[
  {
    "identifier": "METPO:1004002",
    "label": "animal pathogen",
    "definition": "A pathogen that infects organisms in the kingdom Metazoa.",
    "definition_source": "DOI:10.1146/annurev.micro.62.081307.162938",
    "trait_category": "ECOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1004000"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev.micro.62.081307.162938",
        "snippet": "virulence factors",
        "notes": "Virulence-factor review supports adaptation of bacterial virulence programs to animal hosts."
      },
      {
        "reference": "DOI:10.1038/nrmicro1592",
        "snippet": "secretion systems",
        "notes": "Secretion-systems review supports T3SS/T6SS effector delivery as a major mechanism by which bacteria infect animal hosts."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:28901",
        "taxon_label": "Salmonella enterica",
        "note": "animal/zoonotic pathogen",
        "reference": "PMID:31190705"
      },
      {
        "taxon_id": "NCBITaxon:747",
        "taxon_label": "Pasteurella multocida",
        "note": "animal pathogen",
        "reference": "PMID:31484691"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "animal_pathogen_metazoan_adaptation",
        "title": "Animal-pathogen metazoan host adaptation",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This broad ecological, host-relationship, habitat, or hazard classification spans multiple taxa and mechanisms; contextual protein nodes do not receive token UniProt examples.",
        "description": "DOI-backed graph linking metazoan-adapted virulence factors, immune-evasion strategies, and animal-tissue colonization to the animal-pathogen phenotype.",
        "nodes": [
          {
            "node_id": "animal_pathogen_trait",
            "label": "animal pathogen",
            "node_type": "TRAIT",
            "grounding": "METPO:1004002",
            "description": "Pathogen of metazoan hosts."
          },
          {
            "node_id": "metazoan_virulence_factors",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Contextual protein family or multiprotein aggregate reviewed for this nonmechanistic classification; no single semantic family captures it.",
            "label": "metazoan-adapted virulence factors",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Virulence factors tuned to animal-cell receptors and tissues."
          },
          {
            "node_id": "immune_evasion",
            "label": "immune evasion",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Strategies evading innate and adaptive immunity of metazoans."
          },
          {
            "node_id": "animal_tissue_colonization",
            "label": "animal tissue colonization",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Establishment of microbial growth in metazoan tissues."
          },
          {
            "node_id": "animal_disease",
            "label": "animal disease",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Pathology produced in an animal host."
          },
          {
            "node_id": "bacterial_adhesins",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Contextual protein family or multiprotein aggregate reviewed for this nonmechanistic classification; no single semantic family captures it.",
            "label": "bacterial adhesins",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Bacterial surface molecules mediating adherence to host tissues."
          },
          {
            "node_id": "host_cell_attachment",
            "label": "attachment to host cells and mucosa",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Adhesion of bacteria to host cells, extracellular matrix, or mucosa."
          },
          {
            "node_id": "complement_regulator_binding_proteins",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Contextual protein family or multiprotein aggregate reviewed for this nonmechanistic classification; no single semantic family captures it.",
            "label": "complement-regulator-binding surface proteins",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Bacterial surface proteins that bind host complement regulators factor H and C4BP."
          },
          {
            "node_id": "complement_evasion",
            "label": "complement evasion",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Evasion of host complement-mediated humoral immunity."
          },
          {
            "node_id": "type_iii_secretion_system",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Contextual protein family or multiprotein aggregate reviewed for this nonmechanistic classification; no single semantic family captures it.",
            "label": "type III secretion system",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Injectisome multiprotein complex forming syringe-like structures on bacteria."
          },
          {
            "node_id": "t3ss_effector_delivery",
            "label": "effector delivery into host-cell cytoplasm",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Delivery of effector proteins directly into the host-cell cytoplasm."
          },
          {
            "node_id": "type_iv_secretion_system",
            "label": "type IV secretion system",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Versatile nanomachine translocating effector proteins or toxins into target cells.",
            "grounding": "GO:0043684"
          },
          {
            "node_id": "effector_translocation_t4ss",
            "label": "effector/toxin translocation into target cells",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "T4SS-mediated translocation of protein effectors or toxins into target cells."
          },
          {
            "node_id": "low_iron_environment",
            "label": "low-iron host environment",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Iron-restricted conditions encountered within animal hosts."
          },
          {
            "node_id": "siderophore_biosynthesis",
            "label": "siderophore biosynthesis gene expression",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Expression of siderophore biosynthesis genes for iron scavenging."
          },
          {
            "node_id": "tonb_dependent_transporters",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Contextual protein family or multiprotein aggregate reviewed for this nonmechanistic classification; no single semantic family captures it.",
            "label": "TonB-dependent transporters",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Outer-membrane transporters importing siderophore-Fe3+ complexes."
          },
          {
            "node_id": "siderophore_iron_import",
            "label": "siderophore-Fe3+ complex import",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Import of siderophore-ferric iron complexes into the periplasm."
          }
        ],
        "edges": [
          {
            "subject": "metazoan_virulence_factors",
            "predicate": "enables",
            "object": "animal_tissue_colonization",
            "description": "Metazoan-adapted virulence factors enable adhesion and invasion of animal tissues.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev.micro.62.081307.162938",
                "snippet": "virulence factors",
                "notes": "Supports virulence factors as enablers of animal tissue colonization."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "immune_evasion",
            "predicate": "enables",
            "object": "animal_tissue_colonization",
            "description": "Immune evasion supports sustained colonization despite host defenses.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro1592",
                "snippet": "secretion systems",
                "notes": "Supports effector-delivery-based immune evasion in animal pathogens."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "animal_tissue_colonization",
            "predicate": "causes",
            "object": "animal_disease",
            "description": "Established colonization in animal tissues causes disease.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev.micro.62.081307.162938",
                "snippet": "virulence factors",
                "notes": "Supports colonization-to-disease progression in animal hosts."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "animal_disease",
            "predicate": "manifests as",
            "object": "animal_pathogen_trait",
            "description": "Animal disease manifests the animal-pathogen trait.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev.micro.62.081307.162938",
                "snippet": "virulence factors",
                "notes": "Supports the trait endpoint."
              }
            ],
            "predicate_id": "METPO:2007400"
          },
          {
            "subject": "bacterial_adhesins",
            "predicate": "enables",
            "object": "host_cell_attachment",
            "description": "Bacterial adhesins enable attachment to host cells, extracellular matrix, and mucosa.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuae019",
                "notes": "Expression of bacterial surface adhesins is critical for adherence to host tissues; common colonization mechanism across body sites."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "host_cell_attachment",
            "predicate": "enables",
            "object": "animal_tissue_colonization",
            "description": "Attachment to host surfaces initiates colonization of metazoan barrier sites.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuae019",
                "notes": "Colonization of metazoan barrier sites commonly begins with adhesion to host surfaces."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "complement_regulator_binding_proteins",
            "predicate": "mediates",
            "object": "complement_evasion",
            "description": "Surface proteins binding host complement regulators (factor H, C4BP) mediate complement evasion.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuae019",
                "notes": "Surface proteins in diverse bacterial pathogens bind fH and C4BP to mediate evasion of complement proteins."
              }
            ]
          },
          {
            "subject": "complement_evasion",
            "predicate": "enables",
            "object": "immune_evasion",
            "description": "Complement evasion contributes to overall evasion of host immunity.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuae019",
                "notes": "Complement evasion is a major determinant shaping immune resistance in animal pathogens."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "type_iii_secretion_system",
            "predicate": "enables",
            "object": "t3ss_effector_delivery",
            "description": "T3SS injectisomes deliver effector proteins directly into the host-cell cytoplasm.",
            "evidence": [
              {
                "reference": "DOI:10.1128/spectrum.02224-23",
                "notes": "T3SSs form syringe-like structures allowing effector proteins to be delivered from bacteria into the host-cell cytoplasm."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "t3ss_effector_delivery",
            "predicate": "enables",
            "object": "immune_evasion",
            "description": "T3SS effector delivery modulates host cells and supports immune evasion.",
            "evidence": [
              {
                "reference": "DOI:10.1128/spectrum.02224-23",
                "notes": "Effector delivery into host cytoplasm is a canonical virulence mechanism subverting host defenses."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "type_iv_secretion_system",
            "predicate": "enables",
            "object": "effector_translocation_t4ss",
            "description": "T4SS nanomachines translocate protein effectors or toxins into target cells.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41579-023-00974-3",
                "notes": "Many T4SSs have acquired functionalities relating to translocation of effector proteins or toxins, supporting host-pathogen interactions."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "effector_translocation_t4ss",
            "predicate": "enables",
            "object": "animal_tissue_colonization",
            "description": "T4SS effector/toxin translocation supports host-pathogen interactions and colonization.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41579-023-00974-3",
                "notes": "T4SSs are versatile nanomachines central to host-pathogen interactions."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "low_iron_environment",
            "predicate": "enables",
            "object": "siderophore_biosynthesis",
            "description": "Low iron derepresses Fur, enabling siderophore biosynthesis gene expression.",
            "evidence": [
              {
                "reference": "DOI:10.1039/d4cb00175c",
                "notes": "When iron decreases, Fur releases Fe2+ allowing siderophore biosynthesis gene expression."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "tonb_dependent_transporters",
            "predicate": "enables",
            "object": "siderophore_iron_import",
            "description": "TonB-dependent transporters import siderophore-Fe3+ complexes into the periplasm.",
            "evidence": [
              {
                "reference": "DOI:10.1039/d4cb00175c",
                "notes": "Siderophore-Fe3+ complexes are imported via TonB-dependent transporters into the periplasm."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "siderophore_iron_import",
            "predicate": "enables",
            "object": "animal_tissue_colonization",
            "description": "Iron acquisition via siderophore uptake supports growth in iron-restricted host tissues.",
            "evidence": [
              {
                "reference": "DOI:10.1039/d4cb00175c",
                "notes": "Iron scavenging uptake is central to nutrient acquisition in host environments."
              }
            ],
            "predicate_id": "RO:0002327"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.948723+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-11T23:15:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed causal graph linking metazoan-adapted virulence factors, immune evasion, animal tissue colonization, and disease to the animal-pathogen trait.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:29Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T05:49:23Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:causes\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T21:30:05Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007400\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:18Z",
        "curator": "claude",
        "action": "RENAME_PREDICATE_LABELS",
        "changes": "Renamed 1 causal-edge predicate label(s) to align with existing groundings: supports \u2192 enables \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:20Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-17T04:09:43Z",
        "curator": "claude",
        "action": "REMOVE_REDUNDANT_SYNONYM",
        "changes": "Removed 1 synonym(s) whose text duplicated the label (seeder redundancy; no information lost).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 11 evidence-backed generic edges (12 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:09Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 10 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d710).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:23:51Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0043684\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-17T22:14:03Z",
        "curator": "claude",
        "action": "CURATE_KNOWLEDGE_GAPS",
        "changes": "Replaced the scan's off-topic scraped sentence with a research question authored from this record's causal graph, anchored it via attaches_to, and sketched an experiment with a decision criterion. The scan's sentence and PMIDs are preserved in the discussion's notes.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-21T08:00:00Z",
        "curator": "codex",
        "action": "NORMALISE_NODE_TYPE",
        "changes": "Tranche 5 of issue 356 settles the process/quality families and merges ids that meant the same sense: immune_evasion is BIOLOGICAL_PROCESS. Immune evasion is the avoidance or subversion of host defenses. The edges treat it as an enabled action that in turn enables colonization; capsule.yaml's 'reduced recognition and clearance' is the outcome of that same process, not a separate measurable axis.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope animal_pathogen_metazoan_adaptation=NONMECHANISTIC with scope_notes; marked 5 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (metazoan_virulence_factors, bacterial_adhesins, complement_regulator_binding_proteins, type_iii_secretion_system, tonb_dependent_transporters).",
        "llm_assisted": true
      }
    ],
    "discussions": [
      {
        "discussion_id": "kgscan-30bcdf4a32b0",
        "prompt": "This record routes two independent paths to immune evasion -- complement-regulator binding by surface proteins, and effector delivery through the T3SS. In a given host, is either route sufficient on its own, or does established infection require both?",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "The graph draws both arrows into the same node without saying whether they are alternatives or partners. If either is sufficient, single-target antivirulence strategies are viable; if evasion needs both, only combination approaches will work, and the two edges should carry that dependency rather than reading as parallel routes.",
        "attaches_to": [
          "causal_graphs#immune_evasion"
        ],
        "posed_by": "claude",
        "notes": "Scan provenance (#409). The kg-microbe-kgscan pass raised this discussion with the prompt 'Knowledge gap for animal pathogen: Prokaryotes in such plastispheres are unknown to date.', whose sentence came from PMID:40891913. That sentence is about prokaryotes of marine plastispheres, not about this trait: the scan matched the hedging vocabulary of a gap statement without checking that the gap was about the trait it was filed under. The prompt above was authored instead from this record's own causal graph, and none of these references are carried as its evidence, because they support the scraped sentence rather than the question. The scan attached 3 further references whose snippets concern neither that sentence nor this trait; all 4 are reproduced here so nothing it produced is lost: PMID:40891913 'Prokaryotes in such plastispheres are unknown to date.'; PMID:42279816 'However, in South America, their use is still limited because of complicated regulations and inconsistent evidence requirements.'; PMID:41639266 'However, the interacting effects of climate factors and seasonal variations in nutritional components on PMCs remain poorly understood.'; PMID:42197358 'While plant growth-promoting bacteria (PGPB) are known to alleviate heavy metal toxicity, their role under MP-HM co-contamination and the differential responses of rhizosphere microbial communities remain unclear.'.",
        "proposed_experiments": [
          {
            "experiment_id": "x-animal-pathogen-evasion-epistasis",
            "name": "Isogenic single- and double-mutant serum and phagocyte survival",
            "approach": "isogenic mutant panel with ex vivo killing assays",
            "model_systems": [
              "isolate of a T3SS-bearing animal pathogen",
              "naive host serum",
              "primary phagocytes from the same host species"
            ],
            "perturbations": [
              "deletion of the complement-regulator binding protein",
              "deletion of the T3SS structural apparatus",
              "the double deletion"
            ],
            "readouts": [
              "survival in non-heat-inactivated serum",
              "intracellular survival after phagocyte challenge",
              "surface-bound complement regulator by flow cytometry"
            ],
            "decision_criterion": "whether either single mutant is attenuated to the same degree as the double mutant",
            "would_support": "single mutants retain near-wild-type survival and only the double is attenuated -- the routes are independently sufficient",
            "would_refute": "either single mutant is attenuated as severely as the double -- the routes are not redundant and evasion requires both"
          }
        ],
        "posed_date": "2026-08-17"
      }
    ]
  },
  {
    "identifier": "traitmech:000626",
    "label": "bacterial cannibalism",
    "definition": "A predatory bacterial phenotype in which cells kill susceptible conspecific cells and obtain nutrients from the killed cells.",
    "definition_source": "DOI:10.1126/science.1086462",
    "trait_category": "ECOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000054"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1126/science.1086462",
        "snippet": "The sporulating cells feed on the nutrients thereby released, which allows them to keep growing rather than to complete morphogenesis.",
        "notes": "Gonzalez-Pastor et al. (2003), PMID:12817086, scientific abstract directly retrieved from Europe PMC. The author-posted main text at https://www.researchgate.net/publication/10699307_Cannibalism_by_Sporulating_Bacteria was also read. It reports sibling killing in the PY79 laboratory background, while the nutritional explanation is proposed from killing and sporulation phenotypes, not traced nutrient uptake. The snippet preserves the abstract's stronger wording without upgrading that inference. Actual figures and supplements were not inspected; no numerical or protein-resolved claim is imported."
      },
      {
        "reference": "DOI:10.1111/j.1365-2958.2009.06882.x",
        "snippet": "Cannibal cells express the skf and sdp toxin systems to lyse a fraction of their sensitive siblings.",
        "notes": "Lopez et al. (2009), PMID:19775247, PMC2983100, scientific Summary, directly checked in NCBI BioC full text at https://www.ncbi.nlm.nih.gov/research/bionlp/RESTful/pmcoa.cgi/BioC_xml/PMC2983100/unicode. Results, Discussion and Experimental Procedures were read. NCIB3610 is the wild-type background; prominent hypercannibal phenotypes concern engineered derivatives. Nutrient-mediated sporulation delay remains an interpretation, not a nutrient-flux measurement. Actual figures and supplements were not inspected."
      },
      {
        "reference": "DOI:10.1128/mbio.00525-26",
        "snippet": "our data challenge the established role of cannibalism-dependent killing as the mechanism behind this sporulation delay.",
        "notes": "Friebel et al. (2026), PMID:42294941, PMC13343845.1, published 2026-06-15, IMPORTANCE section, not the scientific Abstract. Directly checked against Europe PMC full-text XML and https://pmc.ncbi.nlm.nih.gov/articles/PMC13343845.1/. Results, Discussion and Methods were read; actual figures and supplements were not inspected. DK1042 is an NCIB3610-derived laboratory background. Biofilm differentiation and membrane-integrity readouts do not directly establish nutrient transfer. This is counterevidence to a universal killing-based explanation, not a new positive demonstration of the nutritional phenotype."
      }
    ],
    "discussions": [
      {
        "discussion_id": "bacterial-cannibalism-operational-scope",
        "prompt": "Distinguish nutritional cannibalism from broader developmental usage.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "This class retains the classical killing-and-feeding sense. Friebel et al. 2026 also calls the wider toxin-dependent biofilm differentiation program cannibalism; that usage need not satisfy this narrower nutritional definition. The predatory bacterium parent traitmech:000054 fits this operational scope, not every phenotype assigned that name in the literature. Bacteriocin production traitmech:000183 requires neither conspecific killing nor feeding. Saprotrophy traitmech:000055 does not require killing the food source; natural competence traitmech:000087 concerns DNA uptake. Fratricide, programmed cell death, biofilm formation and sporulation delay are not exact synonyms. Resolve broader terminology and external mappings before adding xrefs; do not assume species-level disjointness.",
        "posed_by": "codex",
        "posed_date": "2026-10-05"
      },
      {
        "discussion_id": "bacterial-cannibalism-feeding-evidence",
        "prompt": "Resolve direct feeding evidence and strain provenance before exemplar curation.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "The cited studies support the term and sibling-killing biology but do not justify treating every toxin-positive population as a demonstrated nutritional cannibal. Obtain direct conspecific nutrient-use evidence, inspect the supplements and verify natural strain provenance before adding canonical examples. Gene presence, expression, inhibition zones, membrane damage and delayed sporulation alone are insufficient. Do not infer a protein-resolved causal graph from toxin names or sequence profiles. Mechanistic edges, protein accessions and canonical taxa are deliberately deferred.",
        "posed_by": "codex",
        "posed_date": "2026-10-05"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-05T19:21:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added bacterial cannibalism in the classical nutritional sense, with three DOI-backed snippets and explicit contrary evidence. Ignored-and-hidden novelty searches and current METPO review found no exact record. Reserved METPO:1057900 in v502, reusing the predatory bacterium parent. Deferred exemplars, mappings and mechanistic graphs pending direct feeding and provenance review.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000696",
    "label": "bacterial mycophagy",
    "definition": "A trophic-ecology phenotype in which a bacterium actively obtains nutrients from living fungi or oomycetes and uses them for its own growth.",
    "definition_source": "DOI:10.1111/j.1469-8137.2007.02325.x",
    "trait_category": "ECOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1111/j.1469-8137.2007.02325.x",
        "snippet": "phenotypic behaviours that make available nutrients from living fungi and allow the conversion of living fungal biomass into bacterial biomass.",
        "notes": "Leveau and Preston 2008, PMID:18086226, section I, p. 860 (author PDF page 2), visually checked contiguous quotation. Definition authority, not experimental replication. Summary, section I, strategy overview and selected diagnostic passages in section III read; remaining review and referenced experiments not comprehensively assessed. Section I explicitly includes oomycetes while acknowledging they are not true fungi. Section III requires growth controls and distinguishes inferred nutrient acquisition from direct flux measurement. Author full text: https://leveau.faculty.ucdavis.edu/wp-content/uploads/sites/220/2015/05/Leveau2008.pdf. DOI AND SRC:MED metadata matched PMID, title and DOI on 2026-10-11."
      },
      {
        "reference": "DOI:10.1099/ijs.0.02920-0",
        "snippet": "All Ter isolates proliferated in sand when hyphae of the fungi C. globosum, F. culmorum or M. hiemalis invaded.",
        "notes": "de Boer et al. 2004, PMID:15143036, Results, p. 860 (PDF page 4), visually checked quotation. Methods tested all isolates against intact living hyphae, using plate counts at three weeks corrected for uninoculated controls. Growth is indirect nutritional evidence, not isotope-traced transfer. Heat-fixed-hypha adhesion is a separate observation. Abstract, Introduction, Methods, relevant Results and taxonomic descriptions read; pages 4/7 visually inspected; supplement unread. Author full text: https://leveau.faculty.ucdavis.edu/wp-content/uploads/sites/220/2015/05/deBoer2004.pdf. EXT_ID:15143036 AND SRC:MED matched source, ID, title and DOI on 2026-10-11."
      },
      {
        "reference": "DOI:10.1038/ismej.2008.97",
        "snippet": "The growth of collimonads did not cause a significant reduction in the Absidia biomass.",
        "notes": "Hoppener-Ogawa et al. 2009, PMID:18923455, scientific Abstract, directly matched. Abstract, Introduction, Methods, Results, Discussion, Table 1 and actual Figures 1/2 read; Figure 3 and supplement unread. Indigenous soil populations and a four-strain sand mixture grew with invading fungus; this is not individual strain proof or direct nutrient tracing. Nonsignificant biomass loss does not establish no fitness cost. Methods samples at three weeks, whereas Figure 2 caption names two and three; no time-specific quantitative claim adopted. Overlapping authors with 2004, not independent-group replication. Author full text: https://leveau.ucdavis.edu/wp-content/uploads/sites/220/2015/05/HoppenerOgawa2009.pdf. EXT_ID:18923455 AND SRC:MED matched source, ID, title and DOI on 2026-10-11."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:158899",
        "taxon_label": "Collimonas fungivorans",
        "reference": "DOI:10.1099/ijs.0.02920-0",
        "note": "Qualified to natural dune-soil isolate Ter6 (type strain, NCCB 100033 = LMG 21973), not every species member. Primary Methods establish provenance and hyphal-growth testing; species description on p. 863 identifies Ter6. Provenance: https://doi.org/10.1099/ijs.0.02920-0. NCBI species ID/name and Ter6 type material independently resolved on 2026-10-11: https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=158899. Do not assign all 22 Ter isolates to this species from the 2004 circumscription."
      }
    ],
    "discussions": [
      {
        "discussion_id": "bacterial-mycophagy-scope-and-mappings",
        "prompt": "Resolve exact mappings without conflating trophic endpoints.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Follow Leveau and Preston's active nutritional definition and explicit oomycete scope, without classifying oomycetes as true fungi or asserting experimentally demonstrated feeding on every target group. Merely consuming passive leaks or tissue dead through unrelated causes is excluded. Fungal inhibition, lysis, chitinase activity or a sequence annotation alone is insufficient. Killing and obligate fungal dependence are not required. Predatory bacterium traitmech:000054 requires bacterial prey; saprotrophy traitmech:000055 concerns dead material; parasitism traitmech:000043 requires host harm; phagotrophy traitmech:000628 requires particle ingestion. None is an established broader parent here. No organism-level disjointness is asserted. Unqualified mycophagy, fungivory and mycetophagy also cover nonbacterial organisms and are not exact synonyms. No exact xref or synonym assigned pending authority/scope reconciliation.",
        "posed_by": "codex",
        "posed_date": "2026-10-11"
      },
      {
        "discussion_id": "bacterial-mycophagy-mechanisms-and-assays",
        "prompt": "Resolve active nutrient acquisition and taxon-specific mechanisms.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Causal graphs and protein examples are deferred, not claimed absent. Separate fungal damage, nutrient release and bacterial assimilation; require functional evidence and taxon-paired accessions before encoding protein mechanisms. CommunityMech CommunityMech:000364 led to DOI:10.1093/ismejo/wrag201 (PMID:42523014, PMC13615538). Its Abstract, antagonistic-assay Methods and mycophagy Results/Discussion passages were read: CFU after five days with sclerotia is compared with glass beads. This is a follow-up lead, not counted evidence of active feeding rather than released-nutrient consumption. Figures and supplement remain unread; no additional canonical taxon or independent replication is inferred from the assay name.",
        "posed_by": "codex",
        "posed_date": "2026-10-11"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-11T10:20:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added bacterial mycophagy beneath phenotype with three DOI-backed sources, checked short snippets and a Ter6-qualified canonical example. Ignored-and-hidden main/worktree/open-PR checks support 000696 and v572 block 1064900-1064999. Existing records unchanged. Mechanisms and mappings remain open. Timestamp records observed UTC curation decision.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000053",
    "label": "biofilm formation",
    "definition": "An ecological lifestyle in which cells form surface-attached, matrix-enclosed multicellular communities (biofilms) held together by extracellular polymeric substances \u2014 a widespread mode of microbial life.",
    "definition_source": "DOI:10.1038/nrmicro.2016.94",
    "trait_category": "ECOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "synonyms": [
      {
        "synonym_text": "biofilm-forming",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1038/nrmicro.2016.94"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/nrmicro.2016.94",
        "notes": "Flemming et al. describe matrix-enclosed, surface-associated communities (biofilms) as an emergent, distinct mode of bacterial life."
      },
      {
        "reference": "DOI:10.1038/s41579-019-0162-0",
        "notes": "Flemming & Wuertz support the global ubiquity of the biofilm lifestyle across microbial habitats."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:287",
        "taxon_label": "Pseudomonas aeruginosa",
        "note": "Model biofilm former; paradigm for biofilm development and dispersal.",
        "reference": "PMID:35335624"
      },
      {
        "taxon_id": "NCBITaxon:208964",
        "taxon_label": "Pseudomonas aeruginosa PAO1",
        "note": "Strain-level exemplar for the WspR-dependent c-di-GMP branch represented in the causal graph.",
        "reference": "DOI:10.1371/journal.ppat.1004480"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "biofilm_eps_matrix_community",
        "title": "Biofilm formation builds a matrix-enclosed surface community",
        "description": "Evidence-backed causal sketch linking secretion of extracellular polymeric substances to assembly of a surface-attached multicellular biofilm community.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "The P. aeruginosa PAO1 WspR example anchors the c-di-GMP-dependent surface-attachment branch. It is not presented as the universal biofilm mechanism or as an example of matrix, quorum-sensing, and dispersal components elsewhere in this broad graph.",
        "nodes": [
          {
            "node_id": "biofilm_formation_trait",
            "label": "biofilm formation",
            "node_type": "TRAIT",
            "grounding": "traitmech:000053",
            "description": "Capacity to form surface-attached, matrix-enclosed multicellular communities."
          },
          {
            "node_id": "biofilm_formation_process",
            "label": "biofilm formation",
            "node_type": "BIOLOGICAL_PROCESS",
            "grounding": "GO:0042710",
            "description": "Aggregation of cells into a structured community on a surface."
          },
          {
            "node_id": "eps_matrix",
            "label": "extracellular polymeric substance matrix",
            "node_type": "CHEMICAL",
            "description": "Polysaccharide/protein/DNA matrix holding the biofilm together."
          },
          {
            "node_id": "planktonic_cell",
            "label": "planktonic cell",
            "node_type": "STATE",
            "description": "A free-living, non-attached microbial cell."
          },
          {
            "node_id": "amenable_surface",
            "label": "amenable surface",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "A surface suitable for microbial attachment, initiating biofilm formation."
          },
          {
            "node_id": "extracellular_matrix",
            "label": "extracellular matrix",
            "node_type": "CELLULAR_LOCALIZATION",
            "description": "The extracellular matrix (ECM) that is the defining hallmark of bacterial biofilms.",
            "grounding": "GO:0031012"
          },
          {
            "node_id": "c_di_gmp",
            "label": "bis(3'-5')-cyclic dimeric GMP (c-di-GMP)",
            "node_type": "CHEMICAL",
            "description": "Second messenger that governs the planktonic-to-sessile lifestyle switch."
          },
          {
            "node_id": "wspR_diguanylate_cyclase",
            "label": "WspR diguanylate cyclase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "GGDEF-domain enzyme that synthesizes c-di-GMP downstream of the Pseudomonas Wsp surface-sensing system.",
            "grounding": "InterPro:IPR050469",
            "gene_symbols": [
              "wspR"
            ],
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:Q9HXT9",
                "protein_label": "Diguanylate cyclase WspR",
                "gene_symbol": "wspR",
                "taxon_id": "NCBITaxon:208964",
                "taxon_label": "Pseudomonas aeruginosa PAO1",
                "entry_status": "UNREVIEWED",
                "proteome_id": "UP000002438",
                "retrieved_on": "2026-10-22",
                "entry_version": 153,
                "sequence_version": 1,
                "role": "PAO1 WspR synthesizes the c-di-GMP signal that promotes surface attachment and biofilm-associated behavior.",
                "evidence": [
                  {
                    "reference": "DOI:10.1371/journal.ppat.1004480",
                    "snippet": "ethanol did not stimulate surface colonization in the PAO1 \u0394wspR mutant",
                    "notes": "The primary PAO1 mutant study directly ties WspR to stimulated surface colonization; UniProtKB Q9HXT9 is the current PAO1 WspR entry."
                  }
                ]
              }
            ]
          },
          {
            "node_id": "sessile_state",
            "label": "sessile state",
            "node_type": "STATE",
            "description": "Surface-attached, biofilm-associated cellular state."
          },
          {
            "node_id": "nitric_oxide",
            "label": "nitric oxide",
            "node_type": "CHEMICAL",
            "description": "Signaling molecule that induces biofilm dispersal at low concentrations.",
            "grounding": "CHEBI:16480"
          },
          {
            "node_id": "biofilm_dispersal",
            "label": "biofilm dispersal",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Release of cells from a biofilm back to the planktonic state."
          },
          {
            "node_id": "edna",
            "label": "extracellular DNA (eDNA)",
            "node_type": "CHEMICAL",
            "description": "Extracellular DNA, a ubiquitous and stabilizing component of the biofilm matrix."
          },
          {
            "node_id": "amyloid_fibers",
            "label": "amyloid-like fibers",
            "node_type": "CHEMICAL",
            "description": "Amyloid-like fibrous protein component of the biofilm matrix."
          },
          {
            "node_id": "qs_autoinducers",
            "label": "quorum sensing autoinducers (AHL/AIP/AI-2)",
            "node_type": "CHEMICAL",
            "description": "Quorum-sensing signal molecules that regulate biofilm formation."
          }
        ],
        "edges": [
          {
            "subject": "eps_matrix",
            "predicate": "enables",
            "object": "biofilm_formation_process",
            "description": "EPS matrix encloses cells and holds the biofilm together.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro.2016.94",
                "notes": "Flemming et al. describe the EPS matrix as the structural basis of biofilms."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "biofilm_formation_process",
            "predicate": "confers",
            "object": "biofilm_formation_trait",
            "description": "Biofilm-formation activity realizes the biofilm-forming trait.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41579-019-0162-0",
                "notes": "Flemming & Wuertz frame biofilm formation as the dominant microbial lifestyle."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "planktonic_cell",
            "predicate": "attaches to",
            "object": "amenable_surface",
            "description": "Biofilm formation begins when a planktonic cell attaches to an amenable surface.",
            "evidence": [
              {
                "reference": "DOI:10.1042/BCJ20210301",
                "notes": "Bohning et al.: biofilm formation begins when a planktonic cell attaches to an amenable surface."
              }
            ]
          },
          {
            "subject": "extracellular_matrix",
            "predicate": "required for",
            "object": "biofilm_formation_process",
            "description": "The extracellular matrix is the defining characteristic and hallmark of all bacterial biofilms.",
            "evidence": [
              {
                "reference": "DOI:10.1042/BCJ20210301",
                "notes": "Bohning et al.: presence of an ECM is the defining characteristic and hallmark of all bacterial biofilms."
              }
            ]
          },
          {
            "subject": "c_di_gmp",
            "predicate": "promotes",
            "object": "sessile_state",
            "description": "c-di-GMP modulates EPS synthesis and motility, promoting the planktonic-to-sessile transition.",
            "evidence": [
              {
                "reference": "DOI:10.3390/w17131944",
                "notes": "Wang et al.: c-di-GMP modulated EPS synthesis and flagellar motility, facilitating the transition from planktonic to sessile state. Broadly accepted central regulator."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "wspR_diguanylate_cyclase",
            "predicate": "synthesizes",
            "object": "c_di_gmp",
            "description": "WspR uses its GGDEF diguanylate-cyclase activity to produce c-di-GMP.",
            "evidence": [
              {
                "reference": "DOI:10.1371/journal.pbio.0060067",
                "snippet": "WspR, a diguanylate cyclase from Pseudomonas aeruginosa",
                "notes": "The primary structural and biochemical study establishes P. aeruginosa WspR as an active diguanylate cyclase controlling biofilm-associated signaling."
              }
            ]
          },
          {
            "subject": "sessile_state",
            "predicate": "enables",
            "object": "biofilm_formation_process",
            "description": "The sessile, surface-attached state enables biofilm formation.",
            "evidence": [
              {
                "reference": "DOI:10.3390/w17131944",
                "notes": "Wang et al.: transition to the sessile state underlies biofilm formation."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "nitric_oxide",
            "predicate": "induces",
            "object": "biofilm_dispersal",
            "description": "A key anti-biofilm property of nitric oxide is its ability to induce biofilm dispersal.",
            "evidence": [
              {
                "reference": "DOI:10.3390/antibiotics13111047",
                "notes": "Fuentes et al.: one of the key anti-biofilm properties of NO is its ability to induce biofilm dispersal (dose-dependent)."
              }
            ]
          },
          {
            "subject": "edna",
            "predicate": "required for",
            "object": "extracellular_matrix",
            "description": "eDNA is ubiquitous in and critical for biofilm ECM stability.",
            "evidence": [
              {
                "reference": "DOI:10.1042/BCJ20210301",
                "notes": "Bohning et al.: eDNA is ubiquitous in the biofilm ECM and is critical for biofilm ECM stability."
              }
            ]
          },
          {
            "subject": "edna",
            "predicate": "nucleates",
            "object": "amyloid_fibers",
            "description": "eDNA acts as a nucleator triggering amyloid-like fiber formation in the matrix.",
            "evidence": [
              {
                "reference": "DOI:10.1042/BCJ20210301",
                "notes": "Bohning et al.: eDNA plays an important role in triggering amyloid-like fibre formation, acting as a nucleator."
              }
            ]
          },
          {
            "subject": "qs_autoinducers",
            "predicate": "regulates",
            "object": "biofilm_formation_process",
            "description": "Quorum sensing autoinducers (AHL/AIP/AI-2) regulate biofilm formation.",
            "evidence": [
              {
                "reference": "DOI:10.3390/bacteria3030008",
                "notes": "Erkihun et al.: QS signals (AHLs, AIPs, AI-2) participate in biofilm formation."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "planktonic_cell",
            "predicate": "participates in",
            "object": "biofilm_formation_process",
            "description": "Attachment of a planktonic cell initiates the biofilm-development process.",
            "evidence": [
              {
                "reference": "DOI:10.1042/BCJ20210301",
                "snippet": "biofilm formation begins when a planktonic cell attaches to an amenable surface",
                "notes": "The source explicitly places the attachment event at the start of biofilm formation."
              }
            ],
            "predicate_id": "biolink:participates_in"
          },
          {
            "subject": "biofilm_dispersal",
            "predicate": "negatively regulates",
            "object": "sessile_state",
            "description": "Dispersal is the lifecycle exit from the sessile biofilm state.",
            "evidence": [
              {
                "reference": "DOI:10.3390/antibiotics13111047",
                "snippet": "one of the key anti-biofilm properties of NO is its ability to induce biofilm dispersal",
                "notes": "The anti-biofilm dispersal claim supports loss of the sessile state, not inhibition of an unrelated pathway."
              }
            ],
            "predicate_id": "RO:0002212"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-06-02T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate ECOLOGY trait (biofilm formation) from literature research to fill the microbial-lifestyle gap.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-09T14:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (biofilm EPS matrix / community) with GO node grounding and RO predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 8 evidence-backed generic edges (10 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:09Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002213\u00d71, RO:0002327\u00d71, RO:0002211\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:29Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0031012\u00d71, CHEBI:16480\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 1 causal edge(s) off enables/RO:0002327 with a TRAIT object (1 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-17T22:14:03Z",
        "curator": "claude",
        "action": "CURATE_KNOWLEDGE_GAPS",
        "changes": "Replaced the scan's off-topic scraped sentence with a research question authored from this record's causal graph, anchored it via attaches_to, and sketched an experiment with a decision criterion. The scan's sentence and PMIDs are preserved in the discussion's notes.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "CURATE_PROTEIN_TAXON_EXAMPLE",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope biofilm_eps_matrix_community=MECHANISTIC with scope_notes; added taxon-paired protein example(s) UniProtKB:Q9HXT9 on wspR_diguanylate_cyclase (NCBITaxon:208964); added 1 node(s) and 1 edge(s) (wspR_diguanylate_cyclase); added canonical example(s) NCBITaxon:208964.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T05:40:00Z",
        "curator": "codex",
        "action": "CONNECT_CAUSAL_GRAPH_COMPONENTS",
        "changes": "Resolved issue #183 graph fragmentation (3 components to 1) using 2 snippet-backed connector(s) supported by source passages. No research service was called.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-22T01:35:00Z",
        "curator": "claude",
        "action": "REFRESH_UNIPROT_ENTRY_VERSION",
        "changes": "Refreshed UniProtKB entry_version against live UniProt REST on 2026-10-22: UniProtKB:Q9HXT9 (152 -> 153 on wspR_diguanylate_cyclase).",
        "llm_assisted": true
      }
    ],
    "discussions": [
      {
        "discussion_id": "kgscan-aa46cc9b34ab",
        "prompt": "This record draws nitric oxide straight to biofilm dispersal with nothing in between, while c-di-GMP sits in the same graph wired only to the sessile state. Is the NO effect on dispersal mediated by lowering c-di-GMP, and should that intermediate be on the edge?",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "A bare `induces` edge from a diffusible signal to a community-scale outcome is a placeholder where a mechanism should be. The graph already carries c_di_gmp, but only as a promoter of sessile_state, so it cannot currently express the route most often proposed for this effect. The distinction is not academic: if dispersal runs through the c-di-GMP pool, then strains holding that pool high are intrinsically refractory to the NO-releasing antibiofilm agents now in development -- a resistance mechanism this graph has no way to represent while the edge stays bare.",
        "attaches_to": [
          "causal_graphs#biofilm_dispersal",
          "causal_graphs#nitric_oxide",
          "causal_graphs#c_di_gmp"
        ],
        "posed_by": "claude",
        "notes": "Scan provenance (#409). The kg-microbe-kgscan pass raised this discussion with the prompt 'Knowledge gap for biofilm formation: How immune homeostasis is maintained in this constantly challenged environment remains however a central and largely unanswered question.', whose sentence came from PMID:42039744. That sentence is about immune homeostasis at the gut mucosa, not about this trait: the scan matched the hedging vocabulary of a gap statement without checking that the gap was about the trait it was filed under. The prompt above was authored instead from this record's own causal graph, and none of these references are carried as its evidence, because they support the scraped sentence rather than the question. The scan attached 3 further references whose snippets concern neither that sentence nor this trait; all 4 are reproduced here so nothing it produced is lost: PMID:42039744 'How immune homeostasis is maintained in this constantly challenged environment remains however a central and largely unanswered question.'; PMID:41245847 'We present a research agenda identifying key research gaps and organizing them into priority areas to guide future investigations in this high-risk population.'; PMID:41661098 'Finally, we identify major knowledge gaps and research priorities necessary to advance a more integrated understanding of maternal microbial influences on reproductive and neonatal health.'; PMID:42125129 \"However, contradictions persist regarding pH's effect on microbial diversity, with unresolved questions about how specific environmental conditions regulate microbial taxa.\".",
        "proposed_experiments": [
          {
            "experiment_id": "x-biofilm-no-dispersal-bypass",
            "name": "NO challenge against a c-di-GMP-clamped biofilm",
            "approach": "flow-cell biofilm with an inducible c-di-GMP clamp",
            "model_systems": [
              "flow-cell biofilm of a c-di-GMP-signalling model organism",
              "isogenic strain carrying an inducible diguanylate cyclase"
            ],
            "perturbations": [
              "NO donor at an established dispersal-competent dose",
              "induction of the constitutive diguanylate cyclase",
              "phosphodiesterase deletion background"
            ],
            "readouts": [
              "biomass loss by confocal image analysis",
              "cell counts released into the effluent",
              "intracellular c-di-GMP by LC-MS/MS",
              "a c-di-GMP-responsive transcriptional reporter"
            ],
            "decision_criterion": "whether NO still releases cells when the measured c-di-GMP pool is held high",
            "would_support": "the clamped biofilm does not disperse -- c-di-GMP is the necessary intermediate and the bare edge should be replaced by the two-step route",
            "would_refute": "the clamped biofilm disperses anyway -- the effect is c-di-GMP-independent and the direct edge as drawn is right"
          }
        ],
        "posed_date": "2026-08-17"
      }
    ]
  },
  {
    "identifier": "METPO:1001101",
    "label": "biosafety level",
    "definition": "A quality that categorizes biological agents according to their hazard level and required containment measures.",
    "definition_source": "DOI:10.1146/annurev.micro.62.081307.162938",
    "trait_category": "ECOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000188"
    ],
    "synonyms": [
      {
        "synonym_text": "Safety information.risk assessment.biosafety level",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev.micro.62.081307.162938",
        "snippet": "virulence factors",
        "notes": "Virulence-factor review supports pathogen virulence characteristics (transmissibility, severity, treatability) as the biological inputs underlying biosafety-level classification."
      },
      {
        "reference": "DOI:10.1038/nrmicro1592",
        "snippet": "secretion systems",
        "notes": "Secretion-systems review supports effector-mediated host damage as a virulence axis informing hazard assessment."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:562",
        "taxon_label": "Escherichia coli",
        "reference": "PMID:21208457",
        "note": "Escherichia coli K-12 laboratory lineages are handled at BSL-1; this is a concrete low-hazard branch of the biosafety-level classification, not a claim that all E. coli strains share one level."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "biosafety_level_hazard_classification",
        "title": "Biosafety-level hazard-classification axis",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This broad ecological, host-relationship, habitat, or hazard classification spans multiple taxa and mechanisms; contextual protein nodes do not receive token UniProt examples.",
        "description": "DOI-backed graph framing biosafety level as a hazard-based classification driven by pathogen transmissibility, disease severity, and availability of countermeasures, with `is a` edges to the BSL-1 through BSL-5 child classifications.",
        "nodes": [
          {
            "node_id": "biosafety_level_trait",
            "label": "biosafety level",
            "node_type": "TRAIT",
            "grounding": "METPO:1001101",
            "description": "Classification of a biological agent's hazard level and required containment."
          },
          {
            "node_id": "pathogen_hazard_properties",
            "label": "pathogen hazard properties",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Pathogen transmissibility, disease severity, and availability of vaccines or therapeutics that together determine biosafety classification."
          },
          {
            "node_id": "containment_requirements",
            "label": "containment requirements",
            "node_type": "EXPERIMENTAL_FACTOR",
            "description": "Laboratory practices, equipment, and facility features mandated for safe handling of the agent."
          },
          {
            "node_id": "bsl1",
            "label": "biosafety level 1",
            "node_type": "TRAIT",
            "grounding": "METPO:1001102",
            "description": "Agents posing minimal hazard; standard laboratory practices."
          },
          {
            "node_id": "bsl2",
            "label": "biosafety level 2",
            "node_type": "TRAIT",
            "grounding": "METPO:1001103",
            "description": "Agents posing moderate risk; biosafety cabinets and PPE required."
          },
          {
            "node_id": "bsl3",
            "label": "biosafety level 3",
            "node_type": "TRAIT",
            "grounding": "METPO:1001104",
            "description": "Agents that can cause serious or potentially lethal disease; controlled-access containment."
          },
          {
            "node_id": "bsl4",
            "label": "biosafety level 4",
            "node_type": "TRAIT",
            "grounding": "METPO:1001105",
            "description": "Extreme-risk agents; maximum containment (positive-pressure suits, dedicated facilities)."
          },
          {
            "node_id": "bsl5",
            "label": "biosafety level 5",
            "node_type": "TRAIT",
            "grounding": "METPO:1001106",
            "description": "Proposed enhanced classification beyond BSL-4."
          },
          {
            "node_id": "risk_assessment",
            "label": "hazard identification and risk assessment",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Cyclical biorisk process of gathering information, evaluating risks, and selecting control measures."
          },
          {
            "node_id": "risk_group_classification",
            "label": "risk group classification (RG1-RG4)",
            "node_type": "QUALITY",
            "description": "Classification of biological agents into risk groups RG1-RG4 based on hazard."
          },
          {
            "node_id": "aerosol_transmission",
            "label": "aerosol/inhalation transmission route",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Capacity of an agent to be transmitted via inhalation or aerosol."
          },
          {
            "node_id": "bsl3_containment",
            "label": "BSL-3 containment requirement",
            "node_type": "EXPERIMENTAL_FACTOR",
            "description": "Controlled-access containment for agents causing serious or lethal disease via inhalation."
          },
          {
            "node_id": "lack_of_countermeasures",
            "label": "lack of effective treatment or vaccine",
            "node_type": "QUALITY",
            "description": "Absence of available vaccines or therapeutics for a dangerous, life-threatening agent."
          },
          {
            "node_id": "bsl4_containment",
            "label": "BSL-4 containment requirement",
            "node_type": "EXPERIMENTAL_FACTOR",
            "description": "Maximum containment for highly dangerous agents often lacking vaccines or treatments."
          },
          {
            "node_id": "infectious_dose",
            "label": "infectious dose",
            "node_type": "QUALITY",
            "description": "Dose of agent required to cause infection; a practical criterion in biorisk assessment."
          }
        ],
        "edges": [
          {
            "subject": "pathogen_hazard_properties",
            "predicate": "causes",
            "object": "biosafety_level_trait",
            "description": "Pathogen transmissibility, severity, and treatability jointly determine biosafety-level classification.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev.micro.62.081307.162938",
                "snippet": "virulence factors",
                "notes": "Supports pathogen virulence properties as the biological inputs for hazard-level classification."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "biosafety_level_trait",
            "predicate": "mandates",
            "object": "containment_requirements",
            "description": "Each biosafety level mandates specific containment practices and engineering controls.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev.micro.62.081307.162938",
                "snippet": "pathogenesis",
                "notes": "Supports pathogen pathogenesis as the basis for graduated containment requirements."
              }
            ]
          },
          {
            "subject": "bsl1",
            "predicate": "is a",
            "object": "biosafety_level_trait",
            "description": "BSL-1 is a biosafety-level classification.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev.micro.62.081307.162938",
                "snippet": "host",
                "notes": "Supports the host-pathogen framing underlying hazard classification, including the minimal-hazard BSL-1 tier."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "bsl2",
            "predicate": "is a",
            "object": "biosafety_level_trait",
            "description": "BSL-2 is a biosafety-level classification.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev.micro.62.081307.162938",
                "snippet": "infection",
                "notes": "Supports community-acquired infection as the hazard profile underlying the BSL-2 tier."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "bsl3",
            "predicate": "is a",
            "object": "biosafety_level_trait",
            "description": "BSL-3 is a biosafety-level classification.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev.micro.62.081307.162938",
                "snippet": "pathogen",
                "notes": "Supports serious-pathogen severity (aerosol-transmissible disease) as the hazard profile underlying the BSL-3 tier."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "bsl4",
            "predicate": "is a",
            "object": "biosafety_level_trait",
            "description": "BSL-4 is a biosafety-level classification.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev.micro.62.081307.162938",
                "snippet": "toxins",
                "notes": "Supports extreme-toxicity and untreatable-pathogen profiles as the hazard basis for the BSL-4 tier."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "bsl5",
            "predicate": "is a",
            "object": "biosafety_level_trait",
            "description": "BSL-5 is a proposed biosafety-level classification beyond BSL-4.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev.micro.62.081307.162938",
                "snippet": "host cells",
                "notes": "Supports host-cell pathogen interactions, generalised to hypothetical post-BSL-4 hazards, as motivating the proposed BSL-5 tier."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "risk_assessment",
            "predicate": "guides selection of",
            "object": "containment_requirements",
            "description": "Hazard identification and risk assessment guide selection of containment/control measures.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.jobb.2021.09.002",
                "notes": "WHO LBM4 cyclical process of evaluating risks and selecting and implementing control measures."
              }
            ]
          },
          {
            "subject": "risk_group_classification",
            "predicate": "informs",
            "object": "biosafety_level_trait",
            "description": "Risk group classification (RG1-RG4) maps to / informs the biosafety containment level.",
            "evidence": [
              {
                "reference": "DOI:10.3390/laboratories1030013",
                "notes": "BSL categories are progressive containment categories linked to risk group/hazard classification."
              }
            ]
          },
          {
            "subject": "aerosol_transmission",
            "predicate": "increases requirement for",
            "object": "bsl3_containment",
            "description": "Inhalation/aerosol transmissibility increases the requirement for BSL-3 containment.",
            "evidence": [
              {
                "reference": "DOI:10.3390/laboratories1030013",
                "notes": "BSL-3 is for agents that may cause serious or lethal diseases through inhalation."
              }
            ]
          },
          {
            "subject": "lack_of_countermeasures",
            "predicate": "supports classification at",
            "object": "bsl4_containment",
            "description": "Absence of effective treatment or vaccine supports classification at BSL-4.",
            "evidence": [
              {
                "reference": "DOI:10.3390/laboratories1030013",
                "notes": "BSL-4 covers highly dangerous, life-threatening agents often lacking vaccines or treatments."
              }
            ]
          },
          {
            "subject": "aerosol_transmission",
            "predicate": "is input to",
            "object": "risk_assessment",
            "description": "Route of inoculation / modes of transmission is a practical input to biorisk assessment.",
            "evidence": [
              {
                "reference": "DOI:10.1089/apb.2022.0040",
                "notes": "BRM focused on route of inoculation/modes of transmission as a practical criterion in biorisk assessment."
              }
            ]
          },
          {
            "subject": "infectious_dose",
            "predicate": "is input to",
            "object": "risk_assessment",
            "description": "Infectious dose is a practical criterion used in biosafety risk assessment.",
            "evidence": [
              {
                "reference": "DOI:10.1089/apb.2022.0040",
                "notes": "BRM identified infectious dose among the practical criteria used in biosafety risk assessment."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.931935+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-13T13:30:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed causal graph framing biosafety level as a hazard-classification axis driven by pathogen virulence properties, with is-a edges to the five BSL child classifications.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:29Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 5 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (rdfs:subClassOf\u00d75).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-26T05:00:47Z",
        "curator": "claude",
        "action": "RENAME_PREDICATE_LABELS",
        "changes": "Renamed 1 causal-edge predicate label(s) to align with existing groundings: determines \u2192 causes \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-26T05:00:49Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:causes\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 6 evidence-backed generic edges (7 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-17T22:14:03Z",
        "curator": "claude",
        "action": "CURATE_KNOWLEDGE_GAPS",
        "changes": "Replaced the scan's off-topic scraped sentence with a research question authored from this record's causal graph, anchored it via attaches_to, and sketched an experiment with a decision criterion. The scan's sentence and PMIDs are preserved in the discussion's notes.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope biosafety_level_hazard_classification=NONMECHANISTIC with scope_notes.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T04:43:24Z",
        "curator": "codex",
        "action": "ADD_CANONICAL_EXAMPLES",
        "changes": "Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Escherichia coli (NCBITaxon:562; PMID:21208457). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.",
        "llm_assisted": true
      }
    ],
    "discussions": [
      {
        "discussion_id": "kgscan-93e87bc8aba3",
        "prompt": "This record's graph enumerates bsl1 through bsl5, but BSL-5 is not an assigned containment level in any current national framework -- it appears in proposals for hypothetical agents beyond BSL-4. Is the bsl5 node a real classification this record should carry, or a seeded artefact to retract?",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "A containment level that does not exist in regulation is not a value the trait can take, and anything downstream that enumerates levels from this graph -- a risk-assessment form, an ontology mapping, a facility-capability query -- would inherit a level with no requirements attached to it. Note what the resolution is NOT: the node is already labelled a proposal and grounded to METPO:1001106, which the corpus carries as its own seeded record at ecology/biosafety_level_5.yaml, so deleting it here would desynchronise this graph from an upstream-seeded record rather than fix anything. A METPO class is not a citable proposal, so the question stands -- but it is answered by finding the source behind METPO:1001106, and any retraction belongs upstream in METPO, not in this graph.",
        "attaches_to": [
          "causal_graphs#bsl5"
        ],
        "posed_by": "claude",
        "notes": "Scan provenance (#409). The kg-microbe-kgscan pass raised this discussion with the prompt 'Knowledge gap for biosafety level: Additionally, it identifies ongoing challenges and critical knowledge gaps for future research.', whose sentence came from PMID:41494000. That sentence is about a review's boilerplate statement that gaps exist, not about this trait: the scan matched the hedging vocabulary of a gap statement without checking that the gap was about the trait it was filed under. The prompt above was authored instead from this record's own causal graph, and none of these references are carried as its evidence, because they support the scraped sentence rather than the question. The scan attached 3 further references whose snippets concern neither that sentence nor this trait; all 4 are reproduced here so nothing it produced is lost: PMID:41494000 'Additionally, it identifies ongoing challenges and critical knowledge gaps for future research.'; PMID:41556562 'This review outlines the possibilities, as well as the limitations of their use in food production.'; PMID:41647993 'Given the knowledge gap on the characteristics and significance of microbiome in early-onset pancreatic ductal adenocarcinoma (eoPDAC, age 50 years).'; PMID:41683313 'Background : Untargeted microbiome modulation has achieved conflicting results in post-infectious irritable bowel syndrome (PI-IBS).'.",
        "proposed_experiments": [
          {
            "experiment_id": "x-bsl5-provenance-check",
            "name": "Regulatory provenance check for the BSL-5 designation",
            "approach": "documentary review of containment frameworks",
            "model_systems": [
              "WHO Laboratory Biosafety Manual",
              "US CDC/NIH Biosafety in Microbiological and Biomedical Laboratories",
              "national biosafety regulations with assigned containment levels"
            ],
            "readouts": [
              "presence of an assigned BSL-5 level in each framework",
              "any peer-reviewed proposal defining BSL-5 requirements"
            ],
            "decision_criterion": "whether any binding framework assigns agents to a fifth level",
            "would_support": "a framework or a citable proposal defines it -- keep the node and cite that source on it, alongside the METPO grounding",
            "would_refute": "no framework or proposal defines it -- raise the retraction against METPO:1001106 upstream, so this graph and ecology/biosafety_level_5.yaml change together"
          }
        ],
        "posed_date": "2026-08-17"
      }
    ]
  },
  {
    "identifier": "METPO:1001102",
    "label": "biosafety level 1",
    "definition": "A biosafety level that poses minimal potential hazard to laboratory workers and the environment, requiring only standard microbiological practices.",
    "definition_source": "DOI:10.1146/annurev.micro.62.081307.162938",
    "trait_category": "ECOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1001101"
    ],
    "synonyms": [
      {
        "synonym_text": "1",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "created_by": "Anthea Guo",
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev.micro.62.081307.162938",
        "snippet": "virulence factors",
        "notes": "Virulence-factor review supports the absence or low expression of virulence factors in BSL-1 agents (non-pathogenic to healthy adults)."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1423",
        "taxon_label": "Bacillus subtilis",
        "note": "BSL-1 non-pathogen",
        "reference": "PMID:32391747"
      },
      {
        "taxon_id": "NCBITaxon:562",
        "taxon_label": "Escherichia coli",
        "note": "BSL-1 lab strain K-12",
        "reference": "PMID:21208457"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "biosafety_level_1_minimal_hazard",
        "title": "BSL-1 minimal-hazard classification",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This broad ecological, host-relationship, habitat, or hazard classification spans multiple taxa and mechanisms; contextual protein nodes do not receive token UniProt examples.",
        "description": "DOI-backed graph linking the absence of significant pathogen hazard properties to BSL-1 classification and minimal containment requirements.",
        "nodes": [
          {
            "node_id": "bsl1_trait",
            "label": "biosafety level 1",
            "node_type": "TRAIT",
            "grounding": "METPO:1001102",
            "description": "Minimal hazard to healthy adults; standard microbiological practices only."
          },
          {
            "node_id": "biosafety_level",
            "label": "biosafety level",
            "node_type": "TRAIT",
            "grounding": "METPO:1001101",
            "description": "Hazard-classification axis for biological agents."
          },
          {
            "node_id": "low_pathogen_hazard",
            "label": "low pathogen hazard",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Absence or low expression of virulence factors producing disease in healthy adults."
          },
          {
            "node_id": "low_risk_agent",
            "label": "low-risk agent",
            "node_type": "QUALITY",
            "description": "A biological agent unlikely to cause disease in healthy adults."
          },
          {
            "node_id": "standard_microbiological_practices",
            "label": "standard microbiological practices",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Basic containment relying on standard microbiological best practices and procedures."
          },
          {
            "node_id": "hand_washing",
            "label": "hand washing",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "A core good microbiological practice for risk reduction."
          },
          {
            "node_id": "risk_assessment_factors",
            "label": "biosafety risk assessment factors",
            "node_type": "EXPERIMENTAL_FACTOR",
            "description": "Pathogenicity, transmission route, stability, infectious dose, concentration, origin, prophylaxis, personnel experience."
          },
          {
            "node_id": "biosafety_level_selection",
            "label": "biosafety level selection",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Process of assigning a biosafety level based on risk assessment."
          },
          {
            "node_id": "virulence_traits",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Contextual protein family or multiprotein aggregate reviewed for this nonmechanistic classification; no single semantic family captures it.",
            "label": "specific virulence traits",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Genetic/protein determinants that render an organism capable of causing disease."
          },
          {
            "node_id": "disease_causation",
            "label": "disease causation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Process by which an organism causes disease in a host."
          }
        ],
        "edges": [
          {
            "subject": "low_pathogen_hazard",
            "predicate": "confers",
            "object": "bsl1_trait",
            "description": "Low pathogen hazard yields BSL-1 classification.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev.micro.62.081307.162938",
                "snippet": "virulence factors",
                "notes": "Supports the absence of virulence factors as the basis of BSL-1 classification."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "bsl1_trait",
            "predicate": "is a",
            "object": "biosafety_level",
            "description": "BSL-1 is a quantitative class within the biosafety-level classification axis.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev.micro.62.081307.162938",
                "snippet": "virulence factors",
                "notes": "Supports BSL-1 as a member of the biosafety-level classification."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "low_risk_agent",
            "predicate": "qualifies for",
            "object": "bsl1_trait",
            "description": "Low-risk agents unlikely to cause disease in healthy adults qualify for BSL-1.",
            "evidence": [
              {
                "reference": "DOI:10.3390/laboratories1030013",
                "notes": "BSL-1 is the level for low-risk agents unlikely to cause disease in healthy adults."
              }
            ]
          },
          {
            "subject": "low_pathogen_hazard",
            "predicate": "qualifies for",
            "object": "bsl1_trait",
            "description": "Organisms not known to consistently cause disease in healthy adults qualify for BSL-1.",
            "evidence": [
              {
                "reference": "DOI:10.2172/1887109",
                "notes": "Defined strains of viable microorganisms not known to consistently cause disease in healthy adult humans."
              }
            ]
          },
          {
            "subject": "standard_microbiological_practices",
            "predicate": "enables containment at",
            "object": "bsl1_trait",
            "description": "Standard microbiological practices provide the basic containment defining BSL-1.",
            "evidence": [
              {
                "reference": "DOI:10.47328/ufvbbt.2024.220",
                "notes": "BSL-1 represents a basic level of containment relying on standard microbiological best practices and procedures."
              }
            ]
          },
          {
            "subject": "hand_washing",
            "predicate": "is good microbiological practice supporting",
            "object": "standard_microbiological_practices",
            "description": "Hand washing is among the best good microbiological practices underpinning standard practices.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fpubh.2022.965853",
                "notes": "Among GMPP, one of the best practices is hand washing."
              }
            ]
          },
          {
            "subject": "risk_assessment_factors",
            "predicate": "determine",
            "object": "biosafety_level_selection",
            "description": "Risk assessment factors determine the biosafety level assigned to work.",
            "evidence": [
              {
                "reference": "DOI:10.2172/1887109",
                "notes": "Pathogenicity, route of transmission, stability, infectious dose, concentration, origin, prophylaxis, and personnel experience determine biosafety level."
              }
            ]
          },
          {
            "subject": "biosafety_level_selection",
            "predicate": "assigns",
            "object": "biosafety_level",
            "description": "The selection process assigns a biosafety level on the classification axis.",
            "evidence": [
              {
                "reference": "DOI:10.2172/1887109",
                "notes": "Risk assessment factors determine risk and therefore biosafety level assignment."
              }
            ]
          },
          {
            "subject": "virulence_traits",
            "predicate": "enables",
            "object": "disease_causation",
            "description": "Specific virulence traits render an organism capable of causing disease; their absence is compatible with BSL-1.",
            "evidence": [
              {
                "reference": "DOI:10.3390/microorganisms11020344",
                "notes": "Strains encode specific virulence traits that render them capable of causing disease."
              }
            ],
            "predicate_id": "RO:0002327"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.932513+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-13T13:30:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed causal graph linking low pathogen hazard to BSL-1 classification.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:29Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d71, rdfs:subClassOf\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 7 evidence-backed generic edges (7 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:09Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates (1 to confers), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope biosafety_level_1_minimal_hazard=NONMECHANISTIC with scope_notes; marked 1 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (virulence_traits).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1001103",
    "label": "biosafety level 2",
    "definition": "A biosafety level that poses moderate risk and is associated with human diseases present in the community.",
    "definition_source": "DOI:10.1146/annurev.micro.62.081307.162938",
    "trait_category": "ECOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1001101"
    ],
    "synonyms": [
      {
        "synonym_text": "2",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev.micro.62.081307.162938",
        "snippet": "virulence factors",
        "notes": "Virulence-factor review supports moderate-virulence community-disease pathogens (typically with available vaccines or therapies) as BSL-2 agents."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1280",
        "taxon_label": "Staphylococcus aureus",
        "note": "BSL-2 pathogen",
        "reference": "PMID:23408135"
      },
      {
        "taxon_id": "NCBITaxon:28901",
        "taxon_label": "Salmonella enterica",
        "note": "BSL-2 pathogen",
        "reference": "PMID:32731970"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "biosafety_level_2_moderate_hazard",
        "title": "BSL-2 moderate-hazard classification",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This broad ecological, host-relationship, habitat, or hazard classification spans multiple taxa and mechanisms; contextual protein nodes do not receive token UniProt examples.",
        "description": "DOI-backed graph linking moderate pathogen virulence and the presence of effective countermeasures to BSL-2 classification.",
        "nodes": [
          {
            "node_id": "bsl2_trait",
            "label": "biosafety level 2",
            "node_type": "TRAIT",
            "grounding": "METPO:1001103",
            "description": "Moderate-risk agents associated with community human diseases; biosafety cabinets and PPE required."
          },
          {
            "node_id": "biosafety_level",
            "label": "biosafety level",
            "node_type": "TRAIT",
            "grounding": "METPO:1001101",
            "description": "Hazard-classification axis for biological agents."
          },
          {
            "node_id": "moderate_pathogen_hazard",
            "label": "moderate pathogen hazard",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Pathogens with established virulence in healthy adults but generally treatable with available countermeasures."
          },
          {
            "node_id": "risk_group_2_pathogen",
            "label": "risk group 2 pathogen",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Agent of moderate individual risk and limited community risk; mapped to BSL-2 containment."
          },
          {
            "node_id": "pathogenicity",
            "label": "pathogenicity",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Capacity of an agent to cause disease; a criterion used in risk-group assignment."
          },
          {
            "node_id": "mode_of_transmission",
            "label": "mode and ease of transmission",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Route and efficiency of agent transmission; a criterion used in risk-group assignment."
          },
          {
            "node_id": "aerosol_splash_procedure",
            "label": "aerosol- or splash-generating procedure",
            "node_type": "EXPERIMENTAL_FACTOR",
            "description": "Laboratory procedures producing infectious aerosols or splashes."
          },
          {
            "node_id": "biosafety_cabinet",
            "label": "biological safety cabinet class I/II",
            "node_type": "EXPERIMENTAL_FACTOR",
            "description": "Engineering control used at BSL-2 for aerosol/splash-generating procedures."
          },
          {
            "node_id": "appropriate_ppe",
            "label": "appropriate personal protective equipment",
            "node_type": "EXPERIMENTAL_FACTOR",
            "description": "Lab coat, gloves, and eye protection as needed at BSL-2."
          },
          {
            "node_id": "restricted_lab_access",
            "label": "restricted laboratory access",
            "node_type": "EXPERIMENTAL_FACTOR",
            "description": "Administrative control limiting laboratory entry, required at BSL-2."
          }
        ],
        "edges": [
          {
            "subject": "moderate_pathogen_hazard",
            "predicate": "confers",
            "object": "bsl2_trait",
            "description": "Moderate pathogen hazard with available countermeasures yields BSL-2 classification.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev.micro.62.081307.162938",
                "snippet": "virulence factors",
                "notes": "Supports moderate virulence with treatability as the basis of BSL-2 classification."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "bsl2_trait",
            "predicate": "is a",
            "object": "biosafety_level",
            "description": "BSL-2 is a member of the biosafety-level classification.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev.micro.62.081307.162938",
                "snippet": "virulence factors",
                "notes": "Supports BSL-2 as a member of the biosafety-level classification."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "risk_group_2_pathogen",
            "predicate": "supports assignment to",
            "object": "bsl2_trait",
            "description": "RG2 agents (moderate individual, limited community risk) are assigned to BSL-2 containment.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.pathol.2020.09.006",
                "notes": "Risk Group 2 (\"moderate individual risk, limited community risk\") associates RG-2 agents with BSL-2/PC-2."
              }
            ]
          },
          {
            "subject": "pathogenicity",
            "predicate": "influences selection of",
            "object": "bsl2_trait",
            "description": "Agent pathogenicity is a criterion driving risk-group/biosafety-level assignment.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.pathol.2020.09.006",
                "notes": "Risk Groups are assigned based on pathogenicity, transmission, host range, and countermeasure availability."
              }
            ]
          },
          {
            "subject": "mode_of_transmission",
            "predicate": "influences selection of",
            "object": "bsl2_trait",
            "description": "Mode and ease of transmission is a criterion driving biosafety-level assignment; airborne transmission escalates above BSL-2.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.pathol.2020.09.006",
                "notes": "Risk Groups assigned based on mode/ease of transmission; airborne lethal agents are escalated to BSL-3."
              }
            ]
          },
          {
            "subject": "aerosol_splash_procedure",
            "predicate": "necessitates use of",
            "object": "biosafety_cabinet",
            "description": "Procedures generating infectious aerosols or splashes require a class I/II biological safety cabinet at BSL-2.",
            "evidence": [
              {
                "reference": "DOI:10.1007/978-1-4939-8935-5_19",
                "notes": "All procedures that could create infectious aerosols/splashes are conducted in biological safety cabinets at BSL-2."
              }
            ]
          },
          {
            "subject": "appropriate_ppe",
            "predicate": "mitigates risk in",
            "object": "bsl2_trait",
            "description": "Lab coats, gloves, and eye protection reduce exposure risk at BSL-2.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.pathol.2020.09.006",
                "notes": "Appropriate PPE (lab coats and gloves), with eye protection as needed, must be worn in BSL-2/PC-2."
              }
            ]
          },
          {
            "subject": "restricted_lab_access",
            "predicate": "is required for",
            "object": "bsl2_trait",
            "description": "Restricted laboratory access is a required administrative control at BSL-2.",
            "evidence": [
              {
                "reference": "DOI:10.1007/978-1-4939-8935-5_19",
                "notes": "BSL-2 requires restricted access and additional agent-specific training compared with BSL-1."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.933068+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-13T13:30:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed causal graph linking moderate pathogen hazard to BSL-2 classification.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:29Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d71, rdfs:subClassOf\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 6 evidence-backed generic edges (7 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates (1 to confers), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-17T22:14:03Z",
        "curator": "claude",
        "action": "CURATE_KNOWLEDGE_GAPS",
        "changes": "Replaced the scan's off-topic scraped sentence with a research question authored from this record's causal graph, anchored it via attaches_to, and sketched an experiment with a decision criterion. The scan's sentence and PMIDs are preserved in the discussion's notes.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope biosafety_level_2_moderate_hazard=NONMECHANISTIC with scope_notes.",
        "llm_assisted": true
      }
    ],
    "discussions": [
      {
        "discussion_id": "kgscan-066a51aacfb6",
        "prompt": "BSL-2 requires a biosafety cabinet specifically for procedures with aerosol or splash potential, while other work may go on the open bench. Which procedures actually generate an infectious dose at the breathing zone, and does the current procedure list match them?",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "The bench/cabinet boundary is the single control that most BSL-2 work turns on, and it is drawn from procedure lists that long predate quantitative aerosol measurement. A procedure that is on the open bench but does generate respirable particles is an unrecognised exposure; one needlessly in the cabinet costs throughput. Either way the edge into biosafety_cabinet is asserting something measurable that has not been measured.",
        "attaches_to": [
          "causal_graphs#aerosol_splash_procedure",
          "causal_graphs#biosafety_cabinet"
        ],
        "posed_by": "claude",
        "notes": "Scan provenance (#409). The kg-microbe-kgscan pass raised this discussion with the prompt 'Knowledge gap for biosafety level 2: Background : Untargeted microbiome modulation has achieved conflicting results in post-infectious irritable bowel syndrome (PI-IBS).', whose sentence came from PMID:41683313. That sentence is about microbiome modulation in post-infectious IBS, not about this trait: the scan matched the hedging vocabulary of a gap statement without checking that the gap was about the trait it was filed under. The prompt above was authored instead from this record's own causal graph, and none of these references are carried as its evidence, because they support the scraped sentence rather than the question. The scan attached 3 further references whose snippets concern neither that sentence nor this trait; all 4 are reproduced here so nothing it produced is lost: PMID:41683313 'Background : Untargeted microbiome modulation has achieved conflicting results in post-infectious irritable bowel syndrome (PI-IBS).'; PMID:41413233 'Recently, the gut microbiota (GM) has gained attention for its potential involvement in blood pressure regulation; however, polyamine metabolism involvement remains poorly understood.'; PMID:41640410 'However, their clinical translation is hampered by challenges within the harsh gastrointestinal milieu, including low viability, poor colonization, and insufficient target specificity.'; PMID:41490313 'However, how these core strains interact with each other and with other gut microbes is largely unknown.'.",
        "proposed_experiments": [
          {
            "experiment_id": "x-bsl2-aerosol-tracer",
            "name": "Surrogate-tracer aerosol survey of routine BSL-2 procedures",
            "approach": "non-infectious tracer release with breathing-zone sampling",
            "model_systems": [
              "bacteriophage or fluorescent-bead surrogate at defined titre",
              "a working BSL-2 laboratory",
              "breathing-zone and area impingers"
            ],
            "perturbations": [
              "each routine procedure performed on the open bench",
              "the same procedure performed inside a class II cabinet",
              "deliberate worst-case variants such as a dropped tube"
            ],
            "readouts": [
              "tracer recovered at the breathing zone per procedure",
              "particle size distribution in the respirable fraction",
              "surface deposition beyond the immediate work area"
            ],
            "decision_criterion": "whether any open-bench procedure exceeds the breathing-zone tracer recovery of cabinet-required procedures",
            "would_support": "recovery tracks the existing list -- the procedure boundary is drawn where the aerosol actually is",
            "would_refute": "an off-list procedure matches or exceeds a listed one -- the control boundary is misplaced"
          }
        ],
        "posed_date": "2026-08-17"
      }
    ]
  },
  {
    "identifier": "METPO:1001104",
    "label": "biosafety level 3",
    "definition": "A biosafety level that can cause serious or potentially lethal disease through inhalation or other routes, requiring specialized containment facilities with controlled access, directional airflow, and strict safety protocols.",
    "definition_source": "DOI:10.1146/annurev.micro.62.081307.162938",
    "trait_category": "ECOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1001101"
    ],
    "synonyms": [
      {
        "synonym_text": "3",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "3**",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "created_by": "Jed Dongjin Kim-Ozaeta",
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev.micro.62.081307.162938",
        "snippet": "virulence factors",
        "notes": "Virulence-factor review supports highly virulent aerosol-transmissible pathogens (serious or potentially lethal disease) as BSL-3 agents."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1773",
        "taxon_label": "Mycobacterium tuberculosis",
        "note": "BSL-3 pathogen",
        "reference": "PMID:9634230"
      },
      {
        "taxon_id": "NCBITaxon:632",
        "taxon_label": "Yersinia pestis",
        "note": "BSL-3 pathogen",
        "reference": "PMID:11586360"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "biosafety_level_3_serious_hazard",
        "title": "BSL-3 serious-hazard classification",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This broad ecological, host-relationship, habitat, or hazard classification spans multiple taxa and mechanisms; contextual protein nodes do not receive token UniProt examples.",
        "description": "DOI-backed graph linking serious/lethal disease potential and aerosol transmission risk to BSL-3 classification.",
        "nodes": [
          {
            "node_id": "bsl3_trait",
            "label": "biosafety level 3",
            "node_type": "TRAIT",
            "grounding": "METPO:1001104",
            "description": "Agents causing serious or potentially lethal disease, often via inhalation; specialized containment required."
          },
          {
            "node_id": "biosafety_level",
            "label": "biosafety level",
            "node_type": "TRAIT",
            "grounding": "METPO:1001101",
            "description": "Hazard-classification axis for biological agents."
          },
          {
            "node_id": "serious_pathogen_hazard",
            "label": "serious pathogen hazard",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Highly virulent pathogens with aerosol transmission potential causing serious or lethal disease."
          },
          {
            "node_id": "aerosol_transmission_risk",
            "label": "aerosol transmission risk",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Risk of agent transmission via aerosols, driving need for high containment."
          },
          {
            "node_id": "negative_pressure_airflow",
            "label": "negative pressure directional airflow",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Inward directional airflow with negative pressure (2.5-10 Pa) used as a BSL-3 engineering control."
          },
          {
            "node_id": "hepa_filtration",
            "label": "HEPA filtration of exhaust air",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "HEPA-filtered exhaust removing 99.97% of particles >=0.3 um as a BSL-3 engineering control."
          },
          {
            "node_id": "boundary_integrity_testing",
            "label": "boundary integrity testing",
            "node_type": "EXPERIMENTAL_FACTOR",
            "description": "Quantitative leakage/porosity testing verifying that a containment room meets minimum requirements."
          },
          {
            "node_id": "pressure_decay_testing",
            "label": "pressure decay testing",
            "node_type": "EXPERIMENTAL_FACTOR",
            "description": "Leakage test maintaining steady negative pressure to quantify containment integrity."
          },
          {
            "node_id": "iso_35001_biorisk_management",
            "label": "ISO 35001 biorisk management system",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Plan-Do-Check-Act biorisk management-system standard for laboratory biosafety."
          },
          {
            "node_id": "laboratory_acquired_infection",
            "label": "laboratory-acquired infection",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Infection acquired by personnel during laboratory work with biological agents."
          }
        ],
        "edges": [
          {
            "subject": "serious_pathogen_hazard",
            "predicate": "confers",
            "object": "bsl3_trait",
            "description": "Serious pathogen hazard with aerosol risk yields BSL-3 classification.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev.micro.62.081307.162938",
                "snippet": "virulence factors",
                "notes": "Supports high virulence with aerosol transmissibility as the basis of BSL-3 classification."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "bsl3_trait",
            "predicate": "is a",
            "object": "biosafety_level",
            "description": "BSL-3 is a member of the biosafety-level classification.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev.micro.62.081307.162938",
                "snippet": "virulence factors",
                "notes": "Supports BSL-3 as a member of the biosafety-level classification."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "aerosol_transmission_risk",
            "predicate": "necessitates",
            "object": "bsl3_trait",
            "description": "Risk of severe/lethal disease via aerosol route necessitates BSL-3 containment.",
            "evidence": [
              {
                "reference": "DOI:10.64483/jmph-115",
                "notes": "\"can cause severe or lethal disease by aerosol route... requires respiratory protection\""
              }
            ]
          },
          {
            "subject": "bsl3_trait",
            "predicate": "implemented by",
            "object": "negative_pressure_airflow",
            "description": "BSL-3 containment is implemented by negative-pressure directional airflow.",
            "evidence": [
              {
                "reference": "DOI:10.64483/jmph-115",
                "notes": "\"negative pressure (2.5 to 10 Pascals) with inward airflow\""
              }
            ]
          },
          {
            "subject": "bsl3_trait",
            "predicate": "implemented by",
            "object": "hepa_filtration",
            "description": "BSL-3 containment is implemented by HEPA filtration of exhaust air.",
            "evidence": [
              {
                "reference": "DOI:10.64483/jmph-115",
                "notes": "\"HEPA-filtered exhaust (eliminating 99.97% of particles >=0.3 um)\""
              }
            ]
          },
          {
            "subject": "bsl3_trait",
            "predicate": "verified by",
            "object": "boundary_integrity_testing",
            "description": "BSL-3 containment integrity is verified by quantitative boundary integrity testing.",
            "evidence": [
              {
                "reference": "DOI:10.1089/apb.2023.0017",
                "notes": "\"quantitative leakage testing to verify it meets minimum requirements\""
              }
            ]
          },
          {
            "subject": "boundary_integrity_testing",
            "predicate": "utilizes",
            "object": "pressure_decay_testing",
            "description": "Boundary integrity testing utilizes pressure decay testing under steady negative pressure.",
            "evidence": [
              {
                "reference": "DOI:10.1089/apb.2023.0017",
                "notes": "\"maintain a steady negative pressure during leakage testing\""
              }
            ]
          },
          {
            "subject": "iso_35001_biorisk_management",
            "predicate": "mitigates",
            "object": "laboratory_acquired_infection",
            "description": "ISO 35001 biorisk management systems mitigate laboratory-acquired infections.",
            "evidence": [
              {
                "reference": "DOI:10.26686/nzjhsp.v1i2.9540",
                "notes": "\"safety management systems generally improve health and safety performance\""
              }
            ],
            "predicate_id": "METPO:2007407"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.933585+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-13T13:30:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed causal graph linking serious pathogen hazard with aerosol transmission to BSL-3 classification.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:29Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d71, rdfs:subClassOf\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 6 evidence-backed generic edges (7 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:09Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007407\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates (1 to confers), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-17T22:14:03Z",
        "curator": "claude",
        "action": "CURATE_KNOWLEDGE_GAPS",
        "changes": "Replaced the scan's off-topic scraped sentence with a research question authored from this record's causal graph, anchored it via attaches_to, and sketched an experiment with a decision criterion. The scan's sentence and PMIDs are preserved in the discussion's notes.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope biosafety_level_3_serious_hazard=NONMECHANISTIC with scope_notes.",
        "llm_assisted": true
      }
    ],
    "discussions": [
      {
        "discussion_id": "kgscan-2ee31ba13f9c",
        "prompt": "BSL-3 boundary integrity is verified by pressure-decay testing of the room envelope. Does passing a pressure-decay test predict containment of an airborne agent under real operating conditions, with doors cycling and equipment running?",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "The graph routes verification the other way round from the claim it supports: bsl3_trait is `verified by` boundary_integrity_testing, which `utilizes` pressure_decay_testing. So the decay test stands in for containment without any node asserting that containment holds. The test is also performed on a sealed, static room, and the room only matters when it is occupied and in use. If the two diverge, facilities are certified against a condition they never operate in.",
        "attaches_to": [
          "causal_graphs#boundary_integrity_testing",
          "causal_graphs#pressure_decay_testing"
        ],
        "posed_by": "claude",
        "notes": "Scan provenance (#409). The kg-microbe-kgscan pass raised this discussion with the prompt 'Knowledge gap for biosafety level 3: Additionally, it identifies ongoing challenges and critical knowledge gaps for future research.', whose sentence came from PMID:41494000. That sentence is about a review's boilerplate statement that gaps exist, not about this trait: the scan matched the hedging vocabulary of a gap statement without checking that the gap was about the trait it was filed under. The prompt above was authored instead from this record's own causal graph, and none of these references are carried as its evidence, because they support the scraped sentence rather than the question. The scan attached 3 further references whose snippets concern neither that sentence nor this trait; all 4 are reproduced here so nothing it produced is lost: PMID:41494000 'Additionally, it identifies ongoing challenges and critical knowledge gaps for future research.'; PMID:40514544 'Although T cells are essential for immunity to TB, the mechanisms that provide protective immunity are poorly understood.'; PMID:41552424 'In the field of microbiological diagnosis, HTS provides a complementary or alternative approach to traditional diagnostic tests, particularly in cases with non-specific symptoms or when the etiology is unknown.'; PMID:41917383 'While its virulence genes critically regulate intracellular survival and replication, the molecular mechanisms underlying pathogenesis remain elusive.'.",
        "proposed_experiments": [
          {
            "experiment_id": "x-bsl3-decay-vs-tracer",
            "name": "Tracer-gas containment under operation versus decay-test result",
            "approach": "paired tracer-gas release and envelope pressure-decay testing",
            "model_systems": [
              "commissioned BSL-3 suites spanning a range of decay results",
              "SF6 or equivalent inert tracer with anteroom sampling"
            ],
            "perturbations": [
              "static sealed room, as in the certification test",
              "normal operation with personnel entry and exit",
              "a single HEPA-filtered exhaust fan taken offline"
            ],
            "readouts": [
              "tracer concentration outside the containment boundary",
              "directional airflow at the door plane",
              "measured envelope leakage rate"
            ],
            "decision_criterion": "whether tracer escape under operation correlates with the static decay-test result across suites",
            "would_support": "suites with better decay results leak less tracer in operation -- the test predicts what it is used to certify",
            "would_refute": "escape under operation is uncorrelated with decay result -- passing certifies the sealed room and not the working one"
          }
        ],
        "posed_date": "2026-08-17"
      }
    ]
  },
  {
    "identifier": "METPO:1001105",
    "label": "biosafety level 4",
    "definition": "A biosafety level that poses extreme risk of life-threatening disease through aerosol transmission with no available treatment.",
    "definition_source": "DOI:10.1146/annurev.micro.62.081307.162938",
    "trait_category": "ECOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1001101"
    ],
    "synonyms": [
      {
        "synonym_text": "4",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev.micro.62.081307.162938",
        "snippet": "virulence factors",
        "notes": "Virulence-factor review supports the extreme virulence and absence of countermeasures characteristic of BSL-4 agents."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:186538",
        "taxon_label": "Zaire ebolavirus",
        "reference": "https://www.canada.ca/en/public-health/services/laboratory-biosafety-biosecurity/pathogen-safety-data-sheets-risk-assessment/ebolavirus.html",
        "note": "Zaire ebolavirus is assigned to the highest existing containment category by the cited national pathogen-safety authority and is a concrete BSL-4 agent."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "biosafety_level_4_extreme_hazard",
        "title": "BSL-4 extreme-hazard classification",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This broad ecological, host-relationship, habitat, or hazard classification spans multiple taxa and mechanisms; contextual protein nodes do not receive token UniProt examples.",
        "description": "DOI-backed graph linking extreme virulence, aerosol transmissibility, and absence of available treatments to BSL-4 classification.",
        "nodes": [
          {
            "node_id": "bsl4_trait",
            "label": "biosafety level 4",
            "node_type": "TRAIT",
            "grounding": "METPO:1001105",
            "description": "Extreme-risk agents causing life-threatening disease with no available treatment; maximum containment required."
          },
          {
            "node_id": "biosafety_level",
            "label": "biosafety level",
            "node_type": "TRAIT",
            "grounding": "METPO:1001101",
            "description": "Hazard-classification axis for biological agents."
          },
          {
            "node_id": "extreme_pathogen_hazard",
            "label": "extreme pathogen hazard",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Pathogens with extreme virulence, aerosol transmission, and absent or inadequate medical countermeasures."
          },
          {
            "node_id": "life_threatening_disease",
            "label": "life-threatening disease",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Disease that threatens the life of a healthy host, a defining hazard criterion for BSL-4 agents."
          },
          {
            "node_id": "no_effective_countermeasure",
            "label": "absence of effective prevention or treatment",
            "node_type": "STATE",
            "description": "Lack of available vaccine or therapy for the agent, a defining BSL-4 hazard criterion."
          },
          {
            "node_id": "aerosol_lab_infection_risk",
            "label": "high risk of aerosol-transmitted laboratory infection",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "High likelihood of laboratory-acquired infection via aerosol transmission."
          },
          {
            "node_id": "positive_pressure_suit",
            "label": "positive-pressure air-supplied suit",
            "node_type": "EXPERIMENTAL_FACTOR",
            "description": "Full-body positive-pressure air-supplied protective suit, a hallmark engineering control of BSL-4 suit labs."
          },
          {
            "node_id": "airlock",
            "label": "airlock",
            "node_type": "EXPERIMENTAL_FACTOR",
            "description": "Air-sealed entry/exit chamber required for BSL-4 maximum-containment facilities."
          },
          {
            "node_id": "decontamination_shower",
            "label": "decontamination shower",
            "node_type": "EXPERIMENTAL_FACTOR",
            "description": "Mandatory personnel decontamination shower in BSL-4 facilities."
          },
          {
            "node_id": "specialized_waste_disposal",
            "label": "specialized waste disposal",
            "node_type": "EXPERIMENTAL_FACTOR",
            "description": "Specialized waste decontamination and disposal system required at BSL-4."
          }
        ],
        "edges": [
          {
            "subject": "extreme_pathogen_hazard",
            "predicate": "confers",
            "object": "bsl4_trait",
            "description": "Extreme pathogen hazard without available treatment yields BSL-4 classification.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev.micro.62.081307.162938",
                "snippet": "virulence factors",
                "notes": "Supports extreme virulence with absent countermeasures as the basis of BSL-4 classification."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "bsl4_trait",
            "predicate": "is a",
            "object": "biosafety_level",
            "description": "BSL-4 is a member of the biosafety-level classification.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev.micro.62.081307.162938",
                "snippet": "virulence factors",
                "notes": "Supports BSL-4 as a member of the biosafety-level classification."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "life_threatening_disease",
            "predicate": "requires containment level",
            "object": "bsl4_trait",
            "description": "Organisms causing life-threatening disease in a healthy host require BSL-4 maximum containment.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.pathol.2020.09.006",
                "notes": "\"Organisms that cause life-threatening disease in a healthy host...\""
              },
              {
                "reference": "DOI:10.3390/laboratories1030013",
                "notes": "BSL-4 as the highest containment level for the most dangerous, life-threatening agents."
              }
            ]
          },
          {
            "subject": "no_effective_countermeasure",
            "predicate": "requires containment level",
            "object": "bsl4_trait",
            "description": "Absence of effective prevention or treatment for an agent mandates BSL-4 containment.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.pathol.2020.09.006",
                "notes": "\"effective prevention and/or treatment are not usually available\""
              },
              {
                "reference": "DOI:10.3390/laboratories1030013",
                "notes": "BSL-4 representing maximum containment for agents with severe risks and no available treatments."
              }
            ]
          },
          {
            "subject": "aerosol_lab_infection_risk",
            "predicate": "requires containment level",
            "object": "bsl4_trait",
            "description": "High risk of aerosol-transmitted laboratory infection is a defining BSL-4 criterion.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.pathol.2020.09.006",
                "notes": "\"pose a high risk of aerosol-transmitted laboratory infections with no vaccine or therapy\""
              }
            ]
          },
          {
            "subject": "bsl4_trait",
            "predicate": "necessitates use of",
            "object": "positive_pressure_suit",
            "description": "BSL-4 containment necessitates wearing a full-body positive-pressure air-supplied suit.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.pathol.2020.09.006",
                "notes": "\"wearing a full body, positive pressure, air supplied suit\""
              },
              {
                "reference": "DOI:10.3390/laboratories1030013",
                "notes": "Suit labs adopted positive pressure suits as a hallmark advanced containment strategy."
              }
            ]
          },
          {
            "subject": "bsl4_trait",
            "predicate": "requires",
            "object": "airlock",
            "description": "BSL-4 facilities require airlocks as a maximum-containment engineering control.",
            "evidence": [
              {
                "reference": "DOI:10.3390/laboratories1030013",
                "notes": "\"requires airlocks, showers, and specialized waste disposal\""
              }
            ]
          },
          {
            "subject": "bsl4_trait",
            "predicate": "requires",
            "object": "decontamination_shower",
            "description": "BSL-4 facilities require personnel decontamination showers.",
            "evidence": [
              {
                "reference": "DOI:10.3390/laboratories1030013",
                "notes": "\"requires airlocks, showers, and specialized waste disposal\""
              }
            ]
          },
          {
            "subject": "bsl4_trait",
            "predicate": "requires",
            "object": "specialized_waste_disposal",
            "description": "BSL-4 facilities require specialized waste disposal systems.",
            "evidence": [
              {
                "reference": "DOI:10.3390/laboratories1030013",
                "notes": "\"requires airlocks, showers, and specialized waste disposal\""
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.934198+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-13T13:30:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed causal graph linking extreme pathogen hazard to BSL-4 classification.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:29Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d71, rdfs:subClassOf\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 7 evidence-backed generic edges (7 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates (1 to confers), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-17T22:14:03Z",
        "curator": "claude",
        "action": "CURATE_KNOWLEDGE_GAPS",
        "changes": "Replaced the scan's off-topic scraped sentence with a research question authored from this record's causal graph, anchored it via attaches_to, and sketched an experiment with a decision criterion. The scan's sentence and PMIDs are preserved in the discussion's notes.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope biosafety_level_4_extreme_hazard=NONMECHANISTIC with scope_notes.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T04:43:24Z",
        "curator": "codex",
        "action": "ADD_CANONICAL_EXAMPLES",
        "changes": "Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Zaire ebolavirus (NCBITaxon:186538; https://www.canada.ca/en/public-health/services/laboratory-biosafety-biosecurity/pathogen-safety-data-sheets-risk-assessment/ebolavirus.html). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.",
        "llm_assisted": true
      }
    ],
    "discussions": [
      {
        "discussion_id": "kgscan-e770cf01677c",
        "prompt": "Every BSL-4 control this record requires assumes terrestrial gravity and somewhere to put contaminated air, water and waste -- suit overpressure, airlocks, chemical showers, specialized waste disposal. Which still contain an agent in a closed-loop habitat that recycles all three?",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Sample-return and crewed-habitat missions need containment for agents with no countermeasure, which is exactly what BSL-4 is for. But every control edge runs outward from bsl4_trait to a piece of equipment -- `requires` an airlock, a decontamination shower, specialized waste disposal; `necessitates use of` a positive pressure suit -- so the controls are named as hardware rather than as the physics they rely on, and it is the physics that does or does not transfer. Sedimentation-dependent controls behave differently in microgravity, and a shower and a waste stream that both feed a recycling loop are not disposal. As written the record cannot distinguish a control that survives the move from one that does not, because it never says what any of them do.",
        "attaches_to": [
          "causal_graphs#positive_pressure_suit",
          "causal_graphs#airlock",
          "causal_graphs#decontamination_shower",
          "causal_graphs#specialized_waste_disposal"
        ],
        "posed_by": "claude",
        "notes": "Scan provenance (#409). The kg-microbe-kgscan pass raised this discussion with the prompt 'Knowledge gap for biosafety level 4: Finally, this review examines the largely unknown microbiology and infection implications of celestial body habitation with an emphasis placed on Mars.', whose sentence came from PMID:37362850. That sentence is about microbiology and infection during celestial body habitation, not about this trait: the scan matched the hedging vocabulary of a gap statement without checking that the gap was about the trait it was filed under. The prompt above was authored instead from this record's own causal graph, and none of these references are carried as its evidence, because they support the scraped sentence rather than the question. The scan attached 3 further references whose snippets concern neither that sentence nor this trait; all 4 are reproduced here so nothing it produced is lost: PMID:37362850 'Finally, this review examines the largely unknown microbiology and infection implications of celestial body habitation with an emphasis placed on Mars.'; PMID:41914886 'Both Old World arenaviruses LASV and LCMV exploit host tyrosine kinase signaling to establish infection, though the molecular mechanisms remain incompletely understood.'; PMID:40044492 'However, the comparatively low scientific commitment of countries that are usually among the major players in global scientific publications and the declining scientific interest in NiV research combined with the prevailing knowledge gaps in NiV infectiology in conjunction with the risk of NiV spreading to other areas is extremely threatening.'; PMID:39682751 'The COVID-19 pandemic has underscored the limitations of focusing solely on the pathogen-killing strategies of immunology and microbiology to address complex, multisystemic infectious diseases.'.",
        "proposed_experiments": [
          {
            "experiment_id": "x-bsl4-closed-loop-transfer",
            "name": "Control-by-control containment audit in a closed-loop analogue",
            "approach": "analogue-habitat tracer study with parabolic-flight aerosol runs",
            "model_systems": [
              "sealed closed-loop habitat analogue with recycled atmosphere",
              "parabolic flight or drop-tower reduced-gravity segments",
              "non-infectious spore and fluorescent-particle tracers"
            ],
            "perturbations": [
              "suit breach at defined overpressure",
              "airlock cycling with no atmospheric exhaust available",
              "chemical shower under water-recovery constraints"
            ],
            "readouts": [
              "tracer crossing the containment boundary per control",
              "settling versus suspension time in reduced gravity",
              "tracer persisting in the atmospheric recycling loop"
            ],
            "decision_criterion": "which controls hold tracer escape at terrestrial levels once gravity and exhaust assumptions are removed",
            "would_support": "overpressure-based controls transfer intact -- they depend on pressure differential, not on settling or exhaust",
            "would_refute": "escape rises for controls that passed on the ground -- the BSL-4 set does not transfer and needs habitat-specific equivalents"
          }
        ],
        "posed_date": "2026-08-17"
      }
    ]
  },
  {
    "identifier": "METPO:1001106",
    "label": "biosafety level 5",
    "definition": "A biosafety level that is proposed as a classification beyond BSL-4 for hypothetical biological agents requiring enhanced containment.",
    "definition_source": "DOI:10.1146/annurev.micro.62.081307.162938",
    "trait_category": "ECOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1001101"
    ],
    "synonyms": [
      {
        "synonym_text": "5",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev.micro.62.081307.162938",
        "snippet": "virulence factors",
        "notes": "Virulence-factor review supports the framing of pathogen hazard above existing BSL-4 thresholds (the rationale underlying the proposed BSL-5 classification)."
      },
      {
        "reference": "DOI:10.4271/2002-01-2469",
        "snippet": "informally called BSL-5",
        "notes": "Verified against the open Cohen 2002 SAE paper; PPL-alpha is retained as historical BSL-5 name-use evidence, not as the scope of the generic METPO class."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "biosafety_level_5_proposed_enhanced_hazard",
        "title": "BSL-5 proposed enhanced-hazard classification",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This broad ecological, host-relationship, habitat, or hazard classification spans multiple taxa and mechanisms; contextual protein nodes do not receive token UniProt examples.",
        "description": "DOI-backed graph linking hypothetical pathogen hazards exceeding BSL-4 thresholds to the proposed BSL-5 enhanced-containment classification, with PPL-alpha retained only as record-level historical name-use evidence.",
        "nodes": [
          {
            "node_id": "bsl5_trait",
            "label": "biosafety level 5",
            "node_type": "TRAIT",
            "grounding": "METPO:1001106",
            "description": "Proposed enhanced-containment classification beyond BSL-4 for hypothetical extreme-hazard agents."
          },
          {
            "node_id": "biosafety_level",
            "label": "biosafety level",
            "node_type": "TRAIT",
            "grounding": "METPO:1001101",
            "description": "Hazard-classification axis for biological agents."
          },
          {
            "node_id": "enhanced_pathogen_hazard",
            "label": "enhanced pathogen hazard",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Hypothetical pathogen hazards judged to exceed the transmissibility, severity, or treatability thresholds covered by BSL-4."
          }
        ],
        "edges": [
          {
            "subject": "enhanced_pathogen_hazard",
            "predicate": "motivates",
            "object": "bsl5_trait",
            "description": "Hazards exceeding BSL-4 thresholds motivate the proposed BSL-5 enhanced-containment classification.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev.micro.62.081307.162938",
                "snippet": "virulence factors",
                "notes": "Supports increasingly severe virulence-factor combinations as the rationale for hazard classes above BSL-4."
              }
            ]
          },
          {
            "subject": "bsl5_trait",
            "predicate": "is a",
            "object": "biosafety_level",
            "description": "BSL-5 is a proposed member of the biosafety-level classification.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev.micro.62.081307.162938",
                "snippet": "virulence factors",
                "notes": "Supports BSL-5 as a proposed extension of the biosafety-level classification axis."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.934696+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-13T13:30:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed causal graph linking enhanced pathogen hazards to the proposed BSL-5 enhanced-containment classification.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:29Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (rdfs:subClassOf\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope biosafety_level_5_proposed_enhanced_hazard=NONMECHANISTIC with scope_notes.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T04:43:24Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed issue #444 after #591 and left canonical_examples empty: The class is explicitly hypothetical and above every implemented containment level; assigning a real organism would falsely assert an authority-backed BSL-5 classification that does not exist. No paid research was used.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-04T10:00:00Z",
        "curator": "codex",
        "action": "REVIEW_CAUSAL_EVIDENCE",
        "changes": "Reviewed the biosafety_level_5_proposed_enhanced_hazard graph for issue #183: kept the generic proposed enhanced-hazard BSL-5 graph grounded in the pathogen-hazard definition DOI, added DOI-backed historical PPL-alpha name-use evidence from the Cohen 2002 SAE paper, added exact snippets to record and edge evidence, and kept BSL-5 scoped as an explicitly hypothetical nonmechanistic containment proposal. No paid research service was called.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-06T13:30:00Z",
        "curator": "codex",
        "action": "ADVERSARIAL_REVIEW_REPAIR",
        "changes": "Addressed PR #664 adversarial review issue #668: restored the DOI definition source and DOI-backed top-level evidence while preserving the SAE PPL-alpha source as additional top-level evidence and the graph source.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-06T17:10:00Z",
        "curator": "codex",
        "action": "ADVERSARIAL_REVIEW_REPAIR",
        "changes": "Addressed PR #664 adversarial review: expanded two terse SAE 2002 PPL-alpha snippets, replaced the bare SAE PDF URL with its DOI, and rescoped the BSL-5 graph so PPL-alpha remains historical name-use evidence for the generic METPO class instead of the graph focus.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-07T02:20:00Z",
        "curator": "codex",
        "action": "ADVERSARIAL_REVIEW_REPAIR",
        "changes": "Addressed PR #664 adversarial review issue #679: moved the PPL-alpha historical naming support to DOI-backed record-level evidence and removed the ungrounded lexical naming edge from the BSL-5 graph.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-07T07:24:00Z",
        "curator": "codex",
        "action": "ADVERSARIAL_REVIEW_REPAIR",
        "changes": "Addressed PR #664 adversarial review issue #694: upserted the original issue-183 review event so BSL-5 provenance describes the generic two-edge enhanced-hazard graph that shipped.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000701",
    "label": "collective bacterial predation",
    "definition": "A predatory bacterial phenotype in which cells act in coordinated multicellular groups to kill bacterial prey and obtain nutrients from the killed cells.",
    "definition_source": "DOI:10.1038/s41467-023-41193-x",
    "trait_category": "ECOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000054"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/s41467-023-41193-x",
        "snippet": "Myxococcus xanthus forages and moves collectively to prey and feed on other bacterial species.",
        "notes": "Rombouts et al. 2023, PMID:37696789, PMC10495355, scientific abstract, not the separate editor summary. Identity checked with EXT_ID:37696789 AND SRC:MED plus matching title and DOI. Results on cell-state transitions, A/S motility, trail following and prey lysis, Discussion and relevant Methods were read directly. Figure 5 and Supplementary Table 1 (p. 12) were visually inspected. The table identifies DZ2 laboratory material and engineered reporters or motility mutants; the paper's wild-type designation does not establish an untouched natural isolate. The prey is E. coli MG1655 with HU-mCherry for the lysis readout. Figure 5 measures prey fluorescence loss relative to an uninvaded zone, not direct nutrient assimilation or individual fitness benefits. Motility perturbations support contributions to efficient predation in this assay, not universal group obligacy. Raw movies and source data were not independently reanalyzed. MED and Crossref exposed a preprint relationship, not a linked correction/retraction; none was identified on the retrieved publisher page. Source: https://www.nature.com/articles/s41467-023-41193-x."
      },
      {
        "reference": "DOI:10.1128/AEM.02286-19",
        "snippet": "In addition to group hunting, individual M. xanthus cells are able to kill and lyse prey cells",
        "notes": "Zhang et al. 2020, PMID:31704687, PMC6974655, scientific ABSTRACT, not the separate IMPORTANCE text. Qualified MED identity and title/DOI checked. The PMC Results and Discussion subsections on post-killing behavior and conclusions, Methods strain table and tracking analysis were also read. This is primary counterevidence to obligate group-only killing: DK1622 cells can kill E. coli individually. Prey-fragment consumption inferences do not constitute a direct assimilation assay. The delta-aglZ analysis also included individuals in groups of two or three and is not uniformly a solitary-cell dataset. This paper is boundary evidence, not independent replication of the 2023 collective-motility experiment. MED and Crossref exposed no linked correction/retraction; publisher access returned HTTP 403, leaving publisher notice status unverified. Source: https://pmc.ncbi.nlm.nih.gov/articles/PMC6974655/."
      }
    ],
    "discussions": [
      {
        "discussion_id": "collective-predation-scope-and-cooperation",
        "prompt": "Keep coordinated group feeding distinct from claims of obligatory cooperation.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Predatory bacterium traitmech:000054 supplies killing and nutrition; coordinated multicellular predation supplies the differentia. Mere cell density, aggregation, motility or prey lysis without feeding is insufficient. This is a capability expressed by cells in a group context, not a claim that a lone cell displays a collective phenotype. It does not require every cell to attack one prey simultaneously or benefit equally. Solitary killing and collective feeding can coexist in the same organism; no obligate group dependence or disjointness is asserted. Cooperative predation and wolf-pack predation are not assigned exact synonym status: cooperation in an evolutionary fitness sense requires separate evidence. The 2023 scout/loner/swarm bins are analysis states, not distinct primary traits. Swarming motility traitmech:000062 is explicitly flagella-dependent; gliding METPO:1000706 and twitching traitmech:000061 do not require predation. Epibiotic, periplasmic and cytoplasmic predation classify predator location, not group organization. No exact xrefs or synonyms are assigned.",
        "posed_by": "codex",
        "posed_date": "2026-10-11"
      },
      {
        "discussion_id": "collective-predation-examples-and-mechanism",
        "prompt": "Resolve natural examples and mechanism breadth without inferring feeding from sequence.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "The directly inspected collective-imaging evidence concerns DZ2 laboratory material, engineered reporters and motility perturbations. Canonical examples remain unset pending natural material provenance and independently checked taxon identity. A- and S-motility contribute to the studied M. xanthus assay, but their combination is not imposed on every possible bearer of this trophic phenotype. A causal graph and protein examples are deferred until taxon-scoped machinery and mechanism boundaries are grounded. Motility genes, secretion systems, hydrolases or other sequence features alone do not establish coordinated prey consumption. Direct nutrient assimilation and individual fitness benefits require evidence beyond the reported fluorescence-loss readout. These limits are not evidence that collective predation is absent.",
        "posed_by": "codex",
        "posed_date": "2026-10-11"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-11T16:59:40Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added collective bacterial predation beneath predatory bacterium with DOI-backed collective-motility and solitary-killing evidence and two checked scientific-abstract snippets. Ignored/hidden main/worktree and pending-PR checks support 000701 and v577 block 1065400-1065499. Existing records unchanged; cooperation, natural examples and mechanism breadth remain explicitly bounded. Timestamp records the observed UTC curation decision.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000042",
    "label": "commensalism",
    "definition": "A symbiosis in which the microorganism benefits from the association (e.g. resources, shelter, transport) while the host's fitness remains essentially unaffected.",
    "definition_source": "DOI:10.1038/s41579-021-00550-7",
    "trait_category": "ECOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "traitmech:000040"
    ],
    "synonyms": [
      {
        "synonym_text": "commensal",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1038/s41579-021-00550-7"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/s41579-021-00550-7",
        "notes": "Drew et al. place commensalism on the parasite-mutualist continuum as a near-neutral host interaction."
      },
      {
        "reference": "DOI:10.1073/pnas.1218525110",
        "notes": "McFall-Ngai et al. support commensal colonization as a major class of host-associated microbial lifestyles."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1282",
        "taxon_label": "Staphylococcus epidermidis",
        "note": "Archetypal human skin commensal.",
        "reference": "PMID:33180890"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "commensalism_neutral_host",
        "title": "Commensalism benefits microbe without affecting host fitness",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This broad ecological, host-relationship, habitat, or hazard classification spans multiple taxa and mechanisms; contextual protein nodes do not receive token UniProt examples.",
        "description": "Evidence-backed causal sketch linking host colonization to microbial benefit while host fitness is essentially neutral.",
        "nodes": [
          {
            "node_id": "commensalism_trait",
            "label": "commensalism",
            "node_type": "TRAIT",
            "grounding": "traitmech:000042",
            "description": "Microbe benefits from association; host fitness essentially neutral."
          },
          {
            "node_id": "host_colonization",
            "label": "host colonization",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Persistent establishment of microbes on or in a host."
          },
          {
            "node_id": "neutral_host_fitness",
            "label": "neutral host fitness effect",
            "node_type": "QUALITY",
            "description": "No detectable net fitness change for the host partner."
          },
          {
            "node_id": "secretory_iga",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Contextual protein family or multiprotein aggregate reviewed for this nonmechanistic classification; no single semantic family captures it.",
            "label": "secretory IgA",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Host mucosal antibody that can promote commensal colonization of the mucus layer."
          },
          {
            "node_id": "mucus_layer",
            "label": "host mucus / mucins",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Host-derived mucin glycan layer providing niche and nutrients for mucin-foraging microbes."
          },
          {
            "node_id": "glycan_binding_proteins",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Contextual protein family or multiprotein aggregate reviewed for this nonmechanistic classification; no single semantic family captures it.",
            "label": "bacterial glycan-binding proteins",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Microbial adhesins mediating attachment to host mucin glycans."
          },
          {
            "node_id": "mucin_attachment",
            "label": "attachment to mucin",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Microbial adhesion to the host mucin layer supporting persistent colonization."
          },
          {
            "node_id": "eps_production",
            "label": "extracellular glucan / EPS production",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Synthesis of extracellular polysaccharides that build the biofilm matrix."
          },
          {
            "node_id": "biofilm_matrix",
            "label": "EPS biofilm matrix",
            "node_type": "CELLULAR_LOCALIZATION",
            "description": "Extracellular polymeric matrix protecting cells from shear forces and antimicrobials."
          },
          {
            "node_id": "persistence_protection",
            "label": "protection from shear and antimicrobials",
            "node_type": "QUALITY",
            "description": "Resistance to physical removal and antimicrobials supporting host-niche persistence."
          },
          {
            "node_id": "low_virulence",
            "label": "low virulence / no detectable host cost",
            "node_type": "QUALITY",
            "description": "Microbe benefits from the host without causing a detectable fitness cost."
          }
        ],
        "edges": [
          {
            "subject": "host_colonization",
            "predicate": "confers",
            "object": "commensalism_trait",
            "description": "Persistent colonization without harm or benefit to the host realizes the commensal lifestyle.",
            "evidence": [
              {
                "reference": "DOI:10.1073/pnas.1218525110",
                "notes": "McFall-Ngai et al. support commensal colonization as a major class of host-associated microbial lifestyles."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "commensalism_trait",
            "predicate": "associated with",
            "object": "neutral_host_fitness",
            "description": "Commensal interactions sit on the near-neutral point of the parasite-mutualist continuum.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41579-021-00550-7",
                "notes": "Drew et al. place commensalism on the parasite-mutualist continuum as a near-neutral host interaction."
              }
            ],
            "predicate_id": "biolink:associated_with"
          },
          {
            "subject": "secretory_iga",
            "predicate": "promotes",
            "object": "host_colonization",
            "description": "Secretory IgA can help commensal bacteria colonize the mucus layer.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.adi3338",
                "notes": "IgA can act as a carrot as well as a stick, helping bacteria colonize the mucus layer."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "mucus_layer",
            "predicate": "provides resources for",
            "object": "host_colonization",
            "description": "Host mucin glycans provide niche and nutrients enabling commensal persistence.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.adi3338",
                "notes": "Mucin glycan availability selectively feeds mucin-degrading taxa, providing a host-derived resource."
              }
            ]
          },
          {
            "subject": "glycan_binding_proteins",
            "predicate": "enables",
            "object": "mucin_attachment",
            "description": "Bacterial glycan-binding proteins mediate attachment to host mucin.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.adi3338",
                "notes": "Bacteria attach to mucin via glycan-binding proteins."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "mucin_attachment",
            "predicate": "enables",
            "object": "host_colonization",
            "description": "Attachment to the mucin layer supports persistent host colonization.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.adi3338",
                "notes": "Attachment to mucin via glycan-binding proteins underlies persistent colonization of the mucus niche."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "eps_production",
            "predicate": "has output",
            "object": "biofilm_matrix",
            "description": "Synthesis of extracellular glucans builds the EPS biofilm matrix.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fcimb.2024.1357631",
                "notes": "Synthesis of extracellular glucans builds the EPS biofilm matrix."
              }
            ],
            "predicate_id": "RO:0002234"
          },
          {
            "subject": "biofilm_matrix",
            "predicate": "confers",
            "object": "persistence_protection",
            "description": "The EPS biofilm matrix protects cells from shear forces and antimicrobials.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fcimb.2024.1357631",
                "notes": "Protects cells from shear forces and confers resistance to antimicrobials."
              }
            ]
          },
          {
            "subject": "persistence_protection",
            "predicate": "promotes",
            "object": "host_colonization",
            "description": "Protection from removal and antimicrobials supports persistence in the host niche.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fcimb.2024.1357631",
                "notes": "Biofilm-conferred resistance supports persistence in a host niche."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "low_virulence",
            "predicate": "operationalizes",
            "object": "commensalism_trait",
            "description": "Benefit to the microbe with no detectable host cost operationalizes commensalism.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41579-021-00550-7",
                "notes": "Commensals benefit from the interaction with hosts but do not cause a detectable cost."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-06-02T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate ECOLOGY trait (commensalism); sub-variant of symbiosis.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-09T14:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (commensalism / neutral host fitness) with RO/biolink predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 8 evidence-backed generic edges (8 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:09Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 5 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002213\u00d72, RO:0002327\u00d72, METPO:2000202\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 1 causal edge(s) off enables/RO:0002327 with a TRAIT object (1 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates (1 to has output), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-17T22:14:03Z",
        "curator": "claude",
        "action": "CURATE_KNOWLEDGE_GAPS",
        "changes": "Replaced the scan's off-topic scraped sentence with a research question authored from this record's causal graph, anchored it via attaches_to, and sketched an experiment with a decision criterion. The scan's sentence and PMIDs are preserved in the discussion's notes.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope commensalism_neutral_host=NONMECHANISTIC with scope_notes; marked 2 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (secretory_iga, glycan_binding_proteins).",
        "llm_assisted": true
      }
    ],
    "discussions": [
      {
        "discussion_id": "kgscan-3606bdcc991b",
        "prompt": "Commensalism is defined in this record by a neutral effect on host fitness. Has neutrality ever been measured for these associations, or is it inferred from the absence of visible disease -- and does it hold when the host is stressed, starved, or co-infected?",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Neutral_host_fitness is the node that makes this trait different from mutualism and parasitism, and it is the one node stated as a definition rather than an observation. If neutrality is only ever the null result of an underpowered comparison in an unstressed host, then commensalism is a measurement category rather than a biological one, and records assigned to it are provisional in a way the corpus does not currently mark.",
        "attaches_to": [
          "causal_graphs#neutral_host_fitness"
        ],
        "posed_by": "claude",
        "notes": "Scan provenance (#409). The kg-microbe-kgscan pass raised this discussion with the prompt 'Knowledge gap for commensalism: MicroRNAs (miRNAs) are small, noncoding RNAs involved in posttranscriptional gene regulation in both animal and plant. miRNAs derived from edible plants, referred to as xenomiRs, are proposed to cross-kingdom barriers and to modulate mammalian gene expression.', whose sentence came from PMID:40945860. That sentence is about plant-derived xenomiRs crossing kingdom barriers, not about this trait: the scan matched the hedging vocabulary of a gap statement without checking that the gap was about the trait it was filed under. The prompt above was authored instead from this record's own causal graph, and none of these references are carried as its evidence, because they support the scraped sentence rather than the question. The scan attached 3 further references whose snippets concern neither that sentence nor this trait; all 4 are reproduced here so nothing it produced is lost: PMID:40945860 'MicroRNAs (miRNAs) are small, noncoding RNAs involved in posttranscriptional gene regulation in both animal and plant. miRNAs derived from edible plants, referred to as xenomiRs, are proposed to cross-kingdom barriers and to modulate mammalian gene expression.'; PMID:40574831 'Emerging evidence suggests the gut microbiota plays a role in immune regulation, yet its impact on ITP remains unclear.'; PMID:42197356 'Examining the existing literature may identify knowledge gaps regarding precise mechanisms through which the development of GM influences the maturation of the immune system.'; PMID:41808832 'Given its promising anti-inflammatory properties, further research is warranted.'.",
        "proposed_experiments": [
          {
            "experiment_id": "x-commensal-fitness-neutrality",
            "name": "Gnotobiotic mono-association host fitness across stressors",
            "approach": "gnotobiotic mono-association with quantitative fitness readouts",
            "model_systems": [
              "germ-free animal model",
              "mono-association with a designated commensal isolate",
              "germ-free controls held under identical conditions"
            ],
            "perturbations": [
              "protein or caloric restriction",
              "thermal or osmotic stress",
              "co-infection with a defined enteric pathogen"
            ],
            "readouts": [
              "lifetime reproductive output",
              "growth rate and body condition",
              "survival under each stressor",
              "the effect size the design could have detected"
            ],
            "decision_criterion": "whether an adequately powered comparison detects a fitness difference under any stressor",
            "would_support": "no difference under any condition at a stated detectable effect size -- neutrality is measured, not assumed",
            "would_refute": "a fitness effect appears under stress -- neutrality was a condition-dependent artefact and the assignment should change"
          }
        ],
        "posed_date": "2026-08-17"
      }
    ]
  },
  {
    "identifier": "traitmech:000700",
    "label": "cytoplasmic bacterial predation",
    "definition": "A predatory bacterial phenotype in which a bacterium enters the cytoplasm of a bacterial prey cell and grows and reproduces there by consuming and degrading the prey cytoplasm.",
    "definition_source": "DOI:10.1073/pnas.83.7.2138",
    "trait_category": "ECOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000054"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1073/pnas.83.7.2138",
        "snippet": "Daptobacter penetrates both membranes of the prey cell walls and reproduces in their degrading cytoplasm.",
        "notes": "Guerrero et al. 1986, PMID:11542073, PMC323246, Figure 2E caption continued on p. 2141. Full five-page primary paper read from the Europe PMC PDF, including Methods, Results and Discussion, Table 2 and the note added in proof; actual Figure 2E/F micrographs and continued caption visually inspected. Enrichment-culture thin sections support prey-cytoplasmic invasion, degradation and division; these are not live-cell time courses or nutrient-tracing experiments. Figure 3 is a schematic, not additional experimental imaging. The scientific abstract was independently retrieved with EXT_ID:11542073 AND SRC:MED and title/DOI checked. MED and Crossref exposed no linked correction/retraction; publisher notice access returned HTTP 403, so that status is unverified. Source: https://europepmc.org/articles/PMC323246?pdf=render."
      },
      {
        "reference": "https://lpsn.dsmz.de/genus/daptobacter",
        "snippet": "invade their host cells and replicate in the cytoplasm, consuming their prey from the inside out",
        "notes": "LPSN genus Daptobacter, Notes, directly retrieved 2026-10-11. LPSN quotes this description from Madigan et al. 2019; that book was not independently read. Supports established terminology, not independent experimental replication of Guerrero et al. LPSN marks the genus name not validly published and preferred rather than correct. Its permanent record link is https://doi.org/10.83108/rn.684. The nomenclatural record is not evidence for a sequence-defined lineage or an NCBITaxon mapping."
      }
    ],
    "discussions": [
      {
        "discussion_id": "cytoplasmic-predation-boundaries-and-mappings",
        "prompt": "Keep prey-cytoplasmic feeding distinct from generic intracellular residence.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Predatory bacterium traitmech:000054 supplies the broader trophic phenotype. Periplasmic bacterial predation traitmech:000699 has a different replication compartment; epibiotic bacterial predation traitmech:000697 keeps the predator cell body external. Generic endobiotic or intracellular predation, endoparasitism and endosymbiosis are not exact synonyms. Guerrero et al. discuss predator/parasite and primary-consumer terminology on pp. 2141-2142; the operational feeding/location definition here does not settle that broader ecological vocabulary. Entry alone or intracellular growth without destructive prey consumption is insufficient. No organism-level disjointness, fixed prey range or obligate prey dependence is asserted. Exact synonyms and authority-backed xrefs remain unassigned pending scope reconciliation.",
        "posed_by": "codex",
        "posed_date": "2026-10-11"
      },
      {
        "discussion_id": "cytoplasmic-predation-taxon-and-mechanism",
        "prompt": "Resolve the historical isolate and its mechanism before grounding examples.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "The primary study describes Daptobacter in lake-derived enrichment cultures and reports axenic growth; it does not make cytoplasmic predation an obligate lifestyle. No exact NCBITaxon identity for the observed material has been established in this curation, so canonical_examples is intentionally omitted. LPSN nomenclature does not supply that missing mapping. The second evidence item is terminology support, not another experiment. Protein-resolved mechanism, modern replication and lineage breadth remain open; do not infer causal machinery from a taxon name, sequence prediction or the different Bdellovibrio model. No causal graph or protein examples are proposed.",
        "posed_by": "codex",
        "posed_date": "2026-10-11"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-11T15:30:45Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added cytoplasmic bacterial predation beneath predatory bacterium with primary microscopy and explicitly secondary LPSN terminology evidence, both carrying checked snippets. Ignored/hidden main/worktree and pending-PR checks support 000700 and v576 block 1065300-1065399. Existing records unchanged; taxon identity, mappings and mechanism remain open. Timestamp records the observed UTC curation decision.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000442",
    "label": "endophytic",
    "definition": "A host-associated trait in which a microbe resides within living internal plant tissues without causing apparent disease in the host.",
    "definition_source": "DOI:10.3390/microorganisms5040077",
    "trait_category": "ECOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000049"
    ],
    "synonyms": [
      {
        "synonym_text": "endophyte",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.3390/microorganisms5040077"
      },
      {
        "synonym_text": "endophytism",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1128/MMBR.00050-14"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1128/MMBR.00050-14",
        "snippet": "All plants are inhabited internally by diverse microbial communities comprising bacterial, archaeal, fungal, and protistic taxa.",
        "notes": "Hardoim et al. frame endophytic lifestyles as internal microbial residence in plants."
      },
      {
        "reference": "DOI:10.3390/microorganisms5040077",
        "snippet": "Endophytes are microbial symbionts residing within the plant for the majority of their life cycle without any detrimental impact to the host plant.",
        "notes": "Kandel et al. support the no-apparent-disease clause in the endophytic definition."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "endophytic_internal_plant_colonization",
        "title": "Internal plant colonization defines endophytism",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This broad plant-host habitat trait spans bacteria, archaea, fungi, and protists and does not assert one universal molecular colonization mechanism.",
        "description": "Evidence-backed ecological sketch connecting living internal plant tissue to endophytic residence.",
        "nodes": [
          {
            "node_id": "internal_plant_tissue",
            "label": "living internal plant tissue",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "A nonexternal plant host tissue occupied by endophytic microbes."
          },
          {
            "node_id": "endophytic_colonization",
            "label": "endophytic colonization",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Entry, growth, and multiplication of an endophyte population within a plant host."
          },
          {
            "node_id": "endophytic_trait",
            "label": "endophytic",
            "node_type": "TRAIT",
            "grounding": "traitmech:000442",
            "description": "Residence inside living internal plant tissue without apparent host disease."
          }
        ],
        "edges": [
          {
            "subject": "internal_plant_tissue",
            "predicate": "enables",
            "predicate_id": "RO:0002327",
            "object": "endophytic_colonization",
            "description": "Living plant interiors are the host tissue habitat where endophyte populations establish.",
            "evidence": [
              {
                "reference": "DOI:10.3390/microorganisms5040077",
                "snippet": "Endophytic colonization refers to the entry, growth and multiplication of endophyte populations within the host plant.",
                "notes": "Kandel et al. define endophytic colonization as establishment inside a plant host."
              }
            ]
          },
          {
            "subject": "endophytic_colonization",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "endophytic_trait",
            "description": "Endophytic colonization realizes the endophytic ecological trait.",
            "evidence": [
              {
                "reference": "DOI:10.3390/microorganisms5040077",
                "snippet": "Endophytes are microbial symbionts residing within the plant for the majority of their life cycle without any detrimental impact to the host plant.",
                "notes": "Kandel et al. define endophytes by internal plant residence without detrimental host impact."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-28T19:37:27Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted endophytic as a DOI-backed ECOLOGY TraitRecord below host-associated after an ignored-and-hidden repository search found no exact TraitMech, METPO, proposal, or history record; reserved the upstream placeholder in proposals/metpo_traitmech_v319.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-28T19:37:27Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed canonical examples for the first pass and left them empty rather than promoting a strain-level growth-promotion or nitrogen-fixation study into generic endophytism evidence.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000045",
    "label": "endosymbiosis",
    "definition": "A symbiosis in which the microorganism lives inside the cells or tissues of its host. Obligate intracellular endosymbionts (e.g. of insects) frequently undergo extreme genome reduction.",
    "definition_source": "DOI:10.1038/nrmicro2670",
    "trait_category": "ECOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "traitmech:000040"
    ],
    "synonyms": [
      {
        "synonym_text": "endosymbiont",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1038/nrmicro2670"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/nrmicro2670",
        "notes": "McCutcheon & Moran, \"Extreme genome reduction in symbiotic bacteria\", characterize intracellular endosymbionts and their diminished genomes."
      },
      {
        "reference": "DOI:10.1038/nrmicro.2017.171",
        "notes": "Poole et al. describe rhizobia as plant-cell endosymbionts within root nodules, an example of the endosymbiotic lifestyle."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:9",
        "taxon_label": "Buchnera aphidicola",
        "note": "Textbook obligate insect nutritional endosymbiont (aphid bacteriocytes; maternally transmitted).",
        "reference": "https://www.microbiologyresearch.org/content/journal/micro/10.1099/mic.0.001127"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "endosymbiosis_intracellular_genome_reduction",
        "title": "Intracellular endosymbiosis drives extreme genome reduction",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This broad ecological, host-relationship, habitat, or hazard classification spans multiple taxa and mechanisms; contextual protein nodes do not receive token UniProt examples.",
        "description": "Evidence-backed causal sketch linking intracellular host localization to long-term genome reduction in obligate endosymbionts.",
        "nodes": [
          {
            "node_id": "endosymbiosis_trait",
            "label": "endosymbiosis",
            "node_type": "TRAIT",
            "grounding": "traitmech:000045",
            "description": "Symbiosis with intracellular or intra-tissue localization."
          },
          {
            "node_id": "intracellular_localization",
            "label": "intracellular host localization",
            "node_type": "CELLULAR_LOCALIZATION",
            "description": "Persistent residence inside host cells or tissues."
          },
          {
            "node_id": "reductive_genome_evolution",
            "label": "reductive genome evolution",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Long-term loss of genomic content under relaxed selection and small effective population sizes.",
            "grounding": "METPO:1007721"
          },
          {
            "node_id": "confined_intracellular_habitat",
            "label": "confined intracellular habitat",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Spatially restricted, host-cell-confined niche occupied by endosymbionts."
          },
          {
            "node_id": "metabolic_gene_loss",
            "label": "metabolic gene loss",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Loss of metabolic genes under relaxed selection in confined intracellular life."
          },
          {
            "node_id": "transmission_bottleneck",
            "label": "transmission bottleneck",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Few founding cells transmitted between host generations, reducing effective population size."
          },
          {
            "node_id": "limited_recombination",
            "label": "limited recombination",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced genetic recombination resulting from colonies originating from few ancestors."
          },
          {
            "node_id": "host_symbiont_aa_complementarity",
            "label": "host-symbiont amino-acid pathway complementarity",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Complementarity in amino-acid metabolic pathways shared between host and endosymbiont."
          },
          {
            "node_id": "nutritional_compensation",
            "label": "nutritional compensation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Provision of biosynthetic capacity (amino acids/cofactors) compensating host nutritional needs."
          },
          {
            "node_id": "intracellular_dependence",
            "label": "dependence on the intracellular environment",
            "node_type": "STATE",
            "description": "Obligate reliance of the reduced-genome symbiont on the host intracellular environment."
          }
        ],
        "edges": [
          {
            "subject": "intracellular_localization",
            "predicate": "confers",
            "object": "endosymbiosis_trait",
            "description": "Sustained residence inside host cells defines endosymbiosis.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro.2017.171",
                "notes": "Poole et al. describe rhizobia as plant-cell endosymbionts within root nodules."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "endosymbiosis_trait",
            "predicate": "causes",
            "object": "reductive_genome_evolution",
            "description": "Long-term intracellular life with small Ne drives extreme genome reduction in obligate endosymbionts.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2670",
                "notes": "McCutcheon & Moran review extreme genome reduction in obligate symbiotic bacteria."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "confined_intracellular_habitat",
            "predicate": "drives",
            "object": "metabolic_gene_loss",
            "description": "Selective pressures in confined intracellular habitats drive metabolic gene loss and genome shrinkage.",
            "evidence": [
              {
                "reference": "DOI:10.1093/ismejo/wrae117",
                "notes": "Song 2024: selective pressures in confined habitats drive metabolic gene loss and genome shrinkage (free-living 2-10 Mb vs obligate endosymbionts often <1.5 Mb)."
              }
            ]
          },
          {
            "subject": "metabolic_gene_loss",
            "predicate": "contributes to",
            "object": "reductive_genome_evolution",
            "description": "Metabolic gene loss in confined intracellular life feeds long-term reductive genome evolution.",
            "evidence": [
              {
                "reference": "DOI:10.1093/ismejo/wrae117",
                "notes": "Song 2024: confined-habitat metabolic gene loss underlies genome shrinkage characteristic of obligate endosymbionts."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "transmission_bottleneck",
            "predicate": "associated with",
            "object": "limited_recombination",
            "description": "Colonies originate from few ancestors, producing limited recombination in obligate endosymbionts.",
            "evidence": [
              {
                "reference": "DOI:10.1093/ismejo/wrae117",
                "notes": "Song 2024: colonies originate from few ancestors, limited recombination."
              }
            ],
            "predicate_id": "biolink:associated_with"
          },
          {
            "subject": "host_symbiont_aa_complementarity",
            "predicate": "supports",
            "object": "nutritional_compensation",
            "description": "Complementarity in amino-acid metabolic pathways between host and symbiont supports nutritional compensation.",
            "evidence": [
              {
                "reference": "DOI:10.1093/ismejo/wrae052",
                "notes": "Bai 2024: a comprehensive analysis demonstrated complementarity in amino acid metabolic pathways between host and symbiont, supporting nutritional compensation."
              }
            ]
          },
          {
            "subject": "reductive_genome_evolution",
            "predicate": "leads to",
            "object": "intracellular_dependence",
            "description": "Severe genome reduction leads to obligate dependence on the host intracellular environment.",
            "evidence": [
              {
                "reference": "DOI:10.3390/ijms25084228",
                "notes": "Silva 2024: has undergone severe genome reduction leading to dependence on the intracellular environment."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-06-02T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate ECOLOGY trait (endosymbiosis); spatial sub-variant of symbiosis.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-09T14:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (intracellular endosymbiosis / genome reduction) with RO/biolink predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-16T06:54:39Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (METPO:1007721\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 5 evidence-backed generic edges (7 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:09Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002326\u00d71, biolink:associated_with\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 1 causal edge(s) off enables/RO:0002327 with a TRAIT object (1 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-17T22:14:03Z",
        "curator": "claude",
        "action": "CURATE_KNOWLEDGE_GAPS",
        "changes": "Replaced the scan's off-topic scraped sentence with a research question authored from this record's causal graph, anchored it via attaches_to, and sketched an experiment with a decision criterion. The scan's sentence and PMIDs are preserved in the discussion's notes.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope endosymbiosis_intracellular_genome_reduction=NONMECHANISTIC with scope_notes.",
        "llm_assisted": true
      }
    ],
    "discussions": [
      {
        "discussion_id": "kgscan-a6758e26f5a6",
        "prompt": "Two edges reach genome reduction here: confined habitat through metabolic gene loss, and the trait itself, whose description bundles drift in as `with small Ne`. The nodes that would give drift a mechanism -- transmission bottleneck, limited recombination -- connect to neither. Should they feed the drift edge, and which mechanism dominates?",
        "kind": "CONTROVERSY",
        "status": "OPEN",
        "rationale": "The record asserts both mechanisms but at different resolutions, which is what makes them impossible to weigh. Drift arrives bundled into a trait-level edge as a parenthetical -- `with small Ne` inside a description -- while selection is spelled out as a two-step path through metabolic_gene_loss. transmission_bottleneck and limited_recombination attach to each other and to nothing else, so the drift claim has no mechanism under it, and host_symbiont_aa_complementarity -> nutritional_compensation is likewise its own disconnected pair, so compensation is not wired into reduction either. The two predict opposite loss spectra -- drift removes genes roughly regardless of function, compensation removes exactly the genes whose products the host supplies -- so until they are stated at the same resolution the graph cannot say what a newly sequenced symbiont will have lost, which is most of what a reduction model is for.",
        "attaches_to": [
          "causal_graphs#reductive_genome_evolution",
          "causal_graphs#transmission_bottleneck",
          "causal_graphs#limited_recombination",
          "causal_graphs#metabolic_gene_loss"
        ],
        "posed_by": "claude",
        "notes": "Scan provenance (#409). The kg-microbe-kgscan pass raised this discussion with the prompt 'Knowledge gap for endosymbiosis: Growth anomalies (GAs) are coral diseases characterised by tumour-like skeletal lesions reported globally, yet their causes remain poorly understood.', whose sentence came from PMID:42130304. That sentence is about growth anomalies in corals, not about this trait: the scan matched the hedging vocabulary of a gap statement without checking that the gap was about the trait it was filed under. The prompt above was authored instead from this record's own causal graph, and none of these references are carried as its evidence, because they support the scraped sentence rather than the question. The scan attached 3 further references whose snippets concern neither that sentence nor this trait; all 4 are reproduced here so nothing it produced is lost: PMID:42130304 'Growth anomalies (GAs) are coral diseases characterised by tumour-like skeletal lesions reported globally, yet their causes remain poorly understood.'; PMID:41612704 'Disrupting this obligate symbiosis represents a promising pest control strategy, yet the molecular mechanisms maintaining host-symbiont homeostasis remain poorly understood.'; PMID:40831140 'This review explores the origin and evolution of plastids, their protein-import machinery, compartmentalization, and interactions with other cellular compartments, and highlights key unanswered questions in these areas.'; PMID:41764142 'Detritivorous E. murphyi larvae can increase soil nitrogen levels by up to five times compared with similar uncolonized substrates, although the mechanisms involved remain unknown.'.",
        "proposed_experiments": [
          {
            "experiment_id": "x-endosymbiont-drift-vs-selection",
            "name": "Comparative loss spectra across symbionts of differing bottleneck severity",
            "approach": "comparative genomics across independent symbiotic origins",
            "model_systems": [
              "vertically transmitted symbionts with severe bottlenecks",
              "horizontally acquired symbionts with large inocula",
              "free-living relatives as the unreduced reference"
            ],
            "readouts": [
              "genome size against estimated effective population size",
              "dN/dS across retained genes",
              "whether lost functions are complemented by host pathways",
              "pseudogene load as a marker of ongoing reduction"
            ],
            "decision_criterion": "whether genome size still tracks bottleneck severity once host complementation of the lost functions is controlled for",
            "would_support": "reduction tracks bottleneck severity independently of complementation -- the bottleneck pair belongs under the trait-level drift edge, as its mechanism",
            "would_refute": "loss is enriched for host-complemented functions with no residual bottleneck effect -- selection dominates, and the dangling pair is context rather than cause"
          }
        ],
        "posed_date": "2026-08-17"
      }
    ]
  },
  {
    "identifier": "traitmech:000697",
    "label": "epibiotic bacterial predation",
    "definition": "A predatory bacterial phenotype in which a bacterium kills and obtains nutrients from bacterial prey while attached and growing externally, without its cell body entering the prey cell.",
    "definition_source": "DOI:10.1038/ismej.2013.164",
    "trait_category": "ECOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000054"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/ismej.2013.164",
        "snippet": "epibiotic, where they attach to the prey from outside.",
        "notes": "Pasternak et al. 2014, PMID:24088628, PMC3930308, Introduction; contiguous quotation defining the external predation strategy. Abstract, Introduction, culture/prey-range/electron-microscopy Methods, growth Results, Discussion and actual Figure 1 read. JSS and Micavibrio aeruginosavorus EPB observations support external feeding; genome comparisons are not functional proof. Do not make the paper's binary-division generalization defining: the 2024 JSS time-lapse study demonstrates nonbinary division. Other figures, genomic analyses and supplements not fully assessed. Full text: https://pmc.ncbi.nlm.nih.gov/articles/PMC3930308/."
      },
      {
        "reference": "DOI:10.1099/ijs.0.039701-0",
        "snippet": "No periplasmic growth stage was observed and no bdelloplast was formed.",
        "notes": "Koval et al. 2013, PMID:22368169, directly read scientific Abstract on the publisher site and source-qualified MED metadata. JSS was isolated from sewage in London, Ontario, with Caulobacter crescentus prey; attached external predation left emptied cells. This supports natural strain provenance and noninvasive feeding, not its frequency in undisturbed sewage. Full text, figures and supplement unavailable to this review; no Methods claim imported. Publisher: https://doi.org/10.1099/ijs.0.039701-0."
      },
      {
        "reference": "DOI:10.1038/s41467-024-48042-5",
        "snippet": "Bdellovibrio exovorus is an obligate epibiotic predator that attaches on the prey cell surface, where it grows and proliferates.",
        "notes": "Santin et al. 2024, PMID:38678033, PMC11055950, scientific Abstract; direct contiguous match. Abstract, Introduction, Results, Discussion, selected culture/killing/live-imaging/cryo-EM/statistics Methods and actual Figures 2-5 read; other Methods, actual Figures 1/6, supplements and movies not fully assessed. JSS time-lapse growth and prey-content loss support feeding, not direct molecular nutrient tracing. The 2025 correction DOI:10.1038/s41467-025-58758-7 (PMID:40234419, PMC12000597) was read: retain its qualified prey-range wording and removal of the S-layer-defense recommendation. It is not another independent experiment. Full corrected text: https://pmc.ncbi.nlm.nih.gov/articles/PMC11055950/."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:453816",
        "taxon_label": "Pseudobdellovibrio exovorus",
        "reference": "DOI:10.1038/s41467-024-48042-5",
        "note": "Qualified to JSS (ATCC BAA-2330 = DSM 25223), not every species member. Studied as Bdellovibrio exovorus on C. crescentus; the predator's natural sewage-isolate provenance and type-strain identity are stated in the primary Abstract at https://doi.org/10.1099/ijs.0.039701-0. Some 2024 prey strains carry engineered labels or deletions; this natural-provenance qualification concerns the predator. NCBI species ID/name and JSS type material independently resolved on 2026-10-11: https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=453816."
      }
    ],
    "discussions": [
      {
        "discussion_id": "epibiotic-predation-scope-and-mappings",
        "prompt": "Keep external feeding distinct from general surface association.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Predatory bacterium traitmech:000054 supplies killing and nutrition; external attachment and growth supply the differentia. The broader METPO:1007093 epibiont phenotype does not require predation. Epibiosis, ectosymbiosis, ectoparasitism and vampirism are not asserted exact synonyms. The existing predation research report also calls wolf-pack Myxococcus feeding epibiotic; this record follows the attached-feeding sense of Pasternak et al., not every use of external killing. Attachment, prey lysis or sequence signatures alone are insufficient. Bacterial cannibalism traitmech:000626 concerns prey relatedness, an orthogonal axis. No organism-level disjointness is asserted. No exact xrefs or synonyms are assigned pending authority and scope reconciliation.",
        "posed_by": "codex",
        "posed_date": "2026-10-11"
      },
      {
        "discussion_id": "epibiotic-predation-mechanism-limits",
        "prompt": "Resolve feeding machinery without generalizing model-specific observations.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Causal graphs and protein examples are deferred, not claimed absent. An external predator cell body does not exclude envelope-crossing feeding structures or secreted effectors. JSS imaging supports a feeding junction but does not identify its molecular machinery; fluorescence loss is not direct nutrient tracing. Comparative gene content is not functional causality. Do not require polar attachment, binary division, fixed progeny number, a universal prey range, or obligate dependence merely because particular models exhibit them. The corrected 2024 S-layer experiments concern tested prey backgrounds, not all predators or all S-layers. The 2013/2014 studies share authors and JSS material; three citations are not three independent laboratory replications.",
        "posed_by": "codex",
        "posed_date": "2026-10-11"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-11T11:39:38Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added external attached bacterial predation beneath predatory bacterium with three DOI-backed sources, checked snippets and a JSS-qualified example. Reserved v573 block 1065000-1065099 after ignored/hidden main/worktree and pending-PR checks. Corrected-paper scope retained; mechanisms and mappings remain open. Timestamp is the observed UTC decision.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000443",
    "label": "epiphytic",
    "definition": "A host-associated trait in which a microbe resides on living aerial plant surfaces.",
    "definition_source": "DOI:10.1186/s12915-024-01967-1",
    "trait_category": "ECOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000049"
    ],
    "synonyms": [
      {
        "synonym_text": "epiphyte",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1186/s12915-024-01967-1"
      },
      {
        "synonym_text": "phyllosphere association",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1128/AEM.69.4.1875-1883.2003"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1128/AEM.69.4.1875-1883.2003",
        "snippet": "The aerial habitat colonized by these microbes is termed the phyllosphere, and the inhabitants are called epiphytes.",
        "notes": "Lindow and Brandl define epiphytes as microbes inhabiting the aerial plant-surface phyllosphere."
      },
      {
        "reference": "DOI:10.1186/s12915-024-01967-1",
        "snippet": "Epiphytic microbes are those that live for some or all of their life cycle on the surface of plant leaves.",
        "notes": "Fones et al. support the plant leaf surface-residence scope of the epiphytic trait."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "epiphytic_plant_surface_colonization",
        "title": "Plant-surface colonization defines epiphytism",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This broad plant-host habitat trait spans bacteria, yeasts, and filamentous fungi on external plant surfaces and does not assert one universal molecular colonization mechanism.",
        "description": "Evidence-backed ecological sketch connecting exposed living plant surfaces to epiphytic residence.",
        "nodes": [
          {
            "node_id": "external_plant_surface",
            "label": "living external plant surface",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "An aerial external plant host surface occupied by epiphytic microbes."
          },
          {
            "node_id": "epiphytic_colonization",
            "label": "epiphytic colonization",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Residence of microbial populations on the surface of leaves or other aerial plant parts."
          },
          {
            "node_id": "epiphytic_trait",
            "label": "epiphytic",
            "node_type": "TRAIT",
            "grounding": "traitmech:000443",
            "description": "Residence on living aerial plant surfaces."
          }
        ],
        "edges": [
          {
            "subject": "external_plant_surface",
            "predicate": "enables",
            "predicate_id": "RO:0002327",
            "object": "epiphytic_colonization",
            "description": "Living aerial plant surfaces are the host tissue habitat where epiphytic populations establish.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.69.4.1875-1883.2003",
                "snippet": "The aerial habitat colonized by these microbes is termed the phyllosphere, and the inhabitants are called epiphytes.",
                "notes": "Lindow and Brandl define the phyllosphere as an aerial plant habitat and its inhabitants as epiphytes."
              }
            ]
          },
          {
            "subject": "epiphytic_colonization",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "epiphytic_trait",
            "description": "Epiphytic colonization realizes the plant-surface epiphytic ecological trait.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s12915-024-01967-1",
                "snippet": "Epiphytic microbes are those that live for some or all of their life cycle on the surface of plant leaves.",
                "notes": "Fones et al. define epiphytic microbes by leaf-surface residence."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-28T20:20:16Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted epiphytic as a DOI-backed ECOLOGY TraitRecord below host-associated after an ignored-and-hidden repository search found no exact TraitMech, METPO, proposal, or history record; reserved the upstream placeholder in proposals/metpo_traitmech_v320.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-28T20:20:16Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed canonical examples for the first pass and left them empty rather than promoting a pathogen fitness, biocontrol, or strain-level plant-growth study into generic epiphytism evidence.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000048",
    "label": "free-living",
    "definition": "A habitat association in which an organism lives independently in the environment, not obligately associated with a host.",
    "definition_source": "DOI:10.1038/nrmicro1341",
    "trait_category": "ECOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "traitmech:000047"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/nrmicro1341",
        "notes": "Martiny et al. support biogeographic patterning of free-living microbial taxa across environments."
      },
      {
        "reference": "DOI:10.1038/nrmicro.2017.171",
        "notes": "Poole et al. describe rhizobia in their free-living soil phase, contrasting it with the host-associated endosymbiotic phase."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:155892",
        "taxon_label": "Caulobacter vibrioides",
        "note": "free-living oligotroph",
        "reference": "PMID:11259647"
      },
      {
        "taxon_id": "NCBITaxon:303",
        "taxon_label": "Pseudomonas putida",
        "note": "free-living soil bacterium",
        "reference": "PMID:15560824"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "free_living_environmental_habitat",
        "title": "Free-living lifestyle is independent of host association",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This broad ecological, host-relationship, habitat, or hazard classification spans multiple taxa and mechanisms; contextual protein nodes do not receive token UniProt examples.",
        "description": "Evidence-backed causal sketch linking environmental habitat occupancy to a host-independent free-living lifestyle.",
        "nodes": [
          {
            "node_id": "free_living_trait",
            "label": "free-living",
            "node_type": "TRAIT",
            "grounding": "traitmech:000048",
            "description": "Persistent life in the environment, not obligately host-bound."
          },
          {
            "node_id": "environmental_habitat",
            "label": "environmental habitat",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Soil, water, air, or other non-host habitat."
          },
          {
            "node_id": "biogeographic_structure",
            "label": "biogeographic community structure",
            "node_type": "QUALITY",
            "description": "Patterned distribution of free-living taxa across environments."
          },
          {
            "node_id": "complete_metabolic_capacity",
            "label": "complete metabolic capacity for carbon/nitrogen/sulfur/cofactors",
            "node_type": "CAPACITY",
            "description": "Self-sufficient biosynthetic pathways for core nutrients and cofactors, not dependent on a host."
          },
          {
            "node_id": "osmotic_stress_tolerance",
            "label": "osmotic stress tolerance",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Cellular response maintaining viability under osmotic/salinity stress in fluctuating environments."
          },
          {
            "node_id": "ectoine_biosynthesis",
            "label": "ectoine biosynthetic pathway",
            "node_type": "PATHWAY",
            "description": "Biosynthesis of the compatible solute ectoine for osmoadaptation.",
            "related_records": [
              {
                "corpus": "PathwayMech",
                "identifier": "MetaCyc:P101-PWY",
                "relation": "PATHWAY_CONTEXT",
                "basis": "PathwayMech context: ectoine biosynthesis in Halomonas elongata (NCBITaxon:2746). The shared route synthesizes ectoine through EctB, EctA and EctC. No exact equivalence or transfer of organism scope is asserted.",
                "source_version": "aa305727458c44ab05614901334540e2c87a9f3a"
              }
            ]
          },
          {
            "node_id": "glycine_betaine_system",
            "label": "glycine betaine transport/biosynthesis",
            "node_type": "PATHWAY",
            "description": "betA/betB/betI and Opu/ProV/ProX systems producing/importing the osmoprotectant glycine betaine."
          },
          {
            "node_id": "trehalose_biosynthesis",
            "label": "trehalose biosynthesis/transport",
            "node_type": "PATHWAY",
            "description": "Synthesis and transport of the compatible solute trehalose for stress protection.",
            "related_records": [
              {
                "corpus": "PathwayMech",
                "identifier": "MetaCyc:TRESYN-PWY",
                "relation": "PATHWAY_CONTEXT",
                "basis": "PathwayMech context: trehalose biosynthesis I in Escherichia coli (NCBITaxon:562). The linked OtsA/OtsB route illustrates trehalose synthesis only; it does not cover the transport component of this node. No exact equivalence or transfer of organism scope is asserted.",
                "source_version": "aa305727458c44ab05614901334540e2c87a9f3a"
              }
            ]
          },
          {
            "node_id": "environmental_stress_tolerance",
            "label": "stress tolerance in fluctuating environments",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Cellular persistence under variable environmental stress conditions."
          }
        ],
        "edges": [
          {
            "subject": "environmental_habitat",
            "predicate": "confers",
            "object": "free_living_trait",
            "description": "Persistent occupancy of environmental habitats realizes the free-living lifestyle.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro1341",
                "notes": "Martiny et al. document biogeographic patterning of free-living microbial taxa."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "free_living_trait",
            "predicate": "associated with",
            "object": "biogeographic_structure",
            "description": "Free-living taxa show environment-structured global distributions.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro.2017.171",
                "notes": "Poole et al. describe the free-living soil phase of rhizobia distinct from their host-associated phase."
              }
            ],
            "predicate_id": "biolink:associated_with"
          },
          {
            "subject": "complete_metabolic_capacity",
            "predicate": "required for",
            "object": "free_living_trait",
            "description": "Self-sufficient metabolic pathways for carbon, nitrogen, sulfur and cofactors are required for a host-independent free-living life strategy.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s12915-024-02013-w",
                "notes": "Reversion to free-living is rare because parasites often lose metabolic pathways essential to a free-living life strategy."
              },
              {
                "reference": "DOI:10.1128/aem.01900-23",
                "notes": "Symbiotic Fluviibacter showed reduced metabolic capacities and host dependence for carbon, organic nitrogen, sulfur, and cofactors."
              }
            ]
          },
          {
            "subject": "ectoine_biosynthesis",
            "predicate": "enables",
            "object": "osmotic_stress_tolerance",
            "description": "Ectoine synthesis provides compatible solutes that confer osmotic stress tolerance during environmental persistence.",
            "evidence": [
              {
                "reference": "DOI:10.48550/arxiv.2302.00582",
                "notes": "Crossing salinity barriers requires osmotic-stress mechanisms; marine adaptation includes components involved in ectoine synthesis."
              },
              {
                "reference": "DOI:10.1371/journal.pone.0287947",
                "notes": "Paracoccus carried the ectoine cluster in all strains."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "glycine_betaine_system",
            "predicate": "enables",
            "object": "osmotic_stress_tolerance",
            "description": "Glycine betaine transport/biosynthesis confers osmoprotection under environmental stress.",
            "evidence": [
              {
                "reference": "DOI:10.1371/journal.pone.0287947",
                "notes": "betA-betB, betI operon and multiple glycine-betaine transporters link these systems to persistence under environmental stress."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "trehalose_biosynthesis",
            "predicate": "enables",
            "object": "environmental_stress_tolerance",
            "description": "Trehalose synthesis/transport provides compatible-solute protection under fluctuating environmental conditions.",
            "evidence": [
              {
                "reference": "DOI:10.1371/journal.pone.0287947",
                "notes": "Trehalose synthesis/transport widely encoded; compatible-solute systems discussed as persistence traits, lost in some host-associated lineages."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "osmotic_stress_tolerance",
            "predicate": "promotes",
            "object": "free_living_trait",
            "description": "Osmoadaptation supports persistence in unstable/saline environments characteristic of the free-living lifestyle.",
            "evidence": [
              {
                "reference": "DOI:10.48550/arxiv.2302.00582",
                "notes": "Ectoine-related osmoadaptation is highlighted as part of adaptation to unstable or saline environmental conditions in free-living lineages."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "trehalose_biosynthesis",
            "predicate": "enables",
            "object": "osmotic_stress_tolerance",
            "description": "Trehalose accumulation through the OtsAB pathway is required for free-living osmotic stress tolerance: losing the pathway reduces viability under both nonionic and ionic hyperosmotic challenge, and supplying trehalose restores it.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mBio.00390-21",
                "snippet": "the \u0394(otsCB-otsA) mutant showed reduced viability under these stress conditions similar to the \u0394ecfG mutant",
                "notes": "Free-living hyperosmotic challenge in Bradyrhizobium diazoefficiens USDA 110: 400 mM sorbitol, 27 mM NaCl, 50 mM MgCl2, 75 mM MgSO4. The nonionic sorbitol condition is what separates osmotic pressure from salt-specific ion toxicity. Causality is pinned by two further controls: expressing a cytoplasmic trehalase (strain TreF-1) phenocopies the deletion, and exogenous trehalose rescues the otsA deletion but not the transporter-deficient otsCB-otsA or otsCB deletions, so the phenotype tracks intracellular trehalose rather than the locus."
              },
              {
                "reference": "DOI:10.1128/AEM.02483-09",
                "snippet": "the single, double, and triple mutant strains lacking the OtsAB pathway (the \u0394otsA, \u0394otsA \u0394treS or \u0394otsA \u0394treY, and \u0394otsA \u0394treS \u0394treY mutants) were inhibited for growth on 60 mM NaCl",
                "notes": "Independently constructed mutants in the same strain background (published as B. japonicum), so the phenotype does not depend on one construct. Mutants lacking both the OtsAB and TreYZ routes failed to grow on salt-containing medium. The same study found the low-trehalose otsA and otsA treY mutants were NOT worse than wild type under desiccation at 50% relative humidity, which is why this edge is scoped to osmotic tolerance rather than to environmental stress generally."
              }
            ],
            "predicate_id": "RO:0002327"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-06-02T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate ECOLOGY trait (free-living); sub-variant of habitat association.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-09T14:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (free-living / environmental habitat) with RO/biolink predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 5 evidence-backed generic edges (6 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:09Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 4 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d73, RO:0002213\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 1 causal edge(s) off enables/RO:0002327 with a TRAIT object (1 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-16T02:00:00Z",
        "curator": "claude",
        "action": "NORMALISE_NODE_TYPE",
        "changes": "Under the PATHWAY-vs-BIOLOGICAL_PROCESS rule, one node_id means one thing corpus-wide (issue 356): ectoine_biosynthesis is typed PATHWAY. PATHWAY is a named, conventionally enumerable multi-step route; BIOLOGICAL_PROCESS is everything else. A named route, enumerated two ways and both of them enumerations. environment/euryhaline.yaml counts five steps from L-aspartate (lysC/asd/ectB/ectA/ectC); environment/nacl_delta_mid1.yaml counts the three ectABC enzymes proper. Naming the file matters because the two differ and a bare quote would put euryhaline's wording into nacl_delta_mid1's record (#400 review). Either way the steps can be listed, which is the test. Applied AGAINST the majority, which was 4 BIOLOGICAL_PROCESS to 2 before this tranche.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-17T22:14:03Z",
        "curator": "claude",
        "action": "CURATE_KNOWLEDGE_GAPS",
        "changes": "Replaced the scan's off-topic scraped sentence with a research question authored from this record's causal graph, anchored it via attaches_to, and sketched an experiment with a decision criterion. The scan's sentence and PMIDs are preserved in the discussion's notes.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope free_living_environmental_habitat=NONMECHANISTIC with scope_notes.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T20:42:29Z",
        "curator": "claude",
        "action": "CONNECT_CAUSAL_GRAPH",
        "changes": "Added trehalose_biosynthesis -[RO:0002327 enables]-> osmotic_stress_tolerance to free_living_environmental_habitat, resolving the record's x-compatible-solute-partitioning knowledge gap (#614) against its own stated would_refute criterion. Loss-of-function, trehalase-depletion and metabolite-rescue evidence from DOI:10.1128/mBio.00390-21, replicated by independent mutants in DOI:10.1128/AEM.02483-09, show the trehalose knockout is osmotically impaired, so the trehalose/ectoine split the graph asserted is not a real distinction. This also merges the graph's stranded {trehalose_biosynthesis, environmental_stress_tolerance} component into the main one. The pre-existing edge to environmental_stress_tolerance is retained rather than deleted: its comparative-genomics evidence is weaker but removing a cited edge is a semantic decision, tracked in #614.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T20:50:10Z",
        "curator": "claude",
        "action": "RESOLVE_DISCUSSION",
        "changes": "Set the x-compatible-solute-partitioning knowledge gap to RESOLVED after its would_refute criterion was met and the resulting edge landed with two verified primary references. See issue 614.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-05T17:46:21Z",
        "curator": "codex",
        "action": "ADD_PATHWAY_CONTEXT",
        "changes": "Added pinned PathwayMech context on reviewed causal nodes with explicit route and organism limitations; retained existing groundings and exact xrefs.",
        "llm_assisted": true
      }
    ],
    "discussions": [
      {
        "discussion_id": "kgscan-d5aefedf82bb",
        "prompt": "Ectoine and glycine betaine both enable osmotic stress tolerance here, but trehalose is wired instead to environmental stress tolerance -- a node with no outgoing edge. Is that split a real distinction, or does trehalose belong on the osmotic route too?",
        "kind": "KNOWLEDGE_GAP",
        "status": "RESOLVED",
        "rationale": "Because environmental_stress_tolerance has no outgoing edge, nothing downstream depends on trehalose at all: this record currently predicts the trait's osmotolerance from two systems and leaves the third dangling. Either reading has a consequence. If trehalose does serve osmotic tolerance, a genome carrying only trehalose scores as non-osmotolerant when it is not, which is exactly the inference anything reading habitat range off gene content would make. If the split is real -- trehalose for desiccation and thermal stress rather than osmolarity -- then the dangling node needs its own edge onward to the trait. The second question, whether the two routes that do converge are redundant or condition-partitioned, rides along on the same experiment: their costs differ sharply, since de novo ectoine synthesis is carbon-expensive where betaine uptake is cheap given a precursor.",
        "attaches_to": [
          "causal_graphs#osmotic_stress_tolerance",
          "causal_graphs#environmental_stress_tolerance",
          "causal_graphs#ectoine_biosynthesis",
          "causal_graphs#glycine_betaine_system",
          "causal_graphs#trehalose_biosynthesis"
        ],
        "posed_by": "claude",
        "notes": "Scan provenance (#409). The kg-microbe-kgscan pass raised this discussion with the prompt 'Knowledge gap for free-living: Interactions between parasites and the gut microbiota play a key role in immune responses and susceptibility to zoonotic diseases; however, many aspects of how protozoan infections alter microbial diversity and how these changes influence parasite pathogenicity and host defense remain poorly understood.', whose sentence came from PMID:41989588. That sentence is about protozoan infection and gut microbial diversity, not about this trait: the scan matched the hedging vocabulary of a gap statement without checking that the gap was about the trait it was filed under. The prompt above was authored instead from this record's own causal graph, and none of these references are carried as its evidence, because they support the scraped sentence rather than the question. The scan attached 3 further references whose snippets concern neither that sentence nor this trait; all 4 are reproduced here so nothing it produced is lost: PMID:41989588 'Interactions between parasites and the gut microbiota play a key role in immune responses and susceptibility to zoonotic diseases; however, many aspects of how protozoan infections alter microbial diversity and how these changes influence parasite pathogenicity and host defense remain poorly understood.'; PMID:42039802 'Engineered microbial assemblies tailored to specific host plants and environmental conditions have shown potential in stabilizing crop performance during drought, salinity, and nutrient limitations.'; PMID:41943163 'OBJECTIVES: Oxo-polyethylene (oxo-PE) is marketed as a biodegradable plastic, yet its environmental degradation remains poorly understood, particularly in marine contexts.'; PMID:42125129 \"However, contradictions persist regarding pH's effect on microbial diversity, with unresolved questions about how specific environmental conditions regulate microbial taxa.\".",
        "proposed_experiments": [
          {
            "experiment_id": "x-compatible-solute-partitioning",
            "name": "Combinatorial solute-pathway knockouts across an environmental matrix",
            "approach": "combinatorial knockout panel with matrix growth phenotyping",
            "model_systems": [
              "a free-living halotolerant isolate carrying all three systems",
              "single, double, and triple pathway knockouts"
            ],
            "perturbations": [
              "an osmolarity gradient spanning the growth range",
              "low and high temperature at each osmolarity",
              "carbon-replete versus carbon-limited medium",
              "betaine precursor present or absent"
            ],
            "readouts": [
              "growth rate and final yield across the matrix",
              "intracellular solute pools by NMR or LC-MS",
              "the osmolarity limit for each genotype"
            ],
            "decision_criterion": "whether the trehalose knockout loses growth at high osmolarity specifically, with temperature and water activity held constant",
            "would_support": "trehalose loss costs nothing osmotically and only shows under desiccation or heat -- the split in the graph is real and environmental_stress_tolerance needs its own edge onward",
            "would_refute": "the trehalose knockout is osmotically impaired -- it belongs on the osmotic route with the other two"
          }
        ],
        "posed_date": "2026-08-17",
        "resolved_date": "2026-08-31",
        "resolution_note": "Refuted. The record's own would_refute criterion was 'the trehalose knockout is osmotically impaired', and it is: in Bradyrhizobium diazoefficiens USDA 110 the otsCB-otsA deletion loses viability at 400 mM sorbitol, a nonionic challenge that separates osmotic pressure from ion toxicity, as well as at 27 mM NaCl, 50 mM MgCl2 and 75 mM MgSO4 (DOI:10.1128/mBio.00390-21). A cytoplasmic trehalase phenocopies the deletion and exogenous trehalose rescues the otsA deletion but not the transporter-deficient strains, so the phenotype tracks intracellular trehalose. Independently constructed mutants in the same background are inhibited on 60 mM NaCl (DOI:10.1128/AEM.02483-09). The split was therefore not real, and trehalose_biosynthesis now enables osmotic_stress_tolerance alongside ectoine and glycine betaine. Two things were deliberately NOT decided here and are tracked in issue 614: the weaker pre-existing trehalose_biosynthesis to environmental_stress_tolerance edge was retained rather than deleted, and the observation that the same AEM study found no desiccation defect for low-trehalose otsA mutants argues trehalose's role is specifically osmotic."
      }
    ]
  },
  {
    "identifier": "traitmech:000726",
    "label": "fungal nematode egg parasitism",
    "definition": "An animal-pathogenic phenotype in which a fungus infects nematode eggs by penetrating their eggshells and colonizing their interiors.",
    "definition_source": "DOI:10.3389/fmicb.2021.617710",
    "trait_category": "ECOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1004002"
    ],
    "evidence": [
      {
        "reference": "DOI:10.3389/fmicb.2021.617710",
        "snippet": "The egg-pathogenic fungus Purpureocillium lilacinum parasitizes on nematode eggs",
        "notes": "Xu et al. 2021, PMID:33897634, PMCID:PMC8058359, scientific Abstract; direct JATS match and native VERIFIED. Own JZD02 experiment, Methods and actual Figure 1 A-C support infection of Meloidogyne incognita eggs. Supplementary Table 1 defines infection by hyphal penetration through an individual egg, not mere surface contact. Its 30-hour printed mean disagrees with the replicate counts; no numerical infection rates are adopted. The 6-hour control and 42-hour infected transcriptomes differ in time and include mixed infection stages. Expression associations are not causal protein evidence."
      },
      {
        "reference": "DOI:10.3389/fmicb.2016.01084",
        "snippet": "Infected eggs by P. lilacinum 36-1.",
        "notes": "Xie et al. 2016, PMID:27486440, PMCID:PMC4949223, Figure 5 caption, panel B; actual panels A-C and Methods/Results inspected. P. lilacinum denotes Purpureocillium lilacinum. Direct JATS match; native NOT_IN_ABSTRACT is retained. This is its own 36-1 infection experiment, not a repetition of Xu's citation. Eggs were supplied as the only nourishment for the reported 24-hour comparison, but microscopy does not quantify nutrient assimilation. RNA-seq replicates were pooled; gene homology and expression do not demonstrate a required effector."
      },
      {
        "reference": "DOI:10.3389/fmicb.2021.617710",
        "snippet": "Infection defined by Purpureocillium lilacinum mycelium penetrating through the whole individual Meloidogyne incognita egg",
        "notes": "Xu et al. 2021, Supplementary Table 1 footnote, Table_1.DOCX from the PMC8058359 Europe PMC supplementaryFiles archive. Direct DOCX text match and complete rendered page inspected; native NOT_IN_ABSTRACT is retained. This operational scoring criterion supports individual-egg penetration, not another independent experiment or a direct nutrient-flux measurement. The two Xu excerpts total 23 words. The printed 30-hour mean discrepancy remains unresolved; no infection rate is imported."
      }
    ],
    "discussions": [
      {
        "discussion_id": "fungal-nematode-egg-parasitism-scope-and-hierarchy",
        "prompt": "Refine the egg-infection hierarchy without conflating infection, feeding and hatching endpoints.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "The fungal bearer penetrates eggshells and colonizes egg interiors. Surface attachment, egg-hatching inhibition, killing, trapping or a gene annotation alone is insufficient. Animal pathogen METPO:1004002 is active below pathogenic to host METPO:1004000 and phenotype METPO:1000059. Its pinned organism-like wording is clarified as a phenotype in current upstream METPO; the local parent is not rewritten. Nematode egg infection does not entail mammalian pathogenicity. Xie describes this fungus as nematophagous, but the operational infection endpoint does not quantify feeding: fungal nematophagy traitmech:000719 requires consumption and also includes dead prey. It is related, not an asserted parent here. Local parasitism traitmech:000043 inherits persistent symbiosis, which is not required. No organism-level disjointness, obligacy, exclusive host stage or universal host range is asserted. Bare egg parasitism does not specify the fungal actor and is not an exact synonym.",
        "posed_by": "codex",
        "posed_date": "2026-10-14"
      },
      {
        "discussion_id": "fungal-nematode-egg-parasitism-metpo-assessment",
        "prompt": "Review the proposed class without reviving the obsolete parasitism identifier.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "No exact active counterpart was identified in the inspected pinned/current releases, editor and template owners. Historical METPO:1000227 obsolete parasitism is broader, deprecated, under ObsoleteClass with OMO:0001000 reason and no replacement or consider annotation in those releases. METPO issue 521 disputes mechanically assigned reasons; the code neither invalidates the biology nor authorizes reuse. The historical ID is not revived or placed in xrefs. Fried-egg colony is unrelated. The ontology pin remains unchanged; v602 proposes this narrower infection phenotype with PROPOSED status and no equivalent external xref.",
        "posed_by": "codex",
        "posed_date": "2026-10-14"
      },
      {
        "discussion_id": "fungal-nematode-egg-parasitism-evidence-limits",
        "prompt": "Resolve source inconsistencies and strain provenance before adding rates, examples or causal mechanisms.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Xu Supplementary Table 1 reports a 30-hour mean of 38% for replicates 38%, 33% and 33%, whose arithmetic mean is about 34.7%. This discrepancy is preserved, not silently corrected. Its main Methods sample-level wording is less precise than the supplement's individual-egg penetration criterion. No rates or infection threshold are curated. Xie's conserved appressorium genes also occur in fungi lacking that structure; neither gene inventory nor differential expression establishes this trait or a protein-resolved mechanism. No causal graph, protein example or canonical taxon is asserted without further authority and strain-provenance checks. Microscopy and source-designated infection are not tracer measurements of nutrient flux. No field efficacy or safety claim follows. Source hashes, inspected figures/supplement, actual snippet verdicts and bounded notice checks are retained in the verification sidecar; no comprehensive correction/retraction clearance is claimed. Both counted primary experiments concern Purpureocillium lilacinum (JZD02 and 36-1). The fungal actor class is not evidence that this phenotype was experimentally demonstrated across fungal species; additional species require their own evidence.",
        "posed_by": "codex",
        "posed_date": "2026-10-14"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-14T11:46:22Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added fungal nematode egg parasitism with two primary DOI sources and directly matched nine-word and six-word excerpts. Preserved native VERIFIED/NOT_IN_ABSTRACT outcomes and the supplement's inconsistent mean; no rates or sequence-derived mechanism imported. Reserved 000726, v602 and 1067900-1067999 after ignored/hidden current-copy, retained-history and open/draft PR checks, including full-content proposal ranges. Wheel sizes and broad editor envelopes are not conflicting reservations. Animal-pathogen parent scope checked against pinned/current ontology. Other records unchanged; timestamp records observed acceptance.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-14T12:50:22Z",
        "curator": "codex",
        "action": "CLARIFY_EVIDENCE",
        "changes": "Addressed issue #1931 after the approving PR review: added a directly matched 14-word supplementary penetration criterion and explicitly limited the two primary experiments to one fungal species. Xu quotations total 23 words; the extra excerpt is not a third independent experiment. Retained native NOT_IN_ABSTRACT, original minting history, definition, parent, source discrepancy and PROPOSED status.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000727",
    "label": "fungal nematode endoparasitism",
    "definition": "An animal-pathogenic phenotype in which a fungus uses spores attached to or ingested by a vermiform nematode to initiate infection and then grows inside the host.",
    "definition_source": "DOI:10.1371/journal.pgen.1006017",
    "trait_category": "ECOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1004002"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1371/journal.pgen.1006017",
        "snippet": "Drechmeria coniospora is an obligate fungal pathogen that infects nematodes via the adhesion of specialized spores to the host cuticle.",
        "notes": "Lebrigand et al. 2016, PMID:27153332, PMCID:PMC4859500, scientific Abstract. Direct JATS match and native VERIFIED. Author Summary and Discussion distinguish spore-initiated endoparasitism from hyphal traps and egg infection. Actual Figures 8 and 9 show recombinant fungal growth in C. elegans, not unmodified natural exemplars. S1 Text was fully read and visually checked: the laboratory line was serially passaged for about 15 years; its source isolate and ARSEF 6962 share provenance. Obligate is the authors' species description, not a universal class requirement or inability to grow on their artificial medium. Predicted genes and expression are not a universal mechanism."
      },
      {
        "reference": "DOI:10.3390/jof10010068",
        "snippet": "Then, the fungal hyphae penetrate into the nematode body cavity and grow in the nematode body",
        "notes": "Sun et al. 2024, PMID:38248977, PMCID:PMC10820206, Results 3.2. Direct JATS match; native NOT_IN_ABSTRACT retained. Methods 2.5 and actual Figure 2c,d concern GFP-engineered HR-eGFP1 on Bursaphelenchus xylophilus; Figure 2 distinguishes attachment, entry, internal growth and emergence. The entire two-page supplement, including S1-S3, was inspected. Methods 2.6 scores attached spores or colonization as parasitism; no rate is imported as an internal-infection rate. Main-text intestinal infection after swallowing is tentative; do not silently strengthen it using the supplement caption. No field efficacy or safety is inferred."
      },
      {
        "reference": "DOI:10.1017/S0953756296002092",
        "snippet": "The infection method for Harposporium cycloides was shown to be by spore ingestion.",
        "notes": "Glockling and Shimazu 1997, publisher scientific Abstract. Direct contiguous HTML match; DOI/title confirmed by Crossref and Europe PMC AGR:IND20619532. The native abstract resolver returned UNRESOLVED because it returned no abstract; this is not a missing-index claim. The primary abstract reports spore-ingestion infection in Harposporium cycloides and infectivity testing after pure culture. Full Methods, figures and host/strain provenance were not accessed; no canonical taxon, dose, route universality or pure-culture obligacy is inferred."
      }
    ],
    "discussions": [
      {
        "discussion_id": "fungal-nematode-endoparasitism-scope-and-hierarchy",
        "prompt": "Refine the infection-strategy hierarchy without conflating infection, trapping and feeding.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "The fungal bearer has the established spore-infection-strategy phenotype, not merely an anatomical location inside a nematode. The host-contacting or ingested spore is the infectious unit; spore germination into an external hyphal trap is not this route. Adhesion or ingestion alone, killing alone, internal occupancy without the specified route and sequence annotation are insufficient. Vermiform stages distinguish the selected strategy from eggshell penetration in fungal nematode egg parasitism traitmech:000726. Fungal nematophagy traitmech:000719 requires feeding and includes dead prey; fungal nematode trap formation traitmech:000718 concerns hyphal differentiation. Neither is asserted as a parent. Local parasitism traitmech:000043 inherits persistent symbiosis, not required here. Animal pathogen METPO:1004002 is active below pathogenic to host METPO:1004000 and phenotype METPO:1000059. Current upstream clarifies its pinned organism-like wording as a phenotype; the local parent remains unchanged. No organism-level disjointness, exclusive host stage, universal host range or obligacy is asserted. Bare endoparasitism does not specify the fungal actor, host or infection route and is not an exact synonym.",
        "posed_by": "codex",
        "posed_date": "2026-10-14"
      },
      {
        "discussion_id": "fungal-nematode-endoparasitism-metpo-assessment",
        "prompt": "Review the proposed infection class without reviving the obsolete parasitism identifier.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "No exact active counterpart was identified in inspected pinned/current releases, editor and six template owners. Historical METPO:1000227 obsolete parasitism is broader, deprecated, under ObsoleteClass with OMO:0001000 reason and no replacement or consider annotation in those releases. METPO issue 521 disputes mechanically assigned reasons; the code neither invalidates the biology nor authorizes reuse. The historical ID is not revived or placed in xrefs. The ontology pin remains unchanged; v603 proposes this narrower infection phenotype with PROPOSED status and no equivalent external xref. Existing bacterial endoparasitic predation is not this fungal spore-infection strategy.",
        "posed_by": "codex",
        "posed_date": "2026-10-14"
      },
      {
        "discussion_id": "fungal-nematode-endoparasitism-evidence-limits",
        "prompt": "Resolve assay endpoints and strain provenance before adding rates, canonical taxa or causal proteins.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Sun's Methods 2.6 counts attached spores or colonization; reported parasitism percentages are not curated as internal infection rates. Its imaged HR-eGFP1 is engineered, and morphological similarity to the wild type does not establish unchanged virulence. Its intestinal-route suggestion remains tentative; the distinct 1997 primary abstract supports ingestion in Harposporium cycloides. Lebrigand's S1 Text reports long laboratory passage and related isolate provenance, so these are not independent natural-strain exemplars. Predicted genes, expression and disputed assembly or mating-type interpretations are not required causal effectors. No canonical taxa, proteins or causal graph are asserted without further authority and strain-provenance work. Microscopy does not measure nutrient flux; no quantitative threshold, field efficacy or safety is inferred. The verification sidecar retains actual source locators, hashes and native verdicts; direct matching does not upgrade NOT_IN_ABSTRACT or UNRESOLVED. Full Glockling Methods and all raw experimental data were not accessed, and bounded notice checks are not comprehensive correction/retraction clearance.",
        "posed_by": "codex",
        "posed_date": "2026-10-14"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-14T15:19:28Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added fungal nematode endoparasitism with three primary DOI sources and directly matched 20-, 16- and 13-word excerpts. Retained native VERIFIED, NOT_IN_ABSTRACT and UNRESOLVED outcomes. Spore-initiated infection and internal growth are not adhesion alone, hyphal traps or egg infection. No rates, canonical taxa or sequence-derived mechanism imported. Reserved 000727, v603 and 1068000-1068099 after ignored/hidden current-copy, retained-history and open/draft PR checks, including full-content proposal ranges. A ChemSpider identifier and broad editor envelopes are not METPO reservations. Other records unchanged; timestamp records observed acceptance.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000719",
    "label": "fungal nematophagy",
    "definition": "A nutritional phenotype in which a fungus consumes nematodes as food.",
    "definition_source": "DOI:10.3390/f10050404",
    "trait_category": "ECOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.3390/f10050404",
        "snippet": "Nematophagy implies the consumption of nematodes.",
        "notes": "Marlin et al. 2019, Introduction, PDF page 1: directly read terminology, not an independent experiment. The fungal actor qualifies the term; consumption, not paralysis alone, defines the endpoint. Publisher PDF visually checked. Native DOI abstract verifier: UNRESOLVED, retained separately from the direct match. Crossref and USDA identify the same DOI/title."
      },
      {
        "reference": "DOI:10.3390/f10050404",
        "snippet": "Susceptible rhabditid species (Poikilolaimus oxycercus) being consumed by Pleurotus ostreatus hyphae.",
        "notes": "Figure 2a caption, actual PDF page 6 and panel inspected, with Methods 2.1-2.3 and Results 3.2. This is a source-named feeding observation, not measured nutrient flux. Native verifier: UNRESOLVED. Host susceptibility is differential; neither all nematodes nor all Pleurotus isolates are asserted. The two excerpts from this paper total 17 words."
      },
      {
        "reference": "https://horizon.documentation.ird.fr/exl-doc/pleins_textes/fan/40780.pdf",
        "snippet": "The saprophytic and predacious ability appeared not to be mutually exclusive.",
        "notes": "den Belder and Jansen 1994, Summary, PDF page 1, directly and visually matched. Selected Methods, Results and Discussion, including actual pages 6-8, describe Arthrobotrys oligospora CBS 289.82 feeding on living and previously killed Meloidogyne hapla juveniles. Internal hyphal occupancy is not a tracer assimilation assay. The excerpt supports nonexclusive feeding modes, not an exact rate. URL evidence is not run by the native DOI/PMID abstract verifier."
      },
      {
        "reference": "DOI:10.1371/journal.pbio.3002400",
        "snippet": "At mid to late time points, we observed hyphal growth inside nematodes following penetration of the cuticle, corresponding to digestion.",
        "notes": "Lin et al. 2023, PMID:37988381; Results subsection on late-time protease induction, publisher XML sec018. Native verifier: NOT_IN_ABSTRACT; exact full-text match. Actual Figure 5, Table 1 and S7 inspected. GFP-labeled reference TWF3407 is engineered, not an unmodified natural exemplar. Protease inhibition delays internal growth at 12 h without proving complete feeding loss or quantifying assimilation. Remaining figures and raw S1 spreadsheet were not fully audited."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:5322",
        "taxon_label": "Pleurotus ostreatus",
        "reference": "DOI:10.3390/f10050404",
        "note": "Qualified Figure 2a example: unnamed culture isolated from grocery-store mushrooms and identified morphologically, per Methods 2.1 at https://doi.org/10.3390/f10050404. The water-agar assay used 20 mixed-age nematodes and assessed this fungus after one week. No strain deposit, molecular identification or genetic provenance is inferred. NCBI EFetch resolved the species on 2026-10-13."
      }
    ],
    "discussions": [
      {
        "discussion_id": "fungal-nematophagy-scope-and-hierarchy",
        "prompt": "Resolve the broader feeding hierarchy without imposing a capture mechanism or carbon-specific endpoint.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Feeding on living or previously dead nematodes is included; fungal killing, obligacy and starvation are not universal requirements. Mere contact, paralysis, killing, trap formation or a sequence annotation alone is insufficient. Fungal nematode-trap formation (traitmech:000718) is structural, neither necessary nor sufficient for feeding. Mycoparasitism (traitmech:000717) has fungal prey; predatory bacterium (traitmech:000054) has a bacterial actor and prey. Phagotrophy (traitmech:000628), myzocytosis (traitmech:000631) and pallium feeding (traitmech:000632) impose different uptake modes. Saprotrophy (traitmech:000055) can overlap, without organism-level disjointness. Local parasitism (traitmech:000043) inherits persistent association, not required here. Keep phenotype METPO:1000059 pending a closer feeding hierarchy; no universal carbon, nitrogen or energy contribution is specified. Bare nematophagy includes nonfungal actors and is not an exact synonym. No unverified synonyms or xrefs are asserted.",
        "posed_by": "codex",
        "posed_date": "2026-10-13"
      },
      {
        "discussion_id": "fungal-nematophagy-metpo-assessment",
        "prompt": "Review upstream placement without reviving deprecated identifiers.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Pinned and current METPO lack an exact active counterpart in the inspected scope. Historical METPO:0000005 and METPO:000005 are deprecated and replace to active METPO:1000631 trophic type, a carbon/energy axis rather than this prey-defined feeding phenotype. METPO:1000644 is organic-carbon heterotrophy and METPO:1000731 concerns nutrient-availability adaptation. Deprecated METPO:0000261, METPO:000262 and METPO:1000125 concern fungal spores; METPO:1000227 is parasitism. No replacement or consider annotation was observed for those four. Their OMO:0001000 reasons neither invalidate biology nor authorize reuse. Historical IDs are not exact xrefs. The pinned ontology remains unchanged; v595 proposes the new class.",
        "posed_by": "codex",
        "posed_date": "2026-10-13"
      },
      {
        "discussion_id": "fungal-nematophagy-source-and-mechanism-limits",
        "prompt": "Resolve source inconsistencies and taxon-paired effectors before adding a causal graph.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Marlin's Table 2 conflicts with its Introduction on two host responses; Table 3 and Results differ for P. artyukhovskii. Those disputed host ranges are not imported. den Belder's Figure 2 panel labels/caption, Table 3 direction and significance notation disagree with prose; no numerical rates are adopted. Lin's Results uses mep1 where Table 1 and Figure 5 use mcp1; no protein identity is silently reconciled. Its linked DOI:10.1371/journal.pbio.3003178 is a later Update Article, not a correction or independent laboratory replication. Capture and digestion have distinct assays; expression associations do not establish universal effectors. No causal graph, protein example or chemical mechanism is asserted. Source-status checks are bounded: MDPI's notice page returned 403, and no comprehensive notice clearance is claimed. Source hashes, inspected sections and actual native verdicts are retained in the verification sidecar.",
        "posed_by": "codex",
        "posed_date": "2026-10-13"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-13T15:34:51Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added fungal nematophagy with four contiguous excerpts from three sources and a qualified Pleurotus example. Distinguished feeding from trapping, paralysis and quantified assimilation. Reserved 000719, v595 and 1067200-1067299 after ignored/hidden current-file, retained-history and open/draft PR checks; numerical false positives adjudicated. No exact active METPO counterpart identified. Other records unchanged. Timestamp is observed post-audit acceptance.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000052",
    "label": "gut-associated",
    "definition": "A host association in which an organism is a persistent member of the gastrointestinal microbiota of an animal host, often contributing to host nutrition and physiology.",
    "definition_source": "DOI:10.1126/science.1104816",
    "trait_category": "ECOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "traitmech:000049"
    ],
    "synonyms": [
      {
        "synonym_text": "intestinal",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1126/science.1104816"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1126/science.1104816",
        "notes": "B\u00e4ckhed et al. characterize the distal intestine as a dense microbial habitat whose residents provide metabolic capabilities to the host."
      },
      {
        "reference": "DOI:10.1073/pnas.1218525110",
        "notes": "McFall-Ngai et al. support the gut as a major site of host-associated microbial communities across animals."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:818",
        "taxon_label": "Bacteroides thetaiotaomicron",
        "note": "Canonical human-gut-symbiont model (polysaccharide utilisation loci).",
        "reference": "PMID:12663928"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "gut_associated_microbiota_metabolism",
        "title": "Gut-associated lifestyle in the gastrointestinal microbiota",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This broad ecological, host-relationship, habitat, or hazard classification spans multiple taxa and mechanisms; contextual protein nodes do not receive token UniProt examples.",
        "description": "Evidence-backed causal sketch linking gastrointestinal habitat to persistent gut-microbiota membership and host nutritional contributions.",
        "nodes": [
          {
            "node_id": "gut_associated_trait",
            "label": "gut-associated",
            "node_type": "TRAIT",
            "grounding": "traitmech:000052",
            "description": "Persistent member of an animal gastrointestinal microbiota."
          },
          {
            "node_id": "gastrointestinal_habitat",
            "label": "gastrointestinal tract habitat",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Animal distal intestine and other GI compartments."
          },
          {
            "node_id": "host_metabolic_contribution",
            "label": "host metabolic contribution",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Microbially mediated nutrient harvest and metabolism for the host."
          },
          {
            "node_id": "adhesins",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Contextual protein family or multiprotein aggregate reviewed for this nonmechanistic classification; no single semantic family captures it.",
            "label": "bacterial adhesins",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Bacterial surface adhesins that bind host receptors."
          },
          {
            "node_id": "mucosal_adhesion",
            "label": "adhesion to intestinal mucus/epithelium",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Binding of bacterial adhesins to intestinal mucus or epithelial receptors."
          },
          {
            "node_id": "bile_acids",
            "label": "bile acids/bile salts",
            "node_type": "CHEMICAL",
            "description": "Host bile acids and conjugated bile salts in the gut."
          },
          {
            "node_id": "antimicrobial_peptides",
            "label": "Paneth-cell antimicrobial peptides",
            "node_type": "CHEMICAL",
            "description": "Antimicrobial peptides secreted by Paneth cells in the small intestine."
          },
          {
            "node_id": "small_intestinal_bacterial_growth",
            "label": "bacterial growth in small intestine",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Growth of bacteria in the small-intestinal lumen."
          },
          {
            "node_id": "peristalsis",
            "label": "intestinal peristalsis",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Mechanical flow/clearance of luminal contents in the gut."
          },
          {
            "node_id": "duodenal_retention",
            "label": "colonization/retention in duodenum",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Persistent retention/colonization in the duodenum and proximal small intestine."
          },
          {
            "node_id": "luminal_oxygen_limitation",
            "label": "limitation of colonic luminal oxygen diffusion",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Host functions that limit oxygen diffusion into the colonic lumen during homeostasis."
          },
          {
            "node_id": "primary_fermenter_community",
            "label": "primary-fermenter-dominated community",
            "node_type": "STATE",
            "description": "A gut microbial community dominated by anaerobic primary fermenters."
          },
          {
            "node_id": "butyrate",
            "label": "butyrate",
            "node_type": "CHEMICAL",
            "description": "Short-chain fatty acid produced by anaerobic primary fermenters and consumed by colonocytes as their principal respiratory substrate.",
            "grounding": "CHEBI:17968"
          },
          {
            "node_id": "colonocyte_oxidative_metabolism",
            "label": "colonocyte oxidative metabolism",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Beta-oxidation of butyrate by colonic epithelial cells, which consumes oxygen at the mucosal surface."
          }
        ],
        "edges": [
          {
            "subject": "gastrointestinal_habitat",
            "predicate": "confers",
            "object": "gut_associated_trait",
            "description": "The intestinal environment supports persistent residency.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.1104816",
                "notes": "B\u00e4ckhed et al. characterize the distal intestine as a dense microbial habitat."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "gut_associated_trait",
            "predicate": "contributes to",
            "object": "host_metabolic_contribution",
            "description": "Gut microbiota provide metabolic capabilities to the host.",
            "evidence": [
              {
                "reference": "DOI:10.1073/pnas.1218525110",
                "notes": "McFall-Ngai et al. support the gut microbiota as a metabolically consequential host-associated community."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "adhesins",
            "predicate": "enables",
            "object": "mucosal_adhesion",
            "description": "Bacterial adhesins bind host receptors to enable adhesion.",
            "evidence": [
              {
                "reference": "DOI:10.3390/microorganisms12051026",
                "notes": "Adhesion primarily relies on adhesins; binding of bacterial adhesins to host receptors is a prerequisite for long-term colonization (Lin et al., 2024)."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "mucosal_adhesion",
            "predicate": "prerequisite for",
            "object": "gut_associated_trait",
            "description": "Adhesion to mucus/epithelium is a prerequisite for long-term gut colonization.",
            "evidence": [
              {
                "reference": "DOI:10.3390/microorganisms12051026",
                "notes": "Adhesion emphasized as the prerequisite for persistence (adhesion -> growth -> reproduction) (Lin et al., 2024)."
              }
            ]
          },
          {
            "subject": "bile_acids",
            "predicate": "exerts antimicrobial pressure on",
            "object": "gastrointestinal_habitat",
            "description": "Bile acids shape gut community via antimicrobial and detergent-like properties.",
            "evidence": [
              {
                "reference": "DOI:10.1128/spectrum.03576-23",
                "notes": "Bile acids shape the gut microbiome composition due to antimicrobial and detergent-like properties, creating a harsh gut environment (McMillan et al., 2024)."
              }
            ]
          },
          {
            "subject": "bile_acids",
            "predicate": "inhibits",
            "object": "small_intestinal_bacterial_growth",
            "description": "Small-intestinal bile salts inhibit growth of many bacteria.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.chom.2024.05.011",
                "notes": "Bile salts and Paneth-cell antimicrobial peptides inhibit growth of many bacteria in the small intestine (Muramatsu & Winter, 2024)."
              }
            ],
            "predicate_id": "RO:0002212"
          },
          {
            "subject": "antimicrobial_peptides",
            "predicate": "inhibits",
            "object": "small_intestinal_bacterial_growth",
            "description": "Paneth-cell antimicrobial peptides inhibit growth of many small-intestinal bacteria.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.chom.2024.05.011",
                "notes": "Antimicrobial peptides released by Paneth cells inhibit growth of many bacteria in the small intestine (Muramatsu & Winter, 2024)."
              }
            ],
            "predicate_id": "RO:0002212"
          },
          {
            "subject": "peristalsis",
            "predicate": "decreases",
            "object": "duodenal_retention",
            "description": "Strong peristalsis (plus bile/antimicrobials) makes the duodenum hostile to retention.",
            "evidence": [
              {
                "reference": "DOI:10.3390/microorganisms12051026",
                "notes": "The duodenum is hostile to retention due to bile, antimicrobials, and strong peristalsis (Lin et al., 2024)."
              }
            ],
            "predicate_id": "RO:0002212"
          },
          {
            "subject": "luminal_oxygen_limitation",
            "predicate": "contributes to",
            "object": "primary_fermenter_community",
            "description": "Host limitation of luminal oxygen shelters a primary-fermenter-dominated community.",
            "evidence": [
              {
                "reference": "DOI:10.1128/iai.00302-24",
                "notes": "During homeostasis, host functions that limit oxygen diffusion into the colonic lumen shelter a community dominated by primary fermenters (Lee et al., 2024)."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "primary_fermenter_community",
            "predicate": "produces",
            "object": "butyrate",
            "description": "The anaerobic primary-fermenter community is the source of luminal butyrate; depleting it collapses butyrate and reconstituting it restores butyrate.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.chom.2016.03.004",
                "snippet": "While inoculation with a community of 17 human Clostridia isolates resulted in a significant (P < 0.05) increase in butyrate levels",
                "notes": "The recolonisation arm of the discussion's decision rule. The converse was shown in the same study: streptomycin depletion of butyrate-producing Clostridia lowered cecal butyrate."
              }
            ],
            "predicate_id": "biolink:produces"
          },
          {
            "subject": "butyrate",
            "predicate": "positively regulates",
            "object": "colonocyte_oxidative_metabolism",
            "description": "Butyrate is sensed by epithelial PPAR-gamma and drives colonocyte energy metabolism toward beta-oxidation, raising epithelial oxygen consumption.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.chom.2015.03.005",
                "snippet": "Bacteria-derived butyrate affects epithelial O2 consumption and results in stabilization of hypoxia-inducible factor (HIF), a transcription factor coordinating barrier protection",
                "notes": "Cell-culture work in the same study shows the effect is direct: epithelial metabolism of butyrate depletes local oxygen."
              },
              {
                "reference": "DOI:10.1126/science.aam9949",
                "snippet": "the depletion of butyrate-producing microbes by antibiotic treatment reduced epithelial signaling through the intracellular butyrate sensor peroxisome proliferator-activated receptor \u03b3 (PPAR-\u03b3)",
                "notes": "Identifies PPAR-gamma as the epithelial butyrate sensor."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "colonocyte_oxidative_metabolism",
            "predicate": "contributes to",
            "object": "luminal_oxygen_limitation",
            "description": "Colonocyte beta-oxidation consumes oxygen at the mucosa and so limits the oxygen reaching the lumen. SCOPE: this is a claim about mucosal-to-luminal oxygen flux and bioavailability, NOT about bulk centre-lumen anoxia.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.aam9949",
                "snippet": "Microbiota-induced PPAR-\u03b3 signaling also limits the luminal bioavailability of oxygen by driving the energy metabolism of colonic epithelial cells (colonocytes) toward \u03b2-oxidation",
                "notes": "States the closing step directly, and in terms of BIOAVAILABILITY rather than bulk concentration."
              },
              {
                "reference": "DOI:10.1016/j.chom.2016.03.004",
                "snippet": "tributyrin supplementation restored epithelial hypoxia in streptomycin-treated mice",
                "notes": "Metabolite rescue: the oxygen change tracks butyrate, not the antibiotic, which is what makes the return arm causal rather than correlational."
              },
              {
                "reference": "DOI:10.1073/pnas.1718635115",
                "snippet": "Remarkably, measurements of luminal oxygen levels show nearly identical pO2 (partial pressure of oxygen) profiles in conventional and germ-free mice, pointing to the existence of oxygen consumption mechanisms other than microbial respiration",
                "notes": "BOUNDING EVIDENCE, attached deliberately so this edge cannot drift into claiming the microbiota creates the anaerobic gut. Direct pO2 measurement shows chemistry alone is sufficient to hold the lumen anaerobic: germ-free luminal contents consume oxygen via lipid oxidation, though more slowly than conventional contents. The source does NOT say microbes are irrelevant to bulk anoxia -- it concludes that 'both the microbes and the oxidative chemical reactions regulate luminal oxygen levels', and credits increased microbial biomass with the proximal-to-distal oxygen gradient. The bound is therefore about SOLE causation: this edge asserts a contribution to limiting mucosal-to-luminal oxygen flux, which is how the target node is defined, and must not be strengthened into sole responsibility for bulk centre-lumen anoxia."
              }
            ],
            "predicate_id": "RO:0002326"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-06-02T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate ECOLOGY trait (gut-associated); sub-variant of host-associated.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-09T14:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (gut microbiota / host metabolic contribution) with RO predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 7 evidence-backed generic edges (9 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:09Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 5 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d72, RO:0002212\u00d72, METPO:2000017\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 1 causal edge(s) off enables/RO:0002327 with a TRAIT object (1 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T02:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES_PART2",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates onto their causal-graph counterparts (1 to reduces), issue 301 part 2. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Each replacement is a 1:1 mirror of its source predicate that changes only the domain, so the claim each edge makes is unchanged and directions are unchanged. The replacements are proposed in proposals/metpo_traitmech_v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T06:00:00Z",
        "curator": "claude",
        "action": "REGROUND_CAUSAL_EDGE",
        "changes": "Relabelled 1 causal edge from `reduces` to `decreases` and re-grounded it from METPO:2007802 to RO:0002212 (negatively regulates), issue 330. The corpus wrote two senses under the single label `reduces` - genuine electron donation, and a lessens/decreases sense - and METPO:2007802 is defined as donating electrons to the object and lowering its oxidation state, which this edge does not assert. The two senses could not be separated mechanically because the label was identical, so they migrated together in issue 329 and were split here by reading each edge. RO:0002212 declares no rdfs:domain or rdfs:range, so this introduces no entailment of the kind issue 301 removed.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-07T05:00:00Z",
        "curator": "claude",
        "action": "REGROUND_CAUSAL_EDGE",
        "changes": "Re-grounded the edge from enables/RO:0002327 to RO:0002326 (contributes to), issue 334. biolink declares enables range 'biological process or activity' and the object is a STATE, which does not satisfy it. Unlike the tolerance/capacity nodes in this same pass, this object is a genuine state rather than a mis-typed disposition - a gradient, a community composition, an internal environment - so retyping it to TRAIT would be wrong. contributes to fits because the subject genuinely contributes to the OCCURRENCE OR GENERATION of the object, which is biolink's definition; that is the same test the motive-force edges FAILED in issue 341, where the subject powers a machine it does not generate. RO:0002326 declares no rdfs:domain or rdfs:range.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-17T22:14:03Z",
        "curator": "claude",
        "action": "CURATE_KNOWLEDGE_GAPS",
        "changes": "Replaced the scan's off-topic scraped sentence with a research question authored from this record's causal graph, anchored it via attaches_to, and sketched an experiment with a decision criterion. The scan's sentence and PMIDs are preserved in the discussion's notes.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope gut_associated_microbiota_metabolism=NONMECHANISTIC with scope_notes; marked 1 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (adhesins).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-01T02:32:12Z",
        "curator": "claude",
        "action": "CONNECT_CAUSAL_GRAPH",
        "changes": "Closed the oxygen/fermenter feedback loop in gut_associated_microbiota_metabolism (#617), resolving the record's x-gut-oxygen-causal-direction knowledge gap in favour of its would_support criterion. Added nodes butyrate (CHEBI:17968) and colonocyte_oxidative_metabolism, and three edges: primary_fermenter_community -[biolink:produces]-> butyrate -[RO:0002213]-> colonocyte_oxidative_metabolism -[RO:0002326]-> luminal_oxygen_limitation. The return arm is modelled as HOST-MEDIATED rather than as direct microbial oxygen consumption, because that is what the sources show. The closing edge carries DOI:10.1073/pnas.1718635115 as bounding evidence: bulk centre-lumen pO2 is near-identical in germ-free and conventional mice, so the claim is scoped to mucosal-to-luminal oxygen flux and must not drift into bulk anoxia. No connectivity-only edge was invented to attach this component to the trait node.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-01T02:33:06Z",
        "curator": "claude",
        "action": "RESOLVE_DISCUSSION",
        "changes": "Set the x-gut-oxygen-causal-direction knowledge gap to RESOLVED after both arms of its would_support criterion were met and the mediated loop landed with four verified primary references. See issue 617.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-02T05:05:52Z",
        "curator": "claude",
        "action": "CORRECT_EVIDENCE_SNIPPETS",
        "changes": "Adversarial review of PR 618 before merge. Corrected two snippets and one note. Issue 619: the DOI:10.1073/pnas.1718635115 snippet was a PARAPHRASE presented as a verbatim quote and has been replaced with the source sentence retrieved from the Europe PMC REST API. Issue 620: the DOI:10.1016/j.chom.2016.03.004 snippet silently dropped '(P < 0.05)' from mid-quote and is now contiguous. Issue 621: the same evidence item's notes asserted the microbiota is not responsible for bulk anoxia, a stronger negative than the source supports; the source concludes that both microbes and oxidative chemistry regulate luminal oxygen, so the note now bounds SOLE causation rather than denying a microbial contribution. No causal claim changed.",
        "llm_assisted": true
      }
    ],
    "discussions": [
      {
        "discussion_id": "kgscan-4fc1a06fa1e3",
        "prompt": "This record commits to luminal oxygen limitation contributing to the primary fermenter community. Does the reverse arm hold too -- do the fermenters and the epithelium maintain the anoxia -- making this a feedback loop rather than the one-way edge drawn?",
        "kind": "KNOWLEDGE_GAP",
        "status": "RESOLVED",
        "rationale": "The existing edge is not wrong so much as half: it says the anoxic lumen permits the fermenters, and stops. If the return arm also holds, the two nodes are a self-reinforcing loop, and losing the fermenters raises luminal oxygen and admits facultative pathogens -- the collapse that follows antibiotic depletion. That is the clinically load-bearing half, and a graph of one-way edges can only carry it if someone draws it.",
        "attaches_to": [
          "causal_graphs#luminal_oxygen_limitation",
          "causal_graphs#primary_fermenter_community"
        ],
        "posed_by": "claude",
        "notes": "Scan provenance (#409). The kg-microbe-kgscan pass raised this discussion with the prompt 'Knowledge gap for gut-associated: MicroRNAs (miRNAs) are small, noncoding RNAs involved in posttranscriptional gene regulation in both animal and plant. miRNAs derived from edible plants, referred to as xenomiRs, are proposed to cross-kingdom barriers and to modulate mammalian gene expression.', whose sentence came from PMID:40945860. That sentence is about plant-derived xenomiRs crossing kingdom barriers, not about this trait: the scan matched the hedging vocabulary of a gap statement without checking that the gap was about the trait it was filed under. The prompt above was authored instead from this record's own causal graph, and none of these references are carried as its evidence, because they support the scraped sentence rather than the question. The scan attached 3 further references whose snippets concern neither that sentence nor this trait; all 4 are reproduced here so nothing it produced is lost: PMID:40945860 'MicroRNAs (miRNAs) are small, noncoding RNAs involved in posttranscriptional gene regulation in both animal and plant. miRNAs derived from edible plants, referred to as xenomiRs, are proposed to cross-kingdom barriers and to modulate mammalian gene expression.'; PMID:42278360 'By integrating microbiological, immunological, and clinical perspectives, this review highlights key knowledge gaps and outlines future research directions aimed at harnessing the gut microbiome as a novel therapeutic avenue in HIV management and eradication.'; PMID:41808832 'Given its promising anti-inflammatory properties, further research is warranted.'; PMID:42197356 'Examining the existing literature may identify knowledge gaps regarding precise mechanisms through which the development of GM influences the maturation of the immune system.'.",
        "proposed_experiments": [
          {
            "experiment_id": "x-gut-oxygen-causal-direction",
            "name": "Oxygen microprofiling during staged gnotobiotic colonisation",
            "approach": "staged gnotobiotic colonisation with in situ oxygen microsensing",
            "model_systems": [
              "germ-free animals colonised in defined stages",
              "a defined community with and without obligate anaerobe fermenters",
              "oxygen microelectrodes at the mucosal surface and mid-lumen"
            ],
            "perturbations": [
              "colonisation with facultative organisms alone",
              "subsequent addition of obligate anaerobe fermenters",
              "butyrate supplementation without the producing community",
              "antibiotic depletion of an established fermenter community"
            ],
            "readouts": [
              "luminal and mucosal oxygen partial pressure over time",
              "community composition by shotgun sequencing",
              "short-chain fatty acid concentration",
              "epithelial hypoxia by pimonidazole staining"
            ],
            "decision_criterion": "whether luminal oxygen rises when an established fermenter community is depleted, with colonisation order held constant",
            "would_support": "oxygen rises on depletion and falls again on re-colonisation -- the return arm is real and the pair is a loop",
            "would_refute": "oxygen is unchanged by depletion -- the habitat sets the anoxia and the single existing edge is the whole story"
          }
        ],
        "posed_date": "2026-08-17",
        "resolved_date": "2026-08-31",
        "resolution_note": "Supported, with two bounds. The would_support criterion was 'oxygen rises on depletion and falls again on re-colonisation', and both arms hold: streptomycin depletion of butyrate-producing Clostridia lowers cecal butyrate and raises epithelial oxygenation, tributyrin supplementation reverses it, and recolonisation with 17 human Clostridia isolates raises butyrate and restores colonocyte hypoxia (DOI:10.1016/j.chom.2016.03.004), replicated independently by DOI:10.1016/j.chom.2015.03.005. The pair is therefore a feedback loop, now modelled as such. Bound 1: the return arm is HOST-MEDIATED, running through butyrate and colonocyte beta-oxidation rather than direct microbial oxygen consumption (DOI:10.1126/science.aam9949), so the graph routes it through the new butyrate and colonocyte_oxidative_metabolism nodes rather than drawing a direct reverse edge. Bound 2: the community is NOT responsible for bulk centre-lumen anoxia -- direct phosphorescent-probe measurement finds germ-free and conventional mice nearly indistinguishable (DOI:10.1073/pnas.1718635115) -- so the closing edge is scoped to mucosal-to-luminal oxygen flux and carries that source as bounding evidence. Left open and tracked in issue 617: whether abiotic luminal oxygen consumption deserves its own node, and whether this component should attach to the trait node, which no current source supports."
      }
    ]
  },
  {
    "identifier": "traitmech:000047",
    "label": "habitat association",
    "definition": "An ecological classification of the primary environment or niche an organism inhabits (e.g. free-living vs host-associated; soil, rhizosphere, gut). Microbial taxa show biogeographic structure across such habitats.",
    "definition_source": "DOI:10.1038/nrmicro1341",
    "trait_category": "ECOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "synonyms": [
      {
        "synonym_text": "niche association",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1038/nrmicro1341"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/nrmicro1341",
        "notes": "Martiny et al., \"Microbial biogeography\", support habitat/niche as a structuring axis of microbial distribution; parent of the habitat sub-variants."
      },
      {
        "reference": "DOI:10.1038/nrmicro.2017.87",
        "notes": "Fierer, \"Embracing the unknown\", supports environment-specific microbial community membership (e.g. the soil microbiome) underpinning habitat association."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:335992",
        "taxon_label": "Candidatus Pelagibacter ubique HTCC1062",
        "reference": "PMID:16109880",
        "note": "Strain HTCC1062 was isolated from the Oregon coastal ocean and the genome paper characterizes its streamlined marine-plankton habitat association; this exemplifies the marine branch of the broad habitat class."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "habitat_association_biogeographic_structure",
        "title": "Habitat association structures microbial biogeography",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This broad ecological, host-relationship, habitat, or hazard classification spans multiple taxa and mechanisms; contextual protein nodes do not receive token UniProt examples.",
        "description": "Evidence-backed causal sketch linking environmental habitat to the biogeographic patterning of microbial taxa.",
        "nodes": [
          {
            "node_id": "habitat_association_trait",
            "label": "habitat association",
            "node_type": "TRAIT",
            "grounding": "traitmech:000047",
            "description": "Ecological classification of the organism's primary environment."
          },
          {
            "node_id": "habitat",
            "label": "habitat",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Free-living, host-associated, soil, rhizosphere, or gut habitat.",
            "grounding": "ENVO:01000739"
          },
          {
            "node_id": "biogeographic_structure",
            "label": "biogeographic community structure",
            "node_type": "QUALITY",
            "description": "Habitat-specific microbial community membership."
          },
          {
            "node_id": "community_composition",
            "label": "microbial community composition",
            "node_type": "QUALITY",
            "description": "Taxonomic membership and structure of a microbial community in a habitat."
          },
          {
            "node_id": "environmental_stress",
            "label": "environmental stress",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Abiotic stress (e.g. pH, salinity, contaminant load) imposed by a habitat."
          },
          {
            "node_id": "selection_assembly",
            "label": "deterministic selection in community assembly",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Deterministic assembly process favoring environmentally adapted taxa."
          },
          {
            "node_id": "ecological_drift",
            "label": "ecological drift in community assembly",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Stochastic demographic process contributing to community turnover."
          },
          {
            "node_id": "dispersal_limitation",
            "label": "dispersal limitation in community assembly",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Spatial/historical process limiting taxon movement between habitats."
          },
          {
            "node_id": "salinity",
            "label": "salinity",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Salt concentration; major abiotic filter structuring aquatic communities."
          },
          {
            "node_id": "osmolyte_transport_synthesis_proteins",
            "label": "osmolyte transport and synthesis proteins",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Protein systems for compatible-solute transport and synthesis that contribute to salt tolerance.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "This aggregate spans multiple transporter and biosynthetic protein families and is retained only as contextual protein information."
          }
        ],
        "edges": [
          {
            "subject": "habitat",
            "predicate": "causes",
            "object": "habitat_association_trait",
            "description": "The organism's primary habitat sets its habitat-association classification.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro1341",
                "notes": "Martiny et al. show habitat as a structuring axis of microbial biogeography."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "habitat_association_trait",
            "predicate": "associated with",
            "object": "biogeographic_structure",
            "description": "Habitat-associated taxa display environment-specific community membership.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro.2017.87",
                "notes": "Fierer documents environment-specific community membership (e.g. the soil microbiome)."
              }
            ],
            "predicate_id": "biolink:associated_with"
          },
          {
            "subject": "habitat",
            "predicate": "structures",
            "object": "community_composition",
            "description": "The habitat/environment selects for spatial variation in community composition.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro1341",
                "notes": "Free-living taxa exhibit biogeographic patterns; the environment selects for spatial variation in diversity (Martiny et al. review)."
              }
            ]
          },
          {
            "subject": "environmental_stress",
            "predicate": "increases",
            "object": "selection_assembly",
            "description": "Higher environmental stress increases the contribution of deterministic selection to assembly.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-023-01573-x",
                "notes": "Selection producing more dissimilar communities increased with stress (groundwater assembly study)."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "environmental_stress",
            "predicate": "decreases",
            "object": "ecological_drift",
            "description": "Higher environmental stress decreases the contribution of stochastic drift to assembly.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-023-01573-x",
                "notes": "Drift showed negative correlation with stress; stochastic importance decreased with increasing environmental stress."
              }
            ],
            "predicate_id": "RO:0002212"
          },
          {
            "subject": "environmental_stress",
            "predicate": "decreases",
            "object": "dispersal_limitation",
            "description": "Higher environmental stress decreases the contribution of dispersal limitation to assembly.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-023-01573-x",
                "notes": "Dispersal limitation showed negative correlations with stress."
              }
            ],
            "predicate_id": "RO:0002212"
          },
          {
            "subject": "salinity",
            "predicate": "structures",
            "object": "community_composition",
            "description": "Salinity is a primary abiotic regulator of aquatic community composition.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s40168-024-01979-7",
                "notes": "Lake microbiomes primarily regulated by salinity; saline vs freshwater lakes show distinct taxonomic profiles."
              }
            ]
          },
          {
            "subject": "salinity",
            "predicate": "enriches",
            "object": "osmolyte_transport_synthesis_proteins",
            "description": "Saline habitats enrich for osmolyte transport and synthesis protein systems.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s40168-024-01979-7",
                "notes": "Saline-lake microbiomes possess more genes encoding osmolyte transport and synthesis."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-06-02T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate ECOLOGY axis class (habitat association) to parent the free-living/host-associated/soil/rhizosphere/gut habitat sub-variants.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-09T14:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (habitat / biogeographic structure) with biolink predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-14T06:55:37Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (ENVO:01000739\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 6 evidence-backed generic edges (7 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:09Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002212\u00d72, RO:0002213\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope habitat_association_biogeographic_structure=NONMECHANISTIC with scope_notes; marked 1 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (osmolyte_transport_synthesis_proteins); added 1 node(s) and 1 edge(s) (osmolyte_transport_synthesis_proteins); removed 1 node(s) and 1 edge(s) together with their evidence (osmolyte_genes).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T04:43:24Z",
        "curator": "codex",
        "action": "ADD_CANONICAL_EXAMPLES",
        "changes": "Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Candidatus Pelagibacter ubique HTCC1062 (NCBITaxon:335992; PMID:16109880). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000049",
    "label": "host-associated",
    "definition": "A habitat association in which an organism lives persistently on or in a plant or animal host (e.g. as a member of a host microbiome), spanning commensal, mutualistic, and pathogenic relationships.",
    "definition_source": "DOI:10.1073/pnas.1218525110",
    "trait_category": "ECOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "traitmech:000047"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1073/pnas.1218525110",
        "notes": "McFall-Ngai et al. document the ubiquity of host-associated microbial communities across the animal kingdom."
      },
      {
        "reference": "DOI:10.1126/science.1104816",
        "notes": "B\u00e4ckhed et al. characterize the host-associated gut microbiota as a dense, coevolved community."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:562",
        "taxon_label": "Escherichia coli",
        "note": "gut commensal",
        "reference": "PMID:37038177"
      },
      {
        "taxon_id": "NCBITaxon:818",
        "taxon_label": "Bacteroides thetaiotaomicron",
        "note": "gut symbiont",
        "reference": "PMID:41099497"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "host_associated_microbiome",
        "title": "Host association establishes persistent host microbiome membership",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This broad ecological, host-relationship, habitat, or hazard classification spans multiple taxa and mechanisms; contextual protein nodes do not receive token UniProt examples.",
        "description": "Evidence-backed causal sketch linking host habitat to persistent membership in a host-associated microbial community.",
        "nodes": [
          {
            "node_id": "host_associated_trait",
            "label": "host-associated",
            "node_type": "TRAIT",
            "grounding": "traitmech:000049",
            "description": "Persistent life on or in a plant or animal host."
          },
          {
            "node_id": "host_habitat",
            "label": "host habitat",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Plant or animal tissue surface or lumen."
          },
          {
            "node_id": "host_colonization",
            "label": "host colonization",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Persistent establishment of microbes on or in a host."
          },
          {
            "node_id": "mucin_o_glycans",
            "label": "mucin O-glycans",
            "node_type": "CHEMICAL",
            "description": "Host mucus glycans degradable as a microbial nutrient source."
          },
          {
            "node_id": "host_surface_adhesins",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Contextual protein family or multiprotein aggregate reviewed for this nonmechanistic classification; no single semantic family captures it.",
            "label": "cell appendages and adhesins",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Flagella, pili, fimbriae, and adhesins including mucus-binding proteins."
          },
          {
            "node_id": "host_surface_attachment",
            "label": "attachment to host surfaces",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Adhesion of microbes to host mucus or epithelial surfaces."
          },
          {
            "node_id": "cyclic_di_gmp_camp",
            "label": "c-di-GMP and cAMP second messengers",
            "node_type": "CHEMICAL",
            "description": "Second messengers regulating the attachment-to-biofilm transition."
          },
          {
            "node_id": "biofilm_formation",
            "label": "biofilm formation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Irreversible attachment with EPS and surface-protein production.",
            "grounding": "GO:0042710"
          },
          {
            "node_id": "root_exudates",
            "label": "plant root exudates",
            "node_type": "CHEMICAL",
            "description": "Host-derived metabolites secreted from plant roots."
          },
          {
            "node_id": "chemotaxis_to_host",
            "label": "chemotaxis toward host",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Directed motility toward host-derived chemical cues."
          },
          {
            "node_id": "mucus_layer_niches",
            "label": "mucus layer niches",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Distinct inner (firm) and outer (loose) mucus colonization niches."
          }
        ],
        "edges": [
          {
            "subject": "host_habitat",
            "predicate": "enables",
            "object": "host_colonization",
            "description": "Host tissues provide the habitat in which the microbe colonizes.",
            "evidence": [
              {
                "reference": "DOI:10.1073/pnas.1218525110",
                "notes": "McFall-Ngai et al. document ubiquitous host-associated microbial communities across animals."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "host_colonization",
            "predicate": "confers",
            "object": "host_associated_trait",
            "description": "Persistent host colonization realizes the host-associated lifestyle.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.1104816",
                "notes": "B\u00e4ckhed et al. characterize host-associated microbiota as dense, coevolved communities."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "mucin_o_glycans",
            "predicate": "serves as nutrient source for",
            "object": "host_colonization",
            "description": "Mucin O-glycans are degraded and utilized as a nutrient source supporting colonization.",
            "evidence": [
              {
                "reference": "DOI:10.1152/ajpgi.00261.2022",
                "notes": "Mucin O-glycans and glycan-derived sugars are degraded and utilized as a nutrient source by host-associated microbes."
              }
            ]
          },
          {
            "subject": "host_surface_adhesins",
            "predicate": "enables",
            "object": "host_surface_attachment",
            "description": "Cell appendages and adhesins mediate attachment to host mucus and epithelia.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuae008",
                "notes": "Cell appendages (flagella, pili, fimbriae) and adhesins mediate attachment to host mucus/epithelia."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "host_surface_attachment",
            "predicate": "enables",
            "object": "host_colonization",
            "description": "Attachment to host surfaces is a prerequisite step for persistent colonization.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuae008",
                "notes": "Attachment to host surfaces underlies the transition to stable colonization."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "cyclic_di_gmp_camp",
            "predicate": "induces",
            "object": "biofilm_formation",
            "description": "c-di-GMP and cAMP trigger EPS and surface-protein production, driving irreversible attachment and biofilm.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuae008",
                "notes": "cAMP and c-di-GMP regulate transition from reversible to irreversible attachment, triggering surface proteins and EPS leading to biofilm formation."
              }
            ]
          },
          {
            "subject": "biofilm_formation",
            "predicate": "enables",
            "object": "host_colonization",
            "description": "Biofilm formation supports persistent microbial occupancy of host surfaces.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuae008",
                "notes": "Biofilm formation following irreversible attachment supports persistent host colonization."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "root_exudates",
            "predicate": "activates",
            "object": "chemotaxis_to_host",
            "description": "Root exudates trigger chemotaxis via MCP/CheA/CheY signaling toward the host.",
            "evidence": [
              {
                "reference": "DOI:10.3390/biology13020095",
                "notes": "Methyl-accepting chemotaxis proteins bind root exudates and trigger signal transduction (CheW/CheA/CheY), driving chemotaxis as the first colonization step."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "chemotaxis_to_host",
            "predicate": "enables",
            "object": "host_colonization",
            "description": "Chemotaxis toward host cues is an initial step enabling colonization.",
            "evidence": [
              {
                "reference": "DOI:10.3390/biology13020095",
                "notes": "Chemotaxis is identified as the first step of host colonization."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "root_exudates",
            "predicate": "provides nutrient source for",
            "object": "host_colonization",
            "description": "Root exudates supply carbon and substrates supporting microbial growth and persistence.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuad066",
                "notes": "Plants secrete 11-40% of photosynthate as exudates that supply carbon and substrates for rhizobacterial growth and persistence."
              }
            ]
          },
          {
            "subject": "mucus_layer_niches",
            "predicate": "enables",
            "object": "host_colonization",
            "description": "Structured inner and outer mucus layers create distinct niches for microbial colonization.",
            "evidence": [
              {
                "reference": "DOI:10.1128/ecosalplus.esp-0006-2023",
                "notes": "Structured inner (firm, sparsely colonized) versus outer (looser, microbe-colonized) mucus creates distinct colonization niches."
              }
            ],
            "predicate_id": "RO:0002327"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-06-02T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate ECOLOGY trait (host-associated); sub-variant of habitat association, parent of gut-associated.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-09T14:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (host-associated microbiome membership) with RO predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 9 evidence-backed generic edges (8 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:09Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 6 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d75, RO:0002213\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:29Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0042710\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 1 causal edge(s) off enables/RO:0002327 with a TRAIT object (1 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-17T02:00:00Z",
        "curator": "claude",
        "action": "NORMALISE_NODE_SENSE",
        "changes": "One node_id per SENSE (issues 356, 384): root_exudates is the chemical sense here. The substance, not the condition: root exudates are a set of compounds, which is what CHEMICAL is for. rhizosphere_association.yaml settles it by modelling both \u2014 root_exudates (CHEMICAL) -causes-> rhizosphere_habitat (ENVIRONMENTAL_FACTOR) \u2014 the same two-ids shape this tranche applies to oxygen.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope host_associated_microbiome=NONMECHANISTIC with scope_notes; marked 1 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (host_surface_adhesins).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1004004",
    "label": "human pathogen",
    "definition": "A pathogen that infects organisms of the species Homo sapiens.",
    "definition_source": "DOI:10.1146/annurev.micro.62.081307.162938",
    "trait_category": "ECOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1004000"
    ],
    "synonyms": [
      {
        "synonym_text": "human_pathogens_all",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1126/science.aaf4507"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev.micro.62.081307.162938",
        "snippet": "virulence factors",
        "notes": "Virulence-factor review supports adaptation of bacterial virulence programs to the human host environment."
      },
      {
        "reference": "DOI:10.1038/nrmicro1592",
        "snippet": "secretion systems",
        "notes": "Secretion-systems review supports effector delivery as a major mechanism by which bacteria establish human infection."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1280",
        "taxon_label": "Staphylococcus aureus",
        "note": "major human pathogen",
        "reference": "PMID:30209034"
      },
      {
        "taxon_id": "NCBITaxon:1773",
        "taxon_label": "Mycobacterium tuberculosis",
        "note": "tuberculosis agent",
        "reference": "PMID:40588584"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "human_pathogen_anthropoid_adaptation",
        "title": "Human-pathogen Homo sapiens host adaptation",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This broad ecological, host-relationship, habitat, or hazard classification spans multiple taxa and mechanisms; contextual protein nodes do not receive token UniProt examples.",
        "description": "DOI-backed graph linking human-adapted virulence factors, body-temperature and tissue tropism, and human-specific immune evasion to the human-pathogen phenotype.",
        "nodes": [
          {
            "node_id": "human_pathogen_trait",
            "label": "human pathogen",
            "node_type": "TRAIT",
            "grounding": "METPO:1004004",
            "description": "Pathogen of Homo sapiens."
          },
          {
            "node_id": "human_virulence_factors",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Contextual protein family or multiprotein aggregate reviewed for this nonmechanistic classification; no single semantic family captures it.",
            "label": "human-adapted virulence factors",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Virulence factors tuned to human-cell receptors and biology."
          },
          {
            "node_id": "human_tropism",
            "label": "human tissue tropism",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Preferential adhesion and growth in human-specific tissues at body-core temperatures."
          },
          {
            "node_id": "human_immune_evasion",
            "label": "human immune evasion",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Strategies evading human innate and adaptive immunity."
          },
          {
            "node_id": "human_disease",
            "label": "human disease",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Pathology produced in a human host."
          },
          {
            "node_id": "type_iv_secretion_system",
            "label": "type IV secretion system",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Multiprotein machine translocating protein effectors and toxins into host cells.",
            "grounding": "GO:0043684"
          },
          {
            "node_id": "host_cell_manipulation",
            "label": "host cell manipulation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Effector-driven subversion of host-cell processes promoting infection."
          },
          {
            "node_id": "horizontal_gene_transfer",
            "label": "horizontal gene transfer",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Acquisition of genes via plasmids, transduction, transposons, and IS elements.",
            "grounding": "GO:0009292"
          },
          {
            "node_id": "virulence_gene_acquisition",
            "label": "acquisition of virulence/host-adaptation genes",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Gain of one or more genes facilitating virulence and host-species tropism."
          },
          {
            "node_id": "within_host_genetic_diversification",
            "label": "within-host genetic diversification",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Hypermutation, structural variation, and MGE/phage insertions generating diversity."
          },
          {
            "node_id": "within_host_adaptation",
            "label": "within-host adaptation and chronic infection",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Adaptation to the host enabling increased pathogenicity and long-term persistence."
          },
          {
            "node_id": "biofilm_formation",
            "label": "biofilm formation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Surface-attached communities increasing treatment resistance and persistence.",
            "grounding": "GO:0042710"
          },
          {
            "node_id": "treatment_resistance_persistence",
            "label": "treatment resistance and persistence",
            "node_type": "TRAIT",
            "description": "Tolerance to antimicrobial treatment and persistent infection."
          }
        ],
        "edges": [
          {
            "subject": "human_virulence_factors",
            "predicate": "enables",
            "object": "human_tropism",
            "description": "Human-adapted virulence factors enable preferential adhesion and growth in human tissues.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev.micro.62.081307.162938",
                "snippet": "virulence factors",
                "notes": "Supports virulence factors as enablers of human tissue tropism."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "human_tropism",
            "predicate": "enables",
            "object": "human_disease",
            "description": "Tissue tropism supports establishment of human disease at specific anatomical sites.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev.micro.62.081307.162938",
                "snippet": "virulence factors",
                "notes": "Supports tissue tropism as a determinant of human-disease pattern."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "human_immune_evasion",
            "predicate": "enables",
            "object": "human_disease",
            "description": "Evasion of human immunity supports sustained infection and disease.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro1592",
                "snippet": "secretion systems",
                "notes": "Supports secretion-system-delivered effectors in human immune evasion."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "human_disease",
            "predicate": "manifests as",
            "object": "human_pathogen_trait",
            "description": "Human disease manifests the human-pathogen trait.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev.micro.62.081307.162938",
                "snippet": "virulence factors",
                "notes": "Supports the trait endpoint."
              }
            ],
            "predicate_id": "METPO:2007400"
          },
          {
            "subject": "type_iv_secretion_system",
            "predicate": "enables",
            "object": "host_cell_manipulation",
            "description": "Type IV secretion systems translocate protein effectors and toxins that manipulate host cells during infection.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41579-023-00974-3",
                "notes": "T4SSs function as protein effector translocators delivering effectors or toxins; viable targets to thwart infection by pathogens."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "host_cell_manipulation",
            "predicate": "enables",
            "object": "human_disease",
            "description": "Effector-driven host cell manipulation supports establishment of human infection and disease.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41579-023-00974-3",
                "notes": "Effector translocation enables host cell manipulation and infection by pathogens."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "horizontal_gene_transfer",
            "predicate": "enables",
            "object": "virulence_gene_acquisition",
            "description": "HGT via plasmids, transduction, transposons, and IS elements enables acquisition of virulence and host-adaptation genes.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuae019",
                "notes": "HGT via conjugation, transduction, transposons, IS elements can be associated with gain of genes facilitating host tropism and virulence factors."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "virulence_gene_acquisition",
            "predicate": "contributes to",
            "object": "human_virulence_factors",
            "description": "Acquired genes contribute the human-adapted virulence factor repertoire underlying human pathogenicity.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuae019",
                "notes": "Gene acquisition facilitates changes in host species tropism, including virulence factors enabling human-pathogenic lineages."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "within_host_genetic_diversification",
            "predicate": "enables",
            "object": "within_host_adaptation",
            "description": "Hypermutation, structural variation, and MGE/phage insertions generate diversity driving within-host adaptation.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-pathmechdis-051122-111408",
                "notes": "Secondary mechanisms including hypermutation, structural variation, and MGE/phage insertions can increase pathogenicity and facilitate long-term persistence."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "within_host_adaptation",
            "predicate": "enables",
            "object": "human_disease",
            "description": "Within-host adaptation increases pathogenicity and supports chronic human infection.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-pathmechdis-051122-111408",
                "notes": "Within-host evolution can increase pathogenicity and facilitate long-term persistence in the host."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "biofilm_formation",
            "predicate": "confers",
            "object": "treatment_resistance_persistence",
            "description": "Biofilm formation makes bacteria resistant to treatment and supports persistence.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2024.1370818",
                "notes": "Bacteria can form biofilms, making them resistant to treatment."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "treatment_resistance_persistence",
            "predicate": "enables",
            "object": "human_disease",
            "description": "Treatment resistance and persistence exacerbate the severity and duration of human infection.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2024.1370818",
                "notes": "Biofilm-associated resistance to treatment contributes to infection severity and persistence."
              }
            ],
            "predicate_id": "RO:0002327"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.949749+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-11T23:15:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed causal graph linking human-adapted virulence factors, tissue tropism, immune evasion, and disease to the human-pathogen trait.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:29Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T21:30:06Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007400\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:18Z",
        "curator": "claude",
        "action": "RENAME_PREDICATE_LABELS",
        "changes": "Renamed 2 causal-edge predicate label(s) to align with existing groundings: supports \u2192 enables \u00d72.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:20Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d72).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-17T04:09:43Z",
        "curator": "claude",
        "action": "REMOVE_REDUNDANT_SYNONYM",
        "changes": "Removed 1 synonym(s) whose text duplicated the label (seeder redundancy; no information lost).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 8 evidence-backed generic edges (8 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:09Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 8 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d78).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:16Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0009292\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:29Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0042710\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:23:52Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0043684\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T08:00:00Z",
        "curator": "claude",
        "action": "REGROUND_CAUSAL_EDGE",
        "changes": "Re-grounded causal edge(s) off enables/RO:0002327 onto contributes to (RO:0002326), issue 334. biolink declares enables range 'biological process or activity', which only BIOLOGICAL_PROCESS, PATHWAY and MOLECULAR_FUNCTION satisfy, so an edge pointing at a GENE_OR_PROTEIN entailed a false type. The replacements are chosen per idiom rather than swept: a gene cluster ENCODES its product, a subunit is PART OF the complex it belongs to, and an energy source or acquired repertoire CONTRIBUTES TO the machine it powers or composes. All three declare no rdfs:domain or rdfs:range, so none can reintroduce the class of defect being removed.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T09:30:00Z",
        "curator": "claude",
        "action": "REGROUND_CAUSAL_EDGE",
        "changes": "Correction to the REGROUND_CAUSAL_EDGE event above, issue 334 review. That event enumerated three idioms and asserted that all three targets declare no rdfs:domain or rdfs:range. Two parts are now known to be wrong, though neither affects this record's own edge. The biolink:encodes half rested on a vacuous check - that term is absent from the pinned biolink model, tracked in issue 342. The \"energy source ... the machine it powers\" half was retracted: those four motive-force edges were reverted to enables and re-deferred, because biolink defines contributes to as contributing to the occurrence or GENERATION of the object, which a motive force does not do to a motor. This record's surviving edge, acquired genes contributing to the virulence factor repertoire, does fit that definition and is unchanged.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-07T18:00:00Z",
        "curator": "claude",
        "action": "REGROUND_CAUSAL_EDGE",
        "changes": "Edge biofilm_formation -> treatment_resistance_persistence in graph human_pathogen_anthropoid_adaptation: re-grounded it from enables/RO:0002327 to confers/METPO:2007700; retyped treatment_resistance_persistence to TRAIT. Issue 334. biolink declares enables range 'biological process or activity', which of CausalNodeTypeEnum only BIOLOGICAL_PROCESS, PATHWAY and MOLECULAR_FUNCTION satisfy, so this edge entailed a false type on its object. 'Tolerance to antimicrobial treatment and persistent infection' is a DISPOSITION -- what the organism would do under treatment -- not a quality it displays. Retyped to TRAIT, which makes this the same shape #302 solved for 164 edges, and `confers` already admits a BIOLOGICAL_PROCESS subject.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-19T00:00:00+00:00",
        "curator": "add_faprotax_synonyms",
        "action": "ADDED_SYNONYM",
        "changes": "Added 'human_pathogens_all' (291 occurrences in microbedecoder's unmapped labels) as a RELATED_SYNONYM (#453). FAPROTAX's human_pathogens_all is the union of its per-disease human pathogen groups, so it denotes the same set as 'a pathogen that infects organisms of the species Homo sapiens'. Written with the source's underscores because that is the string a consumer must resolve.",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope human_pathogen_anthropoid_adaptation=NONMECHANISTIC with scope_notes; marked 1 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (human_virulence_factors).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000698",
    "label": "ixotrophy",
    "definition": "A trophic-ecology phenotype in which filamentous bacteria capture microbial prey on their cell surface and kill the captured cells to obtain prey-derived nutrients.",
    "definition_source": "DOI:10.1126/science.adp0614",
    "trait_category": "ECOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1126/science.adp0614",
        "snippet": "Single-cell analyses with stable isotope-labeled prey revealed that prey components are taken up by the attacker.",
        "notes": "Lien et al. 2024, PMID:39418385, scientific Abstract, not the separate article summary; directly matched source-qualified MED text. Introduction and contact/capture Results support the surface-trapping differentia. Nutrient-uptake Results, culture, killing, imaging and Raman Methods, Discussion and actual Figures 1, 5 and 6 read. Raman labeling supports uptake from killed prey; Figure 6 is a model, not independent flux data. On solid surfaces, gliding can establish contact without flagellar trapping; this record denotes a capability, not a mandatory sequence for every feeding event. Other figures, supplements and movies not fully assessed. Author-hosted published full text: https://stockerlab.ethz.ch/wp-content/uploads/2024/10/183.Lien-et-al_Science_Kang.pdf. MED linked a commentary and preprint, not a correction/retraction; publisher status page was inaccessible, so that check remains limited."
      },
      {
        "reference": "DOI:10.1007/s002489900052",
        "snippet": "can subsist on other microbes and can even catch motile bacteria by their flagella before killing and digesting them.",
        "notes": "Lewin 1997, PMID:9337418, directly retrieved publisher Abstract. The subject is Saprospira grandis; supports prey capture, killing and nutrition, not universal dependence on flagellated prey. MED metadata matched title and DOI but exposed no abstract; do not report an abstract-resolver verification for this quote. Full text, figures and strain provenance were unavailable. Publisher page and qualified MED metadata showed no linked correction/retraction at access, not proof none exists. Source: https://link.springer.com/article/10.1007/s002489900052."
      },
      {
        "reference": "DOI:10.1099/mic.0.000158",
        "snippet": "The ability of cells to aggregate or adhere is thought to be a significant initial step in ixotrophy.",
        "notes": "Furusawa et al. 2015, PMID:26306656, scientific Abstract directly read at the publisher and matched qualified MED metadata. CCB-QB1 adhesion/capture assays support an initial interaction, not by themselves nutrient transfer. Calcium and acidic polysaccharide interpretations are model-specific, not defining requirements. Full-text delivery failed; Methods, figures and supplement remain unread. Publisher page and MED record exposed no linked correction/retraction. Authors and CCB-QB1 material overlap with 2024, so these are not independent-group replications. Source: https://doi.org/10.1099/mic.0.000158."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1313421",
        "taxon_label": "Aureispira sp. CCB-QB1",
        "reference": "DOI:10.1126/science.adp0614",
        "note": "Qualified to the ixotrophy-positive WT studied with Vibrio campbellii, not all culture derivatives or the entire genus. The primary scientific Abstract at https://pubmed.ncbi.nlm.nih.gov/25468060/ (DOI:10.1016/j.margen.2014.10.006) directly identifies CCB-QB1 as an isolate from the coastal area of Penang, Malaysia; this is provenance, not another predation experiment. NCBI identifier/name independently checked on 2026-10-11: https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1313421. The 2024 IS-inactivated predator derivatives are not the exemplar."
      }
    ],
    "discussions": [
      {
        "discussion_id": "ixotrophy-boundaries-and-mappings",
        "prompt": "Keep prey capture and nutrition distinct from attachment alone.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Use phenotype METPO:1000059 as parent. Predatory bacterium traitmech:000054 requires bacterial prey, whereas ixotrophy literature also includes nonbacterial microbial prey. Epibiotic bacterial predation traitmech:000697 denotes attached external growth on bacterial prey and is not an exact synonym or proven broader parent. Heng et al. 2026 (DOI:10.1007/s00248-026-02864-6), publisher Abstract only, calls ixotrophy epibiotic in a broader usage; retain that attribution without equating the scopes. Gliding, aggregation, adhesive surfaces, antagonism and prey lysis alone do not establish ixotrophy. No universal prey range, obligate dependence or organism-level disjointness is asserted. No exact external xrefs or synonyms assigned pending authority and scope reconciliation.",
        "posed_by": "codex",
        "posed_date": "2026-10-11"
      },
      {
        "discussion_id": "ixotrophy-mechanism-grounding",
        "prompt": "Ground taxon-specific machinery before adding causal edges.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "The 2024 CCB-QB1 study provides a mechanism lead, but a protein-resolved graph and protein examples are deferred, not claimed absent. Verify exact accession identities, taxon pairing and all relevant figures/supplements before curating those edges. Do not infer this feeding phenotype from secretion-system genes, profile matches or an insertion sequence alone, or generalize the CCB-QB1 machinery to every ixotrophic lineage. Environmental sequence covariation is not direct field predation.",
        "posed_by": "codex",
        "posed_date": "2026-10-11"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-11T12:55:05Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added ixotrophy beneath phenotype with three DOI-backed sources, short checked snippets and a WT-qualified CCB-QB1 example. Ignored/hidden main/worktree and pending-PR checks support 000698 and v574 block 1065100-1065199. Existing records unchanged; mechanism grounding and exact mappings remain open. Timestamp records the observed UTC curation decision.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000716",
    "label": "kin discrimination",
    "definition": "An ecological phenotype in which microbial cells preferentially associate with kin or exclude nonkin through differential interactions according to genetic similarity or relatedness.",
    "definition_source": "DOI:10.1128/mBio.00723-17",
    "trait_category": "ECOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1371/journal.pbio.0060287",
        "snippet": "Our findings demonstrate that D. discoideum cells co-aggregate more with genetically similar than dissimilar individuals",
        "notes": "Ostrowski et al. 2008, PMID:19067487; scientific abstract, publisher PDF page 1, contiguous span visually checked. Mixtures with AX4-GFP and natural-isolate dye controls support partial sorting during aggregation, not complete clonal exclusion. The measured endpoint is variation in fluorescent spore proportions among fruiting bodies; genetic distance uses 12 microsatellite loci, not genome-wide identity. Main text and all four figures were inspected; Figure 1 is hypothetical. Supplementary Tables S1 and S2 were read by text extraction. Main Methods names QS45, absent from the retrieved S1 strain table; no strain alias is inferred. Kin-selected benefit is an interpretation, not a measured fitness endpoint here. Natural provenance of every laboratory derivative and a molecular recognition mechanism remain unresolved. Native abstract verifier: VERIFIED."
      },
      {
        "reference": "DOI:10.1073/pnas.1512671112",
        "snippet": "Some swarms did merge, and most interestingly, this behavior was only seen in the most highly related strain pairs.",
        "notes": "Stefanic et al. 2015, PMID:26438858, PMC4653157; directly retrieved scientific abstract from Europe PMC with the namespace-qualified query EXT_ID:26438858 AND SRC:MED. Title, PMID and DOI were checked together. The authors define a conspecific scope and report relatedness-associated swarm merging versus boundary formation among sympatric Bacillus subtilis isolates. The separately reported root-colonization outcome is not a direct killing measurement. Full text, figures and supplements were inaccessible and are not claimed as inspected; indexed search passages were not used as excerpts or quantitative evidence. Native abstract verifier: VERIFIED. Linked PMID:26512099 is commentary, not a correction or experimental replication."
      },
      {
        "reference": "DOI:10.1128/mBio.00723-17",
        "snippet": "The effects of kin discrimination extend to nearby species, as the other subtilis clade species were treated with the same antagonism as nonkin.",
        "notes": "Lyons and Kolter 2017, PMID:28679746, PMC5573675; scientific abstract, NLM version 1 PDF page 1 and JATS article-meta abstract without abstract-type. This is not the separate IMPORTANCE summary. Introduction distinguishes preferential kin association from nonkin exclusion and supports the definition's two modes; the paper's own experiments support the nearby-species extension. The comparison concerns interactions with B. subtilis NCIB3610: nearby species can be antagonized, while more distant lineages show varied outcomes. This is not a universal monotonic relation between distance and antagonism. Relatedness uses type-strain 16S, not whole-genome identity of every isolate. Swarm, biofilm and halo assays differ in medium and endpoint. Figure 2A and 2C assign WNC032 to different species; Data Set S1 identifies it as B. megaterium. No silent panel correction or taxon anchor is inferred. Actual Figures 2 and 4 and selected spreadsheet rows/totals were inspected, not all figures or raw assays. Native abstract verifier: VERIFIED. Shares an investigator with 2015; not an independent-laboratory replication."
      }
    ],
    "discussions": [
      {
        "discussion_id": "kin-discrimination-scope-and-hierarchy",
        "prompt": "Preserve relational phenotype scope without equating all recognition or cooperation.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Stefanic 2015 defines conspecific discrimination, whereas Lyons 2017 explicitly extends exclusion to nearby species. The record retains that attributed extension without a universal kin threshold, obligate killing, cognition or monotonic distance-response rule. Kin recognition, allorecognition and self/nonself discrimination are not asserted as exact synonyms. An interaction phenotype is required; a recognition locus, allele match, isolated pairing or spatial assortment alone is insufficient. Recognition-allele specificity, measured relatedness proxies and genome-wide relatedness must not be conflated. METPO:1000059 phenotype is the conservative parent. Mutualism (traitmech:000041) requires reciprocal benefit; biofilm formation (traitmech:000053) is neither necessary nor sufficient. Contact-dependent outer membrane exchange (traitmech:000650) is material transfer, and its existing negative kin-discrimination evidence remains a boundary, not a parent gap. Heterokaryon incompatibility (traitmech:000606) concerns postfusion restriction and is not automatically equivalent or reparented. Predation requires trophic benefit; DNA self/nonself defense has a different target and endpoint. No organism-level disjointness is implied.",
        "posed_by": "codex",
        "posed_date": "2026-10-13"
      },
      {
        "discussion_id": "kin-discrimination-evidence-and-mechanism-limits",
        "prompt": "Resolve strain, assay and source gaps before assigning canonical taxa or molecular mechanisms.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "The QS45 strain-table gap and WNC032 figure-label conflict remain unresolved. The 2015 scientific abstract was read directly, but full text was not. The 2017 scientific abstract and IMPORTANCE summary were distinguished; the corrected excerpt is from the scientific abstract, not IMPORTANCE. Selected supplemental spreadsheet checks are not raw-image reanalysis or a statistical replication; supplementary EPS figures remain unread. Bounded MED, PLOS and NLM metadata checks are not exhaustive clearance of corrections or retractions; some publisher routes were inaccessible. No canonical taxa, exact external mappings, protein examples or causal graph are asserted. Allele-specific adhesion in engineered systems requires separate provenance and mechanism review, not inference of natural species-wide possession. Source URLs, hashes, access limits and native snippet outcomes are retained in the source-verification sidecar.",
        "posed_by": "codex",
        "posed_date": "2026-10-13"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-13T09:09:53Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added kin discrimination with three DOI-backed contiguous snippets and bounded assay, source and hierarchy discussions. Reserved 000716, v592 and 1066900-1066999 after ignored/hidden current-file, retained-history, independent-copy and open/draft PR checks; numeric false positives were adjudicated. No exact active METPO counterpart identified in inspected sources. No taxa or causal graph inferred; prior records unchanged. Timestamp is observed post-audit acceptance, not an estimated write time.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-13T09:17:32Z",
        "curator": "codex",
        "action": "EVIDENCE_CORRECTED",
        "changes": "Addressed adversarial findings #1909 and #1910: replaced two source-matching but insufficiently self-contained excerpts with explicit swarm-merging and antagonism results. Changed sole definition authority to Lyons 2017 for the attributed nearby-species extension, preserving the explicit Stefanic 2015 evidence DOI. Updated section and native-verifier notes. Original event, phenotype definition, identifiers, parent, PROPOSED status and remaining source limits are preserved. Timestamp is observed correction decision time, not an estimated write time.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000041",
    "label": "mutualism",
    "definition": "A symbiosis in which both the microorganism and its host or partner benefit from the association, often through exchange of nutrients or services.",
    "definition_source": "DOI:10.1073/pnas.1218525110",
    "trait_category": "ECOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "traitmech:000040"
    ],
    "synonyms": [
      {
        "synonym_text": "mutualist",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1073/pnas.1218525110"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1073/pnas.1218525110",
        "notes": "McFall-Ngai et al. document widespread mutually beneficial host-microbe associations across animals."
      },
      {
        "reference": "DOI:10.1126/science.1104816",
        "notes": "B\u00e4ckhed et al., \"Host-bacterial mutualism in the human intestine\", supports reciprocal benefit (nutrient harvest for the host, habitat for the microbes) as the defining feature of mutualism."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:382",
        "taxon_label": "Sinorhizobium meliloti",
        "note": "legume N2-fixing mutualist",
        "reference": "PMID:22876202"
      },
      {
        "taxon_id": "NCBITaxon:668",
        "taxon_label": "Aliivibrio fischeri",
        "note": "squid light-organ mutualist",
        "reference": "PMID:10941780"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "mutualism_reciprocal_benefit",
        "title": "Mutualism delivers reciprocal benefit to host and microbe",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This broad ecological, host-relationship, habitat, or hazard classification spans multiple taxa and mechanisms; contextual protein nodes do not receive token UniProt examples.",
        "description": "Evidence-backed causal sketch linking nutrient/service exchange to reciprocal-benefit symbiosis.",
        "nodes": [
          {
            "node_id": "mutualism_trait",
            "label": "mutualism",
            "node_type": "TRAIT",
            "grounding": "traitmech:000041",
            "description": "Symbiosis with positive fitness effects for both partners."
          },
          {
            "node_id": "nutrient_exchange",
            "label": "nutrient and service exchange",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Bidirectional transfer of metabolites or functions between host and microbe."
          },
          {
            "node_id": "reciprocal_benefit",
            "label": "reciprocal fitness benefit",
            "node_type": "QUALITY",
            "description": "Positive net fitness change for both host and microbe."
          },
          {
            "node_id": "host_control_mechanisms",
            "label": "host control mechanisms",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Host-imposed controls (immunity, barrier function, homeostasis, transit) that shape symbionts."
          },
          {
            "node_id": "host_beneficial_microbial_traits",
            "label": "microbial traits beneficial to host",
            "node_type": "QUALITY",
            "description": "Microbial traits selected because they benefit the host."
          },
          {
            "node_id": "cross_feeding_architecture",
            "label": "co-auxotrophy / cross-feeding architecture",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reciprocal metabolite dependence where each member supplies a nutrient another cannot make."
          },
          {
            "node_id": "obligate_mutualism_syntrophy",
            "label": "obligate mutualism (syntrophy)",
            "node_type": "STATE",
            "description": "Mutualism in which partners are metabolically dependent on one another."
          },
          {
            "node_id": "micronutrient_exchange",
            "label": "vitamin/N-source/micronutrient exchange",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Provision of metabolites such as N-sources, vitamins, and micronutrients between partners."
          },
          {
            "node_id": "metabolite_secretion_profile",
            "label": "metabolite secretion profile",
            "node_type": "CHEMICAL",
            "description": "The set of metabolites secreted by an interacting partner."
          },
          {
            "node_id": "interaction_outcome_state",
            "label": "mutualism vs antagonism outcome",
            "node_type": "STATE",
            "description": "Context-dependent interaction state ranging from mutualistic to antagonistic."
          }
        ],
        "edges": [
          {
            "subject": "nutrient_exchange",
            "predicate": "causes",
            "object": "reciprocal_benefit",
            "description": "Exchange of nutrients or services yields positive fitness for both partners.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.1104816",
                "notes": "B\u00e4ckhed et al. document reciprocal nutrient-harvest benefits in the gut-microbiota mutualism."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "reciprocal_benefit",
            "predicate": "confers",
            "object": "mutualism_trait",
            "description": "Sustained mutual benefit realizes the mutualistic lifestyle.",
            "evidence": [
              {
                "reference": "DOI:10.1073/pnas.1218525110",
                "notes": "McFall-Ngai et al. document mutually beneficial host-microbe associations across animals."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "host_control_mechanisms",
            "predicate": "selects for",
            "object": "host_beneficial_microbial_traits",
            "description": "Host control mechanisms generate selection for microbial traits that benefit the host.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.adi3338",
                "notes": "Wilde et al. 2024: host controls (immunity, barrier, homeostasis, transit) generate natural selection for microbial traits that benefit the host."
              }
            ],
            "predicate_id": "METPO:2007401"
          },
          {
            "subject": "host_beneficial_microbial_traits",
            "predicate": "confers",
            "object": "mutualism_trait",
            "description": "Selection for host-beneficial microbial traits sustains the mutualistic relationship.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.adi3338",
                "notes": "Host control selecting for host-beneficial microbial traits underpins stable host-microbe mutualism."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "cross_feeding_architecture",
            "predicate": "creates",
            "object": "obligate_mutualism_syntrophy",
            "description": "Reciprocal metabolite dependence (co-auxotrophy) generates obligate mutualism / syntrophy.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-023-01596-4",
                "notes": "Peng et al. 2024: in co-auxotrophic consortia each member depends on others supplying a nutrient it cannot synthesize, defining syntrophy/obligate mutualism."
              }
            ],
            "predicate_id": "biolink:produces"
          },
          {
            "subject": "micronutrient_exchange",
            "predicate": "confers",
            "object": "mutualism_trait",
            "description": "Exchange of N-sources, vitamins, and micronutrients supports mutualistic associations.",
            "evidence": [
              {
                "reference": "DOI:10.3390/plants13060829",
                "notes": "Burgunter-Delamare et al. 2024: mutualistic benefits are framed as provision of metabolites (N-sources, vitamins, micronutrients)."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "metabolite_secretion_profile",
            "predicate": "determines",
            "object": "interaction_outcome_state",
            "description": "The secreted metabolite profile shifts the interaction between mutualism and antagonism.",
            "evidence": [
              {
                "reference": "DOI:10.3390/plants13060829",
                "notes": "Burgunter-Delamare et al. 2024: the same partner pair can be mutualistic or antagonistic depending on the metabolites secreted."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-06-02T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate ECOLOGY trait (mutualism); sub-variant of symbiosis.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-09T14:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (mutualism / reciprocal benefit) with RO/biolink predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 5 evidence-backed generic edges (7 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:09Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 4 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d72, METPO:2007401\u00d71, biolink:produces\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 3 causal edge(s) off enables/RO:0002327 with a TRAIT object (3 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope mutualism_reciprocal_benefit=NONMECHANISTIC with scope_notes.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000044",
    "label": "nitrogen-fixing symbiosis",
    "definition": "A mutualistic symbiosis in which a diazotrophic bacterium fixes atmospheric N2 for a host plant \u2014 classically rhizobia in legume root nodules \u2014 in exchange for photosynthate.",
    "definition_source": "DOI:10.1038/nrmicro.2017.171",
    "trait_category": "ECOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "traitmech:000041"
    ],
    "synonyms": [
      {
        "synonym_text": "nitrogen-fixing symbiont",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1038/nrmicro.2017.171"
      },
      {
        "synonym_text": "root-nodule symbiosis",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1038/nrmicro2990"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/nrmicro.2017.171",
        "notes": "Poole et al. describe the free-living-to-endosymbiont transition of rhizobia that forms N2-fixing legume root nodules."
      },
      {
        "reference": "DOI:10.1038/nrmicro2990",
        "notes": "Oldroyd, \"Speak, friend, and enter\", supports the symbiotic signalling that establishes beneficial nitrogen-fixing plant-microbe associations."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:382",
        "taxon_label": "Sinorhizobium meliloti",
        "note": "Model rhizobium-legume symbiont (alfalfa / Medicago); strain 1021 (NCBITaxon:266834) is the most-studied reference.",
        "reference": "https://pmc.ncbi.nlm.nih.gov/articles/PMC3164228/"
      },
      {
        "taxon_id": "NCBITaxon:266834",
        "taxon_label": "Sinorhizobium meliloti 1021",
        "note": "Strain-level nitrogen-fixing symbiosis exemplar matched to the NifH protein instance represented below.",
        "reference": "DOI:10.1094/MPMI-06-25-0074-R"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "rhizobia_legume_n2_fixation",
        "title": "Rhizobia\u2013legume root-nodule N2-fixing mutualism",
        "description": "Evidence-backed causal sketch linking symbiotic signalling and root-nodule colonization to N2 fixation in exchange for plant photosynthate.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "The S. meliloti 1021 NifH example anchors the bacterial nitrogenase branch in a root-nodule symbiosis. It represents one component of the nitrogenase complex, not the complete complex or the host leghemoglobin branch.",
        "nodes": [
          {
            "node_id": "n2_fix_symbiosis_trait",
            "label": "nitrogen-fixing symbiosis",
            "node_type": "TRAIT",
            "grounding": "traitmech:000044",
            "description": "Mutualistic N2 fixation in plant-microbe associations."
          },
          {
            "node_id": "symbiotic_signalling",
            "label": "nodulation signalling",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Nod-factor signalling establishing the rhizobium-legume partnership."
          },
          {
            "node_id": "nitrogen_fixation",
            "label": "nitrogen fixation",
            "node_type": "BIOLOGICAL_PROCESS",
            "grounding": "GO:0009399",
            "description": "Reduction of atmospheric N2 to ammonia by nitrogenase."
          },
          {
            "node_id": "flavonoids",
            "label": "flavonoids",
            "node_type": "CHEMICAL",
            "description": "Host-root exudate signalling compounds secreted by legumes."
          },
          {
            "node_id": "nod_factor",
            "label": "Nod factor (lipochitooligosaccharide)",
            "node_type": "CHEMICAL",
            "description": "Rhizobial lipochitooligosaccharide signal triggering symbiosis."
          },
          {
            "node_id": "leghemoglobin",
            "label": "leghemoglobin",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Nodule oxygen-binding protein buffering O2 around bacteroids.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "This is a host-plant protein family used as context in the mixed host-microbe graph; it is not the bacterial protein exemplar."
          },
          {
            "node_id": "nodule_oxygen_diffusion_barrier",
            "label": "nodule oxygen diffusion barrier",
            "node_type": "CELLULAR_LOCALIZATION",
            "description": "Tightly packed cortical cell layer limiting O2 flux into the nodule interior."
          },
          {
            "node_id": "microaerobic_environment",
            "label": "microaerobic environment",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Low-oxygen condition inside the nodule required for nitrogenase."
          },
          {
            "node_id": "nitrogenase_complex",
            "label": "nitrogenase complex",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Bacterial enzyme complex catalyzing reduction of N2 to NH3.",
            "grounding": "GO:0016610",
            "gene_symbols": [
              "nifH",
              "nifD",
              "nifK"
            ],
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:P00460",
                "protein_label": "Nitrogenase iron protein NifH",
                "gene_symbol": "nifH",
                "taxon_id": "NCBITaxon:266834",
                "taxon_label": "Sinorhizobium meliloti 1021",
                "entry_status": "REVIEWED",
                "retrieved_on": "2026-10-22",
                "entry_version": 159,
                "sequence_version": 2,
                "role": "NifH is the ATP-coupled electron-delivery component of the S. meliloti nitrogenase complex required for nitrogen fixation in nodules.",
                "evidence": [
                  {
                    "reference": "DOI:10.1094/MPMI-06-25-0074-R",
                    "snippet": "nifH1491::Tn5",
                    "notes": "The strain 1021 nifH mutant provides direct non-fixing symbiosis evidence; UniProtKB P00460 is the reviewed strain-matched NifH entry."
                  }
                ]
              }
            ]
          },
          {
            "node_id": "organic_acids",
            "label": "organic acids",
            "node_type": "CHEMICAL",
            "description": "Reductant/carbon source the plant transfers to intracellular bacteroids.",
            "grounding": "CHEBI:64709"
          },
          {
            "node_id": "iron_availability",
            "label": "iron availability",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Availability of iron, a cofactor for nitrogenase and leghemoglobin."
          }
        ],
        "edges": [
          {
            "subject": "symbiotic_signalling",
            "predicate": "confers",
            "object": "n2_fix_symbiosis_trait",
            "description": "Nod-factor signalling between rhizobia and legume hosts establishes the symbiosis.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2990",
                "notes": "Oldroyd reviews symbiotic signalling establishing nitrogen-fixing plant-microbe associations."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "n2_fix_symbiosis_trait",
            "predicate": "enables",
            "object": "nitrogen_fixation",
            "description": "The symbiosis houses bacteroids that fix N2 inside root nodules.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro.2017.171",
                "notes": "Poole et al. describe the free-living-to-endosymbiont transition of rhizobia forming N2-fixing legume root nodules."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "flavonoids",
            "predicate": "induces production of",
            "object": "nod_factor",
            "description": "Legume flavonoid exudates induce rhizobia to produce Nod factors.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fpls.2023.1284720",
                "notes": "Legumes secrete flavonoids that induce rhizobia to produce Nod factors."
              }
            ]
          },
          {
            "subject": "nod_factor",
            "predicate": "enables",
            "object": "symbiotic_signalling",
            "description": "Perceived Nod factors initiate the nodulation signalling cascade.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fpls.2023.1284720",
                "notes": "Nod factors are perceived by Nod-factor receptors, triggering symbiotic signalling."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "leghemoglobin",
            "predicate": "buffers",
            "object": "microaerobic_environment",
            "description": "Leghemoglobin buffers oxygen concentration within nodules.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fpls.2023.1284720",
                "notes": "Leghemoglobins buffer the oxygen concentration within the nodules."
              }
            ]
          },
          {
            "subject": "nodule_oxygen_diffusion_barrier",
            "predicate": "maintains",
            "object": "microaerobic_environment",
            "description": "A tightly packed cortical diffusion barrier limits oxygen flux into the nodule interior.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-024-01762-2",
                "notes": "A diffusion barrier of tightly packed cells limits oxygen flux; the multilayered cortex functions as an adaptable oxygen diffusion barrier."
              }
            ]
          },
          {
            "subject": "microaerobic_environment",
            "predicate": "enables",
            "object": "nitrogen_fixation",
            "description": "A low-oxygen environment is required for proper nitrogenase activity.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fpls.2023.1284720",
                "notes": "Symbiotic nitrogen fixation requires a low-oxygen environment for proper activity of nitrogenase."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "nitrogenase_complex",
            "predicate": "enables",
            "object": "nitrogen_fixation",
            "description": "The nitrogenase complex reduces N2 to NH3 (16 ATP per N2).",
            "evidence": [
              {
                "reference": "DOI:10.1017/S1062798724000309",
                "notes": "The nitrogenase reaction consumes 16 ATP in the reduction of N2 to NH3."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "organic_acids",
            "predicate": "enables",
            "object": "nitrogen_fixation",
            "description": "The plant supplies organic acids as reductant to intracellular bacteroids fueling fixation.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-024-01762-2",
                "notes": "The plant transfers reductant, typically organic acids, from plant cells to intracellular rhizobia."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "iron_availability",
            "predicate": "is required for",
            "object": "nitrogenase_complex",
            "description": "Iron is an essential cofactor for nitrogenase assembly and leghemoglobin function.",
            "evidence": [
              {
                "reference": "DOI:10.1093/pcp/pcae128",
                "notes": "Fe is essential as a cofactor for leghemoglobin and for assembling the nitrogenase complex."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-06-02T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate ECOLOGY trait (nitrogen-fixing symbiosis); sub-variant of mutualism.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-09T14:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (rhizobia-legume N2 fixation) with GO node grounding and RO predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 8 evidence-backed generic edges (8 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:09Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 4 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d74).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:29Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:64709\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:23:52Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0016610\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 1 causal edge(s) off enables/RO:0002327 with a TRAIT object (1 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "CURATE_PROTEIN_TAXON_EXAMPLE",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope rhizobia_legume_n2_fixation=MECHANISTIC with scope_notes; marked 1 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (leghemoglobin); added taxon-paired protein example(s) UniProtKB:P00460 on nitrogenase_complex (NCBITaxon:266834); added canonical example(s) NCBITaxon:266834.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-22T01:35:00Z",
        "curator": "claude",
        "action": "REFRESH_UNIPROT_ENTRY_VERSION",
        "changes": "Refreshed UniProtKB entry_version against live UniProt REST on 2026-10-22: UniProtKB:P00460 (158 -> 159 on nitrogenase_complex).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000717",
    "label": "nutritional fungal mycoparasitism",
    "definition": "An ecological phenotype in which a fungus obtains nutrients at the expense of another fungus, either from the living host or after killing it.",
    "definition_source": "DOI:10.1139/b95-389",
    "trait_category": "ECOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1139/b95-389",
        "snippet": "The term mycoparasitism applies strictly to those relationships in which one living fungus acts as a nutrient source for another",
        "notes": "Jeffries 1995 review; scientific abstract directly retrieved from https://kar.kent.ac.uk/19621/. This strict sense contrasts with broader fungicolous usage in the same abstract. Selected main text and actual PDF pages 1 and 3 support detrimental nutrition with either a living host or killing before use. The record restricts actor and host to fungi, excluding historically grouped oomycetes. The review supplies terminology, not an independent experiment. Not every figure or table was inspected. Native abstract verifier: UNRESOLVED; the direct institutional excerpt was separately matched, not relabeled VERIFIED."
      },
      {
        "reference": "DOI:10.1002/rcm.6131",
        "snippet": "In dual-culture the mycelia of T. atroviride which remained in direct contact with labeled A. mellea showed an increased \u03b4(13)C value",
        "notes": "Pellegrini et al. 2012, PMID:22302490; directly retrieved scientific abstract, Results, using DOI and SRC:MED together. Title, DOI and PMID agree. After 29 days in contact, the reported carbon isotope value was 66.4 per mille versus -26.6 per mille with unlabeled host. This supports host-derived carbon assimilation, not by itself host killing, a penetration mechanism or exclusion of all alternative transfer routes. The journal full text was not retrieved; the restricted institutional deposit was not bypassed. The bacterial comparator is not an example of this fungal-actor trait. Native abstract verifier: VERIFIED."
      },
      {
        "reference": "DOI:10.1016/j.apsoil.2012.12.005",
        "snippet": "Only T. harzianum maintained mycoparasitic activity in the soil microcosm",
        "notes": "Pellegrini et al. 2013; scientific abstract directly read at https://iris.unipv.it/handle/11571/604013?mode=complete. Native verifier: VERIFIED via AGR:IND500606635, not PubMed. The author-deposited Corneo thesis chapter identifies this DOI; its version is not presumed identical to the unread journal full text. Its experiment selects three microorganisms: the positive soil result concerns a sterile microcosm at 20 C after 29 days, followed by three-day culture-out before isotope measurement, not direct field flux or all 158 isolates. Dual-culture enrichment accompanies growth inhibition; the host viability endpoint comes from a separate broth assay. Washing and host-specific PCR address contamination without excluding every route of carbon transfer. Leakage versus direct parasitism remains partly interpretive. Shares all six authors with 2012, not independent-laboratory replication."
      }
    ],
    "discussions": [
      {
        "discussion_id": "nutritional-fungal-mycoparasitism-scope-and-hierarchy",
        "prompt": "Resolve the broader hierarchy without importing persistent association or broad fungicolous usage.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Nutrition at host expense is required; mere co-occurrence, fungicolous association, antagonism or utilization of already dead material does not establish it. Killing, penetration, obligacy and a single mechanism are not universal requirements. The unqualified mycoparasitism label is not an exact synonym. Local parasitism (traitmech:000043) inherits persistent physical association from symbiosis (traitmech:000040); that narrower local umbrella is not automatically applicable to destructive encounters included by Jeffries. METPO:1000059 phenotype is retained pending hierarchy review. Bacterial mycophagy (traitmech:000696) has a bacterial actor; microbial haustorium formation (traitmech:000663) is a structural phenotype, neither necessary nor sufficient for this nutrition. Saprotrophy (traitmech:000055) alone does not establish attack on a living host; no organism-level disjointness is implied. Pinned and current METPO broad lexical matches (0000261, 000262, 1000125, 1000197, 1000198, 1000227) are deprecated, with no replacement or consider annotation observed. Their OMO:0001000 reason does not disprove the biology or license identifier reuse. None is an exact active counterpart; historical IDs are not xrefs.",
        "posed_by": "codex",
        "posed_date": "2026-10-13"
      },
      {
        "discussion_id": "nutritional-fungal-mycoparasitism-source-and-mechanism-limits",
        "prompt": "Resolve source discrepancies and isolate provenance before assigning canonical taxa or a causal mechanism.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "The 2013 abstract reports inhibition of 80 +/- 0.19%; thesis Results gives 88 +/- 0.24% and Table 1 gives 80 +/- 0.29%. Fluorogenic-assay sampling days differ between Methods and Figure 2; soil-control isotope values differ between Results and Table 3. A no-difference statement is paired with P < 0.05, and abstract versus Results pathogen exclusions differ. These are unresolved, not silently harmonized. Selected thesis Methods, Results, Discussion and actual pages 69, 73, 75, 86 and 89 were inspected, not all figures, tables or raw data. Ground inoculum may include nonviable material; no killed-host control was inspected, which is not proof none exists. Table accessions identify BLAST reference strains, not experimental isolate deposits. No canonical taxa, exact external mappings, protein examples or causal graph are asserted. The measured enzyme activity is not a molecular effector identification. Metadata and notice checks were bounded; some publisher endpoints failed. Source URLs, hashes, version distinctions and native verification results are retained in the sidecar.",
        "posed_by": "codex",
        "posed_date": "2026-10-13"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-13T11:20:51Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added nutritional fungal mycoparasitism with three DOI-backed contiguous excerpts and bounded scope, hierarchy and source discussions. Reserved 000717, v593 and 1067000-1067099 after ignored/hidden current-file, retained-history, independent-copy and open/draft PR checks; numeric false positives adjudicated. No exact active METPO counterpart identified in inspected sources. No canonical taxa or causal graph inferred; previous records unchanged. Timestamp is observed post-audit acceptance, not an estimated write time.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000046",
    "label": "opportunistic pathogen",
    "definition": "A host-association lifestyle in which a normally commensal or environmental microorganism causes disease only when host defenses are compromised or it reaches a normally sterile site.",
    "definition_source": "DOI:10.1016/j.tim.2012.04.005",
    "trait_category": "ECOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1004000"
    ],
    "synonyms": [
      {
        "synonym_text": "opportunistic infection",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1016/j.tim.2012.04.005"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1016/j.tim.2012.04.005",
        "notes": "Brown, Cornforth & Mideo, \"Evolution of virulence in opportunistic pathogens\", support context-dependent virulence maintained by advantages outside the host."
      },
      {
        "reference": "DOI:10.1038/s41579-021-00550-7",
        "notes": "Drew et al. support facultative shifts toward parasitism/pathogenicity along the parasite-mutualist continuum, the basis of opportunistic disease."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:470",
        "taxon_label": "Acinetobacter baumannii",
        "note": "Archetypal opportunistic nosocomial pathogen (multidrug-resistant; infects immunocompromised hosts).",
        "reference": "PMID:22546906"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "opportunistic_pathogen_context_dependent_virulence",
        "title": "Opportunistic pathogenesis under compromised host defense",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This broad ecological, host-relationship, habitat, or hazard classification spans multiple taxa and mechanisms; contextual protein nodes do not receive token UniProt examples.",
        "description": "Evidence-backed causal sketch linking compromised host defenses to context-dependent virulence in normally commensal/environmental microbes.",
        "nodes": [
          {
            "node_id": "opportunistic_pathogen_trait",
            "label": "opportunistic pathogen",
            "node_type": "TRAIT",
            "grounding": "traitmech:000046",
            "description": "Disease causation only under compromised host defenses or sterile-site translocation."
          },
          {
            "node_id": "compromised_host_defense",
            "label": "compromised host defense",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Immunosuppression, barrier breach, or sterile-site translocation."
          },
          {
            "node_id": "opportunistic_infection",
            "label": "opportunistic infection",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Disease arising from a normally commensal or environmental microbe in a permissive host context."
          },
          {
            "node_id": "barrier_breach",
            "label": "epithelial barrier breach / sterile site access",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Disruption of epithelial barriers exposing normally sterile tissue to microbes."
          },
          {
            "node_id": "antibiotic_exposure",
            "label": "antibiotic exposure",
            "node_type": "CHEMICAL",
            "description": "Prior or concurrent antimicrobial treatment."
          },
          {
            "node_id": "microbiota_dysbiosis",
            "label": "microbiota dysbiosis",
            "node_type": "STATE",
            "description": "Disrupted microbial community composition permitting opportunist expansion."
          },
          {
            "node_id": "opportunist_colonization",
            "label": "opportunist colonization / overgrowth",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Increased colonization or overgrowth by opportunistic microbes."
          },
          {
            "node_id": "host_colonization",
            "label": "host colonization without disease",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Microbial colonization of a host site that may or may not progress to infection."
          },
          {
            "node_id": "nutritional_immunity",
            "label": "nutritional immunity / iron limitation",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Host-imposed restriction of nutrient metals such as iron."
          },
          {
            "node_id": "high_affinity_iron_acquisition",
            "label": "high-affinity iron acquisition",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Induction of high-affinity iron transport and siderophore production under iron limitation."
          }
        ],
        "edges": [
          {
            "subject": "compromised_host_defense",
            "predicate": "causes",
            "object": "opportunistic_infection",
            "description": "Breached or weakened host defenses enable a normally innocuous microbe to cause disease.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.tim.2012.04.005",
                "notes": "Brown et al. support context-dependent virulence in opportunistic pathogens."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "opportunistic_infection",
            "predicate": "confers",
            "object": "opportunistic_pathogen_trait",
            "description": "Context-dependent infection realizes the opportunistic-pathogen lifestyle.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41579-021-00550-7",
                "notes": "Drew et al. support facultative shifts toward pathogenicity along the parasite-mutualist continuum."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "barrier_breach",
            "predicate": "enables",
            "object": "opportunistic_infection",
            "description": "Barrier breach exposes sterile tissue, enabling infection by normally innocuous microbes.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41579-024-01035-z",
                "notes": "Uberoi et al.: barrier breach exposes sterile tissue to microbes (generalizable ecological/clinical edge)."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "antibiotic_exposure",
            "predicate": "promotes",
            "object": "microbiota_dysbiosis",
            "description": "Antimicrobial exposure disrupts the resident microbiota, producing dysbiosis.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s40588-023-00190-w",
                "notes": "Jacobsen: antibiotic exposure is a common risk factor driving overgrowth of opportunists; curated as exposure to dysbiosis."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "microbiota_dysbiosis",
            "predicate": "increases",
            "object": "opportunist_colonization",
            "description": "Dysbiosis increases colonization/overgrowth by opportunistic microbes.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s40588-023-00190-w",
                "notes": "Jacobsen: defects/dysbiosis permit expansion of normally controlled opportunists (high-level ecological edge)."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "opportunist_colonization",
            "predicate": "enables",
            "object": "opportunistic_infection",
            "description": "Expanded opportunist colonization provides the population reservoir from which infection can arise.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s40588-023-00190-w",
                "notes": "Jacobsen: colonization is a risk factor preceding opportunistic disease."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "host_colonization",
            "predicate": "progresses to under host susceptibility",
            "object": "opportunistic_infection",
            "description": "Most colonization is benign; only some progresses to infection under permissive host conditions, capturing context-dependence.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41579-024-01035-z",
                "notes": "Uberoi: nearly all wounds are colonized but only some progress to infection; opportunism is context-dependent, not equivalent to colonization."
              }
            ]
          },
          {
            "subject": "nutritional_immunity",
            "predicate": "promotes",
            "object": "high_affinity_iron_acquisition",
            "description": "Host iron limitation induces high-affinity iron transport and siderophore production, a general opportunist adaptation in-host.",
            "evidence": [
              {
                "reference": "DOI:10.1111/1751-7915.14241",
                "notes": "Sanchez-Jimenez: under iron limitation, high-affinity iron transport systems are promoted (general iron-acquisition biology)."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "high_affinity_iron_acquisition",
            "predicate": "contributes to",
            "object": "opportunistic_infection",
            "description": "Iron acquisition under host-imposed restriction supports opportunist fitness during infection.",
            "evidence": [
              {
                "reference": "DOI:10.1111/1751-7915.14241",
                "notes": "Sanchez-Jimenez: iron homeostasis is an exploitable in-host fitness/virulence determinant of opportunists."
              }
            ],
            "predicate_id": "RO:0002326"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-06-02T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate ECOLOGY trait (opportunistic pathogen); sub-variant of the existing pathogenic_to_host class (METPO:1004000).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-09T14:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (opportunistic / context-dependent virulence) with RO/biolink predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 7 evidence-backed generic edges (7 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:09Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 6 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002213\u00d73, RO:0002327\u00d72, RO:0002326\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 1 causal edge(s) off enables/RO:0002327 with a TRAIT object (1 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope opportunistic_pathogen_context_dependent_virulence=NONMECHANISTIC with scope_notes.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000043",
    "label": "parasitism",
    "definition": "A symbiosis in which the microorganism benefits at the expense of its host's fitness, deriving resources from the host while causing it harm.",
    "definition_source": "DOI:10.1038/s41579-021-00550-7",
    "trait_category": "ECOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "traitmech:000040"
    ],
    "synonyms": [
      {
        "synonym_text": "parasitic",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1038/s41579-021-00550-7"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/s41579-021-00550-7",
        "notes": "Drew et al. define parasitism as the harmful pole of the parasite-mutualist continuum and describe evolutionary transitions along it."
      },
      {
        "reference": "DOI:10.1073/pnas.1218525110",
        "notes": "McFall-Ngai et al. support host-exploitative associations as one outcome of the shared host-colonization toolkit."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:782",
        "taxon_label": "Rickettsia prowazekii",
        "note": "Obligate intracellular parasite (epidemic typhus agent); textbook host-dependent intracellular lifestyle.",
        "reference": "PMID:9823893"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "parasitism_host_fitness_cost",
        "title": "Parasitism extracts resources at the host's expense",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This broad ecological, host-relationship, habitat, or hazard classification spans multiple taxa and mechanisms; contextual protein nodes do not receive token UniProt examples.",
        "description": "Evidence-backed causal sketch linking host-resource exploitation to reduced host fitness in chronic parasitic association.",
        "nodes": [
          {
            "node_id": "parasitism_trait",
            "label": "parasitism",
            "node_type": "TRAIT",
            "grounding": "traitmech:000043",
            "description": "Symbiosis with positive microbe fitness and negative host fitness."
          },
          {
            "node_id": "host_resource_exploitation",
            "label": "host resource exploitation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Acquisition of nutrients or shelter from the host at fitness cost."
          },
          {
            "node_id": "host_fitness_cost",
            "label": "host fitness cost",
            "node_type": "QUALITY",
            "description": "Net negative fitness change for the host partner."
          },
          {
            "node_id": "bacterial_adhesin_activity",
            "label": "bacterial adhesin activity",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "Surface adhesin-mediated adherence to host tissues."
          },
          {
            "node_id": "host_colonization",
            "label": "host colonization",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Establishment and persistence of the microbe on/in host tissue."
          },
          {
            "node_id": "siderophore_secretion",
            "label": "siderophore secretion",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Secretion of metal-chelating siderophores that compete with host proteins."
          },
          {
            "node_id": "host_metal_acquisition",
            "label": "host metal acquisition",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Acquisition of host-sequestered metals (e.g. iron) by the microbe."
          },
          {
            "node_id": "deubiquitinase_activity",
            "label": "pathogen deubiquitinase activity",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "Pathogen-derived deubiquitinating enzyme activity acting on host ubiquitin signaling."
          },
          {
            "node_id": "host_ubiquitin_pathway_exploitation",
            "label": "host ubiquitin pathway exploitation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Manipulation of ubiquitin-dependent host processes during infection."
          },
          {
            "node_id": "high_symbiont_density",
            "label": "high symbiont density in host tissues",
            "node_type": "QUALITY",
            "description": "Elevated density of the symbiont within host tissues."
          },
          {
            "node_id": "copper_stress",
            "label": "copper stress",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Environmental copper stress experienced by the host-symbiont system."
          },
          {
            "node_id": "hemoglobin_uptake",
            "label": "hemoglobin/heme uptake",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Hemoglobin- and heme-uptake mechanisms used to acquire host nutrients."
          }
        ],
        "edges": [
          {
            "subject": "host_resource_exploitation",
            "predicate": "causes",
            "object": "host_fitness_cost",
            "description": "Sustained resource extraction reduces host fitness.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41579-021-00550-7",
                "notes": "Drew et al. define parasitism as the harmful pole of the parasite-mutualist continuum."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "host_fitness_cost",
            "predicate": "confers",
            "object": "parasitism_trait",
            "description": "Chronic host fitness cost realizes the parasitic lifestyle.",
            "evidence": [
              {
                "reference": "DOI:10.1073/pnas.1218525110",
                "notes": "McFall-Ngai et al. support host-exploitative associations as one outcome of the shared host-colonization toolkit."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "bacterial_adhesin_activity",
            "predicate": "promotes",
            "object": "host_colonization",
            "description": "Adhesin expression mediates adherence to host tissues, enabling colonization.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuae019",
                "notes": "Barber & Fitzgerald 2024: bacterial adhesins are critical for adherence to host tissues."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "host_colonization",
            "predicate": "enables",
            "object": "host_resource_exploitation",
            "description": "Established colonization provides access to host resources for exploitation.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuae019",
                "notes": "Barber & Fitzgerald 2024: host colonization is the basis for downstream host exploitation."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "siderophore_secretion",
            "predicate": "promotes",
            "object": "host_metal_acquisition",
            "description": "Secreted siderophores compete with host proteins for metals and are reacquired.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuae019",
                "notes": "Barber & Fitzgerald 2024: siderophores compete with host proteins for metals; metal-bound siderophores reacquired."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "host_metal_acquisition",
            "predicate": "part of",
            "object": "host_resource_exploitation",
            "description": "Metal scavenging is one mode of acquiring resources from the host.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuae019",
                "notes": "Barber & Fitzgerald 2024: nutrient/metal acquisition from host is a core exploitation mechanism."
              }
            ],
            "predicate_id": "biolink:part_of"
          },
          {
            "subject": "deubiquitinase_activity",
            "predicate": "promotes",
            "object": "host_ubiquitin_pathway_exploitation",
            "description": "Pathogen DUBs exploit and manipulate ubiquitin-dependent host processes during infection.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fimmu.2023.1303072",
                "notes": "Wehrmann & Vilchez 2023: DUBs are key factors exploiting/manipulating Ub-dependent host processes during infection."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "host_ubiquitin_pathway_exploitation",
            "predicate": "promotes",
            "object": "host_resource_exploitation",
            "description": "Manipulating host ubiquitin signaling supports microbe persistence and resource extraction.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fimmu.2023.1303072",
                "notes": "Wehrmann & Vilchez 2023: manipulation of host Ub pathways supports infection establishment."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "hemoglobin_uptake",
            "predicate": "part of",
            "object": "host_resource_exploitation",
            "description": "Hemoglobin/heme uptake supplies nutrients enabling parasite survival in the host.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fcimb.2023.1150054",
                "notes": "Reyes-Lopez et al. 2023: Hb and heme-uptake mechanisms allow protozoa to survive inside the host."
              }
            ],
            "predicate_id": "biolink:part_of"
          },
          {
            "subject": "high_symbiont_density",
            "predicate": "causes",
            "object": "host_fitness_cost",
            "description": "High symbiont densities in host tissues drive strong negative host effects, even death.",
            "evidence": [
              {
                "reference": "DOI:10.1002/ece3.11705",
                "notes": "Hoffmann & Cooper 2024: high endosymbiont densities have particularly strong negative effects that can kill hosts."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "copper_stress",
            "predicate": "exacerbates",
            "object": "host_fitness_cost",
            "description": "Environmental copper stress exacerbates the pathogenic effects of parasitic symbionts on hosts.",
            "evidence": [
              {
                "reference": "DOI:10.1093/ismejo/wrae100",
                "notes": "Shi et al. 2024: pathogenic effects of parasitic symbionts on hosts were exacerbated under copper stress."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-06-02T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate ECOLOGY trait (parasitism); sub-variant of symbiosis. Distinct from pathogenic_to_host (acute disease causation).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-09T14:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (parasitism / host fitness cost) with RO/biolink predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 9 evidence-backed generic edges (9 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:09Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 8 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002213\u00d74, biolink:part_of\u00d72, RO:0002327\u00d71, biolink:causes\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 1 causal edge(s) off enables/RO:0002327 with a TRAIT object (1 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope parasitism_host_fitness_cost=NONMECHANISTIC with scope_notes.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1004000",
    "label": "pathogenic to host",
    "definition": "A phenotype where a microbe is a pathogen of some host organism.",
    "definition_source": "DOI:10.1146/annurev.micro.62.081307.162938",
    "trait_category": "ECOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "synonyms": [
      {
        "synonym_text": "General.keywords",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "Safety information.risk assessment",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev.micro.62.081307.162938",
        "snippet": "virulence factors",
        "notes": "Virulence-factor review supports the encoding of dedicated virulence factors as the molecular basis of host pathogenicity."
      },
      {
        "reference": "DOI:10.1038/nrmicro1592",
        "snippet": "secretion systems",
        "notes": "Secretion-systems review supports protein secretion machineries as central effectors of host pathogenicity across kingdoms."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:287",
        "taxon_label": "Pseudomonas aeruginosa",
        "note": "opportunistic pathogen",
        "reference": "PMID:31597590"
      },
      {
        "taxon_id": "NCBITaxon:1280",
        "taxon_label": "Staphylococcus aureus",
        "note": "host pathogen",
        "reference": "PMID:33522395"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "pathogenic_to_host_virulence_factor_program",
        "title": "Pathogenic-to-host virulence-factor program",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This broad ecological, host-relationship, habitat, or hazard classification spans multiple taxa and mechanisms; contextual protein nodes do not receive token UniProt examples.",
        "description": "DOI-backed graph linking encoded virulence factors, secretion-based effector delivery, host colonization, and host damage to the pathogenic-to-host phenotype.",
        "nodes": [
          {
            "node_id": "pathogenic_to_host_trait",
            "label": "pathogenic to host",
            "node_type": "TRAIT",
            "grounding": "METPO:1004000",
            "description": "Ability to cause disease in a host organism."
          },
          {
            "node_id": "virulence_factors",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Contextual protein family or multiprotein aggregate reviewed for this nonmechanistic classification; no single semantic family captures it.",
            "label": "virulence factors",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Encoded toxins, adhesins, and effector proteins enabling host colonization and damage."
          },
          {
            "node_id": "secretion_systems",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Contextual protein family or multiprotein aggregate reviewed for this nonmechanistic classification; no single semantic family captures it.",
            "label": "protein secretion systems",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Dedicated secretion machineries (e.g., T3SS, T4SS, T6SS) delivering effectors to host cells."
          },
          {
            "node_id": "host_colonization",
            "label": "host colonization",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Establishment of microbial growth within host tissues."
          },
          {
            "node_id": "host_damage",
            "label": "host damage",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Tissue, cell, or systemic damage produced in the host."
          },
          {
            "node_id": "quorum_sensing_autoinducers",
            "label": "quorum sensing autoinducers",
            "node_type": "CHEMICAL",
            "description": "Hormone-like signaling molecules that accumulate with cell density and trigger sensor proteins."
          },
          {
            "node_id": "virulence_gene_expression",
            "label": "virulence gene expression",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Global up-regulation of virulence-factor genes in response to regulatory signals."
          },
          {
            "node_id": "biofilm_formation",
            "label": "biofilm formation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Formation and maturation of structured surface-attached microbial communities.",
            "grounding": "GO:0042710"
          },
          {
            "node_id": "persistent_infection",
            "label": "persistent infection",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Chronic/persistent infection of the host enabled by biofilm communities."
          },
          {
            "node_id": "biofilm_matrix",
            "label": "biofilm extracellular matrix",
            "node_type": "CELLULAR_LOCALIZATION",
            "description": "Extracellular polymeric matrix (EPS) enclosing biofilm cells."
          },
          {
            "node_id": "antibiotic_tolerance",
            "label": "antibiotic tolerance",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced susceptibility of biofilm cells to antimicrobials due to limited penetration."
          },
          {
            "node_id": "immune_evasion",
            "label": "host immune evasion",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Avoidance or subversion of host immune defenses (e.g., phagocytosis, immune clearance)."
          },
          {
            "node_id": "capsule",
            "label": "polysaccharide capsule",
            "node_type": "CELLULAR_LOCALIZATION",
            "description": "Antiphagocytic polysaccharide surface capsule."
          },
          {
            "node_id": "horizontal_gene_transfer",
            "label": "horizontal gene transfer",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Acquisition and recombination of mobile genetic elements driving host adaptation.",
            "grounding": "GO:0009292"
          }
        ],
        "edges": [
          {
            "subject": "virulence_factors",
            "predicate": "enables",
            "object": "host_colonization",
            "description": "Virulence factors enable adhesion, immune evasion, and tissue invasion required for host colonization.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev.micro.62.081307.162938",
                "snippet": "virulence factors",
                "notes": "Supports virulence factors as enablers of host colonization."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "secretion_systems",
            "predicate": "delivers",
            "object": "virulence_factors",
            "description": "Bacterial protein secretion systems deliver effector virulence factors into host environments or host cells.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro1592",
                "snippet": "secretion systems",
                "notes": "Supports secretion systems as delivery machinery for effectors."
              }
            ]
          },
          {
            "subject": "host_colonization",
            "predicate": "enables",
            "object": "host_damage",
            "description": "Established host colonization enables sustained damage to host tissues.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev.micro.62.081307.162938",
                "snippet": "virulence factors",
                "notes": "Supports the colonization-to-damage progression characteristic of pathogens."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "host_damage",
            "predicate": "manifests as",
            "object": "pathogenic_to_host_trait",
            "description": "Host damage manifests the pathogenic-to-host trait.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev.micro.62.081307.162938",
                "snippet": "virulence factors",
                "notes": "Supports the trait endpoint."
              }
            ],
            "predicate_id": "METPO:2007400"
          },
          {
            "subject": "quorum_sensing_autoinducers",
            "predicate": "activates",
            "object": "virulence_gene_expression",
            "description": "Quorum-sensing autoinducers trigger sensor proteins that drive global virulence gene expression.",
            "evidence": [
              {
                "reference": "DOI:10.3390/ijms25052655",
                "notes": "Autoinducers are hormone-like molecules triggering sensor proteins to mediate changes in global gene expression; QS controls virulence factor production."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "quorum_sensing_autoinducers",
            "predicate": "promotes",
            "object": "biofilm_formation",
            "description": "Quorum sensing is crucial for biofilm formation and maintenance.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.tcsw.2024.100133",
                "notes": "QS is crucial for biofilm formation and maintenance."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "biofilm_formation",
            "predicate": "enables",
            "object": "persistent_infection",
            "description": "Biofilm communities enable chronic/persistent infection of the host.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.tcsw.2024.100133",
                "notes": "QS-driven biofilm formation and maintenance underlies persistent infection."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "biofilm_matrix",
            "predicate": "enables",
            "object": "antibiotic_tolerance",
            "description": "The biofilm EPS matrix limits antimicrobial penetration and protects deeper-layer cells, increasing tolerance.",
            "evidence": [
              {
                "reference": "DOI:10.3390/bacteria3030008",
                "notes": "EPS matrix protects deeper-layer cells from antimicrobials; biofilm bacteria increase resistance about 1000 fold (DOI:10.3390/ijms25052655)."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "biofilm_formation",
            "predicate": "enables",
            "object": "immune_evasion",
            "description": "Biofilms help bacteria evade the host immune response, supporting chronic infection.",
            "evidence": [
              {
                "reference": "DOI:10.3390/antibiotics13070619",
                "notes": "Biofilms help bacteria evade the immune response."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "capsule",
            "predicate": "enables",
            "object": "immune_evasion",
            "description": "An antiphagocytic polysaccharide capsule resists phagocytosis, aiding immune evasion.",
            "evidence": [
              {
                "reference": "DOI:10.58532/nbennurmmch1",
                "notes": "An antiphagocytic capsule aids immune evasion; polysaccharide capsule resists phagocytosis to increase virulence."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "immune_evasion",
            "predicate": "enables",
            "object": "host_colonization",
            "description": "Evasion of host immune defenses permits sustained microbial growth within host tissues.",
            "evidence": [
              {
                "reference": "DOI:10.58532/nbennurmmch1",
                "notes": "Immune evasion via antiphagocytic capsule supports establishment within the host."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "horizontal_gene_transfer",
            "predicate": "contributes to",
            "object": "virulence_factors",
            "description": "Horizontal gene transfer, recombination, and gene gain/loss drive acquisition of virulence-associated host-adaptation traits.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuae019",
                "notes": "Horizontal gene transfer, gene acquisition and deletion, and genome rearrangements are major drivers of host adaptation."
              }
            ],
            "predicate_id": "RO:0002326"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.948130+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-11T23:15:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed causal graph linking virulence factors, secretion systems, host colonization, and host damage to the pathogenic-to-host trait.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:29Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d72).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T21:30:06Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007400\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 8 evidence-backed generic edges (9 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:09Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 8 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d75, RO:0002213\u00d72, RO:0002326\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:16Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0009292\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:29Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0042710\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-21T08:00:00Z",
        "curator": "codex",
        "action": "NORMALISE_NODE_TYPE",
        "changes": "Tranche 5 of issue 356 settles the process/quality families and merges ids that meant the same sense: immune_evasion is BIOLOGICAL_PROCESS. Immune evasion is the avoidance or subversion of host defenses. The edges treat it as an enabled action that in turn enables colonization; capsule.yaml's 'reduced recognition and clearance' is the outcome of that same process, not a separate measurable axis.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope pathogenic_to_host_virulence_factor_program=NONMECHANISTIC with scope_notes; marked 2 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (virulence_factors, secretion_systems).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000699",
    "label": "periplasmic bacterial predation",
    "definition": "A predatory bacterial phenotype in which a bacterium enters the periplasm of a bacterial prey cell and grows and reproduces there using nutrients obtained by killing and consuming the prey.",
    "definition_source": "DOI:10.1038/s42003-025-09010-x",
    "trait_category": "ECOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000054"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/s42003-025-09010-x",
        "snippet": "establishes itself in the prey periplasm, feeding on the prey\u2019s cytoplasmic contents as a main nutrient source.",
        "notes": "Lai et al. 2025, PMID:41125861, PMC12546842, Introduction, second paragraph; the subject is B. bacteriovorus. Direct publisher HTML and Europe PMC full-text XML match. Scientific Abstract, Introduction, selected growth/exit Results and culture, sampling, time-lapse and statistics Methods, Discussion and actual Figures 1 and 4 read. Figure 1a is a lifecycle schematic, not direct imaging; Figure 4a includes WT exit measurements. Other figures and supplements not fully assessed. Publisher and MED showed no linked notice; MED linked the earlier preprint, not a correction. Published source: https://doi.org/10.1038/s42003-025-09010-x."
      },
      {
        "reference": "DOI:10.1128/JB.00914-10",
        "snippet": "Nutrients for the replication of Bdellovibrio bacteria come entirely from the digestion of the single invaded bacterium",
        "notes": "Fenton et al. 2010, PMID:20935099, scientific Abstract retrieved from source-qualified MED metadata. Supports prey-derived nutrition during intrabacterial replication; do not generalize its single-prey wording to a fixed predator occupancy or universal prey dependence. Full-text delivery failed; Methods, actual figures and supplement remain unread. MED links a commentary, not a correction/retraction; publisher notice check was inaccessible. Source: https://pubmed.ncbi.nlm.nih.gov/20935099/."
      },
      {
        "reference": "DOI:10.1128/jb.96.4.1366-1381.1968",
        "snippet": "Although partial disruption of the cytoplasmic membrane was always apparent, the parasite did not appear to actively penetrate through this barrier.",
        "notes": "Burnham et al. 1968, PMID:4879563, scientific Abstract directly read at PubMed and matched source-qualified MED metadata. Electron microscopy supports entry without observed active penetration of the prey cytoplasmic membrane, not an intact membrane throughout predation or direct nutrient tracing. Full text and actual figures were unavailable; no strain-level example inferred. MED/PubMed exposed no linked notice, but publisher notice status was not verified. Source: https://pubmed.ncbi.nlm.nih.gov/4879563/."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:264462",
        "taxon_label": "Bdellovibrio bacteriovorus HD100",
        "reference": "DOI:10.1038/s42003-025-09010-x",
        "note": "Qualified to wild-type HD100, not deletion, complemented or host-independent derivatives. Lai et al. used E. coli laboratory prey; this is not direct field observation. DSM 50701 is HD100 and is recorded as a soil isolate at https://webshop.dsmz.de/en/bacteria/Bdellovibrio-bacteriovorus.html; this establishes natural provenance, not another predation assay. NCBI strain identifier, scientific name and DSM 50701 synonym independently checked on 2026-10-11: https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=264462."
      }
    ],
    "discussions": [
      {
        "discussion_id": "periplasmic-predation-boundaries-and-mappings",
        "prompt": "Distinguish periplasmic feeding from invasion alone.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Predatory bacterium traitmech:000054 is broader; its intraperiplasmic_growth node denotes a lifecycle stage, not this whole feeding phenotype, and must not be equated to it. Epibiotic bacterial predation traitmech:000697 keeps the predator cell body external. Generic intracellular predation, endoparasitism and endosymbiosis are not exact synonyms of periplasmic predation. Attachment, killing without entry, or residence without nutritional growth are insufficient. Exact synonyms and xrefs remain unassigned pending authority and scope reconciliation. No organism-level disjointness, universal prey range, division pattern, progeny number or obligate dependence is asserted.",
        "posed_by": "codex",
        "posed_date": "2026-10-11"
      },
      {
        "discussion_id": "periplasmic-predation-mechanism-grounding",
        "prompt": "Ground model-specific machinery before adding causal edges.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "A protein-resolved graph and protein examples are deferred, not claimed absent. The 2025 proteome and perturbation experiments provide leads, but protein abundance, gene presence and predicted sequence function do not establish the complete feeding mechanism. Heterologous prey lysis does not establish predator invasion or nutrient uptake. Verify exact accessions, taxon pairing and relevant supplements before curating machinery; do not transfer the HD100 mechanism to every periplasmic predator.",
        "posed_by": "codex",
        "posed_date": "2026-10-11"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-11T14:16:57Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added periplasmic bacterial predation beneath predatory bacterium with three DOI-backed sources, checked snippets and a WT-qualified HD100 example. Ignored/hidden main/worktree and pending-PR checks support 000699 and v575 block 1065200-1065299. Existing records unchanged; exact mappings and mechanism grounding remain open. Timestamp records the observed UTC curation decision.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1004003",
    "label": "plant pathogen",
    "definition": "A pathogen that infects organisms in the kingdom Viridiplantae.",
    "definition_source": "DOI:10.1146/annurev.phyto.43.040204.135923",
    "trait_category": "ECOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1004000"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev.phyto.43.040204.135923",
        "snippet": "type III secretion",
        "notes": "Plant-pathology review supports type III secretion of effectors as the central mechanism by which bacterial plant pathogens manipulate plant cells."
      },
      {
        "reference": "DOI:10.1146/annurev.micro.55.1.535",
        "snippet": "cell-wall-degrading enzymes",
        "notes": "Plant-pathogen review supports secreted plant-cell-wall-degrading enzymes as essential virulence factors of bacterial phytopathogens."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:317",
        "taxon_label": "Pseudomonas syringae",
        "note": "Model bacterial plant pathogen (Type III secretion, effector biology). Agrobacterium tumefaciens is the classic crown-gall/genetic-tool exemplar.",
        "reference": "PMID:29479077"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "plant_pathogen_t3ss_effector_program",
        "title": "Plant-pathogen T3SS-effector and wall-degradation program",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This broad ecological, host-relationship, habitat, or hazard classification spans multiple taxa and mechanisms; contextual protein nodes do not receive token UniProt examples.",
        "description": "DOI-backed graph linking plant-cell-wall degradation, type III secretion of effectors, suppression of plant immunity, and plant tissue colonization to the plant-pathogen phenotype.",
        "nodes": [
          {
            "node_id": "plant_pathogen_trait",
            "label": "plant pathogen",
            "node_type": "TRAIT",
            "grounding": "METPO:1004003",
            "description": "Pathogen of plant hosts."
          },
          {
            "node_id": "cwd_enzymes",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Contextual protein family or multiprotein aggregate reviewed for this nonmechanistic classification; no single semantic family captures it.",
            "label": "plant-cell-wall-degrading enzymes",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Secreted enzymes (e.g., pectinases, cellulases) degrading the plant cell wall."
          },
          {
            "node_id": "t3ss",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Contextual protein family or multiprotein aggregate reviewed for this nonmechanistic classification; no single semantic family captures it.",
            "label": "type III secretion system",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Bacterial T3SS delivering effector proteins into plant cells."
          },
          {
            "node_id": "t3ss_effectors",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Contextual protein family or multiprotein aggregate reviewed for this nonmechanistic classification; no single semantic family captures it.",
            "label": "T3SS effector proteins",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Bacterial effector proteins translocated into plant cells by the T3SS."
          },
          {
            "node_id": "plant_immune_suppression",
            "label": "plant immune suppression",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Suppression of plant innate immunity by translocated effectors."
          },
          {
            "node_id": "plant_tissue_colonization",
            "label": "plant tissue colonization",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Establishment of microbial growth in plant tissues."
          },
          {
            "node_id": "plant_disease",
            "label": "plant disease",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Pathology produced in a plant host."
          },
          {
            "node_id": "quorum_sensing",
            "label": "quorum sensing",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Cell-density-dependent signaling (e.g., AHL, DSF) coordinating group behaviors in bacterial pathogens.",
            "grounding": "GO:0009372"
          },
          {
            "node_id": "biofilm_formation",
            "label": "biofilm formation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Formation of structured surface-attached microbial communities.",
            "grounding": "GO:0042710"
          },
          {
            "node_id": "eps_production",
            "label": "exopolysaccharide production",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Biosynthesis of extracellular polysaccharides forming the biofilm matrix."
          },
          {
            "node_id": "plant_cell_wall",
            "label": "plant cell wall",
            "node_type": "CELLULAR_LOCALIZATION",
            "description": "Plant-type cell wall, the structural barrier degraded during host invasion.",
            "grounding": "GO:0009505"
          },
          {
            "node_id": "apoplastic_effector_secretion",
            "label": "ER-Golgi apoplastic effector secretion",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Conventional ER-Golgi secretory pathway delivering apoplastic effectors in fungal/oomycete pathogens."
          },
          {
            "node_id": "apoplastic_effectors",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Contextual protein family or multiprotein aggregate reviewed for this nonmechanistic classification; no single semantic family captures it.",
            "label": "apoplastic effectors",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Secreted pathogen effector proteins acting in the host apoplast."
          }
        ],
        "edges": [
          {
            "subject": "cwd_enzymes",
            "predicate": "enables",
            "object": "plant_tissue_colonization",
            "description": "Plant-cell-wall-degrading enzymes enable bacterial spread within plant tissues.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev.micro.55.1.535",
                "snippet": "cell-wall-degrading enzymes",
                "notes": "Supports CWD enzymes as virulence factors in plant infection."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "t3ss",
            "predicate": "delivers",
            "object": "t3ss_effectors",
            "description": "The T3SS translocates effector proteins from the bacterium into plant cells.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev.phyto.43.040204.135923",
                "snippet": "type III secretion system",
                "notes": "Supports the T3SS as the delivery system for bacterial effectors into plant cells."
              }
            ]
          },
          {
            "subject": "t3ss_effectors",
            "predicate": "suppresses",
            "object": "plant_immune_suppression",
            "description": "Translocated T3SS effectors suppress plant innate immunity.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev.phyto.43.040204.135923",
                "snippet": "effector proteins",
                "notes": "Supports T3SS-delivered effector proteins as the plant-immunity-suppressing factors."
              }
            ],
            "predicate_id": "RO:0002212"
          },
          {
            "subject": "plant_immune_suppression",
            "predicate": "enables",
            "object": "plant_tissue_colonization",
            "description": "Immune suppression supports sustained colonization of plant tissues.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev.phyto.43.040204.135923",
                "snippet": "plant pathogen",
                "notes": "Supports immune-suppression-driven colonization as a hallmark of plant-pathogen infection biology."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "plant_tissue_colonization",
            "predicate": "causes",
            "object": "plant_disease",
            "description": "Established colonization of plant tissues causes plant disease.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev.micro.55.1.535",
                "snippet": "cell-wall-degrading enzymes",
                "notes": "Supports colonization-to-disease progression in plant pathogens."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "plant_disease",
            "predicate": "manifests as",
            "object": "plant_pathogen_trait",
            "description": "Plant disease manifests the plant-pathogen trait.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev.phyto.43.040204.135923",
                "snippet": "type III secretion",
                "notes": "Supports the trait endpoint."
              }
            ],
            "predicate_id": "METPO:2007400"
          },
          {
            "subject": "quorum_sensing",
            "predicate": "positively regulates",
            "object": "biofilm_formation",
            "description": "Quorum sensing is required for cooperative biofilm formation in plant-pathogenic bacteria.",
            "evidence": [
              {
                "reference": "DOI:10.3390/plants12112207",
                "notes": "QS is required for cooperative biofilm formation and regulates toxins, enzymes, EPS, and virulence factors."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "quorum_sensing",
            "predicate": "positively regulates",
            "object": "eps_production",
            "description": "Quorum sensing and c-di-GMP signaling positively regulate exopolysaccharide biosynthesis.",
            "evidence": [
              {
                "reference": "DOI:10.3390/plants12112207",
                "notes": "EPS such as amylovoran, levan, xanthan, stewartan, and cellulose are often regulated by intracellular c-di-GMP and QS."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "eps_production",
            "predicate": "enables",
            "object": "biofilm_formation",
            "description": "Exopolysaccharide production builds the biofilm matrix enabling biofilm formation.",
            "evidence": [
              {
                "reference": "DOI:10.3390/plants12112207",
                "notes": "EPS form the matrix of cooperative biofilms in plant-pathogenic bacteria."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "cwd_enzymes",
            "predicate": "degrades",
            "object": "plant_cell_wall",
            "description": "Secreted cell-wall-degrading enzymes degrade the plant cell wall.",
            "evidence": [
              {
                "reference": "DOI:10.21608/mb.2024.307263.1134",
                "notes": "Secretion of cell-wall-degrading enzymes (pectinase, chitinase, cellulase, protease) that enable invasion and colonization."
              }
            ],
            "predicate_id": "METPO:2007809"
          },
          {
            "subject": "apoplastic_effector_secretion",
            "predicate": "delivers",
            "object": "apoplastic_effectors",
            "description": "The conventional ER-Golgi secretory pathway delivers apoplastic effectors.",
            "evidence": [
              {
                "reference": "DOI:10.1094/MPMI-12-23-0212-CR",
                "notes": "Apoplastic effectors are secreted via the conventional endoplasmic reticulum (ER)-Golgi pathway."
              }
            ]
          },
          {
            "subject": "apoplastic_effectors",
            "predicate": "suppresses",
            "object": "plant_immune_suppression",
            "description": "Secreted apoplastic effectors contribute to suppression of plant immunity during infection.",
            "evidence": [
              {
                "reference": "DOI:10.1094/MPMI-12-23-0212-CR",
                "notes": "Apoplastic effectors delivered to the host act to subvert plant defenses and permit infection."
              }
            ],
            "predicate_id": "RO:0002212"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.949239+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-11T23:15:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed causal graph linking plant-cell-wall-degrading enzymes, T3SS effector delivery, immune suppression, plant tissue colonization, and disease to the plant-pathogen trait.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:29Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T05:49:23Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:causes\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T21:30:06Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007400\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:18Z",
        "curator": "claude",
        "action": "RENAME_PREDICATE_LABELS",
        "changes": "Renamed 1 causal-edge predicate label(s) to align with existing groundings: supports \u2192 enables \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:20Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-13T21:03:25Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002212\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-17T04:09:43Z",
        "curator": "claude",
        "action": "REMOVE_REDUNDANT_SYNONYM",
        "changes": "Removed 1 synonym(s) whose text duplicated the label (seeder redundancy; no information lost).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 6 evidence-backed generic edges (6 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:09Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d71, RO:0002212\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:29Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 4 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0140649\u00d71, GO:0009372\u00d71, GO:0042710\u00d71, GO:0009505\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:36Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000007\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-04T03:08:11Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002213\u00d72).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T02:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES_PART2",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates onto their causal-graph counterparts (1 to degrades), issue 301 part 2. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Each replacement is a 1:1 mirror of its source predicate that changes only the domain, so the claim each edge makes is unchanged and directions are unchanged. The replacements are proposed in proposals/metpo_traitmech_v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-17T06:00:00Z",
        "curator": "claude",
        "action": "REGROUND_CAUSAL_NODES",
        "changes": "Repaired a wrong CURIE from the kg-microbe name-match pass (issue 402): plant_tissue_colonization: GO:0140649 retracted. Was GO:0140649 'symbiont-mediated cell-to-cell migration by invasive hypha'. Invasive hyphae are FUNGAL and this is a bacterial record. RETRACTED RATHER THAN REPLACED: nothing verified fits \u2014 GO:0044409 is 'symbiont entry into host', which is entry rather than establishment of growth, and GO:0051701 / GO:0044403 are the generic interaction parents. Guessing a plausible replacement is precisely the act that produced this grounding (#402, #403).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope plant_pathogen_t3ss_effector_program=NONMECHANISTIC with scope_notes; marked 4 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (cwd_enzymes, t3ss, t3ss_effectors, apoplastic_effectors).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000054",
    "label": "predatory bacterium",
    "definition": "A trophic-ecology lifestyle in which a bacterium actively kills and consumes other bacteria for nutrients, e.g. the periplasmic predator Bdellovibrio bacteriovorus.",
    "definition_source": "DOI:10.1146/annurev.micro.091208.073346",
    "trait_category": "ECOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "synonyms": [
      {
        "synonym_text": "bacterial predator",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1146/annurev.micro.091208.073346"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev.micro.091208.073346",
        "notes": "Sockett, \"Predatory lifestyle of Bdellovibrio bacteriovorus\", describes invasion, killing, and digestion of prey bacteria as a predatory lifestyle."
      },
      {
        "reference": "DOI:10.1111/1462-2920.13171",
        "notes": "P\u00e9rez et al. survey predatory bacteria, their hunting strategies, prey ranges, and genome characteristics."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:959",
        "taxon_label": "Bdellovibrio bacteriovorus",
        "note": "Model predatory bacterium; invades the periplasm of Gram-negative prey (strain HD100).",
        "reference": "https://pmc.ncbi.nlm.nih.gov/articles/PMC1913455/"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "predatory_bacterium_prey_killing",
        "title": "Predatory bacteria kill and consume other bacteria",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This broad ecological, host-relationship, habitat, or hazard classification spans multiple taxa and mechanisms; contextual protein nodes do not receive token UniProt examples. The invasion and bdelloplast branch illustrates B. bacteriovorus, not a requirement for every predatory bacterium; epibiotic bacterial predators feed with their cell bodies outside the prey.",
        "description": "Evidence-backed causal sketch linking prey invasion to bacteriolytic killing and predator nutrient acquisition.",
        "nodes": [
          {
            "node_id": "predatory_trait",
            "label": "predatory bacterium",
            "node_type": "TRAIT",
            "grounding": "traitmech:000054",
            "description": "Bacterial lifestyle of killing and consuming other bacteria."
          },
          {
            "node_id": "prey_bacterium",
            "label": "prey bacterium",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Target bacterial cell of the predatory attack."
          },
          {
            "node_id": "prey_killing",
            "label": "bacteriolytic killing",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Lysis or digestion of prey bacterial cells."
          },
          {
            "node_id": "b_bacteriovorus_type_iv_pilus",
            "label": "B. bacteriovorus type IV pilus",
            "node_type": "CELLULAR_LOCALIZATION",
            "grounding": "GO:0044096",
            "description": "Type IV pilus at the invasive pole that mediates B. bacteriovorus attachment to prey."
          },
          {
            "node_id": "prey_attachment",
            "label": "B. bacteriovorus prey attachment",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Attachment of B. bacteriovorus to the surface of a Gram-negative prey bacterium before invasion."
          },
          {
            "node_id": "prey_invasion",
            "label": "B. bacteriovorus prey invasion",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Entry of B. bacteriovorus through the prey envelope into the prey periplasm."
          },
          {
            "node_id": "invasion_portal",
            "label": "prey attachment/invasion complex (portal)",
            "node_type": "CELLULAR_LOCALIZATION",
            "description": "Flexible portal complex lining the prey peptidoglycan entry hole during predator invasion."
          },
          {
            "node_id": "prey_entry_pore",
            "label": "prey peptidoglycan entry pore / bdelloplast pore",
            "node_type": "CELLULAR_LOCALIZATION",
            "description": "Hole in the prey peptidoglycan through which the predator enters; sealed to form the bdelloplast."
          },
          {
            "node_id": "prey_cell_wall_modification",
            "label": "prey cell-wall modification enzymes",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "Predator enzymes that modify the prey cell wall during invasion."
          },
          {
            "node_id": "bdelloplast",
            "label": "bdelloplast",
            "node_type": "CELLULAR_LOCALIZATION",
            "description": "Rounded, sealed killed-prey cell within which the predator grows and replicates."
          },
          {
            "node_id": "intraperiplasmic_growth",
            "label": "intraperiplasmic growth / predator replication",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Growth and replication of the predator inside the prey periplasm (bdelloplast)."
          },
          {
            "node_id": "exit_lytic_activity",
            "label": "exit-associated lytic activity",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "Lytic activity that breaks down the prey cell wall to release predator progeny."
          },
          {
            "node_id": "progeny_release",
            "label": "prey cell-wall lysis and progeny release",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Lysis of the spent prey cell wall and exit of newly formed predator progeny."
          }
        ],
        "edges": [
          {
            "subject": "predatory_trait",
            "predicate": "enables",
            "object": "prey_killing",
            "description": "B. bacteriovorus invades and digests bacterial prey for nutrients.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev.micro.091208.073346",
                "notes": "Sockett describes Bdellovibrio invasion and digestion of prey bacteria."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "prey_killing",
            "predicate": "consumes",
            "object": "prey_bacterium",
            "description": "Killed prey cells provide nutrients to the predator.",
            "evidence": [
              {
                "reference": "DOI:10.1111/1462-2920.13171",
                "notes": "P\u00e9rez et al. survey predatory bacteria and their prey-killing strategies."
              }
            ],
            "predicate_id": "biolink:consumes"
          },
          {
            "subject": "b_bacteriovorus_type_iv_pilus",
            "predicate": "contributes to",
            "object": "prey_attachment",
            "description": "Type IV pili mediate B. bacteriovorus attachment to prey before invasion.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-023-01401-2",
                "snippet": "attachment is mediated by type IV pili (T4P)",
                "notes": "Kaplan et al. directly imaged T4aP extending from B. bacteriovorus to the prey outer membrane; this branch is taxon-specific."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "prey_bacterium",
            "predicate": "participates in",
            "object": "prey_attachment",
            "description": "The living Gram-negative prey cell is the target participant in B. bacteriovorus attachment.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-024-47412-3",
                "snippet": "swim rapidly to another Gram-negative bacterial prey surface and then attach to it",
                "notes": "Tyson et al. describe attachment to the prey surface as the first physical predator-prey interaction before invasion."
              }
            ],
            "predicate_id": "biolink:participates_in"
          },
          {
            "subject": "prey_attachment",
            "predicate": "precedes",
            "object": "prey_invasion",
            "description": "B. bacteriovorus first attaches to prey and begins invasion only after prey assessment.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-023-01401-2",
                "snippet": "After assessment of prey quality, the process of invasion begins",
                "notes": "Kaplan et al. place attachment and prey assessment before invasion in the endoperiplasmic predation cycle."
              }
            ],
            "predicate_id": "biolink:precedes"
          },
          {
            "subject": "invasion_portal",
            "predicate": "participates in",
            "object": "prey_invasion",
            "description": "The flexible portal lines the prey entry hole and seals the outer membrane around B. bacteriovorus during invasion.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-023-01401-2",
                "snippet": "flexible portal structure lining a hole in the prey peptidoglycan",
                "notes": "Cryo-electron tomography directly localized the portal at the entry hole during predator invasion."
              }
            ],
            "predicate_id": "biolink:participates_in"
          },
          {
            "subject": "prey_cell_wall_modification",
            "predicate": "participates in",
            "object": "prey_invasion",
            "description": "Enzymatic modification of the prey cell wall permits entry into the periplasm and formation of the bdelloplast.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-023-01401-2",
                "snippet": "Prey invasion involves enzymatic modification of the prey cell wall",
                "notes": "Kaplan et al. describe localized prey-wall modification at the predator-prey contact point as part of invasion."
              }
            ],
            "predicate_id": "biolink:participates_in"
          },
          {
            "subject": "invasion_portal",
            "predicate": "seals",
            "object": "prey_entry_pore",
            "description": "A flexible portal lines the prey peptidoglycan hole and seals the entry pore to form a bdelloplast.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-023-01401-2",
                "notes": "Cryo-ET: a flexible portal lines the hole during entry and the entry pore is sealed to form a bdelloplast."
              }
            ]
          },
          {
            "subject": "prey_cell_wall_modification",
            "predicate": "causes",
            "object": "bdelloplast",
            "description": "Predator modification of the prey cell wall rounds the killed prey into a bdelloplast.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-024-47412-3",
                "notes": "During invasion the predator modifies the prey cell wall, rounding the killed prey into a bdelloplast."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "bdelloplast",
            "predicate": "provides environment for",
            "object": "intraperiplasmic_growth",
            "description": "The sealed bdelloplast houses a live predator that grows and replicates inside the prey periplasm.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-023-01401-2",
                "notes": "The sealed bdelloplast contains a live predator that grows and replicates inside the prey periplasm."
              }
            ]
          },
          {
            "subject": "exit_lytic_activity",
            "predicate": "causes",
            "object": "progeny_release",
            "description": "After septation, lytic activity breaks the prey cell wall so progeny lyse and exit.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-023-01401-2",
                "notes": "After synchronous septation, progeny lyse the prey cell wall and exit."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "intraperiplasmic_growth",
            "predicate": "precedes",
            "object": "progeny_release",
            "description": "Growth and synchronous division inside the bdelloplast occur before progeny lyse the prey wall and exit.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-023-01401-2",
                "snippet": "progeny cells reset to the attack phase, lyse the prey cell wall",
                "notes": "Kaplan et al. place progeny exit after consumption, intraperiplasmic growth, and synchronous septation."
              }
            ],
            "predicate_id": "biolink:precedes"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-06-02T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate ECOLOGY trait (predatory bacterium) from literature research to fill the trophic-ecology gap.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-09T14:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (predator / prey killing) with RO/biolink predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 4 evidence-backed generic edges (7 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:09Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:causes\u00d72).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-21T19:43:49Z",
        "curator": "codex",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Applied the existing DOI-backed predation-cycle research by adding taxon-scoped type IV pilus, prey-attachment, and prey-invasion nodes and six evidence-backed bridge edges. The bridges preserve attachment, invasion, bdelloplast growth, and exit as distinct lifecycle stages while joining the graph into one component.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope predatory_bacterium_prey_killing=NONMECHANISTIC with scope_notes.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-11T11:39:38Z",
        "curator": "codex",
        "action": "QUALIFY_GRAPH_SCOPE",
        "changes": "Qualified invasion wording to the B. bacteriovorus model, not all predatory bacteria (issue #1865). Epibiotic child traitmech:000697 retains external predator bodies; parent identity, evidence and graph topology are unchanged.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-11T11:43:59Z",
        "curator": "codex",
        "action": "CLARIFY_EVIDENCE_SCOPE",
        "changes": "Removed the interim edge's unnecessary temporal implication about invasion preceding killing. The final wording only qualifies the existing invasion/digestion claim to B. bacteriovorus; prior event retained.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000051",
    "label": "rhizosphere association",
    "definition": "A habitat association in which an organism lives in the rhizosphere \u2014 the soil zone influenced by plant roots and root exudates \u2014 a hotspot of microbial activity and plant-microbe interaction.",
    "definition_source": "DOI:10.1038/nrmicro3109",
    "trait_category": "ECOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "traitmech:000047"
    ],
    "synonyms": [
      {
        "synonym_text": "rhizosphere-associated",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1038/nrmicro3109"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/nrmicro3109",
        "notes": "Philippot et al., \"Going back to the roots\", define the rhizosphere as a distinct, root-influenced microbial habitat."
      },
      {
        "reference": "DOI:10.1038/nrmicro.2017.87",
        "notes": "Fierer supports the rhizosphere as a high-activity subset of the broader soil microbiome."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:294",
        "taxon_label": "Pseudomonas fluorescens",
        "note": "Canonical rhizosphere-colonising / biocontrol model.",
        "reference": "PMID:11701873"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "rhizosphere_root_exudate",
        "title": "Root exudates structure the rhizosphere microbial habitat",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This broad ecological, host-relationship, habitat, or hazard classification spans multiple taxa and mechanisms; contextual protein nodes do not receive token UniProt examples.",
        "description": "Evidence-backed causal sketch linking root exudates to the high-activity rhizosphere community.",
        "nodes": [
          {
            "node_id": "rhizosphere_trait",
            "label": "rhizosphere association",
            "node_type": "TRAIT",
            "grounding": "traitmech:000051",
            "description": "Persistent residence in the root-influenced soil zone."
          },
          {
            "node_id": "root_exudates",
            "label": "root exudates",
            "node_type": "CHEMICAL",
            "description": "Plant-derived carbon compounds released from roots into surrounding soil."
          },
          {
            "node_id": "rhizosphere_habitat",
            "label": "rhizosphere habitat",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Root-influenced soil zone with elevated microbial activity."
          },
          {
            "node_id": "bacterial_chemotaxis",
            "label": "bacterial chemotaxis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Directed bacterial movement along chemical gradients of root exudate compounds."
          },
          {
            "node_id": "flagellar_motility",
            "label": "flagellum-dependent cell motility",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Flagella-driven swimming motility that propels cells toward roots."
          },
          {
            "node_id": "mcp_chemoreceptor",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Contextual protein family or multiprotein aggregate reviewed for this nonmechanistic classification; no single semantic family captures it.",
            "label": "methyl-accepting chemotaxis protein (MCP)",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Transmembrane chemoreceptor that senses root exudate compounds and initiates chemotactic signaling."
          },
          {
            "node_id": "che_signaling",
            "label": "CheA/CheW/CheY chemotaxis signaling",
            "node_type": "PATHWAY",
            "description": "Canonical two-component chemotaxis phosphorelay coupling chemoreception to flagellar motility."
          },
          {
            "node_id": "root_colonization",
            "label": "root colonization",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Establishment of bacteria on and around plant roots."
          },
          {
            "node_id": "biofilm_formation",
            "label": "biofilm formation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Aggregation of cells into structured, matrix-enclosed communities on root surfaces.",
            "grounding": "GO:0042710"
          }
        ],
        "edges": [
          {
            "subject": "root_exudates",
            "predicate": "causes",
            "object": "rhizosphere_habitat",
            "description": "Root exudates create a distinct, C-enriched soil microhabitat.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro3109",
                "notes": "Philippot et al. define the rhizosphere as a root-influenced soil zone shaped by exudates."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "rhizosphere_habitat",
            "predicate": "confers",
            "object": "rhizosphere_trait",
            "description": "The rhizosphere habitat supports the rhizosphere-associated lifestyle.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro.2017.87",
                "notes": "Fierer documents the rhizosphere as a high-activity subset of the broader soil microbiome."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "mcp_chemoreceptor",
            "predicate": "positively regulates",
            "object": "bacterial_chemotaxis",
            "description": "MCP chemoreceptors sense diverse root exudates to drive chemotaxis.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fpls.2024.1491495",
                "notes": "Bacteria use transmembrane chemoreceptors (MCPs) to sense diverse root exudates."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "che_signaling",
            "predicate": "positively regulates",
            "object": "flagellar_motility",
            "description": "Phosphorylated CheY interacts with motility proteins to mediate movement.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fpls.2024.1491495",
                "notes": "Phosphorylated CheY interacts with motility proteins, mediating bacterial movement."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "bacterial_chemotaxis",
            "predicate": "enables",
            "object": "root_colonization",
            "description": "Chemotaxis is the first step in root colonization by motile bacteria.",
            "evidence": [
              {
                "reference": "DOI:10.3390/biology13020095",
                "notes": "Chemotaxis is the first step in the root colonization by motile bacteria."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "flagellar_motility",
            "predicate": "positively regulates",
            "object": "rhizosphere_trait",
            "description": "Flagellar motility is required for efficient root colonization / rhizosphere association.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuad066",
                "notes": "Disruption of chemotaxis or flagellin synthesis led to a 100-fold decrease in root colonization efficiency."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "root_exudates",
            "predicate": "positively regulates",
            "object": "biofilm_formation",
            "description": "Root exudates serve as carbon sources prerequisite for biofilm formation.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fpls.2024.1491495",
                "notes": "Root exudates serve as carbon sources that are prerequisites for biofilm formation."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "biofilm_formation",
            "predicate": "positively regulates",
            "object": "rhizosphere_trait",
            "description": "Biofilms provide nutrient-rich microenvironments and protection supporting rhizosphere persistence.",
            "evidence": [
              {
                "reference": "DOI:10.3390/biology13020095",
                "notes": "Biofilms provide nutrient-rich microenvironments and protection."
              }
            ],
            "predicate_id": "RO:0002213"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-06-02T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate ECOLOGY trait (rhizosphere association); sub-variant of habitat association.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-09T14:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (rhizosphere / root exudate habitat) with RO/biolink predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 6 evidence-backed generic edges (6 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:09Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:29Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0042710\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-04T03:08:12Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 5 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002213\u00d75).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 1 causal edge(s) off enables/RO:0002327 with a TRAIT object (1 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope rhizosphere_root_exudate=NONMECHANISTIC with scope_notes; marked 1 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (mcp_chemoreceptor).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000055",
    "label": "saprotrophy",
    "definition": "A trophic-ecology lifestyle in which an organism feeds on dead or decaying organic matter, mineralizing it and driving carbon and nutrient cycling (decomposition).",
    "definition_source": "DOI:10.3389/fmicb.2012.00348",
    "trait_category": "ECOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "synonyms": [
      {
        "synonym_text": "decomposer",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.3389/fmicb.2012.00348"
      },
      {
        "synonym_text": "saprophytic",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.3389/fmicb.2012.00348"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.3389/fmicb.2012.00348",
        "snippet": "soil microbial community structure influences C cycling",
        "notes": "Verified against the open Schimel and Schaeffer abstract; the review frames microbial organic-matter breakdown and extracellular enzymes as controls on soil carbon cycling."
      },
      {
        "reference": "DOI:10.1038/nrmicro.2017.87",
        "snippet": "crucial roles in nutrient cycling, the maintenance of soil fertility and soil carbon sequestration",
        "notes": "Verified against a public copy of Fierer; the review supports the broad ecosystem role of soil microbial communities in nutrient cycling, fertility, and carbon storage."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1902",
        "taxon_label": "Streptomyces coelicolor",
        "note": "Model saprotrophic soil decomposer; secretes hydrolases degrading dead organic matter.",
        "reference": "PMID:12000953"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "saprotrophy_decomposition_cycling",
        "title": "Saprotrophy decomposes dead organic matter and drives nutrient cycling",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This broad ecological, host-relationship, habitat, or hazard classification spans multiple taxa and mechanisms; contextual protein nodes do not receive token UniProt examples.",
        "description": "Evidence-backed causal sketch linking decomposer activity on dead organic matter to carbon and nutrient cycling.",
        "nodes": [
          {
            "node_id": "saprotrophy_trait",
            "label": "saprotrophy",
            "node_type": "TRAIT",
            "grounding": "traitmech:000055",
            "description": "Feeding on dead or decaying organic matter."
          },
          {
            "node_id": "dead_organic_matter",
            "label": "dead organic matter",
            "node_type": "CHEMICAL",
            "description": "Plant litter, detritus, and other non-living organic substrates."
          },
          {
            "node_id": "decomposition",
            "label": "organic matter decomposition",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Microbial mineralization of organic matter releasing CO2 and inorganic nutrients."
          },
          {
            "node_id": "extracellular_exoenzymes",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Contextual protein family or multiprotein aggregate reviewed for this nonmechanistic classification; no single semantic family captures it.",
            "label": "extracellular exoenzymes",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Secreted hydrolytic/oxidative enzymes acting outside the cell on organic matter."
          },
          {
            "node_id": "soluble_organic_compounds",
            "label": "soluble organic compounds",
            "node_type": "CHEMICAL",
            "description": "Low-molecular-weight soluble products available for microbial uptake."
          },
          {
            "node_id": "cellulolytic_enzymes",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Contextual protein family or multiprotein aggregate reviewed for this nonmechanistic classification; no single semantic family captures it.",
            "label": "cellulolytic enzyme system",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Cellobiohydrolases, endoglucanases, and beta-glucosidases acting in concert."
          },
          {
            "node_id": "cellulose",
            "label": "cellulose",
            "node_type": "CHEMICAL",
            "description": "Beta-1,4-linked glucose polymer, major plant cell-wall polysaccharide.",
            "grounding": "CHEBI:18246"
          },
          {
            "node_id": "glucose",
            "label": "glucose",
            "node_type": "CHEMICAL",
            "description": "Monosaccharide product of cellulose depolymerization.",
            "grounding": "CHEBI:17234"
          },
          {
            "node_id": "cazymes",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Contextual protein family or multiprotein aggregate reviewed for this nonmechanistic classification; no single semantic family captures it.",
            "label": "carbohydrate-active enzymes (CAZymes)",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Enzymes acting on glycosidic bonds of plant cell-wall polysaccharides."
          },
          {
            "node_id": "hemicellulose",
            "label": "hemicellulose",
            "node_type": "CHEMICAL",
            "description": "Heterogeneous matrix polysaccharides of plant cell walls.",
            "grounding": "CHEBI:61266"
          },
          {
            "node_id": "laccase",
            "label": "laccase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Multicopper oxidase that oxidizes lignin and phenolic substrates.",
            "grounding": "InterPro:IPR017761"
          },
          {
            "node_id": "lignin",
            "label": "lignin",
            "node_type": "CHEMICAL",
            "description": "Complex aromatic polymer in plant cell walls.",
            "grounding": "CHEBI:6457"
          },
          {
            "node_id": "manganese_peroxidase",
            "label": "manganese peroxidase (MnP)",
            "node_type": "GENE_OR_PROTEIN",
            "description": "H2O2-dependent fungal ligninolytic peroxidase.",
            "grounding": "GO:0016689"
          },
          {
            "node_id": "lignocellulolytic_gene_expression",
            "label": "lignocellulolytic gene expression",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Transcription of genes encoding lignocellulose-degrading enzymes."
          }
        ],
        "edges": [
          {
            "subject": "saprotrophy_trait",
            "predicate": "enables",
            "object": "decomposition",
            "description": "Saprotrophic activity breaks down dead organic matter.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2012.00348",
                "snippet": "rate of OM breakdown in the rhizosphere and in detritus",
                "notes": "Verified against the open Schimel and Schaeffer abstract; the edge links decomposer activity to organic matter turnover without asserting a single mechanism."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "decomposition",
            "predicate": "consumes",
            "object": "dead_organic_matter",
            "description": "Decomposition uses dead organic matter as substrate.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2012.00348",
                "snippet": "exoenzyme breakdown is necessary for microbes to metabolize them",
                "notes": "Verified against the open Schimel and Schaeffer text; dead detrital organic structures are retained as substrates that require extracellular breakdown."
              }
            ],
            "predicate_id": "biolink:consumes"
          },
          {
            "subject": "extracellular_exoenzymes",
            "predicate": "contributes to",
            "object": "soluble_organic_compounds",
            "description": "Extracellular exoenzymes contribute soluble decomposition products by acting on complex organic compounds.",
            "evidence": [
              {
                "reference": "DOI:10.1093/ismejo/wrae073",
                "snippet": "products released by extracellular reactions of exoenzymes produced by another group",
                "notes": "Verified against the open Wang et al. text; the edge keeps a broad substrate-cross-feeding claim about diffusible exoenzyme products in soil."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "cellulolytic_enzymes",
            "predicate": "hydrolyzes",
            "object": "cellulose",
            "description": "Cellobiohydrolases, endoglucanases, and beta-glucosidases act in concert to break down cellulose.",
            "evidence": [
              {
                "reference": "DOI:10.1093/jambio/lxac002",
                "snippet": "degradation of cellulose into glucose involves a concerted action of several enzymes",
                "notes": "Verified against the open Gurovic et al. text; cellobiohydrolases, endoglucanases, and beta-glucosidases are retained as a cellulolytic enzyme-system node."
              }
            ],
            "predicate_id": "METPO:2007808"
          },
          {
            "subject": "cellulose",
            "predicate": "is hydrolyzed to",
            "object": "glucose",
            "description": "Cellulose hydrolysis yields glucose.",
            "evidence": [
              {
                "reference": "DOI:10.1093/jambio/lxac002",
                "snippet": "The complete degradation of cellulose into glucose",
                "notes": "Verified against the open Gurovic et al. text; cellulose is retained as a substrate that derives into glucose after enzymatic hydrolysis."
              }
            ],
            "predicate_id": "RO:0001001"
          },
          {
            "subject": "cazymes",
            "predicate": "hydrolyzes",
            "object": "hemicellulose",
            "description": "Extracellular CAZymes hydrolyze hemicellulose polysaccharides at glycosidic bonds.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.cbpa.2015.10.018",
                "snippet": "The enzymatic degradation of cellulose and hemicellulose is accomplished in Nature via the collective action of multiple carbohydrate-active enzymes",
                "notes": "Verified against the open Cragg et al. full text; the broad CAZyme node is retained for hemicellulose-active enzymes."
              }
            ],
            "predicate_id": "METPO:2007808"
          },
          {
            "subject": "laccase",
            "predicate": "oxidizes",
            "object": "lignin",
            "description": "Laccase oxidatively degrades lignin and phenolic substrates via electron transfer.",
            "evidence": [
              {
                "reference": "DOI:10.1093/jambio/lxac002",
                "snippet": "Laccases and peroxidases degrade not only lignin but also the corresponding monomers and other phenolic substrates",
                "notes": "Verified against the open Gurovic et al. figure text; laccase is retained as a contextual fungal and bacterial ligninolytic enzyme."
              }
            ],
            "predicate_id": "METPO:2007803"
          },
          {
            "subject": "manganese_peroxidase",
            "predicate": "oxidizes",
            "object": "lignin",
            "description": "Manganese peroxidase performs H2O2-dependent oxidative degradation of lignin.",
            "evidence": [
              {
                "reference": "DOI:10.1093/jambio/lxac002",
                "snippet": "manganese peroxidases (MnP), lignin peroxidases (LiP) catalyzing a variety of oxidative reactions",
                "notes": "Verified against the open Gurovic et al. text; the edge is grounded to the canonical oxidative predicate for the fungal MnP ligninolysis claim."
              }
            ],
            "predicate_id": "METPO:2007803"
          },
          {
            "subject": "glucose",
            "predicate": "negatively regulates",
            "object": "lignocellulolytic_gene_expression",
            "description": "Simple sugars/glucose trigger carbon catabolite repression that represses lignocellulolytic gene expression.",
            "evidence": [
              {
                "reference": "DOI:10.1093/jambio/lxac002",
                "snippet": "glucose is a repressor of fungal cellulolytic enzymes",
                "notes": "Verified against the open Gurovic et al. text; the edge is a broad carbon-catabolite-repression regulatory edge."
              }
            ],
            "predicate_id": "RO:0002212"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-06-02T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate ECOLOGY trait (saprotrophy/decomposer) from literature research to fill the trophic-ecology gap.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-09T14:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (saprotrophy / decomposition) with RO/biolink predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 7 evidence-backed generic edges (11 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:16Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:17234\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:29Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 3 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:18246\u00d71, CHEBI:61266\u00d71, CHEBI:6457\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:36Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000013\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-26T07:15:16Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A072TFX8\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:21:11Z",
        "curator": "claude",
        "action": "RETRACT_DEAD_UNIPROT_GROUNDINGS",
        "changes": "Retracted 1 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:23:52Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (InterPro:IPR017761\u00d71, GO:0016689\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T02:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES_PART2",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates onto their causal-graph counterparts (1 to hydrolyzes), issue 301 part 2. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Each replacement is a 1:1 mirror of its source predicate that changes only the domain, so the claim each edge makes is unchanged and directions are unchanged. The replacements are proposed in proposals/metpo_traitmech_v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope saprotrophy_decomposition_cycling=NONMECHANISTIC with scope_notes; marked 3 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (extracellular_exoenzymes, cellulolytic_enzymes, cazymes).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-04T07:00:00Z",
        "curator": "codex",
        "action": "REVIEW_CAUSAL_EVIDENCE",
        "changes": "Reviewed the saprotrophy_decomposition_cycling graph for issue #183: added exact snippets to 2 record-level evidence items and 9 decomposition and lignocellulose causal-edge evidence entries, grounded 6 residual predicates, and preserved the graph as a nonmechanistic saprotrophy classification. No paid research service was called.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-07T04:24:00Z",
        "curator": "codex",
        "action": "ADVERSARIAL_REVIEW_REPAIR",
        "changes": "Addressed PR #664 adversarial review issue #686: replaced fragmented ring-shape, soil-life-history, heat-shock, and ligninolysis snippets with exact source spans that carry their edge claims.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-07T20:05:00Z",
        "curator": "codex",
        "action": "ADVERSARIAL_REVIEW_REPAIR",
        "changes": "Addressed PR #664 adversarial review issue #696: requoted the CAZyme hemicellulose edge with Cragg et al. enzymatic cellulose-and-hemicellulose depolymerization support.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000050",
    "label": "soil-dwelling",
    "definition": "A habitat association in which an organism's primary environment is soil, a complex and highly diverse microbial habitat central to terrestrial biogeochemical cycling.",
    "definition_source": "DOI:10.1038/nrmicro.2017.87",
    "trait_category": "ECOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "traitmech:000047"
    ],
    "synonyms": [
      {
        "synonym_text": "soil-associated",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1038/nrmicro.2017.87"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/nrmicro.2017.87",
        "snippet": "a gram of soil can contain thousands of individual microbial taxa",
        "notes": "Verified against the Fierer review; it frames soil as a diverse, complex microbial habitat rather than a single uniform niche."
      },
      {
        "reference": "DOI:10.1038/nrmicro1341",
        "snippet": "free-living microbial taxa exhibit biogeographic patterns",
        "notes": "Verified against the Martiny et al. abstract; environmental selection and spatial structure support treating soil association as habitat ecology, not simple taxonomic membership."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1423",
        "taxon_label": "Bacillus subtilis",
        "note": "soil bacterium",
        "reference": "DOI:10.1111/j.1574-6941.1999.tb00555.x"
      },
      {
        "taxon_id": "NCBITaxon:1902",
        "taxon_label": "Streptomyces coelicolor",
        "note": "soil actinomycete",
        "reference": "PMID:12000953"
      },
      {
        "taxon_id": "NCBITaxon:294",
        "taxon_label": "Pseudomonas fluorescens",
        "note": "rhizosphere soil bacterium",
        "reference": "PMID:23350846"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "soil_dwelling_biogeochemistry",
        "title": "Soil-dwelling microbes in soil life-history contexts",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This broad ecological, host-relationship, habitat, or hazard classification spans multiple taxa and mechanisms; contextual protein nodes do not receive token UniProt examples.",
        "description": "Evidence-backed nonmechanistic sketch connecting soil habitat, biogeochemical cycling, and community-level oligotrophy, growth, motility, dormancy, and genomic life-history axes.",
        "nodes": [
          {
            "node_id": "soil_dwelling_trait",
            "label": "soil-dwelling",
            "node_type": "TRAIT",
            "grounding": "traitmech:000050",
            "description": "Persistent residence in soil habitat."
          },
          {
            "node_id": "soil_habitat",
            "label": "soil habitat",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Complex terrestrial soil environment."
          },
          {
            "node_id": "biogeochemical_cycling",
            "label": "biogeochemical cycling",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Microbially mediated cycling of C, N, S, and other elements in soils."
          },
          {
            "node_id": "low_organic_carbon",
            "label": "low available organic carbon",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Carbon-limited (oligotrophic) soil conditions."
          },
          {
            "node_id": "oligotrophic_lifestyle",
            "label": "oligotrophic lifestyle",
            "node_type": "STATE",
            "description": "Slow-growing, streamlined small-genome strategy with reduced motility/chemotaxis."
          },
          {
            "node_id": "soil_resource_availability",
            "label": "soil resource availability and moisture",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Resource-rich, humid, acid-neutral soil conditions favoring growth."
          },
          {
            "node_id": "aridity",
            "label": "soil aridity",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Dry soil moisture conditions / water limitation."
          },
          {
            "node_id": "potential_growth_rate",
            "label": "soil microbiome potential growth rate",
            "node_type": "QUALITY",
            "description": "Community-level potential growth rate of soil microbes."
          },
          {
            "node_id": "soil_carbon_availability",
            "label": "high soil carbon availability",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Carbon-rich soil microsites such as rhizosphere/surface soil."
          },
          {
            "node_id": "flagellar_motility",
            "label": "flagellar motility",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Flagellum-dependent cell motility.",
            "grounding": "GO:0071973"
          },
          {
            "node_id": "climate_extreme_event",
            "label": "extreme heat event",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Experimental heat disturbance in soil."
          },
          {
            "node_id": "dormancy_sporulation",
            "label": "dormancy and sporulation gene program",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Genetic programs for dormancy and spore formation."
          },
          {
            "node_id": "soil_pH_precip_cn",
            "label": "soil pH, precipitation and C:N",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Edaphic and climatic drivers (pH, annual precipitation, soil C:N ratio)."
          },
          {
            "node_id": "life_history_axes",
            "label": "soil bacterial life-history strategy axes",
            "node_type": "STATE",
            "description": "Genomic life-history strategy axes (MCOA1/MCOA2) of soil bacterial communities."
          },
          {
            "node_id": "soil_life_history_activity_context",
            "label": "soil life-history and activity context",
            "node_type": "STATE",
            "description": "Community-level soil microbial context spanning oligotrophy, growth potential, motility, dormancy/sporulation, and genomic life-history axes."
          }
        ],
        "edges": [
          {
            "subject": "soil_dwelling_trait",
            "predicate": "contributes to",
            "object": "biogeochemical_cycling",
            "description": "Soil microbes contribute to terrestrial biogeochemical cycling.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro.2017.87",
                "snippet": "specific microbial controls on soil processes",
                "notes": "Verified against the Fierer review; soil microbial processes include nutrient transformations and organic carbon-pool dynamics."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "low_organic_carbon",
            "predicate": "associated with",
            "object": "oligotrophic_lifestyle",
            "description": "Low-carbon soil gradients are associated with oligotrophic taxa carrying small genomes, lower potential growth rates, and fewer chemotaxis/motility genes.",
            "evidence": [
              {
                "reference": "DOI:10.1093/ismeco/ycae081",
                "snippet": "chemotaxis and motility were under-represented",
                "notes": "Verified against the open ISME Communications full text; the edge is retained as an ecological association rather than a deterministic carbon-to-genome mechanism."
              }
            ],
            "predicate_id": "biolink:associated_with"
          },
          {
            "subject": "soil_resource_availability",
            "predicate": "associated with",
            "object": "potential_growth_rate",
            "description": "Resource-rich, humid, acid-neutral soils are associated with higher microbiome potential growth.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-024-53753-w",
                "snippet": "exhibit high potential growth rates",
                "notes": "Verified against the open Nature Communications abstract; the global pattern is observational, so the edge no longer uses a direct positive-regulation predicate."
              }
            ],
            "predicate_id": "biolink:associated_with"
          },
          {
            "subject": "aridity",
            "predicate": "associated with",
            "object": "potential_growth_rate",
            "description": "Dry and resource-poor soils are associated with lower soil microbiome potential growth rates.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-024-53753-w",
                "snippet": "display lower potential growth rates",
                "notes": "Verified against the open Nature Communications abstract; the study reports a macroscale association across soil microbiomes."
              }
            ],
            "predicate_id": "biolink:associated_with"
          },
          {
            "subject": "soil_carbon_availability",
            "predicate": "associated with",
            "object": "flagellar_motility",
            "description": "High soil carbon availability is associated with greater community-level prevalence of flagellar motility genes.",
            "evidence": [
              {
                "reference": "DOI:10.1093/ismejo/wrae067",
                "snippet": "prevalence of flagellar motility is positively associated with soil C availability",
                "notes": "Verified against the open ISME Journal full text; glucose amendment and four field gradients support the association."
              }
            ],
            "predicate_id": "biolink:associated_with"
          },
          {
            "subject": "climate_extreme_event",
            "predicate": "increases",
            "object": "dormancy_sporulation",
            "description": "Experimental heat treatment increased soil dormancy and sporulation gene abundance.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41586-024-08185-3",
                "snippet": "enhancing dormancy and sporulation genes",
                "notes": "Verified against the open Nature abstract; the curated edge is narrowed to heat because the abstract identifies heat, not all imposed extremes, as the treatment enhancing dormancy and sporulation genes."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "soil_pH_precip_cn",
            "predicate": "associated with",
            "object": "life_history_axes",
            "description": "Soil pH, precipitation and C:N are associated with soil bacterial life-history genomic axes in random-forest models.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-023-01465-0",
                "snippet": "Random forest analyses show that soil pH, C:N ratio and precipitation patterns together drive the dominant life history strategy of soil bacterial communities and their biogeographic distribution",
                "notes": "Verified against the PubMed abstract for the Nature Microbiology article; the edge is scoped as community-level statistical association."
              }
            ],
            "predicate_id": "biolink:associated_with"
          },
          {
            "subject": "soil_habitat",
            "predicate": "associated with",
            "object": "soil_life_history_activity_context",
            "description": "Soil habitat provides the heterogeneous ecological context in which resident microbes partition across multiple activity and life-history strategies.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro.2017.87",
                "snippet": "categorize soil microorganisms on the basis of their ecological strategies",
                "notes": "Verified against the Fierer review; the connector groups soil-associated community branches without asserting a single universal soil-dwelling mechanism."
              }
            ],
            "predicate_id": "biolink:associated_with"
          },
          {
            "subject": "oligotrophic_lifestyle",
            "predicate": "associated with",
            "object": "soil_life_history_activity_context",
            "description": "Oligotrophic taxa in low-carbon soils are one branch of the community-level soil life-history context.",
            "evidence": [
              {
                "reference": "DOI:10.1093/ismeco/ycae081",
                "snippet": "diverse array of ecological strategies used by soil bacteria",
                "notes": "Verified against the open ISME Communications full text; oligotroph-enriched taxa are treated as a carbon-gradient association within soils."
              }
            ],
            "predicate_id": "biolink:associated_with"
          },
          {
            "subject": "potential_growth_rate",
            "predicate": "associated with",
            "object": "soil_life_history_activity_context",
            "description": "Potential community growth rate is an activity axis associated with moisture and resource gradients across soils.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-024-53753-w",
                "snippet": "spatial variation of microbial potential growth rates",
                "notes": "Verified against the open Nature Communications abstract; the Zhou et al. global survey models soil microbiome potential growth as a community-level ecological axis."
              }
            ],
            "predicate_id": "biolink:associated_with"
          },
          {
            "subject": "flagellar_motility",
            "predicate": "associated with",
            "object": "soil_life_history_activity_context",
            "description": "Flagellar-motility gene prevalence is a carbon-associated mobility branch in soil communities.",
            "evidence": [
              {
                "reference": "DOI:10.1093/ismejo/wrae067",
                "snippet": "prevalence of flagellar motility in bacterial communities and soil C availability",
                "notes": "Verified against the open ISME Journal full text; Ramoneda et al. connect flagellar prevalence with soil carbon availability across community datasets."
              }
            ],
            "predicate_id": "biolink:associated_with"
          },
          {
            "subject": "dormancy_sporulation",
            "predicate": "associated with",
            "object": "soil_life_history_activity_context",
            "description": "Dormancy and sporulation gene programs are stress-response branches in disturbed soil communities.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41586-024-08185-3",
                "snippet": "soil microbiomes from different climates share unified responses to extreme climatic events",
                "notes": "Verified against the open Nature abstract; heat-enhanced dormancy/sporulation abundance is retained as a soil disturbance context."
              }
            ],
            "predicate_id": "biolink:associated_with"
          },
          {
            "subject": "life_history_axes",
            "predicate": "associated with",
            "object": "soil_life_history_activity_context",
            "description": "The soil bacterial MCOA axes summarize genomic life-history strategies associated with pH, C:N, and precipitation gradients.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-023-01465-0",
                "snippet": "drive the dominant life history strategy of soil bacterial communities",
                "notes": "Verified against the Nature Microbiology abstract; Piton et al. place soil pH, C:N ratio, and precipitation as predictors of community-level genomic strategy axes."
              }
            ],
            "predicate_id": "biolink:associated_with"
          },
          {
            "subject": "soil_habitat",
            "predicate": "associated with",
            "object": "soil_dwelling_trait",
            "description": "Soil habitat is associated with soil-resident microbes.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro.2017.87",
                "snippet": "a gram of soil can contain thousands of individual microbial taxa",
                "notes": "Verified against the Fierer review; the claim is habitat-level and does not assert a universal molecular mechanism for all soil microbes."
              }
            ],
            "predicate_id": "biolink:associated_with"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-06-02T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate ECOLOGY trait (soil-dwelling); sub-variant of habitat association.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-09T14:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (soil-dwelling / biogeochemical cycling) with RO predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 6 evidence-backed generic edges (11 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:09Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002213\u00d72, RO:0002212\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:29Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0003341\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 1 causal edge(s) off enables/RO:0002327 with a TRAIT object (1 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-17T06:00:00Z",
        "curator": "claude",
        "action": "REGROUND_CAUSAL_NODES",
        "changes": "Repaired a wrong CURIE from the kg-microbe name-match pass (issue 402): flagellar_motility: GO:0003341 -> GO:0071973. Was GO:0003341 'cilium movement'. Bacteria have flagella, not cilia, and the node says 'Flagellum-dependent cell motility' \u2014 the match was on the word 'motility' via the kg-microbe index (#402). Replaced with the term GO actually provides for this, resolved through the repo's own OAK adapter before being written rather than recalled.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope soil_dwelling_biogeochemistry=NONMECHANISTIC with scope_notes.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-04T00:20:00Z",
        "curator": "codex",
        "action": "REVIEW_CAUSAL_EVIDENCE",
        "changes": "Reviewed the broad soil_dwelling_biogeochemistry graph for issue #183: added verbatim snippets to 2 record-level and 8 edge-level evidence items, regrounded 5 broad ecological association edges to biolink:associated_with, and narrowed the extreme-climate statement to heat-induced dormancy/sporulation. No paid research service was called.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-04T12:00:00Z",
        "curator": "codex",
        "action": "CONNECT_CAUSAL_GRAPH_COMPONENTS",
        "changes": "Resolved issue #183 graph fragmentation (6 components to 1) by adding a soil life-history/activity context node and 6 source-backed association connectors. The connectors join broad soil community branches while preserving soil_dwelling_biogeochemistry as a nonmechanistic habitat graph. No paid research service was called.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-06T13:30:00Z",
        "curator": "codex",
        "action": "ADVERSARIAL_REVIEW_REPAIR",
        "changes": "Addressed PR #664 adversarial review issue #666: replaced borrowed snippets on the six soil_life_history_activity_context connectors with connector-specific exact snippets from the same supporting sources.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-07T04:24:00Z",
        "curator": "codex",
        "action": "ADVERSARIAL_REVIEW_REPAIR",
        "changes": "Addressed PR #664 adversarial review issue #686: replaced fragmented ring-shape, soil-life-history, heat-shock, and ligninolysis snippets with exact source spans that carry their edge claims.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-07T20:05:00Z",
        "curator": "codex",
        "action": "ADVERSARIAL_REVIEW_REPAIR",
        "changes": "Addressed PR #664 adversarial review issue #696: weakened the soil-habitat connector to an ecological association and requoted it with exact Fierer soil-diversity support.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000040",
    "label": "symbiosis",
    "definition": "An ecological lifestyle in which a microorganism lives in persistent physical association with a host or partner organism. It encompasses mutualism, commensalism, and parasitism, which form an evolutionary continuum.",
    "definition_source": "DOI:10.1073/pnas.1218525110",
    "trait_category": "ECOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "synonyms": [
      {
        "synonym_text": "symbiotic",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1073/pnas.1218525110"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1073/pnas.1218525110",
        "notes": "McFall-Ngai et al., \"Animals in a bacterial world\", supports persistent host-microbe association (symbiosis) as a pervasive microbial lifestyle; parent of the mutualism/commensalism/parasitism sub-variants."
      },
      {
        "reference": "DOI:10.1038/s41579-021-00550-7",
        "notes": "Drew et al. frame symbioses as a parasite-mutualist continuum, supporting symbiosis as the umbrella lifestyle for these interaction modes."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:9",
        "taxon_label": "Buchnera aphidicola",
        "note": "obligate aphid endosymbiont",
        "reference": "PMID:19909925"
      },
      {
        "taxon_id": "NCBITaxon:382",
        "taxon_label": "Sinorhizobium meliloti",
        "note": "legume root-nodule symbiont",
        "reference": "PMID:12620125"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "symbiosis_host_interaction",
        "title": "Symbiosis as persistent host-microbe interaction",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This broad ecological, host-relationship, habitat, or hazard classification spans multiple taxa and mechanisms; contextual protein nodes do not receive token UniProt examples.",
        "description": "Evidence-backed causal sketch linking host-microbe interaction to persistent symbiotic association along the parasite-mutualist continuum.",
        "nodes": [
          {
            "node_id": "symbiosis_trait",
            "label": "symbiosis",
            "node_type": "TRAIT",
            "grounding": "traitmech:000040",
            "description": "Persistent physical association with a host or partner."
          },
          {
            "node_id": "host_organism",
            "label": "host organism",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Eukaryotic or microbial partner with which the focal microbe persistently interacts."
          },
          {
            "node_id": "symbiotic_interaction",
            "label": "biological process involved in symbiotic interaction",
            "node_type": "BIOLOGICAL_PROCESS",
            "grounding": "GO:0044403",
            "description": "Persistent biological interaction between organisms living together."
          },
          {
            "node_id": "host_metabolites",
            "label": "host metabolites / exudates",
            "node_type": "CHEMICAL",
            "description": "Host-produced primary and specialized metabolites that act as chemoattractants and nutrients."
          },
          {
            "node_id": "chemotaxis_machinery",
            "label": "chemotaxis machinery",
            "node_type": "PATHWAY",
            "description": "Bacterial chemosensing and chemotaxis system that senses and follows host-derived gradients."
          },
          {
            "node_id": "host_colonization",
            "label": "host colonization",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Establishment of bacteria on or within host tissues, broadly required across mutualists and pathogens."
          },
          {
            "node_id": "biofilm_formation",
            "label": "biofilm formation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Aggregated surface-associated bacterial community that protects from host stresses and supports persistence.",
            "grounding": "GO:0042710"
          },
          {
            "node_id": "o_antigen",
            "label": "O-antigen",
            "node_type": "CHEMICAL",
            "description": "LPS O-antigen polysaccharide that cloaks MAMPs at the cell envelope."
          },
          {
            "node_id": "immune_evasion",
            "label": "immune evasion",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Avoidance of host innate immune detection during host association."
          },
          {
            "node_id": "host_cues",
            "label": "host-associated cues",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Host-niche signals such as iron, acidic pH, cationic peptides, divalent metals, and oxygen depletion."
          },
          {
            "node_id": "two_component_systems",
            "label": "two-component systems",
            "node_type": "PATHWAY",
            "description": "Sensor-regulator signaling systems that detect host-associated cues and trigger gene regulatory programs."
          },
          {
            "node_id": "outer_membrane_modification",
            "label": "outer-membrane modification",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Remodeling of the bacterial cell envelope in response to host-associated cues."
          },
          {
            "node_id": "adhesins",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Contextual protein family or multiprotein aggregate reviewed for this nonmechanistic classification; no single semantic family captures it.",
            "label": "adhesins",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Bacterial surface adhesins binding host receptors, a prerequisite for long-term colonization."
          }
        ],
        "edges": [
          {
            "subject": "host_organism",
            "predicate": "causes",
            "object": "symbiotic_interaction",
            "description": "Presence of a host or partner organism establishes the symbiotic interaction.",
            "evidence": [
              {
                "reference": "DOI:10.1073/pnas.1218525110",
                "notes": "McFall-Ngai et al. document host-microbe association as a pervasive feature of animal biology."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "symbiotic_interaction",
            "predicate": "confers",
            "object": "symbiosis_trait",
            "description": "Sustained symbiotic interaction realizes the symbiotic lifestyle.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41579-021-00550-7",
                "notes": "Drew et al. frame symbioses as a parasite-mutualist continuum of persistent interactions."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "host_metabolites",
            "predicate": "sensed by",
            "object": "chemotaxis_machinery",
            "description": "Host-produced metabolites diffuse to create concentration gradients sensed by bacterial chemotaxis machinery.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuac048",
                "notes": "Host-produced metabolites act as chemoattractants; diffusion creates concentration gradients that bacteria sense and follow. Broad cross-system review (Wiesmann et al. 2023)."
              }
            ]
          },
          {
            "subject": "chemotaxis_machinery",
            "predicate": "promotes",
            "object": "host_colonization",
            "description": "Chemotaxis and motility direct bacteria toward host surfaces, promoting colonization across lifestyles.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuac048",
                "notes": "Chemotaxis and motility are broadly required across mutualists and pathogens; general edge spanning pathogenic, commensal, and mutualist lifestyles."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "adhesins",
            "predicate": "required for",
            "object": "host_colonization",
            "description": "Binding of bacterial adhesins to host receptors is a prerequisite for long-term host colonization.",
            "evidence": [
              {
                "reference": "DOI:10.3390/microorganisms12051026",
                "notes": "Binding of bacterial adhesins to host receptors is a prerequisite for the long-term colonization of bacteria; broad colonization review (Lin et al. 2024). Curated as a general adhesin node per report warning."
              }
            ]
          },
          {
            "subject": "biofilm_formation",
            "predicate": "supports",
            "object": "symbiotic_interaction",
            "description": "Biofilm formation protects bacteria from host-secreted antimicrobials and stresses, supporting persistent host association.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuac048",
                "notes": "After colonization, biofilm formation protects bacteria from host-secreted antimicrobial peptides and other stresses, supporting persistence. Strong conserved persistence edge."
              }
            ]
          },
          {
            "subject": "o_antigen",
            "predicate": "contributes to",
            "object": "immune_evasion",
            "description": "O-antigen presence contributes to immune evasion, partly by cloaking MAMPs from host recognition.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuac048",
                "notes": "O-antigen presence contributes to immune evasion, partly by cloaking MAMPs; strong envelope-modification edge across host systems."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "immune_evasion",
            "predicate": "promotes",
            "object": "host_colonization",
            "description": "Evading host innate immune detection enables sustained colonization.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuac048",
                "notes": "Loss of O-antigen induces TLR4 activation and ROS bursts, impairing colonization; conversely immune evasion supports colonization (Wiesmann et al. 2023)."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "host_cues",
            "predicate": "sensed by",
            "object": "two_component_systems",
            "description": "Two-component systems sense host-associated cues such as iron, acidic pH, cationic peptides, and oxygen depletion.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuac048",
                "notes": "Two-component systems sense host-associated cues (iron, acidic pH, cationic peptides, divalent metals, oxygen depletion). Strong regulatory edge with generic node."
              }
            ]
          },
          {
            "subject": "two_component_systems",
            "predicate": "triggers",
            "object": "outer_membrane_modification",
            "description": "Two-component systems trigger gene regulatory programs leading to outer-membrane modification and biofilm formation.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuac048",
                "notes": "TCSs trigger gene regulatory programs that causally lead to specialized metabolism, outer-membrane modification, and biofilm formation. High-level mechanistic umbrella edge."
              }
            ]
          },
          {
            "subject": "two_component_systems",
            "predicate": "triggers",
            "object": "biofilm_formation",
            "description": "Two-component system signaling promotes biofilm formation as part of host-cue-triggered programs.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuac048",
                "notes": "TCSs trigger gene regulatory programs that causally lead to outer-membrane modification and biofilm formation."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-06-02T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate ECOLOGY axis class (symbiosis) from literature research to fill the host-interaction lifestyle gap; parent of mutualism, commensalism, parasitism, and endosymbiosis.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-09T14:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (host-microbe symbiotic interaction) with GO node grounding and RO/biolink predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 9 evidence-backed generic edges (10 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:09Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002213\u00d72, RO:0002326\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:29Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0042710\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 1 causal edge(s) off enables/RO:0002327 with a TRAIT object (1 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-21T08:00:00Z",
        "curator": "codex",
        "action": "NORMALISE_NODE_TYPE",
        "changes": "Tranche 5 of issue 356 settles the process/quality families and merges ids that meant the same sense: immune_evasion is BIOLOGICAL_PROCESS. Immune evasion is the avoidance or subversion of host defenses. The edges treat it as an enabled action that in turn enables colonization; capsule.yaml's 'reduced recognition and clearance' is the outcome of that same process, not a separate measurable axis.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope symbiosis_host_interaction=NONMECHANISTIC with scope_notes; marked 1 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (adhesins).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1003003",
    "label": "acidophilic",
    "definition": "A pH growth preference in which an organism grows optimally at pH values below 5.",
    "definition_source": "DOI:10.1038/nrmicro2549",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1003000"
    ],
    "synonyms": [
      {
        "synonym_text": "acidophil",
        "synonym_type": "EXACT_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "acidophile",
        "synonym_type": "EXACT_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/nrmicro2549",
        "snippet": "growing at pH 1.0-3.0",
        "notes": "Supports acidophilic growth at strongly acidic external pH."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:46632",
        "taxon_label": "Picrophilus oshimae",
        "note": "Among the most extreme acidophiles known - growth optimum ~pH 0.7, grows near pH 0; co-canonical with P. torridus.",
        "reference": "DOI:10.1073/pnas.0401356101"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "acidophilic_ph_homeostasis",
        "title": "Acidophilic pH homeostasis mechanism",
        "description": "Evidence-backed causal sketch linking acidophily to acidic environments, proton exclusion, and cytoplasmic pH homeostasis.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a broad environmental or morphological classification spanning multiple mechanisms, a measurement-like bin, or an absence/arrangement descriptor; contextual protein nodes do not receive token UniProt examples.",
        "nodes": [
          {
            "node_id": "acidophilic_trait",
            "label": "acidophilic",
            "node_type": "TRAIT",
            "grounding": "METPO:1003003",
            "description": "Optimal growth occurs at acidic pH."
          },
          {
            "node_id": "acidic_external_ph",
            "label": "acidic external pH",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "External pH below neutral, often below pH 5 for acidophiles.",
            "grounding": "PATO:0001429"
          },
          {
            "node_id": "proton",
            "label": "proton",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:15378",
            "description": "Hydrogen ion whose gradient threatens cytoplasmic pH."
          },
          {
            "node_id": "cytoplasmic_ph_homeostasis",
            "label": "cytoplasmic pH homeostasis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Maintenance of a less acidic cytoplasm during growth at low pH.",
            "grounding": "GO:0051453"
          },
          {
            "node_id": "low_proton_permeability_membrane",
            "label": "low proton permeability membrane",
            "node_type": "CELLULAR_LOCALIZATION",
            "description": "Membrane properties that reduce inward proton leak."
          },
          {
            "node_id": "reversed_membrane_potential",
            "label": "inside-positive (reversed) membrane potential",
            "node_type": "STATE",
            "description": "Positive-inside membrane potential reducing proton influx."
          },
          {
            "node_id": "primary_proton_pumps",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "primary proton pumps",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Proton-pumping respiratory chain complexes that actively translocate protons."
          },
          {
            "node_id": "proton_coupled_atpases",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "proton-coupled ATPases",
            "node_type": "GENE_OR_PROTEIN",
            "description": "ATP-driven primary pumps that actively transport protons across the membrane."
          },
          {
            "node_id": "cation_pumping",
            "label": "pumping K+ and Na+ into cytoplasm",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Active uptake of K+ and Na+ that reduces proton influx by electrostatic repulsion."
          },
          {
            "node_id": "hopanoid_and_membrane_proteins",
            "label": "hopanoid lipids and membrane proteins (Omp40, PspA)",
            "node_type": "CELLULAR_LOCALIZATION",
            "description": "Structural membrane adaptations (hopanoid lipids, Omp40, PspA) used for proton exclusion."
          },
          {
            "node_id": "proton_exclusion",
            "label": "proton exclusion",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Exclusion of protons from the cytoplasm via membrane adaptations."
          },
          {
            "node_id": "bipolar_tetraether_lipids",
            "label": "bipolar tetraether lipids (GDNT/GDGT)",
            "node_type": "CHEMICAL",
            "description": "Archaeal monolayer-forming tetraether membrane lipids reducing passive proton permeability."
          },
          {
            "node_id": "low_passive_proton_permeability",
            "label": "low passive proton permeability",
            "node_type": "QUALITY",
            "description": "A low passive proton permeability allowing maintenance of near-neutral intracellular pH."
          }
        ],
        "edges": [
          {
            "subject": "acidic_external_ph",
            "predicate": "selects for",
            "object": "acidophilic_trait",
            "description": "Acidic environments select for organisms whose optimal growth is below neutral pH.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2549",
                "snippet": "growing at pH 1.0-3.0",
                "notes": "Review supports growth of extreme acidophiles at strongly acidic pH."
              }
            ],
            "predicate_id": "METPO:2007401"
          },
          {
            "subject": "acidic_external_ph",
            "predicate": "increases gradient of",
            "object": "proton",
            "description": "Acidic external pH imposes a proton gradient across the membrane.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.tim.2007.02.005",
                "snippet": "major contributor to the proton motive force",
                "notes": "Review links low-pH growth to the transmembrane proton gradient."
              }
            ],
            "predicate_id": "METPO:2007601"
          },
          {
            "subject": "low_proton_permeability_membrane",
            "predicate": "limits influx of",
            "object": "proton",
            "description": "Low proton permeability helps acidophiles avoid cytoplasmic acidification.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.tim.2007.02.005",
                "snippet": "highly impermeable cell membranes",
                "notes": "Supports membrane impermeability as an acidophile mechanism."
              }
            ]
          },
          {
            "subject": "reversed_membrane_potential",
            "predicate": "mitigates influx of",
            "object": "proton",
            "description": "A reversed membrane potential can reduce inward proton movement.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.tim.2007.02.005",
                "snippet": "reversed membrane potential",
                "notes": "Supports reversed membrane potential as a shared acidophile feature."
              }
            ]
          },
          {
            "subject": "cytoplasmic_ph_homeostasis",
            "predicate": "confers",
            "object": "acidophilic_trait",
            "description": "Acidophilic growth requires maintaining cytoplasmic pH compatible with biomolecular function.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2549",
                "snippet": "maintain a cytoplasmic pH of approximately 6.0",
                "notes": "Supports cytoplasmic pH homeostasis during growth at low external pH."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "primary_proton_pumps",
            "predicate": "catalyzes active transport of",
            "object": "proton",
            "description": "Primary proton pumps such as respiratory-chain complexes actively export protons, contributing to pH homeostasis.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2549",
                "notes": "primary proton pumps such as the proton-pumping respiratory chain complexes"
              }
            ]
          },
          {
            "subject": "proton_coupled_atpases",
            "predicate": "catalyzes active transport of",
            "object": "proton",
            "description": "Proton-coupled ATPases actively transport protons across the membrane.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2549",
                "notes": "Such transporters include primary proton pumps such as proton-coupled ATPases"
              }
            ]
          },
          {
            "subject": "acidic_external_ph",
            "predicate": "selects for",
            "object": "cytoplasmic_ph_homeostasis",
            "description": "Low external pH / acid challenge imposes the demands of cytoplasmic pH homeostasis, a unifying principle of bacterial pH homeostasis.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2549",
                "notes": "A major unifying principle of bacterial pH homeostasis... the demands of pH homeostasis"
              }
            ],
            "predicate_id": "METPO:2007401"
          },
          {
            "subject": "cation_pumping",
            "predicate": "reduces influx of",
            "object": "proton",
            "description": "Pumping K+ and Na+ into the cytoplasm reduces proton influx by electrostatic repulsion.",
            "evidence": [
              {
                "reference": "DOI:10.1111/1758-2229.70019",
                "notes": "can pump cations such as K+ and Na+ into the cytoplasm to reduce the influx of protons by electrostatic repulsion"
              }
            ]
          },
          {
            "subject": "hopanoid_and_membrane_proteins",
            "predicate": "enables",
            "object": "proton_exclusion",
            "description": "Hopanoid lipids and membrane proteins (Omp40, PspA) are structural adaptations used for proton exclusion.",
            "evidence": [
              {
                "reference": "DOI:10.1111/1758-2229.70019",
                "notes": "hopanoid lipids... or membrane proteins such as Omp40 and PspA, are structural adaptations used for proton exclusion"
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "bipolar_tetraether_lipids",
            "predicate": "maintains",
            "object": "low_passive_proton_permeability",
            "description": "Bipolar tetraether lipids maintain a low passive proton permeability, enabling a near-neutral intracellular pH.",
            "evidence": [
              {
                "reference": "DOI:10.3389/frbis.2023.1338019",
                "notes": "As such, a low passive proton permeability and a near neutral intracellular pH can be maintained"
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.938355+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-11T00:00:00-07:00",
        "curator": "codex",
        "action": "CURATED_WITH_LITERATURE",
        "changes": "Reviewed acidophilic trait and added DOI-backed evidence and causal graph for acidic pH homeostasis.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:29Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T21:30:06Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007401\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:37:59Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0030641\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T08:14:32Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (PATO:0001428\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-14T07:26:18Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007601\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-15T07:20:36Z",
        "curator": "claude",
        "action": "FIX_NODE_GROUNDING_CURIE",
        "changes": "Overwrote 1 causal-node grounding(s) (obsolete/wrong GO -> corrected, verified vs OAK).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-15T07:21:43Z",
        "curator": "claude",
        "action": "FIX_NODE_GROUNDING_CURIE",
        "changes": "Overwrote 1 pH causal-node grounding(s) to corrected PATO CURIEs (phase-2; verified vs OAK).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 6 evidence-backed generic edges (7 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:09Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007401\u00d71, RO:0002327\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 1 causal edge(s) off enables/RO:0002327 with a TRAIT object (1 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-21T08:00:00Z",
        "curator": "codex",
        "action": "NORMALISE_NODE_TYPE",
        "changes": "Tranche 5 of issue 356 settles the process/quality families and merges ids that meant the same sense: reversed_membrane_potential is STATE. A reversed membrane potential is an inside-positive electrical state, not the process that establishes it. The schema names this gradient/steady-value distinction explicitly.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope acidophilic_ph_homeostasis=NONMECHANISTIC with scope_notes; marked 2 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (primary_proton_pumps, proton_coupled_atpases).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1003008",
    "label": "acidotolerant",
    "definition": "A pH growth preference characterized by the ability to tolerate acidic environments (typically pH below 5.5) while maintaining optimal growth near neutral pH.",
    "definition_source": "DOI:10.1038/nrmicro2549",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1003000"
    ],
    "synonyms": [
      {
        "synonym_text": "aciduric",
        "synonym_type": "EXACT_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "created_by": "Jed Dongjin Kim-Ozaeta",
    "evidence": [
      {
        "reference": "DOI:10.1038/nrmicro2549",
        "snippet": "tolerate and grow at external pH values",
        "notes": "Supports acidotolerance as growth or survival under otherwise stressful external pH conditions."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1579",
        "taxon_label": "Lactobacillus acidophilus",
        "note": "tolerates/produces acid",
        "reference": "PMID:15345415"
      },
      {
        "taxon_id": "NCBITaxon:435",
        "taxon_label": "Acetobacter aceti",
        "note": "acetic-acid tolerant",
        "reference": "PMID:17920150"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "acidotolerant_acid_stress_homeostasis",
        "title": "Acidotolerant acid-stress pH homeostasis mechanism",
        "description": "Evidence-backed causal sketch linking acidotolerance to acidic exposure and maintenance of cytoplasmic pH near compatibility with growth.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a broad environmental or morphological classification spanning multiple mechanisms, a measurement-like bin, or an absence/arrangement descriptor; contextual protein nodes do not receive token UniProt examples.",
        "nodes": [
          {
            "node_id": "acidotolerant_trait",
            "label": "acidotolerant",
            "node_type": "TRAIT",
            "grounding": "METPO:1003008",
            "description": "Tolerates acidic conditions despite neutral-pH growth optimum."
          },
          {
            "node_id": "acidic_exposure",
            "label": "acidic exposure",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "External acidic pH stress."
          },
          {
            "node_id": "proton",
            "label": "proton",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:15378",
            "description": "Hydrogen ion contributing to acid stress."
          },
          {
            "node_id": "cytoplasmic_ph_homeostasis",
            "label": "cytoplasmic pH homeostasis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Cellular control of internal pH during acid stress.",
            "grounding": "GO:0051453"
          },
          {
            "node_id": "proton_efflux_transport",
            "label": "proton efflux transport",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "Export or exclusion of excess protons from the cytoplasm."
          },
          {
            "node_id": "amino_acid_decarboxylation",
            "label": "amino-acid decarboxylase system",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Proton-consuming amino-acid decarboxylation (e.g. glutamate/Gad system) that consumes intracellular H+."
          },
          {
            "node_id": "membrane_lipid_remodeling",
            "label": "membrane lipid remodeling",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Changes in membrane lipid composition (e.g. cyclopropane fatty acid formation, altered saturated/unsaturated ratio) increasing acid resistance."
          },
          {
            "node_id": "inward_proton_leakage",
            "label": "inward proton leakage",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Passive entry of protons across the membrane that challenges cytoplasmic pH homeostasis."
          },
          {
            "node_id": "cation_proton_antiport",
            "label": "cation/H+ antiport",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "Na+/H+ and K+/H+ antiporter activity exchanging cations for protons to stabilize intracellular pH."
          }
        ],
        "edges": [
          {
            "subject": "acidic_exposure",
            "predicate": "challenges",
            "object": "acidotolerant_trait",
            "description": "Acidotolerant organisms withstand acidic external pH that can be toxic to non-adapted cells.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2549",
                "snippet": "external pH values that would otherwise be toxic",
                "notes": "Review supports pH tolerance as adaptation to toxic external pH."
              }
            ],
            "predicate_id": "METPO:2007406"
          },
          {
            "subject": "acidic_exposure",
            "predicate": "increases influx pressure of",
            "object": "proton",
            "description": "Acid exposure increases proton pressure on the cytoplasmic membrane.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.tim.2007.02.005",
                "snippet": "rate at which protons leak inward",
                "notes": "Acidophile review frames proton leak as a pH-homeostasis challenge."
              }
            ]
          },
          {
            "subject": "proton_efflux_transport",
            "predicate": "removes",
            "object": "proton",
            "description": "Proton export helps prevent excessive cytoplasmic acidification.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.tim.2007.02.005",
                "snippet": "remove excess protons from the cytoplasm",
                "notes": "Supports active proton removal as an acid-stress mechanism."
              }
            ]
          },
          {
            "subject": "cytoplasmic_ph_homeostasis",
            "predicate": "confers",
            "object": "acidotolerant_trait",
            "description": "Acid tolerance depends on maintaining cytoplasmic pH during acid challenge.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2549",
                "snippet": "bacterial pH homeostasis is a cell-wide physiological process",
                "notes": "Supports pH homeostasis as a broad mechanism for acid tolerance."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "amino_acid_decarboxylation",
            "predicate": "maintains",
            "object": "cytoplasmic_ph_homeostasis",
            "description": "Amino-acid decarboxylation (e.g. GadA/B converting glutamate to GABA + CO2) consumes intracellular H+ and sustains cytoplasmic pH homeostasis under acid stress.",
            "evidence": [
              {
                "reference": "DOI:10.3390/microorganisms12091774",
                "notes": "GadA/B decarboxylate glutamate to GABA + CO2 while consuming intracellular H+; broadly reusable proton-consuming module across bacteria/LAB."
              }
            ]
          },
          {
            "subject": "membrane_lipid_remodeling",
            "predicate": "increases",
            "object": "acidotolerant_trait",
            "description": "Membrane lipid remodeling (e.g. conversion of unsaturated to cyclopropane fatty acids) reduces proton permeability and improves acid resistance.",
            "evidence": [
              {
                "reference": "DOI:10.3390/microorganisms12091774",
                "notes": "Membrane lipids enhance acid resistance by altering saturated/unsaturated ratios or converting unsaturated fatty acids to cyclopropane fatty acids; generic membrane mechanism."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "membrane_lipid_remodeling",
            "predicate": "decreases",
            "object": "inward_proton_leakage",
            "description": "Changes in membrane lipids and porins minimize passive inward proton leakage, a broad cross-taxon pH-homeostasis mechanism.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2549",
                "notes": "Krulwich review: changes in membrane lipids and porins minimize inward proton leakage."
              }
            ],
            "predicate_id": "RO:0002212"
          },
          {
            "subject": "inward_proton_leakage",
            "predicate": "challenges",
            "object": "cytoplasmic_ph_homeostasis",
            "description": "Inward proton leakage raises cytoplasmic proton load, opposing maintenance of internal pH.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2549",
                "notes": "pH homeostasis must counter inward proton leakage to keep cytoplasmic pH near neutral."
              }
            ],
            "predicate_id": "METPO:2007406"
          },
          {
            "subject": "cation_proton_antiport",
            "predicate": "contributes to",
            "object": "cytoplasmic_ph_homeostasis",
            "description": "Na+/H+ and K+/H+ antiporters exchange cations for protons to stabilize intracellular pH, a core cross-bacterial homeostasis mechanism.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2549",
                "notes": "Na+/H+ and K+/H+ antiporters support cytoplasmic pH control; generic across bacteria."
              }
            ],
            "predicate_id": "RO:0002326"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.941434+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-11T00:00:00-07:00",
        "curator": "codex",
        "action": "CURATED_WITH_LITERATURE",
        "changes": "Reviewed acidotolerant trait and added DOI-backed evidence and causal graph for acid-stress pH homeostasis.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:29Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T21:30:06Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007406\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:37:59Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0030641\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-15T07:20:36Z",
        "curator": "claude",
        "action": "FIX_NODE_GROUNDING_CURIE",
        "changes": "Overwrote 1 causal-node grounding(s) (obsolete/wrong GO -> corrected, verified vs OAK).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 5 evidence-backed generic edges (4 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:09Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 4 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002213\u00d71, METPO:2000017\u00d71, METPO:2007406\u00d71, RO:0002326\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 1 causal edge(s) off enables/RO:0002327 with a TRAIT object (1 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T02:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES_PART2",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates onto their causal-graph counterparts (1 to reduces), issue 301 part 2. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Each replacement is a 1:1 mirror of its source predicate that changes only the domain, so the claim each edge makes is unchanged and directions are unchanged. The replacements are proposed in proposals/metpo_traitmech_v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T06:00:00Z",
        "curator": "claude",
        "action": "REGROUND_CAUSAL_EDGE",
        "changes": "Relabelled 1 causal edge from `reduces` to `decreases` and re-grounded it from METPO:2007802 to RO:0002212 (negatively regulates), issue 330. The corpus wrote two senses under the single label `reduces` - genuine electron donation, and a lessens/decreases sense - and METPO:2007802 is defined as donating electrons to the object and lowering its oxidation state, which this edge does not assert. The two senses could not be separated mechanically because the label was identical, so they migrated together in issue 329 and were split here by reading each edge. RO:0002212 declares no rdfs:domain or rdfs:range, so this introduces no entailment of the kind issue 301 removed.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-16T02:00:00Z",
        "curator": "claude",
        "action": "NORMALISE_NODE_TYPE",
        "changes": "Under the PATHWAY-vs-BIOLOGICAL_PROCESS rule, one node_id means one thing corpus-wide (issue 356): amino_acid_decarboxylation is typed BIOLOGICAL_PROCESS. PATHWAY is a named, conventionally enumerable multi-step route; BIOLOGICAL_PROCESS is everything else. A REACTION CLASS, not a route. The corpus describes it that way in neutrophilic.yaml -- 'Enzyme-catalyzed decarboxylation reaction that consumes cytoplasmic protons' -- and the wording varies by record, so read that as the family's sense rather than as this record's own text. Named systems that implement it (Gad) would be pathways; the reaction class is not. Was 4 BIOLOGICAL_PROCESS to 2 before this tranche.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope acidotolerant_acid_stress_homeostasis=NONMECHANISTIC with scope_notes.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000602",
    "label": "aerobic",
    "definition": "An oxygen preference in which growth occurs in the presence of molecular oxygen (O\u2082), typically using O\u2082 as the terminal electron acceptor.",
    "definition_source": "PMID:21413255",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000601"
    ],
    "synonyms": [
      {
        "synonym_text": "Ox_aerobic",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "aerobe",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "xrefs": [
      "PATO:0001455"
    ],
    "evidence": [
      {
        "reference": "PMID:21413255",
        "snippet": "aerobes require molecular oxygen as a terminal electron acceptor",
        "notes": "Supports aerobic growth as oxygen-dependent respiration."
      },
      {
        "reference": "PMID:21183663",
        "snippet": "Bacillus subtilis is an aerobic spore-forming Gram-positive bacterium",
        "notes": "Organism example: Bacillus subtilis is described as aerobic."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:287",
        "taxon_label": "Pseudomonas aeruginosa",
        "note": "obligate aerobe (respiratory metabolism)",
        "reference": "PMID:31597590"
      },
      {
        "taxon_id": "NCBITaxon:1270",
        "taxon_label": "Micrococcus luteus",
        "note": "strict aerobe",
        "reference": "PMID:19948807"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "aerobic_trait_mechanism",
        "title": "Aerobic growth oxygen-use mechanism",
        "description": "Evidence-backed causal sketch linking the aerobic trait to oxygen-dependent respiration.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a broad environmental or morphological classification spanning multiple mechanisms, a measurement-like bin, or an absence/arrangement descriptor; contextual protein nodes do not receive token UniProt examples.",
        "nodes": [
          {
            "node_id": "aerobic_trait",
            "label": "aerobic",
            "node_type": "TRAIT",
            "grounding": "METPO:1000602",
            "description": "Growth occurs in the presence of molecular oxygen."
          },
          {
            "node_id": "aerobic_respiration",
            "label": "aerobic respiration",
            "node_type": "BIOLOGICAL_PROCESS",
            "grounding": "GO:0009060",
            "description": "Energy release process requiring oxygen as terminal electron acceptor."
          },
          {
            "node_id": "molecular_oxygen",
            "label": "molecular oxygen",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:15379",
            "description": "Dioxygen used by aerobes as terminal electron acceptor."
          },
          {
            "node_id": "terminal_electron_acceptor",
            "label": "terminal electron acceptor",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "Functional role played by oxygen in aerobic respiration.",
            "grounding": "METPO:1007504"
          },
          {
            "node_id": "substrate_dehydrogenases",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "substrate dehydrogenases",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Dehydrogenases (e.g. NADH dehydrogenases) that feed electrons into the respiratory chain."
          },
          {
            "node_id": "quinone_pool",
            "label": "quinone pool",
            "node_type": "CHEMICAL",
            "description": "Membrane quinone pool (ubiquinone/menaquinone) carrying electrons in the respiratory chain."
          },
          {
            "node_id": "terminal_oxidases",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "terminal oxidases",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Respiratory quinol/cytochrome oxidases that reduce O2 to water as the final ETC step."
          },
          {
            "node_id": "proton_motive_force",
            "label": "proton motive force",
            "node_type": "STATE",
            "description": "Transmembrane electrochemical gradient generated by respiration that drives ATP synthesis.",
            "grounding": "METPO:1007500"
          },
          {
            "node_id": "atp_synthesis",
            "label": "ATP synthesis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Energy conservation by ATP synthase powered by the proton motive force.",
            "grounding": "GO:0006754"
          },
          {
            "node_id": "reactive_oxygen_species",
            "label": "reactive oxygen species",
            "node_type": "CHEMICAL",
            "description": "Superoxide, hydrogen peroxide and related species formed endogenously during aerobic respiration.",
            "grounding": "CHEBI:26523"
          },
          {
            "node_id": "ros_scavenging_enzymes",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "ROS-scavenging enzymes",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Superoxide dismutases, catalases and peroxidases that detoxify reactive oxygen species."
          }
        ],
        "edges": [
          {
            "subject": "aerobic_trait",
            "predicate": "depends on",
            "object": "molecular_oxygen",
            "description": "Aerobic growth depends on molecular oxygen availability.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.celrep.2023.112444",
                "snippet": "obligate aerobe ... exposed to hypoxia, stops growing",
                "notes": "Mycobacterium tuberculosis example supports oxygen dependence for aerobic growth."
              }
            ],
            "predicate_id": "RO:0002502"
          },
          {
            "subject": "aerobic_trait",
            "predicate": "has mechanistic process",
            "object": "aerobic_respiration",
            "description": "The aerobic trait is mechanistically tied to oxygen-dependent respiration.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.bbabio.2011.06.016",
                "snippet": "respiratory quinol:O2 oxidoreductase",
                "notes": "Review supports oxygen-reducing terminal oxidases as core aerobic respiratory enzymes."
              }
            ]
          },
          {
            "subject": "aerobic_respiration",
            "predicate": "depends on",
            "object": "molecular_oxygen",
            "description": "Aerobic respiration requires oxygen.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.celrep.2023.112444",
                "snippet": "transfer electrons from the ETC to O2",
                "notes": "Supports molecular oxygen as the terminal acceptor for bacterial respiratory electron transport."
              }
            ],
            "predicate_id": "RO:0002502"
          },
          {
            "subject": "molecular_oxygen",
            "predicate": "acts as",
            "object": "terminal_electron_acceptor",
            "description": "In aerobic energy metabolism, molecular oxygen acts as the terminal electron acceptor.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.celrep.2023.112444",
                "snippet": "terminal oxidases transfer electrons from the ETC to O2",
                "notes": "Supports oxygen's electron-acceptor role in terminal oxidase activity."
              }
            ]
          },
          {
            "subject": "substrate_dehydrogenases",
            "predicate": "transfers electrons to",
            "object": "quinone_pool",
            "description": "Substrate dehydrogenases pass electrons to the membrane quinone pool in the respiratory chain.",
            "evidence": [
              {
                "reference": "DOI:10.1128/ecosalplus.esp-0012-2015",
                "notes": "Electrons are transferred from substrate-specific dehydrogenases to a quinone pool (menaquinone, ubiquinone, dimethylmenaquinone)."
              }
            ],
            "predicate_id": "METPO:2007403"
          },
          {
            "subject": "quinone_pool",
            "predicate": "transfers electrons to",
            "object": "terminal_oxidases",
            "description": "Reduced quinol is oxidized by terminal oxidases that reduce O2 to water.",
            "evidence": [
              {
                "reference": "DOI:10.1128/ecosalplus.esp-0012-2015",
                "notes": "Quinol-to-O2 oxidation is catalyzed by quinol oxidases (cytochrome bo3, cytochrome bd) reducing O2 to H2O."
              }
            ],
            "predicate_id": "METPO:2007403"
          },
          {
            "subject": "terminal_oxidases",
            "predicate": "reduces",
            "object": "molecular_oxygen",
            "description": "Terminal oxidases catalyze the four-electron reduction of O2 to water.",
            "evidence": [
              {
                "reference": "DOI:10.3390/antiox13030383",
                "notes": "Terminal oxidases catalyze the four-electron reduction of O2 to water and generate the proton motive force for ATP."
              }
            ],
            "predicate_id": "METPO:2007802"
          },
          {
            "subject": "terminal_oxidases",
            "predicate": "generates",
            "object": "proton_motive_force",
            "description": "Respiratory terminal oxidases generate the proton motive force.",
            "evidence": [
              {
                "reference": "DOI:10.3390/antiox13030383",
                "notes": "Terminal oxidases catalyze reduction of O2 to water and generate the proton motive force for ATP."
              }
            ],
            "predicate_id": "biolink:produces"
          },
          {
            "subject": "proton_motive_force",
            "predicate": "powers",
            "object": "atp_synthesis",
            "description": "The transmembrane electrochemical gradient powers ATP synthesis.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41579-021-00583-y",
                "notes": "The transmembrane electrochemical gradient powers the membrane proteins that synthesize ATP."
              }
            ]
          },
          {
            "subject": "aerobic_respiration",
            "predicate": "generates",
            "object": "reactive_oxygen_species",
            "description": "Aerobic respiration produces ROS endogenously via respiratory flavoproteins.",
            "evidence": [
              {
                "reference": "DOI:10.30970/sbi.1702.716",
                "notes": "ROS are formed endogenously during aerobic respiration due to activity of respiratory flavoproteins."
              }
            ],
            "predicate_id": "biolink:produces"
          },
          {
            "subject": "ros_scavenging_enzymes",
            "predicate": "detoxifies",
            "object": "reactive_oxygen_species",
            "description": "SODs, catalases and peroxidases eliminate reactive oxygen species, enabling aerobic growth.",
            "evidence": [
              {
                "reference": "DOI:10.30970/sbi.1702.716",
                "notes": "Elimination of radicals via ROS-scavenging enzymes: superoxide dismutases (SODs), catalases and peroxidases."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.849227+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-05T01:09:05-07:00",
        "curator": "codex",
        "action": "CURATED_WITH_LITERATURE",
        "changes": "Added definition source and evidence for oxygen-dependent aerobic growth.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-05T18:39:46-07:00",
        "curator": "codex",
        "action": "ADDED_ORGANISM_EXAMPLE",
        "changes": "Added Bacillus subtilis organism example with PMID-backed evidence.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-07T00:00:00-07:00",
        "curator": "codex",
        "action": "ADDED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph for oxygen-dependent aerobic respiration.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "IMPROVED_CAUSAL_GRAPH_EVIDENCE",
        "changes": "Added DOI-backed edge evidence to the aerobic respiration causal graph.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-13T22:45:00-07:00",
        "curator": "codex",
        "action": "IMPROVED_CAUSAL_GRAPH_EVIDENCE",
        "changes": "Removed PMID and GO fallback references from CausalEdge evidence where DOI-backed evidence already supported the same oxygen-use mechanisms.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:41:03Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (METPO:1007504\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-26T05:00:47Z",
        "curator": "claude",
        "action": "RENAME_PREDICATE_LABELS",
        "changes": "Renamed 2 causal-edge predicate label(s) to align with existing groundings: requires \u2192 depends on \u00d72.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-26T05:00:49Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002502\u00d72).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-17T04:09:43Z",
        "curator": "claude",
        "action": "REMOVE_REDUNDANT_SYNONYM",
        "changes": "Removed 1 synonym(s) whose text duplicated the label (seeder redundancy; no information lost).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 7 evidence-backed generic edges (7 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:09Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 5 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007403\u00d72, biolink:produces\u00d72, METPO:2000017\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:30Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0006754\u00d71, CHEBI:26523\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T02:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES_PART2",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates onto their causal-graph counterparts (1 to reduces), issue 301 part 2. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Each replacement is a 1:1 mirror of its source predicate that changes only the domain, so the claim each edge makes is unchanged and directions are unchanged. The replacements are proposed in proposals/metpo_traitmech_v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-15T02:00:00Z",
        "curator": "claude",
        "action": "NORMALISE_NODE_TYPE",
        "changes": "Normalised causal-node type(s) so one node_id means one thing corpus-wide (issue 356): proton_motive_force: BIOLOGICAL_PROCESS -> STATE. The schema's OWN example of STATE: 'a bioenergetic or molecular state of the cell (e.g. proton motive force ...) ... the state is the gradient / steady-value, not its establishment'. All 35 occurrences describe the gradient -- every description across all four types reads 'electrochemical proton gradient', including the 13 typed BIOLOGICAL_PROCESS ('Transmembrane electrochemical gradient generated by respiration'), which name the gradient and its provenance rather than the generating process. Nothing here means the establishment, so this is a retype and not a rename; records that DO mean the process already use a separate id (proton_motive_force_generation in ph_delta.yaml). Also settles the one edge #356 was filed for: phototrophic.yaml's CAPACITY typing was blocking `powers` (METPO:2007900), which is gated to BIOLOGICAL_PROCESS|STATE.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-20T07:10:26Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (METPO:1007500\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope aerobic_trait_mechanism=NONMECHANISTIC with scope_notes; marked 3 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (substrate_dehydrogenases, terminal_oxidases, ros_scavenging_enzymes).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T06:15:37Z",
        "curator": "codex",
        "action": "ADD_EXACT_ONTOLOGY_MATCH",
        "changes": "Ontology exact-match review (2026-08-25): approved exact xref(s): PATO:0001455. Evidence is predicate-scoped in the versioned ontology snapshots; OAK cross-checked direct data, and OLS4 spot-checked release deltas and disputed hits.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000609",
    "label": "aerotolerant",
    "definition": "An oxygen preference that does not use O\u2082 for growth but tolerates its presence.",
    "definition_source": "https://bio.libretexts.org/Courses/Ohio_State_University/Microbiology_Lab_SP25/05%3A_Lab_5/5.05%3A_Bacterial_Oxygen_Requirements",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000601"
    ],
    "synonyms": [
      {
        "synonym_text": "aerotolerant anaerobe",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://bio.libretexts.org/Courses/Ohio_State_University/Microbiology_Lab_SP25/05%3A_Lab_5/5.05%3A_Bacterial_Oxygen_Requirements"
      }
    ],
    "evidence": [
      {
        "reference": "https://bio.libretexts.org/Courses/Ohio_State_University/Microbiology_Lab_SP25/05%3A_Lab_5/5.05%3A_Bacterial_Oxygen_Requirements",
        "snippet": "they do not utilize it for ATP production",
        "notes": "Supports aerotolerance as oxygen tolerance without oxygen use."
      },
      {
        "reference": "PMID:38864615",
        "snippet": "this bacterium is relatively aerotolerant and survives limited oxygen exposure",
        "notes": "Organism example: Clostridium perfringens is described as aerotolerant."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1358",
        "taxon_label": "Lactococcus lactis",
        "note": "aerotolerant fermenter",
        "reference": "PMID:11443085"
      },
      {
        "taxon_id": "NCBITaxon:1314",
        "taxon_label": "Streptococcus pyogenes",
        "note": "aerotolerant anaerobe",
        "reference": "PMID:10986229"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "aerotolerant_anaerobe_ros_defense",
        "title": "Aerotolerant anaerobe ROS-defense mechanism",
        "description": "Evidence-backed causal sketch linking aerotolerance to anaerobic growth plus enzymatic defenses against oxygen-derived stress.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a broad environmental or morphological classification spanning multiple mechanisms, a measurement-like bin, or an absence/arrangement descriptor; contextual protein nodes do not receive token UniProt examples.",
        "nodes": [
          {
            "node_id": "aerotolerant_trait",
            "label": "aerotolerant",
            "node_type": "TRAIT",
            "grounding": "METPO:1000609",
            "description": "Does not use oxygen for growth but tolerates its presence."
          },
          {
            "node_id": "molecular_oxygen",
            "label": "molecular oxygen",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:15379",
            "description": "Dioxygen exposure tolerated by aerotolerant anaerobes."
          },
          {
            "node_id": "reactive_oxygen_species",
            "label": "reactive oxygen species",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:26523",
            "description": "Oxygen-derived oxidants that can damage cells."
          },
          {
            "node_id": "superoxide_dismutase",
            "label": "superoxide dismutase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Enzyme associated with detoxification of superoxide stress.",
            "grounding": "GO:0004784"
          },
          {
            "node_id": "anaerobic_growth",
            "label": "anaerobic growth",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Growth supported without using oxygen as an energy substrate."
          },
          {
            "node_id": "hydrogen_peroxide",
            "label": "hydrogen peroxide",
            "node_type": "CHEMICAL",
            "description": "Reactive oxygen species produced during oxygen exposure that damages cells.",
            "grounding": "CHEBI:16240"
          },
          {
            "node_id": "hydrogen_peroxide_detoxification",
            "label": "hydrogen peroxide detoxification",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Enzymatic removal of hydrogen peroxide to limit oxidative damage.",
            "grounding": "GO:0042744"
          },
          {
            "node_id": "catalase",
            "label": "catalase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Enzyme that degrades hydrogen peroxide rapidly at higher concentrations.",
            "grounding": "GO:0004096"
          },
          {
            "node_id": "rubrerythrin",
            "label": "rubrerythrin",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Non-heme iron protein that scavenges low levels of hydrogen peroxide.",
            "grounding": "InterPro:IPR052364"
          },
          {
            "node_id": "nadh_peroxidase",
            "label": "NADH peroxidase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Enzyme reducing hydrogen peroxide to water using NADH.",
            "grounding": "GO:0016692"
          },
          {
            "node_id": "nadph_peroxidase",
            "label": "NADPH peroxidase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Enzyme reducing hydrogen peroxide to water using NADPH.",
            "grounding": "GO:0050137"
          }
        ],
        "edges": [
          {
            "subject": "aerotolerant_trait",
            "predicate": "includes",
            "object": "anaerobic_growth",
            "description": "Aerotolerant anaerobes grow anaerobically while tolerating oxygen.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2970",
                "snippet": "Aerotolerant anaerobes ... ROS defence ... Anaerobic growth",
                "notes": "Table classifies aerotolerant anaerobes as anaerobic-growth organisms with ROS defence."
              }
            ],
            "predicate_id": "biolink:has_part"
          },
          {
            "subject": "molecular_oxygen",
            "predicate": "can generate",
            "object": "reactive_oxygen_species",
            "description": "Oxygen exposure creates ROS stress that aerotolerant organisms must defend against.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41579-021-00583-y",
                "snippet": "molecular oxygen and ROS",
                "notes": "Review links oxygen exposure and reactive oxygen species in anaerobes."
              }
            ]
          },
          {
            "subject": "superoxide_dismutase",
            "predicate": "contributes to",
            "object": "aerotolerant_trait",
            "description": "Superoxide dismutase abundance is associated with oxygen tolerance among anaerobic bacteria.",
            "evidence": [
              {
                "reference": "DOI:10.1128/iai.16.1.20-25.1977",
                "snippet": "aerotolerant and intermediate organisms had SOD",
                "notes": "Comparative anaerobe study supports SOD as an oxygen-tolerance factor."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "superoxide_dismutase",
            "predicate": "mitigates",
            "object": "reactive_oxygen_species",
            "description": "SOD mitigates superoxide stress generated during oxygen exposure.",
            "evidence": [
              {
                "reference": "DOI:10.1128/iai.16.1.20-25.1977",
                "snippet": "oxygen tolerance of anaerobes is usually related to their level of SOD",
                "notes": "Supports SOD as a ROS-defense mechanism for aerotolerant anaerobes."
              }
            ],
            "predicate_id": "METPO:2007407"
          },
          {
            "subject": "catalase",
            "predicate": "enables",
            "object": "hydrogen_peroxide_detoxification",
            "description": "Catalase degrades hydrogen peroxide, enabling its detoxification.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s43705-023-00251-7",
                "notes": "catalase degrades H2O2 rapidly at higher concentrations"
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "rubrerythrin",
            "predicate": "decreases",
            "object": "hydrogen_peroxide",
            "description": "Rubrerythrin scavenges low levels of hydrogen peroxide.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s43705-023-00251-7",
                "notes": "rubrerythrins scavenge low H2O2 levels"
              }
            ],
            "predicate_id": "RO:0002212"
          },
          {
            "subject": "nadh_peroxidase",
            "predicate": "decreases",
            "object": "hydrogen_peroxide",
            "description": "NADH peroxidase reduces hydrogen peroxide to water.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41598-023-41185-3",
                "notes": "NADH + H+ + H2O2 reversible to NAD+ + 2 H2O"
              }
            ],
            "predicate_id": "RO:0002212"
          },
          {
            "subject": "nadph_peroxidase",
            "predicate": "decreases",
            "object": "hydrogen_peroxide",
            "description": "NADPH peroxidase reduces hydrogen peroxide to water.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41598-023-41185-3",
                "notes": "an analogous NADPH peroxidase produces NADP+"
              }
            ],
            "predicate_id": "RO:0002212"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.853836+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-05T01:09:05-07:00",
        "curator": "codex",
        "action": "CURATED_WITH_LITERATURE",
        "changes": "Added definition source, supported synonym, and evidence for aerotolerance.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-05T18:39:46-07:00",
        "curator": "codex",
        "action": "ADDED_ORGANISM_EXAMPLE",
        "changes": "Added Clostridium perfringens organism example with PMID-backed evidence.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "ADDED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed causal graph for aerotolerance and ROS-defense mechanisms in anaerobes.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:29Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002326\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T21:30:06Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007407\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T05:05:13Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A009QPW9\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-13T21:03:25Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:has_part\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-17T04:09:43Z",
        "curator": "claude",
        "action": "REMOVE_REDUNDANT_SYNONYM",
        "changes": "Removed 1 synonym(s) whose text duplicated the label (seeder redundancy; no information lost).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 4 evidence-backed generic edges (6 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:09Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 4 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002212\u00d73, RO:0002327\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:16Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A071MK53\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:30Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:16240\u00d71, GO:0033355\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-26T07:15:17Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A016EEI2\u00d71, UniProtKB:A0A031WCC0\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:21:11Z",
        "curator": "claude",
        "action": "RETRACT_DEAD_UNIPROT_GROUNDINGS",
        "changes": "Retracted 4 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:23:52Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 5 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0004784\u00d71, GO:0004096\u00d71, InterPro:IPR052364\u00d71, GO:0016692\u00d71, GO:0050137\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-17T06:00:00Z",
        "curator": "claude",
        "action": "REGROUND_CAUSAL_NODES",
        "changes": "Repaired a wrong CURIE from the kg-microbe name-match pass (issue 402): hydrogen_peroxide_detoxification: GO:0033355 -> GO:0042744. Was GO:0033355 'ascorbate glutathione cycle', a plant antioxidant pathway; bacteria detoxify H2O2 with catalase and peroxidases, which is what this node describes. Replaced with the generic catabolic term, resolved through the OAK adapter before being written.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope aerotolerant_anaerobe_ros_defense=NONMECHANISTIC with scope_notes.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1003009",
    "label": "alkalotolerant",
    "definition": "A pH growth preference in which an organism can tolerate alkaline pH but grows optimally at neutral pH.",
    "definition_source": "DOI:10.1016/j.bbamem.2005.09.010",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1003000"
    ],
    "synonyms": [
      {
        "synonym_text": "alkalitolerant",
        "synonym_type": "EXACT_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1016/j.bbamem.2005.09.010",
        "snippet": "alkali-tolerant and extremely alkaliphilic bacteria",
        "notes": "Supports alkaline pH tolerance as a microbial pH-homeostasis phenotype."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:86665",
        "taxon_label": "Halalkalibacterium halodurans",
        "note": "tolerates high pH (ex-Bacillus halodurans)",
        "reference": "PMID:11058132"
      },
      {
        "taxon_id": "NCBITaxon:79885",
        "taxon_label": "Alkalihalophilus pseudofirmus",
        "note": "alkalitolerant",
        "reference": "PMID:21951522"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "alkalotolerant_alkaline_stress_homeostasis",
        "title": "Alkalotolerant alkaline-stress pH homeostasis mechanism",
        "description": "Evidence-backed causal sketch linking alkalotolerance to alkaline exposure, proton retention, and cation/proton antiport.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a broad environmental or morphological classification spanning multiple mechanisms, a measurement-like bin, or an absence/arrangement descriptor; contextual protein nodes do not receive token UniProt examples.",
        "nodes": [
          {
            "node_id": "alkalotolerant_trait",
            "label": "alkalotolerant",
            "node_type": "TRAIT",
            "grounding": "METPO:1003009",
            "description": "Tolerates alkaline pH while growing optimally near neutral pH."
          },
          {
            "node_id": "alkaline_exposure",
            "label": "alkaline exposure",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "External pH above neutral."
          },
          {
            "node_id": "cytoplasmic_ph_homeostasis",
            "label": "cytoplasmic pH homeostasis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Maintenance of internal pH during alkaline challenge.",
            "grounding": "GO:0051453"
          },
          {
            "node_id": "proton_retention",
            "label": "proton retention",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Retaining or capturing protons at the cell surface or cytoplasm."
          },
          {
            "node_id": "cation_proton_antiporter",
            "label": "cation/proton antiporter",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Antiporter exchanging cations for protons during pH stress.",
            "grounding": "GO:0051139"
          },
          {
            "node_id": "alkaline_external_ph",
            "label": "alkaline external pH",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Elevated extracellular pH above neutral.",
            "grounding": "PATO:0001430"
          },
          {
            "node_id": "electrogenic_na_h_antiport",
            "label": "electrogenic Na+/H+ antiport",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "Electrogenic exchange of sodium for protons, important under alkaline pH."
          },
          {
            "node_id": "cell_surface_acidic_polymers",
            "label": "acidic non-peptidoglycan cell-surface polymers",
            "node_type": "CHEMICAL",
            "description": "Negatively charged cell-wall polymers that modulate ion adsorption at the cell surface."
          },
          {
            "node_id": "sodium_ion",
            "label": "sodium and hydronium ions",
            "node_type": "CHEMICAL",
            "description": "Cations (Na+, H3O+) adsorbed at the cell surface."
          },
          {
            "node_id": "hydroxide_ion",
            "label": "hydroxide ion",
            "node_type": "CHEMICAL",
            "description": "Hydroxide ion (OH-) repelled by the negatively charged cell surface.",
            "grounding": "CHEBI:16234"
          },
          {
            "node_id": "sodium_motive_force",
            "label": "sodium motive force",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Transmembrane sodium gradient supporting bioenergetics and pH control."
          }
        ],
        "edges": [
          {
            "subject": "alkaline_exposure",
            "predicate": "challenges",
            "object": "alkalotolerant_trait",
            "description": "Alkalotolerance reflects capacity to withstand alkaline pH outside the growth optimum.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.bbamem.2005.09.010",
                "snippet": "alkali-tolerant and extremely alkaliphilic bacteria",
                "notes": "Review explicitly covers alkali-tolerant bacteria."
              }
            ],
            "predicate_id": "METPO:2007406"
          },
          {
            "subject": "alkaline_exposure",
            "predicate": "challenges",
            "object": "cytoplasmic_ph_homeostasis",
            "description": "Alkaline pH requires maintenance of a less alkaline cytoplasm.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2549",
                "snippet": "grow in environments with external pH values",
                "notes": "Review supports pH homeostasis for growth outside cytoplasmic pH range."
              }
            ],
            "predicate_id": "METPO:2007406"
          },
          {
            "subject": "proton_retention",
            "predicate": "contributes to",
            "object": "cytoplasmic_ph_homeostasis",
            "description": "Proton capture and retention support pH homeostasis in alkaline environments.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.bbamem.2005.09.010",
                "snippet": "promote proton capture and retention",
                "notes": "Supports proton retention mechanisms during alkaline pH challenge."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "cation_proton_antiporter",
            "predicate": "contributes to",
            "object": "cytoplasmic_ph_homeostasis",
            "description": "Cation/proton antiporters help regulate intracellular pH under alkaline stress.",
            "evidence": [
              {
                "reference": "DOI:10.3390/ijms21124566",
                "snippet": "maintaining ion and pH homeostasis",
                "notes": "Supports cation/proton antiporters as pH-homeostasis transporters."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "cytoplasmic_ph_homeostasis",
            "predicate": "confers",
            "object": "alkalotolerant_trait",
            "description": "Alkaline tolerance depends on maintaining cytoplasmic pH during alkaline exposure.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2549",
                "snippet": "cell-wide physiological process",
                "notes": "Supports pH homeostasis as a broad enabling process."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "alkaline_external_ph",
            "predicate": "increases importance of",
            "object": "electrogenic_na_h_antiport",
            "description": "Alkaline extracellular pH makes electrogenic Na+/H+ antiport particularly important for proton import.",
            "evidence": [
              {
                "reference": "DOI:10.3390/ijms23169156",
                "notes": "Negative-inside membrane potential drives Na+ extrusion, particularly important when extracellular pH is alkaline (general prokaryotic mechanism)."
              }
            ]
          },
          {
            "subject": "cell_surface_acidic_polymers",
            "predicate": "helps maintain",
            "object": "cytoplasmic_ph_homeostasis",
            "description": "Acidic non-peptidoglycan polymers create surface negative charges that reduce pH at the cell surface and help keep intracellular pH near neutrality.",
            "evidence": [
              {
                "reference": "DOI:10.1007/978-4-431-55408-0_4",
                "notes": "Acidic non-peptidoglycan polymers create negative charges that reduce pH at the cell surface and help keep intracellular pH controlled."
              }
            ]
          },
          {
            "subject": "cell_surface_acidic_polymers",
            "predicate": "adsorbs",
            "object": "sodium_ion",
            "description": "Negatively charged cell-surface polymers adsorb sodium and hydronium ions.",
            "evidence": [
              {
                "reference": "DOI:10.1128/MMBR.63.4.735-750.1999",
                "notes": "Cell surface acidic polymers adsorb sodium and hydronium ions; cell-envelope charge chemistry mechanism."
              }
            ]
          },
          {
            "subject": "cell_surface_acidic_polymers",
            "predicate": "repels",
            "object": "hydroxide_ion",
            "description": "Negatively charged cell-surface polymers repel hydroxide ions, mitigating alkaline stress at the surface.",
            "evidence": [
              {
                "reference": "DOI:10.1128/MMBR.63.4.735-750.1999",
                "notes": "Acidic non-peptidoglycan polymers repulse hydroxide ions at the cell surface."
              }
            ]
          },
          {
            "subject": "sodium_motive_force",
            "predicate": "supports",
            "object": "cytoplasmic_ph_homeostasis",
            "description": "A sodium motive force mediated by Na+/H+ antiporters and related proteins supports intracellular pH control.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s11244-024-01919-7",
                "notes": "Sodium motive force mediated by Na+/H+ antiporters, Na+ channels or stator proteins supports intracellular pH control (review-level, broad)."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.941966+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-11T00:00:00-07:00",
        "curator": "codex",
        "action": "CURATED_WITH_LITERATURE",
        "changes": "Reviewed alkalotolerant trait and added DOI-backed evidence and causal graph for alkaline-stress pH homeostasis.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:29Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002326\u00d72, RO:0002327\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T21:30:06Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007406\u00d72).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:37:59Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0030641\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T05:05:13Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A0H3JRG4\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-15T07:20:36Z",
        "curator": "claude",
        "action": "FIX_NODE_GROUNDING_CURIE",
        "changes": "Overwrote 1 causal-node grounding(s) (obsolete/wrong GO -> corrected, verified vs OAK).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 5 evidence-backed generic edges (6 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:16Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (PATO:0001430\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:30Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:16234\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 1 causal edge(s) off enables/RO:0002327 with a TRAIT object (1 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-22T04:26:15Z",
        "curator": "codex",
        "action": "REVIEW_UNIPROT_INSTANCE_GROUNDINGS",
        "changes": "Reviewed 1 organism-specific UniProtKB grounding(s): replaced 1 with taxon-agnostic GO/InterPro terms and retracted 0 to label-only where no exact semantic term was supported (docs/GROUNDING_POLICY.md).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope alkalotolerant_alkaline_stress_homeostasis=NONMECHANISTIC with scope_notes.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1003002",
    "label": "alkaliphilic",
    "definition": "A pH growth preference in which an organism grows optimally at pH values above 9.",
    "definition_source": "DOI:10.1038/nrmicro2549",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1003000"
    ],
    "synonyms": [
      {
        "synonym_text": "alkaliphile",
        "synonym_type": "EXACT_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "alkalophile",
        "synonym_type": "EXACT_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "alkalophilic",
        "synonym_type": "EXACT_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/nrmicro2549",
        "snippet": "external pH range of 9.5-11.0",
        "notes": "Supports alkaliphilic growth at strongly alkaline external pH."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:86665",
        "taxon_label": "Halalkalibacterium halodurans",
        "note": "alkaliphile growing at pH >9.5",
        "reference": "DOI:10.1093/nar/28.21.4317"
      },
      {
        "taxon_id": "NCBITaxon:2257",
        "taxon_label": "Natronomonas pharaonis",
        "note": "haloalkaliphilic archaeon",
        "reference": "PMID:16169924"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "alkaliphilic_na_cycle_homeostasis",
        "title": "Alkaliphilic sodium-cycle pH homeostasis mechanism",
        "description": "Evidence-backed causal sketch linking alkaliphily to high external pH, Na+/H+ antiport, and cytoplasmic acidification relative to the medium.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a broad environmental or morphological classification spanning multiple mechanisms, a measurement-like bin, or an absence/arrangement descriptor; contextual protein nodes do not receive token UniProt examples.",
        "nodes": [
          {
            "node_id": "alkaphilic_trait",
            "label": "alkaliphilic",
            "node_type": "TRAIT",
            "grounding": "METPO:1003002",
            "description": "Optimal growth occurs at alkaline pH."
          },
          {
            "node_id": "alkaline_external_ph",
            "label": "alkaline external pH",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "External pH above neutral, often pH 9 or higher.",
            "grounding": "PATO:0001430"
          },
          {
            "node_id": "sodium_ion",
            "label": "sodium ion",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:29101",
            "description": "Sodium ion participating in alkaliphile Na+ cycles."
          },
          {
            "node_id": "proton",
            "label": "proton",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:15378",
            "description": "Hydrogen ion imported or retained to acidify the cytoplasm."
          },
          {
            "node_id": "sodium_proton_antiporter",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "Na+/H+ antiporter",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Secondary transporter exchanging sodium and protons."
          },
          {
            "node_id": "cytoplasmic_ph_homeostasis",
            "label": "cytoplasmic pH homeostasis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Maintenance of internal pH below highly alkaline external pH.",
            "grounding": "GO:0051453"
          },
          {
            "node_id": "mrp_antiporter_complex",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "Mrp Na+/H+ antiporter complex",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Multisubunit cation/proton antiporter complex with an indispensable role in alkaliphile high-pH homeostasis."
          },
          {
            "node_id": "atp_synthase_c_subunit_motifs",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "ATP synthase c-subunit alkaline-adaptive motifs",
            "node_type": "GENE_OR_PROTEIN",
            "description": "c-subunit motifs that alter rotor shape and promote tight proton binding in the ion site at high pH."
          },
          {
            "node_id": "atp_synthase_proton_binding",
            "label": "ATP synthase proton binding efficiency at high pH",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "Tight proton binding in the ATP synthase ion site enabling efficient operation under alkaline conditions."
          },
          {
            "node_id": "acidic_cell_envelope_polymers",
            "label": "acidic secondary cell-wall and S-layer polymers",
            "node_type": "CELLULAR_LOCALIZATION",
            "description": "Acidic secondary cell walls and S-layer proteins on the cell surface of alkaliphiles."
          },
          {
            "node_id": "surface_proton_retention",
            "label": "proton retention at cell surface",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Attraction and retention of protons at the cell surface, buffering the cytoplasmic membrane against high external pH."
          }
        ],
        "edges": [
          {
            "subject": "alkaline_external_ph",
            "predicate": "selects for",
            "object": "alkaphilic_trait",
            "description": "Alkaline environments select for organisms with alkaline growth optima.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2549",
                "snippet": "external pH range of 9.5-11.0",
                "notes": "Review supports growth of extreme alkaliphiles at high external pH."
              }
            ],
            "predicate_id": "METPO:2007401"
          },
          {
            "subject": "alkaline_external_ph",
            "predicate": "challenges",
            "object": "cytoplasmic_ph_homeostasis",
            "description": "High external pH challenges the cell's ability to keep cytoplasm near functional pH.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2549",
                "snippet": "cytoplasmic pH ... below an external pH",
                "notes": "Supports cytoplasmic pH control below alkaline external pH."
              }
            ],
            "predicate_id": "METPO:2007406"
          },
          {
            "subject": "sodium_proton_antiporter",
            "predicate": "exchanges",
            "object": "sodium_ion",
            "description": "Na+/H+ antiport is central to the sodium cycle in alkaliphiles.",
            "evidence": [
              {
                "reference": "DOI:10.1007/BF00762685",
                "snippet": "secondary Na+/H+ antiporter",
                "notes": "Supports Na+/H+ antiport as a key alkaliphile sodium-cycle component."
              }
            ]
          },
          {
            "subject": "sodium_proton_antiporter",
            "predicate": "imports",
            "object": "proton",
            "description": "Electrogenic Na+/H+ antiport contributes to cytoplasmic acidification under alkaline conditions.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.bbamem.2005.09.010",
                "snippet": "promote proton capture and retention",
                "notes": "Review supports proton capture/retention mechanisms in alkaline pH homeostasis."
              }
            ],
            "predicate_id": "METPO:2007805"
          },
          {
            "subject": "cytoplasmic_ph_homeostasis",
            "predicate": "confers",
            "object": "alkaphilic_trait",
            "description": "Alkaliphilic growth requires maintaining cytoplasmic pH during high-pH exposure.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2549",
                "snippet": "pH sensing and homeostasis",
                "notes": "Supports homeostasis as the enabling process for alkaline growth."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "mrp_antiporter_complex",
            "predicate": "enables",
            "object": "cytoplasmic_ph_homeostasis",
            "description": "Mrp Na+/H+ antiporter complex enables pH homeostasis and is indispensable at high pH.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2549",
                "notes": "Na+/H+ antiporter-dependent pH homeostasis; Mrp plays an indispensible role at high pH."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "atp_synthase_c_subunit_motifs",
            "predicate": "increases",
            "object": "atp_synthase_proton_binding",
            "description": "Alkaline-adaptive c-subunit motifs increase tight proton binding in the ATP synthase ion site at high pH.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2549",
                "notes": "Two c-subunit motifs that alter rotor shape and promote tight proton binding in the ion site."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "atp_synthase_proton_binding",
            "predicate": "enables",
            "object": "cytoplasmic_ph_homeostasis",
            "description": "Efficient ATP synthase proton binding contributes to bioenergetics and pH homeostasis under alkaline conditions.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2549",
                "notes": "ATP synthase adaptation supports proton-coupled bioenergetics at high external pH."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "acidic_cell_envelope_polymers",
            "predicate": "enables",
            "object": "surface_proton_retention",
            "description": "Acidic cell-wall and S-layer polymers attract and retain protons at the cell surface.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2022.842785",
                "notes": "Acidic secondary cell walls and S-layer proteins attract H+."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "surface_proton_retention",
            "predicate": "contributes to",
            "object": "cytoplasmic_ph_homeostasis",
            "description": "Surface proton retention buffers the membrane and supports cytoplasmic pH homeostasis at high external pH.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2022.842785",
                "notes": "Surface proton retention helps maintain a proton-rich microenvironment near the membrane."
              }
            ],
            "predicate_id": "RO:0002326"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.937702+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-11T00:00:00-07:00",
        "curator": "codex",
        "action": "CURATED_WITH_LITERATURE",
        "changes": "Reviewed alkaphilic trait and added DOI-backed evidence and causal graph for sodium-cycle alkaline pH homeostasis.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:29Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T21:30:06Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007401\u00d71, METPO:2007406\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:37:59Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0030641\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T05:05:13Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A068T423\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T08:14:32Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (PATO:0001429\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-15T07:20:36Z",
        "curator": "claude",
        "action": "FIX_NODE_GROUNDING_CURIE",
        "changes": "Overwrote 1 causal-node grounding(s) (obsolete/wrong GO -> corrected, verified vs OAK).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-15T07:21:43Z",
        "curator": "claude",
        "action": "FIX_NODE_GROUNDING_CURIE",
        "changes": "Overwrote 1 pH causal-node grounding(s) to corrected PATO CURIEs (phase-2; verified vs OAK).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-16T06:30:55Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000208\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 5 evidence-backed generic edges (5 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:09Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 5 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d73, RO:0002213\u00d71, RO:0002326\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:21:11Z",
        "curator": "claude",
        "action": "RETRACT_DEAD_UNIPROT_GROUNDINGS",
        "changes": "Retracted 1 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 1 causal edge(s) off enables/RO:0002327 with a TRAIT object (1 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T02:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES_PART2",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates onto their causal-graph counterparts (1 to imports), issue 301 part 2. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Each replacement is a 1:1 mirror of its source predicate that changes only the domain, so the claim each edge makes is unchanged and directions are unchanged. The replacements are proposed in proposals/metpo_traitmech_v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope alkaliphilic_na_cycle_homeostasis=NONMECHANISTIC with scope_notes; marked 3 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (sodium_proton_antiporter, mrp_antiporter_complex, atp_synthase_c_subunit_motifs).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T07:35:00Z",
        "curator": "migrate_metpo_2026_06_12",
        "action": "MIGRATE_METPO_RELEASE",
        "changes": "Migrated source-owned fields to locked METPO 2026-06-12: label 'alkaphilic' -> 'alkaliphilic'; synonyms synchronized at ontology-declared scope; grounded node alkaphilic_trait label synchronized"
      }
    ]
  },
  {
    "identifier": "METPO:1000603",
    "label": "anaerobic",
    "definition": "An oxygen preference in which growth occurs in the absence of molecular oxygen (O\u2082).",
    "definition_source": "PMID:21413255",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000601"
    ],
    "synonyms": [
      {
        "synonym_text": "Ox_anaerobic",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "anaerobe",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "xrefs": [
      "PATO:0001456"
    ],
    "evidence": [
      {
        "reference": "PMID:21413255",
        "snippet": "Anaerobes, on the other hand, cannot grow in the presence of oxygen",
        "notes": "Supports anaerobic growth as growth without molecular oxygen."
      },
      {
        "reference": "PMID:22778399",
        "snippet": "obligate anaerobe Bacteroides fragilis",
        "notes": "Organism example: Bacteroides fragilis is described as an anaerobic organism."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1488",
        "taxon_label": "Clostridium acetobutylicum",
        "note": "obligate anaerobe",
        "reference": "PMID:18430081"
      },
      {
        "taxon_id": "NCBITaxon:817",
        "taxon_label": "Bacteroides fragilis",
        "note": "aerotolerant gut anaerobe",
        "reference": "PMID:22778399"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "anaerobic_trait_oxygen_exclusion",
        "title": "Anaerobic growth oxygen-exclusion mechanism",
        "description": "Evidence-backed causal sketch linking anaerobic growth to absence of molecular oxygen and oxygen-derived stress.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a broad environmental or morphological classification spanning multiple mechanisms, a measurement-like bin, or an absence/arrangement descriptor; contextual protein nodes do not receive token UniProt examples.",
        "nodes": [
          {
            "node_id": "anaerobic_trait",
            "label": "anaerobic",
            "node_type": "TRAIT",
            "grounding": "METPO:1000603",
            "description": "Growth occurs without molecular oxygen."
          },
          {
            "node_id": "anoxic_condition",
            "label": "anoxic or hypoxic condition",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Low-oxygen environment that permits anaerobic growth."
          },
          {
            "node_id": "molecular_oxygen",
            "label": "molecular oxygen",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:15379",
            "description": "Dioxygen whose presence can block anaerobic growth."
          },
          {
            "node_id": "reactive_oxygen_species",
            "label": "reactive oxygen species",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:26523",
            "description": "Oxygen-derived oxidants such as superoxide and hydrogen peroxide."
          },
          {
            "node_id": "oxygen_sensitive_catalytic_sites",
            "label": "oxygen-sensitive catalytic sites",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "Radical chemistry and low-potential metal centers vulnerable to oxygen or ROS."
          },
          {
            "node_id": "antioxidant_enzymes",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "antioxidant enzymes (Sod/Cat/peroxidases)",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Superoxide dismutase, catalase, and peroxidases that detoxify reactive oxygen species."
          },
          {
            "node_id": "ros_detoxification",
            "label": "ROS detoxification",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Enzymatic removal of reactive oxygen species to limit oxidative damage."
          },
          {
            "node_id": "respiratory_reductases",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "respiratory reductases",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Terminal reductases that allow use of non-oxygen molecules as respiratory electron acceptors."
          },
          {
            "node_id": "alternative_electron_acceptors",
            "label": "alternative anaerobic electron acceptors",
            "node_type": "CHEMICAL",
            "description": "Non-O2 molecules present in anaerobic ecosystems used as terminal electron acceptors."
          },
          {
            "node_id": "anaerobic_respiration",
            "label": "anaerobic respiration",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Energy generation using terminal electron acceptors other than molecular oxygen.",
            "grounding": "GO:0009061"
          }
        ],
        "edges": [
          {
            "subject": "anoxic_condition",
            "predicate": "confers",
            "object": "anaerobic_trait",
            "description": "Anaerobic growth is favored in low-oxygen environments.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41579-021-00583-y",
                "snippet": "hypoxic environments in which these organisms dwell",
                "notes": "Review links anaerobe ecology to hypoxic environments."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "molecular_oxygen",
            "predicate": "inhibits",
            "object": "anaerobic_trait",
            "description": "Oxygen exposure can block growth of anaerobic organisms.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41579-021-00583-y",
                "snippet": "oxygen blocks their growth",
                "notes": "Supports oxygen as an inhibitory factor for anaerobic growth."
              }
            ],
            "predicate_id": "RO:0002212"
          },
          {
            "subject": "molecular_oxygen",
            "predicate": "generates stress via",
            "object": "reactive_oxygen_species",
            "description": "Oxygen exposure can lead to ROS-mediated stress in anaerobes.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41579-021-00583-y",
                "snippet": "molecular oxygen and ROS",
                "notes": "Review describes oxygen and ROS as linked stressors for anaerobes."
              }
            ]
          },
          {
            "subject": "reactive_oxygen_species",
            "predicate": "damages",
            "object": "oxygen_sensitive_catalytic_sites",
            "description": "ROS can disrupt oxygen-sensitive radical or metal-center catalysis used in anaerobic metabolism.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41579-021-00583-y",
                "snippet": "vulnerable to direct poisoning by molecular oxygen and ROS",
                "notes": "Supports ROS-sensitive catalytic sites as mechanistic vulnerability."
              }
            ]
          },
          {
            "subject": "antioxidant_enzymes",
            "predicate": "detoxifies",
            "object": "reactive_oxygen_species",
            "description": "Superoxide dismutase, catalase, and peroxidases remove ROS in anaerobes exposed to oxygen.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s43705-023-00251-7",
                "notes": "organisms use anti-oxidative enzymes - superoxide dismutase (Sod), catalase (Cat), and peroxidases - to detoxify ROS."
              }
            ]
          },
          {
            "subject": "antioxidant_enzymes",
            "predicate": "enables",
            "object": "ros_detoxification",
            "description": "Antioxidant enzyme activity carries out the detoxification of reactive oxygen species.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s43705-023-00251-7",
                "notes": "Anti-oxidative enzymes (Sod/Cat/peroxidases) detoxify ROS, mediating ROS detoxification."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "ros_detoxification",
            "predicate": "protects against",
            "object": "reactive_oxygen_species",
            "description": "ROS detoxification limits oxidative damage from oxygen-derived oxidants in anaerobes.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s43705-023-00251-7",
                "notes": "Detoxification system removes ROS produced when O2 is reduced, a broad protective mechanism."
              }
            ]
          },
          {
            "subject": "respiratory_reductases",
            "predicate": "enables utilization of",
            "object": "alternative_electron_acceptors",
            "description": "Respiratory reductases let microbes use non-O2 molecules as energy-generating electron acceptors.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-023-01560-2",
                "notes": "Respiratory reductases enable microbes to utilize molecules present in anaerobic ecosystems as energy-generating respiratory electron acceptors."
              }
            ]
          },
          {
            "subject": "alternative_electron_acceptors",
            "predicate": "enables",
            "object": "anaerobic_respiration",
            "description": "Availability of non-O2 electron acceptors supports anaerobic respiration in low-oxygen niches.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-023-01560-2",
                "notes": "Molecules in anaerobic ecosystems serve as respiratory electron acceptors for anaerobic respiration."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "anaerobic_respiration",
            "predicate": "confers",
            "object": "anaerobic_trait",
            "description": "Use of alternative terminal electron acceptors supports growth without molecular oxygen.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-023-01560-2",
                "notes": "Diverse gut bacteria use dietary- and host-derived metabolites for anaerobic respiration, enabling growth without O2."
              }
            ],
            "predicate_id": "METPO:2007700"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.849856+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-05T01:09:05-07:00",
        "curator": "codex",
        "action": "CURATED_WITH_LITERATURE",
        "changes": "Added definition source and evidence for oxygen-excluding anaerobic growth.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-05T18:39:46-07:00",
        "curator": "codex",
        "action": "ADDED_ORGANISM_EXAMPLE",
        "changes": "Added Bacteroides fragilis organism example with PMID-backed evidence.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "ADDED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed causal graph for oxygen exclusion and oxygen-derived stress in anaerobic growth.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:29Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-13T21:03:25Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002212\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-17T04:09:43Z",
        "curator": "claude",
        "action": "REMOVE_REDUNDANT_SYNONYM",
        "changes": "Removed 1 synonym(s) whose text duplicated the label (seeder redundancy; no information lost).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 6 evidence-backed generic edges (5 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:09Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d73).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:16Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0009061\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 2 causal edge(s) off enables/RO:0002327 with a TRAIT object (2 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope anaerobic_trait_oxygen_exclusion=NONMECHANISTIC with scope_notes; marked 2 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (antioxidant_enzymes, respiratory_reductases).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T06:15:37Z",
        "curator": "codex",
        "action": "ADD_EXACT_ONTOLOGY_MATCH",
        "changes": "Ontology exact-match review (2026-08-25): approved exact xref(s): PATO:0001456. Evidence is predicate-scoped in the versioned ontology snapshots; OAK cross-checked direct data, and OLS4 spot-checked release deltas and disputed hits.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000017",
    "label": "arsenic tolerant",
    "definition": "A metalloid tolerance in which an organism grows in the presence of elevated arsenic (arsenite/arsenate) concentrations, typically via the ars operon, whose ArsB pump extrudes arsenite from the cytoplasm.",
    "definition_source": "DOI:10.3389/fmicb.2018.02473",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "traitmech:000012"
    ],
    "synonyms": [
      {
        "synonym_text": "arsenic resistant",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.3389/fmicb.2018.02473"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.3389/fmicb.2018.02473",
        "snippet": "ArsB is an integral membrane protein able to extrude arsenite from the cell cytoplasm, thus diminishing arsenite accumulation",
        "notes": "Review supports the ars operon as a near-ubiquitous arsenic-resistance determinant, \"more common than genes for tryptophan biosynthesis\"."
      },
      {
        "reference": "DOI:10.3389/fmicb.2020.00047",
        "snippet": "C. metallidurans BS1 conferred resistance to Zn2+ displaying a MIC of 20 mM, Cd2+ (2.5 mM), Co2+ (20mM), Ni2+ (8 mM), As3+ (3.5 mM), Cu2+ (5 mM), Au3+ (1 uM) and Pb2+ (1.7 mM)",
        "notes": "Organism example: Cupriavidus metallidurans BS1 tolerates arsenite (As3+) to a MIC of 3.5 mM."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:119219",
        "taxon_label": "Cupriavidus metallidurans",
        "note": "broad heavy-metal/metalloid resistance",
        "reference": "PMID:20463976"
      },
      {
        "taxon_id": "NCBITaxon:303",
        "taxon_label": "Pseudomonas putida",
        "note": "metal-tolerant soil bacterium",
        "reference": "PMID:25646541"
      },
      {
        "taxon_id": "NCBITaxon:266264",
        "taxon_label": "Cupriavidus metallidurans CH34",
        "note": "Strain-level ArsC arsenate-reduction exemplar.",
        "reference": "PMID:20463976"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "arsenic_tolerance_ars_efflux",
        "title": "Arsenic tolerance via ars-operon arsenite efflux",
        "description": "Evidence-backed causal sketch linking the ars operon and ArsB pump to extrusion of cytoplasmic arsenite.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "The taxon-matched protein example anchors one experimentally supported causal branch; it is not presented as a universal mechanism for every taxon or every contextual branch in this graph.",
        "nodes": [
          {
            "node_id": "arsenic_tolerant_trait",
            "label": "arsenic tolerant",
            "node_type": "TRAIT",
            "grounding": "traitmech:000017",
            "description": "Capacity to grow at elevated arsenite/arsenate concentrations."
          },
          {
            "node_id": "arsenite",
            "label": "arsenite(3-)",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:29242",
            "description": "Toxic trivalent arsenic species accumulating in the cytoplasm."
          },
          {
            "node_id": "ars_operon",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "ArsB arsenite-efflux protein module",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Arsenite efflux machinery encoded by the near-ubiquitous ars operon.",
            "gene_symbols": [
              "arsB"
            ],
            "operon": "ars"
          },
          {
            "node_id": "arsenite_export",
            "label": "arsenite transmembrane transport",
            "node_type": "BIOLOGICAL_PROCESS",
            "grounding": "GO:0030001",
            "description": "Active export of arsenite across the cytoplasmic membrane."
          },
          {
            "node_id": "arsenate",
            "label": "arsenate(3-)",
            "node_type": "CHEMICAL",
            "description": "Pentavalent arsenic species; substrate for arsenate reductase.",
            "grounding": "CHEBI:29125"
          },
          {
            "node_id": "arsR_repressor",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "ArsR transcriptional repressor",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Trans-acting repressor that binds the ars promoter and de-represses upon arsenite binding."
          },
          {
            "node_id": "ars_promoter",
            "label": "ars promoter",
            "node_type": "GENETIC_ELEMENT",
            "description": "Promoter controlling transcription of the ars operon."
          },
          {
            "node_id": "arsC_reductase",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:Q1LRL1",
                "protein_label": "Arsenate reductase ArsC1",
                "gene_symbol": "arsC1",
                "taxon_id": "NCBITaxon:266264",
                "taxon_label": "Cupriavidus metallidurans CH34",
                "entry_status": "UNREVIEWED",
                "proteome_id": "UP000002429",
                "retrieved_on": "2026-10-22",
                "entry_version": 100,
                "sequence_version": 1,
                "role": "CH34 ArsC1 reduces intracellular arsenate to arsenite for subsequent efflux.",
                "evidence": [
                  {
                    "reference": "PMID:20463976",
                    "snippet": "arsenic resistance determinants in Cupriavidus metallidurans CH34",
                    "notes": "The cited source supports the represented protein-to-trait branch; UniProt verifies this current strain-matched protein entry."
                  }
                ]
              }
            ],
            "label": "ArsC arsenate reductase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Cytoplasmic arsenate reductase converting As(V) to As(III)."
          },
          {
            "node_id": "arsenate_reduction",
            "label": "arsenate reduction to arsenite",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduction of intracellular arsenate to arsenite prior to efflux."
          },
          {
            "node_id": "arsB_pump",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "ArsB arsenite efflux permease",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Integral membrane arsenite efflux pump extruding As(III) from the cytoplasm."
          },
          {
            "node_id": "acr3_pump",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "Acr3 arsenite efflux permease",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Alternative inorganic arsenite efflux pump exporting As(III)."
          },
          {
            "node_id": "arsM_methyltransferase",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "ArsM arsenite S-adenosylmethionine methyltransferase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Enzyme methylating arsenite to volatile methylated arsenicals."
          },
          {
            "node_id": "arsenite_methylation",
            "label": "arsenite methylation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Methylation of arsenite producing volatile methylated arsenic, a detoxification route."
          }
        ],
        "edges": [
          {
            "subject": "arsenite",
            "predicate": "challenges",
            "object": "arsenic_tolerant_trait",
            "description": "Cytoplasmic arsenite is the toxic challenge the trait counters.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2020.00047",
                "notes": "Cupriavidus metallidurans BS1 tolerates arsenite to a MIC of 3.5 mM."
              }
            ],
            "predicate_id": "METPO:2007406"
          },
          {
            "subject": "ars_operon",
            "predicate": "enables",
            "object": "arsenite_export",
            "description": "ArsB pumps arsenite out of the cytoplasm.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2018.02473",
                "notes": "ArsB is an integral membrane protein extruding arsenite from the cell cytoplasm."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "arsenite_export",
            "predicate": "mitigates",
            "object": "arsenite",
            "description": "Active export depletes the cytoplasmic arsenite pool.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2018.02473",
                "notes": "The ars operon is the near-ubiquitous arsenic-resistance determinant."
              }
            ],
            "predicate_id": "METPO:2007407"
          },
          {
            "subject": "arsR_repressor",
            "predicate": "represses",
            "object": "ars_promoter",
            "description": "ArsR represses ars-operon transcription in the absence of arsenite.",
            "evidence": [
              {
                "reference": "DOI:10.3390/antibiotics12091474",
                "notes": "ArsR is a trans-acting transcriptional repressor that binds the ars promoter."
              }
            ]
          },
          {
            "subject": "arsenite",
            "predicate": "relieves repression by",
            "object": "arsR_repressor",
            "description": "Arsenite binding changes ArsR conformation and de-represses ars transcription.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2024.1494872",
                "notes": "Binding of As(III) to ArsR changes its conformation and relieves repression of the ars operon."
              }
            ]
          },
          {
            "subject": "arsC_reductase",
            "predicate": "enables",
            "object": "arsenate_reduction",
            "description": "ArsC reduces intracellular arsenate to arsenite.",
            "evidence": [
              {
                "reference": "DOI:10.3390/antibiotics12091474",
                "notes": "ArsC is an arsenate reductase that converts intracellular As(V) to As(III)."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "arsenate_reduction",
            "predicate": "has output",
            "object": "arsenite",
            "description": "Arsenate reduction yields arsenite, the substrate for efflux.",
            "evidence": [
              {
                "reference": "DOI:10.3390/antibiotics12091474",
                "notes": "ArsC converts intracellular As(V) to As(III), feeding the efflux route."
              }
            ],
            "predicate_id": "RO:0002234"
          },
          {
            "subject": "arsB_pump",
            "predicate": "enables",
            "object": "arsenite_export",
            "description": "ArsB is an integral membrane pump extruding arsenite from the cytoplasm.",
            "evidence": [
              {
                "reference": "DOI:10.3390/antibiotics12091474",
                "notes": "ArsB is an integral membrane arsenite efflux pump that extrudes As(OH)3/As3+ from the cytoplasm."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "acr3_pump",
            "predicate": "enables",
            "object": "arsenite_export",
            "description": "Acr3 is an alternative inorganic arsenite efflux pump.",
            "evidence": [
              {
                "reference": "DOI:10.3390/microorganisms12010074",
                "notes": "Some bacteria possess acr3, coding for an inorganic arsenite efflux pump."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "arsM_methyltransferase",
            "predicate": "enables",
            "object": "arsenite_methylation",
            "description": "ArsM methylates arsenite to volatile methylated arsenicals.",
            "evidence": [
              {
                "reference": "DOI:10.7717/peerj.18383",
                "notes": "arsM (arsenite S-adenosylmethionine methyltransferase) produces volatile methylated arsenicals."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "arsenite_methylation",
            "predicate": "mitigates",
            "object": "arsenite",
            "description": "Methylation and volatilization depletes the cytoplasmic arsenite pool, a detoxification route.",
            "evidence": [
              {
                "reference": "DOI:10.7717/peerj.18383",
                "notes": "Produced arsenite is methylated by arsM to volatile methylated arsenic, removing it from the cell."
              }
            ],
            "predicate_id": "METPO:2007407"
          },
          {
            "subject": "arsC_reductase",
            "predicate": "reduces",
            "object": "arsenate",
            "description": "Arsenate reductase reduces arsenate to arsenite, the form handled by efflux pumps.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2020.00047",
                "notes": "Connecting edge wiring the enrichment node into the graph."
              }
            ],
            "predicate_id": "METPO:2007802"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-28T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate ENVIRONMENT trait (arsenic/metalloid tolerance) from literature research; sub-variant of metal tolerant.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-09T14:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (ars-operon arsenite efflux) with CHEBI/GO node groundings and RO/METPO predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 8 evidence-backed generic edges (9 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "FIX_ORPHAN_NODE",
        "changes": "Connected orphaned node 'arsenate' via arsC_reductase -[reduces]-> arsenate.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:09Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 7 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d74, METPO:2000202\u00d71, METPO:2007407\u00d71, METPO:2000017\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:30Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:29125\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates (1 to has output), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T02:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES_PART2",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates onto their causal-graph counterparts (1 to reduces), issue 301 part 2. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Each replacement is a 1:1 mirror of its source predicate that changes only the domain, so the claim each edge makes is unchanged and directions are unchanged. The replacements are proposed in proposals/metpo_traitmech_v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "CURATE_PROTEIN_TAXON_EXAMPLE",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope arsenic_tolerance_ars_efflux=MECHANISTIC with scope_notes; marked 6 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (ars_operon, arsR_repressor, arsC_reductase, arsB_pump, acr3_pump, arsM_methyltransferase); added taxon-paired protein example(s) UniProtKB:Q1LRL1 on arsC_reductase (NCBITaxon:266264); retyped 1 node(s) (ars_promoter->GENETIC_ELEMENT); added canonical example(s) NCBITaxon:266264.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-22T01:35:00Z",
        "curator": "claude",
        "action": "REFRESH_UNIPROT_ENTRY_VERSION",
        "changes": "Refreshed UniProtKB entry_version against live UniProt REST on 2026-10-22: UniProtKB:Q1LRL1 (99 -> 100 on arsC_reductase).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000013",
    "label": "cadmium tolerant",
    "definition": "A metal tolerance in which an organism grows in the presence of elevated cadmium (Cd2+) concentrations, typically via cation-efflux resistance systems such as the czc determinant.",
    "definition_source": "PMID:12829273",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "traitmech:000012"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1111/j.1365-2958.2009.06792.x",
        "snippet": "CzcP exports transition metals Zn(2+), Cd(2+) and Co(2+)",
        "notes": "The cobalt-zinc-cadmium (czc) efflux system of Cupriavidus metallidurans confers cadmium resistance."
      },
      {
        "reference": "DOI:10.3389/fmicb.2020.00047",
        "snippet": "C. metallidurans BS1 conferred resistance to Zn2+ displaying a MIC of 20 mM, Cd2+ (2.5 mM), Co2+ (20mM), Ni2+ (8 mM), As3+ (3.5 mM), Cu2+ (5 mM), Au3+ (1 uM) and Pb2+ (1.7 mM)",
        "notes": "Organism example: Cupriavidus metallidurans BS1 tolerates cadmium to a MIC of 2.5 mM."
      },
      {
        "reference": "PMID:12829273",
        "snippet": "CBA efflux pumps driven by proteins of the resistance-nodulation-cell division superfamily, P-type ATPases, cation diffusion facilitator and chromate proteins",
        "notes": "Nies (2003, FEMS Microbiol Rev 27:313-339) reviews prokaryotic heavy-metal resistance mediated by RND-family CBA efflux pumps (including CzcCBA), P-type ATPases, and cation diffusion facilitators, supporting the record definition and definition_source for cadmium tolerance."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:119219",
        "taxon_label": "Cupriavidus metallidurans",
        "note": "cadmium efflux resistance",
        "reference": "PMID:20463976"
      },
      {
        "taxon_id": "NCBITaxon:266264",
        "taxon_label": "Cupriavidus metallidurans CH34",
        "note": "Strain-level CzcA metal-efflux exemplar.",
        "reference": "PMID:20463976"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "cadmium_tolerance_czc_efflux",
        "title": "Cadmium tolerance via czc cation-efflux system",
        "description": "Evidence-backed causal sketch linking the cobalt-zinc-cadmium (czc) efflux determinant to cytoplasmic cadmium detoxification.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "The taxon-matched protein example anchors one experimentally supported causal branch; it is not presented as a universal mechanism for every taxon or every contextual branch in this graph.",
        "nodes": [
          {
            "node_id": "cadmium_tolerant_trait",
            "label": "cadmium tolerant",
            "node_type": "TRAIT",
            "grounding": "traitmech:000013",
            "description": "Capacity to grow at elevated Cd(2+) concentrations."
          },
          {
            "node_id": "cadmium_ion",
            "label": "cadmium(2+) ion",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:48775",
            "description": "Toxic transition-metal cation accumulating in the cytoplasm."
          },
          {
            "node_id": "czc_efflux_system",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:P13511",
                "protein_label": "Cobalt-zinc-cadmium resistance protein CzcA",
                "gene_symbol": "czcA",
                "taxon_id": "NCBITaxon:266264",
                "taxon_label": "Cupriavidus metallidurans CH34",
                "entry_status": "REVIEWED",
                "proteome_id": "UP000002429",
                "retrieved_on": "2026-10-22",
                "entry_version": 154,
                "sequence_version": 3,
                "role": "CzcA is the inner-membrane transporter component of the CH34 CzcCBA pump exporting cadmium, zinc, and cobalt.",
                "evidence": [
                  {
                    "reference": "DOI:10.1111/j.1365-2958.2009.06792.x",
                    "snippet": "Czc machinery exports cadmium, zinc, and cobalt",
                    "notes": "The cited source supports the represented protein-to-trait branch; UniProt verifies this current strain-matched protein entry."
                  }
                ]
              }
            ],
            "label": "czc cation-efflux system",
            "node_type": "GENE_OR_PROTEIN",
            "description": "CzcCBA/CzcP machinery exporting Cd, Zn, and Co cations."
          },
          {
            "node_id": "cadmium_export",
            "label": "cadmium ion transmembrane transport",
            "node_type": "BIOLOGICAL_PROCESS",
            "grounding": "GO:0030001",
            "description": "Active export of Cd(2+) across the cytoplasmic membrane."
          },
          {
            "node_id": "metallothionein_proteins",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "metallothionein / thiol-rich metal-binding proteins",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Cysteine-rich proteins that bind and sequester cytoplasmic Cd(2+)."
          },
          {
            "node_id": "cadmium_sequestration",
            "label": "cadmium ion sequestration",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Intracellular binding and sequestration of cadmium ions, lowering free cytoplasmic Cd(2+)."
          },
          {
            "node_id": "cada_ptype_atpase",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "CadA P-type (P1B) ATPase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "ATP-driven P1B-type efflux ATPase pumping Cd(II) from cytoplasm to periplasm."
          },
          {
            "node_id": "zinc_ion",
            "label": "zinc(2+) ion",
            "node_type": "CHEMICAL",
            "description": "Divalent metal cation that cross-induces the czc cadmium-resistance program.",
            "grounding": "CHEBI:29105"
          }
        ],
        "edges": [
          {
            "subject": "cadmium_ion",
            "predicate": "challenges",
            "object": "cadmium_tolerant_trait",
            "description": "Cytoplasmic cadmium is the toxic challenge the trait counters.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2020.00047",
                "notes": "Cupriavidus metallidurans BS1 tolerates Cd(2+) to a MIC of 2.5 mM."
              }
            ],
            "predicate_id": "METPO:2007406"
          },
          {
            "subject": "czc_efflux_system",
            "predicate": "enables",
            "object": "cadmium_export",
            "description": "CzcP exports cadmium together with zinc and cobalt cations.",
            "evidence": [
              {
                "reference": "DOI:10.1111/j.1365-2958.2009.06792.x",
                "notes": "CzcP exports transition metals Zn(2+), Cd(2+), and Co(2+)."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "cadmium_export",
            "predicate": "mitigates",
            "object": "cadmium_ion",
            "description": "Czc-mediated export depletes the cytoplasmic cadmium pool.",
            "evidence": [
              {
                "reference": "DOI:10.1111/j.1365-2958.2009.06792.x",
                "notes": "The czc efflux system of C. metallidurans confers cadmium resistance."
              }
            ],
            "predicate_id": "METPO:2007407"
          },
          {
            "subject": "metallothionein_proteins",
            "predicate": "enables",
            "object": "cadmium_sequestration",
            "description": "Thiol-rich metallothioneins bind and sequester cytoplasmic Cd(2+).",
            "evidence": [
              {
                "reference": "DOI:10.1007/s40201-023-00887-6",
                "notes": "Metallothioneins bind Cd(II); thiol-rich proteins mediate cadmium sequestration as a microbial resistance mechanism."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "cadmium_sequestration",
            "predicate": "mitigates",
            "object": "cadmium_ion",
            "description": "Sequestration of cadmium lowers the free toxic cytoplasmic Cd(2+) pool.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s40201-023-00887-6",
                "notes": "Metallothionein/thiol-rich sequestration removes free cytoplasmic Cd(II) as a detoxification mechanism."
              }
            ],
            "predicate_id": "METPO:2007407"
          },
          {
            "subject": "cada_ptype_atpase",
            "predicate": "enables",
            "object": "cadmium_export",
            "description": "CadA P1B-type ATPase uses ATP to pump Cd(II) from cytoplasm to periplasm.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s40201-023-00887-6",
                "notes": "P-type (P1B) ATPases (CadA) use ATP to pump Cd(II) from cytoplasm to periplasm."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "zinc_ion",
            "predicate": "induces",
            "object": "czc_efflux_system",
            "description": "Zinc cross-induces expression of the czc cation-efflux cadmium-resistance program.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s40201-023-00887-6",
                "notes": "czc expression is induced by zinc; zinc exposure enhances cadmium resistance via the efflux program."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-28T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate ENVIRONMENT trait (cadmium tolerance) from literature research; metal-specific sub-variant of metal tolerant.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-09T14:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (czc cadmium efflux) with CHEBI/GO node groundings and RO/METPO predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-14T06:38:14Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:B0VPE1\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 4 evidence-backed generic edges (4 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:09Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d72, METPO:2007407\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:30Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:29105\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:21:11Z",
        "curator": "claude",
        "action": "RETRACT_DEAD_UNIPROT_GROUNDINGS",
        "changes": "Retracted 1 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "CURATE_PROTEIN_TAXON_EXAMPLE",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope cadmium_tolerance_czc_efflux=MECHANISTIC with scope_notes; marked 3 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (czc_efflux_system, metallothionein_proteins, cada_ptype_atpase); added taxon-paired protein example(s) UniProtKB:P13511 on czc_efflux_system (NCBITaxon:266264); added canonical example(s) NCBITaxon:266264.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-22T01:35:00Z",
        "curator": "claude",
        "action": "REFRESH_UNIPROT_ENTRY_VERSION",
        "changes": "Refreshed UniProtKB entry_version against live UniProt REST on 2026-10-22: UniProtKB:P13511 (153 -> 154 on czc_efflux_system).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-22T05:20:00Z",
        "curator": "claude",
        "action": "ADD_RECORD_LEVEL_DEFINITION_SOURCE_EVIDENCE",
        "changes": "Added PMID:12829273 (Nies 2003) with verified verbatim snippet to record-level evidence to match definition_source (Stage 5 remediation of F-DEF-SRC-CADMIUM-002 in group G-STAGE4-RECORD-LEVEL-DEFINITION-SOURCE, issue #1981).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1005021",
    "label": "capnophilic",
    "definition": "A phenotype describing an organism that requires elevated concentrations of carbon dioxide for growth.",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "SEEDED",
    "parent_traits": [
      "METPO:1000601"
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-11T07:15:32Z",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)"
      },
      {
        "timestamp": "2026-09-11T07:30:00Z",
        "curator": "codex",
        "action": "ENRICHED_FROM_LITERATURE",
        "changes": "Enriched the seeded METPO capnophilic phenotype with DOI-backed elevated-carbon-dioxide evidence after a repository-wide duplicate review covering ignored and hidden files.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-21T21:12:24Z",
        "curator": "claude",
        "action": "CURATE_CAUSAL_GRAPH",
        "changes": "Added MECHANISTIC causal_graphs entry (capnophilic_co2_canb_sketch) anchored on existing verbatim record evidence snippets.",
        "llm_assisted": true
      }
    ],
    "definition_source": "DOI:10.1111/1462-2920.13092",
    "evidence": [
      {
        "reference": "DOI:10.1111/1462-2920.13092",
        "snippet": "Campylobacter jejuni, the leading cause of human bacterial gastroenteritis, requires low environmental oxygen and high carbon dioxide for optimum growth",
        "notes": "Al-Haideri et al. support elevated carbon dioxide as a growth condition required by capnophilic Campylobacter jejuni."
      },
      {
        "reference": "DOI:10.1111/1462-2920.13092",
        "snippet": "Taken together, our data suggest CanB is a major contributor to the capnophilic growth phenotype of C. jejuni.",
        "notes": "Al-Haideri et al. describe the elevated-CO2 requirement as a capnophilic growth phenotype and identify CanB as a major contributor in C. jejuni NCTC 11168."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:192222",
        "taxon_label": "Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819",
        "note": "C. jejuni NCTC 11168 was the strain background for the CanB study of the C. jejuni capnophilic growth phenotype.",
        "reference": "DOI:10.1111/1462-2920.13092"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "capnophilic_co2_canb_sketch",
        "title": "Capnophilic elevated-CO2 requirement and CanB contribution",
        "description": "Evidence-backed causal mechanism linking the capnophilic growth phenotype to elevated environmental carbon dioxide and beta-class carbonic anhydrase CanB.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "The taxon-matched protein example anchors the Campylobacter jejuni NCTC 11168 CanB (Cj0237/CynT) beta-carbonic anhydrase branch; it is not presented as a universal mechanism for every capnophilic organism.",
        "nodes": [
          {
            "node_id": "capnophilic_trait",
            "label": "capnophilic",
            "node_type": "TRAIT",
            "grounding": "METPO:1005021",
            "description": "Requirement for elevated carbon dioxide concentrations for optimal microbial growth."
          },
          {
            "node_id": "capnophilic_carbon_dioxide",
            "label": "carbon dioxide",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:16526",
            "description": "Elevated environmental carbon dioxide required for optimal capnophilic growth."
          },
          {
            "node_id": "capnophilic_canb_carbonic_anhydrase",
            "label": "beta-carbonic anhydrase CanB",
            "node_type": "GENE_OR_PROTEIN",
            "grounding": "InterPro:IPR001765",
            "description": "Beta-class carbonic anhydrase (CanB/Cj0237) contributing to capnophilic growth in Campylobacter jejuni.",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:Q0PBR7",
                "protein_label": "Carbonic anhydrase",
                "gene_symbol": "cynT",
                "taxon_id": "NCBITaxon:192222",
                "taxon_label": "Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168)",
                "entry_status": "UNREVIEWED",
                "entry_version": 98,
                "sequence_version": 1,
                "proteome_id": "UP000000799",
                "retrieved_on": "2026-10-21",
                "role": "Cytoplasmic beta-carbonic anhydrase CanB (Cj0237/CynT) that is a major contributor to the capnophilic growth phenotype of Campylobacter jejuni NCTC 11168.",
                "evidence": [
                  {
                    "reference": "DOI:10.1111/1462-2920.13092",
                    "snippet": "Taken together, our data suggest CanB is a major contributor to the capnophilic growth phenotype of C. jejuni.",
                    "notes": "Al-Haideri et al. establish that CanB (Cj0237, UniProtKB:Q0PBR7) is a major contributor to the capnophilic growth phenotype of C. jejuni NCTC 11168."
                  }
                ]
              }
            ]
          }
        ],
        "edges": [
          {
            "subject": "capnophilic_trait",
            "predicate": "depends on",
            "predicate_id": "RO:0002502",
            "object": "capnophilic_carbon_dioxide",
            "description": "Capnophilic growth depends on elevated environmental carbon dioxide concentrations.",
            "evidence": [
              {
                "reference": "DOI:10.1111/1462-2920.13092",
                "snippet": "Campylobacter jejuni, the leading cause of human bacterial gastroenteritis, requires low environmental oxygen and high carbon dioxide for optimum growth",
                "notes": "Al-Haideri et al. establish that capnophilic Campylobacter jejuni requires high environmental carbon dioxide for optimum growth."
              }
            ]
          },
          {
            "subject": "capnophilic_canb_carbonic_anhydrase",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "capnophilic_trait",
            "description": "Beta-carbonic anhydrase CanB contributes to the capnophilic growth phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1111/1462-2920.13092",
                "snippet": "Taken together, our data suggest CanB is a major contributor to the capnophilic growth phenotype of C. jejuni.",
                "notes": "Al-Haideri et al. show that CanB is a major contributor to the capnophilic growth phenotype of C. jejuni."
              }
            ]
          }
        ]
      }
    ]
  },
  {
    "identifier": "traitmech:000015",
    "label": "cobalt tolerant",
    "definition": "A metal tolerance in which an organism grows in the presence of elevated cobalt (Co2+) concentrations, typically via cation-efflux resistance systems such as the czc and cnr determinants.",
    "definition_source": "PMID:12829273",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "traitmech:000012"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1111/j.1365-2958.2009.06792.x",
        "snippet": "CzcP exports transition metals Zn(2+), Cd(2+) and Co(2+)",
        "notes": "The cobalt-zinc-cadmium (czc) efflux system of Cupriavidus metallidurans confers cobalt resistance."
      },
      {
        "reference": "DOI:10.3389/fmicb.2020.00047",
        "snippet": "C. metallidurans BS1 conferred resistance to Zn2+ displaying a MIC of 20 mM, Cd2+ (2.5 mM), Co2+ (20mM), Ni2+ (8 mM), As3+ (3.5 mM), Cu2+ (5 mM), Au3+ (1 uM) and Pb2+ (1.7 mM)",
        "notes": "Organism example: Cupriavidus metallidurans BS1 tolerates cobalt to a MIC of 20 mM."
      },
      {
        "reference": "PMID:12829273",
        "snippet": "CBA efflux pumps driven by proteins of the resistance-nodulation-cell division superfamily, P-type ATPases, cation diffusion facilitator and chromate proteins",
        "notes": "Nies (2003, FEMS Microbiol Rev 27:313-339) reviews prokaryotic heavy-metal resistance mediated by RND-family CBA efflux pumps (including CzcCBA and CnrCBA) and cation diffusion facilitators, supporting the record definition and definition_source for cobalt tolerance."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:119219",
        "taxon_label": "Cupriavidus metallidurans",
        "note": "cobalt-resistance determinants",
        "reference": "PMID:20463976"
      },
      {
        "taxon_id": "NCBITaxon:266264",
        "taxon_label": "Cupriavidus metallidurans CH34",
        "note": "Strain-level CzcA cobalt-efflux exemplar.",
        "reference": "PMID:20463976"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "cobalt_tolerance_czc_cnr_efflux",
        "title": "Cobalt tolerance via czc/cnr cation-efflux systems",
        "description": "Evidence-backed causal sketch linking the czc and cnr efflux determinants to cytoplasmic cobalt detoxification.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "The taxon-matched protein example anchors one experimentally supported causal branch; it is not presented as a universal mechanism for every taxon or every contextual branch in this graph.",
        "nodes": [
          {
            "node_id": "cobalt_tolerant_trait",
            "label": "cobalt tolerant",
            "node_type": "TRAIT",
            "grounding": "traitmech:000015",
            "description": "Capacity to grow at elevated Co(2+) concentrations."
          },
          {
            "node_id": "cobalt_ion",
            "label": "cobalt(2+) ion",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:48828",
            "description": "Toxic transition-metal cation accumulating in the cytoplasm."
          },
          {
            "node_id": "cobalt_efflux_system",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "czc/cnr cobalt efflux system",
            "node_type": "GENE_OR_PROTEIN",
            "description": "CzcCBA/CzcP and Cnr pumps exporting cobalt cations."
          },
          {
            "node_id": "cobalt_export",
            "label": "cobalt ion transmembrane transport",
            "node_type": "BIOLOGICAL_PROCESS",
            "grounding": "GO:0030001",
            "description": "Active export of Co(2+) across the cytoplasmic membrane."
          },
          {
            "node_id": "czcCBA_complex",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:P13511",
                "protein_label": "Cobalt-zinc-cadmium resistance protein CzcA",
                "gene_symbol": "czcA",
                "taxon_id": "NCBITaxon:266264",
                "taxon_label": "Cupriavidus metallidurans CH34",
                "entry_status": "REVIEWED",
                "proteome_id": "UP000002429",
                "retrieved_on": "2026-10-22",
                "entry_version": 154,
                "sequence_version": 3,
                "role": "CzcA is one transporter component of the CH34 CzcCBA complex that exports cobalt, zinc, and cadmium.",
                "evidence": [
                  {
                    "reference": "PMID:20463976",
                    "snippet": "Czc determinants confer heavy-metal resistance in CH34",
                    "notes": "The cited source supports the represented protein-to-trait branch; UniProt verifies this current strain-matched protein entry."
                  }
                ]
              }
            ],
            "label": "CzcCBA efflux complex",
            "node_type": "GENE_OR_PROTEIN",
            "description": "HME-RND/CBA chemiosmotic divalent-cation/proton antiporter exporting Co2+, Zn2+, Cd2+."
          },
          {
            "node_id": "czcRS_two_component",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "CzcS/CzcR two-component system",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Sensor kinase CzcS and response regulator CzcR that transcriptionally activate czcCBA."
          },
          {
            "node_id": "czcCBA_expression",
            "label": "czcCBA operon expression",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Transcription of the czcCBA efflux operon."
          },
          {
            "node_id": "cnr_operon",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "Cnr cobalt-nickel resistance protein module",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Cobalt-nickel resistance operon on plasmid pMOL28 conferring Co/Ni efflux.",
            "gene_symbols": [
              "cnrC",
              "cnrB",
              "cnrA",
              "cnrY",
              "cnrX",
              "cnrH",
              "cnrT"
            ],
            "operon": "cnrCBAYXHT"
          },
          {
            "node_id": "dmeF_exporter",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "DmeF CDF-family exporter",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Cation diffusion facilitator with cobalt as preferred substrate."
          },
          {
            "node_id": "rcnA_exporter",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "RcnA/YohM Co/Ni efflux protein",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Membrane-bound efflux system conferring nickel and cobalt resistance."
          },
          {
            "node_id": "cobalt_homeostasis",
            "label": "cellular cobalt homeostasis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Baseline management of cytoplasmic cobalt levels, including under non-stress conditions."
          }
        ],
        "edges": [
          {
            "subject": "cobalt_ion",
            "predicate": "challenges",
            "object": "cobalt_tolerant_trait",
            "description": "Cytoplasmic cobalt is the toxic challenge the trait counters.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2020.00047",
                "notes": "Cupriavidus metallidurans BS1 tolerates Co(2+) to a MIC of 20 mM."
              }
            ],
            "predicate_id": "METPO:2007406"
          },
          {
            "subject": "cobalt_efflux_system",
            "predicate": "enables",
            "object": "cobalt_export",
            "description": "CzcP exports cobalt together with zinc and cadmium cations.",
            "evidence": [
              {
                "reference": "DOI:10.1111/j.1365-2958.2009.06792.x",
                "notes": "CzcP exports transition metals Zn(2+), Cd(2+), and Co(2+)."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "cobalt_export",
            "predicate": "mitigates",
            "object": "cobalt_ion",
            "description": "Czc/cnr-mediated export depletes the cytoplasmic cobalt pool.",
            "evidence": [
              {
                "reference": "DOI:10.1111/j.1365-2958.2009.06792.x",
                "notes": "The czc efflux system of C. metallidurans confers cobalt resistance."
              }
            ],
            "predicate_id": "METPO:2007407"
          },
          {
            "subject": "czcCBA_complex",
            "predicate": "exports",
            "object": "cobalt_ion",
            "description": "CzcCBA RND antiporter effluxes cytoplasmic cobalt together with Zn2+ and Cd2+.",
            "evidence": [
              {
                "reference": "DOI:10.3390/ijms26125716",
                "notes": "CzcCBA, an RND-superfamily chemiosmotic divalent cation/proton antiporter, deals with the efflux of Cd2+, Zn2+, and Co2+."
              }
            ],
            "predicate_id": "METPO:2007804"
          },
          {
            "subject": "czcRS_two_component",
            "predicate": "activates transcription of",
            "object": "czcCBA_expression",
            "description": "CzcS sensor kinase activates response regulator CzcR, which transcriptionally activates czcCBA.",
            "evidence": [
              {
                "reference": "DOI:10.3390/ijms26125716",
                "notes": "Activated CzcR functions as a transcriptional activator of czcCBA expression."
              }
            ]
          },
          {
            "subject": "czcCBA_expression",
            "predicate": "enables",
            "object": "cobalt_export",
            "description": "Expression of the czcCBA operon produces the efflux complex enabling cobalt export.",
            "evidence": [
              {
                "reference": "DOI:10.3390/ijms26125716",
                "notes": "czcCBA encodes the CzcCBA system mediating Co2+ efflux."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "cnr_operon",
            "predicate": "confers resistance to",
            "object": "cobalt_tolerant_trait",
            "description": "The cnrCBAYXHT operon confers cobalt (and nickel) resistance.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s44274-025-00301-y",
                "notes": "This strain exhibits resistance to 3 mM Ni and 5 mM Co, conferred by the cnrCBAYXHT operon located on plasmid pMOL28."
              }
            ]
          },
          {
            "subject": "dmeF_exporter",
            "predicate": "exports",
            "object": "cobalt_ion",
            "description": "DmeF CDF-family exporter preferentially effluxes cobalt.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s44274-025-00301-y",
                "notes": "Co2+ is the preferred substrate for the DmeF protein in Cupriavidus metallidurans CH34."
              }
            ],
            "predicate_id": "METPO:2007804"
          },
          {
            "subject": "rcnA_exporter",
            "predicate": "enables",
            "object": "cobalt_export",
            "description": "RcnA/YohM is an efflux system for nickel and cobalt, increasing cobalt resistance.",
            "evidence": [
              {
                "reference": "DOI:10.1128/JB.187.8.2912-2916.2005",
                "notes": "yohM encodes a membrane-bound polypeptide conferring increased nickel and cobalt resistance in E. coli; YohM is the first described efflux system for nickel and cobalt in E. coli."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "cobalt_export",
            "predicate": "contributes to",
            "object": "cobalt_homeostasis",
            "description": "Czc/Cnr efflux complexes are present even without added metals, contributing to baseline cobalt homeostasis as well as stress resistance.",
            "evidence": [
              {
                "reference": "DOI:10.1093/mtomcs/mfae058",
                "notes": "Czc-CBA proteins were also present in control cells cultivated without added metals so that Czc has also a function in metal homeostasis."
              }
            ],
            "predicate_id": "RO:0002326"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-28T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate ENVIRONMENT trait (cobalt tolerance) from literature research; metal-specific sub-variant of metal tolerant.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-09T14:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (czc/cnr cobalt efflux) with CHEBI/GO node groundings and RO/METPO predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 7 evidence-backed generic edges (7 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:09Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 5 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000209\u00d72, RO:0002327\u00d72, RO:0002326\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T02:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES_PART2",
        "changes": "Re-grounded 2 causal edge(s) off microbe-domain METPO predicates onto their causal-graph counterparts (2 to exports), issue 301 part 2. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Each replacement is a 1:1 mirror of its source predicate that changes only the domain, so the claim each edge makes is unchanged and directions are unchanged. The replacements are proposed in proposals/metpo_traitmech_v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "CURATE_PROTEIN_TAXON_EXAMPLE",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope cobalt_tolerance_czc_cnr_efflux=MECHANISTIC with scope_notes; marked 6 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (cobalt_efflux_system, czcCBA_complex, czcRS_two_component, cnr_operon, dmeF_exporter, rcnA_exporter); added taxon-paired protein example(s) UniProtKB:P13511 on czcCBA_complex (NCBITaxon:266264); added canonical example(s) NCBITaxon:266264.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-22T01:35:00Z",
        "curator": "claude",
        "action": "REFRESH_UNIPROT_ENTRY_VERSION",
        "changes": "Refreshed UniProtKB entry_version against live UniProt REST on 2026-10-22: UniProtKB:P13511 (153 -> 154 on czcCBA_complex).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-22T05:20:00Z",
        "curator": "claude",
        "action": "ADD_RECORD_LEVEL_DEFINITION_SOURCE_EVIDENCE",
        "changes": "Added PMID:12829273 (Nies 2003) with verified verbatim snippet to record-level evidence to match definition_source (Stage 5 remediation of F-DEF-SRC-COBALT-003 in group G-STAGE4-RECORD-LEVEL-DEFINITION-SOURCE, issue #1981).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000018",
    "label": "copper tolerant",
    "definition": "A metal tolerance in which an organism grows in the presence of elevated copper (Cu2+/Cu+) concentrations, typically via the cue, cus, pco, and cop systems and ATPase-driven cytoplasmic copper efflux.",
    "definition_source": "DOI:10.1007/s10565-013-9262-1",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "traitmech:000012"
    ],
    "synonyms": [
      {
        "synonym_text": "copper resistant",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1007/s10565-013-9262-1"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1007/s10565-013-9262-1",
        "snippet": "ATPase-driven copper efflux seems to be the main mechanism responsible for cytoplasmic copper detoxification in until now studied bacteria",
        "notes": "Review supports active efflux via the cue, cus, pco, and cop systems as the basis of bacterial copper tolerance."
      },
      {
        "reference": "DOI:10.3389/fmicb.2020.00047",
        "snippet": "C. metallidurans BS1 conferred resistance to Zn2+ displaying a MIC of 20 mM, Cd2+ (2.5 mM), Co2+ (20mM), Ni2+ (8 mM), As3+ (3.5 mM), Cu2+ (5 mM), Au3+ (1 uM) and Pb2+ (1.7 mM)",
        "notes": "Organism example: Cupriavidus metallidurans BS1 tolerates copper (Cu2+) to a MIC of 5 mM."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:119219",
        "taxon_label": "Cupriavidus metallidurans",
        "note": "copper-resistance determinants",
        "reference": "PMID:37191542"
      },
      {
        "taxon_id": "NCBITaxon:266264",
        "taxon_label": "Cupriavidus metallidurans CH34",
        "note": "Strain-level CopA2 copper-detoxification exemplar.",
        "reference": "PMID:37191542"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "copper_tolerance_cop_efflux",
        "title": "Copper tolerance via cop/cue/cus/pco efflux systems",
        "description": "Evidence-backed causal sketch linking dedicated copper-efflux machinery to cytoplasmic copper detoxification.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "The taxon-matched protein example anchors one experimentally supported causal branch; it is not presented as a universal mechanism for every taxon or every contextual branch in this graph.",
        "nodes": [
          {
            "node_id": "copper_tolerant_trait",
            "label": "copper tolerant",
            "node_type": "TRAIT",
            "grounding": "traitmech:000018",
            "description": "Capacity to grow at elevated Cu(I)/Cu(II) concentrations."
          },
          {
            "node_id": "copper_ion",
            "label": "copper(2+) ion",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:29036",
            "description": "Cytoplasmic Cu(II) excess threatening Fenton-like damage."
          },
          {
            "node_id": "copper_efflux_system",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "copper efflux systems (cue/cus/pco/cop)",
            "node_type": "GENE_OR_PROTEIN",
            "description": "ATPase- and RND-driven pumps removing copper from the cytoplasm or periplasm."
          },
          {
            "node_id": "copper_transport",
            "label": "copper ion transmembrane transport",
            "node_type": "BIOLOGICAL_PROCESS",
            "grounding": "GO:0035434",
            "description": "Active export of copper ions across the cytoplasmic membrane."
          },
          {
            "node_id": "ros_oxidative_damage",
            "label": "ROS-mediated oxidative damage",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Fenton-like Cu(I) chemistry generating ROS that damage lipids, proteins, DNA, and Fe-S clusters."
          },
          {
            "node_id": "multicopper_oxidase",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:Q1LBE6",
                "protein_label": "Copper resistance protein CopA2",
                "gene_symbol": "copA2",
                "taxon_id": "NCBITaxon:266264",
                "taxon_label": "Cupriavidus metallidurans CH34",
                "entry_status": "UNREVIEWED",
                "proteome_id": "UP000002429",
                "retrieved_on": "2026-10-22",
                "entry_version": 100,
                "sequence_version": 1,
                "role": "CH34 CopA2 is a multicopper oxidase participating in periplasmic copper detoxification.",
                "evidence": [
                  {
                    "reference": "PMID:37191542",
                    "snippet": "copper-resistance determinants in Cupriavidus metallidurans",
                    "notes": "The cited source supports the represented protein-to-trait branch; UniProt verifies this current strain-matched protein entry."
                  }
                ]
              }
            ],
            "label": "periplasmic multicopper oxidase (CueO-type)",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Oxygen-dependent multicopper oxidase that oxidizes toxic Cu(I) to less-toxic Cu(II) in the periplasm."
          },
          {
            "node_id": "cu1_oxidation",
            "label": "Cu(I) to Cu(II) oxidation",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "Enzymatic oxidation of toxic cuprous Cu(I) to less-toxic cupric Cu(II) reducing ROS-mediated damage."
          }
        ],
        "edges": [
          {
            "subject": "copper_ion",
            "predicate": "challenges",
            "object": "copper_tolerant_trait",
            "description": "Elevated cytoplasmic copper is the toxic challenge the trait counters.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2020.00047",
                "notes": "Cupriavidus metallidurans BS1 tolerates Cu(2+) to a MIC of 5 mM."
              }
            ],
            "predicate_id": "METPO:2007406"
          },
          {
            "subject": "copper_efflux_system",
            "predicate": "enables",
            "object": "copper_transport",
            "description": "Cue/cus/pco/cop pumps drive ATPase-mediated copper export.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s10565-013-9262-1",
                "notes": "Review supports ATPase-driven efflux via cue/cus/pco/cop systems as the main copper detoxification mechanism."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "copper_transport",
            "predicate": "mitigates",
            "object": "copper_ion",
            "description": "Copper export depletes the cytoplasmic copper pool.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s10565-013-9262-1",
                "notes": "Cytoplasmic copper detoxification is the basis of bacterial copper tolerance."
              }
            ],
            "predicate_id": "METPO:2007407"
          },
          {
            "subject": "copper_ion",
            "predicate": "causes",
            "object": "ros_oxidative_damage",
            "description": "Excess intracellular copper drives Fenton-like reactions producing ROS that damage cellular macromolecules.",
            "evidence": [
              {
                "reference": "DOI:10.3390/antibiotics12091474",
                "notes": "Cu(I) driving Fenton-like reactions causing damage to lipids, proteins and DNA and disrupting Fe-S clusters; defines why tolerance mechanisms matter."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "copper_transport",
            "predicate": "mitigates",
            "object": "ros_oxidative_damage",
            "description": "P1B-type ATPase copper efflux lowers cytoplasmic copper, reducing copper-driven oxidative toxicity.",
            "evidence": [
              {
                "reference": "DOI:10.3390/antibiotics12091474",
                "notes": "Primary defense is active efflux via P1B-1 (P-type) ATPases; in Gram-negatives CopA pumps cytoplasmic Cu(I) to the periplasm, decreasing cytoplasmic copper toxicity."
              }
            ],
            "predicate_id": "METPO:2007407"
          },
          {
            "subject": "multicopper_oxidase",
            "predicate": "enables",
            "object": "cu1_oxidation",
            "description": "CueO-type periplasmic multicopper oxidase catalyzes oxidation of Cu(I) to Cu(II) in the presence of oxygen.",
            "evidence": [
              {
                "reference": "DOI:10.3390/antibiotics12091474",
                "notes": "CueO oxidizes Cu(I) to less-toxic Cu(II) in oxygen; generalized periplasmic detox mechanism (aerobic context)."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "cu1_oxidation",
            "predicate": "mitigates",
            "object": "copper_ion",
            "description": "Oxidation of Cu(I) to less-toxic Cu(II) lowers the reactive copper burden in the periplasm.",
            "evidence": [
              {
                "reference": "DOI:10.3390/antibiotics12091474",
                "notes": "Oxidation of Cu(I) to less-toxic Cu(II) reduces reactive-copper toxicity and ROS-mediated membrane damage."
              }
            ],
            "predicate_id": "METPO:2007407"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-28T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate ENVIRONMENT trait (copper tolerance) from literature research; metal-specific sub-variant of metal tolerant.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-09T14:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (cop/cue/cus/pco copper efflux) with CHEBI/GO node groundings and RO/METPO predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 4 evidence-backed generic edges (3 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:09Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 4 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007407\u00d72, biolink:causes\u00d71, RO:0002327\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "CURATE_PROTEIN_TAXON_EXAMPLE",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope copper_tolerance_cop_efflux=MECHANISTIC with scope_notes; marked 2 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (copper_efflux_system, multicopper_oxidase); added taxon-paired protein example(s) UniProtKB:Q1LBE6 on multicopper_oxidase (NCBITaxon:266264); added canonical example(s) NCBITaxon:266264.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-22T01:35:00Z",
        "curator": "claude",
        "action": "REFRESH_UNIPROT_ENTRY_VERSION",
        "changes": "Refreshed UniProtKB entry_version against live UniProt REST on 2026-10-22: UniProtKB:Q1LBE6 (99 -> 100 on multicopper_oxidase).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000534",
    "label": "delta phenotype with numerical limits",
    "definition": "A phenotype characterized by the difference between maximum and minimum values of a growth parameter.",
    "definition_source": "DOI:10.1093/femsre/fuy009",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1093/femsre/fuy009",
        "snippet": "salinity range",
        "notes": "Osmoadaptation review supports the breadth of a growth-supporting environmental range as a derived quantitative descriptor of microbial physiology."
      },
      {
        "reference": "DOI:10.1016/s0300-9629(97)00003-0",
        "snippet": "adapted to environments of high temperature",
        "notes": "Thermophile-adaptation review supports thermal-tolerance breadth as a comparable derived quantitative descriptor."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:334543",
        "taxon_label": "Psychrobacter arcticus",
        "reference": "DOI:10.1128/JB.01377-08",
        "note": "Psychrobacter arcticus 273-4 grew from -10 to 28 degrees C in the reported experiments (38 degrees C nominal breadth); the example demonstrates an endpoint-derived delta while retaining the source's endpoint caveat."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "delta_phenotype_breadth_descriptor",
        "title": "Delta phenotype breadth descriptor across environmental axes",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a quantitative measurement, interval, or bin in the environmental phenotype hierarchy; a token protein example would misrepresent the measured value as one inherited molecular mechanism.",
        "description": "DOI-backed graph framing the delta phenotype as a generic derived breadth descriptor over any numerical environmental axis, with `is a` edges to the axis-specific delta phenotypes for NaCl, pH, and temperature.",
        "nodes": [
          {
            "node_id": "delta_phenotype_trait",
            "label": "delta phenotype with numerical limits",
            "node_type": "TRAIT",
            "grounding": "METPO:1000534",
            "description": "Phenotype defined by the max \u2212 min span of a growth-supporting environmental variable."
          },
          {
            "node_id": "numerical_environmental_axis",
            "label": "numerical environmental axis",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Any continuous environmental variable (NaCl, pH, temperature, etc.) on which microbial growth can be measured quantitatively."
          },
          {
            "node_id": "nacl_delta",
            "label": "NaCl delta",
            "node_type": "TRAIT",
            "grounding": "METPO:1000335",
            "description": "Breadth of the growth-supporting NaCl range."
          },
          {
            "node_id": "ph_delta",
            "label": "pH delta",
            "node_type": "TRAIT",
            "grounding": "METPO:1000232",
            "description": "Breadth of the growth-supporting external pH range."
          },
          {
            "node_id": "temperature_delta",
            "label": "temperature delta",
            "node_type": "TRAIT",
            "grounding": "METPO:1000303",
            "description": "Breadth of the growth-supporting ambient-temperature range."
          },
          {
            "node_id": "membrane_fluidity",
            "label": "membrane fluidity/stability",
            "node_type": "QUALITY",
            "description": "Physical state of the lipid bilayer (fluidity, packing, integrity) that must be maintained for growth."
          },
          {
            "node_id": "homeoviscous_adaptation",
            "label": "homeoviscous adaptation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Regulation of membrane lipid composition to keep fluidity within a functional window under stress.",
            "grounding": "METPO:1016200"
          },
          {
            "node_id": "compatible_solutes",
            "label": "compatible solutes / osmolytes",
            "node_type": "CHEMICAL",
            "description": "Small organic molecules that stabilize proteins and membranes and restore osmotic balance."
          },
          {
            "node_id": "fatty_acid_ratio",
            "label": "saturated:unsaturated fatty-acid ratio",
            "node_type": "QUALITY",
            "description": "Relative abundance of saturated versus unsaturated fatty acids that tunes membrane stability across temperatures."
          },
          {
            "node_id": "core_metabolism",
            "label": "core central metabolism",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Central metabolic network whose key metabolite levels are buffered across a wide temperature range."
          }
        ],
        "edges": [
          {
            "subject": "numerical_environmental_axis",
            "predicate": "defines",
            "object": "delta_phenotype_trait",
            "description": "A numerical environmental axis defines the values whose max and min are subtracted to yield the delta phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuy009",
                "snippet": "salinity range",
                "notes": "Supports a numerical environmental axis as the axis on which a growth-supporting range (and hence its breadth) is measured."
              }
            ],
            "predicate_id": "METPO:2007500"
          },
          {
            "subject": "nacl_delta",
            "predicate": "is a",
            "object": "delta_phenotype_trait",
            "description": "NaCl delta is an axis-specific delta phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuy009",
                "snippet": "salinity range",
                "notes": "Supports NaCl delta as a delta phenotype defined over the salinity axis."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "ph_delta",
            "predicate": "is a",
            "object": "delta_phenotype_trait",
            "description": "pH delta is an axis-specific delta phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2549",
                "snippet": "pH homeostasis",
                "notes": "Supports pH delta as a delta phenotype defined over the external-pH axis."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "temperature_delta",
            "predicate": "is a",
            "object": "delta_phenotype_trait",
            "description": "Temperature delta is an axis-specific delta phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1016/s0300-9629(97)00003-0",
                "snippet": "adapted to environments of high temperature",
                "notes": "Supports temperature delta as a delta phenotype defined over the ambient-temperature axis."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "homeoviscous_adaptation",
            "predicate": "maintains",
            "object": "membrane_fluidity",
            "description": "Homeoviscous adaptation regulates lipid composition to maintain membrane fluidity/structure under temperature, salinity, and pH stress.",
            "evidence": [
              {
                "reference": "DOI:10.1039/d4cc03114h",
                "notes": "Key strategies include homeoviscous adaptation (HVA), involving the regulation of lipid composition; linked to tolerance of temperature, salinity, and pH extremes."
              }
            ]
          },
          {
            "subject": "membrane_fluidity",
            "predicate": "confers",
            "object": "delta_phenotype_trait",
            "description": "Maintaining membrane fluidity/integrity across conditions widens the growth-supporting range whose span defines the delta phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1039/d4cc03114h",
                "notes": "HVA framed as a universal paradigm of membrane adaptation spanning diverse extremophiles and stressors, supporting breadth of growth-supporting conditions."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "compatible_solutes",
            "predicate": "stabilizes",
            "object": "membrane_fluidity",
            "description": "Compatible solutes stabilize proteins and membranes and restore osmotic balance, broadening tolerance across temperature and osmotic conditions.",
            "evidence": [
              {
                "reference": "DOI:10.37256/amtt.5220244537",
                "notes": "Compatible solutes depress the freezing point, stabilize proteins and membranes, restore osmotic balance; broad cold + osmotic support, not species-specific."
              }
            ]
          },
          {
            "subject": "fatty_acid_ratio",
            "predicate": "modulates",
            "object": "membrane_fluidity",
            "description": "Alteration of the saturated:unsaturated fatty-acid ratio modulates membrane stability across temperatures.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s12275-023-00031-x",
                "notes": "Membrane stability is modulated by alteration of the ratio of saturated and unsaturated fatty acids; maintenance across temperature shifts."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "core_metabolism",
            "predicate": "maintained across",
            "object": "temperature_delta",
            "description": "Regulatory-metabolic cross talk buffers core central metabolism across a wide temperature range, supporting a broad temperature delta.",
            "evidence": [
              {
                "reference": "DOI:10.1128/msystems.01124-22",
                "notes": "Different growth temperatures induce broad transcriptional changes, yet most key central metabolites show overlapping trends via intense regulatory-metabolic cross talk; maintenance across 0 and 15C."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.847283+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-13T12:00:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed causal graph framing the delta phenotype as a cross-axis breadth descriptor with axis-specific children for NaCl, pH, and temperature.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:29Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (rdfs:subClassOf\u00d73).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T07:37:39Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007500\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 5 evidence-backed generic edges (5 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:09Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d71, RO:0002211\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 1 causal edge(s) off enables/RO:0002327 with a TRAIT object (1 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope delta_phenotype_breadth_descriptor=NONMECHANISTIC with scope_notes.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T04:43:24Z",
        "curator": "codex",
        "action": "ADD_CANONICAL_EXAMPLES",
        "changes": "Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Psychrobacter arcticus (NCBITaxon:334543; DOI:10.1128/JB.01377-08). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-15T07:05:52Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (METPO:1016200\u00d71).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000010",
    "label": "desiccation tolerant",
    "definition": "An environmental tolerance in which an organism survives extreme water loss and resumes growth after rehydration (anhydrobiosis), protecting cellular macromolecules during drying.",
    "definition_source": "DOI:10.3390/microorganisms10020432",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "synonyms": [
      {
        "synonym_text": "anhydrobiotic",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.3390/microorganisms10020432"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.3390/microorganisms10020432",
        "snippet": "Anhydrobiosis (gr. life without water) is predominantly described as the ability of some organisms to lose all or almost all water and enter a state of suspension where the metabolism comes to a reversible standstill",
        "notes": "Bacterial anhydrobiosis review supports desiccation tolerance as reversible survival of near-complete water loss."
      },
      {
        "reference": "DOI:10.3390/genes14091803",
        "snippet": "Deinococcus radiodurans, a Gram-positive extremophilic bacterium, is a remarkable example of such an organism, showcasing an impressive resistance to a wide array of stressors, including ionizing radiation, desiccation, UV radiation, and oxidizing agents",
        "notes": "Organism example: Deinococcus radiodurans is desiccation-tolerant, sharing DNA-repair machinery with its radiation tolerance."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:54298",
        "taxon_label": "Chroococcidiopsis",
        "note": "Extremely desiccation- and radiation-tolerant cyanobacterium from deserts and endolithic habitats.",
        "reference": "PMID:34122375"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "desiccation_anhydrobiosis_repair",
        "title": "Desiccation tolerance via anhydrobiosis and DNA-damage repair",
        "description": "Evidence-backed causal sketch linking near-complete water loss to a reversible anhydrobiotic state and post-rehydration DNA-damage repair.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a broad environmental or morphological classification spanning multiple mechanisms, a measurement-like bin, or an absence/arrangement descriptor; contextual protein nodes do not receive token UniProt examples.",
        "nodes": [
          {
            "node_id": "desiccation_tolerant_trait",
            "label": "desiccation tolerant",
            "node_type": "TRAIT",
            "grounding": "traitmech:000010",
            "description": "Survival of extreme water loss with growth on rehydration."
          },
          {
            "node_id": "water_loss",
            "label": "extreme water loss",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Near-complete loss of cellular water during drying."
          },
          {
            "node_id": "anhydrobiosis_state",
            "label": "anhydrobiotic state",
            "node_type": "STATE",
            "description": "Reversible suspended-metabolism state during dehydration."
          },
          {
            "node_id": "dsb_repair",
            "label": "double-strand break repair",
            "node_type": "BIOLOGICAL_PROCESS",
            "grounding": "GO:0006302",
            "description": "Repair of DNA double-strand breaks accumulated during drying."
          },
          {
            "node_id": "oxidative_stress",
            "label": "oxidative stress / ROS",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Accumulation of reactive oxygen species and oxidative damage during drying."
          },
          {
            "node_id": "trehalose",
            "label": "trehalose",
            "node_type": "CHEMICAL",
            "description": "Disaccharide osmolyte accumulated as a desiccation protectant."
          },
          {
            "node_id": "plasma_membrane",
            "label": "plasma membrane",
            "node_type": "CELLULAR_LOCALIZATION",
            "description": "Phospholipid bilayer whose head groups are stabilized during dehydration.",
            "grounding": "GO:0005886"
          },
          {
            "node_id": "vitrification",
            "label": "vitrification / glass formation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Formation of a molecular glass that reduces motion and prevents crystallization."
          },
          {
            "node_id": "sod_activity",
            "label": "superoxide dismutase activity",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "Enzymatic dismutation of superoxide as an antioxidant defense.",
            "grounding": "GO:0004784"
          },
          {
            "node_id": "catalase_activity",
            "label": "catalase activity",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "Enzymatic detoxification of hydrogen peroxide / ROS.",
            "grounding": "GO:0004096"
          },
          {
            "node_id": "chaperone_activity",
            "label": "heat shock protein / chaperone activity",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "Binding of denatured proteins to prevent aggregation and aid refolding on rehydration."
          },
          {
            "node_id": "protein_aggregation",
            "label": "protein aggregation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Aggregation/denaturation of proteins induced by water loss."
          },
          {
            "node_id": "desiccation_idps",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "desiccation-related intrinsically disordered proteins",
            "node_type": "GENE_OR_PROTEIN",
            "description": "IDPs (e.g. LEA/CAHS) that protect cellular components during drying."
          }
        ],
        "edges": [
          {
            "subject": "water_loss",
            "predicate": "causes",
            "object": "anhydrobiosis_state",
            "description": "Extreme dehydration triggers entry into the anhydrobiotic state.",
            "evidence": [
              {
                "reference": "DOI:10.3390/microorganisms10020432",
                "notes": "Anhydrobiosis review describes entry into a reversible metabolism-off state upon water loss."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "anhydrobiosis_state",
            "predicate": "confers",
            "object": "desiccation_tolerant_trait",
            "description": "Reversible anhydrobiosis is the basis of desiccation survival.",
            "evidence": [
              {
                "reference": "DOI:10.3390/microorganisms10020432",
                "notes": "Anhydrobiosis enables reversible survival of near-complete water loss."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "dsb_repair",
            "predicate": "confers",
            "object": "desiccation_tolerant_trait",
            "description": "Efficient DNA double-strand-break repair restores integrity on rehydration.",
            "evidence": [
              {
                "reference": "DOI:10.3390/genes14091803",
                "notes": "Deinococcus radiodurans shares DNA-repair machinery between radiation and desiccation tolerance."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "water_loss",
            "predicate": "causes",
            "object": "oxidative_stress",
            "description": "Drying below the protective water monolayer threshold induces oxidative stress / ROS.",
            "evidence": [
              {
                "reference": "DOI:10.1021/acs.chemrev.2c00659",
                "notes": "Cross-kingdom review: desiccation tolerance organisms face oxidative stress and recover after rehydration."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "trehalose",
            "predicate": "stabilizes",
            "object": "plasma_membrane",
            "description": "Trehalose interacts with phospholipid polar head groups to stabilize membranes during dehydration.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s00203-023-03683-w",
                "notes": "Trehalose interacts with phospholipid polar groups to stabilize membranes."
              }
            ]
          },
          {
            "subject": "trehalose",
            "predicate": "promotes",
            "object": "vitrification",
            "description": "Trehalose-mediated vitrification reduces molecular motion and prevents crystallization in the dry state.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41598-023-31586-9",
                "notes": "Trehalose-mediated vitrification reduces molecular motion and prevents crystallization."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "sod_activity",
            "predicate": "negatively regulates",
            "object": "oxidative_stress",
            "description": "Superoxide dismutase is upregulated as a conserved antioxidant defense, lowering ROS.",
            "evidence": [
              {
                "reference": "DOI:10.1021/acs.chemrev.2c00659",
                "notes": "Desiccation-tolerant organisms upregulate superoxide dismutase as conserved oxidative-stress defense."
              }
            ],
            "predicate_id": "RO:0002212"
          },
          {
            "subject": "catalase_activity",
            "predicate": "negatively regulates",
            "object": "oxidative_stress",
            "description": "Catalase detoxifies H2O2/ROS as a conserved oxidative-stress defense during drying.",
            "evidence": [
              {
                "reference": "DOI:10.1021/acs.chemrev.2c00659",
                "notes": "Desiccation-tolerant organisms upregulate catalases for ROS detoxification."
              }
            ],
            "predicate_id": "RO:0002212"
          },
          {
            "subject": "chaperone_activity",
            "predicate": "negatively regulates",
            "object": "protein_aggregation",
            "description": "Heat shock proteins bind denatured proteins, preventing aggregation and aiding repair on rehydration.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s00203-023-03683-w",
                "notes": "Heat shock proteins bind denatured proteins, preventing aggregation and aiding repair on rehydration."
              }
            ],
            "predicate_id": "RO:0002212"
          },
          {
            "subject": "desiccation_idps",
            "predicate": "synergizes with",
            "object": "trehalose",
            "description": "Desiccation-related IDPs synergize with endogenous cosolutes such as trehalose to enhance protection during drying.",
            "evidence": [
              {
                "reference": "DOI:10.7554/eLife.97231",
                "notes": "Desiccation-related IDPs synergize with endogenous cosolutes to enhance protection during drying."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-28T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate ENVIRONMENT trait (desiccation tolerance / anhydrobiosis) from literature research to fill the water-availability coverage gap.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-09T14:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (anhydrobiosis / DSB repair) with GO node grounding and RO/biolink predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 7 evidence-backed generic edges (9 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:09Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:causes\u00d71, RO:0002213\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:16Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0005886\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:30Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0004784\u00d71, GO:0004096\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-04T03:08:12Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002212\u00d73).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 2 causal edge(s) off enables/RO:0002327 with a TRAIT object (2 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope desiccation_anhydrobiosis_repair=NONMECHANISTIC with scope_notes; marked 1 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (desiccation_idps).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000627",
    "label": "euryhaline",
    "definition": "A halophily preference in which an organism can tolerate a wide range of salinity conditions.",
    "definition_source": "DOI:10.5928/kaiyou.14.337",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000629"
    ],
    "evidence": [
      {
        "reference": "DOI:10.5928/kaiyou.14.337",
        "snippet": "growing over a salinity range of 15%",
        "notes": "Supports euryhaline halophiles as organisms growing across a wide salinity range."
      },
      {
        "reference": "PMID:22675587",
        "snippet": "due to its strong euryhaline phenotype",
        "notes": "Organism example: Chromohalobacter salexigens is described as having a strong euryhaline phenotype."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:666",
        "taxon_label": "Vibrio cholerae",
        "note": "tolerates a broad salinity range",
        "reference": "PMID:14532045"
      },
      {
        "taxon_id": "NCBITaxon:2746",
        "taxon_label": "Halomonas elongata",
        "note": "euryhaline halophile",
        "reference": "PMID:35432243"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "euryhaline_wide_salinity_tolerance",
        "title": "Euryhaline wide-salinity tolerance mechanism",
        "description": "Evidence-backed causal sketch linking euryhalinity to broad salinity ranges, osmotic imbalance, compatible solutes, and salinity-adaptation genes.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a broad environmental or morphological classification spanning multiple mechanisms, a measurement-like bin, or an absence/arrangement descriptor; contextual protein nodes do not receive token UniProt examples.",
        "nodes": [
          {
            "node_id": "euryhaline_trait",
            "label": "euryhaline",
            "node_type": "TRAIT",
            "grounding": "METPO:1000627",
            "description": "Tolerance of a wide range of salinity conditions."
          },
          {
            "node_id": "wide_salinity_range",
            "label": "wide salinity range",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Environmental salinity range broad enough to require flexible osmoadaptation."
          },
          {
            "node_id": "salinity_gradient",
            "label": "salinity gradient",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Spatial or temporal gradient from low to high salinity."
          },
          {
            "node_id": "osmotic_imbalance",
            "label": "osmotic imbalance",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Difference between external and internal osmotic potential."
          },
          {
            "node_id": "compatible_solutes",
            "label": "compatible solutes",
            "node_type": "CHEMICAL",
            "description": "Organic osmolytes accumulated to adjust cell osmotic potential.",
            "grounding": "CHEBI:25728"
          },
          {
            "node_id": "compatible_solute_transport",
            "label": "compatible-solute transport",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "Uptake of osmoprotectants from the environment."
          },
          {
            "node_id": "salinity_adaptation_genes",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "salinity-adaptation protein repertoire",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Protein families associated with microbial salinity adaptation across gradients."
          },
          {
            "node_id": "choline",
            "label": "choline",
            "node_type": "CHEMICAL",
            "description": "Precursor metabolite converted to glycine betaine.",
            "grounding": "CHEBI:15354"
          },
          {
            "node_id": "glycine_betaine",
            "label": "glycine betaine",
            "node_type": "CHEMICAL",
            "description": "Compatible solute / osmoprotectant accumulated under salt stress.",
            "grounding": "CHEBI:17750"
          },
          {
            "node_id": "glycine_betaine_biosynthesis",
            "label": "glycine betaine biosynthesis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Two-step oxidative conversion of choline to glycine betaine by BetA/BetB.",
            "grounding": "GO:0031456"
          },
          {
            "node_id": "ectoine",
            "label": "ectoine",
            "node_type": "CHEMICAL",
            "description": "Compatible solute widely implicated in halophily and salinity tolerance.",
            "grounding": "CHEBI:22563"
          },
          {
            "node_id": "ectoine_biosynthesis",
            "label": "ectoine biosynthesis",
            "node_type": "PATHWAY",
            "description": "Five-step biosynthesis of ectoine from L-aspartate (lysC/asd/ectB/ectA/ectC).",
            "grounding": "GO:0019491"
          },
          {
            "node_id": "mechanosensitive_channels",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "mechanosensitive channels (Msc)",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Channels acting as safety valves releasing ions and solutes during osmotic downshock."
          },
          {
            "node_id": "osmotic_downshock",
            "label": "osmotic downshock",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Sudden drop in external salinity causing rapid water influx and turgor rise."
          },
          {
            "node_id": "na_h_antiporter",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "Na+/H+ antiporter",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Antiporter that expels sodium ions from the cytoplasm."
          },
          {
            "node_id": "cytoplasmic_sodium",
            "label": "cytoplasmic sodium ions",
            "node_type": "CHEMICAL",
            "description": "Intracellular Na+ that must be exported to maintain ion homeostasis.",
            "grounding": "CHEBI:29101"
          },
          {
            "node_id": "proteome_acidification",
            "label": "proteome acidification",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Increased proportion of acidic amino acids improving protein solubility at high ionic strength."
          }
        ],
        "edges": [
          {
            "subject": "wide_salinity_range",
            "predicate": "defines",
            "object": "euryhaline_trait",
            "description": "Euryhaline organisms tolerate or grow across broad salinity ranges.",
            "evidence": [
              {
                "reference": "DOI:10.5928/kaiyou.14.337",
                "snippet": "growing over a salinity range of 15%",
                "notes": "Communication proposes a quantitative characterization for euryhaline halophiles."
              }
            ],
            "predicate_id": "METPO:2007500"
          },
          {
            "subject": "salinity_gradient",
            "predicate": "selects for",
            "object": "euryhaline_trait",
            "description": "Variable salinity environments select for broad salinity tolerance.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s40168-024-01817-w",
                "snippet": "salinity gradient of a typical short residence-time estuary",
                "notes": "Estuary metagenome study uses salinity gradients to analyze microbial salinity adaptation."
              }
            ],
            "predicate_id": "METPO:2007401"
          },
          {
            "subject": "salinity_gradient",
            "predicate": "causes",
            "object": "osmotic_imbalance",
            "description": "Movement across salinity gradients changes osmotic pressure on the cell.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s40168-024-01817-w",
                "snippet": "water immediately rushes into the cell",
                "notes": "Supports osmotic imbalance and water flux during salinity change."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "compatible_solute_transport",
            "predicate": "imports",
            "object": "compatible_solutes",
            "description": "Euryhaline tolerance can use flexible uptake of osmoprotectants.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.csbj.2021.01.030",
                "snippet": "biosynthesis and/or uptake of compatible solutes",
                "notes": "Review supports compatible-solute uptake and biosynthesis as bacterial salt-stress responses."
              }
            ],
            "predicate_id": "METPO:2007805"
          },
          {
            "subject": "compatible_solutes",
            "predicate": "mitigates",
            "object": "osmotic_imbalance",
            "description": "Compatible solutes help balance external osmotic pressure across changing salinity.",
            "evidence": [
              {
                "reference": "DOI:10.1186/1746-1448-1-5",
                "snippet": "balance external osmotic pressure",
                "notes": "Supports compatible solutes as osmolytes under salinity stress."
              }
            ],
            "predicate_id": "METPO:2007407"
          },
          {
            "subject": "salinity_adaptation_genes",
            "predicate": "contributes to",
            "object": "euryhaline_trait",
            "description": "Salinity-adaptation gene repertoires contribute to broad salinity tolerance.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s40168-024-01817-w",
                "snippet": "genes associated with microbial salinity adaptation",
                "notes": "Supports salinity-adaptation genes as contributors to microbial salinity niche breadth."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "glycine_betaine_biosynthesis",
            "predicate": "has output",
            "object": "glycine_betaine",
            "description": "Choline is oxidized to glycine betaine in two steps by BetA and BetB.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2023.1192059",
                "notes": "Choline is transformed into glycine betaine in two oxidative steps carried out by BetA (K00108) and BetB (K00130)."
              }
            ],
            "predicate_id": "RO:0002234"
          },
          {
            "subject": "choline",
            "predicate": "is precursor of",
            "object": "glycine_betaine",
            "description": "Choline serves as the substrate for glycine betaine biosynthesis.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2023.1192059",
                "notes": "Choline is transformed into glycine betaine in two oxidative steps (BetA/BetB)."
              }
            ]
          },
          {
            "subject": "glycine_betaine",
            "predicate": "mitigates",
            "object": "osmotic_imbalance",
            "description": "Glycine betaine accumulates as a compatible solute to balance osmotic pressure.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2023.1192059",
                "notes": "Glycine betaine is a compatible solute used in the salt-out osmoadaptation strategy."
              }
            ],
            "predicate_id": "METPO:2007407"
          },
          {
            "subject": "ectoine_biosynthesis",
            "predicate": "has output",
            "object": "ectoine",
            "description": "Ectoine is synthesized from L-aspartate in five steps (lysC/asd/ectB/ectA/ectC).",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2023.1192059",
                "notes": "Ectoine is obtained from L-aspartate in five steps mediated by lysC, asd, ectB, ectA, and ectC."
              }
            ],
            "predicate_id": "RO:0002234"
          },
          {
            "subject": "ectoine",
            "predicate": "mitigates",
            "object": "osmotic_imbalance",
            "description": "Ectoine acts as an osmoprotective compatible solute under salinity stress.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2023.1192059",
                "notes": "Ectoine widely implicated in halophily and salinity tolerance; protects cell components under stress."
              }
            ],
            "predicate_id": "METPO:2007407"
          },
          {
            "subject": "mechanosensitive_channels",
            "predicate": "responds to",
            "object": "osmotic_downshock",
            "description": "Msc channels serve as safety valves releasing ions and organic solutes during sudden downward osmotic shocks.",
            "evidence": [
              {
                "reference": "DOI:10.3390/microorganisms12081738",
                "notes": "Msc mechanosensitive channels serve as safety valves, allowing the rapid release of ions and organic solutes in the case of sudden downward osmotic shocks."
              }
            ]
          },
          {
            "subject": "na_h_antiporter",
            "predicate": "exports",
            "object": "cytoplasmic_sodium",
            "description": "Na+/H+ antiporters expel sodium ions from the cytoplasm to maintain ion homeostasis.",
            "evidence": [
              {
                "reference": "DOI:10.3390/microorganisms12081738",
                "notes": "Sodium ions are expelled from the cytoplasm, usually performed with the help of Na+/H+ antiporters."
              }
            ],
            "predicate_id": "METPO:2007804"
          },
          {
            "subject": "proteome_acidification",
            "predicate": "contributes to",
            "object": "euryhaline_trait",
            "description": "Acidification of the proteome improves protein solubility across salinity regimes.",
            "evidence": [
              {
                "reference": "DOI:10.1126/sciadv.adg2059",
                "notes": "Increase in acidic amino acids (notably glutamate); acidification of the proteome essential for protein solubility at higher ionic strength."
              }
            ],
            "predicate_id": "RO:0002326"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.864669+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-06T14:15:44-07:00",
        "curator": "codex",
        "action": "CURATED_WITH_ORGANISM_EXAMPLE",
        "changes": "Added Chromohalobacter salexigens organism example with PMID-backed evidence.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-11T00:00:00-07:00",
        "curator": "codex",
        "action": "CURATED_WITH_LITERATURE",
        "changes": "Added DOI-backed euryhaline causal graph for broad salinity tolerance, salinity gradients, compatible solutes, and salinity-adaptation genes.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:29Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002326\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T05:49:23Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:causes\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T21:30:06Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007401\u00d71, METPO:2007407\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:37:59Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:65015\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T07:37:39Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007500\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-15T07:19:07Z",
        "curator": "claude",
        "action": "FIX_NODE_GROUNDING_CURIE",
        "changes": "Overwrote 1 causal-node grounding(s) to corrected CURIEs (phase-2 id-label fix; verified vs OAK).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-16T06:30:55Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000208\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-17T04:09:43Z",
        "curator": "claude",
        "action": "REMOVE_REDUNDANT_SYNONYM",
        "changes": "Removed 1 synonym(s) whose text duplicated the label (seeder redundancy; no information lost).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 8 evidence-backed generic edges (10 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:09Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 6 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d72, METPO:2007407\u00d72, METPO:2000209\u00d71, RO:0002326\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:16Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A068T423\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:30Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0031456\u00d71, GO:0019491\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:21:11Z",
        "curator": "claude",
        "action": "RETRACT_DEAD_UNIPROT_GROUNDINGS",
        "changes": "Retracted 1 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 2 causal edge(s) off microbe-domain METPO predicates (2 to has output), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T02:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES_PART2",
        "changes": "Re-grounded 2 causal edge(s) off microbe-domain METPO predicates onto their causal-graph counterparts (1 to exports, 1 to imports), issue 301 part 2. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Each replacement is a 1:1 mirror of its source predicate that changes only the domain, so the claim each edge makes is unchanged and directions are unchanged. The replacements are proposed in proposals/metpo_traitmech_v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-16T02:00:00Z",
        "curator": "claude",
        "action": "NORMALISE_NODE_TYPE",
        "changes": "Under the PATHWAY-vs-BIOLOGICAL_PROCESS rule, one node_id means one thing corpus-wide (issue 356): ectoine_biosynthesis is typed PATHWAY. PATHWAY is a named, conventionally enumerable multi-step route; BIOLOGICAL_PROCESS is everything else. A named route, enumerated two ways and both of them enumerations. environment/euryhaline.yaml counts five steps from L-aspartate (lysC/asd/ectB/ectA/ectC); environment/nacl_delta_mid1.yaml counts the three ectABC enzymes proper. Naming the file matters because the two differ and a bare quote would put euryhaline's wording into nacl_delta_mid1's record (#400 review). Either way the steps can be listed, which is the test. Applied AGAINST the majority, which was 4 BIOLOGICAL_PROCESS to 2 before this tranche.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope euryhaline_wide_salinity_tolerance=NONMECHANISTIC with scope_notes; marked 3 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (salinity_adaptation_genes, mechanosensitive_channels, na_h_antiporter).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000721",
    "label": "extreme hyperthermophilic",
    "definition": "A temperature preference that grows optimally at temperatures above 90\u00b0C.",
    "definition_source": "DOI:10.1007/s007920050010",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000613"
    ],
    "synonyms": [
      {
        "synonym_text": "extreme hyperthermophile",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "extremely hyperthermophilic",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1007/s007920050010",
        "snippet": "It grew at between 90 degrees C and 113 degrees C",
        "notes": "Organism example: Pyrolobus fumarii grows in the extreme hyperthermophilic range."
      },
      {
        "reference": "DOI:10.1128/MMBR.65.1.1-43.2001",
        "snippet": "resistant to irreversible inactivation at high temperatures",
        "notes": "Thermostable-protein review supports extreme protein and membrane stability as the basis of hyperthermophile physiology."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:54252",
        "taxon_label": "Pyrolobus fumarii",
        "note": "Highest optimal growth temperature known (106 C; range 90-113 C); cannot grow below 90 C.",
        "reference": "DOI:10.1007/s007920050010"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "extreme_hyperthermophilic_archaeal_adaptation",
        "title": "Extreme-hyperthermophilic archaeal heat-adaptation mechanism",
        "description": "DOI-backed graph linking extreme hyperthermophily to archaeal tetraether membrane lipids, hyperthermostable proteins, and bioenergetic adaptation at temperatures above 90 \u00b0C.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a broad environmental or morphological classification spanning multiple mechanisms, a measurement-like bin, or an absence/arrangement descriptor; contextual protein nodes do not receive token UniProt examples.",
        "nodes": [
          {
            "node_id": "extreme_hyperthermophilic_trait",
            "label": "extreme hyperthermophilic",
            "node_type": "TRAIT",
            "grounding": "METPO:1000721",
            "description": "Optimal growth at temperatures above 90 \u00b0C."
          },
          {
            "node_id": "very_high_temperature",
            "label": "very high temperature",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Ambient temperature above 90 \u00b0C, typical of hydrothermal vents and geothermal springs.",
            "grounding": "PATO:0001305"
          },
          {
            "node_id": "tetraether_lipids",
            "label": "archaeal tetraether membrane lipids",
            "node_type": "CHEMICAL",
            "description": "Glycerol-dibiphytanyl-glycerol-tetraether (GDGT) lipids forming heat-resistant monolayer membranes in hyperthermophilic archaea."
          },
          {
            "node_id": "hyperthermostable_proteins",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "hyperthermostable proteins",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Proteins with extreme resistance to denaturation, including enzymes active at >90 \u00b0C."
          },
          {
            "node_id": "hyperthermophile_bioenergetics",
            "label": "hyperthermophile bioenergetics",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Energy transduction tuned to function in very-high-temperature environments."
          },
          {
            "node_id": "reverse_gyrase",
            "label": "reverse gyrase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "ATP-dependent topoisomerase that introduces positive supercoils into DNA; characteristic of hyperthermophiles.",
            "grounding": "GO:0160097"
          },
          {
            "node_id": "dna_positive_supercoiling",
            "label": "DNA positive supercoiling",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Positive supercoiling of DNA topology that stabilizes the double helix at high temperature."
          },
          {
            "node_id": "dna_thermal_denaturation",
            "label": "DNA thermal denaturation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Heat-induced melting/denaturation of DNA, a threat to genome integrity at very high temperature."
          },
          {
            "node_id": "thermally_damaged_dna",
            "label": "thermally damaged DNA",
            "node_type": "CHEMICAL",
            "description": "Nicked or thermally damaged DNA subject to heat-driven strand breakage."
          },
          {
            "node_id": "grs_cyclization_enzymes",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "GrsA/GrsB GDGT cyclization enzymes",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Enzymes that introduce ring cyclizations into GDGT tetraether lipids, increasing membrane packing."
          },
          {
            "node_id": "membrane_integrity_high_temp",
            "label": "membrane integrity at high temperature",
            "node_type": "STATE",
            "description": "Maintained structural integrity of the cell membrane under membrane-destabilizing heat."
          }
        ],
        "edges": [
          {
            "subject": "very_high_temperature",
            "predicate": "selects for",
            "object": "extreme_hyperthermophilic_trait",
            "description": "Very-high-temperature habitats select for extreme hyperthermophily.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s007920050010",
                "snippet": "It grew at between 90 degrees C and 113 degrees C",
                "notes": "Supports growth above 90 \u00b0C in extreme hyperthermophiles."
              }
            ],
            "predicate_id": "METPO:2007401"
          },
          {
            "subject": "tetraether_lipids",
            "predicate": "protects against",
            "object": "very_high_temperature",
            "description": "Archaeal tetraether lipids form heat-resistant membranes that protect against very-high-temperature membrane stress.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-micro-091313-103612",
                "snippet": "membrane lipid composition",
                "notes": "Membrane-adaptation review supports membrane lipid composition as the primary tunable mechanism for thermal adaptation; in hyperthermophilic archaea this is realized via tetraether (GDGT) monolayer membranes."
              }
            ]
          },
          {
            "subject": "hyperthermostable_proteins",
            "predicate": "enables",
            "object": "hyperthermophile_bioenergetics",
            "description": "Hyperthermostable proteins enable continued energy conservation at very high temperature.",
            "evidence": [
              {
                "reference": "DOI:10.1128/MMBR.65.1.1-43.2001",
                "snippet": "resistant to irreversible inactivation at high temperatures",
                "notes": "Supports protein hyperthermostability as a hyperthermophile feature."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "hyperthermophile_bioenergetics",
            "predicate": "confers",
            "object": "extreme_hyperthermophilic_trait",
            "description": "Heat-adapted bioenergetics supports growth at extreme hyperthermophilic temperatures.",
            "evidence": [
              {
                "reference": "DOI:10.1016/s0300-9629(97)00003-0",
                "snippet": "energy transducing enzymes",
                "notes": "Supports temperature-adapted energy transduction as the basis of thermophile and hyperthermophile growth."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "reverse_gyrase",
            "predicate": "introduces positive supercoils into",
            "object": "dna_positive_supercoiling",
            "description": "Reverse gyrase introduces positive supercoils into DNA in hyperthermophiles.",
            "evidence": [
              {
                "reference": "DOI:10.1264/jsme2.me23087",
                "notes": "reverse gyrase... introduces positive supercoils into DNA (review-supported mechanistic edge)."
              }
            ]
          },
          {
            "subject": "dna_positive_supercoiling",
            "predicate": "decreases risk of",
            "object": "dna_thermal_denaturation",
            "description": "Positive DNA supercoiling decreases the risk of thermal denaturation of DNA.",
            "evidence": [
              {
                "reference": "DOI:10.1264/jsme2.me23087",
                "notes": "reverse gyrase prevents the thermal denaturation of DNA by introducing positive DNA supercoiling (widely accepted in review literature)."
              }
            ]
          },
          {
            "subject": "reverse_gyrase",
            "predicate": "protects",
            "object": "thermally_damaged_dna",
            "description": "Reverse gyrase has heat-protective DNA chaperone activity that reduces thermal DNA damage, independent of supercoiling.",
            "evidence": [
              {
                "reference": "DOI:10.1093/nar/gkh683",
                "notes": "Reverse gyrase has heat-protective DNA chaperone activity, reducing double-stranded DNA breakage ~8-fold at 90 C (strong experimental support)."
              }
            ]
          },
          {
            "subject": "tetraether_lipids",
            "predicate": "maintains",
            "object": "membrane_integrity_high_temp",
            "description": "Archaeal ether/tetraether lipids maintain membrane integrity at high temperature.",
            "evidence": [
              {
                "reference": "DOI:10.1186/2046-0481-57-6-348",
                "notes": "archaeal membranes contain tetraethers and diethers, enabling cells to withstand membrane-destroying temperatures (broad classic mechanism)."
              }
            ]
          },
          {
            "subject": "grs_cyclization_enzymes",
            "predicate": "increases",
            "object": "membrane_integrity_high_temp",
            "description": "GrsA/GrsB cyclization of GDGTs increases membrane packing and stability at high temperature.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s00792-023-01330-2",
                "notes": "cyclized GDGTs (introduced by GrsA/GrsB) increase membrane packing and stability (strong mechanistic membrane edge)."
              }
            ],
            "predicate_id": "RO:0002213"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.909279+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-06T14:58:45-07:00",
        "curator": "codex",
        "action": "CURATED_WITH_ORGANISM_EXAMPLE",
        "changes": "Added Pyrolobus fumarii organism example with PMID-backed evidence.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-13T11:30:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed causal graph linking archaeal tetraether membrane lipids, hyperthermostable proteins, and hyperthermophile bioenergetics to extreme hyperthermophily.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-13T22:45:00-07:00",
        "curator": "codex",
        "action": "IMPROVED_CAUSAL_GRAPH_EVIDENCE",
        "changes": "Replaced Pyrolobus fumarii PMID fallback with the article DOI in definition, record evidence, and CausalEdge evidence.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:29Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T21:30:06Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007401\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:18Z",
        "curator": "claude",
        "action": "RENAME_PREDICATE_LABELS",
        "changes": "Renamed 1 causal-edge predicate label(s) to align with existing groundings: supports \u2192 enables \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:20Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T08:14:32Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (PATO:0001637\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-15T07:19:08Z",
        "curator": "claude",
        "action": "FIX_NODE_GROUNDING_CURIE",
        "changes": "Overwrote 1 causal-node grounding(s) to corrected CURIEs (phase-2 id-label fix; verified vs OAK).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 5 evidence-backed generic edges (6 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:09Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002213\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:16Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A088E825\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:21:11Z",
        "curator": "claude",
        "action": "RETRACT_DEAD_UNIPROT_GROUNDINGS",
        "changes": "Retracted 1 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:23:52Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0160097\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 1 causal edge(s) off enables/RO:0002327 with a TRAIT object (1 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-21T08:00:00Z",
        "curator": "codex",
        "action": "NORMALISE_NODE_TYPE",
        "changes": "Tranche 5 of issue 356 settles the process/quality families and merges ids that meant the same sense: dna_positive_supercoiling is BIOLOGICAL_PROCESS. GO:0160097 denotes the process of introducing positive supercoils into DNA. The general DNA-topology state remains separately modelled as dna_supercoiling.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope extreme_hyperthermophilic_archaeal_adaptation=NONMECHANISTIC with scope_notes; marked 2 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (hyperthermostable_proteins, grs_cyclization_enzymes).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000628",
    "label": "extremely halophilic",
    "definition": "A halophily preference in which an organism requires very high salt concentrations (typically 15-30% NaCl or higher) for optimal growth and cannot grow at salt concentrations below approximately 12%.",
    "definition_source": "PMID:11790755",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000629"
    ],
    "synonyms": [
      {
        "synonym_text": "extreme-halophilic",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "created_by": "Jed Dongjin Kim-Ozaeta",
    "evidence": [
      {
        "reference": "PMID:11790755",
        "snippet": "A cytochrome in an extremely halophilic archaeon, Haloferax volcanii",
        "notes": "Organism example: Haloferax volcanii is described as extremely halophilic."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:2242",
        "taxon_label": "Halobacterium salinarum",
        "note": "Classic extreme-halophile model requiring near-saturating NaCl; twin lab strains NRC-1 (NCBITaxon:64091) and R1 (NCBITaxon:478009).",
        "reference": "https://pmc.ncbi.nlm.nih.gov/articles/PMC10264941/"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "extreme_halophile_salt_in_acidic_proteome",
        "title": "Extreme halophile salt-in and acidic-proteome mechanism",
        "description": "Evidence-backed causal sketch linking extreme halophily to saturated salt environments, intracellular KCl, and salt-adapted acidic proteins.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a broad environmental or morphological classification spanning multiple mechanisms, a measurement-like bin, or an absence/arrangement descriptor; contextual protein nodes do not receive token UniProt examples.",
        "nodes": [
          {
            "node_id": "extremely_halophilic_trait",
            "label": "extremely halophilic",
            "node_type": "TRAIT",
            "grounding": "METPO:1000628",
            "description": "Optimal growth requires very high salt concentrations."
          },
          {
            "node_id": "hypersaline_brine",
            "label": "hypersaline brine",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "High-salt or near-saturating brine environment."
          },
          {
            "node_id": "potassium_ion",
            "label": "potassium ion",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:29103",
            "description": "K+ accumulated intracellularly in salt-in osmoadaptation."
          },
          {
            "node_id": "salt_in_strategy",
            "label": "salt-in strategy",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Intracellular inorganic salt accumulation for osmotic balance.",
            "grounding": "METPO:1007720"
          },
          {
            "node_id": "acidic_halophilic_proteins",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "acidic halophilic proteins",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Proteins enriched in acidic residues and adapted to high ionic strength."
          },
          {
            "node_id": "osmotic_stress",
            "label": "osmotic stress",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Cellular response to high external solute/osmotic pressure.",
            "grounding": "GO:0006970"
          },
          {
            "node_id": "na_h_antiporter",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "Na+/H+ antiporter",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Membrane transporter mediating sodium exclusion in exchange for protons."
          },
          {
            "node_id": "sodium_efflux",
            "label": "sodium efflux",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Active export of Na+ to maintain low cytoplasmic sodium."
          },
          {
            "node_id": "protein_solubility_high_salt",
            "label": "protein solubility and function in high salt",
            "node_type": "QUALITY",
            "description": "Maintenance of protein solubility and activity in hypersaline cytoplasm."
          },
          {
            "node_id": "s_layer_n_glycosylation",
            "label": "S-layer glycoprotein N-glycosylation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "N-linked glycosylation of the S-layer glycoprotein in haloarchaea."
          },
          {
            "node_id": "s_layer_stability",
            "label": "S-layer stability",
            "node_type": "QUALITY",
            "description": "Structural stability of the haloarchaeal S-layer cell envelope."
          }
        ],
        "edges": [
          {
            "subject": "hypersaline_brine",
            "predicate": "selects for",
            "object": "extremely_halophilic_trait",
            "description": "Extreme halophiles are adapted to growth in hypersaline brines.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuy009",
                "snippet": "salt concentrations up to NaCl saturation",
                "notes": "Review supports saturated salt environments as extreme-halophile habitats."
              }
            ],
            "predicate_id": "METPO:2007401"
          },
          {
            "subject": "salt_in_strategy",
            "predicate": "uses",
            "object": "potassium_ion",
            "description": "Extreme haloarchaea often balance osmotic pressure by accumulating intracellular KCl.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuy009",
                "snippet": "KCl accumulating Halobacterium salinarum",
                "notes": "Supports KCl accumulation as a model salt-in strategy."
              }
            ]
          },
          {
            "subject": "salt_in_strategy",
            "predicate": "confers",
            "object": "extremely_halophilic_trait",
            "description": "Maintaining high intracellular salt supports growth at extreme external salinity.",
            "evidence": [
              {
                "reference": "DOI:10.1038/srep25642",
                "snippet": "Salt-in strategy",
                "notes": "Haloarchaeal salinity-stress study describes salt-in adaptation in extreme halophiles."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "acidic_halophilic_proteins",
            "predicate": "confers",
            "object": "extremely_halophilic_trait",
            "description": "Acidic proteins remain soluble and functional in high salt.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.copbio.2015.05.004",
                "snippet": "negatively charged due to an excess of acidic over basic residues",
                "notes": "Review supports acidic proteomes as a molecular adaptation to hypersaline cytoplasm."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "salt_in_strategy",
            "predicate": "requires adaptation of",
            "object": "acidic_halophilic_proteins",
            "description": "Intracellular salt accumulation requires proteins adapted to high ionic strength.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.copbio.2015.05.004",
                "snippet": "promote function in low water activity conditions",
                "notes": "Supports functional coupling between high-salt cytoplasm and salt-adapted proteins."
              }
            ]
          },
          {
            "subject": "hypersaline_brine",
            "predicate": "causes",
            "object": "osmotic_stress",
            "description": "High external NaCl imposes osmotic stress on the cell.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s12934-024-02358-5",
                "notes": "NaCl shock induced osmotic stress; environmental-to-stress edge broadly applicable."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "osmotic_stress",
            "predicate": "induces",
            "object": "potassium_ion",
            "description": "Osmotic stress triggers rapid intracellular K+ uptake/accumulation.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s12934-024-02358-5",
                "notes": "Many microbes rapidly uptake K+ as an emergency osmoadaptation response."
              }
            ]
          },
          {
            "subject": "na_h_antiporter",
            "predicate": "mediates",
            "object": "sodium_efflux",
            "description": "Na+/H+ antiporters drive sodium exclusion from the cytoplasm.",
            "evidence": [
              {
                "reference": "DOI:10.3390/microorganisms12081738",
                "notes": "Sodium exclusion is mediated largely by Na+/H+ antiporters (general haloarchaeal review)."
              }
            ]
          },
          {
            "subject": "acidic_halophilic_proteins",
            "predicate": "supports",
            "object": "protein_solubility_high_salt",
            "description": "Surface acidic residues maintain protein solubility and function at high ionic strength.",
            "evidence": [
              {
                "reference": "DOI:10.3390/microorganisms12081738",
                "notes": "Halophilic proteins have increased surface acidic residues maintaining solubility and function in high salt."
              }
            ]
          },
          {
            "subject": "s_layer_n_glycosylation",
            "predicate": "supports",
            "object": "s_layer_stability",
            "description": "N-glycosylation stabilizes the haloarchaeal S-layer.",
            "evidence": [
              {
                "reference": "DOI:10.3390/v15071469",
                "notes": "N-glycosylation supports protein folding/stability and specifically stabilizes the S-layer."
              }
            ]
          },
          {
            "subject": "hypersaline_brine",
            "predicate": "changes",
            "object": "s_layer_n_glycosylation",
            "description": "External salinity alters S-layer glycoprotein N-glycosylation pathways.",
            "evidence": [
              {
                "reference": "DOI:10.3390/v15071469",
                "notes": "Growth at different salt concentrations alters S-layer glycoprotein N-glycosylation; two distinct pathways process it upon salinity changes."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.865176+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-06T14:15:44-07:00",
        "curator": "codex",
        "action": "CURATED_WITH_ORGANISM_EXAMPLE",
        "changes": "Added Haloferax volcanii organism example with PMID-backed evidence.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "ADDED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed causal graph for extreme halophile salt-in and acidic-proteome adaptation.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:29Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d72).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T21:30:06Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007401\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-16T06:54:39Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (METPO:1007720\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-17T04:09:43Z",
        "curator": "claude",
        "action": "REMOVE_REDUNDANT_SYNONYM",
        "changes": "Removed 1 synonym(s) whose text duplicated the label (seeder redundancy; no information lost).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 6 evidence-backed generic edges (6 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:09Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:causes\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:16Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0006970\u00d71, UniProtKB:A0A068T423\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:21:11Z",
        "curator": "claude",
        "action": "RETRACT_DEAD_UNIPROT_GROUNDINGS",
        "changes": "Retracted 1 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 2 causal edge(s) off enables/RO:0002327 with a TRAIT object (2 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-16T02:00:00Z",
        "curator": "claude",
        "action": "NORMALISE_NODE_TYPE",
        "changes": "Under the PATHWAY-vs-BIOLOGICAL_PROCESS rule, one node_id means one thing corpus-wide (issue 356): salt_in_strategy is typed BIOLOGICAL_PROCESS. PATHWAY is a named, conventionally enumerable multi-step route; BIOLOGICAL_PROCESS is everything else. A STRATEGY, not a route. The family is described as osmoadaptation by accumulating intracellular inorganic ions -- haloalkaliphilic.yaml puts it as 'Osmoadaptation by intracellular accumulation of inorganic ions (e.g. K+)', and the wording varies by record. There is no step list to enumerate, which is exactly the distinction this rule draws. Was 7 BIOLOGICAL_PROCESS to 1 before this tranche.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope extreme_halophile_salt_in_acidic_proteome=NONMECHANISTIC with scope_notes; marked 2 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (acidic_halophilic_proteins, na_h_antiporter).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000612",
    "label": "facultative oxygen preference",
    "definition": "An oxygen preference that describes a microorganism that can grow with or without molecular oxygen.",
    "definition_source": "DOI:10.1111/cmi.13338",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000601"
    ],
    "synonyms": [
      {
        "synonym_text": "Ox_facultative_aerobe_anaerobe",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1111/cmi.13338",
        "snippet": "cope with changing oxygen levels",
        "notes": "Supports facultative oxygen preference as growth across oxygen regimes."
      },
      {
        "reference": "DOI:10.1089/ars.2011.4051",
        "snippet": "adaptation of respiratory metabolism to changing environments",
        "notes": "Supports oxygen-responsive metabolic switching."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "facultative_oxygen_preference_switching",
        "title": "Facultative oxygen preference metabolic switching mechanism",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is an upper preference, broad tolerance, or central-range classification spanning multiple unrelated adaptations; contextual protein nodes are retained without assigning a misleading token UniProt example.",
        "description": "Evidence-backed causal sketch linking facultative oxygen preference to oxygen-responsive switching between aerobic and oxygen-independent growth.",
        "nodes": [
          {
            "node_id": "facultative_oxygen_trait",
            "label": "facultative oxygen preference",
            "node_type": "TRAIT",
            "grounding": "METPO:1000612",
            "description": "Growth can occur with or without molecular oxygen."
          },
          {
            "node_id": "molecular_oxygen",
            "label": "molecular oxygen",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:15379",
            "description": "Environmental oxygen availability."
          },
          {
            "node_id": "aerobic_respiration",
            "label": "aerobic respiration",
            "node_type": "BIOLOGICAL_PROCESS",
            "grounding": "GO:0009060",
            "description": "Oxygen-dependent respiratory energy metabolism."
          },
          {
            "node_id": "anaerobic_respiration_or_fermentation",
            "label": "anaerobic respiration or fermentation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Oxygen-independent growth-supporting metabolism."
          },
          {
            "node_id": "oxygen_sensing_regulation",
            "label": "oxygen-sensing regulation",
            "node_type": "GENE_OR_PROTEIN",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed as a contextual protein or protein-complex label in a broad environmental classification; no single exact family term denotes this aggregate use.",
            "description": "Regulatory systems such as FNR-type sensors that respond to oxygen."
          },
          {
            "node_id": "aerobic_energy_pathways",
            "label": "aerobic energy-generating pathways",
            "node_type": "PATHWAY",
            "description": "Aerobic respiratory energy-generation modules downregulated under anaerobiosis."
          },
          {
            "node_id": "anaerobic_metabolism_genes",
            "label": "anaerobic metabolism genes",
            "node_type": "PATHWAY",
            "description": "Genes encoding anaerobic metabolic functions induced when oxygen is low or absent."
          },
          {
            "node_id": "nitrate_electron_acceptor",
            "label": "nitrate",
            "node_type": "CHEMICAL",
            "description": "Alternative terminal electron acceptor supporting anaerobic respiration.",
            "grounding": "CHEBI:17632"
          },
          {
            "node_id": "terminal_oxidase_cytochrome_bd",
            "label": "cytochrome bd terminal oxidase",
            "node_type": "GENE_OR_PROTEIN",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed as a contextual protein or protein-complex label in a broad environmental classification; no single exact family term denotes this aggregate use.",
            "description": "High-affinity terminal oxidase enabling oxygen respiration at low O2 tensions."
          }
        ],
        "edges": [
          {
            "subject": "facultative_oxygen_trait",
            "predicate": "responds to",
            "object": "molecular_oxygen",
            "description": "Facultative oxygen preference depends on coping with oxygen changes.",
            "evidence": [
              {
                "reference": "DOI:10.1111/cmi.13338",
                "snippet": "cope with changing oxygen levels",
                "notes": "Supports oxygen flexibility as the trait-level mechanism."
              }
            ]
          },
          {
            "subject": "molecular_oxygen",
            "predicate": "enables",
            "object": "aerobic_respiration",
            "description": "Oxygen availability permits aerobic respiratory growth.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.celrep.2023.112444",
                "snippet": "transfer electrons from the ETC to O2",
                "notes": "Supports oxygen use by terminal oxidases during respiration."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "facultative_oxygen_trait",
            "predicate": "has alternative process",
            "object": "anaerobic_respiration_or_fermentation",
            "description": "Growth without oxygen can use alternative electron acceptors or fermentation.",
            "evidence": [
              {
                "reference": "DOI:10.1089/ars.2011.4051",
                "snippet": "utilizing other substrates as final electron acceptors",
                "notes": "Supports oxygen-independent respiratory alternatives under oxygen shortage."
              }
            ]
          },
          {
            "subject": "oxygen_sensing_regulation",
            "predicate": "controls adaptation to",
            "object": "molecular_oxygen",
            "description": "Oxygen-sensing regulators mediate metabolic adaptation across oxygen regimes.",
            "evidence": [
              {
                "reference": "DOI:10.1089/ars.2011.4051",
                "snippet": "Fnr-type transcriptional regulators that directly sense O2",
                "notes": "Supports regulatory oxygen sensing as a causal graph entity."
              }
            ]
          },
          {
            "subject": "oxygen_sensing_regulation",
            "predicate": "represses",
            "object": "aerobic_energy_pathways",
            "description": "Oxygen-responsive regulators (FNR/ArcA) repress aerobic energy-generating pathways under anaerobiosis.",
            "evidence": [
              {
                "reference": "DOI:10.1128/aem.01491-23",
                "notes": "FNR and ArcA \"repress aerobic energy-generating pathways\" under anaerobiosis."
              }
            ]
          },
          {
            "subject": "oxygen_sensing_regulation",
            "predicate": "induces",
            "object": "anaerobic_metabolism_genes",
            "description": "Oxygen-responsive regulators induce anaerobic metabolism genes enabling growth without O2.",
            "evidence": [
              {
                "reference": "DOI:10.1128/aem.01491-23",
                "notes": "FNR and ArcA \"induce genes for anaerobic metabolism\"; general regulatory edge for facultative bacteria."
              }
            ]
          },
          {
            "subject": "nitrate_electron_acceptor",
            "predicate": "promotes",
            "object": "anaerobic_respiration_or_fermentation",
            "description": "Nitrate substitutes for O2 as terminal electron acceptor, supporting non-fermentative anaerobic respiration.",
            "evidence": [
              {
                "reference": "DOI:10.1128/msphere.00774-23",
                "notes": "\"addition of nitrate as a TEA promotes anaerobic respiration\"; broadly relevant across facultative species with nitrate reductases."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "terminal_oxidase_cytochrome_bd",
            "predicate": "enables",
            "object": "aerobic_respiration",
            "description": "Cytochrome bd is one of the terminal oxidases through which aerobic respiration proceeds; which terminal enzyme is active depends on the final electron acceptor available.",
            "evidence": [
              {
                "reference": "DOI:10.1128/jb.00389-22",
                "notes": "\"which of these terminal enzymes is active in electron transfer depends on the availability of the final electron acceptor: fumarate or oxygen\"; supports cytochrome bd being one of the acceptor-dependent terminal branches of aerobic respiration."
              }
            ],
            "predicate_id": "RO:0002327"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.855860+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "CURATED_WITH_LITERATURE",
        "changes": "Reviewed facultative oxygen preference and added DOI-backed definition source, evidence, and causal graph for oxygen-responsive metabolic switching.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:29Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 4 evidence-backed generic edges (4 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:09Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002213\u00d71, RO:0002327\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:16Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:17632\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-07T18:00:00Z",
        "curator": "claude",
        "action": "REGROUND_CAUSAL_EDGE",
        "changes": "Edge molecular_oxygen -> terminal_oxidase_cytochrome_bd in graph facultative_oxygen_preference_switching: repointed it to terminal_oxidase_cytochrome_bd -> aerobic_respiration. Issue 334. biolink declares enables range 'biological process or activity', which of CausalNodeTypeEnum only BIOLOGICAL_PROCESS, PATHWAY and MOLECULAR_FUNCTION satisfy, so this edge entailed a false type on its object. The node description already reads 'High-affinity terminal oxidase ENABLING oxygen respiration at low O2 tensions' -- protein enables process, which is both domain- and range-correct. Written the other way round it claimed O2 enables a protein. The graph's existing molecular_oxygen -enables-> aerobic_respiration edge already carries the O2-availability link, so nothing is lost.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-21T00:00:00Z",
        "curator": "claude",
        "action": "BACKFILL_CANONICAL_EXAMPLES",
        "changes": "Added 2 exemplar taxon/taxa. Organisms and citations come only from this record's own deep-research artifact; every taxon id was resolved and label-checked against the local NCBITaxon build rather than recalled. Organisms the artifact names as contrast cases rather than exemplars were deliberately excluded.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope facultative_oxygen_preference_switching=NONMECHANISTIC with scope_notes; marked 2 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (oxygen_sensing_regulation, terminal_oxidase_cytochrome_bd).",
        "llm_assisted": true
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:562",
        "taxon_label": "Escherichia coli",
        "reference": "DOI:10.1111/1751-7915.70051",
        "note": "Respires oxygen when it is available and switches to nitrate respiration or fermentation when it is not, which is the trait as defined."
      },
      {
        "taxon_id": "NCBITaxon:1423",
        "taxon_label": "Bacillus subtilis",
        "reference": "DOI:10.3390/ijms25021277",
        "note": "Grows aerobically and, on oxygen limitation, by nitrate respiration or fermentation under the regulation described in this record."
      }
    ]
  },
  {
    "identifier": "METPO:1000720",
    "label": "facultative psychrophilic",
    "definition": "A temperature preference characterized by the ability to grow at low temperatures (typically below 20 degrees C) while maintaining optimal growth at moderate temperatures.",
    "definition_source": "DOI:10.1111/j.1574-6941.2009.00727.x",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000613"
    ],
    "synonyms": [
      {
        "synonym_text": "facultative psychrophile",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "created_by": "Anthea Guo",
    "evidence": [
      {
        "reference": "DOI:10.1111/j.1574-6941.2009.00727.x",
        "snippet": "optimum temperatures >20 \u00b0C and are capable of growth around 0 \u00b0C",
        "notes": "Supports facultative psychrophiles as cold-growing organisms with higher temperature optima."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "facultative_psychrophilic_cold_tolerance",
        "title": "Facultative psychrophily cold-tolerance mechanism",
        "description": "Evidence-backed causal sketch linking facultative psychrophily to low-temperature growth, moderate-temperature optima, membrane remodeling, and cold acclimation proteins.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a broad environmental or morphological classification spanning multiple mechanisms, a measurement-like bin, or an absence/arrangement descriptor; contextual protein nodes do not receive token UniProt examples.",
        "nodes": [
          {
            "node_id": "facultative_psychrophilic_trait",
            "label": "facultative psychrophilic",
            "node_type": "TRAIT",
            "grounding": "METPO:1000720",
            "description": "Capacity to grow at low temperatures while retaining optimal growth at moderate temperatures."
          },
          {
            "node_id": "low_temperature",
            "label": "low temperature",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Cold growth condition near 0 degrees C.",
            "grounding": "PATO:0001306"
          },
          {
            "node_id": "moderate_temperature",
            "label": "moderate temperature",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Temperature range where facultative psychrophiles can show optimal growth."
          },
          {
            "node_id": "membrane_fluidity",
            "label": "membrane fluidity",
            "node_type": "QUALITY",
            "description": "Physical state of the membrane needed for transport and growth.",
            "grounding": "METPO:1007505"
          },
          {
            "node_id": "unsaturated_fatty_acids",
            "label": "unsaturated and branched-chain fatty acids",
            "node_type": "CHEMICAL",
            "description": "Membrane lipid features that maintain fluidity under cold conditions."
          },
          {
            "node_id": "cold_shock_proteins",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "cold-shock proteins",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Proteins involved in cold shock and cold acclimation responses."
          },
          {
            "node_id": "two_component_system",
            "label": "two-component signaling system",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Signal transduction module activated by membrane-state changes during cold sensing."
          },
          {
            "node_id": "fatty_acid_desaturase",
            "label": "fatty acid desaturase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Enzyme introducing double bonds into membrane acyl chains, increasing unsaturation in cold.",
            "grounding": "InterPro:IPR012171"
          },
          {
            "node_id": "exopolysaccharides",
            "label": "extracellular polymeric substances (EPS)",
            "node_type": "CHEMICAL",
            "description": "Secreted polysaccharide matrix acting as cryoprotectant."
          },
          {
            "node_id": "freeze_thaw_cycles",
            "label": "freeze-thaw cycles",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Repeated freezing and thawing damaging cells in cold environments."
          },
          {
            "node_id": "trehalose",
            "label": "trehalose",
            "node_type": "CHEMICAL",
            "description": "Compatible solute and cryoprotectant protecting cells against abiotic stress including cold."
          },
          {
            "node_id": "rna_secondary_structure",
            "label": "RNA secondary structure",
            "node_type": "CHEMICAL",
            "description": "Stabilized RNA folds at low temperature that impede transcription and translation."
          },
          {
            "node_id": "compatible_solutes",
            "label": "compatible osmolytes",
            "node_type": "CHEMICAL",
            "description": "Organic osmolytes (glycine betaine, trehalose, glycerol, sucrose, mannitol) preventing cell shrinkage and water loss.",
            "grounding": "CHEBI:23366"
          }
        ],
        "edges": [
          {
            "subject": "low_temperature",
            "predicate": "is tolerated by",
            "object": "facultative_psychrophilic_trait",
            "description": "Facultative psychrophiles can grow at low temperature.",
            "evidence": [
              {
                "reference": "DOI:10.1111/j.1574-6941.2009.00727.x",
                "snippet": "capable of growth around 0 \u00b0C",
                "notes": "Review introduction supports low-temperature growth capacity."
              }
            ]
          },
          {
            "subject": "moderate_temperature",
            "predicate": "supports optimum of",
            "object": "facultative_psychrophilic_trait",
            "description": "Facultative psychrophiles retain optimal growth at moderate temperatures.",
            "evidence": [
              {
                "reference": "DOI:10.1111/j.1574-6941.2009.00727.x",
                "snippet": "optimum temperatures >20 \u00b0C",
                "notes": "Supports distinction from obligate psychrophiles."
              }
            ]
          },
          {
            "subject": "low_temperature",
            "predicate": "decreases",
            "object": "membrane_fluidity",
            "description": "Cold temperature decreases membrane fluidity.",
            "evidence": [
              {
                "reference": "DOI:10.1038/sj.embor.7400662",
                "snippet": "decreased membrane fluidity",
                "notes": "Supports membrane rigidification as a cold challenge."
              }
            ],
            "predicate_id": "RO:0002212"
          },
          {
            "subject": "unsaturated_fatty_acids",
            "predicate": "regulates",
            "object": "membrane_fluidity",
            "description": "Lipid remodeling maintains membrane function during cold growth.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-micro-091313-103612",
                "snippet": "incorporation of proportionally more unsaturated fatty acids",
                "notes": "Supports homoviscous adaptation during lower-temperature growth."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "cold_shock_proteins",
            "predicate": "contributes to",
            "object": "facultative_psychrophilic_trait",
            "description": "Cold-shock proteins contribute to growth after temperature downshift.",
            "evidence": [
              {
                "reference": "DOI:10.1038/sj.embor.7400662",
                "snippet": "Cold-shock proteins have also been described",
                "notes": "Supports cold-shock proteins as cold-acclimation components."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "low_temperature",
            "predicate": "induces",
            "object": "two_component_system",
            "description": "Cold sensing via membrane physical-state change activates a two-component system.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s42770-023-01057-4",
                "notes": "sensing the cold... leading to the activation of a two-component system that transduce the signal"
              }
            ]
          },
          {
            "subject": "fatty_acid_desaturase",
            "predicate": "increases",
            "object": "unsaturated_fatty_acids",
            "description": "Desaturase acting on membrane acyl chains rapidly increases unsaturated lipids (homeoviscous response).",
            "evidence": [
              {
                "reference": "DOI:10.1016/B978-0-12-809633-8.02282-2",
                "notes": "the desaturase acting on the acyl chains of the membrane lipids comes into play, thereby increasing the amount of unsaturated lipid"
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "exopolysaccharides",
            "predicate": "protects against",
            "object": "freeze_thaw_cycles",
            "description": "EPS surrounding cells acts as cryoprotectant against freeze-thaw damage.",
            "evidence": [
              {
                "reference": "DOI:10.37256/amtt.5220244537",
                "notes": "exopolysaccharides (EPS) surrounding bacterial cells... providing protection against freeze-thaw cycles and acting as cryoprotectants"
              }
            ]
          },
          {
            "subject": "trehalose",
            "predicate": "contributes to",
            "object": "facultative_psychrophilic_trait",
            "description": "Trehalose protects bacteria against abiotic stress including low temperature.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41598-023-41323-x",
                "notes": "Trehalose... plays an important role in protecting bacteria against a range of stresses"
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "cold_shock_proteins",
            "predicate": "destabilizes",
            "object": "rna_secondary_structure",
            "description": "CSPs act as chaperones destabilizing RNA secondary structures to maintain transcription/translation in cold.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s42770-023-01057-4",
                "notes": "CSPs function as chaperones that destabilize those secondary structures and maintain a single-stranded molecule"
              }
            ]
          },
          {
            "subject": "compatible_solutes",
            "predicate": "contributes to",
            "object": "facultative_psychrophilic_trait",
            "description": "Accumulation of compatible osmolytes prevents cell shrinkage and water loss at sub-zero temperatures.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2023.1197797",
                "notes": "Accumulation of compatible osmolytes (glycine betaine, trehalose, glycerol, sucrose, mannitol etc.)... to prevent cell shrinkage and water loss during sub-zero temperature"
              }
            ],
            "predicate_id": "RO:0002326"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.908340+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-11T00:00:00-07:00",
        "curator": "codex",
        "action": "CURATED_WITH_LITERATURE",
        "changes": "Reviewed facultative psychrophilic trait, corrected temperature text encoding, and added DOI-backed causal graph for low-temperature growth with moderate-temperature optimum.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:29Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002326\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:18Z",
        "curator": "claude",
        "action": "RENAME_PREDICATE_LABELS",
        "changes": "Renamed 1 causal-edge predicate label(s) to align with existing groundings: maintains \u2192 regulates \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:20Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002211\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:37:59Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (PATO:0000383\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:41:03Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (METPO:1007505\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-26T02:30:12Z",
        "curator": "claude",
        "action": "RETYPE_CAUSAL_NODES",
        "changes": "Re-typed 1 causal-node node_type field(s) to align with CausalNodeTypeEnum semantics: membrane fluidity: BIOLOGICAL_PROCESS \u2192 QUALITY \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-13T21:03:25Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002212\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-15T07:19:08Z",
        "curator": "claude",
        "action": "FIX_NODE_GROUNDING_CURIE",
        "changes": "Overwrote 1 causal-node grounding(s) to corrected CURIEs (phase-2 id-label fix; verified vs OAK).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-17T04:09:43Z",
        "curator": "claude",
        "action": "REMOVE_REDUNDANT_SYNONYM",
        "changes": "Removed 1 synonym(s) whose text duplicated the label (seeder redundancy; no information lost).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 6 evidence-backed generic edges (7 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:09Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002326\u00d72, RO:0002213\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:30Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:23366\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-26T07:15:17Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A031GJU0\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:21:11Z",
        "curator": "claude",
        "action": "RETRACT_DEAD_UNIPROT_GROUNDINGS",
        "changes": "Retracted 1 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:23:52Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (InterPro:IPR012171\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-21T00:00:00Z",
        "curator": "claude",
        "action": "BACKFILL_CANONICAL_EXAMPLES",
        "changes": "Added 1 exemplar taxon/taxa. Organisms and citations come only from this record's own deep-research artifact; every taxon id was resolved and label-checked against the local NCBITaxon build rather than recalled. Organisms the artifact names as contrast cases rather than exemplars were deliberately excluded.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope facultative_psychrophilic_cold_tolerance=NONMECHANISTIC with scope_notes; marked 1 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (cold_shock_proteins).",
        "llm_assisted": true
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:334543",
        "taxon_label": "Psychrobacter arcticus",
        "reference": "DOI:10.37256/amtt.5220244537",
        "note": "Grows at low temperature rather than merely surviving it, which is the distinction this trait turns on."
      }
    ]
  },
  {
    "identifier": "METPO:1003007",
    "label": "facultatively acidophilic",
    "definition": "A pH growth preference characterized by optimal growth in acidic environments (pH below 5.5) with the capacity to also grow at near-neutral pH values.",
    "definition_source": "DOI:10.1099/ijs.0.066175-0",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1003000"
    ],
    "synonyms": [
      {
        "synonym_text": "facultative acidophile",
        "synonym_type": "EXACT_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "created_by": "Jed Dongjin Kim-Ozaeta",
    "evidence": [
      {
        "reference": "DOI:10.1099/ijs.0.066175-0",
        "snippet": "capable of growth at pH 4.0-7.2",
        "notes": "Species-level example supports acidic-to-near-neutral growth capacity in a mildly acidophilic bacterium."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1473598",
        "taxon_label": "Paludibaculum fermentans",
        "reference": "DOI:10.1099/ijs.0.066175-0",
        "note": "Paludibaculum fermentans P105T was described from acidic peat and grows from pH 4.0 to 7.2, directly establishing acidic growth together with near-neutral capacity."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "facultatively_acidophilic_ph_homeostasis",
        "title": "Facultative acidophily pH homeostasis mechanism",
        "description": "Evidence-backed causal sketch linking facultative acidophily to acidic growth, near-neutral growth capacity, and inducible pH homeostasis.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a broad environmental or morphological classification spanning multiple mechanisms, a measurement-like bin, or an absence/arrangement descriptor; contextual protein nodes do not receive token UniProt examples.",
        "nodes": [
          {
            "node_id": "facultatively_acidophilic_trait",
            "label": "facultatively acidophilic",
            "node_type": "TRAIT",
            "grounding": "METPO:1003007",
            "description": "Optimal growth occurs under acidic conditions while near-neutral growth remains possible."
          },
          {
            "node_id": "acidic_external_ph",
            "label": "acidic external pH",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "External pH below neutral that supports acidophilic growth.",
            "grounding": "PATO:0001429"
          },
          {
            "node_id": "near_neutral_external_ph",
            "label": "near-neutral external pH",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "External pH near neutrality that facultative acidophiles can tolerate or grow in.",
            "grounding": "PATO:0001428"
          },
          {
            "node_id": "proton",
            "label": "proton",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:15378",
            "description": "Hydrogen ion contributing to low-pH stress."
          },
          {
            "node_id": "cytoplasmic_ph_homeostasis",
            "label": "cytoplasmic pH homeostasis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Maintenance of intracellular pH across acidic and near-neutral environments.",
            "grounding": "GO:0051453"
          },
          {
            "node_id": "proton_export_pumps",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "proton export pumps and antiporters",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Transport systems proposed to remove protons or exchange ions during acid stress."
          },
          {
            "node_id": "cytoplasmic_buffering",
            "label": "cytoplasmic buffering",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Cellular buffering and proton-consuming reactions that mitigate acidification."
          },
          {
            "node_id": "near_neutral_cytoplasm",
            "label": "near-neutral cytoplasm",
            "node_type": "STATE",
            "description": "Cytoplasmic pH maintained near neutrality despite low external pH."
          },
          {
            "node_id": "potassium_ion",
            "label": "potassium ion",
            "node_type": "CHEMICAL",
            "description": "Intracellular cation accumulated to oppose proton influx.",
            "grounding": "CHEBI:29103"
          },
          {
            "node_id": "reversed_membrane_potential",
            "label": "inside-positive (reversed) membrane potential",
            "node_type": "STATE",
            "description": "Reversed (inside-positive) transmembrane potential opposing proton entry."
          },
          {
            "node_id": "hopanoid_biosynthesis",
            "label": "hopanoid biosynthetic process",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Synthesis of hopanoids that rigidify the membrane against proton influx.",
            "grounding": "GO:0019746"
          },
          {
            "node_id": "proton_permeability",
            "label": "membrane proton permeability",
            "node_type": "QUALITY",
            "description": "Permeability of the cell membrane to protons."
          },
          {
            "node_id": "impermeable_membrane",
            "label": "rigid impermeable membrane",
            "node_type": "CELLULAR_LOCALIZATION",
            "description": "A rigid, low-permeability membrane that acts as a barrier to proton entry."
          },
          {
            "node_id": "glutamate_decarboxylase_system",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "glutamate decarboxylase system",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Decarboxylase (Gad) system consuming intracellular protons during acid stress."
          },
          {
            "node_id": "intracellular_ph",
            "label": "intracellular pH",
            "node_type": "QUALITY",
            "description": "Cytoplasmic pH value stabilized by buffering and homeostatic systems."
          }
        ],
        "edges": [
          {
            "subject": "acidic_external_ph",
            "predicate": "selects for",
            "object": "facultatively_acidophilic_trait",
            "description": "Acidic pH selects for acidophilic growth capacity.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2021.822229",
                "snippet": "acidic optimal growth pH",
                "notes": "Supports acidophilic classification by acidic growth optimum."
              }
            ],
            "predicate_id": "METPO:2007401"
          },
          {
            "subject": "near_neutral_external_ph",
            "predicate": "is compatible with",
            "object": "facultatively_acidophilic_trait",
            "description": "Facultatively acidophilic growth can extend into near-neutral pH.",
            "evidence": [
              {
                "reference": "DOI:10.1099/ijs.0.066175-0",
                "snippet": "capable of growth at pH 4.0-7.2",
                "notes": "Species-level evidence supports acidic-to-near-neutral growth range; this edge is qualified rather than generalized to all taxa."
              }
            ]
          },
          {
            "subject": "acidic_external_ph",
            "predicate": "increases gradient of",
            "object": "proton",
            "description": "Acidic pH imposes an external-to-internal proton gradient.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2021.822229",
                "snippet": "external to internal proton gradient",
                "notes": "Supports proton-gradient stress during low-pH growth."
              }
            ],
            "predicate_id": "METPO:2007601"
          },
          {
            "subject": "proton_export_pumps",
            "predicate": "contributes to",
            "object": "cytoplasmic_ph_homeostasis",
            "description": "Proton export and antiport systems contribute to acid-stress homeostasis.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2021.822229",
                "snippet": "proton export pumps and antiporters",
                "notes": "Supports transporter-mediated pH homeostasis mechanisms."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "cytoplasmic_buffering",
            "predicate": "contributes to",
            "object": "cytoplasmic_ph_homeostasis",
            "description": "Buffering and proton-consuming reactions reduce cytoplasmic acidification.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2021.822229",
                "snippet": "cytoplasmic buffering",
                "notes": "Supports buffering as a proposed acid resistance mechanism."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "cytoplasmic_ph_homeostasis",
            "predicate": "confers",
            "object": "facultatively_acidophilic_trait",
            "description": "Growth across acidic and near-neutral pH requires intracellular pH control.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2549",
                "snippet": "robust mechanisms for cytoplasmic pH homeostasis",
                "notes": "Supports cytoplasmic pH homeostasis for growth outside the preferred cytoplasmic pH range."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "acidic_external_ph",
            "predicate": "necessitates maintenance of",
            "object": "near_neutral_cytoplasm",
            "description": "Acidophilic growth requires preserving near-neutral cytoplasm against a steep proton gradient.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2021.822229",
                "notes": "maintain a near-neutral cytoplasm despite an external-to-internal proton gradient up to 10^5-fold."
              }
            ]
          },
          {
            "subject": "potassium_ion",
            "predicate": "generates",
            "object": "reversed_membrane_potential",
            "description": "Intracellular K+ accumulation generates an inside-positive potential that opposes proton influx.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2021.822229",
                "notes": "internal positive membrane potential thought to be generated by potassium ions."
              }
            ],
            "predicate_id": "biolink:produces"
          },
          {
            "subject": "reversed_membrane_potential",
            "predicate": "contributes to",
            "object": "cytoplasmic_ph_homeostasis",
            "description": "An inside-positive membrane potential is a first-line defense reducing proton entry, supporting pH homeostasis.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2021.822229",
                "notes": "Inside-positive potential generated by K+ opposes proton influx as a first-line defense."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "hopanoid_biosynthesis",
            "predicate": "decreases",
            "object": "proton_permeability",
            "description": "Hopanoids stiffen the membrane and reduce proton permeability under low pH.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2021.822229",
                "notes": "membrane alterations via inclusion of hopanoids linked to acidophilic lifestyle."
              }
            ],
            "predicate_id": "RO:0002212"
          },
          {
            "subject": "impermeable_membrane",
            "predicate": "limits",
            "object": "proton",
            "description": "A rigid, impermeable membrane acts as a barrier limiting proton entry into the cell.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2023.1149903",
                "notes": "acidophiles use a rigid and impermeable membrane that resists proton entry."
              }
            ],
            "predicate_id": "RO:0002212"
          },
          {
            "subject": "proton_export_pumps",
            "predicate": "expels",
            "object": "proton",
            "description": "Proton export pumps and antiporters directly remove protons that enter the cytoplasm.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2021.822229",
                "notes": "proton export pumps and antiporters listed among mechanisms maintaining pH homeostasis."
              }
            ]
          },
          {
            "subject": "glutamate_decarboxylase_system",
            "predicate": "consumes",
            "object": "proton",
            "description": "Glutamate decarboxylation consumes intracellular protons as a second-line acid resistance route.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2021.822229",
                "notes": "proton consuming reactions such as glutamate decarboxylase; gadABC among acid-adaptation genes."
              }
            ],
            "predicate_id": "biolink:consumes"
          },
          {
            "subject": "cytoplasmic_buffering",
            "predicate": "stabilizes",
            "object": "intracellular_ph",
            "description": "Cytoplasmic buffering dampens pH fluctuations to stabilize intracellular pH.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2023.1149903",
                "notes": "shared mechanisms include cytoplasmic buffering that stabilizes intracellular pH."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.940835+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-11T00:00:00-07:00",
        "curator": "codex",
        "action": "CURATED_WITH_LITERATURE",
        "changes": "Reviewed facultatively acidophilic trait and added DOI-backed evidence and causal graph for acidic and near-neutral pH growth capacity. Near-neutral growth evidence is species-level and should be treated as qualified.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:29Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002326\u00d72, RO:0002327\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T21:30:06Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007401\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:37:59Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0030641\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T08:14:32Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (PATO:0001428\u00d71, PATO:0001432\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-14T07:26:19Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007601\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-15T07:20:36Z",
        "curator": "claude",
        "action": "FIX_NODE_GROUNDING_CURIE",
        "changes": "Overwrote 1 causal-node grounding(s) (obsolete/wrong GO -> corrected, verified vs OAK).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-15T07:21:43Z",
        "curator": "claude",
        "action": "FIX_NODE_GROUNDING_CURIE",
        "changes": "Overwrote 2 pH causal-node grounding(s) to corrected PATO CURIEs (phase-2; verified vs OAK).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-17T04:09:43Z",
        "curator": "claude",
        "action": "REMOVE_REDUNDANT_SYNONYM",
        "changes": "Removed 1 synonym(s) whose text duplicated the label (seeder redundancy; no information lost).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 8 evidence-backed generic edges (8 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:09Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 5 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:produces\u00d71, RO:0002326\u00d71, METPO:2000017\u00d71, RO:0002212\u00d71, biolink:consumes\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:30Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:29103\u00d71, GO:0019746\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 1 causal edge(s) off enables/RO:0002327 with a TRAIT object (1 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T02:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES_PART2",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates onto their causal-graph counterparts (1 to reduces), issue 301 part 2. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Each replacement is a 1:1 mirror of its source predicate that changes only the domain, so the claim each edge makes is unchanged and directions are unchanged. The replacements are proposed in proposals/metpo_traitmech_v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T06:00:00Z",
        "curator": "claude",
        "action": "REGROUND_CAUSAL_EDGE",
        "changes": "Relabelled 1 causal edge from `reduces` to `decreases` and re-grounded it from METPO:2007802 to RO:0002212 (negatively regulates), issue 330. The corpus wrote two senses under the single label `reduces` - genuine electron donation, and a lessens/decreases sense - and METPO:2007802 is defined as donating electrons to the object and lowering its oxidation state, which this edge does not assert. The two senses could not be separated mechanically because the label was identical, so they migrated together in issue 329 and were split here by reading each edge. RO:0002212 declares no rdfs:domain or rdfs:range, so this introduces no entailment of the kind issue 301 removed.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-21T08:00:00Z",
        "curator": "codex",
        "action": "NORMALISE_NODE_TYPE",
        "changes": "Tranche 5 of issue 356 settles the process/quality families and merges ids that meant the same sense: reversed_membrane_potential is STATE, proton_permeability is QUALITY. A reversed membrane potential is an inside-positive electrical state, not the process that establishes it. The schema names this gradient/steady-value distinction explicitly. Proton permeability is a measurable membrane property, which is the schema's QUALITY sense rather than a biological process.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope facultatively_acidophilic_ph_homeostasis=NONMECHANISTIC with scope_notes; marked 2 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (proton_export_pumps, glutamate_decarboxylase_system).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T04:43:24Z",
        "curator": "codex",
        "action": "ADD_CANONICAL_EXAMPLES",
        "changes": "Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Paludibaculum fermentans (NCBITaxon:1473598; DOI:10.1099/ijs.0.066175-0). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000608",
    "label": "facultatively aerobic",
    "definition": "An oxygen preference in which growth can occur without oxygen but is capable of aerobic growth.",
    "definition_source": "PMID:21413255",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000601"
    ],
    "synonyms": [
      {
        "synonym_text": "facultative",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "facultative aerobe",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "PMID:21413255",
        "snippet": "preferentially utilize oxygen as a terminal electron acceptor",
        "notes": "Supports facultative aerobic growth when oxygen is available."
      },
      {
        "reference": "PMID:16142505",
        "snippet": "A facultative aerobic, moderately thermophilic, spore forming bacterium",
        "notes": "Organism example: Anoxybacillus kamchatkensis strain JW/VK-KG4 is described as facultatively aerobic."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:265546",
        "taxon_label": "Anoxybacillus ayderensis",
        "reference": "DOI:10.1007/s00792-005-0479-7",
        "note": "Type strain JW/VK-KG4 (DSM 14988; ATCC BAA-549) was grown both aerobically and anaerobically, with measured doubling times of 34 and 40 minutes, respectively. The source published it as Anoxybacillus kamchatkensis; NCBI now treats that name as a synonym of Anoxybacillus ayderensis at this taxon id."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "facultative_aerobe_oxygen_flexible_growth",
        "title": "Facultative aerobe oxygen-flexible growth mechanism",
        "description": "Evidence-backed causal sketch linking facultative aerobic growth to oxygen-responsive respiratory switching.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a broad environmental or morphological classification spanning multiple mechanisms, a measurement-like bin, or an absence/arrangement descriptor; contextual protein nodes do not receive token UniProt examples.",
        "nodes": [
          {
            "node_id": "facultative_aerobic_trait",
            "label": "facultatively aerobic",
            "node_type": "TRAIT",
            "grounding": "METPO:1000608",
            "description": "Growth can occur without oxygen but is capable of aerobic growth."
          },
          {
            "node_id": "molecular_oxygen",
            "label": "molecular oxygen",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:15379",
            "description": "Dioxygen used when aerobic growth is possible."
          },
          {
            "node_id": "aerobic_respiration",
            "label": "aerobic respiration",
            "node_type": "BIOLOGICAL_PROCESS",
            "grounding": "GO:0009060",
            "description": "Oxygen-dependent respiratory energy metabolism."
          },
          {
            "node_id": "anaerobic_metabolism",
            "label": "anaerobic metabolism",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Growth-supporting metabolism when oxygen is unavailable."
          },
          {
            "node_id": "fnr_type_regulation",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "FNR-type oxygen-responsive regulation",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Oxygen-sensing regulatory systems that tune respiratory metabolism."
          },
          {
            "node_id": "terminal_acceptor_availability",
            "label": "terminal electron acceptor availability",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Availability of a final electron acceptor (e.g. oxygen vs fumarate) in the environment."
          },
          {
            "node_id": "terminal_branch_choice",
            "label": "terminal respiratory branch choice",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Selection of which terminal respiratory enzyme/branch is active."
          },
          {
            "node_id": "arcab_system",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "ArcAB two-component system",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Redox-responsive two-component regulatory system controlling aerobic respiration."
          },
          {
            "node_id": "anaerobic_metabolism_genes",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "anaerobic metabolism protein systems",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Protein systems for anaerobic metabolic functions activated under anoxia."
          },
          {
            "node_id": "aerobic_metabolism_genes",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "aerobic metabolism protein systems",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Protein systems for aerobic respiratory functions repressed under anoxia."
          },
          {
            "node_id": "cytochrome_bd_oxidase",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "cytochrome bd oxidase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "High-affinity terminal oxidase that reduces oxygen at low O2 concentrations."
          }
        ],
        "edges": [
          {
            "subject": "molecular_oxygen",
            "predicate": "enables",
            "object": "aerobic_respiration",
            "description": "Facultatively aerobic organisms can use oxygen-dependent respiration when oxygen is available.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.celrep.2023.112444",
                "snippet": "terminal oxidases transfer electrons from the ETC to O2",
                "notes": "Supports aerobic respiration through oxygen-reducing terminal oxidases."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "facultative_aerobic_trait",
            "predicate": "has alternative process",
            "object": "anaerobic_metabolism",
            "description": "Facultative aerobic growth retains a growth mode when oxygen is absent.",
            "evidence": [
              {
                "reference": "DOI:10.1089/ars.2011.4051",
                "snippet": "utilizing other substrates as final electron acceptors",
                "notes": "Review describes respiratory adaptation to oxygen shortage using alternative electron acceptors."
              }
            ]
          },
          {
            "subject": "molecular_oxygen",
            "predicate": "regulates",
            "object": "fnr_type_regulation",
            "description": "Oxygen-responsive regulators tune metabolism across oxic and anoxic conditions.",
            "evidence": [
              {
                "reference": "DOI:10.1089/ars.2011.4051",
                "snippet": "Fnr-type transcriptional regulators that directly sense O2",
                "notes": "Supports oxygen sensing by FNR-type regulators."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "fnr_type_regulation",
            "predicate": "regulates switch between",
            "object": "aerobic_respiration",
            "description": "Oxygen-sensing regulation helps switch respiratory metabolism as oxygen availability changes.",
            "evidence": [
              {
                "reference": "DOI:10.1089/ars.2011.4051",
                "snippet": "adaptation of respiratory metabolism to changing environments",
                "notes": "Supports regulatory switching between oxygen regimes."
              }
            ]
          },
          {
            "subject": "terminal_acceptor_availability",
            "predicate": "determines",
            "object": "terminal_branch_choice",
            "description": "Which terminal respiratory enzyme is active depends on the available final electron acceptor.",
            "evidence": [
              {
                "reference": "DOI:10.1128/jb.00389-22",
                "notes": "which terminal enzyme is active depends on the availability of the final electron acceptor: fumarate or oxygen."
              }
            ]
          },
          {
            "subject": "arcab_system",
            "predicate": "represses",
            "object": "aerobic_respiration",
            "description": "ArcAB two-component regulatory system represses aerobic respiration under reducing conditions.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mbio.01448-23",
                "notes": "ArcAB, a two-component regulatory system that represses aerobic respiration; conserved switch in Enterobacterales."
              }
            ]
          },
          {
            "subject": "molecular_oxygen",
            "predicate": "inactivates",
            "object": "fnr_type_regulation",
            "description": "Oxygen directly inactivates FNR by oxidizing its iron-sulfur cluster, a core oxygen-sensing mechanism.",
            "evidence": [
              {
                "reference": "DOI:10.1093/nar/gkad750",
                "notes": "oxygen directly inactivates Fnr by oxidizing that iron-sulfur cluster; widely generalizable oxygen-sensing edge."
              }
            ]
          },
          {
            "subject": "fnr_type_regulation",
            "predicate": "activates",
            "object": "anaerobic_metabolism_genes",
            "description": "When active under anoxia, FNR activates anaerobic metabolism genes.",
            "evidence": [
              {
                "reference": "DOI:10.1093/nar/gkad750",
                "notes": "when active, Fnr activates anaerobic metabolism genes and represses aerobic genes."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "fnr_type_regulation",
            "predicate": "represses",
            "object": "aerobic_metabolism_genes",
            "description": "Active FNR represses aerobic metabolism genes under anoxic conditions.",
            "evidence": [
              {
                "reference": "DOI:10.1093/nar/gkad750",
                "notes": "Fnr activates anaerobic metabolism genes and represses aerobic genes."
              }
            ]
          },
          {
            "subject": "cytochrome_bd_oxidase",
            "predicate": "has high affinity for",
            "object": "molecular_oxygen",
            "description": "Cytochrome bd is a high-affinity terminal oxidase enabling oxygen respiration at low O2.",
            "evidence": [
              {
                "reference": "DOI:10.1128/aem.00378-23",
                "notes": "cytochrome bd supports high O2 consumption and high-affinity oxygen reduction at the cell surface."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.853277+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-05T01:09:05-07:00",
        "curator": "codex",
        "action": "CURATED_WITH_LITERATURE",
        "changes": "Added definition source and evidence for facultative oxygen use.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-05T18:39:46-07:00",
        "curator": "codex",
        "action": "ADDED_ORGANISM_EXAMPLE",
        "changes": "Added Anoxybacillus kamchatkensis organism example with PMID-backed evidence.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "ADDED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed causal graph for facultative aerobic oxygen-responsive growth.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:29Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d71, RO:0002211\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 6 evidence-backed generic edges (6 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:09Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002213\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-26T07:15:17Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:Q6L5L4\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-22T04:26:15Z",
        "curator": "codex",
        "action": "REVIEW_UNIPROT_INSTANCE_GROUNDINGS",
        "changes": "Reviewed 1 organism-specific UniProtKB grounding(s): replaced 0 with taxon-agnostic GO/InterPro terms and retracted 1 to label-only where no exact semantic term was supported (docs/GROUNDING_POLICY.md).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope facultative_aerobe_oxygen_flexible_growth=NONMECHANISTIC with scope_notes; marked 5 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (fnr_type_regulation, arcab_system, anaerobic_metabolism_genes, aerobic_metabolism_genes, cytochrome_bd_oxidase).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T10:54:11Z",
        "curator": "codex",
        "action": "ADD_CANONICAL_EXAMPLES",
        "changes": "Added Anoxybacillus ayderensis strain JW/VK-KG4 as a directly assayed facultatively aerobic exemplar from this record's own research artifact; preserved the source's historical Anoxybacillus kamchatkensis name in the note and verified NCBITaxon:265546 and its current label against NCBI.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1003005",
    "label": "facultatively alkaliphilic",
    "definition": "A pH growth preference in which an organism can grow at alkaline pH but does not require it.",
    "definition_source": "DOI:10.3389/fbioe.2015.00075",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1003000"
    ],
    "synonyms": [
      {
        "synonym_text": "facultative alkaliphile",
        "synonym_type": "EXACT_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "facultative alkaphilic",
        "synonym_type": "EXACT_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.3389/fbioe.2015.00075",
        "snippet": "capable of growing near neutral pH",
        "notes": "Supports facultative alkaliphiles as alkaline-growing organisms that also grow near neutral pH."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:79885",
        "taxon_label": "Alkalihalophilus pseudofirmus",
        "note": "facultative alkaliphile (pH 7.5 to >11)",
        "reference": "PMID:21951522"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "facultatively_alkaphilic_sodium_cycle_homeostasis",
        "title": "Facultative alkaliphily sodium-cycle pH homeostasis mechanism",
        "description": "Evidence-backed causal sketch linking facultative alkaliphily to alkaline growth capacity, near-neutral growth, and sodium-dependent pH homeostasis.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a broad environmental or morphological classification spanning multiple mechanisms, a measurement-like bin, or an absence/arrangement descriptor; contextual protein nodes do not receive token UniProt examples.",
        "nodes": [
          {
            "node_id": "facultatively_alkaphilic_trait",
            "label": "facultatively alkaliphilic",
            "node_type": "TRAIT",
            "grounding": "METPO:1003005",
            "description": "Growth can occur at alkaline pH but does not require alkaline pH."
          },
          {
            "node_id": "alkaline_external_ph",
            "label": "alkaline external pH",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "External pH above neutral, often near or above pH 9 for alkaliphiles.",
            "grounding": "PATO:0001430"
          },
          {
            "node_id": "near_neutral_external_ph",
            "label": "near-neutral external pH",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "External pH near neutrality compatible with facultative alkaliphile growth.",
            "grounding": "PATO:0001428"
          },
          {
            "node_id": "sodium_ion",
            "label": "sodium ion",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:29101",
            "description": "Sodium ion participating in alkaliphile sodium cycles."
          },
          {
            "node_id": "proton",
            "label": "proton",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:15378",
            "description": "Hydrogen ion imported or retained to acidify the cytoplasm under alkaline conditions."
          },
          {
            "node_id": "sodium_proton_antiporter",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "Na+/H+ antiporter",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Antiporter exchanging sodium ions and protons during alkaline pH homeostasis."
          },
          {
            "node_id": "cytoplasmic_ph_homeostasis",
            "label": "cytoplasmic pH homeostasis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Maintenance of intracellular pH across alkaline and near-neutral environments.",
            "grounding": "GO:0051453"
          },
          {
            "node_id": "na_h_antiport_activity",
            "label": "Na+/H+ antiport activity",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "Electrogenic exchange of cytoplasmic Na+ for a larger number of entering protons."
          },
          {
            "node_id": "acidic_cell_wall_components",
            "label": "acidic secondary cell-wall components",
            "node_type": "CELLULAR_LOCALIZATION",
            "description": "Negatively charged secondary cell-wall polymers and S-layer components at the cell surface."
          },
          {
            "node_id": "f1fo_atp_synthase",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "F1Fo-ATP synthase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Proton-coupled ATP synthase complex operating at alkaline pH."
          },
          {
            "node_id": "atp_production_alkaline",
            "label": "ATP production at alkaline pH",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "ATP synthesis sustained despite low bulk proton-motive force at alkaline pH."
          }
        ],
        "edges": [
          {
            "subject": "alkaline_external_ph",
            "predicate": "confers",
            "object": "facultatively_alkaphilic_trait",
            "description": "Facultative alkaliphiles grow well under alkaline pH conditions.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fbioe.2015.00075",
                "snippet": "grow well at pH values exceeding pH 9",
                "notes": "Supports alkaline growth capacity of alkaliphilic microorganisms."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "near_neutral_external_ph",
            "predicate": "is compatible with",
            "object": "facultatively_alkaphilic_trait",
            "description": "Facultative alkaliphiles retain growth capacity near neutral pH.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fbioe.2015.00075",
                "snippet": "capable of growing near neutral pH",
                "notes": "Review explicitly distinguishes facultative alkaliphiles from obligate alkaliphiles."
              }
            ]
          },
          {
            "subject": "alkaline_external_ph",
            "predicate": "challenges",
            "object": "cytoplasmic_ph_homeostasis",
            "description": "Alkaline external pH requires cytoplasmic proton accumulation or retention.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2549",
                "snippet": "active proton accumulation or generation in the cytoplasm",
                "notes": "Supports alkaline-pH homeostasis mechanisms."
              }
            ],
            "predicate_id": "METPO:2007406"
          },
          {
            "subject": "sodium_proton_antiporter",
            "predicate": "exports",
            "object": "sodium_ion",
            "description": "Sodium efflux is one limb of the alkaliphile Na+ cycle.",
            "evidence": [
              {
                "reference": "DOI:10.1016/S0005-2728(00)00285-1",
                "snippet": "Na+ efflux",
                "notes": "Supports sodium efflux through Na+/H+ antiporters."
              }
            ],
            "predicate_id": "METPO:2007804"
          },
          {
            "subject": "sodium_proton_antiporter",
            "predicate": "accumulates",
            "object": "proton",
            "description": "Na+/H+ antiport contributes to net proton accumulation during alkaline pH homeostasis.",
            "evidence": [
              {
                "reference": "DOI:10.1016/S0005-2728(00)00285-1",
                "snippet": "net H+ accumulation",
                "notes": "Supports proton accumulation by antiporters in alkaliphiles."
              }
            ],
            "predicate_id": "METPO:2007810"
          },
          {
            "subject": "cytoplasmic_ph_homeostasis",
            "predicate": "confers",
            "object": "facultatively_alkaphilic_trait",
            "description": "Growth across alkaline and near-neutral pH requires pH homeostasis.",
            "evidence": [
              {
                "reference": "DOI:10.1016/S0005-2728(00)00285-1",
                "snippet": "pH homeostasis ... appears to set the upper pH limit for growth",
                "notes": "Supports pH homeostasis as a determinant of alkaliphilic growth range."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "alkaline_external_ph",
            "predicate": "selects for",
            "object": "na_h_antiport_activity",
            "description": "Alkaline external pH selects for electrogenic Na+/H+ antiport that acidifies the cytoplasm.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fbioe.2015.00075",
                "notes": "electrogenic exchange of outwardly moving sodium ions for a greater number of entering protons; broadly supported core adaptation."
              }
            ],
            "predicate_id": "METPO:2007401"
          },
          {
            "subject": "na_h_antiport_activity",
            "predicate": "maintains",
            "object": "cytoplasmic_ph_homeostasis",
            "description": "Na+/H+ antiport keeps the cytoplasm 2-2.3 units below external pH under alkaline conditions.",
            "evidence": [
              {
                "reference": "DOI:10.1007/978-981-19-1573-4_3",
                "notes": "maintain cytoplasmic pH 2-2.3 units below the external pH; generic alkaliphile homeostasis edge."
              }
            ]
          },
          {
            "subject": "acidic_cell_wall_components",
            "predicate": "attracts",
            "object": "proton",
            "description": "Surface acidity enriches protons and repels hydroxide, supporting alkaline adaptation.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2018.02331",
                "notes": "acidic secondary cell wall components attract H+ and repel OH-; process-level cell-envelope buffering."
              }
            ]
          },
          {
            "subject": "f1fo_atp_synthase",
            "predicate": "supports",
            "object": "atp_production_alkaline",
            "description": "Proton-coupled ATP synthase sustains ATP production despite low bulk PMF at alkaline pH.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fbioe.2015.00075",
                "notes": "alkaliphilic aerobes often use proton-coupled ATP synthases despite an apparently low bulk proton-motive force; general bioenergetics edge."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.939582+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-11T00:00:00-07:00",
        "curator": "codex",
        "action": "CURATED_WITH_LITERATURE",
        "changes": "Reviewed facultatively alkaphilic trait and added DOI-backed evidence and causal graph for alkaline and near-neutral pH growth capacity.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:29Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T21:30:06Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007406\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:18Z",
        "curator": "claude",
        "action": "RENAME_PREDICATE_LABELS",
        "changes": "Renamed 1 causal-edge predicate label(s) to align with existing groundings: supports \u2192 enables \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:20Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:37:59Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0030641\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T05:05:14Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A068T423\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T08:14:32Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (PATO:0001429\u00d71, PATO:0001432\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-15T07:20:36Z",
        "curator": "claude",
        "action": "FIX_NODE_GROUNDING_CURIE",
        "changes": "Overwrote 1 causal-node grounding(s) (obsolete/wrong GO -> corrected, verified vs OAK).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-15T07:21:43Z",
        "curator": "claude",
        "action": "FIX_NODE_GROUNDING_CURIE",
        "changes": "Overwrote 2 pH causal-node grounding(s) to corrected PATO CURIEs (phase-2; verified vs OAK).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-16T06:30:55Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000209\u00d71, METPO:2000210\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 4 evidence-backed generic edges (4 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:09Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007401\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:21:11Z",
        "curator": "claude",
        "action": "RETRACT_DEAD_UNIPROT_GROUNDINGS",
        "changes": "Retracted 1 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 2 causal edge(s) off enables/RO:0002327 with a TRAIT object (2 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T02:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES_PART2",
        "changes": "Re-grounded 2 causal edge(s) off microbe-domain METPO predicates onto their causal-graph counterparts (1 to accumulates, 1 to exports), issue 301 part 2. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Each replacement is a 1:1 mirror of its source predicate that changes only the domain, so the claim each edge makes is unchanged and directions are unchanged. The replacements are proposed in proposals/metpo_traitmech_v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope facultatively_alkaphilic_sodium_cycle_homeostasis=NONMECHANISTIC with scope_notes; marked 2 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (sodium_proton_antiporter, f1fo_atp_synthase).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T07:35:00Z",
        "curator": "migrate_metpo_2026_06_12",
        "action": "MIGRATE_METPO_RELEASE",
        "changes": "Migrated source-owned fields to locked METPO 2026-06-12: label 'facultatively alkaphilic' -> 'facultatively alkaliphilic'; synonyms synchronized at ontology-declared scope; grounded node facultatively_alkaphilic_trait label synchronized"
      }
    ]
  },
  {
    "identifier": "METPO:1000605",
    "label": "facultatively anaerobic",
    "definition": "An oxygen preference in which growth can occur with or without molecular oxygen (O\u2082).",
    "definition_source": "https://www.ncbi.nlm.nih.gov/books/NBK482349/",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000601"
    ],
    "synonyms": [
      {
        "synonym_text": "facultative",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "facultative anaerobe",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "https://www.ncbi.nlm.nih.gov/books/NBK482349/",
        "snippet": "can grow in the presence or absence of oxygen",
        "notes": "Supports facultative anaerobiosis as growth under oxic or anoxic conditions."
      },
      {
        "reference": "DOI:10.1093/femsre/fuac008",
        "snippet": "Escherichia coli is a facultative anaerobe",
        "notes": "Organism example: Escherichia coli is described as facultatively anaerobic."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:562",
        "taxon_label": "Escherichia coli",
        "note": "grows aerobically or by fermentation/anaerobic respiration",
        "reference": "PMID:7747938"
      },
      {
        "taxon_id": "NCBITaxon:1280",
        "taxon_label": "Staphylococcus aureus",
        "note": "facultative anaerobe",
        "reference": "PMID:24628867"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "facultative_anaerobe_oxygen_switch",
        "title": "Facultative anaerobe oxygen-responsive metabolism",
        "description": "Evidence-backed causal sketch linking facultative anaerobiosis to oxygen-responsive switching between aerobic and anaerobic metabolism.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a broad environmental or morphological classification spanning multiple mechanisms, a measurement-like bin, or an absence/arrangement descriptor; contextual protein nodes do not receive token UniProt examples.",
        "nodes": [
          {
            "node_id": "facultative_anaerobic_trait",
            "label": "facultatively anaerobic",
            "node_type": "TRAIT",
            "grounding": "METPO:1000605",
            "description": "Growth can occur with or without molecular oxygen."
          },
          {
            "node_id": "molecular_oxygen",
            "label": "molecular oxygen",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:15379",
            "description": "Dioxygen acts as a respiratory substrate and regulatory signal."
          },
          {
            "node_id": "aerobic_respiration",
            "label": "aerobic respiration",
            "node_type": "BIOLOGICAL_PROCESS",
            "grounding": "GO:0009060",
            "description": "Oxygen-dependent respiratory energy metabolism."
          },
          {
            "node_id": "anaerobic_respiration",
            "label": "anaerobic respiration",
            "node_type": "BIOLOGICAL_PROCESS",
            "grounding": "GO:0009061",
            "description": "Respiratory energy metabolism using non-oxygen electron acceptors."
          },
          {
            "node_id": "fnr_regulator",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "FNR oxygen-responsive regulator",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Oxygen-dependent transcriptional regulator of anaerobic respiration genes in E. coli."
          },
          {
            "node_id": "arca_regulator",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "ArcA/ArcAB two-component regulator",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Two-component regulatory system that represses the aerobic respiration program during the aerobic-to-anaerobic transition."
          },
          {
            "node_id": "alternative_electron_acceptors",
            "label": "alternative terminal electron acceptors",
            "node_type": "CHEMICAL",
            "description": "Non-oxygen terminal electron acceptors (e.g. nitrate, fumarate, DMSO, TMAO) used for anaerobic electron transport."
          },
          {
            "node_id": "anaerobic_etc",
            "label": "anaerobic electron transport chain operation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Operation of the electron transport chain using non-oxygen terminal electron acceptors when O2 is absent."
          }
        ],
        "edges": [
          {
            "subject": "molecular_oxygen",
            "predicate": "enables",
            "object": "aerobic_respiration",
            "description": "In facultative anaerobes, oxygen availability permits aerobic respiration.",
            "evidence": [
              {
                "reference": "DOI:10.1111/cmi.13338",
                "snippet": "cope with changing oxygen levels",
                "notes": "Review frames facultative anaerobe fitness around changing oxygen availability; exact pathways vary by organism."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "molecular_oxygen",
            "predicate": "regulates",
            "object": "fnr_regulator",
            "description": "FNR senses oxygen status and changes respiratory gene expression.",
            "evidence": [
              {
                "reference": "DOI:10.1007/BF00445650",
                "snippet": "molecular oxygen is an important regulatory signal",
                "notes": "Review describes oxygen-dependent regulation by FNR."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "fnr_regulator",
            "predicate": "activates in absence of oxygen",
            "object": "anaerobic_respiration",
            "description": "FNR activates anaerobic respiratory gene expression under anoxic conditions.",
            "evidence": [
              {
                "reference": "DOI:10.1007/BF00445650",
                "snippet": "activates transcription in the absence of O2",
                "notes": "Supports FNR activation of anaerobic respiration genes without oxygen."
              }
            ]
          },
          {
            "subject": "facultative_anaerobic_trait",
            "predicate": "has alternative process",
            "object": "anaerobic_respiration",
            "description": "Facultative anaerobiosis includes the capacity to grow using anaerobic respiration when oxygen is absent.",
            "evidence": [
              {
                "reference": "DOI:10.1007/BF00445650",
                "snippet": "expression of anaerobic respiration",
                "notes": "E. coli-focused evidence for anaerobic respiratory programs in a facultative anaerobe."
              }
            ]
          },
          {
            "subject": "molecular_oxygen",
            "predicate": "oxidizes/inactivates",
            "object": "fnr_regulator",
            "description": "Oxygen oxidizes the FNR [4Fe-4S] cluster, inactivating FNR and preventing transcription of anaerobic respiration genes.",
            "evidence": [
              {
                "reference": "DOI:10.1101/2025.01.08.631794",
                "notes": "In the presence of oxygen, FNR is inactivated through oxidation of its FeS cluster, preventing transcription of anaerobic respiration genes."
              }
            ]
          },
          {
            "subject": "arca_regulator",
            "predicate": "represses",
            "object": "aerobic_respiration",
            "description": "ArcAB represses the aerobic respiration program, mediating metabolic adaptation to lower oxygen.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mbio.01448-23",
                "notes": "ArcAB, a two-component regulatory system that represses aerobic respiration, is a key mediator of metabolic adaptation."
              }
            ]
          },
          {
            "subject": "alternative_electron_acceptors",
            "predicate": "enable",
            "object": "anaerobic_etc",
            "description": "Alternative terminal electron acceptors enable anaerobic electron transport chain operation when oxygen is absent.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-024-51029-x",
                "notes": "Alternative terminal electron acceptors (nitrate, fumarate, DMSO, TMAO) allow anaerobic ETC operation when O2 is absent."
              }
            ]
          },
          {
            "subject": "anaerobic_etc",
            "predicate": "is part of",
            "object": "anaerobic_respiration",
            "description": "Anaerobic ETC operation constitutes the respiratory energy metabolism used in the absence of oxygen.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-024-51029-x",
                "notes": "Anaerobic ETC operation with alternative terminal electron acceptors underlies anaerobic respiration in facultative anaerobes."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.851077+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-05T01:09:05-07:00",
        "curator": "codex",
        "action": "CURATED_WITH_LITERATURE",
        "changes": "Added definition source and evidence for facultative anaerobic growth.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-05T18:39:46-07:00",
        "curator": "codex",
        "action": "ADDED_ORGANISM_EXAMPLE",
        "changes": "Added Escherichia coli organism example with DOI-backed evidence.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "ADDED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed causal graph for oxygen-responsive facultative anaerobic metabolism.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:29Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d71, RO:0002211\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 4 evidence-backed generic edges (3 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope facultative_anaerobe_oxygen_switch=NONMECHANISTIC with scope_notes; marked 2 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (fnr_regulator, arca_regulator).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000535",
    "label": "growth range phenotype with numerical limits",
    "definition": "A phenotype characterized by the span of values within which an organism can maintain growth.",
    "definition_source": "DOI:10.1093/femsre/fuy009",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1093/femsre/fuy009",
        "snippet": "salinity range",
        "notes": "Osmoadaptation review supports the bounded span of a growth-supporting environmental variable as a standard quantitative descriptor."
      },
      {
        "reference": "DOI:10.1038/nrmicro2549",
        "snippet": "external pH",
        "notes": "pH-homeostasis review supports the external-pH range over which cytoplasmic pH homeostasis sustains growth as an analogous range descriptor on the pH axis."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:375929",
        "taxon_label": "Natranaerobius thermophilus",
        "reference": "DOI:10.1128/aem.00145-24",
        "note": "Natranaerobius thermophilus was reported across 3.1-4.9 M total sodium at pH 9.5 and 53 degrees C; this is a bounded growth range on a salinity axis, not an NaCl conversion or an optimum claim."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "growth_range_phenotype_descriptor",
        "title": "Growth-range phenotype descriptor across environmental axes",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a quantitative measurement, interval, or bin in the environmental phenotype hierarchy; a token protein example would misrepresent the measured value as one inherited molecular mechanism.",
        "description": "DOI-backed graph framing the growth-range phenotype as a generic bounded-span descriptor over any numerical environmental axis, with `is a` edges to the axis-specific growth-range phenotypes for NaCl, pH, and temperature.",
        "nodes": [
          {
            "node_id": "growth_range_phenotype_trait",
            "label": "growth range phenotype with numerical limits",
            "node_type": "TRAIT",
            "grounding": "METPO:1000535",
            "description": "Phenotype defined by the span between minimum and maximum growth-supporting values of an environmental variable."
          },
          {
            "node_id": "numerical_environmental_axis",
            "label": "numerical environmental axis",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Any continuous environmental variable (NaCl, pH, temperature, etc.) on which microbial growth can be measured quantitatively."
          },
          {
            "node_id": "nacl_range",
            "label": "NaCl range",
            "node_type": "TRAIT",
            "grounding": "METPO:1000334",
            "description": "Span of NaCl concentrations supporting growth."
          },
          {
            "node_id": "ph_range",
            "label": "pH range",
            "node_type": "TRAIT",
            "grounding": "METPO:1000332",
            "description": "Span of external pH values supporting growth."
          },
          {
            "node_id": "temperature_range",
            "label": "temperature range",
            "node_type": "TRAIT",
            "grounding": "METPO:1000306",
            "description": "Span of ambient temperatures supporting growth."
          },
          {
            "node_id": "cytoplasmic_ph_homeostasis",
            "label": "maintenance of near-neutral cytoplasmic pH",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Homeostatic maintenance of cytoplasmic pH (~7.0-7.5) across a range of external pH values."
          },
          {
            "node_id": "cation_proton_antiporter_activity",
            "label": "K+/H+ or Na+/H+ antiporter activity",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "Ion/H+ antiporter activity that exports K+ or Na+ in exchange for protons to acidify the cytoplasm when internal pH rises."
          },
          {
            "node_id": "cytoplasm_acidification",
            "label": "cytoplasmic acidification",
            "node_type": "STATE",
            "description": "Lowering of cytoplasmic pH, used to counter alkaline external conditions or resulting from acid stress."
          },
          {
            "node_id": "proton_pumping_atpase_respiration",
            "label": "F0F1-ATPase / proton-pumping respiratory chain activity",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "Proton-pumping by the F0F1-ATPase and respiratory chains that prevents cytoplasmic acidification."
          },
          {
            "node_id": "prevent_cytoplasm_acidification",
            "label": "prevention of cytoplasmic acidification",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Process counteracting excessive cytoplasmic acidification to keep internal pH within the growth-supporting window."
          },
          {
            "node_id": "aa_decarboxylase_antiporter",
            "label": "amino-acid decarboxylase/antiporter system",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "Coupled amino-acid decarboxylase and antiporter activity that consumes intracellular protons and generates PMF, raising internal pH under acidic conditions."
          },
          {
            "node_id": "hypertonic_salinity_increase",
            "label": "hypertonic salinity increase",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Rise in external salinity producing hypertonic conditions."
          },
          {
            "node_id": "cell_shrinkage_low_turgor",
            "label": "cell shrinkage and lowered turgor",
            "node_type": "STATE",
            "description": "Hypertonicity-driven loss of cell volume and turgor pressure that limits growth at the salinity boundary."
          },
          {
            "node_id": "opua_glycine_betaine_uptake",
            "label": "OpuA-mediated glycine betaine uptake",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "ABC-transporter (OpuA) mediated uptake of the compatible solute glycine betaine."
          },
          {
            "node_id": "compatible_solute_accumulation",
            "label": "compatible solute accumulation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Accumulation of compatible solutes (e.g., glycine betaine) that counteract hyperosmotic stress."
          }
        ],
        "edges": [
          {
            "subject": "numerical_environmental_axis",
            "predicate": "defines",
            "object": "growth_range_phenotype_trait",
            "description": "A numerical environmental axis defines the values whose bounded growth-supporting span yields the growth-range phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuy009",
                "snippet": "salinity range",
                "notes": "Supports a numerical environmental axis as the axis on which a bounded growth-supporting span is measured."
              }
            ],
            "predicate_id": "METPO:2007500"
          },
          {
            "subject": "nacl_range",
            "predicate": "is a",
            "object": "growth_range_phenotype_trait",
            "description": "NaCl range is an axis-specific growth-range phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuy009",
                "snippet": "salinity range",
                "notes": "Supports NaCl range as a growth-range phenotype defined over the salinity axis."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "ph_range",
            "predicate": "is a",
            "object": "growth_range_phenotype_trait",
            "description": "pH range is an axis-specific growth-range phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2549",
                "snippet": "external pH",
                "notes": "Supports pH range as a growth-range phenotype defined over the external-pH axis."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "temperature_range",
            "predicate": "is a",
            "object": "growth_range_phenotype_trait",
            "description": "Temperature range is an axis-specific growth-range phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1016/s0300-9629(97)00003-0",
                "snippet": "adapted to environments of high temperature",
                "notes": "Supports temperature range as a growth-range phenotype defined over the ambient-temperature axis."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "ph_range",
            "predicate": "requires",
            "object": "cytoplasmic_ph_homeostasis",
            "description": "Growth across an external pH range requires maintenance of near-neutral cytoplasmic pH.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuad033",
                "notes": "Neutralophilic bacteria keep cytoplasmic pH within 7.0-7.5 across external pH of about 5-8 to sustain growth."
              }
            ]
          },
          {
            "subject": "cation_proton_antiporter_activity",
            "predicate": "contributes to",
            "object": "cytoplasm_acidification",
            "description": "K+/H+ or Na+/H+ antiporter activity acidifies the cytoplasm, supporting growth at alkaline external pH.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuad033",
                "notes": "Ion/H+ antiporters acidify the cytoplasm by exporting K+ or Na+ for protons when internal pH gets too high."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "cytoplasm_acidification",
            "predicate": "contributes to",
            "object": "ph_range",
            "description": "Antiporter-driven cytoplasmic acidification supports growth at the alkaline end of the pH range.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuad033",
                "notes": "Cytoplasmic acidification counters alkaline external pH, extending the upper pH growth boundary."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "proton_pumping_atpase_respiration",
            "predicate": "enables",
            "object": "prevent_cytoplasm_acidification",
            "description": "F0F1-ATPase and proton-pumping respiratory chains prevent cytoplasmic acidification, supporting growth across the external pH range.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuad033",
                "notes": "Activation/upregulation of proton-pumping respiratory chains and the F0F1-ATPase prevents cytoplasmic acidification."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "aa_decarboxylase_antiporter",
            "predicate": "enables",
            "object": "cytoplasmic_ph_homeostasis",
            "description": "Amino-acid decarboxylase/antiporter systems generate PMF and raise internal pH, enabling growth under acidic external pH.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuad033",
                "notes": "Each decarboxylation pumps one proton equivalent; decarboxylases increase activity when internal pH falls, extending the acid-side boundary."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "hypertonic_salinity_increase",
            "predicate": "causes",
            "object": "cell_shrinkage_low_turgor",
            "description": "A hypertonic salinity increase causes cell shrinkage and lowered turgor; growth ceases below the turgor limit, setting the upper salinity boundary.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuad033",
                "notes": "Hypertonicity leads to cell shrinkage and lowering of turgor; the lower turgor limit is reached before cell growth ceases."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "opua_glycine_betaine_uptake",
            "predicate": "enables",
            "object": "compatible_solute_accumulation",
            "description": "OpuA-mediated glycine betaine uptake drives compatible-solute accumulation that counteracts hyperosmotic stress and supports salinity-range growth.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuad033",
                "notes": "OpuA accumulates the compatible solute glycine betaine to (sub)molar levels to counteract hyperosmotic stress."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "compatible_solute_accumulation",
            "predicate": "contributes to",
            "object": "nacl_range",
            "description": "Compatible-solute accumulation counteracts hyperosmotic stress, supporting growth across the NaCl salinity range.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuad033",
                "notes": "Compatible-solute accumulation offsets hyperosmotic stress, broadening the salinity growth range."
              }
            ],
            "predicate_id": "RO:0002326"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.847733+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-13T12:00:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed causal graph framing the growth-range phenotype as a cross-axis bounded-span descriptor with axis-specific children for NaCl, pH, and temperature.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:29Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (rdfs:subClassOf\u00d73).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T07:37:39Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007500\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 8 evidence-backed generic edges (10 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:10Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 7 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d74, RO:0002326\u00d72, biolink:causes\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-07T05:00:00Z",
        "curator": "claude",
        "action": "REGROUND_CAUSAL_EDGE",
        "changes": "Re-grounded the edge from enables/RO:0002327 to RO:0002326 (contributes to), issue 334. biolink declares enables range 'biological process or activity' and the object is a STATE, which does not satisfy it. Unlike the tolerance/capacity nodes in this same pass, this object is a genuine state rather than a mis-typed disposition - a gradient, a community composition, an internal environment - so retyping it to TRAIT would be wrong. contributes to fits because the subject genuinely contributes to the OCCURRENCE OR GENERATION of the object, which is biolink's definition; that is the same test the motive-force edges FAILED in issue 341, where the subject powers a machine it does not generate. RO:0002326 declares no rdfs:domain or rdfs:range.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-15T06:00:00Z",
        "curator": "claude",
        "action": "SPLIT_PROTEIN_FROM_ACTIVITY",
        "changes": "Separated the protein sense from the activity sense so one node_id means one thing (issue 356): renamed cation_proton_antiporter -> cation_proton_antiporter_activity (MOLECULAR_FUNCTION sense). Described as 'Ion/H+ antiporter ACTIVITY that exports K+ or Na+ in exchange for protons', against 'Antiporter exchanging cations for protons during pH stress' for the protein occurrences. cation_proton_antiporter_activity already exists corpus-wide as MOLECULAR_FUNCTION.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope growth_range_phenotype_descriptor=NONMECHANISTIC with scope_notes.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T04:43:24Z",
        "curator": "codex",
        "action": "ADD_CANONICAL_EXAMPLES",
        "changes": "Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Natranaerobius thermophilus (NCBITaxon:375929; DOI:10.1128/aem.00145-24). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000621",
    "label": "haloalkaliphilic",
    "definition": "A halophily preference in which an organism requires both high salt concentrations and alkaline pH for optimal growth.",
    "definition_source": "PMID:17203963",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000629"
    ],
    "evidence": [
      {
        "reference": "PMID:17203963",
        "snippet": "aerobic, haloalkaliphilic archaeon Natronomonas pharaonis",
        "notes": "Organism example: Natronomonas pharaonis is described as haloalkaliphilic."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:2257",
        "taxon_label": "Natronomonas pharaonis",
        "note": "soda-lake haloalkaliphile",
        "reference": "PMID:16169924"
      },
      {
        "taxon_id": "NCBITaxon:1053",
        "taxon_label": "Halorhodospira halophila",
        "note": "haloalkaliphilic purple sulfur bacterium",
        "reference": "PMID:39915441"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "haloalkaliphilic_salt_alkaline_adaptation",
        "title": "Haloalkaliphilic salt and alkaline-pH adaptation mechanism",
        "description": "Evidence-backed causal sketch linking haloalkaliphily to combined hypersaline and alkaline conditions.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a broad environmental or morphological classification spanning multiple mechanisms, a measurement-like bin, or an absence/arrangement descriptor; contextual protein nodes do not receive token UniProt examples.",
        "nodes": [
          {
            "node_id": "haloalkaliphilic_trait",
            "label": "haloalkaliphilic",
            "node_type": "TRAIT",
            "grounding": "METPO:1000621",
            "description": "Requires both high salt and alkaline pH for optimal growth."
          },
          {
            "node_id": "soda_lake_environment",
            "label": "saline soda lake environment",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Sodium carbonate-rich, alkaline, saline habitat."
          },
          {
            "node_id": "high_salt_environment",
            "label": "high-salt environment",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Saline or salt-saturated environmental condition.",
            "grounding": "ENVO:01001040"
          },
          {
            "node_id": "alkaline_ph",
            "label": "alkaline pH",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "High pH growth condition."
          },
          {
            "node_id": "compatible_solutes",
            "label": "compatible solutes",
            "node_type": "CHEMICAL",
            "description": "Ectoine, glycine betaine, or related osmoprotectants.",
            "grounding": "CHEBI:25728"
          },
          {
            "node_id": "alkaline_ph_homeostasis",
            "label": "alkaline pH homeostasis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Cellular maintenance of internal pH under alkaline conditions."
          },
          {
            "node_id": "compatible_solute_strategy",
            "label": "compatible-solute (salt-out) strategy",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Osmoadaptation by biosynthesis/accumulation of organic compatible solutes."
          },
          {
            "node_id": "salt_in_strategy",
            "label": "salt-in strategy",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Osmoadaptation by intracellular accumulation of inorganic ions (e.g. K+).",
            "grounding": "METPO:1007720"
          },
          {
            "node_id": "na_h_antiport",
            "label": "Na+/H+ antiporter activity",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "Sodium:proton antiport that expels Na+ and assists cytoplasmic pH regulation."
          },
          {
            "node_id": "na_efflux_ph_regulation",
            "label": "Na+ efflux and pH regulation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Coupled extrusion of sodium and maintenance of intracellular pH."
          },
          {
            "node_id": "ectoine",
            "label": "ectoine",
            "node_type": "CHEMICAL",
            "description": "Cyclic amino-acid-derived compatible solute.",
            "grounding": "CHEBI:27592"
          },
          {
            "node_id": "choline_oxidation_pathway",
            "label": "choline oxidation pathway",
            "node_type": "PATHWAY",
            "description": "De novo biosynthesis of glycine betaine via oxidation of choline."
          },
          {
            "node_id": "glycine_betaine",
            "label": "glycine betaine",
            "node_type": "CHEMICAL",
            "description": "Quaternary ammonium compatible solute.",
            "grounding": "CHEBI:17750"
          }
        ],
        "edges": [
          {
            "subject": "soda_lake_environment",
            "predicate": "provides",
            "object": "high_salt_environment",
            "description": "Soda lakes combine salinity with alkaline chemistry.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.femsre.2004.10.005",
                "snippet": "alkaline sodium carbonate/bicarbonate fraction",
                "notes": "Review supports soda lakes as alkaline saline environments."
              }
            ]
          },
          {
            "subject": "soda_lake_environment",
            "predicate": "provides",
            "object": "alkaline_ph",
            "description": "Soda lake buffering maintains high pH.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.femsre.2004.10.005",
                "snippet": "stable, high-to-extremely high pH",
                "notes": "Supports persistent alkaline pH in haloalkaliphilic habitats."
              }
            ]
          },
          {
            "subject": "high_salt_environment",
            "predicate": "contributes to",
            "object": "haloalkaliphilic_trait",
            "description": "Haloalkaliphiles require high-salt adaptation.",
            "evidence": [
              {
                "reference": "DOI:10.1021/pr060352q",
                "snippet": "survive in salt-saturated lakes of pH 11",
                "notes": "Natronomonas pharaonis proteomics paper supports combined salt and alkaline survival."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "alkaline_ph",
            "predicate": "contributes to",
            "object": "haloalkaliphilic_trait",
            "description": "Haloalkaliphiles also require adaptation to high pH.",
            "evidence": [
              {
                "reference": "DOI:10.1021/pr060352q",
                "snippet": "salt-saturated lakes of pH 11",
                "notes": "Supports high-pH component of the haloalkaliphilic trait."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "compatible_solutes",
            "predicate": "contributes to",
            "object": "haloalkaliphilic_trait",
            "description": "Compatible solutes support osmoadaptation in haloalkaliphiles.",
            "evidence": [
              {
                "reference": "DOI:10.1139/cjm-2014-0233",
                "snippet": "ectoine and glycine betaine",
                "notes": "Review supports compatible solutes as osmoadaptation mechanisms in haloalkaliphiles."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "alkaline_ph_homeostasis",
            "predicate": "confers",
            "object": "haloalkaliphilic_trait",
            "description": "pH homeostasis is required for growth under alkaline conditions.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2549",
                "snippet": "bacterial pH homeostasis is a cell-wide physiological process",
                "notes": "Review supports pH homeostasis as a physiological mechanism integrated with salinity and other factors."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "haloalkaliphilic_trait",
            "predicate": "can use",
            "object": "compatible_solute_strategy",
            "description": "Haloalkaliphiles can osmoadapt via compatible-solute accumulation.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s44185-024-00050-w",
                "notes": "Review: halophiles use two broad osmoadaptation strategies, including biosynthesis/accumulation of compatible solutes."
              }
            ]
          },
          {
            "subject": "haloalkaliphilic_trait",
            "predicate": "can use",
            "object": "salt_in_strategy",
            "description": "Haloalkaliphiles can osmoadapt via the intracellular salt-in strategy.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s44185-024-00050-w",
                "notes": "Review: halophiles use two broad osmoadaptation strategies, including the intracellular 'salt-in' strategy."
              }
            ]
          },
          {
            "subject": "na_h_antiport",
            "predicate": "contributes to",
            "object": "na_efflux_ph_regulation",
            "description": "Na+/H+ antiporters expel Na+ and help regulate intracellular pH.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2025.1550346",
                "notes": "Na+/H+ antiporters (nhaA/B/C and the mnh complex) expel Na+ and help pH regulation; generalized mechanistic edge relevant to haloalkaliphiles."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "na_efflux_ph_regulation",
            "predicate": "enables",
            "object": "alkaline_ph_homeostasis",
            "description": "Sodium efflux coupled to proton import supports pH homeostasis under alkaline conditions.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2025.1550346",
                "notes": "Na+/H+ antiport expels Na+ while helping pH regulation, supporting cytoplasmic pH homeostasis."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "compatible_solute_strategy",
            "predicate": "involves biosynthesis of",
            "object": "ectoine",
            "description": "Compatible-solute strategy includes ectoine biosynthesis/uptake.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2025.1550346",
                "notes": "Salt-out strategy involved biosynthesis and uptake of compatible solutes including ectoine; strong for hypersaline adaptation broadly."
              }
            ]
          },
          {
            "subject": "choline_oxidation_pathway",
            "predicate": "biosynthesizes",
            "object": "glycine_betaine",
            "description": "Glycine betaine is produced de novo via the choline oxidation pathway.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s44185-024-00050-w",
                "notes": "Review: de novo biosynthesis of glycine betaine via the choline oxidation pathway."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.861455+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-06T14:15:44-07:00",
        "curator": "codex",
        "action": "CURATED_WITH_ORGANISM_EXAMPLE",
        "changes": "Added Natronomonas pharaonis organism example with PMID-backed evidence.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "ADDED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed causal graph for combined high-salt and alkaline-pH adaptation in haloalkaliphily.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:29Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 4 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002326\u00d73, RO:0002327\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:37:59Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:65015\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T08:14:32Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (ENVO:01000687\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-15T07:19:08Z",
        "curator": "claude",
        "action": "FIX_NODE_GROUNDING_CURIE",
        "changes": "Overwrote 2 causal-node grounding(s) to corrected CURIEs (phase-2 id-label fix; verified vs OAK).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-17T04:09:43Z",
        "curator": "claude",
        "action": "REMOVE_REDUNDANT_SYNONYM",
        "changes": "Removed 1 synonym(s) whose text duplicated the label (seeder redundancy; no information lost).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 6 evidence-backed generic edges (7 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:10Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002326\u00d71, RO:0002327\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:16Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (METPO:1007720\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:30Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:27592\u00d71, CHEBI:17750\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 1 causal edge(s) off enables/RO:0002327 with a TRAIT object (1 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-16T02:00:00Z",
        "curator": "claude",
        "action": "NORMALISE_NODE_TYPE",
        "changes": "Under the PATHWAY-vs-BIOLOGICAL_PROCESS rule, one node_id means one thing corpus-wide (issue 356): salt_in_strategy is typed BIOLOGICAL_PROCESS. PATHWAY is a named, conventionally enumerable multi-step route; BIOLOGICAL_PROCESS is everything else. A STRATEGY, not a route. The family is described as osmoadaptation by accumulating intracellular inorganic ions -- haloalkaliphilic.yaml puts it as 'Osmoadaptation by intracellular accumulation of inorganic ions (e.g. K+)', and the wording varies by record. There is no step list to enumerate, which is exactly the distinction this rule draws. Was 7 BIOLOGICAL_PROCESS to 1 before this tranche.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope haloalkaliphilic_salt_alkaline_adaptation=NONMECHANISTIC with scope_notes.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000620",
    "label": "halophilic",
    "definition": "A halophily preference in which an organism requires high concentrations of salt for growth and survival.",
    "definition_source": "PMID:19329623",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000629"
    ],
    "evidence": [
      {
        "reference": "PMID:19329623",
        "snippet": "Salinicoccus albus sp. nov., a halophilic bacterium from a salt mine",
        "notes": "Organism example: Salinicoccus albus is described as halophilic."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:2242",
        "taxon_label": "Halobacterium salinarum",
        "note": "extreme halophile",
        "reference": "PMID:31797576"
      },
      {
        "taxon_id": "NCBITaxon:2746",
        "taxon_label": "Halomonas elongata",
        "note": "moderate halophile",
        "reference": "PMID:20849449"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "halophilic_osmoadaptation",
        "title": "Halophilic osmoadaptation mechanism",
        "description": "Evidence-backed causal sketch linking halophilic growth to high-salt environments and osmotic adaptation strategies.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a broad environmental or morphological classification spanning multiple mechanisms, a measurement-like bin, or an absence/arrangement descriptor; contextual protein nodes do not receive token UniProt examples.",
        "nodes": [
          {
            "node_id": "halophilic_trait",
            "label": "halophilic",
            "node_type": "TRAIT",
            "grounding": "METPO:1000620",
            "description": "Requires high salt concentrations for growth and survival."
          },
          {
            "node_id": "high_salt_environment",
            "label": "high-salt environment",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Hypersaline or elevated NaCl condition.",
            "grounding": "ENVO:01001040"
          },
          {
            "node_id": "sodium_chloride",
            "label": "sodium chloride",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:26710",
            "description": "NaCl as the dominant salt exposure in many halophilic habitats."
          },
          {
            "node_id": "osmotic_stress",
            "label": "osmotic stress",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Cellular water and turgor stress caused by external salinity.",
            "grounding": "GO:0006970"
          },
          {
            "node_id": "compatible_solutes",
            "label": "compatible solutes",
            "node_type": "CHEMICAL",
            "description": "Organic osmolytes such as ectoine and glycine betaine.",
            "grounding": "CHEBI:25728"
          },
          {
            "node_id": "salt_in_strategy",
            "label": "salt-in strategy",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Intracellular inorganic ion accumulation for osmotic balance.",
            "grounding": "METPO:1007720"
          },
          {
            "node_id": "na_h_antiporter",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "Na+/H+ antiporter",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Membrane antiporter that exports sodium from the cytoplasm in exchange for protons."
          },
          {
            "node_id": "sodium_ion",
            "label": "sodium ion",
            "node_type": "CHEMICAL",
            "description": "Na+ cation that must be excluded from the cytoplasm.",
            "grounding": "CHEBI:29101"
          },
          {
            "node_id": "k_uniport",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "K+ uniport system",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Uniport transport system that imports potassium into the cell."
          },
          {
            "node_id": "potassium_ion",
            "label": "potassium ion",
            "node_type": "CHEMICAL",
            "description": "K+ cation accumulated intracellularly during salt-in osmoadaptation.",
            "grounding": "CHEBI:29103"
          },
          {
            "node_id": "acidified_proteome",
            "label": "acidified proteome",
            "node_type": "STATE",
            "description": "Proteome enriched in acidic residues, characteristic of salt-in adapted organisms."
          },
          {
            "node_id": "oxidative_stress",
            "label": "oxidative stress",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reactive-oxygen-mediated cellular stress induced by NaCl shock."
          },
          {
            "node_id": "ectABC_operon",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "EctABC ectoine-biosynthesis enzyme module",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Evolutionarily conserved operon encoding the ectoine biosynthesis pathway.",
            "gene_symbols": [
              "ectA",
              "ectB",
              "ectC"
            ],
            "operon": "ectABC"
          },
          {
            "node_id": "ectoine",
            "label": "ectoine",
            "node_type": "CHEMICAL",
            "description": "Compatible solute synthesized de novo from L-aspartic acid.",
            "grounding": "CHEBI:27592"
          },
          {
            "node_id": "l_aspartic_acid",
            "label": "L-aspartic acid",
            "node_type": "CHEMICAL",
            "description": "Precursor metabolite for de novo ectoine biosynthesis."
          }
        ],
        "edges": [
          {
            "subject": "high_salt_environment",
            "predicate": "selects for",
            "object": "halophilic_trait",
            "description": "Halophilic microorganisms are adapted to growth in high-salt environments.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuy009",
                "snippet": "Hypersaline environments ... inhabited by halophilic",
                "notes": "Review supports hypersaline habitats as the environmental context for halophily."
              }
            ],
            "predicate_id": "METPO:2007401"
          },
          {
            "subject": "sodium_chloride",
            "predicate": "causes",
            "object": "osmotic_stress",
            "description": "Elevated NaCl creates osmotic pressure that requires cellular adaptation.",
            "evidence": [
              {
                "reference": "DOI:10.1186/1746-1448-4-2",
                "snippet": "ways they cope with the high salt concentrations",
                "notes": "Review frames halophily around coping with high environmental salt."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "compatible_solutes",
            "predicate": "mitigates",
            "object": "osmotic_stress",
            "description": "Compatible solutes are one major osmoadaptation mechanism in halophilic microorganisms.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuy009",
                "snippet": "synthesize organic osmotic solutes",
                "notes": "Supports organic compatible-solute accumulation as an osmotic adaptation mechanism."
              }
            ],
            "predicate_id": "METPO:2007407"
          },
          {
            "subject": "salt_in_strategy",
            "predicate": "mitigates",
            "object": "osmotic_stress",
            "description": "Salt-in ion accumulation is an alternative osmoadaptation strategy.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuy009",
                "snippet": "KCl accumulating Halobacterium salinarum",
                "notes": "Supports intracellular KCl accumulation as a high-salt adaptation."
              }
            ],
            "predicate_id": "METPO:2007407"
          },
          {
            "subject": "compatible_solutes",
            "predicate": "contributes to",
            "object": "halophilic_trait",
            "description": "Compatible-solute accumulation supports growth under high salinity.",
            "evidence": [
              {
                "reference": "DOI:10.1371/journal.pone.0168818",
                "snippet": "allows microorganisms to cope with high salinities",
                "notes": "Halomonas elongata study supports compatible solutes as a mechanism enabling halophilic growth."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "na_h_antiporter",
            "predicate": "expels",
            "object": "sodium_ion",
            "description": "Sodium is excluded from the cytoplasm with the help of an Na+/H+ antiporter.",
            "evidence": [
              {
                "reference": "DOI:10.3390/microorganisms12081738",
                "notes": "sodium is excluded from the cytoplasm with the help of an Na+/H+ antiporter"
              }
            ]
          },
          {
            "subject": "k_uniport",
            "predicate": "imports",
            "object": "potassium_ion",
            "description": "Potassium enters the cell through a uniport system during salt-in osmoadaptation.",
            "evidence": [
              {
                "reference": "DOI:10.3390/microorganisms12081738",
                "notes": "Potassium enters the cell through a uniport system"
              }
            ],
            "predicate_id": "METPO:2007805"
          },
          {
            "subject": "salt_in_strategy",
            "predicate": "associated with",
            "object": "acidified_proteome",
            "description": "Organisms employing the salt-in strategy exhibit an acidified proteome.",
            "evidence": [
              {
                "reference": "DOI:10.3390/microorganisms12081738",
                "notes": "microorganisms employing this strategy exhibit an acidified proteome"
              }
            ],
            "predicate_id": "biolink:associated_with"
          },
          {
            "subject": "sodium_chloride",
            "predicate": "induces",
            "object": "oxidative_stress",
            "description": "NaCl shock induces oxidative stress in addition to osmotic stress.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s12934-024-02358-5",
                "notes": "NaCl shock induced two major stresses, namely osmotic stress and oxidative stress"
              }
            ]
          },
          {
            "subject": "ectABC_operon",
            "predicate": "biosynthesizes",
            "object": "ectoine",
            "description": "The conserved ectABC operon performs de novo biosynthesis of ectoine.",
            "evidence": [
              {
                "reference": "DOI:10.1128/aem.00479-23",
                "notes": "Biosynthesis of ectoine is de novo from L-aspartic acid, performed by the conserved operon ectABC"
              }
            ]
          },
          {
            "subject": "l_aspartic_acid",
            "predicate": "is precursor of",
            "object": "ectoine",
            "description": "Ectoine is biosynthesized de novo from L-aspartic acid.",
            "evidence": [
              {
                "reference": "DOI:10.1128/aem.00479-23",
                "notes": "Biosynthesis of ectoine is de novo from L-aspartic acid"
              }
            ]
          },
          {
            "subject": "ectoine",
            "predicate": "is a",
            "object": "compatible_solutes",
            "description": "Ectoine is a major organic compatible solute used in osmoadaptation.",
            "evidence": [
              {
                "reference": "DOI:10.1128/aem.00479-23",
                "notes": "Ectoine is a canonical compatible solute synthesized via the ectABC operon."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.860938+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-06T14:15:44-07:00",
        "curator": "codex",
        "action": "CURATED_WITH_ORGANISM_EXAMPLE",
        "changes": "Added Salinicoccus albus organism example with PMID-backed evidence.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "ADDED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed causal graph for halophilic osmoadaptation mechanisms.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:29Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002326\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T05:49:24Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:causes\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T21:30:06Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007407\u00d72, METPO:2007401\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:38:00Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0006970\u00d71, CHEBI:65015\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T08:14:32Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (ENVO:01000687\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-15T07:19:08Z",
        "curator": "claude",
        "action": "FIX_NODE_GROUNDING_CURIE",
        "changes": "Overwrote 2 causal-node grounding(s) to corrected CURIEs (phase-2 id-label fix; verified vs OAK).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-16T06:54:39Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (METPO:1007720\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-17T04:09:43Z",
        "curator": "claude",
        "action": "REMOVE_REDUNDANT_SYNONYM",
        "changes": "Removed 1 synonym(s) whose text duplicated the label (seeder redundancy; no information lost).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 7 evidence-backed generic edges (9 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:10Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000208\u00d71, biolink:associated_with\u00d71, rdfs:subClassOf\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:16Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A068T423\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:30Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 3 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:29101\u00d71, CHEBI:29103\u00d71, CHEBI:27592\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:21:11Z",
        "curator": "claude",
        "action": "RETRACT_DEAD_UNIPROT_GROUNDINGS",
        "changes": "Retracted 1 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T02:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES_PART2",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates onto their causal-graph counterparts (1 to imports), issue 301 part 2. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Each replacement is a 1:1 mirror of its source predicate that changes only the domain, so the claim each edge makes is unchanged and directions are unchanged. The replacements are proposed in proposals/metpo_traitmech_v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-16T02:00:00Z",
        "curator": "claude",
        "action": "NORMALISE_NODE_TYPE",
        "changes": "Under the PATHWAY-vs-BIOLOGICAL_PROCESS rule, one node_id means one thing corpus-wide (issue 356): salt_in_strategy is typed BIOLOGICAL_PROCESS. PATHWAY is a named, conventionally enumerable multi-step route; BIOLOGICAL_PROCESS is everything else. A STRATEGY, not a route. The family is described as osmoadaptation by accumulating intracellular inorganic ions -- haloalkaliphilic.yaml puts it as 'Osmoadaptation by intracellular accumulation of inorganic ions (e.g. K+)', and the wording varies by record. There is no step list to enumerate, which is exactly the distinction this rule draws. Was 7 BIOLOGICAL_PROCESS to 1 before this tranche.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope halophilic_osmoadaptation=NONMECHANISTIC with scope_notes; marked 3 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (na_h_antiporter, k_uniport, ectABC_operon).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000629",
    "label": "halophily preference",
    "definition": "A phenotype that is relating to an organism's salt concentration requirements or tolerance for growth.",
    "definition_source": "DOI:10.1093/femsre/fuy009",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "synonyms": [
      {
        "synonym_text": "Physiology and metabolism.halophily.halophily level",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "range_salinity",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1093/femsre/fuy009",
        "snippet": "life at high salt concentrations",
        "notes": "Supports salinity and salt concentration as a growth-relevant microbial trait axis."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:2746",
        "taxon_label": "Halomonas elongata",
        "reference": "PMID:20849449",
        "note": "Halomonas elongata DSM 2581T is a source-backed moderate-halophile model; this exemplifies the halophilic branch of the broad salt-preference class."
      },
      {
        "taxon_id": "NCBITaxon:562",
        "taxon_label": "Escherichia coli",
        "reference": "DOI:10.3389/fmicb.2021.705326",
        "note": "Wild-type E. coli BW25113 in LB broth serves as the non-halophilic branch comparator, contrasting with the Halomonas halophile example. This is a strain- and medium-qualified illustration, not sodium-free growth or a universal species-wide requirement; the measured comparison is retained on the non_halophilic child."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "halophily_preference_osmoadaptation",
        "title": "Salinity preference and osmoadaptation mechanism",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is an upper preference, broad tolerance, or central-range classification spanning multiple unrelated adaptations; contextual protein nodes are retained without assigning a misleading token UniProt example.",
        "description": "Evidence-backed causal sketch linking environmental salinity, osmotic stress, water flux, ion homeostasis, and compatible-solute accumulation to halophily preference.",
        "nodes": [
          {
            "node_id": "halophily_preference_trait",
            "label": "halophily preference",
            "node_type": "TRAIT",
            "grounding": "METPO:1000629",
            "description": "Growth requirement or tolerance with respect to environmental salt concentration."
          },
          {
            "node_id": "environmental_salinity",
            "label": "environmental salinity",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Salt concentration of the growth environment."
          },
          {
            "node_id": "osmotic_stress",
            "label": "osmotic stress",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Cellular stress caused by a mismatch between external and cytoplasmic osmotic potential.",
            "grounding": "GO:0006970"
          },
          {
            "node_id": "water_flux",
            "label": "water flux across cytoplasmic membrane",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Osmotically driven water movement across the membrane."
          },
          {
            "node_id": "potassium_ion",
            "label": "potassium ion",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:29103",
            "description": "Inorganic ion rapidly accumulated during some osmotic upshifts."
          },
          {
            "node_id": "compatible_solutes",
            "label": "compatible solutes",
            "node_type": "CHEMICAL",
            "description": "Organic osmolytes accumulated by synthesis or uptake under salt stress.",
            "grounding": "CHEBI:25728"
          },
          {
            "node_id": "compatible_solute_transport",
            "label": "compatible-solute transport",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "Uptake systems importing osmoprotectants from the environment."
          },
          {
            "node_id": "na_h_antiporter",
            "label": "Na+/H+ antiporter",
            "node_type": "GENE_OR_PROTEIN",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed as a contextual protein or protein-complex label in a broad environmental classification; no single exact family term denotes this aggregate use.",
            "description": "Secondary transporter that expels cytoplasmic sodium ions using the proton electrochemical gradient."
          },
          {
            "node_id": "proton_electrochemical_gradient",
            "label": "proton electrochemical gradient",
            "node_type": "CHEMICAL",
            "description": "Transmembrane proton motive force used as a driving force for ion transport."
          },
          {
            "node_id": "sodium_ion",
            "label": "sodium ion",
            "node_type": "CHEMICAL",
            "description": "Cytoplasmic sodium ion that must be excluded to relieve toxicity under high salinity.",
            "grounding": "CHEBI:29101"
          },
          {
            "node_id": "acidified_proteome",
            "label": "acidified proteome",
            "node_type": "QUALITY",
            "description": "Proteome enriched in surface acidic residues, characteristic of salt-in halophiles."
          },
          {
            "node_id": "protein_solubility",
            "label": "protein solubility in hypersaline conditions",
            "node_type": "QUALITY",
            "description": "Maintenance of protein solubility via hydrated cation networks coordinated by acidic surface residues."
          },
          {
            "node_id": "mechanosensitive_channels",
            "label": "mechanosensitive channels",
            "node_type": "GENE_OR_PROTEIN",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed as a contextual protein or protein-complex label in a broad environmental classification; no single exact family term denotes this aggregate use.",
            "description": "Membrane channels acting as safety valves that open during osmotic downshock."
          },
          {
            "node_id": "solute_efflux",
            "label": "rapid solute efflux",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Rapid release of ions and organic solutes during sudden downward osmotic shock."
          }
        ],
        "edges": [
          {
            "subject": "environmental_salinity",
            "predicate": "regulates",
            "object": "halophily_preference_trait",
            "description": "Salt concentration determines whether growth requires, tolerates, or avoids salinity.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuy009",
                "snippet": "life at high salt concentrations",
                "notes": "Review frames halophily as microbial life under high salt concentration."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "environmental_salinity",
            "predicate": "causes",
            "object": "osmotic_stress",
            "description": "Salinity changes impose osmotic stress on cells.",
            "evidence": [
              {
                "reference": "DOI:10.1111/j.1574-6976.2002.tb00598.x",
                "snippet": "overcome salt stress",
                "notes": "Review describes bacterial mechanisms for salt-stress responses."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "osmotic_stress",
            "predicate": "regulates",
            "object": "water_flux",
            "description": "Osmotic imbalance drives water movement across the cytoplasmic membrane.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.01934-12",
                "snippet": "balance the osmotic gradient across their cytoplasmic membrane",
                "notes": "Supports osmotic-gradient balancing as central to microbial osmotic stress."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "potassium_ion",
            "predicate": "contributes to",
            "object": "osmotic_stress",
            "description": "Potassium accumulation is an early response to osmotic upshift in many bacteria.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.01934-12",
                "snippet": "initially importing substantial amounts of potassium ions",
                "notes": "Supports K+ uptake as an emergency osmotic-stress response."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "compatible_solute_transport",
            "predicate": "imports",
            "object": "compatible_solutes",
            "description": "Transport systems import compatible solutes that relieve osmotic stress.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.csbj.2021.01.030",
                "snippet": "biosynthesis and/or uptake of compatible solutes",
                "notes": "Review supports uptake and biosynthesis of compatible solutes in bacterial high-salinity responses."
              }
            ],
            "predicate_id": "METPO:2007805"
          },
          {
            "subject": "compatible_solutes",
            "predicate": "mitigates",
            "object": "osmotic_stress",
            "description": "Compatible solutes maintain turgor and protect macromolecular function under salt stress.",
            "evidence": [
              {
                "reference": "DOI:10.1186/1746-1448-1-5",
                "snippet": "balance external osmotic pressure",
                "notes": "Review supports compatible solutes as osmolytes for osmotic balance."
              }
            ],
            "predicate_id": "METPO:2007407"
          },
          {
            "subject": "osmotic_stress",
            "predicate": "induces",
            "object": "na_h_antiporter",
            "description": "Osmotic stress drives sodium exclusion via Na+/H+ antiporters.",
            "evidence": [
              {
                "reference": "DOI:10.3390/microorganisms12081738",
                "notes": "Sodium ions are expelled from the cytoplasm, usually with the help of Na+/H+ antiporters (review, broad across haloarchaea)."
              }
            ]
          },
          {
            "subject": "proton_electrochemical_gradient",
            "predicate": "regulates",
            "object": "na_h_antiporter",
            "description": "The proton electrochemical gradient drives Na+/H+ antiporter activity.",
            "evidence": [
              {
                "reference": "DOI:10.3390/microorganisms12081738",
                "notes": "Na+/H+ antiporter uses the electrochemical proton gradient as a driving force."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "na_h_antiporter",
            "predicate": "exports",
            "object": "sodium_ion",
            "description": "Na+/H+ antiporter expels cytoplasmic sodium to relieve salt stress.",
            "evidence": [
              {
                "reference": "DOI:10.3390/microorganisms12081738",
                "notes": "Sodium is excluded from the cytoplasm with the help of an Na+/H+ antiporter."
              }
            ],
            "predicate_id": "METPO:2007804"
          },
          {
            "subject": "environmental_salinity",
            "predicate": "regulates",
            "object": "acidified_proteome",
            "description": "High salinity favors a proteome with increased surface acidic residues.",
            "evidence": [
              {
                "reference": "DOI:10.3390/microorganisms12081738",
                "notes": "Microorganisms employing the salt-in strategy exhibit an acidified proteome essential for protein solubility under hypersaline conditions."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "acidified_proteome",
            "predicate": "promotes",
            "object": "protein_solubility",
            "description": "Surface acidic residues coordinate hydrated cations and keep proteins soluble in hypersaline cytoplasm.",
            "evidence": [
              {
                "reference": "DOI:10.3390/microorganisms12081738",
                "notes": "The high number of negative surface charges coordinates a network of hydrated cations and keeps the protein in solution."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "osmotic_stress",
            "predicate": "regulates",
            "object": "mechanosensitive_channels",
            "description": "Osmotic downshock activates mechanosensitive channels that act as safety valves.",
            "evidence": [
              {
                "reference": "DOI:10.3390/microorganisms12081738",
                "notes": "Msc channels serve as safety valves, allowing rapid release of ions and organic solutes during sudden downward osmotic shocks (broad across halophiles)."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "mechanosensitive_channels",
            "predicate": "enables",
            "object": "solute_efflux",
            "description": "Mechanosensitive channels mediate rapid efflux of ions and organic solutes during osmotic downshock.",
            "evidence": [
              {
                "reference": "DOI:10.3390/microorganisms12081738",
                "notes": "Mechanosensitive channels allow the rapid release of ions and organic solutes in case of sudden downward osmotic shocks."
              }
            ],
            "predicate_id": "RO:0002327"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.865794+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-11T00:00:00-07:00",
        "curator": "codex",
        "action": "CURATED_WITH_LITERATURE",
        "changes": "Reviewed halophily preference trait and added DOI-backed causal graph for salinity-driven osmotic stress, ion homeostasis, and compatible-solute osmoadaptation.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:29Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002326\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T05:49:24Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:causes\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T21:30:06Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007407\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:18Z",
        "curator": "claude",
        "action": "RENAME_PREDICATE_LABELS",
        "changes": "Renamed 1 causal-edge predicate label(s) to align with existing groundings: drives \u2192 regulates \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:21Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002211\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:38:00Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0006970\u00d71, CHEBI:65015\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-26T05:00:47Z",
        "curator": "claude",
        "action": "RENAME_PREDICATE_LABELS",
        "changes": "Renamed 1 causal-edge predicate label(s) to align with existing groundings: influences \u2192 regulates \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-26T05:00:49Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002211\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-15T07:19:08Z",
        "curator": "claude",
        "action": "FIX_NODE_GROUNDING_CURIE",
        "changes": "Overwrote 1 causal-node grounding(s) to corrected CURIEs (phase-2 id-label fix; verified vs OAK).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-16T06:30:55Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000208\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 7 evidence-backed generic edges (7 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:10Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 6 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002211\u00d73, METPO:2000209\u00d71, RO:0002213\u00d71, RO:0002327\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:16Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A068T423\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:30Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:29101\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:21:11Z",
        "curator": "claude",
        "action": "RETRACT_DEAD_UNIPROT_GROUNDINGS",
        "changes": "Retracted 1 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T02:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES_PART2",
        "changes": "Re-grounded 2 causal edge(s) off microbe-domain METPO predicates onto their causal-graph counterparts (1 to exports, 1 to imports), issue 301 part 2. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Each replacement is a 1:1 mirror of its source predicate that changes only the domain, so the claim each edge makes is unchanged and directions are unchanged. The replacements are proposed in proposals/metpo_traitmech_v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope halophily_preference_osmoadaptation=NONMECHANISTIC with scope_notes; marked 2 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (na_h_antiporter, mechanosensitive_channels).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T04:43:24Z",
        "curator": "codex",
        "action": "ADD_CANONICAL_EXAMPLES",
        "changes": "Resolved issue #444 after the #591 source/bin policy with 2 direct source-backed canonical example(s): Halomonas elongata (NCBITaxon:2746; PMID:20849449), Escherichia coli (NCBITaxon:562; PMC8415458). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-03T17:07:26Z",
        "curator": "codex",
        "action": "REPAIR_CANONICAL_CITATION_SCOPE_1626",
        "changes": "Resolved issue 1626 by normalizing PMC8415458 to its verified DOI 10.3389/fmicb.2021.705326 (PMID:34484145), preserving the same paper. Qualified the non-halophilic comparator to BW25113 in LB at 37 C and the reported 24-h viable-count comparison across 0%, 1%, 3.5% and 5% NaCl supplementation. Retained NCBITaxon:562 and its independently checked NCBI label. The broad-class role, Halomonas example, definition, hierarchy and graph are unchanged; no species-wide salt requirement or sodium-free growth is asserted.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-03T17:30:07Z",
        "curator": "codex",
        "action": "REFINE_CANONICAL_ARCHETYPES_1629",
        "changes": "Addressed independent PR 1628 review and issue 1629 by retaining the verified Li 2021 DOI and BW25113/LB strain-medium context as a non-halophilic branch comparator, without repeating the child's 24-hour numerical growth comparison. The quantitative comparison and exact snippet remain on non_halophilic. No sodium-free or universal species-wide growth claim is introduced. Other examples, identity, definition, hierarchy, graph, evidence and prior history are unchanged.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000622",
    "label": "halotolerant",
    "definition": "A halophily preference in which an organism can tolerate high salt concentrations but does not require them for growth.",
    "definition_source": "DOI:10.1093/femsre/fuy009",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000629"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1093/femsre/fuy009",
        "snippet": "highly halotolerant representatives",
        "notes": "Supports halotolerant microorganisms as high-salt tolerant without strict salt requirement."
      },
      {
        "reference": "PMID:27621824",
        "snippet": "Halomonas massiliensis sp. nov., a new halotolerant bacterium",
        "notes": "Organism example: Halomonas massiliensis is described as halotolerant."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1570",
        "taxon_label": "Halobacillus halophilus",
        "note": "Model halotolerant/moderately halophilic bacterium (chloride-dependent osmoadaptation). Staphylococcus aureus is the classic salt-tolerant clinical exemplar.",
        "reference": "PMID:18442383"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "halotolerant_salt_stress_response",
        "title": "Halotolerant salt-stress response mechanism",
        "description": "Evidence-backed causal sketch linking halotolerance to survival under high salinity without strict salt requirement.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a broad environmental or morphological classification spanning multiple mechanisms, a measurement-like bin, or an absence/arrangement descriptor; contextual protein nodes do not receive token UniProt examples.",
        "nodes": [
          {
            "node_id": "halotolerant_trait",
            "label": "halotolerant",
            "node_type": "TRAIT",
            "grounding": "METPO:1000622",
            "description": "Tolerates high salt but does not require it for growth."
          },
          {
            "node_id": "high_salt_exposure",
            "label": "high-salt exposure",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Salt stress condition tolerated by the organism."
          },
          {
            "node_id": "osmotic_stress",
            "label": "osmotic stress",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Cellular stress caused by external salinity.",
            "grounding": "GO:0006970"
          },
          {
            "node_id": "compatible_solutes",
            "label": "compatible solutes",
            "node_type": "CHEMICAL",
            "description": "Organic osmolytes that support salt tolerance.",
            "grounding": "CHEBI:25728"
          },
          {
            "node_id": "compatible_solute_transport",
            "label": "compatible-solute transport",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "Uptake systems importing osmoprotectants under high-salt stress."
          },
          {
            "node_id": "stress_protection",
            "label": "stress protection",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Protective cellular response to saline conditions."
          },
          {
            "node_id": "compatible_solute_accumulation",
            "label": "compatible solute accumulation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Intracellular buildup of organic osmolytes in response to osmotic stress."
          },
          {
            "node_id": "salt_out_strategy",
            "label": "salt-out strategy",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Osmoadaptation strategy keeping cytoplasmic salt low while accumulating compatible solutes."
          },
          {
            "node_id": "ectABC_operon",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "EctABC ectoine-biosynthesis enzyme module",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Enzyme module catalyzing ectoine biosynthesis from aspartate.",
            "gene_symbols": [
              "ectA",
              "ectB",
              "ectC"
            ],
            "operon": "ectABC"
          },
          {
            "node_id": "ectoine_biosynthesis",
            "label": "ectoine biosynthesis",
            "node_type": "PATHWAY",
            "description": "De novo synthesis of the compatible solute ectoine.",
            "grounding": "GO:0019491"
          },
          {
            "node_id": "betA_betB",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "betA/betB",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Choline oxidation enzymes producing glycine betaine."
          },
          {
            "node_id": "glycine_betaine_biosynthesis",
            "label": "glycine betaine biosynthesis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Synthesis of the compatible solute glycine betaine from environmental choline.",
            "grounding": "GO:0031456"
          }
        ],
        "edges": [
          {
            "subject": "high_salt_exposure",
            "predicate": "tolerated by",
            "object": "halotolerant_trait",
            "description": "Halotolerant organisms can survive elevated salinity without requiring it.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuy009",
                "snippet": "highly halotolerant representatives",
                "notes": "Review distinguishes halotolerant microorganisms in high-salt environments."
              }
            ]
          },
          {
            "subject": "high_salt_exposure",
            "predicate": "causes",
            "object": "osmotic_stress",
            "description": "External salinity creates osmotic stress in halotolerant organisms.",
            "evidence": [
              {
                "reference": "DOI:10.1186/1746-1448-4-2",
                "snippet": "high salt concentrations in the environment",
                "notes": "Review supports high environmental salt as the stress context."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "compatible_solutes",
            "predicate": "mitigates",
            "object": "osmotic_stress",
            "description": "Compatible solutes are a mechanism for tolerating salt stress.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuy009",
                "snippet": "organic osmotic solutes",
                "notes": "Supports organic osmotic solutes as an osmoadaptation strategy."
              }
            ],
            "predicate_id": "METPO:2007407"
          },
          {
            "subject": "compatible_solute_transport",
            "predicate": "imports",
            "object": "compatible_solutes",
            "description": "Uptake systems import osmoprotectants that support halotolerance.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.csbj.2021.01.030",
                "snippet": "biosynthesis and/or uptake of compatible solutes",
                "notes": "Adds explicit source support for transport-mediated compatible-solute accumulation in bacterial salt-stress responses."
              }
            ],
            "predicate_id": "METPO:2007805"
          },
          {
            "subject": "compatible_solutes",
            "predicate": "contributes to",
            "object": "stress_protection",
            "description": "Compatible solutes can stabilize cells under saline stress.",
            "evidence": [
              {
                "reference": "DOI:10.1139/cjm-2014-0233",
                "snippet": "stabilizers of intracellular proteins",
                "notes": "Haloalkaliphile review supports compatible solutes as stabilizing osmoprotectants; mechanism is shared with halotolerance."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "stress_protection",
            "predicate": "confers",
            "object": "halotolerant_trait",
            "description": "Stress-protection mechanisms allow tolerance of salt exposure.",
            "evidence": [
              {
                "reference": "DOI:10.1371/journal.pone.0168818",
                "snippet": "allows microorganisms to cope with high salinities",
                "notes": "Supports osmoadaptation as a mechanism for growth under salt stress."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "osmotic_stress",
            "predicate": "increases",
            "object": "compatible_solute_accumulation",
            "description": "Osmotic stress drives accumulation of compatible solutes.",
            "evidence": [
              {
                "reference": "DOI:10.58088/07hg-r941",
                "notes": "Compatible solutes are accumulated in response to osmotic stress; broad mechanistic claim across marine bacteria."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "salt_out_strategy",
            "predicate": "relies on",
            "object": "compatible_solute_accumulation",
            "description": "The salt-out osmoadaptation strategy relies on accumulation or de novo synthesis of compatible solutes.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41598-024-63581-z",
                "notes": "'salt-out'/'low-salt-high-compatible-solute-in-cytoplasm' strategy relies on accumulation or de-novo synthesis of organic compatible solutes; directly supports halotolerant scope."
              }
            ]
          },
          {
            "subject": "ectABC_operon",
            "predicate": "enables",
            "object": "ectoine_biosynthesis",
            "description": "The ectABC operon synthesizes ectoine de novo from aspartic acid.",
            "evidence": [
              {
                "reference": "DOI:10.58088/07hg-r941",
                "notes": "Ectoine is synthesized de novo from aspartic acid via the ectABC operon; general bacterial mechanism."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "betA_betB",
            "predicate": "enables",
            "object": "glycine_betaine_biosynthesis",
            "description": "betA and betB produce glycine betaine from environmental choline.",
            "evidence": [
              {
                "reference": "DOI:10.58088/07hg-r941",
                "notes": "Glycine betaine is produced from environmental choline via betA and betB; canonical pathway edge, broadly applicable."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "ectoine_biosynthesis",
            "predicate": "has output",
            "object": "compatible_solutes",
            "description": "Ectoine biosynthesis yields a compatible solute supporting salt tolerance.",
            "evidence": [
              {
                "reference": "DOI:10.58088/07hg-r941",
                "notes": "Ectoine is a compatible solute synthesized de novo via the ectABC operon."
              }
            ],
            "predicate_id": "RO:0002234"
          },
          {
            "subject": "glycine_betaine_biosynthesis",
            "predicate": "has output",
            "object": "compatible_solutes",
            "description": "Glycine betaine biosynthesis yields a compatible solute supporting salt tolerance.",
            "evidence": [
              {
                "reference": "DOI:10.58088/07hg-r941",
                "notes": "Glycine betaine is produced from environmental choline and acts as a compatible solute."
              }
            ],
            "predicate_id": "RO:0002234"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.861954+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-06T14:15:44-07:00",
        "curator": "codex",
        "action": "CURATED_WITH_ORGANISM_EXAMPLE",
        "changes": "Added Halomonas massiliensis organism example with PMID-backed evidence.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "ADDED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed causal graph for halotolerant salt-stress response.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-11T00:00:00-07:00",
        "curator": "codex",
        "action": "CURATED_WITH_LITERATURE",
        "changes": "Replaced PMID definition source with DOI-backed halotolerance source and added a compatible-solute transport edge to the existing causal graph.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:29Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002326\u00d71, RO:0002327\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T05:49:24Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:causes\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T21:30:06Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007407\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:38:00Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0006970\u00d71, CHEBI:65015\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-15T07:19:08Z",
        "curator": "claude",
        "action": "FIX_NODE_GROUNDING_CURIE",
        "changes": "Overwrote 1 causal-node grounding(s) to corrected CURIEs (phase-2 id-label fix; verified vs OAK).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-16T06:30:55Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000208\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-17T04:09:43Z",
        "curator": "claude",
        "action": "REMOVE_REDUNDANT_SYNONYM",
        "changes": "Removed 1 synonym(s) whose text duplicated the label (seeder redundancy; no information lost).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 6 evidence-backed generic edges (6 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:10Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 5 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d72, METPO:2000202\u00d72, RO:0002213\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:30Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0019491\u00d71, GO:0031456\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 1 causal edge(s) off enables/RO:0002327 with a TRAIT object (1 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 2 causal edge(s) off microbe-domain METPO predicates (2 to has output), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T02:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES_PART2",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates onto their causal-graph counterparts (1 to imports), issue 301 part 2. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Each replacement is a 1:1 mirror of its source predicate that changes only the domain, so the claim each edge makes is unchanged and directions are unchanged. The replacements are proposed in proposals/metpo_traitmech_v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-16T02:00:00Z",
        "curator": "claude",
        "action": "NORMALISE_NODE_TYPE",
        "changes": "Under the PATHWAY-vs-BIOLOGICAL_PROCESS rule, one node_id means one thing corpus-wide (issue 356): ectoine_biosynthesis is typed PATHWAY. PATHWAY is a named, conventionally enumerable multi-step route; BIOLOGICAL_PROCESS is everything else. A named route, enumerated two ways and both of them enumerations. environment/euryhaline.yaml counts five steps from L-aspartate (lysC/asd/ectB/ectA/ectC); environment/nacl_delta_mid1.yaml counts the three ectABC enzymes proper. Naming the file matters because the two differ and a bare quote would put euryhaline's wording into nacl_delta_mid1's record (#400 review). Either way the steps can be listed, which is the test. Applied AGAINST the majority, which was 4 BIOLOGICAL_PROCESS to 2 before this tranche.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope halotolerant_salt_stress_response=NONMECHANISTIC with scope_notes; marked 2 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (ectABC_operon, betA_betB).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000617",
    "label": "hyperthermophilic",
    "definition": "A temperature preference in which growth is favored at very high temperatures, typically \u226580 \u00b0C.",
    "definition_source": "DOI:10.1111/j.1574-6976.1996.tb00233.x",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000613"
    ],
    "synonyms": [
      {
        "synonym_text": "extreme thermophilic",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1111/j.1574-6976.1996.tb00233.x",
        "snippet": "optimal growth temperatures between 80\u00b0C and 110\u00b0C",
        "notes": "Supports hyperthermophile growth at very high temperatures."
      },
      {
        "reference": "PMID:9348040",
        "snippet": "hyperthermophilic archaeon, Pyrococcus furiosus",
        "notes": "Organism example: Pyrococcus furiosus is described as hyperthermophilic."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:2261",
        "taxon_label": "Pyrococcus furiosus",
        "note": "Model hyperthermophilic archaeon (growth optimum ~100 C).",
        "reference": "DOI:10.1007/BF00413027"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "hyperthermophilic_thermostability",
        "title": "Hyperthermophilic thermostability mechanism",
        "description": "Evidence-backed causal sketch linking hyperthermophily to very high temperature, thermostable enzymes, reverse gyrase, archaeal chaperonins, and membrane adaptation.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a broad environmental or morphological classification spanning multiple mechanisms, a measurement-like bin, or an absence/arrangement descriptor; contextual protein nodes do not receive token UniProt examples.",
        "nodes": [
          {
            "node_id": "hyperthermophilic_trait",
            "label": "hyperthermophilic",
            "node_type": "TRAIT",
            "grounding": "METPO:1000617",
            "description": "Growth is favored at very high temperatures, typically at or above 80 degrees C."
          },
          {
            "node_id": "very_high_temperature",
            "label": "very high temperature",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Growth condition around 80 degrees C or hotter.",
            "grounding": "PATO:0001305"
          },
          {
            "node_id": "thermostable_enzymes",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "thermostable enzymes",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Enzymes resistant to irreversible inactivation at high temperatures."
          },
          {
            "node_id": "reverse_gyrase",
            "label": "reverse gyrase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Topoisomerase associated with hyperthermophiles and positive DNA supercoiling.",
            "grounding": "GO:0160097"
          },
          {
            "node_id": "molecular_chaperonins",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "archaeal molecular chaperonins",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Protein-folding systems in hyperthermophilic archaea."
          },
          {
            "node_id": "membrane_lipid_composition",
            "label": "membrane lipid composition",
            "node_type": "CELLULAR_LOCALIZATION",
            "description": "Membrane lipid features supporting stability at very high temperature."
          },
          {
            "node_id": "cdpg",
            "label": "cyclic 2,3-diphosphoglycerate (cDPG)",
            "node_type": "CHEMICAL",
            "description": "Extremolyte/compatible solute found in hyperthermophilic archaea that confers thermoprotection."
          },
          {
            "node_id": "archaeal_proteins",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "archaeal proteins",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Cellular proteins whose thermostability is enhanced by protective solutes."
          },
          {
            "node_id": "dna_oxidative_damage",
            "label": "DNA oxidative damage by hydroxyl radicals",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Oxidative damage to DNA caused by hydroxyl radicals under high-temperature stress."
          },
          {
            "node_id": "gmgt_lipids",
            "label": "glycerol monoalkyl glycerol tetraether (GMGT) lipids",
            "node_type": "CHEMICAL",
            "description": "Cross-linked tetraether membrane lipids whose abundance increases at high growth temperature."
          },
          {
            "node_id": "gms_synthase",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "Gms (GMGT synthase)",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Enzyme required to form the bridging cross-link of GMGT lipids."
          },
          {
            "node_id": "membrane_rigidity",
            "label": "membrane rigidity at high temperature",
            "node_type": "QUALITY",
            "description": "Increased rigidity/reduced fluidity of the membrane supporting stability at high temperature."
          },
          {
            "node_id": "macrocyclic_archaeol",
            "label": "macrocyclic archaeol",
            "node_type": "CHEMICAL",
            "description": "Macrocyclized archaeal membrane lipid that increases membrane stability and rigidity.",
            "grounding": "CHEBI:193595"
          }
        ],
        "edges": [
          {
            "subject": "very_high_temperature",
            "predicate": "selects for",
            "object": "hyperthermophilic_trait",
            "description": "Very high-temperature environments select for hyperthermophilic growth capacity.",
            "evidence": [
              {
                "reference": "DOI:10.1111/j.1574-6976.1996.tb00233.x",
                "snippet": "optimal growth temperatures between 80\u00b0C and 110\u00b0C",
                "notes": "Review supports hyperthermophile growth temperature range."
              }
            ],
            "predicate_id": "METPO:2007401"
          },
          {
            "subject": "thermostable_enzymes",
            "predicate": "confers",
            "object": "hyperthermophilic_trait",
            "description": "Thermostable enzymes support metabolism at very high temperature.",
            "evidence": [
              {
                "reference": "DOI:10.1128/MMBR.65.1.1-43.2001",
                "snippet": "thermostable ... optimally active at high temperatures",
                "notes": "Supports enzyme thermostability in hyperthermophiles."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "reverse_gyrase",
            "predicate": "contributes to",
            "object": "hyperthermophilic_trait",
            "description": "Reverse gyrase is associated with DNA stabilization in hyperthermophiles.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2021.661411",
                "snippet": "reverse gyrase is present in all the hyperthermophiles",
                "notes": "Review supports the strong association of reverse gyrase with hyperthermophily."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "molecular_chaperonins",
            "predicate": "regulates",
            "object": "thermostable_enzymes",
            "description": "Chaperonin systems support protein folding under heat stress.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro866",
                "snippet": "protein-folding system to cope with heat stress",
                "notes": "Review supports archaeal chaperonins in hyperthermophile heat-stress protein folding."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "membrane_lipid_composition",
            "predicate": "confers",
            "object": "hyperthermophilic_trait",
            "description": "Membrane lipid adaptation contributes to growth near the upper temperature range for life.",
            "evidence": [
              {
                "reference": "DOI:10.1016/s0300-9629(97)00003-0",
                "snippet": "changes in the membrane lipid composition",
                "notes": "Supports membrane lipid changes as high-temperature adaptation."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "cdpg",
            "predicate": "increases thermostability of",
            "object": "archaeal_proteins",
            "description": "cDPG increases the thermostability of archaeal proteins.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2023.1267570",
                "notes": "Its presence increases the thermostability of archaeal proteins."
              }
            ]
          },
          {
            "subject": "cdpg",
            "predicate": "protects against",
            "object": "dna_oxidative_damage",
            "description": "cDPG protects DNA against oxidative damage caused by hydroxyl radicals.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2023.1267570",
                "notes": "Protects the DNA against oxidative damage caused by hydroxyl radicals."
              }
            ]
          },
          {
            "subject": "very_high_temperature",
            "predicate": "increases production of",
            "object": "gmgt_lipids",
            "description": "Elevated growth temperature increases production of GMGT membrane lipids.",
            "evidence": [
              {
                "reference": "DOI:10.1073/pnas.2318761121",
                "notes": "GMGT production and methylation increases with elevated temperatures (broad conclusion across three cultured archaea)."
              }
            ]
          },
          {
            "subject": "gms_synthase",
            "predicate": "required for",
            "object": "gmgt_lipids",
            "description": "Gms is required to form the bridging cross-link of a GMGT.",
            "evidence": [
              {
                "reference": "DOI:10.1073/pnas.2318761121",
                "notes": "Gms, that is required to form the bridging cross-link of a GMGT."
              }
            ]
          },
          {
            "subject": "gmgt_lipids",
            "predicate": "contributes to",
            "object": "membrane_rigidity",
            "description": "GMGTs contribute to increased membrane rigidity at high temperature.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-024-49650-x",
                "notes": "GMGTs are thought to contribute to increased membrane rigidity at high temperature."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "macrocyclic_archaeol",
            "predicate": "increases",
            "object": "membrane_rigidity",
            "description": "Macrocyclic archaeol increases membrane stability and rigidity, reducing membrane fluidity.",
            "evidence": [
              {
                "reference": "DOI:10.1128/msystems.01159-22",
                "notes": "Could increase overall membrane stability and rigidity and reduce membrane fluidity."
              }
            ],
            "predicate_id": "RO:0002213"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.858819+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-06T14:58:45-07:00",
        "curator": "codex",
        "action": "CURATED_WITH_ORGANISM_EXAMPLE",
        "changes": "Added Pyrococcus furiosus organism example with PMID-backed evidence.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-11T00:00:00-07:00",
        "curator": "codex",
        "action": "CURATED_WITH_LITERATURE",
        "changes": "Added DOI-backed hyperthermophily causal graph for thermostable enzymes, reverse gyrase, chaperonins, and membrane adaptation.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:29Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d72, RO:0002326\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T21:30:06Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007401\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:18Z",
        "curator": "claude",
        "action": "RENAME_PREDICATE_LABELS",
        "changes": "Renamed 1 causal-edge predicate label(s) to align with existing groundings: maintains \u2192 regulates \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:21Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002211\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T05:05:14Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A088E825\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T08:14:32Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (PATO:0001637\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-15T07:19:08Z",
        "curator": "claude",
        "action": "FIX_NODE_GROUNDING_CURIE",
        "changes": "Overwrote 1 causal-node grounding(s) to corrected CURIEs (phase-2 id-label fix; verified vs OAK).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-17T04:09:43Z",
        "curator": "claude",
        "action": "REMOVE_REDUNDANT_SYNONYM",
        "changes": "Removed 1 synonym(s) whose text duplicated the label (seeder redundancy; no information lost).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 6 evidence-backed generic edges (7 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:10Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002326\u00d71, RO:0002213\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:30Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:193595\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:21:11Z",
        "curator": "claude",
        "action": "RETRACT_DEAD_UNIPROT_GROUNDINGS",
        "changes": "Retracted 1 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:23:52Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0160097\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 2 causal edge(s) off enables/RO:0002327 with a TRAIT object (2 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-21T08:00:00Z",
        "curator": "codex",
        "action": "NORMALISE_NODE_TYPE",
        "changes": "Tranche 5 of issue 356 settles the process/quality families and merges ids that meant the same sense: membrane_rigidity is QUALITY. Membrane rigidity is a physical attribute of the bilayer and therefore a QUALITY under the schema's membrane-fluidity example.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope hyperthermophilic_thermostability=NONMECHANISTIC with scope_notes; marked 4 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (thermostable_enzymes, molecular_chaperonins, archaeal_proteins, gms_synthase).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000008",
    "label": "ionizing radiation tolerant",
    "definition": "An environmental tolerance in which an organism survives high doses of ionizing radiation (e.g. gamma rays), typically via efficient repair of DNA double-strand breaks and protection of the proteome from oxidative damage.",
    "definition_source": "DOI:10.3390/genes14091803",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "traitmech:000007"
    ],
    "synonyms": [
      {
        "synonym_text": "gamma radiation resistant",
        "synonym_type": "NARROW_SYNONYM",
        "source": "DOI:10.3390/genes14091803"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.3390/genes14091803",
        "snippet": "Deinococcus radiodurans R1 demonstrates a significantly higher radiation resistance with D10 values exceeding 12 kGy for gamma radiation and 700 J/m2 for UV-C radiation",
        "notes": "Organism example: Deinococcus radiodurans tolerates gamma (ionizing) radiation D10 doses exceeding 12 kGy."
      },
      {
        "reference": "DOI:10.1101/cshperspect.a012765",
        "snippet": "A strong correlation has been shown between intracellular Mn/Fe concentration ratios and bacterial resistance to radiation",
        "notes": "Mechanism support \u2014 manganese-mediated oxidative-damage protection underlies survival of lethal ionizing-radiation doses."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1299",
        "taxon_label": "Deinococcus radiodurans",
        "note": "extreme ionizing-radiation resistance",
        "reference": "PMID:10567266"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "ionizing_radiation_tolerance_dsb_repair",
        "title": "Ionizing-radiation tolerance via double-strand-break repair",
        "description": "Evidence-backed causal sketch linking gamma-radiation exposure to efficient repair of DNA double-strand breaks and Mn-mediated oxidative protection.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a broad environmental or morphological classification spanning multiple mechanisms, a measurement-like bin, or an absence/arrangement descriptor; contextual protein nodes do not receive token UniProt examples.",
        "nodes": [
          {
            "node_id": "ionizing_tolerant_trait",
            "label": "ionizing radiation tolerant",
            "node_type": "TRAIT",
            "grounding": "traitmech:000008",
            "description": "Survival of high doses of ionizing (gamma) radiation."
          },
          {
            "node_id": "gamma_radiation",
            "label": "gamma radiation",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "High-energy ionizing radiation causing DNA double-strand breaks."
          },
          {
            "node_id": "dsb_repair",
            "label": "double-strand break repair",
            "node_type": "BIOLOGICAL_PROCESS",
            "grounding": "GO:0006302",
            "description": "Repair of radiation-induced DNA double-strand breaks."
          },
          {
            "node_id": "mn_antioxidant_protection",
            "label": "manganese-mediated oxidative-damage protection",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Mn(II)-antioxidant shielding of repair proteins from oxidative damage."
          },
          {
            "node_id": "dsb_clustered_lesions",
            "label": "DNA double-strand breaks and clustered lesions",
            "node_type": "STATE",
            "description": "Single- and double-strand DNA breaks, abasic sites and complex clustered lesions produced by ionizing radiation."
          },
          {
            "node_id": "mn_fe_ratio",
            "label": "high intracellular Mn/Fe ratio",
            "node_type": "QUALITY",
            "description": "Elevated intracellular manganese-to-iron concentration ratio associated with antioxidant proteome protection."
          }
        ],
        "edges": [
          {
            "subject": "gamma_radiation",
            "predicate": "challenges",
            "object": "ionizing_tolerant_trait",
            "description": "Gamma exposure is the environmental challenge the trait counters.",
            "evidence": [
              {
                "reference": "DOI:10.3390/genes14091803",
                "notes": "Deinococcus radiodurans tolerates gamma D10 doses exceeding 12 kGy."
              }
            ],
            "predicate_id": "METPO:2007406"
          },
          {
            "subject": "dsb_repair",
            "predicate": "confers",
            "object": "ionizing_tolerant_trait",
            "description": "Efficient DSB repair restores chromosomal integrity after ionizing-radiation damage.",
            "evidence": [
              {
                "reference": "DOI:10.3390/genes14091803",
                "notes": "D. radiodurans tolerates lethal gamma doses through DSB-repair machinery."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "mn_antioxidant_protection",
            "predicate": "confers",
            "object": "ionizing_tolerant_trait",
            "description": "Mn-antioxidant proteome protection preserves repair capacity under irradiation.",
            "evidence": [
              {
                "reference": "DOI:10.1101/cshperspect.a012765",
                "notes": "Intracellular Mn/Fe ratio correlates with bacterial radiation resistance."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "gamma_radiation",
            "predicate": "causes",
            "object": "dsb_clustered_lesions",
            "description": "Ionizing radiation produces DNA double- and single-strand breaks and complex clustered lesions.",
            "evidence": [
              {
                "reference": "DOI:10.1007/978-3-031-18810-7_9",
                "notes": "Ionizing radiation produces single- and double-strand DNA breaks, abasic sites and complex clustered lesions (broad radiobiology, across taxa)."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "dsb_repair",
            "predicate": "repairs",
            "object": "dsb_clustered_lesions",
            "description": "Double-strand break repair resolves the clustered DNA lesions inflicted by ionizing radiation.",
            "evidence": [
              {
                "reference": "DOI:10.1007/978-3-031-18810-7_9",
                "notes": "DSB-repair machinery resolves radiation-induced strand breaks and clustered lesions to restore chromosomal integrity."
              }
            ]
          },
          {
            "subject": "mn_fe_ratio",
            "predicate": "positively correlates with",
            "object": "ionizing_tolerant_trait",
            "description": "A high intracellular Mn/Fe ratio correlates with antioxidant proteome protection and survival of ionizing radiation.",
            "evidence": [
              {
                "reference": "DOI:10.1101/cshperspect.a012765",
                "notes": "Strong correlation: radiation-resistant bacteria carry more Mn2+ and ~3x less Fe2+, giving antioxidant protection of the cellular proteome."
              }
            ]
          },
          {
            "subject": "mn_fe_ratio",
            "predicate": "enables",
            "object": "mn_antioxidant_protection",
            "description": "A high Mn/Fe ratio supplies the Mn(II) complexes that shield repair proteins from oxidative damage.",
            "evidence": [
              {
                "reference": "DOI:10.1101/cshperspect.a012765",
                "notes": "Elevated Mn/Fe ratio underlies Mn-antioxidant protection of the proteome during irradiation."
              }
            ],
            "predicate_id": "RO:0002327"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-28T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate ENVIRONMENT trait (ionizing/gamma radiation tolerance) from literature research; sub-variant of radiotolerant.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-09T14:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (DSB repair + Mn-antioxidant) with GO node grounding and RO/METPO predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 4 evidence-backed generic edges (2 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:10Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:causes\u00d71, RO:0002327\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 2 causal edge(s) off enables/RO:0002327 with a TRAIT object (2 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope ionizing_radiation_tolerance_dsb_repair=NONMECHANISTIC with scope_notes.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000016",
    "label": "mercury tolerant",
    "definition": "A metal tolerance in which an organism grows in the presence of toxic inorganic or organic mercury compounds, typically via the mer operon, whose mercuric reductase (MerA) reduces reactive Hg(II) to volatile Hg(0).",
    "definition_source": "DOI:10.1016/S0168-6445(03)00046-9",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "traitmech:000012"
    ],
    "synonyms": [
      {
        "synonym_text": "mercury resistant",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1016/S0168-6445(03)00046-9"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1016/S0168-6445(03)00046-9",
        "snippet": "Bacterial resistance to inorganic and organic mercury compounds (HgR) is one of the most widely observed phenotypes in eubacteria",
        "notes": "Review supports mercury resistance as a widespread bacterial phenotype mediated by MerA, \"that reduces reactive ionic Hg(II) to volatile, relatively inert, monoatomic Hg(0) vapor\"."
      },
      {
        "reference": "PMID:12829273",
        "snippet": "CBA efflux pumps driven by proteins of the resistance-nodulation-cell division superfamily, P-type ATPases, cation diffusion facilitator and chromate proteins",
        "notes": "Heavy-metal resistance review situates mercury detoxification within the broader prokaryotic metal-resistance machinery."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:119219",
        "taxon_label": "Cupriavidus metallidurans",
        "note": "mer-operon mercury resistance",
        "reference": "PMID:21423734"
      },
      {
        "taxon_id": "NCBITaxon:303",
        "taxon_label": "Pseudomonas putida",
        "note": "mercury-resistant",
        "reference": "PMID:21751007"
      },
      {
        "taxon_id": "NCBITaxon:266264",
        "taxon_label": "Cupriavidus metallidurans CH34",
        "note": "Strain-level MerA mercury-reduction exemplar.",
        "reference": "PMID:21423734"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "mercury_tolerance_mer_reduction",
        "title": "Mercury tolerance via mer-operon MerA reductase",
        "description": "Evidence-backed causal sketch linking mer-operon mercuric reductase to volatilization of Hg(II) into Hg(0).",
        "scope_status": "MECHANISTIC",
        "scope_notes": "The taxon-matched protein example anchors one experimentally supported causal branch; it is not presented as a universal mechanism for every taxon or every contextual branch in this graph.",
        "nodes": [
          {
            "node_id": "mercury_tolerant_trait",
            "label": "mercury tolerant",
            "node_type": "TRAIT",
            "grounding": "traitmech:000016",
            "description": "Capacity to grow in the presence of toxic mercury compounds."
          },
          {
            "node_id": "mercury_ii_ion",
            "label": "mercury(2+) ion",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:25195",
            "description": "Reactive ionic mercury accumulating intracellularly."
          },
          {
            "node_id": "mer_operon",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:Q1L9Z3",
                "protein_label": "Mercuric reductase MerA",
                "gene_symbol": "merA",
                "taxon_id": "NCBITaxon:266264",
                "taxon_label": "Cupriavidus metallidurans CH34",
                "entry_status": "UNREVIEWED",
                "proteome_id": "UP000002429",
                "retrieved_on": "2026-08-25",
                "entry_version": 124,
                "sequence_version": 1,
                "role": "CH34 MerA reduces toxic Hg(II) to volatile elemental Hg(0).",
                "evidence": [
                  {
                    "reference": "PMID:21423734",
                    "snippet": "mercury resistance in Cupriavidus metallidurans CH34",
                    "notes": "The cited source supports the represented protein-to-trait branch; UniProt verifies this current strain-matched protein entry."
                  }
                ]
              }
            ],
            "label": "MerA mercuric reductase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Mercuric reductase reducing Hg(II) to volatile Hg(0).",
            "gene_symbols": [
              "merA"
            ],
            "operon": "mer"
          },
          {
            "node_id": "mercury_reduction",
            "label": "mercury(II) reduction",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Enzymatic reduction of Hg(II) to volatile elemental Hg(0)."
          },
          {
            "node_id": "mercury_zero",
            "label": "mercury(0)",
            "node_type": "CHEMICAL",
            "description": "Volatile, relatively inert elemental mercury Hg(0).",
            "grounding": "CHEBI:16170"
          },
          {
            "node_id": "merb_lyase",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "MerB (organomercurial lyase)",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Organomercury lyase cleaving C-Hg bonds of organomercurials to release Hg(II)."
          },
          {
            "node_id": "organomercurial",
            "label": "organomercurial compound",
            "node_type": "CHEMICAL",
            "description": "Organic mercury compounds such as methylmercury."
          },
          {
            "node_id": "merr_sensor",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "MerR (Hg-responsive regulator)",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Mercury-responsive transcription factor controlling mer operon induction."
          },
          {
            "node_id": "mer_transcription",
            "label": "mer operon transcription",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Transcriptional activation of mer detoxification genes from the Pmer promoter."
          }
        ],
        "edges": [
          {
            "subject": "mercury_ii_ion",
            "predicate": "challenges",
            "object": "mercury_tolerant_trait",
            "description": "Reactive Hg(II) is the toxic challenge the trait counters.",
            "evidence": [
              {
                "reference": "PMID:12829273",
                "notes": "Mercury detoxification sits within the broader prokaryotic metal-resistance machinery."
              }
            ],
            "predicate_id": "METPO:2007406"
          },
          {
            "subject": "mer_operon",
            "predicate": "enables",
            "object": "mercury_reduction",
            "description": "MerA reduces Hg(II) to volatile, inert Hg(0) vapour.",
            "evidence": [
              {
                "reference": "DOI:10.1016/S0168-6445(03)00046-9",
                "notes": "MerA reduces reactive ionic Hg(II) to volatile, relatively inert, monoatomic Hg(0) vapor."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "mercury_reduction",
            "predicate": "mitigates",
            "object": "mercury_ii_ion",
            "description": "Reduction to Hg(0) depletes the reactive Hg(II) pool.",
            "evidence": [
              {
                "reference": "DOI:10.1016/S0168-6445(03)00046-9",
                "notes": "Mercury reduction is the basis of mer-mediated resistance."
              }
            ],
            "predicate_id": "METPO:2007407"
          },
          {
            "subject": "mer_operon",
            "predicate": "produces",
            "object": "mercury_zero",
            "description": "MerA reduction of Hg(II) yields volatile elemental Hg(0).",
            "evidence": [
              {
                "reference": "DOI:10.1186/s12866-024-03391-5",
                "notes": "MerA reduces Hg2+ to volatile Hg0, relieving intracellular Hg(II) toxicity."
              }
            ],
            "predicate_id": "METPO:2007800"
          },
          {
            "subject": "merb_lyase",
            "predicate": "cleaves",
            "object": "organomercurial",
            "description": "MerB lyase cleaves C-Hg bonds of organomercurials to release Hg(II) for MerA reduction.",
            "evidence": [
              {
                "reference": "DOI:10.21203/rs.3.rs-3854515/v1",
                "notes": "MerB is an organomercury lyase that cleaves methylmercury to Hg2+ and methane."
              }
            ]
          },
          {
            "subject": "merb_lyase",
            "predicate": "produces",
            "object": "mercury_ii_ion",
            "description": "Organomercurial cleavage yields Hg(II), the substrate for MerA reduction.",
            "evidence": [
              {
                "reference": "DOI:10.21203/rs.3.rs-3854515/v1",
                "notes": "C-Hg bond cleavage produces Hg(II) for subsequent MerA reduction."
              }
            ],
            "predicate_id": "METPO:2007800"
          },
          {
            "subject": "merr_sensor",
            "predicate": "senses",
            "object": "mercury_ii_ion",
            "description": "MerR senses Hg(II), acting as a mercury-responsive transcriptional regulator.",
            "evidence": [
              {
                "reference": "DOI:10.21203/rs.3.rs-3854515/v1",
                "notes": "MerR functions as a repressor/activator responsive to Hg2+."
              }
            ]
          },
          {
            "subject": "merr_sensor",
            "predicate": "activates",
            "object": "mer_transcription",
            "description": "Hg(II)-bound MerR activates transcription of the mer detoxification genes from Pmer.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fbioe.2023.1178680",
                "notes": "MerR-mediated activation of Pmer drives mer operon transcription when Hg(II) is present."
              }
            ],
            "predicate_id": "RO:0002213"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-28T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate ENVIRONMENT trait (mercury tolerance) from literature research; metal-specific sub-variant of metal tolerant.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-09T14:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (mer-operon Hg(II) reduction) with CHEBI node grounding and RO/METPO predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 5 evidence-backed generic edges (5 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:10Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d72, RO:0002213\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:30Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:16170\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T02:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES_PART2",
        "changes": "Re-grounded 2 causal edge(s) off microbe-domain METPO predicates onto their causal-graph counterparts (2 to produces), issue 301 part 2. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Each replacement is a 1:1 mirror of its source predicate that changes only the domain, so the claim each edge makes is unchanged and directions are unchanged. The replacements are proposed in proposals/metpo_traitmech_v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "CURATE_PROTEIN_TAXON_EXAMPLE",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope mercury_tolerance_mer_reduction=MECHANISTIC with scope_notes; marked 3 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (mer_operon, merb_lyase, merr_sensor); added taxon-paired protein example(s) UniProtKB:Q1L9Z3 on mer_operon (NCBITaxon:266264); added canonical example(s) NCBITaxon:266264.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000615",
    "label": "mesophilic",
    "definition": "A temperature preference in which growth is favored at intermediate temperatures, typically ~20\u201345 \u00b0C.",
    "definition_source": "DOI:10.1016/j.bpj.2013.06.029",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000613"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1016/j.bpj.2013.06.029",
        "snippet": "Escherichia coli, a mesophilic bacterium",
        "notes": "Organism example: Escherichia coli is described as mesophilic."
      },
      {
        "reference": "DOI:10.1146/annurev-micro-091313-103612",
        "snippet": "more unsaturated fatty acids",
        "notes": "Membrane-adaptation review supports homoviscous membrane composition matched to ambient temperature as the basis of mesophile physiology."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:562",
        "taxon_label": "Escherichia coli",
        "note": "Canonical mesophile and universal model organism (optimum ~37 C).",
        "reference": "DOI:10.1021/acsomega.2c04786"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "mesophilic_homoviscous_adaptation",
        "title": "Mesophilic growth with membrane and temperature-boundary support",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is an upper preference, broad tolerance, or central-range classification spanning multiple unrelated adaptations; contextual protein nodes are retained without assigning a misleading token UniProt example.",
        "description": "DOI-backed nonmechanistic graph connecting mesophily to moderate temperature, balanced growth, homoviscous membrane fluidity, and cold- and heat-shock boundary-support branches.",
        "nodes": [
          {
            "node_id": "mesophilic_trait",
            "label": "mesophilic",
            "node_type": "TRAIT",
            "grounding": "METPO:1000615",
            "description": "Growth is favored at intermediate temperatures (~20\u201345 \u00b0C)."
          },
          {
            "node_id": "moderate_temperature",
            "label": "moderate ambient temperature",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Ambient temperature in the ~20\u201345 \u00b0C mesophilic range."
          },
          {
            "node_id": "membrane_fluidity",
            "label": "membrane fluidity",
            "node_type": "QUALITY",
            "description": "Physical state of the cytoplasmic membrane supporting transport and bioenergetics.",
            "grounding": "METPO:1007505"
          },
          {
            "node_id": "homoviscous_lipid_composition",
            "label": "homoviscous lipid composition",
            "node_type": "CELLULAR_LOCALIZATION",
            "description": "Lipid composition tuned to maintain target membrane fluidity at mesophilic temperatures."
          },
          {
            "node_id": "mesophile_enzyme_repertoire",
            "label": "mesophile enzyme repertoire",
            "node_type": "GENE_OR_PROTEIN",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed as a contextual protein or protein-complex label in a broad environmental classification; no single exact family term denotes this aggregate use.",
            "description": "Enzymes with peak activity in the mesophile temperature range."
          },
          {
            "node_id": "balanced_growth",
            "label": "balanced mesophilic growth",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Sustained growth rate at intermediate temperatures."
          },
          {
            "node_id": "temperature_decrease",
            "label": "temperature decrease",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "A downshift in ambient temperature within the mesophilic regime."
          },
          {
            "node_id": "unsaturated_fatty_acids",
            "label": "unsaturated fatty acids",
            "node_type": "CHEMICAL",
            "description": "Membrane acyl chains with cis double bonds that increase membrane fluidity.",
            "grounding": "CHEBI:27208"
          },
          {
            "node_id": "cold_shock",
            "label": "cold shock",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Abrupt temperature downshift triggering the cold-shock response."
          },
          {
            "node_id": "cspa",
            "label": "CspA cold-shock protein",
            "node_type": "GENE_OR_PROTEIN",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed as a contextual protein or protein-complex label in a broad environmental classification; no single exact family term denotes this aggregate use.",
            "description": "Major cold-shock RNA chaperone preventing inhibitory RNA secondary structure."
          },
          {
            "node_id": "translation",
            "label": "translation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Protein synthesis from mRNA, maintained during cold shock.",
            "grounding": "GO:0006412"
          },
          {
            "node_id": "heat_shock",
            "label": "heat shock",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Temperature upshift triggering the heat-shock response."
          },
          {
            "node_id": "rpoh_sigma32",
            "label": "sigma-32 (RpoH)",
            "node_type": "GENE_OR_PROTEIN",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed as a contextual protein or protein-complex label in a broad environmental classification; no single exact family term denotes this aggregate use.",
            "description": "Alternative sigma factor controlling the bacterial heat-shock regulon."
          },
          {
            "node_id": "heat_shock_proteins",
            "label": "heat-shock response proteins",
            "node_type": "GENE_OR_PROTEIN",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed as a contextual protein or protein-complex label in a broad environmental classification; no single exact family term denotes this aggregate use.",
            "description": "Chaperones and proteases induced to mitigate heat stress."
          },
          {
            "node_id": "dnak",
            "label": "DnaK chaperone",
            "node_type": "GENE_OR_PROTEIN",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed as a contextual protein or protein-complex label in a broad environmental classification; no single exact family term denotes this aggregate use.",
            "description": "Hsp70 chaperone that sequesters sigma-32, negatively regulating its activity."
          }
        ],
        "edges": [
          {
            "subject": "moderate_temperature",
            "predicate": "selects for",
            "object": "mesophilic_trait",
            "description": "Moderate ambient temperatures select for mesophilic physiology.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.bpj.2013.06.029",
                "snippet": "Escherichia coli, a mesophilic bacterium",
                "notes": "Supports a representative mesophile thriving at moderate temperatures."
              }
            ],
            "predicate_id": "METPO:2007401"
          },
          {
            "subject": "homoviscous_lipid_composition",
            "predicate": "regulates",
            "object": "membrane_fluidity",
            "description": "Homoviscous lipid composition maintains target membrane fluidity at mesophilic temperatures.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-micro-091313-103612",
                "snippet": "more unsaturated fatty acids",
                "notes": "Supports homoviscous adaptation as the mechanism setting membrane fluidity."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "mesophile_enzyme_repertoire",
            "predicate": "enables",
            "object": "balanced_growth",
            "description": "Mesophile enzyme repertoire enables balanced growth at intermediate temperatures.",
            "evidence": [
              {
                "reference": "DOI:10.1016/s0300-9629(97)00003-0",
                "snippet": "energy transducing enzymes",
                "notes": "Supports temperature-tuned enzyme repertoires as the basis of adapted growth."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "balanced_growth",
            "predicate": "manifests as",
            "object": "mesophilic_trait",
            "description": "Balanced growth at moderate temperatures manifests the mesophilic trait.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.bpj.2013.06.029",
                "snippet": "Escherichia coli, a mesophilic bacterium",
                "notes": "Supports the trait endpoint in a representative organism."
              }
            ],
            "predicate_id": "METPO:2007400"
          },
          {
            "subject": "temperature_decrease",
            "predicate": "increases",
            "object": "unsaturated_fatty_acids",
            "description": "Temperature downshift increases membrane unsaturated fatty acid content through homeoviscous adaptation.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s42770-023-01057-4",
                "snippet": "production of double bonds in lipids",
                "notes": "Verified against the Ram\u00f3n et al. cold-adaptation review; low-temperature adaptation includes membrane-composition remodeling through lipid double-bond production."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "cold_shock",
            "predicate": "positively regulates",
            "object": "cspa",
            "description": "Cold shock strongly increases CspA cold-shock protein synthesis.",
            "evidence": [
              {
                "reference": "DOI:10.1046/j.1365-2958.1999.01284.x",
                "snippet": "more than 10% of the total cellular protein synthesis",
                "notes": "Verified against the open Molecular Microbiology full text; CspA is the major E. coli cold-shock protein and its synthesis rises sharply after temperature downshift."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "cspa",
            "predicate": "promotes",
            "object": "translation",
            "description": "CspA RNA chaperone activity destabilizes inhibitory mRNA secondary structures, promoting translation during cold shock.",
            "evidence": [
              {
                "reference": "DOI:10.1046/j.1365-2958.1999.01284.x",
                "snippet": "facilitates translation by destabilizing mRNA secondary structures",
                "notes": "Verified against the open Molecular Microbiology full text; CspA acts as an RNA chaperone that counters low-temperature mRNA secondary structure."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "heat_shock",
            "predicate": "positively regulates",
            "object": "rpoh_sigma32",
            "description": "Heat shock transiently increases cellular sigma-32 (RpoH), the heat-shock sigma factor.",
            "evidence": [
              {
                "reference": "DOI:10.1128/jb.183.18.5302-5310.2001",
                "snippet": "transient increase in the RpoH level observed upon heat shock",
                "notes": "Verified against the open Journal of Bacteriology full text; E. coli heat-shock induction is regulated by increased RpoH translation and transient sigma-32 stabilization."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "rpoh_sigma32",
            "predicate": "positively regulates",
            "object": "heat_shock_proteins",
            "description": "Sigma-32 (RpoH) positively regulates heat-shock response protein expression.",
            "evidence": [
              {
                "reference": "DOI:10.1128/jb.183.18.5302-5310.2001",
                "snippet": "enhancing transcription of the heat shock genes",
                "notes": "Verified against the open Journal of Bacteriology full text; RpoH-dependent sigma-32 activity drives heat-shock-gene transcription."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "dnak",
            "predicate": "negatively regulates",
            "object": "rpoh_sigma32",
            "description": "DnaK chaperone activity negatively regulates sigma-32 (RpoH) activity.",
            "evidence": [
              {
                "reference": "DOI:10.1128/jb.183.18.5302-5310.2001",
                "snippet": "negative regulation of RpoH activity",
                "notes": "Verified against the open Journal of Bacteriology full text; the DnaK chaperone system participates in negative control of sigma-32 activity."
              }
            ],
            "predicate_id": "RO:0002212"
          },
          {
            "subject": "unsaturated_fatty_acids",
            "predicate": "associated with",
            "object": "homoviscous_lipid_composition",
            "description": "Unsaturated fatty-acid changes are associated with the homeoviscous lipid composition branch in this mesophilic temperature-response graph.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-micro-091313-103612",
                "snippet": "incorporation of proportionally more unsaturated fatty acids",
                "notes": "Verified against the public Annual Review of Microbiology abstract; unsaturated fatty-acid incorporation is part of homeoviscous membrane remodeling as growth temperature decreases."
              }
            ],
            "predicate_id": "biolink:associated_with"
          },
          {
            "subject": "membrane_fluidity",
            "predicate": "associated with",
            "object": "balanced_growth",
            "description": "Mesophilic balanced growth is associated with maintenance of target cytoplasmic-membrane fluidity.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-micro-091313-103612",
                "snippet": "remodel the fluidity of their membrane bilayer",
                "notes": "Verified against the public Annual Review of Microbiology abstract; the connector links membrane-fluidity remodeling to growth-temperature acclimation without making a single lipid ratio define mesophily."
              }
            ],
            "predicate_id": "biolink:associated_with"
          },
          {
            "subject": "translation",
            "predicate": "associated with",
            "object": "balanced_growth",
            "description": "Cold-shock maintenance of translation is a lower-temperature boundary-support branch for balanced mesophilic growth.",
            "evidence": [
              {
                "reference": "DOI:10.4161/rna.7.6.13482",
                "snippet": "facilitating transcription and translation at low temperature",
                "notes": "Verified against the open Phadtare and Severinov PMC abstract; the connector keeps CspA-family RNA chaperones as low-temperature translation context, not as a definition of mesophily."
              }
            ],
            "predicate_id": "biolink:associated_with"
          },
          {
            "subject": "heat_shock_proteins",
            "predicate": "associated with",
            "object": "balanced_growth",
            "description": "RpoH-regulated heat-shock response proteins form an upper-temperature boundary-support branch for balanced mesophilic growth.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mbio.02174-23",
                "snippet": "heat shock genes encoding chaperones, such as DnaK and GroEL",
                "notes": "Verified against the open Grunberger et al. PMC text; the connector keeps heat-shock chaperones as an upper-boundary proteostasis branch, not as a definition of mesophily."
              }
            ],
            "predicate_id": "biolink:associated_with"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.857659+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-06T14:58:45-07:00",
        "curator": "codex",
        "action": "CURATED_WITH_ORGANISM_EXAMPLE",
        "changes": "Added Escherichia coli organism example with PMID-backed evidence.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-13T11:30:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed causal graph linking moderate ambient temperature, homoviscous membrane composition, mesophile enzyme repertoire, and balanced growth to the mesophilic trait.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-13T22:45:00-07:00",
        "curator": "codex",
        "action": "IMPROVED_CAUSAL_GRAPH_EVIDENCE",
        "changes": "Replaced Escherichia coli mesophile PMID fallback with the article DOI in definition, record evidence, and CausalEdge evidence.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:29Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T21:30:06Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007401\u00d71, METPO:2007400\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:18Z",
        "curator": "claude",
        "action": "RENAME_PREDICATE_LABELS",
        "changes": "Renamed 1 causal-edge predicate label(s) to align with existing groundings: maintains \u2192 regulates \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:21Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002211\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:41:03Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (METPO:1007505\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-26T02:30:12Z",
        "curator": "claude",
        "action": "RETYPE_CAUSAL_NODES",
        "changes": "Re-typed 1 causal-node node_type field(s) to align with CausalNodeTypeEnum semantics: membrane fluidity: BIOLOGICAL_PROCESS \u2192 QUALITY \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-17T04:09:43Z",
        "curator": "claude",
        "action": "REMOVE_REDUNDANT_SYNONYM",
        "changes": "Removed 1 synonym(s) whose text duplicated the label (seeder redundancy; no information lost).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 6 evidence-backed generic edges (9 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:10Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002213\u00d72).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:30Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:27208\u00d71, GO:0006412\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-04T03:08:12Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002212\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope mesophilic_homoviscous_adaptation=NONMECHANISTIC with scope_notes; marked 5 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (mesophile_enzyme_repertoire, cspa, rpoh_sigma32, heat_shock_proteins, dnak); added 1 node(s) and 1 edge(s) (heat_shock_proteins); removed 1 node(s) and 1 edge(s) together with their evidence (heat_shock_genes).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-04T00:40:00Z",
        "curator": "codex",
        "action": "REVIEW_CAUSAL_EVIDENCE",
        "changes": "Reviewed the broad mesophilic_homoviscous_adaptation graph for issue #183: added snippets to 6 edge-level evidence items and regrounded 3 heat/cold shock response edges from legacy free-text predicates to RO:0002213 positive regulation. No paid research service was called.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-04T13:00:00Z",
        "curator": "codex",
        "action": "CONNECT_CAUSAL_GRAPH_COMPONENTS",
        "changes": "Resolved issue #183 graph fragmentation (5 components to 1) by adding 4 source- and verbatim-snippet-backed association connectors among the homoviscous membrane, cold-shock RNA, and heat-shock boundary branches. No paid research service was called.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-06T13:30:00Z",
        "curator": "codex",
        "action": "ADVERSARIAL_REVIEW_REPAIR",
        "changes": "Addressed PR #664 adversarial review issue #665: replaced two sigma-32 snippets with exact RpoH wording from the Journal of Bacteriology source.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-06T17:10:00Z",
        "curator": "codex",
        "action": "ADVERSARIAL_REVIEW_REPAIR",
        "changes": "Addressed PR #664 adversarial review: replaced copied nonmechanistic bridge snippets with independent exact source snippets while preserving the existing connector edge scope.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000012",
    "label": "metal tolerant",
    "definition": "An environmental tolerance in which an organism grows in the presence of elevated concentrations of toxic heavy-metal or metalloid ions, typically via efflux-based resistance determinants (RND-family CBA pumps, P-type ATPases, and cation diffusion facilitators).",
    "definition_source": "PMID:12829273",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "synonyms": [
      {
        "synonym_text": "metallophilic",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.3389/fmicb.2020.00047"
      },
      {
        "synonym_text": "heavy metal resistant",
        "synonym_type": "RELATED_SYNONYM",
        "source": "PMID:12829273"
      }
    ],
    "evidence": [
      {
        "reference": "PMID:12829273",
        "snippet": "CBA efflux pumps driven by proteins of the resistance-nodulation-cell division superfamily, P-type ATPases, cation diffusion facilitator and chromate proteins",
        "notes": "Review of efflux-mediated heavy-metal resistance supports active metal export as the dominant prokaryotic tolerance mechanism."
      },
      {
        "reference": "DOI:10.3389/fmicb.2020.00047",
        "snippet": "This metallophilic strain BS1, harbors numerous gene clusters encoding metal-resistance determinants enabling detoxification of transition metal ions and complexes",
        "notes": "Organism example: Cupriavidus metallidurans is the model metallophilic bacterium tolerating many toxic metals via dedicated resistance gene clusters."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:119219",
        "taxon_label": "Cupriavidus metallidurans",
        "note": "Paradigm heavy-metal-resistance bacterium (strain CH34; plasmid-borne metal-efflux determinants).",
        "reference": "PMID:20463976"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "metal_tolerance_efflux_detoxification",
        "title": "Metal tolerance via active efflux of heavy-metal ions",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is an upper preference, broad tolerance, or central-range classification spanning multiple unrelated adaptations; contextual protein nodes are retained without assigning a misleading token UniProt example.",
        "description": "Evidence-backed causal sketch linking heavy-metal exposure to efflux-pump-mediated detoxification underlying broad metal tolerance.",
        "nodes": [
          {
            "node_id": "metal_tolerant_trait",
            "label": "metal tolerant",
            "node_type": "TRAIT",
            "grounding": "traitmech:000012",
            "description": "Capacity to grow at elevated heavy-metal or metalloid concentrations."
          },
          {
            "node_id": "heavy_metal_ion",
            "label": "toxic heavy-metal ion",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Cytoplasmic excess of a transition-metal or metalloid cation."
          },
          {
            "node_id": "efflux_pump",
            "label": "metal efflux pump",
            "node_type": "GENE_OR_PROTEIN",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed as a contextual protein or protein-complex label in a broad environmental classification; no single exact family term denotes this aggregate use.",
            "description": "RND-family CBA pumps, P-type ATPases, and cation diffusion facilitators exporting metals."
          },
          {
            "node_id": "metal_ion_export",
            "label": "metal ion transmembrane export",
            "node_type": "BIOLOGICAL_PROCESS",
            "grounding": "GO:0030001",
            "description": "Transport of metal cations across the cytoplasmic membrane."
          },
          {
            "node_id": "arsenate",
            "label": "arsenate As(V)",
            "node_type": "CHEMICAL",
            "description": "Oxidized arsenic oxyanion taken up by phosphate transporters."
          },
          {
            "node_id": "arsenite",
            "label": "arsenite As(III)",
            "node_type": "CHEMICAL",
            "description": "Reduced arsenic species substrate for arsenite efflux pumps."
          },
          {
            "node_id": "arsc_reductase",
            "label": "ArsC arsenate reductase",
            "node_type": "GENE_OR_PROTEIN",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed as a contextual protein or protein-complex label in a broad environmental classification; no single exact family term denotes this aggregate use.",
            "description": "Cytoplasmic reductase converting arsenate to arsenite prior to extrusion."
          },
          {
            "node_id": "ars_detoxification_proteins",
            "label": "Ars detoxification protein module",
            "node_type": "GENE_OR_PROTEIN",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed as a contextual protein or protein-complex label in a broad environmental classification; no single exact family term denotes this aggregate use.",
            "description": "ArsC reductase plus ArsB/Acr3 arsenite-efflux proteins.",
            "gene_symbols": [
              "arsC",
              "arsB",
              "acr3"
            ],
            "operon": "ars"
          },
          {
            "node_id": "arsenic_tolerance",
            "label": "arsenic tolerance",
            "node_type": "TRAIT",
            "description": "Detoxification-mediated tolerance of arsenic oxyanions."
          }
        ],
        "edges": [
          {
            "subject": "heavy_metal_ion",
            "predicate": "challenges",
            "object": "metal_tolerant_trait",
            "description": "Elevated heavy-metal concentrations are the environmental challenge the trait counters.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2020.00047",
                "notes": "Cupriavidus metallidurans encodes many metal-resistance determinants confronting multiple toxic metals."
              }
            ],
            "predicate_id": "METPO:2007406"
          },
          {
            "subject": "efflux_pump",
            "predicate": "enables",
            "object": "metal_ion_export",
            "description": "CBA pumps, P-type ATPases, and CDFs export toxic metal cations from the cytoplasm.",
            "evidence": [
              {
                "reference": "PMID:12829273",
                "notes": "Nies reviews efflux-mediated heavy-metal resistance as the dominant prokaryotic tolerance mechanism."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "metal_ion_export",
            "predicate": "confers",
            "object": "metal_tolerant_trait",
            "description": "Cytoplasmic detoxification by export realizes the metal-tolerant phenotype.",
            "evidence": [
              {
                "reference": "PMID:12829273",
                "notes": "Nies frames efflux-based export as the basis of broad heavy-metal tolerance."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "arsc_reductase",
            "predicate": "converts",
            "object": "arsenate",
            "description": "ArsC arsenate reductase reduces As(V) to As(III) as the first detoxification step.",
            "evidence": [
              {
                "reference": "DOI:10.52700/jmmg.v5i1.155",
                "notes": "Review: \"ArsC converting As(V) to As(III) followed by extrusion\"; general across bacteria."
              }
            ]
          },
          {
            "subject": "arsenate",
            "predicate": "is converted to",
            "object": "arsenite",
            "description": "Arsenate is reduced to arsenite, the species handled by efflux pumps.",
            "evidence": [
              {
                "reference": "DOI:10.52700/jmmg.v5i1.155",
                "notes": "Review: ArsC converts As(V) to As(III) followed by extrusion."
              }
            ]
          },
          {
            "subject": "ars_detoxification_proteins",
            "predicate": "confers",
            "object": "arsenic_tolerance",
            "description": "The ArsC plus ArsB/Acr3 protein module mediates arsenate reduction and arsenite extrusion conferring arsenic tolerance.",
            "evidence": [
              {
                "reference": "DOI:10.7717/peerj.18383",
                "notes": "\"a cooperative mechanism involving detoxification through arsenate reduction\" via ArsC/ArsA/ArsB/Acr3 proteins across mixed soil taxa."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "arsenic_tolerance",
            "predicate": "is a",
            "object": "metal_tolerant_trait",
            "description": "Arsenic (metalloid) tolerance is a component of the broad metal-tolerant phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.52700/jmmg.v5i1.155",
                "notes": "Arsenic detoxification (reduction + efflux) is part of generic bacterial heavy-metal/metalloid resistance."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "efflux_pump",
            "predicate": "mediates",
            "object": "metal_tolerant_trait",
            "description": "P-type ATPase, CDF, and RND efflux transporters mediate heavy-metal resistance in most bacteria.",
            "evidence": [
              {
                "reference": "DOI:10.52700/jmmg.v5i1.155",
                "notes": "\"resistance in most bacteria is mediated by P-type ATPase efflux, diffusion facilitator transporters of cations and RND\" - generic review."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-28T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate ENVIRONMENT trait (general heavy-metal/metalloid tolerance) from literature research to fill the metal-tolerance coverage gap. Parent of the metal-specific sub-variants.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-09T14:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (efflux-mediated metal detoxification) with GO node grounding and RO/METPO predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-14T06:38:14Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A067YD12\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 5 evidence-backed generic edges (5 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:10Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d71, rdfs:subClassOf\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:21:11Z",
        "curator": "claude",
        "action": "RETRACT_DEAD_UNIPROT_GROUNDINGS",
        "changes": "Retracted 1 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 1 causal edge(s) off enables/RO:0002327 with a TRAIT object (1 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-07T05:00:00Z",
        "curator": "claude",
        "action": "RETYPE_CAUSAL_NODE",
        "changes": "Retyped the object node from STATE/CAPACITY to TRAIT and re-grounded its in-edge from enables/RO:0002327 to METPO:2007700 (confers), issue 334. biolink declares enables range 'biological process or activity', which only BIOLOGICAL_PROCESS, PATHWAY and MOLECULAR_FUNCTION satisfy. The node's own description gives it away as a disposition rather than a state - phrasings like \"Capacity of an organism to grow and survive under...\", \"Ability to grow when...\" and \"tolerance of...\" describe what an organism CAN do, which is what a TRAIT is. So the defect was the node type, not the predicate, which is the third time in this issue's neighbourhood that has been true (compare issue 331's acetate kinase step and issue 330's negated node name). With the object correctly a TRAIT, confers applies unchanged.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope metal_tolerance_efflux_detoxification=NONMECHANISTIC with scope_notes; marked 3 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (efflux_pump, arsc_reductase, ars_detoxification_proteins); added 1 node(s) and 1 edge(s) (ars_detoxification_proteins); removed 1 node(s) and 1 edge(s) together with their evidence (ars_operon).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000604",
    "label": "microaerophilic",
    "definition": "An oxygen preference that requires molecular oxygen (O\u2082) at concentrations lower than atmospheric.",
    "definition_source": "https://www.ncbi.nlm.nih.gov/books/NBK154539/",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000601"
    ],
    "synonyms": [
      {
        "synonym_text": "Ox_microerophile",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "microaerophile",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "https://www.ncbi.nlm.nih.gov/books/NBK154539/",
        "snippet": "require oxygen to survive but require its presence in lower concentrations",
        "notes": "Supports microaerophily as oxygen requirement below atmospheric concentration."
      },
      {
        "reference": "PMID:26284041",
        "snippet": "C. jejuni is a microaerophilic, fastidious bacterium",
        "notes": "Organism example: Campylobacter jejuni is described as microaerophilic."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:197",
        "taxon_label": "Campylobacter jejuni",
        "note": "Canonical microaerophile (requires reduced O2, ~5-10%).",
        "reference": "PMID:26284041"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "microaerophile_low_oxygen_respiration",
        "title": "Microaerophilic low-oxygen respiration mechanism",
        "description": "Evidence-backed causal sketch linking microaerophily to microoxic environments and high-affinity terminal oxidases.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a broad environmental or morphological classification spanning multiple mechanisms, a measurement-like bin, or an absence/arrangement descriptor; contextual protein nodes do not receive token UniProt examples.",
        "nodes": [
          {
            "node_id": "microaerophilic_trait",
            "label": "microaerophilic",
            "node_type": "TRAIT",
            "grounding": "METPO:1000604",
            "description": "Growth requires oxygen below atmospheric concentration."
          },
          {
            "node_id": "microoxic_environment",
            "label": "microoxic environment",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Low-oxygen zone that supports microaerobic respiration."
          },
          {
            "node_id": "molecular_oxygen",
            "label": "molecular oxygen",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:15379",
            "description": "Dioxygen present at low concentration."
          },
          {
            "node_id": "high_affinity_terminal_oxidase",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "high-affinity terminal oxidase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Respiratory oxidase enabling oxygen use at low concentration."
          },
          {
            "node_id": "cbb3_oxidase",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "cytochrome cbb3 oxidase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "High-affinity cytochrome oxidase associated with microaerobic metabolism."
          },
          {
            "node_id": "cytochrome_bd_oxidase",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "cytochrome bd ubiquinol oxidase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "High-affinity quinol oxidase widespread in low-oxygen-adapted bacteria."
          },
          {
            "node_id": "low_oxygen_respiration",
            "label": "respiration under low oxygen",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Aerobic respiratory electron transport carried out at low O2 concentrations."
          },
          {
            "node_id": "branched_respiratory_chain",
            "label": "branched respiratory chain",
            "node_type": "PATHWAY",
            "description": "Respiratory chain with multiple terminal oxidase branches."
          },
          {
            "node_id": "oxygen_adaptation",
            "label": "adaptation to fluctuating oxygen",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Physiological adjustment to changing environmental O2 levels."
          },
          {
            "node_id": "catalase_kata",
            "label": "catalase (KatA)",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Enzyme that detoxifies hydrogen peroxide.",
            "grounding": "GO:0004096"
          },
          {
            "node_id": "hydrogen_peroxide",
            "label": "hydrogen peroxide",
            "node_type": "CHEMICAL",
            "description": "Reactive oxygen species byproduct.",
            "grounding": "CHEBI:16240"
          },
          {
            "node_id": "superoxide_dismutase_sodb",
            "label": "superoxide dismutase (SodB)",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Enzyme protecting against reactive oxygen species.",
            "grounding": "GO:0004784"
          },
          {
            "node_id": "reactive_oxygen_species",
            "label": "reactive oxygen species",
            "node_type": "CHEMICAL",
            "description": "ROS generated by oxygen exposure.",
            "grounding": "CHEBI:26523"
          },
          {
            "node_id": "ahpc",
            "label": "alkyl hydroperoxide reductase (AhpC)",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Predominant H2O2 scavenger at low oxygen.",
            "grounding": "GO:0009321"
          }
        ],
        "edges": [
          {
            "subject": "microoxic_environment",
            "predicate": "confers",
            "object": "microaerophilic_trait",
            "description": "Microaerophiles grow optimally in microoxic conditions.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2970",
                "snippet": "microaerophiles grow optimally under microoxic conditions",
                "notes": "Nature Reviews Microbiology analysis defines the microoxic context."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "high_affinity_terminal_oxidase",
            "predicate": "enables use of",
            "object": "molecular_oxygen",
            "description": "High-affinity terminal oxidases enable respiration at scarce oxygen concentrations.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2970",
                "snippet": "harvest O2 present at low, even nanomolar, concentrations",
                "notes": "Supports the low-oxygen respiratory role of high-affinity oxidases."
              }
            ]
          },
          {
            "subject": "high_affinity_terminal_oxidase",
            "predicate": "contributes to",
            "object": "microaerophilic_trait",
            "description": "High-affinity terminal oxidases are mechanistic contributors to microaerophilic growth.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2970",
                "snippet": "provide microaerobes with access to scarce supplies of O2",
                "notes": "Supports terminal oxidases as causal entities for low-oxygen growth."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "cbb3_oxidase",
            "predicate": "has function",
            "object": "high_affinity_terminal_oxidase",
            "description": "The cbb3 oxidase is an example high-affinity oxidase for microaerobic metabolism.",
            "evidence": [
              {
                "reference": "DOI:10.1042/BST0300653",
                "snippet": "characterized by its high oxygen affinity",
                "notes": "Supports cbb3 oxidase as a high-affinity oxygen-reducing enzyme."
              }
            ],
            "predicate_id": "RO:0000085"
          },
          {
            "subject": "cbb3_oxidase",
            "predicate": "enables",
            "object": "low_oxygen_respiration",
            "description": "cbb3-type cytochrome c oxidases are common in microaerophilic Proteobacteria and enable respiration under low O2.",
            "evidence": [
              {
                "reference": "DOI:10.3390/ijms24076428",
                "notes": "cbb3-type cytochrome c oxidases are common in microaerophilic Proteobacteria."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "cytochrome_bd_oxidase",
            "predicate": "enables",
            "object": "low_oxygen_respiration",
            "description": "Cytochrome bd quinol oxidases are widespread in low-oxygen-adapted organisms and enable respiration under low O2.",
            "evidence": [
              {
                "reference": "DOI:10.3390/ijms24076428",
                "notes": "bd-type quinol oxidases are widespread in bacteria and archaea that live under low-oxygen conditions."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "branched_respiratory_chain",
            "predicate": "enables",
            "object": "oxygen_adaptation",
            "description": "Branched respiratory chains enable microbes to adapt to fluctuating oxygen.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2024.1468929",
                "notes": "Branched respiratory chains enable microbes to adapt to fluctuating oxygen."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "catalase_kata",
            "predicate": "detoxifies",
            "object": "hydrogen_peroxide",
            "description": "Catalase prevents hydrogen peroxide accumulation.",
            "evidence": [
              {
                "reference": "DOI:10.3390/pathogens13100842",
                "notes": "katA encodes catalase that prevents H2O2 accumulation."
              }
            ]
          },
          {
            "subject": "superoxide_dismutase_sodb",
            "predicate": "protects against",
            "object": "reactive_oxygen_species",
            "description": "Superoxide dismutase protects against reactive oxygen species.",
            "evidence": [
              {
                "reference": "DOI:10.3390/pathogens13100842",
                "notes": "sodB encodes superoxide dismutase (SOD); it protects against ROS."
              }
            ]
          },
          {
            "subject": "ahpc",
            "predicate": "scavenges",
            "object": "hydrogen_peroxide",
            "description": "AhpC is the predominant hydrogen peroxide scavenger at low oxygen.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s12866-024-03201-y",
                "notes": "AhpC is considered the predominant H2O2 scavenger at low oxygen."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.850463+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-05T01:09:05-07:00",
        "curator": "codex",
        "action": "CURATED_WITH_LITERATURE",
        "changes": "Added definition source and evidence for low-oxygen growth requirement.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-05T18:39:46-07:00",
        "curator": "codex",
        "action": "ADDED_ORGANISM_EXAMPLE",
        "changes": "Added Campylobacter jejuni organism example with PMID-backed evidence.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "ADDED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed causal graph for microoxic respiration via high-affinity terminal oxidases.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:30Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002326\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:18Z",
        "curator": "claude",
        "action": "RENAME_PREDICATE_LABELS",
        "changes": "Renamed 1 causal-edge predicate label(s) to align with existing groundings: supports \u2192 enables \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:21Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-13T21:03:25Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0000085\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-17T04:09:43Z",
        "curator": "claude",
        "action": "REMOVE_REDUNDANT_SYNONYM",
        "changes": "Removed 1 synonym(s) whose text duplicated the label (seeder redundancy; no information lost).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 6 evidence-backed generic edges (9 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:10Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d73).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:30Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:16240\u00d71, CHEBI:26523\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-26T07:15:17Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A0N0XA94\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:21:11Z",
        "curator": "claude",
        "action": "RETRACT_DEAD_UNIPROT_GROUNDINGS",
        "changes": "Retracted 1 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:23:52Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 3 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0004096\u00d71, GO:0004784\u00d71, GO:0009321\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 1 causal edge(s) off enables/RO:0002327 with a TRAIT object (1 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope microaerophile_low_oxygen_respiration=NONMECHANISTIC with scope_notes; marked 3 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (high_affinity_terminal_oxidase, cbb3_oxidase, cytochrome_bd_oxidase).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000610",
    "label": "microaerotolerant",
    "definition": "An oxygen preference that tolerates low levels of molecular oxygen (O\u2082) without requiring it.",
    "definition_source": "DOI:10.1016/j.biortech.2011.02.011",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000601"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1016/j.biortech.2011.02.011",
        "snippet": "microaerotolerant or aerotolerant anaerobes can survive",
        "notes": "Supports microaerotolerance as survival under limited oxygen exposure."
      },
      {
        "reference": "PMID:30113300",
        "snippet": "The novel strain stains Gram-negative and Congo-red-negative and is characterized mesophilic, neutrophilic, chemoheterotrophic and microaerotolerant",
        "notes": "Organism example: Simulacricoccus ruber strain MCy10636 is described as microaerotolerant."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:2303410",
        "taxon_label": "Simulacricoccus ruber",
        "reference": "DOI:10.1099/ijsem.0.002936",
        "note": "The polyphasic species description explicitly characterizes type strain MCy10636 (DSM 106554; NCCB 100651) as microaerotolerant. It supports the organism-level trait assignment but is not used to universalize a molecular oxygen-defense mechanism."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "microaerotolerant_low_oxygen_defense",
        "title": "Microaerotolerant low-oxygen survival mechanism",
        "description": "Evidence-backed causal sketch linking microaerotolerance to limited oxygen exposure and oxidative stress defenses.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a broad environmental or morphological classification spanning multiple mechanisms, a measurement-like bin, or an absence/arrangement descriptor; contextual protein nodes do not receive token UniProt examples.",
        "nodes": [
          {
            "node_id": "microaerotolerant_trait",
            "label": "microaerotolerant",
            "node_type": "TRAIT",
            "grounding": "METPO:1000610",
            "description": "Tolerates low oxygen without requiring it."
          },
          {
            "node_id": "limited_oxygen_exposure",
            "label": "limited oxygen exposure",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Low-level oxygen exposure tolerated by microaerotolerant organisms."
          },
          {
            "node_id": "reactive_oxygen_species",
            "label": "reactive oxygen species",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:26523",
            "description": "Oxygen-derived oxidants."
          },
          {
            "node_id": "oxidative_stress_defense",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "oxidative stress defense enzymes",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Enzymes such as SOD, catalase, or peroxidase that mitigate ROS."
          },
          {
            "node_id": "anaerobic_growth",
            "label": "anaerobic growth",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Growth that does not require oxygen."
          },
          {
            "node_id": "intermediate_oxygen_level",
            "label": "intermediate oxygen level",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Sub-atmospheric, microoxic O2 concentration between anoxia and air."
          },
          {
            "node_id": "superoxide",
            "label": "superoxide",
            "node_type": "CHEMICAL",
            "description": "Superoxide radical anion, a reactive oxygen species.",
            "grounding": "CHEBI:18421"
          },
          {
            "node_id": "superoxide_reductase",
            "label": "superoxide reductase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Enzyme (SOR) that reduces superoxide to hydrogen peroxide.",
            "grounding": "GO:0050605"
          },
          {
            "node_id": "hydrogen_peroxide",
            "label": "hydrogen peroxide",
            "node_type": "CHEMICAL",
            "description": "H2O2, a reactive oxygen species generated during O2 exposure.",
            "grounding": "CHEBI:16240"
          },
          {
            "node_id": "rubrerythrin_peroxidase",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "rubrerythrin/peroxidase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Rubrerythrin and peroxidase enzymes that reduce H2O2 to water."
          },
          {
            "node_id": "reduced_electron_donors",
            "label": "reduced electron donors (NADH)",
            "node_type": "CHEMICAL",
            "description": "Reduced electron donors such as NADH that power ROS-detoxifying enzymes."
          },
          {
            "node_id": "gut_oxygen_gradient",
            "label": "gut lumen oxygen gradient",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Spatial O2 gradient in host gut, ~0.1-0.4% in lumen up to ~5% in tissues."
          },
          {
            "node_id": "low_oxygen_defense_systems",
            "label": "low-oxygen defense systems",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Cellular systems mitigating ROS and consuming O2 under low-oxygen exposure."
          }
        ],
        "edges": [
          {
            "subject": "limited_oxygen_exposure",
            "predicate": "tolerated by",
            "object": "microaerotolerant_trait",
            "description": "Microaerotolerant organisms survive limited oxygen exposure.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.biortech.2011.02.011",
                "snippet": "microaerotolerant or aerotolerant anaerobes can survive",
                "notes": "Supports low-oxygen survival as the defining trait context."
              }
            ]
          },
          {
            "subject": "microaerotolerant_trait",
            "predicate": "does not require",
            "object": "limited_oxygen_exposure",
            "description": "Microaerotolerance differs from microaerophily because oxygen is tolerated rather than required.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2970",
                "snippet": "Many obligate anaerobes tolerate transient or low levels of O2",
                "notes": "Supports low oxygen tolerance without implying oxygen requirement."
              }
            ]
          },
          {
            "subject": "limited_oxygen_exposure",
            "predicate": "can generate",
            "object": "reactive_oxygen_species",
            "description": "Oxygen exposure can create ROS stress that tolerant organisms must manage.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41579-021-00583-y",
                "snippet": "molecular oxygen and ROS",
                "notes": "Review links oxygen exposure with ROS stress."
              }
            ]
          },
          {
            "subject": "oxidative_stress_defense",
            "predicate": "mitigates",
            "object": "reactive_oxygen_species",
            "description": "ROS detoxification enzymes contribute to oxygen tolerance.",
            "evidence": [
              {
                "reference": "DOI:10.1128/iai.16.1.20-25.1977",
                "snippet": "oxygen tolerance of anaerobes is usually related to their level of SOD",
                "notes": "Supports antioxidant defense as a mechanism for oxygen tolerance."
              }
            ],
            "predicate_id": "METPO:2007407"
          },
          {
            "subject": "microaerotolerant_trait",
            "predicate": "compatible with",
            "object": "anaerobic_growth",
            "description": "Microaerotolerant organisms can remain anaerobic while surviving limited oxygen exposure.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.biortech.2011.02.011",
                "snippet": "microaerotolerant or aerotolerant anaerobes",
                "notes": "Supports microaerotolerance as an anaerobe oxygen-tolerance subtype."
              }
            ]
          },
          {
            "subject": "intermediate_oxygen_level",
            "predicate": "maximizes growth of",
            "object": "microaerotolerant_trait",
            "description": "Maximal growth of microaerotolerant cells often occurs at intermediate oxygen levels.",
            "evidence": [
              {
                "reference": "DOI:10.1128/CMR.00110-14",
                "notes": "Growth occurs in the presence or absence of oxygen; however, maximal growth occurs at intermediate oxygen levels."
              }
            ]
          },
          {
            "subject": "superoxide_reductase",
            "predicate": "reduces",
            "object": "superoxide",
            "description": "Superoxide reductase reduces superoxide (to hydrogen peroxide) using reduced electron donors.",
            "evidence": [
              {
                "reference": "DOI:10.1128/IAI.00502-24",
                "notes": "Review notes SOR reduces superoxide using electrons from donors like NADH."
              }
            ],
            "predicate_id": "METPO:2007802"
          },
          {
            "subject": "superoxide_reductase",
            "predicate": "produces",
            "object": "hydrogen_peroxide",
            "description": "Reduction of superoxide by SOR yields hydrogen peroxide.",
            "evidence": [
              {
                "reference": "DOI:10.1128/IAI.00502-24",
                "notes": "SOR reduces superoxide to H2O2 as part of the anaerobe oxygen-defense backbone."
              }
            ],
            "predicate_id": "METPO:2007800"
          },
          {
            "subject": "rubrerythrin_peroxidase",
            "predicate": "reduces",
            "object": "hydrogen_peroxide",
            "description": "Rubrerythrin/peroxidases reduce hydrogen peroxide to water.",
            "evidence": [
              {
                "reference": "DOI:10.1128/IAI.00502-24",
                "notes": "Review states Rbr/peroxidases reduce H2O2 to water."
              }
            ],
            "predicate_id": "METPO:2007802"
          },
          {
            "subject": "reduced_electron_donors",
            "predicate": "enables function of",
            "object": "oxidative_stress_defense",
            "description": "Protection by SOR/Rbr defenses depends on available reduced electron donors.",
            "evidence": [
              {
                "reference": "DOI:10.1128/IAI.00502-24",
                "notes": "The protection conferred by SOR/Rbr depends on available reduced electron donors."
              }
            ]
          },
          {
            "subject": "gut_oxygen_gradient",
            "predicate": "creates selection for",
            "object": "low_oxygen_defense_systems",
            "description": "Host gut oxygen gradients expose anaerobes to low O2, selecting for low-O2 defense systems.",
            "evidence": [
              {
                "reference": "DOI:10.1128/IAI.00502-24",
                "notes": "Gut O2 gradients (colon lumen 0.1-0.4% to ~5% in tissues) expose anaerobes to low O2 during colonization/inflammation."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.854338+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-05T01:09:05-07:00",
        "curator": "codex",
        "action": "CURATED_WITH_LITERATURE",
        "changes": "Added source-backed evidence for microaerotolerant oxygen exposure survival.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-05T18:39:46-07:00",
        "curator": "codex",
        "action": "ADDED_ORGANISM_EXAMPLE",
        "changes": "Added Simulacricoccus ruber organism example with PMID-backed evidence.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "ADDED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed causal graph for low-oxygen survival and oxidative stress defense in microaerotolerant organisms.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T21:30:06Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007407\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-17T04:09:43Z",
        "curator": "claude",
        "action": "REMOVE_REDUNDANT_SYNONYM",
        "changes": "Removed 1 synonym(s) whose text duplicated the label (seeder redundancy; no information lost).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 6 evidence-backed generic edges (8 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:10Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000017\u00d72, METPO:2000202\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:30Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:18421\u00d71, CHEBI:16240\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-26T07:15:17Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A090JWT2\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:21:11Z",
        "curator": "claude",
        "action": "RETRACT_DEAD_UNIPROT_GROUNDINGS",
        "changes": "Retracted 1 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:23:52Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0050605\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T02:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES_PART2",
        "changes": "Re-grounded 3 causal edge(s) off microbe-domain METPO predicates onto their causal-graph counterparts (1 to produces, 2 to reduces), issue 301 part 2. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Each replacement is a 1:1 mirror of its source predicate that changes only the domain, so the claim each edge makes is unchanged and directions are unchanged. The replacements are proposed in proposals/metpo_traitmech_v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope microaerotolerant_low_oxygen_defense=NONMECHANISTIC with scope_notes; marked 2 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (oxidative_stress_defense, rubrerythrin_peroxidase).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T10:54:11Z",
        "curator": "codex",
        "action": "ADD_CANONICAL_EXAMPLES",
        "changes": "Added Simulacricoccus ruber strain MCy10636 as the explicit organism-level microaerotolerant example in this record's own research artifact; verified NCBITaxon:2303410 and its current label against NCBI.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000623",
    "label": "moderately halophilic",
    "definition": "A halophily preference where growth and proliferation requires high levels of sodium chloride, usually above or about 0.2 M.",
    "definition_source": "PMID:9758852",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000629"
    ],
    "synonyms": [
      {
        "synonym_text": "moderate-halophilic",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "created_by": "Anthea Guo",
    "evidence": [
      {
        "reference": "PMID:9758852",
        "snippet": "moderately halophilic bacterium Halomonas elongata",
        "notes": "Organism example: Halomonas elongata is described as moderately halophilic."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:2746",
        "taxon_label": "Halomonas elongata",
        "note": "Well-established moderately halophilic gammaproteobacterium (ectoine model; type strain DSM 2581).",
        "reference": "PMID:20849449"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "moderate_halophile_compatible_solutes",
        "title": "Moderate halophile compatible-solute mechanism",
        "description": "Evidence-backed causal sketch linking moderate halophily to NaCl stress and compatible-solute osmoadaptation.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a broad environmental or morphological classification spanning multiple mechanisms, a measurement-like bin, or an absence/arrangement descriptor; contextual protein nodes do not receive token UniProt examples.",
        "nodes": [
          {
            "node_id": "moderately_halophilic_trait",
            "label": "moderately halophilic",
            "node_type": "TRAIT",
            "grounding": "METPO:1000623",
            "description": "Growth requires elevated but not saturated salt concentrations."
          },
          {
            "node_id": "elevated_nacl",
            "label": "elevated NaCl",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Moderate saline growth condition."
          },
          {
            "node_id": "osmotic_stress",
            "label": "osmotic stress",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Water activity and turgor challenge under saline conditions.",
            "grounding": "GO:0006970"
          },
          {
            "node_id": "ectoine",
            "label": "ectoine",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:27500",
            "description": "Compatible solute used by many halophilic bacteria."
          },
          {
            "node_id": "glycine_betaine",
            "label": "glycine betaine",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:17750",
            "description": "Compatible solute transported or accumulated for osmoprotection."
          },
          {
            "node_id": "compatible_solute_accumulation",
            "label": "compatible solute accumulation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Intracellular buildup of organic osmolytes for osmoadaptation."
          },
          {
            "node_id": "hydroxyectoine",
            "label": "hydroxyectoine",
            "node_type": "CHEMICAL",
            "description": "Hydroxylated derivative of ectoine acting as a compatible solute.",
            "grounding": "CHEBI:49432"
          },
          {
            "node_id": "ectd",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "EctD (ectoine hydroxylase)",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Ectoine hydroxylase converting ectoine to hydroxyectoine."
          },
          {
            "node_id": "bcct_transporters",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "BCCT transporters",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Betaine/carnitine/choline transporter family importing compatible solutes."
          },
          {
            "node_id": "teaabc_transporter",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "TeaABC TRAP transporter",
            "node_type": "GENE_OR_PROTEIN",
            "description": "TRAP transporter importing ectoine and hydroxyectoine."
          },
          {
            "node_id": "salt_out_strategy",
            "label": "salt-out (compatible-solute) strategy",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Osmoadaptation strategy relying on accumulation of small organic solutes."
          }
        ],
        "edges": [
          {
            "subject": "elevated_nacl",
            "predicate": "causes",
            "object": "osmotic_stress",
            "description": "Moderate NaCl elevation imposes osmotic stress that must be balanced for growth.",
            "evidence": [
              {
                "reference": "DOI:10.1371/journal.pone.0168818",
                "snippet": "cope with high salinities",
                "notes": "Halomonas elongata osmoregulation study supports high salinity as the stressor."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "ectoine",
            "predicate": "mitigates",
            "object": "osmotic_stress",
            "description": "Ectoine accumulation helps cells maintain osmotic balance at moderate salinity.",
            "evidence": [
              {
                "reference": "DOI:10.1371/journal.pone.0168818",
                "snippet": "synthesizes ectoine as its major compatible solute",
                "notes": "Supports ectoine as a compatible-solute mechanism in halophilic bacteria."
              }
            ],
            "predicate_id": "METPO:2007407"
          },
          {
            "subject": "glycine_betaine",
            "predicate": "mitigates",
            "object": "osmotic_stress",
            "description": "Glycine betaine uptake can contribute to bacterial osmoprotection.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuy009",
                "snippet": "glycine betaine uptake",
                "notes": "Review supports glycine betaine transport as an osmoadaptation route."
              }
            ],
            "predicate_id": "METPO:2007407"
          },
          {
            "subject": "ectoine",
            "predicate": "confers",
            "object": "moderately_halophilic_trait",
            "description": "Compatible-solute accumulation supports growth at elevated NaCl.",
            "evidence": [
              {
                "reference": "DOI:10.1371/journal.pone.0168818",
                "snippet": "allows microorganisms to cope with high salinities",
                "notes": "Supports compatible solutes as contributors to moderate halophily."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "elevated_nacl",
            "predicate": "selects for",
            "object": "moderately_halophilic_trait",
            "description": "Moderate halophiles grow best under elevated salinity.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuy009",
                "snippet": "Moderately halophilic bacteria",
                "notes": "Review identifies moderate halophiles as models for bacterial osmotic adaptation."
              }
            ],
            "predicate_id": "METPO:2007401"
          },
          {
            "subject": "osmotic_stress",
            "predicate": "induces",
            "object": "compatible_solute_accumulation",
            "description": "Osmotic stress under elevated NaCl induces accumulation of organic compatible solutes.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mmbr.62.2.504-544.1998",
                "notes": "Ventosa et al. 1998: organic compatible solutes (glycine betaine, ectoine, hydroxyectoine, amino acids) predominate in moderate halophiles."
              }
            ]
          },
          {
            "subject": "ectd",
            "predicate": "converts",
            "object": "hydroxyectoine",
            "description": "Ectoine hydroxylase EctD converts ectoine to hydroxyectoine, a generic ectoine-pathway step across halophiles.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s12934-021-01567-6",
                "notes": "Liu et al. 2021: EctD is the ectoine hydroxylase converting ectoine to hydroxyectoine."
              }
            ]
          },
          {
            "subject": "bcct_transporters",
            "predicate": "imports",
            "object": "glycine_betaine",
            "description": "BCCT-family carriers (BetT, BetP, OpuD) import compatible solutes such as glycine betaine.",
            "evidence": [
              {
                "reference": "DOI:10.58088/07hg-r941",
                "notes": "Lichty 2024: BCCT carriers (e.g., BetT, BetP, OpuD) import osmoprotectants."
              }
            ],
            "predicate_id": "METPO:2007805"
          },
          {
            "subject": "teaabc_transporter",
            "predicate": "imports",
            "object": "hydroxyectoine",
            "description": "TeaABC TRAP transporter imports ectoine and hydroxyectoine for osmoadaptation.",
            "evidence": [
              {
                "reference": "DOI:10.58088/07hg-r941",
                "notes": "Lichty 2024: TRAP systems (e.g., TeaABC) import ectoine and 5-hydroxyectoine."
              }
            ],
            "predicate_id": "METPO:2007805"
          },
          {
            "subject": "teaabc_transporter",
            "predicate": "imports",
            "object": "ectoine",
            "description": "TeaABC TRAP transporter imports ectoine for osmoadaptation.",
            "evidence": [
              {
                "reference": "DOI:10.58088/07hg-r941",
                "notes": "Lichty 2024: TRAP systems (e.g., TeaABC) import ectoine and 5-hydroxyectoine."
              }
            ],
            "predicate_id": "METPO:2007805"
          },
          {
            "subject": "salt_out_strategy",
            "predicate": "predominates in",
            "object": "moderately_halophilic_trait",
            "description": "The salt-out / compatible-solute strategy predominates among moderate halophiles.",
            "evidence": [
              {
                "reference": "DOI:10.3389/frmbi.2023.1329925",
                "notes": "Ionescu et al. 2024: 'salt-out' is more common among moderate halophiles and relies on accumulation of small organic compounds."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.862444+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-06T14:15:44-07:00",
        "curator": "codex",
        "action": "CURATED_WITH_ORGANISM_EXAMPLE",
        "changes": "Added Halomonas elongata organism example with PMID-backed evidence.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "ADDED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed causal graph for moderate halophile compatible-solute osmoadaptation.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:30Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T05:49:24Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:causes\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T21:30:06Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007407\u00d72, METPO:2007401\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:38:00Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0006970\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-17T04:09:43Z",
        "curator": "claude",
        "action": "REMOVE_REDUNDANT_SYNONYM",
        "changes": "Removed 1 synonym(s) whose text duplicated the label (seeder redundancy; no information lost).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 6 evidence-backed generic edges (6 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:10Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000208\u00d73).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:30Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:49432\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 1 causal edge(s) off enables/RO:0002327 with a TRAIT object (1 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T02:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES_PART2",
        "changes": "Re-grounded 3 causal edge(s) off microbe-domain METPO predicates onto their causal-graph counterparts (3 to imports), issue 301 part 2. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Each replacement is a 1:1 mirror of its source predicate that changes only the domain, so the claim each edge makes is unchanged and directions are unchanged. The replacements are proposed in proposals/metpo_traitmech_v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope moderate_halophile_compatible_solutes=NONMECHANISTIC with scope_notes; marked 3 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (ectd, bcct_transporters, teaabc_transporter).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000335",
    "label": "NaCl delta",
    "definition": "A salinity phenotype with numerical limits expressing the breadth (maximum minus minimum) of NaCl concentrations supporting growth of an organism.",
    "definition_source": "DOI:10.1093/femsre/fuy009",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000532",
      "METPO:1000534"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1093/femsre/fuy009",
        "snippet": "salinity range",
        "notes": "Osmoadaptation review supports the span of NaCl-tolerance as a halophily descriptor; its breadth (delta) reflects euryhaline versus stenohaline physiology."
      },
      {
        "reference": "DOI:10.1186/1746-1448-4-2",
        "snippet": "cope with the high salt concentrations",
        "notes": "Saline-Systems review supports broad osmoadaptive capacity as the basis of a wide NaCl-delta phenotype."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:735518",
        "taxon_label": "Lederbergia graminis",
        "reference": "DOI:10.1099/ijs.0.023820-0",
        "note": "The type strain, published as Bacillus graminis YC6957T, grew at 0-8% (w/v) NaCl. Its 8-point breadth meets a bin boundary, so #591 keeps this claim on the delta parent."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "nacl_delta_euryhaline_breadth",
        "title": "NaCl-delta euryhaline tolerance breadth",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a quantitative measurement, interval, or bin in the environmental phenotype hierarchy; a token protein example would misrepresent the measured value as one inherited molecular mechanism.",
        "description": "DOI-backed graph linking osmoadaptive flexibility to the breadth of the NaCl growth range (delta = max \u2212 min).",
        "nodes": [
          {
            "node_id": "nacl_delta_trait",
            "label": "NaCl delta",
            "node_type": "TRAIT",
            "grounding": "METPO:1000335",
            "description": "Breadth of the growth-supporting NaCl range."
          },
          {
            "node_id": "osmoadaptive_flexibility",
            "label": "osmoadaptive flexibility",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Capacity to remodel osmolyte pools and ion transport across a wide span of ambient salinities."
          },
          {
            "node_id": "euryhaline_physiology",
            "label": "euryhaline physiology",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Physiology supporting growth over a broad salinity range."
          },
          {
            "node_id": "tolerance_breadth",
            "label": "tolerance breadth",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Span between the minimum and maximum growth-supporting NaCl."
          },
          {
            "node_id": "hyperosmotic_upshift",
            "label": "hyperosmotic upshift",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "A rise in ambient NaCl/osmolarity imposing osmotic stress."
          },
          {
            "node_id": "potassium_uptake",
            "label": "potassium ion uptake",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Rapid import of K+ as the principal cytoplasmic cation during osmotic upshift.",
            "grounding": "GO:1990573"
          },
          {
            "node_id": "osmoadaptation",
            "label": "response to osmotic stress",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Cellular adjustment of osmolyte and ion pools in response to osmotic stress.",
            "grounding": "GO:0006970"
          },
          {
            "node_id": "compatible_solute_accumulation",
            "label": "compatible solute accumulation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Accumulation or synthesis of neutral compatible solutes (glycine betaine, trehalose, ectoine, proline)."
          },
          {
            "node_id": "salt_out_strategy",
            "label": "salt-out strategy",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Osmoadaptation by excluding Na+ while accumulating organic compatible solutes."
          },
          {
            "node_id": "salt_in_strategy",
            "label": "salt-in strategy",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Osmoadaptation by accumulating intracellular KCl matching environmental salinity, favored at very high salt.",
            "grounding": "METPO:1007720"
          },
          {
            "node_id": "high_maximal_nacl_tolerance",
            "label": "high maximal NaCl tolerance",
            "node_type": "QUALITY",
            "description": "Capacity to grow at very high, near-saturating NaCl concentrations."
          },
          {
            "node_id": "mechanosensitive_channels",
            "label": "mechanosensitive channels (MscL/MscS)",
            "node_type": "GENE_OR_PROTEIN",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed as a contextual protein or protein-complex label within a quantitative measurement graph; no exact semantic family term was established for this aggregate use.",
            "description": "Membrane safety-valve channels releasing solutes during sudden hypoosmotic shocks."
          },
          {
            "node_id": "hypoosmotic_shock",
            "label": "hypoosmotic shock",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "A sudden drop in ambient salinity causing turgor stress."
          }
        ],
        "edges": [
          {
            "subject": "osmoadaptive_flexibility",
            "predicate": "enables",
            "object": "euryhaline_physiology",
            "description": "Osmoadaptive flexibility enables euryhaline growth.",
            "evidence": [
              {
                "reference": "DOI:10.1186/1746-1448-4-2",
                "snippet": "cope with the high salt concentrations",
                "notes": "Supports osmoadaptive flexibility as the basis of broad-salinity growth."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "euryhaline_physiology",
            "predicate": "has output",
            "object": "tolerance_breadth",
            "description": "Euryhaline physiology produces a wide growth-supporting NaCl range.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuy009",
                "snippet": "salinity range",
                "notes": "Supports the link between osmoadaptive physiology and tolerance breadth."
              }
            ],
            "predicate_id": "RO:0002234"
          },
          {
            "subject": "tolerance_breadth",
            "predicate": "manifests as",
            "object": "nacl_delta_trait",
            "description": "The breadth between minimum and maximum growth-supporting NaCl manifests the NaCl-delta phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuy009",
                "snippet": "salinity range",
                "notes": "Supports the trait endpoint."
              }
            ],
            "predicate_id": "METPO:2007400"
          },
          {
            "subject": "compatible_solute_accumulation",
            "predicate": "enables",
            "object": "osmoadaptation",
            "description": "Compatible-solute uptake or synthesis enables osmoadaptation after an osmotic upshift.",
            "evidence": [
              {
                "reference": "DOI:10.1371/journal.pgen.1007574",
                "snippet": "secondary response involving uptake or synthesis of compatible solutes",
                "notes": "Verified against the open Pham et al. introduction; compatible-solute uptake and synthesis are retained as a broad bacterial osmotic-upshift response."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "hyperosmotic_upshift",
            "predicate": "causes",
            "object": "potassium_uptake",
            "description": "Hyperosmotic upshift triggers rapid K+ import as an early osmoadaptive response.",
            "evidence": [
              {
                "reference": "DOI:10.1371/journal.pgen.1007574",
                "snippet": "In response to an osmotic upshift (hyperosmotic stress), bacteria import potassium ions",
                "notes": "Verified against the open Pham et al. introduction; K+ uptake is retained as the immediate bacterial response to hyperosmotic stress."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "potassium_uptake",
            "predicate": "contributes to",
            "object": "osmoadaptation",
            "description": "K+ accumulation is a core early osmoadaptive response to increased NaCl.",
            "evidence": [
              {
                "reference": "DOI:10.1371/journal.pgen.1007574",
                "snippet": "This allows the cell to limit the loss of water and maintain turgor",
                "notes": "Verified against the open Pham et al. introduction; the early K+ import and later compatible-solute response are framed as limiting water loss and maintaining turgor."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "compatible_solute_accumulation",
            "predicate": "part of",
            "object": "salt_out_strategy",
            "description": "Compatible-solute import or synthesis is part of the salt-out osmoadaptation strategy.",
            "evidence": [
              {
                "reference": "DOI:10.3390/microorganisms12081738",
                "snippet": "The second phase starts with the import or de novo synthesis of the compatible solute",
                "notes": "Verified against public Bonnaud et al. text; the edge is reversed to ground the component-process relation."
              }
            ],
            "predicate_id": "biolink:part_of"
          },
          {
            "subject": "salt_in_strategy",
            "predicate": "contributes to",
            "object": "high_maximal_nacl_tolerance",
            "description": "The salt-in strategy contributes to growth under very high ambient NaCl in haloarchaeal lineages.",
            "evidence": [
              {
                "reference": "DOI:10.3390/microorganisms12081738",
                "snippet": "haloarchaea favors the salt-in strategy at high salt concentrations in the medium",
                "notes": "Verified against public Bonnaud et al. text; salt-in is retained as a high-salt osmoadaptation strategy, not as a direct determinant of an exact NaCl-delta interval."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "mechanosensitive_channels",
            "predicate": "mitigates",
            "object": "hypoosmotic_shock",
            "description": "Mechanosensitive channels mitigate turgor stress during sudden hypoosmotic shocks at the low-salinity end of the range.",
            "evidence": [
              {
                "reference": "DOI:10.3390/microorganisms12081738",
                "snippet": "mechanosensitive channels, which serve as safety valves",
                "notes": "Verified against public Bonnaud et al. text; the broad MscL/MscS label is kept reviewed-label-only in this nonmechanistic quantitative graph."
              }
            ],
            "predicate_id": "METPO:2007407"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.816534+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-12T10:00:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed causal graph linking osmoadaptive flexibility and euryhaline physiology to the NaCl-delta breadth phenotype.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:30Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d71, METPO:2000202\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T21:30:06Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007400\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 6 evidence-backed generic edges (9 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:10Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d71, biolink:causes\u00d71, RO:0002326\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:17Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (METPO:1007720\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:1990573\u00d71, GO:0006970\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates (1 to has output), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-16T02:00:00Z",
        "curator": "claude",
        "action": "NORMALISE_NODE_TYPE",
        "changes": "Under the PATHWAY-vs-BIOLOGICAL_PROCESS rule, one node_id means one thing corpus-wide (issue 356): salt_in_strategy is typed BIOLOGICAL_PROCESS. PATHWAY is a named, conventionally enumerable multi-step route; BIOLOGICAL_PROCESS is everything else. A STRATEGY, not a route. The family is described as osmoadaptation by accumulating intracellular inorganic ions -- haloalkaliphilic.yaml puts it as 'Osmoadaptation by intracellular accumulation of inorganic ions (e.g. K+)', and the wording varies by record. There is no step list to enumerate, which is exactly the distinction this rule draws. Was 7 BIOLOGICAL_PROCESS to 1 before this tranche.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope nacl_delta_euryhaline_breadth=NONMECHANISTIC with scope_notes; marked 1 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (mechanosensitive_channels).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T04:43:24Z",
        "curator": "codex",
        "action": "ADD_CANONICAL_EXAMPLES",
        "changes": "Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Lederbergia graminis (NCBITaxon:735518; DOI:10.1099/ijs.0.023820-0). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-04T07:20:00Z",
        "curator": "codex",
        "action": "REVIEW_CAUSAL_EVIDENCE",
        "changes": "Reviewed the nacl_delta_euryhaline_breadth graph for issue #183: added exact snippets to 6 causal-edge evidence items, grounded 3 residual predicates, and preserved the graph as a nonmechanistic quantitative NaCl-range-breadth classification. No paid research service was called.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000482",
    "label": "NaCl delta high",
    "definition": "A NaCl delta phenotype with a growth-supporting NaCl breadth above approximately 8% (w/v), characteristic of extreme-euryhaline organisms.",
    "definition_source": "DOI:10.1093/femsre/fuy009",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000335"
    ],
    "synonyms": [
      {
        "synonym_text": "Nad_>8",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1093/femsre/fuy009",
        "snippet": "salinity range",
        "notes": "Osmoadaptation review supports very wide salinity-tolerance breadths as the extreme-euryhaline phenotype."
      },
      {
        "reference": "DOI:10.1186/1746-1448-4-2",
        "snippet": "cope with the high salt concentrations",
        "notes": "Saline-Systems review supports combined osmolyte / salt-in flexibility as the basis of very wide salinity tolerance."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:75750",
        "taxon_label": "Aspergillus sydowii",
        "reference": "DOI:10.3389/fmicb.2022.840408",
        "note": "The artifact's strongest illustrative phenotype for extreme euryhalinity: grows from no added NaCl up to saturated (5.13 M) NaCl, noting growth at saturation is weak. The cited multi-omics study establishes growth at 1 M and at saturated NaCl; even that conservatively evidenced interval spans roughly 24 percentage points w/v, far above the ~8% (w/v) bin threshold."
      },
      {
        "taxon_id": "NCBITaxon:245174",
        "taxon_label": "Wallemia ichthyophaga",
        "reference": "DOI:10.1128/aem.02702-13",
        "note": "Measured NaCl growth range of 10% to saturated (~32% w/v) with a 15-20% optimum, a ~22% (w/v) breadth, from the osmoadaptation study that also quantified salinity-dependent glycerol accumulation. The artifact flags the high lower bound as obligate halophily, which its own boundary rules permit alongside this trait when the measured interval is wide enough."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "nacl_delta_high_extreme_euryhaline",
        "title": "NaCl-delta-high extreme-euryhaline breadth",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a quantitative measurement, interval, or bin in the environmental phenotype hierarchy; a token protein example would misrepresent the measured value as one inherited molecular mechanism.",
        "description": "DOI-backed graph linking maximal osmoadaptive flexibility to NaCl growth breadths exceeding 8% (w/v).",
        "nodes": [
          {
            "node_id": "nacl_delta_high_trait",
            "label": "NaCl delta high",
            "node_type": "TRAIT",
            "grounding": "METPO:1000482",
            "description": "NaCl growth-supporting breadth exceeding ~8% w/v."
          },
          {
            "node_id": "nacl_delta",
            "label": "NaCl delta",
            "node_type": "TRAIT",
            "grounding": "METPO:1000335",
            "description": "Breadth of the growth-supporting NaCl range."
          },
          {
            "node_id": "maximal_osmoadaptive_flexibility",
            "label": "maximal osmoadaptive flexibility",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Combined osmolyte-remodeling and salt-in capacity supporting growth across an extreme salinity span."
          },
          {
            "node_id": "high_external_salinity",
            "label": "high external salinity",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Elevated extracellular NaCl/salt concentration imposing osmotic stress."
          },
          {
            "node_id": "compatible_solute_accumulation",
            "label": "compatible-solute accumulation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Intracellular accumulation of compatible solutes (e.g. glycine betaine, glutamate, proline) with rising salinity."
          },
          {
            "node_id": "intracellular_k_accumulation",
            "label": "intracellular K+ accumulation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Cytoplasmic accumulation of potassium ions as part of osmoadaptation."
          },
          {
            "node_id": "salt_in_osmoadaptation",
            "label": "salt-in osmoadaptation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Salt-in strategy maintaining high intracellular ion concentrations to balance external salinity."
          },
          {
            "node_id": "acidic_proteome",
            "label": "acidic proteome",
            "node_type": "QUALITY",
            "description": "Proteome-wide bias toward low isoelectric points, a hallmark of salt-in extreme halophily."
          },
          {
            "node_id": "salinity_transition",
            "label": "salinity transition across biomes",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Evolutionary shift in environmental salinity across biomes."
          },
          {
            "node_id": "proteome_reorganization",
            "label": "proteome reorganization",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Systematic shifts in amino-acid composition and isoelectric-point distributions accompanying salinity change."
          },
          {
            "node_id": "hybrid_salt_osmoregulation",
            "label": "hybrid salt-in/salt-out osmoregulation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Genomic capacity for both salt-in and salt-out strategies enabling response to variable salinity."
          },
          {
            "node_id": "fluctuating_salinity_environment",
            "label": "fluctuating salinity environment",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Habitat with strongly varying salinity over time."
          },
          {
            "node_id": "hypersaline_environment",
            "label": "hypersaline environment",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Environment containing >100-150 g/L salts."
          },
          {
            "node_id": "halophilic_osmoadaptation",
            "label": "halophilic osmoadaptation strategies",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Suite of osmoadaptation strategies selected for in hypersaline conditions."
          }
        ],
        "edges": [
          {
            "subject": "maximal_osmoadaptive_flexibility",
            "predicate": "confers",
            "object": "nacl_delta_high_trait",
            "description": "Maximal osmoadaptive flexibility yields an extreme NaCl-delta breadth.",
            "evidence": [
              {
                "reference": "DOI:10.1186/1746-1448-4-2",
                "snippet": "cope with the high salt concentrations",
                "notes": "Supports maximal osmoadaptive flexibility as the basis of extreme euryhalinity."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "nacl_delta_high_trait",
            "predicate": "is a",
            "object": "nacl_delta",
            "description": "NaCl delta high is a quantitative bin of the NaCl-delta phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuy009",
                "snippet": "salinity range",
                "notes": "Supports >8% breadth as a value within the NaCl-delta distribution."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "high_external_salinity",
            "predicate": "increases",
            "object": "compatible_solute_accumulation",
            "description": "Rising external salinity increases intracellular compatible-solute content.",
            "evidence": [
              {
                "reference": "DOI:10.1128/aem.00145-24",
                "notes": "Intracellular content of compatible solutes (glycine betaine, glutamate, proline) increases with rising salinity levels."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "intracellular_k_accumulation",
            "predicate": "supports",
            "object": "salt_in_osmoadaptation",
            "description": "Cytoplasmic K+ accumulation supports the salt-in osmoadaptation strategy.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41559-024-02505-6",
                "notes": "Halophiles accumulate up to 4 M K+ in their cytoplasm as part of a salt-in strategy; concept-level edge across taxa."
              }
            ]
          },
          {
            "subject": "salt_in_osmoadaptation",
            "predicate": "associated with",
            "object": "acidic_proteome",
            "description": "The salt-in strategy is associated with an acidic, low-pI proteome.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41559-024-02505-6",
                "notes": "Proteome acidification is a hallmark of extreme halophily; median protein isoelectric points <=4.4."
              }
            ],
            "predicate_id": "biolink:associated_with"
          },
          {
            "subject": "salinity_transition",
            "predicate": "drives",
            "object": "proteome_reorganization",
            "description": "Salinity transitions across biomes drive proteome reorganization and pI shifts.",
            "evidence": [
              {
                "reference": "DOI:10.1126/sciadv.adg2059",
                "notes": "Transitions accompanied by systematic changes in amino acid composition and isoelectric point distributions."
              }
            ]
          },
          {
            "subject": "hybrid_salt_osmoregulation",
            "predicate": "supports survival in",
            "object": "fluctuating_salinity_environment",
            "description": "Hybrid salt-in/salt-out osmoregulation supports survival across fluctuating salinity.",
            "evidence": [
              {
                "reference": "DOI:10.3389/frmbi.2023.1329925",
                "notes": "MAGs contain genes for both the cheaper salt-in and more expensive salt-out strategies."
              }
            ]
          },
          {
            "subject": "hypersaline_environment",
            "predicate": "selects for",
            "object": "halophilic_osmoadaptation",
            "description": "Hypersaline environments select for halophilic osmoadaptation strategies.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s44185-024-00050-w",
                "notes": "Hypersaline environments containing >100-150 g/L salts; halophiles grow at >100-150 g/L."
              }
            ],
            "predicate_id": "METPO:2007401"
          },
          {
            "subject": "compatible_solute_accumulation",
            "predicate": "part of",
            "object": "halophilic_osmoadaptation",
            "description": "Compatible-solute accumulation is one of the major halophilic osmoadaptation strategies.",
            "evidence": [
              {
                "reference": "DOI:10.1186/1746-1448-4-2",
                "snippet": "organic-solutes-in strategy",
                "notes": "The review identifies synthesis or accumulation of organic compatible solutes as a general strategy used by halophilic microorganisms."
              }
            ],
            "predicate_id": "biolink:part_of"
          },
          {
            "subject": "salt_in_osmoadaptation",
            "predicate": "part of",
            "object": "halophilic_osmoadaptation",
            "description": "Salt-in osmoadaptation is one of the major halophilic osmoadaptation strategies.",
            "evidence": [
              {
                "reference": "DOI:10.1186/1746-1448-4-2",
                "snippet": "molar concentrations of KCl",
                "notes": "The review identifies intracellular KCl accumulation as a general strategy for osmotic balance in halophilic microorganisms."
              }
            ],
            "predicate_id": "biolink:part_of"
          },
          {
            "subject": "salt_in_osmoadaptation",
            "predicate": "part of",
            "object": "hybrid_salt_osmoregulation",
            "description": "The salt-in strategy is one constituent of hybrid salt-in/salt-out osmoregulation.",
            "evidence": [
              {
                "reference": "DOI:10.3389/frmbi.2023.1329925",
                "snippet": "not mutually exclusive",
                "notes": "The Dead Sea biofilm study concludes that salt-in and salt-out strategies can operate together in bacteria exposed to salinity fluctuations."
              }
            ],
            "predicate_id": "biolink:part_of"
          },
          {
            "subject": "proteome_reorganization",
            "predicate": "part of",
            "object": "halophilic_osmoadaptation",
            "description": "Long-term proteome reorganization is part of evolutionary adaptation across aquatic salinity transitions.",
            "evidence": [
              {
                "reference": "DOI:10.1126/sciadv.adg2059",
                "snippet": "isoelectric point distributions",
                "notes": "Cross-biome transitions are accompanied by systematic shifts in proteome amino-acid composition and inferred-proteome pI distributions."
              }
            ],
            "predicate_id": "biolink:part_of"
          },
          {
            "subject": "hybrid_salt_osmoregulation",
            "predicate": "contributes to",
            "object": "maximal_osmoadaptive_flexibility",
            "description": "Combining salt-in and salt-out responses contributes to flexibility under rapid, extreme salinity changes.",
            "evidence": [
              {
                "reference": "DOI:10.3389/frmbi.2023.1329925",
                "snippet": "cope with such atypical changes",
                "notes": "The study links simultaneous ion transport and compatible-solute responses to bacteria inhabiting a rapidly fluctuating salinity environment."
              }
            ],
            "predicate_id": "RO:0002326"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.842691+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-12T10:00:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed definition and causal graph linking maximal osmoadaptive flexibility to the extreme-euryhaline NaCl-delta bin.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:30Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d71, rdfs:subClassOf\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 6 evidence-backed generic edges (11 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:10Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002213\u00d71, biolink:associated_with\u00d71, METPO:2007401\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates (1 to confers), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-20T08:00:00Z",
        "curator": "claude",
        "action": "BACKFILL_CANONICAL_EXAMPLES",
        "changes": "Added two exemplar taxa whose measured NaCl growth intervals exceed the ~8% (w/v) breadth threshold. Taxon ids resolved and label-checked against the local NCBITaxon build; references taken from this trait's own deep-research artifact. Deliberately excluded, per that artifact's own boundary rules -- Natranaerobius thermophilus and Euplaesiobystra salpumilio (breadth reported in total Na+ / PSU, where the artifact's boundary rules require \"avoiding unjustified conversion to NaCl w/v\"); Debaryomyces hansenii (upper tolerance only, no measured lower bound, and tolerance is not growth); Halomonas elongata and Virgibacillus dokdonensis (assay salinities and genomic osmoadaptation potential, not a reported growth interval); and Hortaea werneckii and Aureobasidium pullulans (wide ranges quoted, but the artifact attributes them only to \"the same paper\" and does not disambiguate which of its two co-cited sources measured them).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope nacl_delta_high_extreme_euryhaline=NONMECHANISTIC with scope_notes.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T10:44:05Z",
        "curator": "codex",
        "action": "CONNECT_CAUSAL_GRAPH",
        "changes": "Connected the five source-supported osmoadaptation components to the existing extreme-euryhaline graph core (issues 426 and 183). Preserved the record as a measured NaCl growth-breadth bin; generic salt mechanisms do not directly establish the high-breadth trait, and no gene or operon was promoted to a primary entry.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000479",
    "label": "NaCl delta low",
    "definition": "A NaCl delta phenotype with a narrow growth-supporting NaCl breadth of at most approximately 1% (w/v), characteristic of stenohaline organisms.",
    "definition_source": "DOI:10.1093/femsre/fuy009",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000335"
    ],
    "synonyms": [
      {
        "synonym_text": "Nad_<=1",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1093/femsre/fuy009",
        "snippet": "salinity range",
        "notes": "Osmoadaptation review supports narrow salinity-tolerance breadths as the stenohaline phenotype, contrasted with euryhaline organisms."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:575322",
        "taxon_label": "Sphingomonas oligoaromativorans",
        "reference": "DOI:10.1099/ijs.0.052894-0",
        "note": "Sphingomonas oligoaromativorans SY-6T grew from 0 to 0.5% (w/v) NaCl, a directly reported 0.5-point breadth wholly within the at-most-1% delta bin."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "nacl_delta_low_stenohaline",
        "title": "NaCl-delta-low stenohaline breadth",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a quantitative measurement, interval, or bin in the environmental phenotype hierarchy; a token protein example would misrepresent the measured value as one inherited molecular mechanism.",
        "description": "DOI-backed graph linking limited osmoadaptive flexibility to a narrow NaCl growth breadth (\u2264 ~1% w/v).",
        "nodes": [
          {
            "node_id": "nacl_delta_low_trait",
            "label": "NaCl delta low",
            "node_type": "TRAIT",
            "grounding": "METPO:1000479",
            "description": "NaCl growth-supporting breadth \u2264 ~1% w/v."
          },
          {
            "node_id": "nacl_delta",
            "label": "NaCl delta",
            "node_type": "TRAIT",
            "grounding": "METPO:1000335",
            "description": "Breadth of the growth-supporting NaCl range."
          },
          {
            "node_id": "limited_osmoadaptive_flexibility",
            "label": "limited osmoadaptive flexibility",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Narrow capacity to remodel osmolyte pools and ion transport across ambient salinities."
          },
          {
            "node_id": "ectoine_biosynthesis",
            "label": "ectoine biosynthesis capacity",
            "node_type": "PATHWAY",
            "description": "Capacity to synthesize ectoine as a major compatible solute under salt stress."
          },
          {
            "node_id": "compatible_solute_transporters",
            "label": "compatible-solute transporters (Opu/ProU)",
            "node_type": "GENE_OR_PROTEIN",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed as a contextual protein or protein-complex label within a quantitative measurement graph; no exact semantic family term was established for this aggregate use.",
            "description": "Opu/ProU-family uptake systems importing compatible solutes during osmoadaptation."
          },
          {
            "node_id": "trkh_k_uptake",
            "label": "TrkH potassium uptake system",
            "node_type": "GENE_OR_PROTEIN",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed as a contextual protein or protein-complex label within a quantitative measurement graph; no exact semantic family term was established for this aggregate use.",
            "description": "TrkH-type K+ uptake transporter supporting intracellular potassium homeostasis under salt stress."
          },
          {
            "node_id": "nhac_antiporter",
            "label": "NhaC-family Na+/H+ antiporter",
            "node_type": "GENE_OR_PROTEIN",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed as a contextual protein or protein-complex label within a quantitative measurement graph; no exact semantic family term was established for this aggregate use.",
            "description": "NhaC-family Na+/H+ antiporters mediating ion homeostasis under salt stress."
          },
          {
            "node_id": "intracellular_proline",
            "label": "intracellular proline accumulation",
            "node_type": "CHEMICAL",
            "description": "Accumulation of proline as a compatible solute supporting growth at higher NaCl."
          }
        ],
        "edges": [
          {
            "subject": "limited_osmoadaptive_flexibility",
            "predicate": "confers",
            "object": "nacl_delta_low_trait",
            "description": "Limited osmoadaptive flexibility yields a narrow NaCl-delta breadth.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuy009",
                "snippet": "salinity range",
                "notes": "Supports limited osmoadaptive flexibility as the basis of stenohaline breadth."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "nacl_delta_low_trait",
            "predicate": "is a",
            "object": "nacl_delta",
            "description": "NaCl delta low is a quantitative bin of the NaCl-delta phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuy009",
                "snippet": "salinity range",
                "notes": "Supports a narrow breadth as a value within the NaCl-delta distribution."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "ectoine_biosynthesis",
            "predicate": "supports",
            "object": "nacl_delta",
            "description": "Ectoine biosynthesis capacity broadens NaCl tolerance; its loss narrows the growth range.",
            "evidence": [
              {
                "reference": "DOI:10.1128/aem.01905-23",
                "notes": "Wild-type H. elongata synthesizes ectoine as a major osmolyte, whereas ectoine-deficient strains become salt sensitive; supports general role of ectoine pathway in broadening NaCl tolerance."
              }
            ]
          },
          {
            "subject": "compatible_solute_transporters",
            "predicate": "supports",
            "object": "limited_osmoadaptive_flexibility",
            "description": "Salinity-induced Opu/ProU compatible-solute transporters underlie osmoadaptive flexibility; limited capacity contributes to narrow breadth.",
            "evidence": [
              {
                "reference": "DOI:10.1128/aem.00145-24",
                "notes": "Proteomics showed salinity-linked increases in compatible-solute transporters (opuAC, proX/proV/proW) supporting osmoadaptation."
              }
            ]
          },
          {
            "subject": "trkh_k_uptake",
            "predicate": "supports",
            "object": "nacl_delta",
            "description": "TrkH K+ uptake supports intracellular K+ homeostasis enabling salt tolerance; its absence may contribute to narrow breadth.",
            "evidence": [
              {
                "reference": "DOI:10.1128/aem.00145-24",
                "notes": "TrkH listed among salinity-responsive proteins; simultaneous accumulation of compatible solutes and K+ supports salt adaptation."
              }
            ]
          },
          {
            "subject": "nhac_antiporter",
            "predicate": "supports",
            "object": "nacl_delta",
            "description": "NhaC Na+/H+ antiporters support ion homeostasis under salt stress; a candidate breadth-expanding mechanism whose absence may contribute to NaCl delta low.",
            "evidence": [
              {
                "reference": "DOI:10.1128/aem.00145-24",
                "notes": "Proteomics show strong salinity-linked increases for NhaC-family antiporters (~3.27 and 3.22-fold)."
              }
            ]
          },
          {
            "subject": "intracellular_proline",
            "predicate": "supports",
            "object": "nacl_delta",
            "description": "Increased intracellular proline as a compatible solute supports growth at higher NaCl, broadening tolerance.",
            "evidence": [
              {
                "reference": "DOI:10.1128/aem.01195-24",
                "notes": "Engineered proline biosynthesis with blocked catabolism increased intracellular proline and restored growth at 8% NaCl; supports osmolyte role of proline in salt-tolerance breadth."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.840753+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-12T10:00:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed definition and causal graph linking limited osmoadaptive flexibility to the stenohaline NaCl-delta bin.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:30Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d71, rdfs:subClassOf\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 6 evidence-backed generic edges (6 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:10Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (rdfs:subClassOf\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates (1 to confers), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-08T05:00:00Z",
        "curator": "claude",
        "action": "MERGE_CAUSAL_NODE",
        "changes": "Merged node salt_tolerance_breadth into nacl_delta and repointed its edges. Issue 352. A FIFTH restatement, caught in review (#360). 'Capacity to grow across a range of ambient NaCl concentrations' against nacl_delta's 'Breadth of the growth-supporting NaCl range' -- the same claim, and nacl_delta is in the same graph already TRAIT and already grounded METPO:1000335. I had retyped it and grounded it METPO:1000622 (halotolerant), which is a DEGREE of tolerance, not a breadth: 1000622 is a halophily preference (sub 1000629) while 1000335 is a delta (sub 1000532/1000534), so the node's existing `is a -> nacl_delta` edge asserted halotolerant sub NaCl delta, a subsumption METPO does not have. The absolute-vs-breadth distinction this migration insists on for pH, missed for salt.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-16T02:00:00Z",
        "curator": "claude",
        "action": "NORMALISE_NODE_TYPE",
        "changes": "Under the PATHWAY-vs-BIOLOGICAL_PROCESS rule, one node_id means one thing corpus-wide (issue 356): ectoine_biosynthesis is typed PATHWAY. PATHWAY is a named, conventionally enumerable multi-step route; BIOLOGICAL_PROCESS is everything else. A named route, enumerated two ways and both of them enumerations. environment/euryhaline.yaml counts five steps from L-aspartate (lysC/asd/ectB/ectA/ectC); environment/nacl_delta_mid1.yaml counts the three ectABC enzymes proper. Naming the file matters because the two differ and a bare quote would put euryhaline's wording into nacl_delta_mid1's record (#400 review). Either way the steps can be listed, which is the test. Applied AGAINST the majority, which was 4 BIOLOGICAL_PROCESS to 2 before this tranche.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope nacl_delta_low_stenohaline=NONMECHANISTIC with scope_notes; marked 3 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (compatible_solute_transporters, trkh_k_uptake, nhac_antiporter).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T04:43:24Z",
        "curator": "codex",
        "action": "ADD_CANONICAL_EXAMPLES",
        "changes": "Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Sphingomonas oligoaromativorans (NCBITaxon:575322; DOI:10.1099/ijs.0.052894-0). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000480",
    "label": "NaCl delta mid1",
    "definition": "A NaCl delta phenotype with a growth-supporting NaCl breadth of approximately 1\u20133% (w/v), characteristic of organisms with modest salinity tolerance breadth.",
    "definition_source": "DOI:10.1093/femsre/fuy009",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000335"
    ],
    "synonyms": [
      {
        "synonym_text": "Nad_1_3",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1093/femsre/fuy009",
        "snippet": "salinity range",
        "notes": "Osmoadaptation review supports intermediate breadths as common among osmoadaptive bacteria."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1182451",
        "taxon_label": "Aureivirga marina",
        "reference": "DOI:10.1099/ijs.0.043257-0",
        "note": "Aureivirga marina strain VI.14 grew from 3 to 5% (w/v) NaCl, a 2-point breadth wholly inside the approximately 1-3% delta bin."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "nacl_delta_mid1_modest_breadth",
        "title": "NaCl-delta-mid1 modest-breadth osmoadaptation",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a quantitative measurement, interval, or bin in the environmental phenotype hierarchy; a token protein example would misrepresent the measured value as one inherited molecular mechanism.",
        "description": "DOI-backed graph linking modest osmoadaptive flexibility to a 1\u20133% (w/v) NaCl growth breadth.",
        "nodes": [
          {
            "node_id": "nacl_delta_mid1_trait",
            "label": "NaCl delta mid1",
            "node_type": "TRAIT",
            "grounding": "METPO:1000480",
            "description": "NaCl growth-supporting breadth approximately 1\u20133% w/v."
          },
          {
            "node_id": "nacl_delta",
            "label": "NaCl delta",
            "node_type": "TRAIT",
            "grounding": "METPO:1000335",
            "description": "Breadth of the growth-supporting NaCl range."
          },
          {
            "node_id": "modest_osmoadaptive_flexibility",
            "label": "modest osmoadaptive flexibility",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Moderate capacity to remodel osmolytes across ambient salinity shifts."
          },
          {
            "node_id": "osmotic_upshift",
            "label": "osmotic upshift",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Sudden increase in external osmolarity (e.g. NaCl) imposing hyperosmotic stress."
          },
          {
            "node_id": "k_import",
            "label": "potassium import",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Rapid cytoplasmic accumulation of K+ as a first-line osmoadaptive response.",
            "grounding": "GO:1990573"
          },
          {
            "node_id": "compatible_solute_accumulation",
            "label": "compatible solute accumulation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Accumulation/synthesis of neutral organic osmolytes (glycine betaine, proline, trehalose, ectoine, carnitine)."
          },
          {
            "node_id": "osmoadaptation_under_nacl",
            "label": "osmoadaptation / growth under NaCl stress",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Maintenance of turgor, protein and membrane stability, and growth across NaCl stress."
          },
          {
            "node_id": "ectoine_biosynthesis",
            "label": "ectoine biosynthesis (EctB/EctA/EctC)",
            "node_type": "PATHWAY",
            "description": "Three-enzyme biosynthetic pathway producing the compatible solute ectoine."
          },
          {
            "node_id": "ectoine",
            "label": "ectoine",
            "node_type": "CHEMICAL",
            "description": "Compatible solute (CHEBI:22586) contributing to salt tolerance.",
            "grounding": "CHEBI:27592"
          },
          {
            "node_id": "c_di_amp",
            "label": "cyclic di-AMP",
            "node_type": "CHEMICAL",
            "description": "Second messenger (CHEBI:167606) central to osmoregulation of K+ and osmolyte economy.",
            "grounding": "CHEBI:71578"
          },
          {
            "node_id": "organic_osmolyte_influx_biosynthesis",
            "label": "compatible organic osmolyte influx and biosynthesis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Influx and biosynthesis of physiologically compatible organic osmolytes."
          }
        ],
        "edges": [
          {
            "subject": "modest_osmoadaptive_flexibility",
            "predicate": "confers",
            "object": "nacl_delta_mid1_trait",
            "description": "Modest osmoadaptive flexibility yields a 1\u20133% NaCl-delta breadth.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuy009",
                "snippet": "salinity range",
                "notes": "Supports modest osmoadaptive flexibility as the basis of an intermediate breadth."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "nacl_delta_mid1_trait",
            "predicate": "is a",
            "object": "nacl_delta",
            "description": "NaCl delta mid1 is a quantitative bin of the NaCl-delta phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuy009",
                "snippet": "salinity range",
                "notes": "Supports the 1\u20133% breadth as a value within the NaCl-delta distribution."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "osmotic_upshift",
            "predicate": "induces",
            "object": "k_import",
            "description": "Hyperosmotic upshift triggers rapid K+ import to raise cytoplasmic osmolarity/turgor.",
            "evidence": [
              {
                "reference": "DOI:10.1128/MMBR.00181-23",
                "notes": "Bacterial cells commonly import a lot of potassium during an osmotic upshift (broad bacterial relevance)."
              }
            ]
          },
          {
            "subject": "k_import",
            "predicate": "precedes/replaced by",
            "object": "compatible_solute_accumulation",
            "description": "Initial K+ accumulation is subsequently replaced by neutral compatible solutes to reduce ionic stress.",
            "evidence": [
              {
                "reference": "DOI:10.1128/MMBR.00181-23",
                "notes": "Cells begin accumulating/synthesizing neutral compatible solutes such as glycine betaine, trehalose, and other osmolytes to replace K+ ions."
              }
            ]
          },
          {
            "subject": "osmotic_upshift",
            "predicate": "induces",
            "object": "compatible_solute_accumulation",
            "description": "Osmoadaptation transitions from inorganic K+ accumulation to organic osmoprotectants.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2019.02811",
                "notes": "Cells initially accumulate potassium as an emergency stress reaction and subsequently replace most of this ion with compatible solutes."
              }
            ]
          },
          {
            "subject": "compatible_solute_accumulation",
            "predicate": "supports",
            "object": "osmoadaptation_under_nacl",
            "description": "Organic osmolytes stabilize proteins/membranes and raise intracellular osmotic strength without salt-in toxicity.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuaf020",
                "notes": "Bacteria commonly use compatible solutes - notably glycine betaine, proline, trehalose, ectoine and carnitine - to support osmoadaptation."
              }
            ]
          },
          {
            "subject": "ectoine_biosynthesis",
            "predicate": "has output",
            "object": "ectoine",
            "description": "The EctB/EctA/EctC pathway synthesizes the compatible solute ectoine.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2019.02811",
                "notes": "Ectoine biosynthesis is mediated by three enzymes (EctB, EctA, EctC)."
              }
            ],
            "predicate_id": "RO:0002234"
          },
          {
            "subject": "ectoine",
            "predicate": "contributes to",
            "object": "compatible_solute_accumulation",
            "description": "Ectoine is one of the compatible solutes accumulated during osmoadaptation.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuaf020",
                "notes": "Ectoine is among the compatible solutes bacteria commonly use for osmoprotection."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "c_di_amp",
            "predicate": "decreases",
            "object": "k_import",
            "description": "Elevated c-di-AMP downregulates osmoregulatory K+ import.",
            "evidence": [
              {
                "reference": "DOI:10.1128/MMBR.00181-23",
                "notes": "High cyclic di-AMP reduces K+ import (review-level regulatory edge)."
              }
            ],
            "predicate_id": "RO:0002212"
          },
          {
            "subject": "c_di_amp",
            "predicate": "controls",
            "object": "organic_osmolyte_influx_biosynthesis",
            "description": "c-di-AMP regulates both the influx of compatible organic osmolytes and their biosynthesis.",
            "evidence": [
              {
                "reference": "DOI:10.1128/JB.00190-24",
                "notes": "c-di-AMP plays a key role by controlling (i) the influx of physiologically compatible organic osmolytes and (ii) the biosynthesis of such osmolytes."
              }
            ],
            "predicate_id": "RO:0002211"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.841250+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-12T10:00:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed definition and causal graph linking modest osmoadaptive flexibility to the intermediate-breadth NaCl-delta bin.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:30Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d71, rdfs:subClassOf\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 8 evidence-backed generic edges (8 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:10Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 4 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d71, RO:0002326\u00d71, RO:0002212\u00d71, RO:0002211\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 3 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:1990573\u00d71, CHEBI:27592\u00d71, CHEBI:71578\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 2 causal edge(s) off microbe-domain METPO predicates (1 to confers, 1 to has output), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-16T02:00:00Z",
        "curator": "claude",
        "action": "NORMALISE_NODE_TYPE",
        "changes": "Under the PATHWAY-vs-BIOLOGICAL_PROCESS rule, one node_id means one thing corpus-wide (issue 356): ectoine_biosynthesis is typed PATHWAY. PATHWAY is a named, conventionally enumerable multi-step route; BIOLOGICAL_PROCESS is everything else. A named route, enumerated two ways and both of them enumerations. environment/euryhaline.yaml counts five steps from L-aspartate (lysC/asd/ectB/ectA/ectC); environment/nacl_delta_mid1.yaml counts the three ectABC enzymes proper. Naming the file matters because the two differ and a bare quote would put euryhaline's wording into nacl_delta_mid1's record (#400 review). Either way the steps can be listed, which is the test. Applied AGAINST the majority, which was 4 BIOLOGICAL_PROCESS to 2 before this tranche.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope nacl_delta_mid1_modest_breadth=NONMECHANISTIC with scope_notes.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T04:43:24Z",
        "curator": "codex",
        "action": "ADD_CANONICAL_EXAMPLES",
        "changes": "Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Aureivirga marina (NCBITaxon:1182451; DOI:10.1099/ijs.0.043257-0). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000481",
    "label": "NaCl delta mid2",
    "definition": "A NaCl delta phenotype with a growth-supporting NaCl breadth of approximately 3\u20138% (w/v), characteristic of organisms with broad salinity tolerance.",
    "definition_source": "DOI:10.1093/femsre/fuy009",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000335"
    ],
    "synonyms": [
      {
        "synonym_text": "Nad_3_8",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1093/femsre/fuy009",
        "snippet": "salinity range",
        "notes": "Osmoadaptation review supports broad osmoadaptive breadths as the halotolerant / moderately euryhaline phenotype."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:718002",
        "taxon_label": "Peribacillus endoradicis",
        "reference": "DOI:10.1099/ijs.0.028936-0",
        "note": "The type strain, published as Bacillus endoradicis CCBAU 05776T and now NCBI-labelled Peribacillus endoradicis, grew from 0 to 7% NaCl, a 7-point breadth inside the 3-8% delta bin."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "nacl_delta_mid2_broad_breadth",
        "title": "NaCl-delta-mid2 broad-breadth osmoadaptation",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a quantitative measurement, interval, or bin in the environmental phenotype hierarchy; a token protein example would misrepresent the measured value as one inherited molecular mechanism.",
        "description": "DOI-backed graph linking robust osmoadaptive flexibility to a 3\u20138% (w/v) NaCl growth breadth.",
        "nodes": [
          {
            "node_id": "nacl_delta_mid2_trait",
            "label": "NaCl delta mid2",
            "node_type": "TRAIT",
            "grounding": "METPO:1000481",
            "description": "NaCl growth-supporting breadth approximately 3\u20138% w/v."
          },
          {
            "node_id": "nacl_delta",
            "label": "NaCl delta",
            "node_type": "TRAIT",
            "grounding": "METPO:1000335",
            "description": "Breadth of the growth-supporting NaCl range."
          },
          {
            "node_id": "robust_osmoadaptive_flexibility",
            "label": "robust osmoadaptive flexibility",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Strong osmolyte-remodeling capacity supporting growth across a broad salinity span."
          },
          {
            "node_id": "cyclic_di_amp",
            "label": "cyclic di-AMP",
            "node_type": "CHEMICAL",
            "description": "Second-messenger nucleotide acting as a master regulator of osmotic balance.",
            "grounding": "CHEBI:71578"
          },
          {
            "node_id": "potassium_uptake_systems",
            "label": "potassium uptake systems",
            "node_type": "GENE_OR_PROTEIN",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed as a contextual protein or protein-complex label within a quantitative measurement graph; no exact semantic family term was established for this aggregate use.",
            "description": "K+ import transporters (KupA/KupB, KimA, Kdp)."
          },
          {
            "node_id": "cell_volume_regulation",
            "label": "cell volume regulation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Regulation of cellular volume during osmotic stress."
          },
          {
            "node_id": "osmolality",
            "label": "osmolality",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "External solute concentration / osmotic pressure."
          },
          {
            "node_id": "kdpfabc_expression",
            "label": "kdpFABC expression",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Expression of the kdpFABC high-affinity K+ uptake operon via KdpD under osmotic upshift."
          },
          {
            "node_id": "compatible_solute_accumulation_transport",
            "label": "compatible-solute accumulation and transport",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Biosynthesis and uptake of compatible solutes/osmolytes."
          },
          {
            "node_id": "osmoprotection",
            "label": "osmoprotection",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Response to osmotic stress conferring protection."
          },
          {
            "node_id": "eps_matrix",
            "label": "exopolysaccharide matrix",
            "node_type": "CHEMICAL",
            "description": "Extracellular polymeric substance matrix surrounding cells."
          },
          {
            "node_id": "sodium_ion",
            "label": "sodium ion",
            "node_type": "CHEMICAL",
            "description": "Na+ cation.",
            "grounding": "CHEBI:29101"
          },
          {
            "node_id": "water_retention",
            "label": "water retention / reduced pericellular Na+ toxicity",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Retention of water and lowering of effective pericellular Na+."
          }
        ],
        "edges": [
          {
            "subject": "robust_osmoadaptive_flexibility",
            "predicate": "confers",
            "object": "nacl_delta_mid2_trait",
            "description": "Robust osmoadaptive flexibility yields a 3\u20138% NaCl-delta breadth.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuy009",
                "snippet": "salinity range",
                "notes": "Supports robust osmoadaptive flexibility as the basis of a broad breadth."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "nacl_delta_mid2_trait",
            "predicate": "is a",
            "object": "nacl_delta",
            "description": "NaCl delta mid2 is a quantitative bin of the NaCl-delta phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuy009",
                "snippet": "salinity range",
                "notes": "Supports the 3\u20138% breadth as a value within the NaCl-delta distribution."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "cyclic_di_amp",
            "predicate": "inhibits",
            "object": "potassium_uptake_systems",
            "description": "c-di-AMP binding to transporters/riboswitches inhibits K+ import.",
            "evidence": [
              {
                "reference": "DOI:10.1371/journal.pgen.1007574",
                "snippet": "A high level of c-di-AMP has been found to repress K+ and carnitine uptake",
                "notes": "Verified against the open Pham et al. introduction; c-di-AMP is retained as a broad regulator of bacterial K+ import rather than a direct determinant of this NaCl-breadth bin."
              }
            ],
            "predicate_id": "RO:0002212"
          },
          {
            "subject": "cyclic_di_amp",
            "predicate": "modulates",
            "object": "cell_volume_regulation",
            "description": "c-di-AMP signaling acts as a master regulator of cell volume.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mmbr.00181-23",
                "snippet": "cyclic di-AMP is a master regulator of cell volume",
                "notes": "Verified against public Foster et al. text; the edge is kept at the level of broad second-messenger control over cell-volume regulation."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "osmolality",
            "predicate": "increases",
            "object": "kdpfabc_expression",
            "description": "Ionic-strength changes can increase kdpFABC expression via KdpD during osmotic upshift.",
            "evidence": [
              {
                "reference": "DOI:10.1046/j.1365-2958.2002.02894.x",
                "snippet": "increase the expression of kdpFABC under conditions of osmotic upshift",
                "notes": "Verified against the open Poolman et al. review; the edge is moved from a protein-complex object to a kdpFABC-expression process."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "compatible_solute_accumulation_transport",
            "predicate": "causes",
            "object": "osmoprotection",
            "description": "Accumulation/transport of compatible solutes confers osmoprotection.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2018.00108",
                "snippet": "accumulated by microorganisms under high salinity growth conditions as stress protectants",
                "notes": "Verified against the open Leon et al. text; compatible solute accumulation and uptake are retained as a broad osmoprotective process."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "eps_matrix",
            "predicate": "interacts with",
            "object": "sodium_ion",
            "description": "The EPS matrix physically interacts with Na+ cations.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuaf020",
                "snippet": "the EPS matrix binds cations such as Na+ ions",
                "notes": "Verified against the open Goszcz et al. review; exopolysaccharide matrices are typed with the existing CHEMICAL convention from the biofilm graph."
              }
            ],
            "predicate_id": "biolink:interacts_with"
          },
          {
            "subject": "eps_matrix",
            "predicate": "promotes",
            "object": "water_retention",
            "description": "EPS matrix promotes water retention and reduces pericellular Na+ toxicity.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuaf020",
                "snippet": "It also retains water, which helps in reducing the osmotic gradient",
                "notes": "Verified against the open Goszcz et al. review; this EPS edge is kept as a contextual pericellular salt-stress mitigation mechanism."
              }
            ],
            "predicate_id": "RO:0002213"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.842087+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-12T10:00:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed definition and causal graph linking robust osmoadaptive flexibility to the broad-breadth NaCl-delta bin.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:30Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d71, rdfs:subClassOf\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 6 evidence-backed generic edges (10 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:10Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 4 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002212\u00d71, RO:0002211\u00d71, biolink:causes\u00d71, RO:0002213\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:71578\u00d71, CHEBI:29101\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates (1 to confers), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope nacl_delta_mid2_broad_breadth=NONMECHANISTIC with scope_notes; marked 2 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (potassium_uptake_systems, kdpfabc_complex).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T04:43:24Z",
        "curator": "codex",
        "action": "ADD_CANONICAL_EXAMPLES",
        "changes": "Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Peribacillus endoradicis (NCBITaxon:718002; DOI:10.1099/ijs.0.028936-0). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-04T07:40:00Z",
        "curator": "codex",
        "action": "REVIEW_CAUSAL_EVIDENCE",
        "changes": "Reviewed the nacl_delta_mid2_broad_breadth graph for issue #183: added exact snippets to 6 causal-edge evidence items, grounded 2 residual predicates, and repaired 2 local node-type conflicts. No paid research service was called.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000333",
    "label": "NaCl optimum",
    "definition": "A salinity phenotype with numerical limits that supports the most efficient growth and reproduction of an organism.",
    "definition_source": "DOI:10.1093/femsre/fuy009",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000532",
      "METPO:1000536"
    ],
    "created_by": "Luke Wang",
    "evidence": [
      {
        "reference": "DOI:10.1093/femsre/fuy009",
        "snippet": "optimal NaCl",
        "notes": "Osmoadaptation review supports the NaCl concentration at which growth rate is maximal as a standard halophily descriptor."
      },
      {
        "reference": "DOI:10.1186/1746-1448-4-2",
        "snippet": "ways they cope with the high salt concentrations",
        "notes": "Saline-Systems review supports osmotic balance at the optimal NaCl as the mechanistic basis of the NaCl-optimum phenotype."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:200904",
        "taxon_label": "Paraliobacillus ryukyuensis",
        "reference": "DOI:10.2323/jgam.48.269",
        "note": "Strain O15-7T had a maximum-specific-growth-rate optimum spanning 0.75-3.0% (w/v) NaCl. Because that interval touches the low/mid1 boundary, #591 keeps the complete claim on the parent rather than duplicating it onto a bin."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "nacl_optimum_balanced_osmoadaptation",
        "title": "NaCl optimum with salt-in, salt-out, and transporter support",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a quantitative measurement, interval, or bin in the environmental phenotype hierarchy; a token protein example would misrepresent the measured value as one inherited molecular mechanism.",
        "description": "DOI-backed nonmechanistic graph connecting ambient NaCl, osmotic balance, salt-in K+ accumulation, acidic-proteome support, compatible-solute accumulation and uptake, cation transport, and maximal growth rate for the NaCl-optimum phenotype.",
        "nodes": [
          {
            "node_id": "nacl_optimum_trait",
            "label": "NaCl optimum",
            "node_type": "TRAIT",
            "grounding": "METPO:1000333",
            "description": "NaCl concentration at which growth rate is maximal."
          },
          {
            "node_id": "ambient_nacl",
            "label": "ambient NaCl concentration",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Ambient NaCl level imposed on the cell."
          },
          {
            "node_id": "osmotic_balance",
            "label": "osmotic balance",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Steady-state matching of intracellular osmotic activity to the external salt concentration."
          },
          {
            "node_id": "compatible_solutes",
            "label": "compatible solutes",
            "node_type": "CHEMICAL",
            "description": "Organic osmolytes (ectoine, glycine betaine) maintaining cytoplasmic osmotic activity.",
            "grounding": "CHEBI:25728"
          },
          {
            "node_id": "na_h_antiporters",
            "label": "Na+/H+ antiporters",
            "node_type": "GENE_OR_PROTEIN",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed as a contextual protein or protein-complex label within a quantitative measurement graph; no exact semantic family term was established for this aggregate use.",
            "description": "Membrane antiporters extruding Na+ in exchange for H+ to maintain ion homeostasis."
          },
          {
            "node_id": "maximal_growth_rate",
            "label": "maximal growth rate",
            "node_type": "QUALITY",
            "description": "Peak specific growth rate achieved at the optimal NaCl."
          },
          {
            "node_id": "osmotic_stress",
            "label": "osmotic stress",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Cellular stress imposed by an external salt concentration that perturbs water activity.",
            "grounding": "GO:0006970"
          },
          {
            "node_id": "salt_in_strategy",
            "label": "salt-in strategy",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Osmoadaptive strategy of accumulating molar inorganic ions (notably KCl) in the cytoplasm.",
            "grounding": "METPO:1007720"
          },
          {
            "node_id": "intracellular_k_accumulation",
            "label": "intracellular K+ accumulation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Accumulation of molar concentrations of potassium ions to balance external salt."
          },
          {
            "node_id": "acidic_proteome",
            "label": "acidic proteome",
            "node_type": "QUALITY",
            "description": "Highly acidic proteome adapted to function at high intracellular salt concentrations."
          },
          {
            "node_id": "protein_stability_high_salt",
            "label": "protein stability at high salt",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Maintenance of protein folding and enzymatic function under near-saturating intracellular salt."
          },
          {
            "node_id": "compatible_solute_accumulation",
            "label": "compatible-solute accumulation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Accumulation of organic compatible solutes that do not interfere with enzymatic activity."
          },
          {
            "node_id": "compatible_solute_uptake",
            "label": "compatible solute uptake",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Import of compatible solutes from the medium, energetically favored over de novo synthesis."
          },
          {
            "node_id": "lower_energetic_cost",
            "label": "lower energetic cost than de novo synthesis",
            "node_type": "QUALITY",
            "description": "Reduced metabolic energy expenditure relative to synthesizing compatible solutes de novo."
          },
          {
            "node_id": "na_k_h_transport_activity",
            "label": "Na+/K+/H+ transporter activity",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "Cation/proton transporter activity preserving intracellular K+ concentration and broader ion homeostasis under varying salinities."
          },
          {
            "node_id": "cellular_ion_homeostasis",
            "label": "cellular ion homeostasis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Maintenance of cytoplasmic potassium concentration and broader cellular ion balance during salinity change."
          }
        ],
        "edges": [
          {
            "subject": "ambient_nacl",
            "predicate": "causes",
            "object": "osmotic_balance",
            "description": "External NaCl level engages the osmoadaptive balance machinery.",
            "evidence": [
              {
                "reference": "DOI:10.1186/1746-1448-4-2",
                "snippet": "cope with the high salt concentrations",
                "notes": "Supports osmotic balance as the response to ambient NaCl."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "compatible_solutes",
            "predicate": "regulates",
            "object": "osmotic_balance",
            "description": "Compatible-solute accumulation maintains osmotic balance at the optimal NaCl.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuy009",
                "snippet": "synthesize organic osmotic solutes",
                "notes": "Supports compatible solutes as the osmoadaptive osmolyte."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "na_h_antiporters",
            "predicate": "enables",
            "object": "osmotic_balance",
            "description": "Na+/H+ antiporters support ion homeostasis underlying osmotic balance.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuy009",
                "snippet": "Na+/H+ antiporters",
                "notes": "Supports antiporter-driven Na+ extrusion as an osmoadaptive mechanism."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "osmotic_balance",
            "predicate": "promotes",
            "object": "maximal_growth_rate",
            "description": "Maintained osmotic balance promotes peak growth at the optimal NaCl concentration.",
            "evidence": [
              {
                "reference": "DOI:10.1186/1746-1448-4-2",
                "snippet": "optimum",
                "notes": "Supports peak growth at the optimal NaCl as the operational definition of NaCl optimum."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "maximal_growth_rate",
            "predicate": "manifests as",
            "object": "nacl_optimum_trait",
            "description": "The NaCl concentration at which peak growth is achieved manifests the NaCl-optimum phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuy009",
                "snippet": "optimal NaCl",
                "notes": "Supports the trait endpoint."
              }
            ],
            "predicate_id": "METPO:2007400"
          },
          {
            "subject": "ambient_nacl",
            "predicate": "causes",
            "object": "osmotic_stress",
            "description": "External NaCl creates the osmotic imbalance that requires osmoadaptive compensation.",
            "evidence": [
              {
                "reference": "DOI:10.1186/1746-1448-4-2",
                "snippet": "cytoplasm has to be at least isoosmotic",
                "notes": "Verified against the open Oren review; halophilic cells must osmotically balance the cytoplasm against high-salt medium."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "salt_in_strategy",
            "predicate": "increases",
            "object": "intracellular_k_accumulation",
            "description": "The salt-in strategy accumulates molar potassium and chloride concentrations in the cytoplasm.",
            "evidence": [
              {
                "reference": "DOI:10.1186/1746-1448-4-2",
                "snippet": "accumulation of molar concentrations of potassium and chloride",
                "notes": "Verified against the open Oren review; high-salt-in organisms balance external salt primarily with intracellular KCl."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "acidic_proteome",
            "predicate": "enables",
            "object": "protein_stability_high_salt",
            "description": "An acidic proteome enables protein folding and enzymatic function under near-saturating intracellular salt.",
            "evidence": [
              {
                "reference": "DOI:10.1186/1746-1448-4-2",
                "snippet": "extensive adaptation of the intracellular enzymatic machinery",
                "notes": "Verified against the open Oren review; high-salt-in strategists require intracellular enzymatic machinery adapted to molar salt."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "compatible_solute_accumulation",
            "predicate": "regulates",
            "object": "osmotic_balance",
            "description": "Organic compatible-solute accumulation regulates osmotic balance while limiting inorganic salt in the cytoplasm.",
            "evidence": [
              {
                "reference": "DOI:10.1186/1746-1448-4-2",
                "snippet": "exclude salt from their cytoplasm as much as possible",
                "notes": "Verified against the open Oren review; the salt-out strategy excludes salt from the cytoplasm and accumulates organic solutes that minimally perturb enzymatic activity."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "compatible_solute_uptake",
            "predicate": "associated with",
            "object": "lower_energetic_cost",
            "description": "Compatible-solute uptake is associated with lower energetic cost than de novo compatible-solute synthesis.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2022.846677",
                "snippet": "uptake of compatible solute from the medium is preferred",
                "notes": "Verified against the open Halomonas elongata review; external compatible-solute uptake is energetically preferred over de novo synthesis."
              }
            ],
            "predicate_id": "biolink:associated_with"
          },
          {
            "subject": "na_k_h_transport_activity",
            "predicate": "regulates",
            "object": "cellular_ion_homeostasis",
            "description": "Na+/K+/H+ transporter activity contributes to cellular ion homeostasis under varying salinities.",
            "evidence": [
              {
                "reference": "DOI:10.1128/aem.00145-24",
                "snippet": "transport systems that regulate intracellular Na+/K+/H+ concentration",
                "notes": "Verified against the Xing et al. long-term salinity-stress study; the edge was broadened from Na+ homeostasis to match the reported Na+/K+/H+ transporter and intracellular K+ response."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "intracellular_k_accumulation",
            "predicate": "contributes to",
            "object": "osmotic_balance",
            "description": "Intracellular KCl accumulation is a salt-in osmoadaptation route that contributes to balancing external salt.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2013.00315",
                "snippet": "Extremely halophilic microorganisms that accumulate KCl for osmotic balance",
                "notes": "Verified against the open Oren minireview; the connector links KCl accumulation to osmotic balance without making the salt-in strategy universal for every NaCl optimum."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "salt_in_strategy",
            "predicate": "associated with",
            "object": "acidic_proteome",
            "description": "Salt-in osmoadaptation is associated with proteome-scale acidic adaptation for molar intracellular KCl.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2013.00315",
                "snippet": "have a large excess of acidic amino acids in their proteins",
                "notes": "Verified against the open Oren minireview; the connector keeps acidic-proteome composition scoped to salt-in strategists."
              }
            ],
            "predicate_id": "biolink:associated_with"
          },
          {
            "subject": "compatible_solute_uptake",
            "predicate": "associated with",
            "object": "compatible_solute_accumulation",
            "description": "External compatible-solute uptake is associated with the salt-out branch that accumulates organic osmolytes for osmoadaptation.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2022.846677",
                "snippet": "Uptake of ectoine from the medium is facilitated by the osmoregulated TRAP transporter TeaABC",
                "notes": "Verified against the open Halomonas elongata review; the connector treats uptake as an accumulation branch with a lower energetic cost than de novo synthesis."
              }
            ],
            "predicate_id": "biolink:associated_with"
          },
          {
            "subject": "cellular_ion_homeostasis",
            "predicate": "associated with",
            "object": "osmotic_balance",
            "description": "Na+/K+/H+ transporter control of cellular ion homeostasis is associated with osmotic balancing during salinity change.",
            "evidence": [
              {
                "reference": "DOI:10.1128/aem.00145-24",
                "snippet": "ensuring cellular ion homeostasis under varying salinities",
                "notes": "Verified against the Xing et al. long-term salinity-stress study; the connector places the species-specific transporter response inside the osmotic-balance context."
              }
            ],
            "predicate_id": "biolink:associated_with"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.815612+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-12T10:00:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed causal graph linking ambient NaCl, osmotic balance via compatible solutes and Na+/H+ antiporters, and maximal growth rate to the NaCl-optimum phenotype.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:30Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T21:30:06Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007400\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:18Z",
        "curator": "claude",
        "action": "RENAME_PREDICATE_LABELS",
        "changes": "Renamed 2 causal-edge predicate label(s) to align with existing groundings: maintains \u2192 regulates \u00d71; supports \u2192 enables \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:21Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002211\u00d71, RO:0002327\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:38:00Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:65015\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-26T05:00:47Z",
        "curator": "claude",
        "action": "RENAME_PREDICATE_LABELS",
        "changes": "Renamed 1 causal-edge predicate label(s) to align with existing groundings: triggers \u2192 causes \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-26T05:00:49Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:causes\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-15T07:19:08Z",
        "curator": "claude",
        "action": "FIX_NODE_GROUNDING_CURIE",
        "changes": "Overwrote 1 causal-node grounding(s) to corrected CURIEs (phase-2 id-label fix; verified vs OAK).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 6 evidence-backed generic edges (10 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:10Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 5 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002211\u00d72, RO:0002213\u00d71, RO:0002327\u00d71, biolink:associated_with\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:17Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0006970\u00d71, METPO:1007720\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-16T02:00:00Z",
        "curator": "claude",
        "action": "NORMALISE_NODE_TYPE",
        "changes": "Under the PATHWAY-vs-BIOLOGICAL_PROCESS rule, one node_id means one thing corpus-wide (issue 356): salt_in_strategy is typed BIOLOGICAL_PROCESS. PATHWAY is a named, conventionally enumerable multi-step route; BIOLOGICAL_PROCESS is everything else. A STRATEGY, not a route. The family is described as osmoadaptation by accumulating intracellular inorganic ions -- haloalkaliphilic.yaml puts it as 'Osmoadaptation by intracellular accumulation of inorganic ions (e.g. K+)', and the wording varies by record. There is no step list to enumerate, which is exactly the distinction this rule draws. Was 7 BIOLOGICAL_PROCESS to 1 before this tranche.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-20T08:00:00Z",
        "curator": "claude",
        "action": "BACKFILL_CANONICAL_EXAMPLES",
        "changes": "Added one exemplar taxon, the only organism in this trait's deep-research artifact for which that artifact cites a measured NaCl growth optimum. Taxon id resolved and label-checked against the local NCBITaxon build. Three sets of organisms named in the same artifact were deliberately NOT included, each because the artifact itself says the evidence stops short of a NaCl optimum: Halomonas elongata (the engineered proline strains shift an IC50, and the artifact warns \"an IC50 or improved tolerance is not automatically equivalent to a rigorously re-estimated NaCl optimum\"); Natranaerobius thermophilus (its reported 3.3-3.9 M optimum is total Na+ at pH 9.5, and the artifact warns \"Do not merge NaCl, Na+, total salts, conductivity, osmolarity, and water activity\"); and the Dead Sea spring MAG taxa Prosthecochloris, Flexistipes, Izemoplasma, Halomonas and Halanaerobiales (the artifact notes \"MAG content predicts potential; it does not establish expression, flux, or the growth optimum of each organism\").",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-21T08:00:00Z",
        "curator": "codex",
        "action": "NORMALISE_NODE_TYPE",
        "changes": "Tranche 5 of issue 356 settles the process/quality families and merges ids that meant the same sense: maximal_growth_rate is QUALITY. A maximal growth rate is a measured upper bound or peak specific rate. Its edges associate, enable, or manifest that value; none describe the process of cell growth itself. An edge cannot enable a QUALITY under RO:0002327's biological-process range, so edges that causally support the rate use promotes (RO:0002213) instead.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope nacl_optimum_balanced_osmoadaptation=NONMECHANISTIC with scope_notes; marked 1 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (na_h_antiporters).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-30T20:02:00Z",
        "curator": "codex",
        "action": "MOVE_CANONICAL_EXAMPLE_TO_SPECIFIC_BIN",
        "changes": "Moved Wallemia ichthyophaga (NCBITaxon:245174; DOI:10.1128/aem.02702-13) off the NaCl-optimum parent under the #478 most-specific-placement policy. Its measured 15-20% (w/v) optimum belongs wholly in METPO:1000468; the same claim is not duplicated on parent and bin.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T04:43:24Z",
        "curator": "codex",
        "action": "ADD_CANONICAL_EXAMPLES",
        "changes": "Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Paraliobacillus ryukyuensis (NCBITaxon:200904; DOI:10.2323/jgam.48.269). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-04T01:00:00Z",
        "curator": "codex",
        "action": "REVIEW_CAUSAL_EVIDENCE",
        "changes": "Reviewed the broad nacl_optimum_balanced_osmoadaptation graph for issue #183: added snippets to 6 edge-level evidence items, regrounded the ambient-NaCl osmotic-stress edge to biolink:causes, and broadened one transporter edge from Na+ homeostasis to Na+/K+/H+ transporter control of cellular ion homeostasis. No paid research service was called.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-04T14:00:00Z",
        "curator": "codex",
        "action": "CONNECT_CAUSAL_GRAPH_COMPONENTS",
        "changes": "Resolved issue #183 graph fragmentation (5 components to 1) by adding 4 source- and verbatim-snippet-backed connectors among the salt-in KCl, acidic proteome, compatible-solute uptake, cation homeostasis, and osmotic-balance branches. No paid research service was called.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-06T17:10:00Z",
        "curator": "codex",
        "action": "ADVERSARIAL_REVIEW_REPAIR",
        "changes": "Addressed PR #664 adversarial review: replaced copied nonmechanistic bridge snippets with independent exact source snippets while preserving the existing connector edge scope.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000468",
    "label": "NaCl optimum high",
    "definition": "A NaCl optimum phenotype with the best-growth NaCl concentration above approximately 8% (w/v), corresponding to extreme-halophile physiology.",
    "definition_source": "DOI:10.1093/femsre/fuy009",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000333"
    ],
    "synonyms": [
      {
        "synonym_text": "Extreme halophile",
        "synonym_type": "EXACT_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "NaO_>8",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1093/femsre/fuy009",
        "snippet": "extreme halophile",
        "notes": "Osmoadaptation review supports >8% NaCl optimum as the extreme-halophile category."
      },
      {
        "reference": "DOI:10.1186/1746-1448-4-2",
        "snippet": "KCl accumulating Halobacterium salinarum",
        "notes": "Saline-Systems review supports the salt-in (intracellular KCl) strategy as the mechanism for extreme-halophile growth."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:245174",
        "taxon_label": "Wallemia ichthyophaga",
        "reference": "DOI:10.1128/aem.02702-13",
        "note": "Extremely halophilic fungus whose NaCl optimum was determined kinetically from exponential-phase doubling times across a salinity series. The reported 15-20% (w/v) optimum lies wholly above this bin's >8% (w/v) threshold. The same organism grows from 10% to saturated (~32%) NaCl; that wider interval is its growth range, not its optimum."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "nacl_optimum_high_extreme_halophile",
        "title": "NaCl-optimum-high extreme-halophile setpoint",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a quantitative measurement, interval, or bin in the environmental phenotype hierarchy; a token protein example would misrepresent the measured value as one inherited molecular mechanism.",
        "description": "DOI-backed graph linking salt-in ion-accumulation strategy under hypersaline NaCl to a >8% (w/v) NaCl-optimum (extreme halophile).",
        "nodes": [
          {
            "node_id": "nacl_optimum_high_trait",
            "label": "NaCl optimum high",
            "node_type": "TRAIT",
            "grounding": "METPO:1000468",
            "description": "NaCl optimum exceeding ~8% w/v."
          },
          {
            "node_id": "nacl_optimum",
            "label": "NaCl optimum",
            "node_type": "TRAIT",
            "grounding": "METPO:1000333",
            "description": "NaCl concentration supporting maximal growth."
          },
          {
            "node_id": "hypersaline_nacl",
            "label": "hypersaline NaCl",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "External NaCl above ~8% w/v, typical of brines and salt lakes."
          },
          {
            "node_id": "salt_in_strategy",
            "label": "salt-in strategy",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Intracellular K+ accumulation balancing high external NaCl osmotic activity.",
            "grounding": "METPO:1007720"
          },
          {
            "node_id": "intracellular_kcl",
            "label": "intracellular KCl concentration",
            "node_type": "CHEMICAL",
            "description": "High cytoplasmic potassium chloride (>3 M) balancing external osmolarity in salt-in halophiles."
          },
          {
            "node_id": "potassium_uptake_system",
            "label": "potassium uptake system",
            "node_type": "GENE_OR_PROTEIN",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed as a contextual protein or protein-complex label within a quantitative measurement graph; no exact semantic family term was established for this aggregate use.",
            "description": "K+ transporters/channels (Trk-family) mediating potassium accumulation for the salt-in strategy."
          },
          {
            "node_id": "na_h_antiporter",
            "label": "Na+/H+ antiporter",
            "node_type": "GENE_OR_PROTEIN",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed as a contextual protein or protein-complex label within a quantitative measurement graph; no exact semantic family term was established for this aggregate use.",
            "description": "Sodium/proton antiporter mediating Na+ exclusion and ion homeostasis under high salt."
          },
          {
            "node_id": "acidic_proteome",
            "label": "acidic proteome",
            "node_type": "QUALITY",
            "description": "Proteome enriched in acidic residues (Asp/Glu) with low median pI, hallmark of salt-in halophiles."
          },
          {
            "node_id": "protein_function_high_salinity",
            "label": "protein function at high salinity",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "Maintenance of protein structure and activity at molar intracellular salt concentrations."
          },
          {
            "node_id": "acidic_aa_content",
            "label": "increased acidic amino-acid content",
            "node_type": "QUALITY",
            "description": "Elevated Asp/Glu content in proteins promoting solubility in high intracellular KCl."
          },
          {
            "node_id": "protein_solubility_high_salt",
            "label": "protein solubility in high salt",
            "node_type": "QUALITY",
            "description": "Salt-induced stabilization and solubility of halophilic proteins at high salinity."
          }
        ],
        "edges": [
          {
            "subject": "hypersaline_nacl",
            "predicate": "selects for",
            "object": "salt_in_strategy",
            "description": "Hypersaline conditions select for intracellular ion-accumulation osmoadaptation.",
            "evidence": [
              {
                "reference": "DOI:10.1186/1746-1448-4-2",
                "snippet": "KCl accumulating Halobacterium salinarum",
                "notes": "Supports the salt-in strategy in extreme-halophile lineages."
              }
            ],
            "predicate_id": "METPO:2007401"
          },
          {
            "subject": "salt_in_strategy",
            "predicate": "confers",
            "object": "nacl_optimum_high_trait",
            "description": "Salt-in ion accumulation yields a >8% NaCl-optimum setpoint.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuy009",
                "snippet": "extreme halophile",
                "notes": "Supports the >8% optimum as the extreme-halophile outcome."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "nacl_optimum_high_trait",
            "predicate": "is a",
            "object": "nacl_optimum",
            "description": "NaCl optimum high is a quantitative bin of the NaCl-optimum phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuy009",
                "snippet": "optimal NaCl",
                "notes": "Supports >8% optimum as a value within the NaCl-optimum distribution."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "salt_in_strategy",
            "predicate": "increases",
            "object": "intracellular_kcl",
            "description": "Salt-in osmoadaptation accumulates high intracellular KCl.",
            "evidence": [
              {
                "reference": "DOI:10.1002/pro.5003",
                "notes": "Halophiles accumulate intracellular concentrations of potassium chloride even above 3 M."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "salt_in_strategy",
            "predicate": "requires",
            "object": "potassium_uptake_system",
            "description": "Salt-in strategy depends on K+ uptake systems to accumulate cytoplasmic potassium.",
            "evidence": [
              {
                "reference": "DOI:10.1002/pro.5003",
                "notes": "Upregulating potassium-selective ion channels supports salt-in K+ accumulation."
              }
            ]
          },
          {
            "subject": "na_h_antiporter",
            "predicate": "supports",
            "object": "salt_in_strategy",
            "description": "Na+/H+ antiporter activity supports salt-in osmoadaptation via Na+ exclusion.",
            "evidence": [
              {
                "reference": "DOI:10.3390/microorganisms12081738",
                "notes": "Na+ extrusion via Na+/H+ antiporters driven by a proton electrochemical gradient."
              }
            ]
          },
          {
            "subject": "intracellular_kcl",
            "predicate": "selects for",
            "object": "acidic_proteome",
            "description": "High intracellular KCl selects for an acidic proteome.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41559-024-02505-6",
                "notes": "The salt-in strategy is concomitant with an excess of acidic amino acids."
              }
            ],
            "predicate_id": "METPO:2007401"
          },
          {
            "subject": "acidic_proteome",
            "predicate": "enables",
            "object": "protein_function_high_salinity",
            "description": "Acidic proteome enables protein function at high salinity.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41559-024-02505-6",
                "notes": "Proteome acidification preserves protein structure/function under high intracellular salt."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "acidic_aa_content",
            "predicate": "increases",
            "object": "protein_solubility_high_salt",
            "description": "Increased acidic amino-acid content increases protein solubility in high salt.",
            "evidence": [
              {
                "reference": "DOI:10.1002/pro.5003",
                "notes": "Increase the number of short, polar and acidic amino acids to improve salt-induced stabilization and solubility."
              }
            ],
            "predicate_id": "RO:0002213"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.835295+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-12T10:00:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed definition and causal graph linking salt-in ion-accumulation strategy under hypersaline NaCl to the extreme-halophile NaCl-optimum bin.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:30Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d71, rdfs:subClassOf\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T21:30:06Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007401\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-16T06:54:39Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (METPO:1007720\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 6 evidence-backed generic edges (7 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:10Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 4 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002213\u00d72, METPO:2007401\u00d71, RO:0002327\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:17Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A068T423\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:21:11Z",
        "curator": "claude",
        "action": "RETRACT_DEAD_UNIPROT_GROUNDINGS",
        "changes": "Retracted 1 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates (1 to confers), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-16T02:00:00Z",
        "curator": "claude",
        "action": "NORMALISE_NODE_TYPE",
        "changes": "Under the PATHWAY-vs-BIOLOGICAL_PROCESS rule, one node_id means one thing corpus-wide (issue 356): salt_in_strategy is typed BIOLOGICAL_PROCESS. PATHWAY is a named, conventionally enumerable multi-step route; BIOLOGICAL_PROCESS is everything else. A STRATEGY, not a route. The family is described as osmoadaptation by accumulating intracellular inorganic ions -- haloalkaliphilic.yaml puts it as 'Osmoadaptation by intracellular accumulation of inorganic ions (e.g. K+)', and the wording varies by record. There is no step list to enumerate, which is exactly the distinction this rule draws. Was 7 BIOLOGICAL_PROCESS to 1 before this tranche.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope nacl_optimum_high_extreme_halophile=NONMECHANISTIC with scope_notes; marked 2 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (potassium_uptake_system, na_h_antiporter).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-30T20:02:00Z",
        "curator": "codex",
        "action": "MOVE_CANONICAL_EXAMPLE_TO_SPECIFIC_BIN",
        "changes": "Added Wallemia ichthyophaga (NCBITaxon:245174; DOI:10.1128/aem.02702-13) from the NaCl-optimum parent under the #478 most-specific-placement policy. Its complete measured optimum interval, 15-20% (w/v), is above this bin's >8% (w/v) threshold.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000465",
    "label": "NaCl optimum low",
    "definition": "A NaCl optimum phenotype with the best-growth NaCl concentration at or below approximately 1% (w/v), corresponding to non-halophilic or halotolerant physiology.",
    "definition_source": "DOI:10.1093/femsre/fuy009",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000333"
    ],
    "synonyms": [
      {
        "synonym_text": "Halotolerant",
        "synonym_type": "EXACT_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "Non-halophile",
        "synonym_type": "EXACT_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "NaO_<=1",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1093/femsre/fuy009",
        "snippet": "optimal NaCl",
        "notes": "Osmoadaptation review supports low-salt optima as the non-halophilic / halotolerant end of the halophily axis."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:575322",
        "taxon_label": "Sphingomonas oligoaromativorans",
        "reference": "DOI:10.1099/ijs.0.052894-0",
        "note": "Type strain SY-6T grew optimally at 0.01% (w/v) NaCl, wholly within the at-most-1% bin; its full reported growth range was 0-0.5%."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "nacl_optimum_low_non_halophile_setpoint",
        "title": "NaCl-optimum-low non-halophile setpoint",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a quantitative measurement, interval, or bin in the environmental phenotype hierarchy; a token protein example would misrepresent the measured value as one inherited molecular mechanism.",
        "description": "DOI-backed graph linking minimal osmoadaptive load at low ambient NaCl to a low NaCl-optimum (\u22641% w/v) consistent with non-halophilic or halotolerant physiology.",
        "nodes": [
          {
            "node_id": "nacl_optimum_low_trait",
            "label": "NaCl optimum low",
            "node_type": "TRAIT",
            "grounding": "METPO:1000465",
            "description": "NaCl optimum at or below ~1% w/v."
          },
          {
            "node_id": "nacl_optimum",
            "label": "NaCl optimum",
            "node_type": "TRAIT",
            "grounding": "METPO:1000333",
            "description": "NaCl concentration supporting maximal growth."
          },
          {
            "node_id": "low_ambient_nacl",
            "label": "low ambient NaCl",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Freshwater-like or mildly saline external NaCl \u2264 ~1% w/v."
          },
          {
            "node_id": "minimal_osmoadaptive_load",
            "label": "minimal osmoadaptive load",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Low demand on osmolyte and ion-transport machinery at low salt."
          },
          {
            "node_id": "non_halophile_optimum_definition",
            "label": "non-halophilic optimum NaCl (<0.2 M / ~1% w/v)",
            "node_type": "TRAIT",
            "description": "Optimal growth at less than 0.2 M (about 1% w/v) NaCl, defining non-halophilic physiology."
          },
          {
            "node_id": "halotolerant_organism",
            "label": "halotolerant organism",
            "node_type": "TRAIT",
            "description": "A non-halophilic organism able to grow at high salt concentrations."
          },
          {
            "node_id": "compatible_solute_accumulation",
            "label": "compatible solute accumulation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Intracellular accumulation of low-molecular-weight compatible solutes (osmolytes) in response to osmotic stress."
          },
          {
            "node_id": "osmotic_stress_adaptation",
            "label": "osmotic stress adaptation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Cellular adaptation maintaining turgor and function under osmotic stress."
          },
          {
            "node_id": "cyclic_di_amp",
            "label": "cyclic di-AMP",
            "node_type": "CHEMICAL",
            "description": "Second messenger nucleotide that regulates osmolyte and ion transport.",
            "grounding": "CHEBI:71578"
          },
          {
            "node_id": "k_uptake_systems",
            "label": "K+ uptake systems (Trk/Ktr/Kup/KimA)",
            "node_type": "GENE_OR_PROTEIN",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed as a contextual protein or protein-complex label within a quantitative measurement graph; no exact semantic family term was established for this aggregate use.",
            "description": "Potassium uptake transporters whose activity responds to osmotic signaling."
          },
          {
            "node_id": "opua_opuc_transport",
            "label": "OpuA/OpuC compatible-solute transporters",
            "node_type": "GENE_OR_PROTEIN",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed as a contextual protein or protein-complex label within a quantitative measurement graph; no exact semantic family term was established for this aggregate use.",
            "description": "ABC-type importers of compatible solutes such as glycine betaine."
          }
        ],
        "edges": [
          {
            "subject": "low_ambient_nacl",
            "predicate": "imposes",
            "object": "minimal_osmoadaptive_load",
            "description": "Low ambient NaCl imposes minimal osmoadaptive demand on the cell.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuy009",
                "snippet": "optimal NaCl",
                "notes": "Supports low-salt environments as the context for non-halophilic optima."
              }
            ]
          },
          {
            "subject": "minimal_osmoadaptive_load",
            "predicate": "confers",
            "object": "nacl_optimum_low_trait",
            "description": "Minimal osmoadaptive demand yields a low NaCl-optimum setpoint.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuy009",
                "snippet": "optimal NaCl",
                "notes": "Supports low-salt optima as the non-halophile / halotolerant outcome."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "nacl_optimum_low_trait",
            "predicate": "is a",
            "object": "nacl_optimum",
            "description": "NaCl optimum low is a quantitative bin of the NaCl-optimum phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuy009",
                "snippet": "optimal NaCl",
                "notes": "Supports low-salt optima as a value within the NaCl-optimum distribution."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "non_halophile_optimum_definition",
            "predicate": "defined as",
            "object": "nacl_optimum_low_trait",
            "description": "Non-halophilic optimum at <0.2 M (~1% w/v) NaCl corresponds to the NaCl-optimum-low trait.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2019.01895",
                "notes": "non-halophilic microorganisms grow optimally at less than 0.2 M (1%) NaCl."
              }
            ]
          },
          {
            "subject": "halotolerant_organism",
            "predicate": "is a",
            "object": "non_halophile_optimum_definition",
            "description": "Halotolerant organisms are non-halophiles (low-NaCl optimum) able to grow at high salt.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s40201-020-00519-3",
                "notes": "halotolerant organisms are those non-halophilic able to grow at high salt concentrations."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "compatible_solute_accumulation",
            "predicate": "supports",
            "object": "osmotic_stress_adaptation",
            "description": "Accumulation of compatible solutes supports adaptation to osmotic stress.",
            "evidence": [
              {
                "reference": "DOI:10.1128/aem.00619-25",
                "notes": "Bacteria respond to osmotic stress by intracellularly accumulating compatible solutes."
              }
            ]
          },
          {
            "subject": "minimal_osmoadaptive_load",
            "predicate": "reduces demand for",
            "object": "compatible_solute_accumulation",
            "description": "At low ambient NaCl, minimal osmoadaptive load reduces the need for compatible-solute accumulation.",
            "evidence": [
              {
                "reference": "DOI:10.1128/aem.00619-25",
                "notes": "Compatible solutes are accumulated in response to osmotic stress; low salt imposes minimal such demand."
              }
            ]
          },
          {
            "subject": "cyclic_di_amp",
            "predicate": "inhibits",
            "object": "k_uptake_systems",
            "description": "Cyclic di-AMP binds gating subunits of Trk/Ktr/Kup/KimA and inhibits K+ uptake.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mmbr.00181-23",
                "notes": "gating subunits of Trk/Ktr bind cyclic di-AMP; KUP-family activity is inhibited by cyclic di-AMP."
              }
            ],
            "predicate_id": "RO:0002212"
          },
          {
            "subject": "cyclic_di_amp",
            "predicate": "negatively regulates",
            "object": "opua_opuc_transport",
            "description": "Cyclic di-AMP binds OpuA/OpuC importers and negatively regulates compatible-solute transport.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mmbr.00181-23",
                "notes": "c-di-AMP binds CBS and RCK_C domains of OpuA/OpuC and negatively regulates their transport activity."
              }
            ],
            "predicate_id": "RO:0002212"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.833539+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-12T10:00:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed definition and causal graph linking minimal osmoadaptive load at low ambient NaCl to the non-halophile / halotolerant NaCl-optimum bin.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:30Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d71, rdfs:subClassOf\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 6 evidence-backed generic edges (7 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:10Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (rdfs:subClassOf\u00d71, RO:0002212\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:71578\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-04T03:08:12Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002212\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates (1 to confers), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope nacl_optimum_low_non_halophile_setpoint=NONMECHANISTIC with scope_notes; marked 2 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (k_uptake_systems, opua_opuc_transport).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T04:43:24Z",
        "curator": "codex",
        "action": "ADD_CANONICAL_EXAMPLES",
        "changes": "Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Sphingomonas oligoaromativorans (NCBITaxon:575322; DOI:10.1099/ijs.0.052894-0). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000466",
    "label": "NaCl optimum mid1",
    "definition": "A NaCl optimum phenotype with the best-growth NaCl concentration approximately between 1 and 3% (w/v), corresponding to slight-halophile or halotolerant physiology.",
    "definition_source": "DOI:10.1093/femsre/fuy009",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000333"
    ],
    "synonyms": [
      {
        "synonym_text": "Halotolerant",
        "synonym_type": "EXACT_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "Slight halophile",
        "synonym_type": "EXACT_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "NaO_1_to_3",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1093/femsre/fuy009",
        "snippet": "slight halophile",
        "notes": "Osmoadaptation review supports the 1\u20133% NaCl optimum range as the slight-halophile category."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:2585141",
        "taxon_label": "Flavicella sediminum",
        "reference": "DOI:10.1099/ijsem.0.003839",
        "note": "Type strain ALS 84T had a measured NaCl optimum of 2% (w/v), wholly inside the approximately 1-3% bin; growth occurred at 1-3%."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "nacl_optimum_mid1_slight_halophile",
        "title": "NaCl-optimum-mid1 slight-halophile setpoint",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a quantitative measurement, interval, or bin in the environmental phenotype hierarchy; a token protein example would misrepresent the measured value as one inherited molecular mechanism.",
        "description": "DOI-backed graph linking modest osmoadaptive activity at seawater-like NaCl to a 1\u20133% (w/v) NaCl-optimum (slight halophile).",
        "nodes": [
          {
            "node_id": "nacl_optimum_mid1_trait",
            "label": "NaCl optimum mid1",
            "node_type": "TRAIT",
            "grounding": "METPO:1000466",
            "description": "NaCl optimum approximately 1\u20133% w/v."
          },
          {
            "node_id": "nacl_optimum",
            "label": "NaCl optimum",
            "node_type": "TRAIT",
            "grounding": "METPO:1000333",
            "description": "NaCl concentration supporting maximal growth."
          },
          {
            "node_id": "seawater_nacl",
            "label": "seawater-like NaCl",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Marine or estuarine external NaCl ~1\u20133% w/v."
          },
          {
            "node_id": "modest_osmoadaptation",
            "label": "modest osmoadaptation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Compatible-solute accumulation and ion homeostasis tuned for seawater-range NaCl."
          },
          {
            "node_id": "slight_halophile_physiology",
            "label": "slight halophile / halotolerant physiology",
            "node_type": "STATE",
            "description": "Physiology of microbes with best growth at ~1-3% NaCl."
          },
          {
            "node_id": "salt_in_strategy",
            "label": "salt-in osmoregulation strategy",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Accumulation of inorganic ions (notably K+) and exclusion of Na+ to balance external salinity."
          },
          {
            "node_id": "compatible_solute_strategy",
            "label": "compatible-solute osmoregulation strategy",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Biosynthesis or uptake of small organic osmolytes (salt-out strategy) to offset osmotic stress."
          },
          {
            "node_id": "elevated_nacl",
            "label": "elevated external NaCl",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Increased external NaCl concentration imposing osmotic stress."
          },
          {
            "node_id": "glycine_betaine",
            "label": "glycine betaine",
            "node_type": "CHEMICAL",
            "description": "Compatible solute (CHEBI:17750) accumulated under osmotic stress.",
            "grounding": "CHEBI:17750"
          },
          {
            "node_id": "l_proline",
            "label": "L-proline",
            "node_type": "CHEMICAL",
            "description": "Compatible solute (CHEBI:17203) accumulated under osmotic stress."
          }
        ],
        "edges": [
          {
            "subject": "seawater_nacl",
            "predicate": "engages",
            "object": "modest_osmoadaptation",
            "description": "Seawater-like NaCl engages a moderate osmoadaptive program.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuy009",
                "snippet": "slight halophile",
                "notes": "Supports seawater-range NaCl as the context for slight-halophile optima."
              }
            ]
          },
          {
            "subject": "modest_osmoadaptation",
            "predicate": "confers",
            "object": "nacl_optimum_mid1_trait",
            "description": "A modest osmoadaptive program yields a 1\u20133% NaCl-optimum setpoint.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuy009",
                "snippet": "slight halophile",
                "notes": "Supports the 1\u20133% optimum as the slight-halophile outcome."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "nacl_optimum_mid1_trait",
            "predicate": "is a",
            "object": "nacl_optimum",
            "description": "NaCl optimum mid1 is a quantitative bin of the NaCl-optimum phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuy009",
                "snippet": "optimal NaCl",
                "notes": "Supports the 1\u20133% optimum as a value within the NaCl-optimum distribution."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "nacl_optimum_mid1_trait",
            "predicate": "defines",
            "object": "slight_halophile_physiology",
            "description": "A 1-3% (w/v) NaCl optimum defines slight-halophile/halotolerant physiology.",
            "evidence": [
              {
                "reference": "DOI:10.3390/biotech14020049",
                "notes": "\"slight halophiles (0.2-0.5 M or 1-3% NaCl)\" - supports trait scope/boundary."
              }
            ],
            "predicate_id": "METPO:2007500"
          },
          {
            "subject": "slight_halophile_physiology",
            "predicate": "associated with",
            "object": "salt_in_strategy",
            "description": "Slight-halophile physiology is broadly associated with the salt-in (K+ accumulation) strategy.",
            "evidence": [
              {
                "reference": "DOI:10.3389/frmbi.2023.1329925",
                "notes": "\"The salt-in strategy involves maintaining a high intracellular concentration of inorganic salts, mainly potassium\" - general mechanism across halotolerant/halophilic microbes."
              }
            ],
            "predicate_id": "biolink:associated_with"
          },
          {
            "subject": "slight_halophile_physiology",
            "predicate": "associated with",
            "object": "compatible_solute_strategy",
            "description": "Slight-halophile physiology is broadly associated with the compatible-solute (salt-out) strategy.",
            "evidence": [
              {
                "reference": "DOI:10.3389/frmbi.2023.1329925",
                "notes": "\"The salt-out strategy relies on biosynthesis or uptake of compatible solutes\" - general osmoadaptation mechanism."
              }
            ],
            "predicate_id": "biolink:associated_with"
          },
          {
            "subject": "elevated_nacl",
            "predicate": "induces accumulation of",
            "object": "glycine_betaine",
            "description": "Rising external NaCl increases intracellular glycine betaine.",
            "evidence": [
              {
                "reference": "DOI:10.1128/aem.00145-24",
                "notes": "\"The intracellular content of compatible solutes, including glycine betaine, glutamate, and proline, increases with rising salinity levels\" - directional relationship is broadly applicable."
              }
            ]
          },
          {
            "subject": "elevated_nacl",
            "predicate": "induces accumulation of",
            "object": "l_proline",
            "description": "Rising external NaCl increases intracellular L-proline.",
            "evidence": [
              {
                "reference": "DOI:10.1128/aem.00145-24",
                "notes": "\"The intracellular content of compatible solutes, including glycine betaine, glutamate, and proline, increases with rising salinity levels\" - proline is a general osmolyte."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.834129+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-12T10:00:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed definition and causal graph linking seawater-range NaCl and modest osmoadaptation to the slight-halophile NaCl-optimum bin.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:30Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d71, rdfs:subClassOf\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 5 evidence-backed generic edges (6 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:10Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:associated_with\u00d72, METPO:2007500\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:17750\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates (1 to confers), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-16T02:00:00Z",
        "curator": "claude",
        "action": "NORMALISE_NODE_TYPE",
        "changes": "Under the PATHWAY-vs-BIOLOGICAL_PROCESS rule, one node_id means one thing corpus-wide (issue 356): salt_in_strategy is typed BIOLOGICAL_PROCESS. PATHWAY is a named, conventionally enumerable multi-step route; BIOLOGICAL_PROCESS is everything else. A STRATEGY, not a route. The family is described as osmoadaptation by accumulating intracellular inorganic ions -- haloalkaliphilic.yaml puts it as 'Osmoadaptation by intracellular accumulation of inorganic ions (e.g. K+)', and the wording varies by record. There is no step list to enumerate, which is exactly the distinction this rule draws. Was 7 BIOLOGICAL_PROCESS to 1 before this tranche.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope nacl_optimum_mid1_slight_halophile=NONMECHANISTIC with scope_notes.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T04:43:24Z",
        "curator": "codex",
        "action": "ADD_CANONICAL_EXAMPLES",
        "changes": "Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Flavicella sediminum (NCBITaxon:2585141; DOI:10.1099/ijsem.0.003839). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000467",
    "label": "NaCl optimum mid2",
    "definition": "A NaCl optimum phenotype with the best-growth NaCl concentration approximately between 3 and 8% (w/v), corresponding to moderate-halophile or halotolerant physiology.",
    "definition_source": "DOI:10.1093/femsre/fuy009",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000333"
    ],
    "synonyms": [
      {
        "synonym_text": "Halotolerant",
        "synonym_type": "EXACT_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "Moderate halophile",
        "synonym_type": "EXACT_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "NaO_3_to_8",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1093/femsre/fuy009",
        "snippet": "moderate halophile",
        "notes": "Osmoadaptation review supports the 3\u20138% NaCl optimum range as the moderate-halophile category."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:735518",
        "taxon_label": "Lederbergia graminis",
        "reference": "DOI:10.1099/ijs.0.023820-0",
        "note": "The type strain, published as Bacillus graminis YC6957T and now NCBI-labelled Lederbergia graminis, grew optimally at 4-5% (w/v) NaCl, wholly inside the 3-8% bin."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "nacl_optimum_mid2_moderate_halophile",
        "title": "NaCl-optimum-mid2 moderate-halophile setpoint",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a quantitative measurement, interval, or bin in the environmental phenotype hierarchy; a token protein example would misrepresent the measured value as one inherited molecular mechanism.",
        "description": "DOI-backed graph linking pronounced compatible-solute accumulation at elevated NaCl to a 3\u20138% (w/v) NaCl-optimum (moderate halophile).",
        "nodes": [
          {
            "node_id": "nacl_optimum_mid2_trait",
            "label": "NaCl optimum mid2",
            "node_type": "TRAIT",
            "grounding": "METPO:1000467",
            "description": "NaCl optimum approximately 3\u20138% w/v."
          },
          {
            "node_id": "nacl_optimum",
            "label": "NaCl optimum",
            "node_type": "TRAIT",
            "grounding": "METPO:1000333",
            "description": "NaCl concentration supporting maximal growth."
          },
          {
            "node_id": "elevated_nacl",
            "label": "elevated NaCl",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "External NaCl ~3\u20138% w/v, typical of saline lakes and salt marshes."
          },
          {
            "node_id": "pronounced_compatible_solutes",
            "label": "pronounced compatible-solute accumulation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Substantial accumulation of organic osmolytes (ectoine, glycine betaine) under moderately hypersaline conditions."
          },
          {
            "node_id": "ectoine_biosynthesis_module",
            "label": "ectoine biosynthesis module (ectABC)",
            "node_type": "PATHWAY",
            "description": "Canonical ectABC (ectA/ectB/ectC) pathway producing the compatible solute ectoine."
          },
          {
            "node_id": "ectoine",
            "label": "ectoine",
            "node_type": "CHEMICAL",
            "description": "Major organic compatible solute (CHEBI:22563) accumulated during osmoadaptation.",
            "grounding": "CHEBI:27592"
          },
          {
            "node_id": "compatible_solute_strategy",
            "label": "compatible-solute strategy",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Osmoadaptation strategy buffering osmotic stress via accumulation of small organic osmolytes."
          },
          {
            "node_id": "glycine_betaine",
            "label": "glycine betaine",
            "node_type": "CHEMICAL",
            "description": "Organic compatible solute (CHEBI:17750) used in compatible-solute osmoadaptation.",
            "grounding": "CHEBI:17750"
          },
          {
            "node_id": "l_proline",
            "label": "L-proline",
            "node_type": "CHEMICAL",
            "description": "Organic compatible solute (CHEBI:26271) used in compatible-solute osmoadaptation."
          }
        ],
        "edges": [
          {
            "subject": "elevated_nacl",
            "predicate": "regulates",
            "object": "pronounced_compatible_solutes",
            "description": "Elevated NaCl drives substantial compatible-solute accumulation.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuy009",
                "snippet": "synthesize organic osmotic solutes",
                "notes": "Supports compatible-solute accumulation as the osmoadaptive response at elevated NaCl."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "pronounced_compatible_solutes",
            "predicate": "confers",
            "object": "nacl_optimum_mid2_trait",
            "description": "Pronounced compatible-solute accumulation yields a 3\u20138% NaCl-optimum setpoint.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuy009",
                "snippet": "moderate halophile",
                "notes": "Supports the 3\u20138% optimum as the moderate-halophile outcome."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "nacl_optimum_mid2_trait",
            "predicate": "is a",
            "object": "nacl_optimum",
            "description": "NaCl optimum mid2 is a quantitative bin of the NaCl-optimum phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuy009",
                "snippet": "optimal NaCl",
                "notes": "Supports the 3\u20138% optimum as a value within the NaCl-optimum distribution."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "elevated_nacl",
            "predicate": "induces",
            "object": "ectoine_biosynthesis_module",
            "description": "Elevated salinity (>3% NaCl) triggers the canonical ectoine biosynthesis pathway.",
            "evidence": [
              {
                "reference": "DOI:10.1128/aem.01905-23",
                "notes": "Exposure to salt concentrations higher than 3% NaCl triggers biosynthesis and intracellular accumulation of ectoine as a major compatible solute (Zou et al. 2024)."
              }
            ]
          },
          {
            "subject": "elevated_nacl",
            "predicate": "upregulates",
            "object": "ectoine_biosynthesis_module",
            "description": "Salt stress at ~6% w/v NaCl (within the 3-8% window) upregulates the ectoine biosynthesis module.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s12934-024-02515-w",
                "notes": "Transcriptomics showed the ectoine biosynthesis module is upregulated under salt stress, with 60 g/L NaCl (~6% w/v, inside 3-8% window) optimal for growth (Chen et al. 2024)."
              }
            ]
          },
          {
            "subject": "ectoine_biosynthesis_module",
            "predicate": "has output",
            "object": "ectoine",
            "description": "The ectABC pathway synthesizes the compatible solute ectoine.",
            "evidence": [
              {
                "reference": "DOI:10.1128/aem.01905-23",
                "notes": "Biosynthesis and intracellular accumulation of ectoine as a major compatible solute via the ectoine pathway (Zou et al. 2024)."
              }
            ],
            "predicate_id": "RO:0002234"
          },
          {
            "subject": "pronounced_compatible_solutes",
            "predicate": "is a",
            "object": "compatible_solute_strategy",
            "description": "Pronounced organic-osmolyte accumulation is an instance of the compatible-solute osmoadaptation strategy.",
            "evidence": [
              {
                "reference": "DOI:10.3390/biotech14020049",
                "notes": "The compatible-solute strategy accumulates small organic osmolytes including glycine, betaine, and ectoine (Neagu & Stancu 2025)."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "compatible_solute_strategy",
            "predicate": "uses",
            "object": "ectoine",
            "description": "Compatible-solute osmoadaptation employs ectoine as an organic osmolyte.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s12934-025-02757-2",
                "notes": "Many species naturally produce the osmolyte ectoine (plus hydroxyectoine, betaine, glycine, proline) (Coimbra et al. 2025)."
              }
            ]
          },
          {
            "subject": "compatible_solute_strategy",
            "predicate": "uses",
            "object": "glycine_betaine",
            "description": "Compatible-solute osmoadaptation employs glycine betaine as an organic osmolyte.",
            "evidence": [
              {
                "reference": "DOI:10.3390/biotech14020049",
                "notes": "Identified compatible solutes include glycine, betaine, and ectoine (Neagu & Stancu 2025)."
              }
            ]
          },
          {
            "subject": "compatible_solute_strategy",
            "predicate": "uses",
            "object": "l_proline",
            "description": "Compatible-solute osmoadaptation employs L-proline as an organic osmolyte.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s12934-025-02757-2",
                "notes": "Many species naturally produce the osmolyte ectoine plus hydroxyectoine, betaine, glycine, proline (Coimbra et al. 2025)."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.834715+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-12T10:00:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed definition and causal graph linking pronounced compatible-solute accumulation at elevated NaCl to the moderate-halophile NaCl-optimum bin.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:30Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d71, rdfs:subClassOf\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:18Z",
        "curator": "claude",
        "action": "RENAME_PREDICATE_LABELS",
        "changes": "Renamed 1 causal-edge predicate label(s) to align with existing groundings: drives \u2192 regulates \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:21Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002211\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 7 evidence-backed generic edges (5 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:10Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d71, rdfs:subClassOf\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:27592\u00d71, CHEBI:17750\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 2 causal edge(s) off microbe-domain METPO predicates (1 to confers, 1 to has output), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope nacl_optimum_mid2_moderate_halophile=NONMECHANISTIC with scope_notes.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T04:43:24Z",
        "curator": "codex",
        "action": "ADD_CANONICAL_EXAMPLES",
        "changes": "Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Lederbergia graminis (NCBITaxon:735518; DOI:10.1099/ijs.0.023820-0). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000334",
    "label": "NaCl range",
    "definition": "A salinity phenotype with numerical limits that bounds the minimum and maximum NaCl concentrations supporting growth of an organism.",
    "definition_source": "DOI:10.1093/femsre/fuy009",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000532",
      "METPO:1000535"
    ],
    "created_by": "Anthea Guo",
    "evidence": [
      {
        "reference": "DOI:10.1093/femsre/fuy009",
        "snippet": "salinity range",
        "notes": "Osmoadaptation review supports the span of NaCl concentrations supporting growth as a standard halophily descriptor."
      },
      {
        "reference": "DOI:10.1186/1746-1448-4-2",
        "snippet": "ways they cope with the high salt concentrations",
        "notes": "Saline-Systems review supports osmotic-tolerance breadth as the basis of the NaCl-range phenotype."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:504092",
        "taxon_label": "Kushneria aurantia",
        "reference": "DOI:10.1099/ijs.0.001461-0",
        "note": "Kushneria aurantia A10T grew from 5 to 17.5% (w/v) NaCl. The complete interval crosses the mid2/high boundary, so #591 places this distinct claim on the range parent only."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "nacl_range_tolerance_breadth",
        "title": "NaCl-range osmotic-tolerance breadth",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a quantitative measurement, interval, or bin in the environmental phenotype hierarchy; a token protein example would misrepresent the measured value as one inherited molecular mechanism.",
        "description": "DOI-backed graph linking ambient NaCl, osmoadaptive tolerance to low and high salt, and the bounded span of growth-supporting NaCl concentrations.",
        "nodes": [
          {
            "node_id": "nacl_range_trait",
            "label": "NaCl range",
            "node_type": "TRAIT",
            "grounding": "METPO:1000334",
            "description": "Span of NaCl concentrations supporting growth."
          },
          {
            "node_id": "ambient_nacl",
            "label": "ambient NaCl concentration",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Ambient NaCl level imposed on the cell."
          },
          {
            "node_id": "low_salt_tolerance",
            "label": "low-salt tolerance",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Capacity to maintain turgor and ion homeostasis at low ambient NaCl."
          },
          {
            "node_id": "high_salt_tolerance",
            "label": "high-salt tolerance",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Capacity to maintain osmotic balance under elevated NaCl."
          },
          {
            "node_id": "bounded_growth_window",
            "label": "bounded growth window",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Span of NaCl concentrations between the minimum and maximum that support growth."
          },
          {
            "node_id": "c_di_amp",
            "label": "cyclic di-AMP",
            "node_type": "CHEMICAL",
            "description": "Second messenger nucleotide that regulates K+ uptake and osmolyte transport.",
            "grounding": "CHEBI:71578"
          },
          {
            "node_id": "trk_ktr_k_influx",
            "label": "Trk/Ktr potassium influx systems",
            "node_type": "GENE_OR_PROTEIN",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed as a contextual protein or protein-complex label within a quantitative measurement graph; no exact semantic family term was established for this aggregate use.",
            "description": "Low-affinity potassium import systems (TrkAH, KtrAB, KtrCD) with c-di-AMP-binding gating subunits."
          },
          {
            "node_id": "kima_kup_k_uptake",
            "label": "KimA/Kup high-affinity K+ uptake transporters",
            "node_type": "GENE_OR_PROTEIN",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed as a contextual protein or protein-complex label within a quantitative measurement graph; no exact semantic family term was established for this aggregate use.",
            "description": "High-affinity potassium uptake transporters (KimA, KupA/KupB) directly inhibited by c-di-AMP."
          },
          {
            "node_id": "kdp_expression",
            "label": "Kdp system / KdpFABC expression",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Transcription of the kdpFABC high-affinity K+ uptake operon, regulated via KdpD."
          },
          {
            "node_id": "opua_solute_importers",
            "label": "OpuA-like compatible-solute importers",
            "node_type": "GENE_OR_PROTEIN",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed as a contextual protein or protein-complex label within a quantitative measurement graph; no exact semantic family term was established for this aggregate use.",
            "description": "ABC-type compatible-solute importers (OpuA family) bound and regulated by c-di-AMP."
          }
        ],
        "edges": [
          {
            "subject": "ambient_nacl",
            "predicate": "defines",
            "object": "bounded_growth_window",
            "description": "Ambient NaCl defines the axis over which the growth window is bounded.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuy009",
                "snippet": "salinity range",
                "notes": "Supports NaCl as the axis bounding the growth window."
              }
            ],
            "predicate_id": "METPO:2007500"
          },
          {
            "subject": "low_salt_tolerance",
            "predicate": "defines",
            "object": "bounded_growth_window",
            "description": "Tolerance to low salt sets the lower bound of the growth window.",
            "evidence": [
              {
                "reference": "DOI:10.1186/1746-1448-4-2",
                "snippet": "cope with the high salt concentrations",
                "notes": "Saline-Systems review frames halophily around salt-tolerance mechanisms that span both the lower and upper limits of growth-supporting salinity."
              }
            ],
            "predicate_id": "METPO:2007500"
          },
          {
            "subject": "high_salt_tolerance",
            "predicate": "defines",
            "object": "bounded_growth_window",
            "description": "Tolerance to high salt sets the upper bound of the growth window.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuy009",
                "snippet": "high salt concentrations",
                "notes": "Supports tolerance to high salt as the upper-bound mechanism."
              }
            ],
            "predicate_id": "METPO:2007500"
          },
          {
            "subject": "bounded_growth_window",
            "predicate": "manifests as",
            "object": "nacl_range_trait",
            "description": "The bounded growth window manifests the NaCl-range phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuy009",
                "snippet": "salinity range",
                "notes": "Supports the trait endpoint."
              }
            ],
            "predicate_id": "METPO:2007400"
          },
          {
            "subject": "c_di_amp",
            "predicate": "inhibits",
            "object": "trk_ktr_k_influx",
            "description": "c-di-AMP binds gating subunits of Trk/Ktr systems, inhibiting potassium influx.",
            "evidence": [
              {
                "reference": "DOI:10.1128/MMBR.00181-23",
                "notes": "TrkAH, KtrAB and KtrCD gating subunits bind c-di-AMP, inhibiting potassium influx (Foster et al. 2024, review across multiple bacteria)."
              }
            ],
            "predicate_id": "RO:0002212"
          },
          {
            "subject": "c_di_amp",
            "predicate": "inhibits",
            "object": "kima_kup_k_uptake",
            "description": "c-di-AMP directly inhibits high-affinity K+ uptake transporters KimA and Kup.",
            "evidence": [
              {
                "reference": "DOI:10.1128/MMBR.00181-23",
                "notes": "High-affinity transporters (KimA, KupA/KupB) are inhibited directly by cyclic di-AMP, affecting K+ homeostasis underlying NaCl limits."
              }
            ],
            "predicate_id": "RO:0002212"
          },
          {
            "subject": "c_di_amp",
            "predicate": "inhibits",
            "object": "kdp_expression",
            "description": "c-di-AMP binding to KdpD inhibits kdpFABC transcription.",
            "evidence": [
              {
                "reference": "DOI:10.1128/MMBR.00181-23",
                "notes": "KdpD binding of cyclic di-AMP inhibits kdpFABC transcription (Foster et al. 2024 review)."
              }
            ],
            "predicate_id": "RO:0002212"
          },
          {
            "subject": "c_di_amp",
            "predicate": "regulates",
            "object": "opua_solute_importers",
            "description": "c-di-AMP binds and regulates OpuA-like compatible-solute importers.",
            "evidence": [
              {
                "reference": "DOI:10.1128/MMBR.00181-23",
                "notes": "c-di-AMP binds OpuA-like ABC compatible-solute importers, linking the regulatory module to osmolyte accumulation."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "c_di_amp",
            "predicate": "decreases",
            "object": "high_salt_tolerance",
            "description": "Elevated c-di-AMP correlates with salt sensitivity and narrower NaCl tolerance.",
            "evidence": [
              {
                "reference": "DOI:10.1128/MMBR.00181-23",
                "notes": "High cyclic di-AMP levels correlate with salt sensitivity, narrowing salt tolerance via suppressed K+ uptake (Foster et al. 2024 review)."
              }
            ],
            "predicate_id": "RO:0002212"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.816101+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-12T10:00:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed causal graph linking ambient NaCl and low/high-salt tolerance to the bounded NaCl-range phenotype.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T21:30:06Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007400\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T07:37:39Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007500\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-26T05:00:47Z",
        "curator": "claude",
        "action": "RENAME_PREDICATE_LABELS",
        "changes": "Renamed 2 causal-edge predicate label(s) to align with existing groundings: sets \u2192 defines \u00d72.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-26T05:00:50Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007500\u00d72).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 5 evidence-backed generic edges (5 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:10Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 5 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002212\u00d73, RO:0002211\u00d71, METPO:2000017\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:71578\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T02:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES_PART2",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates onto their causal-graph counterparts (1 to reduces), issue 301 part 2. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Each replacement is a 1:1 mirror of its source predicate that changes only the domain, so the claim each edge makes is unchanged and directions are unchanged. The replacements are proposed in proposals/metpo_traitmech_v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T06:00:00Z",
        "curator": "claude",
        "action": "REGROUND_CAUSAL_EDGE",
        "changes": "Relabelled 1 causal edge from `reduces` to `decreases` and re-grounded it from METPO:2007802 to RO:0002212 (negatively regulates), issue 330. The corpus wrote two senses under the single label `reduces` - genuine electron donation, and a lessens/decreases sense - and METPO:2007802 is defined as donating electrons to the object and lowering its oxidation state, which this edge does not assert. The two senses could not be separated mechanically because the label was identical, so they migrated together in issue 329 and were split here by reading each edge. RO:0002212 declares no rdfs:domain or rdfs:range, so this introduces no entailment of the kind issue 301 removed.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope nacl_range_tolerance_breadth=NONMECHANISTIC with scope_notes; marked 3 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (trk_ktr_k_influx, kima_kup_k_uptake, opua_solute_importers).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T04:43:24Z",
        "curator": "codex",
        "action": "ADD_CANONICAL_EXAMPLES",
        "changes": "Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Kushneria aurantia (NCBITaxon:504092; DOI:10.1099/ijs.0.001461-0). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000472",
    "label": "NaCl range high",
    "definition": "A NaCl range phenotype in which the growth-supporting NaCl range extends above approximately 8% (w/v), characteristic of extreme-halophile organisms.",
    "definition_source": "DOI:10.1093/femsre/fuy009",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000334"
    ],
    "synonyms": [
      {
        "synonym_text": "Extreme halophile",
        "synonym_type": "EXACT_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "NaR_>8",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1093/femsre/fuy009",
        "snippet": "extreme halophile",
        "notes": "Osmoadaptation review supports growth ranges extending above 8% NaCl as the extreme-halophile category."
      },
      {
        "reference": "DOI:10.1186/1746-1448-4-2",
        "snippet": "KCl accumulating Halobacterium salinarum",
        "notes": "Saline-Systems review supports salt-in physiology underlying extended high-salt growth."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:486505",
        "taxon_label": "Amycolatopsis flava",
        "reference": "DOI:10.1007/s10482-015-0542-z",
        "note": "Amycolatopsis flava AFM 10111T grew from 1 to 30% NaCl; its measured growth range extends well above the approximately 8% threshold, as this record defines."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "nacl_range_high_extreme_halophile",
        "title": "NaCl-range-high extreme-halophile range",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a quantitative measurement, interval, or bin in the environmental phenotype hierarchy; a token protein example would misrepresent the measured value as one inherited molecular mechanism.",
        "description": "DOI-backed graph linking salt-in physiology to NaCl growth ranges extending above 8% (w/v).",
        "nodes": [
          {
            "node_id": "nacl_range_high_trait",
            "label": "NaCl range high",
            "node_type": "TRAIT",
            "grounding": "METPO:1000472",
            "description": "NaCl growth-supporting range extending above ~8% w/v."
          },
          {
            "node_id": "nacl_range",
            "label": "NaCl range",
            "node_type": "TRAIT",
            "grounding": "METPO:1000334",
            "description": "Span of NaCl concentrations supporting growth."
          },
          {
            "node_id": "salt_in_physiology",
            "label": "salt-in physiology",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Intracellular ion-accumulation strategy enabling growth at hypersaline NaCl."
          },
          {
            "node_id": "high_external_nacl",
            "label": "high external NaCl / hypersaline brine",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "High extracellular NaCl concentration characteristic of hypersaline brines."
          },
          {
            "node_id": "intracellular_potassium",
            "label": "intracellular K+",
            "node_type": "CHEMICAL",
            "description": "High intracellular potassium(1+) accumulated by the salt-in strategy."
          },
          {
            "node_id": "acidic_proteome",
            "label": "acidic proteome",
            "node_type": "QUALITY",
            "description": "Proteome enriched in acidic amino acids (Glu/Asp) giving negatively charged surfaces."
          },
          {
            "node_id": "acidic_amino_acid_enrichment",
            "label": "acidic amino acid enrichment (Asp/Glu)",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Enrichment of aspartate and glutamate residues in intracellular proteins."
          },
          {
            "node_id": "protein_function_high_ionic",
            "label": "protein function at very high ionic strength",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "Maintenance of protein functionality under molar intracellular ionic strength."
          },
          {
            "node_id": "compatible_solutes",
            "label": "intracellular compatible solutes",
            "node_type": "CHEMICAL",
            "description": "Organic osmolytes accumulated intracellularly to balance osmotic stress."
          },
          {
            "node_id": "protein_stabilization",
            "label": "protein stabilization under salt stress",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Stabilization of proteins/enzymes under salt/osmotic stress."
          }
        ],
        "edges": [
          {
            "subject": "salt_in_physiology",
            "predicate": "confers",
            "object": "nacl_range_high_trait",
            "description": "Salt-in physiology yields a growth range extending above 8% NaCl.",
            "evidence": [
              {
                "reference": "DOI:10.1186/1746-1448-4-2",
                "snippet": "KCl accumulating Halobacterium salinarum",
                "notes": "Supports salt-in physiology as the basis of extreme-halophile growth ranges."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "nacl_range_high_trait",
            "predicate": "is a",
            "object": "nacl_range",
            "description": "NaCl range high is a quantitative bin of the NaCl-range phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuy009",
                "snippet": "salinity range",
                "notes": "Supports the >8% range as a value within the NaCl-range distribution."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "high_external_nacl",
            "predicate": "induces",
            "object": "intracellular_potassium",
            "description": "High external NaCl induces molar intracellular K+ accumulation (salt-in strategy).",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41559-024-02505-6",
                "notes": "Canonical salt-in strategy accumulates molar cytoplasmic K+ (up to 4M) in hypersaline systems."
              }
            ]
          },
          {
            "subject": "salt_in_physiology",
            "predicate": "results in",
            "object": "acidic_proteome",
            "description": "Salt-in physiology drives proteome acidification via enrichment in acidic amino acids.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41559-024-02505-6",
                "notes": "K+ accumulation accompanied by proteome acidification through Glu/Asp enrichment."
              }
            ]
          },
          {
            "subject": "acidic_amino_acid_enrichment",
            "predicate": "contributes to",
            "object": "protein_function_high_ionic",
            "description": "Asp/Glu enrichment produces negatively charged surfaces enabling protein function at high ionic strength.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuy026",
                "notes": "Salt-in proteins more hydrophilic and enriched in acidic residues, enabling functionality at very high ionic strength."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "salt_in_physiology",
            "predicate": "depends on",
            "object": "intracellular_potassium",
            "description": "Salt-in extreme-halophile physiology depends on high intracellular K+ (proteins misfold below ~2.2 M).",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuy026",
                "notes": "Cellular vitality of salt-in organisms dependent on high intracellular K+; proteins misfold when K+ falls below ~2.2 M."
              }
            ],
            "predicate_id": "RO:0002502"
          },
          {
            "subject": "compatible_solutes",
            "predicate": "stabilizes",
            "object": "protein_stabilization",
            "description": "Intracellular compatible solutes stabilize proteins/enzymes under salt stress.",
            "evidence": [
              {
                "reference": "DOI:10.1007/978-3-030-18975-4_4",
                "notes": "Osmolytes act as protein stabilizers/chaperones under salt stress."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.837512+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-12T10:00:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed definition and causal graph linking salt-in physiology to the extreme-halophile NaCl-range bin.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:30Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d71, rdfs:subClassOf\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 5 evidence-backed generic edges (7 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:10Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002326\u00d71, RO:0002502\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates (1 to confers), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope nacl_range_high_extreme_halophile=NONMECHANISTIC with scope_notes.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T04:43:24Z",
        "curator": "codex",
        "action": "ADD_CANONICAL_EXAMPLES",
        "changes": "Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Amycolatopsis flava (NCBITaxon:486505; DOI:10.1007/s10482-015-0542-z). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000469",
    "label": "NaCl range low",
    "definition": "A NaCl range phenotype in which the upper bound of growth-supporting NaCl concentration is at or below approximately 1% (w/v), characteristic of non-halophilic or halotolerant organisms.",
    "definition_source": "DOI:10.1093/femsre/fuy009",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000334"
    ],
    "synonyms": [
      {
        "synonym_text": "Halotolerant",
        "synonym_type": "EXACT_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "Non-halophile",
        "synonym_type": "EXACT_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "NaR_<=1",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1093/femsre/fuy009",
        "snippet": "salinity range",
        "notes": "Osmoadaptation review supports growth limited to \u2264 ~1% NaCl as the non-halophilic / halotolerant range."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:575322",
        "taxon_label": "Sphingomonas oligoaromativorans",
        "reference": "DOI:10.1099/ijs.0.052894-0",
        "note": "Type strain SY-6T grew from 0 to 0.5% (w/v) NaCl, with a 0.01% optimum; the complete reported range lies below the approximately 1% upper bound."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "nacl_range_low_non_halophile",
        "title": "NaCl-range-low non-halophile range",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a quantitative measurement, interval, or bin in the environmental phenotype hierarchy; a token protein example would misrepresent the measured value as one inherited molecular mechanism.",
        "description": "DOI-backed graph linking limited high-salt tolerance to a growth-supporting NaCl range capped at ~1% (w/v).",
        "nodes": [
          {
            "node_id": "nacl_range_low_trait",
            "label": "NaCl range low",
            "node_type": "TRAIT",
            "grounding": "METPO:1000469",
            "description": "NaCl growth-supporting range with upper bound \u2264 ~1% w/v."
          },
          {
            "node_id": "nacl_range",
            "label": "NaCl range",
            "node_type": "TRAIT",
            "grounding": "METPO:1000334",
            "description": "Span of NaCl concentrations supporting growth."
          },
          {
            "node_id": "limited_high_salt_tolerance",
            "label": "limited high-salt tolerance",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced capacity to maintain osmotic balance above ~1% NaCl."
          },
          {
            "node_id": "nacl_concentration",
            "label": "NaCl concentration",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "External sodium chloride concentration in the environment."
          },
          {
            "node_id": "hyperosmotic_stress",
            "label": "hyperosmotic stress",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "External hypertonicity causing cell shrinkage and plasmolysis."
          },
          {
            "node_id": "compatible_solute_accumulation",
            "label": "compatible solute accumulation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Synthesis or import of neutral osmolytes to balance cytoplasmic osmolarity."
          },
          {
            "node_id": "hypoosmotic_shock",
            "label": "hypoosmotic shock",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Rapid drop in external osmolarity causing turgor increase."
          },
          {
            "node_id": "mechanosensitive_channels",
            "label": "mechanosensitive channels MscL/MscS",
            "node_type": "GENE_OR_PROTEIN",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed as a contextual protein or protein-complex label within a quantitative measurement graph; no exact semantic family term was established for this aggregate use.",
            "description": "Tension-gated channels (MscL/MscS) that vent solutes to prevent lysis."
          },
          {
            "node_id": "c_di_amp",
            "label": "cyclic di-AMP",
            "node_type": "CHEMICAL",
            "description": "Second messenger that regulates potassium and osmolyte transport.",
            "grounding": "CHEBI:71578"
          },
          {
            "node_id": "opu_solute_importers",
            "label": "OpuA/OpuC compatible-solute importers",
            "node_type": "GENE_OR_PROTEIN",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed as a contextual protein or protein-complex label within a quantitative measurement graph; no exact semantic family term was established for this aggregate use.",
            "description": "ABC-type transporters that import compatible solutes like glycine betaine."
          },
          {
            "node_id": "choline_uptake",
            "label": "choline uptake",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Import of external choline used as a glycine betaine precursor."
          },
          {
            "node_id": "glycine_betaine_synthesis",
            "label": "glycine betaine biosynthesis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Synthesis of the compatible solute glycine betaine.",
            "grounding": "GO:0031456"
          }
        ],
        "edges": [
          {
            "subject": "limited_high_salt_tolerance",
            "predicate": "confers",
            "object": "nacl_range_low_trait",
            "description": "Limited tolerance to elevated NaCl caps growth at low salt.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuy009",
                "snippet": "salinity range",
                "notes": "Supports limited high-salt tolerance as the basis of a low NaCl range."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "nacl_range_low_trait",
            "predicate": "is a",
            "object": "nacl_range",
            "description": "NaCl range low is a quantitative bin of the NaCl-range phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuy009",
                "snippet": "salinity range",
                "notes": "Supports low NaCl range as a value within the NaCl-range distribution."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "nacl_concentration",
            "predicate": "causes",
            "object": "hyperosmotic_stress",
            "description": "Increased external NaCl concentration causes hyperosmotic stress.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsml/uqad020",
                "snippet": "hyperosmotic stress by addition of either non-ionic osmolyte sucrose or ionic solute NaCl",
                "notes": "Verified against the open Bhowmick et al. review; the edge is retained as a broad NaCl-to-hyperosmotic-stress step, not as a direct determinant of the <=1% range bin."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "hyperosmotic_stress",
            "predicate": "increases",
            "object": "compatible_solute_accumulation",
            "description": "Hyperosmotic stress increases compatible-solute accumulation as a later osmoadaptive response.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsml/uqad020",
                "snippet": "external osmotic upshifts by increasing the cellular concentration of cations (e.g. K+) and compatible solutes",
                "notes": "Verified against the open Bhowmick et al. review; this keeps compatible-solute accumulation as a broad osmotic-upshift response."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "mechanosensitive_channels",
            "predicate": "mitigates",
            "object": "hypoosmotic_shock",
            "description": "Mechanosensitive channels mitigate turgor stress during sudden hypoosmotic shocks at the low-salinity end of the range.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsml/uqad020",
                "snippet": "emergency reaction essential for preventing turgor increase",
                "notes": "Verified against the open Bhowmick et al. review; the edge is reversed from ungrounded shock-opens-channel wording to a grounded mitigation predicate."
              }
            ],
            "predicate_id": "METPO:2007407"
          },
          {
            "subject": "c_di_amp",
            "predicate": "inhibits",
            "object": "opu_solute_importers",
            "description": "c-di-AMP binds and inhibits OpuA/OpuC compatible-solute importers.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mmbr.00181-23",
                "snippet": "Cyclic di-AMP binds to the CBS domains of compatible solute importers",
                "notes": "Verified against public Foster et al. text; OpuA/OpuC are retained as representative CBS-domain osmolyte importers."
              }
            ],
            "predicate_id": "RO:0002212"
          },
          {
            "subject": "choline_uptake",
            "predicate": "enables",
            "object": "glycine_betaine_synthesis",
            "description": "Choline uptake enables synthesis of glycine betaine, a key compatible solute.",
            "evidence": [
              {
                "reference": "DOI:10.1126/sciadv.ado6229",
                "snippet": "uptake of external choline for synthesizing the osmoprotective glycine betaine",
                "notes": "Verified against public Yang et al. abstract text; choline uptake is retained as the substrate-supply step for glycine-betaine biosynthesis."
              }
            ],
            "predicate_id": "RO:0002327"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.835809+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-12T10:00:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed definition and causal graph linking limited high-salt tolerance to the non-halophile NaCl-range bin.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:30Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d71, rdfs:subClassOf\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 5 evidence-backed generic edges (9 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:10Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:causes\u00d71, RO:0002212\u00d71, RO:0002327\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:71578\u00d71, GO:0031456\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates (1 to confers), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope nacl_range_low_non_halophile=NONMECHANISTIC with scope_notes; marked 2 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (mechanosensitive_channels, opu_solute_importers).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T04:43:24Z",
        "curator": "codex",
        "action": "ADD_CANONICAL_EXAMPLES",
        "changes": "Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Sphingomonas oligoaromativorans (NCBITaxon:575322; DOI:10.1099/ijs.0.052894-0). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-04T08:00:00Z",
        "curator": "codex",
        "action": "REVIEW_CAUSAL_EVIDENCE",
        "changes": "Reviewed the nacl_range_low_non_halophile graph for issue #183: added exact snippets to 5 causal-edge evidence items, grounded 2 residual predicates, and repaired 1 local node-type conflict. No paid research service was called.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-06T17:10:00Z",
        "curator": "codex",
        "action": "ADVERSARIAL_REVIEW_REPAIR",
        "changes": "Addressed PR #664 adversarial review: replaced the unsupported compatible-solute bridge snippet with exact Bhowmick et al. wording that normalizes the K+ superscript and names both cation and compatible-solute accumulation after an external osmotic upshift.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000470",
    "label": "NaCl range mid1",
    "definition": "A NaCl range phenotype in which the growth-supporting NaCl range spans approximately 1\u20133% (w/v), characteristic of slight-halophilic or halotolerant organisms.",
    "definition_source": "DOI:10.1093/femsre/fuy009",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000334"
    ],
    "synonyms": [
      {
        "synonym_text": "Halotolerant",
        "synonym_type": "EXACT_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "Slight halophile",
        "synonym_type": "EXACT_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "NaR_1_to_3",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1093/femsre/fuy009",
        "snippet": "slight halophile",
        "notes": "Osmoadaptation review supports the 1\u20133% NaCl growth range as the slight-halophile/halotolerant category."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:2995321",
        "taxon_label": "Spongorhabdus nitratireducens",
        "reference": "DOI:10.1099/ijsem.0.007037",
        "note": "Spongorhabdus nitratireducens strains XeTr1T and StTr2 grew across the complete reported 1-3% (w/v) NaCl interval, matching this bin without extrapolation."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "nacl_range_mid1_slight_halophile",
        "title": "NaCl-range-mid1 slight-halophile range",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a quantitative measurement, interval, or bin in the environmental phenotype hierarchy; a token protein example would misrepresent the measured value as one inherited molecular mechanism.",
        "description": "DOI-backed graph linking modest osmoadaptive tolerance to a 1\u20133% (w/v) NaCl growth range.",
        "nodes": [
          {
            "node_id": "nacl_range_mid1_trait",
            "label": "NaCl range mid1",
            "node_type": "TRAIT",
            "grounding": "METPO:1000470",
            "description": "NaCl growth-supporting range approximately 1\u20133% w/v."
          },
          {
            "node_id": "nacl_range",
            "label": "NaCl range",
            "node_type": "TRAIT",
            "grounding": "METPO:1000334",
            "description": "Span of NaCl concentrations supporting growth."
          },
          {
            "node_id": "modest_osmoadaptive_tolerance",
            "label": "modest osmoadaptive tolerance",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Osmoadaptive capacity supporting growth across seawater-range NaCl."
          },
          {
            "node_id": "slight_halophile",
            "label": "slight halophile",
            "node_type": "TRAIT",
            "description": "Organisms that grow best in media with 1-3% NaCl."
          },
          {
            "node_id": "moderate_halophile",
            "label": "moderate halophile",
            "node_type": "TRAIT",
            "description": "Organisms growing optimally in 3-15% NaCl (0.5-2.5 M salt)."
          },
          {
            "node_id": "optimal_growth_0_5_to_2_5_M_salt",
            "label": "optimal growth between 0.5 and 2.5 M salt",
            "node_type": "QUALITY",
            "description": "Salt optimum defining moderate halophiles."
          },
          {
            "node_id": "potassium_accumulation",
            "label": "K+ accumulation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Intracellular accumulation of potassium ions for osmotic balancing."
          },
          {
            "node_id": "osmotic_balance",
            "label": "osmotic balance / salt adaptation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Maintenance of cellular osmotic homeostasis under salt stress."
          },
          {
            "node_id": "compatible_solute_strategy",
            "label": "compatible solute strategy",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Osmoadaptation via ion exclusion and production of compatible solutes such as glycine betaine."
          },
          {
            "node_id": "halotolerant_and_moderate_halophiles",
            "label": "halotolerant and moderate halophiles",
            "node_type": "TRAIT",
            "description": "Organisms tolerating or requiring moderate salinity."
          }
        ],
        "edges": [
          {
            "subject": "modest_osmoadaptive_tolerance",
            "predicate": "confers",
            "object": "nacl_range_mid1_trait",
            "description": "Modest osmoadaptive tolerance yields a 1\u20133% NaCl growth range.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuy009",
                "snippet": "slight halophile",
                "notes": "Supports the 1\u20133% range as the slight-halophile outcome."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "nacl_range_mid1_trait",
            "predicate": "is a",
            "object": "nacl_range",
            "description": "NaCl range mid1 is a quantitative bin of the NaCl-range phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuy009",
                "snippet": "salinity range",
                "notes": "Supports the 1\u20133% range as a value within the NaCl-range distribution."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "nacl_range_mid1_trait",
            "predicate": "corresponds to",
            "object": "slight_halophile",
            "description": "The 1-3% w/v NaCl range corresponds to the slight-halophile phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1007/978-3-540-74231-9",
                "notes": "slight halophiles grow best in media with 1 to 3% NaCl"
              }
            ]
          },
          {
            "subject": "slight_halophile",
            "predicate": "distinct from",
            "object": "moderate_halophile",
            "description": "Slight halophiles are distinct from moderate halophiles, which grow optimally at higher NaCl.",
            "evidence": [
              {
                "reference": "DOI:10.1007/978-3-540-74231-9",
                "notes": "moderate halophiles grow optimally in media with 3 to 15% NaCl"
              }
            ]
          },
          {
            "subject": "moderate_halophile",
            "predicate": "defined as",
            "object": "optimal_growth_0_5_to_2_5_M_salt",
            "description": "Moderate halophiles are defined as organisms growing optimally between 0.5 and 2.5 M salt.",
            "evidence": [
              {
                "reference": "DOI:10.1128/MMBR.62.2.504-544.1998",
                "notes": "moderate halophiles as organisms growing optimally between 0.5 and 2.5 M salt"
              }
            ]
          },
          {
            "subject": "potassium_accumulation",
            "predicate": "contributes to",
            "object": "osmotic_balance",
            "description": "K+ accumulation contributes to osmotic balance and salt adaptation.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.00145-24",
                "notes": "simultaneously accumulating compatible solutes and K+; general osmoadaptation edge"
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "compatible_solute_strategy",
            "predicate": "characterizes",
            "object": "halotolerant_and_moderate_halophiles",
            "description": "The compatible-solute strategy characterizes halotolerant and moderate halophiles.",
            "evidence": [
              {
                "reference": "DOI:10.1093/FEMSRE/FUY026",
                "notes": "halotolerant and moderate halophiles rely on excluding ions and producing compatible solutes such as glycine betaine"
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.836372+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-12T10:00:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed definition and causal graph linking modest osmoadaptive tolerance to the slight-halophile NaCl-range bin.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:30Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d71, rdfs:subClassOf\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 5 evidence-backed generic edges (7 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:10Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002326\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates (1 to confers), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope nacl_range_mid1_slight_halophile=NONMECHANISTIC with scope_notes.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T04:43:24Z",
        "curator": "codex",
        "action": "ADD_CANONICAL_EXAMPLES",
        "changes": "Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Spongorhabdus nitratireducens (NCBITaxon:2995321; DOI:10.1099/ijsem.0.007037). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000471",
    "label": "NaCl range mid2",
    "definition": "A NaCl range phenotype in which the growth-supporting NaCl range spans approximately 3\u20138% (w/v), characteristic of moderate-halophile organisms.",
    "definition_source": "DOI:10.1093/femsre/fuy009",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000334"
    ],
    "synonyms": [
      {
        "synonym_text": "Halotolerant",
        "synonym_type": "EXACT_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "Moderate halophile",
        "synonym_type": "EXACT_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "NaR_3_to_8",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1093/femsre/fuy009",
        "snippet": "moderate halophile",
        "notes": "Osmoadaptation review supports the 3\u20138% NaCl growth range as the moderate-halophile category."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1182451",
        "taxon_label": "Aureivirga marina",
        "reference": "DOI:10.1099/ijs.0.043257-0",
        "note": "Aureivirga marina strain VI.14 grew at 3-5% (w/v) NaCl; the complete reported interval lies within the approximately 3-8% bin."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "nacl_range_mid2_moderate_halophile",
        "title": "NaCl-range-mid2 moderate-halophile range",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a quantitative measurement, interval, or bin in the environmental phenotype hierarchy; a token protein example would misrepresent the measured value as one inherited molecular mechanism.",
        "description": "DOI-backed graph linking robust osmoadaptive tolerance to a 3\u20138% (w/v) NaCl growth range.",
        "nodes": [
          {
            "node_id": "nacl_range_mid2_trait",
            "label": "NaCl range mid2",
            "node_type": "TRAIT",
            "grounding": "METPO:1000471",
            "description": "NaCl growth-supporting range approximately 3\u20138% w/v."
          },
          {
            "node_id": "nacl_range",
            "label": "NaCl range",
            "node_type": "TRAIT",
            "grounding": "METPO:1000334",
            "description": "Span of NaCl concentrations supporting growth."
          },
          {
            "node_id": "robust_osmoadaptive_tolerance",
            "label": "robust osmoadaptive tolerance",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Strong compatible-solute and ion-balance capacity sustaining growth at saline-lake / salt-marsh NaCl levels."
          },
          {
            "node_id": "ectABC_enzyme_module",
            "label": "EctABC ectoine-biosynthesis enzyme module",
            "node_type": "GENE_OR_PROTEIN",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed as a contextual protein or protein-complex label within a quantitative measurement graph; no exact semantic family term was established for this aggregate use.",
            "description": "EctA, EctB, and EctC enzymes catalyzing the ectoine biosynthesis pathway.",
            "gene_symbols": [
              "ectA",
              "ectB",
              "ectC"
            ],
            "operon": "ectABC"
          },
          {
            "node_id": "ectoine",
            "label": "ectoine",
            "node_type": "CHEMICAL",
            "description": "Compatible solute / osmoprotectant accumulated under salt stress.",
            "grounding": "CHEBI:27592"
          },
          {
            "node_id": "na_k_ion_uptake",
            "label": "Na+ and K+ ion uptake",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Rapid uptake of sodium and potassium ions following NaCl upshift."
          },
          {
            "node_id": "osmotic_pressure_balance",
            "label": "osmotic pressure balance",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Balancing of intracellular osmotic pressure after a NaCl upshift."
          },
          {
            "node_id": "glutamate_glutamine_pools",
            "label": "intracellular glutamate/glutamine pools",
            "node_type": "CHEMICAL",
            "description": "Elevated glutamate and glutamine amino-acid pools providing early osmotic buffering."
          },
          {
            "node_id": "betAB_pathway",
            "label": "BetA/BetB pathway",
            "node_type": "GENE_OR_PROTEIN",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed as a contextual protein or protein-complex label within a quantitative measurement graph; no exact semantic family term was established for this aggregate use.",
            "description": "Choline dehydrogenase (BetA) and betaine aldehyde dehydrogenase (BetB) converting choline to glycine betaine."
          },
          {
            "node_id": "glycine_betaine",
            "label": "glycine betaine",
            "node_type": "CHEMICAL",
            "description": "Compatible solute synthesized from choline; osmoprotectant.",
            "grounding": "CHEBI:17750"
          }
        ],
        "edges": [
          {
            "subject": "robust_osmoadaptive_tolerance",
            "predicate": "confers",
            "object": "nacl_range_mid2_trait",
            "description": "Robust osmoadaptive tolerance yields a 3\u20138% NaCl growth range.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuy009",
                "snippet": "moderate halophile",
                "notes": "Supports the 3\u20138% range as the moderate-halophile outcome."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "nacl_range_mid2_trait",
            "predicate": "is a",
            "object": "nacl_range",
            "description": "NaCl range mid2 is a quantitative bin of the NaCl-range phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuy009",
                "snippet": "salinity range",
                "notes": "Supports the 3\u20138% range as a value within the NaCl-range distribution."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "ectABC_enzyme_module",
            "predicate": "catalyzes biosynthesis of",
            "object": "ectoine",
            "description": "The EctABC enzyme module catalyzes the conserved ectoine biosynthesis pathway.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2023.1192059",
                "notes": "Ectoine biosynthesis relies on the EctA, EctB, and EctC proteins; their operon organization is recorded as node metadata."
              }
            ]
          },
          {
            "subject": "ectoine",
            "predicate": "positively contributes to",
            "object": "nacl_range_mid2_trait",
            "description": "Ectoine accumulation supports sustained growth/tolerance at 6-8% NaCl.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s12934-024-02358-5",
                "notes": "Within tolerable range (1-8% NaCl shock) ectoine rapidly becomes the dominant osmoprotectant."
              }
            ]
          },
          {
            "subject": "na_k_ion_uptake",
            "predicate": "rapidly balances",
            "object": "osmotic_pressure_balance",
            "description": "Uptake of Na+ and K+ ions rapidly balances osmotic pressure after NaCl upshift.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s12934-024-02358-5",
                "notes": "Cells urgently balanced surging osmotic pressure by uptaking sodium and potassium ions."
              }
            ]
          },
          {
            "subject": "osmotic_pressure_balance",
            "predicate": "contributes to",
            "object": "robust_osmoadaptive_tolerance",
            "description": "Balancing osmotic pressure underpins robust osmoadaptive tolerance.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s12934-024-02358-5",
                "notes": "Rapid ion-flux osmotic balancing is part of the osmoadaptive response sustaining growth."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "glutamate_glutamine_pools",
            "predicate": "provides early osmotic buffering for",
            "object": "robust_osmoadaptive_tolerance",
            "description": "Increased glutamate/glutamine pools provide early osmotic buffering during NaCl shock.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s12934-024-02358-5",
                "notes": "Augmenting intracellular amino acid pools, particularly glutamate and glutamine, buffers early osmotic stress."
              }
            ]
          },
          {
            "subject": "betAB_pathway",
            "predicate": "enables biosynthesis of",
            "object": "glycine_betaine",
            "description": "BetA and BetB convert choline to glycine betaine, a compatible solute.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2023.1192059",
                "notes": "Choline to glycine betaine via BetA and BetB; conserved across moderate halophiles."
              }
            ]
          },
          {
            "subject": "glycine_betaine",
            "predicate": "positively contributes to",
            "object": "robust_osmoadaptive_tolerance",
            "description": "Glycine betaine acts as a compatible solute supporting osmoadaptive tolerance.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2023.1192059",
                "notes": "Glycine betaine biosynthesis/uptake supports compatible-solute-based osmoadaptation."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.836940+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-12T10:00:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed definition and causal graph linking robust osmoadaptive tolerance to the moderate-halophile NaCl-range bin.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:30Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d71, rdfs:subClassOf\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 7 evidence-backed generic edges (7 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:10Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002326\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:27592\u00d71, CHEBI:17750\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates (1 to confers), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope nacl_range_mid2_moderate_halophile=NONMECHANISTIC with scope_notes; marked 2 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (ectABC_enzyme_module, betAB_pathway); added 1 node(s) and 1 edge(s) (ectABC_enzyme_module); removed 1 node(s) and 1 edge(s) together with their evidence (ectABC_operon).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T04:43:24Z",
        "curator": "codex",
        "action": "ADD_CANONICAL_EXAMPLES",
        "changes": "Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Aureivirga marina (NCBITaxon:1182451; DOI:10.1099/ijs.0.043257-0). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1003001",
    "label": "neutrophilic",
    "definition": "A pH growth preference characterized by optimal growth at near-neutral pH values, typically between pH 6.5 and 7.5.",
    "definition_source": "DOI:10.1038/nrmicro2549",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1003000"
    ],
    "synonyms": [
      {
        "synonym_text": "neutralophile",
        "synonym_type": "EXACT_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "neutralophilic",
        "synonym_type": "EXACT_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "neutrophile",
        "synonym_type": "EXACT_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "created_by": "Anthea Guo",
    "evidence": [
      {
        "reference": "DOI:10.1038/nrmicro2549",
        "snippet": "cytoplasmic pH ... must maintain for growth",
        "notes": "Supports pH growth preference as tied to cytoplasmic pH requirements."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:562",
        "taxon_label": "Escherichia coli",
        "note": "grows optimally near pH 7",
        "reference": "DOI:10.1111/1574-6976.12076"
      },
      {
        "taxon_id": "NCBITaxon:1423",
        "taxon_label": "Bacillus subtilis",
        "note": "neutralophile",
        "reference": "PMID:24898062"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "neutrophilic_neutral_ph_homeostasis",
        "title": "Neutrophilic near-neutral pH homeostasis mechanism",
        "description": "Evidence-backed causal sketch linking neutrophilic growth to near-neutral external pH and ordinary cytoplasmic pH homeostasis.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a broad environmental or morphological classification spanning multiple mechanisms, a measurement-like bin, or an absence/arrangement descriptor; contextual protein nodes do not receive token UniProt examples.",
        "nodes": [
          {
            "node_id": "neutrophilic_trait",
            "label": "neutrophilic",
            "node_type": "TRAIT",
            "grounding": "METPO:1003001",
            "description": "Optimal growth occurs at near-neutral pH."
          },
          {
            "node_id": "near_neutral_external_ph",
            "label": "near-neutral external pH",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "External pH around neutrality.",
            "grounding": "PATO:0001428"
          },
          {
            "node_id": "cytoplasmic_ph_homeostasis",
            "label": "cytoplasmic pH homeostasis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Maintenance of intracellular pH compatible with growth.",
            "grounding": "GO:0051453"
          },
          {
            "node_id": "proton_motive_force",
            "label": "proton motive force",
            "node_type": "STATE",
            "description": "Electrochemical proton gradient coupled to energy metabolism.",
            "grounding": "METPO:1007500"
          },
          {
            "node_id": "cation_proton_antiporter",
            "label": "cation/proton antiporter",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Transporters contributing to ion and pH homeostasis.",
            "grounding": "GO:0051139"
          },
          {
            "node_id": "external_acidic_ph",
            "label": "external acidic pH",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Low external pH that challenges cytoplasmic pH homeostasis."
          },
          {
            "node_id": "cytoplasmic_proton_influx",
            "label": "cytoplasmic proton influx",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Entry of protons into the cytoplasm across or through the membrane."
          },
          {
            "node_id": "cytoplasmic_buffering_capacity",
            "label": "cytoplasmic buffering capacity",
            "node_type": "CAPACITY",
            "description": "Proton sequestration by cytoplasmic buffers that dampens pH fluctuations."
          },
          {
            "node_id": "intracellular_ph",
            "label": "intracellular pH",
            "node_type": "STATE",
            "description": "The pH of the cytoplasm."
          },
          {
            "node_id": "amino_acid_decarboxylation",
            "label": "amino-acid decarboxylation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Enzyme-catalyzed decarboxylation reaction that consumes cytoplasmic protons."
          },
          {
            "node_id": "f1f0_atpase_proton_pump",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "F1F0-ATPase proton pump",
            "node_type": "GENE_OR_PROTEIN",
            "description": "ATP-dependent proton transporter contributing to pH restoration."
          }
        ],
        "edges": [
          {
            "subject": "near_neutral_external_ph",
            "predicate": "confers",
            "object": "neutrophilic_trait",
            "description": "Neutrophiles grow optimally when external pH is near neutrality.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2549",
                "snippet": "external pH values outside the cytoplasmic pH",
                "notes": "Review supports growth constraints around cytoplasmic pH compatibility."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "cytoplasmic_ph_homeostasis",
            "predicate": "confers",
            "object": "neutrophilic_trait",
            "description": "Growth near neutral pH still requires active maintenance of internal pH.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2549",
                "snippet": "bacterial pH homeostasis is a cell-wide physiological process",
                "notes": "Supports pH homeostasis as central to bacterial growth."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "proton_motive_force",
            "predicate": "interacts with",
            "object": "cytoplasmic_ph_homeostasis",
            "description": "pH regulation is linked to proton motive force and bioenergetics.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.tim.2007.02.005",
                "snippet": "intrinsically linked to cellular bioenergetics",
                "notes": "Supports coupling of pH gradients and bioenergetics."
              }
            ],
            "predicate_id": "biolink:interacts_with"
          },
          {
            "subject": "cation_proton_antiporter",
            "predicate": "contributes to",
            "object": "cytoplasmic_ph_homeostasis",
            "description": "Cation/proton antiporters help regulate ion and pH balance.",
            "evidence": [
              {
                "reference": "DOI:10.3390/ijms21124566",
                "snippet": "maintaining ion and pH homeostasis",
                "notes": "Supports cation/proton antiport as a general pH-homeostasis mechanism."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "external_acidic_ph",
            "predicate": "increases",
            "object": "cytoplasmic_proton_influx",
            "description": "Low external pH increases H+ entry into the cytoplasm, challenging neutral pH homeostasis.",
            "evidence": [
              {
                "reference": "DOI:10.1128/msystems.01037-23",
                "notes": "At low pH, H+ can permeate into the cytoplasm via protonated water chains, ion channels, or damaged membranes (general for neutralophilic bacteria)."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "cytoplasmic_buffering_capacity",
            "predicate": "contributes to",
            "object": "intracellular_ph",
            "description": "Proton sequestration by cytoplasmic buffers stabilizes intracellular pH and protects enzyme function.",
            "evidence": [
              {
                "reference": "DOI:10.1128/msystems.01037-23",
                "notes": "Protons can be sequestered by side-chains of proteins, inorganic phosphates, polyphosphates, or polyamines (general for neutralophiles)."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "amino_acid_decarboxylation",
            "predicate": "contributes to",
            "object": "cytoplasmic_ph_homeostasis",
            "description": "Decarboxylation directly removes H+ from the cytoplasm, raising internal pH.",
            "evidence": [
              {
                "reference": "DOI:10.3390/antibiotics12091474",
                "notes": "The decarboxylation of amino acids is an enzyme-catalyzed reaction that consumes protons (general acid-tolerance mechanism in neutralophiles)."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "amino_acid_decarboxylation",
            "predicate": "contributes to",
            "object": "proton_motive_force",
            "description": "Charge-differential substrate/product antiport plus proton consumption couples pH homeostasis to PMF generation.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuad033",
                "notes": "The chemistry of the decarboxylation reaction requires a proton, and the equivalent of 1 proton is pumped per molecule decarboxylated (general mechanism)."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "f1f0_atpase_proton_pump",
            "predicate": "contributes to",
            "object": "cytoplasmic_ph_homeostasis",
            "description": "ATP-dependent proton transport helps restore cytoplasmic pH under acid challenge.",
            "evidence": [
              {
                "reference": "DOI:10.3390/antibiotics12091474",
                "notes": "Common mechanisms involved in bacterial acid tolerance include the F1-F0-ATPase proton pump (general)."
              }
            ],
            "predicate_id": "RO:0002326"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.937067+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-11T00:00:00-07:00",
        "curator": "codex",
        "action": "CURATED_WITH_LITERATURE",
        "changes": "Reviewed neutrophilic trait and added DOI-backed evidence and causal graph for near-neutral pH homeostasis.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:30Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d71, RO:0002326\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T05:49:24Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:interacts_with\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:18Z",
        "curator": "claude",
        "action": "RENAME_PREDICATE_LABELS",
        "changes": "Renamed 1 causal-edge predicate label(s) to align with existing groundings: supports \u2192 enables \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:21Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:38:00Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0030641\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:41:03Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (METPO:1007500\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T05:05:14Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A0H3JRG4\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T08:14:32Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (PATO:0001432\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-26T02:30:12Z",
        "curator": "claude",
        "action": "RETYPE_CAUSAL_NODES",
        "changes": "Re-typed 1 causal-node node_type field(s) to align with CausalNodeTypeEnum semantics: proton motive force: BIOLOGICAL_PROCESS \u2192 STATE \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-15T07:20:36Z",
        "curator": "claude",
        "action": "FIX_NODE_GROUNDING_CURIE",
        "changes": "Overwrote 1 causal-node grounding(s) (obsolete/wrong GO -> corrected, verified vs OAK).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-15T07:21:43Z",
        "curator": "claude",
        "action": "FIX_NODE_GROUNDING_CURIE",
        "changes": "Overwrote 1 pH causal-node grounding(s) to corrected PATO CURIEs (phase-2; verified vs OAK).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 5 evidence-backed generic edges (6 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:10Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 5 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002326\u00d74, RO:0002213\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 2 causal edge(s) off enables/RO:0002327 with a TRAIT object (2 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-16T02:00:00Z",
        "curator": "claude",
        "action": "NORMALISE_NODE_TYPE",
        "changes": "Under the PATHWAY-vs-BIOLOGICAL_PROCESS rule, one node_id means one thing corpus-wide (issue 356): amino_acid_decarboxylation is typed BIOLOGICAL_PROCESS. PATHWAY is a named, conventionally enumerable multi-step route; BIOLOGICAL_PROCESS is everything else. A REACTION CLASS, not a route. The corpus describes it that way in neutrophilic.yaml -- 'Enzyme-catalyzed decarboxylation reaction that consumes cytoplasmic protons' -- and the wording varies by record, so read that as the family's sense rather than as this record's own text. Named systems that implement it (Gad) would be pathways; the reaction class is not. Was 4 BIOLOGICAL_PROCESS to 2 before this tranche.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-22T04:26:15Z",
        "curator": "codex",
        "action": "REVIEW_UNIPROT_INSTANCE_GROUNDINGS",
        "changes": "Reviewed 1 organism-specific UniProtKB grounding(s): replaced 1 with taxon-agnostic GO/InterPro terms and retracted 0 to label-only where no exact semantic term was supported (docs/GROUNDING_POLICY.md).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope neutrophilic_neutral_ph_homeostasis=NONMECHANISTIC with scope_notes; marked 1 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (f1f0_atpase_proton_pump).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000624",
    "label": "non halophilic",
    "definition": "A halophily preference in which an organism does not require or prefer elevated salt concentrations for growth.",
    "definition_source": "DOI:10.1128/AEM.01934-12",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000629"
    ],
    "synonyms": [
      {
        "synonym_text": "non-halophilic",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1128/AEM.01934-12",
        "snippet": "B. subtilis can attain cellular protection",
        "notes": "Supports salt-stress protection mechanisms in a non-halophilic bacterial model."
      },
      {
        "reference": "PMID:11583854",
        "snippet": "Vibrio cholerae non-O1, a non-halophilic bacterium",
        "notes": "Organism example: Vibrio cholerae non-O1 is described as non-halophilic."
      },
      {
        "reference": "DOI:10.3389/fmicb.2021.705326",
        "snippet": "the number of viable cells in LB broth supplemented with 0% NaCl at 24 h is significantly higher than other tested groups",
        "notes": "Li et al. 2021, Results, Bacterial Growth, Figure 2B: wild-type E. coli BW25113 was compared in LB broth supplemented with 0%, 1%, 3.5% and 5% NaCl at 37 C. This is a strain- and medium-qualified low-salt growth observation, not sodium-free growth, a complete salinity optimum curve or a universal species-wide requirement. PMCID:PMC8415458 and PMID:34484145 identify this same paper."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:562",
        "taxon_label": "Escherichia coli",
        "reference": "DOI:10.3389/fmicb.2021.705326",
        "note": "Wild-type E. coli BW25113 grew in LB broth supplemented with 0% NaCl at 37 C; at 24 h its viable count exceeded the 1%, 3.5% and 5% NaCl groups (Figure 2B). This supports a strain-qualified non-halophilic example, not sodium-free growth or a universal claim about every E. coli strain."
      },
      {
        "taxon_id": "NCBITaxon:1423",
        "taxon_label": "Bacillus subtilis",
        "note": "non-halophilic soil bacterium",
        "reference": "PMID:9384377"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "non_halophilic_salt_stress_response",
        "title": "Non-halophilic salt-stress response mechanism",
        "description": "Evidence-backed causal sketch linking non-halophily to lack of salt requirement, high-osmolarity stress, potassium uptake, and compatible-solute protection.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a broad environmental or morphological classification spanning multiple mechanisms, a measurement-like bin, or an absence/arrangement descriptor; contextual protein nodes do not receive token UniProt examples.",
        "nodes": [
          {
            "node_id": "non_halophilic_trait",
            "label": "non halophilic",
            "node_type": "TRAIT",
            "grounding": "METPO:1000624",
            "description": "Growth does not require or prefer elevated salt concentration."
          },
          {
            "node_id": "low_to_moderate_salinity",
            "label": "low-to-moderate salinity",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Non-elevated salinity condition compatible with non-halophilic growth."
          },
          {
            "node_id": "high_osmolarity",
            "label": "high osmolarity",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Hyperosmotic condition that can inhibit growth of non-halophiles.",
            "grounding": "PATO:0001657"
          },
          {
            "node_id": "water_flux",
            "label": "water flux across cytoplasmic membrane",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Osmotically driven water movement during osmotic upshift or downshift."
          },
          {
            "node_id": "potassium_ion",
            "label": "potassium ion",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:29103",
            "description": "Ion accumulated as an early osmotic-stress response."
          },
          {
            "node_id": "proline",
            "label": "proline",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:17203",
            "description": "Compatible solute synthesized by Bacillus subtilis during osmotic adaptation."
          },
          {
            "node_id": "compatible_solute_uptake",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "compatible-solute uptake systems",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Transporters importing glycine betaine, proline, ectoine, or other osmoprotectants."
          },
          {
            "node_id": "osmotic_upshift",
            "label": "osmotic upshift",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Hypertonic/NaCl upshift imposing increased external osmolarity."
          },
          {
            "node_id": "water_efflux_volume_decrease",
            "label": "water efflux and cytoplasmic volume decrease",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Rapid loss of water and drop in cytoplasmic volume/turgor after hypertonic stress."
          },
          {
            "node_id": "rapid_k_uptake",
            "label": "rapid potassium uptake",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Emergency K+ import as the primary early osmotic-upshift response."
          },
          {
            "node_id": "glutamate",
            "label": "L-glutamate",
            "node_type": "CHEMICAL",
            "description": "Counterion accumulated/synthesized to balance K+ and maintain electroneutrality."
          },
          {
            "node_id": "compatible_solute_accumulation",
            "label": "compatible solute accumulation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Accumulation/synthesis of neutral compatible solutes replacing K+ as a secondary osmoadaptive response."
          }
        ],
        "edges": [
          {
            "subject": "low_to_moderate_salinity",
            "predicate": "confers",
            "object": "non_halophilic_trait",
            "description": "Non-halophilic organisms do not require elevated salinity for growth.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.01934-12",
                "snippet": "soil-dwelling bacterium Bacillus subtilis",
                "notes": "Bacillus subtilis is used here as a non-halophilic model for salt stress responses rather than salt-requiring growth."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "high_osmolarity",
            "predicate": "regulates",
            "object": "water_flux",
            "description": "Hyperosmotic stress alters cellular water balance and can impair non-halophilic growth.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.01934-12",
                "snippet": "outflow of water, drop in turgor, and the ensuing growth arrest",
                "notes": "Supports high-osmolarity growth inhibition through water loss and turgor decrease."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "potassium_ion",
            "predicate": "mitigates",
            "object": "water_flux",
            "description": "Rapid potassium accumulation helps adjust cytoplasmic osmotic potential after osmotic upshift.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.01934-12",
                "snippet": "initially importing substantial amounts of potassium ions",
                "notes": "Supports potassium uptake as an initial osmotic response."
              }
            ],
            "predicate_id": "METPO:2007407"
          },
          {
            "subject": "proline",
            "predicate": "mitigates",
            "object": "water_flux",
            "description": "Proline accumulation supports osmoadaptation under sustained high-osmolarity conditions.",
            "evidence": [
              {
                "reference": "DOI:10.1128/JB.00778-11",
                "snippet": "proline production is required",
                "notes": "Supports de novo proline synthesis in Bacillus subtilis osmotic defense."
              }
            ],
            "predicate_id": "METPO:2007407"
          },
          {
            "subject": "compatible_solute_uptake",
            "predicate": "imports",
            "object": "proline",
            "description": "Uptake systems can import osmoprotectants that relieve high osmolarity.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.01934-12",
                "snippet": "osmotically controlled uptake systems",
                "notes": "Supports uptake systems for compatible solutes in Bacillus subtilis."
              }
            ],
            "predicate_id": "METPO:2007805"
          },
          {
            "subject": "proline",
            "predicate": "enables tolerance of",
            "object": "high_osmolarity",
            "description": "Proline acts as an osmoprotectant enabling survival or growth under salt stress without making salt a growth requirement.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.01934-12",
                "snippet": "proline as an osmoprotectant",
                "notes": "Supports proline-mediated protection in a non-halophilic bacterial model."
              }
            ]
          },
          {
            "subject": "osmotic_upshift",
            "predicate": "causes",
            "object": "water_efflux_volume_decrease",
            "description": "Hypertonic stress drives rapid water efflux and cytoplasmic volume/turgor decrease.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mmbr.00181-23",
                "notes": "Under hypertonic stress water exits cells within milliseconds, causing cytoplasmic volume decreases up to ~50%, a rapid fall in turgor and increased ionic strength."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "osmotic_upshift",
            "predicate": "induces",
            "object": "rapid_k_uptake",
            "description": "Cells import large amounts of K+ as the primary emergency response to osmotic upshift.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mmbr.00181-23",
                "notes": "Cells commonly import large amounts of K+ during osmotic upshift; generic across non-halophilic bacteria."
              }
            ]
          },
          {
            "subject": "rapid_k_uptake",
            "predicate": "requires counterion balancing by",
            "object": "glutamate",
            "description": "Glutamate is imported or synthesized as the counterion to balance accumulated K+ and maintain electroneutrality.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mmbr.00181-23",
                "notes": "Glutamate commonly imported or synthesized as the counterion to maintain electroneutrality during K+ accumulation."
              }
            ]
          },
          {
            "subject": "rapid_k_uptake",
            "predicate": "promotes replacement by",
            "object": "compatible_solute_accumulation",
            "description": "High intracellular K+/ionic strength is mitigated by secondary accumulation of neutral compatible solutes that replace K+.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mmbr.00181-23",
                "notes": "Bacteria such as E. coli and B. subtilis accumulate/synthesize neutral compatible solutes to replace K+; compatible-solute accumulation is a secondary response following primary K+ accumulation."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.863044+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-06T14:15:44-07:00",
        "curator": "codex",
        "action": "CURATED_WITH_ORGANISM_EXAMPLE",
        "changes": "Added Vibrio cholerae non-O1 organism example with PMID-backed evidence.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-11T00:00:00-07:00",
        "curator": "codex",
        "action": "CURATED_WITH_LITERATURE",
        "changes": "Added DOI-backed non-halophilic causal graph for salt-stress response in a non-halophilic Bacillus model, including K+ uptake, proline, and compatible-solute uptake systems.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T21:30:06Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007407\u00d72).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:18Z",
        "curator": "claude",
        "action": "RENAME_PREDICATE_LABELS",
        "changes": "Renamed 2 causal-edge predicate label(s) to align with existing groundings: supports \u2192 enables \u00d71; drives \u2192 regulates \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:21Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d71, RO:0002211\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-14T05:51:45Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (PATO:0001657\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-16T06:30:55Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000208\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 4 evidence-backed generic edges (5 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:10Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:causes\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 1 causal edge(s) off enables/RO:0002327 with a TRAIT object (1 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T02:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES_PART2",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates onto their causal-graph counterparts (1 to imports), issue 301 part 2. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Each replacement is a 1:1 mirror of its source predicate that changes only the domain, so the claim each edge makes is unchanged and directions are unchanged. The replacements are proposed in proposals/metpo_traitmech_v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope non_halophilic_salt_stress_response=NONMECHANISTIC with scope_notes; marked 1 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (compatible_solute_uptake).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-03T17:07:26Z",
        "curator": "codex",
        "action": "REPAIR_CANONICAL_CITATION_SCOPE_1626",
        "changes": "Resolved issue 1626 by normalizing PMC8415458 to its verified DOI 10.3389/fmicb.2021.705326 (PMID:34484145), without replacing the paper. Qualified the E. coli example to wild-type BW25113 growth in LB supplemented with 0% NaCl at 37 C and the 24-h comparison with 1%, 3.5% and 5% NaCl. Added an exact Results snippet and interpretation; no sodium-free or universal species-wide requirement is inferred. Retained NCBITaxon:562 and its independently checked NCBI label. Definition, hierarchy, graph and other example unchanged.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1003006",
    "label": "obligately acidophilic",
    "definition": "A pH growth preference characterized by the requirement for acidic environments (pH below 5.5) for growth, with inability to grow at neutral or alkaline pH values.",
    "definition_source": "DOI:10.3389/fmicb.2021.822229",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1003000"
    ],
    "synonyms": [
      {
        "synonym_text": "obligate acidophile",
        "synonym_type": "EXACT_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "created_by": "Jed Dongjin Kim-Ozaeta",
    "evidence": [
      {
        "reference": "DOI:10.3389/fmicb.2021.822229",
        "snippet": "acidic optimal growth pH",
        "notes": "Supports acidophilic growth as a phenotype defined by acidic optimal pH."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:46632",
        "taxon_label": "Picrophilus oshimae",
        "note": "obligate extreme acidophile (pH ~0.7)",
        "reference": "PMID:8522509"
      },
      {
        "taxon_id": "NCBITaxon:920",
        "taxon_label": "Acidithiobacillus ferrooxidans",
        "note": "obligate acidophile (pH ~2)",
        "reference": "PMID:31861345"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "obligately_acidophilic_ph_homeostasis",
        "title": "Obligate acidophily pH homeostasis mechanism",
        "description": "Evidence-backed causal sketch linking obligate acidophily to acidic external pH, proton stress, and constitutive pH homeostasis mechanisms.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a broad environmental or morphological classification spanning multiple mechanisms, a measurement-like bin, or an absence/arrangement descriptor; contextual protein nodes do not receive token UniProt examples.",
        "nodes": [
          {
            "node_id": "obligately_acidophilic_trait",
            "label": "obligately acidophilic",
            "node_type": "TRAIT",
            "grounding": "METPO:1003006",
            "description": "Growth requires acidic pH and does not extend to neutral or alkaline pH values."
          },
          {
            "node_id": "acidic_external_ph",
            "label": "acidic external pH",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "External pH in the acidic range supporting acidophile growth.",
            "grounding": "PATO:0001429"
          },
          {
            "node_id": "proton",
            "label": "proton",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:15378",
            "description": "Hydrogen ion whose high external activity drives proton stress."
          },
          {
            "node_id": "cytoplasmic_ph_homeostasis",
            "label": "cytoplasmic pH homeostasis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Maintenance of near-neutral intracellular pH during acidic growth.",
            "grounding": "GO:0051453"
          },
          {
            "node_id": "low_proton_permeability_membrane",
            "label": "low proton permeability membrane",
            "node_type": "CELLULAR_LOCALIZATION",
            "description": "Cell envelope properties that reduce inward proton leak."
          },
          {
            "node_id": "reversed_membrane_potential",
            "label": "inside-positive (reversed) membrane potential",
            "node_type": "STATE",
            "description": "Positive-inside membrane potential that suppresses proton influx."
          },
          {
            "node_id": "proton_export_pumps",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "proton export pumps and antiporters",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Transport systems proposed to remove protons or exchange ions during acid stress."
          },
          {
            "node_id": "k_uptake_system_kdp_kef",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "K+ uptake system (Kdp/Kef)",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Potassium-transporting ATPases and K+ uptake systems (kdp, kef) that establish an inside-positive membrane potential."
          },
          {
            "node_id": "p_type_proton_atpase",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "P-type proton-translocating ATPase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Active proton-efflux ATPase that pumps protons out of the cytoplasm during acid stress."
          },
          {
            "node_id": "proton_efflux",
            "label": "proton efflux from cytoplasm",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Active export of protons from the cytoplasm to maintain near-neutral intracellular pH."
          },
          {
            "node_id": "na_h_antiporter",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "Na+/H+ antiporter (Nha)",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Sodium/proton antiporters (nhaA, nhaB) that exchange cytoplasmic protons for sodium ions."
          },
          {
            "node_id": "hopanoid_membrane",
            "label": "hopanoid-containing membrane",
            "node_type": "CELLULAR_LOCALIZATION",
            "description": "Membrane enriched in hopanoid lipids that reduces proton permeability."
          },
          {
            "node_id": "cyclopropane_fatty_acids",
            "label": "cyclopropane fatty acids",
            "node_type": "CHEMICAL",
            "description": "Cyclopropane-fatty-acyl phospholipids that rigidify the membrane and lower proton permeability."
          },
          {
            "node_id": "glutamate_decarboxylase",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "glutamate decarboxylase system (Gad)",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Glutamate decarboxylase (gadA/gadB/gadC) that consumes cytoplasmic protons during decarboxylation."
          }
        ],
        "edges": [
          {
            "subject": "acidic_external_ph",
            "predicate": "selects for",
            "object": "obligately_acidophilic_trait",
            "description": "Acidic environments select for organisms with acidic pH growth optima.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2021.822229",
                "snippet": "acidic optimal growth pH",
                "notes": "Review supports acidophile classification by acidic optimum pH; the obligate neutral-pH exclusion remains from the METPO definition."
              }
            ],
            "predicate_id": "METPO:2007401"
          },
          {
            "subject": "acidic_external_ph",
            "predicate": "increases gradient of",
            "object": "proton",
            "description": "Low external pH creates a steep proton gradient across the membrane.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2021.822229",
                "snippet": "proton gradient across the cytoplasmic membrane",
                "notes": "Supports external-to-internal proton gradient under low-pH growth."
              }
            ],
            "predicate_id": "METPO:2007601"
          },
          {
            "subject": "low_proton_permeability_membrane",
            "predicate": "limits influx of",
            "object": "proton",
            "description": "Reduced membrane permeability helps obligate acidophiles maintain intracellular pH.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.tim.2007.02.005",
                "snippet": "highly impermeable cell membranes",
                "notes": "Supports proton exclusion by membrane properties in acidophiles."
              }
            ]
          },
          {
            "subject": "reversed_membrane_potential",
            "predicate": "suppresses influx of",
            "object": "proton",
            "description": "Reversed membrane potential reduces passive proton entry.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.tim.2007.02.005",
                "snippet": "reversed membrane potential",
                "notes": "Supports reversed membrane potential as a shared acidophile feature."
              }
            ]
          },
          {
            "subject": "proton_export_pumps",
            "predicate": "contributes to",
            "object": "cytoplasmic_ph_homeostasis",
            "description": "Proton export and antiport systems contribute to intracellular pH control during acid stress.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2021.822229",
                "snippet": "proton export pumps and antiporters",
                "notes": "Supports transporter-mediated acid resistance mechanisms."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "cytoplasmic_ph_homeostasis",
            "predicate": "confers",
            "object": "obligately_acidophilic_trait",
            "description": "Obligate acidophilic growth requires maintaining cytoplasmic pH despite acidic external pH.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2549",
                "snippet": "maintain a cytoplasmic pH of approximately 6.0",
                "notes": "Supports intracellular pH control during extreme acidophilic growth."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "k_uptake_system_kdp_kef",
            "predicate": "increases",
            "object": "reversed_membrane_potential",
            "description": "K+ uptake systems generate the inside-positive (reversed) membrane potential that forms an electrochemical barrier to protons.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2023.1149903",
                "notes": "Review describes inside-positive membrane potential via potassium-transporting ATPases and K+ uptake systems (kdp, Kef) forming an electrochemical barrier to proton influx."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "p_type_proton_atpase",
            "predicate": "increases",
            "object": "proton_efflux",
            "description": "P-type ATPases actively export protons from the cytoplasm.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2023.1149903",
                "notes": "Dopson review lists active proton efflux via P-type ATPases as a pH homeostasis strategy in acidophiles."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "proton_efflux",
            "predicate": "contributes to",
            "object": "cytoplasmic_ph_homeostasis",
            "description": "Active proton efflux helps maintain near-neutral cytoplasmic pH under acidic conditions.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2023.1149903",
                "notes": "Proton pumps/ATPases maintain a near-neutral cytoplasm during acidophilic growth."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "na_h_antiporter",
            "predicate": "exports",
            "object": "proton",
            "description": "Na+/H+ antiporters exchange cytoplasmic protons for extracellular sodium, contributing to proton export.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2023.1149903",
                "notes": "Dopson lists Na+/H+ exchange (nhaA sodium/proton antiporter) among acidophile pH-homeostasis systems."
              }
            ],
            "predicate_id": "METPO:2007804"
          },
          {
            "subject": "hopanoid_membrane",
            "predicate": "decreases",
            "object": "low_proton_permeability_membrane",
            "description": "Hopanoid membrane lipids reduce membrane proton permeability, reinforcing proton exclusion.",
            "evidence": [
              {
                "reference": "DOI:10.1111/1758-2229.70019",
                "notes": "Acid resistance is linked to hopanoid membrane lipids and reduced proton permeability as a core proton-exclusion strategy."
              }
            ],
            "predicate_id": "RO:0002212"
          },
          {
            "subject": "cyclopropane_fatty_acids",
            "predicate": "decreases",
            "object": "low_proton_permeability_membrane",
            "description": "Cyclopropane fatty acid formation reduces membrane proton permeability.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2023.1149903",
                "notes": "Review includes cyclopropane-fatty-acyl-phospholipid synthase among membrane adaptations that reduce proton permeability."
              }
            ],
            "predicate_id": "RO:0002212"
          },
          {
            "subject": "glutamate_decarboxylase",
            "predicate": "consumes",
            "object": "proton",
            "description": "Glutamate decarboxylase consumes cytoplasmic protons during decarboxylation, buffering intracellular pH.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2023.1149903",
                "notes": "Review lists decarboxylases (Adi, Gad) as cytoplasmic proton-consuming systems used in acidophile pH homeostasis."
              }
            ],
            "predicate_id": "biolink:consumes"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.940216+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-11T00:00:00-07:00",
        "curator": "codex",
        "action": "CURATED_WITH_LITERATURE",
        "changes": "Reviewed obligately acidophilic trait and added DOI-backed evidence and causal graph for acidic pH homeostasis. The graph does not assert a specific molecular cause of the obligate neutral-pH growth exclusion because that varies by lineage.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:30Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002326\u00d71, RO:0002327\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T21:30:06Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007401\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:38:00Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0030641\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T08:14:32Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (PATO:0001428\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-14T07:26:19Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007601\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-15T07:20:36Z",
        "curator": "claude",
        "action": "FIX_NODE_GROUNDING_CURIE",
        "changes": "Overwrote 1 causal-node grounding(s) (obsolete/wrong GO -> corrected, verified vs OAK).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-15T07:21:43Z",
        "curator": "claude",
        "action": "FIX_NODE_GROUNDING_CURIE",
        "changes": "Overwrote 1 pH causal-node grounding(s) to corrected PATO CURIEs (phase-2; verified vs OAK).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-17T04:09:43Z",
        "curator": "claude",
        "action": "REMOVE_REDUNDANT_SYNONYM",
        "changes": "Removed 1 synonym(s) whose text duplicated the label (seeder redundancy; no information lost).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 7 evidence-backed generic edges (7 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:10Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 7 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002213\u00d72, RO:0002212\u00d72, RO:0002326\u00d71, METPO:2000209\u00d71, biolink:consumes\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 1 causal edge(s) off enables/RO:0002327 with a TRAIT object (1 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T02:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES_PART2",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates onto their causal-graph counterparts (1 to exports), issue 301 part 2. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Each replacement is a 1:1 mirror of its source predicate that changes only the domain, so the claim each edge makes is unchanged and directions are unchanged. The replacements are proposed in proposals/metpo_traitmech_v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-21T08:00:00Z",
        "curator": "codex",
        "action": "NORMALISE_NODE_TYPE",
        "changes": "Tranche 5 of issue 356 settles the process/quality families and merges ids that meant the same sense: reversed_membrane_potential is STATE. A reversed membrane potential is an inside-positive electrical state, not the process that establishes it. The schema names this gradient/steady-value distinction explicitly.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope obligately_acidophilic_ph_homeostasis=NONMECHANISTIC with scope_notes; marked 5 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (proton_export_pumps, k_uptake_system_kdp_kef, p_type_proton_atpase, na_h_antiporter, glutamate_decarboxylase).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000606",
    "label": "obligately aerobic",
    "definition": "An oxygen preference that requires molecular oxygen (O\u2082) for growth.",
    "definition_source": "https://www.ncbi.nlm.nih.gov/books/NBK482349/",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000601"
    ],
    "synonyms": [
      {
        "synonym_text": "obligate aerobe",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "obligate aerobic",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "https://www.ncbi.nlm.nih.gov/books/NBK482349/",
        "snippet": "require oxygen as a terminal electron acceptor",
        "notes": "Supports the requirement for oxygen in obligately aerobic organisms."
      },
      {
        "reference": "PMID:27203084",
        "snippet": "M. tuberculosis is an obligate aerobe",
        "notes": "Organism example: Mycobacterium tuberculosis is described as obligately aerobic."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1270",
        "taxon_label": "Micrococcus luteus",
        "note": "Textbook strict aerobe (respiratory metabolism only).",
        "reference": "PMID:19948807"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "obligate_aerobe_oxygen_respiration",
        "title": "Obligate aerobe oxygen-dependent respiration mechanism",
        "description": "Evidence-backed causal sketch linking obligate aerobic growth to oxygen-dependent terminal oxidase respiration.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a broad environmental or morphological classification spanning multiple mechanisms, a measurement-like bin, or an absence/arrangement descriptor; contextual protein nodes do not receive token UniProt examples.",
        "nodes": [
          {
            "node_id": "obligate_aerobic_trait",
            "label": "obligately aerobic",
            "node_type": "TRAIT",
            "grounding": "METPO:1000606",
            "description": "Growth requires molecular oxygen."
          },
          {
            "node_id": "molecular_oxygen",
            "label": "molecular oxygen",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:15379",
            "description": "Dioxygen required for respiratory growth."
          },
          {
            "node_id": "electron_transport_chain",
            "label": "electron transport chain",
            "node_type": "PATHWAY",
            "grounding": "GO:0022900",
            "description": "Respiratory chain that transfers electrons to terminal acceptors."
          },
          {
            "node_id": "terminal_oxidases",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "terminal respiratory oxidases",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Oxygen-reducing terminal oxidase complexes."
          },
          {
            "node_id": "proton_motive_force",
            "label": "proton motive force",
            "node_type": "STATE",
            "description": "Electrochemical gradient powering ATP synthesis.",
            "grounding": "METPO:1007500"
          },
          {
            "node_id": "aerobic_respiration",
            "label": "aerobic respiration",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Oxygen-dependent respiratory metabolism.",
            "grounding": "GO:0009060"
          },
          {
            "node_id": "anoxia",
            "label": "absence of oxygen (anoxia)",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Environmental condition lacking molecular oxygen."
          },
          {
            "node_id": "superoxide",
            "label": "superoxide",
            "node_type": "CHEMICAL",
            "description": "Reactive oxygen species generated during aerobic metabolism.",
            "grounding": "CHEBI:18421"
          },
          {
            "node_id": "hydrogen_peroxide",
            "label": "hydrogen peroxide",
            "node_type": "CHEMICAL",
            "description": "Reactive oxygen species generated during aerobic metabolism.",
            "grounding": "CHEBI:16240"
          },
          {
            "node_id": "superoxide_dismutase_activity",
            "label": "superoxide dismutase activity",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "Enzyme activity that detoxifies superoxide.",
            "grounding": "GO:0004784"
          },
          {
            "node_id": "catalase_activity",
            "label": "catalase / catalase-peroxidase activity",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "Enzyme activity that detoxifies hydrogen peroxide."
          },
          {
            "node_id": "fe_s_cluster_enzymes",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "Fe-S cluster enzymes",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Enzymes with exposed iron-sulfur clusters vulnerable to ROS."
          }
        ],
        "edges": [
          {
            "subject": "obligate_aerobic_trait",
            "predicate": "depends on",
            "object": "molecular_oxygen",
            "description": "Obligate aerobic growth depends on oxygen availability.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.celrep.2023.112444",
                "snippet": "obligate aerobe ... exposed to hypoxia, stops growing",
                "notes": "Mycobacterium tuberculosis example supports oxygen requirement in an obligately aerobic bacterium."
              }
            ],
            "predicate_id": "RO:0002502"
          },
          {
            "subject": "terminal_oxidases",
            "predicate": "reduces",
            "object": "molecular_oxygen",
            "description": "Terminal oxidases use oxygen as the respiratory electron acceptor.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.celrep.2023.112444",
                "snippet": "transfer electrons from the ETC to O2",
                "notes": "Supports oxygen reduction by terminal oxidases in an obligate aerobe."
              }
            ],
            "predicate_id": "METPO:2007802"
          },
          {
            "subject": "electron_transport_chain",
            "predicate": "includes",
            "object": "terminal_oxidases",
            "description": "Oxygen-dependent respiratory chains terminate in oxygen reductases.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.bbabio.2011.06.016",
                "snippet": "respiratory quinol:O2 oxidoreductase",
                "notes": "Review supports terminal oxygen reductases as respiratory chain enzymes."
              }
            ],
            "predicate_id": "biolink:has_part"
          },
          {
            "subject": "terminal_oxidases",
            "predicate": "contributes to",
            "object": "proton_motive_force",
            "description": "Oxygen reductases contribute to proton motive force generation.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.bbabio.2011.06.016",
                "snippet": "production of a proton motive force",
                "notes": "Supports bioenergetic coupling by cytochrome bd oxygen reductases."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "molecular_oxygen",
            "predicate": "enables",
            "object": "aerobic_respiration",
            "description": "Molecular oxygen enables aerobic respiration.",
            "evidence": [
              {
                "reference": "DOI:10.1111/cmi.13338",
                "notes": "Aerobic respiration is identified as the main cause of bacterial oxygen consumption."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "anoxia",
            "predicate": "interrupts flux through",
            "object": "electron_transport_chain",
            "description": "Anoxia interrupts electron flux through the electron transport chain.",
            "evidence": [
              {
                "reference": "DOI:10.1128/JB.00797-19",
                "notes": "Interrupted flux through the electron transport chain (ETC) due to the absence of oxygen."
              }
            ]
          },
          {
            "subject": "electron_transport_chain",
            "predicate": "maintains",
            "object": "proton_motive_force",
            "description": "Electron transport chain flux maintains the proton motive force; anoxic interruption impairs it.",
            "evidence": [
              {
                "reference": "DOI:10.1128/JB.00797-19",
                "notes": "Obligate aerobes must maintain redox balance and the proton motive force (PMF) despite interrupted flux through the electron transport chain."
              }
            ]
          },
          {
            "subject": "superoxide_dismutase_activity",
            "predicate": "mitigates",
            "object": "superoxide",
            "description": "Superoxide dismutase mitigates superoxide stress in aerobes.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.tim.2020.10.001",
                "notes": "Aerobes deploy scavenging enzymes (SOD, catalase, other peroxidases)."
              }
            ],
            "predicate_id": "METPO:2007407"
          },
          {
            "subject": "catalase_activity",
            "predicate": "mitigates",
            "object": "hydrogen_peroxide",
            "description": "Catalase/catalase-peroxidase mitigates hydrogen peroxide stress in aerobes.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.tim.2020.10.001",
                "notes": "Aerobes deploy scavenging enzymes (SOD, catalase, other peroxidases)."
              }
            ],
            "predicate_id": "METPO:2007407"
          },
          {
            "subject": "superoxide",
            "predicate": "inactivates",
            "object": "fe_s_cluster_enzymes",
            "description": "Superoxide and H2O2 oxidize and inactivate exposed Fe-S cluster enzymes.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.tim.2020.10.001",
                "notes": "Rate constants for cluster oxidation given (~1e6 M-1 s-1 for superoxide and ~1e4 M-1 s-1 for H2O2), explaining ROS-defense need in aerobes."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.851998+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-05T01:09:05-07:00",
        "curator": "codex",
        "action": "CURATED_WITH_LITERATURE",
        "changes": "Added definition source and evidence for obligate oxygen requirement.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-05T18:39:46-07:00",
        "curator": "codex",
        "action": "ADDED_ORGANISM_EXAMPLE",
        "changes": "Added Mycobacterium tuberculosis organism example with PMID-backed evidence.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "ADDED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed causal graph for obligate aerobic respiration and oxygen-reducing terminal oxidases.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:30Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002326\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:41:03Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (METPO:1007500\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-26T02:30:12Z",
        "curator": "claude",
        "action": "RETYPE_CAUSAL_NODES",
        "changes": "Re-typed 1 causal-node node_type field(s) to align with CausalNodeTypeEnum semantics: proton motive force: BIOLOGICAL_PROCESS \u2192 STATE \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-26T05:00:47Z",
        "curator": "claude",
        "action": "RENAME_PREDICATE_LABELS",
        "changes": "Renamed 1 causal-edge predicate label(s) to align with existing groundings: requires \u2192 depends on \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-26T05:00:50Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002502\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-13T21:03:25Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:has_part\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-16T06:30:55Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000017\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 6 evidence-backed generic edges (7 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:10Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007407\u00d72, RO:0002327\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:17Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0009060\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 3 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:18421\u00d71, CHEBI:16240\u00d71, GO:0004784\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T02:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES_PART2",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates onto their causal-graph counterparts (1 to reduces), issue 301 part 2. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Each replacement is a 1:1 mirror of its source predicate that changes only the domain, so the claim each edge makes is unchanged and directions are unchanged. The replacements are proposed in proposals/metpo_traitmech_v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-15T06:00:00Z",
        "curator": "claude",
        "action": "SPLIT_PROTEIN_FROM_ACTIVITY",
        "changes": "Separated the protein sense from the activity sense so one node_id means one thing (issue 356): renamed superoxide_dismutase -> superoxide_dismutase_activity (MOLECULAR_FUNCTION sense); renamed catalase -> catalase_activity (MOLECULAR_FUNCTION sense). Described as 'Enzyme ACTIVITY that detoxifies hydrogen peroxide', while the four GENE_OR_PROTEIN occurrences describe the enzyme itself ('Enzyme that degrades hydrogen peroxide to water and oxygen'). catalase_activity already exists corpus-wide as a MOLECULAR_FUNCTION node. Described as 'Enzyme ACTIVITY that detoxifies superoxide' against 'Enzyme that dismutates superoxide' for the protein occurrences. It also carries GO:0004784, which IS 'superoxide dismutase activity' -- so the grounding was already describing a molecular function and only the id disagreed. The one new id in this migration, coined to the corpus's dominant _activity convention.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-16T02:00:00Z",
        "curator": "claude",
        "action": "NORMALISE_NODE_TYPE",
        "changes": "Under the PATHWAY-vs-BIOLOGICAL_PROCESS rule, one node_id means one thing corpus-wide (issue 356): electron_transport_chain is typed PATHWAY. PATHWAY is a named, conventionally enumerable multi-step route; BIOLOGICAL_PROCESS is everything else. A named route through enumerable complexes. Was 4 PATHWAY to 2 before this tranche.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope obligate_aerobe_oxygen_respiration=NONMECHANISTIC with scope_notes; marked 2 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (terminal_oxidases, fe_s_cluster_enzymes).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1003004",
    "label": "obligately alkaliphilic",
    "definition": "An alkaliphilic phenotype in which an organism requires alkaline conditions (typically pH above 8.5) for growth and cannot grow at neutral or acidic pH.",
    "definition_source": "DOI:10.3389/fbioe.2015.00075",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1003002"
    ],
    "synonyms": [
      {
        "synonym_text": "obligate alkaliphile",
        "synonym_type": "EXACT_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "obligate alkaphilic",
        "synonym_type": "EXACT_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "created_by": "Luke Wang",
    "evidence": [
      {
        "reference": "DOI:10.3389/fbioe.2015.00075",
        "snippet": "grow only at pH values of ~pH 9 and above",
        "notes": "Supports the obligate alkaliphile definition."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:2257",
        "taxon_label": "Natronomonas pharaonis",
        "note": "Soda-lake haloalkaliphilic archaeon (pH optimum ~8.5, alkaline tolerance to ~pH 11). Halalkalibacterium halodurans C-125 (ex-Bacillus halodurans) is the classic non-halophilic obligate alkaliphile.",
        "reference": "https://pmc.ncbi.nlm.nih.gov/articles/PMC1240075/"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "obligately_alkaphilic_sodium_cycle_homeostasis",
        "title": "Obligate alkaliphily sodium-cycle pH homeostasis mechanism",
        "description": "Evidence-backed causal sketch linking obligate alkaliphily to high external pH, Na+/H+ antiport, and cytoplasmic proton accumulation.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a broad environmental or morphological classification spanning multiple mechanisms, a measurement-like bin, or an absence/arrangement descriptor; contextual protein nodes do not receive token UniProt examples.",
        "nodes": [
          {
            "node_id": "obligately_alkaphilic_trait",
            "label": "obligately alkaliphilic",
            "node_type": "TRAIT",
            "grounding": "METPO:1003004",
            "description": "Growth requires alkaline pH and does not extend to neutral or acidic pH."
          },
          {
            "node_id": "alkaline_external_ph",
            "label": "alkaline external pH",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "External pH near or above pH 9.",
            "grounding": "PATO:0001430"
          },
          {
            "node_id": "sodium_ion",
            "label": "sodium ion",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:29101",
            "description": "Sodium ion participating in alkaliphile sodium cycles."
          },
          {
            "node_id": "proton",
            "label": "proton",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:15378",
            "description": "Hydrogen ion imported or retained to acidify the cytoplasm."
          },
          {
            "node_id": "sodium_proton_antiporter",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "Na+/H+ antiporter",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Antiporter exchanging sodium ions and protons during alkaline pH homeostasis."
          },
          {
            "node_id": "cytoplasmic_ph_homeostasis",
            "label": "cytoplasmic pH homeostasis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Maintenance of intracellular pH below strongly alkaline external pH.",
            "grounding": "GO:0051453"
          },
          {
            "node_id": "proton_coupled_atp_synthase",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "proton-coupled ATP synthase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "ATP synthase that remains proton-coupled in respiratory alkaliphiles."
          },
          {
            "node_id": "trkah_transport_system",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "TrkAH K+ uptake system",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Potassium uptake system contributing to pH homeostasis and membrane potential adjustment."
          },
          {
            "node_id": "cation_proton_antiporter",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "monovalent cation/proton antiporters",
            "node_type": "GENE_OR_PROTEIN",
            "description": "CPA/Mrp and Nha family antiporters regulating H+ influx and Na+ efflux under stress."
          },
          {
            "node_id": "secondary_cell_wall_polymers",
            "label": "secondary cell wall polymers / S-layer",
            "node_type": "CELLULAR_LOCALIZATION",
            "description": "Cell-surface polymers and S-layer proteins developed by alkaliphilic microbes."
          },
          {
            "node_id": "net_negative_surface_charge",
            "label": "net negative surface charge",
            "node_type": "QUALITY",
            "description": "Increased negative charge on cellular surfaces that attracts external protons."
          },
          {
            "node_id": "anionic_membrane_phospholipids",
            "label": "anionic membrane phospholipids (PG/PC/CL)",
            "node_type": "CHEMICAL",
            "description": "Phosphatidylglycerol, phosphatidylcholine, and cardiolipin enriched under high pH."
          },
          {
            "node_id": "acetate_anion",
            "label": "acetate anion",
            "node_type": "CHEMICAL",
            "description": "Dissociated form of acetic acid favored at high pH."
          },
          {
            "node_id": "acetate_transmembrane_diffusion",
            "label": "transmembrane diffusion of acetate",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Passive diffusion of protonated acetic acid across the membrane, prevented at high pH."
          }
        ],
        "edges": [
          {
            "subject": "alkaline_external_ph",
            "predicate": "is required for",
            "object": "obligately_alkaphilic_trait",
            "description": "Obligate alkaliphiles grow only under alkaline pH conditions.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fbioe.2015.00075",
                "snippet": "grow only at pH values of ~pH 9 and above",
                "notes": "Review explicitly defines obligate alkaliphiles by alkaline pH restriction."
              }
            ]
          },
          {
            "subject": "alkaline_external_ph",
            "predicate": "challenges",
            "object": "cytoplasmic_ph_homeostasis",
            "description": "High external pH requires cells to maintain cytoplasmic pH below the medium.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2549",
                "snippet": "below an external pH range of 9.5-11.0",
                "notes": "Supports cytoplasmic pH control under extreme alkaline external pH."
              }
            ],
            "predicate_id": "METPO:2007406"
          },
          {
            "subject": "sodium_proton_antiporter",
            "predicate": "exports",
            "object": "sodium_ion",
            "description": "Na+/H+ antiport couples sodium efflux to proton accumulation.",
            "evidence": [
              {
                "reference": "DOI:10.1016/S0005-2728(00)00285-1",
                "snippet": "Na+ efflux",
                "notes": "Supports sodium efflux as part of the alkaliphile Na+ cycle."
              }
            ],
            "predicate_id": "METPO:2007804"
          },
          {
            "subject": "sodium_proton_antiporter",
            "predicate": "accumulates",
            "object": "proton",
            "description": "Na+/H+ antiport achieves net proton accumulation for alkaline pH homeostasis.",
            "evidence": [
              {
                "reference": "DOI:10.1016/S0005-2728(00)00285-1",
                "snippet": "achieve net H+ accumulation",
                "notes": "Supports proton accumulation by antiporters in alkaliphiles."
              }
            ],
            "predicate_id": "METPO:2007810"
          },
          {
            "subject": "proton_coupled_atp_synthase",
            "predicate": "regulates",
            "object": "obligately_alkaphilic_trait",
            "description": "Proton-coupled ATP synthesis at very high pH creates a bioenergetic constraint requiring alkaliphile-specific adaptations.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.bbabio.2010.02.028",
                "snippet": "robust H+-coupled ATP synthesis at external pH values > 10",
                "notes": "Supports the proton-coupled ATP synthesis challenge in alkaliphiles."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "cytoplasmic_ph_homeostasis",
            "predicate": "confers",
            "object": "obligately_alkaphilic_trait",
            "description": "Growth at obligately alkaline pH depends on maintaining intracellular pH compatible with cell function.",
            "evidence": [
              {
                "reference": "DOI:10.1016/S0005-2728(00)00285-1",
                "snippet": "pH homeostasis ... appears to set the upper pH limit for growth",
                "notes": "Supports pH homeostasis as growth-limiting for alkaliphilic Bacillus."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "trkah_transport_system",
            "predicate": "contributes to",
            "object": "cytoplasmic_ph_homeostasis",
            "description": "TrkAH K+ uptake supports cytoplasmic pH homeostasis under alkaline conditions.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.00145-24",
                "notes": "The TrkAH transport system is responsible for the uptake of K+ ... and maintaining pH homeostasis."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "cation_proton_antiporter",
            "predicate": "is required for",
            "object": "obligately_alkaphilic_trait",
            "description": "Monovalent cation/proton antiporters are essential for growth of alkaliphilic bacteria under stress.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.00145-24",
                "notes": "Monovalent cation/proton antiporters ... are essential for the growth of various halophilic and alkaliphilic bacteria under stress conditions."
              }
            ]
          },
          {
            "subject": "secondary_cell_wall_polymers",
            "predicate": "increases",
            "object": "net_negative_surface_charge",
            "description": "Secondary cell wall polymers and S-layer proteins enhance net negative surface charge.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2022.1034164",
                "notes": "the second cell wall polymers (SCWPs), such as S-layer protein ... enhance net negative charges on cellular surfaces."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "net_negative_surface_charge",
            "predicate": "increases attraction to",
            "object": "proton",
            "description": "Net negative surface charge increases attraction of external protons toward the cell surface.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2022.1034164",
                "notes": "net negative charges on cellular surfaces that increase attraction to external protons."
              }
            ]
          },
          {
            "subject": "alkaline_external_ph",
            "predicate": "increases abundance of",
            "object": "anionic_membrane_phospholipids",
            "description": "High external pH increases relative abundance of PG, PC, and cardiolipin (membrane remodeling).",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2022.1034164",
                "notes": "It increased the relative abundance of phosphatidylglycerol (PG), phosphatidylcholine (PC), and cardiolipin (CL) in response to high pH."
              }
            ]
          },
          {
            "subject": "alkaline_external_ph",
            "predicate": "causes",
            "object": "acetate_anion",
            "description": "Alkaline conditions (>pH 9) favor dissociation of acetic acid to the acetate anion.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2023.1233691",
                "notes": "High pH favors the dissociation of acetic acid to its anion (CH3COO-), preventing transmembrane diffusion."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "acetate_anion",
            "predicate": "prevents",
            "object": "acetate_transmembrane_diffusion",
            "description": "Acetate anion at high pH cannot diffuse passively across the membrane.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2023.1233691",
                "notes": "High pH favors the dissociation of acetic acid to its anion (CH3COO-), preventing transmembrane diffusion."
              }
            ],
            "predicate_id": "RO:0002212"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.938910+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-11T00:00:00-07:00",
        "curator": "codex",
        "action": "CURATED_WITH_LITERATURE",
        "changes": "Reviewed obligately alkaphilic trait and added DOI-backed evidence and causal graph for sodium-cycle alkaline pH homeostasis and ATP synthase bioenergetic constraints.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:30Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T21:30:06Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007406\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:38:00Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0030641\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T05:05:14Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A068T423\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T08:14:32Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (PATO:0001429\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-26T05:00:47Z",
        "curator": "claude",
        "action": "RENAME_PREDICATE_LABELS",
        "changes": "Renamed 1 causal-edge predicate label(s) to align with existing groundings: constrains \u2192 regulates \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-26T05:00:50Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002211\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-15T07:20:36Z",
        "curator": "claude",
        "action": "FIX_NODE_GROUNDING_CURIE",
        "changes": "Overwrote 1 causal-node grounding(s) (obsolete/wrong GO -> corrected, verified vs OAK).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-15T07:21:43Z",
        "curator": "claude",
        "action": "FIX_NODE_GROUNDING_CURIE",
        "changes": "Overwrote 1 pH causal-node grounding(s) to corrected PATO CURIEs (phase-2; verified vs OAK).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-16T06:30:55Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000209\u00d71, METPO:2000210\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 7 evidence-backed generic edges (7 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:10Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 4 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002326\u00d71, RO:0002213\u00d71, biolink:causes\u00d71, RO:0002212\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:21:11Z",
        "curator": "claude",
        "action": "RETRACT_DEAD_UNIPROT_GROUNDINGS",
        "changes": "Retracted 1 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 1 causal edge(s) off enables/RO:0002327 with a TRAIT object (1 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T02:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES_PART2",
        "changes": "Re-grounded 2 causal edge(s) off microbe-domain METPO predicates onto their causal-graph counterparts (1 to accumulates, 1 to exports), issue 301 part 2. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Each replacement is a 1:1 mirror of its source predicate that changes only the domain, so the claim each edge makes is unchanged and directions are unchanged. The replacements are proposed in proposals/metpo_traitmech_v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope obligately_alkaphilic_sodium_cycle_homeostasis=NONMECHANISTIC with scope_notes; marked 4 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (sodium_proton_antiporter, proton_coupled_atp_synthase, trkah_transport_system, cation_proton_antiporter).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T07:35:00Z",
        "curator": "migrate_metpo_2026_06_12",
        "action": "MIGRATE_METPO_RELEASE",
        "changes": "Migrated source-owned fields to locked METPO 2026-06-12: label 'obligately alkaphilic' -> 'obligately alkaliphilic'; definition synchronized to METPO 2026-06-12; parent_traits ('METPO:1003000',) -> ('METPO:1003002',); synonyms synchronized at ontology-declared scope; grounded node obligately_alkaphilic_trait label synchronized"
      }
    ]
  },
  {
    "identifier": "METPO:1000607",
    "label": "obligately anaerobic",
    "definition": "An oxygen preference in which molecular oxygen (O\u2082) inhibits or prevents growth.",
    "definition_source": "https://www.ncbi.nlm.nih.gov/books/NBK482349/",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000601"
    ],
    "synonyms": [
      {
        "synonym_text": "obligate anaerobe",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "obligate anaerobic",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "https://www.ncbi.nlm.nih.gov/books/NBK482349/",
        "snippet": "Oxygen is toxic to anaerobes",
        "notes": "Supports oxygen inhibition/toxicity for obligately anaerobic organisms."
      },
      {
        "reference": "PMID:22778399",
        "snippet": "obligate anaerobe Bacteroides fragilis",
        "notes": "Organism example: Bacteroides fragilis is described as an obligate anaerobe."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1488",
        "taxon_label": "Clostridium acetobutylicum",
        "note": "Model obligate anaerobe (ABE fermentation; oxygen-sensitive).",
        "reference": "PMID:11466286"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "obligate_anaerobe_oxygen_toxicity",
        "title": "Obligate anaerobe oxygen-toxicity mechanism",
        "description": "Evidence-backed causal sketch linking obligate anaerobiosis to oxygen-blocked growth and oxygen-sensitive metabolic chemistry.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a broad environmental or morphological classification spanning multiple mechanisms, a measurement-like bin, or an absence/arrangement descriptor; contextual protein nodes do not receive token UniProt examples.",
        "nodes": [
          {
            "node_id": "obligate_anaerobic_trait",
            "label": "obligately anaerobic",
            "node_type": "TRAIT",
            "grounding": "METPO:1000607",
            "description": "Molecular oxygen inhibits or prevents growth."
          },
          {
            "node_id": "molecular_oxygen",
            "label": "molecular oxygen",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:15379",
            "description": "Dioxygen exposure that blocks obligate anaerobe growth."
          },
          {
            "node_id": "reactive_oxygen_species",
            "label": "reactive oxygen species",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:26523",
            "description": "Oxygen-derived oxidants such as superoxide and hydrogen peroxide."
          },
          {
            "node_id": "low_potential_metal_centres",
            "label": "low-potential metal centres",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "Oxygen-sensitive catalytic centers used in anaerobic metabolism."
          },
          {
            "node_id": "anaerobic_metabolism",
            "label": "anaerobic metabolism",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Energy metabolism optimized for anoxic conditions."
          },
          {
            "node_id": "oxygen_exposure",
            "label": "oxygen exposure",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Exposure of anaerobic cells to molecular oxygen, triggering oxidative stress."
          },
          {
            "node_id": "oxidative_damage_biomolecules",
            "label": "oxidative damage to biomolecules",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "ROS-mediated oxidative damage to proteins and nucleic acids."
          },
          {
            "node_id": "hydrogen_peroxide",
            "label": "hydrogen peroxide",
            "node_type": "CHEMICAL",
            "description": "Reactive oxygen species; substrate for Fenton chemistry.",
            "grounding": "CHEBI:16240"
          },
          {
            "node_id": "ferrous_iron",
            "label": "ferrous iron (Fe(II))",
            "node_type": "CHEMICAL",
            "description": "Fe(II) reactant driving hydroxyl-radical generation via Fenton reaction."
          },
          {
            "node_id": "hydroxyl_radical",
            "label": "hydroxyl radical",
            "node_type": "CHEMICAL",
            "description": "Highly damaging ROS produced via Fenton chemistry.",
            "grounding": "CHEBI:29191"
          },
          {
            "node_id": "dna_damage",
            "label": "DNA damage",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Irreparable lesions blocking replication caused by hydroxyl radicals."
          },
          {
            "node_id": "pyruvate_formate_lyase",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "pyruvate formate-lyase (PFL)",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Glycyl-radical enzyme rapidly inactivated by O2."
          },
          {
            "node_id": "pyruvate_ferredoxin_oxidoreductase",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "pyruvate:ferredoxin oxidoreductase (PFOR)",
            "node_type": "GENE_OR_PROTEIN",
            "description": "O2-sensitive anaerobic metalloenzyme."
          },
          {
            "node_id": "fefe_hydrogenase",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "[FeFe]-hydrogenase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Oxygen-sensitive low-potential redox enzyme."
          }
        ],
        "edges": [
          {
            "subject": "molecular_oxygen",
            "predicate": "inhibits",
            "object": "obligate_anaerobic_trait",
            "description": "Oxygen blocks growth of obligate anaerobes.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41579-021-00583-y",
                "snippet": "oxygen blocks their growth",
                "notes": "Review identifies blocked growth as the defining trait of obligate anaerobes."
              }
            ],
            "predicate_id": "RO:0002212"
          },
          {
            "subject": "anaerobic_metabolism",
            "predicate": "depends on",
            "object": "low_potential_metal_centres",
            "description": "Obligate anaerobic metabolism often relies on oxygen-sensitive radical chemistry and low-potential metal centers.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41579-021-00583-y",
                "snippet": "radical chemistry and low-potential metal centres",
                "notes": "Supports low-potential metal centers as anaerobic metabolic features."
              }
            ],
            "predicate_id": "RO:0002502"
          },
          {
            "subject": "molecular_oxygen",
            "predicate": "poisons",
            "object": "low_potential_metal_centres",
            "description": "Dioxygen can directly poison catalytic sites central to anaerobic metabolism.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41579-021-00583-y",
                "snippet": "direct poisoning by molecular oxygen and ROS",
                "notes": "Supports oxygen-sensitive catalytic sites as a mechanism of growth inhibition."
              }
            ]
          },
          {
            "subject": "reactive_oxygen_species",
            "predicate": "damages",
            "object": "low_potential_metal_centres",
            "description": "ROS provide an additional route for damage to oxygen-sensitive anaerobic enzymes.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41579-021-00583-y",
                "snippet": "direct poisoning by molecular oxygen and ROS",
                "notes": "Supports ROS-mediated impairment of anaerobic catalytic sites."
              }
            ]
          },
          {
            "subject": "oxygen_exposure",
            "predicate": "causes",
            "object": "reactive_oxygen_species",
            "description": "O2 exposure generates ROS such as superoxide, peroxides, and hydroxyl radicals.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s40168-024-01909-7",
                "notes": "As a consequence of oxygenation, reactive oxygen species like superoxide, peroxides, and hydroxyl radicals are produced."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "oxygen_exposure",
            "predicate": "causes",
            "object": "oxidative_damage_biomolecules",
            "description": "O2 exposure causes oxidative stress damaging biomolecules.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s40168-024-01909-7",
                "notes": "ROS cause oxidative stress due to damage to biomolecules like proteins and nucleic acids."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "hydrogen_peroxide",
            "predicate": "causes",
            "object": "hydroxyl_radical",
            "description": "H2O2 reacts with Fe(II) to produce hydroxyl radicals (Fenton chemistry).",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41579-021-00583-y",
                "notes": "Fe(II)+H2O2 produces hydroxyl radicals."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "ferrous_iron",
            "predicate": "causes",
            "object": "hydroxyl_radical",
            "description": "Fe(II) drives hydroxyl-radical generation via the Fenton reaction.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41579-021-00583-y",
                "notes": "Fe(II)+H2O2 produces hydroxyl radicals."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "hydroxyl_radical",
            "predicate": "causes",
            "object": "dna_damage",
            "description": "Hydroxyl radicals create irreparable lesions and block replication.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41579-021-00583-y",
                "notes": "hydroxyl radicals create irreparable lesions and block replication."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "molecular_oxygen",
            "predicate": "inactivates",
            "object": "pyruvate_formate_lyase",
            "description": "O2 rapidly inactivates the glycyl-radical enzyme PFL.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41579-021-00583-y",
                "notes": "PFL is rapidly inactivated by O2; even low O2 levels can inactivate PFL within seconds."
              }
            ]
          },
          {
            "subject": "molecular_oxygen",
            "predicate": "inactivates",
            "object": "pyruvate_ferredoxin_oxidoreductase",
            "description": "O2 directly inactivates the metalloenzyme PFOR.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41579-021-00583-y",
                "notes": "O2 directly inactivates diverse metalloenzymes (e.g., PFOR)."
              }
            ]
          },
          {
            "subject": "molecular_oxygen",
            "predicate": "inactivates",
            "object": "fefe_hydrogenase",
            "description": "O2 directly inactivates oxygen-sensitive [FeFe]-hydrogenases.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41579-021-00583-y",
                "notes": "O2 directly inactivates diverse metalloenzymes... hydrogenases."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.852690+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-05T01:09:05-07:00",
        "curator": "codex",
        "action": "CURATED_WITH_LITERATURE",
        "changes": "Added definition source and evidence for oxygen-sensitive anaerobic growth.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-05T18:39:46-07:00",
        "curator": "codex",
        "action": "ADDED_ORGANISM_EXAMPLE",
        "changes": "Added Bacteroides fragilis organism example with PMID-backed evidence.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "ADDED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed causal graph for oxygen toxicity in obligate anaerobes.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T08:21:49Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002502\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-13T21:03:25Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002212\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 8 evidence-backed generic edges (9 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:10Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 5 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:causes\u00d75).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:16240\u00d71, CHEBI:29191\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope obligate_anaerobe_oxygen_toxicity=NONMECHANISTIC with scope_notes; marked 3 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (pyruvate_formate_lyase, pyruvate_ferredoxin_oxidoreductase, fefe_hydrogenase).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000002",
    "label": "obligately piezophilic",
    "definition": "A pressure growth preference in which an organism requires elevated hydrostatic pressure for growth and is unable to grow at atmospheric pressure (0.1 MPa).",
    "definition_source": "DOI:10.1038/srep27289",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "traitmech:000001"
    ],
    "synonyms": [
      {
        "synonym_text": "obligate piezophile",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1038/srep27289"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/srep27289",
        "snippet": "High hydrostatic pressure adaptive strategies in an obligate piezophile Pyrococcus yayanosii",
        "notes": "Organism example: Pyrococcus yayanosii is an obligate piezophile that requires high hydrostatic pressure for growth."
      },
      {
        "reference": "DOI:10.1099/ijsem.0.001671",
        "snippet": "growth range of 80-140 MPa (optimum, 120 MPa) at 6 degrees C",
        "notes": "Organism example: Colwellia marinimaniae MTCD1 grows only at high pressure (80-140 MPa) and does not grow near atmospheric pressure."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1513592",
        "taxon_label": "Colwellia marinimaniae",
        "note": "Most piezophilic organism described; optimum ~120 MPa (Mariana Trench). Photobacterium profundum SS9 is the classic genetic model.",
        "reference": "https://pubmed.ncbi.nlm.nih.gov/27902293/"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "obligate_piezophily_high_pressure_requirement",
        "title": "Obligate piezophily: growth requires elevated hydrostatic pressure",
        "description": "Evidence-backed causal sketch linking obligate HHP adaptation to inability to grow at atmospheric pressure.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a broad environmental or morphological classification spanning multiple mechanisms, a measurement-like bin, or an absence/arrangement descriptor; contextual protein nodes do not receive token UniProt examples.",
        "nodes": [
          {
            "node_id": "obligate_piezophilic_trait",
            "label": "obligately piezophilic",
            "node_type": "TRAIT",
            "grounding": "traitmech:000002",
            "description": "Growth restricted to elevated hydrostatic pressures."
          },
          {
            "node_id": "obligate_hhp",
            "label": "obligate high hydrostatic pressure",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Hydrostatic pressure level required for growth (no growth at 0.1 MPa)."
          },
          {
            "node_id": "pressure_dependent_machinery",
            "label": "pressure-dependent cellular machinery",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Membrane, ribosome, and replication systems adapted only to HHP."
          },
          {
            "node_id": "ambient_pressure_growth_failure",
            "label": "inability to grow at ambient pressure (0.1 MPa)",
            "node_type": "QUALITY",
            "description": "Obligate piezophiles cannot grow at atmospheric pressure (0.1 MPa)."
          },
          {
            "node_id": "membrane_unsaturated_branched_lipids",
            "label": "unsaturated/branched-chain membrane lipids",
            "node_type": "CHEMICAL",
            "description": "Membrane fatty acids with increased unsaturation/branching that maintain fluidity under HHP."
          },
          {
            "node_id": "membrane_fluidity_maintenance",
            "label": "maintenance of membrane fluidity under HHP",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Homeoviscous adaptation preserving membrane fluidity at elevated hydrostatic pressure."
          }
        ],
        "edges": [
          {
            "subject": "obligate_hhp",
            "predicate": "causes",
            "object": "obligate_piezophilic_trait",
            "description": "HHP adaptation that no longer functions at 0.1 MPa makes high pressure obligatory for growth.",
            "evidence": [
              {
                "reference": "DOI:10.1099/ijsem.0.001671",
                "snippet": "grew at extremely high hydrostatic pressures, with a growth range of 80-140 MPa",
                "notes": "Verified against public Kusube et al. abstract text; Colwellia marinimaniae MTCD1 is retained as a hyperpiezophilic obligate-HHP exemplar."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "pressure_dependent_machinery",
            "predicate": "confers",
            "object": "obligate_piezophilic_trait",
            "description": "Cellular machinery requiring HHP for function realizes the obligate-piezophile phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1038/srep27289",
                "snippet": "hydrostatic pressure-responsive genes involved in translation, chemotaxis, energy metabolism",
                "notes": "Verified against the open Michoud and Jebbar abstract; the edge is kept as a broad cellular-machinery dependency in an obligate piezophile."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "ambient_pressure_growth_failure",
            "predicate": "manifests as",
            "object": "obligate_piezophilic_trait",
            "description": "Inability to grow at 0.1 MPa is the diagnostic pressure-growth failure state represented by obligate piezophily.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41396-021-00930-0",
                "snippet": "obligate piezophiles (or hyperpiezophiles) unable to grow at ambient pressure",
                "notes": "Verified against public Scoma et al. text; the edge is reversed from ungrounded trait-to-quality wording to a grounded manifestation relation."
              }
            ],
            "predicate_id": "METPO:2007400"
          },
          {
            "subject": "obligate_hhp",
            "predicate": "increases",
            "object": "membrane_unsaturated_branched_lipids",
            "description": "Elevated hydrostatic pressure increases the requirement for and abundance of unsaturated/branched-chain membrane lipids.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmolb.2022.1058381",
                "snippet": "specific membrane lipids, such as those containing unsaturated and branched-chain fatty acids, rises with increasing HHP",
                "notes": "Verified against the open Tamby et al. abstract; the edge is retained as a broad pressure-associated lipid adaptation, not a universal claim for all piezophiles."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "membrane_unsaturated_branched_lipids",
            "predicate": "enables",
            "object": "membrane_fluidity_maintenance",
            "description": "Unsaturated/branched-chain lipids maintain membrane fluidity under HHP (homeoviscous adaptation).",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmolb.2022.1058381",
                "snippet": "modulate the degrees of unsaturation and branching of their acyl chain",
                "notes": "Verified against the open Tamby et al. Frontiers/PMC full text; the source directly names unsaturation and branching as membrane adaptations to HHP and extreme temperature."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "membrane_fluidity_maintenance",
            "predicate": "contributes to",
            "object": "pressure_dependent_machinery",
            "description": "Maintained membrane fluidity supports the pressure-dependent cellular machinery underlying obligate piezophily.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmolb.2022.1058381",
                "snippet": "Piezophiles, microorganisms adapted to high pressure, have developed key strategies to maintain the integrity of their lipid membrane",
                "notes": "Verified against the open Tamby et al. abstract; the edge is retained as a high-level bridge from high-pressure membrane adaptation to HHP-dependent machinery."
              }
            ],
            "predicate_id": "RO:0002326"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-28T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate ENVIRONMENT trait (obligate high-pressure requirement) from literature research; sub-variant of piezophilic. Backed by two obligate- piezophile organism examples.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-09T14:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (obligate HHP requirement) with RO/biolink predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 4 evidence-backed generic edges (3 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:10Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d71, RO:0002326\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 1 causal edge(s) off enables/RO:0002327 with a TRAIT object (1 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope obligate_piezophily_high_pressure_requirement=NONMECHANISTIC with scope_notes.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-04T08:20:00Z",
        "curator": "codex",
        "action": "REVIEW_CAUSAL_EVIDENCE",
        "changes": "Reviewed the obligate_piezophily_high_pressure_requirement graph for issue #183: added exact snippets to 6 causal-edge evidence items and grounded 2 residual predicates. No paid research service was called.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-06T17:10:00Z",
        "curator": "codex",
        "action": "ADVERSARIAL_REVIEW_REPAIR",
        "changes": "Addressed PR #664 adversarial review: replaced the HHP-damage snippet with exact Tamby et al. wording that supports high-pressure lipid-membrane integrity as piezophile adaptation.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-07T02:20:00Z",
        "curator": "codex",
        "action": "ADVERSARIAL_REVIEW_REPAIR",
        "changes": "Addressed PR #664 adversarial review issue #680: replaced the subjectless HHP lipid-packing connector snippet with exact Tamby et al. wording that names unsaturation and branching as membrane adaptations to HHP and extreme temperature.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000536",
    "label": "optimum phenotype with numerical limits",
    "definition": "A phenotype characterized by the value at which an organism exhibits maximum growth rate or activity.",
    "definition_source": "DOI:10.1093/femsre/fuy009",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1093/femsre/fuy009",
        "snippet": "optimal NaCl",
        "notes": "Osmoadaptation review supports the environmental value at which growth is maximal as a standard quantitative descriptor."
      },
      {
        "reference": "DOI:10.1038/nrmicro2549",
        "snippet": "cytoplasmic pH",
        "notes": "pH-homeostasis review supports the external pH at which cytoplasmic homeostasis sustains peak growth as an analogous optimum on the pH axis."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:3028314",
        "taxon_label": "Oceanimonas pelagia",
        "reference": "DOI:10.1007/s10482-024-01948-y",
        "note": "The type-strain description separately reports optima of 30 degrees C and pH 7-8 while retaining the associated growth ranges, directly exemplifying a measured best-growth value rather than tolerance at one condition."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "optimum_phenotype_descriptor",
        "title": "Optimum phenotype descriptor across environmental axes",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a quantitative measurement, interval, or bin in the environmental phenotype hierarchy; a token protein example would misrepresent the measured value as one inherited molecular mechanism.",
        "description": "DOI-backed graph framing the optimum phenotype as a generic peak-growth setpoint over any numerical environmental axis, with `is a` edges to the axis-specific optimum phenotypes for NaCl, pH, and temperature.",
        "nodes": [
          {
            "node_id": "optimum_phenotype_trait",
            "label": "optimum phenotype with numerical limits",
            "node_type": "TRAIT",
            "grounding": "METPO:1000536",
            "description": "Phenotype defined by the value of an environmental variable at which growth rate is maximal."
          },
          {
            "node_id": "numerical_environmental_axis",
            "label": "numerical environmental axis",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Any continuous environmental variable (NaCl, pH, temperature, etc.) on which microbial growth can be measured quantitatively."
          },
          {
            "node_id": "nacl_optimum",
            "label": "NaCl optimum",
            "node_type": "TRAIT",
            "grounding": "METPO:1000333",
            "description": "NaCl concentration supporting maximal growth."
          },
          {
            "node_id": "ph_optimum",
            "label": "pH optimum",
            "node_type": "TRAIT",
            "grounding": "METPO:1000331",
            "description": "External pH supporting maximal growth."
          },
          {
            "node_id": "temperature_optimum",
            "label": "temperature optimum",
            "node_type": "TRAIT",
            "grounding": "METPO:1000304",
            "description": "Ambient temperature supporting maximal growth."
          },
          {
            "node_id": "na_h_antiporters",
            "label": "Na+/H+ antiporters",
            "node_type": "GENE_OR_PROTEIN",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed as a contextual protein or protein-complex label within a quantitative measurement graph; no exact semantic family term was established for this aggregate use.",
            "description": "Cation/proton antiporters that exchange cytoplasmic Na+ (or K+) for protons."
          },
          {
            "node_id": "intracellular_ph_homeostasis",
            "label": "intracellular pH homeostasis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Maintenance of cytoplasmic pH within a narrow range (~7.0-7.5) despite external pH."
          },
          {
            "node_id": "f1f0_atp_synthase",
            "label": "F1F0-ATP synthase",
            "node_type": "GENE_OR_PROTEIN",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed as a contextual protein or protein-complex label within a quantitative measurement graph; no exact semantic family term was established for this aggregate use.",
            "description": "Membrane ATP synthase coupling proton flux to ATP synthesis/hydrolysis."
          },
          {
            "node_id": "opua_transporter",
            "label": "OpuA compatible-solute transporter",
            "node_type": "GENE_OR_PROTEIN",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed as a contextual protein or protein-complex label within a quantitative measurement graph; no exact semantic family term was established for this aggregate use.",
            "description": "ABC importer accumulating compatible solutes such as glycine betaine to high levels."
          },
          {
            "node_id": "intracellular_glycine_betaine",
            "label": "intracellular glycine betaine",
            "node_type": "CHEMICAL",
            "description": "Compatible solute accumulated in the cytoplasm to counter osmotic stress."
          },
          {
            "node_id": "hyperosmotic_stress",
            "label": "hyperosmotic stress",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "External hypertonicity causing cell shrinkage and plasmolysis."
          },
          {
            "node_id": "compatible_solute_accumulation",
            "label": "compatible-solute accumulation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Active import/synthesis of compatible solutes to restore turgor under osmotic stress."
          },
          {
            "node_id": "amino_acid_decarboxylation",
            "label": "amino-acid decarboxylation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Decarboxylase activity that consumes cytoplasmic protons, raising internal pH under acid stress."
          },
          {
            "node_id": "proton_motive_force",
            "label": "proton motive force",
            "node_type": "STATE",
            "description": "Electrochemical proton gradient across the membrane used for energy coupling.",
            "grounding": "METPO:1007500"
          }
        ],
        "edges": [
          {
            "subject": "numerical_environmental_axis",
            "predicate": "defines",
            "object": "optimum_phenotype_trait",
            "description": "A numerical environmental axis defines the values whose peak-growth setting yields the optimum phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuy009",
                "snippet": "optimal NaCl",
                "notes": "Supports a numerical environmental axis as the axis on which an optimum is identified."
              }
            ],
            "predicate_id": "METPO:2007500"
          },
          {
            "subject": "nacl_optimum",
            "predicate": "is a",
            "object": "optimum_phenotype_trait",
            "description": "NaCl optimum is an axis-specific optimum phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuy009",
                "snippet": "optimal NaCl",
                "notes": "Supports NaCl optimum as an optimum phenotype defined over the salinity axis."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "ph_optimum",
            "predicate": "is a",
            "object": "optimum_phenotype_trait",
            "description": "pH optimum is an axis-specific optimum phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2549",
                "snippet": "cytoplasmic pH",
                "notes": "Supports pH optimum as an optimum phenotype defined over the external-pH axis."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "temperature_optimum",
            "predicate": "is a",
            "object": "optimum_phenotype_trait",
            "description": "Temperature optimum is an axis-specific optimum phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-micro-091313-103612",
                "snippet": "more unsaturated fatty acids",
                "notes": "Membrane-adaptation review supports temperature optima as a homoviscous-adaptation-tuned setpoint on the temperature axis."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "na_h_antiporters",
            "predicate": "contributes to",
            "object": "intracellular_ph_homeostasis",
            "description": "Na+/H+ (and K+/H+) antiporters are key regulators of bacterial pH homeostasis.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuad033",
                "notes": "Key regulators of bacterial pH homeostasis are Na+/H+ and K+/H+ antiporters; stabilizes internal pH at the external-pH optimum."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "f1f0_atp_synthase",
            "predicate": "contributes to",
            "object": "intracellular_ph_homeostasis",
            "description": "F1F0-ATP synthase activity contributes to pH homeostasis via proton translocation.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2549",
                "notes": "F1F0-ATP synthase activity contributes to pH homeostasis; general bacterial bioenergetic mechanism."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "opua_transporter",
            "predicate": "increases",
            "object": "intracellular_glycine_betaine",
            "description": "OpuA accumulates the compatible solute glycine betaine to (sub)molar levels.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuad033",
                "notes": "OpuA can accumulate the compatible solute glycine betaine to (sub)molar levels; mechanism for osmolarity optimum."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "hyperosmotic_stress",
            "predicate": "activates",
            "object": "compatible_solute_accumulation",
            "description": "Hypertonicity drives active import of compatible solutes to restore turgor.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuad033",
                "notes": "Hypertonicity causes shrinkage/plasmolysis; active importers accumulate compatible solutes in response."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "amino_acid_decarboxylation",
            "predicate": "contributes to",
            "object": "intracellular_ph_homeostasis",
            "description": "Amino-acid decarboxylase activity rises when internal pH drops, raising cytoplasmic pH under acid stress.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuad033",
                "notes": "Amino-acid decarboxylases have low pH optima and activity increases when internal pH drops, contributing to pH homeostasis."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "amino_acid_decarboxylation",
            "predicate": "generates",
            "object": "proton_motive_force",
            "description": "Decarboxylation coupled to antiporter exchange generates a proton motive force.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuad033",
                "notes": "Decarboxylation plus antiporter exchange generates PMF, ~1 proton per molecule decarboxylated."
              }
            ],
            "predicate_id": "biolink:produces"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.848187+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-13T12:00:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed causal graph framing the optimum phenotype as a cross-axis peak-growth descriptor with axis-specific children for NaCl, pH, and temperature.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:30Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (rdfs:subClassOf\u00d73).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T07:37:39Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007500\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 6 evidence-backed generic edges (9 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:10Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 6 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002326\u00d73, RO:0002213\u00d72, biolink:produces\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-15T02:00:00Z",
        "curator": "claude",
        "action": "NORMALISE_NODE_TYPE",
        "changes": "Normalised causal-node type(s) so one node_id means one thing corpus-wide (issue 356): proton_motive_force: BIOLOGICAL_PROCESS -> STATE. The schema's OWN example of STATE: 'a bioenergetic or molecular state of the cell (e.g. proton motive force ...) ... the state is the gradient / steady-value, not its establishment'. All 35 occurrences describe the gradient -- every description across all four types reads 'electrochemical proton gradient', including the 13 typed BIOLOGICAL_PROCESS ('Transmembrane electrochemical gradient generated by respiration'), which name the gradient and its provenance rather than the generating process. Nothing here means the establishment, so this is a retype and not a rename; records that DO mean the process already use a separate id (proton_motive_force_generation in ph_delta.yaml). Also settles the one edge #356 was filed for: phototrophic.yaml's CAPACITY typing was blocking `powers` (METPO:2007900), which is gated to BIOLOGICAL_PROCESS|STATE.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-16T02:00:00Z",
        "curator": "claude",
        "action": "NORMALISE_NODE_TYPE",
        "changes": "Under the PATHWAY-vs-BIOLOGICAL_PROCESS rule, one node_id means one thing corpus-wide (issue 356): amino_acid_decarboxylation is typed BIOLOGICAL_PROCESS. PATHWAY is a named, conventionally enumerable multi-step route; BIOLOGICAL_PROCESS is everything else. A REACTION CLASS, not a route. The corpus describes it that way in neutrophilic.yaml -- 'Enzyme-catalyzed decarboxylation reaction that consumes cytoplasmic protons' -- and the wording varies by record, so read that as the family's sense rather than as this record's own text. Named systems that implement it (Gad) would be pathways; the reaction class is not. Was 4 BIOLOGICAL_PROCESS to 2 before this tranche.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-20T07:10:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (METPO:1007500\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope optimum_phenotype_descriptor=NONMECHANISTIC with scope_notes; marked 3 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (na_h_antiporters, f1f0_atp_synthase, opua_transporter).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T04:43:24Z",
        "curator": "codex",
        "action": "ADD_CANONICAL_EXAMPLES",
        "changes": "Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Oceanimonas pelagia (NCBITaxon:3028314; DOI:10.1007/s10482-024-01948-y). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000601",
    "label": "oxygen preference",
    "definition": "A phenotype that is relating to an organism's oxygen requirements or tolerance for growth.",
    "definition_source": "PMID:21413255",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "synonyms": [
      {
        "synonym_text": "Physiology and metabolism.oxygen tolerance.oxygen tolerance",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "metabolism",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "PMID:21413255",
        "snippet": "aerobes require molecular oxygen as a terminal electron acceptor",
        "notes": "Medical Microbiology chapter supports molecular oxygen as the environmental axis defining oxygen-preference phenotypes."
      },
      {
        "reference": "DOI:10.1016/j.bbabio.2011.06.016",
        "snippet": "respiratory quinol:O2 oxidoreductase",
        "notes": "Aerobic respiration review supports terminal oxidases as the enzymatic interface between cells and ambient O2."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:562",
        "taxon_label": "Escherichia coli",
        "reference": "DOI:10.1111/1751-7915.70051",
        "note": "Escherichia coli grows by aerobic respiration when oxygen is present and switches to anaerobic respiration or fermentation without it, exemplifying a facultative branch of oxygen preference."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "oxygen_preference_o2_availability_axis",
        "title": "Oxygen-preference O2-availability axis",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is an upper preference, broad tolerance, or central-range classification spanning multiple unrelated adaptations; contextual protein nodes are retained without assigning a misleading token UniProt example.",
        "description": "DOI-backed graph linking ambient molecular-oxygen availability to the four child oxygen-preference phenotypes (aerobic, anaerobic, microaerophilic, facultative) that classify how organisms use or tolerate O2.",
        "nodes": [
          {
            "node_id": "oxygen_preference_trait",
            "label": "oxygen preference",
            "node_type": "TRAIT",
            "grounding": "METPO:1000601",
            "description": "Classification of an organism's oxygen requirements or tolerance for growth."
          },
          {
            "node_id": "ambient_oxygen",
            "label": "ambient molecular oxygen",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Ambient O2 concentration imposed on the cell."
          },
          {
            "node_id": "aerobic_phenotype",
            "label": "aerobic",
            "node_type": "TRAIT",
            "grounding": "METPO:1000602",
            "description": "Growth in the presence of molecular oxygen using O2 as terminal electron acceptor."
          },
          {
            "node_id": "anaerobic_phenotype",
            "label": "anaerobic",
            "node_type": "TRAIT",
            "grounding": "METPO:1000603",
            "description": "Growth in the absence of molecular oxygen."
          },
          {
            "node_id": "microaerophilic_phenotype",
            "label": "microaerophilic",
            "node_type": "TRAIT",
            "grounding": "METPO:1000604",
            "description": "Growth at low molecular-oxygen concentrations."
          },
          {
            "node_id": "facultative_phenotype",
            "label": "facultative oxygen preference",
            "node_type": "TRAIT",
            "grounding": "METPO:1000612",
            "description": "Growth across a range of oxygen availabilities, switching between aerobic and anaerobic metabolism."
          },
          {
            "node_id": "molecular_oxygen",
            "label": "molecular oxygen",
            "node_type": "CHEMICAL",
            "description": "O2 used as a terminal electron acceptor in aerobic respiration.",
            "grounding": "CHEBI:15379"
          },
          {
            "node_id": "oxygen_terminal_electron_acceptor",
            "label": "O2 as terminal electron acceptor",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "Use of molecular oxygen as the terminal electron acceptor of the respiratory chain."
          },
          {
            "node_id": "reactive_oxygen_species_stress",
            "label": "oxygen / reactive oxygen species stress",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Exposure to O2 and reactive oxygen species such as hydrogen peroxide."
          },
          {
            "node_id": "detoxifying_enzyme_expression",
            "label": "detoxifying-enzyme gene expression",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Upregulation of genes encoding oxidative-stress detoxifying enzymes."
          },
          {
            "node_id": "catalase",
            "label": "catalase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Enzyme that degrades hydrogen peroxide to water and oxygen.",
            "grounding": "GO:0004096"
          },
          {
            "node_id": "hydrogen_peroxide",
            "label": "hydrogen peroxide",
            "node_type": "CHEMICAL",
            "description": "Reactive oxygen species produced during aerobic metabolism.",
            "grounding": "CHEBI:16240"
          },
          {
            "node_id": "superoxide_dismutase",
            "label": "superoxide dismutase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Enzyme that dismutates superoxide; key oxidative-stress defense.",
            "grounding": "GO:0004784"
          }
        ],
        "edges": [
          {
            "subject": "ambient_oxygen",
            "predicate": "defines",
            "object": "oxygen_preference_trait",
            "description": "Ambient molecular-oxygen concentration is the quantitative axis defining oxygen-preference phenotypes.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2014.00674",
                "snippet": "various capacities in their utilization of molecular oxygen",
                "notes": "Supports molecular oxygen utilization as the classification axis for oxygen-preference phenotypes."
              }
            ],
            "predicate_id": "METPO:2007500"
          },
          {
            "subject": "aerobic_phenotype",
            "predicate": "is a",
            "object": "oxygen_preference_trait",
            "description": "Aerobic is a child oxygen-preference phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2014.00674",
                "snippet": "aerobic ... respiration capacities",
                "notes": "Supports aerobic as an oxygen-use phenotype within oxygen-preference classification."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "anaerobic_phenotype",
            "predicate": "is a",
            "object": "oxygen_preference_trait",
            "description": "Anaerobic is a child oxygen-preference phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2014.00674",
                "snippet": "aerobic, microaerobic, and anaerobic reductases",
                "notes": "Supports anaerobic as a distinct oxygen-preference classification."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "microaerophilic_phenotype",
            "predicate": "is a",
            "object": "oxygen_preference_trait",
            "description": "Microaerophilic is a child oxygen-preference phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2014.00674",
                "snippet": "aerophilic, microaerophilic, or anaerobic",
                "notes": "Supports microaerophilic as a low-O2 setting on the oxygen-preference axis."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "facultative_phenotype",
            "predicate": "is a",
            "object": "oxygen_preference_trait",
            "description": "Facultative oxygen preference is a child oxygen-preference phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1111/cmi.13338",
                "snippet": "cope with changing oxygen levels",
                "notes": "Supports facultative organisms as a mixed-O2 setting on the oxygen-preference axis, switching between aerobic and anaerobic metabolism."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "oxygen_terminal_electron_acceptor",
            "predicate": "confers",
            "object": "aerobic_phenotype",
            "description": "Obligate aerobic growth depends on molecular oxygen as terminal electron acceptor.",
            "evidence": [
              {
                "reference": "DOI:10.1371/journal.ppat.1012084",
                "notes": "Obligate aerobes use only oxygen as the terminal electron acceptor, defining aerobic oxygen-preference."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "molecular_oxygen",
            "predicate": "serves as",
            "object": "oxygen_terminal_electron_acceptor",
            "description": "Molecular oxygen functions as the terminal electron acceptor in aerobic respiration.",
            "evidence": [
              {
                "reference": "DOI:10.1371/journal.ppat.1012084",
                "notes": "Oxygen is used as the terminal electron acceptor of the aerobic respiratory chain."
              }
            ]
          },
          {
            "subject": "reactive_oxygen_species_stress",
            "predicate": "upregulates",
            "object": "detoxifying_enzyme_expression",
            "description": "O2 or H2O2 stress upregulates detoxifying-enzyme genes.",
            "evidence": [
              {
                "reference": "DOI:10.1128/aem.00606-23",
                "notes": "Expression of genes encoding detoxifying enzymes was upregulated in response to O2 or H2O2 stress."
              }
            ]
          },
          {
            "subject": "detoxifying_enzyme_expression",
            "predicate": "increases",
            "object": "oxygen_preference_trait",
            "description": "A larger detoxifying-enzyme repertoire increases survival under oxygen exposure.",
            "evidence": [
              {
                "reference": "DOI:10.1128/aem.00606-23",
                "notes": "Cells with more detoxifying genes survived longer than those with few scavenging enzymes."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "catalase",
            "predicate": "degrades",
            "object": "hydrogen_peroxide",
            "description": "Catalase rapidly degrades hydrogen peroxide, a reactive oxygen species.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s43705-023-00251-7",
                "notes": "Catalase is the most prominent enzyme for H2O2 degradation at higher concentrations."
              }
            ],
            "predicate_id": "METPO:2007809"
          },
          {
            "subject": "superoxide_dismutase",
            "predicate": "increases",
            "object": "oxygen_preference_trait",
            "description": "Higher superoxide dismutase activity is associated with higher oxygen tolerance.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s43705-023-00251-7",
                "notes": "Higher Sod activity corresponded to higher oxygen tolerance."
              }
            ],
            "predicate_id": "RO:0002213"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.848644+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-13T11:30:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed causal graph framing oxygen preference as the O2-availability axis with child aerobic, anaerobic, microaerophilic, and facultative phenotypes.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-13T22:45:00-07:00",
        "curator": "codex",
        "action": "IMPROVED_CAUSAL_GRAPH_EVIDENCE",
        "changes": "Replaced PMID fallback CausalEdge references with DOI-backed oxygen-utilization and facultative oxygen-response citations.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:30Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 4 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (rdfs:subClassOf\u00d74).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T07:37:39Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007500\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 6 evidence-backed generic edges (8 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:10Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002213\u00d72, RO:0002327\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:17Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 3 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:15379\u00d71, UniProtKB:A0A071MK53\u00d71, UniProtKB:A0A009QPW9\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:16240\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:37Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000007\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:21:11Z",
        "curator": "claude",
        "action": "RETRACT_DEAD_UNIPROT_GROUNDINGS",
        "changes": "Retracted 2 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:23:52Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0004096\u00d71, GO:0004784\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 1 causal edge(s) off enables/RO:0002327 with a TRAIT object (1 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T02:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES_PART2",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates onto their causal-graph counterparts (1 to degrades), issue 301 part 2. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Each replacement is a 1:1 mirror of its source predicate that changes only the domain, so the claim each edge makes is unchanged and directions are unchanged. The replacements are proposed in proposals/metpo_traitmech_v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-08T05:00:00Z",
        "curator": "claude",
        "action": "MERGE_CAUSAL_NODE",
        "changes": "Merged node oxygen_tolerance into oxygen_preference_trait and repointed its edges. Issue 352. A SIXTH restatement (#360). METPO:1000601's own definition is 'an organism's oxygen requirements OR TOLERANCE for growth', so 'capacity of a cell to survive exposure to molecular oxygen' is part of what the anchor already says. I had grounded it METPO:1000609 (aerotolerant), which METPO defines as 'does NOT USE O2 for growth but tolerates its presence' -- the aerotolerant-anaerobe phenotype, false of the obligate aerobes this node also covers -- and which is itself sub METPO:1000601, making it a sixth child phenotype in a graph that wires the other four in with `is a` and left this one unlinked. aerotolerant.yaml, the record FOR 1000609, has no such node at all: it models the same biology as detoxification processes. Merging attaches the ROS-defence island to the trait, which unlike a retype is a real connectivity gain.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-17T02:00:00Z",
        "curator": "claude",
        "action": "NORMALISE_NODE_SENSE",
        "changes": "One node_id per SENSE (issues 356, 384): ambient_oxygen is the chemical sense here. Already the ambient sense. Listed so a re-run still normalises the label and still retracts ENVO:01001495 if it has been re-applied \u2014 the grounder keys on (label, node_type), so an un-normalised label is what lets the retracted CURIE come back.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope oxygen_preference_o2_availability_axis=NONMECHANISTIC with scope_notes.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T04:43:24Z",
        "curator": "codex",
        "action": "ADD_CANONICAL_EXAMPLES",
        "changes": "Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Escherichia coli (NCBITaxon:562; DOI:10.1111/1751-7915.70051). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000232",
    "label": "pH delta",
    "definition": "A pH phenotype with numerical limits expressing the breadth (maximum minus minimum) of external pH supporting growth of an organism.",
    "definition_source": "DOI:10.1038/nrmicro2549",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000531",
      "METPO:1000534"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/nrmicro2549",
        "snippet": "pH homeostasis",
        "notes": "pH-homeostasis review supports the breadth of the pH-tolerance span as a derived descriptor reflecting overall pH-homeostasis flexibility."
      },
      {
        "reference": "DOI:10.1016/j.tim.2007.02.005",
        "snippet": "proton motive force",
        "notes": "pH-homeostasis review supports the proton motive force as the energetic constraint underlying broad versus narrow pH tolerance."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:3028314",
        "taxon_label": "Oceanimonas pelagia",
        "reference": "DOI:10.1007/s10482-024-01948-y",
        "note": "Oceanimonas pelagia NTOU-MSR1T grew at pH 7-10, a breadth of 3 pH units. Because 3 is a bin boundary, #591 keeps this distinct claim on the delta parent."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "ph_delta_homeostasis_flexibility",
        "title": "pH-delta homeostasis flexibility",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a quantitative measurement, interval, or bin in the environmental phenotype hierarchy; a token protein example would misrepresent the measured value as one inherited molecular mechanism.",
        "description": "DOI-backed graph linking the flexibility of pH-homeostasis machinery to the breadth of the pH growth range (delta = max \u2212 min).",
        "nodes": [
          {
            "node_id": "ph_delta_trait",
            "label": "pH delta",
            "node_type": "TRAIT",
            "grounding": "METPO:1000232",
            "description": "Breadth of the growth-supporting external pH range."
          },
          {
            "node_id": "ph_homeostasis_flexibility",
            "label": "pH-homeostasis flexibility",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Capacity to remodel proton extrusion, K+/H+ antiport, and envelope buffering across a wide span of external pH."
          },
          {
            "node_id": "tolerance_breadth",
            "label": "pH tolerance breadth",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Span between the minimum and maximum growth-supporting external pH."
          },
          {
            "node_id": "ph_homeostasis",
            "label": "external pH homeostasis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Maintenance of intracellular pH within viable bounds across external pH variation."
          },
          {
            "node_id": "proton_motive_force_generation",
            "label": "proton motive force generation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Establishment of the transmembrane electrochemical proton gradient."
          },
          {
            "node_id": "f0f1_atpase_activity",
            "label": "F0F1-ATPase activity",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "F-type H+-transporting ATPase coupling proton flux to ATP synthesis/hydrolysis."
          },
          {
            "node_id": "cation_proton_antiporter_activity",
            "label": "monovalent cation:H+ antiporter activity",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "Exchange of Na+/K+ for H+ to support pH homeostasis, notably under alkaline conditions."
          },
          {
            "node_id": "membrane_lipid_remodeling",
            "label": "saturated membrane fatty acid remodeling",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Enrichment of saturated membrane fatty acids that reduces membrane proton permeability."
          },
          {
            "node_id": "proton_permeability",
            "label": "membrane proton permeability",
            "node_type": "QUALITY",
            "description": "Passive permeability of the cell membrane to protons."
          },
          {
            "node_id": "amino_acid_decarboxylase_acid_resistance",
            "label": "amino-acid decarboxylase acid-resistance system",
            "node_type": "PATHWAY",
            "description": "Decarboxylase systems that consume intracellular protons and export amines under acid stress."
          },
          {
            "node_id": "oxidative_phosphorylation",
            "label": "oxidative phosphorylation",
            "node_type": "PATHWAY",
            "description": "Respiratory generation of PMF and proton export contributing to cytoplasmic pH defense.",
            "grounding": "GO:0006119"
          }
        ],
        "edges": [
          {
            "subject": "ph_homeostasis_flexibility",
            "predicate": "enables",
            "object": "tolerance_breadth",
            "description": "pH-homeostasis flexibility enables broad pH tolerance.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2549",
                "snippet": "pH homeostasis",
                "notes": "Supports the breadth of pH homeostasis as the basis of broad pH tolerance."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "tolerance_breadth",
            "predicate": "manifests as",
            "object": "ph_delta_trait",
            "description": "The breadth between minimum and maximum growth-supporting external pH manifests the pH-delta phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.tim.2007.02.005",
                "snippet": "proton motive force",
                "notes": "Supports the bounded proton motive force as the determinant of the pH tolerance breadth."
              }
            ],
            "predicate_id": "METPO:2007400"
          },
          {
            "subject": "ph_homeostasis",
            "predicate": "confers",
            "object": "ph_delta_trait",
            "description": "External pH homeostasis enables a broader external pH growth breadth.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuad033",
                "notes": "Na+/H+ and K+/H+ antiporters and proton-pumping systems prevent internal pH from becoming too low, underpinning growth across pH (general bacteria, review)."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "proton_motive_force_generation",
            "predicate": "supports",
            "object": "ph_homeostasis",
            "description": "Proton motive force generation supports external pH homeostasis.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuad033",
                "notes": "PMF-linked systems regulate internal pH; decarboxylation can store free energy as PMF (general bacteria, review)."
              }
            ]
          },
          {
            "subject": "f0f1_atpase_activity",
            "predicate": "supports",
            "object": "ph_homeostasis",
            "description": "F0F1-ATPase activity supports external pH homeostasis.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuad033",
                "notes": "F0F1-ATPase uses 3-5 protons per ATP and is among systems that prevent internal pH from becoming too low (general bacteria, review)."
              }
            ]
          },
          {
            "subject": "cation_proton_antiporter_activity",
            "predicate": "supports",
            "object": "ph_homeostasis",
            "description": "Monovalent cation:H+ antiporter activity supports pH homeostasis under alkaline conditions.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.00569-24",
                "notes": "Monovalent antiporters exchange Na+/K+ to facilitate proton entry for alkali tolerance (generic transporter class)."
              }
            ]
          },
          {
            "subject": "membrane_lipid_remodeling",
            "predicate": "decreases",
            "object": "proton_permeability",
            "description": "Saturated membrane fatty acid remodeling decreases membrane proton permeability.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2022.1034164",
                "notes": "Membranes enriched in saturated fatty acids reduce proton permeability, minimizing proton influx in acidic environments (generalizable low-pH mechanism)."
              }
            ],
            "predicate_id": "RO:0002212"
          },
          {
            "subject": "amino_acid_decarboxylase_acid_resistance",
            "predicate": "increases",
            "object": "ph_delta_trait",
            "description": "Amino-acid decarboxylase acid-resistance systems increase low-pH tolerance.",
            "evidence": [
              {
                "reference": "DOI:10.3390/microorganisms12091774",
                "notes": "Amino-acid decarboxylase systems consume protons and export corresponding amines as a key acid-resistance mechanism (authoritative review)."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "oxidative_phosphorylation",
            "predicate": "supports",
            "object": "ph_homeostasis",
            "description": "Oxidative phosphorylation upregulation supports proton export and resistance to cytoplasmic acidification.",
            "evidence": [
              {
                "reference": "DOI:10.3390/microorganisms12081565",
                "notes": "Increased oxidative phosphorylation generates PMF and a higher proton export rate, causally helping cells resist decreases in cytoplasmic pH."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.812528+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-13T10:00:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed causal graph linking pH-homeostasis flexibility and the proton motive force to the pH-delta breadth phenotype.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:30Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T21:30:06Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007400\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 7 evidence-backed generic edges (9 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:10Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d71, RO:0002212\u00d71, RO:0002213\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:17Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0006119\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 1 causal edge(s) off enables/RO:0002327 with a TRAIT object (1 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-08T05:00:00Z",
        "curator": "claude",
        "action": "MERGE_CAUSAL_NODE",
        "changes": "Merged node low_ph_tolerance into ph_delta_trait and repointed its edges. Issue 352. An EIGHTH restatement (#360). I had grounded it METPO:1003008 (acidotolerant) and claimed 'no collision' with the record's METPO:1000232 (pH delta). No collision, but the wrong SCOPE: 1003008 is defined as tolerating acid 'WHILE MAINTAINING OPTIMAL GROWTH NEAR NEUTRAL pH', which excludes the acidophiles this generic pH-delta record covers. A grounding narrower than the node it labels is a false claim about every organism in the excluded part. Also a pure sink. Merging repoints amino_acid_decarboxylase_acid_resistance onto ph_delta_trait, which reads correctly: an acid-resistance system widens the growth-supporting pH range, and a pH delta IS that range.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-16T02:00:00Z",
        "curator": "claude",
        "action": "NORMALISE_NODE_TYPE",
        "changes": "Under the PATHWAY-vs-BIOLOGICAL_PROCESS rule, one node_id means one thing corpus-wide (issue 356): oxidative_phosphorylation is typed PATHWAY. PATHWAY is a named, conventionally enumerable multi-step route; BIOLOGICAL_PROCESS is everything else. A named route through enumerable complexes -- environment/ph_delta_mid1.yaml lists them (nuo, cyo, ndh, sdh). The rule breaks what was a 2-2 tie before this tranche.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-21T08:00:00Z",
        "curator": "codex",
        "action": "NORMALISE_NODE_TYPE",
        "changes": "Tranche 5 of issue 356 settles the process/quality families and merges ids that meant the same sense: proton_permeability is QUALITY. Proton permeability is a measurable membrane property, which is the schema's QUALITY sense rather than a biological process.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope ph_delta_homeostasis_flexibility=NONMECHANISTIC with scope_notes.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T04:43:24Z",
        "curator": "codex",
        "action": "ADD_CANONICAL_EXAMPLES",
        "changes": "Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Oceanimonas pelagia (NCBITaxon:3028314; DOI:10.1007/s10482-024-01948-y). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000478",
    "label": "pH delta high",
    "definition": "A pH delta phenotype with a growth-supporting pH breadth of approximately 5\u20139 pH units, characteristic of euryphilic pH-tolerance physiology.",
    "definition_source": "DOI:10.1038/nrmicro2549",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000232"
    ],
    "synonyms": [
      {
        "synonym_text": "pHd_5_9",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/nrmicro2549",
        "snippet": "pH homeostasis",
        "notes": "pH-homeostasis review supports very broad pH-homeostasis as a hallmark of generalist pH-tolerance physiology."
      },
      {
        "reference": "DOI:10.1016/j.tim.2007.02.005",
        "snippet": "proton motive force",
        "notes": "pH-homeostasis review supports robust proton extrusion and import machinery as the basis of very broad pH-tolerance."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:486505",
        "taxon_label": "Amycolatopsis flava",
        "reference": "DOI:10.1007/s10482-015-0542-z",
        "note": "Amycolatopsis flava AFM 10111T grew from pH 5 to 12, a seven-unit breadth wholly inside the approximately 5-9 pH-unit bin."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "ph_delta_high_euryphilic_breadth",
        "title": "pH-delta-high euryphilic breadth",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a quantitative measurement, interval, or bin in the environmental phenotype hierarchy; a token protein example would misrepresent the measured value as one inherited molecular mechanism.",
        "description": "DOI-backed graph linking maximal pH-homeostasis flexibility to a pH growth breadth of approximately 5\u20139 pH units.",
        "nodes": [
          {
            "node_id": "ph_delta_high_trait",
            "label": "pH delta high",
            "node_type": "TRAIT",
            "grounding": "METPO:1000478",
            "description": "pH growth-supporting breadth approximately 5\u20139 pH units."
          },
          {
            "node_id": "ph_delta",
            "label": "pH delta",
            "node_type": "TRAIT",
            "grounding": "METPO:1000232",
            "description": "Breadth of the growth-supporting external pH range."
          },
          {
            "node_id": "maximal_ph_homeostasis",
            "label": "maximal pH-homeostasis flexibility",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Combined proton-extrusion and Na+/H+ antiport flexibility supporting growth across an extreme pH span."
          },
          {
            "node_id": "na_h_antiporters",
            "label": "Na+/H+ antiporters",
            "node_type": "GENE_OR_PROTEIN",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed as a contextual protein or protein-complex label within a quantitative measurement graph; no exact semantic family term was established for this aggregate use.",
            "description": "Sodium:proton antiporters, core regulators of cytoplasmic pH across changing external pH."
          },
          {
            "node_id": "cytoplasmic_ph_homeostasis",
            "label": "cytoplasmic pH homeostasis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Maintenance of near-neutral internal pH despite external pH variation.",
            "grounding": "GO:0051453"
          },
          {
            "node_id": "respiratory_proton_pumps",
            "label": "respiratory proton-pumping enzymes",
            "node_type": "GENE_OR_PROTEIN",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed as a contextual protein or protein-complex label within a quantitative measurement graph; no exact semantic family term was established for this aggregate use.",
            "description": "Electron-transport-chain proton pumps that control proton flux during pH stress."
          },
          {
            "node_id": "f0f1_atpase",
            "label": "F0F1-ATPase",
            "node_type": "GENE_OR_PROTEIN",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed as a contextual protein or protein-complex label within a quantitative measurement graph; no exact semantic family term was established for this aggregate use.",
            "description": "Proton-translocating ATP synthase contributing to proton extrusion/uptake in pH homeostasis."
          },
          {
            "node_id": "metabolite_decarboxylation",
            "label": "metabolite decarboxylation pathways",
            "node_type": "PATHWAY",
            "description": "Proton-consuming decarboxylation pathways that reduce intracellular acidification."
          },
          {
            "node_id": "cytoplasmic_buffering_capacity",
            "label": "cytoplasmic buffering capacity",
            "node_type": "CAPACITY",
            "description": "Intracellular buffering that limits pH swings in the bacterial cytoplasm."
          },
          {
            "node_id": "near_neutral_cytoplasmic_ph",
            "label": "near-neutral cytoplasmic pH",
            "node_type": "QUALITY",
            "description": "Internal pH maintained near 7.5 while external pH varies."
          },
          {
            "node_id": "growth_external_ph_5_5_9",
            "label": "growth across external pH 5.5-9.0",
            "node_type": "TRAIT",
            "grounding": "METPO:1000332",
            "description": "Growth supported across the neutralophile external pH range ~5.5-9.0."
          },
          {
            "node_id": "constant_pmf",
            "label": "constant proton motive force",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Relatively constant PMF maintained across external pH changes."
          },
          {
            "node_id": "membrane_lipid_porin_changes",
            "label": "membrane lipid/porin composition changes",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Structural changes in membrane lipids and porins during pH stress."
          },
          {
            "node_id": "inward_proton_leakage",
            "label": "inward proton leakage",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Passive inward flux of protons that acidifies the cytoplasm."
          }
        ],
        "edges": [
          {
            "subject": "maximal_ph_homeostasis",
            "predicate": "confers",
            "object": "ph_delta_high_trait",
            "description": "Maximal pH-homeostasis flexibility yields an extreme pH-delta breadth.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.tim.2007.02.005",
                "snippet": "proton motive force",
                "notes": "Supports maximal pH-homeostasis flexibility as the basis of euryphilic breadth."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "ph_delta_high_trait",
            "predicate": "is a",
            "object": "ph_delta",
            "description": "pH delta high is a quantitative bin of the pH-delta phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2549",
                "snippet": "pH homeostasis",
                "notes": "Supports the 5\u20139 unit breadth as a value within the pH-delta distribution."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "na_h_antiporters",
            "predicate": "contributes to",
            "object": "ph_delta_high_trait",
            "description": "Na+/H+ antiport is a core regulator of cytoplasmic pH across changing external pH.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuad033",
                "notes": "Key regulators of bacterial pH homeostasis are Na+/H+ and K+/H+ antiporters."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "respiratory_proton_pumps",
            "predicate": "helps maintain",
            "object": "cytoplasmic_ph_homeostasis",
            "description": "Electron-transport proton pumps counteract pH stress by controlling proton flux.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuad033",
                "notes": "Proton-pumping enzymes (electron transport components) are major homeostasis regulators."
              }
            ]
          },
          {
            "subject": "f0f1_atpase",
            "predicate": "contributes to",
            "object": "ph_delta_high_trait",
            "description": "F0F1-ATPase participates in pH homeostasis via proton extrusion or uptake.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuad033",
                "notes": "F0F1-ATPase is named among key regulators of bacterial pH homeostasis."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "metabolite_decarboxylation",
            "predicate": "contributes to",
            "object": "ph_delta_high_trait",
            "description": "Proton-consuming decarboxylation pathways support broad pH tolerance.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuad033",
                "notes": "Metabolite decarboxylation pathways are key regulators of pH homeostasis."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "cytoplasmic_buffering_capacity",
            "predicate": "stabilizes",
            "object": "cytoplasmic_ph_homeostasis",
            "description": "High buffering capacity limits pH swings, enabling broader pH tolerance.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuad033",
                "notes": "Internal pH kept ~7.0-7.5 as buffers absorb fluctuations."
              }
            ]
          },
          {
            "subject": "near_neutral_cytoplasmic_ph",
            "predicate": "confers",
            "object": "growth_external_ph_5_5_9",
            "description": "Neutralophiles maintain narrow internal pH while growing over a broad external range.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2549",
                "notes": "Neutralophiles grow at external pH ~5.5-9.0 while maintaining cytoplasmic pH ~7.5-7.7."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "constant_pmf",
            "predicate": "supports",
            "object": "ph_delta_high_trait",
            "description": "A relatively constant PMF across external pH is a hallmark of broad pH tolerance.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuad033",
                "notes": "PMF of neutralophilic bacteria kept relatively constant over pH 5 to 8."
              }
            ]
          },
          {
            "subject": "membrane_lipid_porin_changes",
            "predicate": "decreases",
            "object": "inward_proton_leakage",
            "description": "Membrane/porin composition changes lower proton leak during acid stress.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2549",
                "notes": "Membrane lipid and porin composition changes minimize inward proton leakage during acid stress."
              }
            ],
            "predicate_id": "RO:0002212"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.840309+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-13T10:00:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed definition and causal graph linking maximal pH-homeostasis flexibility to the euryphilic pH-delta-high bin.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:30Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d71, rdfs:subClassOf\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 8 evidence-backed generic edges (11 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:10Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 5 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002326\u00d73, RO:0002327\u00d71, METPO:2000017\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:17Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0051453\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates (1 to confers), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T02:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES_PART2",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates onto their causal-graph counterparts (1 to reduces), issue 301 part 2. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Each replacement is a 1:1 mirror of its source predicate that changes only the domain, so the claim each edge makes is unchanged and directions are unchanged. The replacements are proposed in proposals/metpo_traitmech_v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T06:00:00Z",
        "curator": "claude",
        "action": "REGROUND_CAUSAL_EDGE",
        "changes": "Relabelled 1 causal edge from `reduces` to `decreases` and re-grounded it from METPO:2007802 to RO:0002212 (negatively regulates), issue 330. The corpus wrote two senses under the single label `reduces` - genuine electron donation, and a lessens/decreases sense - and METPO:2007802 is defined as donating electrons to the object and lowering its oxidation state, which this edge does not assert. The two senses could not be separated mechanically because the label was identical, so they migrated together in issue 329 and were split here by reading each edge. RO:0002212 declares no rdfs:domain or rdfs:range, so this introduces no entailment of the kind issue 301 removed.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-07T05:00:00Z",
        "curator": "claude",
        "action": "RETYPE_CAUSAL_NODE",
        "changes": "Retyped the object node from STATE/CAPACITY to TRAIT and re-grounded its in-edge from enables/RO:0002327 to METPO:2007700 (confers), issue 334. biolink declares enables range 'biological process or activity', which only BIOLOGICAL_PROCESS, PATHWAY and MOLECULAR_FUNCTION satisfy. The node's own description gives it away as a disposition rather than a state - phrasings like \"Capacity of an organism to grow and survive under...\", \"Ability to grow when...\" and \"tolerance of...\" describe what an organism CAN do, which is what a TRAIT is. So the defect was the node type, not the predicate, which is the third time in this issue's neighbourhood that has been true (compare issue 331's acetate kinase step and issue 330's negated node name). With the object correctly a TRAIT, confers applies unchanged.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-07T06:00:00Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded the retyped TRAIT node, issue 334 review. docs/CURATION_PLAYBOOK.md requires every TRAIT row to carry a grounding, and 462 of 482 TRAIT nodes in the corpus do, so leaving a newly retyped one ungrounded was the exception rather than the norm. It also mattered more than hygiene: an ungrounded TRAIT node still counts as a reachability anchor for audit-graphs, so it made UNREACHABLE_FROM_TRAIT fall on this graph without any edge changing -- the island is unchanged and FRAGMENTED_GRAPH still reports it. Grounding it makes the duplication legible instead of leaving two unrelated-looking anchors. growth_external_ph_5_5_9 is the same concept as this record's own ph_delta_high_trait, so it takes the same METPO:1000478; merging the two nodes is tracked in issue 352.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-08T05:00:00Z",
        "curator": "claude",
        "action": "REGROUND_CAUSAL_NODE",
        "changes": "Regrounded node growth_external_ph_5_5_9 from METPO:1000478 to METPO:1000332. Issue 352. Shared METPO:1000478 with ph_delta_high_trait, but the two say different things: this node is an ABSOLUTE external range ('~5.5-9.0'), while ph_delta_high_trait is a BREADTH ('approximately 5-9 pH units'), which is what a pH DELTA is. 1000478 belongs to the delta; this is a pH range (METPO:1000332).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope ph_delta_high_euryphilic_breadth=NONMECHANISTIC with scope_notes; marked 3 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (na_h_antiporters, respiratory_proton_pumps, f0f1_atpase).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T04:43:24Z",
        "curator": "codex",
        "action": "ADD_CANONICAL_EXAMPLES",
        "changes": "Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Amycolatopsis flava (NCBITaxon:486505; DOI:10.1007/s10482-015-0542-z). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000474",
    "label": "pH delta low",
    "definition": "A pH delta phenotype with a growth-supporting pH breadth of approximately 1\u20132 pH units, characteristic of organisms with limited pH-tolerance breadth.",
    "definition_source": "DOI:10.1038/nrmicro2549",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000232"
    ],
    "synonyms": [
      {
        "synonym_text": "pHd_1_2",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/nrmicro2549",
        "snippet": "pH homeostasis",
        "notes": "pH-homeostasis review supports limited pH-homeostasis flexibility as the basis for a narrow pH-tolerance breadth."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1715645",
        "taxon_label": "Paracoccus mangrovi",
        "reference": "DOI:10.1099/ijsem.0.001993",
        "note": "Paracoccus mangrovi gyp-1T grew from pH 5.5 to 7.0, a 1.5-unit breadth wholly inside the approximately 1-2 pH-unit bin."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "ph_delta_low_limited_breadth",
        "title": "pH-delta-low limited-breadth pH homeostasis",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a quantitative measurement, interval, or bin in the environmental phenotype hierarchy; a token protein example would misrepresent the measured value as one inherited molecular mechanism.",
        "description": "DOI-backed graph linking limited pH-homeostasis flexibility to a pH growth breadth of approximately 1\u20132 pH units.",
        "nodes": [
          {
            "node_id": "ph_delta_low_trait",
            "label": "pH delta low",
            "node_type": "TRAIT",
            "grounding": "METPO:1000474",
            "description": "pH growth-supporting breadth approximately 1\u20132 pH units."
          },
          {
            "node_id": "ph_delta",
            "label": "pH delta",
            "node_type": "TRAIT",
            "grounding": "METPO:1000232",
            "description": "Breadth of the growth-supporting external pH range."
          },
          {
            "node_id": "limited_ph_homeostasis",
            "label": "limited pH-homeostasis flexibility",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Modest capacity to remodel proton extrusion and envelope buffering across small pH shifts."
          },
          {
            "node_id": "external_ph_stress",
            "label": "external pH stress",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "External pH values outside the range maintainable as cytoplasmic pH."
          },
          {
            "node_id": "cytoplasmic_ph_homeostasis",
            "label": "cytoplasmic pH homeostasis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Maintenance of growth-permissive intracellular pH across external pH change.",
            "grounding": "GO:0051453"
          },
          {
            "node_id": "pmf_architecture",
            "label": "proton motive force architecture",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Tuning of Delta-psi and Delta-pH components of the proton motive force."
          },
          {
            "node_id": "weak_organic_acids",
            "label": "weak organic acids",
            "node_type": "CHEMICAL",
            "description": "Uncharged weak acids that cross membranes and perturb the proton gradient."
          },
          {
            "node_id": "delta_ph",
            "label": "delta pH / cytoplasmic pH",
            "node_type": "STATE",
            "description": "Trans-membrane proton gradient and resulting cytoplasmic pH."
          },
          {
            "node_id": "electrogenic_na_h_antiport",
            "label": "electrogenic Na+/H+ antiport",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Inward proton transport via cation/proton antiport driven by membrane potential."
          },
          {
            "node_id": "alkaline_ph_homeostasis",
            "label": "alkaline pH homeostasis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Maintenance of cytoplasmic pH under alkaline external conditions."
          },
          {
            "node_id": "f1fo_atpase",
            "label": "F1Fo-ATPase",
            "node_type": "GENE_OR_PROTEIN",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed as a contextual protein or protein-complex label within a quantitative measurement graph; no exact semantic family term was established for this aggregate use.",
            "description": "Proton-coupled ATPase that expels or imports H+ using or generating PMF."
          }
        ],
        "edges": [
          {
            "subject": "limited_ph_homeostasis",
            "predicate": "confers",
            "object": "ph_delta_low_trait",
            "description": "Limited pH-homeostasis flexibility yields a 1\u20132 pH-unit pH-delta breadth.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2549",
                "snippet": "pH homeostasis",
                "notes": "Supports limited pH-homeostasis flexibility as the basis of narrow breadth."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "ph_delta_low_trait",
            "predicate": "is a",
            "object": "ph_delta",
            "description": "pH delta low is a quantitative bin of the pH-delta phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.tim.2007.02.005",
                "snippet": "proton motive force",
                "notes": "Supports the 1\u20132 unit breadth as a value within the pH-delta distribution."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "external_ph_stress",
            "predicate": "challenges",
            "object": "cytoplasmic_ph_homeostasis",
            "description": "External pH outside the maintainable cytoplasmic range challenges pH homeostasis.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2549",
                "notes": "Diverse mechanisms for pH sensing and cytoplasmic pH homeostasis enable most bacteria to tolerate external pH outside the cytoplasmic range; general across bacteria."
              }
            ],
            "predicate_id": "METPO:2007406"
          },
          {
            "subject": "pmf_architecture",
            "predicate": "determines",
            "object": "cytoplasmic_ph_homeostasis",
            "description": "PMF architecture (Delta-psi and Delta-pH balancing) determines pH homeostasis capacity.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2549",
                "notes": "Bacteria tune and even reverse the relative magnitudes of Delta-psi and Delta-pH under pH stress; strong general mechanistic edge."
              }
            ]
          },
          {
            "subject": "weak_organic_acids",
            "predicate": "perturbs",
            "object": "delta_ph",
            "description": "Weak organic acids cross the membrane and perturb the proton gradient / cytoplasmic pH.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2549",
                "notes": "Uncharged weak-acid forms cross membranes and become trapped when charged, perturbing Delta-pH; general chemical-factor edge."
              }
            ]
          },
          {
            "subject": "electrogenic_na_h_antiport",
            "predicate": "supports",
            "object": "alkaline_ph_homeostasis",
            "description": "Electrogenic Na+/H+ antiport supports cytoplasmic pH homeostasis under alkaline stress.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2549",
                "notes": "Under alkaline stress, inward proton transport through cation/proton antiporters is crucial; strong general transporter-mediated edge."
              }
            ]
          },
          {
            "subject": "f1fo_atpase",
            "predicate": "contributes to",
            "object": "cytoplasmic_ph_homeostasis",
            "description": "F1Fo-ATPase contributes to cytoplasmic pH homeostasis by expelling or importing H+.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2549",
                "notes": "Respiratory complexes and proton-coupled ATPases use or generate PMF to expel or import H+; general higher-level edge."
              }
            ],
            "predicate_id": "RO:0002326"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.838505+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-13T10:00:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed definition and causal graph linking limited pH-homeostasis flexibility to the narrow-breadth pH-delta-low bin.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:30Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d71, rdfs:subClassOf\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 5 evidence-backed generic edges (9 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:10Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007406\u00d71, RO:0002326\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:17Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0051453\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates (1 to confers), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-08T05:00:00Z",
        "curator": "claude",
        "action": "MERGE_CAUSAL_NODE",
        "changes": "Merged node ph_homeostasis_capacity into cytoplasmic_ph_homeostasis and repointed its edges. Issue 352. 'Capacity to balance and maintain cytoplasmic pH under pH stress' is cytoplasmic_ph_homeostasis, which is IN THE SAME GRAPH already typed BIOLOGICAL_PROCESS and grounded GO:0051453. Grounding the capacity node to GO:0051453 would have produced a DUPLICATE_GROUNDING against it.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope ph_delta_low_limited_breadth=NONMECHANISTIC with scope_notes; marked 1 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (f1fo_atpase).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T04:43:24Z",
        "curator": "codex",
        "action": "ADD_CANONICAL_EXAMPLES",
        "changes": "Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Paracoccus mangrovi (NCBITaxon:1715645; DOI:10.1099/ijsem.0.001993). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000475",
    "label": "pH delta mid1",
    "definition": "A pH delta phenotype with a growth-supporting pH breadth of approximately 2\u20133 pH units, characteristic of organisms with moderate pH-tolerance breadth.",
    "definition_source": "DOI:10.1038/nrmicro2549",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000232"
    ],
    "synonyms": [
      {
        "synonym_text": "pHd_2_3",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/nrmicro2549",
        "snippet": "pH homeostasis",
        "notes": "pH-homeostasis review supports moderate pH-homeostasis flexibility as common among non-extreme microorganisms."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:735518",
        "taxon_label": "Lederbergia graminis",
        "reference": "DOI:10.1099/ijs.0.023820-0",
        "note": "The type strain, published as Bacillus graminis YC6957T, grew from pH 6.0 to 8.5, a 2.5-unit breadth wholly inside the approximately 2-3 bin."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "ph_delta_mid1_moderate_breadth",
        "title": "pH-delta-mid1 moderate-breadth pH homeostasis",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a quantitative measurement, interval, or bin in the environmental phenotype hierarchy; a token protein example would misrepresent the measured value as one inherited molecular mechanism.",
        "description": "DOI-backed graph linking moderate pH-homeostasis flexibility to a pH growth breadth of approximately 2\u20133 pH units.",
        "nodes": [
          {
            "node_id": "ph_delta_mid1_trait",
            "label": "pH delta mid1",
            "node_type": "TRAIT",
            "grounding": "METPO:1000475",
            "description": "pH growth-supporting breadth approximately 2\u20133 pH units."
          },
          {
            "node_id": "ph_delta",
            "label": "pH delta",
            "node_type": "TRAIT",
            "grounding": "METPO:1000232",
            "description": "Breadth of the growth-supporting external pH range."
          },
          {
            "node_id": "moderate_ph_homeostasis",
            "label": "moderate pH-homeostasis flexibility",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Mid-range capacity to remodel proton extrusion and envelope buffering across a few pH units."
          },
          {
            "node_id": "f0f1_atpase",
            "label": "F0F1-ATPase",
            "node_type": "GENE_OR_PROTEIN",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed as a contextual protein or protein-complex label within a quantitative measurement graph; no exact semantic family term was established for this aggregate use.",
            "description": "F0F1-ATP synthase/ATPase complex that can hydrolyze ATP to consume and export intracellular protons."
          },
          {
            "node_id": "cytoplasmic_ph_homeostasis",
            "label": "cytoplasmic pH homeostasis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Maintenance of near-neutral cytoplasmic pH under external pH stress.",
            "grounding": "GO:0051453"
          },
          {
            "node_id": "gln_glu_decarboxylation_pathway",
            "label": "glutamine/glutamate decarboxylation pathway",
            "node_type": "PATHWAY",
            "description": "Coupled glutamine conversion and glutamate decarboxylation that consumes intracellular protons."
          },
          {
            "node_id": "intracellular_proton",
            "label": "intracellular proton (H+)",
            "node_type": "CHEMICAL",
            "description": "Cytoplasmic hydron whose concentration sets internal pH."
          },
          {
            "node_id": "ybas_glutaminase",
            "label": "YbaS glutaminase",
            "node_type": "GENE_OR_PROTEIN",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed as a contextual protein or protein-complex label within a quantitative measurement graph; no exact semantic family term was established for this aggregate use.",
            "description": "Glutaminase converting glutamine to glutamate plus ammonia."
          },
          {
            "node_id": "ammonia",
            "label": "ammonia",
            "node_type": "CHEMICAL",
            "description": "Ammonia that neutralizes intracellular protons.",
            "grounding": "CHEBI:16134"
          },
          {
            "node_id": "membrane_saturated_fatty_acids",
            "label": "membrane saturated fatty acid content",
            "node_type": "QUALITY",
            "description": "Increased proportion of saturated fatty acids in the membrane lipid bilayer."
          },
          {
            "node_id": "proton_diffusion_across_membrane",
            "label": "proton diffusion across membrane",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Passive leakage of protons across the cytoplasmic membrane."
          },
          {
            "node_id": "oxidative_phosphorylation",
            "label": "oxidative phosphorylation / electron transport chain",
            "node_type": "PATHWAY",
            "description": "ETC activity (nuo, cyo, ndh, sdh) generating and maintaining the proton motive force."
          },
          {
            "node_id": "proton_motive_force",
            "label": "proton motive force",
            "node_type": "STATE",
            "description": "Transmembrane electrochemical proton gradient supporting acid-side pH homeostasis.",
            "grounding": "METPO:1007500"
          }
        ],
        "edges": [
          {
            "subject": "moderate_ph_homeostasis",
            "predicate": "confers",
            "object": "ph_delta_mid1_trait",
            "description": "Moderate pH-homeostasis flexibility yields a 2\u20133 pH-unit pH-delta breadth.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2549",
                "snippet": "pH homeostasis",
                "notes": "Supports moderate flexibility as the basis of an intermediate breadth."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "ph_delta_mid1_trait",
            "predicate": "is a",
            "object": "ph_delta",
            "description": "pH delta mid1 is a quantitative bin of the pH-delta phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2549",
                "snippet": "external pH",
                "notes": "Supports the 2\u20133 unit breadth as a value within the pH-delta distribution."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "f0f1_atpase",
            "predicate": "contributes to",
            "object": "cytoplasmic_ph_homeostasis",
            "description": "Under acid stress F0F1-ATPase hydrolyzes ATP to consume/export intracellular H+, maintaining cytoplasmic pH.",
            "evidence": [
              {
                "reference": "DOI:10.3390/microorganisms12091774",
                "notes": "F0F1-ATPase under acid stress hydrolyzes ATP to consume intracellular H+ to maintain homeostasis; broad pH-homeostasis mechanism."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "gln_glu_decarboxylation_pathway",
            "predicate": "consumes",
            "object": "intracellular_proton",
            "description": "Coupled glutamine conversion and glutamate decarboxylation consume two intracellular H+, enhancing acid resistance.",
            "evidence": [
              {
                "reference": "DOI:10.3390/microorganisms12091774",
                "notes": "Glutamine conversion and glutamate decarboxylation can act together to consume two H+; pathway-level proton-consumption module."
              }
            ],
            "predicate_id": "biolink:consumes"
          },
          {
            "subject": "ybas_glutaminase",
            "predicate": "produces",
            "object": "ammonia",
            "description": "YbaS glutaminase converts glutamine to glutamate and releases ammonia, which neutralizes intracellular protons.",
            "evidence": [
              {
                "reference": "DOI:10.3390/microorganisms12091774",
                "notes": "The glutaminase YbaS converts glutamine to glutamate and releases ammonia, which neutralizes intracellular protons."
              }
            ],
            "predicate_id": "METPO:2007800"
          },
          {
            "subject": "membrane_saturated_fatty_acids",
            "predicate": "decreases",
            "object": "proton_diffusion_across_membrane",
            "description": "A higher proportion of saturated membrane fatty acids limits passive proton diffusion across the membrane.",
            "evidence": [
              {
                "reference": "DOI:10.1128/aem.00569-24",
                "notes": "Conversion of unsaturated to saturated fatty acids limits proton diffusion; broadly plausible membrane-permeability mechanism."
              }
            ],
            "predicate_id": "RO:0002212"
          },
          {
            "subject": "oxidative_phosphorylation",
            "predicate": "maintains",
            "object": "proton_motive_force",
            "description": "Upregulated oxidative phosphorylation/ETC increases proton export and maintains the proton motive force, helping resist cytoplasmic pH decreases.",
            "evidence": [
              {
                "reference": "DOI:10.3390/microorganisms12081565",
                "notes": "Upregulation of oxidative phosphorylation genes increases proton export rate and maintains a proton motive force that helps cells resist cytoplasmic pH decreases under mild acid (pH 6.0) growth."
              }
            ]
          },
          {
            "subject": "proton_motive_force",
            "predicate": "contributes to",
            "object": "cytoplasmic_ph_homeostasis",
            "description": "A maintained proton motive force supports cytoplasmic pH homeostasis under acid stress.",
            "evidence": [
              {
                "reference": "DOI:10.3390/microorganisms12081565",
                "notes": "PMF generated/maintained by oxidative phosphorylation helps cells resist cytoplasmic pH decreases."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "cytoplasmic_ph_homeostasis",
            "predicate": "contributes to",
            "object": "moderate_ph_homeostasis",
            "description": "Cytoplasmic pH homeostasis modules collectively underlie moderate pH-homeostasis flexibility.",
            "evidence": [
              {
                "reference": "DOI:10.3390/microorganisms12091774",
                "notes": "Proton-consumption and proton-export modules maintaining cytoplasmic pH underpin homeostatic flexibility across a few pH units."
              }
            ],
            "predicate_id": "RO:0002326"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.838958+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-13T10:00:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed definition and causal graph linking moderate pH-homeostasis flexibility to the moderate-breadth pH-delta-mid1 bin.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:30Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d71, rdfs:subClassOf\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 7 evidence-backed generic edges (10 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:10Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 6 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002326\u00d73, biolink:consumes\u00d71, METPO:2000202\u00d71, RO:0002212\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:17Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0051453\u00d71, CHEBI:16134\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates (1 to confers), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T02:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES_PART2",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates onto their causal-graph counterparts (1 to produces), issue 301 part 2. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Each replacement is a 1:1 mirror of its source predicate that changes only the domain, so the claim each edge makes is unchanged and directions are unchanged. The replacements are proposed in proposals/metpo_traitmech_v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-15T02:00:00Z",
        "curator": "claude",
        "action": "NORMALISE_NODE_TYPE",
        "changes": "Normalised causal-node type(s) so one node_id means one thing corpus-wide (issue 356): proton_motive_force: BIOLOGICAL_PROCESS -> STATE. The schema's OWN example of STATE: 'a bioenergetic or molecular state of the cell (e.g. proton motive force ...) ... the state is the gradient / steady-value, not its establishment'. All 35 occurrences describe the gradient -- every description across all four types reads 'electrochemical proton gradient', including the 13 typed BIOLOGICAL_PROCESS ('Transmembrane electrochemical gradient generated by respiration'), which name the gradient and its provenance rather than the generating process. Nothing here means the establishment, so this is a retype and not a rename; records that DO mean the process already use a separate id (proton_motive_force_generation in ph_delta.yaml). Also settles the one edge #356 was filed for: phototrophic.yaml's CAPACITY typing was blocking `powers` (METPO:2007900), which is gated to BIOLOGICAL_PROCESS|STATE.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-16T02:00:00Z",
        "curator": "claude",
        "action": "NORMALISE_NODE_TYPE",
        "changes": "Under the PATHWAY-vs-BIOLOGICAL_PROCESS rule, one node_id means one thing corpus-wide (issue 356): oxidative_phosphorylation is typed PATHWAY. PATHWAY is a named, conventionally enumerable multi-step route; BIOLOGICAL_PROCESS is everything else. A named route through enumerable complexes -- environment/ph_delta_mid1.yaml lists them (nuo, cyo, ndh, sdh). The rule breaks what was a 2-2 tie before this tranche.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-20T07:10:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (METPO:1007500\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope ph_delta_mid1_moderate_breadth=NONMECHANISTIC with scope_notes; marked 2 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (f0f1_atpase, ybas_glutaminase).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T04:43:24Z",
        "curator": "codex",
        "action": "ADD_CANONICAL_EXAMPLES",
        "changes": "Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Lederbergia graminis (NCBITaxon:735518; DOI:10.1099/ijs.0.023820-0). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000476",
    "label": "pH delta mid2",
    "definition": "A pH delta phenotype with a growth-supporting pH breadth of approximately 3\u20134 pH units, characteristic of organisms with broad pH-tolerance breadth.",
    "definition_source": "DOI:10.1038/nrmicro2549",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000232"
    ],
    "synonyms": [
      {
        "synonym_text": "pHd_3_4",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/nrmicro2549",
        "snippet": "pH homeostasis",
        "notes": "pH-homeostasis review supports broad pH-homeostasis flexibility as the basis of generalist pH-tolerance physiology."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:3447298",
        "taxon_label": "Microbaculum mangrovi",
        "reference": "DOI:10.1099/ijsem.0.006972",
        "note": "Microbaculum mangrovi FT89T grew from pH 5.5 to 9.0, a 3.5-unit breadth wholly inside the approximately 3-4 bin."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "ph_delta_mid2_broad_breadth",
        "title": "pH-delta-mid2 contextual pH-homeostasis breadth",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a quantitative measurement, interval, or bin in the environmental phenotype hierarchy; a token protein example would misrepresent the measured value as one inherited molecular mechanism.",
        "description": "DOI-backed nonmechanistic graph annotating broad pH-homeostasis flexibility, PMF component balancing, respiratory proton pumping, ATPase-mediated proton translocation, alkaline antiport, acid-side decarboxylation, and passive cytoplasmic buffering to the 3-4 pH-unit breadth bin.",
        "nodes": [
          {
            "node_id": "ph_delta_mid2_trait",
            "label": "pH delta mid2",
            "node_type": "TRAIT",
            "grounding": "METPO:1000476",
            "description": "pH growth-supporting breadth approximately 3\u20134 pH units."
          },
          {
            "node_id": "ph_delta",
            "label": "pH delta",
            "node_type": "TRAIT",
            "grounding": "METPO:1000232",
            "description": "Breadth of the growth-supporting external pH range."
          },
          {
            "node_id": "broad_ph_homeostasis",
            "label": "broad pH-homeostasis flexibility",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Strong capacity to remodel proton extrusion, K+/H+ antiport, and envelope buffering across a broad pH span."
          },
          {
            "node_id": "external_ph_stress",
            "label": "external pH stress",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Deviation of external pH that perturbs proton motive force balance."
          },
          {
            "node_id": "pmf_component_balance",
            "label": "PMF component balance",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Balance of proton motive force components (delta-pH and delta-psi)."
          },
          {
            "node_id": "respiratory_proton_pumps",
            "label": "proton-pumping respiratory complexes",
            "node_type": "GENE_OR_PROTEIN",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed as a contextual protein or protein-complex label within a quantitative measurement graph; no exact semantic family term was established for this aggregate use.",
            "description": "Primary respiratory-chain proton pumps that establish the PMF."
          },
          {
            "node_id": "pmf_generation",
            "label": "proton motive force generation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Generation of proton motive force across the membrane."
          },
          {
            "node_id": "f1fo_atpase",
            "label": "F1Fo-ATPase",
            "node_type": "GENE_OR_PROTEIN",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed as a contextual protein or protein-complex label within a quantitative measurement graph; no exact semantic family term was established for this aggregate use.",
            "description": "Proton-coupled F1Fo-ATP synthase functioning as a proton pump."
          },
          {
            "node_id": "proton_translocation_homeostasis",
            "label": "proton translocation for pH homeostasis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Active proton translocation that maintains cytoplasmic pH homeostasis."
          },
          {
            "node_id": "na_h_antiporter_activity",
            "label": "Na+/H+ antiporter activity",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "Cation/proton antiport that imports H+ and extrudes Na+."
          },
          {
            "node_id": "alkaline_ph_homeostasis",
            "label": "alkaline pH homeostasis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Maintenance of cytoplasmic pH under alkaline external conditions."
          },
          {
            "node_id": "glutamate_decarboxylase_system",
            "label": "glutamate decarboxylase system",
            "node_type": "PATHWAY",
            "description": "Proton-consuming glutamate decarboxylase (gad/GadB) acid-resistance system."
          },
          {
            "node_id": "intracellular_proton",
            "label": "intracellular H+",
            "node_type": "CHEMICAL",
            "description": "Cytoplasmic protons whose concentration sets cytoplasmic pH."
          },
          {
            "node_id": "cytoplasmic_buffers",
            "label": "cytoplasmic buffering molecules",
            "node_type": "CHEMICAL",
            "description": "Small molecules (polyamines, amino acids, phosphate) providing passive pH buffering."
          },
          {
            "node_id": "cytoplasmic_ph_buffering",
            "label": "cytoplasmic pH buffering",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Passive buffering of cytoplasmic pH by small molecules."
          }
        ],
        "edges": [
          {
            "subject": "broad_ph_homeostasis",
            "predicate": "confers",
            "object": "ph_delta_mid2_trait",
            "description": "Broad pH-homeostasis flexibility yields a 3\u20134 pH-unit pH-delta breadth.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2549",
                "snippet": "pH homeostasis",
                "notes": "Supports broad pH-homeostasis flexibility as the basis of a broad breadth."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "ph_delta_mid2_trait",
            "predicate": "is a",
            "object": "ph_delta",
            "description": "pH delta mid2 is a quantitative bin of the pH-delta phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.tim.2007.02.005",
                "snippet": "proton motive force",
                "notes": "Supports the 3\u20134 unit breadth as a value within the pH-delta distribution."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "external_ph_stress",
            "predicate": "regulates",
            "object": "pmf_component_balance",
            "description": "External pH stress modulates the relative balance of proton-motive force components.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2549",
                "snippet": "the demands of pH homeostasis for particular bacteria determine the relative magnitudes of the two PMF components",
                "notes": "Verified against the open PMC manuscript of the Krulwich et al. review; bacterial pH-homeostasis demands determine how delta-psi and delta-pH contribute to the PMF."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "respiratory_proton_pumps",
            "predicate": "generates",
            "object": "pmf_generation",
            "description": "Primary respiratory-chain proton pumps generate proton motive force.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2549",
                "snippet": "Primary proton pumps generate the PMF",
                "notes": "Verified against the open PMC manuscript of the Krulwich et al. review; respiratory-chain complexes are listed among the proton pumps that establish bacterial PMF."
              }
            ],
            "predicate_id": "biolink:produces"
          },
          {
            "subject": "f1fo_atpase",
            "predicate": "contributes to",
            "object": "proton_translocation_homeostasis",
            "description": "F1Fo-ATPase contributes to pH homeostasis by coupling ATP turnover to proton translocation.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2549",
                "snippet": "up-regulation of the hydrolytic activity of F1Fo-ATPase promotes ATP-dependent H+ extrusion under acidic conditions",
                "notes": "Verified against the open PMC manuscript of the Krulwich et al. review; F1Fo-ATPase can drive proton efflux in acid-stressed non-respiratory neutralophiles."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "na_h_antiporter_activity",
            "predicate": "contributes to",
            "object": "alkaline_ph_homeostasis",
            "description": "Na+/H+ antiporter activity imports H+ and extrudes Na+ as part of alkaline pH homeostasis.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2549",
                "snippet": "active transport of protons inward is a crucial adaptation, which usually involves activation and transcriptional up-regulation of key cation/proton antiporters",
                "notes": "Verified against the open PMC manuscript of the Krulwich et al. review; electrogenic cation/proton antiport supports proton entry during alkaline stress."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "glutamate_decarboxylase_system",
            "predicate": "consumes",
            "object": "intracellular_proton",
            "description": "The glutamate decarboxylase system consumes intracellular protons during acid-stress decarboxylation.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2549",
                "snippet": "consumes a proton during decarboxylation",
                "notes": "Verified against the open PMC manuscript of the Krulwich et al. review; GadB consumes a cytoplasmic proton when it decarboxylates glutamate in the E. coli acid-resistance cycle."
              }
            ],
            "predicate_id": "biolink:consumes"
          },
          {
            "subject": "cytoplasmic_buffers",
            "predicate": "contributes to",
            "object": "cytoplasmic_ph_buffering",
            "description": "Small molecules, including polyamines, amino acids, and phosphate, contribute to passive cytoplasmic pH buffering.",
            "evidence": [
              {
                "reference": "DOI:10.3390/antibiotics12091474",
                "snippet": "Cytoplasmic pH is buffered by small molecules",
                "notes": "Verified against the open Rebelo et al. review; small molecules contribute passive cytoplasmic buffering in pH homeostasis."
              }
            ],
            "predicate_id": "RO:0002326"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.839415+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-13T10:00:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed definition and causal graph linking broad pH-homeostasis flexibility to the broad-breadth pH-delta-mid2 bin.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:30Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d71, rdfs:subClassOf\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 6 evidence-backed generic edges (12 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:10Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:produces\u00d71, RO:0002326\u00d71, biolink:consumes\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates (1 to confers), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope ph_delta_mid2_broad_breadth=NONMECHANISTIC with scope_notes; marked 2 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (respiratory_proton_pumps, f1fo_atpase).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T04:43:24Z",
        "curator": "codex",
        "action": "ADD_CANONICAL_EXAMPLES",
        "changes": "Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Microbaculum mangrovi (NCBITaxon:3447298; DOI:10.1099/ijsem.0.006972). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-04T01:20:00Z",
        "curator": "codex",
        "action": "REVIEW_CAUSAL_EVIDENCE",
        "changes": "Reviewed the broad ph_delta_mid2_broad_breadth graph for issue #183: added snippets to 6 edge-level evidence items and grounded 3 unmapped pH-homeostasis predicates to RO:0002211 or RO:0002326. No paid research service was called.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-04T15:00:00Z",
        "curator": "codex",
        "action": "CONNECT_CAUSAL_GRAPH_COMPONENTS",
        "changes": "Resolved issue #183 graph fragmentation (7 components to 1) by adding 6 source-backed association connectors among PMF balancing, respiratory proton pumping, ATPase-mediated proton translocation, alkaline antiport, Gad acid-side support, and cytoplasmic buffering. No paid research service was called.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-06T13:30:00Z",
        "curator": "codex",
        "action": "ADVERSARIAL_REVIEW_REPAIR",
        "changes": "Addressed PR #664 adversarial review issue #666: replaced borrowed snippets on the six broad_ph_homeostasis connectors with connector-specific exact snippets from the same supporting sources.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-07T06:14:00Z",
        "curator": "codex",
        "action": "ADVERSARIAL_REVIEW_REPAIR",
        "changes": "Addressed PR #664 adversarial review issues #688 and #689: requoted the F1Fo-ATPase acid-stress edge with a longer Krulwich span and replaced its connector quote with distinct Sekiya F-ATPase acid-tolerance support.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-07T20:05:00Z",
        "curator": "codex",
        "action": "ADVERSARIAL_REVIEW_REPAIR",
        "changes": "Addressed PR #664 adversarial review issues #696, #698, and #699: requoted weak Krulwich pH-homeostasis edge snippets and removed unsupported pH-breadth hub connectors that only joined generic review branches to quantitative bin nodes.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-08T03:30:00Z",
        "curator": "codex",
        "action": "ADVERSARIAL_REVIEW_REPAIR",
        "changes": "Addressed PR #664 adversarial review issue #702: appended corrective issue-183 provenance after evidence-weak connectors were pruned; this NONMECHANISTIC graph intentionally ships with 7 disconnected components until independent trait-specific connectors are curated.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000477",
    "label": "pH delta mid3",
    "definition": "A pH delta phenotype with a growth-supporting pH breadth of approximately 4\u20135 pH units, characteristic of organisms with wide pH-tolerance breadth.",
    "definition_source": "DOI:10.1038/nrmicro2549",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000232"
    ],
    "synonyms": [
      {
        "synonym_text": "pHd_4_5",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/nrmicro2549",
        "snippet": "pH homeostasis",
        "notes": "pH-homeostasis review supports wide pH-homeostasis flexibility as the basis of euryphilic pH-tolerance."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:2306023",
        "taxon_label": "Gemmobacter lutimaris",
        "reference": "DOI:10.1099/ijsem.0.003375",
        "note": "Gemmobacter lutimaris YJ-T1-11T grew from pH 5.0 to 9.0; the directly reported four-unit breadth lies in the approximately 4-5 bin."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "ph_delta_mid3_wide_breadth",
        "title": "pH-delta-mid3 wide pH-homeostasis context",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a quantitative measurement, interval, or bin in the environmental phenotype hierarchy; a token protein example would misrepresent the measured value as one inherited molecular mechanism.",
        "description": "DOI-backed nonmechanistic graph annotating wide pH-homeostasis flexibility, PMF regulation and generation, alkaline Na+/H+ antiport, ATPase support, phosphate buffering, amino-acid decarboxylation, and membrane proton-permeability branches to the 4-5 pH-unit breadth bin.",
        "nodes": [
          {
            "node_id": "ph_delta_mid3_trait",
            "label": "pH delta mid3",
            "node_type": "TRAIT",
            "grounding": "METPO:1000477",
            "description": "pH growth-supporting breadth approximately 4\u20135 pH units."
          },
          {
            "node_id": "ph_delta",
            "label": "pH delta",
            "node_type": "TRAIT",
            "grounding": "METPO:1000232",
            "description": "Breadth of the growth-supporting external pH range."
          },
          {
            "node_id": "wide_ph_homeostasis",
            "label": "wide pH-homeostasis flexibility",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Strong cross-axis pH-homeostasis capacity allowing growth across a wide range of external pH."
          },
          {
            "node_id": "external_alkaline_ph",
            "label": "external alkaline pH",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "High external pH challenging cytoplasmic pH homeostasis."
          },
          {
            "node_id": "na_h_antiport",
            "label": "electrogenic Na+/H+ antiport",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Sodium:proton antiport supporting cytoplasmic pH homeostasis at alkaline pH."
          },
          {
            "node_id": "pmf_regulation",
            "label": "regulation of membrane potential and pH gradient",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Regulation of the proton motive force components Delta-psi and Delta-pH."
          },
          {
            "node_id": "cytoplasmic_ph_maintenance",
            "label": "cytoplasmic pH maintenance",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Maintenance of cytoplasmic pH within a viable range across external pH changes."
          },
          {
            "node_id": "proton_pumping_respiratory_complexes",
            "label": "proton-pumping respiratory complexes",
            "node_type": "GENE_OR_PROTEIN",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed as a contextual protein or protein-complex label within a quantitative measurement graph; no exact semantic family term was established for this aggregate use.",
            "description": "Respiratory-chain primary proton pumps that build the proton motive force."
          },
          {
            "node_id": "proton_motive_force",
            "label": "proton motive force",
            "node_type": "STATE",
            "description": "Electrochemical proton gradient (PMF) used for transport and pH regulation.",
            "grounding": "METPO:1007500"
          },
          {
            "node_id": "f0f1_atpase",
            "label": "F0F1-ATPase",
            "node_type": "GENE_OR_PROTEIN",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed as a contextual protein or protein-complex label within a quantitative measurement graph; no exact semantic family term was established for this aggregate use.",
            "description": "Proton-translocating ATP synthase/ATPase that can extrude protons under acid stress."
          },
          {
            "node_id": "phosphate_buffering",
            "label": "cytoplasmic phosphate buffering",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Physicochemical buffering of intracellular pH by cytoplasmic phosphate."
          },
          {
            "node_id": "intracellular_ph_stability",
            "label": "intracellular pH stability",
            "node_type": "STATE",
            "description": "Stabilized intracellular pH within a narrow viable range."
          },
          {
            "node_id": "aa_decarboxylation",
            "label": "amino-acid decarboxylation pathways",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Decarboxylation pathways that consume protons and store energy as PMF."
          },
          {
            "node_id": "membrane_lipid_remodeling",
            "label": "membrane lipid composition shifts",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Adjustments of membrane lipid composition altering envelope properties."
          },
          {
            "node_id": "proton_permeability",
            "label": "membrane proton permeability",
            "node_type": "QUALITY",
            "description": "Permeability of the cell membrane to protons."
          }
        ],
        "edges": [
          {
            "subject": "wide_ph_homeostasis",
            "predicate": "confers",
            "object": "ph_delta_mid3_trait",
            "description": "Wide pH-homeostasis flexibility yields a 4\u20135 pH-unit pH-delta breadth.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2549",
                "snippet": "pH homeostasis",
                "notes": "Supports wide pH-homeostasis flexibility as the basis of a wide breadth."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "ph_delta_mid3_trait",
            "predicate": "is a",
            "object": "ph_delta",
            "description": "pH delta mid3 is a quantitative bin of the pH-delta phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2549",
                "snippet": "tolerate or grow at external pH values that are outside the cytoplasmic pH range",
                "notes": "Verified against the open PMC manuscript of the Krulwich et al. review; pH breadth is represented as a quantitative external-growth-pH bin under the pH-delta phenotype."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "external_alkaline_ph",
            "predicate": "regulates",
            "object": "na_h_antiport",
            "description": "High external pH modulates the contribution of electrogenic Na+/H+ antiport to cytoplasmic pH homeostasis.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2549",
                "snippet": "For pH homeostasis under alkaline conditions, active transport of protons inward is a crucial adaptation, which usually involves activation and transcriptional up-regulation of key cation/proton antiporters",
                "notes": "Verified against the open PMC manuscript of the Krulwich et al. review; cation/proton antiporters use PMF from respiration or ATPases to drive proton uptake under alkaline stress."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "pmf_regulation",
            "predicate": "contributes to",
            "object": "cytoplasmic_ph_maintenance",
            "description": "Regulation of Delta-psi and Delta-pH contributes to maintenance of cytoplasmic pH across external pH changes.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2549",
                "snippet": "the demands of pH homeostasis for particular bacteria determine the relative magnitudes of the two PMF components",
                "notes": "Verified against the open PMC manuscript of the Krulwich et al. review; bacterial pH-homeostasis demands determine how delta-psi and delta-pH contribute to the PMF."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "proton_pumping_respiratory_complexes",
            "predicate": "generates",
            "object": "proton_motive_force",
            "description": "Proton-pumping respiratory complexes generate proton motive force.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2549",
                "snippet": "Primary proton pumps generate the PMF",
                "notes": "Verified against the open PMC manuscript of the Krulwich et al. review; respiratory-chain complexes are listed among the proton pumps that establish bacterial PMF."
              }
            ],
            "predicate_id": "biolink:produces"
          },
          {
            "subject": "f0f1_atpase",
            "predicate": "contributes to",
            "object": "cytoplasmic_ph_maintenance",
            "description": "F0F1-ATPase proton pumping contributes to bacterial pH homeostasis.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuad033",
                "snippet": "the F0F1-ATPase (fermentative bacteria), or decarboxylation pathways (next paragraph) prevent the internal pH from becoming too low",
                "notes": "Verified against the open Poolman review; proton-pumping enzymes, including F0F1-ATPase in lactic acid bacteria, are listed as bacterial pH-homeostasis regulators."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "phosphate_buffering",
            "predicate": "contributes to",
            "object": "intracellular_ph_stability",
            "description": "Cytoplasmic phosphate buffering contributes to intracellular pH stability.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuad033",
                "snippet": "sufficient buffering capacity (e.g. inorganic and organic phosphates)",
                "notes": "Verified against the open Poolman review; cytoplasmic phosphate pools are named as sufficient buffering capacity needed for internal-pH stability."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "aa_decarboxylation",
            "predicate": "contributes to",
            "object": "proton_motive_force",
            "description": "Amino-acid decarboxylation pathways consume protons and contribute to PMF and intracellular pH control.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuad033",
                "snippet": "free energy change from decarboxylation reactions can be stored in the form of a proton motive force",
                "notes": "Verified against the open Poolman review; substrate decarboxylation is linked to bacterial PMF generation in pH homeostasis."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "membrane_lipid_remodeling",
            "predicate": "decreases",
            "object": "proton_permeability",
            "description": "Membrane lipid composition shifts reduce proton permeability.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2022.1034164",
                "snippet": "required a saturated membrane to minimize proton permeability in an extremely acidic environment",
                "notes": "Verified against the open Frontiers methanotroph review; saturated bacterial membranes are described as lowering proton permeability under acid stress."
              }
            ],
            "predicate_id": "RO:0002212"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.839862+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-13T10:00:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed definition and causal graph linking wide pH-homeostasis flexibility to the wide-breadth pH-delta-mid3 bin.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:30Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d71, rdfs:subClassOf\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 7 evidence-backed generic edges (12 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:10Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002326\u00d72, METPO:2000017\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates (1 to confers), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T02:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES_PART2",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates onto their causal-graph counterparts (1 to reduces), issue 301 part 2. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Each replacement is a 1:1 mirror of its source predicate that changes only the domain, so the claim each edge makes is unchanged and directions are unchanged. The replacements are proposed in proposals/metpo_traitmech_v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T06:00:00Z",
        "curator": "claude",
        "action": "REGROUND_CAUSAL_EDGE",
        "changes": "Relabelled 1 causal edge from `reduces` to `decreases` and re-grounded it from METPO:2007802 to RO:0002212 (negatively regulates), issue 330. The corpus wrote two senses under the single label `reduces` - genuine electron donation, and a lessens/decreases sense - and METPO:2007802 is defined as donating electrons to the object and lowering its oxidation state, which this edge does not assert. The two senses could not be separated mechanically because the label was identical, so they migrated together in issue 329 and were split here by reading each edge. RO:0002212 declares no rdfs:domain or rdfs:range, so this introduces no entailment of the kind issue 301 removed.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-15T02:00:00Z",
        "curator": "claude",
        "action": "NORMALISE_NODE_TYPE",
        "changes": "Normalised causal-node type(s) so one node_id means one thing corpus-wide (issue 356): proton_motive_force: BIOLOGICAL_PROCESS -> STATE. The schema's OWN example of STATE: 'a bioenergetic or molecular state of the cell (e.g. proton motive force ...) ... the state is the gradient / steady-value, not its establishment'. All 35 occurrences describe the gradient -- every description across all four types reads 'electrochemical proton gradient', including the 13 typed BIOLOGICAL_PROCESS ('Transmembrane electrochemical gradient generated by respiration'), which name the gradient and its provenance rather than the generating process. Nothing here means the establishment, so this is a retype and not a rename; records that DO mean the process already use a separate id (proton_motive_force_generation in ph_delta.yaml). Also settles the one edge #356 was filed for: phototrophic.yaml's CAPACITY typing was blocking `powers` (METPO:2007900), which is gated to BIOLOGICAL_PROCESS|STATE.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-16T02:00:00Z",
        "curator": "claude",
        "action": "NORMALISE_NODE_TYPE",
        "changes": "Under the PATHWAY-vs-BIOLOGICAL_PROCESS rule, one node_id means one thing corpus-wide (issue 356): aa_decarboxylation is typed BIOLOGICAL_PROCESS. PATHWAY is a named, conventionally enumerable multi-step route; BIOLOGICAL_PROCESS is everything else. The same concept as amino_acid_decarboxylation under a shorter id, with a BYTE-IDENTICAL label ('amino-acid decarboxylation pathways') and a reaction-class description ('Decarboxylation pathways that consume protons and store energy as PMF'). Caught in review (#394): both this table and INCONSISTENT_NODE_TYPE key on node_id, so retyping the long-named one would have created a fresh split between two ids nothing compares. Included here rather than left, because this tranche is what would have caused it.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-20T07:10:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (METPO:1007500\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-21T08:00:00Z",
        "curator": "codex",
        "action": "NORMALISE_NODE_TYPE",
        "changes": "Tranche 5 of issue 356 settles the process/quality families and merges ids that meant the same sense: phosphate_buffering is BIOLOGICAL_PROCESS, proton_permeability is QUALITY. Both occurrences describe cytoplasmic phosphate pools buffering protons and stabilizing pH: the buffering action, not the size of a buffer reservoir. The distinct cytoplasmic_buffering_capacity id remains CAPACITY for that quantity sense. Proton permeability is a measurable membrane property, which is the schema's QUALITY sense rather than a biological process.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope ph_delta_mid3_wide_breadth=NONMECHANISTIC with scope_notes; marked 2 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (proton_pumping_respiratory_complexes, f0f1_atpase).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T04:43:24Z",
        "curator": "codex",
        "action": "ADD_CANONICAL_EXAMPLES",
        "changes": "Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Gemmobacter lutimaris (NCBITaxon:2306023; DOI:10.1099/ijsem.0.003375). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-04T01:40:00Z",
        "curator": "codex",
        "action": "REVIEW_CAUSAL_EVIDENCE",
        "changes": "Reviewed the wide ph_delta_mid3_wide_breadth graph for issue #183: added snippets to 8 edge-level evidence items and grounded 4 unmapped pH-homeostasis predicates to RO:0002211, RO:0002326, or biolink:produces. No paid research service was called.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-04T16:00:00Z",
        "curator": "codex",
        "action": "CONNECT_CAUSAL_GRAPH_COMPONENTS",
        "changes": "Resolved issue #183 graph fragmentation (6 components to 1) by adding 5 source- and verbatim-snippet-backed association connectors among the PMF generation, PMF regulation, alkaline Na+/H+ antiport, ATPase, phosphate-buffering, amino-acid decarboxylation, and membrane proton-permeability branches. No paid research service was called.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-06T17:10:00Z",
        "curator": "codex",
        "action": "ADVERSARIAL_REVIEW_REPAIR",
        "changes": "Addressed PR #664 adversarial review: replaced the weak Poolman section-heading snippets with exact text supporting F0F1-ATPase pH-homeostasis and decarboxylation-driven PMF edges.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-07T03:40:00Z",
        "curator": "codex",
        "action": "ADVERSARIAL_REVIEW_REPAIR",
        "changes": "Addressed PR #664 adversarial review issue #683: normalized the Poolman F0F1-ATPase evidence snippet by removing MathML brace markup so the snippet matches the source text.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-07T04:24:00Z",
        "curator": "codex",
        "action": "ADVERSARIAL_REVIEW_REPAIR",
        "changes": "Addressed PR #664 adversarial review issue #685: replaced weak pH edge snippets with exact source spans that carry their edge claims, and left derived pH-axis bin membership in notes instead of fragment snippets.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-07T06:14:00Z",
        "curator": "codex",
        "action": "ADVERSARIAL_REVIEW_REPAIR",
        "changes": "Addressed PR #664 adversarial review issues #688 and #690: restored a supporting Krulwich snippet on the pH-delta bin membership edge and requoted the Poolman phosphate-buffering edge from the primary source text.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-07T20:05:00Z",
        "curator": "codex",
        "action": "ADVERSARIAL_REVIEW_REPAIR",
        "changes": "Addressed PR #664 adversarial review issues #696, #698, and #699: requoted weak Krulwich pH-homeostasis edge snippets and removed unsupported pH-breadth hub connectors that only joined generic review branches to quantitative bin nodes.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-08T03:30:00Z",
        "curator": "codex",
        "action": "ADVERSARIAL_REVIEW_REPAIR",
        "changes": "Addressed PR #664 adversarial review issue #702: appended corrective issue-183 provenance after evidence-weak connectors were pruned; this NONMECHANISTIC graph intentionally ships with 6 disconnected components until independent trait-specific connectors are curated.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000473",
    "label": "pH delta very low",
    "definition": "A pH delta phenotype with a very narrow growth-supporting pH breadth of at most approximately 1 pH unit, characteristic of stenotopic pH-sensitive physiology.",
    "definition_source": "DOI:10.1038/nrmicro2549",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000232"
    ],
    "synonyms": [
      {
        "synonym_text": "pHd_<=1",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/nrmicro2549",
        "snippet": "pH homeostasis",
        "notes": "pH-homeostasis review supports very narrow pH-tolerance breadths as the stenotopic / pH-sensitive phenotype."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:575322",
        "taxon_label": "Sphingomonas oligoaromativorans",
        "reference": "DOI:10.1099/ijs.0.052894-0",
        "note": "Sphingomonas oligoaromativorans SY-6T grew from pH 6.0 to 7.0, a directly reported breadth of one pH unit inside the at-most-1 bin."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "ph_delta_very_low_stenotopic",
        "title": "pH-delta-very-low stenotopic pH-homeostasis context",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a quantitative measurement, interval, or bin in the environmental phenotype hierarchy; a token protein example would misrepresent the measured value as one inherited molecular mechanism.",
        "description": "DOI-backed nonmechanistic graph annotating very limited pH-homeostasis flexibility, PMF partitioning, constitutive pH-homeostatic expression cost, alkaline antiport, F1Fo acid-side pumping, and Gad proton-consumption branches to the at-most-1 pH-unit breadth bin.",
        "nodes": [
          {
            "node_id": "ph_delta_very_low_trait",
            "label": "pH delta very low",
            "node_type": "TRAIT",
            "grounding": "METPO:1000473",
            "description": "pH growth-supporting breadth \u2264 ~1 pH unit."
          },
          {
            "node_id": "ph_delta",
            "label": "pH delta",
            "node_type": "TRAIT",
            "grounding": "METPO:1000232",
            "description": "Breadth of the growth-supporting external pH range."
          },
          {
            "node_id": "very_limited_ph_homeostasis",
            "label": "very limited pH-homeostasis flexibility",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Narrow capacity to remodel proton extrusion and envelope buffering across changes in external pH."
          },
          {
            "node_id": "external_ph_stress",
            "label": "external pH stress",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Deviation of external pH from the cytoplasmic optimum imposing stress on the cell."
          },
          {
            "node_id": "pmf_partitioning",
            "label": "PMF partitioning (delta-pH / delta-psi)",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Adjustable partitioning of the proton motive force between the transmembrane pH gradient and membrane potential."
          },
          {
            "node_id": "constitutive_ph_homeostasis_expression",
            "label": "constitutive pH-homeostasis machinery expression",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Constitutive expression of pH-homeostatic machinery typical of pH extremophiles."
          },
          {
            "node_id": "energetic_cost",
            "label": "energetic cost on growth near neutral pH",
            "node_type": "STATE",
            "description": "Energetic/proteomic cost that impairs growth at near-neutral pH."
          },
          {
            "node_id": "na_h_antiporter_activity",
            "label": "Na+/H+ antiporter activity",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "Sodium:proton antiporter activity contributing to pH homeostasis."
          },
          {
            "node_id": "alkaline_ph_homeostasis",
            "label": "alkaline pH homeostasis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Maintenance of cytoplasmic pH under alkaline external conditions."
          },
          {
            "node_id": "f1fo_atpase_proton_pumping",
            "label": "F1Fo-ATPase hydrolytic proton pumping",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "ATP-dependent hydrolytic proton extrusion by the F1Fo-ATPase under acid stress."
          },
          {
            "node_id": "acid_stress_survival",
            "label": "acid stress survival",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Survival of the cell under low external pH (acid) stress."
          },
          {
            "node_id": "glutamate_decarboxylase_system",
            "label": "glutamate decarboxylase GadB + GABA/glutamate antiporter",
            "node_type": "PATHWAY",
            "description": "Decarboxylase/antiporter acid-resistance module that consumes cytoplasmic protons."
          },
          {
            "node_id": "cytoplasmic_proton_consumption",
            "label": "cytoplasmic proton consumption",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Consumption of cytoplasmic protons buffering internal acidification."
          }
        ],
        "edges": [
          {
            "subject": "very_limited_ph_homeostasis",
            "predicate": "confers",
            "object": "ph_delta_very_low_trait",
            "description": "Very limited pH-homeostasis flexibility yields a narrow pH-delta breadth.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2549",
                "snippet": "pH homeostasis",
                "notes": "Supports very limited pH-homeostasis flexibility as the basis of stenotopic breadth."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "ph_delta_very_low_trait",
            "predicate": "is a",
            "object": "ph_delta",
            "description": "pH delta very low is a quantitative bin of the pH-delta phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.tim.2007.02.005",
                "snippet": "proton motive force",
                "notes": "Supports a very narrow breadth as a value within the pH-delta distribution."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "external_ph_stress",
            "predicate": "regulates",
            "object": "pmf_partitioning",
            "description": "External pH stress modulates partitioning of the proton motive force between Delta-pH and Delta-psi.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2549",
                "snippet": "Under significant pH stress conditions, both neutralophiles and extremophiles exhibit reversal of the orientation of a PMF component",
                "notes": "Verified against the open PMC manuscript of the Krulwich et al. review; bacterial pH-homeostasis demands determine how delta-psi and delta-pH contribute to the PMF."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "constitutive_ph_homeostasis_expression",
            "predicate": "causes",
            "object": "energetic_cost",
            "description": "Constitutive expression of pH-homeostatic machinery can impose a growth cost near neutral pH.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2549",
                "snippet": "energetic cost of expressing proteins",
                "notes": "Verified against the open PMC manuscript of the Krulwich et al. review; constitutive pH-homeostatic preparedness in extremophiles can negatively affect growth near neutral pH."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "na_h_antiporter_activity",
            "predicate": "contributes to",
            "object": "alkaline_ph_homeostasis",
            "description": "Na+/H+ antiporter activity contributes to alkaline pH homeostasis.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2549",
                "snippet": "active transport of protons inward is a crucial adaptation, which usually involves activation and transcriptional up-regulation of key cation/proton antiporters",
                "notes": "Verified against the open PMC manuscript of the Krulwich et al. review; electrogenic cation/proton antiport supports proton entry during alkaline stress."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "f1fo_atpase_proton_pumping",
            "predicate": "contributes to",
            "object": "acid_stress_survival",
            "description": "Hydrolytic F1Fo-ATPase proton pumping contributes to acid-stress survival.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2549",
                "snippet": "up-regulation of the hydrolytic activity of F1Fo-ATPase promotes ATP-dependent H+ extrusion under acidic conditions",
                "notes": "Verified against the open PMC manuscript of the Krulwich et al. review; F1Fo-ATPase can drive proton efflux in acid-stressed non-respiratory neutralophiles."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "glutamate_decarboxylase_system",
            "predicate": "contributes to",
            "object": "cytoplasmic_proton_consumption",
            "description": "Glutamate decarboxylase GadB coupled with a GABA/glutamate antiporter contributes to cytoplasmic proton consumption.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2549",
                "snippet": "consumes a proton during decarboxylation",
                "notes": "Verified against the open PMC manuscript of the Krulwich et al. review; GadB consumes a cytoplasmic proton when it decarboxylates glutamate in the E. coli acid-resistance cycle."
              }
            ],
            "predicate_id": "RO:0002326"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.838042+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-13T10:00:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed definition and causal graph linking very limited pH-homeostasis flexibility to the stenotopic pH-delta-very-low bin.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:30Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d71, rdfs:subClassOf\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 5 evidence-backed generic edges (10 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:10Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d71, RO:0002213\u00d71, biolink:consumes\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates (1 to confers), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope ph_delta_very_low_stenotopic=NONMECHANISTIC with scope_notes.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T04:43:24Z",
        "curator": "codex",
        "action": "ADD_CANONICAL_EXAMPLES",
        "changes": "Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Sphingomonas oligoaromativorans (NCBITaxon:575322; DOI:10.1099/ijs.0.052894-0). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-04T02:00:00Z",
        "curator": "codex",
        "action": "REVIEW_CAUSAL_EVIDENCE",
        "changes": "Reviewed the very-low ph_delta_very_low_stenotopic graph for issue #183: added snippets to 5 edge-level evidence items, grounded 2 unmapped predicates, and narrowed 3 broad pH-homeostasis predicates to RO:0002326. No paid research service was called.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-04T17:00:00Z",
        "curator": "codex",
        "action": "CONNECT_CAUSAL_GRAPH_COMPONENTS",
        "changes": "Resolved issue #183 graph fragmentation (6 components to 1) by adding 5 source- and verbatim-snippet-backed association connectors among PMF partitioning, constitutive cost, alkaline antiport, F1Fo acid-survival support, and Gad proton-consumption branches. No paid research service was called.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-06T17:10:00Z",
        "curator": "codex",
        "action": "ADVERSARIAL_REVIEW_REPAIR",
        "changes": "Addressed PR #664 adversarial review: replaced copied nonmechanistic bridge snippets with independent exact source snippets while preserving the existing connector edge scope.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-07T06:14:00Z",
        "curator": "codex",
        "action": "ADVERSARIAL_REVIEW_REPAIR",
        "changes": "Addressed PR #664 adversarial review issues #688 and #689: requoted the F1Fo-ATPase acid-stress edge with a longer Krulwich span and replaced its connector quote with distinct Sekiya F-ATPase acid-tolerance support.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-07T20:05:00Z",
        "curator": "codex",
        "action": "ADVERSARIAL_REVIEW_REPAIR",
        "changes": "Addressed PR #664 adversarial review issues #696, #698, and #699: requoted weak Krulwich pH-homeostasis edge snippets and removed unsupported pH-breadth hub connectors that only joined generic review branches to quantitative bin nodes.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-08T03:30:00Z",
        "curator": "codex",
        "action": "ADVERSARIAL_REVIEW_REPAIR",
        "changes": "Addressed PR #664 adversarial review issue #702: appended corrective issue-183 provenance after evidence-weak connectors were pruned; this NONMECHANISTIC graph intentionally ships with 6 disconnected components until independent trait-specific connectors are curated.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1003000",
    "label": "pH growth preference",
    "definition": "A phenotype that describes how the rate and extent of population growth are affected by environmental pH.",
    "definition_source": "DOI:10.1038/nrmicro2549",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/nrmicro2549",
        "snippet": "external pH values that are outside the cytoplasmic pH range",
        "notes": "Supports environmental pH as a growth-relevant condition requiring pH homeostasis."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:46632",
        "taxon_label": "Picrophilus oshimae",
        "reference": "DOI:10.1007/s007920050044",
        "note": "Picrophilus oshimae, with a growth optimum near pH 0.7, exemplifies the acidophilic branch of pH growth preference."
      },
      {
        "taxon_id": "NCBITaxon:2069301",
        "taxon_label": "Evansella tamaricis",
        "reference": "DOI:10.1099/ijsem.0.002543",
        "note": "Evansella tamaricis EGI 80668T, published as Bacillus tamaricis, grew at pH 8-10 with optimum pH 9 and exemplifies an alkaliphilic branch."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "ph_growth_preference_homeostasis",
        "title": "Environmental pH control of growth preference",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is an upper preference, broad tolerance, or central-range classification spanning multiple unrelated adaptations; contextual protein nodes are retained without assigning a misleading token UniProt example.",
        "description": "Evidence-backed causal sketch linking environmental pH, pH sensing, and cytoplasmic pH homeostasis to growth preference phenotypes.",
        "nodes": [
          {
            "node_id": "ph_growth_preference_trait",
            "label": "pH growth preference",
            "node_type": "TRAIT",
            "grounding": "METPO:1003000",
            "description": "Growth-rate and growth-extent phenotype shaped by environmental pH."
          },
          {
            "node_id": "environmental_ph",
            "label": "environmental pH",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Acidity or alkalinity of the growth environment."
          },
          {
            "node_id": "acidic_external_ph",
            "label": "acidic external pH",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "External pH below the cytoplasmic pH range compatible with growth.",
            "grounding": "PATO:0001429"
          },
          {
            "node_id": "alkaline_external_ph",
            "label": "alkaline external pH",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "External pH above the cytoplasmic pH range compatible with growth.",
            "grounding": "PATO:0001430"
          },
          {
            "node_id": "ph_sensing",
            "label": "pH sensing",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "Detection of external or envelope pH change by regulatory proteins and transporters."
          },
          {
            "node_id": "cytoplasmic_ph_homeostasis",
            "label": "cytoplasmic pH homeostasis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Maintenance of intracellular pH within a range compatible with growth.",
            "grounding": "GO:0051453"
          },
          {
            "node_id": "f1f0_atpase",
            "label": "proton-translocating F1F0-ATPase",
            "node_type": "GENE_OR_PROTEIN",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed as a contextual protein or protein-complex label in a broad environmental classification; no single exact family term denotes this aggregate use.",
            "description": "F-type ATP synthase/ATPase that translocates protons across the membrane, contributing to pH homeostasis."
          },
          {
            "node_id": "amino_acid_decarboxylase_systems",
            "label": "amino-acid decarboxylase systems",
            "node_type": "PATHWAY",
            "description": "Inducible decarboxylase systems (e.g. GAD, arginine/agmatine) that consume cytoplasmic protons."
          },
          {
            "node_id": "amino_acid_decarboxylation",
            "label": "amino-acid decarboxylation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Decarboxylation of amino acids that consumes protons and raises cytoplasmic alkalinity."
          },
          {
            "node_id": "na_h_antiport",
            "label": "Na+/H+ antiport",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "Sodium/proton antiporter activity (e.g. Mrp system) coupling Na+ efflux to H+ import."
          },
          {
            "node_id": "proton_consuming_enzyme_modules",
            "label": "proton-consuming enzyme modules",
            "node_type": "GENE_OR_PROTEIN",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed as a contextual protein or protein-complex label in a broad environmental classification; no single exact family term denotes this aggregate use.",
            "description": "Decarboxylase and deaminase protein families carrying out proton-consuming reactions."
          },
          {
            "node_id": "na_h_antiporter_proteins",
            "label": "Na+/H+ antiporter proteins",
            "node_type": "GENE_OR_PROTEIN",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed as a contextual protein or protein-complex label in a broad environmental classification; no single exact family term denotes this aggregate use.",
            "description": "Na+/H+ antiporter protein families (e.g. Mrp/Mnh/Nha) associated with pH preference."
          }
        ],
        "edges": [
          {
            "subject": "environmental_ph",
            "predicate": "regulates",
            "object": "ph_growth_preference_trait",
            "description": "Environmental pH determines which pH conditions support growth.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2549",
                "snippet": "tolerate or grow at external pH values",
                "notes": "Review frames pH growth as a response to external pH outside the cytoplasmic range."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "acidic_external_ph",
            "predicate": "challenges",
            "object": "cytoplasmic_ph_homeostasis",
            "description": "Acidic environments impose inward proton stress that must be managed for growth.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2549",
                "snippet": "acid challenge conditions include increased expression and activity",
                "notes": "Supports active mechanisms under acid challenge."
              }
            ],
            "predicate_id": "METPO:2007406"
          },
          {
            "subject": "alkaline_external_ph",
            "predicate": "challenges",
            "object": "cytoplasmic_ph_homeostasis",
            "description": "Alkaline environments require active proton accumulation or generation to maintain cytoplasmic pH.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2549",
                "snippet": "active proton accumulation or generation in the cytoplasm",
                "notes": "Supports alkaline-pH homeostasis as a growth-enabling process."
              }
            ],
            "predicate_id": "METPO:2007406"
          },
          {
            "subject": "ph_sensing",
            "predicate": "regulates",
            "object": "cytoplasmic_ph_homeostasis",
            "description": "pH-sensing and signalling systems regulate homeostasis responses to acid or alkali.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2549",
                "snippet": "pH-sensing and signalling capabilities",
                "notes": "Supports regulatory sensing as part of homeostasis."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "cytoplasmic_ph_homeostasis",
            "predicate": "confers",
            "object": "ph_growth_preference_trait",
            "description": "Growth at preferred pH depends on maintaining intracellular pH compatible with cellular processes.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2549",
                "snippet": "robust mechanisms for cytoplasmic pH homeostasis",
                "notes": "Supports cytoplasmic pH homeostasis as central to growth under pH stress."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "f1f0_atpase",
            "predicate": "contributes to",
            "object": "cytoplasmic_ph_homeostasis",
            "description": "The proton-translocating F1F0-ATPase mediates pH homeostasis supporting growth under low pH.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuad062",
                "notes": "pH homeostasis mediated by the proton-translocating F1F0-ATPase; general across taxa."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "acidic_external_ph",
            "predicate": "induces",
            "object": "amino_acid_decarboxylase_systems",
            "description": "Low external pH induces amino-acid decarboxylase systems that consume protons.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuad062",
                "notes": "amino-acid decarboxylase systems (GAD, agmatine/arginine decarboxylation) that consume protons and raise cytoplasmic alkalinity."
              }
            ]
          },
          {
            "subject": "amino_acid_decarboxylase_systems",
            "predicate": "enables",
            "object": "amino_acid_decarboxylation",
            "description": "Decarboxylase systems carry out amino-acid decarboxylation.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuad062",
                "notes": "amino-acid decarboxylase systems that consume protons and raise cytoplasmic alkalinity."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "amino_acid_decarboxylation",
            "predicate": "contributes to",
            "object": "cytoplasmic_ph_homeostasis",
            "description": "Amino-acid decarboxylation consumes protons and raises cytoplasmic alkalinity, aiding pH homeostasis.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuad062",
                "notes": "consume protons and raise cytoplasmic alkalinity."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "na_h_antiport",
            "predicate": "contributes to",
            "object": "cytoplasmic_ph_homeostasis",
            "description": "Na+/H+ antiport (notably the Mrp system) is the major mechanism for alkaline pH homeostasis.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2549",
                "notes": "Na+/H+ antiporters (notably the multicomponent Mrp system) are the major mechanism for alkaliphile pH homeostasis."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "proton_consuming_enzyme_modules",
            "predicate": "associated with",
            "object": "acidic_external_ph",
            "description": "Enzymes for proton-consuming reactions (decarboxylases/deaminases) are consistently associated with lower pH preference.",
            "evidence": [
              {
                "reference": "DOI:10.1126/sciadv.adf8998",
                "notes": "proton-consuming reactions (decarboxylases, deaminases) consistently associated with pH preference across environments."
              }
            ],
            "predicate_id": "biolink:associated_with"
          },
          {
            "subject": "na_h_antiporter_proteins",
            "predicate": "associated with",
            "object": "alkaline_external_ph",
            "description": "Na+/H+ antiporter proteins (PhaGF/MnhG/MrpF/YufB) are associated with higher pH preference.",
            "evidence": [
              {
                "reference": "DOI:10.1126/sciadv.adf8998",
                "notes": "Na+/H+ antiporters PhaGF, MnhG, MrpF, YufB associated with higher pH preference."
              }
            ],
            "predicate_id": "biolink:associated_with"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.936639+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-11T00:00:00-07:00",
        "curator": "codex",
        "action": "CURATED_WITH_LITERATURE",
        "changes": "Reviewed pH growth preference trait and added DOI-backed evidence and causal graph for pH sensing and cytoplasmic pH homeostasis.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:30Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002211\u00d71, RO:0002327\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T21:30:06Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007406\u00d72).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:38:00Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0030641\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T08:14:32Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (PATO:0001428\u00d71, PATO:0001429\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-26T05:00:47Z",
        "curator": "claude",
        "action": "RENAME_PREDICATE_LABELS",
        "changes": "Renamed 1 causal-edge predicate label(s) to align with existing groundings: influences \u2192 regulates \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-26T05:00:50Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002211\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-15T07:20:36Z",
        "curator": "claude",
        "action": "FIX_NODE_GROUNDING_CURIE",
        "changes": "Overwrote 1 causal-node grounding(s) (obsolete/wrong GO -> corrected, verified vs OAK).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-15T07:21:43Z",
        "curator": "claude",
        "action": "FIX_NODE_GROUNDING_CURIE",
        "changes": "Overwrote 2 pH causal-node grounding(s) to corrected PATO CURIEs (phase-2; verified vs OAK).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 7 evidence-backed generic edges (6 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:10Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 6 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002326\u00d73, biolink:associated_with\u00d72, RO:0002327\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 1 causal edge(s) off enables/RO:0002327 with a TRAIT object (1 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-16T02:00:00Z",
        "curator": "claude",
        "action": "NORMALISE_NODE_TYPE",
        "changes": "Under the PATHWAY-vs-BIOLOGICAL_PROCESS rule, one node_id means one thing corpus-wide (issue 356): amino_acid_decarboxylation is typed BIOLOGICAL_PROCESS. PATHWAY is a named, conventionally enumerable multi-step route; BIOLOGICAL_PROCESS is everything else. A REACTION CLASS, not a route. The corpus describes it that way in neutrophilic.yaml -- 'Enzyme-catalyzed decarboxylation reaction that consumes cytoplasmic protons' -- and the wording varies by record, so read that as the family's sense rather than as this record's own text. Named systems that implement it (Gad) would be pathways; the reaction class is not. Was 4 BIOLOGICAL_PROCESS to 2 before this tranche.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope ph_growth_preference_homeostasis=NONMECHANISTIC with scope_notes; marked 3 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (f1f0_atpase, proton_consuming_enzyme_modules, na_h_antiporter_proteins); added 2 node(s) and 2 edge(s) (proton_consuming_enzyme_modules, na_h_antiporter_proteins); removed 2 node(s) and 2 edge(s) together with their evidence (na_h_antiporter_genes, proton_consuming_reaction_genes).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T04:43:24Z",
        "curator": "codex",
        "action": "ADD_CANONICAL_EXAMPLES",
        "changes": "Resolved issue #444 after the #591 source/bin policy with 2 direct source-backed canonical example(s): Picrophilus oshimae (NCBITaxon:46632; DOI:10.1007/s007920050044), Evansella tamaricis (NCBITaxon:2069301; DOI:10.1099/ijsem.0.002543). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000331",
    "label": "pH optimum",
    "definition": "A pH phenotype with numerical limits that represents the external pH conditions at which an organism exhibits the most efficient growth and reproduction.",
    "definition_source": "DOI:10.1038/nrmicro2549",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000531",
      "METPO:1000536"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/nrmicro2549",
        "snippet": "cytoplasmic pH",
        "notes": "pH-homeostasis review supports the external pH at which cytoplasmic pH is best maintained as the operational definition of pH optimum."
      },
      {
        "reference": "DOI:10.1016/j.tim.2007.02.005",
        "snippet": "proton motive force",
        "notes": "pH-homeostasis review supports the balanced proton motive force at the optimal external pH as the mechanism enabling maximal growth."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:3447298",
        "taxon_label": "Microbaculum mangrovi",
        "reference": "DOI:10.1099/ijsem.0.006972",
        "note": "Microbaculum mangrovi FT89T had a reported optimum interval of pH 6.0-7.0. Because the interval touches the low/mid1 boundary, #591 keeps this claim on the optimum parent."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "ph_optimum_balanced_homeostasis",
        "title": "pH-optimum balanced cytoplasmic homeostasis",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a quantitative measurement, interval, or bin in the environmental phenotype hierarchy; a token protein example would misrepresent the measured value as one inherited molecular mechanism.",
        "description": "DOI-backed graph linking the external pH at which cytoplasmic pH-homeostasis machinery operates with minimal load to maximal growth and the pH-optimum phenotype.",
        "nodes": [
          {
            "node_id": "ph_optimum_trait",
            "label": "pH optimum",
            "node_type": "TRAIT",
            "grounding": "METPO:1000331",
            "description": "External pH at which growth rate is maximal."
          },
          {
            "node_id": "external_ph",
            "label": "external pH",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Ambient proton activity (pH) imposed on the cell."
          },
          {
            "node_id": "proton",
            "label": "proton",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:15378",
            "description": "H+ ion whose transmembrane gradient drives the proton motive force."
          },
          {
            "node_id": "cytoplasmic_ph_homeostasis",
            "label": "cytoplasmic pH homeostasis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Maintenance of a near-neutral cytoplasmic pH against the external H+ gradient.",
            "grounding": "GO:0051453"
          },
          {
            "node_id": "proton_motive_force",
            "label": "proton motive force",
            "node_type": "STATE",
            "description": "Electrochemical proton gradient powering ATP synthesis and transport.",
            "grounding": "METPO:1007500"
          },
          {
            "node_id": "maximal_growth_rate",
            "label": "maximal growth rate",
            "node_type": "QUALITY",
            "description": "Peak specific growth rate achieved at the optimal external pH."
          },
          {
            "node_id": "atp_synthesis",
            "label": "ATP synthesis by F0F1-ATP synthase",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Synthesis of ATP driven by proton flux through the F0F1-ATP synthase."
          },
          {
            "node_id": "na_h_antiporter_activity",
            "label": "Na+/H+ antiporter activity",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "Proton-sensing antiporter that exports Na+/K+ in exchange for protons to acidify the cytoplasm."
          },
          {
            "node_id": "cytoplasm_acidification",
            "label": "cytoplasm acidification",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Lowering of cytoplasmic pH when internal pH becomes too high."
          },
          {
            "node_id": "decarboxylation_pathways",
            "label": "metabolite decarboxylation pathways",
            "node_type": "PATHWAY",
            "description": "Proton-consuming decarboxylation reactions that contribute to pH homeostasis and energy conservation."
          },
          {
            "node_id": "cytoplasmic_buffering_capacity",
            "label": "cytoplasmic buffering capacity",
            "node_type": "CAPACITY",
            "description": "Capacity of cytoplasmic buffers (e.g. inorganic/organic phosphates) to absorb pH fluctuations."
          },
          {
            "node_id": "internal_ph",
            "label": "internal pH",
            "node_type": "STATE",
            "description": "Cytoplasmic proton activity (pH) maintained near neutrality."
          }
        ],
        "edges": [
          {
            "subject": "external_ph",
            "predicate": "imposes gradient of",
            "object": "proton",
            "description": "External pH imposes a transmembrane H+ gradient on the cell.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.tim.2007.02.005",
                "snippet": "major contributor to the proton motive force",
                "notes": "Supports the transmembrane H+ gradient as the determinant of the proton motive force."
              }
            ],
            "predicate_id": "METPO:2007601"
          },
          {
            "subject": "cytoplasmic_ph_homeostasis",
            "predicate": "regulates",
            "object": "proton_motive_force",
            "description": "Cytoplasmic pH homeostasis maintains a balanced proton motive force at the optimal external pH.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2549",
                "snippet": "pH homeostasis",
                "notes": "Supports pH homeostasis as the mechanism balancing the proton motive force."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "proton_motive_force",
            "predicate": "promotes",
            "object": "maximal_growth_rate",
            "description": "A balanced proton motive force promotes peak growth.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.tim.2007.02.005",
                "snippet": "proton motive force",
                "notes": "Supports the proton motive force as the energetic basis of growth at the optimal external pH."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "maximal_growth_rate",
            "predicate": "manifests as",
            "object": "ph_optimum_trait",
            "description": "The external pH supporting peak growth manifests the pH-optimum phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2549",
                "snippet": "cytoplasmic pH",
                "notes": "Supports the trait endpoint."
              }
            ],
            "predicate_id": "METPO:2007400"
          },
          {
            "subject": "external_ph",
            "predicate": "contributes to",
            "object": "proton_motive_force",
            "description": "The external pH largely determines the magnitude of the pH gradient (\u0394pH) component of the proton motive force.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuad033",
                "notes": "Cells maintain cytoplasmic pH near neutral, so the magnitude of the pH gradient is largely determined by the external pH."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "proton_motive_force",
            "predicate": "drives",
            "object": "atp_synthesis",
            "description": "The proton motive force drives ATP synthesis via the F0F1-ATP synthase.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuad033",
                "notes": "PMF drives the synthesis of ATP; the F0F1-ATP synthase uses three to five protons to synthesize one ATP."
              }
            ]
          },
          {
            "subject": "na_h_antiporter_activity",
            "predicate": "enables",
            "object": "cytoplasm_acidification",
            "description": "Proton-sensing Na+/H+ (and K+/H+) antiporters acidify the cytoplasm when internal pH gets too high.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuad033",
                "notes": "Proton-sensing ion/H+ antiporters acidify the cytoplasm by exporting K+ or Na+ in exchange for protons when the internal pH gets too high."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "cytoplasm_acidification",
            "predicate": "regulates",
            "object": "cytoplasmic_ph_homeostasis",
            "description": "Antiporter-driven cytoplasm acidification contributes to cytoplasmic pH homeostasis.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuad033",
                "notes": "Acidifying the cytoplasm when internal pH gets too high is a homeostatic mechanism maintaining near-neutral cytoplasmic pH."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "decarboxylation_pathways",
            "predicate": "contributes to",
            "object": "cytoplasmic_ph_homeostasis",
            "description": "Proton-consuming decarboxylation reactions raise the internal pH and contribute to pH homeostasis.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuad033",
                "notes": "The chemistry of the decarboxylation reaction requires a proton, raising internal pH, and the enzymes have a built-in self-regulatory mechanism contributing to pH homeostasis."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "decarboxylation_pathways",
            "predicate": "generates",
            "object": "proton_motive_force",
            "description": "Free energy from decarboxylation reactions can be stored as a proton motive force.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuad033",
                "notes": "The free energy change from decarboxylation reactions can be stored in the form of a proton motive force."
              }
            ],
            "predicate_id": "biolink:produces"
          },
          {
            "subject": "cytoplasmic_buffering_capacity",
            "predicate": "regulates",
            "object": "internal_ph",
            "description": "Cytoplasmic buffering capacity stabilizes the internal pH by absorbing pH fluctuations.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuad033",
                "notes": "The buffering capacity of the cytoplasm is important in absorbing pH fluctuations (e.g. inorganic and organic phosphates)."
              }
            ],
            "predicate_id": "RO:0002211"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.814691+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-13T10:00:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed causal graph linking external pH, cytoplasmic pH homeostasis, the proton motive force, and maximal growth to the pH-optimum phenotype.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:30Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T21:30:06Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007400\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:18Z",
        "curator": "claude",
        "action": "RENAME_PREDICATE_LABELS",
        "changes": "Renamed 1 causal-edge predicate label(s) to align with existing groundings: maintains \u2192 regulates \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:21Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002211\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:38:00Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0030641\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:41:03Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (METPO:1007500\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-26T02:30:12Z",
        "curator": "claude",
        "action": "RETYPE_CAUSAL_NODES",
        "changes": "Re-typed 1 causal-node node_type field(s) to align with CausalNodeTypeEnum semantics: proton motive force: BIOLOGICAL_PROCESS \u2192 STATE \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-14T07:26:19Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007601\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-15T07:20:36Z",
        "curator": "claude",
        "action": "FIX_NODE_GROUNDING_CURIE",
        "changes": "Overwrote 1 causal-node grounding(s) (obsolete/wrong GO -> corrected, verified vs OAK).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 7 evidence-backed generic edges (6 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:10Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 6 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002326\u00d72, RO:0002211\u00d72, RO:0002327\u00d71, biolink:produces\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-21T08:00:00Z",
        "curator": "codex",
        "action": "NORMALISE_NODE_TYPE",
        "changes": "Tranche 5 of issue 356 settles the process/quality families and merges ids that meant the same sense: maximal_growth_rate is QUALITY. A maximal growth rate is a measured upper bound or peak specific rate. Its edges associate, enable, or manifest that value; none describe the process of cell growth itself. An edge cannot enable a QUALITY under RO:0002327's biological-process range, so edges that causally support the rate use promotes (RO:0002213) instead.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope ph_optimum_balanced_homeostasis=NONMECHANISTIC with scope_notes.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T04:43:24Z",
        "curator": "codex",
        "action": "ADD_CANONICAL_EXAMPLES",
        "changes": "Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Microbaculum mangrovi (NCBITaxon:3447298; DOI:10.1099/ijsem.0.006972). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000458",
    "label": "pH optimum high",
    "definition": "A pH optimum phenotype with the best-growth external pH above approximately 8, corresponding to alkaliphilic or extreme-alkaliphilic physiology.",
    "definition_source": "DOI:10.1038/nrmicro2549",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000331"
    ],
    "synonyms": [
      {
        "synonym_text": "Alkali Tolerant",
        "synonym_type": "EXACT_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "Alkaliphile",
        "synonym_type": "EXACT_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "Extreme Alkaliphile",
        "synonym_type": "EXACT_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "pHO_8_to_14",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/nrmicro2549",
        "snippet": "alkaliphiles",
        "notes": "pH-homeostasis review supports alkaliphile and extreme-alkaliphile physiology growing at high external pH."
      },
      {
        "reference": "DOI:10.1016/j.tim.2007.02.005",
        "snippet": "proton motive force",
        "notes": "pH-homeostasis review supports Na+/H+ antiporters re-importing protons as the alkaliphile mechanism sustaining the proton motive force at high external pH."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "ph_optimum_high_alkaliphile_setpoint",
        "title": "pH-optimum-high alkaliphile setpoint",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a quantitative measurement, interval, or bin in the environmental phenotype hierarchy; a token protein example would misrepresent the measured value as one inherited molecular mechanism.",
        "description": "DOI-backed graph linking alkaliphile cytoplasmic pH homeostasis via Na+/H+ antiporters to a pH-optimum above 8 (alkaliphile / extreme alkaliphile).",
        "nodes": [
          {
            "node_id": "ph_optimum_high_trait",
            "label": "pH optimum high",
            "node_type": "TRAIT",
            "grounding": "METPO:1000458",
            "description": "pH optimum above ~8."
          },
          {
            "node_id": "ph_optimum",
            "label": "pH optimum",
            "node_type": "TRAIT",
            "grounding": "METPO:1000331",
            "description": "External pH supporting maximal growth."
          },
          {
            "node_id": "alkaline_external_ph",
            "label": "alkaline external pH",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "External pH > ~8, typical of soda lakes and other alkaline habitats.",
            "grounding": "PATO:0001430"
          },
          {
            "node_id": "na_h_antiporters",
            "label": "Na+/H+ antiporters",
            "node_type": "GENE_OR_PROTEIN",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed as a contextual protein or protein-complex label within a quantitative measurement graph; no exact semantic family term was established for this aggregate use.",
            "description": "Membrane antiporters importing H+ in exchange for Na+ to acidify the cytoplasm at high external pH."
          },
          {
            "node_id": "alkaliphile_homeostasis",
            "label": "alkaliphile cytoplasmic pH homeostasis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Maintenance of a less alkaline cytoplasm than the external environment by proton re-import."
          },
          {
            "node_id": "cpa_nha_antiporters",
            "label": "CPA/Nha family Na+/H+ antiporters",
            "node_type": "GENE_OR_PROTEIN",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed as a contextual protein or protein-complex label within a quantitative measurement graph; no exact semantic family term was established for this aggregate use.",
            "description": "Monovalent cation/proton antiporter family exporting Na+ and importing H+."
          },
          {
            "node_id": "intracellular_na",
            "label": "intracellular Na+ concentration",
            "node_type": "CHEMICAL",
            "description": "Cytoplasmic sodium ion concentration."
          },
          {
            "node_id": "trkah_k_uptake",
            "label": "TrkAH K+ uptake system",
            "node_type": "GENE_OR_PROTEIN",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed as a contextual protein or protein-complex label within a quantitative measurement graph; no exact semantic family term was established for this aggregate use.",
            "description": "Potassium uptake transport system aiding membrane potential and pH homeostasis."
          },
          {
            "node_id": "rnf_complex",
            "label": "Rnf complex",
            "node_type": "GENE_OR_PROTEIN",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed as a contextual protein or protein-complex label within a quantitative measurement graph; no exact semantic family term was established for this aggregate use.",
            "description": "Ferredoxin:NAD oxidoreductase that pumps Na+ to build a transmembrane Na+ gradient."
          },
          {
            "node_id": "transmembrane_na_gradient",
            "label": "transmembrane Na+ gradient",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Electrochemical sodium ion gradient across the membrane."
          },
          {
            "node_id": "terminal_oxidases",
            "label": "branched respiratory chain terminal oxidases",
            "node_type": "GENE_OR_PROTEIN",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed as a contextual protein or protein-complex label within a quantitative measurement graph; no exact semantic family term was established for this aggregate use.",
            "description": "Terminal oxidases (aa3/ba3/bb3) that pump protons with differing efficiencies."
          },
          {
            "node_id": "proton_motive_force",
            "label": "proton motive force",
            "node_type": "STATE",
            "description": "Electrochemical proton gradient powering bioenergetics.",
            "grounding": "METPO:1007500"
          },
          {
            "node_id": "acidic_membrane_polymers",
            "label": "acidic plasma membrane polymers",
            "node_type": "CHEMICAL",
            "description": "Acidic cell-envelope polymers (teichuronopeptide, peptidoglycan, teichuronic acid)."
          },
          {
            "node_id": "organic_acid_secretion",
            "label": "organic acid secretion",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Secretion of metabolic organic acids that helps counter alkaline stress."
          },
          {
            "node_id": "ph_balance",
            "label": "pH balance",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Maintenance of cytoplasmic pH balance under alkaline stress."
          }
        ],
        "edges": [
          {
            "subject": "alkaline_external_ph",
            "predicate": "selects for",
            "object": "alkaliphile_homeostasis",
            "description": "Alkaline environments select for alkaliphile cytoplasmic pH homeostasis.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2549",
                "snippet": "alkaliphiles",
                "notes": "Supports the alkaliphile regime as the environmental context for high-pH optima."
              }
            ],
            "predicate_id": "METPO:2007401"
          },
          {
            "subject": "na_h_antiporters",
            "predicate": "regulates",
            "object": "alkaliphile_homeostasis",
            "description": "Na+/H+ antiporters drive proton re-import that acidifies the cytoplasm relative to the alkaline external pH.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.tim.2007.02.005",
                "snippet": "proton motive force",
                "notes": "Supports antiporter-driven proton re-import as the alkaliphile mechanism for maintaining the proton motive force."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "alkaliphile_homeostasis",
            "predicate": "confers",
            "object": "ph_optimum_high_trait",
            "description": "Alkaliphile pH homeostasis yields an alkaline pH-optimum setpoint.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2549",
                "snippet": "alkaliphiles",
                "notes": "Supports a high-pH optimum as the alkaliphile / extreme-alkaliphile outcome."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "ph_optimum_high_trait",
            "predicate": "is a",
            "object": "ph_optimum",
            "description": "pH optimum high is a quantitative bin of the pH-optimum phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2549",
                "snippet": "cytoplasmic pH",
                "notes": "Supports an alkaline optimum as a value within the pH-optimum distribution."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "cpa_nha_antiporters",
            "predicate": "decreases",
            "object": "intracellular_na",
            "description": "CPA/Nha family Na+/H+ antiporters export Na+, lowering intracellular Na+ as part of pH homeostasis.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.00145-24",
                "notes": "Monovalent cation/proton antiporters import H+ and efflux Na+; Na+/H+ antiporters effectively decrease the intracellular Na+ concentration."
              }
            ],
            "predicate_id": "RO:0002212"
          },
          {
            "subject": "trkah_k_uptake",
            "predicate": "maintains",
            "object": "alkaliphile_homeostasis",
            "description": "TrkAH K+ uptake supports membrane potential adjustment and cytoplasmic pH homeostasis.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.00145-24",
                "notes": "TrkAH transport system takes up K+ and maintains pH homeostasis, adjusting membrane potential."
              }
            ]
          },
          {
            "subject": "rnf_complex",
            "predicate": "generates",
            "object": "transmembrane_na_gradient",
            "description": "Rnf complex expels sodium ions to establish a transmembrane Na+ gradient usable for bioenergetics at high pH.",
            "evidence": [
              {
                "reference": "DOI:10.1515/hsz-2015-0137",
                "notes": "Rnf transfers electrons from reduced ferredoxin to NAD and uses the redox difference to expel sodium, establishing a transmembrane sodium gradient."
              }
            ],
            "predicate_id": "biolink:produces"
          },
          {
            "subject": "terminal_oxidases",
            "predicate": "produces",
            "object": "proton_motive_force",
            "description": "Branched respiratory chain terminal oxidases pump protons (with varying efficiencies) to sustain proton motive force at high pH.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2024.1468929",
                "notes": "Cyt. aa3 pumps protons at 0.7 H+/electron; ba3 and bb3 pump at 0.5 H+/electron, supporting usable PMF at high pH."
              }
            ],
            "predicate_id": "METPO:2007800"
          },
          {
            "subject": "acidic_membrane_polymers",
            "predicate": "enhances",
            "object": "proton_motive_force",
            "description": "Acidic plasma-membrane polymers aid proton retention and enhance proton motive force generation at high external pH.",
            "evidence": [
              {
                "reference": "DOI:10.3390/min14090861",
                "notes": "Alkaliphilic Bacillus enhances proton motive force generation by synthesis of acidic plasma membrane (teichuronopeptide, peptidoglycan, teichuronic acid)."
              }
            ]
          },
          {
            "subject": "organic_acid_secretion",
            "predicate": "regulates",
            "object": "ph_balance",
            "description": "Secretion of organic acids by alkaliphiles permits cytoplasmic pH balance against alkaline stress.",
            "evidence": [
              {
                "reference": "DOI:10.3390/min14090861",
                "notes": "Secretion of organic acids by alkaliphilic microbes is a crucial metabolic activity that permits pH balance."
              }
            ],
            "predicate_id": "RO:0002211"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.828378+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-13T10:00:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed definition and causal graph linking Na+/H+ antiporter-driven alkaliphile pH homeostasis to the alkaliphile / extreme-alkaliphile pH-optimum-high bin.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:30Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d71, rdfs:subClassOf\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T21:30:06Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007401\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:18Z",
        "curator": "claude",
        "action": "RENAME_PREDICATE_LABELS",
        "changes": "Renamed 1 causal-edge predicate label(s) to align with existing groundings: drives \u2192 regulates \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:21Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002211\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T08:14:32Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (PATO:0001429\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-15T07:21:43Z",
        "curator": "claude",
        "action": "FIX_NODE_GROUNDING_CURIE",
        "changes": "Overwrote 1 pH causal-node grounding(s) to corrected PATO CURIEs (phase-2; verified vs OAK).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 6 evidence-backed generic edges (10 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:10Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 4 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002212\u00d71, biolink:produces\u00d71, METPO:2000202\u00d71, RO:0002211\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates (1 to confers), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T02:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES_PART2",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates onto their causal-graph counterparts (1 to produces), issue 301 part 2. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Each replacement is a 1:1 mirror of its source predicate that changes only the domain, so the claim each edge makes is unchanged and directions are unchanged. The replacements are proposed in proposals/metpo_traitmech_v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-15T02:00:00Z",
        "curator": "claude",
        "action": "NORMALISE_NODE_TYPE",
        "changes": "Normalised causal-node type(s) so one node_id means one thing corpus-wide (issue 356): proton_motive_force: BIOLOGICAL_PROCESS -> STATE. The schema's OWN example of STATE: 'a bioenergetic or molecular state of the cell (e.g. proton motive force ...) ... the state is the gradient / steady-value, not its establishment'. All 35 occurrences describe the gradient -- every description across all four types reads 'electrochemical proton gradient', including the 13 typed BIOLOGICAL_PROCESS ('Transmembrane electrochemical gradient generated by respiration'), which name the gradient and its provenance rather than the generating process. Nothing here means the establishment, so this is a retype and not a rename; records that DO mean the process already use a separate id (proton_motive_force_generation in ph_delta.yaml). Also settles the one edge #356 was filed for: phototrophic.yaml's CAPACITY typing was blocking `powers` (METPO:2007900), which is gated to BIOLOGICAL_PROCESS|STATE.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-20T07:10:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (METPO:1007500\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-21T00:00:00Z",
        "curator": "claude",
        "action": "BACKFILL_CANONICAL_EXAMPLES",
        "changes": "Added 1 exemplar taxon/taxa. Organisms and citations come only from this record's own deep-research artifact; every taxon id was resolved and label-checked against the local NCBITaxon build rather than recalled. Organisms the artifact names as contrast cases rather than exemplars were deliberately excluded.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope ph_optimum_high_alkaliphile_setpoint=NONMECHANISTIC with scope_notes; marked 5 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (na_h_antiporters, cpa_nha_antiporters, trkah_k_uptake, rnf_complex, terminal_oxidases).",
        "llm_assisted": true
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1463663",
        "taxon_label": "Bacillus aequororis",
        "reference": "DOI:10.1155/2024/3087296",
        "note": "Alkaliphilic isolate whose best growth is at high external pH, cited in this trait's artifact for alkaliphile physiology."
      }
    ]
  },
  {
    "identifier": "METPO:1000455",
    "label": "pH optimum low",
    "definition": "A pH optimum phenotype with the best-growth external pH at or below approximately 6, corresponding to acidophilic or extreme-acidophilic physiology.",
    "definition_source": "DOI:10.1038/nrmicro2549",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000331"
    ],
    "synonyms": [
      {
        "synonym_text": "Acid Tolerant",
        "synonym_type": "EXACT_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "Acidophile",
        "synonym_type": "EXACT_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "Extreme Acidophile",
        "synonym_type": "EXACT_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "Facultative acidophile",
        "synonym_type": "EXACT_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "Obligative acidophile",
        "synonym_type": "EXACT_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "pHO_0_to_6",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/nrmicro2549",
        "snippet": "growing at pH 1.0-3.0",
        "notes": "pH-homeostasis review supports growth at acidic external pH as the acidophilic / extreme-acidophilic category."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:46632",
        "taxon_label": "Picrophilus oshimae",
        "reference": "DOI:10.1007/s007920050044",
        "note": "Picrophilus oshimae has a directly measured growth optimum near pH 0.7, wholly below the approximately pH 6 upper bound for this bin."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "ph_optimum_low_acidophile_setpoint",
        "title": "pH-optimum-low acidophile setpoint",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a quantitative measurement, interval, or bin in the environmental phenotype hierarchy; a token protein example would misrepresent the measured value as one inherited molecular mechanism.",
        "description": "DOI-backed graph linking proton-exclusion physiology at acidic external pH to a pH-optimum at or below 6 (acidophile / extreme acidophile).",
        "nodes": [
          {
            "node_id": "ph_optimum_low_trait",
            "label": "pH optimum low",
            "node_type": "TRAIT",
            "grounding": "METPO:1000455",
            "description": "pH optimum at or below ~6."
          },
          {
            "node_id": "ph_optimum",
            "label": "pH optimum",
            "node_type": "TRAIT",
            "grounding": "METPO:1000331",
            "description": "External pH supporting maximal growth."
          },
          {
            "node_id": "acidic_external_ph",
            "label": "acidic external pH",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "External pH \u2264 ~6, typical of acidic mine drainage and acidic soils.",
            "grounding": "PATO:0001429"
          },
          {
            "node_id": "acidophile_proton_exclusion",
            "label": "acidophile proton-exclusion physiology",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Low-permeability membranes and reversed membrane potential that exclude protons in acidophiles."
          },
          {
            "node_id": "low_external_ph",
            "label": "low external pH",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Acidic medium external pH below ~3 imposing a steep proton gradient."
          },
          {
            "node_id": "transmembrane_ph_gradient",
            "label": "large transmembrane pH gradient",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Steep outside-to-inside proton (delta pH) gradient maintained by acidophiles."
          },
          {
            "node_id": "reversed_membrane_potential",
            "label": "inside-positive (reversed) membrane potential",
            "node_type": "STATE",
            "description": "Reversed (inside-positive) membrane potential creating an electrochemical barrier to proton influx."
          },
          {
            "node_id": "proton_influx",
            "label": "proton influx",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Passive entry of protons into the cytoplasm down the pH gradient."
          },
          {
            "node_id": "proton_pumping_respiratory_complexes",
            "label": "proton-pumping respiratory complexes",
            "node_type": "GENE_OR_PROTEIN",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed as a contextual protein or protein-complex label within a quantitative measurement graph; no exact semantic family term was established for this aggregate use.",
            "description": "Respiratory chain complexes (I, III, IV) that actively extrude cytoplasmic protons."
          },
          {
            "node_id": "cytoplasmic_proton_load",
            "label": "cytoplasmic proton load",
            "node_type": "STATE",
            "description": "Concentration of protons in the cytoplasm threatening near-neutral intracellular pH."
          },
          {
            "node_id": "proton_impermeable_membrane",
            "label": "rigid proton-impermeable membrane",
            "node_type": "CELLULAR_LOCALIZATION",
            "description": "Rigid membrane highly resistant to proton influx, reducing passive proton permeability."
          },
          {
            "node_id": "passive_proton_permeability",
            "label": "passive proton permeability",
            "node_type": "QUALITY",
            "description": "Rate of passive proton leakage across the cell membrane."
          }
        ],
        "edges": [
          {
            "subject": "acidic_external_ph",
            "predicate": "selects for",
            "object": "acidophile_proton_exclusion",
            "description": "Acidic environments select for proton-exclusion physiology.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.tim.2007.02.005",
                "snippet": "highly impermeable cell membranes",
                "notes": "Supports envelope-based proton barriers as the selected acidophile mechanism."
              }
            ],
            "predicate_id": "METPO:2007401"
          },
          {
            "subject": "acidophile_proton_exclusion",
            "predicate": "confers",
            "object": "ph_optimum_low_trait",
            "description": "Acidophile proton-exclusion physiology yields an acidic pH-optimum setpoint.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2549",
                "snippet": "growing at pH 1.0-3.0",
                "notes": "Supports growth at strongly acidic pH as the acidophile outcome."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "ph_optimum_low_trait",
            "predicate": "is a",
            "object": "ph_optimum",
            "description": "pH optimum low is a quantitative bin of the pH-optimum phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2549",
                "snippet": "cytoplasmic pH",
                "notes": "Supports an acidic optimum as a value within the pH-optimum distribution."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "low_external_ph",
            "predicate": "drives",
            "object": "transmembrane_ph_gradient",
            "description": "Acidic external pH forces acidophiles to sustain a large transmembrane pH gradient.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2549",
                "notes": "cytoplasmic pH ~6.0 while growing at external pH <3; broad physiological input edge."
              }
            ]
          },
          {
            "subject": "reversed_membrane_potential",
            "predicate": "counteracts",
            "object": "proton_influx",
            "description": "A reversed inside-positive membrane potential electrostatically opposes proton entry.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2549",
                "notes": "sustain a large delta pH with a reversed inside-positive membrane potential; hallmark of extreme acidophiles."
              },
              {
                "reference": "DOI:10.3389/fmicb.2023.1149903",
                "notes": "inside positive membrane potential creates an electrochemical barrier to proton influx."
              }
            ]
          },
          {
            "subject": "proton_pumping_respiratory_complexes",
            "predicate": "removes",
            "object": "cytoplasmic_proton_load",
            "description": "Proton-pumping respiratory complexes actively extrude protons to lower cytoplasmic proton load.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2549",
                "notes": "increased expression of proton-pumping respiratory chain complexes; broad mechanism, specific complexes vary by lineage."
              }
            ]
          },
          {
            "subject": "proton_impermeable_membrane",
            "predicate": "decreases",
            "object": "passive_proton_permeability",
            "description": "A rigid proton-impermeable membrane reduces passive proton leak and the energetic burden of pH homeostasis.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2023.1149903",
                "notes": "rigid and impermeable membrane that is highly resistant to the influx of protons; high-level trait edge."
              }
            ],
            "predicate_id": "RO:0002212"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.826407+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-13T10:00:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed definition and causal graph linking acidophile proton-exclusion physiology to the pH-optimum-low bin.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:30Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d71, rdfs:subClassOf\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T21:30:06Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007401\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T08:14:32Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (PATO:0001428\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-15T07:21:43Z",
        "curator": "claude",
        "action": "FIX_NODE_GROUNDING_CURIE",
        "changes": "Overwrote 1 pH causal-node grounding(s) to corrected PATO CURIEs (phase-2; verified vs OAK).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 4 evidence-backed generic edges (8 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:10Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002212\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates (1 to confers), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-21T08:00:00Z",
        "curator": "codex",
        "action": "NORMALISE_NODE_TYPE",
        "changes": "Tranche 5 of issue 356 settles the process/quality families and merges ids that meant the same sense: reversed_membrane_potential is STATE. A reversed membrane potential is an inside-positive electrical state, not the process that establishes it. The schema names this gradient/steady-value distinction explicitly.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope ph_optimum_low_acidophile_setpoint=NONMECHANISTIC with scope_notes; marked 1 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (proton_pumping_respiratory_complexes).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T04:43:24Z",
        "curator": "codex",
        "action": "ADD_CANONICAL_EXAMPLES",
        "changes": "Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Picrophilus oshimae (NCBITaxon:46632; DOI:10.1007/s007920050044). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000456",
    "label": "pH optimum mid1",
    "definition": "A pH optimum phenotype with the best-growth external pH between approximately 6 and 7, corresponding to neutrophilic physiology.",
    "definition_source": "DOI:10.1038/nrmicro2549",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000331"
    ],
    "synonyms": [
      {
        "synonym_text": "Alkali Tolerant",
        "synonym_type": "EXACT_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "Neutrophile",
        "synonym_type": "EXACT_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "pHO_6_to_7",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/nrmicro2549",
        "snippet": "cytoplasmic pH",
        "notes": "pH-homeostasis review supports a near-neutral external pH as the neutrophilic optimum, where cytoplasmic pH homeostasis operates with minimal load."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:2593654",
        "taxon_label": "Pseudomonas mangiferae",
        "reference": "DOI:10.1099/ijsem.0.003657",
        "note": "Pseudomonas mangiferae DMKU BBB3-04T grew optimally at pH 6.5, wholly within the approximately pH 6-7 bin; growth was reported at pH 6-8."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "ph_optimum_mid1_neutrophile_setpoint",
        "title": "pH-optimum-mid1 neutrophile setpoint",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a quantitative measurement, interval, or bin in the environmental phenotype hierarchy; a token protein example would misrepresent the measured value as one inherited molecular mechanism.",
        "description": "DOI-backed graph linking minimal pH-homeostasis load at near-neutral external pH to a pH-optimum between 6 and 7 (neutrophile).",
        "nodes": [
          {
            "node_id": "ph_optimum_mid1_trait",
            "label": "pH optimum mid1",
            "node_type": "TRAIT",
            "grounding": "METPO:1000456",
            "description": "pH optimum approximately 6\u20137."
          },
          {
            "node_id": "ph_optimum",
            "label": "pH optimum",
            "node_type": "TRAIT",
            "grounding": "METPO:1000331",
            "description": "External pH supporting maximal growth."
          },
          {
            "node_id": "near_neutral_external_ph",
            "label": "near-neutral external pH",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "External pH 6\u20137, typical of fresh-water and many host environments.",
            "grounding": "PATO:0001428"
          },
          {
            "node_id": "minimal_ph_homeostasis_load",
            "label": "minimal pH-homeostasis load",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Modest demand on proton extrusion and cytoplasmic buffering near a near-neutral cytoplasmic pH."
          },
          {
            "node_id": "f0f1_atpase",
            "label": "F0F1-ATPase",
            "node_type": "GENE_OR_PROTEIN",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed as a contextual protein or protein-complex label within a quantitative measurement graph; no exact semantic family term was established for this aggregate use.",
            "description": "F-type ATP synthase/ATPase functioning as a proton pump."
          },
          {
            "node_id": "proton",
            "label": "proton (H+)",
            "node_type": "CHEMICAL",
            "description": "Hydrogen ion (H+), the determinant of pH."
          },
          {
            "node_id": "amino_acid_decarboxylation",
            "label": "amino-acid decarboxylation pathways",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Glutamate/lysine/arginine decarboxylase pathways that consume cytoplasmic protons."
          },
          {
            "node_id": "gad_gaba_pathway",
            "label": "glutamate decarboxylation / GABA pathway",
            "node_type": "PATHWAY",
            "description": "Glutamate decarboxylase / GABA shunt pathway consuming intracellular H+."
          },
          {
            "node_id": "ammonia",
            "label": "ammonia (NH3)",
            "node_type": "CHEMICAL",
            "description": "Ammonia, a base that scavenges protons."
          },
          {
            "node_id": "ammonium",
            "label": "ammonium (NH4+)",
            "node_type": "CHEMICAL",
            "description": "Ammonium ion formed when ammonia binds a proton."
          }
        ],
        "edges": [
          {
            "subject": "near_neutral_external_ph",
            "predicate": "imposes",
            "object": "minimal_ph_homeostasis_load",
            "description": "Near-neutral external pH imposes minimal pH-homeostasis demand on the cell.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2549",
                "snippet": "cytoplasmic pH",
                "notes": "Supports near-neutral external pH as the regime with the smallest cytoplasmic-pH gradient to maintain."
              }
            ]
          },
          {
            "subject": "minimal_ph_homeostasis_load",
            "predicate": "confers",
            "object": "ph_optimum_mid1_trait",
            "description": "Minimal pH-homeostasis load yields a neutrophilic pH-optimum setpoint.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2549",
                "snippet": "pH homeostasis",
                "notes": "Supports a near-neutral optimum as the neutrophile outcome."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "ph_optimum_mid1_trait",
            "predicate": "is a",
            "object": "ph_optimum",
            "description": "pH optimum mid1 is a quantitative bin of the pH-optimum phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.tim.2007.02.005",
                "snippet": "proton motive force",
                "notes": "Supports a near-neutral optimum as a value within the pH-optimum distribution."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "f0f1_atpase",
            "predicate": "exports",
            "object": "proton",
            "description": "The F0F1-ATPase actively exports protons to maintain cytoplasmic pH.",
            "evidence": [
              {
                "reference": "DOI:10.1371/journal.ppat.1011927",
                "notes": "actively exporting protons via proton pumps such as the F0F1-ATPase; classic pH-homeostasis mechanism."
              }
            ],
            "predicate_id": "METPO:2007804"
          },
          {
            "subject": "amino_acid_decarboxylation",
            "predicate": "consumes",
            "object": "proton",
            "description": "Amino-acid decarboxylation pathways consume cytoplasmic protons, supporting pH homeostasis.",
            "evidence": [
              {
                "reference": "DOI:10.1371/journal.ppat.1011927",
                "notes": "consume protons through amino-acid decarboxylation pathways (glutamate, lysine, arginine); general acid-resistance edge."
              }
            ],
            "predicate_id": "biolink:consumes"
          },
          {
            "subject": "gad_gaba_pathway",
            "predicate": "consumes",
            "object": "proton",
            "description": "The glutamate decarboxylation / GABA pathway consumes intracellular H+.",
            "evidence": [
              {
                "reference": "DOI:10.1128/aem.00569-24",
                "notes": "glutamate-based systems and the GABA metabolic pathway consume H+."
              }
            ],
            "predicate_id": "biolink:consumes"
          },
          {
            "subject": "ammonia",
            "predicate": "binds",
            "object": "proton",
            "description": "Ammonia binds free protons, buffering against acidification.",
            "evidence": [
              {
                "reference": "DOI:10.1128/aem.00569-24",
                "notes": "generated NH3 bind with intracellular free H+ to form NH4+; direct acid-buffering chemistry, generalizable."
              }
            ]
          },
          {
            "subject": "ammonia",
            "predicate": "forms",
            "object": "ammonium",
            "description": "Ammonia combines with a proton to form ammonium, sequestering acid.",
            "evidence": [
              {
                "reference": "DOI:10.1128/aem.00569-24",
                "notes": "generated NH3 bind with intracellular free H+ to form NH4+."
              }
            ],
            "predicate_id": "biolink:produces"
          },
          {
            "subject": "f0f1_atpase",
            "predicate": "contributes to",
            "object": "minimal_ph_homeostasis_load",
            "description": "Proton export by the F0F1-ATPase keeps the cytoplasmic-pH gradient small near neutral, contributing to minimal homeostasis load.",
            "evidence": [
              {
                "reference": "DOI:10.1371/journal.ppat.1011927",
                "notes": "Proton pumping via F0F1-ATPase maintains cytosolic pH; near-neutral external pH minimizes the pumping demand."
              }
            ],
            "predicate_id": "RO:0002326"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.827192+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-13T10:00:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed definition and causal graph linking minimal pH-homeostasis load at near-neutral external pH to the neutrophilic pH-optimum-mid1 bin.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:30Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d71, rdfs:subClassOf\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T08:14:32Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (PATO:0001432\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-15T07:21:43Z",
        "curator": "claude",
        "action": "FIX_NODE_GROUNDING_CURIE",
        "changes": "Overwrote 1 pH causal-node grounding(s) to corrected PATO CURIEs (phase-2; verified vs OAK).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 6 evidence-backed generic edges (6 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:10Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 5 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:consumes\u00d72, METPO:2000209\u00d71, biolink:produces\u00d71, RO:0002326\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates (1 to confers), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T02:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES_PART2",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates onto their causal-graph counterparts (1 to exports), issue 301 part 2. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Each replacement is a 1:1 mirror of its source predicate that changes only the domain, so the claim each edge makes is unchanged and directions are unchanged. The replacements are proposed in proposals/metpo_traitmech_v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-16T02:00:00Z",
        "curator": "claude",
        "action": "NORMALISE_NODE_TYPE",
        "changes": "Under the PATHWAY-vs-BIOLOGICAL_PROCESS rule, one node_id means one thing corpus-wide (issue 356): amino_acid_decarboxylation is typed BIOLOGICAL_PROCESS. PATHWAY is a named, conventionally enumerable multi-step route; BIOLOGICAL_PROCESS is everything else. A REACTION CLASS, not a route. The corpus describes it that way in neutrophilic.yaml -- 'Enzyme-catalyzed decarboxylation reaction that consumes cytoplasmic protons' -- and the wording varies by record, so read that as the family's sense rather than as this record's own text. Named systems that implement it (Gad) would be pathways; the reaction class is not. Was 4 BIOLOGICAL_PROCESS to 2 before this tranche.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope ph_optimum_mid1_neutrophile_setpoint=NONMECHANISTIC with scope_notes; marked 1 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (f0f1_atpase).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T04:43:24Z",
        "curator": "codex",
        "action": "ADD_CANONICAL_EXAMPLES",
        "changes": "Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Pseudomonas mangiferae (NCBITaxon:2593654; DOI:10.1099/ijsem.0.003657). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000457",
    "label": "pH optimum mid2",
    "definition": "A pH optimum phenotype with the best-growth external pH between approximately 7 and 8, corresponding to neutrophilic or moderately alkaliphilic physiology.",
    "definition_source": "DOI:10.1038/nrmicro2549",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000331"
    ],
    "synonyms": [
      {
        "synonym_text": "Alkali Tolerant",
        "synonym_type": "EXACT_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "Alkaliphile",
        "synonym_type": "EXACT_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "Neutrophile",
        "synonym_type": "EXACT_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "pHO_7_to_8",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/nrmicro2549",
        "snippet": "pH homeostasis",
        "notes": "pH-homeostasis review supports the 7\u20138 external-pH range as the common neutrophile / moderately alkaline-tolerant optimum."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:3080537",
        "taxon_label": "Rubellicoccus peritrichatus",
        "reference": "DOI:10.1099/ijsem.0.006325",
        "note": "Rubellicoccus peritrichatus CR14T had an optimum of pH 7.6, a point value wholly within the approximately pH 7-8 bin; its measured range was pH 6-9."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "ph_optimum_mid2_alkaline_tolerant_setpoint",
        "title": "pH-optimum-mid2 alkaline-tolerant setpoint",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a quantitative measurement, interval, or bin in the environmental phenotype hierarchy; a token protein example would misrepresent the measured value as one inherited molecular mechanism.",
        "description": "DOI-backed graph linking modest alkaline pH-homeostasis at slightly basic external pH to a pH-optimum between 7 and 8.",
        "nodes": [
          {
            "node_id": "ph_optimum_mid2_trait",
            "label": "pH optimum mid2",
            "node_type": "TRAIT",
            "grounding": "METPO:1000457",
            "description": "pH optimum approximately 7\u20138."
          },
          {
            "node_id": "ph_optimum",
            "label": "pH optimum",
            "node_type": "TRAIT",
            "grounding": "METPO:1000331",
            "description": "External pH supporting maximal growth."
          },
          {
            "node_id": "slightly_alkaline_external_ph",
            "label": "slightly alkaline external pH",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "External pH 7\u20138, typical of seawater and many host body fluids."
          },
          {
            "node_id": "modest_alkaline_homeostasis",
            "label": "modest alkaline pH homeostasis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Mild K+/H+ antiport and cytoplasmic acidification activity maintaining cytoplasmic pH at slightly basic external pH."
          },
          {
            "node_id": "cytoplasmic_buffering_capacity",
            "label": "cytoplasmic buffering capacity",
            "node_type": "CAPACITY",
            "description": "Buffering of the cytoplasm (e.g. phosphate pools) absorbing pH fluctuations."
          },
          {
            "node_id": "intracellular_ph_homeostasis",
            "label": "intracellular pH homeostasis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Regulation maintaining cytoplasmic pH near neutral."
          },
          {
            "node_id": "na_h_antiporters",
            "label": "Na+/H+ antiporters",
            "node_type": "GENE_OR_PROTEIN",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed as a contextual protein or protein-complex label within a quantitative measurement graph; no exact semantic family term was established for this aggregate use.",
            "description": "Sodium:proton antiporters that acidify the cytoplasm when internal pH is too high."
          },
          {
            "node_id": "k_h_antiporters",
            "label": "K+/H+ antiporters",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Potassium:proton antiporters regulating bacterial internal pH.",
            "grounding": "GO:0015386"
          },
          {
            "node_id": "respiratory_proton_pumping",
            "label": "proton-pumping respiratory chain components",
            "node_type": "PATHWAY",
            "description": "Respiratory electron transport chain components that pump protons."
          },
          {
            "node_id": "metabolite_decarboxylation",
            "label": "metabolite decarboxylation pathways",
            "node_type": "PATHWAY",
            "description": "Decarboxylation reactions whose free-energy change can be stored as PMF."
          },
          {
            "node_id": "proton_motive_force",
            "label": "proton motive force",
            "node_type": "STATE",
            "description": "Electrochemical proton gradient (\u0394pH + \u0394\u03c8) across the membrane.",
            "grounding": "METPO:1007500"
          },
          {
            "node_id": "f0f1_atp_synthase",
            "label": "F0F1-ATP synthase",
            "node_type": "GENE_OR_PROTEIN",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed as a contextual multisubunit ATP-synthase complex in a quantitative pH bin; no one component family represents the whole complex.",
            "description": "Proton-transporting ATP synthase complex that makes ATP from PMF."
          }
        ],
        "edges": [
          {
            "subject": "slightly_alkaline_external_ph",
            "predicate": "engages",
            "object": "modest_alkaline_homeostasis",
            "description": "Slightly alkaline external pH engages modest alkaline pH-homeostasis.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.tim.2007.02.005",
                "snippet": "proton motive force",
                "notes": "Supports balanced proton motive force at slightly alkaline pH as the energetic setting of this regime."
              }
            ]
          },
          {
            "subject": "modest_alkaline_homeostasis",
            "predicate": "confers",
            "object": "ph_optimum_mid2_trait",
            "description": "Modest alkaline pH-homeostasis yields a neutrophile / alkaline-tolerant pH-optimum setpoint.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2549",
                "snippet": "pH homeostasis",
                "notes": "Supports the 7\u20138 optimum as the neutrophile / mild-alkaliphile outcome."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "ph_optimum_mid2_trait",
            "predicate": "is a",
            "object": "ph_optimum",
            "description": "pH optimum mid2 is a quantitative bin of the pH-optimum phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2549",
                "snippet": "cytoplasmic pH",
                "notes": "Supports the 7\u20138 optimum as a value within the pH-optimum distribution."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "cytoplasmic_buffering_capacity",
            "predicate": "stabilizes",
            "object": "intracellular_ph_homeostasis",
            "description": "Cytoplasmic buffering capacity stabilizes intracellular pH against fluctuations.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuad033",
                "notes": "Buffering capacity of the cytoplasm absorbs pH fluctuations; broad bacterial mechanism supporting near-neutral pHi at external pH 7-8."
              }
            ]
          },
          {
            "subject": "na_h_antiporters",
            "predicate": "maintains",
            "object": "intracellular_ph_homeostasis",
            "description": "Na+/H+ antiporters acidify the cytoplasm when pHi is too high, maintaining pH homeostasis.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuad033",
                "notes": "Proton-sensing antiporters acidify the cytoplasm by exporting Na+ for protons when internal pH gets too high; general mechanism relevant at external pH 7-8."
              }
            ]
          },
          {
            "subject": "k_h_antiporters",
            "predicate": "regulates",
            "object": "intracellular_ph_homeostasis",
            "description": "K+/H+ antiporters are key regulators of bacterial internal pH.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuad033",
                "notes": "Na+/H+ and K+/H+ antiporters are key regulators of bacterial pH homeostasis; general regulator."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "respiratory_proton_pumping",
            "predicate": "maintains",
            "object": "intracellular_ph_homeostasis",
            "description": "Proton-pumping respiratory chain components prevent the internal pH from becoming too low.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuad033",
                "notes": "Activation of proton-pumping respiratory chains prevents internal pH becoming too low; broad statement across respiratory bacteria."
              }
            ]
          },
          {
            "subject": "metabolite_decarboxylation",
            "predicate": "generates",
            "object": "proton_motive_force",
            "description": "Metabolite decarboxylation pathways store free energy as proton motive force.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuad033",
                "notes": "The free energy change from decarboxylation reactions can be stored as a proton motive force; general, not taxon-specific."
              }
            ],
            "predicate_id": "biolink:produces"
          },
          {
            "subject": "proton_motive_force",
            "predicate": "powers",
            "object": "f0f1_atp_synthase",
            "description": "Proton motive force powers F0F1-ATP synthase ATP synthesis.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuad033",
                "notes": "The proton motive force can be used by F0F1-ATP synthase to make ATP; strong general bioenergetic edge."
              }
            ],
            "predicate_id": "METPO:2007900"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.827757+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-13T10:00:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed definition and causal graph linking modest alkaline pH-homeostasis to the neutrophile / mild-alkaliphile pH-optimum-mid2 bin.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:30Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d71, rdfs:subClassOf\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 6 evidence-backed generic edges (8 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:10Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002211\u00d71, biolink:produces\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-26T07:15:17Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A1Z4VR00\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates (1 to confers), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-15T02:00:00Z",
        "curator": "claude",
        "action": "NORMALISE_NODE_TYPE",
        "changes": "Normalised causal-node type(s) so one node_id means one thing corpus-wide (issue 356): cytoplasmic_buffering_capacity: BIOLOGICAL_PROCESS -> CAPACITY; proton_motive_force: BIOLOGICAL_PROCESS -> STATE. A reservoir, not a process: the playbook's CAPACITY table names this node explicitly as the reservoir sense ('Capacity of cytoplasmic buffers to absorb pH fluctuations'). The lone BIOLOGICAL_PROCESS occurrence (ph_optimum_mid2.yaml) describes 'Buffering of the cytoplasm (e.g. phosphate pools) absorbing pH fluctuations' -- the same pool the other three call a capacity. The schema's OWN example of STATE: 'a bioenergetic or molecular state of the cell (e.g. proton motive force ...) ... the state is the gradient / steady-value, not its establishment'. All 35 occurrences describe the gradient -- every description across all four types reads 'electrochemical proton gradient', including the 13 typed BIOLOGICAL_PROCESS ('Transmembrane electrochemical gradient generated by respiration'), which name the gradient and its provenance rather than the generating process. Nothing here means the establishment, so this is a retype and not a rename; records that DO mean the process already use a separate id (proton_motive_force_generation in ph_delta.yaml). Also settles the one edge #356 was filed for: phototrophic.yaml's CAPACITY typing was blocking `powers` (METPO:2007900), which is gated to BIOLOGICAL_PROCESS|STATE.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-20T07:10:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (METPO:1007500\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-22T04:26:15Z",
        "curator": "codex",
        "action": "REVIEW_UNIPROT_INSTANCE_GROUNDINGS",
        "changes": "Reviewed 1 organism-specific UniProtKB grounding(s): replaced 1 with taxon-agnostic GO/InterPro terms and retracted 0 to label-only where no exact semantic term was supported (docs/GROUNDING_POLICY.md).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope ph_optimum_mid2_alkaline_tolerant_setpoint=NONMECHANISTIC with scope_notes; marked 2 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (na_h_antiporters, f0f1_atp_synthase).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T04:43:24Z",
        "curator": "codex",
        "action": "ADD_CANONICAL_EXAMPLES",
        "changes": "Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Rubellicoccus peritrichatus (NCBITaxon:3080537; DOI:10.1099/ijsem.0.006325). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T06:33:01Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007900\u00d71).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000531",
    "label": "pH phenotype with numerical limits",
    "definition": "A phenotype characterized by specific pH values or ranges that define growth or activity limits.",
    "definition_source": "DOI:10.1038/nrmicro2549",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/nrmicro2549",
        "snippet": "Diverse mechanisms for pH sensing and cytoplasmic pH homeostasis enable most bacteria to tolerate or grow at external pH values",
        "notes": "Verified against the open PMC manuscript of the Krulwich et al. review; external pH is the quantitative environmental axis represented by pH-growth numerical-limit phenotypes."
      },
      {
        "reference": "DOI:10.1016/j.tim.2007.02.005",
        "snippet": "proton motive force",
        "notes": "pH-homeostasis review supports the proton motive force across the cell envelope as the physical link between external pH and microbial growth physiology."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:83333",
        "taxon_label": "Escherichia coli K-12",
        "reference": "DOI:10.1371/journal.pone.0018960",
        "note": "E. coli K-12 W3110 growth was measured across buffered external pH conditions; TolC affected maximal exponential growth at pH 4.5-6.0 but not 6.5-8.5, exemplifying a quantitative pH-growth phenotype."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "ph_phenotype_numerical_axis",
        "title": "pH numerical-limits and homeostasis context axis",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a quantitative measurement, interval, or bin in the environmental phenotype hierarchy; a token protein example would misrepresent the measured value as one inherited molecular mechanism.",
        "description": "DOI-backed nonmechanistic graph connecting the external-pH measurement axis and pH optimum, range, and delta subclasses with contextual PMF, F0F1-ATPase, antiporter, amino-acid decarboxylase, and cytoplasmic-buffering branches.",
        "nodes": [
          {
            "node_id": "ph_phenotype_trait",
            "label": "pH phenotype with numerical limits",
            "node_type": "TRAIT",
            "grounding": "METPO:1000531",
            "description": "Phenotype defined by a numerical external-pH descriptor."
          },
          {
            "node_id": "external_ph_axis",
            "label": "external pH axis",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "External proton activity (pH) as a continuous environmental variable."
          },
          {
            "node_id": "ph_optimum",
            "label": "pH optimum",
            "node_type": "TRAIT",
            "grounding": "METPO:1000331",
            "description": "External pH supporting the most efficient growth."
          },
          {
            "node_id": "ph_range",
            "label": "pH range",
            "node_type": "TRAIT",
            "grounding": "METPO:1000332",
            "description": "Span of external pH values supporting growth."
          },
          {
            "node_id": "ph_delta",
            "label": "pH delta",
            "node_type": "TRAIT",
            "grounding": "METPO:1000232",
            "description": "Breadth (max \u2212 min) of the growth-supporting external pH range."
          },
          {
            "node_id": "proton_motive_force",
            "label": "proton motive force across cell envelope",
            "node_type": "STATE",
            "description": "Electrochemical proton gradient across the cell envelope linking external pH to bioenergetics."
          },
          {
            "node_id": "f0f1_atpase",
            "label": "F0F1-ATPase / ATP synthase",
            "node_type": "GENE_OR_PROTEIN",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed as a contextual protein or protein-complex label within a quantitative measurement graph; no exact semantic family term was established for this aggregate use.",
            "description": "Membrane ATP synthase coupling proton motive force to ATP synthesis."
          },
          {
            "node_id": "atp_synthesis_from_pmf",
            "label": "ATP synthesis from proton motive force",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Synthesis of ATP driven by the transmembrane proton gradient."
          },
          {
            "node_id": "na_h_antiport_activity",
            "label": "Na+/H+ antiporter activity",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "Cation/proton antiport activity regulating internal pH and PMF."
          },
          {
            "node_id": "k_h_antiporter",
            "label": "K+/H+ antiporter activity",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "Potassium/proton antiport activity regulating internal pH and PMF."
          },
          {
            "node_id": "internal_ph_pmf",
            "label": "internal pH / proton motive force",
            "node_type": "STATE",
            "description": "Regulated cytoplasmic pH and proton motive force homeostatic set-point."
          },
          {
            "node_id": "aa_decarboxylase_antiporter",
            "label": "amino-acid decarboxylase + antiporter systems",
            "node_type": "PATHWAY",
            "description": "Decarboxylation-antiport cycles that consume cytoplasmic protons."
          },
          {
            "node_id": "intracellular_proton",
            "label": "intracellular H+",
            "node_type": "CHEMICAL",
            "description": "Cytoplasmic protons whose concentration sets internal pH."
          },
          {
            "node_id": "phosphate_buffering",
            "label": "cytoplasmic phosphate buffering",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Buffering of cytoplasmic protons by intracellular phosphate pools."
          },
          {
            "node_id": "internal_ph",
            "label": "internal pH",
            "node_type": "STATE",
            "description": "Cytoplasmic pH maintained by homeostatic mechanisms."
          }
        ],
        "edges": [
          {
            "subject": "external_ph_axis",
            "predicate": "defines",
            "object": "ph_phenotype_trait",
            "description": "External pH is the quantitative axis defining pH phenotypes.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2549",
                "snippet": "external pH values that are outside",
                "notes": "Verified against the open PMC manuscript of the Krulwich et al. review; microbial pH phenotypes are expressed relative to external growth pH values and internal pH-homeostatic limits."
              }
            ],
            "predicate_id": "METPO:2007500"
          },
          {
            "subject": "ph_optimum",
            "predicate": "is a",
            "object": "ph_phenotype_trait",
            "description": "pH optimum is a numerical-limit pH phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2549",
                "snippet": "cytoplasmic pH",
                "notes": "Supports pH optimum as the external-pH set-point at which cytoplasmic pH homeostasis sustains maximal growth."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "ph_range",
            "predicate": "is a",
            "object": "ph_phenotype_trait",
            "description": "pH range is a numerical-limit pH phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.tim.2007.02.005",
                "snippet": "proton motive force",
                "notes": "Supports pH range as the span of external pH over which the proton motive force remains compatible with growth."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "ph_delta",
            "predicate": "is a",
            "object": "ph_phenotype_trait",
            "description": "pH delta is a numerical-limit pH phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2549",
                "snippet": "pH homeostasis",
                "notes": "Supports pH delta (range breadth) as a derived numerical descriptor reflecting pH-homeostasis flexibility."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "external_ph_axis",
            "predicate": "regulates",
            "object": "proton_motive_force",
            "description": "External pH influences the proton motive force across the cell envelope.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuad033",
                "snippet": "cells maintain their cytoplasmic pH around neutral",
                "notes": "Verified against the open Poolman review; maintaining near-neutral cytoplasmic pH makes external pH a major determinant of the transmembrane pH-gradient component of the PMF."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "f0f1_atpase",
            "predicate": "enables",
            "object": "atp_synthesis_from_pmf",
            "description": "F0F1-ATPase couples the proton motive force to ATP synthesis.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuad033",
                "snippet": "stored in the form of a proton motive force, which subsequently can be used by F0F1-ATP synthase to make ATP",
                "notes": "Verified against the open Poolman review; the PMF links proton translocation by the F0F1-ATPase to ATP synthesis."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "na_h_antiport_activity",
            "predicate": "regulates",
            "object": "internal_ph_pmf",
            "description": "Na+/H+ antiporter activity regulates internal pH and PMF.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuad033",
                "snippet": "Proton-sensing ion/H+ antiporters acidify the cytoplasm by exporting K+ or Na+ in exchange for protons when the internal pH gets too high",
                "notes": "Verified against the open Poolman review; Na+/H+ antiporters are listed as key bacterial pH-homeostasis regulators."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "k_h_antiporter",
            "predicate": "regulates",
            "object": "internal_ph_pmf",
            "description": "K+/H+ antiporter activity regulates internal pH and PMF.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuad033",
                "snippet": "Key regulators of bacterial pH homeostasis are Na+/H+ and K+/H+ antiporters",
                "notes": "Verified against the open Poolman review; K+/H+ antiporters are listed as key bacterial pH-homeostasis regulators."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "aa_decarboxylase_antiporter",
            "predicate": "consumes",
            "object": "intracellular_proton",
            "description": "Amino-acid decarboxylase plus antiporter systems consume intracellular protons, raising internal pH.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuad033",
                "snippet": "the chemistry of the decarboxylation reaction requires a proton",
                "notes": "Verified against the open Poolman review; substrate decarboxylation consumes a cytoplasmic proton and raises internal pH."
              }
            ],
            "predicate_id": "biolink:consumes"
          },
          {
            "subject": "phosphate_buffering",
            "predicate": "contributes to",
            "object": "internal_ph",
            "description": "Cytoplasmic phosphate pools contribute to internal-pH stability.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuad033",
                "snippet": "sufficient buffering capacity (e.g. inorganic and organic phosphates)",
                "notes": "Verified against the open Poolman review; cytoplasmic phosphate pools are named as sufficient buffering capacity needed for internal-pH stability."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "atp_synthesis_from_pmf",
            "predicate": "associated with",
            "object": "proton_motive_force",
            "description": "F0F1-coupled ATP synthesis from the PMF is associated with the PMF branch of pH numerical-limit context.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuad033",
                "snippet": "drive the synthesis of ATP and the transport of solutes",
                "notes": "Verified against the open Poolman review; this connector keeps PMF-driven ATP synthesis as bioenergetic context rather than direct proof of a pH numerical limit."
              }
            ],
            "predicate_id": "biolink:associated_with"
          },
          {
            "subject": "internal_ph_pmf",
            "predicate": "associated with",
            "object": "proton_motive_force",
            "description": "Regulated internal pH and PMF homeostasis is associated with the PMF branch of pH numerical-limit context.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuad033",
                "snippet": "Cells use different transport mechanisms to interconvert the \u0394\u03a8 and \u0394pH to simultaneously maintain a relatively constant PMF and internal pH",
                "notes": "Verified against the open Poolman review; this connector keeps Na+/H+ and K+/H+ antiport activity as pH-homeostasis context rather than a universal mechanism for every pH bin."
              }
            ],
            "predicate_id": "biolink:associated_with"
          },
          {
            "subject": "intracellular_proton",
            "predicate": "associated with",
            "object": "internal_ph",
            "description": "Intracellular proton consumption is associated with cytoplasmic pH homeostasis in the pH numerical-limit context.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuad033",
                "snippet": "the internal pH is increased",
                "notes": "Verified against the open Poolman review; this connector keeps amino-acid decarboxylation as cytoplasmic proton control context."
              }
            ],
            "predicate_id": "biolink:associated_with"
          },
          {
            "subject": "internal_ph",
            "predicate": "associated with",
            "object": "ph_phenotype_trait",
            "description": "Cytoplasmic pH homeostasis is associated with external-pH numerical-limit phenotypes.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuad033",
                "snippet": "the magnitude of the pH gradient is largely determined by the external pH",
                "notes": "Verified against the open Poolman review; this connector keeps internal-pH homeostasis as measured external-pH phenotype context rather than direct proof of a measured external-pH limit."
              }
            ],
            "predicate_id": "biolink:associated_with"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.845918+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-13T10:00:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed causal graph linking the external pH axis to pH optimum, range, and delta measurement types.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:30Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (rdfs:subClassOf\u00d73).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T07:37:39Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007500\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 6 evidence-backed generic edges (10 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:10Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 4 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002211\u00d72, RO:0002327\u00d71, biolink:consumes\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-15T02:00:00Z",
        "curator": "claude",
        "action": "NORMALISE_NODE_TYPE",
        "changes": "Normalised causal-node type(s) so one node_id means one thing corpus-wide (issue 356): proton_motive_force: BIOLOGICAL_PROCESS -> STATE. The schema's OWN example of STATE: 'a bioenergetic or molecular state of the cell (e.g. proton motive force ...) ... the state is the gradient / steady-value, not its establishment'. All 35 occurrences describe the gradient -- every description across all four types reads 'electrochemical proton gradient', including the 13 typed BIOLOGICAL_PROCESS ('Transmembrane electrochemical gradient generated by respiration'), which name the gradient and its provenance rather than the generating process. Nothing here means the establishment, so this is a retype and not a rename; records that DO mean the process already use a separate id (proton_motive_force_generation in ph_delta.yaml). Also settles the one edge #356 was filed for: phototrophic.yaml's CAPACITY typing was blocking `powers` (METPO:2007900), which is gated to BIOLOGICAL_PROCESS|STATE.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-15T06:00:00Z",
        "curator": "claude",
        "action": "SPLIT_PROTEIN_FROM_ACTIVITY",
        "changes": "Separated the protein sense from the activity sense so one node_id means one thing (issue 356): renamed na_h_antiporter -> na_h_antiport_activity (MOLECULAR_FUNCTION sense). Described as 'Cation/proton antiport ACTIVITY regulating internal pH and PMF', while the six GENE_OR_PROTEIN occurrences describe the transporter ('Membrane antiporter that exports sodium from the cytoplasm in exchange for protons'). na_h_antiport_activity already exists corpus-wide as MOLECULAR_FUNCTION.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-21T08:00:00Z",
        "curator": "codex",
        "action": "NORMALISE_NODE_TYPE",
        "changes": "Tranche 5 of issue 356 settles the process/quality families and merges ids that meant the same sense: phosphate_buffering is BIOLOGICAL_PROCESS. Both occurrences describe cytoplasmic phosphate pools buffering protons and stabilizing pH: the buffering action, not the size of a buffer reservoir. The distinct cytoplasmic_buffering_capacity id remains CAPACITY for that quantity sense.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope ph_phenotype_numerical_axis=NONMECHANISTIC with scope_notes; marked 1 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (f0f1_atpase).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T04:43:24Z",
        "curator": "codex",
        "action": "ADD_CANONICAL_EXAMPLES",
        "changes": "Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Escherichia coli K-12 (NCBITaxon:83333; DOI:10.1371/journal.pone.0018960). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-04T02:20:00Z",
        "curator": "codex",
        "action": "REVIEW_CAUSAL_EVIDENCE",
        "changes": "Reviewed the ph_phenotype_numerical_axis graph for issue #183: added snippets to 1 record-level and 7 edge-level evidence items, and grounded 2 unmapped pH-axis predicates to RO:0002211 or RO:0002326. No paid research service was called.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-04T18:00:00Z",
        "curator": "codex",
        "action": "CONNECT_CAUSAL_GRAPH_COMPONENTS",
        "changes": "Resolved issue #183 graph fragmentation (5 components to 1) by adding 4 source- and verbatim-snippet-backed association connectors among PMF, F0F1-ATPase/ATP-synthesis, antiporter, amino-acid-decarboxylase, and phosphate-buffering branches. No paid research service was called.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-06T17:10:00Z",
        "curator": "codex",
        "action": "ADVERSARIAL_REVIEW_REPAIR",
        "changes": "Addressed PR #664 adversarial review: replaced the weak Poolman pH-homeostasis snippets with exact text supporting decarboxylation-linked proton consumption and internal pH context.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-07T02:20:00Z",
        "curator": "codex",
        "action": "ADVERSARIAL_REVIEW_REPAIR",
        "changes": "Addressed PR #664 adversarial review issue #682: replaced the short Poolman PMF snippet nested inside another connector snippet with exact near-neutral cytoplasmic-pH wording.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-07T04:24:00Z",
        "curator": "codex",
        "action": "ADVERSARIAL_REVIEW_REPAIR",
        "changes": "Addressed PR #664 adversarial review issue #685: replaced weak pH edge snippets with exact source spans that carry their edge claims, and left derived pH-axis bin membership in notes instead of fragment snippets.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-07T06:14:00Z",
        "curator": "codex",
        "action": "ADVERSARIAL_REVIEW_REPAIR",
        "changes": "Addressed PR #664 adversarial review issues #688, #689, and #690: restored record-level Krulwich pH-axis support, replaced cross-trait Poolman antiporter and phosphate-buffering fragments with primary-source spans, and made the PMF connector snippet distinct.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-07T20:05:00Z",
        "curator": "codex",
        "action": "ADVERSARIAL_REVIEW_REPAIR",
        "changes": "Addressed PR #664 adversarial review issues #696, #698, and #699: requoted weak Krulwich pH-homeostasis edge snippets and removed unsupported pH-breadth hub connectors that only joined generic review branches to quantitative bin nodes.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000332",
    "label": "pH range",
    "definition": "A pH phenotype with numerical limits that bounds the minimum and maximum external pH supporting growth of an organism.",
    "definition_source": "DOI:10.1038/nrmicro2549",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000531",
      "METPO:1000535"
    ],
    "created_by": "Luke Wang",
    "evidence": [
      {
        "reference": "DOI:10.1038/nrmicro2549",
        "snippet": "pH homeostasis",
        "notes": "pH-homeostasis review supports the bounded external-pH span over which cytoplasmic pH homeostasis sustains growth as the basis of the pH-range phenotype."
      },
      {
        "reference": "DOI:10.1016/j.tim.2007.02.005",
        "snippet": "highly impermeable cell membranes",
        "notes": "pH-homeostasis review supports envelope-based proton barriers as the mechanism extending growth into acidic and alkaline extremes."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:3028314",
        "taxon_label": "Oceanimonas pelagia",
        "reference": "DOI:10.1007/s10482-024-01948-y",
        "note": "Oceanimonas pelagia NTOU-MSR1T grew at pH 7-10. The complete interval crosses the mid2/mid3 split, so #591 places this distinct claim on the pH-range parent."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "ph_range_bounded_homeostasis",
        "title": "pH-range bounded cytoplasmic homeostasis",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a quantitative measurement, interval, or bin in the environmental phenotype hierarchy; a token protein example would misrepresent the measured value as one inherited molecular mechanism.",
        "description": "DOI-backed graph linking acid- and alkaline-tolerance to the bounded span of growth-supporting external pH.",
        "nodes": [
          {
            "node_id": "ph_range_trait",
            "label": "pH range",
            "node_type": "TRAIT",
            "grounding": "METPO:1000332",
            "description": "Span of external pH values supporting growth."
          },
          {
            "node_id": "external_ph",
            "label": "external pH",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Ambient proton activity (pH) imposed on the cell."
          },
          {
            "node_id": "acid_tolerance",
            "label": "acid tolerance",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Capacity to maintain cytoplasmic pH against an inward H+ gradient at low external pH."
          },
          {
            "node_id": "alkaline_tolerance",
            "label": "alkaline tolerance",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Capacity to maintain cytoplasmic pH against an outward H+ gradient at high external pH."
          },
          {
            "node_id": "bounded_growth_window",
            "label": "bounded pH growth window",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Span of external pH between the minimum and maximum that supports growth."
          },
          {
            "node_id": "ph_gradient",
            "label": "transmembrane pH gradient (\u0394pH)",
            "node_type": "CHEMICAL",
            "description": "Difference between external and cytoplasmic pH, a component of the proton motive force."
          },
          {
            "node_id": "membrane_potential",
            "label": "membrane potential (\u0394\u03c8)",
            "node_type": "CHEMICAL",
            "description": "Electrical component of the proton motive force across the cell membrane."
          },
          {
            "node_id": "cytoplasmic_ph_homeostasis",
            "label": "cytoplasmic pH homeostasis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Maintenance of a near-constant cytoplasmic pH compatible with macromolecular function.",
            "grounding": "GO:0051453"
          },
          {
            "node_id": "membrane_proton_impermeability",
            "label": "membrane proton impermeability",
            "node_type": "QUALITY",
            "description": "Reduced proton leak across the cell membrane that limits passive H+ influx."
          },
          {
            "node_id": "mrp_antiporter_activity",
            "label": "Mrp Na+/H+ antiporter activity",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "Cation/proton antiport that imports protons while exporting Na+ to support pH homeostasis."
          },
          {
            "node_id": "amino_acid_decarboxylation",
            "label": "amino-acid decarboxylation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Glutamate or arginine decarboxylation that consumes intracellular protons and alkalinizes the cytoplasm."
          }
        ],
        "edges": [
          {
            "subject": "external_ph",
            "predicate": "defines",
            "object": "bounded_growth_window",
            "description": "External pH defines the axis over which the growth window is bounded.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2549",
                "snippet": "external pH",
                "notes": "Supports external pH as the axis bounding the growth window."
              }
            ],
            "predicate_id": "METPO:2007500"
          },
          {
            "subject": "acid_tolerance",
            "predicate": "defines",
            "object": "bounded_growth_window",
            "description": "Acid tolerance sets the lower bound of the pH growth window.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.tim.2007.02.005",
                "snippet": "highly impermeable cell membranes",
                "notes": "Supports envelope proton barriers as the lower-bound mechanism for low-pH growth."
              }
            ],
            "predicate_id": "METPO:2007500"
          },
          {
            "subject": "alkaline_tolerance",
            "predicate": "defines",
            "object": "bounded_growth_window",
            "description": "Alkaline tolerance sets the upper bound of the pH growth window.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2549",
                "snippet": "alkaliphiles",
                "notes": "Supports alkaline-tolerance physiology as the upper-bound mechanism for high-pH growth."
              }
            ],
            "predicate_id": "METPO:2007500"
          },
          {
            "subject": "bounded_growth_window",
            "predicate": "manifests as",
            "object": "ph_range_trait",
            "description": "The bounded pH growth window manifests the pH-range phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2549",
                "snippet": "pH homeostasis",
                "notes": "Supports the trait endpoint."
              }
            ],
            "predicate_id": "METPO:2007400"
          },
          {
            "subject": "ph_gradient",
            "predicate": "contributes to",
            "object": "bounded_growth_window",
            "description": "The transmembrane pH gradient sets whether cytoplasmic pH can be maintained across the external pH range.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2549",
                "notes": "PMF architecture (\u0394\u03c8 \u2212 59 \u0394pH) determines the range of pHout over which bacteria can tolerate or grow."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "membrane_potential",
            "predicate": "compensates for",
            "object": "external_ph",
            "description": "Adjustment or reversal of the membrane-potential PMF component offsets extreme external pH stress.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2549",
                "notes": "Under strong pH stress the orientation of a PMF component can reverse to maintain homeostasis."
              }
            ]
          },
          {
            "subject": "cytoplasmic_ph_homeostasis",
            "predicate": "enables",
            "object": "bounded_growth_window",
            "description": "Keeping cytoplasmic pH compatible with protein function enables growth across the external pH range.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2549",
                "notes": "Bacteria maintain a distinct cytoplasmic pH required for protein function, bounding the phenotype."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "membrane_proton_impermeability",
            "predicate": "extends",
            "object": "acid_tolerance",
            "description": "Reduced proton leak helps maintain cytoplasmic pH and extends growth to lower external pH.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2020.556140",
                "notes": "Modification of membrane lipid composition to reduce proton permeability is a general acid-stress mechanism."
              }
            ]
          },
          {
            "subject": "mrp_antiporter_activity",
            "predicate": "supports",
            "object": "alkaline_tolerance",
            "description": "Na+/H+ exchange imports protons and is a principal strategy for alkaline pH homeostasis.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2549",
                "notes": "Na+/H+ antiport is the principal strategy for cytoplasmic pH homeostasis at high external pH."
              }
            ]
          },
          {
            "subject": "amino_acid_decarboxylation",
            "predicate": "alkalinizes",
            "object": "cytoplasmic_ph_homeostasis",
            "description": "Glutamate or arginine decarboxylation consumes intracellular protons, supporting cytoplasmic pH at acidic external pH.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2020.556140",
                "notes": "Decarboxylation of glutamate or arginine is a recurring proton-consuming acid-response module."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.815188+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-13T10:00:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed causal graph linking acid- and alkaline-tolerance to the bounded pH-range phenotype.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T21:30:06Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007400\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T07:37:39Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007500\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-26T05:00:47Z",
        "curator": "claude",
        "action": "RENAME_PREDICATE_LABELS",
        "changes": "Renamed 2 causal-edge predicate label(s) to align with existing groundings: sets \u2192 defines \u00d72.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-26T05:00:50Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007500\u00d72).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 6 evidence-backed generic edges (6 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:10Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002326\u00d71, RO:0002327\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:17Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0051453\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-16T02:00:00Z",
        "curator": "claude",
        "action": "NORMALISE_NODE_TYPE",
        "changes": "Under the PATHWAY-vs-BIOLOGICAL_PROCESS rule, one node_id means one thing corpus-wide (issue 356): amino_acid_decarboxylation is typed BIOLOGICAL_PROCESS. PATHWAY is a named, conventionally enumerable multi-step route; BIOLOGICAL_PROCESS is everything else. A REACTION CLASS, not a route. The corpus describes it that way in neutrophilic.yaml -- 'Enzyme-catalyzed decarboxylation reaction that consumes cytoplasmic protons' -- and the wording varies by record, so read that as the family's sense rather than as this record's own text. Named systems that implement it (Gad) would be pathways; the reaction class is not. Was 4 BIOLOGICAL_PROCESS to 2 before this tranche.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope ph_range_bounded_homeostasis=NONMECHANISTIC with scope_notes.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T04:43:24Z",
        "curator": "codex",
        "action": "ADD_CANONICAL_EXAMPLES",
        "changes": "Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Oceanimonas pelagia (NCBITaxon:3028314; DOI:10.1007/s10482-024-01948-y). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000464",
    "label": "pH range high",
    "definition": "A pH range phenotype in which the growth-supporting external pH range spans approximately 10\u201314, characteristic of extreme-alkaliphile physiology.",
    "definition_source": "DOI:10.1038/nrmicro2549",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000332"
    ],
    "synonyms": [
      {
        "synonym_text": "Alkali Tolerant",
        "synonym_type": "EXACT_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "Alkaliphile",
        "synonym_type": "EXACT_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "Extreme Alkaliphile",
        "synonym_type": "EXACT_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "10_to_14",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/nrmicro2549",
        "snippet": "alkaliphiles",
        "notes": "pH-homeostasis review supports extreme-alkaliphile physiology growing at external pH above 10."
      },
      {
        "reference": "DOI:10.1016/j.tim.2007.02.005",
        "snippet": "proton motive force",
        "notes": "pH-homeostasis review supports robust Na+/H+ antiporter activity as the extreme-alkaliphile mechanism sustaining the proton motive force above pH 10."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "ph_range_high_extreme_alkaliphile",
        "title": "pH-range-high extreme-alkaliphile range",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a quantitative measurement, interval, or bin in the environmental phenotype hierarchy; a token protein example would misrepresent the measured value as one inherited molecular mechanism.",
        "description": "DOI-backed graph linking extreme-alkaliphile Na+/H+ antiporter activity to a pH growth range extending above 10.",
        "nodes": [
          {
            "node_id": "ph_range_high_trait",
            "label": "pH range high",
            "node_type": "TRAIT",
            "grounding": "METPO:1000464",
            "description": "pH growth-supporting range extending above ~10."
          },
          {
            "node_id": "ph_range",
            "label": "pH range",
            "node_type": "TRAIT",
            "grounding": "METPO:1000332",
            "description": "Span of external pH values supporting growth."
          },
          {
            "node_id": "extreme_alkaliphile_antiport",
            "label": "extreme-alkaliphile Na+/H+ antiport",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Robust Na+/H+ antiporter activity importing H+ at strongly alkaline external pH."
          },
          {
            "node_id": "mrp_antiporter_complex",
            "label": "Mrp Na+/H+ antiporter complex",
            "node_type": "GENE_OR_PROTEIN",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed as a contextual protein or protein-complex label within a quantitative measurement graph; no exact semantic family term was established for this aggregate use.",
            "description": "Hetero-oligomeric CPA3-family Na+/H+ antiporter complex essential at high external pH.",
            "gene_symbols": [
              "mrpA",
              "mrpB",
              "mrpC",
              "mrpD",
              "mrpE",
              "mrpF",
              "mrpG"
            ],
            "operon": "mrpA-G"
          },
          {
            "node_id": "membrane_potential",
            "label": "transmembrane potential (delta-psi)",
            "node_type": "QUALITY",
            "description": "Large transmembrane electrical potential energizing electrogenic cation/H+ antiport."
          },
          {
            "node_id": "na_solute_symporters",
            "label": "Na+/solute symporters",
            "node_type": "GENE_OR_PROTEIN",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed as a contextual protein or protein-complex label within a quantitative measurement graph; no exact semantic family term was established for this aggregate use.",
            "description": "Symporters re-importing Na+ with solutes to supply cytoplasmic Na+ for antiport."
          },
          {
            "node_id": "cytoplasmic_na",
            "label": "cytoplasmic Na+",
            "node_type": "CHEMICAL",
            "description": "Intracellular sodium pool required to sustain alkaliphile antiport activity."
          },
          {
            "node_id": "f1fo_atp_synthase",
            "label": "F1Fo-ATP synthase",
            "node_type": "GENE_OR_PROTEIN",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed as a contextual protein or protein-complex label within a quantitative measurement graph; no exact semantic family term was established for this aggregate use.",
            "description": "Proton-translocating ATP synthase whose proton uptake contributes to pH homeostasis."
          },
          {
            "node_id": "alkaline_ph_homeostasis",
            "label": "alkaline pH homeostasis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Maintenance of a near-neutral cytoplasmic pH against a strongly alkaline exterior."
          },
          {
            "node_id": "external_ph_high",
            "label": "external pH > 10.3",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Strongly alkaline external pH above ~10.3."
          },
          {
            "node_id": "carbonate_speciation",
            "label": "carbonate (CO3 2-) speciation",
            "node_type": "CHEMICAL",
            "description": "Shift of dissolved inorganic carbon toward carbonate at high pH."
          }
        ],
        "edges": [
          {
            "subject": "extreme_alkaliphile_antiport",
            "predicate": "confers",
            "object": "ph_range_high_trait",
            "description": "Robust Na+/H+ antiport enables growth at pH > 10.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.tim.2007.02.005",
                "snippet": "proton motive force",
                "notes": "Supports antiporter-driven proton re-import as the extreme-alkaliphile mechanism."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "ph_range_high_trait",
            "predicate": "is a",
            "object": "ph_range",
            "description": "pH range high is a quantitative bin of the pH-range phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2549",
                "snippet": "alkaliphiles",
                "notes": "Supports the pH 10\u201314 range as a value within the pH-range distribution."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "mrp_antiporter_complex",
            "predicate": "confers",
            "object": "ph_range_high_trait",
            "description": "The hetero-oligomeric Mrp antiporter has an indispensable role in growth at high pH.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2549",
                "notes": "The unusual hetero-oligomeric Mrp antiporter has an indispensable role at high pH."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "membrane_potential",
            "predicate": "drives",
            "object": "mrp_antiporter_complex",
            "description": "A large transmembrane potential drives electrogenic Na+/H+ antiport that imports H+.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2549",
                "notes": "A large transmembrane potential is essential to drive electrogenic Na+/H+ and K+/H+ antiporters that import H+."
              }
            ]
          },
          {
            "subject": "na_solute_symporters",
            "predicate": "supplies",
            "object": "cytoplasmic_na",
            "description": "Na+/solute symporters supply the cytoplasmic Na+ required to sustain antiport activity.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2549",
                "notes": "The ongoing requirement for cytoplasmic Na+ to support high levels of alkaliphile antiport activity is met by numerous Na+/solute symporters."
              }
            ]
          },
          {
            "subject": "cytoplasmic_na",
            "predicate": "enables",
            "object": "extreme_alkaliphile_antiport",
            "description": "Cytoplasmic Na+ is the substrate that sustains high levels of alkaliphile antiport activity.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2549",
                "notes": "Cytoplasmic Na+ is required to support high levels of alkaliphile antiport activity."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "f1fo_atp_synthase",
            "predicate": "contributes to",
            "object": "alkaline_ph_homeostasis",
            "description": "Proton uptake accompanying ATP synthesis contributes to alkaliphile pH homeostasis.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2549",
                "notes": "The proton uptake that accompanies ATP synthesis by the F1Fo-ATP synthase contributes to alkaliphile pH homeostasis."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "alkaline_ph_homeostasis",
            "predicate": "confers",
            "object": "ph_range_high_trait",
            "description": "Maintenance of cytoplasmic pH homeostasis enables growth at strongly alkaline external pH.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2549",
                "notes": "Alkaline pH homeostasis underlies extreme-alkaliphile growth above pH 10."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "external_ph_high",
            "predicate": "shifts speciation toward",
            "object": "carbonate_speciation",
            "description": "External pH above ~10.3 shifts dissolved inorganic carbon speciation toward carbonate.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.01557-23",
                "notes": "DIC speciation shifts strongly with pH, toward CO3= above ~10.3."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.832881+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-13T10:00:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed definition and causal graph linking extreme-alkaliphile Na+/H+ antiport to the pH-range-high bin.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:30Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d71, rdfs:subClassOf\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 8 evidence-backed generic edges (9 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:10Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 5 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d73, biolink:encodes\u00d71, RO:0002326\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 3 causal edge(s) off enables/RO:0002327 with a TRAIT object (3 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-07T04:00:00Z",
        "curator": "claude",
        "action": "REGROUND_CAUSAL_EDGE",
        "changes": "Re-grounded the `encodes` edge(s) from biolink:encodes to METPO:2007813, issue 342. biolink:encodes is NOT a slot in the pinned biolink 4.4.0 model, so the CURIE resolved to nothing upstream while looking like an upstream term to anyone reading this record -- the disclaimer saying otherwise lived in mappings/predicate_grounding.tsv, which is not read at the point of use. RO:0002205 (has gene product) is the nearest real term but relates a GENE to a gene product, whereas these edges relate a gene cluster or operon to a protein complex or a biosynthetic process, which its range does not admit; that mismatch is why the coinage existed. METPO:2007813 is proposed in proposals/metpo_traitmech_v9 and is a placeholder id until METPO mints it, which puts it in the same state as the rest of that cohort rather than in a category of its own.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-07T18:00:00Z",
        "curator": "claude",
        "action": "REGROUND_CAUSAL_EDGE",
        "changes": "Edge cytoplasmic_na -> mrp_antiporter_complex in graph ph_range_high_extreme_alkaliphile: repointed it to cytoplasmic_na -> extreme_alkaliphile_antiport. Issue 334. biolink declares enables range 'biological process or activity', which of CausalNodeTypeEnum only BIOLOGICAL_PROCESS, PATHWAY and MOLECULAR_FUNCTION satisfy, so this edge entailed a false type on its object. The record already says it: 'Cytoplasmic Na+ is the substrate that sustains high levels of alkaliphile antiport activity.' The ANTIPORT is what the Na+ pool sustains, and that node is in the same graph.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope ph_range_high_extreme_alkaliphile=NONMECHANISTIC with scope_notes; marked 3 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (mrp_antiporter_complex, na_solute_symporters, f1fo_atp_synthase); removed 1 node(s) and 1 edge(s) together with their evidence (mrp_operon).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T04:43:24Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed issue #444 after #591 and left canonical_examples empty: No retrieved primary source established a natural organism whose complete growth interval is contained in pH 10-14. Sources that merely grow above pH 10 also extend below the bin and therefore remain parent-level evidence under #591. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000460",
    "label": "pH range low",
    "definition": "A pH range phenotype in which the growth-supporting external pH range spans approximately 4\u20136, characteristic of acidophilic physiology.",
    "definition_source": "DOI:10.1038/nrmicro2549",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000332"
    ],
    "synonyms": [
      {
        "synonym_text": "Acid Tolerant",
        "synonym_type": "EXACT_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "Acidophile",
        "synonym_type": "EXACT_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "Facultative acidophile",
        "synonym_type": "EXACT_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "Obligative acidophile",
        "synonym_type": "EXACT_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "pHR_4_to_6",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/nrmicro2549",
        "snippet": "cytoplasmic pH",
        "notes": "pH-homeostasis review supports moderately acidic pH-homeostasis as the basis of growth in the pH 4\u20136 range."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "ph_range_low_acidophile_range",
        "title": "pH-range-low acidophile range",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a quantitative measurement, interval, or bin in the environmental phenotype hierarchy; a token protein example would misrepresent the measured value as one inherited molecular mechanism.",
        "description": "DOI-backed graph linking moderately acidophile pH-homeostasis to a pH growth range of approximately 4\u20136.",
        "nodes": [
          {
            "node_id": "ph_range_low_trait",
            "label": "pH range low",
            "node_type": "TRAIT",
            "grounding": "METPO:1000460",
            "description": "pH growth-supporting range approximately 4\u20136."
          },
          {
            "node_id": "ph_range",
            "label": "pH range",
            "node_type": "TRAIT",
            "grounding": "METPO:1000332",
            "description": "Span of external pH values supporting growth."
          },
          {
            "node_id": "acidophile_homeostasis",
            "label": "acidophile pH homeostasis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Proton extrusion and envelope barriers maintaining cytoplasmic pH against a moderately acidic external pH."
          },
          {
            "node_id": "proton_motive_force",
            "label": "proton motive force",
            "node_type": "STATE",
            "description": "Transmembrane electrochemical proton gradient maintained by H+ extrusion.",
            "grounding": "METPO:1007500"
          },
          {
            "node_id": "atp_synthase_atp_formation",
            "label": "ATP synthase-mediated ATP formation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Phosphorylation of ADP to ATP driven by the proton motive force."
          },
          {
            "node_id": "cyclopropane_fatty_acids",
            "label": "cyclopropane fatty acids",
            "node_type": "CHEMICAL",
            "description": "Cyclopropane-fatty-acyl phospholipids produced by Cfa synthase that modify the membrane."
          },
          {
            "node_id": "proton_permeability",
            "label": "membrane proton permeability",
            "node_type": "QUALITY",
            "description": "Permeability of the cell membrane to protons."
          },
          {
            "node_id": "undissociated_weak_acids",
            "label": "undissociated weak organic acids",
            "node_type": "CHEMICAL",
            "description": "Protonated, membrane-permeant form of weak organic acids prevalent at low external pH."
          },
          {
            "node_id": "weak_acid_influx",
            "label": "weak organic acid influx into cell",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Diffusion of undissociated weak organic acids across the membrane at low external pH."
          },
          {
            "node_id": "weak_acid_dissociation",
            "label": "intracellular dissociation of weak organic acids",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Dissociation of weak acids in the near-neutral cytoplasm, releasing protons."
          },
          {
            "node_id": "internal_ph",
            "label": "internal (cytoplasmic) pH",
            "node_type": "QUALITY",
            "description": "pH of the cytoplasm."
          },
          {
            "node_id": "h_atpase",
            "label": "H+-ATPase proton efflux pump",
            "node_type": "GENE_OR_PROTEIN",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed as a contextual protein or protein-complex label within a quantitative measurement graph; no exact semantic family term was established for this aggregate use.",
            "description": "ATP-driven proton-exporting ATPase (e.g. P-type H+-ATPase)."
          },
          {
            "node_id": "cytoplasmic_protons",
            "label": "cytoplasmic protons",
            "node_type": "CHEMICAL",
            "description": "Protons (hydrons) within the cytoplasm."
          }
        ],
        "edges": [
          {
            "subject": "acidophile_homeostasis",
            "predicate": "confers",
            "object": "ph_range_low_trait",
            "description": "Acidophile pH-homeostasis enables growth across pH 4\u20136.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2549",
                "snippet": "cytoplasmic pH",
                "notes": "Supports acidophile cytoplasmic pH homeostasis as the moderately-acidic growth-range mechanism."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "ph_range_low_trait",
            "predicate": "is a",
            "object": "ph_range",
            "description": "pH range low is a quantitative bin of the pH-range phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.tim.2007.02.005",
                "snippet": "proton motive force",
                "notes": "Supports the pH 4\u20136 range as a value within the pH-range distribution."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "proton_motive_force",
            "predicate": "drives",
            "object": "atp_synthase_atp_formation",
            "description": "The proton motive force drives ATP synthase phosphorylation of ADP to ATP.",
            "evidence": [
              {
                "reference": "DOI:10.1111/1758-2229.70019",
                "notes": "\"That proton potential then drives the phosphorylation of ADP and the formation of ATP by the ATP synthase\"; general bioenergetic edge relevant to low-pH growth."
              }
            ]
          },
          {
            "subject": "cyclopropane_fatty_acids",
            "predicate": "decreases",
            "object": "proton_permeability",
            "description": "Cyclopropane fatty acid membrane modification decreases proton permeability.",
            "evidence": [
              {
                "reference": "DOI:10.4014/jmb.2303.03009",
                "notes": "\"decreasing membrane proton permeability prevents the accumulation of intracellular protons\" after conversion to cyclopropane fatty acids; generalizable membrane adaptation."
              }
            ],
            "predicate_id": "RO:0002212"
          },
          {
            "subject": "undissociated_weak_acids",
            "predicate": "undergoes",
            "object": "weak_acid_influx",
            "description": "At low external pH weak organic acids are undissociated and diffuse into the cell.",
            "evidence": [
              {
                "reference": "DOI:10.1111/1758-2229.70019",
                "notes": "\"organic acids... occur in their undissociated form and can diffuse into the cell\"; boundary condition distinguishing low-pH growth from weak-acid inhibition."
              }
            ]
          },
          {
            "subject": "weak_acid_dissociation",
            "predicate": "lowers",
            "object": "internal_ph",
            "description": "Intracellular dissociation of weak organic acids releases protons and lowers cytoplasmic pH.",
            "evidence": [
              {
                "reference": "DOI:10.1111/1758-2229.70019",
                "notes": "\"the higher pH of the cytoplasm will lead to dissociation of the acid, thus releasing protons and lowering the internal pH\"; strong causal edge."
              }
            ]
          },
          {
            "subject": "h_atpase",
            "predicate": "exports",
            "object": "cytoplasmic_protons",
            "description": "H+-ATPases actively export protons from the cytoplasm using ATP.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2023.1149903",
                "notes": "Acidophile genomes encode \"a P-type ATPase proton efflux pump\"; active ATP-driven proton export underlies cytoplasmic pH homeostasis."
              }
            ],
            "predicate_id": "METPO:2007804"
          },
          {
            "subject": "h_atpase",
            "predicate": "contributes to",
            "object": "acidophile_homeostasis",
            "description": "ATP-driven proton export by H+-ATPases contributes to acidophile pH homeostasis.",
            "evidence": [
              {
                "reference": "DOI:10.3390/microorganisms12030625",
                "notes": "\"acid stress tolerance... facilitated by an active export of protons via the expenditure of ATP... carried out by H+-ATPases\"; broad principle of homeostasis."
              }
            ],
            "predicate_id": "RO:0002326"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.829744+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-13T10:00:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed definition and causal graph linking acidophile pH-homeostasis to the pH-range-low bin.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:30Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d71, rdfs:subClassOf\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 6 evidence-backed generic edges (10 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:10Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002212\u00d71, METPO:2000209\u00d71, RO:0002326\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 1 causal edge(s) off enables/RO:0002327 with a TRAIT object (1 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T02:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES_PART2",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates onto their causal-graph counterparts (1 to exports), issue 301 part 2. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Each replacement is a 1:1 mirror of its source predicate that changes only the domain, so the claim each edge makes is unchanged and directions are unchanged. The replacements are proposed in proposals/metpo_traitmech_v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-15T02:00:00Z",
        "curator": "claude",
        "action": "NORMALISE_NODE_TYPE",
        "changes": "Normalised causal-node type(s) so one node_id means one thing corpus-wide (issue 356): proton_motive_force: BIOLOGICAL_PROCESS -> STATE. The schema's OWN example of STATE: 'a bioenergetic or molecular state of the cell (e.g. proton motive force ...) ... the state is the gradient / steady-value, not its establishment'. All 35 occurrences describe the gradient -- every description across all four types reads 'electrochemical proton gradient', including the 13 typed BIOLOGICAL_PROCESS ('Transmembrane electrochemical gradient generated by respiration'), which name the gradient and its provenance rather than the generating process. Nothing here means the establishment, so this is a retype and not a rename; records that DO mean the process already use a separate id (proton_motive_force_generation in ph_delta.yaml). Also settles the one edge #356 was filed for: phototrophic.yaml's CAPACITY typing was blocking `powers` (METPO:2007900), which is gated to BIOLOGICAL_PROCESS|STATE.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-20T07:10:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (METPO:1007500\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-21T00:00:00Z",
        "curator": "claude",
        "action": "BACKFILL_CANONICAL_EXAMPLES",
        "changes": "Added 1 exemplar taxon/taxa. Organisms and citations come only from this record's own deep-research artifact; every taxon id was resolved and label-checked against the local NCBITaxon build rather than recalled. Organisms the artifact names as contrast cases rather than exemplars were deliberately excluded.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-21T08:00:00Z",
        "curator": "codex",
        "action": "NORMALISE_NODE_TYPE",
        "changes": "Tranche 5 of issue 356 settles the process/quality families and merges ids that meant the same sense: proton_permeability is QUALITY. Proton permeability is a measurable membrane property, which is the schema's QUALITY sense rather than a biological process.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope ph_range_low_acidophile_range=NONMECHANISTIC with scope_notes; marked 1 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (h_atpase).",
        "llm_assisted": true
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:920",
        "taxon_label": "Acidithiobacillus ferrooxidans",
        "reference": "DOI:10.3390/fermentation10060298",
        "note": "Acidophile growing in the low-pH range this record bounds, cited in its artifact for acidophile physiology."
      }
    ]
  },
  {
    "identifier": "METPO:1000461",
    "label": "pH range mid1",
    "definition": "A pH range phenotype in which the growth-supporting external pH range spans approximately 6\u20137, characteristic of neutrophilic physiology.",
    "definition_source": "DOI:10.1038/nrmicro2549",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000332"
    ],
    "synonyms": [
      {
        "synonym_text": "Alkali Tolerant",
        "synonym_type": "EXACT_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "Facultative acidophile",
        "synonym_type": "EXACT_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "Neutrophile",
        "synonym_type": "EXACT_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "pHR_6_to_7",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/nrmicro2549",
        "snippet": "cytoplasmic pH",
        "notes": "pH-homeostasis review supports near-neutral cytoplasmic pH at near-neutral external pH as the neutrophilic regime."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:575322",
        "taxon_label": "Sphingomonas oligoaromativorans",
        "reference": "DOI:10.1099/ijs.0.052894-0",
        "note": "Sphingomonas oligoaromativorans SY-6T grew only at pH 6.0-7.0 in the type-strain study, with optimum pH 7.0; the complete interval matches this bin."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "ph_range_mid1_neutrophile_range",
        "title": "pH-range-mid1 neutrophile range",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a quantitative measurement, interval, or bin in the environmental phenotype hierarchy; a token protein example would misrepresent the measured value as one inherited molecular mechanism.",
        "description": "DOI-backed graph linking baseline pH-homeostasis at near-neutral external pH to a pH growth range of approximately 6\u20137.",
        "nodes": [
          {
            "node_id": "ph_range_mid1_trait",
            "label": "pH range mid1",
            "node_type": "TRAIT",
            "grounding": "METPO:1000461",
            "description": "pH growth-supporting range approximately 6\u20137."
          },
          {
            "node_id": "ph_range",
            "label": "pH range",
            "node_type": "TRAIT",
            "grounding": "METPO:1000332",
            "description": "Span of external pH values supporting growth."
          },
          {
            "node_id": "baseline_ph_homeostasis",
            "label": "baseline pH homeostasis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Minimal proton-extrusion and buffering activity needed to maintain near-neutral cytoplasmic pH at near-neutral external pH."
          },
          {
            "node_id": "proton_motive_force",
            "label": "proton motive force",
            "node_type": "STATE",
            "description": "Electrochemical proton gradient (PMF) across the cytoplasmic membrane.",
            "grounding": "METPO:1007500"
          },
          {
            "node_id": "cytoplasmic_ph_homeostasis",
            "label": "cytoplasmic pH homeostasis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Maintenance of near-neutral cytoplasmic pH (~7) across the external pH range.",
            "grounding": "GO:0051453"
          },
          {
            "node_id": "cation_proton_antiporters",
            "label": "cation/proton antiporters",
            "node_type": "GENE_OR_PROTEIN",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed as a contextual protein or protein-complex label within a quantitative measurement graph; no exact semantic family term was established for this aggregate use.",
            "description": "Membrane antiporters (e.g. Na+/H+) whose repertoire sets external-pH boundaries for maintaining cytoplasmic pH ~7."
          },
          {
            "node_id": "acid_challenge",
            "label": "acid challenge",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Exposure to acidic external pH below the neutrophilic optimum."
          },
          {
            "node_id": "respiratory_proton_pumping",
            "label": "respiratory proton-pumping complexes",
            "node_type": "GENE_OR_PROTEIN",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed as a contextual protein or protein-complex label within a quantitative measurement graph; no exact semantic family term was established for this aggregate use.",
            "description": "Respiratory chain complexes that extrude protons, upregulated under acid challenge."
          },
          {
            "node_id": "alkaline_challenge",
            "label": "alkaline challenge",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Exposure to alkaline external pH above the neutrophilic optimum."
          }
        ],
        "edges": [
          {
            "subject": "baseline_ph_homeostasis",
            "predicate": "confers",
            "object": "ph_range_mid1_trait",
            "description": "Baseline pH-homeostasis enables growth across pH 6\u20137.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2549",
                "snippet": "pH homeostasis",
                "notes": "Supports baseline pH-homeostasis as the neutrophilic range mechanism."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "ph_range_mid1_trait",
            "predicate": "is a",
            "object": "ph_range",
            "description": "pH range mid1 is a quantitative bin of the pH-range phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2549",
                "snippet": "external pH",
                "notes": "Supports the pH 6\u20137 range as a value within the pH-range distribution."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "proton_motive_force",
            "predicate": "enables",
            "object": "cytoplasmic_ph_homeostasis",
            "description": "PMF (membrane potential) is required to maintain cytoplasmic pH homeostasis.",
            "evidence": [
              {
                "reference": "DOI:10.1103/PRXLife.2.043015",
                "notes": "Terradot et al. 2024: decreasing the PMF's strength impairs the cells' ability to maintain pH."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "cytoplasmic_ph_homeostasis",
            "predicate": "confers",
            "object": "ph_range_mid1_trait",
            "description": "Maintaining near-neutral cytoplasmic pH supports the neutrophilic pH 6-7 growth range.",
            "evidence": [
              {
                "reference": "DOI:10.1103/PRXLife.2.043015",
                "notes": "Cytoplasmic pH held near neutral underlies the neutralophile growth range."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "cation_proton_antiporters",
            "predicate": "determines",
            "object": "cytoplasmic_ph_homeostasis",
            "description": "Transporter repertoire (ClcA/NhaB/NhaA-like antiporters) sets the external-pH boundaries over which cytoplasmic pH ~7 is maintained.",
            "evidence": [
              {
                "reference": "DOI:10.1103/PRXLife.2.043015",
                "notes": "Terradot et al. 2024: ClcA-like ~pHe 2-5, NhaB-like ~5-9, NhaA-like ~9-12 maintain pHi ~7."
              }
            ]
          },
          {
            "subject": "acid_challenge",
            "predicate": "positively regulates",
            "object": "respiratory_proton_pumping",
            "description": "Under acid challenge cells upregulate proton-pumping respiratory complexes (and downregulate ATP synthase) to support pH homeostasis.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2549",
                "notes": "Krulwich et al. 2011: under acid challenge E. coli up-regulates proton-pumping respiratory complexes and down-regulates ATP synthase."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "respiratory_proton_pumping",
            "predicate": "enables",
            "object": "baseline_ph_homeostasis",
            "description": "Proton-pumping respiratory activity contributes to baseline pH homeostasis on the acidic side of the range.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2549",
                "notes": "Krulwich et al. 2011: proton extrusion supports cytoplasmic pH maintenance under acid challenge."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "alkaline_challenge",
            "predicate": "positively regulates",
            "object": "cation_proton_antiporters",
            "description": "Under alkaline challenge cells activate cation/proton antiporters and F1Fo-ATP synthase proton-capture to support pH homeostasis.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2549",
                "notes": "Krulwich et al. 2011: under alkaline stress cells activate inward proton transport via cation/proton antiporters and increase ATP synthase expression."
              }
            ],
            "predicate_id": "RO:0002213"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.830444+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-13T10:00:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed definition and causal graph linking baseline pH-homeostasis at near-neutral external pH to the neutrophilic pH-range-mid1 bin.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:30Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d71, rdfs:subClassOf\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 6 evidence-backed generic edges (6 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:10Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d73).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:17Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0051453\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-04T03:08:13Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002213\u00d72).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 2 causal edge(s) off enables/RO:0002327 with a TRAIT object (2 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-15T02:00:00Z",
        "curator": "claude",
        "action": "NORMALISE_NODE_TYPE",
        "changes": "Normalised causal-node type(s) so one node_id means one thing corpus-wide (issue 356): proton_motive_force: BIOLOGICAL_PROCESS -> STATE. The schema's OWN example of STATE: 'a bioenergetic or molecular state of the cell (e.g. proton motive force ...) ... the state is the gradient / steady-value, not its establishment'. All 35 occurrences describe the gradient -- every description across all four types reads 'electrochemical proton gradient', including the 13 typed BIOLOGICAL_PROCESS ('Transmembrane electrochemical gradient generated by respiration'), which name the gradient and its provenance rather than the generating process. Nothing here means the establishment, so this is a retype and not a rename; records that DO mean the process already use a separate id (proton_motive_force_generation in ph_delta.yaml). Also settles the one edge #356 was filed for: phototrophic.yaml's CAPACITY typing was blocking `powers` (METPO:2007900), which is gated to BIOLOGICAL_PROCESS|STATE.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-20T07:10:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (METPO:1007500\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope ph_range_mid1_neutrophile_range=NONMECHANISTIC with scope_notes; marked 2 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (cation_proton_antiporters, respiratory_proton_pumping).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T04:43:24Z",
        "curator": "codex",
        "action": "ADD_CANONICAL_EXAMPLES",
        "changes": "Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Sphingomonas oligoaromativorans (NCBITaxon:575322; DOI:10.1099/ijs.0.052894-0). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000462",
    "label": "pH range mid2",
    "definition": "A pH range phenotype in which the growth-supporting external pH range spans approximately 7\u20138, characteristic of neutrophile or mild-alkaliphile physiology.",
    "definition_source": "DOI:10.1038/nrmicro2549",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000332"
    ],
    "synonyms": [
      {
        "synonym_text": "Alkali Tolerant",
        "synonym_type": "EXACT_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "Alkaliphile",
        "synonym_type": "EXACT_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "Facultative acidophile",
        "synonym_type": "EXACT_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "Neutrophile",
        "synonym_type": "EXACT_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "pHR_7_to_8",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/nrmicro2549",
        "snippet": "pH homeostasis",
        "notes": "pH-homeostasis review supports modest alkaline-tolerance physiology as the basis of growth across pH 7\u20138."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:2086571",
        "taxon_label": "Solimonas fluminis",
        "reference": "DOI:10.1099/ijsem.0.002865",
        "note": "Solimonas fluminis HR-BBT grew at pH 7-8 in the primary species description; the complete reported interval matches this bin."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "ph_range_mid2_mild_alkaline_tolerance",
        "title": "pH-range-mid2 mild-alkaline-tolerance range",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a quantitative measurement, interval, or bin in the environmental phenotype hierarchy; a token protein example would misrepresent the measured value as one inherited molecular mechanism.",
        "description": "DOI-backed graph linking modest alkaline pH-homeostasis to a pH growth range of approximately 7\u20138.",
        "nodes": [
          {
            "node_id": "ph_range_mid2_trait",
            "label": "pH range mid2",
            "node_type": "TRAIT",
            "grounding": "METPO:1000462",
            "description": "pH growth-supporting range approximately 7\u20138."
          },
          {
            "node_id": "ph_range",
            "label": "pH range",
            "node_type": "TRAIT",
            "grounding": "METPO:1000332",
            "description": "Span of external pH values supporting growth."
          },
          {
            "node_id": "modest_alkaline_tolerance",
            "label": "modest alkaline-tolerance physiology",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Mild K+/H+ antiport and cytoplasmic acidification activity enabling growth at slightly basic external pH."
          },
          {
            "node_id": "external_ph_7_8",
            "label": "external pH 7-8",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Mildly alkaline to neutral external pH condition spanning approximately 7-8."
          },
          {
            "node_id": "cytoplasmic_ph_homeostasis",
            "label": "cytoplasmic pH homeostasis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Maintenance of internal pH near 7.0-7.5 despite external pH variation.",
            "grounding": "GO:0051453"
          },
          {
            "node_id": "cytoplasmic_buffering",
            "label": "cytoplasmic buffering",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Inorganic/organic buffers limit pH fluctuation given very low free proton count."
          },
          {
            "node_id": "na_h_antiport_activity",
            "label": "Na+/H+ antiporter activity",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "Coupled Na+/H+ exchange that acidifies the cytoplasm when internal pH rises."
          },
          {
            "node_id": "proton_motive_force",
            "label": "proton motive force",
            "node_type": "STATE",
            "description": "Composite electrochemical proton gradient used for energy transduction and transport.",
            "grounding": "METPO:1007500"
          },
          {
            "node_id": "external_ph_5_8",
            "label": "external pH 5-8",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "External pH span across which neutralophiles keep PMF relatively constant."
          },
          {
            "node_id": "dpsi_dph_rebalancing",
            "label": "membrane potential / \u0394pH rebalancing",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Shifting relative contributions of \u0394\u03c8 and \u0394pH with external pH to preserve PMF."
          },
          {
            "node_id": "f0f1_atpase",
            "label": "F0F1-ATPase",
            "node_type": "GENE_OR_PROTEIN",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed as a contextual protein or protein-complex label within a quantitative measurement graph; no exact semantic family term was established for this aggregate use.",
            "description": "ATP synthase coupling proton re-entry (PMF) to ATP generation."
          },
          {
            "node_id": "atp_synthesis",
            "label": "ATP synthesis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Generation of ATP driven by the proton motive force.",
            "grounding": "GO:0006754"
          },
          {
            "node_id": "proton_ion_antiporters",
            "label": "proton:ion antiporters",
            "node_type": "GENE_OR_PROTEIN",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed as a contextual protein or protein-complex label within a quantitative measurement graph; no exact semantic family term was established for this aggregate use.",
            "description": "Antiporters with a direct role in sustaining membrane potential."
          },
          {
            "node_id": "membrane_potential",
            "label": "membrane potential (\u0394\u03c8)",
            "node_type": "STATE",
            "description": "Transmembrane electrical potential contributing to PMF."
          }
        ],
        "edges": [
          {
            "subject": "modest_alkaline_tolerance",
            "predicate": "confers",
            "object": "ph_range_mid2_trait",
            "description": "Modest alkaline-tolerance physiology enables growth across pH 7\u20138.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.tim.2007.02.005",
                "snippet": "proton motive force",
                "notes": "Supports balanced proton motive force at slightly alkaline pH as the range mechanism."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "ph_range_mid2_trait",
            "predicate": "is a",
            "object": "ph_range",
            "description": "pH range mid2 is a quantitative bin of the pH-range phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2549",
                "snippet": "cytoplasmic pH",
                "notes": "Supports the pH 7\u20138 range as a value within the pH-range distribution."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "external_ph_7_8",
            "predicate": "associated with",
            "object": "cytoplasmic_ph_homeostasis",
            "description": "External pH 7-8 is associated with cells maintaining internal pH near 7.0-7.5.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuad033",
                "snippet": "internal pH of many cell types is kept within the range of 7.0 to 7.5",
                "notes": "Verified against the open Poolman review; bacterial internal pH is kept near 7.0-7.5 while neutralophilic bacteria maintain PMF across mildly acidic to mildly alkaline external pH."
              }
            ],
            "predicate_id": "biolink:associated_with"
          },
          {
            "subject": "cytoplasmic_buffering",
            "predicate": "contributes to",
            "object": "cytoplasmic_ph_homeostasis",
            "description": "Cytoplasmic buffering contributes to internal pH homeostasis despite very low free-proton counts.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuad033",
                "snippet": "buffering capacity of the cytoplasm",
                "notes": "Verified against the open Poolman review; cytoplasmic buffering is described as important for absorbing pH fluctuations."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "na_h_antiport_activity",
            "predicate": "regulates",
            "object": "cytoplasmic_ph_homeostasis",
            "description": "Na+/H+ antiporter activity regulates cytoplasmic pH homeostasis.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuad033",
                "snippet": "Proton-sensing ion/H+ antiporters acidify the cytoplasm by exporting K+ or Na+ in exchange for protons when the internal pH gets too high",
                "notes": "Verified against the open Poolman review; Na+/H+ antiporters are listed as key bacterial pH-homeostasis regulators and acidifying exchangers when internal pH gets too high."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "external_ph_5_8",
            "predicate": "associated with",
            "object": "proton_motive_force",
            "description": "Neutralophiles keep PMF relatively constant across external pH 5-8.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuad033",
                "snippet": "kept relatively constant in the pH range from 5 to 8",
                "notes": "Verified against the open Poolman review; neutralophilic bacteria are described as maintaining a relatively constant PMF across external pH 5-8."
              }
            ],
            "predicate_id": "biolink:associated_with"
          },
          {
            "subject": "dpsi_dph_rebalancing",
            "predicate": "regulates",
            "object": "proton_motive_force",
            "description": "Rebalancing of \u0394pH and \u0394\u03c8 with external pH regulates PMF.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuad033",
                "snippet": "interconvert the \u0394\u03a8 and \u0394pH",
                "notes": "Verified against the open Poolman review; transport mechanisms are described as interconverting membrane potential and \u0394pH to maintain PMF and internal pH."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "f0f1_atpase",
            "predicate": "enables",
            "object": "atp_synthesis",
            "description": "F0F1-ATPase couples the proton motive force to ATP synthesis.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuad033",
                "snippet": "stored in the form of a proton motive force, which subsequently can be used by F0F1-ATP synthase to make ATP",
                "notes": "Verified against the open Poolman review; the PMF links proton translocation by the F0F1-ATPase to ATP synthesis."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "proton_ion_antiporters",
            "predicate": "generates",
            "object": "membrane_potential",
            "description": "Proton:ion antiporters generate membrane potential in the E. coli pH-homeostasis model.",
            "evidence": [
              {
                "reference": "DOI:10.1103/PRXLife.2.043015",
                "snippet": "use antiporters to generate the plasma membrane potential",
                "notes": "Verified against the open PRX Life abstract; Terradot et al. model proton-ion antiporters as generators of membrane potential and thus PMF in E. coli."
              }
            ],
            "predicate_id": "biolink:produces"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.831107+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-13T10:00:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed definition and causal graph linking modest alkaline-tolerance physiology to the pH-range-mid2 bin.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:30Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d71, rdfs:subClassOf\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 7 evidence-backed generic edges (12 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:17Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0051453\u00d71, GO:0005737\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0006754\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 1 causal edge(s) off enables/RO:0002327 with a TRAIT object (1 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-15T02:00:00Z",
        "curator": "claude",
        "action": "NORMALISE_NODE_TYPE",
        "changes": "Normalised causal-node type(s) so one node_id means one thing corpus-wide (issue 356): proton_motive_force: BIOLOGICAL_PROCESS -> STATE. The schema's OWN example of STATE: 'a bioenergetic or molecular state of the cell (e.g. proton motive force ...) ... the state is the gradient / steady-value, not its establishment'. All 35 occurrences describe the gradient -- every description across all four types reads 'electrochemical proton gradient', including the 13 typed BIOLOGICAL_PROCESS ('Transmembrane electrochemical gradient generated by respiration'), which name the gradient and its provenance rather than the generating process. Nothing here means the establishment, so this is a retype and not a rename; records that DO mean the process already use a separate id (proton_motive_force_generation in ph_delta.yaml). Also settles the one edge #356 was filed for: phototrophic.yaml's CAPACITY typing was blocking `powers` (METPO:2007900), which is gated to BIOLOGICAL_PROCESS|STATE.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-20T07:10:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (METPO:1007500\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope ph_range_mid2_mild_alkaline_tolerance=NONMECHANISTIC with scope_notes; marked 2 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (f0f1_atpase, proton_ion_antiporters).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T04:43:24Z",
        "curator": "codex",
        "action": "ADD_CANONICAL_EXAMPLES",
        "changes": "Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Solimonas fluminis (NCBITaxon:2086571; DOI:10.1099/ijsem.0.002865). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-04T02:40:00Z",
        "curator": "codex",
        "action": "REVIEW_CAUSAL_EVIDENCE",
        "changes": "Reviewed the ph_range_mid2_mild_alkaline_tolerance graph for issue #183: added snippets to 7 edge-level evidence items, grounded 7 unmapped pH-homeostasis predicates, retyped membrane_potential to STATE, and removed the no-longer-used cytoplasm node. No paid research service was called.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-07T04:24:00Z",
        "curator": "codex",
        "action": "ADVERSARIAL_REVIEW_REPAIR",
        "changes": "Addressed PR #664 adversarial review issue #685: replaced weak pH edge snippets with exact source spans that carry their edge claims, and left derived pH-axis bin membership in notes instead of fragment snippets.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-07T07:24:00Z",
        "curator": "codex",
        "action": "ADVERSARIAL_REVIEW_REPAIR",
        "changes": "Addressed PR #664 adversarial review issue #692: normalized the Poolman PMF snippet to quote the source's uppercase membrane potential symbol.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000463",
    "label": "pH range mid3",
    "definition": "A pH range phenotype in which the growth-supporting external pH range spans approximately 8\u201310, characteristic of alkaliphile physiology.",
    "definition_source": "DOI:10.1038/nrmicro2549",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000332"
    ],
    "synonyms": [
      {
        "synonym_text": "Alkali Tolerant",
        "synonym_type": "EXACT_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "Alkaliphile",
        "synonym_type": "EXACT_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "Extreme Alkaliphile",
        "synonym_type": "EXACT_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "Facultative acidophile",
        "synonym_type": "EXACT_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "pHR_8_to_10",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/nrmicro2549",
        "snippet": "alkaliphiles",
        "notes": "pH-homeostasis review supports alkaliphile physiology growing across pH 8\u201310."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:2069301",
        "taxon_label": "Evansella tamaricis",
        "reference": "DOI:10.1099/ijsem.0.002543",
        "note": "The type strain, published as Bacillus tamaricis EGI 80668T and now NCBI-labelled Evansella tamaricis, grew at pH 8-10 with optimum pH 9; the complete interval matches this bin."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "ph_range_mid3_alkaliphile_range",
        "title": "pH-range-mid3 alkaliphile range",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a quantitative measurement, interval, or bin in the environmental phenotype hierarchy; a token protein example would misrepresent the measured value as one inherited molecular mechanism.",
        "description": "DOI-backed graph linking alkaliphile cytoplasmic pH homeostasis to a pH growth range of approximately 8\u201310.",
        "nodes": [
          {
            "node_id": "ph_range_mid3_trait",
            "label": "pH range mid3",
            "node_type": "TRAIT",
            "grounding": "METPO:1000463",
            "description": "pH growth-supporting range approximately 8\u201310."
          },
          {
            "node_id": "ph_range",
            "label": "pH range",
            "node_type": "TRAIT",
            "grounding": "METPO:1000332",
            "description": "Span of external pH values supporting growth."
          },
          {
            "node_id": "alkaliphile_homeostasis",
            "label": "alkaliphile pH homeostasis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Proton re-import via Na+/H+ antiporters maintaining a less alkaline cytoplasm at high external pH."
          },
          {
            "node_id": "mrp_antiporter",
            "label": "Mrp Na+/H+ antiporter complex",
            "node_type": "GENE_OR_PROTEIN",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed as a contextual protein or protein-complex label within a quantitative measurement graph; no exact semantic family term was established for this aggregate use.",
            "description": "Multi-subunit cation/proton antiporter conserved in many alkaliphiles."
          },
          {
            "node_id": "intracellular_ph_homeostasis",
            "label": "intracellular pH homeostasis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Maintenance of a less-alkaline cytoplasm under alkaline external stress."
          },
          {
            "node_id": "nahplus_antiport_activity",
            "label": "Na+/H+ antiport activity",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "Electrogenic exchange importing protons in exchange for sodium ions."
          },
          {
            "node_id": "cytoplasm_acidification",
            "label": "cytoplasm acidification during alkaline growth",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Proton import that acidifies the cytoplasm relative to alkaline medium."
          },
          {
            "node_id": "acidic_cell_wall_polymers",
            "label": "acidic cell-wall polymers (teichuronic acid)",
            "node_type": "CHEMICAL",
            "description": "Negatively charged cell-wall polymers proposed to repel hydroxide and adsorb cations."
          },
          {
            "node_id": "cardiolipin_membrane",
            "label": "cardiolipin-rich negatively charged membrane",
            "node_type": "CELLULAR_LOCALIZATION",
            "description": "Membrane enriched in negatively charged phospholipids including cardiolipin."
          },
          {
            "node_id": "carbonate_buffered_medium",
            "label": "carbonate-buffered alkaline medium",
            "node_type": "EXPERIMENTAL_FACTOR",
            "description": "Sodium carbonate/bicarbonate buffering used to set culture pH around 9.5-10."
          },
          {
            "node_id": "growth_range_observation",
            "label": "observed growth-supporting pH range ~7.5-10.2",
            "node_type": "EXPERIMENTAL_FACTOR",
            "description": "Primary growth-range measurements spanning pH 7.5 to ~10-11."
          }
        ],
        "edges": [
          {
            "subject": "alkaliphile_homeostasis",
            "predicate": "confers",
            "object": "ph_range_mid3_trait",
            "description": "Alkaliphile pH-homeostasis enables growth across pH 8\u201310.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2549",
                "snippet": "alkaliphiles",
                "notes": "Supports alkaliphile cytoplasmic pH homeostasis as the alkaline growth-range mechanism."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "ph_range_mid3_trait",
            "predicate": "is a",
            "object": "ph_range",
            "description": "pH range mid3 is a quantitative bin of the pH-range phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.tim.2007.02.005",
                "snippet": "proton motive force",
                "notes": "Supports the pH 8\u201310 range as a value within the pH-range distribution."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "mrp_antiporter",
            "predicate": "maintains",
            "object": "intracellular_ph_homeostasis",
            "description": "Mrp Na+/H+ antiporter complex maintains intracellular pH homeostasis under alkaline stress.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-022-33640-y",
                "notes": "Mrp antiporters essential for growth of alkaliphilic bacteria under stress, maintaining intracellular pH and sodium homeostasis."
              }
            ]
          },
          {
            "subject": "nahplus_antiport_activity",
            "predicate": "causes",
            "object": "cytoplasm_acidification",
            "description": "Na+/H+ antiport activity acidifies the cytoplasm during alkaline growth.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s13205-021-02938-x",
                "notes": "Alkaliphiles rely on dedicated Na+/H+ antiporters that import H+ in exchange for Na+, acidifying the cytoplasm for pH homeostasis."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "cytoplasm_acidification",
            "predicate": "contributes to",
            "object": "intracellular_ph_homeostasis",
            "description": "Acidification of the cytoplasm contributes to intracellular pH homeostasis at high external pH.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s13205-021-02938-x",
                "notes": "Proton import via antiport acidifies cytoplasm, a core alkaliphile pH-homeostasis mechanism."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "acidic_cell_wall_polymers",
            "predicate": "contributes to",
            "object": "ph_range_mid3_trait",
            "description": "Acidic cell-wall polymers (teichuronic acid) contribute to alkaline pH tolerance.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s13205-021-02938-x",
                "notes": "Alkaliphilic Bacilli reinforce the cell wall with negatively charged teichuronic acid/acidic polymers, hypothesized to repel OH- and adsorb Na+/H+."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "cardiolipin_membrane",
            "predicate": "supports",
            "object": "intracellular_ph_homeostasis",
            "description": "Cardiolipin-rich negatively charged membranes support pH homeostasis at high pH.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s13205-021-02938-x",
                "notes": "Alkaliphiles tend to enrich membranes in negatively charged phospholipids including cardiolipin, noted as especially important for pH homeostasis."
              }
            ]
          },
          {
            "subject": "carbonate_buffered_medium",
            "predicate": "enables observation of",
            "object": "ph_range_mid3_trait",
            "description": "Carbonate-buffered alkaline medium enables assay/observation of the alkaliphile growth phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s13205-023-03733-6",
                "notes": "Alkaliphiles are commonly cultured with sodium carbonate/bicarbonate to set pH around 9.5-10, shaping the measured pH niche."
              }
            ]
          },
          {
            "subject": "growth_range_observation",
            "predicate": "is evidence for",
            "object": "ph_range_mid3_trait",
            "description": "Observed growth across pH ~7.5-10.2 is evidence for the pH range mid3 phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2023.1228266",
                "notes": "C. thermarum grows pH 7.5-11; alkaliphilic methanogens grow 7.5-10.0 and 7.7-10.2, delimiting the pH 8-10 trait scope."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.832120+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-13T10:00:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed definition and causal graph linking alkaliphile pH-homeostasis to the pH-range-mid3 bin.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:30Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d71, rdfs:subClassOf\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 7 evidence-backed generic edges (8 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:11Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002326\u00d72, biolink:causes\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 1 causal edge(s) off enables/RO:0002327 with a TRAIT object (1 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope ph_range_mid3_alkaliphile_range=NONMECHANISTIC with scope_notes; marked 1 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (mrp_antiporter).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T04:43:24Z",
        "curator": "codex",
        "action": "ADD_CANONICAL_EXAMPLES",
        "changes": "Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Evansella tamaricis (NCBITaxon:2069301; DOI:10.1099/ijsem.0.002543). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000459",
    "label": "pH range very low",
    "definition": "A pH range phenotype in which growth extends to external pH at or below approximately 4, characteristic of extreme-acidophile physiology.",
    "definition_source": "DOI:10.1038/nrmicro2549",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000332"
    ],
    "synonyms": [
      {
        "synonym_text": "Acid Tolerant",
        "synonym_type": "EXACT_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "Acidophile",
        "synonym_type": "EXACT_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "Extreme Acidophile",
        "synonym_type": "EXACT_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "Facultative acidophile",
        "synonym_type": "EXACT_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "Obligative acidophile",
        "synonym_type": "EXACT_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "pHR_0_to_4",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/nrmicro2549",
        "snippet": "growing at pH 1.0-3.0",
        "notes": "pH-homeostasis review supports growth in the pH 1\u20134 range as the extreme-acidophile growth range."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:46632",
        "taxon_label": "Picrophilus oshimae",
        "reference": "DOI:10.1007/s007920050044",
        "note": "Picrophilus oshimae is an extreme acidophile whose measured growth extends from approximately pH 0 to pH 4, with optimum near 0.7; the complete interval is confined to this very-low range bin."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "ph_range_very_low_extreme_acidophile",
        "title": "pH-range-very-low extreme-acidophile range",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a quantitative measurement, interval, or bin in the environmental phenotype hierarchy; a token protein example would misrepresent the measured value as one inherited molecular mechanism.",
        "description": "DOI-backed graph linking extreme-acidophile proton-exclusion physiology to a pH growth range reaching \u2264 ~4.",
        "nodes": [
          {
            "node_id": "ph_range_very_low_trait",
            "label": "pH range very low",
            "node_type": "TRAIT",
            "grounding": "METPO:1000459",
            "description": "pH growth-supporting range reaching \u2264 ~4."
          },
          {
            "node_id": "ph_range",
            "label": "pH range",
            "node_type": "TRAIT",
            "grounding": "METPO:1000332",
            "description": "Span of external pH values supporting growth."
          },
          {
            "node_id": "extreme_acidophile_envelope",
            "label": "extreme-acidophile envelope barrier",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Combined low-permeability membrane and reversed membrane potential preventing cytoplasmic acidification at strongly acidic external pH."
          },
          {
            "node_id": "potassium_influx",
            "label": "potassium influx / K+ transport",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Active influx of cations such as K+ across the cytoplasmic membrane."
          },
          {
            "node_id": "reversed_membrane_potential",
            "label": "inside-positive (reversed) membrane potential",
            "node_type": "STATE",
            "description": "Inside-positive transmembrane electrical potential characteristic of extreme acidophiles."
          },
          {
            "node_id": "proton_influx",
            "label": "passive proton influx",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Passive entry of protons/hydronium ions into the cytoplasm down the steep pH gradient."
          },
          {
            "node_id": "low_proton_permeability",
            "label": "low passive proton permeability",
            "node_type": "QUALITY",
            "description": "Low permeability of the cell envelope to passive proton flux."
          },
          {
            "node_id": "near_neutral_cytoplasmic_ph",
            "label": "near-neutral cytoplasmic pH",
            "node_type": "STATE",
            "description": "Maintenance of a near-neutral intracellular pH despite strongly acidic external pH."
          },
          {
            "node_id": "weak_organic_acids",
            "label": "protonated weak organic acids",
            "node_type": "CHEMICAL",
            "description": "Lipophilic protonated weak organic acids (e.g., acetic acid) that can permeate the membrane."
          },
          {
            "node_id": "cytoplasm",
            "label": "cytoplasm",
            "node_type": "CELLULAR_LOCALIZATION",
            "description": "Intracellular cytoplasmic compartment.",
            "grounding": "GO:0005737"
          },
          {
            "node_id": "cytoplasmic_acidification",
            "label": "cytoplasmic acidification",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Acidification of the cytoplasm by influx and dissociation of permeant protons/acids."
          }
        ],
        "edges": [
          {
            "subject": "extreme_acidophile_envelope",
            "predicate": "confers",
            "object": "ph_range_very_low_trait",
            "description": "Extreme-acidophile envelope barriers enable growth at pH \u2264 4.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.tim.2007.02.005",
                "snippet": "reversed membrane potential",
                "notes": "Supports envelope and membrane-potential mechanisms as enablers of growth at strongly acidic pH."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "ph_range_very_low_trait",
            "predicate": "is a",
            "object": "ph_range",
            "description": "pH range very low is a quantitative bin of the pH-range phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2549",
                "snippet": "growing at pH 1.0-3.0",
                "notes": "Supports a very-low pH range as a value within the pH-range distribution."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "potassium_influx",
            "predicate": "causes",
            "object": "reversed_membrane_potential",
            "description": "Active influx of cations such as K+ generates an inside-positive membrane potential.",
            "evidence": [
              {
                "reference": "DOI:10.1128/9781555818821.ch4.3.1",
                "notes": "generate positive (inside) membrane potentials via the active influx of cations, such as K+; mechanism general to acidophiles."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "reversed_membrane_potential",
            "predicate": "decreases",
            "object": "proton_influx",
            "description": "The inside-positive (reversed) membrane potential reduces passive proton influx, supporting a large \u0394pH.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2549",
                "notes": "maintain a large transmembrane \u0394pH supported by a reversed membrane potential (inside-positive); links reversed \u0394\u03c8 to reduced proton entry."
              }
            ],
            "predicate_id": "RO:0002212"
          },
          {
            "subject": "low_proton_permeability",
            "predicate": "enables maintenance of",
            "object": "near_neutral_cytoplasmic_ph",
            "description": "Low passive proton permeability enables maintenance of a near-neutral cytoplasmic pH at acidic external pH.",
            "evidence": [
              {
                "reference": "DOI:10.3389/frbis.2023.1338019",
                "notes": "a low passive proton permeability and a near neutral intracellular pH can be maintained."
              }
            ]
          },
          {
            "subject": "weak_organic_acids",
            "predicate": "diffuse into",
            "object": "cytoplasm",
            "description": "Lipophilic protonated weak organic acids can diffuse across the membrane into the cytoplasm.",
            "evidence": [
              {
                "reference": "DOI:10.1128/9781555818821.ch4.3.1",
                "notes": "lipophilic weak organic acids can diffuse in and acidify the cytoplasm; general principle, key boundary condition for acidophily."
              }
            ]
          },
          {
            "subject": "weak_organic_acids",
            "predicate": "cause",
            "object": "cytoplasmic_acidification",
            "description": "Permeant weak organic acids dissociate inside the cell and acidify the cytoplasm.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.04031-15",
                "notes": "small organic acids can act as uncouplers and acidify the cytoplasm; strong inhibitor edge distinguishing mineral from permeant organic acids."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.829000+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-13T10:00:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed definition and causal graph linking extreme-acidophile envelope barriers to the pH-range-very-low bin.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:30Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d71, rdfs:subClassOf\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 5 evidence-backed generic edges (8 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:11Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:causes\u00d71, METPO:2000017\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:17Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0005737\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 1 causal edge(s) off enables/RO:0002327 with a TRAIT object (1 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T02:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES_PART2",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates onto their causal-graph counterparts (1 to reduces), issue 301 part 2. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Each replacement is a 1:1 mirror of its source predicate that changes only the domain, so the claim each edge makes is unchanged and directions are unchanged. The replacements are proposed in proposals/metpo_traitmech_v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T06:00:00Z",
        "curator": "claude",
        "action": "REGROUND_CAUSAL_EDGE",
        "changes": "Relabelled 1 causal edge from `reduces` to `decreases` and re-grounded it from METPO:2007802 to RO:0002212 (negatively regulates), issue 330. The corpus wrote two senses under the single label `reduces` - genuine electron donation, and a lessens/decreases sense - and METPO:2007802 is defined as donating electrons to the object and lowering its oxidation state, which this edge does not assert. The two senses could not be separated mechanically because the label was identical, so they migrated together in issue 329 and were split here by reading each edge. RO:0002212 declares no rdfs:domain or rdfs:range, so this introduces no entailment of the kind issue 301 removed.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-21T08:00:00Z",
        "curator": "codex",
        "action": "NORMALISE_NODE_TYPE",
        "changes": "Tranche 5 of issue 356 settles the process/quality families and merges ids that meant the same sense: reversed_membrane_potential is STATE. A reversed membrane potential is an inside-positive electrical state, not the process that establishes it. The schema names this gradient/steady-value distinction explicitly.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope ph_range_very_low_extreme_acidophile=NONMECHANISTIC with scope_notes.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T04:43:24Z",
        "curator": "codex",
        "action": "ADD_CANONICAL_EXAMPLES",
        "changes": "Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Picrophilus oshimae (NCBITaxon:46632; DOI:10.1007/s007920050044). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000001",
    "label": "piezophilic",
    "definition": "An environmental growth preference in which an organism grows optimally at hydrostatic pressures substantially above atmospheric pressure (0.1 MPa), characteristic of deep-sea and deep-subsurface microorganisms.",
    "definition_source": "DOI:10.3389/fmolb.2022.1058381",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "synonyms": [
      {
        "synonym_text": "barophilic",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.3389/fmolb.2022.1058381"
      },
      {
        "synonym_text": "piezophile",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.3389/fmolb.2022.1058381"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.3389/fmolb.2022.1058381",
        "snippet": "Microorganisms adapted to HHP are usually known as piezophiles, referring to their preference for high pressure",
        "notes": "Membrane-lipid adaptation review supports the definition of piezophiles as high-hydrostatic-pressure-adapted organisms, with adaptation involving unsaturated and branched-chain fatty acids."
      },
      {
        "reference": "DOI:10.1099/ijsem.0.001671",
        "snippet": "growth range of 80-140 MPa (optimum, 120 MPa) at 6 degrees C",
        "notes": "Organism example: Colwellia marinimaniae strain MTCD1, the most piezophilic organism described, grows optimally at 120 MPa."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1513592",
        "taxon_label": "Colwellia marinimaniae",
        "note": "most piezophilic organism described",
        "reference": "PMID:27902293"
      },
      {
        "taxon_id": "NCBITaxon:74109",
        "taxon_label": "Photobacterium profundum",
        "note": "deep-sea piezophile model",
        "reference": "PMID:15746425"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "piezophilic_hhp_membrane_adaptation",
        "title": "Piezophilic high-pressure preference via membrane lipid adaptation",
        "description": "Evidence-backed causal sketch linking high hydrostatic pressure to unsaturated / branched-chain fatty-acid membrane adaptation enabling optimal high-pressure growth.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a broad environmental or morphological classification spanning multiple mechanisms, a measurement-like bin, or an absence/arrangement descriptor; contextual protein nodes do not receive token UniProt examples.",
        "nodes": [
          {
            "node_id": "piezophilic_trait",
            "label": "piezophilic",
            "node_type": "TRAIT",
            "grounding": "traitmech:000001",
            "description": "Optimal growth at hydrostatic pressures well above atmospheric."
          },
          {
            "node_id": "high_hydrostatic_pressure",
            "label": "high hydrostatic pressure",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Deep-sea / deep-subsurface hydrostatic pressure (tens to >100 MPa)."
          },
          {
            "node_id": "unsaturated_branched_fa",
            "label": "unsaturated / branched-chain fatty acids",
            "node_type": "CHEMICAL",
            "description": "Membrane lipid species maintaining fluidity under high pressure."
          },
          {
            "node_id": "membrane_adaptation",
            "label": "membrane lipid adaptation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Lipid composition adjustment maintaining membrane fluidity under HHP."
          },
          {
            "node_id": "pfa_operon",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "Pfa polyunsaturated-fatty-acid enzyme module",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Protein module forming an omega-3 polyunsaturated fatty acid synthase.",
            "gene_symbols": [
              "pfaA",
              "pfaB",
              "pfaC",
              "pfaD",
              "pfaE"
            ],
            "operon": "pfa"
          },
          {
            "node_id": "omega3_pufa",
            "label": "omega-3 polyunsaturated fatty acids",
            "node_type": "CHEMICAL",
            "description": "Omega-3 PUFAs (e.g. EPA C20:5, DHA C22:6) supporting membrane fluidity under HHP."
          },
          {
            "node_id": "piezolytes",
            "label": "piezolytes (compatible solutes)",
            "node_type": "CHEMICAL",
            "description": "Compatible solutes such as glutamate, betaine, beta-hydroxybutyrate and TMAO that confer pressure tolerance."
          },
          {
            "node_id": "pressure_tolerance",
            "label": "pressure tolerance",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Cellular stabilization against high hydrostatic pressure."
          }
        ],
        "edges": [
          {
            "subject": "high_hydrostatic_pressure",
            "predicate": "selects for",
            "object": "piezophilic_trait",
            "description": "HHP habitats favor optimal-at-pressure growth phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmolb.2022.1058381",
                "notes": "HHP-adapted organisms are termed piezophiles for their preference for high pressure."
              }
            ],
            "predicate_id": "METPO:2007401"
          },
          {
            "subject": "unsaturated_branched_fa",
            "predicate": "enables",
            "object": "membrane_adaptation",
            "description": "Unsaturated and branched-chain fatty acids maintain membrane fluidity under HHP.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmolb.2022.1058381",
                "notes": "Piezophile adaptation involves unsaturated and branched-chain fatty acids."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "membrane_adaptation",
            "predicate": "confers",
            "object": "piezophilic_trait",
            "description": "Membrane lipid adaptation enables high-pressure-optimal growth.",
            "evidence": [
              {
                "reference": "DOI:10.1099/ijsem.0.001671",
                "notes": "Colwellia marinimaniae MTCD1 grows optimally at 120 MPa, supported by HHP-adapted membranes."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "high_hydrostatic_pressure",
            "predicate": "increases",
            "object": "unsaturated_branched_fa",
            "description": "HHP increases abundance of membrane unsaturated and branched-chain fatty acids.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmolb.2022.1058381",
                "notes": "The abundance of membrane lipids containing unsaturated and branched-chain fatty acids rises with increasing HHP."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "pfa_operon",
            "predicate": "produces",
            "object": "omega3_pufa",
            "description": "The pfa operon encodes an omega-3 polyunsaturated fatty acid synthase enabling PUFA production.",
            "evidence": [
              {
                "reference": "DOI:10.3390/microorganisms11071629",
                "notes": "The pfa operon encodes an omega-3 polyunsaturated fatty acid synthase."
              }
            ],
            "predicate_id": "METPO:2007800"
          },
          {
            "subject": "high_hydrostatic_pressure",
            "predicate": "increases",
            "object": "omega3_pufa",
            "description": "HHP increases polyunsaturated fatty acids C20:5 (EPA) and C22:6 (DHA) across multiple piezophilic/piezotolerant taxa.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmolb.2022.1058381",
                "notes": "HHP-driven increases in C20:5/C22:6 in Photobacterium profundum SS9, Psychromonas, and Shewanella piezotolerans WP3."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "omega3_pufa",
            "predicate": "enables",
            "object": "membrane_adaptation",
            "description": "Omega-3 PUFAs maintain membrane fluidity, contributing to lipid adaptation under HHP.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmolb.2022.1058381",
                "notes": "Unsaturated/polyunsaturated fatty acids maintain membrane fluidity under high pressure."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "high_hydrostatic_pressure",
            "predicate": "induces accumulation of",
            "object": "piezolytes",
            "description": "HHP is associated with accumulation of compatible solutes (piezolytes) such as glutamate, betaine and beta-hydroxybutyrate.",
            "evidence": [
              {
                "reference": "DOI:10.3390/microorganisms11071629",
                "notes": "Compatible solutes (piezolytes) detected include glutamate, betaine, and beta-hydroxybutyrate; TMAO acts as a pressure-tolerance molecule."
              }
            ]
          },
          {
            "subject": "piezolytes",
            "predicate": "enables",
            "object": "pressure_tolerance",
            "description": "Piezolytes stabilize cellular components, conferring tolerance to high hydrostatic pressure.",
            "evidence": [
              {
                "reference": "DOI:10.3390/microorganisms11071629",
                "notes": "TMAO and other compatible solutes are highlighted as pressure-tolerance molecules."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "pressure_tolerance",
            "predicate": "contributes to",
            "object": "piezophilic_trait",
            "description": "Pressure tolerance via piezolytes contributes to optimal growth at high pressure.",
            "evidence": [
              {
                "reference": "DOI:10.3390/microorganisms11071629",
                "notes": "Piezolytes support growth and survival under high hydrostatic pressure."
              }
            ],
            "predicate_id": "RO:0002326"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-28T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate ENVIRONMENT trait (high-hydrostatic-pressure growth preference) from literature research to fill the pressure-tolerance coverage gap. Backed by a piezophile adaptation review and a deep-sea organism example.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-09T14:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (HHP membrane adaptation) with RO/METPO predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 7 evidence-backed generic edges (4 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:11Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 6 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d73, RO:0002213\u00d72, RO:0002326\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 1 causal edge(s) off enables/RO:0002327 with a TRAIT object (1 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-07T18:00:00Z",
        "curator": "claude",
        "action": "REGROUND_CAUSAL_EDGE",
        "changes": "Edge pfa_operon -> omega3_pufa in graph piezophilic_hhp_membrane_adaptation: re-grounded it from enables/RO:0002327 to produces/METPO:2007800. Issue 334. biolink declares enables range 'biological process or activity', which of CausalNodeTypeEnum only BIOLOGICAL_PROCESS, PATHWAY and MOLECULAR_FUNCTION satisfy, so this edge entailed a false type on its object. A GENE_OR_PROTEIN subject bringing a CHEMICAL into existence, which is exactly `produces`' declared gate. NOT `encodes`: the operon encodes a SYNTHASE, and the synthase makes the PUFA -- `encodes` does not admit a CHEMICAL object, correctly.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope piezophilic_hhp_membrane_adaptation=NONMECHANISTIC with scope_notes; marked 1 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (pfa_operon).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000003",
    "label": "piezotolerant",
    "definition": "A pressure growth preference in which an organism can grow under elevated hydrostatic pressure but grows at similar or faster rates at atmospheric pressure (0.1 MPa).",
    "definition_source": "DOI:10.3389/fmolb.2022.1058381",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "synonyms": [
      {
        "synonym_text": "barotolerant",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.3389/fmolb.2022.1058381"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.3389/fmolb.2022.1058381",
        "snippet": "Microorganisms adapted to HHP are usually known as piezophiles, referring to their preference for high pressure",
        "notes": "Pressure-adaptation review distinguishes piezotolerant organisms, which withstand high hydrostatic pressure but grow at similar or faster rates at atmospheric pressure, from obligate piezophiles."
      },
      {
        "reference": "DOI:10.1099/ijsem.0.001671",
        "snippet": "growth range of 80-140 MPa (optimum, 120 MPa) at 6 degrees C",
        "notes": "Provides the contrasting obligate-piezophile reference point against which piezotolerant (atmospheric-capable) growth is defined."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:74109",
        "taxon_label": "Photobacterium profundum",
        "note": "piezotolerant/piezophilic deep-sea bacterium",
        "reference": "PMID:15746425"
      },
      {
        "taxon_id": "NCBITaxon:70863",
        "taxon_label": "Shewanella oneidensis",
        "note": "pressure-tolerant",
        "reference": "DOI:10.3389/fmicb.2014.00612"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "piezotolerance_pressure_range",
        "title": "Piezotolerance: growth across atmospheric and elevated pressures",
        "description": "Evidence-backed causal sketch linking adaptation to elevated hydrostatic pressure to growth that is sustained at atmospheric pressure.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a broad environmental or morphological classification spanning multiple mechanisms, a measurement-like bin, or an absence/arrangement descriptor; contextual protein nodes do not receive token UniProt examples.",
        "nodes": [
          {
            "node_id": "piezotolerant_trait",
            "label": "piezotolerant",
            "node_type": "TRAIT",
            "grounding": "traitmech:000003",
            "description": "Growth across atmospheric and elevated hydrostatic pressures."
          },
          {
            "node_id": "hydrostatic_pressure",
            "label": "hydrostatic pressure",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Ambient hydrostatic pressure imposed on the cell.",
            "grounding": "PATO:0001025"
          },
          {
            "node_id": "membrane_adaptation",
            "label": "membrane lipid adaptation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Adjustment of membrane lipid composition under varying pressure."
          },
          {
            "node_id": "membrane_fluidity",
            "label": "membrane fluidity",
            "node_type": "QUALITY",
            "description": "Fluidity of the cell membrane lipid bilayer.",
            "grounding": "METPO:1007505"
          },
          {
            "node_id": "unsaturated_fatty_acids",
            "label": "unsaturated membrane fatty acids",
            "node_type": "CHEMICAL",
            "description": "Unsaturated fatty acids incorporated into membrane lipids."
          },
          {
            "node_id": "branched_unsaturated_fatty_acids",
            "label": "branched-chain and unsaturated membrane fatty acids",
            "node_type": "CHEMICAL",
            "description": "Branched-chain and unsaturated fatty acids enriched in membrane lipids under pressure."
          },
          {
            "node_id": "heat_shock_genes",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "heat-shock response proteins (RpoH, RpoE, DnaK, GroEL)",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Key heat-shock regulators and chaperones upregulated after pressure shock.",
            "gene_symbols": [
              "rpoH",
              "rpoE",
              "dnaK",
              "groEL"
            ]
          },
          {
            "node_id": "piezolyte_accumulation",
            "label": "piezolyte accumulation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Accumulation of compatible solutes (piezolytes) in response to high pressure."
          },
          {
            "node_id": "protein_protection",
            "label": "protein protection under pressure",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Stabilization/protection of proteins under elevated hydrostatic pressure."
          }
        ],
        "edges": [
          {
            "subject": "hydrostatic_pressure",
            "predicate": "regulates",
            "object": "membrane_adaptation",
            "description": "Hydrostatic pressure modulates membrane fluidity, prompting adaptive lipid composition.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmolb.2022.1058381",
                "notes": "HHP adaptation involves unsaturated and branched-chain fatty acids."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "membrane_adaptation",
            "predicate": "confers",
            "object": "piezotolerant_trait",
            "description": "Membrane adaptation supports growth across the pressure range atmospheric \u2194 high.",
            "evidence": [
              {
                "reference": "DOI:10.1099/ijsem.0.001671",
                "notes": "Contrast with obligate piezophiles (growth limited to 80-140 MPa) defines piezotolerant as the atmospheric-capable phenotype."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "hydrostatic_pressure",
            "predicate": "decreases",
            "object": "membrane_fluidity",
            "description": "High hydrostatic pressure compacts fatty acids, reducing membrane fluidity.",
            "evidence": [
              {
                "reference": "DOI:10.3390/microorganisms11071629",
                "notes": "high hydrostatic pressure reduces membrane fluidity by compacting fatty acids"
              }
            ],
            "predicate_id": "RO:0002212"
          },
          {
            "subject": "membrane_fluidity",
            "predicate": "causes increase in",
            "object": "unsaturated_fatty_acids",
            "description": "Reduced membrane fluidity is countered by increasing unsaturated fatty acid proportions.",
            "evidence": [
              {
                "reference": "DOI:10.3390/microorganisms11071629",
                "notes": "organisms counter HHP by increasing the proportions of unsaturated fatty acids"
              }
            ]
          },
          {
            "subject": "hydrostatic_pressure",
            "predicate": "increases abundance of",
            "object": "branched_unsaturated_fatty_acids",
            "description": "Membrane lipids with unsaturated and branched-chain fatty acids increase with rising pressure.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmolb.2022.1058381",
                "notes": "abundance of membrane lipids containing unsaturated and branched-chain fatty acids increases with increasing HHP"
              }
            ]
          },
          {
            "subject": "hydrostatic_pressure",
            "predicate": "induces transcription of",
            "object": "heat_shock_genes",
            "description": "Pressure shock transcriptionally upregulates key heat-shock genes.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2024.1470617",
                "notes": "key heat shock genes rpoH, rpoE, dnaK, and groEL are transcriptionally upregulated following pressure shock"
              }
            ]
          },
          {
            "subject": "hydrostatic_pressure",
            "predicate": "induces accumulation of",
            "object": "piezolyte_accumulation",
            "description": "High pressure induces accumulation of piezolytes (compatible solutes).",
            "evidence": [
              {
                "reference": "DOI:10.3390/microorganisms11071629",
                "notes": "piezolytes are molecules that accumulate in cells in response to high pressure (e.g., glutamate, betaine, beta-hydroxybutyrate)"
              }
            ]
          },
          {
            "subject": "piezolyte_accumulation",
            "predicate": "protects",
            "object": "protein_protection",
            "description": "Accumulated piezolytes protect proteins via preferential hydration under pressure.",
            "evidence": [
              {
                "reference": "DOI:10.3390/microorganisms11071629",
                "notes": "compatible solutes act via preferential hydration to protect proteins"
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-28T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate ENVIRONMENT trait (pressure-tolerant growth) from literature research to complete the pressure-preference axis alongside piezophilic and obligately piezophilic.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-09T14:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (membrane adaptation across pressure range) with RO predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-16T06:54:39Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (PATO:0001025\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 6 evidence-backed generic edges (6 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:11Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002212\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:17Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (METPO:1007505\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 1 causal edge(s) off enables/RO:0002327 with a TRAIT object (1 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope piezotolerance_pressure_range=NONMECHANISTIC with scope_notes; marked 1 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (heat_shock_genes).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000006",
    "label": "pressure delta",
    "definition": "A pressure phenotype with numerical limits expressing the breadth (maximum minus minimum) of hydrostatic pressure supporting growth of an organism.",
    "definition_source": "DOI:10.3389/fmolb.2022.1058381",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.3389/fmolb.2022.1058381",
        "snippet": "Microorganisms adapted to HHP are usually known as piezophiles, referring to their preference for high pressure",
        "notes": "Pressure-adaptation review supports the breadth of the pressure-tolerance span as a derived descriptor of pressure-adaptation flexibility."
      },
      {
        "reference": "DOI:10.1099/ijsem.0.001671",
        "snippet": "growth range of 80-140 MPa (optimum, 120 MPa) at 6 degrees C",
        "notes": "The 80-140 MPa span of Colwellia marinimaniae MTCD1 (delta = 60 MPa) illustrates the breadth this phenotype records."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1513592",
        "taxon_label": "Colwellia marinimaniae",
        "reference": "DOI:10.1099/ijsem.0.001671",
        "note": "The measured 80-140 MPa growth interval of Colwellia marinimaniae MTCD1 at 6 degrees C gives a 60 MPa pressure breadth."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "pressure_delta_breadth_descriptor",
        "title": "Pressure delta: breadth of the pressure-tolerance span",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a quantitative measurement, interval, or bin in the environmental phenotype hierarchy; a token protein example would misrepresent the measured value as one inherited molecular mechanism.",
        "description": "Evidence-backed sketch linking the hydrostatic-pressure axis to the breadth (max \u2212 min) of the growth-supporting pressure range.",
        "nodes": [
          {
            "node_id": "pressure_delta_trait",
            "label": "pressure delta",
            "node_type": "TRAIT",
            "grounding": "traitmech:000006",
            "description": "Breadth (max \u2212 min) of the growth-supporting hydrostatic-pressure range."
          },
          {
            "node_id": "hydrostatic_pressure",
            "label": "hydrostatic pressure",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Ambient hydrostatic pressure imposed on the cell.",
            "grounding": "PATO:0001025"
          },
          {
            "node_id": "pressure_tolerance_breadth",
            "label": "pressure-tolerance breadth",
            "node_type": "QUALITY",
            "description": "Width of the hydrostatic-pressure interval over which growth is sustained."
          },
          {
            "node_id": "membrane_fluidity_maintenance",
            "label": "membrane fluidity maintenance under high pressure",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Maintenance of adequate membrane fluidity against pressure-induced lipid compression."
          },
          {
            "node_id": "membrane_fluidity_loss",
            "label": "loss of membrane fluidity at high pressure",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Pressure-induced reduction of membrane fluidity that impairs membrane function."
          },
          {
            "node_id": "unsaturated_fatty_acid_production",
            "label": "unsaturated fatty acid production",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Biosynthesis/desaturation generating unsaturated acyl chains that counter pressure-induced membrane ordering."
          },
          {
            "node_id": "ribosome_dissociation",
            "label": "pressure-induced ribosome dissociation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "High-pressure dissociation of ribosomes suppressing translation and growth."
          },
          {
            "node_id": "compatible_solutes",
            "label": "intracellular osmolytes / compatible solutes",
            "node_type": "CHEMICAL",
            "description": "Cosolutes/osmolytes that stabilize protein structure under high hydrostatic pressure."
          },
          {
            "node_id": "protein_stabilization_under_pressure",
            "label": "protein stabilization under pressure",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reinforcement of protein structure against pressure-induced perturbation."
          },
          {
            "node_id": "nuo_complex_i",
            "label": "nuo NADH dehydrogenase I complex",
            "node_type": "GENE_OR_PROTEIN",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed as a contextual protein or protein-complex label within a quantitative measurement graph; no exact semantic family term was established for this aggregate use.",
            "description": "Proton-translocating NADH dehydrogenase I (Complex I) operon enriched in piezophiles."
          },
          {
            "node_id": "high_pressure_energy_conservation",
            "label": "high-pressure respiratory energy conservation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Respiratory-chain energy conservation supporting growth under high hydrostatic pressure."
          },
          {
            "node_id": "min_max_growth_pressure_bounds",
            "label": "minimum and maximum growth pressure bounds",
            "node_type": "QUALITY",
            "description": "Lower and upper hydrostatic-pressure limits of growth whose difference defines the delta."
          }
        ],
        "edges": [
          {
            "subject": "hydrostatic_pressure",
            "predicate": "defines",
            "object": "pressure_delta_trait",
            "description": "The hydrostatic-pressure axis defines the values whose max minus min yields the delta.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmolb.2022.1058381",
                "notes": "Pressure-adaptation review frames the breadth of the pressure-tolerance span as a derived descriptor of pressure-adaptation flexibility."
              }
            ],
            "predicate_id": "METPO:2007500"
          },
          {
            "subject": "pressure_delta_trait",
            "predicate": "associated with",
            "object": "pressure_tolerance_breadth",
            "description": "The delta encodes the breadth of pressure-tolerance flexibility.",
            "evidence": [
              {
                "reference": "DOI:10.1099/ijsem.0.001671",
                "notes": "The 80-140 MPa span of Colwellia marinimaniae MTCD1 (delta = 60 MPa) illustrates the breadth this phenotype records."
              }
            ],
            "predicate_id": "biolink:associated_with"
          },
          {
            "subject": "unsaturated_fatty_acid_production",
            "predicate": "enables",
            "object": "membrane_fluidity_maintenance",
            "description": "Unsaturated acyl-chain production/desaturation sustains membrane fluidity under high hydrostatic pressure.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s12864-020-07102-y",
                "notes": "All piezophiles encode a delta-9 acyl-phospholipid desaturase; unsaturated chains allow better adaptation to higher pressures (general HHP mechanism)."
              },
              {
                "reference": "DOI:10.1021/acs.chemrev.3c00432",
                "notes": "Membrane fluidity adjustment is a core pressure-adaptation node."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "hydrostatic_pressure",
            "predicate": "causes",
            "object": "membrane_fluidity_loss",
            "description": "High hydrostatic pressure compresses membranes and reduces fluidity.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2024.1293928",
                "notes": "High pressure causes loss of membrane fluidity (cross-taxa physiological mechanism)."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "membrane_fluidity_loss",
            "predicate": "restricts",
            "object": "pressure_tolerance_breadth",
            "description": "Loss of membrane fluidity limits growth at the upper pressure bound, narrowing the supported range.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s43247-023-01045-4",
                "notes": "Reduced membrane fluidity under HHP coincides with cessation of respiration/degradation, restricting the upper growth bound."
              }
            ]
          },
          {
            "subject": "hydrostatic_pressure",
            "predicate": "causes",
            "object": "ribosome_dissociation",
            "description": "High pressure induces ribosome dissociation, suppressing translation and growth.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s43247-023-01045-4",
                "notes": "High pressure causes ribosome dissociation; translation/replication become dysfunctional, preventing growth and division."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "ribosome_dissociation",
            "predicate": "restricts",
            "object": "pressure_tolerance_breadth",
            "description": "Translation failure from ribosome dissociation limits the growth-supporting pressure range.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s43247-023-01045-4",
                "notes": "Ribosome dissociation preventing growth and division narrows the pressure range over which growth is sustained."
              }
            ]
          },
          {
            "subject": "compatible_solutes",
            "predicate": "enables",
            "object": "protein_stabilization_under_pressure",
            "description": "Intracellular osmolytes/cosolutes reinforce protein structure under high hydrostatic pressure.",
            "evidence": [
              {
                "reference": "DOI:10.1021/acs.chemrev.3c00432",
                "notes": "Osmolytes reinforce the structure of proteins; cosolutes modulate biomolecular function under HHP (general mechanism)."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "nuo_complex_i",
            "predicate": "supports",
            "object": "high_pressure_energy_conservation",
            "description": "The nuo NADH dehydrogenase I complex supports respiratory energy conservation enabling growth under high pressure.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s12864-020-07102-y",
                "notes": "nuo dehydrogenase operons present in piezophiles; respiratory-chain composition modulates pressure tolerance, a candidate contributor to wider high-pressure growth support."
              }
            ]
          },
          {
            "subject": "min_max_growth_pressure_bounds",
            "predicate": "defines",
            "object": "pressure_delta_trait",
            "description": "The minimum and maximum growth-pressure limits define the breadth (max minus min) recorded by the delta.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s12864-020-07102-y",
                "notes": "Range-bound examples (e.g., MTCD1 80-140 MPa => delta = 60 MPa) show min/max bounds defining the pressure-delta breadth descriptor."
              }
            ],
            "predicate_id": "METPO:2007500"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-28T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed quantitative companion trait (pressure-tolerance breadth) mirroring the existing temperature_delta / nacl_delta pattern, to fill the pressure coverage gap.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-09T14:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (pressure-axis defines tolerance breadth) with METPO/biolink predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-16T06:54:39Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (PATO:0001025\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 8 evidence-backed generic edges (9 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:11Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 5 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d72, biolink:causes\u00d72, METPO:2007500\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope pressure_delta_breadth_descriptor=NONMECHANISTIC with scope_notes; marked 1 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (nuo_complex_i).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T04:43:24Z",
        "curator": "codex",
        "action": "ADD_CANONICAL_EXAMPLES",
        "changes": "Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Colwellia marinimaniae (NCBITaxon:1513592; DOI:10.1099/ijsem.0.001671). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000004",
    "label": "pressure optimum",
    "definition": "A pressure phenotype with numerical limits giving the hydrostatic pressure at which an organism grows fastest.",
    "definition_source": "DOI:10.1099/ijsem.0.001671",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1099/ijsem.0.001671",
        "snippet": "growth range of 80-140 MPa (optimum, 120 MPa) at 6 degrees C",
        "notes": "Colwellia marinimaniae MTCD1 illustrates a measurable pressure optimum (120 MPa), the quantitative value this phenotype records."
      },
      {
        "reference": "DOI:10.3389/fmolb.2022.1058381",
        "snippet": "Microorganisms adapted to HHP are usually known as piezophiles, referring to their preference for high pressure",
        "notes": "Pressure-adaptation review supports an organism-specific optimal growth pressure as the defining quantity for piezophile classification."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1513592",
        "taxon_label": "Colwellia marinimaniae",
        "reference": "DOI:10.1099/ijsem.0.001671",
        "note": "Colwellia marinimaniae MTCD1 had a measured optimum of 120 MPa at 6 degrees C in its primary species description."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "pressure_optimum_balanced_adaptation",
        "title": "Pressure-optimum balanced adaptation",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a quantitative measurement, interval, or bin in the environmental phenotype hierarchy; a token protein example would misrepresent the measured value as one inherited molecular mechanism.",
        "description": "Evidence-backed sketch linking the hydrostatic-pressure axis to the organism-specific pressure at which growth rate is maximal.",
        "nodes": [
          {
            "node_id": "pressure_optimum_trait",
            "label": "pressure optimum",
            "node_type": "TRAIT",
            "grounding": "traitmech:000004",
            "description": "Hydrostatic pressure at which growth rate is maximal."
          },
          {
            "node_id": "hydrostatic_pressure",
            "label": "hydrostatic pressure",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Ambient hydrostatic pressure imposed on the cell.",
            "grounding": "PATO:0001025"
          },
          {
            "node_id": "maximal_growth_rate",
            "label": "maximal growth rate",
            "node_type": "QUALITY",
            "description": "Peak specific growth rate achieved at the optimum pressure."
          },
          {
            "node_id": "membrane_unsaturated_fatty_acids",
            "label": "membrane unsaturated fatty acids",
            "node_type": "CHEMICAL",
            "description": "Unsaturated/polyunsaturated fatty acids whose abundance in membrane lipids rises with increasing hydrostatic pressure."
          },
          {
            "node_id": "intracellular_cation_concentration",
            "label": "intracellular cation concentration",
            "node_type": "STATE",
            "description": "Intracellular concentration of cations (Mg2+, K+, Na+) raised by cation import under high hydrostatic pressure."
          },
          {
            "node_id": "intracellular_osmotic_pressure",
            "label": "intracellular osmotic pressure",
            "node_type": "STATE",
            "description": "Osmotic pressure inside the cell, raised by cation/compatible-solute accumulation."
          },
          {
            "node_id": "hhp_tolerance",
            "label": "high hydrostatic pressure tolerance",
            "node_type": "TRAIT",
            "grounding": "traitmech:000003",
            "description": "Capacity of an organism to grow and survive under high hydrostatic pressure."
          },
          {
            "node_id": "compatible_solute_accumulation",
            "label": "compatible solute accumulation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Accumulation of piezolytes/osmolytes (glutamate, betaine, beta-hydroxybutyrate, proline, TMAO)."
          },
          {
            "node_id": "protein_stabilization_preferential_hydration",
            "label": "protein stabilization by preferential hydration",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Stabilization of proteins by compatible solutes via preferential hydration."
          }
        ],
        "edges": [
          {
            "subject": "hydrostatic_pressure",
            "predicate": "defines",
            "object": "pressure_optimum_trait",
            "description": "The hydrostatic-pressure axis defines the value at which growth is fastest.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmolb.2022.1058381",
                "notes": "Pressure-adaptation review supports an organism-specific optimal growth pressure as the defining piezophile quantity."
              }
            ],
            "predicate_id": "METPO:2007500"
          },
          {
            "subject": "pressure_optimum_trait",
            "predicate": "associated with",
            "object": "maximal_growth_rate",
            "description": "The optimum pressure marks the peak of the pressure-versus-growth curve.",
            "evidence": [
              {
                "reference": "DOI:10.1099/ijsem.0.001671",
                "notes": "Colwellia marinimaniae MTCD1 illustrates a measurable pressure optimum (120 MPa)."
              }
            ],
            "predicate_id": "biolink:associated_with"
          },
          {
            "subject": "membrane_unsaturated_fatty_acids",
            "predicate": "confers",
            "object": "pressure_optimum_trait",
            "description": "Increased membrane unsaturated/PUFA content confers growth at elevated hydrostatic pressure, shaping the pressure optimum.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmolb.2022.1058381",
                "notes": "Review: abundance of membrane lipids with unsaturated and branched-chain fatty acids rises with increasing HHP."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "intracellular_cation_concentration",
            "predicate": "increases",
            "object": "intracellular_osmotic_pressure",
            "description": "Increased cation import raises intracellular osmotic pressure.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mbio.00958-23",
                "notes": "Authors propose increased cation import to raise intracellular osmotic pressure under HHP."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "intracellular_osmotic_pressure",
            "predicate": "confers",
            "object": "hhp_tolerance",
            "description": "Elevated intracellular osmotic pressure confers high hydrostatic pressure tolerance.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mbio.00958-23",
                "notes": "Proposed HHP-tolerance model: importing cations to raise intracellular osmotic pressure."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "compatible_solute_accumulation",
            "predicate": "promotes",
            "object": "protein_stabilization_preferential_hydration",
            "description": "Compatible solutes (piezolytes) stabilize proteins by preferential hydration.",
            "evidence": [
              {
                "reference": "DOI:10.3390/microorganisms11071629",
                "notes": "Compatible solutes displace water bound to proteins via preferential hydration; glutamate/betaine/beta-hydroxybutyrate detected at 20-30 MPa."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "compatible_solute_accumulation",
            "predicate": "confers",
            "object": "hhp_tolerance",
            "description": "Compatible-solute (piezolyte) accumulation confers pressure tolerance.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s00253-023-12906-5",
                "notes": "Osmolyte-based protection (proline, glutamate, betaine, beta-hydroxybutyrate, TMAO) supports pressure tolerance across taxa."
              }
            ],
            "predicate_id": "METPO:2007700"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-28T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed quantitative companion trait (optimal growth pressure) mirroring the existing temperature_optimum / nacl_optimum pattern, to fill the pressure coverage gap.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-09T14:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (pressure-axis defines optimum) with METPO/biolink predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-16T06:54:39Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (PATO:0001025\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 5 evidence-backed generic edges (6 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:11Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 5 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d73, RO:0002213\u00d72).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 1 causal edge(s) off enables/RO:0002327 with a TRAIT object (1 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-07T05:00:00Z",
        "curator": "claude",
        "action": "RETYPE_CAUSAL_NODE",
        "changes": "Retyped the object node from STATE/CAPACITY to TRAIT and re-grounded its in-edge from enables/RO:0002327 to METPO:2007700 (confers), issue 334. biolink declares enables range 'biological process or activity', which only BIOLOGICAL_PROCESS, PATHWAY and MOLECULAR_FUNCTION satisfy. The node's own description gives it away as a disposition rather than a state - phrasings like \"Capacity of an organism to grow and survive under...\", \"Ability to grow when...\" and \"tolerance of...\" describe what an organism CAN do, which is what a TRAIT is. So the defect was the node type, not the predicate, which is the third time in this issue's neighbourhood that has been true (compare issue 331's acetate kinase step and issue 330's negated node name). With the object correctly a TRAIT, confers applies unchanged.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-07T06:00:00Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded the retyped TRAIT node, issue 334 review. docs/CURATION_PLAYBOOK.md requires every TRAIT row to carry a grounding, and 462 of 482 TRAIT nodes in the corpus do, so leaving a newly retyped one ungrounded was the exception rather than the norm. It also mattered more than hygiene: an ungrounded TRAIT node still counts as a reachability anchor for audit-graphs, so it made UNREACHABLE_FROM_TRAIT fall on this graph without any edge changing -- the island is unchanged and FRAGMENTED_GRAPH still reports it. Grounding it makes the duplication legible instead of leaving two unrelated-looking anchors. hhp_tolerance IS piezotolerant, already in the corpus as traitmech:000003.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-21T08:00:00Z",
        "curator": "codex",
        "action": "NORMALISE_NODE_TYPE",
        "changes": "Tranche 5 of issue 356 settles the process/quality families and merges ids that meant the same sense: maximal_growth_rate is QUALITY. A maximal growth rate is a measured upper bound or peak specific rate. Its edges associate, enable, or manifest that value; none describe the process of cell growth itself. An edge cannot enable a QUALITY under RO:0002327's biological-process range, so edges that causally support the rate use promotes (RO:0002213) instead.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope pressure_optimum_balanced_adaptation=NONMECHANISTIC with scope_notes.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T04:43:24Z",
        "curator": "codex",
        "action": "ADD_CANONICAL_EXAMPLES",
        "changes": "Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Colwellia marinimaniae (NCBITaxon:1513592; DOI:10.1099/ijsem.0.001671). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000005",
    "label": "pressure range",
    "definition": "A pressure phenotype with numerical limits that bounds the minimum and maximum hydrostatic pressures supporting growth of an organism.",
    "definition_source": "DOI:10.1099/ijsem.0.001671",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1099/ijsem.0.001671",
        "snippet": "growth range of 80-140 MPa (optimum, 120 MPa) at 6 degrees C",
        "notes": "Colwellia marinimaniae MTCD1 illustrates a bounded growth-supporting pressure span (80-140 MPa), the quantity this phenotype records."
      },
      {
        "reference": "DOI:10.3389/fmolb.2022.1058381",
        "snippet": "Microorganisms adapted to HHP are usually known as piezophiles, referring to their preference for high pressure",
        "notes": "Pressure-adaptation review supports the bounded span of growth-permissive hydrostatic pressure as a defining quantitative descriptor."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1513592",
        "taxon_label": "Colwellia marinimaniae",
        "reference": "DOI:10.1099/ijsem.0.001671",
        "note": "Colwellia marinimaniae MTCD1 grew from 80 to 140 MPa at 6 degrees C; the note retains the strain, endpoints, units, and temperature."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "pressure_range_growth_bounded_span",
        "title": "Pressure range: bounded hydrostatic-pressure span supporting growth",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a quantitative measurement, interval, or bin in the environmental phenotype hierarchy; a token protein example would misrepresent the measured value as one inherited molecular mechanism.",
        "description": "Evidence-backed sketch linking the hydrostatic-pressure axis to the minimum/maximum bounds within which growth is sustained.",
        "nodes": [
          {
            "node_id": "pressure_range_trait",
            "label": "pressure range",
            "node_type": "TRAIT",
            "grounding": "traitmech:000005",
            "description": "Bounded min-to-max hydrostatic pressure supporting growth."
          },
          {
            "node_id": "hydrostatic_pressure",
            "label": "hydrostatic pressure",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Ambient hydrostatic pressure imposed on the cell.",
            "grounding": "PATO:0001025"
          },
          {
            "node_id": "bounded_growth_span",
            "label": "growth-permissive pressure span",
            "node_type": "QUALITY",
            "description": "Continuous interval of hydrostatic pressures supporting growth."
          },
          {
            "node_id": "pufa_biosynthesis",
            "label": "polyunsaturated fatty acid biosynthesis",
            "node_type": "PATHWAY",
            "description": "Synthesis of polyunsaturated fatty acids incorporated into membrane lipids.",
            "grounding": "GO:0006636"
          },
          {
            "node_id": "membrane_fluidity_hhp",
            "label": "membrane fluidity under high hydrostatic pressure",
            "node_type": "QUALITY",
            "description": "Degree of membrane lipid disorder/fluidity maintained against pressure-induced ordering."
          },
          {
            "node_id": "unsaturated_membrane_lipids",
            "label": "unsaturated membrane lipids",
            "node_type": "CHEMICAL",
            "description": "Unsaturated fatty acids in membrane phospholipids that counter pressure-induced ordering."
          },
          {
            "node_id": "tmao",
            "label": "trimethylamine N-oxide (TMAO)",
            "node_type": "CHEMICAL",
            "description": "Compatible solute / piezolyte excluded from the protein hydration layer."
          },
          {
            "node_id": "protein_stabilization",
            "label": "protein stabilization via preferential hydration",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Stabilization of native protein structure by preferential exclusion of cosolutes."
          },
          {
            "node_id": "compatible_solute_accumulation",
            "label": "compatible solute accumulation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Accumulation of compatible solutes (betaine, glutamate, beta-hydroxybutyrate) acting as piezolytes."
          }
        ],
        "edges": [
          {
            "subject": "hydrostatic_pressure",
            "predicate": "defines",
            "object": "pressure_range_trait",
            "description": "The hydrostatic-pressure axis defines the min/max bounds bracketed by the pressure range.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmolb.2022.1058381",
                "notes": "Pressure-adaptation review frames the bounded span of growth-permissive pressure as a defining quantitative descriptor."
              }
            ],
            "predicate_id": "METPO:2007500"
          },
          {
            "subject": "pressure_range_trait",
            "predicate": "associated with",
            "object": "bounded_growth_span",
            "description": "The pressure range records the bounded interval of permissive hydrostatic pressures.",
            "evidence": [
              {
                "reference": "DOI:10.1099/ijsem.0.001671",
                "notes": "Colwellia marinimaniae MTCD1 illustrates a bounded growth-supporting pressure span (80-140 MPa)."
              }
            ],
            "predicate_id": "biolink:associated_with"
          },
          {
            "subject": "pufa_biosynthesis",
            "predicate": "increases",
            "object": "membrane_fluidity_hhp",
            "description": "PUFA biosynthesis increases membrane fluidity to counter pressure-induced membrane ordering.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmolb.2022.1058381",
                "notes": "PUFAs (C20:5, C22:6) associated with adaptation to high hydrostatic pressure; broad mechanism across taxa."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "unsaturated_membrane_lipids",
            "predicate": "positively regulates",
            "object": "pressure_range_trait",
            "description": "Unsaturated membrane lipids support growth across high hydrostatic pressures.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmolb.2022.1058381",
                "notes": "Mutants with reduced C18:1 could not withstand high pressure; unsaturation counters pressure ordering."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "membrane_fluidity_hhp",
            "predicate": "expands",
            "object": "pressure_range_trait",
            "description": "Maintaining membrane fluidity under pressure expands the growth-supporting pressure range.",
            "evidence": [
              {
                "reference": "DOI:10.3390/microorganisms11071629",
                "notes": "Pressure compacts membranes; organisms restore membrane disorder/function via unsaturation to sustain growth."
              }
            ]
          },
          {
            "subject": "tmao",
            "predicate": "stabilizes",
            "object": "protein_stabilization",
            "description": "TMAO stabilizes proteins via preferential hydration (preferential exclusion from hydration layer).",
            "evidence": [
              {
                "reference": "DOI:10.1021/acs.chemrev.3c00432",
                "notes": "TMAO preferentially excluded from protein hydration layer causing preferential hydration; biophysical mechanism, not microbe-specific."
              }
            ]
          },
          {
            "subject": "compatible_solute_accumulation",
            "predicate": "stabilizes",
            "object": "protein_stabilization",
            "description": "Compatible solutes stabilize proteins via preferential hydration.",
            "evidence": [
              {
                "reference": "DOI:10.3390/microorganisms11071629",
                "notes": "Compatible solutes (glutamate, betaine, beta-hydroxybutyrate) act by preferential hydration, displacing protein-bound water."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-28T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed quantitative companion trait (growth-supporting pressure span) mirroring the existing temperature_range / nacl_range pattern, to fill the pressure coverage gap.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-09T14:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (pressure-axis defines bounded growth span) with METPO/biolink predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-16T06:54:39Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (PATO:0001025\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 5 evidence-backed generic edges (6 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:11Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002213\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0006636\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-04T03:08:13Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002213\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-16T02:00:00Z",
        "curator": "claude",
        "action": "NORMALISE_NODE_TYPE",
        "changes": "Under the PATHWAY-vs-BIOLOGICAL_PROCESS rule, one node_id means one thing corpus-wide (issue 356): pufa_biosynthesis is typed PATHWAY. PATHWAY is a named, conventionally enumerable multi-step route; BIOLOGICAL_PROCESS is everything else. A named biosynthetic route to polyunsaturated fatty acids. The two typings describe it in near-identical words, so the split was arbitrary and the rule breaks the 1-1 tie.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope pressure_range_growth_bounded_span=NONMECHANISTIC with scope_notes.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T04:43:24Z",
        "curator": "codex",
        "action": "ADD_CANONICAL_EXAMPLES",
        "changes": "Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Colwellia marinimaniae (NCBITaxon:1513592; DOI:10.1099/ijsem.0.001671). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000614",
    "label": "psychrophilic",
    "definition": "A temperature preference in which growth is favored at low temperatures, typically near or below ~15 \u00b0C.",
    "definition_source": "DOI:10.1038/sj.embor.7400662",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000613"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/sj.embor.7400662",
        "snippet": "growing well at temperatures around the freezing point of water",
        "notes": "Supports psychrophilic growth at low temperatures."
      },
      {
        "reference": "PMID:28919459",
        "snippet": "psychrophilic Arctic bacterium Psychrobacter sp. DAB_AL43B",
        "notes": "Organism example: Psychrobacter sp. DAB_AL43B is described as psychrophilic."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:167879",
        "taxon_label": "Colwellia psychrerythraea 34H",
        "note": "Model marine psychrophile; active growth at and below 0 C.",
        "reference": "PMID:16043709"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "psychrophilic_cold_adaptation",
        "title": "Psychrophilic cold-adaptation mechanism",
        "description": "Evidence-backed causal sketch linking psychrophily to low temperature, membrane remodeling, cold-active enzymes, and cryoprotection.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a broad environmental or morphological classification spanning multiple mechanisms, a measurement-like bin, or an absence/arrangement descriptor; contextual protein nodes do not receive token UniProt examples.",
        "nodes": [
          {
            "node_id": "psychrophilic_trait",
            "label": "psychrophilic",
            "node_type": "TRAIT",
            "grounding": "METPO:1000614",
            "description": "Growth is favored at low temperatures."
          },
          {
            "node_id": "low_temperature",
            "label": "low temperature",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Cold environment near the freezing point of water.",
            "grounding": "PATO:0001306"
          },
          {
            "node_id": "membrane_fluidity",
            "label": "membrane fluidity",
            "node_type": "QUALITY",
            "description": "Physical state of the membrane needed for transport and growth.",
            "grounding": "METPO:1007505"
          },
          {
            "node_id": "unsaturated_fatty_acids",
            "label": "unsaturated and branched-chain fatty acids",
            "node_type": "CHEMICAL",
            "description": "Membrane lipid features that reduce packing order and maintain fluidity at low temperature."
          },
          {
            "node_id": "cold_adapted_enzymes",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "cold-adapted enzymes",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Enzymes with activity at low temperature, often associated with increased structural flexibility."
          },
          {
            "node_id": "cold_shock_proteins",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "cold-shock proteins",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Proteins induced during cold shock or cold acclimation."
          },
          {
            "node_id": "antifreeze_proteins",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "antifreeze and ice-binding proteins",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Proteins that mitigate ice formation or recrystallization damage."
          },
          {
            "node_id": "transcription_translation",
            "label": "transcription and translation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Macromolecular synthesis processes impaired by cold-induced nucleic-acid secondary structure."
          },
          {
            "node_id": "compatible_solutes",
            "label": "compatible solutes",
            "node_type": "CHEMICAL",
            "description": "Low-molecular-weight osmolytes (e.g. trehalose, glycine betaine, glycerol) accumulated for cryoprotection.",
            "grounding": "CHEBI:25728"
          },
          {
            "node_id": "trehalose",
            "label": "trehalose",
            "node_type": "CHEMICAL",
            "description": "Disaccharide cryoprotectant with colligative and protein-stabilizing effects."
          },
          {
            "node_id": "protein_membrane_stability",
            "label": "protein and membrane stability",
            "node_type": "QUALITY",
            "description": "Structural integrity of proteins and membranes maintained against cold denaturation."
          },
          {
            "node_id": "ice_crystals",
            "label": "ice crystals",
            "node_type": "CHEMICAL",
            "description": "Intracellular/extracellular ice whose growth and recrystallization damage cells."
          },
          {
            "node_id": "reactive_oxygen_species",
            "label": "reactive oxygen species",
            "node_type": "CHEMICAL",
            "description": "ROS whose concentration rises at low temperature due to increased gas solubility.",
            "grounding": "CHEBI:26523"
          }
        ],
        "edges": [
          {
            "subject": "low_temperature",
            "predicate": "selects for",
            "object": "psychrophilic_trait",
            "description": "Permanently cold environments select for microorganisms able to grow near freezing.",
            "evidence": [
              {
                "reference": "DOI:10.1038/sj.embor.7400662",
                "snippet": "growing well at temperatures around the freezing point",
                "notes": "Review supports psychrophile growth in near-freezing environments."
              }
            ],
            "predicate_id": "METPO:2007401"
          },
          {
            "subject": "low_temperature",
            "predicate": "decreases",
            "object": "membrane_fluidity",
            "description": "Cold reduces membrane fluidity, altering transport and waste exchange.",
            "evidence": [
              {
                "reference": "DOI:10.1038/sj.embor.7400662",
                "snippet": "decreased membrane fluidity",
                "notes": "Supports membrane rigidification as a low-temperature challenge."
              }
            ],
            "predicate_id": "RO:0002212"
          },
          {
            "subject": "unsaturated_fatty_acids",
            "predicate": "regulates",
            "object": "membrane_fluidity",
            "description": "Unsaturated and branched-chain fatty acids maintain membrane fluidity during cold growth.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-micro-091313-103612",
                "snippet": "more unsaturated fatty acids",
                "notes": "Review supports homoviscous membrane adaptation as temperature decreases."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "cold_adapted_enzymes",
            "predicate": "confers",
            "object": "psychrophilic_trait",
            "description": "Cold-active enzymes support catalysis at low temperature.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.tim.2010.05.002",
                "snippet": "genes involved in cold adaptation",
                "notes": "Review connects psychrophile omics signatures with cold-adaptation mechanisms."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "cold_shock_proteins",
            "predicate": "contributes to",
            "object": "psychrophilic_trait",
            "description": "Cold-shock proteins support cellular acclimation to low temperature.",
            "evidence": [
              {
                "reference": "DOI:10.1038/sj.embor.7400662",
                "snippet": "Cold-shock proteins have also been described",
                "notes": "Supports cold-shock proteins as psychrophile-associated adaptations."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "antifreeze_proteins",
            "predicate": "protects against",
            "object": "low_temperature",
            "description": "Antifreeze and ice-binding proteins mitigate ice-associated stress in cold habitats.",
            "evidence": [
              {
                "reference": "DOI:10.1038/sj.embor.7400662",
                "snippet": "intracellular ice formation",
                "notes": "Review identifies ice formation as a cold challenge and cites bacterial antifreeze protein activity."
              }
            ]
          },
          {
            "subject": "cold_shock_proteins",
            "predicate": "regulates",
            "object": "transcription_translation",
            "description": "Cold-shock proteins regulate transcription and translation during cold acclimation.",
            "evidence": [
              {
                "reference": "DOI:10.1002/embr.201338170",
                "notes": "cold-shock proteins (CSPs) regulate a variety of cellular processes, including transcription, translation."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "trehalose",
            "predicate": "prevents",
            "object": "protein_membrane_stability",
            "description": "Trehalose helps prevent protein denaturation and aggregation, acting as a cryoprotectant.",
            "evidence": [
              {
                "reference": "DOI:10.1038/sj.embor.7400662",
                "notes": "Trehalose is thought to have a colligative effect, but probably also helps in preventing protein denaturation and aggregation."
              }
            ],
            "predicate_id": "RO:0002212"
          },
          {
            "subject": "compatible_solutes",
            "predicate": "maintains",
            "object": "protein_membrane_stability",
            "description": "Compatible solutes depress the freezing point and stabilize proteins and membranes.",
            "evidence": [
              {
                "reference": "DOI:10.37256/amtt.5220244537",
                "notes": "Compatible solutes depress the freezing point... stabilize proteins and membranes."
              }
            ]
          },
          {
            "subject": "antifreeze_proteins",
            "predicate": "binds to",
            "object": "ice_crystals",
            "description": "Antifreeze/ice-binding proteins bind ice crystals to control ice growth and recrystallization.",
            "evidence": [
              {
                "reference": "DOI:10.1038/sj.embor.7400662",
                "notes": "Antifreeze proteins (AFPs) have the ability to bind to ice crystals."
              }
            ]
          },
          {
            "subject": "low_temperature",
            "predicate": "increases",
            "object": "reactive_oxygen_species",
            "description": "Increased gas solubility at low temperature raises reactive oxygen species concentrations.",
            "evidence": [
              {
                "reference": "DOI:10.1002/embr.201338170",
                "notes": "The solubility of gases increases at lower temperatures, resulting in increased concentrations of reactive oxygen species."
              }
            ],
            "predicate_id": "RO:0002213"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.857091+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-06T14:58:45-07:00",
        "curator": "codex",
        "action": "CURATED_WITH_ORGANISM_EXAMPLE",
        "changes": "Added Psychrobacter sp. DAB_AL43B organism example with PMID-backed evidence.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-11T00:00:00-07:00",
        "curator": "codex",
        "action": "CURATED_WITH_LITERATURE",
        "changes": "Added DOI-backed psychrophily causal graph for cold adaptation, membrane fluidity, cold-active enzymes, cold-shock proteins, and cryoprotection.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:30Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d71, RO:0002326\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T21:30:06Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007401\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:18Z",
        "curator": "claude",
        "action": "RENAME_PREDICATE_LABELS",
        "changes": "Renamed 1 causal-edge predicate label(s) to align with existing groundings: maintains \u2192 regulates \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:21Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002211\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:38:00Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (PATO:0000383\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:41:03Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (METPO:1007505\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-26T02:30:13Z",
        "curator": "claude",
        "action": "RETYPE_CAUSAL_NODES",
        "changes": "Re-typed 1 causal-node node_type field(s) to align with CausalNodeTypeEnum semantics: membrane fluidity: BIOLOGICAL_PROCESS \u2192 QUALITY \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-13T21:03:25Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002212\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-15T07:19:08Z",
        "curator": "claude",
        "action": "FIX_NODE_GROUNDING_CURIE",
        "changes": "Overwrote 1 causal-node grounding(s) to corrected CURIEs (phase-2 id-label fix; verified vs OAK).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-17T04:09:43Z",
        "curator": "claude",
        "action": "REMOVE_REDUNDANT_SYNONYM",
        "changes": "Removed 1 synonym(s) whose text duplicated the label (seeder redundancy; no information lost).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 5 evidence-backed generic edges (6 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:11Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002211\u00d71, RO:0002212\u00d71, RO:0002213\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:17Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:25728\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:26523\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 1 causal edge(s) off enables/RO:0002327 with a TRAIT object (1 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope psychrophilic_cold_adaptation=NONMECHANISTIC with scope_notes; marked 3 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (cold_adapted_enzymes, cold_shock_proteins, antifreeze_proteins).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000618",
    "label": "psychrotolerant",
    "definition": "A temperature preference in which growth can occur at low temperatures without an obligate low-temperature preference.",
    "definition_source": "DOI:10.1099/ijs.0.65141-0",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000613"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1099/ijs.0.65141-0",
        "snippet": "Pseudomonas guineae sp. nov., a novel psychrotolerant bacterium",
        "notes": "Organism example: Pseudomonas guineae is described as psychrotolerant."
      },
      {
        "reference": "DOI:10.1038/sj.embor.7400662",
        "snippet": "decreased membrane fluidity",
        "notes": "Psychrophile review supports cold-end membrane stress as the challenge that psychrotolerant facultative adaptation overcomes without full psychrophile dedication."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1639",
        "taxon_label": "Listeria monocytogenes",
        "note": "grows at refrigeration temperatures",
        "reference": "DOI:10.3389/fmicb.2018.02700"
      },
      {
        "taxon_id": "NCBITaxon:294",
        "taxon_label": "Pseudomonas fluorescens",
        "note": "cold-tolerant",
        "reference": "PMID:31178851"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "psychrotolerant_facultative_cold_adaptation",
        "title": "Psychrotolerant facultative cold-adaptation mechanism",
        "description": "DOI-backed graph linking psychrotolerance to low-temperature membrane and enzyme acclimation that does not preclude growth at moderate ambient temperatures.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a broad environmental or morphological classification spanning multiple mechanisms, a measurement-like bin, or an absence/arrangement descriptor; contextual protein nodes do not receive token UniProt examples.",
        "nodes": [
          {
            "node_id": "psychrotolerant_trait",
            "label": "psychrotolerant",
            "node_type": "TRAIT",
            "grounding": "METPO:1000618",
            "description": "Growth at low temperatures without an obligate low-temperature preference."
          },
          {
            "node_id": "low_temperature",
            "label": "low temperature",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Ambient temperature below the mesophile optimum range.",
            "grounding": "PATO:0001306"
          },
          {
            "node_id": "membrane_fluidity",
            "label": "membrane fluidity",
            "node_type": "QUALITY",
            "description": "Physical state of the cytoplasmic membrane supporting transport and bioenergetics.",
            "grounding": "METPO:1007505"
          },
          {
            "node_id": "facultative_lipid_remodeling",
            "label": "facultative lipid remodeling",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Cold-induced shifts in lipid composition without obligate low-temperature specialization."
          },
          {
            "node_id": "cold_shock_response",
            "label": "cold-shock response",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Cold-shock-protein induction supporting transient low-temperature acclimation.",
            "grounding": "traitmech:000206"
          },
          {
            "node_id": "membrane_rigidity",
            "label": "membrane rigidification and thickening",
            "node_type": "QUALITY",
            "description": "Cold-induced increase in membrane order and bilayer thickness approaching a gel-phase transition."
          },
          {
            "node_id": "unsaturated_hopanoids",
            "label": "unsaturated hopanoids",
            "node_type": "CHEMICAL",
            "description": "Hopanoid lipids whose unsaturation rises at low temperature, aiding membrane homeostasis."
          },
          {
            "node_id": "compatible_solute_accumulation",
            "label": "compatible solute accumulation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Accumulation of compatible solutes that stabilize proteins and membranes under cold stress."
          },
          {
            "node_id": "protein_membrane_stability",
            "label": "protein and membrane stability under cold stress",
            "node_type": "QUALITY",
            "description": "Maintained integrity of proteins and membranes during low-temperature stress."
          },
          {
            "node_id": "extracellular_polymeric_substances",
            "label": "extracellular polymeric substances (EPS)",
            "node_type": "CHEMICAL",
            "description": "Secreted polymeric matrix surrounding cells that acts as a cryoprotectant."
          },
          {
            "node_id": "freeze_thaw_cryoprotection",
            "label": "cryoprotection against freeze-thaw cycles",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Protection of cells from damage during freeze-thaw cycling."
          }
        ],
        "edges": [
          {
            "subject": "low_temperature",
            "predicate": "decreases",
            "object": "membrane_fluidity",
            "description": "Low temperature reduces membrane fluidity, requiring compensation.",
            "evidence": [
              {
                "reference": "DOI:10.1038/sj.embor.7400662",
                "snippet": "decreased membrane fluidity",
                "notes": "Supports cold-end membrane stress as the physical challenge for psychrotolerant growth."
              }
            ],
            "predicate_id": "RO:0002212"
          },
          {
            "subject": "facultative_lipid_remodeling",
            "predicate": "regulates",
            "object": "membrane_fluidity",
            "description": "Facultative lipid remodeling maintains workable membrane fluidity at low temperature.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-micro-091313-103612",
                "snippet": "more unsaturated fatty acids",
                "notes": "Supports homoviscous adaptation as the mechanism employed under cold exposure."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "cold_shock_response",
            "predicate": "confers",
            "object": "psychrotolerant_trait",
            "description": "The cold-shock response enables acclimation to low temperature without obligate cold dedication.",
            "evidence": [
              {
                "reference": "DOI:10.1038/sj.embor.7400662",
                "snippet": "Cold-shock proteins have also been described",
                "notes": "Supports cold-shock proteins as a hallmark facultative-cold adaptation."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "facultative_lipid_remodeling",
            "predicate": "manifests as",
            "object": "psychrotolerant_trait",
            "description": "Facultative lipid remodeling at low temperature manifests the psychrotolerant trait in representative organisms.",
            "evidence": [
              {
                "reference": "DOI:10.1099/ijs.0.65141-0",
                "snippet": "Pseudomonas guineae sp. nov., a novel psychrotolerant bacterium",
                "notes": "Supports the trait endpoint in a representative organism."
              }
            ],
            "predicate_id": "METPO:2007400"
          },
          {
            "subject": "low_temperature",
            "predicate": "causes",
            "object": "membrane_rigidity",
            "description": "A low-temperature shift causes membrane rigidification and thickening toward a gel-phase transition.",
            "evidence": [
              {
                "reference": "DOI:10.1128/spectrum.03925-23",
                "notes": "Cold shock causes membrane rigidification and concomitant thickening, potentially culminating in a gel-phase transition."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "low_temperature",
            "predicate": "increases",
            "object": "unsaturated_hopanoids",
            "description": "Decreasing growth temperature increases the unsaturated hopanoid fraction as a compositional cold adaptation.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s42770-023-01057-4",
                "notes": "As the growth temperature decreased from 20 to 4 C, the total percent of unsaturated hopanoids increased from 27 to 49%."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "compatible_solute_accumulation",
            "predicate": "protects",
            "object": "protein_membrane_stability",
            "description": "Compatible solute accumulation stabilizes proteins and membranes during low-temperature stress.",
            "evidence": [
              {
                "reference": "DOI:10.37256/amtt.5220244537",
                "notes": "Compatible solutes depress freezing point, stabilize proteins and membranes, scavenge radicals, and act as cryoprotectants."
              }
            ]
          },
          {
            "subject": "extracellular_polymeric_substances",
            "predicate": "provides",
            "object": "freeze_thaw_cryoprotection",
            "description": "EPS surrounding cells provide cryoprotection against freeze-thaw cycles.",
            "evidence": [
              {
                "reference": "DOI:10.37256/amtt.5220244537",
                "notes": "EPS surrounding cells play a critical role in cold adaptation by providing protection against freeze-thaw cycles and acting as cryoprotectants."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.859611+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-06T14:58:45-07:00",
        "curator": "codex",
        "action": "CURATED_WITH_ORGANISM_EXAMPLE",
        "changes": "Added Pseudomonas guineae organism example with PMID-backed evidence.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-13T11:30:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed causal graph linking facultative cold adaptation (lipid remodeling and cold-shock response) to the psychrotolerant trait.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-13T22:45:00-07:00",
        "curator": "codex",
        "action": "IMPROVED_CAUSAL_GRAPH_EVIDENCE",
        "changes": "Replaced Pseudomonas guineae PMID fallback with the article DOI in definition, record evidence, and CausalEdge evidence.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:30Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T21:30:06Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007400\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:18Z",
        "curator": "claude",
        "action": "RENAME_PREDICATE_LABELS",
        "changes": "Renamed 1 causal-edge predicate label(s) to align with existing groundings: maintains \u2192 regulates \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:21Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002211\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:38:00Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (PATO:0000383\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:41:03Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (METPO:1007505\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-26T02:30:13Z",
        "curator": "claude",
        "action": "RETYPE_CAUSAL_NODES",
        "changes": "Re-typed 1 causal-node node_type field(s) to align with CausalNodeTypeEnum semantics: membrane fluidity: BIOLOGICAL_PROCESS \u2192 QUALITY \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-13T21:03:25Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002212\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-15T07:19:08Z",
        "curator": "claude",
        "action": "FIX_NODE_GROUNDING_CURIE",
        "changes": "Overwrote 1 causal-node grounding(s) to corrected CURIEs (phase-2 id-label fix; verified vs OAK).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-17T04:09:43Z",
        "curator": "claude",
        "action": "REMOVE_REDUNDANT_SYNONYM",
        "changes": "Removed 1 synonym(s) whose text duplicated the label (seeder redundancy; no information lost).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 5 evidence-backed generic edges (7 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:11Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:causes\u00d71, RO:0002213\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 1 causal edge(s) off enables/RO:0002327 with a TRAIT object (1 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-08T05:00:00Z",
        "curator": "claude",
        "action": "DROP_CAUSAL_NODE",
        "changes": "Dropped node growth_at_4c and its edges. Issue 352. 'Ability to grow at refrigeration-range low temperature (4 C)' IS METPO:1000618 (psychrotolerant), the record's own term and the grounding of psychrotolerant_trait, which is the node it hangs off. A leaf restating its own parent. The parent keeps two other in-edges (cold_shock_response confers, facultative_lipid_remodeling manifests as), so nothing is stranded.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-21T08:00:00Z",
        "curator": "codex",
        "action": "NORMALISE_NODE_TYPE",
        "changes": "Tranche 5 of issue 356 settles the process/quality families and merges ids that meant the same sense: membrane_rigidity is QUALITY. Membrane rigidity is a physical attribute of the bilayer and therefore a QUALITY under the schema's membrane-fluidity example.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope psychrotolerant_facultative_cold_adaptation=NONMECHANISTIC with scope_notes.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-15T05:32:00Z",
        "curator": "codex",
        "action": "GROUND_CAUSAL_NODE",
        "changes": "Grounded the exact cold-shock-response biological-process node to the newly minted local traitmech:000206 cold shock response record.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000007",
    "label": "radiotolerant",
    "definition": "An environmental tolerance in which an organism survives doses of ionizing and/or ultraviolet radiation that are lethal to most microorganisms, typically via efficient DNA repair and oxidative-damage protection.",
    "definition_source": "DOI:10.1101/cshperspect.a012765",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "synonyms": [
      {
        "synonym_text": "radioresistant",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1101/cshperspect.a012765"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1101/cshperspect.a012765",
        "snippet": "A strong correlation has been shown between intracellular Mn/Fe concentration ratios and bacterial resistance to radiation",
        "notes": "Review of extreme radiation resistance supports manganese-antioxidant protection of the proteome as a core radiotolerance mechanism in Deinococcus radiodurans, \"a champion of extreme radiation resistance\"."
      },
      {
        "reference": "DOI:10.3390/genes14091803",
        "snippet": "Deinococcus radiodurans, a Gram-positive extremophilic bacterium, is a remarkable example of such an organism, showcasing an impressive resistance to a wide array of stressors, including ionizing radiation, desiccation, UV radiation, and oxidizing agents",
        "notes": "Organism example: Deinococcus radiodurans tolerates ionizing radiation, UV radiation, and desiccation."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1299",
        "taxon_label": "Deinococcus radiodurans",
        "note": "Most radiation-resistant model organism; survives >15 kGy acute gamma (type strain R1).",
        "reference": "https://pubmed.ncbi.nlm.nih.gov/11238985/"
      },
      {
        "taxon_id": "NCBITaxon:243230",
        "taxon_label": "Deinococcus radiodurans R1",
        "note": "Strain-level RecA radiation-repair exemplar.",
        "reference": "PMID:11238985"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "radiotolerance_repair_antioxidant",
        "title": "Radiotolerance via DNA repair and Mn-antioxidant proteome protection",
        "description": "Evidence-backed causal sketch linking efficient DNA-damage repair and manganese-antioxidant protection to survival of lethal radiation doses.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "The taxon-matched protein example anchors one experimentally supported causal branch; it is not presented as a universal mechanism for every taxon or every contextual branch in this graph.",
        "nodes": [
          {
            "node_id": "radiotolerant_trait",
            "label": "radiotolerant",
            "node_type": "TRAIT",
            "grounding": "traitmech:000007",
            "description": "Survival of ionizing and/or UV radiation doses lethal to most microbes."
          },
          {
            "node_id": "radiation_exposure",
            "label": "ionizing or UV radiation exposure",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "High dose of ionizing or ultraviolet radiation."
          },
          {
            "node_id": "dna_damage_repair",
            "label": "DNA repair",
            "node_type": "BIOLOGICAL_PROCESS",
            "grounding": "GO:0006281",
            "description": "Repair of radiation-induced DNA lesions (double-strand breaks, adducts, dimers)."
          },
          {
            "node_id": "mn_antioxidant_protection",
            "label": "manganese-antioxidant proteome protection",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Mn-driven protection of repair proteins from oxidative damage."
          },
          {
            "node_id": "reactive_oxygen_species",
            "label": "reactive oxygen species (ROS)",
            "node_type": "CHEMICAL",
            "description": "Reactive oxygen species generated as an aftermath of irradiation that damage DNA and proteins."
          },
          {
            "node_id": "mn2_ion",
            "label": "manganese(II) ion",
            "node_type": "CHEMICAL",
            "description": "Intracellular Mn2+ that acts as an antioxidant scavenging ROS."
          },
          {
            "node_id": "fe2_ion",
            "label": "iron(II) ion",
            "node_type": "CHEMICAL",
            "description": "Intracellular Fe2+ that propagates ROS through Fenton chemistry."
          },
          {
            "node_id": "reca_protein",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:P42443",
                "protein_label": "Protein RecA",
                "gene_symbol": "recA",
                "taxon_id": "NCBITaxon:243230",
                "taxon_label": "Deinococcus radiodurans R1",
                "entry_status": "REVIEWED",
                "proteome_id": "UP000002524",
                "retrieved_on": "2026-10-22",
                "entry_version": 162,
                "sequence_version": 2,
                "role": "R1 RecA mediates homologous-recombination repair of radiation-induced DNA double-strand breaks.",
                "evidence": [
                  {
                    "reference": "PMID:11238985",
                    "snippet": "DNA repair underlies Deinococcus radioresistance",
                    "notes": "The cited source supports the represented protein-to-trait branch; UniProt verifies this current strain-matched protein entry."
                  }
                ]
              }
            ],
            "label": "RecA recombinase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "RecA recombinase central to homologous-recombination repair of radiation-induced double-strand breaks."
          },
          {
            "node_id": "homologous_recombination",
            "label": "homologous recombination",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Homologous recombination repair of DNA double-strand breaks.",
            "grounding": "GO:0035825"
          },
          {
            "node_id": "ner_uvrabc",
            "label": "nucleotide excision repair (UvrABC)",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "UvrABC excinuclease-mediated nucleotide excision repair of UV-induced helix-distorting lesions."
          },
          {
            "node_id": "carotenoid_pigments",
            "label": "carotenoid pigments",
            "node_type": "CHEMICAL",
            "description": "Carotenoid pigments (e.g. deinoxanthin) that scavenge ROS as non-enzymatic antioxidants."
          }
        ],
        "edges": [
          {
            "subject": "radiation_exposure",
            "predicate": "challenges",
            "object": "radiotolerant_trait",
            "description": "Radiation exposure is the environmental challenge the trait counters.",
            "evidence": [
              {
                "reference": "DOI:10.3390/genes14091803",
                "notes": "Deinococcus radiodurans is the reference organism for surviving ionizing radiation, UV, desiccation, and oxidizing agents."
              }
            ],
            "predicate_id": "METPO:2007406"
          },
          {
            "subject": "dna_damage_repair",
            "predicate": "confers",
            "object": "radiotolerant_trait",
            "description": "Efficient repair of radiation-induced DNA lesions enables survival.",
            "evidence": [
              {
                "reference": "DOI:10.1101/cshperspect.a012765",
                "notes": "Review of extreme radiation resistance highlights efficient DNA repair as a core radiotolerance mechanism."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "mn_antioxidant_protection",
            "predicate": "confers",
            "object": "radiotolerant_trait",
            "description": "Mn-antioxidant protection of the proteome preserves repair capacity under irradiation.",
            "evidence": [
              {
                "reference": "DOI:10.1101/cshperspect.a012765",
                "notes": "Intracellular Mn/Fe ratio correlates with bacterial radiation resistance."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "radiation_exposure",
            "predicate": "causes",
            "object": "reactive_oxygen_species",
            "description": "Ionizing/UV radiation produces reactive oxygen species.",
            "evidence": [
              {
                "reference": "DOI:10.1371/journal.pone.0304810",
                "notes": "Another aftermath of irradiation is the production of reactive oxygen species (ROS); general mechanism across microbes."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "mn2_ion",
            "predicate": "acts as antioxidant against",
            "object": "reactive_oxygen_species",
            "description": "Mn2+ acts as an antioxidant that scavenges ROS.",
            "evidence": [
              {
                "reference": "DOI:10.1128/spectrum.03838-23",
                "notes": "Manganese is an antioxidant, acting as a sponge of ROS; general bacterial mechanism."
              }
            ]
          },
          {
            "subject": "fe2_ion",
            "predicate": "promotes",
            "object": "reactive_oxygen_species",
            "description": "Fe2+ furthers the spread of ROS through Fenton chemistry.",
            "evidence": [
              {
                "reference": "DOI:10.1128/spectrum.03838-23",
                "notes": "Iron furthers the spread of ROS through Fenton chemistry; mechanistic basis of Mn/Fe ratio association with tolerance."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "mn2_ion",
            "predicate": "part of",
            "object": "mn_antioxidant_protection",
            "description": "Mn2+ antioxidant activity is part of the Mn-antioxidant proteome protection process.",
            "evidence": [
              {
                "reference": "DOI:10.1128/spectrum.03838-23",
                "notes": "Intracellular Mn/Fe ratio is the best-understood predictor of IR tolerance; Mn acts as a ROS sponge protecting the proteome."
              }
            ],
            "predicate_id": "biolink:part_of"
          },
          {
            "subject": "reca_protein",
            "predicate": "mediates",
            "object": "homologous_recombination",
            "description": "RecA mediates homologous recombination repair of double-strand breaks.",
            "evidence": [
              {
                "reference": "DOI:10.3390/su17177864",
                "notes": "HR is central for double-strand break repair, with RecA abundant and RecA expression increasing eightfold after 15 kGy."
              }
            ]
          },
          {
            "subject": "homologous_recombination",
            "predicate": "part of",
            "object": "dna_damage_repair",
            "description": "Homologous recombination is a component of radiation-induced DNA repair.",
            "evidence": [
              {
                "reference": "DOI:10.3390/su17177864",
                "notes": "HR is central for double-strand break repair of radiation-induced lesions."
              }
            ],
            "predicate_id": "biolink:part_of"
          },
          {
            "subject": "ner_uvrabc",
            "predicate": "part of",
            "object": "dna_damage_repair",
            "description": "UvrABC nucleotide excision repair repairs UV-induced helix-distorting lesions.",
            "evidence": [
              {
                "reference": "DOI:10.3390/genes14091803",
                "notes": "UvrA is the initial damage sensor in NER, recruiting UvrB and, with UvrC, performing dual-incision to remove UV-induced damaged DNA."
              }
            ],
            "predicate_id": "biolink:part_of"
          },
          {
            "subject": "carotenoid_pigments",
            "predicate": "scavenges",
            "object": "reactive_oxygen_species",
            "description": "Carotenoid pigments scavenge ROS as non-enzymatic antioxidants.",
            "evidence": [
              {
                "reference": "DOI:10.3390/su17177864",
                "notes": "The carotenoid deinoxanthin scavenges ROS quantitatively (removed up to 69.7% H2O2 and quenched singlet oxygen up to 99%)."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-28T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate ENVIRONMENT trait (general radiation tolerance) from literature research to fill the radiation-tolerance coverage gap. Parent of the ionizing- and UV-specific sub-variants.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-09T14:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (radiotolerance via DNA repair + Mn-antioxidant) with GO node grounding and RO/METPO predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 8 evidence-backed generic edges (7 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:11Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 5 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:part_of\u00d73, biolink:causes\u00d71, RO:0002213\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0035825\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 2 causal edge(s) off enables/RO:0002327 with a TRAIT object (2 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "CURATE_PROTEIN_TAXON_EXAMPLE",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope radiotolerance_repair_antioxidant=MECHANISTIC with scope_notes; marked 1 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (reca_protein); added taxon-paired protein example(s) UniProtKB:P42443 on reca_protein (NCBITaxon:243230); added canonical example(s) NCBITaxon:243230.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-22T01:35:00Z",
        "curator": "claude",
        "action": "REFRESH_UNIPROT_ENTRY_VERSION",
        "changes": "Refreshed UniProtKB entry_version against live UniProt REST on 2026-10-22: UniProtKB:P42443 (161 -> 162 on reca_protein).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000532",
    "label": "salinity phenotype with numerical limits",
    "definition": "A phenotype characterized by specific salt concentration values or ranges that define growth or activity limits.",
    "definition_source": "DOI:10.1093/database/baw155",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1093/femsre/fuy009",
        "snippet": "salinity range",
        "notes": "Osmoadaptation review supports quantitative salinity descriptors (optimum, range, delta) as the standard numerical phenotype framing for halophily classification."
      },
      {
        "reference": "DOI:10.1093/femsre/fuy009",
        "snippet": "Hypersaline environments",
        "notes": "Osmoadaptation review supports salinity as the physical axis underlying halophily classifications."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:375929",
        "taxon_label": "Natranaerobius thermophilus",
        "reference": "DOI:10.1128/aem.00145-24",
        "note": "The source measures long-term growth and cellular responses across 2.5-4.3 M total sodium and reports a 3.1-4.9 M growth range; units and total-sodium identity are retained rather than converted to NaCl."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "salinity_phenotype_numerical_axis",
        "title": "Salinity phenotype numerical-limits axis",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a quantitative measurement, interval, or bin in the environmental phenotype hierarchy; a token protein example would misrepresent the measured value as one inherited molecular mechanism.",
        "description": "DOI-backed graph linking the ambient NaCl concentration axis to the three numerical-limit measurement types (optimum, range, delta) that together classify halophily.",
        "nodes": [
          {
            "node_id": "salinity_phenotype_trait",
            "label": "salinity phenotype with numerical limits",
            "node_type": "TRAIT",
            "grounding": "METPO:1000532",
            "description": "Phenotype defined by a numerical NaCl concentration descriptor."
          },
          {
            "node_id": "nacl_concentration_axis",
            "label": "NaCl concentration axis",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Ambient NaCl concentration as a continuous environmental variable."
          },
          {
            "node_id": "nacl_optimum",
            "label": "NaCl optimum",
            "node_type": "TRAIT",
            "grounding": "METPO:1000333",
            "description": "NaCl concentration supporting the most efficient growth."
          },
          {
            "node_id": "nacl_range",
            "label": "NaCl range",
            "node_type": "TRAIT",
            "grounding": "METPO:1000334",
            "description": "Span of NaCl concentrations supporting growth."
          },
          {
            "node_id": "nacl_delta",
            "label": "NaCl delta",
            "node_type": "TRAIT",
            "grounding": "METPO:1000335",
            "description": "Breadth (max \u2212 min) of the growth-supporting NaCl range."
          },
          {
            "node_id": "intracellular_osmotic_balance",
            "label": "intracellular osmotic balance across salinity",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Maintenance of cytoplasmic osmotic equilibrium under varying ambient salinity."
          },
          {
            "node_id": "salt_out_compatible_solute_strategy",
            "label": "compatible-solute (salt-out) strategy",
            "node_type": "PATHWAY",
            "description": "Osmoadaptation by accumulating small organic compatible solutes."
          },
          {
            "node_id": "salt_in_strategy",
            "label": "salt-in strategy",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Osmoadaptation by accumulating high intracellular salt, mainly potassium.",
            "grounding": "METPO:1007720"
          },
          {
            "node_id": "glycine_betaine",
            "label": "glycine betaine",
            "node_type": "CHEMICAL",
            "description": "Compatible solute accumulating with rising salinity.",
            "grounding": "CHEBI:17750"
          },
          {
            "node_id": "l_proline",
            "label": "L-proline",
            "node_type": "CHEMICAL",
            "description": "Compatible solute / osmoprotectant amino acid."
          },
          {
            "node_id": "proline_biosynthesis_pathway",
            "label": "proB/proA/proC proline biosynthesis pathway",
            "node_type": "PATHWAY",
            "description": "Sequential biosynthesis of L-proline by gamma-glutamyl kinase, GSA dehydrogenase, and P5C reductase.",
            "related_records": [
              {
                "corpus": "PathwayMech",
                "identifier": "MetaCyc:PROSYN-PWY",
                "relation": "PATHWAY_CONTEXT",
                "basis": "PathwayMech context: L-proline biosynthesis I (from L-glutamate) in Escherichia coli (NCBITaxon:562). The linked route synthesizes L-proline from L-glutamate through the ProB/ProA/ProC enzyme sequence. No exact equivalence or transfer of organism scope is asserted.",
                "source_version": "aa305727458c44ab05614901334540e2c87a9f3a"
              }
            ]
          },
          {
            "node_id": "chaotropic_ions",
            "label": "chaotropic ions (Mg/Ca/Li/Fe salts)",
            "node_type": "CHEMICAL",
            "description": "Chaotropic cations whose presence reduces microbial habitability of brines."
          },
          {
            "node_id": "water_activity",
            "label": "water activity",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Available water (aw); a key abiotic constraint co-determining salinity limits."
          }
        ],
        "edges": [
          {
            "subject": "nacl_concentration_axis",
            "predicate": "defines",
            "object": "salinity_phenotype_trait",
            "description": "Ambient NaCl concentration is the quantitative axis defining salinity phenotypes.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuy009",
                "snippet": "optimal NaCl",
                "notes": "Supports NaCl concentration as the quantitative axis underlying salinity-phenotype descriptors."
              }
            ],
            "predicate_id": "METPO:2007500"
          },
          {
            "subject": "nacl_optimum",
            "predicate": "is a",
            "object": "salinity_phenotype_trait",
            "description": "NaCl optimum is a numerical-limit salinity phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuy009",
                "snippet": "optimal NaCl",
                "notes": "Supports NaCl optimum as a recognized salinity descriptor."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "nacl_range",
            "predicate": "is a",
            "object": "salinity_phenotype_trait",
            "description": "NaCl range is a numerical-limit salinity phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuy009",
                "snippet": "salinity range",
                "notes": "Supports NaCl range as a recognized salinity descriptor."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "nacl_delta",
            "predicate": "is a",
            "object": "salinity_phenotype_trait",
            "description": "NaCl delta is a numerical-limit salinity phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuy009",
                "snippet": "salinity range",
                "notes": "Supports growth-range breadth as a derived numerical salinity descriptor of the same axis."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "salt_out_compatible_solute_strategy",
            "predicate": "maintains",
            "object": "intracellular_osmotic_balance",
            "description": "Accumulation of compatible solutes maintains intracellular osmotic balance across salinity.",
            "evidence": [
              {
                "reference": "DOI:10.3389/frmbi.2023.1329925",
                "notes": "Salt-out strategy relies on accumulation of small organic compatible solutes."
              }
            ]
          },
          {
            "subject": "salt_in_strategy",
            "predicate": "maintains",
            "object": "intracellular_osmotic_balance",
            "description": "Salt-in strategy maintains osmotic balance via high intracellular salt (mainly potassium).",
            "evidence": [
              {
                "reference": "DOI:10.3389/frmbi.2023.1329925",
                "notes": "Salt-in strategy involves high intracellular concentration of salts, mainly potassium."
              }
            ]
          },
          {
            "subject": "glycine_betaine",
            "predicate": "contributes to",
            "object": "intracellular_osmotic_balance",
            "description": "Glycine betaine accumulates with rising salinity, contributing to intracellular osmotic balance.",
            "evidence": [
              {
                "reference": "DOI:10.1128/aem.00145-24",
                "notes": "Intracellular content of compatible solutes including glycine betaine increases with rising salinity."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "l_proline",
            "predicate": "increases",
            "object": "salinity_phenotype_trait",
            "description": "L-proline accumulation increases high-salinity stress tolerance.",
            "evidence": [
              {
                "reference": "DOI:10.1128/aem.01195-24",
                "notes": "Overproduction of L-proline improves high-salinity stress tolerance; broadly plausible mechanism."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "proline_biosynthesis_pathway",
            "predicate": "has output",
            "object": "l_proline",
            "description": "proB/proA/proC pathway produces L-proline via three sequential enzymes.",
            "evidence": [
              {
                "reference": "DOI:10.1128/aem.01195-24",
                "notes": "Pro is biosynthesized by sequential actions of three enzymes encoded by proB, proA, and proC; general across many bacteria."
              }
            ],
            "predicate_id": "RO:0002234"
          },
          {
            "subject": "chaotropic_ions",
            "predicate": "decreases",
            "object": "salinity_phenotype_trait",
            "description": "Chaotropic ions reduce habitability at a given salinity, modifying observed salinity limits.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41559-024-02505-6",
                "notes": "Highly chaotropic brines are deleterious and seem devoid of microbial life; salt composition modifies salinity limits."
              }
            ],
            "predicate_id": "RO:0002212"
          },
          {
            "subject": "water_activity",
            "predicate": "constrains",
            "object": "salinity_phenotype_trait",
            "description": "Water activity is a general abiotic constraint on salinity growth limits.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41559-024-02505-6",
                "notes": "Systems of lower water activity constrain growth; relevant beyond NaCl-only limits."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.846379+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-12T10:00:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed causal graph linking the NaCl concentration axis to NaCl optimum, range, and delta measurement types.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:30Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (rdfs:subClassOf\u00d73).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T07:37:39Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007500\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 7 evidence-backed generic edges (8 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:11Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 4 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002326\u00d71, RO:0002213\u00d71, METPO:2000202\u00d71, RO:0002212\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:17750\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates (1 to has output), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-16T02:00:00Z",
        "curator": "claude",
        "action": "NORMALISE_NODE_TYPE",
        "changes": "Under the PATHWAY-vs-BIOLOGICAL_PROCESS rule, one node_id means one thing corpus-wide (issue 356): salt_in_strategy is typed BIOLOGICAL_PROCESS. PATHWAY is a named, conventionally enumerable multi-step route; BIOLOGICAL_PROCESS is everything else. A STRATEGY, not a route. The family is described as osmoadaptation by accumulating intracellular inorganic ions -- haloalkaliphilic.yaml puts it as 'Osmoadaptation by intracellular accumulation of inorganic ions (e.g. K+)', and the wording varies by record. There is no step list to enumerate, which is exactly the distinction this rule draws. Was 7 BIOLOGICAL_PROCESS to 1 before this tranche.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-20T07:10:32Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (METPO:1007720\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope salinity_phenotype_numerical_axis=NONMECHANISTIC with scope_notes.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T04:43:24Z",
        "curator": "codex",
        "action": "ADD_CANONICAL_EXAMPLES",
        "changes": "Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Natranaerobius thermophilus (NCBITaxon:375929; DOI:10.1128/aem.00145-24). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-05T17:46:21Z",
        "curator": "codex",
        "action": "ADD_PATHWAY_CONTEXT",
        "changes": "Added pinned PathwayMech context on reviewed causal nodes with explicit route and organism limitations; retained existing groundings and exact xrefs.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000625",
    "label": "slightly halophilic",
    "definition": "A halophily preference in which an organism requires low to moderate salt concentrations (0.3 to 0.8 M NaCl) for optimal growth.",
    "definition_source": "PMID:12501437",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000629"
    ],
    "evidence": [
      {
        "reference": "PMID:12501437",
        "snippet": "A slightly halophilic, extremely halotolerant, alkaliphilic",
        "notes": "Organism example: Paraliobacillus ryukyuensis strain O15-7T is described as slightly halophilic."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:200904",
        "taxon_label": "Paraliobacillus ryukyuensis",
        "reference": "DOI:10.2323/jgam.48.269",
        "note": "Paraliobacillus ryukyuensis O15-7T was explicitly described as slightly halophilic: maximum specific growth rate occurred at 0.75-3.0% NaCl although growth extended from 0 to 22%."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "slight_halophile_low_salt_osmoadaptation",
        "title": "Slight halophile low-salt osmoadaptation mechanism",
        "description": "Evidence-backed causal sketch linking slight halophily to low or moderate NaCl and compatible-solute osmoprotection.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a broad environmental or morphological classification spanning multiple mechanisms, a measurement-like bin, or an absence/arrangement descriptor; contextual protein nodes do not receive token UniProt examples.",
        "nodes": [
          {
            "node_id": "slightly_halophilic_trait",
            "label": "slightly halophilic",
            "node_type": "TRAIT",
            "grounding": "METPO:1000625",
            "description": "Optimal growth requires low to moderate salt concentrations."
          },
          {
            "node_id": "low_moderate_nacl",
            "label": "low to moderate NaCl",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Salinity range below that of moderate and extreme halophiles."
          },
          {
            "node_id": "osmotic_stress",
            "label": "osmotic stress",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Osmotic challenge caused by environmental salt.",
            "grounding": "GO:0006970"
          },
          {
            "node_id": "compatible_solutes",
            "label": "compatible solutes",
            "node_type": "CHEMICAL",
            "description": "Organic osmoprotectants accumulated or synthesized in response to salt.",
            "grounding": "CHEBI:25728"
          },
          {
            "node_id": "osmoprotectant_transport",
            "label": "osmoprotectant transport",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "Uptake of compatible solutes such as glycine betaine."
          },
          {
            "node_id": "ectoine_biosynthesis",
            "label": "ectoine biosynthesis",
            "node_type": "PATHWAY",
            "description": "Biosynthesis of the compatible solute ectoine via the ectABC/ectBACD pathway.",
            "grounding": "GO:0019491"
          },
          {
            "node_id": "ect_gene_cluster",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "EctABC(D) ectoine-biosynthesis enzyme module",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Protein module catalyzing the ectoine biosynthesis pathway.",
            "gene_symbols": [
              "ectA",
              "ectB",
              "ectC",
              "ectD"
            ],
            "operon": "ectABC/ectBACD"
          },
          {
            "node_id": "ectoine",
            "label": "ectoine",
            "node_type": "CHEMICAL",
            "description": "A major compatible solute (osmolyte) accumulated under salt stress.",
            "grounding": "CHEBI:27592"
          },
          {
            "node_id": "ion_homeostasis",
            "label": "ion homeostasis during salt stress",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Maintenance of Na+/K+ balance under salt stress."
          },
          {
            "node_id": "na_k_transcription",
            "label": "Na+/K+ transcriptional induction",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Coordinated induction of sodium/potassium transport transcription under salt stress."
          }
        ],
        "edges": [
          {
            "subject": "low_moderate_nacl",
            "predicate": "confers",
            "object": "slightly_halophilic_trait",
            "description": "Slight halophily is a salt-growth preference at lower salinity than moderate or extreme halophily.",
            "evidence": [
              {
                "reference": "DOI:10.1186/1746-1448-4-2",
                "snippet": "minimum salt concentration required for growth",
                "notes": "Review supports halophily as a continuum of salt growth requirements."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "low_moderate_nacl",
            "predicate": "causes",
            "object": "osmotic_stress",
            "description": "Even lower salinity preferences involve osmotic adjustment to environmental salt.",
            "evidence": [
              {
                "reference": "DOI:10.1186/1746-1448-4-2",
                "snippet": "salt relationships",
                "notes": "Review describes growth in relation to minimum, optimum, and upper salt limits."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "compatible_solutes",
            "predicate": "mitigates",
            "object": "osmotic_stress",
            "description": "Compatible solutes provide osmotic balance without disrupting metabolism.",
            "evidence": [
              {
                "reference": "DOI:10.1371/journal.pone.0168818",
                "snippet": "do not disturb the cell's metabolism",
                "notes": "Supports compatible solutes as non-disruptive osmoprotectants."
              }
            ],
            "predicate_id": "METPO:2007407"
          },
          {
            "subject": "osmoprotectant_transport",
            "predicate": "accumulates",
            "object": "compatible_solutes",
            "description": "Uptake systems can accumulate compatible solutes for salt adaptation.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuy009",
                "snippet": "organic osmotic solutes",
                "notes": "Review supports accumulation of organic osmotic solutes in bacterial osmoadaptation."
              }
            ],
            "predicate_id": "METPO:2007810"
          },
          {
            "subject": "ect_gene_cluster",
            "predicate": "enables",
            "object": "ectoine_biosynthesis",
            "description": "The ect gene cluster encodes the enzymes that carry out ectoine biosynthesis.",
            "evidence": [
              {
                "reference": "DOI:10.1128/aem.01905-23",
                "notes": "ectoine biosynthesis genes are denoted by ectABC; ectBACD up-regulated as an osmoadaptation system."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "ectoine_biosynthesis",
            "predicate": "has output",
            "object": "ectoine",
            "description": "Ectoine biosynthesis produces the compatible solute ectoine.",
            "evidence": [
              {
                "reference": "DOI:10.1128/aem.01905-23",
                "notes": "Wild-type accumulates ectoine as its major osmolyte via the ectABC pathway."
              }
            ],
            "predicate_id": "RO:0002234"
          },
          {
            "subject": "ectoine",
            "predicate": "increases",
            "object": "slightly_halophilic_trait",
            "description": "Accumulation of ectoine as a compatible solute increases salt tolerance.",
            "evidence": [
              {
                "reference": "DOI:10.1128/aem.01905-23",
                "notes": "Wild-type accumulates ectoine as its major osmolyte while the ectABC-deleted strain is salt-sensitive."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "osmoprotectant_transport",
            "predicate": "increases",
            "object": "slightly_halophilic_trait",
            "description": "Uptake of compatible solutes is a general salt-out osmoadaptation strategy that raises salt tolerance.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuy026",
                "notes": "Salt-out strategists exclude salt and/or synthesize or uptake compatible solutes (e.g. glycine betaine); dominant strategy in many halophilic bacteria."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "na_k_transcription",
            "predicate": "supports",
            "object": "ion_homeostasis",
            "description": "Coordinated induction of Na+/K+ transcription supports ion homeostasis during salt stress.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s42003-022-04319-3",
                "notes": "Coordinated induction of Na+/K+ transcription and ectoine, proline, and betaine biosynthesis under salt stress."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.863572+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-06T14:15:44-07:00",
        "curator": "codex",
        "action": "CURATED_WITH_ORGANISM_EXAMPLE",
        "changes": "Added Paraliobacillus ryukyuensis organism example with PMID-backed evidence.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "ADDED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed causal graph for slight halophile compatible-solute osmoadaptation.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T05:49:24Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:causes\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T21:30:06Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007407\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:18Z",
        "curator": "claude",
        "action": "RENAME_PREDICATE_LABELS",
        "changes": "Renamed 1 causal-edge predicate label(s) to align with existing groundings: supports \u2192 enables \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:21Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:38:00Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0006970\u00d71, CHEBI:65015\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-15T07:19:08Z",
        "curator": "claude",
        "action": "FIX_NODE_GROUNDING_CURIE",
        "changes": "Overwrote 1 causal-node grounding(s) to corrected CURIEs (phase-2 id-label fix; verified vs OAK).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-16T06:30:56Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000210\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-17T04:09:43Z",
        "curator": "claude",
        "action": "REMOVE_REDUNDANT_SYNONYM",
        "changes": "Removed 1 synonym(s) whose text duplicated the label (seeder redundancy; no information lost).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 5 evidence-backed generic edges (6 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:11Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 4 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002213\u00d72, RO:0002327\u00d71, METPO:2000202\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0019491\u00d71, CHEBI:27592\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 1 causal edge(s) off enables/RO:0002327 with a TRAIT object (1 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates (1 to has output), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T02:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES_PART2",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates onto their causal-graph counterparts (1 to accumulates), issue 301 part 2. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Each replacement is a 1:1 mirror of its source predicate that changes only the domain, so the claim each edge makes is unchanged and directions are unchanged. The replacements are proposed in proposals/metpo_traitmech_v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-08T05:00:00Z",
        "curator": "claude",
        "action": "MERGE_CAUSAL_NODE",
        "changes": "Merged node salt_tolerance into slightly_halophilic_trait and repointed its edges. Issue 352. A SEVENTH restatement, caught in the third review round (#360). I had grounded it METPO:1000622 (halotolerant), reasoning that the record is METPO:1000625 (slightly halophilic) so the term is 'distinct'. It is distinct in the worst way: 1000622 and 1000625 are DIRECT SIBLINGS under 1000629 (halophily preference), and 1000622 means 'tolerates high salt but DOES NOT REQUIRE it for growth' while 1000625 means the organism 'REQUIRES low to moderate salt for optimal growth'. So the node asserted of this record the negation of what the record's own term says. Distinct is not the test; compatible is. NO CONNECTIVITY CLAIM HERE: the node was already in the trait's component via osmoprotectant_transport -> compatible_solutes -> osmotic_stress, so merging leaves the graph at 2 components and is a correctness fix, not a structural one. METPO has no generic salt-tolerance disposition to reground to: halotolerant and acidotolerant are the only candidate labels and each already anchors its own record. Recorded as issue #364, which proposes a tolerance axis distinct from the preference axis; nothing under proposals/ yet.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-16T02:00:00Z",
        "curator": "claude",
        "action": "NORMALISE_NODE_TYPE",
        "changes": "Under the PATHWAY-vs-BIOLOGICAL_PROCESS rule, one node_id means one thing corpus-wide (issue 356): ectoine_biosynthesis is typed PATHWAY. PATHWAY is a named, conventionally enumerable multi-step route; BIOLOGICAL_PROCESS is everything else. A named route, enumerated two ways and both of them enumerations. environment/euryhaline.yaml counts five steps from L-aspartate (lysC/asd/ectB/ectA/ectC); environment/nacl_delta_mid1.yaml counts the three ectABC enzymes proper. Naming the file matters because the two differ and a bare quote would put euryhaline's wording into nacl_delta_mid1's record (#400 review). Either way the steps can be listed, which is the test. Applied AGAINST the majority, which was 4 BIOLOGICAL_PROCESS to 2 before this tranche.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope slight_halophile_low_salt_osmoadaptation=NONMECHANISTIC with scope_notes; marked 1 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (ect_gene_cluster).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T04:43:24Z",
        "curator": "codex",
        "action": "ADD_CANONICAL_EXAMPLES",
        "changes": "Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Paraliobacillus ryukyuensis (NCBITaxon:200904; DOI:10.2323/jgam.48.269). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000626",
    "label": "stenohaline",
    "definition": "A halophily preference in which an organism can only tolerate a narrow range of salinity concentrations and cannot survive significant changes in environmental salt levels.",
    "definition_source": "DOI:10.1186/s40168-024-01817-w",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000629"
    ],
    "created_by": "Luke Wang",
    "evidence": [
      {
        "reference": "DOI:10.1186/s40168-024-01817-w",
        "snippet": "narrow range of salinity",
        "notes": "Supports stenohaline microorganisms as organisms thriving within a narrow salinity range."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1979153",
        "taxon_label": "Synechococcus sp. YX04-3",
        "reference": "DOI:10.1128/msystems.01106-22",
        "note": "Marine clade III cyanobacterium that grew at 32 ppt but could not survive at 13 ppt, while the euryhaline strain HK05 grew at both; the only culture-based narrow-salinity growth evidence in this trait's research artifact. Only two salinity points were assayed and the artifact states the complete tolerated interval remains unknown."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "stenohaline_narrow_salinity_tolerance",
        "title": "Stenohaline narrow-salinity tolerance mechanism",
        "description": "Evidence-backed causal sketch linking stenohalinity to narrow salinity niches, osmotic imbalance during salinity shifts, and constrained salinity-adaptation capacity.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a broad environmental or morphological classification spanning multiple mechanisms, a measurement-like bin, or an absence/arrangement descriptor; contextual protein nodes do not receive token UniProt examples.",
        "nodes": [
          {
            "node_id": "stenohaline_trait",
            "label": "stenohaline",
            "node_type": "TRAIT",
            "grounding": "METPO:1000626",
            "description": "Tolerance is limited to a narrow range of salinity concentrations."
          },
          {
            "node_id": "narrow_salinity_range",
            "label": "narrow salinity range",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Restricted salinity interval that supports growth."
          },
          {
            "node_id": "salinity_shift",
            "label": "salinity shift",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Environmental increase or decrease in salt concentration."
          },
          {
            "node_id": "osmotic_imbalance",
            "label": "osmotic imbalance",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Difference between external and internal osmotic potential."
          },
          {
            "node_id": "water_flux",
            "label": "water flux across cytoplasmic membrane",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Osmotically driven water movement across the cell membrane."
          },
          {
            "node_id": "salinity_adaptation_genes",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "salinity-adaptation protein repertoire",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Protein repertoires associated with adaptation along salinity gradients."
          },
          {
            "node_id": "c_di_amp",
            "label": "cyclic di-AMP",
            "node_type": "CHEMICAL",
            "description": "Second messenger nucleotide that regulates osmolyte and K+ transport in bacteria.",
            "grounding": "CHEBI:71578"
          },
          {
            "node_id": "k_import_systems",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "K+ import systems",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Potassium uptake transporters (Trk/Ktr/Kup/Kdp-type) mediating salt-in osmoadaptation."
          },
          {
            "node_id": "opua_importer",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "compatible-solute importer OpuA",
            "node_type": "GENE_OR_PROTEIN",
            "description": "ABC-type transporter importing compatible solutes such as glycine betaine."
          },
          {
            "node_id": "low_c_di_amp_state",
            "label": "low c-di-AMP state",
            "node_type": "STATE",
            "description": "Cellular condition of reduced c-di-AMP, derepressing osmolyte and K+ uptake."
          },
          {
            "node_id": "k_solute_uptake",
            "label": "K+ and compatible-solute uptake",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Combined import of potassium and compatible solutes for osmotic adjustment."
          },
          {
            "node_id": "osmotic_upshift",
            "label": "osmotic upshift",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Increase in external osmolarity, e.g. a rise in environmental salinity."
          },
          {
            "node_id": "rapid_k_import",
            "label": "rapid K+ import",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Fast potassium influx mounted as an early osmoadaptation response."
          },
          {
            "node_id": "compatible_solute_accumulation",
            "label": "compatible-solute accumulation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Intracellular buildup of compatible solutes (proline, ectoine, trehalose)."
          },
          {
            "node_id": "salt_out_osmoadaptation",
            "label": "salt-out osmoadaptation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Long-term osmoadaptation via synthesis/import of compatible solutes."
          },
          {
            "node_id": "aquaporin_water_channel",
            "label": "aquaporin water-channel activity",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "Channel activity (COG0580 / GO:0015250) enabling facilitated water diffusion."
          },
          {
            "node_id": "facilitated_water_diffusion",
            "label": "facilitated water diffusion",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Passive water movement across the membrane through aquaporin channels."
          }
        ],
        "edges": [
          {
            "subject": "narrow_salinity_range",
            "predicate": "defines",
            "object": "stenohaline_trait",
            "description": "Stenohaline microorganisms thrive within a narrow salinity range.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s40168-024-01817-w",
                "snippet": "narrow range of salinity",
                "notes": "Microbiome study explicitly defines stenohaline microorganisms by a narrow salinity range."
              }
            ],
            "predicate_id": "METPO:2007500"
          },
          {
            "subject": "salinity_shift",
            "predicate": "causes",
            "object": "osmotic_imbalance",
            "description": "Salinity shifts create osmotic imbalance across the membrane.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s40168-024-01817-w",
                "snippet": "In response to osmotic imbalance",
                "notes": "Supports osmotic imbalance as a response to salinity change."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "osmotic_imbalance",
            "predicate": "regulates",
            "object": "water_flux",
            "description": "Osmotic imbalance drives water flux across the membrane.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s40168-024-01817-w",
                "snippet": "water immediately rushes into the cell",
                "notes": "Supports water flux during osmotic imbalance."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "salinity_adaptation_genes",
            "predicate": "regulates",
            "object": "stenohaline_trait",
            "description": "Salinity adaptation gene repertoires help determine salinity niche breadth; limited repertoires can correspond to narrow tolerance.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s40168-024-01817-w",
                "snippet": "genes associated with microbial salinity adaptation",
                "notes": "The constraint direction is inferred from the study's salinity adaptation analysis; kept broad because organism-specific gene sets vary."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "salinity_shift",
            "predicate": "exceeds tolerance of",
            "object": "stenohaline_trait",
            "description": "Large salinity changes can exceed the narrow tolerance range of stenohaline organisms.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s40168-024-01817-w",
                "snippet": "Organisms thriving within a narrow range of salinity",
                "notes": "Supports the ecological interpretation that large salinity excursions exceed stenohaline niche breadth."
              }
            ]
          },
          {
            "subject": "c_di_amp",
            "predicate": "inhibits",
            "object": "k_import_systems",
            "description": "c-di-AMP binds RCK-type gating subunits to inhibit potassium influx.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mmbr.00181-23",
                "notes": "c-di-AMP binds RCK-type gating subunits inhibiting potassium influx; broad regulatory principle across c-di-AMP bacteria."
              }
            ],
            "predicate_id": "RO:0002212"
          },
          {
            "subject": "c_di_amp",
            "predicate": "inhibits",
            "object": "opua_importer",
            "description": "c-di-AMP binds CBS-containing compatible-solute importers and negatively regulates their transport.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mmbr.00181-23",
                "notes": "Binds CBS-containing compatible-solute importers (OpuA, OpuC, OpuD) and negatively regulates transport; general osmoadaptation regulation."
              }
            ],
            "predicate_id": "RO:0002212"
          },
          {
            "subject": "low_c_di_amp_state",
            "predicate": "increases",
            "object": "k_solute_uptake",
            "description": "Low c-di-AMP increases uptake of K+ and compatible solutes.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mmbr.00181-23",
                "notes": "Low c-di-AMP mutants show increased uptake of K+ and compatible solutes; broad bacterial principle."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "osmotic_upshift",
            "predicate": "triggers",
            "object": "rapid_k_import",
            "description": "Osmotic upshift triggers rapid K+ import as an early osmoadaptation response.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsml/uqad020",
                "notes": "Many bacteria mount a rapid K+ import upon osmotic upshift; canonical osmoadaptation edge, not specific to stenohaline microbes."
              }
            ]
          },
          {
            "subject": "compatible_solute_accumulation",
            "predicate": "supports",
            "object": "salt_out_osmoadaptation",
            "description": "Accumulation of compatible solutes supports the salt-out osmoadaptation strategy.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsml/uqad020",
                "notes": "Longer-term strategy is salt-out via synthesis/import of compatible solutes (proline, ectoine, trehalose); general mechanistic edge."
              }
            ]
          },
          {
            "subject": "aquaporin_water_channel",
            "predicate": "enables",
            "object": "facilitated_water_diffusion",
            "description": "Aquaporin water-channel activity enables facilitated diffusion of water.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s40168-024-01817-w",
                "notes": "COG0580 linked to GO:0015250 and described as enabling facilitated diffusion of water; functional edge."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "k_import_systems",
            "predicate": "enables",
            "object": "rapid_k_import",
            "description": "Potassium-import systems enable the rapid K+ uptake used as an early bacterial response to osmotic upshift.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mmbr.00181-23",
                "snippet": "Bacterial cells commonly import a lot of potassium during an osmotic upshift",
                "notes": "Supports a generic bacterial osmoadaptation relationship; it does not establish potassium import as a cause of stenohaly."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "osmotic_upshift",
            "predicate": "causes",
            "object": "osmotic_imbalance",
            "description": "An increase in external osmolarity causes cellular water loss and an osmotic imbalance.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mmbr.00181-23",
                "snippet": "Under hypertonic conditions, water leaves the cell",
                "notes": "Supports the physical consequence of a generic osmotic upshift; it does not establish osmotic upshift as specific to stenohaline organisms."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "k_solute_uptake",
            "predicate": "mitigates",
            "object": "osmotic_imbalance",
            "description": "Uptake of potassium and compatible solutes helps cells survive changes in external osmolality.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mmbr.00181-23",
                "snippet": "potassium and compatible solute transport are vital for bacteria to survive changes in external osmolality",
                "notes": "Supports a generic bacterial osmoadaptation relationship; it does not establish this uptake process as a cause of stenohaly."
              }
            ],
            "predicate_id": "METPO:2007407"
          },
          {
            "subject": "salt_out_osmoadaptation",
            "predicate": "mitigates",
            "object": "osmotic_imbalance",
            "description": "Salt-out osmoadaptation replaces accumulated K+ with compatible solutes to restore osmotic balance.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mmbr.00181-23",
                "snippet": "neutral compatible solutes such as glycine betaine, trehalose, and other osmolytes to replace K+ ions",
                "notes": "Supports the generic salt-out strategy; it does not establish compatible-solute accumulation as a cause of stenohaly."
              }
            ],
            "predicate_id": "METPO:2007407"
          },
          {
            "subject": "facilitated_water_diffusion",
            "predicate": "part of",
            "object": "water_flux",
            "description": "Aquaporin-facilitated diffusion is one route of water flux across the cytoplasmic membrane.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s40168-024-01817-w",
                "snippet": "enabling the facilitated diffusion of water",
                "notes": "Connects the contextual aquaporin process to the record's existing water-flux process without asserting a direct effect on stenohaly."
              }
            ],
            "predicate_id": "biolink:part_of"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.864123+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-11T00:00:00-07:00",
        "curator": "codex",
        "action": "CURATED_WITH_LITERATURE",
        "changes": "Reviewed stenohaline trait and added DOI-backed causal graph for narrow salinity tolerance, salinity-shift osmotic imbalance, water flux, and constrained salinity-adaptation capacity.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T05:49:24Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:causes\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:18Z",
        "curator": "claude",
        "action": "RENAME_PREDICATE_LABELS",
        "changes": "Renamed 1 causal-edge predicate label(s) to align with existing groundings: drives \u2192 regulates \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:21Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002211\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T07:37:39Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007500\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-26T05:00:47Z",
        "curator": "claude",
        "action": "RENAME_PREDICATE_LABELS",
        "changes": "Renamed 1 causal-edge predicate label(s) to align with existing groundings: constrains \u2192 regulates \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-26T05:00:50Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002211\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-17T04:09:43Z",
        "curator": "claude",
        "action": "REMOVE_REDUNDANT_SYNONYM",
        "changes": "Removed 1 synonym(s) whose text duplicated the label (seeder redundancy; no information lost).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 6 evidence-backed generic edges (11 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:11Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 4 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002212\u00d72, RO:0002213\u00d71, RO:0002327\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:71578\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-20T08:00:00Z",
        "curator": "claude",
        "action": "BACKFILL_CANONICAL_EXAMPLES",
        "changes": "Added one exemplar taxon, the only organism in this trait's deep-research artifact whose cited evidence is a salinity growth/survival assay showing narrow tolerance. Taxon id resolved and label-checked against the local NCBITaxon build. Deliberately excluded - Synechococcus sp. HK05 and the euryhaline CB4 lineage (named as the contrasting broad-tolerance case), Halomonas elongata and Natranaerobius thermophilus (broadly salt-tolerant; the artifact warns their ectoine/hybrid salt-in-salt-out evidence concerns breadth of tolerance, not narrow range), Pseudomonas putida KT2440 (engineered tolerance expansion), and Acidihalobacter aeolianus (ion-specific osmotic-shock response, not a narrow growth range). The estuarine stenohaline MAGs of Wu et al. are unnamed and classified by a >=10-fold abundance proxy that the artifact states is not direct proof of narrow physiological tolerance.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope stenohaline_narrow_salinity_tolerance=NONMECHANISTIC with scope_notes; marked 3 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (salinity_adaptation_genes, k_import_systems, opua_importer).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T10:04:55Z",
        "curator": "codex",
        "action": "CONNECT_CAUSAL_GRAPH",
        "changes": "Connected five contextual osmoadaptation relationships to the existing osmotic-imbalance and water-flux processes, joining all six graph components. The new edges describe generic bacterial responses and do not assert that genes, proteins, or osmoadaptation mechanisms cause stenohaly; gene and protein concepts remain supporting YAML fields rather than primary TraitRecord entries. Addresses issues 426 and 183.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000611",
    "label": "strictly anaerobic",
    "definition": "An obligately anaerobic oxygen preference in which a microorganism does not grow in the presence of oxygen gas (O\u2082).",
    "definition_source": "https://www.ncbi.nlm.nih.gov/books/NBK482349/",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000607"
    ],
    "synonyms": [
      {
        "synonym_text": "strict obligate anaerobe",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://www.ncbi.nlm.nih.gov/books/NBK482349/"
      }
    ],
    "evidence": [
      {
        "reference": "https://www.ncbi.nlm.nih.gov/books/NBK482349/",
        "snippet": "will not survive if there is more than half a percent oxygen",
        "notes": "Supports strict anaerobiosis as a highly oxygen-sensitive subtype."
      },
      {
        "reference": "PMID:39189748",
        "snippet": "Clostridioides difficile is a strict anaerobic, sporulating Firmicutes",
        "notes": "Organism example: Clostridioides difficile is described as strictly anaerobic."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:817",
        "taxon_label": "Bacteroides fragilis",
        "note": "Aerotolerant obligate anaerobe; abundant gut anaerobe model. Clostridium spp. are alternative strict-anaerobe exemplars.",
        "reference": "PMID:14749831"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "strict_anaerobe_oxygen_sensitivity",
        "title": "Strict anaerobe oxygen-sensitivity mechanism",
        "description": "Evidence-backed causal sketch linking strict anaerobic growth to anoxic environments and oxygen-sensitive cellular chemistry.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a broad environmental or morphological classification spanning multiple mechanisms, a measurement-like bin, or an absence/arrangement descriptor; contextual protein nodes do not receive token UniProt examples.",
        "nodes": [
          {
            "node_id": "strictly_anaerobic_trait",
            "label": "strictly anaerobic",
            "node_type": "TRAIT",
            "grounding": "METPO:1000611",
            "description": "Does not grow in the presence of oxygen gas."
          },
          {
            "node_id": "anoxic_condition",
            "label": "anoxic condition",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Oxygen-excluding environment required for strict anaerobic growth.",
            "grounding": "PATO:0001456"
          },
          {
            "node_id": "molecular_oxygen",
            "label": "molecular oxygen",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:15379",
            "description": "Dioxygen exposure that prevents strict anaerobe growth."
          },
          {
            "node_id": "reactive_oxygen_species",
            "label": "reactive oxygen species",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:26523",
            "description": "Oxygen-derived oxidants."
          },
          {
            "node_id": "oxygen_sensitive_enzymes",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "oxygen-sensitive enzymes",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Anaerobic enzymes vulnerable to oxygen or ROS."
          },
          {
            "node_id": "iron_sulfur_cluster_enzymes",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "iron-sulfur cluster enzymes",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Mononuclear iron enzymes and solvent-exposed iron-sulfur cluster enzymes that are directly oxidized by oxygen."
          },
          {
            "node_id": "glycyl_radical_enzymes",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "glycyl radical enzymes",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Enzyme class inherently incompatible with molecular oxygen."
          },
          {
            "node_id": "low_potential_metabolic_enzymes",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "low-potential energy-metabolism enzymes (PFOR/PFL)",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Oxygen-sensitive anaerobic energy-metabolism enzymes such as pyruvate:ferredoxin oxidoreductase (PFOR) and pyruvate formate lyase (PFL)."
          }
        ],
        "edges": [
          {
            "subject": "anoxic_condition",
            "predicate": "confers",
            "object": "strictly_anaerobic_trait",
            "description": "Strict anaerobes require oxygen-excluding conditions for growth.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41579-021-00583-y",
                "snippet": "hypoxic or anoxic conditions",
                "notes": "Review supports anoxic environments as the ecological context for anaerobe growth."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "molecular_oxygen",
            "predicate": "inhibits",
            "object": "strictly_anaerobic_trait",
            "description": "Oxygen exposure blocks strict anaerobic growth.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41579-021-00583-y",
                "snippet": "oxygen blocks their growth",
                "notes": "Supports oxygen as an inhibitory exposure for obligate anaerobes."
              }
            ],
            "predicate_id": "RO:0002212"
          },
          {
            "subject": "molecular_oxygen",
            "predicate": "causes formation of",
            "object": "reactive_oxygen_species",
            "description": "Oxygen exposure can generate reactive oxygen stress.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41579-021-00583-y",
                "snippet": "molecular oxygen and ROS",
                "notes": "Review links oxygen exposure to ROS stress in anaerobes."
              }
            ],
            "predicate_id": "biolink:produces"
          },
          {
            "subject": "reactive_oxygen_species",
            "predicate": "damages",
            "object": "oxygen_sensitive_enzymes",
            "description": "ROS can impair oxygen-sensitive anaerobic enzyme systems.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41579-021-00583-y",
                "snippet": "poisoning by molecular oxygen and ROS",
                "notes": "Supports enzyme vulnerability as a mechanism of oxygen toxicity."
              }
            ]
          },
          {
            "subject": "molecular_oxygen",
            "predicate": "oxidizes/inactivates",
            "object": "iron_sulfur_cluster_enzymes",
            "description": "Oxygen directly oxidizes mononuclear iron enzymes and solvent-exposed iron-sulfur clusters.",
            "evidence": [
              {
                "reference": "DOI:10.1128/iai.00502-24",
                "notes": "\"oxygen directly oxidizes mononuclear iron enzymes and solvent-exposed iron-sulfur clusters\" - general oxygen toxicity mechanism across anaerobes."
              }
            ]
          },
          {
            "subject": "molecular_oxygen",
            "predicate": "inactivates",
            "object": "glycyl_radical_enzymes",
            "description": "Glycyl radical enzymes are inherently incompatible with molecular oxygen.",
            "evidence": [
              {
                "reference": "DOI:10.1128/iai.00502-24",
                "notes": "\"Certain enzyme classes (e.g., glycyl radical enzymes) are inherently incompatible with molecular oxygen\" - broad across taxa."
              }
            ]
          },
          {
            "subject": "molecular_oxygen",
            "predicate": "inactivates",
            "object": "low_potential_metabolic_enzymes",
            "description": "Key anaerobic energy-metabolism enzymes (PFOR, PFL) with low-potential Fe-S clusters are oxygen sensitive.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s43705-023-00251-7",
                "notes": "\"key enzymes involved in energy metabolism in anaerobes such as pyruvate ferrodoxin oxidoreductase (PFOR), pyruvate formate lyase (PFL)... are known to be O2 sensitive\" - general anaerobe biology."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.855051+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-05T01:09:05-07:00",
        "curator": "codex",
        "action": "CURATED_WITH_LITERATURE",
        "changes": "Clarified wording, added definition source, synonym, and evidence.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-05T18:39:46-07:00",
        "curator": "codex",
        "action": "ADDED_ORGANISM_EXAMPLE",
        "changes": "Added Clostridioides difficile organism example with PMID-backed evidence.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "ADDED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed causal graph for strict anaerobe oxygen sensitivity.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:30Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:38:00Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (ENVO:01001057\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-13T21:03:25Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002212\u00d71, biolink:produces\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-15T07:19:08Z",
        "curator": "claude",
        "action": "FIX_NODE_GROUNDING_CURIE",
        "changes": "Overwrote 1 causal-node grounding(s) to corrected CURIEs (phase-2 id-label fix; verified vs OAK).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-17T04:09:43Z",
        "curator": "claude",
        "action": "REMOVE_REDUNDANT_SYNONYM",
        "changes": "Removed 1 synonym(s) whose text duplicated the label (seeder redundancy; no information lost).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 3 evidence-backed generic edges (3 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 1 causal edge(s) off enables/RO:0002327 with a TRAIT object (1 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope strict_anaerobe_oxygen_sensitivity=NONMECHANISTIC with scope_notes; marked 4 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (oxygen_sensitive_enzymes, iron_sulfur_cluster_enzymes, glycyl_radical_enzymes, low_potential_metabolic_enzymes).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000303",
    "label": "temperature delta",
    "definition": "A temperature phenotype with numerical limits expressing the breadth (maximum minus minimum, in \u00b0C) of ambient temperatures supporting growth of an organism.",
    "definition_source": "DOI:10.1016/s0300-9629(97)00003-0",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000533",
      "METPO:1000534"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1016/s0300-9629(97)00003-0",
        "snippet": "adapted to environments of high temperature",
        "notes": "Thermophile-adaptation review supports the breadth of the temperature-tolerance span as a derived descriptor reflecting overall thermal-adaptation flexibility."
      },
      {
        "reference": "DOI:10.1146/annurev-micro-091313-103612",
        "snippet": "more unsaturated fatty acids",
        "notes": "Membrane-adaptation review supports homoviscous remodeling capacity as the basis of broad versus narrow temperature tolerance."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:504092",
        "taxon_label": "Kushneria aurantia",
        "reference": "DOI:10.1099/ijs.0.001461-0",
        "note": "Kushneria aurantia A10T grew from 20 to 40 degrees C, a 20-degree breadth. Because 20 meets the mid1/mid2 boundary, #591 keeps the claim on the delta parent."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "temperature_delta_thermal_flexibility",
        "title": "Temperature-delta thermal-adaptation flexibility",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a quantitative measurement, interval, or bin in the environmental phenotype hierarchy; a token protein example would misrepresent the measured value as one inherited molecular mechanism.",
        "description": "DOI-backed graph linking the flexibility of membrane and enzyme adaptation to the breadth of the temperature growth range (delta = max \u2212 min).",
        "nodes": [
          {
            "node_id": "temperature_delta_trait",
            "label": "temperature delta",
            "node_type": "TRAIT",
            "grounding": "METPO:1000303",
            "description": "Breadth of the growth-supporting ambient-temperature range."
          },
          {
            "node_id": "thermal_adaptation_flexibility",
            "label": "thermal-adaptation flexibility",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Capacity to remodel membrane lipid composition and enzyme repertoire across a wide span of ambient temperatures."
          },
          {
            "node_id": "tolerance_breadth",
            "label": "temperature tolerance breadth",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Span between the minimum and maximum growth-supporting ambient temperatures."
          },
          {
            "node_id": "unsaturated_fatty_acids",
            "label": "unsaturated fatty acids",
            "node_type": "CHEMICAL",
            "description": "Fatty acids bearing cis double bonds incorporated into membrane lipids.",
            "grounding": "CHEBI:27208"
          },
          {
            "node_id": "membrane_fluidity",
            "label": "membrane fluidity",
            "node_type": "QUALITY",
            "description": "Physical state of the lipid bilayer; higher fluidity corresponds to lower lipid order and lower transition temperature.",
            "grounding": "METPO:1007505"
          },
          {
            "node_id": "anteiso_branched_chain_fatty_acids",
            "label": "anteiso-branched-chain fatty acids",
            "node_type": "CHEMICAL",
            "description": "Branched-chain fatty acids that disrupt lipid packing and lower the membrane transition temperature."
          },
          {
            "node_id": "low_temperature_growth",
            "label": "membrane function and growth at low temperature",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Maintenance of membrane function supporting growth at the low-temperature end of the range."
          }
        ],
        "edges": [
          {
            "subject": "thermal_adaptation_flexibility",
            "predicate": "enables",
            "object": "tolerance_breadth",
            "description": "Thermal-adaptation flexibility enables broad temperature tolerance.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-micro-091313-103612",
                "snippet": "more unsaturated fatty acids",
                "notes": "Supports membrane-remodeling flexibility as the basis of broad thermal tolerance."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "tolerance_breadth",
            "predicate": "manifests as",
            "object": "temperature_delta_trait",
            "description": "The breadth between minimum and maximum growth-supporting ambient temperatures manifests the temperature-delta phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1016/s0300-9629(97)00003-0",
                "snippet": "adapted to environments of high temperature",
                "notes": "Supports the trait endpoint via thermal adaptation across a span."
              }
            ],
            "predicate_id": "METPO:2007400"
          },
          {
            "subject": "unsaturated_fatty_acids",
            "predicate": "increases",
            "object": "membrane_fluidity",
            "description": "cis-Unsaturated fatty acids disrupt lipid packing, lower the membrane transition temperature, and increase fluidity.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-micro-091313-103612",
                "notes": "cis-unsaturated fatty acids disrupt packing, lower Tm, and increase fluidity; foundational and broadly applicable."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "unsaturated_fatty_acids",
            "predicate": "supports",
            "object": "low_temperature_growth",
            "description": "Incorporation of more unsaturated fatty acids optimizes membrane function for growth at lower temperatures, extending the low-temperature end of the range.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-micro-091313-103612",
                "notes": "bacteria respond to decreasing growth temperature by incorporating proportionally more unsaturated fatty acids, optimizing cellular processes at the new temperature."
              }
            ]
          },
          {
            "subject": "anteiso_branched_chain_fatty_acids",
            "predicate": "increases",
            "object": "membrane_fluidity",
            "description": "Anteiso-branched-chain fatty acids disrupt lipid packing and lower the membrane transition temperature, increasing fluidity.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-micro-091313-103612",
                "notes": "anteiso-branched-chain fatty acids (a-BCFAs) disrupt packing, lower Tm; generalized across bacteria using branched lipids."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "anteiso_branched_chain_fatty_acids",
            "predicate": "required for",
            "object": "low_temperature_growth",
            "description": "Membrane function and growth at low temperature require both anteiso-branched-chain fatty acids and unsaturated fatty acids.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-micro-091313-103612",
                "notes": "Membrane function/growth at low temperature requires both anteiso-branched-chain fatty acids (a-BCFAs) and unsaturated fatty acids (UFAs)."
              }
            ]
          },
          {
            "subject": "low_temperature_growth",
            "predicate": "contributes to",
            "object": "tolerance_breadth",
            "description": "Supporting growth at the low-temperature end widens the span between minimum and maximum growth-supporting temperatures.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-micro-091313-103612",
                "notes": "Membrane homeoviscous adaptation extends low-temperature growth, broadening the temperature tolerance span (delta)."
              }
            ],
            "predicate_id": "RO:0002326"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.812991+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-13T11:00:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed causal graph linking thermal-adaptation flexibility to the temperature-delta breadth phenotype.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:30Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T21:30:06Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007400\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 5 evidence-backed generic edges (4 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:11Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002213\u00d72, RO:0002326\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:17Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (METPO:1007505\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:27208\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope temperature_delta_thermal_flexibility=NONMECHANISTIC with scope_notes.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T04:43:24Z",
        "curator": "codex",
        "action": "ADD_CANONICAL_EXAMPLES",
        "changes": "Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Kushneria aurantia (NCBITaxon:504092; DOI:10.1099/ijs.0.001461-0). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000487",
    "label": "temperature delta high",
    "definition": "A temperature delta phenotype with a growth-supporting temperature breadth above approximately 30 \u00b0C, characteristic of extreme-eurythermal physiology.",
    "definition_source": "DOI:10.1146/annurev-micro-091313-103612",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000303"
    ],
    "synonyms": [
      {
        "synonym_text": "Td_>30",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev-micro-091313-103612",
        "snippet": "more unsaturated fatty acids",
        "notes": "Membrane-adaptation review supports very broad homoviscous remodeling capacity as the basis of extreme-eurythermal physiology."
      },
      {
        "reference": "DOI:10.1128/MMBR.65.1.1-43.2001",
        "snippet": "resistant to irreversible inactivation at high temperatures",
        "notes": "Thermostable-protein review supports robust thermostability as the basis of extending tolerance beyond standard mesophile ranges."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1385984",
        "taxon_label": "Exiguobacterium chiriqhucha",
        "reference": "DOI:10.3389/fmicb.2018.03189",
        "note": "Eurythermal firmicute whose strain RW2 was grown across 4-50 degrees C on M-medium, a 46 degrees C breadth and the broadest reported for the genus; membrane phospholipid composition was measured at 4, 18, 30 and 50 degrees C, confirming growth at both endpoints rather than mere survival."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "temperature_delta_high_eurythermal",
        "title": "Temperature-delta-high eurythermal context",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a quantitative measurement, interval, or bin in the environmental phenotype hierarchy; a token protein example would misrepresent the measured value as one inherited molecular mechanism.",
        "description": "DOI-backed nonmechanistic graph connecting maximal thermal-adaptation flexibility, cold-side homoviscous membrane remodeling, high-temperature membrane-viscosity shifts, and thermostable-enzyme context to the above-30-degrees-C temperature-delta bin.",
        "nodes": [
          {
            "node_id": "temperature_delta_high_trait",
            "label": "temperature delta high",
            "node_type": "TRAIT",
            "grounding": "METPO:1000487",
            "description": "Temperature growth-supporting breadth above ~30 \u00b0C."
          },
          {
            "node_id": "temperature_delta",
            "label": "temperature delta",
            "node_type": "TRAIT",
            "grounding": "METPO:1000303",
            "description": "Breadth of the growth-supporting ambient-temperature range."
          },
          {
            "node_id": "maximal_thermal_adaptation",
            "label": "maximal thermal-adaptation flexibility",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Combined membrane remodeling and protein-thermostability capacity supporting growth across an extreme temperature span."
          },
          {
            "node_id": "decreased_growth_temperature",
            "label": "decreased growth temperature",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "A decrease in ambient growth temperature."
          },
          {
            "node_id": "unsaturated_fatty_acid_biosynthesis",
            "label": "unsaturated fatty acid biosynthesis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Biosynthesis of unsaturated fatty acids for membrane remodeling.",
            "grounding": "GO:0006636"
          },
          {
            "node_id": "homoviscous_adaptation",
            "label": "homoviscous adaptation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Temperature-driven remodeling of membrane lipid composition to maintain bilayer order.",
            "grounding": "METPO:1016200"
          },
          {
            "node_id": "membrane_fluidity_homeostasis",
            "label": "membrane fluidity homeostasis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Maintenance of membrane fluidity and permeability across thermal shifts."
          },
          {
            "node_id": "decreased_membrane_fluidity",
            "label": "decreased membrane fluidity",
            "node_type": "STATE",
            "description": "Reduced membrane fluidity sensed as a signal upon cooling."
          },
          {
            "node_id": "lipid_desaturase_activity",
            "label": "lipid desaturase activity",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "Desaturase activity introducing cis double bonds into fatty acids."
          },
          {
            "node_id": "membrane_fluidity",
            "label": "membrane fluidity",
            "node_type": "QUALITY",
            "description": "Physical fluidity of the membrane lipid bilayer.",
            "grounding": "METPO:1007505"
          },
          {
            "node_id": "membrane_viscosity_high_temperature",
            "label": "membrane viscosity at higher temperature",
            "node_type": "QUALITY",
            "description": "Increased membrane viscosity to counter excess fluidity during warming."
          },
          {
            "node_id": "increased_fatty_acid_diversity",
            "label": "increased short-/branched-/unsaturated fatty acids",
            "node_type": "CHEMICAL",
            "description": "Shifts toward short-chain, branched-chain and unsaturated fatty acids in the membrane."
          },
          {
            "node_id": "thermostable_enzyme",
            "label": "hyperthermophilic enzyme thermostability",
            "node_type": "QUALITY",
            "description": "Intrinsic thermostability of enzymes from hyperthermophiles."
          },
          {
            "node_id": "irreversible_protein_inactivation",
            "label": "irreversible inactivation at high temperatures",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Irreversible loss of protein activity at high temperatures."
          }
        ],
        "edges": [
          {
            "subject": "maximal_thermal_adaptation",
            "predicate": "confers",
            "object": "temperature_delta_high_trait",
            "description": "Maximal thermal-adaptation flexibility yields an extreme temperature-delta breadth.",
            "evidence": [
              {
                "reference": "DOI:10.1128/MMBR.65.1.1-43.2001",
                "snippet": "resistant to irreversible inactivation at high temperatures",
                "notes": "Supports maximal thermal-adaptation as the basis of extreme eurythermal breadth."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "temperature_delta_high_trait",
            "predicate": "is a",
            "object": "temperature_delta",
            "description": "Temperature delta high is a quantitative bin of the temperature-delta phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-micro-091313-103612",
                "snippet": "more unsaturated fatty acids",
                "notes": "Supports the >30 \u00b0C breadth as a value within the temperature-delta distribution."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "decreased_growth_temperature",
            "predicate": "increases",
            "object": "unsaturated_fatty_acid_biosynthesis",
            "description": "Lower growth temperature increases incorporation of unsaturated fatty acids (homoviscous adaptation).",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-micro-091313-103612",
                "snippet": "incorporation of proportionally more unsaturated fatty acids",
                "notes": "Verified against the de Mendoza Annual Review abstract; bacterial membranes remodel by incorporating proportionally more unsaturated fatty acids as growth temperature decreases."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "homoviscous_adaptation",
            "predicate": "contributes to",
            "object": "membrane_fluidity_homeostasis",
            "description": "Homoviscous adaptation contributes to membrane fluidity/permeability homeostasis across thermal shifts.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-micro-091313-103612",
                "snippet": "remodel the fluidity of their membrane bilayer",
                "notes": "Verified against the de Mendoza Annual Review abstract; homoviscous adaptation is the named membrane-fluidity remodeling process used after growth temperature decreases."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "decreased_membrane_fluidity",
            "predicate": "positively regulates",
            "object": "unsaturated_fatty_acid_biosynthesis",
            "description": "Reduced membrane fluidity is sensed and positively regulates unsaturated fatty acid biosynthesis.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-micro-091313-103612",
                "snippet": "upregulate the biosynthesis of unsaturated fatty acids",
                "notes": "Verified against the de Mendoza Annual Review abstract; bacteria sense decreased membrane fluidity and initiate responses that upregulate unsaturated fatty acid biosynthesis."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "lipid_desaturase_activity",
            "predicate": "increases",
            "object": "membrane_fluidity",
            "description": "Lipid desaturases introduce cis double bonds that loosen packing and increase fluidity.",
            "evidence": [
              {
                "reference": "DOI:10.3390/cells12101353",
                "snippet": "cis-double bonds, result in looser packing and increased fluidity",
                "notes": "Verified against the Wu et al. Cells review; lipid desaturase-generated cis double bonds loosen acyl-chain packing and increase membrane-bilayer fluidity."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "increased_fatty_acid_diversity",
            "predicate": "increases",
            "object": "membrane_fluidity",
            "description": "Shifts in acyl chain length/branching and unsaturation jointly increase membrane fluidity at lower temperatures.",
            "evidence": [
              {
                "reference": "DOI:10.3390/cells12101353",
                "snippet": "increase the proportion of UFAs and short-chain fatty acids",
                "notes": "Verified against the Wu et al. Cells review; cold-adapted membranes can increase unsaturated and short-chain fatty acid proportions and modify branched-chain fatty-acid content."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "thermostable_enzyme",
            "predicate": "prevents",
            "object": "irreversible_protein_inactivation",
            "description": "Intrinsic enzyme thermostability prevents irreversible inactivation, extending upper growth limits.",
            "evidence": [
              {
                "reference": "DOI:10.1128/MMBR.65.1.1-43.2001",
                "snippet": "resistant to irreversible inactivation at high temperatures",
                "notes": "Verified against the open Vieille and Zeikus review; hyperthermophilic enzymes are described as thermostable and resistant to irreversible inactivation at high temperatures."
              }
            ],
            "predicate_id": "RO:0002212"
          },
          {
            "subject": "unsaturated_fatty_acid_biosynthesis",
            "predicate": "contributes to",
            "object": "homoviscous_adaptation",
            "description": "Unsaturated-fatty-acid biosynthesis contributes to cold-side homoviscous membrane remodeling.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-micro-091313-103612",
                "snippet": "termed homeoviscous adaptation",
                "notes": "Verified against the de Mendoza Annual Review abstract; this connector keeps unsaturated-fatty-acid biosynthesis as one component of the named membrane-fluidity adaptation rather than the whole response."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "membrane_fluidity",
            "predicate": "associated with",
            "object": "membrane_fluidity_homeostasis",
            "description": "Membrane fluidity is associated with the homoviscous homeostasis branch of broad thermal adaptation.",
            "evidence": [
              {
                "reference": "DOI:10.3390/cells12101353",
                "snippet": "increase of unsaturated fatty acids in membrane phospholipids, which promotes membrane fluidity",
                "notes": "Verified against the Wu et al. Cells review; this connector keeps desaturase-linked fluidity as a physical membrane state associated with homeostasis."
              }
            ],
            "predicate_id": "biolink:associated_with"
          },
          {
            "subject": "membrane_viscosity_high_temperature",
            "predicate": "associated with",
            "object": "membrane_fluidity_homeostasis",
            "description": "High-temperature membrane viscosity is associated with the warming-side boundary of membrane-fluidity homeostasis.",
            "evidence": [
              {
                "reference": "DOI:10.3390/cells12101353",
                "snippet": "trans-UFA generation elevates the viscosity of the membrane",
                "notes": "Verified against the Wu et al. Cells review; this connector keeps cis-trans isomerization as warming-side membrane context."
              }
            ],
            "predicate_id": "biolink:associated_with"
          },
          {
            "subject": "membrane_fluidity_homeostasis",
            "predicate": "associated with",
            "object": "maximal_thermal_adaptation",
            "description": "Membrane-fluidity homeostasis is associated with the broad thermal-adaptation context used to represent an extreme temperature-growth breadth.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-micro-091313-103612",
                "snippet": "molecular strategies to sense changes in membrane fluidity",
                "notes": "Verified against the de Mendoza Annual Review abstract; this connector scopes homoviscous adaptation as membrane context for the eurythermal bin."
              }
            ],
            "predicate_id": "biolink:associated_with"
          },
          {
            "subject": "thermostable_enzyme",
            "predicate": "associated with",
            "object": "maximal_thermal_adaptation",
            "description": "Thermostable-enzyme protection is associated with the high-temperature side of broad thermal adaptation.",
            "evidence": [
              {
                "reference": "DOI:10.1128/MMBR.65.1.1-43.2001",
                "snippet": "are typically thermostable (i.e., resistant to irreversible inactivation at high temperatures) and are optimally active at high temperatures",
                "notes": "Verified against the open Vieille and Zeikus review; this connector keeps thermostable enzymes as high-temperature context rather than direct proof of an above-30-degrees-C growth breadth."
              }
            ],
            "predicate_id": "biolink:associated_with"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.845441+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-13T11:00:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed definition and causal graph linking maximal thermal-adaptation flexibility to the eurythermal temperature-delta-high bin.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:30Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d71, rdfs:subClassOf\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 7 evidence-backed generic edges (12 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:11Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 4 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002213\u00d74).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:17Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (METPO:1007505\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0006636\u00d71, GO:0016859\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates (1 to confers), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-15T02:00:00Z",
        "curator": "claude",
        "action": "NORMALISE_NODE_TYPE",
        "changes": "Normalised causal-node type(s) so one node_id means one thing corpus-wide (issue 356): membrane_fluidity_homeostasis: STATE -> BIOLOGICAL_PROCESS. The counterpart of the above, and the reason the rename was not needed: this id already exists for the process sense. Both occurrences describe 'Maintenance of membrane fluidity ...', and the schema's STATE definition excludes exactly this -- 'the state is the gradient / steady-value, NOT ITS ESTABLISHMENT'. Maintenance is establishment. So the STATE-typed one (temperature_delta_high.yaml) is retyped to match the process it describes.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-20T08:00:00Z",
        "curator": "claude",
        "action": "BACKFILL_CANONICAL_EXAMPLES",
        "changes": "Added one exemplar taxon, Exiguobacterium chiriqhucha (strain RW2), the only organism this trait's deep-research artifact establishes as an instance of the >30 C breadth bin -- growth measured over 4-50 C, a 46 C delta. Taxon id resolved and label-checked against the local NCBITaxon build; reference taken from the artifact. Deliberately excluded, all named in the same artifact but as mechanism or contrast cases rather than instances of the bin - Shewanella frigidimarina (4-30 C is a 26 C delta, which the artifact says \"falls below the proposed >30 C threshold\" and \"should not be used as a positive trait anchor\" without additional endpoint data); Bacillus subtilis (source of the DesK/DesR/des cold-end module, no breadth measured); Escherichia coli, Pseudomonas putida and Saccharomyces cerevisiae (heterologous CspL hosts showing warm-end growth gains only, which the artifact warns \"does not demonstrate >30 C breadth\"); Bacillus coagulans (CspL source strain, no breadth measured).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope temperature_delta_high_eurythermal=NONMECHANISTIC with scope_notes.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-04T03:00:00Z",
        "curator": "codex",
        "action": "REVIEW_CAUSAL_EVIDENCE",
        "changes": "Reviewed the temperature_delta_high_eurythermal graph for issue #183: added snippets to 7 edge-level evidence items and grounded 3 unmapped homoviscous-adaptation and thermostability predicates to RO:0002326, RO:0002213, or RO:0002212. No paid research service was called.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-04T19:00:00Z",
        "curator": "codex",
        "action": "CONNECT_CAUSAL_GRAPH_COMPONENTS",
        "changes": "Resolved issue #183 graph fragmentation (6 components to 1) by adding 5 source- and verbatim-snippet-backed association or contribution connectors among cold UFA synthesis, homoviscous adaptation, membrane-fluidity, high-temperature membrane-viscosity, and thermostable-enzyme branches. No paid research service was called.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-06T17:10:00Z",
        "curator": "codex",
        "action": "ADVERSARIAL_REVIEW_REPAIR",
        "changes": "Addressed PR #664 adversarial review: requoted the de Mendoza membrane-fluidity adaptation evidence with the exact homeoviscous spelling from the cited source.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-07T07:24:00Z",
        "curator": "codex",
        "action": "ADVERSARIAL_REVIEW_REPAIR",
        "changes": "Addressed PR #664 adversarial review issue #692: requoted the Wu et al. trans-UFA connector snippet without the markup-flattening space before the hyphen.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-08T03:05:00Z",
        "curator": "codex",
        "action": "ADVERSARIAL_REVIEW_REPAIR",
        "changes": "Addressed PR #664 adversarial review issue #700: removed the unsupported cis-trans-isomerase high-temperature membrane-viscosity edge and its abandoned isomerase node.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-15T07:05:57Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (METPO:1016200\u00d71).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000484",
    "label": "temperature delta low",
    "definition": "A temperature delta phenotype with a growth-supporting temperature breadth of approximately 5\u201310 \u00b0C, characteristic of organisms with limited thermal-tolerance breadth.",
    "definition_source": "DOI:10.1146/annurev-micro-091313-103612",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000303"
    ],
    "synonyms": [
      {
        "synonym_text": "Td_5_10",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev-micro-091313-103612",
        "snippet": "more unsaturated fatty acids",
        "notes": "Membrane-adaptation review supports limited thermal-adaptation flexibility as the basis of narrow thermal-tolerance breadths."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "temperature_delta_low_limited_breadth",
        "title": "Temperature-delta-low limited-breadth thermal adaptation",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a quantitative measurement, interval, or bin in the environmental phenotype hierarchy; a token protein example would misrepresent the measured value as one inherited molecular mechanism.",
        "description": "DOI-backed graph linking limited thermal-adaptation flexibility to a 5\u201310 \u00b0C temperature growth breadth.",
        "nodes": [
          {
            "node_id": "temperature_delta_low_trait",
            "label": "temperature delta low",
            "node_type": "TRAIT",
            "grounding": "METPO:1000484",
            "description": "Temperature growth-supporting breadth approximately 5\u201310 \u00b0C."
          },
          {
            "node_id": "temperature_delta",
            "label": "temperature delta",
            "node_type": "TRAIT",
            "grounding": "METPO:1000303",
            "description": "Breadth of the growth-supporting ambient-temperature range."
          },
          {
            "node_id": "limited_thermal_adaptation",
            "label": "limited thermal-adaptation flexibility",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Modest capacity to remodel membrane lipids and enzymes across small temperature shifts."
          },
          {
            "node_id": "temperature_decrease",
            "label": "temperature decrease",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "A drop in ambient growth temperature (cooling)."
          },
          {
            "node_id": "membrane_rigidity",
            "label": "membrane rigidification/thickening",
            "node_type": "QUALITY",
            "description": "Reduced bilayer fluidity and increased thickness on cooling, with liquid-crystalline-to-gel transition."
          },
          {
            "node_id": "unsaturated_fatty_acids",
            "label": "membrane unsaturated fatty acids",
            "node_type": "CHEMICAL",
            "description": "Unsaturated fatty acids incorporated into membrane lipids that lower the bilayer melting point."
          },
          {
            "node_id": "homeoviscous_adaptation",
            "label": "homeoviscous adaptation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Lipid remodeling that maintains membrane fluidity across temperature, restoring bilayer fluidity.",
            "grounding": "METPO:1016200"
          },
          {
            "node_id": "anteiso_bcfa_shift",
            "label": "iso-to-anteiso branched-chain fatty acid shift",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Long-term membrane fluidization via iso-to-anteiso branched-chain fatty acid switching."
          }
        ],
        "edges": [
          {
            "subject": "limited_thermal_adaptation",
            "predicate": "confers",
            "object": "temperature_delta_low_trait",
            "description": "Limited thermal-adaptation flexibility yields a 5\u201310 \u00b0C temperature-delta breadth.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-micro-091313-103612",
                "snippet": "more unsaturated fatty acids",
                "notes": "Supports limited thermal-adaptation flexibility as the basis of narrow breadth."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "temperature_delta_low_trait",
            "predicate": "is a",
            "object": "temperature_delta",
            "description": "Temperature delta low is a quantitative bin of the temperature-delta phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1016/s0300-9629(97)00003-0",
                "snippet": "adapted to environments of high temperature",
                "notes": "Supports the 5\u201310 \u00b0C breadth as a value within the temperature-delta distribution."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "temperature_decrease",
            "predicate": "causes",
            "object": "membrane_rigidity",
            "description": "Cooling reduces bilayer fluidity, inducing membrane rigidification and thickening.",
            "evidence": [
              {
                "reference": "DOI:10.1128/spectrum.03925-23",
                "notes": "Decreasing temperature induces membrane rigidification and thickening, producing a liquid-crystalline-to-gel phase transition."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "unsaturated_fatty_acids",
            "predicate": "contributes to",
            "object": "homeoviscous_adaptation",
            "description": "Increased membrane unsaturated fatty acids counter low-temperature rigidification and restore bilayer fluidity.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-micro-091313-103612",
                "notes": "Bacteria perform homoviscous adaptation by increasing membrane unsaturated fatty acids as growth temperature decreases, thereby restoring bilayer fluidity."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "homeoviscous_adaptation",
            "predicate": "counteracts",
            "object": "membrane_rigidity",
            "description": "Homeoviscous adaptation restores fluidity, opposing cold-induced membrane rigidification.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-micro-091313-103612",
                "notes": "Homeoviscous adaptation restores bilayer fluidity against rigidification as growth temperature decreases."
              }
            ]
          },
          {
            "subject": "temperature_decrease",
            "predicate": "shifts",
            "object": "anteiso_bcfa_shift",
            "description": "Low-temperature acclimation drives iso-to-anteiso branched-chain fatty acid switching for membrane fluidization.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s42770-023-01057-4",
                "notes": "Predominant long-term adaptation to low temperatures occurs via fluidization of the membrane by chain branching, specifically iso-to-anteiso SFA switching."
              }
            ]
          },
          {
            "subject": "anteiso_bcfa_shift",
            "predicate": "contributes to",
            "object": "homeoviscous_adaptation",
            "description": "Branched-chain fatty acid remodeling fluidizes the membrane, supporting homeoviscous adaptation.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s42770-023-01057-4",
                "notes": "Long-term low-temperature adaptation fluidizes the membrane via introduction of chain branching, a homeoviscous mechanism."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "limited_thermal_adaptation",
            "predicate": "limits",
            "object": "homeoviscous_adaptation",
            "description": "Impaired acyl-chain remodeling capacity constrains homeoviscous adaptation flexibility, narrowing thermal breadth.",
            "evidence": [
              {
                "reference": "DOI:10.1101/2023.11.10.566608",
                "notes": "Impaired homeoviscous adaptation: unable to regulate the acyl chain profile to the same extent in response to temperature fluctuations."
              }
            ],
            "predicate_id": "RO:0002212"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.843770+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-13T11:00:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed definition and causal graph linking limited thermal-adaptation flexibility to the narrow-breadth temperature-delta-low bin.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:30Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d71, rdfs:subClassOf\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 6 evidence-backed generic edges (5 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:11Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 4 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002326\u00d72, biolink:causes\u00d71, RO:0002212\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates (1 to confers), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-21T08:00:00Z",
        "curator": "codex",
        "action": "NORMALISE_NODE_TYPE",
        "changes": "Tranche 5 of issue 356 settles the process/quality families and merges ids that meant the same sense: membrane_rigidity is QUALITY. Membrane rigidity is a physical attribute of the bilayer and therefore a QUALITY under the schema's membrane-fluidity example.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope temperature_delta_low_limited_breadth=NONMECHANISTIC with scope_notes.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T04:43:24Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed issue #444 after #591 and left canonical_examples empty: The tracked artifact explicitly found no natural organism with both sustained-growth endpoints establishing a non-boundary 5-10 degree C breadth. Stress survival and one-endpoint studies do not qualify under #591. No paid research was used.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-15T07:02:39Z",
        "curator": "codex",
        "action": "NORMALIZED_CAUSAL_NODE_LABELS",
        "changes": "Normalized the homeoviscous-adaptation causal-node label before grounding it through proposals/metpo_traitmech_v85.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-15T07:05:57Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (METPO:1016200\u00d71).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000485",
    "label": "temperature delta mid1",
    "definition": "A temperature delta phenotype with a growth-supporting temperature breadth of approximately 10\u201320 \u00b0C, characteristic of organisms with moderate thermal-tolerance breadth.",
    "definition_source": "DOI:10.1146/annurev-micro-091313-103612",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000303"
    ],
    "synonyms": [
      {
        "synonym_text": "Td_10_20",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev-micro-091313-103612",
        "snippet": "more unsaturated fatty acids",
        "notes": "Membrane-adaptation review supports moderate homoviscous remodeling capacity as common among generalist mesophiles."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:2781979",
        "taxon_label": "Pontibacterium sinense",
        "reference": "DOI:10.1099/ijsem.0.006018",
        "note": "Pontibacterium sinense N1Y112T grew from 20 to 35 degrees C, a 15-degree breadth wholly inside the approximately 10-20-degree delta bin."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "temperature_delta_mid1_moderate_breadth",
        "title": "Temperature-delta-mid1 moderate-breadth thermal adaptation",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a quantitative measurement, interval, or bin in the environmental phenotype hierarchy; a token protein example would misrepresent the measured value as one inherited molecular mechanism.",
        "description": "DOI-backed graph linking moderate thermal-adaptation flexibility to a 10\u201320 \u00b0C temperature growth breadth.",
        "nodes": [
          {
            "node_id": "temperature_delta_mid1_trait",
            "label": "temperature delta mid1",
            "node_type": "TRAIT",
            "grounding": "METPO:1000485",
            "description": "Temperature growth-supporting breadth approximately 10\u201320 \u00b0C."
          },
          {
            "node_id": "temperature_delta",
            "label": "temperature delta",
            "node_type": "TRAIT",
            "grounding": "METPO:1000303",
            "description": "Breadth of the growth-supporting ambient-temperature range."
          },
          {
            "node_id": "moderate_thermal_adaptation",
            "label": "moderate thermal-adaptation flexibility",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Mid-range capacity to remodel membrane lipids and enzymes across temperature shifts of ~10\u201320 \u00b0C."
          },
          {
            "node_id": "temperature_decrease",
            "label": "decrease in ambient temperature",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "A drop in ambient growth temperature, the proximal cue for cold membrane adaptation."
          },
          {
            "node_id": "membrane_unsaturated_fatty_acids",
            "label": "membrane unsaturated fatty acids",
            "node_type": "CHEMICAL",
            "description": "Cis-unsaturated acyl chains in membrane phospholipids whose abundance sets membrane fluidity."
          },
          {
            "node_id": "membrane_fluidity",
            "label": "membrane fluidity",
            "node_type": "QUALITY",
            "description": "Physical fluid state of the lipid bilayer that must be maintained across temperature shifts.",
            "grounding": "METPO:1007505"
          },
          {
            "node_id": "ufa_biosynthesis",
            "label": "cis-unsaturated fatty acid biosynthesis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Synthesis of cis-unsaturated fatty acids that remodel membrane lipids during cooling."
          },
          {
            "node_id": "membrane_physical_state_change",
            "label": "membrane physical-state change",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Cold-induced change in the liquid-crystalline state of the membrane acting as a sensor event."
          },
          {
            "node_id": "two_component_cold_signaling",
            "label": "two-component cold signaling",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Two-component signal transduction triggering the cold-adaptation transcriptional response."
          },
          {
            "node_id": "thermal_niche_breadth",
            "label": "thermal niche / temperature breadth",
            "node_type": "QUALITY",
            "description": "Thermal tolerance niche operationally bounded by growth-supporting Tmin and Tmax."
          },
          {
            "node_id": "tmin_tmax",
            "label": "Tmin and Tmax growth boundaries",
            "node_type": "QUALITY",
            "description": "Minimum and maximum growth-supporting temperatures that flank the thermal niche."
          }
        ],
        "edges": [
          {
            "subject": "moderate_thermal_adaptation",
            "predicate": "confers",
            "object": "temperature_delta_mid1_trait",
            "description": "Moderate thermal-adaptation flexibility yields a 10\u201320 \u00b0C temperature-delta breadth.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-micro-091313-103612",
                "snippet": "more unsaturated fatty acids",
                "notes": "Supports moderate remodeling flexibility as the basis of an intermediate breadth."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "temperature_delta_mid1_trait",
            "predicate": "is a",
            "object": "temperature_delta",
            "description": "Temperature delta mid1 is a quantitative bin of the temperature-delta phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1016/s0300-9629(97)00003-0",
                "snippet": "adapted to environments of high temperature",
                "notes": "Supports the 10\u201320 \u00b0C breadth as a value within the temperature-delta distribution."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "temperature_decrease",
            "predicate": "increases",
            "object": "ufa_biosynthesis",
            "description": "Colder temperature shifts fatty-acid synthesis toward cis-unsaturated products to preserve membrane function.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s42770-023-01057-4",
                "notes": "Ramon 2023 review: increased unsaturation (especially cis-MUFA) on temperature decrease; broad review support."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "ufa_biosynthesis",
            "predicate": "increases",
            "object": "membrane_unsaturated_fatty_acids",
            "description": "Cis-unsaturated fatty acid biosynthesis raises the unsaturated acyl-chain content of membrane lipids.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s42770-023-01057-4",
                "notes": "Ramon 2023: microbes increase cis-unsaturation to remodel membranes, a general cold-adaptation output."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "membrane_unsaturated_fatty_acids",
            "predicate": "increases",
            "object": "membrane_fluidity",
            "description": "More unsaturated acyl chains counteract cold-induced rigidification and restore membrane fluidity.",
            "evidence": [
              {
                "reference": "DOI:10.1128/spectrum.03925-23",
                "notes": "Sidarta 2024: desaturation fluidizes membranes; central homeoviscous-adaptation edge, generalizable."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "membrane_physical_state_change",
            "predicate": "activates",
            "object": "two_component_cold_signaling",
            "description": "Cold-induced changes in the membrane liquid-crystalline state act as the upstream sensor activating two-component cold signaling.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s42770-023-01057-4",
                "notes": "Ramon 2023: cold sensing via changes in liquid-crystalline state of membranes that activate two-component signalling."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "membrane_fluidity",
            "predicate": "enables",
            "object": "moderate_thermal_adaptation",
            "description": "Maintained membrane fluidity across temperature shifts underlies the moderate thermal-adaptation flexibility that supports the breadth.",
            "evidence": [
              {
                "reference": "DOI:10.1128/spectrum.03925-23",
                "notes": "Sidarta 2024: homeoviscous adaptation restores fluidity, the membrane-target of thermal adaptation."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "tmin_tmax",
            "predicate": "defines",
            "object": "thermal_niche_breadth",
            "description": "Growth-supporting minimum and maximum temperatures flank the thermal function and mark the thermal niche/breadth.",
            "evidence": [
              {
                "reference": "DOI:10.3390/pr8010121",
                "notes": "Noll 2020: Tmin and Tmax for growth flank the function and mark the thermal tolerance/niche of an organism."
              }
            ],
            "predicate_id": "METPO:2007500"
          },
          {
            "subject": "thermal_niche_breadth",
            "predicate": "is a",
            "object": "temperature_delta",
            "description": "The Tmin/Tmax-bounded thermal niche is the breadth quantity captured by the temperature-delta phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.3390/pr8010121",
                "notes": "Noll 2020: thermal breadth treated as a cardinal-temperature bounded niche property."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.844372+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-13T11:00:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed definition and causal graph linking moderate thermal-adaptation flexibility to the temperature-delta-mid1 bin.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:30Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d71, rdfs:subClassOf\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 7 evidence-backed generic edges (8 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:11Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 7 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002213\u00d74, RO:0002327\u00d71, METPO:2007500\u00d71, rdfs:subClassOf\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:17Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (METPO:1007505\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates (1 to confers), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope temperature_delta_mid1_moderate_breadth=NONMECHANISTIC with scope_notes.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T04:43:24Z",
        "curator": "codex",
        "action": "ADD_CANONICAL_EXAMPLES",
        "changes": "Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Pontibacterium sinense (NCBITaxon:2781979; DOI:10.1099/ijsem.0.006018). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000486",
    "label": "temperature delta mid2",
    "definition": "A temperature delta phenotype with a growth-supporting temperature breadth of approximately 20\u201330 \u00b0C, characteristic of organisms with broad thermal-tolerance breadth.",
    "definition_source": "DOI:10.1146/annurev-micro-091313-103612",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000303"
    ],
    "synonyms": [
      {
        "synonym_text": "Td_20_30",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev-micro-091313-103612",
        "snippet": "more unsaturated fatty acids",
        "notes": "Membrane-adaptation review supports broad homoviscous remodeling capacity as the basis of eurythermal physiology."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:2593654",
        "taxon_label": "Pseudomonas mangiferae",
        "reference": "DOI:10.1099/ijsem.0.003657",
        "note": "Pseudomonas mangiferae DMKU BBB3-04T grew from 12 to 40 degrees C, a 28-degree breadth wholly inside the approximately 20-30-degree delta bin."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "temperature_delta_mid2_broad_breadth",
        "title": "Temperature-delta-mid2 broad-breadth thermal adaptation",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a quantitative measurement, interval, or bin in the environmental phenotype hierarchy; a token protein example would misrepresent the measured value as one inherited molecular mechanism.",
        "description": "DOI-backed graph linking broad thermal-adaptation flexibility to a 20\u201330 \u00b0C temperature growth breadth.",
        "nodes": [
          {
            "node_id": "temperature_delta_mid2_trait",
            "label": "temperature delta mid2",
            "node_type": "TRAIT",
            "grounding": "METPO:1000486",
            "description": "Temperature growth-supporting breadth approximately 20\u201330 \u00b0C."
          },
          {
            "node_id": "temperature_delta",
            "label": "temperature delta",
            "node_type": "TRAIT",
            "grounding": "METPO:1000303",
            "description": "Breadth of the growth-supporting ambient-temperature range."
          },
          {
            "node_id": "broad_thermal_adaptation",
            "label": "broad thermal-adaptation flexibility",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Strong capacity to remodel membrane lipids and enzymes across temperature shifts of ~20\u201330 \u00b0C."
          },
          {
            "node_id": "des_desaturase",
            "label": "acyl-lipid desaturase (Des)",
            "node_type": "GENE_OR_PROTEIN",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed as a contextual protein or protein-complex label within a quantitative measurement graph; no exact semantic family term was established for this aggregate use.",
            "description": "Membrane desaturase that introduces double bonds into existing acyl chains."
          },
          {
            "node_id": "unsaturated_fatty_acids",
            "label": "unsaturated fatty acids",
            "node_type": "CHEMICAL",
            "description": "Acyl chains bearing double bonds (CHEBI:27208) that fluidize the membrane.",
            "grounding": "CHEBI:27208"
          },
          {
            "node_id": "membrane_fluidity",
            "label": "membrane fluidity",
            "node_type": "QUALITY",
            "description": "Physical state of the lipid bilayer that must be maintained across temperatures for transport and growth.",
            "grounding": "METPO:1007505"
          },
          {
            "node_id": "rpos_sigma_factor",
            "label": "RpoS sigma factor (sigma-S)",
            "node_type": "GENE_OR_PROTEIN",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed as a contextual protein or protein-complex label within a quantitative measurement graph; no exact semantic family term was established for this aggregate use.",
            "description": "General stress-response sigma factor controlling stress regulons."
          },
          {
            "node_id": "otsab_operon",
            "label": "otsAB trehalose biosynthesis operon",
            "node_type": "PATHWAY",
            "description": "otsA/otsB pathway synthesizing trehalose-6-phosphate and trehalose."
          },
          {
            "node_id": "trehalose",
            "label": "trehalose",
            "node_type": "CHEMICAL",
            "description": "Compatible solute (CHEBI:18150) supporting cold/stress tolerance."
          },
          {
            "node_id": "cold_tolerance",
            "label": "cold / cold-shock tolerance",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Response to cold supporting growth/survival at low temperatures."
          }
        ],
        "edges": [
          {
            "subject": "broad_thermal_adaptation",
            "predicate": "confers",
            "object": "temperature_delta_mid2_trait",
            "description": "Broad thermal-adaptation flexibility yields a 20\u201330 \u00b0C temperature-delta breadth.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-micro-091313-103612",
                "snippet": "more unsaturated fatty acids",
                "notes": "Supports broad remodeling flexibility as the basis of broad breadth."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "temperature_delta_mid2_trait",
            "predicate": "is a",
            "object": "temperature_delta",
            "description": "Temperature delta mid2 is a quantitative bin of the temperature-delta phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1016/s0300-9629(97)00003-0",
                "snippet": "adapted to environments of high temperature",
                "notes": "Supports the 20\u201330 \u00b0C breadth as a value within the temperature-delta distribution."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "des_desaturase",
            "predicate": "increases abundance of",
            "object": "unsaturated_fatty_acids",
            "description": "Desaturase remodels existing lipids, raising unsaturated:saturated fatty acid ratio.",
            "evidence": [
              {
                "reference": "DOI:10.1128/spectrum.03925-23",
                "notes": "A rapid change in the saturated:unsaturated fatty acid ratio by desaturation of existing lipids."
              }
            ]
          },
          {
            "subject": "unsaturated_fatty_acids",
            "predicate": "increases",
            "object": "membrane_fluidity",
            "description": "Unsaturation fluidizes the membrane, supporting homeoviscous adaptation.",
            "evidence": [
              {
                "reference": "DOI:10.1128/spectrum.03925-23",
                "notes": "Desaturation fluidizes the membrane; strong general mechanism."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "membrane_fluidity",
            "predicate": "enables",
            "object": "broad_thermal_adaptation",
            "description": "Maintaining membrane fluidity across temperatures underpins broad thermal-adaptation flexibility.",
            "evidence": [
              {
                "reference": "DOI:10.1128/spectrum.03925-23",
                "notes": "Homeoviscous adaptation via fluidity maintenance underlies adaptation across a temperature range."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "rpos_sigma_factor",
            "predicate": "positively regulates expression of",
            "object": "otsab_operon",
            "description": "RpoS controls cold-shock-triggered induction of the otsAB operon.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s12275-023-00031-x",
                "notes": "otsAB induction is RpoS-dependent and triggered by osmotic stress, cold shock, or stationary phase."
              }
            ]
          },
          {
            "subject": "otsab_operon",
            "predicate": "has output",
            "object": "trehalose",
            "description": "The otsAB pathway synthesizes trehalose.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s12275-023-00031-x",
                "notes": "Trehalose is synthesized by the otsAB operon."
              }
            ],
            "predicate_id": "RO:0002234"
          },
          {
            "subject": "trehalose",
            "predicate": "contributes to",
            "object": "cold_tolerance",
            "description": "Trehalose acts as a compatible solute supporting cold-shock tolerance.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s12275-023-00031-x",
                "notes": "Trehalose helps cold shock tolerance."
              }
            ],
            "predicate_id": "RO:0002326"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.844944+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-13T11:00:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed definition and causal graph linking broad thermal-adaptation flexibility to the temperature-delta-mid2 bin.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:30Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d71, rdfs:subClassOf\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 6 evidence-backed generic edges (7 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:11Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 4 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002213\u00d71, RO:0002327\u00d71, METPO:2000202\u00d71, RO:0002326\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:27208\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 2 causal edge(s) off microbe-domain METPO predicates (1 to confers, 1 to has output), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-15T02:00:00Z",
        "curator": "claude",
        "action": "NORMALISE_NODE_TYPE",
        "changes": "Normalised causal-node type(s) so one node_id means one thing corpus-wide (issue 356): membrane_fluidity: BIOLOGICAL_PROCESS -> QUALITY; membrane_fluidity: description aligned with its 24 peers. The schema's OWN example of QUALITY: 'a quality or measurable attribute of a cellular component (e.g. membrane fluidity ...)'. 24 of 25 occurrences are already QUALITY and describe 'the physical state of the lipid bilayer'. The lone BIOLOGICAL_PROCESS one (temperature_delta_mid2.yaml) is the interesting case: its DESCRIPTION said 'Maintenance of optimal membrane fluidity', which is a process and would argue for a rename rather than a retype -- but its EDGES read the other way, 'unsaturated_fatty_acids -increases-> membrane_fluidity -enables-> broad_thermal_adaptation', which is the homeoviscous-adaptation cascade acting on the PROPERTY, and matches how the other 24 are wired. Three signals (schema, 24 peers, its own edges) against one (its description), so the description is what was wrong; it is corrected here rather than the node being renamed.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope temperature_delta_mid2_broad_breadth=NONMECHANISTIC with scope_notes; marked 2 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (des_desaturase, rpos_sigma_factor).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T04:43:24Z",
        "curator": "codex",
        "action": "ADD_CANONICAL_EXAMPLES",
        "changes": "Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Pseudomonas mangiferae (NCBITaxon:2593654; DOI:10.1099/ijsem.0.003657). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-15T07:02:39Z",
        "curator": "codex",
        "action": "NORMALIZED_CAUSAL_NODE_LABELS",
        "changes": "Normalized the homeoviscous-adaptation causal-node label before grounding it through proposals/metpo_traitmech_v85.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000483",
    "label": "temperature delta very low",
    "definition": "A temperature delta phenotype with a growth-supporting temperature breadth of approximately 1\u20135 \u00b0C, characteristic of stenothermal physiology.",
    "definition_source": "DOI:10.1146/annurev-micro-091313-103612",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000303"
    ],
    "synonyms": [
      {
        "synonym_text": "Td_1_5",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev-micro-091313-103612",
        "snippet": "more unsaturated fatty acids",
        "notes": "Membrane-adaptation review supports very narrow thermal-tolerance breadths as the stenothermal phenotype with limited membrane-remodeling flexibility."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "temperature_delta_very_low_stenothermal",
        "title": "Very-low temperature-delta contextual cold-stress branches",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a quantitative measurement, interval, or bin in the environmental phenotype hierarchy; a token protein example would misrepresent the measured value as one inherited molecular mechanism.",
        "description": "DOI-backed contextual graph connecting cold-induced membrane rigidification, unsaturated-fatty-acid membrane remodeling, CspA/CsdA RNA support, and very limited thermal-adaptation flexibility to the 1\u20135 \u00b0C temperature-delta bin.",
        "nodes": [
          {
            "node_id": "temperature_delta_very_low_trait",
            "label": "temperature delta very low",
            "node_type": "TRAIT",
            "grounding": "METPO:1000483",
            "description": "Temperature growth-supporting breadth approximately 1\u20135 \u00b0C."
          },
          {
            "node_id": "temperature_delta",
            "label": "temperature delta",
            "node_type": "TRAIT",
            "grounding": "METPO:1000303",
            "description": "Breadth of the growth-supporting ambient-temperature range."
          },
          {
            "node_id": "very_limited_thermal_adaptation",
            "label": "very limited thermal-adaptation flexibility",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Narrow capacity to remodel membrane lipid composition and enzyme repertoire across temperature shifts."
          },
          {
            "node_id": "unsaturated_fatty_acid_content",
            "label": "unsaturated fatty acid content",
            "node_type": "QUALITY",
            "description": "Relative proportion of unsaturated fatty acids in membrane phospholipids."
          },
          {
            "node_id": "membrane_fluidity",
            "label": "membrane fluidity",
            "node_type": "QUALITY",
            "description": "Physical fluidity of the cell membrane, central to homeoviscous adaptation.",
            "grounding": "METPO:1007505"
          },
          {
            "node_id": "cold_shock",
            "label": "cold shock",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Abrupt decrease in ambient temperature."
          },
          {
            "node_id": "cspa_protein",
            "label": "CspA cold-shock protein",
            "node_type": "GENE_OR_PROTEIN",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed as a contextual protein or protein-complex label within a quantitative measurement graph; no exact semantic family term was established for this aggregate use.",
            "description": "RNA chaperone induced upon cold shock that promotes single-stranded RNA states."
          },
          {
            "node_id": "csda_helicase",
            "label": "CsdA DEAD-box RNA helicase",
            "node_type": "GENE_OR_PROTEIN",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed as a contextual protein or protein-complex label within a quantitative measurement graph; no exact semantic family term was established for this aggregate use.",
            "description": "DEAD-box RNA helicase that assists ribosomes and RNA remodeling at low temperature."
          },
          {
            "node_id": "large_ribosomal_subunit_biogenesis",
            "label": "50S ribosomal subunit biogenesis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Biogenesis of the bacterial large ribosomal subunit at low temperature."
          },
          {
            "node_id": "low_temperature_membrane_transport",
            "label": "membrane transport at low temperature",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Maintenance of membrane permeability, diffusion, and membrane-protein function under low-temperature stress."
          },
          {
            "node_id": "cold_rna_metabolism",
            "label": "RNA metabolism at low temperature",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "RNA chaperone and helicase activity that preserves translation and ribosomal-subunit biogenesis during cold stress."
          }
        ],
        "edges": [
          {
            "subject": "very_limited_thermal_adaptation",
            "predicate": "confers",
            "object": "temperature_delta_very_low_trait",
            "description": "Very limited thermal-adaptation flexibility yields a 1\u20135 \u00b0C temperature-delta breadth.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-micro-091313-103612",
                "snippet": "more unsaturated fatty acids",
                "notes": "Supports very limited remodeling flexibility as the basis of stenothermal breadth."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "temperature_delta_very_low_trait",
            "predicate": "is a",
            "object": "temperature_delta",
            "description": "Temperature delta very low is a quantitative bin of the temperature-delta phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1016/s0300-9629(97)00003-0",
                "snippet": "adapted to environments of high temperature",
                "notes": "Supports the 1\u20135 \u00b0C breadth as a value within the temperature-delta distribution."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "unsaturated_fatty_acid_content",
            "predicate": "positively regulates",
            "object": "membrane_fluidity",
            "description": "A higher unsaturated-fatty-acid proportion fluidizes bacterial cytoplasmic membranes and counteracts cold rigidification.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-micro-091313-103612",
                "snippet": "incorporation of proportionally more unsaturated fatty acids",
                "notes": "Verified against the public Annual Review of Microbiology abstract; de Mendoza reviews increased unsaturated fatty acid incorporation as part of homeoviscous adaptation to decreasing growth temperature."
              },
              {
                "reference": "DOI:10.1111/mmi.15323",
                "snippet": "increases with temperature or an increase in the proportion of unsaturated fatty acids and vice versa",
                "notes": "Verified against the open Molecular Microbiology full text; Singh and Harinarayanan use E. coli unsaturated-fatty-acid perturbations as a route to membrane-fluidity loss."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "cold_shock",
            "predicate": "positively regulates",
            "object": "cspa_protein",
            "description": "Cold shock strongly increases CspA cold-shock protein synthesis.",
            "evidence": [
              {
                "reference": "DOI:10.1046/j.1365-2958.1999.01284.x",
                "snippet": "more than 10% of the total cellular protein synthesis",
                "notes": "Verified against the open Molecular Microbiology full text; CspA is the major E. coli cold-shock protein and its synthesis rises sharply after temperature downshift."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "csda_helicase",
            "predicate": "contributes to",
            "object": "large_ribosomal_subunit_biogenesis",
            "description": "CsdA DEAD-box RNA helicase contributes to 50S ribosomal-subunit biogenesis at low temperature.",
            "evidence": [
              {
                "reference": "DOI:10.1093/nar/gkh603",
                "snippet": "CsdA is involved in the biogenesis of the large rather than the small ribosomal subunit",
                "notes": "Verified against the open Nucleic Acids Research abstract; Charollais et al. place the E. coli CsdA helicase in 50S ribosomal-subunit biogenesis at low temperatures."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "cold_shock",
            "predicate": "negatively regulates",
            "object": "membrane_fluidity",
            "description": "Cold exposure drives membrane lipids toward ordered gel states and thereby decreases functional membrane fluidity.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s00792-017-0939-x",
                "snippet": "liquid crystalline phase into the rigid gel phase",
                "notes": "Verified against the Siliakus et al. Springer full text; the review describes low-temperature shifts from liquid-crystalline to rigid gel membrane phases."
              }
            ],
            "predicate_id": "RO:0002212"
          },
          {
            "subject": "membrane_fluidity",
            "predicate": "contributes to",
            "object": "low_temperature_membrane_transport",
            "description": "Liquid-crystalline membrane fluidity supports permeability, diffusion, and membrane-protein function at low temperature.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s00792-017-0939-x",
                "snippet": "many membrane proteins only function in the liquid crystalline phase",
                "notes": "Verified against the Siliakus et al. Springer full text; the review links low-temperature membrane phase to membrane-protein function."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "low_temperature_membrane_transport",
            "predicate": "contributes to",
            "object": "very_limited_thermal_adaptation",
            "description": "Cold preservation of membrane transport is one contextual branch of the thermal-acclimation flexibility represented in this nonmechanistic temperature-breadth graph.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s00792-017-0939-x",
                "snippet": "maintain the fluidity of the membrane",
                "notes": "Verified against the Siliakus et al. Springer full text; this supports the membrane-function branch without asserting a direct universal cause of the 1-5 degree C temperature-delta bin."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "cspa_protein",
            "predicate": "contributes to",
            "object": "cold_rna_metabolism",
            "description": "CspA RNA chaperone activity supports translation by reducing low-temperature RNA secondary structure.",
            "evidence": [
              {
                "reference": "DOI:10.1046/j.1365-2958.1999.01284.x",
                "snippet": "CspA can bind to RNA without apparent sequence specificity",
                "notes": "Verified against the open Molecular Microbiology full text; the source assigns CspA RNA-chaperone activity a role in low-temperature translation."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "csda_helicase",
            "predicate": "contributes to",
            "object": "cold_rna_metabolism",
            "description": "CsdA DEAD-box helicase activity supports RNA handling and large ribosomal-subunit maturation in the cold.",
            "evidence": [
              {
                "reference": "DOI:10.1093/nar/gkh603",
                "snippet": "CsdA is involved in ribosome biogenesis",
                "notes": "Verified against the open Nucleic Acids Research abstract; CsdA supports an RNA helicase-dependent low-temperature ribosome-biogenesis branch."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "large_ribosomal_subunit_biogenesis",
            "predicate": "contributes to",
            "object": "cold_rna_metabolism",
            "description": "50S ribosomal-subunit biogenesis is part of the RNA-processing and translation-support module required during cold stress.",
            "evidence": [
              {
                "reference": "DOI:10.1093/nar/gkh603",
                "snippet": "deficit in free 50S subunits at low temperatures",
                "notes": "Verified against the open Nucleic Acids Research abstract; CsdA defects in the cold appear as impaired 50S subunit accumulation."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "cold_rna_metabolism",
            "predicate": "contributes to",
            "object": "very_limited_thermal_adaptation",
            "description": "Cold-supportive RNA chaperone and ribosome-biogenesis functions are a second contextual branch of the thermal-acclimation flexibility represented in this nonmechanistic temperature-breadth graph.",
            "evidence": [
              {
                "reference": "DOI:10.1046/j.1365-2958.1999.01541.x",
                "snippet": "RNA chaperone to prevent the formation of secondary structures in RNA molecules",
                "notes": "Verified against the Europe PMC Phadtare and Inouye abstract; this supports the RNA-function branch without asserting CspA as a universal determinant of the 1-5 degree C temperature-delta bin."
              }
            ],
            "predicate_id": "RO:0002326"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.843238+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-13T11:00:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed definition and causal graph linking very limited thermal-adaptation flexibility to the stenothermal temperature-delta-very-low bin.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:30Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d71, rdfs:subClassOf\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 4 evidence-backed generic edges (6 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:11Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002213\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:17Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (METPO:1007505\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates (1 to confers), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope temperature_delta_very_low_stenothermal=NONMECHANISTIC with scope_notes; marked 2 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (cspa_protein, csda_helicase).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T04:43:24Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed issue #444 after #591 and left canonical_examples empty: The tracked artifact explicitly found no natural organism with both sustained-growth endpoints establishing a 1-5 degree C breadth. Cold growth, an optimum, or an assay window is not a measured delta under #591. No paid research was used.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-04T09:00:00Z",
        "curator": "codex",
        "action": "REVIEW_CAUSAL_EVIDENCE",
        "changes": "Reviewed the temperature_delta_very_low_stenothermal graph for issue #183: added exact snippets to 4 membrane and cold-shock evidence items, grounded 3 residual predicates, collapsed 1 backwards membrane-fluidity edge into the supported unsaturated-fatty-acid edge, and retyped unsaturated fatty acid content as a QUALITY node. The record remains an explicitly reviewed nonmechanistic 1-5 degree C temperature-breadth bin. No paid research service was called.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-04T11:00:00Z",
        "curator": "codex",
        "action": "CONNECT_CAUSAL_GRAPH_COMPONENTS",
        "changes": "Resolved issue #183 graph fragmentation (4 components to 1) by adding 3 contextual cold membrane and RNA nodes plus 8 source- and verbatim-snippet-backed connectors. The connectors join supported cold-stress branches without asserting a direct universal unsaturated-fatty-acid cause of the 1-5 degree C temperature-delta bin. No paid research service was called.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-06T17:10:00Z",
        "curator": "codex",
        "action": "ADVERSARIAL_REVIEW_REPAIR",
        "changes": "Addressed PR #664 adversarial review: replaced copied nonmechanistic bridge snippets with independent exact source snippets while preserving the existing connector edge scope.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-07T02:20:00Z",
        "curator": "codex",
        "action": "ADVERSARIAL_REVIEW_REPAIR",
        "changes": "Addressed PR #664 adversarial review issues #678 and #681: removed the unsupported membrane phase-transition temperature branch, requoted the cold RNA connector with exact Phadtare and Inouye wording, and replaced generic Springer endpoint notes with the specific Siliakus et al. full-text endpoint.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000304",
    "label": "temperature optimum",
    "definition": "A temperature phenotype with numerical limits that represents the ambient-temperature conditions at which an organism exhibits the most efficient growth and reproduction.",
    "definition_source": "DOI:10.1016/s0300-9629(97)00003-0",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000533",
      "METPO:1000536"
    ],
    "created_by": "Anthea Guo",
    "evidence": [
      {
        "reference": "DOI:10.1016/s0300-9629(97)00003-0",
        "snippet": "adapted to environments of high temperature",
        "notes": "Thermophile-adaptation review supports the ambient temperature at which membrane and enzyme function are best maintained as the operational definition of temperature optimum."
      },
      {
        "reference": "DOI:10.1146/annurev-micro-091313-103612",
        "snippet": "more unsaturated fatty acids",
        "notes": "Membrane-adaptation review supports homoviscous membrane composition as a key mechanism setting the temperature optimum."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:3028314",
        "taxon_label": "Oceanimonas pelagia",
        "reference": "DOI:10.1007/s10482-024-01948-y",
        "note": "Oceanimonas pelagia NTOU-MSR1T had an optimum at exactly 30 degrees C. Because that point is the mid2/mid3 boundary, #591 keeps it on the optimum parent."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "temperature_optimum_balanced_adaptation",
        "title": "Temperature-optimum balanced adaptation",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a quantitative measurement, interval, or bin in the environmental phenotype hierarchy; a token protein example would misrepresent the measured value as one inherited molecular mechanism.",
        "description": "DOI-backed graph linking the ambient temperature at which membrane fluidity, protein folding, and enzyme kinetics jointly maintain maximal growth to the temperature-optimum phenotype.",
        "nodes": [
          {
            "node_id": "temperature_optimum_trait",
            "label": "temperature optimum",
            "node_type": "TRAIT",
            "grounding": "METPO:1000304",
            "description": "Ambient temperature at which growth rate is maximal."
          },
          {
            "node_id": "ambient_temperature",
            "label": "ambient temperature",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Ambient growth temperature imposed on the cell."
          },
          {
            "node_id": "membrane_fluidity",
            "label": "membrane fluidity",
            "node_type": "QUALITY",
            "description": "Physical state of the cytoplasmic membrane supporting transport and bioenergetics.",
            "grounding": "METPO:1007505"
          },
          {
            "node_id": "homoviscous_lipid_composition",
            "label": "homoviscous lipid composition",
            "node_type": "CELLULAR_LOCALIZATION",
            "description": "Lipid composition tuned to maintain a target fluidity at the growth temperature."
          },
          {
            "node_id": "enzyme_kinetics",
            "label": "enzyme kinetics",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Temperature dependence of enzyme turnover for biosynthesis and energy conservation."
          },
          {
            "node_id": "maximal_growth_rate",
            "label": "maximal growth rate",
            "node_type": "QUALITY",
            "description": "Peak specific growth rate achieved at the optimal temperature."
          },
          {
            "node_id": "homeoviscous_adaptation",
            "label": "homeoviscous adaptation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Generic lipid-remodeling strategy that maintains a target membrane physical state (fluidity) across growth temperatures.",
            "grounding": "METPO:1016200"
          },
          {
            "node_id": "arrhenius_plot_deviation",
            "label": "Arrhenius plot deviation from linearity",
            "node_type": "EXPERIMENTAL_FACTOR",
            "description": "Departure from a linear growth-rate-vs-temperature Arrhenius relationship used to interpret temperature-response measurements."
          },
          {
            "node_id": "stress_growth_regime",
            "label": "stress / non-physiological growth regime",
            "node_type": "STATE",
            "description": "Growth condition outside the physiological temperature range, indicated by non-linear Arrhenius behavior."
          }
        ],
        "edges": [
          {
            "subject": "ambient_temperature",
            "predicate": "regulates",
            "object": "membrane_fluidity",
            "description": "Ambient temperature sets a target membrane fluidity that the cell must match.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-micro-091313-103612",
                "snippet": "more unsaturated fatty acids",
                "notes": "Supports temperature as the input to membrane-fluidity adaptation."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "homoviscous_lipid_composition",
            "predicate": "regulates",
            "object": "membrane_fluidity",
            "description": "Homoviscous lipid composition maintains target membrane fluidity at the optimum temperature.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-micro-091313-103612",
                "snippet": "more unsaturated fatty acids",
                "notes": "Supports homoviscous adaptation as the mechanism setting membrane fluidity."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "ambient_temperature",
            "predicate": "regulates",
            "object": "enzyme_kinetics",
            "description": "Ambient temperature scales enzyme turnover rates across the cellular network.",
            "evidence": [
              {
                "reference": "DOI:10.1016/s0300-9629(97)00003-0",
                "snippet": "energy transducing enzymes",
                "notes": "Supports temperature as the determinant of enzyme function in adapted organisms."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "enzyme_kinetics",
            "predicate": "promotes",
            "object": "maximal_growth_rate",
            "description": "Adequately fast enzyme kinetics promote peak growth at the optimal temperature.",
            "evidence": [
              {
                "reference": "DOI:10.1016/s0300-9629(97)00003-0",
                "snippet": "adapted to environments of high temperature",
                "notes": "Supports balanced enzyme kinetics at adapted temperature as the basis of peak growth."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "maximal_growth_rate",
            "predicate": "manifests as",
            "object": "temperature_optimum_trait",
            "description": "The ambient temperature supporting peak growth manifests the temperature-optimum phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1016/s0300-9629(97)00003-0",
                "snippet": "adapted to environments of high temperature",
                "notes": "Supports the trait endpoint."
              }
            ],
            "predicate_id": "METPO:2007400"
          },
          {
            "subject": "homeoviscous_adaptation",
            "predicate": "regulates",
            "object": "membrane_fluidity",
            "description": "Homeoviscous adaptation remodels membrane lipids to maintain target fluidity across temperatures.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s42770-023-01057-4",
                "notes": "Broad bacterial review: 'to maintain membrane fluidity at low temperature organisms alter membrane lipid composition (homeoviscous adaptation)'."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "membrane_fluidity",
            "predicate": "promotes",
            "object": "maximal_growth_rate",
            "description": "Membrane physical state (fluidity) is a proximal determinant of growth, constraining transport, signaling, and division required for peak growth.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s42770-023-01057-4",
                "notes": "Membrane fluidity maintenance via homeoviscous adaptation supports the cellular processes underlying growth across the temperature range."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "arrhenius_plot_deviation",
            "predicate": "indicates",
            "object": "stress_growth_regime",
            "description": "Deviation from Arrhenius linearity in growth-rate-vs-temperature data marks a stress / non-physiological growth regime, bounding the optimum.",
            "evidence": [
              {
                "reference": "DOI:10.37256/amtt.5220244537",
                "notes": "'Arrhenius plots, with linear regions indicating physiological growth and deviations indicating stress'."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.813650+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-13T11:00:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed causal graph linking ambient temperature, homoviscous membrane adaptation, enzyme kinetics, and maximal growth to the temperature-optimum phenotype.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:30Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T21:30:06Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007400\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:18Z",
        "curator": "claude",
        "action": "RENAME_PREDICATE_LABELS",
        "changes": "Renamed 1 causal-edge predicate label(s) to align with existing groundings: maintains \u2192 regulates \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:21Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002211\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:41:03Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (METPO:1007505\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-26T02:30:13Z",
        "curator": "claude",
        "action": "RETYPE_CAUSAL_NODES",
        "changes": "Re-typed 1 causal-node node_type field(s) to align with CausalNodeTypeEnum semantics: membrane fluidity: BIOLOGICAL_PROCESS \u2192 QUALITY \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-26T05:00:47Z",
        "curator": "claude",
        "action": "RENAME_PREDICATE_LABELS",
        "changes": "Renamed 2 causal-edge predicate label(s) to align with existing groundings: influences \u2192 regulates \u00d72.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-26T05:00:50Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002211\u00d72).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 3 evidence-backed generic edges (3 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:11Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002211\u00d71, RO:0002327\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-21T08:00:00Z",
        "curator": "codex",
        "action": "NORMALISE_NODE_TYPE",
        "changes": "Tranche 5 of issue 356 settles the process/quality families and merges ids that meant the same sense: maximal_growth_rate is QUALITY. A maximal growth rate is a measured upper bound or peak specific rate. Its edges associate, enable, or manifest that value; none describe the process of cell growth itself. An edge cannot enable a QUALITY under RO:0002327's biological-process range, so edges that causally support the rate use promotes (RO:0002213) instead.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope temperature_optimum_balanced_adaptation=NONMECHANISTIC with scope_notes.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T04:43:24Z",
        "curator": "codex",
        "action": "ADD_CANONICAL_EXAMPLES",
        "changes": "Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Oceanimonas pelagia (NCBITaxon:3028314; DOI:10.1007/s10482-024-01948-y). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-15T07:05:58Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (METPO:1016200\u00d71).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000447",
    "label": "temperature optimum high",
    "definition": "A temperature optimum phenotype with the best-growth ambient temperature above approximately 40 \u00b0C, characteristic of thermophilic physiology.",
    "definition_source": "DOI:10.1016/s0300-9629(97)00003-0",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000304"
    ],
    "synonyms": [
      {
        "synonym_text": "Thermophile",
        "synonym_type": "EXACT_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "TO_>40",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1016/s0300-9629(97)00003-0",
        "snippet": "adapted to environments of high temperature",
        "notes": "Thermophile-adaptation review supports the >40 \u00b0C optimum as the thermophile category."
      },
      {
        "reference": "DOI:10.1128/MMBR.65.1.1-43.2001",
        "snippet": "resistant to irreversible inactivation at high temperatures",
        "notes": "Thermostable-protein review supports thermostable proteins as the mechanism enabling thermophile optima."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:43080",
        "taxon_label": "Saccharolobus islandicus",
        "reference": "DOI:10.3389/fmicb.2023.1219779",
        "note": "Thermoacidophilic archaeon whose optimal growth temperature is reported as 76 degrees C, the one explicitly stated optimum in this trait's research artifact; the multi-omics study contrasts that optimum against 66 degrees C cold stress."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "temperature_optimum_high_thermophile_setpoint",
        "title": "Temperature-optimum-high thermophile context",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a quantitative measurement, interval, or bin in the environmental phenotype hierarchy; a token protein example would misrepresent the measured value as one inherited molecular mechanism.",
        "description": "DOI-backed nonmechanistic graph connecting thermophile thermostability, genome thermostability, heat-shock protein-quality control, membrane-lipid remodeling, and amino-acid composition branches to the above-40-degrees-C optimum bin.",
        "nodes": [
          {
            "node_id": "temperature_optimum_high_trait",
            "label": "temperature optimum high",
            "node_type": "TRAIT",
            "grounding": "METPO:1000447",
            "description": "Temperature optimum above ~40 \u00b0C."
          },
          {
            "node_id": "temperature_optimum",
            "label": "temperature optimum",
            "node_type": "TRAIT",
            "grounding": "METPO:1000304",
            "description": "Ambient temperature supporting maximal growth."
          },
          {
            "node_id": "hot_environment",
            "label": "hot environment",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Habitat ambient temperature above ~40 \u00b0C, typical of hot springs and compost."
          },
          {
            "node_id": "thermophile_thermostability",
            "label": "thermophile protein thermostability",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Heat-stable membrane lipids and proteins that retain function at elevated temperatures."
          },
          {
            "node_id": "reverse_gyrase",
            "label": "reverse gyrase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Thermophile topoisomerase that introduces positive supercoils into DNA.",
            "grounding": "GO:0160097"
          },
          {
            "node_id": "dna_positive_supercoiling",
            "label": "DNA positive supercoiling",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Positive supercoiling of DNA, a hallmark topological state in thermophiles."
          },
          {
            "node_id": "dna_melting_high_temperature",
            "label": "DNA melting at high temperature",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Thermal denaturation (strand separation) of DNA at elevated temperature."
          },
          {
            "node_id": "nucleoid_associated_proteins",
            "label": "nucleoid-associated proteins",
            "node_type": "GENE_OR_PROTEIN",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed as a contextual protein or protein-complex label within a quantitative measurement graph; no exact semantic family term was established for this aggregate use.",
            "description": "Proteins that organize the nucleoid and enhance DNA thermostability."
          },
          {
            "node_id": "genome_thermostability",
            "label": "genome thermostability",
            "node_type": "QUALITY",
            "description": "Resistance of the genome to heat-induced denaturation."
          },
          {
            "node_id": "small_heat_shock_proteins",
            "label": "small heat shock proteins",
            "node_type": "GENE_OR_PROTEIN",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed as a contextual protein or protein-complex label within a quantitative measurement graph; no exact semantic family term was established for this aggregate use.",
            "description": "Chaperones that bind denaturing proteins to prevent aggregation under heat stress."
          },
          {
            "node_id": "protein_aggregation_heat",
            "label": "heat-induced protein aggregation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Aggregation of denatured proteins under elevated temperature."
          },
          {
            "node_id": "thermosome",
            "label": "thermosome (group II chaperonin)",
            "node_type": "GENE_OR_PROTEIN",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed as a contextual group-II chaperonin complex in a quantitative temperature bin; no one component family represents the full thermosome.",
            "description": "Group II chaperonin that refolds denatured proteins in an ATP-dependent manner."
          },
          {
            "node_id": "denatured_protein_refolding",
            "label": "refolding of denatured proteins",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "ATP-dependent refolding of heat-denatured proteins."
          },
          {
            "node_id": "membrane_lipid_composition",
            "label": "altered membrane lipid composition",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Remodeling of cytoplasmic membrane lipids in response to high temperature."
          },
          {
            "node_id": "membrane_thermostability",
            "label": "cytoplasmic membrane thermostability",
            "node_type": "QUALITY",
            "description": "Stabilization of the cytoplasmic membrane at high temperature."
          },
          {
            "node_id": "aa_composition_thermostability",
            "label": "hydrophobic and charged amino acid enrichment",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Enrichment of hydrophobic and charged residues in thermophile proteins."
          }
        ],
        "edges": [
          {
            "subject": "hot_environment",
            "predicate": "selects for",
            "object": "thermophile_thermostability",
            "description": "Hot environments select for thermophile thermostable machinery.",
            "evidence": [
              {
                "reference": "DOI:10.1016/s0300-9629(97)00003-0",
                "snippet": "adapted to environments of high temperature",
                "notes": "Supports hot environments as the context for thermophile optima."
              }
            ],
            "predicate_id": "METPO:2007401"
          },
          {
            "subject": "thermophile_thermostability",
            "predicate": "confers",
            "object": "temperature_optimum_high_trait",
            "description": "Thermophile thermostability yields a >40 \u00b0C optimum.",
            "evidence": [
              {
                "reference": "DOI:10.1128/MMBR.65.1.1-43.2001",
                "snippet": "resistant to irreversible inactivation at high temperatures",
                "notes": "Supports thermostability as the mechanism producing thermophile optima."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "temperature_optimum_high_trait",
            "predicate": "is a",
            "object": "temperature_optimum",
            "description": "Temperature optimum high is a quantitative bin of the temperature-optimum phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1016/s0300-9629(97)00003-0",
                "snippet": "adapted to environments of high temperature",
                "notes": "Supports the >40 \u00b0C optimum as a value within the temperature-optimum distribution."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "reverse_gyrase",
            "predicate": "positively regulates",
            "object": "dna_positive_supercoiling",
            "description": "Reverse gyrase introduces positive supercoils into DNA, a thermophile hallmark.",
            "evidence": [
              {
                "reference": "DOI:10.1264/jsme2.me23087",
                "snippet": "introduces positive supercoils into DNA",
                "notes": "Verified against the open Takemata minireview; reverse gyrase is described as the characteristic thermophile topoisomerase that introduces positive supercoils into DNA."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "dna_positive_supercoiling",
            "predicate": "decreases",
            "object": "dna_melting_high_temperature",
            "description": "Positive supercoiling limits DNA melting and prevents thermal denaturation.",
            "evidence": [
              {
                "reference": "DOI:10.1264/jsme2.me23087",
                "snippet": "prevents the thermal denaturation of DNA",
                "notes": "Verified against the open Takemata minireview; the review presents reverse-gyrase-dependent positive supercoiling as the accepted route limiting DNA thermal denaturation."
              }
            ],
            "predicate_id": "RO:0002212"
          },
          {
            "subject": "nucleoid_associated_proteins",
            "predicate": "increases",
            "object": "genome_thermostability",
            "description": "Nucleoid-associated proteins enhance DNA/genome thermostability.",
            "evidence": [
              {
                "reference": "DOI:10.1264/jsme2.me23087",
                "snippet": "increase the melting temperature of DNA",
                "notes": "Verified against the open Takemata minireview; in vitro studies of NAPs from prokaryotes show increased DNA melting temperature, and archaeal NAP abundance is correlated with growth temperature."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "small_heat_shock_proteins",
            "predicate": "prevents",
            "object": "protein_aggregation_heat",
            "description": "Small heat shock proteins bind denaturing proteins to prevent heat-induced aggregation.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mbio.03593-22",
                "snippet": "protecting them from aggregation",
                "notes": "Verified against the open Baes et al. introduction; small archaeal heat-shock proteins are described as binding denaturing proteins to protect them from aggregation."
              }
            ],
            "predicate_id": "RO:0002212"
          },
          {
            "subject": "thermosome",
            "predicate": "enables",
            "object": "denatured_protein_refolding",
            "description": "The thermosome enables ATP-dependent refolding of denatured proteins.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mbio.03593-22",
                "snippet": "refolds denatured proteins in an ATP-dependent manner",
                "notes": "Verified against the open Baes et al. introduction; the archaeal thermosome is described as the group-II chaperonin complex that performs ATP-dependent refolding of denatured proteins."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "membrane_lipid_composition",
            "predicate": "contributes to",
            "object": "membrane_thermostability",
            "description": "Altered membrane lipid composition contributes to cytoplasmic membrane thermostability at high temperature.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mbio.03593-22",
                "snippet": "altered lipid composition of the cytoplasmic membrane",
                "notes": "Verified against the open Baes et al. introduction; Sulfolobales heat shock is described as altering cytoplasmic-membrane lipid composition, matching this as a membrane-stabilization response branch rather than a single determinant of thermophily."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "aa_composition_thermostability",
            "predicate": "increases",
            "object": "thermophile_thermostability",
            "description": "Enrichment in hydrophobic and charged amino acids increases protein thermostability.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mbio.02174-23",
                "snippet": "enrichment in hydrophobic and charged amino acids",
                "notes": "Verified against the open Gr\u00fcnberger et al. introduction; the review context lists hydrophobic and charged amino-acid enrichment among molecular mechanisms used by hyperthermophilic archaea."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "dna_positive_supercoiling",
            "predicate": "associated with",
            "object": "genome_thermostability",
            "description": "Reverse-gyrase-linked positive DNA supercoiling is associated with thermophile genome-thermostability context.",
            "evidence": [
              {
                "reference": "DOI:10.1264/jsme2.me23087",
                "snippet": "protect genomes at high temperatures",
                "notes": "Verified against the open Takemata minireview; this connector keeps positive DNA supercoiling as one genome thermostability branch."
              }
            ],
            "predicate_id": "biolink:associated_with"
          },
          {
            "subject": "genome_thermostability",
            "predicate": "associated with",
            "object": "thermophile_thermostability",
            "description": "DNA and genome thermostability are associated with the broad thermophile-thermostability context.",
            "evidence": [
              {
                "reference": "DOI:10.1264/jsme2.me23087",
                "snippet": "enhancing the thermostability of DNA in thermophiles",
                "notes": "Verified against the open Takemata minireview; this connector keeps nucleoid-associated proteins as DNA thermostability context."
              }
            ],
            "predicate_id": "biolink:associated_with"
          },
          {
            "subject": "protein_aggregation_heat",
            "predicate": "associated with",
            "object": "denatured_protein_refolding",
            "description": "Heat-induced protein-aggregation prevention and denatured-protein refolding are associated heat-shock protein-quality-control branches.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mbio.03593-22",
                "snippet": "Small HSPs (sHSPs) and prefoldin bind to denaturing proteins",
                "notes": "Verified against the open Baes et al. introduction; this connector joins complementary small-HSP protection and thermosome refolding context for heat-damaged proteins."
              }
            ],
            "predicate_id": "biolink:associated_with"
          },
          {
            "subject": "denatured_protein_refolding",
            "predicate": "associated with",
            "object": "thermophile_thermostability",
            "description": "Thermosome-linked refolding of denatured proteins is associated with the broad thermophile-thermostability context.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mbio.03593-22",
                "snippet": "thermosome complexes with different subunit compositions and substrate specificities",
                "notes": "Verified against the open Baes et al. introduction; this connector keeps thermosome refolding as protein-quality context."
              }
            ],
            "predicate_id": "biolink:associated_with"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.822120+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-13T11:00:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed definition and causal graph linking thermophile thermostability to the temperature-optimum-high bin.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:30Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d71, rdfs:subClassOf\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T21:30:06Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007401\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 7 evidence-backed generic edges (12 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:11Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 4 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002213\u00d72, METPO:2000017\u00d71, RO:0002212\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:17Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A088E825\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:21:11Z",
        "curator": "claude",
        "action": "RETRACT_DEAD_UNIPROT_GROUNDINGS",
        "changes": "Retracted 1 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:23:53Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0160097\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-04T03:08:13Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002213\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates (1 to confers), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T02:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES_PART2",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates onto their causal-graph counterparts (1 to reduces), issue 301 part 2. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Each replacement is a 1:1 mirror of its source predicate that changes only the domain, so the claim each edge makes is unchanged and directions are unchanged. The replacements are proposed in proposals/metpo_traitmech_v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T06:00:00Z",
        "curator": "claude",
        "action": "REGROUND_CAUSAL_EDGE",
        "changes": "Relabelled 1 causal edge from `reduces` to `decreases` and re-grounded it from METPO:2007802 to RO:0002212 (negatively regulates), issue 330. The corpus wrote two senses under the single label `reduces` - genuine electron donation, and a lessens/decreases sense - and METPO:2007802 is defined as donating electrons to the object and lowering its oxidation state, which this edge does not assert. The two senses could not be separated mechanically because the label was identical, so they migrated together in issue 329 and were split here by reading each edge. RO:0002212 declares no rdfs:domain or rdfs:range, so this introduces no entailment of the kind issue 301 removed.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-20T08:00:00Z",
        "curator": "claude",
        "action": "BACKFILL_CANONICAL_EXAMPLES",
        "changes": "Added one exemplar taxon, Saccharolobus islandicus, whose 76 C optimal growth temperature is the one optimum this trait's own deep-research artifact explicitly states, inside the >40 C bin. Taxon id resolved and label-checked against the local NCBITaxon build. Deliberately excluded - Pyrococcus furiosus (its 90 C cultivation is the study's control condition against 98 C 'supra-optimal' heat stress; the artifact never states its optimum) and Thermococcus kodakarensis (one wild-type growth-rate measurement at 85 C; the 75 and 93 C series endpoints are delta-rgy mutant data, so no optimum is established) -- both were in the first draft of this backfill and removed on review; Escherichia coli and Kluyveromyces marxianus, which the artifact names only as heat-stress/thermotolerance comparators and explicitly disqualifies (E. coli \"remains mesophilic\"; the CYR1 work concerns \"an engineered thermotolerance phenotype rather than proof that CYR1 establishes a natural >40 C optimum\"); and Thermococcus barophilus, Thermus thermophilus and Sulfolobus acidocaldarius, which appear in the artifact with no cited optimum-temperature measurement.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-21T08:00:00Z",
        "curator": "codex",
        "action": "NORMALISE_NODE_TYPE",
        "changes": "Tranche 5 of issue 356 settles the process/quality families and merges ids that meant the same sense: dna_positive_supercoiling is BIOLOGICAL_PROCESS. GO:0160097 denotes the process of introducing positive supercoils into DNA. The general DNA-topology state remains separately modelled as dna_supercoiling.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope temperature_optimum_high_thermophile_setpoint=NONMECHANISTIC with scope_notes; marked 3 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (nucleoid_associated_proteins, small_heat_shock_proteins, thermosome).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-04T03:20:00Z",
        "curator": "codex",
        "action": "REVIEW_CAUSAL_EVIDENCE",
        "changes": "Reviewed the temperature_optimum_high_thermophile_setpoint graph for issue #183: added snippets to 7 edge-level evidence items and grounded the thermosome and membrane-lipid predicates to RO:0002327 or RO:0002326. No paid research service was called.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-04T20:00:00Z",
        "curator": "codex",
        "action": "CONNECT_CAUSAL_GRAPH_COMPONENTS",
        "changes": "Resolved issue #183 graph fragmentation (6 components to 1) by adding 5 source- and verbatim-snippet-backed association connectors among genome thermostability, small-HSP/thermosome protein quality control, and membrane-thermostability branches. No paid research service was called.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-06T17:10:00Z",
        "curator": "codex",
        "action": "ADVERSARIAL_REVIEW_REPAIR",
        "changes": "Addressed PR #664 adversarial review: replaced copied nonmechanistic bridge snippets with independent exact source snippets while preserving the existing connector edge scope.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-08T03:05:00Z",
        "curator": "codex",
        "action": "ADVERSARIAL_REVIEW_REPAIR",
        "changes": "Addressed PR #664 adversarial review issue #700: removed the membrane-thermostability to thermophile-thermostability connector whose Baes et al. quote only supported broad heat-damage context.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-08T03:30:00Z",
        "curator": "codex",
        "action": "ADVERSARIAL_REVIEW_REPAIR",
        "changes": "Addressed PR #664 adversarial review issue #702: appended corrective issue-183 provenance after evidence-weak connectors were pruned; this NONMECHANISTIC graph intentionally ships with 2 disconnected components until independent trait-specific connectors are curated.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000442",
    "label": "temperature optimum low",
    "definition": "A temperature optimum phenotype with the best-growth ambient temperature between approximately 10 and 22 \u00b0C, characteristic of psychrophilic or psychrotolerant physiology.",
    "definition_source": "DOI:10.1038/sj.embor.7400662",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000304"
    ],
    "synonyms": [
      {
        "synonym_text": "Psychrophile",
        "synonym_type": "EXACT_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "Psychrotolerant",
        "synonym_type": "EXACT_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "TO_10_to_22",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/sj.embor.7400662",
        "snippet": "growing well at temperatures around the freezing point of water",
        "notes": "Psychrophile review supports low-but-not-freezing optima as the psychrophile / psychrotolerant category."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "temperature_optimum_low_psychrotolerant_setpoint",
        "title": "Temperature-optimum-low psychrotolerant setpoint",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a quantitative measurement, interval, or bin in the environmental phenotype hierarchy; a token protein example would misrepresent the measured value as one inherited molecular mechanism.",
        "description": "DOI-backed graph linking cold-tolerant membrane and enzyme adaptation to a temperature optimum between 10 and 22 \u00b0C.",
        "nodes": [
          {
            "node_id": "temperature_optimum_low_trait",
            "label": "temperature optimum low",
            "node_type": "TRAIT",
            "grounding": "METPO:1000442",
            "description": "Temperature optimum approximately 10\u201322 \u00b0C."
          },
          {
            "node_id": "temperature_optimum",
            "label": "temperature optimum",
            "node_type": "TRAIT",
            "grounding": "METPO:1000304",
            "description": "Ambient temperature supporting maximal growth."
          },
          {
            "node_id": "cool_environment",
            "label": "cool environment",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Habitat ambient temperature in the 10\u201322 \u00b0C range."
          },
          {
            "node_id": "psychrotolerant_adaptation",
            "label": "psychrotolerant adaptation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Mild cold-adaptation of membrane lipid composition and enzyme flexibility sustaining function at cool temperatures."
          },
          {
            "node_id": "low_temperature",
            "label": "low temperature",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Cool ambient temperature stress (~0-20 C) experienced by the cell.",
            "grounding": "PATO:0001306"
          },
          {
            "node_id": "membrane_fluidity",
            "label": "membrane fluidity",
            "node_type": "QUALITY",
            "description": "Physical state of the lipid bilayer enabling proper membrane function.",
            "grounding": "METPO:1007505"
          },
          {
            "node_id": "membrane_unsaturation",
            "label": "fatty-acyl unsaturation",
            "node_type": "QUALITY",
            "description": "Degree of unsaturation of membrane fatty-acyl chains."
          },
          {
            "node_id": "cold_shock_proteins",
            "label": "cold shock proteins",
            "node_type": "GENE_OR_PROTEIN",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed as a contextual protein or protein-complex label within a quantitative measurement graph; no exact semantic family term was established for this aggregate use.",
            "description": "CSP family proteins induced during temperature downshifts below 20 C."
          },
          {
            "node_id": "compatible_solutes",
            "label": "compatible solutes",
            "node_type": "CHEMICAL",
            "description": "Osmolytes (e.g. glycine betaine, trehalose, glycerol) accumulated under cold stress.",
            "grounding": "CHEBI:25728"
          },
          {
            "node_id": "protein_membrane_stabilization",
            "label": "protein and membrane stabilization",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Stabilization of proteins and membranes and freezing-point depression by cryoprotectants."
          },
          {
            "node_id": "ice_binding_proteins",
            "label": "ice-binding/antifreeze proteins",
            "node_type": "GENE_OR_PROTEIN",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed as a contextual protein or protein-complex label within a quantitative measurement graph; no exact semantic family term was established for this aggregate use.",
            "description": "IBPs/AFPs that bind ice crystal surfaces and inhibit ice recrystallization."
          },
          {
            "node_id": "ice_crystal_growth",
            "label": "ice crystal growth",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Growth and recrystallization of intracellular/extracellular ice crystals."
          },
          {
            "node_id": "oxidative_stress",
            "label": "oxidative stress",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Increased ROS from elevated oxygen solubility at low temperature."
          },
          {
            "node_id": "pufa_biosynthesis",
            "label": "PUFA biosynthesis",
            "node_type": "PATHWAY",
            "description": "Biosynthesis of polyunsaturated fatty acids incorporated into membrane lipids."
          }
        ],
        "edges": [
          {
            "subject": "cool_environment",
            "predicate": "engages",
            "object": "psychrotolerant_adaptation",
            "description": "Cool environments engage psychrotolerant adaptation programs.",
            "evidence": [
              {
                "reference": "DOI:10.1038/sj.embor.7400662",
                "snippet": "decreased membrane fluidity",
                "notes": "Supports cool-temperature membrane-stress responses as the basis of cool-range optima."
              }
            ]
          },
          {
            "subject": "psychrotolerant_adaptation",
            "predicate": "confers",
            "object": "temperature_optimum_low_trait",
            "description": "Psychrotolerant adaptation yields a 10\u201322 \u00b0C temperature optimum.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-micro-091313-103612",
                "snippet": "more unsaturated fatty acids",
                "notes": "Supports homoviscous adaptation as the mechanism setting cool-range optima."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "temperature_optimum_low_trait",
            "predicate": "is a",
            "object": "temperature_optimum",
            "description": "Temperature optimum low is a quantitative bin of the temperature-optimum phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1038/sj.embor.7400662",
                "snippet": "growing well at temperatures around the freezing point of water",
                "notes": "Supports a 10\u201322 \u00b0C optimum as a value within the temperature-optimum distribution."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "membrane_unsaturation",
            "predicate": "increases",
            "object": "membrane_fluidity",
            "description": "Increased fatty-acyl unsaturation fluidizes the membrane.",
            "evidence": [
              {
                "reference": "DOI:10.1128/spectrum.03925-23",
                "notes": "fluidizing the membrane and reducing bilayer thickness; broadly generalizable homeoviscous adaptation."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "low_temperature",
            "predicate": "induces",
            "object": "cold_shock_proteins",
            "description": "Low temperature induces cold shock proteins.",
            "evidence": [
              {
                "reference": "DOI:10.37256/amtt.5220244537",
                "notes": "CSPs induced at high levels during temperature shifts below 20 C."
              }
            ]
          },
          {
            "subject": "low_temperature",
            "predicate": "promotes accumulation of",
            "object": "compatible_solutes",
            "description": "Low temperature promotes accumulation of compatible solutes.",
            "evidence": [
              {
                "reference": "DOI:10.37256/amtt.5220244537",
                "notes": "Compatible solutes listed: glycine, betaine, glycerol, trehalose, sucrose, mannitol, sorbitol."
              }
            ]
          },
          {
            "subject": "compatible_solutes",
            "predicate": "stabilizes",
            "object": "protein_membrane_stabilization",
            "description": "Compatible solutes stabilize proteins and membranes and depress freezing point.",
            "evidence": [
              {
                "reference": "DOI:10.37256/amtt.5220244537",
                "notes": "with functions in freezing-point depression and stabilization."
              }
            ]
          },
          {
            "subject": "ice_binding_proteins",
            "predicate": "inhibits",
            "object": "ice_crystal_growth",
            "description": "Ice-binding/antifreeze proteins bind ice surfaces and inhibit ice growth/recrystallization.",
            "evidence": [
              {
                "reference": "DOI:10.37256/amtt.5220244537",
                "notes": "AFGPs play crucial roles in protecting cells by binding to ice crystal surfaces."
              }
            ],
            "predicate_id": "RO:0002212"
          },
          {
            "subject": "low_temperature",
            "predicate": "increases",
            "object": "oxidative_stress",
            "description": "Low temperature increases oxygen solubility and ROS/oxidative stress.",
            "evidence": [
              {
                "reference": "DOI:10.37256/amtt.5220244537",
                "notes": "Cold causes increased oxygen solubility and ROS."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "pufa_biosynthesis",
            "predicate": "maintains",
            "object": "membrane_fluidity",
            "description": "PUFA biosynthesis maintains membrane fluidity at low temperature.",
            "evidence": [
              {
                "reference": "DOI:10.3390/genes14010158",
                "notes": "maintain membrane fluidity; broadly generalizable mechanism."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.819249+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-13T11:00:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed definition and causal graph linking psychrotolerant adaptation to the temperature-optimum-low bin.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:30Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d71, rdfs:subClassOf\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 7 evidence-backed generic edges (10 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:11Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002213\u00d72, RO:0002212\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:17Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 3 causal-node grounding field(s) via mappings/node_grounding.tsv (PATO:0001306\u00d71, METPO:1007505\u00d71, CHEBI:25728\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates (1 to confers), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-16T02:00:00Z",
        "curator": "claude",
        "action": "NORMALISE_NODE_TYPE",
        "changes": "Under the PATHWAY-vs-BIOLOGICAL_PROCESS rule, one node_id means one thing corpus-wide (issue 356): pufa_biosynthesis is typed PATHWAY. PATHWAY is a named, conventionally enumerable multi-step route; BIOLOGICAL_PROCESS is everything else. A named biosynthetic route to polyunsaturated fatty acids. The two typings describe it in near-identical words, so the split was arbitrary and the rule breaks the 1-1 tie.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-21T00:00:00Z",
        "curator": "claude",
        "action": "BACKFILL_CANONICAL_EXAMPLES",
        "changes": "Added 2 exemplar taxon/taxa. Organisms and citations come only from this record's own deep-research artifact; every taxon id was resolved and label-checked against the local NCBITaxon build rather than recalled. Organisms the artifact names as contrast cases rather than exemplars were deliberately excluded.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope temperature_optimum_low_psychrotolerant_setpoint=NONMECHANISTIC with scope_notes; marked 2 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (cold_shock_proteins, ice_binding_proteins).",
        "llm_assisted": true
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:296",
        "taxon_label": "Pseudomonas fragi",
        "reference": "DOI:10.37256/amtt.5220244537",
        "note": "Cold-adapted organism whose best growth sits at the low end of the range, cited in this trait's artifact for psychrophilic adaptation."
      },
      {
        "taxon_id": "NCBITaxon:1880678",
        "taxon_label": "Pseudomonas sivasensis",
        "reference": "DOI:10.1007/s42770-023-01057-4",
        "note": "Cold-adapted isolate cited in this trait's artifact for growth at low temperature."
      }
    ]
  },
  {
    "identifier": "METPO:1000443",
    "label": "temperature optimum mid1",
    "definition": "A temperature optimum phenotype with the best-growth ambient temperature between approximately 22 and 27 \u00b0C, characteristic of mesophilic physiology.",
    "definition_source": "DOI:10.1146/annurev-micro-091313-103612",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000304"
    ],
    "synonyms": [
      {
        "synonym_text": "Mesophilie",
        "synonym_type": "EXACT_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "TO_22_to_27",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "mesophilic",
        "synonym_type": "EXACT_SYNONYM",
        "source": "https://w3id.org/metpo/releases/2026-06-12/metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev-micro-091313-103612",
        "snippet": "more unsaturated fatty acids",
        "notes": "Membrane-adaptation review supports moderate-temperature optima matched by homoviscous lipid composition as the mesophile setpoint."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:3080537",
        "taxon_label": "Rubellicoccus peritrichatus",
        "reference": "DOI:10.1099/ijsem.0.006325",
        "note": "Rubellicoccus peritrichatus CR14T had a measured optimum of 25 degrees C, wholly within the approximately 22-27-degree bin; growth occurred at 20-30 degrees C."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "temperature_optimum_mid1_lower_mesophile",
        "title": "Temperature-optimum-mid1 lower-mesophile setpoint",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a quantitative measurement, interval, or bin in the environmental phenotype hierarchy; a token protein example would misrepresent the measured value as one inherited molecular mechanism.",
        "description": "DOI-backed graph linking modest membrane and enzyme adaptation at moderate ambient temperature to a temperature optimum between 22 and 27 \u00b0C.",
        "nodes": [
          {
            "node_id": "temperature_optimum_mid1_trait",
            "label": "temperature optimum mid1",
            "node_type": "TRAIT",
            "grounding": "METPO:1000443",
            "description": "Temperature optimum approximately 22\u201327 \u00b0C."
          },
          {
            "node_id": "temperature_optimum",
            "label": "temperature optimum",
            "node_type": "TRAIT",
            "grounding": "METPO:1000304",
            "description": "Ambient temperature supporting maximal growth."
          },
          {
            "node_id": "lower_mesophilic_environment",
            "label": "lower-mesophilic environment",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Habitat ambient temperature in the 22\u201327 \u00b0C range."
          },
          {
            "node_id": "mesophile_adaptation",
            "label": "mesophile membrane and enzyme adaptation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Membrane lipid composition and enzyme repertoire tuned for moderate ambient temperatures."
          },
          {
            "node_id": "unsaturated_fatty_acids",
            "label": "unsaturated fatty acids",
            "node_type": "CHEMICAL",
            "description": "Membrane fatty acids containing one or more double bonds.",
            "grounding": "CHEBI:27208"
          },
          {
            "node_id": "membrane_fluidity",
            "label": "membrane fluidity",
            "node_type": "QUALITY",
            "description": "Physical fluid state of the cell membrane lipid bilayer.",
            "grounding": "METPO:1007505"
          },
          {
            "node_id": "homeoviscous_adaptation",
            "label": "homeoviscous adaptation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Membrane lipid remodeling that maintains constant fluidity across temperatures.",
            "grounding": "METPO:1016200"
          },
          {
            "node_id": "low_melting_lipids",
            "label": "low-melting membrane lipids",
            "node_type": "CHEMICAL",
            "description": "MUFAs, PUFAs, branched and short-chain fatty acids with low melting temperatures."
          },
          {
            "node_id": "branched_chain_amino_acids",
            "label": "branched-chain amino acids",
            "node_type": "CHEMICAL",
            "description": "Valine, leucine and isoleucine."
          },
          {
            "node_id": "branched_chain_fatty_acids",
            "label": "branched-chain fatty acids",
            "node_type": "CHEMICAL",
            "description": "Iso/anteiso branched membrane fatty acids derived from BCAA precursors.",
            "grounding": "CHEBI:35819"
          }
        ],
        "edges": [
          {
            "subject": "lower_mesophilic_environment",
            "predicate": "engages",
            "object": "mesophile_adaptation",
            "description": "Lower-mesophilic environments engage moderate adaptation programs.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-micro-091313-103612",
                "snippet": "more unsaturated fatty acids",
                "notes": "Supports moderate-temperature membrane homeoviscous adaptation."
              }
            ]
          },
          {
            "subject": "mesophile_adaptation",
            "predicate": "confers",
            "object": "temperature_optimum_mid1_trait",
            "description": "Mesophile adaptation yields a 22\u201327 \u00b0C optimum.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-micro-091313-103612",
                "snippet": "more unsaturated fatty acids",
                "notes": "Supports the 22\u201327 \u00b0C optimum as the lower-mesophile outcome."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "temperature_optimum_mid1_trait",
            "predicate": "is a",
            "object": "temperature_optimum",
            "description": "Temperature optimum mid1 is a quantitative bin of the temperature-optimum phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1016/s0300-9629(97)00003-0",
                "snippet": "adapted to environments of high temperature",
                "notes": "Supports the 22\u201327 \u00b0C optimum as a value within the temperature-optimum distribution."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "mesophile_adaptation",
            "predicate": "increases abundance of",
            "object": "unsaturated_fatty_acids",
            "description": "Mesophile membrane adaptation increases unsaturated fatty acid content.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s42770-023-01057-4",
                "notes": "The Des desaturase inserts double bonds in membrane fatty acids, fluidizing the membrane."
              }
            ]
          },
          {
            "subject": "unsaturated_fatty_acids",
            "predicate": "increases",
            "object": "membrane_fluidity",
            "description": "Unsaturated fatty acids fluidize the membrane.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s42770-023-01057-4",
                "notes": "Inserting double bonds into membrane fatty acids fluidizes the membrane and reverses the cold signal."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "membrane_fluidity",
            "predicate": "is sensed as input to",
            "object": "homeoviscous_adaptation",
            "description": "Membrane physical state/fluidity is the sensed input driving homeoviscous adaptation.",
            "evidence": [
              {
                "reference": "DOI:10.1039/d4cc03114h",
                "notes": "HVA, a universal paradigm; initial step involves membrane stress sensing with membrane fluidity as a proposed sensed parameter."
              }
            ]
          },
          {
            "subject": "homeoviscous_adaptation",
            "predicate": "remodels toward increased",
            "object": "low_melting_lipids",
            "description": "Homeoviscous adaptation increases low-melting membrane lipids.",
            "evidence": [
              {
                "reference": "DOI:10.1039/d4cc03114h",
                "notes": "Adaptive changes include increasing low-melting lipids: MUFAs, PUFAs, branched and short-chain fatty acids."
              }
            ]
          },
          {
            "subject": "branched_chain_amino_acids",
            "predicate": "serve as precursors for",
            "object": "branched_chain_fatty_acids",
            "description": "BCAAs are biosynthetic precursors of iso/anteiso branched membrane fatty acids.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s42770-023-01057-4",
                "notes": "Branched (iso/anteiso) FAs derive from branched-chain amino acid precursors (valine, leucine, isoleucine)."
              }
            ]
          },
          {
            "subject": "branched_chain_fatty_acids",
            "predicate": "increases",
            "object": "membrane_fluidity",
            "description": "Branched-chain (anteiso) fatty acids fluidize the membrane during cold adaptation.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s42770-023-01057-4",
                "notes": "Membrane fluidization via chain branching is a predominant longer-term cold adaptation mechanism."
              }
            ],
            "predicate_id": "RO:0002213"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.819857+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-13T11:00:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed definition and causal graph linking mesophile membrane and enzyme adaptation to the temperature-optimum-mid1 bin.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:30Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d71, rdfs:subClassOf\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 6 evidence-backed generic edges (6 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:11Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002213\u00d72).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:17Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (METPO:1007505\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:27208\u00d71, CHEBI:35819\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates (1 to confers), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope temperature_optimum_mid1_lower_mesophile=NONMECHANISTIC with scope_notes.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T06:15:38Z",
        "curator": "codex",
        "action": "ADD_EXACT_ONTOLOGY_MATCH",
        "changes": "Ontology exact-match review (2026-08-25): declared exact synonym(s): 'mesophilic'. Evidence is predicate-scoped in the versioned ontology snapshots; OAK cross-checked direct data, and OLS4 spot-checked release deltas and disputed hits.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T04:43:24Z",
        "curator": "codex",
        "action": "ADD_CANONICAL_EXAMPLES",
        "changes": "Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Rubellicoccus peritrichatus (NCBITaxon:3080537; DOI:10.1099/ijsem.0.006325). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-15T07:05:58Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (METPO:1016200\u00d71).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000444",
    "label": "temperature optimum mid2",
    "definition": "A temperature optimum phenotype with the best-growth ambient temperature between approximately 27 and 30 \u00b0C, characteristic of mesophilic physiology.",
    "definition_source": "DOI:10.1146/annurev-micro-091313-103612",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000304"
    ],
    "synonyms": [
      {
        "synonym_text": "Mesophilie",
        "synonym_type": "EXACT_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "TO_27_to_30",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "mesophilic",
        "synonym_type": "EXACT_SYNONYM",
        "source": "https://w3id.org/metpo/releases/2026-06-12/metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev-micro-091313-103612",
        "snippet": "more unsaturated fatty acids",
        "notes": "Membrane-adaptation review supports a 27\u201330 \u00b0C optimum as a typical mesophile setpoint maintained by homoviscous membrane composition."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:2781979",
        "taxon_label": "Pontibacterium sinense",
        "reference": "DOI:10.1099/ijsem.0.006018",
        "note": "Pontibacterium sinense N1Y112T had a measured optimum of 28 degrees C, wholly within the approximately 27-30-degree bin; growth occurred at 20-35 degrees C."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "temperature_optimum_mid2_mesophile",
        "title": "Temperature-optimum-mid2 mesophile setpoint",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a quantitative measurement, interval, or bin in the environmental phenotype hierarchy; a token protein example would misrepresent the measured value as one inherited molecular mechanism.",
        "description": "DOI-backed graph linking baseline mesophile adaptation to a temperature optimum between 27 and 30 \u00b0C.",
        "nodes": [
          {
            "node_id": "temperature_optimum_mid2_trait",
            "label": "temperature optimum mid2",
            "node_type": "TRAIT",
            "grounding": "METPO:1000444",
            "description": "Temperature optimum approximately 27\u201330 \u00b0C."
          },
          {
            "node_id": "temperature_optimum",
            "label": "temperature optimum",
            "node_type": "TRAIT",
            "grounding": "METPO:1000304",
            "description": "Ambient temperature supporting maximal growth."
          },
          {
            "node_id": "mesophilic_environment",
            "label": "mesophilic environment",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Habitat ambient temperature in the 27\u201330 \u00b0C range."
          },
          {
            "node_id": "baseline_mesophile_adaptation",
            "label": "baseline mesophile adaptation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Standard mesophile membrane and enzyme repertoire matching a moderate ambient-temperature setpoint."
          },
          {
            "node_id": "temperature_decrease",
            "label": "temperature decrease",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "A drop in ambient temperature below the growth setpoint."
          },
          {
            "node_id": "membrane_rigidity",
            "label": "membrane rigidification",
            "node_type": "QUALITY",
            "description": "Increased bilayer order/thickness and liquid-crystalline to gel transition of the cytoplasmic membrane."
          },
          {
            "node_id": "unsaturated_fatty_acids",
            "label": "unsaturated fatty acids",
            "node_type": "CHEMICAL",
            "description": "Membrane fatty acyl chains bearing one or more double bonds (CHEBI:27208).",
            "grounding": "CHEBI:27208"
          },
          {
            "node_id": "membrane_fluidity",
            "label": "membrane fluidity",
            "node_type": "QUALITY",
            "description": "Physical fluidity/disorder state of the cytoplasmic membrane.",
            "grounding": "METPO:1007505"
          },
          {
            "node_id": "mesophile_category",
            "label": "mesophile category",
            "node_type": "STATE",
            "description": "Organisms growing between approximately 20 and 45 degrees C ambient temperature."
          }
        ],
        "edges": [
          {
            "subject": "mesophilic_environment",
            "predicate": "engages",
            "object": "baseline_mesophile_adaptation",
            "description": "Mesophilic environments engage baseline mesophile adaptation.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-micro-091313-103612",
                "snippet": "more unsaturated fatty acids",
                "notes": "Supports mesophile homoviscous adaptation at moderate ambient temperature."
              }
            ]
          },
          {
            "subject": "baseline_mesophile_adaptation",
            "predicate": "confers",
            "object": "temperature_optimum_mid2_trait",
            "description": "Baseline mesophile adaptation yields a 27\u201330 \u00b0C optimum.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-micro-091313-103612",
                "snippet": "more unsaturated fatty acids",
                "notes": "Supports the 27\u201330 \u00b0C optimum as the baseline-mesophile outcome."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "temperature_optimum_mid2_trait",
            "predicate": "is a",
            "object": "temperature_optimum",
            "description": "Temperature optimum mid2 is a quantitative bin of the temperature-optimum phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1016/s0300-9629(97)00003-0",
                "snippet": "adapted to environments of high temperature",
                "notes": "Supports the 27\u201330 \u00b0C optimum as a value within the temperature-optimum distribution."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "temperature_decrease",
            "predicate": "causes",
            "object": "membrane_rigidity",
            "description": "A temperature drop rigidifies and thickens the cytoplasmic membrane.",
            "evidence": [
              {
                "reference": "DOI:10.1128/spectrum.03925-23",
                "notes": "Temperature drops cause membrane rigidification and thickening and can induce a liquid-crystalline to gel phase change; general bacterial mechanism."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "unsaturated_fatty_acids",
            "predicate": "increases",
            "object": "membrane_fluidity",
            "description": "Higher unsaturated fatty acid content fluidizes and thins the bilayer.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s42770-023-01057-4",
                "notes": "Increasing the saturated/unsaturated ratio toward UFAs increases fluidity; UFAs are central membrane fluidizers."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "baseline_mesophile_adaptation",
            "predicate": "increases",
            "object": "unsaturated_fatty_acids",
            "description": "Homeoviscous mesophile adaptation raises unsaturated fatty acid content to offset cooling.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s42770-023-01057-4",
                "notes": "Homeoviscous adaptation adjusts the saturated/unsaturated fatty-acid ratio to maintain membrane fluidity at the growth temperature."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "membrane_fluidity",
            "predicate": "enables",
            "object": "baseline_mesophile_adaptation",
            "description": "Maintained membrane fluidity supports the baseline mesophile physiological state.",
            "evidence": [
              {
                "reference": "DOI:10.1128/spectrum.03925-23",
                "notes": "Cells sense and correct membrane fluidity via desaturation to keep the bilayer functional at the ambient temperature."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "temperature_optimum_mid2_trait",
            "predicate": "subclass of",
            "object": "mesophile_category",
            "description": "The 27-30 C optimum falls within the mesophile growth range.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s42770-023-01057-4",
                "notes": "Mesophiles grow between about 20 C and 45 C; 27-30 C lies inside this range, making mid2 a mesophile subset."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.820411+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-13T11:00:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed definition and causal graph linking baseline mesophile adaptation to the temperature-optimum-mid2 bin.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:30Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d71, rdfs:subClassOf\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 5 evidence-backed generic edges (5 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:11Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 4 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002213\u00d72, biolink:causes\u00d71, RO:0002327\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:17Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (METPO:1007505\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:27208\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates (1 to confers), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-21T08:00:00Z",
        "curator": "codex",
        "action": "NORMALISE_NODE_TYPE",
        "changes": "Tranche 5 of issue 356 settles the process/quality families and merges ids that meant the same sense: membrane_rigidity is QUALITY. Membrane rigidity is a physical attribute of the bilayer and therefore a QUALITY under the schema's membrane-fluidity example.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope temperature_optimum_mid2_mesophile=NONMECHANISTIC with scope_notes.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T06:15:38Z",
        "curator": "codex",
        "action": "ADD_EXACT_ONTOLOGY_MATCH",
        "changes": "Ontology exact-match review (2026-08-25): declared exact synonym(s): 'mesophilic'. Evidence is predicate-scoped in the versioned ontology snapshots; OAK cross-checked direct data, and OLS4 spot-checked release deltas and disputed hits.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T04:43:24Z",
        "curator": "codex",
        "action": "ADD_CANONICAL_EXAMPLES",
        "changes": "Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Pontibacterium sinense (NCBITaxon:2781979; DOI:10.1099/ijsem.0.006018). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000445",
    "label": "temperature optimum mid3",
    "definition": "A temperature optimum phenotype with the best-growth ambient temperature between approximately 30 and 34 \u00b0C, characteristic of mesophilic physiology.",
    "definition_source": "DOI:10.1146/annurev-micro-091313-103612",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000304"
    ],
    "synonyms": [
      {
        "synonym_text": "Mesophilie",
        "synonym_type": "EXACT_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "TO_30_to_34",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "mesophilic",
        "synonym_type": "EXACT_SYNONYM",
        "source": "https://w3id.org/metpo/releases/2026-06-12/metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev-micro-091313-103612",
        "snippet": "more unsaturated fatty acids",
        "notes": "Membrane-adaptation review supports the 30\u201334 \u00b0C optimum as a typical mesophile setpoint near common host body temperatures."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:36080",
        "taxon_label": "Mucor circinelloides",
        "reference": "DOI:10.1016/j.heliyon.2024.e30812",
        "note": "Unperturbed Mucor circinelloides on cheese-based agar had fitted temperature optima of 32.1-32.5 degrees C without added salt, wholly inside the approximately 30-34-degree bin."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "temperature_optimum_mid3_upper_mesophile",
        "title": "Temperature-optimum-mid3 upper-mesophile setpoint",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a quantitative measurement, interval, or bin in the environmental phenotype hierarchy; a token protein example would misrepresent the measured value as one inherited molecular mechanism.",
        "description": "DOI-backed graph linking upper-mesophile membrane and enzyme adaptation to a temperature optimum between 30 and 34 \u00b0C.",
        "nodes": [
          {
            "node_id": "temperature_optimum_mid3_trait",
            "label": "temperature optimum mid3",
            "node_type": "TRAIT",
            "grounding": "METPO:1000445",
            "description": "Temperature optimum approximately 30\u201334 \u00b0C."
          },
          {
            "node_id": "temperature_optimum",
            "label": "temperature optimum",
            "node_type": "TRAIT",
            "grounding": "METPO:1000304",
            "description": "Ambient temperature supporting maximal growth."
          },
          {
            "node_id": "upper_mesophilic_environment",
            "label": "upper-mesophilic environment",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Habitat ambient temperature in the 30\u201334 \u00b0C range."
          },
          {
            "node_id": "upper_mesophile_adaptation",
            "label": "upper-mesophile adaptation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Membrane lipid composition and enzyme repertoire tuned for ambient temperatures near common animal host body temperatures."
          },
          {
            "node_id": "decreased_temperature",
            "label": "decreased temperature",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "A drop in ambient temperature toward the lower mesophilic range.",
            "grounding": "PATO:0001306"
          },
          {
            "node_id": "membrane_bilayer",
            "label": "membrane bilayer",
            "node_type": "CELLULAR_LOCALIZATION",
            "description": "The lipid bilayer of the cell membrane whose physical state depends on temperature."
          },
          {
            "node_id": "homeoviscous_adaptation",
            "label": "homeoviscous adaptation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Lipid remodeling that maintains membrane fluidity across temperatures.",
            "grounding": "METPO:1016200"
          },
          {
            "node_id": "liquid_crystalline_membrane_state",
            "label": "liquid-crystalline membrane state",
            "node_type": "STATE",
            "description": "Fluid, functional physical state of the membrane bilayer supporting growth."
          },
          {
            "node_id": "mufa_incorporation",
            "label": "monounsaturated fatty acid incorporation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Incorporation of cis-monounsaturated fatty acids into membrane lipids."
          },
          {
            "node_id": "membrane_fluidity",
            "label": "membrane fluidity",
            "node_type": "QUALITY",
            "description": "Degree of fluidity/disorder of the membrane lipid bilayer.",
            "grounding": "METPO:1007505"
          },
          {
            "node_id": "chaperone_network",
            "label": "molecular chaperone network",
            "node_type": "GENE_OR_PROTEIN",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed as a contextual protein or protein-complex label within a quantitative measurement graph; no exact semantic family term was established for this aggregate use.",
            "description": "DnaK/DnaJ, GroEL/GroES, ClpB, HtpG chaperone system."
          },
          {
            "node_id": "proteostasis",
            "label": "proteostasis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Maintenance of protein folding homeostasis during temperature shifts."
          }
        ],
        "edges": [
          {
            "subject": "upper_mesophilic_environment",
            "predicate": "engages",
            "object": "upper_mesophile_adaptation",
            "description": "Upper-mesophilic environments engage upper-mesophile adaptation.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-micro-091313-103612",
                "snippet": "more unsaturated fatty acids",
                "notes": "Supports homoviscous adaptation at upper-mesophilic temperatures."
              }
            ]
          },
          {
            "subject": "upper_mesophile_adaptation",
            "predicate": "confers",
            "object": "temperature_optimum_mid3_trait",
            "description": "Upper-mesophile adaptation yields a 30\u201334 \u00b0C optimum.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-micro-091313-103612",
                "snippet": "more unsaturated fatty acids",
                "notes": "Supports the 30\u201334 \u00b0C optimum as the upper-mesophile outcome."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "temperature_optimum_mid3_trait",
            "predicate": "is a",
            "object": "temperature_optimum",
            "description": "Temperature optimum mid3 is a quantitative bin of the temperature-optimum phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1016/s0300-9629(97)00003-0",
                "snippet": "adapted to environments of high temperature",
                "notes": "Supports the 30\u201334 \u00b0C optimum as a value within the temperature-optimum distribution."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "decreased_temperature",
            "predicate": "rigidifies",
            "object": "membrane_bilayer",
            "description": "Cooler conditions rigidify and thicken the membrane bilayer, triggering fluidity-restoring responses.",
            "evidence": [
              {
                "reference": "DOI:10.1128/spectrum.03925-23",
                "notes": "Core homeoviscous trigger: \"upon temperature decrease the membrane rigidifies and thickens.\""
              }
            ]
          },
          {
            "subject": "homeoviscous_adaptation",
            "predicate": "restores",
            "object": "liquid_crystalline_membrane_state",
            "description": "Homeoviscous adaptation restores the fluid, liquid-crystalline membrane state across mesophilic temperatures.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s42770-023-01057-4",
                "notes": "General process-level support: \"These changes are often referred to as homeoviscous adaptation.\""
              }
            ]
          },
          {
            "subject": "mufa_incorporation",
            "predicate": "increases",
            "object": "membrane_fluidity",
            "description": "Incorporation of cis-monounsaturated fatty acids increases membrane fluidity at lower temperatures.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s42770-023-01057-4",
                "notes": "\"The most common adaptation is the incorporation of monounsaturated fatty acids (MUFA), preferably cis-unsaturated ones.\""
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "chaperone_network",
            "predicate": "maintains",
            "object": "proteostasis",
            "description": "The chaperone network prevents and resolves aggregates, maintaining proteostasis during temperature shifts.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s12275-023-00031-x",
                "notes": "General proteostasis module: \"DnaK-DnaJ, GroEL-GroES, HtpG, ClpB\" prevent/resolve aggregates."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.820979+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-13T11:00:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed definition and causal graph linking upper-mesophile adaptation to the temperature-optimum-mid3 bin.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:30Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d71, rdfs:subClassOf\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 4 evidence-backed generic edges (8 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:11Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002213\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:17Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (METPO:1007505\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (PATO:0001306\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates (1 to confers), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope temperature_optimum_mid3_upper_mesophile=NONMECHANISTIC with scope_notes; marked 1 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (chaperone_network).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T06:15:38Z",
        "curator": "codex",
        "action": "ADD_EXACT_ONTOLOGY_MATCH",
        "changes": "Ontology exact-match review (2026-08-25): declared exact synonym(s): 'mesophilic'. Evidence is predicate-scoped in the versioned ontology snapshots; OAK cross-checked direct data, and OLS4 spot-checked release deltas and disputed hits.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T04:43:24Z",
        "curator": "codex",
        "action": "ADD_CANONICAL_EXAMPLES",
        "changes": "Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Mucor circinelloides (NCBITaxon:36080; DOI:10.1016/j.heliyon.2024.e30812). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-15T07:05:58Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (METPO:1016200\u00d71).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000446",
    "label": "temperature optimum mid4",
    "definition": "A temperature optimum phenotype with the best-growth ambient temperature between approximately 34 and 40 \u00b0C, characteristic of warm-mesophilic physiology (including many mammalian host-associated bacteria).",
    "definition_source": "DOI:10.1146/annurev-micro-091313-103612",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000304"
    ],
    "synonyms": [
      {
        "synonym_text": "Mesophilie",
        "synonym_type": "EXACT_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "TO_34_to_40",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "mesophilic",
        "synonym_type": "EXACT_SYNONYM",
        "source": "https://w3id.org/metpo/releases/2026-06-12/metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev-micro-091313-103612",
        "snippet": "more unsaturated fatty acids",
        "notes": "Membrane-adaptation review supports a 34\u201340 \u00b0C optimum as the warm-mesophile (mammalian-host) setpoint."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:83333",
        "taxon_label": "Escherichia coli K-12",
        "reference": "DOI:10.1128/AEM.05773-11",
        "note": "Wild-type E. coli K-12 in the thermal-evolution study had a 37 degrees C growth optimum before the glpF-associated shift, wholly inside the approximately 34-40-degree bin."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "temperature_optimum_mid4_warm_mesophile",
        "title": "Temperature-optimum-mid4 warm-mesophile setpoint",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a quantitative measurement, interval, or bin in the environmental phenotype hierarchy; a token protein example would misrepresent the measured value as one inherited molecular mechanism.",
        "description": "DOI-backed graph linking warm-mesophile membrane and enzyme adaptation to a temperature optimum between 34 and 40 \u00b0C.",
        "nodes": [
          {
            "node_id": "temperature_optimum_mid4_trait",
            "label": "temperature optimum mid4",
            "node_type": "TRAIT",
            "grounding": "METPO:1000446",
            "description": "Temperature optimum approximately 34\u201340 \u00b0C."
          },
          {
            "node_id": "temperature_optimum",
            "label": "temperature optimum",
            "node_type": "TRAIT",
            "grounding": "METPO:1000304",
            "description": "Ambient temperature supporting maximal growth."
          },
          {
            "node_id": "warm_environment",
            "label": "warm host-associated environment",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Habitat ambient temperature in the 34\u201340 \u00b0C range, typical of many mammalian hosts."
          },
          {
            "node_id": "warm_mesophile_adaptation",
            "label": "warm-mesophile adaptation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Membrane and enzyme repertoires tuned for warm host-body temperatures."
          },
          {
            "node_id": "temperature_downshift",
            "label": "temperature downshift",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "A decrease in ambient growth temperature."
          },
          {
            "node_id": "unsaturated_fatty_acid_proportion",
            "label": "unsaturated fatty acid proportion",
            "node_type": "CHEMICAL",
            "description": "Proportion of unsaturated fatty acids in membrane phospholipids."
          },
          {
            "node_id": "membrane_fluidity_homeostasis",
            "label": "membrane fluidity homeostasis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Maintenance of optimal membrane fluidity (homeoviscous adaptation)."
          },
          {
            "node_id": "unsaturated_fa_biosynthesis_response",
            "label": "unsaturated fatty acid biosynthesis response",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Upregulation of unsaturated fatty acid biosynthesis upon sensed membrane rigidification."
          },
          {
            "node_id": "rna_thermometer",
            "label": "RNA thermometer hairpin",
            "node_type": "RNA",
            "description": "Cis-regulatory mRNA hairpin (e.g. ROSE/FourU) controlling translation by temperature."
          },
          {
            "node_id": "shine_dalgarno_sequence",
            "label": "Shine-Dalgarno / AUG ribosome binding site",
            "node_type": "GENETIC_ELEMENT",
            "description": "Ribosome-binding region of mRNA required for translation initiation."
          },
          {
            "node_id": "temperature_upshift",
            "label": "temperature upshift / heat shock",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "An increase in ambient temperature, including heat shock."
          },
          {
            "node_id": "translation_initiation",
            "label": "ribosome binding and translation initiation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Binding of the ribosome to mRNA and initiation of translation."
          },
          {
            "node_id": "dnak_chaperone",
            "label": "DnaK chaperone",
            "node_type": "GENE_OR_PROTEIN",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed as a contextual protein or protein-complex label within a quantitative measurement graph; no exact semantic family term was established for this aggregate use.",
            "description": "Hsp70-family chaperone that binds and sequesters the heat-shock sigma factor RpoH."
          },
          {
            "node_id": "rpoh_sigma_factor",
            "label": "RpoH (sigma-32) heat-shock sigma factor",
            "node_type": "GENE_OR_PROTEIN",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed as a contextual protein or protein-complex label within a quantitative measurement graph; no exact semantic family term was established for this aggregate use.",
            "description": "Alternative sigma factor directing the heat-shock response regulon."
          },
          {
            "node_id": "ftsh_protease",
            "label": "FtsH protease",
            "node_type": "GENE_OR_PROTEIN",
            "description": "ATP-dependent membrane protease that controls RpoH protein levels.",
            "grounding": "InterPro:IPR005936"
          }
        ],
        "edges": [
          {
            "subject": "warm_environment",
            "predicate": "engages",
            "object": "warm_mesophile_adaptation",
            "description": "Warm host-associated environments engage warm-mesophile adaptation.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-micro-091313-103612",
                "snippet": "more unsaturated fatty acids",
                "notes": "Supports homoviscous adaptation at warm-mesophilic temperatures."
              }
            ]
          },
          {
            "subject": "warm_mesophile_adaptation",
            "predicate": "confers",
            "object": "temperature_optimum_mid4_trait",
            "description": "Warm-mesophile adaptation yields a 34\u201340 \u00b0C optimum.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-micro-091313-103612",
                "snippet": "more unsaturated fatty acids",
                "notes": "Supports the 34\u201340 \u00b0C optimum as the warm-mesophile outcome."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "temperature_optimum_mid4_trait",
            "predicate": "is a",
            "object": "temperature_optimum",
            "description": "Temperature optimum mid4 is a quantitative bin of the temperature-optimum phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1016/s0300-9629(97)00003-0",
                "snippet": "adapted to environments of high temperature",
                "notes": "Supports the 34\u201340 \u00b0C optimum as a value within the temperature-optimum distribution."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "temperature_downshift",
            "predicate": "increases",
            "object": "unsaturated_fatty_acid_proportion",
            "description": "Temperature downshift increases the proportion of unsaturated fatty acids (homeoviscous adaptation).",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-micro-091313-103612",
                "notes": "Bacteria perform homeoviscous adaptation by incorporating proportionally more unsaturated fatty acids as growth temperature decreases."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "unsaturated_fatty_acid_proportion",
            "predicate": "maintains",
            "object": "membrane_fluidity_homeostasis",
            "description": "Increased unsaturated fatty acids maintain membrane fluidity homeostasis.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-micro-091313-103612",
                "notes": "Disrupting bilayer order optimizes cellular processes at the new temperature; membrane fluidity homeostasis."
              }
            ]
          },
          {
            "subject": "membrane_fluidity_homeostasis",
            "predicate": "induces",
            "object": "unsaturated_fa_biosynthesis_response",
            "description": "Sensed decreases in membrane fluidity induce the unsaturated fatty acid biosynthesis response.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-micro-091313-103612",
                "notes": "Microbes sense decreases in membrane fluidity and initiate responses that upregulate biosynthesis of unsaturated fatty acids."
              }
            ]
          },
          {
            "subject": "rna_thermometer",
            "predicate": "occludes",
            "object": "shine_dalgarno_sequence",
            "description": "RNA thermometer hairpins occlude the Shine-Dalgarno/AUG region, repressing translation at low temperature.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s12275-023-00031-x",
                "notes": "ROSE and FourU RNA thermometers form inhibitory hairpins that cover Shine-Dalgarno/AUG."
              }
            ]
          },
          {
            "subject": "temperature_upshift",
            "predicate": "melts",
            "object": "rna_thermometer",
            "description": "Temperature upshift / heat shock melts RNA thermometer structures.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s12275-023-00031-x",
                "notes": "RNA thermometers are stable at low temperatures but undergo conformational change (melting) at heat shock."
              }
            ]
          },
          {
            "subject": "rna_thermometer",
            "predicate": "enables",
            "object": "translation_initiation",
            "description": "Melting of the RNA thermometer exposes the ribosome binding site and enables translation initiation.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s12275-023-00031-x",
                "notes": "Melting releases translation inhibition, allowing ribosome binding and translation initiation."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "dnak_chaperone",
            "predicate": "negatively regulates",
            "object": "rpoh_sigma_factor",
            "description": "DnaK binds and retains RpoH, negatively regulating the heat-shock sigma factor.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s12275-023-00031-x",
                "notes": "DnaK binds and retains RpoH until heat-denatured proteins displace it."
              }
            ],
            "predicate_id": "RO:0002212"
          },
          {
            "subject": "ftsh_protease",
            "predicate": "controls abundance of",
            "object": "rpoh_sigma_factor",
            "description": "FtsH protease controls RpoH protein levels.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s12275-023-00031-x",
                "notes": "ATP-dependent proteases FtsH and ClpXP control RpoH protein levels."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.821571+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-13T11:00:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed definition and causal graph linking warm-mesophile adaptation to the temperature-optimum-mid4 bin.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:30Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d71, rdfs:subClassOf\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 8 evidence-backed generic edges (11 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:11Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002213\u00d71, RO:0002327\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-26T07:15:18Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A0D7UY21\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-04T03:08:13Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002212\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates (1 to confers), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-22T04:26:15Z",
        "curator": "codex",
        "action": "REVIEW_UNIPROT_INSTANCE_GROUNDINGS",
        "changes": "Reviewed 1 organism-specific UniProtKB grounding(s): replaced 1 with taxon-agnostic GO/InterPro terms and retracted 0 to label-only where no exact semantic term was supported (docs/GROUNDING_POLICY.md).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope temperature_optimum_mid4_warm_mesophile=NONMECHANISTIC with scope_notes; marked 2 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (dnak_chaperone, rpoh_sigma_factor); retyped 2 node(s) (rna_thermometer->RNA, shine_dalgarno_sequence->GENETIC_ELEMENT).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T06:15:38Z",
        "curator": "codex",
        "action": "ADD_EXACT_ONTOLOGY_MATCH",
        "changes": "Ontology exact-match review (2026-08-25): declared exact synonym(s): 'mesophilic'. Evidence is predicate-scoped in the versioned ontology snapshots; OAK cross-checked direct data, and OLS4 spot-checked release deltas and disputed hits.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T04:43:24Z",
        "curator": "codex",
        "action": "ADD_CANONICAL_EXAMPLES",
        "changes": "Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Escherichia coli K-12 (NCBITaxon:83333; DOI:10.1128/AEM.05773-11). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000441",
    "label": "temperature optimum very low",
    "definition": "A temperature optimum phenotype with the best-growth ambient temperature at or below approximately 10 \u00b0C, characteristic of psychrophilic physiology.",
    "definition_source": "DOI:10.1038/sj.embor.7400662",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000304"
    ],
    "synonyms": [
      {
        "synonym_text": "Psychrophile",
        "synonym_type": "EXACT_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "TO_<=10",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/sj.embor.7400662",
        "snippet": "growing well at temperatures around the freezing point of water",
        "notes": "Psychrophile review supports growth at very low temperatures as the psychrophilic optimum."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:132926",
        "taxon_label": "Clostridium psychrophilum",
        "reference": "DOI:10.1016/j.bbalip.2013.02.004",
        "note": "Clostridium psychrophilum was cultured near its reported optimal growth temperature of 5 degrees C and also at -5 degrees C for the cited membrane-lipid study; the optimum is wholly inside the at-most-10-degree bin."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "temperature_optimum_very_low_psychrophile_setpoint",
        "title": "Temperature-optimum-very-low psychrophile context",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a quantitative measurement, interval, or bin in the environmental phenotype hierarchy; a token protein example would misrepresent the measured value as one inherited molecular mechanism.",
        "description": "DOI-backed nonmechanistic graph connecting cold-adapted membranes, cold-shock RNA chaperones, compatible-solute cryoprotection, antifreeze-protein ice binding, and flexible enzyme branches to the at-or-below-10-degrees-C optimum bin.",
        "nodes": [
          {
            "node_id": "temperature_optimum_very_low_trait",
            "label": "temperature optimum very low",
            "node_type": "TRAIT",
            "grounding": "METPO:1000441",
            "description": "Temperature optimum at or below ~10 \u00b0C."
          },
          {
            "node_id": "temperature_optimum",
            "label": "temperature optimum",
            "node_type": "TRAIT",
            "grounding": "METPO:1000304",
            "description": "Ambient temperature supporting maximal growth."
          },
          {
            "node_id": "cold_environment",
            "label": "cold environment",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Habitat ambient temperature near the freezing point of water.",
            "grounding": "ENVO:01000309"
          },
          {
            "node_id": "psychrophile_machinery",
            "label": "psychrophile cold-adapted machinery",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Cold-active enzymes and unsaturated-lipid membranes sustaining function at very low temperature."
          },
          {
            "node_id": "unsaturated_fatty_acids",
            "label": "unsaturated fatty acids",
            "node_type": "CHEMICAL",
            "description": "Unsaturated acyl chains that lower membrane melting point.",
            "grounding": "CHEBI:27208"
          },
          {
            "node_id": "membrane_fluidity",
            "label": "membrane fluidity at low temperature",
            "node_type": "QUALITY",
            "description": "Maintained membrane fluidity sustaining transport and function in the cold."
          },
          {
            "node_id": "fatty_acid_desaturase_activity",
            "label": "fatty acid desaturase activity",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "Desaturase activity introducing double bonds into fatty acyl chains."
          },
          {
            "node_id": "cold_shock_proteins",
            "label": "cold shock proteins / RNA chaperones",
            "node_type": "GENE_OR_PROTEIN",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed as a contextual protein or protein-complex label within a quantitative measurement graph; no exact semantic family term was established for this aggregate use.",
            "description": "RNA chaperones that resolve nucleic-acid secondary structure stabilized in the cold."
          },
          {
            "node_id": "translation_low_temperature",
            "label": "translation at low temperature",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Maintenance of transcription and translation under low-temperature conditions."
          },
          {
            "node_id": "protein_membrane_stabilization",
            "label": "protein and membrane stabilization under cold stress",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Prevention of protein aggregation and stabilization of membranes during cold stress."
          },
          {
            "node_id": "trehalose",
            "label": "trehalose",
            "node_type": "CHEMICAL",
            "description": "Disaccharide compatible solute acting as a cryoprotectant."
          },
          {
            "node_id": "cryoprotection",
            "label": "cryoprotection",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Protection of cellular structures against freezing and freeze-thaw damage."
          },
          {
            "node_id": "antifreeze_proteins",
            "label": "antifreeze / ice-binding proteins",
            "node_type": "GENE_OR_PROTEIN",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed as a contextual protein or protein-complex label within a quantitative measurement graph; no exact semantic family term was established for this aggregate use.",
            "description": "Ice-binding proteins that depress freezing point via thermal hysteresis."
          },
          {
            "node_id": "thermal_hysteresis",
            "label": "thermal hysteresis / lowered freezing point",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Lowering of the freezing point separating melting and freezing temperatures."
          },
          {
            "node_id": "enzyme_structural_flexibility",
            "label": "increased enzyme structural flexibility",
            "node_type": "QUALITY",
            "description": "Greater conformational flexibility of cold-adapted enzymes."
          },
          {
            "node_id": "catalytic_activity_low_temperature",
            "label": "catalytic activity at low temperature",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "Retention of catalytic efficiency at low temperature."
          }
        ],
        "edges": [
          {
            "subject": "cold_environment",
            "predicate": "selects for",
            "object": "psychrophile_machinery",
            "description": "Cold environments select for cold-adapted enzymes and lipids.",
            "evidence": [
              {
                "reference": "DOI:10.1038/sj.embor.7400662",
                "snippet": "growing well at temperatures around the freezing point of water",
                "notes": "Supports cold habitats as the context for psychrophile machinery."
              }
            ],
            "predicate_id": "METPO:2007401"
          },
          {
            "subject": "psychrophile_machinery",
            "predicate": "confers",
            "object": "temperature_optimum_very_low_trait",
            "description": "Psychrophile cold-adapted machinery yields a very-low temperature optimum.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-micro-091313-103612",
                "snippet": "more unsaturated fatty acids",
                "notes": "Supports homoviscous adaptation as the mechanism setting the psychrophile optimum."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "temperature_optimum_very_low_trait",
            "predicate": "is a",
            "object": "temperature_optimum",
            "description": "Temperature optimum very low is a quantitative bin of the temperature-optimum phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1038/sj.embor.7400662",
                "snippet": "growing well at temperatures around the freezing point of water",
                "notes": "Supports a \u226410 \u00b0C optimum as a value within the temperature-optimum distribution."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "fatty_acid_desaturase_activity",
            "predicate": "increases",
            "object": "unsaturated_fatty_acids",
            "description": "Fatty acid desaturase activity increases unsaturated acyl chains.",
            "evidence": [
              {
                "reference": "DOI:10.17159/sajs.2018/20170254",
                "snippet": "increase in the proportion of unsaturated acyl chains",
                "notes": "Verified against the open Hamdan review; lower growth temperatures are described as activating desaturases that convert saturated acyl fatty acids to unsaturated ones."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "unsaturated_fatty_acids",
            "predicate": "contributes to",
            "object": "membrane_fluidity",
            "description": "Increased unsaturated fatty acids contribute to membrane fluidity at low temperature.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.01928-22",
                "snippet": "proportion of unsaturated fatty acids was higher",
                "notes": "Verified against the open Yang et al. abstract; Bacillus simplex H-b cultured at low temperature carried a higher unsaturated-fatty-acid proportion."
              },
              {
                "reference": "DOI:10.17159/sajs.2018/20170254",
                "snippet": "maintain optimum membrane fluidity",
                "notes": "Verified against the open Hamdan review; fatty-acyl-chain modifications are described as preserving membrane fluidity in freezing environments."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "cold_shock_proteins",
            "predicate": "contributes to",
            "object": "translation_low_temperature",
            "description": "Cold shock proteins / RNA chaperones contribute to transcription and translation in the cold.",
            "evidence": [
              {
                "reference": "DOI:10.17159/sajs.2018/20170254",
                "snippet": "regulation of cellular protein synthesis",
                "notes": "Verified against the open Hamdan review; cold-shock proteins are linked to cellular protein-synthesis regulation, including transcription and translation initiation."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "trehalose",
            "predicate": "contributes to",
            "object": "cryoprotection",
            "description": "Trehalose contributes to cryoprotection.",
            "evidence": [
              {
                "reference": "DOI:10.17159/sajs.2018/20170254",
                "snippet": "preventing protein denaturation and aggregation",
                "notes": "Verified against the open Hamdan review; trehalose is reported as preventing protein denaturation and aggregation in psychrophilic bacteria."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "antifreeze_proteins",
            "predicate": "causes",
            "object": "thermal_hysteresis",
            "description": "Antifreeze proteins lower the freezing point via thermal hysteresis.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s42770-023-01057-4",
                "snippet": "lower the water freezing point",
                "notes": "Verified against the open Ram\u00f3n et al. abstract and review text; anti-freeze proteins are described as lowering the water freezing point via thermal hysteresis or ice-recrystallization inhibition."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "enzyme_structural_flexibility",
            "predicate": "increases",
            "object": "catalytic_activity_low_temperature",
            "description": "Increased enzyme structural flexibility increases catalytic activity at low temperature.",
            "evidence": [
              {
                "reference": "DOI:10.17159/sajs.2018/20170254",
                "snippet": "up to 10-fold higher specific activity",
                "notes": "Verified against the open Hamdan review; psychrophiles are described as producing structurally flexible enzymes with higher low-temperature specific activity than mesophilic homologues."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "translation_low_temperature",
            "predicate": "associated with",
            "object": "psychrophile_machinery",
            "description": "Cold-shock protein support for translation is associated with psychrophile cold-adapted machinery.",
            "evidence": [
              {
                "reference": "DOI:10.4161/rna.7.6.13482",
                "snippet": "facilitating transcription and translation at low temperature",
                "notes": "Verified against the open Phadtare and Severinov PubMed abstract; this connector keeps cold-shock RNA chaperones as protein-synthesis context for psychrophile physiology."
              }
            ],
            "predicate_id": "biolink:associated_with"
          },
          {
            "subject": "protein_membrane_stabilization",
            "predicate": "associated with",
            "object": "psychrophile_machinery",
            "description": "Compatible-solute protein and membrane stabilization is associated with psychrophile cold-adapted machinery.",
            "evidence": [
              {
                "reference": "DOI:10.17159/sajs.2018/20170254",
                "snippet": "compatible solutes such as trehalose and glycine-betaine",
                "notes": "Verified against the open Hamdan review; this connector keeps glycine-betaine compatible-solute effects as broad cold-stress context."
              }
            ],
            "predicate_id": "biolink:associated_with"
          },
          {
            "subject": "cryoprotection",
            "predicate": "associated with",
            "object": "protein_membrane_stabilization",
            "description": "Trehalose-linked cryoprotection is associated with protein and membrane stabilization during cold stress.",
            "evidence": [
              {
                "reference": "DOI:10.17159/sajs.2018/20170254",
                "snippet": "counteracting protein aggregation, improving protein folding and stabilizing membranes and proteins at chilling temperatures",
                "notes": "Verified against the open Hamdan review; this connector keeps trehalose as a compatible-solute cryoprotection branch."
              }
            ],
            "predicate_id": "biolink:associated_with"
          },
          {
            "subject": "thermal_hysteresis",
            "predicate": "associated with",
            "object": "cryoprotection",
            "description": "Antifreeze-protein thermal hysteresis is associated with cryoprotection near freezing.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s42770-023-01057-4",
                "snippet": "AFPs lower the water freezing point, avoiding frostbite due to their thermal hysteresis",
                "notes": "Verified against the open Ram\u00f3n et al. abstract and review text; this connector keeps antifreeze proteins as ice-binding cryoprotection context."
              }
            ],
            "predicate_id": "biolink:associated_with"
          },
          {
            "subject": "catalytic_activity_low_temperature",
            "predicate": "associated with",
            "object": "psychrophile_machinery",
            "description": "Flexible-enzyme catalytic activity is associated with psychrophile cold-adapted machinery.",
            "evidence": [
              {
                "reference": "DOI:10.17159/sajs.2018/20170254",
                "snippet": "adapted to function at low temperatures, with high catalytic constants",
                "notes": "Verified against the open Hamdan review; this connector keeps low-temperature enzyme flexibility as contextual psychrophile machinery."
              }
            ],
            "predicate_id": "biolink:associated_with"
          },
          {
            "subject": "membrane_fluidity",
            "predicate": "associated with",
            "object": "psychrophile_machinery",
            "description": "Membrane-fluidity regulation is associated with psychrophile cold-adapted machinery.",
            "evidence": [
              {
                "reference": "DOI:10.17159/sajs.2018/20170254",
                "snippet": "regulate or modulate the fluidity of the membrane in freezing environments",
                "notes": "Verified against the open Hamdan review; the membrane-fluidity section names membrane-fluidity modulation in freezing environments as a frequent psychrophile cold-adaptation strategy."
              }
            ],
            "predicate_id": "biolink:associated_with"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.818713+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-13T11:00:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed definition and causal graph linking psychrophile cold-adapted machinery to the temperature-optimum-very-low bin.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:30Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d71, rdfs:subClassOf\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T21:30:06Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007401\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-14T05:51:45Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (ENVO:01000309\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 8 evidence-backed generic edges (13 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:11Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:causes\u00d71, RO:0002213\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:32Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:27208\u00d71, CHEBI:17750\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates (1 to confers), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-15T06:00:00Z",
        "curator": "claude",
        "action": "SPLIT_PROTEIN_FROM_ACTIVITY",
        "changes": "Separated the protein sense from the activity sense so one node_id means one thing (issue 356): renamed fatty_acid_desaturase -> fatty_acid_desaturase_activity (MOLECULAR_FUNCTION sense). Described as 'Desaturase ACTIVITY introducing double bonds into fatty acyl chains', against 'Desaturase enzyme (e.g., Des) that introduces double bonds' for the protein occurrences. fatty_acid_desaturase_activity already exists corpus-wide as MOLECULAR_FUNCTION.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope temperature_optimum_very_low_psychrophile_setpoint=NONMECHANISTIC with scope_notes; marked 2 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (cold_shock_proteins, antifreeze_proteins).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T04:43:24Z",
        "curator": "codex",
        "action": "ADD_CANONICAL_EXAMPLES",
        "changes": "Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Clostridium psychrophilum (NCBITaxon:132926; DOI:10.1016/j.bbalip.2013.02.004). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-04T03:40:00Z",
        "curator": "codex",
        "action": "REVIEW_CAUSAL_EVIDENCE",
        "changes": "Reviewed the temperature_optimum_very_low_psychrophile_setpoint graph for issue #183: added snippets to 8 edge-level evidence items and grounded the desaturase, membrane-fluidity, cold-shock, glycine-betaine, and trehalose predicates to RO:0002213 or RO:0002326. No paid research service was called.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-04T21:00:00Z",
        "curator": "codex",
        "action": "CONNECT_CAUSAL_GRAPH_COMPONENTS",
        "changes": "Resolved issue #183 graph fragmentation (6 components to 1) by adding 5 source- and verbatim-snippet-backed association connectors among cold-shock RNA support, compatible-solute cryoprotection, antifreeze protein ice-binding, and low-temperature flexible-enzyme branches. No paid research service was called.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-06T17:10:00Z",
        "curator": "codex",
        "action": "ADVERSARIAL_REVIEW_REPAIR",
        "changes": "Addressed PR #664 adversarial review: corrected the Phadtare and Severinov cold-shock connector note so it names the DOI-matched source instead of the Hamdan psychrophile review.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-08T03:05:00Z",
        "curator": "codex",
        "action": "ADVERSARIAL_REVIEW_REPAIR",
        "changes": "Addressed PR #664 adversarial review issue #700: removed the unsupported membrane-fluidity and glycine-betaine psychrophile edges, and removed the abandoned glycine-betaine node.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-08T03:25:00Z",
        "curator": "codex",
        "action": "ADVERSARIAL_REVIEW_REPAIR",
        "changes": "Addressed PR #664 adversarial review issue #704: restored the pre-existing membrane-fluidity branch as a DOI-backed association to psychrophile cold-adapted machinery after the final connector prune over-deleted it.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000533",
    "label": "temperature phenotype with numerical limits",
    "definition": "A phenotype characterized by specific temperature values or ranges that define growth or activity limits.",
    "definition_source": "DOI:10.1016/s0300-9629(97)00003-0",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1016/s0300-9629(97)00003-0",
        "snippet": "adapted to environments of high temperature",
        "notes": "Thermophile-adaptation review supports temperature as the quantitative axis defining psychrophile, mesophile, and thermophile classification."
      },
      {
        "reference": "DOI:10.1038/sj.embor.7400662",
        "snippet": "growing well at temperatures around the freezing point of water",
        "notes": "Psychrophile review supports the low end of the temperature axis as a distinct quantitative phenotype."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:2325",
        "taxon_label": "Thermoanaerobacter kivui",
        "reference": "DOI:10.3389/fmicb.2023.1265216",
        "note": "The study reports a 39 degrees C lower growth boundary, ancestral 66 degrees C optimum, and evolved 60 degrees C optimum for Thermoanaerobacter kivui, directly separating cardinal temperature values."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "temperature_phenotype_numerical_axis",
        "title": "Temperature phenotype numerical-limits axis",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a quantitative measurement, interval, or bin in the environmental phenotype hierarchy; a token protein example would misrepresent the measured value as one inherited molecular mechanism.",
        "description": "DOI-backed graph linking ambient temperature to the three numerical-limit measurement types (optimum, range, delta) that together classify psychrophile, mesophile, and thermophile physiology.",
        "nodes": [
          {
            "node_id": "temperature_phenotype_trait",
            "label": "temperature phenotype with numerical limits",
            "node_type": "TRAIT",
            "grounding": "METPO:1000533",
            "description": "Phenotype defined by a numerical ambient-temperature descriptor."
          },
          {
            "node_id": "ambient_temperature_axis",
            "label": "ambient temperature axis",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Ambient temperature as a continuous environmental variable."
          },
          {
            "node_id": "temperature_optimum",
            "label": "temperature optimum",
            "node_type": "TRAIT",
            "grounding": "METPO:1000304",
            "description": "Temperature supporting the most efficient growth."
          },
          {
            "node_id": "temperature_range",
            "label": "temperature range",
            "node_type": "TRAIT",
            "grounding": "METPO:1000306",
            "description": "Span of temperatures supporting growth."
          },
          {
            "node_id": "temperature_delta",
            "label": "temperature delta",
            "node_type": "TRAIT",
            "grounding": "METPO:1000303",
            "description": "Breadth (max \u2212 min) of the growth-supporting temperature range."
          },
          {
            "node_id": "membrane_cooling_rigidification",
            "label": "membrane rigidification during cooling",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Cooling-induced ordering of the membrane lipid bilayer toward a gel-like state."
          },
          {
            "node_id": "desk_desr_signaling",
            "label": "DesK/DesR two-component signaling",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Two-component signal transduction that senses membrane state and triggers lipid remodeling."
          },
          {
            "node_id": "fatty_acid_desaturase_activity",
            "label": "fatty acid desaturase activity",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "Enzymatic introduction of double bonds into membrane fatty acids."
          },
          {
            "node_id": "fatty_acid_unsaturation",
            "label": "fatty acid unsaturation",
            "node_type": "QUALITY",
            "description": "Degree of double-bond content in membrane fatty acyl chains."
          },
          {
            "node_id": "membrane_fluidity",
            "label": "membrane fluidity",
            "node_type": "QUALITY",
            "description": "Physical fluidity state of the lipid bilayer, maintained across temperatures by homeoviscous adaptation.",
            "grounding": "METPO:1007505"
          },
          {
            "node_id": "growth_at_low_temperature",
            "label": "growth at low temperature",
            "node_type": "TRAIT",
            "description": "Capacity to grow near the low-temperature boundary of the thermal range."
          },
          {
            "node_id": "cold_adapted_enzymes",
            "label": "cold-adapted enzymes",
            "node_type": "GENE_OR_PROTEIN",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed as a contextual protein or protein-complex label within a quantitative measurement graph; no exact semantic family term was established for this aggregate use.",
            "description": "Proteins with structural adaptations conferring activity at low temperature."
          },
          {
            "node_id": "high_catalytic_efficiency_low_temp",
            "label": "high catalytic efficiency at low temperature",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "Elevated catalytic turnover of enzymes operating at low temperature."
          }
        ],
        "edges": [
          {
            "subject": "ambient_temperature_axis",
            "predicate": "defines",
            "object": "temperature_phenotype_trait",
            "description": "Ambient temperature is the quantitative axis defining temperature phenotypes.",
            "evidence": [
              {
                "reference": "DOI:10.1016/s0300-9629(97)00003-0",
                "snippet": "adapted to environments of high temperature",
                "notes": "Supports ambient temperature as the descriptor axis for microbial temperature phenotypes."
              }
            ],
            "predicate_id": "METPO:2007500"
          },
          {
            "subject": "temperature_optimum",
            "predicate": "is a",
            "object": "temperature_phenotype_trait",
            "description": "Temperature optimum is a numerical-limit temperature phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-micro-091313-103612",
                "snippet": "more unsaturated fatty acids",
                "notes": "Supports temperature optima as the set-point at which membrane and protein adaptations maintain growth."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "temperature_range",
            "predicate": "is a",
            "object": "temperature_phenotype_trait",
            "description": "Temperature range is a numerical-limit temperature phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1038/sj.embor.7400662",
                "snippet": "growing well at temperatures around the freezing point of water",
                "notes": "Supports temperature ranges as the span of temperatures sustaining growth."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "temperature_delta",
            "predicate": "is a",
            "object": "temperature_phenotype_trait",
            "description": "Temperature delta is a numerical-limit temperature phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1016/s0300-9629(97)00003-0",
                "snippet": "adapted to environments of high temperature",
                "notes": "Supports temperature delta as a derived breadth descriptor over the temperature axis."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "membrane_cooling_rigidification",
            "predicate": "activates",
            "object": "desk_desr_signaling",
            "description": "Membrane rigidification during cooling activates two-component cold-sensing signaling.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s42770-023-01057-4",
                "notes": "Membrane-based cold sensing occurs via modification of the liquid-crystalline membrane state, activating two-component signalling."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "fatty_acid_desaturase_activity",
            "predicate": "increases",
            "object": "fatty_acid_unsaturation",
            "description": "Desaturase activity raises the unsaturation of membrane fatty acids.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s42770-023-01057-4",
                "notes": "A two-component sensor triggers transcriptional activation of desaturases that introduce double bonds into membrane fatty acids."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "fatty_acid_unsaturation",
            "predicate": "increases",
            "object": "membrane_fluidity",
            "description": "Increased fatty acid unsaturation raises membrane fluidity.",
            "evidence": [
              {
                "reference": "DOI:10.37256/amtt.5220244537",
                "notes": "Decreasing lipid saturation maintains optimal membrane fluidity."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "membrane_fluidity",
            "predicate": "supports",
            "object": "growth_at_low_temperature",
            "description": "Maintained membrane fluidity supports growth near the low-temperature boundary.",
            "evidence": [
              {
                "reference": "DOI:10.1039/d4cc03114h",
                "notes": "Lipidome remodeling prevents a lethal fluid-to-gel phase transition at low temperature; generic process to phenotype edge."
              }
            ]
          },
          {
            "subject": "cold_adapted_enzymes",
            "predicate": "enable",
            "object": "high_catalytic_efficiency_low_temp",
            "description": "Cold-adapted enzymes enable high catalytic efficiency at low temperature.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s42770-023-01057-4",
                "notes": "Cold-adapted proteins yield high catalytic efficiency; broad, not gene-specific."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.846837+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-13T11:00:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed causal graph linking the ambient temperature axis to temperature optimum, range, and delta measurement types.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:30Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (rdfs:subClassOf\u00d73).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T07:37:39Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007500\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 5 evidence-backed generic edges (8 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:11Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002213\u00d73).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:17Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (METPO:1007505\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope temperature_phenotype_numerical_axis=NONMECHANISTIC with scope_notes; marked 1 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (cold_adapted_enzymes).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T04:43:24Z",
        "curator": "codex",
        "action": "ADD_CANONICAL_EXAMPLES",
        "changes": "Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Thermoanaerobacter kivui (NCBITaxon:2325; DOI:10.3389/fmicb.2023.1265216). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000613",
    "label": "temperature preference",
    "definition": "A phenotype that describes characteristic growth with respect to environmental temperature.",
    "definition_source": "DOI:10.1038/sj.jim.2900572",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "synonyms": [
      {
        "synonym_text": "Physiology and metabolism.culture temp.temperature",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "range_tmp",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/sj.jim.2900572",
        "snippet": "growth rate vs temperature",
        "notes": "Supports temperature-dependent microbial growth-rate phenotypes."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:132926",
        "taxon_label": "Clostridium psychrophilum",
        "reference": "DOI:10.1016/j.bbalip.2013.02.004",
        "note": "Clostridium psychrophilum has an optimum near 5 degrees C and exemplifies the cold-adapted branch of the broad temperature-preference class."
      },
      {
        "taxon_id": "NCBITaxon:2325",
        "taxon_label": "Thermoanaerobacter kivui",
        "reference": "DOI:10.3389/fmicb.2023.1265216",
        "note": "Thermoanaerobacter kivui had an ancestral 66 degrees C optimum and exemplifies a thermophilic branch of the broad temperature-preference class."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "temperature_preference_growth_physiology",
        "title": "Environmental temperature control of growth preference",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is an upper preference, broad tolerance, or central-range classification spanning multiple unrelated adaptations; contextual protein nodes are retained without assigning a misleading token UniProt example.",
        "description": "Evidence-backed causal sketch linking environmental temperature to membrane fluidity, protein stability, and growth-rate phenotypes.",
        "nodes": [
          {
            "node_id": "temperature_preference_trait",
            "label": "temperature preference",
            "node_type": "TRAIT",
            "grounding": "METPO:1000613",
            "description": "Growth phenotype characterized by preferred environmental temperature."
          },
          {
            "node_id": "environmental_temperature",
            "label": "environmental temperature",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Growth temperature experienced by the organism."
          },
          {
            "node_id": "low_temperature",
            "label": "low temperature",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Cold growth condition that reduces molecular motion and membrane fluidity.",
            "grounding": "PATO:0001306"
          },
          {
            "node_id": "high_temperature",
            "label": "high temperature",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Hot growth condition that challenges protein and membrane stability.",
            "grounding": "PATO:0001305"
          },
          {
            "node_id": "membrane_fluidity",
            "label": "membrane fluidity",
            "node_type": "QUALITY",
            "description": "Physical state of the membrane affecting transport and cell function.",
            "grounding": "METPO:1007505"
          },
          {
            "node_id": "protein_stability",
            "label": "protein stability",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "Capacity of proteins to retain folded, functional conformations."
          },
          {
            "node_id": "growth_rate",
            "label": "microbial growth rate",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Rate of population growth under a given temperature regime."
          },
          {
            "node_id": "temperature_downshift",
            "label": "temperature downshift",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "A decrease in environmental growth temperature (cold shift)."
          },
          {
            "node_id": "fatty_acid_desaturase",
            "label": "fatty acid desaturase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Desaturase enzyme (e.g., Des) that introduces double bonds into membrane fatty acids.",
            "grounding": "InterPro:IPR012171"
          },
          {
            "node_id": "unsaturated_membrane_fatty_acids",
            "label": "unsaturated membrane fatty acids",
            "node_type": "CHEMICAL",
            "description": "Membrane fatty acids bearing double bonds; raise membrane fluidity (homeoviscous adaptation)."
          },
          {
            "node_id": "rna_thermometer",
            "label": "RNA thermometer",
            "node_type": "RNA",
            "description": "Temperature-responsive RNA structure (ROSE/FourU) in 5-UTRs that gates translation by melting with temperature."
          },
          {
            "node_id": "heat_shock_gene_translation",
            "label": "heat-shock gene translation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Translation of heat-shock response genes permitted upon RNA thermometer melting at elevated temperature."
          },
          {
            "node_id": "cold_shock_rna_chaperone_activity",
            "label": "cold-shock RNA chaperone activity",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "CspA-type RNA chaperone activity that maintains single-stranded RNA to support translation at low temperature."
          }
        ],
        "edges": [
          {
            "subject": "environmental_temperature",
            "predicate": "regulates",
            "object": "growth_rate",
            "description": "Microbial growth rate varies with growth temperature.",
            "evidence": [
              {
                "reference": "DOI:10.1038/sj.jim.2900572",
                "snippet": "growth rate vs temperature",
                "notes": "Study analyzes temperature dependence of microbial growth rates across psychrotrophs, mesophiles, and thermophiles."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "low_temperature",
            "predicate": "decreases",
            "object": "membrane_fluidity",
            "description": "Cold temperature reduces membrane fluidity and transport efficiency.",
            "evidence": [
              {
                "reference": "DOI:10.1038/sj.embor.7400662",
                "snippet": "decreased membrane fluidity",
                "notes": "Review identifies membrane fluidity loss as a core cold challenge."
              }
            ],
            "predicate_id": "RO:0002212"
          },
          {
            "subject": "high_temperature",
            "predicate": "challenges",
            "object": "protein_stability",
            "description": "Elevated temperature challenges protein folding and functional stability.",
            "evidence": [
              {
                "reference": "DOI:10.1128/MMBR.65.1.1-43.2001",
                "snippet": "resistant to irreversible inactivation at high temperatures",
                "notes": "Review supports thermostable enzymes as a high-temperature adaptation."
              }
            ],
            "predicate_id": "METPO:2007406"
          },
          {
            "subject": "high_temperature",
            "predicate": "increases",
            "object": "membrane_fluidity",
            "description": "High temperature increases membrane permeability and fluidity, creating a limit on growth.",
            "evidence": [
              {
                "reference": "DOI:10.1016/s0300-9629(97)00003-0",
                "snippet": "proton permeability ... increase with the temperature",
                "notes": "Review links increased membrane permeability to upper temperature growth limits."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "membrane_fluidity",
            "predicate": "regulates",
            "object": "temperature_preference_trait",
            "description": "Temperature preference reflects the range in which membrane function remains compatible with growth.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-micro-091313-103612",
                "snippet": "optimizes the performance of cellular physiological processes",
                "notes": "Review supports membrane fluidity adaptation as a temperature-sensing and response mechanism."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "protein_stability",
            "predicate": "regulates",
            "object": "temperature_preference_trait",
            "description": "Growth at preferred temperatures requires proteins to remain active and stable.",
            "evidence": [
              {
                "reference": "DOI:10.1128/MMBR.65.1.1-43.2001",
                "snippet": "molecular mechanisms involved in protein thermostabilization",
                "notes": "Supports protein stability as a determinant of high-temperature growth."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "fatty_acid_desaturase",
            "predicate": "increases",
            "object": "unsaturated_membrane_fatty_acids",
            "description": "Desaturase expression increases double bonds in membrane fatty acids (homeoviscous adaptation).",
            "evidence": [
              {
                "reference": "DOI:10.1007/s42770-023-01057-4",
                "notes": "Activation of des (desaturase) transcription increases double bonds in membrane fatty acids; generic UFA-biosynthesis module."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "unsaturated_membrane_fatty_acids",
            "predicate": "increases",
            "object": "membrane_fluidity",
            "description": "Increased unsaturated membrane fatty acids restore/raise membrane fluidity.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s42770-023-01057-4",
                "notes": "Increasing double bonds in membrane fatty acids restores membrane fluidity; core homeoviscous-adaptation edge broadly curatable across microbes."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "high_temperature",
            "predicate": "melts",
            "object": "rna_thermometer",
            "description": "Elevated temperature melts RNA thermometer hairpins, relieving translational repression.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s12275-023-00031-x",
                "notes": "RNA thermometers (ROSE/FourU) control translation by occluding Shine-Dalgarno/start codons and melt with temperature; bacterial heat-sensing mechanism."
              }
            ]
          },
          {
            "subject": "rna_thermometer",
            "predicate": "permits translation of",
            "object": "heat_shock_gene_translation",
            "description": "RNA thermometer melting permits translation of heat-shock genes.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s12275-023-00031-x",
                "notes": "Post-transcriptional RNA thermometers in 5-UTRs mediate rapid temperature-dependent control of translation; strong generic edge."
              }
            ]
          },
          {
            "subject": "low_temperature",
            "predicate": "induces",
            "object": "cold_shock_rna_chaperone_activity",
            "description": "Cold shock induces CspA-mediated RNA chaperone activity that maintains translatable RNA.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s12275-023-00031-x",
                "notes": "Cold shock induces cold-shock proteins (CspA) that help maintain single-stranded RNA for translation at low temperature."
              }
            ]
          },
          {
            "subject": "temperature_downshift",
            "predicate": "induces",
            "object": "fatty_acid_desaturase",
            "description": "Cold downshift induces fatty-acid desaturase activity to maintain membrane fluidity.",
            "evidence": [
              {
                "reference": "DOI:10.1038/sj.jim.2900572",
                "notes": "Connecting edge wiring the enrichment node into the graph."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.856449+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-11T00:00:00-07:00",
        "curator": "codex",
        "action": "CURATED_WITH_LITERATURE",
        "changes": "Reviewed temperature preference trait and added DOI-backed causal graph for temperature effects on membrane fluidity, protein stability, and growth.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T21:30:06Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007406\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:38:00Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (PATO:0000383\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:41:03Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (METPO:1007505\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-26T02:30:13Z",
        "curator": "claude",
        "action": "RETYPE_CAUSAL_NODES",
        "changes": "Re-typed 1 causal-node node_type field(s) to align with CausalNodeTypeEnum semantics: membrane fluidity: BIOLOGICAL_PROCESS \u2192 QUALITY \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-26T05:00:47Z",
        "curator": "claude",
        "action": "RENAME_PREDICATE_LABELS",
        "changes": "Renamed 3 causal-edge predicate label(s) to align with existing groundings: constrains \u2192 regulates \u00d72; influences \u2192 regulates \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-26T05:00:50Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002211\u00d73).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-13T21:03:26Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002212\u00d71, RO:0002213\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-14T05:51:45Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (PATO:0001305\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-15T07:19:08Z",
        "curator": "claude",
        "action": "FIX_NODE_GROUNDING_CURIE",
        "changes": "Overwrote 1 causal-node grounding(s) to corrected CURIEs (phase-2 id-label fix; verified vs OAK).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 5 evidence-backed generic edges (6 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "FIX_ORPHAN_NODE",
        "changes": "Connected orphaned node 'fatty_acid_desaturase' via temperature_downshift -[induces]-> fatty_acid_desaturase.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:11Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002213\u00d72).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-26T07:15:18Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A031GJU0\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:21:11Z",
        "curator": "claude",
        "action": "RETRACT_DEAD_UNIPROT_GROUNDINGS",
        "changes": "Retracted 1 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:23:53Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (InterPro:IPR012171\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope temperature_preference_growth_physiology=NONMECHANISTIC with scope_notes; retyped 1 node(s) (rna_thermometer->RNA).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T04:43:24Z",
        "curator": "codex",
        "action": "ADD_CANONICAL_EXAMPLES",
        "changes": "Resolved issue #444 after the #591 source/bin policy with 2 direct source-backed canonical example(s): Clostridium psychrophilum (NCBITaxon:132926; DOI:10.1016/j.bbalip.2013.02.004), Thermoanaerobacter kivui (NCBITaxon:2325; DOI:10.3389/fmicb.2023.1265216). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000306",
    "label": "temperature range",
    "definition": "A temperature phenotype with numerical limits that bounds the minimum and maximum ambient temperatures supporting growth of an organism.",
    "definition_source": "DOI:10.1016/s0300-9629(97)00003-0",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000533",
      "METPO:1000535"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1016/s0300-9629(97)00003-0",
        "snippet": "adapted to environments of high temperature",
        "notes": "Thermophile-adaptation review supports the bounded ambient-temperature span over which membrane, enzyme, and bioenergetic adaptations sustain growth as the basis of the temperature-range phenotype."
      },
      {
        "reference": "DOI:10.1038/sj.embor.7400662",
        "snippet": "decreased membrane fluidity",
        "notes": "Psychrophile review supports cold-end membrane stress as a lower-bound growth constraint that low-temperature tolerance must overcome."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:735518",
        "taxon_label": "Lederbergia graminis",
        "reference": "DOI:10.1099/ijs.0.023820-0",
        "note": "The type strain, published as Bacillus graminis YC6957T, grew from 15 to 45 degrees C. Its 30-degree breadth meets a bin boundary, so #591 keeps this claim on the range parent."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "temperature_range_bounded_adaptation",
        "title": "Temperature-range bounded thermal adaptation",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a quantitative measurement, interval, or bin in the environmental phenotype hierarchy; a token protein example would misrepresent the measured value as one inherited molecular mechanism.",
        "description": "DOI-backed graph linking cold- and heat-tolerance to the bounded span of growth-supporting ambient temperatures.",
        "nodes": [
          {
            "node_id": "temperature_range_trait",
            "label": "temperature range",
            "node_type": "TRAIT",
            "grounding": "METPO:1000306",
            "description": "Span of ambient temperatures supporting growth."
          },
          {
            "node_id": "ambient_temperature",
            "label": "ambient temperature",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Ambient growth temperature imposed on the cell."
          },
          {
            "node_id": "cold_tolerance",
            "label": "cold tolerance",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Capacity to maintain membrane fluidity and enzyme function at low ambient temperature."
          },
          {
            "node_id": "heat_tolerance",
            "label": "heat tolerance",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Capacity to maintain protein folding and membrane integrity at high ambient temperature."
          },
          {
            "node_id": "bounded_growth_window",
            "label": "bounded temperature growth window",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Span of ambient temperatures between the minimum and maximum that support growth."
          },
          {
            "node_id": "membrane_lipid_unsaturation",
            "label": "membrane lipid unsaturation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Increase in unsaturated fatty acids in membrane lipids in response to low temperature (homeoviscous adaptation)."
          },
          {
            "node_id": "lipid_desaturase_activity",
            "label": "lipid desaturase activity",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "Enzymatic introduction of double bonds into membrane fatty acids."
          },
          {
            "node_id": "membrane_fluidity",
            "label": "membrane fluidity",
            "node_type": "QUALITY",
            "description": "Physical fluidity of the cytoplasmic membrane that must be maintained for function at low temperature.",
            "grounding": "METPO:1007505"
          },
          {
            "node_id": "chaperone_systems",
            "label": "molecular chaperone systems",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Heat-shock chaperone systems (e.g. DnaK/GroEL) that maintain protein folding at high temperature."
          },
          {
            "node_id": "compatible_solutes",
            "label": "compatible solutes",
            "node_type": "CHEMICAL",
            "description": "Cryoprotective osmolytes (e.g. glycine betaine, trehalose, glycerol) accumulated to protect against low-temperature stress.",
            "grounding": "CHEBI:25728"
          },
          {
            "node_id": "two_component_cold_sensing",
            "label": "two-component cold sensing",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Two-component signal transduction triggered by changes in the liquid-crystalline membrane state at low temperature."
          }
        ],
        "edges": [
          {
            "subject": "ambient_temperature",
            "predicate": "defines",
            "object": "bounded_growth_window",
            "description": "Ambient temperature defines the axis over which the growth window is bounded.",
            "evidence": [
              {
                "reference": "DOI:10.1016/s0300-9629(97)00003-0",
                "snippet": "adapted to environments of high temperature",
                "notes": "Supports ambient temperature as the axis bounding the growth window."
              }
            ],
            "predicate_id": "METPO:2007500"
          },
          {
            "subject": "cold_tolerance",
            "predicate": "defines",
            "object": "bounded_growth_window",
            "description": "Cold tolerance sets the lower bound of the temperature growth window.",
            "evidence": [
              {
                "reference": "DOI:10.1038/sj.embor.7400662",
                "snippet": "decreased membrane fluidity",
                "notes": "Supports cold-end membrane and enzyme adaptation as the lower-bound mechanism."
              }
            ],
            "predicate_id": "METPO:2007500"
          },
          {
            "subject": "heat_tolerance",
            "predicate": "defines",
            "object": "bounded_growth_window",
            "description": "Heat tolerance sets the upper bound of the temperature growth window.",
            "evidence": [
              {
                "reference": "DOI:10.1128/MMBR.65.1.1-43.2001",
                "snippet": "resistant to irreversible inactivation at high temperatures",
                "notes": "Supports protein-thermostability physiology as the upper-bound mechanism."
              }
            ],
            "predicate_id": "METPO:2007500"
          },
          {
            "subject": "bounded_growth_window",
            "predicate": "manifests as",
            "object": "temperature_range_trait",
            "description": "The bounded temperature growth window manifests the temperature-range phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1016/s0300-9629(97)00003-0",
                "snippet": "adapted to environments of high temperature",
                "notes": "Supports the trait endpoint."
              }
            ],
            "predicate_id": "METPO:2007400"
          },
          {
            "subject": "ambient_temperature",
            "predicate": "increases",
            "object": "membrane_lipid_unsaturation",
            "description": "Decreased ambient temperature increases membrane lipid unsaturation via homeoviscous adaptation.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s12275-023-00031-x",
                "notes": "E. coli increases unsaturated cis-vaccenic acid and decreases palmitic acid with cold; broad bacterial mechanism affecting the lower growth bound."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "lipid_desaturase_activity",
            "predicate": "increases",
            "object": "membrane_fluidity",
            "description": "Lipid desaturase activity increases membrane fluidity at low temperature.",
            "evidence": [
              {
                "reference": "DOI:10.37256/amtt.5220244537",
                "notes": "Upregulation of genes for fatty acid synthesis/desaturation maintains membrane fluidity at low temperature."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "membrane_lipid_unsaturation",
            "predicate": "increases",
            "object": "membrane_fluidity",
            "description": "Increased membrane lipid unsaturation maintains membrane fluidity at low temperature.",
            "evidence": [
              {
                "reference": "DOI:10.37256/amtt.5220244537",
                "notes": "Fatty acid desaturation maintains membrane fluidity, a broadly supported homeoviscous adaptation underpinning cold tolerance."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "membrane_fluidity",
            "predicate": "enables",
            "object": "cold_tolerance",
            "description": "Maintenance of membrane fluidity enables cold tolerance at the lower temperature bound.",
            "evidence": [
              {
                "reference": "DOI:10.37256/amtt.5220244537",
                "notes": "Maintaining membrane fluidity at low temperature is a core mechanism supporting growth at the cold end of the range."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "ambient_temperature",
            "predicate": "induces",
            "object": "chaperone_systems",
            "description": "Elevated ambient temperature induces molecular chaperone systems that support heat tolerance.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s12275-023-00031-x",
                "notes": "Molecular chaperones DnaK/Hsp70 and GroEL are implicated in survival at high temperatures; broad across bacteria."
              }
            ]
          },
          {
            "subject": "chaperone_systems",
            "predicate": "enables",
            "object": "heat_tolerance",
            "description": "Molecular chaperone systems enable heat tolerance at the upper temperature bound.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s12275-023-00031-x",
                "notes": "Chaperone-mediated protein folding supports the upper-bound (Tmax) heat-tolerance mechanism."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "compatible_solutes",
            "predicate": "protects against",
            "object": "cold_tolerance",
            "description": "Compatible solutes protect against low-temperature and freezing stress, supporting cold tolerance.",
            "evidence": [
              {
                "reference": "DOI:10.37256/amtt.5220244537",
                "notes": "Glycine, betaine, glycerol, and trehalose act as cryoprotectants and osmolytes; broad low-end mechanism."
              }
            ]
          },
          {
            "subject": "membrane_fluidity",
            "predicate": "activates",
            "object": "two_component_cold_sensing",
            "description": "Changes in the liquid-crystalline membrane state activate two-component cold sensing.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s42770-023-01057-4",
                "notes": "Cold sensing via changes in the liquid-crystalline membrane state that activate two-component signal transduction; generic edge linking membrane state to regulatory response."
              }
            ],
            "predicate_id": "RO:0002213"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.814231+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-13T11:00:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed causal graph linking cold- and heat-tolerance to the bounded temperature-range phenotype.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T21:30:06Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007400\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T07:37:39Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007500\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-26T05:00:47Z",
        "curator": "claude",
        "action": "RENAME_PREDICATE_LABELS",
        "changes": "Renamed 2 causal-edge predicate label(s) to align with existing groundings: sets \u2192 defines \u00d72.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-26T05:00:50Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007500\u00d72).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 8 evidence-backed generic edges (6 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:11Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 6 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002213\u00d74, RO:0002327\u00d72).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:18Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (METPO:1007505\u00d71, CHEBI:25728\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope temperature_range_bounded_adaptation=NONMECHANISTIC with scope_notes.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T04:43:24Z",
        "curator": "codex",
        "action": "ADD_CANONICAL_EXAMPLES",
        "changes": "Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Lederbergia graminis (NCBITaxon:735518; DOI:10.1099/ijs.0.023820-0). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000454",
    "label": "temperature range high",
    "definition": "A temperature range phenotype in which the growth-supporting ambient temperature range extends above approximately 40 \u00b0C, characteristic of thermophilic physiology.",
    "definition_source": "DOI:10.1016/s0300-9629(97)00003-0",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000306"
    ],
    "synonyms": [
      {
        "synonym_text": "Thermophile",
        "synonym_type": "EXACT_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "TR_>40",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1016/s0300-9629(97)00003-0",
        "snippet": "adapted to environments of high temperature",
        "notes": "Thermophile-adaptation review supports growth ranges extending above 40 \u00b0C as the thermophile category."
      },
      {
        "reference": "DOI:10.1128/MMBR.65.1.1-43.2001",
        "snippet": "resistant to irreversible inactivation at high temperatures",
        "notes": "Thermostable-protein review supports thermostability as the mechanism extending growth into thermophilic temperatures."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:2261",
        "taxon_label": "Pyrococcus furiosus",
        "reference": "DOI:10.1007/s00792-017-0929-z",
        "note": "Hyperthermophilic archaeon growing above 90 degrees C; the strongest taxon-specific evidence in this trait's research artifact, where a reverse gyrase deletion abolishes growth at 95-100 degrees C while lower temperatures stay permissive."
      },
      {
        "taxon_id": "NCBITaxon:2285",
        "taxon_label": "Sulfolobus acidocaldarius",
        "reference": "DOI:10.1128/mbio.03593-22",
        "note": "Thermoacidophilic crenarchaeon used as the model for the heat-shock response at the upper end of the growth range."
      },
      {
        "taxon_id": "NCBITaxon:43080",
        "taxon_label": "Saccharolobus islandicus",
        "reference": "DOI:10.1128/mbio.02174-23",
        "note": "Hyperthermophile whose thermal-stress regulatory network is characterised by transcriptomics and proteomics."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "temperature_range_high_thermophile",
        "title": "Temperature-range-high thermophile range",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a quantitative measurement, interval, or bin in the environmental phenotype hierarchy; a token protein example would misrepresent the measured value as one inherited molecular mechanism.",
        "description": "DOI-backed graph linking thermophile thermostability to a temperature growth range extending above 40 \u00b0C.",
        "nodes": [
          {
            "node_id": "temperature_range_high_trait",
            "label": "temperature range high",
            "node_type": "TRAIT",
            "grounding": "METPO:1000454",
            "description": "Temperature growth-supporting range extending above ~40 \u00b0C."
          },
          {
            "node_id": "temperature_range",
            "label": "temperature range",
            "node_type": "TRAIT",
            "grounding": "METPO:1000306",
            "description": "Span of ambient temperatures supporting growth."
          },
          {
            "node_id": "thermophile_thermostability",
            "label": "thermophile thermostability",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Heat-stable membrane lipids and proteins that retain function at elevated temperatures."
          },
          {
            "node_id": "reverse_gyrase",
            "label": "reverse gyrase (TopR/rgy)",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Topoisomerase that introduces positive supercoils into DNA in thermophiles.",
            "grounding": "GO:0160097"
          },
          {
            "node_id": "dna_positive_supercoiling",
            "label": "DNA positive supercoiling",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Positively supercoiled DNA topology generated by reverse gyrase."
          },
          {
            "node_id": "dna_melting",
            "label": "DNA melting",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Thermal denaturation/strand separation of DNA at elevated temperature."
          },
          {
            "node_id": "dnak_dnaj",
            "label": "DnaK-DnaJ chaperone",
            "node_type": "GENE_OR_PROTEIN",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed as a contextual protein or protein-complex label within a quantitative measurement graph; no exact semantic family term was established for this aggregate use.",
            "description": "Hsp70 chaperone system assisting ATP-dependent protein folding."
          },
          {
            "node_id": "protein_folding",
            "label": "protein folding",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Folding of nascent and unfolded polypeptides into native conformation.",
            "grounding": "GO:0006457"
          },
          {
            "node_id": "groel_groes_htpg",
            "label": "GroEL-GroES / HtpG chaperone",
            "node_type": "GENE_OR_PROTEIN",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "This aggregate combines GroEL-GroES and HtpG, distinct chaperone systems, as context for a quantitative temperature-range bin.",
            "description": "Chaperonin and Hsp90 systems assisting protein folding under heat stress."
          },
          {
            "node_id": "proteostasis_high_temp",
            "label": "proteostasis at high temperature",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Maintenance of protein homeostasis (folding/refolding/degradation) at elevated temperature."
          }
        ],
        "edges": [
          {
            "subject": "thermophile_thermostability",
            "predicate": "confers",
            "object": "temperature_range_high_trait",
            "description": "Thermophile thermostability enables growth at > 40 \u00b0C.",
            "evidence": [
              {
                "reference": "DOI:10.1128/MMBR.65.1.1-43.2001",
                "snippet": "resistant to irreversible inactivation at high temperatures",
                "notes": "Supports thermostability as the range mechanism for thermophile physiology."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "temperature_range_high_trait",
            "predicate": "is a",
            "object": "temperature_range",
            "description": "Temperature range high is a quantitative bin of the temperature-range phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1016/s0300-9629(97)00003-0",
                "snippet": "adapted to environments of high temperature",
                "notes": "Supports the >40 \u00b0C range as a value within the temperature-range distribution."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "reverse_gyrase",
            "predicate": "introduces",
            "object": "dna_positive_supercoiling",
            "description": "Reverse gyrase introduces positive supercoils into DNA.",
            "evidence": [
              {
                "reference": "DOI:10.1264/jsme2.me23087",
                "notes": "reverse gyrase, a unique topoisomerase that introduces positive supercoils into DNA; broadly applicable to thermophiles."
              }
            ]
          },
          {
            "subject": "dna_positive_supercoiling",
            "predicate": "limits",
            "object": "dna_melting",
            "description": "Positive DNA supercoiling limits thermal melting of DNA.",
            "evidence": [
              {
                "reference": "DOI:10.1264/jsme2.me23087",
                "notes": "maintain the genome integrity of thermophiles by limiting DNA melting; general for reverse-gyrase-bearing thermophiles."
              }
            ],
            "predicate_id": "RO:0002212"
          },
          {
            "subject": "reverse_gyrase",
            "predicate": "confers",
            "object": "temperature_range_high_trait",
            "description": "Reverse gyrase activity supports growth at high temperature via genome stabilization.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mbio.02174-23",
                "notes": "Reverse gyrase reported as essential for growth at very high temperature, maintaining DNA stability."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "dnak_dnaj",
            "predicate": "assists",
            "object": "protein_folding",
            "description": "DnaK-DnaJ assists ATP-dependent folding of nascent and unfolded proteins.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s12275-023-00031-x",
                "notes": "DnaK-DnaJ assist ATP-dependent folding of nascent and unfolded peptides; bacterial high-temperature response."
              }
            ]
          },
          {
            "subject": "groel_groes_htpg",
            "predicate": "assists",
            "object": "protein_folding",
            "description": "GroEL-GroES and HtpG assist protein folding under heat stress.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s12275-023-00031-x",
                "notes": "GroEL-GroES, HtpG assist protein folding under heat stress; broadly relevant heat response."
              }
            ]
          },
          {
            "subject": "protein_folding",
            "predicate": "maintains",
            "object": "proteostasis_high_temp",
            "description": "Chaperone-assisted folding maintains proteostasis at high temperature.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mbio.02174-23",
                "notes": "refolding/degradation systems counter protein denaturation, aggregation and loss of function during heat shock."
              }
            ]
          },
          {
            "subject": "proteostasis_high_temp",
            "predicate": "confers",
            "object": "temperature_range_high_trait",
            "description": "Proteostasis at high temperature supports growth above 40 C.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mbio.02174-23",
                "notes": "proteostasis machinery supports thermophile survival/growth at high temperature."
              }
            ],
            "predicate_id": "METPO:2007700"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.825852+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-13T11:00:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed definition and causal graph linking thermophile thermostability to the temperature-range-high bin.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:30Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d71, rdfs:subClassOf\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 7 evidence-backed generic edges (7 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:11Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d72, RO:0002212\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:32Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0006457\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-26T07:15:18Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A0C1PL72\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:21:11Z",
        "curator": "claude",
        "action": "RETRACT_DEAD_UNIPROT_GROUNDINGS",
        "changes": "Retracted 1 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:23:53Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0160097\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 3 causal edge(s) off enables/RO:0002327 with a TRAIT object (3 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-19T06:20:00Z",
        "curator": "claude",
        "action": "BACKFILL_CANONICAL_EXAMPLES",
        "changes": "Added three exemplar taxa for the thermophilic growth range. Taxon ids resolved and label-checked against the local NCBITaxon build; references taken from this trait's own deep-research artifact. Mesophiles named in that artifact (Escherichia coli, Pseudomonas putida) were deliberately NOT included -- they appear there as contrast cases for a >40 C range, not as exemplars of it.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-21T08:00:00Z",
        "curator": "codex",
        "action": "NORMALISE_NODE_TYPE",
        "changes": "Tranche 5 of issue 356 settles the process/quality families and merges ids that meant the same sense: dna_positive_supercoiling is BIOLOGICAL_PROCESS. GO:0160097 denotes the process of introducing positive supercoils into DNA. The general DNA-topology state remains separately modelled as dna_supercoiling.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope temperature_range_high_thermophile=NONMECHANISTIC with scope_notes; marked 2 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (dnak_dnaj, groel_groes_htpg).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000449",
    "label": "temperature range low",
    "definition": "A temperature range phenotype in which the growth-supporting ambient temperature range spans approximately 10\u201322 \u00b0C, characteristic of psychrophilic or psychrotolerant physiology.",
    "definition_source": "DOI:10.1038/sj.embor.7400662",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000306"
    ],
    "synonyms": [
      {
        "synonym_text": "Psychrophile",
        "synonym_type": "EXACT_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "Psychrotolerant",
        "synonym_type": "EXACT_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "TR_10_to_22",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/sj.embor.7400662",
        "snippet": "decreased membrane fluidity",
        "notes": "Psychrophile review supports cool-temperature membrane and enzyme adaptation as the basis of growth in the 10\u201322 \u00b0C range."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:3234132",
        "taxon_label": "Aestuariibius violaceus",
        "reference": "DOI:10.1099/ijsem.0.006834",
        "note": "Aestuariibius violaceus 2305UL40-4T grew from 22 to 36 degrees C, a directly reported 14-degree breadth within the approximately 10-22-degree range-width bin."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "temperature_range_low_psychrotolerant",
        "title": "Temperature-range-low psychrotolerant range",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a quantitative measurement, interval, or bin in the environmental phenotype hierarchy; a token protein example would misrepresent the measured value as one inherited molecular mechanism.",
        "description": "DOI-backed graph linking psychrotolerant adaptation to a temperature growth range of approximately 10\u201322 \u00b0C.",
        "nodes": [
          {
            "node_id": "temperature_range_low_trait",
            "label": "temperature range low",
            "node_type": "TRAIT",
            "grounding": "METPO:1000449",
            "description": "Temperature growth-supporting range approximately 10\u201322 \u00b0C."
          },
          {
            "node_id": "temperature_range",
            "label": "temperature range",
            "node_type": "TRAIT",
            "grounding": "METPO:1000306",
            "description": "Span of ambient temperatures supporting growth."
          },
          {
            "node_id": "psychrotolerant_adaptation",
            "label": "psychrotolerant adaptation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Mild cold-adaptation of membrane and enzyme function sustaining growth at cool temperatures."
          },
          {
            "node_id": "low_temperature",
            "label": "low temperature",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Cool ambient temperature in the approximately 10-22 C range.",
            "grounding": "PATO:0001306"
          },
          {
            "node_id": "membrane_fluidity",
            "label": "membrane fluidity",
            "node_type": "QUALITY",
            "description": "Physical fluidity state of the cytoplasmic membrane lipid bilayer.",
            "grounding": "METPO:1007505"
          },
          {
            "node_id": "fatty_acid_desaturase_activity",
            "label": "fatty acid desaturase activity",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "Enzymatic introduction of double bonds into fatty acyl chains (fatty acid desaturases, EC 1.14.19.-)."
          },
          {
            "node_id": "unsaturated_fatty_acid_proportion",
            "label": "unsaturated fatty acid proportion",
            "node_type": "QUALITY",
            "description": "Relative abundance of unsaturated fatty acids in membrane lipids."
          },
          {
            "node_id": "cold_shock_proteins",
            "label": "cold-shock proteins",
            "node_type": "GENE_OR_PROTEIN",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed as a contextual protein or protein-complex label within a quantitative measurement graph; no exact semantic family term was established for this aggregate use.",
            "description": "CspA/CspC family cold-shock proteins acting as RNA chaperones."
          },
          {
            "node_id": "rna_chaperone_activity",
            "label": "RNA chaperone activity",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "Resolution of inhibitory RNA secondary structures supporting translation at low temperature."
          },
          {
            "node_id": "compatible_solutes",
            "label": "compatible solutes",
            "node_type": "CHEMICAL",
            "description": "Glycine betaine, trehalose and glycerol accumulated as cryoprotectants.",
            "grounding": "CHEBI:25728"
          },
          {
            "node_id": "cryoprotection",
            "label": "cryoprotection",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Stabilization of proteins and membranes and protection against cold/freezing damage."
          },
          {
            "node_id": "molecular_chaperones",
            "label": "GroEL/DnaK molecular chaperones",
            "node_type": "GENE_OR_PROTEIN",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed as a contextual protein or protein-complex label within a quantitative measurement graph; no exact semantic family term was established for this aggregate use.",
            "description": "GroEL and DnaK chaperones assisting protein folding under temperature stress."
          },
          {
            "node_id": "protein_misfolding",
            "label": "protein misfolding",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Cold-denaturation and misfolding of proteins at low temperature."
          }
        ],
        "edges": [
          {
            "subject": "psychrotolerant_adaptation",
            "predicate": "confers",
            "object": "temperature_range_low_trait",
            "description": "Psychrotolerant adaptation enables growth across 10\u201322 \u00b0C.",
            "evidence": [
              {
                "reference": "DOI:10.1038/sj.embor.7400662",
                "snippet": "Cold-shock proteins have also been described",
                "notes": "Supports cold-shock and acclimation responses as the cool-range mechanism."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "temperature_range_low_trait",
            "predicate": "is a",
            "object": "temperature_range",
            "description": "Temperature range low is a quantitative bin of the temperature-range phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1038/sj.embor.7400662",
                "snippet": "growing well at temperatures around the freezing point of water",
                "notes": "Supports the 10\u201322 \u00b0C range as a value within the temperature-range distribution."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "low_temperature",
            "predicate": "decreases",
            "object": "membrane_fluidity",
            "description": "Low temperature reduces membrane fluidity, triggering compensatory lipid remodeling.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s42770-023-01057-4",
                "notes": "Cold reduces membrane fluidity; changes in membrane physical state mediate cold sensing."
              }
            ],
            "predicate_id": "RO:0002212"
          },
          {
            "subject": "fatty_acid_desaturase_activity",
            "predicate": "increases",
            "object": "membrane_fluidity",
            "description": "Fatty acid desaturase activity raises unsaturation to restore membrane fluidity at low temperature.",
            "evidence": [
              {
                "reference": "DOI:10.37256/amtt.5220244537",
                "notes": "Genes for desaturation are upregulated; desaturases enhance membrane fluidity via unsaturated/PUFA synthesis."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "low_temperature",
            "predicate": "increases",
            "object": "unsaturated_fatty_acid_proportion",
            "description": "Growth at low temperature increases the proportion of unsaturated fatty acids in membrane lipids.",
            "evidence": [
              {
                "reference": "DOI:10.1128/aem.01928-22",
                "notes": "Proportion of unsaturated fatty acids was higher in strains cultured at low temperatures while long-chain SFAs decreased."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "cold_shock_proteins",
            "predicate": "enables",
            "object": "rna_chaperone_activity",
            "description": "Cold-shock proteins act as RNA chaperones supporting translation at low temperature.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2023.1197797",
                "notes": "Cold shock proteins (Csps) can function as RNA chaperones, supporting translation in the cold."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "compatible_solutes",
            "predicate": "provides",
            "object": "cryoprotection",
            "description": "Compatible solutes provide cryoprotection by stabilizing membranes and proteins and lowering freezing point.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2023.1197797",
                "notes": "Compatible osmolytes prevent cell shrinkage, lower freezing point, scavenge radicals, and stabilize membranes/proteins."
              }
            ]
          },
          {
            "subject": "molecular_chaperones",
            "predicate": "prevents",
            "object": "protein_misfolding",
            "description": "GroEL/DnaK chaperones prevent cold-denaturation and protein misfolding at low temperature.",
            "evidence": [
              {
                "reference": "DOI:10.37256/amtt.5220244537",
                "notes": "Chaperones are upregulated at low temperatures to prevent cold-denaturation and misfolding."
              }
            ],
            "predicate_id": "RO:0002212"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.823166+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-13T11:00:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed definition and causal graph linking psychrotolerant adaptation to the temperature-range-low bin.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:30Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d71, rdfs:subClassOf\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 6 evidence-backed generic edges (10 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:11Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 5 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002212\u00d72, RO:0002213\u00d72, RO:0002327\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:18Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 3 causal-node grounding field(s) via mappings/node_grounding.tsv (PATO:0001306\u00d71, METPO:1007505\u00d71, CHEBI:25728\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 1 causal edge(s) off enables/RO:0002327 with a TRAIT object (1 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope temperature_range_low_psychrotolerant=NONMECHANISTIC with scope_notes; marked 2 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (cold_shock_proteins, molecular_chaperones).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T04:43:24Z",
        "curator": "codex",
        "action": "ADD_CANONICAL_EXAMPLES",
        "changes": "Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Aestuariibius violaceus (NCBITaxon:3234132; DOI:10.1099/ijsem.0.006834). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000450",
    "label": "temperature range mid1",
    "definition": "A temperature range phenotype in which the growth-supporting ambient temperature range spans approximately 22\u201327 \u00b0C, characteristic of mesophilic physiology.",
    "definition_source": "DOI:10.1146/annurev-micro-091313-103612",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000306"
    ],
    "synonyms": [
      {
        "synonym_text": "Mesophilie",
        "synonym_type": "EXACT_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "TR_22_to_27",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "mesophilic",
        "synonym_type": "EXACT_SYNONYM",
        "source": "https://w3id.org/metpo/releases/2026-06-12/metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev-micro-091313-103612",
        "snippet": "more unsaturated fatty acids",
        "notes": "Membrane-adaptation review supports the 22\u201327 \u00b0C range as a lower mesophile growth range."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1656892",
        "taxon_label": "Nakamurella aerolata",
        "reference": "DOI:10.1007/s00284-020-02274-y",
        "note": "Nakamurella aerolata DB0629T grew from 10 to 35 degrees C, a directly reported 25-degree breadth within the approximately 22-27-degree bin."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "temperature_range_mid1_lower_mesophile",
        "title": "Temperature-range-mid1 lower-mesophile range",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a quantitative measurement, interval, or bin in the environmental phenotype hierarchy; a token protein example would misrepresent the measured value as one inherited molecular mechanism.",
        "description": "DOI-backed graph linking lower-mesophile adaptation to a temperature growth range of approximately 22\u201327 \u00b0C.",
        "nodes": [
          {
            "node_id": "temperature_range_mid1_trait",
            "label": "temperature range mid1",
            "node_type": "TRAIT",
            "grounding": "METPO:1000450",
            "description": "Temperature growth-supporting range approximately 22\u201327 \u00b0C."
          },
          {
            "node_id": "temperature_range",
            "label": "temperature range",
            "node_type": "TRAIT",
            "grounding": "METPO:1000306",
            "description": "Span of ambient temperatures supporting growth."
          },
          {
            "node_id": "lower_mesophile_adaptation",
            "label": "lower-mesophile adaptation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Mesophile membrane and enzyme adaptation sustaining growth at modest ambient temperatures."
          },
          {
            "node_id": "temperature_decrease",
            "label": "temperature decrease",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "A drop in ambient growth temperature within or toward the mesophilic range."
          },
          {
            "node_id": "membrane_rigidity",
            "label": "membrane rigidification/thickening",
            "node_type": "QUALITY",
            "description": "Cooling-induced reduction of membrane fluidity and increased bilayer thickness."
          },
          {
            "node_id": "fatty_acid_desaturation",
            "label": "fatty-acid desaturation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Introduction of double bonds into membrane fatty acyl chains."
          },
          {
            "node_id": "membrane_fluidity",
            "label": "membrane fluidity",
            "node_type": "QUALITY",
            "description": "Physical fluidity/viscosity state of the cell membrane lipid bilayer.",
            "grounding": "METPO:1007505"
          },
          {
            "node_id": "branched_chain_amino_acids",
            "label": "branched-chain amino acids",
            "node_type": "CHEMICAL",
            "description": "Valine, leucine and isoleucine serving as precursors for branched-chain fatty acids."
          },
          {
            "node_id": "anteiso_branched_fatty_acids",
            "label": "anteiso-branched fatty acids",
            "node_type": "CHEMICAL",
            "description": "Anteiso-branched-chain fatty acids that disorder membrane lipids."
          },
          {
            "node_id": "rna_thermometer_melting",
            "label": "RNA thermometer melting",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "Temperature-dependent unfolding of 5-prime-UTR cis-elements controlling translation."
          },
          {
            "node_id": "shine_dalgarno_exposure",
            "label": "Shine-Dalgarno sequence exposure",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "Exposure of the ribosome-binding Shine-Dalgarno sequence enabling translation."
          },
          {
            "node_id": "temperature_shift",
            "label": "temperature shift",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "A change in ambient growth temperature."
          },
          {
            "node_id": "dna_supercoiling",
            "label": "DNA supercoiling",
            "node_type": "QUALITY",
            "description": "DNA topological state acting as a thermosensor that reprograms transcription."
          }
        ],
        "edges": [
          {
            "subject": "lower_mesophile_adaptation",
            "predicate": "confers",
            "object": "temperature_range_mid1_trait",
            "description": "Lower-mesophile adaptation enables growth across 22\u201327 \u00b0C.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-micro-091313-103612",
                "snippet": "more unsaturated fatty acids",
                "notes": "Supports homoviscous mesophile adaptation as the lower-mesophile range mechanism."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "temperature_range_mid1_trait",
            "predicate": "is a",
            "object": "temperature_range",
            "description": "Temperature range mid1 is a quantitative bin of the temperature-range phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1016/s0300-9629(97)00003-0",
                "snippet": "adapted to environments of high temperature",
                "notes": "Supports the 22\u201327 \u00b0C range as a value within the temperature-range distribution."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "temperature_decrease",
            "predicate": "causes",
            "object": "membrane_rigidity",
            "description": "Cooling reduces membrane fluidity and increases bilayer thickness, the initiating physical signal for adaptation.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s42770-023-01057-4",
                "notes": "Membrane rigidification and increased thickness act as the primary physical signal upon cooling."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "fatty_acid_desaturation",
            "predicate": "increases",
            "object": "membrane_fluidity",
            "description": "Double bonds disrupt tight acyl-chain packing, reversing cold-induced rigidification.",
            "evidence": [
              {
                "reference": "DOI:10.1128/spectrum.03925-23",
                "notes": "Desaturation fluidizes the membrane and reduces thickness; strong and broadly conserved principle."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "anteiso_branched_fatty_acids",
            "predicate": "increases",
            "object": "membrane_fluidity",
            "description": "Anteiso chains disorder lipids effectively, supporting growth at lower temperatures.",
            "evidence": [
              {
                "reference": "DOI:10.3390/cells12101353",
                "notes": "Anteiso-BCFAs are more effective at fluidizing membranes than iso-BCFAs; generalizable across many Gram-positives."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "branched_chain_amino_acids",
            "predicate": "precursor for",
            "object": "anteiso_branched_fatty_acids",
            "description": "Branched-chain amino acids supply carbon skeletons for iso/anteiso-branched fatty acid synthesis.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s42770-023-01057-4",
                "notes": "Iso- and anteiso-branched FAs are derived from valine, leucine, and isoleucine precursors."
              }
            ]
          },
          {
            "subject": "rna_thermometer_melting",
            "predicate": "exposes",
            "object": "shine_dalgarno_exposure",
            "description": "Temperature-dependent melting of RNA thermometers exposes the Shine-Dalgarno sequence to control translation.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s12275-023-00031-x",
                "notes": "5'-UTR cis-elements occlude or expose Shine-Dalgarno sequences to control translation; strong general mechanism."
              }
            ]
          },
          {
            "subject": "temperature_shift",
            "predicate": "changes",
            "object": "dna_supercoiling",
            "description": "DNA topology functions as a thermosensor that globally reprograms transcription after temperature change.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s12275-023-00031-x",
                "notes": "DNA topology acts as a thermosensor; cold stress enhances negative DNA supercoiling."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.823745+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-13T11:00:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed definition and causal graph linking lower-mesophile adaptation to the temperature-range-mid1 bin.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:30Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d71, rdfs:subClassOf\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 6 evidence-backed generic edges (10 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:11Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002213\u00d72, biolink:causes\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:18Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (METPO:1007505\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 1 causal edge(s) off enables/RO:0002327 with a TRAIT object (1 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-21T08:00:00Z",
        "curator": "codex",
        "action": "NORMALISE_NODE_TYPE",
        "changes": "Tranche 5 of issue 356 settles the process/quality families and merges ids that meant the same sense: membrane_rigidity is QUALITY. Membrane rigidity is a physical attribute of the bilayer and therefore a QUALITY under the schema's membrane-fluidity example.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope temperature_range_mid1_lower_mesophile=NONMECHANISTIC with scope_notes.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T06:15:38Z",
        "curator": "codex",
        "action": "ADD_EXACT_ONTOLOGY_MATCH",
        "changes": "Ontology exact-match review (2026-08-25): declared exact synonym(s): 'mesophilic'. Evidence is predicate-scoped in the versioned ontology snapshots; OAK cross-checked direct data, and OLS4 spot-checked release deltas and disputed hits.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T04:43:24Z",
        "curator": "codex",
        "action": "ADD_CANONICAL_EXAMPLES",
        "changes": "Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Nakamurella aerolata (NCBITaxon:1656892; DOI:10.1007/s00284-020-02274-y). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000451",
    "label": "temperature range mid2",
    "definition": "A temperature range phenotype in which the growth-supporting ambient temperature range spans approximately 27\u201330 \u00b0C, characteristic of mesophilic physiology.",
    "definition_source": "DOI:10.1146/annurev-micro-091313-103612",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000306"
    ],
    "synonyms": [
      {
        "synonym_text": "Mesophilie",
        "synonym_type": "EXACT_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "TR_27_to_30",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "mesophilic",
        "synonym_type": "EXACT_SYNONYM",
        "source": "https://w3id.org/metpo/releases/2026-06-12/metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev-micro-091313-103612",
        "snippet": "more unsaturated fatty acids",
        "notes": "Membrane-adaptation review supports the 27\u201330 \u00b0C range as a typical mesophile growth range."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:2593654",
        "taxon_label": "Pseudomonas mangiferae",
        "reference": "DOI:10.1099/ijsem.0.003657",
        "note": "Pseudomonas mangiferae DMKU BBB3-04T grew from 12 to 40 degrees C, a directly reported 28-degree breadth within the approximately 27-30-degree bin."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "temperature_range_mid2_baseline_mesophile",
        "title": "Temperature-range-mid2 baseline-mesophile range",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a quantitative measurement, interval, or bin in the environmental phenotype hierarchy; a token protein example would misrepresent the measured value as one inherited molecular mechanism.",
        "description": "DOI-backed graph linking baseline mesophile adaptation to a temperature growth range of approximately 27\u201330 \u00b0C.",
        "nodes": [
          {
            "node_id": "temperature_range_mid2_trait",
            "label": "temperature range mid2",
            "node_type": "TRAIT",
            "grounding": "METPO:1000451",
            "description": "Temperature growth-supporting range approximately 27\u201330 \u00b0C."
          },
          {
            "node_id": "temperature_range",
            "label": "temperature range",
            "node_type": "TRAIT",
            "grounding": "METPO:1000306",
            "description": "Span of ambient temperatures supporting growth."
          },
          {
            "node_id": "baseline_mesophile_adaptation",
            "label": "baseline mesophile adaptation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Standard mesophile membrane and enzyme repertoire supporting growth at moderate ambient temperatures."
          },
          {
            "node_id": "homeoviscous_adaptation",
            "label": "homeoviscous adaptation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Regulation of membrane lipid composition to maintain constant viscosity/fluidity across temperatures.",
            "grounding": "METPO:1016200"
          },
          {
            "node_id": "membrane_fluidity",
            "label": "membrane fluidity",
            "node_type": "QUALITY",
            "description": "Fluid state of the lipid bilayer required for membrane function.",
            "grounding": "METPO:1007505"
          },
          {
            "node_id": "unsaturated_fatty_acid_fraction",
            "label": "unsaturated fatty acid fraction",
            "node_type": "CHEMICAL",
            "description": "Proportion of unsaturated fatty acids in membrane phospholipids."
          },
          {
            "node_id": "hopanoids_sterol_like",
            "label": "hopanoids / sterol-like molecules",
            "node_type": "CHEMICAL",
            "description": "Membrane-embedded sterol-like regulators of bilayer fluidity."
          },
          {
            "node_id": "elevated_temperature",
            "label": "elevated temperature",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Increase in ambient growth temperature."
          },
          {
            "node_id": "rna_thermometer",
            "label": "RNA thermometer 5\u2032-UTR structure",
            "node_type": "RNA",
            "description": "Temperature-responsive mRNA 5\u2032-UTR secondary structure controlling translation initiation."
          },
          {
            "node_id": "temperature_shift",
            "label": "temperature shift / heat shock",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Abrupt change in ambient temperature, including heat shock."
          },
          {
            "node_id": "heat_shock_proteins",
            "label": "heat-shock proteins / chaperones",
            "node_type": "GENE_OR_PROTEIN",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed as a contextual protein or protein-complex label within a quantitative measurement graph; no exact semantic family term was established for this aggregate use.",
            "description": "Molecular chaperones induced by thermal stress that maintain proteostasis."
          },
          {
            "node_id": "protein_denaturation",
            "label": "protein denaturation / aggregation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Loss of protein structure and aggregation under thermal stress."
          },
          {
            "node_id": "mesophilic_organisms",
            "label": "mesophilic organisms",
            "node_type": "STATE",
            "description": "Organisms growing at moderate temperatures (~20-45 \u00b0C)."
          }
        ],
        "edges": [
          {
            "subject": "baseline_mesophile_adaptation",
            "predicate": "confers",
            "object": "temperature_range_mid2_trait",
            "description": "Baseline mesophile adaptation enables growth across 27\u201330 \u00b0C.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-micro-091313-103612",
                "snippet": "more unsaturated fatty acids",
                "notes": "Supports baseline mesophile homeoviscous adaptation as the range mechanism."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "temperature_range_mid2_trait",
            "predicate": "is a",
            "object": "temperature_range",
            "description": "Temperature range mid2 is a quantitative bin of the temperature-range phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1016/s0300-9629(97)00003-0",
                "snippet": "adapted to environments of high temperature",
                "notes": "Supports the 27\u201330 \u00b0C range as a value within the temperature-range distribution."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "homeoviscous_adaptation",
            "predicate": "maintains",
            "object": "membrane_fluidity",
            "description": "Homeoviscous adaptation maintains membrane lipid viscosity/fluidity.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s42770-023-01057-4",
                "notes": "Homeoviscous adaptation regulates membrane lipid viscosity; generic background mechanism for mesophilic temperature tolerance."
              }
            ]
          },
          {
            "subject": "unsaturated_fatty_acid_fraction",
            "predicate": "increases",
            "object": "membrane_fluidity",
            "description": "Increased unsaturated fatty acid fraction increases membrane fluidity.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s12275-023-00031-x",
                "notes": "Higher unsaturated content increases fluidity; canonical general bacterial thermoadaptation mechanism."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "hopanoids_sterol_like",
            "predicate": "regulates",
            "object": "membrane_fluidity",
            "description": "Hopanoids / sterol-like molecules regulate membrane fluidity.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s42770-023-01057-4",
                "notes": "Hopanoids and sterol-like molecules act as regulators of membrane fluidity; broad membrane-modulator edge."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "membrane_fluidity",
            "predicate": "confers",
            "object": "temperature_range_mid2_trait",
            "description": "Maintained membrane fluidity enables growth across the mid2 temperature range.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-micro-091313-103612",
                "notes": "Functional membrane fluidity underlies homeoviscous adaptation supporting the mesophile range."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "elevated_temperature",
            "predicate": "opens",
            "object": "rna_thermometer",
            "description": "Elevated temperature melts/opens RNA thermometer 5\u2032-UTR secondary structure.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s12551-025-01290-1",
                "notes": "5\u2032-UTR secondary structures melt upon heat exposure, exposing ribosome binding sites; broad review-level support."
              }
            ]
          },
          {
            "subject": "temperature_shift",
            "predicate": "induces",
            "object": "heat_shock_proteins",
            "description": "Temperature shift / heat shock induces heat-shock proteins and chaperones.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s12275-023-00031-x",
                "notes": "Temperature shifts induce heat- and cold-shock proteins; high-confidence general stress-response edge."
              }
            ]
          },
          {
            "subject": "heat_shock_proteins",
            "predicate": "counteracts",
            "object": "protein_denaturation",
            "description": "Heat-shock proteins / chaperones counteract protein denaturation and aggregation.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s12275-023-00031-x",
                "notes": "Chaperones counteract denaturation and aid tolerance; strong general proteostasis edge."
              }
            ]
          },
          {
            "subject": "baseline_mesophile_adaptation",
            "predicate": "characterizes",
            "object": "mesophilic_organisms",
            "description": "Mesophilic organisms grow between ~20 \u00b0C and ~45 \u00b0C, bracketing the mid2 range.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s42770-023-01057-4",
                "notes": "Mesophiles grow between room temperature (~20 \u00b0C) and ~45 \u00b0C; scope-defining edge placing 27-30 \u00b0C within mesophily."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.824255+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-13T11:00:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed definition and causal graph linking baseline mesophile adaptation to the temperature-range-mid2 bin.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:30Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d71, rdfs:subClassOf\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 8 evidence-backed generic edges (10 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:11Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002213\u00d71, RO:0002211\u00d71, RO:0002327\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:18Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (METPO:1007505\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 2 causal edge(s) off enables/RO:0002327 with a TRAIT object (2 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope temperature_range_mid2_baseline_mesophile=NONMECHANISTIC with scope_notes; marked 1 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (heat_shock_proteins); retyped 1 node(s) (rna_thermometer->RNA).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T06:15:38Z",
        "curator": "codex",
        "action": "ADD_EXACT_ONTOLOGY_MATCH",
        "changes": "Ontology exact-match review (2026-08-25): declared exact synonym(s): 'mesophilic'. Evidence is predicate-scoped in the versioned ontology snapshots; OAK cross-checked direct data, and OLS4 spot-checked release deltas and disputed hits.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T04:43:24Z",
        "curator": "codex",
        "action": "ADD_CANONICAL_EXAMPLES",
        "changes": "Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Pseudomonas mangiferae (NCBITaxon:2593654; DOI:10.1099/ijsem.0.003657). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-15T07:05:58Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (METPO:1016200\u00d71).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000452",
    "label": "temperature range mid3",
    "definition": "A temperature range phenotype in which the growth-supporting ambient temperature range spans approximately 30\u201334 \u00b0C, characteristic of mesophilic physiology.",
    "definition_source": "DOI:10.1146/annurev-micro-091313-103612",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000306"
    ],
    "synonyms": [
      {
        "synonym_text": "Mesophilie",
        "synonym_type": "EXACT_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "TR_30_to_34",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "mesophilic",
        "synonym_type": "EXACT_SYNONYM",
        "source": "https://w3id.org/metpo/releases/2026-06-12/metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev-micro-091313-103612",
        "snippet": "more unsaturated fatty acids",
        "notes": "Membrane-adaptation review supports the 30\u201334 \u00b0C range as the upper-mesophile growth range."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1793963",
        "taxon_label": "Bacillus nakamurai",
        "reference": "DOI:10.1099/ijsem.0.001135",
        "note": "Bacillus nakamurai NRRL B-41091T grew from 17 to 50 degrees C in its primary species description, a directly reported 33-degree breadth within the approximately 30-34-degree range-width bin."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "temperature_range_mid3_upper_mesophile",
        "title": "Temperature-range-mid3 upper-mesophile context",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a quantitative measurement, interval, or bin in the environmental phenotype hierarchy; a token protein example would misrepresent the measured value as one inherited molecular mechanism.",
        "description": "DOI-backed nonmechanistic graph annotating upper-mesophile growth-range context, the DesK/DesR membrane-order sensor, des expression, cooling-induced membrane rigidification, and homeoviscous liquid-crystalline membrane maintenance.",
        "nodes": [
          {
            "node_id": "temperature_range_mid3_trait",
            "label": "temperature range mid3",
            "node_type": "TRAIT",
            "grounding": "METPO:1000452",
            "description": "Temperature growth-supporting range approximately 30\u201334 \u00b0C."
          },
          {
            "node_id": "temperature_range",
            "label": "temperature range",
            "node_type": "TRAIT",
            "grounding": "METPO:1000306",
            "description": "Span of ambient temperatures supporting growth."
          },
          {
            "node_id": "upper_mesophile_adaptation",
            "label": "upper-mesophile adaptation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Mesophile membrane and enzyme tuning for ambient temperatures near common animal host body temperatures."
          },
          {
            "node_id": "membrane_order",
            "label": "membrane order / fluidity state",
            "node_type": "QUALITY",
            "description": "Physical order/fluidity state of the membrane bilayer; the proximate signal for thermosensing."
          },
          {
            "node_id": "desk_kinase_state",
            "label": "DesK kinase-dominant state",
            "node_type": "STATE",
            "description": "Membrane thickness sensor DesK in its autophosphorylating kinase-dominant conformation."
          },
          {
            "node_id": "desk",
            "label": "DesK",
            "node_type": "GENE_OR_PROTEIN",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed as a contextual protein or protein-complex label within a quantitative measurement graph; no exact semantic family term was established for this aggregate use.",
            "description": "Membrane-bound histidine kinase that senses membrane order/thickness."
          },
          {
            "node_id": "phospho_desr",
            "label": "phosphorylated DesR",
            "node_type": "STATE",
            "description": "Phosphorylated DesR that tetramerizes and binds the des promoter."
          },
          {
            "node_id": "des_gene",
            "label": "des (acyl-lipid desaturase)",
            "node_type": "GENE_OR_PROTEIN",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed as a contextual protein or protein-complex label within a quantitative measurement graph; no exact semantic family term was established for this aggregate use.",
            "description": "Fatty-acid desaturase that introduces double bonds to fluidize the membrane."
          },
          {
            "node_id": "membrane_fatty_acyl_chains",
            "label": "membrane fatty acyl chains",
            "node_type": "CHEMICAL",
            "description": "Fatty acyl chains of membrane phospholipids whose unsaturation modulates fluidity."
          },
          {
            "node_id": "membrane_rigidity",
            "label": "membrane rigidification and increased thickness",
            "node_type": "QUALITY",
            "description": "Cooling-induced membrane rigidification and bilayer thickening, the general homeoviscous sensing signal."
          },
          {
            "node_id": "temperature_decrease",
            "label": "temperature decrease",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Drop in ambient temperature within/near the mesophilic range."
          },
          {
            "node_id": "homeoviscous_adaptation",
            "label": "homeoviscous adaptation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Adjustment of membrane lipid composition to maintain constant fluidity across temperatures.",
            "grounding": "METPO:1016200"
          },
          {
            "node_id": "liquid_crystalline_membrane",
            "label": "liquid-crystalline membrane state",
            "node_type": "STATE",
            "description": "Functional liquid-crystalline phase of the membrane required for growth."
          }
        ],
        "edges": [
          {
            "subject": "upper_mesophile_adaptation",
            "predicate": "confers",
            "object": "temperature_range_mid3_trait",
            "description": "Upper-mesophile adaptation enables growth across 30\u201334 \u00b0C.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-micro-091313-103612",
                "snippet": "more unsaturated fatty acids",
                "notes": "Supports upper-mesophile homeoviscous adaptation as the range mechanism."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "temperature_range_mid3_trait",
            "predicate": "is a",
            "object": "temperature_range",
            "description": "Temperature range mid3 is a quantitative bin of the temperature-range phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1016/s0300-9629(97)00003-0",
                "snippet": "adapted to environments of high temperature",
                "notes": "Supports the 30\u201334 \u00b0C range as a value within the temperature-range distribution."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "membrane_order",
            "predicate": "positively regulates",
            "object": "desk_kinase_state",
            "description": "Increased membrane order (reduced fluidity) promotes the DesK kinase-dominant state; membrane physical state is the proximate signal.",
            "evidence": [
              {
                "reference": "DOI:10.1128/spectrum.03925-23",
                "snippet": "Upon temperature decrease, the membrane rigidifies and increases in thickness, resulting in activation of the kinase-dominant state of DesK",
                "notes": "Verified against the open Sidarta et al. introduction; the current Des model links temperature-decrease-driven membrane rigidification/thickening to the active kinase-dominant state."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "phospho_desr",
            "predicate": "positively regulates",
            "object": "des_gene",
            "description": "DesR-P tetramerizes, binds the des promoter, and positively regulates des expression for lipid desaturation.",
            "evidence": [
              {
                "reference": "DOI:10.1128/spectrum.03925-23",
                "snippet": "activating expression of the des gene",
                "notes": "Verified against the open Sidarta et al. introduction; phosphorylated DesR tetramers bind Pdes and activate des transcription."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "des_gene",
            "predicate": "regulates",
            "object": "membrane_fatty_acyl_chains",
            "description": "Des-mediated unsaturation regulates membrane fatty acyl chains, fluidizing the membrane and reducing bilayer thickness.",
            "evidence": [
              {
                "reference": "DOI:10.1128/spectrum.03925-23",
                "snippet": "desaturates the fatty acyl chains",
                "notes": "Verified against the open Sidarta et al. introduction; Des desaturates membrane-lipid fatty acyl chains as the effector of the DesK/DesR temperature-sensing system."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "temperature_decrease",
            "predicate": "causes",
            "object": "membrane_rigidity",
            "description": "A temperature decrease causes membrane rigidification and increased thickness, a physical trigger for homeoviscous adaptation.",
            "evidence": [
              {
                "reference": "DOI:10.1128/spectrum.03925-23",
                "snippet": "rigidification and concomitant thickening",
                "notes": "Verified against the open Sidarta et al. introduction; temperature decrease is described as causing cell-membrane rigidification and thickening."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "homeoviscous_adaptation",
            "predicate": "contributes to",
            "object": "liquid_crystalline_membrane",
            "description": "Homeoviscous adaptation contributes to a functional liquid-crystalline membrane state at low temperature.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s42770-023-01057-4",
                "snippet": "maintain the liquid crystalline phase",
                "notes": "Verified against the open Ram\u00f3n et al. review; organisms in cold environments are described as adapting their membrane composition to maintain a liquid-crystalline state."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "membrane_rigidity",
            "predicate": "associated with",
            "object": "membrane_order",
            "description": "Cooling-induced membrane rigidification is associated with the ordered membrane state sensed by DesK.",
            "evidence": [
              {
                "reference": "DOI:10.1128/spectrum.03925-23",
                "snippet": "membrane rigidifies and increases in thickness",
                "notes": "Verified against the open Sidarta et al. introduction; this connector joins the cooling membrane signal to the DesK kinase-state branch."
              }
            ],
            "predicate_id": "biolink:associated_with"
          },
          {
            "subject": "membrane_fatty_acyl_chains",
            "predicate": "associated with",
            "object": "homeoviscous_adaptation",
            "description": "Des-mediated fatty-acyl-chain unsaturation is associated with homeoviscous membrane adaptation.",
            "evidence": [
              {
                "reference": "DOI:10.1128/spectrum.03925-23",
                "snippet": "resulting in membrane fluidization and concomitant decrease of bilayer thickness",
                "notes": "Verified against the open Sidarta et al. introduction; this connector keeps des expression as membrane-fatty-acyl remodeling context."
              }
            ],
            "predicate_id": "biolink:associated_with"
          },
          {
            "subject": "desk",
            "predicate": "regulates",
            "object": "phospho_desr",
            "description": "DesK regulates DesR phosphorylation in the core two-component signaling step linking membrane physical state to transcriptional response.",
            "evidence": [
              {
                "reference": "DOI:10.1128/spectrum.03925-23",
                "snippet": "phosphorylating or dephosphorylating DesR",
                "notes": "Verified against the open Sidarta et al. introduction; DesK is described as a membrane-associated histidine kinase that phosphorylates or dephosphorylates DesR in a temperature-dependent manner."
              }
            ],
            "predicate_id": "RO:0002211"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.824789+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-13T11:00:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed definition and causal graph linking upper-mesophile adaptation to the temperature-range-mid3 bin.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:30Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d71, rdfs:subClassOf\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 6 evidence-backed generic edges (11 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:11Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:causes\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-26T07:15:18Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A067Z5N7\u00d71, UniProtKB:A0A067Z2X2\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:21:11Z",
        "curator": "claude",
        "action": "RETRACT_DEAD_UNIPROT_GROUNDINGS",
        "changes": "Retracted 2 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 1 causal edge(s) off enables/RO:0002327 with a TRAIT object (1 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-21T08:00:00Z",
        "curator": "codex",
        "action": "NORMALISE_NODE_TYPE",
        "changes": "Tranche 5 of issue 356 settles the process/quality families and merges ids that meant the same sense: membrane_rigidity is QUALITY. Membrane rigidity is a physical attribute of the bilayer and therefore a QUALITY under the schema's membrane-fluidity example.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope temperature_range_mid3_upper_mesophile=NONMECHANISTIC with scope_notes; marked 3 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (desk, desr, des_gene).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T06:15:38Z",
        "curator": "codex",
        "action": "ADD_EXACT_ONTOLOGY_MATCH",
        "changes": "Ontology exact-match review (2026-08-25): declared exact synonym(s): 'mesophilic'. Evidence is predicate-scoped in the versioned ontology snapshots; OAK cross-checked direct data, and OLS4 spot-checked release deltas and disputed hits.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T04:43:24Z",
        "curator": "codex",
        "action": "ADD_CANONICAL_EXAMPLES",
        "changes": "Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Bacillus nakamurai (NCBITaxon:1793963; DOI:10.1099/ijsem.0.001135). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-04T04:00:00Z",
        "curator": "codex",
        "action": "REVIEW_CAUSAL_EVIDENCE",
        "changes": "Reviewed the temperature_range_mid3_upper_mesophile graph for issue #183: added snippets to 6 edge-level evidence items and grounded the DesK/DesR thermosensing predicates to RO:0002213, RO:0002211, or RO:0002326. No paid research service was called.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-04T22:00:00Z",
        "curator": "codex",
        "action": "CONNECT_CAUSAL_GRAPH_COMPONENTS",
        "changes": "Resolved issue #183 graph fragmentation (5 components to 1) by adding 4 source- and verbatim-snippet-backed association connectors among DesK/DesR membrane-order sensing, des expression, cooling-induced membrane rigidification, and homeoviscous liquid-crystalline membrane branches. No paid research service was called.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-06T17:10:00Z",
        "curator": "codex",
        "action": "ADVERSARIAL_REVIEW_REPAIR",
        "changes": "Addressed PR #664 adversarial review: replaced copied nonmechanistic bridge snippets with independent exact source snippets while preserving the existing connector edge scope.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-07T07:24:00Z",
        "curator": "codex",
        "action": "ADVERSARIAL_REVIEW_REPAIR",
        "changes": "Addressed PR #664 adversarial review issue #693: replaced weak DesK/DesR connector edges by routing DesK directly to phosphorylated DesR, removed the redundant unphosphorylated DesR node, and updated the original connector history.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-07T20:05:00Z",
        "curator": "codex",
        "action": "ADVERSARIAL_REVIEW_REPAIR",
        "changes": "Addressed PR #664 adversarial review issues #696, #698, and #699: strengthened the DesK kinase-state snippet and removed weak association connectors to DesK and upper-mesophile adaptation.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-08T03:30:00Z",
        "curator": "codex",
        "action": "ADVERSARIAL_REVIEW_REPAIR",
        "changes": "Addressed PR #664 adversarial review issue #702: appended corrective issue-183 provenance after evidence-weak connectors were pruned; this NONMECHANISTIC graph intentionally ships with 3 disconnected components until independent trait-specific connectors are curated.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-15T07:05:59Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (METPO:1016200\u00d71).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000453",
    "label": "temperature range mid4",
    "definition": "A temperature range phenotype in which the growth-supporting ambient temperature range spans approximately 34\u201340 \u00b0C, characteristic of warm-mesophilic physiology (including many mammalian host-associated bacteria).",
    "definition_source": "DOI:10.1146/annurev-micro-091313-103612",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000306"
    ],
    "synonyms": [
      {
        "synonym_text": "Mesophilie",
        "synonym_type": "EXACT_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "TR_34_to_40",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "mesophilic",
        "synonym_type": "EXACT_SYNONYM",
        "source": "https://w3id.org/metpo/releases/2026-06-12/metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev-micro-091313-103612",
        "snippet": "more unsaturated fatty acids",
        "notes": "Membrane-adaptation review supports the 34\u201340 \u00b0C range as the warm-mesophile (mammalian-host) growth range."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:3028314",
        "taxon_label": "Oceanimonas pelagia",
        "reference": "DOI:10.1007/s10482-024-01948-y",
        "note": "Oceanimonas pelagia NTOU-MSR1T grew from 10 to 45 degrees C, a directly reported 35-degree breadth within the approximately 34-40-degree bin."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "temperature_range_mid4_warm_mesophile",
        "title": "Temperature-range-mid4 warm-mesophile context",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a quantitative measurement, interval, or bin in the environmental phenotype hierarchy; a token protein example would misrepresent the measured value as one inherited molecular mechanism.",
        "description": "DOI-backed nonmechanistic graph annotating warm-mesophile growth-range context, Fab-mediated homeoviscous membrane adaptation, compensatory membrane-fluidity restoration, high-temperature protein damage, and RpoH-governed heat-shock protection branches.",
        "nodes": [
          {
            "node_id": "temperature_range_mid4_trait",
            "label": "temperature range mid4",
            "node_type": "TRAIT",
            "grounding": "METPO:1000453",
            "description": "Temperature growth-supporting range approximately 34\u201340 \u00b0C."
          },
          {
            "node_id": "temperature_range",
            "label": "temperature range",
            "node_type": "TRAIT",
            "grounding": "METPO:1000306",
            "description": "Span of ambient temperatures supporting growth."
          },
          {
            "node_id": "warm_mesophile_adaptation",
            "label": "warm-mesophile adaptation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Membrane and enzyme repertoires tuned for warm host-body temperatures."
          },
          {
            "node_id": "fab_branchpoint_valve",
            "label": "FabI/FabB fatty-acid branchpoint valve",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Temperature-sensitive metabolic valve at the fatty-acid branchpoint reallocating flux between saturated and unsaturated synthesis via FabI and FabB."
          },
          {
            "node_id": "homeoviscous_adaptation",
            "label": "homeoviscous adaptation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Compensatory adjustment of membrane lipid composition to maintain optimal fluidity across temperatures.",
            "grounding": "METPO:1016200"
          },
          {
            "node_id": "fab_c10_competition",
            "label": "FabA/FabI/FabB competition for C10:1 pool",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "FabA, FabI and FabB compete for a common C10:1 acyl-ACP pool, shifting flux between saturated and unsaturated fatty acids."
          },
          {
            "node_id": "saturated_unsaturated_membrane_lipid_composition",
            "label": "saturated/unsaturated membrane lipid composition",
            "node_type": "QUALITY",
            "description": "Saturated/unsaturated phospholipid makeup of the cell membrane."
          },
          {
            "node_id": "membrane_fluidity_restoration",
            "label": "membrane fluidity restoration",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Restoration of optimal membrane fluidity within a single generation after a temperature shock via the valve and transcriptional feedback."
          },
          {
            "node_id": "growth_after_temperature_shock",
            "label": "growth after temperature shock",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Continued growth following a rapid change in ambient temperature."
          },
          {
            "node_id": "heat_stress",
            "label": "heat stress",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Elevated ambient temperature near or above the warm-mesophile upper growth limit."
          },
          {
            "node_id": "protein_unfolding_aggregation",
            "label": "protein unfolding and aggregation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Loss of native protein structure and formation of aggregates caused by high temperature."
          },
          {
            "node_id": "mesophile_growth_impairment",
            "label": "impaired mesophile growth",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduction of growth in warm-mesophiles unless protein-damage is compensated."
          },
          {
            "node_id": "membrane_fluidity",
            "label": "membrane fluidity",
            "node_type": "QUALITY",
            "description": "Physical fluidity of the lipid bilayer, increased by high temperature.",
            "grounding": "METPO:1007505"
          },
          {
            "node_id": "compensatory_adaptation",
            "label": "compensatory membrane adaptation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Adaptive response required to counter temperature-driven membrane fluidity changes."
          },
          {
            "node_id": "rpoh_regulon",
            "label": "sigma-32 (RpoH) heat-shock regulon",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Heat-shock regulon driven by the alternative sigma factor sigma-32/RpoH."
          },
          {
            "node_id": "heat_shock_chaperone_systems",
            "label": "DnaK/DnaJ/GrpE and GroES/GroEL chaperone systems",
            "node_type": "GENE_OR_PROTEIN",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed as a contextual protein or protein-complex label within a quantitative measurement graph; no exact semantic family term was established for this aggregate use.",
            "description": "Protective heat-shock chaperone systems that refold stress-damaged proteins."
          },
          {
            "node_id": "heat_stress_protection",
            "label": "protection against heat stress",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Cellular protection against heat-induced protein damage."
          }
        ],
        "edges": [
          {
            "subject": "warm_mesophile_adaptation",
            "predicate": "confers",
            "object": "temperature_range_mid4_trait",
            "description": "Warm-mesophile adaptation enables growth across 34\u201340 \u00b0C.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-micro-091313-103612",
                "snippet": "more unsaturated fatty acids",
                "notes": "Supports warm-mesophile homeoviscous adaptation as the range mechanism."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "temperature_range_mid4_trait",
            "predicate": "is a",
            "object": "temperature_range",
            "description": "Temperature range mid4 is a quantitative bin of the temperature-range phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1016/s0300-9629(97)00003-0",
                "snippet": "adapted to environments of high temperature",
                "notes": "Supports the 34\u201340 \u00b0C range as a value within the temperature-range distribution."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "fab_branchpoint_valve",
            "predicate": "enables",
            "object": "homeoviscous_adaptation",
            "description": "The FabI/FabB branchpoint valve reallocates flux between saturated and unsaturated fatty acid synthesis, enabling homeoviscous adaptation.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-024-53677-5",
                "snippet": "A first element of this regulatory system is a temperature-sensitive metabolic valve that allocates flux between the saturated and unsaturated fatty acid synthesis pathways via the branchpoint enzymes FabI and FabB",
                "notes": "Verified against the open Hoogerland et al. abstract; the E. coli temperature-sensitive metabolic valve allocates fatty-acid synthesis flux through FabI and FabB."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "fab_c10_competition",
            "predicate": "regulates",
            "object": "saturated_unsaturated_membrane_lipid_composition",
            "description": "Competition of FabA/FabI/FabB for the common C10:1 pool shifts flux between saturated and unsaturated fatty acids, changing saturated/unsaturated membrane lipid composition.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-024-53677-5",
                "snippet": "compete for a common pool of substrates",
                "notes": "Verified against the open Hoogerland et al. Figure 1 legend; FabA interconverts the C10:1 acyl-ACP substrates used by FabI and FabB, making the enzymes indirectly compete for one pool."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "membrane_fluidity_restoration",
            "predicate": "contributes to",
            "object": "growth_after_temperature_shock",
            "description": "Valve plus transcriptional feedback restores optimal membrane fluidity within a single generation, contributing to growth after a temperature shock.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-024-53677-5",
                "snippet": "restores optimal membrane fluidity within a single generation",
                "notes": "Verified against the open Hoogerland et al. abstract; the measured E. coli fatty-acid and phospholipid pathway connects membrane-fluidity restoration to recovery from temperature shock."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "heat_stress",
            "predicate": "causes",
            "object": "protein_unfolding_aggregation",
            "description": "High temperatures cause protein unfolding and aggregation.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s12864-023-09266-9",
                "snippet": "unfold or misfold proteins",
                "notes": "Verified against the open McGuire and Nano introduction; the review context lists unfolding, misfolding, and aggregation among the high-temperature cellular problems near TMAX."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "protein_unfolding_aggregation",
            "predicate": "contributes to",
            "object": "mesophile_growth_impairment",
            "description": "Protein unfolding and aggregation contributes to mesophile growth impairment unless compensated.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s12864-023-09266-9",
                "notes": "Verified against the open McGuire and Nano introduction; the paper frames high-temperature RNA, protein, lipid, and DNA effects as cellular problems near the maximum growth temperature."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "heat_stress",
            "predicate": "positively regulates",
            "object": "membrane_fluidity",
            "description": "High temperatures increase membrane fluidity, requiring compensatory adaptation.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s12864-023-09266-9",
                "snippet": "cause increased membrane fluidity",
                "notes": "Verified against the open McGuire and Nano introduction; increased membrane fluidity is listed as a high-temperature effect on cells."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "compensatory_adaptation",
            "predicate": "regulates",
            "object": "membrane_fluidity",
            "description": "Compensatory membrane adaptation regulates temperature-driven membrane-fluidity changes.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-024-53677-5",
                "snippet": "hard-wired parameters calibrate the system to generate membrane compositions that maintain constant fluidity",
                "notes": "Verified against the open Hoogerland et al. introduction; homeoviscous adaptation counteracts temperature by varying unsaturated, branched-chain, or chain-length lipid features to stabilize viscosity."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "rpoh_regulon",
            "predicate": "positively regulates",
            "object": "heat_shock_chaperone_systems",
            "description": "The sigma-32/RpoH regulon positively regulates the DnaK/DnaJ/GrpE and GroES/GroEL chaperone systems.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mbio.03105-23",
                "snippet": "the alternative sigma factor \u03c332 (RpoH) that drives the expression of protective heat shock proteins (HSPs), such as the molecular chaperone systems DnaK/DnaJ/GrpE and GroES/GroEL",
                "notes": "Verified against the open Berdejo et al. introduction; RpoH is described as the main governor of the Salmonella Typhimurium heat-shock response and as driving protective heat-shock-protein expression."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "heat_shock_chaperone_systems",
            "predicate": "enables",
            "object": "heat_stress_protection",
            "description": "The DnaK/DnaJ/GrpE and GroES/GroEL chaperone systems protect against heat stress.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mbio.03105-23",
                "snippet": "protective heat shock proteins",
                "notes": "Verified against the open Berdejo et al. introduction; DnaK/DnaJ/GrpE and GroES/GroEL are named as molecular chaperone systems in the protective heat-shock-protein response."
              }
            ],
            "predicate_id": "RO:0002327"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.825319+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-13T11:00:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed definition and causal graph linking warm-mesophile adaptation to the temperature-range-mid4 bin.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:30Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d71, rdfs:subClassOf\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 9 evidence-backed generic edges (14 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:11Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 7 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d73, biolink:causes\u00d73, RO:0002211\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:18Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (METPO:1007505\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 1 causal edge(s) off enables/RO:0002327 with a TRAIT object (1 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope temperature_range_mid4_warm_mesophile=NONMECHANISTIC with scope_notes; marked 1 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (chaperone_systems).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T06:15:38Z",
        "curator": "codex",
        "action": "ADD_EXACT_ONTOLOGY_MATCH",
        "changes": "Ontology exact-match review (2026-08-25): declared exact synonym(s): 'mesophilic'. Evidence is predicate-scoped in the versioned ontology snapshots; OAK cross-checked direct data, and OLS4 spot-checked release deltas and disputed hits.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T04:43:24Z",
        "curator": "codex",
        "action": "ADD_CANONICAL_EXAMPLES",
        "changes": "Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Oceanimonas pelagia (NCBITaxon:3028314; DOI:10.1007/s10482-024-01948-y). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-04T04:20:00Z",
        "curator": "codex",
        "action": "REVIEW_CAUSAL_EVIDENCE",
        "changes": "Reviewed the temperature_range_mid4_warm_mesophile graph for issue #183: reviewed 9 edge-level evidence items, grounded the RpoH and compensatory-adaptation predicates, retained exact snippets where source wording directly supported the edge, and narrowed 2 local node identifiers to avoid cross-record type collisions. No paid research service was called.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-04T23:00:00Z",
        "curator": "codex",
        "action": "CONNECT_CAUSAL_GRAPH_COMPONENTS",
        "changes": "Resolved issue #183 graph fragmentation (6 components to 1) by adding 5 source- and verbatim-snippet-backed association connectors among Fab-mediated membrane adaptation, compensatory membrane-fluidity restoration, high-temperature protein damage, and RpoH heat-shock protection branches. No paid research service was called.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-06T13:30:00Z",
        "curator": "codex",
        "action": "ADVERSARIAL_REVIEW_REPAIR",
        "changes": "Addressed PR #664 adversarial review issue #667: dropped the weak protein-damage snippet from the protein_unfolding_aggregation to mesophile_growth_impairment edge while preserving its reference-backed review notes.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-06T17:10:00Z",
        "curator": "codex",
        "action": "ADVERSARIAL_REVIEW_REPAIR",
        "changes": "Addressed PR #664 adversarial review: replaced copied nonmechanistic bridge snippets with independent exact source snippets while preserving the existing connector edge scope.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-07T04:24:00Z",
        "curator": "codex",
        "action": "ADVERSARIAL_REVIEW_REPAIR",
        "changes": "Addressed PR #664 adversarial review issue #686: replaced fragmented ring-shape, soil-life-history, heat-shock, and ligninolysis snippets with exact source spans that carry their edge claims.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-07T06:14:00Z",
        "curator": "codex",
        "action": "ADVERSARIAL_REVIEW_REPAIR",
        "changes": "Addressed PR #664 adversarial review issue #689: expanded the Hoogerland FabI/FabB branch quote and replaced the warm-mesophile connector quote with an independent homeoviscous-adaptation span.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-07T20:05:00Z",
        "curator": "codex",
        "action": "ADVERSARIAL_REVIEW_REPAIR",
        "changes": "Addressed PR #664 adversarial review issues #698 and #699: removed sliced Hoogerland and heat-protection hub connectors and requoted the remaining compensatory membrane-fluidity edge.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-08T03:30:00Z",
        "curator": "codex",
        "action": "ADVERSARIAL_REVIEW_REPAIR",
        "changes": "Addressed PR #664 adversarial review issue #702: appended corrective issue-183 provenance after evidence-weak connectors were pruned; this NONMECHANISTIC graph intentionally ships with 6 disconnected components until independent trait-specific connectors are curated.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-15T07:05:59Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (METPO:1016200\u00d71).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000448",
    "label": "temperature range very low",
    "definition": "A temperature range phenotype in which growth extends to ambient temperatures at or below approximately 10 \u00b0C, characteristic of psychrophilic growth ranges.",
    "definition_source": "DOI:10.1038/sj.embor.7400662",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000306"
    ],
    "synonyms": [
      {
        "synonym_text": "Psychrophile",
        "synonym_type": "EXACT_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "TR_<=10",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/sj.embor.7400662",
        "snippet": "growing well at temperatures around the freezing point of water",
        "notes": "Psychrophile review supports growth at very low temperatures as the psychrophilic range."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:357794",
        "taxon_label": "Psychromonas ingrahamii",
        "reference": "DOI:10.1099/ijs.0.64068-0",
        "note": "Psychromonas ingrahamii strain 37T grew from -12 to 10 degrees C in its primary species description, directly establishing growth at and below this bin's 10-degree threshold."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "temperature_range_very_low_psychrophile",
        "title": "Temperature-range-very-low psychrophile context",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a quantitative measurement, interval, or bin in the environmental phenotype hierarchy; a token protein example would misrepresent the measured value as one inherited molecular mechanism.",
        "description": "DOI-backed nonmechanistic graph connecting membrane desaturation, two-component cold signaling, CspA-family RNA chaperones, cold proteostasis, compatible-solute stabilization, and ice-binding protein branches to the at-or-below-10-degrees-C growth-range bin.",
        "nodes": [
          {
            "node_id": "temperature_range_very_low_trait",
            "label": "temperature range very low",
            "node_type": "TRAIT",
            "grounding": "METPO:1000448",
            "description": "Temperature growth-supporting range reaching \u2264 ~10 \u00b0C."
          },
          {
            "node_id": "temperature_range",
            "label": "temperature range",
            "node_type": "TRAIT",
            "grounding": "METPO:1000306",
            "description": "Span of ambient temperatures supporting growth."
          },
          {
            "node_id": "psychrophile_machinery",
            "label": "psychrophile cold-adapted machinery",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Cold-active enzymes and unsaturated-lipid membranes that sustain function near freezing."
          },
          {
            "node_id": "low_temperature",
            "label": "low temperature",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Ambient temperature at or below ~10 C imposing cold stress.",
            "grounding": "PATO:0001306"
          },
          {
            "node_id": "membrane_fatty_acid_desaturation",
            "label": "membrane fatty-acid desaturation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Introduction of double bonds into membrane lipids during cold adaptation."
          },
          {
            "node_id": "membrane_fluidity",
            "label": "membrane fluidity",
            "node_type": "QUALITY",
            "description": "Physical fluidity of the membrane bilayer required for function in the cold.",
            "grounding": "METPO:1007505"
          },
          {
            "node_id": "two_component_cold_signaling",
            "label": "two-component cold signaling",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Two-component regulatory systems triggered by cold-induced membrane state changes."
          },
          {
            "node_id": "cold_shock_proteins",
            "label": "cold-shock proteins (CspA-family)",
            "node_type": "GENE_OR_PROTEIN",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed as a contextual protein or protein-complex label within a quantitative measurement graph; no exact semantic family term was established for this aggregate use.",
            "description": "CspA-family RNA chaperones that bind nucleic acids during cold acclimation."
          },
          {
            "node_id": "cold_stabilized_rna_secondary_structure",
            "label": "cold-stabilized mRNA/RNA secondary structure",
            "node_type": "QUALITY",
            "description": "Cold-stabilized RNA secondary structures impeding translation."
          },
          {
            "node_id": "molecular_chaperones",
            "label": "molecular chaperones (DnaK/GroEL/GroES/Clp/TF)",
            "node_type": "GENE_OR_PROTEIN",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed as a contextual protein or protein-complex label within a quantitative measurement graph; no exact semantic family term was established for this aggregate use.",
            "description": "Chaperone and protease systems maintaining proteostasis under cold."
          },
          {
            "node_id": "proteostasis_cold",
            "label": "protein folding and proteostasis in the cold",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Maintenance of correct protein folding despite cold-slowed folding kinetics."
          },
          {
            "node_id": "compatible_solutes",
            "label": "compatible solutes (glycine betaine/trehalose/glycerol)",
            "node_type": "CHEMICAL",
            "description": "Osmolytes that lower freezing damage and stabilize macromolecules."
          },
          {
            "node_id": "protein_membrane_stabilization",
            "label": "protein and membrane stabilization",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Stabilization of proteins and membranes against cold/freezing damage."
          },
          {
            "node_id": "ice_binding_proteins",
            "label": "ice-binding/antifreeze proteins",
            "node_type": "GENE_OR_PROTEIN",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed as a contextual protein or protein-complex label within a quantitative measurement graph; no exact semantic family term was established for this aggregate use.",
            "description": "AFPs/IBPs that bind ice and inhibit ice-crystal growth."
          },
          {
            "node_id": "ice_crystal_growth",
            "label": "ice-crystal growth/recrystallization",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Damaging ice-crystal growth and recrystallization around cells."
          }
        ],
        "edges": [
          {
            "subject": "psychrophile_machinery",
            "predicate": "confers",
            "object": "temperature_range_very_low_trait",
            "description": "Psychrophile cold-adapted machinery enables growth at \u2264 10 \u00b0C.",
            "evidence": [
              {
                "reference": "DOI:10.1038/sj.embor.7400662",
                "snippet": "decreased membrane fluidity",
                "notes": "Supports cold-adapted membranes and enzymes as enablers of growth at very low temperatures."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "temperature_range_very_low_trait",
            "predicate": "is a",
            "object": "temperature_range",
            "description": "Temperature range very low is a quantitative bin of the temperature-range phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1038/sj.embor.7400662",
                "snippet": "growing well at temperatures around the freezing point of water",
                "notes": "Supports a \u226410 \u00b0C range as a value within the temperature-range distribution."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "membrane_fatty_acid_desaturation",
            "predicate": "increases",
            "object": "membrane_fluidity",
            "description": "Homeoviscous adaptation via lipid desaturation maintains membrane fluidity in the cold.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s42770-023-01057-4",
                "snippet": "production of double bonds in lipids",
                "notes": "Verified against the open Ram\u00f3n et al. PubMed abstract; the multifactorial cold-adaptation model lists membrane composition adaptation by producing lipid double bonds."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "low_temperature",
            "predicate": "activates",
            "object": "two_component_cold_signaling",
            "description": "Cold-induced membrane state changes activate two-component cold signaling.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s42770-023-01057-4",
                "snippet": "activation of a two-component system",
                "notes": "Verified against the open Ram\u00f3n et al. PubMed abstract; cold sensing is described as occurring mainly through liquid-crystalline membrane-state changes that activate a two-component signal-transduction system."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "cold_shock_proteins",
            "predicate": "regulates",
            "object": "cold_stabilized_rna_secondary_structure",
            "description": "CspA-family RNA chaperones regulate cold-stabilized RNA structures to sustain translation.",
            "evidence": [
              {
                "reference": "DOI:10.4161/rna.7.6.13482",
                "snippet": "through their RNA chaperoning function",
                "notes": "Verified against the open Phadtare and Severinov PubMed abstract; CspA-family cold-shock proteins are described as RNA-modulating proteins affecting low-temperature transcription and possibly translation through RNA chaperoning."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "molecular_chaperones",
            "predicate": "contributes to",
            "object": "proteostasis_cold",
            "description": "Chaperone/protease systems contribute to proteostasis by countering cold-slowed folding and misfolding risk.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2023.1197797",
                "snippet": "heat shock proteins associated to folding",
                "notes": "Verified against the open Ramasamy et al. PMC text; the Antarctic psychrophile review discusses heat-shock proteins associated with protein folding in 4 \u00b0C versus 18 \u00b0C Pseudoalteromonas haloplanktis TAC125."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "compatible_solutes",
            "predicate": "contributes to",
            "object": "protein_membrane_stabilization",
            "description": "Osmolytes contribute to protein and membrane stabilization while lowering freezing damage.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2023.1197797",
                "snippet": "counteracting protein aggregation, improving protein folding",
                "notes": "Verified against the open Ramasamy et al. PMC text; Antarctic compatible osmolytes are described as counteracting protein aggregation and improving protein folding."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "ice_binding_proteins",
            "predicate": "inhibits",
            "object": "ice_crystal_growth",
            "description": "AFPs/IBPs bind ice and inhibit ice-crystal growth and recrystallization.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2023.1197797",
                "snippet": "inhibits the growth of ice crystals",
                "notes": "Verified against the open Ramasamy et al. PMC text; ice binding proteins are described as antifreeze proteins that bind ice, inhibit ice-crystal growth, lower freezing temperature, create a thermal hysteresis gap, and display ice-recrystallization inhibition activity."
              }
            ],
            "predicate_id": "RO:0002212"
          },
          {
            "subject": "membrane_fluidity",
            "predicate": "associated with",
            "object": "psychrophile_machinery",
            "description": "Membrane fatty-acid desaturation is associated with the cold-adapted machinery supporting psychrophile growth ranges.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s42770-023-01057-4",
                "snippet": "maintain the liquid crystalline phase",
                "notes": "Verified against the open Ram\u00f3n et al. PubMed abstract; this connector keeps membrane desaturation as cold membrane-adaptation context."
              }
            ],
            "predicate_id": "biolink:associated_with"
          },
          {
            "subject": "two_component_cold_signaling",
            "predicate": "associated with",
            "object": "psychrophile_machinery",
            "description": "Two-component cold signaling is associated with psychrophile cold-adapted machinery.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s42770-023-01057-4",
                "snippet": "When the temperature drops, DesK/DesR is the two-component system involved in membrane adaptation",
                "notes": "Verified against the open Ram\u00f3n et al. PubMed abstract; this connector keeps low-temperature membrane sensing as cold-acclimation context."
              }
            ],
            "predicate_id": "biolink:associated_with"
          },
          {
            "subject": "cold_stabilized_rna_secondary_structure",
            "predicate": "associated with",
            "object": "psychrophile_machinery",
            "description": "CspA-family regulation of cold-stabilized RNA structure is associated with psychrophile cold-adapted machinery.",
            "evidence": [
              {
                "reference": "DOI:10.4161/rna.7.6.13482",
                "snippet": "CspA, the main cold shock protein, and its homologs act as RNA chaperones",
                "notes": "Verified against the open Phadtare and Severinov PubMed abstract; this connector keeps CspA-family RNA chaperones as low-temperature transcript context."
              }
            ],
            "predicate_id": "biolink:associated_with"
          },
          {
            "subject": "proteostasis_cold",
            "predicate": "associated with",
            "object": "psychrophile_machinery",
            "description": "Cold proteostasis support is associated with the psychrophile machinery context.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2023.1197797",
                "snippet": "ice binding, cold shock and heat shock proteins to sustain their physiological state",
                "notes": "Verified against the open Ramasamy et al. PMC text; this connector keeps chaperone/protease systems as protein-folding context."
              }
            ],
            "predicate_id": "biolink:associated_with"
          },
          {
            "subject": "protein_membrane_stabilization",
            "predicate": "associated with",
            "object": "psychrophile_machinery",
            "description": "Compatible-solute stabilization is associated with psychrophile cold-adapted machinery.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2023.1197797",
                "snippet": "scavenging free radicals, counteracting protein aggregation",
                "notes": "Verified against the open Ramasamy et al. PMC text; this connector keeps compatible osmolytes as stabilization context."
              }
            ],
            "predicate_id": "biolink:associated_with"
          },
          {
            "subject": "ice_crystal_growth",
            "predicate": "associated with",
            "object": "psychrophile_machinery",
            "description": "Ice-binding protein inhibition of ice-crystal growth is associated with psychrophile cold-adapted machinery.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2023.1197797",
                "snippet": "This ceases ice growth by creating a thermal hysteresis gap",
                "notes": "Verified against the open Ramasamy et al. PMC text; this connector keeps ice-binding proteins as freezing-protection context."
              }
            ],
            "predicate_id": "biolink:associated_with"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.822647+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-13T11:00:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed definition and causal graph linking psychrophile cold-adapted machinery to the temperature-range-very-low bin.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:30Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d71, rdfs:subClassOf\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 6 evidence-backed generic edges (12 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:11Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002213\u00d72, RO:0002212\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:18Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (PATO:0001306\u00d71, METPO:1007505\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 1 causal edge(s) off enables/RO:0002327 with a TRAIT object (1 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope temperature_range_very_low_psychrophile=NONMECHANISTIC with scope_notes; marked 3 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (cold_shock_proteins, molecular_chaperones, ice_binding_proteins).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T04:43:24Z",
        "curator": "codex",
        "action": "ADD_CANONICAL_EXAMPLES",
        "changes": "Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Psychromonas ingrahamii (NCBITaxon:357794; DOI:10.1099/ijs.0.64068-0). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-04T04:40:00Z",
        "curator": "codex",
        "action": "REVIEW_CAUSAL_EVIDENCE",
        "changes": "Reviewed the temperature_range_very_low_psychrophile graph for issue #183: added snippets to 6 edge-level evidence items, grounded 3 residual predicates, and narrowed 1 local node identifier and type for cold-stabilized RNA secondary structure. No paid research service was called.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-04T23:20:00Z",
        "curator": "codex",
        "action": "CONNECT_CAUSAL_GRAPH_COMPONENTS",
        "changes": "Resolved issue #183 graph fragmentation (7 components to 1) by adding 6 source- and verbatim-snippet-backed association connectors among membrane desaturation, two-component cold signaling, CspA-family RNA chaperone, cold proteostasis, compatible-solute, and ice-binding protein branches. No paid research service was called.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-06T17:10:00Z",
        "curator": "codex",
        "action": "ADVERSARIAL_REVIEW_REPAIR",
        "changes": "Addressed PR #664 adversarial review: replaced copied Ramasamy cold-adaptation snippets with independent exact text supporting compatible-osmolyte and ice-binding-protein context edges.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000616",
    "label": "thermophilic",
    "definition": "A temperature preference in which growth is favored at elevated temperatures, typically \u226545 \u00b0C.",
    "definition_source": "DOI:10.1016/s0300-9629(97)00003-0",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000613"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1016/s0300-9629(97)00003-0",
        "snippet": "adapted to environments of high temperature",
        "notes": "Supports thermophilic growth as adaptation to elevated temperature."
      },
      {
        "reference": "PMID:24058645",
        "snippet": "Geobacillus stearothermophilus is a gram-positive, thermophilic bacterium",
        "notes": "Organism example: Geobacillus stearothermophilus is described as thermophilic."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:274",
        "taxon_label": "Thermus thermophilus",
        "note": "Model thermophile (~65-72 C); Taq relative and structural-biology workhorse.",
        "reference": "DOI:10.1007/s00792-009-0226-6"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "thermophilic_heat_adaptation",
        "title": "Thermophilic heat-adaptation mechanism",
        "description": "Evidence-backed causal sketch linking thermophily to elevated temperature, membrane lipid adaptation, thermostable proteins, and energy transduction constraints.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a broad environmental or morphological classification spanning multiple mechanisms, a measurement-like bin, or an absence/arrangement descriptor; contextual protein nodes do not receive token UniProt examples.",
        "nodes": [
          {
            "node_id": "thermophilic_trait",
            "label": "thermophilic",
            "node_type": "TRAIT",
            "grounding": "METPO:1000616",
            "description": "Growth is favored at elevated temperatures."
          },
          {
            "node_id": "high_temperature",
            "label": "high temperature",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Elevated-temperature growth condition.",
            "grounding": "PATO:0001305"
          },
          {
            "node_id": "membrane_lipid_composition",
            "label": "membrane lipid composition",
            "node_type": "CELLULAR_LOCALIZATION",
            "description": "Membrane lipid features altered during high-temperature adaptation."
          },
          {
            "node_id": "proton_permeability",
            "label": "membrane proton permeability",
            "node_type": "QUALITY",
            "description": "Proton leakiness of the cytoplasmic membrane at elevated temperature."
          },
          {
            "node_id": "thermostable_proteins",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "thermostable proteins",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Proteins with increased resistance to thermal denaturation."
          },
          {
            "node_id": "energy_transducing_enzymes",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "energy-transducing enzymes",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Enzymes involved in membrane bioenergetics at elevated temperature."
          },
          {
            "node_id": "reverse_gyrase",
            "label": "reverse gyrase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "ATP-dependent topoisomerase that introduces positive DNA supercoils, characteristic of thermophiles.",
            "grounding": "GO:0160097"
          },
          {
            "node_id": "dna_positive_supercoiling",
            "label": "DNA positive supercoiling",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Introduction of positive supercoils into genomic DNA."
          },
          {
            "node_id": "dna_melting",
            "label": "DNA melting",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Thermal denaturation/strand separation of DNA at elevated temperature."
          },
          {
            "node_id": "genome_integrity",
            "label": "genome integrity maintenance",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Maintenance of genome integrity including DNA repair under thermal stress."
          },
          {
            "node_id": "group_ii_chaperonin",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "group II chaperonin (thermosome)",
            "node_type": "GENE_OR_PROTEIN",
            "description": "HSP60-type group II chaperonin that refolds denatured proteins in an ATP-dependent manner."
          },
          {
            "node_id": "denatured_proteins",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "denatured proteins",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Proteins unfolded or denatured during thermal stress."
          },
          {
            "node_id": "cyclopentane_ring_number",
            "label": "tetraether lipid cyclopentane ring number",
            "node_type": "QUALITY",
            "description": "Number of cyclopentane rings in archaeal tetraether membrane lipids."
          },
          {
            "node_id": "membrane_rigidity",
            "label": "membrane rigidity",
            "node_type": "QUALITY",
            "description": "Membrane condensation, packing tightness, and rigidity."
          }
        ],
        "edges": [
          {
            "subject": "high_temperature",
            "predicate": "selects for",
            "object": "thermophilic_trait",
            "description": "High-temperature environments select for thermophilic growth capacity.",
            "evidence": [
              {
                "reference": "DOI:10.1016/s0300-9629(97)00003-0",
                "snippet": "adapted to environments of high temperature",
                "notes": "Review supports thermophile adaptation to high-temperature environments."
              }
            ],
            "predicate_id": "METPO:2007401"
          },
          {
            "subject": "high_temperature",
            "predicate": "increases",
            "object": "proton_permeability",
            "description": "Elevated temperature increases proton permeability of the cytoplasmic membrane.",
            "evidence": [
              {
                "reference": "DOI:10.1016/s0300-9629(97)00003-0",
                "snippet": "proton permeability ... increase with the temperature",
                "notes": "Supports membrane proton permeability as a high-temperature growth constraint."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "membrane_lipid_composition",
            "predicate": "limits",
            "object": "proton_permeability",
            "description": "Lipid composition changes can reduce high-temperature membrane leakiness.",
            "evidence": [
              {
                "reference": "DOI:10.1016/s0300-9629(97)00003-0",
                "snippet": "changing the lipid composition",
                "notes": "Supports lipid composition as an adaptation to membrane permeability."
              }
            ],
            "predicate_id": "RO:0002212"
          },
          {
            "subject": "thermostable_proteins",
            "predicate": "confers",
            "object": "thermophilic_trait",
            "description": "Thermostable proteins retain function during elevated-temperature growth.",
            "evidence": [
              {
                "reference": "DOI:10.1128/MMBR.65.1.1-43.2001",
                "snippet": "resistant to irreversible inactivation at high temperatures",
                "notes": "Supports thermostability as a high-temperature enzyme feature."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "energy_transducing_enzymes",
            "predicate": "confers",
            "object": "thermophilic_trait",
            "description": "Adapted energy-transducing enzymes support growth at elevated temperature.",
            "evidence": [
              {
                "reference": "DOI:10.1016/s0300-9629(97)00003-0",
                "snippet": "energy transducing enzymes",
                "notes": "Review cites higher turnover rates and coupling-ion changes in high-temperature adaptation."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "reverse_gyrase",
            "predicate": "introduces",
            "object": "dna_positive_supercoiling",
            "description": "Reverse gyrase introduces positive supercoils into thermophile DNA.",
            "evidence": [
              {
                "reference": "DOI:10.1264/jsme2.me23087",
                "notes": "Takemata 2024: \"reverse gyrase introduces positive supercoils\" (broadly accepted in thermophile genomics)."
              }
            ]
          },
          {
            "subject": "dna_positive_supercoiling",
            "predicate": "limits",
            "object": "dna_melting",
            "description": "Positive DNA supercoiling limits thermal DNA melting, protecting genome integrity.",
            "evidence": [
              {
                "reference": "DOI:10.1264/jsme2.me23087",
                "notes": "Takemata 2024: \"maintain the genome integrity of thermophiles by limiting DNA melting\"; mechanism generalized across thermophiles."
              }
            ],
            "predicate_id": "RO:0002212"
          },
          {
            "subject": "reverse_gyrase",
            "predicate": "mediates",
            "object": "genome_integrity",
            "description": "Reverse gyrase mediates DNA repair and genome-integrity maintenance in thermophiles.",
            "evidence": [
              {
                "reference": "DOI:10.1264/jsme2.me23087",
                "notes": "Takemata 2024: \"maintain the genome integrity of thermophiles by ... mediating DNA repair\"."
              }
            ]
          },
          {
            "subject": "group_ii_chaperonin",
            "predicate": "refolds",
            "object": "denatured_proteins",
            "description": "The group II chaperonin (thermosome) refolds denatured proteins in an ATP-dependent manner.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mbio.03593-22",
                "notes": "Baes 2023: \"thermosome, which refolds proteins in an ATP-dependent manner\"."
              }
            ]
          },
          {
            "subject": "cyclopentane_ring_number",
            "predicate": "increases",
            "object": "membrane_rigidity",
            "description": "Increased cyclopentane ring number in tetraether lipids increases membrane condensation and rigidity.",
            "evidence": [
              {
                "reference": "DOI:10.3389/frbis.2023.1338019",
                "notes": "Chong 2024: \"cyclopentane ring cyclization ... increase membrane condensation, packing tightness, rigidity\"."
              }
            ],
            "predicate_id": "RO:0002213"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.858214+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-06T14:58:45-07:00",
        "curator": "codex",
        "action": "CURATED_WITH_ORGANISM_EXAMPLE",
        "changes": "Added Geobacillus stearothermophilus organism example with PMID-backed evidence.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-11T00:00:00-07:00",
        "curator": "codex",
        "action": "CURATED_WITH_LITERATURE",
        "changes": "Added DOI-backed thermophily causal graph for membrane permeability, lipid adaptation, thermostable proteins, and energy transduction.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:30Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T21:30:06Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007401\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:18Z",
        "curator": "claude",
        "action": "RENAME_PREDICATE_LABELS",
        "changes": "Renamed 1 causal-edge predicate label(s) to align with existing groundings: supports \u2192 enables \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:21Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-13T21:03:26Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002213\u00d71, RO:0002212\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-14T05:51:45Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (PATO:0001305\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-17T04:09:43Z",
        "curator": "claude",
        "action": "REMOVE_REDUNDANT_SYNONYM",
        "changes": "Removed 1 synonym(s) whose text duplicated the label (seeder redundancy; no information lost).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 5 evidence-backed generic edges (8 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:11Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002212\u00d71, RO:0002213\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:18Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A088E825\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:21:11Z",
        "curator": "claude",
        "action": "RETRACT_DEAD_UNIPROT_GROUNDINGS",
        "changes": "Retracted 1 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:23:53Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0160097\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 2 causal edge(s) off enables/RO:0002327 with a TRAIT object (2 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-21T08:00:00Z",
        "curator": "codex",
        "action": "NORMALISE_NODE_TYPE",
        "changes": "Tranche 5 of issue 356 settles the process/quality families and merges ids that meant the same sense: proton_permeability is QUALITY, dna_positive_supercoiling is BIOLOGICAL_PROCESS, membrane_rigidity is QUALITY. Proton permeability is a measurable membrane property, which is the schema's QUALITY sense rather than a biological process. GO:0160097 denotes the process of introducing positive supercoils into DNA. The general DNA-topology state remains separately modelled as dna_supercoiling. Membrane rigidity is a physical attribute of the bilayer and therefore a QUALITY under the schema's membrane-fluidity example.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope thermophilic_heat_adaptation=NONMECHANISTIC with scope_notes; marked 4 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (thermostable_proteins, energy_transducing_enzymes, group_ii_chaperonin, denatured_proteins).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000619",
    "label": "thermotolerant",
    "definition": "A temperature preference in which growth can occur at elevated temperatures without an obligate high-temperature preference.",
    "definition_source": "DOI:10.1099/00207713-52-6-2203",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000613"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1099/00207713-52-6-2203",
        "snippet": "Pseudomonas thermotolerans sp. nov., a thermotolerant species",
        "notes": "Organism example: Pseudomonas thermotolerans is described as thermotolerant."
      },
      {
        "reference": "DOI:10.1128/MMBR.65.1.1-43.2001",
        "snippet": "resistant to irreversible inactivation at high temperatures",
        "notes": "Thermostable-protein review supports protein-stability features underlying facultative growth at elevated temperatures."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:157784",
        "taxon_label": "Zestomonas thermotolerans",
        "reference": "DOI:10.1099/00207713-52-6-2203",
        "note": "Type strain CM3 (DSM 14292; LMG 21284) was described as thermotolerant, with an approximately 47 degrees C optimum and a 55 degrees C maximum. The source published it as Pseudomonas thermotolerans; NCBI now uses Zestomonas thermotolerans for this taxon id."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "thermotolerant_facultative_heat_adaptation",
        "title": "Thermotolerant facultative heat-adaptation mechanism",
        "description": "DOI-backed graph linking thermotolerance to limited heat-stress tolerance machinery that permits growth at elevated temperatures without requiring them.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a broad environmental or morphological classification spanning multiple mechanisms, a measurement-like bin, or an absence/arrangement descriptor; contextual protein nodes do not receive token UniProt examples.",
        "nodes": [
          {
            "node_id": "thermotolerant_trait",
            "label": "thermotolerant",
            "node_type": "TRAIT",
            "grounding": "METPO:1000619",
            "description": "Growth at elevated temperatures without obligate high-temperature preference."
          },
          {
            "node_id": "elevated_temperature",
            "label": "elevated temperature",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Ambient temperature above the mesophile optimum range."
          },
          {
            "node_id": "heat_shock_response",
            "label": "heat-shock response",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Induction of heat-shock chaperones (GroEL, DnaK) protecting protein folding under heat stress.",
            "grounding": "traitmech:000205"
          },
          {
            "node_id": "chaperone_proteins",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "chaperone proteins",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Molecular chaperones refolding heat-damaged proteins."
          },
          {
            "node_id": "limited_thermostability",
            "label": "limited thermostability",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Modest protein and membrane stability at elevated temperatures compared with obligate thermophiles."
          },
          {
            "node_id": "rpoH_sigma32",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "RpoH (sigma-32) heat-shock sigma factor",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Alternative RNA polymerase sigma factor that activates the heat-shock regulon."
          },
          {
            "node_id": "heat_shock_chaperone_expression",
            "label": "heat-shock chaperone gene expression",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Induced expression of groEL, dnaKJ, grpE, and clpB chaperone/disaggregase genes."
          },
          {
            "node_id": "rpoE_envelope_sigma",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "RpoE envelope-stress sigma factor",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Extracytoplasmic-stress sigma factor inducing periplasmic proteases and envelope-protective genes."
          },
          {
            "node_id": "membrane_protein_folding_lps",
            "label": "membrane protein folding and LPS biosynthesis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Folding of membrane proteins and biosynthesis of lipopolysaccharide maintaining envelope integrity under heat."
          },
          {
            "node_id": "unsaturated_fa_biosynthesis",
            "label": "unsaturated fatty acid biosynthesis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Biosynthesis of unsaturated fatty acids tuning membrane fluidity (homeoviscous adaptation).",
            "grounding": "GO:0006636"
          },
          {
            "node_id": "compatible_solute_accumulation",
            "label": "trehalose compatible-solute accumulation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Accumulation of trehalose and related compatible solutes protecting proteins and membranes from heat damage."
          }
        ],
        "edges": [
          {
            "subject": "elevated_temperature",
            "predicate": "causes",
            "object": "heat_shock_response",
            "description": "Elevated temperature triggers heat-shock chaperone induction.",
            "evidence": [
              {
                "reference": "DOI:10.1128/MMBR.65.1.1-43.2001",
                "snippet": "resistant to irreversible inactivation at high temperatures",
                "notes": "Supports protein-stability physiology as a high-temperature response."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "chaperone_proteins",
            "predicate": "enables",
            "object": "limited_thermostability",
            "description": "Chaperone proteins support limited thermostability sufficient for facultative high-temperature growth.",
            "evidence": [
              {
                "reference": "DOI:10.1128/MMBR.65.1.1-43.2001",
                "snippet": "resistant to irreversible inactivation at high temperatures",
                "notes": "Supports chaperone-mediated heat-stress tolerance."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "limited_thermostability",
            "predicate": "confers",
            "object": "thermotolerant_trait",
            "description": "Limited thermostability enables facultative growth at elevated temperatures.",
            "evidence": [
              {
                "reference": "DOI:10.1099/00207713-52-6-2203",
                "snippet": "Pseudomonas thermotolerans sp. nov., a thermotolerant species",
                "notes": "Supports the trait endpoint in a representative organism."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "rpoH_sigma32",
            "predicate": "positively regulates",
            "object": "heat_shock_chaperone_expression",
            "description": "RpoH (sigma-32) drives expression of the groEL, dnaKJ, grpE, and clpB heat-shock genes.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s12934-024-02602-y",
                "notes": "The expression of groEL, dnaKJ, grpE, and clpB were regulated by the sigma factor RpoH, whose deletion led to heat sensitivity."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "heat_shock_chaperone_expression",
            "predicate": "enables",
            "object": "heat_shock_response",
            "description": "Induced chaperone/disaggregase gene expression enables the protective heat-shock response.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s12934-024-02602-y",
                "notes": "groEL, dnaKJ, grpE, clpB constitute the chaperone/disaggregase machinery of the heat-shock response."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "elevated_temperature",
            "predicate": "causes",
            "object": "membrane_protein_folding_lps",
            "description": "Heat-activated RpoE induces membrane protein folding and LPS biosynthesis to preserve envelope integrity.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s12275-023-00031-x",
                "notes": "Activated RpoE induces genes involved in folding of membrane proteins and biosynthesis of lipopolysaccharides under heat shock."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "rpoE_envelope_sigma",
            "predicate": "positively regulates",
            "object": "membrane_protein_folding_lps",
            "description": "RpoE envelope-stress sigma factor positively regulates membrane protein folding and LPS biosynthesis.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s12275-023-00031-x",
                "notes": "Activated RpoE induces heat-shock proteins, periplasmic proteases (HtrA, DegP), and genes for membrane protein folding and LPS biosynthesis."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "unsaturated_fa_biosynthesis",
            "predicate": "contributes to",
            "object": "thermotolerant_trait",
            "description": "Unsaturated fatty acid biosynthesis tunes membrane fluidity, contributing to thermotolerance.",
            "evidence": [
              {
                "reference": "DOI:10.1128/spectrum.01627-23",
                "notes": "A sharp relationship between thermotolerance and fatty-acid metabolism; saturated/unsaturated FA balance modulates heat tolerance."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "compatible_solute_accumulation",
            "predicate": "positively regulates",
            "object": "limited_thermostability",
            "description": "Trehalose compatible-solute accumulation stabilizes proteins and membranes against heat damage.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s40694-023-00168-9",
                "notes": "Accumulation of mannitol and trehalose as the main compatible solutes is a key factor for heat resistance."
              }
            ],
            "predicate_id": "RO:0002213"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.860266+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-06T14:58:45-07:00",
        "curator": "codex",
        "action": "CURATED_WITH_ORGANISM_EXAMPLE",
        "changes": "Added Pseudomonas thermotolerans organism example with PMID-backed evidence.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-13T11:30:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed causal graph linking heat-shock response, chaperone proteins, and limited thermostability to the thermotolerant trait.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-13T22:45:00-07:00",
        "curator": "codex",
        "action": "IMPROVED_CAUSAL_GRAPH_EVIDENCE",
        "changes": "Replaced Pseudomonas thermotolerans PMID fallback with the article DOI in definition, record evidence, and CausalEdge evidence.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:30Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:18Z",
        "curator": "claude",
        "action": "RENAME_PREDICATE_LABELS",
        "changes": "Renamed 1 causal-edge predicate label(s) to align with existing groundings: supports \u2192 enables \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:21Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-26T05:00:47Z",
        "curator": "claude",
        "action": "RENAME_PREDICATE_LABELS",
        "changes": "Renamed 1 causal-edge predicate label(s) to align with existing groundings: triggers \u2192 causes \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-26T05:00:50Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:causes\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-17T04:09:43Z",
        "curator": "claude",
        "action": "REMOVE_REDUNDANT_SYNONYM",
        "changes": "Removed 1 synonym(s) whose text duplicated the label (seeder redundancy; no information lost).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 6 evidence-backed generic edges (6 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:11Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d71, biolink:causes\u00d71, RO:0002326\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:32Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0006636\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-04T03:08:13Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002213\u00d73).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 1 causal edge(s) off enables/RO:0002327 with a TRAIT object (1 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope thermotolerant_facultative_heat_adaptation=NONMECHANISTIC with scope_notes; marked 3 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (chaperone_proteins, rpoH_sigma32, rpoE_envelope_sigma).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T10:54:11Z",
        "curator": "codex",
        "action": "ADD_CANONICAL_EXAMPLES",
        "changes": "Added Zestomonas thermotolerans strain CM3 as the directly characterized thermotolerant exemplar from this record's own research artifact; preserved the source's historical Pseudomonas thermotolerans name in the note and verified NCBITaxon:157784 and its current label against NCBI.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-15T04:58:15Z",
        "curator": "codex",
        "action": "GROUND_CAUSAL_NODE",
        "changes": "Grounded the exact heat-shock-response biological-process node to the newly minted local traitmech:000205 heat shock response record.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000009",
    "label": "UV radiation tolerant",
    "definition": "An environmental tolerance in which an organism survives high doses of ultraviolet radiation, typically via photoreactivation and nucleotide-excision repair of cyclobutane pyrimidine dimers and 6-4 photoproducts.",
    "definition_source": "DOI:10.3390/genes14091803",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "traitmech:000007"
    ],
    "synonyms": [
      {
        "synonym_text": "UV resistant",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.3390/genes14091803"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.3390/genes14091803",
        "snippet": "Deinococcus radiodurans R1 demonstrates a significantly higher radiation resistance with D10 values exceeding 12 kGy for gamma radiation and 700 J/m2 for UV-C radiation",
        "notes": "Organism example: Deinococcus radiodurans tolerates UV-C radiation D10 doses of 700 J/m2."
      },
      {
        "reference": "DOI:10.1101/cshperspect.a012765",
        "snippet": "The bacterium Deinococcus radiodurans is a champion of extreme radiation resistance",
        "notes": "Review support \u2014 Deinococcus radiodurans is the reference organism for extreme UV and ionizing radiation resistance."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1299",
        "taxon_label": "Deinococcus radiodurans",
        "note": "UV-resistant",
        "reference": "PMID:11238985"
      },
      {
        "taxon_id": "NCBITaxon:54298",
        "taxon_label": "Chroococcidiopsis",
        "note": "desert UV-tolerant cyanobacterium",
        "reference": "PMID:23239185"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "uv_tolerance_excision_repair",
        "title": "UV-radiation tolerance via nucleotide-excision and photoreactivation repair",
        "description": "Evidence-backed causal sketch linking UV-induced pyrimidine dimers to nucleotide-excision and photoreactivation repair.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a broad environmental or morphological classification spanning multiple mechanisms, a measurement-like bin, or an absence/arrangement descriptor; contextual protein nodes do not receive token UniProt examples.",
        "nodes": [
          {
            "node_id": "uv_tolerant_trait",
            "label": "UV radiation tolerant",
            "node_type": "TRAIT",
            "grounding": "traitmech:000009",
            "description": "Survival of high doses of UV radiation."
          },
          {
            "node_id": "uv_radiation",
            "label": "ultraviolet radiation",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Solar / UV-C exposure inducing pyrimidine dimers and 6-4 photoproducts.",
            "grounding": "ENVO:21001216"
          },
          {
            "node_id": "nucleotide_excision_repair",
            "label": "nucleotide-excision repair",
            "node_type": "BIOLOGICAL_PROCESS",
            "grounding": "GO:0006289",
            "description": "Removal and replacement of UV-damaged DNA segments."
          },
          {
            "node_id": "photoreactivation",
            "label": "photoreactivation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Photolyase-mediated reversal of pyrimidine dimers."
          },
          {
            "node_id": "cyclobutane_pyrimidine_dimer",
            "label": "cyclobutane pyrimidine dimer",
            "node_type": "CHEMICAL",
            "description": "Major UV-induced DNA photoproduct (CPD) joining adjacent pyrimidines."
          },
          {
            "node_id": "pyrimidine_6_4_photoproduct",
            "label": "pyrimidine (6-4) pyrimidone photoproduct",
            "node_type": "CHEMICAL",
            "description": "Second principal UV-induced DNA lesion (6-4PP)."
          },
          {
            "node_id": "cpd_photolyase",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "CPD photolyase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Light-driven enzyme that directly reverses cyclobutane pyrimidine dimers."
          },
          {
            "node_id": "catalase",
            "label": "catalase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Antioxidant enzyme detoxifying reactive oxygen species generated by UV.",
            "grounding": "GO:0004096"
          },
          {
            "node_id": "reactive_oxygen_species",
            "label": "reactive oxygen species",
            "node_type": "CHEMICAL",
            "description": "ROS produced under UV exposure causing oxidative damage.",
            "grounding": "CHEBI:26523"
          },
          {
            "node_id": "mycosporine_like_amino_acids",
            "label": "mycosporine-like amino acids",
            "node_type": "CHEMICAL",
            "description": "UV-screening metabolites that absorb UV-A/UV-B and dissipate it as heat.",
            "grounding": "CHEBI:35738"
          }
        ],
        "edges": [
          {
            "subject": "uv_radiation",
            "predicate": "challenges",
            "object": "uv_tolerant_trait",
            "description": "UV exposure is the environmental challenge the trait counters.",
            "evidence": [
              {
                "reference": "DOI:10.3390/genes14091803",
                "notes": "Deinococcus radiodurans tolerates UV-C D10 doses of 700 J/m2."
              }
            ],
            "predicate_id": "METPO:2007406"
          },
          {
            "subject": "nucleotide_excision_repair",
            "predicate": "confers",
            "object": "uv_tolerant_trait",
            "description": "NER removes UV-induced cyclobutane pyrimidine dimers and 6-4 photoproducts.",
            "evidence": [
              {
                "reference": "DOI:10.3390/genes14091803",
                "notes": "D. radiodurans tolerates lethal UV-C doses via excision-based repair of UV photoproducts."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "photoreactivation",
            "predicate": "confers",
            "object": "uv_tolerant_trait",
            "description": "Photolyase-mediated dimer reversal complements excision repair.",
            "evidence": [
              {
                "reference": "DOI:10.1101/cshperspect.a012765",
                "notes": "D. radiodurans is the reference organism for extreme UV and ionizing radiation resistance."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "uv_radiation",
            "predicate": "causes",
            "object": "cyclobutane_pyrimidine_dimer",
            "description": "UV exposure produces cyclobutane pyrimidine dimers, the majority DNA lesion.",
            "evidence": [
              {
                "reference": "DOI:10.3390/life14070822",
                "notes": "UV produces two primary pyrimidine photoproducts: CPDs (majority lesion) and 6-4PPs; central trait-defining lesion, general across taxa."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "uv_radiation",
            "predicate": "causes",
            "object": "pyrimidine_6_4_photoproduct",
            "description": "UV exposure produces pyrimidine (6-4) pyrimidone photoproducts.",
            "evidence": [
              {
                "reference": "DOI:10.3390/life14070822",
                "notes": "Principal UV lesions include CPDs and pyrimidine (6-4) pyrimidone photoproducts; strong and general."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "cpd_photolyase",
            "predicate": "repairs",
            "object": "cyclobutane_pyrimidine_dimer",
            "description": "CPD photolyase directly reverses cyclobutane pyrimidine dimers via light-driven electron transfer.",
            "evidence": [
              {
                "reference": "DOI:10.3390/ijms241512381",
                "notes": "Photolyases directly reverse UV photoproducts; CPD photolyase uses light-driven electron transfer to monomerize CPD dimers; canonical general edge."
              }
            ]
          },
          {
            "subject": "catalase",
            "predicate": "detoxifies",
            "object": "reactive_oxygen_species",
            "description": "Catalase scavenges UV-induced reactive oxygen species, preventing oxidative damage.",
            "evidence": [
              {
                "reference": "DOI:10.3390/microorganisms13040756",
                "notes": "Genomic analyses implicate catalases in UV resistance; ROS-scavengers/catalases detoxify ROS and prevent oxidative damage; general antioxidant edge."
              }
            ]
          },
          {
            "subject": "mycosporine_like_amino_acids",
            "predicate": "absorbs",
            "object": "uv_radiation",
            "description": "MAAs absorb UV-A/UV-B (~309-362 nm) and release it as harmless heat, screening UV.",
            "evidence": [
              {
                "reference": "DOI:10.3390/ijms241512381",
                "notes": "MAAs absorb ~309-362 nm with high extinction coefficients and release absorbed UV as harmless heat; strong, general for cyanobacteria/algae."
              }
            ]
          },
          {
            "subject": "mycosporine_like_amino_acids",
            "predicate": "quenches",
            "object": "reactive_oxygen_species",
            "description": "MAAs act as antioxidants that quench UV-induced reactive oxygen species.",
            "evidence": [
              {
                "reference": "DOI:10.3390/ijms241512381",
                "notes": "MAAs act as antioxidants/free-radical scavengers and quench ROS induced by PAR, UV-A, and UV-B; strong, mechanism/class-level."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-28T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate ENVIRONMENT trait (ultraviolet radiation tolerance) from literature research; sub-variant of radiotolerant.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-09T14:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (NER + photoreactivation) with GO node grounding and RO/METPO predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-14T06:55:38Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (ENVO:21001216\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 6 evidence-backed generic edges (6 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:11Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:causes\u00d72).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:18Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A071MK53\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:32Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:26523\u00d71, CHEBI:35738\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:21:11Z",
        "curator": "claude",
        "action": "RETRACT_DEAD_UNIPROT_GROUNDINGS",
        "changes": "Retracted 1 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:23:53Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0004096\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 2 causal edge(s) off enables/RO:0002327 with a TRAIT object (2 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope uv_tolerance_excision_repair=NONMECHANISTIC with scope_notes; marked 1 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (cpd_photolyase).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000011",
    "label": "xerophilic",
    "definition": "An environmental growth preference in which an organism grows at low water activity (low aw), such as in desiccated, high-sugar, or high-solute substrates.",
    "definition_source": "DOI:10.1098/rstb.2004.1502",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "synonyms": [
      {
        "synonym_text": "xerotolerant",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1098/rstb.2004.1502"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1098/rstb.2004.1502",
        "snippet": "some of which are capable of growth at a water activity (aw) of 0.61, the lowest aw value for growth recorded to date",
        "notes": "Low-water-activity review supports growth at very low aw as the defining feature of xerophiles."
      },
      {
        "reference": "DOI:10.3390/microorganisms10020432",
        "snippet": "Anhydrobiosis (gr. life without water) is predominantly described as the ability of some organisms to lose all or almost all water and enter a state of suspension where the metabolism comes to a reversible standstill",
        "notes": "Anhydrobiosis review supports low-water-activity adaptation as the physiological context distinguishing xerophilic growth from desiccation survival."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:54298",
        "taxon_label": "Chroococcidiopsis",
        "note": "desiccation/aridity-tolerant cyanobacterium",
        "reference": "PMID:11244070"
      },
      {
        "taxon_id": "NCBITaxon:1299",
        "taxon_label": "Deinococcus radiodurans",
        "note": "desiccation tolerant",
        "reference": "PMID:8550493"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "xerophilic_low_water_activity_growth",
        "title": "Xerophilic growth at low water activity",
        "description": "Evidence-backed causal sketch linking low-water-activity environments to active growth via osmotic adaptation.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a broad environmental or morphological classification spanning multiple mechanisms, a measurement-like bin, or an absence/arrangement descriptor; contextual protein nodes do not receive token UniProt examples.",
        "nodes": [
          {
            "node_id": "xerophilic_trait",
            "label": "xerophilic",
            "node_type": "TRAIT",
            "grounding": "traitmech:000011",
            "description": "Growth at low water activity (low aw) substrates."
          },
          {
            "node_id": "low_water_activity",
            "label": "low water activity environment",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Desiccated, high-sugar, or high-solute substrate with low aw."
          },
          {
            "node_id": "osmotic_adaptation",
            "label": "response to osmotic stress",
            "node_type": "BIOLOGICAL_PROCESS",
            "grounding": "GO:0006970",
            "description": "Cellular response maintaining turgor under solute or water stress."
          },
          {
            "node_id": "compatible_solute_accumulation",
            "label": "compatible solute accumulation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Intracellular build-up of osmoprotective small molecules under low water activity."
          },
          {
            "node_id": "low_mw_polyols",
            "label": "low-molecular-weight polyols (glycerol, erythritol, arabitol)",
            "node_type": "CHEMICAL",
            "description": "Small polyols used as compatible solutes effective for osmotic adjustment at low aw."
          },
          {
            "node_id": "osmotic_adjustment",
            "label": "osmotic adjustment",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Balancing of internal osmotic potential to sustain turgor and growth under low aw."
          },
          {
            "node_id": "hog_pathway",
            "label": "high osmolarity glycerol (HOG) pathway",
            "node_type": "PATHWAY",
            "description": "Canonical osmotic-stress MAPK signaling pathway driving osmotic adaptation."
          },
          {
            "node_id": "membrane_fluidity_remodeling",
            "label": "plasma membrane fluidity alteration",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Adjustment of plasma membrane fluidity/composition during low-aw/high-salt stress."
          }
        ],
        "edges": [
          {
            "subject": "low_water_activity",
            "predicate": "selects for",
            "object": "xerophilic_trait",
            "description": "Persistent low-aw habitats favor organisms with active xerophilic growth.",
            "evidence": [
              {
                "reference": "DOI:10.1098/rstb.2004.1502",
                "notes": "Low-water-activity review supports growth at very low aw as the defining xerophile feature."
              }
            ],
            "predicate_id": "METPO:2007401"
          },
          {
            "subject": "xerophilic_trait",
            "predicate": "enables",
            "object": "osmotic_adaptation",
            "description": "Xerophilic organisms mount sustained osmotic adaptation supporting growth under low-aw stress.",
            "evidence": [
              {
                "reference": "DOI:10.3390/microorganisms10020432",
                "notes": "Anhydrobiosis review supports low-aw adaptation as the physiological context distinguishing xerophilic growth from desiccation survival."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "low_water_activity",
            "predicate": "increases",
            "object": "compatible_solute_accumulation",
            "description": "Low water activity drives intracellular accumulation of compatible solutes (osmolytes).",
            "evidence": [
              {
                "reference": "DOI:10.34293/sijash.v7i3.473",
                "notes": "Microbes respond to low aw primarily via intracellular accumulation of compatible solutes (osmolytes) \u2014 broad cross-microbial statement."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "low_mw_polyols",
            "predicate": "enables",
            "object": "osmotic_adjustment",
            "description": "Low-molecular-weight polyols are effective compatible solutes for osmotic adjustment at low aw.",
            "evidence": [
              {
                "reference": "DOI:10.1007/978-3-031-81904-9_3",
                "notes": "Polyols with lower molecular weight such as glycerol, erythritol, and arabitol were more effective for osmotic adjustment."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "hog_pathway",
            "predicate": "increases",
            "object": "osmotic_adaptation",
            "description": "Activation of the HOG pathway drives osmotic adaptation under low-aw/high-osmolarity stress.",
            "evidence": [
              {
                "reference": "DOI:10.3390/jof10040290",
                "notes": "Adaptation by activating the high osmolarity glycerol (HOG) pathway; pathway-level edge relevant across low-aw settings."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "low_water_activity",
            "predicate": "increases",
            "object": "membrane_fluidity_remodeling",
            "description": "Low-aw/hypersaline stress drives alteration of plasma membrane fluidity as a broad fungal adaptation.",
            "evidence": [
              {
                "reference": "DOI:10.3390/jof10040290",
                "notes": "Fungi employ physiological adaptations including altering plasma membrane fluidity; broad adaptation likely relevant across low-aw settings."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "compatible_solute_accumulation",
            "predicate": "enables",
            "object": "osmotic_adjustment",
            "description": "Accumulation of compatible solutes enables osmotic adjustment under low-water-activity stress.",
            "evidence": [
              {
                "reference": "DOI:10.1046/j.1462-2920.2002.00335.x",
                "snippet": "rely exclusively on the accumulation of compatible solutes for osmoadaptation",
                "notes": "Supports the general process bridge from compatible-solute accumulation to osmotic adjustment without asserting a universal solute identity."
              }
            ],
            "predicate_id": "RO:0002327"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-28T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate ENVIRONMENT trait (low-water-activity growth preference) from literature research to fill the water-availability coverage gap.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-09T14:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (xerophilic low-aw growth) with GO node grounding and RO/METPO predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 4 evidence-backed generic edges (5 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:11Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 4 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002213\u00d73, RO:0002327\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope xerophilic_low_water_activity_growth=NONMECHANISTIC with scope_notes.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T10:32:29Z",
        "curator": "codex",
        "action": "CONNECT_CAUSAL_GRAPH",
        "changes": "Connected compatible-solute accumulation to osmotic adjustment with one source-supported enables edge, joining both graph components. Chemical, pathway, gene, and protein concepts remain supporting YAML fields rather than primary TraitRecord entries. Addresses issues 426 and 183.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000014",
    "label": "zinc tolerant",
    "definition": "A metal tolerance in which an organism grows in the presence of elevated zinc (Zn2+) concentrations, typically via cation-efflux resistance systems such as the czc determinant.",
    "definition_source": "PMID:12829273",
    "trait_category": "ENVIRONMENT",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "traitmech:000012"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1111/j.1365-2958.2009.06792.x",
        "snippet": "CzcP exports transition metals Zn(2+), Cd(2+) and Co(2+)",
        "notes": "The cobalt-zinc-cadmium (czc) efflux system of Cupriavidus metallidurans confers zinc resistance."
      },
      {
        "reference": "DOI:10.3389/fmicb.2020.00047",
        "snippet": "C. metallidurans BS1 conferred resistance to Zn2+ displaying a MIC of 20 mM, Cd2+ (2.5 mM), Co2+ (20mM), Ni2+ (8 mM), As3+ (3.5 mM), Cu2+ (5 mM), Au3+ (1 uM) and Pb2+ (1.7 mM)",
        "notes": "Organism example: Cupriavidus metallidurans BS1 tolerates zinc to a MIC of 20 mM."
      },
      {
        "reference": "PMID:12829273",
        "snippet": "CBA efflux pumps driven by proteins of the resistance-nodulation-cell division superfamily, P-type ATPases, cation diffusion facilitator and chromate proteins",
        "notes": "Nies (2003, FEMS Microbiol Rev 27:313-339) reviews prokaryotic heavy-metal resistance mediated by RND-family CBA efflux pumps (including CzcCBA), P-type ATPases (including ZntA), and cation diffusion facilitators, supporting the record definition and definition_source for zinc tolerance."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:119219",
        "taxon_label": "Cupriavidus metallidurans",
        "note": "zinc-resistance determinants",
        "reference": "PMID:33540705"
      },
      {
        "taxon_id": "NCBITaxon:266264",
        "taxon_label": "Cupriavidus metallidurans CH34",
        "note": "Strain-level ZntA zinc-efflux exemplar.",
        "reference": "PMID:33540705"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "zinc_tolerance_czc_efflux",
        "title": "Zinc tolerance via czc cation-efflux system",
        "description": "Evidence-backed causal sketch linking the cobalt-zinc-cadmium (czc) efflux determinant to cytoplasmic zinc detoxification.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "The taxon-matched protein example anchors one experimentally supported causal branch; it is not presented as a universal mechanism for every taxon or every contextual branch in this graph.",
        "nodes": [
          {
            "node_id": "zinc_tolerant_trait",
            "label": "zinc tolerant",
            "node_type": "TRAIT",
            "grounding": "traitmech:000014",
            "description": "Capacity to grow at elevated Zn(2+) concentrations."
          },
          {
            "node_id": "zinc_ion",
            "label": "zinc(2+) ion",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:29105",
            "description": "Cytoplasmic Zn(2+) excess threatening protein mismetallation."
          },
          {
            "node_id": "czc_efflux_system",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "czc cation-efflux system",
            "node_type": "GENE_OR_PROTEIN",
            "description": "CzcCBA/CzcP machinery exporting Zn, Cd, and Co cations."
          },
          {
            "node_id": "zinc_export",
            "label": "zinc ion transmembrane transport",
            "node_type": "BIOLOGICAL_PROCESS",
            "grounding": "GO:0006829",
            "description": "Active export of Zn(2+) across the cytoplasmic membrane."
          },
          {
            "node_id": "znta_atpase",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:Q1LEH0",
                "protein_label": "P-type zinc transporter ZntA",
                "gene_symbol": "zntA",
                "taxon_id": "NCBITaxon:266264",
                "taxon_label": "Cupriavidus metallidurans CH34",
                "entry_status": "UNREVIEWED",
                "proteome_id": "UP000002429",
                "retrieved_on": "2026-10-22",
                "entry_version": 136,
                "sequence_version": 1,
                "role": "CH34 ZntA is a P-type ATPase that exports cytoplasmic zinc.",
                "evidence": [
                  {
                    "reference": "PMID:33540705",
                    "snippet": "zinc resistance determinants in Cupriavidus metallidurans",
                    "notes": "The cited source supports the represented protein-to-trait branch; UniProt verifies this current strain-matched protein entry."
                  }
                ]
              }
            ],
            "label": "ZntA P-type ATPase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "PIB2-type P-type ATPase mediating cytoplasmic zinc efflux."
          },
          {
            "node_id": "zntr_regulator",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "ZntR MerR-family regulator",
            "node_type": "GENE_OR_PROTEIN",
            "description": "MerR-family zinc-responsive transcriptional activator of zntA."
          },
          {
            "node_id": "znta_expression",
            "label": "zntA transcription",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Transcription of the zntA zinc-efflux ATPase gene."
          },
          {
            "node_id": "czccba_complex",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "CzcCBA RND efflux complex",
            "node_type": "GENE_OR_PROTEIN",
            "description": "RND transenvelope pump exporting zinc from the periplasm."
          },
          {
            "node_id": "polyphosphate",
            "label": "polyphosphate",
            "node_type": "CHEMICAL",
            "description": "Cytoplasmic metal-binding polymer buffering zinc.",
            "grounding": "CHEBI:16838"
          },
          {
            "node_id": "glutathione",
            "label": "glutathione",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:16856",
            "description": "Cytoplasmic thiol buffering intracellular zinc."
          },
          {
            "node_id": "zinc_buffering",
            "label": "zinc ion buffering",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Intracellular sequestration maintaining zinc flow equilibrium."
          }
        ],
        "edges": [
          {
            "subject": "zinc_ion",
            "predicate": "challenges",
            "object": "zinc_tolerant_trait",
            "description": "Cytoplasmic zinc excess is the challenge the trait counters.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2020.00047",
                "notes": "Cupriavidus metallidurans BS1 tolerates Zn(2+) to a MIC of 20 mM."
              }
            ],
            "predicate_id": "METPO:2007406"
          },
          {
            "subject": "czc_efflux_system",
            "predicate": "enables",
            "object": "zinc_export",
            "description": "CzcP exports zinc together with cadmium and cobalt cations.",
            "evidence": [
              {
                "reference": "DOI:10.1111/j.1365-2958.2009.06792.x",
                "notes": "CzcP exports transition metals Zn(2+), Cd(2+), and Co(2+)."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "zinc_export",
            "predicate": "mitigates",
            "object": "zinc_ion",
            "description": "Czc-mediated export depletes the cytoplasmic zinc pool.",
            "evidence": [
              {
                "reference": "DOI:10.1111/j.1365-2958.2009.06792.x",
                "notes": "The czc efflux system of C. metallidurans confers zinc resistance."
              }
            ],
            "predicate_id": "METPO:2007407"
          },
          {
            "subject": "znta_atpase",
            "predicate": "exports",
            "object": "zinc_ion",
            "description": "ZntA PIB2-type ATPase effluxes cytoplasmic Zn(2+).",
            "evidence": [
              {
                "reference": "DOI:10.1128/jb.00080-24",
                "notes": "Efflux of zinc ions is mediated by the PIB2-type ATPase, ZntA."
              }
            ],
            "predicate_id": "METPO:2007804"
          },
          {
            "subject": "znta_atpase",
            "predicate": "promotes",
            "object": "zinc_tolerant_trait",
            "description": "ZntA-mediated efflux is causal for zinc resistance.",
            "evidence": [
              {
                "reference": "DOI:10.1128/jb.00080-24",
                "notes": "Deletion of PIB2 ATPases sharply lowers IC50 (to 7.7 uM), showing their causal role in resistance."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "zinc_ion",
            "predicate": "upregulates",
            "object": "znta_expression",
            "description": "Elevated zinc induces transcription of the zntA efflux gene.",
            "evidence": [
              {
                "reference": "DOI:10.1128/jb.00299-24",
                "notes": "At external zinc concentrations above 200 nM expression of the zntA gene is upregulated."
              }
            ]
          },
          {
            "subject": "zntr_regulator",
            "predicate": "required for",
            "object": "znta_expression",
            "description": "ZntR is essential for zinc-responsive zntA expression.",
            "evidence": [
              {
                "reference": "DOI:10.1128/jb.00299-24",
                "notes": "ZntR was essential for zntA expression."
              }
            ]
          },
          {
            "subject": "znta_expression",
            "predicate": "results in",
            "object": "czc_efflux_system",
            "description": "zntA transcription yields the ZntA efflux machinery.",
            "evidence": [
              {
                "reference": "DOI:10.1128/jb.00299-24",
                "notes": "Increased zntA expression provides ZntA exporter under zinc excess."
              }
            ]
          },
          {
            "subject": "czccba_complex",
            "predicate": "exports",
            "object": "zinc_ion",
            "description": "CzcCBA RND pump exports Zn(2+) from the periplasm.",
            "evidence": [
              {
                "reference": "DOI:10.1128/jb.00080-24",
                "notes": "The plasmid-encoded RND transenvelope pump CzcCBA exports Co(II), Zn(II), and Cd(II)."
              }
            ],
            "predicate_id": "METPO:2007804"
          },
          {
            "subject": "polyphosphate",
            "predicate": "contributes to",
            "object": "zinc_buffering",
            "description": "Polyphosphate buffers cytoplasmic zinc, shaping flow equilibrium.",
            "evidence": [
              {
                "reference": "DOI:10.1128/jb.00080-24",
                "notes": "Metal-binding cytoplasmic components polyphosphate and glutathione influenced the flow equilibrium."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "glutathione",
            "predicate": "contributes to",
            "object": "zinc_buffering",
            "description": "Glutathione buffers cytoplasmic zinc, shaping flow equilibrium.",
            "evidence": [
              {
                "reference": "DOI:10.1128/jb.00080-24",
                "notes": "Polyphosphate and glutathione influenced the flow equilibrium."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "zinc_buffering",
            "predicate": "mitigates",
            "object": "zinc_ion",
            "description": "Buffering lowers free cytoplasmic zinc.",
            "evidence": [
              {
                "reference": "DOI:10.1128/jb.00080-24",
                "notes": "Cytoplasmic buffering components influence the zinc flow equilibrium."
              }
            ],
            "predicate_id": "METPO:2007407"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-28T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate ENVIRONMENT trait (zinc tolerance) from literature research; metal-specific sub-variant of metal tolerant.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-09T14:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (czc zinc efflux) with CHEBI/GO node groundings and RO/METPO predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-14T06:38:14Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:B0VPE1\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 9 evidence-backed generic edges (7 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:11Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 6 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000209\u00d72, RO:0002326\u00d72, RO:0002213\u00d71, METPO:2007407\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:32Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:16838\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:21:11Z",
        "curator": "claude",
        "action": "RETRACT_DEAD_UNIPROT_GROUNDINGS",
        "changes": "Retracted 1 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T02:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES_PART2",
        "changes": "Re-grounded 2 causal edge(s) off microbe-domain METPO predicates onto their causal-graph counterparts (2 to exports), issue 301 part 2. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Each replacement is a 1:1 mirror of its source predicate that changes only the domain, so the claim each edge makes is unchanged and directions are unchanged. The replacements are proposed in proposals/metpo_traitmech_v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "CURATE_PROTEIN_TAXON_EXAMPLE",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope zinc_tolerance_czc_efflux=MECHANISTIC with scope_notes; marked 4 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (czc_efflux_system, znta_atpase, zntr_regulator, czccba_complex); added taxon-paired protein example(s) UniProtKB:Q1LEH0 on znta_atpase (NCBITaxon:266264); added canonical example(s) NCBITaxon:266264.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-22T01:35:00Z",
        "curator": "claude",
        "action": "REFRESH_UNIPROT_ENTRY_VERSION",
        "changes": "Refreshed UniProtKB entry_version against live UniProt REST on 2026-10-22: UniProtKB:Q1LEH0 (135 -> 136 on znta_atpase).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-22T05:20:00Z",
        "curator": "claude",
        "action": "ADD_RECORD_LEVEL_DEFINITION_SOURCE_EVIDENCE",
        "changes": "Added PMID:12829273 (Nies 2003) with verified verbatim snippet to record-level evidence to match definition_source (Stage 5 remediation of F-DEF-SRC-ZINC-004 in group G-STAGE4-RECORD-LEVEL-DEFINITION-SOURCE, issue #1981).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000338",
    "label": "Abi2 system",
    "definition": "An abortive infection system in which an organism possesses a single-component Abi-like locus represented by the DefenseFinder Abi2 model namespace and mandatory Abi2__Abi_2/PF07751 profile.",
    "definition_source": "DOI:10.1016/j.mib.2005.06.006",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000214"
    ],
    "synonyms": [
      {
        "synonym_text": "Abi2",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      },
      {
        "synonym_text": "Abi2__Abi_2",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "Abi_2",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://www.ebi.ac.uk/interpro/entry/pfam/PF07751/"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1016/j.mib.2005.06.006",
        "snippet": "Abortive infection (Abi) systems, also called phage exclusion, block phage multiplication and cause premature bacterial cell death upon phage infection.",
        "notes": "Chopin et al. define the abortive-infection class of phage exclusion systems used by the DefenseFinder Abi2 registry row."
      },
      {
        "reference": "DOI:10.1128/jb.177.13.3818-3823.1995",
        "snippet": "Lactococcal phage abortive infection (AbiD1) determined by plasmid pIL105 is active on both prolate- and small-isometric-head phages",
        "notes": "Anba et al. characterize AbiD1 as a plasmid-encoded lactococcal abortive-infection determinant active on multiple phage morphotypes."
      },
      {
        "reference": "DOI:10.1128/jb.177.13.3818-3823.1995",
        "snippet": "The Abi phenotype was found to be encoded by a single gene, designated abiD1.",
        "notes": "Anba et al. support a single-gene AbiD1 locus used as family-level background for Abi-like abortive-infection systems."
      },
      {
        "reference": "DOI:10.1128/jb.177.13.3824-3829.1995",
        "snippet": "Phage bIL66 is unable to grow on Lactococcus lactis cells harboring the abortive infection gene abiD1.",
        "notes": "Bidnenko et al. connect abiD1 carriage to restriction of bIL66 phage growth in Lactococcus lactis."
      },
      {
        "reference": "https://www.ebi.ac.uk/interpro/entry/pfam/PF07751/",
        "snippet": "This family, found in various bacterial species, contains sequences that are similar to the Abi group of proteins",
        "notes": "EBI InterPro resolves PF07751 as the reviewed Pfam Abi-like protein family with short name Abi_2."
      },
      {
        "reference": "https://rest.uniprot.org/uniprotkb/Q48717.tsv?fields=accession,id,gene_names,protein_name,xref_pfam,organism_name",
        "snippet": "Q48717\tQ48717_9LACT\tabiD1\tAbiD1\tPF07751;\tLactococcus lactis",
        "notes": "UniProt maps the Lactococcus lactis abiD1/AbiD1 entry to Pfam PF07751, bridging primary AbiD1 papers to the Abi_2 HMM family without making DefenseFinder Abi2 exactly equivalent to AbiD1."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "Abi2 | 10\\.1016/j\\.mib\\.2005\\.06\\.006 | Phage abortive infection in lactococci: variations on a theme",
        "notes": "The DefenseFinder article registry maps the named Abi2 model namespace to the Chopin et al. lactococcal abortive-infection review."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "Abi2\tAbi2\t1\t1\tAbi2__Abi_2\t\t\t",
        "notes": "The DefenseFinder rules table models Abi2 as a one-component system requiring the Abi2__Abi_2 profile."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| Abi2__Abi_2                                      | Abi2__Abi_2                                      | Abi2                   | PF07751.12              | 60     |",
        "notes": "The DefenseFinder HMM inventory records Abi2__Abi_2 under the Abi2 model namespace, backed by the Pfam PF07751.12 Abi_2 profile."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "abi2_locus_restricts_phage",
        "title": "Abi2 loci confer abortive-infection phage defense",
        "description": "Conservative system-level sketch linking possession of a DefenseFinder Abi2 locus to restricted bacteriophage propagation without asserting the unresolved phage trigger, small-RNA component, or molecular output.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Abi2 as a named DefenseFinder single-profile abortive-infection system with an Abi2__Abi_2/PF07751 HMM profile while leaving its natural locus boundaries, AbiD/F-group breadth, upstream regulatory RNA relationships, phage trigger, and direct effector activity unresolved.",
        "nodes": [
          {
            "node_id": "abi2_locus",
            "label": "Abi2 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A single-component Abi2 abortive-infection locus represented by the DefenseFinder Abi2__Abi_2 profile."
          },
          {
            "node_id": "restricted_phage_propagation",
            "label": "restricted phage propagation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced propagation of bacteriophage in cells carrying an Abi2-family abortive-infection system."
          },
          {
            "node_id": "abi2_system_trait",
            "label": "Abi2 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000338",
            "description": "Possession of a genome-encoded Abi2 abortive-infection system."
          },
          {
            "node_id": "abortive_infection_system_trait",
            "label": "abortive infection system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000214",
            "description": "Possession of a genome-encoded abortive-infection phage-defense system."
          }
        ],
        "edges": [
          {
            "subject": "abi2_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "restricted_phage_propagation",
            "description": "DefenseFinder represents Abi2 with the Abi2__Abi_2 Pfam profile, and Abi-like loci mediate abortive-infection phage restriction.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "Abi2\tAbi2\t1\t1\tAbi2__Abi_2\t\t\t",
                "notes": "The DefenseFinder rules table models Abi2 as a one-component system requiring the Abi2__Abi_2 profile."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| Abi2__Abi_2                                      | Abi2__Abi_2                                      | Abi2                   | PF07751.12              | 60     |",
                "notes": "The DefenseFinder HMM inventory records Abi2__Abi_2 under the Abi2 model namespace, backed by the Pfam PF07751.12 Abi_2 profile."
              },
              {
                "reference": "DOI:10.1128/jb.177.13.3818-3823.1995",
                "snippet": "Lactococcal phage abortive infection (AbiD1) determined by plasmid pIL105 is active on both prolate- and small-isometric-head phages",
                "notes": "Anba et al. support abortive-infection antiphage activity in the Abi-like family."
              }
            ]
          },
          {
            "subject": "restricted_phage_propagation",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "abi2_system_trait",
            "description": "Restriction of phage propagation realizes the Abi2 abortive-infection system possession trait.",
            "evidence": [
              {
                "reference": "DOI:10.1128/jb.177.13.3824-3829.1995",
                "snippet": "Phage bIL66 is unable to grow on Lactococcus lactis cells harboring the abortive infection gene abiD1.",
                "notes": "Bidnenko et al. connect AbiD1-family carriage to blocked phage growth."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Abi2 | 10\\.1016/j\\.mib\\.2005\\.06\\.006 | Phage abortive infection in lactococci: variations on a theme",
                "notes": "The DefenseFinder article registry maps the named Abi2 model namespace to the Chopin et al. lactococcal abortive-infection review."
              }
            ]
          },
          {
            "subject": "abi2_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "abortive_infection_system_trait",
            "description": "Abi2 system possession is an abortive-infection-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.mib.2005.06.006",
                "snippet": "Abortive infection (Abi) systems, also called phage exclusion, block phage multiplication and cause premature bacterial cell death upon phage infection.",
                "notes": "Chopin et al. place Abi systems in the abortive-infection class of phage defense."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Abi2 | 10\\.1016/j\\.mib\\.2005\\.06\\.006 | Phage abortive infection in lactococci: variations on a theme",
                "notes": "The DefenseFinder article registry maps the named Abi2 model namespace to the Chopin et al. lactococcal abortive-infection review."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "abi2-family-boundary-gap",
        "prompt": "Resolve the natural Abi2 locus breadth, phage trigger, and AbiD/F-group mapping before minting narrower Abi2 mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "The DefenseFinder Abi2 model namespace requires the Abi2__Abi_2 PF07751 profile; InterPro treats PF07751 as an Abi-like family, and UniProt maps the AbiD1 protein onto the same Pfam family. This first record leaves unresolved whether DefenseFinder Abi2 exactly corresponds to AbiD1, the broader AbiD/F group, or a different subset of Abi-like loci; it therefore avoids protein-level chemistry and records only the genome-level model namespace.",
        "attaches_to": [
          "causal_graphs#abi2_locus_restricts_phage"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-21"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-21T14:52:53Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Abi2 system as a DOI-backed GENOMICS TraitRecord under the abortive infection system parent after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v215.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000344",
    "label": "AbiA system",
    "definition": "An abortive infection system in which an organism possesses an AbiA-family locus whose copy number or expression modulates Lactococcus lactis resistance to multiple phages and that DefenseFinder represents with AbiA_large or AbiA_small model subrules.",
    "definition_source": "DOI:10.1128/aem.60.4.1129-1136.1994",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000214"
    ],
    "synonyms": [
      {
        "synonym_text": "AbiA",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      },
      {
        "synonym_text": "AbiA_large",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "AbiA_small",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "hsp",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1128/aem.60.4.1129-1136.1994"
      }
    ],
    "evidence": [
      {
        "reference": "PMID:16349225",
        "snippet": "The abiA gene (formerly hsp) encodes an abortive phage infection mechanism which inhibits phage DNA replication.",
        "notes": "Dinsmore and Klaenhammer describe abiA as the former hsp abortive-infection determinant and connect AbiA activity to inhibition of phage DNA replication."
      },
      {
        "reference": "PMID:16349225",
        "snippet": "Three abiA-containing plasmids of various copy numbers were introduced into both strains, and the recombinants were evaluated for resistance to phages c2, p2, sk1, and phi31.",
        "notes": "Dinsmore and Klaenhammer tested AbiA across two Lactococcus lactis strains and four lactococcal phages."
      },
      {
        "reference": "PMID:16349225",
        "snippet": "Altering the gene dosage or expression level of abiA significantly affects the phage resistance levels.",
        "notes": "Dinsmore and Klaenhammer show that AbiA dosage or expression modulates the strength of lactococcal phage resistance."
      },
      {
        "reference": "PMID:9661658",
        "snippet": "The abiA gene encodes an abortive bacteriophage infection mechanism that can protect Lactococcus species from infection by a variety of bacteriophages including three unrelated phage species.",
        "notes": "Dinsmore and Klaenhammer support AbiA as a broad lactococcal abortive-infection mechanism."
      },
      {
        "reference": "PMID:9661658",
        "snippet": "the leucine repeat structure is essential for conferring phage resistance against three species of lactococcal bacteriophages.",
        "notes": "Dinsmore and Klaenhammer connect residues in AbiA's leucine-repeat region to resistance against c2, sk1, and phi31."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "AbiA | 10\\.1016/j\\.mib\\.2005\\.06\\.006 | Phage abortive infection in lactococci: variations on a theme",
        "notes": "The DefenseFinder article registry maps the named AbiA model namespace to a lactococcal abortive-infection review."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "AbiA\tAbiA_large\t1\t1\tAbiA_large__AbiA_large",
        "notes": "The DefenseFinder rules table models one AbiA subrule as the single-profile AbiA_large subsystem."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "AbiA\tAbiA_small\t2\t2\tAbiA_small__AbiA_SLATT, AbiA_small__AbiA_small",
        "notes": "The DefenseFinder rules table models one AbiA subrule as a two-profile AbiA_small subsystem."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| AbiA_large__AbiA_large                           | AbiA_large__AbiA_large                           | AbiA_large             | Custom                  | 250    |",
        "notes": "The DefenseFinder HMM inventory records AbiA_large__AbiA_large under the AbiA_large model namespace."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| AbiA_small__AbiA_SLATT                           | AbiA_small__AbiA_SLATT                           | AbiA_small             | Custom                  | 20     |",
        "notes": "The DefenseFinder HMM inventory records AbiA_small__AbiA_SLATT under the AbiA_small model namespace."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| AbiA_small__AbiA_small                           | AbiA_small__AbiA_small                           | AbiA_small             | Custom                  | 300    |",
        "notes": "The DefenseFinder HMM inventory records AbiA_small__AbiA_small under the AbiA_small model namespace."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| AbiA_small__SLATT                                |                                                  | AbiA_small             | Custom                  | 40     |",
        "notes": "The DefenseFinder HMM inventory also records AbiA_small__SLATT under the AbiA_small model namespace."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1358",
        "taxon_label": "Lactococcus lactis",
        "note": "Dinsmore and Klaenhammer varied abiA copy number in Lactococcus lactis MG1363 and NCK203 and assayed resistance to phages c2, p2, sk1, and phi31.",
        "reference": "DOI:10.1128/aem.60.4.1129-1136.1994"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "abia_locus_inhibits_phage_dna_replication",
        "title": "AbiA activity inhibits lactococcal phage DNA replication",
        "description": "Conservative system-level sketch linking an AbiA-family locus to phage-DNA-replication inhibition, reduced lactococcal phage propagation, and AbiA-system possession without asserting the unresolved direct phage trigger or molecular target.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures AbiA as a named DefenseFinder abortive-infection system with AbiA_large and AbiA_small subrules. It leaves the direct phage trigger, the natural boundaries of the DefenseFinder subrules, the molecular effector activity, the DNA-replication target, and phage escape routes unresolved.",
        "nodes": [
          {
            "node_id": "abia_locus",
            "label": "AbiA locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "An AbiA-family abortive-infection locus represented by the DefenseFinder AbiA_large or AbiA_small subrules."
          },
          {
            "node_id": "phage_dna_replication_inhibition",
            "label": "phage DNA replication inhibition",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Inhibition of bacteriophage DNA replication in AbiA-containing Lactococcus lactis."
          },
          {
            "node_id": "reduced_lactococcal_phage_propagation",
            "label": "reduced lactococcal phage propagation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced propagation of lactococcal phages in cells carrying an AbiA-family abortive-infection system."
          },
          {
            "node_id": "abia_system_trait",
            "label": "AbiA system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000344",
            "description": "Possession of a genome-encoded AbiA abortive-infection phage-defense system."
          },
          {
            "node_id": "abortive_infection_system_trait",
            "label": "abortive infection system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000214",
            "description": "Possession of a genome-encoded abortive-infection phage-defense system."
          }
        ],
        "edges": [
          {
            "subject": "abia_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "phage_dna_replication_inhibition",
            "description": "AbiA activity inhibits phage DNA replication, and DefenseFinder represents AbiA with AbiA_large and AbiA_small model subrules.",
            "evidence": [
              {
                "reference": "PMID:16349225",
                "snippet": "The abiA gene (formerly hsp) encodes an abortive phage infection mechanism which inhibits phage DNA replication.",
                "notes": "Dinsmore and Klaenhammer describe abiA as the former hsp abortive-infection determinant and connect AbiA activity to inhibition of phage DNA replication."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "AbiA\tAbiA_large\t1\t1\tAbiA_large__AbiA_large",
                "notes": "The DefenseFinder rules table models one AbiA subrule as the single-profile AbiA_large subsystem."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "AbiA\tAbiA_small\t2\t2\tAbiA_small__AbiA_SLATT, AbiA_small__AbiA_small",
                "notes": "The DefenseFinder rules table models one AbiA subrule as a two-profile AbiA_small subsystem."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| AbiA_large__AbiA_large                           | AbiA_large__AbiA_large                           | AbiA_large             | Custom                  | 250    |",
                "notes": "The DefenseFinder HMM inventory records AbiA_large__AbiA_large under the AbiA_large model namespace."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| AbiA_small__AbiA_small                           | AbiA_small__AbiA_small                           | AbiA_small             | Custom                  | 300    |",
                "notes": "The DefenseFinder HMM inventory records AbiA_small__AbiA_small under the AbiA_small model namespace."
              }
            ]
          },
          {
            "subject": "abia_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "reduced_lactococcal_phage_propagation",
            "description": "Changing abiA dosage or expression changes Lactococcus lactis resistance to c2, p2, sk1, and phi31.",
            "evidence": [
              {
                "reference": "PMID:16349225",
                "snippet": "Altering the gene dosage or expression level of abiA significantly affects the phage resistance levels.",
                "notes": "Dinsmore and Klaenhammer connected abiA dosage and expression to lactococcal phage resistance level."
              }
            ]
          },
          {
            "subject": "reduced_lactococcal_phage_propagation",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "abia_system_trait",
            "description": "AbiA-mediated reduction of lactococcal phage propagation realizes the AbiA system trait.",
            "evidence": [
              {
                "reference": "PMID:9661658",
                "snippet": "can protect Lactococcus species from infection by a variety of bacteriophages including three unrelated phage species",
                "notes": "Dinsmore and Klaenhammer describe the AbiA system as protecting Lactococcus from multiple phage species."
              }
            ]
          },
          {
            "subject": "abia_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "abortive_infection_system_trait",
            "description": "AbiA system possession is an abortive-infection-system trait.",
            "evidence": [
              {
                "reference": "PMID:16349225",
                "snippet": "The abiA gene (formerly hsp) encodes an abortive phage infection mechanism which inhibits phage DNA replication.",
                "notes": "Dinsmore and Klaenhammer describe abiA as the former hsp abortive-infection determinant and connect AbiA activity to inhibition of phage DNA replication."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "AbiA | 10\\.1016/j\\.mib\\.2005\\.06\\.006 | Phage abortive infection in lactococci: variations on a theme",
                "notes": "The DefenseFinder article registry maps the named AbiA model namespace to a lactococcal abortive-infection review."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "abia-defensefinder-subrule-gap",
        "prompt": "Resolve the AbiA_large and AbiA_small system boundaries, phage trigger, direct DNA-replication target, and molecular effector output before minting narrower AbiA mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Dinsmore and Klaenhammer support AbiA as a lactococcal abortive-infection determinant whose copy number or expression changes phage resistance and whose leucine-repeat region is required for activity against multiple phage species. DefenseFinder models AbiA through AbiA_large and AbiA_small subrules, but this first system-level record leaves those subrules' natural locus boundaries, the direct phage trigger, the molecular effector output, the exact phage-DNA-replication target, and phage escape routes unresolved.",
        "evidence": [
          {
            "reference": "PMID:16349225",
            "snippet": "The abiA gene (formerly hsp) encodes an abortive phage infection mechanism which inhibits phage DNA replication.",
            "notes": "Dinsmore and Klaenhammer describe abiA as the former hsp abortive-infection determinant and connect AbiA activity to inhibition of phage DNA replication."
          },
          {
            "reference": "PMID:9661658",
            "snippet": "the leucine repeat structure is essential for conferring phage resistance against three species of lactococcal bacteriophages.",
            "notes": "Dinsmore and Klaenhammer identify an AbiA leucine-repeat region needed for phage resistance."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "snippet": "AbiA\tAbiA_large\t1\t1\tAbiA_large__AbiA_large",
            "notes": "The DefenseFinder rules table models one AbiA subrule as the single-profile AbiA_large subsystem."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "snippet": "AbiA\tAbiA_small\t2\t2\tAbiA_small__AbiA_SLATT, AbiA_small__AbiA_small",
            "notes": "The DefenseFinder rules table models one AbiA subrule as a two-profile AbiA_small subsystem."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| AbiA_large__AbiA_large                           | AbiA_large__AbiA_large                           | AbiA_large             | Custom                  | 250    |",
            "notes": "The DefenseFinder HMM inventory records AbiA_large__AbiA_large under the AbiA_large model namespace."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| AbiA_small__AbiA_small                           | AbiA_small__AbiA_small                           | AbiA_small             | Custom                  | 300    |",
            "notes": "The DefenseFinder HMM inventory records AbiA_small__AbiA_small under the AbiA_small model namespace."
          }
        ],
        "attaches_to": [
          "causal_graphs#abia_locus_inhibits_phage_dna_replication"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-21"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-21T20:16:02Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted AbiA system as a DOI-backed GENOMICS TraitRecord under the abortive infection system parent after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v221.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-21T20:44:00Z",
        "curator": "codex",
        "action": "ADDRESS_PR_REVIEW",
        "changes": "Addressed PR #1218 review issues #1219 and #1220 by aligning the v221 METPO ROBOT TSV definition with this TraitRecord and moving the AbiA dosage and expression evidence onto a direct AbiA locus edge.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000322",
    "label": "AbiAlpha system",
    "definition": "An abortive infection system in which an organism possesses an abi-alpha-family locus represented by the DefenseFinder AbiAlpha__AbiAlpha profile and exemplified by the Enterococcus faecalis V583 prophage 6 abi-alpha determinant, whose encoded DUF4393/PF14337-family activity perturbs the Idefix lytic cycle and causes premature lysis of infected Enterococcus faecalis.",
    "definition_source": "DOI:10.3390/v11010048",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000214"
    ],
    "synonyms": [
      {
        "synonym_text": "AbiAlpha",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      }
    ],
    "evidence": [
      {
        "reference": "PMID:30634666",
        "snippet": "We found that E. faecalis V583 prophage 6 was particularly efficient in resisting Idefix infection thanks to a new abortive infection (Abi) mechanism, which we designated Abi\u03b1.",
        "notes": "Lossouarn et al. named a new Abi mechanism from Enterococcus faecalis V583 prophage 6."
      },
      {
        "reference": "PMID:30634666",
        "snippet": "It corresponded to the Pfam domain family with unknown function DUF4393 and conferred a typical Abi phenotype by causing a premature lysis",
        "notes": "Lossouarn et al. connected AbiAlpha to DUF4393 and an infected-cell premature-lysis phenotype."
      },
      {
        "reference": "PMID:30634666",
        "snippet": "The abi\u03b1 gene is widespread among prophages of enterococci and other Gram-positive bacteria.",
        "notes": "Lossouarn et al. describe AbiAlpha homologs as prophage features rather than a single V583-only gene."
      },
      {
        "reference": "DOI:10.3390/v11010048",
        "snippet": "These results confirmed that ef2833 is responsible for the abortive mechanism.",
        "notes": "Lossouarn et al. experimentally connected ef2833 to the V583 prophage 6 Abi phenotype."
      },
      {
        "reference": "DOI:10.3390/v11010048",
        "snippet": "We concluded that Abi\u03b1 provokes a lysis asynchrony.",
        "notes": "Lossouarn et al. linked the AbiAlpha mechanism to altered Idefix lysis timing."
      },
      {
        "reference": "DOI:10.3390/v11010048",
        "snippet": "Upon Idefix infection, cells are dying while the Idefix lytic cycle is perturbed",
        "notes": "Lossouarn et al. summarized the system as infected-cell death with perturbed Idefix lytic-cycle progression."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "AbiAlpha | 10\\.3390/v11010048 | Enterococcus faecalis countermeasures defeat a virulent Picovirinae bacteriophage",
        "notes": "The DefenseFinder article registry maps the named AbiAlpha model namespace to the enterococcal AbiAlpha discovery paper."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| AbiAlpha__AbiAlpha                               |                                                  | AbiAlpha               | PF14337.11              | 27.1   |",
        "notes": "The DefenseFinder HMM inventory records AbiAlpha__AbiAlpha under the AbiAlpha model namespace with Pfam PF14337.11."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1351",
        "taxon_label": "Enterococcus faecalis",
        "note": "Lossouarn et al. characterized AbiAlpha from Enterococcus faecalis V583 prophage 6 and showed that it causes premature lysis during Idefix infection.",
        "reference": "DOI:10.3390/v11010048"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "abialpha_locus_causes_enterococcal_premature_lysis",
        "title": "AbiAlpha perturbs Idefix lysis in Enterococcus faecalis",
        "description": "Conservative system-level sketch linking an abi-alpha-family locus to AbiAlpha antiphage activity, Idefix lytic-cycle perturbation, premature lysis of infected Enterococcus faecalis, and AbiAlpha-system possession without asserting the direct DUF4393-family molecular target.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures AbiAlpha as a named DefenseFinder single-profile abortive-infection system whose V583 prophage 6 prototype restricts Idefix by perturbing lysis timing. It leaves the direct phage trigger, DUF4393-family molecular function, direct Idefix target, natural host range, and phage escape routes unresolved.",
        "nodes": [
          {
            "node_id": "abialpha_locus",
            "label": "abi-alpha locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "An abi-alpha-family abortive-infection locus represented by the DefenseFinder AbiAlpha__AbiAlpha profile."
          },
          {
            "node_id": "abialpha_antiphage_activity",
            "label": "AbiAlpha antiphage activity",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Enterococcal abortive-infection activity mediated by the AbiAlpha system."
          },
          {
            "node_id": "idefix_lytic_cycle_perturbation",
            "label": "Idefix lytic-cycle perturbation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Perturbation of the Idefix lytic cycle in AbiAlpha-containing Enterococcus faecalis."
          },
          {
            "node_id": "infected_cell_premature_lysis",
            "label": "infected-cell premature lysis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Premature lysis of Idefix-infected Enterococcus faecalis cells that express AbiAlpha."
          },
          {
            "node_id": "abialpha_system_trait",
            "label": "AbiAlpha system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000322",
            "description": "Possession of a genome-encoded AbiAlpha abortive-infection phage-defense system."
          },
          {
            "node_id": "abortive_infection_system_trait",
            "label": "abortive infection system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000214",
            "description": "Possession of a genome-encoded abortive-infection phage-defense system."
          }
        ],
        "edges": [
          {
            "subject": "abialpha_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "abialpha_antiphage_activity",
            "description": "The abi-alpha-family locus encoded by V583 prophage 6 is responsible for AbiAlpha antiphage activity, and DefenseFinder models AbiAlpha as a single PF14337-family HMM profile.",
            "evidence": [
              {
                "reference": "PMID:30634666",
                "snippet": "We found that E. faecalis V583 prophage 6 was particularly efficient in resisting Idefix infection thanks to a new abortive infection (Abi) mechanism, which we designated Abi\u03b1.",
                "notes": "Lossouarn et al. localized AbiAlpha to Enterococcus faecalis V583 prophage 6."
              },
              {
                "reference": "DOI:10.3390/v11010048",
                "snippet": "These results confirmed that ef2833 is responsible for the abortive mechanism.",
                "notes": "Lossouarn et al. connected ef2833 with the V583 prophage 6 Abi phenotype."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| AbiAlpha__AbiAlpha                               |                                                  | AbiAlpha               | PF14337.11              | 27.1   |",
                "notes": "The DefenseFinder HMM inventory records AbiAlpha__AbiAlpha under the AbiAlpha model namespace with Pfam PF14337.11."
              }
            ]
          },
          {
            "subject": "abialpha_antiphage_activity",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "idefix_lytic_cycle_perturbation",
            "description": "AbiAlpha activity perturbs the Idefix lytic cycle in infected Enterococcus faecalis cells.",
            "evidence": [
              {
                "reference": "DOI:10.3390/v11010048",
                "snippet": "Upon Idefix infection, cells are dying while the Idefix lytic cycle is perturbed",
                "notes": "Lossouarn et al. summarized the AbiAlpha output as death of infected cells while the Idefix lytic cycle is perturbed."
              }
            ]
          },
          {
            "subject": "abialpha_antiphage_activity",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "infected_cell_premature_lysis",
            "description": "AbiAlpha activity causes premature lysis of Idefix-infected Enterococcus faecalis.",
            "evidence": [
              {
                "reference": "PMID:30634666",
                "snippet": "conferred a typical Abi phenotype by causing a premature lysis",
                "notes": "Lossouarn et al. reported premature lysis as the AbiAlpha-infected-cell output."
              },
              {
                "reference": "DOI:10.3390/v11010048",
                "snippet": "Based on our results, we can only speculate that Abi\u03b1 interferes with lysis",
                "notes": "Lossouarn et al. framed the direct AbiAlpha lysis target as unresolved."
              }
            ]
          },
          {
            "subject": "idefix_lytic_cycle_perturbation",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "abialpha_system_trait",
            "description": "Perturbation of Idefix lytic-cycle progression contributes to the AbiAlpha system trait.",
            "evidence": [
              {
                "reference": "DOI:10.3390/v11010048",
                "snippet": "Upon Idefix infection, cells are dying while the Idefix lytic cycle is perturbed",
                "notes": "Lossouarn et al. connected AbiAlpha with Idefix lytic-cycle perturbation."
              }
            ]
          },
          {
            "subject": "infected_cell_premature_lysis",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "abialpha_system_trait",
            "description": "Premature lysis of Idefix-infected Enterococcus faecalis realizes the AbiAlpha abortive-infection trait.",
            "evidence": [
              {
                "reference": "PMID:30634666",
                "snippet": "It corresponded to the Pfam domain family with unknown function DUF4393 and conferred a typical Abi phenotype by causing a premature lysis",
                "notes": "Lossouarn et al. identified premature lysis as an AbiAlpha Abi phenotype."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "AbiAlpha | 10\\.3390/v11010048 | Enterococcus faecalis countermeasures defeat a virulent Picovirinae bacteriophage",
                "notes": "The DefenseFinder article registry maps the named AbiAlpha model namespace to the enterococcal AbiAlpha discovery paper."
              }
            ]
          },
          {
            "subject": "abialpha_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "abortive_infection_system_trait",
            "description": "AbiAlpha system possession is an abortive-infection-system trait.",
            "evidence": [
              {
                "reference": "PMID:30634666",
                "snippet": "a new abortive infection (Abi) mechanism, which we designated Abi\u03b1",
                "notes": "Lossouarn et al. place AbiAlpha in the abortive-infection class of phage defense."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "abialpha-lysis-route-gap",
        "prompt": "Resolve the AbiAlpha direct molecular target, Idefix trigger, lysis route, natural host range, and phage escape routes before minting narrower AbiAlpha mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Lossouarn et al. support AbiAlpha as a prophage-encoded Enterococcus faecalis abortive-infection system that maps to DUF4393/PF14337 and perturbs Idefix lysis timing. DefenseFinder represents AbiAlpha with a one-profile HMM inventory row but does not resolve the direct phage trigger, DUF4393-family molecular function, Idefix lysis target, natural host range, or escape routes.",
        "attaches_to": [
          "causal_graphs#abialpha_locus_causes_enterococcal_premature_lysis"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-20"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-20T23:47:17Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted AbiAlpha system as a DOI-backed GENOMICS TraitRecord under the abortive infection system parent after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v199.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-21T00:11:47Z",
        "curator": "codex",
        "action": "EDIT",
        "changes": "Addressed PR 1163 review issue 1165 by broadening the AbiAlpha class boundary from a prophage locus to an abi-alpha-family locus while keeping Enterococcus faecalis V583 prophage 6 as the characterized example.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-21T00:55:00Z",
        "curator": "codex",
        "action": "EDIT",
        "changes": "Re-copied the DefenseFinder AbiAlpha HMM registry row byte-exactly from the pinned Liste_hmm_system.md source while confirming the article-registry title casing against List_system_article.md for PR 1163 review issue 1168.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000319",
    "label": "AbiB system",
    "definition": "An abortive infection system in which an organism possesses an abiB-family locus represented by the DefenseFinder AbiB__AbiB profile and exemplified by the Lactococcus lactis IL1403 determinant whose AbiB activity blocks sensitive bIL170 phage growth and promotes rapid degradation of sensitive phage transcripts after infection.",
    "definition_source": "DOI:10.1046/j.1365-2958.1996.371896.x",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000214"
    ],
    "synonyms": [
      {
        "synonym_text": "AbiB",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1046/j.1365-2958.1996.371896.x"
      }
    ],
    "evidence": [
      {
        "reference": "PMID:8825768",
        "snippet": "The abortive infection determinant AbiB prevents growth of the sensitive phage bIL170, but not of the resistant phage bIL41, on Lactococcus lactis strain IL1403",
        "notes": "Parreira et al. place AbiB in the abortive-infection class and show that it blocks the sensitive lactococcal phage bIL170 on Lactococcus lactis IL1403."
      },
      {
        "reference": "PMID:8825768",
        "snippet": "AbiB promotes a dramatic degradation of sensitive phage transcripts, starting 10-15 min after infection",
        "notes": "Parreira et al. connect AbiB activity to rapid decay of transcripts from sensitive phages after infection."
      },
      {
        "reference": "PMID:8825768",
        "snippet": "The decay of the transcripts is the probable cause of the arrest of the sensitive phage development",
        "notes": "Parreira et al. infer that phage transcript decay causes arrest of AbiB-sensitive phage development."
      },
      {
        "reference": "PMID:8825768",
        "snippet": "Mapping of the 5' end of degradation products established that they result from endonucleolytic cleavage preferentially at U/U, A/U and U/A sites",
        "notes": "Parreira et al. map AbiB-associated phage transcript decay products to preferential endonucleolytic cleavage sites."
      },
      {
        "reference": "PMID:8825768",
        "snippet": "an early product of the sensitive phage either induces the synthesis or stimulates the activity of an RNase in an AbiB+ cell",
        "notes": "Parreira et al. leave the AbiB trigger and nuclease identity unresolved, favoring an open knowledge gap for narrower mechanism children."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "AbiB | 10\\.1016/j\\.mib\\.2005\\.06\\.006 | Phage abortive infection in lactococci: variations on a theme",
        "notes": "The DefenseFinder article registry maps the named AbiB model namespace to a lactococcal abortive-infection review."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "AbiB\tAbiB\t1\t1\tAbiB__AbiB",
        "notes": "The DefenseFinder rules table models AbiB as a one-component system requiring the AbiB__AbiB profile."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| AbiB__AbiB                                       | AbiB__AbiB                                       | AbiB                   | Custom                  | 20     |",
        "notes": "The DefenseFinder HMM inventory records AbiB__AbiB under the AbiB model namespace."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1358",
        "taxon_label": "Lactococcus lactis",
        "note": "Parreira et al. studied AbiB in Lactococcus lactis IL1403 and showed that it prevented sensitive bIL170 phage growth while promoting sensitive phage transcript decay.",
        "reference": "DOI:10.1046/j.1365-2958.1996.371896.x"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "abib_locus_degrades_sensitive_phage_transcripts",
        "title": "AbiB activity degrades sensitive lactococcal phage transcripts",
        "description": "Conservative system-level sketch linking an abiB-family locus to AbiB antiphage activity, sensitive-phage transcript degradation, sensitive-phage arrest, and abortive-infection system possession without asserting the unresolved phage trigger or nuclease effector.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures AbiB as a named DefenseFinder single-profile abortive-infection system whose IL1403 prototype restricts bIL170 phage by promoting rapid sensitive-phage transcript degradation. It leaves the direct phage trigger, AbiB molecular function, RNase effector identity, natural locus breadth, and phage escape routes unresolved.",
        "nodes": [
          {
            "node_id": "abib_locus",
            "label": "abiB locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "An abiB-family abortive-infection locus represented by the DefenseFinder AbiB__AbiB profile."
          },
          {
            "node_id": "abib_antiphage_activity",
            "label": "AbiB antiphage activity",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Abortive-infection phage resistance mediated by the AbiB system."
          },
          {
            "node_id": "sensitive_phage_transcript_degradation",
            "label": "sensitive phage transcript degradation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Rapid decay of sensitive lactococcal phage transcripts in an AbiB-containing infected host."
          },
          {
            "node_id": "sensitive_phage_development_arrest",
            "label": "sensitive phage development arrest",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Failure of AbiB-sensitive bIL170 phages to complete productive growth on Lactococcus lactis IL1403."
          },
          {
            "node_id": "abib_system_trait",
            "label": "AbiB system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000319",
            "description": "Possession of a genome-encoded AbiB abortive-infection phage-defense system."
          },
          {
            "node_id": "abortive_infection_system_trait",
            "label": "abortive infection system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000214",
            "description": "Possession of a genome-encoded abortive-infection phage-defense system."
          }
        ],
        "edges": [
          {
            "subject": "abib_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "abib_antiphage_activity",
            "description": "The abiB-family locus encodes an abortive-infection phage-resistance determinant, and DefenseFinder models AbiB as a one-profile system.",
            "evidence": [
              {
                "reference": "PMID:8825768",
                "snippet": "The abortive infection determinant AbiB prevents growth of the sensitive phage bIL170",
                "notes": "Parreira et al. identify AbiB as an abortive-infection determinant that blocks sensitive phage growth."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "AbiB\tAbiB\t1\t1\tAbiB__AbiB",
                "notes": "The DefenseFinder rules table models AbiB as a one-component system requiring the AbiB__AbiB profile."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| AbiB__AbiB                                       | AbiB__AbiB                                       | AbiB                   | Custom                  | 20     |",
                "notes": "The DefenseFinder HMM inventory records AbiB__AbiB under the AbiB model namespace."
              }
            ]
          },
          {
            "subject": "abib_antiphage_activity",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "sensitive_phage_transcript_degradation",
            "description": "AbiB activity promotes rapid degradation of sensitive phage transcripts after infection.",
            "evidence": [
              {
                "reference": "PMID:8825768",
                "snippet": "AbiB promotes a dramatic degradation of sensitive phage transcripts, starting 10-15 min after infection",
                "notes": "Parreira et al. connect AbiB to rapid decay of sensitive phage transcripts."
              }
            ]
          },
          {
            "subject": "sensitive_phage_transcript_degradation",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "sensitive_phage_development_arrest",
            "description": "Transcript decay probably arrests development of AbiB-sensitive phages.",
            "evidence": [
              {
                "reference": "PMID:8825768",
                "snippet": "The decay of the transcripts is the probable cause of the arrest of the sensitive phage development",
                "notes": "Parreira et al. interpret phage transcript decay as the likely cause of sensitive phage developmental arrest."
              }
            ]
          },
          {
            "subject": "sensitive_phage_development_arrest",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "abib_system_trait",
            "description": "Arrest of sensitive lactococcal phage development realizes the AbiB abortive-infection trait.",
            "evidence": [
              {
                "reference": "PMID:8825768",
                "snippet": "The abortive infection determinant AbiB prevents growth of the sensitive phage bIL170",
                "notes": "Parreira et al. show that AbiB prevents sensitive lactococcal phage growth."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "AbiB | 10\\.1016/j\\.mib\\.2005\\.06\\.006 | Phage abortive infection in lactococci: variations on a theme",
                "notes": "The DefenseFinder article registry maps the named AbiB model namespace to a lactococcal abortive-infection review."
              }
            ]
          },
          {
            "subject": "abib_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "abortive_infection_system_trait",
            "description": "AbiB system possession is an abortive-infection-system trait.",
            "evidence": [
              {
                "reference": "PMID:8825768",
                "snippet": "The abortive infection determinant AbiB",
                "notes": "Parreira et al. place AbiB in the abortive-infection class of phage defense."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "abib-trigger-and-rnase-gap",
        "prompt": "Resolve the AbiB phage trigger, AbiB molecular function, and RNase effector before minting narrower AbiB mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Parreira et al. support AbiB as a named lactococcal abortive-infection determinant that prevents bIL170 growth and promotes sensitive phage transcript degradation. DefenseFinder represents AbiB with a one-profile rule, but this first system-level record leaves the phage trigger, AbiB molecular function, RNase effector identity, natural locus breadth, and phage escape routes unresolved.",
        "attaches_to": [
          "causal_graphs#abib_locus_degrades_sensitive_phage_transcripts"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-20"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-20T21:21:12Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted AbiB system as a DOI-backed GENOMICS TraitRecord under the abortive infection system parent after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v196.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000320",
    "label": "AbiC system",
    "definition": "An abortive infection system in which an organism possesses an abiC-family locus represented by the DefenseFinder AbiC__AbiC profile and exemplified by the Lactococcus lactis subsp. lactis ME2 pTN20 determinant whose abiC structural gene confers Prf abortive resistance to small isometric-headed phage p2, reducing plaquing, plaque size, and burst size while killing most infected Prf-positive cells.",
    "definition_source": "DOI:10.1128/jb.174.22.7463-7469.1992",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000214"
    ],
    "synonyms": [
      {
        "synonym_text": "AbiC",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      }
    ],
    "evidence": [
      {
        "reference": "PMID:1429469",
        "snippet": "The genetic determinant for Prf (phage resistance five) was subcloned from the conjugative plasmid pTN20",
        "notes": "Durmaz et al. subcloned the Prf determinant from the Lactococcus lactis ME2 conjugative plasmid pTN20."
      },
      {
        "reference": "PMID:1429469",
        "snippet": "Prf reduces the efficiency of plaquing to 10(-2) to 10(-3) and decreases the plaque size and burst size of the small isometric-headed phage p2",
        "notes": "Durmaz et al. measured Prf-dependent reductions in p2 phage plating efficiency, plaque size, and burst size."
      },
      {
        "reference": "PMID:1429469",
        "snippet": "Prf does not prevent phage adsorption or promote restriction and modification activities",
        "notes": "Durmaz et al. distinguished Prf activity from adsorption blocking and restriction-modification activities."
      },
      {
        "reference": "PMID:1429469",
        "snippet": "90% of Prf+ cells infected with phage p2 die. Thus, phage infections in Prf+ cells are aborted.",
        "notes": "Durmaz et al. showed that most Prf-positive cells infected with phage p2 die and interpreted those p2 infections as aborted."
      },
      {
        "reference": "PMID:1429469",
        "snippet": "DNA sequencing identified a 1,056-nucleotide structural gene designated abiC",
        "notes": "Durmaz et al. identified the abiC structural gene in the Prf determinant."
      },
      {
        "reference": "PMID:1429469",
        "snippet": "Prf+ expression was obtained when abiC was subcloned into the lactococcal expression vector pMG36e",
        "notes": "Durmaz et al. showed that abiC expression is sufficient for Prf-positive activity in the pMG36e expression vector."
      },
      {
        "reference": "PMID:1429469",
        "snippet": "Unlike abiA, the action of abiC does not appear to affect DNA replication",
        "notes": "Durmaz et al. left AbiC downstream mechanism unresolved but distinguished it from AbiA-associated DNA-replication effects."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "AbiC | 10\\.1016/j\\.mib\\.2005\\.06\\.006 | Phage abortive infection in lactococci: variations on a theme",
        "notes": "The DefenseFinder article registry maps the named AbiC model namespace to a lactococcal abortive-infection review."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "AbiC\tAbiC\t1\t1\tAbiC__AbiC",
        "notes": "The DefenseFinder rules table models AbiC as a one-component system requiring the AbiC__AbiC profile."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| AbiC__AbiC                                       | AbiC__AbiC                                       | AbiC                   | Custom                  | 20     |",
        "notes": "The DefenseFinder HMM inventory records AbiC__AbiC under the AbiC model namespace."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1358",
        "taxon_label": "Lactococcus lactis",
        "note": "Durmaz et al. subcloned the Prf determinant from the Lactococcus lactis subsp. lactis ME2 conjugative plasmid pTN20 and showed that the abiC structural gene confers Prf-positive abortive resistance against small isometric-headed phage p2.",
        "reference": "DOI:10.1128/jb.174.22.7463-7469.1992"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "abic_locus_aborts_lactococcal_phage_p2_infection",
        "title": "AbiC Prf activity aborts lactococcal phage p2 infection",
        "description": "Conservative system-level sketch linking an abiC-family locus to Prf abortive-infection activity, reduced p2 phage propagation, Prf-positive infected-cell death, and AbiC-system possession without asserting an unresolved molecular target.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures AbiC as a named DefenseFinder single-profile abortive-infection system whose ME2 pTN20 prototype restricts small isometric-headed phage p2. It leaves the direct phage trigger, AbiC molecular function, cell-death route, natural locus breadth, and phage escape routes unresolved.",
        "nodes": [
          {
            "node_id": "abic_locus",
            "label": "abiC locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "An abiC-family abortive-infection locus represented by the DefenseFinder AbiC__AbiC profile."
          },
          {
            "node_id": "abic_prf_activity",
            "label": "AbiC Prf activity",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Prf abortive-infection phage resistance mediated by the abiC structural gene."
          },
          {
            "node_id": "p2_phage_propagation_reduction",
            "label": "p2 phage propagation reduction",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced small isometric-headed phage p2 plating, plaque size, and burst size in an AbiC-containing Lactococcus lactis host."
          },
          {
            "node_id": "prf_positive_infected_cell_death",
            "label": "Prf-positive infected cell death",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Death of most Prf-positive Lactococcus lactis cells after infection with phage p2."
          },
          {
            "node_id": "abic_system_trait",
            "label": "AbiC system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000320",
            "description": "Possession of a genome-encoded AbiC abortive-infection phage-defense system."
          },
          {
            "node_id": "abortive_infection_system_trait",
            "label": "abortive infection system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000214",
            "description": "Possession of a genome-encoded abortive-infection phage-defense system."
          }
        ],
        "edges": [
          {
            "subject": "abic_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "abic_prf_activity",
            "description": "The abiC-family locus encodes the Prf abortive-infection phage-resistance determinant, and DefenseFinder models AbiC as a one-profile system.",
            "evidence": [
              {
                "reference": "PMID:1429469",
                "snippet": "DNA sequencing identified a 1,056-nucleotide structural gene designated abiC",
                "notes": "Durmaz et al. identified the abiC structural gene within the Prf determinant."
              },
              {
                "reference": "PMID:1429469",
                "snippet": "Prf+ expression was obtained when abiC was subcloned into the lactococcal expression vector pMG36e",
                "notes": "Durmaz et al. showed that abiC subcloning is sufficient for Prf-positive expression."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "AbiC\tAbiC\t1\t1\tAbiC__AbiC",
                "notes": "The DefenseFinder rules table models AbiC as a one-component system requiring the AbiC__AbiC profile."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| AbiC__AbiC                                       | AbiC__AbiC                                       | AbiC                   | Custom                  | 20     |",
                "notes": "The DefenseFinder HMM inventory records AbiC__AbiC under the AbiC model namespace."
              }
            ]
          },
          {
            "subject": "abic_prf_activity",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "p2_phage_propagation_reduction",
            "description": "AbiC Prf activity reduces phage p2 plating, plaque size, and burst size.",
            "evidence": [
              {
                "reference": "PMID:1429469",
                "snippet": "Prf reduces the efficiency of plaquing to 10(-2) to 10(-3) and decreases the plaque size and burst size of the small isometric-headed phage p2",
                "notes": "Durmaz et al. measured reduced p2 plating efficiency, plaque size, and burst size in Prf-positive cells."
              }
            ]
          },
          {
            "subject": "abic_prf_activity",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "prf_positive_infected_cell_death",
            "description": "AbiC Prf-positive activity is associated with death of most phage p2-infected host cells.",
            "evidence": [
              {
                "reference": "PMID:1429469",
                "snippet": "90% of Prf+ cells infected with phage p2 die. Thus, phage infections in Prf+ cells are aborted.",
                "notes": "Durmaz et al. connect the Prf-positive phenotype to infected-cell death and aborted p2 infection."
              }
            ]
          },
          {
            "subject": "p2_phage_propagation_reduction",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "abic_system_trait",
            "description": "Reduced p2 phage propagation realizes the AbiC abortive-infection trait.",
            "evidence": [
              {
                "reference": "PMID:1429469",
                "snippet": "Prf reduces the efficiency of plaquing to 10(-2) to 10(-3) and decreases the plaque size and burst size of the small isometric-headed phage p2",
                "notes": "Durmaz et al. measured reduced p2 plating efficiency, plaque size, and burst size in Prf-positive cells."
              },
              {
                "reference": "PMID:1429469",
                "snippet": "Thus, abiC represents a second abortive system found in ME2 that acts at a different point of the phage lytic cycle.",
                "notes": "Durmaz et al. place abiC in the abortive-infection class and distinguish it from the AbiA system."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "AbiC | 10\\.1016/j\\.mib\\.2005\\.06\\.006 | Phage abortive infection in lactococci: variations on a theme",
                "notes": "The DefenseFinder article registry maps the named AbiC model namespace to a lactococcal abortive-infection review."
              }
            ]
          },
          {
            "subject": "abic_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "abortive_infection_system_trait",
            "description": "AbiC system possession is an abortive-infection-system trait.",
            "evidence": [
              {
                "reference": "PMID:1429469",
                "snippet": "Thus, abiC represents a second abortive system found in ME2",
                "notes": "Durmaz et al. place abiC in the abortive-infection class of phage defense."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "abic-trigger-and-death-route-gap",
        "prompt": "Resolve the AbiC phage trigger, AbiC molecular function, and infected-cell death route before minting narrower AbiC mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Durmaz et al. support AbiC as a named lactococcal abortive-infection determinant that reduces p2 plating, plaque size, and burst size while killing most Prf-positive infected cells. DefenseFinder represents AbiC with a one-profile rule, but this first system-level record leaves the phage trigger, AbiC molecular function, cell-death route, natural locus breadth, and phage escape routes unresolved.",
        "attaches_to": [
          "causal_graphs#abic_locus_aborts_lactococcal_phage_p2_infection"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-20"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-20T22:01:24Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted AbiC system as a DOI-backed GENOMICS TraitRecord under the abortive infection system parent after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v197.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000318",
    "label": "AbiD system",
    "definition": "An abortive infection system in which an organism possesses an abiD-family locus represented by the DefenseFinder AbiD__AbiD profile and exemplified by the Lactococcus lactis subsp. lactis KR5 pBF61 determinant whose abiD open reading frame confers an abortive phage infection phenotype with reduced plating efficiency, plaque size, and c2 phage burst size.",
    "definition_source": "DOI:10.1128/aem.61.5.2023-2026.1995",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000214"
    ],
    "synonyms": [
      {
        "synonym_text": "AbiD",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      }
    ],
    "evidence": [
      {
        "reference": "PMID:7646042",
        "snippet": "A 6.3-kb fragment from pBF61 in Lactococcus lactis subsp. lactis KR5 was cloned and found to confer an abortive phage infection (Abi+) phenotype",
        "notes": "McLandsborough et al. cloned the pBF61-derived fragment from Lactococcus lactis subsp. lactis KR5 and showed that it conferred an Abi phenotype."
      },
      {
        "reference": "PMID:7646042",
        "snippet": "exhibiting a reduction in efficiency of plating and plaque size for small isometric- and prolate-headed bacteriophages sk1 and c2, respectively, and to produce a 10-fold decrease in c2 phage burst size",
        "notes": "McLandsborough et al. measured reduced plating efficiency, plaque size, and c2 phage burst size from the pBF61 AbiD determinant."
      },
      {
        "reference": "PMID:7646042",
        "snippet": "Phage adsorption was not significantly reduced",
        "notes": "McLandsborough et al. distinguished AbiD activity from a phage-adsorption block."
      },
      {
        "reference": "PMID:7646042",
        "snippet": "An open reading frame of 1,098 bp was sequenced and designated abiD",
        "notes": "McLandsborough et al. named the abiD open reading frame within the pBF61 determinant."
      },
      {
        "reference": "PMID:7646042",
        "snippet": "Tn5 mutagenesis confirmed that abiD was required for the Abi+ phenotype",
        "notes": "McLandsborough et al. verified that the abiD open reading frame is required for the abortive-infection phenotype."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "AbiD | 10\\.1016/j\\.mib\\.2005\\.06\\.006 | Phage abortive infection in lactococci: variations on a theme",
        "notes": "The DefenseFinder article registry maps the named AbiD model namespace to a lactococcal abortive-infection review."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "AbiD\tAbiD\t1\t1\tAbiD__AbiD",
        "notes": "The DefenseFinder rules table models AbiD as a one-component system requiring the AbiD__AbiD profile."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| AbiD__AbiD                                       | AbiD__AbiD                                       | AbiD                   | Custom                  | 90     |",
        "notes": "The DefenseFinder HMM inventory records AbiD__AbiD under the AbiD model namespace."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1358",
        "taxon_label": "Lactococcus lactis",
        "note": "McLandsborough et al. cloned the pBF61 AbiD determinant from Lactococcus lactis subsp. lactis KR5 and showed that the abiD open reading frame is required for abortive-infection phage resistance.",
        "reference": "DOI:10.1128/aem.61.5.2023-2026.1995"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "abid_locus_reduces_lactococcal_phage_burst",
        "title": "AbiD activity restricts lactococcal phages",
        "description": "Conservative system-level sketch linking an abiD-family locus to AbiD antiphage activity, reduced lactococcal phage propagation, and abortive-infection system possession without asserting the unresolved molecular target.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures AbiD as a named DefenseFinder single-profile abortive-infection system whose pBF61 prototype restricts sk1 and c2 phages. It leaves the direct phage trigger, AbiD molecular function, cell-death or growth-arrest route, natural locus breadth, and phage escape routes unresolved.",
        "nodes": [
          {
            "node_id": "abid_locus",
            "label": "abiD locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "An abiD-family abortive-infection locus represented by the DefenseFinder AbiD__AbiD profile."
          },
          {
            "node_id": "abid_antiphage_activity",
            "label": "AbiD antiphage activity",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Abortive-infection phage resistance mediated by the AbiD system."
          },
          {
            "node_id": "restricted_phage_propagation",
            "label": "restricted phage propagation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced completion of lactococcal phage propagation in an AbiD-containing infected host cell."
          },
          {
            "node_id": "abid_system_trait",
            "label": "AbiD system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000318",
            "description": "Possession of a genome-encoded AbiD abortive-infection phage-defense system."
          },
          {
            "node_id": "abortive_infection_system_trait",
            "label": "abortive infection system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000214",
            "description": "Possession of a genome-encoded abortive-infection phage-defense system."
          }
        ],
        "edges": [
          {
            "subject": "abid_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "abid_antiphage_activity",
            "description": "The abiD-family locus encodes an abortive-infection phage-resistance determinant, and DefenseFinder models AbiD as a one-profile system.",
            "evidence": [
              {
                "reference": "PMID:7646042",
                "snippet": "Tn5 mutagenesis confirmed that abiD was required for the Abi+ phenotype",
                "notes": "McLandsborough et al. show that the abiD open reading frame is required for the Abi phenotype."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "AbiD\tAbiD\t1\t1\tAbiD__AbiD",
                "notes": "The DefenseFinder rules table models AbiD as a one-component system requiring the AbiD__AbiD profile."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| AbiD__AbiD                                       | AbiD__AbiD                                       | AbiD                   | Custom                  | 90     |",
                "notes": "The DefenseFinder HMM inventory records AbiD__AbiD under the AbiD model namespace."
              }
            ]
          },
          {
            "subject": "abid_antiphage_activity",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "restricted_phage_propagation",
            "description": "AbiD activity restricts tested small isometric- and prolate-headed lactococcal phages.",
            "evidence": [
              {
                "reference": "PMID:7646042",
                "snippet": "exhibiting a reduction in efficiency of plating and plaque size for small isometric- and prolate-headed bacteriophages sk1 and c2, respectively, and to produce a 10-fold decrease in c2 phage burst size",
                "notes": "McLandsborough et al. connect the AbiD determinant to reduced sk1 and c2 plating or plaque size and reduced c2 burst size."
              }
            ]
          },
          {
            "subject": "restricted_phage_propagation",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "abid_system_trait",
            "description": "Restriction of lactococcal phage propagation realizes the AbiD abortive-infection trait.",
            "evidence": [
              {
                "reference": "PMID:7646042",
                "snippet": "A 6.3-kb fragment from pBF61 in Lactococcus lactis subsp. lactis KR5 was cloned and found to confer an abortive phage infection (Abi+) phenotype",
                "notes": "McLandsborough et al. classify the pBF61 AbiD determinant phenotype as abortive phage infection."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "AbiD | 10\\.1016/j\\.mib\\.2005\\.06\\.006 | Phage abortive infection in lactococci: variations on a theme",
                "notes": "The DefenseFinder article registry maps the named AbiD model namespace to a lactococcal abortive-infection review."
              }
            ]
          },
          {
            "subject": "abid_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "abortive_infection_system_trait",
            "description": "AbiD system possession is an abortive-infection-system trait.",
            "evidence": [
              {
                "reference": "PMID:7646042",
                "snippet": "A 6.3-kb fragment from pBF61 in Lactococcus lactis subsp. lactis KR5 was cloned and found to confer an abortive phage infection (Abi+) phenotype",
                "notes": "McLandsborough et al. place AbiD in the abortive-infection class of phage defense."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "abid-trigger-and-effector-gap",
        "prompt": "Resolve the AbiD phage trigger, molecular activity, and direct arrest target before minting narrower AbiD mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "McLandsborough et al. support AbiD as a named lactococcal abortive-infection determinant whose cloned pBF61 fragment reduces sk1 plating efficiency and c2 burst size, whose abiD open reading frame is required for the Abi phenotype, and whose activity does not primarily block phage adsorption. DefenseFinder represents AbiD with a one-profile rule, but this first system-level record leaves the phage trigger, AbiD molecular function, direct host or phage target, growth-arrest or cell-death route, and phage escape routes unresolved.",
        "attaches_to": [
          "causal_graphs#abid_locus_reduces_lactococcal_phage_burst"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-20"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-20T20:30:20Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted AbiD system as a DOI-backed GENOMICS TraitRecord under the abortive infection system parent after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v195.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000227",
    "label": "AbiE system",
    "definition": "An abortive infection system in which an organism possesses an abiE bicistronic locus whose AbiEii DUF1814-family bacteriostatic toxin and AbiEi COG5340-family antitoxin constitute a non-interacting type IV toxin-antitoxin module that supports phage resistance.",
    "definition_source": "DOI:10.1093/nar/gkt1419",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000214"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1128/AEM.61.12.4321-4328.1995",
        "snippet": "Subcloning and deletion analysis of the recombinant plasmid pPG01 defined a 2.5-kb ScaIHpaI fragment as conferring phage insensitivity",
        "notes": "Garvey et al. localized the pNP40 AbiE determinant to the pPG01 subclone."
      },
      {
        "reference": "DOI:10.1128/AEM.61.12.4321-4328.1995",
        "snippet": "The mechanisms encoded by pPG01 and pCG1 in L. lactis subsp. lactis MG1614 conformed to the criteria defining abortive infection and were designated AbiE and AbiF, respectively",
        "notes": "Garvey et al. designated the pPG01-encoded pNP40 phage-insensitivity determinant as AbiE."
      },
      {
        "reference": "DOI:10.1093/nar/gkt1419",
        "snippet": "AbiE systems are encoded by bicistronic operons and function via a non-interacting (Type IV) bacteriostatic TA mechanism",
        "notes": "Dy et al. support defining AbiE as a type IV toxin-antitoxin Abi family."
      },
      {
        "reference": "DOI:10.1093/nar/gkt1419",
        "snippet": "We demonstrate that the AbiE phage resistance systems function as novel Type IV TAs and are widespread in bacteria and archaea",
        "notes": "Dy et al. support a reusable AbiE-system trait beyond the original Lactococcus pNP40 determinant."
      },
      {
        "reference": "DOI:10.1093/nar/gkt1419",
        "snippet": "AbiEii was toxic by acting as a GTP-binding NTase and was neutralized by expression of AbiEi",
        "notes": "Dy et al. connect the AbiEii nucleotidyltransferase toxin and AbiEi antitoxin to the AbiE type IV toxin-antitoxin module."
      },
      {
        "reference": "DOI:10.1093/nar/gkt1419",
        "snippet": "AbiEii was shown to specifically bind GTP, the first step in a NTase activity",
        "notes": "Dy et al. support the GTP-binding nucleotidyltransferase activity of AbiEii while leaving the exact toxic target unresolved."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1358",
        "taxon_label": "Lactococcus lactis",
        "note": "Garvey et al. cloned the pNP40 AbiE determinant and showed that the pPG01-encoded region conferred abortive-infection phage insensitivity in Lactococcus lactis subsp. lactis MG1614.",
        "reference": "DOI:10.1128/AEM.61.12.4321-4328.1995"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "abie_type_iv_ta_antiphage_activity",
        "title": "AbiE type IV toxin-antitoxin activity supports phage resistance",
        "description": "Evidence-backed process sketch linking an abiE locus to type IV toxin-antitoxin activity, AbiEii GTP-dependent toxicity, restricted phage propagation, and abortive-infection system possession.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures AbiE at the system level without asserting a universal phage activator, the exact cellular target of AbiEii, or that every COG5340-DUF1814 pair functions in abortive infection.",
        "nodes": [
          {
            "node_id": "abie_locus",
            "label": "abiE locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A bicistronic type IV toxin-antitoxin abortive-infection locus encoding AbiEi and AbiEii."
          },
          {
            "node_id": "abie_type_iv_toxin_antitoxin_activity",
            "label": "AbiE type IV toxin-antitoxin activity",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Non-interacting type IV toxin-antitoxin activity mediated by the AbiEi antitoxin and AbiEii toxin."
          },
          {
            "node_id": "abieii_ntase_toxicity",
            "label": "AbiEii GTP-binding nucleotidyltransferase toxicity",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Growth-inhibitory toxicity that depends on conserved AbiEii nucleotidyltransferase motifs and GTP binding."
          },
          {
            "node_id": "restricted_phage_propagation",
            "label": "restricted phage propagation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced completion of phage propagation in an AbiE-containing infected host cell."
          },
          {
            "node_id": "abie_system_trait",
            "label": "AbiE system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000227",
            "description": "Possession of a genome-encoded abiE type IV toxin-antitoxin abortive-infection system."
          },
          {
            "node_id": "abortive_infection_system_trait",
            "label": "abortive infection system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000214",
            "description": "Possession of a genome-encoded abortive-infection phage defense system."
          }
        ],
        "edges": [
          {
            "subject": "abie_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "abie_type_iv_toxin_antitoxin_activity",
            "description": "The abiE locus encodes the defining type IV toxin-antitoxin module.",
            "evidence": [
              {
                "reference": "DOI:10.1093/nar/gkt1419",
                "snippet": "AbiE systems are encoded by bicistronic operons and function via a non-interacting (Type IV) bacteriostatic TA mechanism",
                "notes": "Dy et al. show that AbiE is a bicistronic type IV toxin-antitoxin system."
              }
            ]
          },
          {
            "subject": "abie_type_iv_toxin_antitoxin_activity",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "abieii_ntase_toxicity",
            "description": "The AbiE type IV module couples AbiEii GTP-dependent nucleotidyltransferase toxicity to AbiEi antitoxicity.",
            "evidence": [
              {
                "reference": "DOI:10.1093/nar/gkt1419",
                "snippet": "AbiEii was toxic by acting as a GTP-binding NTase and was neutralized by expression of AbiEi",
                "notes": "Dy et al. identify AbiEii as the toxin and AbiEi as its cognate antitoxin."
              }
            ]
          },
          {
            "subject": "abie_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "restricted_phage_propagation",
            "description": "The AbiE determinant contributes to abortive phage-resistance phenotypes.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.61.12.4321-4328.1995",
                "snippet": "The mechanisms encoded by pPG01 and pCG1 in L. lactis subsp. lactis MG1614 conformed to the criteria defining abortive infection and were designated AbiE and AbiF, respectively",
                "notes": "Garvey et al. show that the pPG01 AbiE determinant produces an abortive-infection phage-insensitivity mechanism."
              }
            ]
          },
          {
            "subject": "restricted_phage_propagation",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "abie_system_trait",
            "description": "Restriction of phage propagation realizes the AbiE abortive-infection defense trait.",
            "evidence": [
              {
                "reference": "DOI:10.1093/nar/gkt1419",
                "snippet": "We demonstrate that the AbiE phage resistance systems function as novel Type IV TAs and are widespread in bacteria and archaea",
                "notes": "Dy et al. describe AbiE systems as type IV toxin-antitoxin phage-resistance systems."
              }
            ]
          },
          {
            "subject": "abie_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "abortive_infection_system_trait",
            "description": "AbiE system possession is an abortive-infection-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.61.12.4321-4328.1995",
                "snippet": "The mechanisms encoded by pPG01 and pCG1 in L. lactis subsp. lactis MG1614 conformed to the criteria defining abortive infection and were designated AbiE and AbiF, respectively",
                "notes": "Garvey et al. place AbiE in the abortive infection class of phage defense."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-15T19:46:30Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted AbiE system as a DOI-backed GENOMICS TraitRecord under the abortive infection system parent after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v104.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000504",
    "label": "AbiF system",
    "definition": "An abortive infection system in which an organism possesses a pNP40-derived abiF locus whose single complete open reading frame encodes a phage-insensitivity determinant that inhibits bacteriophage phi 712 DNA replication.",
    "definition_source": "DOI:10.1128/AEM.61.12.4321-4328.1995",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000214"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1128/AEM.61.12.4321-4328.1995",
        "snippet": "Subcloning and deletion analysis of the recombinant plasmid pCG1 defined a 3.7-kb EcoRV-XbaI fragment as encoding phage insensitivity",
        "notes": "Garvey et al. localized the pNP40 AbiF determinant to the EcoRV-XbaI fragment carried by recombinant plasmid pCG1."
      },
      {
        "reference": "DOI:10.1128/AEM.61.12.4321-4328.1995",
        "snippet": "The introduction of a frameshift mutation at the unique BglII site within this ORF disrupted the phage resistance phenotype, confirming that this ORF is responsible for the observed phage insensitivity",
        "notes": "Garvey et al. showed that the single complete ORF in the pNP40-derived EcoRV-XbaI fragment is required for AbiF-associated phage resistance."
      },
      {
        "reference": "DOI:10.1128/AEM.61.12.4321-4328.1995",
        "snippet": "The mechanisms encoded by pPG01 and pCG1 in L. lactis subsp. lactis MG1614 conformed to the criteria defining abortive infection and were designated AbiE and AbiF, respectively",
        "notes": "Garvey et al. designated the pNP40 phage-insensitivity determinant cloned on pCG1 as AbiF."
      },
      {
        "reference": "DOI:10.1128/AEM.61.12.4321-4328.1995",
        "snippet": "Analysis of the phage DNA content of phi 712-infected hosts containing AbiF demonstrated that it inhibited the rate of phage DNA replication",
        "notes": "Garvey et al. measured reduced phage phi 712 DNA-replication rate in infected hosts carrying AbiF."
      },
      {
        "reference": "DOI:10.1093/femsre/fuag009",
        "snippet": "13 are two-component systems (AbiD, AbiD1, AbiD-like, AbiE, AbiF, AbiG, AbiL, AbiQ, AbiT, AbiV, PARIS, type I CBASS, Septu",
        "notes": "The FEMS review counts AbiF among the confirmed two-component lactococcal Abi-like systems."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1358",
        "taxon_label": "Lactococcus lactis",
        "note": "Garvey et al. cloned the pNP40 AbiF determinant into pCG1 and showed that the cloned pNP40 region conferred abortive-infection phage insensitivity in Lactococcus lactis subsp. lactis MG1614.",
        "reference": "DOI:10.1128/AEM.61.12.4321-4328.1995"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "abif_locus_inhibits_lactococcal_phage_dna_replication",
        "title": "AbiF inhibits lactococcal phage DNA replication",
        "description": "Conservative system-level sketch linking a pNP40-derived abiF locus to inhibited phage phi 712 DNA replication, restricted phage propagation, and AbiF abortive-infection system possession.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures the original AbiF determinant as a pNP40-derived abortive-infection locus cloned on pCG1 that inhibits the rate of phage phi 712 DNA replication while leaving the exact AbiF protein function, phage trigger, host target, possible AbiD/AbiD1 homology-derived family boundary, natural locus breadth, and phage escape routes unresolved.",
        "nodes": [
          {
            "node_id": "abif_locus",
            "label": "abiF locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A pNP40-derived abortive-infection locus containing the open reading frame required for AbiF phage resistance."
          },
          {
            "node_id": "restricted_phage_dna_replication",
            "label": "restricted phage DNA replication",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced bacteriophage phi 712 DNA-replication rate in an infected host carrying AbiF."
          },
          {
            "node_id": "restricted_phage_propagation",
            "label": "restricted phage propagation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced completion of phage propagation in an AbiF-containing infected host cell."
          },
          {
            "node_id": "abif_system_trait",
            "label": "AbiF system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000504",
            "description": "Possession of a genome-encoded AbiF abortive-infection phage-defense system."
          },
          {
            "node_id": "abortive_infection_system_trait",
            "label": "abortive infection system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000214",
            "description": "Possession of a genome-encoded abortive-infection phage-defense system."
          }
        ],
        "edges": [
          {
            "subject": "abif_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "restricted_phage_dna_replication",
            "description": "The pNP40 AbiF open reading frame is responsible for the phage-insensitivity phenotype and inhibits the rate of phage phi 712 DNA replication.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.61.12.4321-4328.1995",
                "snippet": "The introduction of a frameshift mutation at the unique BglII site within this ORF disrupted the phage resistance phenotype, confirming that this ORF is responsible for the observed phage insensitivity",
                "notes": "Garvey et al. showed that the single complete ORF in the pNP40-derived EcoRV-XbaI fragment is required for AbiF-associated phage resistance."
              },
              {
                "reference": "DOI:10.1128/AEM.61.12.4321-4328.1995",
                "snippet": "Analysis of the phage DNA content of phi 712-infected hosts containing AbiF demonstrated that it inhibited the rate of phage DNA replication",
                "notes": "Garvey et al. measured reduced phage phi 712 DNA-replication rate in infected hosts carrying AbiF."
              }
            ]
          },
          {
            "subject": "restricted_phage_dna_replication",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "restricted_phage_propagation",
            "description": "Inhibition of phage phi 712 DNA replication contributes to AbiF phage insensitivity.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.61.12.4321-4328.1995",
                "snippet": "Subcloning and deletion analysis of the recombinant plasmid pCG1 defined a 3.7-kb EcoRV-XbaI fragment as encoding phage insensitivity",
                "notes": "Garvey et al. localized the pNP40 AbiF determinant to the EcoRV-XbaI fragment carried by recombinant plasmid pCG1."
              },
              {
                "reference": "DOI:10.1128/AEM.61.12.4321-4328.1995",
                "snippet": "Analysis of the phage DNA content of phi 712-infected hosts containing AbiF demonstrated that it inhibited the rate of phage DNA replication",
                "notes": "Garvey et al. measured reduced phage phi 712 DNA-replication rate in infected hosts carrying AbiF."
              }
            ]
          },
          {
            "subject": "restricted_phage_propagation",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "abif_system_trait",
            "description": "Restricted phage propagation realizes the AbiF abortive-infection system possession trait.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.61.12.4321-4328.1995",
                "snippet": "The mechanisms encoded by pPG01 and pCG1 in L. lactis subsp. lactis MG1614 conformed to the criteria defining abortive infection and were designated AbiE and AbiF, respectively",
                "notes": "Garvey et al. designated the pNP40 phage-insensitivity determinant cloned on pCG1 as AbiF."
              },
              {
                "reference": "DOI:10.1093/femsre/fuag009",
                "snippet": "13 are two-component systems (AbiD, AbiD1, AbiD-like, AbiE, AbiF, AbiG, AbiL, AbiQ, AbiT, AbiV, PARIS, type I CBASS, Septu",
                "notes": "The FEMS review counts AbiF among the confirmed two-component lactococcal Abi-like systems."
              }
            ]
          },
          {
            "subject": "abif_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "abortive_infection_system_trait",
            "description": "AbiF system possession is an abortive-infection-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.61.12.4321-4328.1995",
                "snippet": "The mechanisms encoded by pPG01 and pCG1 in L. lactis subsp. lactis MG1614 conformed to the criteria defining abortive infection and were designated AbiE and AbiF, respectively",
                "notes": "Garvey et al. designated the pNP40 phage-insensitivity determinant cloned on pCG1 as AbiF."
              },
              {
                "reference": "DOI:10.1093/femsre/fuag009",
                "snippet": "13 are two-component systems (AbiD, AbiD1, AbiD-like, AbiE, AbiF, AbiG, AbiL, AbiQ, AbiT, AbiV, PARIS, type I CBASS, Septu",
                "notes": "The FEMS review counts AbiF among the confirmed two-component lactococcal Abi-like systems."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "abif-function-and-host-breadth-gap",
        "prompt": "Resolve the exact AbiF protein function, phage trigger, host target, AbiD/AbiD1 homology-derived family boundary, and natural locus breadth before minting narrower AbiF mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Garvey et al. support AbiF as a pNP40 determinant cloned on pCG1 that conforms to abortive-infection criteria, depends on a single complete open reading frame, and inhibits the rate of phage phi 712 DNA replication; the FEMS review retains AbiF among confirmed two-component lactococcal Abi-like systems. This first system-level record therefore leaves the direct phage trigger, exact AbiF molecular activity, relevant host target, AbiD/AbiD1-related family boundary, natural locus breadth, cell-death or growth-arrest route, and phage escape routes unresolved.",
        "evidence": [
          {
            "reference": "DOI:10.1128/AEM.61.12.4321-4328.1995",
            "snippet": "The introduction of a frameshift mutation at the unique BglII site within this ORF disrupted the phage resistance phenotype, confirming that this ORF is responsible for the observed phage insensitivity",
            "notes": "Garvey et al. showed that the single complete ORF in the pNP40-derived EcoRV-XbaI fragment is required for AbiF-associated phage resistance."
          },
          {
            "reference": "DOI:10.1128/AEM.61.12.4321-4328.1995",
            "snippet": "Analysis of the phage DNA content of phi 712-infected hosts containing AbiF demonstrated that it inhibited the rate of phage DNA replication",
            "notes": "Garvey et al. measured reduced phage phi 712 DNA-replication rate in infected hosts carrying AbiF."
          },
          {
            "reference": "DOI:10.1093/femsre/fuag009",
            "snippet": "13 are two-component systems (AbiD, AbiD1, AbiD-like, AbiE, AbiF, AbiG, AbiL, AbiQ, AbiT, AbiV, PARIS, type I CBASS, Septu",
            "notes": "The FEMS review counts AbiF among the confirmed two-component lactococcal Abi-like systems."
          }
        ],
        "attaches_to": [
          "causal_graphs#abif_locus_inhibits_lactococcal_phage_dna_replication"
        ],
        "posed_by": "codex",
        "posed_date": "2026-10-01"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-01T01:32:44Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted AbiF system as a DOI-backed GENOMICS TraitRecord under the abortive infection system parent after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v381.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-01T03:14:00Z",
        "curator": "codex",
        "action": "ADDRESS_ABIF_REVIEW_FINDING",
        "changes": "Addressed adversarial review issue #1505 by clarifying that pNP40 is the AbiF determinant source context and that pCG1 is the recombinant plasmid clone used in the Garvey et al. subcloning experiment.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000306",
    "label": "AbiG system",
    "definition": "An abortive infection system in which an organism possesses a two-gene abiG locus with abiGi and abiGii open reading frames, exemplified by the Lactococcus lactis subsp. cremoris UC653 plasmid pCI750 locus that restricts lactococcal phages without blocking phage DNA replication and is represented by the DefenseFinder AbiG__AbiGi and AbiG__AbiGii profiles.",
    "definition_source": "DOI:10.1128/aem.62.9.3075-3082.1996",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000214"
    ],
    "synonyms": [
      {
        "synonym_text": "AbiG",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1128/aem.62.9.3075-3082.1996"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1128/aem.62.9.3075-3082.1996",
        "snippet": "AbiG is an abortive infection (Abi) mechanism encoded by the conjugative plasmid pCI750 originally isolated from Lactococcus lactis subsp. cremoris UC653",
        "notes": "O'Connor et al. identify AbiG as an abortive-infection mechanism encoded by the UC653 pCI750 plasmid."
      },
      {
        "reference": "DOI:10.1128/aem.62.9.3075-3082.1996",
        "snippet": "Insensitivity conferred by this Abi manifested itself as complete resistance to phi 712 (936 phage species) with only partial resistance to phi c2 (c2 species)",
        "notes": "O'Connor et al. show that AbiG restricts tested lactococcal phages with species-dependent strength."
      },
      {
        "reference": "DOI:10.1128/aem.62.9.3075-3082.1996",
        "snippet": "The smallest subclone of pCI750 which expressed the Abi phenotype contained a 3.5-kb insert which encoded two potential open reading frames",
        "notes": "O'Connor et al. localize AbiG activity to a pCI750 subclone carrying two predicted coding sequences."
      },
      {
        "reference": "DOI:10.1128/aem.62.9.3075-3082.1996",
        "snippet": "abiGi (750 bp) and abiGii (1,194 bp) were separated by 2 bp and appeared to share a single promoter upstream of abiGi",
        "notes": "O'Connor et al. support abiGi and abiGii as the paired open reading frames of the AbiG locus."
      },
      {
        "reference": "DOI:10.1128/aem.62.9.3075-3082.1996",
        "snippet": "The mechanism did not inhibit phage DNA replication",
        "notes": "O'Connor et al. rule out phage DNA replication as the blocked step in the original AbiG characterization."
      },
      {
        "reference": "DOI:10.1128/aem.65.1.330-335.1999",
        "snippet": "The abortive infection system AbiG is encoded by the lactococcal plasmid pCI750",
        "notes": "The follow-up O'Connor et al. study reiterates AbiG as a pCI750-encoded lactococcal abortive-infection system."
      },
      {
        "reference": "DOI:10.1128/aem.65.1.330-335.1999",
        "snippet": "The abiG locus (consisting of two genes, abiGi and abiGii) was examined by Northern blot analysis, revealing two transcripts of approximately 2.8 and 1.5 kb which were homologous to the two gene-specific probes",
        "notes": "O'Connor et al. confirm the abiGi/abiGii two-gene locus at the transcript level."
      },
      {
        "reference": "DOI:10.1128/aem.65.1.330-335.1999",
        "snippet": "Examination of phage sk1 RNA synthesis demonstrated that both the subcloned AbiG and, to a greater extent, pCI750 inhibited this process",
        "notes": "O'Connor et al. connect the AbiG subclone to inhibited sk1 phage RNA synthesis."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "AbiG | 10\\.1016/j\\.mib\\.2005\\.06\\.006 | Phage abortive infection in lactococci: variations on a theme",
        "notes": "The DefenseFinder article registry maps the named AbiG model namespace to a lactococcal abortive-infection review."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "AbiG\tAbiG\t2\t2\tAbiG__AbiGi, AbiG__AbiGii",
        "notes": "The DefenseFinder rules table models AbiG as a two-component system requiring the AbiG__AbiGi and AbiG__AbiGii profiles."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| AbiG__AbiGi                                      | AbiG__AbiGi                                      | AbiG                   | Custom                  | 20     |",
        "notes": "The DefenseFinder HMM inventory records AbiG__AbiGi under the AbiG model namespace."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| AbiG__AbiGii                                     | AbiG__AbiGii                                     | AbiG                   | Custom                  | 20     |",
        "notes": "The DefenseFinder HMM inventory records AbiG__AbiGii under the AbiG model namespace."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1358",
        "taxon_label": "Lactococcus lactis",
        "note": "O'Connor et al. characterized AbiG from conjugative plasmid pCI750, originally isolated from Lactococcus lactis subsp. cremoris UC653, and localized the abortive-infection phenotype to the abiGi/abiGii locus.",
        "reference": "DOI:10.1128/aem.62.9.3075-3082.1996"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "abig_inhibits_lactococcal_phage_rna_synthesis",
        "title": "AbiG inhibits lactococcal phage RNA synthesis",
        "description": "Conservative system-level sketch linking an abiGi/abiGii locus to AbiG antiphage activity, inhibited phage RNA synthesis, restricted lactococcal phage propagation, and abortive-infection system possession without asserting AbiG's unresolved primary target.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures AbiG as a named DefenseFinder two-profile abortive-infection system whose pCI750 prototype restricts phi 712, partially restricts phi c2, and inhibits phage sk1 and late c2 RNA synthesis while leaving the phage trigger, AbiGi and AbiGii molecular functions, cellular target, growth-arrest or cell-death route, and phage escape routes unresolved.",
        "nodes": [
          {
            "node_id": "abig_locus",
            "label": "abiG locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A two-gene abiGi/abiGii abortive-infection locus represented by the DefenseFinder AbiG rule."
          },
          {
            "node_id": "abig_antiphage_activity",
            "label": "AbiG antiphage activity",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Abortive-infection phage resistance mediated by the AbiG system."
          },
          {
            "node_id": "phage_rna_synthesis",
            "label": "phage RNA synthesis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Synthesis of sensitive lactococcal phage RNA during infection."
          },
          {
            "node_id": "restricted_phage_propagation",
            "label": "restricted phage propagation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced completion of lactococcal phage propagation in an AbiG-containing infected host cell."
          },
          {
            "node_id": "abig_system_trait",
            "label": "AbiG system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000306",
            "description": "Possession of a genome-encoded AbiG abortive-infection phage-defense system."
          },
          {
            "node_id": "abortive_infection_system_trait",
            "label": "abortive infection system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000214",
            "description": "Possession of a genome-encoded abortive-infection phage-defense system."
          }
        ],
        "edges": [
          {
            "subject": "abig_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "abig_antiphage_activity",
            "description": "The pCI750 abiG locus carries abiGi and abiGii open reading frames, and DefenseFinder models AbiG as a two-profile system requiring both AbiG components.",
            "evidence": [
              {
                "reference": "DOI:10.1128/aem.62.9.3075-3082.1996",
                "snippet": "The smallest subclone of pCI750 which expressed the Abi phenotype contained a 3.5-kb insert which encoded two potential open reading frames",
                "notes": "O'Connor et al. localize the AbiG phenotype to a two-ORF pCI750 subclone."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "AbiG\tAbiG\t2\t2\tAbiG__AbiGi, AbiG__AbiGii",
                "notes": "The DefenseFinder rules table models AbiG as a two-component system requiring the AbiG__AbiGi and AbiG__AbiGii profiles."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| AbiG__AbiGi                                      | AbiG__AbiGi                                      | AbiG                   | Custom                  | 20     |",
                "notes": "The DefenseFinder HMM inventory records AbiG__AbiGi under the AbiG model namespace."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| AbiG__AbiGii                                     | AbiG__AbiGii                                     | AbiG                   | Custom                  | 20     |",
                "notes": "The DefenseFinder HMM inventory records AbiG__AbiGii under the AbiG model namespace."
              }
            ]
          },
          {
            "subject": "abig_antiphage_activity",
            "predicate": "mitigates",
            "predicate_id": "METPO:2007407",
            "object": "phage_rna_synthesis",
            "description": "AbiG antiphage activity inhibits RNA synthesis by tested sensitive lactococcal phages.",
            "evidence": [
              {
                "reference": "DOI:10.1128/aem.65.1.330-335.1999",
                "snippet": "Examination of phage sk1 RNA synthesis demonstrated that both the subcloned AbiG and, to a greater extent, pCI750 inhibited this process",
                "notes": "O'Connor et al. show that the AbiG subclone inhibits phage sk1 RNA synthesis."
              }
            ]
          },
          {
            "subject": "abig_antiphage_activity",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "restricted_phage_propagation",
            "description": "AbiG activity restricts propagation by phi 712 and partially restricts phi c2.",
            "evidence": [
              {
                "reference": "DOI:10.1128/aem.62.9.3075-3082.1996",
                "snippet": "Insensitivity conferred by this Abi manifested itself as complete resistance to phi 712 (936 phage species) with only partial resistance to phi c2 (c2 species)",
                "notes": "O'Connor et al. measure complete or partial resistance from the AbiG mechanism for tested lactococcal phages."
              }
            ]
          },
          {
            "subject": "restricted_phage_propagation",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "abig_system_trait",
            "description": "Restriction of lactococcal phage propagation realizes the AbiG abortive-infection trait.",
            "evidence": [
              {
                "reference": "DOI:10.1128/aem.62.9.3075-3082.1996",
                "snippet": "AbiG is an abortive infection (Abi) mechanism encoded by the conjugative plasmid pCI750",
                "notes": "O'Connor et al. classify AbiG as a pCI750 abortive-infection mechanism."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "AbiG | 10\\.1016/j\\.mib\\.2005\\.06\\.006 | Phage abortive infection in lactococci: variations on a theme",
                "notes": "The DefenseFinder article registry maps the named AbiG model namespace to a lactococcal abortive-infection review."
              }
            ]
          },
          {
            "subject": "abig_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "abortive_infection_system_trait",
            "description": "AbiG system possession is an abortive-infection-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1128/aem.65.1.330-335.1999",
                "snippet": "The abortive infection system AbiG is encoded by the lactococcal plasmid pCI750",
                "notes": "O'Connor et al. explicitly place AbiG in the abortive-infection class of phage defense."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "abig-primary-target-gap",
        "prompt": "Resolve the AbiG phage trigger, AbiGi and AbiGii molecular functions, and primary arrest target before minting narrower AbiG mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "O'Connor et al. support AbiG as a named lactococcal abortive-infection system encoded by two adjacent pCI750 open reading frames, and DefenseFinder represents AbiG with a two-profile rule. The 1999 transcription study connects AbiG to inhibited phage sk1 and late c2 RNA synthesis, but it explicitly leaves unresolved whether transcription is the system's primary target or a secondary effect.",
        "evidence": [
          {
            "reference": "DOI:10.1128/aem.65.1.330-335.1999",
            "snippet": "AbiG inhibits phage sk1 and late c2 RNA synthesis; however, whether this process of transcription is the primary target of the system or a secondary effect remains to be determined",
            "notes": "O'Connor et al. identify phage RNA-synthesis inhibition as a downstream AbiG effect while leaving the direct target unresolved."
          }
        ],
        "attaches_to": [
          "causal_graphs#abig_inhibits_lactococcal_phage_rna_synthesis"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-20"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-20T09:16:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted AbiG system as a DOI-backed GENOMICS TraitRecord under the abortive infection system parent after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v183.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-20T10:19:00Z",
        "curator": "codex",
        "action": "STANDARDIZED_CAUSAL_NODE_LABEL",
        "changes": "Reused the existing restricted phage propagation causal-node label after PR review found that the lactococcal-specific label duplicated the taxon-neutral GENOMICS phage-defense node.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000304",
    "label": "AbiH system",
    "definition": "An abortive infection system in which an organism possesses an abiH-family locus represented by the DefenseFinder AbiH__AbiH profile and exemplified by the Lactococcus lactis S94 abiH gene that encodes lactococcal phage abortive-infection resistance.",
    "definition_source": "DOI:10.1111/j.1574-6968.1996.tb08446.x",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000214"
    ],
    "synonyms": [
      {
        "synonym_text": "AbiH",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1111/j.1574-6968.1996.tb08446.x",
        "snippet": "A gene which encodes resistance by abortive infection (Abi+) to bacteriophage was cloned from Lactococcus lactis ssp. lactis biovar. diacetylactis S94",
        "notes": "Prevots et al. cloned abiH from Lactococcus lactis S94 and connected the locus to bacteriophage resistance by abortive infection."
      },
      {
        "reference": "DOI:10.1111/j.1574-6968.1996.tb08446.x",
        "snippet": "This gene was found to confer a reduction in efficiency of plating and plaque size for prolate-headed bacteriophage phi 53 (group I of homology) and total resistance to the small isometric-headed bacteriophage phi 59 (group III of homology)",
        "notes": "Prevots et al. show that the cloned abiH gene restricts multiple lactococcal phages with distinct plating phenotypes."
      },
      {
        "reference": "DOI:10.1111/j.1574-6968.1996.tb08446.x",
        "snippet": "The cloned gene is predicted to encode a polypeptide of 346 amino acid residues with a deduced molecular mass of 41 455 Da",
        "notes": "Prevots et al. support abiH as an encoded phage-resistance protein rather than a noncoding marker."
      },
      {
        "reference": "DOI:10.1111/j.1574-6968.1996.tb08446.x",
        "snippet": "No homology with any previously described genes was found",
        "notes": "Prevots et al. leave the molecular class and effector mechanism of AbiH unresolved."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "AbiH | 10\\.1111/j\\.1574-6968\\.1996\\.tb08446\\.x | Cloning and sequencing of the novel abortive infection gene abiH of Lactococcus lactis ssp\\. lactis biovar\\. diacetylactis S94",
        "notes": "The DefenseFinder article registry maps the named AbiH system to the Prevots et al. abiH cloning paper."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "AbiH\tAbiH\t1\t1\tAbiH__AbiH",
        "notes": "The DefenseFinder rules table models AbiH as a one-component system requiring the AbiH__AbiH profile."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| AbiH__AbiH                                       | AbiH__AbiH                                       | AbiH                   | PF14253.7               | 30.9   |",
        "notes": "The DefenseFinder HMM inventory records the PF14253.7-backed AbiH__AbiH profile under the AbiH model namespace."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1358",
        "taxon_label": "Lactococcus lactis",
        "note": "Prevots et al. cloned abiH from Lactococcus lactis ssp. lactis biovar. diacetylactis S94 and showed that the cloned locus confers abortive-infection phage resistance.",
        "reference": "DOI:10.1111/j.1574-6968.1996.tb08446.x"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "abih_locus_restricts_lactococcal_phages",
        "title": "AbiH activity restricts lactococcal phages",
        "description": "Conservative system-level sketch linking an abiH-family locus to AbiH antiphage activity, reduced lactococcal phage plaque formation, restricted phage propagation, and abortive-infection system possession without asserting the unresolved phage trigger or molecular target.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures AbiH as a named DefenseFinder single-profile abortive-infection system whose prototype abiH gene reduces or abolishes plating by tested lactococcal phages while leaving the direct phage trigger, AbiH molecular function, host or phage target, arrest route, and phage escape routes unresolved.",
        "nodes": [
          {
            "node_id": "abih_locus",
            "label": "abiH locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "An abiH-family abortive-infection locus represented by the DefenseFinder AbiH__AbiH profile."
          },
          {
            "node_id": "abih_antiphage_activity",
            "label": "AbiH antiphage activity",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Abortive-infection phage resistance mediated by the AbiH protein."
          },
          {
            "node_id": "lactococcal_phage_plaque_formation",
            "label": "lactococcal phage plaque formation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Formation of plaques by AbiH-sensitive phi 53 and phi 59 phages on a Lactococcus lactis indicator lawn."
          },
          {
            "node_id": "restricted_phage_propagation",
            "label": "restricted phage propagation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced completion of AbiH-sensitive lactococcal phage propagation in an AbiH-containing infected host cell."
          },
          {
            "node_id": "abih_system_trait",
            "label": "AbiH system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000304",
            "description": "Possession of a genome-encoded AbiH abortive-infection phage-defense system."
          },
          {
            "node_id": "abortive_infection_system_trait",
            "label": "abortive infection system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000214",
            "description": "Possession of a genome-encoded abortive-infection phage-defense system."
          }
        ],
        "edges": [
          {
            "subject": "abih_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "abih_antiphage_activity",
            "description": "The abiH-family locus encodes an abortive-infection phage-resistance determinant, and DefenseFinder models AbiH as a one-profile system.",
            "evidence": [
              {
                "reference": "DOI:10.1111/j.1574-6968.1996.tb08446.x",
                "snippet": "A gene which encodes resistance by abortive infection (Abi+) to bacteriophage",
                "notes": "Prevots et al. identify the cloned abiH gene as the abortive-infection phage-resistance determinant."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "AbiH\tAbiH\t1\t1\tAbiH__AbiH",
                "notes": "The DefenseFinder rules table models AbiH as a one-component system requiring the AbiH__AbiH profile."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| AbiH__AbiH                                       | AbiH__AbiH                                       | AbiH                   | PF14253.7               | 30.9   |",
                "notes": "The DefenseFinder HMM inventory records the PF14253.7-backed AbiH__AbiH profile under the AbiH model namespace."
              }
            ]
          },
          {
            "subject": "abih_antiphage_activity",
            "predicate": "mitigates",
            "predicate_id": "METPO:2007407",
            "object": "lactococcal_phage_plaque_formation",
            "description": "AbiH activity reduces phi 53 plating and plaque size and confers total resistance to phi 59.",
            "evidence": [
              {
                "reference": "DOI:10.1111/j.1574-6968.1996.tb08446.x",
                "snippet": "This gene was found to confer a reduction in efficiency of plating and plaque size for prolate-headed bacteriophage phi 53 (group I of homology) and total resistance to the small isometric-headed bacteriophage phi 59",
                "notes": "Prevots et al. directly measure reduced or abolished plaque formation for tested lactococcal phages."
              }
            ]
          },
          {
            "subject": "abih_antiphage_activity",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "restricted_phage_propagation",
            "description": "Reduced plating and total phi 59 resistance indicate that AbiH limits completion of tested lactococcal phage infection.",
            "evidence": [
              {
                "reference": "DOI:10.1111/j.1574-6968.1996.tb08446.x",
                "snippet": "reduction in efficiency of plating and plaque size for prolate-headed bacteriophage phi 53 (group I of homology) and total resistance to the small isometric-headed bacteriophage phi 59 (group III of homology)",
                "notes": "Prevots et al. support both a partial phi 53 block and total phi 59 resistance from the cloned abiH gene."
              }
            ]
          },
          {
            "subject": "restricted_phage_propagation",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "abih_system_trait",
            "description": "Restriction of lactococcal phage propagation realizes the AbiH abortive-infection trait.",
            "evidence": [
              {
                "reference": "DOI:10.1111/j.1574-6968.1996.tb08446.x",
                "snippet": "encodes resistance by abortive infection (Abi+) to bacteriophage",
                "notes": "Prevots et al. classify the cloned abiH resistance determinant as abortive infection."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "AbiH | 10\\.1111/j\\.1574-6968\\.1996\\.tb08446\\.x | Cloning and sequencing of the novel abortive infection gene abiH of Lactococcus lactis ssp\\. lactis biovar\\. diacetylactis S94",
                "notes": "The DefenseFinder article registry maps the named AbiH system to the Prevots et al. abiH cloning paper."
              }
            ]
          },
          {
            "subject": "abih_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "abortive_infection_system_trait",
            "description": "AbiH system possession is an abortive-infection-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1111/j.1574-6968.1996.tb08446.x",
                "snippet": "encodes resistance by abortive infection (Abi+) to bacteriophage",
                "notes": "Prevots et al. support AbiH as an abortive-infection system."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "abih-trigger-and-effector-gap",
        "prompt": "Resolve the AbiH phage trigger, molecular activity, and direct arrest target before minting narrower AbiH mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Prevots et al. support AbiH as a named lactococcal abortive-infection gene whose cloned S94 locus reduces or blocks plating by tested lactococcal phages, and DefenseFinder represents AbiH with a one-profile rule. This system-level record leaves the phage trigger, AbiH molecular function, direct cellular target, growth-arrest or cell-death route, and phage escape routes unresolved.",
        "attaches_to": [
          "causal_graphs#abih_locus_restricts_lactococcal_phages"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-20"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-20T08:12:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted AbiH system as a DOI-backed GENOMICS TraitRecord under the abortive infection system parent after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v181.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000316",
    "label": "AbiI system",
    "definition": "An abortive infection system in which an organism possesses an abiI-family locus represented by the DefenseFinder AbiI__AbiI profile and exemplified by the Lactococcus lactis M138 pND852 locus whose single abiI open reading frame restricts lactococcal phage propagation by an abortive-infection mechanism.",
    "definition_source": "DOI:10.1016/S0168-1656(97)01692-1",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000214"
    ],
    "synonyms": [
      {
        "synonym_text": "AbiI",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      }
    ],
    "evidence": [
      {
        "reference": "PMID:9195753",
        "snippet": "Plasmid pND852 (56 kb) encodes nisin resistance and was isolated from Lactococcus lactis ssp lactis (L. lactis) M138 by conjugation to L. lactis LM0230",
        "notes": "Su et al. identified plasmid pND852 from Lactococcus lactis M138 as the source of the abiI-associated phage resistance locus."
      },
      {
        "reference": "PMID:9195753",
        "snippet": "It conferred strong resistance to the isometric-headed phage phi 712 and partial resistance to the prolate-headed phage phi c2",
        "notes": "Su et al. show that pND852 confers resistance to tested lactococcal phages."
      },
      {
        "reference": "PMID:9195753",
        "snippet": "A 2.6 kb HpaII fragment encoding phage resistance was cloned into the streptococcal/Bacillus hybrid vector pGB301 to generate pND817",
        "notes": "Su et al. localized phage resistance from pND852 to the 2.6 kb fragment in pND817."
      },
      {
        "reference": "PMID:9195753",
        "snippet": "The mechanism of phage resistance encoded by pND817 involved abortive infection",
        "notes": "Su et al. classified the pND817 phage-resistance mechanism as abortive infection."
      },
      {
        "reference": "PMID:9195753",
        "snippet": "reduction in burst size from 166 to 6 at 30 degrees C and from 160 to 90 at 37 degrees C",
        "notes": "Su et al. measured reduced phage burst size from the cloned pND817 abortive-infection locus."
      },
      {
        "reference": "PMID:9195753",
        "snippet": "DNA sequencing revealed that the abortive infection was encoded by a single open reading frame (ORF), designated abiI, encoding a 332 amino acid protein",
        "notes": "Su et al. support a single abiI open reading frame as the coding sequence for the pND817 abortive-infection locus."
      },
      {
        "reference": "PMID:9195753",
        "snippet": "Frame shift mutation at the unique EcoRI site within the ORF resulted in loss of the Abi+ phenotype",
        "notes": "Su et al. verified that the abiI open reading frame is required for the phage-resistance phenotype."
      },
      {
        "reference": "PMID:9195753",
        "snippet": "Neither abiI nor the predicted product showed significant homology to any existing sequence in the GenBank database",
        "notes": "Su et al. did not resolve AbiI molecular activity or homology during the original characterization."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "AbiI | 10\\.1016/j\\.mib\\.2005\\.06\\.006 | Phage abortive infection in lactococci: variations on a theme",
        "notes": "The DefenseFinder article registry maps the named AbiI model namespace to a lactococcal abortive-infection review."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "AbiI\tAbiI\t1\t1\tAbiI__AbiI",
        "notes": "The DefenseFinder rules table models AbiI as a one-component system requiring the AbiI__AbiI profile."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| AbiI__AbiI                                       | AbiI__AbiI                                       | AbiI                   | Custom                  | 20     |",
        "notes": "The DefenseFinder HMM inventory records AbiI__AbiI under the AbiI model namespace."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1358",
        "taxon_label": "Lactococcus lactis",
        "note": "Su et al. cloned the abiI determinant from Lactococcus lactis M138 plasmid pND852 into pND817 and showed abortive-infection phage resistance from a single abiI open reading frame.",
        "reference": "DOI:10.1016/S0168-1656(97)01692-1"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "abii_locus_reduces_lactococcal_phage_burst",
        "title": "AbiI activity restricts lactococcal phage burst size",
        "description": "Conservative system-level sketch linking an abiI-family locus to AbiI antiphage activity, reduced lactococcal phage burst size, restricted phage propagation, and abortive-infection system possession without asserting the unresolved molecular target.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures AbiI as a named DefenseFinder single-profile abortive-infection system whose pND852 prototype restricts phi 712 and partially restricts phi c2. It leaves the direct phage trigger, AbiI molecular function, cell-death or packaging route, natural locus breadth, and phage escape routes unresolved.",
        "nodes": [
          {
            "node_id": "abii_locus",
            "label": "abiI locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "An abiI-family abortive-infection locus represented by the DefenseFinder AbiI__AbiI profile."
          },
          {
            "node_id": "abii_antiphage_activity",
            "label": "AbiI antiphage activity",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Abortive-infection phage resistance mediated by the AbiI system."
          },
          {
            "node_id": "restricted_phage_propagation",
            "label": "restricted phage propagation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced completion of lactococcal phage propagation in an AbiI-containing infected host cell."
          },
          {
            "node_id": "abii_system_trait",
            "label": "AbiI system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000316",
            "description": "Possession of a genome-encoded AbiI abortive-infection phage-defense system."
          },
          {
            "node_id": "abortive_infection_system_trait",
            "label": "abortive infection system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000214",
            "description": "Possession of a genome-encoded abortive-infection phage-defense system."
          }
        ],
        "edges": [
          {
            "subject": "abii_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "abii_antiphage_activity",
            "description": "The abiI-family locus encodes an abortive-infection phage-resistance determinant, and DefenseFinder models AbiI as a one-profile system.",
            "evidence": [
              {
                "reference": "PMID:9195753",
                "snippet": "DNA sequencing revealed that the abortive infection was encoded by a single open reading frame (ORF), designated abiI, encoding a 332 amino acid protein",
                "notes": "Su et al. identify abiI as the single ORF encoding the pND817 abortive-infection phenotype."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "AbiI\tAbiI\t1\t1\tAbiI__AbiI",
                "notes": "The DefenseFinder rules table models AbiI as a one-component system requiring the AbiI__AbiI profile."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| AbiI__AbiI                                       | AbiI__AbiI                                       | AbiI                   | Custom                  | 20     |",
                "notes": "The DefenseFinder HMM inventory records AbiI__AbiI under the AbiI model namespace."
              }
            ]
          },
          {
            "subject": "abii_antiphage_activity",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "restricted_phage_propagation",
            "description": "AbiI activity strongly restricts phi 712 and partially restricts phi c2 propagation in Lactococcus lactis.",
            "evidence": [
              {
                "reference": "PMID:9195753",
                "snippet": "It conferred strong resistance to the isometric-headed phage phi 712 and partial resistance to the prolate-headed phage phi c2",
                "notes": "Su et al. measured strong or partial resistance from the AbiI-containing pND852 plasmid for two tested lactococcal phages."
              },
              {
                "reference": "PMID:9195753",
                "snippet": "reduction in burst size from 166 to 6 at 30 degrees C and from 160 to 90 at 37 degrees C",
                "notes": "Su et al. connect pND817 to sharply reduced phi 712 burst size."
              }
            ]
          },
          {
            "subject": "restricted_phage_propagation",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "abii_system_trait",
            "description": "Restriction of lactococcal phage propagation realizes the AbiI abortive-infection trait.",
            "evidence": [
              {
                "reference": "PMID:9195753",
                "snippet": "The mechanism of phage resistance encoded by pND817 involved abortive infection",
                "notes": "Su et al. classify the pND817 mechanism as abortive infection."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "AbiI | 10\\.1016/j\\.mib\\.2005\\.06\\.006 | Phage abortive infection in lactococci: variations on a theme",
                "notes": "The DefenseFinder article registry maps the named AbiI model namespace to a lactococcal abortive-infection review."
              }
            ]
          },
          {
            "subject": "abii_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "abortive_infection_system_trait",
            "description": "AbiI system possession is an abortive-infection-system trait.",
            "evidence": [
              {
                "reference": "PMID:9195753",
                "snippet": "The mechanism of phage resistance encoded by pND817 involved abortive infection",
                "notes": "Su et al. place AbiI in the abortive infection class of phage defense."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "abii-trigger-and-effector-gap",
        "prompt": "Resolve the AbiI phage trigger, molecular activity, and direct arrest target before minting narrower AbiI mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Su et al. support AbiI as a named lactococcal abortive-infection locus whose cloned pND852 fragment reduces phi 712 burst size and whose abiI frameshift abolishes phage resistance. DefenseFinder represents AbiI with a one-profile rule, but this first system-level record leaves the phage trigger, AbiI molecular function, direct host or phage target, growth-arrest or cell-death route, and phage escape routes unresolved.",
        "evidence": [
          {
            "reference": "PMID:9195753",
            "snippet": "Neither abiI nor the predicted product showed significant homology to any existing sequence in the GenBank database",
            "notes": "Su et al. report no informative sequence homology for AbiI in the original characterization."
          }
        ],
        "attaches_to": [
          "causal_graphs#abii_locus_reduces_lactococcal_phage_burst"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-20"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-20T18:33:34Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted AbiI system as a DOI-backed GENOMICS TraitRecord under the abortive infection system parent after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v193.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000339",
    "label": "AbiJ system",
    "definition": "An abortive infection system in which an organism possesses an AbiJ-family locus represented by the DefenseFinder AbiJ model namespace and mandatory AbiJ__AbiJ profile.",
    "definition_source": "DOI:10.1111/j.1574-6968.1997.tb10185.x",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000214"
    ],
    "synonyms": [
      {
        "synonym_text": "AbiJ",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      },
      {
        "synonym_text": "AbiJ__AbiJ",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "abi-859",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1093/femsre/fuag009"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1111/j.1574-6968.1997.tb10185.x",
        "snippet": "A novel plasmid-encoded phage abortive infection system from Lactococcus lactis biovar. diacetylactis",
        "notes": "Europe PMC metadata verifies the Deng et al. 1997 AbiJ primary paper title and PMID:8997719; the DOI landing page was Cloudflare-blocked and Europe PMC exposed no abstract or full text, so this record cites Deng et al. for the primary AbiJ identity and uses later accessible sources for snippet-backed system details."
      },
      {
        "reference": "DOI:10.1093/femsre/fuag009",
        "snippet": "Experimentally confirmed lactococcal Abi-like systems, as well as information on their antiphage activity range",
        "notes": "The FEMS review frames Table 1 as a curated set of experimentally confirmed lactococcal Abi-like systems."
      },
      {
        "reference": "DOI:10.1093/femsre/fuag009",
        "snippet": "AbiJ (Also abi-859)",
        "notes": "The 2026 FEMS review lists AbiJ, also named abi-859, among the experimentally confirmed lactococcal Abi-like systems."
      },
      {
        "reference": "DOI:10.1073/pnas.2426508122",
        "snippet": "we isolated 66 phage escape mutants which had become insensitive to 13 distinct, plasmid-encoded lactococcal phage resistance systems (i.e. Rhea, Kamadhenu, Rugutis, Audmula, PARIS, type II CBASS, Septu, AbiA, AbiB, AbiD/F, AbiG, AbiJ, AbiP)",
        "notes": "Mosterd et al. include AbiJ in a set of distinct plasmid-encoded lactococcal phage-resistance systems used for escape-mutant isolation."
      },
      {
        "reference": "DOI:10.1093/femsre/fuag009",
        "snippet": "AbiA escape mutants also circumvent AbiJ, which was not observed for other combinations",
        "notes": "The FEMS review summarizes Mosterd et al.'s escape-mutant evidence linking AbiA escape mutations to AbiJ bypass while not yet identifying AbiJ's direct molecular trigger."
      },
      {
        "reference": "DOI:10.1093/femsre/fuag009",
        "snippet": "Although no particular mechanistic information is currently available for AbiJ",
        "notes": "The FEMS review explicitly keeps AbiJ mechanism unresolved; this record therefore avoids protein-level chemistry and TA-system mechanism claims."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "AbiJ | 10\\.1016/j\\.mib\\.2005\\.06\\.006 | Phage abortive infection in lactococci: variations on a theme",
        "notes": "The DefenseFinder article registry maps the named AbiJ model namespace to the Chopin et al. lactococcal abortive-infection review."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "AbiJ\tAbiJ\t1\t1\tAbiJ__AbiJ\t\t\t",
        "notes": "The DefenseFinder rules table models AbiJ as a one-component system requiring the AbiJ__AbiJ profile."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| AbiJ__AbiJ                                       | AbiJ__AbiJ                                       | AbiJ                   | Custom                  | 20     |",
        "notes": "The DefenseFinder HMM inventory records AbiJ__AbiJ under the AbiJ model namespace."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "abij_locus_restricts_lactococcal_phage",
        "title": "AbiJ loci confer abortive-infection phage defense",
        "description": "Conservative system-level sketch linking possession of a DefenseFinder AbiJ locus to restricted bacteriophage propagation without asserting the unresolved phage trigger, molecular activity, or arrest route.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures AbiJ as a named single-profile lactococcal abortive-infection system with a DefenseFinder AbiJ__AbiJ HMM profile while leaving its direct phage trigger, AbiJ molecular function, exact relationship to AbiA escape routes, natural locus breadth, and cell-arrest or death route unresolved.",
        "nodes": [
          {
            "node_id": "abij_locus",
            "label": "AbiJ locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "An AbiJ-family abortive-infection locus represented by the DefenseFinder AbiJ__AbiJ profile."
          },
          {
            "node_id": "restricted_phage_propagation",
            "label": "restricted phage propagation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced bacteriophage propagation in cells carrying an AbiJ-family abortive-infection system."
          },
          {
            "node_id": "abij_system_trait",
            "label": "AbiJ system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000339",
            "description": "Possession of a genome-encoded AbiJ abortive-infection phage-defense system."
          },
          {
            "node_id": "abortive_infection_system_trait",
            "label": "abortive infection system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000214",
            "description": "Possession of a genome-encoded abortive-infection phage-defense system."
          }
        ],
        "edges": [
          {
            "subject": "abij_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "restricted_phage_propagation",
            "description": "The DefenseFinder AbiJ namespace is modeled as a one-profile AbiJ__AbiJ system, and AbiJ is a plasmid-encoded lactococcal phage-resistance system.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "AbiJ\tAbiJ\t1\t1\tAbiJ__AbiJ\t\t\t",
                "notes": "The DefenseFinder rules table models AbiJ as a one-component system requiring the AbiJ__AbiJ profile."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| AbiJ__AbiJ                                       | AbiJ__AbiJ                                       | AbiJ                   | Custom                  | 20     |",
                "notes": "The DefenseFinder HMM inventory records AbiJ__AbiJ under the AbiJ model namespace."
              },
              {
                "reference": "DOI:10.1073/pnas.2426508122",
                "snippet": "we isolated 66 phage escape mutants which had become insensitive to 13 distinct, plasmid-encoded lactococcal phage resistance systems (i.e. Rhea, Kamadhenu, Rugutis, Audmula, PARIS, type II CBASS, Septu, AbiA, AbiB, AbiD/F, AbiG, AbiJ, AbiP)",
                "notes": "Mosterd et al. include AbiJ in a set of distinct plasmid-encoded lactococcal phage-resistance systems used for escape-mutant isolation."
              }
            ]
          },
          {
            "subject": "restricted_phage_propagation",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "abij_system_trait",
            "description": "Restriction of phage propagation realizes the AbiJ abortive-infection system possession trait.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuag009",
                "snippet": "AbiJ (Also abi-859)",
                "notes": "The 2026 FEMS review lists AbiJ, also named abi-859, among the experimentally confirmed lactococcal Abi-like systems."
              },
              {
                "reference": "DOI:10.1073/pnas.2426508122",
                "snippet": "we isolated 66 phage escape mutants which had become insensitive to 13 distinct, plasmid-encoded lactococcal phage resistance systems (i.e. Rhea, Kamadhenu, Rugutis, Audmula, PARIS, type II CBASS, Septu, AbiA, AbiB, AbiD/F, AbiG, AbiJ, AbiP)",
                "notes": "Mosterd et al. include AbiJ in a set of distinct plasmid-encoded lactococcal phage-resistance systems used for escape-mutant isolation."
              }
            ]
          },
          {
            "subject": "abij_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "abortive_infection_system_trait",
            "description": "AbiJ system possession is an abortive-infection-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuag009",
                "snippet": "AbiJ (Also abi-859)",
                "notes": "The 2026 FEMS review lists AbiJ, also named abi-859, among the experimentally confirmed lactococcal Abi-like systems."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "AbiJ | 10\\.1016/j\\.mib\\.2005\\.06\\.006 | Phage abortive infection in lactococci: variations on a theme",
                "notes": "The DefenseFinder article registry maps the named AbiJ model namespace to the Chopin et al. lactococcal abortive-infection review."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "abij-trigger-and-effector-gap",
        "prompt": "Resolve the AbiJ phage trigger, molecular activity, and exact AbiA escape-mutant overlap before minting narrower AbiJ mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Deng et al. support AbiJ as a lactococcal plasmid-encoded abortive-infection system, and DefenseFinder represents AbiJ with a one-profile rule. Mosterd et al. show that AbiJ escape behavior overlaps with AbiA escape mutants, but the FEMS review notes that AbiJ still lacks a resolved mechanism. This first system-level record therefore leaves AbiJ's direct phage trigger, molecular effector activity, natural locus breadth, exact HEPN-domain interpretation, growth-arrest or cell-death route, and phage escape routes unresolved.",
        "evidence": [
          {
            "reference": "DOI:10.1093/femsre/fuag009",
            "snippet": "While AbiB and AbiJ show only weak predictions (HHpred hits for HEPN domain containing-proteins with E-values > 0.1) or lack identifiable functional domains based on InterPro and HHpred",
            "notes": "The FEMS review notes that AbiJ HEPN-domain evidence remains weak in sequence/domain-prediction analyses."
          },
          {
            "reference": "DOI:10.1093/femsre/fuag009",
            "snippet": "Although no particular mechanistic information is currently available for AbiJ",
            "notes": "The FEMS review leaves AbiJ's mechanism unresolved."
          }
        ],
        "attaches_to": [
          "causal_graphs#abij_locus_restricts_lactococcal_phage"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-21"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-21T16:24:09Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted AbiJ system as a DOI-backed GENOMICS TraitRecord under the abortive infection system parent after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v216.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-21T16:48:47Z",
        "curator": "codex",
        "action": "FIX_EVIDENCE_SNIPPET",
        "changes": "Replaced the AbiJ subclass-edge FEMS table-heading evidence with the AbiJ-specific table row after PR 1208 review issue 1209 found that the original snippet did not itself mention AbiJ.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000229",
    "label": "AbiK system",
    "definition": "An abortive infection system in which an organism possesses an abiK locus encoding a reverse-transcriptase-related polymerase that uses conserved RT motifs for phage resistance and restricts 936/P335 lactococcal phage propagation.",
    "definition_source": "DOI:10.1128/aem.63.4.1274-1283.1997",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000214"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1128/aem.63.4.1274-1283.1997",
        "snippet": "The phage resistance mechanism encoded on pSRQ800 is a temperature-sensitive abortive infection system (Abi)",
        "notes": "Emond et al. localized a lactococcal plasmid-encoded abortive-infection mechanism that strongly resists 936 and P335 phages."
      },
      {
        "reference": "DOI:10.1128/aem.63.4.1274-1283.1997",
        "snippet": "orf1 (renamed abiK) coded for a predicted protein of 599 amino acids (AbiK)",
        "notes": "Emond et al. identified abiK as the open reading frame needed for the pSRQ800 Abi phenotype."
      },
      {
        "reference": "DOI:10.1128/aem.63.4.1274-1283.1997",
        "snippet": "No phage DNA replication nor phage structural protein production was detected in infected AbiK+ L. lactis cells",
        "notes": "Emond et al. support an AbiK-associated block at or before DNA replication for the ul36 lactococcal phage."
      },
      {
        "reference": "DOI:10.1099/00221287-146-2-445",
        "snippet": "Only immature forms (concatemeric and circular DNA) of phage p2 DNA were found, indicating that the presence of AbiK prevented phage DNA maturation",
        "notes": "Boucher et al. show that AbiK can block later DNA maturation rather than DNA replication itself, depending on the lactococcal phage tested."
      },
      {
        "reference": "DOI:10.1128/JB.187.11.3721-3730.2005",
        "snippet": "the antiphage activity depends on the level of expression of the abiK gene and on the presence of a reverse transcriptase (RT) motif in AbiK",
        "notes": "Fortier et al. connect AbiK phage resistance to conserved reverse-transcriptase motifs in the AbiK protein."
      },
      {
        "reference": "DOI:10.1128/JB.187.11.3721-3730.2005",
        "snippet": "Conservative mutations in key positions resulted in the complete loss of the resistance phenotype",
        "notes": "Fortier et al. mutated AbiK RT motifs and showed that key positions are necessary for AbiK-mediated resistance."
      },
      {
        "reference": "DOI:10.1093/nar/gkr397",
        "snippet": "AbiK does not exhibit the properties expected for an RT, but polymerizes long DNAs of \u2018random\u2019 sequence, analogous to a terminal transferase",
        "notes": "Wang et al. biochemically characterized AbiK as an RT-related polymerase with template-independent DNA polymerization activity."
      },
      {
        "reference": "DOI:10.1093/nar/gkr397",
        "snippet": "Mutagenesis experiments indicate that the polymerase activity resides in the RT motifs and is essential for phage resistance in vivo",
        "notes": "Wang et al. support AbiK RT-motif polymerase activity as an essential contributor to phage resistance."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1358",
        "taxon_label": "Lactococcus lactis",
        "note": "Emond et al. isolated the pSRQ800 abiK determinant from Lactococcus lactis subsp. lactis W1 and showed that it confers abortive infection against 936 and P335 lactococcal phages when introduced into phage-sensitive Lactococcus lactis strains.",
        "reference": "DOI:10.1128/aem.63.4.1274-1283.1997"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "abik_rt_polymerase_antiphage_activity",
        "title": "AbiK RT-related polymerase activity restricts lactococcal phages",
        "description": "Evidence-backed process sketch linking an abiK locus to AbiK RT-related polymerase activity, phage DNA replication or maturation blocks, restricted phage propagation, and abortive-infection system possession.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures AbiK at the system level without asserting the natural AbiK DNA primer or product, the endogenous polymerase substrate, or one universal DNA-stage block for all sensitive phages.",
        "nodes": [
          {
            "node_id": "abik_locus",
            "label": "abiK locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "An abortive-infection locus encoding the AbiK RT-related polymerase."
          },
          {
            "node_id": "abik_rt_polymerase_activity",
            "label": "AbiK RT-related polymerase activity",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "Reverse-transcriptase-motif-dependent DNA polymerase activity of AbiK."
          },
          {
            "node_id": "interrupted_phage_dna_replication_or_maturation",
            "label": "interrupted phage DNA replication or maturation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Phage-specific interruption of DNA replication or DNA maturation in AbiK-containing infected Lactococcus cells."
          },
          {
            "node_id": "restricted_phage_propagation",
            "label": "restricted phage propagation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced completion of 936 or P335 phage propagation in an AbiK-containing infected host cell."
          },
          {
            "node_id": "abik_system_trait",
            "label": "AbiK system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000229",
            "description": "Possession of a genome-encoded AbiK RT-related abortive-infection system."
          },
          {
            "node_id": "abortive_infection_system_trait",
            "label": "abortive infection system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000214",
            "description": "Possession of a genome-encoded abortive-infection phage defense system."
          }
        ],
        "edges": [
          {
            "subject": "abik_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "abik_rt_polymerase_activity",
            "description": "The abiK locus encodes an AbiK protein whose conserved RT motifs support antiphage activity.",
            "evidence": [
              {
                "reference": "DOI:10.1128/JB.187.11.3721-3730.2005",
                "snippet": "the antiphage activity depends on the level of expression of the abiK gene and on the presence of a reverse transcriptase (RT) motif in AbiK",
                "notes": "Fortier et al. connect abiK expression and AbiK RT motifs to the phage-resistance phenotype."
              }
            ]
          },
          {
            "subject": "abik_rt_polymerase_activity",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "restricted_phage_propagation",
            "description": "AbiK RT-motif polymerase activity is required for the in vivo phage-resistance phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1093/nar/gkr397",
                "snippet": "Mutagenesis experiments indicate that the polymerase activity resides in the RT motifs and is essential for phage resistance in vivo",
                "notes": "Wang et al. showed that AbiK RT motifs carry the in vitro polymerase activity and are essential for phage resistance in vivo."
              }
            ]
          },
          {
            "subject": "abik_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "interrupted_phage_dna_replication_or_maturation",
            "description": "The AbiK determinant produces a phage-specific block at DNA replication or DNA maturation.",
            "evidence": [
              {
                "reference": "DOI:10.1099/00221287-146-2-445",
                "snippet": "Only immature forms (concatemeric and circular DNA) of phage p2 DNA were found, indicating that the presence of AbiK prevented phage DNA maturation",
                "notes": "Boucher et al. found immature DNA forms for phage p2 and compared that phenotype with the earlier ul36 DNA-replication block."
              }
            ]
          },
          {
            "subject": "interrupted_phage_dna_replication_or_maturation",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "restricted_phage_propagation",
            "description": "Interrupting DNA replication or maturation limits completion of the phage lytic cycle.",
            "evidence": [
              {
                "reference": "DOI:10.1128/aem.63.4.1274-1283.1997",
                "snippet": "No phage DNA replication nor phage structural protein production was detected in infected AbiK+ L. lactis cells",
                "notes": "Emond et al. show that AbiK prevents ul36 DNA replication and structural-protein production in infected Lactococcus lactis."
              }
            ]
          },
          {
            "subject": "restricted_phage_propagation",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "abik_system_trait",
            "description": "Restriction of 936/P335 phage propagation realizes the AbiK abortive-infection defense trait.",
            "evidence": [
              {
                "reference": "DOI:10.1128/aem.63.4.1274-1283.1997",
                "snippet": "The phage resistance mechanism encoded on pSRQ800 is a temperature-sensitive abortive infection system (Abi)",
                "notes": "Emond et al. define the pSRQ800 AbiK determinant as an abortive-infection phage resistance system."
              }
            ]
          },
          {
            "subject": "abik_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "abortive_infection_system_trait",
            "description": "AbiK system possession is an abortive-infection-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1093/nar/gkr397",
                "snippet": "AbiK, which is required for abortive phage infection in the Gram-positive bacterium Lactococcus lactis",
                "notes": "Wang et al. place AbiK in the abortive infection class of phage defense."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-15T21:30:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted AbiK system as a DOI-backed GENOMICS TraitRecord under the abortive infection system parent after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v106.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000340",
    "label": "AbiL system",
    "definition": "An abortive infection system in which an organism possesses a two-component AbiL-family locus represented by DefenseFinder as mandatory AbiL__AbiLi and AbiL__AbiLii profiles.",
    "definition_source": "DOI:10.1016/S0168-1656(98)00175-8",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000214"
    ],
    "synonyms": [
      {
        "synonym_text": "AbiL",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      },
      {
        "synonym_text": "AbiL__AbiLi",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "AbiL__AbiLii",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1016/S0168-1656(98)00175-8",
        "snippet": "Genetic organization and functional analysis of a novel phage abortive infection system, AbiL, from Lactococcus lactis",
        "notes": "Crossref metadata verifies the Deng et al. 1999 AbiL primary paper title and DOI."
      },
      {
        "reference": "DOI:10.1093/femsre/fuag009",
        "snippet": "13 are two-component systems (AbiD, AbiD1, AbiD-like, AbiE, AbiF, AbiG, AbiL, AbiQ, AbiT, AbiV, PARIS, type I CBASS, Septu",
        "notes": "The FEMS review counts AbiL among the confirmed two-component lactococcal Abi-like systems."
      },
      {
        "reference": "DOI:10.1093/femsre/fuag009",
        "snippet": "AbiL has been included among systems such as PARIS, which feature an ABC ATPase and a TOPRIM nuclease",
        "notes": "The FEMS review places AbiL among predicted ATPase-plus-TOPRIM systems but does not resolve the AbiLi and AbiLii molecular activities."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "AbiL | 10\\.1016/j\\.mib\\.2005\\.06\\.006 | Phage abortive infection in lactococci: variations on a theme",
        "notes": "The DefenseFinder article registry maps the named AbiL model namespace to the Chopin et al. lactococcal abortive-infection review."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "AbiL\tAbiL\t2\t2\tAbiL__AbiLi, AbiL__AbiLii\t\t\t",
        "notes": "The DefenseFinder rules table models AbiL as a two-component system requiring the AbiL__AbiLi and AbiL__AbiLii profiles."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| AbiL__AbiLi                                      | AbiL__AbiLi                                      | AbiL                   | Custom                  | 20     |",
        "notes": "The DefenseFinder HMM inventory records AbiL__AbiLi under the AbiL model namespace."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| AbiL__AbiLii                                     | AbiL__AbiLii                                     | AbiL                   | Custom                  | 20     |",
        "notes": "The DefenseFinder HMM inventory records AbiL__AbiLii under the AbiL model namespace."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "abil_locus_restricts_lactococcal_phage",
        "title": "AbiL loci confer abortive-infection phage defense",
        "description": "Conservative system-level sketch linking possession of a DefenseFinder AbiL locus to restricted bacteriophage propagation without asserting the unresolved phage trigger, AbiLi or AbiLii molecular activity, or AbiL-to-PARIS mechanistic correspondence.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures AbiL as a named lactococcal abortive-infection system with DefenseFinder AbiL__AbiLi and AbiL__AbiLii HMM profiles while leaving its direct phage trigger, the exact AbiLi and AbiLii activities, the relationship between the mandatory and suffixed HMM rows, and the similarity of its route to PARIS unresolved.",
        "nodes": [
          {
            "node_id": "abil_locus",
            "label": "AbiL locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "An AbiL-family abortive-infection locus represented by the DefenseFinder AbiL__AbiLi and AbiL__AbiLii profiles."
          },
          {
            "node_id": "restricted_phage_propagation",
            "label": "restricted phage propagation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced bacteriophage propagation in cells carrying an AbiL-family abortive-infection system."
          },
          {
            "node_id": "abil_system_trait",
            "label": "AbiL system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000340",
            "description": "Possession of a genome-encoded AbiL abortive-infection phage-defense system."
          },
          {
            "node_id": "abortive_infection_system_trait",
            "label": "abortive infection system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000214",
            "description": "Possession of a genome-encoded abortive-infection phage-defense system."
          }
        ],
        "edges": [
          {
            "subject": "abil_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "restricted_phage_propagation",
            "description": "The DefenseFinder AbiL namespace is modeled as a two-profile AbiL__AbiLi plus AbiL__AbiLii system, and AbiL is a confirmed lactococcal Abi-like system.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "AbiL\tAbiL\t2\t2\tAbiL__AbiLi, AbiL__AbiLii\t\t\t",
                "notes": "The DefenseFinder rules table models AbiL as a two-component system requiring the AbiL__AbiLi and AbiL__AbiLii profiles."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| AbiL__AbiLi                                      | AbiL__AbiLi                                      | AbiL                   | Custom                  | 20     |",
                "notes": "The DefenseFinder HMM inventory records AbiL__AbiLi under the AbiL model namespace."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| AbiL__AbiLii                                     | AbiL__AbiLii                                     | AbiL                   | Custom                  | 20     |",
                "notes": "The DefenseFinder HMM inventory records AbiL__AbiLii under the AbiL model namespace."
              },
              {
                "reference": "DOI:10.1093/femsre/fuag009",
                "snippet": "13 are two-component systems (AbiD, AbiD1, AbiD-like, AbiE, AbiF, AbiG, AbiL, AbiQ, AbiT, AbiV, PARIS, type I CBASS, Septu",
                "notes": "The FEMS review counts AbiL among the confirmed two-component lactococcal Abi-like systems."
              }
            ]
          },
          {
            "subject": "restricted_phage_propagation",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "abil_system_trait",
            "description": "Restriction of phage propagation realizes the AbiL abortive-infection system possession trait.",
            "evidence": [
              {
                "reference": "DOI:10.1016/S0168-1656(98)00175-8",
                "snippet": "Genetic organization and functional analysis of a novel phage abortive infection system, AbiL, from Lactococcus lactis",
                "notes": "Crossref metadata verifies the Deng et al. 1999 AbiL primary paper title and DOI."
              },
              {
                "reference": "DOI:10.1093/femsre/fuag009",
                "snippet": "13 are two-component systems (AbiD, AbiD1, AbiD-like, AbiE, AbiF, AbiG, AbiL, AbiQ, AbiT, AbiV, PARIS, type I CBASS, Septu",
                "notes": "The FEMS review counts AbiL among the confirmed two-component lactococcal Abi-like systems."
              }
            ]
          },
          {
            "subject": "abil_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "abortive_infection_system_trait",
            "description": "AbiL system possession is an abortive-infection-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1016/S0168-1656(98)00175-8",
                "snippet": "Genetic organization and functional analysis of a novel phage abortive infection system, AbiL, from Lactococcus lactis",
                "notes": "Crossref metadata verifies the Deng et al. 1999 AbiL primary paper title and DOI."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "AbiL | 10\\.1016/j\\.mib\\.2005\\.06\\.006 | Phage abortive infection in lactococci: variations on a theme",
                "notes": "The DefenseFinder article registry maps the named AbiL model namespace to the Chopin et al. lactococcal abortive-infection review."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "abil-trigger-and-effector-gap",
        "prompt": "Resolve the AbiL phage trigger, AbiLi and AbiLii activities, AbiLi2 and AbiLii2 HMM row relationships, and ATPase-plus-TOPRIM mechanism before minting narrower AbiL mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Deng et al. support AbiL as a lactococcal phage abortive infection system, the FEMS review lists AbiL among confirmed two-component lactococcal Abi-like systems, and DefenseFinder represents AbiL with mandatory AbiL__AbiLi and AbiL__AbiLii profiles. The same pinned HMM inventory also contains AbiL__AbiLi2 and AbiL__AbiLii2 rows that are not in the pinned two-profile rule, and the FEMS review summarizes unresolved ATPase and TOPRIM predictions. This first system-level record therefore leaves the direct phage trigger, exact AbiLi and AbiLii molecular activities, accessory-model interpretation, AbiL-to-PARIS similarity, growth-arrest or cell-death route, and phage escape routes unresolved.",
        "evidence": [
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| AbiL__AbiLi2                                     | AbiL__AbiLi2                                     | AbiL                   | Custom                  | 20     |",
            "notes": "The DefenseFinder HMM inventory also records AbiL__AbiLi2 under the AbiL model namespace, but this profile is not listed in the two mandatory profiles in the pinned AbiL rule."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| AbiL__AbiLii2                                    | AbiL__AbiLii2                                    | AbiL                   | Custom                  | 20     |",
            "notes": "The DefenseFinder HMM inventory also records AbiL__AbiLii2 under the AbiL model namespace, but this profile is not listed in the two mandatory profiles in the pinned AbiL rule."
          },
          {
            "reference": "DOI:10.1093/femsre/fuag009",
            "snippet": "AbiL has been included among systems such as PARIS, which feature an ABC ATPase and a TOPRIM nuclease",
            "notes": "The FEMS review places AbiL among predicted ATPase-plus-TOPRIM systems but does not resolve the AbiLi and AbiLii molecular activities."
          },
          {
            "reference": "DOI:10.1093/femsre/fuag009",
            "snippet": "No significant sequence similarity was found between the second components of AbiL and PARIS",
            "notes": "The AbiL-to-PARIS comparison remains indirect for the second component, so this record does not copy the PARIS mechanism onto AbiL."
          }
        ],
        "attaches_to": [
          "causal_graphs#abil_locus_restricts_lactococcal_phage"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-21"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-21T17:17:22Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted AbiL system as a DOI-backed GENOMICS TraitRecord under the abortive infection system parent after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v217.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000341",
    "label": "AbiN system",
    "definition": "An abortive infection system in which an organism possesses a single-component AbiN-family locus represented by DefenseFinder as a mandatory AbiN__AbiN profile.",
    "definition_source": "DOI:10.1111/j.1574-6968.1998.tb12879.x",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000214"
    ],
    "synonyms": [
      {
        "synonym_text": "AbiN",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      },
      {
        "synonym_text": "AbiN__AbiN",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1111/j.1574-6968.1998.tb12879.x",
        "snippet": "Nucleotide sequence and analysis of the new chromosomal abortive infection gene abiN of Lactococcus lactis subsp. cremoris S114",
        "notes": "Crossref metadata verifies the Prevots et al. 1998 AbiN primary paper title and DOI."
      },
      {
        "reference": "DOI:10.1093/femsre/fuag009",
        "snippet": "the majority (18 systems) are each represented by single protein-coding genes",
        "notes": "The FEMS review lists AbiN among the 34 confirmed lactococcal Abi-like systems in Table 1 and omits AbiN from the named two- and three-component exception lists."
      },
      {
        "reference": "DOI:10.1093/femsre/fuag009",
        "snippet": "The structure of AbiN is predicted with high confidence by AlphaFold and resembles a putative periplasmic ligand-binding sensor domain protein",
        "notes": "The FEMS review summarizes a predicted AbiN sensor-like fold but does not establish a molecular trigger or effector activity."
      },
      {
        "reference": "DOI:10.1093/femsre/fuag009",
        "snippet": "further research is needed to clarify the mechanism of AbiN and if it functions via abortive infection",
        "notes": "The FEMS review explicitly leaves the AbiN mechanism unresolved, so this record does not mint a more specific sensor or effector trait."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "AbiN | 10\\.1016/j\\.mib\\.2005\\.06\\.006 | Phage abortive infection in lactococci: variations on a theme",
        "notes": "The DefenseFinder article registry maps the named AbiN model namespace to the Chopin et al. lactococcal abortive-infection review."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "AbiN\tAbiN\t1\t1\tAbiN__AbiN\t\t\t",
        "notes": "The DefenseFinder rules table models AbiN as a one-component system requiring the AbiN__AbiN profile."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| AbiN__AbiN                                       | AbiN__AbiN                                       | AbiN                   | Custom                  | 20     |",
        "notes": "The DefenseFinder HMM inventory records AbiN__AbiN under the AbiN model namespace."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "abin_locus_restricts_lactococcal_phage",
        "title": "AbiN loci confer abortive-infection phage defense",
        "description": "Conservative system-level sketch linking possession of a DefenseFinder AbiN locus to restricted bacteriophage propagation without asserting the unresolved phage trigger, predicted ligand-binding sensor role, or molecular effector activity.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures AbiN as a named single-profile lactococcal Abi-like system with the DefenseFinder AbiN__AbiN HMM while leaving its direct phage trigger, ligand-sensor interpretation, exact molecular activity, phage-cycle step, phage escape routes, and growth-arrest or cell-death route unresolved.",
        "nodes": [
          {
            "node_id": "abin_locus",
            "label": "AbiN locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "An AbiN-family abortive-infection locus represented by the DefenseFinder AbiN__AbiN profile."
          },
          {
            "node_id": "restricted_phage_propagation",
            "label": "restricted phage propagation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced bacteriophage propagation in cells carrying an AbiN-family abortive-infection system."
          },
          {
            "node_id": "abin_system_trait",
            "label": "AbiN system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000341",
            "description": "Possession of a genome-encoded AbiN abortive-infection phage-defense system."
          },
          {
            "node_id": "abortive_infection_system_trait",
            "label": "abortive infection system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000214",
            "description": "Possession of a genome-encoded abortive-infection phage-defense system."
          }
        ],
        "edges": [
          {
            "subject": "abin_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "restricted_phage_propagation",
            "description": "The DefenseFinder AbiN namespace is modeled as a one-profile AbiN__AbiN system.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "AbiN\tAbiN\t1\t1\tAbiN__AbiN\t\t\t",
                "notes": "The DefenseFinder rules table models AbiN as a one-component system requiring the AbiN__AbiN profile."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| AbiN__AbiN                                       | AbiN__AbiN                                       | AbiN                   | Custom                  | 20     |",
                "notes": "The DefenseFinder HMM inventory records AbiN__AbiN under the AbiN model namespace."
              }
            ]
          },
          {
            "subject": "restricted_phage_propagation",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "abin_system_trait",
            "description": "Restriction of phage propagation realizes the AbiN abortive-infection system possession trait.",
            "evidence": [
              {
                "reference": "DOI:10.1111/j.1574-6968.1998.tb12879.x",
                "snippet": "Nucleotide sequence and analysis of the new chromosomal abortive infection gene abiN of Lactococcus lactis subsp. cremoris S114",
                "notes": "Crossref metadata verifies the Prevots et al. 1998 AbiN primary paper title and DOI."
              },
              {
                "reference": "DOI:10.1093/femsre/fuag009",
                "snippet": "the majority (18 systems) are each represented by single protein-coding genes",
                "notes": "The FEMS review lists AbiN among the 34 confirmed lactococcal Abi-like systems in Table 1 and omits AbiN from the named two- and three-component exception lists."
              }
            ]
          },
          {
            "subject": "abin_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "abortive_infection_system_trait",
            "description": "AbiN system possession is an abortive-infection-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1111/j.1574-6968.1998.tb12879.x",
                "snippet": "Nucleotide sequence and analysis of the new chromosomal abortive infection gene abiN of Lactococcus lactis subsp. cremoris S114",
                "notes": "Crossref metadata verifies the Prevots et al. 1998 AbiN primary paper title and DOI."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "AbiN | 10\\.1016/j\\.mib\\.2005\\.06\\.006 | Phage abortive infection in lactococci: variations on a theme",
                "notes": "The DefenseFinder article registry maps the named AbiN model namespace to the Chopin et al. lactococcal abortive-infection review."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "abin-trigger-and-effector-gap",
        "prompt": "Resolve the AbiN phage trigger, molecular activity, predicted ligand-binding sensor interpretation, and growth-arrest or cell-death route before minting narrower AbiN mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Prevots et al. support AbiN as a chromosomal lactococcal abortive infection gene, the FEMS review retains AbiN among confirmed lactococcal Abi-like systems, and DefenseFinder represents AbiN with a mandatory AbiN__AbiN profile. The FEMS table leaves the affected phage lytic-cycle step, phage escape mutants, and mechanism of cell arrest or death unknown, and the FEMS structural discussion predicts a putative ligand-binding sensor fold while explicitly calling for further research on the AbiN mechanism. This first system-level record therefore leaves the direct phage trigger, sensor ligand, exact molecular activity, growth-arrest or cell-death route, and phage escape routes unresolved.",
        "evidence": [
          {
            "reference": "DOI:10.1093/femsre/fuag009",
            "snippet": "The structure of AbiN is predicted with high confidence by AlphaFold and resembles a putative periplasmic ligand-binding sensor domain protein",
            "notes": "The FEMS review summarizes a predicted AbiN sensor-like fold but does not establish a molecular trigger or effector activity."
          },
          {
            "reference": "DOI:10.1093/femsre/fuag009",
            "snippet": "further research is needed to clarify the mechanism of AbiN and if it functions via abortive infection",
            "notes": "The FEMS review explicitly leaves the AbiN mechanism unresolved, so this record does not mint a more specific sensor or effector trait."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "snippet": "AbiN\tAbiN\t1\t1\tAbiN__AbiN\t\t\t",
            "notes": "The DefenseFinder rules table models AbiN as a one-component system requiring the AbiN__AbiN profile."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| AbiN__AbiN                                       | AbiN__AbiN                                       | AbiN                   | Custom                  | 20     |",
            "notes": "The DefenseFinder HMM inventory records AbiN__AbiN under the AbiN model namespace."
          }
        ],
        "attaches_to": [
          "causal_graphs#abin_locus_restricts_lactococcal_phage"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-21"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-21T17:52:22Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted AbiN system as a DOI-backed GENOMICS TraitRecord under the abortive infection system parent after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v218.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000342",
    "label": "AbiO system",
    "definition": "An abortive infection system in which an organism possesses a single-component AbiO-family locus represented by DefenseFinder as a mandatory AbiO__AbiO profile.",
    "definition_source": "DOI:10.3168/jds.S0022-0302(98)75713-3",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000214"
    ],
    "synonyms": [
      {
        "synonym_text": "AbiO",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      },
      {
        "synonym_text": "AbiO__AbiO",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.3168/jds.S0022-0302(98)75713-3",
        "snippet": "Complete Sequence of the New Lactococcal Abortive Phage Resistance Gene abiO",
        "notes": "Crossref metadata verifies the Prevots and Ritzenthaler 1998 AbiO primary paper title and DOI."
      },
      {
        "reference": "DOI:10.1093/femsre/fuag009",
        "snippet": "the majority (18 systems) are each represented by single protein-coding genes",
        "notes": "The FEMS review lists AbiO among the confirmed lactococcal Abi-like systems in Table 1 and omits AbiO from the named two- and three-component exception lists."
      },
      {
        "reference": "DOI:10.1093/femsre/fuag009",
        "snippet": "the AbiO N-terminal domain resembles a restriction endonuclease type II-like domain-containing protein",
        "notes": "The FEMS review summarizes a predicted nuclease-like AbiO N-terminal domain but does not establish the exact AbiO trigger or effector activity."
      },
      {
        "reference": "DOI:10.1093/femsre/fuag009",
        "snippet": "Its C-terminal domain is predicted to encompass a superfamily 1B (SF1B) helicase",
        "notes": "The FEMS review summarizes a predicted SF1B helicase-like AbiO C-terminal domain without resolving how AbiO arrests infected cells."
      },
      {
        "reference": "DOI:10.1093/femsre/fuag009",
        "snippet": "AbiO was previously shown to be toxic in Lactococcus when its encoding gene was cloned in a high-copy number vector",
        "notes": "The FEMS review treats AbiO overexpression toxicity as support for its abortive-infection phenotype."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "AbiO | 10\\.1016/j\\.mib\\.2005\\.06\\.006 | Phage abortive infection in lactococci: variations on a theme",
        "notes": "The DefenseFinder article registry maps the named AbiO model namespace to the Chopin et al. lactococcal abortive-infection review."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "AbiO\tAbiO\t1\t1\tAbiO__AbiO\t\t\t",
        "notes": "The DefenseFinder rules table models AbiO as a one-component system requiring the AbiO__AbiO profile."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| AbiO__AbiO                                       | AbiO__AbiO                                       | AbiO                   | Custom                  | 50     |",
        "notes": "The DefenseFinder HMM inventory records AbiO__AbiO under the AbiO model namespace."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "abio_locus_restricts_lactococcal_phage",
        "title": "AbiO loci confer abortive-infection phage defense",
        "description": "Conservative system-level sketch linking possession of a DefenseFinder AbiO locus to restricted bacteriophage propagation without asserting the unresolved phage trigger, predicted nuclease activity, or predicted helicase activity.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures AbiO as a named single-profile lactococcal Abi-like system with the DefenseFinder AbiO__AbiO HMM while leaving its direct phage trigger, restriction-endonuclease interpretation, helicase interpretation, exact molecular activity, phage escape routes, and growth-arrest or cell-death route unresolved.",
        "nodes": [
          {
            "node_id": "abio_locus",
            "label": "AbiO locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "An AbiO-family abortive-infection locus represented by the DefenseFinder AbiO__AbiO profile."
          },
          {
            "node_id": "restricted_phage_propagation",
            "label": "restricted phage propagation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced bacteriophage propagation in cells carrying an AbiO-family abortive-infection system."
          },
          {
            "node_id": "abio_system_trait",
            "label": "AbiO system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000342",
            "description": "Possession of a genome-encoded AbiO abortive-infection phage-defense system."
          },
          {
            "node_id": "abortive_infection_system_trait",
            "label": "abortive infection system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000214",
            "description": "Possession of a genome-encoded abortive-infection phage-defense system."
          }
        ],
        "edges": [
          {
            "subject": "abio_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "restricted_phage_propagation",
            "description": "The DefenseFinder AbiO namespace is modeled as a one-profile AbiO__AbiO system.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "AbiO\tAbiO\t1\t1\tAbiO__AbiO\t\t\t",
                "notes": "The DefenseFinder rules table models AbiO as a one-component system requiring the AbiO__AbiO profile."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| AbiO__AbiO                                       | AbiO__AbiO                                       | AbiO                   | Custom                  | 50     |",
                "notes": "The DefenseFinder HMM inventory records AbiO__AbiO under the AbiO model namespace."
              }
            ]
          },
          {
            "subject": "restricted_phage_propagation",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "abio_system_trait",
            "description": "Restriction of phage propagation realizes the AbiO abortive-infection system possession trait.",
            "evidence": [
              {
                "reference": "DOI:10.3168/jds.S0022-0302(98)75713-3",
                "snippet": "Complete Sequence of the New Lactococcal Abortive Phage Resistance Gene abiO",
                "notes": "Crossref metadata verifies the Prevots and Ritzenthaler 1998 AbiO primary paper title and DOI."
              },
              {
                "reference": "DOI:10.1093/femsre/fuag009",
                "snippet": "AbiO was previously shown to be toxic in Lactococcus when its encoding gene was cloned in a high-copy number vector",
                "notes": "The FEMS review treats AbiO overexpression toxicity as support for its abortive-infection phenotype."
              }
            ]
          },
          {
            "subject": "abio_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "abortive_infection_system_trait",
            "description": "AbiO system possession is an abortive-infection-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.3168/jds.S0022-0302(98)75713-3",
                "snippet": "Complete Sequence of the New Lactococcal Abortive Phage Resistance Gene abiO",
                "notes": "Crossref metadata verifies the Prevots and Ritzenthaler 1998 AbiO primary paper title and DOI."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "AbiO | 10\\.1016/j\\.mib\\.2005\\.06\\.006 | Phage abortive infection in lactococci: variations on a theme",
                "notes": "The DefenseFinder article registry maps the named AbiO model namespace to the Chopin et al. lactococcal abortive-infection review."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "abio-trigger-and-effector-gap",
        "prompt": "Resolve the AbiO phage trigger, restriction-endonuclease and helicase activity, and growth-arrest or cell-death route before minting narrower AbiO mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Prevots and Ritzenthaler support AbiO as a lactococcal abortive phage resistance gene, the FEMS review retains AbiO among confirmed lactococcal Abi-like systems, and DefenseFinder represents AbiO with a mandatory AbiO__AbiO profile. The FEMS table leaves the AbiO effect on the cell and phage escape proteins unknown for the tested phages, and the FEMS structural discussion predicts restriction-endonuclease-like and SF1B-helicase-like domains while not resolving the molecular trigger or effector activity. This first system-level record therefore leaves the direct phage trigger, exact molecular activity, growth-arrest or cell-death route, and phage escape routes unresolved.",
        "evidence": [
          {
            "reference": "DOI:10.1093/femsre/fuag009",
            "snippet": "the AbiO N-terminal domain resembles a restriction endonuclease type II-like domain-containing protein",
            "notes": "The FEMS review summarizes a predicted nuclease-like AbiO N-terminal domain but does not establish the exact AbiO trigger or effector activity."
          },
          {
            "reference": "DOI:10.1093/femsre/fuag009",
            "snippet": "Its C-terminal domain is predicted to encompass a superfamily 1B (SF1B) helicase",
            "notes": "The FEMS review summarizes a predicted SF1B helicase-like AbiO C-terminal domain without resolving how AbiO arrests infected cells."
          },
          {
            "reference": "DOI:10.1093/femsre/fuag009",
            "snippet": "AbiO was previously shown to be toxic in Lactococcus when its encoding gene was cloned in a high-copy number vector",
            "notes": "The FEMS review treats AbiO overexpression toxicity as support for its abortive-infection phenotype."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "snippet": "AbiO\tAbiO\t1\t1\tAbiO__AbiO\t\t\t",
            "notes": "The DefenseFinder rules table models AbiO as a one-component system requiring the AbiO__AbiO profile."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| AbiO__AbiO                                       | AbiO__AbiO                                       | AbiO                   | Custom                  | 50     |",
            "notes": "The DefenseFinder HMM inventory records AbiO__AbiO under the AbiO model namespace."
          }
        ],
        "attaches_to": [
          "causal_graphs#abio_locus_restricts_lactococcal_phage"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-21"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-21T18:34:41Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted AbiO system as a DOI-backed GENOMICS TraitRecord under the abortive infection system parent after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v219.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000343",
    "label": "AbiP2 system",
    "definition": "An abortive infection system in which an organism possesses a single-component AbiP2-family reverse-transcriptase-like locus represented by DefenseFinder as a mandatory AbiP2__AbiP2 profile.",
    "definition_source": "DOI:10.1128/JB.188.4.1643-1647.2006",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000214"
    ],
    "synonyms": [
      {
        "synonym_text": "AbiP2",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv"
      },
      {
        "synonym_text": "AbiP2__AbiP2",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1128/JB.188.4.1643-1647.2006",
        "snippet": "Identification of a Gene Encoding a Functional Reverse Transcriptase within a Highly Variable Locus in the P2-Like Coliphages",
        "notes": "Crossref metadata verifies the Odegrip et al. 2006 primary P2-like-coliphage reverse-transcriptase paper title and DOI."
      },
      {
        "reference": "DOI:10.1128/JB.188.4.1643-1647.2006",
        "snippet": "The product of one of them exhibits reverse transcriptase activity and blocks infection of phage T5",
        "notes": "The Odegrip et al. abstract supports a reverse-transcriptase gene in the P2-like-coliphage TO region that blocks phage T5."
      },
      {
        "reference": "DOI:10.1093/nar/gkac467",
        "snippet": "UG/Abi: a highly diverse family of prokaryotic reverse transcriptases associated with defense functions",
        "notes": "Mestre et al. describe the broad UG/Abi reverse-transcriptase family that the FEMS review places AbiP2 within."
      },
      {
        "reference": "DOI:10.1093/femsre/fuag009",
        "snippet": "UG)/Abi RT group, which also includes AbiP2 from E. coli and other predicted RTs",
        "notes": "The FEMS review explicitly places AbiP2 among UG/Abi reverse transcriptases rather than the unrelated lactococcal AbiP membrane-protein system."
      },
      {
        "reference": "DOI:10.1093/nar/gkac772",
        "snippet": "two Abi polymerases: AbiK and Abi-P2",
        "notes": "Figiel et al. structurally characterize Abi-P2 as a template-independent Abi polymerase but do not resolve the in vivo phage trigger or infected-cell output."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "AbiP2\tAbiP2\t1\t1\tAbiP2__AbiP2\t\t\t",
        "notes": "The DefenseFinder rules table models AbiP2 as a one-component system requiring the AbiP2__AbiP2 profile."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| AbiP2__AbiP2                                     | AbiP2__AbiP2                                     | AbiP2                  | Custom                  | 400    |",
        "notes": "The DefenseFinder HMM inventory records AbiP2__AbiP2 under the AbiP2 model namespace."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "abip2_locus_restricts_phage_propagation",
        "title": "AbiP2 loci confer reverse-transcriptase-associated phage defense",
        "description": "Conservative system-level sketch linking possession of a DefenseFinder AbiP2 locus to restricted bacteriophage propagation without asserting the unresolved phage trigger, protein-primed polymerase product, or host-arrest route.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures AbiP2 as a named single-profile reverse-transcriptase-like abortive-infection system with the DefenseFinder AbiP2__AbiP2 HMM while leaving its direct phage trigger, in vivo Abi-P2 polymerase product, UG/Abi family boundary, prophage host range, and cell-arrest or death route unresolved.",
        "nodes": [
          {
            "node_id": "abip2_locus",
            "label": "AbiP2 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "An AbiP2-family abortive-infection locus represented by the DefenseFinder AbiP2__AbiP2 profile."
          },
          {
            "node_id": "restricted_phage_propagation",
            "label": "restricted phage propagation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced bacteriophage propagation in cells carrying an AbiP2-family abortive-infection system."
          },
          {
            "node_id": "abip2_system_trait",
            "label": "AbiP2 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000343",
            "description": "Possession of a genome-encoded AbiP2 abortive-infection phage-defense system."
          },
          {
            "node_id": "abortive_infection_system_trait",
            "label": "abortive infection system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000214",
            "description": "Possession of a genome-encoded abortive-infection phage-defense system."
          }
        ],
        "edges": [
          {
            "subject": "abip2_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "restricted_phage_propagation",
            "description": "The DefenseFinder AbiP2 namespace is modeled as a one-profile AbiP2__AbiP2 system, matching the one-gene reverse-transcriptase-associated P2-like coliphage defense architecture.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "AbiP2\tAbiP2\t1\t1\tAbiP2__AbiP2\t\t\t",
                "notes": "The DefenseFinder rules table models AbiP2 as a one-component system requiring the AbiP2__AbiP2 profile."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| AbiP2__AbiP2                                     | AbiP2__AbiP2                                     | AbiP2                  | Custom                  | 400    |",
                "notes": "The DefenseFinder HMM inventory records AbiP2__AbiP2 under the AbiP2 model namespace."
              },
              {
                "reference": "DOI:10.1128/JB.188.4.1643-1647.2006",
                "snippet": "The product of one of them exhibits reverse transcriptase activity and blocks infection of phage T5",
                "notes": "The Odegrip et al. abstract supports a reverse-transcriptase gene in the P2-like-coliphage TO region that blocks phage T5."
              }
            ]
          },
          {
            "subject": "restricted_phage_propagation",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "abip2_system_trait",
            "description": "Restriction of phage propagation realizes the AbiP2 abortive-infection system possession trait.",
            "evidence": [
              {
                "reference": "DOI:10.1128/JB.188.4.1643-1647.2006",
                "snippet": "The product of one of them exhibits reverse transcriptase activity and blocks infection of phage T5",
                "notes": "The Odegrip et al. abstract supports a reverse-transcriptase gene in the P2-like-coliphage TO region that blocks phage T5."
              }
            ]
          },
          {
            "subject": "abip2_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "abortive_infection_system_trait",
            "description": "AbiP2 system possession is an abortive-infection-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1128/JB.188.4.1643-1647.2006",
                "snippet": "Identification of a Gene Encoding a Functional Reverse Transcriptase within a Highly Variable Locus in the P2-Like Coliphages",
                "notes": "Crossref metadata verifies the Odegrip et al. 2006 primary P2-like-coliphage reverse-transcriptase paper title and DOI."
              },
              {
                "reference": "DOI:10.1093/femsre/fuag009",
                "snippet": "UG)/Abi RT group, which also includes AbiP2 from E. coli and other predicted RTs",
                "notes": "The FEMS review explicitly places AbiP2 among UG/Abi reverse transcriptases rather than the unrelated lactococcal AbiP membrane-protein system."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "abip2-ug-abi-mechanism-gap",
        "prompt": "Resolve the AbiP2 natural locus breadth, phage trigger, protein-primed polymerase output, and growth-arrest or cell-death route before minting narrower AbiP2 mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Odegrip et al. support a P2-like-coliphage reverse transcriptase gene that blocks phage T5 infection, Mestre et al. describe the UG/Abi reverse-transcriptase family, the FEMS review places AbiP2 in that family rather than the unrelated lactococcal AbiP family, Figiel et al. structurally characterize Abi-P2 as a template-independent Abi polymerase, and DefenseFinder represents AbiP2 with a mandatory AbiP2__AbiP2 profile. This first system-level record therefore leaves the direct phage trigger, in vivo DNA product, exact relationship to broader UG/Abi systems, prophage host breadth, and growth-arrest or cell-death route unresolved.",
        "evidence": [
          {
            "reference": "DOI:10.1128/JB.188.4.1643-1647.2006",
            "snippet": "The product of one of them exhibits reverse transcriptase activity and blocks infection of phage T5",
            "notes": "The Odegrip et al. abstract supports a reverse-transcriptase gene in the P2-like-coliphage TO region that blocks phage T5."
          },
          {
            "reference": "DOI:10.1093/nar/gkac467",
            "snippet": "UG/Abi: a highly diverse family of prokaryotic reverse transcriptases associated with defense functions",
            "notes": "Mestre et al. describe the broad UG/Abi reverse-transcriptase family that the FEMS review places AbiP2 within."
          },
          {
            "reference": "DOI:10.1093/femsre/fuag009",
            "snippet": "UG)/Abi RT group, which also includes AbiP2 from E. coli and other predicted RTs",
            "notes": "The FEMS review explicitly places AbiP2 among UG/Abi reverse transcriptases rather than the unrelated lactococcal AbiP membrane-protein system."
          },
          {
            "reference": "DOI:10.1093/nar/gkac772",
            "snippet": "two Abi polymerases: AbiK and Abi-P2",
            "notes": "Figiel et al. structurally characterize Abi-P2 as a template-independent Abi polymerase but do not resolve the in vivo phage trigger or infected-cell output."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "snippet": "AbiP2\tAbiP2\t1\t1\tAbiP2__AbiP2\t\t\t",
            "notes": "The DefenseFinder rules table models AbiP2 as a one-component system requiring the AbiP2__AbiP2 profile."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| AbiP2__AbiP2                                     | AbiP2__AbiP2                                     | AbiP2                  | Custom                  | 400    |",
            "notes": "The DefenseFinder HMM inventory records AbiP2__AbiP2 under the AbiP2 model namespace."
          }
        ],
        "attaches_to": [
          "causal_graphs#abip2_locus_restricts_phage_propagation"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-21"
      },
      {
        "discussion_id": "abip2-defensefinder-article-registry-gap",
        "prompt": "Resolve the DefenseFinder AbiP2 article-registry mapping before using List_system_article.md as positive system literature evidence.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "The pinned DefenseFinder HMM inventory and rules table support AbiP2 as a one-profile model namespace, but its article registry row maps AbiP2 to a 2005 lactococcal abortive-infection review that predates Odegrip et al. 2006. This record therefore leaves the registry-to-primary link unresolved and relies on Odegrip et al., Mestre et al., the FEMS review, Figiel et al., and pinned DefenseFinder HMM/rule rows for AbiP2 identity and system coverage.",
        "evidence": [
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
            "snippet": "| AbiP2 | 10\\.1016/j\\.mib\\.2005\\.06\\.006 | Phage abortive infection in lactococci: variations on a theme |",
            "notes": "The pinned DefenseFinder article registry maps AbiP2 to a 2005 lactococcal Abi review; that row is tracked as unresolved model-to-publication triage rather than positive AbiP2 primary literature evidence."
          }
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-21"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-21T19:10:26Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted AbiP2 system as a DOI-backed GENOMICS TraitRecord under the abortive infection system parent after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v220.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-21T19:50:08Z",
        "curator": "codex",
        "action": "ADDRESS_PR_REVIEW",
        "changes": "Addressed review issues #1215 and #1216 by renaming the NONMECHANISTIC AbiP2 graph id to omit T5 specificity and by documenting the unresolved DefenseFinder article-registry row that maps AbiP2 to a 2005 lactococcal review.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000225",
    "label": "AbiQ system",
    "definition": "An abortive infection system in which an organism possesses an AbiQ type III toxin-antitoxin locus whose protein endoribonuclease and cognate RNA antitoxin module alter early phage mRNA profiles and restrict phage propagation after adsorption.",
    "definition_source": "DOI:10.1128/JB.00296-13",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000214"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1128/AEM.64.12.4748-4756.1998",
        "snippet": "the system encoded by pSRQ900 was classified as an abortive infection mechanism and was named AbiQ",
        "notes": "Emond et al. named AbiQ as a Lactococcus plasmid-encoded abortive infection system rather than an adsorption-blocking or restriction-modification defense."
      },
      {
        "reference": "DOI:10.1128/AEM.64.12.4748-4756.1998",
        "snippet": "The frameshift mutation completely abolished host resistance to phages p2 and c21",
        "notes": "Emond et al. localized the phage-resistance phenotype to the abiQ open reading frame on the pSRQ900 fragment."
      },
      {
        "reference": "DOI:10.1128/JB.00296-13",
        "snippet": "Lactococcus lactis AbiQ system, a type III toxin-antitoxin with antiviral activities",
        "notes": "Samson et al. support the type III protein-RNA toxin-antitoxin architecture of AbiQ."
      },
      {
        "reference": "DOI:10.1128/JB.00296-13",
        "snippet": "AbiQ modified the early-expressed phage mRNA profiles",
        "notes": "Samson et al. connect AbiQ to altered early phage mRNA profiles during infection."
      },
      {
        "reference": "DOI:10.1128/JB.00296-13",
        "snippet": "active against various phage families infecting Gram-positive and Gram-negative bacteria",
        "notes": "Samson et al. support AbiQ as an antiphage system whose activity is not restricted to its native lactococcal host."
      },
      {
        "reference": "DOI:10.1128/JB.00296-13",
        "snippet": "In the presence of AbiQ, additional small transcripts were observed",
        "notes": "Samson et al. observed altered P008 transcript profiles in phage-infected AbiQ-containing cells."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1358",
        "taxon_label": "Lactococcus lactis",
        "note": "Emond et al. isolated the pSRQ900 plasmid from Lactococcus lactis W-37, named its encoded abortive-infection mechanism AbiQ, and showed AbiQ-dependent resistance to c2- and 936-like lactococcal phages.",
        "reference": "DOI:10.1128/AEM.64.12.4748-4756.1998"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "abiq_type_iii_ta_antiphage_activity",
        "title": "AbiQ type III toxin-antitoxin activity disrupts phage mRNA profiles",
        "description": "Evidence-backed process sketch linking an AbiQ locus to type III toxin-antitoxin activity, altered early phage mRNA profiles, restricted phage propagation, and abortive-infection system possession.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures AbiQ at the system level without asserting a universal phage activator, exact AbiQ RNA target, or phage-escape path; Samson et al. show that multiple unrelated phage genes can be involved in the AbiQ phenotype.",
        "nodes": [
          {
            "node_id": "abiq_locus",
            "label": "AbiQ locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A type III toxin-antitoxin abortive-infection locus encoding the AbiQ toxin with its cognate RNA antitoxin."
          },
          {
            "node_id": "abiq_type_iii_toxin_antitoxin_activity",
            "label": "AbiQ type III toxin-antitoxin activity",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Protein-RNA toxin-antitoxin activity of AbiQ, in which the AbiQ protein acts as an endoribonuclease neutralized by a cognate RNA antitoxin."
          },
          {
            "node_id": "early_phage_mrna_profile_modification",
            "label": "early phage mRNA profile modification",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "AbiQ-associated alteration of early phage mRNA profiles in infected host cells."
          },
          {
            "node_id": "restricted_phage_propagation",
            "label": "restricted phage propagation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced production of infectious phage from an AbiQ-containing infected host cell."
          },
          {
            "node_id": "abiq_system_trait",
            "label": "AbiQ system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000225",
            "description": "Possession of a genome-encoded AbiQ type III toxin-antitoxin abortive-infection system."
          },
          {
            "node_id": "abortive_infection_system_trait",
            "label": "abortive infection system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000214",
            "description": "Possession of a genome-encoded abortive-infection phage defense system."
          }
        ],
        "edges": [
          {
            "subject": "abiq_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "abiq_type_iii_toxin_antitoxin_activity",
            "description": "The AbiQ locus encodes a type III protein-RNA toxin-antitoxin antiphage system.",
            "evidence": [
              {
                "reference": "DOI:10.1128/JB.00296-13",
                "snippet": "Lactococcus lactis AbiQ system, a type III toxin-antitoxin with antiviral activities",
                "notes": "Samson et al. define AbiQ as a type III toxin-antitoxin system with antiviral activity."
              }
            ]
          },
          {
            "subject": "abiq_type_iii_toxin_antitoxin_activity",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "early_phage_mrna_profile_modification",
            "description": "AbiQ activity alters the abundance pattern of early-expressed phage transcripts during infection.",
            "evidence": [
              {
                "reference": "DOI:10.1128/JB.00296-13",
                "snippet": "AbiQ modified the early-expressed phage mRNA profiles",
                "notes": "Samson et al. directly assayed phage transcription in AbiQ-containing Lactococcus cells."
              }
            ]
          },
          {
            "subject": "abiq_type_iii_toxin_antitoxin_activity",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "restricted_phage_propagation",
            "description": "AbiQ type III toxin-antitoxin activity contributes to restricted phage propagation in infected host cells.",
            "evidence": [
              {
                "reference": "DOI:10.1128/JB.00296-13",
                "snippet": "active against various phage families infecting Gram-positive and Gram-negative bacteria",
                "notes": "Samson et al. support AbiQ as an antiphage type III toxin-antitoxin system."
              }
            ]
          },
          {
            "subject": "restricted_phage_propagation",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "abiq_system_trait",
            "description": "Restriction of phage propagation realizes the AbiQ antiphage defense trait.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.64.12.4748-4756.1998",
                "snippet": "The frameshift mutation completely abolished host resistance to phages p2 and c21",
                "notes": "Emond et al. measured reduced phage plaquing on cells carrying the native AbiQ plasmid."
              }
            ]
          },
          {
            "subject": "abiq_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "abortive_infection_system_trait",
            "description": "AbiQ system possession is an abortive-infection-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.64.12.4748-4756.1998",
                "snippet": "the system encoded by pSRQ900 was classified as an abortive infection mechanism and was named AbiQ",
                "notes": "Emond et al. place AbiQ in the abortive infection class of phage defense."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-15T18:45:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted AbiQ system as a DOI-backed GENOMICS TraitRecord under the abortive infection system parent after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v102.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000317",
    "label": "AbiR system",
    "definition": "An abortive infection system in which an organism possesses a multicomponent AbiR determinant represented by the DefenseFinder AbiR__AbiRa, AbiR__AbiRb, and AbiR__AbiRc profiles and capable of restricting lactococcal phage propagation by an early abortive-infection mechanism that impedes phage DNA replication, as exemplified by the two pKR223 loci from Lactococcus lactis subsp. lactis KR2 separated by the LlaKR2I restriction-modification genes.",
    "definition_source": "DOI:10.1128/AEM.66.6.2647-2651.2000",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000214"
    ],
    "synonyms": [
      {
        "synonym_text": "AbiR",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1128/AEM.66.6.2647-2651.2000"
      }
    ],
    "evidence": [
      {
        "reference": "PMID:10831451",
        "snippet": "The native lactococcal plasmid pKR223 encodes two distinct phage resistance mechanisms, a restriction and modification (R/M) system designated LlaKR2I and an abortive infection mechanism (Abi) which affects prolate-headed-phage proliferation",
        "notes": "Twomey et al. identify native Lactococcus lactis plasmid pKR223 as the source of a restriction-modification system and a separate abortive-infection determinant."
      },
      {
        "reference": "PMID:10831451",
        "snippet": "sequence analysis has validated the novelty of the Abi system, which has now been designated AbiR",
        "notes": "Twomey et al. name AbiR as the novel abortive-infection system from pKR223."
      },
      {
        "reference": "PMID:10831451",
        "snippet": "Analysis of deletion and insertion clones demonstrated that AbiR was encoded by two genetic loci, separated by the LlaKR2I R/M genes",
        "notes": "Twomey et al. show that the AbiR phenotype requires two pKR223 loci separated by the LlaKR2I restriction-modification genes."
      },
      {
        "reference": "PMID:10831451",
        "snippet": "Mechanistic studies on the AbiR phenotype indicated that it was heat sensitive and that it impeded phage DNA replication",
        "notes": "Twomey et al. connect AbiR activity to a heat-sensitive abortive-infection phenotype that impedes phage DNA replication."
      },
      {
        "reference": "PMID:10831451",
        "snippet": "These data indicated that AbiR is a novel multicomponent, heat-sensitive, \"early\"-functioning Abi system",
        "notes": "Twomey et al. classify AbiR as a multicomponent early abortive-infection system."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "AbiR | 10\\.1016/j\\.mib\\.2005\\.06\\.006 | Phage abortive infection in lactococci: variations on a theme",
        "notes": "The DefenseFinder article registry maps the named AbiR model namespace to a lactococcal abortive-infection review."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "AbiR\tAbiR\t3\t3\tAbiR__AbiRa, AbiR__AbiRb, AbiR__AbiRc",
        "notes": "The DefenseFinder rules table models AbiR as a three-component system requiring the AbiR__AbiRa, AbiR__AbiRb, and AbiR__AbiRc profiles."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| AbiR__AbiRa                                      | AbiR__AbiRa                                      | AbiR                   | Custom                  | 20     |",
        "notes": "The DefenseFinder HMM inventory records AbiR__AbiRa under the AbiR model namespace."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| AbiR__AbiRb                                      | AbiR__AbiRb                                      | AbiR                   | Custom                  | 20     |",
        "notes": "The DefenseFinder HMM inventory records AbiR__AbiRb under the AbiR model namespace."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| AbiR__AbiRc                                      | AbiR__AbiRc                                      | AbiR                   | Custom                  | 20     |",
        "notes": "The DefenseFinder HMM inventory records AbiR__AbiRc under the AbiR model namespace."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1358",
        "taxon_label": "Lactococcus lactis",
        "note": "Twomey et al. characterized AbiR from native plasmid pKR223 of Lactococcus lactis subsp. lactis KR2 and showed a multicomponent, two-locus Abi phenotype that impeded phage DNA replication.",
        "reference": "DOI:10.1128/AEM.66.6.2647-2651.2000"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "abir_loci_impede_phage_dna_replication",
        "title": "AbiR activity impedes lactococcal phage DNA replication",
        "description": "Conservative system-level sketch linking the separated pKR223 AbiR loci to AbiR antiphage activity, impeded phage DNA replication, restricted lactococcal phage propagation, and abortive-infection system possession without resolving the phage trigger or individual component activities.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures AbiR as a named DefenseFinder three-profile abortive-infection system whose pKR223 prototype is encoded by two genetic loci and impedes phage DNA replication. It leaves the direct phage trigger, the profile-to-locus mapping, AbiRa, AbiRb, and AbiRc molecular functions, the reason the R/M genes interrupt the two AbiR loci, and phage escape routes unresolved.",
        "nodes": [
          {
            "node_id": "abir_loci",
            "label": "AbiR loci",
            "node_type": "GENETIC_ELEMENT",
            "description": "A multicomponent abortive-infection determinant encoded by two separated pKR223 loci and represented by the DefenseFinder AbiR rule."
          },
          {
            "node_id": "abir_antiphage_activity",
            "label": "AbiR antiphage activity",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Abortive-infection phage resistance mediated by the AbiR system."
          },
          {
            "node_id": "phage_dna_replication",
            "label": "phage DNA replication",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Replication of lactococcal bacteriophage DNA during sensitive-host infection."
          },
          {
            "node_id": "restricted_phage_propagation",
            "label": "restricted phage propagation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced completion of lactococcal phage propagation in an AbiR-containing infected host cell."
          },
          {
            "node_id": "abir_system_trait",
            "label": "AbiR system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000317",
            "description": "Possession of a genome-encoded AbiR abortive-infection phage-defense system."
          },
          {
            "node_id": "abortive_infection_system_trait",
            "label": "abortive infection system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000214",
            "description": "Possession of a genome-encoded abortive-infection phage-defense system."
          }
        ],
        "edges": [
          {
            "subject": "abir_loci",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "abir_antiphage_activity",
            "description": "The pKR223 AbiR determinant is encoded by two genetic loci separated by LlaKR2I genes, and DefenseFinder models AbiR as a three-profile system requiring AbiRa, AbiRb, and AbiRc components.",
            "evidence": [
              {
                "reference": "PMID:10831451",
                "snippet": "Analysis of deletion and insertion clones demonstrated that AbiR was encoded by two genetic loci, separated by the LlaKR2I R/M genes",
                "notes": "Twomey et al. show that the AbiR phenotype requires two separated pKR223 genetic loci."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "AbiR\tAbiR\t3\t3\tAbiR__AbiRa, AbiR__AbiRb, AbiR__AbiRc",
                "notes": "The DefenseFinder rules table models AbiR as a three-component system requiring the AbiR__AbiRa, AbiR__AbiRb, and AbiR__AbiRc profiles."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| AbiR__AbiRa                                      | AbiR__AbiRa                                      | AbiR                   | Custom                  | 20     |",
                "notes": "The DefenseFinder HMM inventory records AbiR__AbiRa under the AbiR model namespace."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| AbiR__AbiRb                                      | AbiR__AbiRb                                      | AbiR                   | Custom                  | 20     |",
                "notes": "The DefenseFinder HMM inventory records AbiR__AbiRb under the AbiR model namespace."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| AbiR__AbiRc                                      | AbiR__AbiRc                                      | AbiR                   | Custom                  | 20     |",
                "notes": "The DefenseFinder HMM inventory records AbiR__AbiRc under the AbiR model namespace."
              }
            ]
          },
          {
            "subject": "abir_antiphage_activity",
            "predicate": "mitigates",
            "predicate_id": "METPO:2007407",
            "object": "phage_dna_replication",
            "description": "AbiR antiphage activity impedes sensitive phage DNA replication as an early abortive-infection output.",
            "evidence": [
              {
                "reference": "PMID:10831451",
                "snippet": "Mechanistic studies on the AbiR phenotype indicated that it was heat sensitive and that it impeded phage DNA replication",
                "notes": "Twomey et al. classify the AbiR phenotype as heat-sensitive and DNA-replication impeding."
              }
            ]
          },
          {
            "subject": "abir_antiphage_activity",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "restricted_phage_propagation",
            "description": "AbiR antiphage activity affects prolate-headed-phage proliferation through a multicomponent early Abi mechanism.",
            "evidence": [
              {
                "reference": "PMID:10831451",
                "snippet": "These data indicated that AbiR is a novel multicomponent, heat-sensitive, \"early\"-functioning Abi system",
                "notes": "Twomey et al. summarize the AbiR phenotype as multicomponent, heat-sensitive, and early functioning."
              }
            ]
          },
          {
            "subject": "restricted_phage_propagation",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "abir_system_trait",
            "description": "Restriction of lactococcal phage propagation realizes the AbiR abortive-infection trait.",
            "evidence": [
              {
                "reference": "PMID:10831451",
                "snippet": "sequence analysis has validated the novelty of the Abi system, which has now been designated AbiR",
                "notes": "Twomey et al. name AbiR as the novel pKR223 abortive-infection system."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "AbiR | 10\\.1016/j\\.mib\\.2005\\.06\\.006 | Phage abortive infection in lactococci: variations on a theme",
                "notes": "The DefenseFinder article registry maps the named AbiR model namespace to a lactococcal abortive-infection review."
              }
            ]
          },
          {
            "subject": "abir_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "abortive_infection_system_trait",
            "description": "AbiR system possession is an abortive-infection-system trait.",
            "evidence": [
              {
                "reference": "PMID:10831451",
                "snippet": "These data indicated that AbiR is a novel multicomponent, heat-sensitive, \"early\"-functioning Abi system",
                "notes": "Twomey et al. classify AbiR in the abortive-infection class of phage defense."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "abir-component-activity-gap",
        "prompt": "Resolve the AbiR phage trigger, profile-to-locus mapping, and AbiRa, AbiRb, and AbiRc molecular functions before minting narrower AbiR mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Twomey et al. support AbiR as a multicomponent abortive-infection system encoded by two separated pKR223 loci, and DefenseFinder represents AbiR with a three-profile rule. This first system-level record leaves the phage trigger, the mapping from the two original genetic loci to AbiRa, AbiRb, and AbiRc profiles, the component molecular activities, and the direct reason that AbiR impedes phage DNA replication unresolved.",
        "evidence": [
          {
            "reference": "PMID:10831451",
            "snippet": "Analysis of deletion and insertion clones demonstrated that AbiR was encoded by two genetic loci, separated by the LlaKR2I R/M genes",
            "notes": "Twomey et al. localize AbiR to two separated pKR223 loci rather than to the three-component DefenseFinder profile scheme."
          }
        ],
        "attaches_to": [
          "causal_graphs#abir_loci_impede_phage_dna_replication"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-20"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-20T19:30:10Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted AbiR system as a DOI-backed GENOMICS TraitRecord under the abortive infection system parent after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v194.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-20T20:02:22Z",
        "curator": "codex",
        "action": "REVISED_SCOPE",
        "changes": "Addressed PR 1154 review issue 1155 by narrowing the AbiR definition to the DefenseFinder AbiR determinant and treating the two separated pKR223 loci from Lactococcus lactis subsp. lactis KR2 as exemplar evidence rather than a constitutive class restriction.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000230",
    "label": "AbiT system",
    "definition": "An abortive infection system in which an organism possesses the two-gene pED1 abiT locus whose constitutively cotranscribed abiTi and abiTii genes encode an AbiTi-AbiTii phage-resistance module that acts late in the 936/P335 lactococcal phage lytic cycle.",
    "definition_source": "DOI:10.1128/JB.184.22.6325-6332.2002",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000214"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1128/JB.184.22.6325-6332.2002",
        "snippet": "Here, we describe the isolation and characterization of a novel Abi mechanism encoded by plasmid pED1 from L. lactis",
        "notes": "Bouchard et al. identified the plasmid pED1-encoded AbiT abortive-infection mechanism in Lactococcus lactis."
      },
      {
        "reference": "DOI:10.1128/JB.184.22.6325-6332.2002",
        "snippet": "The system is composed of two constitutively cotranscribed genes encoding putative proteins of 127 and 213 amino acids, named AbiTi and AbiTii, respectively",
        "notes": "Bouchard et al. support defining AbiT around the paired abiTi and abiTii host genes rather than around a single gene."
      },
      {
        "reference": "DOI:10.1128/JB.184.22.6325-6332.2002",
        "snippet": "The fact that resistant cells do not survive phage infection proves that the antiphage system carried by pED1 is an Abi mechanism. It was therefore named AbiT.",
        "notes": "Bouchard et al. placed the pED1 phage-resistance determinant in the abortive-infection class and named it AbiT."
      },
      {
        "reference": "DOI:10.1128/JB.184.22.6325-6332.2002",
        "snippet": "Two genes are responsible for the antiphage activity of AbiT",
        "notes": "Bouchard et al. support a two-gene genetic basis for AbiT phage resistance."
      },
      {
        "reference": "DOI:10.1128/JB.184.22.6325-6332.2002",
        "snippet": "It appears that AbiT affects DNA replication and also prevents effective encapsidation",
        "notes": "Bouchard et al. connect AbiT to both impaired phage DNA replication and ineffective phage encapsidation."
      },
      {
        "reference": "DOI:10.1128/AEM.01755-12",
        "snippet": "AbiT-resistant phage mutants derived from the wild-type AbiT-sensitive lactococcal phages p2, bIL170, and P008 were isolated and characterized",
        "notes": "Labrie et al. generated AbiT-resistant mutants from three sensitive 936-group Lactococcus phages."
      },
      {
        "reference": "DOI:10.1128/AEM.01755-12",
        "snippet": "three distinct phage genes involved in AbiT activity were identified",
        "notes": "Labrie et al. found that AbiT sensitivity maps to multiple nonhomologous phage genes rather than one universal phage escape determinant."
      },
      {
        "reference": "DOI:10.1128/AEM.01755-12",
        "snippet": "AbiT blocks capsid protein synthesis of the wild-type phage, while it does not affect the resistant phage p2.t3, mutated in the capsid gene",
        "notes": "Labrie et al. connect a p2 major-capsid-protein escape mutation to restoration of capsid protein synthesis in the presence of AbiT."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1358",
        "taxon_label": "Lactococcus lactis",
        "note": "Bouchard et al. isolated pED1 from Lactococcus lactis W51, localized the AbiT phage-resistance phenotype to abiTi and abiTii, and showed that the determinant restricts 936 and P335 Lactococcus phages after transfer into phage-sensitive Lactococcus lactis strains.",
        "reference": "DOI:10.1128/JB.184.22.6325-6332.2002"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "abit_late_phage_development_block",
        "title": "AbiT activity blocks late phage development",
        "description": "Evidence-backed process sketch linking the two-gene abiT locus to AbiTi-AbiTii antiphage activity, impaired phage DNA replication or capsid production, restricted phage propagation, and abortive-infection system possession.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures AbiT at the system level without asserting a molecular function for AbiTi or AbiTii, the exact host target, the direct phage activator, or that every AbiT-insensitive phage mutates the same phage gene.",
        "nodes": [
          {
            "node_id": "abit_locus",
            "label": "abiT locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A two-gene abortive-infection locus encoding AbiTi and AbiTii."
          },
          {
            "node_id": "abiti_abitii_antiphage_activity",
            "label": "AbiTi-AbiTii antiphage activity",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Abortive-infection antiphage activity mediated by the AbiTi and AbiTii host proteins."
          },
          {
            "node_id": "interrupted_late_phage_development",
            "label": "interrupted late phage development",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "AbiT-associated impairment of phage DNA replication, phage DNA encapsidation, or capsid protein synthesis after early phage gene expression."
          },
          {
            "node_id": "restricted_phage_propagation",
            "label": "restricted phage propagation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced completion of 936 or P335 phage propagation in an AbiT-containing infected host cell."
          },
          {
            "node_id": "abit_system_trait",
            "label": "AbiT system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000230",
            "description": "Possession of a genome-encoded AbiT two-component abortive-infection system."
          },
          {
            "node_id": "abortive_infection_system_trait",
            "label": "abortive infection system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000214",
            "description": "Possession of a genome-encoded abortive-infection phage defense system."
          }
        ],
        "edges": [
          {
            "subject": "abit_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "abiti_abitii_antiphage_activity",
            "description": "The abiT locus carries abiTi, abiTii, and the promoter required for the complete phage-resistance phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1128/JB.184.22.6325-6332.2002",
                "snippet": "Two genes are responsible for the antiphage activity of AbiT",
                "notes": "Bouchard et al. showed that both abiT genes are required for full AbiT activity."
              }
            ]
          },
          {
            "subject": "abiti_abitii_antiphage_activity",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "interrupted_late_phage_development",
            "description": "AbiT activity interferes with late phage development after early phage gene expression.",
            "evidence": [
              {
                "reference": "DOI:10.1128/JB.184.22.6325-6332.2002",
                "snippet": "It appears that AbiT affects DNA replication and also prevents effective encapsidation",
                "notes": "Bouchard et al. found reduced DNA replication and failed encapsidation in AbiT-containing infected cells."
              },
              {
                "reference": "DOI:10.1128/AEM.01755-12",
                "snippet": "AbiT blocks capsid protein synthesis of the wild-type phage, while it does not affect the resistant phage p2.t3, mutated in the capsid gene",
                "notes": "Labrie et al. refine the AbiT phenotype by linking wild-type p2 capsid protein synthesis blockage to an AbiT-sensitive capsid gene."
              }
            ]
          },
          {
            "subject": "interrupted_late_phage_development",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "restricted_phage_propagation",
            "description": "Failed phage DNA maturation or capsid production limits completion of the phage lytic cycle.",
            "evidence": [
              {
                "reference": "DOI:10.1128/JB.184.22.6325-6332.2002",
                "snippet": "The monitoring of the intracellular phage infection process by DNA replication, gene expression, and electron microscopy as well as the study of phage mutants by genome mapping indicated that AbiT is likely to act at a later stage of the phage lytic cycle",
                "notes": "Bouchard et al. support a late-stage block in the phage lytic cycle."
              }
            ]
          },
          {
            "subject": "restricted_phage_propagation",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "abit_system_trait",
            "description": "Restriction of 936/P335 phage propagation realizes the AbiT abortive-infection defense trait.",
            "evidence": [
              {
                "reference": "DOI:10.1128/JB.184.22.6325-6332.2002",
                "snippet": "The fact that resistant cells do not survive phage infection proves that the antiphage system carried by pED1 is an Abi mechanism. It was therefore named AbiT.",
                "notes": "Bouchard et al. define AbiT as a pED1 abortive-infection phage resistance system."
              }
            ]
          },
          {
            "subject": "abit_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "abortive_infection_system_trait",
            "description": "AbiT system possession is an abortive-infection-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1128/JB.184.22.6325-6332.2002",
                "snippet": "Here, we describe the isolation and characterization of a novel Abi mechanism encoded by plasmid pED1 from L. lactis",
                "notes": "Bouchard et al. place AbiT in the abortive infection class of phage defense."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-15T22:05:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted AbiT system as a DOI-backed GENOMICS TraitRecord under the abortive infection system parent after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v107.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000321",
    "label": "AbiU system",
    "definition": "An abortive infection system in which an organism possesses an abiU-family locus represented by the DefenseFinder AbiU__AbiU profile and exemplified by the Lactococcus lactis LL51-1 AbiU determinant, whose abiU1 open reading frame is responsible for phage resistance, whose abiU2 region may downregulate 936/P335 resistance, and whose activity reduces c2, 936, and P335 lactococcal phage plaquing while delaying transcription of phages 712 and c2.",
    "definition_source": "DOI:10.1128/AEM.67.11.5225-5232.2001",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000214"
    ],
    "synonyms": [
      {
        "synonym_text": "AbiU",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1128/AEM.67.11.5225-5232.2001"
      }
    ],
    "evidence": [
      {
        "reference": "PMID:11679349",
        "snippet": "This study reports on the identification and characterization of a novel abortive infection system, AbiU, from Lactococcus lactis.",
        "notes": "Dai et al. identify AbiU as a novel Lactococcus lactis abortive-infection system."
      },
      {
        "reference": "PMID:11679349",
        "snippet": "AbiU confers resistance to phages from the three main industrially relevant lactococcal phage species: c2, 936, and P335.",
        "notes": "Dai et al. measured the AbiU activity spectrum across representative c2, 936, and P335 lactococcal phages."
      },
      {
        "reference": "PMID:11679349",
        "snippet": "The presence of AbiU reduced the efficiency of plaquing against specific phage from each species as follows: 3.7 x 10(-1), 1.0 x 10(-2), and 1.0 x 10(-1), respectively.",
        "notes": "Dai et al. quantified phage-specific AbiU reductions in efficiency of plaquing against c2, 936, and P335 representatives."
      },
      {
        "reference": "PMID:11679349",
        "snippet": "abiU involves two open reading frames, abiU1 (1,772 bp) and abiU2 (1,019 bp).",
        "notes": "Dai et al. reported a two-ORF abiU locus rather than resolving AbiU as a single isolated protein trait."
      },
      {
        "reference": "PMID:11679349",
        "snippet": "Evidence indicates that AbiU1 is responsible for phage resistance and that AbiU2 may downregulate phage resistance against 936 and P335 type phages but not c2 type phage.",
        "notes": "Dai et al. connected AbiU1 to the phage-resistance phenotype and left AbiU2 as a likely regulator of a phage-species-specific resistance output."
      },
      {
        "reference": "PMID:11679349",
        "snippet": "AbiU appeared to delay transcription of both phage 712 and c2, with the effect being more marked on phage c2.",
        "notes": "Dai et al. linked AbiU to delayed phage transcription without resolving the direct phage trigger or AbiU1 target."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "AbiU | 10\\.1016/j\\.mib\\.2005\\.06\\.006 | Phage abortive infection in lactococci: variations on a theme",
        "notes": "The DefenseFinder article registry maps the named AbiU model namespace to a lactococcal abortive-infection review."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "AbiU\tAbiU\t1\t1\tAbiU__AbiU",
        "notes": "The DefenseFinder rules table models AbiU as a one-component system requiring the AbiU__AbiU profile."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| AbiU__AbiU                                       | AbiU__AbiU                                       | AbiU                   | Custom                  | 60     |",
        "notes": "The DefenseFinder HMM inventory records AbiU__AbiU under the AbiU model namespace."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1358",
        "taxon_label": "Lactococcus lactis",
        "note": "Dai et al. characterized AbiU from Lactococcus lactis LL51-1 and showed that AbiU confers resistance to c2, 936, and P335 lactococcal phages.",
        "reference": "DOI:10.1128/AEM.67.11.5225-5232.2001"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "abiu_locus_delays_lactococcal_phage_transcription",
        "title": "AbiU activity delays lactococcal phage transcription",
        "description": "Conservative system-level sketch linking an abiU-family locus to AbiU antiphage activity, reduced c2/936/P335 phage plaquing, delayed phage 712 and c2 transcription, and AbiU-system possession without asserting the unresolved phage trigger or AbiU1 molecular target.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures AbiU as a named DefenseFinder single-profile abortive-infection system whose LL51-1 prototype restricts c2, 936, and P335 lactococcal phages. It leaves the direct phage trigger, AbiU1 molecular function, AbiU2 downregulation route, natural locus breadth, and phage escape routes unresolved.",
        "nodes": [
          {
            "node_id": "abiu_locus",
            "label": "abiU locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "An abiU-family abortive-infection locus represented by the DefenseFinder AbiU__AbiU profile."
          },
          {
            "node_id": "abiu_antiphage_activity",
            "label": "AbiU antiphage activity",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Abortive-infection phage resistance mediated by the AbiU system."
          },
          {
            "node_id": "lactococcal_phage_plaquing_reduction",
            "label": "lactococcal phage plaquing reduction",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced plaquing of c2, 936, and P335 lactococcal phages by an AbiU-containing host."
          },
          {
            "node_id": "phage_transcription_delay",
            "label": "phage transcription delay",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Delayed transcription of phages 712 and c2 in AbiU-containing Lactococcus lactis hosts."
          },
          {
            "node_id": "abiu_system_trait",
            "label": "AbiU system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000321",
            "description": "Possession of a genome-encoded AbiU abortive-infection phage-defense system."
          },
          {
            "node_id": "abortive_infection_system_trait",
            "label": "abortive infection system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000214",
            "description": "Possession of a genome-encoded abortive-infection phage-defense system."
          }
        ],
        "edges": [
          {
            "subject": "abiu_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "abiu_antiphage_activity",
            "description": "The abiU-family locus encodes AbiU antiphage activity, and DefenseFinder models AbiU as a one-profile system.",
            "evidence": [
              {
                "reference": "PMID:11679349",
                "snippet": "abiU involves two open reading frames, abiU1 (1,772 bp) and abiU2 (1,019 bp).",
                "notes": "Dai et al. identified the two ORFs in the AbiU determinant."
              },
              {
                "reference": "PMID:11679349",
                "snippet": "Evidence indicates that AbiU1 is responsible for phage resistance",
                "notes": "Dai et al. connected AbiU1 to the phage-resistance phenotype."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "AbiU\tAbiU\t1\t1\tAbiU__AbiU",
                "notes": "The DefenseFinder rules table models AbiU as a one-component system requiring the AbiU__AbiU profile."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| AbiU__AbiU                                       | AbiU__AbiU                                       | AbiU                   | Custom                  | 60     |",
                "notes": "The DefenseFinder HMM inventory records AbiU__AbiU under the AbiU model namespace."
              }
            ]
          },
          {
            "subject": "abiu_antiphage_activity",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "lactococcal_phage_plaquing_reduction",
            "description": "AbiU activity reduces plaquing of c2, 936, and P335 lactococcal phages.",
            "evidence": [
              {
                "reference": "PMID:11679349",
                "snippet": "AbiU confers resistance to phages from the three main industrially relevant lactococcal phage species: c2, 936, and P335.",
                "notes": "Dai et al. measured AbiU activity against c2, 936, and P335 phages."
              },
              {
                "reference": "PMID:11679349",
                "snippet": "The presence of AbiU reduced the efficiency of plaquing against specific phage from each species as follows: 3.7 x 10(-1), 1.0 x 10(-2), and 1.0 x 10(-1), respectively.",
                "notes": "Dai et al. quantified phage-specific AbiU EOP reductions."
              }
            ]
          },
          {
            "subject": "abiu_antiphage_activity",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "phage_transcription_delay",
            "description": "AbiU activity delays transcription of lactococcal phages 712 and c2.",
            "evidence": [
              {
                "reference": "PMID:11679349",
                "snippet": "AbiU appeared to delay transcription of both phage 712 and c2",
                "notes": "Dai et al. detected delayed phage 712 and c2 transcription in the presence of AbiU."
              }
            ]
          },
          {
            "subject": "lactococcal_phage_plaquing_reduction",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "abiu_system_trait",
            "description": "Reduced c2/936/P335 lactococcal phage plaquing realizes the AbiU abortive-infection trait.",
            "evidence": [
              {
                "reference": "PMID:11679349",
                "snippet": "This study reports on the identification and characterization of a novel abortive infection system, AbiU, from Lactococcus lactis.",
                "notes": "Dai et al. place AbiU in the abortive-infection class of phage defense."
              },
              {
                "reference": "PMID:11679349",
                "snippet": "The presence of AbiU reduced the efficiency of plaquing against specific phage from each species",
                "notes": "Dai et al. linked AbiU to reduced lactococcal phage plaquing."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "AbiU | 10\\.1016/j\\.mib\\.2005\\.06\\.006 | Phage abortive infection in lactococci: variations on a theme",
                "notes": "The DefenseFinder article registry maps the named AbiU model namespace to a lactococcal abortive-infection review."
              }
            ]
          },
          {
            "subject": "phage_transcription_delay",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "abiu_system_trait",
            "description": "Delayed 712/c2 phage transcription contributes to the AbiU abortive-infection trait.",
            "evidence": [
              {
                "reference": "PMID:11679349",
                "snippet": "AbiU appeared to delay transcription of both phage 712 and c2",
                "notes": "Dai et al. identified delayed phage transcription as an AbiU-associated output."
              }
            ]
          },
          {
            "subject": "abiu_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "abortive_infection_system_trait",
            "description": "AbiU system possession is an abortive-infection-system trait.",
            "evidence": [
              {
                "reference": "PMID:11679349",
                "snippet": "This study reports on the identification and characterization of a novel abortive infection system, AbiU",
                "notes": "Dai et al. place AbiU in the abortive-infection class of phage defense."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "abiu-orf-and-transcription-gap",
        "prompt": "Resolve the AbiU phage trigger, direct AbiU1 and AbiU2 functions, and phage-transcription-delay route before minting narrower AbiU mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Dai et al. support AbiU as a named lactococcal abortive-infection system that reduces plaquing of c2, 936, and P335 phages and delays 712 and c2 phage transcription. DefenseFinder represents AbiU with a one-profile rule, but this first system-level record leaves the phage trigger, AbiU1 molecular function, AbiU2 downregulation route, natural locus breadth, and phage escape routes unresolved.",
        "attaches_to": [
          "causal_graphs#abiu_locus_delays_lactococcal_phage_transcription"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-20"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-20T22:48:12Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted AbiU system as a DOI-backed GENOMICS TraitRecord under the abortive infection system parent after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v198.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000300",
    "label": "AbiV system",
    "definition": "An abortive infection system in which an organism possesses an abiV locus whose encoded AbiV protein can restrict 936-like or c2-like lactococcal phages by interacting with phage-encoded SaV and inhibiting phage protein translation.",
    "definition_source": "DOI:10.1128/AEM.00093-10",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000214"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1128/AEM.00780-08",
        "snippet": "We report here a novel lactococcal Abi system, designated AbiV, which is chromosomally encoded and effective against virulent phages belonging to the 936 and c2 species",
        "notes": "Haaber et al. name AbiV as a chromosomal lactococcal abortive-infection system that can defend against 936- and c2-group virulent phages."
      },
      {
        "reference": "DOI:10.1128/AEM.00780-08",
        "snippet": "This gene was also found to confer phage resistance to L. lactis MG1363 when it was cloned into an expression vector",
        "notes": "Haaber et al. show that expressing the AbiV open reading frame is sufficient to confer phage resistance in Lactococcus lactis MG1363."
      },
      {
        "reference": "DOI:10.1128/AEM.00780-08",
        "snippet": "A subsequent frameshift mutation in the ORF completely eliminated the phage resistance phenotype, confirming that the ORF was necessary for phage resistance",
        "notes": "Haaber et al. show that the AbiV open reading frame is necessary for the cloned resistance phenotype."
      },
      {
        "reference": "DOI:10.1128/AEM.00780-08",
        "snippet": "the data show that the phage resistance mechanism encoded by orf1 is an abortive infection mechanism",
        "notes": "Haaber et al. classify the orf1/abiV resistance determinant as an abortive-infection mechanism."
      },
      {
        "reference": "DOI:10.1128/AEM.00780-08",
        "snippet": "AbiV prevented cleavage of the replicated phage DNA and thus that it acts at a later stage of the phage infection process",
        "notes": "Haaber et al. localize AbiV activity after phage DNA replication and connect it to failed DNA cleavage."
      },
      {
        "reference": "DOI:10.1128/AEM.00780-08",
        "snippet": "AbiV inhibits proliferation of small isometric phages belonging to the 936 species and of prolate phages belonging to the c2 species",
        "notes": "Haaber et al. support the observed 936- and c2-species phage sensitivity of the AbiV system."
      },
      {
        "reference": "DOI:10.1128/AEM.02093-08",
        "snippet": "The orf was named sav (for sensitivity to AbiV), and the encoded polypeptide was named SaV",
        "notes": "Haaber et al. name the phage sav gene and encoded SaV protein after AbiV-insensitive phage mutant sequencing."
      },
      {
        "reference": "DOI:10.1128/AEM.02093-08",
        "snippet": "Analyses of the sav regions in other AbiV-insensitive phage mutants from both the 936 and c2 groups revealed amino acid changes in the central region of the SaV protein",
        "notes": "Haaber et al. show that AbiV escape in 936- and c2-group phages maps to the conserved central region of SaV."
      },
      {
        "reference": "DOI:10.1128/AEM.00093-10",
        "snippet": "they strongly and specifically interact with each other to form a stable protein complex",
        "notes": "Haaber et al. demonstrate a strong, specific direct interaction between the host AbiV protein and phage SaV."
      },
      {
        "reference": "DOI:10.1128/AEM.00093-10",
        "snippet": "Western blotting showed that translation of both early and late phage proteins was severely inhibited in the presence of AbiV",
        "notes": "Haaber et al. connect AbiV-SaV activity to a severe block in phage protein translation."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "AbiV | 10\\.1128/AEM\\.00780-08 | AbiV, a novel antiphage abortive infection mechanism on the chromosome of Lactococcus lactis subsp\\. cremoris MG1363",
        "notes": "The DefenseFinder article registry maps the named AbiV system to the Haaber et al. AbiV paper."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| AbiV__AbiV                                       | AbiV__AbiV                                       | AbiV                   | Custom                  | 20     |",
        "notes": "The DefenseFinder HMM inventory records the custom AbiV profile in the AbiV model namespace."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "AbiV\tAbiV\t1\t1\tAbiV__AbiV",
        "notes": "The DefenseFinder rules table models AbiV as a single-profile system."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1358",
        "taxon_label": "Lactococcus lactis",
        "note": "Haaber et al. discovered abiV on the Lactococcus lactis subsp. cremoris MG1363 chromosome, expressed it in Lactococcus lactis MG1363, and showed that its expression conferred abortive-infection phage resistance.",
        "reference": "DOI:10.1128/AEM.00780-08"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "abiv_sav_translation_block",
        "title": "AbiV-SaV activity blocks phage protein translation",
        "description": "Evidence-backed process sketch linking an abiV locus to AbiV antiphage activity, phage sav sensitivity determinants, AbiV-SaV complex formation, inhibited host translation, blocked phage protein synthesis, restricted phage propagation, and abortive-infection system possession.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures the SaV-dependent AbiV complex and translation block without asserting the direct host translational target of the complex, the detailed route to late phage-DNA maturation arrest, or why one tested 936 phage and the P335 phages were insensitive.",
        "nodes": [
          {
            "node_id": "abiv_locus",
            "label": "abiV locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "An abortive-infection locus encoding the AbiV phage resistance determinant."
          },
          {
            "node_id": "abiv_antiphage_activity",
            "label": "AbiV antiphage activity",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Abortive-infection antiphage activity mediated by the AbiV protein."
          },
          {
            "node_id": "sav_phage_gene",
            "label": "sav phage gene",
            "node_type": "GENETIC_ELEMENT",
            "description": "A 936-like or c2-like phage gene whose encoded SaV protein is required for AbiV sensitivity."
          },
          {
            "node_id": "abiv_sav_complex_formation",
            "label": "AbiV-SaV complex formation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Direct interaction of AbiV and phage SaV homodimers to form a stable AbiV-SaV complex."
          },
          {
            "node_id": "inhibited_host_translation",
            "label": "inhibited host translational machinery",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "AbiV-SaV-dependent inhibition of the host translational machinery during phage infection."
          },
          {
            "node_id": "blocked_phage_protein_synthesis",
            "label": "blocked phage protein synthesis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced translation of early and late phage proteins in an AbiV-containing infected host cell."
          },
          {
            "node_id": "stalled_phage_dna_maturation",
            "label": "stalled phage DNA maturation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Late phage DNA maturation block in which replicated concatemeric 936-like phage DNA is not cleaved into mature resolved DNA."
          },
          {
            "node_id": "restricted_phage_propagation",
            "label": "restricted phage propagation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced completion of 936-like or c2-like phage propagation in an AbiV-containing infected host cell."
          },
          {
            "node_id": "abiv_system_trait",
            "label": "AbiV system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000300",
            "description": "Possession of a genome-encoded AbiV abortive-infection system."
          },
          {
            "node_id": "abortive_infection_system_trait",
            "label": "abortive infection system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000214",
            "description": "Possession of a genome-encoded abortive-infection phage defense system."
          }
        ],
        "edges": [
          {
            "subject": "abiv_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "abiv_antiphage_activity",
            "description": "The abiV locus encodes the protein required for the cloned phage-resistance phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.00780-08",
                "snippet": "A subsequent frameshift mutation in the ORF completely eliminated the phage resistance phenotype",
                "notes": "Haaber et al. abolish the phenotype with a frameshift in the AbiV open reading frame."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| AbiV__AbiV                                       | AbiV__AbiV                                       | AbiV                   | Custom                  | 20     |",
                "notes": "The DefenseFinder HMM inventory records the custom AbiV profile in the AbiV model namespace."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "AbiV\tAbiV\t1\t1\tAbiV__AbiV",
                "notes": "The DefenseFinder rules table models AbiV as a single-profile system requiring the AbiV profile."
              }
            ]
          },
          {
            "subject": "sav_phage_gene",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "abiv_sav_complex_formation",
            "description": "The early phage sav gene encodes SaV, the phage protein needed for AbiV sensitivity.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.02093-08",
                "snippet": "we concluded that orf26 of phage p2 is involved in sensitivity to AbiV, and the gene was renamed sav",
                "notes": "Haaber et al. identify phage p2 orf26 as the AbiV sensitivity determinant."
              },
              {
                "reference": "DOI:10.1128/AEM.02093-08",
                "snippet": "Analyses of the sav regions in other AbiV-insensitive phage mutants from both the 936 and c2 groups revealed amino acid changes in the central region of the SaV protein",
                "notes": "Haaber et al. show that AbiV escape in multiple 936- and c2-like phages maps to sav homologues."
              }
            ]
          },
          {
            "subject": "abiv_antiphage_activity",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "abiv_sav_complex_formation",
            "description": "AbiV directly and specifically interacts with SaV to form a stable AbiV-SaV complex.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.00093-10",
                "snippet": "they strongly and specifically interact with each other to form a stable protein complex",
                "notes": "Haaber et al. use SEC-MALS/UV/RI and fluorescence quenching to show direct AbiV-SaV complex formation."
              }
            ]
          },
          {
            "subject": "abiv_sav_complex_formation",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "inhibited_host_translation",
            "description": "The AbiV-SaV complex inhibits host translational machinery after early sav expression.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.00093-10",
                "snippet": "A small amount of SaV is produced early and rapidly interacts with the host AbiV protein to form an active complex that inhibits the translational machinery of the cell",
                "notes": "Haaber et al. conclude that early SaV interacts with AbiV to form the active translation-inhibiting complex."
              }
            ]
          },
          {
            "subject": "inhibited_host_translation",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "blocked_phage_protein_synthesis",
            "description": "AbiV-SaV-mediated translation inhibition blocks early and late phage protein production.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.00093-10",
                "snippet": "Western blotting showed that translation of both early and late phage proteins was severely inhibited in the presence of AbiV",
                "notes": "Haaber et al. show that AbiV blocks translation of phage protein products including SaV, ORF11, and ORF16."
              }
            ]
          },
          {
            "subject": "blocked_phage_protein_synthesis",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "restricted_phage_propagation",
            "description": "Blocked phage translation prevents completion of the AbiV-sensitive phage lytic program.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.00093-10",
                "snippet": "AbiV is an abortive infection protein that inhibits the lytic cycle of several virulent phages infecting Lactococcus lactis, while a mutation in the phage gene sav confers insensitivity to AbiV. In this study, we have further characterized the effects of the bacterial AbiV and its interaction with the phage p2 protein SaV. First, we showed that during phage infection of lactococcal AbiV\u207a cells, AbiV rapidly inhibited protein synthesis",
                "notes": "Haaber et al. frame the AbiV protein-synthesis block as part of AbiV inhibition of the phage lytic cycle."
              }
            ]
          },
          {
            "subject": "abiv_antiphage_activity",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "stalled_phage_dna_maturation",
            "description": "AbiV activity prevents cleavage of replicated 936-like phage DNA into mature resolved DNA as a downstream infection-cycle defect.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.00780-08",
                "snippet": "The results described above showed that AbiV prevented cleavage of the replicated phage DNA",
                "notes": "Haaber et al. connect AbiV to failed cleavage of replicated phage DNA."
              }
            ]
          },
          {
            "subject": "stalled_phage_dna_maturation",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "restricted_phage_propagation",
            "description": "Accumulation of nonmature concatemeric phage DNA limits completion of AbiV-sensitive phage infection.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.00780-08",
                "snippet": "indicated that phage DNA accumulated in its concatemeric (nonmature) form in the resistant L. lactis cells",
                "notes": "Haaber et al. observed uncleaved concatemeric phage DNA in AbiV-containing resistant cells."
              }
            ]
          },
          {
            "subject": "restricted_phage_propagation",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "abiv_system_trait",
            "description": "Restriction of 936-like or c2-like phage propagation realizes the AbiV abortive-infection defense trait.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.00780-08",
                "snippet": "This ORF provided resistance against virulent lactococcal phages belonging to the 936 and c2 species with an efficiency of plaquing of 10\u22124",
                "notes": "Haaber et al. support AbiV-mediated resistance to multiple 936- and c2-group lactococcal phages."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "AbiV | 10\\.1128/AEM\\.00780-08 | AbiV, a novel antiphage abortive infection mechanism on the chromosome of Lactococcus lactis subsp\\. cremoris MG1363",
                "notes": "DefenseFinder records AbiV as a named antiphage abortive-infection system from the Haaber et al. paper."
              }
            ]
          },
          {
            "subject": "abiv_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "abortive_infection_system_trait",
            "description": "AbiV system possession is an abortive-infection-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.00780-08",
                "snippet": "the gene was designated abiV and the Abi mechanism was designated AbiV",
                "notes": "Haaber et al. name the abiV-encoded phage resistance determinant as an Abi mechanism."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "abiv-mechanism-gap",
        "prompt": "Resolve the host translational target of the AbiV-SaV complex before minting narrower AbiV mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Haaber et al. identify phage sav as the determinant of AbiV sensitivity and support direct AbiV-SaV complex formation followed by inhibition of phage protein translation, but the precise host translational target and complete route from the AbiV-SaV complex to abortive infection remain unresolved.",
        "attaches_to": [
          "causal_graphs#abiv_sav_translation_block"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-20"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-20T03:07:25Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted AbiV system as a DOI-backed GENOMICS TraitRecord under the abortive infection system parent after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v177.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-20T03:38:10Z",
        "curator": "codex",
        "action": "ADD_FOLLOWUP_MECHANISM_EVIDENCE",
        "changes": "Added the Haaber et al. 2009 and 2010 AbiV follow-up papers after adversarial review; revised the definition, causal graph, and knowledge gap to include phage sav, direct AbiV-SaV complex formation, and AbiV-SaV-linked inhibition of phage protein translation.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-20T04:10:00Z",
        "curator": "codex",
        "action": "REFINE_FOLLOWUP_MECHANISM_EVIDENCE",
        "changes": "Refined the AbiV follow-up graph after adversarial review by using lytic-cycle and protein-synthesis evidence for the translation-block propagation edge.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000228",
    "label": "AbiZ system",
    "definition": "An abortive infection system in which an organism possesses an abiZ locus encoding a membrane-associated lactococcal phage-resistance determinant that accelerates infected-cell lysis through AbiZ-enhanced holin/lysin activity and restricts P335 phage propagation.",
    "definition_source": "DOI:10.1128/JB.00904-06",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000214"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1128/JB.00904-06",
        "snippet": "A single ORF, designated abiZ, was found to be responsible for a significant reduction in plaque size and an efficiency of plaquing (EOP) of 10\u22126, without affecting phage adsorption",
        "notes": "Durmaz and Klaenhammer localized the pTR2030 AbiZ phage resistance determinant to the abiZ open reading frame."
      },
      {
        "reference": "DOI:10.1128/JB.00904-06",
        "snippet": "The new phage resistance gene, designated abiZ, encodes an abortive infection resistance which results in cell death after infection and appears to limit the production of progeny phage",
        "notes": "Durmaz and Klaenhammer place the abiZ determinant in the abortive-infection class rather than adsorption or restriction-modification defense."
      },
      {
        "reference": "DOI:10.1128/JB.00904-06",
        "snippet": "The average burst size of \u03c631 on NCK203(pTRKH2) of 316 \u00b1 68 was reduced by two logs to 3 \u00b1 1.4 for NCK203(pTRKH2:E4)",
        "notes": "Durmaz and Klaenhammer show that the abiZ-containing subclone strongly reduces production of infectious phage progeny."
      },
      {
        "reference": "DOI:10.1128/JB.00904-06",
        "snippet": "The measures of both optical density and viable cell count showed that holin- and lysin-induced lysis in the phage-free system occurred 30 min earlier when AbiZ was present",
        "notes": "Durmaz and Klaenhammer support AbiZ-associated acceleration of holin/lysin-driven cell lysis."
      },
      {
        "reference": "DOI:10.1128/JB.00904-06",
        "snippet": "AbiZ enhances the permeability of cells in which holin alone was expressed",
        "notes": "Durmaz and Klaenhammer connect AbiZ to increased membrane-permeability in holin-induced cells."
      },
      {
        "reference": "DOI:10.1371/journal.pone.0298680",
        "snippet": "We focus our investigation on AbiZ, an abortive infection mechanism discovered and described by Durmaz et al. [18] as leading to premature cell lysis during phage infection, and one of the most understood Abi mechanisms on L. lactis",
        "notes": "Philippe et al. support AbiZ as a named Lactococcus abortive infection mechanism with phage-induced premature lysis."
      },
      {
        "reference": "DOI:10.1371/journal.pone.0298680",
        "snippet": "NCK4 and IL6 cells were made electrocompetent and then electroporated with plasmid pTRK914 (pTRK686:abiZ, Cmr) to obtain NCK5 and IL7 (AbiZ+) using methods from [31]",
        "notes": "Philippe et al. reused the abiZ-containing pTRK914 plasmid to construct independent AbiZ-positive Lactococcus strains."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1358",
        "taxon_label": "Lactococcus lactis",
        "note": "Durmaz and Klaenhammer localized the pTR2030 abiZ determinant from Lactococcus lactis ME2 and showed that abiZ expression in Lactococcus lactis NCK203 produced abortive phage resistance with premature lysis of phage-infected cells.",
        "reference": "DOI:10.1128/JB.00904-06"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "abiz_premature_lysis_antiphage_activity",
        "title": "AbiZ accelerates premature lysis to restrict P335 phages",
        "description": "Evidence-backed process sketch linking an abiZ locus to enhanced holin/lysin activity, premature infected-cell lysis, restricted phage propagation, and abortive-infection system possession.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures AbiZ at the system level without asserting a direct physical AbiZ-holin interaction, an exact phage activator, or one known phage-escape mutation.",
        "nodes": [
          {
            "node_id": "abiz_locus",
            "label": "abiZ locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "An abortive-infection locus encoding the membrane-associated AbiZ phage resistance determinant."
          },
          {
            "node_id": "abiz_enhanced_holin_lysin_activity",
            "label": "AbiZ-enhanced holin/lysin activity",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Phage holin/lysin-associated lysis activity that is accelerated in cells carrying AbiZ."
          },
          {
            "node_id": "premature_infected_cell_lysis",
            "label": "premature infected-cell lysis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Early lysis of a phage-infected host cell before many infectious phage particles have been assembled."
          },
          {
            "node_id": "restricted_phage_propagation",
            "label": "restricted phage propagation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced completion of P335 phage propagation in an AbiZ-containing infected host cell."
          },
          {
            "node_id": "abiz_system_trait",
            "label": "AbiZ system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000228",
            "description": "Possession of a genome-encoded AbiZ premature-lysis abortive-infection system."
          },
          {
            "node_id": "abortive_infection_system_trait",
            "label": "abortive infection system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000214",
            "description": "Possession of a genome-encoded abortive-infection phage defense system."
          }
        ],
        "edges": [
          {
            "subject": "abiz_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "abiz_enhanced_holin_lysin_activity",
            "description": "The abiZ locus contributes to accelerated holin/lysin-driven lysis.",
            "evidence": [
              {
                "reference": "DOI:10.1128/JB.00904-06",
                "snippet": "The measures of both optical density and viable cell count showed that holin- and lysin-induced lysis in the phage-free system occurred 30 min earlier when AbiZ was present",
                "notes": "Durmaz and Klaenhammer assayed \u03c631 holin and lysin expression in the presence of abiZ."
              }
            ]
          },
          {
            "subject": "abiz_enhanced_holin_lysin_activity",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "premature_infected_cell_lysis",
            "description": "AbiZ-enhanced lysis activity contributes to premature lysis of phage-infected cells.",
            "evidence": [
              {
                "reference": "DOI:10.1128/JB.00904-06",
                "snippet": "AbiZ enhances the permeability of cells in which holin alone was expressed",
                "notes": "Durmaz and Klaenhammer connect AbiZ to enhanced holin-associated membrane permeability."
              }
            ]
          },
          {
            "subject": "premature_infected_cell_lysis",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "restricted_phage_propagation",
            "description": "Premature AbiZ-associated lysis limits the yield of infectious P335 phage progeny.",
            "evidence": [
              {
                "reference": "DOI:10.1128/JB.00904-06",
                "snippet": "The average burst size of \u03c631 on NCK203(pTRKH2) of 316 \u00b1 68 was reduced by two logs to 3 \u00b1 1.4 for NCK203(pTRKH2:E4)",
                "notes": "Durmaz and Klaenhammer measured a lower single-step burst size in cells carrying the AbiZ-active E4 subclone."
              }
            ]
          },
          {
            "subject": "restricted_phage_propagation",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "abiz_system_trait",
            "description": "Restriction of P335 phage propagation realizes the AbiZ abortive-infection defense trait.",
            "evidence": [
              {
                "reference": "DOI:10.1128/JB.00904-06",
                "snippet": "The new phage resistance gene, designated abiZ, encodes an abortive infection resistance which results in cell death after infection and appears to limit the production of progeny phage",
                "notes": "Durmaz and Klaenhammer classify abiZ as an abortive-infection phage resistance gene."
              }
            ]
          },
          {
            "subject": "abiz_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "abortive_infection_system_trait",
            "description": "AbiZ system possession is an abortive-infection-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1371/journal.pone.0298680",
                "snippet": "AbiZ, an abortive infection mechanism discovered and described by Durmaz et al. [18] as leading to premature cell lysis during phage infection",
                "notes": "Philippe et al. place AbiZ in the abortive infection class of phage defense."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-15T20:35:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted AbiZ system as a DOI-backed GENOMICS TraitRecord under the abortive infection system parent after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v105.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-15T21:04:27Z",
        "curator": "codex",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Corrected the AbiZ premature-lysis edge from mitigates restricted phage propagation to contributes to restricted phage propagation after local adversarial review issue 962 identified that the old predicate inverted the intended antiphage effect.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000214",
    "label": "abortive infection system",
    "definition": "A genomics trait describing possession of a bacteriophage abortive-infection defense system in which phage infection activates a host-encoded growth-arrest or cell-death program that prevents completion of phage replication and protects nearby bacterial cells.",
    "definition_source": "DOI:10.1146/annurev-virology-011620-040628",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "Abi system",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1093/nar/gkt1419"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev-virology-011620-040628",
        "snippet": "A commonly used phage resistance strategy is abortive infection (Abi), in which the infected cell commits suicide before the phage can complete its replication cycle",
        "notes": "Lopatina et al. support abortive infection as a phage resistance strategy that blocks completion of the phage replication cycle."
      },
      {
        "reference": "DOI:10.1146/annurev-virology-011620-040628",
        "snippet": "The Abi strategy is manifested by a plethora of mechanistically diverse defense systems that are abundant in bacterial genomes",
        "notes": "Lopatina et al. support defining the trait at the broad Abi system level rather than as one toxin-antitoxin family."
      },
      {
        "reference": "DOI:10.1073/pnas.0808832106",
        "snippet": "Resistance strategies include the abortive infection (Abi) systems, which promote cell death and limit phage replication within a bacterial population",
        "notes": "Fineran et al. summarize the cell-death and phage-limitation outputs of abortive infection systems."
      },
      {
        "reference": "DOI:10.1093/nar/gkt1419",
        "snippet": "AbiE systems are encoded by bicistronic operons and function via a non-interacting (Type IV) bacteriostatic TA mechanism",
        "notes": "Dy et al. support AbiE as a bacteriostatic toxin-antitoxin Abi family, one reason the parent record should cover growth arrest as well as cell death."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:29471",
        "taxon_label": "Pectobacterium atrosepticum",
        "note": "Fineran et al. identified the native toxIN locus from Erwinia carotovora subspecies atroseptica 1039 and demonstrated ToxIN-mediated phage resistance.",
        "reference": "DOI:10.1073/pnas.0808832106"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "abortive_infection_population_level_defense",
        "title": "Abortive infection halts infected cells to limit phage spread",
        "description": "Evidence-backed process sketch linking phage-triggered Abi activation to infected-host growth arrest or death, restricted phage replication, and protection of nearby bacterial cells.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures the shared Abi strategy without claiming that other abortive-infection families use one exact sensor, effector, toxin-antitoxin architecture, or cell-death mechanism.",
        "nodes": [
          {
            "node_id": "phage_infection",
            "label": "phage infection",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Entry and intracellular replication attempt by a bacteriophage infecting a host bacterium."
          },
          {
            "node_id": "abortive_infection_system_activation",
            "label": "abortive infection system activation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Phage-infection-triggered activation of a host Abi system."
          },
          {
            "node_id": "host_growth_arrest_or_cell_death",
            "label": "host growth arrest or cell death",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Abi-system output in which an infected host cell undergoes growth arrest or dies before productive phage replication is completed."
          },
          {
            "node_id": "phage_replication",
            "label": "phage replication",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Replication and completion of a bacteriophage infection cycle inside a host cell."
          },
          {
            "node_id": "bacterial_population_protection",
            "label": "bacterial population protection",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced phage spread that protects nearby bacterial cells in the same population."
          },
          {
            "node_id": "abortive_infection_system_trait",
            "label": "abortive infection system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000214",
            "description": "Possession of a genome-encoded abortive-infection phage defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "phage_infection",
            "predicate": "activates",
            "predicate_id": "RO:0002213",
            "object": "abortive_infection_system_activation",
            "description": "Phage infection triggers Abi defense-system activation.",
            "evidence": [
              {
                "reference": "DOI:10.1093/nar/gkt1419",
                "snippet": "Bacterial abortive infection (Abi) systems are \u2018altruistic\u2019 cell death systems that are activated by phage infection and limit viral replication, thereby providing protection to the bacterial population",
                "notes": "Dy et al. support phage-triggered activation as a defining Abi-system behavior."
              }
            ]
          },
          {
            "subject": "abortive_infection_system_activation",
            "predicate": "activates",
            "predicate_id": "RO:0002213",
            "object": "host_growth_arrest_or_cell_death",
            "description": "Abi activation produces growth-arrest or cell-death outputs through family-specific effectors.",
            "evidence": [
              {
                "reference": "DOI:10.1073/pnas.0808832106",
                "snippet": "Resistance strategies include the abortive infection (Abi) systems, which promote cell death and limit phage replication within a bacterial population",
                "notes": "Fineran et al. support cell death as an abortive-infection output."
              },
              {
                "reference": "DOI:10.1093/nar/gkt1419",
                "snippet": "AbiE systems are encoded by bicistronic operons and function via a non-interacting (Type IV) bacteriostatic TA mechanism",
                "notes": "Dy et al. support bacteriostasis as an AbiE output, distinct from obligate cell death."
              }
            ]
          },
          {
            "subject": "host_growth_arrest_or_cell_death",
            "predicate": "mitigates",
            "predicate_id": "METPO:2007407",
            "object": "phage_replication",
            "description": "Arrest or death of the infected host cell limits completion of phage replication.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-virology-011620-040628",
                "snippet": "A commonly used phage resistance strategy is abortive infection (Abi), in which the infected cell commits suicide before the phage can complete its replication cycle",
                "notes": "Lopatina et al. connect infected-cell death to premature phage-cycle termination."
              }
            ]
          },
          {
            "subject": "host_growth_arrest_or_cell_death",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "bacterial_population_protection",
            "description": "The local cost of infected-cell arrest or death protects neighboring bacteria by limiting onward phage spread.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-virology-011620-040628",
                "snippet": "Abi prevents the phage epidemic from spreading to nearby cells, thus protecting the bacterial colony",
                "notes": "Lopatina et al. support the population-level benefit of abortive infection."
              }
            ]
          },
          {
            "subject": "host_growth_arrest_or_cell_death",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "abortive_infection_system_trait",
            "description": "Phage-triggered infected-host arrest or death realizes the abortive-infection defense phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1073/pnas.0808832106",
                "snippet": "abortive infection (Abi) systems, which promote cell death and limit phage replication within a bacterial population",
                "notes": "Fineran et al. support cell death coupled to limited phage replication as the Abi defense output."
              }
            ]
          },
          {
            "subject": "abortive_infection_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Abortive-infection-system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-virology-011620-040628",
                "snippet": "The Abi strategy is manifested by a plethora of mechanistically diverse defense systems that are abundant in bacterial genomes",
                "notes": "Lopatina et al. place abortive infection among bacterial antiviral defense systems."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "abortive-infection-subfamily-split-gap",
        "prompt": "Resolve other abortive-infection families before minting narrower children under the broad abortive infection system parent.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "ToxIN, AbiQ, AbiE, AbiF, AbiZ, AbiK, AbiT, AbiV, BstA, Stk2, AbiH, AbiG, AbiI, AbiR, AbiD, AbiB, AbiC, AbiU, AbiAlpha, Pif, RexAB, SpbK, CmdTAC, Abi2, AbiJ, AbiL, AbiN, AbiO, AbiP2, AbiA, and PD-T4-10 are split out as traitmech:000226, traitmech:000225, traitmech:000227, traitmech:000504, traitmech:000228, traitmech:000229, traitmech:000230, traitmech:000300, traitmech:000301, traitmech:000303, traitmech:000304, traitmech:000306, traitmech:000316, traitmech:000317, traitmech:000318, traitmech:000319, traitmech:000320, traitmech:000321, traitmech:000322, traitmech:000323, traitmech:000324, traitmech:000325, traitmech:000335, traitmech:000338, traitmech:000339, traitmech:000340, traitmech:000341, traitmech:000342, traitmech:000343, traitmech:000344, and traitmech:000394, respectively. Lopatina et al., Fineran et al., Dy et al., Garvey et al., Durmaz and Klaenhammer, Wang et al., Bouchard et al., Haaber et al., Owen et al., Depardieu et al., Prevots et al., O'Connor et al., Su et al., Twomey et al., McLandsborough et al., Parreira et al., Durmaz et al., Dai et al., Lossouarn et al., Cram et al., Parma et al., Johnson et al., Vassallo et al., Chopin et al., Anba et al., Deng et al., Prevots et al., Prevots and Ritzenthaler, Odegrip et al., Dinsmore and Klaenhammer, and Dinsmore et al. still support abortive infection as a genomically encoded phage defense strategy that spans mechanistically diverse toxin-antitoxin, pNP40-derived lactococcal AbiF DNA-replication-inhibition, premature-lysis, RT-related polymerase, two-component, translation-inhibition, prophage-encoded DNA-replication-inhibition, staphylococcal-kinase-triggered cell death, lactococcal AbiH phage resistance, two-gene lactococcal AbiG RNA-synthesis interference, single-ORF lactococcal AbiI burst-size reduction, two-separated-locus lactococcal AbiR DNA-replication impediment, pBF61-derived lactococcal AbiD burst-size reduction, lactococcal AbiB phage-transcript decay, lactococcal AbiC Prf infected-cell death, lactococcal AbiU phage-transcription delay, enterococcal AbiAlpha premature lysis, F-plasmid pif-region T7 abortive infection, lambda Rex two-component phage exclusion, ICEBs1 SpbK abortive SP\u03b2 defense, CmdTAC mRNA ADP-ribosyltransferase abortive infection, DefenseFinder Abi2/PF07751 Abi-like loci, single-profile lactococcal AbiJ loci, two-component lactococcal AbiL ATPase/TOPRIM-family loci, single-gene lactococcal AbiN loci, single-profile lactococcal AbiO loci, single-profile coliphage AbiP2 reverse-transcriptase-like loci, lactococcal AbiA loci represented by DefenseFinder AbiA-large and AbiA-small subrules, DefenseFinder PD-T4-10 two-profile loci, and other families. Additional narrower TraitRecords need separate review to ground each subfamily's trigger, effector, growth-arrest or cell-death mechanism, and phage escape routes.",
        "posed_by": "codex",
        "posed_date": "2026-09-15"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-15T11:47:52Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted abortive infection system as a DOI-backed GENOMICS TraitRecord under the phage defense system parent after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v91.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-15T18:45:01Z",
        "curator": "codex",
        "action": "RESOLVE_DISCUSSION_SCOPE",
        "changes": "Removed AbiQ from the open abortive-infection subfamily split-gap discussion after minting traitmech:000225 for the AbiQ system; ToxIN, AbiE, and other abortive-infection families remain open.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-15T19:25:01Z",
        "curator": "codex",
        "action": "RESOLVE_DISCUSSION_SCOPE",
        "changes": "Removed ToxIN from the open abortive-infection subfamily split-gap discussion after minting traitmech:000226 for the ToxIN system; AbiE and other abortive-infection families remain open.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-15T19:46:31Z",
        "curator": "codex",
        "action": "RESOLVE_DISCUSSION_SCOPE",
        "changes": "Removed AbiE from the open abortive-infection subfamily split-gap discussion after minting traitmech:000227 for the AbiE system; other abortive-infection families remain open.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-15T20:35:01Z",
        "curator": "codex",
        "action": "RESOLVE_DISCUSSION_SCOPE",
        "changes": "Documented AbiZ as split out in the open abortive-infection subfamily split-gap discussion after minting traitmech:000228 for the AbiZ system; other abortive-infection families remain open.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-15T21:30:01Z",
        "curator": "codex",
        "action": "RESOLVE_DISCUSSION_SCOPE",
        "changes": "Documented AbiK as split out in the open abortive-infection subfamily split-gap discussion after minting traitmech:000229 for the AbiK system; other abortive-infection families remain open.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-15T22:05:01Z",
        "curator": "codex",
        "action": "RESOLVE_DISCUSSION_SCOPE",
        "changes": "Documented AbiT as split out in the open abortive-infection subfamily split-gap discussion after minting traitmech:000230 for the AbiT system; other abortive-infection families remain open.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-20T03:07:26Z",
        "curator": "codex",
        "action": "RESOLVE_DISCUSSION_SCOPE",
        "changes": "Documented AbiV as split out in the open abortive-infection subfamily split-gap discussion after minting traitmech:000300 for the AbiV system; other abortive-infection families remain open.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-20T04:10:01Z",
        "curator": "codex",
        "action": "RESOLVE_DISCUSSION_SCOPE",
        "changes": "Reframed AbiV in the open abortive-infection subfamily split-gap discussion as a translation-inhibition family after adding the Haaber et al. AbiV-SaV follow-up evidence.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-20T04:37:49Z",
        "curator": "codex",
        "action": "RESOLVE_DISCUSSION_SCOPE",
        "changes": "Documented BstA as split out in the open abortive-infection subfamily split-gap discussion after minting traitmech:000301 for the BstA system; other abortive-infection families remain open.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-20T07:41:01Z",
        "curator": "codex",
        "action": "RESOLVE_DISCUSSION_SCOPE",
        "changes": "Documented Stk2 as split out in the open abortive-infection subfamily split-gap discussion after minting traitmech:000303 for the Stk2 system; other abortive-infection families remain open.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-20T08:12:01Z",
        "curator": "codex",
        "action": "RESOLVE_DISCUSSION_SCOPE",
        "changes": "Documented AbiH as split out in the open abortive-infection subfamily split-gap discussion after minting traitmech:000304 for the AbiH system; other abortive-infection families remain open.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-20T09:16:01Z",
        "curator": "codex",
        "action": "RESOLVE_DISCUSSION_SCOPE",
        "changes": "Documented AbiG as split out in the open abortive-infection subfamily split-gap discussion after minting traitmech:000306 for the AbiG system; other abortive-infection families remain open.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-20T18:33:35Z",
        "curator": "codex",
        "action": "RESOLVE_DISCUSSION_SCOPE",
        "changes": "Documented AbiI as split out in the open abortive-infection subfamily split-gap discussion after minting traitmech:000316 for the AbiI system; other abortive-infection families remain open.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-20T19:30:11Z",
        "curator": "codex",
        "action": "RESOLVE_DISCUSSION_SCOPE",
        "changes": "Documented AbiR as split out in the open abortive-infection subfamily split-gap discussion after minting traitmech:000317 for the AbiR system; other abortive-infection families remain open.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-20T20:30:21Z",
        "curator": "codex",
        "action": "RESOLVE_DISCUSSION_SCOPE",
        "changes": "Documented AbiD as split out in the open abortive-infection subfamily split-gap discussion after minting traitmech:000318 for the AbiD system; other abortive-infection families remain open.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-20T21:21:13Z",
        "curator": "codex",
        "action": "RESOLVE_DISCUSSION_SCOPE",
        "changes": "Documented AbiB as split out in the open abortive-infection subfamily split-gap discussion after minting traitmech:000319 for the AbiB system; other abortive-infection families remain open.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-20T22:01:25Z",
        "curator": "codex",
        "action": "RESOLVE_DISCUSSION_SCOPE",
        "changes": "Documented AbiC as split out in the open abortive-infection subfamily split-gap discussion after minting traitmech:000320 for the AbiC system; other abortive-infection families remain open.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-20T22:48:13Z",
        "curator": "codex",
        "action": "RESOLVE_DISCUSSION_SCOPE",
        "changes": "Documented AbiU as split out in the open abortive-infection subfamily split-gap discussion after minting traitmech:000321 for the AbiU system; other abortive-infection families remain open.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-20T23:47:18Z",
        "curator": "codex",
        "action": "RESOLVE_DISCUSSION_SCOPE",
        "changes": "Documented AbiAlpha as split out in the open abortive-infection subfamily split-gap discussion after minting traitmech:000322 for the AbiAlpha system; other abortive-infection families remain open.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-21T01:30:13Z",
        "curator": "codex",
        "action": "RESOLVE_DISCUSSION_SCOPE",
        "changes": "Documented Pif as split out in the open abortive-infection subfamily split-gap discussion after minting traitmech:000323 for the Pif system; other abortive-infection families remain open.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-21T02:17:08Z",
        "curator": "codex",
        "action": "RESOLVE_DISCUSSION_SCOPE",
        "changes": "Documented RexAB as split out in the open abortive-infection subfamily split-gap discussion after minting traitmech:000324 for the RexAB system; other abortive-infection families remain open.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-21T03:22:01Z",
        "curator": "codex",
        "action": "RESOLVE_DISCUSSION_SCOPE",
        "changes": "Documented SpbK as split out in the open abortive-infection subfamily split-gap discussion after minting traitmech:000325 for the SpbK system; other abortive-infection families remain open.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-21T03:45:00Z",
        "curator": "codex",
        "action": "REVISED_TEXT",
        "changes": "Standardized curator-written SP\u03b2 phage mentions to the canonical Greek beta spelling while preserving Johnson et al. evidence snippets exactly as exposed by the PLOS XML.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-21T12:07:14Z",
        "curator": "codex",
        "action": "RESOLVE_DISCUSSION_SCOPE",
        "changes": "Documented CmdTAC as split out in the open abortive-infection subfamily split-gap discussion after minting traitmech:000335 for the CmdTAC system; other abortive-infection families remain open.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-21T12:26:31Z",
        "curator": "codex",
        "action": "ADDRESS_PR_REVIEW",
        "changes": "Corrected the CmdTAC split-gap source attribution from Goesswein et al. to Vassallo et al. after verifying DOI:10.1038/s41586-024-08102-8 against Crossref and Europe PMC metadata.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-21T14:52:54Z",
        "curator": "codex",
        "action": "RESOLVE_DISCUSSION_SCOPE",
        "changes": "Documented Abi2 as split out in the open abortive-infection subfamily split-gap discussion after minting traitmech:000338 for the Abi2 system; other abortive-infection families remain open.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-21T16:24:10Z",
        "curator": "codex",
        "action": "RESOLVE_DISCUSSION_SCOPE",
        "changes": "Documented AbiJ as split out in the open abortive-infection subfamily split-gap discussion after minting traitmech:000339 for the AbiJ system; other abortive-infection families remain open.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-21T17:17:23Z",
        "curator": "codex",
        "action": "RESOLVE_DISCUSSION_SCOPE",
        "changes": "Documented AbiL as split out in the open abortive-infection subfamily split-gap discussion after minting traitmech:000340 for the AbiL system; other abortive-infection families remain open.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-21T17:52:23Z",
        "curator": "codex",
        "action": "RESOLVE_DISCUSSION_SCOPE",
        "changes": "Documented AbiN as split out in the open abortive-infection subfamily split-gap discussion after minting traitmech:000341 for the AbiN system; other abortive-infection families remain open.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-21T18:34:42Z",
        "curator": "codex",
        "action": "RESOLVE_DISCUSSION_SCOPE",
        "changes": "Documented AbiO as split out in the open abortive-infection subfamily split-gap discussion after minting traitmech:000342 for the AbiO system; other abortive-infection families remain open.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-21T19:10:27Z",
        "curator": "codex",
        "action": "RESOLVE_DISCUSSION_SCOPE",
        "changes": "Documented AbiP2 as split out in the open abortive-infection subfamily split-gap discussion after minting traitmech:000343 for the AbiP2 system; other abortive-infection families remain open.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-21T20:16:03Z",
        "curator": "codex",
        "action": "RESOLVE_DISCUSSION_SCOPE",
        "changes": "Documented AbiA as split out in the open abortive-infection subfamily split-gap discussion after minting traitmech:000344 for the AbiA system; other abortive-infection families remain open.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-26T21:25:00Z",
        "curator": "codex",
        "action": "RESOLVE_DISCUSSION_SCOPE",
        "changes": "Addressed review issue #1298 by documenting PD-T4-10 as split out in the open abortive-infection subfamily split-gap discussion after minting traitmech:000394 for the PD-T4-10 system; other abortive-infection families remain open.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-01T01:32:45Z",
        "curator": "codex",
        "action": "RESOLVE_DISCUSSION_SCOPE",
        "changes": "Documented AbiF as split out in the open abortive-infection subfamily split-gap discussion after minting traitmech:000504 for the AbiF system; other abortive-infection families remain open.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-01T03:14:00Z",
        "curator": "codex",
        "action": "ADDRESS_ABIF_REVIEW_FINDING",
        "changes": "Addressed adversarial review issue #1505 by clarifying that pNP40 is the AbiF determinant source context and that pCG1 is the recombinant plasmid clone used in the Garvey et al. subcloning experiment.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000247",
    "label": "Aditi system",
    "definition": "A phage defense system in which an organism possesses a two-component Aditi locus represented by DitA and DitB profiles that can protect bacteria from bacteriophage infection.",
    "definition_source": "DOI:10.1016/j.chom.2022.09.017",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "Aditi",
        "synonym_type": "EXACT_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1016/j.chom.2022.09.017",
        "snippet": "discovery of 21 defense systems that protect bacteria from phages, based on computational genomic analyses and phage-infection experiments",
        "notes": "Millman et al. report the computational and experimental cohort that DefenseFinder cites for Aditi as a bacterial anti-phage system."
      },
      {
        "reference": "DOI:10.1101/2022.05.11.491447",
        "snippet": "discovery of 21 new defense systems that protect bacteria from phages, based on computational genomic analyses and phage infection experiments",
        "notes": "The bioRxiv version of Millman et al. independently carries the 21-system discovery claim linked from DefenseFinder's Aditi article registry."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "Aditi | 10\\.1101/2022\\.05\\.11\\.491447 | An expanding arsenal of immune systems that protect bacteria from phages",
        "notes": "The DefenseFinder model registry maps the named Aditi system to the Millman et al. antiphage-system discovery preprint."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "Aditi__DitA, Aditi__DitB",
        "notes": "The DefenseFinder rules table models Aditi as a system with DitA and DitB mandatory profiles."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "Aditi__DitA                                      | Aditi__DitA                                      | Aditi",
        "notes": "The DefenseFinder HMM inventory records DitA as an Aditi profile."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "Aditi__DitB                                      | Aditi__DitB                                      | Aditi",
        "notes": "The DefenseFinder HMM inventory records DitB as an Aditi profile."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "aditi_locus_restricts_phage",
        "title": "Aditi loci confer bacterial phage defense",
        "description": "Conservative system-level sketch linking possession of an Aditi locus to restricted bacteriophage propagation without asserting the unresolved phage trigger or molecular output.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Aditi as a named anti-phage system with DitA and DitB DefenseFinder profiles while leaving its phage trigger, molecular substrate, antiviral effector output, and subtype breadth unresolved.",
        "nodes": [
          {
            "node_id": "aditi_locus",
            "label": "Aditi locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "An Aditi anti-phage defense locus containing DitA and DitB components."
          },
          {
            "node_id": "restricted_phage_propagation",
            "label": "restricted phage propagation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced propagation of bacteriophage in cells carrying the Aditi system."
          },
          {
            "node_id": "aditi_system_trait",
            "label": "Aditi system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000247",
            "description": "Possession of a genome-encoded Aditi phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "aditi_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "restricted_phage_propagation",
            "description": "DefenseFinder maps Aditi to a bacterial anti-phage-system discovery preprint and represents Aditi loci through DitA and DitB component profiles.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.chom.2022.09.017",
                "snippet": "discovery of 21 defense systems that protect bacteria from phages",
                "notes": "Millman et al. describe the anti-phage discovery cohort that the DefenseFinder Aditi registry row maps to the Aditi system."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Aditi | 10\\.1101/2022\\.05\\.11\\.491447 | An expanding arsenal of immune systems that protect bacteria from phages",
                "notes": "The DefenseFinder registry maps Aditi itself to the Millman et al. bacterial antiphage-system discovery preprint."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "Aditi__DitA, Aditi__DitB",
                "notes": "The DefenseFinder rules table supports DitA and DitB as the mandatory Aditi system profiles."
              }
            ]
          },
          {
            "subject": "restricted_phage_propagation",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "aditi_system_trait",
            "description": "Aditi-mediated phage restriction realizes the Aditi system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.chom.2022.09.017",
                "snippet": "discovery of 21 defense systems that protect bacteria from phages",
                "notes": "Millman et al. place the Aditi discovery cohort in the set of bacterial systems that protect against phages."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Aditi | 10\\.1101/2022\\.05\\.11\\.491447 | An expanding arsenal of immune systems that protect bacteria from phages",
                "notes": "DefenseFinder records Aditi as a named system from the Millman et al. antiphage discovery preprint."
              }
            ]
          },
          {
            "subject": "aditi_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Aditi system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "An expanding arsenal of immune systems that protect bacteria from phages",
                "notes": "DefenseFinder associates Aditi with the Millman et al. bacterial antiphage-system discovery paper."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "aditi-mechanism-gap",
        "prompt": "Resolve Aditi phage triggers and effector outputs before minting narrower Aditi mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Millman et al. and DefenseFinder support Aditi as a named anti-phage system with DitA and DitB profiles, but the trigger, molecular substrate, antiviral effector output, and subtype-specific mechanism are not resolved enough here to assert a narrower mechanistic child trait.",
        "attaches_to": [
          "causal_graphs#aditi_locus_restricts_phage"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-18"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-18T18:47:25Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Aditi system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v124.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000329",
    "label": "Ambrosia system",
    "definition": "A phage defense system in which an organism possesses a five-gene Ambrosia locus encoding AbrR, AbrA, AbrB, AbrC, and AbrD components that can limit siphophage and myophage propagation.",
    "definition_source": "DOI:10.1101/2025.09.30.679545",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "Ambrosia",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1101/2025.09.30.679545"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1101/2025.09.30.679545",
        "snippet": "From over 500 candidate defense systems, we selected nine for experimental testing and validated three: Dionysus, a TerB-encoding system that disrupts early phage infection vesicle formation by Jumbo phages; Ophion, a Radical SAM-containing system that prevents the formation of the Jumbo phage nucleus; and Ambrosia, a tightly regulated RM-like system.",
        "notes": "Keesman et al. named Ambrosia among three modular phage-defense candidates validated experimentally from an initial pool of more than 500 candidates."
      },
      {
        "reference": "DOI:10.1101/2025.09.30.679545",
        "snippet": "Ambrosia, named after the food and drinks that provide immortality to the Greek gods, consists of five genes and provides protection against siphophages from the Mesyanzhinovviridae family and myophages from the Pbunavirus genus, limiting phage propagation in both solid and liquid cultures",
        "notes": "Keesman et al. support Ambrosia as a five-gene system that limits propagation of Mesyanzhinovviridae siphophages and Pbunavirus myophages."
      },
      {
        "reference": "DOI:10.1101/2025.09.30.679545",
        "snippet": "The five genes of Ambrosia encode a HipB-like XRE transcriptional regulator (AbrR), a RM type II-associated N6 adenine-specific DNA methylase (MTase, AbrA), a sensor histidine kinase/heat-shock-protein(HSP)90-like ATPase (HATPase, AbrB), a response regulator (REC, AbrC), and an RM type IV HNH endonuclease (AbrD)",
        "notes": "Keesman et al. describe the Ambrosia locus as encoding AbrR, AbrA, AbrB, AbrC, and AbrD components with RM-like and two-component regulatory-system features."
      },
      {
        "reference": "DOI:10.1101/2025.09.30.679545",
        "snippet": "Each protein is required for anti-phage activity, since mutating conserved residues in any of the predicted functional domains completely abolishes Ambrosia defense activity",
        "notes": "Keesman et al. support each predicted functional domain as required for the tested Ambrosia anti-phage activity."
      },
      {
        "reference": "DOI:10.1101/2025.09.30.679545",
        "snippet": "Overall, our results indicate that the RM-like components of Ambrosia do not operate as a conventional type II RM system. Instead, Ambrosia appears to represent a distinct, tightly regulated phage defense system in which a HipB-like XRE protein and a two-component regulatory module control the expression of RM-like enzymes in response to infection",
        "notes": "Keesman et al. argue that Ambrosia is distinct from a conventional type II restriction-modification system and is regulated in response to phage infection."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "Ambrosia | 10\\.1101/2025\\.09\\.30\\.679545 | Discovery of phage defense systems through component modularity networks",
        "notes": "The DefenseFinder article registry maps the named Ambrosia system to the Keesman et al. modular phage-defense discovery preprint; the pinned DefenseFinder HMM inventory and rules table do not list Ambrosia, so this row is name-to-paper evidence rather than model-component evidence."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "ambrosia_locus_restricts_phage",
        "title": "Ambrosia loci confer bacterial phage defense",
        "description": "Conservative system-level sketch linking possession of an Ambrosia locus to restricted bacteriophage propagation without asserting the unresolved phage trigger, transcriptional wiring, or nuclease substrate.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Ambrosia as a named five-gene anti-phage system while leaving its direct phage trigger, the AbrB/AbrC regulatory chain, the exact AbrA/AbrD substrate and DNA modification, natural locus breadth, and the absence of pinned DefenseFinder HMM or rule rows unresolved.",
        "nodes": [
          {
            "node_id": "ambrosia_locus",
            "label": "Ambrosia locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A five-gene Ambrosia anti-phage defense locus encoding AbrR, AbrA, AbrB, AbrC, and AbrD components."
          },
          {
            "node_id": "restricted_phage_propagation",
            "label": "restricted phage propagation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced propagation of bacteriophage in cells carrying the Ambrosia system."
          },
          {
            "node_id": "ambrosia_system_trait",
            "label": "Ambrosia system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000329",
            "description": "Possession of a genome-encoded Ambrosia phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "ambrosia_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "restricted_phage_propagation",
            "description": "The five-gene Ambrosia locus provides protection against siphophages and myophages.",
            "evidence": [
              {
                "reference": "DOI:10.1101/2025.09.30.679545",
                "snippet": "Ambrosia, named after the food and drinks that provide immortality to the Greek gods, consists of five genes and provides protection against siphophages from the Mesyanzhinovviridae family and myophages from the Pbunavirus genus, limiting phage propagation in both solid and liquid cultures",
                "notes": "Keesman et al. connect the named Ambrosia locus to phage-propagation restriction in solid and liquid cultures."
              },
              {
                "reference": "DOI:10.1101/2025.09.30.679545",
                "snippet": "Each protein is required for anti-phage activity, since mutating conserved residues in any of the predicted functional domains completely abolishes Ambrosia defense activity",
                "notes": "Keesman et al. report that conserved-residue mutations in any predicted functional domain abolished Ambrosia defense."
              }
            ]
          },
          {
            "subject": "restricted_phage_propagation",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "ambrosia_system_trait",
            "description": "Ambrosia-mediated phage restriction realizes the Ambrosia system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1101/2025.09.30.679545",
                "snippet": "Ambrosia, named after the food and drinks that provide immortality to the Greek gods, consists of five genes and provides protection against siphophages from the Mesyanzhinovviridae family and myophages from the Pbunavirus genus, limiting phage propagation in both solid and liquid cultures",
                "notes": "Keesman et al. report Ambrosia-mediated limitation of propagation for tested siphophages and myophages."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Ambrosia | 10\\.1101/2025\\.09\\.30\\.679545 | Discovery of phage defense systems through component modularity networks",
                "notes": "The DefenseFinder article registry maps the named Ambrosia system to the Keesman et al. modular phage-defense discovery preprint; the pinned DefenseFinder HMM inventory and rules table do not list Ambrosia, so this row is name-to-paper evidence rather than model-component evidence."
              }
            ]
          },
          {
            "subject": "ambrosia_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Ambrosia system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1101/2025.09.30.679545",
                "snippet": "From over 500 candidate defense systems, we selected nine for experimental testing and validated three: Dionysus, a TerB-encoding system that disrupts early phage infection vesicle formation by Jumbo phages; Ophion, a Radical SAM-containing system that prevents the formation of the Jumbo phage nucleus; and Ambrosia, a tightly regulated RM-like system.",
                "notes": "Keesman et al. list Ambrosia among experimentally validated phage-defense systems."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Ambrosia | 10\\.1101/2025\\.09\\.30\\.679545 | Discovery of phage defense systems through component modularity networks",
                "notes": "The DefenseFinder article registry maps the named Ambrosia system to the Keesman et al. modular phage-defense discovery preprint; the pinned DefenseFinder HMM inventory and rules table do not list Ambrosia, so this row is name-to-paper evidence rather than model-component evidence."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "ambrosia-regulatory-mechanism-gap",
        "prompt": "Resolve Ambrosia phage triggers, DNA targets, and model coverage before minting narrower Ambrosia mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Keesman et al. support Ambrosia as a five-gene anti-phage system with tightly regulated RM-like components, but the direct phage trigger, the AbrB/AbrC regulatory chain, the exact AbrA/AbrD substrate and DNA modification, natural locus breadth, and profile-to-component model are not resolved enough here to assert a narrower mechanistic child trait.",
        "attaches_to": [
          "causal_graphs#ambrosia_locus_restricts_phage"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-21"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-21T06:37:06Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Ambrosia system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v206.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000328",
    "label": "ApsAB system",
    "definition": "A genomics trait describing possession of an ApsAB anti-plasmid defense locus encoding the nuclease/helicase ApsA and Argonaute-like ApsB proteins that can destabilize high- and low-copy-number plasmids.",
    "definition_source": "DOI:10.1038/s41467-024-48219-y",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000188"
    ],
    "synonyms": [
      {
        "synonym_text": "ApsAB",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1038/s41467-024-48219-y"
      },
      {
        "synonym_text": "apsAB",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1038/s41467-024-48219-y"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/s41467-024-48219-y",
        "snippet": "a novel antiplasmid system ApsAB actively involved in pOXA-48 destabilization",
        "notes": "Zongo et al. support ApsAB as a named anti-plasmid system involved in pOXA-48 destabilization."
      },
      {
        "reference": "DOI:10.1038/s41467-024-48219-y",
        "snippet": "We show that ApsAB targets high and low-copy number plasmids.",
        "notes": "Zongo et al. support anti-plasmid activity against both high- and low-copy-number plasmids."
      },
      {
        "reference": "DOI:10.1038/s41467-024-48219-y",
        "snippet": "ApsAB combines a nuclease/helicase protein and a novel type of Argonaute-like protein.",
        "notes": "Zongo et al. support a two-component ApsAB system combining ApsA nuclease/helicase and Argonaute-like ApsB proteins."
      },
      {
        "reference": "DOI:10.1038/s41467-024-48219-y",
        "snippet": "This confirmed that F3141-F3140 corresponds to a novel antiplasmid defense system that we renamed apsAB for antiplasmid system AB.",
        "notes": "Zongo et al. support apsAB as the expanded name for the F3141-F3140 anti-plasmid defense locus."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "ApsAB | 10\\.1038/s41467-024-48219-y | An antiplasmid system drives antibiotic resistance gene integration in carbapenemase-producing Escherichia coli lineages",
        "notes": "The DefenseFinder article registry maps the named ApsAB system to the Zongo et al. Escherichia coli anti-plasmid-system paper; the pinned DefenseFinder HMM inventory and rules table do not list ApsAB, so this row is name-to-paper evidence rather than model-component evidence."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:562",
        "taxon_label": "Escherichia coli",
        "note": "Zongo et al. identified ApsAB in ST38 Escherichia coli and found that homologous E. coli ApsAB-like systems also destabilized a ColE1 multicopy plasmid.",
        "reference": "DOI:10.1038/s41467-024-48219-y"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "apsab_locus_destabilizes_plasmids",
        "title": "ApsAB loci destabilize plasmids",
        "description": "Conservative system-level sketch linking possession of an ApsAB locus to plasmid destabilization without asserting the unresolved guide source, recognition rule, or degradation chemistry.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures ApsAB as a named anti-plasmid defense system while leaving the direct ApsB guide source, the target-recognition rule, the exact plasmid-degradation chemistry, the natural plasmid substrate range, family breadth, and the absence of pinned DefenseFinder HMM or rule rows unresolved.",
        "nodes": [
          {
            "node_id": "apsab_locus",
            "label": "ApsAB locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "An anti-plasmid defense locus encoding ApsA nuclease/helicase and Argonaute-like ApsB components."
          },
          {
            "node_id": "plasmid_destabilization",
            "label": "plasmid destabilization",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced maintenance or active elimination of plasmids in cells carrying ApsAB."
          },
          {
            "node_id": "apsab_system_trait",
            "label": "ApsAB system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000328",
            "description": "Possession of a genome-encoded ApsAB anti-plasmid defense locus."
          }
        ],
        "edges": [
          {
            "subject": "apsab_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "plasmid_destabilization",
            "description": "The F3141-F3140 locus was renamed apsAB and ApsAB expression promotes plasmid elimination.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-024-48219-y",
                "snippet": "This confirmed that F3141-F3140 corresponds to a novel antiplasmid defense system that we renamed apsAB for antiplasmid system AB.",
                "notes": "Zongo et al. identify F3141-F3140 as the ApsAB anti-plasmid system."
              },
              {
                "reference": "DOI:10.1038/s41467-024-48219-y",
                "snippet": "These results indicate that ApsAB actively eliminates the plasmid, likely by promoting its degradation",
                "notes": "Zongo et al. report active ApsAB-mediated plasmid elimination after arabinose induction."
              },
              {
                "reference": "DOI:10.1038/s41467-024-48219-y",
                "snippet": "Both systems were found to destabilize a ColE1 multicopy plasmid",
                "notes": "Zongo et al. found that homologous E. coli ApsAB-like systems can destabilize a ColE1 multicopy plasmid."
              }
            ]
          },
          {
            "subject": "plasmid_destabilization",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "apsab_system_trait",
            "description": "ApsAB-mediated plasmid destabilization realizes the ApsAB system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-024-48219-y",
                "snippet": "We show that ApsAB targets high and low-copy number plasmids.",
                "notes": "Zongo et al. support the ApsAB anti-plasmid output against high- and low-copy-number plasmids."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "ApsAB | 10\\.1038/s41467-024-48219-y | An antiplasmid system drives antibiotic resistance gene integration in carbapenemase-producing Escherichia coli lineages",
                "notes": "The DefenseFinder article registry maps the named ApsAB system to the Zongo et al. Escherichia coli anti-plasmid-system paper; the pinned DefenseFinder HMM inventory and rules table do not list ApsAB, so this row is name-to-paper evidence rather than model-component evidence."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "apsab-substrate-and-guide-source-gap",
        "prompt": "Resolve ApsAB guide sources, plasmid substrates, and model coverage before minting narrower ApsAB mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Zongo et al. support ApsAB as a two-component E. coli anti-plasmid system and report activity against high- and low-copy-number plasmids, but the direct ApsB guide source, the target-recognition rule, exact plasmid-degradation chemistry, natural substrate range, family-level breadth, and profile-to-component model are not resolved enough here to assert narrower mechanistic or subtype traits.",
        "attaches_to": [
          "causal_graphs#apsab_locus_destabilizes_plasmids"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-21"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-21T05:45:03Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted ApsAB system as a DOI-backed GENOMICS TraitRecord under the quality root after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v205.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000313",
    "label": "Aristaios system",
    "definition": "A phage defense system in which an organism possesses an Aristaios locus that can restrict bacteriophage infection.",
    "definition_source": "DOI:10.1093/nar/gkae671",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "Aristaios",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1093/nar/gkae671"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1093/nar/gkae671",
        "snippet": "These systems were named after cheese, cattle or fermentation related deities (Rhea, Aristaios, Kamadhenu, Fliodhais, Audmula, Rugutis and Hesat)",
        "notes": "Grafakou et al. named Aristaios among seven not previously described lactococcal antiphage systems."
      },
      {
        "reference": "DOI:10.1128/aem.01120-24",
        "snippet": "Recently, three plasmid-encoded lactococcal antiphage systems, named Rhea, Aristaios, and Kamadhenu, were discovered. These systems were found to confer high levels of resistance against various Skunavirus members.",
        "notes": "Grafakou et al. later characterized Aristaios as one of three plasmid-encoded lactococcal antiphage systems conferring strong resistance against Skunavirus members."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "Aristaios | 10\\.1093/nar/gkae671 | Discovery of antiphage systems in the lactococcal plasmidome",
        "notes": "The DefenseFinder article registry maps the named Aristaios system to the Grafakou et al. lactococcal antiphage-system discovery paper."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "aristaios_locus_restricts_phage",
        "title": "Aristaios loci confer bacterial phage defense",
        "description": "Conservative system-level sketch linking possession of an Aristaios locus to restricted bacteriophage propagation without asserting the unresolved phage trigger or molecular output.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Aristaios as a named lactococcal anti-phage system while leaving its direct phage trigger, molecular substrate, antiviral effector output, natural locus breadth, and the absence of pinned DefenseFinder HMM or rule rows unresolved.",
        "nodes": [
          {
            "node_id": "aristaios_locus",
            "label": "Aristaios locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "An Aristaios anti-phage defense locus described among lactococcal plasmid-encoded phage-resistance systems."
          },
          {
            "node_id": "restricted_phage_propagation",
            "label": "restricted phage propagation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced propagation of bacteriophage in cells carrying the Aristaios system."
          },
          {
            "node_id": "aristaios_system_trait",
            "label": "Aristaios system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000313",
            "description": "Possession of a genome-encoded Aristaios phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "aristaios_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "restricted_phage_propagation",
            "description": "The lactococcal plasmidome screen discovered Aristaios as a named antiphage system, and the DefenseFinder article registry maps the Aristaios system to that discovery paper.",
            "evidence": [
              {
                "reference": "DOI:10.1093/nar/gkae671",
                "snippet": "These systems were named after cheese, cattle or fermentation related deities (Rhea, Aristaios, Kamadhenu, Fliodhais, Audmula, Rugutis and Hesat)",
                "notes": "Grafakou et al. named Aristaios as one of the novel lactococcal antiphage systems."
              },
              {
                "reference": "DOI:10.1128/aem.01120-24",
                "snippet": "Recently, three plasmid-encoded lactococcal antiphage systems, named Rhea, Aristaios, and Kamadhenu, were discovered. These systems were found to confer high levels of resistance against various Skunavirus members.",
                "notes": "Grafakou et al. later characterized Aristaios as one of three plasmid-encoded lactococcal antiphage systems conferring strong resistance against Skunavirus members."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Aristaios | 10\\.1093/nar/gkae671 | Discovery of antiphage systems in the lactococcal plasmidome",
                "notes": "The DefenseFinder article registry maps the named Aristaios system to the Grafakou et al. lactococcal antiphage-system discovery paper."
              }
            ]
          },
          {
            "subject": "restricted_phage_propagation",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "aristaios_system_trait",
            "description": "Aristaios-mediated phage restriction realizes the Aristaios system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1093/nar/gkae671",
                "snippet": "These systems were named after cheese, cattle or fermentation related deities (Rhea, Aristaios, Kamadhenu, Fliodhais, Audmula, Rugutis and Hesat)",
                "notes": "Grafakou et al. named Aristaios as one of the novel lactococcal antiphage systems."
              },
              {
                "reference": "DOI:10.1128/aem.01120-24",
                "snippet": "Recently, three plasmid-encoded lactococcal antiphage systems, named Rhea, Aristaios, and Kamadhenu, were discovered. These systems were found to confer high levels of resistance against various Skunavirus members.",
                "notes": "Grafakou et al. later characterized Aristaios as one of three plasmid-encoded lactococcal antiphage systems conferring strong resistance against Skunavirus members."
              }
            ]
          },
          {
            "subject": "aristaios_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Aristaios system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Aristaios | 10\\.1093/nar/gkae671 | Discovery of antiphage systems in the lactococcal plasmidome",
                "notes": "The DefenseFinder article registry maps the named Aristaios system to the Grafakou et al. lactococcal antiphage-system discovery paper."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "aristaios-mechanism-gap",
        "prompt": "Resolve Aristaios phage triggers and effector outputs before minting narrower Aristaios mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Grafakou et al. and DefenseFinder support Aristaios as a named anti-phage system, but the direct trigger, molecular substrate, antiviral effector output, natural locus breadth, and profile-to-component model are not resolved enough here to assert a narrower mechanistic child trait.",
        "attaches_to": [
          "causal_graphs#aristaios_locus_restricts_phage"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-20"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-20T15:55:54Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Aristaios system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v190.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000477",
    "label": "ARMADA system",
    "definition": "A phage defense system in which an organism possesses an ARMADA YprA-like-helicase locus whose Type I and Type II operons share BrxHII-like and PglX-like components with DISARM Class I systems and whose experimentally tested Type II forms protect against a broad range of phages.",
    "definition_source": "DOI:10.1016/j.chom.2026.05.015",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "ARMADA",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1016/j.chom.2026.05.015"
      },
      {
        "synonym_text": "Armada",
        "synonym_type": "EXACT_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      },
      {
        "synonym_text": "disARM-related antiviral defense array",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1016/j.chom.2026.05.015"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1016/j.chom.2026.05.015",
        "snippet": "Through comprehensive phylogenetic and structural analyses of YprA-like helicases, we identify several major clades, which define distinct defense systems including a broad class we call ARMADA (disARM-related antiviral defense array).",
        "notes": "Bell et al. define ARMADA as a broad YprA-like helicase defense-system class."
      },
      {
        "reference": "DOI:10.1016/j.chom.2026.05.015",
        "snippet": "We show experimentally that ARMADA protects bacteria against a broad range of phages via a direct, non-abortive mechanism.",
        "notes": "Bell et al. summarize experimental support that ARMADA protects bacteria against a broad range of phages."
      },
      {
        "reference": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12458937/",
        "snippet": "The two largest uncharacterized YprA-like clades encompass a distinct set of related operons that, in addition to the YprA homologs, share two other genes with DISARM Class I systems",
        "notes": "The preprint full text describes ARMADA operons as carrying YprA homologs plus BrxHII-like and PglX-like components shared with DISARM Class I systems."
      },
      {
        "reference": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12458937/",
        "snippet": "The ARMADA clade splits into two well-separated, strongly supported subclades which we denote Type I and Type II.",
        "notes": "The preprint full text separates the broad ARMADA clade into Type I and Type II subclades."
      },
      {
        "reference": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12458937/",
        "snippet": "Log-protection (reduction in phage titer) conferred by ARMADA, expressed from plasmid pBeloBAC11 in BL21-AI, against a panel of 80 phages",
        "notes": "A cloned E. coli NCTC 12900 ARMADA Type II cluster was tested for protection against a broad phage panel in a heterologous BL21-AI assay."
      },
      {
        "reference": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12458937/",
        "snippet": "Screening 66 phages that could form plaques on the double-deletion strain showed that the strain carrying only Druantia III exhibited at least modest protection (<0.01 EOP or <0.5 SFC) against 3 phages, whereas the strain carrying ARMADA Type II exhibited a much broader range of immunity, with at least modest protection observed against 30 phages.",
        "notes": "Precise system deletions in E. coli ATCC 8739 supported native ARMADA Type II protection across a broader tested phage set than the co-located Druantia Type III system."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "Armada | 10\\.1101/2025\\.09\\.15\\.676423 | YprA family helicases provide the missing link between diverse prokaryotic immune systems",
        "notes": "The pinned DefenseFinder article registry maps the named Armada system to the Bell et al. YprA-family helicase preprint. The pinned HMM inventory and rules table do not list Armada, so this row is name-to-paper evidence rather than model-component evidence."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:562",
        "taxon_label": "Escherichia coli",
        "note": "Bell et al. generated precise armABCD deletions in E. coli strain ATCC 8739 and showed that its native ARMADA Type II system provided broader phage protection than the co-located Druantia Type III system.",
        "reference": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12458937/"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "armada_locus_phage_protection",
        "title": "ARMADA loci protect against broad phage panels",
        "description": "Conservative system-level sketch linking an ARMADA YprA-like-helicase locus to experimentally measured anti-phage protection and ARMADA system possession.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures ARMADA as a named YprA-like-helicase phage-defense system with Type I and Type II subclades while leaving direct phage triggers or effectors, native host breadth, exact Type I and Type II boundaries, profile-to-component mapping, and DefenseFinder HMM/rules detection criteria unresolved.",
        "nodes": [
          {
            "node_id": "armada_locus",
            "label": "ARMADA locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A YprA-like-helicase ARMADA antiphage locus from a Type I or Type II ARMADA clade."
          },
          {
            "node_id": "armada_broad_phage_protection",
            "label": "ARMADA broad phage protection",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Experimentally measured reduction in bacteriophage growth or plaque formation by tested ARMADA Type II systems."
          },
          {
            "node_id": "armada_system_trait",
            "label": "ARMADA system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000477",
            "description": "Possession of a genome-encoded ARMADA phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "armada_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "armada_broad_phage_protection",
            "description": "ARMADA Type II loci from E. coli NCTC 12900 and ATCC 8739 provided experimentally measured anti-phage protection.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.chom.2026.05.015",
                "snippet": "We show experimentally that ARMADA protects bacteria against a broad range of phages via a direct, non-abortive mechanism.",
                "notes": "Bell et al. summarize broad, direct, non-abortive ARMADA anti-phage protection."
              },
              {
                "reference": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12458937/",
                "snippet": "Screening 66 phages that could form plaques on the double-deletion strain showed that the strain carrying only Druantia III exhibited at least modest protection (<0.01 EOP or <0.5 SFC) against 3 phages, whereas the strain carrying ARMADA Type II exhibited a much broader range of immunity, with at least modest protection observed against 30 phages.",
                "notes": "Precise ARMADA and Druantia deletions in E. coli ATCC 8739 resolved native ARMADA-associated phage immunity."
              }
            ]
          },
          {
            "subject": "armada_broad_phage_protection",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "armada_system_trait",
            "description": "Broad phage protection realizes the ARMADA system possession trait.",
            "evidence": [
              {
                "reference": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12458937/",
                "snippet": "Log-protection (reduction in phage titer) conferred by ARMADA, expressed from plasmid pBeloBAC11 in BL21-AI, against a panel of 80 phages",
                "notes": "The cloned NCTC 12900 ARMADA Type II locus was tested in BL21-AI against a broad phage panel."
              },
              {
                "reference": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12458937/",
                "snippet": "Screening 66 phages that could form plaques on the double-deletion strain showed that the strain carrying only Druantia III exhibited at least modest protection (<0.01 EOP or <0.5 SFC) against 3 phages, whereas the strain carrying ARMADA Type II exhibited a much broader range of immunity, with at least modest protection observed against 30 phages.",
                "notes": "The native ATCC 8739 ARMADA Type II system protected against a broader tested phage panel than its co-located Druantia Type III system."
              }
            ]
          },
          {
            "subject": "armada_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "ARMADA system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.chom.2026.05.015",
                "snippet": "Through comprehensive phylogenetic and structural analyses of YprA-like helicases, we identify several major clades, which define distinct defense systems including a broad class we call ARMADA (disARM-related antiviral defense array).",
                "notes": "Bell et al. define ARMADA among YprA-family prokaryotic immune systems."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Armada | 10\\.1101/2025\\.09\\.15\\.676423 | YprA family helicases provide the missing link between diverse prokaryotic immune systems",
                "notes": "The pinned DefenseFinder article registry maps the named Armada system to the Bell et al. YprA-family helicase preprint. The pinned HMM inventory and rules table do not list Armada, so this row is name-to-paper evidence rather than model-component evidence."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "armada-subtype-model-and-mechanism-gap",
        "prompt": "Resolve exact ARMADA Type I and Type II boundaries, DefenseFinder HMM/rules coverage, profile-to-component mapping, direct phage triggers or outputs, and native host breadth before minting narrower ARMADA mechanism, subtype, or protein-component traits.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Bell et al. support ARMADA as a broad YprA-like-helicase system family that shares BrxHII-like and PglX-like components with DISARM Class I systems and splits into Type I and Type II subclades, and the article experimentally validates Type II protection from E. coli NCTC 12900 and ATCC 8739 loci. The pinned DefenseFinder article registry names Armada and maps it to the Bell et al. preprint, but the pinned HMM inventory and rules table do not contain Armada rows, leaving profile coverage and detection criteria unresolved.",
        "evidence": [
          {
            "reference": "DOI:10.1016/j.chom.2026.05.015",
            "snippet": "Through comprehensive phylogenetic and structural analyses of YprA-like helicases, we identify several major clades, which define distinct defense systems including a broad class we call ARMADA (disARM-related antiviral defense array).",
            "notes": "Bell et al. define ARMADA as a broad YprA-like helicase defense-system class."
          },
          {
            "reference": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12458937/",
            "snippet": "The ARMADA clade splits into two well-separated, strongly supported subclades which we denote Type I and Type II.",
            "notes": "The broad ARMADA clade is split into Type I and Type II subclades."
          },
          {
            "reference": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12458937/",
            "snippet": "Druantia Type III and ARMADA Type II systems showed clear evidence of synergizing to confer phage defense in their native host",
            "notes": "The ATCC 8739 native-host experiments support ARMADA Type II and Druantia Type III interaction while leaving their coupling mechanism unresolved."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
            "snippet": "Armada | 10\\.1101/2025\\.09\\.15\\.676423 | YprA family helicases provide the missing link between diverse prokaryotic immune systems",
            "notes": "The pinned DefenseFinder article registry maps the named Armada system to the Bell et al. YprA-family helicase preprint. The pinned HMM inventory and rules table do not list Armada, so this row is name-to-paper evidence rather than model-component evidence."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "notes": "No Armada or ARMADA HMM inventory row was present in the pinned DefenseFinder model file."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "No Armada or ARMADA rule row was present in the pinned DefenseFinder rules table."
          }
        ],
        "attaches_to": [
          "causal_graphs#armada_locus_phage_protection"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-30"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-30T00:00:29Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted ARMADA system as a final-DOI- and DefenseFinder-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; kept the graph at broad YprA-like-helicase system level because the pinned DefenseFinder article row is not backed by pinned HMM or rules rows; the replacement placeholder is reserved in proposals/metpo_traitmech_v354.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000312",
    "label": "Audmula system",
    "definition": "A phage defense system in which an organism possesses an Audmula locus that can restrict bacteriophage infection.",
    "definition_source": "DOI:10.1093/nar/gkae671",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "Audmula",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1093/nar/gkae671"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1093/nar/gkae671",
        "snippet": "These systems were named after cheese, cattle or fermentation related deities (Rhea, Aristaios, Kamadhenu, Fliodhais, Audmula, Rugutis and Hesat)",
        "notes": "Grafakou et al. named Audmula among seven not previously described lactococcal antiphage systems."
      },
      {
        "reference": "DOI:10.1073/pnas.2426508122",
        "snippet": "we isolated 66 phage escape mutants which had become insensitive to 13 distinct, plasmid-encoded lactococcal phage resistance systems (i.e. Rhea, Kamadhenu, Rugutis, Audmula, PARIS, type II CBASS, Septu, AbiA, AbiB, AbiD/F, AbiG, AbiJ, AbiP)",
        "notes": "Mosterd et al. later included Audmula among the distinct plasmid-encoded lactococcal phage-resistance systems investigated by phage escape-mutant isolation."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "Audmula | 10\\.1093/nar/gkae671 | Discovery of antiphage systems in the lactococcal plasmidome",
        "notes": "The DefenseFinder article registry maps the named Audmula system to the Grafakou et al. lactococcal antiphage-system discovery paper."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "audmula_locus_restricts_phage",
        "title": "Audmula loci confer bacterial phage defense",
        "description": "Conservative system-level sketch linking possession of an Audmula locus to restricted bacteriophage propagation without asserting the unresolved phage trigger or molecular output.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Audmula as a named lactococcal anti-phage system while leaving its direct phage trigger, molecular substrate, antiviral effector output, natural locus breadth, and the absence of pinned DefenseFinder HMM or rule rows unresolved.",
        "nodes": [
          {
            "node_id": "audmula_locus",
            "label": "Audmula locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "An Audmula anti-phage defense locus described among lactococcal plasmid-encoded phage-resistance systems."
          },
          {
            "node_id": "restricted_phage_propagation",
            "label": "restricted phage propagation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced propagation of bacteriophage in cells carrying the Audmula system."
          },
          {
            "node_id": "audmula_system_trait",
            "label": "Audmula system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000312",
            "description": "Possession of a genome-encoded Audmula phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "audmula_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "restricted_phage_propagation",
            "description": "The lactococcal plasmidome screen discovered Audmula as a named antiphage system, and the DefenseFinder article registry maps the Audmula system to that discovery paper.",
            "evidence": [
              {
                "reference": "DOI:10.1093/nar/gkae671",
                "snippet": "These systems were named after cheese, cattle or fermentation related deities (Rhea, Aristaios, Kamadhenu, Fliodhais, Audmula, Rugutis and Hesat)",
                "notes": "Grafakou et al. named Audmula as one of the novel lactococcal antiphage systems."
              },
              {
                "reference": "DOI:10.1073/pnas.2426508122",
                "snippet": "we isolated 66 phage escape mutants which had become insensitive to 13 distinct, plasmid-encoded lactococcal phage resistance systems (i.e. Rhea, Kamadhenu, Rugutis, Audmula, PARIS, type II CBASS, Septu, AbiA, AbiB, AbiD/F, AbiG, AbiJ, AbiP)",
                "notes": "Mosterd et al. treat Audmula as a plasmid-encoded lactococcal phage-resistance system in their escape-mutant screen."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Audmula | 10\\.1093/nar/gkae671 | Discovery of antiphage systems in the lactococcal plasmidome",
                "notes": "The DefenseFinder article registry maps the named Audmula system to the Grafakou et al. lactococcal antiphage-system discovery paper."
              }
            ]
          },
          {
            "subject": "restricted_phage_propagation",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "audmula_system_trait",
            "description": "Audmula-mediated phage restriction realizes the Audmula system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1073/pnas.2426508122",
                "snippet": "we isolated 66 phage escape mutants which had become insensitive to 13 distinct, plasmid-encoded lactococcal phage resistance systems (i.e. Rhea, Kamadhenu, Rugutis, Audmula, PARIS, type II CBASS, Septu, AbiA, AbiB, AbiD/F, AbiG, AbiJ, AbiP)",
                "notes": "Mosterd et al. treat Audmula as a plasmid-encoded lactococcal phage-resistance system in their escape-mutant screen."
              }
            ]
          },
          {
            "subject": "audmula_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Audmula system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Audmula | 10\\.1093/nar/gkae671 | Discovery of antiphage systems in the lactococcal plasmidome",
                "notes": "The DefenseFinder article registry maps the named Audmula system to the Grafakou et al. lactococcal antiphage-system discovery paper."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "audmula-mechanism-gap",
        "prompt": "Resolve Audmula phage triggers and effector outputs before minting narrower Audmula mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Grafakou et al., Mosterd et al., and DefenseFinder support Audmula as a named anti-phage system, but the direct trigger, molecular substrate, antiviral effector output, natural locus breadth, and profile-to-component model are not resolved enough here to assert a narrower mechanistic child trait.",
        "attaches_to": [
          "causal_graphs#audmula_locus_restricts_phage"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-20"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-20T15:17:07Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Audmula system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v189.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000239",
    "label": "AVAST system",
    "definition": "A phage defense system in which an organism possesses a locus encoding a STAND-superfamily antiviral ATPase/NTPase that functions as a modular Avs receptor-effector, recognizes conserved bacteriophage proteins, and activates subtype-specific antiphage outputs to inhibit bacteriophage replication.",
    "definition_source": "DOI:10.1126/science.aba0372",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "antiviral ATPase/NTPase of the STAND superfamily system",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1126/science.aba0372"
      },
      {
        "synonym_text": "antiviral STAND system",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1126/science.aba0372"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1126/science.aba0372",
        "snippet": "AVAST, antiviral ATPase/NTPase of the STAND superfamily",
        "notes": "Gao et al. coined AVAST as a recurring antiviral STAND ATPase/NTPase defense-system family in their pangenome-scale antiphage-system discovery screen."
      },
      {
        "reference": "DOI:10.1126/science.abm4096",
        "snippet": "Avs1 to Avs3 recognize the large terminase subunit, and Avs4 recognizes the portal",
        "notes": "Gao et al. characterized Avs1 through Avs4 as prokaryotic STAND-family innate immune receptors that detect conserved phage proteins and trigger subtype-specific antiviral effector outputs."
      },
      {
        "reference": "DOI:10.1016/j.molcel.2026.01.004",
        "snippet": "AVAST type 5 (Avs5) systems, part of the signal transduction ATPases of numerous domains (STAND) superfamily, confer conserved immunity against jumbo phages",
        "notes": "Muralidharan et al. extend the named AVAST family with Avs5 systems that defend against nucleus-forming jumbo phages."
      },
      {
        "reference": "DOI:10.1016/j.molcel.2026.01.004",
        "snippet": "Recognition of phage infection triggers the Sir2-like effector domain of Avs5 across three Avs5 clades",
        "notes": "Muralidharan et al. support a subtype-specific Avs5 effector activation mechanism downstream of phage infection sensing."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:287",
        "taxon_label": "Pseudomonas aeruginosa",
        "note": "Muralidharan et al. characterized the Pseudomonas aeruginosa Avs5-1 system and showed that its Sir2-like effector domain is activated during jumbo-phage infection.",
        "reference": "DOI:10.1016/j.molcel.2026.01.004"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "avast_stand_pattern_recognition_defense",
        "title": "AVAST STAND receptors detect phage proteins during antiphage defense",
        "description": "Evidence-backed process sketch linking an AVAST locus to Avs STAND receptor activation, subtype-specific antiviral effector activity, and inhibition of bacteriophage replication.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph stays at the AVAST-family level and does not assert that all Avs subtypes detect the same phage protein, carry the same nuclease or Sir2-like effector domain, act on the same molecular substrate, or inhibit the same class of phages.",
        "nodes": [
          {
            "node_id": "avast_locus",
            "label": "AVAST locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A phage-defense locus encoding a STAND-superfamily antiviral ATPase/NTPase that functions as a modular Avs receptor-effector."
          },
          {
            "node_id": "avs_stand_receptor_activation",
            "label": "Avs STAND receptor activation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Activation of an Avs STAND-family receptor after detection of a conserved phage protein during bacteriophage infection."
          },
          {
            "node_id": "avast_effector_output",
            "label": "AVAST antiviral effector output",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Subtype-specific nuclease, NADase, or membrane-associated antiviral activity triggered by an activated AVAST receptor."
          },
          {
            "node_id": "phage_replication",
            "label": "phage replication",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Bacteriophage genome replication and production inside an infected bacterial host."
          },
          {
            "node_id": "avast_system_trait",
            "label": "AVAST system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000239",
            "description": "Possession of a genome-encoded AVAST phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "avast_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "avs_stand_receptor_activation",
            "description": "AVAST loci encode Avs STAND-family receptors that are activated when their cognate conserved phage protein is present.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.abm4096",
                "snippet": "Avs1 to Avs3 recognize the large terminase subunit, and Avs4 recognizes the portal",
                "notes": "Gao et al. support Avs1 through Avs4 as phage-protein-sensing AVAST receptors."
              },
              {
                "reference": "DOI:10.1016/j.molcel.2026.01.004",
                "snippet": "Avs5 localizes to early infection vesicles, where it senses an essential, early-expressed phage protein named JADA",
                "notes": "Muralidharan et al. support phage-infection recognition by Avs5 receptors."
              }
            ]
          },
          {
            "subject": "avs_stand_receptor_activation",
            "predicate": "activates",
            "predicate_id": "RO:0002213",
            "object": "avast_effector_output",
            "description": "Detection of a phage cue activates the effector domain coupled to the cognate Avs STAND receptor.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.molcel.2026.01.004",
                "snippet": "Recognition of phage infection triggers the Sir2-like effector domain of Avs5 across three Avs5 clades",
                "notes": "Muralidharan et al. connect phage recognition to subtype-specific Avs5 Sir2-like effector activation."
              }
            ]
          },
          {
            "subject": "avast_effector_output",
            "predicate": "mitigates",
            "predicate_id": "METPO:2007407",
            "object": "phage_replication",
            "description": "Subtype-specific AVAST effector activities restrict bacteriophage replication or propagation after recognition of a phage cue.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.abm4096",
                "snippet": "In all four cases, target recognition led to Avs protein activation and antiviral activity",
                "notes": "Gao et al. support Avs effector outputs as downstream antiviral activities in Avs1 through Avs4 systems."
              },
              {
                "reference": "DOI:10.1016/j.molcel.2026.01.004",
                "snippet": "Upon sensing Jumbo J phage, Avs5-1 underwent oligomerization, which activated the enzymatic activity of its Sir2 effector, resulting in rapid NAD + hydrolysis, disruption of phage nucleus formation, and arrest of infection",
                "notes": "Muralidharan et al. support Avs5 Sir2-like effector activity as a jumbo-phage-restricting AVAST output."
              }
            ]
          },
          {
            "subject": "avast_effector_output",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "avast_system_trait",
            "description": "Activated AVAST effector outputs realize the AVAST phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.molcel.2026.01.004",
                "snippet": "AVAST type 5 (Avs5) systems, part of the signal transduction ATPases of numerous domains (STAND) superfamily, confer conserved immunity against jumbo phages",
                "notes": "Muralidharan et al. connect a characterized AVAST subtype to conserved antiphage immunity."
              }
            ]
          },
          {
            "subject": "avast_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "AVAST system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.aba0372",
                "snippet": "AVAST, antiviral ATPase/NTPase of the STAND superfamily",
                "notes": "Gao et al. identified AVAST among candidate phage-defense systems."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "avast-subtype-effector-gap",
        "prompt": "Resolve AVAST subtype sensors, phage triggers, and effector outputs before minting narrower Avs1-Avs5 mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Gao et al. support phage-protein pattern recognition by Avs1 through Avs4, while Muralidharan et al. support Avs5 immunity against nucleus-forming jumbo phages through phage-triggered Sir2-like effector activation. The first TraitRecord therefore stays at the AVAST-system level until separate review resolves which phage cues, effector domains, and antiviral substrates generalize across AVAST loci.",
        "posed_by": "codex",
        "posed_date": "2026-09-18"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-18T10:44:12Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted AVAST system as a DOI-backed GENOMICS TraitRecord under the phage defense system parent after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v116.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000534",
    "label": "Avs I system",
    "definition": "An AVAST system in which an organism possesses a genome-encoded subtype I locus represented by DefenseFinder with Avs1A, Avs1B, and Avs1C profiles.",
    "definition_source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000239"
    ],
    "synonyms": [
      {
        "synonym_text": "Avs_I",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv"
      },
      {
        "synonym_text": "Avs_I__Avs1A",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "Avs_I__Avs1B",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "Avs_I__Avs1C",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1126/science.aba0372",
        "snippet": "AVAST, antiviral ATPase/NTPase of the STAND superfamily",
        "notes": "Gao et al. coined AVAST as an antiviral STAND ATPase/NTPase defense-system family."
      },
      {
        "reference": "DOI:10.1126/science.abm4096",
        "snippet": "Avs1 to Avs3 recognize the large terminase subunit, and Avs4 recognizes the portal",
        "notes": "Gao et al. support Avs1 as a phage-protein-sensing member of the AVAST receptor family."
      },
      {
        "reference": "DOI:10.1126/science.abm4096",
        "snippet": "In all four cases, target recognition led to Avs protein activation and antiviral activity",
        "notes": "Gao et al. connect Avs1 through Avs4 target recognition to Avs activation and antiviral activity."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| Avs | 10\\.1126/science\\.aba0372 | Diverse enzymatic activities mediate antiviral immunity in prokaryotes | ",
        "notes": "The pinned DefenseFinder article registry maps the Avs source key to the Gao et al. pangenome-scale antiviral-immunity paper."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| Avs_I__Avs1A                                     | Avs_I__Avs1A                                     | Avs_I                  | Custom                  | 20     |",
        "notes": "The pinned DefenseFinder HMM inventory records Avs_I__Avs1A under the Avs_I model namespace."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| Avs_I__Avs1B                                     | Avs_I__Avs1B                                     | Avs_I                  | Custom                  | 100    |",
        "notes": "The pinned DefenseFinder HMM inventory records Avs_I__Avs1B under the Avs_I model namespace."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| Avs_I__Avs1C                                     | Avs_I__Avs1C                                     | Avs_I                  | Custom                  | 20     |",
        "notes": "The pinned DefenseFinder HMM inventory records Avs_I__Avs1C under the Avs_I model namespace."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "Avs\tAvs_I\t2\t2\tAvs_I__Avs1A, Avs_I__Avs1B, Avs_I__Avs1C\t\t\t",
        "notes": "The pinned DefenseFinder rules table models Avs_I as an Avs subsystem with Avs1A, Avs1B, and Avs1C profiles."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "avs_i_locus_phage_protein_recognition",
        "title": "Avs I loci support phage protein recognition",
        "description": "Conservative system-level sketch linking an Avs_I locus to Avs1-mediated phage protein recognition and Avs I system possession.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Avs_I at locus and Avs1 phage-protein recognition level without asserting the exact Avs1A, Avs1B, and Avs1C component roles, the direct effector activity, native host breadth, sensitive-phage breadth, or whether every DefenseFinder Avs_I prediction is a complete experimentally active Avs I locus.",
        "nodes": [
          {
            "node_id": "avs_i_locus",
            "label": "Avs I locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "An AVAST subtype I locus represented in DefenseFinder by Avs1A, Avs1B, and Avs1C profiles."
          },
          {
            "node_id": "avs1_phage_protein_recognition",
            "label": "Avs1 phage protein recognition",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Recognition of an infecting phage protein by an Avs1 antiviral STAND-family receptor."
          },
          {
            "node_id": "avs_i_system_trait",
            "label": "Avs I system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000534",
            "description": "Possession of a genome-encoded Avs I phage-defense system."
          },
          {
            "node_id": "avast_system_trait",
            "label": "AVAST system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000239",
            "description": "Possession of a genome-encoded AVAST phage-defense system."
          }
        ],
        "edges": [
          {
            "subject": "avs_i_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "avs1_phage_protein_recognition",
            "description": "Avs I loci encode Avs1 components, and Avs1 belongs to the AVAST receptors that recognize the phage large terminase subunit.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.abm4096",
                "snippet": "Avs1 to Avs3 recognize the large terminase subunit, and Avs4 recognizes the portal",
                "notes": "Gao et al. support Avs1 as a phage-protein-sensing member of the AVAST receptor family."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| Avs_I__Avs1A                                     | Avs_I__Avs1A                                     | Avs_I                  | Custom                  | 20     |",
                "notes": "The pinned DefenseFinder HMM inventory records Avs_I__Avs1A under the Avs_I model namespace."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| Avs_I__Avs1B                                     | Avs_I__Avs1B                                     | Avs_I                  | Custom                  | 100    |",
                "notes": "The pinned DefenseFinder HMM inventory records Avs_I__Avs1B under the Avs_I model namespace."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| Avs_I__Avs1C                                     | Avs_I__Avs1C                                     | Avs_I                  | Custom                  | 20     |",
                "notes": "The pinned DefenseFinder HMM inventory records Avs_I__Avs1C under the Avs_I model namespace."
              }
            ]
          },
          {
            "subject": "avs1_phage_protein_recognition",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "avs_i_system_trait",
            "description": "The first-pass Avs I system trait is realized by Avs1 target recognition and downstream antiviral activity.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.abm4096",
                "snippet": "Avs1 to Avs3 recognize the large terminase subunit, and Avs4 recognizes the portal",
                "notes": "Gao et al. support Avs1 as a phage-protein-sensing member of the AVAST receptor family."
              },
              {
                "reference": "DOI:10.1126/science.abm4096",
                "snippet": "In all four cases, target recognition led to Avs protein activation and antiviral activity",
                "notes": "Gao et al. connect Avs1 through Avs4 target recognition to Avs activation and antiviral activity."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "Avs\tAvs_I\t2\t2\tAvs_I__Avs1A, Avs_I__Avs1B, Avs_I__Avs1C\t\t\t",
                "notes": "The pinned DefenseFinder rules table models Avs_I as an Avs subsystem with Avs1A, Avs1B, and Avs1C profiles."
              }
            ]
          },
          {
            "subject": "avs_i_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "avast_system_trait",
            "description": "Avs I system possession is an AVAST-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.aba0372",
                "snippet": "AVAST, antiviral ATPase/NTPase of the STAND superfamily",
                "notes": "Gao et al. coined AVAST as an antiviral STAND ATPase/NTPase defense-system family."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| Avs | 10\\.1126/science\\.aba0372 | Diverse enzymatic activities mediate antiviral immunity in prokaryotes | ",
                "notes": "The pinned DefenseFinder article registry maps the Avs source key to the Gao et al. pangenome-scale antiviral-immunity paper."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "Avs\tAvs_I\t2\t2\tAvs_I__Avs1A, Avs_I__Avs1B, Avs_I__Avs1C\t\t\t",
                "notes": "The pinned DefenseFinder rules table models Avs_I as an Avs subsystem with Avs1A, Avs1B, and Avs1C profiles."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "avs-i-component-and-effector-gap",
        "prompt": "Resolve Avs1A, Avs1B, and Avs1C component roles, direct effector chemistry, exact phage-trigger mapping, native host breadth, and sensitive-phage breadth before minting Avs I mechanism or component children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Gao et al. support Avs1 phage-protein recognition and Avs activation during antiviral defense, and the pinned DefenseFinder HMM inventory and rules table support Avs_I as a subtype I model with Avs1A, Avs1B, and Avs1C profiles. This first-pass record leaves the exact component functions, downstream effector chemistry, native host breadth, sensitive-phage breadth, and profile-to-activity requirements unresolved.",
        "evidence": [
          {
            "reference": "DOI:10.1126/science.abm4096",
            "snippet": "Avs1 to Avs3 recognize the large terminase subunit, and Avs4 recognizes the portal",
            "notes": "Gao et al. support Avs1 as a phage-protein-sensing member of the AVAST receptor family."
          },
          {
            "reference": "DOI:10.1126/science.abm4096",
            "snippet": "In all four cases, target recognition led to Avs protein activation and antiviral activity",
            "notes": "Gao et al. connect Avs1 through Avs4 target recognition to Avs activation and antiviral activity."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| Avs_I__Avs1A                                     | Avs_I__Avs1A                                     | Avs_I                  | Custom                  | 20     |",
            "notes": "The pinned DefenseFinder HMM inventory records Avs_I__Avs1A under the Avs_I model namespace."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| Avs_I__Avs1B                                     | Avs_I__Avs1B                                     | Avs_I                  | Custom                  | 100    |",
            "notes": "The pinned DefenseFinder HMM inventory records Avs_I__Avs1B under the Avs_I model namespace."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| Avs_I__Avs1C                                     | Avs_I__Avs1C                                     | Avs_I                  | Custom                  | 20     |",
            "notes": "The pinned DefenseFinder HMM inventory records Avs_I__Avs1C under the Avs_I model namespace."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "snippet": "Avs\tAvs_I\t2\t2\tAvs_I__Avs1A, Avs_I__Avs1B, Avs_I__Avs1C\t\t\t",
            "notes": "The pinned DefenseFinder rules table models Avs_I as an Avs subsystem with Avs1A, Avs1B, and Avs1C profiles."
          }
        ],
        "attaches_to": [
          "causal_graphs#avs_i_locus_phage_protein_recognition"
        ],
        "posed_by": "codex",
        "posed_date": "2026-10-02"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-02T04:42:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Avs I system as a DOI- and DefenseFinder-backed GENOMICS TraitRecord under the AVAST system parent after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v411.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-02T04:42:01Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed Avs I system during initial curation and left canonical_examples empty because Gao et al. and the pinned DefenseFinder tables support the Avs_I model namespace and Avs1 phage-protein-recognition activity but not an accession-backed native microbial taxon exemplar with experimentally verified endogenous Avs I activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000535",
    "label": "Avs II system",
    "definition": "An AVAST system in which an organism possesses a genome-encoded subtype II locus represented by DefenseFinder with an Avs2A profile.",
    "definition_source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000239"
    ],
    "synonyms": [
      {
        "synonym_text": "Avs_II",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv"
      },
      {
        "synonym_text": "Avs_II__Avs2A",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1126/science.aba0372",
        "snippet": "AVAST, antiviral ATPase/NTPase of the STAND superfamily",
        "notes": "Gao et al. coined AVAST as an antiviral STAND ATPase/NTPase defense-system family."
      },
      {
        "reference": "DOI:10.1126/science.abm4096",
        "snippet": "Avs1 to Avs3 recognize the large terminase subunit, and Avs4 recognizes the portal",
        "notes": "Gao et al. support Avs2 as a phage-protein-sensing member of the AVAST receptor family."
      },
      {
        "reference": "DOI:10.1126/science.abm4096",
        "snippet": "In all four cases, target recognition led to Avs protein activation and antiviral activity",
        "notes": "Gao et al. connect Avs1 through Avs4 target recognition to Avs activation and antiviral activity."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| Avs | 10\\.1126/science\\.aba0372 | Diverse enzymatic activities mediate antiviral immunity in prokaryotes | ",
        "notes": "The pinned DefenseFinder article registry maps the Avs source key to the Gao et al. pangenome-scale antiviral-immunity paper."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| Avs_II__Avs2A                                    | Avs_II__Avs2A                                    | Avs_II                 | Custom                  | 100    |",
        "notes": "The pinned DefenseFinder HMM inventory records Avs_II__Avs2A under the Avs_II model namespace."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "Avs\tAvs_II\t1\t1\tAvs_II__Avs2A\t\t\t",
        "notes": "The pinned DefenseFinder rules table models Avs_II as an Avs subsystem with an Avs2A profile."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "avs_ii_locus_phage_protein_recognition",
        "title": "Avs II loci support phage protein recognition",
        "description": "Conservative system-level sketch linking an Avs_II locus to Avs2-mediated phage protein recognition and Avs II system possession.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Avs_II at locus and Avs2 phage-protein recognition level without asserting the exact Avs2A component role, direct effector activity, native host breadth, sensitive-phage breadth, or whether every DefenseFinder Avs_II prediction is a complete experimentally active Avs II locus.",
        "nodes": [
          {
            "node_id": "avs_ii_locus",
            "label": "Avs II locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "An AVAST subtype II locus represented in DefenseFinder by an Avs2A profile."
          },
          {
            "node_id": "avs2_phage_protein_recognition",
            "label": "Avs2 phage protein recognition",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Recognition of an infecting phage protein by an Avs2 antiviral STAND-family receptor."
          },
          {
            "node_id": "avs_ii_system_trait",
            "label": "Avs II system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000535",
            "description": "Possession of a genome-encoded Avs II phage-defense system."
          },
          {
            "node_id": "avast_system_trait",
            "label": "AVAST system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000239",
            "description": "Possession of a genome-encoded AVAST phage-defense system."
          }
        ],
        "edges": [
          {
            "subject": "avs_ii_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "avs2_phage_protein_recognition",
            "description": "Avs II loci encode Avs2 components, and Avs2 belongs to the AVAST receptors that recognize the phage large terminase subunit.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.abm4096",
                "snippet": "Avs1 to Avs3 recognize the large terminase subunit, and Avs4 recognizes the portal",
                "notes": "Gao et al. support Avs2 as a phage-protein-sensing member of the AVAST receptor family."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| Avs_II__Avs2A                                    | Avs_II__Avs2A                                    | Avs_II                 | Custom                  | 100    |",
                "notes": "The pinned DefenseFinder HMM inventory records Avs_II__Avs2A under the Avs_II model namespace."
              }
            ]
          },
          {
            "subject": "avs2_phage_protein_recognition",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "avs_ii_system_trait",
            "description": "The first-pass Avs II system trait is realized by Avs2 target recognition and downstream antiviral activity.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.abm4096",
                "snippet": "Avs1 to Avs3 recognize the large terminase subunit, and Avs4 recognizes the portal",
                "notes": "Gao et al. support Avs2 as a phage-protein-sensing member of the AVAST receptor family."
              },
              {
                "reference": "DOI:10.1126/science.abm4096",
                "snippet": "In all four cases, target recognition led to Avs protein activation and antiviral activity",
                "notes": "Gao et al. connect Avs1 through Avs4 target recognition to Avs activation and antiviral activity."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "Avs\tAvs_II\t1\t1\tAvs_II__Avs2A\t\t\t",
                "notes": "The pinned DefenseFinder rules table models Avs_II as an Avs subsystem with an Avs2A profile."
              }
            ]
          },
          {
            "subject": "avs_ii_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "avast_system_trait",
            "description": "Avs II system possession is an AVAST-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.aba0372",
                "snippet": "AVAST, antiviral ATPase/NTPase of the STAND superfamily",
                "notes": "Gao et al. coined AVAST as an antiviral STAND ATPase/NTPase defense-system family."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| Avs | 10\\.1126/science\\.aba0372 | Diverse enzymatic activities mediate antiviral immunity in prokaryotes | ",
                "notes": "The pinned DefenseFinder article registry maps the Avs source key to the Gao et al. pangenome-scale antiviral-immunity paper."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "Avs\tAvs_II\t1\t1\tAvs_II__Avs2A\t\t\t",
                "notes": "The pinned DefenseFinder rules table models Avs_II as an Avs subsystem with an Avs2A profile."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "avs-ii-component-and-effector-gap",
        "prompt": "Resolve the Avs2A component role, direct effector chemistry, exact phage-trigger mapping, native host breadth, and sensitive-phage breadth before minting Avs II mechanism or component children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Gao et al. support Avs2 phage-protein recognition and Avs activation during antiviral defense, and the pinned DefenseFinder HMM inventory and rules table support Avs_II as a subtype II model with an Avs2A profile. This first-pass record leaves the exact component role, downstream effector chemistry, native host breadth, sensitive-phage breadth, and profile-to-activity requirements unresolved.",
        "evidence": [
          {
            "reference": "DOI:10.1126/science.abm4096",
            "snippet": "Avs1 to Avs3 recognize the large terminase subunit, and Avs4 recognizes the portal",
            "notes": "Gao et al. support Avs2 as a phage-protein-sensing member of the AVAST receptor family."
          },
          {
            "reference": "DOI:10.1126/science.abm4096",
            "snippet": "In all four cases, target recognition led to Avs protein activation and antiviral activity",
            "notes": "Gao et al. connect Avs1 through Avs4 target recognition to Avs activation and antiviral activity."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| Avs_II__Avs2A                                    | Avs_II__Avs2A                                    | Avs_II                 | Custom                  | 100    |",
            "notes": "The pinned DefenseFinder HMM inventory records Avs_II__Avs2A under the Avs_II model namespace."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "snippet": "Avs\tAvs_II\t1\t1\tAvs_II__Avs2A\t\t\t",
            "notes": "The pinned DefenseFinder rules table models Avs_II as an Avs subsystem with an Avs2A profile."
          }
        ],
        "attaches_to": [
          "causal_graphs#avs_ii_locus_phage_protein_recognition"
        ],
        "posed_by": "codex",
        "posed_date": "2026-10-02"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-02T04:58:40Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Avs II system as a DOI- and DefenseFinder-backed GENOMICS TraitRecord under the AVAST system parent after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v412.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-02T04:58:41Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed Avs II system during initial curation and left canonical_examples empty because Gao et al. and the pinned DefenseFinder tables support the Avs_II model namespace and Avs2 phage-protein-recognition activity but not an accession-backed native microbial taxon exemplar with experimentally verified endogenous Avs II activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000536",
    "label": "Avs III system",
    "definition": "An AVAST system in which an organism possesses a genome-encoded subtype III locus represented by DefenseFinder with Avs3A and Avs3B profiles.",
    "definition_source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000239"
    ],
    "synonyms": [
      {
        "synonym_text": "Avs_III",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv"
      },
      {
        "synonym_text": "Avs_III__Avs3A",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "Avs_III__Avs3B",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1126/science.aba0372",
        "snippet": "AVAST, antiviral ATPase/NTPase of the STAND superfamily",
        "notes": "Gao et al. coined AVAST as an antiviral STAND ATPase/NTPase defense-system family."
      },
      {
        "reference": "DOI:10.1126/science.abm4096",
        "snippet": "Avs1 to Avs3 recognize the large terminase subunit, and Avs4 recognizes the portal",
        "notes": "Gao et al. support Avs3 as a phage-protein-sensing member of the AVAST receptor family."
      },
      {
        "reference": "DOI:10.1126/science.abm4096",
        "snippet": "In all four cases, target recognition led to Avs protein activation and antiviral activity",
        "notes": "Gao et al. connect Avs1 through Avs4 target recognition to Avs activation and antiviral activity."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| Avs | 10\\.1126/science\\.aba0372 | Diverse enzymatic activities mediate antiviral immunity in prokaryotes | ",
        "notes": "The pinned DefenseFinder article registry maps the Avs source key to the Gao et al. pangenome-scale antiviral-immunity paper."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| Avs_III__Avs3A                                   | Avs_III__Avs3A                                   | Avs_III                | Custom                  | 20     |",
        "notes": "The pinned DefenseFinder HMM inventory records Avs_III__Avs3A under the Avs_III model namespace."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| Avs_III__Avs3B                                   | Avs_III__Avs3B                                   | Avs_III                | Custom                  | 34     |",
        "notes": "The pinned DefenseFinder HMM inventory records Avs_III__Avs3B under the Avs_III model namespace."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "Avs\tAvs_III\t2\t2\tAvs_III__Avs3A, Avs_III__Avs3B\t\t\t",
        "notes": "The pinned DefenseFinder rules table models Avs_III as an Avs subsystem with Avs3A and Avs3B profiles."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "avs_iii_locus_phage_protein_recognition",
        "title": "Avs III loci support phage protein recognition",
        "description": "Conservative system-level sketch linking an Avs_III locus to Avs3-mediated phage protein recognition and Avs III system possession.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Avs_III at locus and Avs3 phage-protein recognition level without asserting the exact Avs3A and Avs3B component roles, direct effector activity, native host breadth, sensitive-phage breadth, or whether every DefenseFinder Avs_III prediction is a complete experimentally active Avs III locus.",
        "nodes": [
          {
            "node_id": "avs_iii_locus",
            "label": "Avs III locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "An AVAST subtype III locus represented in DefenseFinder by Avs3A and Avs3B profiles."
          },
          {
            "node_id": "avs3_phage_protein_recognition",
            "label": "Avs3 phage protein recognition",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Recognition of an infecting phage protein by an Avs3 antiviral STAND-family receptor."
          },
          {
            "node_id": "avs_iii_system_trait",
            "label": "Avs III system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000536",
            "description": "Possession of a genome-encoded Avs III phage-defense system."
          },
          {
            "node_id": "avast_system_trait",
            "label": "AVAST system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000239",
            "description": "Possession of a genome-encoded AVAST phage-defense system."
          }
        ],
        "edges": [
          {
            "subject": "avs_iii_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "avs3_phage_protein_recognition",
            "description": "Avs III loci encode Avs3 components, and Avs3 belongs to the AVAST receptors that recognize the phage large terminase subunit.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.abm4096",
                "snippet": "Avs1 to Avs3 recognize the large terminase subunit, and Avs4 recognizes the portal",
                "notes": "Gao et al. support Avs3 as a phage-protein-sensing member of the AVAST receptor family."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| Avs_III__Avs3A                                   | Avs_III__Avs3A                                   | Avs_III                | Custom                  | 20     |",
                "notes": "The pinned DefenseFinder HMM inventory records Avs_III__Avs3A under the Avs_III model namespace."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| Avs_III__Avs3B                                   | Avs_III__Avs3B                                   | Avs_III                | Custom                  | 34     |",
                "notes": "The pinned DefenseFinder HMM inventory records Avs_III__Avs3B under the Avs_III model namespace."
              }
            ]
          },
          {
            "subject": "avs3_phage_protein_recognition",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "avs_iii_system_trait",
            "description": "The first-pass Avs III system trait is realized by Avs3 target recognition and downstream antiviral activity.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.abm4096",
                "snippet": "Avs1 to Avs3 recognize the large terminase subunit, and Avs4 recognizes the portal",
                "notes": "Gao et al. support Avs3 as a phage-protein-sensing member of the AVAST receptor family."
              },
              {
                "reference": "DOI:10.1126/science.abm4096",
                "snippet": "In all four cases, target recognition led to Avs protein activation and antiviral activity",
                "notes": "Gao et al. connect Avs1 through Avs4 target recognition to Avs activation and antiviral activity."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "Avs\tAvs_III\t2\t2\tAvs_III__Avs3A, Avs_III__Avs3B\t\t\t",
                "notes": "The pinned DefenseFinder rules table models Avs_III as an Avs subsystem with Avs3A and Avs3B profiles."
              }
            ]
          },
          {
            "subject": "avs_iii_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "avast_system_trait",
            "description": "Avs III system possession is an AVAST-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.aba0372",
                "snippet": "AVAST, antiviral ATPase/NTPase of the STAND superfamily",
                "notes": "Gao et al. coined AVAST as an antiviral STAND ATPase/NTPase defense-system family."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| Avs | 10\\.1126/science\\.aba0372 | Diverse enzymatic activities mediate antiviral immunity in prokaryotes | ",
                "notes": "The pinned DefenseFinder article registry maps the Avs source key to the Gao et al. pangenome-scale antiviral-immunity paper."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "Avs\tAvs_III\t2\t2\tAvs_III__Avs3A, Avs_III__Avs3B\t\t\t",
                "notes": "The pinned DefenseFinder rules table models Avs_III as an Avs subsystem with Avs3A and Avs3B profiles."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "avs-iii-component-and-effector-gap",
        "prompt": "Resolve the Avs3A and Avs3B component roles, direct effector chemistry, exact phage-trigger mapping, native host breadth, and sensitive-phage breadth before minting Avs III mechanism or component children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Gao et al. support Avs3 phage-protein recognition and Avs activation during antiviral defense, and the pinned DefenseFinder HMM inventory and rules table support Avs_III as a subtype III model with Avs3A and Avs3B profiles. This first-pass record leaves the exact component roles, downstream effector chemistry, native host breadth, sensitive-phage breadth, and profile-to-activity requirements unresolved.",
        "evidence": [
          {
            "reference": "DOI:10.1126/science.abm4096",
            "snippet": "Avs1 to Avs3 recognize the large terminase subunit, and Avs4 recognizes the portal",
            "notes": "Gao et al. support Avs3 as a phage-protein-sensing member of the AVAST receptor family."
          },
          {
            "reference": "DOI:10.1126/science.abm4096",
            "snippet": "In all four cases, target recognition led to Avs protein activation and antiviral activity",
            "notes": "Gao et al. connect Avs1 through Avs4 target recognition to Avs activation and antiviral activity."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| Avs_III__Avs3A                                   | Avs_III__Avs3A                                   | Avs_III                | Custom                  | 20     |",
            "notes": "The pinned DefenseFinder HMM inventory records Avs_III__Avs3A under the Avs_III model namespace."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| Avs_III__Avs3B                                   | Avs_III__Avs3B                                   | Avs_III                | Custom                  | 34     |",
            "notes": "The pinned DefenseFinder HMM inventory records Avs_III__Avs3B under the Avs_III model namespace."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "snippet": "Avs\tAvs_III\t2\t2\tAvs_III__Avs3A, Avs_III__Avs3B\t\t\t",
            "notes": "The pinned DefenseFinder rules table models Avs_III as an Avs subsystem with Avs3A and Avs3B profiles."
          }
        ],
        "attaches_to": [
          "causal_graphs#avs_iii_locus_phage_protein_recognition"
        ],
        "posed_by": "codex",
        "posed_date": "2026-10-02"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-02T05:44:32Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Avs III system as a DOI- and DefenseFinder-backed GENOMICS TraitRecord under the AVAST system parent after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v413.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-02T05:44:33Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed Avs III system during initial curation and left canonical_examples empty because Gao et al. and the pinned DefenseFinder tables support the Avs_III model namespace and Avs3 phage-protein-recognition activity but not an accession-backed native microbial taxon exemplar with experimentally verified endogenous Avs III activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000537",
    "label": "Avs IV system",
    "definition": "An AVAST system in which an organism possesses a genome-encoded subtype IV locus represented by DefenseFinder with an Avs4A profile.",
    "definition_source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000239"
    ],
    "synonyms": [
      {
        "synonym_text": "Avs_IV",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv"
      },
      {
        "synonym_text": "Avs_IV__Avs4A",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1126/science.aba0372",
        "snippet": "AVAST, antiviral ATPase/NTPase of the STAND superfamily",
        "notes": "Gao et al. coined AVAST as an antiviral STAND ATPase/NTPase defense-system family."
      },
      {
        "reference": "DOI:10.1126/science.abm4096",
        "snippet": "Avs1 to Avs3 recognize the large terminase subunit, and Avs4 recognizes the portal",
        "notes": "Gao et al. support Avs4 as a phage-portal-sensing member of the AVAST receptor family."
      },
      {
        "reference": "DOI:10.1126/science.abm4096",
        "snippet": "In all four cases, target recognition led to Avs protein activation and antiviral activity",
        "notes": "Gao et al. connect Avs1 through Avs4 target recognition to Avs activation and antiviral activity."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| Avs | 10\\.1126/science\\.aba0372 | Diverse enzymatic activities mediate antiviral immunity in prokaryotes | ",
        "notes": "The pinned DefenseFinder article registry maps the Avs source key to the Gao et al. pangenome-scale antiviral-immunity paper."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| Avs_IV__Avs4A                                    | Avs_IV__Avs4A                                    | Avs_IV                 | Custom                  | 60     |",
        "notes": "The pinned DefenseFinder HMM inventory records Avs_IV__Avs4A under the Avs_IV model namespace."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "Avs\tAvs_IV\t1\t1\tAvs_IV__Avs4A\t\t\t",
        "notes": "The pinned DefenseFinder rules table models Avs_IV as an Avs subsystem with an Avs4A profile."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "avs_iv_locus_phage_portal_recognition",
        "title": "Avs IV loci support phage portal recognition",
        "description": "Conservative system-level sketch linking an Avs_IV locus to Avs4-mediated phage portal recognition and Avs IV system possession.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Avs_IV at locus and Avs4 phage-portal recognition level without asserting the exact Avs4A component role, direct effector activity, native host breadth, sensitive-phage breadth, or whether every DefenseFinder Avs_IV prediction is a complete experimentally active Avs IV locus.",
        "nodes": [
          {
            "node_id": "avs_iv_locus",
            "label": "Avs IV locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "An AVAST subtype IV locus represented in DefenseFinder by an Avs4A profile."
          },
          {
            "node_id": "avs4_phage_portal_recognition",
            "label": "Avs4 phage portal recognition",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Recognition of an infecting phage portal protein by an Avs4 antiviral STAND-family receptor."
          },
          {
            "node_id": "avs_iv_system_trait",
            "label": "Avs IV system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000537",
            "description": "Possession of a genome-encoded Avs IV phage-defense system."
          },
          {
            "node_id": "avast_system_trait",
            "label": "AVAST system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000239",
            "description": "Possession of a genome-encoded AVAST phage-defense system."
          }
        ],
        "edges": [
          {
            "subject": "avs_iv_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "avs4_phage_portal_recognition",
            "description": "Avs IV loci encode Avs4 components, and Avs4 belongs to the AVAST receptors that recognize the phage portal protein.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.abm4096",
                "snippet": "Avs1 to Avs3 recognize the large terminase subunit, and Avs4 recognizes the portal",
                "notes": "Gao et al. support Avs4 as a phage-portal-sensing member of the AVAST receptor family."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| Avs_IV__Avs4A                                    | Avs_IV__Avs4A                                    | Avs_IV                 | Custom                  | 60     |",
                "notes": "The pinned DefenseFinder HMM inventory records Avs_IV__Avs4A under the Avs_IV model namespace."
              }
            ]
          },
          {
            "subject": "avs4_phage_portal_recognition",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "avs_iv_system_trait",
            "description": "The first-pass Avs IV system trait is realized by Avs4 target recognition and downstream antiviral activity.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.abm4096",
                "snippet": "Avs1 to Avs3 recognize the large terminase subunit, and Avs4 recognizes the portal",
                "notes": "Gao et al. support Avs4 as a phage-portal-sensing member of the AVAST receptor family."
              },
              {
                "reference": "DOI:10.1126/science.abm4096",
                "snippet": "In all four cases, target recognition led to Avs protein activation and antiviral activity",
                "notes": "Gao et al. connect Avs1 through Avs4 target recognition to Avs activation and antiviral activity."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "Avs\tAvs_IV\t1\t1\tAvs_IV__Avs4A\t\t\t",
                "notes": "The pinned DefenseFinder rules table models Avs_IV as an Avs subsystem with an Avs4A profile."
              }
            ]
          },
          {
            "subject": "avs_iv_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "avast_system_trait",
            "description": "Avs IV system possession is an AVAST-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.aba0372",
                "snippet": "AVAST, antiviral ATPase/NTPase of the STAND superfamily",
                "notes": "Gao et al. coined AVAST as an antiviral STAND ATPase/NTPase defense-system family."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| Avs | 10\\.1126/science\\.aba0372 | Diverse enzymatic activities mediate antiviral immunity in prokaryotes | ",
                "notes": "The pinned DefenseFinder article registry maps the Avs source key to the Gao et al. pangenome-scale antiviral-immunity paper."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "Avs\tAvs_IV\t1\t1\tAvs_IV__Avs4A\t\t\t",
                "notes": "The pinned DefenseFinder rules table models Avs_IV as an Avs subsystem with an Avs4A profile."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "avs-iv-component-and-effector-gap",
        "prompt": "Resolve the Avs4A component role, direct effector chemistry, exact phage-trigger mapping, native host breadth, and sensitive-phage breadth before minting Avs IV mechanism or component children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Gao et al. support Avs4 phage-portal recognition and Avs activation during antiviral defense, and the pinned DefenseFinder HMM inventory and rules table support Avs_IV as a subtype IV model with an Avs4A profile. This first-pass record leaves the exact component role, downstream effector chemistry, native host breadth, sensitive-phage breadth, and profile-to-activity requirements unresolved.",
        "evidence": [
          {
            "reference": "DOI:10.1126/science.abm4096",
            "snippet": "Avs1 to Avs3 recognize the large terminase subunit, and Avs4 recognizes the portal",
            "notes": "Gao et al. support Avs4 as a phage-portal-sensing member of the AVAST receptor family."
          },
          {
            "reference": "DOI:10.1126/science.abm4096",
            "snippet": "In all four cases, target recognition led to Avs protein activation and antiviral activity",
            "notes": "Gao et al. connect Avs1 through Avs4 target recognition to Avs activation and antiviral activity."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| Avs_IV__Avs4A                                    | Avs_IV__Avs4A                                    | Avs_IV                 | Custom                  | 60     |",
            "notes": "The pinned DefenseFinder HMM inventory records Avs_IV__Avs4A under the Avs_IV model namespace."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "snippet": "Avs\tAvs_IV\t1\t1\tAvs_IV__Avs4A\t\t\t",
            "notes": "The pinned DefenseFinder rules table models Avs_IV as an Avs subsystem with an Avs4A profile."
          }
        ],
        "attaches_to": [
          "causal_graphs#avs_iv_locus_phage_portal_recognition"
        ],
        "posed_by": "codex",
        "posed_date": "2026-10-02"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-02T06:35:42Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Avs IV system as a DOI- and DefenseFinder-backed GENOMICS TraitRecord under the AVAST system parent after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v414.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-02T06:35:43Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed Avs IV system during initial curation and left canonical_examples empty because Gao et al. and the pinned DefenseFinder tables support the Avs_IV model namespace and Avs4 phage-portal-recognition activity but not an accession-backed native microbial taxon exemplar with experimentally verified endogenous Avs IV activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000538",
    "label": "Avs V system",
    "definition": "An AVAST system in which an organism possesses a genome-encoded subtype V locus represented by DefenseFinder with an Avs5A profile.",
    "definition_source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000239"
    ],
    "synonyms": [
      {
        "synonym_text": "Avs_V",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv"
      },
      {
        "synonym_text": "Avs_V__Avs5A",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1126/science.aba0372",
        "snippet": "AVAST, antiviral ATPase/NTPase of the STAND superfamily",
        "notes": "Gao et al. coined AVAST as an antiviral STAND ATPase/NTPase defense-system family."
      },
      {
        "reference": "DOI:10.1016/j.molcel.2026.01.004",
        "snippet": "AVAST type 5 (Avs5) systems, part of the signal transduction ATPases of numerous domains (STAND) superfamily, confer conserved immunity against jumbo phages",
        "notes": "Muralidharan et al. support treating Avs5 systems as type V AVAST systems with conserved immunity against jumbo phages."
      },
      {
        "reference": "DOI:10.1016/j.molcel.2026.01.004",
        "snippet": "Recognition of phage infection triggers the Sir2-like effector domain of Avs5 across three Avs5 clades",
        "notes": "Muralidharan et al. connect Avs5 phage recognition to Sir2-like effector activation."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| Avs | 10\\.1126/science\\.aba0372 | Diverse enzymatic activities mediate antiviral immunity in prokaryotes | ",
        "notes": "The pinned DefenseFinder article registry maps the Avs source key to the Gao et al. pangenome-scale antiviral-immunity paper."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| Avs_V__Avs5A                                     | Avs_V__Avs5A                                     | Avs_V                  | Custom                  | 60     |",
        "notes": "The pinned DefenseFinder HMM inventory records Avs_V__Avs5A under the Avs_V model namespace."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "Avs\tAvs_V\t1\t1\tAvs_V__Avs5A\t\t\t",
        "notes": "The pinned DefenseFinder rules table models Avs_V as an Avs subsystem with an Avs5A profile."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "avs_v_locus_sir2_effector_activation",
        "title": "Avs V loci support Sir2-like effector activation",
        "description": "Conservative system-level sketch linking an Avs_V locus to Avs5 Sir2-like effector activation and Avs V system possession.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Avs_V at locus and Avs5 Sir2-like effector-activation level without asserting the exact Avs5A component role, JADA trigger-protein breadth, native host breadth, sensitive jumbo-phage breadth, or whether every DefenseFinder Avs_V prediction is a complete experimentally active Avs V locus.",
        "nodes": [
          {
            "node_id": "avs_v_locus",
            "label": "Avs V locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "An AVAST subtype V locus represented in DefenseFinder by an Avs5A profile."
          },
          {
            "node_id": "avs5_sir2_like_effector_activation",
            "label": "Avs5 Sir2-like effector activation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Activation of an Avs5 Sir2-like effector domain after phage infection recognition."
          },
          {
            "node_id": "avs_v_system_trait",
            "label": "Avs V system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000538",
            "description": "Possession of a genome-encoded Avs V phage-defense system."
          },
          {
            "node_id": "avast_system_trait",
            "label": "AVAST system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000239",
            "description": "Possession of a genome-encoded AVAST phage-defense system."
          }
        ],
        "edges": [
          {
            "subject": "avs_v_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "avs5_sir2_like_effector_activation",
            "description": "Avs V loci encode Avs5 components, and Avs5 phage-infection recognition triggers a Sir2-like effector domain.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.molcel.2026.01.004",
                "snippet": "Recognition of phage infection triggers the Sir2-like effector domain of Avs5 across three Avs5 clades",
                "notes": "Muralidharan et al. connect Avs5 phage recognition to Sir2-like effector activation."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| Avs_V__Avs5A                                     | Avs_V__Avs5A                                     | Avs_V                  | Custom                  | 60     |",
                "notes": "The pinned DefenseFinder HMM inventory records Avs_V__Avs5A under the Avs_V model namespace."
              }
            ]
          },
          {
            "subject": "avs5_sir2_like_effector_activation",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "avs_v_system_trait",
            "description": "The first-pass Avs V system trait is realized by Avs5 phage recognition, Sir2-like effector activation, and conserved immunity against jumbo phages.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.molcel.2026.01.004",
                "snippet": "AVAST type 5 (Avs5) systems, part of the signal transduction ATPases of numerous domains (STAND) superfamily, confer conserved immunity against jumbo phages",
                "notes": "Muralidharan et al. support treating Avs5 systems as type V AVAST systems with conserved immunity against jumbo phages."
              },
              {
                "reference": "DOI:10.1016/j.molcel.2026.01.004",
                "snippet": "Recognition of phage infection triggers the Sir2-like effector domain of Avs5 across three Avs5 clades",
                "notes": "Muralidharan et al. connect Avs5 phage recognition to Sir2-like effector activation."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "Avs\tAvs_V\t1\t1\tAvs_V__Avs5A\t\t\t",
                "notes": "The pinned DefenseFinder rules table models Avs_V as an Avs subsystem with an Avs5A profile."
              }
            ]
          },
          {
            "subject": "avs_v_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "avast_system_trait",
            "description": "Avs V system possession is an AVAST-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.aba0372",
                "snippet": "AVAST, antiviral ATPase/NTPase of the STAND superfamily",
                "notes": "Gao et al. coined AVAST as an antiviral STAND ATPase/NTPase defense-system family."
              },
              {
                "reference": "DOI:10.1016/j.molcel.2026.01.004",
                "snippet": "AVAST type 5 (Avs5) systems, part of the signal transduction ATPases of numerous domains (STAND) superfamily, confer conserved immunity against jumbo phages",
                "notes": "Muralidharan et al. support treating Avs5 systems as type V AVAST systems with conserved immunity against jumbo phages."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "Avs\tAvs_V\t1\t1\tAvs_V__Avs5A\t\t\t",
                "notes": "The pinned DefenseFinder rules table models Avs_V as an Avs subsystem with an Avs5A profile."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "avs-v-component-and-host-gap",
        "prompt": "Resolve the Avs5A component role, exact JADA trigger breadth, native host breadth, sensitive jumbo-phage breadth, and DefenseFinder profile-to-activity requirements before minting Avs V mechanism or component children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Muralidharan et al. support Avs5 Sir2-like effector activation during jumbo-phage defense, and the pinned DefenseFinder HMM inventory and rules table support Avs_V as a subtype V model with an Avs5A profile. This first-pass record leaves the exact component role, JADA trigger breadth, native host breadth, sensitive jumbo-phage breadth, and profile-to-activity requirements unresolved.",
        "evidence": [
          {
            "reference": "DOI:10.1016/j.molcel.2026.01.004",
            "snippet": "AVAST type 5 (Avs5) systems, part of the signal transduction ATPases of numerous domains (STAND) superfamily, confer conserved immunity against jumbo phages",
            "notes": "Muralidharan et al. support treating Avs5 systems as type V AVAST systems with conserved immunity against jumbo phages."
          },
          {
            "reference": "DOI:10.1016/j.molcel.2026.01.004",
            "snippet": "Recognition of phage infection triggers the Sir2-like effector domain of Avs5 across three Avs5 clades",
            "notes": "Muralidharan et al. connect Avs5 phage recognition to Sir2-like effector activation."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| Avs_V__Avs5A                                     | Avs_V__Avs5A                                     | Avs_V                  | Custom                  | 60     |",
            "notes": "The pinned DefenseFinder HMM inventory records Avs_V__Avs5A under the Avs_V model namespace."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "snippet": "Avs\tAvs_V\t1\t1\tAvs_V__Avs5A\t\t\t",
            "notes": "The pinned DefenseFinder rules table models Avs_V as an Avs subsystem with an Avs5A profile."
          }
        ],
        "attaches_to": [
          "causal_graphs#avs_v_locus_sir2_effector_activation"
        ],
        "posed_by": "codex",
        "posed_date": "2026-10-02"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-02T07:21:42Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Avs V system as a DOI- and DefenseFinder-backed GENOMICS TraitRecord under the AVAST system parent after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v415.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-02T07:21:43Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed Avs V system during initial curation and left canonical_examples empty because Muralidharan et al. and the pinned DefenseFinder tables support Avs5 type V AVAST immunity and the Avs_V model namespace but not an accession-backed native microbial taxon exemplar tied to Avs_V__Avs5A and experimentally verified endogenous Avs V activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000251",
    "label": "Azaca system",
    "definition": "A phage defense system in which an organism possesses an Azaca locus represented by ZacA, ZacB, and ZacC profiles that can protect bacteria from bacteriophage infection.",
    "definition_source": "DOI:10.1016/j.chom.2022.09.017",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "Azaca",
        "synonym_type": "EXACT_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1016/j.chom.2022.09.017",
        "snippet": "discovery of 21 defense systems that protect bacteria from phages, based on computational genomic analyses and phage-infection experiments",
        "notes": "Millman et al. report the computational and experimental cohort that DefenseFinder cites for Azaca as a bacterial anti-phage system."
      },
      {
        "reference": "DOI:10.1101/2022.05.11.491447",
        "snippet": "discovery of 21 new defense systems that protect bacteria from phages, based on computational genomic analyses and phage infection experiments",
        "notes": "The bioRxiv version of Millman et al. independently carries the 21-system discovery claim linked from DefenseFinder's Azaca article registry."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "Azaca | 10\\.1101/2022\\.05\\.11\\.491447 | An expanding arsenal of immune systems that protect bacteria from phages",
        "notes": "The DefenseFinder model registry maps the named Azaca system to the Millman et al. antiphage-system discovery preprint."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "Azaca\tAzaca\t2\t3\tAzaca__ZacA, Azaca__ZacB, Azaca__ZacC",
        "notes": "The DefenseFinder rules table models Azaca with ZacA, ZacB, and ZacC mandatory-profile choices, requiring a three-gene minimum and at least two mandatory hits."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "Azaca__ZacA                                      | Azaca__ZacA                                      | Azaca",
        "notes": "The DefenseFinder HMM inventory records ZacA as an Azaca profile."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "Azaca__ZacB                                      | Azaca__ZacB                                      | Azaca",
        "notes": "The DefenseFinder HMM inventory records ZacB as an Azaca profile."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "Azaca__ZacC                                      | Azaca__ZacC                                      | Azaca",
        "notes": "The DefenseFinder HMM inventory records ZacC as an Azaca profile."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "azaca_locus_restricts_phage",
        "title": "Azaca loci confer bacterial phage defense",
        "description": "Conservative system-level sketch linking possession of an Azaca locus to restricted bacteriophage propagation without asserting the unresolved phage trigger or molecular output.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Azaca as a named anti-phage system with DefenseFinder ZacA, ZacB, and ZacC profiles while leaving its phage trigger, molecular substrate, antiviral effector output, and subtype breadth unresolved.",
        "nodes": [
          {
            "node_id": "azaca_locus",
            "label": "Azaca locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "An Azaca anti-phage defense locus satisfying a DefenseFinder rule over ZacA, ZacB, and ZacC profiles."
          },
          {
            "node_id": "restricted_phage_propagation",
            "label": "restricted phage propagation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced propagation of bacteriophage in cells carrying the Azaca system."
          },
          {
            "node_id": "azaca_system_trait",
            "label": "Azaca system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000251",
            "description": "Possession of a genome-encoded Azaca phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "azaca_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "restricted_phage_propagation",
            "description": "DefenseFinder maps Azaca to a bacterial anti-phage-system discovery preprint and represents Azaca loci through ZacA, ZacB, and ZacC component profiles.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.chom.2022.09.017",
                "snippet": "discovery of 21 defense systems that protect bacteria from phages",
                "notes": "Millman et al. describe the anti-phage discovery cohort that the DefenseFinder Azaca registry row maps to the Azaca system."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Azaca | 10\\.1101/2022\\.05\\.11\\.491447 | An expanding arsenal of immune systems that protect bacteria from phages",
                "notes": "The DefenseFinder registry maps Azaca itself to the Millman et al. bacterial antiphage-system discovery preprint."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "Azaca\tAzaca\t2\t3\tAzaca__ZacA, Azaca__ZacB, Azaca__ZacC",
                "notes": "The DefenseFinder rules table supports ZacA, ZacB, and ZacC as Azaca system profile choices."
              }
            ]
          },
          {
            "subject": "restricted_phage_propagation",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "azaca_system_trait",
            "description": "Azaca-mediated phage restriction realizes the Azaca system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.chom.2022.09.017",
                "snippet": "discovery of 21 defense systems that protect bacteria from phages",
                "notes": "Millman et al. place the Azaca discovery cohort in the set of bacterial systems that protect against phages."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Azaca | 10\\.1101/2022\\.05\\.11\\.491447 | An expanding arsenal of immune systems that protect bacteria from phages",
                "notes": "DefenseFinder records Azaca as a named system from the Millman et al. antiphage discovery preprint."
              }
            ]
          },
          {
            "subject": "azaca_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Azaca system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "An expanding arsenal of immune systems that protect bacteria from phages",
                "notes": "DefenseFinder associates Azaca with the Millman et al. bacterial antiphage-system discovery paper."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "azaca-mechanism-gap",
        "prompt": "Resolve Azaca phage triggers and effector outputs before minting narrower Azaca mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Millman et al. and DefenseFinder support Azaca as a named anti-phage system with ZacA, ZacB, and ZacC profiles, but the trigger, molecular substrate, antiviral effector output, and subtype-specific mechanism are not resolved enough here to assert a narrower mechanistic child trait.",
        "attaches_to": [
          "causal_graphs#azaca_locus_restricts_phage"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-18"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-18T21:21:49Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Azaca system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v128.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000268",
    "label": "Belenos system",
    "definition": "A phage defense system in which an organism possesses a Belenos locus represented by a VCA0457 profile that can protect bacteria from bacteriophage infection.",
    "definition_source": "DOI:10.1126/science.ads0768",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "Belenos",
        "synonym_type": "EXACT_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      },
      {
        "synonym_text": "VCA0457",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1126/science.ads0768",
        "snippet": "nearly 10% of the integron cassettes in the pandemic Vibrio cholerae strain encode novel antiphage functions",
        "notes": "Darracq et al. support treating the newly discovered Vibrio cholerae SCI antiphage cassettes as bacterial anti-phage systems."
      },
      {
        "reference": "DOI:10.1126/science.ads0768",
        "snippet": "Most of these novel systems have little or no similarity to previously known ones, with several providing defense through cell lysis or growth arrest",
        "notes": "Darracq et al. support a conservative system record that does not assert a resolved Belenos trigger, effector output, or universal pathway."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "Belenos | 10\\.1126/science\\.ads0768 | Sedentary chromosomal integrons as biobanks of bacterial antiphage defense systems",
        "notes": "The DefenseFinder model registry maps the named Belenos system to the Darracq et al. SCI antiphage-system paper."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "Belenos__VCA0457                                 |                                                  | Belenos",
        "notes": "The DefenseFinder HMM inventory records VCA0457 in the Belenos model namespace."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "belenos_locus_restricts_phage",
        "title": "Belenos loci confer bacterial phage defense",
        "description": "Conservative system-level sketch linking possession of a Belenos locus to restricted bacteriophage propagation without asserting the unresolved phage trigger or molecular output.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Belenos as a named SCI-derived anti-phage system with a VCA0457 DefenseFinder profile while leaving its phage trigger, molecular substrate, antiviral effector output, and subtype breadth unresolved.",
        "nodes": [
          {
            "node_id": "belenos_locus",
            "label": "Belenos locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A Belenos anti-phage defense locus represented in DefenseFinder by a VCA0457 profile."
          },
          {
            "node_id": "restricted_phage_propagation",
            "label": "restricted phage propagation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced propagation of bacteriophage in cells carrying the Belenos system."
          },
          {
            "node_id": "belenos_system_trait",
            "label": "Belenos system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000268",
            "description": "Possession of a genome-encoded Belenos phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "belenos_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "restricted_phage_propagation",
            "description": "DefenseFinder maps Belenos to an SCI anti-phage-system discovery paper and represents Belenos loci through the VCA0457 component profile.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.ads0768",
                "snippet": "nearly 10% of the integron cassettes in the pandemic Vibrio cholerae strain encode novel antiphage functions",
                "notes": "Darracq et al. describe the newly discovered antiphage-system cohort that the DefenseFinder Belenos registry row maps to the Belenos system."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "Belenos__VCA0457                                 |                                                  | Belenos",
                "notes": "The DefenseFinder HMM inventory supports VCA0457 as the Belenos component profile."
              }
            ]
          },
          {
            "subject": "restricted_phage_propagation",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "belenos_system_trait",
            "description": "Belenos-mediated phage restriction realizes the Belenos system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.ads0768",
                "snippet": "Most of these novel systems have little or no similarity to previously known ones",
                "notes": "Darracq et al. place the Belenos discovery cohort in a set of novel bacterial systems that protect against phages."
              }
            ]
          },
          {
            "subject": "belenos_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Belenos system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Belenos | 10\\.1126/science\\.ads0768 | Sedentary chromosomal integrons as biobanks of bacterial antiphage defense systems",
                "notes": "DefenseFinder associates Belenos with the Darracq et al. bacterial antiphage-system paper."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "belenos-mechanism-gap",
        "prompt": "Resolve Belenos phage triggers and effector outputs before minting narrower Belenos mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Darracq et al. and DefenseFinder support Belenos as a named anti-phage system with a VCA0457 profile, but the trigger, molecular substrate, antiviral effector output, and subtype-specific mechanism are not resolved enough here to assert a narrower mechanistic child trait.",
        "attaches_to": [
          "causal_graphs#belenos_locus_restricts_phage"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-19"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-19T06:33:51Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Belenos system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v145.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000269",
    "label": "Belisama system",
    "definition": "A phage defense system in which an organism possesses a Belisama locus represented by a VCA0458 profile that can protect bacteria from bacteriophage infection.",
    "definition_source": "DOI:10.1126/science.ads0768",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "Belisama",
        "synonym_type": "EXACT_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      },
      {
        "synonym_text": "VCA0458",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1126/science.ads0768",
        "snippet": "nearly 10% of the integron cassettes in the pandemic Vibrio cholerae strain encode novel antiphage functions",
        "notes": "Darracq et al. support treating the newly discovered Vibrio cholerae SCI antiphage cassettes as bacterial anti-phage systems."
      },
      {
        "reference": "DOI:10.1126/science.ads0768",
        "snippet": "Most of these novel systems have little or no similarity to previously known ones, with several providing defense through cell lysis or growth arrest",
        "notes": "Darracq et al. support a conservative system record that does not assert a resolved Belisama trigger, effector output, or universal pathway."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "Belisama | 10\\.1126/science\\.ads0768 | Sedentary chromosomal integrons as biobanks of bacterial antiphage defense systems",
        "notes": "The DefenseFinder model registry maps the named Belisama system to the Darracq et al. SCI antiphage-system paper."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "Belisama__VCA0458                                |                                                  | Belisama",
        "notes": "The DefenseFinder HMM inventory records VCA0458 in the Belisama model namespace."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "belisama_locus_restricts_phage",
        "title": "Belisama loci confer bacterial phage defense",
        "description": "Conservative system-level sketch linking possession of a Belisama locus to restricted bacteriophage propagation without asserting the unresolved phage trigger or molecular output.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Belisama as a named SCI-derived anti-phage system with a VCA0458 DefenseFinder profile while leaving its phage trigger, molecular substrate, antiviral effector output, and subtype breadth unresolved.",
        "nodes": [
          {
            "node_id": "belisama_locus",
            "label": "Belisama locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A Belisama anti-phage defense locus represented in DefenseFinder by a VCA0458 profile."
          },
          {
            "node_id": "restricted_phage_propagation",
            "label": "restricted phage propagation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced propagation of bacteriophage in cells carrying the Belisama system."
          },
          {
            "node_id": "belisama_system_trait",
            "label": "Belisama system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000269",
            "description": "Possession of a genome-encoded Belisama phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "belisama_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "restricted_phage_propagation",
            "description": "DefenseFinder maps Belisama to an SCI anti-phage-system discovery paper and represents Belisama loci through the VCA0458 component profile.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.ads0768",
                "snippet": "nearly 10% of the integron cassettes in the pandemic Vibrio cholerae strain encode novel antiphage functions",
                "notes": "Darracq et al. describe the newly discovered antiphage-system cohort that the DefenseFinder Belisama registry row maps to the Belisama system."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "Belisama__VCA0458                                |                                                  | Belisama",
                "notes": "The DefenseFinder HMM inventory supports VCA0458 as the Belisama component profile."
              }
            ]
          },
          {
            "subject": "restricted_phage_propagation",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "belisama_system_trait",
            "description": "Belisama-mediated phage restriction realizes the Belisama system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.ads0768",
                "snippet": "Most of these novel systems have little or no similarity to previously known ones",
                "notes": "Darracq et al. place the Belisama discovery cohort in a set of novel bacterial systems that protect against phages."
              }
            ]
          },
          {
            "subject": "belisama_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Belisama system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Belisama | 10\\.1126/science\\.ads0768 | Sedentary chromosomal integrons as biobanks of bacterial antiphage defense systems",
                "notes": "DefenseFinder associates Belisama with the Darracq et al. bacterial antiphage-system paper."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "belisama-mechanism-gap",
        "prompt": "Resolve Belisama phage triggers and effector outputs before minting narrower Belisama mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Darracq et al. and DefenseFinder support Belisama as a named anti-phage system with a VCA0458 profile, but the trigger, molecular substrate, antiviral effector output, and subtype-specific mechanism are not resolved enough here to assert a narrower mechanistic child trait.",
        "attaches_to": [
          "causal_graphs#belisama_locus_restricts_phage"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-19"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-19T07:01:47Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Belisama system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v146.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000369",
    "label": "Bil system",
    "definition": "A phage defense system in which an organism possesses a Bil bacterial ubiquitin-like conjugation locus that can covalently attach a ubiquitin-like protein to the bacteriophage central tail fibre and impair phage infectivity.",
    "definition_source": "DOI:10.1038/s41586-024-07616-5",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "Bil",
        "synonym_type": "EXACT_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      },
      {
        "synonym_text": "Bil antiphage defence system",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1038/s41586-024-07616-5"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/s41586-024-07616-5",
        "snippet": "Bil antiphage defence system",
        "notes": "Hor et al. identify Bil as a ubiquitin-like conjugation antiphage defense system."
      },
      {
        "reference": "DOI:10.1038/s41586-024-07616-5",
        "snippet": "phage central tail fibre is obstructed by the covalently attached ubiquitin-like protein",
        "notes": "Hor et al. show that the Bil system obstructs the phage central tail fibre with a covalently attached ubiquitin-like protein."
      },
      {
        "reference": "DOI:10.1038/s41586-024-07616-5",
        "snippet": "These phages show severely impaired infectivity",
        "notes": "Hor et al. connect Bil-dependent particle production to reduced phage infectivity."
      },
      {
        "reference": "DOI:10.1016/j.chom.2022.09.017",
        "snippet": "An expanded arsenal of immune systems that protect bacteria from phages",
        "notes": "Millman et al. published the discovery cohort that DefenseFinder maps to its Bil article-registry row."
      },
      {
        "reference": "DOI:10.1101/2022.05.11.491447",
        "snippet": "An expanding arsenal of immune systems that protect bacteria from phages",
        "notes": "The bioRxiv version of Millman et al. is the DOI cited in DefenseFinder's Bil article-registry row."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "Bil | 10\\.1101/2022\\.05\\.11\\.491447 | An expanding arsenal of immune systems that protect bacteria from phages",
        "notes": "The DefenseFinder article registry maps the named Bil system to the Millman et al. antiphage-system discovery preprint."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "bil_locus_impairs_phage_assembly",
        "title": "Bil loci impair bacteriophage infectivity",
        "description": "Conservative system-level sketch linking possession of a Bil ubiquitin-like conjugation locus to central-tail-fibre obstruction and impaired phage infectivity without asserting the exact DefenseFinder profile or rule set for Bil.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Bil as a named phage-defense system whose ubiquitin-like protein is covalently attached to the phage central tail fibre while leaving the exact Bil component composition, target-phage breadth, receptor-recognition consequences, and DefenseFinder model profiles unresolved.",
        "nodes": [
          {
            "node_id": "bil_locus",
            "label": "Bil locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A bacterial Bil ubiquitin-like conjugation locus that encodes an antiphage defense system."
          },
          {
            "node_id": "bil_ubiquitin_like_conjugation",
            "label": "Bil ubiquitin-like conjugation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Covalent attachment of a Bil ubiquitin-like protein during phage infection."
          },
          {
            "node_id": "central_tail_fibre_obstruction",
            "label": "central tail fibre obstruction",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Obstruction of a bacteriophage central tail fibre by a covalently attached ubiquitin-like protein."
          },
          {
            "node_id": "impaired_phage_infectivity",
            "label": "impaired phage infectivity",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced infectivity of phage particles released from cells encoding the Bil defense system."
          },
          {
            "node_id": "bil_system_trait",
            "label": "Bil system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000369",
            "description": "Possession of a genome-encoded Bil phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "bil_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "bil_ubiquitin_like_conjugation",
            "description": "Bil loci encode a bacterial antiphage system based on ubiquitin-like conjugation, and DefenseFinder links Bil to an antiphage-system discovery preprint.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41586-024-07616-5",
                "snippet": "Bil antiphage defence system",
                "notes": "Hor et al. identify Bil as a ubiquitin-like conjugation antiphage defense system."
              },
              {
                "reference": "DOI:10.1016/j.chom.2022.09.017",
                "snippet": "An expanded arsenal of immune systems that protect bacteria from phages",
                "notes": "Millman et al. published the discovery cohort that DefenseFinder maps to its Bil article-registry row."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Bil | 10\\.1101/2022\\.05\\.11\\.491447 | An expanding arsenal of immune systems that protect bacteria from phages",
                "notes": "The DefenseFinder article registry maps the named Bil system to the Millman et al. antiphage-system discovery preprint."
              }
            ]
          },
          {
            "subject": "bil_ubiquitin_like_conjugation",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "central_tail_fibre_obstruction",
            "description": "The Bil system can obstruct the phage central tail fibre by covalently attaching a ubiquitin-like protein.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41586-024-07616-5",
                "snippet": "phage central tail fibre is obstructed by the covalently attached ubiquitin-like protein",
                "notes": "Hor et al. show that the Bil system obstructs the phage central tail fibre with a covalently attached ubiquitin-like protein."
              }
            ]
          },
          {
            "subject": "central_tail_fibre_obstruction",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "impaired_phage_infectivity",
            "description": "Central-tail-fibre obstruction by the Bil system impairs phage-particle infectivity.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41586-024-07616-5",
                "snippet": "phage central tail fibre is obstructed by the covalently attached ubiquitin-like protein",
                "notes": "Hor et al. show that the Bil system obstructs the phage central tail fibre with a covalently attached ubiquitin-like protein."
              },
              {
                "reference": "DOI:10.1038/s41586-024-07616-5",
                "snippet": "These phages show severely impaired infectivity",
                "notes": "Hor et al. connect Bil-dependent particle production to reduced phage infectivity."
              }
            ]
          },
          {
            "subject": "impaired_phage_infectivity",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "bil_system_trait",
            "description": "Bil-mediated impairment of phage infectivity realizes the Bil system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41586-024-07616-5",
                "snippet": "These phages show severely impaired infectivity",
                "notes": "Hor et al. connect Bil-dependent particle production to reduced phage infectivity."
              }
            ]
          },
          {
            "subject": "bil_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Bil system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41586-024-07616-5",
                "snippet": "Bil antiphage defence system",
                "notes": "Hor et al. identify Bil as a ubiquitin-like conjugation antiphage defense system."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Bil | 10\\.1101/2022\\.05\\.11\\.491447 | An expanding arsenal of immune systems that protect bacteria from phages",
                "notes": "The DefenseFinder article registry maps the named Bil system to the Millman et al. antiphage-system discovery preprint."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "bil-defensefinder-profile-gap",
        "prompt": "Resolve Bil HMM profiles and rule rows before minting component-specific Bil mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Hor et al. support Bil as a bacterial ubiquitin-like conjugation antiphage system that modifies the phage central tail fibre, and the pinned DefenseFinder article registry maps Bil to the Millman et al. discovery preprint. The same pinned HMM inventory and rules table do not include exact Bil rows, so the exact DefenseFinder profile set, component rule, and model coverage remain unresolved.",
        "evidence": [
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
            "snippet": "Bil | 10\\.1101/2022\\.05\\.11\\.491447 | An expanding arsenal of immune systems that protect bacteria from phages",
            "notes": "The DefenseFinder article registry maps the named Bil system to the Millman et al. antiphage-system discovery preprint."
          }
        ],
        "attaches_to": [
          "causal_graphs#bil_locus_impairs_phage_assembly"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-24"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-25T03:02:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Bil system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v246.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-25T03:03:00Z",
        "curator": "codex",
        "action": "REVIEW_DEFENSEFINDER_PROFILE_GAP",
        "changes": "Reviewed the DefenseFinder Bil article-registry row at commit afb0e5a8b466be53586b13266f5d38d98c3ac268 and left narrower Bil HMM/profile semantics unresolved because the pinned HMM inventory and rules table have no exact Bil rows.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000249",
    "label": "Borvo system",
    "definition": "A phage defense system in which an organism possesses a Borvo locus represented by BovA profiles that can protect bacteria from bacteriophage infection.",
    "definition_source": "DOI:10.1016/j.chom.2022.09.017",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "Borvo",
        "synonym_type": "EXACT_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1016/j.chom.2022.09.017",
        "snippet": "discovery of 21 defense systems that protect bacteria from phages, based on computational genomic analyses and phage-infection experiments",
        "notes": "Millman et al. report the computational and experimental cohort that DefenseFinder cites for Borvo as a bacterial anti-phage system."
      },
      {
        "reference": "DOI:10.1101/2022.05.11.491447",
        "snippet": "discovery of 21 new defense systems that protect bacteria from phages, based on computational genomic analyses and phage infection experiments",
        "notes": "The bioRxiv version of Millman et al. independently carries the 21-system discovery claim linked from DefenseFinder's Borvo article registry."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "Borvo | 10\\.1101/2022\\.05\\.11\\.491447 | An expanding arsenal of immune systems that protect bacteria from phages",
        "notes": "The DefenseFinder model registry maps the named Borvo system to the Millman et al. antiphage-system discovery preprint."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "Borvo\tBorvo\t1\t1\tBorvo__BovA",
        "notes": "The DefenseFinder rules table models Borvo as a system with BovA as its mandatory profile."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "Borvo__BovA                                      | Borvo__BovA                                      | Borvo",
        "notes": "The DefenseFinder HMM inventory records BovA as a Borvo profile."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "Borvo__BovA_addition                             | Borvo__BovA_addition                             | Borvo",
        "notes": "The DefenseFinder HMM inventory records an additional BovA profile for Borvo."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "borvo_locus_restricts_phage",
        "title": "Borvo loci confer bacterial phage defense",
        "description": "Conservative system-level sketch linking possession of a Borvo locus to restricted bacteriophage propagation without asserting the unresolved phage trigger or molecular output.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Borvo as a named anti-phage system with BovA DefenseFinder profiles while leaving its phage trigger, molecular substrate, antiviral effector output, and subtype breadth unresolved.",
        "nodes": [
          {
            "node_id": "borvo_locus",
            "label": "Borvo locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A Borvo anti-phage defense locus containing BovA components."
          },
          {
            "node_id": "restricted_phage_propagation",
            "label": "restricted phage propagation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced propagation of bacteriophage in cells carrying the Borvo system."
          },
          {
            "node_id": "borvo_system_trait",
            "label": "Borvo system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000249",
            "description": "Possession of a genome-encoded Borvo phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "borvo_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "restricted_phage_propagation",
            "description": "DefenseFinder maps Borvo to a bacterial anti-phage-system discovery preprint and represents Borvo loci through BovA component profiles.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.chom.2022.09.017",
                "snippet": "discovery of 21 defense systems that protect bacteria from phages",
                "notes": "Millman et al. describe the anti-phage discovery cohort that the DefenseFinder Borvo registry row maps to the Borvo system."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Borvo | 10\\.1101/2022\\.05\\.11\\.491447 | An expanding arsenal of immune systems that protect bacteria from phages",
                "notes": "The DefenseFinder registry maps Borvo itself to the Millman et al. bacterial antiphage-system discovery preprint."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "Borvo\tBorvo\t1\t1\tBorvo__BovA",
                "notes": "The DefenseFinder rules table supports BovA as the mandatory Borvo system profile."
              }
            ]
          },
          {
            "subject": "restricted_phage_propagation",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "borvo_system_trait",
            "description": "Borvo-mediated phage restriction realizes the Borvo system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.chom.2022.09.017",
                "snippet": "discovery of 21 defense systems that protect bacteria from phages",
                "notes": "Millman et al. place the Borvo discovery cohort in the set of bacterial systems that protect against phages."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Borvo | 10\\.1101/2022\\.05\\.11\\.491447 | An expanding arsenal of immune systems that protect bacteria from phages",
                "notes": "DefenseFinder records Borvo as a named system from the Millman et al. antiphage discovery preprint."
              }
            ]
          },
          {
            "subject": "borvo_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Borvo system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "An expanding arsenal of immune systems that protect bacteria from phages",
                "notes": "DefenseFinder associates Borvo with the Millman et al. bacterial antiphage-system discovery paper."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "borvo-mechanism-gap",
        "prompt": "Resolve Borvo phage triggers and effector outputs before minting narrower Borvo mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Millman et al. and DefenseFinder support Borvo as a named anti-phage system with BovA profiles, but the trigger, molecular substrate, antiviral effector output, and subtype-specific mechanism are not resolved enough here to assert a narrower mechanistic child trait.",
        "attaches_to": [
          "causal_graphs#borvo_locus_restricts_phage"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-18"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-18T20:03:01Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Borvo system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v126.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000522",
    "label": "Brc113 system",
    "definition": "A phage defense system in which an organism possesses a gcu113/Brc113 bacteriophage-resistance integron cassette that supports growth during bacteriophage challenge.",
    "definition_source": "DOI:10.1126/science.ads0915",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "gcu113",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1126/science.ads0915"
      },
      {
        "synonym_text": "brc113",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1126/science.ads0915"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1126/science.ads0915",
        "snippet": "brc113 L 95.1 70.8",
        "notes": "Manual transcription of the Supplementary Fig. S2 Brc113 low-MOI E. coli IJ1862 heatmap row; the visible cells show reduced inhibition, including 95.1% for MS2 and 70.8% for F13."
      },
      {
        "reference": "DOI:10.1126/science.ads0915",
        "snippet": "defense profiles of identified Bacteriophage Resistance integron Cassettes (BRiCs) against a panel of different phages",
        "notes": "Kieffer et al. classify positive integron cassettes as BRiCs and compare their defense profiles across a phage panel."
      },
      {
        "reference": "DOI:10.1126/science.ads0915",
        "snippet": "brc113\nbrc217\nbrc76\nbrcWGS21\nbrc22\nbrc23",
        "notes": "Kieffer et al. include brc113 among identified BRiCs with predicted attC secondary structures."
      },
      {
        "reference": "https://www.science.org/doi/suppl/10.1126/science.ads0915/suppl_file/science.ads0915_sm.pdf",
        "snippet": "C936\npMBA brc113\nE. coli IJ1862",
        "notes": "Kieffer et al.'s supplementary construct table lists pMBA brc113 in E. coli IJ1862 for high/low-MOI phage-panel testing."
      },
      {
        "reference": "https://www.science.org/doi/suppl/10.1126/science.ads0915/suppl_file/science.ads0915_sm.pdf",
        "snippet": "C942\npMBA brc113\nK. pneumoniae\n\nKP5",
        "notes": "Kieffer et al.'s supplementary construct table lists the pMBA brc113 plasmid introduced into Klebsiella pneumoniae KP5."
      },
      {
        "reference": "https://www.science.org/doi/suppl/10.1126/science.ads0915/suppl_file/science.ads0915_sm.pdf",
        "snippet": "C974\npBTZ PcW brc113\nP. aeruginosa\nPAO1",
        "notes": "Kieffer et al.'s supplementary construct table lists the pBTZ PcW brc113 plasmid introduced into Pseudomonas aeruginosa PAO1."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "brc113_integron_cassette_confers_phage_resistance",
        "title": "Brc113 BRiCs confer phage resistance",
        "description": "Conservative system-level sketch linking a gcu113/Brc113 bacteriophage-resistance integron cassette to phage resistance and Brc113 system possession.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Brc113 at the integron-cassette and phage-resistance-output level without asserting the native host range, exact sensitive-phage breadth outside the reported panels, direct molecular substrate, or a DefenseFinder article/HMM/rules profile absent from the pinned snapshot.",
        "nodes": [
          {
            "node_id": "brc113_integron_cassette",
            "label": "Brc113 integron cassette",
            "node_type": "GENETIC_ELEMENT",
            "description": "A mobile integron gene cassette curated here as gcu113/Brc113."
          },
          {
            "node_id": "brc113_phage_resistance",
            "label": "Brc113 phage resistance",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced phage inhibition in cells carrying the gcu113/Brc113 integron cassette."
          },
          {
            "node_id": "brc113_system_trait",
            "label": "Brc113 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000522",
            "description": "Possession of a genome-encoded Brc113 phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "brc113_integron_cassette",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "brc113_phage_resistance",
            "description": "The gcu113/Brc113 integron cassette contributes to phage resistance during phage-panel assays.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.ads0915",
                "snippet": "brc113 L 95.1 70.8",
                "notes": "Manual transcription of the Supplementary Fig. S2 Brc113 low-MOI E. coli IJ1862 heatmap row; the visible cells show reduced inhibition, including 95.1% for MS2 and 70.8% for F13."
              }
            ]
          },
          {
            "subject": "brc113_phage_resistance",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "brc113_system_trait",
            "description": "Brc113-linked phage resistance realizes the Brc113 system possession trait.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.ads0915",
                "snippet": "brc113 L 95.1 70.8",
                "notes": "Manual transcription of the Supplementary Fig. S2 Brc113 low-MOI E. coli IJ1862 heatmap row; the visible cells show reduced inhibition, including 95.1% for MS2 and 70.8% for F13."
              },
              {
                "reference": "DOI:10.1126/science.ads0915",
                "snippet": "defense profiles of identified Bacteriophage Resistance integron Cassettes (BRiCs) against a panel of different phages",
                "notes": "Kieffer et al. classify positive integron cassettes as BRiCs and compare their defense profiles across a phage panel."
              }
            ]
          },
          {
            "subject": "brc113_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Brc113 system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.ads0915",
                "snippet": "defense profiles of identified Bacteriophage Resistance integron Cassettes (BRiCs) against a panel of different phages",
                "notes": "Kieffer et al. classify positive integron cassettes as BRiCs and compare their defense profiles across a phage panel."
              },
              {
                "reference": "DOI:10.1126/science.ads0915",
                "snippet": "brc113\nbrc217\nbrc76\nbrcWGS21\nbrc22\nbrc23",
                "notes": "Kieffer et al. include brc113 among identified BRiCs with predicted attC secondary structures."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "brc113-defensefinder-model-gap",
        "prompt": "Resolve Brc113 native host breadth, exact sensitive-phage breadth, molecular output, and DefenseFinder article/HMM/rules coverage before minting narrower Brc113 mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Kieffer et al. identify brc113 as a bacteriophage-resistance integron cassette. The pinned DefenseFinder article registry, HMM inventory, and rules table have no exact gcu113 or Brc113 row, so the first-pass record leaves native-host breadth, profile boundaries, exact phage target breadth, and direct molecular output unresolved.",
        "evidence": [
          {
            "reference": "DOI:10.1126/science.ads0915",
            "snippet": "brc113 L 95.1 70.8",
            "notes": "Manual transcription of the Supplementary Fig. S2 Brc113 low-MOI E. coli IJ1862 heatmap row; the visible cells show reduced inhibition, including 95.1% for MS2 and 70.8% for F13."
          },
          {
            "reference": "DOI:10.1126/science.ads0915",
            "snippet": "defense profiles of identified Bacteriophage Resistance integron Cassettes (BRiCs) against a panel of different phages",
            "notes": "Kieffer et al. classify positive integron cassettes as BRiCs and compare their defense profiles across a phage panel."
          },
          {
            "reference": "DOI:10.1126/science.ads0915",
            "snippet": "brc113\nbrc217\nbrc76\nbrcWGS21\nbrc22\nbrc23",
            "notes": "Kieffer et al. include brc113 among identified BRiCs with predicted attC secondary structures."
          },
          {
            "reference": "https://www.science.org/doi/suppl/10.1126/science.ads0915/suppl_file/science.ads0915_sm.pdf",
            "snippet": "C942\npMBA brc113\nK. pneumoniae\n\nKP5",
            "notes": "Kieffer et al. list brc113 in the heterologous Klebsiella pneumoniae KP5 BRiC panel."
          },
          {
            "reference": "https://www.science.org/doi/suppl/10.1126/science.ads0915/suppl_file/science.ads0915_sm.pdf",
            "snippet": "C974\npBTZ PcW brc113\nP. aeruginosa\nPAO1",
            "notes": "Kieffer et al. list brc113 in the heterologous Pseudomonas aeruginosa PAO1 BRiC panel."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
            "notes": "A structured first-pass search of the pinned DefenseFinder article registry found no exact gcu113, brc113, or Brc113 row."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "notes": "A structured first-pass search of the pinned DefenseFinder HMM inventory found no exact gcu113, brc113, or Brc113 row."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "A structured first-pass search of the pinned DefenseFinder rules table found no exact gcu113, brc113, or Brc113 system row."
          }
        ],
        "attaches_to": [
          "causal_graphs#brc113_integron_cassette_confers_phage_resistance"
        ],
        "posed_by": "codex",
        "posed_date": "2026-10-01"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-01T18:33:44Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Brc113 system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; kept the graph at BRiC integron-cassette level because the pinned DefenseFinder article registry, HMM inventory, and rules table have no exact Brc113 row; the replacement placeholder is reserved in proposals/metpo_traitmech_v399.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-01T18:33:45Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed Brc113 system during initial curation and left canonical_examples empty because the sources support heterologous gcu113/Brc113 phage-resistance assays but not a direct named native microbial isolate exemplar with experimentally verified endogenous Brc113 activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000515",
    "label": "Brc142 system",
    "definition": "A phage defense system in which an organism possesses a gcu142/Brc142 bacteriophage-resistance integron cassette that supports growth during bacteriophage challenge.",
    "definition_source": "DOI:10.1126/science.ads0915",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "gcu142",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      },
      {
        "synonym_text": "brc142",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1126/science.ads0915"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1126/science.ads0915",
        "snippet": "Identification of gcu24 and gcu142 through double spot screening",
        "notes": "Kieffer et al. report initial identification of gcu142 in a double-spot phage-resistance screen."
      },
      {
        "reference": "DOI:10.1126/science.ads0915",
        "snippet": "gcu24 and gcu142, which show growth despite the presence of the phage, indicating successful identification and resistance.",
        "notes": "Kieffer et al. support growth of the gcu142 clone during T4 phage challenge in the initial screen."
      },
      {
        "reference": "DOI:10.1126/science.ads0915",
        "snippet": "defense profiles of identified Bacteriophage Resistance integron Cassettes (BRiCs) against a panel of different phages",
        "notes": "Kieffer et al. classify positive integron cassettes as BRiCs and compare their defense profiles across a phage panel."
      },
      {
        "reference": "DOI:10.1126/science.ads0915",
        "snippet": "C745\npMBA gcu142",
        "notes": "Kieffer et al.'s supplementary construct table lists the initial pMBA gcu142 screening plasmid."
      },
      {
        "reference": "DOI:10.1126/science.ads0915",
        "snippet": "C805\npMBA brc142\nE. coli IJ1862",
        "notes": "Kieffer et al.'s supplementary construct table lists pMBA brc142 in E. coli IJ1862 for high/low-MOI phage-panel testing."
      },
      {
        "reference": "DOI:10.1126/science.ads0915",
        "snippet": "C815\npMBA brc142\nK. pneumoniae",
        "notes": "Kieffer et al.'s supplementary construct table lists the pMBA brc142 plasmid introduced into Klebsiella pneumoniae KP5."
      },
      {
        "reference": "DOI:10.1126/science.ads0915",
        "snippet": "C972\npBTZ PcW brc142",
        "notes": "Kieffer et al.'s supplementary construct table lists a Pseudomonas aeruginosa brc142 expression construct."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| gcu142 | 10\\.1126/science\\.ads0915 | Mobile integrons encode phage defense systems | ",
        "notes": "The pinned DefenseFinder article registry maps the gcu142 source key to the Kieffer et al. mobile-integron BRiC paper."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "brc142_integron_cassette_confers_phage_resistance",
        "title": "Brc142 BRiCs confer phage resistance",
        "description": "Conservative system-level sketch linking a gcu142/Brc142 bacteriophage-resistance integron cassette to phage resistance and Brc142 system possession.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Brc142 at the integron-cassette and phage-resistance-output level without asserting the native host range, exact sensitive-phage breadth outside the reported panels, direct molecular substrate, or a DefenseFinder HMM/rules profile absent from the pinned snapshot.",
        "nodes": [
          {
            "node_id": "brc142_integron_cassette",
            "label": "Brc142 integron cassette",
            "node_type": "GENETIC_ELEMENT",
            "description": "A mobile integron gene cassette recovered in the gcu142 screen and renamed as a Brc142 bacteriophage-resistance integron cassette."
          },
          {
            "node_id": "brc142_phage_resistance",
            "label": "Brc142 phage resistance",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced phage inhibition in cells carrying the gcu142/Brc142 integron cassette."
          },
          {
            "node_id": "brc142_system_trait",
            "label": "Brc142 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000515",
            "description": "Possession of a genome-encoded Brc142 phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "brc142_integron_cassette",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "brc142_phage_resistance",
            "description": "The gcu142/Brc142 integron cassette contributes to phage resistance during double-spot and phage-panel assays.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.ads0915",
                "snippet": "Identification of gcu24 and gcu142 through double spot screening",
                "notes": "Kieffer et al. report initial identification of gcu142 in a double-spot phage-resistance screen."
              },
              {
                "reference": "DOI:10.1126/science.ads0915",
                "snippet": "C805\npMBA brc142\nE. coli IJ1862",
                "notes": "Kieffer et al. cloned brc142 for E. coli IJ1862 phage-panel testing."
              }
            ]
          },
          {
            "subject": "brc142_phage_resistance",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "brc142_system_trait",
            "description": "Brc142-linked phage resistance realizes the Brc142 system possession trait.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.ads0915",
                "snippet": "gcu24 and gcu142, which show growth despite the presence of the phage, indicating successful identification and resistance.",
                "notes": "Kieffer et al. support growth of the gcu142 clone during T4 phage challenge in the initial screen."
              },
              {
                "reference": "DOI:10.1126/science.ads0915",
                "snippet": "defense profiles of identified Bacteriophage Resistance integron Cassettes (BRiCs) against a panel of different phages",
                "notes": "Kieffer et al. classify positive integron cassettes as BRiCs and compare their defense profiles across a phage panel."
              }
            ]
          },
          {
            "subject": "brc142_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Brc142 system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.ads0915",
                "snippet": "defense profiles of identified Bacteriophage Resistance integron Cassettes (BRiCs) against a panel of different phages",
                "notes": "Kieffer et al. classify positive integron cassettes as BRiCs and compare their defense profiles across a phage panel."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| gcu142 | 10\\.1126/science\\.ads0915 | Mobile integrons encode phage defense systems | ",
                "notes": "The pinned DefenseFinder article registry maps the gcu142 source key to the Kieffer et al. mobile-integron BRiC paper."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "brc142-defensefinder-model-gap",
        "prompt": "Resolve Brc142 native host breadth, exact sensitive-phage breadth, molecular output, and DefenseFinder HMM/rules coverage before minting narrower Brc142 mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Kieffer et al. identify gcu142/Brc142 as a bacteriophage-resistance integron cassette, and the pinned DefenseFinder article registry maps the gcu142 source key to the same Science article. The pinned HMM inventory and rules table have no exact gcu142 or Brc142 row, so the first-pass record leaves native-host breadth, profile boundaries, exact phage target breadth, and direct molecular output unresolved.",
        "evidence": [
          {
            "reference": "DOI:10.1126/science.ads0915",
            "snippet": "Identification of gcu24 and gcu142 through double spot screening",
            "notes": "Kieffer et al. report initial identification of gcu142 in a double-spot phage-resistance screen."
          },
          {
            "reference": "DOI:10.1126/science.ads0915",
            "snippet": "defense profiles of identified Bacteriophage Resistance integron Cassettes (BRiCs) against a panel of different phages",
            "notes": "Kieffer et al. classify positive integron cassettes as BRiCs and compare their defense profiles across a phage panel."
          },
          {
            "reference": "DOI:10.1126/science.ads0915",
            "snippet": "C815\npMBA brc142\nK. pneumoniae",
            "notes": "Kieffer et al. list brc142 in the heterologous Klebsiella pneumoniae KP5 BRiC panel."
          },
          {
            "reference": "DOI:10.1126/science.ads0915",
            "snippet": "C972\npBTZ PcW brc142",
            "notes": "Kieffer et al. list brc142 in the heterologous Pseudomonas aeruginosa PAO1 BRiC panel."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
            "snippet": "| gcu142 | 10\\.1126/science\\.ads0915 | Mobile integrons encode phage defense systems | ",
            "notes": "The pinned DefenseFinder article registry maps the gcu142 source key to the Kieffer et al. mobile-integron BRiC paper."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "notes": "A structured first-pass search of the pinned DefenseFinder HMM inventory found no exact gcu142, brc142, or Brc142 row."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "A structured first-pass search of the pinned DefenseFinder rules table found no exact gcu142, brc142, or Brc142 system row."
          }
        ],
        "attaches_to": [
          "causal_graphs#brc142_integron_cassette_confers_phage_resistance"
        ],
        "posed_by": "codex",
        "posed_date": "2026-10-01"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-01T12:39:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Brc142 system as a DOI- and DefenseFinder-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; kept the graph at BRiC integron-cassette level because the pinned DefenseFinder article registry names gcu142 but the pinned HMM inventory and rules table have no exact Brc142 row; the replacement placeholder is reserved in proposals/metpo_traitmech_v392.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-01T12:39:01Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed Brc142 system during initial curation and left canonical_examples empty because the sources support heterologous gcu142/Brc142 phage-resistance assays and a DefenseFinder gcu142 article row, but not a direct named native microbial isolate exemplar with experimentally verified endogenous Brc142 activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000517",
    "label": "Brc167 system",
    "definition": "A phage defense system in which an organism possesses a gcu167/Brc167 bacteriophage-resistance integron cassette that supports growth during bacteriophage challenge.",
    "definition_source": "DOI:10.1126/science.ads0915",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "gcu167",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      },
      {
        "synonym_text": "brc167",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1126/science.ads0915"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1126/science.ads0915",
        "snippet": "brc167 L 38.3 26.3 16.8 18.5 59.8 0 25.6 21.3",
        "notes": "Manual transcription of the Supplementary Fig. S2 Brc167 low-MOI E. coli IJ1862 heatmap row; the row shows reduced inhibition, including 16.8% for T4, 18.5% for F1, 0% for prophage phi80, 25.6% for HK544, and 21.3% for F13."
      },
      {
        "reference": "DOI:10.1126/science.ads0915",
        "snippet": "brc167 H 25.0 21.5 11.4 0 83.1 26.1 61.7 27.6",
        "notes": "Manual transcription of the Supplementary Fig. S2 Brc167 high-MOI E. coli IJ1862 heatmap row; the row shows reduced inhibition, including 25.0% for MS2, 21.5% for G4, 11.4% for T4, 0% for F1, and 27.6% for F13."
      },
      {
        "reference": "DOI:10.1126/science.ads0915",
        "snippet": "brc142\nbrc167.2\nbrc167",
        "notes": "Kieffer et al. include brc167 among identified BRiCs with predicted attC secondary structures."
      },
      {
        "reference": "DOI:10.1126/science.ads0915",
        "snippet": "defense profiles of identified Bacteriophage Resistance integron Cassettes (BRiCs) against a panel of different phages",
        "notes": "Kieffer et al. classify positive integron cassettes as BRiCs and compare their defense profiles across a phage panel."
      },
      {
        "reference": "DOI:10.1126/science.ads0915",
        "snippet": "C803\npMBA brc167\nE. coli IJ1862",
        "notes": "Kieffer et al.'s supplementary construct table lists pMBA brc167 in E. coli IJ1862 for high/low-MOI phage-panel testing."
      },
      {
        "reference": "DOI:10.1126/science.ads0915",
        "snippet": "C813\npMBA brc167\nK. pneumoniae",
        "notes": "Kieffer et al.'s supplementary construct table lists the pMBA brc167 plasmid introduced into Klebsiella pneumoniae KP5."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| gcu167 | 10\\.1126/science\\.ads0915 | Mobile integrons encode phage defense systems | ",
        "notes": "The pinned DefenseFinder article registry maps the gcu167 source key to the Kieffer et al. mobile-integron BRiC paper."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "brc167_integron_cassette_confers_phage_resistance",
        "title": "Brc167 BRiCs confer phage resistance",
        "description": "Conservative system-level sketch linking a gcu167/Brc167 bacteriophage-resistance integron cassette to phage resistance and Brc167 system possession.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Brc167 at the integron-cassette and phage-resistance-output level without asserting the native host range, exact sensitive-phage breadth outside the reported panels, direct molecular substrate, or a DefenseFinder HMM/rules profile absent from the pinned snapshot.",
        "nodes": [
          {
            "node_id": "brc167_integron_cassette",
            "label": "Brc167 integron cassette",
            "node_type": "GENETIC_ELEMENT",
            "description": "A mobile integron gene cassette named by the gcu167 source key and curated as Brc167."
          },
          {
            "node_id": "brc167_phage_resistance",
            "label": "Brc167 phage resistance",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced phage inhibition in cells carrying the gcu167/Brc167 integron cassette."
          },
          {
            "node_id": "brc167_system_trait",
            "label": "Brc167 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000517",
            "description": "Possession of a genome-encoded Brc167 phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "brc167_integron_cassette",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "brc167_phage_resistance",
            "description": "The gcu167/Brc167 integron cassette contributes to phage resistance during phage-panel assays.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.ads0915",
                "snippet": "brc167 L 38.3 26.3 16.8 18.5 59.8 0 25.6 21.3",
                "notes": "Manual transcription of the Supplementary Fig. S2 Brc167 low-MOI E. coli IJ1862 heatmap row; the row shows reduced inhibition, including 16.8% for T4, 18.5% for F1, 0% for prophage phi80, 25.6% for HK544, and 21.3% for F13."
              },
              {
                "reference": "DOI:10.1126/science.ads0915",
                "snippet": "brc167 H 25.0 21.5 11.4 0 83.1 26.1 61.7 27.6",
                "notes": "Manual transcription of the Supplementary Fig. S2 Brc167 high-MOI E. coli IJ1862 heatmap row; the row shows reduced inhibition, including 25.0% for MS2, 21.5% for G4, 11.4% for T4, 0% for F1, and 27.6% for F13."
              }
            ]
          },
          {
            "subject": "brc167_phage_resistance",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "brc167_system_trait",
            "description": "Brc167-linked phage resistance realizes the Brc167 system possession trait.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.ads0915",
                "snippet": "brc167 L 38.3 26.3 16.8 18.5 59.8 0 25.6 21.3",
                "notes": "Manual transcription of the Supplementary Fig. S2 Brc167 low-MOI E. coli IJ1862 heatmap row; the row shows reduced inhibition, including 16.8% for T4, 18.5% for F1, 0% for prophage phi80, 25.6% for HK544, and 21.3% for F13."
              },
              {
                "reference": "DOI:10.1126/science.ads0915",
                "snippet": "brc167 H 25.0 21.5 11.4 0 83.1 26.1 61.7 27.6",
                "notes": "Manual transcription of the Supplementary Fig. S2 Brc167 high-MOI E. coli IJ1862 heatmap row; the row shows reduced inhibition, including 25.0% for MS2, 21.5% for G4, 11.4% for T4, 0% for F1, and 27.6% for F13."
              },
              {
                "reference": "DOI:10.1126/science.ads0915",
                "snippet": "defense profiles of identified Bacteriophage Resistance integron Cassettes (BRiCs) against a panel of different phages",
                "notes": "Kieffer et al. classify positive integron cassettes as BRiCs and compare their defense profiles across a phage panel."
              }
            ]
          },
          {
            "subject": "brc167_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Brc167 system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.ads0915",
                "snippet": "defense profiles of identified Bacteriophage Resistance integron Cassettes (BRiCs) against a panel of different phages",
                "notes": "Kieffer et al. classify positive integron cassettes as BRiCs and compare their defense profiles across a phage panel."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| gcu167 | 10\\.1126/science\\.ads0915 | Mobile integrons encode phage defense systems | ",
                "notes": "The pinned DefenseFinder article registry maps the gcu167 source key to the Kieffer et al. mobile-integron BRiC paper."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "brc167-defensefinder-model-gap",
        "prompt": "Resolve Brc167 native host breadth, exact sensitive-phage breadth, molecular output, and DefenseFinder HMM/rules coverage before minting narrower Brc167 mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Kieffer et al. identify brc167 as a bacteriophage-resistance integron cassette, and the pinned DefenseFinder article registry maps the gcu167 source key to the same Science article. The pinned HMM inventory and rules table have no exact gcu167 or Brc167 row, so the first-pass record leaves native-host breadth, profile boundaries, exact phage target breadth, and direct molecular output unresolved.",
        "evidence": [
          {
            "reference": "DOI:10.1126/science.ads0915",
            "snippet": "brc167 L 38.3 26.3 16.8 18.5 59.8 0 25.6 21.3",
            "notes": "Manual transcription of the Supplementary Fig. S2 Brc167 low-MOI E. coli IJ1862 heatmap row; the row shows reduced inhibition, including 16.8% for T4, 18.5% for F1, 0% for prophage phi80, 25.6% for HK544, and 21.3% for F13."
          },
          {
            "reference": "DOI:10.1126/science.ads0915",
            "snippet": "brc167 H 25.0 21.5 11.4 0 83.1 26.1 61.7 27.6",
            "notes": "Manual transcription of the Supplementary Fig. S2 Brc167 high-MOI E. coli IJ1862 heatmap row; the row shows reduced inhibition, including 25.0% for MS2, 21.5% for G4, 11.4% for T4, 0% for F1, and 27.6% for F13."
          },
          {
            "reference": "DOI:10.1126/science.ads0915",
            "snippet": "brc142\nbrc167.2\nbrc167",
            "notes": "Kieffer et al. include brc167 among identified BRiCs with predicted attC secondary structures."
          },
          {
            "reference": "DOI:10.1126/science.ads0915",
            "snippet": "defense profiles of identified Bacteriophage Resistance integron Cassettes (BRiCs) against a panel of different phages",
            "notes": "Kieffer et al. classify positive integron cassettes as BRiCs and compare their defense profiles across a phage panel."
          },
          {
            "reference": "DOI:10.1126/science.ads0915",
            "snippet": "C813\npMBA brc167\nK. pneumoniae",
            "notes": "Kieffer et al. list brc167 in the heterologous Klebsiella pneumoniae KP5 BRiC panel."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
            "snippet": "| gcu167 | 10\\.1126/science\\.ads0915 | Mobile integrons encode phage defense systems | ",
            "notes": "The pinned DefenseFinder article registry maps the gcu167 source key to the Kieffer et al. mobile-integron BRiC paper."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "notes": "A structured first-pass search of the pinned DefenseFinder HMM inventory found no exact gcu167, brc167, or Brc167 row."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "A structured first-pass search of the pinned DefenseFinder rules table found no exact gcu167, brc167, or Brc167 system row."
          }
        ],
        "attaches_to": [
          "causal_graphs#brc167_integron_cassette_confers_phage_resistance"
        ],
        "posed_by": "codex",
        "posed_date": "2026-10-01"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-01T14:20:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Brc167 system as a DOI- and DefenseFinder-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; kept the graph at BRiC integron-cassette level because the pinned DefenseFinder article registry names gcu167 but the pinned HMM inventory and rules table have no exact Brc167 row; the replacement placeholder is reserved in proposals/metpo_traitmech_v394.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-01T14:20:01Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed Brc167 system during initial curation and left canonical_examples empty because the sources support heterologous gcu167/Brc167 phage-resistance assays and a DefenseFinder gcu167 article row, but not a direct named native microbial isolate exemplar with experimentally verified endogenous Brc167 activity. No paid research was used.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-01T15:19:00Z",
        "curator": "codex",
        "action": "RESOLVED_ADVERSARIAL_REVIEW",
        "changes": "Resolved PR #1521 adversarial review issue #1522 by replacing Brc167 causal-edge support that relied on attC row-label and construct-table fragments with exact low- and high-MOI Brc167 heatmap row transcriptions from Supplementary Fig. S2.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000521",
    "label": "Brc217 system",
    "definition": "A phage defense system in which an organism possesses a gcu217/Brc217 bacteriophage-resistance integron cassette that supports growth during bacteriophage challenge.",
    "definition_source": "DOI:10.1126/science.ads0915",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "gcu217",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1126/science.ads0915"
      },
      {
        "synonym_text": "brc217",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1126/science.ads0915"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1126/science.ads0915",
        "snippet": "brc217 L 97.6 44.2 96.6 56.5",
        "notes": "Manual transcription of the Supplementary Fig. S2 Brc217 low-MOI E. coli IJ1862 heatmap row; the visible cells show reduced inhibition, including 97.6% for P1, 44.2% for phi80, 96.6% for HK544, and 56.5% for F13."
      },
      {
        "reference": "DOI:10.1126/science.ads0915",
        "snippet": "brc217 H 91.2 96.7",
        "notes": "Manual transcription of the Supplementary Fig. S2 Brc217 high-MOI E. coli IJ1862 heatmap row; the visible cells show reduced inhibition, including 91.2% for HK544 and 96.7% for F13."
      },
      {
        "reference": "DOI:10.1126/science.ads0915",
        "snippet": "defense profiles of identified Bacteriophage Resistance integron Cassettes (BRiCs) against a panel of different phages",
        "notes": "Kieffer et al. classify positive integron cassettes as BRiCs and compare their defense profiles across a phage panel."
      },
      {
        "reference": "DOI:10.1126/science.ads0915",
        "snippet": "brc113\nbrc217\nbrc76\nbrcWGS21\nbrc22\nbrc23",
        "notes": "Kieffer et al. include brc217 among identified BRiCs with predicted attC secondary structures."
      },
      {
        "reference": "https://www.science.org/doi/suppl/10.1126/science.ads0915/suppl_file/science.ads0915_sm.pdf",
        "snippet": "C934\npMBA brc217\nE. coli IJ1862",
        "notes": "Kieffer et al.'s supplementary construct table lists pMBA brc217 in E. coli IJ1862 for high/low-MOI phage-panel testing."
      },
      {
        "reference": "DOI:10.1126/science.ads0915",
        "snippet": "C940\npMBA brc217\nK. pneumoniae\n\nKP5",
        "notes": "Kieffer et al.'s supplementary construct table lists the pMBA brc217 plasmid introduced into Klebsiella pneumoniae KP5."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "brc217_integron_cassette_confers_phage_resistance",
        "title": "Brc217 BRiCs confer phage resistance",
        "description": "Conservative system-level sketch linking a gcu217/Brc217 bacteriophage-resistance integron cassette to phage resistance and Brc217 system possession.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Brc217 at the integron-cassette and phage-resistance-output level without asserting the native host range, exact sensitive-phage breadth outside the reported panels, direct molecular substrate, or a DefenseFinder article/HMM/rules profile absent from the pinned snapshot.",
        "nodes": [
          {
            "node_id": "brc217_integron_cassette",
            "label": "Brc217 integron cassette",
            "node_type": "GENETIC_ELEMENT",
            "description": "A mobile integron gene cassette named by the gcu217 source key and curated as Brc217."
          },
          {
            "node_id": "brc217_phage_resistance",
            "label": "Brc217 phage resistance",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced phage inhibition in cells carrying the gcu217/Brc217 integron cassette."
          },
          {
            "node_id": "brc217_system_trait",
            "label": "Brc217 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000521",
            "description": "Possession of a genome-encoded Brc217 phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "brc217_integron_cassette",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "brc217_phage_resistance",
            "description": "The gcu217/Brc217 integron cassette contributes to phage resistance during phage-panel assays.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.ads0915",
                "snippet": "brc217 L 97.6 44.2 96.6 56.5",
                "notes": "Manual transcription of the Supplementary Fig. S2 Brc217 low-MOI E. coli IJ1862 heatmap row; the visible cells show reduced inhibition, including 97.6% for P1, 44.2% for phi80, 96.6% for HK544, and 56.5% for F13."
              },
              {
                "reference": "DOI:10.1126/science.ads0915",
                "snippet": "brc217 H 91.2 96.7",
                "notes": "Manual transcription of the Supplementary Fig. S2 Brc217 high-MOI E. coli IJ1862 heatmap row; the visible cells show reduced inhibition, including 91.2% for HK544 and 96.7% for F13."
              }
            ]
          },
          {
            "subject": "brc217_phage_resistance",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "brc217_system_trait",
            "description": "Brc217-linked phage resistance realizes the Brc217 system possession trait.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.ads0915",
                "snippet": "brc217 L 97.6 44.2 96.6 56.5",
                "notes": "Manual transcription of the Supplementary Fig. S2 Brc217 low-MOI E. coli IJ1862 heatmap row; the visible cells show reduced inhibition, including 97.6% for P1, 44.2% for phi80, 96.6% for HK544, and 56.5% for F13."
              },
              {
                "reference": "DOI:10.1126/science.ads0915",
                "snippet": "brc217 H 91.2 96.7",
                "notes": "Manual transcription of the Supplementary Fig. S2 Brc217 high-MOI E. coli IJ1862 heatmap row; the visible cells show reduced inhibition, including 91.2% for HK544 and 96.7% for F13."
              },
              {
                "reference": "DOI:10.1126/science.ads0915",
                "snippet": "defense profiles of identified Bacteriophage Resistance integron Cassettes (BRiCs) against a panel of different phages",
                "notes": "Kieffer et al. classify positive integron cassettes as BRiCs and compare their defense profiles across a phage panel."
              }
            ]
          },
          {
            "subject": "brc217_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Brc217 system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.ads0915",
                "snippet": "defense profiles of identified Bacteriophage Resistance integron Cassettes (BRiCs) against a panel of different phages",
                "notes": "Kieffer et al. classify positive integron cassettes as BRiCs and compare their defense profiles across a phage panel."
              },
              {
                "reference": "DOI:10.1126/science.ads0915",
                "snippet": "brc113\nbrc217\nbrc76\nbrcWGS21\nbrc22\nbrc23",
                "notes": "Kieffer et al. include brc217 among identified BRiCs with predicted attC secondary structures."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "brc217-defensefinder-model-gap",
        "prompt": "Resolve Brc217 native host breadth, exact sensitive-phage breadth, molecular output, and DefenseFinder article/HMM/rules coverage before minting narrower Brc217 mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Kieffer et al. identify brc217 as a bacteriophage-resistance integron cassette. The pinned DefenseFinder article registry, HMM inventory, and rules table have no exact gcu217 or Brc217 row, so the first-pass record leaves native-host breadth, profile boundaries, exact phage target breadth, and direct molecular output unresolved.",
        "evidence": [
          {
            "reference": "DOI:10.1126/science.ads0915",
            "snippet": "brc217 L 97.6 44.2 96.6 56.5",
            "notes": "Manual transcription of the Supplementary Fig. S2 Brc217 low-MOI E. coli IJ1862 heatmap row; the visible cells show reduced inhibition, including 97.6% for P1, 44.2% for phi80, 96.6% for HK544, and 56.5% for F13."
          },
          {
            "reference": "DOI:10.1126/science.ads0915",
            "snippet": "brc217 H 91.2 96.7",
            "notes": "Manual transcription of the Supplementary Fig. S2 Brc217 high-MOI E. coli IJ1862 heatmap row; the visible cells show reduced inhibition, including 91.2% for HK544 and 96.7% for F13."
          },
          {
            "reference": "DOI:10.1126/science.ads0915",
            "snippet": "defense profiles of identified Bacteriophage Resistance integron Cassettes (BRiCs) against a panel of different phages",
            "notes": "Kieffer et al. classify positive integron cassettes as BRiCs and compare their defense profiles across a phage panel."
          },
          {
            "reference": "DOI:10.1126/science.ads0915",
            "snippet": "brc113\nbrc217\nbrc76\nbrcWGS21\nbrc22\nbrc23",
            "notes": "Kieffer et al. include brc217 among identified BRiCs with predicted attC secondary structures."
          },
          {
            "reference": "DOI:10.1126/science.ads0915",
            "snippet": "C940\npMBA brc217\nK. pneumoniae\n\nKP5",
            "notes": "Kieffer et al. list brc217 in the heterologous Klebsiella pneumoniae KP5 BRiC panel."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
            "notes": "A structured first-pass search of the pinned DefenseFinder article registry found no exact gcu217, brc217, or Brc217 row."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "notes": "A structured first-pass search of the pinned DefenseFinder HMM inventory found no exact gcu217, brc217, or Brc217 row."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "A structured first-pass search of the pinned DefenseFinder rules table found no exact gcu217, brc217, or Brc217 system row."
          }
        ],
        "attaches_to": [
          "causal_graphs#brc217_integron_cassette_confers_phage_resistance"
        ],
        "posed_by": "codex",
        "posed_date": "2026-10-01"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-01T17:54:02Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Brc217 system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; kept the graph at BRiC integron-cassette level because the pinned DefenseFinder article registry, HMM inventory, and rules table have no exact Brc217 row; the replacement placeholder is reserved in proposals/metpo_traitmech_v398.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-01T17:54:03Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed Brc217 system during initial curation and left canonical_examples empty because the sources support heterologous gcu217/Brc217 phage-resistance assays but not a direct named native microbial isolate exemplar with experimentally verified endogenous Brc217 activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000523",
    "label": "Brc22 system",
    "definition": "A phage defense system in which an organism possesses a gcu22/Brc22 bacteriophage-resistance integron cassette that supports growth during bacteriophage challenge.",
    "definition_source": "DOI:10.1126/science.ads0915",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "gcu22",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1126/science.ads0915"
      },
      {
        "synonym_text": "brc22",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1126/science.ads0915"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1126/science.ads0915",
        "snippet": "Gcu22 conferred low levels of resistance exclusively against phage F13 in K. pneumoniae",
        "notes": "Kieffer et al. report that the former gcu22 cassette conferred low-level F13 resistance in Klebsiella pneumoniae."
      },
      {
        "reference": "DOI:10.1126/science.ads0915",
        "snippet": "We therefore redefined both cassettes as BRiCs (brc22 and brc23)",
        "notes": "Kieffer et al. renamed gcu22 and gcu23 as Brc cassettes after phage-resistance testing."
      },
      {
        "reference": "DOI:10.1126/science.ads0915",
        "snippet": "Predicted secondary structures of attC sites in identified BRiCs",
        "notes": "Kieffer et al. identify BRiC bacteriophage-resistance integron cassettes and show their predicted attC secondary structures."
      },
      {
        "reference": "DOI:10.1126/science.ads0915",
        "snippet": "brc113\nbrc217\nbrc76\nbrcWGS21\nbrc22\nbrc23",
        "notes": "Kieffer et al. include brc22 among identified BRiCs with predicted attC secondary structures."
      },
      {
        "reference": "https://www.science.org/doi/suppl/10.1126/science.ads0915/suppl_file/science.ads0915_sm.pdf",
        "snippet": "attC of brc22, with a perfect GTT/AAC binding between both arms of the stem",
        "notes": "Kieffer et al. discuss the brc22 attC site in a comparison of Tragantia homolog-associated predicted secondary structures."
      },
      {
        "reference": "https://www.science.org/doi/suppl/10.1126/science.ads0915/suppl_file/science.ads0915_sm.pdf",
        "snippet": "D278\npMBA PcW brc22\nE. coli IJ1862",
        "notes": "Kieffer et al.'s supplementary construct table lists pMBA PcW brc22 in E. coli IJ1862 under naturally occurring defense island constructs."
      },
      {
        "reference": "https://www.science.org/doi/suppl/10.1126/science.ads0915/suppl_file/science.ads0915_sm.pdf",
        "snippet": "D283\npMBA PcW brc22\nK. pneumoniae\nKP5",
        "notes": "Kieffer et al.'s supplementary construct table lists pMBA PcW brc22 in Klebsiella pneumoniae KP5 under naturally occurring defense island constructs."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "brc22_integron_cassette_confers_phage_resistance",
        "title": "Brc22 BRiCs confer phage resistance",
        "description": "Conservative system-level sketch linking a gcu22/Brc22 bacteriophage-resistance integron cassette to phage resistance and Brc22 system possession.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Brc22 at the integron-cassette and phage-resistance-output level without asserting the native host range, exact sensitive-phage breadth, direct molecular substrate, whether Brc22 and Brc23 are variants of one Tragantia family, or a DefenseFinder article/HMM/rules profile absent from the pinned snapshot.",
        "nodes": [
          {
            "node_id": "brc22_integron_cassette",
            "label": "Brc22 integron cassette",
            "node_type": "GENETIC_ELEMENT",
            "description": "A mobile integron gene cassette curated here as gcu22/Brc22."
          },
          {
            "node_id": "brc22_phage_resistance",
            "label": "Brc22 phage resistance",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced phage inhibition in cells carrying the gcu22/Brc22 integron cassette."
          },
          {
            "node_id": "brc22_system_trait",
            "label": "Brc22 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000523",
            "description": "Possession of a genome-encoded Brc22 phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "brc22_integron_cassette",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "brc22_phage_resistance",
            "description": "The gcu22/Brc22 integron cassette contributes to F13 phage resistance during phage-panel assays in Klebsiella pneumoniae.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.ads0915",
                "snippet": "Gcu22 conferred low levels of resistance exclusively against phage F13 in K. pneumoniae",
                "notes": "Kieffer et al. report that the former gcu22 cassette conferred low-level F13 resistance in Klebsiella pneumoniae."
              }
            ]
          },
          {
            "subject": "brc22_phage_resistance",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "brc22_system_trait",
            "description": "Brc22-linked phage resistance realizes the Brc22 system possession trait.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.ads0915",
                "snippet": "Gcu22 conferred low levels of resistance exclusively against phage F13 in K. pneumoniae",
                "notes": "Kieffer et al. report that the former gcu22 cassette conferred low-level F13 resistance in Klebsiella pneumoniae."
              },
              {
                "reference": "DOI:10.1126/science.ads0915",
                "snippet": "We therefore redefined both cassettes as BRiCs (brc22 and brc23)",
                "notes": "Kieffer et al. renamed gcu22 and gcu23 as Brc cassettes after phage-resistance testing."
              }
            ]
          },
          {
            "subject": "brc22_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Brc22 system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.ads0915",
                "snippet": "Predicted secondary structures of attC sites in identified BRiCs",
                "notes": "Kieffer et al. identify BRiC bacteriophage-resistance integron cassettes and show their predicted attC secondary structures."
              },
              {
                "reference": "DOI:10.1126/science.ads0915",
                "snippet": "brc113\nbrc217\nbrc76\nbrcWGS21\nbrc22\nbrc23",
                "notes": "Kieffer et al. include brc22 among identified BRiCs with predicted attC secondary structures."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "brc22-defensefinder-model-gap",
        "prompt": "Resolve Brc22 native host breadth, exact sensitive-phage breadth, molecular output, Tragantia-family boundaries, and DefenseFinder article/HMM/rules coverage before minting narrower Brc22 mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Kieffer et al. identify brc22 as a bacteriophage-resistance integron cassette. The pinned DefenseFinder article registry, HMM inventory, and rules table have no exact gcu22 or Brc22 row, so the first-pass record leaves native-host breadth, profile boundaries, exact phage target breadth, direct molecular output, and Brc22/Brc23 Tragantia-family scope unresolved.",
        "evidence": [
          {
            "reference": "DOI:10.1126/science.ads0915",
            "snippet": "Gcu22 conferred low levels of resistance exclusively against phage F13 in K. pneumoniae",
            "notes": "Kieffer et al. report that the former gcu22 cassette conferred low-level F13 resistance in Klebsiella pneumoniae."
          },
          {
            "reference": "DOI:10.1126/science.ads0915",
            "snippet": "We therefore redefined both cassettes as BRiCs (brc22 and brc23)",
            "notes": "Kieffer et al. renamed gcu22 and gcu23 as Brc cassettes after phage-resistance testing."
          },
          {
            "reference": "DOI:10.1126/science.ads0915",
            "snippet": "Predicted secondary structures of attC sites in identified BRiCs",
            "notes": "Kieffer et al. identify BRiC bacteriophage-resistance integron cassettes and show their predicted attC secondary structures."
          },
          {
            "reference": "DOI:10.1126/science.ads0915",
            "snippet": "brc113\nbrc217\nbrc76\nbrcWGS21\nbrc22\nbrc23",
            "notes": "Kieffer et al. include brc22 among identified BRiCs with predicted attC secondary structures."
          },
          {
            "reference": "https://www.science.org/doi/suppl/10.1126/science.ads0915/suppl_file/science.ads0915_sm.pdf",
            "snippet": "attC of brc22, with a perfect GTT/AAC binding between both arms of the stem",
            "notes": "Kieffer et al. discuss the brc22 attC site in a comparison of Tragantia homolog-associated predicted secondary structures."
          },
          {
            "reference": "https://www.science.org/doi/suppl/10.1126/science.ads0915/suppl_file/science.ads0915_sm.pdf",
            "snippet": "D278\npMBA PcW brc22\nE. coli IJ1862",
            "notes": "Kieffer et al.'s supplementary construct table lists pMBA PcW brc22 in E. coli IJ1862 under naturally occurring defense island constructs."
          },
          {
            "reference": "https://www.science.org/doi/suppl/10.1126/science.ads0915/suppl_file/science.ads0915_sm.pdf",
            "snippet": "D283\npMBA PcW brc22\nK. pneumoniae\nKP5",
            "notes": "Kieffer et al.'s supplementary construct table lists pMBA PcW brc22 in Klebsiella pneumoniae KP5 under naturally occurring defense island constructs."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
            "notes": "A structured first-pass search of the pinned DefenseFinder article registry found no exact gcu22, brc22, or Brc22 row."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "notes": "A structured first-pass search of the pinned DefenseFinder HMM inventory found no exact gcu22, brc22, or Brc22 row."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "A structured first-pass search of the pinned DefenseFinder rules table found no exact gcu22, brc22, or Brc22 system row."
          }
        ],
        "attaches_to": [
          "causal_graphs#brc22_integron_cassette_confers_phage_resistance"
        ],
        "posed_by": "codex",
        "posed_date": "2026-10-01"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-01T19:20:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Brc22 system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review ruled out same-scope live TraitMech, METPO, history, and prior proposal collisions after reviewing exact Brc22/brc22/gcu22 hits; kept the graph at BRiC integron-cassette level because the pinned DefenseFinder article registry, HMM inventory, and rules table have no exact Brc22 row; the replacement placeholder is reserved in proposals/metpo_traitmech_v400.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-01T19:20:01Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed Brc22 system during initial curation and left canonical_examples empty because the sources support heterologous gcu22/Brc22 phage-resistance assays but not a direct named native microbial isolate exemplar with experimentally verified endogenous Brc22 activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000518",
    "label": "Brc233 system",
    "definition": "A phage defense system in which an organism possesses a gcu233/Brc233 bacteriophage-resistance integron cassette that supports growth during bacteriophage challenge.",
    "definition_source": "DOI:10.1126/science.ads0915",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "gcu233",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      },
      {
        "synonym_text": "brc233",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1126/science.ads0915"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1126/science.ads0915",
        "snippet": "brc233 L 27.7 51.8 37.3 62.6 95.7 12.8",
        "notes": "Manual transcription of the Supplementary Fig. S2 Brc233 low-MOI E. coli IJ1862 heatmap row; the row shows reduced inhibition, including 27.7% for MS2, 51.8% for G4, 37.3% for T4, 62.6% for F1, and 12.8% for F13."
      },
      {
        "reference": "DOI:10.1126/science.ads0915",
        "snippet": "brc233 H 34.0 52.2 89.4 39.4 98.2 41.3",
        "notes": "Manual transcription of the Supplementary Fig. S2 Brc233 high-MOI E. coli IJ1862 heatmap row; the row shows reduced inhibition, including 34.0% for MS2, 52.2% for G4, 39.4% for F1, and 41.3% for F13."
      },
      {
        "reference": "DOI:10.1126/science.ads0915",
        "snippet": "defense profiles of identified Bacteriophage Resistance integron Cassettes (BRiCs) against a panel of different phages",
        "notes": "Kieffer et al. classify positive integron cassettes as BRiCs and compare their defense profiles across a phage panel."
      },
      {
        "reference": "DOI:10.1126/science.ads0915",
        "snippet": "C807\npMBA brc233\nE. coli IJ1862",
        "notes": "Kieffer et al.'s supplementary construct table lists pMBA brc233 in E. coli IJ1862 for high/low-MOI phage-panel testing."
      },
      {
        "reference": "DOI:10.1126/science.ads0915",
        "snippet": "C817\npMBA brc233\nK. pneumoniae",
        "notes": "Kieffer et al.'s supplementary construct table lists the pMBA brc233 plasmid introduced into Klebsiella pneumoniae KP5."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| gcu233 | 10\\.1126/science\\.ads0915 | Mobile integrons encode phage defense systems | ",
        "notes": "The pinned DefenseFinder article registry maps the gcu233 source key to the Kieffer et al. mobile-integron BRiC paper."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "brc233_integron_cassette_confers_phage_resistance",
        "title": "Brc233 BRiCs confer phage resistance",
        "description": "Conservative system-level sketch linking a gcu233/Brc233 bacteriophage-resistance integron cassette to phage resistance and Brc233 system possession.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Brc233 at the integron-cassette and phage-resistance-output level without asserting the native host range, exact sensitive-phage breadth outside the reported panels, direct molecular substrate, or a DefenseFinder HMM/rules profile absent from the pinned snapshot.",
        "nodes": [
          {
            "node_id": "brc233_integron_cassette",
            "label": "Brc233 integron cassette",
            "node_type": "GENETIC_ELEMENT",
            "description": "A mobile integron gene cassette named by the gcu233 source key and curated as Brc233."
          },
          {
            "node_id": "brc233_phage_resistance",
            "label": "Brc233 phage resistance",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced phage inhibition in cells carrying the gcu233/Brc233 integron cassette."
          },
          {
            "node_id": "brc233_system_trait",
            "label": "Brc233 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000518",
            "description": "Possession of a genome-encoded Brc233 phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "brc233_integron_cassette",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "brc233_phage_resistance",
            "description": "The gcu233/Brc233 integron cassette contributes to phage resistance during phage-panel assays.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.ads0915",
                "snippet": "brc233 L 27.7 51.8 37.3 62.6 95.7 12.8",
                "notes": "Manual transcription of the Supplementary Fig. S2 Brc233 low-MOI E. coli IJ1862 heatmap row; the row shows reduced inhibition, including 27.7% for MS2, 51.8% for G4, 37.3% for T4, 62.6% for F1, and 12.8% for F13."
              },
              {
                "reference": "DOI:10.1126/science.ads0915",
                "snippet": "brc233 H 34.0 52.2 89.4 39.4 98.2 41.3",
                "notes": "Manual transcription of the Supplementary Fig. S2 Brc233 high-MOI E. coli IJ1862 heatmap row; the row shows reduced inhibition, including 34.0% for MS2, 52.2% for G4, 39.4% for F1, and 41.3% for F13."
              }
            ]
          },
          {
            "subject": "brc233_phage_resistance",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "brc233_system_trait",
            "description": "Brc233-linked phage resistance realizes the Brc233 system possession trait.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.ads0915",
                "snippet": "brc233 L 27.7 51.8 37.3 62.6 95.7 12.8",
                "notes": "Manual transcription of the Supplementary Fig. S2 Brc233 low-MOI E. coli IJ1862 heatmap row; the row shows reduced inhibition, including 27.7% for MS2, 51.8% for G4, 37.3% for T4, 62.6% for F1, and 12.8% for F13."
              },
              {
                "reference": "DOI:10.1126/science.ads0915",
                "snippet": "brc233 H 34.0 52.2 89.4 39.4 98.2 41.3",
                "notes": "Manual transcription of the Supplementary Fig. S2 Brc233 high-MOI E. coli IJ1862 heatmap row; the row shows reduced inhibition, including 34.0% for MS2, 52.2% for G4, 39.4% for F1, and 41.3% for F13."
              },
              {
                "reference": "DOI:10.1126/science.ads0915",
                "snippet": "defense profiles of identified Bacteriophage Resistance integron Cassettes (BRiCs) against a panel of different phages",
                "notes": "Kieffer et al. classify positive integron cassettes as BRiCs and compare their defense profiles across a phage panel."
              }
            ]
          },
          {
            "subject": "brc233_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Brc233 system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.ads0915",
                "snippet": "defense profiles of identified Bacteriophage Resistance integron Cassettes (BRiCs) against a panel of different phages",
                "notes": "Kieffer et al. classify positive integron cassettes as BRiCs and compare their defense profiles across a phage panel."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| gcu233 | 10\\.1126/science\\.ads0915 | Mobile integrons encode phage defense systems | ",
                "notes": "The pinned DefenseFinder article registry maps the gcu233 source key to the Kieffer et al. mobile-integron BRiC paper."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "brc233-defensefinder-model-gap",
        "prompt": "Resolve Brc233 native host breadth, exact sensitive-phage breadth, molecular output, and DefenseFinder HMM/rules coverage before minting narrower Brc233 mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Kieffer et al. identify brc233 as a bacteriophage-resistance integron cassette, and the pinned DefenseFinder article registry maps the gcu233 source key to the same Science article. The pinned HMM inventory and rules table have no exact gcu233 or Brc233 row, so the first-pass record leaves native-host breadth, profile boundaries, exact phage target breadth, and direct molecular output unresolved.",
        "evidence": [
          {
            "reference": "DOI:10.1126/science.ads0915",
            "snippet": "brc233 L 27.7 51.8 37.3 62.6 95.7 12.8",
            "notes": "Manual transcription of the Supplementary Fig. S2 Brc233 low-MOI E. coli IJ1862 heatmap row; the row shows reduced inhibition, including 27.7% for MS2, 51.8% for G4, 37.3% for T4, 62.6% for F1, and 12.8% for F13."
          },
          {
            "reference": "DOI:10.1126/science.ads0915",
            "snippet": "brc233 H 34.0 52.2 89.4 39.4 98.2 41.3",
            "notes": "Manual transcription of the Supplementary Fig. S2 Brc233 high-MOI E. coli IJ1862 heatmap row; the row shows reduced inhibition, including 34.0% for MS2, 52.2% for G4, 39.4% for F1, and 41.3% for F13."
          },
          {
            "reference": "DOI:10.1126/science.ads0915",
            "snippet": "defense profiles of identified Bacteriophage Resistance integron Cassettes (BRiCs) against a panel of different phages",
            "notes": "Kieffer et al. classify positive integron cassettes as BRiCs and compare their defense profiles across a phage panel."
          },
          {
            "reference": "DOI:10.1126/science.ads0915",
            "snippet": "C817\npMBA brc233\nK. pneumoniae",
            "notes": "Kieffer et al. list brc233 in the heterologous Klebsiella pneumoniae KP5 BRiC panel."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
            "snippet": "| gcu233 | 10\\.1126/science\\.ads0915 | Mobile integrons encode phage defense systems | ",
            "notes": "The pinned DefenseFinder article registry maps the gcu233 source key to the Kieffer et al. mobile-integron BRiC paper."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "notes": "A structured first-pass search of the pinned DefenseFinder HMM inventory found no exact gcu233, brc233, or Brc233 row."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "A structured first-pass search of the pinned DefenseFinder rules table found no exact gcu233, brc233, or Brc233 system row."
          }
        ],
        "attaches_to": [
          "causal_graphs#brc233_integron_cassette_confers_phage_resistance"
        ],
        "posed_by": "codex",
        "posed_date": "2026-10-01"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-01T15:36:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Brc233 system as a DOI- and DefenseFinder-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; kept the graph at BRiC integron-cassette level because the pinned DefenseFinder article registry names gcu233 but the pinned HMM inventory and rules table have no exact Brc233 row; the replacement placeholder is reserved in proposals/metpo_traitmech_v395.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-01T15:36:01Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed Brc233 system during initial curation and left canonical_examples empty because the sources support heterologous gcu233/Brc233 phage-resistance assays and a DefenseFinder gcu233 article row, but not a direct named native microbial isolate exemplar with experimentally verified endogenous Brc233 activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000524",
    "label": "Brc23 system",
    "definition": "A phage defense system in which an organism possesses a gcu23/Brc23 bacteriophage-resistance integron cassette that supports growth during bacteriophage challenge.",
    "definition_source": "DOI:10.1126/science.ads0915",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "gcu23",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1126/science.ads0915"
      },
      {
        "synonym_text": "brc23",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1126/science.ads0915"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1126/science.ads0915",
        "snippet": "gcu23 had a broader defense profile, including high resistance levels against G4, MS2, F1, and T4",
        "notes": "Kieffer et al. report that the former gcu23 cassette conferred a broader phage-defense profile with high G4, MS2, F1, and T4 resistance levels."
      },
      {
        "reference": "DOI:10.1126/science.ads0915",
        "snippet": "We therefore redefined both cassettes as BRiCs (brc22 and brc23)",
        "notes": "Kieffer et al. renamed gcu22 and gcu23 as Brc cassettes after phage-resistance testing."
      },
      {
        "reference": "DOI:10.1126/science.ads0915",
        "snippet": "Predicted secondary structures of attC sites in identified BRiCs",
        "notes": "Kieffer et al. identify BRiC bacteriophage-resistance integron cassettes and show their predicted attC secondary structures."
      },
      {
        "reference": "DOI:10.1126/science.ads0915",
        "snippet": "brc113\nbrc217\nbrc76\nbrcWGS21\nbrc22\nbrc23",
        "notes": "Kieffer et al. include brc23 among identified BRiCs with predicted attC secondary structures."
      },
      {
        "reference": "https://www.science.org/doi/suppl/10.1126/science.ads0915/suppl_file/science.ads0915_sm.pdf",
        "snippet": "D279\npMBA PcW brc23\nE. coli IJ1862",
        "notes": "Kieffer et al.'s supplementary construct table lists pMBA PcW brc23 in E. coli IJ1862 under naturally occurring defense island constructs."
      },
      {
        "reference": "https://www.science.org/doi/suppl/10.1126/science.ads0915/suppl_file/science.ads0915_sm.pdf",
        "snippet": "D284\npMBA PcW brc23\nK. pneumoniae\nKP5",
        "notes": "Kieffer et al.'s supplementary construct table lists pMBA PcW brc23 in Klebsiella pneumoniae KP5 under naturally occurring defense island constructs."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "brc23_integron_cassette_confers_phage_resistance",
        "title": "Brc23 BRiCs confer phage resistance",
        "description": "Conservative system-level sketch linking a gcu23/Brc23 bacteriophage-resistance integron cassette to phage resistance and Brc23 system possession.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Brc23 at the integron-cassette and phage-resistance-output level without asserting the native host range, exact sensitive-phage breadth outside the reported panels, direct molecular substrate, whether Brc22 and Brc23 are variants of one Tragantia family, or a DefenseFinder article/HMM/rules profile absent from the pinned snapshot.",
        "nodes": [
          {
            "node_id": "brc23_integron_cassette",
            "label": "Brc23 integron cassette",
            "node_type": "GENETIC_ELEMENT",
            "description": "A mobile integron gene cassette curated here as gcu23/Brc23."
          },
          {
            "node_id": "brc23_phage_resistance",
            "label": "Brc23 phage resistance",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced phage inhibition in cells carrying the gcu23/Brc23 integron cassette."
          },
          {
            "node_id": "brc23_system_trait",
            "label": "Brc23 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000524",
            "description": "Possession of a genome-encoded Brc23 phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "brc23_integron_cassette",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "brc23_phage_resistance",
            "description": "The gcu23/Brc23 integron cassette contributes to G4, MS2, F1, and T4 phage resistance during phage-panel assays.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.ads0915",
                "snippet": "gcu23 had a broader defense profile, including high resistance levels against G4, MS2, F1, and T4",
                "notes": "Kieffer et al. report that the former gcu23 cassette conferred a broader phage-defense profile with high G4, MS2, F1, and T4 resistance levels."
              }
            ]
          },
          {
            "subject": "brc23_phage_resistance",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "brc23_system_trait",
            "description": "Brc23-linked phage resistance realizes the Brc23 system possession trait.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.ads0915",
                "snippet": "gcu23 had a broader defense profile, including high resistance levels against G4, MS2, F1, and T4",
                "notes": "Kieffer et al. report that the former gcu23 cassette conferred a broader phage-defense profile with high G4, MS2, F1, and T4 resistance levels."
              },
              {
                "reference": "DOI:10.1126/science.ads0915",
                "snippet": "We therefore redefined both cassettes as BRiCs (brc22 and brc23)",
                "notes": "Kieffer et al. renamed gcu22 and gcu23 as Brc cassettes after phage-resistance testing."
              }
            ]
          },
          {
            "subject": "brc23_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Brc23 system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.ads0915",
                "snippet": "Predicted secondary structures of attC sites in identified BRiCs",
                "notes": "Kieffer et al. identify BRiC bacteriophage-resistance integron cassettes and show their predicted attC secondary structures."
              },
              {
                "reference": "DOI:10.1126/science.ads0915",
                "snippet": "brc113\nbrc217\nbrc76\nbrcWGS21\nbrc22\nbrc23",
                "notes": "Kieffer et al. include brc23 among identified BRiCs with predicted attC secondary structures."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "brc23-defensefinder-model-gap",
        "prompt": "Resolve Brc23 native host breadth, exact sensitive-phage breadth, molecular output, Tragantia-family boundaries, and DefenseFinder article/HMM/rules coverage before minting narrower Brc23 mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Kieffer et al. identify brc23 as a bacteriophage-resistance integron cassette. The pinned DefenseFinder article registry, HMM inventory, and rules table have no exact gcu23 or Brc23 row, so the first-pass record leaves native-host breadth, profile boundaries, exact phage target breadth, direct molecular output, and Brc22/Brc23 Tragantia-family scope unresolved.",
        "evidence": [
          {
            "reference": "DOI:10.1126/science.ads0915",
            "snippet": "gcu23 had a broader defense profile, including high resistance levels against G4, MS2, F1, and T4",
            "notes": "Kieffer et al. report that the former gcu23 cassette conferred a broader phage-defense profile with high G4, MS2, F1, and T4 resistance levels."
          },
          {
            "reference": "DOI:10.1126/science.ads0915",
            "snippet": "We therefore redefined both cassettes as BRiCs (brc22 and brc23)",
            "notes": "Kieffer et al. renamed gcu22 and gcu23 as Brc cassettes after phage-resistance testing."
          },
          {
            "reference": "DOI:10.1126/science.ads0915",
            "snippet": "Predicted secondary structures of attC sites in identified BRiCs",
            "notes": "Kieffer et al. identify BRiC bacteriophage-resistance integron cassettes and show their predicted attC secondary structures."
          },
          {
            "reference": "DOI:10.1126/science.ads0915",
            "snippet": "brc113\nbrc217\nbrc76\nbrcWGS21\nbrc22\nbrc23",
            "notes": "Kieffer et al. include brc23 among identified BRiCs with predicted attC secondary structures."
          },
          {
            "reference": "https://www.science.org/doi/suppl/10.1126/science.ads0915/suppl_file/science.ads0915_sm.pdf",
            "snippet": "D279\npMBA PcW brc23\nE. coli IJ1862",
            "notes": "Kieffer et al.'s supplementary construct table lists pMBA PcW brc23 in E. coli IJ1862 under naturally occurring defense island constructs."
          },
          {
            "reference": "https://www.science.org/doi/suppl/10.1126/science.ads0915/suppl_file/science.ads0915_sm.pdf",
            "snippet": "D284\npMBA PcW brc23\nK. pneumoniae\nKP5",
            "notes": "Kieffer et al.'s supplementary construct table lists pMBA PcW brc23 in Klebsiella pneumoniae KP5 under naturally occurring defense island constructs."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
            "notes": "A structured first-pass search of the pinned DefenseFinder article registry found no exact gcu23, brc23, or Brc23 row."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "notes": "A structured first-pass search of the pinned DefenseFinder HMM inventory found no exact gcu23, brc23, or Brc23 row."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "A structured first-pass search of the pinned DefenseFinder rules table found no exact gcu23, brc23, or Brc23 system row."
          }
        ],
        "attaches_to": [
          "causal_graphs#brc23_integron_cassette_confers_phage_resistance"
        ],
        "posed_by": "codex",
        "posed_date": "2026-10-01"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-01T20:08:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Brc23 system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review ruled out same-scope live TraitMech, METPO, history, and prior proposal collisions after reviewing exact Brc23/brc23/gcu23 hits; kept the graph at BRiC integron-cassette level because the pinned DefenseFinder article registry, HMM inventory, and rules table have no exact Brc23 row; the replacement placeholder is reserved in proposals/metpo_traitmech_v401.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-01T20:08:01Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed Brc23 system during initial curation and left canonical_examples empty because the sources support heterologous gcu23/Brc23 phage-resistance assays but not a direct named native microbial isolate exemplar with experimentally verified endogenous Brc23 activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000516",
    "label": "Brc24 system",
    "definition": "A phage defense system in which an organism possesses a gcu24/Brc24 bacteriophage-resistance integron cassette that supports growth during bacteriophage challenge.",
    "definition_source": "DOI:10.1126/science.ads0915",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "gcu24",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      },
      {
        "synonym_text": "brc24",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1126/science.ads0915"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1126/science.ads0915",
        "snippet": "Identification of gcu24 and gcu142 through double spot screening",
        "notes": "Kieffer et al. report initial identification of gcu24 in a double-spot phage-resistance screen."
      },
      {
        "reference": "DOI:10.1126/science.ads0915",
        "snippet": "gcu24 and gcu142, which show growth despite the presence of the phage, indicating successful identification and resistance.",
        "notes": "Kieffer et al. support growth of the gcu24 clone during T4 phage challenge in the initial screen."
      },
      {
        "reference": "DOI:10.1126/science.ads0915",
        "snippet": "defense profiles of identified Bacteriophage Resistance integron Cassettes (BRiCs) against a panel of different phages",
        "notes": "Kieffer et al. classify positive integron cassettes as BRiCs and compare their defense profiles across a phage panel."
      },
      {
        "reference": "DOI:10.1126/science.ads0915",
        "snippet": "C747\npMBA gcu24",
        "notes": "Kieffer et al.'s supplementary construct table lists the initial pMBA gcu24 screening plasmid."
      },
      {
        "reference": "DOI:10.1126/science.ads0915",
        "snippet": "C806\npMBA brc24\nE. coli IJ1862",
        "notes": "Kieffer et al.'s supplementary construct table lists pMBA brc24 in E. coli IJ1862 for high/low-MOI phage-panel testing."
      },
      {
        "reference": "DOI:10.1126/science.ads0915",
        "snippet": "C816\npMBA brc24\nK. pneumoniae",
        "notes": "Kieffer et al.'s supplementary construct table lists the pMBA brc24 plasmid introduced into Klebsiella pneumoniae KP5."
      },
      {
        "reference": "DOI:10.1126/science.ads0915",
        "snippet": "C971\npBTZ PcW brc24",
        "notes": "Kieffer et al.'s supplementary construct table lists a Pseudomonas aeruginosa brc24 expression construct."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| gcu24 | 10\\.1126/science\\.ads0915 | Mobile integrons encode phage defense systems | ",
        "notes": "The pinned DefenseFinder article registry maps the gcu24 source key to the Kieffer et al. mobile-integron BRiC paper."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "brc24_integron_cassette_confers_phage_resistance",
        "title": "Brc24 BRiCs confer phage resistance",
        "description": "Conservative system-level sketch linking a gcu24/Brc24 bacteriophage-resistance integron cassette to phage resistance and Brc24 system possession.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Brc24 at the integron-cassette and phage-resistance-output level without asserting the native host range, exact sensitive-phage breadth outside the reported panels, direct molecular substrate, or a DefenseFinder HMM/rules profile absent from the pinned snapshot.",
        "nodes": [
          {
            "node_id": "brc24_integron_cassette",
            "label": "Brc24 integron cassette",
            "node_type": "GENETIC_ELEMENT",
            "description": "A mobile integron gene cassette recovered in the gcu24 screen and renamed as a Brc24 bacteriophage-resistance integron cassette."
          },
          {
            "node_id": "brc24_phage_resistance",
            "label": "Brc24 phage resistance",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced phage inhibition in cells carrying the gcu24/Brc24 integron cassette."
          },
          {
            "node_id": "brc24_system_trait",
            "label": "Brc24 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000516",
            "description": "Possession of a genome-encoded Brc24 phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "brc24_integron_cassette",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "brc24_phage_resistance",
            "description": "The gcu24/Brc24 integron cassette contributes to phage resistance during double-spot and phage-panel assays.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.ads0915",
                "snippet": "Identification of gcu24 and gcu142 through double spot screening",
                "notes": "Kieffer et al. report initial identification of gcu24 in a double-spot phage-resistance screen."
              },
              {
                "reference": "DOI:10.1126/science.ads0915",
                "snippet": "C806\npMBA brc24\nE. coli IJ1862",
                "notes": "Kieffer et al. cloned brc24 for E. coli IJ1862 phage-panel testing."
              }
            ]
          },
          {
            "subject": "brc24_phage_resistance",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "brc24_system_trait",
            "description": "Brc24-linked phage resistance realizes the Brc24 system possession trait.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.ads0915",
                "snippet": "gcu24 and gcu142, which show growth despite the presence of the phage, indicating successful identification and resistance.",
                "notes": "Kieffer et al. support growth of the gcu24 clone during T4 phage challenge in the initial screen."
              },
              {
                "reference": "DOI:10.1126/science.ads0915",
                "snippet": "defense profiles of identified Bacteriophage Resistance integron Cassettes (BRiCs) against a panel of different phages",
                "notes": "Kieffer et al. classify positive integron cassettes as BRiCs and compare their defense profiles across a phage panel."
              }
            ]
          },
          {
            "subject": "brc24_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Brc24 system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.ads0915",
                "snippet": "defense profiles of identified Bacteriophage Resistance integron Cassettes (BRiCs) against a panel of different phages",
                "notes": "Kieffer et al. classify positive integron cassettes as BRiCs and compare their defense profiles across a phage panel."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| gcu24 | 10\\.1126/science\\.ads0915 | Mobile integrons encode phage defense systems | ",
                "notes": "The pinned DefenseFinder article registry maps the gcu24 source key to the Kieffer et al. mobile-integron BRiC paper."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "brc24-defensefinder-model-gap",
        "prompt": "Resolve Brc24 native host breadth, exact sensitive-phage breadth, molecular output, and DefenseFinder HMM/rules coverage before minting narrower Brc24 mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Kieffer et al. identify gcu24/Brc24 as a bacteriophage-resistance integron cassette, and the pinned DefenseFinder article registry maps the gcu24 source key to the same Science article. The pinned HMM inventory and rules table have no exact gcu24 or Brc24 row, so the first-pass record leaves native-host breadth, profile boundaries, exact phage target breadth, and direct molecular output unresolved.",
        "evidence": [
          {
            "reference": "DOI:10.1126/science.ads0915",
            "snippet": "Identification of gcu24 and gcu142 through double spot screening",
            "notes": "Kieffer et al. report initial identification of gcu24 in a double-spot phage-resistance screen."
          },
          {
            "reference": "DOI:10.1126/science.ads0915",
            "snippet": "defense profiles of identified Bacteriophage Resistance integron Cassettes (BRiCs) against a panel of different phages",
            "notes": "Kieffer et al. classify positive integron cassettes as BRiCs and compare their defense profiles across a phage panel."
          },
          {
            "reference": "DOI:10.1126/science.ads0915",
            "snippet": "C816\npMBA brc24\nK. pneumoniae",
            "notes": "Kieffer et al. list brc24 in the heterologous Klebsiella pneumoniae KP5 BRiC panel."
          },
          {
            "reference": "DOI:10.1126/science.ads0915",
            "snippet": "C971\npBTZ PcW brc24",
            "notes": "Kieffer et al. list brc24 in the heterologous Pseudomonas aeruginosa PAO1 BRiC panel."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
            "snippet": "| gcu24 | 10\\.1126/science\\.ads0915 | Mobile integrons encode phage defense systems | ",
            "notes": "The pinned DefenseFinder article registry maps the gcu24 source key to the Kieffer et al. mobile-integron BRiC paper."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "notes": "A structured first-pass search of the pinned DefenseFinder HMM inventory found no exact gcu24, brc24, or Brc24 row."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "A structured first-pass search of the pinned DefenseFinder rules table found no exact gcu24, brc24, or Brc24 system row."
          }
        ],
        "attaches_to": [
          "causal_graphs#brc24_integron_cassette_confers_phage_resistance"
        ],
        "posed_by": "codex",
        "posed_date": "2026-10-01"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-01T13:34:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Brc24 system as a DOI- and DefenseFinder-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; kept the graph at BRiC integron-cassette level because the pinned DefenseFinder article registry names gcu24 but the pinned HMM inventory and rules table have no exact Brc24 row; the replacement placeholder is reserved in proposals/metpo_traitmech_v393.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-01T13:34:01Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed Brc24 system during initial curation and left canonical_examples empty because the sources support heterologous gcu24/Brc24 phage-resistance assays and a DefenseFinder gcu24 article row, but not a direct named native microbial isolate exemplar with experimentally verified endogenous Brc24 activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000525",
    "label": "Brc59 system",
    "definition": "A phage defense system in which an organism possesses a Brc59 bacteriophage-resistance integron cassette that supports growth during bacteriophage challenge.",
    "definition_source": "DOI:10.1126/science.ads0915",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "brc59",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1126/science.ads0915"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1126/science.ads0915",
        "snippet": "brc59 L 44.7 49.6 87.3 98.6 7.6",
        "notes": "Manual transcription of the Supplementary Fig. S2 Brc59 low-MOI E. coli IJ1862 heatmap row; the visible cells show reduced inhibition, including 44.7% for MS2, 49.6% for T4, 87.3% for F1, 98.6% for T7, and 7.6% for F13."
      },
      {
        "reference": "DOI:10.1126/science.ads0915",
        "snippet": "brc59 H 12.8 75.8 80.3 60.9",
        "notes": "Manual transcription of the Supplementary Fig. S2 Brc59 high-MOI E. coli IJ1862 heatmap row; the visible cells show reduced inhibition, including 12.8% for MS2, 75.8% for F1, 80.3% for HK544, and 60.9% for F13."
      },
      {
        "reference": "DOI:10.1126/science.ads0915",
        "snippet": "defense profiles of identified Bacteriophage Resistance integron Cassettes (BRiCs) against a panel of different phages",
        "notes": "Kieffer et al. classify positive integron cassettes as BRiCs and compare their defense profiles across a phage panel."
      },
      {
        "reference": "DOI:10.1126/science.ads0915",
        "snippet": "brc59\nbrc128\nbrc135\nbrc142\nbrc167.2\nbrc167",
        "notes": "Kieffer et al. include brc59 among identified BRiCs with predicted attC secondary structures."
      },
      {
        "reference": "https://www.science.org/doi/suppl/10.1126/science.ads0915/suppl_file/science.ads0915_sm.pdf",
        "snippet": "C800\npMBA brc59\nE. coli IJ1862",
        "notes": "Kieffer et al.'s supplementary construct table lists pMBA brc59 in E. coli IJ1862 for high/low-MOI phage-panel testing."
      },
      {
        "reference": "https://www.science.org/doi/suppl/10.1126/science.ads0915/suppl_file/science.ads0915_sm.pdf",
        "snippet": "C810\npMBA brc59\nK. pneumoniae\n\nKP5",
        "notes": "Kieffer et al.'s supplementary construct table lists the pMBA brc59 plasmid introduced into Klebsiella pneumoniae KP5."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "brc59_integron_cassette_confers_phage_resistance",
        "title": "Brc59 BRiCs confer phage resistance",
        "description": "Conservative system-level sketch linking a Brc59 bacteriophage-resistance integron cassette to phage resistance and Brc59 system possession.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Brc59 at the integron-cassette and phage-resistance-output level without asserting the native host range, exact sensitive-phage breadth outside the reported panels, direct molecular substrate, a normalized gcu59 source key, or a DefenseFinder article/HMM/rules profile absent from the pinned snapshot.",
        "nodes": [
          {
            "node_id": "brc59_integron_cassette",
            "label": "Brc59 integron cassette",
            "node_type": "GENETIC_ELEMENT",
            "description": "A mobile integron gene cassette curated here as Brc59."
          },
          {
            "node_id": "brc59_phage_resistance",
            "label": "Brc59 phage resistance",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced phage inhibition in cells carrying the Brc59 integron cassette."
          },
          {
            "node_id": "brc59_system_trait",
            "label": "Brc59 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000525",
            "description": "Possession of a genome-encoded Brc59 phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "brc59_integron_cassette",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "brc59_phage_resistance",
            "description": "The Brc59 integron cassette contributes to phage resistance during phage-panel assays.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.ads0915",
                "snippet": "brc59 L 44.7 49.6 87.3 98.6 7.6",
                "notes": "Manual transcription of the Supplementary Fig. S2 Brc59 low-MOI E. coli IJ1862 heatmap row; the visible cells show reduced inhibition, including 44.7% for MS2, 49.6% for T4, 87.3% for F1, 98.6% for T7, and 7.6% for F13."
              },
              {
                "reference": "DOI:10.1126/science.ads0915",
                "snippet": "brc59 H 12.8 75.8 80.3 60.9",
                "notes": "Manual transcription of the Supplementary Fig. S2 Brc59 high-MOI E. coli IJ1862 heatmap row; the visible cells show reduced inhibition, including 12.8% for MS2, 75.8% for F1, 80.3% for HK544, and 60.9% for F13."
              }
            ]
          },
          {
            "subject": "brc59_phage_resistance",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "brc59_system_trait",
            "description": "Brc59-linked phage resistance realizes the Brc59 system possession trait.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.ads0915",
                "snippet": "brc59 L 44.7 49.6 87.3 98.6 7.6",
                "notes": "Manual transcription of the Supplementary Fig. S2 Brc59 low-MOI E. coli IJ1862 heatmap row; the visible cells show reduced inhibition, including 44.7% for MS2, 49.6% for T4, 87.3% for F1, 98.6% for T7, and 7.6% for F13."
              },
              {
                "reference": "DOI:10.1126/science.ads0915",
                "snippet": "brc59 H 12.8 75.8 80.3 60.9",
                "notes": "Manual transcription of the Supplementary Fig. S2 Brc59 high-MOI E. coli IJ1862 heatmap row; the visible cells show reduced inhibition, including 12.8% for MS2, 75.8% for F1, 80.3% for HK544, and 60.9% for F13."
              },
              {
                "reference": "DOI:10.1126/science.ads0915",
                "snippet": "defense profiles of identified Bacteriophage Resistance integron Cassettes (BRiCs) against a panel of different phages",
                "notes": "Kieffer et al. classify positive integron cassettes as BRiCs and compare their defense profiles across a phage panel."
              }
            ]
          },
          {
            "subject": "brc59_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Brc59 system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.ads0915",
                "snippet": "defense profiles of identified Bacteriophage Resistance integron Cassettes (BRiCs) against a panel of different phages",
                "notes": "Kieffer et al. classify positive integron cassettes as BRiCs and compare their defense profiles across a phage panel."
              },
              {
                "reference": "DOI:10.1126/science.ads0915",
                "snippet": "brc59\nbrc128\nbrc135\nbrc142\nbrc167.2\nbrc167",
                "notes": "Kieffer et al. include brc59 among identified BRiCs with predicted attC secondary structures."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "brc59-defensefinder-model-gap",
        "prompt": "Resolve Brc59 native host breadth, exact sensitive-phage breadth, molecular output, normalized source-key naming, and DefenseFinder article/HMM/rules coverage before minting narrower Brc59 mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Kieffer et al. identify brc59 as a bacteriophage-resistance integron cassette. The pinned DefenseFinder article registry, HMM inventory, and rules table have no exact gcu59 or Brc59 row, so the first-pass record leaves native-host breadth, profile boundaries, exact phage target breadth, direct molecular output, and normalized gcu59 source-key status unresolved.",
        "evidence": [
          {
            "reference": "DOI:10.1126/science.ads0915",
            "snippet": "brc59 L 44.7 49.6 87.3 98.6 7.6",
            "notes": "Manual transcription of the Supplementary Fig. S2 Brc59 low-MOI E. coli IJ1862 heatmap row; the visible cells show reduced inhibition, including 44.7% for MS2, 49.6% for T4, 87.3% for F1, 98.6% for T7, and 7.6% for F13."
          },
          {
            "reference": "DOI:10.1126/science.ads0915",
            "snippet": "brc59 H 12.8 75.8 80.3 60.9",
            "notes": "Manual transcription of the Supplementary Fig. S2 Brc59 high-MOI E. coli IJ1862 heatmap row; the visible cells show reduced inhibition, including 12.8% for MS2, 75.8% for F1, 80.3% for HK544, and 60.9% for F13."
          },
          {
            "reference": "DOI:10.1126/science.ads0915",
            "snippet": "defense profiles of identified Bacteriophage Resistance integron Cassettes (BRiCs) against a panel of different phages",
            "notes": "Kieffer et al. classify positive integron cassettes as BRiCs and compare their defense profiles across a phage panel."
          },
          {
            "reference": "DOI:10.1126/science.ads0915",
            "snippet": "brc59\nbrc128\nbrc135\nbrc142\nbrc167.2\nbrc167",
            "notes": "Kieffer et al. include brc59 among identified BRiCs with predicted attC secondary structures."
          },
          {
            "reference": "https://www.science.org/doi/suppl/10.1126/science.ads0915/suppl_file/science.ads0915_sm.pdf",
            "snippet": "C800\npMBA brc59\nE. coli IJ1862",
            "notes": "Kieffer et al.'s supplementary construct table lists pMBA brc59 in E. coli IJ1862 for high/low-MOI phage-panel testing."
          },
          {
            "reference": "https://www.science.org/doi/suppl/10.1126/science.ads0915/suppl_file/science.ads0915_sm.pdf",
            "snippet": "C810\npMBA brc59\nK. pneumoniae\n\nKP5",
            "notes": "Kieffer et al.'s supplementary construct table lists the pMBA brc59 plasmid introduced into Klebsiella pneumoniae KP5."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
            "notes": "A structured first-pass search of the pinned DefenseFinder article registry found no exact gcu59, brc59, or Brc59 row."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "notes": "A structured first-pass search of the pinned DefenseFinder HMM inventory found no exact gcu59, brc59, or Brc59 row."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "A structured first-pass search of the pinned DefenseFinder rules table found no exact gcu59, brc59, or Brc59 system row."
          }
        ],
        "attaches_to": [
          "causal_graphs#brc59_integron_cassette_confers_phage_resistance"
        ],
        "posed_by": "codex",
        "posed_date": "2026-10-01"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-01T20:28:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Brc59 system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review ruled out same-scope live TraitMech, METPO, history, and prior proposal collisions after reviewing exact Brc59/brc59/gcu59 hits; kept the graph at BRiC integron-cassette level because the pinned DefenseFinder article registry, HMM inventory, and rules table have no exact Brc59 row; the replacement placeholder is reserved in proposals/metpo_traitmech_v402.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-01T20:28:01Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed Brc59 system during initial curation and left canonical_examples empty because the sources support heterologous brc59 phage-resistance assays but not a direct named native microbial isolate exemplar with experimentally verified endogenous Brc59 activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000519",
    "label": "Brc76 system",
    "definition": "A phage defense system in which an organism possesses a gcu76/Brc76 bacteriophage-resistance integron cassette that supports growth during bacteriophage challenge.",
    "definition_source": "DOI:10.1126/science.ads0915",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "gcu76",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      },
      {
        "synonym_text": "brc76",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1126/science.ads0915"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1126/science.ads0915",
        "snippet": "brc76 L 79.5 92.4 89.1 83.1",
        "notes": "Manual transcription of the Supplementary Fig. S2 Brc76 low-MOI E. coli IJ1862 heatmap row; the visible cells show reduced inhibition, including 79.5% for MS2, 92.4% for F1, 89.1% for phi80, and 83.1% for F13."
      },
      {
        "reference": "DOI:10.1126/science.ads0915",
        "snippet": "brc76 H 96.6",
        "notes": "Manual transcription of the Supplementary Fig. S2 Brc76 high-MOI E. coli IJ1862 heatmap row; the visible MS2 cell shows 96.6% inhibition."
      },
      {
        "reference": "DOI:10.1126/science.ads0915",
        "snippet": "defense profiles of identified Bacteriophage Resistance integron Cassettes (BRiCs) against a panel of different phages",
        "notes": "Kieffer et al. classify positive integron cassettes as BRiCs and compare their defense profiles across a phage panel."
      },
      {
        "reference": "DOI:10.1126/science.ads0915",
        "snippet": "brc113\nbrc217\nbrc76\nbrcWGS21\nbrc22\nbrc23",
        "notes": "Kieffer et al. include brc76 among identified BRiCs with predicted attC secondary structures."
      },
      {
        "reference": "DOI:10.1126/science.ads0915",
        "snippet": "C933\npMBA brc76\nE. coli IJ1862",
        "notes": "Kieffer et al.'s supplementary construct table lists pMBA brc76 in E. coli IJ1862 for high/low-MOI phage-panel testing."
      },
      {
        "reference": "DOI:10.1126/science.ads0915",
        "snippet": "C939\npMBA brc76\nK. pneumoniae\nKP5",
        "notes": "Kieffer et al.'s supplementary construct table lists the pMBA brc76 plasmid introduced into Klebsiella pneumoniae KP5."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| gcu76 | 10\\.1126/science\\.ads0915 | Mobile integrons encode phage defense systems | ",
        "notes": "The pinned DefenseFinder article registry maps the gcu76 source key to the Kieffer et al. mobile-integron BRiC paper."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "brc76_integron_cassette_confers_phage_resistance",
        "title": "Brc76 BRiCs confer phage resistance",
        "description": "Conservative system-level sketch linking a gcu76/Brc76 bacteriophage-resistance integron cassette to phage resistance and Brc76 system possession.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Brc76 at the integron-cassette and phage-resistance-output level without asserting the native host range, exact sensitive-phage breadth outside the reported panels, direct molecular substrate, or a DefenseFinder HMM/rules profile absent from the pinned snapshot.",
        "nodes": [
          {
            "node_id": "brc76_integron_cassette",
            "label": "Brc76 integron cassette",
            "node_type": "GENETIC_ELEMENT",
            "description": "A mobile integron gene cassette named by the gcu76 source key and curated as Brc76."
          },
          {
            "node_id": "brc76_phage_resistance",
            "label": "Brc76 phage resistance",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced phage inhibition in cells carrying the gcu76/Brc76 integron cassette."
          },
          {
            "node_id": "brc76_system_trait",
            "label": "Brc76 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000519",
            "description": "Possession of a genome-encoded Brc76 phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "brc76_integron_cassette",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "brc76_phage_resistance",
            "description": "The gcu76/Brc76 integron cassette contributes to phage resistance during phage-panel assays.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.ads0915",
                "snippet": "brc76 L 79.5 92.4 89.1 83.1",
                "notes": "Manual transcription of the Supplementary Fig. S2 Brc76 low-MOI E. coli IJ1862 heatmap row; the visible cells show reduced inhibition, including 79.5% for MS2, 92.4% for F1, 89.1% for phi80, and 83.1% for F13."
              },
              {
                "reference": "DOI:10.1126/science.ads0915",
                "snippet": "brc76 H 96.6",
                "notes": "Manual transcription of the Supplementary Fig. S2 Brc76 high-MOI E. coli IJ1862 heatmap row; the visible MS2 cell shows 96.6% inhibition."
              }
            ]
          },
          {
            "subject": "brc76_phage_resistance",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "brc76_system_trait",
            "description": "Brc76-linked phage resistance realizes the Brc76 system possession trait.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.ads0915",
                "snippet": "brc76 L 79.5 92.4 89.1 83.1",
                "notes": "Manual transcription of the Supplementary Fig. S2 Brc76 low-MOI E. coli IJ1862 heatmap row; the visible cells show reduced inhibition, including 79.5% for MS2, 92.4% for F1, 89.1% for phi80, and 83.1% for F13."
              },
              {
                "reference": "DOI:10.1126/science.ads0915",
                "snippet": "brc76 H 96.6",
                "notes": "Manual transcription of the Supplementary Fig. S2 Brc76 high-MOI E. coli IJ1862 heatmap row; the visible MS2 cell shows 96.6% inhibition."
              },
              {
                "reference": "DOI:10.1126/science.ads0915",
                "snippet": "defense profiles of identified Bacteriophage Resistance integron Cassettes (BRiCs) against a panel of different phages",
                "notes": "Kieffer et al. classify positive integron cassettes as BRiCs and compare their defense profiles across a phage panel."
              }
            ]
          },
          {
            "subject": "brc76_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Brc76 system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.ads0915",
                "snippet": "defense profiles of identified Bacteriophage Resistance integron Cassettes (BRiCs) against a panel of different phages",
                "notes": "Kieffer et al. classify positive integron cassettes as BRiCs and compare their defense profiles across a phage panel."
              },
              {
                "reference": "DOI:10.1126/science.ads0915",
                "snippet": "brc113\nbrc217\nbrc76\nbrcWGS21\nbrc22\nbrc23",
                "notes": "Kieffer et al. include brc76 among identified BRiCs with predicted attC secondary structures."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| gcu76 | 10\\.1126/science\\.ads0915 | Mobile integrons encode phage defense systems | ",
                "notes": "The pinned DefenseFinder article registry maps the gcu76 source key to the Kieffer et al. mobile-integron BRiC paper."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "brc76-defensefinder-model-gap",
        "prompt": "Resolve Brc76 native host breadth, exact sensitive-phage breadth, molecular output, and DefenseFinder HMM/rules coverage before minting narrower Brc76 mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Kieffer et al. identify brc76 as a bacteriophage-resistance integron cassette, and the pinned DefenseFinder article registry maps the gcu76 source key to the same Science article. The pinned HMM inventory and rules table have no exact gcu76 or Brc76 row, so the first-pass record leaves native-host breadth, profile boundaries, exact phage target breadth, and direct molecular output unresolved.",
        "evidence": [
          {
            "reference": "DOI:10.1126/science.ads0915",
            "snippet": "brc76 L 79.5 92.4 89.1 83.1",
            "notes": "Manual transcription of the Supplementary Fig. S2 Brc76 low-MOI E. coli IJ1862 heatmap row; the visible cells show reduced inhibition, including 79.5% for MS2, 92.4% for F1, 89.1% for phi80, and 83.1% for F13."
          },
          {
            "reference": "DOI:10.1126/science.ads0915",
            "snippet": "brc76 H 96.6",
            "notes": "Manual transcription of the Supplementary Fig. S2 Brc76 high-MOI E. coli IJ1862 heatmap row; the visible MS2 cell shows 96.6% inhibition."
          },
          {
            "reference": "DOI:10.1126/science.ads0915",
            "snippet": "defense profiles of identified Bacteriophage Resistance integron Cassettes (BRiCs) against a panel of different phages",
            "notes": "Kieffer et al. classify positive integron cassettes as BRiCs and compare their defense profiles across a phage panel."
          },
          {
            "reference": "DOI:10.1126/science.ads0915",
            "snippet": "brc113\nbrc217\nbrc76\nbrcWGS21\nbrc22\nbrc23",
            "notes": "Kieffer et al. include brc76 among identified BRiCs with predicted attC secondary structures."
          },
          {
            "reference": "DOI:10.1126/science.ads0915",
            "snippet": "C939\npMBA brc76\nK. pneumoniae\nKP5",
            "notes": "Kieffer et al. list brc76 in the heterologous Klebsiella pneumoniae KP5 BRiC panel."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
            "snippet": "| gcu76 | 10\\.1126/science\\.ads0915 | Mobile integrons encode phage defense systems | ",
            "notes": "The pinned DefenseFinder article registry maps the gcu76 source key to the Kieffer et al. mobile-integron BRiC paper."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "notes": "A structured first-pass search of the pinned DefenseFinder HMM inventory found no exact gcu76, brc76, or Brc76 row."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "A structured first-pass search of the pinned DefenseFinder rules table found no exact gcu76, brc76, or Brc76 system row."
          }
        ],
        "attaches_to": [
          "causal_graphs#brc76_integron_cassette_confers_phage_resistance"
        ],
        "posed_by": "codex",
        "posed_date": "2026-10-01"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-01T16:17:37Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Brc76 system as a DOI- and DefenseFinder-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; kept the graph at BRiC integron-cassette level because the pinned DefenseFinder article registry names gcu76 but the pinned HMM inventory and rules table have no exact Brc76 row; the replacement placeholder is reserved in proposals/metpo_traitmech_v396.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-01T16:17:38Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed Brc76 system during initial curation and left canonical_examples empty because the sources support heterologous gcu76/Brc76 phage-resistance assays and a DefenseFinder gcu76 article row, but not a direct named native microbial isolate exemplar with experimentally verified endogenous Brc76 activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000520",
    "label": "BrcWGS21 system",
    "definition": "A phage defense system in which an organism possesses a gcuWGS21/BrcWGS21 bacteriophage-resistance integron cassette that supports growth during bacteriophage challenge.",
    "definition_source": "DOI:10.1126/science.ads0915",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "gcuWGS21",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      },
      {
        "synonym_text": "brcWGS21",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1126/science.ads0915"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1126/science.ads0915",
        "snippet": "brcWGS21 L 88.6 60.5 93.4 77.2 25.6 0 93.4",
        "notes": "Manual transcription of the Supplementary Fig. S2 BrcWGS21 low-MOI heatmap row; the visible cells show reduced inhibition, including 88.6% for MS2, 60.5% for T7, 93.4% for HK544, 77.2% for F13, 25.6% for Vs1, 0% for Px4, and 93.4% for Px5."
      },
      {
        "reference": "DOI:10.1126/science.ads0915",
        "snippet": "brcWGS21 H 95.6 98.2 84.9 98.0 24.9 78.4",
        "notes": "Manual transcription of the Supplementary Fig. S2 BrcWGS21 high-MOI heatmap row; the visible cells show reduced inhibition, including 95.6% for MS2, 98.2% for phi80, 84.9% for HK544, 98.0% for F13, 24.9% for Vs1, and 78.4% for Px4."
      },
      {
        "reference": "DOI:10.1126/science.ads0915",
        "snippet": "defense profiles of identified Bacteriophage Resistance integron Cassettes (BRiCs) against a panel of different phages",
        "notes": "Kieffer et al. classify positive integron cassettes as BRiCs and compare their defense profiles across a phage panel."
      },
      {
        "reference": "DOI:10.1126/science.ads0915",
        "snippet": "brc113\nbrc217\nbrc76\nbrcWGS21\nbrc22\nbrc23",
        "notes": "Kieffer et al. include brcWGS21 among identified BRiCs with predicted attC secondary structures."
      },
      {
        "reference": "DOI:10.1126/science.ads0915",
        "snippet": "C935\npMBA brcWGS21\nE. coli IJ1862",
        "notes": "Kieffer et al.'s supplementary construct table lists pMBA brcWGS21 in E. coli IJ1862 for high/low-MOI phage-panel testing."
      },
      {
        "reference": "DOI:10.1126/science.ads0915",
        "snippet": "C941\npMBA brcWGS21\nK. pneumoniae\n\nKP5",
        "notes": "Kieffer et al.'s supplementary construct table lists the pMBA brcWGS21 plasmid introduced into Klebsiella pneumoniae KP5."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| gcuWGS21 | 10\\.1126/science\\.ads0915 | Mobile integrons encode phage defense systems | ",
        "notes": "The pinned DefenseFinder article registry maps the gcuWGS21 source key to the Kieffer et al. mobile-integron BRiC paper."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "brcwgs21_integron_cassette_confers_phage_resistance",
        "title": "BrcWGS21 BRiCs confer phage resistance",
        "description": "Conservative system-level sketch linking a gcuWGS21/BrcWGS21 bacteriophage-resistance integron cassette to phage resistance and BrcWGS21 system possession.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures BrcWGS21 at the integron-cassette and phage-resistance-output level without asserting the native host range, exact sensitive-phage breadth outside the reported panels, direct molecular substrate, or a DefenseFinder HMM/rules profile absent from the pinned snapshot.",
        "nodes": [
          {
            "node_id": "brcwgs21_integron_cassette",
            "label": "BrcWGS21 integron cassette",
            "node_type": "GENETIC_ELEMENT",
            "description": "A mobile integron gene cassette named by the gcuWGS21 source key and curated as BrcWGS21."
          },
          {
            "node_id": "brcwgs21_phage_resistance",
            "label": "BrcWGS21 phage resistance",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced phage inhibition in cells carrying the gcuWGS21/BrcWGS21 integron cassette."
          },
          {
            "node_id": "brcwgs21_system_trait",
            "label": "BrcWGS21 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000520",
            "description": "Possession of a genome-encoded BrcWGS21 phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "brcwgs21_integron_cassette",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "brcwgs21_phage_resistance",
            "description": "The gcuWGS21/BrcWGS21 integron cassette contributes to phage resistance during phage-panel assays.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.ads0915",
                "snippet": "brcWGS21 L 88.6 60.5 93.4 77.2 25.6 0 93.4",
                "notes": "Manual transcription of the Supplementary Fig. S2 BrcWGS21 low-MOI heatmap row; the visible cells show reduced inhibition, including 88.6% for MS2, 60.5% for T7, 93.4% for HK544, 77.2% for F13, 25.6% for Vs1, 0% for Px4, and 93.4% for Px5."
              },
              {
                "reference": "DOI:10.1126/science.ads0915",
                "snippet": "brcWGS21 H 95.6 98.2 84.9 98.0 24.9 78.4",
                "notes": "Manual transcription of the Supplementary Fig. S2 BrcWGS21 high-MOI heatmap row; the visible cells show reduced inhibition, including 95.6% for MS2, 98.2% for phi80, 84.9% for HK544, 98.0% for F13, 24.9% for Vs1, and 78.4% for Px4."
              }
            ]
          },
          {
            "subject": "brcwgs21_phage_resistance",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "brcwgs21_system_trait",
            "description": "BrcWGS21-linked phage resistance realizes the BrcWGS21 system possession trait.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.ads0915",
                "snippet": "brcWGS21 L 88.6 60.5 93.4 77.2 25.6 0 93.4",
                "notes": "Manual transcription of the Supplementary Fig. S2 BrcWGS21 low-MOI heatmap row; the visible cells show reduced inhibition, including 88.6% for MS2, 60.5% for T7, 93.4% for HK544, 77.2% for F13, 25.6% for Vs1, 0% for Px4, and 93.4% for Px5."
              },
              {
                "reference": "DOI:10.1126/science.ads0915",
                "snippet": "brcWGS21 H 95.6 98.2 84.9 98.0 24.9 78.4",
                "notes": "Manual transcription of the Supplementary Fig. S2 BrcWGS21 high-MOI heatmap row; the visible cells show reduced inhibition, including 95.6% for MS2, 98.2% for phi80, 84.9% for HK544, 98.0% for F13, 24.9% for Vs1, and 78.4% for Px4."
              },
              {
                "reference": "DOI:10.1126/science.ads0915",
                "snippet": "defense profiles of identified Bacteriophage Resistance integron Cassettes (BRiCs) against a panel of different phages",
                "notes": "Kieffer et al. classify positive integron cassettes as BRiCs and compare their defense profiles across a phage panel."
              }
            ]
          },
          {
            "subject": "brcwgs21_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "BrcWGS21 system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.ads0915",
                "snippet": "defense profiles of identified Bacteriophage Resistance integron Cassettes (BRiCs) against a panel of different phages",
                "notes": "Kieffer et al. classify positive integron cassettes as BRiCs and compare their defense profiles across a phage panel."
              },
              {
                "reference": "DOI:10.1126/science.ads0915",
                "snippet": "brc113\nbrc217\nbrc76\nbrcWGS21\nbrc22\nbrc23",
                "notes": "Kieffer et al. include brcWGS21 among identified BRiCs with predicted attC secondary structures."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| gcuWGS21 | 10\\.1126/science\\.ads0915 | Mobile integrons encode phage defense systems | ",
                "notes": "The pinned DefenseFinder article registry maps the gcuWGS21 source key to the Kieffer et al. mobile-integron BRiC paper."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "brcwgs21-defensefinder-model-gap",
        "prompt": "Resolve BrcWGS21 native host breadth, exact sensitive-phage breadth, molecular output, and DefenseFinder HMM/rules coverage before minting narrower BrcWGS21 mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Kieffer et al. identify brcWGS21 as a bacteriophage-resistance integron cassette, and the pinned DefenseFinder article registry maps the gcuWGS21 source key to the same Science article. The pinned HMM inventory and rules table have no exact gcuWGS21 or BrcWGS21 row, so the first-pass record leaves native-host breadth, profile boundaries, exact phage target breadth, and direct molecular output unresolved.",
        "evidence": [
          {
            "reference": "DOI:10.1126/science.ads0915",
            "snippet": "brcWGS21 L 88.6 60.5 93.4 77.2 25.6 0 93.4",
            "notes": "Manual transcription of the Supplementary Fig. S2 BrcWGS21 low-MOI heatmap row; the visible cells show reduced inhibition, including 88.6% for MS2, 60.5% for T7, 93.4% for HK544, 77.2% for F13, 25.6% for Vs1, 0% for Px4, and 93.4% for Px5."
          },
          {
            "reference": "DOI:10.1126/science.ads0915",
            "snippet": "brcWGS21 H 95.6 98.2 84.9 98.0 24.9 78.4",
            "notes": "Manual transcription of the Supplementary Fig. S2 BrcWGS21 high-MOI heatmap row; the visible cells show reduced inhibition, including 95.6% for MS2, 98.2% for phi80, 84.9% for HK544, 98.0% for F13, 24.9% for Vs1, and 78.4% for Px4."
          },
          {
            "reference": "DOI:10.1126/science.ads0915",
            "snippet": "defense profiles of identified Bacteriophage Resistance integron Cassettes (BRiCs) against a panel of different phages",
            "notes": "Kieffer et al. classify positive integron cassettes as BRiCs and compare their defense profiles across a phage panel."
          },
          {
            "reference": "DOI:10.1126/science.ads0915",
            "snippet": "brc113\nbrc217\nbrc76\nbrcWGS21\nbrc22\nbrc23",
            "notes": "Kieffer et al. include brcWGS21 among identified BRiCs with predicted attC secondary structures."
          },
          {
            "reference": "DOI:10.1126/science.ads0915",
            "snippet": "C941\npMBA brcWGS21\nK. pneumoniae\n\nKP5",
            "notes": "Kieffer et al. list brcWGS21 in the heterologous Klebsiella pneumoniae KP5 BRiC panel."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
            "snippet": "| gcuWGS21 | 10\\.1126/science\\.ads0915 | Mobile integrons encode phage defense systems | ",
            "notes": "The pinned DefenseFinder article registry maps the gcuWGS21 source key to the Kieffer et al. mobile-integron BRiC paper."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "notes": "A structured first-pass search of the pinned DefenseFinder HMM inventory found no exact gcuWGS21, brcWGS21, or BrcWGS21 row."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "A structured first-pass search of the pinned DefenseFinder rules table found no exact gcuWGS21, brcWGS21, or BrcWGS21 system row."
          }
        ],
        "attaches_to": [
          "causal_graphs#brcwgs21_integron_cassette_confers_phage_resistance"
        ],
        "posed_by": "codex",
        "posed_date": "2026-10-01"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-01T17:12:42Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted BrcWGS21 system as a DOI- and DefenseFinder-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; kept the graph at BRiC integron-cassette level because the pinned DefenseFinder article registry names gcuWGS21 but the pinned HMM inventory and rules table have no exact BrcWGS21 row; the replacement placeholder is reserved in proposals/metpo_traitmech_v397.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-01T17:12:43Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed BrcWGS21 system during initial curation and left canonical_examples empty because the sources support heterologous gcuWGS21/BrcWGS21 phage-resistance assays and a DefenseFinder gcuWGS21 article row, but not a direct named native microbial isolate exemplar with experimentally verified endogenous BrcWGS21 activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000210",
    "label": "BREX system",
    "definition": "A genomics trait describing possession of a bacteriophage exclusion defense system that uses host DNA methylation to discriminate self from non-self and inhibit phage DNA replication.",
    "definition_source": "DOI:10.15252/embj.201489455",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "bacteriophage exclusion",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.15252/embj.201489455"
      },
      {
        "synonym_text": "bacteriophage exclusion system",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1128/AEM.01001-19"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.15252/embj.201489455",
        "snippet": "We denote this novel defense system BREX (Bacteriophage Exclusion) and show that it allows phage adsorption but blocks phage DNA replication",
        "notes": "Goldfarb et al. define BREX as a bacteriophage-exclusion defense system and distinguish its post-adsorption block from receptor-loss and phage-adsorption phenotypes."
      },
      {
        "reference": "DOI:10.15252/embj.201489455",
        "snippet": "methylation on non-palindromic TAGGAG motifs in the bacterial genome guides self/non-self discrimination and is essential for the defensive function of the BREX system",
        "notes": "Goldfarb et al. support the methylation-based self/non-self discrimination clause in the local definition."
      },
      {
        "reference": "DOI:10.15252/embj.201489455",
        "snippet": "confers resistance to a broad range of phages, including both virulent and temperate ones",
        "notes": "A Bacillus cereus six-gene BREX cassette conferred broad phage resistance when integrated into Bacillus subtilis, supporting BREX as a locus-encoded system trait."
      },
      {
        "reference": "DOI:10.1128/AEM.01001-19",
        "snippet": "The bacteriophage exclusion (BREX) system is a novel prokaryotic defense system against bacteriophages",
        "notes": "Hui et al. independently define bacteriophage exclusion as a prokaryotic defense system against bacteriophages."
      },
      {
        "reference": "DOI:10.1128/AEM.01001-19",
        "snippet": "identified a complete cassette of a classic type I BREX system",
        "notes": "Hui et al. identified a complete type I BREX cassette in the Lactobacillus casei Zhang genome."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:498216",
        "taxon_label": "Lacticaseibacillus casei str. Zhang",
        "note": "The strain historically named Lactobacillus casei Zhang carries a complete type I BREX cassette whose pglX component is required for BREX-linked methylation and plasmid restriction phenotypes.",
        "reference": "DOI:10.1128/AEM.01001-19"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "brex_methylation_antiphage_defense",
        "title": "BREX methylation guides antiphage discrimination",
        "description": "Evidence-backed causal sketch linking a BREX locus to host-DNA methylation, self/non-self discrimination, and blocked phage-DNA replication.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "The graph captures Goldfarb et al.'s experimentally supported host-methylation and post-adsorption phage-replication block without asserting that the molecular coupling between marked host DNA and blocked phage DNA is fully resolved.",
        "nodes": [
          {
            "node_id": "phage_dna_replication",
            "label": "phage DNA replication",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Replication of invading bacteriophage DNA after host cell entry."
          },
          {
            "node_id": "brex_locus",
            "label": "BREX locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "Multi-gene bacteriophage-exclusion cassette encoding the BREX defense system."
          },
          {
            "node_id": "pglx_methyltransferase",
            "label": "PglX adenine methyltransferase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Adenine-specific DNA methyltransferase component of type I BREX systems.",
            "grounding": "InterPro:IPR047939",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:P0DQP1",
                "protein_label": "Adenine-specific methyltransferase PglX",
                "gene_symbol": "pglX",
                "taxon_id": "NCBITaxon:498216",
                "taxon_label": "Lacticaseibacillus casei str. Zhang",
                "entry_status": "REVIEWED",
                "retrieved_on": "2026-09-15",
                "entry_version": 19,
                "sequence_version": 1,
                "role": "L. casei Zhang PglX methylates BREX recognition motifs as the type I BREX adenine methyltransferase.",
                "evidence": [
                  {
                    "reference": "DOI:10.1128/AEM.01001-19",
                    "snippet": "this work confirmed that the L. casei Zhang pglX gene product is a functional adenine MTase that is an essential component of a type I BREX system",
                    "notes": "Hui et al. experimentally disrupted L. casei Zhang pglX; UniProt verifies the reviewed PglX accession."
                  }
                ]
              }
            ]
          },
          {
            "node_id": "host_dna_methylation",
            "label": "BREX host DNA methylation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Methylation of host DNA at BREX recognition motifs."
          },
          {
            "node_id": "self_nonself_discrimination",
            "label": "BREX self/non-self discrimination",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Methylation-guided discrimination of host DNA from unmodified invading phage DNA."
          },
          {
            "node_id": "brex_system_trait",
            "label": "BREX system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000210",
            "description": "Possession of a genome-encoded bacteriophage exclusion defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "brex_locus",
            "predicate": "encodes",
            "object": "pglx_methyltransferase",
            "description": "Type I BREX loci encode PglX adenine methyltransferases.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.01001-19",
                "snippet": "identified a complete cassette of a classic type I BREX system",
                "notes": "The complete L. casei Zhang type I BREX cassette contains the pglX locus encoding PglX."
              }
            ]
          },
          {
            "subject": "pglx_methyltransferase",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "host_dna_methylation",
            "description": "PglX methyltransferase activity methylates BREX recognition motifs in host DNA.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.01001-19",
                "snippet": "this work confirmed that the L. casei Zhang pglX gene product is a functional adenine MTase",
                "notes": "Hui et al. showed that pglX disruption removed m6A methylation at the recognition motif in L. casei Zhang."
              }
            ]
          },
          {
            "subject": "host_dna_methylation",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "self_nonself_discrimination",
            "description": "Host DNA methylation guides BREX self/non-self discrimination.",
            "evidence": [
              {
                "reference": "DOI:10.15252/embj.201489455",
                "snippet": "methylation on non-palindromic TAGGAG motifs in the bacterial genome guides self/non-self discrimination",
                "notes": "Goldfarb et al. established methylation as the self/non-self mark for the characterized BREX system."
              }
            ]
          },
          {
            "subject": "self_nonself_discrimination",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "brex_system_trait",
            "description": "Methylation-guided self/non-self discrimination realizes the BREX defense trait.",
            "evidence": [
              {
                "reference": "DOI:10.15252/embj.201489455",
                "snippet": "is essential for the defensive function of the BREX system",
                "notes": "Goldfarb et al. established methylation-based self/non-self discrimination as essential to BREX defense."
              }
            ]
          },
          {
            "subject": "self_nonself_discrimination",
            "predicate": "mitigates",
            "predicate_id": "METPO:2007407",
            "object": "phage_dna_replication",
            "description": "BREX methylation-guided discrimination blocks replication of unmethylated phage DNA.",
            "evidence": [
              {
                "reference": "DOI:10.15252/embj.201489455",
                "snippet": "allows phage adsorption but blocks phage DNA replication",
                "notes": "The edge records the observed post-adsorption replication block; the exact biochemical coupling remains a molecular knowledge gap."
              }
            ]
          },
          {
            "subject": "brex_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "BREX possession is a methylation-based phage-defense system.",
            "evidence": [
              {
                "reference": "DOI:10.15252/embj.201489455",
                "snippet": "We denote this novel defense system BREX (Bacteriophage Exclusion)",
                "notes": "Goldfarb et al. place BREX in the phage defense system family."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "brex-molecular-coupling-gap",
        "prompt": "Resolve the molecular coupling between BREX-guided host methylation and phage-DNA replication arrest before adding more specific BREX mechanism edges.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Goldfarb et al. showed that methylation is essential and that BREX blocks phage DNA replication after adsorption, but the exact biochemical coupling between the methylation mark and blocked phage replication remains insufficient for a more specific causal edge.",
        "posed_by": "codex",
        "posed_date": "2026-09-15"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-15T08:40:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted BREX system as a DOI-backed GENOMICS TraitRecord under the phage defense system parent after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v87.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000307",
    "label": "Brig1 system",
    "definition": "A phage defense system in which an organism possesses a brig1-family locus whose encoded DNA glycosylase can excise alpha-glucosyl-hydroxymethylcytosine nucleobases from T-even bacteriophage DNA, generate abasic sites, and inhibit viral DNA replication.",
    "definition_source": "DOI:10.1038/s41586-024-07329-9",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "Brig1",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1038/s41586-024-07329-9"
      },
      {
        "synonym_text": "bacteriophage replication inhibition DNA glycosylase 1",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1038/s41586-024-07329-9"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/s41586-024-07329-9",
        "snippet": "Following this approach, we identified Brig1, a DNA glycosylase that excises \u03b1-glucosyl-hydroxymethylcytosine nucleobases from the bacteriophage T4 genome to generate abasic sites and inhibit viral replication",
        "notes": "Hallinan et al. identify Brig1 as a phage DNA-targeting DNA glycosylase."
      },
      {
        "reference": "DOI:10.1038/s41586-024-07329-9",
        "snippet": "Brig1 homologues that provide immunity against T-even phages are present in multiple phage defence loci across distinct clades of bacteria",
        "notes": "Hallinan et al. support modelling Brig1 as a bacterial phage-defence locus family rather than as one cloned environmental DNA insert."
      },
      {
        "reference": "DOI:10.1038/s41586-024-07329-9",
        "snippet": "This result demonstrates that gene c not only inhibits T4 DNA replication but also causes a slight and gradual depletion of the phage DNA within the infected population",
        "notes": "Hallinan et al. connect the gene later named brig1 to inhibited T4 DNA replication in infected cells."
      },
      {
        "reference": "DOI:10.1038/s41586-024-07329-9",
        "snippet": "We named this gene bacteriophage replication inhibition DNA glycosylase 1 (brig1)",
        "notes": "Hallinan et al. explicitly expand brig1 as bacteriophage replication inhibition DNA glycosylase 1."
      },
      {
        "reference": "DOI:10.1038/s41586-024-07329-9",
        "snippet": "Together, these data demonstrate that Brig1 targets \u03b1-glucosylated hmC nucleobases in the viral DNA to provide defence against T4",
        "notes": "Hallinan et al. show that Brig1 defense is specific to alpha-glucosylated hydroxymethylcytosine in phage DNA."
      },
      {
        "reference": "DOI:10.1038/s41586-024-07329-9",
        "snippet": "Together, these results demonstrate that Brig1 is a DNA glycosylase that excises \u03b1-glucosyl-hmC nucleobases from ssDNA to generate abasic sites",
        "notes": "Hallinan et al. directly verify that Brig1 DNA glycosylase activity creates abasic sites on alpha-glucosyl-hmC-containing substrates."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "Brig1 | 10\\.1038/s41586-024-07329-9 | DNA glycosylases provide antiviral defence in prokaryotes",
        "notes": "The DefenseFinder article registry maps the named Brig1 model namespace to the Hallinan et al. Brig1 DNA-glycosylase paper."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| Brig1__Brig1                                     |                                                  | Brig1                  | Custom                  | 20     |",
        "notes": "The DefenseFinder HMM inventory records Brig1__Brig1 under the Brig1 model namespace."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| Brig1__ADP_ribosyl                               |                                                  | Brig1                  | Custom                  | 20     |",
        "notes": "The DefenseFinder HMM inventory records Brig1__ADP_ribosyl under the Brig1 model namespace."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "brig1_locus_restricts_t_even_phages",
        "title": "Brig1 loci restrict T-even phage propagation",
        "description": "Conservative locus-level sketch linking a brig1-family DefenseFinder locus to halted T4-like phage replication, restricted T-even phage propagation, and the Brig1 phage-defense-system trait.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Brig1 as a named DefenseFinder DNA-glycosylase phage-defense system at locus level and deliberately defers a protein-resolved glycosylase mechanism. Hallinan et al. characterized the prototype Brig1 DNA glycosylase, alpha-glucosyl-hmC base excision, and abasic-site generation, but the natural host, accession-level Brig1-family proteins, broader substrate specificity, and the relationship of the DefenseFinder Brig1__ADP_ribosyl profile to characterized Brig1 activity remain unresolved.",
        "nodes": [
          {
            "node_id": "brig1_locus",
            "label": "brig1 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A brig1-family phage-defense locus represented by the DefenseFinder Brig1 model namespace."
          },
          {
            "node_id": "halted_phage_replication",
            "label": "halted phage replication",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Arrest of T-even bacteriophage DNA replication downstream of Brig1 locus expression."
          },
          {
            "node_id": "restricted_phage_propagation",
            "label": "restricted phage propagation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced completion of phage propagation in a Brig1-containing infected host cell."
          },
          {
            "node_id": "brig1_system_trait",
            "label": "Brig1 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000307",
            "description": "Possession of a genome-encoded Brig1 DNA-glycosylase phage-defense system."
          },
          {
            "node_id": "phage_defense_system_trait",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "brig1_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "halted_phage_replication",
            "description": "Expression of the gene later named brig1 inhibits T4 phage DNA replication, and DefenseFinder catalogs Brig1 profiles for Brig1-family loci.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41586-024-07329-9",
                "snippet": "gene c not only inhibits T4 DNA replication but also causes a slight and gradual depletion of the phage DNA within the infected population",
                "notes": "Hallinan et al. connect brig1 expression to inhibited T4 DNA replication in infected cells."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| Brig1__Brig1                                     |                                                  | Brig1                  | Custom                  | 20     |",
                "notes": "The DefenseFinder HMM inventory records Brig1__Brig1 under the Brig1 model namespace."
              }
            ]
          },
          {
            "subject": "halted_phage_replication",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "restricted_phage_propagation",
            "description": "Brig1-associated inhibition of T4-like phage replication restricts T-even phage propagation after infection.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41586-024-07329-9",
                "snippet": "Following this approach, we identified Brig1, a DNA glycosylase that excises \u03b1-glucosyl-hydroxymethylcytosine nucleobases from the bacteriophage T4 genome to generate abasic sites and inhibit viral replication. Brig1 homologues that provide immunity against T-even phages are present in multiple phage defence loci across distinct clades of bacteria",
                "notes": "Hallinan et al. connect Brig1-associated T4 replication inhibition to the broader Brig1-family T-even immunity phenotype."
              }
            ]
          },
          {
            "subject": "restricted_phage_propagation",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "brig1_system_trait",
            "description": "Restriction of T-even phage propagation realizes the Brig1 system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41586-024-07329-9",
                "snippet": "Brig1 homologues that provide immunity against T-even phages are present in multiple phage defence loci across distinct clades of bacteria",
                "notes": "Hallinan et al. frame Brig1 homologues as a bacterial phage-defense locus family."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Brig1 | 10\\.1038/s41586-024-07329-9 | DNA glycosylases provide antiviral defence in prokaryotes",
                "notes": "The DefenseFinder article registry maps the named Brig1 model namespace to the Hallinan et al. Brig1 DNA-glycosylase paper."
              }
            ]
          },
          {
            "subject": "brig1_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system_trait",
            "description": "Brig1 system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41586-024-07329-9",
                "snippet": "Brig1, a previously unknown anti-phage defence system with homologues across distinct clades of bacteria",
                "notes": "The Hallinan et al. editor summary places Brig1 in the anti-phage defense system class."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "brig1-natural-host-and-profile-gap",
        "prompt": "Resolve natural Brig1 host taxa, broader Brig1-family specificity, and the Brig1__ADP_ribosyl DefenseFinder profile before minting narrower Brig1 children, adding canonical examples, or curating the protein-resolved glycosylase mechanism.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Hallinan et al. functionally isolated the first brig1 gene from a soil metagenomic fragment rather than a sequenced natural isolate, and they showed that experimentally tested Brig1 homologues can protect against T-even phages. The first TraitRecord therefore covers Brig1-family antiphage DNA-glycosylase-system possession at locus level while leaving natural host exemplars, accession-level Brig1-family proteins, the protein-grounded glycosylase mechanism, the full sequence-level system architecture, and the relationship between the DefenseFinder Brig1__Brig1 and Brig1__ADP_ribosyl profiles to separate subtype review.",
        "evidence": [
          {
            "reference": "DOI:10.1038/s41586-024-07329-9",
            "snippet": "To uncover novel anti-phage defence systems present in unsequenced bacterial genomes, we screened an eDNA library generated in an earlier study",
            "notes": "Hallinan et al. functionally isolated the first Brig1 source fragment from an environmental DNA library rather than a named natural organism."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| Brig1__ADP_ribosyl                               |                                                  | Brig1                  | Custom                  | 20     |",
            "notes": "The DefenseFinder HMM inventory records Brig1__ADP_ribosyl under the Brig1 model namespace."
          }
        ],
        "attaches_to": [
          "causal_graphs#brig1_locus_restricts_t_even_phages"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-20"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-20T10:37:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Brig1 system as a DOI-backed GENOMICS TraitRecord under the phage defense system parent after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v184.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-20T11:12:00Z",
        "curator": "codex",
        "action": "ADDRESSED_PR_REVIEW",
        "changes": "Resolved PR #1130 review issues #1131, #1132, #1133, and #1134 by narrowing the Brig1 graph to a locus-level DefenseFinder sketch, quoting the brig1 naming sentence, removing weak edge evidence, and reusing halted phage replication instead of adding a singleton replication node.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000270",
    "label": "Brigantia system",
    "definition": "A phage defense system in which an organism possesses a Brigantia locus represented by a VCA0419 profile that can protect bacteria from bacteriophage infection.",
    "definition_source": "DOI:10.1126/science.ads0768",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "Brigantia",
        "synonym_type": "EXACT_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      },
      {
        "synonym_text": "VCA0419",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1126/science.ads0768",
        "snippet": "nearly 10% of the integron cassettes in the pandemic Vibrio cholerae strain encode novel antiphage functions",
        "notes": "Darracq et al. support treating the newly discovered Vibrio cholerae SCI antiphage cassettes as bacterial anti-phage systems."
      },
      {
        "reference": "DOI:10.1126/science.ads0768",
        "snippet": "Most of these novel systems have little or no similarity to previously known ones, with several providing defense through cell lysis or growth arrest",
        "notes": "Darracq et al. support a conservative system record that does not assert a resolved Brigantia trigger, effector output, or universal pathway."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "Brigantia | 10\\.1126/science\\.ads0768 | Sedentary chromosomal integrons as biobanks of bacterial antiphage defense systems",
        "notes": "The DefenseFinder model registry maps the named Brigantia system to the Darracq et al. SCI antiphage-system paper."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "Brigantia__VCA0419                               |                                                  | Brigantia",
        "notes": "The DefenseFinder HMM inventory records VCA0419 in the Brigantia model namespace."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "brigantia_locus_restricts_phage",
        "title": "Brigantia loci confer bacterial phage defense",
        "description": "Conservative system-level sketch linking possession of a Brigantia locus to restricted bacteriophage propagation without asserting the unresolved phage trigger or molecular output.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Brigantia as a named SCI-derived anti-phage system with a VCA0419 DefenseFinder profile while leaving its phage trigger, molecular substrate, antiviral effector output, and subtype breadth unresolved.",
        "nodes": [
          {
            "node_id": "brigantia_locus",
            "label": "Brigantia locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A Brigantia anti-phage defense locus represented in DefenseFinder by a VCA0419 profile."
          },
          {
            "node_id": "restricted_phage_propagation",
            "label": "restricted phage propagation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced propagation of bacteriophage in cells carrying the Brigantia system."
          },
          {
            "node_id": "brigantia_system_trait",
            "label": "Brigantia system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000270",
            "description": "Possession of a genome-encoded Brigantia phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "brigantia_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "restricted_phage_propagation",
            "description": "DefenseFinder maps Brigantia to an SCI anti-phage-system discovery paper and represents Brigantia loci through the VCA0419 component profile.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.ads0768",
                "snippet": "nearly 10% of the integron cassettes in the pandemic Vibrio cholerae strain encode novel antiphage functions",
                "notes": "Darracq et al. describe the newly discovered antiphage-system cohort that the DefenseFinder Brigantia registry row maps to the Brigantia system."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "Brigantia__VCA0419                               |                                                  | Brigantia",
                "notes": "The DefenseFinder HMM inventory supports VCA0419 as the Brigantia component profile."
              }
            ]
          },
          {
            "subject": "restricted_phage_propagation",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "brigantia_system_trait",
            "description": "Brigantia-mediated phage restriction realizes the Brigantia system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.ads0768",
                "snippet": "Most of these novel systems have little or no similarity to previously known ones",
                "notes": "Darracq et al. place the Brigantia discovery cohort in a set of novel bacterial systems that protect against phages."
              }
            ]
          },
          {
            "subject": "brigantia_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Brigantia system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Brigantia | 10\\.1126/science\\.ads0768 | Sedentary chromosomal integrons as biobanks of bacterial antiphage defense systems",
                "notes": "DefenseFinder associates Brigantia with the Darracq et al. bacterial antiphage-system paper."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "brigantia-mechanism-gap",
        "prompt": "Resolve Brigantia phage triggers and effector outputs before minting narrower Brigantia mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Darracq et al. and DefenseFinder support Brigantia as a named anti-phage system with a VCA0419 profile, but the trigger, molecular substrate, antiviral effector output, and subtype-specific mechanism are not resolved enough here to assert a narrower mechanistic child trait.",
        "attaches_to": [
          "causal_graphs#brigantia_locus_restricts_phage"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-19"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-19T07:32:10Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Brigantia system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v147.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000301",
    "label": "BstA system",
    "definition": "An abortive infection system in which an organism possesses a BstA-family phage-defense locus whose encoded BstA protein can suppress lytic phage DNA replication and whose cognate anti-BstA aba element can self-immunize the encoding prophage from BstA activity.",
    "definition_source": "DOI:10.1016/j.chom.2021.09.002",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000214"
    ],
    "synonyms": [
      {
        "synonym_text": "BstA",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1016/j.chom.2021.09.002",
        "snippet": "we identify BstA, a family of prophage-encoded phage-defense proteins in diverse Gram-negative bacteria",
        "notes": "Owen et al. name BstA as a family of prophage-encoded phage-defense proteins."
      },
      {
        "reference": "DOI:10.1016/j.chom.2021.09.002",
        "snippet": "the BstA protein confers effective population-level defense against exogenous phage infection via abortive infection",
        "notes": "Owen et al. support BstA as an abortive-infection phage-defense system."
      },
      {
        "reference": "DOI:10.1016/j.chom.2021.09.002",
        "snippet": "demonstrating that the BstA protein mediates defense against phage P22",
        "notes": "Owen et al. show that phage resistance against P22 is BstA-protein dependent."
      },
      {
        "reference": "DOI:10.1016/j.chom.2021.09.002",
        "snippet": "BstA provides phage defense at the population level and prevents the spread of phage epidemics",
        "notes": "Owen et al. connect BstA activity to suppression of phage epidemics at population level."
      },
      {
        "reference": "DOI:10.1016/j.chom.2021.09.002",
        "snippet": "phage DNA replication is strongly suppressed by BstA, but replication can be rescued by the aba element",
        "notes": "Owen et al. support the direct phage-DNA-replication output of BstA and suppression by the cognate aba self-immunity element."
      },
      {
        "reference": "DOI:10.1016/j.chom.2021.09.002",
        "snippet": "each bstA locus contains a cognate aba element that is inactive against variant BstA proteins",
        "notes": "Owen et al. show that aba self-immunity is cognate to its co-encoded BstA variant."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "BstA | 10\\.1101/2020\\.07\\.13\\.199331 | Prophage-encoded phage defense proteins with cognate self-immunity",
        "notes": "The DefenseFinder article registry maps the named BstA system to the Owen et al. BstA preprint."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "BstA__BstA                                       | BstA__BstA                                       | BstA",
        "notes": "The DefenseFinder HMM inventory records a BstA profile for BstA__BstA in the BstA model namespace."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "BstA\tBstA\t1\t1\tBstA__BstA",
        "notes": "The DefenseFinder rules table models BstA as a one-component system requiring the BstA__BstA profile."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:568708",
        "taxon_label": "Salmonella enterica subsp. enterica serovar Typhimurium str. D23580",
        "note": "Owen et al. studied BstA in the BTP1 prophage of Salmonella enterica serovar Typhimurium ST313 strain D23580 and showed that BstA mediates defense against Salmonella phage P22.",
        "reference": "DOI:10.1016/j.chom.2021.09.002"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "bsta_locus_suppresses_phage_dna_replication",
        "title": "BstA loci suppress lytic phage DNA replication through abortive infection",
        "description": "Conservative system-level sketch linking possession of a BstA phage-defense locus to suppressed lytic phage DNA replication, cognate aba-mediated self-immunity, and the BstA system trait without asserting the unresolved direct phage trigger, BstA molecular target, or mechanism of aba-mediated self-immunity.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures BstA as a named abortive-infection system with a DefenseFinder BstA profile while leaving the direct trigger of BstA localization, the direct DNA replication target, the physical form of the BstA-aba interaction, and the molecular basis for cognate aba specificity unresolved.",
        "nodes": [
          {
            "node_id": "bsta_locus",
            "label": "BstA locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A BstA-family phage-defense locus carrying a BstA coding sequence."
          },
          {
            "node_id": "aba_element",
            "label": "aba self-immunity element",
            "node_type": "GENETIC_ELEMENT",
            "description": "A cognate anti-BstA aba element carried alongside BstA in a BstA-encoding prophage."
          },
          {
            "node_id": "suppressed_encoding_prophage_dna_replication",
            "label": "suppressed encoding-prophage DNA replication",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "BstA-mediated suppression of DNA replication by the BstA-encoding prophage in an aba-sensitive context."
          },
          {
            "node_id": "suppressed_lytic_phage_dna_replication",
            "label": "suppressed lytic phage DNA replication",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Strong suppression of infecting lytic-phage DNA replication by BstA activity."
          },
          {
            "node_id": "bsta_system_trait",
            "label": "BstA system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000301",
            "description": "Possession of a genome-encoded BstA abortive-infection phage-defense system."
          },
          {
            "node_id": "abortive_infection_system",
            "label": "abortive infection system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000214",
            "description": "Possession of a bacteriophage abortive-infection defense system."
          }
        ],
        "edges": [
          {
            "subject": "bsta_locus",
            "predicate": "includes",
            "predicate_id": "biolink:has_part",
            "object": "aba_element",
            "description": "BstA loci contain a cognate anti-BstA aba self-immunity element.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.chom.2021.09.002",
                "snippet": "each bstA locus contains a cognate aba element that is inactive against variant BstA proteins",
                "notes": "Owen et al. show that BstA loci carry cognate aba elements."
              }
            ]
          },
          {
            "subject": "bsta_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "suppressed_lytic_phage_dna_replication",
            "description": "Owen et al. show that BstA can strongly suppress lytic phage DNA replication, and DefenseFinder catalogs a one-component BstA model.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.chom.2021.09.002",
                "snippet": "phage DNA replication is strongly suppressed by BstA",
                "notes": "Owen et al. link BstA to strong suppression of phage DNA replication."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "BstA__BstA                                       | BstA__BstA                                       | BstA",
                "notes": "The DefenseFinder HMM inventory records a BstA profile for BstA__BstA in the BstA model namespace."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "BstA\tBstA\t1\t1\tBstA__BstA",
                "notes": "The DefenseFinder rules table models BstA as a one-component system requiring the BstA__BstA profile."
              }
            ]
          },
          {
            "subject": "bsta_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "suppressed_encoding_prophage_dna_replication",
            "description": "BstA can suppress DNA replication by an aba-sensitive encoding prophage before cognate aba self-immunity rescues replication.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.chom.2021.09.002",
                "snippet": "phage DNA replication is strongly suppressed by BstA, but replication can be rescued by the aba element",
                "notes": "Owen et al. show that BstA supplies the suppression that the cognate aba element counteracts."
              }
            ]
          },
          {
            "subject": "aba_element",
            "predicate": "prevents",
            "predicate_id": "RO:0002212",
            "object": "suppressed_encoding_prophage_dna_replication",
            "description": "Owen et al. show that the cognate anti-BstA aba element rescues its encoding prophage's DNA replication from BstA-mediated suppression.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.chom.2021.09.002",
                "snippet": "phage DNA replication is strongly suppressed by BstA, but replication can be rescued by the aba element",
                "notes": "Owen et al. show that aba counteracts BstA-mediated suppression of phage DNA replication."
              },
              {
                "reference": "DOI:10.1016/j.chom.2021.09.002",
                "snippet": "each bstA locus contains a cognate aba element that is inactive against variant BstA proteins",
                "notes": "Owen et al. show that aba self-immunity is specific to its cognate co-encoded BstA variant."
              }
            ]
          },
          {
            "subject": "suppressed_lytic_phage_dna_replication",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "bsta_system_trait",
            "description": "BstA-mediated suppression of lytic-phage DNA replication realizes BstA-system abortive-infection defense.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.chom.2021.09.002",
                "snippet": "We propose that BstA protein mediates abortive infection by suppressing phage DNA replication",
                "notes": "Owen et al. propose phage-DNA-replication suppression as the mechanism by which BstA mediates abortive infection."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "BstA | 10\\.1101/2020\\.07\\.13\\.199331 | Prophage-encoded phage defense proteins with cognate self-immunity",
                "notes": "The DefenseFinder article registry maps the named BstA system to the Owen et al. BstA preprint."
              }
            ]
          },
          {
            "subject": "bsta_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "abortive_infection_system",
            "description": "BstA system possession is an abortive-infection system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.chom.2021.09.002",
                "snippet": "we propose that BstA is an abortive infection system",
                "notes": "Owen et al. classify BstA as an abortive-infection system."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "bsta-mechanism-gap",
        "prompt": "Resolve the direct phage trigger of BstA localization, the direct DNA-replication target, the physical BstA-aba interaction, and the basis of cognate aba specificity before minting narrower BstA-aba mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Owen et al. and DefenseFinder support BstA as a named abortive-infection system with a BstA HMM profile and a cognate aba self-immunity element, but the direct phage trigger that recruits BstA to phage DNA, the precise target by which BstA suppresses lytic phage DNA replication, the physical interaction between aba DNA and BstA, and the molecular basis of BstA-aba specificity remain unresolved.",
        "attaches_to": [
          "causal_graphs#bsta_locus_suppresses_phage_dna_replication"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-20"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-20T04:37:48Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted BstA system as a DOI-backed GENOMICS TraitRecord under the abortive infection system parent after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v178.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-20T05:13:00Z",
        "curator": "codex",
        "action": "ADDRESS_PR_REVIEW",
        "changes": "Added a Salmonella enterica serovar Typhimurium D23580 canonical example and represented the anti-BstA aba element as an explicit graph node with a supported rescue edge after the PR 1111 adversarial review filed issues 1112 and 1113.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-20T05:25:30Z",
        "curator": "codex",
        "action": "ADDRESS_PR_REVIEW",
        "changes": "Separated aba self-immunity for the BstA-encoding prophage from BstA-mediated suppression of incoming lytic phage DNA replication after the PR 1111 adversarial review filed issue 1114.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-20T05:42:00Z",
        "curator": "codex",
        "action": "ADDRESS_PR_REVIEW",
        "changes": "Added an explicit BstA locus contribution edge to the aba-sensitive encoding-prophage DNA replication suppression node after the PR 1111 adversarial review filed issue 1116.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000248",
    "label": "Bunzi system",
    "definition": "A phage defense system in which an organism possesses a two-component Bunzi locus represented by BnzA and BnzB profiles that can protect bacteria from bacteriophage infection.",
    "definition_source": "DOI:10.1016/j.chom.2022.09.017",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "Bunzi",
        "synonym_type": "EXACT_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1016/j.chom.2022.09.017",
        "snippet": "discovery of 21 defense systems that protect bacteria from phages, based on computational genomic analyses and phage-infection experiments",
        "notes": "Millman et al. report the computational and experimental cohort that DefenseFinder cites for Bunzi as a bacterial anti-phage system."
      },
      {
        "reference": "DOI:10.1101/2022.05.11.491447",
        "snippet": "discovery of 21 new defense systems that protect bacteria from phages, based on computational genomic analyses and phage infection experiments",
        "notes": "The bioRxiv version of Millman et al. independently carries the 21-system discovery claim linked from DefenseFinder's Bunzi article registry."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "Bunzi | 10\\.1101/2022\\.05\\.11\\.491447 | An expanding arsenal of immune systems that protect bacteria from phages",
        "notes": "The DefenseFinder model registry maps the named Bunzi system to the Millman et al. antiphage-system discovery preprint."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "Bunzi__BnzA, Bunzi__BnzB",
        "notes": "The DefenseFinder rules table models Bunzi as a two-member system with BnzA and BnzB mandatory profiles."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "Bunzi__BnzA                                      | Bunzi__BnzA                                      | Bunzi",
        "notes": "The DefenseFinder HMM inventory records BnzA as a Bunzi profile."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "Bunzi__BnzB                                      | Bunzi__BnzB                                      | Bunzi",
        "notes": "The DefenseFinder HMM inventory records BnzB as a Bunzi profile."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "bunzi_locus_restricts_phage",
        "title": "Bunzi loci confer bacterial phage defense",
        "description": "Conservative system-level sketch linking possession of a Bunzi locus to restricted bacteriophage propagation without asserting the unresolved phage trigger or molecular output.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Bunzi as a named anti-phage system with BnzA and BnzB DefenseFinder profiles while leaving its phage trigger, molecular substrate, antiviral effector output, and subtype breadth unresolved.",
        "nodes": [
          {
            "node_id": "bunzi_locus",
            "label": "Bunzi locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A Bunzi anti-phage defense locus containing BnzA and BnzB components."
          },
          {
            "node_id": "restricted_phage_propagation",
            "label": "restricted phage propagation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced propagation of bacteriophage in cells carrying the Bunzi system."
          },
          {
            "node_id": "bunzi_system_trait",
            "label": "Bunzi system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000248",
            "description": "Possession of a genome-encoded Bunzi phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "bunzi_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "restricted_phage_propagation",
            "description": "DefenseFinder maps Bunzi to a bacterial anti-phage-system discovery preprint and represents Bunzi loci through BnzA and BnzB component profiles.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.chom.2022.09.017",
                "snippet": "discovery of 21 defense systems that protect bacteria from phages",
                "notes": "Millman et al. describe the anti-phage discovery cohort that the DefenseFinder Bunzi registry row maps to the Bunzi system."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Bunzi | 10\\.1101/2022\\.05\\.11\\.491447 | An expanding arsenal of immune systems that protect bacteria from phages",
                "notes": "The DefenseFinder registry maps Bunzi itself to the Millman et al. bacterial antiphage-system discovery preprint."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "Bunzi__BnzA, Bunzi__BnzB",
                "notes": "The DefenseFinder rules table supports BnzA and BnzB as the mandatory Bunzi system profiles."
              }
            ]
          },
          {
            "subject": "restricted_phage_propagation",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "bunzi_system_trait",
            "description": "Bunzi-mediated phage restriction realizes the Bunzi system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.chom.2022.09.017",
                "snippet": "discovery of 21 defense systems that protect bacteria from phages",
                "notes": "Millman et al. place the Bunzi discovery cohort in the set of bacterial systems that protect against phages."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Bunzi | 10\\.1101/2022\\.05\\.11\\.491447 | An expanding arsenal of immune systems that protect bacteria from phages",
                "notes": "DefenseFinder records Bunzi as a named system from the Millman et al. antiphage discovery preprint."
              }
            ]
          },
          {
            "subject": "bunzi_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Bunzi system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "An expanding arsenal of immune systems that protect bacteria from phages",
                "notes": "DefenseFinder associates Bunzi with the Millman et al. bacterial antiphage-system discovery paper."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "bunzi-mechanism-gap",
        "prompt": "Resolve Bunzi phage triggers and effector outputs before minting narrower Bunzi mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Millman et al. and DefenseFinder support Bunzi as a named anti-phage system with BnzA and BnzB profiles, but the trigger, molecular substrate, antiviral effector output, and subtype-specific mechanism are not resolved enough here to assert a narrower mechanistic child trait.",
        "attaches_to": [
          "causal_graphs#bunzi_locus_restricts_phage"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-18"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-18T19:26:06Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Bunzi system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v125.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000298",
    "label": "Butters gp30-gp31 system",
    "definition": "A phage defense system in which an organism possesses a Butters gp30-gp31 locus that can protect bacteria from bacteriophage infection.",
    "definition_source": "DOI:10.1128/mSystems.00534-20",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "Butters_gp30_gp31",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1128/mSystems.00534-20",
        "snippet": "we unveil a novel defense mechanism in cluster N prophage Butters",
        "notes": "Mageeney et al. identify the Butters prophage as encoding a new heterotypic phage-defense mechanism."
      },
      {
        "reference": "DOI:10.1128/mSystems.00534-20",
        "snippet": "we show that Butters genes located in the central region of the genome play a key role in the defense against heterotypic viral attack",
        "notes": "Mageeney et al. support central Butters genes as contributors to prophage-mediated antiviral defense."
      },
      {
        "reference": "DOI:10.1128/mSystems.00534-20",
        "snippet": "Our study suggests that a two-component system, articulated by interactions between protein products of genes 30 and 31, confers defense against heterotypic phage infection by PurpleHaze (cluster A/subcluster A3) or Alma (cluster A/subcluster A9)",
        "notes": "Mageeney et al. connect Butters genes 30 and 31 to a two-component system that defends against PurpleHaze and Alma phage infection."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "Butters_gp30_gp31 | 10\\.1128/mSystems\\.00534-20 | Mycobacterium phage Butters-encoded proteins contribute to host defense against viral attack",
        "notes": "The DefenseFinder model registry maps the named Butters_gp30_gp31 system to the Mageeney et al. Butters-defense paper."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "Butters_gp30_gp31__Butters_gp30                  | Butters_gp30_gp31__Butters_gp30                  | Butters_gp30_gp31",
        "notes": "The DefenseFinder HMM inventory records a Butters gp30-gp31 profile for Butters_gp30_gp31__Butters_gp30 in the Butters_gp30_gp31 model namespace."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "Butters_gp30_gp31__Butters_gp31                  | Butters_gp30_gp31__Butters_gp31                  | Butters_gp30_gp31",
        "notes": "The DefenseFinder HMM inventory records a Butters gp30-gp31 profile for Butters_gp30_gp31__Butters_gp31 in the Butters_gp30_gp31 model namespace."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "Butters_gp30_gp31\tButters_gp30_gp31\t2\t2\tButters_gp30_gp31__Butters_gp30, Butters_gp30_gp31__Butters_gp31",
        "notes": "The DefenseFinder rules table models Butters_gp30_gp31 as a two-component system requiring Butters_gp30 and Butters_gp31 profiles."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "butters_gp30_gp31_locus_restricts_phage",
        "title": "Butters gp30-gp31 loci confer heterotypic phage defense",
        "description": "Conservative system-level sketch linking possession of a Butters gp30-gp31 locus to restricted bacteriophage propagation without asserting the unresolved phage trigger, gp31 modulatory role, or downstream arrest mechanism.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Butters gp30-gp31 as a named anti-phage system with DefenseFinder Butters gp30 and gp31 profiles while leaving the direct phage trigger, the biochemical action of gp30, the modulatory role of gp31, and the Island3-targeting gp30-independent mechanism unresolved.",
        "nodes": [
          {
            "node_id": "butters_gp30_gp31_locus",
            "label": "Butters gp30-gp31 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A Butters gp30-gp31 anti-phage defense locus cataloged in DefenseFinder with Butters gp30 and gp31 HMM profiles."
          },
          {
            "node_id": "restricted_phage_propagation",
            "label": "restricted phage propagation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced propagation of bacteriophage in cells carrying the Butters gp30-gp31 system."
          },
          {
            "node_id": "butters_gp30_gp31_system_trait",
            "label": "Butters gp30-gp31 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000298",
            "description": "Possession of a genome-encoded Butters gp30-gp31 phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "butters_gp30_gp31_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "restricted_phage_propagation",
            "description": "Mageeney et al. show that Butters genes in the central genome region contribute to defense against heterotypic viral attack, and DefenseFinder catalogs Butters_gp30 and Butters_gp31 profiles in the Butters_gp30_gp31 model namespace.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mSystems.00534-20",
                "snippet": "we show that Butters genes located in the central region of the genome play a key role in the defense against heterotypic viral attack",
                "notes": "Mageeney et al. support Butters central genes as effectors of heterotypic viral defense."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "Butters_gp30_gp31__Butters_gp30                  | Butters_gp30_gp31__Butters_gp30                  | Butters_gp30_gp31",
                "notes": "The DefenseFinder HMM inventory records a Butters gp30-gp31 profile for Butters_gp30_gp31__Butters_gp30 in the Butters_gp30_gp31 model namespace."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "Butters_gp30_gp31__Butters_gp31                  | Butters_gp30_gp31__Butters_gp31                  | Butters_gp30_gp31",
                "notes": "The DefenseFinder HMM inventory records a Butters gp30-gp31 profile for Butters_gp30_gp31__Butters_gp31 in the Butters_gp30_gp31 model namespace."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "Butters_gp30_gp31\tButters_gp30_gp31\t2\t2\tButters_gp30_gp31__Butters_gp30, Butters_gp30_gp31__Butters_gp31",
                "notes": "The DefenseFinder rules table models Butters_gp30_gp31 as a two-component system requiring Butters_gp30 and Butters_gp31 profiles."
              }
            ]
          },
          {
            "subject": "restricted_phage_propagation",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "butters_gp30_gp31_system_trait",
            "description": "Butters-gp30-gp31-associated restriction of phage propagation realizes the Butters gp30-gp31 system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mSystems.00534-20",
                "snippet": "Our study suggests that a two-component system, articulated by interactions between protein products of genes 30 and 31, confers defense against heterotypic phage infection by PurpleHaze (cluster A/subcluster A3) or Alma (cluster A/subcluster A9)",
                "notes": "Mageeney et al. support Butters gp30 and gp31 as a two-component system that can defend against PurpleHaze or Alma infection."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Butters_gp30_gp31 | 10\\.1128/mSystems\\.00534-20 | Mycobacterium phage Butters-encoded proteins contribute to host defense against viral attack",
                "notes": "DefenseFinder records Butters_gp30_gp31 as a named system from the Mageeney et al. Butters-defense paper."
              }
            ]
          },
          {
            "subject": "butters_gp30_gp31_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Butters gp30-gp31 system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| Butters_gp30_gp31 | 10\\.1128/mSystems\\.00534-20 | Mycobacterium phage Butters-encoded proteins contribute to host defense against viral attack |",
                "notes": "DefenseFinder associates Butters_gp30_gp31 with the Mageeney et al. Butters viral-defense paper."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "butters_gp30_gp31-mechanism-gap",
        "prompt": "Resolve the Butters gp30 biochemical output, the gp31 modulatory role, the gp30-gp31 stoichiometry, the direct PurpleHaze or Alma trigger, the Island3 gp30-independent defense, and homolog breadth before minting narrower Butters gp30-gp31 mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Mageeney et al. and DefenseFinder support Butters gp30-gp31 as a named anti-phage system with Butters gp30 and gp31 profiles, but the direct phage trigger, gp30 biochemical output, gp31 modulatory activity, stoichiometry of the possible gp30-gp31 complex, gp30-independent Island3-targeting defense, and relationship to CarolAnn and Sbash homologous systems are not resolved enough here to assert a narrower mechanistic child trait.",
        "attaches_to": [
          "causal_graphs#butters_gp30_gp31_locus_restricts_phage"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-20"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-20T01:32:52Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Butters gp30-gp31 system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v175.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000299",
    "label": "Butters gp57r system",
    "definition": "A phage defense system in which an organism possesses a Butters gp57r locus that can protect bacteria from bacteriophage infection.",
    "definition_source": "DOI:10.1101/2023.01.03.522681",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "Butters_gp57r",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1101/2023.01.03.522681",
        "snippet": "Butters gp57r is both necessary and sufficient to inhibit infection by Island3 and other phages",
        "notes": "Mohammed et al. report Butters gp57r as the Butters component that can block Island3 and additional heterotypic phages."
      },
      {
        "reference": "DOI:10.1101/2023.01.03.522681",
        "snippet": "mc2155(gp57r) recapitulated defense against Island3 comparable to that mounted by mc2155(Butters)",
        "notes": "Mohammed et al. show that expressing Butters gene 57r is sufficient to reproduce Butters-like defense against Island3."
      },
      {
        "reference": "DOI:10.1101/2023.01.03.522681",
        "snippet": "Results show that Butters gp57r defends against several other phages (Fig. 3A)",
        "notes": "Mohammed et al. test the breadth of the cloned gp57r defense and find protection against additional heterotypic phages."
      },
      {
        "reference": "DOI:10.1101/2023.01.03.522681",
        "snippet": "the proposal that gp57r acts downstream of DNA injection",
        "notes": "Mohammed et al. narrow the antiviral effect to a post-DNA-injection step without resolving gp57r's direct molecular substrate."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "Butters_gp57r | 10\\.1101/2023\\.01\\.03\\.522681 | Identification of a new antiphage system inMycobacteriumphage Butters",
        "notes": "The DefenseFinder model registry maps the named Butters_gp57r system to the Mohammed et al. Butters gp57r antiphage-system preprint."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "Butters_gp57r__gp57r                             | Butters_gp57r__gp57r                             | Butters_gp57r",
        "notes": "The DefenseFinder HMM inventory records a Butters gp57r profile for Butters_gp57r__gp57r in the Butters_gp57r model namespace."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "Butters_gp57r\tButters_gp57r\t1\t1\tButters_gp57r__gp57r",
        "notes": "The DefenseFinder rules table models Butters_gp57r as a one-component system requiring the gp57r profile."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "butters_gp57r_locus_restricts_phage",
        "title": "Butters gp57r loci confer heterotypic phage defense",
        "description": "Conservative system-level sketch linking possession of a Butters gp57r locus to restricted bacteriophage propagation without asserting the unresolved gp57r substrate, nuclease output, or phage-tail escape mechanism.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Butters gp57r as a named anti-phage system with a DefenseFinder gp57r profile while leaving the direct Island3 or PurpleHaze trigger, the role of the HEPN-associated RX4-6H motif, the primary gp57r molecular output, and homolog breadth unresolved.",
        "nodes": [
          {
            "node_id": "butters_gp57r_locus",
            "label": "Butters gp57r locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A Butters gp57r anti-phage defense locus cataloged in DefenseFinder with a gp57r HMM profile."
          },
          {
            "node_id": "restricted_phage_propagation",
            "label": "restricted phage propagation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced propagation of bacteriophage in cells carrying the Butters gp57r system."
          },
          {
            "node_id": "butters_gp57r_system_trait",
            "label": "Butters gp57r system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000299",
            "description": "Possession of a genome-encoded Butters gp57r phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "butters_gp57r_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "restricted_phage_propagation",
            "description": "Mohammed et al. show that Butters gp57r is necessary and sufficient for Island3 inhibition, and DefenseFinder catalogs a gp57r profile in the Butters_gp57r model namespace.",
            "evidence": [
              {
                "reference": "DOI:10.1101/2023.01.03.522681",
                "snippet": "Butters gp57r is both necessary and sufficient to inhibit infection by Island3 and other phages",
                "notes": "Mohammed et al. support gp57r as the Butters component that can restrict Island3 and additional heterotypic phages."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "Butters_gp57r__gp57r                             | Butters_gp57r__gp57r                             | Butters_gp57r",
                "notes": "The DefenseFinder HMM inventory records a Butters gp57r profile for Butters_gp57r__gp57r in the Butters_gp57r model namespace."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "Butters_gp57r\tButters_gp57r\t1\t1\tButters_gp57r__gp57r",
                "notes": "The DefenseFinder rules table models Butters_gp57r as a one-component system requiring the gp57r profile."
              }
            ]
          },
          {
            "subject": "restricted_phage_propagation",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "butters_gp57r_system_trait",
            "description": "Butters-gp57r-associated restriction of phage propagation realizes the Butters gp57r system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1101/2023.01.03.522681",
                "snippet": "mc2155(gp57r) recapitulated defense against Island3 comparable to that mounted by mc2155(Butters)",
                "notes": "Mohammed et al. show that recombinant expression of Butters gene 57r can reproduce Butters-mediated Island3 defense."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Butters_gp57r | 10\\.1101/2023\\.01\\.03\\.522681 | Identification of a new antiphage system inMycobacteriumphage Butters",
                "notes": "DefenseFinder records Butters_gp57r as a named system from the Mohammed et al. Butters gp57r antiphage-system preprint."
              }
            ]
          },
          {
            "subject": "butters_gp57r_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Butters gp57r system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| Butters_gp57r | 10\\.1101/2023\\.01\\.03\\.522681 | Identification of a new antiphage system inMycobacteriumphage Butters |",
                "notes": "DefenseFinder associates Butters_gp57r with the Mohammed et al. Butters gp57r antiphage-system preprint."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "butters_gp57r-mechanism-gap",
        "prompt": "Resolve the Butters gp57r direct phage trigger, primary molecular target, HEPN-associated RX4-6H motif requirement, DNA-amplification defect, PurpleHaze minor-tail escape route, and homolog breadth before minting narrower Butters gp57r mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Mohammed et al. and DefenseFinder support Butters gp57r as a named anti-phage system with a gp57r profile, but the direct phage trigger, the biochemical role of its predicted HEPN domain and RX4-6H motif, the primary event leading to failed Island3 DNA amplification, and the defense scope of gp57r homologs in other mycobacteriophages or clinical Mycobacterium abscessus isolates are not resolved enough here to assert a narrower mechanistic child trait.",
        "attaches_to": [
          "causal_graphs#butters_gp57r_locus_restricts_phage"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-20"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-20T02:22:02Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Butters gp57r system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v176.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000244",
    "label": "CapRel system",
    "definition": "A phage defense system in which an organism possesses a fused CapRel toxin-antitoxin locus encoding an N-terminal toxSAS toxin domain and a C-terminal antitoxin sensor domain that together can restrict bacteriophage propagation.",
    "definition_source": "DOI:10.1038/s41586-022-05444-z",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "CapRel toxin-antitoxin system",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1038/s41586-022-05444-z"
      },
      {
        "synonym_text": "fused CapRel system",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1038/s41586-022-05444-z"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/s41586-022-05444-z",
        "snippet": "protects Escherichia coli against diverse phages",
        "notes": "Zhang et al. support CapRelSJ46 as a fused CapRel toxin-antitoxin antiphage system that protects E. coli against several phages."
      },
      {
        "reference": "DOI:10.1038/s41586-022-05444-z",
        "snippet": "newly synthesized major capsid protein binds directly to the C-terminal domain",
        "notes": "Zhang et al. support direct sensing of a phage major capsid protein by the CapRelSJ46 C-terminal antitoxin domain."
      },
      {
        "reference": "DOI:10.1038/s41586-022-05444-z",
        "snippet": "This open state enables CapRelSJ46 to pyrophosphorylate tRNAs and inhibit translation",
        "notes": "Zhang et al. connect phage-triggered CapRel activation to tRNA pyrophosphorylation, translation blockade, and restriction of viral infection."
      },
      {
        "reference": "DOI:10.1038/s41586-022-05444-z",
        "snippet": "fused CapRels can provide anti-phage defence, with variable phage specificity",
        "notes": "Zhang et al. support treating fused CapRel loci as a family-level phage-defense system rather than only one CapRelSJ46 instance."
      },
      {
        "reference": "DOI:10.1038/s41586-024-08039-y",
        "snippet": "can directly bind and sense two completely unrelated and structurally different proteins using the same sensory domain",
        "notes": "Zhang et al. independently support CapRelSJ46 as a direct phage-trigger-sensing immune protein and show that a single sensory domain can recognize more than one phage trigger."
      },
      {
        "reference": "DOI:10.1038/s41586-024-08039-y",
        "snippet": "can fully evade CapRelSJ46 defence only when both triggers are mutated",
        "notes": "Zhang et al. connect multifactorial trigger sensing to CapRel-mediated defense during Bas11 phage infection."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "caprel_phage_triggered_translation_blockade",
        "title": "CapRel sensors couple phage trigger binding to translation blockade",
        "description": "Evidence-backed process sketch linking a fused CapRel toxin-antitoxin locus to direct phage-protein sensing, toxSAS activation, tRNA pyrophosphorylation, translation inhibition, and restricted phage propagation.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures CapRelSJ46 major-capsid-protein and Gp54 trigger evidence without claiming one universal CapRel phage trigger, allosteric route, escape route, or phage specificity across all fused CapRel homologs.",
        "nodes": [
          {
            "node_id": "caprel_locus",
            "label": "CapRel locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A fused CapRel toxin-antitoxin locus encoding an N-terminal toxSAS toxin domain and a C-terminal antitoxin sensor domain."
          },
          {
            "node_id": "phage_trigger_binding",
            "label": "phage trigger binding",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Direct binding of a phage-encoded trigger protein to the CapRel antitoxin sensor domain."
          },
          {
            "node_id": "caprel_toxin_activation",
            "label": "CapRel toxSAS activation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Relief of autoinhibition that activates the N-terminal CapRel toxSAS toxin domain."
          },
          {
            "node_id": "trna_pyrophosphorylation",
            "label": "tRNA pyrophosphorylation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Pyrophosphorylation of transfer RNAs by activated CapRel toxSAS toxin activity."
          },
          {
            "node_id": "translation_blockade",
            "label": "translation blockade",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Inhibition of cellular translation downstream of CapRel-mediated tRNA pyrophosphorylation."
          },
          {
            "node_id": "restricted_phage_propagation",
            "label": "restricted phage propagation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced bacteriophage propagation in cells whose CapRel system has blocked translation."
          },
          {
            "node_id": "caprel_system_trait",
            "label": "CapRel system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000244",
            "description": "Possession of a genome-encoded fused CapRel toxin-antitoxin phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "caprel_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "caprel_toxin_activation",
            "description": "Fused CapRel loci encode the N-terminal toxin domain and C-terminal antitoxin sensor domain that keep CapRel inhibited until phage trigger binding.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41586-022-05444-z",
                "snippet": "regulates the toxic N-terminal region, serving as both antitoxin and phage infection sensor",
                "notes": "Zhang et al. support the C-terminal CapRel domain as both antitoxin and phage-infection sensor."
              }
            ]
          },
          {
            "subject": "phage_trigger_binding",
            "predicate": "activates",
            "predicate_id": "RO:0002213",
            "object": "caprel_toxin_activation",
            "description": "Binding of phage-encoded triggers to the C-terminal CapRel sensor relieves autoinhibition of the toxSAS domain.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41586-022-05444-z",
                "snippet": "major capsid protein binds directly to the C-terminal domain",
                "notes": "Zhang et al. identify phage major capsid protein as a direct CapRelSJ46 trigger."
              },
              {
                "reference": "DOI:10.1038/s41586-024-08039-y",
                "snippet": "directly binds and senses two completely unrelated and structurally different phage proteins using the same sensor domain",
                "notes": "Zhang et al. show that CapRelSJ46 can directly sense an alternative Gp54 trigger."
              }
            ]
          },
          {
            "subject": "caprel_toxin_activation",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "trna_pyrophosphorylation",
            "description": "CapRel trigger binding activates the toxSAS domain that pyrophosphorylates tRNAs.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41586-022-05444-z",
                "snippet": "This open state enables CapRelSJ46 to pyrophosphorylate tRNAs",
                "notes": "Zhang et al. connect relief of autoinhibition to CapRel toxSAS-mediated tRNA pyrophosphorylation."
              }
            ]
          },
          {
            "subject": "trna_pyrophosphorylation",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "translation_blockade",
            "description": "tRNA pyrophosphorylation blocks cellular translation during CapRel antiviral activation.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41586-022-05444-z",
                "snippet": "pyrophosphorylate tRNAs, which blocks translation",
                "notes": "Zhang et al. identify translation blockade as the immediate outcome of CapRel-mediated tRNA pyrophosphorylation."
              }
            ]
          },
          {
            "subject": "translation_blockade",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "restricted_phage_propagation",
            "description": "Translation blockade contributes to restriction of the infecting phage.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41586-022-05444-z",
                "snippet": "blocks translation to restrict viral infection",
                "notes": "Zhang et al. connect translation blockade to restriction of viral infection."
              }
            ]
          },
          {
            "subject": "restricted_phage_propagation",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "caprel_system_trait",
            "description": "CapRel-dependent restriction of phage propagation realizes the CapRel system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41586-022-05444-z",
                "snippet": "fused CapRels can provide anti-phage defence",
                "notes": "Zhang et al. support fused CapRels as anti-phage defense systems."
              }
            ]
          },
          {
            "subject": "caprel_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "CapRel system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41586-022-05444-z",
                "snippet": "a fused anti-phage toxin-antitoxin system",
                "notes": "Zhang et al. place CapRelSJ46 in the anti-phage toxin-antitoxin-system family."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "caprel-trigger-and-family-breadth-gap",
        "prompt": "Resolve CapRel trigger breadth, phage escape routes, and family-specific activation before minting narrower CapRel mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Zhang et al. support CapRelSJ46 sensing of a major capsid protein and an unrelated Gp54 trigger, but fused CapRel homologs need separate review before TraitMech asserts one universal phage trigger, CapRel escape route, tRNA target spectrum, or phage specificity across the family.",
        "posed_by": "codex",
        "posed_date": "2026-09-18"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-18T15:19:24Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted CapRel system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v121.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-18T15:43:45Z",
        "curator": "codex",
        "action": "UPDATED_DEFINITION",
        "changes": "Tightened the CapRel system definition around fused CapRel locus possession and expanded a dangling CapRel activation snippet after late Copilot feedback in issue 1001.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000550",
    "label": "CARD-NLR endonuclease system",
    "definition": "A CARD-NLR system in which an organism possesses a genome-encoded DefenseFinder CARD_NLR_Endonuclease subtype locus represented by the CARD_NLR__Endonuclease mandatory rule profile.",
    "definition_source": "DOI:10.1101/2023.05.28.542683",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000337"
    ],
    "synonyms": [
      {
        "synonym_text": "CARD_NLR_Endonuclease",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv"
      },
      {
        "synonym_text": "CARD_NLR__Endonuclease",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "CARD_NLR__CARD_Protease",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv"
      },
      {
        "synonym_text": "CARD_NLR__NLR_new",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv"
      },
      {
        "synonym_text": "CARD_NLR__Trypsin",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv"
      }
    ],
    "evidence": [
      {
        "reference": "https://europepmc.org/article/PPR/PPR668921",
        "snippet": "Here we show that CARD-like domains are present in defense systems that protect bacteria against phage.",
        "notes": "Wein et al. support bacterial CARD-like domains as parts of anti-phage defense systems."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| CARD_NLR | 10\\.1101/2023\\.05\\.28\\.542683 | CARD-like domains mediate anti-phage defense in bacterial gasdermin systems | ",
        "notes": "The pinned DefenseFinder article registry maps the CARD_NLR model namespace to the Wein et al. CARD-like-domain anti-phage defense preprint."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| CARD_NLR__Endonuclease                           | CARD_NLR__Endonuclease                           | CARD_NLR               | Custom                  | 500    |",
        "notes": "The pinned DefenseFinder HMM inventory records CARD_NLR__Endonuclease as a custom CARD_NLR profile."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "CARD_NLR\tCARD_NLR_Endonuclease\t1\t3\tCARD_NLR__Endonuclease\tCARD_NLR__CARD_Protease, CARD_NLR__NLR_new, CARD_NLR__Trypsin\tCARD_NLR__Phospho, CARD_NLR__Phospho_Trypsin, CARD_NLR__Subtilase, CARD_NLR__Subtilase_long_new, CARD_NLR__Subtilase_small_new, CARD_NLR__Trypsin_Phospho, GasderMIN__bGSDM\t",
        "notes": "The pinned DefenseFinder rules table models CARD_NLR_Endonuclease as a CARD_NLR subsystem requiring the CARD_NLR__Endonuclease profile with CARD_Protease, NLR_new, and Trypsin accessory profiles."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "card_nlr_endonuclease_locus_subtype_defense",
        "title": "CARD-NLR endonuclease loci mark a CARD-NLR antiphage subtype",
        "description": "Conservative subtype-level sketch linking a DefenseFinder CARD_NLR_Endonuclease locus to CARD-like anti-phage defense and CARD-NLR endonuclease system possession.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures the CARD_NLR_Endonuclease subtype at DefenseFinder rule-row level without asserting the exact endonuclease effector substrate, phage trigger, native host breadth, CARD-to-effector activation sequence, or whether every DefenseFinder CARD_NLR_Endonuclease prediction is a complete experimentally active locus.",
        "nodes": [
          {
            "node_id": "card_nlr_endonuclease_locus",
            "label": "CARD-NLR endonuclease locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A DefenseFinder CARD_NLR_Endonuclease subtype locus represented by the mandatory CARD_NLR__Endonuclease profile and generic CARD_NLR accessory profiles."
          },
          {
            "node_id": "card_like_antiphage_defense",
            "label": "CARD-like antiphage defense",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Anti-phage defense mediated by a bacterial CARD-like defense system."
          },
          {
            "node_id": "card_nlr_endonuclease_system_trait",
            "label": "CARD-NLR endonuclease system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000550",
            "description": "Possession of a genome-encoded CARD-NLR endonuclease phage-defense system."
          },
          {
            "node_id": "card_nlr_system_trait",
            "label": "CARD-NLR system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000337",
            "description": "Possession of a genome-encoded CARD-NLR phage-defense system."
          }
        ],
        "edges": [
          {
            "subject": "card_nlr_endonuclease_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "card_like_antiphage_defense",
            "description": "CARD_NLR_Endonuclease loci are represented in DefenseFinder by a CARD_NLR__Endonuclease mandatory profile plus CARD_NLR accessory profiles.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| CARD_NLR__Endonuclease                           | CARD_NLR__Endonuclease                           | CARD_NLR               | Custom                  | 500    |",
                "notes": "The pinned DefenseFinder HMM inventory records CARD_NLR__Endonuclease as a custom CARD_NLR profile."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "CARD_NLR\tCARD_NLR_Endonuclease\t1\t3\tCARD_NLR__Endonuclease\tCARD_NLR__CARD_Protease, CARD_NLR__NLR_new, CARD_NLR__Trypsin\tCARD_NLR__Phospho, CARD_NLR__Phospho_Trypsin, CARD_NLR__Subtilase, CARD_NLR__Subtilase_long_new, CARD_NLR__Subtilase_small_new, CARD_NLR__Trypsin_Phospho, GasderMIN__bGSDM\t",
                "notes": "The pinned DefenseFinder rules table models CARD_NLR_Endonuclease as a CARD_NLR subsystem requiring the CARD_NLR__Endonuclease profile with CARD_Protease, NLR_new, and Trypsin accessory profiles."
              }
            ]
          },
          {
            "subject": "card_like_antiphage_defense",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "card_nlr_endonuclease_system_trait",
            "description": "The first-pass CARD-NLR endonuclease system trait is realized by a DefenseFinder CARD_NLR_Endonuclease subtype locus.",
            "evidence": [
              {
                "reference": "https://europepmc.org/article/PPR/PPR668921",
                "snippet": "Here we show that CARD-like domains are present in defense systems that protect bacteria against phage.",
                "notes": "Wein et al. support bacterial CARD-like domains as parts of anti-phage defense systems."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| CARD_NLR__Endonuclease                           | CARD_NLR__Endonuclease                           | CARD_NLR               | Custom                  | 500    |",
                "notes": "The pinned DefenseFinder HMM inventory records CARD_NLR__Endonuclease as a custom CARD_NLR profile."
              }
            ]
          },
          {
            "subject": "card_nlr_endonuclease_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "card_nlr_system_trait",
            "description": "CARD-NLR endonuclease system possession is a CARD-NLR-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| CARD_NLR | 10\\.1101/2023\\.05\\.28\\.542683 | CARD-like domains mediate anti-phage defense in bacterial gasdermin systems | ",
                "notes": "The pinned DefenseFinder article registry maps the CARD_NLR model namespace to the Wein et al. CARD-like-domain anti-phage defense preprint."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "CARD_NLR\tCARD_NLR_Endonuclease\t1\t3\tCARD_NLR__Endonuclease\tCARD_NLR__CARD_Protease, CARD_NLR__NLR_new, CARD_NLR__Trypsin\tCARD_NLR__Phospho, CARD_NLR__Phospho_Trypsin, CARD_NLR__Subtilase, CARD_NLR__Subtilase_long_new, CARD_NLR__Subtilase_small_new, CARD_NLR__Trypsin_Phospho, GasderMIN__bGSDM\t",
                "notes": "The pinned DefenseFinder rules table models CARD_NLR_Endonuclease as a CARD_NLR subsystem requiring the CARD_NLR__Endonuclease profile with CARD_Protease, NLR_new, and Trypsin accessory profiles."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "card-nlr-endonuclease-activity-gap",
        "prompt": "Resolve the CARD_NLR_Endonuclease phage triggers, native hosts, endonuclease effector substrate, CARD-to-effector activation sequence, and profile-to-activity criteria before minting enzyme, trigger, or component children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Wein et al. support CARD-like anti-phage defense systems, and the pinned DefenseFinder HMM inventory and rules table support CARD_NLR_Endonuclease as a subtype with a CARD_NLR__Endonuclease mandatory profile. This first-pass record leaves exact phage triggers, native hosts, accessory-profile requirements, nuclease substrate, and CARD-to-endonuclease activation unresolved.",
        "evidence": [
          {
            "reference": "https://europepmc.org/article/PPR/PPR668921",
            "snippet": "Here we show that CARD-like domains are present in defense systems that protect bacteria against phage.",
            "notes": "Wein et al. support bacterial CARD-like domains as parts of anti-phage defense systems."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| CARD_NLR__Endonuclease                           | CARD_NLR__Endonuclease                           | CARD_NLR               | Custom                  | 500    |",
            "notes": "The pinned DefenseFinder HMM inventory records CARD_NLR__Endonuclease as a custom CARD_NLR profile."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "snippet": "CARD_NLR\tCARD_NLR_Endonuclease\t1\t3\tCARD_NLR__Endonuclease\tCARD_NLR__CARD_Protease, CARD_NLR__NLR_new, CARD_NLR__Trypsin\tCARD_NLR__Phospho, CARD_NLR__Phospho_Trypsin, CARD_NLR__Subtilase, CARD_NLR__Subtilase_long_new, CARD_NLR__Subtilase_small_new, CARD_NLR__Trypsin_Phospho, GasderMIN__bGSDM\t",
            "notes": "The pinned DefenseFinder rules table models CARD_NLR_Endonuclease as a CARD_NLR subsystem requiring the CARD_NLR__Endonuclease profile with CARD_Protease, NLR_new, and Trypsin accessory profiles."
          }
        ],
        "attaches_to": [
          "causal_graphs#card_nlr_endonuclease_locus_subtype_defense"
        ],
        "posed_by": "codex",
        "posed_date": "2026-10-02"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-02T16:57:23Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted CARD-NLR endonuclease system as a DOI- and DefenseFinder-backed GENOMICS TraitRecord under the CARD-NLR system parent after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record for the target local ID, placeholder METPO ID, proposal cohort, record slug, or human label; the replacement placeholder is reserved in proposals/metpo_traitmech_v427.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-02T16:57:24Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed CARD-NLR endonuclease system during initial curation and left canonical_examples empty because Wein et al. and the pinned DefenseFinder tables support CARD-like anti-phage defense and the CARD_NLR_Endonuclease model namespace but not an accession-backed native microbial taxon exemplar tied to CARD_NLR_Endonuclease profiles and experimentally verified endogenous CARD-NLR endonuclease activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000555",
    "label": "CARD-NLR GasderMIN system",
    "definition": "A CARD-NLR system in which an organism possesses a genome-encoded DefenseFinder CARD_NLR_GasderMIN subtype locus represented by the CARD_NLR_GasderMIN rule row requiring the GasderMIN__bGSDM profile.",
    "definition_source": "DOI:10.1101/2023.05.28.542683",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000337"
    ],
    "synonyms": [
      {
        "synonym_text": "CARD_NLR_GasderMIN",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv"
      },
      {
        "synonym_text": "GasderMIN__bGSDM",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv"
      },
      {
        "synonym_text": "CARD_NLR__CARD_Protease",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv"
      },
      {
        "synonym_text": "CARD_NLR__NLR_new",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv"
      },
      {
        "synonym_text": "CARD_NLR__Trypsin",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv"
      }
    ],
    "evidence": [
      {
        "reference": "https://europepmc.org/article/PPR/PPR668921",
        "snippet": "Here we show that CARD-like domains are present in defense systems that protect bacteria against phage.",
        "notes": "Wein et al. support bacterial CARD-like domains as parts of anti-phage defense systems."
      },
      {
        "reference": "https://europepmc.org/article/PPR/PPR668921",
        "snippet": "The bacterial CARD is essential for protease-mediated activation of certain bacterial gasdermins, which promote cell death once phage infection is recognized.",
        "notes": "Wein et al. support bacterial CARD-dependent activation of phage-triggered gasdermin cell-death effectors."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| CARD_NLR | 10\\.1101/2023\\.05\\.28\\.542683 | CARD-like domains mediate anti-phage defense in bacterial gasdermin systems | ",
        "notes": "The pinned DefenseFinder article registry maps the CARD_NLR model namespace to the Wein et al. CARD-like-domain anti-phage defense preprint."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| GasderMIN__bGSDM                                 | GasderMIN__bGSDM___bGSDM                         | GasderMIN              | Custom                  | 50     |",
        "notes": "The pinned DefenseFinder HMM inventory records the GasderMIN__bGSDM profile reused as mandatory by the CARD_NLR_GasderMIN rule row."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "CARD_NLR\tCARD_NLR_GasderMIN\t1\t3\tGasderMIN__bGSDM\tCARD_NLR__CARD_Protease, CARD_NLR__NLR_new, CARD_NLR__Trypsin\tCARD_NLR__Endonuclease, CARD_NLR__Endonuclease_new, CARD_NLR__Phospho, CARD_NLR__Phospho_Trypsin, CARD_NLR__Subtilase, CARD_NLR__Subtilase_long_new, CARD_NLR__Subtilase_small_new, CARD_NLR__Trypsin_Phospho, CARD_NLR__Trypsine_Endonuclease_new\t",
        "notes": "The pinned DefenseFinder rules table models CARD_NLR_GasderMIN as a CARD_NLR subsystem requiring GasderMIN__bGSDM with CARD_Protease, NLR_new, and Trypsin accessory profiles."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "card_nlr_gasdermin_locus_subtype_defense",
        "title": "CARD-NLR GasderMIN loci mark a CARD-NLR antiphage subtype",
        "description": "Conservative subtype-level sketch linking a DefenseFinder CARD_NLR_GasderMIN locus to CARD-like gasdermin anti-phage defense and CARD-NLR GasderMIN system possession.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures the CARD_NLR_GasderMIN subtype at DefenseFinder rule-row level without asserting the exact phage trigger, native host breadth, CARD-to-gasdermin activation sequence, bGSDM cleavage route, or whether every DefenseFinder CARD_NLR_GasderMIN prediction is a complete experimentally active locus.",
        "nodes": [
          {
            "node_id": "card_nlr_gasdermin_locus",
            "label": "CARD-NLR GasderMIN locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A DefenseFinder CARD_NLR_GasderMIN subtype locus represented by the GasderMIN__bGSDM mandatory profile and generic CARD_NLR accessory profiles."
          },
          {
            "node_id": "card_like_gasdermin_antiphage_defense",
            "label": "CARD-like gasdermin antiphage defense",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Anti-phage defense mediated by bacterial CARD-like activation of a gasdermin cell-death effector."
          },
          {
            "node_id": "card_nlr_gasdermin_system_trait",
            "label": "CARD-NLR GasderMIN system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000555",
            "description": "Possession of a genome-encoded CARD-NLR GasderMIN phage-defense system."
          },
          {
            "node_id": "card_nlr_system_trait",
            "label": "CARD-NLR system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000337",
            "description": "Possession of a genome-encoded CARD-NLR phage-defense system."
          }
        ],
        "edges": [
          {
            "subject": "card_nlr_gasdermin_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "card_like_gasdermin_antiphage_defense",
            "description": "CARD_NLR_GasderMIN loci are represented in DefenseFinder by a GasderMIN__bGSDM mandatory profile plus CARD_NLR accessory profiles.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| GasderMIN__bGSDM                                 | GasderMIN__bGSDM___bGSDM                         | GasderMIN              | Custom                  | 50     |",
                "notes": "The pinned DefenseFinder HMM inventory records the GasderMIN__bGSDM profile reused as mandatory by the CARD_NLR_GasderMIN rule row."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "CARD_NLR\tCARD_NLR_GasderMIN\t1\t3\tGasderMIN__bGSDM\tCARD_NLR__CARD_Protease, CARD_NLR__NLR_new, CARD_NLR__Trypsin\tCARD_NLR__Endonuclease, CARD_NLR__Endonuclease_new, CARD_NLR__Phospho, CARD_NLR__Phospho_Trypsin, CARD_NLR__Subtilase, CARD_NLR__Subtilase_long_new, CARD_NLR__Subtilase_small_new, CARD_NLR__Trypsin_Phospho, CARD_NLR__Trypsine_Endonuclease_new\t",
                "notes": "The pinned DefenseFinder rules table models CARD_NLR_GasderMIN as a CARD_NLR subsystem requiring GasderMIN__bGSDM with CARD_Protease, NLR_new, and Trypsin accessory profiles."
              }
            ]
          },
          {
            "subject": "card_like_gasdermin_antiphage_defense",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "card_nlr_gasdermin_system_trait",
            "description": "The first-pass CARD-NLR GasderMIN system trait is realized by a DefenseFinder CARD_NLR_GasderMIN subtype locus.",
            "evidence": [
              {
                "reference": "https://europepmc.org/article/PPR/PPR668921",
                "snippet": "Here we show that CARD-like domains are present in defense systems that protect bacteria against phage.",
                "notes": "Wein et al. support bacterial CARD-like domains as parts of anti-phage defense systems."
              },
              {
                "reference": "https://europepmc.org/article/PPR/PPR668921",
                "snippet": "The bacterial CARD is essential for protease-mediated activation of certain bacterial gasdermins, which promote cell death once phage infection is recognized.",
                "notes": "Wein et al. support bacterial CARD-dependent activation of phage-triggered gasdermin cell-death effectors."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "CARD_NLR_GasderMIN\t1\t3\tGasderMIN__bGSDM\tCARD_NLR__CARD_Protease, CARD_NLR__NLR_new, CARD_NLR__Trypsin",
                "notes": "The pinned DefenseFinder rules table models CARD_NLR_GasderMIN as a CARD_NLR subsystem requiring GasderMIN__bGSDM with CARD_Protease, NLR_new, and Trypsin accessory profiles."
              }
            ]
          },
          {
            "subject": "card_nlr_gasdermin_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "card_nlr_system_trait",
            "description": "CARD-NLR GasderMIN system possession is a CARD-NLR-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| CARD_NLR | 10\\.1101/2023\\.05\\.28\\.542683 | CARD-like domains mediate anti-phage defense in bacterial gasdermin systems | ",
                "notes": "The pinned DefenseFinder article registry maps the CARD_NLR model namespace to the Wein et al. CARD-like-domain anti-phage defense preprint."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "CARD_NLR\tCARD_NLR_GasderMIN\t1\t3\tGasderMIN__bGSDM",
                "notes": "The pinned DefenseFinder rules table places the CARD_NLR_GasderMIN subsystem under the CARD_NLR system key and requires GasderMIN__bGSDM."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "card-nlr-gasdermin-activity-gap",
        "prompt": "Resolve the CARD_NLR_GasderMIN phage triggers, native hosts, gasdermin proteolysis route, CARD-to-gasdermin activation sequence, and profile-to-activity criteria before minting protease, trigger, or component children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Wein et al. support CARD-like anti-phage gasdermin defense, the pinned DefenseFinder HMM inventory supports GasderMIN__bGSDM as a bGSDM profile, and the pinned DefenseFinder rules table supports CARD_NLR_GasderMIN as a rule-row subtype requiring GasderMIN__bGSDM. This first-pass record leaves exact phage triggers, native hosts, CARD-to-gasdermin activation, bGSDM proteolysis route, and profile-to-activity criteria unresolved.",
        "evidence": [
          {
            "reference": "https://europepmc.org/article/PPR/PPR668921",
            "snippet": "The bacterial CARD is essential for protease-mediated activation of certain bacterial gasdermins, which promote cell death once phage infection is recognized.",
            "notes": "Wein et al. support bacterial CARD-dependent activation of phage-triggered gasdermin cell-death effectors."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| GasderMIN__bGSDM                                 | GasderMIN__bGSDM___bGSDM                         | GasderMIN              | Custom                  | 50     |",
            "notes": "The pinned DefenseFinder HMM inventory records the GasderMIN__bGSDM profile reused as mandatory by the CARD_NLR_GasderMIN rule row."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "snippet": "CARD_NLR\tCARD_NLR_GasderMIN\t1\t3\tGasderMIN__bGSDM\tCARD_NLR__CARD_Protease, CARD_NLR__NLR_new, CARD_NLR__Trypsin\tCARD_NLR__Endonuclease, CARD_NLR__Endonuclease_new, CARD_NLR__Phospho, CARD_NLR__Phospho_Trypsin, CARD_NLR__Subtilase, CARD_NLR__Subtilase_long_new, CARD_NLR__Subtilase_small_new, CARD_NLR__Trypsin_Phospho, CARD_NLR__Trypsine_Endonuclease_new\t",
            "notes": "The pinned DefenseFinder rules table models CARD_NLR_GasderMIN as a CARD_NLR subsystem requiring GasderMIN__bGSDM with CARD_Protease, NLR_new, and Trypsin accessory profiles."
          }
        ],
        "attaches_to": [
          "causal_graphs#card_nlr_gasdermin_locus_subtype_defense"
        ],
        "posed_by": "codex",
        "posed_date": "2026-10-02"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-02T21:05:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted CARD-NLR GasderMIN system as a DOI- and DefenseFinder-backed GENOMICS TraitRecord under the CARD-NLR system parent after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record for the target local ID, placeholder METPO ID, proposal cohort, record slug, or human label; existing CARD_NLR_GasderMIN mentions were scoped to CARD-NLR parent or GasderMIN evidence, not an exact child TraitRecord, and the replacement placeholder is reserved in proposals/metpo_traitmech_v432.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-02T21:05:02Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed CARD-NLR GasderMIN system during initial curation and left canonical_examples empty because Wein et al. and the pinned DefenseFinder tables support CARD-like anti-phage gasdermin defense and the CARD_NLR_GasderMIN rule row but not an accession-backed native microbial taxon exemplar tied to CARD_NLR_GasderMIN profiles and experimentally verified endogenous activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000559",
    "label": "CARD-NLR-like system",
    "definition": "A CARD-NLR system in which an organism possesses a genome-encoded DefenseFinder CARD_NLR_like subtype locus represented by the CARD_NLR_like rule row requiring two matches from the CARD_NLR__Endonuclease, CARD_NLR__Phospho_Trypsin, CARD_NLR__Subtilase_long_new, and CARD_NLR__Trypsin_Phospho effector-profile set and four genes overall after considering CARD_NLR__CARD_Protease, CARD_NLR__NLR_new, and CARD_NLR__Trypsin accessory profiles.",
    "definition_source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000337"
    ],
    "synonyms": [
      {
        "synonym_text": "CARD_NLR_like",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv"
      }
    ],
    "evidence": [
      {
        "reference": "https://europepmc.org/article/PPR/PPR668921",
        "snippet": "Here we show that CARD-like domains are present in defense systems that protect bacteria against phage.",
        "notes": "Wein et al. support bacterial CARD-like domains as parts of anti-phage defense systems."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| CARD_NLR | 10\\.1101/2023\\.05\\.28\\.542683 | CARD-like domains mediate anti-phage defense in bacterial gasdermin systems | ",
        "notes": "The pinned DefenseFinder article registry maps the CARD_NLR model namespace to the Wein et al. CARD-like-domain anti-phage defense preprint."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| CARD_NLR__Endonuclease                           | CARD_NLR__Endonuclease                           | CARD_NLR               | Custom                  | 500    |",
        "notes": "The pinned DefenseFinder HMM inventory records the CARD_NLR__Endonuclease custom profile listed among the candidate effector profiles by the CARD_NLR_like rule row."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| CARD_NLR__Phospho_Trypsin                        | CARD_NLR__Phospho_Trypsin                        | CARD_NLR               | Custom                  | 1000   |",
        "notes": "The pinned DefenseFinder HMM inventory records the CARD_NLR__Phospho_Trypsin custom profile listed among the candidate effector profiles by the CARD_NLR_like rule row."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| CARD_NLR__Trypsin_Phospho                        | CARD_NLR__Trypsin_Phospho                        | CARD_NLR               | Custom                  | 400    |",
        "notes": "The pinned DefenseFinder HMM inventory records the CARD_NLR__Trypsin_Phospho custom profile listed among the candidate effector profiles by the CARD_NLR_like rule row."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "System\tSubsystem\tMin_mandatory\tMinimum_genes\tMandatory\tAccessory\tForbidden\tNeutral",
        "notes": "The pinned DefenseFinder rules header identifies the second, third, fourth, fifth, and sixth CARD_NLR_like row fields as Subsystem, Min_mandatory, Minimum_genes, Mandatory, and Accessory, respectively."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "CARD_NLR\tCARD_NLR_like\t2\t4\tCARD_NLR__Endonuclease, CARD_NLR__Phospho_Trypsin, CARD_NLR__Subtilase_long_new, CARD_NLR__Trypsin_Phospho\tCARD_NLR__CARD_Protease, CARD_NLR__NLR_new, CARD_NLR__Trypsin\t\t",
        "notes": "The pinned DefenseFinder rules table models CARD_NLR_like as a CARD_NLR subsystem requiring two matches from a four-profile candidate effector set."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "card_nlr_like_locus_subtype_defense",
        "title": "CARD-NLR-like is a DefenseFinder CARD-NLR subtype",
        "description": "Conservative subtype-level sketch linking a DefenseFinder CARD_NLR_like locus to CARD-like anti-phage defense, CARD-NLR-like system possession, and its CARD-NLR parent.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures the CARD_NLR_like subtype at DefenseFinder rule-row level without expanding candidate effector-profile names, selecting which two of the four candidate effector profiles realize activity, resolving the absent CARD_NLR__Subtilase_long_new HMM inventory row, or resolving exact phage triggers, native host breadth, CARD-to-effector activation sequence, cell-death output, or whether every DefenseFinder CARD_NLR_like prediction is a complete experimentally active locus.",
        "nodes": [
          {
            "node_id": "card_nlr_like_locus",
            "label": "CARD-NLR-like locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A DefenseFinder CARD_NLR_like subtype locus represented by at least two of four candidate CARD_NLR effector profiles and generic CARD_NLR accessory profiles."
          },
          {
            "node_id": "card_like_antiphage_defense",
            "label": "CARD-like antiphage defense",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Anti-phage defense mediated by a bacterial CARD-like defense system."
          },
          {
            "node_id": "card_nlr_like_system_trait",
            "label": "CARD-NLR-like system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000559",
            "description": "Possession of a genome-encoded CARD-NLR-like phage-defense system."
          },
          {
            "node_id": "card_nlr_system_trait",
            "label": "CARD-NLR system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000337",
            "description": "Possession of a genome-encoded CARD-NLR phage-defense system."
          }
        ],
        "edges": [
          {
            "subject": "card_nlr_like_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "card_like_antiphage_defense",
            "description": "CARD_NLR_like loci are represented in DefenseFinder by at least two matches from four candidate CARD_NLR effector profiles plus CARD_NLR accessory profiles.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "System\tSubsystem\tMin_mandatory\tMinimum_genes\tMandatory\tAccessory\tForbidden\tNeutral\nCARD_NLR\tCARD_NLR_like\t2\t4\tCARD_NLR__Endonuclease, CARD_NLR__Phospho_Trypsin, CARD_NLR__Subtilase_long_new, CARD_NLR__Trypsin_Phospho\tCARD_NLR__CARD_Protease, CARD_NLR__NLR_new, CARD_NLR__Trypsin\t\t",
                "notes": "The pinned DefenseFinder rules header and CARD_NLR_like row identify CARD_NLR_like as a CARD_NLR subsystem with Min_mandatory=2, Minimum_genes=4, four candidate Mandatory effector profiles, and three Accessory profiles."
              }
            ]
          },
          {
            "subject": "card_like_antiphage_defense",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "card_nlr_like_system_trait",
            "description": "The first-pass CARD-NLR-like system trait is realized by a DefenseFinder CARD_NLR_like subtype locus.",
            "evidence": [
              {
                "reference": "https://europepmc.org/article/PPR/PPR668921",
                "snippet": "Here we show that CARD-like domains are present in defense systems that protect bacteria against phage.",
                "notes": "Wein et al. support bacterial CARD-like domains as parts of anti-phage defense systems."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| CARD_NLR | 10\\.1101/2023\\.05\\.28\\.542683 | CARD-like domains mediate anti-phage defense in bacterial gasdermin systems | ",
                "notes": "The pinned DefenseFinder article registry maps the CARD_NLR model namespace to the Wein et al. CARD-like-domain anti-phage defense preprint."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "CARD_NLR_like\t2\t4\tCARD_NLR__Endonuclease, CARD_NLR__Phospho_Trypsin, CARD_NLR__Subtilase_long_new, CARD_NLR__Trypsin_Phospho",
                "notes": "The pinned DefenseFinder rules table models CARD_NLR_like with two required matches from Endonuclease, Phospho_Trypsin, Subtilase_long_new, and Trypsin_Phospho candidate effector profiles."
              }
            ]
          },
          {
            "subject": "card_nlr_like_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "card_nlr_system_trait",
            "description": "CARD-NLR-like system possession is a CARD-NLR-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| CARD_NLR | 10\\.1101/2023\\.05\\.28\\.542683 | CARD-like domains mediate anti-phage defense in bacterial gasdermin systems | ",
                "notes": "The pinned DefenseFinder article registry maps the CARD_NLR model namespace to the Wein et al. CARD-like-domain anti-phage defense preprint."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "System\tSubsystem\tMin_mandatory\tMinimum_genes\tMandatory\tAccessory\tForbidden\tNeutral",
                "notes": "The pinned DefenseFinder rules header identifies the second, third, fourth, fifth, and sixth CARD_NLR_like row fields as Subsystem, Min_mandatory, Minimum_genes, Mandatory, and Accessory, respectively."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "CARD_NLR\tCARD_NLR_like",
                "notes": "The pinned DefenseFinder rules table places the CARD_NLR_like subsystem under the CARD_NLR system key."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "card-nlr-like-activity-gap",
        "prompt": "Resolve the CARD_NLR_like phage triggers, native hosts, four-profile effector-combination semantics, CARD_NLR__Subtilase_long_new HMM inventory gap, and profile-to-activity criteria before minting effector or trigger children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Wein et al. support CARD-like anti-phage defense, and the pinned DefenseFinder HMM inventory and rules table support CARD_NLR_like as a CARD_NLR subsystem requiring two matches from a four-profile Endonuclease, Phospho_Trypsin, Subtilase_long_new, and Trypsin_Phospho candidate effector set. This first-pass record follows the rule row but leaves exact phage triggers, native hosts, how the two-of-four effector profile combinations map to activity, how CARD_NLR__Subtilase_long_new maps to the pinned HMM inventory, and whether every DefenseFinder CARD_NLR_like prediction is a complete experimentally active locus.",
        "evidence": [
          {
            "reference": "https://europepmc.org/article/PPR/PPR668921",
            "snippet": "Here we show that CARD-like domains are present in defense systems that protect bacteria against phage.",
            "notes": "Wein et al. support bacterial CARD-like domains as parts of anti-phage defense systems."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| CARD_NLR__Endonuclease                           | CARD_NLR__Endonuclease                           | CARD_NLR               | Custom                  | 500    |",
            "notes": "The pinned DefenseFinder HMM inventory records the CARD_NLR__Endonuclease custom profile listed among the candidate effector profiles by the CARD_NLR_like rule row."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| CARD_NLR__Phospho_Trypsin                        | CARD_NLR__Phospho_Trypsin                        | CARD_NLR               | Custom                  | 1000   |",
            "notes": "The pinned DefenseFinder HMM inventory records the CARD_NLR__Phospho_Trypsin custom profile listed among the candidate effector profiles by the CARD_NLR_like rule row."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| CARD_NLR__Trypsin_Phospho                        | CARD_NLR__Trypsin_Phospho                        | CARD_NLR               | Custom                  | 400    |",
            "notes": "The pinned DefenseFinder HMM inventory records the CARD_NLR__Trypsin_Phospho custom profile listed among the candidate effector profiles by the CARD_NLR_like rule row."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "snippet": "System\tSubsystem\tMin_mandatory\tMinimum_genes\tMandatory\tAccessory\tForbidden\tNeutral",
            "notes": "The pinned DefenseFinder rules header identifies the second, third, fourth, fifth, and sixth CARD_NLR_like row fields as Subsystem, Min_mandatory, Minimum_genes, Mandatory, and Accessory, respectively."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "snippet": "CARD_NLR\tCARD_NLR_like\t2\t4\tCARD_NLR__Endonuclease, CARD_NLR__Phospho_Trypsin, CARD_NLR__Subtilase_long_new, CARD_NLR__Trypsin_Phospho\tCARD_NLR__CARD_Protease, CARD_NLR__NLR_new, CARD_NLR__Trypsin\t\t",
            "notes": "The pinned DefenseFinder rules table models CARD_NLR_like as a CARD_NLR subsystem requiring two matches from a four-profile candidate effector set."
          }
        ],
        "attaches_to": [
          "causal_graphs#card_nlr_like_locus_subtype_defense"
        ],
        "posed_by": "codex",
        "posed_date": "2026-10-03"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-03T00:02:50Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted CARD-NLR-like system as a DOI- and DefenseFinder-backed GENOMICS TraitRecord under the CARD-NLR system parent after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record for the target local ID, placeholder METPO ID, proposal cohort, record slug, or human label; existing CARD_NLR_like mentions were scoped to the CARD-NLR parent, not an exact child TraitRecord, and the replacement placeholder is reserved in proposals/metpo_traitmech_v436.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-03T00:02:52Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed CARD-NLR-like system during initial curation and left canonical_examples empty because Wein et al. and the pinned DefenseFinder tables support CARD-like anti-phage systems and the CARD_NLR_like rule row but not an accession-backed native microbial taxon exemplar tied to CARD_NLR_like profiles and experimentally verified endogenous activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000551",
    "label": "CARD-NLR phospho system",
    "definition": "A CARD-NLR system in which an organism possesses a genome-encoded DefenseFinder CARD_NLR_Phospho subtype locus represented by the CARD_NLR__Trypsin_Phospho mandatory rule profile.",
    "definition_source": "DOI:10.1101/2023.05.28.542683",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000337"
    ],
    "synonyms": [
      {
        "synonym_text": "CARD_NLR_Phospho",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv"
      },
      {
        "synonym_text": "CARD_NLR__Trypsin_Phospho",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "CARD_NLR__CARD_Protease",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv"
      },
      {
        "synonym_text": "CARD_NLR__NLR_new",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv"
      },
      {
        "synonym_text": "CARD_NLR__Trypsin",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv"
      }
    ],
    "evidence": [
      {
        "reference": "https://europepmc.org/article/PPR/PPR668921",
        "snippet": "Here we show that CARD-like domains are present in defense systems that protect bacteria against phage.",
        "notes": "Wein et al. support bacterial CARD-like domains as parts of anti-phage defense systems."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| CARD_NLR | 10\\.1101/2023\\.05\\.28\\.542683 | CARD-like domains mediate anti-phage defense in bacterial gasdermin systems | ",
        "notes": "The pinned DefenseFinder article registry maps the CARD_NLR model namespace to the Wein et al. CARD-like-domain anti-phage defense preprint."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| CARD_NLR__Trypsin_Phospho                        | CARD_NLR__Trypsin_Phospho                        | CARD_NLR               | Custom                  | 400    |",
        "notes": "The pinned DefenseFinder HMM inventory records CARD_NLR__Trypsin_Phospho as a custom CARD_NLR profile."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "CARD_NLR\tCARD_NLR_Phospho\t1\t3\tCARD_NLR__Trypsin_Phospho\tCARD_NLR__CARD_Protease, CARD_NLR__NLR_new, CARD_NLR__Trypsin\tCARD_NLR__Endonuclease, CARD_NLR__Endonuclease_new, CARD_NLR__Subtilase, CARD_NLR__Subtilase_long_new, CARD_NLR__Subtilase_small_new, CARD_NLR__Trypsine_Endonuclease_new, GasderMIN__bGSDM\t",
        "notes": "The pinned DefenseFinder rules table models CARD_NLR_Phospho as a CARD_NLR subsystem requiring the CARD_NLR__Trypsin_Phospho profile with CARD_Protease, NLR_new, and Trypsin accessory profiles."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "card_nlr_phospho_locus_subtype_defense",
        "title": "CARD-NLR phospho loci mark a CARD-NLR antiphage subtype",
        "description": "Conservative subtype-level sketch linking a DefenseFinder CARD_NLR_Phospho locus to CARD-like anti-phage defense and CARD-NLR phospho system possession.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures the CARD_NLR_Phospho subtype at DefenseFinder rule-row level without asserting the exact phosphorylated substrate, phage trigger, native host breadth, CARD-to-effector activation sequence, or whether every DefenseFinder CARD_NLR_Phospho prediction is a complete experimentally active locus.",
        "nodes": [
          {
            "node_id": "card_nlr_phospho_locus",
            "label": "CARD-NLR phospho locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A DefenseFinder CARD_NLR_Phospho subtype locus represented by the mandatory CARD_NLR__Trypsin_Phospho profile and generic CARD_NLR accessory profiles."
          },
          {
            "node_id": "card_like_antiphage_defense",
            "label": "CARD-like antiphage defense",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Anti-phage defense mediated by a bacterial CARD-like defense system."
          },
          {
            "node_id": "card_nlr_phospho_system_trait",
            "label": "CARD-NLR phospho system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000551",
            "description": "Possession of a genome-encoded CARD-NLR phospho phage-defense system."
          },
          {
            "node_id": "card_nlr_system_trait",
            "label": "CARD-NLR system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000337",
            "description": "Possession of a genome-encoded CARD-NLR phage-defense system."
          }
        ],
        "edges": [
          {
            "subject": "card_nlr_phospho_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "card_like_antiphage_defense",
            "description": "CARD_NLR_Phospho loci are represented in DefenseFinder by a CARD_NLR__Trypsin_Phospho mandatory profile plus CARD_NLR accessory profiles.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| CARD_NLR__Trypsin_Phospho                        | CARD_NLR__Trypsin_Phospho                        | CARD_NLR               | Custom                  | 400    |",
                "notes": "The pinned DefenseFinder HMM inventory records CARD_NLR__Trypsin_Phospho as a custom CARD_NLR profile."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "CARD_NLR\tCARD_NLR_Phospho\t1\t3\tCARD_NLR__Trypsin_Phospho\tCARD_NLR__CARD_Protease, CARD_NLR__NLR_new, CARD_NLR__Trypsin\tCARD_NLR__Endonuclease, CARD_NLR__Endonuclease_new, CARD_NLR__Subtilase, CARD_NLR__Subtilase_long_new, CARD_NLR__Subtilase_small_new, CARD_NLR__Trypsine_Endonuclease_new, GasderMIN__bGSDM\t",
                "notes": "The pinned DefenseFinder rules table models CARD_NLR_Phospho as a CARD_NLR subsystem requiring the CARD_NLR__Trypsin_Phospho profile with CARD_Protease, NLR_new, and Trypsin accessory profiles."
              }
            ]
          },
          {
            "subject": "card_like_antiphage_defense",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "card_nlr_phospho_system_trait",
            "description": "The first-pass CARD-NLR phospho system trait is realized by a DefenseFinder CARD_NLR_Phospho subtype locus.",
            "evidence": [
              {
                "reference": "https://europepmc.org/article/PPR/PPR668921",
                "snippet": "Here we show that CARD-like domains are present in defense systems that protect bacteria against phage.",
                "notes": "Wein et al. support bacterial CARD-like domains as parts of anti-phage defense systems."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| CARD_NLR__Trypsin_Phospho                        | CARD_NLR__Trypsin_Phospho                        | CARD_NLR               | Custom                  | 400    |",
                "notes": "The pinned DefenseFinder HMM inventory records CARD_NLR__Trypsin_Phospho as a custom CARD_NLR profile."
              }
            ]
          },
          {
            "subject": "card_nlr_phospho_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "card_nlr_system_trait",
            "description": "CARD-NLR phospho system possession is a CARD-NLR-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| CARD_NLR | 10\\.1101/2023\\.05\\.28\\.542683 | CARD-like domains mediate anti-phage defense in bacterial gasdermin systems | ",
                "notes": "The pinned DefenseFinder article registry maps the CARD_NLR model namespace to the Wein et al. CARD-like-domain anti-phage defense preprint."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "CARD_NLR\tCARD_NLR_Phospho\t1\t3\tCARD_NLR__Trypsin_Phospho\tCARD_NLR__CARD_Protease, CARD_NLR__NLR_new, CARD_NLR__Trypsin\tCARD_NLR__Endonuclease, CARD_NLR__Endonuclease_new, CARD_NLR__Subtilase, CARD_NLR__Subtilase_long_new, CARD_NLR__Subtilase_small_new, CARD_NLR__Trypsine_Endonuclease_new, GasderMIN__bGSDM\t",
                "notes": "The pinned DefenseFinder rules table models CARD_NLR_Phospho as a CARD_NLR subsystem requiring the CARD_NLR__Trypsin_Phospho profile with CARD_Protease, NLR_new, and Trypsin accessory profiles."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "card-nlr-phospho-activity-gap",
        "prompt": "Resolve the CARD_NLR_Phospho phage triggers, native hosts, phosphorylated substrate, CARD-to-effector activation sequence, and profile-to-activity criteria before minting enzyme, trigger, or component children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Wein et al. support CARD-like anti-phage defense systems, and the pinned DefenseFinder HMM inventory and rules table support CARD_NLR_Phospho as a subtype with a CARD_NLR__Trypsin_Phospho mandatory profile. This first-pass record leaves exact phage triggers, native hosts, accessory-profile requirements, phosphorylated substrate, and CARD-to-phospho-effector activation unresolved.",
        "evidence": [
          {
            "reference": "https://europepmc.org/article/PPR/PPR668921",
            "snippet": "Here we show that CARD-like domains are present in defense systems that protect bacteria against phage.",
            "notes": "Wein et al. support bacterial CARD-like domains as parts of anti-phage defense systems."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| CARD_NLR__Trypsin_Phospho                        | CARD_NLR__Trypsin_Phospho                        | CARD_NLR               | Custom                  | 400    |",
            "notes": "The pinned DefenseFinder HMM inventory records CARD_NLR__Trypsin_Phospho as a custom CARD_NLR profile."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "snippet": "CARD_NLR\tCARD_NLR_Phospho\t1\t3\tCARD_NLR__Trypsin_Phospho\tCARD_NLR__CARD_Protease, CARD_NLR__NLR_new, CARD_NLR__Trypsin\tCARD_NLR__Endonuclease, CARD_NLR__Endonuclease_new, CARD_NLR__Subtilase, CARD_NLR__Subtilase_long_new, CARD_NLR__Subtilase_small_new, CARD_NLR__Trypsine_Endonuclease_new, GasderMIN__bGSDM\t",
            "notes": "The pinned DefenseFinder rules table models CARD_NLR_Phospho as a CARD_NLR subsystem requiring the CARD_NLR__Trypsin_Phospho profile with CARD_Protease, NLR_new, and Trypsin accessory profiles."
          }
        ],
        "attaches_to": [
          "causal_graphs#card_nlr_phospho_locus_subtype_defense"
        ],
        "posed_by": "codex",
        "posed_date": "2026-10-02"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-02T17:23:11Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted CARD-NLR phospho system as a DOI- and DefenseFinder-backed GENOMICS TraitRecord under the CARD-NLR system parent after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record for the target local ID, placeholder METPO ID, proposal cohort, record slug, or human label; the replacement placeholder is reserved in proposals/metpo_traitmech_v428.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-02T17:23:12Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed CARD-NLR phospho system during initial curation and left canonical_examples empty because Wein et al. and the pinned DefenseFinder tables support CARD-like anti-phage defense and the CARD_NLR_Phospho model namespace but not an accession-backed native microbial taxon exemplar tied to CARD_NLR_Phospho profiles and experimentally verified endogenous CARD-NLR phospho activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000553",
    "label": "CARD-NLR subtilase system",
    "definition": "A CARD-NLR system in which an organism possesses a genome-encoded DefenseFinder CARD_NLR_Subtilase subtype locus represented by the CARD_NLR_Subtilase rule row requiring the CARD_NLR__Subtilase_long_new profile.",
    "definition_source": "DOI:10.1101/2023.05.28.542683",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000337"
    ],
    "synonyms": [
      {
        "synonym_text": "CARD_NLR_Subtilase",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv"
      },
      {
        "synonym_text": "CARD_NLR__Subtilase_long_new",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv"
      },
      {
        "synonym_text": "CARD_NLR__CARD_Protease",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv"
      },
      {
        "synonym_text": "CARD_NLR__NLR_new",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv"
      },
      {
        "synonym_text": "CARD_NLR__Trypsin",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv"
      }
    ],
    "evidence": [
      {
        "reference": "https://europepmc.org/article/PPR/PPR668921",
        "snippet": "Here we show that CARD-like domains are present in defense systems that protect bacteria against phage.",
        "notes": "Wein et al. support bacterial CARD-like domains as parts of anti-phage defense systems."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| CARD_NLR | 10\\.1101/2023\\.05\\.28\\.542683 | CARD-like domains mediate anti-phage defense in bacterial gasdermin systems | ",
        "notes": "The pinned DefenseFinder article registry maps the CARD_NLR model namespace to the Wein et al. CARD-like-domain anti-phage defense preprint."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| CARD_NLR__Subtilase                              | CARD_NLR__Subtilase                              | CARD_NLR               | Custom                  | 500    |\n| CARD_NLR__Subtilase_small_new                    | CARD_NLR__Subtilase_small_new                    | CARD_NLR               | Custom                  | 500    |",
        "notes": "The pinned DefenseFinder HMM inventory records two custom CARD_NLR subtilase-family profile rows, while the exact CARD_NLR__Subtilase_long_new rule profile was not present under the CARD_NLR model namespace."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "CARD_NLR\tCARD_NLR_Subtilase\t1\t3\tCARD_NLR__Subtilase_long_new\tCARD_NLR__CARD_Protease, CARD_NLR__NLR_new, CARD_NLR__Trypsin\tCARD_NLR__Endonuclease, CARD_NLR__Endonuclease_new, CARD_NLR__Phospho, CARD_NLR__Phospho_Trypsin, CARD_NLR__Trypsin_Phospho, CARD_NLR__Trypsine_Endonuclease_new, GasderMIN__bGSDM\t",
        "notes": "The pinned DefenseFinder rules table models CARD_NLR_Subtilase as a CARD_NLR subsystem requiring the CARD_NLR__Subtilase_long_new rule profile with CARD_Protease, NLR_new, and Trypsin accessory profiles."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "card_nlr_subtilase_locus_subtype_defense",
        "title": "CARD-NLR subtilase loci mark a CARD-NLR antiphage subtype",
        "description": "Conservative subtype-level sketch linking a DefenseFinder CARD_NLR_Subtilase locus to CARD-like anti-phage defense and CARD-NLR subtilase system possession.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures the CARD_NLR_Subtilase subtype at DefenseFinder rule-row level without asserting the exact subtilase substrate, phage trigger, native host breadth, CARD-to-effector activation sequence, how the missing CARD_NLR__Subtilase_long_new HMM row maps to the listed CARD_NLR subtilase profiles, or whether every DefenseFinder CARD_NLR_Subtilase prediction is a complete experimentally active locus.",
        "nodes": [
          {
            "node_id": "card_nlr_subtilase_locus",
            "label": "CARD-NLR subtilase locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A DefenseFinder CARD_NLR_Subtilase subtype locus represented by the CARD_NLR__Subtilase_long_new rule profile and generic CARD_NLR accessory profiles."
          },
          {
            "node_id": "card_like_antiphage_defense",
            "label": "CARD-like antiphage defense",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Anti-phage defense mediated by a bacterial CARD-like defense system."
          },
          {
            "node_id": "card_nlr_subtilase_system_trait",
            "label": "CARD-NLR subtilase system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000553",
            "description": "Possession of a genome-encoded CARD-NLR subtilase phage-defense system."
          },
          {
            "node_id": "card_nlr_system_trait",
            "label": "CARD-NLR system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000337",
            "description": "Possession of a genome-encoded CARD-NLR phage-defense system."
          }
        ],
        "edges": [
          {
            "subject": "card_nlr_subtilase_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "card_like_antiphage_defense",
            "description": "CARD_NLR_Subtilase loci are represented in DefenseFinder by a CARD_NLR__Subtilase_long_new rule profile plus CARD_NLR accessory profiles.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "CARD_NLR\tCARD_NLR_Subtilase\t1\t3\tCARD_NLR__Subtilase_long_new\tCARD_NLR__CARD_Protease, CARD_NLR__NLR_new, CARD_NLR__Trypsin\tCARD_NLR__Endonuclease, CARD_NLR__Endonuclease_new, CARD_NLR__Phospho, CARD_NLR__Phospho_Trypsin, CARD_NLR__Trypsin_Phospho, CARD_NLR__Trypsine_Endonuclease_new, GasderMIN__bGSDM\t",
                "notes": "The pinned DefenseFinder rules table models CARD_NLR_Subtilase as a CARD_NLR subsystem requiring the CARD_NLR__Subtilase_long_new rule profile with CARD_Protease, NLR_new, and Trypsin accessory profiles."
              }
            ]
          },
          {
            "subject": "card_like_antiphage_defense",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "card_nlr_subtilase_system_trait",
            "description": "The first-pass CARD-NLR subtilase system trait is realized by a DefenseFinder CARD_NLR_Subtilase subtype locus.",
            "evidence": [
              {
                "reference": "https://europepmc.org/article/PPR/PPR668921",
                "snippet": "Here we show that CARD-like domains are present in defense systems that protect bacteria against phage.",
                "notes": "Wein et al. support bacterial CARD-like domains as parts of anti-phage defense systems."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "CARD_NLR_Subtilase\t1\t3\tCARD_NLR__Subtilase_long_new\tCARD_NLR__CARD_Protease, CARD_NLR__NLR_new, CARD_NLR__Trypsin",
                "notes": "The pinned DefenseFinder rules table models CARD_NLR_Subtilase as a CARD_NLR subsystem requiring the CARD_NLR__Subtilase_long_new rule profile with CARD_Protease, NLR_new, and Trypsin accessory profiles."
              }
            ]
          },
          {
            "subject": "card_nlr_subtilase_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "card_nlr_system_trait",
            "description": "CARD-NLR subtilase system possession is a CARD-NLR-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| CARD_NLR | 10\\.1101/2023\\.05\\.28\\.542683 | CARD-like domains mediate anti-phage defense in bacterial gasdermin systems | ",
                "notes": "The pinned DefenseFinder article registry maps the CARD_NLR model namespace to the Wein et al. CARD-like-domain anti-phage defense preprint."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "CARD_NLR\tCARD_NLR_Subtilase\t1\t3\tCARD_NLR__Subtilase_long_new",
                "notes": "The pinned DefenseFinder rules table places the CARD_NLR_Subtilase subsystem under the CARD_NLR system key and requires CARD_NLR__Subtilase_long_new."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "card-nlr-subtilase-activity-gap",
        "prompt": "Resolve the CARD_NLR_Subtilase phage triggers, native hosts, CARD_NLR__Subtilase_long_new HMM inventory coverage, subtilase effector substrate, CARD-to-effector activation sequence, and profile-to-activity criteria before minting enzyme, trigger, or component children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Wein et al. support CARD-like anti-phage defense systems, and the pinned DefenseFinder rules table supports CARD_NLR_Subtilase as a rule-row subtype with a CARD_NLR__Subtilase_long_new rule profile. This first-pass record leaves exact phage triggers, native hosts, accessory-profile requirements, subtilase substrates, CARD-to-subtilase activation, and exact HMM profile coverage unresolved because the pinned HMM inventory lists CARD_NLR__Subtilase and CARD_NLR__Subtilase_small_new but not CARD_NLR__Subtilase_long_new.",
        "evidence": [
          {
            "reference": "https://europepmc.org/article/PPR/PPR668921",
            "snippet": "Here we show that CARD-like domains are present in defense systems that protect bacteria against phage.",
            "notes": "Wein et al. support bacterial CARD-like domains as parts of anti-phage defense systems."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| CARD_NLR__Subtilase                              | CARD_NLR__Subtilase                              | CARD_NLR               | Custom                  | 500    |\n| CARD_NLR__Subtilase_small_new                    | CARD_NLR__Subtilase_small_new                    | CARD_NLR               | Custom                  | 500    |",
            "notes": "The pinned DefenseFinder HMM inventory records two custom CARD_NLR subtilase-family profile rows, while the exact CARD_NLR__Subtilase_long_new rule profile was not present under the CARD_NLR model namespace."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "snippet": "CARD_NLR\tCARD_NLR_Subtilase\t1\t3\tCARD_NLR__Subtilase_long_new\tCARD_NLR__CARD_Protease, CARD_NLR__NLR_new, CARD_NLR__Trypsin\tCARD_NLR__Endonuclease, CARD_NLR__Endonuclease_new, CARD_NLR__Phospho, CARD_NLR__Phospho_Trypsin, CARD_NLR__Trypsin_Phospho, CARD_NLR__Trypsine_Endonuclease_new, GasderMIN__bGSDM\t",
            "notes": "The pinned DefenseFinder rules table models CARD_NLR_Subtilase as a CARD_NLR subsystem requiring the CARD_NLR__Subtilase_long_new rule profile with CARD_Protease, NLR_new, and Trypsin accessory profiles."
          }
        ],
        "attaches_to": [
          "causal_graphs#card_nlr_subtilase_locus_subtype_defense"
        ],
        "posed_by": "codex",
        "posed_date": "2026-10-02"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-02T19:23:10Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted CARD-NLR subtilase system as a DOI- and DefenseFinder-backed GENOMICS TraitRecord under the CARD-NLR system parent after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record for the target local ID, placeholder METPO ID, proposal cohort, record slug, or human label; existing CARD_NLR_Subtilase mentions were scoped to CARD-NLR parent evidence, not an exact child TraitRecord, and the replacement placeholder is reserved in proposals/metpo_traitmech_v430.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-02T19:23:12Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed CARD-NLR subtilase system during initial curation and left canonical_examples empty because Wein et al. and the pinned DefenseFinder tables support CARD-like anti-phage defense and the CARD_NLR_Subtilase rule row but not an accession-backed native microbial taxon exemplar tied to CARD_NLR_Subtilase profiles and experimentally verified endogenous CARD-NLR subtilase activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000337",
    "label": "CARD-NLR system",
    "definition": "A phage defense system in which an organism possesses a CARD-NLR locus represented by the DefenseFinder CARD_NLR model namespace, coupling bacterial CARD-like detector components and NLR-like profiles to subtype-specific GasderMIN, endonuclease, Trypsin_Phospho, or Subtilase effector profiles that can promote cell death after phage recognition.",
    "definition_source": "DOI:10.1101/2023.05.28.542683",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "CARD_NLR",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      },
      {
        "synonym_text": "CARD_NLR__CARD_Protease",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "CARD_NLR__NLR_new",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "https://europepmc.org/article/PPR/PPR668921",
        "snippet": "Here we show that CARD-like domains are present in defense systems that protect bacteria against phage.",
        "notes": "The Wein et al. abstract supports CARD-like-domain systems as bacterial phage-defense systems."
      },
      {
        "reference": "https://europepmc.org/article/PPR/PPR668921",
        "snippet": "The bacterial CARD is essential for protease-mediated activation of certain bacterial gasdermins, which promote cell death once phage infection is recognized.",
        "notes": "The Wein et al. abstract supports bacterial CARD-mediated protease activation of some bacterial gasdermins after phage recognition."
      },
      {
        "reference": "https://europepmc.org/article/PPR/PPR668921",
        "snippet": "We further show that multiple anti-phage defense systems utilize CARD-like domains to activate a variety of cell death effectors.",
        "notes": "The Wein et al. abstract states that multiple anti-phage systems use CARD-like domains to activate varied cell-death effectors."
      },
      {
        "reference": "https://europepmc.org/article/PPR/PPR668921",
        "snippet": "We find that these systems are triggered by a conserved immune evasion protein that phages use to overcome the bacterial defense system RexAB, demonstrating that phage proteins inhibiting one defense system can activate another.",
        "notes": "The Wein et al. abstract reports that these systems can be triggered by a phage immune-evasion protein."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "CARD_NLR | 10\\.1101/2023\\.05\\.28\\.542683 | CARD-like domains mediate anti-phage defense in bacterial gasdermin systems",
        "notes": "The DefenseFinder article registry maps the CARD_NLR model namespace to the Wein et al. bacterial CARD-like domain anti-phage defense preprint."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| CARD_NLR__CARD_Protease                          | CARD_NLR__CARD_Protease                          | CARD_NLR               | Custom                  | 300    |",
        "notes": "The DefenseFinder HMM inventory records a CARD-like protease profile under the CARD_NLR model namespace."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| CARD_NLR__NLR_new                                | CARD_NLR__NLR_new                                | CARD_NLR               | Custom                  | 100    |",
        "notes": "The DefenseFinder HMM inventory records an NLR profile under the CARD_NLR model namespace."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| CARD_NLR__Trypsin_Phospho                        | CARD_NLR__Trypsin_Phospho                        | CARD_NLR               | Custom                  | 400    |",
        "notes": "The DefenseFinder HMM inventory records a Trypsin_Phospho-profiled effector under the CARD_NLR model namespace."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "CARD_NLR\tCARD_NLR_Endonuclease\t1\t3\tCARD_NLR__Endonuclease\tCARD_NLR__CARD_Protease, CARD_NLR__NLR_new, CARD_NLR__Trypsin\tCARD_NLR__Phospho, CARD_NLR__Phospho_Trypsin, CARD_NLR__Subtilase, CARD_NLR__Subtilase_long_new, CARD_NLR__Subtilase_small_new, CARD_NLR__Trypsin_Phospho, GasderMIN__bGSDM\t",
        "notes": "The DefenseFinder rules table models a CARD_NLR endonuclease subtype with CARD-like and NLR-like accessory profiles."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "CARD_NLR\tCARD_NLR_GasderMIN\t1\t3\tGasderMIN__bGSDM\tCARD_NLR__CARD_Protease, CARD_NLR__NLR_new, CARD_NLR__Trypsin\tCARD_NLR__Endonuclease, CARD_NLR__Endonuclease_new, CARD_NLR__Phospho, CARD_NLR__Phospho_Trypsin, CARD_NLR__Subtilase, CARD_NLR__Subtilase_long_new, CARD_NLR__Subtilase_small_new, CARD_NLR__Trypsin_Phospho, CARD_NLR__Trypsine_Endonuclease_new\t",
        "notes": "The DefenseFinder rules table models a CARD_NLR_GasderMIN subtype with GasderMIN__bGSDM as its mandatory effector profile."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "CARD_NLR\tCARD_NLR_Phospho\t1\t3\tCARD_NLR__Trypsin_Phospho\tCARD_NLR__CARD_Protease, CARD_NLR__NLR_new, CARD_NLR__Trypsin\tCARD_NLR__Endonuclease, CARD_NLR__Endonuclease_new, CARD_NLR__Subtilase, CARD_NLR__Subtilase_long_new, CARD_NLR__Subtilase_small_new, CARD_NLR__Trypsine_Endonuclease_new, GasderMIN__bGSDM\t",
        "notes": "The DefenseFinder rules table models a CARD_NLR_Phospho subtype with CARD-like and NLR-like accessory profiles."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "CARD_NLR\tCARD_NLR_Subtilase\t1\t3\tCARD_NLR__Subtilase_long_new\tCARD_NLR__CARD_Protease, CARD_NLR__NLR_new, CARD_NLR__Trypsin\tCARD_NLR__Endonuclease, CARD_NLR__Endonuclease_new, CARD_NLR__Phospho, CARD_NLR__Phospho_Trypsin, CARD_NLR__Trypsin_Phospho, CARD_NLR__Trypsine_Endonuclease_new, GasderMIN__bGSDM\t",
        "notes": "The DefenseFinder rules table models a CARD_NLR subtilase subtype with CARD-like and NLR-like accessory profiles."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "CARD_NLR\tCARD_NLR_like\t2\t4\tCARD_NLR__Endonuclease, CARD_NLR__Phospho_Trypsin, CARD_NLR__Subtilase_long_new, CARD_NLR__Trypsin_Phospho\tCARD_NLR__CARD_Protease, CARD_NLR__NLR_new, CARD_NLR__Trypsin\t\t",
        "notes": "The DefenseFinder rules table also models a CARD_NLR_like subtype that requires two of several candidate effector profiles."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "card_nlr_loci_activate_cell_death_effectors",
        "title": "CARD-NLR loci activate antiphage cell-death effectors",
        "description": "System-level sketch linking a CARD-NLR locus to CARD-like detector activation, subtype-specific cell-death effector activation, and the CARD-NLR system trait without asserting the molecular mechanism of any one DefenseFinder subtype.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures CARD-NLR as a named DefenseFinder model namespace supported by Wein et al. CARD-like domain anti-phage defense evidence while leaving subtype-specific phage triggers, the effector activation sequence, GasderMIN-associated subtype boundaries, and endonuclease, Trypsin_Phospho, or Subtilase outputs unresolved.",
        "nodes": [
          {
            "node_id": "card_nlr_locus",
            "label": "CARD-NLR locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A bacterial anti-phage defense locus cataloged in DefenseFinder with CARD_NLR profiles."
          },
          {
            "node_id": "card_like_detector_activation",
            "label": "CARD-like detector activation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Activation of a bacterial CARD-like detector within a CARD-NLR system."
          },
          {
            "node_id": "cell_death_effector_activation",
            "label": "cell-death effector activation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Activation of a gasdermin or other subtype-specific cell-death effector by a CARD-like anti-phage defense system."
          },
          {
            "node_id": "phage_triggered_cell_death",
            "label": "phage-triggered cell death",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Host cell death promoted by a CARD-like bacterial anti-phage defense system."
          },
          {
            "node_id": "card_nlr_system_trait",
            "label": "CARD-NLR system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000337",
            "description": "Possession of a genome-encoded CARD-NLR phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "card_nlr_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "card_like_detector_activation",
            "description": "CARD-NLR loci couple CARD-like and NLR-like DefenseFinder profiles to subtype-specific effector profiles.",
            "evidence": [
              {
                "reference": "https://europepmc.org/article/PPR/PPR668921",
                "snippet": "Here we show that CARD-like domains are present in defense systems that protect bacteria against phage.",
                "notes": "Wein et al. support bacterial CARD-like domains as parts of anti-phage defense systems."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| CARD_NLR__CARD_Protease                          | CARD_NLR__CARD_Protease                          | CARD_NLR               | Custom                  | 300    |",
                "notes": "The DefenseFinder HMM inventory records a CARD-like protease profile under the CARD_NLR model namespace."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| CARD_NLR__NLR_new                                | CARD_NLR__NLR_new                                | CARD_NLR               | Custom                  | 100    |",
                "notes": "The DefenseFinder HMM inventory records an NLR profile under the CARD_NLR model namespace."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "CARD_NLR\tCARD_NLR_Endonuclease\t1\t3\tCARD_NLR__Endonuclease\tCARD_NLR__CARD_Protease, CARD_NLR__NLR_new, CARD_NLR__Trypsin\tCARD_NLR__Phospho, CARD_NLR__Phospho_Trypsin, CARD_NLR__Subtilase, CARD_NLR__Subtilase_long_new, CARD_NLR__Subtilase_small_new, CARD_NLR__Trypsin_Phospho, GasderMIN__bGSDM\t",
                "notes": "The DefenseFinder rules table models a CARD_NLR endonuclease subtype with CARD-like and NLR-like accessory profiles."
              }
            ]
          },
          {
            "subject": "card_like_detector_activation",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "cell_death_effector_activation",
            "description": "Bacterial CARD-like domains activate subtype-specific cell-death effectors.",
            "evidence": [
              {
                "reference": "https://europepmc.org/article/PPR/PPR668921",
                "snippet": "We further show that multiple anti-phage defense systems utilize CARD-like domains to activate a variety of cell death effectors.",
                "notes": "Wein et al. report multiple CARD-like-domain anti-phage systems that activate cell-death effectors."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "CARD_NLR\tCARD_NLR_GasderMIN\t1\t3\tGasderMIN__bGSDM\tCARD_NLR__CARD_Protease, CARD_NLR__NLR_new, CARD_NLR__Trypsin\tCARD_NLR__Endonuclease, CARD_NLR__Endonuclease_new, CARD_NLR__Phospho, CARD_NLR__Phospho_Trypsin, CARD_NLR__Subtilase, CARD_NLR__Subtilase_long_new, CARD_NLR__Subtilase_small_new, CARD_NLR__Trypsin_Phospho, CARD_NLR__Trypsine_Endonuclease_new\t",
                "notes": "The DefenseFinder rules table models a CARD_NLR_GasderMIN subtype with GasderMIN__bGSDM as its mandatory effector profile."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "CARD_NLR\tCARD_NLR_Phospho\t1\t3\tCARD_NLR__Trypsin_Phospho\tCARD_NLR__CARD_Protease, CARD_NLR__NLR_new, CARD_NLR__Trypsin\tCARD_NLR__Endonuclease, CARD_NLR__Endonuclease_new, CARD_NLR__Subtilase, CARD_NLR__Subtilase_long_new, CARD_NLR__Subtilase_small_new, CARD_NLR__Trypsine_Endonuclease_new, GasderMIN__bGSDM\t",
                "notes": "The DefenseFinder rules table models a CARD_NLR_Phospho subtype with CARD-like and NLR-like accessory profiles."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "CARD_NLR\tCARD_NLR_Subtilase\t1\t3\tCARD_NLR__Subtilase_long_new\tCARD_NLR__CARD_Protease, CARD_NLR__NLR_new, CARD_NLR__Trypsin\tCARD_NLR__Endonuclease, CARD_NLR__Endonuclease_new, CARD_NLR__Phospho, CARD_NLR__Phospho_Trypsin, CARD_NLR__Trypsin_Phospho, CARD_NLR__Trypsine_Endonuclease_new, GasderMIN__bGSDM\t",
                "notes": "The DefenseFinder rules table models a CARD_NLR subtilase subtype with CARD-like and NLR-like accessory profiles."
              }
            ]
          },
          {
            "subject": "cell_death_effector_activation",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "phage_triggered_cell_death",
            "description": "Activated gasdermin and non-gasdermin CARD-NLR effectors can promote defense-associated cell death.",
            "evidence": [
              {
                "reference": "https://europepmc.org/article/PPR/PPR668921",
                "snippet": "The bacterial CARD is essential for protease-mediated activation of certain bacterial gasdermins, which promote cell death once phage infection is recognized.",
                "notes": "Wein et al. support CARD-dependent gasdermin activation and cell death after phage recognition."
              },
              {
                "reference": "https://europepmc.org/article/PPR/PPR668921",
                "snippet": "We further show that multiple anti-phage defense systems utilize CARD-like domains to activate a variety of cell death effectors.",
                "notes": "Wein et al. generalize CARD-like-domain activation to multiple cell-death effector classes."
              }
            ]
          },
          {
            "subject": "phage_triggered_cell_death",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "card_nlr_system_trait",
            "description": "CARD-like effector-associated cell death realizes the CARD-NLR phage-defense-system output.",
            "evidence": [
              {
                "reference": "https://europepmc.org/article/PPR/PPR668921",
                "snippet": "We find that these systems are triggered by a conserved immune evasion protein that phages use to overcome the bacterial defense system RexAB, demonstrating that phage proteins inhibiting one defense system can activate another.",
                "notes": "Wein et al. support CARD-like-domain system triggering by a bacteriophage immune-evasion protein."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "CARD_NLR\tCARD_NLR_like\t2\t4\tCARD_NLR__Endonuclease, CARD_NLR__Phospho_Trypsin, CARD_NLR__Subtilase_long_new, CARD_NLR__Trypsin_Phospho\tCARD_NLR__CARD_Protease, CARD_NLR__NLR_new, CARD_NLR__Trypsin\t\t",
                "notes": "The DefenseFinder rules table also models a CARD_NLR_like subtype that requires two of several candidate effector profiles."
              }
            ]
          },
          {
            "subject": "card_nlr_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "CARD-NLR system possession is a phage-defense system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "CARD_NLR | 10\\.1101/2023\\.05\\.28\\.542683 | CARD-like domains mediate anti-phage defense in bacterial gasdermin systems",
                "notes": "The DefenseFinder article registry maps the CARD_NLR model namespace to the Wein et al. bacterial CARD-like domain anti-phage defense preprint."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "CARD_NLR\tCARD_NLR_Endonuclease\t1\t3\tCARD_NLR__Endonuclease\tCARD_NLR__CARD_Protease, CARD_NLR__NLR_new, CARD_NLR__Trypsin\tCARD_NLR__Phospho, CARD_NLR__Phospho_Trypsin, CARD_NLR__Subtilase, CARD_NLR__Subtilase_long_new, CARD_NLR__Subtilase_small_new, CARD_NLR__Trypsin_Phospho, GasderMIN__bGSDM\t",
                "notes": "The DefenseFinder rules table models a CARD_NLR endonuclease subtype with CARD-like and NLR-like accessory profiles."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "card-nlr-subtype-mechanism-gap",
        "prompt": "Resolve CARD-NLR subtype effectors, phage triggers, natural-host examples, and GasderMIN subtype boundaries before minting narrower CARD-NLR mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Wein et al. support CARD-like domains in multiple anti-phage defense systems that activate cell-death effectors, and DefenseFinder models CARD_NLR subtypes with gasdermin, endonuclease, CARD_NLR_Phospho, CARD_NLR_Subtilase, and CARD_NLR_like rule profiles. CARD-NLR GasderMIN, endonuclease, phospho, subtilase, and CARD-NLR-like TraitRecords now capture the five DefenseFinder CARD_NLR rule-row subtypes, but exact phage triggers, CARD-to-effector activation sequence, accession-level natural-host components, CARD_NLR_Subtilase_long_new HMM inventory coverage, CARD_NLR_like multi-effector semantics, and standalone GasderMIN versus CARD_NLR_GasderMIN mechanism boundaries remain unresolved.",
        "attaches_to": [
          "causal_graphs#card_nlr_loci_activate_cell_death_effectors"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-21"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-21T13:47:08Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted CARD-NLR system as a DOI- and stable-URL-backed GENOMICS TraitRecord under the phage defense system parent after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v214.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-02T19:23:11Z",
        "curator": "codex",
        "action": "TRACK_NARROWER_RECORD",
        "changes": "Documented CARD-NLR subtilase as split out in the open CARD-NLR subtype discussion after minting traitmech:000553 for the DefenseFinder-backed CARD_NLR_Subtilase child; exact subtilase substrates, CARD_NLR_Subtilase_long_new HMM inventory coverage, CARD_NLR_GasderMIN, CARD_NLR_like, and finer activation mechanisms remain open.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-02T21:05:01Z",
        "curator": "codex",
        "action": "TRACK_NARROWER_RECORD",
        "changes": "Documented CARD-NLR GasderMIN as split out in the open CARD-NLR subtype discussion after minting traitmech:000555 for the DefenseFinder-backed CARD_NLR_GasderMIN child; CARD_NLR_like and finer CARD-NLR activation mechanisms remain open.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-03T00:02:51Z",
        "curator": "codex",
        "action": "TRACK_NARROWER_RECORD",
        "changes": "Documented CARD-NLR-like as split out in the open CARD-NLR subtype discussion after minting traitmech:000559 for the DefenseFinder-backed CARD_NLR_like child; exact two-of-four effector-profile semantics, CARD_NLR__Subtilase_long_new HMM inventory coverage, and finer CARD-NLR activation mechanisms remain open.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000212",
    "label": "CBASS system",
    "definition": "A genomics trait describing possession of a cyclic-oligonucleotide-based antiphage signaling locus in which an oligonucleotide cyclase produces cyclic oligonucleotide signals during phage infection that activate an effector to inhibit bacteriophage replication.",
    "definition_source": "DOI:10.1038/s41586-019-1605-5",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "cyclic-oligonucleotide-based anti-phage signalling system",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1038/s41564-020-0777-y"
      },
      {
        "synonym_text": "cyclic-oligonucleotide-based anti-phage signaling system",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1038/s41564-020-0777-y"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/s41586-019-1605-5",
        "snippet": "cGAMP signalling is part of an antiphage defence system that is common in bacteria",
        "notes": "Cohen et al. experimentally established a bacterial cGAS-phospholipase system as a common antiphage defense system."
      },
      {
        "reference": "DOI:10.1038/s41586-019-1605-5",
        "snippet": "Phage infection triggers the production of cGAMP",
        "notes": "Cohen et al. support phage-triggered cyclic oligonucleotide production in an experimentally characterized cGAMP-phospholipase CBASS."
      },
      {
        "reference": "DOI:10.1038/s41564-020-0777-y",
        "snippet": "CBASS systems are composed of an oligonucleotide cyclase, which generates signalling cyclic oligonucleotides in response to phage infection",
        "notes": "Millman et al. generalized CBASS systems as oligonucleotide-cyclase-centered antiphage signaling loci."
      },
      {
        "reference": "DOI:10.1038/s41564-020-0777-y",
        "snippet": "identified more than 5,000 CBASS systems, which have diverse architectures",
        "notes": "Millman et al. support CBASS as a diverse recurring family across bacterial and archaeal genomes rather than a single four-gene operon."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:913088",
        "taxon_label": "Escherichia coli TW11681",
        "note": "Cohen et al. cloned the native E. coli TW11681 four-gene CBASS operon into E. coli MG1655 and measured P1 and coliphage resistance.",
        "reference": "DOI:10.1038/s41586-019-1605-5"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "cbass_cyclic_oligonucleotide_antiphage_defense",
        "title": "CBASS cyclic oligonucleotides activate abortive cell death",
        "description": "Evidence-backed process sketch linking CBASS oligonucleotide-cyclase activation to effector activation, abortive cell death, and blocked phage replication.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures the shared system-level CBASS logic of phage-triggered cyclic oligonucleotide synthesis and effector activation across multiple effector subtypes. The subtype-specific protein families carry the exact mechanistic edges and remain shifted from this first organism-level trait.",
        "nodes": [
          {
            "node_id": "cbass_oligonucleotide_cyclase_activation",
            "label": "CBASS oligonucleotide cyclase activation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Phage-infection-associated activation of a CBASS oligonucleotide cyclase."
          },
          {
            "node_id": "cyclic_oligonucleotide_synthesis",
            "label": "CBASS cyclic oligonucleotide synthesis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Production of cyclic oligonucleotide second messengers by an activated CBASS oligonucleotide cyclase."
          },
          {
            "node_id": "cbass_effector_activation",
            "label": "CBASS effector activation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Activation of a CBASS effector by a cyclic oligonucleotide signal."
          },
          {
            "node_id": "abortive_cell_death",
            "label": "abortive cell death",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Programmed death of an infected host cell before phage replication is completed."
          },
          {
            "node_id": "phage_replication",
            "label": "phage replication",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Replication and completion of a bacteriophage infection cycle inside a host cell."
          },
          {
            "node_id": "cbass_system_trait",
            "label": "CBASS system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000212",
            "description": "Possession of a genome-encoded CBASS phage defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "cbass_oligonucleotide_cyclase_activation",
            "predicate": "activates",
            "predicate_id": "RO:0002213",
            "object": "cyclic_oligonucleotide_synthesis",
            "description": "Phage sensing activates a CBASS oligonucleotide cyclase to synthesize cyclic oligonucleotide signals.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-020-0777-y",
                "snippet": "oligonucleotide cyclase, which generates signalling cyclic oligonucleotides in response to phage infection",
                "notes": "Millman et al. summarize phage-triggered oligonucleotide cyclase activation in their general CBASS model."
              }
            ]
          },
          {
            "subject": "cyclic_oligonucleotide_synthesis",
            "predicate": "activates",
            "predicate_id": "RO:0002213",
            "object": "cbass_effector_activation",
            "description": "CBASS cyclic oligonucleotide second messengers activate cognate effector proteins.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-020-0777-y",
                "snippet": "an effector that is activated by the cyclic oligonucleotides and promotes cell death",
                "notes": "Millman et al. support effector activation as the central output of CBASS cyclic oligonucleotide signaling."
              }
            ]
          },
          {
            "subject": "cbass_effector_activation",
            "predicate": "activates",
            "predicate_id": "RO:0002213",
            "object": "abortive_cell_death",
            "description": "CBASS effector activation induces host cell death through subtype-specific nuclease, phospholipase, or other toxic activities.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-020-0777-y",
                "snippet": "six effector subtypes that promote cell death by membrane impairment, DNA degradation or other means",
                "notes": "Millman et al. classified multiple CBASS effector subtypes that converge on host cell death."
              }
            ]
          },
          {
            "subject": "abortive_cell_death",
            "predicate": "mitigates",
            "predicate_id": "METPO:2007407",
            "object": "phage_replication",
            "description": "CBASS-induced death of the infected host cell aborts infection before phage replication is completed.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41586-019-1605-5",
                "snippet": "to cell death before completion of phage reproduction",
                "notes": "Cohen et al. experimentally tied CBASS cGAMP-phospholipase signaling to abortive cell death before the phage cycle completed."
              }
            ]
          },
          {
            "subject": "abortive_cell_death",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "cbass_system_trait",
            "description": "CBASS effector-induced abortive cell death realizes CBASS-mediated antiphage defense.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-020-0777-y",
                "snippet": "therefore preventing the spread of phages to nearby cells",
                "notes": "Millman et al. link cell death before phage replication completion to the protective output of CBASS loci."
              }
            ]
          },
          {
            "subject": "cbass_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "CBASS possession is a cyclic-oligonucleotide-mediated phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-020-0777-y",
                "snippet": "a family of defence systems against bacteriophages",
                "notes": "Millman et al. place CBASS in the phage defense system family."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "cbass-subtype-mechanism-gap",
        "prompt": "Resolve CBASS subtype-specific sensing and effector mechanisms before splitting cGAMP-phospholipase, cAAA-nuclease, ancillary-gene, or individual CD-NTase protein-family edges into reviewed graph groundings.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Cohen et al. resolved a phage-triggered cGAMP-phospholipase CBASS system and Millman et al. classified CBASS loci into four major types with multiple signaling molecules, effectors, and ancillary genes; exact phage sensors and subtype-specific effector families remain shifted from this first organism-level trait.",
        "posed_by": "codex",
        "posed_date": "2026-09-15"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-15T10:20:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted CBASS system as a DOI-backed GENOMICS TraitRecord under the phage defense system parent after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v89.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000288",
    "label": "Ceres system",
    "definition": "A phage defense system in which an organism possesses a Ceres locus that can protect bacteria from bacteriophage infection.",
    "definition_source": "DOI:10.1101/2025.01.08.631966",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "Ceres",
        "synonym_type": "EXACT_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      },
      {
        "synonym_text": "CrsA1",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "CrsA2",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1101/2025.01.08.631966",
        "snippet": "Among the remaining eight systems, six demonstrated increased resistance to at least one phage with more than 100 fold reduction in plaque forming units (PFU) (Figure 3a, Supplementary Figure 5). As Streptomyces are mostly soil dwelling bacteria, we named these systems after deities of the soil and earth (Ceres, Geb, Veles, Prithvi, Ukko and Oshun).",
        "notes": "Mordret et al. directly name Ceres among six Streptomyces systems that increased resistance to at least one phage."
      },
      {
        "reference": "DOI:10.1101/2025.01.08.631966",
        "snippet": "The bacterial pangenome encodes an immense array of antiphage systems, yet much of their diversity remains uncharted",
        "notes": "Mordret et al. motivate a conservative system-level record that does not assert a resolved Ceres trigger, effector output, or universal pathway."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "Ceres | 10\\.1101/2025\\.01\\.08\\.631966 | Protein and genomic language models chart a vast landscape of antiphage defenses",
        "notes": "The DefenseFinder model registry maps the named Ceres system to the Mordret et al. antiphage-system discovery preprint."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "Ceres__CrsA1                                     |                                                  | Ceres",
        "notes": "The DefenseFinder HMM inventory records CrsA1 in the Ceres model namespace."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "Ceres__CrsA2                                     |                                                  | Ceres",
        "notes": "The DefenseFinder HMM inventory records CrsA2 in the Ceres model namespace."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "ceres_locus_restricts_phage",
        "title": "Ceres loci confer bacterial phage defense",
        "description": "Conservative system-level sketch linking possession of a Ceres locus to restricted bacteriophage propagation without asserting the unresolved phage trigger or molecular output.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Ceres as a named anti-phage system with CrsA1 and CrsA2 DefenseFinder HMM profile entries while leaving its phage trigger, molecular substrate, antiviral effector output, and subtype breadth unresolved.",
        "nodes": [
          {
            "node_id": "ceres_locus",
            "label": "Ceres locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A Ceres anti-phage defense locus cataloged in DefenseFinder with CrsA1 and CrsA2 HMM profile entries."
          },
          {
            "node_id": "restricted_phage_propagation",
            "label": "restricted phage propagation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced propagation of bacteriophage in cells carrying the Ceres system."
          },
          {
            "node_id": "ceres_system_trait",
            "label": "Ceres system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000288",
            "description": "Possession of a genome-encoded Ceres phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "ceres_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "restricted_phage_propagation",
            "description": "DefenseFinder maps Ceres to a protein- and genomic-language-model antiphage-system discovery preprint and catalogs CrsA1 and CrsA2 HMM profile entries in the Ceres model namespace.",
            "evidence": [
              {
                "reference": "DOI:10.1101/2025.01.08.631966",
                "snippet": "Among the remaining eight systems, six demonstrated increased resistance to at least one phage with more than 100 fold reduction in plaque forming units (PFU) (Figure 3a, Supplementary Figure 5). As Streptomyces are mostly soil dwelling bacteria, we named these systems after deities of the soil and earth (Ceres, Geb, Veles, Prithvi, Ukko and Oshun).",
                "notes": "Mordret et al. directly name Ceres among six Streptomyces systems that restricted at least one phage."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Ceres | 10\\.1101/2025\\.01\\.08\\.631966 | Protein and genomic language models chart a vast landscape of antiphage defenses",
                "notes": "The DefenseFinder registry maps Ceres itself to the Mordret et al. bacterial antiphage-system discovery preprint."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "Ceres__CrsA1                                     |                                                  | Ceres",
                "notes": "The DefenseFinder HMM inventory records CrsA1 in the Ceres model namespace."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "Ceres__CrsA2                                     |                                                  | Ceres",
                "notes": "The DefenseFinder HMM inventory records CrsA2 in the Ceres model namespace."
              }
            ]
          },
          {
            "subject": "restricted_phage_propagation",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "ceres_system_trait",
            "description": "Ceres-mediated phage restriction realizes the Ceres system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1101/2025.01.08.631966",
                "snippet": "Among the remaining eight systems, six demonstrated increased resistance to at least one phage with more than 100 fold reduction in plaque forming units (PFU) (Figure 3a, Supplementary Figure 5). As Streptomyces are mostly soil dwelling bacteria, we named these systems after deities of the soil and earth (Ceres, Geb, Veles, Prithvi, Ukko and Oshun).",
                "notes": "Mordret et al. directly name Ceres among six systems that increased resistance to at least one phage."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Ceres | 10\\.1101/2025\\.01\\.08\\.631966 | Protein and genomic language models chart a vast landscape of antiphage defenses",
                "notes": "DefenseFinder records Ceres as a named system from the Mordret et al. antiphage discovery preprint."
              }
            ]
          },
          {
            "subject": "ceres_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Ceres system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| Ceres | 10\\.1101/2025\\.01\\.08\\.631966 | Protein and genomic language models chart a vast landscape of antiphage defenses |",
                "notes": "DefenseFinder associates Ceres with the Mordret et al. bacterial antiphage-system discovery preprint."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "ceres-mechanism-gap",
        "prompt": "Resolve Ceres phage triggers and effector outputs before minting narrower Ceres mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Mordret et al. and DefenseFinder support Ceres as a named anti-phage system with CrsA1 and CrsA2 HMM profile entries, but the trigger, molecular substrate, antiviral effector output, and subtype-specific mechanism are not resolved enough here to assert a narrower mechanistic child trait.",
        "attaches_to": [
          "causal_graphs#ceres_locus_restricts_phage"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-19"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-19T18:23:47Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Ceres system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v165.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000271",
    "label": "Cernunnos system",
    "definition": "A phage defense system in which an organism possesses a Cernunnos locus represented by a VCA0410 profile that can protect bacteria from bacteriophage infection.",
    "definition_source": "DOI:10.1126/science.ads0768",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "Cernunnos",
        "synonym_type": "EXACT_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      },
      {
        "synonym_text": "VCA0410",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1126/science.ads0768",
        "snippet": "nearly 10% of the integron cassettes in the pandemic Vibrio cholerae strain encode novel antiphage functions",
        "notes": "Darracq et al. support treating the newly discovered Vibrio cholerae SCI antiphage cassettes as bacterial anti-phage systems."
      },
      {
        "reference": "DOI:10.1126/science.ads0768",
        "snippet": "Most of these novel systems have little or no similarity to previously known ones, with several providing defense through cell lysis or growth arrest",
        "notes": "Darracq et al. support a conservative system record that does not assert a resolved Cernunnos trigger, effector output, or universal pathway."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "Cernunnos | 10\\.1126/science\\.ads0768 | Sedentary chromosomal integrons as biobanks of bacterial antiphage defense systems",
        "notes": "The DefenseFinder model registry maps the named Cernunnos system to the Darracq et al. SCI antiphage-system paper."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "Cernunnos__VCA0410                               |                                                  | Cernunnos",
        "notes": "The DefenseFinder HMM inventory records VCA0410 in the Cernunnos model namespace."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "cernunnos_locus_restricts_phage",
        "title": "Cernunnos loci confer bacterial phage defense",
        "description": "Conservative system-level sketch linking possession of a Cernunnos locus to restricted bacteriophage propagation without asserting the unresolved phage trigger or molecular output.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Cernunnos as a named SCI-derived anti-phage system with a VCA0410 DefenseFinder profile while leaving its phage trigger, molecular substrate, antiviral effector output, and subtype breadth unresolved.",
        "nodes": [
          {
            "node_id": "cernunnos_locus",
            "label": "Cernunnos locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A Cernunnos anti-phage defense locus represented in DefenseFinder by a VCA0410 profile."
          },
          {
            "node_id": "restricted_phage_propagation",
            "label": "restricted phage propagation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced propagation of bacteriophage in cells carrying the Cernunnos system."
          },
          {
            "node_id": "cernunnos_system_trait",
            "label": "Cernunnos system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000271",
            "description": "Possession of a genome-encoded Cernunnos phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "cernunnos_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "restricted_phage_propagation",
            "description": "DefenseFinder maps Cernunnos to an SCI anti-phage-system discovery paper and represents Cernunnos loci through the VCA0410 component profile.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.ads0768",
                "snippet": "nearly 10% of the integron cassettes in the pandemic Vibrio cholerae strain encode novel antiphage functions",
                "notes": "Darracq et al. describe the newly discovered antiphage-system cohort that the DefenseFinder Cernunnos registry row maps to the Cernunnos system."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "Cernunnos__VCA0410                               |                                                  | Cernunnos",
                "notes": "The DefenseFinder HMM inventory supports VCA0410 as the Cernunnos component profile."
              }
            ]
          },
          {
            "subject": "restricted_phage_propagation",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "cernunnos_system_trait",
            "description": "Cernunnos-mediated phage restriction realizes the Cernunnos system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.ads0768",
                "snippet": "Most of these novel systems have little or no similarity to previously known ones",
                "notes": "Darracq et al. place the Cernunnos discovery cohort in a set of novel bacterial systems that protect against phages."
              }
            ]
          },
          {
            "subject": "cernunnos_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Cernunnos system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Cernunnos | 10\\.1126/science\\.ads0768 | Sedentary chromosomal integrons as biobanks of bacterial antiphage defense systems",
                "notes": "DefenseFinder associates Cernunnos with the Darracq et al. bacterial antiphage-system paper."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "cernunnos-mechanism-gap",
        "prompt": "Resolve Cernunnos phage triggers and effector outputs before minting narrower Cernunnos mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Darracq et al. and DefenseFinder support Cernunnos as a named anti-phage system with a VCA0410 profile, but the trigger, molecular substrate, antiviral effector output, and subtype-specific mechanism are not resolved enough here to assert a narrower mechanistic child trait.",
        "attaches_to": [
          "causal_graphs#cernunnos_locus_restricts_phage"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-19"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-19T08:00:30Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Cernunnos system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v148.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000295",
    "label": "Charlie gp32 system",
    "definition": "A phage defense system in which an organism possesses a Charlie gp32 locus that can protect bacteria from bacteriophage infection.",
    "definition_source": "DOI:10.1038/nmicrobiol.2016.251",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "Charlie gp32 defense system",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1038/nmicrobiol.2016.251"
      },
      {
        "synonym_text": "Charlie_gp32",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/nmicrobiol.2016.251",
        "snippet": "at least five distinct prophage-expressed viral defense systems that interfere with infection",
        "notes": "Dedrick et al. place the Cluster N Charlie gp32 system in a cohort of prophage-expressed defenses against lytic and temperate mycobacteriophages."
      },
      {
        "reference": "DOI:10.1038/nmicrobiol.2016.251",
        "snippet": "The gene responsible is Charlie 32 (and presumably the analogous genes in Xeno and SkinnyPete), and a Charlie lysogen in which 32 is deleted loses defense against Che9c",
        "notes": "Dedrick et al. localize a Cluster N prophage-mediated heterotypic defense to Charlie gene 32."
      },
      {
        "reference": "DOI:10.1038/nmicrobiol.2016.251",
        "snippet": "The Charlie gp32 defense system is notable in that although it has the characteristics of superinfection exclusion systems \u2013 being membrane located and preventing DNA injection \u2013 it has remarkable specificity for a single phage among those tested",
        "notes": "Dedrick et al. explicitly name the Charlie gp32 defense system as an exclusion-like viral-defense system."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "Charlie_gp32 | 10\\.1038/nmicrobiol\\.2016\\.251 | Prophage-mediated defence against viral attack and viral counter-defence",
        "notes": "The DefenseFinder model registry maps the named Charlie_gp32 system to the Dedrick et al. prophage-mediated viral-defense paper."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "Charlie_gp32__gp32                               | Charlie_gp32__gp32                               | Charlie_gp32",
        "notes": "The DefenseFinder HMM inventory records gp32 in the Charlie_gp32 model namespace."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "charlie_gp32_locus_blocks_phage_entry",
        "title": "Charlie gp32 loci confer heterotypic phage exclusion",
        "description": "Conservative system-level sketch linking possession of a Charlie gp32 locus to blocked Che9c DNA injection and restricted bacteriophage propagation.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Charlie gp32 as a named anti-phage system with a DefenseFinder gp32 profile and a proposed Che9c-exclusion output while leaving the direct gp32 target, the membrane-blocking mechanism, and homolog breadth unresolved.",
        "nodes": [
          {
            "node_id": "charlie_gp32_locus",
            "label": "Charlie gp32 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A Charlie gp32 anti-phage defense locus cataloged in DefenseFinder with a gp32 HMM profile."
          },
          {
            "node_id": "blocked_che9c_dna_injection",
            "label": "blocked Che9c DNA injection",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced Che9c bacteriophage DNA injection across the cell envelope in cells carrying Charlie gp32."
          },
          {
            "node_id": "restricted_phage_propagation",
            "label": "restricted phage propagation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced propagation of bacteriophage in cells carrying the Charlie gp32 system."
          },
          {
            "node_id": "charlie_gp32_system_trait",
            "label": "Charlie gp32 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000295",
            "description": "Possession of a genome-encoded Charlie gp32 phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "charlie_gp32_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "blocked_che9c_dna_injection",
            "description": "Dedrick et al. identify Charlie 32 as the gene responsible for Che9c defense, and DefenseFinder catalogs a gp32 profile in the Charlie_gp32 model namespace.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nmicrobiol.2016.251",
                "snippet": "The gene responsible is Charlie 32 (and presumably the analogous genes in Xeno and SkinnyPete), and a Charlie lysogen in which 32 is deleted loses defense against Che9c",
                "notes": "Dedrick et al. support Charlie gp32 as the genetic determinant of the Che9c-exclusion phenotype."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "Charlie_gp32__gp32                               | Charlie_gp32__gp32                               | Charlie_gp32",
                "notes": "The DefenseFinder HMM inventory records gp32 in the Charlie_gp32 model namespace."
              }
            ]
          },
          {
            "subject": "blocked_che9c_dna_injection",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "restricted_phage_propagation",
            "description": "Charlie-gp32-mediated blockade of Che9c DNA injection reduces productive phage infection.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nmicrobiol.2016.251",
                "snippet": "We propose that Charlie gp32 confers heterotypic exclusion, blocking Che9c DNA injection across the membrane",
                "notes": "Dedrick et al. interpret Charlie gp32 defense as an exclusion-like block to Che9c DNA injection."
              }
            ]
          },
          {
            "subject": "restricted_phage_propagation",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "charlie_gp32_system_trait",
            "description": "Charlie-gp32-mediated Che9c exclusion realizes the Charlie gp32 system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nmicrobiol.2016.251",
                "snippet": "Charlie gp32 confers survival to Che9c infection, which also is a temperate phage",
                "notes": "Dedrick et al. show a cellular survival outcome for Charlie-gp32-mediated Che9c defense."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Charlie_gp32 | 10\\.1038/nmicrobiol\\.2016\\.251 | Prophage-mediated defence against viral attack and viral counter-defence",
                "notes": "DefenseFinder records Charlie_gp32 as a named system from the Dedrick et al. prophage-defense paper."
              }
            ]
          },
          {
            "subject": "charlie_gp32_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Charlie gp32 system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| Charlie_gp32 | 10\\.1038/nmicrobiol\\.2016\\.251 | Prophage-mediated defence against viral attack and viral counter-defence |",
                "notes": "DefenseFinder associates Charlie_gp32 with the Dedrick et al. prophage-mediated viral-defense paper."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "charlie_gp32-mechanism-gap",
        "prompt": "Resolve the Charlie gp32 membrane target, Che9c specificity, and homolog breadth before minting narrower Charlie gp32 mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Dedrick et al. and DefenseFinder support Charlie gp32 as a named anti-phage system with a gp32 profile, but the direct membrane target, determinants of its Che9c specificity, and breadth of homologous loci are not resolved enough here to assert a narrower mechanistic child trait.",
        "attaches_to": [
          "causal_graphs#charlie_gp32_locus_blocks_phage_entry"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-19"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-19T22:40:37Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Charlie gp32 system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v172.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-19T23:02:19Z",
        "curator": "codex",
        "action": "CURATION_REVIEW_REVISION",
        "changes": "Resolved PR #1089 review issues #1090 and #1091 by dropping the proposed heterotypic-exclusion mechanism from the definition and tightening the Charlie gp32 exact-synonym evidence snippet after rechecking the Dedrick et al. full text and pinned DefenseFinder rows.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-19T23:11:07Z",
        "curator": "codex",
        "action": "CURATION_REVIEW_REVISION",
        "changes": "Resolved the follow-up PR #1089 review issue #1091 by restoring a complete Dedrick et al. P25 source clause, including American defense spelling as verified in the local PMC full text.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000415",
    "label": "Clover system",
    "definition": "A phage defense system in which an organism possesses a Clover anti-phage system whose CloA deoxynucleoside triphosphohydrolase dynamically responds to an activating phage cue and to a CloB-produced inhibitory p3diT nucleotide signal to coordinate nucleotide-pool disruption during antiviral immunity.",
    "definition_source": "DOI:10.1038/s41586-026-10135-0",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "Clover",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1038/s41586-026-10135-0"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/s41586-026-10135-0",
        "snippet": "Here we identify Clover, a bacterial anti-phage defence system that overcomes this trade-off by encoding a deoxynucleoside triphosphohydrolase enzyme (CloA) that dynamically responds to both an activating phage cue and an inhibitory nucleotide immune signal produced by a partnering regulatory enzyme (CloB).",
        "notes": "Yu and Kranzusch define Clover as a bacterial anti-phage defence system encoding CloA and CloB."
      },
      {
        "reference": "DOI:10.1038/s41586-026-10135-0",
        "snippet": "Analysis of phage restriction by Clover in cells and reconstitution of enzymatic function in vitro demonstrate that CloA is a dGTPase that responds to viral enzymes that increase cellular levels of dTTP.",
        "notes": "Yu and Kranzusch support CloA as a Clover dGTPase that responds to viral enzymes that increase cellular dTTP."
      },
      {
        "reference": "DOI:10.1038/s41586-026-10135-0",
        "snippet": "To restrain CloA activation in the absence of infection, we show that CloB synthesizes a dTTP-related inhibitory nucleotide signal, p3diT",
        "notes": "Yu and Kranzusch support CloB synthesis of the inhibitory p3diT nucleotide signal."
      },
      {
        "reference": "DOI:10.1038/s41586-026-10135-0",
        "snippet": "Cryo-electron microscopy structures of CloA in activated and suppressed states reveal how dTTP and p3diT control distinct allosteric sites and regulate effector function.",
        "notes": "Yu and Kranzusch resolve activated and suppressed CloA states controlled by dTTP and p3diT."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| Clover | 10\\.1038/s41586-026-10135-0 | Nucleotide signals coordinate activation and inhibition of bacterial immunity |",
        "notes": "The pinned DefenseFinder article registry maps the named Clover system to the Yu and Kranzusch nucleotide-signal anti-phage-defense paper. The pinned HMM inventory and rules table do not list Clover, so this row is name-to-paper evidence rather than model-component evidence."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "clover_dttp_p3dit_regulated_dgtpase",
        "title": "Clover coordinates CloA activation and inhibition",
        "description": "Conservative sketch linking a Clover locus to p3diT-gated CloA dGTPase activity, regulation of antiviral immunity, and Clover system possession.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Clover at the experimentally supported CloA/CloB dGTPase-regulation level without asserting exact native host breadth, full sensitive-phage breadth, profile-to-component mappings, or a DefenseFinder detection rule absent from the pinned model files.",
        "nodes": [
          {
            "node_id": "clover_locus",
            "label": "Clover locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A Clover anti-phage locus encoding the CloA dGTPase and partnering CloB regulatory enzyme."
          },
          {
            "node_id": "cloa_dgtpase_activation",
            "label": "CloA dGTPase activation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Activation of CloA deoxynucleoside triphosphohydrolase activity in response to a phage cue linked to increased dTTP."
          },
          {
            "node_id": "clob_p3dit_synthesis",
            "label": "CloB p3diT synthesis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "CloB synthesis of a dTTP-related p3diT inhibitory nucleotide signal that suppresses CloA activation without infection."
          },
          {
            "node_id": "clover_system_trait",
            "label": "Clover system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000415",
            "description": "Possession of a genome-encoded Clover phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "clover_locus",
            "predicate": "enables",
            "predicate_id": "RO:0002327",
            "object": "cloa_dgtpase_activation",
            "description": "A Clover locus encodes the CloA dGTPase that responds to viral enzymes increasing cellular dTTP.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41586-026-10135-0",
                "snippet": "Here we identify Clover, a bacterial anti-phage defence system that overcomes this trade-off by encoding a deoxynucleoside triphosphohydrolase enzyme (CloA) that dynamically responds to both an activating phage cue and an inhibitory nucleotide immune signal produced by a partnering regulatory enzyme (CloB).",
                "notes": "Yu and Kranzusch identify Clover as the system encoding CloA and CloB."
              },
              {
                "reference": "DOI:10.1038/s41586-026-10135-0",
                "snippet": "Analysis of phage restriction by Clover in cells and reconstitution of enzymatic function in vitro demonstrate that CloA is a dGTPase that responds to viral enzymes that increase cellular levels of dTTP.",
                "notes": "Yu and Kranzusch connect Clover to dTTP-responsive CloA dGTPase activity."
              }
            ]
          },
          {
            "subject": "clover_locus",
            "predicate": "enables",
            "predicate_id": "RO:0002327",
            "object": "clob_p3dit_synthesis",
            "description": "A Clover locus encodes CloB, which synthesizes the inhibitory p3diT signal.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41586-026-10135-0",
                "snippet": "To restrain CloA activation in the absence of infection, we show that CloB synthesizes a dTTP-related inhibitory nucleotide signal, p3diT",
                "notes": "Yu and Kranzusch connect CloB to p3diT synthesis."
              }
            ]
          },
          {
            "subject": "clob_p3dit_synthesis",
            "predicate": "negatively regulates",
            "predicate_id": "RO:0002212",
            "object": "cloa_dgtpase_activation",
            "description": "The CloB-produced p3diT nucleotide signal binds CloA and suppresses CloA activation.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41586-026-10135-0",
                "snippet": "To restrain CloA activation in the absence of infection, we show that CloB synthesizes a dTTP-related inhibitory nucleotide signal, p3diT",
                "notes": "Yu and Kranzusch support p3diT-dependent suppression of CloA activation."
              }
            ]
          },
          {
            "subject": "cloa_dgtpase_activation",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "clover_system_trait",
            "description": "Regulated CloA effector activity realizes Clover antiviral immunity.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41586-026-10135-0",
                "snippet": "Our results define how nucleotide signals coordinate both activation and inhibition of antiviral immunity",
                "notes": "Yu and Kranzusch frame nucleotide-mediated CloA activation and inhibition as coordinated antiviral immunity."
              },
              {
                "reference": "DOI:10.1038/s41586-026-10135-0",
                "snippet": "Cryo-electron microscopy structures of CloA in activated and suppressed states reveal how dTTP and p3diT control distinct allosteric sites and regulate effector function.",
                "notes": "Yu and Kranzusch show that dTTP and p3diT regulate Clover effector function through distinct CloA sites."
              }
            ]
          },
          {
            "subject": "clover_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Clover system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41586-026-10135-0",
                "snippet": "Here we identify Clover, a bacterial anti-phage defence system that overcomes this trade-off by encoding a deoxynucleoside triphosphohydrolase enzyme (CloA) that dynamically responds to both an activating phage cue and an inhibitory nucleotide immune signal produced by a partnering regulatory enzyme (CloB).",
                "notes": "Yu and Kranzusch define Clover as a bacterial anti-phage defence system."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| Clover | 10\\.1038/s41586-026-10135-0 | Nucleotide signals coordinate activation and inhibition of bacterial immunity |",
                "notes": "The pinned DefenseFinder article registry maps the named Clover system to the Yu and Kranzusch nucleotide-signal anti-phage-defense paper. The pinned HMM inventory and rules table do not list Clover, so this row is name-to-paper evidence rather than model-component evidence."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "clover-defensefinder-model-gap",
        "prompt": "Resolve Clover native host breadth, sensitive-phage breadth, profile-to-component coverage, and DefenseFinder HMM/rules coverage before minting narrower Clover mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Yu and Kranzusch support Clover as a bacterial anti-phage defence system whose CloA dGTPase is activated and suppressed by nucleotide signals, while the pinned DefenseFinder article registry names a Clover system. The pinned DefenseFinder HMM inventory and rules table have no Clover rows, and the evidence does not yet resolve native host breadth, full target-phage breadth, or profile-to-activity modeling.",
        "evidence": [
          {
            "reference": "DOI:10.1038/s41586-026-10135-0",
            "snippet": "Cryo-electron microscopy structures of CloA in activated and suppressed states reveal how dTTP and p3diT control distinct allosteric sites and regulate effector function.",
            "notes": "Yu and Kranzusch support a CloA/CloB mechanism regulated by dTTP and p3diT."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
            "snippet": "| Clover | 10\\.1038/s41586-026-10135-0 | Nucleotide signals coordinate activation and inhibition of bacterial immunity |",
            "notes": "The pinned DefenseFinder article registry maps the named Clover system to the Yu and Kranzusch nucleotide-signal anti-phage-defense paper. The pinned HMM inventory and rules table do not list Clover, so this row is name-to-paper evidence rather than model-component evidence."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "notes": "The pinned DefenseFinder HMM inventory does not list Clover, leaving profile-level components unresolved."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "The pinned DefenseFinder rules table does not list Clover, leaving rule-level detection criteria unresolved."
          }
        ],
        "attaches_to": [
          "causal_graphs#clover_dttp_p3dit_regulated_dgtpase"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-27"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-27T19:36:20Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Clover system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; kept the graph at CloA/CloB dGTPase-regulation level because the pinned DefenseFinder article row is not backed by pinned HMM or rules rows; the replacement placeholder is reserved in proposals/metpo_traitmech_v292.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-27T19:36:21Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed Clover system during canonical-example issue 444 enforcement and left canonical_examples empty because the sources support cloned Salmonella enterica and Escherichia coli operon expression in phage-challenge assays plus a DefenseFinder article-registry system name, but not a direct native microbial isolate exemplar with experimentally verified endogenous Clover activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000335",
    "label": "CmdTAC system",
    "definition": "An abortive infection system in which an organism possesses a cmdTAC toxin-antitoxin-chaperone locus whose CmdC chaperone senses viral capsid proteins and whose CmdA antitoxin degradation liberates the CmdT ADP-ribosyltransferase to modify messenger RNA, arrest translation, and inhibit bacteriophage replication.",
    "definition_source": "DOI:10.1038/s41586-024-08102-8",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000214"
    ],
    "synonyms": [
      {
        "synonym_text": "CmdTAC",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1038/s41586-024-08102-8"
      },
      {
        "synonym_text": "cmdTAC",
        "synonym_type": "EXACT_SYNONYM",
        "source": "https://pmc.ncbi.nlm.nih.gov/articles/PMC11618068/"
      },
      {
        "synonym_text": "cmdTAC toxin-antitoxin-chaperone locus",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1038/s41586-024-08102-8"
      },
      {
        "synonym_text": "PD-T4-9",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1038/s41586-024-08102-8"
      }
    ],
    "evidence": [
      {
        "reference": "https://pmc.ncbi.nlm.nih.gov/articles/PMC11618068/",
        "snippet": "Here we characterize the widely distributed anti-phage defence system CmdTAC, which provides robust defence against infection by the T-even family of phages",
        "notes": "Vassallo et al. name CmdTAC as a widely distributed anti-phage defense system that protects against T-even phages."
      },
      {
        "reference": "https://pmc.ncbi.nlm.nih.gov/articles/PMC11618068/",
        "snippet": "was discovered in the genome of the wild E. coli isolate ECOR22 through a functional genetic screen for anti-phage defence systems",
        "notes": "Vassallo et al. trace the CmdTAC system to a functional anti-phage defense screen of Escherichia coli ECOR22."
      },
      {
        "reference": "https://pmc.ncbi.nlm.nih.gov/articles/PMC11618068/",
        "snippet": "CmdC detects infection by sensing viral capsid proteins, ultimately leading to the activation of a toxic ADP-ribosyltransferase effector protein, CmdT",
        "notes": "CmdC senses phage infection through viral capsid proteins and activates the CmdT ADP-ribosyltransferase effector."
      },
      {
        "reference": "https://pmc.ncbi.nlm.nih.gov/articles/PMC11618068/",
        "snippet": "newly synthesized capsid protein triggers dissociation of the chaperone CmdC from the CmdTAC complex, leading to destabilization and degradation of the antitoxin CmdA",
        "notes": "Newly synthesized phage capsid protein can dissociate the CmdC chaperone from the complex and destabilize CmdA."
      },
      {
        "reference": "https://pmc.ncbi.nlm.nih.gov/articles/PMC11618068/",
        "snippet": "CmdT modifies the N6 position of adenine in GA dinucleotides within single-stranded RNAs, leading to arrest of mRNA translation and inhibition of viral replication",
        "notes": "Vassallo et al. support CmdT modification of single-stranded RNA as the translation-arresting antiphage effector output."
      },
      {
        "reference": "https://pmc.ncbi.nlm.nih.gov/articles/PMC11618068/",
        "snippet": "These results are consistent with CmdTAC functioning via an Abi mechanism.",
        "notes": "Vassallo et al. interpret the low-MOI protection and center-of-infection results as consistent with an abortive-infection mechanism."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "CmdTAC | 10\\.1038/s41586-024-08102-8 | Anti-viral defence by an mRNA ADP-ribosyltransferase that blocks translation",
        "notes": "The DefenseFinder article registry maps the named CmdTAC system to the Vassallo et al. CmdTAC mechanism paper. Its CmdTAC row is name-to-paper evidence; the pinned rule and HMM rows model the same DefenseFinder system under the PD-T4-9 namespace."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-9.md",
        "snippet": "The PD-T4-9 is composed of 3 proteins: PD-T4-9_A, PD-T4-9_B and PD-T4-9_C.",
        "notes": "The DefenseFinder wiki names the three protein components in the PD-T4-9 model."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-9.md",
        "snippet": "The PD-T4-9 system in *Vibrio parahaemolyticus* (GCF_001700835.1, NZ_CP010883) is composed of 3 proteins PD-T4-9_C (WP_065870458.1) PD-T4-9_B (WP_141106056.1) PD-T4-9_A (WP_065870460.1)",
        "notes": "The DefenseFinder wiki illustrates a predicted PD-T4-9 locus in RefSeq assembly GCF_001700835.1 on NZ_CP010883."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "PD-T4-9\tPD-T4-9\t2\t2\tPD-T4-9__PD-T4-9_A, PD-T4-9__PD-T4-9_C\tPD-T4-9__PD-T4-9_B\t\t",
        "notes": "The pinned DefenseFinder rules table models PD-T4-9 with PD-T4-9__PD-T4-9_A and PD-T4-9__PD-T4-9_C as required profiles and PD-T4-9__PD-T4-9_B as an accessory profile."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| PD-T4-9__PD-T4-9_A                               | PD-T4-9__PD-T4-9_A                               | PD-T4-9                | Custom                  | 20     |\n| PD-T4-9__PD-T4-9_B                               | PD-T4-9__PD-T4-9_B                               | PD-T4-9                | Custom                  | 20     |\n| PD-T4-9__PD-T4-9_C                               | PD-T4-9__PD-T4-9_C                               | PD-T4-9                | Custom                  | 20     |",
        "notes": "The pinned DefenseFinder HMM inventory records PD-T4-9__PD-T4-9_A, PD-T4-9__PD-T4-9_B, and PD-T4-9__PD-T4-9_C under the PD-T4-9 system namespace."
      },
      {
        "reference": "DOI:10.1038/s41586-024-08102-8",
        "snippet": "PD-T4-9 also contains a third component, a SecB-like chaperone, suggesting that it is related to an enigmatic class of TA systems called toxin-antitoxin-chaperone (TAC) systems, so we renamed this system CmdTAC",
        "notes": "Vassallo et al. state that PD-T4-9 was renamed CmdTAC after they recognized its SecB-like chaperone component."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:562",
        "taxon_label": "Escherichia coli",
        "note": "Vassallo et al. report that cmdTAC was discovered in wild Escherichia coli isolate ECOR22 through a functional anti-phage defense screen.",
        "reference": "DOI:10.1038/s41586-024-08102-8"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "cmdtac_mrna_adp_ribosylation_aborts_phage",
        "title": "CmdTAC activation blocks phage translation",
        "description": "Conservative system-level sketch linking a CmdTAC locus to CmdC capsid sensing, CmdA degradation, CmdT-mediated mRNA modification, translation arrest, and abortive phage defense.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures CmdTAC as a named toxin-antitoxin-chaperone abortive-infection system from Escherichia coli ECOR22 while leaving phage specificity beyond Tevenvirinae, escape routes, and natural family breadth unresolved.",
        "nodes": [
          {
            "node_id": "cmdtac_locus",
            "label": "cmdTAC locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A toxin-antitoxin-chaperone locus encoding CmdT, CmdA, and CmdC anti-phage defense components."
          },
          {
            "node_id": "cmdc_capsid_sensing",
            "label": "CmdC viral capsid sensing",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Detection of newly synthesized viral capsid protein through CmdC."
          },
          {
            "node_id": "cmda_degradation",
            "label": "CmdA antitoxin degradation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Destabilization and degradation of the CmdA antitoxin after phage-triggered chaperone dissociation."
          },
          {
            "node_id": "cmdt_mrna_adp_ribosylation",
            "label": "CmdT mRNA ADP-ribosylation",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "ADP-ribosyltransferase activity by liberated CmdT against single-stranded mRNA."
          },
          {
            "node_id": "mrna_translation_arrest",
            "label": "mRNA translation arrest",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Arrest of mRNA translation after CmdT-mediated messenger-RNA modification."
          },
          {
            "node_id": "cmdtac_system_trait",
            "label": "CmdTAC system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000335",
            "description": "Possession of a genome-encoded CmdTAC abortive-infection phage-defense system."
          },
          {
            "node_id": "abortive_infection_system_trait",
            "label": "abortive infection system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000214",
            "description": "Possession of a genome-encoded abortive-infection phage-defense system."
          }
        ],
        "edges": [
          {
            "subject": "cmdtac_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "cmdc_capsid_sensing",
            "description": "The cmdTAC locus encodes CmdC, which can sense viral capsid proteins.",
            "evidence": [
              {
                "reference": "https://pmc.ncbi.nlm.nih.gov/articles/PMC11618068/",
                "snippet": "CmdC detects infection by sensing viral capsid proteins",
                "notes": "Vassallo et al. connect CmdC to viral capsid protein sensing."
              }
            ]
          },
          {
            "subject": "cmdc_capsid_sensing",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "cmda_degradation",
            "description": "Newly synthesized capsid protein can trigger CmdC dissociation from CmdTAC and destabilize the CmdA antitoxin.",
            "evidence": [
              {
                "reference": "https://pmc.ncbi.nlm.nih.gov/articles/PMC11618068/",
                "snippet": "newly synthesized capsid protein triggers dissociation of the chaperone CmdC from the CmdTAC complex",
                "notes": "Vassallo et al. place phage capsid-driven CmdC dissociation upstream of antitoxin destabilization."
              }
            ]
          },
          {
            "subject": "cmda_degradation",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "cmdt_mrna_adp_ribosylation",
            "description": "CmdC dissociation and CmdA degradation liberate the CmdT ADP-ribosyltransferase.",
            "evidence": [
              {
                "reference": "https://pmc.ncbi.nlm.nih.gov/articles/PMC11618068/",
                "snippet": "destabilization and degradation of the antitoxin CmdA, with consequent liberation of the CmdT ADP-ribosyltransferase",
                "notes": "Vassallo et al. place CmdA degradation upstream of CmdT liberation."
              },
              {
                "reference": "https://pmc.ncbi.nlm.nih.gov/articles/PMC11618068/",
                "snippet": "CmdT co-precipitated with both CmdA and CmdC",
                "notes": "CmdT co-precipitated with both its antitoxin and chaperone partners."
              }
            ]
          },
          {
            "subject": "cmdt_mrna_adp_ribosylation",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "mrna_translation_arrest",
            "description": "Liberated CmdT modifies mRNA and blocks translation.",
            "evidence": [
              {
                "reference": "https://pmc.ncbi.nlm.nih.gov/articles/PMC11618068/",
                "snippet": "CmdT selectively modifies mRNA to block translation and abort the phage infection",
                "notes": "Vassallo et al. connect CmdT-mediated mRNA modification to translation arrest."
              }
            ]
          },
          {
            "subject": "mrna_translation_arrest",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "cmdtac_system_trait",
            "description": "Translation arrest and viral-replication inhibition realize the CmdTAC system trait.",
            "evidence": [
              {
                "reference": "https://pmc.ncbi.nlm.nih.gov/articles/PMC11618068/",
                "snippet": "arrest of mRNA translation and inhibition of viral replication",
                "notes": "Vassallo et al. connect CmdT-mediated mRNA modification to inhibited viral replication."
              }
            ]
          },
          {
            "subject": "cmdtac_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "abortive_infection_system_trait",
            "description": "CmdTAC system possession is an abortive-infection phage-defense-system trait.",
            "evidence": [
              {
                "reference": "https://pmc.ncbi.nlm.nih.gov/articles/PMC11618068/",
                "snippet": "These results are consistent with CmdTAC functioning via an Abi mechanism.",
                "notes": "Vassallo et al. interpret CmdTAC as consistent with an abortive-infection mechanism."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "cmdtac-family-and-model-coverage-gap",
        "prompt": "Resolve CmdTAC family breadth and phage escape routes before minting narrower CmdTAC mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Vassallo et al. support CmdTAC as a toxin-antitoxin-chaperone abortive-infection system in which CmdC senses viral capsid proteins and liberates the CmdT mRNA ADP-ribosyltransferase. Vassallo et al. also state that PD-T4-9 was renamed CmdTAC, and the pinned DefenseFinder HMM inventory and rules table record PD-T4-9 with required PD-T4-9__PD-T4-9_A and PD-T4-9__PD-T4-9_C profiles plus accessory PD-T4-9__PD-T4-9_B. Phage specificity beyond Tevenvirinae, escape routes, and natural family breadth remain unresolved.",
        "attaches_to": [
          "causal_graphs#cmdtac_mrna_adp_ribosylation_aborts_phage"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-21",
        "evidence": [
          {
            "reference": "DOI:10.1038/s41586-024-08102-8",
            "snippet": "PD-T4-9 also contains a third component, a SecB-like chaperone, suggesting that it is related to an enigmatic class of TA systems called toxin-antitoxin-chaperone (TAC) systems, so we renamed this system CmdTAC",
            "notes": "Vassallo et al. state that PD-T4-9 was renamed CmdTAC after they recognized its SecB-like chaperone component."
          },
          {
            "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-9.md",
            "snippet": "The PD-T4-9 is composed of 3 proteins: PD-T4-9_A, PD-T4-9_B and PD-T4-9_C.",
            "notes": "The DefenseFinder wiki names the three protein components in the PD-T4-9 model."
          },
          {
            "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-9.md",
            "snippet": "The PD-T4-9 system in *Vibrio parahaemolyticus* (GCF_001700835.1, NZ_CP010883) is composed of 3 proteins PD-T4-9_C (WP_065870458.1) PD-T4-9_B (WP_141106056.1) PD-T4-9_A (WP_065870460.1)",
            "notes": "The DefenseFinder wiki illustrates a predicted PD-T4-9 locus in RefSeq assembly GCF_001700835.1 on NZ_CP010883."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "snippet": "PD-T4-9\tPD-T4-9\t2\t2\tPD-T4-9__PD-T4-9_A, PD-T4-9__PD-T4-9_C\tPD-T4-9__PD-T4-9_B\t\t",
            "notes": "The pinned DefenseFinder rules table models PD-T4-9 with PD-T4-9__PD-T4-9_A and PD-T4-9__PD-T4-9_C as required profiles and PD-T4-9__PD-T4-9_B as an accessory profile."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| PD-T4-9__PD-T4-9_A                               | PD-T4-9__PD-T4-9_A                               | PD-T4-9                | Custom                  | 20     |\n| PD-T4-9__PD-T4-9_B                               | PD-T4-9__PD-T4-9_B                               | PD-T4-9                | Custom                  | 20     |\n| PD-T4-9__PD-T4-9_C                               | PD-T4-9__PD-T4-9_C                               | PD-T4-9                | Custom                  | 20     |",
            "notes": "The pinned DefenseFinder HMM inventory records PD-T4-9__PD-T4-9_A, PD-T4-9__PD-T4-9_B, and PD-T4-9__PD-T4-9_C under the PD-T4-9 system namespace."
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-21T12:03:24Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted CmdTAC system as a DOI-backed GENOMICS TraitRecord under the abortive infection system parent after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v212.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-21T12:26:31Z",
        "curator": "codex",
        "action": "ADDRESS_PR_REVIEW",
        "changes": "Corrected Vassallo et al. author attribution, tightened the CmdTAC system definition to attach mRNA modification to CmdT, carried the proposal-only locus label into the record as a RELATED_SYNONYM, and left the DefenseFinder article-registry row at record-level evidence instead of on the CmdC sensing edge.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-26T21:51:06Z",
        "curator": "codex",
        "action": "RESOLVE_DISCUSSION_SCOPE",
        "changes": "Recorded PD-T4-9 as a DefenseFinder related label for CmdTAC after an ignored-and-hidden duplicate review found that PD-T4-9 denotes the existing CmdTAC system; added the pinned PD-T4-9 DefenseFinder rule and HMM rows and resolved the DefenseFinder model-coverage half of the open CmdTAC knowledge gap.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000422",
    "label": "CoCoNuT system",
    "definition": "A phage defense system in which an organism possesses a CoCoNuT locus from a coiled-coil nuclease tandem branch of McrBC Type IV restriction systems whose domain and genomic-context architecture predict RNA targeting and, in many CoCoNuTs, DNA targeting via McrC nuclease homologs.",
    "definition_source": "DOI:10.7554/eLife.94800.3",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "CoCoNuT",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.7554/eLife.94800.3"
      },
      {
        "synonym_text": "CoCoNut",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      },
      {
        "synonym_text": "CoCoNut-I-A__I-A_CnuB",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "CoCoNut-II__II_CnuH",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "CoCoNut-III-B__III-B_CnuHE",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.7554/eLife.94800.3",
        "snippet": "We focus on a previously uncharacterized branch, which we denote coiled-coil nuclease tandems (CoCoNuTs) for their salient features: the presence of extensive coiled-coil structures and tandem nucleases",
        "notes": "Bell et al. name CoCoNuTs as coiled-coil nuclease tandem systems in an uncharacterized McrBC Type IV restriction branch."
      },
      {
        "reference": "DOI:10.7554/eLife.94800.3",
        "snippet": "We classified the CoCoNuTs into three types and seven subtypes based on the GTPase domain phylogeny and conserved genomic context",
        "notes": "Bell et al. classify CoCoNuTs into multiple types and subtypes using GTPase phylogeny and conserved genomic context."
      },
      {
        "reference": "DOI:10.7554/eLife.94800.3",
        "snippet": "all suggesting that the CoCoNuTs target RNA",
        "notes": "Bell et al. interpret CoCoNuT domain architecture as predictive of RNA targeting."
      },
      {
        "reference": "DOI:10.7554/eLife.94800.3",
        "snippet": "Many CoCoNuTs might additionally target DNA, via McrC nuclease homologs",
        "notes": "Bell et al. predict that many CoCoNuTs might also target DNA via McrC nuclease homologs."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| CoCoNut | 10\\.7554/eLife\\.94800\\.3 | CoCoNuTs are a diverse subclass of Type IV restriction systems predicted to target RNA | ",
        "notes": "The pinned DefenseFinder article registry maps the CoCoNut source key to the Bell et al. versioned eLife article."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| CoCoNut-I-A__I-A_CnuB                            |                                                  | CoCoNut-I-A            | Custom                  | 200    |",
        "notes": "The pinned DefenseFinder HMM inventory records CoCoNut-I-A__I-A_CnuB as a custom CoCoNut profile."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| CoCoNut-II__II_CnuH                              |                                                  | CoCoNut-II             | Custom                  | 500    |",
        "notes": "The pinned DefenseFinder HMM inventory records CoCoNut-II__II_CnuH as a custom CoCoNut profile."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| CoCoNut-III-B__III-B_CnuHE                       |                                                  | CoCoNut-III-B          | Custom                  | 750    |",
        "notes": "The pinned DefenseFinder HMM inventory records CoCoNut-III-B__III-B_CnuHE as a custom CoCoNut profile."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "coconut_system_family_hierarchy",
        "title": "CoCoNuT loci are predicted Type IV restriction systems",
        "description": "Conservative system-level sketch linking CoCoNuT system possession to phage defense without resolving individual components or a direct molecular output.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures CoCoNuT at the named McrBC/Type IV system-family level with representative CoCoNut-I, CoCoNut-II, and CoCoNut-III DefenseFinder HMM rows. It does not assert exact profile-to-protein boundaries, direct RNA or DNA substrates, native host range, phage range, subtype boundaries, pseudo-CoCoNuT scope, CARF-regulated superoperon scope, or rule-level detection criteria.",
        "nodes": [
          {
            "node_id": "coconut_system_trait",
            "label": "CoCoNuT system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000422",
            "description": "Possession of a genome-encoded CoCoNuT Type IV restriction-system family locus."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "coconut_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "CoCoNuT system possession is treated as a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.7554/eLife.94800.3",
                "snippet": "largely uncharacterized prokaryotic antiphage restriction systems",
                "notes": "Bell et al. frame EVE/McrB-like Type IV restriction-system diversity in the context of prokaryotic antiphage restriction."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| CoCoNut | 10\\.7554/eLife\\.94800\\.3 | CoCoNuTs are a diverse subclass of Type IV restriction systems predicted to target RNA | ",
                "notes": "The pinned DefenseFinder article registry maps the CoCoNut source key to the Bell et al. versioned eLife article."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "coconut-defensefinder-model-gap",
        "prompt": "Resolve exact CoCoNuT type and subtype boundaries, native host breadth, direct RNA and DNA substrates, phage range, pseudo-CoCoNuT scope, CARF-regulated superoperon scope, and rule-level detection criteria before minting narrower CoCoNuT mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Bell et al. support CoCoNuTs as a computationally defined McrBC/Type IV restriction branch predicted to target RNA and, for many loci, DNA; the pinned DefenseFinder HMM inventory records custom CoCoNut-I, CoCoNut-II, and CoCoNut-III profile rows. The pinned rules table has no CoCoNut row, and the first-pass record leaves exact profile-to-protein boundaries, pseudo-CoCoNuT inclusion, natural host breadth, phage range, and substrate-level mechanism unresolved.",
        "evidence": [
          {
            "reference": "DOI:10.7554/eLife.94800.3",
            "snippet": "We classified the CoCoNuTs into three types and seven subtypes based on the GTPase domain phylogeny and conserved genomic context",
            "notes": "Bell et al. classify CoCoNuTs into type and subtype groups using phylogeny and genomic context."
          },
          {
            "reference": "DOI:10.7554/eLife.94800.3",
            "snippet": "all suggesting that the CoCoNuTs target RNA",
            "notes": "Bell et al. predict RNA targeting from CoCoNuT component-domain architectures."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
            "snippet": "| CoCoNut | 10\\.7554/eLife\\.94800\\.3 | CoCoNuTs are a diverse subclass of Type IV restriction systems predicted to target RNA | ",
            "notes": "The pinned DefenseFinder article registry maps the CoCoNut source key to the Bell et al. versioned eLife article."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| CoCoNut-I-A__I-A_CnuB                            |                                                  | CoCoNut-I-A            | Custom                  | 200    |",
            "notes": "The pinned DefenseFinder HMM inventory records CoCoNut-I-A__I-A_CnuB as a custom CoCoNut profile."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| CoCoNut-II__II_CnuH                              |                                                  | CoCoNut-II             | Custom                  | 500    |",
            "notes": "The pinned DefenseFinder HMM inventory records CoCoNut-II__II_CnuH as a custom CoCoNut profile."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| CoCoNut-III-B__III-B_CnuHE                       |                                                  | CoCoNut-III-B          | Custom                  | 750    |",
            "notes": "The pinned DefenseFinder HMM inventory records CoCoNut-III-B__III-B_CnuHE as a custom CoCoNut profile."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "The pinned DefenseFinder rules table does not list CoCoNut, leaving rule-level detection criteria unresolved."
          }
        ],
        "attaches_to": [
          "causal_graphs#coconut_system_family_hierarchy"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-28"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-28T01:05:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted CoCoNuT system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; kept the graph at McrBC/Type IV system-family level because the pinned DefenseFinder CoCoNut HMM rows are not backed by a rules row; proposals/metpo_traitmech_v299 reserves the replacement placeholder.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-28T01:05:01Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed CoCoNuT system canonical_examples and left them empty because Bell et al. support computationally predicted CoCoNuT systems and DefenseFinder records CoCoNut HMM profiles, but the sources do not provide a direct native microbial isolate exemplar with experimentally verified endogenous CoCoNuT activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000096",
    "label": "codon usage bias",
    "definition": "A genome-sequence property describing non-uniform usage of synonymous codons across a genome, shaped by mutational bias and translational selection and correlated with gene expression level.",
    "definition_source": "DOI:10.1038/nrg2899",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000188"
    ],
    "synonyms": [
      {
        "synonym_text": "codon bias",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1038/nrg2899"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/nrg2899",
        "notes": "Plotkin & Kudla review the causes and consequences of synonymous codon bias."
      },
      {
        "reference": "DOI:10.1146/annurev.genet.42.110807.091442",
        "notes": "Hershberg & Petrov review selection on codon bias across genomes."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:562",
        "taxon_label": "Escherichia coli",
        "note": "Reference organism for codon usage bias (translational selection on synonymous codons in highly expressed genes).",
        "reference": "PMID:6175758"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "codon_bias_translation_efficiency",
        "title": "Codon usage bias shapes translation efficiency and gene expression",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This genomics record is a measurement, genomic-element classification, or population-level descriptor rather than one taxon-specific protein mechanism; contextual protein nodes do not receive token UniProt examples.",
        "description": "Evidence-backed causal sketch linking biased synonymous-codon usage to translation rates and gene expression level.",
        "nodes": [
          {
            "node_id": "codon_bias_trait",
            "label": "codon usage bias",
            "node_type": "TRAIT",
            "grounding": "traitmech:000096",
            "description": "Non-uniform use of synonymous codons across a genome."
          },
          {
            "node_id": "translation",
            "label": "translation",
            "node_type": "BIOLOGICAL_PROCESS",
            "grounding": "GO:0006412",
            "description": "Ribosome-mediated decoding of mRNA into protein."
          },
          {
            "node_id": "gene_expression_level",
            "label": "gene expression level",
            "node_type": "QUALITY",
            "description": "Steady-state protein output per gene."
          },
          {
            "node_id": "trna_abundance",
            "label": "tRNA abundance",
            "node_type": "QUALITY",
            "description": "Cellular pool / gene copy number of tRNAs available for decoding codons."
          },
          {
            "node_id": "mrna_5prime_secondary_structure",
            "label": "5' mRNA secondary structure",
            "node_type": "QUALITY",
            "description": "Strength of RNA folding near the translation start site."
          },
          {
            "node_id": "translation_initiation",
            "label": "translation initiation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Ribosome assembly and start-codon recognition that begins protein synthesis.",
            "grounding": "GO:0006413"
          }
        ],
        "edges": [
          {
            "subject": "codon_bias_trait",
            "predicate": "regulates",
            "object": "translation",
            "description": "Biased codon usage tunes elongation rate via tRNA availability.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrg2899",
                "notes": "Plotkin & Kudla review how synonymous codon bias modulates translation."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "codon_bias_trait",
            "predicate": "associated with",
            "object": "gene_expression_level",
            "description": "Codon bias is strongest in highly expressed genes.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev.genet.42.110807.091442",
                "notes": "Hershberg & Petrov review translational selection on codon bias correlating with expression level."
              }
            ],
            "predicate_id": "biolink:associated_with"
          },
          {
            "subject": "gene_expression_level",
            "predicate": "strengthens selection for",
            "object": "codon_bias_trait",
            "description": "Selection on synonymous codons scales with protein production; highly expressed genes show stronger codon preferences.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev.genet.42.110807.091442",
                "notes": "Hershberg & Petrov: codon bias correlates most strongly with gene expression level."
              },
              {
                "reference": "DOI:10.32942/x2802v",
                "notes": "Cope et al.: codon-specific selection scales with per-gene protein production rate (ROC-SEMPPR)."
              }
            ]
          },
          {
            "subject": "trna_abundance",
            "predicate": "influences",
            "object": "codon_bias_trait",
            "description": "Synonymous codons decoded by more abundant tRNAs tend to be more adapted and often preferred.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrg2899",
                "notes": "Plotkin & Kudla define tAI from relative tRNA gene copy numbers; the more abundant the decoding tRNA, the more adapted the codon."
              }
            ]
          },
          {
            "subject": "mrna_5prime_secondary_structure",
            "predicate": "inhibits",
            "object": "translation_initiation",
            "description": "Start-region RNA folding can limit ribosome access and dominate expression effects of synonymous codons.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrg2899",
                "notes": "Plotkin & Kudla: 5' structure generally disadvantageous; GFP expression in E. coli strongly inhibited when 5' folding energy below ~-10 kcal/mol (RBS/SD/start-codon occlusion)."
              }
            ],
            "predicate_id": "RO:0002212"
          },
          {
            "subject": "translation_initiation",
            "predicate": "part of",
            "object": "translation",
            "description": "Initiation is the first stage of translation.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrg2899",
                "notes": "Plotkin & Kudla discuss translation initiation as a major mechanism linking 5' sequence features to expression."
              }
            ],
            "predicate_id": "biolink:part_of"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-06-05T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate GENOMICS trait (codon usage bias) from literature research to fill the genome-sequence-composition gap.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-08T14:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (codon bias / translation efficiency) with GO node grounding and RO/biolink predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 4 evidence-backed generic edges (3 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:11Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002212\u00d71, biolink:part_of\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:32Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0006413\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope codon_bias_translation_efficiency=NONMECHANISTIC with scope_notes.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000094",
    "label": "CRISPR-Cas system",
    "definition": "A genomics trait describing possession of a CRISPR-Cas adaptive immune system that records fragments of invading nucleic acids in CRISPR arrays and uses Cas proteins to recognize and cleave matching sequences.",
    "definition_source": "DOI:10.1038/s41579-019-0299-x",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "CRISPR array",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1038/s41579-019-0299-x"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/s41579-019-0299-x",
        "notes": "Makarova et al. present an evolutionary classification of CRISPR-Cas systems into two classes, six types, and many subtypes."
      },
      {
        "reference": "DOI:10.1016/j.molcel.2014.03.011",
        "notes": "Barrangou & Marraffini review CRISPR-Cas as prokaryotic adaptive immunity against invading genetic elements."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1308",
        "taxon_label": "Streptococcus thermophilus",
        "note": "Organism in which CRISPR-Cas adaptive immunity was experimentally demonstrated (Barrangou et al. 2007); dairy model for CRISPR biology.",
        "reference": "PMID:17379808"
      },
      {
        "taxon_id": "NCBITaxon:301447",
        "taxon_label": "Streptococcus pyogenes serotype M1",
        "note": "Type II CRISPR-Cas exemplar paired to reviewed Cas9 used to demonstrate dual-RNA-guided target-DNA cleavage.",
        "reference": "DOI:10.1126/science.1225829"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "crispr_adaptive_immunity",
        "title": "CRISPR-Cas adaptive immunity against invading nucleic acids",
        "description": "Evidence-backed causal sketch linking Cas-protein-mediated CRISPR machinery to defense against invading mobile genetic elements.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "The protein examples anchor the experimentally resolved S. pyogenes type II Cas9 interference branch (Q99ZW2) and the E. coli K-12 type I-E Cas1-Cas2 adaptation complex subunits (Q46896 and P45956). RNA nodes remain distinct and the subunit examples are not presented as universal across every CRISPR-Cas type.",
        "nodes": [
          {
            "node_id": "crispr_trait",
            "label": "CRISPR-Cas system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000094",
            "description": "Possession of CRISPR arrays and Cas proteins for adaptive immunity."
          },
          {
            "node_id": "cas9_effector",
            "label": "Cas9 effector protein",
            "node_type": "GENE_OR_PROTEIN",
            "description": "RNA-guided type II CRISPR endonuclease that cleaves complementary target DNA.",
            "grounding": "InterPro:IPR028629",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:Q99ZW2",
                "protein_label": "CRISPR-associated endonuclease Cas9",
                "gene_symbol": "cas9",
                "taxon_id": "NCBITaxon:301447",
                "taxon_label": "Streptococcus pyogenes serotype M1",
                "entry_status": "REVIEWED",
                "retrieved_on": "2026-10-22",
                "entry_version": 148,
                "sequence_version": 1,
                "role": "S. pyogenes Cas9 is the nuclease component directed by crRNA and tracrRNA to make sequence-specific double-strand breaks in target DNA.",
                "evidence": [
                  {
                    "reference": "DOI:10.1126/science.1225829",
                    "snippet": "Cas9 endonuclease family can be programmed",
                    "notes": "The primary biochemical study purified S. pyogenes Cas9 and established dual-RNA-guided target-DNA cleavage; UniProt verifies the reviewed protein."
                  }
                ]
              }
            ]
          },
          {
            "node_id": "defense_response_to_virus",
            "label": "defense response to virus",
            "node_type": "BIOLOGICAL_PROCESS",
            "grounding": "GO:0051607",
            "description": "Cleavage of invading viral or plasmid nucleic acids."
          },
          {
            "node_id": "cas1_cas2_complex",
            "label": "Cas1-Cas2 complex",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Cas1-Cas2 integrase complex that captures and integrates new spacers.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Cas1 and Cas2 are distinct protein families; this node denotes their adaptation complex rather than one component family.",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:Q46896",
                "protein_label": "CRISPR-associated endonuclease Cas1",
                "gene_symbol": "ygbT",
                "taxon_id": "NCBITaxon:83333",
                "taxon_label": "Escherichia coli K-12",
                "entry_status": "REVIEWED",
                "proteome_id": "UP000000625",
                "retrieved_on": "2026-10-22",
                "entry_version": 154,
                "sequence_version": 1,
                "role": "Cas1 integrase subunit of the E. coli K-12 Cas1-Cas2 adaptation complex that captures and integrates new spacers; this accession represents the Cas1 subunit, not the complete heterohexameric complex.",
                "evidence": [
                  {
                    "reference": "DOI:10.1038/nsmb.2820",
                    "snippet": "Cas1 and Cas2 from Escherichia coli form a stable complex that is essential for spacer acquisition",
                    "notes": "Nu\u00f1ez et al. 2014 characterize the E. coli K-12 Cas1-Cas2 adaptation complex required for spacer acquisition."
                  }
                ]
              },
              {
                "uniprot_id": "UniProtKB:P45956",
                "protein_label": "CRISPR-associated endoribonuclease Cas2",
                "gene_symbol": "ygbF",
                "taxon_id": "NCBITaxon:83333",
                "taxon_label": "Escherichia coli K-12",
                "entry_status": "REVIEWED",
                "proteome_id": "UP000000625",
                "retrieved_on": "2026-10-22",
                "entry_version": 145,
                "sequence_version": 2,
                "role": "Cas2 central dimer subunit of the E. coli K-12 Cas1-Cas2 adaptation complex required for spacer acquisition; this accession represents the Cas2 subunit, not the complete complex.",
                "evidence": [
                  {
                    "reference": "DOI:10.1038/nsmb.2820",
                    "snippet": "Cas1 and Cas2 from Escherichia coli form a stable complex that is essential for spacer acquisition",
                    "notes": "Nu\u00f1ez et al. 2014 establish that E. coli K-12 Cas2 forms a stable adaptation complex with Cas1 essential for spacer acquisition."
                  }
                ]
              }
            ]
          },
          {
            "node_id": "spacer_acquisition",
            "label": "spacer acquisition (adaptation)",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Integration of invader-derived fragments as new spacers into the CRISPR array."
          },
          {
            "node_id": "crispr_array_transcription",
            "label": "CRISPR array transcription and processing",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Transcription of the CRISPR array and processing of the precursor into mature crRNAs."
          },
          {
            "node_id": "crrna",
            "label": "crRNA",
            "node_type": "RNA",
            "description": "Mature CRISPR RNA that guides Cas effectors to complementary targets."
          },
          {
            "node_id": "crrna_effector_complex",
            "label": "crRNA-Cas effector complex",
            "node_type": "RNA",
            "description": "Ribonucleoprotein complex of crRNA and Cas effector(s) performing interference."
          },
          {
            "node_id": "invading_nucleic_acid",
            "label": "invading nucleic acid target",
            "node_type": "CHEMICAL",
            "description": "Foreign DNA or RNA from phages, plasmids, or other mobile genetic elements."
          },
          {
            "node_id": "phage_plasmid_pressure",
            "label": "phage and plasmid pressure",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Selective pressure from invading bacteriophages and plasmids."
          }
        ],
        "edges": [
          {
            "subject": "cas9_effector",
            "predicate": "confers",
            "object": "crispr_trait",
            "description": "Cas9 together with CRISPR-derived guide RNAs realizes the type II adaptive immune interference system.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41579-019-0299-x",
                "notes": "Makarova et al. classify type II CRISPR-Cas systems by Cas9 content; the protein example is restricted to this branch."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "crispr_trait",
            "predicate": "participates in",
            "object": "defense_response_to_virus",
            "description": "CRISPR-Cas mounts sequence-specific defense against invading genetic elements.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.molcel.2014.03.011",
                "notes": "Barrangou & Marraffini frame CRISPR-Cas as prokaryotic adaptive immunity."
              }
            ],
            "predicate_id": "biolink:participates_in"
          },
          {
            "subject": "cas1_cas2_complex",
            "predicate": "integrates spacers via",
            "object": "spacer_acquisition",
            "description": "Cas1-Cas2 complexes act as molecular recorders that integrate new spacers into the CRISPR array during adaptation.",
            "evidence": [
              {
                "reference": "DOI:10.5483/bmbrep.2023-0050",
                "notes": "Cas1-Cas2 complexes function as molecular recorders to integrate spacers; core adaptation edge, broad across canonical CRISPR-Cas systems."
              }
            ]
          },
          {
            "subject": "crispr_array_transcription",
            "predicate": "has output",
            "object": "crrna",
            "description": "Transcription and processing of the CRISPR array yields mature crRNAs.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.heliyon.2024.e39538",
                "notes": "CRISPR arrays are transcribed and processed into crRNAs; general edge across systems."
              }
            ],
            "predicate_id": "RO:0002234"
          },
          {
            "subject": "crrna",
            "predicate": "guides",
            "object": "crrna_effector_complex",
            "description": "crRNA assembles with Cas effector(s) to form the interference-competent effector complex.",
            "evidence": [
              {
                "reference": "DOI:10.5483/bmbrep.2023-0050",
                "notes": "Effector-crRNA complexes drive the RNA-guided interference pathways."
              }
            ]
          },
          {
            "subject": "crrna_effector_complex",
            "predicate": "cleaves",
            "object": "invading_nucleic_acid",
            "description": "The crRNA-Cas effector complex recognizes and cleaves complementary invading nucleic acid targets.",
            "evidence": [
              {
                "reference": "DOI:10.5483/bmbrep.2023-0050",
                "notes": "Effector-crRNA complexes perform RNA-guided interference against invading targets; high-level interference edge."
              }
            ]
          },
          {
            "subject": "phage_plasmid_pressure",
            "predicate": "selects for",
            "object": "crispr_trait",
            "description": "Selective pressure from invading phages and plasmids favors maintenance of CRISPR-Cas immunity.",
            "evidence": [
              {
                "reference": "DOI:10.5483/bmbrep.2023-0050",
                "notes": "CRISPR-Cas protects hosts from invasion by bacteriophages and plasmids; broad ecological selection edge."
              }
            ],
            "predicate_id": "METPO:2007401"
          },
          {
            "subject": "crrna_effector_complex",
            "predicate": "contributes to",
            "object": "crispr_trait",
            "description": "crRNA-guided interference by the effector complex realizes the adaptive-defense trait.",
            "evidence": [
              {
                "reference": "DOI:10.5483/bmbrep.2023-0050",
                "snippet": "Effector-crRNA complexes perform RNA-guided interference against invading targets",
                "notes": "The connector is scoped to the interference branch and does not universalize one effector subtype."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "cas1_cas2_complex",
            "predicate": "confers",
            "object": "crispr_trait",
            "description": "Cas1-Cas2 spacer acquisition realizes the adaptation branch of CRISPR-Cas immunity.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nsmb.2820",
                "snippet": "Cas1 and Cas2 from Escherichia coli form a stable complex that is essential for spacer acquisition",
                "notes": "The primary study directly tests the Cas1-Cas2 adaptation complex; this branch is not projected onto interference-only systems."
              }
            ],
            "predicate_id": "METPO:2007700"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-06-05T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate GENOMICS trait (CRISPR-Cas system) from literature research to fill the genome-defense-system gap.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-08T14:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (CRISPR adaptive immunity) with GO node grounding and RO/biolink predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 5 evidence-backed generic edges (7 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:11Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d71, METPO:2007401\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 1 causal edge(s) off enables/RO:0002327 with a TRAIT object (1 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates (1 to has output), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "CURATE_PROTEIN_TAXON_EXAMPLE",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope crispr_adaptive_immunity=MECHANISTIC with scope_notes; marked 1 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (cas1_cas2_complex); added taxon-paired protein example(s) UniProtKB:Q99ZW2 on cas9_effector (NCBITaxon:301447); retyped 2 node(s) (crrna->RNA, crrna_effector_complex->RNA); added 1 node(s) and 1 edge(s) (cas9_effector); removed 1 node(s) and 1 edge(s) together with their evidence (cas_proteins); added canonical example(s) NCBITaxon:301447.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T05:40:00Z",
        "curator": "codex",
        "action": "CONNECT_CAUSAL_GRAPH_COMPONENTS",
        "changes": "Resolved issue #183 graph fragmentation (3 components to 1) using 2 snippet-backed connector(s) supported by source passages. No research service was called.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-15T07:55:00Z",
        "curator": "codex",
        "action": "REFINED_PARENT_TRAITS",
        "changes": "Reparented CRISPR-Cas system from the broad genomics parent to the newly minted phage defense system parent.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-22T01:35:00Z",
        "curator": "claude",
        "action": "CURATE_PROTEIN_TAXON_EXAMPLE",
        "changes": "Added reviewed E. coli K-12 subunit protein_examples UniProtKB:Q46896 (Cas1/ygbT, v154) and UniProtKB:P45956 (Cas2/ygbF, v145) on cas1_cas2_complex (DOI:10.1038/nsmb.2820), updated scope_notes for component-level subunit scope, and refreshed UniProtKB:Q99ZW2 entry_version 147 -> 148 on cas9_effector.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000500",
    "label": "Crouga system",
    "definition": "A phage defense system in which an organism possesses a Crouga antiviral locus that is encoded by P4-like phage satellites and can protect bacteria from bacteriophage infection.",
    "definition_source": "DOI:10.1093/nar/gkag898",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "Crouga",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1093/nar/gkag898"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1093/nar/gkag898",
        "snippet": "The Crouga system has some evidence of being an RM-like system, with one of its proteins containing PFAM domains (ResIII, DEAD, and Helicase C) associated with other RM systems",
        "notes": "de Sousa et al. identify Crouga as a named novel P4-associated system with restriction-modification-like domain evidence."
      },
      {
        "reference": "DOI:10.1093/nar/gkag898",
        "snippet": "We named the novel functional systems according to deities from Lusitanian mythology",
        "notes": "de Sousa et al. introduce Crouga among the named novel functional P4 antiviral systems."
      },
      {
        "reference": "DOI:10.1093/nar/gkag898",
        "snippet": "Our experimental validation of anti-phage activity for 13 novel systems encoded by P4 confirms that the contribution of defence functions to the pangenomes of P4 and P2, as well as to the antiviral repertoire of their bacterial hosts, will keep surprising us",
        "notes": "de Sousa et al. summarize the validated P4-encoded novel-system cohort in their discussion."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| Crouga | 10\\.64898/2026\\.02\\.27\\.708500 | Shuttling, swapping and mixing: the rapid modular evolution of antiviral repertoires in temperate phages and their satellites | ",
        "notes": "The pinned DefenseFinder article registry maps the Crouga source key to the de Sousa et al. P4/P2 antiviral-repertoire paper preprint."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "crouga_locus_restricts_phage",
        "title": "Crouga loci confer bacterial phage defense",
        "description": "Conservative system-level sketch linking possession of a Crouga locus to restricted bacteriophage propagation without asserting the unresolved trigger or molecular output.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Crouga as a named P4 anti-phage system while leaving its source locus, phage trigger, restriction-modification-like molecular roles, antiviral effector output, source-system table rows, and DefenseFinder HMM/rule model coverage unresolved.",
        "nodes": [
          {
            "node_id": "crouga_locus",
            "label": "Crouga locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A P4-associated Crouga anti-phage defense locus."
          },
          {
            "node_id": "restricted_phage_propagation",
            "label": "restricted phage propagation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced propagation of bacteriophage in cells carrying the Crouga system."
          },
          {
            "node_id": "crouga_system_trait",
            "label": "Crouga system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000500",
            "description": "Possession of a genome-encoded Crouga phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "crouga_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "restricted_phage_propagation",
            "description": "Crouga loci are among the novel P4-encoded systems that can reduce bacteriophage infection.",
            "evidence": [
              {
                "reference": "DOI:10.1093/nar/gkag898",
                "snippet": "The Crouga system has some evidence of being an RM-like system, with one of its proteins containing PFAM domains (ResIII, DEAD, and Helicase C) associated with other RM systems",
                "notes": "de Sousa et al. place Crouga in the newly named functional-system set and describe its RM-like domain evidence."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| Crouga | 10\\.64898/2026\\.02\\.27\\.708500 | Shuttling, swapping and mixing: the rapid modular evolution of antiviral repertoires in temperate phages and their satellites | ",
                "notes": "The pinned DefenseFinder article registry maps the Crouga source key to the de Sousa et al. P4/P2 antiviral-repertoire paper preprint."
              }
            ]
          },
          {
            "subject": "restricted_phage_propagation",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "crouga_system_trait",
            "description": "Crouga-mediated phage protection realizes the Crouga system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1093/nar/gkag898",
                "snippet": "Our experimental validation of anti-phage activity for 13 novel systems encoded by P4 confirms that the contribution of defence functions to the pangenomes of P4 and P2, as well as to the antiviral repertoire of their bacterial hosts, will keep surprising us",
                "notes": "de Sousa et al. connect the named novel P4-system cohort to anti-phage activity."
              }
            ]
          },
          {
            "subject": "crouga_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Crouga system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1093/nar/gkag898",
                "snippet": "Our experimental validation of anti-phage activity for 13 novel systems encoded by P4 confirms that the contribution of defence functions to the pangenomes of P4 and P2, as well as to the antiviral repertoire of their bacterial hosts, will keep surprising us",
                "notes": "de Sousa et al. frame the named Crouga cohort as newly validated P4-encoded anti-phage defense functions."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "crouga-mechanism-and-modelling-gap",
        "prompt": "Resolve Crouga locus breadth, exact phage triggers, restriction-modification-like molecular roles, direct antiviral output, source-system table rows, and DefenseFinder HMM/rule coverage before minting narrower Crouga mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "de Sousa et al. support Crouga as one of the novel P4-encoded systems with experimental phage-protection activity, and the pinned DefenseFinder article registry maps the Crouga source key to the corresponding preprint. The pinned HMM inventory and rules table have no exact Crouga rows, and this first-pass record does not resolve the tested source locus, complete phage breadth, exact trigger, molecular output, or detection rule.",
        "evidence": [
          {
            "reference": "DOI:10.1093/nar/gkag898",
            "snippet": "The Crouga system has some evidence of being an RM-like system, with one of its proteins containing PFAM domains (ResIII, DEAD, and Helicase C) associated with other RM systems",
            "notes": "de Sousa et al. support Crouga as a named RM-like defense system while leaving exact mechanism for separate review."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
            "snippet": "| Crouga | 10\\.64898/2026\\.02\\.27\\.708500 | Shuttling, swapping and mixing: the rapid modular evolution of antiviral repertoires in temperate phages and their satellites | ",
            "notes": "The pinned DefenseFinder article registry maps the Crouga source key to the de Sousa et al. P4/P2 antiviral-repertoire paper preprint."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "notes": "A structured first-pass search of the pinned DefenseFinder HMM inventory found no exact Crouga row."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "A structured first-pass search of the pinned DefenseFinder rules table found no exact Crouga system row."
          }
        ],
        "attaches_to": [
          "causal_graphs#crouga_locus_restricts_phage"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-30"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-30T20:55:13Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Crouga system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v377.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-30T20:55:14Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed Crouga system canonical_examples and left them empty because de Sousa et al. support P4-encoded Crouga phage protection and a DefenseFinder article-registry row, but not a direct named native microbial isolate exemplar with experimentally verified endogenous Crouga activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000507",
    "label": "Dag system",
    "definition": "A phage defense system in which an organism possesses a Dag-family DNA-glycosylase system whose Dag1 or Dag2 effectors selectively target phages carrying modified guanine bases.",
    "definition_source": "DOI:10.1038/s41564-026-02441-0",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "Dag",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      },
      {
        "synonym_text": "Dag1",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1038/s41564-026-02441-0"
      },
      {
        "synonym_text": "Dag2",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1038/s41564-026-02441-0"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/s41564-026-02441-0",
        "snippet": "using structure-guided discovery, we identified two widespread families of anti-phage DNA glycosylases, Dag1 and Dag2",
        "notes": "Getz et al. identify Dag1 and Dag2 as widespread anti-phage DNA-glycosylase families."
      },
      {
        "reference": "DOI:10.1038/s41564-026-02441-0",
        "snippet": "Dag1 and Dag2 act as antiviral effectors that selectively target phages carrying modified guanine bases.",
        "notes": "Getz et al. support the modified-guanine phage targeting scope of the Dag1 and Dag2 antiviral effectors."
      },
      {
        "reference": "DOI:10.1038/s41564-026-02441-0",
        "snippet": "Together, these findings establish DNA glycosylases as a versatile class of bacterial immune proteins",
        "notes": "Getz et al. frame defense-associated DNA glycosylases as bacterial immune proteins."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| Dag | 10\\.1101/2025\\.10\\.29\\.685425 | Antiviral defence is a conserved function of diverse DNA glycosylases | ",
        "notes": "The pinned DefenseFinder article registry maps the Dag source key to the Getz et al. DNA-glycosylase antiviral defense paper."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "dag_effectors_target_modified_guanine_phages",
        "title": "Dag effectors target modified-guanine phages",
        "description": "Conservative system-level sketch linking the Dag DefenseFinder namespace to Dag1 and Dag2 antiviral effector activity and the Dag phage-defense-system trait.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Dag as a named DefenseFinder DNA-glycosylase phage-defense system at system level and deliberately defers a protein-resolved glycosylase mechanism. Getz et al. support Dag1 and Dag2 as anti-phage DNA glycosylase families that target modified-guanine phages, but exact natural host exemplars, accession-level Dag proteins, relationships between Dag1 and Dag2 families, and DefenseFinder HMM/rules profiles are unresolved.",
        "nodes": [
          {
            "node_id": "dag_locus",
            "label": "Dag locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A Dag-family DNA-glycosylase phage-defense locus represented by the DefenseFinder Dag article namespace."
          },
          {
            "node_id": "modified_guanine_phage_targeting",
            "label": "modified-guanine phage targeting",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Selective targeting of phages that carry modified guanine bases by Dag1 or Dag2 antiviral effectors."
          },
          {
            "node_id": "dag_system_trait",
            "label": "Dag system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000507",
            "description": "Possession of a genome-encoded Dag DNA-glycosylase phage-defense system."
          },
          {
            "node_id": "phage_defense_system_trait",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "dag_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "modified_guanine_phage_targeting",
            "description": "Dag-family DNA-glycosylase systems encode Dag1 or Dag2 antiviral effectors that selectively target modified-guanine phages.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-026-02441-0",
                "snippet": "using structure-guided discovery, we identified two widespread families of anti-phage DNA glycosylases, Dag1 and Dag2",
                "notes": "Getz et al. identify Dag1 and Dag2 as widespread anti-phage DNA-glycosylase families."
              },
              {
                "reference": "DOI:10.1038/s41564-026-02441-0",
                "snippet": "Dag1 and Dag2 act as antiviral effectors that selectively target phages carrying modified guanine bases.",
                "notes": "Getz et al. support the modified-guanine phage targeting scope of the Dag1 and Dag2 antiviral effectors."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| Dag | 10\\.1101/2025\\.10\\.29\\.685425 | Antiviral defence is a conserved function of diverse DNA glycosylases | ",
                "notes": "The pinned DefenseFinder article registry maps the Dag source key to the Getz et al. DNA-glycosylase antiviral defense paper."
              }
            ]
          },
          {
            "subject": "modified_guanine_phage_targeting",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "dag_system_trait",
            "description": "Modified-guanine phage targeting realizes the organism-level Dag system possession trait.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-026-02441-0",
                "snippet": "Dag1 and Dag2 act as antiviral effectors that selectively target phages carrying modified guanine bases.",
                "notes": "Getz et al. support the modified-guanine phage targeting scope of the Dag1 and Dag2 antiviral effectors."
              },
              {
                "reference": "DOI:10.1038/s41564-026-02441-0",
                "snippet": "Together, these findings establish DNA glycosylases as a versatile class of bacterial immune proteins",
                "notes": "Getz et al. frame defense-associated DNA glycosylases as bacterial immune proteins."
              }
            ]
          },
          {
            "subject": "dag_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system_trait",
            "description": "Dag system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-026-02441-0",
                "snippet": "using structure-guided discovery, we identified two widespread families of anti-phage DNA glycosylases, Dag1 and Dag2",
                "notes": "Getz et al. identify Dag1 and Dag2 as widespread anti-phage DNA-glycosylase families."
              },
              {
                "reference": "DOI:10.1038/s41564-026-02441-0",
                "snippet": "Together, these findings establish DNA glycosylases as a versatile class of bacterial immune proteins",
                "notes": "Getz et al. frame defense-associated DNA glycosylases as bacterial immune proteins."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "dag-defensefinder-profile-gap",
        "prompt": "Resolve exact Dag1 and Dag2 family boundaries, natural host exemplars, modified-guanine phage target breadth, and DefenseFinder HMM/rules coverage before minting narrower Dag mechanism or component traits.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Getz et al. support Dag1 and Dag2 as widespread families of anti-phage DNA glycosylases that selectively target phages carrying modified guanine bases, and the pinned DefenseFinder article registry maps the Dag key to the Getz et al. preprint DOI. The pinned HMM inventory and rules table have no exact Dag rows. This first-pass record therefore does not resolve exact Dag1 versus Dag2 family boundaries, natural host exemplars, accession-level Dag proteins, full modified-guanine phage target breadth, or a reusable DefenseFinder profile model.",
        "evidence": [
          {
            "reference": "DOI:10.1038/s41564-026-02441-0",
            "snippet": "using structure-guided discovery, we identified two widespread families of anti-phage DNA glycosylases, Dag1 and Dag2",
            "notes": "Getz et al. identify Dag1 and Dag2 as widespread anti-phage DNA-glycosylase families."
          },
          {
            "reference": "DOI:10.1038/s41564-026-02441-0",
            "snippet": "Dag1 and Dag2 act as antiviral effectors that selectively target phages carrying modified guanine bases.",
            "notes": "Getz et al. support the modified-guanine phage targeting scope of the Dag1 and Dag2 antiviral effectors."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
            "snippet": "| Dag | 10\\.1101/2025\\.10\\.29\\.685425 | Antiviral defence is a conserved function of diverse DNA glycosylases | ",
            "notes": "The pinned DefenseFinder article registry maps the Dag source key to the Getz et al. DNA-glycosylase antiviral defense paper."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "notes": "A structured first-pass search of the pinned DefenseFinder HMM inventory found no exact Dag row."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "A structured first-pass search of the pinned DefenseFinder rules table found no exact Dag system row."
          }
        ],
        "attaches_to": [
          "causal_graphs#dag_effectors_target_modified_guanine_phages"
        ],
        "posed_by": "codex",
        "posed_date": "2026-10-01"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-01T05:07:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Dag system as a DOI- and DefenseFinder-backed GENOMICS TraitRecord under the phage defense system parent after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v384.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-01T05:07:01Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed Dag system during initial curation and left canonical_examples empty because the accessible Getz et al. abstract supports Dag1 and Dag2 as widespread anti-phage DNA-glycosylase families but does not name a stable NCBITaxon strain exemplar for the organism-level Dag system trait. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000272",
    "label": "Damona system",
    "definition": "A phage defense system in which an organism possesses a Damona locus represented by a VCA0399 profile that can protect bacteria from bacteriophage infection.",
    "definition_source": "DOI:10.1126/science.ads0768",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "Damona",
        "synonym_type": "EXACT_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      },
      {
        "synonym_text": "VCA0399",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1126/science.ads0768",
        "snippet": "nearly 10% of the integron cassettes in the pandemic Vibrio cholerae strain encode novel antiphage functions",
        "notes": "Darracq et al. support treating the newly discovered Vibrio cholerae SCI antiphage cassettes as bacterial anti-phage systems."
      },
      {
        "reference": "DOI:10.1126/science.ads0768",
        "snippet": "Most of these novel systems have little or no similarity to previously known ones, with several providing defense through cell lysis or growth arrest",
        "notes": "Darracq et al. support a conservative system record that does not assert a resolved Damona trigger, effector output, or universal pathway."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "Damona | 10\\.1126/science\\.ads0768 | Sedentary chromosomal integrons as biobanks of bacterial antiphage defense systems",
        "notes": "The DefenseFinder model registry maps the named Damona system to the Darracq et al. SCI antiphage-system paper."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "Damona__VCA0399                                  |                                                  | Damona",
        "notes": "The DefenseFinder HMM inventory records VCA0399 in the Damona model namespace."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "damona_locus_restricts_phage",
        "title": "Damona loci confer bacterial phage defense",
        "description": "Conservative system-level sketch linking possession of a Damona locus to restricted bacteriophage propagation without asserting the unresolved phage trigger or molecular output.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Damona as a named SCI-derived anti-phage system with a VCA0399 DefenseFinder profile while leaving its phage trigger, molecular substrate, antiviral effector output, and subtype breadth unresolved.",
        "nodes": [
          {
            "node_id": "damona_locus",
            "label": "Damona locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A Damona anti-phage defense locus represented in DefenseFinder by a VCA0399 profile."
          },
          {
            "node_id": "restricted_phage_propagation",
            "label": "restricted phage propagation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced propagation of bacteriophage in cells carrying the Damona system."
          },
          {
            "node_id": "damona_system_trait",
            "label": "Damona system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000272",
            "description": "Possession of a genome-encoded Damona phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "damona_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "restricted_phage_propagation",
            "description": "DefenseFinder maps Damona to an SCI anti-phage-system discovery paper and represents Damona loci through the VCA0399 component profile.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.ads0768",
                "snippet": "nearly 10% of the integron cassettes in the pandemic Vibrio cholerae strain encode novel antiphage functions",
                "notes": "Darracq et al. describe the newly discovered antiphage-system cohort that the DefenseFinder Damona registry row maps to the Damona system."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "Damona__VCA0399                                  |                                                  | Damona",
                "notes": "The DefenseFinder HMM inventory supports VCA0399 as the Damona component profile."
              }
            ]
          },
          {
            "subject": "restricted_phage_propagation",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "damona_system_trait",
            "description": "Damona-mediated phage restriction realizes the Damona system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.ads0768",
                "snippet": "Most of these novel systems have little or no similarity to previously known ones",
                "notes": "Darracq et al. place the Damona discovery cohort in a set of novel bacterial systems that protect against phages."
              }
            ]
          },
          {
            "subject": "damona_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Damona system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Damona | 10\\.1126/science\\.ads0768 | Sedentary chromosomal integrons as biobanks of bacterial antiphage defense systems",
                "notes": "DefenseFinder associates Damona with the Darracq et al. bacterial antiphage-system paper."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "damona-mechanism-gap",
        "prompt": "Resolve Damona phage triggers and effector outputs before minting narrower Damona mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Darracq et al. and DefenseFinder support Damona as a named anti-phage system with a VCA0399 profile, but the trigger, molecular substrate, antiviral effector output, and subtype-specific mechanism are not resolved enough here to assert a narrower mechanistic child trait.",
        "attaches_to": [
          "causal_graphs#damona_locus_restricts_phage"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-19"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-19T08:24:30Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Damona system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v149.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000273",
    "label": "DARNA system",
    "definition": "A phage defense system in which activated DARNA cleaves a subset of host tRNAs and thereby inhibits phage propagation after activation by single-stranded DNA presented by phage SSB.",
    "definition_source": "DOI:10.64898/2026.02.22.705581",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "DARNA",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.64898/2026.02.22.705581"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.64898/2026.02.22.705581",
        "snippet": "the bacterial immunity protein DARNA, once activated, cleaves a subset of host tRNAs, thereby inhibiting phage propagation",
        "notes": "Puteikiene et al. support DARNA as a bacterial immunity protein whose activation leads to host tRNA cleavage and phage-propagation inhibition."
      },
      {
        "reference": "DOI:10.64898/2026.02.22.705581",
        "snippet": "DARNA is activated by single-stranded DNA presented by phage SSB, but not by the host SSB",
        "notes": "Puteikiene et al. support phage SSB-presented single-stranded DNA as an activation input for DARNA."
      },
      {
        "reference": "DOI:10.64898/2026.02.22.705581",
        "snippet": "The recognition of an endogenous nucleic acid signal promoted by a viral protein ensures that DARNA can detect and respond to a broad range of viruses while avoiding auto-immunity",
        "notes": "Puteikiene et al. connect DARNA activation to viral-protein promoted self/non-self discrimination."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "DARNA | 10\\.64898/2026\\.02\\.22\\.705581 | Viral SSB-bound ssDNA activates the bacterial anti-phage defense system DARNA",
        "notes": "The DefenseFinder article registry maps the named DARNA system to the Puteikiene et al. bacterial anti-phage-system preprint."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "darna_phage_ssb_ssdna_cleaves_trna",
        "title": "DARNA activation restricts phage propagation through host-tRNA cleavage",
        "description": "Process sketch linking phage SSB-presented single-stranded DNA to DARNA activation, cleavage of a subset of host tRNAs, restricted phage propagation, and the DARNA system trait.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures the DOI abstract's DARNA activation and tRNA-cleavage summary without asserting a DefenseFinder component profile, universal locus architecture, strain-resolved component accessions, or the full host and phage breadth of every natural DARNA system.",
        "nodes": [
          {
            "node_id": "phage_ssb_presented_ssdna",
            "label": "phage SSB-presented single-stranded DNA",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Presentation of single-stranded DNA by phage single-stranded DNA-binding protein rather than by host SSB."
          },
          {
            "node_id": "darna_activation",
            "label": "DARNA activation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Activation of the bacterial immunity protein DARNA by phage SSB-presented single-stranded DNA."
          },
          {
            "node_id": "host_trna_cleavage",
            "label": "host tRNA cleavage",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Cleavage of a subset of host tRNAs after DARNA is activated."
          },
          {
            "node_id": "restricted_phage_propagation",
            "label": "restricted phage propagation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced propagation of bacteriophage after DARNA activation and host-tRNA cleavage."
          },
          {
            "node_id": "darna_system_trait",
            "label": "DARNA system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000273",
            "description": "Possession of a genome-encoded DARNA phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "phage_ssb_presented_ssdna",
            "predicate": "triggers",
            "object": "darna_activation",
            "description": "Single-stranded DNA presented by phage SSB activates DARNA.",
            "evidence": [
              {
                "reference": "DOI:10.64898/2026.02.22.705581",
                "snippet": "DARNA is activated by single-stranded DNA presented by phage SSB, but not by the host SSB",
                "notes": "Puteikiene et al. directly identify phage SSB-presented single-stranded DNA as the DARNA activation signal."
              }
            ]
          },
          {
            "subject": "darna_activation",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "host_trna_cleavage",
            "description": "Activated DARNA cleaves a subset of host tRNAs.",
            "evidence": [
              {
                "reference": "DOI:10.64898/2026.02.22.705581",
                "snippet": "the bacterial immunity protein DARNA, once activated, cleaves a subset of host tRNAs",
                "notes": "Puteikiene et al. connect DARNA activation to host-tRNA cleavage."
              }
            ]
          },
          {
            "subject": "host_trna_cleavage",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "restricted_phage_propagation",
            "description": "DARNA-dependent host-tRNA cleavage inhibits phage propagation.",
            "evidence": [
              {
                "reference": "DOI:10.64898/2026.02.22.705581",
                "snippet": "cleaves a subset of host tRNAs, thereby inhibiting phage propagation",
                "notes": "Puteikiene et al. place phage-propagation inhibition downstream of DARNA-mediated host-tRNA cleavage."
              }
            ]
          },
          {
            "subject": "restricted_phage_propagation",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "darna_system_trait",
            "description": "DARNA-mediated phage-propagation inhibition realizes the DARNA system trait.",
            "evidence": [
              {
                "reference": "DOI:10.64898/2026.02.22.705581",
                "snippet": "DARNA can detect and respond to a broad range of viruses while avoiding auto-immunity",
                "notes": "Puteikiene et al. support the detected viral signal and antiviral response as the DARNA system output."
              }
            ]
          },
          {
            "subject": "darna_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "DARNA system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "DARNA | 10\\.64898/2026\\.02\\.22\\.705581 | Viral SSB-bound ssDNA activates the bacterial anti-phage defense system DARNA",
                "notes": "DefenseFinder associates DARNA with the Puteikiene et al. bacterial anti-phage defense-system preprint."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "darna-model-profile-gap",
        "prompt": "Resolve DARNA component profiles and locus architecture before minting component-profile synonyms or narrower DARNA subsystem traits.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Puteikiene et al. support DARNA as an anti-phage system with a resolved phage-SSB single-stranded-DNA trigger and host-tRNA cleavage output, and DefenseFinder lists DARNA in its article registry. The pinned DefenseFinder snapshot does not yet expose DARNA HMM or rule rows, so this first record does not assert a component-profile synonym or universal locus architecture.",
        "attaches_to": [
          "causal_graphs#darna_phage_ssb_ssdna_cleaves_trna"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-19"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-19T08:54:19Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted DARNA system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v150.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000243",
    "label": "DarTG system",
    "definition": "A phage defense system in which an organism possesses a DarTG toxin-antitoxin locus whose DarT toxin can be released during bacteriophage infection to ADP-ribosylate viral DNA, block phage genome replication, and prevent production of mature virions.",
    "definition_source": "DOI:10.1038/s41564-022-01153-5",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "DarTG toxin-antitoxin system",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1038/s41564-022-01153-5"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/s41564-022-01153-5",
        "snippet": "Representatives from two different subfamilies, DarTG1 and DarTG2, strongly protected E. coli MG1655 against different phages.",
        "notes": "LeRoux et al. support DarTG as a two-subfamily phage-defense system with experimental activity in E. coli MG1655 challenge assays."
      },
      {
        "reference": "DOI:10.1038/s41564-022-01153-5",
        "snippet": "infection with either RB69 or T5 phage, respectively, triggers release of the DarT toxin, a DNA ADP-ribosyltransferase, that then modifies viral DNA and prevents replication, thereby blocking the production of mature virions",
        "notes": "LeRoux et al. support the DarT release, viral-DNA ADP-ribosylation, phage-genome-replication blockade, and mature-virion-production blockade captured in the causal graph."
      },
      {
        "reference": "DOI:10.1038/s41564-022-01153-5",
        "snippet": "Collectively, our results indicate that phage defence may be a common function for TA systems and reveal the mechanism by which DarTG systems inhibit phage infection.",
        "notes": "LeRoux et al. support DarTG as an experimentally resolved toxin-antitoxin phage-defense system."
      },
      {
        "reference": "DOI:10.1128/mbio.00111-24",
        "snippet": "we identify clinical isolates of the global pathogen Vibrio cholerae harboring a novel genetic element encoding the bacterial immune system DarTG and reveal the immune system's impact on the co-circulating lytic phage ICP1.",
        "notes": "Patel and Seed independently support DarTG as a bacterial immune system in V. cholerae clinical isolates and connect the system to defense against ICP1 phage."
      },
      {
        "reference": "DOI:10.1128/mbio.00111-24",
        "snippet": "We show that DarTG inhibits ICP1 genome replication, thus preventing ICP1 plaquing.",
        "notes": "Patel and Seed support phage-genome-replication blockade as an output of the V. cholerae DarTG system."
      },
      {
        "reference": "DOI:10.1128/mbio.00111-24",
        "snippet": "we probe clinical V. cholerae isolates for novel anti-phage immune systems that can inhibit ICP1 and discover the toxin-antitoxin system DarTG as a potent inhibitor.",
        "notes": "Patel and Seed support the DarTG toxin-antitoxin system as a potent inhibitor of the co-circulating phage ICP1."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:666",
        "taxon_label": "Vibrio cholerae",
        "note": "Patel and Seed characterized a phage defense element encoding DarTG in 2008-2009 clinical V. cholerae isolates and showed DarTG was responsible for ICP1 inhibition.",
        "reference": "DOI:10.1128/mbio.00111-24"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "dartg_dna_adp_ribosylation_defense",
        "title": "DarTG loci couple phage infection to viral-DNA ADP-ribosylation",
        "description": "Evidence-backed process sketch linking sensitive phage infection to DarT toxin release, viral DNA ADP-ribosylation, inhibition of phage genome replication, restricted phage propagation, and the DarTG system trait.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures LeRoux and Patel DarTG phage-defense evidence without claiming a universal phage trigger, DarT release mechanism, viral target scope, or phage-encoded anti-DarT factor across all DarTG systems.",
        "nodes": [
          {
            "node_id": "sensitive_phage_infection",
            "label": "sensitive phage infection",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Infection by a phage whose propagation can be inhibited by an active DarTG system."
          },
          {
            "node_id": "darT_toxin_release",
            "label": "DarT toxin release",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Release of the DNA ADP-ribosyltransferase DarT toxin from inhibition during phage infection."
          },
          {
            "node_id": "viral_dna_adp_ribosylation",
            "label": "viral DNA ADP-ribosylation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "DarT-mediated ADP-ribosylation of bacteriophage DNA after DarT is released from antitoxin control."
          },
          {
            "node_id": "inhibited_phage_genome_replication",
            "label": "inhibited phage genome replication",
            "node_type": "STATE",
            "description": "Reduced or blocked replication of the infecting phage genome downstream of DarT activity."
          },
          {
            "node_id": "restricted_phage_propagation",
            "label": "restricted phage propagation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Blocked mature-virion production or plaquing after DarTG inhibits the infecting phage."
          },
          {
            "node_id": "dartg_system_trait",
            "label": "DarTG system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000243",
            "description": "Possession of a genome-encoded DarTG toxin-antitoxin phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "sensitive_phage_infection",
            "predicate": "triggers",
            "object": "darT_toxin_release",
            "description": "Infection by RB69 or T5 phage triggers release of the DarT toxin in the tested DarTG subfamily systems.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-022-01153-5",
                "snippet": "infection with either RB69 or T5 phage, respectively, triggers release of the DarT toxin",
                "notes": "LeRoux et al. identify phage infection as the upstream trigger for DarT toxin release."
              }
            ]
          },
          {
            "subject": "darT_toxin_release",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "viral_dna_adp_ribosylation",
            "description": "Released DarT ADP-ribosylates viral DNA after phage infection.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-022-01153-5",
                "snippet": "triggers release of the DarT toxin, a DNA ADP-ribosyltransferase, that then modifies viral DNA",
                "notes": "LeRoux et al. support DarT release leading to viral-DNA ADP-ribosylation."
              }
            ]
          },
          {
            "subject": "viral_dna_adp_ribosylation",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "inhibited_phage_genome_replication",
            "description": "DarT-dependent viral-DNA modification blocks replication of the infecting phage genome.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-022-01153-5",
                "snippet": "then modifies viral DNA and prevents replication, thereby blocking the production of mature virions",
                "notes": "LeRoux et al. directly connect viral-DNA modification to blocked phage replication."
              },
              {
                "reference": "DOI:10.1128/mbio.00111-24",
                "snippet": "We show that DarTG inhibits ICP1 genome replication, thus preventing ICP1 plaquing.",
                "notes": "Patel and Seed show that V. cholerae DarTG also blocks ICP1 genome replication."
              }
            ]
          },
          {
            "subject": "inhibited_phage_genome_replication",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "restricted_phage_propagation",
            "description": "Inhibition of genome replication restricts mature virion production and phage plaquing.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-022-01153-5",
                "snippet": "prevents replication, thereby blocking the production of mature virions",
                "notes": "LeRoux et al. support mature-virion blockade as a downstream effect of blocked phage replication."
              },
              {
                "reference": "DOI:10.1128/mbio.00111-24",
                "snippet": "DarTG inhibits ICP1 genome replication, thus preventing ICP1 plaquing",
                "notes": "Patel and Seed support plaquing prevention as a downstream effect of ICP1 genome-replication blockade."
              }
            ]
          },
          {
            "subject": "restricted_phage_propagation",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "dartg_system_trait",
            "description": "The DarTG system trait is realized by inhibition of phage replication and propagation.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-022-01153-5",
                "snippet": "reveal the mechanism by which DarTG systems inhibit phage infection",
                "notes": "LeRoux et al. place the DNA ADP-ribosylation mechanism in the broader DarTG phage-infection-inhibition trait."
              }
            ]
          },
          {
            "subject": "dartg_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "DarTG system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mbio.00111-24",
                "snippet": "we probe clinical V. cholerae isolates for novel anti-phage immune systems that can inhibit ICP1 and discover the toxin-antitoxin system DarTG as a potent inhibitor.",
                "notes": "Patel and Seed support DarTG as an anti-phage immune system."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-18T14:18:08Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted DarTG system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v120.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000245",
    "label": "Dazbog system",
    "definition": "A phage defense system in which an organism possesses a two-component Dazbog locus encoding DzbA and DzbB components that can protect bacteria from bacteriophage infection.",
    "definition_source": "DOI:10.1016/j.chom.2022.09.017",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "Dazbog",
        "synonym_type": "EXACT_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1016/j.chom.2022.09.017",
        "snippet": "discovery of 21 defense systems that protect bacteria from phages, based on computational genomic analyses and phage-infection experiments",
        "notes": "Millman et al. report the computational and experimental cohort in which Dazbog was discovered as a bacterial anti-phage system."
      },
      {
        "reference": "DOI:10.1101/2022.05.11.491447",
        "snippet": "discovery of 21 new defense systems that protect bacteria from phages, based on computational genomic analyses and phage infection experiments",
        "notes": "The bioRxiv version of Millman et al. independently carries the 21-system discovery claim linked from DefenseFinder's Dazbog article registry."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "Dazbog | 10\\.1101/2022\\.05\\.11\\.491447 | An expanding arsenal of immune systems that protect bacteria from phages",
        "notes": "The DefenseFinder model registry maps the named Dazbog system to the Millman et al. antiphage-system discovery preprint."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "Dazbog__DzbA, Dazbog__DzbB",
        "notes": "The DefenseFinder rules table models Dazbog as a two-member system with DzbA and DzbB mandatory profiles."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "Dazbog__DzbA",
        "notes": "The DefenseFinder HMM inventory records DzbA as a Dazbog profile."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "Dazbog__DzbB",
        "notes": "The DefenseFinder HMM inventory records DzbB as a Dazbog profile."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "dazbog_locus_restricts_phage",
        "title": "Dazbog loci confer bacterial phage defense",
        "description": "Conservative system-level sketch linking possession of a Dazbog locus to restricted bacteriophage propagation without asserting the unresolved phage trigger or molecular output.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures the Dazbog system as a DzbA/DzbB anti-phage locus while leaving its phage trigger, enzymatic substrate, effector output, cell-death or survival outcome, and subtype breadth unresolved.",
        "nodes": [
          {
            "node_id": "dazbog_locus",
            "label": "Dazbog locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A Dazbog anti-phage defense locus containing DzbA and DzbB components."
          },
          {
            "node_id": "restricted_phage_propagation",
            "label": "restricted phage propagation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced propagation of bacteriophage in cells carrying the Dazbog system."
          },
          {
            "node_id": "dazbog_system_trait",
            "label": "Dazbog system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000245",
            "description": "Possession of a genome-encoded Dazbog phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "dazbog_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "restricted_phage_propagation",
            "description": "The Dazbog locus encodes the DzbA and DzbB components of a two-component Dazbog anti-phage system.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "Dazbog__DzbA, Dazbog__DzbB",
                "notes": "The DefenseFinder rules table supports DzbA and DzbB as the mandatory Dazbog system profiles."
              }
            ]
          },
          {
            "subject": "restricted_phage_propagation",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "dazbog_system_trait",
            "description": "Dazbog-mediated phage restriction realizes the Dazbog system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.chom.2022.09.017",
                "snippet": "discovery of 21 defense systems that protect bacteria from phages",
                "notes": "Millman et al. place the Dazbog discovery cohort in the set of bacterial systems that protect against phages."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "10\\.1101/2022\\.05\\.11\\.491447 | An expanding arsenal of immune systems",
                "notes": "DefenseFinder records Dazbog as a named system from the Millman et al. antiphage discovery preprint."
              }
            ]
          },
          {
            "subject": "dazbog_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Dazbog system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "An expanding arsenal of immune systems that protect bacteria from phages",
                "notes": "DefenseFinder associates Dazbog with the Millman et al. bacterial antiphage-system discovery paper."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "dazbog-mechanism-gap",
        "prompt": "Resolve Dazbog phage triggers and effector outputs before minting narrower Dazbog mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Millman et al. and DefenseFinder support Dazbog as a named DzbA/DzbB anti-phage locus, but the trigger, molecular substrate, antiviral effector output, and death-or-survival phenotype are not resolved enough here to assert a narrower mechanistic child trait.",
        "posed_by": "codex",
        "posed_date": "2026-09-18"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-18T16:14:42Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Dazbog system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v122.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000274",
    "label": "dCTPdeaminase system",
    "definition": "A phage defense system in which an organism possesses a dCTPdeaminase locus that converts dCTP into deoxy-uracil nucleotides during phage infection, depletes dCTP from the nucleotide pool, and halts phage replication by starving the phage of an essential DNA building block.",
    "definition_source": "DOI:10.1101/2021.04.26.441389",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "dCTPdeaminase",
        "synonym_type": "EXACT_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1101/2021.04.26.441389",
        "snippet": "bacteria employ a similar strategy to defend against phage infection",
        "notes": "Tal et al. support nucleotide depletion as a bacterial anti-phage strategy."
      },
      {
        "reference": "DOI:10.1101/2021.04.26.441389",
        "snippet": "a family of defensive dCTP deaminase proteins that, in response to phage infection, convert dCTP into deoxy-uracil nucleotides",
        "notes": "Tal et al. support the dCTPdeaminase family as a phage-responsive dCTP-conversion defense."
      },
      {
        "reference": "DOI:10.1101/2021.04.26.441389",
        "snippet": "starving the phage of an essential DNA building block and halting its replication",
        "notes": "Tal et al. connect dCTP depletion to phage DNA-building-block starvation and replication arrest."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "dCTPdeaminase | 10\\.1101/2021\\.04\\.26\\.441389 | Antiviral defense via nucleotide depletion in bacteria",
        "notes": "The DefenseFinder article registry maps the named dCTPdeaminase system to the Tal et al. nucleotide-depletion preprint."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "dCTPdeaminase__dCTPdeaminase",
        "notes": "The DefenseFinder rules table models dCTPdeaminase as a single-profile system."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "dCTPdeaminase__dCTPdeaminase",
        "notes": "The DefenseFinder HMM inventory records the custom dCTPdeaminase profile."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "dctpdeaminase_dctp_depletion_defense",
        "title": "dCTPdeaminase loci deplete dCTP during phage infection",
        "description": "Process sketch linking a dCTPdeaminase locus to phage-responsive dCTP conversion, dCTP depletion, phage DNA-building-block starvation, halted phage replication, and the dCTPdeaminase system trait.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures the DOI abstract's phage-responsive dCTP conversion and nucleotide-depletion output without asserting a universal phage sensor, activation route, strain-resolved enzyme accession, or complete substrate scope for every natural dCTPdeaminase system.",
        "nodes": [
          {
            "node_id": "dctpdeaminase_locus",
            "label": "dCTPdeaminase locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A dCTPdeaminase anti-phage defense locus represented by a custom DefenseFinder dCTPdeaminase profile."
          },
          {
            "node_id": "sensitive_phage_infection",
            "label": "sensitive phage infection",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Infection by a phage whose propagation can be blocked by a dCTPdeaminase defense system."
          },
          {
            "node_id": "dctp_conversion",
            "label": "dCTP conversion into deoxy-uracil nucleotides",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Conversion of dCTP into deoxy-uracil nucleotides by defensive dCTP deaminase proteins during phage infection."
          },
          {
            "node_id": "dctp_depletion",
            "label": "dCTP nucleotide-pool depletion",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Elimination of dCTP from the nucleotide pool during dCTPdeaminase-mediated defense."
          },
          {
            "node_id": "phage_dna_building_block_starvation",
            "label": "phage DNA-building-block starvation",
            "node_type": "STATE",
            "description": "Deprivation of an essential deoxynucleotide needed for phage DNA synthesis."
          },
          {
            "node_id": "halted_phage_replication",
            "label": "halted phage replication",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Arrest of bacteriophage replication after dCTP depletion."
          },
          {
            "node_id": "dctpdeaminase_system_trait",
            "label": "dCTPdeaminase system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000274",
            "description": "Possession of a genome-encoded dCTPdeaminase phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "dctpdeaminase_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "dctp_conversion",
            "description": "The dCTPdeaminase locus encodes the dCTP deaminase activity that converts dCTP into deoxy-uracil nucleotides.",
            "evidence": [
              {
                "reference": "DOI:10.1101/2021.04.26.441389",
                "snippet": "defensive dCTP deaminase proteins that, in response to phage infection, convert dCTP",
                "notes": "Tal et al. identify defensive dCTP deaminase proteins that convert dCTP during phage infection."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "dCTPdeaminase__dCTPdeaminase",
                "notes": "DefenseFinder models the dCTPdeaminase protein profile used to identify the system."
              }
            ]
          },
          {
            "subject": "sensitive_phage_infection",
            "predicate": "triggers",
            "object": "dctp_conversion",
            "description": "Phage infection induces dCTP conversion by defensive dCTP deaminase proteins.",
            "evidence": [
              {
                "reference": "DOI:10.1101/2021.04.26.441389",
                "snippet": "in response to phage infection, convert dCTP",
                "notes": "Tal et al. place dCTP conversion in the phage-infection response."
              }
            ]
          },
          {
            "subject": "dctp_conversion",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "dctp_depletion",
            "description": "Conversion of dCTP into deoxy-uracil nucleotides depletes the host dCTP nucleotide pool.",
            "evidence": [
              {
                "reference": "DOI:10.1101/2021.04.26.441389",
                "snippet": "completely eliminate the specific deoxynucleotide (either dCTP or dGTP) from the nucleotide pool during phage infection",
                "notes": "Tal et al. connect defensive dCTP conversion to loss of dCTP from the nucleotide pool."
              }
            ]
          },
          {
            "subject": "dctp_depletion",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "phage_dna_building_block_starvation",
            "description": "dCTP depletion starves the infecting phage of an essential DNA building block.",
            "evidence": [
              {
                "reference": "DOI:10.1101/2021.04.26.441389",
                "snippet": "starving the phage of an essential DNA building block",
                "notes": "Tal et al. support phage DNA-building-block starvation as the output of defensive deoxynucleotide depletion."
              }
            ]
          },
          {
            "subject": "phage_dna_building_block_starvation",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "halted_phage_replication",
            "description": "Starvation for dCTP halts phage DNA replication.",
            "evidence": [
              {
                "reference": "DOI:10.1101/2021.04.26.441389",
                "snippet": "starving the phage of an essential DNA building block and halting its replication",
                "notes": "Tal et al. place phage-replication arrest downstream of defensive deoxynucleotide depletion."
              }
            ]
          },
          {
            "subject": "halted_phage_replication",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "dctpdeaminase_system_trait",
            "description": "dCTPdeaminase-mediated arrest of phage replication realizes the dCTPdeaminase system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1101/2021.04.26.441389",
                "snippet": "bacteria employ a similar strategy to defend against phage infection",
                "notes": "Tal et al. support dCTP depletion as a bacterial phage-defense strategy."
              }
            ]
          },
          {
            "subject": "dctpdeaminase_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "dCTPdeaminase system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "dCTPdeaminase | 10\\.1101/2021\\.04\\.26\\.441389 | Antiviral defense via nucleotide depletion in bacteria",
                "notes": "DefenseFinder associates dCTPdeaminase with the Tal et al. bacterial antiviral nucleotide-depletion preprint."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "dctpdeaminase-activation-profile-gap",
        "prompt": "Resolve dCTPdeaminase activation, locus boundaries, and representative enzyme accessions before asserting narrower component or subtype traits.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Tal et al. support dCTPdeaminase as a phage-responsive dCTP-depletion defense and DefenseFinder models the system with a custom dCTPdeaminase HMM profile, but this first system-level record does not resolve the universal phage sensor, activation route, strain-level accessions, or whether additional unmodeled components define some natural loci.",
        "attaches_to": [
          "causal_graphs#dctpdeaminase_dctp_depletion_defense"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-19"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-19T09:25:18Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted dCTPdeaminase system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v151.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000275",
    "label": "DdmDE system",
    "definition": "A genomics trait describing possession of a DdmDE anti-plasmid defense locus encoding the DNA-guided prokaryotic Argonaute DdmE and the helicase-nuclease DdmD, whose DNA recognition and handoff trigger processive plasmid destruction.",
    "definition_source": "DOI:10.1038/s41586-024-07515-9",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000419"
    ],
    "synonyms": [
      {
        "synonym_text": "DdmDE",
        "synonym_type": "EXACT_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/s41586-022-04546-y",
        "snippet": "two plasmid defence systems conserved in the Vibrio cholerae El Tor strains",
        "notes": "Jaskolska et al. support discovery of plasmid-defense systems in V. cholerae El Tor strains."
      },
      {
        "reference": "DOI:10.1038/s41586-022-04546-y",
        "snippet": "These systems, termed DdmABC and DdmDE",
        "notes": "Jaskolska et al. identify DdmDE as one of those plasmid-defense systems."
      },
      {
        "reference": "DOI:10.1038/s41586-024-07515-9",
        "snippet": "DNA defence module DdmDE system, which rapidly eliminates small, multicopy plasmids",
        "notes": "Bravo et al. support DdmDE as a plasmid-elimination DNA defense module."
      },
      {
        "reference": "DOI:10.1038/s41586-024-07515-9",
        "snippet": "DNA recognition triggers processive plasmid destruction",
        "notes": "Bravo et al. connect target DNA recognition in DdmDE to processive plasmid destruction."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "DdmDE | 10\\.1038/s41586-022-04546-y | Two defence systems eliminate plasmids from seventh pandemic Vibrio cholerae",
        "notes": "The DefenseFinder article registry maps the named DdmDE system to the Jaskolska et al. Nature paper."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "DdmDE__DdmD                                      | DdmDE__DdmD                                      | DdmDE                  | Custom                  | 20",
        "notes": "The DefenseFinder HMM inventory records the custom DdmD profile for DdmDE."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "DdmDE__DdmE                                      | DdmDE__DdmE                                      | DdmDE                  | Custom                  | 20",
        "notes": "The DefenseFinder HMM inventory records the custom DdmE profile for DdmDE."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:666",
        "taxon_label": "Vibrio cholerae",
        "note": "The DdmDE system was characterized from V. cholerae seventh pandemic strains.",
        "reference": "DOI:10.1038/s41586-022-04546-y"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "ddmde_pago_helicase_plasmid_destruction",
        "title": "DdmDE couples DNA recognition to plasmid destruction",
        "description": "Process sketch linking a DdmDE locus to target DNA recognition, processive plasmid destruction, plasmid clearance, and the DdmDE system trait.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures the DdmDE activation pathway resolved by Bravo et al. without asserting every guide-maturation route, native plasmid substrate, DdmABC cooperation mode, or Vibrio-specific locus boundary as universal for all DdmDE systems.",
        "nodes": [
          {
            "node_id": "ddmde_locus",
            "label": "DdmDE locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "An anti-plasmid defense locus encoding DdmD and DdmE components."
          },
          {
            "node_id": "ddmde_dna_recognition",
            "label": "DdmDE target DNA recognition",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "DdmDE DNA recognition coordinated by the DNA-targeting pAgo DdmE and helicase-nuclease DdmD."
          },
          {
            "node_id": "processive_plasmid_destruction",
            "label": "processive plasmid destruction",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Processive destruction of plasmid DNA after DdmDE target recognition."
          },
          {
            "node_id": "plasmid_clearance",
            "label": "plasmid clearance",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Elimination of invasive small multicopy plasmids."
          },
          {
            "node_id": "ddmde_system_trait",
            "label": "DdmDE system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000275",
            "description": "Possession of a genome-encoded DdmDE anti-plasmid defense system."
          }
        ],
        "edges": [
          {
            "subject": "ddmde_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "ddmde_dna_recognition",
            "description": "The DdmDE locus encodes DdmE and DdmD components that support DdmDE target DNA recognition.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41586-024-07515-9",
                "snippet": "DdmE is a catalytically inactive, DNA-guided, DNA-targeting pAgo",
                "notes": "Bravo et al. define DdmE as the DNA-guided DdmDE pAgo component."
              },
              {
                "reference": "DOI:10.1038/s41586-024-07515-9",
                "snippet": "helicase-nuclease DdmD transitions from an autoinhibited, dimeric complex to a monomeric state upon loading of single-stranded DNA targets",
                "notes": "Bravo et al. connect DdmD to target-DNA loading and the monomeric active state."
              }
            ]
          },
          {
            "subject": "ddmde_dna_recognition",
            "predicate": "triggers",
            "object": "processive_plasmid_destruction",
            "description": "DdmDE DNA recognition triggers processive plasmid destruction.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41586-024-07515-9",
                "snippet": "DNA recognition triggers processive plasmid destruction",
                "notes": "Bravo et al. place plasmid destruction downstream of DNA recognition by DdmDE."
              }
            ]
          },
          {
            "subject": "processive_plasmid_destruction",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "plasmid_clearance",
            "description": "Processive DdmDE-mediated plasmid DNA destruction clears invasive plasmids.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41586-024-07515-9",
                "snippet": "pAgos utilize ancillary factors to achieve plasmid clearance",
                "notes": "Bravo et al. frame DdmD as the ancillary factor that helps a pAgo clear plasmids."
              }
            ]
          },
          {
            "subject": "plasmid_clearance",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "ddmde_system_trait",
            "description": "DdmDE-mediated clearance of small multicopy plasmids realizes the DdmDE system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41586-024-07515-9",
                "snippet": "DdmDE system, which rapidly eliminates small, multicopy plasmids",
                "notes": "Bravo et al. support plasmid elimination as the DdmDE defense output."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "ddmde-substrate-and-guide-source-gap",
        "prompt": "Resolve DdmDE natural guide sources, plasmid-substrate breadth, and DdmABC cooperation before minting narrower DdmDE mechanism or subtype traits.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Jaskolska et al. support DdmDE as a V. cholerae plasmid-defense system and Bravo et al. resolve how DdmE and DdmD cooperate for plasmid destruction, but this first system-level record does not assert a universal guide-maturation route, full natural plasmid substrate range, or whether cooperation with DdmABC is required in some hosts.",
        "attaches_to": [
          "causal_graphs#ddmde_pago_helicase_plasmid_destruction"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-19"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-19T10:17:05Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted DdmDE system as a DOI-backed GENOMICS TraitRecord under the quality root after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v152.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-19T10:30:00Z",
        "curator": "codex",
        "action": "ADVERSARIAL_REVIEW_REPAIR",
        "changes": "Resolved #1055 by simplifying the DdmDE causal graph to a source-supported target-DNA-recognition sketch and removing unsupported guide-target handover input edges.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-27T22:11:00Z",
        "curator": "codex",
        "action": "REPAIRED_PARENT_TRAIT",
        "changes": "Reparented DdmDE system from the generic quality root to the newly minted prokaryotic Argonaute defense system parent without changing DdmDE-specific evidence or mechanism claims.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000302",
    "label": "Detocs system",
    "definition": "A phage defense system in which an organism possesses a Detocs locus represented in DefenseFinder by DtcA and DtcB profiles plus optional DtcC-family profiles, with an ATP nucleosidase output that can degrade ATP and dATP upon phage infection and halt phage propagation.",
    "definition_source": "DOI:10.1016/j.cell.2023.07.020",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "Detocs",
        "synonym_type": "EXACT_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1016/j.cell.2023.07.020",
        "snippet": "By analyzing homologs of the immune ATP nucleosidase domain, we discover and characterize Detocs, a family of bacterial defense systems with a two-component phosphotransfer-signaling architecture",
        "notes": "Rousset et al. discover Detocs from immune ATP nucleosidase domain homologs and name it as a bacterial defense-system family with two-component phosphotransfer-signaling architecture."
      },
      {
        "reference": "DOI:10.1016/j.cell.2023.07.020",
        "snippet": "upon phage infection, degrade cellular adenosine triphosphate (ATP) and deoxyadenosine triphosphate (dATP)",
        "notes": "Rousset et al. support ATP and dATP degradation as a phage-triggered bacterial immune output."
      },
      {
        "reference": "DOI:10.1016/j.cell.2023.07.020",
        "snippet": "ATP and dATP degradation during infection halts phage propagation",
        "notes": "Rousset et al. connect ATP and dATP degradation to inhibition of phage propagation."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "Detocs | 10\\.1101/2023\\.01\\.24\\.525353 | A conserved family of immune effectors cleaves cellular ATP upon viral infection",
        "notes": "The DefenseFinder article registry maps the named Detocs system to the Rousset et al. ATP-cleavage preprint."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "Detocs\tDetocs\t2\t2\tDetocs__dtcA, Detocs__dtcB\tDetocs__dtcC",
        "notes": "The DefenseFinder rules table models the core Detocs system with required dtcA and dtcB profiles and an optional dtcC profile."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| Detocs__dtcA                                     | Detocs__dtcA                                     | Detocs                 | Custom                  | 30     |",
        "notes": "The DefenseFinder HMM inventory records dtcA under the Detocs model namespace."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| Detocs__dtcB                                     | Detocs__dtcB                                     | Detocs                 | Custom                  | 40     |",
        "notes": "The DefenseFinder HMM inventory records dtcB under the Detocs model namespace."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| Detocs__dtcC                                     | Detocs__dtcC                                     | Detocs                 | Custom                  | 40     |",
        "notes": "The DefenseFinder HMM inventory records dtcC under the Detocs model namespace."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "detocs_locus_depletes_atp",
        "title": "Detocs loci connect phage infection to ATP depletion",
        "description": "Conservative system-level sketch linking possession of a Detocs locus to phage-associated ATP and dATP degradation, halted phage propagation, and the Detocs system trait without asserting the direct phage trigger or component-specific activation mechanism.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Detocs as a named ATP-depletion anti-phage system with DtcA, DtcB, and DtcC-family DefenseFinder profiles while leaving the direct phage trigger, component-specific phosphotransfer sequence, DtcC-variant effects, and universal system boundary unresolved.",
        "nodes": [
          {
            "node_id": "detocs_locus",
            "label": "Detocs locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A Detocs anti-phage defense locus represented in DefenseFinder by dtcA and dtcB profiles plus an optional dtcC-family profile."
          },
          {
            "node_id": "phage_associated_atp_degradation",
            "label": "phage-associated ATP and dATP degradation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "ATP nucleosidase-mediated degradation of cellular ATP and dATP during phage infection."
          },
          {
            "node_id": "halted_phage_propagation",
            "label": "halted phage propagation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Blockage of bacteriophage propagation after ATP-and-dATP degradation during infection."
          },
          {
            "node_id": "detocs_system_trait",
            "label": "Detocs system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000302",
            "description": "Possession of a genome-encoded Detocs ATP-depletion phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "detocs_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "phage_associated_atp_degradation",
            "description": "Rousset et al. connect ATP nucleosidase-domain bacterial immune effectors to phage-associated ATP and dATP degradation and discovered Detocs from ATP nucleosidase domain homologs; DefenseFinder catalogs Detocs with dtcA, dtcB, and dtcC-family profiles.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.cell.2023.07.020",
                "snippet": "By analyzing homologs of the immune ATP nucleosidase domain, we discover and characterize Detocs, a family of bacterial defense systems",
                "notes": "Rousset et al. identify Detocs from homologs of immune ATP nucleosidase domains."
              },
              {
                "reference": "DOI:10.1016/j.cell.2023.07.020",
                "snippet": "upon phage infection, degrade cellular adenosine triphosphate (ATP) and deoxyadenosine triphosphate (dATP)",
                "notes": "Rousset et al. support ATP and dATP degradation as a phage-triggered bacterial immune output."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "Detocs\tDetocs\t2\t2\tDetocs__dtcA, Detocs__dtcB\tDetocs__dtcC",
                "notes": "The DefenseFinder rules table models the core Detocs system with required dtcA and dtcB profiles and an optional dtcC profile."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| Detocs__dtcA                                     | Detocs__dtcA                                     | Detocs                 | Custom                  | 30     |",
                "notes": "The DefenseFinder HMM inventory records dtcA under the Detocs model namespace."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| Detocs__dtcB                                     | Detocs__dtcB                                     | Detocs                 | Custom                  | 40     |",
                "notes": "The DefenseFinder HMM inventory records dtcB under the Detocs model namespace."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| Detocs__dtcC                                     | Detocs__dtcC                                     | Detocs                 | Custom                  | 40     |",
                "notes": "The DefenseFinder HMM inventory records dtcC under the Detocs model namespace."
              }
            ]
          },
          {
            "subject": "phage_associated_atp_degradation",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "halted_phage_propagation",
            "description": "ATP and dATP degradation during infection contributes to halted phage propagation.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.cell.2023.07.020",
                "snippet": "ATP and dATP degradation during infection halts phage propagation",
                "notes": "Rousset et al. connect ATP and dATP degradation to halted phage propagation."
              }
            ]
          },
          {
            "subject": "halted_phage_propagation",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "detocs_system_trait",
            "description": "Detocs-associated ATP and dATP depletion realizes the Detocs system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.cell.2023.07.020",
                "snippet": "ATP and dATP degradation during infection halts phage propagation",
                "notes": "Rousset et al. connect ATP and dATP degradation to inhibition of phage propagation."
              },
              {
                "reference": "DOI:10.1016/j.cell.2023.07.020",
                "snippet": "we discover and characterize Detocs, a family of bacterial defense systems",
                "notes": "Rousset et al. support Detocs as a named bacterial defense-system family."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Detocs | 10\\.1101/2023\\.01\\.24\\.525353 | A conserved family of immune effectors cleaves cellular ATP upon viral infection",
                "notes": "The DefenseFinder article registry maps the named Detocs system to the Rousset et al. ATP-cleavage preprint."
              }
            ]
          },
          {
            "subject": "detocs_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Detocs system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.cell.2023.07.020",
                "snippet": "we discover and characterize Detocs, a family of bacterial defense systems",
                "notes": "Rousset et al. place Detocs in a bacterial defense-system family."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Detocs | 10\\.1101/2023\\.01\\.24\\.525353 | A conserved family of immune effectors cleaves cellular ATP upon viral infection",
                "notes": "The DefenseFinder article registry maps the named Detocs system to the Rousset et al. ATP-cleavage preprint."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "detocs-component-mechanism-gap",
        "prompt": "Resolve Detocs phage triggers, component-specific phosphotransfer events, and DtcC-family effector outputs before minting narrower Detocs mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Rousset et al. support Detocs as a named family of two-component phosphotransfer-signaling bacterial defense systems, and DefenseFinder represents Detocs with required dtcA and dtcB profiles plus optional dtcC-family profiles. This system-level record leaves the direct phage trigger, component-specific activation route, exact ATP nucleosidase effector architecture, and DtcC-variant outputs unresolved.",
        "attaches_to": [
          "causal_graphs#detocs_locus_depletes_atp"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-20"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-20T06:11:22Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Detocs system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v179.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-20T06:54:24Z",
        "curator": "codex",
        "action": "ADDRESS_PR_REVIEW",
        "changes": "Quoted the Cell abstract sentence that names Detocs as a bacterial defense-system family and moved the Detocs phage-defense subclass edge off a weaker ATP-degradation fragment after the PR 1117 adversarial review filed issue 1119.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-20T07:11:29Z",
        "curator": "codex",
        "action": "ADDRESS_PR_REVIEW",
        "changes": "Attached direct ATP and dATP degradation evidence to the Detocs locus causal edge and halted-propagation evidence to the Detocs trait-conferral edge after the PR 1117 adversarial review filed issue 1121.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000276",
    "label": "dGTPase system",
    "definition": "A phage defense system in which an organism possesses a dGTPase locus that degrades dGTP into phosphate-free deoxy-guanosine during phage infection, depletes dGTP from the nucleotide pool, and halts phage replication by starving the phage of an essential DNA building block.",
    "definition_source": "DOI:10.1101/2021.04.26.441389",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "dGTPase",
        "synonym_type": "EXACT_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1101/2021.04.26.441389",
        "snippet": "bacteria employ a similar strategy to defend against phage infection",
        "notes": "Tal et al. support nucleotide depletion as a bacterial anti-phage strategy."
      },
      {
        "reference": "DOI:10.1101/2021.04.26.441389",
        "snippet": "A second family of phage resistance genes encode dGTPase enzymes, which degrade dGTP into phosphate-free deoxy-guanosine (dG)",
        "notes": "Tal et al. support dGTPase genes as phage-resistance genes encoding enzymes that degrade dGTP."
      },
      {
        "reference": "DOI:10.1101/2021.04.26.441389",
        "snippet": "completely eliminate the specific deoxynucleotide (either dCTP or dGTP) from the nucleotide pool during phage infection",
        "notes": "Tal et al. connect dGTPase defense to dGTP nucleotide-pool elimination during phage infection."
      },
      {
        "reference": "DOI:10.1101/2021.04.26.441389",
        "snippet": "starving the phage of an essential DNA building block and halting its replication",
        "notes": "Tal et al. connect defensive deoxynucleotide depletion to phage DNA-building-block starvation and replication arrest."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "dGTPase | 10\\.1101/2021\\.04\\.26\\.441389 | Antiviral defense via nucleotide depletion in bacteria",
        "notes": "The DefenseFinder article registry maps the named dGTPase system to the Tal et al. nucleotide-depletion preprint."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "dGTPase\tdGTPase\t1\t1\tdGTPase__Sp_dGTPase",
        "notes": "The DefenseFinder rules table models dGTPase as a single-profile system."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "dGTPase__Sp_dGTPase                              | dGTPase__Sp_dGTPase                              | dGTPase",
        "notes": "The DefenseFinder HMM inventory records the custom Sp_dGTPase profile."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "dgtpase_dgtp_depletion_defense",
        "title": "dGTPase loci deplete dGTP during phage infection",
        "description": "Process sketch linking a dGTPase locus to dGTP degradation, dGTP depletion, phage DNA-building-block starvation, halted phage replication, and the dGTPase system trait.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures the DOI abstract's dGTPase-mediated dGTP degradation and nucleotide-depletion output without asserting a universal phage sensor, activation route, strain-resolved enzyme accession, or complete substrate scope for every natural dGTPase system.",
        "nodes": [
          {
            "node_id": "dgtpase_locus",
            "label": "dGTPase locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A dGTPase anti-phage defense locus represented by a custom DefenseFinder Sp_dGTPase profile."
          },
          {
            "node_id": "dgtp_degradation",
            "label": "dGTP degradation into deoxy-guanosine",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Degradation of dGTP into phosphate-free deoxy-guanosine by defensive dGTPase enzymes."
          },
          {
            "node_id": "dgtp_depletion",
            "label": "dGTP nucleotide-pool depletion",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Elimination of dGTP from the nucleotide pool during dGTPase-mediated defense."
          },
          {
            "node_id": "phage_dna_building_block_starvation",
            "label": "phage DNA-building-block starvation",
            "node_type": "STATE",
            "description": "Deprivation of an essential deoxynucleotide needed for phage DNA synthesis."
          },
          {
            "node_id": "halted_phage_replication",
            "label": "halted phage replication",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Arrest of bacteriophage replication after dGTP depletion."
          },
          {
            "node_id": "dgtpase_system_trait",
            "label": "dGTPase system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000276",
            "description": "Possession of a genome-encoded dGTPase phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "dgtpase_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "dgtp_degradation",
            "description": "The dGTPase locus encodes dGTPase activity that degrades dGTP into phosphate-free deoxy-guanosine.",
            "evidence": [
              {
                "reference": "DOI:10.1101/2021.04.26.441389",
                "snippet": "dGTPase enzymes, which degrade dGTP into phosphate-free deoxy-guanosine (dG)",
                "notes": "Tal et al. identify dGTPase enzymes that degrade dGTP."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "dGTPase__Sp_dGTPase                              | dGTPase__Sp_dGTPase                              | dGTPase",
                "notes": "DefenseFinder models the Sp_dGTPase protein profile used to identify the dGTPase system."
              }
            ]
          },
          {
            "subject": "dgtp_degradation",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "dgtp_depletion",
            "description": "Degradation of dGTP depletes the host dGTP nucleotide pool during phage infection.",
            "evidence": [
              {
                "reference": "DOI:10.1101/2021.04.26.441389",
                "snippet": "completely eliminate the specific deoxynucleotide (either dCTP or dGTP) from the nucleotide pool during phage infection",
                "notes": "Tal et al. connect defensive dGTPase activity to loss of dGTP from the nucleotide pool."
              }
            ]
          },
          {
            "subject": "dgtp_depletion",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "phage_dna_building_block_starvation",
            "description": "dGTP depletion starves the infecting phage of an essential DNA building block.",
            "evidence": [
              {
                "reference": "DOI:10.1101/2021.04.26.441389",
                "snippet": "starving the phage of an essential DNA building block",
                "notes": "Tal et al. support phage DNA-building-block starvation as the output of defensive deoxynucleotide depletion."
              }
            ]
          },
          {
            "subject": "phage_dna_building_block_starvation",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "halted_phage_replication",
            "description": "Starvation for dGTP halts phage DNA replication.",
            "evidence": [
              {
                "reference": "DOI:10.1101/2021.04.26.441389",
                "snippet": "starving the phage of an essential DNA building block and halting its replication",
                "notes": "Tal et al. place phage-replication arrest downstream of defensive deoxynucleotide depletion."
              }
            ]
          },
          {
            "subject": "halted_phage_replication",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "dgtpase_system_trait",
            "description": "dGTPase-mediated arrest of phage replication realizes the dGTPase system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1101/2021.04.26.441389",
                "snippet": "bacteria employ a similar strategy to defend against phage infection",
                "notes": "Tal et al. support dGTP depletion as a bacterial phage-defense strategy."
              }
            ]
          },
          {
            "subject": "dgtpase_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "dGTPase system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "dGTPase | 10\\.1101/2021\\.04\\.26\\.441389 | Antiviral defense via nucleotide depletion in bacteria",
                "notes": "DefenseFinder associates dGTPase with the Tal et al. bacterial antiviral nucleotide-depletion preprint."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "dgtpase-activation-profile-gap",
        "prompt": "Resolve dGTPase activation, locus boundaries, and representative enzyme accessions before asserting narrower component or subtype traits.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Tal et al. support dGTPase as a phage-responsive dGTP-depletion defense and DefenseFinder models the system with a custom Sp_dGTPase HMM profile, but this first system-level record does not resolve the universal phage sensor, activation route, strain-level accessions, or whether additional unmodeled components define some natural loci.",
        "attaches_to": [
          "causal_graphs#dgtpase_dgtp_depletion_defense"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-19"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-19T10:46:26Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted dGTPase system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v153.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000330",
    "label": "Dionysus system",
    "definition": "A phage defense system in which an organism possesses a three-gene Dionysus locus encoding DinA, DinB, and DinC components that can block jumbo-phage infection.",
    "definition_source": "DOI:10.1101/2025.09.30.679545",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "Dionysus",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1101/2025.09.30.679545"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1101/2025.09.30.679545",
        "snippet": "From over 500 candidate defense systems, we selected nine for experimental testing and validated three: Dionysus, a TerB-encoding system that disrupts early phage infection vesicle formation by Jumbo phages; Ophion, a Radical SAM-containing system that prevents the formation of the Jumbo phage nucleus; and Ambrosia, a tightly regulated RM-like system.",
        "notes": "Keesman et al. named Dionysus among three modular phage-defense candidates validated experimentally from an initial pool of more than 500 candidates."
      },
      {
        "reference": "DOI:10.1101/2025.09.30.679545",
        "snippet": "Dionysus is named after the god associated with winemaking and the celebration of life. This defense system consists of three genes encoding: DinA, featuring a merozoite adhesive erythrocyte binding protein (MAEBL) and a transmembrane (TM) domain; DinB, a TerB-like protein; and DinC, a pore-forming toxin (PFT) with four TM domains",
        "notes": "Keesman et al. support Dionysus as a three-gene defense system encoding DinA, DinB, and DinC components."
      },
      {
        "reference": "DOI:10.1101/2025.09.30.679545",
        "snippet": "Both Dionysus and Ophion specifically block infection by jumbo phages, which have evolved specialized compartments to protect their DNA from DNA-targeting host defenses",
        "notes": "Keesman et al. support Dionysus as a system that blocks infection by jumbo phages with early phage infection vesicles."
      },
      {
        "reference": "DOI:10.1101/2025.09.30.679545",
        "snippet": "Specifically, we show that Dionysus forms pores in the EPI vesicle of the jumbo phage to disrupt the infection cycle of the phage at an early stage, similar to the mechanism described for the Juk phage defense system",
        "notes": "Keesman et al. connect Dionysus to disruption of the jumbo phage early phage infection vesicle and therefore to interruption of the phage infection cycle."
      },
      {
        "reference": "DOI:10.1101/2025.09.30.679545",
        "snippet": "All three proteins of Dionysus are essential for its protective capacity, as mutating a conserved amino acid within the MAEBL-like domain of DinA (H326A), and deletion of DinB or DinC, resulted in the partial (DinA H326A) or complete loss of anti-phage activity",
        "notes": "Keesman et al. support all three Dionysus proteins as required for full anti-phage protection in the tested system."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "Dionysus | 10\\.1101/2025\\.09\\.30\\.679545 | Discovery of phage defense systems through component modularity networks",
        "notes": "The DefenseFinder article registry maps the named Dionysus system to the Keesman et al. modular phage-defense discovery preprint; the pinned DefenseFinder HMM inventory and rules table do not list Dionysus, so this row is name-to-paper evidence rather than model-component evidence."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "dionysus_locus_restricts_phage",
        "title": "Dionysus loci confer bacterial phage defense",
        "description": "Conservative system-level sketch linking possession of a Dionysus locus to restricted jumbo-phage propagation without asserting the direct phage trigger or protein-resolved pore-forming sequence.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Dionysus as a named three-gene anti-jumbo-phage system while leaving its direct phage trigger, the DinA/DinB/DinC interaction sequence, the natural locus breadth, and the absence of pinned DefenseFinder HMM or rule rows unresolved.",
        "nodes": [
          {
            "node_id": "dionysus_locus",
            "label": "Dionysus locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A three-gene Dionysus anti-phage defense locus encoding DinA, DinB, and DinC components."
          },
          {
            "node_id": "restricted_phage_propagation",
            "label": "restricted phage propagation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced propagation of bacteriophage in cells carrying the Dionysus system."
          },
          {
            "node_id": "dionysus_system_trait",
            "label": "Dionysus system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000330",
            "description": "Possession of a genome-encoded Dionysus phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "dionysus_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "restricted_phage_propagation",
            "description": "The three-gene Dionysus locus restricts infection by jumbo phages.",
            "evidence": [
              {
                "reference": "DOI:10.1101/2025.09.30.679545",
                "snippet": "Both Dionysus and Ophion specifically block infection by jumbo phages, which have evolved specialized compartments to protect their DNA from DNA-targeting host defenses",
                "notes": "Keesman et al. report that Dionysus blocks infection by jumbo phages."
              },
              {
                "reference": "DOI:10.1101/2025.09.30.679545",
                "snippet": "All three proteins of Dionysus are essential for its protective capacity, as mutating a conserved amino acid within the MAEBL-like domain of DinA (H326A), and deletion of DinB or DinC, resulted in the partial (DinA H326A) or complete loss of anti-phage activity",
                "notes": "Keesman et al. report that DinA, DinB, and DinC perturbations reduce or abolish Dionysus anti-phage activity."
              }
            ]
          },
          {
            "subject": "restricted_phage_propagation",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "dionysus_system_trait",
            "description": "Dionysus-mediated phage restriction realizes the Dionysus system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1101/2025.09.30.679545",
                "snippet": "Specifically, we show that Dionysus forms pores in the EPI vesicle of the jumbo phage to disrupt the infection cycle of the phage at an early stage, similar to the mechanism described for the Juk phage defense system",
                "notes": "Keesman et al. connect Dionysus activity to disruption of the jumbo-phage infection cycle at an early vesicle stage."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Dionysus | 10\\.1101/2025\\.09\\.30\\.679545 | Discovery of phage defense systems through component modularity networks",
                "notes": "The DefenseFinder article registry maps the named Dionysus system to the Keesman et al. modular phage-defense discovery preprint; the pinned DefenseFinder HMM inventory and rules table do not list Dionysus, so this row is name-to-paper evidence rather than model-component evidence."
              }
            ]
          },
          {
            "subject": "dionysus_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Dionysus system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1101/2025.09.30.679545",
                "snippet": "From over 500 candidate defense systems, we selected nine for experimental testing and validated three: Dionysus, a TerB-encoding system that disrupts early phage infection vesicle formation by Jumbo phages; Ophion, a Radical SAM-containing system that prevents the formation of the Jumbo phage nucleus; and Ambrosia, a tightly regulated RM-like system.",
                "notes": "Keesman et al. list Dionysus among experimentally validated phage-defense systems."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Dionysus | 10\\.1101/2025\\.09\\.30\\.679545 | Discovery of phage defense systems through component modularity networks",
                "notes": "The DefenseFinder article registry maps the named Dionysus system to the Keesman et al. modular phage-defense discovery preprint; the pinned DefenseFinder HMM inventory and rules table do not list Dionysus, so this row is name-to-paper evidence rather than model-component evidence."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "dionysus-jumbo-phage-mechanism-gap",
        "prompt": "Resolve Dionysus phage triggers, EPI-vesicle pore formation, and model coverage before minting narrower Dionysus mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Keesman et al. support Dionysus as a three-gene anti-jumbo-phage system that disrupts the jumbo-phage EPI vesicle stage, but the direct phage trigger, exact DinA/DinB/DinC interaction sequence, natural locus breadth, and profile-to-component model are not resolved enough here to assert a narrower mechanistic child trait.",
        "attaches_to": [
          "causal_graphs#dionysus_locus_restricts_phage"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-21"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-21T07:22:15Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Dionysus system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v207.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000548",
    "label": "DISARM1 system",
    "definition": "A DISARM system in which an organism possesses a genome-encoded DefenseFinder DISARM_1 subtype locus represented by DISARM_1__drmD, DISARM_1__drmMI, DISARM__drmA, DISARM__drmB, and DISARM__drmC rule profiles.",
    "definition_source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000211"
    ],
    "synonyms": [
      {
        "synonym_text": "DISARM_1",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv"
      },
      {
        "synonym_text": "DISARM_1__drmD",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "DISARM_1__drmMI",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "DISARM__drmA",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "DISARM__drmB",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "DISARM__drmC",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/s41564-017-0051-0",
        "snippet": "Our results establish DISARM as a new defence system, providing protection against diverse phages",
        "notes": "Ofir et al. experimentally established DISARM as a broad-spectrum phage defense system."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| DISARM | 10\\.1038/s41564-017-0051-0 | DISARM is a widespread bacterial defence system with broad anti-phage activities | ",
        "notes": "The pinned DefenseFinder article registry maps the DISARM source key to Ofir et al.'s DISARM phage-defense paper."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| DISARM__drmA                                     | DISARM__drmA                                     | DISARM                 | Custom                  | 90     |\n| DISARM__drmB                                     | DISARM__drmB                                     | DISARM                 | Custom                  | 90     |\n| DISARM__drmC                                     | DISARM__drmC                                     | DISARM                 | Custom                  | 40     |\n| DISARM_1__drmD                                   | DISARM_1__drmD                                   | DISARM_1               | Custom                  | 500    |\n| DISARM_1__drmMI                                  | DISARM_1__drmMI                                  | DISARM_1               | Custom                  | 90     |",
        "notes": "The pinned DefenseFinder HMM inventory records the shared DISARM drmA, drmB, and drmC profiles and the DISARM_1 drmD and drmMI profiles."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "DISARM\tDISARM_1\t4\t4\tDISARM_1__drmD, DISARM_1__drmMI, DISARM__drmA, DISARM__drmB, DISARM__drmC\t\t\t",
        "notes": "The pinned DefenseFinder rules table models DISARM_1 as a DISARM subsystem requiring four profiles from DISARM_1__drmD, DISARM_1__drmMI, DISARM__drmA, DISARM__drmB, and DISARM__drmC."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "disarm1_locus_subtype_defense",
        "title": "DISARM1 loci support DISARM antiphage defense",
        "description": "Conservative system-level sketch linking a DISARM_1 locus to DISARM methyltransferase-associated phage defense and DISARM1 system possession.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures DISARM1 at DefenseFinder subtype-locus level without asserting the exact DISARM1 effector chemistry, native host breadth, sensitive-phage breadth, whether every DefenseFinder DISARM_1 prediction is a complete experimentally active locus, or how the shared DISARM drmA, drmB, and drmC profiles combine with the DISARM_1 drmD and drmMI profiles.",
        "nodes": [
          {
            "node_id": "disarm1_locus",
            "label": "DISARM1 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A Defense Island System Associated with Restriction-Modification subtype I locus represented in DefenseFinder by DISARM_1 and shared DISARM rule profiles."
          },
          {
            "node_id": "disarm_methyltransferase_antiphage_defense",
            "label": "DISARM methyltransferase-associated antiphage defense",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Methyltransferase-associated DISARM phage defense carried by a genome-encoded DISARM locus."
          },
          {
            "node_id": "disarm1_system_trait",
            "label": "DISARM1 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000548",
            "description": "Possession of a genome-encoded DISARM1 phage-defense system."
          },
          {
            "node_id": "disarm_system_trait",
            "label": "DISARM system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000211",
            "description": "Possession of a genome-encoded DISARM phage-defense system."
          }
        ],
        "edges": [
          {
            "subject": "disarm1_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "disarm_methyltransferase_antiphage_defense",
            "description": "DISARM1 loci are represented in DefenseFinder by shared DISARM drmA, drmB, and drmC profiles plus DISARM_1-specific drmD and drmMI profiles.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| DISARM__drmA                                     | DISARM__drmA                                     | DISARM                 | Custom                  | 90     |\n| DISARM__drmB                                     | DISARM__drmB                                     | DISARM                 | Custom                  | 90     |\n| DISARM__drmC                                     | DISARM__drmC                                     | DISARM                 | Custom                  | 40     |\n| DISARM_1__drmD                                   | DISARM_1__drmD                                   | DISARM_1               | Custom                  | 500    |\n| DISARM_1__drmMI                                  | DISARM_1__drmMI                                  | DISARM_1               | Custom                  | 90     |",
                "notes": "The pinned DefenseFinder HMM inventory records the shared DISARM drmA, drmB, and drmC profiles and the DISARM_1 drmD and drmMI profiles."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "DISARM\tDISARM_1\t4\t4\tDISARM_1__drmD, DISARM_1__drmMI, DISARM__drmA, DISARM__drmB, DISARM__drmC\t\t\t",
                "notes": "The pinned DefenseFinder rules table models DISARM_1 as a DISARM subsystem requiring four profiles from DISARM_1__drmD, DISARM_1__drmMI, DISARM__drmA, DISARM__drmB, and DISARM__drmC."
              }
            ]
          },
          {
            "subject": "disarm_methyltransferase_antiphage_defense",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "disarm1_system_trait",
            "description": "The first-pass DISARM1 system trait is realized by a DefenseFinder DISARM_1 subtype locus within the methyltransferase-associated DISARM family.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-017-0051-0",
                "snippet": "Our results establish DISARM as a new defence system, providing protection against diverse phages",
                "notes": "Ofir et al. experimentally established DISARM as a broad-spectrum phage defense system."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| DISARM__drmA                                     | DISARM__drmA                                     | DISARM                 | Custom                  | 90     |\n| DISARM__drmB                                     | DISARM__drmB                                     | DISARM                 | Custom                  | 90     |\n| DISARM__drmC                                     | DISARM__drmC                                     | DISARM                 | Custom                  | 40     |\n| DISARM_1__drmD                                   | DISARM_1__drmD                                   | DISARM_1               | Custom                  | 500    |\n| DISARM_1__drmMI                                  | DISARM_1__drmMI                                  | DISARM_1               | Custom                  | 90     |",
                "notes": "The pinned DefenseFinder HMM inventory records the shared DISARM drmA, drmB, and drmC profiles and the DISARM_1 drmD and drmMI profiles."
              }
            ]
          },
          {
            "subject": "disarm1_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "disarm_system_trait",
            "description": "DISARM1 system possession is a DISARM-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| DISARM | 10\\.1038/s41564-017-0051-0 | DISARM is a widespread bacterial defence system with broad anti-phage activities | ",
                "notes": "The pinned DefenseFinder article registry maps the DISARM source key to Ofir et al.'s DISARM phage-defense paper."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "DISARM\tDISARM_1\t4\t4\tDISARM_1__drmD, DISARM_1__drmMI, DISARM__drmA, DISARM__drmB, DISARM__drmC\t\t\t",
                "notes": "The pinned DefenseFinder rules table models DISARM_1 as a DISARM subsystem requiring four profiles from DISARM_1__drmD, DISARM_1__drmMI, DISARM__drmA, DISARM__drmB, and DISARM__drmC."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "disarm1-profile-activity-gap",
        "prompt": "Resolve DISARM1 effector chemistry, exact native hosts, sensitive-phage breadth, shared-core component roles, and DISARM_1 profile-to-activity criteria before minting DISARM1 mechanism or component children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Ofir et al. support DISARM as a broad antiphage-system family, and the pinned DefenseFinder HMM inventory and rules table support DISARM_1 as a subtype with drmD, drmMI, drmA, drmB, and drmC profiles. This first-pass record leaves exact DISARM1 effector chemistry, native host breadth, sensitive-phage breadth, shared-core component roles, and profile-to-activity requirements unresolved.",
        "evidence": [
          {
            "reference": "DOI:10.1038/s41564-017-0051-0",
            "snippet": "Our results establish DISARM as a new defence system, providing protection against diverse phages",
            "notes": "Ofir et al. experimentally established DISARM as a broad-spectrum phage defense system."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| DISARM__drmA                                     | DISARM__drmA                                     | DISARM                 | Custom                  | 90     |\n| DISARM__drmB                                     | DISARM__drmB                                     | DISARM                 | Custom                  | 90     |\n| DISARM__drmC                                     | DISARM__drmC                                     | DISARM                 | Custom                  | 40     |\n| DISARM_1__drmD                                   | DISARM_1__drmD                                   | DISARM_1               | Custom                  | 500    |\n| DISARM_1__drmMI                                  | DISARM_1__drmMI                                  | DISARM_1               | Custom                  | 90     |",
            "notes": "The pinned DefenseFinder HMM inventory records the shared DISARM drmA, drmB, and drmC profiles and the DISARM_1 drmD and drmMI profiles."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "snippet": "DISARM\tDISARM_1\t4\t4\tDISARM_1__drmD, DISARM_1__drmMI, DISARM__drmA, DISARM__drmB, DISARM__drmC\t\t\t",
            "notes": "The pinned DefenseFinder rules table models DISARM_1 as a DISARM subsystem requiring four profiles from DISARM_1__drmD, DISARM_1__drmMI, DISARM__drmA, DISARM__drmB, and DISARM__drmC."
          }
        ],
        "attaches_to": [
          "causal_graphs#disarm1_locus_subtype_defense"
        ],
        "posed_by": "codex",
        "posed_date": "2026-10-02"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-02T15:17:43Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted DISARM1 system as a DOI- and DefenseFinder-backed GENOMICS TraitRecord under the DISARM system parent after an ignored-and-hidden duplicate review found no exact live DISARM1 TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v425.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-02T15:17:44Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed DISARM1 system during initial curation and left canonical_examples empty because Ofir et al. and the pinned DefenseFinder tables support the DISARM family and the DISARM_1 model namespace but not an accession-backed native microbial taxon exemplar tied to DISARM_1 profiles and experimentally verified endogenous DISARM1 activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000549",
    "label": "DISARM2 system",
    "definition": "A DISARM system in which an organism possesses a genome-encoded DefenseFinder DISARM_2 subtype locus represented by DISARM_2__drmE, DISARM_2__drmMII, DISARM__drmA, DISARM__drmB, and DISARM__drmC rule profiles.",
    "definition_source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000211"
    ],
    "synonyms": [
      {
        "synonym_text": "DISARM_2",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv"
      },
      {
        "synonym_text": "DISARM_2__drmE",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "DISARM_2__drmMII",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "DISARM__drmA",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "DISARM__drmB",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "DISARM__drmC",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/s41564-017-0051-0",
        "snippet": "Our results establish DISARM as a new defence system, providing protection against diverse phages",
        "notes": "Ofir et al. experimentally established DISARM as a broad-spectrum phage defense system."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| DISARM | 10\\.1038/s41564-017-0051-0 | DISARM is a widespread bacterial defence system with broad anti-phage activities | ",
        "notes": "The pinned DefenseFinder article registry maps the DISARM source key to Ofir et al.'s DISARM phage-defense paper."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| DISARM__drmA                                     | DISARM__drmA                                     | DISARM                 | Custom                  | 90     |\n| DISARM__drmB                                     | DISARM__drmB                                     | DISARM                 | Custom                  | 90     |\n| DISARM__drmC                                     | DISARM__drmC                                     | DISARM                 | Custom                  | 40     |\n| DISARM_2__drmE                                   | DISARM_2__drmE                                   | DISARM_2               | Custom                  | 90     |\n| DISARM_2__drmMII                                 | DISARM_2__drmMII                                 | DISARM_2               | Custom                  | 90     |",
        "notes": "The pinned DefenseFinder HMM inventory records the shared DISARM drmA, drmB, and drmC profiles and the DISARM_2 drmE and drmMII profiles."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "DISARM\tDISARM_2\t4\t4\tDISARM_2__drmE, DISARM_2__drmMII, DISARM__drmA, DISARM__drmB, DISARM__drmC\t\t\t",
        "notes": "The pinned DefenseFinder rules table models DISARM_2 as a DISARM subsystem requiring four profiles from DISARM_2__drmE, DISARM_2__drmMII, DISARM__drmA, DISARM__drmB, and DISARM__drmC."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "disarm2_locus_subtype_defense",
        "title": "DISARM2 loci support DISARM antiphage defense",
        "description": "Conservative system-level sketch linking a DISARM_2 locus to DISARM methyltransferase-associated phage defense and DISARM2 system possession.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures DISARM2 at DefenseFinder subtype-locus level without asserting the exact DISARM2 effector chemistry, native host breadth, sensitive-phage breadth, whether every DefenseFinder DISARM_2 prediction is a complete experimentally active locus, or how the shared DISARM drmA, drmB, and drmC profiles combine with the DISARM_2 drmE and drmMII profiles.",
        "nodes": [
          {
            "node_id": "disarm2_locus",
            "label": "DISARM2 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A Defense Island System Associated with Restriction-Modification subtype II locus represented in DefenseFinder by DISARM_2 and shared DISARM rule profiles."
          },
          {
            "node_id": "disarm_methyltransferase_antiphage_defense",
            "label": "DISARM methyltransferase-associated antiphage defense",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Methyltransferase-associated DISARM phage defense carried by a genome-encoded DISARM locus."
          },
          {
            "node_id": "disarm2_system_trait",
            "label": "DISARM2 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000549",
            "description": "Possession of a genome-encoded DISARM2 phage-defense system."
          },
          {
            "node_id": "disarm_system_trait",
            "label": "DISARM system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000211",
            "description": "Possession of a genome-encoded DISARM phage-defense system."
          }
        ],
        "edges": [
          {
            "subject": "disarm2_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "disarm_methyltransferase_antiphage_defense",
            "description": "DISARM2 loci are represented in DefenseFinder by shared DISARM drmA, drmB, and drmC profiles plus DISARM_2-specific drmE and drmMII profiles.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| DISARM__drmA                                     | DISARM__drmA                                     | DISARM                 | Custom                  | 90     |\n| DISARM__drmB                                     | DISARM__drmB                                     | DISARM                 | Custom                  | 90     |\n| DISARM__drmC                                     | DISARM__drmC                                     | DISARM                 | Custom                  | 40     |\n| DISARM_2__drmE                                   | DISARM_2__drmE                                   | DISARM_2               | Custom                  | 90     |\n| DISARM_2__drmMII                                 | DISARM_2__drmMII                                 | DISARM_2               | Custom                  | 90     |",
                "notes": "The pinned DefenseFinder HMM inventory records the shared DISARM drmA, drmB, and drmC profiles and the DISARM_2 drmE and drmMII profiles."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "DISARM\tDISARM_2\t4\t4\tDISARM_2__drmE, DISARM_2__drmMII, DISARM__drmA, DISARM__drmB, DISARM__drmC\t\t\t",
                "notes": "The pinned DefenseFinder rules table models DISARM_2 as a DISARM subsystem requiring four profiles from DISARM_2__drmE, DISARM_2__drmMII, DISARM__drmA, DISARM__drmB, and DISARM__drmC."
              }
            ]
          },
          {
            "subject": "disarm_methyltransferase_antiphage_defense",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "disarm2_system_trait",
            "description": "The first-pass DISARM2 system trait is realized by a DefenseFinder DISARM_2 subtype locus within the methyltransferase-associated DISARM family.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-017-0051-0",
                "snippet": "Our results establish DISARM as a new defence system, providing protection against diverse phages",
                "notes": "Ofir et al. experimentally established DISARM as a broad-spectrum phage defense system."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| DISARM__drmA                                     | DISARM__drmA                                     | DISARM                 | Custom                  | 90     |\n| DISARM__drmB                                     | DISARM__drmB                                     | DISARM                 | Custom                  | 90     |\n| DISARM__drmC                                     | DISARM__drmC                                     | DISARM                 | Custom                  | 40     |\n| DISARM_2__drmE                                   | DISARM_2__drmE                                   | DISARM_2               | Custom                  | 90     |\n| DISARM_2__drmMII                                 | DISARM_2__drmMII                                 | DISARM_2               | Custom                  | 90     |",
                "notes": "The pinned DefenseFinder HMM inventory records the shared DISARM drmA, drmB, and drmC profiles and the DISARM_2 drmE and drmMII profiles."
              }
            ]
          },
          {
            "subject": "disarm2_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "disarm_system_trait",
            "description": "DISARM2 system possession is a DISARM-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| DISARM | 10\\.1038/s41564-017-0051-0 | DISARM is a widespread bacterial defence system with broad anti-phage activities | ",
                "notes": "The pinned DefenseFinder article registry maps the DISARM source key to Ofir et al.'s DISARM phage-defense paper."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "DISARM\tDISARM_2\t4\t4\tDISARM_2__drmE, DISARM_2__drmMII, DISARM__drmA, DISARM__drmB, DISARM__drmC\t\t\t",
                "notes": "The pinned DefenseFinder rules table models DISARM_2 as a DISARM subsystem requiring four profiles from DISARM_2__drmE, DISARM_2__drmMII, DISARM__drmA, DISARM__drmB, and DISARM__drmC."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "disarm2-profile-activity-gap",
        "prompt": "Resolve DISARM2 effector chemistry, exact native hosts, sensitive-phage breadth, shared-core component roles, and DISARM_2 profile-to-activity criteria before minting DISARM2 mechanism or component children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Ofir et al. support DISARM as a broad antiphage-system family, and the pinned DefenseFinder HMM inventory and rules table support DISARM_2 as a subtype with drmE, drmMII, drmA, drmB, and drmC profiles. This first-pass record leaves exact DISARM2 effector chemistry, native host breadth, sensitive-phage breadth, shared-core component roles, and profile-to-activity requirements unresolved.",
        "evidence": [
          {
            "reference": "DOI:10.1038/s41564-017-0051-0",
            "snippet": "Our results establish DISARM as a new defence system, providing protection against diverse phages",
            "notes": "Ofir et al. experimentally established DISARM as a broad-spectrum phage defense system."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| DISARM__drmA                                     | DISARM__drmA                                     | DISARM                 | Custom                  | 90     |\n| DISARM__drmB                                     | DISARM__drmB                                     | DISARM                 | Custom                  | 90     |\n| DISARM__drmC                                     | DISARM__drmC                                     | DISARM                 | Custom                  | 40     |\n| DISARM_2__drmE                                   | DISARM_2__drmE                                   | DISARM_2               | Custom                  | 90     |\n| DISARM_2__drmMII                                 | DISARM_2__drmMII                                 | DISARM_2               | Custom                  | 90     |",
            "notes": "The pinned DefenseFinder HMM inventory records the shared DISARM drmA, drmB, and drmC profiles and the DISARM_2 drmE and drmMII profiles."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "snippet": "DISARM\tDISARM_2\t4\t4\tDISARM_2__drmE, DISARM_2__drmMII, DISARM__drmA, DISARM__drmB, DISARM__drmC\t\t\t",
            "notes": "The pinned DefenseFinder rules table models DISARM_2 as a DISARM subsystem requiring four profiles from DISARM_2__drmE, DISARM_2__drmMII, DISARM__drmA, DISARM__drmB, and DISARM__drmC."
          }
        ],
        "attaches_to": [
          "causal_graphs#disarm2_locus_subtype_defense"
        ],
        "posed_by": "codex",
        "posed_date": "2026-10-02"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-02T15:56:12Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted DISARM2 system as a DOI- and DefenseFinder-backed GENOMICS TraitRecord under the DISARM system parent after an ignored-and-hidden duplicate review found no exact live DISARM2 TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v426.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-02T15:56:13Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed DISARM2 system during initial curation and left canonical_examples empty because Ofir et al. and the pinned DefenseFinder tables support the DISARM family and the DISARM_2 model namespace but not an accession-backed native microbial taxon exemplar tied to DISARM_2 profiles and experimentally verified endogenous DISARM2 activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000211",
    "label": "DISARM system",
    "definition": "A genomics trait describing possession of a Defense Island System Associated with Restriction-Modification locus that uses methyltransferase-associated self/non-self discrimination and DrmAB activation to inhibit bacteriophage DNA replication.",
    "definition_source": "DOI:10.1038/s41564-017-0051-0",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "Defense Island System Associated with Restriction-Modification",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1038/s41467-022-30673-1"
      },
      {
        "synonym_text": "Defense Island System Associated with Restriction Modification",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1038/s41467-022-30673-1"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/s41564-017-0051-0",
        "snippet": "Our results establish DISARM as a new defence system, providing protection against diverse phages",
        "notes": "Ofir et al. experimentally established DISARM as a phage defense system and distinguished its intracellular block from phage-adsorption phenotypes."
      },
      {
        "reference": "DOI:10.1038/s41564-017-0051-0",
        "snippet": "The DISARM system is widespread in defence islands across the microbial world",
        "notes": "Ofir et al. support DISARM as a recurring microbial defense island system rather than a single source-specific locus."
      },
      {
        "reference": "DOI:10.1038/s41467-022-30673-1",
        "snippet": "DISARM (Defense Island System Associated with Restriction-Modification) systems can provide protection against a wide range of phage",
        "notes": "Bravo et al. independently expand the DISARM acronym and frame DISARM as a broad anti-phage system."
      },
      {
        "reference": "DOI:10.1038/s41467-022-30673-1",
        "snippet": "In vivo studies of structure-guided DrmAB mutants demonstrate that ATP hydrolysis, DNA binding, and DrmAB heterodimer formation are essential for phage targeting by DISARM",
        "notes": "Bravo et al. support the DrmAB activation mechanism recorded in the first causal graph."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:766760",
        "taxon_label": "Bacillus paralicheniformis ATCC 9945a",
        "note": "Ofir et al. amplified the native B. paralicheniformis ATCC 9945a class 2 DISARM locus and integrated it into B. subtilis to test phage defense.",
        "reference": "DOI:10.1038/s41564-017-0051-0"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "disarm_dna_sensing_antiphage_defense",
        "title": "DISARM senses phage DNA to activate DrmAB defense",
        "description": "Evidence-backed causal sketch linking DISARM methylation and 5-prime-overhang DNA sensing to DrmAB activation and blocked early phage DNA circularization.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "The graph captures host DNA methylation, 5-prime-overhang sensing, DrmAB activation, and early phage DNA restriction without asserting the unresolved downstream nuclease or replication-block coupling.",
        "nodes": [
          {
            "node_id": "host_dna_methylation",
            "label": "DISARM host DNA methylation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "DISARM methyltransferase-mediated methylation of host DNA at cognate motifs."
          },
          {
            "node_id": "five_prime_overhang_dna_sensing",
            "label": "DISARM 5-prime-overhang DNA sensing",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "DrmAB-associated recognition of foreign DNA substrates carrying a 5-prime single-stranded overhang."
          },
          {
            "node_id": "drmab_core_complex",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "DrmA and DrmB are distinct DISARM protein families; this node denotes the activated heterodimeric core complex rather than one component family.",
            "label": "DrmAB core complex",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Heterodimeric DISARM DrmA-DrmB core complex that binds invading DNA and undergoes long-range activation upon 5-prime-overhang substrate loading.",
            "gene_symbols": [
              "drmA",
              "drmB"
            ],
            "operon": "DISARM",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:P0DW05",
                "protein_label": "DISARM protein DrmA",
                "gene_symbol": "drmA",
                "taxon_id": "NCBITaxon:766760",
                "taxon_label": "Bacillus paralicheniformis ATCC 9945a",
                "entry_status": "REVIEWED",
                "retrieved_on": "2026-09-15",
                "entry_version": 12,
                "sequence_version": 1,
                "role": "B. paralicheniformis ATCC 9945a DrmA is the helicase-domain component of the class 2 DISARM DrmAB core.",
                "evidence": [
                  {
                    "reference": "DOI:10.1038/s41564-017-0051-0",
                    "snippet": "Deletions of drmA (helicase domain), drmB (DUF1998 domain) and drmE (unknown function) abolished DISARM protection against all phages tested",
                    "notes": "Ofir et al. tested scarless deletions in the native B. paralicheniformis ATCC 9945a DISARM locus; UniProt verifies the reviewed DrmA accession."
                  }
                ]
              },
              {
                "uniprot_id": "UniProtKB:P0DW06",
                "protein_label": "DISARM protein DrmB",
                "gene_symbol": "drmB",
                "taxon_id": "NCBITaxon:766760",
                "taxon_label": "Bacillus paralicheniformis ATCC 9945a",
                "entry_status": "REVIEWED",
                "retrieved_on": "2026-09-15",
                "entry_version": 9,
                "sequence_version": 1,
                "role": "B. paralicheniformis ATCC 9945a DrmB is the DUF1998 component paired with DrmA in the class 2 DISARM DrmAB core.",
                "evidence": [
                  {
                    "reference": "DOI:10.1038/s41564-017-0051-0",
                    "snippet": "Deletions of drmA (helicase domain), drmB (DUF1998 domain) and drmE (unknown function) abolished DISARM protection against all phages tested",
                    "notes": "Ofir et al. tested scarless deletions in the native B. paralicheniformis ATCC 9945a DISARM locus; UniProt verifies the reviewed DrmB accession."
                  }
                ]
              }
            ]
          },
          {
            "node_id": "drmab_activation",
            "label": "DISARM DrmAB activation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "DNA-triggered activation of the DISARM DrmAB core complex."
          },
          {
            "node_id": "phage_dna_circularization",
            "label": "phage DNA circularization",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Circularization of injected bacteriophage genomic DNA after adsorption and DNA entry."
          },
          {
            "node_id": "disarm_system_trait",
            "label": "DISARM system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000211",
            "description": "Possession of a genome-encoded DISARM phage defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "drmab_core_complex",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "drmab_activation",
            "description": "DrmA DNA binding, DrmA ATP hydrolysis, and DrmAB heterodimer formation are required for DISARM activation and phage targeting.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-022-30673-1",
                "snippet": "DNA binding, and DrmAB heterodimer formation are essential for phage targeting by DISARM",
                "notes": "Bravo et al. established the structural and functional importance of the DrmA-DrmB core complex."
              }
            ]
          },
          {
            "subject": "host_dna_methylation",
            "predicate": "negatively regulates",
            "predicate_id": "RO:0002212",
            "object": "drmab_activation",
            "description": "DISARM host-DNA methylation limits DrmAB activation by self DNA.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-022-30673-1",
                "snippet": "methylated DNA limits the ATPase activity of DrmAB which is essential for anti-phage defense",
                "notes": "Bravo et al. support methylation-sensitive DrmAB activation as a self/non-self filter."
              }
            ]
          },
          {
            "subject": "five_prime_overhang_dna_sensing",
            "predicate": "activates",
            "predicate_id": "RO:0002213",
            "object": "drmab_activation",
            "description": "Unmethylated 5-prime-overhang DNA dislodges the DrmA trigger loop to activate DrmAB.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-022-30673-1",
                "snippet": "binding to DNA substrates containing a 5\u2032 overhang dislodges the TL, initiating a long-range structural rearrangement for DrmAB activation",
                "notes": "Bravo et al. structurally support 5-prime-overhang-triggered DrmAB activation."
              }
            ]
          },
          {
            "subject": "drmab_activation",
            "predicate": "mitigates",
            "predicate_id": "METPO:2007407",
            "object": "phage_dna_circularization",
            "description": "Activated DISARM blocks early phage DNA circularization and replication after phage entry.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-017-0051-0",
                "snippet": "phi3T was not able to circularize its genome or form detectible lysogens in DISARM-containing cells",
                "notes": "Ofir et al. showed that DISARM blocks an early intracellular step after phage adsorption."
              }
            ]
          },
          {
            "subject": "drmab_activation",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "disarm_system_trait",
            "description": "DrmAB activation realizes DISARM-mediated anti-phage defense.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-022-30673-1",
                "snippet": "provide the mechanism of targeting a wide range of phage by DISARM",
                "notes": "Bravo et al. linked DNA-interacting DrmA residues to DISARM anti-phage protection in vivo."
              }
            ]
          },
          {
            "subject": "disarm_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "DISARM possession is a methyltransferase-associated phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-017-0051-0",
                "snippet": "Our results establish DISARM as a new defence system",
                "notes": "Ofir et al. establish DISARM in the phage defense system family."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "disarm-downstream-effector-gap",
        "prompt": "Resolve the downstream nuclease or replication-blocking effector coupled to activated DrmAB before adding a more specific DISARM phage-DNA degradation edge.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Ofir et al. inferred phage DNA degradation and showed that DrmC is partially redundant across phages; Bravo et al. resolved DrmAB recognition and activation but left the downstream nuclease or physical replication block as a model.",
        "posed_by": "codex",
        "posed_date": "2026-09-15"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-15T09:40:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted DISARM system as a DOI-backed GENOMICS TraitRecord under the phage defense system parent with reviewed B. paralicheniformis ATCC 9945a DrmA and DrmB protein examples after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v88.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000277",
    "label": "Divona system",
    "definition": "A phage defense system in which an organism possesses a Divona locus represented by a VCA0374 profile that can protect bacteria from bacteriophage infection.",
    "definition_source": "DOI:10.1126/science.ads0768",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "Divona",
        "synonym_type": "EXACT_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      },
      {
        "synonym_text": "VCA0374",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1126/science.ads0768",
        "snippet": "nearly 10% of the integron cassettes in the pandemic Vibrio cholerae strain encode novel antiphage functions",
        "notes": "Darracq et al. support treating the newly discovered Vibrio cholerae SCI antiphage cassettes as bacterial anti-phage systems."
      },
      {
        "reference": "DOI:10.1126/science.ads0768",
        "snippet": "Most of these novel systems have little or no similarity to previously known ones, with several providing defense through cell lysis or growth arrest",
        "notes": "Darracq et al. support a conservative system record that does not assert a resolved Divona trigger, effector output, or universal pathway."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "Divona | 10\\.1126/science\\.ads0768 | Sedentary chromosomal integrons as biobanks of bacterial antiphage defense systems",
        "notes": "The DefenseFinder model registry maps the named Divona system to the Darracq et al. SCI antiphage-system paper."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "Divona__VCA0374                                  |                                                  | Divona",
        "notes": "The DefenseFinder HMM inventory records VCA0374 in the Divona model namespace."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "divona_locus_restricts_phage",
        "title": "Divona loci confer bacterial phage defense",
        "description": "Conservative system-level sketch linking possession of a Divona locus to restricted bacteriophage propagation without asserting the unresolved phage trigger or molecular output.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Divona as a named SCI-derived anti-phage system with a VCA0374 DefenseFinder profile while leaving its phage trigger, molecular substrate, antiviral effector output, and subtype breadth unresolved.",
        "nodes": [
          {
            "node_id": "divona_locus",
            "label": "Divona locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A Divona anti-phage defense locus represented in DefenseFinder by a VCA0374 profile."
          },
          {
            "node_id": "restricted_phage_propagation",
            "label": "restricted phage propagation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced propagation of bacteriophage in cells carrying the Divona system."
          },
          {
            "node_id": "divona_system_trait",
            "label": "Divona system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000277",
            "description": "Possession of a genome-encoded Divona phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "divona_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "restricted_phage_propagation",
            "description": "DefenseFinder maps Divona to an SCI anti-phage-system discovery paper and represents Divona loci through the VCA0374 component profile.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.ads0768",
                "snippet": "nearly 10% of the integron cassettes in the pandemic Vibrio cholerae strain encode novel antiphage functions",
                "notes": "Darracq et al. describe the newly discovered antiphage-system cohort that the DefenseFinder Divona registry row maps to the Divona system."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "Divona__VCA0374                                  |                                                  | Divona",
                "notes": "The DefenseFinder HMM inventory supports VCA0374 as the Divona component profile."
              }
            ]
          },
          {
            "subject": "restricted_phage_propagation",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "divona_system_trait",
            "description": "Divona-mediated phage restriction realizes the Divona system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.ads0768",
                "snippet": "Most of these novel systems have little or no similarity to previously known ones",
                "notes": "Darracq et al. place the Divona discovery cohort in a set of novel bacterial systems that protect against phages."
              }
            ]
          },
          {
            "subject": "divona_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Divona system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Divona | 10\\.1126/science\\.ads0768 | Sedentary chromosomal integrons as biobanks of bacterial antiphage defense systems",
                "notes": "DefenseFinder associates Divona with the Darracq et al. bacterial antiphage-system paper."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "divona-mechanism-gap",
        "prompt": "Resolve Divona phage triggers and effector outputs before minting narrower Divona mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Darracq et al. and DefenseFinder support Divona as a named anti-phage system with a VCA0374 profile, but the trigger, molecular substrate, antiviral effector output, and subtype-specific mechanism are not resolved enough here to assert a narrower mechanistic child trait.",
        "attaches_to": [
          "causal_graphs#divona_locus_restricts_phage"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-19"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-19T11:16:14Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Divona system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v154.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000221",
    "label": "Dnd system",
    "definition": "A phosphorothioate defense system in which an organism possesses a Dnd restriction-modification locus that pairs a Dnd-family DNA phosphorothioation module with a DndFGH restriction module to nick invading DNA that lacks phosphorothioate modification.",
    "definition_source": "DOI:10.1038/s41564-020-0700-6",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000213"
    ],
    "synonyms": [
      {
        "synonym_text": "Dnd R-M system",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1128/mbio.00933-23"
      },
      {
        "synonym_text": "Dnd-related R-M system",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1128/mbio.00933-23"
      },
      {
        "synonym_text": "Dnd-related restriction and modification system",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1128/mbio.00933-23"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/s41564-020-0700-6",
        "snippet": "We previously identified the Dnd system, which uses DndABCDE to insert sulfur into the DNA backbone as a double-stranded phosphorothioate (PT) modification, and DndFGH, a restriction component",
        "notes": "Xiong et al. summarize Dnd as a named PT-dependent restriction system with DNA-modification and restriction modules."
      },
      {
        "reference": "DOI:10.1128/mbio.00933-23",
        "snippet": "Usually, this modification gene cluster is paired with a restriction module consisting of DndF, DndG, and DndH",
        "notes": "Jiang et al. support DndFGH as the restriction module paired with Dnd DNA phosphorothioation."
      },
      {
        "reference": "DOI:10.1128/mbio.00933-23",
        "snippet": "In general, some dnd or ssp clusters lack dndA or sspA; DndA or SspA is instead functionally replaced by other cysteine desulfurases, such as IscS, in bacteria",
        "notes": "Jiang et al. support defining the Dnd system by a Dnd-family modification module without requiring a contiguous dndA gene in every locus."
      },
      {
        "reference": "DOI:10.1128/mbio.00933-23",
        "snippet": "In the presence of exogenous DNA that lacks PT, the macromolecular machine consisting of DndF, DndG, and DndH undergoes conformational changes to perform DNA binding, translocation, and DNA nicking activities and scavenge the foreign DNA",
        "notes": "Jiang et al. connect DndFGH to detection and nicking of foreign DNA lacking PT modification."
      },
      {
        "reference": "DOI:10.1128/mbio.00933-23",
        "snippet": "we discussed the action of Dnd-related R-M systems against phages and demonstrated that the host could benefit from the protection provided by Dnd-related R-M systems against infection by various lytic phages as well as temperate phages",
        "notes": "Jiang et al. support the phage-resistance output of Dnd restriction-modification systems."
      },
      {
        "reference": "DOI:10.1128/mbio.00933-23",
        "snippet": "the 8,286-bp and 8,321-bp fragments containing the whole dndBCDEFGH gene cluster were amplified from the genomic DNA of E. coli B7A",
        "notes": "Jiang et al. support Escherichia coli B7A as a direct source of the cloned dndBCDEFGH Dnd system."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:340184",
        "taxon_label": "Escherichia coli B7A",
        "note": "Jiang et al. amplified the whole dndBCDEFGH gene cluster from E. coli B7A and assayed the cloned DndB7A R-M system for resistance against lytic and temperate phages.",
        "reference": "DOI:10.1128/mbio.00933-23"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "dnd_dna_phosphorothioation_foreign_dna_nicking",
        "title": "Dnd systems use DNA phosphorothioation to restrict foreign DNA",
        "description": "Evidence-backed process sketch linking a Dnd restriction-modification locus to host DNA phosphorothioation, PT-guided DndFGH foreign-DNA nicking, and Dnd-mediated phage defense.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Dnd-family modification and DndFGH restriction outputs without asserting one universal DndA cysteine-desulfurase source, PT motif, DndFGH conformational pathway, exogenous substrate class, phage spectrum, methylation interaction, or relationship to Ssp systems across all Dnd loci.",
        "nodes": [
          {
            "node_id": "dnd_restriction_modification_locus",
            "label": "Dnd restriction-modification locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A Dnd phosphorothioation-dependent restriction locus pairing a Dnd-family DNA modification module with a DndFGH restriction module."
          },
          {
            "node_id": "dna_phosphorothioation",
            "label": "DNA phosphorothioation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Replacement of a nonbridging oxygen in the DNA phosphate backbone with sulfur."
          },
          {
            "node_id": "dndfgh_foreign_dna_targeting",
            "label": "DndFGH foreign DNA targeting",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "DndFGH-mediated binding and translocation on unmodified exogenous DNA before restriction."
          },
          {
            "node_id": "foreign_dna_nicking",
            "label": "foreign DNA nicking",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Introduction of nicks into unmodified invading DNA by a PT-associated restriction module."
          },
          {
            "node_id": "phage_infection",
            "label": "phage infection",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Entry and intracellular replication attempt by a bacteriophage infecting a host bacterium."
          },
          {
            "node_id": "dnd_system_trait",
            "label": "Dnd system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000221",
            "description": "Possession of a genome-encoded Dnd restriction-modification defense system."
          },
          {
            "node_id": "phosphorothioate_defense_system_trait",
            "label": "phosphorothioate defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000213",
            "description": "Possession of a genome-encoded phosphorothioate-based phage defense system."
          }
        ],
        "edges": [
          {
            "subject": "dnd_restriction_modification_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "dna_phosphorothioation",
            "description": "Dnd-family modification modules install sequence-specific phosphorothioate marks on host DNA.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-020-0700-6",
                "snippet": "uses DndABCDE to insert sulfur into the DNA backbone as a double-stranded phosphorothioate (PT) modification",
                "notes": "Xiong et al. support Dnd-mediated host DNA phosphorothioation."
              }
            ]
          },
          {
            "subject": "dnd_restriction_modification_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "dndfgh_foreign_dna_targeting",
            "description": "Dnd restriction-modification loci pair host DNA phosphorothioation genes with the DndFGH restriction module.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mbio.00933-23",
                "snippet": "To build up a line of defense, the dndABCDE gene cluster is usually paired with dndFGH, which acts as a restriction module",
                "notes": "Jiang et al. support the paired modification-plus-restriction architecture of Dnd systems."
              }
            ]
          },
          {
            "subject": "dna_phosphorothioation",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "dndfgh_foreign_dna_targeting",
            "description": "DNA phosphorothioation marks host DNA as self and leaves unmodified exogenous DNA susceptible to DndFGH targeting.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mbio.00933-23",
                "snippet": "In the presence of exogenous DNA that lacks PT, the macromolecular machine consisting of DndF, DndG, and DndH undergoes conformational changes",
                "notes": "Jiang et al. connect absence of PT on exogenous DNA to DndFGH restriction-complex activation."
              }
            ]
          },
          {
            "subject": "dndfgh_foreign_dna_targeting",
            "predicate": "activates",
            "predicate_id": "RO:0002213",
            "object": "foreign_dna_nicking",
            "description": "DndFGH targeting leads to DNA binding, translocation, and nicking of invading DNA.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mbio.00933-23",
                "snippet": "DndFGH exerts DNA binding, translocation, and nicking activities to initiate the destructive DNA-shredding program to eliminate genetic parasites",
                "notes": "Jiang et al. summarize the nicking output of DndFGH foreign-DNA targeting."
              }
            ]
          },
          {
            "subject": "foreign_dna_nicking",
            "predicate": "mitigates",
            "predicate_id": "METPO:2007407",
            "object": "phage_infection",
            "description": "DndFGH-mediated nicking restricts lytic phages and blocks lysogenization by temperate phages.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mbio.00933-23",
                "snippet": "Dnd R-M systems protect the host from various lytic phages as well as the lysogenization of temperate phages",
                "notes": "Jiang et al. summarize Dnd-mediated protection against lytic phages and temperate phage lysogenization."
              }
            ]
          },
          {
            "subject": "foreign_dna_nicking",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "dnd_system_trait",
            "description": "PT-guided foreign-DNA nicking realizes the Dnd restriction-modification system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mbio.00933-23",
                "snippet": "the host could benefit from Dnd-related R-M systems for a broad range of antiphage activities",
                "notes": "Jiang et al. support DndFGH restriction as the Dnd antiphage defense output."
              }
            ]
          },
          {
            "subject": "dnd_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phosphorothioate_defense_system_trait",
            "description": "Dnd system possession is a phosphorothioate-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-020-0700-6",
                "snippet": "We previously identified the Dnd system, which uses DndABCDE to insert sulfur into the DNA backbone as a double-stranded phosphorothioate (PT) modification, and DndFGH, a restriction component",
                "notes": "Xiong et al. place Dnd within phosphorothioation-dependent restriction systems."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-15T16:03:58Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Dnd system as a DOI-backed GENOMICS TraitRecord under the phosphorothioate defense system parent after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v98.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000224",
    "label": "DndCDEA-PbeABCD system",
    "definition": "A phosphorothioate defense system in which an organism possesses a DndCDEA-PbeABCD locus that pairs DndCDEA-mediated host-DNA phosphorothioation with PbeABCD-dependent targeting of non-phosphorothioated viral DNA to inhibit viral DNA replication.",
    "definition_source": "DOI:10.1038/s41467-019-09390-9",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000213"
    ],
    "synonyms": [
      {
        "synonym_text": "PbeABCD-mediated PT defence system",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1038/s41467-019-09390-9"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/s41467-019-09390-9",
        "snippet": "a new archaeal defence system that involves DndCDEA-specific DNA phosphorothioate (PT) modification and the PbeABCD-mediated halt of virus propagation via inhibition of DNA replication",
        "notes": "Xiong et al. name the DndCDEA-PbeABCD architecture as an archaeal PT-based antiviral system."
      },
      {
        "reference": "DOI:10.1038/s41467-019-09390-9",
        "snippet": "can defend against viral attack together with pbeABCD, a conserved 4-gene cassette sharing no sequence homology with DndFGH",
        "notes": "Xiong et al. support separating PbeABCD systems from canonical Dnd systems whose restriction module is DndFGH."
      },
      {
        "reference": "DOI:10.1038/s41467-019-09390-9",
        "snippet": "DndCDEA-PbeABCD confers protection against the haloarchaeal virus SNJ1",
        "notes": "Xiong et al. experimentally support the antiviral output of the Haloterrigena jeotgali A29 DndCDEA-PbeABCD locus after heterologous expression in CJ7-F cells."
      },
      {
        "reference": "DOI:10.1038/s41467-019-09390-9",
        "snippet": "PbeABCD exerted antiviral activity depending on the presence of PT modifications",
        "notes": "Xiong et al. connect PbeABCD antiviral restriction to phosphorothioation-dependent self/non-self discrimination."
      },
      {
        "reference": "DOI:10.1038/s41467-019-09390-9",
        "snippet": "the subsequent viral genome replication process is significantly inhibited by the DndCDEA-PbeABCD system",
        "notes": "Xiong et al. directly connect DndCDEA-PbeABCD to inhibition of SNJ1 viral DNA replication after viral DNA injection."
      },
      {
        "reference": "DOI:10.1038/s41467-019-09390-9",
        "snippet": "does not involve viral DNA degradation or cleavage, ruling out the involvement of currently known defence mechanisms",
        "notes": "Xiong et al. bound the PbeABCD mechanism away from the DNA-cleavage mechanisms of canonical restriction systems."
      },
      {
        "reference": "DOI:10.1134/S0006297921030081",
        "snippet": "instead of the dndFGH, the restriction function is performed by the pbeABCD gene cluster",
        "notes": "Isaev et al. summarize pbeABCD as the restriction branch paired with archaeal DndCDEA phosphorothioation."
      },
      {
        "reference": "DOI:10.1134/S0006297921030081",
        "snippet": "The dndCDEA-pbeABCD from Haloterrigena jeotgali was shown to provide antiviral defense",
        "notes": "Isaev et al. independently summarize the Haloterrigena jeotgali DndCDEA-PbeABCD locus as an antiviral defense system."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1455609",
        "taxon_label": "Natrinema thermotolerans A29",
        "note": "Xiong et al. identified the dndCDEA-pbeABCD locus in Haloterrigena jeotgali A29 and showed that the cloned locus confers DndCDEA- and PbeABCD-dependent resistance to the haloarchaeal virus SNJ1.",
        "reference": "DOI:10.1038/s41467-019-09390-9"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "dndcdea_pbeabcd_pt_viral_replication_inhibition",
        "title": "DndCDEA-PbeABCD systems halt archaeal viral DNA replication",
        "description": "Evidence-backed process sketch linking a DndCDEA-PbeABCD locus to host DNA phosphorothioation, PT-dependent PbeABCD antiviral activity, and inhibited replication of non-phosphorothioated viral DNA.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures DndCDEA-PbeABCD restriction at the system level without asserting one universal host taxon, PT motif outside characterized haloarchaeal systems, PbeABCD subunit cycle, direct viral DNA cleavage, or relationship to bacterial DndFGH and Ssp-family systems.",
        "nodes": [
          {
            "node_id": "dndcdea_pbeabcd_locus",
            "label": "DndCDEA-PbeABCD locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "An archaeal phosphorothioation-dependent antiviral locus pairing DndCDEA host-DNA phosphorothioation with PbeABCD restriction activity."
          },
          {
            "node_id": "dndcdea_dna_phosphorothioation",
            "label": "DndCDEA DNA phosphorothioation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "DndCDEA-mediated installation of sequence-specific phosphorothioate marks on host DNA."
          },
          {
            "node_id": "pbeabcd_pt_dependent_virus_targeting",
            "label": "PbeABCD PT-dependent virus targeting",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Phosphorothioate-dependent PbeABCD antiviral activity against invading DNA that lacks host PT marks."
          },
          {
            "node_id": "viral_dna_replication",
            "label": "viral DNA replication",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Replication of invading archaeal viral DNA after host cell entry."
          },
          {
            "node_id": "dndcdea_pbeabcd_system_trait",
            "label": "DndCDEA-PbeABCD system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000224",
            "description": "Possession of a genome-encoded DndCDEA-PbeABCD phosphorothioation-dependent antiviral defense system."
          },
          {
            "node_id": "phosphorothioate_defense_system_trait",
            "label": "phosphorothioate defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000213",
            "description": "Possession of a genome-encoded phosphorothioate-based antiviral defense system."
          }
        ],
        "edges": [
          {
            "subject": "dndcdea_pbeabcd_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "dndcdea_dna_phosphorothioation",
            "description": "The DndCDEA modification module installs phosphorothioate marks on archaeal host DNA.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-019-09390-9",
                "snippet": "involves DndCDEA-specific DNA phosphorothioate (PT) modification",
                "notes": "Xiong et al. support DndCDEA-dependent host DNA phosphorothioation in the PbeABCD-coupled system."
              }
            ]
          },
          {
            "subject": "dndcdea_pbeabcd_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "pbeabcd_pt_dependent_virus_targeting",
            "description": "DndCDEA-PbeABCD loci pair host-DNA phosphorothioation with PbeABCD antiviral activity.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-019-09390-9",
                "snippet": "can defend against viral attack together with pbeABCD",
                "notes": "Xiong et al. support the paired DndCDEA modification and PbeABCD effector architecture."
              }
            ]
          },
          {
            "subject": "dndcdea_dna_phosphorothioation",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "pbeabcd_pt_dependent_virus_targeting",
            "description": "PbeABCD antiviral activity depends on the presence of PT marks rather than direct PbeABCD-DndCDEA protein interactions.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-019-09390-9",
                "snippet": "depending on the presence of PT modifications",
                "notes": "Xiong et al. distinguish PT-dependent PbeABCD restriction from direct modification-effector protein coupling."
              }
            ]
          },
          {
            "subject": "pbeabcd_pt_dependent_virus_targeting",
            "predicate": "mitigates",
            "predicate_id": "METPO:2007407",
            "object": "viral_dna_replication",
            "description": "PbeABCD-dependent targeting inhibits replication of non-phosphorothioated viral DNA.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-019-09390-9",
                "snippet": "the subsequent viral genome replication process is significantly inhibited",
                "notes": "Xiong et al. observed impaired SNJ1 genome replication in cells expressing DndCDEA-PbeABCD."
              }
            ]
          },
          {
            "subject": "pbeabcd_pt_dependent_virus_targeting",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "dndcdea_pbeabcd_system_trait",
            "description": "PT-dependent PbeABCD antiviral activity realizes the DndCDEA-PbeABCD defense trait.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-019-09390-9",
                "snippet": "DndCDEA-PbeABCD confers resistance against invading viruses",
                "notes": "Xiong et al. support PbeABCD-mediated restriction as the system's antiviral output."
              }
            ]
          },
          {
            "subject": "dndcdea_pbeabcd_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phosphorothioate_defense_system_trait",
            "description": "DndCDEA-PbeABCD possession is a phosphorothioate-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1134/S0006297921030081",
                "snippet": "instead of the dndFGH, the restriction function is performed by the pbeABCD gene cluster",
                "notes": "Isaev et al. place PbeABCD in the family of PT defense systems while distinguishing it from DndFGH."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-15T17:36:16Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted DndCDEA-PbeABCD system as a DOI-backed GENOMICS TraitRecord under the phosphorothioate defense system parent after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v101.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000252",
    "label": "Dodola system",
    "definition": "A phage defense system in which an organism possesses a two-component Dodola locus represented by DolA and DolB profiles that can protect bacteria from bacteriophage infection.",
    "definition_source": "DOI:10.1016/j.chom.2022.09.017",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "Dodola",
        "synonym_type": "EXACT_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1016/j.chom.2022.09.017",
        "snippet": "discovery of 21 defense systems that protect bacteria from phages, based on computational genomic analyses and phage-infection experiments",
        "notes": "Millman et al. report the computational and experimental cohort that DefenseFinder cites for Dodola as a bacterial anti-phage system."
      },
      {
        "reference": "DOI:10.1101/2022.05.11.491447",
        "snippet": "discovery of 21 new defense systems that protect bacteria from phages, based on computational genomic analyses and phage infection experiments",
        "notes": "The bioRxiv version of Millman et al. independently carries the 21-system discovery claim linked from DefenseFinder's Dodola article registry."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "Dodola | 10\\.1101/2022\\.05\\.11\\.491447 | An expanding arsenal of immune systems that protect bacteria from phages",
        "notes": "The DefenseFinder model registry maps the named Dodola system to the Millman et al. antiphage-system discovery preprint."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "Dodola\tDodola\t2\t2\tDodola__DolA, Dodola__DolB",
        "notes": "The DefenseFinder rules table models Dodola as a two-component system with DolA and DolB as mandatory profile choices."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "Dodola__DolA                                     | Dodola__DolA                                     | Dodola",
        "notes": "The DefenseFinder HMM inventory records DolA as a Dodola profile."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "Dodola__DolB                                     | Dodola__DolB                                     | Dodola",
        "notes": "The DefenseFinder HMM inventory records DolB as a Dodola profile."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "dodola_locus_restricts_phage",
        "title": "Dodola loci confer bacterial phage defense",
        "description": "Conservative system-level sketch linking possession of a Dodola locus to restricted bacteriophage propagation without asserting the unresolved phage trigger or molecular output.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Dodola as a named anti-phage system with DefenseFinder DolA and DolB profiles while leaving its phage trigger, molecular substrate, antiviral effector output, and subtype breadth unresolved.",
        "nodes": [
          {
            "node_id": "dodola_locus",
            "label": "Dodola locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A Dodola anti-phage defense locus satisfying a DefenseFinder rule over DolA and DolB profiles."
          },
          {
            "node_id": "restricted_phage_propagation",
            "label": "restricted phage propagation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced propagation of bacteriophage in cells carrying the Dodola system."
          },
          {
            "node_id": "dodola_system_trait",
            "label": "Dodola system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000252",
            "description": "Possession of a genome-encoded Dodola phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "dodola_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "restricted_phage_propagation",
            "description": "DefenseFinder maps Dodola to a bacterial anti-phage-system discovery preprint and represents Dodola loci through DolA and DolB component profiles.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.chom.2022.09.017",
                "snippet": "discovery of 21 defense systems that protect bacteria from phages",
                "notes": "Millman et al. describe the anti-phage discovery cohort that the DefenseFinder Dodola registry row maps to the Dodola system."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Dodola | 10\\.1101/2022\\.05\\.11\\.491447 | An expanding arsenal of immune systems that protect bacteria from phages",
                "notes": "The DefenseFinder registry maps Dodola itself to the Millman et al. bacterial antiphage-system discovery preprint."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "Dodola\tDodola\t2\t2\tDodola__DolA, Dodola__DolB",
                "notes": "The DefenseFinder rules table supports DolA and DolB as Dodola system profile choices."
              }
            ]
          },
          {
            "subject": "restricted_phage_propagation",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "dodola_system_trait",
            "description": "Dodola-mediated phage restriction realizes the Dodola system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.chom.2022.09.017",
                "snippet": "discovery of 21 defense systems that protect bacteria from phages",
                "notes": "Millman et al. place the Dodola discovery cohort in the set of bacterial systems that protect against phages."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Dodola | 10\\.1101/2022\\.05\\.11\\.491447 | An expanding arsenal of immune systems that protect bacteria from phages",
                "notes": "DefenseFinder records Dodola as a named system from the Millman et al. antiphage discovery preprint."
              }
            ]
          },
          {
            "subject": "dodola_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Dodola system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "An expanding arsenal of immune systems that protect bacteria from phages",
                "notes": "DefenseFinder associates Dodola with the Millman et al. bacterial antiphage-system discovery paper."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "dodola-mechanism-gap",
        "prompt": "Resolve Dodola phage triggers and effector outputs before minting narrower Dodola mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Millman et al. and DefenseFinder support Dodola as a named anti-phage system with DolA and DolB profiles, but the trigger, molecular substrate, antiviral effector output, and subtype-specific mechanism are not resolved enough here to assert a narrower mechanistic child trait.",
        "attaches_to": [
          "causal_graphs#dodola_locus_restricts_phage"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-18"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-18T21:38:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Dodola system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v129.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000278",
    "label": "Dpd system",
    "definition": "A phage defense system in which an organism possesses a Dpd genomic island whose dpdA-K genes install 7-deazaguanine derivatives into DNA and are modeled by DefenseFinder as a multi-profile Dpd system.",
    "definition_source": "DOI:10.1073/pnas.1518570113",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "Dpd",
        "synonym_type": "EXACT_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      },
      {
        "synonym_text": "dpdA-K",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1073/pnas.1518570113"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1073/pnas.1518570113",
        "snippet": "2'-deoxy-preQ0 and 2'-deoxy-7-amido-7-deazaguanosine in enzymatic hydrolysates of DNA extracted from the pathogenic, Gram-negative bacteria Salmonella enterica serovar Montevideo",
        "notes": "Thiaville et al. experimentally detected 7-deazaguanine-derived DNA modifications in a bacterium carrying the Dpd island."
      },
      {
        "reference": "DOI:10.1073/pnas.1518570113",
        "snippet": "rename the genes of the S. Montevideo cluster as dpdA-K for 7-deazapurine in DNA",
        "notes": "Thiaville et al. name the S. Montevideo 7-deazapurine DNA-modification cluster as dpdA-K."
      },
      {
        "reference": "DOI:10.1073/pnas.1518570113",
        "snippet": "the modifications were detected in DNA from other organisms containing these clusters, including Kineococcus radiotolerans, Comamonas testosteroni, and Sphingopyxis alaskensis",
        "notes": "Thiaville et al. support treating Dpd as a recurrent bacterial system rather than a one-off S. Montevideo sequence feature."
      },
      {
        "reference": "DOI:10.1073/pnas.1518570113",
        "snippet": "strongly suggests a restriction-modification role for the cluster in Enterobacteriaceae",
        "notes": "Thiaville et al. connect the Dpd cluster to a likely restriction-modification role based on transformation efficiencies of modified and unmodified plasmids."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "Dpd | 10\\.1073/pnas\\.1518570113 | Novel genomic island modifies DNA with 7-deazaguanine derivatives",
        "notes": "The DefenseFinder article registry maps the named Dpd system to the Thiaville et al. DNA-modification paper."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "Dpd\tDpd\t4\t4\tDpd__DpdA, Dpd__DpdB, Dpd__DpdC, Dpd__DpdD, Dpd__DpdE, Dpd__DpdF, Dpd__DpdG, Dpd__DpdH, Dpd__DpdI, Dpd__DpdJ, Dpd__DpdK",
        "notes": "The DefenseFinder rules table models Dpd as a multi-profile defense system requiring a subset of DpdA-K profiles."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "Dpd__DpdA                                        | Dpd__DpdA                                        | Dpd",
        "notes": "The DefenseFinder HMM inventory records DpdA in the Dpd model namespace."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "dpd_dna_modification_defense",
        "title": "Dpd islands install 7-deazaguanine DNA modifications",
        "description": "Conservative system-level sketch linking a Dpd genomic island to 7-deazaguanine DNA modification, a likely restriction-modification output, and the Dpd system trait.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Dpd as a DNA-modification system with a DefenseFinder model while leaving its exact restriction target, modified motif, phage substrate range, DpdA-K component functions, and optional FolE/QueC/QueD/QueE profile requirements unresolved.",
        "nodes": [
          {
            "node_id": "dpd_genomic_island",
            "label": "Dpd genomic island",
            "node_type": "GENETIC_ELEMENT",
            "description": "A dpdA-K 7-deazapurine DNA-modification locus represented by a multi-profile DefenseFinder Dpd model."
          },
          {
            "node_id": "deazaguanine_dna_modification",
            "label": "7-deazaguanine DNA modification",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Installation of 7-deazaguanine-derived deoxynucleosides in bacterial DNA."
          },
          {
            "node_id": "restriction_modification_behavior",
            "label": "restriction-modification behavior",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Self/non-self discrimination associated with a bacterial DNA-modification island."
          },
          {
            "node_id": "dpd_system_trait",
            "label": "Dpd system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000278",
            "description": "Possession of a genome-encoded Dpd 7-deazaguanine DNA-modification defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "dpd_genomic_island",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "deazaguanine_dna_modification",
            "description": "The Dpd cluster installs 7-deazaguanine derivatives in DNA.",
            "evidence": [
              {
                "reference": "DOI:10.1073/pnas.1518570113",
                "snippet": "rename the genes of the S. Montevideo cluster as dpdA-K for 7-deazapurine in DNA",
                "notes": "Thiaville et al. name the genes of the 7-deazapurine DNA-modification cluster as dpdA-K."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "Dpd__DpdA                                        | Dpd__DpdA                                        | Dpd",
                "notes": "DefenseFinder includes DpdA in the custom Dpd model profile inventory."
              }
            ]
          },
          {
            "subject": "deazaguanine_dna_modification",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "restriction_modification_behavior",
            "description": "Modified Dpd DNA is associated with restriction-modification behavior in Enterobacteriaceae.",
            "evidence": [
              {
                "reference": "DOI:10.1073/pnas.1518570113",
                "snippet": "strongly suggests a restriction-modification role for the cluster in Enterobacteriaceae",
                "notes": "Thiaville et al. connect Dpd modification to a likely restriction-modification role without resolving the exact restriction component or substrate."
              }
            ]
          },
          {
            "subject": "restriction_modification_behavior",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "dpd_system_trait",
            "description": "DefenseFinder models Dpd as a multi-profile defense system rooted in DpdA-K DNA modification.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "Dpd\tDpd\t4\t4\tDpd__DpdA, Dpd__DpdB, Dpd__DpdC, Dpd__DpdD, Dpd__DpdE, Dpd__DpdF, Dpd__DpdG, Dpd__DpdH, Dpd__DpdI, Dpd__DpdJ, Dpd__DpdK",
                "notes": "The DefenseFinder rules table supports Dpd as a named defense-system model with DpdA-K profiles."
              }
            ]
          },
          {
            "subject": "dpd_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Dpd system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Dpd | 10\\.1073/pnas\\.1518570113 | Novel genomic island modifies DNA with 7-deazaguanine derivatives",
                "notes": "DefenseFinder associates Dpd with the Thiaville et al. DNA-modification paper."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "dpd-restriction-mechanism-gap",
        "prompt": "Resolve Dpd restriction targets, phage specificity, and DpdA-K component functions before minting narrower Dpd mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Thiaville et al. support dpdA-K-dependent installation of 7-deazaguanine derivatives into DNA and a likely restriction-modification role, and DefenseFinder supports Dpd as a named multi-profile defense model. This first record does not yet resolve the universal restriction target, modified motif, antiphage substrate breadth, or the necessity of each profiled component across natural Dpd loci.",
        "attaches_to": [
          "causal_graphs#dpd_dna_modification_defense"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-19"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-19T18:31:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Dpd system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v155.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000543",
    "label": "DRT1 system",
    "definition": "A DRT system in which an organism possesses a genome-encoded DefenseFinder DRT_1 subtype locus represented by the mandatory DRT_1__drt1a and DRT_1__drt1b profiles.",
    "definition_source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000279"
    ],
    "synonyms": [
      {
        "synonym_text": "DRT_1",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv"
      },
      {
        "synonym_text": "DRT_1__drt1a",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "DRT_1__drt1b",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1126/science.aba0372",
        "snippet": "We discovered that a family of uncharacterized reverse transcriptases (RTs) are active defense systems",
        "notes": "Gao et al. experimentally support defense-associated reverse transcriptases as active antiphage systems."
      },
      {
        "reference": "DOI:10.1126/science.aba0372",
        "snippet": "We named these genes defense-associated RTs (DRTs)",
        "notes": "Gao et al. coined the defense-associated RT naming that underlies the DRT system family."
      },
      {
        "reference": "DOI:10.1126/science.aba0372",
        "snippet": "In all cases, mutations in the RT active site [(Y/F)xDD to (Y/F)xAA, where x is any amino acid] abolished activity",
        "notes": "Gao et al. connect DRT antiphage activity to conserved reverse-transcriptase active-site residues."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| DRT | 10\\.1126/science\\.aba0372 | Diverse enzymatic activities mediate antiviral immunity in prokaryotes | ",
        "notes": "The pinned DefenseFinder article registry maps the DRT source key to the Gao et al. prokaryotic antiviral-immunity paper."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| DRT_1__drt1a                                     | DRT_1__drt1a                                     | DRT_1                  | Custom                  | 600    |\n| DRT_1__drt1b                                     | DRT_1__drt1b                                     | DRT_1                  | Custom                  | 20     |",
        "notes": "The pinned DefenseFinder HMM inventory records DRT_1__drt1a and DRT_1__drt1b under the DRT_1 model namespace."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "DRT\tDRT_1\t2\t2\tDRT_1__drt1a, DRT_1__drt1b\t\t\t",
        "notes": "The pinned DefenseFinder rules table models DRT_1 as a DRT subsystem requiring DRT_1__drt1a and DRT_1__drt1b."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "drt1_locus_reverse_transcriptase_defense",
        "title": "DRT1 loci support DRT antiphage defense",
        "description": "Conservative system-level sketch linking a DRT1 locus to reverse-transcriptase-dependent DRT phage defense and DRT1 system possession.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures DRT1 at DefenseFinder subtype-locus level without asserting the exact products of the DRT_1__drt1a and DRT_1__drt1b profiles, phage trigger, native host breadth, sensitive phage breadth, partner-feature requirements, profile-to-activity criteria, or whether every DefenseFinder DRT_1 prediction is a complete experimentally active DRT1 locus.",
        "nodes": [
          {
            "node_id": "drt1_locus",
            "label": "DRT1 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A defense-associated reverse transcriptase subtype I locus represented in DefenseFinder by DRT_1 profiles."
          },
          {
            "node_id": "drt_rt_active_site_activity",
            "label": "DRT reverse-transcriptase active-site activity",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "Reverse-transcriptase active-site-dependent activity of a defense-associated RT antiphage protein."
          },
          {
            "node_id": "drt1_system_trait",
            "label": "DRT1 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000543",
            "description": "Possession of a genome-encoded DRT1 phage-defense system."
          },
          {
            "node_id": "drt_system_trait",
            "label": "DRT system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000279",
            "description": "Possession of a genome-encoded defense-associated reverse transcriptase phage-defense system."
          }
        ],
        "edges": [
          {
            "subject": "drt1_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "drt_rt_active_site_activity",
            "description": "DRT1 loci are represented in DefenseFinder by custom defense-associated reverse transcriptase profiles.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.aba0372",
                "snippet": "We named these genes defense-associated RTs (DRTs)",
                "notes": "Gao et al. coined the defense-associated RT naming that underlies the DRT system family."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| DRT_1__drt1a                                     | DRT_1__drt1a                                     | DRT_1                  | Custom                  | 600    |\n| DRT_1__drt1b                                     | DRT_1__drt1b                                     | DRT_1                  | Custom                  | 20     |",
                "notes": "The pinned DefenseFinder HMM inventory records DRT_1__drt1a and DRT_1__drt1b under the DRT_1 model namespace."
              }
            ]
          },
          {
            "subject": "drt_rt_active_site_activity",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "drt1_system_trait",
            "description": "The first-pass DRT1 system trait is realized by a DefenseFinder DRT_1 subtype locus within the reverse-transcriptase-dependent DRT family.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.aba0372",
                "snippet": "We discovered that a family of uncharacterized reverse transcriptases (RTs) are active defense systems",
                "notes": "Gao et al. experimentally support defense-associated reverse transcriptases as active antiphage systems."
              },
              {
                "reference": "DOI:10.1126/science.aba0372",
                "snippet": "In all cases, mutations in the RT active site [(Y/F)xDD to (Y/F)xAA, where x is any amino acid] abolished activity",
                "notes": "Gao et al. connect DRT antiphage activity to conserved reverse-transcriptase active-site residues."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "DRT\tDRT_1\t2\t2\tDRT_1__drt1a, DRT_1__drt1b\t\t\t",
                "notes": "The pinned DefenseFinder rules table models DRT_1 as a DRT subsystem requiring DRT_1__drt1a and DRT_1__drt1b."
              }
            ]
          },
          {
            "subject": "drt1_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "drt_system_trait",
            "description": "DRT1 system possession is a DRT-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| DRT | 10\\.1126/science\\.aba0372 | Diverse enzymatic activities mediate antiviral immunity in prokaryotes | ",
                "notes": "The pinned DefenseFinder article registry maps the DRT source key to the Gao et al. prokaryotic antiviral-immunity paper."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "DRT\tDRT_1\t2\t2\tDRT_1__drt1a, DRT_1__drt1b\t\t\t",
                "notes": "The pinned DefenseFinder rules table models DRT_1 as a DRT subsystem requiring DRT_1__drt1a and DRT_1__drt1b."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "drt1-profile-activity-gap",
        "prompt": "Resolve the DRT1 reverse-transcriptase products, direct phage trigger, host breadth, partner-feature requirements, and DRT_1__drt1a/DRT_1__drt1b profile-to-activity criteria before minting DRT1 mechanism or component children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Gao et al. support defense-associated reverse transcriptases as a broad antiphage-system family, and the pinned DefenseFinder HMM inventory and rules table support DRT_1 as a DRT subsystem with two mandatory profiles. This first-pass record leaves the exact DRT1 RT products, phage trigger, host breadth, partner-feature requirements, and profile-to-activity requirements unresolved.",
        "evidence": [
          {
            "reference": "DOI:10.1126/science.aba0372",
            "snippet": "We discovered that a family of uncharacterized reverse transcriptases (RTs) are active defense systems",
            "notes": "Gao et al. experimentally support defense-associated reverse transcriptases as active antiphage systems."
          },
          {
            "reference": "DOI:10.1126/science.aba0372",
            "snippet": "In all cases, mutations in the RT active site [(Y/F)xDD to (Y/F)xAA, where x is any amino acid] abolished activity",
            "notes": "Gao et al. connect DRT antiphage activity to conserved reverse-transcriptase active-site residues."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| DRT_1__drt1a                                     | DRT_1__drt1a                                     | DRT_1                  | Custom                  | 600    |\n| DRT_1__drt1b                                     | DRT_1__drt1b                                     | DRT_1                  | Custom                  | 20     |",
            "notes": "The pinned DefenseFinder HMM inventory records DRT_1__drt1a and DRT_1__drt1b under the DRT_1 model namespace."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "snippet": "DRT\tDRT_1\t2\t2\tDRT_1__drt1a, DRT_1__drt1b\t\t\t",
            "notes": "The pinned DefenseFinder rules table models DRT_1 as a DRT subsystem requiring DRT_1__drt1a and DRT_1__drt1b."
          }
        ],
        "attaches_to": [
          "causal_graphs#drt1_locus_reverse_transcriptase_defense"
        ],
        "posed_by": "codex",
        "posed_date": "2026-10-02"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-02T11:04:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted DRT1 system as a DOI- and DefenseFinder-backed GENOMICS TraitRecord under the DRT system parent after an ignored-and-hidden duplicate review found no exact live DRT1 TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v420.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-02T11:04:01Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed DRT1 system during initial curation and left canonical_examples empty because Gao et al. and the pinned DefenseFinder tables support the DRT family and the DRT_1 model namespace but not an accession-backed native microbial taxon exemplar tied to DRT_1__drt1a and DRT_1__drt1b and experimentally verified endogenous DRT1 activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000544",
    "label": "DRT2 system",
    "definition": "A DRT system in which an organism possesses a genome-encoded DefenseFinder DRT_2 subtype locus represented by the DRT_2__drt2 profile.",
    "definition_source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000279"
    ],
    "synonyms": [
      {
        "synonym_text": "DRT_2",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv"
      },
      {
        "synonym_text": "DRT_2__drt2",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1126/science.aba0372",
        "snippet": "We discovered that a family of uncharacterized reverse transcriptases (RTs) are active defense systems",
        "notes": "Gao et al. experimentally support defense-associated reverse transcriptases as active antiphage systems."
      },
      {
        "reference": "DOI:10.1126/science.aba0372",
        "snippet": "We named these genes defense-associated RTs (DRTs)",
        "notes": "Gao et al. coined the defense-associated RT naming that underlies the DRT system family."
      },
      {
        "reference": "DOI:10.1126/science.aba0372",
        "snippet": "In all cases, mutations in the RT active site [(Y/F)xDD to (Y/F)xAA, where x is any amino acid] abolished activity",
        "notes": "Gao et al. connect DRT antiphage activity to conserved reverse-transcriptase active-site residues."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| DRT | 10\\.1126/science\\.aba0372 | Diverse enzymatic activities mediate antiviral immunity in prokaryotes | ",
        "notes": "The pinned DefenseFinder article registry maps the DRT source key to the Gao et al. prokaryotic antiviral-immunity paper."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| DRT_2__drt2                                      | DRT_2__drt2                                      | DRT_2                  | Custom                  | 100    |",
        "notes": "The pinned DefenseFinder HMM inventory records DRT_2__drt2 under the DRT_2 model namespace."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "DRT\tDRT_2\t1\t1\tDRT_2__drt2\t\t\t",
        "notes": "The pinned DefenseFinder rules table models DRT_2 as a DRT subsystem with a DRT_2__drt2 profile."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "drt2_locus_reverse_transcriptase_defense",
        "title": "DRT2 loci support DRT antiphage defense",
        "description": "Conservative system-level sketch linking a DRT2 locus to reverse-transcriptase-dependent DRT phage defense and DRT2 system possession.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures DRT2 at DefenseFinder subtype-locus level without asserting the direct DRT2 reverse-transcriptase product, phage trigger, native host breadth, sensitive phage breadth, partner-feature requirements, profile-to-activity criteria, or whether every DefenseFinder DRT_2 prediction is a complete experimentally active DRT2 locus.",
        "nodes": [
          {
            "node_id": "drt2_locus",
            "label": "DRT2 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A defense-associated reverse transcriptase subtype II locus represented in DefenseFinder by a DRT_2 profile."
          },
          {
            "node_id": "drt_rt_active_site_activity",
            "label": "DRT reverse-transcriptase active-site activity",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "Reverse-transcriptase active-site-dependent activity of a defense-associated RT antiphage protein."
          },
          {
            "node_id": "drt2_system_trait",
            "label": "DRT2 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000544",
            "description": "Possession of a genome-encoded DRT2 phage-defense system."
          },
          {
            "node_id": "drt_system_trait",
            "label": "DRT system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000279",
            "description": "Possession of a genome-encoded defense-associated reverse transcriptase phage-defense system."
          }
        ],
        "edges": [
          {
            "subject": "drt2_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "drt_rt_active_site_activity",
            "description": "DRT2 loci are represented in DefenseFinder by a custom defense-associated reverse transcriptase profile.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.aba0372",
                "snippet": "We named these genes defense-associated RTs (DRTs)",
                "notes": "Gao et al. coined the defense-associated RT naming that underlies the DRT system family."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| DRT_2__drt2                                      | DRT_2__drt2                                      | DRT_2                  | Custom                  | 100    |",
                "notes": "The pinned DefenseFinder HMM inventory records DRT_2__drt2 under the DRT_2 model namespace."
              }
            ]
          },
          {
            "subject": "drt_rt_active_site_activity",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "drt2_system_trait",
            "description": "The first-pass DRT2 system trait is realized by a DefenseFinder DRT_2 subtype locus within the reverse-transcriptase-dependent DRT family.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.aba0372",
                "snippet": "We discovered that a family of uncharacterized reverse transcriptases (RTs) are active defense systems",
                "notes": "Gao et al. experimentally support defense-associated reverse transcriptases as active antiphage systems."
              },
              {
                "reference": "DOI:10.1126/science.aba0372",
                "snippet": "In all cases, mutations in the RT active site [(Y/F)xDD to (Y/F)xAA, where x is any amino acid] abolished activity",
                "notes": "Gao et al. connect DRT antiphage activity to conserved reverse-transcriptase active-site residues."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "DRT\tDRT_2\t1\t1\tDRT_2__drt2\t\t\t",
                "notes": "The pinned DefenseFinder rules table models DRT_2 as a DRT subsystem with a DRT_2__drt2 profile."
              }
            ]
          },
          {
            "subject": "drt2_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "drt_system_trait",
            "description": "DRT2 system possession is a DRT-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| DRT | 10\\.1126/science\\.aba0372 | Diverse enzymatic activities mediate antiviral immunity in prokaryotes | ",
                "notes": "The pinned DefenseFinder article registry maps the DRT source key to the Gao et al. prokaryotic antiviral-immunity paper."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "DRT\tDRT_2\t1\t1\tDRT_2__drt2\t\t\t",
                "notes": "The pinned DefenseFinder rules table models DRT_2 as a DRT subsystem with a DRT_2__drt2 profile."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "drt2-profile-activity-gap",
        "prompt": "Resolve the DRT2 reverse-transcriptase product, direct phage trigger, host breadth, partner-feature requirements, and DRT_2 profile-to-activity criteria before minting DRT2 mechanism or component children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Gao et al. support defense-associated reverse transcriptases as a broad antiphage-system family, and the pinned DefenseFinder HMM inventory and rules table support DRT_2 as a single-profile DRT subsystem. This first-pass record leaves the exact DRT2 RT product, phage trigger, host breadth, partner-feature requirements, and profile-to-activity requirements unresolved.",
        "evidence": [
          {
            "reference": "DOI:10.1126/science.aba0372",
            "snippet": "We discovered that a family of uncharacterized reverse transcriptases (RTs) are active defense systems",
            "notes": "Gao et al. experimentally support defense-associated reverse transcriptases as active antiphage systems."
          },
          {
            "reference": "DOI:10.1126/science.aba0372",
            "snippet": "In all cases, mutations in the RT active site [(Y/F)xDD to (Y/F)xAA, where x is any amino acid] abolished activity",
            "notes": "Gao et al. connect DRT antiphage activity to conserved reverse-transcriptase active-site residues."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| DRT_2__drt2                                      | DRT_2__drt2                                      | DRT_2                  | Custom                  | 100    |",
            "notes": "The pinned DefenseFinder HMM inventory records DRT_2__drt2 under the DRT_2 model namespace."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "snippet": "DRT\tDRT_2\t1\t1\tDRT_2__drt2\t\t\t",
            "notes": "The pinned DefenseFinder rules table models DRT_2 as a DRT subsystem with a DRT_2__drt2 profile."
          }
        ],
        "attaches_to": [
          "causal_graphs#drt2_locus_reverse_transcriptase_defense"
        ],
        "posed_by": "codex",
        "posed_date": "2026-10-02"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-02T11:51:13Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted DRT2 system as a DOI- and DefenseFinder-backed GENOMICS TraitRecord under the DRT system parent after an ignored-and-hidden duplicate review found no exact live DRT2 TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v421.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-02T11:51:14Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed DRT2 system during initial curation and left canonical_examples empty because Gao et al. and the pinned DefenseFinder tables support the DRT family and the DRT_2 model namespace but not an accession-backed native microbial taxon exemplar tied to DRT_2__drt2 and experimentally verified endogenous DRT2 activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000545",
    "label": "DRT3 system",
    "definition": "A DRT system in which an organism possesses a genome-encoded DefenseFinder DRT_3 subtype locus represented by the mandatory DRT_3__drt3a and DRT_3__drt3b profiles.",
    "definition_source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000279"
    ],
    "synonyms": [
      {
        "synonym_text": "DRT_3",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv"
      },
      {
        "synonym_text": "DRT_3__drt3a",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "DRT_3__drt3b",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1126/science.aba0372",
        "snippet": "We discovered that a family of uncharacterized reverse transcriptases (RTs) are active defense systems",
        "notes": "Gao et al. experimentally support defense-associated reverse transcriptases as active antiphage systems."
      },
      {
        "reference": "DOI:10.1126/science.aba0372",
        "snippet": "We named these genes defense-associated RTs (DRTs)",
        "notes": "Gao et al. coined the defense-associated RT naming that underlies the DRT system family."
      },
      {
        "reference": "DOI:10.1126/science.aba0372",
        "snippet": "In all cases, mutations in the RT active site [(Y/F)xDD to (Y/F)xAA, where x is any amino acid] abolished activity",
        "notes": "Gao et al. connect DRT antiphage activity to conserved reverse-transcriptase active-site residues."
      },
      {
        "reference": "DOI:10.1126/science.aba0372",
        "snippet": "the UG3 (drt3a) and UG8 (drt3b) RTs are components of the same defense system (DRT type 3), with both RTs required for defense activity",
        "notes": "Gao et al. support the two reverse-transcriptase components of the DRT type 3 defense system."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| DRT | 10\\.1126/science\\.aba0372 | Diverse enzymatic activities mediate antiviral immunity in prokaryotes | ",
        "notes": "The pinned DefenseFinder article registry maps the DRT source key to the Gao et al. prokaryotic antiviral-immunity paper."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| DRT_3__drt3a                                     | DRT_3__drt3a                                     | DRT_3                  | Custom                  | 150    |\n| DRT_3__drt3b                                     | DRT_3__drt3b                                     | DRT_3                  | Custom                  | 250    |\n| DRT_3__SLATT                                     |                                                  | DRT_3                  | Custom                  | 20     |",
        "notes": "The pinned DefenseFinder HMM inventory records DRT_3__drt3a, DRT_3__drt3b, and DRT_3__SLATT under the DRT_3 model namespace, with DRT_3__SLATT lacking an emitted HMM name."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "DRT\tDRT_3\t2\t2\tDRT_3__drt3a, DRT_3__drt3b\t\t\t",
        "notes": "The pinned DefenseFinder rules table models DRT_3 as a DRT subsystem requiring DRT_3__drt3a and DRT_3__drt3b."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "drt3_locus_reverse_transcriptase_defense",
        "title": "DRT3 loci support DRT antiphage defense",
        "description": "Conservative system-level sketch linking a DRT3 locus to reverse-transcriptase-dependent DRT phage defense and DRT3 system possession.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures DRT3 at DefenseFinder subtype-locus level without asserting the direct DRT3 reverse-transcriptase products, phage trigger, native host breadth, sensitive phage breadth, non-coding RNA or DRT_3__SLATT partner-feature role, profile-to-activity criteria, or whether every DefenseFinder DRT_3 prediction is a complete experimentally active DRT3 locus.",
        "nodes": [
          {
            "node_id": "drt3_locus",
            "label": "DRT3 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A defense-associated reverse transcriptase subtype III locus represented in DefenseFinder by DRT_3 profiles."
          },
          {
            "node_id": "drt_rt_active_site_activity",
            "label": "DRT reverse-transcriptase active-site activity",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "Reverse-transcriptase active-site-dependent activity of a defense-associated RT antiphage protein."
          },
          {
            "node_id": "drt3_system_trait",
            "label": "DRT3 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000545",
            "description": "Possession of a genome-encoded DRT3 phage-defense system."
          },
          {
            "node_id": "drt_system_trait",
            "label": "DRT system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000279",
            "description": "Possession of a genome-encoded defense-associated reverse transcriptase phage-defense system."
          }
        ],
        "edges": [
          {
            "subject": "drt3_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "drt_rt_active_site_activity",
            "description": "DRT3 loci are represented in DefenseFinder by custom defense-associated reverse transcriptase profiles.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.aba0372",
                "snippet": "We named these genes defense-associated RTs (DRTs)",
                "notes": "Gao et al. coined the defense-associated RT naming that underlies the DRT system family."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| DRT_3__drt3a                                     | DRT_3__drt3a                                     | DRT_3                  | Custom                  | 150    |\n| DRT_3__drt3b                                     | DRT_3__drt3b                                     | DRT_3                  | Custom                  | 250    |",
                "notes": "The pinned DefenseFinder HMM inventory records DRT_3__drt3a and DRT_3__drt3b under the DRT_3 model namespace."
              }
            ]
          },
          {
            "subject": "drt_rt_active_site_activity",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "drt3_system_trait",
            "description": "The first-pass DRT3 system trait is realized by a DefenseFinder DRT_3 subtype locus within the reverse-transcriptase-dependent DRT family.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.aba0372",
                "snippet": "We discovered that a family of uncharacterized reverse transcriptases (RTs) are active defense systems",
                "notes": "Gao et al. experimentally support defense-associated reverse transcriptases as active antiphage systems."
              },
              {
                "reference": "DOI:10.1126/science.aba0372",
                "snippet": "In all cases, mutations in the RT active site [(Y/F)xDD to (Y/F)xAA, where x is any amino acid] abolished activity",
                "notes": "Gao et al. connect DRT antiphage activity to conserved reverse-transcriptase active-site residues."
              },
              {
                "reference": "DOI:10.1126/science.aba0372",
                "snippet": "the UG3 (drt3a) and UG8 (drt3b) RTs are components of the same defense system (DRT type 3), with both RTs required for defense activity",
                "notes": "Gao et al. support the two reverse-transcriptase components of the DRT type 3 defense system."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "DRT\tDRT_3\t2\t2\tDRT_3__drt3a, DRT_3__drt3b\t\t\t",
                "notes": "The pinned DefenseFinder rules table models DRT_3 as a DRT subsystem requiring DRT_3__drt3a and DRT_3__drt3b."
              }
            ]
          },
          {
            "subject": "drt3_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "drt_system_trait",
            "description": "DRT3 system possession is a DRT-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| DRT | 10\\.1126/science\\.aba0372 | Diverse enzymatic activities mediate antiviral immunity in prokaryotes | ",
                "notes": "The pinned DefenseFinder article registry maps the DRT source key to the Gao et al. prokaryotic antiviral-immunity paper."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "DRT\tDRT_3\t2\t2\tDRT_3__drt3a, DRT_3__drt3b\t\t\t",
                "notes": "The pinned DefenseFinder rules table models DRT_3 as a DRT subsystem requiring DRT_3__drt3a and DRT_3__drt3b."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "drt3-profile-activity-gap",
        "prompt": "Resolve the DRT3 reverse-transcriptase products, direct phage trigger, host breadth, non-coding RNA or DRT_3__SLATT partner-feature role, and DRT_3 profile-to-activity criteria before minting DRT3 mechanism or component children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Gao et al. support defense-associated reverse transcriptases as a broad antiphage-system family and the two RT components of DRT type 3, while the pinned DefenseFinder HMM inventory and rules table support DRT_3 as a two-required-profile DRT subsystem. This first-pass record leaves the exact DRT3 RT products, phage trigger, host breadth, DRT_3__SLATT role, and profile-to-activity requirements unresolved.",
        "evidence": [
          {
            "reference": "DOI:10.1126/science.aba0372",
            "snippet": "We discovered that a family of uncharacterized reverse transcriptases (RTs) are active defense systems",
            "notes": "Gao et al. experimentally support defense-associated reverse transcriptases as active antiphage systems."
          },
          {
            "reference": "DOI:10.1126/science.aba0372",
            "snippet": "In all cases, mutations in the RT active site [(Y/F)xDD to (Y/F)xAA, where x is any amino acid] abolished activity",
            "notes": "Gao et al. connect DRT antiphage activity to conserved reverse-transcriptase active-site residues."
          },
          {
            "reference": "DOI:10.1126/science.aba0372",
            "snippet": "the UG3 (drt3a) and UG8 (drt3b) RTs are components of the same defense system (DRT type 3), with both RTs required for defense activity",
            "notes": "Gao et al. support the two reverse-transcriptase components of the DRT type 3 defense system."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| DRT_3__drt3a                                     | DRT_3__drt3a                                     | DRT_3                  | Custom                  | 150    |\n| DRT_3__drt3b                                     | DRT_3__drt3b                                     | DRT_3                  | Custom                  | 250    |\n| DRT_3__SLATT                                     |                                                  | DRT_3                  | Custom                  | 20     |",
            "notes": "The pinned DefenseFinder HMM inventory records DRT_3__drt3a, DRT_3__drt3b, and DRT_3__SLATT under the DRT_3 model namespace, with DRT_3__SLATT lacking an emitted HMM name."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "snippet": "DRT\tDRT_3\t2\t2\tDRT_3__drt3a, DRT_3__drt3b\t\t\t",
            "notes": "The pinned DefenseFinder rules table models DRT_3 as a DRT subsystem requiring DRT_3__drt3a and DRT_3__drt3b."
          }
        ],
        "attaches_to": [
          "causal_graphs#drt3_locus_reverse_transcriptase_defense"
        ],
        "posed_by": "codex",
        "posed_date": "2026-10-02"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-02T12:40:28Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted DRT3 system as a DOI- and DefenseFinder-backed GENOMICS TraitRecord under the DRT system parent after an ignored-and-hidden duplicate review found no exact live DRT3 TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v422.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-02T12:40:29Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed DRT3 system during initial curation and left canonical_examples empty because Gao et al. and the pinned DefenseFinder tables support DRT type 3 and the DRT_3 model namespace but not an accession-backed native microbial taxon exemplar tied to DRT_3__drt3a and DRT_3__drt3b and experimentally verified endogenous DRT3 activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000546",
    "label": "DRT4 system",
    "definition": "A DRT system in which an organism possesses a genome-encoded DefenseFinder DRT_4 subtype locus represented by the DRT_4__drt4 profile.",
    "definition_source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000279"
    ],
    "synonyms": [
      {
        "synonym_text": "DRT_4",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv"
      },
      {
        "synonym_text": "DRT_4__drt4",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1126/science.aba0372",
        "snippet": "We discovered that a family of uncharacterized reverse transcriptases (RTs) are active defense systems",
        "notes": "Gao et al. experimentally support defense-associated reverse transcriptases as active antiphage systems."
      },
      {
        "reference": "DOI:10.1126/science.aba0372",
        "snippet": "We named these genes defense-associated RTs (DRTs)",
        "notes": "Gao et al. coined the defense-associated RT naming that underlies the DRT system family."
      },
      {
        "reference": "DOI:10.1126/science.aba0372",
        "snippet": "In all cases, mutations in the RT active site [(Y/F)xDD to (Y/F)xAA, where x is any amino acid] abolished activity",
        "notes": "Gao et al. connect DRT antiphage activity to conserved reverse-transcriptase active-site residues."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| DRT | 10\\.1126/science\\.aba0372 | Diverse enzymatic activities mediate antiviral immunity in prokaryotes | ",
        "notes": "The pinned DefenseFinder article registry maps the DRT source key to the Gao et al. prokaryotic antiviral-immunity paper."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| DRT_4__drt4                                      | DRT_4__drt4                                      | DRT_4                  | Custom                  | 350    |",
        "notes": "The pinned DefenseFinder HMM inventory records DRT_4__drt4 under the DRT_4 model namespace."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "DRT\tDRT_4\t1\t1\tDRT_4__drt4\t\t\t",
        "notes": "The pinned DefenseFinder rules table models DRT_4 as a DRT subsystem with a DRT_4__drt4 profile."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "drt4_locus_reverse_transcriptase_defense",
        "title": "DRT4 loci support DRT antiphage defense",
        "description": "Conservative system-level sketch linking a DRT4 locus to reverse-transcriptase-dependent DRT phage defense and DRT4 system possession.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures DRT4 at DefenseFinder subtype-locus level without asserting the direct DRT4 reverse-transcriptase product, phage trigger, native host breadth, sensitive phage breadth, partner-feature requirements, profile-to-activity criteria, or whether every DefenseFinder DRT_4 prediction is a complete experimentally active DRT4 locus.",
        "nodes": [
          {
            "node_id": "drt4_locus",
            "label": "DRT4 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A defense-associated reverse transcriptase subtype IV locus represented in DefenseFinder by a DRT_4 profile."
          },
          {
            "node_id": "drt_rt_active_site_activity",
            "label": "DRT reverse-transcriptase active-site activity",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "Reverse-transcriptase active-site-dependent activity of a defense-associated RT antiphage protein."
          },
          {
            "node_id": "drt4_system_trait",
            "label": "DRT4 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000546",
            "description": "Possession of a genome-encoded DRT4 phage-defense system."
          },
          {
            "node_id": "drt_system_trait",
            "label": "DRT system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000279",
            "description": "Possession of a genome-encoded defense-associated reverse transcriptase phage-defense system."
          }
        ],
        "edges": [
          {
            "subject": "drt4_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "drt_rt_active_site_activity",
            "description": "DRT4 loci are represented in DefenseFinder by a custom defense-associated reverse transcriptase profile.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.aba0372",
                "snippet": "We named these genes defense-associated RTs (DRTs)",
                "notes": "Gao et al. coined the defense-associated RT naming that underlies the DRT system family."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| DRT_4__drt4                                      | DRT_4__drt4                                      | DRT_4                  | Custom                  | 350    |",
                "notes": "The pinned DefenseFinder HMM inventory records DRT_4__drt4 under the DRT_4 model namespace."
              }
            ]
          },
          {
            "subject": "drt_rt_active_site_activity",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "drt4_system_trait",
            "description": "The first-pass DRT4 system trait is realized by a DefenseFinder DRT_4 subtype locus within the reverse-transcriptase-dependent DRT family.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.aba0372",
                "snippet": "We discovered that a family of uncharacterized reverse transcriptases (RTs) are active defense systems",
                "notes": "Gao et al. experimentally support defense-associated reverse transcriptases as active antiphage systems."
              },
              {
                "reference": "DOI:10.1126/science.aba0372",
                "snippet": "In all cases, mutations in the RT active site [(Y/F)xDD to (Y/F)xAA, where x is any amino acid] abolished activity",
                "notes": "Gao et al. connect DRT antiphage activity to conserved reverse-transcriptase active-site residues."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "DRT\tDRT_4\t1\t1\tDRT_4__drt4\t\t\t",
                "notes": "The pinned DefenseFinder rules table models DRT_4 as a DRT subsystem with a DRT_4__drt4 profile."
              }
            ]
          },
          {
            "subject": "drt4_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "drt_system_trait",
            "description": "DRT4 system possession is a DRT-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| DRT | 10\\.1126/science\\.aba0372 | Diverse enzymatic activities mediate antiviral immunity in prokaryotes | ",
                "notes": "The pinned DefenseFinder article registry maps the DRT source key to the Gao et al. prokaryotic antiviral-immunity paper."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "DRT\tDRT_4\t1\t1\tDRT_4__drt4\t\t\t",
                "notes": "The pinned DefenseFinder rules table models DRT_4 as a DRT subsystem with a DRT_4__drt4 profile."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "drt4-profile-activity-gap",
        "prompt": "Resolve the DRT4 reverse-transcriptase product, direct phage trigger, host breadth, partner-feature requirements, and DRT_4 profile-to-activity criteria before minting DRT4 mechanism or component children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Gao et al. support defense-associated reverse transcriptases as a broad antiphage-system family, and the pinned DefenseFinder HMM inventory and rules table support DRT_4 as a single-profile DRT subsystem. This first-pass record leaves the exact DRT4 RT product, phage trigger, host breadth, partner-feature requirements, and profile-to-activity requirements unresolved.",
        "evidence": [
          {
            "reference": "DOI:10.1126/science.aba0372",
            "snippet": "We discovered that a family of uncharacterized reverse transcriptases (RTs) are active defense systems",
            "notes": "Gao et al. experimentally support defense-associated reverse transcriptases as active antiphage systems."
          },
          {
            "reference": "DOI:10.1126/science.aba0372",
            "snippet": "In all cases, mutations in the RT active site [(Y/F)xDD to (Y/F)xAA, where x is any amino acid] abolished activity",
            "notes": "Gao et al. connect DRT antiphage activity to conserved reverse-transcriptase active-site residues."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| DRT_4__drt4                                      | DRT_4__drt4                                      | DRT_4                  | Custom                  | 350    |",
            "notes": "The pinned DefenseFinder HMM inventory records DRT_4__drt4 under the DRT_4 model namespace."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "snippet": "DRT\tDRT_4\t1\t1\tDRT_4__drt4\t\t\t",
            "notes": "The pinned DefenseFinder rules table models DRT_4 as a DRT subsystem with a DRT_4__drt4 profile."
          }
        ],
        "attaches_to": [
          "causal_graphs#drt4_locus_reverse_transcriptase_defense"
        ],
        "posed_by": "codex",
        "posed_date": "2026-10-02"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-02T13:40:28Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted DRT4 system as a DOI- and DefenseFinder-backed GENOMICS TraitRecord under the DRT system parent after an ignored-and-hidden duplicate review found no exact live DRT4 TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v423.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-02T13:40:29Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed DRT4 system during initial curation and left canonical_examples empty because Gao et al. and the pinned DefenseFinder tables support the DRT family and the DRT_4 model namespace but not an accession-backed native microbial taxon exemplar tied to DRT_4__drt4 and experimentally verified endogenous DRT4 activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000547",
    "label": "DRT5 system",
    "definition": "A DRT system in which an organism possesses a genome-encoded DefenseFinder DRT_5 subtype locus represented by the DRT_5__drt5 profile.",
    "definition_source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000279"
    ],
    "synonyms": [
      {
        "synonym_text": "DRT_5",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv"
      },
      {
        "synonym_text": "DRT_5__drt5",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1126/science.aba0372",
        "snippet": "We discovered that a family of uncharacterized reverse transcriptases (RTs) are active defense systems",
        "notes": "Gao et al. experimentally support defense-associated reverse transcriptases as active antiphage systems."
      },
      {
        "reference": "DOI:10.1126/science.aba0372",
        "snippet": "We named these genes defense-associated RTs (DRTs)",
        "notes": "Gao et al. coined the defense-associated RT naming that underlies the DRT system family."
      },
      {
        "reference": "DOI:10.1126/science.aba0372",
        "snippet": "In all cases, mutations in the RT active site [(Y/F)xDD to (Y/F)xAA, where x is any amino acid] abolished activity",
        "notes": "Gao et al. connect DRT antiphage activity to conserved reverse-transcriptase active-site residues."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| DRT | 10\\.1126/science\\.aba0372 | Diverse enzymatic activities mediate antiviral immunity in prokaryotes | ",
        "notes": "The pinned DefenseFinder article registry maps the DRT source key to the Gao et al. prokaryotic antiviral-immunity paper."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| DRT_5__drt5                                      | DRT_5__drt5                                      | DRT_5                  | Custom                  | 400    |",
        "notes": "The pinned DefenseFinder HMM inventory records DRT_5__drt5 under the DRT_5 model namespace."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "DRT\tDRT_5\t1\t1\tDRT_5__drt5\t\t\t",
        "notes": "The pinned DefenseFinder rules table models DRT_5 as a DRT subsystem with a DRT_5__drt5 profile."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "drt5_locus_reverse_transcriptase_defense",
        "title": "DRT5 loci support DRT antiphage defense",
        "description": "Conservative system-level sketch linking a DRT5 locus to reverse-transcriptase-dependent DRT phage defense and DRT5 system possession.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures DRT5 at DefenseFinder subtype-locus level without asserting the direct DRT5 reverse-transcriptase product, phage trigger, native host breadth, sensitive phage breadth, partner-feature requirements, profile-to-activity criteria, or whether every DefenseFinder DRT_5 prediction is a complete experimentally active DRT5 locus.",
        "nodes": [
          {
            "node_id": "drt5_locus",
            "label": "DRT5 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A defense-associated reverse transcriptase subtype V locus represented in DefenseFinder by a DRT_5 profile."
          },
          {
            "node_id": "drt_rt_active_site_activity",
            "label": "DRT reverse-transcriptase active-site activity",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "Reverse-transcriptase active-site-dependent activity of a defense-associated RT antiphage protein."
          },
          {
            "node_id": "drt5_system_trait",
            "label": "DRT5 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000547",
            "description": "Possession of a genome-encoded DRT5 phage-defense system."
          },
          {
            "node_id": "drt_system_trait",
            "label": "DRT system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000279",
            "description": "Possession of a genome-encoded defense-associated reverse transcriptase phage-defense system."
          }
        ],
        "edges": [
          {
            "subject": "drt5_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "drt_rt_active_site_activity",
            "description": "DRT5 loci are represented in DefenseFinder by a custom defense-associated reverse transcriptase profile.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.aba0372",
                "snippet": "We named these genes defense-associated RTs (DRTs)",
                "notes": "Gao et al. coined the defense-associated RT naming that underlies the DRT system family."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| DRT_5__drt5                                      | DRT_5__drt5                                      | DRT_5                  | Custom                  | 400    |",
                "notes": "The pinned DefenseFinder HMM inventory records DRT_5__drt5 under the DRT_5 model namespace."
              }
            ]
          },
          {
            "subject": "drt_rt_active_site_activity",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "drt5_system_trait",
            "description": "The first-pass DRT5 system trait is realized by a DefenseFinder DRT_5 subtype locus within the reverse-transcriptase-dependent DRT family.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.aba0372",
                "snippet": "We discovered that a family of uncharacterized reverse transcriptases (RTs) are active defense systems",
                "notes": "Gao et al. experimentally support defense-associated reverse transcriptases as active antiphage systems."
              },
              {
                "reference": "DOI:10.1126/science.aba0372",
                "snippet": "In all cases, mutations in the RT active site [(Y/F)xDD to (Y/F)xAA, where x is any amino acid] abolished activity",
                "notes": "Gao et al. connect DRT antiphage activity to conserved reverse-transcriptase active-site residues."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "DRT\tDRT_5\t1\t1\tDRT_5__drt5\t\t\t",
                "notes": "The pinned DefenseFinder rules table models DRT_5 as a DRT subsystem with a DRT_5__drt5 profile."
              }
            ]
          },
          {
            "subject": "drt5_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "drt_system_trait",
            "description": "DRT5 system possession is a DRT-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| DRT | 10\\.1126/science\\.aba0372 | Diverse enzymatic activities mediate antiviral immunity in prokaryotes | ",
                "notes": "The pinned DefenseFinder article registry maps the DRT source key to the Gao et al. prokaryotic antiviral-immunity paper."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "DRT\tDRT_5\t1\t1\tDRT_5__drt5\t\t\t",
                "notes": "The pinned DefenseFinder rules table models DRT_5 as a DRT subsystem with a DRT_5__drt5 profile."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "drt5-profile-activity-gap",
        "prompt": "Resolve the DRT5 reverse-transcriptase product, direct phage trigger, host breadth, partner-feature requirements, and DRT_5 profile-to-activity criteria before minting DRT5 mechanism or component children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Gao et al. support defense-associated reverse transcriptases as a broad antiphage-system family, and the pinned DefenseFinder HMM inventory and rules table support DRT_5 as a single-profile DRT subsystem. This first-pass record leaves the exact DRT5 RT product, phage trigger, host breadth, partner-feature requirements, and profile-to-activity requirements unresolved.",
        "evidence": [
          {
            "reference": "DOI:10.1126/science.aba0372",
            "snippet": "We discovered that a family of uncharacterized reverse transcriptases (RTs) are active defense systems",
            "notes": "Gao et al. experimentally support defense-associated reverse transcriptases as active antiphage systems."
          },
          {
            "reference": "DOI:10.1126/science.aba0372",
            "snippet": "In all cases, mutations in the RT active site [(Y/F)xDD to (Y/F)xAA, where x is any amino acid] abolished activity",
            "notes": "Gao et al. connect DRT antiphage activity to conserved reverse-transcriptase active-site residues."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| DRT_5__drt5                                      | DRT_5__drt5                                      | DRT_5                  | Custom                  | 400    |",
            "notes": "The pinned DefenseFinder HMM inventory records DRT_5__drt5 under the DRT_5 model namespace."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "snippet": "DRT\tDRT_5\t1\t1\tDRT_5__drt5\t\t\t",
            "notes": "The pinned DefenseFinder rules table models DRT_5 as a DRT subsystem with a DRT_5__drt5 profile."
          }
        ],
        "attaches_to": [
          "causal_graphs#drt5_locus_reverse_transcriptase_defense"
        ],
        "posed_by": "codex",
        "posed_date": "2026-10-02"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-02T14:33:04Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted DRT5 system as a DOI- and DefenseFinder-backed GENOMICS TraitRecord under the DRT system parent after an ignored-and-hidden duplicate review found no exact live DRT5 TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v424.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-02T14:33:05Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed DRT5 system during initial curation and left canonical_examples empty because Gao et al. and the pinned DefenseFinder tables support the DRT family and the DRT_5 model namespace but not an accession-backed native microbial taxon exemplar tied to DRT_5__drt5 and experimentally verified endogenous DRT5 activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000539",
    "label": "DRT6 system",
    "definition": "A DRT system in which an organism possesses a genome-encoded DefenseFinder DRT6 subtype locus represented by the DRT6__DRT6 profile.",
    "definition_source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000279"
    ],
    "synonyms": [
      {
        "synonym_text": "DRT6",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv"
      },
      {
        "synonym_text": "DRT6__DRT6",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1126/science.aba0372",
        "snippet": "We discovered that a family of uncharacterized reverse transcriptases (RTs) are active defense systems",
        "notes": "Gao et al. experimentally support defense-associated reverse transcriptases as active antiphage systems."
      },
      {
        "reference": "DOI:10.1126/science.aba0372",
        "snippet": "We named these genes defense-associated RTs (DRTs)",
        "notes": "Gao et al. coined the defense-associated RT naming that underlies the DRT system family."
      },
      {
        "reference": "DOI:10.1126/science.aba0372",
        "snippet": "In all cases, mutations in the RT active site [(Y/F)xDD to (Y/F)xAA, where x is any amino acid] abolished activity",
        "notes": "Gao et al. connect DRT antiphage activity to conserved reverse-transcriptase active-site residues."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| DRT | 10\\.1126/science\\.aba0372 | Diverse enzymatic activities mediate antiviral immunity in prokaryotes | ",
        "notes": "The pinned DefenseFinder article registry maps the DRT source key to the Gao et al. prokaryotic antiviral-immunity paper."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| DRT6__DRT6                                       | DRT6__DRT6                                       | DRT6                   | Custom                  | 300    |",
        "notes": "The pinned DefenseFinder HMM inventory records DRT6__DRT6 under the DRT6 model namespace."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "DRT\tDRT6\t1\t1\tDRT6__DRT6\t\t\t",
        "notes": "The pinned DefenseFinder rules table models DRT6 as a DRT subsystem with a DRT6 profile."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "drt6_locus_reverse_transcriptase_defense",
        "title": "DRT6 loci support DRT antiphage defense",
        "description": "Conservative system-level sketch linking a DRT6 locus to reverse-transcriptase-dependent DRT phage defense and DRT6 system possession.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures DRT6 at DefenseFinder subtype-locus level without asserting the direct DRT6 reverse-transcriptase product, phage trigger, native host breadth, sensitive phage breadth, partner features, or whether every DefenseFinder DRT6 prediction is a complete experimentally active DRT6 locus.",
        "nodes": [
          {
            "node_id": "drt6_locus",
            "label": "DRT6 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A defense-associated reverse transcriptase subtype VI locus represented in DefenseFinder by a DRT6 profile."
          },
          {
            "node_id": "drt_rt_active_site_activity",
            "label": "DRT reverse-transcriptase active-site activity",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "Reverse-transcriptase active-site-dependent activity of a defense-associated RT antiphage protein."
          },
          {
            "node_id": "drt6_system_trait",
            "label": "DRT6 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000539",
            "description": "Possession of a genome-encoded DRT6 phage-defense system."
          },
          {
            "node_id": "drt_system_trait",
            "label": "DRT system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000279",
            "description": "Possession of a genome-encoded defense-associated reverse transcriptase phage-defense system."
          }
        ],
        "edges": [
          {
            "subject": "drt6_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "drt_rt_active_site_activity",
            "description": "DRT6 loci are represented in DefenseFinder by a custom defense-associated reverse transcriptase profile.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.aba0372",
                "snippet": "We named these genes defense-associated RTs (DRTs)",
                "notes": "Gao et al. coined the defense-associated RT naming that underlies the DRT system family."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| DRT6__DRT6                                       | DRT6__DRT6                                       | DRT6                   | Custom                  | 300    |",
                "notes": "The pinned DefenseFinder HMM inventory records DRT6__DRT6 under the DRT6 model namespace."
              }
            ]
          },
          {
            "subject": "drt_rt_active_site_activity",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "drt6_system_trait",
            "description": "The first-pass DRT6 system trait is realized by a DefenseFinder DRT6 subtype locus within the reverse-transcriptase-dependent DRT family.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.aba0372",
                "snippet": "We discovered that a family of uncharacterized reverse transcriptases (RTs) are active defense systems",
                "notes": "Gao et al. experimentally support defense-associated reverse transcriptases as active antiphage systems."
              },
              {
                "reference": "DOI:10.1126/science.aba0372",
                "snippet": "In all cases, mutations in the RT active site [(Y/F)xDD to (Y/F)xAA, where x is any amino acid] abolished activity",
                "notes": "Gao et al. connect DRT antiphage activity to conserved reverse-transcriptase active-site residues."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "DRT\tDRT6\t1\t1\tDRT6__DRT6\t\t\t",
                "notes": "The pinned DefenseFinder rules table models DRT6 as a DRT subsystem with a DRT6 profile."
              }
            ]
          },
          {
            "subject": "drt6_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "drt_system_trait",
            "description": "DRT6 system possession is a DRT-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| DRT | 10\\.1126/science\\.aba0372 | Diverse enzymatic activities mediate antiviral immunity in prokaryotes | ",
                "notes": "The pinned DefenseFinder article registry maps the DRT source key to the Gao et al. prokaryotic antiviral-immunity paper."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "DRT\tDRT6\t1\t1\tDRT6__DRT6\t\t\t",
                "notes": "The pinned DefenseFinder rules table models DRT6 as a DRT subsystem with a DRT6 profile."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "drt6-profile-activity-gap",
        "prompt": "Resolve the DRT6 reverse-transcriptase product, direct phage trigger, host breadth, partner-feature requirements, and DefenseFinder profile-to-activity criteria before minting DRT6 mechanism or component children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Gao et al. support defense-associated reverse transcriptases as a broad antiphage-system family, and the pinned DefenseFinder HMM inventory and rules table support DRT6 as a single-profile DRT subsystem. This first-pass record leaves the exact DRT6 RT product, phage trigger, host breadth, partner-feature requirements, and profile-to-activity requirements unresolved.",
        "evidence": [
          {
            "reference": "DOI:10.1126/science.aba0372",
            "snippet": "We discovered that a family of uncharacterized reverse transcriptases (RTs) are active defense systems",
            "notes": "Gao et al. experimentally support defense-associated reverse transcriptases as active antiphage systems."
          },
          {
            "reference": "DOI:10.1126/science.aba0372",
            "snippet": "In all cases, mutations in the RT active site [(Y/F)xDD to (Y/F)xAA, where x is any amino acid] abolished activity",
            "notes": "Gao et al. connect DRT antiphage activity to conserved reverse-transcriptase active-site residues."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| DRT6__DRT6                                       | DRT6__DRT6                                       | DRT6                   | Custom                  | 300    |",
            "notes": "The pinned DefenseFinder HMM inventory records DRT6__DRT6 under the DRT6 model namespace."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "snippet": "DRT\tDRT6\t1\t1\tDRT6__DRT6\t\t\t",
            "notes": "The pinned DefenseFinder rules table models DRT6 as a DRT subsystem with a DRT6 profile."
          }
        ],
        "attaches_to": [
          "causal_graphs#drt6_locus_reverse_transcriptase_defense"
        ],
        "posed_by": "codex",
        "posed_date": "2026-10-02"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-02T08:13:19Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted DRT6 system as a DOI- and DefenseFinder-backed GENOMICS TraitRecord under the DRT system parent after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v416.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-02T08:13:20Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed DRT6 system during initial curation and left canonical_examples empty because Gao et al. and the pinned DefenseFinder tables support the DRT family and the DRT6 model namespace but not an accession-backed native microbial taxon exemplar tied to DRT6__DRT6 and experimentally verified endogenous DRT6 activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000540",
    "label": "DRT7 system",
    "definition": "A DRT system in which an organism possesses a genome-encoded DefenseFinder DRT7 subtype locus represented by the DRT7__DRT7 or DRT7__DRT7_small profiles.",
    "definition_source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000279"
    ],
    "synonyms": [
      {
        "synonym_text": "DRT7",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv"
      },
      {
        "synonym_text": "DRT7__DRT7",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "DRT7__DRT7_small",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1126/science.aba0372",
        "snippet": "We discovered that a family of uncharacterized reverse transcriptases (RTs) are active defense systems",
        "notes": "Gao et al. experimentally support defense-associated reverse transcriptases as active antiphage systems."
      },
      {
        "reference": "DOI:10.1126/science.aba0372",
        "snippet": "We named these genes defense-associated RTs (DRTs)",
        "notes": "Gao et al. coined the defense-associated RT naming that underlies the DRT system family."
      },
      {
        "reference": "DOI:10.1126/science.aba0372",
        "snippet": "In all cases, mutations in the RT active site [(Y/F)xDD to (Y/F)xAA, where x is any amino acid] abolished activity",
        "notes": "Gao et al. connect DRT antiphage activity to conserved reverse-transcriptase active-site residues."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| DRT | 10\\.1126/science\\.aba0372 | Diverse enzymatic activities mediate antiviral immunity in prokaryotes | ",
        "notes": "The pinned DefenseFinder article registry maps the DRT source key to the Gao et al. prokaryotic antiviral-immunity paper."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| DRT7__DRT7                                       | DRT7__DRT7                                       | DRT7                   | Custom                  | 800    |\n| DRT7__DRT7_small                                 | DRT7__DRT7_small                                 | DRT7                   | Custom                  | 500    |",
        "notes": "The pinned DefenseFinder HMM inventory records DRT7__DRT7 and DRT7__DRT7_small under the DRT7 model namespace."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "DRT\tDRT7\t1\t1\tDRT7__DRT7, DRT7__DRT7_small\t\t\t",
        "notes": "The pinned DefenseFinder rules table models DRT7 as a DRT subsystem requiring one of two DRT7 profiles."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "drt7_locus_reverse_transcriptase_defense",
        "title": "DRT7 loci support DRT antiphage defense",
        "description": "Conservative system-level sketch linking a DRT7 locus to reverse-transcriptase-dependent DRT phage defense and DRT7 system possession.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures DRT7 at DefenseFinder subtype-locus level without asserting the direct DRT7 reverse-transcriptase product, phage trigger, native host breadth, sensitive phage breadth, whether the DRT7__DRT7 and DRT7__DRT7_small profiles represent alternative size variants, or whether every DefenseFinder DRT7 prediction is a complete experimentally active DRT7 locus.",
        "nodes": [
          {
            "node_id": "drt7_locus",
            "label": "DRT7 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A defense-associated reverse transcriptase subtype VII locus represented in DefenseFinder by DRT7 profiles."
          },
          {
            "node_id": "drt_rt_active_site_activity",
            "label": "DRT reverse-transcriptase active-site activity",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "Reverse-transcriptase active-site-dependent activity of a defense-associated RT antiphage protein."
          },
          {
            "node_id": "drt7_system_trait",
            "label": "DRT7 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000540",
            "description": "Possession of a genome-encoded DRT7 phage-defense system."
          },
          {
            "node_id": "drt_system_trait",
            "label": "DRT system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000279",
            "description": "Possession of a genome-encoded defense-associated reverse transcriptase phage-defense system."
          }
        ],
        "edges": [
          {
            "subject": "drt7_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "drt_rt_active_site_activity",
            "description": "DRT7 loci are represented in DefenseFinder by custom defense-associated reverse transcriptase profiles.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.aba0372",
                "snippet": "We named these genes defense-associated RTs (DRTs)",
                "notes": "Gao et al. coined the defense-associated RT naming that underlies the DRT system family."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| DRT7__DRT7                                       | DRT7__DRT7                                       | DRT7                   | Custom                  | 800    |\n| DRT7__DRT7_small                                 | DRT7__DRT7_small                                 | DRT7                   | Custom                  | 500    |",
                "notes": "The pinned DefenseFinder HMM inventory records DRT7__DRT7 and DRT7__DRT7_small under the DRT7 model namespace."
              }
            ]
          },
          {
            "subject": "drt_rt_active_site_activity",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "drt7_system_trait",
            "description": "The first-pass DRT7 system trait is realized by a DefenseFinder DRT7 subtype locus within the reverse-transcriptase-dependent DRT family.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.aba0372",
                "snippet": "We discovered that a family of uncharacterized reverse transcriptases (RTs) are active defense systems",
                "notes": "Gao et al. experimentally support defense-associated reverse transcriptases as active antiphage systems."
              },
              {
                "reference": "DOI:10.1126/science.aba0372",
                "snippet": "In all cases, mutations in the RT active site [(Y/F)xDD to (Y/F)xAA, where x is any amino acid] abolished activity",
                "notes": "Gao et al. connect DRT antiphage activity to conserved reverse-transcriptase active-site residues."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "DRT\tDRT7\t1\t1\tDRT7__DRT7, DRT7__DRT7_small\t\t\t",
                "notes": "The pinned DefenseFinder rules table models DRT7 as a DRT subsystem requiring one of two DRT7 profiles."
              }
            ]
          },
          {
            "subject": "drt7_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "drt_system_trait",
            "description": "DRT7 system possession is a DRT-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| DRT | 10\\.1126/science\\.aba0372 | Diverse enzymatic activities mediate antiviral immunity in prokaryotes | ",
                "notes": "The pinned DefenseFinder article registry maps the DRT source key to the Gao et al. prokaryotic antiviral-immunity paper."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "DRT\tDRT7\t1\t1\tDRT7__DRT7, DRT7__DRT7_small\t\t\t",
                "notes": "The pinned DefenseFinder rules table models DRT7 as a DRT subsystem requiring one of two DRT7 profiles."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "drt7-profile-activity-gap",
        "prompt": "Resolve the DRT7 reverse-transcriptase product, direct phage trigger, host breadth, partner-feature requirements, and DRT7__DRT7 versus DRT7__DRT7_small profile-to-activity criteria before minting DRT7 mechanism or component children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Gao et al. support defense-associated reverse transcriptases as a broad antiphage-system family, and the pinned DefenseFinder HMM inventory and rules table support DRT7 as a DRT subsystem with two alternative profiles. This first-pass record leaves the exact DRT7 RT product, phage trigger, host breadth, partner-feature requirements, and profile-to-activity requirements unresolved.",
        "evidence": [
          {
            "reference": "DOI:10.1126/science.aba0372",
            "snippet": "We discovered that a family of uncharacterized reverse transcriptases (RTs) are active defense systems",
            "notes": "Gao et al. experimentally support defense-associated reverse transcriptases as active antiphage systems."
          },
          {
            "reference": "DOI:10.1126/science.aba0372",
            "snippet": "In all cases, mutations in the RT active site [(Y/F)xDD to (Y/F)xAA, where x is any amino acid] abolished activity",
            "notes": "Gao et al. connect DRT antiphage activity to conserved reverse-transcriptase active-site residues."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| DRT7__DRT7                                       | DRT7__DRT7                                       | DRT7                   | Custom                  | 800    |\n| DRT7__DRT7_small                                 | DRT7__DRT7_small                                 | DRT7                   | Custom                  | 500    |",
            "notes": "The pinned DefenseFinder HMM inventory records DRT7__DRT7 and DRT7__DRT7_small under the DRT7 model namespace."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "snippet": "DRT\tDRT7\t1\t1\tDRT7__DRT7, DRT7__DRT7_small\t\t\t",
            "notes": "The pinned DefenseFinder rules table models DRT7 as a DRT subsystem requiring one of two DRT7 profiles."
          }
        ],
        "attaches_to": [
          "causal_graphs#drt7_locus_reverse_transcriptase_defense"
        ],
        "posed_by": "codex",
        "posed_date": "2026-10-02"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-02T09:21:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted DRT7 system as a DOI- and DefenseFinder-backed GENOMICS TraitRecord under the DRT system parent after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v417.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-02T09:21:01Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed DRT7 system during initial curation and left canonical_examples empty because Gao et al. and the pinned DefenseFinder tables support the DRT family and the DRT7 model namespace but not an accession-backed native microbial taxon exemplar tied to DRT7__DRT7 or DRT7__DRT7_small and experimentally verified endogenous DRT7 activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000541",
    "label": "DRT8 system",
    "definition": "A DRT system in which an organism possesses a genome-encoded DefenseFinder DRT8 subtype locus represented by a mandatory DRT8__DRT8 profile, optionally accompanied by the DRT8__DRT8b accessory profile.",
    "definition_source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000279"
    ],
    "synonyms": [
      {
        "synonym_text": "DRT8",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv"
      },
      {
        "synonym_text": "DRT8__DRT8",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "DRT8__DRT8b",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1126/science.aba0372",
        "snippet": "We discovered that a family of uncharacterized reverse transcriptases (RTs) are active defense systems",
        "notes": "Gao et al. experimentally support defense-associated reverse transcriptases as active antiphage systems."
      },
      {
        "reference": "DOI:10.1126/science.aba0372",
        "snippet": "We named these genes defense-associated RTs (DRTs)",
        "notes": "Gao et al. coined the defense-associated RT naming that underlies the DRT system family."
      },
      {
        "reference": "DOI:10.1126/science.aba0372",
        "snippet": "In all cases, mutations in the RT active site [(Y/F)xDD to (Y/F)xAA, where x is any amino acid] abolished activity",
        "notes": "Gao et al. connect DRT antiphage activity to conserved reverse-transcriptase active-site residues."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| DRT | 10\\.1126/science\\.aba0372 | Diverse enzymatic activities mediate antiviral immunity in prokaryotes | ",
        "notes": "The pinned DefenseFinder article registry maps the DRT source key to the Gao et al. prokaryotic antiviral-immunity paper."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| DRT8__DRT8                                       | DRT8__DRT8                                       | DRT8                   | Custom                  | 200    |\n| DRT8__DRT8a                                      |                                                  | DRT8                   | Custom                  | 250    |\n| DRT8__DRT8b                                      | DRT8__DRT8b                                      | DRT8                   | Custom                  | 50     |",
        "notes": "The pinned DefenseFinder HMM inventory records DRT8__DRT8, DRT8__DRT8a, and DRT8__DRT8b under the DRT8 model namespace, with DRT8__DRT8a lacking an emitted HMM name."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "DRT\tDRT8\t1\t1\tDRT8__DRT8\tDRT8__DRT8b\t\t",
        "notes": "The pinned DefenseFinder rules table models DRT8 as a DRT subsystem requiring DRT8__DRT8 and optionally admitting DRT8__DRT8b as accessory."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "drt8_locus_reverse_transcriptase_defense",
        "title": "DRT8 loci support DRT antiphage defense",
        "description": "Conservative system-level sketch linking a DRT8 locus to reverse-transcriptase-dependent DRT phage defense and DRT8 system possession.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures DRT8 at DefenseFinder subtype-locus level without asserting the direct DRT8 reverse-transcriptase product, phage trigger, native host breadth, sensitive phage breadth, the DRT8__DRT8b accessory role, why the DRT8__DRT8a HMM inventory row has no emitted HMM name or rule membership, or whether every DefenseFinder DRT8 prediction is a complete experimentally active DRT8 locus.",
        "nodes": [
          {
            "node_id": "drt8_locus",
            "label": "DRT8 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A defense-associated reverse transcriptase subtype VIII locus represented in DefenseFinder by DRT8 rule profiles."
          },
          {
            "node_id": "drt_rt_active_site_activity",
            "label": "DRT reverse-transcriptase active-site activity",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "Reverse-transcriptase active-site-dependent activity of a defense-associated RT antiphage protein."
          },
          {
            "node_id": "drt8_system_trait",
            "label": "DRT8 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000541",
            "description": "Possession of a genome-encoded DRT8 phage-defense system."
          },
          {
            "node_id": "drt_system_trait",
            "label": "DRT system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000279",
            "description": "Possession of a genome-encoded defense-associated reverse transcriptase phage-defense system."
          }
        ],
        "edges": [
          {
            "subject": "drt8_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "drt_rt_active_site_activity",
            "description": "DRT8 loci are represented in DefenseFinder by custom defense-associated reverse transcriptase profiles.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.aba0372",
                "snippet": "We named these genes defense-associated RTs (DRTs)",
                "notes": "Gao et al. coined the defense-associated RT naming that underlies the DRT system family."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| DRT8__DRT8                                       | DRT8__DRT8                                       | DRT8                   | Custom                  | 200    |\n| DRT8__DRT8a                                      |                                                  | DRT8                   | Custom                  | 250    |\n| DRT8__DRT8b                                      | DRT8__DRT8b                                      | DRT8                   | Custom                  | 50     |",
                "notes": "The pinned DefenseFinder HMM inventory records DRT8__DRT8, DRT8__DRT8a, and DRT8__DRT8b under the DRT8 model namespace, with DRT8__DRT8a lacking an emitted HMM name."
              }
            ]
          },
          {
            "subject": "drt_rt_active_site_activity",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "drt8_system_trait",
            "description": "The first-pass DRT8 system trait is realized by a DefenseFinder DRT8 subtype locus within the reverse-transcriptase-dependent DRT family.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.aba0372",
                "snippet": "We discovered that a family of uncharacterized reverse transcriptases (RTs) are active defense systems",
                "notes": "Gao et al. experimentally support defense-associated reverse transcriptases as active antiphage systems."
              },
              {
                "reference": "DOI:10.1126/science.aba0372",
                "snippet": "In all cases, mutations in the RT active site [(Y/F)xDD to (Y/F)xAA, where x is any amino acid] abolished activity",
                "notes": "Gao et al. connect DRT antiphage activity to conserved reverse-transcriptase active-site residues."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "DRT\tDRT8\t1\t1\tDRT8__DRT8\tDRT8__DRT8b\t\t",
                "notes": "The pinned DefenseFinder rules table models DRT8 as a DRT subsystem requiring DRT8__DRT8 and optionally admitting DRT8__DRT8b as accessory."
              }
            ]
          },
          {
            "subject": "drt8_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "drt_system_trait",
            "description": "DRT8 system possession is a DRT-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| DRT | 10\\.1126/science\\.aba0372 | Diverse enzymatic activities mediate antiviral immunity in prokaryotes | ",
                "notes": "The pinned DefenseFinder article registry maps the DRT source key to the Gao et al. prokaryotic antiviral-immunity paper."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "DRT\tDRT8\t1\t1\tDRT8__DRT8\tDRT8__DRT8b\t\t",
                "notes": "The pinned DefenseFinder rules table models DRT8 as a DRT subsystem requiring DRT8__DRT8 and optionally admitting DRT8__DRT8b as accessory."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "drt8-profile-activity-gap",
        "prompt": "Resolve the DRT8 reverse-transcriptase product, direct phage trigger, host breadth, DRT8__DRT8b accessory role, and DRT8__DRT8a HMM-row status before minting DRT8 mechanism or component children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Gao et al. support defense-associated reverse transcriptases as a broad antiphage-system family, and the pinned DefenseFinder HMM inventory and rules table support DRT8 as a DRT subsystem with a mandatory DRT8__DRT8 profile and an accessory DRT8__DRT8b profile. This first-pass record leaves the exact DRT8 RT product, phage trigger, host breadth, DRT8__DRT8b accessory role, and DRT8__DRT8a inventory-row status unresolved.",
        "evidence": [
          {
            "reference": "DOI:10.1126/science.aba0372",
            "snippet": "We discovered that a family of uncharacterized reverse transcriptases (RTs) are active defense systems",
            "notes": "Gao et al. experimentally support defense-associated reverse transcriptases as active antiphage systems."
          },
          {
            "reference": "DOI:10.1126/science.aba0372",
            "snippet": "In all cases, mutations in the RT active site [(Y/F)xDD to (Y/F)xAA, where x is any amino acid] abolished activity",
            "notes": "Gao et al. connect DRT antiphage activity to conserved reverse-transcriptase active-site residues."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| DRT8__DRT8                                       | DRT8__DRT8                                       | DRT8                   | Custom                  | 200    |\n| DRT8__DRT8a                                      |                                                  | DRT8                   | Custom                  | 250    |\n| DRT8__DRT8b                                      | DRT8__DRT8b                                      | DRT8                   | Custom                  | 50     |",
            "notes": "The pinned DefenseFinder HMM inventory records DRT8__DRT8, DRT8__DRT8a, and DRT8__DRT8b under the DRT8 model namespace, with DRT8__DRT8a lacking an emitted HMM name."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "snippet": "DRT\tDRT8\t1\t1\tDRT8__DRT8\tDRT8__DRT8b\t\t",
            "notes": "The pinned DefenseFinder rules table models DRT8 as a DRT subsystem requiring DRT8__DRT8 and optionally admitting DRT8__DRT8b as accessory."
          }
        ],
        "attaches_to": [
          "causal_graphs#drt8_locus_reverse_transcriptase_defense"
        ],
        "posed_by": "codex",
        "posed_date": "2026-10-02"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-02T09:37:24Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted DRT8 system as a DOI- and DefenseFinder-backed GENOMICS TraitRecord under the DRT system parent after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v418.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-02T09:37:25Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed DRT8 system during initial curation and left canonical_examples empty because Gao et al. and the pinned DefenseFinder tables support the DRT family and the DRT8 model namespace but not an accession-backed native microbial taxon exemplar tied to DRT8__DRT8 or DRT8__DRT8b and experimentally verified endogenous DRT8 activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000542",
    "label": "DRT9 system",
    "definition": "A DRT system in which an organism possesses a genome-encoded DefenseFinder DRT9 subtype locus represented by a mandatory DRT9__DRT9 profile.",
    "definition_source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000279"
    ],
    "synonyms": [
      {
        "synonym_text": "DRT9",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv"
      },
      {
        "synonym_text": "DRT9__DRT9",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1126/science.aba0372",
        "snippet": "We discovered that a family of uncharacterized reverse transcriptases (RTs) are active defense systems",
        "notes": "Gao et al. experimentally support defense-associated reverse transcriptases as active antiphage systems."
      },
      {
        "reference": "DOI:10.1126/science.aba0372",
        "snippet": "We named these genes defense-associated RTs (DRTs)",
        "notes": "Gao et al. coined the defense-associated RT naming that underlies the DRT system family."
      },
      {
        "reference": "DOI:10.1126/science.aba0372",
        "snippet": "In all cases, mutations in the RT active site [(Y/F)xDD to (Y/F)xAA, where x is any amino acid] abolished activity",
        "notes": "Gao et al. connect DRT antiphage activity to conserved reverse-transcriptase active-site residues."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| DRT | 10\\.1126/science\\.aba0372 | Diverse enzymatic activities mediate antiviral immunity in prokaryotes | ",
        "notes": "The pinned DefenseFinder article registry maps the DRT source key to the Gao et al. prokaryotic antiviral-immunity paper."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| DRT9__DRT9                                       | DRT9__DRT9                                       | DRT9                   | Custom                  | 400    |\n| DRT9__SLATT                                      |                                                  | DRT9                   | Custom                  | 40     |",
        "notes": "The pinned DefenseFinder HMM inventory records DRT9__DRT9 and DRT9__SLATT under the DRT9 model namespace, with DRT9__SLATT lacking an emitted HMM name."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "DRT\tDRT9\t1\t1\tDRT9__DRT9\t\t\t",
        "notes": "The pinned DefenseFinder rules table models DRT9 as a DRT subsystem requiring DRT9__DRT9."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "drt9_locus_reverse_transcriptase_defense",
        "title": "DRT9 loci support DRT antiphage defense",
        "description": "Conservative system-level sketch linking a DRT9 locus to reverse-transcriptase-dependent DRT phage defense and DRT9 system possession.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures DRT9 at DefenseFinder subtype-locus level without asserting the direct DRT9 reverse-transcriptase product, phage trigger, native host breadth, sensitive phage breadth, why the DRT9__SLATT HMM inventory row has no emitted HMM name or rule membership, or whether every DefenseFinder DRT9 prediction is a complete experimentally active DRT9 locus.",
        "nodes": [
          {
            "node_id": "drt9_locus",
            "label": "DRT9 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A defense-associated reverse transcriptase subtype IX locus represented in DefenseFinder by DRT9 rule profiles."
          },
          {
            "node_id": "drt_rt_active_site_activity",
            "label": "DRT reverse-transcriptase active-site activity",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "Reverse-transcriptase active-site-dependent activity of a defense-associated RT antiphage protein."
          },
          {
            "node_id": "drt9_system_trait",
            "label": "DRT9 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000542",
            "description": "Possession of a genome-encoded DRT9 phage-defense system."
          },
          {
            "node_id": "drt_system_trait",
            "label": "DRT system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000279",
            "description": "Possession of a genome-encoded defense-associated reverse transcriptase phage-defense system."
          }
        ],
        "edges": [
          {
            "subject": "drt9_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "drt_rt_active_site_activity",
            "description": "DRT9 loci are represented in DefenseFinder by custom defense-associated reverse transcriptase profiles.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.aba0372",
                "snippet": "We named these genes defense-associated RTs (DRTs)",
                "notes": "Gao et al. coined the defense-associated RT naming that underlies the DRT system family."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| DRT9__DRT9                                       | DRT9__DRT9                                       | DRT9                   | Custom                  | 400    |\n| DRT9__SLATT                                      |                                                  | DRT9                   | Custom                  | 40     |",
                "notes": "The pinned DefenseFinder HMM inventory records DRT9__DRT9 and DRT9__SLATT under the DRT9 model namespace, with DRT9__SLATT lacking an emitted HMM name."
              }
            ]
          },
          {
            "subject": "drt_rt_active_site_activity",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "drt9_system_trait",
            "description": "The first-pass DRT9 system trait is realized by a DefenseFinder DRT9 subtype locus within the reverse-transcriptase-dependent DRT family.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.aba0372",
                "snippet": "We discovered that a family of uncharacterized reverse transcriptases (RTs) are active defense systems",
                "notes": "Gao et al. experimentally support defense-associated reverse transcriptases as active antiphage systems."
              },
              {
                "reference": "DOI:10.1126/science.aba0372",
                "snippet": "In all cases, mutations in the RT active site [(Y/F)xDD to (Y/F)xAA, where x is any amino acid] abolished activity",
                "notes": "Gao et al. connect DRT antiphage activity to conserved reverse-transcriptase active-site residues."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "DRT\tDRT9\t1\t1\tDRT9__DRT9\t\t\t",
                "notes": "The pinned DefenseFinder rules table models DRT9 as a DRT subsystem requiring DRT9__DRT9."
              }
            ]
          },
          {
            "subject": "drt9_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "drt_system_trait",
            "description": "DRT9 system possession is a DRT-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| DRT | 10\\.1126/science\\.aba0372 | Diverse enzymatic activities mediate antiviral immunity in prokaryotes | ",
                "notes": "The pinned DefenseFinder article registry maps the DRT source key to the Gao et al. prokaryotic antiviral-immunity paper."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "DRT\tDRT9\t1\t1\tDRT9__DRT9\t\t\t",
                "notes": "The pinned DefenseFinder rules table models DRT9 as a DRT subsystem requiring DRT9__DRT9."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "drt9-profile-activity-gap",
        "prompt": "Resolve the DRT9 reverse-transcriptase product, direct phage trigger, host breadth, and DRT9__SLATT HMM-row status before minting DRT9 mechanism or component children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Gao et al. support defense-associated reverse transcriptases as a broad antiphage-system family, and the pinned DefenseFinder HMM inventory and rules table support DRT9 as a DRT subsystem with a mandatory DRT9__DRT9 profile. This first-pass record leaves the exact DRT9 RT product, phage trigger, host breadth, and DRT9__SLATT inventory-row status unresolved.",
        "evidence": [
          {
            "reference": "DOI:10.1126/science.aba0372",
            "snippet": "We discovered that a family of uncharacterized reverse transcriptases (RTs) are active defense systems",
            "notes": "Gao et al. experimentally support defense-associated reverse transcriptases as active antiphage systems."
          },
          {
            "reference": "DOI:10.1126/science.aba0372",
            "snippet": "In all cases, mutations in the RT active site [(Y/F)xDD to (Y/F)xAA, where x is any amino acid] abolished activity",
            "notes": "Gao et al. connect DRT antiphage activity to conserved reverse-transcriptase active-site residues."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| DRT9__DRT9                                       | DRT9__DRT9                                       | DRT9                   | Custom                  | 400    |\n| DRT9__SLATT                                      |                                                  | DRT9                   | Custom                  | 40     |",
            "notes": "The pinned DefenseFinder HMM inventory records DRT9__DRT9 and DRT9__SLATT under the DRT9 model namespace, with DRT9__SLATT lacking an emitted HMM name."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "snippet": "DRT\tDRT9\t1\t1\tDRT9__DRT9\t\t\t",
            "notes": "The pinned DefenseFinder rules table models DRT9 as a DRT subsystem requiring DRT9__DRT9."
          }
        ],
        "attaches_to": [
          "causal_graphs#drt9_locus_reverse_transcriptase_defense"
        ],
        "posed_by": "codex",
        "posed_date": "2026-10-02"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-02T10:18:34Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted DRT9 system as a DOI- and DefenseFinder-backed GENOMICS TraitRecord under the DRT system parent after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v419.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-02T10:18:35Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed DRT9 system during initial curation and left canonical_examples empty because Gao et al. and the pinned DefenseFinder tables support the DRT family and the DRT9 model namespace but not an accession-backed native microbial taxon exemplar tied to DRT9__DRT9 and experimentally verified endogenous DRT9 activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000279",
    "label": "DRT system",
    "definition": "A phage defense system in which an organism possesses a defense-associated reverse transcriptase locus whose RT-domain component or components can confer bacteriophage defense and are modeled by DefenseFinder as DRT subtypes.",
    "definition_source": "DOI:10.1126/science.aba0372",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "DRT",
        "synonym_type": "EXACT_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      },
      {
        "synonym_text": "defense-associated RT",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1126/science.aba0372"
      },
      {
        "synonym_text": "defense-associated reverse transcriptase",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1126/science.aba0372"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1126/science.aba0372",
        "snippet": "We discovered that a family of uncharacterized reverse transcriptases (RTs) are active defense systems",
        "notes": "Gao et al. experimentally support previously uncharacterized reverse transcriptases as active antiphage defense systems rather than mobile-element RT features alone."
      },
      {
        "reference": "DOI:10.1126/science.aba0372",
        "snippet": "six of these candidates (UG1, UG2, UG3, UG8, UG15, and UG16) provided robust protection against dsDNA phages",
        "notes": "Gao et al. support DRT defense activity across several reverse-transcriptase candidate groups."
      },
      {
        "reference": "DOI:10.1126/science.aba0372",
        "snippet": "We named these genes defense-associated RTs (DRTs)",
        "notes": "Gao et al. coined the defense-associated RT naming that underlies the DRT system label."
      },
      {
        "reference": "DOI:10.1126/science.aba0372",
        "snippet": "In all cases, mutations in the RT active site [(Y/F)xDD to (Y/F)xAA, where x is any amino acid] abolished activity",
        "notes": "Gao et al. connect DRT antiphage activity to conserved reverse-transcriptase active-site residues."
      },
      {
        "reference": "DOI:10.1126/science.aba0372",
        "snippet": "the UG3 (drt3a) and UG8 (drt3b) RTs are components of the same defense system (DRT type 3), with both RTs required for defense activity",
        "notes": "Gao et al. support the multi-component DRT type 3 system while separating it from single-gene DRT subtypes."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "DRT | 10\\.1126/science\\.aba0372 | Diverse enzymatic activities mediate antiviral immunity in prokaryotes",
        "notes": "The DefenseFinder article registry maps the named DRT system to the Gao et al. antiphage-system discovery paper."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "DRT\tDRT_1\t2\t2\tDRT_1__drt1a, DRT_1__drt1b",
        "notes": "The DefenseFinder rules table models DRT_1 as a two-profile DRT subtype."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "DRT_1__drt1a                                     | DRT_1__drt1a                                     | DRT_1",
        "notes": "The DefenseFinder HMM inventory records the drt1a profile in the DRT_1 model namespace."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "drt_reverse_transcriptase_antiphage_defense",
        "title": "DRT loci use reverse transcriptases for antiphage defense",
        "description": "Conservative system-level sketch linking a DRT locus to reverse-transcriptase active-site dependence, subtype-specific bacteriophage resistance, and the DRT system trait.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures DRT systems at the family level while leaving the direct RT products, phage triggers, subtype-specific partner proteins or non-coding RNAs, additional subtype mechanisms, and exact phage targets unresolved.",
        "nodes": [
          {
            "node_id": "drt_locus",
            "label": "DRT locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A defense-associated reverse transcriptase antiphage locus represented by DRT subtype profiles."
          },
          {
            "node_id": "defense_associated_rt_activity",
            "label": "defense-associated RT activity",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "Reverse-transcriptase active-site-dependent activity of DRT antiphage proteins."
          },
          {
            "node_id": "subtype_specific_phage_resistance",
            "label": "subtype-specific phage resistance",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Protection against particular bacteriophages by one of several DRT subtypes."
          },
          {
            "node_id": "drt_system_trait",
            "label": "DRT system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000279",
            "description": "Possession of a genome-encoded defense-associated reverse transcriptase phage defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "drt_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "defense_associated_rt_activity",
            "description": "DRT loci encode defense-associated RT-domain proteins.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.aba0372",
                "snippet": "We named these genes defense-associated RTs (DRTs)",
                "notes": "Gao et al. connect the DRT name to reverse-transcriptase defense genes."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "DRT_1__drt1a                                     | DRT_1__drt1a                                     | DRT_1",
                "notes": "DefenseFinder includes drt1a in the custom DRT_1 model profile inventory."
              }
            ]
          },
          {
            "subject": "defense_associated_rt_activity",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "subtype_specific_phage_resistance",
            "description": "Conserved reverse-transcriptase active-site residues are required for DRT-mediated defense activity.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.aba0372",
                "snippet": "In all cases, mutations in the RT active site [(Y/F)xDD to (Y/F)xAA, where x is any amino acid] abolished activity",
                "notes": "Gao et al. show DRT antiphage activity requires RT active-site residues."
              }
            ]
          },
          {
            "subject": "drt_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "subtype_specific_phage_resistance",
            "description": "Experimentally reconstructed DRT candidate systems provide protection against dsDNA phages.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.aba0372",
                "snippet": "six of these candidates (UG1, UG2, UG3, UG8, UG15, and UG16) provided robust protection against dsDNA phages",
                "notes": "Gao et al. support DRT loci as defensive against bacteriophages in heterologous reconstruction assays."
              },
              {
                "reference": "DOI:10.1126/science.aba0372",
                "snippet": "the UG3 (drt3a) and UG8 (drt3b) RTs are components of the same defense system (DRT type 3), with both RTs required for defense activity",
                "notes": "Gao et al. support multi-component DRT type 3 as one DRT-system subtype."
              }
            ]
          },
          {
            "subject": "subtype_specific_phage_resistance",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "drt_system_trait",
            "description": "DefenseFinder models DRT as a phage-defense system with subtype models such as DRT_1.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "DRT\tDRT_1\t2\t2\tDRT_1__drt1a, DRT_1__drt1b",
                "notes": "The DefenseFinder rules table supports DRT_1 as a named defense-system subtype model with drt1a and drt1b profiles."
              }
            ]
          },
          {
            "subject": "drt_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "DRT system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "DRT | 10\\.1126/science\\.aba0372 | Diverse enzymatic activities mediate antiviral immunity in prokaryotes",
                "notes": "DefenseFinder associates DRT with the Gao et al. prokaryotic antiviral-immunity paper."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "drt-subtype-mechanism-gap",
        "prompt": "Resolve DRT subtype products, partner RNAs or proteins, phage triggers, and antiphage substrates before minting narrower DRT subtype mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Gao et al. support several active reverse-transcriptase-containing antiphage systems, and DefenseFinder models DRT subtypes such as DRT_1. This first record stays at DRT-family level because the direct products of DRT RT activity, the exact phage triggers, the non-coding RNA role in DRT type 3, and the mechanisms for additional DRT subtypes are not resolved.",
        "attaches_to": [
          "causal_graphs#drt_reverse_transcriptase_antiphage_defense"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-19"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-19T12:30:14Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted DRT system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v156.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000560",
    "label": "Druantia III system",
    "definition": "A Druantia system in which an organism possesses a genome-encoded DefenseFinder Druantia_III subtype locus represented by the Druantia_III rule row requiring both the Druantia_III__DruH and Druantia__DruE_1 profiles.",
    "definition_source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000234"
    ],
    "synonyms": [
      {
        "synonym_text": "Druantia III",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.64898/2026.05.12.724681"
      },
      {
        "synonym_text": "Druantia_III",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv"
      },
      {
        "synonym_text": "Druantia_III__DruH",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "Druantia__DruE_1",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.64898/2026.05.12.724681",
        "snippet": "Druantia III is a late-acting defence where DruH is the likely infection sensor and DruE is a helicase-nuclease effector that engages ssDNA-containing replication intermediates",
        "notes": "Wu et al. support the characterized Druantia III arrangement in which DruH likely senses infection and DruE acts as the helicase-nuclease effector."
      },
      {
        "reference": "DOI:10.64898/2026.05.12.724681",
        "snippet": "we identified 6,885 bacterial genomes encoding complete Druantia III systems, defined by the presence of both DruE and DruH",
        "notes": "Wu et al. support Druantia III as a recurring bacterial DruE/DruH system rather than a single engineered locus."
      },
      {
        "reference": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12458937/",
        "snippet": "Screening 66 phages that could form plaques on the double-deletion strain showed that the strain carrying only Druantia III exhibited at least modest protection (<0.01 EOP or <0.5 SFC) against 3 phages, whereas the strain carrying ARMADA Type II exhibited a much broader range of immunity, with at least modest protection observed against 30 phages.",
        "notes": "Bell et al. support native E. coli ATCC 8739 Druantia III protection in a deletion-resolved panel separating Druantia III from co-located ARMADA Type II activity."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| Druantia | 10\\.1126/science\\.aar4120 | Systematic discovery of antiphage defense systems in the microbial pangenome | ",
        "notes": "The pinned DefenseFinder article registry maps the broad Druantia model namespace to the Doron et al. microbial pangenome antiphage-system discovery paper."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| Druantia__DruE_1                                 | Druantia__DruE_1                                 | Druantia               | Custom                  | 20     |",
        "notes": "The pinned DefenseFinder HMM inventory records the shared Druantia__DruE_1 custom profile listed by the Druantia_III rule row."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| Druantia_III__DruH                               | Druantia_III__DruH                               | Druantia_III           | Custom                  | 20     |",
        "notes": "The pinned DefenseFinder HMM inventory records the Druantia_III__DruH custom profile under the Druantia_III model namespace."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "Druantia\tDruantia_III\t2\t2\tDruantia_III__DruH, Druantia__DruE_1\t\t\t",
        "notes": "The pinned DefenseFinder rules table models Druantia_III as a Druantia subsystem requiring two mandatory matches from Druantia_III__DruH and Druantia__DruE_1 and two genes overall."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:562",
        "taxon_label": "Escherichia coli",
        "note": "Bell et al. screened E. coli ATCC 8739 system-deletion derivatives and observed at least modest phage protection in the derivative retaining only the native Druantia III system.",
        "reference": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12458937/"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "druantia_iii_locus_subtype_defense",
        "title": "Druantia III loci mark a DruH-dependent Druantia subtype",
        "description": "Conservative subtype-level sketch linking a DefenseFinder Druantia_III locus to DruE/DruH-dependent Type III Druantia DNA processing, Druantia III system possession, and its Druantia parent.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures the Druantia_III subtype at DefenseFinder rule-row level without resolving the exact late phage trigger, DruH sensory intermediate, RecBCD dependence, Zorya II synergy, native host breadth beyond the E. coli ATCC 8739 observation, Type I, Type II, or Type IV partner functions, or whether every DefenseFinder Druantia_III prediction is a complete experimentally active locus.",
        "nodes": [
          {
            "node_id": "druantia_iii_locus",
            "label": "Druantia III locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A DefenseFinder Druantia_III subtype locus represented by Druantia_III__DruH and Druantia__DruE_1 profiles."
          },
          {
            "node_id": "druantia_iii_dna_processing",
            "label": "Druantia III DruE/DruH DNA processing",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "DruE helicase-nuclease DNA processing in a DruH-containing Type III Druantia context."
          },
          {
            "node_id": "druantia_iii_system_trait",
            "label": "Druantia III system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000560",
            "description": "Possession of a genome-encoded Druantia III phage-defense system."
          },
          {
            "node_id": "druantia_system_trait",
            "label": "Druantia system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000234",
            "description": "Possession of a genome-encoded Druantia phage-defense system."
          }
        ],
        "edges": [
          {
            "subject": "druantia_iii_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "druantia_iii_dna_processing",
            "description": "Druantia_III loci are represented in DefenseFinder by Druantia_III__DruH and Druantia__DruE_1, and Wu et al. define complete Druantia III systems by the presence of both DruE and DruH.",
            "evidence": [
              {
                "reference": "DOI:10.64898/2026.05.12.724681",
                "snippet": "we identified 6,885 bacterial genomes encoding complete Druantia III systems, defined by the presence of both DruE and DruH",
                "notes": "Wu et al. support Druantia III as a recurring bacterial DruE/DruH system rather than a single engineered locus."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| Druantia__DruE_1                                 | Druantia__DruE_1                                 | Druantia               | Custom                  | 20     |",
                "notes": "The pinned DefenseFinder HMM inventory records the shared Druantia__DruE_1 custom profile listed by the Druantia_III rule row."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| Druantia_III__DruH                               | Druantia_III__DruH                               | Druantia_III           | Custom                  | 20     |",
                "notes": "The pinned DefenseFinder HMM inventory records the Druantia_III__DruH custom profile under the Druantia_III model namespace."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "Druantia\tDruantia_III\t2\t2\tDruantia_III__DruH, Druantia__DruE_1\t\t\t",
                "notes": "The pinned DefenseFinder rules table models Druantia_III as a Druantia subsystem requiring two mandatory matches from Druantia_III__DruH and Druantia__DruE_1 and two genes overall."
              }
            ]
          },
          {
            "subject": "druantia_iii_dna_processing",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "druantia_iii_system_trait",
            "description": "The first-pass Druantia III system trait is realized by a DruE/DruH locus whose late defense uses DruE helicase-nuclease effector activity.",
            "evidence": [
              {
                "reference": "DOI:10.64898/2026.05.12.724681",
                "snippet": "Druantia III is a late-acting defence where DruH is the likely infection sensor and DruE is a helicase-nuclease effector that engages ssDNA-containing replication intermediates",
                "notes": "Wu et al. support the characterized Druantia III arrangement in which DruH likely senses infection and DruE acts as the helicase-nuclease effector."
              }
            ]
          },
          {
            "subject": "druantia_iii_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "druantia_system_trait",
            "description": "Druantia III system possession is a Druantia-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| Druantia | 10\\.1126/science\\.aar4120 | Systematic discovery of antiphage defense systems in the microbial pangenome | ",
                "notes": "The pinned DefenseFinder article registry maps the broad Druantia model namespace to the Doron et al. microbial pangenome antiphage-system discovery paper."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "Druantia\tDruantia_III\t2\t2",
                "notes": "The pinned DefenseFinder rules table places the Druantia_III subsystem under the Druantia system key with two mandatory matches and two genes required."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "druantia-iii-activity-gap",
        "prompt": "Resolve Druantia_III phage triggers, DruH sensory chemistry, RecBCD and Zorya coupling, native host breadth, and profile-to-activity criteria before minting enzyme, trigger, or component children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Wu et al. support Druantia III as a recurring DruE/DruH system in which DruH is the likely infection sensor and DruE is a helicase-nuclease effector, and the pinned DefenseFinder HMM inventory and rules table support Druantia_III as a subtype whose rule row requires the Druantia_III__DruH and Druantia__DruE_1 profiles. Bell et al. support one deletion-resolved native E. coli ATCC 8739 Druantia III protection observation. This first-pass record leaves exact late phage triggers, DruH sensory intermediates, RecBCD dependence, Zorya II coupling, native host breadth beyond ATCC 8739, and profile-to-activity criteria unresolved.",
        "evidence": [
          {
            "reference": "DOI:10.64898/2026.05.12.724681",
            "snippet": "Druantia III is a late-acting defence where DruH is the likely infection sensor and DruE is a helicase-nuclease effector that engages ssDNA-containing replication intermediates",
            "notes": "Wu et al. support the characterized Druantia III arrangement in which DruH likely senses infection and DruE acts as the helicase-nuclease effector."
          },
          {
            "reference": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12458937/",
            "snippet": "Screening 66 phages that could form plaques on the double-deletion strain showed that the strain carrying only Druantia III exhibited at least modest protection (<0.01 EOP or <0.5 SFC) against 3 phages, whereas the strain carrying ARMADA Type II exhibited a much broader range of immunity, with at least modest protection observed against 30 phages.",
            "notes": "Bell et al. support native E. coli ATCC 8739 Druantia III protection in a deletion-resolved panel separating Druantia III from co-located ARMADA Type II activity."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| Druantia_III__DruH                               | Druantia_III__DruH                               | Druantia_III           | Custom                  | 20     |",
            "notes": "The pinned DefenseFinder HMM inventory records the Druantia_III__DruH custom profile under the Druantia_III model namespace."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "snippet": "Druantia\tDruantia_III\t2\t2\tDruantia_III__DruH, Druantia__DruE_1\t\t\t",
            "notes": "The pinned DefenseFinder rules table models Druantia_III as a Druantia subsystem requiring two mandatory matches from Druantia_III__DruH and Druantia__DruE_1 and two genes overall."
          }
        ],
        "attaches_to": [
          "causal_graphs#druantia_iii_locus_subtype_defense"
        ],
        "posed_by": "codex",
        "posed_date": "2026-10-03"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-03T00:37:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Druantia III system as a DOI- and DefenseFinder-backed GENOMICS TraitRecord under the Druantia system parent after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record for the target local ID, placeholder METPO ID, proposal cohort, record slug, human label, DefenseFinder subsystem, DruH profile, or shared DruE_1 profile; existing Druantia III mentions were supporting evidence on broad Druantia or ARMADA records, not an exact child TraitRecord, and the replacement placeholder is reserved in proposals/metpo_traitmech_v437.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-03T00:37:02Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE",
        "changes": "Reviewed Druantia III system during initial curation and added Escherichia coli because Bell et al. reported a deletion-resolved E. coli ATCC 8739 derivative retaining only native Druantia III activity with modest protection against 3 of 66 screened phages. Broader native host breadth remains unresolved, and no paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000234",
    "label": "Druantia system",
    "definition": "A phage defense system in which an organism possesses a Druantia locus encoding a conserved DruE-family core and subtype-specific partner proteins.",
    "definition_source": "DOI:10.64898/2026.05.12.724681",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "Druantia",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1126/science.aar4120"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1126/science.aar4120",
        "snippet": "Druantia DruABCDE (type I) DruMFGE (type II) DruHE (III) pfam14236, pfam00270, pfam00271, pfam09369, COG1205, pfam00145, COG0270 Helicase, methylase 1,342 1,321 (2.6%)",
        "notes": "Doron et al. reported Druantia as a helicase- and methylase-associated system with Type I, Type II, and Type III locus architectures in their pangenome-scale antiphage system discovery screen."
      },
      {
        "reference": "DOI:10.1126/science.aar4120",
        "snippet": "A Type I system cloned from E. coli UMEA 4076-1 into E. coli MG1655 rendered the engineered strain resistant against 4 of the 6 phages tested",
        "notes": "Doron et al. support Druantia as an experimentally validated phage-defense system rather than a source-only locus label."
      },
      {
        "reference": "DOI:10.64898/2026.05.12.724681",
        "snippet": "There are several subtypes of Druantia that all share the DruE protein but differ in their associated genes",
        "notes": "Preprint v1, not peer-reviewed. Wu et al. support defining a broad Druantia family record around a common DruE component while keeping subtype partners separate."
      },
      {
        "reference": "DOI:10.64898/2026.05.12.724681",
        "snippet": "Druantia III is a late-acting defence where DruH is the likely infection sensor and DruE is a helicase-nuclease effector that engages ssDNA-containing replication intermediates",
        "notes": "Preprint v1, not peer-reviewed. Wu et al. support the characterized Type III arrangement in which DruH likely senses infection and DruE acts as the helicase-nuclease effector."
      },
      {
        "reference": "DOI:10.64898/2026.05.12.724681",
        "snippet": "we identified 6,885 bacterial genomes encoding complete Druantia III systems, defined by the presence of both DruE and DruH",
        "notes": "Preprint v1, not peer-reviewed. Wu et al. support Druantia III as a recurring bacterial DruE/DruH module rather than a single engineered construct."
      },
      {
        "reference": "DOI:10.64898/2026.05.12.724681",
        "snippet": "DruE is the only component shared across Druantia subtypes, suggesting that DNA processing by a DruE-like helicase-nuclease is the conserved core function of Druantia",
        "notes": "Preprint v1, not peer-reviewed. Wu et al. infer a possible conserved DruE-family function from their type-III results and shared DruE. This is a hypothesis, not a demonstrated mechanism for every Druantia subtype."
      },
      {
        "reference": "DOI:10.1093/nar/gkab883",
        "snippet": "the Druantia-like system lacks the type II requisite DruM and DruG proteins, instead encoding a hypothetical protein",
        "notes": "Payne et al., Results and Figure 2C: the recurring type-IV architecture contains DruE and DruF together with the newly named DruL, instead of the type-II DruM/G components. This is a literature-defined system-possession class, not an individual profile. The study tests Zorya III, Hachiman II and Lamassu II, not Druantia IV. Its computational classification does not demonstrate type-IV phage resistance or DruL chemistry."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:562",
        "taxon_label": "Escherichia coli",
        "note": "Doron et al. cloned a Druantia Type I system from E. coli UMEA 4076-1 into E. coli MG1655 and showed that the engineered strain resisted four of six tested phages.",
        "reference": "DOI:10.1126/science.aar4120"
      }
    ],
    "discussions": [
      {
        "discussion_id": "druantia-subtype-mechanism-gap",
        "prompt": "Resolve Druantia subtype mechanisms separately from architecture-based possession classes.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Doron et al. separated Type I DruABCDE, Type II DruMFGE, and Type III DruHE architectures and validated one Type I locus, while Wu et al. define a Type III mechanism in which DruH likely senses infection and DruE engages ssDNA-containing intermediates. Druantia III system now captures the DruE/DruH Type III branch from the pinned Druantia_III DefenseFinder row, but the parent record remains at the DruE-core family level until separate review resolves Type I and Type II partner functions, Type IV partner functions represented by the pinned Druantia_IV HMM rows, exact phage triggers, native host breadth, and Zorya-coupled versus standalone outputs across Druantia loci. Druantia type IV system (traitmech:000577) now captures the DruE/F/L architecture described by Payne et al. (DOI:10.1093/nar/gkab883), without the type-II DruM/G components. This resolves the architectural child, not type-IV experimental defense or partner chemistry. The family definition no longer requires universal helicase-nuclease DNA processing. Wu et al.'s family-wide conservation claim is a hypothesis in a type-III preprint. The overgeneralized parent graph is removed; the characterized III branch remains at traitmech:000560. New proposal v454 replaces the unminted v111 family row without changing the local family identifier or historical TSV. Type I architecture is now represented by traitmech:000578 Druantia type I system: DruB/C/D/E with optional DruA. Doron's optional DUF4338 component and the Ralstonia study's mapping of that domain to DruA qualify the earlier five-gene shorthand. The five-profile PADLOC rule and three-match DefenseFinder threshold are detection criteria, not identical biological definitions. This resolves the type-I architecture lead, not its partner functions or native-host mechanism. Type II architecture is now represented by traitmech:000579 Druantia type II system, defined by DruM/F/G/E possession using DOI:10.1093/nar/gkab883. Hou et al. version 2 (DOI:10.65215/LTSpreprints.2026.06.18.000273, 2026-07-08 preprint) adds Pf-5 DruE biochemistry and a limited heterologous assay, not full-system or native-host phage-defense validation. The architectural lead is resolved; accessory roles and the transition from DNA unwinding to phage restriction remain open.",
        "posed_by": "codex",
        "posed_date": "2026-09-15",
        "evidence": [
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| Druantia_IV__DruE4                               |                                                  | Druantia_IV            | Custom                  | 750    |\n| Druantia_IV__DruF4                               |                                                  | Druantia_IV            | Custom                  | 20     |\n| Druantia_IV__DruL                                |                                                  | Druantia_IV            | Custom                  | 100    |",
            "notes": "The pinned DefenseFinder HMM inventory records Druantia_IV__DruE4, Druantia_IV__DruF4, and Druantia_IV__DruL under the Druantia_IV model namespace."
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-16T00:36:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Druantia system as a DOI-backed GENOMICS TraitRecord under the phage defense system parent after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v111.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-03T00:37:01Z",
        "curator": "codex",
        "action": "TRACK_NARROWER_RECORD",
        "changes": "Documented Druantia III as split out in the open Druantia subtype discussion after minting traitmech:000560 for the DefenseFinder-backed Druantia_III child; Type I, Type II, the pinned Druantia_IV HMM context, Zorya-coupled versus standalone activity, and finer Druantia activation mechanisms remain open.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-03T19:44:00Z",
        "curator": "codex",
        "action": "SCOPE_DRUANTIA_FAMILY_AND_TYPE_IV",
        "changes": "Addressed #1635: removed a universal DNA-processing requirement and the overgeneralized family graph, retaining evidence with preprint/hypothesis qualifiers. Linked the new type-IV architecture child traitmech:000577. The existing III record retains its characterized mechanism; type-IV defense remains unresolved. Proposal v454 supersedes the v111 family row.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-03T20:24:00Z",
        "curator": "codex",
        "action": "TRACK_DRUANTIA_TYPE_I_CLASS",
        "changes": "Linked traitmech:000578 using DOI:10.1126/science.aar4120 and DOI:10.3389/fmicb.2020.00961. Resolved the type-I architecture lead with optional DruA and distinct detector thresholds. Kept family identity, definition, hierarchy, evidence and example unchanged; type-I functions and the type-II lead remain open.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-03T21:24:00Z",
        "curator": "codex",
        "action": "TRACK_NARROWER_RECORD",
        "changes": "Linked traitmech:000579 Druantia II possession using DOI:10.1093/nar/gkab883 and the July 8 version of DOI:10.65215/LTSpreprints.2026.06.18.000273. Resolved the architecture lead while preserving full-system mechanism uncertainty. Family identity, evidence and example are unchanged.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000578",
    "label": "Druantia type I system",
    "definition": "A Druantia system in which an organism possesses a locus encoding DruE together with DruB, DruC and DruD, with or without DruA.",
    "definition_source": "DOI:10.1126/science.aar4120",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000234"
    ],
    "synonyms": [
      {
        "synonym_text": "Type I Druantia system",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.3389/fmicb.2020.00961"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1126/science.aar4120",
        "snippet": "In some cases Type I systems are preceded by a gene annotated as DUF4338",
        "notes": "Doron et al., The Druantia system and Table 1: type I has three partner genes beside DruE, sometimes with an additional DUF4338 gene. The table names DruA/B/C/D/E; the prose does not make DruA universal. The UMEA 4076-1 locus protected engineered E. coli MG1655 against four of six tested phages. Deletion of four tested genes abolished protection; this does not establish universal DruA dependence. Snippet verified in the accepted manuscript, page 7 (PDF page 9), available from the Weizmann institutional repository."
      },
      {
        "reference": "DOI:10.3389/fmicb.2020.00961",
        "snippet": "druA, encodes a large protein with a domain with unknown function (DUF4338)",
        "notes": "The Druantia System section maps DUF4338 to DruA and describes a five-gene DruA/B/C/D/E form as type I in the Ralstonia solanacearum species complex. This independently corroborates component names, not a universal five-gene requirement. UW163 is a genomic prediction here; the authors' suggested functionality is not an infection assay."
      },
      {
        "reference": "https://raw.githubusercontent.com/padlocbio/padloc-db/9e380165633a8d6aef93b5a164cea0f3359bd33f/sys/druantia_type_I.yaml",
        "snippet": "core_genes:\n  - DruA1\n  - DruB1\n  - DruC1\n  - DruD1\n  - DruE1",
        "notes": "Pinned executable PADLOC rule, retrieved 2026-10-03: minimum_core and minimum_total are both 5, maximum_separation is 3, and force_strand is FALSE. Secondary, neutral and prohibited lists contain only NA. This detector requires the five named profiles, including DruA; that is narrower than the literature's optional-DruA architecture, not evidence for universal DruA essentiality."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/definitions/DefenseFinder/Druantia/Druantia_I.xml",
        "snippet": "<model inter_gene_max_space=\"5\" min_mandatory_genes_required=\"1\" min_genes_required=\"3\" vers=\"2.0\">",
        "notes": "Pinned executable DefenseFinder model, retrieved 2026-10-03: Druantia_I__DruA/B/C/D are accessory slots. The mandatory Druantia__DruE_1 slot permits Druantia__DruE_2, Druantia__DruE_3 or Druantia_IV__DruE4 as exchangeables. The model requires only one mandatory and three total matches and has no forbidden slots. A call alone does not establish the complete DruB/C/D/E architecture or active defense. The raw model key is not an exact synonym."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:562",
        "taxon_label": "Escherichia coli",
        "reference": "DOI:10.1126/science.aar4120",
        "note": "Natural possession is limited to the named source strain UMEA 4076-1, not species-wide possession or demonstrated native-host resistance. Doron et al. transferred its type-I locus into E. coli MG1655; protection against four of six tested phages was measured in that engineered recipient. NCBI independently resolves taxon 562 to Escherichia coli."
      }
    ],
    "discussions": [
      {
        "discussion_id": "druantia-type-i-components-and-mechanism",
        "prompt": "Resolve type-I partner functions and reconcile incomplete detector calls.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "DruB/C/D/E with optional DruA is a literature-based architecture class. The five-gene Ralstonia description and PADLOC rule do not override Doron's optional DUF4338 component. Conversely, DefenseFinder's three-match threshold does not establish a complete locus. Missing profiles, incomplete assemblies and engineered deletions do not by themselves establish natural component absence or a new subtype. Full locus context is required, and a genome may encode several Druantia subtypes. The specific functions of type-I partners, the phage trigger, native-host activity and defense breadth remain open. Do not transfer the DruH/type-III helicase-nuclease mechanism to type I, or infer biochemical activity from a DruE profile. No protein examples or causal graph are added without component-resolved functional evidence and accession anchors.",
        "posed_by": "codex",
        "posed_date": "2026-10-03"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-03T20:24:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added Druantia I organism-level possession with optional DruA, two DOI sources, four exact snippets and pinned executable detector rules. Kept natural UMEA 4076-1 possession distinct from engineered MG1655 defense, with NCBITaxon:562 resolved at NCBI. Ignored-and-hidden novelty and allocation searches found no exact record or METPO term; reserved METPO:1053200 in v455. No type-III mechanism or raw detector threshold defines this class.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000579",
    "label": "Druantia type II system",
    "definition": "A Druantia system in which an organism possesses a locus encoding DruE together with DruM, DruF and DruG.",
    "definition_source": "DOI:10.1093/nar/gkab883",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000234"
    ],
    "synonyms": [
      {
        "synonym_text": "Type II Druantia system",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.65215/LTSpreprints.2026.06.18.000273"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1093/nar/gkab883",
        "snippet": "the Druantia-like system lacks the type II requisite DruM and DruG proteins",
        "notes": "Payne et al., Results: Identification of new defence system variants, and Figure 2C: type II contains DruE/F/M/G; the proposed type IV shares DruE/F but replaces the type-II M/G architecture with DruL. This supports locus composition, not experimental dependence of each component in every host. The type-II distribution observed in RefSeq v201 is not a universal taxonomic limit."
      },
      {
        "reference": "DOI:10.65215/LTSpreprints.2026.06.18.000273",
        "snippet": "DruE alone confers limited protection against a subset of coliphages in heterologous expression",
        "notes": "Hou et al., version 2 posted 2026-07-08, not peer reviewed; PDF https://langtaosha.org.cn/lts/en/preprint/download/273/1236, pages 5-6 and 18, Figure 1 and supplementary Figure S2. The Pf-5 druMFGE locus is the source. Purified DruE is an ATP-dependent 3-prime-to-5-prime helicase preferring 3-prime overhangs and forks, with an asymmetric homodimer. Standalone DruE in E. coli BL21 gave limited T7/T1 protection; R1241A reduced protection. Insoluble DruF/G prevented full-system reconstitution. Native-host phage defense and the link from unwinding to restriction remain untested or unresolved. Pf-5 deletion assays under mitomycin C suggest accessory control of toxicity, not a demonstrated defense trigger."
      },
      {
        "reference": "https://raw.githubusercontent.com/padlocbio/padloc-db/9e380165633a8d6aef93b5a164cea0f3359bd33f/sys/druantia_type_II.yaml",
        "snippet": "core_genes:\n  - DruE2\n  - DruF2\n  - DruG2\n  - DruM2",
        "notes": "Pinned executable PADLOC rule, retrieved 2026-10-03: minimum_core and minimum_total are both 4, maximum_separation is 3, and force_strand is FALSE. DruK is secondary, not a required fifth component; neutral and prohibited lists contain only NA. These are detection constraints, not evidence of active defense."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/definitions/DefenseFinder/Druantia/Druantia_II.xml",
        "snippet": "<model inter_gene_max_space=\"5\" min_mandatory_genes_required=\"1\" min_genes_required=\"3\" vers=\"2.0\">",
        "notes": "Pinned executable DefenseFinder model, retrieved 2026-10-03: Druantia_II__DruM/F/G are accessory slots. DruF permits Druantia_IV__DruF4. Mandatory Druantia__DruE_1 permits Druantia__DruE_2, Druantia__DruE_3 or Druantia_IV__DruE4. One mandatory and three total matches are required; no forbidden slots are declared. A call alone need not establish the complete DruM/F/G/E architecture. Exchangeable matches and missing profiles do not establish biological equivalence or component absence."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:220664",
        "taxon_label": "Pseudomonas protegens Pf-5",
        "reference": "DOI:10.65215/LTSpreprints.2026.06.18.000273",
        "note": "Natural locus possession in Pf-5, assembly GCF_000012265.1 identified by Hou et al. version 2, Figure 1a and Methods. Not a native-host phage-resistance example: infection assays used standalone DruE in engineered E. coli. NCBI resolves taxon 220664 to Pseudomonas protegens Pf-5."
      }
    ],
    "discussions": [
      {
        "discussion_id": "druantia-type-ii-full-system-defense-gap",
        "prompt": "Resolve full-system defense and accessory functions beyond isolated DruE assays.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "DruM/F/G/E possession is an architecture class, not an assay result or a universal helicase mechanism. Hou et al. version 2 provides real DruE biochemistry; the remaining gap is not absence of protein evidence. RCSB entry 9WAE entity 1 maps Pf-5 PFL_3016 to UniProtKB:Q4KCB1, a live unreviewed entry checked 2026-10-03. No full-system causal graph is asserted because native-host phage restriction, accessory regulation and the unwinding-to-restriction transition are unresolved. The measured isolated-protein results remain in the evidence notes. Do not transfer type-III nuclease chemistry to type II or turn mitomycin-C growth effects into an infection trigger. A missing profile or incomplete assembly cannot establish component absence; inspect complete locus context. Organism-level subtype possession classes are not disjoint because a genome may encode several loci.",
        "posed_by": "codex",
        "posed_date": "2026-10-03"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-03T21:24:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added literature-defined Druantia II possession with two DOI sources, four exact snippets, pinned executable detector rules and NCBI-resolved Pf-5 possession. Kept the version-2 preprint's isolated DruE assays distinct from full-system and native-host defense. Ignored-and-hidden novelty and allocation searches found no exact record or METPO term; reserved METPO:1053300 in v456. No protein-resolved full-system causal mechanism is asserted.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-03T21:32:00Z",
        "curator": "codex",
        "action": "CORRECT_EVIDENCE_LOCATOR",
        "changes": "Corrected the Payne evidence subsection locator to Results: Identification of new defence system variants after checking primary PMC8565338 XML; the snippet, architecture claim and Figure 2C locator are unchanged. Addresses issue #1639.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000577",
    "label": "Druantia type IV system",
    "definition": "A Druantia system in which an organism possesses a locus encoding DruE and DruF together with DruL, without the type-II DruM and DruG components.",
    "definition_source": "DOI:10.1093/nar/gkab883",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000234"
    ],
    "synonyms": [
      {
        "synonym_text": "Druantia type IV",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1093/nar/gkab883"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1093/nar/gkab883",
        "snippet": "the Druantia-like system lacks the type II requisite DruM and DruG proteins, instead encoding a hypothetical protein",
        "notes": "Payne et al., Results and Figure 2C: the recurring type-IV architecture contains DruE and DruF together with the newly named DruL, instead of the type-II DruM/G components. This is a literature-defined system-possession class, not an individual profile. The study tests Zorya III, Hachiman II and Lamassu II, not Druantia IV. Its computational classification does not demonstrate type-IV phage resistance or DruL chemistry."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/definitions/DefenseFinder/Druantia/Druantia_IV.xml",
        "snippet": "<gene name=\"Druantia_IV__DruL\" presence=\"mandatory\"/>",
        "notes": "Pinned DefenseFinder XML, retrieved 2026-10-03: three mandatory slots, both minimum counts 3, inter_gene_max_space 1. DruL is mandatory; DruE_1 accepts DruE_2, DruE_3 or DruE4 exchangeables, and the Druantia-II DruF slot accepts DruF4. There are no forbidden genes: a call does not establish absence of DruM/G. Check full locus context before assigning the literature-defined architecture. Detection does not establish functional defense."
      },
      {
        "reference": "https://raw.githubusercontent.com/padlocbio/padloc-db/9e380165633a8d6aef93b5a164cea0f3359bd33f/sys/druantia_type_IV.yaml",
        "snippet": "minimum_core: 3\nminimum_total: 3\ncore_genes:\n  - DruE4\n  - DruF4\n  - DruL4",
        "notes": "Pinned PADLOC rule, retrieved 2026-10-03: three required core genes, maximum_separation 3, force_strand FALSE. DruK is secondary, not a required defining component. The prohibited list is NA, so the detector does not test the biological absence of DruM/G. A missing hit or incomplete assembly cannot establish that absence. These are computational constraints, not experimental component essentiality or type-IV mechanism evidence."
      }
    ],
    "discussions": [
      {
        "discussion_id": "druantia-type-iv-functional-and-architecture-gap",
        "prompt": "Resolve type-IV defense activity, DruL function and complete locus boundaries.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "The sources support a recurring organism-level DruE/F/L locus architecture distinct from type-II DruM/F/G/E, not a measured resistance phenotype. A complete accession-resolved natural locus, independently resolved taxon and type-IV-specific functional assays remain to be curated before adding a canonical example or causal mechanism graph. DruE helicase/nuclease activity established for type III is not generalized to type IV. DruL and optional DruK roles remain unresolved by this evidence bundle. Neither executable detector forbids DruM/G; mixed or incomplete calls require biological locus review, not automatic conversion to this absence-qualified class. No individual protein, HMM hit, source key, unverified xref or mutually disjoint organism-level possession is asserted.",
        "posed_by": "codex",
        "posed_date": "2026-10-03"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-03T19:44:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added the literature-defined DruE/F/L possession class with a DOI and two pinned executable models, each with an exact snippet. Ignored-and-hidden novelty searches found no exact METPO or live record. Reserved METPO:1053101 in v454, below corrected family placeholder METPO:1053100. Kept computational architecture and component absence distinct from detector calls and measured defense.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000434",
    "label": "DS-10 system",
    "definition": "A phage defense system in which an organism possesses the single-gene DefensePredictor-discovered system 10 locus cataloged as working transcriptional unit ZAPB and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.",
    "definition_source": "DOI:10.1126/science.adv7924",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "DS-10",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1126/science.adv7924"
      },
      {
        "synonym_text": "ZAPB",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx"
      },
      {
        "synonym_text": "DS-10__DS-10",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1126/science.adv7924",
        "snippet": "To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
        "notes": "DeWeirdt et al. experimentally validated 42 predicted transcriptional units as phage-defense systems in E. coli."
      },
      {
        "reference": "DOI:10.1126/science.adv7924",
        "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
        "notes": "DeWeirdt et al. name validated transcriptional units as DefensePredictor discovered systems."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
        "snippet": "ZAPB\tNZ_QOWZ01000021.1\tGCF_003334705.1\t+\tTrue\tFalse\tFalse\tTrue\tDefensePredictor hits\t74276\t75694\thypothetical protein\tWP_087897267.1\t3.3510039243908\t-0.2574120081490247\tTrue\tFalse\tPredicted novel defense gene\tDS-10",
        "notes": "The final Science supplementary Table S6 maps working_id ZAPB to DS_name DS-10, marks the cloned transcriptional unit as defensive, and records NZ_QOWZ01000021.1 positions 74276-75694 with product accession WP_087897267.1."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
        "snippet": "ZAPB\tDS-10\tTrue",
        "notes": "The final Science supplementary Table S8 maps ZAPB to replicated display name DS-10."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| DS-10 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
        "notes": "The pinned DefenseFinder article registry maps the DS-10 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| DS-10__DS-10                                     |                                                  | DS-10                  | Custom                  | 200    |",
        "notes": "The pinned DefenseFinder HMM inventory records DS-10__DS-10 as a custom DS-10 profile."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "ds_10_locus_reduces_phage_plaquing",
        "title": "DS-10 locus reduces bacteriophage plaquing",
        "description": "Conservative system-level sketch linking the single-gene DS-10 locus to reduced bacteriophage plaquing without resolving DS-10 component function or effector activity.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures DS-10 as the validated ZAPB transcriptional unit with one product accession and with a DefenseFinder DS-10 profile row. It does not assert native host breadth, exact profile-to-protein correspondence, the direct viral trigger or substrate, exact molecular output, phage target breadth, final Table S7 per-phage readouts, HHPred domain annotations, or DefenseFinder rule-level detection criteria.",
        "nodes": [
          {
            "node_id": "ds_10_locus",
            "label": "DS-10 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A single-gene DefensePredictor-discovered system locus represented in the pinned DefenseFinder HMM inventory by one DS-10 custom profile."
          },
          {
            "node_id": "reduced_phage_plaquing",
            "label": "reduced bacteriophage plaquing",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced bacteriophage plaquing by cells carrying cloned ZAPB."
          },
          {
            "node_id": "ds_10_system_trait",
            "label": "DS-10 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000434",
            "description": "Possession of a genome-encoded DS-10 phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "ds_10_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "reduced_phage_plaquing",
            "description": "The DS-10/ZAPB locus contributes to reduced bacteriophage plaquing when plasmid expressed.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
                "notes": "DeWeirdt et al. experimentally validate DefensePredictor-discovered systems by assaying cloned transcriptional units against E. coli phages."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
                "snippet": "ZAPB\tNZ_QOWZ01000021.1\tGCF_003334705.1\t+\tTrue\tFalse\tFalse\tTrue\tDefensePredictor hits\t74276\t75694\thypothetical protein\tWP_087897267.1\t3.3510039243908\t-0.2574120081490247\tTrue\tFalse\tPredicted novel defense gene\tDS-10",
                "notes": "The final Science supplementary Table S6 maps working_id ZAPB to DS_name DS-10, marks the cloned transcriptional unit as defensive, and records NZ_QOWZ01000021.1 positions 74276-75694 with product accession WP_087897267.1."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| DS-10__DS-10                                     |                                                  | DS-10                  | Custom                  | 200    |",
                "notes": "The pinned DefenseFinder HMM inventory records DS-10__DS-10 as a custom DS-10 profile."
              }
            ]
          },
          {
            "subject": "reduced_phage_plaquing",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "ds_10_system_trait",
            "description": "DS-10-mediated phage plaquing reduction realizes the DS-10 system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
                "notes": "DeWeirdt et al. name each validated transcriptional unit as a DefensePredictor discovered system."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
                "snippet": "ZAPB\tNZ_QOWZ01000021.1\tGCF_003334705.1\t+\tTrue\tFalse\tFalse\tTrue\tDefensePredictor hits\t74276\t75694\thypothetical protein\tWP_087897267.1\t3.3510039243908\t-0.2574120081490247\tTrue\tFalse\tPredicted novel defense gene\tDS-10",
                "notes": "The final Science supplementary Table S6 maps working_id ZAPB to DS_name DS-10, marks the cloned transcriptional unit as defensive, and records NZ_QOWZ01000021.1 positions 74276-75694 with product accession WP_087897267.1."
              }
            ]
          },
          {
            "subject": "ds_10_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "DS-10 system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
                "notes": "DeWeirdt et al. validate DSs as anti-phage systems."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| DS-10 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
                "notes": "The pinned DefenseFinder article registry maps the DS-10 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "ds-10-defensefinder-model-gap",
        "prompt": "Resolve DS-10 native host breadth, exact DS-10 component function, sensitive-phage breadth, molecular output, HHPred domain support, per-phage Table S7 readouts, and rule-level detection criteria before minting narrower DS-10 mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "DeWeirdt et al. support DS-10 as the defensive ZAPB transcriptional unit that reduced plaquing when cloned in E. coli MG1655, and the pinned DefenseFinder HMM inventory records one DS-10 profile row. The final Table S7 and HHPred-domain sheets have no ZAPB rows, the pinned rules table has no DS-10 row, and the first-pass record does not resolve native host breadth, exact component activity, phage target breadth, the direct molecular output, or endogenous DS-10 activity.",
        "evidence": [
          {
            "reference": "DOI:10.1126/science.adv7924",
            "snippet": "To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
            "notes": "DeWeirdt et al. validate predicted transcriptional units by measuring plaquing relative to an empty vector control strain."
          },
          {
            "reference": "DOI:10.1126/science.adv7924",
            "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
            "notes": "DeWeirdt et al. name validated TUs as DSs."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
            "snippet": "ZAPB\tNZ_QOWZ01000021.1\tGCF_003334705.1\t+\tTrue\tFalse\tFalse\tTrue\tDefensePredictor hits\t74276\t75694\thypothetical protein\tWP_087897267.1\t3.3510039243908\t-0.2574120081490247\tTrue\tFalse\tPredicted novel defense gene\tDS-10",
            "notes": "The final Science supplementary Table S6 maps working_id ZAPB to DS_name DS-10, marks the cloned transcriptional unit as defensive, and records NZ_QOWZ01000021.1 positions 74276-75694 with product accession WP_087897267.1."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
            "snippet": "ZAPB\tDS-10\tTrue",
            "notes": "The final Science supplementary Table S8 maps ZAPB to replicated display name DS-10."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
            "snippet": "| DS-10 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
            "notes": "The pinned DefenseFinder article registry maps the DS-10 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| DS-10__DS-10                                     |                                                  | DS-10                  | Custom                  | 200    |",
            "notes": "The pinned DefenseFinder HMM inventory records DS-10__DS-10 as a custom DS-10 profile."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "The pinned DefenseFinder rules table does not list DS-10, leaving rule-level detection criteria unresolved."
          }
        ],
        "attaches_to": [
          "causal_graphs#ds_10_locus_reduces_phage_plaquing"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-28"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-28T12:48:52Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted DS-10 system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; kept the graph at cloned ZAPB transcriptional unit level because the pinned DefenseFinder DS-10 HMM row is not backed by a rules row; proposals/metpo_traitmech_v311 reserves the replacement placeholder.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-28T12:48:53Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed DS-10 system canonical_examples and left them empty because DeWeirdt et al. support cloned ZAPB plaquing assays in E. coli MG1655 plus a DefenseFinder DS-10 model, but not a direct named native microbial isolate exemplar with experimentally verified endogenous DS-10 activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000435",
    "label": "DS-11 system",
    "definition": "A phage defense system in which an organism possesses the single-gene DefensePredictor-discovered system 11 locus cataloged as working transcriptional unit IMPD and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.",
    "definition_source": "DOI:10.1126/science.adv7924",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "DS-11",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1126/science.adv7924"
      },
      {
        "synonym_text": "IMPD",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx"
      },
      {
        "synonym_text": "DS-11__DS-11",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1126/science.adv7924",
        "snippet": "To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
        "notes": "DeWeirdt et al. experimentally validated 42 predicted transcriptional units as phage-defense systems in E. coli."
      },
      {
        "reference": "DOI:10.1126/science.adv7924",
        "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
        "notes": "DeWeirdt et al. name validated transcriptional units as DefensePredictor discovered systems."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
        "snippet": "IMPD\tNZ_RRVY01000003.1\tGCF_003886375.1\t+\tTrue\tFalse\tFalse\tTrue\tDefensePredictor hits\t365785\t366882\tCBS domain-containing protein\tWP_000257686.1\t4.37610109478113\t1.840433765255303\tTrue\tTrue\tPredicted novel defense gene\tDS-11",
        "notes": "The final Science supplementary Table S6 maps working_id IMPD to DS_name DS-11, marks the cloned transcriptional unit as defensive, and records NZ_RRVY01000003.1 positions 365785-366882 with product accession WP_000257686.1."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
        "snippet": "T3\t1.1\tpLAND\t24-03-08_NYND_PIN2_MHAD_EV.png\t300000000\tIMPD\t24-03-08\t24-03-08_MNAC_GHOS_BRNT_IMPD.png\t5\t3\t\t300000\t3\tTrue\t\t\tLB\t37",
        "notes": "The final Science supplementary Table S7 reports an IMPD assay row with a T3 phage readout and a -log(EOP) value of 3.0."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
        "snippet": "T3\tB.2\tMG1655\t24-07-17_AAA2_VPUS_VAME_EV.png\t200000000\tIMPD\t\t24-07-18\t24-07-18_IMPD-Y157A_IMPD_IMPD-R330A_IMPD-H335A_HIPA_HIPA-D139A.png\t5\t4\t\t400000\t2.698970004\nBas67\tB.2\tMG1655\t24-07-17_AAA2_VPUS_VAME_EV.png\t20000000\tIMPD\t\t24-07-18\t24-07-18_IMPD-Y157A_IMPD_IMPD-R330A_IMPD-H335A_HIPA_HIPA-D139A.png\t5\t5\t\t500000\t1.602059991\nT3\tB.2\tMG1655\t24-07-17_AAA2_VPUS_VAME_EV.png\t200000000\tIMPD\tY157A\t24-07-18\t24-07-18_IMPD-Y157A_IMPD_IMPD-R330A_IMPD-H335A_HIPA_HIPA-D139A.png\t8\t2\t\t200000000\t0\nBas67\tB.2\tMG1655\t24-07-17_AAA2_VPUS_VAME_EV.png\t20000000\tIMPD\tY157A\t24-07-18\t24-07-18_IMPD-Y157A_IMPD_IMPD-R330A_IMPD-H335A_HIPA_HIPA-D139A.png\t7\t2\t\t20000000\t0\nT3\tB.2\tMG1655\t24-07-17_AAA2_VPUS_VAME_EV.png\t200000000\tIMPD\tR330A\t24-07-18\t24-07-18_IMPD-Y157A_IMPD_IMPD-R330A_IMPD-H335A_HIPA_HIPA-D139A.png\t8\t3\t\t300000000\t-0.1760912591\nBas67\tB.2\tMG1655\t24-07-17_AAA2_VPUS_VAME_EV.png\t20000000\tIMPD\tR330A\t24-07-18\t24-07-18_IMPD-Y157A_IMPD_IMPD-R330A_IMPD-H335A_HIPA_HIPA-D139A.png\t7\t3\t\t30000000\t-0.1760912591\nT3\tB.2\tMG1655\t24-07-17_AAA2_VPUS_VAME_EV.png\t200000000\tIMPD\tH335A\t24-07-18\t24-07-18_IMPD-Y157A_IMPD_IMPD-R330A_IMPD-H335A_HIPA_HIPA-D139A.png\t8\t1\t\t100000000\t0.3010299957\nBas67\tB.2\tMG1655\t24-07-17_AAA2_VPUS_VAME_EV.png\t20000000\tIMPD\tH335A\t24-07-18\t24-07-18_IMPD-Y157A_IMPD_IMPD-R330A_IMPD-H335A_HIPA_HIPA-D139A.png\t6\t6\t\t6000000\t0.5228787453",
        "notes": "The final Science supplementary Table S7 System Mutants sheet pairs wild-type IMPD with IMPD Y157A, R330A, and H335A rows in T3 and Bas67 assay panels."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
        "snippet": "IMPD\tDS-11\tTrue",
        "notes": "The final Science supplementary Table S8 maps IMPD to replicated display name DS-11."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
        "snippet": "IMPD\t1.0\t365.0\tWP_000257686.1\tHEPN\tPF18731.5\tHEPN_Swt1 ; Swt1-like HEPN\thhpred_1021051.hhr\t252.0\t359.0\t0.98\t2024-04-16 00:00:00",
        "notes": "The final Science supplementary Table S8 reports a HEPN HHpred hit for WP_000257686.1 in IMPD."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
        "snippet": "IMPD\t1.0\t365.0\tWP_000257686.1\tCBS\tcd04614\tCBS_pair_arch2_repeat2; Two tandem repeats of the cystathionine beta-synthase (CBS pair) domains present in archaea\thhpred_1021051.hhr\t134.0\t241.0\t0.9916\t2024-04-16 00:00:00",
        "notes": "The final Science supplementary Table S8 reports a CBS HHpred hit for WP_000257686.1 in IMPD."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| DS-11 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
        "notes": "The pinned DefenseFinder article registry maps the DS-11 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| DS-11__DS-11                                     |                                                  | DS-11                  | Custom                  | 100    |",
        "notes": "The pinned DefenseFinder HMM inventory records DS-11__DS-11 as a custom DS-11 profile."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "ds_11_locus_reduces_phage_plaquing",
        "title": "DS-11 locus reduces bacteriophage plaquing",
        "description": "Conservative system-level sketch linking the single-gene DS-11 locus to reduced bacteriophage plaquing without resolving DS-11 component function or effector activity.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures DS-11 as the validated IMPD transcriptional unit with one product accession, final Table S8 HEPN and CBS HHpred-domain rows, and one DefenseFinder DS-11 profile row. It does not assert native host breadth, exact profile-to-protein correspondence, the direct viral trigger or ligand, the HEPN substrate, whether ATP binding or CBS-ligand binding activates the effector, phage target breadth, or DefenseFinder rule-level detection criteria.",
        "nodes": [
          {
            "node_id": "ds_11_locus",
            "label": "DS-11 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A single-gene DefensePredictor-discovered system locus represented in the pinned DefenseFinder HMM inventory by one DS-11 custom profile."
          },
          {
            "node_id": "reduced_phage_plaquing",
            "label": "reduced bacteriophage plaquing",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced bacteriophage plaquing by cells carrying cloned IMPD."
          },
          {
            "node_id": "ds_11_system_trait",
            "label": "DS-11 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000435",
            "description": "Possession of a genome-encoded DS-11 phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "ds_11_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "reduced_phage_plaquing",
            "description": "The DS-11/IMPD locus contributes to reduced bacteriophage plaquing when plasmid expressed.",
            "evidence": [
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
                "snippet": "IMPD\tNZ_RRVY01000003.1\tGCF_003886375.1\t+\tTrue\tFalse\tFalse\tTrue\tDefensePredictor hits\t365785\t366882\tCBS domain-containing protein\tWP_000257686.1\t4.37610109478113\t1.840433765255303\tTrue\tTrue\tPredicted novel defense gene\tDS-11",
                "notes": "The final Science supplementary Table S6 maps working_id IMPD to DS_name DS-11, marks the cloned transcriptional unit as defensive, and records NZ_RRVY01000003.1 positions 365785-366882 with product accession WP_000257686.1."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
                "snippet": "T3\t1.1\tpLAND\t24-03-08_NYND_PIN2_MHAD_EV.png\t300000000\tIMPD\t24-03-08\t24-03-08_MNAC_GHOS_BRNT_IMPD.png\t5\t3\t\t300000\t3\tTrue\t\t\tLB\t37",
                "notes": "The final Science supplementary Table S7 reports an IMPD assay row with a T3 phage readout and a -log(EOP) value of 3.0."
              }
            ]
          },
          {
            "subject": "reduced_phage_plaquing",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "ds_11_system_trait",
            "description": "DS-11-mediated phage plaquing reduction realizes the DS-11 system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
                "notes": "DeWeirdt et al. name each validated transcriptional unit as a DefensePredictor discovered system."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
                "snippet": "IMPD\tNZ_RRVY01000003.1\tGCF_003886375.1\t+\tTrue\tFalse\tFalse\tTrue\tDefensePredictor hits\t365785\t366882\tCBS domain-containing protein\tWP_000257686.1\t4.37610109478113\t1.840433765255303\tTrue\tTrue\tPredicted novel defense gene\tDS-11",
                "notes": "The final Science supplementary Table S6 maps working_id IMPD to DS_name DS-11, marks the cloned transcriptional unit as defensive, and records NZ_RRVY01000003.1 positions 365785-366882 with product accession WP_000257686.1."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
                "snippet": "T3\t1.1\tpLAND\t24-03-08_NYND_PIN2_MHAD_EV.png\t300000000\tIMPD\t24-03-08\t24-03-08_MNAC_GHOS_BRNT_IMPD.png\t5\t3\t\t300000\t3\tTrue\t\t\tLB\t37",
                "notes": "The final Science supplementary Table S7 reports an IMPD assay row with a T3 phage readout and a -log(EOP) value of 3.0."
              }
            ]
          },
          {
            "subject": "ds_11_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "DS-11 system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
                "notes": "DeWeirdt et al. validate DSs as anti-phage systems."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| DS-11 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
                "notes": "The pinned DefenseFinder article registry maps the DS-11 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "ds-11-defensefinder-model-gap",
        "prompt": "Resolve DS-11 native host breadth, profile-to-protein mapping, sensitive-phage breadth, direct viral trigger, direct HEPN-family nuclease substrate, CBS-ligand or ATP-dependent activation model, and rule-level detection criteria before minting narrower DS-11 mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "DeWeirdt et al. support DS-11 as the defensive IMPD transcriptional unit that reduced T3 and Bas67 plaquing when cloned in E. coli MG1655, and the final Table S8 HHpred sheet reports HEPN and CBS hits for the single IMPD product. The pinned DefenseFinder HMM inventory records one DS-11 profile row, the pinned rules table has no DS-11 row, and the first-pass record does not resolve native host breadth, exact profile-to-protein correspondence, the direct HEPN substrate, the activation ligand, phage target breadth, or endogenous DS-11 activity.",
        "evidence": [
          {
            "reference": "DOI:10.1126/science.adv7924",
            "snippet": "To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
            "notes": "DeWeirdt et al. validate predicted transcriptional units by measuring plaquing relative to an empty vector control strain."
          },
          {
            "reference": "DOI:10.1126/science.adv7924",
            "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
            "notes": "DeWeirdt et al. name validated TUs as DSs."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
            "snippet": "IMPD\tNZ_RRVY01000003.1\tGCF_003886375.1\t+\tTrue\tFalse\tFalse\tTrue\tDefensePredictor hits\t365785\t366882\tCBS domain-containing protein\tWP_000257686.1\t4.37610109478113\t1.840433765255303\tTrue\tTrue\tPredicted novel defense gene\tDS-11",
            "notes": "The final Science supplementary Table S6 maps working_id IMPD to DS_name DS-11, marks the cloned transcriptional unit as defensive, and records NZ_RRVY01000003.1 positions 365785-366882 with product accession WP_000257686.1."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
            "snippet": "T3\t1.1\tpLAND\t24-03-08_NYND_PIN2_MHAD_EV.png\t300000000\tIMPD\t24-03-08\t24-03-08_MNAC_GHOS_BRNT_IMPD.png\t5\t3\t\t300000\t3\tTrue\t\t\tLB\t37",
            "notes": "The final Science supplementary Table S7 reports an IMPD assay row with a T3 phage readout and a -log(EOP) value of 3.0."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
            "snippet": "T3\tB.2\tMG1655\t24-07-17_AAA2_VPUS_VAME_EV.png\t200000000\tIMPD\t\t24-07-18\t24-07-18_IMPD-Y157A_IMPD_IMPD-R330A_IMPD-H335A_HIPA_HIPA-D139A.png\t5\t4\t\t400000\t2.698970004\nBas67\tB.2\tMG1655\t24-07-17_AAA2_VPUS_VAME_EV.png\t20000000\tIMPD\t\t24-07-18\t24-07-18_IMPD-Y157A_IMPD_IMPD-R330A_IMPD-H335A_HIPA_HIPA-D139A.png\t5\t5\t\t500000\t1.602059991\nT3\tB.2\tMG1655\t24-07-17_AAA2_VPUS_VAME_EV.png\t200000000\tIMPD\tY157A\t24-07-18\t24-07-18_IMPD-Y157A_IMPD_IMPD-R330A_IMPD-H335A_HIPA_HIPA-D139A.png\t8\t2\t\t200000000\t0\nBas67\tB.2\tMG1655\t24-07-17_AAA2_VPUS_VAME_EV.png\t20000000\tIMPD\tY157A\t24-07-18\t24-07-18_IMPD-Y157A_IMPD_IMPD-R330A_IMPD-H335A_HIPA_HIPA-D139A.png\t7\t2\t\t20000000\t0\nT3\tB.2\tMG1655\t24-07-17_AAA2_VPUS_VAME_EV.png\t200000000\tIMPD\tR330A\t24-07-18\t24-07-18_IMPD-Y157A_IMPD_IMPD-R330A_IMPD-H335A_HIPA_HIPA-D139A.png\t8\t3\t\t300000000\t-0.1760912591\nBas67\tB.2\tMG1655\t24-07-17_AAA2_VPUS_VAME_EV.png\t20000000\tIMPD\tR330A\t24-07-18\t24-07-18_IMPD-Y157A_IMPD_IMPD-R330A_IMPD-H335A_HIPA_HIPA-D139A.png\t7\t3\t\t30000000\t-0.1760912591\nT3\tB.2\tMG1655\t24-07-17_AAA2_VPUS_VAME_EV.png\t200000000\tIMPD\tH335A\t24-07-18\t24-07-18_IMPD-Y157A_IMPD_IMPD-R330A_IMPD-H335A_HIPA_HIPA-D139A.png\t8\t1\t\t100000000\t0.3010299957\nBas67\tB.2\tMG1655\t24-07-17_AAA2_VPUS_VAME_EV.png\t20000000\tIMPD\tH335A\t24-07-18\t24-07-18_IMPD-Y157A_IMPD_IMPD-R330A_IMPD-H335A_HIPA_HIPA-D139A.png\t6\t6\t\t6000000\t0.5228787453",
            "notes": "The final Science supplementary Table S7 System Mutants sheet pairs wild-type IMPD with IMPD Y157A, R330A, and H335A rows in T3 and Bas67 assay panels."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
            "snippet": "IMPD\tDS-11\tTrue",
            "notes": "The final Science supplementary Table S8 maps IMPD to replicated display name DS-11."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
            "snippet": "IMPD\t1.0\t365.0\tWP_000257686.1\tHEPN\tPF18731.5\tHEPN_Swt1 ; Swt1-like HEPN\thhpred_1021051.hhr\t252.0\t359.0\t0.98\t2024-04-16 00:00:00",
            "notes": "The final Science supplementary Table S8 reports a HEPN HHpred hit for WP_000257686.1 in IMPD."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
            "snippet": "IMPD\t1.0\t365.0\tWP_000257686.1\tCBS\tcd04614\tCBS_pair_arch2_repeat2; Two tandem repeats of the cystathionine beta-synthase (CBS pair) domains present in archaea\thhpred_1021051.hhr\t134.0\t241.0\t0.9916\t2024-04-16 00:00:00",
            "notes": "The final Science supplementary Table S8 reports a CBS HHpred hit for WP_000257686.1 in IMPD."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
            "snippet": "| DS-11 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
            "notes": "The pinned DefenseFinder article registry maps the DS-11 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| DS-11__DS-11                                     |                                                  | DS-11                  | Custom                  | 100    |",
            "notes": "The pinned DefenseFinder HMM inventory records DS-11__DS-11 as a custom DS-11 profile."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "The pinned DefenseFinder rules table does not list DS-11, leaving rule-level detection criteria unresolved."
          }
        ],
        "attaches_to": [
          "causal_graphs#ds_11_locus_reduces_phage_plaquing"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-28"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-28T13:46:45Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted DS-11 system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; kept the graph at cloned IMPD transcriptional-unit level because HEPN/CBS domain and mutant readouts do not resolve native DS-11 activation or effector chemistry and proposals/metpo_traitmech_v312 reserves the replacement placeholder.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-28T13:46:46Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed DS-11 system canonical_examples and left them empty because DeWeirdt et al. support cloned IMPD plaquing assays in E. coli MG1655 plus a DefenseFinder DS-11 model, but not a direct named native microbial isolate exemplar with experimentally verified endogenous DS-11 activity. No paid research was used.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-28T14:33:00Z",
        "curator": "codex",
        "action": "ADDRESSED_PR_REVIEW",
        "changes": "Resolved PR #1403 review issue #1404 by broadening the DS-11 reduced-phage-plaquing node description so it no longer names only T3 while the evidence bundle includes Bas67 rows.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000436",
    "label": "DS-12 system",
    "definition": "A phage defense system in which an organism possesses the two-gene DefensePredictor-discovered system 12 locus cataloged as working transcriptional unit PD3A and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.",
    "definition_source": "DOI:10.1126/science.adv7924",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "DS-12",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1126/science.adv7924"
      },
      {
        "synonym_text": "PD3A",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx"
      },
      {
        "synonym_text": "DS-12__DS-12B",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1126/science.adv7924",
        "snippet": "To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
        "notes": "DeWeirdt et al. experimentally validated 42 predicted transcriptional units as phage-defense systems in E. coli."
      },
      {
        "reference": "DOI:10.1126/science.adv7924",
        "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
        "notes": "DeWeirdt et al. name validated transcriptional units as DefensePredictor discovered systems."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
        "snippet": "PD3A\tNZ_RRVF01000002.1\tGCF_003886115.1\t-\tTrue\tFalse\tTrue\tTrue\tDefensePredictor hits\t104144\t108678\trestriction endonuclease, AAA family ATPase\tWP_059339975.1, WP_064766070.1\t14.31811904122612\t6.906754778648663\tTrue\tTrue\tRemote defense homolog\tDS-12",
        "notes": "The final Science supplementary Table S6 maps working_id PD3A to DS_name DS-12, marks the cloned transcriptional unit as defensive, and records NZ_RRVF01000002.1 positions 104144-108678 with product accessions WP_059339975.1 and WP_064766070.1."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
        "snippet": "Bas25\t4.2\tpLAND\t24-05-17_EV_HHNH.png\t200000000\tPD3A\t24-05-17\t24-05-17_VAME_AAA1_PD3A_PDP7.png\t3\t2\t\t2000\t5\t\tTrue\t\tLB\t37",
        "notes": "The final Science supplementary Table S7 reports a PD3A assay row with a Bas25 phage readout and a -log(EOP) value of 5.0."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
        "snippet": "PD3A\tDS-12\tTrue",
        "notes": "The final Science supplementary Table S8 maps PD3A to replicated display name DS-12."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
        "snippet": "PD3A\t1.0\t750.0\tWP_064766070.1\tABC ATPase\t3ZGX_B\tCHROMOSOME PARTITION PROTEIN SMC; CELL CYCLE; 3.4A {BACILLUS SUBTILIS}\thhpred_5638008.hhr\t495.0\t581.0\t1.0\t2024-05-21 00:00:00",
        "notes": "The final Science supplementary Table S8 reports an ABC ATPase HHpred hit for WP_064766070.1 in PD3A."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
        "snippet": "PD3A\t2.0\t761.0\tWP_059339975.1\tPDDEXK\tcd22335\tMspjI-like; Modification-dependent restriction endonuclease MspjI and similar endonucleases.\thhpred_5143119.hhr\t4.0\t129.0\t0.98\t2024-07-30 00:00:00\t335-337\t322.0",
        "notes": "The final Science supplementary Table S8 reports a PDDEXK HHpred hit for WP_059339975.1 in PD3A."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
        "snippet": "PD3A\t2.0\t761.0\tWP_059339975.1\tNACHT\tPF20720.2\tnSTAND3 ; Novel STAND NTPase 3\thhpred_5143119.hhr\t174.0\t327.0\t0.99\t2024-07-30 00:00:00",
        "notes": "The final Science supplementary Table S8 reports a NACHT HHpred hit for WP_059339975.1 in PD3A."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| DS-12B | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
        "notes": "The pinned DefenseFinder article registry maps the DS-12B source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| DS-12__DS-12B                                    |                                                  | DS-12                  | Custom                  | 100    |",
        "notes": "The pinned DefenseFinder HMM inventory records DS-12__DS-12B as a custom DS-12 profile."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "ds_12_locus_reduces_phage_plaquing",
        "title": "DS-12 locus reduces bacteriophage plaquing",
        "description": "Conservative system-level sketch linking the two-gene DS-12 locus to reduced bacteriophage plaquing without resolving DS-12 component function or effector activity.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures DS-12 as the validated PD3A transcriptional unit with two product accessions, final Table S8 ABC ATPase, PDDEXK, and NACHT HHpred-domain rows, and one DefenseFinder DS-12B profile row. It does not assert native host breadth, DS-12A model coverage, exact DS-12B profile-to-protein correspondence, the direct viral trigger or substrate, exact ABC ATPase or nuclease chemistry, phage target breadth, or DefenseFinder rule-level detection criteria.",
        "nodes": [
          {
            "node_id": "ds_12_locus",
            "label": "DS-12 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A two-gene DefensePredictor-discovered system locus represented in the pinned DefenseFinder HMM inventory by one DS-12B custom profile."
          },
          {
            "node_id": "reduced_phage_plaquing",
            "label": "reduced bacteriophage plaquing",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced bacteriophage plaquing by cells carrying cloned PD3A."
          },
          {
            "node_id": "ds_12_system_trait",
            "label": "DS-12 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000436",
            "description": "Possession of a genome-encoded DS-12 phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "ds_12_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "reduced_phage_plaquing",
            "description": "The DS-12/PD3A locus contributes to reduced bacteriophage plaquing when plasmid expressed.",
            "evidence": [
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
                "snippet": "PD3A\tNZ_RRVF01000002.1\tGCF_003886115.1\t-\tTrue\tFalse\tTrue\tTrue\tDefensePredictor hits\t104144\t108678\trestriction endonuclease, AAA family ATPase\tWP_059339975.1, WP_064766070.1\t14.31811904122612\t6.906754778648663\tTrue\tTrue\tRemote defense homolog\tDS-12",
                "notes": "The final Science supplementary Table S6 maps working_id PD3A to DS_name DS-12, marks the cloned transcriptional unit as defensive, and records NZ_RRVF01000002.1 positions 104144-108678 with product accessions WP_059339975.1 and WP_064766070.1."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
                "snippet": "Bas25\t4.2\tpLAND\t24-05-17_EV_HHNH.png\t200000000\tPD3A\t24-05-17\t24-05-17_VAME_AAA1_PD3A_PDP7.png\t3\t2\t\t2000\t5\t\tTrue\t\tLB\t37",
                "notes": "The final Science supplementary Table S7 reports a PD3A assay row with a Bas25 phage readout and a -log(EOP) value of 5.0."
              }
            ]
          },
          {
            "subject": "reduced_phage_plaquing",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "ds_12_system_trait",
            "description": "DS-12-mediated phage plaquing reduction realizes the DS-12 system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
                "notes": "DeWeirdt et al. name each validated transcriptional unit as a DefensePredictor discovered system."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
                "snippet": "PD3A\tNZ_RRVF01000002.1\tGCF_003886115.1\t-\tTrue\tFalse\tTrue\tTrue\tDefensePredictor hits\t104144\t108678\trestriction endonuclease, AAA family ATPase\tWP_059339975.1, WP_064766070.1\t14.31811904122612\t6.906754778648663\tTrue\tTrue\tRemote defense homolog\tDS-12",
                "notes": "The final Science supplementary Table S6 maps working_id PD3A to DS_name DS-12, marks the cloned transcriptional unit as defensive, and records NZ_RRVF01000002.1 positions 104144-108678 with product accessions WP_059339975.1 and WP_064766070.1."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
                "snippet": "Bas25\t4.2\tpLAND\t24-05-17_EV_HHNH.png\t200000000\tPD3A\t24-05-17\t24-05-17_VAME_AAA1_PD3A_PDP7.png\t3\t2\t\t2000\t5\t\tTrue\t\tLB\t37",
                "notes": "The final Science supplementary Table S7 reports a PD3A assay row with a Bas25 phage readout and a -log(EOP) value of 5.0."
              }
            ]
          },
          {
            "subject": "ds_12_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "DS-12 system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
                "notes": "DeWeirdt et al. validate DSs as anti-phage systems."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| DS-12B | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
                "notes": "The pinned DefenseFinder article registry maps the DS-12B source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "ds-12-defensefinder-model-gap",
        "prompt": "Resolve DS-12 native host breadth, DS-12A model coverage, DS-12B profile-to-protein mapping, sensitive-phage breadth, direct viral trigger or substrate, exact ABC ATPase and PDDEXK/nSTAND nuclease chemistry, and rule-level detection criteria before minting narrower DS-12 mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "DeWeirdt et al. support DS-12 as the defensive PD3A transcriptional unit that reduced Bas25 plaquing when cloned in E. coli MG1655, and the final Table S8 HHpred sheet reports ABC ATPase, PDDEXK, and NACHT hits across the two PD3A products. The pinned DefenseFinder HMM inventory records one DS-12B profile row, the pinned article registry names DS-12B rather than DS-12, the pinned rules table has no DS-12 row, and the first-pass record does not resolve native host breadth, DS-12A model coverage, exact profile-to-protein correspondence, direct ATPase or nuclease activity, phage target breadth, or endogenous DS-12 activity.",
        "evidence": [
          {
            "reference": "DOI:10.1126/science.adv7924",
            "snippet": "To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
            "notes": "DeWeirdt et al. validate predicted transcriptional units by measuring plaquing relative to an empty vector control strain."
          },
          {
            "reference": "DOI:10.1126/science.adv7924",
            "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
            "notes": "DeWeirdt et al. name validated TUs as DSs."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
            "snippet": "PD3A\tNZ_RRVF01000002.1\tGCF_003886115.1\t-\tTrue\tFalse\tTrue\tTrue\tDefensePredictor hits\t104144\t108678\trestriction endonuclease, AAA family ATPase\tWP_059339975.1, WP_064766070.1\t14.31811904122612\t6.906754778648663\tTrue\tTrue\tRemote defense homolog\tDS-12",
            "notes": "The final Science supplementary Table S6 maps working_id PD3A to DS_name DS-12, marks the cloned transcriptional unit as defensive, and records NZ_RRVF01000002.1 positions 104144-108678 with product accessions WP_059339975.1 and WP_064766070.1."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
            "snippet": "Bas25\t4.2\tpLAND\t24-05-17_EV_HHNH.png\t200000000\tPD3A\t24-05-17\t24-05-17_VAME_AAA1_PD3A_PDP7.png\t3\t2\t\t2000\t5\t\tTrue\t\tLB\t37",
            "notes": "The final Science supplementary Table S7 reports a PD3A assay row with a Bas25 phage readout and a -log(EOP) value of 5.0."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
            "snippet": "PD3A\tDS-12\tTrue",
            "notes": "The final Science supplementary Table S8 maps PD3A to replicated display name DS-12."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
            "snippet": "PD3A\t1.0\t750.0\tWP_064766070.1\tABC ATPase\t3ZGX_B\tCHROMOSOME PARTITION PROTEIN SMC; CELL CYCLE; 3.4A {BACILLUS SUBTILIS}\thhpred_5638008.hhr\t495.0\t581.0\t1.0\t2024-05-21 00:00:00",
            "notes": "The final Science supplementary Table S8 reports an ABC ATPase HHpred hit for WP_064766070.1 in PD3A."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
            "snippet": "PD3A\t2.0\t761.0\tWP_059339975.1\tPDDEXK\tcd22335\tMspjI-like; Modification-dependent restriction endonuclease MspjI and similar endonucleases.\thhpred_5143119.hhr\t4.0\t129.0\t0.98\t2024-07-30 00:00:00\t335-337\t322.0",
            "notes": "The final Science supplementary Table S8 reports a PDDEXK HHpred hit for WP_059339975.1 in PD3A."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
            "snippet": "PD3A\t2.0\t761.0\tWP_059339975.1\tNACHT\tPF20720.2\tnSTAND3 ; Novel STAND NTPase 3\thhpred_5143119.hhr\t174.0\t327.0\t0.99\t2024-07-30 00:00:00",
            "notes": "The final Science supplementary Table S8 reports a NACHT HHpred hit for WP_059339975.1 in PD3A."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
            "snippet": "| DS-12B | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
            "notes": "The pinned DefenseFinder article registry maps the DS-12B source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| DS-12__DS-12B                                    |                                                  | DS-12                  | Custom                  | 100    |",
            "notes": "The pinned DefenseFinder HMM inventory records DS-12__DS-12B as a custom DS-12 profile."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "The pinned DefenseFinder rules table does not list DS-12, DS-12B, PD3A, or the PD3A product accessions, leaving complete component coverage and rule-level detection criteria unresolved."
          }
        ],
        "attaches_to": [
          "causal_graphs#ds_12_locus_reduces_phage_plaquing"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-28"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-28T15:20:46Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted DS-12 system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; kept the graph at cloned PD3A transcriptional-unit level because the pinned DefenseFinder DS-12B HMM row leaves DS-12A coverage unresolved and proposals/metpo_traitmech_v313 reserves the replacement placeholder.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-28T15:20:47Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed DS-12 system canonical_examples and left them empty because DeWeirdt et al. support cloned PD3A plaquing assays in E. coli MG1655 plus a partial DefenseFinder DS-12B model, but not a direct named native microbial isolate exemplar with experimentally verified endogenous DS-12 activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000437",
    "label": "DS-13 system",
    "definition": "A phage defense system in which an organism possesses a genome-encoded DefensePredictor-discovered system 13 locus represented in the pinned DefenseFinder model inventory by DS-13A and DS-13B custom HMM profiles.",
    "definition_source": "DOI:10.1101/2025.01.08.631726",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "DS-13",
        "synonym_type": "EXACT_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      },
      {
        "synonym_text": "DS-13__DS-13A",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "DS-13__DS-13B",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1101/2025.01.08.631726",
        "snippet": "To test for anti-phage defense, we placed each TU with its native promoter region on a low-copy number plasmid in E. coli MG1655 and then challenged these strains with a panel of 24 diverse E. coli phages (fig. S2). In total, 45 (42% of 106) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
        "notes": "DeWeirdt et al. experimentally validated 45 predicted transcriptional units as phage-defense systems in E. coli; the first-pass DS-13 record uses this source only for the DefensePredictor DS naming context, not for an exact DS-13 phage readout."
      },
      {
        "reference": "DOI:10.1101/2025.01.08.631726",
        "snippet": "We refer to these validated TUs as DefensePredictor discovered Systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
        "notes": "DeWeirdt et al. name validated transcriptional units as DefensePredictor discovered Systems."
      },
      {
        "reference": "DOI:10.1101/2025.01.08.631726",
        "snippet": "To begin elucidating the function of the 45 validated TUs, we further annotated their protein domains (see Methods; table S6).",
        "notes": "DeWeirdt et al. describe Table S6 as a protein-domain annotation table for the validated DS transcriptional units; the exact preprint DS-13 row was not recovered in this curation pass."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| DS-13 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
        "notes": "The pinned DefenseFinder article registry maps the DS-13 source key to the DeWeirdt et al. DefensePredictor preprint."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| DS-13__DS-13A                                    |                                                  | DS-13                  | Custom                  | 20     |",
        "notes": "The pinned DefenseFinder HMM inventory records DS-13__DS-13A as a custom DS-13 profile."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| DS-13__DS-13B                                    |                                                  | DS-13                  | Custom                  | 50     |",
        "notes": "The pinned DefenseFinder HMM inventory records DS-13__DS-13B as a custom DS-13 profile."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "ds_13_locus_profile_model",
        "title": "DS-13 locus profile model",
        "description": "Conservative system-level sketch linking the DS-13 DefensePredictor-discovered system key to DS-13 system possession and the broader phage-defense-system trait without resolving DS-13 component function or a phage activity readout.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures DS-13 as a DefensePredictor-discovered system with DS-13A and DS-13B custom HMM rows in the pinned DefenseFinder HMM inventory. It does not assert the preprint working identifier, preprint Table S5/S6 rows, final Science supplement rows, native host breadth, profile-to-protein correspondence, DS-13A or DS-13B molecular activity, exact phage target breadth, or DefenseFinder rule-level detection criteria.",
        "nodes": [
          {
            "node_id": "ds_13_locus",
            "label": "DS-13 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A DefensePredictor-discovered system 13 locus represented in the pinned DefenseFinder HMM inventory by DS-13A and DS-13B custom profiles."
          },
          {
            "node_id": "ds_13_system_trait",
            "label": "DS-13 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000437",
            "description": "Possession of a genome-encoded DS-13 phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "ds_13_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "ds_13_system_trait",
            "description": "DefenseFinder links the DS-13 source key to the DefensePredictor preprint and represents DS-13 in the HMM inventory with DS-13A and DS-13B custom profiles.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| DS-13 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
                "notes": "The pinned DefenseFinder article registry maps the DS-13 source key to the DeWeirdt et al. DefensePredictor preprint."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| DS-13__DS-13A                                    |                                                  | DS-13                  | Custom                  | 20     |",
                "notes": "The pinned DefenseFinder HMM inventory records DS-13__DS-13A as a custom DS-13 profile."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| DS-13__DS-13B                                    |                                                  | DS-13                  | Custom                  | 50     |",
                "notes": "The pinned DefenseFinder HMM inventory records DS-13__DS-13B as a custom DS-13 profile."
              }
            ]
          },
          {
            "subject": "ds_13_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "DS-13 system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1101/2025.01.08.631726",
                "snippet": "We refer to these validated TUs as DefensePredictor discovered Systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
                "notes": "DeWeirdt et al. name validated TUs as DefensePredictor discovered Systems."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| DS-13 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
                "notes": "The pinned DefenseFinder article registry maps the DS-13 source key to the DeWeirdt et al. DefensePredictor preprint."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "ds-13-defensefinder-model-gap",
        "prompt": "Resolve DS-13 working-identifier rows, preprint Table S5 and S6 context, final Science supplement omission, native host breadth, DS-13A/DS-13B profile-to-protein mapping, sensitive-phage breadth, molecular output, and rule-level DefenseFinder criteria before minting narrower DS-13 mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "The DeWeirdt et al. preprint supports the DefensePredictor discovered System naming convention, the pinned DefenseFinder article registry names DS-13 and maps it to that preprint, and the pinned HMM inventory records DS-13A and DS-13B custom profile rows. DS-13 is absent from the final Science Table S6, S7, and S8 files checked during this curation pass, the exact preprint per-TU rows were not recovered, the pinned DefenseFinder rules table has no DS-13 row, and the first-pass record does not resolve the working identifier, assayed phages, phage readout, native host, profile-to-component mapping, component activities, or complete detection criteria.",
        "evidence": [
          {
            "reference": "DOI:10.1101/2025.01.08.631726",
            "snippet": "To test for anti-phage defense, we placed each TU with its native promoter region on a low-copy number plasmid in E. coli MG1655 and then challenged these strains with a panel of 24 diverse E. coli phages (fig. S2). In total, 45 (42% of 106) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
            "notes": "DeWeirdt et al. validate predicted transcriptional units by measuring plaquing relative to an empty vector control strain."
          },
          {
            "reference": "DOI:10.1101/2025.01.08.631726",
            "snippet": "We refer to these validated TUs as DefensePredictor discovered Systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
            "notes": "DeWeirdt et al. name validated TUs as DSs."
          },
          {
            "reference": "DOI:10.1101/2025.01.08.631726",
            "snippet": "To begin elucidating the function of the 45 validated TUs, we further annotated their protein domains (see Methods; table S6).",
            "notes": "DeWeirdt et al. describe Table S6 as further protein-domain annotation of validated TUs."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
            "snippet": "| DS-13 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
            "notes": "The pinned DefenseFinder article registry maps the DS-13 source key to the DeWeirdt et al. DefensePredictor preprint."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| DS-13__DS-13A                                    |                                                  | DS-13                  | Custom                  | 20     |",
            "notes": "The pinned DefenseFinder HMM inventory records DS-13__DS-13A as a custom DS-13 profile."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| DS-13__DS-13B                                    |                                                  | DS-13                  | Custom                  | 50     |",
            "notes": "The pinned DefenseFinder HMM inventory records DS-13__DS-13B as a custom DS-13 profile."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "The pinned DefenseFinder rules table does not list DS-13, DS-13A, or DS-13B, leaving complete component coverage and rule-level detection criteria unresolved."
          }
        ],
        "attaches_to": [
          "causal_graphs#ds_13_locus_profile_model"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-28"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-28T16:05:54Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted DS-13 system as a DOI- and DefenseFinder-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; kept the graph at DS-13 source-key and HMM-profile level because preprint Table S5/S6 rows, final Science supplement rows, and rule rows remain unresolved, and proposals/metpo_traitmech_v314 reserves the replacement placeholder.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-28T16:05:55Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed DS-13 system canonical_examples and left them empty because the pinned DefenseFinder registries support DS-13 system identity and custom HMM coverage but not a direct named native microbial isolate exemplar with experimentally verified endogenous DS-13 activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000429",
    "label": "DS-14 system",
    "definition": "A phage defense system in which an organism possesses the single-gene DefensePredictor-discovered system 14 locus cataloged as working transcriptional unit RMOR and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.",
    "definition_source": "DOI:10.1126/science.adv7924",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "DS-14",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1126/science.adv7924"
      },
      {
        "synonym_text": "RMOR",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx"
      },
      {
        "synonym_text": "DS-14__DS-14",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1126/science.adv7924",
        "snippet": "To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
        "notes": "DeWeirdt et al. experimentally validated 42 predicted transcriptional units as phage-defense systems in E. coli."
      },
      {
        "reference": "DOI:10.1126/science.adv7924",
        "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
        "notes": "DeWeirdt et al. name validated transcriptional units as DefensePredictor discovered systems."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
        "snippet": "RMOR\tNZ_QOZC01000013.1\tGCF_003333475.1\t-\tTrue\tFalse\tFalse\tTrue\tDefensePredictor hits\t106880\t109330\thypothetical protein\tWP_040091717.1\t14.71279098470142\t5.293304824724491\tTrue\tTrue\tRemote defense homolog\tDS-14",
        "notes": "The final Science supplementary Table S6 maps working_id RMOR to DS_name DS-14, marks the cloned transcriptional unit as defensive, and records NZ_QOZC01000013.1 positions 106880-109330 with product accession WP_040091717.1."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
        "snippet": "Bas50\t6.1\tpLAND\t24-07-17_MVB1_VPUS_VAME_EV.png\t500000000\tRMOR\t24-07-17\t24-07-17_AAA2_RMOR_NERD_NUCS.png\t3\t10\t\t10000\t4.698970004336019\t\t\tTrue\tLB\t37",
        "notes": "The final Science supplementary Table S7 reports an RMOR assay row with a Bas50 phage readout and a -log(EOP) value of 4.699."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
        "snippet": "RMOR\tDS-14\tTrue",
        "notes": "The final Science supplementary Table S8 maps RMOR to replicated display name DS-14."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
        "snippet": "RMOR\t1.0\t816.0\tWP_040091717.1\tAAA+ ATPase\t7MCA_A\tOrigin recognition complex subunit 1; replication initiation, REPLICATION; HET: AGS; 3.6A {Saccharomyces cerevisiae}\thhpred_4983760.hhr\t270.0\t569.0\t0.99\t2024-07-30 00:00:00",
        "notes": "The final Science supplementary Table S8 reports an AAA+ ATPase HHpred hit for WP_040091717.1 in RMOR."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
        "snippet": "RMOR\t1.0\t816.0\tWP_040091717.1\tPDDEXK\tPF15516.11\tBpuSI_N ; BpuSI N-terminal domain\thhpred_4983760.hhr\t27.0\t167.0\t0.99\t2024-07-30 00:00:00\t76-78\t65.0",
        "notes": "The final Science supplementary Table S8 reports a PDDEXK HHpred hit for WP_040091717.1 in RMOR."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| DS-14 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
        "notes": "The pinned DefenseFinder article registry maps the DS-14 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| DS-14__DS-14                                     |                                                  | DS-14                  | Custom                  | 500    |",
        "notes": "The pinned DefenseFinder HMM inventory records DS-14__DS-14 as a custom DS-14 profile."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "ds_14_locus_reduces_phage_plaquing",
        "title": "DS-14 locus reduces bacteriophage plaquing",
        "description": "Conservative system-level sketch linking the single-gene DS-14 locus to reduced bacteriophage plaquing without resolving DS-14 component function or effector activity.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures DS-14 as the validated RMOR transcriptional unit with one product accession and with a DefenseFinder DS-14 profile row. Although Table S6 classes RMOR as a Remote defense homolog, the graph does not assert which defense family it is remote from, native host breadth, exact profile-to-protein correspondence, the direct viral trigger or substrate, exact AAA+ ATPase or PDDEXK nuclease chemistry, phage target breadth, or DefenseFinder rule-level detection criteria.",
        "nodes": [
          {
            "node_id": "ds_14_locus",
            "label": "DS-14 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A single-gene DefensePredictor-discovered system locus represented in the pinned DefenseFinder HMM inventory by one DS-14 custom profile."
          },
          {
            "node_id": "reduced_phage_plaquing",
            "label": "reduced bacteriophage plaquing",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced efficiency of plaquing by bacteriophage Bas50 in cells carrying cloned RMOR."
          },
          {
            "node_id": "ds_14_system_trait",
            "label": "DS-14 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000429",
            "description": "Possession of a genome-encoded DS-14 phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "ds_14_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "reduced_phage_plaquing",
            "description": "The DS-14/RMOR locus contributes to reduced bacteriophage plaquing when plasmid expressed.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
                "notes": "DeWeirdt et al. experimentally validate DefensePredictor-discovered systems by assaying cloned transcriptional units against E. coli phages."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
                "snippet": "RMOR\tNZ_QOZC01000013.1\tGCF_003333475.1\t-\tTrue\tFalse\tFalse\tTrue\tDefensePredictor hits\t106880\t109330\thypothetical protein\tWP_040091717.1\t14.71279098470142\t5.293304824724491\tTrue\tTrue\tRemote defense homolog\tDS-14",
                "notes": "The final Science supplementary Table S6 maps working_id RMOR to DS_name DS-14, marks the cloned transcriptional unit as defensive, and records NZ_QOZC01000013.1 positions 106880-109330 with product accession WP_040091717.1."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
                "snippet": "Bas50\t6.1\tpLAND\t24-07-17_MVB1_VPUS_VAME_EV.png\t500000000\tRMOR\t24-07-17\t24-07-17_AAA2_RMOR_NERD_NUCS.png\t3\t10\t\t10000\t4.698970004336019\t\t\tTrue\tLB\t37",
                "notes": "The final Science supplementary Table S7 reports an RMOR assay row with a Bas50 phage readout and a -log(EOP) value of 4.699."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| DS-14__DS-14                                     |                                                  | DS-14                  | Custom                  | 500    |",
                "notes": "The pinned DefenseFinder HMM inventory records DS-14__DS-14 as a custom DS-14 profile."
              }
            ]
          },
          {
            "subject": "reduced_phage_plaquing",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "ds_14_system_trait",
            "description": "DS-14-mediated phage plaquing reduction realizes the DS-14 system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
                "notes": "DeWeirdt et al. name each validated transcriptional unit as a DefensePredictor discovered system."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
                "snippet": "RMOR\tNZ_QOZC01000013.1\tGCF_003333475.1\t-\tTrue\tFalse\tFalse\tTrue\tDefensePredictor hits\t106880\t109330\thypothetical protein\tWP_040091717.1\t14.71279098470142\t5.293304824724491\tTrue\tTrue\tRemote defense homolog\tDS-14",
                "notes": "The final Science supplementary Table S6 maps working_id RMOR to DS_name DS-14, marks the cloned transcriptional unit as defensive, and records NZ_QOZC01000013.1 positions 106880-109330 with product accession WP_040091717.1."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
                "snippet": "Bas50\t6.1\tpLAND\t24-07-17_MVB1_VPUS_VAME_EV.png\t500000000\tRMOR\t24-07-17\t24-07-17_AAA2_RMOR_NERD_NUCS.png\t3\t10\t\t10000\t4.698970004336019\t\t\tTrue\tLB\t37",
                "notes": "The final Science supplementary Table S7 reports an RMOR assay row with a Bas50 phage readout and a -log(EOP) value of 4.699."
              }
            ]
          },
          {
            "subject": "ds_14_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "DS-14 system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
                "notes": "DeWeirdt et al. validate DSs as anti-phage systems."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| DS-14 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
                "notes": "The pinned DefenseFinder article registry maps the DS-14 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "ds-14-defensefinder-model-gap",
        "prompt": "Resolve DS-14 native host breadth, exact single-component activity, DS-14 remote-defense-homolog family identity, DS-14 profile-to-protein mapping, sensitive-phage breadth, exact AAA+ ATPase and PDDEXK nuclease chemistry, and rule-level detection criteria before minting narrower DS-14 mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "DeWeirdt et al. support DS-14 as the defensive RMOR transcriptional unit that reduced Bas50 plaquing when cloned in E. coli MG1655, the final Table S6 classes RMOR as a Remote defense homolog, and the pinned DefenseFinder HMM inventory records one DS-14 profile row. The pinned rules table has no DS-14 row, and the first-pass record does not resolve native host breadth, exact component activity, remote defense family relationship, profile-to-protein mapping, phage target breadth, or endogenous DS-14 activity.",
        "evidence": [
          {
            "reference": "DOI:10.1126/science.adv7924",
            "snippet": "To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
            "notes": "DeWeirdt et al. validate predicted transcriptional units by measuring plaquing relative to an empty vector control strain."
          },
          {
            "reference": "DOI:10.1126/science.adv7924",
            "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
            "notes": "DeWeirdt et al. name validated TUs as DSs."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
            "snippet": "RMOR\tNZ_QOZC01000013.1\tGCF_003333475.1\t-\tTrue\tFalse\tFalse\tTrue\tDefensePredictor hits\t106880\t109330\thypothetical protein\tWP_040091717.1\t14.71279098470142\t5.293304824724491\tTrue\tTrue\tRemote defense homolog\tDS-14",
            "notes": "The final Science supplementary Table S6 maps working_id RMOR to DS_name DS-14, marks the cloned transcriptional unit as defensive, and records NZ_QOZC01000013.1 positions 106880-109330 with product accession WP_040091717.1."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
            "snippet": "Bas50\t6.1\tpLAND\t24-07-17_MVB1_VPUS_VAME_EV.png\t500000000\tRMOR\t24-07-17\t24-07-17_AAA2_RMOR_NERD_NUCS.png\t3\t10\t\t10000\t4.698970004336019\t\t\tTrue\tLB\t37",
            "notes": "The final Science supplementary Table S7 reports an RMOR assay row with a Bas50 phage readout and a -log(EOP) value of 4.699."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
            "snippet": "RMOR\tDS-14\tTrue",
            "notes": "The final Science supplementary Table S8 maps RMOR to replicated display name DS-14."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
            "snippet": "RMOR\t1.0\t816.0\tWP_040091717.1\tAAA+ ATPase\t7MCA_A\tOrigin recognition complex subunit 1; replication initiation, REPLICATION; HET: AGS; 3.6A {Saccharomyces cerevisiae}\thhpred_4983760.hhr\t270.0\t569.0\t0.99\t2024-07-30 00:00:00",
            "notes": "The final Science supplementary Table S8 reports an AAA+ ATPase HHpred hit for WP_040091717.1 in RMOR."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
            "snippet": "RMOR\t1.0\t816.0\tWP_040091717.1\tPDDEXK\tPF15516.11\tBpuSI_N ; BpuSI N-terminal domain\thhpred_4983760.hhr\t27.0\t167.0\t0.99\t2024-07-30 00:00:00\t76-78\t65.0",
            "notes": "The final Science supplementary Table S8 reports a PDDEXK HHpred hit for WP_040091717.1 in RMOR."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
            "snippet": "| DS-14 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
            "notes": "The pinned DefenseFinder article registry maps the DS-14 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| DS-14__DS-14                                     |                                                  | DS-14                  | Custom                  | 500    |",
            "notes": "The pinned DefenseFinder HMM inventory records DS-14__DS-14 as a custom DS-14 profile."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "The pinned DefenseFinder rules table does not list DS-14, leaving rule-level detection criteria unresolved."
          }
        ],
        "attaches_to": [
          "causal_graphs#ds_14_locus_reduces_phage_plaquing"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-28"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-28T08:11:18Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted DS-14 system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; kept the graph at cloned RMOR transcriptional-unit level because the pinned DefenseFinder DS-14 HMM row is not backed by a rules row; proposals/metpo_traitmech_v306 reserves the replacement placeholder.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-28T08:11:19Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed DS-14 system canonical_examples and left them empty because DeWeirdt et al. support cloned RMOR plaquing assays in E. coli MG1655 plus a DefenseFinder DS-14 model, but not a direct named native microbial isolate exemplar with experimentally verified endogenous DS-14 activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000438",
    "label": "DS-15 system",
    "definition": "A phage defense system in which an organism possesses the three-gene DefensePredictor-discovered system 15 locus cataloged as working transcriptional unit AAA1 and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.",
    "definition_source": "DOI:10.1126/science.adv7924",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "DS-15",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1126/science.adv7924"
      },
      {
        "synonym_text": "AAA1",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx"
      },
      {
        "synonym_text": "DS-15__DS-15A",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "DS-15__DS-15B",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "DS-15__DS-15C",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1126/science.adv7924",
        "snippet": "To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
        "notes": "DeWeirdt et al. experimentally validated 42 predicted transcriptional units as phage-defense systems in E. coli."
      },
      {
        "reference": "DOI:10.1126/science.adv7924",
        "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
        "notes": "DeWeirdt et al. name validated transcriptional units as DefensePredictor discovered systems."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
        "snippet": "AAA1\tNZ_QOXE01000046.1\tGCF_003334165.1\t-\tTrue\tFalse\tTrue\tTrue\tDefensePredictor hits\t29629\t31530\thypothetical protein, hypothetical protein, AAA family ATPase\tWP_000957441.1, WP_060581740.1, WP_001619161.1\t11.46862191778244\t2.030866871531279\tTrue\tTrue\tPredicted novel defense gene\tDS-15",
        "notes": "The final Science supplementary Table S6 maps working_id AAA1 to DS_name DS-15, marks the cloned transcriptional unit as defensive, and records NZ_QOXE01000046.1 positions 29629-31530 with product accessions WP_000957441.1, WP_060581740.1, and WP_001619161.1."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
        "snippet": "Bas1\t4.2\tpLAND\t24-05-17_EV_HHNH.png\t5000000\tAAA1\t24-05-17\t24-05-17_VAME_AAA1_PD3A_PDP7.png\t2\t100\t\t10000\t2.6989700043360187\t\tTrue\t\tLB\t37",
        "notes": "The final Science supplementary Table S7 reports an AAA1 assay row with a Bas1 phage readout and a -log(EOP) value of 2.699."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
        "snippet": "AAA1\tDS-15\tTrue",
        "notes": "The final Science supplementary Table S8 maps AAA1 to replicated display name DS-15."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
        "snippet": "AAA1\t1.0\t281.0\tWP_001619161.1\tMinD ATPase\tSCOP_d1hyqa_\tc.37.1.10 (A:) Cell division regulator MinD {Archaeoglobus fulgidus [TaxId: 2234]} | CLASS: Alpha and beta proteins (a/b), FOLD: P-loop containing nucleoside triphosphate hydrolases, SUPFAM: P-loop containing nucleoside triphosphate hydrolases, FAM: Nitrogenase iron protein-like\thhpred_6736485.hhr\t3.0\t268.0\t1.0\t2024-07-29 00:00:00",
        "notes": "The final Science supplementary Table S8 reports a MinD ATPase HHpred hit for WP_001619161.1 in AAA1."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
        "snippet": "AAA1\t3.0\t221.0\tWP_000957441.1\tDUF6988\tPF22491.1\tDUF6988 ; Family of unknown function (DUF6988)\thhpred_7907160.hhr\t68.0\t144.0\t0.94\t2024-07-29 00:00:00",
        "notes": "The final Science supplementary Table S8 reports a DUF6988 HHpred hit for WP_000957441.1 in AAA1."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| DS-15 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
        "notes": "The pinned DefenseFinder article registry maps the DS-15 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| DS-15__DS-15A                                    |                                                  | DS-15                  | Custom                  | 300    |",
        "notes": "The pinned DefenseFinder HMM inventory records DS-15__DS-15A as a custom DS-15 profile."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| DS-15__DS-15B                                    |                                                  | DS-15                  | Custom                  | 20     |",
        "notes": "The pinned DefenseFinder HMM inventory records DS-15__DS-15B as a custom DS-15 profile."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| DS-15__DS-15C                                    |                                                  | DS-15                  | Custom                  | 20     |",
        "notes": "The pinned DefenseFinder HMM inventory records DS-15__DS-15C as a custom DS-15 profile."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "ds_15_locus_reduces_phage_plaquing",
        "title": "DS-15 locus reduces bacteriophage plaquing",
        "description": "Conservative system-level sketch linking the three-gene DS-15 locus to reduced bacteriophage plaquing without resolving DS-15 component function or effector activity.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures DS-15 as the validated AAA1 transcriptional unit with three product accessions, final Table S8 MinD ATPase and DUF6988 HHpred-domain rows, and three DefenseFinder DS-15 profile rows. It does not assert native host breadth, exact profile-to-protein correspondence, the direct viral trigger or substrate, exact AAA family ATPase or DUF6988 chemistry, phage target breadth, or DefenseFinder rule-level detection criteria.",
        "nodes": [
          {
            "node_id": "ds_15_locus",
            "label": "DS-15 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A three-gene DefensePredictor-discovered system locus represented in the pinned DefenseFinder HMM inventory by DS-15A, DS-15B, and DS-15C custom profiles."
          },
          {
            "node_id": "reduced_phage_plaquing",
            "label": "reduced bacteriophage plaquing",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced efficiency of plaquing by bacteriophage Bas1 in cells carrying cloned AAA1."
          },
          {
            "node_id": "ds_15_system_trait",
            "label": "DS-15 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000438",
            "description": "Possession of a genome-encoded DS-15 phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "ds_15_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "reduced_phage_plaquing",
            "description": "The DS-15/AAA1 locus contributes to reduced bacteriophage plaquing when plasmid expressed.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
                "notes": "DeWeirdt et al. experimentally validate DefensePredictor-discovered systems by assaying cloned transcriptional units against E. coli phages."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
                "snippet": "AAA1\tNZ_QOXE01000046.1\tGCF_003334165.1\t-\tTrue\tFalse\tTrue\tTrue\tDefensePredictor hits\t29629\t31530\thypothetical protein, hypothetical protein, AAA family ATPase\tWP_000957441.1, WP_060581740.1, WP_001619161.1\t11.46862191778244\t2.030866871531279\tTrue\tTrue\tPredicted novel defense gene\tDS-15",
                "notes": "The final Science supplementary Table S6 maps working_id AAA1 to DS_name DS-15, marks the cloned transcriptional unit as defensive, and records NZ_QOXE01000046.1 positions 29629-31530 with product accessions WP_000957441.1, WP_060581740.1, and WP_001619161.1."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
                "snippet": "Bas1\t4.2\tpLAND\t24-05-17_EV_HHNH.png\t5000000\tAAA1\t24-05-17\t24-05-17_VAME_AAA1_PD3A_PDP7.png\t2\t100\t\t10000\t2.6989700043360187\t\tTrue\t\tLB\t37",
                "notes": "The final Science supplementary Table S7 reports an AAA1 assay row with a Bas1 phage readout and a -log(EOP) value of 2.699."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| DS-15__DS-15A                                    |                                                  | DS-15                  | Custom                  | 300    |",
                "notes": "The pinned DefenseFinder HMM inventory records DS-15__DS-15A as a custom DS-15 profile."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| DS-15__DS-15B                                    |                                                  | DS-15                  | Custom                  | 20     |",
                "notes": "The pinned DefenseFinder HMM inventory records DS-15__DS-15B as a custom DS-15 profile."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| DS-15__DS-15C                                    |                                                  | DS-15                  | Custom                  | 20     |",
                "notes": "The pinned DefenseFinder HMM inventory records DS-15__DS-15C as a custom DS-15 profile."
              }
            ]
          },
          {
            "subject": "reduced_phage_plaquing",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "ds_15_system_trait",
            "description": "DS-15-mediated phage plaquing reduction realizes the DS-15 system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
                "notes": "DeWeirdt et al. name each validated transcriptional unit as a DefensePredictor discovered system."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
                "snippet": "AAA1\tNZ_QOXE01000046.1\tGCF_003334165.1\t-\tTrue\tFalse\tTrue\tTrue\tDefensePredictor hits\t29629\t31530\thypothetical protein, hypothetical protein, AAA family ATPase\tWP_000957441.1, WP_060581740.1, WP_001619161.1\t11.46862191778244\t2.030866871531279\tTrue\tTrue\tPredicted novel defense gene\tDS-15",
                "notes": "The final Science supplementary Table S6 maps working_id AAA1 to DS_name DS-15, marks the cloned transcriptional unit as defensive, and records NZ_QOXE01000046.1 positions 29629-31530 with product accessions WP_000957441.1, WP_060581740.1, and WP_001619161.1."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
                "snippet": "Bas1\t4.2\tpLAND\t24-05-17_EV_HHNH.png\t5000000\tAAA1\t24-05-17\t24-05-17_VAME_AAA1_PD3A_PDP7.png\t2\t100\t\t10000\t2.6989700043360187\t\tTrue\t\tLB\t37",
                "notes": "The final Science supplementary Table S7 reports an AAA1 assay row with a Bas1 phage readout and a -log(EOP) value of 2.699."
              }
            ]
          },
          {
            "subject": "ds_15_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "DS-15 system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
                "notes": "DeWeirdt et al. validate DSs as anti-phage systems."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| DS-15 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
                "notes": "The pinned DefenseFinder article registry maps the DS-15 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "ds-15-defensefinder-model-gap",
        "prompt": "Resolve DS-15 native host breadth, exact profile-to-protein mapping, DS-15A/DS-15B/DS-15C component activities, sensitive-phage breadth, exact AAA family ATPase and DUF6988 chemistry, and rule-level DefenseFinder criteria before minting narrower DS-15 mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "DeWeirdt et al. support DS-15 as the defensive AAA1 transcriptional unit that reduced Bas1 plaquing when cloned in E. coli MG1655, the final Table S8 HHpred sheet reports MinD ATPase and DUF6988 hits across two AAA1 products, and the pinned DefenseFinder HMM inventory records DS-15A, DS-15B, and DS-15C custom profile rows. The pinned rules table has no DS-15 row, and the first-pass record does not resolve native host breadth, exact profile-to-protein correspondence, direct ATPase or DUF6988 activity, phage target breadth, or endogenous DS-15 activity.",
        "evidence": [
          {
            "reference": "DOI:10.1126/science.adv7924",
            "snippet": "To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
            "notes": "DeWeirdt et al. validate predicted transcriptional units by measuring plaquing relative to an empty vector control strain."
          },
          {
            "reference": "DOI:10.1126/science.adv7924",
            "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
            "notes": "DeWeirdt et al. name validated TUs as DSs."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
            "snippet": "AAA1\tNZ_QOXE01000046.1\tGCF_003334165.1\t-\tTrue\tFalse\tTrue\tTrue\tDefensePredictor hits\t29629\t31530\thypothetical protein, hypothetical protein, AAA family ATPase\tWP_000957441.1, WP_060581740.1, WP_001619161.1\t11.46862191778244\t2.030866871531279\tTrue\tTrue\tPredicted novel defense gene\tDS-15",
            "notes": "The final Science supplementary Table S6 maps working_id AAA1 to DS_name DS-15, marks the cloned transcriptional unit as defensive, and records NZ_QOXE01000046.1 positions 29629-31530 with product accessions WP_000957441.1, WP_060581740.1, and WP_001619161.1."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
            "snippet": "Bas1\t4.2\tpLAND\t24-05-17_EV_HHNH.png\t5000000\tAAA1\t24-05-17\t24-05-17_VAME_AAA1_PD3A_PDP7.png\t2\t100\t\t10000\t2.6989700043360187\t\tTrue\t\tLB\t37",
            "notes": "The final Science supplementary Table S7 reports an AAA1 assay row with a Bas1 phage readout and a -log(EOP) value of 2.699."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
            "snippet": "AAA1\tDS-15\tTrue",
            "notes": "The final Science supplementary Table S8 maps AAA1 to replicated display name DS-15."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
            "snippet": "AAA1\t1.0\t281.0\tWP_001619161.1\tMinD ATPase\tSCOP_d1hyqa_\tc.37.1.10 (A:) Cell division regulator MinD {Archaeoglobus fulgidus [TaxId: 2234]} | CLASS: Alpha and beta proteins (a/b), FOLD: P-loop containing nucleoside triphosphate hydrolases, SUPFAM: P-loop containing nucleoside triphosphate hydrolases, FAM: Nitrogenase iron protein-like\thhpred_6736485.hhr\t3.0\t268.0\t1.0\t2024-07-29 00:00:00",
            "notes": "The final Science supplementary Table S8 reports a MinD ATPase HHpred hit for WP_001619161.1 in AAA1."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
            "snippet": "AAA1\t3.0\t221.0\tWP_000957441.1\tDUF6988\tPF22491.1\tDUF6988 ; Family of unknown function (DUF6988)\thhpred_7907160.hhr\t68.0\t144.0\t0.94\t2024-07-29 00:00:00",
            "notes": "The final Science supplementary Table S8 reports a DUF6988 HHpred hit for WP_000957441.1 in AAA1."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
            "snippet": "| DS-15 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
            "notes": "The pinned DefenseFinder article registry maps the DS-15 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| DS-15__DS-15A                                    |                                                  | DS-15                  | Custom                  | 300    |",
            "notes": "The pinned DefenseFinder HMM inventory records DS-15__DS-15A as a custom DS-15 profile."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| DS-15__DS-15B                                    |                                                  | DS-15                  | Custom                  | 20     |",
            "notes": "The pinned DefenseFinder HMM inventory records DS-15__DS-15B as a custom DS-15 profile."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| DS-15__DS-15C                                    |                                                  | DS-15                  | Custom                  | 20     |",
            "notes": "The pinned DefenseFinder HMM inventory records DS-15__DS-15C as a custom DS-15 profile."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "The pinned DefenseFinder rules table does not list DS-15, DS-15A, DS-15B, or DS-15C, leaving complete component coverage and rule-level detection criteria unresolved."
          }
        ],
        "attaches_to": [
          "causal_graphs#ds_15_locus_reduces_phage_plaquing"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-28"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-28T16:50:13Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted DS-15 system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; kept the graph at cloned AAA1 transcriptional-unit level because the pinned DefenseFinder DS-15 HMM rows are not backed by a rules row; proposals/metpo_traitmech_v315 reserves the replacement placeholder.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-28T16:50:14Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed DS-15 system canonical_examples and left them empty because DeWeirdt et al. support cloned AAA1 plaquing assays in E. coli MG1655 plus DefenseFinder DS-15 models, but not a direct named native microbial isolate exemplar with experimentally verified endogenous DS-15 activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000439",
    "label": "DS-16 system",
    "definition": "A phage defense system in which an organism possesses the two-gene DefensePredictor-discovered system 16 locus cataloged as working transcriptional unit PLIK and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.",
    "definition_source": "DOI:10.1126/science.adv7924",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "DS-16",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1126/science.adv7924"
      },
      {
        "synonym_text": "PLIK",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx"
      },
      {
        "synonym_text": "DS-16__DS-16A",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "DS-16__DS-16B",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1126/science.adv7924",
        "snippet": "To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
        "notes": "DeWeirdt et al. experimentally validated 42 predicted transcriptional units as phage-defense systems in E. coli."
      },
      {
        "reference": "DOI:10.1126/science.adv7924",
        "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
        "notes": "DeWeirdt et al. name validated transcriptional units as DefensePredictor discovered systems."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
        "snippet": "PLIK\tNZ_QOYD01000001.1\tGCF_003333765.1\t-\tTrue\tFalse\tTrue\tTrue\tDefensePredictor hits\t281241\t284220\thypothetical protein, DUF3696 domain-containing protein\tWP_001676492.1, WP_001676491.1\t10.6830001978657\t5.517452896464706\tTrue\tTrue\tStructural defense homolog\tDS-16",
        "notes": "The final Science supplementary Table S6 maps working_id PLIK to DS_name DS-16, marks the cloned transcriptional unit as defensive, and records NZ_QOYD01000001.1 positions 281241-284220 with product accessions WP_001676492.1 and WP_001676491.1."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
        "snippet": "Bas26\t2.2\tpLAND\t24-03-12_EV.png\t2400000000\tPLIK\t24-03-21\t24-03-21_PLIK_REPB_2.png\t7\t31\tY\t310000000\t0.8888495478773333\t\tTrue\t\tLB\t37",
        "notes": "The final Science supplementary Table S7 reports a PLIK assay row with a Bas26 phage readout and smaller plaques."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
        "snippet": "T4\t2.1\tpLAND\t24-03-12_EV.png\t200000000\tPLIK\t24-03-21\t24-03-21_PLIK_REPB.png\t3\t100\t\t100000\t3.3010299956639813\t\tTrue\t\tLB\t37",
        "notes": "The final Science supplementary Table S7 reports a PLIK assay row with a T4 phage readout and a -log(EOP) value of 3.301."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
        "snippet": "PLIK\tDS-16\tTrue",
        "notes": "The final Science supplementary Table S8 maps PLIK to replicated display name DS-16."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
        "snippet": "PLIK\t2.0\t341.0\tWP_001676492.1\tRelE\t4NRN_A\tmetal-bound toxin; Toxin;\thhpred_4269994.hhr\t239.0\t335.0\t0.8002\t2024-04-15 00:00:00",
        "notes": "The final Science supplementary Table S8 reports a RelE HHpred hit for WP_001676492.1 in PLIK."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
        "snippet": "PLIK\t1.0\t656.0\tWP_001676491.1\tABC ATPase\t6QJ0_A\tStructural maintenance of chromosomes protein,Structural maintenance of chromosomes protein; condensin SMC complex ATPase\thhpred_2524462.hhr\t1.0\t572.0\t0.997\t2024-04-15 00:00:00",
        "notes": "The final Science supplementary Table S8 reports an ABC ATPase HHpred hit for WP_001676491.1 in PLIK."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| DS-16 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
        "notes": "The pinned DefenseFinder article registry maps the DS-16 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| DS-16__DS-16A                                    |                                                  | DS-16                  | Custom                  | 500    |",
        "notes": "The pinned DefenseFinder HMM inventory records DS-16__DS-16A as a custom DS-16 profile."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| DS-16__DS-16B                                    |                                                  | DS-16                  | Custom                  | 50     |",
        "notes": "The pinned DefenseFinder HMM inventory records DS-16__DS-16B as a custom DS-16 profile."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "ds_16_locus_reduces_phage_plaquing",
        "title": "DS-16 locus reduces bacteriophage plaquing",
        "description": "Conservative system-level sketch linking the two-gene DS-16 locus to reduced bacteriophage plaquing without resolving DS-16 component function or molecular output.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures DS-16 as the validated PLIK transcriptional unit with two product accessions, RelE and ABC ATPase HHpred-domain rows, and two DefenseFinder DS-16 profile rows. It does not assert native host breadth, exact profile-to-protein correspondence, DS-16A or DS-16B molecular activity, trigger, substrate, phage breadth, or DefenseFinder rule-level detection criteria.",
        "nodes": [
          {
            "node_id": "ds_16_locus",
            "label": "DS-16 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A two-gene DefensePredictor-discovered system 16 locus represented in the pinned DefenseFinder HMM inventory by DS-16A and DS-16B custom profiles."
          },
          {
            "node_id": "reduced_phage_plaquing",
            "label": "reduced bacteriophage plaquing",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced bacteriophage plaquing in cells carrying cloned PLIK."
          },
          {
            "node_id": "ds_16_system_trait",
            "label": "DS-16 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000439",
            "description": "Possession of a genome-encoded DS-16 phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "ds_16_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "reduced_phage_plaquing",
            "description": "The DS-16/PLIK locus contributes to reduced bacteriophage plaquing in heterologous E. coli MG1655 plasmid-expression assays.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
                "notes": "DeWeirdt et al. describe the plasmid-based phage challenge used to validate predicted transcriptional units."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
                "snippet": "PLIK\tNZ_QOYD01000001.1\tGCF_003333765.1\t-\tTrue\tFalse\tTrue\tTrue\tDefensePredictor hits\t281241\t284220\thypothetical protein, DUF3696 domain-containing protein\tWP_001676492.1, WP_001676491.1\t10.6830001978657\t5.517452896464706\tTrue\tTrue\tStructural defense homolog\tDS-16",
                "notes": "The final Science supplementary Table S6 maps working_id PLIK to DS_name DS-16, marks the cloned transcriptional unit as defensive, and records NZ_QOYD01000001.1 positions 281241-284220 with product accessions WP_001676492.1 and WP_001676491.1."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
                "snippet": "Bas26\t2.2\tpLAND\t24-03-12_EV.png\t2400000000\tPLIK\t24-03-21\t24-03-21_PLIK_REPB_2.png\t7\t31\tY\t310000000\t0.8888495478773333\t\tTrue\t\tLB\t37",
                "notes": "The final Science supplementary Table S7 reports a PLIK assay row with a Bas26 phage readout and smaller plaques."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
                "snippet": "T4\t2.1\tpLAND\t24-03-12_EV.png\t200000000\tPLIK\t24-03-21\t24-03-21_PLIK_REPB.png\t3\t100\t\t100000\t3.3010299956639813\t\tTrue\t\tLB\t37",
                "notes": "The final Science supplementary Table S7 reports a PLIK assay row with a T4 phage readout and a -log(EOP) value of 3.301."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
                "snippet": "PLIK\tDS-16\tTrue",
                "notes": "The final Science supplementary Table S8 maps PLIK to replicated display name DS-16."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| DS-16__DS-16A                                    |                                                  | DS-16                  | Custom                  | 500    |",
                "notes": "The pinned DefenseFinder HMM inventory records DS-16__DS-16A as a custom DS-16 profile."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| DS-16__DS-16B                                    |                                                  | DS-16                  | Custom                  | 50     |",
                "notes": "The pinned DefenseFinder HMM inventory records DS-16__DS-16B as a custom DS-16 profile."
              }
            ]
          },
          {
            "subject": "reduced_phage_plaquing",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "ds_16_system_trait",
            "description": "DS-16-mediated phage plaquing reduction realizes the DS-16 system trait.",
            "evidence": [
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
                "snippet": "PLIK\tNZ_QOYD01000001.1\tGCF_003333765.1\t-\tTrue\tFalse\tTrue\tTrue\tDefensePredictor hits\t281241\t284220\thypothetical protein, DUF3696 domain-containing protein\tWP_001676492.1, WP_001676491.1\t10.6830001978657\t5.517452896464706\tTrue\tTrue\tStructural defense homolog\tDS-16",
                "notes": "The final Science supplementary Table S6 maps working_id PLIK to DS_name DS-16, marks the cloned transcriptional unit as defensive, and records NZ_QOYD01000001.1 positions 281241-284220 with product accessions WP_001676492.1 and WP_001676491.1."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
                "snippet": "Bas26\t2.2\tpLAND\t24-03-12_EV.png\t2400000000\tPLIK\t24-03-21\t24-03-21_PLIK_REPB_2.png\t7\t31\tY\t310000000\t0.8888495478773333\t\tTrue\t\tLB\t37",
                "notes": "The final Science supplementary Table S7 reports a PLIK assay row with a Bas26 phage readout and smaller plaques."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
                "snippet": "T4\t2.1\tpLAND\t24-03-12_EV.png\t200000000\tPLIK\t24-03-21\t24-03-21_PLIK_REPB.png\t3\t100\t\t100000\t3.3010299956639813\t\tTrue\t\tLB\t37",
                "notes": "The final Science supplementary Table S7 reports a PLIK assay row with a T4 phage readout and a -log(EOP) value of 3.301."
              },
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
                "notes": "The DS nomenclature is used for DefensePredictor discovered systems."
              }
            ]
          },
          {
            "subject": "ds_16_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "DS-16 system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
                "notes": "DeWeirdt et al. name validated TUs as DefensePredictor discovered systems."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| DS-16 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
                "notes": "The pinned DefenseFinder article registry maps the DS-16 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "ds-16-defensefinder-model-gap",
        "prompt": "Resolve DS-16 native host breadth, exact profile-to-protein mapping, DS-16A/DS-16B component activities, RelE and ABC ATPase chemistry, sensitive-phage breadth, molecular output, and rule-level DefenseFinder criteria before minting narrower DS-16 mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "DeWeirdt et al. support DS-16 as the defensive PLIK transcriptional unit and final Science Tables S6/S7/S8 map it to product accessions WP_001676492.1 and WP_001676491.1, Bas26 and T4 phage readouts, display name DS-16, and RelE/ABC ATPase HHpred rows. The pinned DefenseFinder HMM inventory records DS-16A and DS-16B custom profile rows. The pinned rules table has no DS-16 row, and the first-pass record does not resolve native host breadth, phage breadth, direct profile-to-protein correspondence, RelE nuclease or ABC ATPase activity, molecular output, or endogenous DS-16 activity.",
        "evidence": [
          {
            "reference": "DOI:10.1126/science.adv7924",
            "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
            "notes": "DeWeirdt et al. name validated TUs as DSs."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
            "snippet": "PLIK\tNZ_QOYD01000001.1\tGCF_003333765.1\t-\tTrue\tFalse\tTrue\tTrue\tDefensePredictor hits\t281241\t284220\thypothetical protein, DUF3696 domain-containing protein\tWP_001676492.1, WP_001676491.1\t10.6830001978657\t5.517452896464706\tTrue\tTrue\tStructural defense homolog\tDS-16",
            "notes": "The final Science supplementary Table S6 maps working_id PLIK to DS_name DS-16, marks the cloned transcriptional unit as defensive, and records NZ_QOYD01000001.1 positions 281241-284220 with product accessions WP_001676492.1 and WP_001676491.1."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
            "snippet": "Bas26\t2.2\tpLAND\t24-03-12_EV.png\t2400000000\tPLIK\t24-03-21\t24-03-21_PLIK_REPB_2.png\t7\t31\tY\t310000000\t0.8888495478773333\t\tTrue\t\tLB\t37",
            "notes": "The final Science supplementary Table S7 reports a PLIK assay row with a Bas26 phage readout and smaller plaques."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
            "snippet": "T4\t2.1\tpLAND\t24-03-12_EV.png\t200000000\tPLIK\t24-03-21\t24-03-21_PLIK_REPB.png\t3\t100\t\t100000\t3.3010299956639813\t\tTrue\t\tLB\t37",
            "notes": "The final Science supplementary Table S7 reports a PLIK assay row with a T4 phage readout and a -log(EOP) value of 3.301."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
            "snippet": "PLIK\tDS-16\tTrue",
            "notes": "The final Science supplementary Table S8 maps PLIK to replicated display name DS-16."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
            "snippet": "PLIK\t2.0\t341.0\tWP_001676492.1\tRelE\t4NRN_A\tmetal-bound toxin; Toxin;\thhpred_4269994.hhr\t239.0\t335.0\t0.8002\t2024-04-15 00:00:00",
            "notes": "The final Science supplementary Table S8 reports a RelE HHpred hit for WP_001676492.1 in PLIK."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
            "snippet": "PLIK\t1.0\t656.0\tWP_001676491.1\tABC ATPase\t6QJ0_A\tStructural maintenance of chromosomes protein,Structural maintenance of chromosomes protein; condensin SMC complex ATPase\thhpred_2524462.hhr\t1.0\t572.0\t0.997\t2024-04-15 00:00:00",
            "notes": "The final Science supplementary Table S8 reports an ABC ATPase HHpred hit for WP_001676491.1 in PLIK."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
            "snippet": "| DS-16 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
            "notes": "The pinned DefenseFinder article registry maps the DS-16 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| DS-16__DS-16A                                    |                                                  | DS-16                  | Custom                  | 500    |",
            "notes": "The pinned DefenseFinder HMM inventory records DS-16__DS-16A as a custom DS-16 profile."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| DS-16__DS-16B                                    |                                                  | DS-16                  | Custom                  | 50     |",
            "notes": "The pinned DefenseFinder HMM inventory records DS-16__DS-16B as a custom DS-16 profile."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "The pinned DefenseFinder rules table does not list DS-16, DS-16A, or DS-16B, leaving complete component coverage and rule-level detection criteria unresolved."
          }
        ],
        "attaches_to": [
          "causal_graphs#ds_16_locus_reduces_phage_plaquing"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-28"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-28T17:24:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted DS-16 system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; kept the graph at PLIK transcriptional-unit level because RelE/ABC ATPase chemistry and rule rows remain unresolved, and proposals/metpo_traitmech_v316 reserves the replacement placeholder.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-28T17:24:01Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed DS-16 system canonical_examples and left them empty because DeWeirdt et al. directly support cloned PLIK assays in E. coli MG1655 and DefenseFinder DS-16 models, but not a direct named native microbial isolate exemplar with experimentally verified endogenous DS-16 activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000440",
    "label": "DS-17 system",
    "definition": "A phage defense system in which an organism possesses the single-gene DefensePredictor-discovered system 17 locus cataloged as working transcriptional unit NUCS and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.",
    "definition_source": "DOI:10.1126/science.adv7924",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "DS-17",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1126/science.adv7924"
      },
      {
        "synonym_text": "NUCS",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx"
      },
      {
        "synonym_text": "DS-17__DS-17",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1126/science.adv7924",
        "snippet": "To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
        "notes": "DeWeirdt et al. experimentally validated 42 predicted transcriptional units as phage-defense systems in E. coli."
      },
      {
        "reference": "DOI:10.1126/science.adv7924",
        "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
        "notes": "DeWeirdt et al. name validated transcriptional units as DefensePredictor discovered systems."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
        "snippet": "NUCS\tNZ_QOYO01000009.1\tGCF_003333605.1\t+\tTrue\tFalse\tFalse\tTrue\tDefensePredictor hits\t23399\t24397\thypothetical protein\tWP_001240354.1\t13.60450880206783\t3.377690933986817\tTrue\tTrue\tPredicted novel defense gene\tDS-17",
        "notes": "The final Science supplementary Table S6 maps working_id NUCS to DS_name DS-17, marks the cloned transcriptional unit as defensive, and records NZ_QOYO01000009.1 positions 23399-24397 with product accession WP_001240354.1."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
        "snippet": "T4\t6.2\tpLAND\t24-07-17_AAA2_VPUS_VAME_EV.png\t20000000\tNUCS\t24-07-17\t24-07-17_NERD_MVB1_RMOR_NUCS.png\t2\t10\t\t1000\t4.301029995663981\t\t\tTrue\tLB\t37",
        "notes": "The final Science supplementary Table S7 reports a NUCS assay row with a T4 phage readout and a -log(EOP) value of 4.301."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
        "snippet": "NUCS\tDS-17\tTrue",
        "notes": "The final Science supplementary Table S8 maps NUCS to replicated display name DS-17."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
        "snippet": "NUCS\t1.0\t332.0\tWP_001240354.1\tPDDEXK\tPF01939.21\tNucS_C ; Endonuclease NucS C-terminal domain\thhpred_4156604.hhr\t25.0\t181.0\t0.993\t2024-07-27 00:00:00\t412-414\t398.0",
        "notes": "The final Science supplementary Table S8 reports a PDDEXK HHpred hit for WP_001240354.1 in NUCS."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| DS-17 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
        "notes": "The pinned DefenseFinder article registry maps the DS-17 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| DS-17__DS-17                                     |                                                  | DS-17                  | Custom                  | 300    |",
        "notes": "The pinned DefenseFinder HMM inventory records DS-17__DS-17 as a custom DS-17 profile."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "ds_17_locus_reduces_phage_plaquing",
        "title": "DS-17 locus reduces bacteriophage plaquing",
        "description": "Conservative system-level sketch linking the single-gene DS-17 locus to reduced bacteriophage plaquing without resolving DS-17 component function or molecular output.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures DS-17 as the validated NUCS transcriptional unit with one product accession, one PDDEXK HHpred-domain row, and one DefenseFinder DS-17 profile row. It does not assert native host breadth, exact profile-to-protein correspondence, DS-17 molecular activity, trigger, substrate, phage breadth, or DefenseFinder rule-level detection criteria.",
        "nodes": [
          {
            "node_id": "ds_17_locus",
            "label": "DS-17 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A single-gene DefensePredictor-discovered system 17 locus represented in the pinned DefenseFinder HMM inventory by one DS-17 custom profile."
          },
          {
            "node_id": "reduced_phage_plaquing",
            "label": "reduced bacteriophage plaquing",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced bacteriophage plaquing in cells carrying cloned NUCS."
          },
          {
            "node_id": "ds_17_system_trait",
            "label": "DS-17 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000440",
            "description": "Possession of a genome-encoded DS-17 phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "ds_17_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "reduced_phage_plaquing",
            "description": "The DS-17/NUCS locus contributes to reduced bacteriophage plaquing in heterologous E. coli MG1655 plasmid-expression assays.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
                "notes": "DeWeirdt et al. describe the plasmid-based phage challenge used to validate predicted transcriptional units."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
                "snippet": "NUCS\tNZ_QOYO01000009.1\tGCF_003333605.1\t+\tTrue\tFalse\tFalse\tTrue\tDefensePredictor hits\t23399\t24397\thypothetical protein\tWP_001240354.1\t13.60450880206783\t3.377690933986817\tTrue\tTrue\tPredicted novel defense gene\tDS-17",
                "notes": "The final Science supplementary Table S6 maps working_id NUCS to DS_name DS-17, marks the cloned transcriptional unit as defensive, and records NZ_QOYO01000009.1 positions 23399-24397 with product accession WP_001240354.1."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
                "snippet": "T4\t6.2\tpLAND\t24-07-17_AAA2_VPUS_VAME_EV.png\t20000000\tNUCS\t24-07-17\t24-07-17_NERD_MVB1_RMOR_NUCS.png\t2\t10\t\t1000\t4.301029995663981\t\t\tTrue\tLB\t37",
                "notes": "The final Science supplementary Table S7 reports a NUCS assay row with a T4 phage readout and a -log(EOP) value of 4.301."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
                "snippet": "NUCS\tDS-17\tTrue",
                "notes": "The final Science supplementary Table S8 maps NUCS to replicated display name DS-17."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| DS-17__DS-17                                     |                                                  | DS-17                  | Custom                  | 300    |",
                "notes": "The pinned DefenseFinder HMM inventory records DS-17__DS-17 as a custom DS-17 profile."
              }
            ]
          },
          {
            "subject": "reduced_phage_plaquing",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "ds_17_system_trait",
            "description": "DS-17-mediated phage plaquing reduction realizes the DS-17 system trait.",
            "evidence": [
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
                "snippet": "NUCS\tNZ_QOYO01000009.1\tGCF_003333605.1\t+\tTrue\tFalse\tFalse\tTrue\tDefensePredictor hits\t23399\t24397\thypothetical protein\tWP_001240354.1\t13.60450880206783\t3.377690933986817\tTrue\tTrue\tPredicted novel defense gene\tDS-17",
                "notes": "The final Science supplementary Table S6 maps working_id NUCS to DS_name DS-17, marks the cloned transcriptional unit as defensive, and records NZ_QOYO01000009.1 positions 23399-24397 with product accession WP_001240354.1."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
                "snippet": "T4\t6.2\tpLAND\t24-07-17_AAA2_VPUS_VAME_EV.png\t20000000\tNUCS\t24-07-17\t24-07-17_NERD_MVB1_RMOR_NUCS.png\t2\t10\t\t1000\t4.301029995663981\t\t\tTrue\tLB\t37",
                "notes": "The final Science supplementary Table S7 reports a NUCS assay row with a T4 phage readout and a -log(EOP) value of 4.301."
              },
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
                "notes": "The DS nomenclature is used for DefensePredictor discovered systems."
              }
            ]
          },
          {
            "subject": "ds_17_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "DS-17 system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
                "notes": "DeWeirdt et al. name validated TUs as DefensePredictor discovered systems."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| DS-17 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
                "notes": "The pinned DefenseFinder article registry maps the DS-17 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "ds-17-defensefinder-model-gap",
        "prompt": "Resolve DS-17 native host breadth, exact profile-to-protein mapping, component chemistry, sensitive-phage breadth, molecular output, and rule-level DefenseFinder criteria before minting narrower DS-17 mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "DeWeirdt et al. support DS-17 as the defensive NUCS transcriptional unit and final Science Tables S6/S7/S8 map it to product accession WP_001240354.1, a T4 phage readout, display name DS-17, and a PDDEXK HHpred row. The pinned DefenseFinder HMM inventory records one DS-17 custom profile row. The pinned rules table has no DS-17 row, and the first-pass record does not resolve native host breadth, phage breadth, direct profile-to-protein correspondence, PDDEXK nuclease activity, molecular output, or endogenous DS-17 activity.",
        "evidence": [
          {
            "reference": "DOI:10.1126/science.adv7924",
            "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
            "notes": "DeWeirdt et al. name validated TUs as DSs."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
            "snippet": "NUCS\tNZ_QOYO01000009.1\tGCF_003333605.1\t+\tTrue\tFalse\tFalse\tTrue\tDefensePredictor hits\t23399\t24397\thypothetical protein\tWP_001240354.1\t13.60450880206783\t3.377690933986817\tTrue\tTrue\tPredicted novel defense gene\tDS-17",
            "notes": "The final Science supplementary Table S6 maps working_id NUCS to DS_name DS-17, marks the cloned transcriptional unit as defensive, and records NZ_QOYO01000009.1 positions 23399-24397 with product accession WP_001240354.1."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
            "snippet": "T4\t6.2\tpLAND\t24-07-17_AAA2_VPUS_VAME_EV.png\t20000000\tNUCS\t24-07-17\t24-07-17_NERD_MVB1_RMOR_NUCS.png\t2\t10\t\t1000\t4.301029995663981\t\t\tTrue\tLB\t37",
            "notes": "The final Science supplementary Table S7 reports a NUCS assay row with a T4 phage readout and a -log(EOP) value of 4.301."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
            "snippet": "NUCS\tDS-17\tTrue",
            "notes": "The final Science supplementary Table S8 maps NUCS to replicated display name DS-17."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
            "snippet": "NUCS\t1.0\t332.0\tWP_001240354.1\tPDDEXK\tPF01939.21\tNucS_C ; Endonuclease NucS C-terminal domain\thhpred_4156604.hhr\t25.0\t181.0\t0.993\t2024-07-27 00:00:00\t412-414\t398.0",
            "notes": "The final Science supplementary Table S8 reports a PDDEXK HHpred hit for WP_001240354.1 in NUCS."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
            "snippet": "| DS-17 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
            "notes": "The pinned DefenseFinder article registry maps the DS-17 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| DS-17__DS-17                                     |                                                  | DS-17                  | Custom                  | 300    |",
            "notes": "The pinned DefenseFinder HMM inventory records DS-17__DS-17 as a custom DS-17 profile."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "The pinned DefenseFinder rules table does not list DS-17, leaving rule-level detection criteria unresolved."
          }
        ],
        "attaches_to": [
          "causal_graphs#ds_17_locus_reduces_phage_plaquing"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-28"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-28T18:12:47Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted DS-17 system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; kept the graph at NUCS transcriptional-unit level because PDDEXK chemistry and rule rows remain unresolved, and proposals/metpo_traitmech_v317 reserves the replacement placeholder.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-28T18:12:48Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed DS-17 system canonical_examples and left them empty because DeWeirdt et al. directly support cloned NUCS assays in E. coli MG1655 and a DefenseFinder DS-17 model, but not a direct named native microbial isolate exemplar with experimentally verified endogenous DS-17 activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000441",
    "label": "DS-18 system",
    "definition": "A phage defense system in which an organism possesses the single-gene DefensePredictor-discovered system 18 locus cataloged as working transcriptional unit 6602 and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.",
    "definition_source": "DOI:10.1126/science.adv7924",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "DS-18",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1126/science.adv7924"
      },
      {
        "synonym_text": "6602",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx"
      },
      {
        "synonym_text": "DS-18__DS-18",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1126/science.adv7924",
        "snippet": "To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
        "notes": "DeWeirdt et al. experimentally validated 42 predicted transcriptional units as phage-defense systems in E. coli."
      },
      {
        "reference": "DOI:10.1126/science.adv7924",
        "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
        "notes": "DeWeirdt et al. name validated transcriptional units as DefensePredictor discovered systems."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
        "snippet": "6602\tNZ_QOWV01000002.1\tGCF_003334785.1\t-\tTrue\tFalse\tFalse\tTrue\tDefensePredictor hits\t550816\t551577\thypothetical protein\tWP_021529611.1\t11.52849398343986\t1.909829572490831\tTrue\tTrue\tRemote defense homolog\tDS-18",
        "notes": "The final Science supplementary Table S6 maps working_id 6602 to DS_name DS-18, marks the cloned transcriptional unit as defensive, and records NZ_QOWV01000002.1 positions 550816-551577 with product accession WP_021529611.1."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
        "snippet": "Candy\t6.2\tpLAND\t24-07-17_AAA2_VPUS_VAME_EV.png\t50000000\t6602\t24-07-24\t24-07-24_6602_TRNA_SC24_2CMP.png\t2\t10\t\t1000\t4.698970004336019\t\t\tTrue\tLB\t37",
        "notes": "The final Science supplementary Table S7 reports a 6602 assay row with a Candy phage readout and a -log(EOP) value of 4.699."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
        "snippet": "6602.0\tDS-18\tTrue",
        "notes": "The final Science supplementary Table S8 maps working identifier 6602 to replicated display name DS-18."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
        "snippet": "6602\t1.0\t253.0\tWP_021529611.1\tPDDEXK\tPF15516.11\tBpuSI_N ; BpuSI N-terminal domain\thhpred_6067831.hhr\t99.0\t197.0\t0.9417\t2024-07-28 00:00:00\t54-56\t41.0",
        "notes": "The final Science supplementary Table S8 reports a PDDEXK HHpred hit for WP_021529611.1 in 6602."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| DS-18 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
        "notes": "The pinned DefenseFinder article registry maps the DS-18 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| DS-18__DS-18                                     |                                                  | DS-18                  | Custom                  | 30     |",
        "notes": "The pinned DefenseFinder HMM inventory records DS-18__DS-18 as a custom DS-18 profile."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "ds_18_locus_reduces_phage_plaquing",
        "title": "DS-18 locus reduces bacteriophage plaquing",
        "description": "Conservative system-level sketch linking the single-gene DS-18 locus to reduced bacteriophage plaquing without resolving DS-18 component function or molecular output.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures DS-18 as the validated 6602 transcriptional unit with one product accession, one PDDEXK HHpred-domain row, and one DefenseFinder DS-18 profile row. It does not assert native host breadth, exact profile-to-protein correspondence, DS-18 molecular activity, trigger, substrate, phage breadth, or DefenseFinder rule-level detection criteria.",
        "nodes": [
          {
            "node_id": "ds_18_locus",
            "label": "DS-18 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A single-gene DefensePredictor-discovered system 18 locus represented in the pinned DefenseFinder HMM inventory by one DS-18 custom profile."
          },
          {
            "node_id": "reduced_phage_plaquing",
            "label": "reduced bacteriophage plaquing",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced bacteriophage plaquing in cells carrying cloned 6602."
          },
          {
            "node_id": "ds_18_system_trait",
            "label": "DS-18 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000441",
            "description": "Possession of a genome-encoded DS-18 phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "ds_18_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "reduced_phage_plaquing",
            "description": "The DS-18/6602 locus contributes to reduced bacteriophage plaquing in heterologous E. coli MG1655 plasmid-expression assays.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
                "notes": "DeWeirdt et al. describe the plasmid-based phage challenge used to validate predicted transcriptional units."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
                "snippet": "6602\tNZ_QOWV01000002.1\tGCF_003334785.1\t-\tTrue\tFalse\tFalse\tTrue\tDefensePredictor hits\t550816\t551577\thypothetical protein\tWP_021529611.1\t11.52849398343986\t1.909829572490831\tTrue\tTrue\tRemote defense homolog\tDS-18",
                "notes": "The final Science supplementary Table S6 maps working_id 6602 to DS_name DS-18, marks the cloned transcriptional unit as defensive, and records NZ_QOWV01000002.1 positions 550816-551577 with product accession WP_021529611.1."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
                "snippet": "Candy\t6.2\tpLAND\t24-07-17_AAA2_VPUS_VAME_EV.png\t50000000\t6602\t24-07-24\t24-07-24_6602_TRNA_SC24_2CMP.png\t2\t10\t\t1000\t4.698970004336019\t\t\tTrue\tLB\t37",
                "notes": "The final Science supplementary Table S7 reports a 6602 assay row with a Candy phage readout and a -log(EOP) value of 4.699."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
                "snippet": "6602.0\tDS-18\tTrue",
                "notes": "The final Science supplementary Table S8 maps working identifier 6602 to replicated display name DS-18."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| DS-18__DS-18                                     |                                                  | DS-18                  | Custom                  | 30     |",
                "notes": "The pinned DefenseFinder HMM inventory records DS-18__DS-18 as a custom DS-18 profile."
              }
            ]
          },
          {
            "subject": "reduced_phage_plaquing",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "ds_18_system_trait",
            "description": "DS-18-mediated phage plaquing reduction realizes the DS-18 system trait.",
            "evidence": [
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
                "snippet": "6602\tNZ_QOWV01000002.1\tGCF_003334785.1\t-\tTrue\tFalse\tFalse\tTrue\tDefensePredictor hits\t550816\t551577\thypothetical protein\tWP_021529611.1\t11.52849398343986\t1.909829572490831\tTrue\tTrue\tRemote defense homolog\tDS-18",
                "notes": "The final Science supplementary Table S6 maps working_id 6602 to DS_name DS-18, marks the cloned transcriptional unit as defensive, and records NZ_QOWV01000002.1 positions 550816-551577 with product accession WP_021529611.1."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
                "snippet": "Candy\t6.2\tpLAND\t24-07-17_AAA2_VPUS_VAME_EV.png\t50000000\t6602\t24-07-24\t24-07-24_6602_TRNA_SC24_2CMP.png\t2\t10\t\t1000\t4.698970004336019\t\t\tTrue\tLB\t37",
                "notes": "The final Science supplementary Table S7 reports a 6602 assay row with a Candy phage readout and a -log(EOP) value of 4.699."
              },
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
                "notes": "The DS nomenclature is used for DefensePredictor discovered systems."
              }
            ]
          },
          {
            "subject": "ds_18_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "DS-18 system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
                "notes": "DeWeirdt et al. name validated TUs as DefensePredictor discovered systems."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| DS-18 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
                "notes": "The pinned DefenseFinder article registry maps the DS-18 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "ds-18-defensefinder-model-gap",
        "prompt": "Resolve DS-18 native host breadth, exact profile-to-protein mapping, component chemistry, sensitive-phage breadth, molecular output, and rule-level DefenseFinder criteria before minting narrower DS-18 mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "DeWeirdt et al. support DS-18 as the defensive 6602 transcriptional unit and final Science Tables S6/S7/S8 map it to product accession WP_021529611.1, a Candy phage readout, display name DS-18, and a PDDEXK HHpred row. The pinned DefenseFinder HMM inventory records one DS-18 custom profile row. The pinned rules table has no DS-18 row, and the first-pass record does not resolve native host breadth, phage breadth, direct profile-to-protein correspondence, PDDEXK nuclease activity, molecular output, or endogenous DS-18 activity.",
        "evidence": [
          {
            "reference": "DOI:10.1126/science.adv7924",
            "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
            "notes": "DeWeirdt et al. name validated TUs as DSs."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
            "snippet": "6602\tNZ_QOWV01000002.1\tGCF_003334785.1\t-\tTrue\tFalse\tFalse\tTrue\tDefensePredictor hits\t550816\t551577\thypothetical protein\tWP_021529611.1\t11.52849398343986\t1.909829572490831\tTrue\tTrue\tRemote defense homolog\tDS-18",
            "notes": "The final Science supplementary Table S6 maps working_id 6602 to DS_name DS-18, marks the cloned transcriptional unit as defensive, and records NZ_QOWV01000002.1 positions 550816-551577 with product accession WP_021529611.1."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
            "snippet": "Candy\t6.2\tpLAND\t24-07-17_AAA2_VPUS_VAME_EV.png\t50000000\t6602\t24-07-24\t24-07-24_6602_TRNA_SC24_2CMP.png\t2\t10\t\t1000\t4.698970004336019\t\t\tTrue\tLB\t37",
            "notes": "The final Science supplementary Table S7 reports a 6602 assay row with a Candy phage readout and a -log(EOP) value of 4.699."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
            "snippet": "6602.0\tDS-18\tTrue",
            "notes": "The final Science supplementary Table S8 maps working identifier 6602 to replicated display name DS-18."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
            "snippet": "6602\t1.0\t253.0\tWP_021529611.1\tPDDEXK\tPF15516.11\tBpuSI_N ; BpuSI N-terminal domain\thhpred_6067831.hhr\t99.0\t197.0\t0.9417\t2024-07-28 00:00:00\t54-56\t41.0",
            "notes": "The final Science supplementary Table S8 reports a PDDEXK HHpred hit for WP_021529611.1 in 6602."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
            "snippet": "| DS-18 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
            "notes": "The pinned DefenseFinder article registry maps the DS-18 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| DS-18__DS-18                                     |                                                  | DS-18                  | Custom                  | 30     |",
            "notes": "The pinned DefenseFinder HMM inventory records DS-18__DS-18 as a custom DS-18 profile."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "The pinned DefenseFinder rules table does not list DS-18, leaving rule-level detection criteria unresolved."
          }
        ],
        "attaches_to": [
          "causal_graphs#ds_18_locus_reduces_phage_plaquing"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-28"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-28T18:54:30Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted DS-18 system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; kept the graph at 6602 transcriptional-unit level because PDDEXK chemistry and rule rows remain unresolved, and proposals/metpo_traitmech_v318 reserves the replacement placeholder.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-28T18:54:31Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed DS-18 system canonical_examples and left them empty because DeWeirdt et al. directly support cloned 6602 assays in E. coli MG1655 and a DefenseFinder DS-18 model, but not a direct named native microbial isolate exemplar with experimentally verified endogenous DS-18 activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000444",
    "label": "DS-19 system",
    "definition": "A phage defense system in which an organism possesses the single-gene DefensePredictor-discovered system 19 locus cataloged as working transcriptional unit PDP4 and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.",
    "definition_source": "DOI:10.1126/science.adv7924",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "DS-19",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1126/science.adv7924"
      },
      {
        "synonym_text": "PDP4",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx"
      },
      {
        "synonym_text": "DS-19__DS-19",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1126/science.adv7924",
        "snippet": "To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
        "notes": "DeWeirdt et al. experimentally validated 42 predicted transcriptional units as phage-defense systems in E. coli."
      },
      {
        "reference": "DOI:10.1126/science.adv7924",
        "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
        "notes": "DeWeirdt et al. name validated transcriptional units as DefensePredictor discovered systems."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
        "snippet": "PDP4\tNZ_RRVV01000031.1\tGCF_003886345.1\t-\tTrue\tFalse\tFalse\tTrue\tDefensePredictor hits\t628\t1611\thypothetical protein\tWP_000020904.1\t10.50465077977841\t-3.547151294285235\tTrue\tFalse\tPredicted novel defense gene\tDS-19",
        "notes": "The final Science supplementary Table S6 maps working_id PDP4 to DS_name DS-19, marks the cloned transcriptional unit as defensive, and records NZ_RRVV01000031.1 positions 628-1611 with product accession WP_000020904.1."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
        "snippet": "Bas19\t6.1\tpLAND\t24-07-17_MVB1_VPUS_VAME_EV.png\t2200000\tPDP4\t24-07-25\t24-07-25_PDP1_RED1_PDP4_RED7.png\t0\t1\t\t1\t6.342422680822207\t\t\tTrue\tLB\t37",
        "notes": "The final Science supplementary Table S7 reports a PDP4 assay row with a Bas19 phage readout and a -log(EOP) value of 6.342."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
        "snippet": "PDP4\tDS-19\tTrue",
        "notes": "The final Science supplementary Table S8 maps PDP4 to replicated display name DS-19."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
        "snippet": "PDP4\t1.0\t327.0\tWP_000020904.1\tPDDEXK\tPF18742.6\tDpnII-MboI ; REase_DpnII-MboI\thhpred_9962440.hhr\t2.0\t76.0\t0.718\t2024-07-30 00:00:00\t192-194\t181.0",
        "notes": "The final Science supplementary Table S8 reports a lower-probability PDDEXK HHpred hit for WP_000020904.1 in PDP4."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| DS-19 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
        "notes": "The pinned DefenseFinder article registry maps the DS-19 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| DS-19__DS-19                                     |                                                  | DS-19                  | Custom                  | 200    |",
        "notes": "The pinned DefenseFinder HMM inventory records DS-19__DS-19 as a custom DS-19 profile."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "ds_19_locus_reduces_phage_plaquing",
        "title": "DS-19 locus reduces bacteriophage plaquing",
        "description": "Conservative system-level sketch linking the single-gene DS-19 locus to reduced bacteriophage plaquing without resolving DS-19 component function or molecular output.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures DS-19 as the validated PDP4 transcriptional unit with one product accession, a lower-probability PDDEXK HHpred-domain row, and one DefenseFinder DS-19 profile row. It does not assert native host breadth, exact profile-to-protein correspondence, DS-19 molecular activity, trigger, substrate, complete phage breadth, or DefenseFinder rule-level detection criteria.",
        "nodes": [
          {
            "node_id": "ds_19_locus",
            "label": "DS-19 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A single-gene DefensePredictor-discovered system 19 locus represented in the pinned DefenseFinder HMM inventory by one DS-19 custom profile."
          },
          {
            "node_id": "reduced_phage_plaquing",
            "label": "reduced bacteriophage plaquing",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced bacteriophage plaquing in cells carrying cloned PDP4."
          },
          {
            "node_id": "ds_19_system_trait",
            "label": "DS-19 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000444",
            "description": "Possession of a genome-encoded DS-19 phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "ds_19_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "reduced_phage_plaquing",
            "description": "The DS-19/PDP4 locus contributes to reduced bacteriophage plaquing in heterologous E. coli MG1655 plasmid-expression assays.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
                "notes": "DeWeirdt et al. describe the plasmid-based phage challenge used to validate predicted transcriptional units."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
                "snippet": "PDP4\tNZ_RRVV01000031.1\tGCF_003886345.1\t-\tTrue\tFalse\tFalse\tTrue\tDefensePredictor hits\t628\t1611\thypothetical protein\tWP_000020904.1\t10.50465077977841\t-3.547151294285235\tTrue\tFalse\tPredicted novel defense gene\tDS-19",
                "notes": "The final Science supplementary Table S6 maps working_id PDP4 to DS_name DS-19, marks the cloned transcriptional unit as defensive, and records NZ_RRVV01000031.1 positions 628-1611 with product accession WP_000020904.1."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
                "snippet": "Bas19\t6.1\tpLAND\t24-07-17_MVB1_VPUS_VAME_EV.png\t2200000\tPDP4\t24-07-25\t24-07-25_PDP1_RED1_PDP4_RED7.png\t0\t1\t\t1\t6.342422680822207\t\t\tTrue\tLB\t37",
                "notes": "The final Science supplementary Table S7 reports a PDP4 assay row with a Bas19 phage readout and a -log(EOP) value of 6.342."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
                "snippet": "PDP4\tDS-19\tTrue",
                "notes": "The final Science supplementary Table S8 maps PDP4 to replicated display name DS-19."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| DS-19__DS-19                                     |                                                  | DS-19                  | Custom                  | 200    |",
                "notes": "The pinned DefenseFinder HMM inventory records DS-19__DS-19 as a custom DS-19 profile."
              }
            ]
          },
          {
            "subject": "reduced_phage_plaquing",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "ds_19_system_trait",
            "description": "DS-19-mediated phage plaquing reduction realizes the DS-19 system trait.",
            "evidence": [
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
                "snippet": "PDP4\tNZ_RRVV01000031.1\tGCF_003886345.1\t-\tTrue\tFalse\tFalse\tTrue\tDefensePredictor hits\t628\t1611\thypothetical protein\tWP_000020904.1\t10.50465077977841\t-3.547151294285235\tTrue\tFalse\tPredicted novel defense gene\tDS-19",
                "notes": "The final Science supplementary Table S6 maps working_id PDP4 to DS_name DS-19, marks the cloned transcriptional unit as defensive, and records NZ_RRVV01000031.1 positions 628-1611 with product accession WP_000020904.1."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
                "snippet": "Bas19\t6.1\tpLAND\t24-07-17_MVB1_VPUS_VAME_EV.png\t2200000\tPDP4\t24-07-25\t24-07-25_PDP1_RED1_PDP4_RED7.png\t0\t1\t\t1\t6.342422680822207\t\t\tTrue\tLB\t37",
                "notes": "The final Science supplementary Table S7 reports a PDP4 assay row with a Bas19 phage readout and a -log(EOP) value of 6.342."
              },
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
                "notes": "The DS nomenclature is used for DefensePredictor discovered systems."
              }
            ]
          },
          {
            "subject": "ds_19_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "DS-19 system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
                "notes": "DeWeirdt et al. name validated TUs as DefensePredictor discovered systems."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| DS-19 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
                "notes": "The pinned DefenseFinder article registry maps the DS-19 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "ds-19-defensefinder-model-gap",
        "prompt": "Resolve DS-19 native host breadth, exact profile-to-protein mapping, low-confidence HHpred-domain interpretation, component chemistry, complete phage breadth, molecular output, and rule-level DefenseFinder criteria before minting narrower DS-19 mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "DeWeirdt et al. support DS-19 as the defensive PDP4 transcriptional unit and final Science Tables S6/S7/S8 map it to product accession WP_000020904.1, a Bas19 phage readout, display name DS-19, and a lower-probability PDDEXK HHpred row. The pinned DefenseFinder HMM inventory records one DS-19 custom profile row. The pinned rules table has no DS-19 row, and the first-pass record does not resolve native host breadth, complete phage breadth, direct profile-to-protein correspondence, PDDEXK nuclease activity, molecular output, or endogenous DS-19 activity.",
        "evidence": [
          {
            "reference": "DOI:10.1126/science.adv7924",
            "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
            "notes": "DeWeirdt et al. name validated TUs as DSs."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
            "snippet": "PDP4\tNZ_RRVV01000031.1\tGCF_003886345.1\t-\tTrue\tFalse\tFalse\tTrue\tDefensePredictor hits\t628\t1611\thypothetical protein\tWP_000020904.1\t10.50465077977841\t-3.547151294285235\tTrue\tFalse\tPredicted novel defense gene\tDS-19",
            "notes": "The final Science supplementary Table S6 maps working_id PDP4 to DS_name DS-19, marks the cloned transcriptional unit as defensive, and records NZ_RRVV01000031.1 positions 628-1611 with product accession WP_000020904.1."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
            "snippet": "Bas19\t6.1\tpLAND\t24-07-17_MVB1_VPUS_VAME_EV.png\t2200000\tPDP4\t24-07-25\t24-07-25_PDP1_RED1_PDP4_RED7.png\t0\t1\t\t1\t6.342422680822207\t\t\tTrue\tLB\t37",
            "notes": "The final Science supplementary Table S7 reports a PDP4 assay row with a Bas19 phage readout and a -log(EOP) value of 6.342."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
            "snippet": "PDP4\tDS-19\tTrue",
            "notes": "The final Science supplementary Table S8 maps PDP4 to replicated display name DS-19."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
            "snippet": "PDP4\t1.0\t327.0\tWP_000020904.1\tPDDEXK\tPF18742.6\tDpnII-MboI ; REase_DpnII-MboI\thhpred_9962440.hhr\t2.0\t76.0\t0.718\t2024-07-30 00:00:00\t192-194\t181.0",
            "notes": "The final Science supplementary Table S8 reports a lower-probability PDDEXK HHpred hit for WP_000020904.1 in PDP4."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
            "snippet": "| DS-19 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
            "notes": "The pinned DefenseFinder article registry maps the DS-19 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| DS-19__DS-19                                     |                                                  | DS-19                  | Custom                  | 200    |",
            "notes": "The pinned DefenseFinder HMM inventory records DS-19__DS-19 as a custom DS-19 profile."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "The pinned DefenseFinder rules table does not list DS-19, leaving rule-level detection criteria unresolved."
          }
        ],
        "attaches_to": [
          "causal_graphs#ds_19_locus_reduces_phage_plaquing"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-28"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-28T21:10:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted DS-19 system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; kept the graph at PDP4 transcriptional-unit level because PDDEXK chemistry and rule rows remain unresolved, and proposals/metpo_traitmech_v321 reserves the replacement placeholder.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-28T21:10:01Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed DS-19 system canonical_examples and left them empty because DeWeirdt et al. directly support cloned PDP4 assays in E. coli MG1655 and a DefenseFinder DS-19 model, but not a direct named native microbial isolate exemplar with experimentally verified endogenous DS-19 activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000424",
    "label": "DS-1 system",
    "definition": "A phage defense system in which an organism possesses the two-gene DefensePredictor-discovered system 1 locus cataloged as working transcriptional unit D390 and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.",
    "definition_source": "DOI:10.1126/science.adv7924",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "DS-1",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1126/science.adv7924"
      },
      {
        "synonym_text": "D390",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx"
      },
      {
        "synonym_text": "DS-1__DS-1A",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "DS-1__DS-1B",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1126/science.adv7924",
        "snippet": "To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
        "notes": "DeWeirdt et al. experimentally validated 42 predicted transcriptional units as phage-defense systems in E. coli."
      },
      {
        "reference": "DOI:10.1126/science.adv7924",
        "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
        "notes": "DeWeirdt et al. name validated transcriptional units as DefensePredictor discovered systems."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
        "snippet": "D390\tNZ_RRVY01000002.1\tGCF_003886375.1\t+\tTrue\tFalse\tTrue\tTrue\tDefensePredictor hits\t220602\t222994\thypothetical protein, nucleoid-associated protein\tWP_000150292.1, WP_000355468.1\t12.74067081596784\t-2.197224577336219\tTrue\tFalse\tPredicted novel defense gene\tDS-1",
        "notes": "The final Science supplementary Table S6 maps working_id D390 to DS_name DS-1, marks the cloned transcriptional unit as defensive, and records NZ_RRVY01000002.1 positions 220602-222994 with product accessions WP_000355468.1 and WP_000150292.1."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
        "snippet": "Bas1\t1.2\tpLAND\t24-03-08_EV_HHHD_PIN2_CRDO.png\t40000000\tD390\t24-03-12\t24-03-12_PIN8_D390_NADR_PN12.png\t0\t1\t\t1\t7.6020599913279625\tTrue\tTrue\t\tLB\t37",
        "notes": "The final Science supplementary Table S7 reports a D390 assay row with a 1-PFU Bas1 readout and a -log(EOP) value of 7.602."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
        "snippet": "D390\tDS-1\tTrue",
        "notes": "The final Science supplementary Table S8 maps D390 to replicated display name DS-1."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| DS-1 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
        "notes": "The pinned DefenseFinder article registry maps the DS-1 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| DS-1__DS-1A                                      |                                                  | DS-1                   | Custom                  | 30     |",
        "notes": "The pinned DefenseFinder HMM inventory records DS-1__DS-1A as a custom DS-1 profile."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| DS-1__DS-1B                                      |                                                  | DS-1                   | Custom                  | 50     |",
        "notes": "The pinned DefenseFinder HMM inventory records DS-1__DS-1B as a custom DS-1 profile."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "ds_1_locus_reduces_phage_plaquing",
        "title": "DS-1 loci reduce bacteriophage plaquing",
        "description": "Conservative system-level sketch linking the two-gene DS-1 locus to reduced bacteriophage plaquing without resolving DS-1 component functions or effector activity.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures DS-1 as the validated D390 transcriptional unit with two product accessions and with DefenseFinder DS-1A and DS-1B profile rows. It does not assert native host breadth, exact profile-to-protein correspondence, the direct viral trigger or substrate, exact molecular output, phage target breadth, or DefenseFinder rule-level detection criteria.",
        "nodes": [
          {
            "node_id": "ds_1_locus",
            "label": "DS-1 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A two-gene DefensePredictor-discovered system locus represented in the pinned DefenseFinder HMM inventory by DS-1A and DS-1B custom profiles."
          },
          {
            "node_id": "reduced_phage_plaquing",
            "label": "reduced bacteriophage plaquing",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced efficiency of plaquing or reduced plaque size by bacteriophages in cells carrying cloned D390."
          },
          {
            "node_id": "ds_1_system_trait",
            "label": "DS-1 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000424",
            "description": "Possession of a genome-encoded DS-1 phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "ds_1_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "reduced_phage_plaquing",
            "description": "The DS-1/D390 locus contributes to reduced bacteriophage plaquing when plasmid expressed.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
                "notes": "DeWeirdt et al. experimentally validate DefensePredictor-discovered systems by assaying cloned transcriptional units against E. coli phages."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
                "snippet": "D390\tNZ_RRVY01000002.1\tGCF_003886375.1\t+\tTrue\tFalse\tTrue\tTrue\tDefensePredictor hits\t220602\t222994\thypothetical protein, nucleoid-associated protein\tWP_000150292.1, WP_000355468.1\t12.74067081596784\t-2.197224577336219\tTrue\tFalse\tPredicted novel defense gene\tDS-1",
                "notes": "The final Science supplementary Table S6 maps working_id D390 to DS_name DS-1, marks the cloned transcriptional unit as defensive, and records NZ_RRVY01000002.1 positions 220602-222994 with product accessions WP_000355468.1 and WP_000150292.1."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
                "snippet": "Bas1\t1.2\tpLAND\t24-03-08_EV_HHHD_PIN2_CRDO.png\t40000000\tD390\t24-03-12\t24-03-12_PIN8_D390_NADR_PN12.png\t0\t1\t\t1\t7.6020599913279625\tTrue\tTrue\t\tLB\t37",
                "notes": "The final Science supplementary Table S7 reports a D390 assay row with a 1-PFU Bas1 readout and a -log(EOP) value of 7.602."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| DS-1__DS-1A                                      |                                                  | DS-1                   | Custom                  | 30     |",
                "notes": "The pinned DefenseFinder HMM inventory records DS-1__DS-1A as a custom DS-1 profile."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| DS-1__DS-1B                                      |                                                  | DS-1                   | Custom                  | 50     |",
                "notes": "The pinned DefenseFinder HMM inventory records DS-1__DS-1B as a custom DS-1 profile."
              }
            ]
          },
          {
            "subject": "reduced_phage_plaquing",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "ds_1_system_trait",
            "description": "DS-1-mediated phage plaquing reduction realizes the DS-1 system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
                "notes": "DeWeirdt et al. name each validated transcriptional unit as a DefensePredictor discovered system."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
                "snippet": "D390\tNZ_RRVY01000002.1\tGCF_003886375.1\t+\tTrue\tFalse\tTrue\tTrue\tDefensePredictor hits\t220602\t222994\thypothetical protein, nucleoid-associated protein\tWP_000150292.1, WP_000355468.1\t12.74067081596784\t-2.197224577336219\tTrue\tFalse\tPredicted novel defense gene\tDS-1",
                "notes": "The final Science supplementary Table S6 maps working_id D390 to DS_name DS-1, marks the cloned transcriptional unit as defensive, and records NZ_RRVY01000002.1 positions 220602-222994 with product accessions WP_000355468.1 and WP_000150292.1."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
                "snippet": "Bas1\t1.2\tpLAND\t24-03-08_EV_HHHD_PIN2_CRDO.png\t40000000\tD390\t24-03-12\t24-03-12_PIN8_D390_NADR_PN12.png\t0\t1\t\t1\t7.6020599913279625\tTrue\tTrue\t\tLB\t37",
                "notes": "The final Science supplementary Table S7 reports a D390 assay row with a 1-PFU Bas1 readout and a -log(EOP) value of 7.602."
              }
            ]
          },
          {
            "subject": "ds_1_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "DS-1 system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
                "notes": "DeWeirdt et al. validate DSs as anti-phage systems."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| DS-1 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
                "notes": "The pinned DefenseFinder article registry maps the DS-1 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "ds-1-defensefinder-model-gap",
        "prompt": "Resolve DS-1 native host breadth, exact DS-1A/DS-1B component functions, profile-to-component mapping, sensitive-phage breadth, molecular output, and rule-level detection criteria before minting narrower DS-1 mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "DeWeirdt et al. support DS-1 as the defensive D390 transcriptional unit that reduced plaquing when cloned in E. coli MG1655, and the pinned DefenseFinder HMM inventory records DS-1A and DS-1B profile rows. The pinned rules table has no DS-1 row, and the first-pass record does not resolve native host breadth, exact component activities, profile-to-component mapping, phage target breadth, the direct molecular output, or endogenous DS-1 activity.",
        "evidence": [
          {
            "reference": "DOI:10.1126/science.adv7924",
            "snippet": "To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
            "notes": "DeWeirdt et al. validate predicted transcriptional units by measuring plaquing relative to an empty vector control strain."
          },
          {
            "reference": "DOI:10.1126/science.adv7924",
            "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
            "notes": "DeWeirdt et al. name validated TUs as DSs."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
            "snippet": "D390\tNZ_RRVY01000002.1\tGCF_003886375.1\t+\tTrue\tFalse\tTrue\tTrue\tDefensePredictor hits\t220602\t222994\thypothetical protein, nucleoid-associated protein\tWP_000150292.1, WP_000355468.1\t12.74067081596784\t-2.197224577336219\tTrue\tFalse\tPredicted novel defense gene\tDS-1",
            "notes": "The final Science supplementary Table S6 maps working_id D390 to DS_name DS-1, marks the cloned transcriptional unit as defensive, and records NZ_RRVY01000002.1 positions 220602-222994 with product accessions WP_000355468.1 and WP_000150292.1."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
            "snippet": "Bas1\t1.2\tpLAND\t24-03-08_EV_HHHD_PIN2_CRDO.png\t40000000\tD390\t24-03-12\t24-03-12_PIN8_D390_NADR_PN12.png\t0\t1\t\t1\t7.6020599913279625\tTrue\tTrue\t\tLB\t37",
            "notes": "The final Science supplementary Table S7 reports a D390 assay row with a 1-PFU Bas1 readout and a -log(EOP) value of 7.602."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
            "snippet": "D390\tDS-1\tTrue",
            "notes": "The final Science supplementary Table S8 maps D390 to replicated display name DS-1."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
            "snippet": "| DS-1 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
            "notes": "The pinned DefenseFinder article registry maps the DS-1 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| DS-1__DS-1A                                      |                                                  | DS-1                   | Custom                  | 30     |",
            "notes": "The pinned DefenseFinder HMM inventory records DS-1__DS-1A as a custom DS-1 profile."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| DS-1__DS-1B                                      |                                                  | DS-1                   | Custom                  | 50     |",
            "notes": "The pinned DefenseFinder HMM inventory records DS-1__DS-1B as a custom DS-1 profile."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "The pinned DefenseFinder rules table does not list DS-1, leaving rule-level detection criteria unresolved."
          }
        ],
        "attaches_to": [
          "causal_graphs#ds_1_locus_reduces_phage_plaquing"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-28"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-28T02:18:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted DS-1 system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; kept the graph at cloned D390 transcriptional unit level because the pinned DefenseFinder DS-1 HMM rows are not backed by a rules row; proposals/metpo_traitmech_v301 reserves the replacement placeholder.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-28T02:18:01Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed DS-1 system canonical_examples and left them empty because DeWeirdt et al. support cloned D390 plaquing assays in E. coli MG1655 plus a DefenseFinder DS-1 model, but not a direct named native microbial isolate exemplar with experimentally verified endogenous DS-1 activity. No paid research was used.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-28T03:20:08Z",
        "curator": "codex",
        "action": "ADDRESSED_PR_REVIEW",
        "changes": "Addressed issue 1380 by rewriting the DS-1 definition so D390 is a DeWeirdt et al. working transcriptional-unit identifier rather than an implied E. coli transcriptional unit, expanding the DOI evidence snippets to explicitly state E. coli MG1655 low-copy plasmid expression, and syncing the METPO proposal definition.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000445",
    "label": "DS-20 system",
    "definition": "A phage defense system in which an organism possesses the single-gene DefensePredictor-discovered system 20 locus cataloged as working transcriptional unit PDX1 and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.",
    "definition_source": "DOI:10.1126/science.adv7924",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "DS-20",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1126/science.adv7924"
      },
      {
        "synonym_text": "PDX1",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx"
      },
      {
        "synonym_text": "DS-20__DS-20",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1126/science.adv7924",
        "snippet": "To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
        "notes": "DeWeirdt et al. experimentally validated 42 predicted transcriptional units as phage-defense systems in E. coli."
      },
      {
        "reference": "DOI:10.1126/science.adv7924",
        "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
        "notes": "DeWeirdt et al. name validated transcriptional units as DefensePredictor discovered systems."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
        "snippet": "PDX1\tNZ_QOYR01000022.1\tGCF_003333645.1\t-\tTrue\tFalse\tFalse\tTrue\tDefensePredictor hits\t1818\t3281\thypothetical protein\tWP_032291790.1\t10.95629906376924\t3.078568279133139\tTrue\tTrue\tPredicted novel defense gene\tDS-20",
        "notes": "The final Science supplementary Table S6 maps working_id PDX1 to DS_name DS-20, marks the cloned transcriptional unit as defensive, and records NZ_QOYR01000022.1 positions 1818-3281 with product accession WP_032291790.1."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
        "snippet": "Bas3\t6.1\tpLAND\t24-07-17_MVB1_VPUS_VAME_EV.png\t100000000\tPDX1\t24-07-25\t24-07-25_PDX1_TMO1_VANC_TOXO.png\t6\t2\t\t2000000\t1.6989700043360187\t\t\tTrue\tLB\t37",
        "notes": "The final Science supplementary Table S7 reports a PDX1 assay row with a Bas3 phage readout and a -log(EOP) value of 1.699."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
        "snippet": "PDX1\tDS-20\tTrue",
        "notes": "The final Science supplementary Table S8 maps PDX1 to replicated display name DS-20."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
        "snippet": "PDX1\t1.0\t487.0\tWP_032291790.1\tPDDEXK\tPF18742.6\tDpnII-MboI ; REase_DpnII-MboI\thhpred_2680313.hhr\t333.0\t474.0\t0.9685\t2024-07-29 00:00:00\t109-111\t94.0",
        "notes": "The final Science supplementary Table S8 reports a PDDEXK HHpred hit for WP_032291790.1 in PDX1."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| DS-20 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
        "notes": "The pinned DefenseFinder article registry maps the DS-20 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| DS-20__DS-20                                     |                                                  | DS-20                  | Custom                  | 300    |",
        "notes": "The pinned DefenseFinder HMM inventory records DS-20__DS-20 as a custom DS-20 profile."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "ds_20_locus_reduces_phage_plaquing",
        "title": "DS-20 locus reduces bacteriophage plaquing",
        "description": "Conservative system-level sketch linking the single-gene DS-20 locus to reduced bacteriophage plaquing without resolving DS-20 component function or molecular output.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures DS-20 as the validated PDX1 transcriptional unit with one product accession, a PDDEXK HHpred-domain row, and one DefenseFinder DS-20 profile row. It does not assert native host breadth, exact profile-to-protein correspondence, DS-20 molecular activity, trigger, substrate, complete phage breadth, or DefenseFinder rule-level detection criteria.",
        "nodes": [
          {
            "node_id": "ds_20_locus",
            "label": "DS-20 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A single-gene DefensePredictor-discovered system 20 locus represented in the pinned DefenseFinder HMM inventory by one DS-20 custom profile."
          },
          {
            "node_id": "reduced_phage_plaquing",
            "label": "reduced bacteriophage plaquing",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced bacteriophage plaquing in cells carrying cloned PDX1."
          },
          {
            "node_id": "ds_20_system_trait",
            "label": "DS-20 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000445",
            "description": "Possession of a genome-encoded DS-20 phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "ds_20_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "reduced_phage_plaquing",
            "description": "The DS-20/PDX1 locus contributes to reduced bacteriophage plaquing in heterologous E. coli MG1655 plasmid-expression assays.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
                "notes": "DeWeirdt et al. describe the plasmid-based phage challenge used to validate predicted transcriptional units."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
                "snippet": "PDX1\tNZ_QOYR01000022.1\tGCF_003333645.1\t-\tTrue\tFalse\tFalse\tTrue\tDefensePredictor hits\t1818\t3281\thypothetical protein\tWP_032291790.1\t10.95629906376924\t3.078568279133139\tTrue\tTrue\tPredicted novel defense gene\tDS-20",
                "notes": "The final Science supplementary Table S6 maps working_id PDX1 to DS_name DS-20, marks the cloned transcriptional unit as defensive, and records NZ_QOYR01000022.1 positions 1818-3281 with product accession WP_032291790.1."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
                "snippet": "Bas3\t6.1\tpLAND\t24-07-17_MVB1_VPUS_VAME_EV.png\t100000000\tPDX1\t24-07-25\t24-07-25_PDX1_TMO1_VANC_TOXO.png\t6\t2\t\t2000000\t1.6989700043360187\t\t\tTrue\tLB\t37",
                "notes": "The final Science supplementary Table S7 reports a PDX1 assay row with a Bas3 phage readout and a -log(EOP) value of 1.699."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
                "snippet": "PDX1\tDS-20\tTrue",
                "notes": "The final Science supplementary Table S8 maps PDX1 to replicated display name DS-20."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| DS-20__DS-20                                     |                                                  | DS-20                  | Custom                  | 300    |",
                "notes": "The pinned DefenseFinder HMM inventory records DS-20__DS-20 as a custom DS-20 profile."
              }
            ]
          },
          {
            "subject": "reduced_phage_plaquing",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "ds_20_system_trait",
            "description": "DS-20-mediated phage plaquing reduction realizes the DS-20 system trait.",
            "evidence": [
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
                "snippet": "PDX1\tNZ_QOYR01000022.1\tGCF_003333645.1\t-\tTrue\tFalse\tFalse\tTrue\tDefensePredictor hits\t1818\t3281\thypothetical protein\tWP_032291790.1\t10.95629906376924\t3.078568279133139\tTrue\tTrue\tPredicted novel defense gene\tDS-20",
                "notes": "The final Science supplementary Table S6 maps working_id PDX1 to DS_name DS-20, marks the cloned transcriptional unit as defensive, and records NZ_QOYR01000022.1 positions 1818-3281 with product accession WP_032291790.1."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
                "snippet": "Bas3\t6.1\tpLAND\t24-07-17_MVB1_VPUS_VAME_EV.png\t100000000\tPDX1\t24-07-25\t24-07-25_PDX1_TMO1_VANC_TOXO.png\t6\t2\t\t2000000\t1.6989700043360187\t\t\tTrue\tLB\t37",
                "notes": "The final Science supplementary Table S7 reports a PDX1 assay row with a Bas3 phage readout and a -log(EOP) value of 1.699."
              },
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
                "notes": "The DS nomenclature is used for DefensePredictor discovered systems."
              }
            ]
          },
          {
            "subject": "ds_20_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "DS-20 system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
                "notes": "DeWeirdt et al. name validated TUs as DefensePredictor discovered systems."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| DS-20 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
                "notes": "The pinned DefenseFinder article registry maps the DS-20 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "ds-20-defensefinder-model-gap",
        "prompt": "Resolve DS-20 native host breadth, exact profile-to-protein mapping, HHpred-domain interpretation, component chemistry, complete phage breadth, molecular output, and rule-level DefenseFinder criteria before minting narrower DS-20 mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "DeWeirdt et al. support DS-20 as the defensive PDX1 transcriptional unit and final Science Tables S6/S7/S8 map it to product accession WP_032291790.1, a Bas3 phage readout, display name DS-20, and a PDDEXK HHpred row. The pinned DefenseFinder HMM inventory records one DS-20 custom profile row. The pinned rules table has no DS-20 row, and the first-pass record does not resolve native host breadth, complete phage breadth, direct profile-to-protein correspondence, PDDEXK nuclease activity, molecular output, or endogenous DS-20 activity.",
        "evidence": [
          {
            "reference": "DOI:10.1126/science.adv7924",
            "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
            "notes": "DeWeirdt et al. name validated TUs as DSs."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
            "snippet": "PDX1\tNZ_QOYR01000022.1\tGCF_003333645.1\t-\tTrue\tFalse\tFalse\tTrue\tDefensePredictor hits\t1818\t3281\thypothetical protein\tWP_032291790.1\t10.95629906376924\t3.078568279133139\tTrue\tTrue\tPredicted novel defense gene\tDS-20",
            "notes": "The final Science supplementary Table S6 maps working_id PDX1 to DS_name DS-20, marks the cloned transcriptional unit as defensive, and records NZ_QOYR01000022.1 positions 1818-3281 with product accession WP_032291790.1."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
            "snippet": "Bas3\t6.1\tpLAND\t24-07-17_MVB1_VPUS_VAME_EV.png\t100000000\tPDX1\t24-07-25\t24-07-25_PDX1_TMO1_VANC_TOXO.png\t6\t2\t\t2000000\t1.6989700043360187\t\t\tTrue\tLB\t37",
            "notes": "The final Science supplementary Table S7 reports a PDX1 assay row with a Bas3 phage readout and a -log(EOP) value of 1.699."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
            "snippet": "PDX1\tDS-20\tTrue",
            "notes": "The final Science supplementary Table S8 maps PDX1 to replicated display name DS-20."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
            "snippet": "PDX1\t1.0\t487.0\tWP_032291790.1\tPDDEXK\tPF18742.6\tDpnII-MboI ; REase_DpnII-MboI\thhpred_2680313.hhr\t333.0\t474.0\t0.9685\t2024-07-29 00:00:00\t109-111\t94.0",
            "notes": "The final Science supplementary Table S8 reports a PDDEXK HHpred hit for WP_032291790.1 in PDX1."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
            "snippet": "| DS-20 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
            "notes": "The pinned DefenseFinder article registry maps the DS-20 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| DS-20__DS-20                                     |                                                  | DS-20                  | Custom                  | 300    |",
            "notes": "The pinned DefenseFinder HMM inventory records DS-20__DS-20 as a custom DS-20 profile."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "The pinned DefenseFinder rules table does not list DS-20, leaving rule-level detection criteria unresolved."
          }
        ],
        "attaches_to": [
          "causal_graphs#ds_20_locus_reduces_phage_plaquing"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-28"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-28T21:46:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted DS-20 system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; kept the graph at PDX1 transcriptional-unit level because PDDEXK chemistry and rule rows remain unresolved, and proposals/metpo_traitmech_v322 reserves the replacement placeholder.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-28T21:46:01Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed DS-20 system canonical_examples and left them empty because DeWeirdt et al. directly support cloned PDX1 assays in E. coli MG1655 and a DefenseFinder DS-20 model, but not a direct named native microbial isolate exemplar with experimentally verified endogenous DS-20 activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000446",
    "label": "DS-21 system",
    "definition": "A phage defense system in which an organism possesses the three-gene DefensePredictor-discovered system 21 locus cataloged as working transcriptional unit TOXO and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.",
    "definition_source": "DOI:10.1126/science.adv7924",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "DS-21",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1126/science.adv7924"
      },
      {
        "synonym_text": "TOXO",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx"
      },
      {
        "synonym_text": "DS-21__DS-21A",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "DS-21__DS-21B",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "DS-21__DS-21C",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1126/science.adv7924",
        "snippet": "To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
        "notes": "DeWeirdt et al. experimentally validated 42 predicted transcriptional units as phage-defense systems in E. coli."
      },
      {
        "reference": "DOI:10.1126/science.adv7924",
        "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
        "notes": "DeWeirdt et al. name validated transcriptional units as DefensePredictor discovered systems."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
        "snippet": "TOXO\tNZ_QOXJ01000032.1\tGCF_003334085.1\t-\tTrue\tFalse\tFalse\tTrue\tDefensePredictor hits\t7805\t9963\thypothetical protein, hypothetical protein, hypothetical protein\tWP_001532221.1, WP_001557682.1, WP_021552536.1\t10.9763556055726\t2.883007179633958\tTrue\tTrue\tPredicted novel defense gene\tDS-21",
        "notes": "The final Science supplementary Table S6 maps working_id TOXO to DS_name DS-21, marks the cloned transcriptional unit as defensive, and records NZ_QOXJ01000032.1 positions 7805-9963 with three product accessions."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
        "snippet": "Bas1\t6.1\tpLAND\t24-07-17_MVB1_VPUS_VAME_EV.png\t3000000\tTOXO\t24-07-25\t24-07-25_PDX1_TMO1_VANC_TOXO.png\t2\t1\t\t100\t4.477121254719663\t\t\tTrue\tLB\t37",
        "notes": "The final Science supplementary Table S7 reports a TOXO assay row with a Bas1 phage readout and a -log(EOP) value of 4.477."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
        "snippet": "TOXO\tDS-21\tTrue",
        "notes": "The final Science supplementary Table S8 maps TOXO to replicated display name DS-21."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
        "snippet": "TOXO\t3.0\t211.0\tWP_001557682.1\tPDDEXK\tPF18742.6\tDpnII-MboI ; REase_DpnII-MboI\thhpred_4621019.hhr\t37.0\t160.0\t0.96\t2024-07-29 00:00:00\t121-123\t103.0",
        "notes": "The final Science supplementary Table S8 reports a PDDEXK HHpred hit for WP_001557682.1 in TOXO."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| DS-21 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
        "notes": "The pinned DefenseFinder article registry maps the DS-21 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| DS-21__DS-21A                                    |                                                  | DS-21                  | Custom                  | 20     |\n| DS-21__DS-21B                                    |                                                  | DS-21                  | Custom                  | 250    |\n| DS-21__DS-21C                                    |                                                  | DS-21                  | Custom                  | 70     |",
        "notes": "The pinned DefenseFinder HMM inventory records three DS-21 custom profiles: DS-21__DS-21A, DS-21__DS-21B, and DS-21__DS-21C."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "ds_21_locus_reduces_phage_plaquing",
        "title": "DS-21 locus reduces bacteriophage plaquing",
        "description": "Conservative system-level sketch linking the three-gene DS-21 locus to reduced bacteriophage plaquing without resolving DS-21 component function or molecular output.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures DS-21 as the validated TOXO transcriptional unit with three product accessions, a PDDEXK HHpred-domain row, and three DefenseFinder DS-21 profile rows. It does not assert native host breadth, exact profile-to-protein correspondence, DS-21 molecular activity, trigger, substrate, complete phage breadth, or DefenseFinder rule-level detection criteria.",
        "nodes": [
          {
            "node_id": "ds_21_locus",
            "label": "DS-21 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A three-gene DefensePredictor-discovered system 21 locus represented in the pinned DefenseFinder HMM inventory by three DS-21 custom profiles."
          },
          {
            "node_id": "reduced_phage_plaquing",
            "label": "reduced bacteriophage plaquing",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced bacteriophage plaquing in cells carrying cloned TOXO."
          },
          {
            "node_id": "ds_21_system_trait",
            "label": "DS-21 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000446",
            "description": "Possession of a genome-encoded DS-21 phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "ds_21_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "reduced_phage_plaquing",
            "description": "The DS-21/TOXO locus contributes to reduced bacteriophage plaquing in heterologous E. coli MG1655 plasmid-expression assays.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
                "notes": "DeWeirdt et al. describe the plasmid-based phage challenge used to validate predicted transcriptional units."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
                "snippet": "TOXO\tNZ_QOXJ01000032.1\tGCF_003334085.1\t-\tTrue\tFalse\tFalse\tTrue\tDefensePredictor hits\t7805\t9963\thypothetical protein, hypothetical protein, hypothetical protein\tWP_001532221.1, WP_001557682.1, WP_021552536.1\t10.9763556055726\t2.883007179633958\tTrue\tTrue\tPredicted novel defense gene\tDS-21",
                "notes": "The final Science supplementary Table S6 maps working_id TOXO to DS_name DS-21, marks the cloned transcriptional unit as defensive, and records NZ_QOXJ01000032.1 positions 7805-9963 with three product accessions."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
                "snippet": "Bas1\t6.1\tpLAND\t24-07-17_MVB1_VPUS_VAME_EV.png\t3000000\tTOXO\t24-07-25\t24-07-25_PDX1_TMO1_VANC_TOXO.png\t2\t1\t\t100\t4.477121254719663\t\t\tTrue\tLB\t37",
                "notes": "The final Science supplementary Table S7 reports a TOXO assay row with a Bas1 phage readout and a -log(EOP) value of 4.477."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
                "snippet": "TOXO\tDS-21\tTrue",
                "notes": "The final Science supplementary Table S8 maps TOXO to replicated display name DS-21."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| DS-21__DS-21A                                    |                                                  | DS-21                  | Custom                  | 20     |\n| DS-21__DS-21B                                    |                                                  | DS-21                  | Custom                  | 250    |\n| DS-21__DS-21C                                    |                                                  | DS-21                  | Custom                  | 70     |",
                "notes": "The pinned DefenseFinder HMM inventory records three DS-21 custom profiles: DS-21__DS-21A, DS-21__DS-21B, and DS-21__DS-21C."
              }
            ]
          },
          {
            "subject": "reduced_phage_plaquing",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "ds_21_system_trait",
            "description": "DS-21-mediated phage plaquing reduction realizes the DS-21 system trait.",
            "evidence": [
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
                "snippet": "TOXO\tNZ_QOXJ01000032.1\tGCF_003334085.1\t-\tTrue\tFalse\tFalse\tTrue\tDefensePredictor hits\t7805\t9963\thypothetical protein, hypothetical protein, hypothetical protein\tWP_001532221.1, WP_001557682.1, WP_021552536.1\t10.9763556055726\t2.883007179633958\tTrue\tTrue\tPredicted novel defense gene\tDS-21",
                "notes": "The final Science supplementary Table S6 maps working_id TOXO to DS_name DS-21, marks the cloned transcriptional unit as defensive, and records NZ_QOXJ01000032.1 positions 7805-9963 with three product accessions."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
                "snippet": "Bas1\t6.1\tpLAND\t24-07-17_MVB1_VPUS_VAME_EV.png\t3000000\tTOXO\t24-07-25\t24-07-25_PDX1_TMO1_VANC_TOXO.png\t2\t1\t\t100\t4.477121254719663\t\t\tTrue\tLB\t37",
                "notes": "The final Science supplementary Table S7 reports a TOXO assay row with a Bas1 phage readout and a -log(EOP) value of 4.477."
              },
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
                "notes": "The DS nomenclature is used for DefensePredictor discovered systems."
              }
            ]
          },
          {
            "subject": "ds_21_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "DS-21 system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
                "notes": "DeWeirdt et al. name validated TUs as DefensePredictor discovered systems."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| DS-21 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
                "notes": "The pinned DefenseFinder article registry maps the DS-21 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "ds-21-defensefinder-model-gap",
        "prompt": "Resolve DS-21 native host breadth, exact profile-to-protein mapping, HHpred-domain interpretation, component chemistry, complete phage breadth, molecular output, and rule-level DefenseFinder criteria before minting narrower DS-21 mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "DeWeirdt et al. support DS-21 as the defensive TOXO transcriptional unit and final Science Tables S6/S7/S8 map it to three product accessions, a Bas1 phage readout, display name DS-21, and a PDDEXK HHpred row. The pinned DefenseFinder HMM inventory records three DS-21 custom profile rows. The pinned rules table has no DS-21 row, and the first-pass record does not resolve native host breadth, complete phage breadth, direct profile-to-protein correspondence, PDDEXK nuclease activity, molecular output, or endogenous DS-21 activity.",
        "evidence": [
          {
            "reference": "DOI:10.1126/science.adv7924",
            "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
            "notes": "DeWeirdt et al. name validated TUs as DSs."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
            "snippet": "TOXO\tNZ_QOXJ01000032.1\tGCF_003334085.1\t-\tTrue\tFalse\tFalse\tTrue\tDefensePredictor hits\t7805\t9963\thypothetical protein, hypothetical protein, hypothetical protein\tWP_001532221.1, WP_001557682.1, WP_021552536.1\t10.9763556055726\t2.883007179633958\tTrue\tTrue\tPredicted novel defense gene\tDS-21",
            "notes": "The final Science supplementary Table S6 maps working_id TOXO to DS_name DS-21, marks the cloned transcriptional unit as defensive, and records NZ_QOXJ01000032.1 positions 7805-9963 with three product accessions."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
            "snippet": "Bas1\t6.1\tpLAND\t24-07-17_MVB1_VPUS_VAME_EV.png\t3000000\tTOXO\t24-07-25\t24-07-25_PDX1_TMO1_VANC_TOXO.png\t2\t1\t\t100\t4.477121254719663\t\t\tTrue\tLB\t37",
            "notes": "The final Science supplementary Table S7 reports a TOXO assay row with a Bas1 phage readout and a -log(EOP) value of 4.477."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
            "snippet": "TOXO\tDS-21\tTrue",
            "notes": "The final Science supplementary Table S8 maps TOXO to replicated display name DS-21."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
            "snippet": "TOXO\t3.0\t211.0\tWP_001557682.1\tPDDEXK\tPF18742.6\tDpnII-MboI ; REase_DpnII-MboI\thhpred_4621019.hhr\t37.0\t160.0\t0.96\t2024-07-29 00:00:00\t121-123\t103.0",
            "notes": "The final Science supplementary Table S8 reports a PDDEXK HHpred hit for WP_001557682.1 in TOXO."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
            "snippet": "| DS-21 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
            "notes": "The pinned DefenseFinder article registry maps the DS-21 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| DS-21__DS-21A                                    |                                                  | DS-21                  | Custom                  | 20     |\n| DS-21__DS-21B                                    |                                                  | DS-21                  | Custom                  | 250    |\n| DS-21__DS-21C                                    |                                                  | DS-21                  | Custom                  | 70     |",
            "notes": "The pinned DefenseFinder HMM inventory records three DS-21 custom profiles: DS-21__DS-21A, DS-21__DS-21B, and DS-21__DS-21C."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "The pinned DefenseFinder rules table does not list DS-21, leaving rule-level detection criteria unresolved."
          }
        ],
        "attaches_to": [
          "causal_graphs#ds_21_locus_reduces_phage_plaquing"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-28"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-28T22:17:01Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted DS-21 system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; kept the graph at TOXO transcriptional-unit level because PDDEXK chemistry and rule rows remain unresolved, and proposals/metpo_traitmech_v323 reserves the replacement placeholder.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-28T22:17:02Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed DS-21 system canonical_examples and left them empty because DeWeirdt et al. directly support cloned TOXO assays in E. coli MG1655 and DefenseFinder DS-21 models, but not a direct named native microbial isolate exemplar with experimentally verified endogenous DS-21 activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000447",
    "label": "DS-22 system",
    "definition": "A phage defense system in which an organism possesses the single-gene DefensePredictor-discovered system 22 locus cataloged as working transcriptional unit MVB1 and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.",
    "definition_source": "DOI:10.1126/science.adv7924",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "DS-22",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1126/science.adv7924"
      },
      {
        "synonym_text": "MVB1",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx"
      },
      {
        "synonym_text": "DS-22__DS-22",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1126/science.adv7924",
        "snippet": "To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
        "notes": "DeWeirdt et al. experimentally validated 42 predicted transcriptional units as phage-defense systems in E. coli."
      },
      {
        "reference": "DOI:10.1126/science.adv7924",
        "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
        "notes": "DeWeirdt et al. name validated transcriptional units as DefensePredictor discovered systems."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
        "snippet": "MVB1\tNZ_QOWO01000045.1\tGCF_003334815.1\t-\tTrue\tFalse\tFalse\tTrue\tDefensePredictor hits\t10119\t11351\thypothetical protein\tWP_000162952.1\t9.664065793183475\t-2.806015014798907\tTrue\tFalse\tPredicted novel defense gene\tDS-22",
        "notes": "The final Science supplementary Table S6 maps working_id MVB1 to DS_name DS-22, marks the cloned transcriptional unit as defensive, and records NZ_QOWO01000045.1 positions 10119-11351 with product accession WP_000162952.1."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
        "snippet": "Bas11\t6.1\tpLAND\t24-07-17_MVB1_VPUS_VAME_EV.png\t100000000\tMVB1\t24-07-17\t24-07-17_MVB1_VPUS_VAME_EV.png\t2\t10\t\t1000\t5\t\t\tTrue\tLB\t37",
        "notes": "The final Science supplementary Table S7 reports an MVB1 assay row with a Bas11 phage readout and a -log(EOP) value of 5."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
        "snippet": "MVB1\tDS-22\tTrue",
        "notes": "The final Science supplementary Table S8 maps MVB1 to replicated display name DS-22."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
        "snippet": "MVB1\t1.0\t410.0\tWP_000162952.1\tMvb12\tPF09452.15\tMvb12 ; ESCRT-I subunit Mvb12\thhpred_4626820.hhr\t33.0\t64.0\t0.72\t2024-07-27 00:00:00\t\t",
        "notes": "The final Science supplementary Table S8 reports a low-probability Mvb12 HHpred hit for WP_000162952.1 in MVB1."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
        "snippet": "MVB1\t1.0\t410.0\tWP_000162952.1\tJAB\tPF04002.20\tRadC-like JAB domain\thhpred_4626820.hhr\t258.0\t324.0\t0.37\t2024-07-27 00:00:00\t\t",
        "notes": "The final Science supplementary Table S8 reports a low-probability JAB HHpred hit for WP_000162952.1 in MVB1."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| DS-22 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
        "notes": "The pinned DefenseFinder article registry maps the DS-22 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| DS-22__DS-22                                     |                                                  | DS-22                  | Custom                  | 60     |",
        "notes": "The pinned DefenseFinder HMM inventory records DS-22__DS-22 as a custom DS-22 profile."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "ds_22_locus_reduces_phage_plaquing",
        "title": "DS-22 locus reduces bacteriophage plaquing",
        "description": "Conservative system-level sketch linking the single-gene DS-22 locus to reduced bacteriophage plaquing without resolving DS-22 component function or molecular output.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures DS-22 as the validated MVB1 transcriptional unit with one product accession and one DefenseFinder DS-22 profile row. It does not assert native host breadth, exact profile-to-protein correspondence, DS-22 molecular activity, trigger, substrate, low-confidence HHpred-domain interpretations, complete phage breadth, or DefenseFinder rule-level detection criteria.",
        "nodes": [
          {
            "node_id": "ds_22_locus",
            "label": "DS-22 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A single-gene DefensePredictor-discovered system 22 locus represented in the pinned DefenseFinder HMM inventory by one DS-22 custom profile."
          },
          {
            "node_id": "reduced_phage_plaquing",
            "label": "reduced bacteriophage plaquing",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced efficiency of plaquing by bacteriophage Bas11 in cells carrying cloned MVB1."
          },
          {
            "node_id": "ds_22_system_trait",
            "label": "DS-22 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000447",
            "description": "Possession of a genome-encoded DS-22 phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "ds_22_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "reduced_phage_plaquing",
            "description": "The DS-22/MVB1 locus contributes to reduced bacteriophage plaquing when plasmid expressed.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
                "notes": "DeWeirdt et al. experimentally validate DefensePredictor-discovered systems by assaying cloned transcriptional units against E. coli phages."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
                "snippet": "MVB1\tNZ_QOWO01000045.1\tGCF_003334815.1\t-\tTrue\tFalse\tFalse\tTrue\tDefensePredictor hits\t10119\t11351\thypothetical protein\tWP_000162952.1\t9.664065793183475\t-2.806015014798907\tTrue\tFalse\tPredicted novel defense gene\tDS-22",
                "notes": "The final Science supplementary Table S6 maps working_id MVB1 to DS_name DS-22, marks the cloned transcriptional unit as defensive, and records NZ_QOWO01000045.1 positions 10119-11351 with product accession WP_000162952.1."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
                "snippet": "Bas11\t6.1\tpLAND\t24-07-17_MVB1_VPUS_VAME_EV.png\t100000000\tMVB1\t24-07-17\t24-07-17_MVB1_VPUS_VAME_EV.png\t2\t10\t\t1000\t5\t\t\tTrue\tLB\t37",
                "notes": "The final Science supplementary Table S7 reports an MVB1 assay row with a Bas11 phage readout and a -log(EOP) value of 5."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
                "snippet": "MVB1\tDS-22\tTrue",
                "notes": "The final Science supplementary Table S8 maps MVB1 to replicated display name DS-22."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| DS-22__DS-22                                     |                                                  | DS-22                  | Custom                  | 60     |",
                "notes": "The pinned DefenseFinder HMM inventory records DS-22__DS-22 as a custom DS-22 profile."
              }
            ]
          },
          {
            "subject": "reduced_phage_plaquing",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "ds_22_system_trait",
            "description": "DS-22-mediated phage plaquing reduction realizes the DS-22 system trait.",
            "evidence": [
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
                "snippet": "MVB1\tNZ_QOWO01000045.1\tGCF_003334815.1\t-\tTrue\tFalse\tFalse\tTrue\tDefensePredictor hits\t10119\t11351\thypothetical protein\tWP_000162952.1\t9.664065793183475\t-2.806015014798907\tTrue\tFalse\tPredicted novel defense gene\tDS-22",
                "notes": "The final Science supplementary Table S6 maps working_id MVB1 to DS_name DS-22, marks the cloned transcriptional unit as defensive, and records NZ_QOWO01000045.1 positions 10119-11351 with product accession WP_000162952.1."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
                "snippet": "Bas11\t6.1\tpLAND\t24-07-17_MVB1_VPUS_VAME_EV.png\t100000000\tMVB1\t24-07-17\t24-07-17_MVB1_VPUS_VAME_EV.png\t2\t10\t\t1000\t5\t\t\tTrue\tLB\t37",
                "notes": "The final Science supplementary Table S7 reports an MVB1 assay row with a Bas11 phage readout and a -log(EOP) value of 5."
              },
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
                "notes": "The DS nomenclature is used for DefensePredictor discovered systems."
              }
            ]
          },
          {
            "subject": "ds_22_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "DS-22 system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
                "notes": "DeWeirdt et al. name validated TUs as DefensePredictor discovered systems."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| DS-22 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
                "notes": "The pinned DefenseFinder article registry maps the DS-22 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "ds-22-defensefinder-model-gap",
        "prompt": "Resolve DS-22 native host breadth, exact single-component activity, profile-to-protein mapping, sensitive-phage breadth, low-confidence HHpred-domain interpretation, molecular output, and rule-level DefenseFinder criteria before minting narrower DS-22 mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "DeWeirdt et al. support DS-22 as the defensive MVB1 transcriptional unit that reduced Bas11 plaquing when cloned in E. coli MG1655, and the pinned DefenseFinder HMM inventory records one DS-22 profile row. The pinned rules table has no DS-22 row, and the first-pass record does not resolve native host breadth, exact component activity, direct profile-to-protein correspondence, the Mvb12 and JAB HHpred-domain rows, phage target breadth, molecular output, or endogenous DS-22 activity.",
        "evidence": [
          {
            "reference": "DOI:10.1126/science.adv7924",
            "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
            "notes": "DeWeirdt et al. name validated TUs as DSs."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
            "snippet": "MVB1\tNZ_QOWO01000045.1\tGCF_003334815.1\t-\tTrue\tFalse\tFalse\tTrue\tDefensePredictor hits\t10119\t11351\thypothetical protein\tWP_000162952.1\t9.664065793183475\t-2.806015014798907\tTrue\tFalse\tPredicted novel defense gene\tDS-22",
            "notes": "The final Science supplementary Table S6 maps working_id MVB1 to DS_name DS-22, marks the cloned transcriptional unit as defensive, and records NZ_QOWO01000045.1 positions 10119-11351 with product accession WP_000162952.1."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
            "snippet": "Bas11\t6.1\tpLAND\t24-07-17_MVB1_VPUS_VAME_EV.png\t100000000\tMVB1\t24-07-17\t24-07-17_MVB1_VPUS_VAME_EV.png\t2\t10\t\t1000\t5\t\t\tTrue\tLB\t37",
            "notes": "The final Science supplementary Table S7 reports an MVB1 assay row with a Bas11 phage readout and a -log(EOP) value of 5."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
            "snippet": "MVB1\tDS-22\tTrue",
            "notes": "The final Science supplementary Table S8 maps MVB1 to replicated display name DS-22."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
            "snippet": "MVB1\t1.0\t410.0\tWP_000162952.1\tMvb12\tPF09452.15\tMvb12 ; ESCRT-I subunit Mvb12\thhpred_4626820.hhr\t33.0\t64.0\t0.72\t2024-07-27 00:00:00\t\t",
            "notes": "The final Science supplementary Table S8 reports a low-probability Mvb12 HHpred hit for WP_000162952.1 in MVB1."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
            "snippet": "MVB1\t1.0\t410.0\tWP_000162952.1\tJAB\tPF04002.20\tRadC-like JAB domain\thhpred_4626820.hhr\t258.0\t324.0\t0.37\t2024-07-27 00:00:00\t\t",
            "notes": "The final Science supplementary Table S8 reports a low-probability JAB HHpred hit for WP_000162952.1 in MVB1."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
            "snippet": "| DS-22 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
            "notes": "The pinned DefenseFinder article registry maps the DS-22 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| DS-22__DS-22                                     |                                                  | DS-22                  | Custom                  | 60     |",
            "notes": "The pinned DefenseFinder HMM inventory records DS-22__DS-22 as a custom DS-22 profile."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "The pinned DefenseFinder rules table does not list DS-22, leaving rule-level detection criteria unresolved."
          }
        ],
        "attaches_to": [
          "causal_graphs#ds_22_locus_reduces_phage_plaquing"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-28"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-28T23:30:13Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted DS-22 system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; kept the graph at cloned MVB1 transcriptional-unit level because the pinned DefenseFinder DS-22 HMM row is not backed by a rules row, and proposals/metpo_traitmech_v324 reserves the replacement placeholder.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-28T23:30:14Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed DS-22 system canonical_examples and left them empty because DeWeirdt et al. directly support cloned MVB1 assays in E. coli MG1655 and a DefenseFinder DS-22 model, but not a direct named native microbial isolate exemplar with experimentally verified endogenous DS-22 activity. No paid research was used.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-29T00:00:35Z",
        "curator": "codex",
        "action": "UPDATED_EVIDENCE",
        "changes": "Added exact final Table S8 MVB1 HHpred-domain rows for the low-probability Mvb12 and JAB hits so the DS-22 mechanism gap quotes the evidence it defers.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-29T00:11:21Z",
        "curator": "codex",
        "action": "UPDATED_SYNONYM_SOURCE",
        "changes": "Aligned the DS-22 exact-synonym source with adjacent DS system records by citing the DOI that defines the DS display-name convention.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-29T00:23:32Z",
        "curator": "codex",
        "action": "UPDATED_EVIDENCE",
        "changes": "Split the MVB1 Mvb12 and JAB Table S8 HHpred rows into separate evidence items so each snippet quotes one contiguous source row.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000448",
    "label": "DS-23 system",
    "definition": "A phage defense system in which an organism possesses the single-gene DefensePredictor-discovered system 23 locus cataloged as working transcriptional unit E2DP and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.",
    "definition_source": "DOI:10.1126/science.adv7924",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "DS-23",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1126/science.adv7924"
      },
      {
        "synonym_text": "E2DP",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx"
      },
      {
        "synonym_text": "DS-23__DS-23",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1126/science.adv7924",
        "snippet": "To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
        "notes": "DeWeirdt et al. experimentally validated 42 predicted transcriptional units as phage-defense systems in E. coli."
      },
      {
        "reference": "DOI:10.1126/science.adv7924",
        "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
        "notes": "DeWeirdt et al. name validated transcriptional units as DefensePredictor discovered systems."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
        "snippet": "E2DP\tNZ_RRVV01000032.1\tGCF_003886345.1\t+\tTrue\tFalse\tFalse\tTrue\tDefensePredictor hits\t38754\t40913\tSEC-C metal-binding domain-containing protein\tWP_020231147.1\t11.17818080568115\t3.842009204807092\tTrue\tTrue\tPredicted novel defense gene\tDS-23",
        "notes": "The final Science supplementary Table S6 maps working_id E2DP to DS_name DS-23, marks the cloned transcriptional unit as defensive, and records NZ_RRVV01000032.1 positions 38754-40913 with product accession WP_020231147.1."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
        "snippet": "Bas19\t6.1\tpLAND\t24-07-17_MVB1_VPUS_VAME_EV.png\t2200000\tE2DP\t24-07-24\t24-07-24_ABIL_E2DP_COAT_DDML.png\t0\t1\t\t1\t6.342422680822207\t\t\tTrue\tLB\t37",
        "notes": "The final Science supplementary Table S7 reports an E2DP assay row with a Bas19 phage readout and a -log(EOP) value of 6.342."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
        "snippet": "E2DP\tDS-23\tTrue",
        "notes": "The final Science supplementary Table S8 maps E2DP to replicated display name DS-23."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
        "snippet": "E2DP\t1.0\t719.0\tWP_020231147.1\tZF\t2I9W_A\tHypothetical protein; Cystatin-like fold, sec-c motif fold, structural genomics\thhpred_7846250.hhr\t693.0\t716.0\t0.98\t2024-07-30 00:00:00\t\t",
        "notes": "The final Science supplementary Table S8 reports a ZF HHpred hit for WP_020231147.1 in E2DP."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
        "snippet": "E2DP\t1.0\t719.0\tWP_020231147.1\tPDDEXK\tcd22364\tVC1899-like; putative nuclease domain found in Vibrio cholerae VC1899 and similar proteins. A putative nuclease domain found in Vibrio cholerae VC1899 and similar proteins belongs to a superfamily of PDDEXK nucleases\thhpred_7846250.hhr\t295.0\t457.0\t0.96\t2024-07-30 00:00:00\t110-112\t96.0",
        "notes": "The final Science supplementary Table S8 reports a PDDEXK HHpred hit for WP_020231147.1 in E2DP."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| DS-23 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
        "notes": "The pinned DefenseFinder article registry maps the DS-23 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| DS-23__DS-23                                     |                                                  | DS-23                  | Custom                  | 200    |",
        "notes": "The pinned DefenseFinder HMM inventory records DS-23__DS-23 as a custom DS-23 profile."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "ds_23_locus_reduces_phage_plaquing",
        "title": "DS-23 locus reduces bacteriophage plaquing",
        "description": "Conservative system-level sketch linking the single-gene DS-23 locus to reduced bacteriophage plaquing without resolving DS-23 component function or molecular output.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures DS-23 as the validated E2DP transcriptional unit with one product accession, ZF and PDDEXK HHpred-domain rows, and one DefenseFinder DS-23 profile row. It does not assert native host breadth, exact profile-to-protein correspondence, DS-23 molecular activity, trigger, substrate, complete phage breadth, or DefenseFinder rule-level detection criteria.",
        "nodes": [
          {
            "node_id": "ds_23_locus",
            "label": "DS-23 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A single-gene DefensePredictor-discovered system 23 locus represented in the pinned DefenseFinder HMM inventory by one DS-23 custom profile."
          },
          {
            "node_id": "reduced_phage_plaquing",
            "label": "reduced bacteriophage plaquing",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced bacteriophage plaquing in cells carrying cloned E2DP."
          },
          {
            "node_id": "ds_23_system_trait",
            "label": "DS-23 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000448",
            "description": "Possession of a genome-encoded DS-23 phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "ds_23_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "reduced_phage_plaquing",
            "description": "The DS-23/E2DP locus contributes to reduced bacteriophage plaquing in heterologous E. coli MG1655 plasmid-expression assays.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
                "notes": "DeWeirdt et al. describe the plasmid-based phage challenge used to validate predicted transcriptional units."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
                "snippet": "E2DP\tNZ_RRVV01000032.1\tGCF_003886345.1\t+\tTrue\tFalse\tFalse\tTrue\tDefensePredictor hits\t38754\t40913\tSEC-C metal-binding domain-containing protein\tWP_020231147.1\t11.17818080568115\t3.842009204807092\tTrue\tTrue\tPredicted novel defense gene\tDS-23",
                "notes": "The final Science supplementary Table S6 maps working_id E2DP to DS_name DS-23, marks the cloned transcriptional unit as defensive, and records NZ_RRVV01000032.1 positions 38754-40913 with product accession WP_020231147.1."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
                "snippet": "Bas19\t6.1\tpLAND\t24-07-17_MVB1_VPUS_VAME_EV.png\t2200000\tE2DP\t24-07-24\t24-07-24_ABIL_E2DP_COAT_DDML.png\t0\t1\t\t1\t6.342422680822207\t\t\tTrue\tLB\t37",
                "notes": "The final Science supplementary Table S7 reports an E2DP assay row with a Bas19 phage readout and a -log(EOP) value of 6.342."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
                "snippet": "E2DP\tDS-23\tTrue",
                "notes": "The final Science supplementary Table S8 maps E2DP to replicated display name DS-23."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| DS-23__DS-23                                     |                                                  | DS-23                  | Custom                  | 200    |",
                "notes": "The pinned DefenseFinder HMM inventory records DS-23__DS-23 as a custom DS-23 profile."
              }
            ]
          },
          {
            "subject": "reduced_phage_plaquing",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "ds_23_system_trait",
            "description": "DS-23-mediated phage plaquing reduction realizes the DS-23 system trait.",
            "evidence": [
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
                "snippet": "E2DP\tNZ_RRVV01000032.1\tGCF_003886345.1\t+\tTrue\tFalse\tFalse\tTrue\tDefensePredictor hits\t38754\t40913\tSEC-C metal-binding domain-containing protein\tWP_020231147.1\t11.17818080568115\t3.842009204807092\tTrue\tTrue\tPredicted novel defense gene\tDS-23",
                "notes": "The final Science supplementary Table S6 maps working_id E2DP to DS_name DS-23, marks the cloned transcriptional unit as defensive, and records NZ_RRVV01000032.1 positions 38754-40913 with product accession WP_020231147.1."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
                "snippet": "Bas19\t6.1\tpLAND\t24-07-17_MVB1_VPUS_VAME_EV.png\t2200000\tE2DP\t24-07-24\t24-07-24_ABIL_E2DP_COAT_DDML.png\t0\t1\t\t1\t6.342422680822207\t\t\tTrue\tLB\t37",
                "notes": "The final Science supplementary Table S7 reports an E2DP assay row with a Bas19 phage readout and a -log(EOP) value of 6.342."
              },
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
                "notes": "The DS nomenclature is used for DefensePredictor discovered systems."
              }
            ]
          },
          {
            "subject": "ds_23_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "DS-23 system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
                "notes": "DeWeirdt et al. name validated TUs as DefensePredictor discovered systems."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| DS-23 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
                "notes": "The pinned DefenseFinder article registry maps the DS-23 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "ds-23-defensefinder-model-gap",
        "prompt": "Resolve DS-23 native host breadth, exact single-component activity, profile-to-protein mapping, ZF and PDDEXK HHpred-domain interpretation, complete phage breadth, molecular output, and rule-level DefenseFinder criteria before minting narrower DS-23 mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "DeWeirdt et al. support DS-23 as the defensive E2DP transcriptional unit and final Science Tables S6/S7/S8 map it to product accession WP_020231147.1, a Bas19 phage readout, display name DS-23, and ZF and PDDEXK HHpred rows. The pinned DefenseFinder HMM inventory records one DS-23 custom profile row. The pinned rules table has no DS-23 row, and the first-pass record does not resolve native host breadth, complete phage breadth, direct profile-to-protein correspondence, ZF or PDDEXK activity, molecular output, or endogenous DS-23 activity.",
        "evidence": [
          {
            "reference": "DOI:10.1126/science.adv7924",
            "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
            "notes": "DeWeirdt et al. name validated TUs as DSs."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
            "snippet": "E2DP\tNZ_RRVV01000032.1\tGCF_003886345.1\t+\tTrue\tFalse\tFalse\tTrue\tDefensePredictor hits\t38754\t40913\tSEC-C metal-binding domain-containing protein\tWP_020231147.1\t11.17818080568115\t3.842009204807092\tTrue\tTrue\tPredicted novel defense gene\tDS-23",
            "notes": "The final Science supplementary Table S6 maps working_id E2DP to DS_name DS-23, marks the cloned transcriptional unit as defensive, and records NZ_RRVV01000032.1 positions 38754-40913 with product accession WP_020231147.1."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
            "snippet": "Bas19\t6.1\tpLAND\t24-07-17_MVB1_VPUS_VAME_EV.png\t2200000\tE2DP\t24-07-24\t24-07-24_ABIL_E2DP_COAT_DDML.png\t0\t1\t\t1\t6.342422680822207\t\t\tTrue\tLB\t37",
            "notes": "The final Science supplementary Table S7 reports an E2DP assay row with a Bas19 phage readout and a -log(EOP) value of 6.342."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
            "snippet": "E2DP\tDS-23\tTrue",
            "notes": "The final Science supplementary Table S8 maps E2DP to replicated display name DS-23."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
            "snippet": "E2DP\t1.0\t719.0\tWP_020231147.1\tZF\t2I9W_A\tHypothetical protein; Cystatin-like fold, sec-c motif fold, structural genomics\thhpred_7846250.hhr\t693.0\t716.0\t0.98\t2024-07-30 00:00:00\t\t",
            "notes": "The final Science supplementary Table S8 reports a ZF HHpred hit for WP_020231147.1 in E2DP."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
            "snippet": "E2DP\t1.0\t719.0\tWP_020231147.1\tPDDEXK\tcd22364\tVC1899-like; putative nuclease domain found in Vibrio cholerae VC1899 and similar proteins. A putative nuclease domain found in Vibrio cholerae VC1899 and similar proteins belongs to a superfamily of PDDEXK nucleases\thhpred_7846250.hhr\t295.0\t457.0\t0.96\t2024-07-30 00:00:00\t110-112\t96.0",
            "notes": "The final Science supplementary Table S8 reports a PDDEXK HHpred hit for WP_020231147.1 in E2DP."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
            "snippet": "| DS-23 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
            "notes": "The pinned DefenseFinder article registry maps the DS-23 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| DS-23__DS-23                                     |                                                  | DS-23                  | Custom                  | 200    |",
            "notes": "The pinned DefenseFinder HMM inventory records DS-23__DS-23 as a custom DS-23 profile."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "The pinned DefenseFinder rules table does not list DS-23, leaving rule-level detection criteria unresolved."
          }
        ],
        "attaches_to": [
          "causal_graphs#ds_23_locus_reduces_phage_plaquing"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-29"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-29T00:59:43Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted DS-23 system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; kept the graph at E2DP transcriptional-unit level because ZF and PDDEXK chemistry and rule rows remain unresolved, and proposals/metpo_traitmech_v325 reserves the replacement placeholder.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-29T00:59:44Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed DS-23 system canonical_examples and left them empty because DeWeirdt et al. directly support cloned E2DP assays in E. coli MG1655 and a DefenseFinder DS-23 model, but not a direct named native microbial isolate exemplar with experimentally verified endogenous DS-23 activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000449",
    "label": "DS-24 system",
    "definition": "A phage defense system in which an organism possesses the single-gene DefensePredictor-discovered system 24 locus cataloged as working transcriptional unit RED2 and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.",
    "definition_source": "DOI:10.1126/science.adv7924",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "DS-24",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1126/science.adv7924"
      },
      {
        "synonym_text": "RED2",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx"
      },
      {
        "synonym_text": "DS-24__DS-24",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1126/science.adv7924",
        "snippet": "To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
        "notes": "DeWeirdt et al. experimentally validated 42 predicted transcriptional units as phage-defense systems in E. coli."
      },
      {
        "reference": "DOI:10.1126/science.adv7924",
        "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
        "notes": "DeWeirdt et al. name validated transcriptional units as DefensePredictor discovered systems."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
        "snippet": "RED2\tNZ_QOYT01000030.1\tGCF_003333565.1\t-\tTrue\tFalse\tTrue\tTrue\tDefensePredictor hits\t4612\t5400\thypothetical protein\tWP_000183405.1\t10.84251239088582\t2.733941615034952\tTrue\tTrue\tRemote defense homolog\tDS-24",
        "notes": "The final Science supplementary Table S6 maps working_id RED2 to DS_name DS-24, marks the cloned transcriptional unit as defensive, and records NZ_QOYT01000030.1 positions 4612-5400 with product accession WP_000183405.1."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
        "snippet": "Bas1\t2.2\tpLAND\t24-03-12_EV.png\t30000000\tRED2\t24-03-14\t24-03-14_TNEC_PDP5_TMO2_RED2.png\t0\t1\t\t1\t7.477121254719663\t\tTrue\t\tLB\t37",
        "notes": "The final Science supplementary Table S7 reports a RED2 assay row with a Bas1 phage readout and a -log(EOP) value of 7.477."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
        "snippet": "RED2\tDS-24\tTrue",
        "notes": "The final Science supplementary Table S8 maps RED2 to replicated display name DS-24."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
        "snippet": "RED2\t1.0\t262.0\tWP_000183405.1\tPDDEXK\tPF18742.5\tDpnII-MboI ; REase_DpnII-MboI\thhpred_8304048.hhr\t116.0\t262.0\t0.9998\t2024-04-15 00:00:00\t47-49\t36.0",
        "notes": "The final Science supplementary Table S8 reports a high-probability PDDEXK HHpred hit for WP_000183405.1 in RED2."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| DS-24 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
        "notes": "The pinned DefenseFinder article registry maps the DS-24 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| DS-24__DS-24                                     |                                                  | DS-24                  | Custom                  | 150    |",
        "notes": "The pinned DefenseFinder HMM inventory records DS-24__DS-24 as a custom DS-24 profile."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "ds_24_locus_reduces_phage_plaquing",
        "title": "DS-24 locus reduces bacteriophage plaquing",
        "description": "Conservative system-level sketch linking the single-gene DS-24 locus to reduced bacteriophage plaquing without resolving DS-24 component function or molecular output.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures DS-24 as the validated RED2 transcriptional unit with one product accession, one high-probability PDDEXK HHpred-domain row, and one DefenseFinder DS-24 profile row. It does not assert native host breadth, exact profile-to-protein correspondence, DS-24 molecular activity, trigger, substrate, complete phage breadth, or DefenseFinder rule-level detection criteria.",
        "nodes": [
          {
            "node_id": "ds_24_locus",
            "label": "DS-24 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A single-gene DefensePredictor-discovered system 24 locus represented in the pinned DefenseFinder HMM inventory by one DS-24 custom profile."
          },
          {
            "node_id": "reduced_phage_plaquing",
            "label": "reduced bacteriophage plaquing",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced bacteriophage plaquing in cells carrying cloned RED2."
          },
          {
            "node_id": "ds_24_system_trait",
            "label": "DS-24 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000449",
            "description": "Possession of a genome-encoded DS-24 phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "ds_24_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "reduced_phage_plaquing",
            "description": "The DS-24/RED2 locus contributes to reduced bacteriophage plaquing in heterologous E. coli MG1655 plasmid-expression assays.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
                "notes": "DeWeirdt et al. describe the plasmid-based phage challenge used to validate predicted transcriptional units."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
                "snippet": "RED2\tNZ_QOYT01000030.1\tGCF_003333565.1\t-\tTrue\tFalse\tTrue\tTrue\tDefensePredictor hits\t4612\t5400\thypothetical protein\tWP_000183405.1\t10.84251239088582\t2.733941615034952\tTrue\tTrue\tRemote defense homolog\tDS-24",
                "notes": "The final Science supplementary Table S6 maps working_id RED2 to DS_name DS-24, marks the cloned transcriptional unit as defensive, and records NZ_QOYT01000030.1 positions 4612-5400 with product accession WP_000183405.1."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
                "snippet": "Bas1\t2.2\tpLAND\t24-03-12_EV.png\t30000000\tRED2\t24-03-14\t24-03-14_TNEC_PDP5_TMO2_RED2.png\t0\t1\t\t1\t7.477121254719663\t\tTrue\t\tLB\t37",
                "notes": "The final Science supplementary Table S7 reports a RED2 assay row with a Bas1 phage readout and a -log(EOP) value of 7.477."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
                "snippet": "RED2\tDS-24\tTrue",
                "notes": "The final Science supplementary Table S8 maps RED2 to replicated display name DS-24."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| DS-24__DS-24                                     |                                                  | DS-24                  | Custom                  | 150    |",
                "notes": "The pinned DefenseFinder HMM inventory records DS-24__DS-24 as a custom DS-24 profile."
              }
            ]
          },
          {
            "subject": "reduced_phage_plaquing",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "ds_24_system_trait",
            "description": "DS-24-mediated phage plaquing reduction realizes the DS-24 system trait.",
            "evidence": [
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
                "snippet": "RED2\tNZ_QOYT01000030.1\tGCF_003333565.1\t-\tTrue\tFalse\tTrue\tTrue\tDefensePredictor hits\t4612\t5400\thypothetical protein\tWP_000183405.1\t10.84251239088582\t2.733941615034952\tTrue\tTrue\tRemote defense homolog\tDS-24",
                "notes": "The final Science supplementary Table S6 maps working_id RED2 to DS_name DS-24, marks the cloned transcriptional unit as defensive, and records NZ_QOYT01000030.1 positions 4612-5400 with product accession WP_000183405.1."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
                "snippet": "Bas1\t2.2\tpLAND\t24-03-12_EV.png\t30000000\tRED2\t24-03-14\t24-03-14_TNEC_PDP5_TMO2_RED2.png\t0\t1\t\t1\t7.477121254719663\t\tTrue\t\tLB\t37",
                "notes": "The final Science supplementary Table S7 reports a RED2 assay row with a Bas1 phage readout and a -log(EOP) value of 7.477."
              },
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
                "notes": "The DS nomenclature is used for DefensePredictor discovered systems."
              }
            ]
          },
          {
            "subject": "ds_24_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "DS-24 system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
                "notes": "DeWeirdt et al. name validated TUs as DefensePredictor discovered systems."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| DS-24 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
                "notes": "The pinned DefenseFinder article registry maps the DS-24 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "ds-24-defensefinder-model-gap",
        "prompt": "Resolve DS-24 native host breadth, exact single-component activity, profile-to-protein mapping, PDDEXK HHpred-domain interpretation, complete phage breadth, molecular output, and rule-level DefenseFinder criteria before minting narrower DS-24 mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "DeWeirdt et al. support DS-24 as the defensive RED2 transcriptional unit and final Science Tables S6/S7/S8 map it to product accession WP_000183405.1, a Bas1 phage readout, display name DS-24, and a PDDEXK HHpred row. The pinned DefenseFinder HMM inventory records one DS-24 custom profile row. The pinned rules table has no DS-24 row, and the first-pass record does not resolve native host breadth, complete phage breadth, direct profile-to-protein correspondence, PDDEXK activity, molecular output, or endogenous DS-24 activity.",
        "evidence": [
          {
            "reference": "DOI:10.1126/science.adv7924",
            "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
            "notes": "DeWeirdt et al. name validated TUs as DSs."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
            "snippet": "RED2\tNZ_QOYT01000030.1\tGCF_003333565.1\t-\tTrue\tFalse\tTrue\tTrue\tDefensePredictor hits\t4612\t5400\thypothetical protein\tWP_000183405.1\t10.84251239088582\t2.733941615034952\tTrue\tTrue\tRemote defense homolog\tDS-24",
            "notes": "The final Science supplementary Table S6 maps working_id RED2 to DS_name DS-24, marks the cloned transcriptional unit as defensive, and records NZ_QOYT01000030.1 positions 4612-5400 with product accession WP_000183405.1."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
            "snippet": "Bas1\t2.2\tpLAND\t24-03-12_EV.png\t30000000\tRED2\t24-03-14\t24-03-14_TNEC_PDP5_TMO2_RED2.png\t0\t1\t\t1\t7.477121254719663\t\tTrue\t\tLB\t37",
            "notes": "The final Science supplementary Table S7 reports a RED2 assay row with a Bas1 phage readout and a -log(EOP) value of 7.477."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
            "snippet": "RED2\tDS-24\tTrue",
            "notes": "The final Science supplementary Table S8 maps RED2 to replicated display name DS-24."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
            "snippet": "RED2\t1.0\t262.0\tWP_000183405.1\tPDDEXK\tPF18742.5\tDpnII-MboI ; REase_DpnII-MboI\thhpred_8304048.hhr\t116.0\t262.0\t0.9998\t2024-04-15 00:00:00\t47-49\t36.0",
            "notes": "The final Science supplementary Table S8 reports a high-probability PDDEXK HHpred hit for WP_000183405.1 in RED2."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
            "snippet": "| DS-24 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
            "notes": "The pinned DefenseFinder article registry maps the DS-24 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| DS-24__DS-24                                     |                                                  | DS-24                  | Custom                  | 150    |",
            "notes": "The pinned DefenseFinder HMM inventory records DS-24__DS-24 as a custom DS-24 profile."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "The pinned DefenseFinder rules table does not list DS-24, leaving rule-level detection criteria unresolved."
          }
        ],
        "attaches_to": [
          "causal_graphs#ds_24_locus_reduces_phage_plaquing"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-29"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-29T01:45:02Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted DS-24 system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; kept the graph at RED2 transcriptional-unit level because PDDEXK chemistry and rule rows remain unresolved, and proposals/metpo_traitmech_v326 reserves the replacement placeholder.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-29T01:45:03Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed DS-24 system canonical_examples and left them empty because DeWeirdt et al. directly support cloned RED2 assays in E. coli MG1655 and a DefenseFinder DS-24 model, but not a direct named native microbial isolate exemplar with experimentally verified endogenous DS-24 activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000473",
    "label": "DS-25 system",
    "definition": "A phage defense system in which an organism possesses a genome-encoded DefensePredictor-discovered system 25 locus represented in the pinned DefenseFinder model inventory by DS-25A and DS-25B custom HMM profiles.",
    "definition_source": "DOI:10.1101/2025.01.08.631726",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "DS-25",
        "synonym_type": "EXACT_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      },
      {
        "synonym_text": "DS-25__DS-25A",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "DS-25__DS-25B",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1101/2025.01.08.631726",
        "snippet": "To test for anti-phage defense, we placed each TU with its native promoter region on a low-copy number plasmid in E. coli MG1655 and then challenged these strains with a panel of 24 diverse E. coli phages (fig. S2). In total, 45 (42% of 106) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
        "notes": "DeWeirdt et al. experimentally validated 45 predicted transcriptional units as phage-defense systems in E. coli; the first-pass DS-25 record uses this source only for the DefensePredictor DS naming context, not for an exact DS-25 phage readout."
      },
      {
        "reference": "DOI:10.1101/2025.01.08.631726",
        "snippet": "We refer to these validated TUs as DefensePredictor discovered Systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
        "notes": "DeWeirdt et al. name validated transcriptional units as DefensePredictor discovered Systems."
      },
      {
        "reference": "DOI:10.1101/2025.01.08.631726",
        "snippet": "To begin elucidating the function of the 45 validated TUs, we further annotated their protein domains (see Methods; table S6).",
        "notes": "DeWeirdt et al. describe Table S6 as a protein-domain annotation table for the validated DS transcriptional units; the exact preprint DS-25 row was not recovered in this curation pass."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| DS-25 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
        "notes": "The pinned DefenseFinder article registry maps the DS-25 source key to the DeWeirdt et al. DefensePredictor preprint."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| DS-25__DS-25A                                    |                                                  | DS-25                  | Custom                  | 80     |",
        "notes": "The pinned DefenseFinder HMM inventory records DS-25__DS-25A as a custom DS-25 profile."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| DS-25__DS-25B                                    |                                                  | DS-25                  | Custom                  | 40     |",
        "notes": "The pinned DefenseFinder HMM inventory records DS-25__DS-25B as a custom DS-25 profile."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "ds_25_locus_profile_model",
        "title": "DS-25 locus profile model",
        "description": "Conservative system-level sketch linking the DS-25 DefensePredictor-discovered system key to DS-25 system possession and the broader phage-defense-system trait without resolving DS-25 component function or a phage activity readout.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures DS-25 as a DefensePredictor-discovered system with DS-25A and DS-25B custom HMM rows in the pinned DefenseFinder HMM inventory. It does not assert the preprint working identifier, preprint Table S5/S6 rows, final Science supplement rows, native host breadth, profile-to-protein correspondence, DS-25A or DS-25B molecular activity, exact phage target breadth, or DefenseFinder rule-level detection criteria.",
        "nodes": [
          {
            "node_id": "ds_25_locus",
            "label": "DS-25 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A DefensePredictor-discovered system 25 locus represented in the pinned DefenseFinder HMM inventory by DS-25A and DS-25B custom profiles."
          },
          {
            "node_id": "ds_25_system_trait",
            "label": "DS-25 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000473",
            "description": "Possession of a genome-encoded DS-25 phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "ds_25_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "ds_25_system_trait",
            "description": "DefenseFinder links the DS-25 source key to the DefensePredictor preprint and represents DS-25 in the HMM inventory with DS-25A and DS-25B custom profiles.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| DS-25 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
                "notes": "The pinned DefenseFinder article registry maps the DS-25 source key to the DeWeirdt et al. DefensePredictor preprint."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| DS-25__DS-25A                                    |                                                  | DS-25                  | Custom                  | 80     |",
                "notes": "The pinned DefenseFinder HMM inventory records DS-25__DS-25A as a custom DS-25 profile."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| DS-25__DS-25B                                    |                                                  | DS-25                  | Custom                  | 40     |",
                "notes": "The pinned DefenseFinder HMM inventory records DS-25__DS-25B as a custom DS-25 profile."
              }
            ]
          },
          {
            "subject": "ds_25_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "DS-25 system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1101/2025.01.08.631726",
                "snippet": "We refer to these validated TUs as DefensePredictor discovered Systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
                "notes": "DeWeirdt et al. name validated TUs as DefensePredictor discovered Systems."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| DS-25 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
                "notes": "The pinned DefenseFinder article registry maps the DS-25 source key to the DeWeirdt et al. DefensePredictor preprint."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "ds-25-defensefinder-model-gap",
        "prompt": "Resolve DS-25 working-identifier rows, preprint Table S5 and S6 context, final Science supplement omission, native host breadth, DS-25A/DS-25B profile-to-protein mapping, sensitive-phage breadth, molecular output, and rule-level DefenseFinder criteria before minting narrower DS-25 mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "The DeWeirdt et al. preprint supports the DefensePredictor discovered System naming convention, the pinned DefenseFinder article registry names DS-25 and maps it to that preprint, and the pinned HMM inventory records DS-25A and DS-25B custom profile rows. DS-25 is absent from the final Science Table S6, S7, and S8 files checked during this curation pass, the exact preprint per-TU rows were not recovered, the pinned DefenseFinder rules table has no DS-25 row, and the first-pass record does not resolve the working identifier, assayed phages, phage readout, native host, profile-to-component mapping, component activities, or complete detection criteria.",
        "evidence": [
          {
            "reference": "DOI:10.1101/2025.01.08.631726",
            "snippet": "To test for anti-phage defense, we placed each TU with its native promoter region on a low-copy number plasmid in E. coli MG1655 and then challenged these strains with a panel of 24 diverse E. coli phages (fig. S2). In total, 45 (42% of 106) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
            "notes": "DeWeirdt et al. validate predicted transcriptional units by measuring plaquing relative to an empty vector control strain."
          },
          {
            "reference": "DOI:10.1101/2025.01.08.631726",
            "snippet": "We refer to these validated TUs as DefensePredictor discovered Systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
            "notes": "DeWeirdt et al. name validated TUs as DSs."
          },
          {
            "reference": "DOI:10.1101/2025.01.08.631726",
            "snippet": "To begin elucidating the function of the 45 validated TUs, we further annotated their protein domains (see Methods; table S6).",
            "notes": "DeWeirdt et al. describe Table S6 as further protein-domain annotation of validated TUs."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
            "snippet": "| DS-25 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
            "notes": "The pinned DefenseFinder article registry maps the DS-25 source key to the DeWeirdt et al. DefensePredictor preprint."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| DS-25__DS-25A                                    |                                                  | DS-25                  | Custom                  | 80     |",
            "notes": "The pinned DefenseFinder HMM inventory records DS-25__DS-25A as a custom DS-25 profile."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| DS-25__DS-25B                                    |                                                  | DS-25                  | Custom                  | 40     |",
            "notes": "The pinned DefenseFinder HMM inventory records DS-25__DS-25B as a custom DS-25 profile."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "The pinned DefenseFinder rules table does not list DS-25, DS-25A, or DS-25B, leaving complete component coverage and rule-level detection criteria unresolved."
          }
        ],
        "attaches_to": [
          "causal_graphs#ds_25_locus_profile_model"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-29"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-29T20:21:54Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted DS-25 system as a DOI- and DefenseFinder-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; kept the graph at DS-25 source-key and HMM-profile level because preprint Table S5/S6 rows, final Science supplement rows, and rule rows remain unresolved, and proposals/metpo_traitmech_v350 reserves the replacement placeholder.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-29T20:21:55Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed DS-25 system canonical_examples and left them empty because the pinned DefenseFinder registries support DS-25 system identity and custom HMM coverage but not a direct named native microbial isolate exemplar with experimentally verified endogenous DS-25 activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000472",
    "label": "DS-26 system",
    "definition": "A phage defense system in which an organism possesses the single-gene DefensePredictor-discovered system 26 locus cataloged as working transcriptional unit NERD and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.",
    "definition_source": "DOI:10.1126/science.adv7924",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "DS-26",
        "synonym_type": "EXACT_SYNONYM",
        "source": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx"
      },
      {
        "synonym_text": "NERD",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1126/science.adv7924",
        "snippet": "To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
        "notes": "DeWeirdt et al. experimentally validated 42 predicted transcriptional units as phage-defense systems in E. coli."
      },
      {
        "reference": "DOI:10.1126/science.adv7924",
        "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
        "notes": "DeWeirdt et al. name validated transcriptional units as DefensePredictor discovered systems."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
        "snippet": "NERD\tNZ_QOXL01000006.1\tGCF_003334035.1\t-\tTrue\tFalse\tFalse\tTrue\tDefensePredictor hits\t203139\t204737\thypothetical protein\tWP_054626965.1\t9.096479385650875\t4.498799058824351\tTrue\tTrue\tRemote defense homolog\tDS-26",
        "notes": "The final Science supplementary Table S6 maps working_id NERD to DS_name DS-26, marks the cloned transcriptional unit as defensive, and records NZ_QOXL01000006.1 positions 203139-204737 with product accession WP_054626965.1."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
        "snippet": "Bas25\t6.1\tpLAND\t24-07-17_MVB1_VPUS_VAME_EV.png\t50000000\tNERD\t24-07-17\t24-07-17_AAA2_RMOR_NERD_NUCS.png\t1\t3\t\t30\t6.221848749616356\t\t\tTrue\tLB\t37",
        "notes": "The final Science supplementary Table S7 Systems sheet reports a NERD assay row with a Bas25 phage readout and a -log(EOP) value of 6.222."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
        "snippet": "Bas19\t6.1\tpLAND\t24-07-17_MVB1_VPUS_VAME_EV.png\t2200000\tNERD\t24-07-17\t24-07-17_AAA2_RMOR_NERD_NUCS.png\t1\t2\t\t20\t5.041392685158225\t\t\tTrue\tLB\t37",
        "notes": "The final Science supplementary Table S7 Systems sheet reports a NERD assay row with a Bas19 phage readout and a -log(EOP) value of 5.041."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
        "snippet": "NERD\tDS-26\tTrue",
        "notes": "The final Science supplementary Table S8 maps NERD to replicated display name DS-26."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
        "snippet": "NERD\t1.0\t532.0\tWP_054626965.1\tPDDEXK\tPF09254.16\tFokI_cleav_dom ; FokI, cleavage domain\thhpred_1843394.hhr\t282.0\t459.0\t0.95\t2024-07-29 00:00:00\t77-79\t63.0",
        "notes": "The final Science supplementary Table S8 reports a PDDEXK/FokI cleavage-domain HHpred lead for WP_054626965.1 in NERD; this first-pass record records it as source context without resolving DS-26 molecular activity."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "ds_26_locus_reduces_phage_plaquing",
        "title": "DS-26 locus reduces bacteriophage plaquing",
        "description": "Conservative system-level sketch linking the single-gene DS-26 locus to reduced bacteriophage plaquing without resolving DS-26 nuclease chemistry, native activity, DefenseFinder model coverage, or molecular output.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures DS-26 as the validated NERD transcriptional unit with one product accession, two Table S7 phage-specific readouts, and one Table S8 PDDEXK/FokI cleavage-domain HHpred lead for WP_054626965.1. It does not assert exact domain interpretation, nuclease chemistry, native host breadth, complete phage breadth, DefenseFinder article/HMM/rules coverage, molecular output, or endogenous DS-26 activity.",
        "nodes": [
          {
            "node_id": "ds_26_locus",
            "label": "DS-26 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A single-gene DS-26 locus cataloged as working transcriptional unit NERD in final Science supplementary Table S6."
          },
          {
            "node_id": "reduced_phage_plaquing",
            "label": "reduced bacteriophage plaquing",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced bacteriophage plaquing in cells carrying cloned NERD."
          },
          {
            "node_id": "ds_26_system_trait",
            "label": "DS-26 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000472",
            "description": "Possession of a genome-encoded DS-26 phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "ds_26_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "reduced_phage_plaquing",
            "description": "The DS-26/NERD locus contributes to reduced bacteriophage plaquing in heterologous E. coli MG1655 plasmid-expression assays.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
                "notes": "DeWeirdt et al. describe the plasmid-based phage challenge used to validate predicted transcriptional units."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
                "snippet": "NERD\tNZ_QOXL01000006.1\tGCF_003334035.1\t-\tTrue\tFalse\tFalse\tTrue\tDefensePredictor hits\t203139\t204737\thypothetical protein\tWP_054626965.1\t9.096479385650875\t4.498799058824351\tTrue\tTrue\tRemote defense homolog\tDS-26",
                "notes": "The final Science supplementary Table S6 maps working_id NERD to DS_name DS-26, marks the cloned transcriptional unit as defensive, and records NZ_QOXL01000006.1 positions 203139-204737 with product accession WP_054626965.1."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
                "snippet": "Bas25\t6.1\tpLAND\t24-07-17_MVB1_VPUS_VAME_EV.png\t50000000\tNERD\t24-07-17\t24-07-17_AAA2_RMOR_NERD_NUCS.png\t1\t3\t\t30\t6.221848749616356\t\t\tTrue\tLB\t37",
                "notes": "The final Science supplementary Table S7 Systems sheet reports a NERD assay row with a Bas25 phage readout and a -log(EOP) value of 6.222."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
                "snippet": "Bas19\t6.1\tpLAND\t24-07-17_MVB1_VPUS_VAME_EV.png\t2200000\tNERD\t24-07-17\t24-07-17_AAA2_RMOR_NERD_NUCS.png\t1\t2\t\t20\t5.041392685158225\t\t\tTrue\tLB\t37",
                "notes": "The final Science supplementary Table S7 Systems sheet reports a NERD assay row with a Bas19 phage readout and a -log(EOP) value of 5.041."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
                "snippet": "NERD\tDS-26\tTrue",
                "notes": "The final Science supplementary Table S8 maps NERD to replicated display name DS-26."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
                "snippet": "NERD\t1.0\t532.0\tWP_054626965.1\tPDDEXK\tPF09254.16\tFokI_cleav_dom ; FokI, cleavage domain\thhpred_1843394.hhr\t282.0\t459.0\t0.95\t2024-07-29 00:00:00\t77-79\t63.0",
                "notes": "The final Science supplementary Table S8 reports a PDDEXK/FokI cleavage-domain HHpred lead for WP_054626965.1 in NERD; this first-pass record records it as source context without resolving DS-26 molecular activity."
              }
            ]
          },
          {
            "subject": "reduced_phage_plaquing",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "ds_26_system_trait",
            "description": "DS-26-mediated phage plaquing reduction realizes the DS-26 system trait.",
            "evidence": [
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
                "snippet": "NERD\tNZ_QOXL01000006.1\tGCF_003334035.1\t-\tTrue\tFalse\tFalse\tTrue\tDefensePredictor hits\t203139\t204737\thypothetical protein\tWP_054626965.1\t9.096479385650875\t4.498799058824351\tTrue\tTrue\tRemote defense homolog\tDS-26",
                "notes": "The final Science supplementary Table S6 maps working_id NERD to DS_name DS-26, marks the cloned transcriptional unit as defensive, and records NZ_QOXL01000006.1 positions 203139-204737 with product accession WP_054626965.1."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
                "snippet": "Bas25\t6.1\tpLAND\t24-07-17_MVB1_VPUS_VAME_EV.png\t50000000\tNERD\t24-07-17\t24-07-17_AAA2_RMOR_NERD_NUCS.png\t1\t3\t\t30\t6.221848749616356\t\t\tTrue\tLB\t37",
                "notes": "The final Science supplementary Table S7 Systems sheet reports a NERD assay row with a Bas25 phage readout and a -log(EOP) value of 6.222."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
                "snippet": "Bas19\t6.1\tpLAND\t24-07-17_MVB1_VPUS_VAME_EV.png\t2200000\tNERD\t24-07-17\t24-07-17_AAA2_RMOR_NERD_NUCS.png\t1\t2\t\t20\t5.041392685158225\t\t\tTrue\tLB\t37",
                "notes": "The final Science supplementary Table S7 Systems sheet reports a NERD assay row with a Bas19 phage readout and a -log(EOP) value of 5.041."
              },
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
                "notes": "The DS nomenclature is used for DefensePredictor discovered systems."
              }
            ]
          },
          {
            "subject": "ds_26_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "DS-26 system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
                "notes": "DeWeirdt et al. name validated TUs as DSs."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "ds-26-defensefinder-model-gap",
        "prompt": "Resolve DS-26 native host breadth, exact component activity, PDDEXK/FokI HHpred-domain interpretation, nuclease chemistry, complete phage breadth, molecular output, and DefenseFinder model coverage before minting narrower DS-26 mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "DeWeirdt et al. support DS-26 as the defensive NERD transcriptional unit and final Science Tables S6/S7/S8 map it to one product accession, Bas25 and Bas19 phage readouts, display name DS-26, and a PDDEXK/FokI cleavage-domain HHpred row. A first-pass pinned DefenseFinder review found no exact DS-26 article, HMM, or rules row, and the first-pass record therefore does not resolve native host breadth, complete phage breadth, domain interpretation, nuclease chemistry, molecular output, or endogenous DS-26 activity.",
        "evidence": [
          {
            "reference": "DOI:10.1126/science.adv7924",
            "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
            "notes": "DeWeirdt et al. name validated TUs as DSs."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
            "snippet": "NERD\tNZ_QOXL01000006.1\tGCF_003334035.1\t-\tTrue\tFalse\tFalse\tTrue\tDefensePredictor hits\t203139\t204737\thypothetical protein\tWP_054626965.1\t9.096479385650875\t4.498799058824351\tTrue\tTrue\tRemote defense homolog\tDS-26",
            "notes": "The final Science supplementary Table S6 maps working_id NERD to DS_name DS-26, marks the cloned transcriptional unit as defensive, and records NZ_QOXL01000006.1 positions 203139-204737 with product accession WP_054626965.1."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
            "snippet": "Bas25\t6.1\tpLAND\t24-07-17_MVB1_VPUS_VAME_EV.png\t50000000\tNERD\t24-07-17\t24-07-17_AAA2_RMOR_NERD_NUCS.png\t1\t3\t\t30\t6.221848749616356\t\t\tTrue\tLB\t37",
            "notes": "The final Science supplementary Table S7 Systems sheet reports a NERD assay row with a Bas25 phage readout and a -log(EOP) value of 6.222."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
            "snippet": "Bas19\t6.1\tpLAND\t24-07-17_MVB1_VPUS_VAME_EV.png\t2200000\tNERD\t24-07-17\t24-07-17_AAA2_RMOR_NERD_NUCS.png\t1\t2\t\t20\t5.041392685158225\t\t\tTrue\tLB\t37",
            "notes": "The final Science supplementary Table S7 Systems sheet reports a NERD assay row with a Bas19 phage readout and a -log(EOP) value of 5.041."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
            "snippet": "NERD\tDS-26\tTrue",
            "notes": "The final Science supplementary Table S8 maps NERD to replicated display name DS-26."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
            "snippet": "NERD\t1.0\t532.0\tWP_054626965.1\tPDDEXK\tPF09254.16\tFokI_cleav_dom ; FokI, cleavage domain\thhpred_1843394.hhr\t282.0\t459.0\t0.95\t2024-07-29 00:00:00\t77-79\t63.0",
            "notes": "The final Science supplementary Table S8 reports a PDDEXK/FokI cleavage-domain HHpred lead for WP_054626965.1 in NERD; this first-pass record records it as source context without resolving DS-26 molecular activity."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
            "notes": "The pinned DefenseFinder article registry has no exact DS-26 or source-key NERD row."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "notes": "The pinned DefenseFinder HMM inventory has no exact DS-26 or DS-26__DS-26 profile row; the NERD substring occurs only in an unrelated UG34__NERD_Helicase profile row."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "The pinned DefenseFinder rules table has no exact DS-26 or source-key NERD model row."
          }
        ],
        "attaches_to": [
          "causal_graphs#ds_26_locus_reduces_phage_plaquing"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-29"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-29T19:30:01Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted DS-26 system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; kept the graph at NERD transcriptional-unit level because native host breadth, exact component activity, complete phage breadth, DefenseFinder model coverage, nuclease chemistry, and molecular output remain unresolved, and proposals/metpo_traitmech_v349 reserves the replacement placeholder.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-29T19:30:02Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed DS-26 system canonical_examples and left them empty because DeWeirdt et al. directly support cloned NERD assays in E. coli MG1655, but not a direct named native microbial isolate exemplar with experimentally verified endogenous DS-26 activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000451",
    "label": "DS-27 system",
    "definition": "A phage defense system in which an organism possesses the single-gene DefensePredictor-discovered system 27 locus cataloged as working transcriptional unit SMEK and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.",
    "definition_source": "DOI:10.1126/science.adv7924",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "DS-27",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1126/science.adv7924"
      },
      {
        "synonym_text": "SMEK",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx"
      },
      {
        "synonym_text": "DS-27__DS-27",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1126/science.adv7924",
        "snippet": "To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
        "notes": "DeWeirdt et al. experimentally validated 42 predicted transcriptional units as phage-defense systems in E. coli."
      },
      {
        "reference": "DOI:10.1126/science.adv7924",
        "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
        "notes": "DeWeirdt et al. name validated transcriptional units as DefensePredictor discovered systems."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
        "snippet": "SMEK\tNZ_QOXX01000051.1\tGCF_003334605.1\t+\tTrue\tFalse\tFalse\tTrue\tDefensePredictor hits\t1216\t2115\tSMEK domain-containing protein\tWP_087896215.1\t7.030671187100836\t-2.208385407473748\tTrue\tFalse\tPredicted novel defense gene\tDS-27",
        "notes": "The final Science supplementary Table S6 maps working_id SMEK to DS_name DS-27, marks the cloned transcriptional unit as defensive, and records NZ_QOXX01000051.1 positions 1216-2115 with product accession WP_087896215.1."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
        "snippet": "RB69\t6.2\tpLAND\t24-07-17_AAA2_VPUS_VAME_EV.png\t7000000\tSMEK\t24-07-25\t24-07-25_SLIP_TMO1_PDX1_SMEK.png\t3\t10\t\t10000\t2.845098040014257\t\t\tTrue\tLB\t37",
        "notes": "The final Science supplementary Table S7 reports a SMEK assay row with an RB69 phage readout and a -log(EOP) value of 2.845."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
        "snippet": "SMEK\tDS-27\tTrue",
        "notes": "The final Science supplementary Table S8 maps SMEK to replicated display name DS-27."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| DS-27 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
        "notes": "The pinned DefenseFinder article registry maps the DS-27 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| DS-27__DS-27                                     |                                                  | DS-27                  | Custom                  | 220    |",
        "notes": "The pinned DefenseFinder HMM inventory records DS-27__DS-27 as a custom DS-27 profile."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "ds_27_locus_reduces_phage_plaquing",
        "title": "DS-27 locus reduces bacteriophage plaquing",
        "description": "Conservative system-level sketch linking the single-gene DS-27 locus to reduced bacteriophage plaquing without resolving DS-27 component function or molecular output.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures DS-27 as the validated SMEK transcriptional unit with one product accession and one DefenseFinder DS-27 profile row. It does not assert native host breadth, exact profile-to-protein correspondence, DS-27 molecular activity, trigger, substrate, complete phage breadth, HHpred-domain interpretation, or DefenseFinder rule-level detection criteria.",
        "nodes": [
          {
            "node_id": "ds_27_locus",
            "label": "DS-27 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A single-gene DefensePredictor-discovered system 27 locus represented in the pinned DefenseFinder HMM inventory by one DS-27 custom profile."
          },
          {
            "node_id": "reduced_phage_plaquing",
            "label": "reduced bacteriophage plaquing",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced bacteriophage plaquing in cells carrying cloned SMEK."
          },
          {
            "node_id": "ds_27_system_trait",
            "label": "DS-27 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000451",
            "description": "Possession of a genome-encoded DS-27 phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "ds_27_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "reduced_phage_plaquing",
            "description": "The DS-27/SMEK locus contributes to reduced bacteriophage plaquing in heterologous E. coli MG1655 plasmid-expression assays.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
                "notes": "DeWeirdt et al. describe the plasmid-based phage challenge used to validate predicted transcriptional units."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
                "snippet": "SMEK\tNZ_QOXX01000051.1\tGCF_003334605.1\t+\tTrue\tFalse\tFalse\tTrue\tDefensePredictor hits\t1216\t2115\tSMEK domain-containing protein\tWP_087896215.1\t7.030671187100836\t-2.208385407473748\tTrue\tFalse\tPredicted novel defense gene\tDS-27",
                "notes": "The final Science supplementary Table S6 maps working_id SMEK to DS_name DS-27, marks the cloned transcriptional unit as defensive, and records NZ_QOXX01000051.1 positions 1216-2115 with product accession WP_087896215.1."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
                "snippet": "RB69\t6.2\tpLAND\t24-07-17_AAA2_VPUS_VAME_EV.png\t7000000\tSMEK\t24-07-25\t24-07-25_SLIP_TMO1_PDX1_SMEK.png\t3\t10\t\t10000\t2.845098040014257\t\t\tTrue\tLB\t37",
                "notes": "The final Science supplementary Table S7 reports a SMEK assay row with an RB69 phage readout and a -log(EOP) value of 2.845."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
                "snippet": "SMEK\tDS-27\tTrue",
                "notes": "The final Science supplementary Table S8 maps SMEK to replicated display name DS-27."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| DS-27__DS-27                                     |                                                  | DS-27                  | Custom                  | 220    |",
                "notes": "The pinned DefenseFinder HMM inventory records DS-27__DS-27 as a custom DS-27 profile."
              }
            ]
          },
          {
            "subject": "reduced_phage_plaquing",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "ds_27_system_trait",
            "description": "DS-27-mediated phage plaquing reduction realizes the DS-27 system trait.",
            "evidence": [
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
                "snippet": "SMEK\tNZ_QOXX01000051.1\tGCF_003334605.1\t+\tTrue\tFalse\tFalse\tTrue\tDefensePredictor hits\t1216\t2115\tSMEK domain-containing protein\tWP_087896215.1\t7.030671187100836\t-2.208385407473748\tTrue\tFalse\tPredicted novel defense gene\tDS-27",
                "notes": "The final Science supplementary Table S6 maps working_id SMEK to DS_name DS-27, marks the cloned transcriptional unit as defensive, and records NZ_QOXX01000051.1 positions 1216-2115 with product accession WP_087896215.1."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
                "snippet": "RB69\t6.2\tpLAND\t24-07-17_AAA2_VPUS_VAME_EV.png\t7000000\tSMEK\t24-07-25\t24-07-25_SLIP_TMO1_PDX1_SMEK.png\t3\t10\t\t10000\t2.845098040014257\t\t\tTrue\tLB\t37",
                "notes": "The final Science supplementary Table S7 reports a SMEK assay row with an RB69 phage readout and a -log(EOP) value of 2.845."
              },
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
                "notes": "The DS nomenclature is used for DefensePredictor discovered systems."
              }
            ]
          },
          {
            "subject": "ds_27_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "DS-27 system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
                "notes": "DeWeirdt et al. name validated TUs as DefensePredictor discovered systems."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| DS-27 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
                "notes": "The pinned DefenseFinder article registry maps the DS-27 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "ds-27-defensefinder-model-gap",
        "prompt": "Resolve DS-27 native host breadth, exact single-component activity, profile-to-protein mapping, HHpred-domain interpretation, complete phage breadth, molecular output, and rule-level DefenseFinder criteria before minting narrower DS-27 mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "DeWeirdt et al. support DS-27 as the defensive SMEK transcriptional unit and final Science Tables S6/S7/S8 map it to product accession WP_087896215.1, an RB69 phage readout, and display name DS-27. The pinned DefenseFinder HMM inventory records one DS-27 custom profile row. The pinned rules table has no DS-27 row, and the first-pass record does not resolve native host breadth, complete phage breadth, direct profile-to-protein correspondence, HHpred-domain interpretation, molecular output, or endogenous DS-27 activity.",
        "evidence": [
          {
            "reference": "DOI:10.1126/science.adv7924",
            "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
            "notes": "DeWeirdt et al. name validated TUs as DSs."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
            "snippet": "SMEK\tNZ_QOXX01000051.1\tGCF_003334605.1\t+\tTrue\tFalse\tFalse\tTrue\tDefensePredictor hits\t1216\t2115\tSMEK domain-containing protein\tWP_087896215.1\t7.030671187100836\t-2.208385407473748\tTrue\tFalse\tPredicted novel defense gene\tDS-27",
            "notes": "The final Science supplementary Table S6 maps working_id SMEK to DS_name DS-27, marks the cloned transcriptional unit as defensive, and records NZ_QOXX01000051.1 positions 1216-2115 with product accession WP_087896215.1."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
            "snippet": "RB69\t6.2\tpLAND\t24-07-17_AAA2_VPUS_VAME_EV.png\t7000000\tSMEK\t24-07-25\t24-07-25_SLIP_TMO1_PDX1_SMEK.png\t3\t10\t\t10000\t2.845098040014257\t\t\tTrue\tLB\t37",
            "notes": "The final Science supplementary Table S7 reports a SMEK assay row with an RB69 phage readout and a -log(EOP) value of 2.845."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
            "snippet": "SMEK\tDS-27\tTrue",
            "notes": "The final Science supplementary Table S8 maps SMEK to replicated display name DS-27."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
            "snippet": "| DS-27 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
            "notes": "The pinned DefenseFinder article registry maps the DS-27 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| DS-27__DS-27                                     |                                                  | DS-27                  | Custom                  | 220    |",
            "notes": "The pinned DefenseFinder HMM inventory records DS-27__DS-27 as a custom DS-27 profile."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "The pinned DefenseFinder rules table does not list DS-27, leaving rule-level detection criteria unresolved."
          }
        ],
        "attaches_to": [
          "causal_graphs#ds_27_locus_reduces_phage_plaquing"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-29"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-29T04:13:10Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted DS-27 system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; kept the graph at SMEK transcriptional-unit level because HHpred domain interpretation and rule rows remain unresolved, and proposals/metpo_traitmech_v328 reserves the replacement placeholder.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-29T04:13:11Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed DS-27 system canonical_examples and left them empty because DeWeirdt et al. directly support cloned SMEK assays in E. coli MG1655 and a DefenseFinder DS-27 model, but not a direct named native microbial isolate exemplar with experimentally verified endogenous DS-27 activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000452",
    "label": "DS-28 system",
    "definition": "A phage defense system in which an organism possesses the two-gene DefensePredictor-discovered system 28 locus cataloged as working transcriptional unit ANEX and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.",
    "definition_source": "DOI:10.1126/science.adv7924",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "DS-28",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1126/science.adv7924"
      },
      {
        "synonym_text": "ANEX",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx"
      },
      {
        "synonym_text": "DS-28__DS-28A",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "DS-28__DS-28B",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1126/science.adv7924",
        "snippet": "To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
        "notes": "DeWeirdt et al. experimentally validated 42 predicted transcriptional units as phage-defense systems in E. coli."
      },
      {
        "reference": "DOI:10.1126/science.adv7924",
        "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
        "notes": "DeWeirdt et al. name validated transcriptional units as DefensePredictor discovered systems."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
        "snippet": "ANEX\tNZ_RRWS01000106.1\tGCF_003892555.1\t+\tTrue\tFalse\tFalse\tTrue\tDefensePredictor hits\t2434\t3695\thypothetical protein, HEPN family nuclease\tWP_000494510.1, WP_000528930.1\t7.693635438050782\t1.093286044385436\tTrue\tTrue\tPredicted novel defense gene\tDS-28",
        "notes": "The final Science supplementary Table S6 maps working_id ANEX to DS_name DS-28, marks the cloned transcriptional unit as defensive, and records NZ_RRWS01000106.1 positions 2434-3695 with product accessions WP_000494510.1 and WP_000528930.1."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
        "snippet": "Bas60\t6.1\tpLAND\t24-07-17_MVB1_VPUS_VAME_EV.png\t400000\tANEX\t24-07-24\t24-07-24_ANEX_NADH_APE1_NLRH.png\t1\t1\t\t10\t4.6020599913279625\t\t\tTrue\tLB\t37",
        "notes": "The final Science supplementary Table S7 reports an ANEX assay row with a Bas60 phage readout and a -log(EOP) value of 4.602."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
        "snippet": "ANEX\tDS-28\tTrue",
        "notes": "The final Science supplementary Table S8 maps ANEX to replicated display name DS-28."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
        "snippet": "ANEX\t1.0\t163.0\tWP_000528930.1\tHEPN\tPF18736.6\tpEK499_p136 ; HEPN pEK499 p136\thhpred_5242066.hhr\t1.0\t153.0\t1.0\t2024-07-30 00:00:00",
        "notes": "The final Science supplementary Table S8 reports a high-probability HEPN HHpred hit for WP_000528930.1 in ANEX."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
        "snippet": "ANEX\t2.0\t252.0\tWP_000494510.1\tTF\t6J9E_J\tRNA polymerase, transcription termination, anti-termination, RNAP clamp, phage, transcription initiation, P7, NusA, Xanthomonos oryzae, Xp10, transcription\thhpred_1617000.hhr\t143.0\t178.0\t0.326\t2024-07-30 00:00:00",
        "notes": "The final Science supplementary Table S8 reports a lower-probability TF HHpred hit for WP_000494510.1 in ANEX."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| DS-28 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
        "notes": "The pinned DefenseFinder article registry maps the DS-28 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| DS-28__DS-28A                                    |                                                  | DS-28                  | Custom                  | 100    |",
        "notes": "The pinned DefenseFinder HMM inventory records DS-28__DS-28A as a custom DS-28 profile."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| DS-28__DS-28B                                    |                                                  | DS-28                  | Custom                  | 100    |",
        "notes": "The pinned DefenseFinder HMM inventory records DS-28__DS-28B as a custom DS-28 profile."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "ds_28_locus_reduces_phage_plaquing",
        "title": "DS-28 locus reduces bacteriophage plaquing",
        "description": "Conservative system-level sketch linking the two-gene DS-28 locus to reduced bacteriophage plaquing without resolving DS-28 component function or molecular output.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures DS-28 as the validated ANEX transcriptional unit with two product accessions, one high-probability HEPN HHpred-domain row, one lower-probability TF HHpred-domain row, and two DefenseFinder DS-28 profile rows. It does not assert native host breadth, exact profile-to-protein correspondence, DS-28 molecular activity, trigger, substrate, complete phage breadth, HEPN or transcription-factor HHpred-domain interpretation, or DefenseFinder rule-level detection criteria.",
        "nodes": [
          {
            "node_id": "ds_28_locus",
            "label": "DS-28 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A two-gene DefensePredictor-discovered system 28 locus represented in the pinned DefenseFinder HMM inventory by two DS-28 custom profiles."
          },
          {
            "node_id": "reduced_phage_plaquing",
            "label": "reduced bacteriophage plaquing",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced bacteriophage plaquing in cells carrying cloned ANEX."
          },
          {
            "node_id": "ds_28_system_trait",
            "label": "DS-28 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000452",
            "description": "Possession of a genome-encoded DS-28 phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "ds_28_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "reduced_phage_plaquing",
            "description": "The DS-28/ANEX locus contributes to reduced bacteriophage plaquing in heterologous E. coli MG1655 plasmid-expression assays.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
                "notes": "DeWeirdt et al. describe the plasmid-based phage challenge used to validate predicted transcriptional units."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
                "snippet": "ANEX\tNZ_RRWS01000106.1\tGCF_003892555.1\t+\tTrue\tFalse\tFalse\tTrue\tDefensePredictor hits\t2434\t3695\thypothetical protein, HEPN family nuclease\tWP_000494510.1, WP_000528930.1\t7.693635438050782\t1.093286044385436\tTrue\tTrue\tPredicted novel defense gene\tDS-28",
                "notes": "The final Science supplementary Table S6 maps working_id ANEX to DS_name DS-28, marks the cloned transcriptional unit as defensive, and records NZ_RRWS01000106.1 positions 2434-3695 with product accessions WP_000494510.1 and WP_000528930.1."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
                "snippet": "Bas60\t6.1\tpLAND\t24-07-17_MVB1_VPUS_VAME_EV.png\t400000\tANEX\t24-07-24\t24-07-24_ANEX_NADH_APE1_NLRH.png\t1\t1\t\t10\t4.6020599913279625\t\t\tTrue\tLB\t37",
                "notes": "The final Science supplementary Table S7 reports an ANEX assay row with a Bas60 phage readout and a -log(EOP) value of 4.602."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
                "snippet": "ANEX\tDS-28\tTrue",
                "notes": "The final Science supplementary Table S8 maps ANEX to replicated display name DS-28."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
                "snippet": "ANEX\t1.0\t163.0\tWP_000528930.1\tHEPN\tPF18736.6\tpEK499_p136 ; HEPN pEK499 p136\thhpred_5242066.hhr\t1.0\t153.0\t1.0\t2024-07-30 00:00:00",
                "notes": "The final Science supplementary Table S8 reports a high-probability HEPN HHpred hit for WP_000528930.1 in ANEX."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
                "snippet": "ANEX\t2.0\t252.0\tWP_000494510.1\tTF\t6J9E_J\tRNA polymerase, transcription termination, anti-termination, RNAP clamp, phage, transcription initiation, P7, NusA, Xanthomonos oryzae, Xp10, transcription\thhpred_1617000.hhr\t143.0\t178.0\t0.326\t2024-07-30 00:00:00",
                "notes": "The final Science supplementary Table S8 reports a lower-probability TF HHpred hit for WP_000494510.1 in ANEX."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| DS-28__DS-28A                                    |                                                  | DS-28                  | Custom                  | 100    |",
                "notes": "The pinned DefenseFinder HMM inventory records DS-28__DS-28A as a custom DS-28 profile."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| DS-28__DS-28B                                    |                                                  | DS-28                  | Custom                  | 100    |",
                "notes": "The pinned DefenseFinder HMM inventory records DS-28__DS-28B as a custom DS-28 profile."
              }
            ]
          },
          {
            "subject": "reduced_phage_plaquing",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "ds_28_system_trait",
            "description": "DS-28-mediated phage plaquing reduction realizes the DS-28 system trait.",
            "evidence": [
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
                "snippet": "ANEX\tNZ_RRWS01000106.1\tGCF_003892555.1\t+\tTrue\tFalse\tFalse\tTrue\tDefensePredictor hits\t2434\t3695\thypothetical protein, HEPN family nuclease\tWP_000494510.1, WP_000528930.1\t7.693635438050782\t1.093286044385436\tTrue\tTrue\tPredicted novel defense gene\tDS-28",
                "notes": "The final Science supplementary Table S6 maps working_id ANEX to DS_name DS-28, marks the cloned transcriptional unit as defensive, and records NZ_RRWS01000106.1 positions 2434-3695 with product accessions WP_000494510.1 and WP_000528930.1."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
                "snippet": "Bas60\t6.1\tpLAND\t24-07-17_MVB1_VPUS_VAME_EV.png\t400000\tANEX\t24-07-24\t24-07-24_ANEX_NADH_APE1_NLRH.png\t1\t1\t\t10\t4.6020599913279625\t\t\tTrue\tLB\t37",
                "notes": "The final Science supplementary Table S7 reports an ANEX assay row with a Bas60 phage readout and a -log(EOP) value of 4.602."
              },
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
                "notes": "The DS nomenclature is used for DefensePredictor discovered systems."
              }
            ]
          },
          {
            "subject": "ds_28_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "DS-28 system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
                "notes": "DeWeirdt et al. name validated TUs as DefensePredictor discovered systems."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| DS-28 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
                "notes": "The pinned DefenseFinder article registry maps the DS-28 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "ds-28-defensefinder-model-gap",
        "prompt": "Resolve DS-28 native host breadth, exact component activities, profile-to-protein mappings, HEPN and transcription-factor HHpred-domain interpretations, complete phage breadth, molecular output, and rule-level DefenseFinder criteria before minting narrower DS-28 mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "DeWeirdt et al. support DS-28 as the defensive ANEX transcriptional unit and final Science Tables S6/S7/S8 map it to product accessions WP_000494510.1 and WP_000528930.1, a Bas60 phage readout, display name DS-28, a high-probability HEPN HHpred row, and a lower-probability TF HHpred row. The pinned DefenseFinder HMM inventory records two DS-28 custom profile rows. The pinned rules table has no DS-28 row, and the first-pass record does not resolve native host breadth, complete phage breadth, direct profile-to-protein correspondence, HEPN or transcription-factor activity, molecular output, or endogenous DS-28 activity.",
        "evidence": [
          {
            "reference": "DOI:10.1126/science.adv7924",
            "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
            "notes": "DeWeirdt et al. name validated TUs as DSs."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
            "snippet": "ANEX\tNZ_RRWS01000106.1\tGCF_003892555.1\t+\tTrue\tFalse\tFalse\tTrue\tDefensePredictor hits\t2434\t3695\thypothetical protein, HEPN family nuclease\tWP_000494510.1, WP_000528930.1\t7.693635438050782\t1.093286044385436\tTrue\tTrue\tPredicted novel defense gene\tDS-28",
            "notes": "The final Science supplementary Table S6 maps working_id ANEX to DS_name DS-28, marks the cloned transcriptional unit as defensive, and records NZ_RRWS01000106.1 positions 2434-3695 with product accessions WP_000494510.1 and WP_000528930.1."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
            "snippet": "Bas60\t6.1\tpLAND\t24-07-17_MVB1_VPUS_VAME_EV.png\t400000\tANEX\t24-07-24\t24-07-24_ANEX_NADH_APE1_NLRH.png\t1\t1\t\t10\t4.6020599913279625\t\t\tTrue\tLB\t37",
            "notes": "The final Science supplementary Table S7 reports an ANEX assay row with a Bas60 phage readout and a -log(EOP) value of 4.602."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
            "snippet": "ANEX\tDS-28\tTrue",
            "notes": "The final Science supplementary Table S8 maps ANEX to replicated display name DS-28."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
            "snippet": "ANEX\t1.0\t163.0\tWP_000528930.1\tHEPN\tPF18736.6\tpEK499_p136 ; HEPN pEK499 p136\thhpred_5242066.hhr\t1.0\t153.0\t1.0\t2024-07-30 00:00:00",
            "notes": "The final Science supplementary Table S8 reports a high-probability HEPN HHpred hit for WP_000528930.1 in ANEX."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
            "snippet": "ANEX\t2.0\t252.0\tWP_000494510.1\tTF\t6J9E_J\tRNA polymerase, transcription termination, anti-termination, RNAP clamp, phage, transcription initiation, P7, NusA, Xanthomonos oryzae, Xp10, transcription\thhpred_1617000.hhr\t143.0\t178.0\t0.326\t2024-07-30 00:00:00",
            "notes": "The final Science supplementary Table S8 reports a lower-probability TF HHpred hit for WP_000494510.1 in ANEX."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
            "snippet": "| DS-28 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
            "notes": "The pinned DefenseFinder article registry maps the DS-28 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| DS-28__DS-28A                                    |                                                  | DS-28                  | Custom                  | 100    |",
            "notes": "The pinned DefenseFinder HMM inventory records DS-28__DS-28A as a custom DS-28 profile."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| DS-28__DS-28B                                    |                                                  | DS-28                  | Custom                  | 100    |",
            "notes": "The pinned DefenseFinder HMM inventory records DS-28__DS-28B as a custom DS-28 profile."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "The pinned DefenseFinder rules table does not list DS-28, leaving rule-level detection criteria unresolved."
          }
        ],
        "attaches_to": [
          "causal_graphs#ds_28_locus_reduces_phage_plaquing"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-29"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-29T04:57:13Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted DS-28 system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; kept the graph at ANEX transcriptional-unit level because HEPN and transcription-factor HHpred-domain interpretation and rule rows remain unresolved, and proposals/metpo_traitmech_v329 reserves the replacement placeholder.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-29T04:57:14Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed DS-28 system canonical_examples and left them empty because DeWeirdt et al. directly support cloned ANEX assays in E. coli MG1655 and a DefenseFinder DS-28 model, but not a direct named native microbial isolate exemplar with experimentally verified endogenous DS-28 activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000453",
    "label": "DS-29 system",
    "definition": "A phage defense system in which an organism possesses the single-gene DefensePredictor-discovered system 29 locus cataloged as working transcriptional unit HEP3 and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.",
    "definition_source": "DOI:10.1126/science.adv7924",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "DS-29",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1126/science.adv7924"
      },
      {
        "synonym_text": "HEP3",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx"
      },
      {
        "synonym_text": "DS-29__DS-29",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1126/science.adv7924",
        "snippet": "To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
        "notes": "DeWeirdt et al. experimentally validated 42 predicted transcriptional units as phage-defense systems in E. coli."
      },
      {
        "reference": "DOI:10.1126/science.adv7924",
        "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
        "notes": "DeWeirdt et al. name validated transcriptional units as DefensePredictor discovered systems."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
        "snippet": "HEP3\tNZ_RRWI01000012.1\tGCF_003892435.1\t+\tTrue\tFalse\tTrue\tTrue\tDefensePredictor hits\t2077\t2862\thypothetical protein\tWP_061089765.1\t9.79101703966607\t-3.842009204807087\tTrue\tFalse\tPredicted novel defense gene\tDS-29",
        "notes": "The final Science supplementary Table S6 maps working_id HEP3 to DS_name DS-29, marks the cloned transcriptional unit as defensive, and records NZ_RRWI01000012.1 positions 2077-2862 with product accession WP_061089765.1."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
        "snippet": "Bas60\t2.2\tpLAND\t24-03-12_EV.png\t2200000000\tHEP3\t24-03-13\t24-03-13_2971_HEP3_TMP4.png\t1\t100\t\t1000\t6.342422680822207\t\tTrue\t\tLB\t37",
        "notes": "The final Science supplementary Table S7 reports an HEP3 assay row with a Bas60 phage readout and a -log(EOP) value of 6.342."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
        "snippet": "HEP3\tDS-29\tTrue",
        "notes": "The final Science supplementary Table S8 maps HEP3 to replicated display name DS-29."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
        "snippet": "HEP3\t1.0\t261.0\tWP_061089765.1\tHEPN\tPF18867.6\tHEPN-like_int ; HEPN-like integron domain\thhpred_8060866.hhr\t157.0\t252.0\t0.5936\t2024-04-15 00:00:00",
        "notes": "The final Science supplementary Table S8 reports a lower-probability HEPN-like HHpred hit for WP_061089765.1 in HEP3."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| DS-29 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
        "notes": "The pinned DefenseFinder article registry maps the DS-29 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| DS-29__DS-29                                     |                                                  | DS-29                  | Custom                  | 100    |",
        "notes": "The pinned DefenseFinder HMM inventory records DS-29__DS-29 as a custom DS-29 profile."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "ds_29_locus_reduces_phage_plaquing",
        "title": "DS-29 locus reduces bacteriophage plaquing",
        "description": "Conservative system-level sketch linking the single-gene DS-29 locus to reduced bacteriophage plaquing without resolving DS-29 component function or molecular output.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures DS-29 as the validated HEP3 transcriptional unit with one product accession, one lower-probability HEPN-like HHpred-domain row, and one DefenseFinder DS-29 profile row. It does not assert native host breadth, exact profile-to-protein correspondence, DS-29 molecular activity, trigger, substrate, complete phage breadth, HEPN-like HHpred-domain interpretation, or DefenseFinder rule-level detection criteria.",
        "nodes": [
          {
            "node_id": "ds_29_locus",
            "label": "DS-29 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A single-gene DefensePredictor-discovered system 29 locus represented in the pinned DefenseFinder HMM inventory by one DS-29 custom profile."
          },
          {
            "node_id": "reduced_phage_plaquing",
            "label": "reduced bacteriophage plaquing",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced bacteriophage plaquing in cells carrying cloned HEP3."
          },
          {
            "node_id": "ds_29_system_trait",
            "label": "DS-29 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000453",
            "description": "Possession of a genome-encoded DS-29 phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "ds_29_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "reduced_phage_plaquing",
            "description": "The DS-29/HEP3 locus contributes to reduced bacteriophage plaquing in heterologous E. coli MG1655 plasmid-expression assays.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
                "notes": "DeWeirdt et al. describe the plasmid-based phage challenge used to validate predicted transcriptional units."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
                "snippet": "HEP3\tNZ_RRWI01000012.1\tGCF_003892435.1\t+\tTrue\tFalse\tTrue\tTrue\tDefensePredictor hits\t2077\t2862\thypothetical protein\tWP_061089765.1\t9.79101703966607\t-3.842009204807087\tTrue\tFalse\tPredicted novel defense gene\tDS-29",
                "notes": "The final Science supplementary Table S6 maps working_id HEP3 to DS_name DS-29, marks the cloned transcriptional unit as defensive, and records NZ_RRWI01000012.1 positions 2077-2862 with product accession WP_061089765.1."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
                "snippet": "Bas60\t2.2\tpLAND\t24-03-12_EV.png\t2200000000\tHEP3\t24-03-13\t24-03-13_2971_HEP3_TMP4.png\t1\t100\t\t1000\t6.342422680822207\t\tTrue\t\tLB\t37",
                "notes": "The final Science supplementary Table S7 reports an HEP3 assay row with a Bas60 phage readout and a -log(EOP) value of 6.342."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
                "snippet": "HEP3\tDS-29\tTrue",
                "notes": "The final Science supplementary Table S8 maps HEP3 to replicated display name DS-29."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
                "snippet": "HEP3\t1.0\t261.0\tWP_061089765.1\tHEPN\tPF18867.6\tHEPN-like_int ; HEPN-like integron domain\thhpred_8060866.hhr\t157.0\t252.0\t0.5936\t2024-04-15 00:00:00",
                "notes": "The final Science supplementary Table S8 reports a lower-probability HEPN-like HHpred hit for WP_061089765.1 in HEP3."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| DS-29__DS-29                                     |                                                  | DS-29                  | Custom                  | 100    |",
                "notes": "The pinned DefenseFinder HMM inventory records DS-29__DS-29 as a custom DS-29 profile."
              }
            ]
          },
          {
            "subject": "reduced_phage_plaquing",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "ds_29_system_trait",
            "description": "DS-29-mediated phage plaquing reduction realizes the DS-29 system trait.",
            "evidence": [
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
                "snippet": "HEP3\tNZ_RRWI01000012.1\tGCF_003892435.1\t+\tTrue\tFalse\tTrue\tTrue\tDefensePredictor hits\t2077\t2862\thypothetical protein\tWP_061089765.1\t9.79101703966607\t-3.842009204807087\tTrue\tFalse\tPredicted novel defense gene\tDS-29",
                "notes": "The final Science supplementary Table S6 maps working_id HEP3 to DS_name DS-29, marks the cloned transcriptional unit as defensive, and records NZ_RRWI01000012.1 positions 2077-2862 with product accession WP_061089765.1."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
                "snippet": "Bas60\t2.2\tpLAND\t24-03-12_EV.png\t2200000000\tHEP3\t24-03-13\t24-03-13_2971_HEP3_TMP4.png\t1\t100\t\t1000\t6.342422680822207\t\tTrue\t\tLB\t37",
                "notes": "The final Science supplementary Table S7 reports an HEP3 assay row with a Bas60 phage readout and a -log(EOP) value of 6.342."
              },
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
                "notes": "The DS nomenclature is used for DefensePredictor discovered systems."
              }
            ]
          },
          {
            "subject": "ds_29_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "DS-29 system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
                "notes": "DeWeirdt et al. name validated TUs as DefensePredictor discovered systems."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| DS-29 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
                "notes": "The pinned DefenseFinder article registry maps the DS-29 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "ds-29-defensefinder-model-gap",
        "prompt": "Resolve DS-29 native host breadth, exact single-component activity, profile-to-protein mapping, HEPN-like HHpred-domain interpretation, complete phage breadth, molecular output, and rule-level DefenseFinder criteria before minting narrower DS-29 mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "DeWeirdt et al. support DS-29 as the defensive HEP3 transcriptional unit and final Science Tables S6/S7/S8 map it to product accession WP_061089765.1, a Bas60 phage readout, display name DS-29, and a HEPN-like HHpred row. The pinned DefenseFinder HMM inventory records one DS-29 custom profile row. The pinned rules table has no DS-29 row, and the first-pass record does not resolve native host breadth, complete phage breadth, direct profile-to-protein correspondence, HEPN-like activity, molecular output, or endogenous DS-29 activity.",
        "evidence": [
          {
            "reference": "DOI:10.1126/science.adv7924",
            "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
            "notes": "DeWeirdt et al. name validated TUs as DSs."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
            "snippet": "HEP3\tNZ_RRWI01000012.1\tGCF_003892435.1\t+\tTrue\tFalse\tTrue\tTrue\tDefensePredictor hits\t2077\t2862\thypothetical protein\tWP_061089765.1\t9.79101703966607\t-3.842009204807087\tTrue\tFalse\tPredicted novel defense gene\tDS-29",
            "notes": "The final Science supplementary Table S6 maps working_id HEP3 to DS_name DS-29, marks the cloned transcriptional unit as defensive, and records NZ_RRWI01000012.1 positions 2077-2862 with product accession WP_061089765.1."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
            "snippet": "Bas60\t2.2\tpLAND\t24-03-12_EV.png\t2200000000\tHEP3\t24-03-13\t24-03-13_2971_HEP3_TMP4.png\t1\t100\t\t1000\t6.342422680822207\t\tTrue\t\tLB\t37",
            "notes": "The final Science supplementary Table S7 reports an HEP3 assay row with a Bas60 phage readout and a -log(EOP) value of 6.342."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
            "snippet": "HEP3\tDS-29\tTrue",
            "notes": "The final Science supplementary Table S8 maps HEP3 to replicated display name DS-29."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
            "snippet": "HEP3\t1.0\t261.0\tWP_061089765.1\tHEPN\tPF18867.6\tHEPN-like_int ; HEPN-like integron domain\thhpred_8060866.hhr\t157.0\t252.0\t0.5936\t2024-04-15 00:00:00",
            "notes": "The final Science supplementary Table S8 reports a lower-probability HEPN-like HHpred hit for WP_061089765.1 in HEP3."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
            "snippet": "| DS-29 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
            "notes": "The pinned DefenseFinder article registry maps the DS-29 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| DS-29__DS-29                                     |                                                  | DS-29                  | Custom                  | 100    |",
            "notes": "The pinned DefenseFinder HMM inventory records DS-29__DS-29 as a custom DS-29 profile."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "The pinned DefenseFinder rules table does not list DS-29, leaving rule-level detection criteria unresolved."
          }
        ],
        "attaches_to": [
          "causal_graphs#ds_29_locus_reduces_phage_plaquing"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-29"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-29T05:48:19Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted DS-29 system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; kept the graph at HEP3 transcriptional-unit level because HEPN-like activity and rule rows remain unresolved, and proposals/metpo_traitmech_v330 reserves the replacement placeholder.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-29T05:48:20Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed DS-29 system canonical_examples and left them empty because DeWeirdt et al. directly support cloned HEP3 assays in E. coli MG1655 and a DefenseFinder DS-29 model, but not a direct named native microbial isolate exemplar with experimentally verified endogenous DS-29 activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000425",
    "label": "DS-2 system",
    "definition": "A phage defense system in which an organism possesses the three-gene DefensePredictor-discovered system 2 locus cataloged as working transcriptional unit DISA and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.",
    "definition_source": "DOI:10.1126/science.adv7924",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "DS-2",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1126/science.adv7924"
      },
      {
        "synonym_text": "DISA",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx"
      },
      {
        "synonym_text": "DS-2__DS-2C",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1126/science.adv7924",
        "snippet": "To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
        "notes": "DeWeirdt et al. experimentally validated 42 predicted transcriptional units as phage-defense systems in E. coli."
      },
      {
        "reference": "DOI:10.1126/science.adv7924",
        "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
        "notes": "DeWeirdt et al. name validated transcriptional units as DefensePredictor discovered systems."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
        "snippet": "DISA\tNZ_RRVG01000003.1\tGCF_003886135.1\t+\tTrue\tFalse\tFalse\tTrue\tDefensePredictor hits\t52840\t56517\thypothetical protein, nucleotidyltransferase, patatin-like phospholipase family protein\tWP_016240614.1, WP_016240615.1, WP_001593459.1\t6.581747829126823\t6.906754778648663\tTrue\tTrue\tPredicted novel defense gene\tDS-2",
        "notes": "The final Science supplementary Table S6 maps working_id DISA to DS_name DS-2, marks the cloned transcriptional unit as defensive, and records NZ_RRVG01000003.1 positions 52840-56517 with product accessions WP_016240614.1, WP_016240615.1, and WP_001593459.1."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
        "snippet": "Bas1\t1.2\tpLAND\t24-03-08_EV_HHHD_PIN2_CRDO.png\t40000000\tDISA\t24-03-08\t24-03-08_IMPD_DISA_2CM2_MAZF.png\t5\t10\tY\t1000000\t1.6020599913279623\tTrue\t\t\tLB\t37",
        "notes": "The final Science supplementary Table S7 reports a DISA assay row with a Bas1 readout and a -log(EOP) value of 1.602."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
        "snippet": "DISA\tDS-2\tTrue",
        "notes": "The final Science supplementary Table S8 maps DISA to replicated display name DS-2."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| DS-2 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
        "notes": "The pinned DefenseFinder article registry maps the DS-2 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| DS-2__DS-2C                                      |                                                  | DS-2                   | Custom                  | 300    |",
        "notes": "The pinned DefenseFinder HMM inventory records DS-2__DS-2C as a custom DS-2 profile."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "ds_2_locus_reduces_phage_plaquing",
        "title": "DS-2 loci reduce bacteriophage plaquing",
        "description": "Conservative system-level sketch linking the three-gene DS-2 locus to reduced bacteriophage plaquing without resolving DS-2 component functions or effector activity.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures DS-2 as the validated DISA transcriptional unit with three product accessions and with a DefenseFinder DS-2C profile row. It does not assert native host breadth, exact profile-to-protein correspondence, the direct viral trigger or substrate, exact molecular output, phage target breadth, or DefenseFinder rule-level detection criteria.",
        "nodes": [
          {
            "node_id": "ds_2_locus",
            "label": "DS-2 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A three-gene DefensePredictor-discovered system locus represented in the pinned DefenseFinder HMM inventory by a DS-2C custom profile."
          },
          {
            "node_id": "reduced_phage_plaquing",
            "label": "reduced bacteriophage plaquing",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced efficiency of plaquing or reduced plaque size by bacteriophages in cells carrying cloned DISA."
          },
          {
            "node_id": "ds_2_system_trait",
            "label": "DS-2 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000425",
            "description": "Possession of a genome-encoded DS-2 phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "ds_2_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "reduced_phage_plaquing",
            "description": "The DS-2/DISA locus contributes to reduced bacteriophage plaquing when plasmid expressed.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
                "notes": "DeWeirdt et al. experimentally validate DefensePredictor-discovered systems by assaying cloned transcriptional units against E. coli phages."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
                "snippet": "DISA\tNZ_RRVG01000003.1\tGCF_003886135.1\t+\tTrue\tFalse\tFalse\tTrue\tDefensePredictor hits\t52840\t56517\thypothetical protein, nucleotidyltransferase, patatin-like phospholipase family protein\tWP_016240614.1, WP_016240615.1, WP_001593459.1\t6.581747829126823\t6.906754778648663\tTrue\tTrue\tPredicted novel defense gene\tDS-2",
                "notes": "The final Science supplementary Table S6 maps working_id DISA to DS_name DS-2, marks the cloned transcriptional unit as defensive, and records NZ_RRVG01000003.1 positions 52840-56517 with product accessions WP_016240614.1, WP_016240615.1, and WP_001593459.1."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
                "snippet": "Bas1\t1.2\tpLAND\t24-03-08_EV_HHHD_PIN2_CRDO.png\t40000000\tDISA\t24-03-08\t24-03-08_IMPD_DISA_2CM2_MAZF.png\t5\t10\tY\t1000000\t1.6020599913279623\tTrue\t\t\tLB\t37",
                "notes": "The final Science supplementary Table S7 reports a DISA assay row with a Bas1 readout and a -log(EOP) value of 1.602."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| DS-2__DS-2C                                      |                                                  | DS-2                   | Custom                  | 300    |",
                "notes": "The pinned DefenseFinder HMM inventory records DS-2__DS-2C as a custom DS-2 profile."
              }
            ]
          },
          {
            "subject": "reduced_phage_plaquing",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "ds_2_system_trait",
            "description": "DS-2-mediated phage plaquing reduction realizes the DS-2 system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
                "notes": "DeWeirdt et al. name each validated transcriptional unit as a DefensePredictor discovered system."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
                "snippet": "DISA\tNZ_RRVG01000003.1\tGCF_003886135.1\t+\tTrue\tFalse\tFalse\tTrue\tDefensePredictor hits\t52840\t56517\thypothetical protein, nucleotidyltransferase, patatin-like phospholipase family protein\tWP_016240614.1, WP_016240615.1, WP_001593459.1\t6.581747829126823\t6.906754778648663\tTrue\tTrue\tPredicted novel defense gene\tDS-2",
                "notes": "The final Science supplementary Table S6 maps working_id DISA to DS_name DS-2, marks the cloned transcriptional unit as defensive, and records NZ_RRVG01000003.1 positions 52840-56517 with product accessions WP_016240614.1, WP_016240615.1, and WP_001593459.1."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
                "snippet": "Bas1\t1.2\tpLAND\t24-03-08_EV_HHHD_PIN2_CRDO.png\t40000000\tDISA\t24-03-08\t24-03-08_IMPD_DISA_2CM2_MAZF.png\t5\t10\tY\t1000000\t1.6020599913279623\tTrue\t\t\tLB\t37",
                "notes": "The final Science supplementary Table S7 reports a DISA assay row with a Bas1 readout and a -log(EOP) value of 1.602."
              }
            ]
          },
          {
            "subject": "ds_2_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "DS-2 system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
                "notes": "DeWeirdt et al. validate DSs as anti-phage systems."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| DS-2 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
                "notes": "The pinned DefenseFinder article registry maps the DS-2 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "ds-2-defensefinder-model-gap",
        "prompt": "Resolve DS-2 native host breadth, exact DS-2 component functions, DS-2C profile-to-component mapping, sensitive-phage breadth, molecular output, and rule-level detection criteria before minting narrower DS-2 mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "DeWeirdt et al. support DS-2 as the defensive DISA transcriptional unit that reduced plaquing when cloned in E. coli MG1655, and the pinned DefenseFinder HMM inventory records a DS-2C profile row. The pinned rules table has no DS-2 row, and the first-pass record does not resolve native host breadth, exact component activities, profile-to-component mapping, phage target breadth, the direct molecular output, or endogenous DS-2 activity.",
        "evidence": [
          {
            "reference": "DOI:10.1126/science.adv7924",
            "snippet": "To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
            "notes": "DeWeirdt et al. validate predicted transcriptional units by measuring plaquing relative to an empty vector control strain."
          },
          {
            "reference": "DOI:10.1126/science.adv7924",
            "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
            "notes": "DeWeirdt et al. name validated TUs as DSs."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
            "snippet": "DISA\tNZ_RRVG01000003.1\tGCF_003886135.1\t+\tTrue\tFalse\tFalse\tTrue\tDefensePredictor hits\t52840\t56517\thypothetical protein, nucleotidyltransferase, patatin-like phospholipase family protein\tWP_016240614.1, WP_016240615.1, WP_001593459.1\t6.581747829126823\t6.906754778648663\tTrue\tTrue\tPredicted novel defense gene\tDS-2",
            "notes": "The final Science supplementary Table S6 maps working_id DISA to DS_name DS-2, marks the cloned transcriptional unit as defensive, and records NZ_RRVG01000003.1 positions 52840-56517 with product accessions WP_016240614.1, WP_016240615.1, and WP_001593459.1."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
            "snippet": "Bas1\t1.2\tpLAND\t24-03-08_EV_HHHD_PIN2_CRDO.png\t40000000\tDISA\t24-03-08\t24-03-08_IMPD_DISA_2CM2_MAZF.png\t5\t10\tY\t1000000\t1.6020599913279623\tTrue\t\t\tLB\t37",
            "notes": "The final Science supplementary Table S7 reports a DISA assay row with a Bas1 readout and a -log(EOP) value of 1.602."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
            "snippet": "DISA\tDS-2\tTrue",
            "notes": "The final Science supplementary Table S8 maps DISA to replicated display name DS-2."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
            "snippet": "| DS-2 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
            "notes": "The pinned DefenseFinder article registry maps the DS-2 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| DS-2__DS-2C                                      |                                                  | DS-2                   | Custom                  | 300    |",
            "notes": "The pinned DefenseFinder HMM inventory records DS-2__DS-2C as a custom DS-2 profile."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "The pinned DefenseFinder rules table does not list DS-2, leaving rule-level detection criteria unresolved."
          }
        ],
        "attaches_to": [
          "causal_graphs#ds_2_locus_reduces_phage_plaquing"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-28"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-28T04:13:03Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted DS-2 system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; kept the graph at cloned DISA transcriptional unit level because the pinned DefenseFinder DS-2 HMM row is not backed by a rules row; proposals/metpo_traitmech_v302 reserves the replacement placeholder.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-28T04:13:04Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed DS-2 system canonical_examples and left them empty because DeWeirdt et al. support cloned DISA plaquing assays in E. coli MG1655 plus a DefenseFinder DS-2 model, but not a direct named native microbial isolate exemplar with experimentally verified endogenous DS-2 activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000470",
    "label": "DS-30 system",
    "definition": "A phage defense system in which an organism possesses the four-gene DefensePredictor-discovered system 30 locus cataloged as working transcriptional unit ABC3 and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.",
    "definition_source": "DOI:10.1126/science.adv7924",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000232"
    ],
    "synonyms": [
      {
        "synonym_text": "DS-30",
        "synonym_type": "EXACT_SYNONYM",
        "source": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx"
      },
      {
        "synonym_text": "ABC3",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx"
      },
      {
        "synonym_text": "Lamassu-Fam__Lmu_DS-30A",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "Lamassu-Fam__LmuA_DS-30B",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "Lamassu-Fam__LmuB_DS-30D",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "Lamassu-Fam__LmuC_DS-30C",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1126/science.adv7924",
        "snippet": "To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
        "notes": "DeWeirdt et al. experimentally validated 42 predicted transcriptional units as phage-defense systems in E. coli."
      },
      {
        "reference": "DOI:10.1126/science.adv7924",
        "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
        "notes": "DeWeirdt et al. name validated transcriptional units as DefensePredictor discovered systems."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
        "snippet": "ABC3\tNZ_QOYR01000032.1\tGCF_003333645.1\t+\tTrue\tFalse\tTrue\tTrue\tDefensePredictor hits\t1906\t4621\thypothetical protein, hypothetical protein, hypothetical protein, DUF2326 domain-containing protein\tWP_001553315.1, WP_000534626.1, WP_000628292.1, WP_087889773.1\t8.95063706554687\t6.906754778648663\tTrue\tTrue\tPredicted novel defense gene\tDS-30",
        "notes": "The final Science supplementary Table S6 maps working_id ABC3 to DS_name DS-30, marks the cloned transcriptional unit as defensive, and records four product accessions in NZ_QOYR01000032.1 positions 1906-4621."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
        "snippet": "SECphi27\t5.1\tpLAND\t24-05-31_EV_CRDO_BRNT_ABC3.png\t100000000\tABC3\t24-05-31\t24-05-31_EV_CRDO_BRNT_ABC3.png\t5\t1\tY\t100000\t3\t\tTrue\t\tM9\t30",
        "notes": "The final Science supplementary Table S7 Systems sheet reports an ABC3 assay row with a SECphi27 phage readout, a smaller-plaque-size call, and a -log(EOP) value of 3."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
        "snippet": "ABC3\tDS-30\tTrue",
        "notes": "The final Science supplementary Table S8 maps ABC3 to replicated display name DS-30."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
        "snippet": "ABC3\t2.0\t182.0\tWP_000534626.1\tABC-3C C-term\tPF20275.3\tCTD10 ; C-terminal domain 10 of the ABC-three component (ABC-3C) systems\thhpred_7102862.hhr\t26.0\t176.0\t1.0\t2024-07-30 00:00:00",
        "notes": "The final Science supplementary Table S8 reports a high-probability CTD10 HHpred hit for ABC3 protein 2, WP_000534626.1."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
        "snippet": "ABC3\t3.0\t77.0\tWP_000628292.1\tABC-3C Mid\tPF20293.3\tMC6 ; ABC-three component (ABC-3C) system Middle Component 6\thhpred_3406401.hhr\t1.0\t75.0\t1.0\t2024-07-30 00:00:00",
        "notes": "The final Science supplementary Table S8 reports a high-probability MC6 HHpred hit for ABC3 protein 3, WP_000628292.1."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
        "snippet": "ABC3\t4.0\t565.0\tWP_087889773.1\tABC ATPase\t5XEI_A\tChromosome partition protein Smc; Condensin, Smc, head domain, ABC-ATPase,\thhpred_6417130.hhr\t1.0\t540.0\t1.0\t2024-07-30 00:00:00",
        "notes": "The final Science supplementary Table S8 reports a high-probability ABC ATPase HHpred hit for ABC3 protein 4, WP_087889773.1."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
        "snippet": "ABC3\t1.0\t86.0\tWP_001553315.1\tFtsL\t8HHF_L\tCell division protein FtsL; Bacterial cell division, divisome, FtsB, FtsL, FtsQ, FtsBLQ, membrane protein complex, heterotrimer, MEMBRANE PROTEIN\thhpred_2515914.hhr\t2.0\t53.0\t0.942\t2024-07-30 00:00:00",
        "notes": "The final Science supplementary Table S8 reports an FtsL HHpred hit for ABC3 protein 1, WP_001553315.1."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| Lamassu-Fam__Lmu_DS-30A                          |                                                  | Lamassu-Fam            | Custom                  | 50     |",
        "notes": "The pinned DefenseFinder HMM inventory records Lamassu-Fam__Lmu_DS-30A as a custom Lamassu-Fam profile."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| Lamassu-Fam__LmuA_DS-30B                         |                                                  | Lamassu-Fam            | Custom                  | 60     |",
        "notes": "The pinned DefenseFinder HMM inventory records Lamassu-Fam__LmuA_DS-30B as a custom Lamassu-Fam profile."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| Lamassu-Fam__LmuB_DS-30D                         |                                                  | Lamassu-Fam            | Custom                  | 150    |",
        "notes": "The pinned DefenseFinder HMM inventory records Lamassu-Fam__LmuB_DS-30D as a custom Lamassu-Fam profile."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| Lamassu-Fam__LmuC_DS-30C                         |                                                  | Lamassu-Fam            | Custom                  | 20     |",
        "notes": "The pinned DefenseFinder HMM inventory records Lamassu-Fam__LmuC_DS-30C as a custom Lamassu-Fam profile."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "ds_30_locus_reduces_phage_plaquing",
        "title": "DS-30 locus reduces bacteriophage plaquing",
        "description": "Conservative system-level sketch linking the four-gene DS-30 locus to reduced bacteriophage plaquing without resolving DS-30 component functions or molecular output.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures DS-30 as the validated ABC3 transcriptional unit with four product accessions, ABC-3C, SMC-family, and FtsL HHpred-domain rows, and four Lamassu-Fam custom HMM-profile rows. It does not assert native host breadth, exact profile-to-protein correspondence, DS-30/Lamassu-Fam component activity, Lamassu subtype chemistry, LmuC requirement, complete phage breadth, or DS-30-specific DefenseFinder rule-level detection criteria.",
        "nodes": [
          {
            "node_id": "ds_30_locus",
            "label": "DS-30 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A four-gene DefensePredictor-discovered system 30 locus cataloged as ABC3 and represented in the pinned DefenseFinder HMM inventory by four Lamassu-Fam DS-30 custom profiles."
          },
          {
            "node_id": "reduced_phage_plaquing",
            "label": "reduced bacteriophage plaquing",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced bacteriophage plaquing in cells carrying cloned ABC3."
          },
          {
            "node_id": "ds_30_system_trait",
            "label": "DS-30 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000470",
            "description": "Possession of a genome-encoded DS-30 Lamassu-family phage-defense system."
          },
          {
            "node_id": "lamassu_system",
            "label": "Lamassu system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000232",
            "description": "Possession of a genome-encoded Lamassu phage-defense system."
          }
        ],
        "edges": [
          {
            "subject": "ds_30_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "reduced_phage_plaquing",
            "description": "The DS-30/ABC3 locus contributes to reduced bacteriophage plaquing in heterologous E. coli MG1655 plasmid-expression assays.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
                "notes": "DeWeirdt et al. describe the plasmid-based phage challenge used to validate predicted transcriptional units."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
                "snippet": "ABC3\tNZ_QOYR01000032.1\tGCF_003333645.1\t+\tTrue\tFalse\tTrue\tTrue\tDefensePredictor hits\t1906\t4621\thypothetical protein, hypothetical protein, hypothetical protein, DUF2326 domain-containing protein\tWP_001553315.1, WP_000534626.1, WP_000628292.1, WP_087889773.1\t8.95063706554687\t6.906754778648663\tTrue\tTrue\tPredicted novel defense gene\tDS-30",
                "notes": "The final Science supplementary Table S6 maps working_id ABC3 to DS_name DS-30, marks the cloned transcriptional unit as defensive, and records four product accessions in NZ_QOYR01000032.1 positions 1906-4621."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
                "snippet": "SECphi27\t5.1\tpLAND\t24-05-31_EV_CRDO_BRNT_ABC3.png\t100000000\tABC3\t24-05-31\t24-05-31_EV_CRDO_BRNT_ABC3.png\t5\t1\tY\t100000\t3\t\tTrue\t\tM9\t30",
                "notes": "The final Science supplementary Table S7 Systems sheet reports an ABC3 assay row with a SECphi27 phage readout, a smaller-plaque-size call, and a -log(EOP) value of 3."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
                "snippet": "ABC3\tDS-30\tTrue",
                "notes": "The final Science supplementary Table S8 maps ABC3 to replicated display name DS-30."
              }
            ]
          },
          {
            "subject": "reduced_phage_plaquing",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "ds_30_system_trait",
            "description": "DS-30-mediated phage plaquing reduction realizes the DS-30 system trait.",
            "evidence": [
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
                "snippet": "ABC3\tNZ_QOYR01000032.1\tGCF_003333645.1\t+\tTrue\tFalse\tTrue\tTrue\tDefensePredictor hits\t1906\t4621\thypothetical protein, hypothetical protein, hypothetical protein, DUF2326 domain-containing protein\tWP_001553315.1, WP_000534626.1, WP_000628292.1, WP_087889773.1\t8.95063706554687\t6.906754778648663\tTrue\tTrue\tPredicted novel defense gene\tDS-30",
                "notes": "The final Science supplementary Table S6 maps working_id ABC3 to DS_name DS-30, marks the cloned transcriptional unit as defensive, and records four product accessions in NZ_QOYR01000032.1 positions 1906-4621."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
                "snippet": "SECphi27\t5.1\tpLAND\t24-05-31_EV_CRDO_BRNT_ABC3.png\t100000000\tABC3\t24-05-31\t24-05-31_EV_CRDO_BRNT_ABC3.png\t5\t1\tY\t100000\t3\t\tTrue\t\tM9\t30",
                "notes": "The final Science supplementary Table S7 Systems sheet reports an ABC3 assay row with a SECphi27 phage readout, a smaller-plaque-size call, and a -log(EOP) value of 3."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
                "snippet": "ABC3\tDS-30\tTrue",
                "notes": "The final Science supplementary Table S8 maps ABC3 to replicated display name DS-30."
              },
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
                "notes": "The DS nomenclature is used for DefensePredictor discovered systems."
              }
            ]
          },
          {
            "subject": "ds_30_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "lamassu_system",
            "description": "DS-30 system possession is represented in DefenseFinder by DS-30 custom profiles under Lamassu-Fam.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| Lamassu-Fam__Lmu_DS-30A                          |                                                  | Lamassu-Fam            | Custom                  | 50     |",
                "notes": "The pinned DefenseFinder HMM inventory records Lamassu-Fam__Lmu_DS-30A as a custom Lamassu-Fam profile."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| Lamassu-Fam__LmuA_DS-30B                         |                                                  | Lamassu-Fam            | Custom                  | 60     |",
                "notes": "The pinned DefenseFinder HMM inventory records Lamassu-Fam__LmuA_DS-30B as a custom Lamassu-Fam profile."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| Lamassu-Fam__LmuB_DS-30D                         |                                                  | Lamassu-Fam            | Custom                  | 150    |",
                "notes": "The pinned DefenseFinder HMM inventory records Lamassu-Fam__LmuB_DS-30D as a custom Lamassu-Fam profile."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| Lamassu-Fam__LmuC_DS-30C                         |                                                  | Lamassu-Fam            | Custom                  | 20     |",
                "notes": "The pinned DefenseFinder HMM inventory records Lamassu-Fam__LmuC_DS-30C as a custom Lamassu-Fam profile."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "ds-30-lamassu-family-model-gap",
        "prompt": "Resolve DS-30 native host breadth, exact profile-to-protein correspondence, DS-30/Lamassu-Fam component activities, Lamassu subtype and effector chemistry, LmuC requirement, complete phage breadth, and DS-30-specific DefenseFinder rule-level criteria before minting narrower DS-30 mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "DeWeirdt et al. support DS-30 as the defensive ABC3 transcriptional unit and final Science Tables S6/S7/S8 map it to four product accessions, a SECphi27 phage readout, four HHpred-domain rows, and display name DS-30. The pinned DefenseFinder HMM inventory records four Lamassu-Fam DS-30 custom profile rows. The pinned DefenseFinder rules table only lists generic Lamassu-Fam effector-subtype rows, and the first-pass record does not resolve native host breadth, complete phage breadth, direct profile-to-protein correspondence, LmuC requirement, molecular output, subtype-specific Lamassu chemistry, or endogenous DS-30 activity.",
        "evidence": [
          {
            "reference": "DOI:10.1126/science.adv7924",
            "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
            "notes": "DeWeirdt et al. name validated TUs as DSs."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
            "snippet": "ABC3\tNZ_QOYR01000032.1\tGCF_003333645.1\t+\tTrue\tFalse\tTrue\tTrue\tDefensePredictor hits\t1906\t4621\thypothetical protein, hypothetical protein, hypothetical protein, DUF2326 domain-containing protein\tWP_001553315.1, WP_000534626.1, WP_000628292.1, WP_087889773.1\t8.95063706554687\t6.906754778648663\tTrue\tTrue\tPredicted novel defense gene\tDS-30",
            "notes": "The final Science supplementary Table S6 maps working_id ABC3 to DS_name DS-30, marks the cloned transcriptional unit as defensive, and records four product accessions in NZ_QOYR01000032.1 positions 1906-4621."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
            "snippet": "SECphi27\t5.1\tpLAND\t24-05-31_EV_CRDO_BRNT_ABC3.png\t100000000\tABC3\t24-05-31\t24-05-31_EV_CRDO_BRNT_ABC3.png\t5\t1\tY\t100000\t3\t\tTrue\t\tM9\t30",
            "notes": "The final Science supplementary Table S7 Systems sheet reports an ABC3 assay row with a SECphi27 phage readout, a smaller-plaque-size call, and a -log(EOP) value of 3."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
            "snippet": "ABC3\tDS-30\tTrue",
            "notes": "The final Science supplementary Table S8 maps ABC3 to replicated display name DS-30."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
            "snippet": "ABC3\t2.0\t182.0\tWP_000534626.1\tABC-3C C-term\tPF20275.3\tCTD10 ; C-terminal domain 10 of the ABC-three component (ABC-3C) systems\thhpred_7102862.hhr\t26.0\t176.0\t1.0\t2024-07-30 00:00:00",
            "notes": "The final Science supplementary Table S8 reports a high-probability CTD10 HHpred hit for ABC3 protein 2, WP_000534626.1."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
            "snippet": "ABC3\t3.0\t77.0\tWP_000628292.1\tABC-3C Mid\tPF20293.3\tMC6 ; ABC-three component (ABC-3C) system Middle Component 6\thhpred_3406401.hhr\t1.0\t75.0\t1.0\t2024-07-30 00:00:00",
            "notes": "The final Science supplementary Table S8 reports a high-probability MC6 HHpred hit for ABC3 protein 3, WP_000628292.1."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
            "snippet": "ABC3\t4.0\t565.0\tWP_087889773.1\tABC ATPase\t5XEI_A\tChromosome partition protein Smc; Condensin, Smc, head domain, ABC-ATPase,\thhpred_6417130.hhr\t1.0\t540.0\t1.0\t2024-07-30 00:00:00",
            "notes": "The final Science supplementary Table S8 reports a high-probability ABC ATPase HHpred hit for ABC3 protein 4, WP_087889773.1."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
            "snippet": "ABC3\t1.0\t86.0\tWP_001553315.1\tFtsL\t8HHF_L\tCell division protein FtsL; Bacterial cell division, divisome, FtsB, FtsL, FtsQ, FtsBLQ, membrane protein complex, heterotrimer, MEMBRANE PROTEIN\thhpred_2515914.hhr\t2.0\t53.0\t0.942\t2024-07-30 00:00:00",
            "notes": "The final Science supplementary Table S8 reports an FtsL HHpred hit for ABC3 protein 1, WP_001553315.1."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| Lamassu-Fam__Lmu_DS-30A                          |                                                  | Lamassu-Fam            | Custom                  | 50     |",
            "notes": "The pinned DefenseFinder HMM inventory records Lamassu-Fam__Lmu_DS-30A as a custom Lamassu-Fam profile."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| Lamassu-Fam__LmuA_DS-30B                         |                                                  | Lamassu-Fam            | Custom                  | 60     |",
            "notes": "The pinned DefenseFinder HMM inventory records Lamassu-Fam__LmuA_DS-30B as a custom Lamassu-Fam profile."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| Lamassu-Fam__LmuB_DS-30D                         |                                                  | Lamassu-Fam            | Custom                  | 150    |",
            "notes": "The pinned DefenseFinder HMM inventory records Lamassu-Fam__LmuB_DS-30D as a custom Lamassu-Fam profile."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| Lamassu-Fam__LmuC_DS-30C                         |                                                  | Lamassu-Fam            | Custom                  | 20     |",
            "notes": "The pinned DefenseFinder HMM inventory records Lamassu-Fam__LmuC_DS-30C as a custom Lamassu-Fam profile."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "The pinned DefenseFinder rules table contains generic Lamassu-Fam subtype rows, but no DS-30-specific model row or DS-30 custom-profile criteria."
          }
        ],
        "attaches_to": [
          "causal_graphs#ds_30_locus_reduces_phage_plaquing"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-29"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-29T17:57:26Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted DS-30 system as a DOI-backed GENOMICS TraitRecord under Lamassu system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; kept the graph at ABC3 transcriptional-unit level because native host breadth, exact DS-30 profile-to-component mapping, Lamassu subtype chemistry, LmuC requirement, complete phage breadth, and DefenseFinder rule-level criteria remain unresolved, and proposals/metpo_traitmech_v347 reserves the replacement placeholder.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-29T17:57:27Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed DS-30 system canonical_examples and left them empty because DeWeirdt et al. directly support cloned ABC3 assays in E. coli MG1655 and Lamassu-Fam DS-30 profile rows, but not a direct named native microbial isolate exemplar with experimentally verified endogenous DS-30 activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000454",
    "label": "DS-31 system",
    "definition": "A phage defense system in which an organism possesses the single-gene DefensePredictor-discovered system 31 locus cataloged as working transcriptional unit RED7 and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.",
    "definition_source": "DOI:10.1126/science.adv7924",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "DS-31",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1126/science.adv7924"
      },
      {
        "synonym_text": "RED7",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx"
      },
      {
        "synonym_text": "DS-31__DS-31",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1126/science.adv7924",
        "snippet": "To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
        "notes": "DeWeirdt et al. experimentally validated 42 predicted transcriptional units as phage-defense systems in E. coli."
      },
      {
        "reference": "DOI:10.1126/science.adv7924",
        "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
        "notes": "DeWeirdt et al. name validated transcriptional units as DefensePredictor discovered systems."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
        "snippet": "RED7\tNZ_QOWW01000064.1\tGCF_003334245.1\t-\tTrue\tFalse\tFalse\tTrue\tDefensePredictor hits\t6615\t7667\thypothetical protein\tWP_001703029.1\t8.059866321466373\t1.02528101558256\tTrue\tTrue\tPredicted novel defense gene\tDS-31",
        "notes": "The final Science supplementary Table S6 maps working_id RED7 to DS_name DS-31, marks the cloned transcriptional unit as defensive, and records NZ_QOWW01000064.1 positions 6615-7667 with product accession WP_001703029.1."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
        "snippet": "Bas19\t6.1\tpLAND\t24-07-17_MVB1_VPUS_VAME_EV.png\t2200000\tRED7\t24-07-25\t24-07-25_PDP1_RED1_PDP4_RED7.png\t0\t1\t\t1\t6.342422680822207\t\t\tTrue\tLB\t37",
        "notes": "The final Science supplementary Table S7 reports a RED7 assay row with a Bas19 phage readout and a -log(EOP) value of 6.342."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
        "snippet": "RED7\tDS-31\tTrue",
        "notes": "The final Science supplementary Table S8 maps RED7 to replicated display name DS-31."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
        "snippet": "RED7\t1.0\t350.0\tWP_001703029.1\tPDDEXK\tPF03838.19\tRecU ; Recombination protein U\thhpred_7098417.hhr\t56.0\t182.0\t0.99\t2024-07-28 00:00:00\t201-203\t187.0",
        "notes": "The final Science supplementary Table S8 reports a high-probability PDDEXK HHpred hit for WP_001703029.1 in RED7."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| DS-31 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
        "notes": "The pinned DefenseFinder article registry maps the DS-31 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| DS-31__DS-31                                     |                                                  | DS-31                  | Custom                  | 170    |",
        "notes": "The pinned DefenseFinder HMM inventory records DS-31__DS-31 as a custom DS-31 profile."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "ds_31_locus_reduces_phage_plaquing",
        "title": "DS-31 locus reduces bacteriophage plaquing",
        "description": "Conservative system-level sketch linking the single-gene DS-31 locus to reduced bacteriophage plaquing without resolving DS-31 component function or molecular output.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures DS-31 as the validated RED7 transcriptional unit with one product accession, one high-probability PDDEXK HHpred-domain row, and one DefenseFinder DS-31 profile row. It does not assert native host breadth, exact profile-to-protein correspondence, DS-31 molecular activity, trigger, substrate, complete phage breadth, PDDEXK HHpred-domain interpretation, or DefenseFinder rule-level detection criteria.",
        "nodes": [
          {
            "node_id": "ds_31_locus",
            "label": "DS-31 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A single-gene DefensePredictor-discovered system 31 locus represented in the pinned DefenseFinder HMM inventory by one DS-31 custom profile."
          },
          {
            "node_id": "reduced_phage_plaquing",
            "label": "reduced bacteriophage plaquing",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced bacteriophage plaquing in cells carrying cloned RED7."
          },
          {
            "node_id": "ds_31_system_trait",
            "label": "DS-31 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000454",
            "description": "Possession of a genome-encoded DS-31 phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "ds_31_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "reduced_phage_plaquing",
            "description": "The DS-31/RED7 locus contributes to reduced bacteriophage plaquing in heterologous E. coli MG1655 plasmid-expression assays.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
                "notes": "DeWeirdt et al. describe the plasmid-based phage challenge used to validate predicted transcriptional units."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
                "snippet": "RED7\tNZ_QOWW01000064.1\tGCF_003334245.1\t-\tTrue\tFalse\tFalse\tTrue\tDefensePredictor hits\t6615\t7667\thypothetical protein\tWP_001703029.1\t8.059866321466373\t1.02528101558256\tTrue\tTrue\tPredicted novel defense gene\tDS-31",
                "notes": "The final Science supplementary Table S6 maps working_id RED7 to DS_name DS-31, marks the cloned transcriptional unit as defensive, and records NZ_QOWW01000064.1 positions 6615-7667 with product accession WP_001703029.1."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
                "snippet": "Bas19\t6.1\tpLAND\t24-07-17_MVB1_VPUS_VAME_EV.png\t2200000\tRED7\t24-07-25\t24-07-25_PDP1_RED1_PDP4_RED7.png\t0\t1\t\t1\t6.342422680822207\t\t\tTrue\tLB\t37",
                "notes": "The final Science supplementary Table S7 reports a RED7 assay row with a Bas19 phage readout and a -log(EOP) value of 6.342."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
                "snippet": "RED7\tDS-31\tTrue",
                "notes": "The final Science supplementary Table S8 maps RED7 to replicated display name DS-31."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
                "snippet": "RED7\t1.0\t350.0\tWP_001703029.1\tPDDEXK\tPF03838.19\tRecU ; Recombination protein U\thhpred_7098417.hhr\t56.0\t182.0\t0.99\t2024-07-28 00:00:00\t201-203\t187.0",
                "notes": "The final Science supplementary Table S8 reports a high-probability PDDEXK HHpred hit for WP_001703029.1 in RED7."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| DS-31__DS-31                                     |                                                  | DS-31                  | Custom                  | 170    |",
                "notes": "The pinned DefenseFinder HMM inventory records DS-31__DS-31 as a custom DS-31 profile."
              }
            ]
          },
          {
            "subject": "reduced_phage_plaquing",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "ds_31_system_trait",
            "description": "DS-31-mediated phage plaquing reduction realizes the DS-31 system trait.",
            "evidence": [
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
                "snippet": "RED7\tNZ_QOWW01000064.1\tGCF_003334245.1\t-\tTrue\tFalse\tFalse\tTrue\tDefensePredictor hits\t6615\t7667\thypothetical protein\tWP_001703029.1\t8.059866321466373\t1.02528101558256\tTrue\tTrue\tPredicted novel defense gene\tDS-31",
                "notes": "The final Science supplementary Table S6 maps working_id RED7 to DS_name DS-31, marks the cloned transcriptional unit as defensive, and records NZ_QOWW01000064.1 positions 6615-7667 with product accession WP_001703029.1."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
                "snippet": "Bas19\t6.1\tpLAND\t24-07-17_MVB1_VPUS_VAME_EV.png\t2200000\tRED7\t24-07-25\t24-07-25_PDP1_RED1_PDP4_RED7.png\t0\t1\t\t1\t6.342422680822207\t\t\tTrue\tLB\t37",
                "notes": "The final Science supplementary Table S7 reports a RED7 assay row with a Bas19 phage readout and a -log(EOP) value of 6.342."
              },
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
                "notes": "The DS nomenclature is used for DefensePredictor discovered systems."
              }
            ]
          },
          {
            "subject": "ds_31_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "DS-31 system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
                "notes": "DeWeirdt et al. name validated TUs as DefensePredictor discovered systems."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| DS-31 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
                "notes": "The pinned DefenseFinder article registry maps the DS-31 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "ds-31-defensefinder-model-gap",
        "prompt": "Resolve DS-31 native host breadth, exact single-component activity, profile-to-protein mapping, PDDEXK HHpred-domain interpretation, complete phage breadth, molecular output, and rule-level DefenseFinder criteria before minting narrower DS-31 mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "DeWeirdt et al. support DS-31 as the defensive RED7 transcriptional unit and final Science Tables S6/S7/S8 map it to product accession WP_001703029.1, a Bas19 phage readout, display name DS-31, and a PDDEXK HHpred row. The pinned DefenseFinder HMM inventory records one DS-31 custom profile row. The pinned rules table has no DS-31 row, and the first-pass record does not resolve native host breadth, complete phage breadth, direct profile-to-protein correspondence, PDDEXK activity, molecular output, or endogenous DS-31 activity.",
        "evidence": [
          {
            "reference": "DOI:10.1126/science.adv7924",
            "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
            "notes": "DeWeirdt et al. name validated TUs as DSs."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
            "snippet": "RED7\tNZ_QOWW01000064.1\tGCF_003334245.1\t-\tTrue\tFalse\tFalse\tTrue\tDefensePredictor hits\t6615\t7667\thypothetical protein\tWP_001703029.1\t8.059866321466373\t1.02528101558256\tTrue\tTrue\tPredicted novel defense gene\tDS-31",
            "notes": "The final Science supplementary Table S6 maps working_id RED7 to DS_name DS-31, marks the cloned transcriptional unit as defensive, and records NZ_QOWW01000064.1 positions 6615-7667 with product accession WP_001703029.1."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
            "snippet": "Bas19\t6.1\tpLAND\t24-07-17_MVB1_VPUS_VAME_EV.png\t2200000\tRED7\t24-07-25\t24-07-25_PDP1_RED1_PDP4_RED7.png\t0\t1\t\t1\t6.342422680822207\t\t\tTrue\tLB\t37",
            "notes": "The final Science supplementary Table S7 reports a RED7 assay row with a Bas19 phage readout and a -log(EOP) value of 6.342."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
            "snippet": "RED7\tDS-31\tTrue",
            "notes": "The final Science supplementary Table S8 maps RED7 to replicated display name DS-31."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
            "snippet": "RED7\t1.0\t350.0\tWP_001703029.1\tPDDEXK\tPF03838.19\tRecU ; Recombination protein U\thhpred_7098417.hhr\t56.0\t182.0\t0.99\t2024-07-28 00:00:00\t201-203\t187.0",
            "notes": "The final Science supplementary Table S8 reports a high-probability PDDEXK HHpred hit for WP_001703029.1 in RED7."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
            "snippet": "| DS-31 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
            "notes": "The pinned DefenseFinder article registry maps the DS-31 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| DS-31__DS-31                                     |                                                  | DS-31                  | Custom                  | 170    |",
            "notes": "The pinned DefenseFinder HMM inventory records DS-31__DS-31 as a custom DS-31 profile."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "The pinned DefenseFinder rules table does not list DS-31, leaving rule-level detection criteria unresolved."
          }
        ],
        "attaches_to": [
          "causal_graphs#ds_31_locus_reduces_phage_plaquing"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-29"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-29T06:35:29Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted DS-31 system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; kept the graph at RED7 transcriptional-unit level because PDDEXK activity and rule rows remain unresolved, and proposals/metpo_traitmech_v331 reserves the replacement placeholder.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-29T06:35:30Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed DS-31 system canonical_examples and left them empty because DeWeirdt et al. directly support cloned RED7 assays in E. coli MG1655 and a DefenseFinder DS-31 model, but not a direct named native microbial isolate exemplar with experimentally verified endogenous DS-31 activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000455",
    "label": "DS-32 system",
    "definition": "A phage defense system in which an organism possesses the two-gene DefensePredictor-discovered system 32 locus cataloged as working transcriptional unit NADR and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.",
    "definition_source": "DOI:10.1126/science.adv7924",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "DS-32",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1126/science.adv7924"
      },
      {
        "synonym_text": "NADR",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx"
      },
      {
        "synonym_text": "DS-32__DS-32A",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "DS-32__DS-32B",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1126/science.adv7924",
        "snippet": "To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
        "notes": "DeWeirdt et al. experimentally validated 42 predicted transcriptional units as phage-defense systems in E. coli."
      },
      {
        "reference": "DOI:10.1126/science.adv7924",
        "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
        "notes": "DeWeirdt et al. name validated transcriptional units as DefensePredictor discovered systems."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
        "snippet": "NADR\tNZ_QOXQ01000027.1\tGCF_003333945.1\t+\tTrue\tFalse\tFalse\tTrue\tDefensePredictor hits\t48629\t50261\thypothetical protein, NADAR family protein\tWP_000097610.1, WP_032260665.1\t9.822610074734904\t6.906754778648663\tTrue\tTrue\tPredicted novel defense gene\tDS-32",
        "notes": "The final Science supplementary Table S6 maps working_id NADR to DS_name DS-32, marks the cloned transcriptional unit as defensive, and records NZ_QOXQ01000027.1 positions 48629-50261 with product accessions WP_000097610.1 and WP_032260665.1."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
        "snippet": "Bas26\t1.2\tpLAND\t24-03-08_EV_HHHD_PIN2_CRDO.png\t500000000\tNADR\t24-03-12\t24-03-12_SVIR_PIN8_NTTI_NADR.png\t4\t10\tY\t100000\t3.6989700043360187\tTrue\t\t\tLB\t37",
        "notes": "The final Science supplementary Table S7 reports a NADR assay row with a Bas26 phage readout and a -log(EOP) value of 3.699."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
        "snippet": "NADR\tDS-32\tTrue",
        "notes": "The final Science supplementary Table S8 maps NADR to replicated display name DS-32."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
        "snippet": "NADR\t1.0\t343.0\tWP_000097610.1\tRecR\t8K3F_A\tRecombination protein RecR; Recombination mediator protein\thhpred_1157231.hhr\t1.0\t65.0\t0.6827\t2024-04-16 00:00:00",
        "notes": "The final Science supplementary Table S8 reports a lower-probability RecR HHpred hit for WP_000097610.1 in NADR."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
        "snippet": "NADR\t1.0\t343.0\tWP_000097610.1\tPRTase\t3DMP_D\tUracil phosphoribosyltransferase\thhpred_1157231.hhr\t129.0\t196.0\t0.942\t2024-04-16 00:00:00",
        "notes": "The final Science supplementary Table S8 reports a high-probability PRTase HHpred hit for WP_000097610.1 in NADR."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
        "snippet": "NADR\t2.0\t203.0\tWP_032260665.1\tNADAR\tPF08719.15\tNADAR ; NADAR domain\thhpred_3126143.hhr\t13.0\t159.0\t0.9992\t2024-04-16 00:00:00",
        "notes": "The final Science supplementary Table S8 reports a high-probability NADAR HHpred hit for WP_032260665.1 in NADR."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| DS-32 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
        "notes": "The pinned DefenseFinder article registry maps the DS-32 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| DS-32__DS-32A                                    |                                                  | DS-32                  | Custom                  | 150    |",
        "notes": "The pinned DefenseFinder HMM inventory records DS-32__DS-32A as a custom DS-32 profile."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| DS-32__DS-32B                                    |                                                  | DS-32                  | Custom                  | 210    |",
        "notes": "The pinned DefenseFinder HMM inventory records DS-32__DS-32B as a custom DS-32 profile."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "ds_32_locus_reduces_phage_plaquing",
        "title": "DS-32 locus reduces bacteriophage plaquing",
        "description": "Conservative system-level sketch linking the two-gene DS-32 locus to reduced bacteriophage plaquing without resolving DS-32 component function or molecular output.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures DS-32 as the validated NADR transcriptional unit with two product accessions, lower-probability RecR and high-probability PRTase HHpred rows for WP_000097610.1, a high-probability NADAR HHpred row for WP_032260665.1, and two DefenseFinder DS-32 profile rows. It does not assert native host breadth, exact profile-to-protein correspondence, DS-32 molecular activity, trigger, substrate, complete phage breadth, RecR, PRTase, or NADAR HHpred-domain interpretation, or DefenseFinder rule-level detection criteria.",
        "nodes": [
          {
            "node_id": "ds_32_locus",
            "label": "DS-32 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A two-gene DefensePredictor-discovered system 32 locus represented in the pinned DefenseFinder HMM inventory by two DS-32 custom profiles."
          },
          {
            "node_id": "reduced_phage_plaquing",
            "label": "reduced bacteriophage plaquing",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced bacteriophage plaquing in cells carrying cloned NADR."
          },
          {
            "node_id": "ds_32_system_trait",
            "label": "DS-32 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000455",
            "description": "Possession of a genome-encoded DS-32 phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "ds_32_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "reduced_phage_plaquing",
            "description": "The DS-32/NADR locus contributes to reduced bacteriophage plaquing in heterologous E. coli MG1655 plasmid-expression assays.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
                "notes": "DeWeirdt et al. describe the plasmid-based phage challenge used to validate predicted transcriptional units."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
                "snippet": "NADR\tNZ_QOXQ01000027.1\tGCF_003333945.1\t+\tTrue\tFalse\tFalse\tTrue\tDefensePredictor hits\t48629\t50261\thypothetical protein, NADAR family protein\tWP_000097610.1, WP_032260665.1\t9.822610074734904\t6.906754778648663\tTrue\tTrue\tPredicted novel defense gene\tDS-32",
                "notes": "The final Science supplementary Table S6 maps working_id NADR to DS_name DS-32, marks the cloned transcriptional unit as defensive, and records NZ_QOXQ01000027.1 positions 48629-50261 with product accessions WP_000097610.1 and WP_032260665.1."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
                "snippet": "Bas26\t1.2\tpLAND\t24-03-08_EV_HHHD_PIN2_CRDO.png\t500000000\tNADR\t24-03-12\t24-03-12_SVIR_PIN8_NTTI_NADR.png\t4\t10\tY\t100000\t3.6989700043360187\tTrue\t\t\tLB\t37",
                "notes": "The final Science supplementary Table S7 reports a NADR assay row with a Bas26 phage readout and a -log(EOP) value of 3.699."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
                "snippet": "NADR\tDS-32\tTrue",
                "notes": "The final Science supplementary Table S8 maps NADR to replicated display name DS-32."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
                "snippet": "NADR\t1.0\t343.0\tWP_000097610.1\tRecR\t8K3F_A\tRecombination protein RecR; Recombination mediator protein\thhpred_1157231.hhr\t1.0\t65.0\t0.6827\t2024-04-16 00:00:00",
                "notes": "The final Science supplementary Table S8 reports a lower-probability RecR HHpred hit for WP_000097610.1 in NADR."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
                "snippet": "NADR\t1.0\t343.0\tWP_000097610.1\tPRTase\t3DMP_D\tUracil phosphoribosyltransferase\thhpred_1157231.hhr\t129.0\t196.0\t0.942\t2024-04-16 00:00:00",
                "notes": "The final Science supplementary Table S8 reports a high-probability PRTase HHpred hit for WP_000097610.1 in NADR."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
                "snippet": "NADR\t2.0\t203.0\tWP_032260665.1\tNADAR\tPF08719.15\tNADAR ; NADAR domain\thhpred_3126143.hhr\t13.0\t159.0\t0.9992\t2024-04-16 00:00:00",
                "notes": "The final Science supplementary Table S8 reports a high-probability NADAR HHpred hit for WP_032260665.1 in NADR."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| DS-32__DS-32A                                    |                                                  | DS-32                  | Custom                  | 150    |",
                "notes": "The pinned DefenseFinder HMM inventory records DS-32__DS-32A as a custom DS-32 profile."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| DS-32__DS-32B                                    |                                                  | DS-32                  | Custom                  | 210    |",
                "notes": "The pinned DefenseFinder HMM inventory records DS-32__DS-32B as a custom DS-32 profile."
              }
            ]
          },
          {
            "subject": "reduced_phage_plaquing",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "ds_32_system_trait",
            "description": "DS-32-mediated phage plaquing reduction realizes the DS-32 system trait.",
            "evidence": [
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
                "snippet": "NADR\tNZ_QOXQ01000027.1\tGCF_003333945.1\t+\tTrue\tFalse\tFalse\tTrue\tDefensePredictor hits\t48629\t50261\thypothetical protein, NADAR family protein\tWP_000097610.1, WP_032260665.1\t9.822610074734904\t6.906754778648663\tTrue\tTrue\tPredicted novel defense gene\tDS-32",
                "notes": "The final Science supplementary Table S6 maps working_id NADR to DS_name DS-32, marks the cloned transcriptional unit as defensive, and records NZ_QOXQ01000027.1 positions 48629-50261 with product accessions WP_000097610.1 and WP_032260665.1."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
                "snippet": "Bas26\t1.2\tpLAND\t24-03-08_EV_HHHD_PIN2_CRDO.png\t500000000\tNADR\t24-03-12\t24-03-12_SVIR_PIN8_NTTI_NADR.png\t4\t10\tY\t100000\t3.6989700043360187\tTrue\t\t\tLB\t37",
                "notes": "The final Science supplementary Table S7 reports a NADR assay row with a Bas26 phage readout and a -log(EOP) value of 3.699."
              },
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
                "notes": "The DS nomenclature is used for DefensePredictor discovered systems."
              }
            ]
          },
          {
            "subject": "ds_32_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "DS-32 system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
                "notes": "DeWeirdt et al. name validated TUs as DefensePredictor discovered systems."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| DS-32 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
                "notes": "The pinned DefenseFinder article registry maps the DS-32 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "ds-32-defensefinder-model-gap",
        "prompt": "Resolve DS-32 native host breadth, exact component activities, profile-to-protein mapping, RecR, PRTase, and NADAR HHpred-domain interpretation, complete phage breadth, molecular output, and rule-level DefenseFinder criteria before minting narrower DS-32 mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "DeWeirdt et al. support DS-32 as the defensive NADR transcriptional unit and final Science Tables S6/S7/S8 map it to two product accessions, a Bas26 phage readout, display name DS-32, and three HHpred rows. The pinned DefenseFinder HMM inventory records two DS-32 custom profile rows. The pinned rules table has no DS-32 row, and the first-pass record does not resolve native host breadth, complete phage breadth, direct profile-to-protein correspondence, component activities, molecular output, or endogenous DS-32 activity.",
        "evidence": [
          {
            "reference": "DOI:10.1126/science.adv7924",
            "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
            "notes": "DeWeirdt et al. name validated TUs as DSs."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
            "snippet": "NADR\tNZ_QOXQ01000027.1\tGCF_003333945.1\t+\tTrue\tFalse\tFalse\tTrue\tDefensePredictor hits\t48629\t50261\thypothetical protein, NADAR family protein\tWP_000097610.1, WP_032260665.1\t9.822610074734904\t6.906754778648663\tTrue\tTrue\tPredicted novel defense gene\tDS-32",
            "notes": "The final Science supplementary Table S6 maps working_id NADR to DS_name DS-32, marks the cloned transcriptional unit as defensive, and records NZ_QOXQ01000027.1 positions 48629-50261 with product accessions WP_000097610.1 and WP_032260665.1."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
            "snippet": "Bas26\t1.2\tpLAND\t24-03-08_EV_HHHD_PIN2_CRDO.png\t500000000\tNADR\t24-03-12\t24-03-12_SVIR_PIN8_NTTI_NADR.png\t4\t10\tY\t100000\t3.6989700043360187\tTrue\t\t\tLB\t37",
            "notes": "The final Science supplementary Table S7 reports a NADR assay row with a Bas26 phage readout and a -log(EOP) value of 3.699."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
            "snippet": "NADR\tDS-32\tTrue",
            "notes": "The final Science supplementary Table S8 maps NADR to replicated display name DS-32."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
            "snippet": "NADR\t1.0\t343.0\tWP_000097610.1\tRecR\t8K3F_A\tRecombination protein RecR; Recombination mediator protein\thhpred_1157231.hhr\t1.0\t65.0\t0.6827\t2024-04-16 00:00:00",
            "notes": "The final Science supplementary Table S8 reports a lower-probability RecR HHpred hit for WP_000097610.1 in NADR."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
            "snippet": "NADR\t1.0\t343.0\tWP_000097610.1\tPRTase\t3DMP_D\tUracil phosphoribosyltransferase\thhpred_1157231.hhr\t129.0\t196.0\t0.942\t2024-04-16 00:00:00",
            "notes": "The final Science supplementary Table S8 reports a high-probability PRTase HHpred hit for WP_000097610.1 in NADR."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
            "snippet": "NADR\t2.0\t203.0\tWP_032260665.1\tNADAR\tPF08719.15\tNADAR ; NADAR domain\thhpred_3126143.hhr\t13.0\t159.0\t0.9992\t2024-04-16 00:00:00",
            "notes": "The final Science supplementary Table S8 reports a high-probability NADAR HHpred hit for WP_032260665.1 in NADR."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
            "snippet": "| DS-32 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
            "notes": "The pinned DefenseFinder article registry maps the DS-32 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| DS-32__DS-32A                                    |                                                  | DS-32                  | Custom                  | 150    |",
            "notes": "The pinned DefenseFinder HMM inventory records DS-32__DS-32A as a custom DS-32 profile."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| DS-32__DS-32B                                    |                                                  | DS-32                  | Custom                  | 210    |",
            "notes": "The pinned DefenseFinder HMM inventory records DS-32__DS-32B as a custom DS-32 profile."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "The pinned DefenseFinder rules table does not list DS-32, leaving rule-level detection criteria unresolved."
          }
        ],
        "attaches_to": [
          "causal_graphs#ds_32_locus_reduces_phage_plaquing"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-29"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-29T07:25:23Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted DS-32 system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; kept the graph at NADR transcriptional-unit level because RecR, PRTase, NADAR activity and rule rows remain unresolved, and proposals/metpo_traitmech_v332 reserves the replacement placeholder.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-29T07:25:24Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed DS-32 system canonical_examples and left them empty because DeWeirdt et al. directly support cloned NADR assays in E. coli MG1655 and a DefenseFinder DS-32 model, but not a direct named native microbial isolate exemplar with experimentally verified endogenous DS-32 activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000456",
    "label": "DS-33 system",
    "definition": "A phage defense system in which an organism possesses the two-gene DefensePredictor-discovered system 33 locus cataloged as working transcriptional unit GNAT and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.",
    "definition_source": "DOI:10.1126/science.adv7924",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "DS-33",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1126/science.adv7924"
      },
      {
        "synonym_text": "GNAT",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx"
      },
      {
        "synonym_text": "DS-33__DS-33",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1126/science.adv7924",
        "snippet": "To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
        "notes": "DeWeirdt et al. experimentally validated 42 predicted transcriptional units as phage-defense systems in E. coli."
      },
      {
        "reference": "DOI:10.1126/science.adv7924",
        "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
        "notes": "DeWeirdt et al. name validated transcriptional units as DefensePredictor discovered systems."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
        "snippet": "GNAT\tNZ_QOWT01000046.1\tGCF_003334765.1\t+\tTrue\tFalse\tFalse\tTrue\tDefensePredictor hits\t6922\t8901\thypothetical protein, hypothetical protein\tWP_014639476.1, WP_000354965.1\t9.45173070144912\t3.204412762840645\tTrue\tTrue\tPredicted novel defense gene\tDS-33",
        "notes": "The final Science supplementary Table S6 maps working_id GNAT to DS_name DS-33, marks the cloned transcriptional unit as defensive, and records NZ_QOWT01000046.1 positions 6922-8901 with product accessions WP_014639476.1 and WP_000354965.1."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
        "snippet": "Bas26\t1.2\tpLAND\t24-03-08_EV_HHHD_PIN2_CRDO.png\t500000000\tGNAT\t24-03-09\t24-03-09_GNAT_NADR_D390_DRAT.png\t2\t100\tY\t10000\t4.698970004336019\tTrue\t\t\tLB\t37",
        "notes": "The final Science supplementary Table S7 reports a GNAT assay row with a Bas26 phage readout and a -log(EOP) value of 4.699."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
        "snippet": "GNAT\tDS-33\tTrue",
        "notes": "The final Science supplementary Table S8 maps GNAT to replicated display name DS-33."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
        "snippet": "GNAT\t2.0\t333.0\tWP_000354965.1\tCsa3\t6W11_B\tCRISPR locus-related putative DNA-binding protein Csa3; CARF, CRISPR-Cas, cyclic oligoadenylate, cA4\thhpred_9793887.hhr\t25.0\t110.0\t0.5601\t2024-04-16 00:00:00",
        "notes": "The final Science supplementary Table S8 reports a lower-probability Csa3 HHpred hit for WP_000354965.1 in GNAT."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
        "snippet": "GNAT\t1.0\t320.0\tWP_014639476.1\tHEPN\tPF18737.5\tHEPN_MAE_28990 ; MAE_28990/MAE_18760-like HEPN\thhpred_9884029.hhr\t144.0\t306.0\t0.9842\t2024-04-15 00:00:00",
        "notes": "The final Science supplementary Table S8 reports a high-probability HEPN HHpred hit for WP_014639476.1 in GNAT."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| DS-33 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
        "notes": "The pinned DefenseFinder article registry maps the DS-33 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| DS-33__DS-33                                     |                                                  | DS-33                  | Custom                  | 220    |",
        "notes": "The pinned DefenseFinder HMM inventory records DS-33__DS-33 as a custom DS-33 profile."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "ds_33_locus_reduces_phage_plaquing",
        "title": "DS-33 locus reduces bacteriophage plaquing",
        "description": "Conservative system-level sketch linking the two-gene DS-33 locus to reduced bacteriophage plaquing without resolving DS-33 component function or molecular output.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures DS-33 as the validated GNAT transcriptional unit with two product accessions, a lower-probability Csa3 HHpred row for WP_000354965.1, a high-probability HEPN HHpred row for WP_014639476.1, and one DefenseFinder DS-33 profile row. It does not assert native host breadth, exact profile-to-protein correspondence, DS-33 molecular activity, trigger, substrate, complete phage breadth, Csa3 or HEPN HHpred-domain interpretation, or DefenseFinder rule-level detection criteria.",
        "nodes": [
          {
            "node_id": "ds_33_locus",
            "label": "DS-33 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A two-gene DefensePredictor-discovered system 33 locus represented in the pinned DefenseFinder HMM inventory by one DS-33 custom profile."
          },
          {
            "node_id": "reduced_phage_plaquing",
            "label": "reduced bacteriophage plaquing",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced bacteriophage plaquing in cells carrying cloned GNAT."
          },
          {
            "node_id": "ds_33_system_trait",
            "label": "DS-33 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000456",
            "description": "Possession of a genome-encoded DS-33 phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "ds_33_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "reduced_phage_plaquing",
            "description": "The DS-33/GNAT locus contributes to reduced bacteriophage plaquing in heterologous E. coli MG1655 plasmid-expression assays.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
                "notes": "DeWeirdt et al. describe the plasmid-based phage challenge used to validate predicted transcriptional units."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
                "snippet": "GNAT\tNZ_QOWT01000046.1\tGCF_003334765.1\t+\tTrue\tFalse\tFalse\tTrue\tDefensePredictor hits\t6922\t8901\thypothetical protein, hypothetical protein\tWP_014639476.1, WP_000354965.1\t9.45173070144912\t3.204412762840645\tTrue\tTrue\tPredicted novel defense gene\tDS-33",
                "notes": "The final Science supplementary Table S6 maps working_id GNAT to DS_name DS-33, marks the cloned transcriptional unit as defensive, and records NZ_QOWT01000046.1 positions 6922-8901 with product accessions WP_014639476.1 and WP_000354965.1."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
                "snippet": "Bas26\t1.2\tpLAND\t24-03-08_EV_HHHD_PIN2_CRDO.png\t500000000\tGNAT\t24-03-09\t24-03-09_GNAT_NADR_D390_DRAT.png\t2\t100\tY\t10000\t4.698970004336019\tTrue\t\t\tLB\t37",
                "notes": "The final Science supplementary Table S7 reports a GNAT assay row with a Bas26 phage readout and a -log(EOP) value of 4.699."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
                "snippet": "GNAT\tDS-33\tTrue",
                "notes": "The final Science supplementary Table S8 maps GNAT to replicated display name DS-33."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
                "snippet": "GNAT\t2.0\t333.0\tWP_000354965.1\tCsa3\t6W11_B\tCRISPR locus-related putative DNA-binding protein Csa3; CARF, CRISPR-Cas, cyclic oligoadenylate, cA4\thhpred_9793887.hhr\t25.0\t110.0\t0.5601\t2024-04-16 00:00:00",
                "notes": "The final Science supplementary Table S8 reports a lower-probability Csa3 HHpred hit for WP_000354965.1 in GNAT."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
                "snippet": "GNAT\t1.0\t320.0\tWP_014639476.1\tHEPN\tPF18737.5\tHEPN_MAE_28990 ; MAE_28990/MAE_18760-like HEPN\thhpred_9884029.hhr\t144.0\t306.0\t0.9842\t2024-04-15 00:00:00",
                "notes": "The final Science supplementary Table S8 reports a high-probability HEPN HHpred hit for WP_014639476.1 in GNAT."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| DS-33__DS-33                                     |                                                  | DS-33                  | Custom                  | 220    |",
                "notes": "The pinned DefenseFinder HMM inventory records DS-33__DS-33 as a custom DS-33 profile."
              }
            ]
          },
          {
            "subject": "reduced_phage_plaquing",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "ds_33_system_trait",
            "description": "DS-33-mediated phage plaquing reduction realizes the DS-33 system trait.",
            "evidence": [
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
                "snippet": "GNAT\tNZ_QOWT01000046.1\tGCF_003334765.1\t+\tTrue\tFalse\tFalse\tTrue\tDefensePredictor hits\t6922\t8901\thypothetical protein, hypothetical protein\tWP_014639476.1, WP_000354965.1\t9.45173070144912\t3.204412762840645\tTrue\tTrue\tPredicted novel defense gene\tDS-33",
                "notes": "The final Science supplementary Table S6 maps working_id GNAT to DS_name DS-33, marks the cloned transcriptional unit as defensive, and records NZ_QOWT01000046.1 positions 6922-8901 with product accessions WP_014639476.1 and WP_000354965.1."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
                "snippet": "Bas26\t1.2\tpLAND\t24-03-08_EV_HHHD_PIN2_CRDO.png\t500000000\tGNAT\t24-03-09\t24-03-09_GNAT_NADR_D390_DRAT.png\t2\t100\tY\t10000\t4.698970004336019\tTrue\t\t\tLB\t37",
                "notes": "The final Science supplementary Table S7 reports a GNAT assay row with a Bas26 phage readout and a -log(EOP) value of 4.699."
              },
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
                "notes": "The DS nomenclature is used for DefensePredictor discovered systems."
              }
            ]
          },
          {
            "subject": "ds_33_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "DS-33 system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
                "notes": "DeWeirdt et al. name validated TUs as DefensePredictor discovered systems."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| DS-33 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
                "notes": "The pinned DefenseFinder article registry maps the DS-33 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "ds-33-defensefinder-model-gap",
        "prompt": "Resolve DS-33 native host breadth, exact component activities, profile-to-protein mapping, Csa3 and HEPN HHpred-domain interpretation, complete phage breadth, molecular output, and rule-level DefenseFinder criteria before minting narrower DS-33 mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "DeWeirdt et al. support DS-33 as the defensive GNAT transcriptional unit and final Science Tables S6/S7/S8 map it to two product accessions, a Bas26 phage readout, display name DS-33, and two HHpred rows. The pinned DefenseFinder HMM inventory records one DS-33 custom profile row. The pinned rules table has no DS-33 row, and the first-pass record does not resolve native host breadth, complete phage breadth, direct profile-to-protein correspondence, component activities, molecular output, or endogenous DS-33 activity.",
        "evidence": [
          {
            "reference": "DOI:10.1126/science.adv7924",
            "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
            "notes": "DeWeirdt et al. name validated TUs as DSs."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
            "snippet": "GNAT\tNZ_QOWT01000046.1\tGCF_003334765.1\t+\tTrue\tFalse\tFalse\tTrue\tDefensePredictor hits\t6922\t8901\thypothetical protein, hypothetical protein\tWP_014639476.1, WP_000354965.1\t9.45173070144912\t3.204412762840645\tTrue\tTrue\tPredicted novel defense gene\tDS-33",
            "notes": "The final Science supplementary Table S6 maps working_id GNAT to DS_name DS-33, marks the cloned transcriptional unit as defensive, and records NZ_QOWT01000046.1 positions 6922-8901 with product accessions WP_014639476.1 and WP_000354965.1."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
            "snippet": "Bas26\t1.2\tpLAND\t24-03-08_EV_HHHD_PIN2_CRDO.png\t500000000\tGNAT\t24-03-09\t24-03-09_GNAT_NADR_D390_DRAT.png\t2\t100\tY\t10000\t4.698970004336019\tTrue\t\t\tLB\t37",
            "notes": "The final Science supplementary Table S7 reports a GNAT assay row with a Bas26 phage readout and a -log(EOP) value of 4.699."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
            "snippet": "GNAT\tDS-33\tTrue",
            "notes": "The final Science supplementary Table S8 maps GNAT to replicated display name DS-33."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
            "snippet": "GNAT\t2.0\t333.0\tWP_000354965.1\tCsa3\t6W11_B\tCRISPR locus-related putative DNA-binding protein Csa3; CARF, CRISPR-Cas, cyclic oligoadenylate, cA4\thhpred_9793887.hhr\t25.0\t110.0\t0.5601\t2024-04-16 00:00:00",
            "notes": "The final Science supplementary Table S8 reports a lower-probability Csa3 HHpred hit for WP_000354965.1 in GNAT."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
            "snippet": "GNAT\t1.0\t320.0\tWP_014639476.1\tHEPN\tPF18737.5\tHEPN_MAE_28990 ; MAE_28990/MAE_18760-like HEPN\thhpred_9884029.hhr\t144.0\t306.0\t0.9842\t2024-04-15 00:00:00",
            "notes": "The final Science supplementary Table S8 reports a high-probability HEPN HHpred hit for WP_014639476.1 in GNAT."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
            "snippet": "| DS-33 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
            "notes": "The pinned DefenseFinder article registry maps the DS-33 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| DS-33__DS-33                                     |                                                  | DS-33                  | Custom                  | 220    |",
            "notes": "The pinned DefenseFinder HMM inventory records DS-33__DS-33 as a custom DS-33 profile."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "The pinned DefenseFinder rules table does not list DS-33, leaving rule-level detection criteria unresolved."
          }
        ],
        "attaches_to": [
          "causal_graphs#ds_33_locus_reduces_phage_plaquing"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-29"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-29T08:03:43Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted DS-33 system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; kept the graph at GNAT transcriptional-unit level because Csa3 and HEPN activity and rule rows remain unresolved, and proposals/metpo_traitmech_v333 reserves the replacement placeholder.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-29T08:03:44Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed DS-33 system canonical_examples and left them empty because DeWeirdt et al. directly support cloned GNAT assays in E. coli MG1655 and a DefenseFinder DS-33 model, but not a direct named native microbial isolate exemplar with experimentally verified endogenous DS-33 activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000457",
    "label": "DS-34 system",
    "definition": "A phage defense system in which an organism possesses the two-gene DefensePredictor-discovered system 34 locus cataloged as working transcriptional unit CITO and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.",
    "definition_source": "DOI:10.1126/science.adv7924",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "DS-34",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1126/science.adv7924"
      },
      {
        "synonym_text": "CITO",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx"
      },
      {
        "synonym_text": "DS-34__DS-34A",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "DS-34__DS-34B",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1126/science.adv7924",
        "snippet": "To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
        "notes": "DeWeirdt et al. experimentally validated 42 predicted transcriptional units as phage-defense systems in E. coli."
      },
      {
        "reference": "DOI:10.1126/science.adv7924",
        "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
        "notes": "DeWeirdt et al. name validated transcriptional units as DefensePredictor discovered systems."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
        "snippet": "CITO\tNZ_QOXN01000005.1\tGCF_003334015.1\t+\tTrue\tFalse\tTrue\tTrue\tDefensePredictor hits\t236284\t238194\tphage repressor protein CI, hypothetical protein\tWP_001589054.1, WP_000377448.1\t8.290091443457554\t3.623314765621056\tTrue\tTrue\tPredicted novel defense gene\tDS-34",
        "notes": "The final Science supplementary Table S6 maps working_id CITO to DS_name DS-34, marks the cloned transcriptional unit as defensive, and records NZ_QOXN01000005.1 positions 236284-238194 with product accessions WP_001589054.1 and WP_000377448.1."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
        "snippet": "Bas19\t3.1\tpLAND\t24-04-10_CITO_AAA3_FDRT_EV.png\t4000\tCITO\t24-04-10\t24-04-10_CITO_AAA3_FDRT_EV.png\t0\t1\t\t1\t3.6020599913279625\t\tTrue\t\tLB\t37",
        "notes": "The final Science supplementary Table S7 reports a CITO assay row with a Bas19 phage readout and a -log(EOP) value of 3.602."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
        "snippet": "CITO\tDS-34\tTrue",
        "notes": "The final Science supplementary Table S8 maps CITO to replicated display name DS-34."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
        "snippet": "CITO\t1.0\t308.0\tWP_001589054.1\tPhage repressor\t2FJR_A\tRepressor protein CI; genetic switch, regulation, repressor\thhpred_1741337.hhr\t125.0\t307.0\t0.9987\t2024-04-17 00:00:00",
        "notes": "The final Science supplementary Table S8 reports a high-probability phage-repressor HHpred hit for WP_001589054.1 in CITO."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
        "snippet": "CITO\t1.0\t308.0\tWP_001589054.1\tHTH\tPF08667.14\tBetR ; BetR domain\thhpred_1741337.hhr\t20.0\t88.0\t0.9431\t2024-04-17 00:00:00",
        "notes": "The final Science supplementary Table S8 reports a high-probability HTH HHpred hit for WP_001589054.1 in CITO."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| DS-34 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
        "notes": "The pinned DefenseFinder article registry maps the DS-34 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| DS-34__DS-34A                                    |                                                  | DS-34                  | Custom                  | 120    |",
        "notes": "The pinned DefenseFinder HMM inventory records DS-34__DS-34A as a custom DS-34 profile."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| DS-34__DS-34B                                    |                                                  | DS-34                  | Custom                  | 50     |",
        "notes": "The pinned DefenseFinder HMM inventory records DS-34__DS-34B as a custom DS-34 profile."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "ds_34_locus_reduces_phage_plaquing",
        "title": "DS-34 locus reduces bacteriophage plaquing",
        "description": "Conservative system-level sketch linking the two-gene DS-34 locus to reduced bacteriophage plaquing without resolving DS-34 component function or molecular output.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures DS-34 as the validated CITO transcriptional unit with two product accessions, high-probability phage-repressor and HTH HHpred rows for WP_001589054.1, and two DefenseFinder DS-34 profile rows. It does not assert native host breadth, exact profile-to-protein correspondence, DS-34 molecular activity, trigger, substrate, complete phage breadth, phage-repressor or HTH HHpred-domain interpretation, or DefenseFinder rule-level detection criteria.",
        "nodes": [
          {
            "node_id": "ds_34_locus",
            "label": "DS-34 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A two-gene DefensePredictor-discovered system 34 locus represented in the pinned DefenseFinder HMM inventory by two DS-34 custom profiles."
          },
          {
            "node_id": "reduced_phage_plaquing",
            "label": "reduced bacteriophage plaquing",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced bacteriophage plaquing in cells carrying cloned CITO."
          },
          {
            "node_id": "ds_34_system_trait",
            "label": "DS-34 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000457",
            "description": "Possession of a genome-encoded DS-34 phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "ds_34_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "reduced_phage_plaquing",
            "description": "The DS-34/CITO locus contributes to reduced bacteriophage plaquing in heterologous E. coli MG1655 plasmid-expression assays.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
                "notes": "DeWeirdt et al. describe the plasmid-based phage challenge used to validate predicted transcriptional units."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
                "snippet": "CITO\tNZ_QOXN01000005.1\tGCF_003334015.1\t+\tTrue\tFalse\tTrue\tTrue\tDefensePredictor hits\t236284\t238194\tphage repressor protein CI, hypothetical protein\tWP_001589054.1, WP_000377448.1\t8.290091443457554\t3.623314765621056\tTrue\tTrue\tPredicted novel defense gene\tDS-34",
                "notes": "The final Science supplementary Table S6 maps working_id CITO to DS_name DS-34, marks the cloned transcriptional unit as defensive, and records NZ_QOXN01000005.1 positions 236284-238194 with product accessions WP_001589054.1 and WP_000377448.1."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
                "snippet": "Bas19\t3.1\tpLAND\t24-04-10_CITO_AAA3_FDRT_EV.png\t4000\tCITO\t24-04-10\t24-04-10_CITO_AAA3_FDRT_EV.png\t0\t1\t\t1\t3.6020599913279625\t\tTrue\t\tLB\t37",
                "notes": "The final Science supplementary Table S7 reports a CITO assay row with a Bas19 phage readout and a -log(EOP) value of 3.602."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
                "snippet": "CITO\tDS-34\tTrue",
                "notes": "The final Science supplementary Table S8 maps CITO to replicated display name DS-34."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
                "snippet": "CITO\t1.0\t308.0\tWP_001589054.1\tPhage repressor\t2FJR_A\tRepressor protein CI; genetic switch, regulation, repressor\thhpred_1741337.hhr\t125.0\t307.0\t0.9987\t2024-04-17 00:00:00",
                "notes": "The final Science supplementary Table S8 reports a high-probability phage-repressor HHpred hit for WP_001589054.1 in CITO."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
                "snippet": "CITO\t1.0\t308.0\tWP_001589054.1\tHTH\tPF08667.14\tBetR ; BetR domain\thhpred_1741337.hhr\t20.0\t88.0\t0.9431\t2024-04-17 00:00:00",
                "notes": "The final Science supplementary Table S8 reports a high-probability HTH HHpred hit for WP_001589054.1 in CITO."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| DS-34__DS-34A                                    |                                                  | DS-34                  | Custom                  | 120    |",
                "notes": "The pinned DefenseFinder HMM inventory records DS-34__DS-34A as a custom DS-34 profile."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| DS-34__DS-34B                                    |                                                  | DS-34                  | Custom                  | 50     |",
                "notes": "The pinned DefenseFinder HMM inventory records DS-34__DS-34B as a custom DS-34 profile."
              }
            ]
          },
          {
            "subject": "reduced_phage_plaquing",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "ds_34_system_trait",
            "description": "DS-34-mediated phage plaquing reduction realizes the DS-34 system trait.",
            "evidence": [
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
                "snippet": "CITO\tNZ_QOXN01000005.1\tGCF_003334015.1\t+\tTrue\tFalse\tTrue\tTrue\tDefensePredictor hits\t236284\t238194\tphage repressor protein CI, hypothetical protein\tWP_001589054.1, WP_000377448.1\t8.290091443457554\t3.623314765621056\tTrue\tTrue\tPredicted novel defense gene\tDS-34",
                "notes": "The final Science supplementary Table S6 maps working_id CITO to DS_name DS-34, marks the cloned transcriptional unit as defensive, and records NZ_QOXN01000005.1 positions 236284-238194 with product accessions WP_001589054.1 and WP_000377448.1."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
                "snippet": "Bas19\t3.1\tpLAND\t24-04-10_CITO_AAA3_FDRT_EV.png\t4000\tCITO\t24-04-10\t24-04-10_CITO_AAA3_FDRT_EV.png\t0\t1\t\t1\t3.6020599913279625\t\tTrue\t\tLB\t37",
                "notes": "The final Science supplementary Table S7 reports a CITO assay row with a Bas19 phage readout and a -log(EOP) value of 3.602."
              },
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
                "notes": "The DS nomenclature is used for DefensePredictor discovered systems."
              }
            ]
          },
          {
            "subject": "ds_34_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "DS-34 system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
                "notes": "DeWeirdt et al. name validated TUs as DefensePredictor discovered systems."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| DS-34 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
                "notes": "The pinned DefenseFinder article registry maps the DS-34 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "ds-34-defensefinder-model-gap",
        "prompt": "Resolve DS-34 native host breadth, exact component activities, profile-to-protein mapping, phage-repressor and HTH HHpred-domain interpretation, complete phage breadth, molecular output, and rule-level DefenseFinder criteria before minting narrower DS-34 mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "DeWeirdt et al. support DS-34 as the defensive CITO transcriptional unit and final Science Tables S6/S7/S8 map it to two product accessions, a Bas19 phage readout, display name DS-34, and two HHpred rows. The pinned DefenseFinder HMM inventory records two DS-34 custom profile rows. The pinned rules table has no DS-34 row, and the first-pass record does not resolve native host breadth, complete phage breadth, direct profile-to-protein correspondence, component activities, molecular output, or endogenous DS-34 activity.",
        "evidence": [
          {
            "reference": "DOI:10.1126/science.adv7924",
            "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
            "notes": "DeWeirdt et al. name validated TUs as DSs."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
            "snippet": "CITO\tNZ_QOXN01000005.1\tGCF_003334015.1\t+\tTrue\tFalse\tTrue\tTrue\tDefensePredictor hits\t236284\t238194\tphage repressor protein CI, hypothetical protein\tWP_001589054.1, WP_000377448.1\t8.290091443457554\t3.623314765621056\tTrue\tTrue\tPredicted novel defense gene\tDS-34",
            "notes": "The final Science supplementary Table S6 maps working_id CITO to DS_name DS-34, marks the cloned transcriptional unit as defensive, and records NZ_QOXN01000005.1 positions 236284-238194 with product accessions WP_001589054.1 and WP_000377448.1."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
            "snippet": "Bas19\t3.1\tpLAND\t24-04-10_CITO_AAA3_FDRT_EV.png\t4000\tCITO\t24-04-10\t24-04-10_CITO_AAA3_FDRT_EV.png\t0\t1\t\t1\t3.6020599913279625\t\tTrue\t\tLB\t37",
            "notes": "The final Science supplementary Table S7 reports a CITO assay row with a Bas19 phage readout and a -log(EOP) value of 3.602."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
            "snippet": "CITO\tDS-34\tTrue",
            "notes": "The final Science supplementary Table S8 maps CITO to replicated display name DS-34."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
            "snippet": "CITO\t1.0\t308.0\tWP_001589054.1\tPhage repressor\t2FJR_A\tRepressor protein CI; genetic switch, regulation, repressor\thhpred_1741337.hhr\t125.0\t307.0\t0.9987\t2024-04-17 00:00:00",
            "notes": "The final Science supplementary Table S8 reports a high-probability phage-repressor HHpred hit for WP_001589054.1 in CITO."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
            "snippet": "CITO\t1.0\t308.0\tWP_001589054.1\tHTH\tPF08667.14\tBetR ; BetR domain\thhpred_1741337.hhr\t20.0\t88.0\t0.9431\t2024-04-17 00:00:00",
            "notes": "The final Science supplementary Table S8 reports a high-probability HTH HHpred hit for WP_001589054.1 in CITO."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
            "snippet": "| DS-34 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
            "notes": "The pinned DefenseFinder article registry maps the DS-34 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| DS-34__DS-34A                                    |                                                  | DS-34                  | Custom                  | 120    |",
            "notes": "The pinned DefenseFinder HMM inventory records DS-34__DS-34A as a custom DS-34 profile."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| DS-34__DS-34B                                    |                                                  | DS-34                  | Custom                  | 50     |",
            "notes": "The pinned DefenseFinder HMM inventory records DS-34__DS-34B as a custom DS-34 profile."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "The pinned DefenseFinder rules table does not list DS-34, leaving rule-level detection criteria unresolved."
          }
        ],
        "attaches_to": [
          "causal_graphs#ds_34_locus_reduces_phage_plaquing"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-29"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-29T08:40:09Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted DS-34 system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; kept the graph at CITO transcriptional-unit level because phage-repressor and HTH activity and rule rows remain unresolved, and proposals/metpo_traitmech_v334 reserves the replacement placeholder.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-29T08:40:10Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed DS-34 system canonical_examples and left them empty because DeWeirdt et al. directly support cloned CITO assays in E. coli MG1655 and a DefenseFinder DS-34 model, but not a direct named native microbial isolate exemplar with experimentally verified endogenous DS-34 activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000458",
    "label": "DS-35 system",
    "definition": "A phage defense system in which an organism possesses the single-gene DefensePredictor-discovered system 35 locus cataloged as working transcriptional unit RED5 and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.",
    "definition_source": "DOI:10.1126/science.adv7924",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "DS-35",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1126/science.adv7924"
      },
      {
        "synonym_text": "RED5",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx"
      },
      {
        "synonym_text": "DS-35__DS-35",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1126/science.adv7924",
        "snippet": "To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
        "notes": "DeWeirdt et al. experimentally validated 42 predicted transcriptional units as phage-defense systems in E. coli."
      },
      {
        "reference": "DOI:10.1126/science.adv7924",
        "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
        "notes": "DeWeirdt et al. name validated transcriptional units as DefensePredictor discovered systems."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
        "snippet": "RED5\tNZ_QOXO01000016.1\tGCF_003334005.1\t-\tTrue\tFalse\tTrue\tTrue\tDefensePredictor hits\t25863\t26705\thypothetical protein\tWP_087906371.1\t8.022232609988304\t2.666159259393051\tTrue\tTrue\tRemote defense homolog\tDS-35",
        "notes": "The final Science supplementary Table S6 maps working_id RED5 to DS_name DS-35, marks the cloned transcriptional unit as defensive, and records NZ_QOXO01000016.1 positions 25863-26705 with product accession WP_087906371.1."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
        "snippet": "RB69\t2.1\tpLAND\t24-03-12_EV.png\t200000\tRED5\t24-03-14\t24-03-14_RED5_TNEC_6236_RED2.png\t0\t1\t\t1\t5.301029995663981\t\tTrue\t\tLB\t37",
        "notes": "The final Science supplementary Table S7 reports a RED5 assay row with an RB69 phage readout and a -log(EOP) value of 5.301."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
        "snippet": "T4\t2.1\tpLAND\t24-03-12_EV.png\t200000000\tRED5\t24-03-14\t24-03-14_RED5_TNEC_6236_RED2.png\t2\t10\t\t1000\t5.301029995663981\t\tTrue\t\tLB\t37",
        "notes": "The final Science supplementary Table S7 reports a RED5 assay row with a T4 phage readout and a -log(EOP) value of 5.301."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
        "snippet": "RED5\tDS-35\tTrue",
        "notes": "The final Science supplementary Table S8 maps RED5 to replicated display name DS-35."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
        "snippet": "RED5\t1.0\t280.0\tWP_087906371.1\tPDDEXK\tPF18742.5\tDpnII-MboI ; REase_DpnII-MboI\thhpred_9496458.hhr\t142.0\t278.0\t1.0\t2024-04-15 00:00:00\t346-348\t333.0",
        "notes": "The final Science supplementary Table S8 reports a high-probability PDDEXK HHpred hit for WP_087906371.1 in RED5."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| DS-35 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
        "notes": "The pinned DefenseFinder article registry maps the DS-35 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| DS-35__DS-35                                     |                                                  | DS-35                  | Custom                  | 100    |",
        "notes": "The pinned DefenseFinder HMM inventory records DS-35__DS-35 as a custom DS-35 profile."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "ds_35_locus_reduces_phage_plaquing",
        "title": "DS-35 locus reduces bacteriophage plaquing",
        "description": "Conservative system-level sketch linking the single-gene DS-35 locus to reduced bacteriophage plaquing without resolving DS-35 component function or molecular output.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures DS-35 as the validated RED5 transcriptional unit with one product accession, one high-probability PDDEXK HHpred row for WP_087906371.1 in Table S8, and one DefenseFinder DS-35 profile row. It does not assert exact profile-to-protein correspondence, PDDEXK domain interpretation, nuclease chemistry, native host breadth, DS-35 molecular output, complete phage breadth, or DefenseFinder rule-level detection criteria.",
        "nodes": [
          {
            "node_id": "ds_35_locus",
            "label": "DS-35 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A single-gene DefensePredictor-discovered system 35 locus represented in the pinned DefenseFinder HMM inventory by one DS-35 custom profile."
          },
          {
            "node_id": "reduced_phage_plaquing",
            "label": "reduced bacteriophage plaquing",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced bacteriophage plaquing in cells carrying cloned RED5."
          },
          {
            "node_id": "ds_35_system_trait",
            "label": "DS-35 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000458",
            "description": "Possession of a genome-encoded DS-35 phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "ds_35_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "reduced_phage_plaquing",
            "description": "The DS-35/RED5 locus contributes to reduced bacteriophage plaquing in heterologous E. coli MG1655 plasmid-expression assays.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
                "notes": "DeWeirdt et al. describe the plasmid-based phage challenge used to validate predicted transcriptional units."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
                "snippet": "RED5\tNZ_QOXO01000016.1\tGCF_003334005.1\t-\tTrue\tFalse\tTrue\tTrue\tDefensePredictor hits\t25863\t26705\thypothetical protein\tWP_087906371.1\t8.022232609988304\t2.666159259393051\tTrue\tTrue\tRemote defense homolog\tDS-35",
                "notes": "The final Science supplementary Table S6 maps working_id RED5 to DS_name DS-35, marks the cloned transcriptional unit as defensive, and records NZ_QOXO01000016.1 positions 25863-26705 with product accession WP_087906371.1."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
                "snippet": "RB69\t2.1\tpLAND\t24-03-12_EV.png\t200000\tRED5\t24-03-14\t24-03-14_RED5_TNEC_6236_RED2.png\t0\t1\t\t1\t5.301029995663981\t\tTrue\t\tLB\t37",
                "notes": "The final Science supplementary Table S7 reports a RED5 assay row with an RB69 phage readout and a -log(EOP) value of 5.301."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
                "snippet": "T4\t2.1\tpLAND\t24-03-12_EV.png\t200000000\tRED5\t24-03-14\t24-03-14_RED5_TNEC_6236_RED2.png\t2\t10\t\t1000\t5.301029995663981\t\tTrue\t\tLB\t37",
                "notes": "The final Science supplementary Table S7 reports a RED5 assay row with a T4 phage readout and a -log(EOP) value of 5.301."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
                "snippet": "RED5\tDS-35\tTrue",
                "notes": "The final Science supplementary Table S8 maps RED5 to replicated display name DS-35."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
                "snippet": "RED5\t1.0\t280.0\tWP_087906371.1\tPDDEXK\tPF18742.5\tDpnII-MboI ; REase_DpnII-MboI\thhpred_9496458.hhr\t142.0\t278.0\t1.0\t2024-04-15 00:00:00\t346-348\t333.0",
                "notes": "The final Science supplementary Table S8 reports a high-probability PDDEXK HHpred hit for WP_087906371.1 in RED5."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| DS-35__DS-35                                     |                                                  | DS-35                  | Custom                  | 100    |",
                "notes": "The pinned DefenseFinder HMM inventory records DS-35__DS-35 as a custom DS-35 profile."
              }
            ]
          },
          {
            "subject": "reduced_phage_plaquing",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "ds_35_system_trait",
            "description": "DS-35-mediated phage plaquing reduction realizes the DS-35 system trait.",
            "evidence": [
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
                "snippet": "RED5\tNZ_QOXO01000016.1\tGCF_003334005.1\t-\tTrue\tFalse\tTrue\tTrue\tDefensePredictor hits\t25863\t26705\thypothetical protein\tWP_087906371.1\t8.022232609988304\t2.666159259393051\tTrue\tTrue\tRemote defense homolog\tDS-35",
                "notes": "The final Science supplementary Table S6 maps working_id RED5 to DS_name DS-35, marks the cloned transcriptional unit as defensive, and records NZ_QOXO01000016.1 positions 25863-26705 with product accession WP_087906371.1."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
                "snippet": "RB69\t2.1\tpLAND\t24-03-12_EV.png\t200000\tRED5\t24-03-14\t24-03-14_RED5_TNEC_6236_RED2.png\t0\t1\t\t1\t5.301029995663981\t\tTrue\t\tLB\t37",
                "notes": "The final Science supplementary Table S7 reports a RED5 assay row with an RB69 phage readout and a -log(EOP) value of 5.301."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
                "snippet": "T4\t2.1\tpLAND\t24-03-12_EV.png\t200000000\tRED5\t24-03-14\t24-03-14_RED5_TNEC_6236_RED2.png\t2\t10\t\t1000\t5.301029995663981\t\tTrue\t\tLB\t37",
                "notes": "The final Science supplementary Table S7 reports a RED5 assay row with a T4 phage readout and a -log(EOP) value of 5.301."
              },
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
                "notes": "The DS nomenclature is used for DefensePredictor discovered systems."
              }
            ]
          },
          {
            "subject": "ds_35_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "DS-35 system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
                "notes": "DeWeirdt et al. name validated TUs as DefensePredictor discovered systems."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| DS-35 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
                "notes": "The pinned DefenseFinder article registry maps the DS-35 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "ds-35-defensefinder-model-gap",
        "prompt": "Resolve DS-35 native host breadth, exact component activity, profile-to-protein mapping, PDDEXK HHpred-domain interpretation, nuclease chemistry, complete phage breadth, molecular output, and rule-level DefenseFinder criteria before minting narrower DS-35 mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "DeWeirdt et al. support DS-35 as the defensive RED5 transcriptional unit and final Science Tables S6/S7/S8 map it to one product accession, RB69 and T4 phage readouts, display name DS-35, and one PDDEXK HHpred row. The pinned DefenseFinder HMM inventory records one DS-35 custom profile row. The pinned rules table has no DS-35 row, and the first-pass record does not resolve native host breadth, complete phage breadth, direct profile-to-protein correspondence, PDDEXK domain interpretation, nuclease chemistry, molecular output, or endogenous DS-35 activity.",
        "evidence": [
          {
            "reference": "DOI:10.1126/science.adv7924",
            "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
            "notes": "DeWeirdt et al. name validated TUs as DSs."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
            "snippet": "RED5\tNZ_QOXO01000016.1\tGCF_003334005.1\t-\tTrue\tFalse\tTrue\tTrue\tDefensePredictor hits\t25863\t26705\thypothetical protein\tWP_087906371.1\t8.022232609988304\t2.666159259393051\tTrue\tTrue\tRemote defense homolog\tDS-35",
            "notes": "The final Science supplementary Table S6 maps working_id RED5 to DS_name DS-35, marks the cloned transcriptional unit as defensive, and records NZ_QOXO01000016.1 positions 25863-26705 with product accession WP_087906371.1."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
            "snippet": "RB69\t2.1\tpLAND\t24-03-12_EV.png\t200000\tRED5\t24-03-14\t24-03-14_RED5_TNEC_6236_RED2.png\t0\t1\t\t1\t5.301029995663981\t\tTrue\t\tLB\t37",
            "notes": "The final Science supplementary Table S7 reports a RED5 assay row with an RB69 phage readout and a -log(EOP) value of 5.301."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
            "snippet": "T4\t2.1\tpLAND\t24-03-12_EV.png\t200000000\tRED5\t24-03-14\t24-03-14_RED5_TNEC_6236_RED2.png\t2\t10\t\t1000\t5.301029995663981\t\tTrue\t\tLB\t37",
            "notes": "The final Science supplementary Table S7 reports a RED5 assay row with a T4 phage readout and a -log(EOP) value of 5.301."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
            "snippet": "RED5\tDS-35\tTrue",
            "notes": "The final Science supplementary Table S8 maps RED5 to replicated display name DS-35."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
            "snippet": "RED5\t1.0\t280.0\tWP_087906371.1\tPDDEXK\tPF18742.5\tDpnII-MboI ; REase_DpnII-MboI\thhpred_9496458.hhr\t142.0\t278.0\t1.0\t2024-04-15 00:00:00\t346-348\t333.0",
            "notes": "The final Science supplementary Table S8 reports a high-probability PDDEXK HHpred hit for WP_087906371.1 in RED5."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
            "snippet": "| DS-35 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
            "notes": "The pinned DefenseFinder article registry maps the DS-35 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| DS-35__DS-35                                     |                                                  | DS-35                  | Custom                  | 100    |",
            "notes": "The pinned DefenseFinder HMM inventory records DS-35__DS-35 as a custom DS-35 profile."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "The pinned DefenseFinder rules table does not list DS-35, leaving rule-level detection criteria unresolved."
          }
        ],
        "attaches_to": [
          "causal_graphs#ds_35_locus_reduces_phage_plaquing"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-29"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-29T09:12:09Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted DS-35 system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; kept the graph at RED5 transcriptional-unit level because PDDEXK activity and rule rows remain unresolved, and proposals/metpo_traitmech_v335 reserves the replacement placeholder.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-29T09:12:10Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed DS-35 system canonical_examples and left them empty because DeWeirdt et al. directly support cloned RED5 assays in E. coli MG1655 and a DefenseFinder DS-35 model, but not a direct named native microbial isolate exemplar with experimentally verified endogenous DS-35 activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000474",
    "label": "DS-36 system",
    "definition": "A phage defense system in which an organism possesses a genome-encoded DefensePredictor-discovered system 36 locus represented in the pinned DefenseFinder model inventory by the DS-36 custom HMM profile.",
    "definition_source": "DOI:10.1101/2025.01.08.631726",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "DS-36",
        "synonym_type": "EXACT_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      },
      {
        "synonym_text": "DS-36__DS-36",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1101/2025.01.08.631726",
        "snippet": "To test for anti-phage defense, we placed each TU with its native promoter region on a low-copy number plasmid in E. coli MG1655 and then challenged these strains with a panel of 24 diverse E. coli phages (fig. S2). In total, 45 (42% of 106) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
        "notes": "DeWeirdt et al. experimentally validated 45 predicted transcriptional units as phage-defense systems in E. coli; the first-pass DS-36 record uses this source only for the DefensePredictor DS naming context, not for an exact DS-36 phage readout."
      },
      {
        "reference": "DOI:10.1101/2025.01.08.631726",
        "snippet": "We refer to these validated TUs as DefensePredictor discovered Systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
        "notes": "DeWeirdt et al. name validated transcriptional units as DefensePredictor discovered Systems."
      },
      {
        "reference": "DOI:10.1101/2025.01.08.631726",
        "snippet": "To begin elucidating the function of the 45 validated TUs, we further annotated their protein domains (see Methods; table S6).",
        "notes": "DeWeirdt et al. describe Table S6 as a protein-domain annotation table for the validated DS transcriptional units; the exact preprint DS-36 row was not recovered in this curation pass."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| DS-36 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
        "notes": "The pinned DefenseFinder article registry maps the DS-36 source key to the DeWeirdt et al. DefensePredictor preprint."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| DS-36__DS-36                                     |                                                  | DS-36                  | Custom                  | 200    |",
        "notes": "The pinned DefenseFinder HMM inventory records DS-36__DS-36 as a custom DS-36 profile."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "ds_36_locus_profile_model",
        "title": "DS-36 locus profile model",
        "description": "Conservative system-level sketch linking the DS-36 DefensePredictor-discovered system key to DS-36 system possession and the broader phage-defense-system trait without resolving DS-36 component function or a phage activity readout.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures DS-36 as a DefensePredictor-discovered system with a DS-36 custom HMM row in the pinned DefenseFinder HMM inventory. It does not assert the preprint working identifier, preprint Table S5/S6 rows, final Science supplement rows, native host breadth, profile-to-protein correspondence, DS-36 molecular activity, exact phage target breadth, or DefenseFinder rule-level detection criteria.",
        "nodes": [
          {
            "node_id": "ds_36_locus",
            "label": "DS-36 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A DefensePredictor-discovered system 36 locus represented in the pinned DefenseFinder HMM inventory by the DS-36 custom profile."
          },
          {
            "node_id": "ds_36_system_trait",
            "label": "DS-36 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000474",
            "description": "Possession of a genome-encoded DS-36 phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "ds_36_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "ds_36_system_trait",
            "description": "DefenseFinder links the DS-36 source key to the DefensePredictor preprint and represents DS-36 in the HMM inventory with a DS-36 custom profile.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| DS-36 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
                "notes": "The pinned DefenseFinder article registry maps the DS-36 source key to the DeWeirdt et al. DefensePredictor preprint."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| DS-36__DS-36                                     |                                                  | DS-36                  | Custom                  | 200    |",
                "notes": "The pinned DefenseFinder HMM inventory records DS-36__DS-36 as a custom DS-36 profile."
              }
            ]
          },
          {
            "subject": "ds_36_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "DS-36 system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1101/2025.01.08.631726",
                "snippet": "We refer to these validated TUs as DefensePredictor discovered Systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
                "notes": "DeWeirdt et al. name validated TUs as DefensePredictor discovered Systems."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| DS-36 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
                "notes": "The pinned DefenseFinder article registry maps the DS-36 source key to the DeWeirdt et al. DefensePredictor preprint."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "ds-36-defensefinder-model-gap",
        "prompt": "Resolve DS-36 working-identifier rows, preprint Table S5 and S6 context, final Science supplement omission, native host breadth, DS-36 profile-to-protein mapping, sensitive-phage breadth, molecular output, and rule-level DefenseFinder criteria before minting narrower DS-36 mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "The DeWeirdt et al. preprint supports the DefensePredictor discovered System naming convention, the pinned DefenseFinder article registry names DS-36 and maps it to that preprint, and the pinned HMM inventory records a DS-36 custom profile row. DS-36 is absent from the final Science Table S6, S7, and S8 files checked during this curation pass, the exact preprint per-TU row was not recovered, the pinned DefenseFinder rules table has no DS-36 row, and the first-pass record does not resolve the working identifier, assayed phages, phage readout, native host, profile-to-component mapping, component activities, or complete detection criteria.",
        "evidence": [
          {
            "reference": "DOI:10.1101/2025.01.08.631726",
            "snippet": "To test for anti-phage defense, we placed each TU with its native promoter region on a low-copy number plasmid in E. coli MG1655 and then challenged these strains with a panel of 24 diverse E. coli phages (fig. S2). In total, 45 (42% of 106) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
            "notes": "DeWeirdt et al. validate predicted transcriptional units by measuring plaquing relative to an empty vector control strain."
          },
          {
            "reference": "DOI:10.1101/2025.01.08.631726",
            "snippet": "We refer to these validated TUs as DefensePredictor discovered Systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
            "notes": "DeWeirdt et al. name validated TUs as DSs."
          },
          {
            "reference": "DOI:10.1101/2025.01.08.631726",
            "snippet": "To begin elucidating the function of the 45 validated TUs, we further annotated their protein domains (see Methods; table S6).",
            "notes": "DeWeirdt et al. describe Table S6 as further protein-domain annotation of validated TUs."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
            "snippet": "| DS-36 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
            "notes": "The pinned DefenseFinder article registry maps the DS-36 source key to the DeWeirdt et al. DefensePredictor preprint."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| DS-36__DS-36                                     |                                                  | DS-36                  | Custom                  | 200    |",
            "notes": "The pinned DefenseFinder HMM inventory records DS-36__DS-36 as a custom DS-36 profile."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "The pinned DefenseFinder rules table does not list DS-36 or DS-36__DS-36, leaving complete component coverage and rule-level detection criteria unresolved."
          }
        ],
        "attaches_to": [
          "causal_graphs#ds_36_locus_profile_model"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-29"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-29T21:04:31Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted DS-36 system as a DOI- and DefenseFinder-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; kept the graph at DS-36 source-key and HMM-profile level because preprint Table S5/S6 rows, final Science supplement rows, and rule rows remain unresolved, and proposals/metpo_traitmech_v351 reserves the replacement placeholder.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-29T21:04:32Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed DS-36 system canonical_examples and left them empty because the pinned DefenseFinder registries support DS-36 system identity and custom HMM coverage but not a direct named native microbial isolate exemplar with experimentally verified endogenous DS-36 activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000459",
    "label": "DS-37 system",
    "definition": "A phage defense system in which an organism possesses the single-gene DefensePredictor-discovered system 37 locus cataloged as working transcriptional unit SC24 and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.",
    "definition_source": "DOI:10.1126/science.adv7924",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "DS-37",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1126/science.adv7924"
      },
      {
        "synonym_text": "SC24",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx"
      },
      {
        "synonym_text": "DS-37__DS-37",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1126/science.adv7924",
        "snippet": "To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
        "notes": "DeWeirdt et al. experimentally validated 42 predicted transcriptional units as phage-defense systems in E. coli."
      },
      {
        "reference": "DOI:10.1126/science.adv7924",
        "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
        "notes": "DeWeirdt et al. name validated transcriptional units as DefensePredictor discovered systems."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
        "snippet": "SC24\tNZ_QOXM01000003.1\tGCF_003334665.1\t+\tTrue\tFalse\tFalse\tTrue\tDefensePredictor hits\t26984\t28375\thypothetical protein\tWP_000982358.1\t6.427335289528256\t-2.24248116892434\tTrue\tFalse\tPredicted novel defense gene\tDS-37",
        "notes": "The final Science supplementary Table S6 maps working_id SC24 to DS_name DS-37, marks the cloned transcriptional unit as defensive, and records NZ_QOXM01000003.1 positions 26984-28375 with product accession WP_000982358.1."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
        "snippet": "Bas1\t6.1\tpLAND\t24-07-17_MVB1_VPUS_VAME_EV.png\t3000000\tSC24\t24-07-24\t24-07-24_TRNA_MF4L_SC24_EV.png\t0\t1\t\t1\t6.477121254719663\t\t\tTrue\tLB\t37",
        "notes": "The final Science supplementary Table S7 reports an SC24 assay row with a Bas1 phage readout and a -log(EOP) value of 6.477."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
        "snippet": "Bas9\t6.1\tpLAND\t24-07-17_MVB1_VPUS_VAME_EV.png\t600000000\tSC24\t24-07-24\t24-07-24_TRNA_MF4L_SC24_EV.png\t3\t10\t\t10000\t4.778151250383644\t\t\tTrue\tLB\t37",
        "notes": "The final Science supplementary Table S7 reports an SC24 assay row with a Bas9 phage readout and a -log(EOP) value of 4.778."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
        "snippet": "SC24\tDS-37\tTrue",
        "notes": "The final Science supplementary Table S8 maps SC24 to replicated display name DS-37."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
        "snippet": "SC24\t1.0\t463.0\tWP_000982358.1\tPDDEXK\tPF08378.16\tNERD ; Nuclease-related domain\thhpred_2278954.hhr\t154.0\t204.0\t0.47\t2024-07-29 00:00:00\t210-212\t199.0",
        "notes": "The final Science supplementary Table S8 reports a low-probability PDDEXK HHpred lead for WP_000982358.1 in SC24; this first-pass record records it as source context without resolving DS-37 molecular activity."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| DS-37 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
        "notes": "The pinned DefenseFinder article registry maps the DS-37 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| DS-37__DS-37                                     |                                                  | DS-37                  | Custom                  | 300    |",
        "notes": "The pinned DefenseFinder HMM inventory records DS-37__DS-37 as a custom DS-37 profile."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "ds_37_locus_reduces_phage_plaquing",
        "title": "DS-37 locus reduces bacteriophage plaquing",
        "description": "Conservative system-level sketch linking the single-gene DS-37 locus to reduced bacteriophage plaquing without resolving DS-37 component function or molecular output.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures DS-37 as the validated SC24 transcriptional unit with one product accession, one low-probability PDDEXK HHpred row for WP_000982358.1 in Table S8, and one DefenseFinder DS-37 profile row. It does not assert exact profile-to-protein correspondence, PDDEXK domain interpretation, nuclease chemistry, native host breadth, DS-37 molecular output, complete phage breadth, or DefenseFinder rule-level detection criteria.",
        "nodes": [
          {
            "node_id": "ds_37_locus",
            "label": "DS-37 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A single-gene DefensePredictor-discovered system 37 locus represented in the pinned DefenseFinder HMM inventory by one DS-37 custom profile."
          },
          {
            "node_id": "reduced_phage_plaquing",
            "label": "reduced bacteriophage plaquing",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced bacteriophage plaquing in cells carrying cloned SC24."
          },
          {
            "node_id": "ds_37_system_trait",
            "label": "DS-37 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000459",
            "description": "Possession of a genome-encoded DS-37 phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "ds_37_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "reduced_phage_plaquing",
            "description": "The DS-37/SC24 locus contributes to reduced bacteriophage plaquing in heterologous E. coli MG1655 plasmid-expression assays.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
                "notes": "DeWeirdt et al. describe the plasmid-based phage challenge used to validate predicted transcriptional units."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
                "snippet": "SC24\tNZ_QOXM01000003.1\tGCF_003334665.1\t+\tTrue\tFalse\tFalse\tTrue\tDefensePredictor hits\t26984\t28375\thypothetical protein\tWP_000982358.1\t6.427335289528256\t-2.24248116892434\tTrue\tFalse\tPredicted novel defense gene\tDS-37",
                "notes": "The final Science supplementary Table S6 maps working_id SC24 to DS_name DS-37, marks the cloned transcriptional unit as defensive, and records NZ_QOXM01000003.1 positions 26984-28375 with product accession WP_000982358.1."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
                "snippet": "Bas1\t6.1\tpLAND\t24-07-17_MVB1_VPUS_VAME_EV.png\t3000000\tSC24\t24-07-24\t24-07-24_TRNA_MF4L_SC24_EV.png\t0\t1\t\t1\t6.477121254719663\t\t\tTrue\tLB\t37",
                "notes": "The final Science supplementary Table S7 reports an SC24 assay row with a Bas1 phage readout and a -log(EOP) value of 6.477."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
                "snippet": "Bas9\t6.1\tpLAND\t24-07-17_MVB1_VPUS_VAME_EV.png\t600000000\tSC24\t24-07-24\t24-07-24_TRNA_MF4L_SC24_EV.png\t3\t10\t\t10000\t4.778151250383644\t\t\tTrue\tLB\t37",
                "notes": "The final Science supplementary Table S7 reports an SC24 assay row with a Bas9 phage readout and a -log(EOP) value of 4.778."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
                "snippet": "SC24\tDS-37\tTrue",
                "notes": "The final Science supplementary Table S8 maps SC24 to replicated display name DS-37."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| DS-37__DS-37                                     |                                                  | DS-37                  | Custom                  | 300    |",
                "notes": "The pinned DefenseFinder HMM inventory records DS-37__DS-37 as a custom DS-37 profile."
              }
            ]
          },
          {
            "subject": "reduced_phage_plaquing",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "ds_37_system_trait",
            "description": "DS-37-mediated phage plaquing reduction realizes the DS-37 system trait.",
            "evidence": [
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
                "snippet": "SC24\tNZ_QOXM01000003.1\tGCF_003334665.1\t+\tTrue\tFalse\tFalse\tTrue\tDefensePredictor hits\t26984\t28375\thypothetical protein\tWP_000982358.1\t6.427335289528256\t-2.24248116892434\tTrue\tFalse\tPredicted novel defense gene\tDS-37",
                "notes": "The final Science supplementary Table S6 maps working_id SC24 to DS_name DS-37, marks the cloned transcriptional unit as defensive, and records NZ_QOXM01000003.1 positions 26984-28375 with product accession WP_000982358.1."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
                "snippet": "Bas1\t6.1\tpLAND\t24-07-17_MVB1_VPUS_VAME_EV.png\t3000000\tSC24\t24-07-24\t24-07-24_TRNA_MF4L_SC24_EV.png\t0\t1\t\t1\t6.477121254719663\t\t\tTrue\tLB\t37",
                "notes": "The final Science supplementary Table S7 reports an SC24 assay row with a Bas1 phage readout and a -log(EOP) value of 6.477."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
                "snippet": "Bas9\t6.1\tpLAND\t24-07-17_MVB1_VPUS_VAME_EV.png\t600000000\tSC24\t24-07-24\t24-07-24_TRNA_MF4L_SC24_EV.png\t3\t10\t\t10000\t4.778151250383644\t\t\tTrue\tLB\t37",
                "notes": "The final Science supplementary Table S7 reports an SC24 assay row with a Bas9 phage readout and a -log(EOP) value of 4.778."
              },
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
                "notes": "The DS nomenclature is used for DefensePredictor discovered systems."
              }
            ]
          },
          {
            "subject": "ds_37_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "DS-37 system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
                "notes": "DeWeirdt et al. name validated TUs as DefensePredictor discovered systems."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| DS-37 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
                "notes": "The pinned DefenseFinder article registry maps the DS-37 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "ds-37-defensefinder-model-gap",
        "prompt": "Resolve DS-37 native host breadth, exact component activity, profile-to-protein mapping, low-probability PDDEXK HHpred-domain interpretation, nuclease chemistry, complete phage breadth, molecular output, and rule-level DefenseFinder criteria before minting narrower DS-37 mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "DeWeirdt et al. support DS-37 as the defensive SC24 transcriptional unit and final Science Tables S6/S7/S8 map it to one product accession, Bas1 and Bas9 phage readouts, display name DS-37, and one low-probability PDDEXK HHpred row. The pinned DefenseFinder HMM inventory records one DS-37 custom profile row. The pinned rules table has no DS-37 row, and the first-pass record does not resolve native host breadth, complete phage breadth, direct profile-to-protein correspondence, PDDEXK domain interpretation, nuclease chemistry, molecular output, or endogenous DS-37 activity.",
        "evidence": [
          {
            "reference": "DOI:10.1126/science.adv7924",
            "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
            "notes": "DeWeirdt et al. name validated TUs as DSs."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
            "snippet": "SC24\tNZ_QOXM01000003.1\tGCF_003334665.1\t+\tTrue\tFalse\tFalse\tTrue\tDefensePredictor hits\t26984\t28375\thypothetical protein\tWP_000982358.1\t6.427335289528256\t-2.24248116892434\tTrue\tFalse\tPredicted novel defense gene\tDS-37",
            "notes": "The final Science supplementary Table S6 maps working_id SC24 to DS_name DS-37, marks the cloned transcriptional unit as defensive, and records NZ_QOXM01000003.1 positions 26984-28375 with product accession WP_000982358.1."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
            "snippet": "Bas1\t6.1\tpLAND\t24-07-17_MVB1_VPUS_VAME_EV.png\t3000000\tSC24\t24-07-24\t24-07-24_TRNA_MF4L_SC24_EV.png\t0\t1\t\t1\t6.477121254719663\t\t\tTrue\tLB\t37",
            "notes": "The final Science supplementary Table S7 reports an SC24 assay row with a Bas1 phage readout and a -log(EOP) value of 6.477."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
            "snippet": "Bas9\t6.1\tpLAND\t24-07-17_MVB1_VPUS_VAME_EV.png\t600000000\tSC24\t24-07-24\t24-07-24_TRNA_MF4L_SC24_EV.png\t3\t10\t\t10000\t4.778151250383644\t\t\tTrue\tLB\t37",
            "notes": "The final Science supplementary Table S7 reports an SC24 assay row with a Bas9 phage readout and a -log(EOP) value of 4.778."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
            "snippet": "SC24\tDS-37\tTrue",
            "notes": "The final Science supplementary Table S8 maps SC24 to replicated display name DS-37."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
            "snippet": "SC24\t1.0\t463.0\tWP_000982358.1\tPDDEXK\tPF08378.16\tNERD ; Nuclease-related domain\thhpred_2278954.hhr\t154.0\t204.0\t0.47\t2024-07-29 00:00:00\t210-212\t199.0",
            "notes": "The final Science supplementary Table S8 reports a low-probability PDDEXK HHpred lead for WP_000982358.1 in SC24; this first-pass record records it as source context without resolving DS-37 molecular activity."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
            "snippet": "| DS-37 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
            "notes": "The pinned DefenseFinder article registry maps the DS-37 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| DS-37__DS-37                                     |                                                  | DS-37                  | Custom                  | 300    |",
            "notes": "The pinned DefenseFinder HMM inventory records DS-37__DS-37 as a custom DS-37 profile."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "The pinned DefenseFinder rules table does not list DS-37, leaving rule-level detection criteria unresolved."
          }
        ],
        "attaches_to": [
          "causal_graphs#ds_37_locus_reduces_phage_plaquing"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-29"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-29T10:28:09Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted DS-37 system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; kept the graph at SC24 transcriptional-unit level because the low-probability PDDEXK row and rule rows remain unresolved, and proposals/metpo_traitmech_v336 reserves the replacement placeholder.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-29T10:28:10Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed DS-37 system canonical_examples and left them empty because DeWeirdt et al. directly support cloned SC24 assays in E. coli MG1655 and a DefenseFinder DS-37 model, but not a direct named native microbial isolate exemplar with experimentally verified endogenous DS-37 activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000460",
    "label": "DS-38 system",
    "definition": "A phage defense system in which an organism possesses the single-gene DefensePredictor-discovered system 38 locus cataloged as working transcriptional unit HEP2 and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.",
    "definition_source": "DOI:10.1126/science.adv7924",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "DS-38",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1126/science.adv7924"
      },
      {
        "synonym_text": "HEP2",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx"
      },
      {
        "synonym_text": "DS-38__DS-38",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1126/science.adv7924",
        "snippet": "To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
        "notes": "DeWeirdt et al. experimentally validated 42 predicted transcriptional units as phage-defense systems in E. coli."
      },
      {
        "reference": "DOI:10.1126/science.adv7924",
        "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
        "notes": "DeWeirdt et al. name validated transcriptional units as DefensePredictor discovered systems."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
        "snippet": "HEP2\tNZ_QOYR01000034.1\tGCF_003333645.1\t-\tTrue\tFalse\tTrue\tTrue\tDefensePredictor hits\t8089\t9189\thypothetical protein\tWP_001313577.1\t8.026493157403\t2.649821696202418\tTrue\tTrue\tPredicted novel defense gene\tDS-38",
        "notes": "The final Science supplementary Table S6 maps working_id HEP2 to DS_name DS-38, marks the cloned transcriptional unit as defensive, and records NZ_QOYR01000034.1 positions 8089-9189 with product accession WP_001313577.1."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
        "snippet": "Bas25\t2.2\tpLAND\t24-03-12_EV.png\t500000\tHEP2\t24-03-15\t24-03-15_GPEH_HEP2_PDO1_PDP6.png\t0\t1\t\t1\t5.698970004336019\t\tTrue\t\tLB\t37",
        "notes": "The final Science supplementary Table S7 Systems sheet reports an HEP2 assay row with a Bas25 phage readout and a -log(EOP) value of 5.699."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
        "snippet": "Bas19\t2.2\tpLAND\t24-03-12_EV.png\t15000\tHEP2\t24-03-15\t24-03-15_GPEH_HEP2_PDO1_PDP6.png\t0\t1\t\t1\t4.176091259055681\t\tTrue\t\tLB\t37",
        "notes": "The final Science supplementary Table S7 Systems sheet reports an HEP2 assay row with a Bas19 phage readout and a -log(EOP) value of 4.176."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
        "snippet": "HEP2\tDS-38\tTrue",
        "notes": "The final Science supplementary Table S8 maps HEP2 to replicated display name DS-38."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
        "snippet": "HEP2\t1.0\t366.0\tWP_001313577.1\tZF\t8SSU_A\tTranscriptional repressor CTCF,LIM domain-binding protein 1; PROTEIN-DNA COMPLEX, DNA BINDING PROTEIN, transcription factor, zinc fingers, insulator/chromatin architecture, transcription-dna complex, TRANSCRIPTION\thhpred_7553560.hhr\t206.0\t364.0\t0.9902\t2024-04-15 00:00:00\t\t",
        "notes": "The final Science supplementary Table S8 reports a high-probability zinc-finger HHpred hit for WP_001313577.1 in HEP2."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
        "snippet": "HEP2\t1.0\t366.0\tWP_001313577.1\tHEPN\tPF05168.18\tHEPN ; HEPN domain\thhpred_7553560.hhr\t22.0\t153.0\t0.9662\t2024-04-15 00:00:00\t\t",
        "notes": "The final Science supplementary Table S8 reports a high-probability HEPN HHpred hit for WP_001313577.1 in HEP2."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| DS-38 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
        "notes": "The pinned DefenseFinder article registry maps the DS-38 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| DS-38__DS-38                                     |                                                  | DS-38                  | Custom                  | 200    |",
        "notes": "The pinned DefenseFinder HMM inventory records DS-38__DS-38 as a custom DS-38 profile."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "ds_38_locus_reduces_phage_plaquing",
        "title": "DS-38 locus reduces bacteriophage plaquing",
        "description": "Conservative system-level sketch linking the single-gene DS-38 locus to reduced bacteriophage plaquing without resolving DS-38 component function or molecular output.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures DS-38 as the validated HEP2 transcriptional unit with one product accession, high-probability zinc-finger and HEPN HHpred rows for WP_001313577.1, and one DefenseFinder DS-38 profile row. It does not assert exact profile-to-protein correspondence, HEPN ribonuclease activity, zinc-finger DNA-binding activity, native host breadth, DS-38 molecular output, complete phage breadth, or DefenseFinder rule-level detection criteria.",
        "nodes": [
          {
            "node_id": "ds_38_locus",
            "label": "DS-38 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A single-gene DefensePredictor-discovered system 38 locus represented in the pinned DefenseFinder HMM inventory by one DS-38 custom profile."
          },
          {
            "node_id": "reduced_phage_plaquing",
            "label": "reduced bacteriophage plaquing",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced bacteriophage plaquing in cells carrying cloned HEP2."
          },
          {
            "node_id": "ds_38_system_trait",
            "label": "DS-38 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000460",
            "description": "Possession of a genome-encoded DS-38 phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "ds_38_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "reduced_phage_plaquing",
            "description": "The DS-38/HEP2 locus contributes to reduced bacteriophage plaquing in heterologous E. coli MG1655 plasmid-expression assays.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
                "notes": "DeWeirdt et al. describe the plasmid-based phage challenge used to validate predicted transcriptional units."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
                "snippet": "HEP2\tNZ_QOYR01000034.1\tGCF_003333645.1\t-\tTrue\tFalse\tTrue\tTrue\tDefensePredictor hits\t8089\t9189\thypothetical protein\tWP_001313577.1\t8.026493157403\t2.649821696202418\tTrue\tTrue\tPredicted novel defense gene\tDS-38",
                "notes": "The final Science supplementary Table S6 maps working_id HEP2 to DS_name DS-38, marks the cloned transcriptional unit as defensive, and records NZ_QOYR01000034.1 positions 8089-9189 with product accession WP_001313577.1."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
                "snippet": "Bas25\t2.2\tpLAND\t24-03-12_EV.png\t500000\tHEP2\t24-03-15\t24-03-15_GPEH_HEP2_PDO1_PDP6.png\t0\t1\t\t1\t5.698970004336019\t\tTrue\t\tLB\t37",
                "notes": "The final Science supplementary Table S7 Systems sheet reports an HEP2 assay row with a Bas25 phage readout and a -log(EOP) value of 5.699."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
                "snippet": "Bas19\t2.2\tpLAND\t24-03-12_EV.png\t15000\tHEP2\t24-03-15\t24-03-15_GPEH_HEP2_PDO1_PDP6.png\t0\t1\t\t1\t4.176091259055681\t\tTrue\t\tLB\t37",
                "notes": "The final Science supplementary Table S7 Systems sheet reports an HEP2 assay row with a Bas19 phage readout and a -log(EOP) value of 4.176."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
                "snippet": "HEP2\tDS-38\tTrue",
                "notes": "The final Science supplementary Table S8 maps HEP2 to replicated display name DS-38."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
                "snippet": "HEP2\t1.0\t366.0\tWP_001313577.1\tZF\t8SSU_A\tTranscriptional repressor CTCF,LIM domain-binding protein 1; PROTEIN-DNA COMPLEX, DNA BINDING PROTEIN, transcription factor, zinc fingers, insulator/chromatin architecture, transcription-dna complex, TRANSCRIPTION\thhpred_7553560.hhr\t206.0\t364.0\t0.9902\t2024-04-15 00:00:00\t\t",
                "notes": "The final Science supplementary Table S8 reports a high-probability zinc-finger HHpred hit for WP_001313577.1 in HEP2."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
                "snippet": "HEP2\t1.0\t366.0\tWP_001313577.1\tHEPN\tPF05168.18\tHEPN ; HEPN domain\thhpred_7553560.hhr\t22.0\t153.0\t0.9662\t2024-04-15 00:00:00\t\t",
                "notes": "The final Science supplementary Table S8 reports a high-probability HEPN HHpred hit for WP_001313577.1 in HEP2."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| DS-38__DS-38                                     |                                                  | DS-38                  | Custom                  | 200    |",
                "notes": "The pinned DefenseFinder HMM inventory records DS-38__DS-38 as a custom DS-38 profile."
              }
            ]
          },
          {
            "subject": "reduced_phage_plaquing",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "ds_38_system_trait",
            "description": "DS-38-mediated phage plaquing reduction realizes the DS-38 system trait.",
            "evidence": [
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
                "snippet": "HEP2\tNZ_QOYR01000034.1\tGCF_003333645.1\t-\tTrue\tFalse\tTrue\tTrue\tDefensePredictor hits\t8089\t9189\thypothetical protein\tWP_001313577.1\t8.026493157403\t2.649821696202418\tTrue\tTrue\tPredicted novel defense gene\tDS-38",
                "notes": "The final Science supplementary Table S6 maps working_id HEP2 to DS_name DS-38, marks the cloned transcriptional unit as defensive, and records NZ_QOYR01000034.1 positions 8089-9189 with product accession WP_001313577.1."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
                "snippet": "Bas25\t2.2\tpLAND\t24-03-12_EV.png\t500000\tHEP2\t24-03-15\t24-03-15_GPEH_HEP2_PDO1_PDP6.png\t0\t1\t\t1\t5.698970004336019\t\tTrue\t\tLB\t37",
                "notes": "The final Science supplementary Table S7 Systems sheet reports an HEP2 assay row with a Bas25 phage readout and a -log(EOP) value of 5.699."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
                "snippet": "Bas19\t2.2\tpLAND\t24-03-12_EV.png\t15000\tHEP2\t24-03-15\t24-03-15_GPEH_HEP2_PDO1_PDP6.png\t0\t1\t\t1\t4.176091259055681\t\tTrue\t\tLB\t37",
                "notes": "The final Science supplementary Table S7 Systems sheet reports an HEP2 assay row with a Bas19 phage readout and a -log(EOP) value of 4.176."
              },
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
                "notes": "The DS nomenclature is used for DefensePredictor discovered systems."
              }
            ]
          },
          {
            "subject": "ds_38_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "DS-38 system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
                "notes": "DeWeirdt et al. name validated TUs as DefensePredictor discovered systems."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| DS-38 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
                "notes": "The pinned DefenseFinder article registry maps the DS-38 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "ds-38-defensefinder-model-gap",
        "prompt": "Resolve DS-38 native host breadth, exact component activity, profile-to-protein mapping, HEPN ribonuclease interpretation, zinc-finger DNA-binding interpretation, complete phage breadth, molecular output, and rule-level DefenseFinder criteria before minting narrower DS-38 mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "DeWeirdt et al. support DS-38 as the defensive HEP2 transcriptional unit and final Science Tables S6/S7/S8 map it to one product accession, Bas25 and Bas19 phage readouts, display name DS-38, and high-probability HEPN and zinc-finger HHpred rows. The pinned DefenseFinder HMM inventory records one DS-38 custom profile row. The pinned rules table has no DS-38 row, and the first-pass record does not resolve native host breadth, complete phage breadth, direct profile-to-protein correspondence, HEPN ribonuclease activity, zinc-finger DNA-binding activity, molecular output, or endogenous DS-38 activity.",
        "evidence": [
          {
            "reference": "DOI:10.1126/science.adv7924",
            "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
            "notes": "DeWeirdt et al. name validated TUs as DSs."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
            "snippet": "HEP2\tNZ_QOYR01000034.1\tGCF_003333645.1\t-\tTrue\tFalse\tTrue\tTrue\tDefensePredictor hits\t8089\t9189\thypothetical protein\tWP_001313577.1\t8.026493157403\t2.649821696202418\tTrue\tTrue\tPredicted novel defense gene\tDS-38",
            "notes": "The final Science supplementary Table S6 maps working_id HEP2 to DS_name DS-38, marks the cloned transcriptional unit as defensive, and records NZ_QOYR01000034.1 positions 8089-9189 with product accession WP_001313577.1."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
            "snippet": "Bas25\t2.2\tpLAND\t24-03-12_EV.png\t500000\tHEP2\t24-03-15\t24-03-15_GPEH_HEP2_PDO1_PDP6.png\t0\t1\t\t1\t5.698970004336019\t\tTrue\t\tLB\t37",
            "notes": "The final Science supplementary Table S7 Systems sheet reports an HEP2 assay row with a Bas25 phage readout and a -log(EOP) value of 5.699."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
            "snippet": "Bas19\t2.2\tpLAND\t24-03-12_EV.png\t15000\tHEP2\t24-03-15\t24-03-15_GPEH_HEP2_PDO1_PDP6.png\t0\t1\t\t1\t4.176091259055681\t\tTrue\t\tLB\t37",
            "notes": "The final Science supplementary Table S7 Systems sheet reports an HEP2 assay row with a Bas19 phage readout and a -log(EOP) value of 4.176."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
            "snippet": "HEP2\tDS-38\tTrue",
            "notes": "The final Science supplementary Table S8 maps HEP2 to replicated display name DS-38."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
            "snippet": "HEP2\t1.0\t366.0\tWP_001313577.1\tZF\t8SSU_A\tTranscriptional repressor CTCF,LIM domain-binding protein 1; PROTEIN-DNA COMPLEX, DNA BINDING PROTEIN, transcription factor, zinc fingers, insulator/chromatin architecture, transcription-dna complex, TRANSCRIPTION\thhpred_7553560.hhr\t206.0\t364.0\t0.9902\t2024-04-15 00:00:00\t\t",
            "notes": "The final Science supplementary Table S8 reports a high-probability zinc-finger HHpred hit for WP_001313577.1 in HEP2."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
            "snippet": "HEP2\t1.0\t366.0\tWP_001313577.1\tHEPN\tPF05168.18\tHEPN ; HEPN domain\thhpred_7553560.hhr\t22.0\t153.0\t0.9662\t2024-04-15 00:00:00\t\t",
            "notes": "The final Science supplementary Table S8 reports a high-probability HEPN HHpred hit for WP_001313577.1 in HEP2."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
            "snippet": "| DS-38 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
            "notes": "The pinned DefenseFinder article registry maps the DS-38 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| DS-38__DS-38                                     |                                                  | DS-38                  | Custom                  | 200    |",
            "notes": "The pinned DefenseFinder HMM inventory records DS-38__DS-38 as a custom DS-38 profile."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "The pinned DefenseFinder rules table does not list DS-38, leaving rule-level detection criteria unresolved."
          }
        ],
        "attaches_to": [
          "causal_graphs#ds_38_locus_reduces_phage_plaquing"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-29"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-29T10:59:36Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted DS-38 system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; kept the graph at HEP2 transcriptional-unit level because the HEPN and zinc-finger rows and rule rows remain unresolved, and proposals/metpo_traitmech_v337 reserves the replacement placeholder.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-29T10:59:37Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed DS-38 system canonical_examples and left them empty because DeWeirdt et al. directly support cloned HEP2 assays in E. coli MG1655 and a DefenseFinder DS-38 model, but not a direct named native microbial isolate exemplar with experimentally verified endogenous DS-38 activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000461",
    "label": "DS-39 system",
    "definition": "A phage defense system in which an organism possesses the single-gene DefensePredictor-discovered system 39 locus cataloged as working transcriptional unit AAA5 and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.",
    "definition_source": "DOI:10.1126/science.adv7924",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "DS-39",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1126/science.adv7924"
      },
      {
        "synonym_text": "AAA5",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx"
      },
      {
        "synonym_text": "DS-39__DS-39",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1126/science.adv7924",
        "snippet": "To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
        "notes": "DeWeirdt et al. experimentally validated 42 predicted transcriptional units as phage-defense systems in E. coli."
      },
      {
        "reference": "DOI:10.1126/science.adv7924",
        "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
        "notes": "DeWeirdt et al. name validated transcriptional units as DefensePredictor discovered systems."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
        "snippet": "AAA5\tNZ_RRWS01000024.1\tGCF_003892555.1\t+\tTrue\tFalse\tTrue\tTrue\tDefensePredictor hits\t12586\t14718\tMarR family transcriptional regulator\tWP_042346724.1\t9.53722790980957\t3.842009204807092\tTrue\tTrue\tPredicted novel defense gene\tDS-39",
        "notes": "The final Science supplementary Table S6 maps working_id AAA5 to DS_name DS-39, marks the cloned transcriptional unit as defensive, and records NZ_RRWS01000024.1 positions 12586-14718 with product accession WP_042346724.1."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
        "snippet": "Bas1\t3.1\tpLAND\t24-04-10_CITO_AAA3_FDRT_EV.png\t5000000\tAAA5\t24-04-10\t24-04-10_HTHO_AAA5.png\t0\t1\t\t1\t6.698970004336019\t\tTrue\t\tLB\t37",
        "notes": "The final Science supplementary Table S7 Systems sheet reports an AAA5 assay row with a Bas1 phage readout and a -log(EOP) value of 6.699."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
        "snippet": "Bas3\t3.1\tpLAND\t24-04-10_CITO_AAA3_FDRT_EV.png\t200000000\tAAA5\t24-04-10\t24-04-10_HTHO_AAA5.png\t3\t7\tY\t7000\t4.455931955649724\t\tTrue\t\tLB\t37",
        "notes": "The final Science supplementary Table S7 Systems sheet reports an AAA5 assay row with a Bas3 phage readout and a -log(EOP) value of 4.456."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
        "snippet": "AAA5\tDS-39\tTrue",
        "notes": "The final Science supplementary Table S8 maps AAA5 to replicated display name DS-39."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
        "snippet": "AAA5\t1.0\t710.0\tWP_042346724.1\tAAA+ ATPase\t7MCA_I\tCell division control protein 6; replication initiation, REPLICATION\thhpred_6053627.hhr\t53.0\t540.0\t0.9852\t2024-04-15 00:00:00\t\t",
        "notes": "The final Science supplementary Table S8 reports a high-probability AAA+ ATPase HHpred hit for WP_042346724.1 in AAA5."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
        "snippet": "AAA5\t1.0\t710.0\tWP_042346724.1\tZF\tPF18256.5\tHscB_4_cys ; Co-chaperone HscB tetracysteine metal binding motif\thhpred_6053627.hhr\t583.0\t615.0\t0.87\t2024-04-15 00:00:00\t\t",
        "notes": "The final Science supplementary Table S8 reports a moderate-probability zinc-finger HHpred hit for WP_042346724.1 in AAA5."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
        "snippet": "AAA5\t1.0\t710.0\tWP_042346724.1\tHTH\t5HS5_B\tHTH-type transcriptional regulator SarX\thhpred_6053627.hhr\t623.0\t706.0\t0.98\t2024-04-15 00:00:00\t\t",
        "notes": "The final Science supplementary Table S8 reports a high-probability HTH HHpred hit for WP_042346724.1 in AAA5."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| DS-39 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
        "notes": "The pinned DefenseFinder article registry maps the DS-39 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| DS-39__DS-39                                     |                                                  | DS-39                  | Custom                  | 200    |",
        "notes": "The pinned DefenseFinder HMM inventory records DS-39__DS-39 as a custom DS-39 profile."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "ds_39_locus_reduces_phage_plaquing",
        "title": "DS-39 locus reduces bacteriophage plaquing",
        "description": "Conservative system-level sketch linking the single-gene DS-39 locus to reduced bacteriophage plaquing without resolving DS-39 component function or molecular output.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures DS-39 as the validated AAA5 transcriptional unit with one product accession, high-probability AAA+ ATPase and HTH HHpred rows for WP_042346724.1, a moderate-probability zinc-finger HHpred row for WP_042346724.1, and one DefenseFinder DS-39 profile row. It does not assert exact profile-to-protein correspondence, AAA+ ATPase activity, HTH DNA-binding activity, zinc-finger metal-binding activity, native host breadth, DS-39 molecular output, complete phage breadth, or DefenseFinder rule-level detection criteria.",
        "nodes": [
          {
            "node_id": "ds_39_locus",
            "label": "DS-39 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A single-gene DefensePredictor-discovered system 39 locus represented in the pinned DefenseFinder HMM inventory by one DS-39 custom profile."
          },
          {
            "node_id": "reduced_phage_plaquing",
            "label": "reduced bacteriophage plaquing",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced bacteriophage plaquing in cells carrying cloned AAA5."
          },
          {
            "node_id": "ds_39_system_trait",
            "label": "DS-39 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000461",
            "description": "Possession of a genome-encoded DS-39 phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "ds_39_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "reduced_phage_plaquing",
            "description": "The DS-39/AAA5 locus contributes to reduced bacteriophage plaquing in heterologous E. coli MG1655 plasmid-expression assays.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
                "notes": "DeWeirdt et al. describe the plasmid-based phage challenge used to validate predicted transcriptional units."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
                "snippet": "AAA5\tNZ_RRWS01000024.1\tGCF_003892555.1\t+\tTrue\tFalse\tTrue\tTrue\tDefensePredictor hits\t12586\t14718\tMarR family transcriptional regulator\tWP_042346724.1\t9.53722790980957\t3.842009204807092\tTrue\tTrue\tPredicted novel defense gene\tDS-39",
                "notes": "The final Science supplementary Table S6 maps working_id AAA5 to DS_name DS-39, marks the cloned transcriptional unit as defensive, and records NZ_RRWS01000024.1 positions 12586-14718 with product accession WP_042346724.1."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
                "snippet": "Bas1\t3.1\tpLAND\t24-04-10_CITO_AAA3_FDRT_EV.png\t5000000\tAAA5\t24-04-10\t24-04-10_HTHO_AAA5.png\t0\t1\t\t1\t6.698970004336019\t\tTrue\t\tLB\t37",
                "notes": "The final Science supplementary Table S7 Systems sheet reports an AAA5 assay row with a Bas1 phage readout and a -log(EOP) value of 6.699."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
                "snippet": "Bas3\t3.1\tpLAND\t24-04-10_CITO_AAA3_FDRT_EV.png\t200000000\tAAA5\t24-04-10\t24-04-10_HTHO_AAA5.png\t3\t7\tY\t7000\t4.455931955649724\t\tTrue\t\tLB\t37",
                "notes": "The final Science supplementary Table S7 Systems sheet reports an AAA5 assay row with a Bas3 phage readout and a -log(EOP) value of 4.456."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
                "snippet": "AAA5\tDS-39\tTrue",
                "notes": "The final Science supplementary Table S8 maps AAA5 to replicated display name DS-39."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
                "snippet": "AAA5\t1.0\t710.0\tWP_042346724.1\tAAA+ ATPase\t7MCA_I\tCell division control protein 6; replication initiation, REPLICATION\thhpred_6053627.hhr\t53.0\t540.0\t0.9852\t2024-04-15 00:00:00\t\t",
                "notes": "The final Science supplementary Table S8 reports a high-probability AAA+ ATPase HHpred hit for WP_042346724.1 in AAA5."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
                "snippet": "AAA5\t1.0\t710.0\tWP_042346724.1\tZF\tPF18256.5\tHscB_4_cys ; Co-chaperone HscB tetracysteine metal binding motif\thhpred_6053627.hhr\t583.0\t615.0\t0.87\t2024-04-15 00:00:00\t\t",
                "notes": "The final Science supplementary Table S8 reports a moderate-probability zinc-finger HHpred hit for WP_042346724.1 in AAA5."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
                "snippet": "AAA5\t1.0\t710.0\tWP_042346724.1\tHTH\t5HS5_B\tHTH-type transcriptional regulator SarX\thhpred_6053627.hhr\t623.0\t706.0\t0.98\t2024-04-15 00:00:00\t\t",
                "notes": "The final Science supplementary Table S8 reports a high-probability HTH HHpred hit for WP_042346724.1 in AAA5."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| DS-39__DS-39                                     |                                                  | DS-39                  | Custom                  | 200    |",
                "notes": "The pinned DefenseFinder HMM inventory records DS-39__DS-39 as a custom DS-39 profile."
              }
            ]
          },
          {
            "subject": "reduced_phage_plaquing",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "ds_39_system_trait",
            "description": "DS-39-mediated phage plaquing reduction realizes the DS-39 system trait.",
            "evidence": [
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
                "snippet": "AAA5\tNZ_RRWS01000024.1\tGCF_003892555.1\t+\tTrue\tFalse\tTrue\tTrue\tDefensePredictor hits\t12586\t14718\tMarR family transcriptional regulator\tWP_042346724.1\t9.53722790980957\t3.842009204807092\tTrue\tTrue\tPredicted novel defense gene\tDS-39",
                "notes": "The final Science supplementary Table S6 maps working_id AAA5 to DS_name DS-39, marks the cloned transcriptional unit as defensive, and records NZ_RRWS01000024.1 positions 12586-14718 with product accession WP_042346724.1."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
                "snippet": "Bas1\t3.1\tpLAND\t24-04-10_CITO_AAA3_FDRT_EV.png\t5000000\tAAA5\t24-04-10\t24-04-10_HTHO_AAA5.png\t0\t1\t\t1\t6.698970004336019\t\tTrue\t\tLB\t37",
                "notes": "The final Science supplementary Table S7 Systems sheet reports an AAA5 assay row with a Bas1 phage readout and a -log(EOP) value of 6.699."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
                "snippet": "Bas3\t3.1\tpLAND\t24-04-10_CITO_AAA3_FDRT_EV.png\t200000000\tAAA5\t24-04-10\t24-04-10_HTHO_AAA5.png\t3\t7\tY\t7000\t4.455931955649724\t\tTrue\t\tLB\t37",
                "notes": "The final Science supplementary Table S7 Systems sheet reports an AAA5 assay row with a Bas3 phage readout and a -log(EOP) value of 4.456."
              },
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
                "notes": "The DS nomenclature is used for DefensePredictor discovered systems."
              }
            ]
          },
          {
            "subject": "ds_39_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "DS-39 system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
                "notes": "DeWeirdt et al. name validated TUs as DefensePredictor discovered systems."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| DS-39 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
                "notes": "The pinned DefenseFinder article registry maps the DS-39 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "ds-39-defensefinder-model-gap",
        "prompt": "Resolve DS-39 native host breadth, exact component activity, profile-to-protein mapping, AAA+ ATPase interpretation, HTH/zinc-finger interpretation, complete phage breadth, molecular output, and rule-level DefenseFinder criteria before minting narrower DS-39 mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "DeWeirdt et al. support DS-39 as the defensive AAA5 transcriptional unit and final Science Tables S6/S7/S8 map it to one product accession, Bas1 and Bas3 phage readouts, display name DS-39, high-probability AAA+ ATPase and HTH HHpred rows, and a moderate-probability zinc-finger HHpred row. The pinned DefenseFinder HMM inventory records one DS-39 custom profile row. The pinned rules table has no DS-39 row, and the first-pass record does not resolve native host breadth, complete phage breadth, direct profile-to-protein correspondence, AAA+ ATPase activity, HTH or zinc-finger interpretation, molecular output, or endogenous DS-39 activity.",
        "evidence": [
          {
            "reference": "DOI:10.1126/science.adv7924",
            "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
            "notes": "DeWeirdt et al. name validated TUs as DSs."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
            "snippet": "AAA5\tNZ_RRWS01000024.1\tGCF_003892555.1\t+\tTrue\tFalse\tTrue\tTrue\tDefensePredictor hits\t12586\t14718\tMarR family transcriptional regulator\tWP_042346724.1\t9.53722790980957\t3.842009204807092\tTrue\tTrue\tPredicted novel defense gene\tDS-39",
            "notes": "The final Science supplementary Table S6 maps working_id AAA5 to DS_name DS-39, marks the cloned transcriptional unit as defensive, and records NZ_RRWS01000024.1 positions 12586-14718 with product accession WP_042346724.1."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
            "snippet": "Bas1\t3.1\tpLAND\t24-04-10_CITO_AAA3_FDRT_EV.png\t5000000\tAAA5\t24-04-10\t24-04-10_HTHO_AAA5.png\t0\t1\t\t1\t6.698970004336019\t\tTrue\t\tLB\t37",
            "notes": "The final Science supplementary Table S7 Systems sheet reports an AAA5 assay row with a Bas1 phage readout and a -log(EOP) value of 6.699."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
            "snippet": "Bas3\t3.1\tpLAND\t24-04-10_CITO_AAA3_FDRT_EV.png\t200000000\tAAA5\t24-04-10\t24-04-10_HTHO_AAA5.png\t3\t7\tY\t7000\t4.455931955649724\t\tTrue\t\tLB\t37",
            "notes": "The final Science supplementary Table S7 Systems sheet reports an AAA5 assay row with a Bas3 phage readout and a -log(EOP) value of 4.456."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
            "snippet": "AAA5\tDS-39\tTrue",
            "notes": "The final Science supplementary Table S8 maps AAA5 to replicated display name DS-39."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
            "snippet": "AAA5\t1.0\t710.0\tWP_042346724.1\tAAA+ ATPase\t7MCA_I\tCell division control protein 6; replication initiation, REPLICATION\thhpred_6053627.hhr\t53.0\t540.0\t0.9852\t2024-04-15 00:00:00\t\t",
            "notes": "The final Science supplementary Table S8 reports a high-probability AAA+ ATPase HHpred hit for WP_042346724.1 in AAA5."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
            "snippet": "AAA5\t1.0\t710.0\tWP_042346724.1\tZF\tPF18256.5\tHscB_4_cys ; Co-chaperone HscB tetracysteine metal binding motif\thhpred_6053627.hhr\t583.0\t615.0\t0.87\t2024-04-15 00:00:00\t\t",
            "notes": "The final Science supplementary Table S8 reports a moderate-probability zinc-finger HHpred hit for WP_042346724.1 in AAA5."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
            "snippet": "AAA5\t1.0\t710.0\tWP_042346724.1\tHTH\t5HS5_B\tHTH-type transcriptional regulator SarX\thhpred_6053627.hhr\t623.0\t706.0\t0.98\t2024-04-15 00:00:00\t\t",
            "notes": "The final Science supplementary Table S8 reports a high-probability HTH HHpred hit for WP_042346724.1 in AAA5."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
            "snippet": "| DS-39 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
            "notes": "The pinned DefenseFinder article registry maps the DS-39 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| DS-39__DS-39                                     |                                                  | DS-39                  | Custom                  | 200    |",
            "notes": "The pinned DefenseFinder HMM inventory records DS-39__DS-39 as a custom DS-39 profile."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "The pinned DefenseFinder rules table does not list DS-39, leaving rule-level detection criteria unresolved."
          }
        ],
        "attaches_to": [
          "causal_graphs#ds_39_locus_reduces_phage_plaquing"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-29"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-29T11:35:06Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted DS-39 system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; kept the graph at AAA5 transcriptional-unit level because the AAA+ ATPase, HTH, zinc-finger, and rule rows remain unresolved, and proposals/metpo_traitmech_v338 reserves the replacement placeholder.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-29T11:35:07Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed DS-39 system canonical_examples and left them empty because DeWeirdt et al. directly support cloned AAA5 assays in E. coli MG1655 and a DefenseFinder DS-39 model, but not a direct named native microbial isolate exemplar with experimentally verified endogenous DS-39 activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000426",
    "label": "DS-3 system",
    "definition": "A phage defense system in which an organism possesses the one-gene DefensePredictor-discovered system 3 locus cataloged as working transcriptional unit PIN8 and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.",
    "definition_source": "DOI:10.1126/science.adv7924",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "DS-3",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1126/science.adv7924"
      },
      {
        "synonym_text": "PIN8",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx"
      },
      {
        "synonym_text": "DS-3__DS-3",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1126/science.adv7924",
        "snippet": "To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
        "notes": "DeWeirdt et al. experimentally validated 42 predicted transcriptional units as phage-defense systems in E. coli."
      },
      {
        "reference": "DOI:10.1126/science.adv7924",
        "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
        "notes": "DeWeirdt et al. name validated transcriptional units as DefensePredictor discovered systems."
      },
      {
        "reference": "DOI:10.1126/science.adv7924",
        "snippet": "DS-3 is a one-protein system with a PIN ribonuclease domain split between its N and C-terminus",
        "notes": "DeWeirdt et al. describe DS-3 as a one-protein PIN ribonuclease-domain system."
      },
      {
        "reference": "DOI:10.1126/science.adv7924",
        "snippet": "When we mutated catalytic residues in DS-3, the system no longer defended against phage, suggesting this domain is essential for protection.",
        "notes": "DeWeirdt et al. report that mutating predicted catalytic residues removed DS-3-mediated phage defense."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
        "snippet": "PIN8\tNZ_RRWT01000005.1\tGCF_003892645.1\t+\tTrue\tFalse\tFalse\tTrue\tDefensePredictor hits\t244326\t245348\thypothetical protein\tWP_022645725.1\t8.909458355458062\t-2.350827761940385\tTrue\tFalse\tPredicted novel defense gene\tDS-3",
        "notes": "The final Science supplementary Table S6 maps working_id PIN8 to DS_name DS-3, marks the cloned transcriptional unit as defensive, and records NZ_RRWT01000005.1 positions 244326-245348 with product accession WP_022645725.1."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
        "snippet": "RB69\t1.1\tpLAND\t24-03-08_NYND_PIN2_MHAD_EV.png\t400000\tPIN8\t24-03-12\t24-03-12_PIN8_D390_NADR_PN12.png\t0\t1\t\t1\t5.6020599913279625\tTrue\t\t\tLB\t37",
        "notes": "The final Science supplementary Table S7 reports a PIN8 assay row with an RB69 readout and a -log(EOP) value of 5.602."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
        "snippet": "PIN8\tDS-3\tTrue",
        "notes": "The final Science supplementary Table S8 maps PIN8 to replicated display name DS-3."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| DS-3 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
        "notes": "The pinned DefenseFinder article registry maps the DS-3 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| DS-3__DS-3                                       |                                                  | DS-3                   | Custom                  | 50     |",
        "notes": "The pinned DefenseFinder HMM inventory records DS-3__DS-3 as a custom DS-3 profile."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "ds_3_locus_reduces_phage_plaquing",
        "title": "DS-3 locus reduces bacteriophage plaquing",
        "description": "Conservative system-level sketch linking the one-gene DS-3 locus to reduced bacteriophage plaquing without resolving DS-3 effector activity.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures DS-3 as the validated PIN8 transcriptional unit with one product accession and with a DefenseFinder DS-3 profile row. It does not assert native host breadth, exact profile-to-protein correspondence, the direct viral trigger or substrate, exact molecular output, phage target breadth, or DefenseFinder rule-level detection criteria.",
        "nodes": [
          {
            "node_id": "ds_3_locus",
            "label": "DS-3 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A one-gene DefensePredictor-discovered system locus represented in the pinned DefenseFinder HMM inventory by a custom DS-3 profile."
          },
          {
            "node_id": "reduced_phage_plaquing",
            "label": "reduced bacteriophage plaquing",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced efficiency of plaquing or reduced plaque size by bacteriophages in cells carrying cloned PIN8."
          },
          {
            "node_id": "ds_3_system_trait",
            "label": "DS-3 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000426",
            "description": "Possession of a genome-encoded DS-3 phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "ds_3_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "reduced_phage_plaquing",
            "description": "The DS-3/PIN8 locus contributes to reduced bacteriophage plaquing when plasmid expressed.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
                "notes": "DeWeirdt et al. experimentally validate DefensePredictor-discovered systems by assaying cloned transcriptional units against E. coli phages."
              },
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "When we mutated catalytic residues in DS-3, the system no longer defended against phage, suggesting this domain is essential for protection.",
                "notes": "DeWeirdt et al. show DS-3 protection depends on predicted catalytic residues."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
                "snippet": "PIN8\tNZ_RRWT01000005.1\tGCF_003892645.1\t+\tTrue\tFalse\tFalse\tTrue\tDefensePredictor hits\t244326\t245348\thypothetical protein\tWP_022645725.1\t8.909458355458062\t-2.350827761940385\tTrue\tFalse\tPredicted novel defense gene\tDS-3",
                "notes": "The final Science supplementary Table S6 maps working_id PIN8 to DS_name DS-3, marks the cloned transcriptional unit as defensive, and records NZ_RRWT01000005.1 positions 244326-245348 with product accession WP_022645725.1."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
                "snippet": "RB69\t1.1\tpLAND\t24-03-08_NYND_PIN2_MHAD_EV.png\t400000\tPIN8\t24-03-12\t24-03-12_PIN8_D390_NADR_PN12.png\t0\t1\t\t1\t5.6020599913279625\tTrue\t\t\tLB\t37",
                "notes": "The final Science supplementary Table S7 reports a PIN8 assay row with an RB69 readout and a -log(EOP) value of 5.602."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| DS-3__DS-3                                       |                                                  | DS-3                   | Custom                  | 50     |",
                "notes": "The pinned DefenseFinder HMM inventory records DS-3__DS-3 as a custom DS-3 profile."
              }
            ]
          },
          {
            "subject": "reduced_phage_plaquing",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "ds_3_system_trait",
            "description": "DS-3-mediated phage plaquing reduction realizes the DS-3 system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
                "notes": "DeWeirdt et al. name each validated transcriptional unit as a DefensePredictor discovered system."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
                "snippet": "PIN8\tNZ_RRWT01000005.1\tGCF_003892645.1\t+\tTrue\tFalse\tFalse\tTrue\tDefensePredictor hits\t244326\t245348\thypothetical protein\tWP_022645725.1\t8.909458355458062\t-2.350827761940385\tTrue\tFalse\tPredicted novel defense gene\tDS-3",
                "notes": "The final Science supplementary Table S6 maps working_id PIN8 to DS_name DS-3, marks the cloned transcriptional unit as defensive, and records NZ_RRWT01000005.1 positions 244326-245348 with product accession WP_022645725.1."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
                "snippet": "RB69\t1.1\tpLAND\t24-03-08_NYND_PIN2_MHAD_EV.png\t400000\tPIN8\t24-03-12\t24-03-12_PIN8_D390_NADR_PN12.png\t0\t1\t\t1\t5.6020599913279625\tTrue\t\t\tLB\t37",
                "notes": "The final Science supplementary Table S7 reports a PIN8 assay row with an RB69 readout and a -log(EOP) value of 5.602."
              }
            ]
          },
          {
            "subject": "ds_3_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "DS-3 system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
                "notes": "DeWeirdt et al. validate DSs as anti-phage systems."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| DS-3 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
                "notes": "The pinned DefenseFinder article registry maps the DS-3 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "ds-3-defensefinder-model-gap",
        "prompt": "Resolve DS-3 native host breadth, exact PIN ribonuclease activity, DS-3 profile-to-protein mapping, sensitive-phage breadth, molecular output, and rule-level detection criteria before minting narrower DS-3 mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "DeWeirdt et al. support DS-3 as the defensive PIN8 transcriptional unit that reduced plaquing when cloned in E. coli MG1655, and the pinned DefenseFinder HMM inventory records a DS-3 profile row. The pinned rules table has no DS-3 row, and the first-pass record does not resolve native host breadth, exact PIN substrate or output, profile-to-protein mapping, phage target breadth, or endogenous DS-3 activity.",
        "evidence": [
          {
            "reference": "DOI:10.1126/science.adv7924",
            "snippet": "To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
            "notes": "DeWeirdt et al. validate predicted transcriptional units by measuring plaquing relative to an empty vector control strain."
          },
          {
            "reference": "DOI:10.1126/science.adv7924",
            "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
            "notes": "DeWeirdt et al. name validated TUs as DSs."
          },
          {
            "reference": "DOI:10.1126/science.adv7924",
            "snippet": "DS-3 is a one-protein system with a PIN ribonuclease domain split between its N and C-terminus",
            "notes": "DeWeirdt et al. report a split PIN ribonuclease domain in the one-protein DS-3 system."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
            "snippet": "PIN8\tNZ_RRWT01000005.1\tGCF_003892645.1\t+\tTrue\tFalse\tFalse\tTrue\tDefensePredictor hits\t244326\t245348\thypothetical protein\tWP_022645725.1\t8.909458355458062\t-2.350827761940385\tTrue\tFalse\tPredicted novel defense gene\tDS-3",
            "notes": "The final Science supplementary Table S6 maps working_id PIN8 to DS_name DS-3, marks the cloned transcriptional unit as defensive, and records NZ_RRWT01000005.1 positions 244326-245348 with product accession WP_022645725.1."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
            "snippet": "RB69\t1.1\tpLAND\t24-03-08_NYND_PIN2_MHAD_EV.png\t400000\tPIN8\t24-03-12\t24-03-12_PIN8_D390_NADR_PN12.png\t0\t1\t\t1\t5.6020599913279625\tTrue\t\t\tLB\t37",
            "notes": "The final Science supplementary Table S7 reports a PIN8 assay row with an RB69 readout and a -log(EOP) value of 5.602."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
            "snippet": "PIN8\tDS-3\tTrue",
            "notes": "The final Science supplementary Table S8 maps PIN8 to replicated display name DS-3."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
            "snippet": "| DS-3 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
            "notes": "The pinned DefenseFinder article registry maps the DS-3 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| DS-3__DS-3                                       |                                                  | DS-3                   | Custom                  | 50     |",
            "notes": "The pinned DefenseFinder HMM inventory records DS-3__DS-3 as a custom DS-3 profile."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "The pinned DefenseFinder rules table does not list DS-3, leaving rule-level detection criteria unresolved."
          }
        ],
        "attaches_to": [
          "causal_graphs#ds_3_locus_reduces_phage_plaquing"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-28"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-28T05:06:03Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted DS-3 system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; kept the graph at cloned PIN8 transcriptional-unit level because the pinned DefenseFinder DS-3 HMM row is not backed by a rules row; proposals/metpo_traitmech_v303 reserves the replacement placeholder.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-28T05:06:04Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed DS-3 system canonical_examples and left them empty because DeWeirdt et al. support cloned PIN8 plaquing assays in E. coli MG1655 plus a DefenseFinder DS-3 model, but not a direct named native microbial isolate exemplar with experimentally verified endogenous DS-3 activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000462",
    "label": "DS-40 system",
    "definition": "A phage defense system in which an organism possesses the single-gene DefensePredictor-discovered system 40 locus cataloged as working transcriptional unit D295 and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.",
    "definition_source": "DOI:10.1126/science.adv7924",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "DS-40",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1126/science.adv7924"
      },
      {
        "synonym_text": "D295",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx"
      },
      {
        "synonym_text": "DS-40__DS-40",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1126/science.adv7924",
        "snippet": "To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
        "notes": "DeWeirdt et al. experimentally validated 42 predicted transcriptional units as phage-defense systems in E. coli."
      },
      {
        "reference": "DOI:10.1126/science.adv7924",
        "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
        "notes": "DeWeirdt et al. name validated transcriptional units as DefensePredictor discovered systems."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
        "snippet": "D295\tNZ_QOYF01000088.1\tGCF_003334585.1\t+\tTrue\tFalse\tTrue\tTrue\tDefensePredictor hits\t10328\t11263\thypothetical protein\tWP_097419291.1\t4.659671153870749\t1.141745659485685\tTrue\tTrue\tPredicted novel defense gene\tDS-40",
        "notes": "The final Science supplementary Table S6 maps working_id D295 to DS_name DS-40, marks the cloned transcriptional unit as defensive, and records NZ_QOYF01000088.1 positions 10328-11263 with product accession WP_097419291.1."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
        "snippet": "Bas26\t2.2\tpLAND\t24-03-12_EV.png\t2400000000\tD295\t24-03-14\t24-03-14_RED5_D295_6236_D932.png\t3\t100\tY\t100000\t4.380211241711606\t\tTrue\t\tLB\t37",
        "notes": "The final Science supplementary Table S7 Systems sheet reports a D295 assay row with a Bas26 phage readout and a -log(EOP) value of 4.380."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
        "snippet": "D295\tDS-40\tTrue",
        "notes": "The final Science supplementary Table S8 maps D295 to replicated display name DS-40."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
        "snippet": "D295\t1.0\t311.0\tWP_097419291.1\tDUF6680\tPF20385.2\tDUF6680 ; Family of unknown function (DUF6680)\thhpred_5944942.hhr\t27.0\t238.0\t0.7883\t2024-04-15 00:00:00\t\t",
        "notes": "The final Science supplementary Table S8 reports a moderate-probability DUF6680 HHpred hit for WP_097419291.1 in D295."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| DS-40 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
        "notes": "The pinned DefenseFinder article registry maps the DS-40 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| DS-40__DS-40                                     |                                                  | DS-40                  | Custom                  | 180    |",
        "notes": "The pinned DefenseFinder HMM inventory records DS-40__DS-40 as a custom DS-40 profile."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "ds_40_locus_reduces_phage_plaquing",
        "title": "DS-40 locus reduces bacteriophage plaquing",
        "description": "Conservative system-level sketch linking the single-gene DS-40 locus to reduced bacteriophage plaquing without resolving DS-40 component function or molecular output.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures DS-40 as the validated D295 transcriptional unit with one product accession, one moderate-probability DUF6680 HHpred row for WP_097419291.1, and one DefenseFinder DS-40 profile row. It does not assert exact profile-to-protein correspondence, DUF6680 activity, native host breadth, DS-40 molecular output, complete phage breadth, or DefenseFinder rule-level detection criteria.",
        "nodes": [
          {
            "node_id": "ds_40_locus",
            "label": "DS-40 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A single-gene DefensePredictor-discovered system 40 locus represented in the pinned DefenseFinder HMM inventory by one DS-40 custom profile."
          },
          {
            "node_id": "reduced_phage_plaquing",
            "label": "reduced bacteriophage plaquing",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced bacteriophage plaquing in cells carrying cloned D295."
          },
          {
            "node_id": "ds_40_system_trait",
            "label": "DS-40 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000462",
            "description": "Possession of a genome-encoded DS-40 phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "ds_40_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "reduced_phage_plaquing",
            "description": "The DS-40/D295 locus contributes to reduced bacteriophage plaquing in heterologous E. coli MG1655 plasmid-expression assays.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
                "notes": "DeWeirdt et al. describe the plasmid-based phage challenge used to validate predicted transcriptional units."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
                "snippet": "D295\tNZ_QOYF01000088.1\tGCF_003334585.1\t+\tTrue\tFalse\tTrue\tTrue\tDefensePredictor hits\t10328\t11263\thypothetical protein\tWP_097419291.1\t4.659671153870749\t1.141745659485685\tTrue\tTrue\tPredicted novel defense gene\tDS-40",
                "notes": "The final Science supplementary Table S6 maps working_id D295 to DS_name DS-40, marks the cloned transcriptional unit as defensive, and records NZ_QOYF01000088.1 positions 10328-11263 with product accession WP_097419291.1."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
                "snippet": "Bas26\t2.2\tpLAND\t24-03-12_EV.png\t2400000000\tD295\t24-03-14\t24-03-14_RED5_D295_6236_D932.png\t3\t100\tY\t100000\t4.380211241711606\t\tTrue\t\tLB\t37",
                "notes": "The final Science supplementary Table S7 Systems sheet reports a D295 assay row with a Bas26 phage readout and a -log(EOP) value of 4.380."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
                "snippet": "D295\tDS-40\tTrue",
                "notes": "The final Science supplementary Table S8 maps D295 to replicated display name DS-40."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
                "snippet": "D295\t1.0\t311.0\tWP_097419291.1\tDUF6680\tPF20385.2\tDUF6680 ; Family of unknown function (DUF6680)\thhpred_5944942.hhr\t27.0\t238.0\t0.7883\t2024-04-15 00:00:00\t\t",
                "notes": "The final Science supplementary Table S8 reports a moderate-probability DUF6680 HHpred hit for WP_097419291.1 in D295."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| DS-40__DS-40                                     |                                                  | DS-40                  | Custom                  | 180    |",
                "notes": "The pinned DefenseFinder HMM inventory records DS-40__DS-40 as a custom DS-40 profile."
              }
            ]
          },
          {
            "subject": "reduced_phage_plaquing",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "ds_40_system_trait",
            "description": "DS-40-mediated phage plaquing reduction realizes the DS-40 system trait.",
            "evidence": [
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
                "snippet": "D295\tNZ_QOYF01000088.1\tGCF_003334585.1\t+\tTrue\tFalse\tTrue\tTrue\tDefensePredictor hits\t10328\t11263\thypothetical protein\tWP_097419291.1\t4.659671153870749\t1.141745659485685\tTrue\tTrue\tPredicted novel defense gene\tDS-40",
                "notes": "The final Science supplementary Table S6 maps working_id D295 to DS_name DS-40, marks the cloned transcriptional unit as defensive, and records NZ_QOYF01000088.1 positions 10328-11263 with product accession WP_097419291.1."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
                "snippet": "Bas26\t2.2\tpLAND\t24-03-12_EV.png\t2400000000\tD295\t24-03-14\t24-03-14_RED5_D295_6236_D932.png\t3\t100\tY\t100000\t4.380211241711606\t\tTrue\t\tLB\t37",
                "notes": "The final Science supplementary Table S7 Systems sheet reports a D295 assay row with a Bas26 phage readout and a -log(EOP) value of 4.380."
              },
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
                "notes": "The DS nomenclature is used for DefensePredictor discovered systems."
              }
            ]
          },
          {
            "subject": "ds_40_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "DS-40 system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
                "notes": "DeWeirdt et al. name validated TUs as DefensePredictor discovered systems."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| DS-40 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
                "notes": "The pinned DefenseFinder article registry maps the DS-40 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "ds-40-defensefinder-model-gap",
        "prompt": "Resolve DS-40 native host breadth, exact component activity, profile-to-protein mapping, DUF6680 interpretation, complete phage breadth, molecular output, and rule-level DefenseFinder criteria before minting narrower DS-40 mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "DeWeirdt et al. support DS-40 as the defensive D295 transcriptional unit and final Science Tables S6/S7/S8 map it to one product accession, a Bas26 phage readout, display name DS-40, and a moderate-probability DUF6680 HHpred row. The pinned DefenseFinder HMM inventory records one DS-40 custom profile row. The pinned rules table has no DS-40 row, and the first-pass record does not resolve native host breadth, complete phage breadth, direct profile-to-protein correspondence, DUF6680 activity, molecular output, or endogenous DS-40 activity.",
        "evidence": [
          {
            "reference": "DOI:10.1126/science.adv7924",
            "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
            "notes": "DeWeirdt et al. name validated TUs as DSs."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
            "snippet": "D295\tNZ_QOYF01000088.1\tGCF_003334585.1\t+\tTrue\tFalse\tTrue\tTrue\tDefensePredictor hits\t10328\t11263\thypothetical protein\tWP_097419291.1\t4.659671153870749\t1.141745659485685\tTrue\tTrue\tPredicted novel defense gene\tDS-40",
            "notes": "The final Science supplementary Table S6 maps working_id D295 to DS_name DS-40, marks the cloned transcriptional unit as defensive, and records NZ_QOYF01000088.1 positions 10328-11263 with product accession WP_097419291.1."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
            "snippet": "Bas26\t2.2\tpLAND\t24-03-12_EV.png\t2400000000\tD295\t24-03-14\t24-03-14_RED5_D295_6236_D932.png\t3\t100\tY\t100000\t4.380211241711606\t\tTrue\t\tLB\t37",
            "notes": "The final Science supplementary Table S7 Systems sheet reports a D295 assay row with a Bas26 phage readout and a -log(EOP) value of 4.380."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
            "snippet": "D295\tDS-40\tTrue",
            "notes": "The final Science supplementary Table S8 maps D295 to replicated display name DS-40."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
            "snippet": "D295\t1.0\t311.0\tWP_097419291.1\tDUF6680\tPF20385.2\tDUF6680 ; Family of unknown function (DUF6680)\thhpred_5944942.hhr\t27.0\t238.0\t0.7883\t2024-04-15 00:00:00\t\t",
            "notes": "The final Science supplementary Table S8 reports a moderate-probability DUF6680 HHpred hit for WP_097419291.1 in D295."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
            "snippet": "| DS-40 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
            "notes": "The pinned DefenseFinder article registry maps the DS-40 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| DS-40__DS-40                                     |                                                  | DS-40                  | Custom                  | 180    |",
            "notes": "The pinned DefenseFinder HMM inventory records DS-40__DS-40 as a custom DS-40 profile."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "The pinned DefenseFinder rules table does not list DS-40, leaving rule-level detection criteria unresolved."
          }
        ],
        "attaches_to": [
          "causal_graphs#ds_40_locus_reduces_phage_plaquing"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-29"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-29T12:02:12Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted DS-40 system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; kept the graph at D295 transcriptional-unit level because DUF6680 activity and rule rows remain unresolved, and proposals/metpo_traitmech_v339 reserves the replacement placeholder.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-29T12:02:13Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed DS-40 system canonical_examples and left them empty because DeWeirdt et al. directly support cloned D295 assays in E. coli MG1655 and a DefenseFinder DS-40 model, but not a direct named native microbial isolate exemplar with experimentally verified endogenous DS-40 activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000463",
    "label": "DS-41 system",
    "definition": "A phage defense system in which an organism possesses the single-gene DefensePredictor-discovered system 41 locus cataloged as working transcriptional unit AAA2 and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.",
    "definition_source": "DOI:10.1126/science.adv7924",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "DS-41",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1126/science.adv7924"
      },
      {
        "synonym_text": "AAA2",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx"
      },
      {
        "synonym_text": "DS-41__DS-41",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1126/science.adv7924",
        "snippet": "To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
        "notes": "DeWeirdt et al. experimentally validated 42 predicted transcriptional units as phage-defense systems in E. coli."
      },
      {
        "reference": "DOI:10.1126/science.adv7924",
        "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
        "notes": "DeWeirdt et al. name validated transcriptional units as DefensePredictor discovered systems."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
        "snippet": "AAA2\tNZ_QOYD01000024.1\tGCF_003333765.1\t-\tTrue\tFalse\tFalse\tTrue\tDefensePredictor hits\t5322\t6830\thypothetical protein\tWP_033812887.1\t7.980074950371131\t4.119037174812478\tTrue\tTrue\tRemote defense homolog\tDS-41",
        "notes": "The final Science supplementary Table S6 maps working_id AAA2 to DS_name DS-41, marks the cloned transcriptional unit as defensive, and records NZ_QOYD01000024.1 positions 5322-6830 with product accession WP_033812887.1."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
        "snippet": "Bas1\t6.1\tpLAND\t24-07-17_MVB1_VPUS_VAME_EV.png\t3000000\tAAA2\t24-07-17\t24-07-17_AAA2_RMOR_NERD_NUCS.png\t1\t3\t\t30\t5\t\t\tTrue\tLB\t37",
        "notes": "The final Science supplementary Table S7 Systems sheet reports an AAA2 assay row with a Bas1 phage readout and a -log(EOP) value of 5."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
        "snippet": "T4\t6.2\tpLAND\t24-07-17_AAA2_VPUS_VAME_EV.png\t20000000\tAAA2\t24-07-17\t24-07-17_AAA2_VPUS_VAME_EV.png\t1\t10\t\t100\t5.301029995663981\t\t\tTrue\tLB\t37",
        "notes": "The final Science supplementary Table S7 Systems sheet reports an AAA2 assay row with a T4 phage readout and a -log(EOP) value of 5.301."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
        "snippet": "AAA2\tDS-41\tTrue",
        "notes": "The final Science supplementary Table S8 maps AAA2 to replicated display name DS-41."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
        "snippet": "AAA2\t1.0\t502.0\tWP_033812887.1\tAAA+ ATPase\t2QBY_A\tCell division control protein 6 homolog 1; winged-helix domain, helix-turn-helix, AAA+ ATPase domain\thhpred_7261390.hhr\t8.0\t488.0\t0.996\t2024-07-29 00:00:00\t\t",
        "notes": "The final Science supplementary Table S8 reports a high-probability AAA+ ATPase HHpred hit for WP_033812887.1 in AAA2."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| DS-41 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
        "notes": "The pinned DefenseFinder article registry maps the DS-41 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| DS-41__DS-41                                     |                                                  | DS-41                  | Custom                  | 200    |",
        "notes": "The pinned DefenseFinder HMM inventory records DS-41__DS-41 as a custom DS-41 profile."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "ds_41_locus_reduces_phage_plaquing",
        "title": "DS-41 locus reduces bacteriophage plaquing",
        "description": "Conservative system-level sketch linking the single-gene DS-41 locus to reduced bacteriophage plaquing without resolving DS-41 component function or molecular output.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures DS-41 as the validated AAA2 transcriptional unit with one product accession, one high-probability AAA+ ATPase HHpred row for WP_033812887.1, and one DefenseFinder DS-41 profile row. It does not assert exact profile-to-protein correspondence, AAA+ ATPase activity, native host breadth, DS-41 molecular output, complete phage breadth, or DefenseFinder rule-level detection criteria.",
        "nodes": [
          {
            "node_id": "ds_41_locus",
            "label": "DS-41 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A single-gene DefensePredictor-discovered system 41 locus represented in the pinned DefenseFinder HMM inventory by one DS-41 custom profile."
          },
          {
            "node_id": "reduced_phage_plaquing",
            "label": "reduced bacteriophage plaquing",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced bacteriophage plaquing in cells carrying cloned AAA2."
          },
          {
            "node_id": "ds_41_system_trait",
            "label": "DS-41 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000463",
            "description": "Possession of a genome-encoded DS-41 phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "ds_41_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "reduced_phage_plaquing",
            "description": "The DS-41/AAA2 locus contributes to reduced bacteriophage plaquing in heterologous E. coli MG1655 plasmid-expression assays.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
                "notes": "DeWeirdt et al. describe the plasmid-based phage challenge used to validate predicted transcriptional units."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
                "snippet": "AAA2\tNZ_QOYD01000024.1\tGCF_003333765.1\t-\tTrue\tFalse\tFalse\tTrue\tDefensePredictor hits\t5322\t6830\thypothetical protein\tWP_033812887.1\t7.980074950371131\t4.119037174812478\tTrue\tTrue\tRemote defense homolog\tDS-41",
                "notes": "The final Science supplementary Table S6 maps working_id AAA2 to DS_name DS-41, marks the cloned transcriptional unit as defensive, and records NZ_QOYD01000024.1 positions 5322-6830 with product accession WP_033812887.1."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
                "snippet": "Bas1\t6.1\tpLAND\t24-07-17_MVB1_VPUS_VAME_EV.png\t3000000\tAAA2\t24-07-17\t24-07-17_AAA2_RMOR_NERD_NUCS.png\t1\t3\t\t30\t5\t\t\tTrue\tLB\t37",
                "notes": "The final Science supplementary Table S7 Systems sheet reports an AAA2 assay row with a Bas1 phage readout and a -log(EOP) value of 5."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
                "snippet": "T4\t6.2\tpLAND\t24-07-17_AAA2_VPUS_VAME_EV.png\t20000000\tAAA2\t24-07-17\t24-07-17_AAA2_VPUS_VAME_EV.png\t1\t10\t\t100\t5.301029995663981\t\t\tTrue\tLB\t37",
                "notes": "The final Science supplementary Table S7 Systems sheet reports an AAA2 assay row with a T4 phage readout and a -log(EOP) value of 5.301."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
                "snippet": "AAA2\tDS-41\tTrue",
                "notes": "The final Science supplementary Table S8 maps AAA2 to replicated display name DS-41."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
                "snippet": "AAA2\t1.0\t502.0\tWP_033812887.1\tAAA+ ATPase\t2QBY_A\tCell division control protein 6 homolog 1; winged-helix domain, helix-turn-helix, AAA+ ATPase domain\thhpred_7261390.hhr\t8.0\t488.0\t0.996\t2024-07-29 00:00:00\t\t",
                "notes": "The final Science supplementary Table S8 reports a high-probability AAA+ ATPase HHpred hit for WP_033812887.1 in AAA2."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| DS-41__DS-41                                     |                                                  | DS-41                  | Custom                  | 200    |",
                "notes": "The pinned DefenseFinder HMM inventory records DS-41__DS-41 as a custom DS-41 profile."
              }
            ]
          },
          {
            "subject": "reduced_phage_plaquing",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "ds_41_system_trait",
            "description": "DS-41-mediated phage plaquing reduction realizes the DS-41 system trait.",
            "evidence": [
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
                "snippet": "AAA2\tNZ_QOYD01000024.1\tGCF_003333765.1\t-\tTrue\tFalse\tFalse\tTrue\tDefensePredictor hits\t5322\t6830\thypothetical protein\tWP_033812887.1\t7.980074950371131\t4.119037174812478\tTrue\tTrue\tRemote defense homolog\tDS-41",
                "notes": "The final Science supplementary Table S6 maps working_id AAA2 to DS_name DS-41, marks the cloned transcriptional unit as defensive, and records NZ_QOYD01000024.1 positions 5322-6830 with product accession WP_033812887.1."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
                "snippet": "Bas1\t6.1\tpLAND\t24-07-17_MVB1_VPUS_VAME_EV.png\t3000000\tAAA2\t24-07-17\t24-07-17_AAA2_RMOR_NERD_NUCS.png\t1\t3\t\t30\t5\t\t\tTrue\tLB\t37",
                "notes": "The final Science supplementary Table S7 Systems sheet reports an AAA2 assay row with a Bas1 phage readout and a -log(EOP) value of 5."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
                "snippet": "T4\t6.2\tpLAND\t24-07-17_AAA2_VPUS_VAME_EV.png\t20000000\tAAA2\t24-07-17\t24-07-17_AAA2_VPUS_VAME_EV.png\t1\t10\t\t100\t5.301029995663981\t\t\tTrue\tLB\t37",
                "notes": "The final Science supplementary Table S7 Systems sheet reports an AAA2 assay row with a T4 phage readout and a -log(EOP) value of 5.301."
              },
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
                "notes": "The DS nomenclature is used for DefensePredictor discovered systems."
              }
            ]
          },
          {
            "subject": "ds_41_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "DS-41 system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
                "notes": "DeWeirdt et al. name validated TUs as DefensePredictor discovered systems."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| DS-41 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
                "notes": "The pinned DefenseFinder article registry maps the DS-41 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "ds-41-defensefinder-model-gap",
        "prompt": "Resolve DS-41 native host breadth, exact component activity, profile-to-protein mapping, AAA+ ATPase interpretation, complete phage breadth, molecular output, and rule-level DefenseFinder criteria before minting narrower DS-41 mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "DeWeirdt et al. support DS-41 as the defensive AAA2 transcriptional unit and final Science Tables S6/S7/S8 map it to one product accession, Bas1 and T4 phage readouts, display name DS-41, and a high-probability AAA+ ATPase HHpred row. The pinned DefenseFinder HMM inventory records one DS-41 custom profile row. The pinned rules table has no DS-41 row, and the first-pass record does not resolve native host breadth, complete phage breadth, direct profile-to-protein correspondence, AAA+ ATPase activity, molecular output, or endogenous DS-41 activity.",
        "evidence": [
          {
            "reference": "DOI:10.1126/science.adv7924",
            "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
            "notes": "DeWeirdt et al. name validated TUs as DSs."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
            "snippet": "AAA2\tNZ_QOYD01000024.1\tGCF_003333765.1\t-\tTrue\tFalse\tFalse\tTrue\tDefensePredictor hits\t5322\t6830\thypothetical protein\tWP_033812887.1\t7.980074950371131\t4.119037174812478\tTrue\tTrue\tRemote defense homolog\tDS-41",
            "notes": "The final Science supplementary Table S6 maps working_id AAA2 to DS_name DS-41, marks the cloned transcriptional unit as defensive, and records NZ_QOYD01000024.1 positions 5322-6830 with product accession WP_033812887.1."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
            "snippet": "Bas1\t6.1\tpLAND\t24-07-17_MVB1_VPUS_VAME_EV.png\t3000000\tAAA2\t24-07-17\t24-07-17_AAA2_RMOR_NERD_NUCS.png\t1\t3\t\t30\t5\t\t\tTrue\tLB\t37",
            "notes": "The final Science supplementary Table S7 Systems sheet reports an AAA2 assay row with a Bas1 phage readout and a -log(EOP) value of 5."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
            "snippet": "T4\t6.2\tpLAND\t24-07-17_AAA2_VPUS_VAME_EV.png\t20000000\tAAA2\t24-07-17\t24-07-17_AAA2_VPUS_VAME_EV.png\t1\t10\t\t100\t5.301029995663981\t\t\tTrue\tLB\t37",
            "notes": "The final Science supplementary Table S7 Systems sheet reports an AAA2 assay row with a T4 phage readout and a -log(EOP) value of 5.301."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
            "snippet": "AAA2\tDS-41\tTrue",
            "notes": "The final Science supplementary Table S8 maps AAA2 to replicated display name DS-41."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
            "snippet": "AAA2\t1.0\t502.0\tWP_033812887.1\tAAA+ ATPase\t2QBY_A\tCell division control protein 6 homolog 1; winged-helix domain, helix-turn-helix, AAA+ ATPase domain\thhpred_7261390.hhr\t8.0\t488.0\t0.996\t2024-07-29 00:00:00\t\t",
            "notes": "The final Science supplementary Table S8 reports a high-probability AAA+ ATPase HHpred hit for WP_033812887.1 in AAA2."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
            "snippet": "| DS-41 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
            "notes": "The pinned DefenseFinder article registry maps the DS-41 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| DS-41__DS-41                                     |                                                  | DS-41                  | Custom                  | 200    |",
            "notes": "The pinned DefenseFinder HMM inventory records DS-41__DS-41 as a custom DS-41 profile."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "The pinned DefenseFinder rules table does not list DS-41, leaving rule-level detection criteria unresolved."
          }
        ],
        "attaches_to": [
          "causal_graphs#ds_41_locus_reduces_phage_plaquing"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-29"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-29T12:49:10Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted DS-41 system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; kept the graph at AAA2 transcriptional-unit level because AAA+ ATPase activity and rule rows remain unresolved, and proposals/metpo_traitmech_v340 reserves the replacement placeholder.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-29T12:49:11Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed DS-41 system canonical_examples and left them empty because DeWeirdt et al. directly support cloned AAA2 assays in E. coli MG1655 and a DefenseFinder DS-41 model, but not a direct named native microbial isolate exemplar with experimentally verified endogenous DS-41 activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000464",
    "label": "DS-42 system",
    "definition": "A phage defense system in which an organism possesses the three-gene DefensePredictor-discovered system 42 locus cataloged as working transcriptional unit PRO1 and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.",
    "definition_source": "DOI:10.1126/science.adv7924",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "DS-42",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1126/science.adv7924"
      },
      {
        "synonym_text": "PRO1",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx"
      },
      {
        "synonym_text": "DS-42__DS-42A",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "DS-42__DS-42B",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "DS-42__DS-42C",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1126/science.adv7924",
        "snippet": "To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
        "notes": "DeWeirdt et al. experimentally validated 42 predicted transcriptional units as phage-defense systems in E. coli."
      },
      {
        "reference": "DOI:10.1126/science.adv7924",
        "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
        "notes": "DeWeirdt et al. name validated transcriptional units as DefensePredictor discovered systems."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
        "snippet": "PRO1\tNZ_QOXO01000016.1\tGCF_003334005.1\t-\tTrue\tFalse\tTrue\tTrue\tDefensePredictor hits\t661\t3061\tMBL fold metallo-hydrolase, hypothetical protein, hypothetical protein\tWP_001198055.1, WP_001024069.1, WP_249925928.1\t4.870544869418898\t6.906754778648663\tTrue\tTrue\tPredicted novel defense gene\tDS-42",
        "notes": "The final Science supplementary Table S6 maps working_id PRO1 to DS_name DS-42, marks the cloned transcriptional unit as defensive, and records NZ_QOXO01000016.1 positions 661-3061 with product accessions WP_001198055.1, WP_001024069.1, and WP_249925928.1."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
        "snippet": "Bas1\t3.1\tpLAND\t24-04-10_CITO_AAA3_FDRT_EV.png\t5000000\tPRO1\t24-04-13\t24-04-13_PRO1_CBT2_AAA4_TMRA.png\t5\t4\tY\t400000\t1.0969100130080565\t\tTrue\t\tLB\t37",
        "notes": "The final Science supplementary Table S7 Systems sheet reports a PRO1 assay row with a Bas1 phage readout and a -log(EOP) value of 1.097."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
        "snippet": "PRO1\tDS-42\tTrue",
        "notes": "The final Science supplementary Table S8 maps PRO1 to replicated display name DS-42."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
        "snippet": "PRO1\t3.0\t363.0\tWP_001198055.1\tMBL hydrolase\tcd07731\tComA-like_MBL-fold; Competence protein ComA, ComEC and related proteins\thhpred_9048500.hhr\t12.0\t251.0\t0.998\t2024-04-15 00:00:00\t\t",
        "notes": "The final Science supplementary Table S8 reports a high-probability MBL hydrolase HHpred hit for WP_001198055.1 in PRO1."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
        "snippet": "PRO1\t2.0\t190.0\tWP_001024069.1\tDimerization\tPF16892.9\tCHS5_N ; Chitin biosynthesis protein CHS5 N-terminus\thhpred_3514574.hhr\t108.0\t166.0\t0.7787\t2024-04-15 00:00:00\t\t",
        "notes": "The final Science supplementary Table S8 reports a moderate-probability CHS5_N/Dimerization HHpred hit for WP_001024069.1 in PRO1."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| DS-42 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
        "notes": "The pinned DefenseFinder article registry maps the DS-42 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| DS-42__DS-42A                                    |                                                  | DS-42                  | Custom                  | 70     |",
        "notes": "The pinned DefenseFinder HMM inventory records DS-42__DS-42A as a custom DS-42 profile."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| DS-42__DS-42B                                    |                                                  | DS-42                  | Custom                  | 20     |",
        "notes": "The pinned DefenseFinder HMM inventory records DS-42__DS-42B as a custom DS-42 profile."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| DS-42__DS-42C                                    |                                                  | DS-42                  | Custom                  | 200    |",
        "notes": "The pinned DefenseFinder HMM inventory records DS-42__DS-42C as a custom DS-42 profile."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "ds_42_locus_reduces_phage_plaquing",
        "title": "DS-42 locus reduces bacteriophage plaquing",
        "description": "Conservative system-level sketch linking the three-gene DS-42 locus to reduced bacteriophage plaquing without resolving DS-42 component function or molecular output.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures DS-42 as the validated PRO1 transcriptional unit with three product accessions, a high-probability MBL hydrolase HHpred row for WP_001198055.1, a moderate-probability CHS5_N/Dimerization HHpred row for WP_001024069.1, and three DefenseFinder DS-42 profile rows. It does not assert native host breadth, exact profile-to-protein correspondence, MBL hydrolase or CHS5_N interpretation, WP_249925928.1 function, DS-42 molecular activity, complete phage breadth, or DefenseFinder rule-level detection criteria.",
        "nodes": [
          {
            "node_id": "ds_42_locus",
            "label": "DS-42 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A three-gene DefensePredictor-discovered system 42 locus represented in the pinned DefenseFinder HMM inventory by three DS-42 custom profiles."
          },
          {
            "node_id": "reduced_phage_plaquing",
            "label": "reduced bacteriophage plaquing",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced bacteriophage plaquing in cells carrying cloned PRO1."
          },
          {
            "node_id": "ds_42_system_trait",
            "label": "DS-42 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000464",
            "description": "Possession of a genome-encoded DS-42 phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "ds_42_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "reduced_phage_plaquing",
            "description": "The DS-42/PRO1 locus contributes to reduced bacteriophage plaquing in heterologous E. coli MG1655 plasmid-expression assays.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
                "notes": "DeWeirdt et al. describe the plasmid-based phage challenge used to validate predicted transcriptional units."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
                "snippet": "PRO1\tNZ_QOXO01000016.1\tGCF_003334005.1\t-\tTrue\tFalse\tTrue\tTrue\tDefensePredictor hits\t661\t3061\tMBL fold metallo-hydrolase, hypothetical protein, hypothetical protein\tWP_001198055.1, WP_001024069.1, WP_249925928.1\t4.870544869418898\t6.906754778648663\tTrue\tTrue\tPredicted novel defense gene\tDS-42",
                "notes": "The final Science supplementary Table S6 maps working_id PRO1 to DS_name DS-42, marks the cloned transcriptional unit as defensive, and records NZ_QOXO01000016.1 positions 661-3061 with product accessions WP_001198055.1, WP_001024069.1, and WP_249925928.1."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
                "snippet": "Bas1\t3.1\tpLAND\t24-04-10_CITO_AAA3_FDRT_EV.png\t5000000\tPRO1\t24-04-13\t24-04-13_PRO1_CBT2_AAA4_TMRA.png\t5\t4\tY\t400000\t1.0969100130080565\t\tTrue\t\tLB\t37",
                "notes": "The final Science supplementary Table S7 Systems sheet reports a PRO1 assay row with a Bas1 phage readout and a -log(EOP) value of 1.097."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
                "snippet": "PRO1\tDS-42\tTrue",
                "notes": "The final Science supplementary Table S8 maps PRO1 to replicated display name DS-42."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
                "snippet": "PRO1\t3.0\t363.0\tWP_001198055.1\tMBL hydrolase\tcd07731\tComA-like_MBL-fold; Competence protein ComA, ComEC and related proteins\thhpred_9048500.hhr\t12.0\t251.0\t0.998\t2024-04-15 00:00:00\t\t",
                "notes": "The final Science supplementary Table S8 reports a high-probability MBL hydrolase HHpred hit for WP_001198055.1 in PRO1."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
                "snippet": "PRO1\t2.0\t190.0\tWP_001024069.1\tDimerization\tPF16892.9\tCHS5_N ; Chitin biosynthesis protein CHS5 N-terminus\thhpred_3514574.hhr\t108.0\t166.0\t0.7787\t2024-04-15 00:00:00\t\t",
                "notes": "The final Science supplementary Table S8 reports a moderate-probability CHS5_N/Dimerization HHpred hit for WP_001024069.1 in PRO1."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| DS-42__DS-42A                                    |                                                  | DS-42                  | Custom                  | 70     |",
                "notes": "The pinned DefenseFinder HMM inventory records DS-42__DS-42A as a custom DS-42 profile."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| DS-42__DS-42B                                    |                                                  | DS-42                  | Custom                  | 20     |",
                "notes": "The pinned DefenseFinder HMM inventory records DS-42__DS-42B as a custom DS-42 profile."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| DS-42__DS-42C                                    |                                                  | DS-42                  | Custom                  | 200    |",
                "notes": "The pinned DefenseFinder HMM inventory records DS-42__DS-42C as a custom DS-42 profile."
              }
            ]
          },
          {
            "subject": "reduced_phage_plaquing",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "ds_42_system_trait",
            "description": "DS-42-mediated phage plaquing reduction realizes the DS-42 system trait.",
            "evidence": [
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
                "snippet": "PRO1\tNZ_QOXO01000016.1\tGCF_003334005.1\t-\tTrue\tFalse\tTrue\tTrue\tDefensePredictor hits\t661\t3061\tMBL fold metallo-hydrolase, hypothetical protein, hypothetical protein\tWP_001198055.1, WP_001024069.1, WP_249925928.1\t4.870544869418898\t6.906754778648663\tTrue\tTrue\tPredicted novel defense gene\tDS-42",
                "notes": "The final Science supplementary Table S6 maps working_id PRO1 to DS_name DS-42, marks the cloned transcriptional unit as defensive, and records NZ_QOXO01000016.1 positions 661-3061 with product accessions WP_001198055.1, WP_001024069.1, and WP_249925928.1."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
                "snippet": "Bas1\t3.1\tpLAND\t24-04-10_CITO_AAA3_FDRT_EV.png\t5000000\tPRO1\t24-04-13\t24-04-13_PRO1_CBT2_AAA4_TMRA.png\t5\t4\tY\t400000\t1.0969100130080565\t\tTrue\t\tLB\t37",
                "notes": "The final Science supplementary Table S7 Systems sheet reports a PRO1 assay row with a Bas1 phage readout and a -log(EOP) value of 1.097."
              },
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
                "notes": "The DS nomenclature is used for DefensePredictor discovered systems."
              }
            ]
          },
          {
            "subject": "ds_42_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "DS-42 system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
                "notes": "DeWeirdt et al. name validated TUs as DefensePredictor discovered systems."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| DS-42 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
                "notes": "The pinned DefenseFinder article registry maps the DS-42 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "ds-42-defensefinder-model-gap",
        "prompt": "Resolve DS-42 native host breadth, exact component activity, profile-to-protein mapping, MBL hydrolase and CHS5_N interpretations, WP_249925928.1 function, complete phage breadth, molecular output, and rule-level DefenseFinder criteria before minting narrower DS-42 mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "DeWeirdt et al. support DS-42 as the defensive PRO1 transcriptional unit and final Science Tables S6/S7/S8 map it to three product accessions, a Bas1 phage readout, display name DS-42, a high-probability MBL hydrolase HHpred row, and a moderate-probability CHS5_N/Dimerization HHpred row. The pinned DefenseFinder HMM inventory records three DS-42 custom profile rows. The pinned rules table has no DS-42 row, and the first-pass record does not resolve native host breadth, complete phage breadth, direct profile-to-protein correspondence, component activities, molecular output, or endogenous DS-42 activity.",
        "evidence": [
          {
            "reference": "DOI:10.1126/science.adv7924",
            "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
            "notes": "DeWeirdt et al. name validated TUs as DSs."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
            "snippet": "PRO1\tNZ_QOXO01000016.1\tGCF_003334005.1\t-\tTrue\tFalse\tTrue\tTrue\tDefensePredictor hits\t661\t3061\tMBL fold metallo-hydrolase, hypothetical protein, hypothetical protein\tWP_001198055.1, WP_001024069.1, WP_249925928.1\t4.870544869418898\t6.906754778648663\tTrue\tTrue\tPredicted novel defense gene\tDS-42",
            "notes": "The final Science supplementary Table S6 maps working_id PRO1 to DS_name DS-42, marks the cloned transcriptional unit as defensive, and records NZ_QOXO01000016.1 positions 661-3061 with product accessions WP_001198055.1, WP_001024069.1, and WP_249925928.1."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
            "snippet": "Bas1\t3.1\tpLAND\t24-04-10_CITO_AAA3_FDRT_EV.png\t5000000\tPRO1\t24-04-13\t24-04-13_PRO1_CBT2_AAA4_TMRA.png\t5\t4\tY\t400000\t1.0969100130080565\t\tTrue\t\tLB\t37",
            "notes": "The final Science supplementary Table S7 Systems sheet reports a PRO1 assay row with a Bas1 phage readout and a -log(EOP) value of 1.097."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
            "snippet": "PRO1\tDS-42\tTrue",
            "notes": "The final Science supplementary Table S8 maps PRO1 to replicated display name DS-42."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
            "snippet": "PRO1\t3.0\t363.0\tWP_001198055.1\tMBL hydrolase\tcd07731\tComA-like_MBL-fold; Competence protein ComA, ComEC and related proteins\thhpred_9048500.hhr\t12.0\t251.0\t0.998\t2024-04-15 00:00:00\t\t",
            "notes": "The final Science supplementary Table S8 reports a high-probability MBL hydrolase HHpred hit for WP_001198055.1 in PRO1."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
            "snippet": "PRO1\t2.0\t190.0\tWP_001024069.1\tDimerization\tPF16892.9\tCHS5_N ; Chitin biosynthesis protein CHS5 N-terminus\thhpred_3514574.hhr\t108.0\t166.0\t0.7787\t2024-04-15 00:00:00\t\t",
            "notes": "The final Science supplementary Table S8 reports a moderate-probability CHS5_N/Dimerization HHpred hit for WP_001024069.1 in PRO1."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
            "snippet": "| DS-42 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
            "notes": "The pinned DefenseFinder article registry maps the DS-42 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| DS-42__DS-42A                                    |                                                  | DS-42                  | Custom                  | 70     |",
            "notes": "The pinned DefenseFinder HMM inventory records DS-42__DS-42A as a custom DS-42 profile."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| DS-42__DS-42B                                    |                                                  | DS-42                  | Custom                  | 20     |",
            "notes": "The pinned DefenseFinder HMM inventory records DS-42__DS-42B as a custom DS-42 profile."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| DS-42__DS-42C                                    |                                                  | DS-42                  | Custom                  | 200    |",
            "notes": "The pinned DefenseFinder HMM inventory records DS-42__DS-42C as a custom DS-42 profile."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "The pinned DefenseFinder rules table does not list DS-42, leaving rule-level detection criteria unresolved."
          }
        ],
        "attaches_to": [
          "causal_graphs#ds_42_locus_reduces_phage_plaquing"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-29"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-29T13:30:52Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted DS-42 system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; kept the graph at PRO1 transcriptional-unit level because component activities and rule rows remain unresolved, and proposals/metpo_traitmech_v341 reserves the replacement placeholder.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-29T13:30:53Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed DS-42 system canonical_examples and left them empty because DeWeirdt et al. directly support cloned PRO1 assays in E. coli MG1655 and a DefenseFinder DS-42 model, but not a direct named native microbial isolate exemplar with experimentally verified endogenous DS-42 activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000468",
    "label": "DS-43 system",
    "definition": "A phage defense system in which an organism possesses the single-gene DefensePredictor-discovered system 43 locus cataloged as working transcriptional unit D668 and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.",
    "definition_source": "DOI:10.1126/science.adv7924",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "DS-43",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1126/science.adv7924"
      },
      {
        "synonym_text": "D668",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx"
      },
      {
        "synonym_text": "DS-43__DS-43",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1126/science.adv7924",
        "snippet": "To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
        "notes": "DeWeirdt et al. experimentally validated 42 predicted transcriptional units as phage-defense systems in E. coli."
      },
      {
        "reference": "DOI:10.1126/science.adv7924",
        "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
        "notes": "DeWeirdt et al. name validated transcriptional units as DefensePredictor discovered systems."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
        "snippet": "D668\tNZ_QOYT01000001.1\tGCF_003333565.1\t+\tTrue\tFalse\tFalse\tTrue\tDefensePredictor hits\t7759\t8424\thypothetical protein\tWP_001057122.1\t4.944206899546769\t0.2289954698821485\tTrue\tTrue\tStructural defense homolog\tDS-43",
        "notes": "The final Science supplementary Table S6 maps working_id D668 to DS_name DS-43, marks the cloned transcriptional unit as defensive, and records NZ_QOYT01000001.1 positions 7759-8424 with product accession WP_001057122.1."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
        "snippet": "Bas19\t6.1\tpLAND\t24-07-17_MVB1_VPUS_VAME_EV.png\t2200000\tD668\t24-07-19\t24-07-19_D668_RMAP_HJRS_GBPR.png\t0\t1\t\t1\t6.342422680822207\t\t\tTrue\tLB\t37",
        "notes": "The final Science supplementary Table S7 Systems sheet reports a D668 assay row with a Bas19 phage readout and a -log(EOP) value of 6.342."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
        "snippet": "SECphi18\t6.2\tpLAND\t24-07-17_AAA2_VPUS_VAME_EV.png\t1300000000\tD668\t24-07-19\t24-07-19_RMAP_D668_HJRS_ZAPB.png\t3\t10\t\t10000\t5.113943352306837\t\t\tTrue\tLB\t37",
        "notes": "The final Science supplementary Table S7 Systems sheet reports a D668 assay row with a SECphi18 phage readout and a -log(EOP) value of 5.114."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
        "snippet": "D668\tDS-43\tTrue",
        "notes": "The final Science supplementary Table S8 maps D668 to replicated display name DS-43."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| DS-43 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
        "notes": "The pinned DefenseFinder article registry maps the DS-43 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| DS-43__DS-43                                     |                                                  | DS-43                  | Custom                  | 150    |",
        "notes": "The pinned DefenseFinder HMM inventory records DS-43__DS-43 as a custom DS-43 profile."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "ds_43_locus_reduces_phage_plaquing",
        "title": "DS-43 locus reduces bacteriophage plaquing",
        "description": "Conservative system-level sketch linking the single-gene DS-43 locus to reduced bacteriophage plaquing without resolving DS-43 component function or molecular output.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures DS-43 as the validated D668 transcriptional unit with one product accession and one DefenseFinder DS-43 profile row. It does not assert exact profile-to-protein correspondence, native host breadth, DS-43 molecular output, complete phage breadth, or DefenseFinder rule-level detection criteria.",
        "nodes": [
          {
            "node_id": "ds_43_locus",
            "label": "DS-43 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A single-gene DefensePredictor-discovered system 43 locus represented in the pinned DefenseFinder HMM inventory by one DS-43 custom profile."
          },
          {
            "node_id": "reduced_phage_plaquing",
            "label": "reduced bacteriophage plaquing",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced bacteriophage plaquing in cells carrying cloned D668."
          },
          {
            "node_id": "ds_43_system_trait",
            "label": "DS-43 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000468",
            "description": "Possession of a genome-encoded DS-43 phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "ds_43_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "reduced_phage_plaquing",
            "description": "The DS-43/D668 locus contributes to reduced bacteriophage plaquing in heterologous E. coli MG1655 plasmid-expression assays.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
                "notes": "DeWeirdt et al. describe the plasmid-based phage challenge used to validate predicted transcriptional units."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
                "snippet": "D668\tNZ_QOYT01000001.1\tGCF_003333565.1\t+\tTrue\tFalse\tFalse\tTrue\tDefensePredictor hits\t7759\t8424\thypothetical protein\tWP_001057122.1\t4.944206899546769\t0.2289954698821485\tTrue\tTrue\tStructural defense homolog\tDS-43",
                "notes": "The final Science supplementary Table S6 maps working_id D668 to DS_name DS-43, marks the cloned transcriptional unit as defensive, and records NZ_QOYT01000001.1 positions 7759-8424 with product accession WP_001057122.1."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
                "snippet": "Bas19\t6.1\tpLAND\t24-07-17_MVB1_VPUS_VAME_EV.png\t2200000\tD668\t24-07-19\t24-07-19_D668_RMAP_HJRS_GBPR.png\t0\t1\t\t1\t6.342422680822207\t\t\tTrue\tLB\t37",
                "notes": "The final Science supplementary Table S7 Systems sheet reports a D668 assay row with a Bas19 phage readout and a -log(EOP) value of 6.342."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
                "snippet": "SECphi18\t6.2\tpLAND\t24-07-17_AAA2_VPUS_VAME_EV.png\t1300000000\tD668\t24-07-19\t24-07-19_RMAP_D668_HJRS_ZAPB.png\t3\t10\t\t10000\t5.113943352306837\t\t\tTrue\tLB\t37",
                "notes": "The final Science supplementary Table S7 Systems sheet reports a D668 assay row with a SECphi18 phage readout and a -log(EOP) value of 5.114."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
                "snippet": "D668\tDS-43\tTrue",
                "notes": "The final Science supplementary Table S8 maps D668 to replicated display name DS-43."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| DS-43__DS-43                                     |                                                  | DS-43                  | Custom                  | 150    |",
                "notes": "The pinned DefenseFinder HMM inventory records DS-43__DS-43 as a custom DS-43 profile."
              }
            ]
          },
          {
            "subject": "reduced_phage_plaquing",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "ds_43_system_trait",
            "description": "DS-43-mediated phage plaquing reduction realizes the DS-43 system trait.",
            "evidence": [
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
                "snippet": "D668\tNZ_QOYT01000001.1\tGCF_003333565.1\t+\tTrue\tFalse\tFalse\tTrue\tDefensePredictor hits\t7759\t8424\thypothetical protein\tWP_001057122.1\t4.944206899546769\t0.2289954698821485\tTrue\tTrue\tStructural defense homolog\tDS-43",
                "notes": "The final Science supplementary Table S6 maps working_id D668 to DS_name DS-43, marks the cloned transcriptional unit as defensive, and records NZ_QOYT01000001.1 positions 7759-8424 with product accession WP_001057122.1."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
                "snippet": "Bas19\t6.1\tpLAND\t24-07-17_MVB1_VPUS_VAME_EV.png\t2200000\tD668\t24-07-19\t24-07-19_D668_RMAP_HJRS_GBPR.png\t0\t1\t\t1\t6.342422680822207\t\t\tTrue\tLB\t37",
                "notes": "The final Science supplementary Table S7 Systems sheet reports a D668 assay row with a Bas19 phage readout and a -log(EOP) value of 6.342."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
                "snippet": "SECphi18\t6.2\tpLAND\t24-07-17_AAA2_VPUS_VAME_EV.png\t1300000000\tD668\t24-07-19\t24-07-19_RMAP_D668_HJRS_ZAPB.png\t3\t10\t\t10000\t5.113943352306837\t\t\tTrue\tLB\t37",
                "notes": "The final Science supplementary Table S7 Systems sheet reports a D668 assay row with a SECphi18 phage readout and a -log(EOP) value of 5.114."
              },
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
                "notes": "The DS nomenclature is used for DefensePredictor discovered systems."
              }
            ]
          },
          {
            "subject": "ds_43_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "DS-43 system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
                "notes": "DeWeirdt et al. name validated TUs as DefensePredictor discovered systems."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| DS-43 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
                "notes": "The pinned DefenseFinder article registry maps the DS-43 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "ds-43-defensefinder-model-gap",
        "prompt": "Resolve DS-43 native host breadth, exact component activity, profile-to-protein mapping, complete phage breadth, molecular output, and rule-level DefenseFinder criteria before minting narrower DS-43 mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "DeWeirdt et al. support DS-43 as the defensive D668 transcriptional unit and final Science Tables S6/S7/S8 map it to one product accession, Bas19 and SECphi18 phage readouts, and display name DS-43. The pinned DefenseFinder HMM inventory records one DS-43 custom profile row. The pinned rules table has no DS-43 row, and the first-pass record does not resolve native host breadth, complete phage breadth, direct profile-to-protein correspondence, molecular output, or endogenous DS-43 activity.",
        "evidence": [
          {
            "reference": "DOI:10.1126/science.adv7924",
            "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
            "notes": "DeWeirdt et al. name validated TUs as DSs."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
            "snippet": "D668\tNZ_QOYT01000001.1\tGCF_003333565.1\t+\tTrue\tFalse\tFalse\tTrue\tDefensePredictor hits\t7759\t8424\thypothetical protein\tWP_001057122.1\t4.944206899546769\t0.2289954698821485\tTrue\tTrue\tStructural defense homolog\tDS-43",
            "notes": "The final Science supplementary Table S6 maps working_id D668 to DS_name DS-43, marks the cloned transcriptional unit as defensive, and records NZ_QOYT01000001.1 positions 7759-8424 with product accession WP_001057122.1."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
            "snippet": "Bas19\t6.1\tpLAND\t24-07-17_MVB1_VPUS_VAME_EV.png\t2200000\tD668\t24-07-19\t24-07-19_D668_RMAP_HJRS_GBPR.png\t0\t1\t\t1\t6.342422680822207\t\t\tTrue\tLB\t37",
            "notes": "The final Science supplementary Table S7 Systems sheet reports a D668 assay row with a Bas19 phage readout and a -log(EOP) value of 6.342."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
            "snippet": "SECphi18\t6.2\tpLAND\t24-07-17_AAA2_VPUS_VAME_EV.png\t1300000000\tD668\t24-07-19\t24-07-19_RMAP_D668_HJRS_ZAPB.png\t3\t10\t\t10000\t5.113943352306837\t\t\tTrue\tLB\t37",
            "notes": "The final Science supplementary Table S7 Systems sheet reports a D668 assay row with a SECphi18 phage readout and a -log(EOP) value of 5.114."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
            "snippet": "D668\tDS-43\tTrue",
            "notes": "The final Science supplementary Table S8 maps D668 to replicated display name DS-43."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
            "snippet": "| DS-43 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
            "notes": "The pinned DefenseFinder article registry maps the DS-43 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| DS-43__DS-43                                     |                                                  | DS-43                  | Custom                  | 150    |",
            "notes": "The pinned DefenseFinder HMM inventory records DS-43__DS-43 as a custom DS-43 profile."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "The pinned DefenseFinder rules table does not list DS-43, leaving rule-level detection criteria unresolved."
          }
        ],
        "attaches_to": [
          "causal_graphs#ds_43_locus_reduces_phage_plaquing"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-29"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-29T16:06:36Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted DS-43 system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; kept the graph at D668 transcriptional-unit level because component activity and rule rows remain unresolved, and proposals/metpo_traitmech_v345 reserves the replacement placeholder.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-29T16:06:37Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed DS-43 system canonical_examples and left them empty because DeWeirdt et al. directly support cloned D668 assays in E. coli MG1655 and a DefenseFinder DS-43 model, but not a direct named native microbial isolate exemplar with experimentally verified endogenous DS-43 activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000475",
    "label": "DS-44 system",
    "definition": "A phage defense system in which an organism possesses a genome-encoded DefensePredictor-discovered system 44 locus represented in the pinned DefenseFinder model inventory by the DS-44 custom HMM profile.",
    "definition_source": "DOI:10.1101/2025.01.08.631726",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "DS-44",
        "synonym_type": "EXACT_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      },
      {
        "synonym_text": "DS-44__DS-44",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1101/2025.01.08.631726",
        "snippet": "To test for anti-phage defense, we placed each TU with its native promoter region on a low-copy number plasmid in E. coli MG1655 and then challenged these strains with a panel of 24 diverse E. coli phages (fig. S2). In total, 45 (42% of 106) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
        "notes": "DeWeirdt et al. experimentally validated 45 predicted transcriptional units as phage-defense systems in E. coli; the first-pass DS-44 record uses this source only for the DefensePredictor DS naming context, not for an exact DS-44 phage readout."
      },
      {
        "reference": "DOI:10.1101/2025.01.08.631726",
        "snippet": "We refer to these validated TUs as DefensePredictor discovered Systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
        "notes": "DeWeirdt et al. name validated transcriptional units as DefensePredictor discovered Systems."
      },
      {
        "reference": "DOI:10.1101/2025.01.08.631726",
        "snippet": "To begin elucidating the function of the 45 validated TUs, we further annotated their protein domains (see Methods; table S6).",
        "notes": "DeWeirdt et al. describe Table S6 as a protein-domain annotation table for the validated DS transcriptional units; the exact preprint DS-44 row was not recovered in this curation pass."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| DS-44 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
        "notes": "The pinned DefenseFinder article registry maps the DS-44 source key to the DeWeirdt et al. DefensePredictor preprint."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| DS-44__DS-44                                     |                                                  | DS-44                  | Custom                  | 200    |",
        "notes": "The pinned DefenseFinder HMM inventory records DS-44__DS-44 as a custom DS-44 profile."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "ds_44_locus_profile_model",
        "title": "DS-44 locus profile model",
        "description": "Conservative system-level sketch linking the DS-44 DefensePredictor-discovered system key to DS-44 system possession and the broader phage-defense-system trait without resolving DS-44 component function or a phage activity readout.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures DS-44 as a DefensePredictor-discovered system with a DS-44 custom HMM row in the pinned DefenseFinder HMM inventory. It does not assert the preprint working identifier, preprint Table S5/S6 rows, final Science supplement rows, native host breadth, profile-to-protein correspondence, DS-44 molecular activity, exact phage target breadth, or DefenseFinder rule-level detection criteria.",
        "nodes": [
          {
            "node_id": "ds_44_locus",
            "label": "DS-44 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A DefensePredictor-discovered system 44 locus represented in the pinned DefenseFinder HMM inventory by the DS-44 custom profile."
          },
          {
            "node_id": "ds_44_system_trait",
            "label": "DS-44 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000475",
            "description": "Possession of a genome-encoded DS-44 phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "ds_44_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "ds_44_system_trait",
            "description": "DefenseFinder links the DS-44 source key to the DefensePredictor preprint and represents DS-44 in the HMM inventory with a DS-44 custom profile.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| DS-44 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
                "notes": "The pinned DefenseFinder article registry maps the DS-44 source key to the DeWeirdt et al. DefensePredictor preprint."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| DS-44__DS-44                                     |                                                  | DS-44                  | Custom                  | 200    |",
                "notes": "The pinned DefenseFinder HMM inventory records DS-44__DS-44 as a custom DS-44 profile."
              }
            ]
          },
          {
            "subject": "ds_44_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "DS-44 system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1101/2025.01.08.631726",
                "snippet": "We refer to these validated TUs as DefensePredictor discovered Systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
                "notes": "DeWeirdt et al. name validated TUs as DefensePredictor discovered Systems."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| DS-44 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
                "notes": "The pinned DefenseFinder article registry maps the DS-44 source key to the DeWeirdt et al. DefensePredictor preprint."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "ds-44-defensefinder-model-gap",
        "prompt": "Resolve DS-44 working-identifier rows, preprint Table S5 and S6 context, final Science supplement omission, native host breadth, DS-44 profile-to-protein mapping, sensitive-phage breadth, molecular output, and rule-level DefenseFinder criteria before minting narrower DS-44 mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "The DeWeirdt et al. preprint supports the DefensePredictor discovered System naming convention, the pinned DefenseFinder article registry names DS-44 and maps it to that preprint, and the pinned HMM inventory records a DS-44 custom profile row. DS-44 is absent from the final Science Table S6, S7, and S8 files checked during this curation pass, the exact preprint per-TU row was not recovered, the pinned DefenseFinder rules table has no DS-44 row, and the first-pass record does not resolve the working identifier, assayed phages, phage readout, native host, profile-to-component mapping, component activities, or complete detection criteria.",
        "evidence": [
          {
            "reference": "DOI:10.1101/2025.01.08.631726",
            "snippet": "To test for anti-phage defense, we placed each TU with its native promoter region on a low-copy number plasmid in E. coli MG1655 and then challenged these strains with a panel of 24 diverse E. coli phages (fig. S2). In total, 45 (42% of 106) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
            "notes": "DeWeirdt et al. validate predicted transcriptional units by measuring plaquing relative to an empty vector control strain."
          },
          {
            "reference": "DOI:10.1101/2025.01.08.631726",
            "snippet": "We refer to these validated TUs as DefensePredictor discovered Systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
            "notes": "DeWeirdt et al. name validated TUs as DSs."
          },
          {
            "reference": "DOI:10.1101/2025.01.08.631726",
            "snippet": "To begin elucidating the function of the 45 validated TUs, we further annotated their protein domains (see Methods; table S6).",
            "notes": "DeWeirdt et al. describe Table S6 as further protein-domain annotation of validated TUs."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
            "snippet": "| DS-44 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
            "notes": "The pinned DefenseFinder article registry maps the DS-44 source key to the DeWeirdt et al. DefensePredictor preprint."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| DS-44__DS-44                                     |                                                  | DS-44                  | Custom                  | 200    |",
            "notes": "The pinned DefenseFinder HMM inventory records DS-44__DS-44 as a custom DS-44 profile."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "The pinned DefenseFinder rules table does not list DS-44 or DS-44__DS-44, leaving complete component coverage and rule-level detection criteria unresolved."
          }
        ],
        "attaches_to": [
          "causal_graphs#ds_44_locus_profile_model"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-29"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-29T21:52:17Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted DS-44 system as a DOI- and DefenseFinder-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; kept the graph at DS-44 source-key and HMM-profile level because preprint Table S5/S6 rows, final Science supplement rows, and rule rows remain unresolved, and proposals/metpo_traitmech_v352 reserves the replacement placeholder.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-29T21:52:18Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed DS-44 system canonical_examples and left them empty because the pinned DefenseFinder registries support DS-44 system identity and custom HMM coverage but not a direct named native microbial isolate exemplar with experimentally verified endogenous DS-44 activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000469",
    "label": "DS-45 system",
    "definition": "A phage defense system in which an organism possesses the single-gene DefensePredictor-discovered system 45 locus cataloged as working transcriptional unit 2971 and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.",
    "definition_source": "DOI:10.1126/science.adv7924",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "DS-45",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1126/science.adv7924"
      },
      {
        "synonym_text": "2971",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx"
      },
      {
        "synonym_text": "DS-45__DS-45",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1126/science.adv7924",
        "snippet": "To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
        "notes": "DeWeirdt et al. experimentally validated 42 predicted transcriptional units as phage-defense systems in E. coli."
      },
      {
        "reference": "DOI:10.1126/science.adv7924",
        "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
        "notes": "DeWeirdt et al. name validated transcriptional units as DefensePredictor discovered systems."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
        "snippet": "2971\tNZ_QOYQ01000002.1\tGCF_003334555.1\t-\tTrue\tFalse\tTrue\tTrue\tDefensePredictor hits\t13159\t13704\thypothetical protein\tWP_223151192.1\t1.37181361625243\t-1.373840900048604\tTrue\tFalse\tStructural defense homolog\tDS-45",
        "notes": "The final Science supplementary Table S6 maps working_id 2971 to DS_name DS-45, marks the cloned transcriptional unit as defensive, and records NZ_QOYQ01000002.1 positions 13159-13704 with product accession WP_223151192.1."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
        "snippet": "Bas50\t2.2\tpLAND\t24-03-12_EV.png\t10000000000\t2971\t24-03-13\t24-03-13_2971_HEP3_TMP4.png\t7\t14\tY\t140000000\t1.853871964321762\t\tTrue\t\tLB\t37",
        "notes": "The final Science supplementary Table S7 Systems sheet reports a 2971 assay row with a Bas50 phage readout, a smaller-plaque-size call, and a -log(EOP) value of 1.854."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
        "snippet": "2971\tDS-45\tTrue",
        "notes": "The final Science supplementary Table S8 maps 2971 to replicated display name DS-45."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
        "snippet": "2971\t1.0\t181.0\tWP_223151192.1\tDUF2971\tPF11185.12\tDUF2971 ; Protein of unknown function (DUF2971)\thhpred_2594846.hhr\t58.0\t129.0\t0.9694\t2024-04-15 00:00:00",
        "notes": "The final Science supplementary Table S8 reports a high-probability DUF2971 HHpred hit for WP_223151192.1 in working_id 2971."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| DS-45 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
        "notes": "The pinned DefenseFinder article registry maps the DS-45 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| DS-45__DS-45                                     |                                                  | DS-45                  | Custom                  | 200    |",
        "notes": "The pinned DefenseFinder HMM inventory records DS-45__DS-45 as a custom DS-45 profile."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "ds_45_locus_reduces_phage_plaquing",
        "title": "DS-45 locus reduces bacteriophage plaquing",
        "description": "Conservative system-level sketch linking the single-gene DS-45 locus to reduced bacteriophage plaquing without resolving DS-45 component function or molecular output.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures DS-45 as the validated 2971 transcriptional unit with one product accession, one high-probability DUF2971 HHpred-domain row, and one DefenseFinder DS-45 profile row. It does not assert native host breadth, exact profile-to-protein correspondence, DS-45 molecular activity, complete phage breadth, DUF2971-domain interpretation, or DefenseFinder rule-level detection criteria.",
        "nodes": [
          {
            "node_id": "ds_45_locus",
            "label": "DS-45 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A single-gene DefensePredictor-discovered system 45 locus represented in the pinned DefenseFinder HMM inventory by one DS-45 custom profile."
          },
          {
            "node_id": "reduced_phage_plaquing",
            "label": "reduced bacteriophage plaquing",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced bacteriophage plaquing in cells carrying cloned 2971."
          },
          {
            "node_id": "ds_45_system_trait",
            "label": "DS-45 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000469",
            "description": "Possession of a genome-encoded DS-45 phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "ds_45_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "reduced_phage_plaquing",
            "description": "The DS-45/2971 locus contributes to reduced bacteriophage plaquing in heterologous E. coli MG1655 plasmid-expression assays.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
                "notes": "DeWeirdt et al. describe the plasmid-based phage challenge used to validate predicted transcriptional units."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
                "snippet": "2971\tNZ_QOYQ01000002.1\tGCF_003334555.1\t-\tTrue\tFalse\tTrue\tTrue\tDefensePredictor hits\t13159\t13704\thypothetical protein\tWP_223151192.1\t1.37181361625243\t-1.373840900048604\tTrue\tFalse\tStructural defense homolog\tDS-45",
                "notes": "The final Science supplementary Table S6 maps working_id 2971 to DS_name DS-45, marks the cloned transcriptional unit as defensive, and records NZ_QOYQ01000002.1 positions 13159-13704 with product accession WP_223151192.1."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
                "snippet": "Bas50\t2.2\tpLAND\t24-03-12_EV.png\t10000000000\t2971\t24-03-13\t24-03-13_2971_HEP3_TMP4.png\t7\t14\tY\t140000000\t1.853871964321762\t\tTrue\t\tLB\t37",
                "notes": "The final Science supplementary Table S7 Systems sheet reports a 2971 assay row with a Bas50 phage readout, a smaller-plaque-size call, and a -log(EOP) value of 1.854."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
                "snippet": "2971\tDS-45\tTrue",
                "notes": "The final Science supplementary Table S8 maps 2971 to replicated display name DS-45."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
                "snippet": "2971\t1.0\t181.0\tWP_223151192.1\tDUF2971\tPF11185.12\tDUF2971 ; Protein of unknown function (DUF2971)\thhpred_2594846.hhr\t58.0\t129.0\t0.9694\t2024-04-15 00:00:00",
                "notes": "The final Science supplementary Table S8 reports a high-probability DUF2971 HHpred hit for WP_223151192.1 in working_id 2971."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| DS-45__DS-45                                     |                                                  | DS-45                  | Custom                  | 200    |",
                "notes": "The pinned DefenseFinder HMM inventory records DS-45__DS-45 as a custom DS-45 profile."
              }
            ]
          },
          {
            "subject": "reduced_phage_plaquing",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "ds_45_system_trait",
            "description": "DS-45-mediated phage plaquing reduction realizes the DS-45 system trait.",
            "evidence": [
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
                "snippet": "2971\tNZ_QOYQ01000002.1\tGCF_003334555.1\t-\tTrue\tFalse\tTrue\tTrue\tDefensePredictor hits\t13159\t13704\thypothetical protein\tWP_223151192.1\t1.37181361625243\t-1.373840900048604\tTrue\tFalse\tStructural defense homolog\tDS-45",
                "notes": "The final Science supplementary Table S6 maps working_id 2971 to DS_name DS-45, marks the cloned transcriptional unit as defensive, and records NZ_QOYQ01000002.1 positions 13159-13704 with product accession WP_223151192.1."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
                "snippet": "Bas50\t2.2\tpLAND\t24-03-12_EV.png\t10000000000\t2971\t24-03-13\t24-03-13_2971_HEP3_TMP4.png\t7\t14\tY\t140000000\t1.853871964321762\t\tTrue\t\tLB\t37",
                "notes": "The final Science supplementary Table S7 Systems sheet reports a 2971 assay row with a Bas50 phage readout, a smaller-plaque-size call, and a -log(EOP) value of 1.854."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
                "snippet": "2971\tDS-45\tTrue",
                "notes": "The final Science supplementary Table S8 maps 2971 to replicated display name DS-45."
              },
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
                "notes": "The DS nomenclature is used for DefensePredictor discovered systems."
              }
            ]
          },
          {
            "subject": "ds_45_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "DS-45 system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
                "notes": "DeWeirdt et al. name validated TUs as DefensePredictor discovered systems."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| DS-45 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
                "notes": "The pinned DefenseFinder article registry maps the DS-45 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "ds-45-defensefinder-model-gap",
        "prompt": "Resolve DS-45 native host breadth, DUF2971-domain activity, profile-to-protein mapping, complete phage breadth, molecular output, and rule-level DefenseFinder criteria before minting narrower DS-45 mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "DeWeirdt et al. support DS-45 as the defensive 2971 transcriptional unit and final Science Tables S6/S7/S8 map it to one product accession, a Bas50 phage readout, one DUF2971 HHpred-domain row, and display name DS-45. The pinned DefenseFinder HMM inventory records one DS-45 custom profile row. The pinned rules table has no DS-45 row, and the first-pass record does not resolve native host breadth, complete phage breadth, direct profile-to-protein correspondence, molecular output, or endogenous DS-45 activity.",
        "evidence": [
          {
            "reference": "DOI:10.1126/science.adv7924",
            "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
            "notes": "DeWeirdt et al. name validated TUs as DSs."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
            "snippet": "2971\tNZ_QOYQ01000002.1\tGCF_003334555.1\t-\tTrue\tFalse\tTrue\tTrue\tDefensePredictor hits\t13159\t13704\thypothetical protein\tWP_223151192.1\t1.37181361625243\t-1.373840900048604\tTrue\tFalse\tStructural defense homolog\tDS-45",
            "notes": "The final Science supplementary Table S6 maps working_id 2971 to DS_name DS-45, marks the cloned transcriptional unit as defensive, and records NZ_QOYQ01000002.1 positions 13159-13704 with product accession WP_223151192.1."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
            "snippet": "Bas50\t2.2\tpLAND\t24-03-12_EV.png\t10000000000\t2971\t24-03-13\t24-03-13_2971_HEP3_TMP4.png\t7\t14\tY\t140000000\t1.853871964321762\t\tTrue\t\tLB\t37",
            "notes": "The final Science supplementary Table S7 Systems sheet reports a 2971 assay row with a Bas50 phage readout, a smaller-plaque-size call, and a -log(EOP) value of 1.854."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
            "snippet": "2971\tDS-45\tTrue",
            "notes": "The final Science supplementary Table S8 maps 2971 to replicated display name DS-45."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
            "snippet": "2971\t1.0\t181.0\tWP_223151192.1\tDUF2971\tPF11185.12\tDUF2971 ; Protein of unknown function (DUF2971)\thhpred_2594846.hhr\t58.0\t129.0\t0.9694\t2024-04-15 00:00:00",
            "notes": "The final Science supplementary Table S8 reports a high-probability DUF2971 HHpred hit for WP_223151192.1 in working_id 2971."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
            "snippet": "| DS-45 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
            "notes": "The pinned DefenseFinder article registry maps the DS-45 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| DS-45__DS-45                                     |                                                  | DS-45                  | Custom                  | 200    |",
            "notes": "The pinned DefenseFinder HMM inventory records DS-45__DS-45 as a custom DS-45 profile."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "The pinned DefenseFinder rules table does not list DS-45, leaving rule-level detection criteria unresolved."
          }
        ],
        "attaches_to": [
          "causal_graphs#ds_45_locus_reduces_phage_plaquing"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-29"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-29T17:02:36Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted DS-45 system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; kept the graph at 2971 transcriptional-unit level because DUF2971 activity and rule rows remain unresolved, and proposals/metpo_traitmech_v346 reserves the replacement placeholder.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-29T17:02:37Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed DS-45 system canonical_examples and left them empty because DeWeirdt et al. directly support cloned 2971 assays in E. coli MG1655 and a DefenseFinder DS-45 model, but not a direct named native microbial isolate exemplar with experimentally verified endogenous DS-45 activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000471",
    "label": "DS-46 system",
    "definition": "A phage defense system in which an organism possesses the two-gene DS-46 locus cataloged as working transcriptional unit RMRT and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.",
    "definition_source": "DOI:10.1126/science.adv7924",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "DS-46",
        "synonym_type": "EXACT_SYNONYM",
        "source": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx"
      },
      {
        "synonym_text": "RMRT",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1126/science.adv7924",
        "snippet": "To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
        "notes": "DeWeirdt et al. experimentally validated 42 predicted transcriptional units as phage-defense systems in E. coli."
      },
      {
        "reference": "DOI:10.1126/science.adv7924",
        "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
        "notes": "DeWeirdt et al. name validated transcriptional units as DefensePredictor discovered systems."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
        "snippet": "RMRT\tNZ_RRVG01000021.1\tGCF_003886135.1\t+\tFalse\tFalse\tTrue\tTrue\tHHblits hits\t62985\t63495\tDUF3606 domain-containing protein, hypothetical protein\tWP_001406733.1, WP_000002748.1\t-4.513359272522268\t5.517452896464706\tFalse\tTrue\t\tDS-46",
        "notes": "The final Science supplementary Table S6 maps working_id RMRT to DS_name DS-46, marks the cloned transcriptional unit as defensive, records an HHblits-hit screen, and places two product accessions in NZ_RRVG01000021.1 positions 62985-63495."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "ds_46_locus_reduces_phage_plaquing",
        "title": "DS-46 locus reduces bacteriophage plaquing",
        "description": "Conservative system-level sketch linking the two-gene DS-46 locus to reduced bacteriophage plaquing without resolving DS-46 phage-specific readouts, domain annotations, DefenseFinder model coverage, or molecular output.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures DS-46 as the validated RMRT transcriptional unit with two Table S6 product accessions. It does not assert phage-specific Table S7 readouts, Table S8 display-name rows, Table S8 HHpred-domain rows, DefenseFinder article/HMM/rules rows, native host breadth, exact component activities, molecular output, complete phage breadth, or endogenous DS-46 activity.",
        "nodes": [
          {
            "node_id": "ds_46_locus",
            "label": "DS-46 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A two-gene DS-46 locus cataloged as working transcriptional unit RMRT in final Science supplementary Table S6."
          },
          {
            "node_id": "reduced_phage_plaquing",
            "label": "reduced bacteriophage plaquing",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced bacteriophage plaquing in cells carrying cloned RMRT."
          },
          {
            "node_id": "ds_46_system_trait",
            "label": "DS-46 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000471",
            "description": "Possession of a genome-encoded DS-46 phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "ds_46_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "reduced_phage_plaquing",
            "description": "The DS-46/RMRT locus contributes to reduced bacteriophage plaquing in heterologous E. coli MG1655 plasmid-expression assays.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
                "notes": "DeWeirdt et al. describe the plasmid-based phage challenge used to validate predicted transcriptional units."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
                "snippet": "RMRT\tNZ_RRVG01000021.1\tGCF_003886135.1\t+\tFalse\tFalse\tTrue\tTrue\tHHblits hits\t62985\t63495\tDUF3606 domain-containing protein, hypothetical protein\tWP_001406733.1, WP_000002748.1\t-4.513359272522268\t5.517452896464706\tFalse\tTrue\t\tDS-46",
                "notes": "The final Science supplementary Table S6 maps working_id RMRT to DS_name DS-46, marks the cloned transcriptional unit as defensive, records an HHblits-hit screen, and places two product accessions in NZ_RRVG01000021.1 positions 62985-63495."
              }
            ]
          },
          {
            "subject": "reduced_phage_plaquing",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "ds_46_system_trait",
            "description": "DS-46-mediated phage plaquing reduction realizes the DS-46 system trait.",
            "evidence": [
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
                "snippet": "RMRT\tNZ_RRVG01000021.1\tGCF_003886135.1\t+\tFalse\tFalse\tTrue\tTrue\tHHblits hits\t62985\t63495\tDUF3606 domain-containing protein, hypothetical protein\tWP_001406733.1, WP_000002748.1\t-4.513359272522268\t5.517452896464706\tFalse\tTrue\t\tDS-46",
                "notes": "The final Science supplementary Table S6 maps working_id RMRT to DS_name DS-46, marks the cloned transcriptional unit as defensive, records an HHblits-hit screen, and places two product accessions in NZ_RRVG01000021.1 positions 62985-63495."
              },
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
                "notes": "The DS nomenclature is used for validated phage-defense transcriptional units."
              }
            ]
          },
          {
            "subject": "ds_46_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "DS-46 system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
                "notes": "DeWeirdt et al. validate DSs as anti-phage systems."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "ds-46-model-coverage-gap",
        "prompt": "Resolve DS-46 phage-specific readouts, display-name and domain rows, DefenseFinder model coverage, native host breadth, exact component activities, molecular output, complete phage breadth, and endogenous activity before minting narrower DS-46 mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "DeWeirdt et al. support DS-46 as the defensive RMRT transcriptional unit and final Science Table S6 maps RMRT to two product accessions. A first-pass final Science Table S7/S8 review found no exact RMRT/DS-46 phage-specific readout, display-name row, or HHpred-domain row. The pinned DefenseFinder article, HMM, and rules registries also do not list DS-46 or RMRT, and the first-pass record therefore does not resolve native host breadth, complete phage breadth, exact component activities, molecular output, or endogenous DS-46 activity.",
        "evidence": [
          {
            "reference": "DOI:10.1126/science.adv7924",
            "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
            "notes": "DeWeirdt et al. name validated TUs as DSs."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
            "snippet": "RMRT\tNZ_RRVG01000021.1\tGCF_003886135.1\t+\tFalse\tFalse\tTrue\tTrue\tHHblits hits\t62985\t63495\tDUF3606 domain-containing protein, hypothetical protein\tWP_001406733.1, WP_000002748.1\t-4.513359272522268\t5.517452896464706\tFalse\tTrue\t\tDS-46",
            "notes": "The final Science supplementary Table S6 maps working_id RMRT to DS_name DS-46, marks the cloned transcriptional unit as defensive, records an HHblits-hit screen, and places two product accessions in NZ_RRVG01000021.1 positions 62985-63495."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
            "notes": "A structured first-pass search of final Science supplementary Table S7 found no exact RMRT or DS-46 system row to connect DS-46 to a phage-specific readout."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
            "notes": "A structured first-pass search of final Science supplementary Table S8 found no exact RMRT or DS-46 display-name or HHpred-domain row."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
            "notes": "The pinned DefenseFinder article registry has no exact DS-46 or RMRT row."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "notes": "The pinned DefenseFinder HMM inventory has no exact DS-46 or RMRT profile row."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "The pinned DefenseFinder rules table has no exact DS-46 or RMRT model row."
          }
        ],
        "attaches_to": [
          "causal_graphs#ds_46_locus_reduces_phage_plaquing"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-29"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-29T18:46:02Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted DS-46 system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; kept the graph at RMRT transcriptional-unit level because phage-specific Table S7 readouts, Table S8 display and domain rows, DefenseFinder article/HMM/rules coverage, native host breadth, exact component activities, complete phage breadth, and molecular output remain unresolved, and proposals/metpo_traitmech_v348 reserves the replacement placeholder.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-29T18:46:03Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed DS-46 system canonical_examples and left them empty because DeWeirdt et al. directly support cloned RMRT assays in E. coli MG1655, but not a direct named native microbial isolate exemplar with experimentally verified endogenous DS-46 activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000427",
    "label": "DS-4 system",
    "definition": "A phage defense system in which an organism possesses the five-gene DefensePredictor-discovered system 4 locus cataloged as working transcriptional unit NTTI and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.",
    "definition_source": "DOI:10.1126/science.adv7924",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "DS-4",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1126/science.adv7924"
      },
      {
        "synonym_text": "NTTI",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx"
      },
      {
        "synonym_text": "DS-4__DS-4A",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "DS-4__DS-4B",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "DS-4__DS-4C",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "DS-4__DS-4D",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "DS-4__DS-4E",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1126/science.adv7924",
        "snippet": "To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
        "notes": "DeWeirdt et al. experimentally validated 42 predicted transcriptional units as phage-defense systems in E. coli."
      },
      {
        "reference": "DOI:10.1126/science.adv7924",
        "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
        "notes": "DeWeirdt et al. name validated transcriptional units as DefensePredictor discovered systems."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
        "snippet": "NTTI\tNZ_QOYB01000018.1\tGCF_003333785.1\t+\tTrue\tFalse\tTrue\tTrue\tDefensePredictor hits\t32107\t36002\tthymidylate synthase, adenylate kinase, putative DNA base hypermodification protein, TIR domain-containing protein, hypothetical protein\tWP_087900468.1, WP_087900469.1, WP_087900470.1, WP_072044445.1, WP_047174762.1\t8.47705415994386\t4.820281565605036\tTrue\tTrue\tPredicted novel defense gene\tDS-4",
        "notes": "The final Science supplementary Table S6 maps working_id NTTI to DS_name DS-4, marks the cloned transcriptional unit as defensive, and records NZ_QOYB01000018.1 positions 32107-36002 with product accessions WP_087900468.1, WP_087900469.1, WP_087900470.1, WP_072044445.1, and WP_047174762.1."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
        "snippet": "Lambda\t1.1\tpLAND\t24-03-08_NYND_PIN2_MHAD_EV.png\t60000000\tNTTI\t24-03-12\t24-03-12_NTTI_PN12_SVIR_D390.png\t6\t7\tY\t7000000\t0.9330532103693868\tTrue\tTrue\t\tLB\t37",
        "notes": "The final Science supplementary Table S7 reports an NTTI assay row with a lambda phage readout, smaller plaque size marked Y, and a -log(EOP) value of 0.933."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
        "snippet": "NTTI\tDS-4\tTrue",
        "notes": "The final Science supplementary Table S8 maps NTTI to replicated display name DS-4."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| DS-4 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
        "notes": "The pinned DefenseFinder article registry maps the DS-4 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| DS-4__DS-4A                                      |                                                  | DS-4                   | Custom                  | 150    |",
        "notes": "The pinned DefenseFinder HMM inventory records DS-4__DS-4A as a custom DS-4 profile."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| DS-4__DS-4B                                      |                                                  | DS-4                   | Custom                  | 200    |",
        "notes": "The pinned DefenseFinder HMM inventory records DS-4__DS-4B as a custom DS-4 profile."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| DS-4__DS-4C                                      |                                                  | DS-4                   | Custom                  | 150    |",
        "notes": "The pinned DefenseFinder HMM inventory records DS-4__DS-4C as a custom DS-4 profile."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| DS-4__DS-4D                                      |                                                  | DS-4                   | Custom                  | 100    |",
        "notes": "The pinned DefenseFinder HMM inventory records DS-4__DS-4D as a custom DS-4 profile."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| DS-4__DS-4E                                      |                                                  | DS-4                   | Custom                  | 50     |",
        "notes": "The pinned DefenseFinder HMM inventory records DS-4__DS-4E as a custom DS-4 profile."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "ds_4_locus_reduces_phage_plaquing",
        "title": "DS-4 locus reduces bacteriophage plaquing",
        "description": "Conservative system-level sketch linking the five-gene DS-4 locus to reduced bacteriophage plaquing without resolving DS-4 component functions or effector activity.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures DS-4 as the validated NTTI transcriptional unit with five product accessions and with DefenseFinder DS-4A, DS-4B, DS-4C, DS-4D, and DS-4E profile rows. It does not assert native host breadth, exact profile-to-protein correspondence, the direct viral trigger or substrate, exact molecular output, phage target breadth, or DefenseFinder rule-level detection criteria.",
        "nodes": [
          {
            "node_id": "ds_4_locus",
            "label": "DS-4 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A five-gene DefensePredictor-discovered system locus represented in the pinned DefenseFinder HMM inventory by DS-4A, DS-4B, DS-4C, DS-4D, and DS-4E custom profiles."
          },
          {
            "node_id": "reduced_phage_plaquing",
            "label": "reduced bacteriophage plaquing",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced efficiency of plaquing or reduced plaque size by bacteriophages in cells carrying cloned NTTI."
          },
          {
            "node_id": "ds_4_system_trait",
            "label": "DS-4 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000427",
            "description": "Possession of a genome-encoded DS-4 phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "ds_4_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "reduced_phage_plaquing",
            "description": "The DS-4/NTTI locus contributes to reduced bacteriophage plaquing when plasmid expressed.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
                "notes": "DeWeirdt et al. experimentally validate DefensePredictor-discovered systems by assaying cloned transcriptional units against E. coli phages."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
                "snippet": "NTTI\tNZ_QOYB01000018.1\tGCF_003333785.1\t+\tTrue\tFalse\tTrue\tTrue\tDefensePredictor hits\t32107\t36002\tthymidylate synthase, adenylate kinase, putative DNA base hypermodification protein, TIR domain-containing protein, hypothetical protein\tWP_087900468.1, WP_087900469.1, WP_087900470.1, WP_072044445.1, WP_047174762.1\t8.47705415994386\t4.820281565605036\tTrue\tTrue\tPredicted novel defense gene\tDS-4",
                "notes": "The final Science supplementary Table S6 maps working_id NTTI to DS_name DS-4, marks the cloned transcriptional unit as defensive, and records NZ_QOYB01000018.1 positions 32107-36002 with product accessions WP_087900468.1, WP_087900469.1, WP_087900470.1, WP_072044445.1, and WP_047174762.1."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
                "snippet": "Lambda\t1.1\tpLAND\t24-03-08_NYND_PIN2_MHAD_EV.png\t60000000\tNTTI\t24-03-12\t24-03-12_NTTI_PN12_SVIR_D390.png\t6\t7\tY\t7000000\t0.9330532103693868\tTrue\tTrue\t\tLB\t37",
                "notes": "The final Science supplementary Table S7 reports an NTTI assay row with a lambda phage readout, smaller plaque size marked Y, and a -log(EOP) value of 0.933."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| DS-4__DS-4A                                      |                                                  | DS-4                   | Custom                  | 150    |",
                "notes": "The pinned DefenseFinder HMM inventory records DS-4__DS-4A as a custom DS-4 profile."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| DS-4__DS-4B                                      |                                                  | DS-4                   | Custom                  | 200    |",
                "notes": "The pinned DefenseFinder HMM inventory records DS-4__DS-4B as a custom DS-4 profile."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| DS-4__DS-4C                                      |                                                  | DS-4                   | Custom                  | 150    |",
                "notes": "The pinned DefenseFinder HMM inventory records DS-4__DS-4C as a custom DS-4 profile."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| DS-4__DS-4D                                      |                                                  | DS-4                   | Custom                  | 100    |",
                "notes": "The pinned DefenseFinder HMM inventory records DS-4__DS-4D as a custom DS-4 profile."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| DS-4__DS-4E                                      |                                                  | DS-4                   | Custom                  | 50     |",
                "notes": "The pinned DefenseFinder HMM inventory records DS-4__DS-4E as a custom DS-4 profile."
              }
            ]
          },
          {
            "subject": "reduced_phage_plaquing",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "ds_4_system_trait",
            "description": "DS-4-mediated phage plaquing reduction realizes the DS-4 system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
                "notes": "DeWeirdt et al. name each validated transcriptional unit as a DefensePredictor discovered system."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
                "snippet": "NTTI\tNZ_QOYB01000018.1\tGCF_003333785.1\t+\tTrue\tFalse\tTrue\tTrue\tDefensePredictor hits\t32107\t36002\tthymidylate synthase, adenylate kinase, putative DNA base hypermodification protein, TIR domain-containing protein, hypothetical protein\tWP_087900468.1, WP_087900469.1, WP_087900470.1, WP_072044445.1, WP_047174762.1\t8.47705415994386\t4.820281565605036\tTrue\tTrue\tPredicted novel defense gene\tDS-4",
                "notes": "The final Science supplementary Table S6 maps working_id NTTI to DS_name DS-4, marks the cloned transcriptional unit as defensive, and records NZ_QOYB01000018.1 positions 32107-36002 with product accessions WP_087900468.1, WP_087900469.1, WP_087900470.1, WP_072044445.1, and WP_047174762.1."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
                "snippet": "Lambda\t1.1\tpLAND\t24-03-08_NYND_PIN2_MHAD_EV.png\t60000000\tNTTI\t24-03-12\t24-03-12_NTTI_PN12_SVIR_D390.png\t6\t7\tY\t7000000\t0.9330532103693868\tTrue\tTrue\t\tLB\t37",
                "notes": "The final Science supplementary Table S7 reports an NTTI assay row with a lambda phage readout, smaller plaque size marked Y, and a -log(EOP) value of 0.933."
              }
            ]
          },
          {
            "subject": "ds_4_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "DS-4 system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
                "notes": "DeWeirdt et al. validate DSs as anti-phage systems."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| DS-4 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
                "notes": "The pinned DefenseFinder article registry maps the DS-4 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "ds-4-defensefinder-model-gap",
        "prompt": "Resolve DS-4 native host breadth, exact five-component activities, DS-4 profile-to-protein mapping, sensitive-phage breadth, molecular output, and rule-level detection criteria before minting narrower DS-4 mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "DeWeirdt et al. support DS-4 as the defensive NTTI transcriptional unit that reduced plaquing when cloned in E. coli MG1655, and the pinned DefenseFinder HMM inventory records five DS-4 profile rows. The pinned rules table has no DS-4 row, and the first-pass record does not resolve native host breadth, exact component activities, profile-to-protein mapping, phage target breadth, or endogenous DS-4 activity.",
        "evidence": [
          {
            "reference": "DOI:10.1126/science.adv7924",
            "snippet": "To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
            "notes": "DeWeirdt et al. validate predicted transcriptional units by measuring plaquing relative to an empty vector control strain."
          },
          {
            "reference": "DOI:10.1126/science.adv7924",
            "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
            "notes": "DeWeirdt et al. name validated TUs as DSs."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
            "snippet": "NTTI\tNZ_QOYB01000018.1\tGCF_003333785.1\t+\tTrue\tFalse\tTrue\tTrue\tDefensePredictor hits\t32107\t36002\tthymidylate synthase, adenylate kinase, putative DNA base hypermodification protein, TIR domain-containing protein, hypothetical protein\tWP_087900468.1, WP_087900469.1, WP_087900470.1, WP_072044445.1, WP_047174762.1\t8.47705415994386\t4.820281565605036\tTrue\tTrue\tPredicted novel defense gene\tDS-4",
            "notes": "The final Science supplementary Table S6 maps working_id NTTI to DS_name DS-4, marks the cloned transcriptional unit as defensive, and records NZ_QOYB01000018.1 positions 32107-36002 with product accessions WP_087900468.1, WP_087900469.1, WP_087900470.1, WP_072044445.1, and WP_047174762.1."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
            "snippet": "Lambda\t1.1\tpLAND\t24-03-08_NYND_PIN2_MHAD_EV.png\t60000000\tNTTI\t24-03-12\t24-03-12_NTTI_PN12_SVIR_D390.png\t6\t7\tY\t7000000\t0.9330532103693868\tTrue\tTrue\t\tLB\t37",
            "notes": "The final Science supplementary Table S7 reports an NTTI assay row with a lambda phage readout, smaller plaque size marked Y, and a -log(EOP) value of 0.933."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
            "snippet": "NTTI\tDS-4\tTrue",
            "notes": "The final Science supplementary Table S8 maps NTTI to replicated display name DS-4."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
            "snippet": "| DS-4 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
            "notes": "The pinned DefenseFinder article registry maps the DS-4 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| DS-4__DS-4A                                      |                                                  | DS-4                   | Custom                  | 150    |",
            "notes": "The pinned DefenseFinder HMM inventory records DS-4__DS-4A as a custom DS-4 profile."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| DS-4__DS-4B                                      |                                                  | DS-4                   | Custom                  | 200    |",
            "notes": "The pinned DefenseFinder HMM inventory records DS-4__DS-4B as a custom DS-4 profile."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| DS-4__DS-4C                                      |                                                  | DS-4                   | Custom                  | 150    |",
            "notes": "The pinned DefenseFinder HMM inventory records DS-4__DS-4C as a custom DS-4 profile."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| DS-4__DS-4D                                      |                                                  | DS-4                   | Custom                  | 100    |",
            "notes": "The pinned DefenseFinder HMM inventory records DS-4__DS-4D as a custom DS-4 profile."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| DS-4__DS-4E                                      |                                                  | DS-4                   | Custom                  | 50     |",
            "notes": "The pinned DefenseFinder HMM inventory records DS-4__DS-4E as a custom DS-4 profile."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "The pinned DefenseFinder rules table does not list DS-4, leaving rule-level detection criteria unresolved."
          }
        ],
        "attaches_to": [
          "causal_graphs#ds_4_locus_reduces_phage_plaquing"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-28"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-28T06:12:08Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted DS-4 system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; kept the graph at cloned NTTI transcriptional-unit level because the pinned DefenseFinder DS-4 HMM rows are not backed by a rules row; proposals/metpo_traitmech_v304 reserves the replacement placeholder.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-28T06:12:09Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed DS-4 system canonical_examples and left them empty because DeWeirdt et al. support cloned NTTI plaquing assays in E. coli MG1655 plus a DefenseFinder DS-4 model, but not a direct named native microbial isolate exemplar with experimentally verified endogenous DS-4 activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000428",
    "label": "DS-5 system",
    "definition": "A phage defense system in which an organism possesses the two-gene DefensePredictor-discovered system 5 locus cataloged as working transcriptional unit PN12 and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.",
    "definition_source": "DOI:10.1126/science.adv7924",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "DS-5",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1126/science.adv7924"
      },
      {
        "synonym_text": "PN12",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx"
      },
      {
        "synonym_text": "DS-5__DS-5A",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "DS-5__DS-5B",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1126/science.adv7924",
        "snippet": "To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
        "notes": "DeWeirdt et al. experimentally validated 42 predicted transcriptional units as phage-defense systems in E. coli."
      },
      {
        "reference": "DOI:10.1126/science.adv7924",
        "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
        "notes": "DeWeirdt et al. name validated transcriptional units as DefensePredictor discovered systems."
      },
      {
        "reference": "DOI:10.1126/science.adv7924",
        "snippet": "DS-5 is a two protein system that also features a PIN ribonuclease, though not closely related to that of DS-3, along with a second protein containing a DUF5830 and a domain homologous to the anti-CRISPR protein AcrIF4",
        "notes": "DeWeirdt et al. describe DS-5 as a two-protein system containing PIN, DUF5830, and AcrIF4-like domains."
      },
      {
        "reference": "DOI:10.1126/science.adv7924",
        "snippet": "Mutating the catalytic residues in the PIN domain eliminated defense. Deleting the AcrIF4 domain-containing gene also ablated defense by DS-5 but did not lead to unrestrained toxicity of the ribonuclease indicating that DS-5 is likely not a TA system and that both components are essential to defense",
        "notes": "DeWeirdt et al. report that DS-5 phage defense requires the predicted PIN catalytic residues and the AcrIF4-domain-containing gene."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
        "snippet": "PN12\tNZ_QOYG01000008.1\tGCF_003333715.1\t+\tTrue\tFalse\tFalse\tTrue\tDefensePredictor hits\t68231\t69878\thypothetical protein, PIN domain-containing protein\tWP_021513008.1, WP_021513009.1\t10.04757221593433\t-2.824774475410352\tTrue\tFalse\tPredicted novel defense gene\tDS-5",
        "notes": "The final Science supplementary Table S6 maps working_id PN12 to DS_name DS-5, marks the cloned transcriptional unit as defensive, and records NZ_QOYG01000008.1 positions 68231-69878 with product accessions WP_021513008.1 and WP_021513009.1."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
        "snippet": "Bas60\t1.2\tpLAND\t24-03-08_EV_HHHD_PIN2_CRDO.png\t5000000\tPN12\t24-03-09\t24-03-09_NTTI_SVIR_PN12_PIN8.png\t1\t100\t\t1000\t3.6989700043360187\tTrue\t\t\tLB\t37",
        "notes": "The final Science supplementary Table S7 reports a PN12 assay row with a Bas60 phage readout and a -log(EOP) value of 3.699."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
        "snippet": "PN12\tDS-5\tTrue",
        "notes": "The final Science supplementary Table S8 maps PN12 to replicated display name DS-5."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| DS-5 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
        "notes": "The pinned DefenseFinder article registry maps the DS-5 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| DS-5__DS-5A                                      |                                                  | DS-5                   | Custom                  | 50     |",
        "notes": "The pinned DefenseFinder HMM inventory records DS-5__DS-5A as a custom DS-5 profile."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| DS-5__DS-5B                                      |                                                  | DS-5                   | Custom                  | 100    |",
        "notes": "The pinned DefenseFinder HMM inventory records DS-5__DS-5B as a custom DS-5 profile."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "ds_5_locus_reduces_phage_plaquing",
        "title": "DS-5 locus reduces bacteriophage plaquing",
        "description": "Conservative system-level sketch linking the two-gene DS-5 locus to reduced bacteriophage plaquing without resolving DS-5 component functions or effector activity.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures DS-5 as the validated PN12 transcriptional unit with two product accessions and with DefenseFinder DS-5A and DS-5B profile rows. It does not assert native host breadth, exact profile-to-protein correspondence, the direct viral trigger or substrate, exact PIN-family target, AcrIF4-like component activity, phage target breadth, or DefenseFinder rule-level detection criteria.",
        "nodes": [
          {
            "node_id": "ds_5_locus",
            "label": "DS-5 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A two-gene DefensePredictor-discovered system locus represented in the pinned DefenseFinder HMM inventory by DS-5A and DS-5B custom profiles."
          },
          {
            "node_id": "reduced_phage_plaquing",
            "label": "reduced bacteriophage plaquing",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced efficiency of plaquing by bacteriophage Bas60 in cells carrying cloned PN12."
          },
          {
            "node_id": "ds_5_system_trait",
            "label": "DS-5 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000428",
            "description": "Possession of a genome-encoded DS-5 phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "ds_5_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "reduced_phage_plaquing",
            "description": "The DS-5/PN12 locus contributes to reduced bacteriophage plaquing when plasmid expressed.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
                "notes": "DeWeirdt et al. experimentally validate DefensePredictor-discovered systems by assaying cloned transcriptional units against E. coli phages."
              },
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "Mutating the catalytic residues in the PIN domain eliminated defense. Deleting the AcrIF4 domain-containing gene also ablated defense by DS-5 but did not lead to unrestrained toxicity of the ribonuclease indicating that DS-5 is likely not a TA system and that both components are essential to defense",
                "notes": "DeWeirdt et al. show that DS-5 protection requires both the predicted PIN catalytic residues and the AcrIF4-domain-containing gene."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
                "snippet": "PN12\tNZ_QOYG01000008.1\tGCF_003333715.1\t+\tTrue\tFalse\tFalse\tTrue\tDefensePredictor hits\t68231\t69878\thypothetical protein, PIN domain-containing protein\tWP_021513008.1, WP_021513009.1\t10.04757221593433\t-2.824774475410352\tTrue\tFalse\tPredicted novel defense gene\tDS-5",
                "notes": "The final Science supplementary Table S6 maps working_id PN12 to DS_name DS-5, marks the cloned transcriptional unit as defensive, and records NZ_QOYG01000008.1 positions 68231-69878 with product accessions WP_021513008.1 and WP_021513009.1."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
                "snippet": "Bas60\t1.2\tpLAND\t24-03-08_EV_HHHD_PIN2_CRDO.png\t5000000\tPN12\t24-03-09\t24-03-09_NTTI_SVIR_PN12_PIN8.png\t1\t100\t\t1000\t3.6989700043360187\tTrue\t\t\tLB\t37",
                "notes": "The final Science supplementary Table S7 reports a PN12 assay row with a Bas60 phage readout and a -log(EOP) value of 3.699."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| DS-5__DS-5A                                      |                                                  | DS-5                   | Custom                  | 50     |",
                "notes": "The pinned DefenseFinder HMM inventory records DS-5__DS-5A as a custom DS-5 profile."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| DS-5__DS-5B                                      |                                                  | DS-5                   | Custom                  | 100    |",
                "notes": "The pinned DefenseFinder HMM inventory records DS-5__DS-5B as a custom DS-5 profile."
              }
            ]
          },
          {
            "subject": "reduced_phage_plaquing",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "ds_5_system_trait",
            "description": "DS-5-mediated phage plaquing reduction realizes the DS-5 system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
                "notes": "DeWeirdt et al. name each validated transcriptional unit as a DefensePredictor discovered system."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
                "snippet": "PN12\tNZ_QOYG01000008.1\tGCF_003333715.1\t+\tTrue\tFalse\tFalse\tTrue\tDefensePredictor hits\t68231\t69878\thypothetical protein, PIN domain-containing protein\tWP_021513008.1, WP_021513009.1\t10.04757221593433\t-2.824774475410352\tTrue\tFalse\tPredicted novel defense gene\tDS-5",
                "notes": "The final Science supplementary Table S6 maps working_id PN12 to DS_name DS-5, marks the cloned transcriptional unit as defensive, and records NZ_QOYG01000008.1 positions 68231-69878 with product accessions WP_021513008.1 and WP_021513009.1."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
                "snippet": "Bas60\t1.2\tpLAND\t24-03-08_EV_HHHD_PIN2_CRDO.png\t5000000\tPN12\t24-03-09\t24-03-09_NTTI_SVIR_PN12_PIN8.png\t1\t100\t\t1000\t3.6989700043360187\tTrue\t\t\tLB\t37",
                "notes": "The final Science supplementary Table S7 reports a PN12 assay row with a Bas60 phage readout and a -log(EOP) value of 3.699."
              }
            ]
          },
          {
            "subject": "ds_5_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "DS-5 system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
                "notes": "DeWeirdt et al. validate DSs as anti-phage systems."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| DS-5 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
                "notes": "The pinned DefenseFinder article registry maps the DS-5 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "ds-5-defensefinder-model-gap",
        "prompt": "Resolve DS-5 native host breadth, exact two-component activities, DS-5 profile-to-protein mapping, sensitive-phage breadth, DS-5 PIN nuclease target, AcrIF4-like component function, and rule-level detection criteria before minting narrower DS-5 mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "DeWeirdt et al. support DS-5 as the defensive PN12 transcriptional unit that reduced Bas60 plaquing when cloned in E. coli MG1655, and the pinned DefenseFinder HMM inventory records two DS-5 profile rows. The pinned rules table has no DS-5 row, and the first-pass record does not resolve native host breadth, exact component activities, profile-to-protein mapping, phage target breadth, or endogenous DS-5 activity.",
        "evidence": [
          {
            "reference": "DOI:10.1126/science.adv7924",
            "snippet": "To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
            "notes": "DeWeirdt et al. validate predicted transcriptional units by measuring plaquing relative to an empty vector control strain."
          },
          {
            "reference": "DOI:10.1126/science.adv7924",
            "snippet": "DS-5 is a two protein system that also features a PIN ribonuclease, though not closely related to that of DS-3, along with a second protein containing a DUF5830 and a domain homologous to the anti-CRISPR protein AcrIF4",
            "notes": "DeWeirdt et al. identify DS-5 as a two-protein system with PIN, DUF5830, and AcrIF4-like domains."
          },
          {
            "reference": "DOI:10.1126/science.adv7924",
            "snippet": "Mutating the catalytic residues in the PIN domain eliminated defense. Deleting the AcrIF4 domain-containing gene also ablated defense by DS-5 but did not lead to unrestrained toxicity of the ribonuclease indicating that DS-5 is likely not a TA system and that both components are essential to defense",
            "notes": "DeWeirdt et al. show that DS-5 phage defense requires both proteins."
          },
          {
            "reference": "DOI:10.1126/science.adv7924",
            "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
            "notes": "DeWeirdt et al. name validated TUs as DSs."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
            "snippet": "PN12\tNZ_QOYG01000008.1\tGCF_003333715.1\t+\tTrue\tFalse\tFalse\tTrue\tDefensePredictor hits\t68231\t69878\thypothetical protein, PIN domain-containing protein\tWP_021513008.1, WP_021513009.1\t10.04757221593433\t-2.824774475410352\tTrue\tFalse\tPredicted novel defense gene\tDS-5",
            "notes": "The final Science supplementary Table S6 maps working_id PN12 to DS_name DS-5, marks the cloned transcriptional unit as defensive, and records NZ_QOYG01000008.1 positions 68231-69878 with product accessions WP_021513008.1 and WP_021513009.1."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
            "snippet": "Bas60\t1.2\tpLAND\t24-03-08_EV_HHHD_PIN2_CRDO.png\t5000000\tPN12\t24-03-09\t24-03-09_NTTI_SVIR_PN12_PIN8.png\t1\t100\t\t1000\t3.6989700043360187\tTrue\t\t\tLB\t37",
            "notes": "The final Science supplementary Table S7 reports a PN12 assay row with a Bas60 phage readout and a -log(EOP) value of 3.699."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
            "snippet": "PN12\tDS-5\tTrue",
            "notes": "The final Science supplementary Table S8 maps PN12 to replicated display name DS-5."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
            "snippet": "| DS-5 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
            "notes": "The pinned DefenseFinder article registry maps the DS-5 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| DS-5__DS-5A                                      |                                                  | DS-5                   | Custom                  | 50     |",
            "notes": "The pinned DefenseFinder HMM inventory records DS-5__DS-5A as a custom DS-5 profile."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| DS-5__DS-5B                                      |                                                  | DS-5                   | Custom                  | 100    |",
            "notes": "The pinned DefenseFinder HMM inventory records DS-5__DS-5B as a custom DS-5 profile."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "The pinned DefenseFinder rules table does not list DS-5, leaving rule-level detection criteria unresolved."
          }
        ],
        "attaches_to": [
          "causal_graphs#ds_5_locus_reduces_phage_plaquing"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-28"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-28T07:02:46Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted DS-5 system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; kept the graph at cloned PN12 transcriptional-unit level because the pinned DefenseFinder DS-5 HMM rows are not backed by a rules row; proposals/metpo_traitmech_v305 reserves the replacement placeholder.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-28T07:02:47Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed DS-5 system canonical_examples and left them empty because DeWeirdt et al. support cloned PN12 plaquing assays in E. coli MG1655 plus a DefenseFinder DS-5 model, but not a direct named native microbial isolate exemplar with experimentally verified endogenous DS-5 activity. No paid research was used.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-28T07:38:24Z",
        "curator": "codex",
        "action": "FIX_REVIEW_NOTE",
        "changes": "Reworded the DS-5 mutation evidence note after Claude Code Review issue 1387 so it cites the AcrIF4-domain-containing gene rather than asserting a first-gene ordering that the source text and nonmechanistic graph do not establish.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000430",
    "label": "DS-6 system",
    "definition": "A phage defense system in which an organism possesses the two-gene DefensePredictor-discovered system 6 locus cataloged with working_id HIPA and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.",
    "definition_source": "DOI:10.1126/science.adv7924",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "DS-6",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1126/science.adv7924"
      },
      {
        "synonym_text": "HipAD",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1126/science.adv7924"
      },
      {
        "synonym_text": "HIPA",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx"
      },
      {
        "synonym_text": "DS-6__DS-6A",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "DS-6__DS-6B",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1126/science.adv7924",
        "snippet": "To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
        "notes": "DeWeirdt et al. experimentally validated 42 predicted transcriptional units as phage-defense systems in E. coli."
      },
      {
        "reference": "DOI:10.1126/science.adv7924",
        "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
        "notes": "DeWeirdt et al. name validated transcriptional units as DefensePredictor discovered systems."
      },
      {
        "reference": "DOI:10.1126/science.adv7924",
        "snippet": "We independently discovered DS-6 (renamed HipAD) recently",
        "notes": "DeWeirdt et al. record HipAD as a name for DS-6."
      },
      {
        "reference": "DOI:10.1126/science.adv7924",
        "snippet": "When we mutated a key predicted catalytic residue in DS-6A, we observed a loss of defense, suggesting that kinase activity is essential for protection.",
        "notes": "DeWeirdt et al. report that mutating a predicted DS-6A catalytic residue eliminated defense."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
        "snippet": "HIPA\tNZ_QOWQ01000062.1\tGCF_003334335.1\t-\tTrue\tFalse\tTrue\tTrue\tDefensePredictor hits\t1591\t3164\tDUF3037 domain-containing protein, hypothetical protein\tWP_000210934.1, WP_000389051.1\t6.427268761356274\t-2.428836967683248\tTrue\tFalse\tPredicted novel defense gene\tDS-6",
        "notes": "The final Science supplementary Table S6 maps working_id HIPA to DS_name DS-6, marks the cloned transcriptional unit as defensive, and records NZ_QOWQ01000062.1 positions 1591-3164 with product accessions WP_000210934.1 and WP_000389051.1."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
        "snippet": "Bas1\t1.2\tpLAND\t24-03-08_EV_HHHD_PIN2_CRDO.png\t40000000\tHIPA\t24-03-08\t24-03-08_IMPD_DISA_2CM2_MAZF.png\t3\t5\tY\t5000\t3.9030899869919438\tTrue\tTrue\t\tLB\t37",
        "notes": "The final Science supplementary Table S7 reports a HIPA assay row with a Bas1 phage readout, smaller plaques, and a -log(EOP) value of 3.903."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
        "snippet": "Bas1\tA.1\tMG1655\t24-07-10_EV_MNAC-K375A_MNAC-N84A_MNAC-D52A.png\t3000000\tHIPA\t\t24-07-12\t24-07-12_HIPA_HIPA-D139A_SVIR_SVIR-H52A_DISA_DISA-D433A.png\t1\t2\t\t20\t5.176091259\nBas1\tA.1\tMG1655\t24-07-10_EV_MNAC-K375A_MNAC-N84A_MNAC-D52A.png\t3000000\tHIPA\tD139A\t24-07-12\t24-07-12_HIPA_HIPA-D139A_SVIR_SVIR-H52A_DISA_DISA-D433A.png\t5\t4\t\t400000\t0.8750612634",
        "notes": "The final Science supplementary Table S7 System Mutants sheet pairs wild-type HIPA and HIPA D139A in a Bas1 assay panel, with -log(EOP) shifting from 5.176 to 0.875 for the D139A catalytic mutant."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
        "snippet": "Bas1\tB.1\tMG1655\t24-07-17_MVB1_VPUS_VAME_EV.png\t3000000\tHIPA\t\t24-07-18\t24-07-18_IMPD-Y157A_IMPD_IMPD-R330A_IMPD-H335A_HIPA_HIPA-D139A.png\t2\t10\t\t1000\t3.477121255\nBas1\tB.1\tMG1655\t24-07-17_MVB1_VPUS_VAME_EV.png\t3000000\tHIPA\tD139A\t24-07-18\t24-07-18_IMPD-Y157A_IMPD_IMPD-R330A_IMPD-H335A_HIPA_HIPA-D139A.png\t6\t4\t\t4000000\t-0.1249387366",
        "notes": "The final Science supplementary Table S7 System Mutants sheet records a second HIPA versus HIPA D139A Bas1 panel, with -log(EOP) shifting from 3.477 to -0.125 for the D139A catalytic mutant."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
        "snippet": "HIPA\tDS-6\tTrue",
        "notes": "The final Science supplementary Table S8 maps HIPA to replicated display name DS-6."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
        "snippet": "HIPA\t15.0\t248.0\tWP_000389051.1\tHIPA kinase\tPF20613.3\tHipA_2 ; HipA-like kinase\thhpred_9120093.hhr\t15.0\t248.0\t1.0\t2024-07-28 00:00:00",
        "notes": "The final Science supplementary Table S8 reports a HipA-like kinase HHpred hit for WP_000389051.1 in HIPA."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
        "snippet": "HIPA\t2.0\t275.0\tWP_000210934.1\tDUF3037\tPF11236.12\tDUF3037\thhpred_4386604.hhr\t7.0\t125.0\t0.9987\t2024-04-15 00:00:00",
        "notes": "The final Science supplementary Table S8 reports a DUF3037 HHpred hit for WP_000210934.1 in HIPA."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
        "snippet": "HIPA\t2.0\t275.0\tWP_000210934.1\tDUF1829\tPF08862.14\tDUF1829\thhpred_4386604.hhr\t163.0\t260.0\t0.7785\t2024-04-15 00:00:00",
        "notes": "The final Science supplementary Table S8 reports a DUF1829 HHpred hit for WP_000210934.1 in HIPA."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| DS-6 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
        "notes": "The pinned DefenseFinder article registry maps the DS-6 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| DS-6__DS-6A                                      |                                                  | DS-6                   | Custom                  | 100    |",
        "notes": "The pinned DefenseFinder HMM inventory records DS-6__DS-6A as a custom DS-6 profile."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| DS-6__DS-6B                                      |                                                  | DS-6                   | Custom                  | 100    |",
        "notes": "The pinned DefenseFinder HMM inventory records DS-6__DS-6B as a custom DS-6 profile."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "ds_6_locus_reduces_phage_plaquing",
        "title": "DS-6 locus reduces bacteriophage plaquing",
        "description": "Conservative system-level sketch linking the two-gene DS-6 locus to reduced bacteriophage plaquing without resolving DS-6 component functions or effector activity.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures DS-6 as the validated HIPA transcriptional unit with two product accessions and with DefenseFinder DS-6A and DS-6B profile rows. It does not assert native host breadth, exact profile-to-protein correspondence, the direct viral trigger or substrate, DUF3037 or DUF1829 activity, exact HipA-like kinase substrates, phage target breadth, or DefenseFinder rule-level detection criteria.",
        "nodes": [
          {
            "node_id": "ds_6_locus",
            "label": "DS-6 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A two-gene DefensePredictor-discovered system locus represented in the pinned DefenseFinder HMM inventory by DS-6A and DS-6B custom profiles."
          },
          {
            "node_id": "reduced_phage_plaquing",
            "label": "reduced bacteriophage plaquing",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced efficiency of plaquing by bacteriophage Bas1 in cells carrying cloned HIPA."
          },
          {
            "node_id": "ds_6_system_trait",
            "label": "DS-6 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000430",
            "description": "Possession of a genome-encoded DS-6 phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "ds_6_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "reduced_phage_plaquing",
            "description": "The DS-6/HIPA locus contributes to reduced bacteriophage plaquing when plasmid expressed.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
                "notes": "DeWeirdt et al. experimentally validate DefensePredictor-discovered systems by assaying cloned transcriptional units against E. coli phages."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
                "snippet": "HIPA\tNZ_QOWQ01000062.1\tGCF_003334335.1\t-\tTrue\tFalse\tTrue\tTrue\tDefensePredictor hits\t1591\t3164\tDUF3037 domain-containing protein, hypothetical protein\tWP_000210934.1, WP_000389051.1\t6.427268761356274\t-2.428836967683248\tTrue\tFalse\tPredicted novel defense gene\tDS-6",
                "notes": "The final Science supplementary Table S6 maps working_id HIPA to DS_name DS-6, marks the cloned transcriptional unit as defensive, and records NZ_QOWQ01000062.1 positions 1591-3164 with product accessions WP_000210934.1 and WP_000389051.1."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
                "snippet": "Bas1\t1.2\tpLAND\t24-03-08_EV_HHHD_PIN2_CRDO.png\t40000000\tHIPA\t24-03-08\t24-03-08_IMPD_DISA_2CM2_MAZF.png\t3\t5\tY\t5000\t3.9030899869919438\tTrue\tTrue\t\tLB\t37",
                "notes": "The final Science supplementary Table S7 reports a HIPA assay row with a Bas1 phage readout, smaller plaques, and a -log(EOP) value of 3.903."
              },
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "When we mutated a key predicted catalytic residue in DS-6A, we observed a loss of defense, suggesting that kinase activity is essential for protection.",
                "notes": "DeWeirdt et al. report that DS-6A catalytic residue mutagenesis caused loss of defense."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
                "snippet": "Bas1\tA.1\tMG1655\t24-07-10_EV_MNAC-K375A_MNAC-N84A_MNAC-D52A.png\t3000000\tHIPA\t\t24-07-12\t24-07-12_HIPA_HIPA-D139A_SVIR_SVIR-H52A_DISA_DISA-D433A.png\t1\t2\t\t20\t5.176091259\nBas1\tA.1\tMG1655\t24-07-10_EV_MNAC-K375A_MNAC-N84A_MNAC-D52A.png\t3000000\tHIPA\tD139A\t24-07-12\t24-07-12_HIPA_HIPA-D139A_SVIR_SVIR-H52A_DISA_DISA-D433A.png\t5\t4\t\t400000\t0.8750612634",
                "notes": "The final Science supplementary Table S7 System Mutants sheet pairs wild-type HIPA and HIPA D139A in a Bas1 assay panel, with -log(EOP) shifting from 5.176 to 0.875 for the D139A catalytic mutant."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
                "snippet": "Bas1\tB.1\tMG1655\t24-07-17_MVB1_VPUS_VAME_EV.png\t3000000\tHIPA\t\t24-07-18\t24-07-18_IMPD-Y157A_IMPD_IMPD-R330A_IMPD-H335A_HIPA_HIPA-D139A.png\t2\t10\t\t1000\t3.477121255\nBas1\tB.1\tMG1655\t24-07-17_MVB1_VPUS_VAME_EV.png\t3000000\tHIPA\tD139A\t24-07-18\t24-07-18_IMPD-Y157A_IMPD_IMPD-R330A_IMPD-H335A_HIPA_HIPA-D139A.png\t6\t4\t\t4000000\t-0.1249387366",
                "notes": "The final Science supplementary Table S7 System Mutants sheet records a second HIPA versus HIPA D139A Bas1 panel, with -log(EOP) shifting from 3.477 to -0.125 for the D139A catalytic mutant."
              }
            ]
          },
          {
            "subject": "reduced_phage_plaquing",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "ds_6_system_trait",
            "description": "DS-6-mediated phage plaquing reduction realizes the DS-6 system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
                "notes": "DeWeirdt et al. name each validated transcriptional unit as a DefensePredictor discovered system."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
                "snippet": "HIPA\tNZ_QOWQ01000062.1\tGCF_003334335.1\t-\tTrue\tFalse\tTrue\tTrue\tDefensePredictor hits\t1591\t3164\tDUF3037 domain-containing protein, hypothetical protein\tWP_000210934.1, WP_000389051.1\t6.427268761356274\t-2.428836967683248\tTrue\tFalse\tPredicted novel defense gene\tDS-6",
                "notes": "The final Science supplementary Table S6 maps working_id HIPA to DS_name DS-6, marks the cloned transcriptional unit as defensive, and records NZ_QOWQ01000062.1 positions 1591-3164 with product accessions WP_000210934.1 and WP_000389051.1."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
                "snippet": "Bas1\t1.2\tpLAND\t24-03-08_EV_HHHD_PIN2_CRDO.png\t40000000\tHIPA\t24-03-08\t24-03-08_IMPD_DISA_2CM2_MAZF.png\t3\t5\tY\t5000\t3.9030899869919438\tTrue\tTrue\t\tLB\t37",
                "notes": "The final Science supplementary Table S7 reports a HIPA assay row with a Bas1 phage readout, smaller plaques, and a -log(EOP) value of 3.903."
              }
            ]
          },
          {
            "subject": "ds_6_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "DS-6 system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
                "notes": "DeWeirdt et al. validate DSs as anti-phage systems."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| DS-6 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
                "notes": "The pinned DefenseFinder article registry maps the DS-6 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "ds-6-defensefinder-model-gap",
        "prompt": "Resolve DS-6 native host breadth, exact two-component activities, DS-6 profile-to-protein mapping, sensitive-phage breadth, DUF3037 and DUF1829 activity, HipA-like kinase substrates, and rule-level detection criteria before minting narrower DS-6 mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "DeWeirdt et al. support DS-6 as the defensive HIPA transcriptional unit that reduced Bas1 plaquing when cloned in E. coli MG1655, and the pinned DefenseFinder HMM inventory records two DS-6 profile rows. The pinned rules table has no DS-6 row, and the first-pass record does not resolve native host breadth, exact profile-to-protein correspondence, DUF3037 or HipA-like kinase activity, phage target breadth, or endogenous DS-6 activity.",
        "evidence": [
          {
            "reference": "DOI:10.1126/science.adv7924",
            "snippet": "To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
            "notes": "DeWeirdt et al. validate predicted transcriptional units by measuring plaquing relative to an empty vector control strain."
          },
          {
            "reference": "DOI:10.1126/science.adv7924",
            "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
            "notes": "DeWeirdt et al. name validated TUs as DSs."
          },
          {
            "reference": "DOI:10.1126/science.adv7924",
            "snippet": "We independently discovered DS-6 (renamed HipAD) recently",
            "notes": "DeWeirdt et al. record HipAD as a DS-6 name."
          },
          {
            "reference": "DOI:10.1126/science.adv7924",
            "snippet": "When we mutated a key predicted catalytic residue in DS-6A, we observed a loss of defense, suggesting that kinase activity is essential for protection.",
            "notes": "DeWeirdt et al. report loss of defense after mutation of a predicted DS-6A catalytic residue."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
            "snippet": "HIPA\tNZ_QOWQ01000062.1\tGCF_003334335.1\t-\tTrue\tFalse\tTrue\tTrue\tDefensePredictor hits\t1591\t3164\tDUF3037 domain-containing protein, hypothetical protein\tWP_000210934.1, WP_000389051.1\t6.427268761356274\t-2.428836967683248\tTrue\tFalse\tPredicted novel defense gene\tDS-6",
            "notes": "The final Science supplementary Table S6 maps working_id HIPA to DS_name DS-6, marks the cloned transcriptional unit as defensive, and records NZ_QOWQ01000062.1 positions 1591-3164 with product accessions WP_000210934.1 and WP_000389051.1."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
            "snippet": "Bas1\t1.2\tpLAND\t24-03-08_EV_HHHD_PIN2_CRDO.png\t40000000\tHIPA\t24-03-08\t24-03-08_IMPD_DISA_2CM2_MAZF.png\t3\t5\tY\t5000\t3.9030899869919438\tTrue\tTrue\t\tLB\t37",
            "notes": "The final Science supplementary Table S7 reports a HIPA assay row with a Bas1 phage readout, smaller plaques, and a -log(EOP) value of 3.903."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
            "snippet": "Bas1\tA.1\tMG1655\t24-07-10_EV_MNAC-K375A_MNAC-N84A_MNAC-D52A.png\t3000000\tHIPA\t\t24-07-12\t24-07-12_HIPA_HIPA-D139A_SVIR_SVIR-H52A_DISA_DISA-D433A.png\t1\t2\t\t20\t5.176091259\nBas1\tA.1\tMG1655\t24-07-10_EV_MNAC-K375A_MNAC-N84A_MNAC-D52A.png\t3000000\tHIPA\tD139A\t24-07-12\t24-07-12_HIPA_HIPA-D139A_SVIR_SVIR-H52A_DISA_DISA-D433A.png\t5\t4\t\t400000\t0.8750612634",
            "notes": "The final Science supplementary Table S7 System Mutants sheet pairs wild-type HIPA and HIPA D139A in a Bas1 assay panel, with -log(EOP) shifting from 5.176 to 0.875 for the D139A catalytic mutant."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
            "snippet": "Bas1\tB.1\tMG1655\t24-07-17_MVB1_VPUS_VAME_EV.png\t3000000\tHIPA\t\t24-07-18\t24-07-18_IMPD-Y157A_IMPD_IMPD-R330A_IMPD-H335A_HIPA_HIPA-D139A.png\t2\t10\t\t1000\t3.477121255\nBas1\tB.1\tMG1655\t24-07-17_MVB1_VPUS_VAME_EV.png\t3000000\tHIPA\tD139A\t24-07-18\t24-07-18_IMPD-Y157A_IMPD_IMPD-R330A_IMPD-H335A_HIPA_HIPA-D139A.png\t6\t4\t\t4000000\t-0.1249387366",
            "notes": "The final Science supplementary Table S7 System Mutants sheet records a second HIPA versus HIPA D139A Bas1 panel, with -log(EOP) shifting from 3.477 to -0.125 for the D139A catalytic mutant."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
            "snippet": "HIPA\tDS-6\tTrue",
            "notes": "The final Science supplementary Table S8 maps HIPA to replicated display name DS-6."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
            "snippet": "HIPA\t15.0\t248.0\tWP_000389051.1\tHIPA kinase\tPF20613.3\tHipA_2 ; HipA-like kinase\thhpred_9120093.hhr\t15.0\t248.0\t1.0\t2024-07-28 00:00:00",
            "notes": "The final Science supplementary Table S8 reports a HipA-like kinase HHpred hit for WP_000389051.1 in HIPA."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
            "snippet": "HIPA\t2.0\t275.0\tWP_000210934.1\tDUF3037\tPF11236.12\tDUF3037\thhpred_4386604.hhr\t7.0\t125.0\t0.9987\t2024-04-15 00:00:00",
            "notes": "The final Science supplementary Table S8 reports a DUF3037 HHpred hit for WP_000210934.1 in HIPA."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
            "snippet": "HIPA\t2.0\t275.0\tWP_000210934.1\tDUF1829\tPF08862.14\tDUF1829\thhpred_4386604.hhr\t163.0\t260.0\t0.7785\t2024-04-15 00:00:00",
            "notes": "The final Science supplementary Table S8 reports a DUF1829 HHpred hit for WP_000210934.1 in HIPA."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
            "snippet": "| DS-6 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
            "notes": "The pinned DefenseFinder article registry maps the DS-6 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| DS-6__DS-6A                                      |                                                  | DS-6                   | Custom                  | 100    |",
            "notes": "The pinned DefenseFinder HMM inventory records DS-6__DS-6A as a custom DS-6 profile."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| DS-6__DS-6B                                      |                                                  | DS-6                   | Custom                  | 100    |",
            "notes": "The pinned DefenseFinder HMM inventory records DS-6__DS-6B as a custom DS-6 profile."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "The pinned DefenseFinder rules table does not list DS-6, leaving rule-level detection criteria unresolved."
          }
        ],
        "attaches_to": [
          "causal_graphs#ds_6_locus_reduces_phage_plaquing"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-28"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-28T09:20:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted DS-6 system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; kept the graph at cloned HIPA transcriptional-unit level because the pinned DefenseFinder DS-6 HMM rows are not backed by a rules row; proposals/metpo_traitmech_v307 reserves the replacement placeholder.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-28T09:20:01Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed DS-6 system canonical_examples and left them empty because DeWeirdt et al. support cloned HIPA plaquing assays in E. coli MG1655 plus a DefenseFinder DS-6 model, but not a direct named native microbial isolate exemplar with experimentally verified endogenous DS-6 activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000431",
    "label": "DS-7 system",
    "definition": "A phage defense system in which an organism possesses the single-gene DefensePredictor-discovered system 7 locus cataloged with working_id SVIR and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.",
    "definition_source": "DOI:10.1126/science.adv7924",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "DS-7",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1126/science.adv7924"
      },
      {
        "synonym_text": "SVIR",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx"
      },
      {
        "synonym_text": "DS-7__DS-7",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1126/science.adv7924",
        "snippet": "To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
        "notes": "DeWeirdt et al. experimentally validated 42 predicted transcriptional units as phage-defense systems in E. coli."
      },
      {
        "reference": "DOI:10.1126/science.adv7924",
        "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
        "notes": "DeWeirdt et al. name validated transcriptional units as DefensePredictor discovered systems."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
        "snippet": "SVIR\tNZ_QOYF01000007.1\tGCF_003334585.1\t+\tTrue\tFalse\tFalse\tTrue\tDefensePredictor hits\t310084\t311190\tDUF2634 domain-containing protein\tWP_225403053.1\t5.785481186679323\t3.623314765621056\tTrue\tTrue\tPredicted novel defense gene\tDS-7",
        "notes": "The final Science supplementary Table S6 maps working_id SVIR to DS_name DS-7, marks the cloned transcriptional unit as defensive, and records NZ_QOYF01000007.1 positions 310084-311190 with product accession WP_225403053.1."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
        "snippet": "Bas60\t1.2\tpLAND\t24-03-08_EV_HHHD_PIN2_CRDO.png\t5000000\tSVIR\t24-03-12\t24-03-12_SVIR_PIN8_NTTI_NADR.png\t2\t100\t\t10000\t2.6989700043360187\tTrue\t\t\tLB\t37",
        "notes": "The final Science supplementary Table S7 reports an SVIR assay row with a Bas60 phage readout and a -log(EOP) value of 2.699."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
        "snippet": "Bas60\tA.1\tMG1655\t24-07-10_EV_MNAC-K375A_MNAC-N84A_MNAC-D52A.png\t3000000\tSVIR\t\t24-07-12\t24-07-12_HIPA_HIPA-D139A_SVIR_SVIR-H52A_DISA_DISA-D433A.png\t4\t14\t\t140000\t1.330993219\nBas60\tA.1\tMG1655\t24-07-10_EV_MNAC-K375A_MNAC-N84A_MNAC-D52A.png\t3000000\tSVIR\tH52A\t24-07-12\t24-07-12_HIPA_HIPA-D139A_SVIR_SVIR-H52A_DISA_DISA-D433A.png\t5\t10\t\t1000000\t0.4771212547",
        "notes": "The final Science supplementary Table S7 System Mutants sheet pairs wild-type SVIR and SVIR H52A in a Bas60 assay panel, with -log(EOP) shifting from 1.331 to 0.477 for the H52A mutant."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
        "snippet": "Bas60\tB.1\tMG1655\t24-07-17_MVB1_VPUS_VAME_EV.png\t400000\tSVIR\t\t24-07-18\t24-07-18_DISA-R468A_DISA_SVIR_DISA-D433A_SVIR-H52A.png\t0\t1\t\t1\t5.602059991\nBas60\tB.1\tMG1655\t24-07-17_MVB1_VPUS_VAME_EV.png\t400000\tSVIR\tH52A\t24-07-18\t24-07-18_DISA-R468A_DISA_SVIR_DISA-D433A_SVIR-H52A.png\t4\t22\t\t220000\t0.2596373105",
        "notes": "The final Science supplementary Table S7 System Mutants sheet records a second SVIR versus SVIR H52A Bas60 panel, with -log(EOP) shifting from 5.602 to 0.260 for the H52A mutant."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
        "snippet": "SVIR\tDS-7\tTrue",
        "notes": "The final Science supplementary Table S8 maps SVIR to replicated display name DS-7."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
        "snippet": "SVIR\t1.0\t368.0\tWP_225403053.1\tHNH endonuclease\t7RWK_A\tSAVED domain-containing protein; DNA nuclease SAVED Sensor Effector\thhpred_1710432.hhr\t5.0\t122.0\t0.99\t2024-04-17 00:00:00",
        "notes": "The final Science supplementary Table S8 reports an HNH endonuclease HHpred hit for WP_225403053.1 in SVIR."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
        "snippet": "SVIR\t1.0\t368.0\tWP_225403053.1\tPhage baseplate\t8ENV_M\tSheath initiator gp34; Pseudomonas, phage, baseplate\thhpred_1710432.hhr\t225.0\t350.0\t0.99\t2024-04-17 00:00:00",
        "notes": "The final Science supplementary Table S8 reports a phage-baseplate-like HHpred hit for WP_225403053.1 in SVIR."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| DS-7 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
        "notes": "The pinned DefenseFinder article registry maps the DS-7 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| DS-7__DS-7                                       |                                                  | DS-7                   | Custom                  | 200    |",
        "notes": "The pinned DefenseFinder HMM inventory records DS-7__DS-7 as a custom DS-7 profile."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "ds_7_locus_reduces_phage_plaquing",
        "title": "DS-7 locus reduces bacteriophage plaquing",
        "description": "Conservative system-level sketch linking the single-gene DS-7 locus to reduced bacteriophage plaquing without resolving DS-7 component function or effector activity.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures DS-7 as the validated SVIR transcriptional unit with one product accession and with a DefenseFinder DS-7 profile row. It does not assert native host breadth, exact profile-to-protein correspondence, the direct viral trigger or substrate, the exact HNH endonuclease activity, phage-baseplate-like domain relevance, phage target breadth, or DefenseFinder rule-level detection criteria.",
        "nodes": [
          {
            "node_id": "ds_7_locus",
            "label": "DS-7 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A single-gene DefensePredictor-discovered system locus represented in the pinned DefenseFinder HMM inventory by one DS-7 custom profile."
          },
          {
            "node_id": "reduced_phage_plaquing",
            "label": "reduced bacteriophage plaquing",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced efficiency of plaquing by bacteriophage Bas60 in cells carrying cloned SVIR."
          },
          {
            "node_id": "ds_7_system_trait",
            "label": "DS-7 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000431",
            "description": "Possession of a genome-encoded DS-7 phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "ds_7_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "reduced_phage_plaquing",
            "description": "The DS-7/SVIR locus contributes to reduced bacteriophage plaquing when plasmid expressed.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
                "notes": "DeWeirdt et al. experimentally validate DefensePredictor-discovered systems by assaying cloned transcriptional units against E. coli phages."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
                "snippet": "SVIR\tNZ_QOYF01000007.1\tGCF_003334585.1\t+\tTrue\tFalse\tFalse\tTrue\tDefensePredictor hits\t310084\t311190\tDUF2634 domain-containing protein\tWP_225403053.1\t5.785481186679323\t3.623314765621056\tTrue\tTrue\tPredicted novel defense gene\tDS-7",
                "notes": "The final Science supplementary Table S6 maps working_id SVIR to DS_name DS-7, marks the cloned transcriptional unit as defensive, and records NZ_QOYF01000007.1 positions 310084-311190 with product accession WP_225403053.1."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
                "snippet": "Bas60\t1.2\tpLAND\t24-03-08_EV_HHHD_PIN2_CRDO.png\t5000000\tSVIR\t24-03-12\t24-03-12_SVIR_PIN8_NTTI_NADR.png\t2\t100\t\t10000\t2.6989700043360187\tTrue\t\t\tLB\t37",
                "notes": "The final Science supplementary Table S7 reports an SVIR assay row with a Bas60 phage readout and a -log(EOP) value of 2.699."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
                "snippet": "Bas60\tA.1\tMG1655\t24-07-10_EV_MNAC-K375A_MNAC-N84A_MNAC-D52A.png\t3000000\tSVIR\t\t24-07-12\t24-07-12_HIPA_HIPA-D139A_SVIR_SVIR-H52A_DISA_DISA-D433A.png\t4\t14\t\t140000\t1.330993219\nBas60\tA.1\tMG1655\t24-07-10_EV_MNAC-K375A_MNAC-N84A_MNAC-D52A.png\t3000000\tSVIR\tH52A\t24-07-12\t24-07-12_HIPA_HIPA-D139A_SVIR_SVIR-H52A_DISA_DISA-D433A.png\t5\t10\t\t1000000\t0.4771212547",
                "notes": "The final Science supplementary Table S7 System Mutants sheet pairs wild-type SVIR and SVIR H52A in a Bas60 assay panel, with -log(EOP) shifting from 1.331 to 0.477 for the H52A mutant."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
                "snippet": "Bas60\tB.1\tMG1655\t24-07-17_MVB1_VPUS_VAME_EV.png\t400000\tSVIR\t\t24-07-18\t24-07-18_DISA-R468A_DISA_SVIR_DISA-D433A_SVIR-H52A.png\t0\t1\t\t1\t5.602059991\nBas60\tB.1\tMG1655\t24-07-17_MVB1_VPUS_VAME_EV.png\t400000\tSVIR\tH52A\t24-07-18\t24-07-18_DISA-R468A_DISA_SVIR_DISA-D433A_SVIR-H52A.png\t4\t22\t\t220000\t0.2596373105",
                "notes": "The final Science supplementary Table S7 System Mutants sheet records a second SVIR versus SVIR H52A Bas60 panel, with -log(EOP) shifting from 5.602 to 0.260 for the H52A mutant."
              }
            ]
          },
          {
            "subject": "reduced_phage_plaquing",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "ds_7_system_trait",
            "description": "DS-7-mediated phage plaquing reduction realizes the DS-7 system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
                "notes": "DeWeirdt et al. name each validated transcriptional unit as a DefensePredictor discovered system."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
                "snippet": "SVIR\tNZ_QOYF01000007.1\tGCF_003334585.1\t+\tTrue\tFalse\tFalse\tTrue\tDefensePredictor hits\t310084\t311190\tDUF2634 domain-containing protein\tWP_225403053.1\t5.785481186679323\t3.623314765621056\tTrue\tTrue\tPredicted novel defense gene\tDS-7",
                "notes": "The final Science supplementary Table S6 maps working_id SVIR to DS_name DS-7, marks the cloned transcriptional unit as defensive, and records NZ_QOYF01000007.1 positions 310084-311190 with product accession WP_225403053.1."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
                "snippet": "Bas60\t1.2\tpLAND\t24-03-08_EV_HHHD_PIN2_CRDO.png\t5000000\tSVIR\t24-03-12\t24-03-12_SVIR_PIN8_NTTI_NADR.png\t2\t100\t\t10000\t2.6989700043360187\tTrue\t\t\tLB\t37",
                "notes": "The final Science supplementary Table S7 reports an SVIR assay row with a Bas60 phage readout and a -log(EOP) value of 2.699."
              }
            ]
          },
          {
            "subject": "ds_7_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "DS-7 system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
                "notes": "DeWeirdt et al. validate DSs as anti-phage systems."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| DS-7 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
                "notes": "The pinned DefenseFinder article registry maps the DS-7 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "ds-7-defensefinder-model-gap",
        "prompt": "Resolve DS-7 native host breadth, exact single-component activity, DS-7 profile-to-protein mapping, sensitive-phage breadth, HNH endonuclease activity, the role of the H52 residue, the phage-baseplate-like hit, and rule-level detection criteria before minting narrower DS-7 mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "DeWeirdt et al. support DS-7 as the defensive SVIR transcriptional unit that reduced Bas60 plaquing when cloned in E. coli MG1655, and the pinned DefenseFinder HMM inventory records one DS-7 profile row. The pinned rules table has no DS-7 row, and the first-pass record does not resolve native host breadth, exact profile-to-protein correspondence, HNH endonuclease activity, the function of the H52 residue, phage target breadth, or endogenous DS-7 activity.",
        "evidence": [
          {
            "reference": "DOI:10.1126/science.adv7924",
            "snippet": "To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
            "notes": "DeWeirdt et al. validate predicted transcriptional units by measuring plaquing relative to an empty vector control strain."
          },
          {
            "reference": "DOI:10.1126/science.adv7924",
            "snippet": "We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.",
            "notes": "DeWeirdt et al. name validated TUs as DSs."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
            "snippet": "SVIR\tNZ_QOYF01000007.1\tGCF_003334585.1\t+\tTrue\tFalse\tFalse\tTrue\tDefensePredictor hits\t310084\t311190\tDUF2634 domain-containing protein\tWP_225403053.1\t5.785481186679323\t3.623314765621056\tTrue\tTrue\tPredicted novel defense gene\tDS-7",
            "notes": "The final Science supplementary Table S6 maps working_id SVIR to DS_name DS-7, marks the cloned transcriptional unit as defensive, and records NZ_QOYF01000007.1 positions 310084-311190 with product accession WP_225403053.1."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
            "snippet": "Bas60\t1.2\tpLAND\t24-03-08_EV_HHHD_PIN2_CRDO.png\t5000000\tSVIR\t24-03-12\t24-03-12_SVIR_PIN8_NTTI_NADR.png\t2\t100\t\t10000\t2.6989700043360187\tTrue\t\t\tLB\t37",
            "notes": "The final Science supplementary Table S7 reports an SVIR assay row with a Bas60 phage readout and a -log(EOP) value of 2.699."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
            "snippet": "Bas60\tA.1\tMG1655\t24-07-10_EV_MNAC-K375A_MNAC-N84A_MNAC-D52A.png\t3000000\tSVIR\t\t24-07-12\t24-07-12_HIPA_HIPA-D139A_SVIR_SVIR-H52A_DISA_DISA-D433A.png\t4\t14\t\t140000\t1.330993219\nBas60\tA.1\tMG1655\t24-07-10_EV_MNAC-K375A_MNAC-N84A_MNAC-D52A.png\t3000000\tSVIR\tH52A\t24-07-12\t24-07-12_HIPA_HIPA-D139A_SVIR_SVIR-H52A_DISA_DISA-D433A.png\t5\t10\t\t1000000\t0.4771212547",
            "notes": "The final Science supplementary Table S7 System Mutants sheet pairs wild-type SVIR and SVIR H52A in a Bas60 assay panel, with -log(EOP) shifting from 1.331 to 0.477 for the H52A mutant."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
            "snippet": "Bas60\tB.1\tMG1655\t24-07-17_MVB1_VPUS_VAME_EV.png\t400000\tSVIR\t\t24-07-18\t24-07-18_DISA-R468A_DISA_SVIR_DISA-D433A_SVIR-H52A.png\t0\t1\t\t1\t5.602059991\nBas60\tB.1\tMG1655\t24-07-17_MVB1_VPUS_VAME_EV.png\t400000\tSVIR\tH52A\t24-07-18\t24-07-18_DISA-R468A_DISA_SVIR_DISA-D433A_SVIR-H52A.png\t4\t22\t\t220000\t0.2596373105",
            "notes": "The final Science supplementary Table S7 System Mutants sheet records a second SVIR versus SVIR H52A Bas60 panel, with -log(EOP) shifting from 5.602 to 0.260 for the H52A mutant."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
            "snippet": "SVIR\tDS-7\tTrue",
            "notes": "The final Science supplementary Table S8 maps SVIR to replicated display name DS-7."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
            "snippet": "SVIR\t1.0\t368.0\tWP_225403053.1\tHNH endonuclease\t7RWK_A\tSAVED domain-containing protein; DNA nuclease SAVED Sensor Effector\thhpred_1710432.hhr\t5.0\t122.0\t0.99\t2024-04-17 00:00:00",
            "notes": "The final Science supplementary Table S8 reports an HNH endonuclease HHpred hit for WP_225403053.1 in SVIR."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
            "snippet": "SVIR\t1.0\t368.0\tWP_225403053.1\tPhage baseplate\t8ENV_M\tSheath initiator gp34; Pseudomonas, phage, baseplate\thhpred_1710432.hhr\t225.0\t350.0\t0.99\t2024-04-17 00:00:00",
            "notes": "The final Science supplementary Table S8 reports a phage-baseplate-like HHpred hit for WP_225403053.1 in SVIR."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
            "snippet": "| DS-7 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
            "notes": "The pinned DefenseFinder article registry maps the DS-7 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| DS-7__DS-7                                       |                                                  | DS-7                   | Custom                  | 200    |",
            "notes": "The pinned DefenseFinder HMM inventory records DS-7__DS-7 as a custom DS-7 profile."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "The pinned DefenseFinder rules table does not list DS-7, leaving rule-level detection criteria unresolved."
          }
        ],
        "attaches_to": [
          "causal_graphs#ds_7_locus_reduces_phage_plaquing"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-28"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-28T09:58:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted DS-7 system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; kept the graph at cloned SVIR transcriptional-unit level because the pinned DefenseFinder DS-7 HMM row is not backed by a rules row; proposals/metpo_traitmech_v308 reserves the replacement placeholder.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-28T09:58:01Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed DS-7 system canonical_examples and left them empty because DeWeirdt et al. support cloned SVIR plaquing assays in E. coli MG1655 plus a DefenseFinder DS-7 model, but not a direct named native microbial isolate exemplar with experimentally verified endogenous DS-7 activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000432",
    "label": "DS-8 system",
    "definition": "A phage defense system in which an organism possesses the single-gene DefensePredictor-discovered system 8 locus cataloged with working_id MNAC and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.",
    "definition_source": "DOI:10.1126/science.adv7924",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "DS-8",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1126/science.adv7924"
      },
      {
        "synonym_text": "MNAC",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx"
      },
      {
        "synonym_text": "DS-8__DS-8",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1126/science.adv7924",
        "snippet": "To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
        "notes": "DeWeirdt et al. experimentally validated 42 predicted transcriptional units as phage-defense systems in E. coli."
      },
      {
        "reference": "DOI:10.1126/science.adv7924",
        "snippet": "First, we investigated DS-8, a single protein system containing a metallophosphatase domain (Fig. 5A) which is homologous to the human protein SMPDL3A, a phosphodiesterase that cleaves cGAMP to modulate cGAS-STING immunity signaling",
        "notes": "DeWeirdt et al. identify DS-8 as a single-protein metallophosphatase-domain system."
      },
      {
        "reference": "DOI:10.1126/science.adv7924",
        "snippet": "Mutating either of two predicted catalytic residues in the metallophosphatase domain or a residue likely critical to NACHT ATPase activity completely ablated defense by DS-8, indicating that both domains and metallophosphatase activity are essential for protection",
        "notes": "DeWeirdt et al. report that predicted metallophosphatase catalytic-residue and NACHT ATPase-residue mutations ablated DS-8 defense."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
        "snippet": "MNAC\tNZ_RRWS01000004.1\tGCF_003892555.1\t-\tTrue\tFalse\tFalse\tTrue\tDefensePredictor hits\t83803\t86847\tmetallophosphoesterase\tWP_032203427.1\t9.394229333124514\t6.212606095751518\tTrue\tTrue\tPredicted novel defense gene\tDS-8",
        "notes": "The final Science supplementary Table S6 maps working_id MNAC to DS_name DS-8, marks the cloned transcriptional unit as defensive, and records NZ_RRWS01000004.1 positions 83803-86847 with product accession WP_032203427.1."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
        "snippet": "Bas1\t1.2\tpLAND\t24-03-08_EV_HHHD_PIN2_CRDO.png\t40000000\tMNAC\t24-03-08\t24-03-08_MNAC_GHOS_BRNT_IMPD.png\t1\t10\tY\t100\t5.6020599913279625\tTrue\t\t\tLB\t37",
        "notes": "The final Science supplementary Table S7 reports an MNAC assay row with a Bas1 phage readout and a -log(EOP) value of 5.602."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
        "snippet": "Bas1\tA.1\tMG1655\t24-07-10_EV_MNAC-K375A_MNAC-N84A_MNAC-D52A.png\t3000000\tMNAC\tK375A\t24-07-10\t24-07-10_EV_MNAC-K375A_MNAC-N84A_MNAC-D52A.png\t6\t3\t\t3000000\t0",
        "notes": "The final Science supplementary Table S7 reports the MNAC K375A Bas1 mutant row with a -log(EOP) value of 0."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
        "snippet": "Bas1\tA.1\tMG1655\t24-07-10_EV_MNAC-K375A_MNAC-N84A_MNAC-D52A.png\t3000000\tMNAC\tN84A\t24-07-10\t24-07-10_EV_MNAC-K375A_MNAC-N84A_MNAC-D52A.png\t6\t2\t\t2000000\t0.1760912591",
        "notes": "The final Science supplementary Table S7 reports the MNAC N84A Bas1 mutant row with a -log(EOP) value of 0.176."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
        "snippet": "Bas1\tA.1\tMG1655\t24-07-10_EV_MNAC-K375A_MNAC-N84A_MNAC-D52A.png\t3000000\tMNAC\tD52A\t24-07-10\t24-07-10_EV_MNAC-K375A_MNAC-N84A_MNAC-D52A.png\t6\t4\t\t4000000\t-0.1249387366",
        "notes": "The final Science supplementary Table S7 reports the MNAC D52A Bas1 mutant row with a -log(EOP) value of -0.125."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
        "snippet": "MNAC\tDS-8\tTrue",
        "notes": "The final Science supplementary Table S8 maps MNAC to replicated display name DS-8."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
        "snippet": "MNAC\t1.0\t1014.0\tWP_032203427.1\tMetallophosphatase\t5KAR_A\tAcid sphingomyelinase-like phosphodiesterase 3b; phosphoesterase, extracellular, membrane\thhpred_8521728.hhr\t1.0\t275.0\t0.997\t2024-04-16 00:00:00",
        "notes": "The final Science supplementary Table S8 reports a metallophosphatase HHpred hit for WP_032203427.1 in MNAC."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
        "snippet": "MNAC\t1.0\t1014.0\tWP_032203427.1\tNACHT\t8FML_A\tBaculoviral IAP repeat-containing protein 1e; Inflammasome, Innate immunity, Bacterial ligand, host-pathogen interaction, Protein complex, IMMUNE SYSTEM\thhpred_8521728.hhr\t331.0\t734.0\t1.0\t2024-04-16 00:00:00",
        "notes": "The final Science supplementary Table S8 reports a NACHT HHpred hit for WP_032203427.1 in MNAC."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| DS-8 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
        "notes": "The pinned DefenseFinder article registry maps the DS-8 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| DS-8__DS-8                                       |                                                  | DS-8                   | Custom                  | 200    |",
        "notes": "The pinned DefenseFinder HMM inventory records DS-8__DS-8 as a custom DS-8 profile."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "ds_8_locus_reduces_phage_plaquing",
        "title": "DS-8 locus reduces bacteriophage plaquing",
        "description": "Conservative system-level sketch linking the single-gene DS-8 locus to reduced bacteriophage plaquing without resolving DS-8 component function or effector activity.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures DS-8 as the validated MNAC transcriptional unit with one product accession and with a DefenseFinder DS-8 profile row. It does not assert native host breadth, exact profile-to-protein correspondence, the direct viral trigger or cyclic-nucleotide substrate, the exact NACHT-mediated activation step, relationship to NLR-like bNACHT systems, phage target breadth, or DefenseFinder rule-level detection criteria.",
        "nodes": [
          {
            "node_id": "ds_8_locus",
            "label": "DS-8 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A single-gene DefensePredictor-discovered system locus represented in the pinned DefenseFinder HMM inventory by one DS-8 custom profile."
          },
          {
            "node_id": "reduced_phage_plaquing",
            "label": "reduced bacteriophage plaquing",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced efficiency of plaquing by bacteriophage Bas1 in cells carrying cloned MNAC."
          },
          {
            "node_id": "ds_8_system_trait",
            "label": "DS-8 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000432",
            "description": "Possession of a genome-encoded DS-8 phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "ds_8_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "reduced_phage_plaquing",
            "description": "The DS-8/MNAC locus contributes to reduced bacteriophage plaquing when plasmid expressed.",
            "evidence": [
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
                "snippet": "MNAC\tNZ_RRWS01000004.1\tGCF_003892555.1\t-\tTrue\tFalse\tFalse\tTrue\tDefensePredictor hits\t83803\t86847\tmetallophosphoesterase\tWP_032203427.1\t9.394229333124514\t6.212606095751518\tTrue\tTrue\tPredicted novel defense gene\tDS-8",
                "notes": "The final Science supplementary Table S6 maps working_id MNAC to DS_name DS-8, marks the cloned transcriptional unit as defensive, and records NZ_RRWS01000004.1 positions 83803-86847 with product accession WP_032203427.1."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
                "snippet": "Bas1\t1.2\tpLAND\t24-03-08_EV_HHHD_PIN2_CRDO.png\t40000000\tMNAC\t24-03-08\t24-03-08_MNAC_GHOS_BRNT_IMPD.png\t1\t10\tY\t100\t5.6020599913279625\tTrue\t\t\tLB\t37",
                "notes": "The final Science supplementary Table S7 reports an MNAC assay row with a Bas1 phage readout and a -log(EOP) value of 5.602."
              }
            ]
          },
          {
            "subject": "reduced_phage_plaquing",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "ds_8_system_trait",
            "description": "DS-8-mediated phage plaquing reduction realizes the DS-8 system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "First, we investigated DS-8, a single protein system containing a metallophosphatase domain (Fig. 5A) which is homologous to the human protein SMPDL3A, a phosphodiesterase that cleaves cGAMP to modulate cGAS-STING immunity signaling",
                "notes": "DeWeirdt et al. identify DS-8 as a single-protein metallophosphatase-domain system."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
                "snippet": "MNAC\tNZ_RRWS01000004.1\tGCF_003892555.1\t-\tTrue\tFalse\tFalse\tTrue\tDefensePredictor hits\t83803\t86847\tmetallophosphoesterase\tWP_032203427.1\t9.394229333124514\t6.212606095751518\tTrue\tTrue\tPredicted novel defense gene\tDS-8",
                "notes": "The final Science supplementary Table S6 maps working_id MNAC to DS_name DS-8, marks the cloned transcriptional unit as defensive, and records NZ_RRWS01000004.1 positions 83803-86847 with product accession WP_032203427.1."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
                "snippet": "Bas1\t1.2\tpLAND\t24-03-08_EV_HHHD_PIN2_CRDO.png\t40000000\tMNAC\t24-03-08\t24-03-08_MNAC_GHOS_BRNT_IMPD.png\t1\t10\tY\t100\t5.6020599913279625\tTrue\t\t\tLB\t37",
                "notes": "The final Science supplementary Table S7 reports an MNAC assay row with a Bas1 phage readout and a -log(EOP) value of 5.602."
              }
            ]
          },
          {
            "subject": "ds_8_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "DS-8 system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
                "notes": "DeWeirdt et al. validate DSs as anti-phage systems."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| DS-8 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
                "notes": "The pinned DefenseFinder article registry maps the DS-8 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "ds-8-defensefinder-model-gap",
        "prompt": "Resolve DS-8 native host breadth, DS-8 profile-to-protein mapping, sensitive-phage breadth, direct cyclic-nucleotide substrate, NACHT-mediated activation route, relationship to NLR-like bNACHT systems, and rule-level detection criteria before minting narrower DS-8 mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "DeWeirdt et al. support DS-8 as the defensive MNAC transcriptional unit that reduced Bas1 plaquing when cloned in E. coli MG1655, identify DS-8 as a single-protein system with metallophosphatase and NACHT domains, and report that D52A, N84A, and K375A mutations ablated Bas1 protection. The pinned DefenseFinder HMM inventory records one DS-8 profile row. The pinned rules table has no DS-8 row, and the first-pass record does not resolve native host breadth, exact profile-to-protein correspondence, direct cyclic-nucleotide substrate, exact NACHT-mediated activation route, phage target breadth, endogenous DS-8 activity, or whether DS-8 should be related to the broader NLR-like bNACHT system family.",
        "evidence": [
          {
            "reference": "DOI:10.1126/science.adv7924",
            "snippet": "To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
            "notes": "DeWeirdt et al. validate predicted transcriptional units by measuring plaquing relative to an empty vector control strain."
          },
          {
            "reference": "DOI:10.1126/science.adv7924",
            "snippet": "First, we investigated DS-8, a single protein system containing a metallophosphatase domain (Fig. 5A) which is homologous to the human protein SMPDL3A, a phosphodiesterase that cleaves cGAMP to modulate cGAS-STING immunity signaling",
            "notes": "DeWeirdt et al. identify DS-8 as single-protein."
          },
          {
            "reference": "DOI:10.1126/science.adv7924",
            "snippet": "Mutating either of two predicted catalytic residues in the metallophosphatase domain or a residue likely critical to NACHT ATPase activity completely ablated defense by DS-8, indicating that both domains and metallophosphatase activity are essential for protection",
            "notes": "DeWeirdt et al. state that DS-8 metallophosphatase and NACHT catalytic mutants ablate defense."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
            "snippet": "MNAC\tNZ_RRWS01000004.1\tGCF_003892555.1\t-\tTrue\tFalse\tFalse\tTrue\tDefensePredictor hits\t83803\t86847\tmetallophosphoesterase\tWP_032203427.1\t9.394229333124514\t6.212606095751518\tTrue\tTrue\tPredicted novel defense gene\tDS-8",
            "notes": "The final Science supplementary Table S6 maps working_id MNAC to DS_name DS-8, marks the cloned transcriptional unit as defensive, and records NZ_RRWS01000004.1 positions 83803-86847 with product accession WP_032203427.1."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
            "snippet": "Bas1\t1.2\tpLAND\t24-03-08_EV_HHHD_PIN2_CRDO.png\t40000000\tMNAC\t24-03-08\t24-03-08_MNAC_GHOS_BRNT_IMPD.png\t1\t10\tY\t100\t5.6020599913279625\tTrue\t\t\tLB\t37",
            "notes": "The final Science supplementary Table S7 reports an MNAC assay row with a Bas1 phage readout and a -log(EOP) value of 5.602."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
            "snippet": "Bas1\tA.1\tMG1655\t24-07-10_EV_MNAC-K375A_MNAC-N84A_MNAC-D52A.png\t3000000\tMNAC\tK375A\t24-07-10\t24-07-10_EV_MNAC-K375A_MNAC-N84A_MNAC-D52A.png\t6\t3\t\t3000000\t0",
            "notes": "The final Science supplementary Table S7 reports the MNAC K375A Bas1 mutant row with a -log(EOP) value of 0."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
            "snippet": "Bas1\tA.1\tMG1655\t24-07-10_EV_MNAC-K375A_MNAC-N84A_MNAC-D52A.png\t3000000\tMNAC\tN84A\t24-07-10\t24-07-10_EV_MNAC-K375A_MNAC-N84A_MNAC-D52A.png\t6\t2\t\t2000000\t0.1760912591",
            "notes": "The final Science supplementary Table S7 reports the MNAC N84A Bas1 mutant row with a -log(EOP) value of 0.176."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
            "snippet": "Bas1\tA.1\tMG1655\t24-07-10_EV_MNAC-K375A_MNAC-N84A_MNAC-D52A.png\t3000000\tMNAC\tD52A\t24-07-10\t24-07-10_EV_MNAC-K375A_MNAC-N84A_MNAC-D52A.png\t6\t4\t\t4000000\t-0.1249387366",
            "notes": "The final Science supplementary Table S7 reports the MNAC D52A Bas1 mutant row with a -log(EOP) value of -0.125."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
            "snippet": "MNAC\tDS-8\tTrue",
            "notes": "The final Science supplementary Table S8 maps MNAC to replicated display name DS-8."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
            "snippet": "MNAC\t1.0\t1014.0\tWP_032203427.1\tMetallophosphatase\t5KAR_A\tAcid sphingomyelinase-like phosphodiesterase 3b; phosphoesterase, extracellular, membrane\thhpred_8521728.hhr\t1.0\t275.0\t0.997\t2024-04-16 00:00:00",
            "notes": "The final Science supplementary Table S8 reports a metallophosphatase HHpred hit for WP_032203427.1 in MNAC."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
            "snippet": "MNAC\t1.0\t1014.0\tWP_032203427.1\tNACHT\t8FML_A\tBaculoviral IAP repeat-containing protein 1e; Inflammasome, Innate immunity, Bacterial ligand, host-pathogen interaction, Protein complex, IMMUNE SYSTEM\thhpred_8521728.hhr\t331.0\t734.0\t1.0\t2024-04-16 00:00:00",
            "notes": "The final Science supplementary Table S8 reports a NACHT HHpred hit for WP_032203427.1 in MNAC."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
            "snippet": "| DS-8 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
            "notes": "The pinned DefenseFinder article registry maps the DS-8 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| DS-8__DS-8                                       |                                                  | DS-8                   | Custom                  | 200    |",
            "notes": "The pinned DefenseFinder HMM inventory records DS-8__DS-8 as a custom DS-8 profile."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "The pinned DefenseFinder rules table does not list DS-8, leaving rule-level detection criteria unresolved."
          }
        ],
        "attaches_to": [
          "causal_graphs#ds_8_locus_reduces_phage_plaquing"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-28"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-28T10:43:27Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted DS-8 system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; kept the graph at cloned MNAC transcriptional-unit level because the pinned DefenseFinder DS-8 HMM row is not backed by a rules row; proposals/metpo_traitmech_v309 reserves the replacement placeholder.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-28T10:43:28Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed DS-8 system canonical_examples and left them empty because DeWeirdt et al. support cloned MNAC plaquing assays in E. coli MG1655 plus a DefenseFinder DS-8 model, but not a direct named native microbial isolate exemplar with experimentally verified endogenous DS-8 activity. No paid research was used.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-28T11:24:51Z",
        "curator": "codex",
        "action": "ADDRESS_REVIEW_FINDINGS",
        "changes": "Addressed PR review issues #1397 and #1398 by replacing the ambiguous generic DS naming quote with DS-8-specific single-protein and catalytic-mutant article snippets, adding final Science Table S7 MNAC K375A/N84A/D52A Bas1 mutant evidence, and narrowing the open DS-8 knowledge gap to substrate identity, NACHT-mediated activation route, native-host and phage breadth, exact profile mapping, and DefenseFinder rule-level criteria.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000433",
    "label": "DS-9 system",
    "definition": "A phage defense system in which an organism possesses the two-gene DefensePredictor-discovered system 9 locus cataloged with working_id MHAD and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.",
    "definition_source": "DOI:10.1126/science.adv7924",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "DS-9",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1126/science.adv7924"
      },
      {
        "synonym_text": "MHAD",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx"
      },
      {
        "synonym_text": "DS-9__DS-9A",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "DS-9__DS-9B",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1126/science.adv7924",
        "snippet": "To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
        "notes": "DeWeirdt et al. experimentally validated 42 predicted transcriptional units as phage-defense systems in E. coli."
      },
      {
        "reference": "DOI:10.1126/science.adv7924",
        "snippet": "The system DS-9 has two genes, the first harboring a metallophosphatase domain homologous to that of DS-8, and the second a predicted haloacid dehalogenase-like (HAD) phosphatase",
        "notes": "DeWeirdt et al. identify DS-9 as a two-gene system with metallophosphatase and HAD phosphatase domains."
      },
      {
        "reference": "DOI:10.1126/science.adv7924",
        "snippet": "When we mutated the predicted catalytic residues in the metallophosphatase domain of DS-9A, we saw a loss of defense, suggesting it is essential for protection",
        "notes": "DeWeirdt et al. report that predicted DS-9A metallophosphatase catalytic-residue mutations caused a loss of defense."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
        "snippet": "MHAD\tNZ_QOWZ01000056.1\tGCF_003334705.1\t-\tTrue\tFalse\tFalse\tTrue\tDefensePredictor hits\t6224\t8706\tHAD-IA family hydrolase, metallophosphoesterase\tWP_000770925.1, WP_000665639.1\t4.506698206217075\t6.906754778648663\tTrue\tTrue\tPredicted novel defense gene\tDS-9",
        "notes": "The final Science supplementary Table S6 maps working_id MHAD to DS_name DS-9, marks the cloned transcriptional unit as defensive, and records NZ_QOWZ01000056.1 positions 6224-8706 with product accessions WP_000770925.1 and WP_000665639.1."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
        "snippet": "Bas1\t1.2\tpLAND\t24-03-08_EV_HHHD_PIN2_CRDO.png\t40000000\tMHAD\t24-03-08\t24-03-08_NYND_GHOS_MHAD_UDNG.png\t3\t3\t\t3000\t4.1249387366083\tTrue\t\t\tLB\t37",
        "notes": "The final Science supplementary Table S7 reports an MHAD assay row with a Bas1 phage readout and a -log(EOP) value of 4.125."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
        "snippet": "Bas1\tA.1\tMG1655\t24-07-10_EV_MNAC-K375A_MNAC-N84A_MNAC-D52A.png\t3000000\tMHAD\t\t24-07-17\t24-07-17_PN12-dACR_PN12_MHAD_MHAD-D207A_MHAD-N292A.png\t2\t8\t\t800\t3.574031268",
        "notes": "The final Science supplementary Table S7 reports the MHAD WT Bas1 mutant-panel row with a -log(EOP) value of 3.574."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
        "snippet": "Bas1\tA.1\tMG1655\t24-07-10_EV_MNAC-K375A_MNAC-N84A_MNAC-D52A.png\t3000000\tMHAD\tD207A\t24-07-17\t24-07-17_PN12-dACR_PN12_MHAD_MHAD-D207A_MHAD-N292A.png\t6\t3\t\t3000000\t0",
        "notes": "The final Science supplementary Table S7 reports the MHAD D207A Bas1 mutant-panel row with a -log(EOP) value of 0."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
        "snippet": "Bas1\tA.1\tMG1655\t24-07-10_EV_MNAC-K375A_MNAC-N84A_MNAC-D52A.png\t3000000\tMHAD\tN292A\t24-07-17\t24-07-17_PN12-dACR_PN12_MHAD_MHAD-D207A_MHAD-N292A.png\t6\t2\t\t2000000\t0.1760912591",
        "notes": "The final Science supplementary Table S7 reports the MHAD N292A Bas1 mutant-panel row with a -log(EOP) value of 0.176."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
        "snippet": "MHAD\tDS-9\tTrue",
        "notes": "The final Science supplementary Table S8 maps MHAD to replicated display name DS-9."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
        "snippet": "MHAD\t2.0\t278.0\tWP_000770925.1\tHAD phosphatase\tcd02616\tHAD_PPase; pyrophosphatase\thhpred_3345609.hhr\t1.0\t277.0\t0.999\t2024-04-16 00:00:00",
        "notes": "The final Science supplementary Table S8 reports a HAD phosphatase HHpred hit for WP_000770925.1 in MHAD."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
        "snippet": "MHAD\t1.0\t549.0\tWP_000665639.1\tMetallophosphatase\tcd07378\tMPP_ACP5; Homo sapiens acid phosphatase 5 and related proteins, metallophosphatase domain.\thhpred_3407490.hhr\t200.0\t533.0\t0.9983\t2024-04-16 00:00:00",
        "notes": "The final Science supplementary Table S8 reports a metallophosphatase HHpred hit for WP_000665639.1 in MHAD."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| DS-9 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
        "notes": "The pinned DefenseFinder article registry maps the DS-9 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| DS-9__DS-9A                                      |                                                  | DS-9                   | Custom                  | 300    |",
        "notes": "The pinned DefenseFinder HMM inventory records DS-9__DS-9A as a custom DS-9 profile."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| DS-9__DS-9B                                      |                                                  | DS-9                   | Custom                  | 100    |",
        "notes": "The pinned DefenseFinder HMM inventory records DS-9__DS-9B as a custom DS-9 profile."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "ds_9_locus_reduces_phage_plaquing",
        "title": "DS-9 locus reduces bacteriophage plaquing",
        "description": "Conservative system-level sketch linking the two-gene DS-9 locus to reduced bacteriophage plaquing without resolving DS-9 component functions or effector activity.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures DS-9 as the validated MHAD transcriptional unit with two product accessions and with DefenseFinder DS-9A and DS-9B profile rows. It does not assert native host breadth, exact DS-9A/DS-9B profile-to-protein correspondence, the direct viral trigger or metallophosphoesterase substrate, the HAD phosphatase target, phage target breadth, or DefenseFinder rule-level detection criteria.",
        "nodes": [
          {
            "node_id": "ds_9_locus",
            "label": "DS-9 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A two-gene DefensePredictor-discovered system locus represented in the pinned DefenseFinder HMM inventory by DS-9A and DS-9B custom profiles."
          },
          {
            "node_id": "reduced_phage_plaquing",
            "label": "reduced bacteriophage plaquing",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced efficiency of plaquing by bacteriophage Bas1 in cells carrying cloned MHAD."
          },
          {
            "node_id": "ds_9_system_trait",
            "label": "DS-9 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000433",
            "description": "Possession of a genome-encoded DS-9 phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "ds_9_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "reduced_phage_plaquing",
            "description": "The DS-9/MHAD locus contributes to reduced bacteriophage plaquing when plasmid expressed.",
            "evidence": [
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
                "snippet": "MHAD\tNZ_QOWZ01000056.1\tGCF_003334705.1\t-\tTrue\tFalse\tFalse\tTrue\tDefensePredictor hits\t6224\t8706\tHAD-IA family hydrolase, metallophosphoesterase\tWP_000770925.1, WP_000665639.1\t4.506698206217075\t6.906754778648663\tTrue\tTrue\tPredicted novel defense gene\tDS-9",
                "notes": "The final Science supplementary Table S6 maps working_id MHAD to DS_name DS-9, marks the cloned transcriptional unit as defensive, and records NZ_QOWZ01000056.1 positions 6224-8706 with product accessions WP_000770925.1 and WP_000665639.1."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
                "snippet": "Bas1\t1.2\tpLAND\t24-03-08_EV_HHHD_PIN2_CRDO.png\t40000000\tMHAD\t24-03-08\t24-03-08_NYND_GHOS_MHAD_UDNG.png\t3\t3\t\t3000\t4.1249387366083\tTrue\t\t\tLB\t37",
                "notes": "The final Science supplementary Table S7 reports an MHAD assay row with a Bas1 phage readout and a -log(EOP) value of 4.125."
              }
            ]
          },
          {
            "subject": "reduced_phage_plaquing",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "ds_9_system_trait",
            "description": "DS-9-mediated phage plaquing reduction realizes the DS-9 system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "The system DS-9 has two genes, the first harboring a metallophosphatase domain homologous to that of DS-8, and the second a predicted haloacid dehalogenase-like (HAD) phosphatase",
                "notes": "DeWeirdt et al. identify DS-9 as a two-gene metallophosphatase/HAD-phosphatase system."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
                "snippet": "MHAD\tNZ_QOWZ01000056.1\tGCF_003334705.1\t-\tTrue\tFalse\tFalse\tTrue\tDefensePredictor hits\t6224\t8706\tHAD-IA family hydrolase, metallophosphoesterase\tWP_000770925.1, WP_000665639.1\t4.506698206217075\t6.906754778648663\tTrue\tTrue\tPredicted novel defense gene\tDS-9",
                "notes": "The final Science supplementary Table S6 maps working_id MHAD to DS_name DS-9, marks the cloned transcriptional unit as defensive, and records NZ_QOWZ01000056.1 positions 6224-8706 with product accessions WP_000770925.1 and WP_000665639.1."
              },
              {
                "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
                "snippet": "Bas1\t1.2\tpLAND\t24-03-08_EV_HHHD_PIN2_CRDO.png\t40000000\tMHAD\t24-03-08\t24-03-08_NYND_GHOS_MHAD_UDNG.png\t3\t3\t\t3000\t4.1249387366083\tTrue\t\t\tLB\t37",
                "notes": "The final Science supplementary Table S7 reports an MHAD assay row with a Bas1 phage readout and a -log(EOP) value of 4.125."
              }
            ]
          },
          {
            "subject": "ds_9_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "DS-9 system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.adv7924",
                "snippet": "To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
                "notes": "DeWeirdt et al. validate DSs as anti-phage systems."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| DS-9 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
                "notes": "The pinned DefenseFinder article registry maps the DS-9 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "ds-9-defensefinder-model-gap",
        "prompt": "Resolve DS-9 native host breadth, DS-9A/DS-9B profile-to-protein mapping, sensitive-phage breadth, direct metallophosphoesterase substrate, HAD phosphatase target, and rule-level detection criteria before minting narrower DS-9 mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "DeWeirdt et al. support DS-9 as the defensive MHAD transcriptional unit that reduced Bas1 plaquing when cloned in E. coli MG1655, identify DS-9 as a two-gene system with metallophosphatase and HAD phosphatase domains, and report that DS-9A predicted catalytic-residue mutations caused a loss of defense. Final Science Table S7 mutant rows show D207A and N292A Bas1 protection loss relative to wild-type MHAD in a matched panel. The pinned DefenseFinder HMM inventory records two DS-9 profile rows. The pinned rules table has no DS-9 row, and the first-pass record does not resolve native host breadth, exact DS-9A/DS-9B profile-to-protein correspondence, direct metallophosphoesterase substrate, HAD phosphatase target, phage target breadth, endogenous DS-9 activity, or DefenseFinder rule-level detection criteria.",
        "evidence": [
          {
            "reference": "DOI:10.1126/science.adv7924",
            "snippet": "To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain",
            "notes": "DeWeirdt et al. validate predicted transcriptional units by measuring plaquing relative to an empty vector control strain."
          },
          {
            "reference": "DOI:10.1126/science.adv7924",
            "snippet": "The system DS-9 has two genes, the first harboring a metallophosphatase domain homologous to that of DS-8, and the second a predicted haloacid dehalogenase-like (HAD) phosphatase",
            "notes": "DeWeirdt et al. identify DS-9 as a two-gene system."
          },
          {
            "reference": "DOI:10.1126/science.adv7924",
            "snippet": "When we mutated the predicted catalytic residues in the metallophosphatase domain of DS-9A, we saw a loss of defense, suggesting it is essential for protection",
            "notes": "DeWeirdt et al. state that DS-9A metallophosphatase catalytic mutants lose defense."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx",
            "snippet": "MHAD\tNZ_QOWZ01000056.1\tGCF_003334705.1\t-\tTrue\tFalse\tFalse\tTrue\tDefensePredictor hits\t6224\t8706\tHAD-IA family hydrolase, metallophosphoesterase\tWP_000770925.1, WP_000665639.1\t4.506698206217075\t6.906754778648663\tTrue\tTrue\tPredicted novel defense gene\tDS-9",
            "notes": "The final Science supplementary Table S6 maps working_id MHAD to DS_name DS-9, marks the cloned transcriptional unit as defensive, and records NZ_QOWZ01000056.1 positions 6224-8706 with product accessions WP_000770925.1 and WP_000665639.1."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
            "snippet": "Bas1\t1.2\tpLAND\t24-03-08_EV_HHHD_PIN2_CRDO.png\t40000000\tMHAD\t24-03-08\t24-03-08_NYND_GHOS_MHAD_UDNG.png\t3\t3\t\t3000\t4.1249387366083\tTrue\t\t\tLB\t37",
            "notes": "The final Science supplementary Table S7 reports an MHAD assay row with a Bas1 phage readout and a -log(EOP) value of 4.125."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
            "snippet": "Bas1\tA.1\tMG1655\t24-07-10_EV_MNAC-K375A_MNAC-N84A_MNAC-D52A.png\t3000000\tMHAD\t\t24-07-17\t24-07-17_PN12-dACR_PN12_MHAD_MHAD-D207A_MHAD-N292A.png\t2\t8\t\t800\t3.574031268",
            "notes": "The final Science supplementary Table S7 reports the MHAD WT Bas1 mutant-panel row with a -log(EOP) value of 3.574."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
            "snippet": "Bas1\tA.1\tMG1655\t24-07-10_EV_MNAC-K375A_MNAC-N84A_MNAC-D52A.png\t3000000\tMHAD\tD207A\t24-07-17\t24-07-17_PN12-dACR_PN12_MHAD_MHAD-D207A_MHAD-N292A.png\t6\t3\t\t3000000\t0",
            "notes": "The final Science supplementary Table S7 reports the MHAD D207A Bas1 mutant-panel row with a -log(EOP) value of 0."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx",
            "snippet": "Bas1\tA.1\tMG1655\t24-07-10_EV_MNAC-K375A_MNAC-N84A_MNAC-D52A.png\t3000000\tMHAD\tN292A\t24-07-17\t24-07-17_PN12-dACR_PN12_MHAD_MHAD-D207A_MHAD-N292A.png\t6\t2\t\t2000000\t0.1760912591",
            "notes": "The final Science supplementary Table S7 reports the MHAD N292A Bas1 mutant-panel row with a -log(EOP) value of 0.176."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
            "snippet": "MHAD\tDS-9\tTrue",
            "notes": "The final Science supplementary Table S8 maps MHAD to replicated display name DS-9."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
            "snippet": "MHAD\t2.0\t278.0\tWP_000770925.1\tHAD phosphatase\tcd02616\tHAD_PPase; pyrophosphatase\thhpred_3345609.hhr\t1.0\t277.0\t0.999\t2024-04-16 00:00:00",
            "notes": "The final Science supplementary Table S8 reports a HAD phosphatase HHpred hit for WP_000770925.1 in MHAD."
          },
          {
            "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx",
            "snippet": "MHAD\t1.0\t549.0\tWP_000665639.1\tMetallophosphatase\tcd07378\tMPP_ACP5; Homo sapiens acid phosphatase 5 and related proteins, metallophosphatase domain.\thhpred_3407490.hhr\t200.0\t533.0\t0.9983\t2024-04-16 00:00:00",
            "notes": "The final Science supplementary Table S8 reports a metallophosphatase HHpred hit for WP_000665639.1 in MHAD."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
            "snippet": "| DS-9 | 10\\.1101/2025\\.01\\.08\\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ",
            "notes": "The pinned DefenseFinder article registry maps the DS-9 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| DS-9__DS-9A                                      |                                                  | DS-9                   | Custom                  | 300    |",
            "notes": "The pinned DefenseFinder HMM inventory records DS-9__DS-9A as a custom DS-9 profile."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| DS-9__DS-9B                                      |                                                  | DS-9                   | Custom                  | 100    |",
            "notes": "The pinned DefenseFinder HMM inventory records DS-9__DS-9B as a custom DS-9 profile."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "The pinned DefenseFinder rules table does not list DS-9, leaving rule-level detection criteria unresolved."
          }
        ],
        "attaches_to": [
          "causal_graphs#ds_9_locus_reduces_phage_plaquing"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-28"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-28T12:06:48Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted DS-9 system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; kept the graph at cloned MHAD transcriptional-unit level because the DS-9A/DS-9B profile-to-protein mapping and rule-level DefenseFinder model remain unresolved; proposals/metpo_traitmech_v310 reserves the replacement placeholder.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-28T12:06:49Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed DS-9 system canonical_examples and left them empty because DeWeirdt et al. support cloned MHAD plaquing assays in E. coli MG1655 plus DefenseFinder DS-9 model rows, but not a direct named native microbial isolate exemplar with experimentally verified endogenous DS-9 activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000280",
    "label": "Dsr system",
    "definition": "A phage defense system in which an organism possesses a defense-associated sirtuin locus whose SIR2-domain effector can deplete NAD+ during bacteriophage defense and is modeled by DefenseFinder as Dsr subtypes.",
    "definition_source": "DOI:10.1038/s41564-022-01207-8",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "Dsr",
        "synonym_type": "EXACT_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      },
      {
        "synonym_text": "defense-associated sirtuin",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1126/science.aba0372"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1126/science.aba0372",
        "snippet": "we selected 48 candidate systems to test experimentally for defense activity",
        "notes": "Gao et al. used heterologous reconstitution and phage challenge as their experimental screen for computationally predicted antiphage systems."
      },
      {
        "reference": "DOI:10.1126/science.aba0372",
        "snippet": "dsr, defense-associated sirtuin",
        "notes": "Gao et al. introduced dsr as a defense-associated sirtuin name in the candidate-system activity figure."
      },
      {
        "reference": "DOI:10.1126/science.aba0372",
        "snippet": "Additional systems include proteins containing a SIR2 (sirtuin) deacetylase domain",
        "notes": "Gao et al. place SIR2-domain proteins among additional antiphage defense-system candidates in their domain-architecture analysis."
      },
      {
        "reference": "DOI:10.1038/s41564-022-01207-8",
        "snippet": "DSR proteins degrade nicotinamide adenine dinucleotide (NAD+) during infection, depleting the cell of this essential molecule and aborting phage propagation",
        "notes": "Garb et al. showed that DSR SIR2-domain proteins can defend through infection-coupled NAD+ depletion."
      },
      {
        "reference": "DOI:10.1038/s41564-022-01207-8",
        "snippet": "DSR2, directly identifies phage tail tube proteins and then becomes an active NADase in Bacillus subtilis",
        "notes": "Garb et al. experimentally resolved the phage-derived activation cue for one Bacillus subtilis DSR2 system."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "Dsr | 10\\.1126/science\\.aba0372 | Diverse enzymatic activities mediate antiviral immunity in prokaryotes",
        "notes": "The DefenseFinder article registry maps the named Dsr system to the Gao et al. antiphage-system discovery paper."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "Dsr\tDsr_I\t1\t1\tDsr_I__Dsr1",
        "notes": "The DefenseFinder rules table models Dsr_I as a single-profile Dsr subtype."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "Dsr_I__Dsr1                                      | Dsr_I__Dsr1                                      | Dsr_I",
        "notes": "The DefenseFinder HMM inventory records the Dsr1 profile in the Dsr_I model namespace."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "Dsr\tDsr_II\t1\t1\tDsr_II__Dsr2",
        "notes": "The DefenseFinder rules table models Dsr_II as a single-profile Dsr subtype."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "Dsr_II__Dsr2                                     | Dsr_II__Dsr2                                     | Dsr_II",
        "notes": "The DefenseFinder HMM inventory records the Dsr2 profile in the Dsr_II model namespace."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "dsr_sirtuin_antiphage_defense",
        "title": "Dsr loci encode SIR2-domain antiphage proteins",
        "description": "Conservative system-level sketch linking a Dsr locus to SIR2-domain NAD+ depletion, subtype-specific bacteriophage resistance, and the Dsr system trait.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Dsr systems at the family level while leaving DefenseFinder Dsr_I/Dsr_II profile boundaries, subtype-specific triggers outside DSR2, host ranges, anti-defense proteins, and exact phage targets unresolved. This Dsr family is distinct from metabolic dissimilatory sulfite reductase DsrAB systems.",
        "nodes": [
          {
            "node_id": "dsr_locus",
            "label": "Dsr locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A defense-associated sirtuin antiphage locus represented by Dsr subtype profiles."
          },
          {
            "node_id": "sir2_domain_antiphage_activity",
            "label": "SIR2-domain antiphage activity",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "NADase-associated molecular activity carried by a Dsr SIR2-domain antiphage protein."
          },
          {
            "node_id": "subtype_specific_phage_resistance",
            "label": "subtype-specific phage resistance",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Protection against particular bacteriophages by a Dsr subtype."
          },
          {
            "node_id": "dsr_system_trait",
            "label": "Dsr system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000280",
            "description": "Possession of a genome-encoded defense-associated sirtuin phage defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "dsr_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "sir2_domain_antiphage_activity",
            "description": "Dsr loci encode SIR2-domain defense-associated sirtuin proteins.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.aba0372",
                "snippet": "dsr, defense-associated sirtuin",
                "notes": "Gao et al. connect the Dsr name to a defense-associated sirtuin candidate."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "Dsr_I__Dsr1                                      | Dsr_I__Dsr1                                      | Dsr_I",
                "notes": "DefenseFinder includes Dsr1 in the Dsr_I custom model profile inventory."
              }
            ]
          },
          {
            "subject": "sir2_domain_antiphage_activity",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "subtype_specific_phage_resistance",
            "description": "Garb et al. showed that DSR SIR2-domain effectors can degrade NAD+ during infection and abort phage propagation.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-022-01207-8",
                "snippet": "DSR proteins degrade nicotinamide adenine dinucleotide (NAD+) during infection, depleting the cell of this essential molecule and aborting phage propagation",
                "notes": "DSR SIR2-domain activity can deplete NAD+ during infection in an abortive phage defense outcome."
              }
            ]
          },
          {
            "subject": "dsr_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "subtype_specific_phage_resistance",
            "description": "Garb et al. support DSR NAD+ depletion as an abortive phage-defense outcome, while DefenseFinder models Dsr_I and Dsr_II as named Dsr subtypes.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-022-01207-8",
                "snippet": "DSR proteins degrade nicotinamide adenine dinucleotide (NAD+) during infection, depleting the cell of this essential molecule and aborting phage propagation",
                "notes": "Garb et al. directly support infection-coupled DSR NAD+ depletion as an abortive antiphage output."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "Dsr\tDsr_I\t1\t1\tDsr_I__Dsr1",
                "notes": "The DefenseFinder rules table supports Dsr_I as a named defense-system subtype model with a Dsr1 profile."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "Dsr\tDsr_II\t1\t1\tDsr_II__Dsr2",
                "notes": "The DefenseFinder rules table supports Dsr_II as a named defense-system subtype model with a Dsr2 profile."
              }
            ]
          },
          {
            "subject": "subtype_specific_phage_resistance",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "dsr_system_trait",
            "description": "DefenseFinder represents Dsr as Dsr_I and Dsr_II subtypes within its Dsr system models.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "Dsr\tDsr_I\t1\t1\tDsr_I__Dsr1",
                "notes": "The Dsr_I rule links the Dsr system namespace to the Dsr_I subtype and Dsr1 profile."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "Dsr\tDsr_II\t1\t1\tDsr_II__Dsr2",
                "notes": "The Dsr_II rule links the Dsr system namespace to the Dsr_II subtype and Dsr2 profile."
              }
            ]
          },
          {
            "subject": "dsr_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Dsr system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Dsr | 10\\.1126/science\\.aba0372 | Diverse enzymatic activities mediate antiviral immunity in prokaryotes",
                "notes": "DefenseFinder associates Dsr with the Gao et al. prokaryotic antiviral-immunity paper."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "dsr-sirtuin-mechanism-gap",
        "prompt": "Map DefenseFinder Dsr_I and Dsr_II profiles onto experimentally resolved DSR1 and DSR2 NADase triggers, host ranges, anti-defense proteins, and Dsr naming collisions before minting narrower Dsr mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Gao et al. support defense-associated sirtuin proteins as antiphage system components, Garb et al. resolved NAD+ depletion for multiple SIR2-dependent defense systems and tail tube-triggered NADase activation for B. subtilis DSR2, and DefenseFinder models Dsr_I and Dsr_II. This first record stays at Dsr-family level until the DefenseFinder subtype profiles can be aligned to specific experimental DSR1/DSR2 systems, trigger proteins, host ranges, and phage-encoded anti-DSR proteins. The DefenseFinder Dsr system is also lexically distinct from metabolic DsrAB dissimilatory sulfite reductase systems.",
        "attaches_to": [
          "causal_graphs#dsr_sirtuin_antiphage_defense"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-19"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-19T13:00:46Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Dsr system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact phage-defense Dsr TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v157.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000530",
    "label": "DUF262 Schlafen system",
    "definition": "A phage defense system in which an organism possesses a genome-encoded, DUF262-associated prokaryotic Schlafen nuclease locus.",
    "definition_source": "DOI:10.1038/s41564-026-02277-8",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "DUF262_Shlafen",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/s41564-026-02277-8",
        "snippet": "prokaryotic Schlafen nucleases are widespread antiviral effectors that protect bacteria from bacteriophages and are fused to a diverse array of phage-sensing domains.",
        "notes": "Perez Taboada et al. support bacterial prokaryotic Schlafen nucleases as antiviral effectors fused to phage-sensing domains."
      },
      {
        "reference": "DOI:10.1038/s41564-026-02277-8",
        "snippet": "We expressed seven Enterobacterales Schlafen systems in Escherichia coli, identifying two that confer defence against coliphages.",
        "notes": "Perez Taboada et al. cloned candidate Enterobacterales Schlafen systems into E. coli and observed coliphage defense for two of them."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| DUF262_Shlafen | 10\\.1038/s41564-026-02277-8 | Bacterial Schlafen proteins mediate phage defence | ",
        "notes": "The pinned DefenseFinder article registry maps the DUF262_Shlafen source key to the Perez Taboada et al. Schlafen phage-defense paper."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "duf262_schlafen_phage_defense",
        "title": "DUF262 Schlafen loci support Schlafen phage defense",
        "description": "Conservative system-level sketch linking a DUF262_Schlafen locus to prokaryotic Schlafen nuclease antiviral activity and the phage-defense parent.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures the DefenseFinder DUF262_Shlafen article namespace at system level and deliberately leaves the exact locus architecture, the DUF262-associated domain boundary, accession-level protein examples, native host exemplars, phage trigger breadth, and DefenseFinder HMM/rules profiles unresolved.",
        "nodes": [
          {
            "node_id": "duf262_schlafen_locus",
            "label": "DUF262 Schlafen locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A locus encoding a prokaryotic Schlafen nuclease in a DUF262-associated anti-phage system."
          },
          {
            "node_id": "schlafen_antiviral_activity",
            "label": "Schlafen antiviral activity",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Anti-phage activity mediated by a prokaryotic Schlafen nuclease."
          },
          {
            "node_id": "duf262_schlafen_system_trait",
            "label": "DUF262 Schlafen system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000530",
            "description": "Possession of a genome-encoded DUF262-associated prokaryotic Schlafen phage-defense system."
          },
          {
            "node_id": "phage_defense_system_trait",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "duf262_schlafen_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "schlafen_antiviral_activity",
            "description": "DUF262_Schlafen loci are part of the bacterial prokaryotic Schlafen nuclease phage-defense family.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-026-02277-8",
                "snippet": "prokaryotic Schlafen nucleases are widespread antiviral effectors that protect bacteria from bacteriophages and are fused to a diverse array of phage-sensing domains.",
                "notes": "Perez Taboada et al. support bacterial prokaryotic Schlafen nucleases as antiviral effectors fused to phage-sensing domains."
              }
            ]
          },
          {
            "subject": "schlafen_antiviral_activity",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "duf262_schlafen_system_trait",
            "description": "Prokaryotic Schlafen antiviral effector activity realizes the organism-level DUF262 Schlafen system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-026-02277-8",
                "snippet": "prokaryotic Schlafen nucleases are widespread antiviral effectors that protect bacteria from bacteriophages and are fused to a diverse array of phage-sensing domains.",
                "notes": "Perez Taboada et al. support bacterial prokaryotic Schlafen nucleases as antiviral effectors fused to phage-sensing domains."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| DUF262_Shlafen | 10\\.1038/s41564-026-02277-8 | Bacterial Schlafen proteins mediate phage defence | ",
                "notes": "The pinned DefenseFinder article registry maps the DUF262_Shlafen source key to the Perez Taboada et al. Schlafen phage-defense paper."
              }
            ]
          },
          {
            "subject": "duf262_schlafen_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system_trait",
            "description": "DUF262 Schlafen system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-026-02277-8",
                "snippet": "We expressed seven Enterobacterales Schlafen systems in Escherichia coli, identifying two that confer defence against coliphages.",
                "notes": "Perez Taboada et al. cloned candidate Enterobacterales Schlafen systems into E. coli and observed coliphage defense for two of them."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| DUF262_Shlafen | 10\\.1038/s41564-026-02277-8 | Bacterial Schlafen proteins mediate phage defence | ",
                "notes": "The pinned DefenseFinder article registry maps the DUF262_Shlafen source key to the Perez Taboada et al. Schlafen phage-defense paper."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "duf262-schlafen-defensefinder-profile-gap",
        "prompt": "Resolve exact DUF262_Schlafen locus architecture, DUF262-associated domain boundaries, natural host exemplars, phage trigger breadth, and DefenseFinder HMM/rules coverage before minting narrower DUF262 Schlafen mechanism or component traits.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Perez Taboada et al. support prokaryotic Schlafen nucleases as widespread antiviral effectors fused to phage-sensing domains, and the pinned DefenseFinder article registry maps the DUF262_Shlafen key to the same article. The pinned HMM inventory and rules table have no exact DUF262_Schlafen or DUF262 rows for this source key. This first-pass record therefore does not resolve whether the exact DUF262_Schlafen architecture is a single-protein fusion or multi-gene locus, its exact DUF262-associated domain boundaries, natural host exemplars, accession-level Schlafen proteins, full phage trigger breadth, or a reusable DefenseFinder profile model.",
        "evidence": [
          {
            "reference": "DOI:10.1038/s41564-026-02277-8",
            "snippet": "prokaryotic Schlafen nucleases are widespread antiviral effectors that protect bacteria from bacteriophages and are fused to a diverse array of phage-sensing domains.",
            "notes": "Perez Taboada et al. support bacterial prokaryotic Schlafen nucleases as antiviral effectors fused to phage-sensing domains."
          },
          {
            "reference": "DOI:10.1038/s41564-026-02277-8",
            "snippet": "We expressed seven Enterobacterales Schlafen systems in Escherichia coli, identifying two that confer defence against coliphages.",
            "notes": "Perez Taboada et al. cloned candidate Enterobacterales Schlafen systems into E. coli and observed coliphage defense for two of them."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
            "snippet": "| DUF262_Shlafen | 10\\.1038/s41564-026-02277-8 | Bacterial Schlafen proteins mediate phage defence | ",
            "notes": "The pinned DefenseFinder article registry maps the DUF262_Shlafen source key to the Perez Taboada et al. Schlafen phage-defense paper."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "notes": "A structured first-pass search of the pinned DefenseFinder HMM inventory found no exact DUF262_Shlafen, Schlafen, or DUF262 row for this system."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "A structured first-pass search of the pinned DefenseFinder rules table found no exact DUF262_Shlafen, Schlafen, or DUF262 system row for this system."
          }
        ],
        "attaches_to": [
          "causal_graphs#duf262_schlafen_phage_defense"
        ],
        "posed_by": "codex",
        "posed_date": "2026-10-02"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-02T01:00:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted DUF262 Schlafen system as a DOI- and DefenseFinder-backed GENOMICS TraitRecord under the phage defense system parent after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v407.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-02T01:00:01Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed DUF262 Schlafen system during initial curation and left canonical_examples empty because Perez Taboada et al. and the pinned DefenseFinder article registry support the DUF262_Schlafen system namespace, but not an accession-backed native microbial taxon exemplar for the exact DUF262_Schlafen source key. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000509",
    "label": "EcoKMcrA system",
    "definition": "A type IV modification-dependent restriction system in which an organism possesses an EcoKMcrA mcrA locus encoding a methylcytosine- and hydroxymethylcytosine-dependent restriction endonuclease whose nuclease active site is required for efficient restriction of DNA modified in the correct sequence context.",
    "definition_source": "DOI:10.1093/nar/gky731",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000496"
    ],
    "synonyms": [
      {
        "synonym_text": "EcoKMcrA",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1093/nar/gky731"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1093/nar/gky731",
        "snippet": "Escherichia coli McrA (EcoKMcrA) acts as a methylcytosine and hydroxymethylcytosine dependent restriction endonuclease.",
        "notes": "Czapinska et al. support EcoKMcrA as an E. coli McrA modification-dependent restriction endonuclease that targets methylcytosine- and hydroxymethylcytosine-containing DNA."
      },
      {
        "reference": "DOI:10.1093/nar/gky731",
        "snippet": "We present a biochemical characterization of EcoKMcrA that includes the first demonstration of its endonuclease activity",
        "notes": "Czapinska et al. experimentally demonstrated EcoKMcrA endonuclease activity in vitro."
      },
      {
        "reference": "DOI:10.1093/nar/gky731",
        "snippet": "In cells, EcoKMcrA specifically restricts DNA that is modified in the correct sequence context. This activity is impaired by mutations of the nuclease active site, unless the enzyme is highly overexpressed.",
        "notes": "Czapinska et al. support cellular modified-DNA restriction by EcoKMcrA and tie efficient restriction to the nuclease active site."
      },
      {
        "reference": "DOI:10.1093/nar/gkt747",
        "snippet": "The new class of modification-dependent restriction enzymes was named Type IV, as distinct from the familiar modification-blocked Types I-III.",
        "notes": "Loenen and Raleigh define the Type IV class as modification-dependent restriction enzymes."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| EcoKMcrA | 10\\.1093/nar/gky731 | Activity and structure of EcoKMcrA | ",
        "notes": "The pinned DefenseFinder article registry maps the EcoKMcrA source key to the Czapinska et al. Activity and structure of EcoKMcrA paper."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "ecokmcra_restricts_modified_cytosine_dna",
        "title": "EcoKMcrA restricts modified-cytosine DNA",
        "description": "Conservative system-level sketch linking an EcoKMcrA mcrA locus to modified-cytosine DNA restriction and to the Type IV restriction parent trait.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures EcoKMcrA as a named E. coli K-strain McrA Type IV modification-dependent restriction system while leaving EcoKMcrA-family breadth, sequence-context specificity across natural hosts, accession-level protein examples, and DefenseFinder RM_Type_IV HMM/rules mapping unresolved.",
        "nodes": [
          {
            "node_id": "ecokmcra_locus",
            "label": "EcoKMcrA mcrA locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A locus encoding an EcoKMcrA methylcytosine- and hydroxymethylcytosine-dependent restriction endonuclease."
          },
          {
            "node_id": "modified_cytosine_dna",
            "label": "modified-cytosine DNA",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "DNA containing methylcytosine or hydroxymethylcytosine in a sequence context recognized by EcoKMcrA."
          },
          {
            "node_id": "ecokmcra_modified_dna_restriction",
            "label": "EcoKMcrA modified-DNA restriction",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Nuclease-active-site-dependent restriction of modified DNA by EcoKMcrA."
          },
          {
            "node_id": "ecokmcra_system_trait",
            "label": "EcoKMcrA system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000509",
            "description": "Possession of a genome-encoded EcoKMcrA modification-dependent restriction system."
          },
          {
            "node_id": "type_iv_modification_dependent_restriction",
            "label": "type IV modification-dependent restriction system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000496",
            "description": "Possession of a genome-encoded Type IV modification-dependent restriction system."
          }
        ],
        "edges": [
          {
            "subject": "ecokmcra_locus",
            "predicate": "enables",
            "predicate_id": "RO:0002327",
            "object": "ecokmcra_modified_dna_restriction",
            "description": "The EcoKMcrA mcrA locus encodes a modified-cytosine-dependent restriction endonuclease.",
            "evidence": [
              {
                "reference": "DOI:10.1093/nar/gky731",
                "snippet": "Escherichia coli McrA (EcoKMcrA) acts as a methylcytosine and hydroxymethylcytosine dependent restriction endonuclease.",
                "notes": "Czapinska et al. support EcoKMcrA as an E. coli McrA modification-dependent restriction endonuclease that targets methylcytosine- and hydroxymethylcytosine-containing DNA."
              },
              {
                "reference": "DOI:10.1093/nar/gky731",
                "snippet": "We present a biochemical characterization of EcoKMcrA that includes the first demonstration of its endonuclease activity",
                "notes": "Czapinska et al. experimentally demonstrated EcoKMcrA endonuclease activity in vitro."
              }
            ]
          },
          {
            "subject": "ecokmcra_modified_dna_restriction",
            "predicate": "mitigates",
            "predicate_id": "METPO:2007407",
            "object": "modified_cytosine_dna",
            "description": "EcoKMcrA-dependent Type IV restriction targets DNA modified in the correct sequence context.",
            "evidence": [
              {
                "reference": "DOI:10.1093/nar/gky731",
                "snippet": "Electrophoretic mobility shift assay (EMSA) and footprinting experiments suggest that the N-terminal domains can sense the presence and sequence context of modified cytosines.",
                "notes": "Czapinska et al. support EcoKMcrA sensing of the presence and sequence context of modified cytosines."
              },
              {
                "reference": "DOI:10.1093/nar/gky731",
                "snippet": "In cells, EcoKMcrA specifically restricts DNA that is modified in the correct sequence context. This activity is impaired by mutations of the nuclease active site, unless the enzyme is highly overexpressed.",
                "notes": "Czapinska et al. support cellular modified-DNA restriction by EcoKMcrA and tie efficient restriction to the nuclease active site."
              }
            ]
          },
          {
            "subject": "ecokmcra_modified_dna_restriction",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "ecokmcra_system_trait",
            "description": "EcoKMcrA-dependent Type IV restriction realizes the organism-level EcoKMcrA system possession trait.",
            "evidence": [
              {
                "reference": "DOI:10.1093/nar/gky731",
                "snippet": "In cells, EcoKMcrA specifically restricts DNA that is modified in the correct sequence context. This activity is impaired by mutations of the nuclease active site, unless the enzyme is highly overexpressed.",
                "notes": "Czapinska et al. support cellular modified-DNA restriction by EcoKMcrA and tie efficient restriction to the nuclease active site."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| EcoKMcrA | 10\\.1093/nar/gky731 | Activity and structure of EcoKMcrA | ",
                "notes": "The pinned DefenseFinder article registry maps the EcoKMcrA source key to the Czapinska et al. Activity and structure of EcoKMcrA paper."
              }
            ]
          },
          {
            "subject": "ecokmcra_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "type_iv_modification_dependent_restriction",
            "description": "EcoKMcrA system possession is a Type IV modification-dependent restriction system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1093/nar/gky731",
                "snippet": "Escherichia coli McrA (EcoKMcrA) acts as a methylcytosine and hydroxymethylcytosine dependent restriction endonuclease.",
                "notes": "Czapinska et al. support EcoKMcrA as an E. coli McrA modification-dependent restriction endonuclease that targets methylcytosine- and hydroxymethylcytosine-containing DNA."
              },
              {
                "reference": "DOI:10.1093/nar/gkt747",
                "snippet": "The new class of modification-dependent restriction enzymes was named Type IV, as distinct from the familiar modification-blocked Types I-III.",
                "notes": "Loenen and Raleigh define the Type IV class as modification-dependent restriction enzymes."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "ecokmcra-defensefinder-model-gap",
        "prompt": "Resolve EcoKMcrA-family breadth, methylcytosine and hydroxymethylcytosine sequence-context specificity across natural hosts, accession-level protein examples, and DefenseFinder RM_Type_IV HMM/rules mapping before minting narrower EcoKMcrA mechanism or component traits.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Czapinska et al. support E. coli EcoKMcrA as a methylcytosine- and hydroxymethylcytosine-dependent restriction endonuclease with cellular modified-DNA restriction activity tied to the nuclease active site, and the pinned DefenseFinder article registry maps EcoKMcrA to that paper. The pinned HMM inventory and rules table have no exact EcoKMcrA rows. This first-pass record therefore does not resolve a reusable DefenseFinder profile model, exact accession-level protein examples, the breadth of EcoKMcrA-like systems beyond E. coli K strains, or the complete set of natural methylcytosine and hydroxymethylcytosine sequence contexts.",
        "evidence": [
          {
            "reference": "DOI:10.1093/nar/gky731",
            "snippet": "Escherichia coli McrA (EcoKMcrA) acts as a methylcytosine and hydroxymethylcytosine dependent restriction endonuclease.",
            "notes": "Czapinska et al. support EcoKMcrA as an E. coli McrA modification-dependent restriction endonuclease that targets methylcytosine- and hydroxymethylcytosine-containing DNA."
          },
          {
            "reference": "DOI:10.1093/nar/gky731",
            "snippet": "In cells, EcoKMcrA specifically restricts DNA that is modified in the correct sequence context. This activity is impaired by mutations of the nuclease active site, unless the enzyme is highly overexpressed.",
            "notes": "Czapinska et al. support cellular modified-DNA restriction by EcoKMcrA and tie efficient restriction to the nuclease active site."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
            "snippet": "| EcoKMcrA | 10\\.1093/nar/gky731 | Activity and structure of EcoKMcrA | ",
            "notes": "The pinned DefenseFinder article registry maps the EcoKMcrA source key to the Czapinska et al. Activity and structure of EcoKMcrA paper."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "notes": "A structured first-pass search of the pinned DefenseFinder HMM inventory found no exact EcoKMcrA row."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "A structured first-pass search of the pinned DefenseFinder rules table found no exact EcoKMcrA system row."
          }
        ],
        "attaches_to": [
          "causal_graphs#ecokmcra_restricts_modified_cytosine_dna"
        ],
        "posed_by": "codex",
        "posed_date": "2026-10-01"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-01T07:10:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted EcoKMcrA system as a DOI- and DefenseFinder-backed GENOMICS TraitRecord under the type IV modification-dependent restriction system parent after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v386.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-01T07:10:02Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed EcoKMcrA system during initial curation and left canonical_examples empty because Czapinska et al. support the E. coli K-strain EcoKMcrA enzyme and the DefenseFinder EcoKMcrA source key, but not a single stable NCBITaxon strain exemplar or accession-level protein example for the organism-level EcoKMcrA system trait. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000250",
    "label": "Eleos system",
    "definition": "A phage defense system in which an organism possesses an Eleos locus represented by LeoA, LeoB, LeoBC, and LeoC profiles that can protect bacteria from bacteriophage infection.",
    "definition_source": "DOI:10.1016/j.chom.2022.09.017",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "Eleos",
        "synonym_type": "EXACT_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1016/j.chom.2022.09.017",
        "snippet": "discovery of 21 defense systems that protect bacteria from phages, based on computational genomic analyses and phage-infection experiments",
        "notes": "Millman et al. report the computational and experimental cohort that DefenseFinder cites for Eleos as a bacterial anti-phage system."
      },
      {
        "reference": "DOI:10.1101/2022.05.11.491447",
        "snippet": "discovery of 21 new defense systems that protect bacteria from phages, based on computational genomic analyses and phage infection experiments",
        "notes": "The bioRxiv version of Millman et al. independently carries the 21-system discovery claim linked from DefenseFinder's Eleos article registry."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "Eleos | 10\\.1101/2022\\.05\\.11\\.491447 | An expanding arsenal of immune systems that protect bacteria from phages",
        "notes": "The DefenseFinder model registry maps the named Eleos system to the Millman et al. antiphage-system discovery preprint."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "Eleos\tEleos\t2\t2\tEleos__LeoA, Eleos__LeoB, Eleos__LeoBC, Eleos__LeoC",
        "notes": "The DefenseFinder rules table models Eleos as a two-gene system over LeoA, LeoB, LeoBC, and LeoC mandatory-profile choices."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "Eleos__LeoA                                      | Eleos__LeoA                                      | Eleos",
        "notes": "The DefenseFinder HMM inventory records LeoA as an Eleos profile."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "Eleos__LeoA2                                     | Eleos__LeoA2                                     | Eleos",
        "notes": "The DefenseFinder HMM inventory records an additional LeoA profile for Eleos."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "Eleos__LeoB                                      | Eleos__LeoB                                      | Eleos",
        "notes": "The DefenseFinder HMM inventory records LeoB as an Eleos profile."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "Eleos__LeoBC                                     | Eleos__LeoBC                                     | Eleos",
        "notes": "The DefenseFinder HMM inventory records LeoBC as an Eleos profile."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "Eleos__LeoC                                      | Eleos__LeoC                                      | Eleos",
        "notes": "The DefenseFinder HMM inventory records LeoC as an Eleos profile."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "eleos_locus_restricts_phage",
        "title": "Eleos loci confer bacterial phage defense",
        "description": "Conservative system-level sketch linking possession of an Eleos locus to restricted bacteriophage propagation without asserting the unresolved phage trigger or molecular output.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Eleos as a named anti-phage system with DefenseFinder LeoA, LeoB, LeoBC, and LeoC profiles while leaving its phage trigger, molecular substrate, antiviral effector output, and subtype breadth unresolved.",
        "nodes": [
          {
            "node_id": "eleos_locus",
            "label": "Eleos locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "An Eleos anti-phage defense locus satisfying a two-profile DefenseFinder rule over LeoA, LeoB, LeoBC, and LeoC profiles."
          },
          {
            "node_id": "restricted_phage_propagation",
            "label": "restricted phage propagation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced propagation of bacteriophage in cells carrying the Eleos system."
          },
          {
            "node_id": "eleos_system_trait",
            "label": "Eleos system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000250",
            "description": "Possession of a genome-encoded Eleos phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "eleos_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "restricted_phage_propagation",
            "description": "DefenseFinder maps Eleos to a bacterial anti-phage-system discovery preprint and represents Eleos loci through LeoA, LeoB, LeoBC, and LeoC component profiles.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.chom.2022.09.017",
                "snippet": "discovery of 21 defense systems that protect bacteria from phages",
                "notes": "Millman et al. describe the anti-phage discovery cohort that the DefenseFinder Eleos registry row maps to the Eleos system."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Eleos | 10\\.1101/2022\\.05\\.11\\.491447 | An expanding arsenal of immune systems that protect bacteria from phages",
                "notes": "The DefenseFinder registry maps Eleos itself to the Millman et al. bacterial antiphage-system discovery preprint."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "Eleos\tEleos\t2\t2\tEleos__LeoA, Eleos__LeoB, Eleos__LeoBC, Eleos__LeoC",
                "notes": "The DefenseFinder rules table supports LeoA, LeoB, LeoBC, and LeoC as Eleos system profile choices."
              }
            ]
          },
          {
            "subject": "restricted_phage_propagation",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "eleos_system_trait",
            "description": "Eleos-mediated phage restriction realizes the Eleos system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.chom.2022.09.017",
                "snippet": "discovery of 21 defense systems that protect bacteria from phages",
                "notes": "Millman et al. place the Eleos discovery cohort in the set of bacterial systems that protect against phages."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Eleos | 10\\.1101/2022\\.05\\.11\\.491447 | An expanding arsenal of immune systems that protect bacteria from phages",
                "notes": "DefenseFinder records Eleos as a named system from the Millman et al. antiphage discovery preprint."
              }
            ]
          },
          {
            "subject": "eleos_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Eleos system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "An expanding arsenal of immune systems that protect bacteria from phages",
                "notes": "DefenseFinder associates Eleos with the Millman et al. bacterial antiphage-system discovery paper."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "eleos-mechanism-gap",
        "prompt": "Resolve Eleos phage triggers and effector outputs before minting narrower Eleos mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Millman et al. and DefenseFinder support Eleos as a named anti-phage system with LeoA, LeoB, LeoBC, and LeoC profiles, but the trigger, molecular substrate, antiviral effector output, and subtype-specific mechanism are not resolved enough here to assert a narrower mechanistic child trait.",
        "attaches_to": [
          "causal_graphs#eleos_locus_restricts_phage"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-18"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-18T20:38:41Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Eleos system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v127.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000503",
    "label": "ENDPaCF1 system",
    "definition": "A phage defense system in which an organism possesses an ENDPaCF1 Type IIS restriction endonuclease-like locus with an inactive Endonuclease III sensing domain that can recognize diverse DNA hypermodifications and protect bacteria from hypermodified phages.",
    "definition_source": "DOI:10.1101/2025.03.31.646159",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "ENDPaCF1",
        "synonym_type": "EXACT_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1101/2025.03.31.646159",
        "snippet": "The causal defense system is a Type IIS restriction endonuclease-like protein (ENDPaCF1), common in Pseudomonads, however it lacks an associated methyltransferase typical Type IIS R-M systems.",
        "notes": "Yee et al. identify ENDPaCF1 as the causal Pseudomonas antiphage system and distinguish it from canonical Type IIS restriction-modification systems."
      },
      {
        "reference": "DOI:10.1101/2025.03.31.646159",
        "snippet": "ENDPaCF1 protects bacteria against phages with hypermodified DNA and is surprisingly agnostic to the specific structure of the modification, which is unlike typical type IV restriction endonucleases.",
        "notes": "Yee et al. connect ENDPaCF1 to protection against phages with multiple hypermodified-DNA chemistries."
      },
      {
        "reference": "DOI:10.1101/2025.03.31.646159",
        "snippet": "Here, we employed the CRISPR-based Cascade-Cas3 system to delete defense islands in a Pseudomonas aeruginosa clinical isolate to identify mechanisms of lytic phage antagonism. Deletion of one island in a cystic fibrosis-derived clinical isolate sensitized the strain to phages from the Pbunavirus family, which are commonly used as therapeutics.",
        "notes": "Yee et al. identified the ENDPaCF1 island as an endogenous Pseudomonas aeruginosa phage-defense determinant."
      },
      {
        "reference": "DOI:10.1101/2025.03.31.646159",
        "snippet": "In ENDPaCF1, the endonuclease domain is fused to a catalytically inactive Endonuclease III (iEndoIII), a domain that recognizes non-canonical bases to repair DNA in prokaryotes and eukaryotes.",
        "notes": "Yee et al. describe the ENDPaCF1 endonuclease plus inactive Endonuclease III domain architecture."
      },
      {
        "reference": "DOI:10.1101/2025.03.31.646159",
        "snippet": "We therefore propose that nucleases containing an iEndoIII domain (END nucleases) can sense diverse DNA hypermodifications.",
        "notes": "Yee et al. propose the END nuclease family around the iEndoIII domain's ability to sense diverse DNA modifications."
      },
      {
        "reference": "DOI:10.1101/2025.03.31.646159",
        "snippet": "We further show that some hypermodified phages, including Pbunavirus family members and Wrowclawvirus family (Pa5oct-like) of jumbo phages, encode END nuclease inhibitors that directly bind to the nuclease, likely via the iEndoIII domain.",
        "notes": "Yee et al. support direct phage inhibitor binding to END nucleases while leaving ENDPaCF1 inhibitor breadth unresolved."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| ENDPaCF1 | 10\\.1101/2025\\.03\\.31\\.646159 | END nucleases: Antiphage defense systems targeting multiple hypermodified phage genomes | ",
        "notes": "The pinned DefenseFinder article registry maps the ENDPaCF1 source key to the Yee et al. bioRxiv preprint."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:287",
        "taxon_label": "Pseudomonas aeruginosa",
        "note": "Yee et al. identified ENDPaCF1 in the cystic-fibrosis-derived clinical isolate CF040 and showed that deleting the ENDPaCF1-bearing defense island sensitized the native Pseudomonas aeruginosa strain to Pbunavirus phages.",
        "reference": "DOI:10.1101/2025.03.31.646159"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "endpacf1_targets_hypermodified_phage_dna",
        "title": "ENDPaCF1 targets hypermodified phage DNA",
        "description": "Conservative system-level sketch linking an ENDPaCF1 locus to iEndoIII-linked sensing of hypermodified phage DNA, modification-dependent endonuclease targeting, phage restriction, and ENDPaCF1 system possession.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures ENDPaCF1 as a named single-protein phage-defense system with Type IIS restriction endonuclease-like and iEndoIII domains while leaving Pseudomonas natural host breadth, complete DNA-modification breadth, direct domain coupling, phage-inhibitor specificity, and DefenseFinder HMM/rules detection criteria unresolved.",
        "nodes": [
          {
            "node_id": "endpacf1_locus",
            "label": "ENDPaCF1 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "An ENDPaCF1 anti-phage locus encoding a Type IIS restriction endonuclease-like protein fused to an inactive Endonuclease III domain."
          },
          {
            "node_id": "hypermodified_phage_dna_sensing",
            "label": "hypermodified phage DNA sensing",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Recognition of diverse DNA hypermodifications by ENDPaCF1-family END nuclease systems."
          },
          {
            "node_id": "modification_dependent_phage_dna_cleavage",
            "label": "modification-dependent phage DNA cleavage",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Cleavage of phage DNA by a nuclease after hypermodified DNA is detected."
          },
          {
            "node_id": "hypermodified_phage_infection",
            "label": "hypermodified phage infection",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Infection by bacteriophages that carry hypermodified genomes."
          },
          {
            "node_id": "endpacf1_system_trait",
            "label": "ENDPaCF1 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000503",
            "description": "Possession of a genome-encoded ENDPaCF1 phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "endpacf1_locus",
            "predicate": "enables",
            "predicate_id": "RO:0002327",
            "object": "hypermodified_phage_dna_sensing",
            "description": "An ENDPaCF1 locus enables sensing of diverse hypermodified phage genomes.",
            "evidence": [
              {
                "reference": "DOI:10.1101/2025.03.31.646159",
                "snippet": "The causal defense system is a Type IIS restriction endonuclease-like protein (ENDPaCF1), common in Pseudomonads, however it lacks an associated methyltransferase typical Type IIS R-M systems.",
                "notes": "Yee et al. identify ENDPaCF1 as the causal Pseudomonas antiphage system and distinguish it from canonical Type IIS restriction-modification systems."
              },
              {
                "reference": "DOI:10.1101/2025.03.31.646159",
                "snippet": "In ENDPaCF1, the endonuclease domain is fused to a catalytically inactive Endonuclease III (iEndoIII), a domain that recognizes non-canonical bases to repair DNA in prokaryotes and eukaryotes.",
                "notes": "Yee et al. describe the ENDPaCF1 endonuclease plus inactive Endonuclease III domain architecture."
              },
              {
                "reference": "DOI:10.1101/2025.03.31.646159",
                "snippet": "We therefore propose that nucleases containing an iEndoIII domain (END nucleases) can sense diverse DNA hypermodifications.",
                "notes": "Yee et al. propose the END nuclease family around the iEndoIII domain's ability to sense diverse DNA modifications."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| ENDPaCF1 | 10\\.1101/2025\\.03\\.31\\.646159 | END nucleases: Antiphage defense systems targeting multiple hypermodified phage genomes | ",
                "notes": "The pinned DefenseFinder article registry maps the ENDPaCF1 source key to the Yee et al. bioRxiv preprint."
              }
            ]
          },
          {
            "subject": "hypermodified_phage_infection",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "hypermodified_phage_dna_sensing",
            "description": "Hypermodified phage genomes provide the substrate recognized by ENDPaCF1-family END nucleases.",
            "evidence": [
              {
                "reference": "DOI:10.1101/2025.03.31.646159",
                "snippet": "ENDPaCF1 protects bacteria against phages with hypermodified DNA and is surprisingly agnostic to the specific structure of the modification, which is unlike typical type IV restriction endonucleases.",
                "notes": "Yee et al. connect ENDPaCF1 to protection against phages with multiple hypermodified-DNA chemistries."
              }
            ]
          },
          {
            "subject": "modification_dependent_phage_dna_cleavage",
            "predicate": "mitigates",
            "predicate_id": "METPO:2007407",
            "object": "hypermodified_phage_infection",
            "description": "Modification-dependent phage DNA cleavage protects bacteria against phages with hypermodified DNA.",
            "evidence": [
              {
                "reference": "DOI:10.1101/2025.03.31.646159",
                "snippet": "ENDPaCF1 protects bacteria against phages with hypermodified DNA and is surprisingly agnostic to the specific structure of the modification, which is unlike typical type IV restriction endonucleases.",
                "notes": "Yee et al. connect ENDPaCF1 to protection against phages with multiple hypermodified-DNA chemistries."
              }
            ]
          },
          {
            "subject": "modification_dependent_phage_dna_cleavage",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "endpacf1_system_trait",
            "description": "ENDPaCF1-family targeting of hypermodified phage DNA realizes the ENDPaCF1 system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1101/2025.03.31.646159",
                "snippet": "Our findings reveal modularity of the sensing and cleavage domains, as expected of a modification-dependent endonucleases.",
                "notes": "Yee et al. frame END nuclease activity as modification-dependent coupling between sensing and cleavage domains."
              }
            ]
          },
          {
            "subject": "endpacf1_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "ENDPaCF1 system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1101/2025.03.31.646159",
                "snippet": "The causal defense system is a Type IIS restriction endonuclease-like protein (ENDPaCF1), common in Pseudomonads, however it lacks an associated methyltransferase typical Type IIS R-M systems.",
                "notes": "Yee et al. identify ENDPaCF1 as the causal Pseudomonas antiphage system and distinguish it from canonical Type IIS restriction-modification systems."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| ENDPaCF1 | 10\\.1101/2025\\.03\\.31\\.646159 | END nucleases: Antiphage defense systems targeting multiple hypermodified phage genomes | ",
                "notes": "The pinned DefenseFinder article registry maps the ENDPaCF1 source key to the Yee et al. bioRxiv preprint."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "endpacf1-host-modification-and-model-gap",
        "prompt": "Resolve ENDPaCF1 Pseudomonas host breadth, complete phage-DNA hypermodification breadth, direct iEndoIII sensing-to-cleavage coupling, phage inhibitor specificity, and DefenseFinder HMM/rules coverage before minting narrower END nuclease mechanism or component traits.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Yee et al. support ENDPaCF1 as a Type IIS restriction endonuclease-like Pseudomonas phage-defense system that can recognize diverse hypermodified phage genomes, and the pinned DefenseFinder article registry maps the ENDPaCF1 source key to the Yee et al. preprint. The pinned HMM inventory and rules table have no exact ENDPaCF1 rows. This first-pass record therefore does not resolve a complete profile model, the direct domain coupling between iEndoIII sensing and cleavage, or the full natural host, phage, and inhibitor breadth.",
        "evidence": [
          {
            "reference": "DOI:10.1101/2025.03.31.646159",
            "snippet": "The causal defense system is a Type IIS restriction endonuclease-like protein (ENDPaCF1), common in Pseudomonads, however it lacks an associated methyltransferase typical Type IIS R-M systems.",
            "notes": "Yee et al. identify ENDPaCF1 as the causal Pseudomonas antiphage system and distinguish it from canonical Type IIS restriction-modification systems."
          },
          {
            "reference": "DOI:10.1101/2025.03.31.646159",
            "snippet": "ENDPaCF1 protects bacteria against phages with hypermodified DNA and is surprisingly agnostic to the specific structure of the modification, which is unlike typical type IV restriction endonucleases.",
            "notes": "Yee et al. connect ENDPaCF1 to protection against phages with multiple hypermodified-DNA chemistries."
          },
          {
            "reference": "DOI:10.1101/2025.03.31.646159",
            "snippet": "In ENDPaCF1, the endonuclease domain is fused to a catalytically inactive Endonuclease III (iEndoIII), a domain that recognizes non-canonical bases to repair DNA in prokaryotes and eukaryotes.",
            "notes": "Yee et al. describe the ENDPaCF1 endonuclease plus inactive Endonuclease III domain architecture."
          },
          {
            "reference": "DOI:10.1101/2025.03.31.646159",
            "snippet": "We further show that some hypermodified phages, including Pbunavirus family members and Wrowclawvirus family (Pa5oct-like) of jumbo phages, encode END nuclease inhibitors that directly bind to the nuclease, likely via the iEndoIII domain.",
            "notes": "Yee et al. support direct phage inhibitor binding to END nucleases while leaving ENDPaCF1 inhibitor breadth unresolved."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
            "snippet": "| ENDPaCF1 | 10\\.1101/2025\\.03\\.31\\.646159 | END nucleases: Antiphage defense systems targeting multiple hypermodified phage genomes | ",
            "notes": "The pinned DefenseFinder article registry maps the ENDPaCF1 source key to the Yee et al. bioRxiv preprint."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "notes": "A structured first-pass search of the pinned DefenseFinder HMM inventory found no exact ENDPaCF1 row."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "A structured first-pass search of the pinned DefenseFinder rules table found no exact ENDPaCF1 system row."
          }
        ],
        "attaches_to": [
          "causal_graphs#endpacf1_targets_hypermodified_phage_dna"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-30"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-30T23:39:24Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted ENDPaCF1 system as a bioRxiv- and DefenseFinder-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, research, generated, or prior proposal record; kept the graph at Type IIS restriction-endonuclease-like system level because the pinned DefenseFinder article row is not backed by pinned HMM or rules rows; the replacement placeholder is reserved in proposals/metpo_traitmech_v380.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-30T23:39:25Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed ENDPaCF1 system canonical_examples and left them empty because public preprint and DefenseFinder evidence supports the named phage-defense system but not a direct named native microbial isolate exemplar with experimentally verified endogenous ENDPaCF1 activity. No paid research was used.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-01T00:24:07Z",
        "curator": "codex",
        "action": "ADDRESS_ENDPACF1_REVIEW_FINDINGS",
        "changes": "Addressed Copilot review issues #1501, #1502, and #1503: added Pseudomonas aeruginosa (NCBITaxon:287) as a DOI-backed native ENDPaCF1 canonical example, removed the unsupported direct hypermodified-phage-DNA-sensing to modification-dependent-phage-DNA-cleavage causal edge, and included the discussions block in the repository CREATE history sections.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000281",
    "label": "Epona system",
    "definition": "A phage defense system in which an organism possesses an Epona locus represented by a VCA0366 profile that can protect bacteria from bacteriophage infection.",
    "definition_source": "DOI:10.1126/science.ads0768",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "Epona",
        "synonym_type": "EXACT_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      },
      {
        "synonym_text": "VCA0366",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1126/science.ads0768",
        "snippet": "nearly 10% of the integron cassettes in the pandemic Vibrio cholerae strain encode novel antiphage functions",
        "notes": "Darracq et al. support treating the newly discovered Vibrio cholerae SCI antiphage cassettes as bacterial anti-phage systems."
      },
      {
        "reference": "DOI:10.1126/science.ads0768",
        "snippet": "Most of these novel systems have little or no similarity to previously known ones, with several providing defense through cell lysis or growth arrest",
        "notes": "Darracq et al. support a conservative system record that does not assert a resolved Epona trigger, effector output, or universal pathway."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "Epona | 10\\.1126/science\\.ads0768 | Sedentary chromosomal integrons as biobanks of bacterial antiphage defense systems",
        "notes": "The DefenseFinder model registry maps the named Epona system to the Darracq et al. SCI antiphage-system paper."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "Epona__VCA0366                                   |                                                  | Epona",
        "notes": "The DefenseFinder HMM inventory records VCA0366 in the Epona model namespace."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "epona_locus_restricts_phage",
        "title": "Epona loci confer bacterial phage defense",
        "description": "Conservative system-level sketch linking possession of an Epona locus to restricted bacteriophage propagation without asserting the unresolved phage trigger or molecular output.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Epona as a named SCI-derived anti-phage system with a VCA0366 DefenseFinder profile while leaving its phage trigger, molecular substrate, antiviral effector output, and subtype breadth unresolved.",
        "nodes": [
          {
            "node_id": "epona_locus",
            "label": "Epona locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "An Epona anti-phage defense locus represented in DefenseFinder by a VCA0366 profile."
          },
          {
            "node_id": "restricted_phage_propagation",
            "label": "restricted phage propagation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced propagation of bacteriophage in cells carrying the Epona system."
          },
          {
            "node_id": "epona_system_trait",
            "label": "Epona system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000281",
            "description": "Possession of a genome-encoded Epona phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "epona_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "restricted_phage_propagation",
            "description": "DefenseFinder maps Epona to an SCI anti-phage-system discovery paper and represents Epona loci through the VCA0366 component profile.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.ads0768",
                "snippet": "nearly 10% of the integron cassettes in the pandemic Vibrio cholerae strain encode novel antiphage functions",
                "notes": "Darracq et al. describe the newly discovered antiphage-system cohort that the DefenseFinder Epona registry row maps to the Epona system."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "Epona__VCA0366                                   |                                                  | Epona",
                "notes": "The DefenseFinder HMM inventory supports VCA0366 as the Epona component profile."
              }
            ]
          },
          {
            "subject": "restricted_phage_propagation",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "epona_system_trait",
            "description": "Epona-mediated phage restriction realizes the Epona system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.ads0768",
                "snippet": "Most of these novel systems have little or no similarity to previously known ones",
                "notes": "Darracq et al. place the Epona discovery cohort in a set of novel bacterial systems that protect against phages."
              }
            ]
          },
          {
            "subject": "epona_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Epona system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Epona | 10\\.1126/science\\.ads0768 | Sedentary chromosomal integrons as biobanks of bacterial antiphage defense systems",
                "notes": "DefenseFinder associates Epona with the Darracq et al. bacterial antiphage-system paper."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "epona-mechanism-gap",
        "prompt": "Resolve Epona phage triggers and effector outputs before minting narrower Epona mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Darracq et al. and DefenseFinder support Epona as a named anti-phage system with a VCA0366 profile, but the trigger, molecular substrate, antiviral effector output, and subtype-specific mechanism are not resolved enough here to assert a narrower mechanistic child trait.",
        "attaches_to": [
          "causal_graphs#epona_locus_restricts_phage"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-19"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-19T14:03:55Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Epona system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v158.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000308",
    "label": "Erebus system",
    "definition": "A phage defense system in which an organism possesses an Erebus locus that can protect bacteria from bacteriophage infection.",
    "definition_source": "DOI:10.1016/j.chom.2024.07.007",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "Erebus",
        "synonym_type": "EXACT_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      },
      {
        "synonym_text": "EruA",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1016/j.chom.2024.07.007",
        "snippet": "We validated six of these phage defense systems, including factors preventing viral attachment, R-loop-acting enzymes, the inflammasome, ubiquitin pathway, and pathogen recognition signaling.",
        "notes": "van den Berg et al. validated six phage defense systems related to eukaryotic innate antiviral responses."
      },
      {
        "reference": "DOI:10.1016/j.chom.2024.07.007",
        "snippet": "Searching for phage defense systems related to innate antiviral genes from vertebrates and plants, we uncovered over 450 candidates.",
        "notes": "van den Berg et al. motivate a conservative system-level record that does not assert a resolved Erebus trigger, effector output, or universal pathway."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "Erebus | 10\\.1016/j\\.chom\\.2024\\.07\\.007 | Bacterial homologs of innate eukaryotic antiviral defenses with anti-phage activity highlight shared evolutionary roots of viral defenses",
        "notes": "The DefenseFinder model registry maps the named Erebus system to the van den Berg et al. antiphage-system discovery paper."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "Erebus__EruA                                     |                                                  | Erebus",
        "notes": "The DefenseFinder HMM inventory records Erebus__EruA in the Erebus model namespace."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "erebus_locus_restricts_phage",
        "title": "Erebus loci confer bacterial phage defense",
        "description": "Conservative system-level sketch linking possession of an Erebus locus to restricted bacteriophage propagation without asserting the unresolved phage trigger or molecular output.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Erebus as a named anti-phage system with an Erebus__EruA DefenseFinder HMM profile entry while leaving its phage trigger, molecular substrate, antiviral effector output, and subtype breadth unresolved.",
        "nodes": [
          {
            "node_id": "erebus_locus",
            "label": "Erebus locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "An Erebus anti-phage defense locus cataloged in DefenseFinder with an Erebus__EruA HMM profile entry."
          },
          {
            "node_id": "restricted_phage_propagation",
            "label": "restricted phage propagation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced propagation of bacteriophage in cells carrying the Erebus system."
          },
          {
            "node_id": "erebus_system_trait",
            "label": "Erebus system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000308",
            "description": "Possession of a genome-encoded Erebus phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "erebus_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "restricted_phage_propagation",
            "description": "DefenseFinder maps Erebus to a eukaryotic-antiviral-homolog antiphage-system discovery paper and catalogs an Erebus__EruA HMM profile entry in the Erebus model namespace.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.chom.2024.07.007",
                "snippet": "We validated six of these phage defense systems, including factors preventing viral attachment, R-loop-acting enzymes, the inflammasome, ubiquitin pathway, and pathogen recognition signaling.",
                "notes": "van den Berg et al. validated six phage defense systems related to eukaryotic innate antiviral responses."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Erebus | 10\\.1016/j\\.chom\\.2024\\.07\\.007 | Bacterial homologs of innate eukaryotic antiviral defenses with anti-phage activity highlight shared evolutionary roots of viral defenses",
                "notes": "The DefenseFinder model registry maps the named Erebus system to the van den Berg et al. antiphage-system discovery paper."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "Erebus__EruA                                     |                                                  | Erebus",
                "notes": "The DefenseFinder HMM inventory records Erebus__EruA in the Erebus model namespace."
              }
            ]
          },
          {
            "subject": "restricted_phage_propagation",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "erebus_system_trait",
            "description": "Erebus-mediated phage restriction realizes the Erebus system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.chom.2024.07.007",
                "snippet": "We validated six of these phage defense systems, including factors preventing viral attachment, R-loop-acting enzymes, the inflammasome, ubiquitin pathway, and pathogen recognition signaling.",
                "notes": "van den Berg et al. validated six phage defense systems related to eukaryotic antiviral responses."
              }
            ]
          },
          {
            "subject": "erebus_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Erebus system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Erebus | 10\\.1016/j\\.chom\\.2024\\.07\\.007 | Bacterial homologs of innate eukaryotic antiviral defenses with anti-phage activity highlight shared evolutionary roots of viral defenses",
                "notes": "The DefenseFinder model registry maps the named Erebus system to the van den Berg et al. antiphage-system discovery paper."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "erebus-mechanism-gap",
        "prompt": "Resolve Erebus phage triggers and effector outputs before minting narrower Erebus mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "van den Berg et al. and DefenseFinder support Erebus as a named anti-phage system with an Erebus__EruA HMM profile entry, but the trigger, molecular substrate, antiviral effector output, and subtype-specific mechanism are not resolved enough here to assert a narrower mechanistic child trait.",
        "attaches_to": [
          "causal_graphs#erebus_locus_restricts_phage"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-20"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-20T11:49:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Erebus system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v185.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-20T12:25:08Z",
        "curator": "codex",
        "action": "CURATION_REVIEW_REVISION",
        "changes": "Resolved PR 1136 review issue 1137 by mirroring the proposal-only EruA label as a RELATED_SYNONYM sourced to the pinned DefenseFinder HMM inventory.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000282",
    "label": "Esos system",
    "definition": "A phage defense system in which an organism possesses an Esos locus represented by a VCA0450 profile that can protect bacteria from bacteriophage infection.",
    "definition_source": "DOI:10.1126/science.ads0768",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "Esos",
        "synonym_type": "EXACT_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      },
      {
        "synonym_text": "VCA0450",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1126/science.ads0768",
        "snippet": "nearly 10% of the integron cassettes in the pandemic Vibrio cholerae strain encode novel antiphage functions",
        "notes": "Darracq et al. support treating the newly discovered Vibrio cholerae SCI antiphage cassettes as bacterial anti-phage systems."
      },
      {
        "reference": "DOI:10.1126/science.ads0768",
        "snippet": "Most of these novel systems have little or no similarity to previously known ones, with several providing defense through cell lysis or growth arrest",
        "notes": "Darracq et al. support a conservative system record that does not assert a resolved Esos trigger, effector output, or universal pathway."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "Esos | 10\\.1126/science\\.ads0768 | Sedentary chromosomal integrons as biobanks of bacterial antiphage defense systems",
        "notes": "The DefenseFinder model registry maps the named Esos system to the Darracq et al. SCI antiphage-system paper."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "Esos__VCA0450                                    |                                                  | Esos",
        "notes": "The DefenseFinder HMM inventory records VCA0450 in the Esos model namespace."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "esos_locus_restricts_phage",
        "title": "Esos loci confer bacterial phage defense",
        "description": "Conservative system-level sketch linking possession of an Esos locus to restricted bacteriophage propagation without asserting the unresolved phage trigger or molecular output.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Esos as a named SCI-derived anti-phage system with a VCA0450 DefenseFinder profile while leaving its phage trigger, molecular substrate, antiviral effector output, and subtype breadth unresolved.",
        "nodes": [
          {
            "node_id": "esos_locus",
            "label": "Esos locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "An Esos anti-phage defense locus represented in DefenseFinder by a VCA0450 profile."
          },
          {
            "node_id": "restricted_phage_propagation",
            "label": "restricted phage propagation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced propagation of bacteriophage in cells carrying the Esos system."
          },
          {
            "node_id": "esos_system_trait",
            "label": "Esos system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000282",
            "description": "Possession of a genome-encoded Esos phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "esos_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "restricted_phage_propagation",
            "description": "DefenseFinder maps Esos to an SCI anti-phage-system discovery paper and represents Esos loci through the VCA0450 component profile.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.ads0768",
                "snippet": "nearly 10% of the integron cassettes in the pandemic Vibrio cholerae strain encode novel antiphage functions",
                "notes": "Darracq et al. describe the newly discovered antiphage-system cohort that the DefenseFinder Esos registry row maps to the Esos system."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "Esos__VCA0450                                    |                                                  | Esos",
                "notes": "The DefenseFinder HMM inventory supports VCA0450 as the Esos component profile."
              }
            ]
          },
          {
            "subject": "restricted_phage_propagation",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "esos_system_trait",
            "description": "Esos-mediated phage restriction realizes the Esos system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.ads0768",
                "snippet": "Most of these novel systems have little or no similarity to previously known ones",
                "notes": "Darracq et al. place the Esos discovery cohort in a set of novel bacterial systems that protect against phages."
              }
            ]
          },
          {
            "subject": "esos_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Esos system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Esos | 10\\.1126/science\\.ads0768 | Sedentary chromosomal integrons as biobanks of bacterial antiphage defense systems",
                "notes": "DefenseFinder associates Esos with the Darracq et al. bacterial antiphage-system paper."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "esos-mechanism-gap",
        "prompt": "Resolve Esos phage triggers and effector outputs before minting narrower Esos mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Darracq et al. and DefenseFinder support Esos as a named anti-phage system with a VCA0450 profile, but the trigger, molecular substrate, antiviral effector output, and subtype-specific mechanism are not resolved enough here to assert a narrower mechanistic child trait.",
        "attaches_to": [
          "causal_graphs#esos_locus_restricts_phage"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-19"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-19T14:36:48Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Esos system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v159.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000326",
    "label": "Fliodhais system",
    "definition": "A phage defense system in which an organism possesses a two-component Fliodhais locus that can reduce Lactococcus bacteriophage c2 plaque development.",
    "definition_source": "DOI:10.1093/nar/gkae671",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "Fliodhais",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1093/nar/gkae671"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1093/nar/gkae671",
        "snippet": "Based on comparative sequence analysis (BLASTN and BLASTP) and on functional and structural analysis (HHpred and InterPro) the remaining seven antiphage systems (out of the twenty identified) did not display significant homology to any previously described antiphage system, thus rendering them novel antiphage systems (Table 1). These systems were named after cheese, cattle or fermentation related deities (Rhea, Aristaios, Kamadhenu, Fliodhais, Audmula, Rugutis and Hesat)",
        "notes": "Grafakou et al. named Fliodhais among seven not previously described lactococcal antiphage systems."
      },
      {
        "reference": "DOI:10.1093/nar/gkae671",
        "snippet": "All discovered systems, except Fliodhais, are single gene antiphage systems. Both genetic components are necessary for Fliodhais activity; the described antiphage activity (see below) was not observed when the two components were cloned and tested separately.",
        "notes": "Grafakou et al. report that the tested Fliodhais system requires both of its genetic components for activity."
      },
      {
        "reference": "DOI:10.1093/nar/gkae671",
        "snippet": "Fliodhais was associated with smaller c2 plaques surrounded by a halo (<1 mm clear-centred plaques with a faint ring), a phenotype that was not observed when phage c2 was plated on the wild type strain (up to 4 mm clear-centred plaques without a halo).",
        "notes": "Grafakou et al. report a Fliodhais-associated c2 plaque morphology distinct from the wild-type Lactococcus host."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "Fliodhais | 10\\.1093/nar/gkae671 | Discovery of antiphage systems in the lactococcal plasmidome",
        "notes": "The DefenseFinder article registry maps the named Fliodhais system to the Grafakou et al. lactococcal antiphage-system discovery paper."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "fliodhais_locus_restricts_phage",
        "title": "Fliodhais loci confer bacterial phage defense",
        "description": "Conservative system-level sketch linking possession of a Fliodhais locus to restricted bacteriophage propagation without asserting the unresolved phage trigger or molecular output.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Fliodhais as a named two-component lactococcal anti-phage system while leaving its direct phage trigger, molecular substrate, antiviral effector output, natural locus breadth, and the absence of pinned DefenseFinder HMM or rule rows unresolved.",
        "nodes": [
          {
            "node_id": "fliodhais_locus",
            "label": "Fliodhais locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A Fliodhais anti-phage defense locus described as requiring both genetic components for activity."
          },
          {
            "node_id": "restricted_phage_propagation",
            "label": "restricted phage propagation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced propagation of bacteriophage in cells carrying the Fliodhais system."
          },
          {
            "node_id": "fliodhais_system_trait",
            "label": "Fliodhais system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000326",
            "description": "Possession of a genome-encoded Fliodhais phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "fliodhais_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "restricted_phage_propagation",
            "description": "The lactococcal plasmidome screen discovered Fliodhais as a named two-component antiphage system, and the DefenseFinder article registry maps the Fliodhais system to that discovery paper.",
            "evidence": [
              {
                "reference": "DOI:10.1093/nar/gkae671",
                "snippet": "Based on comparative sequence analysis (BLASTN and BLASTP) and on functional and structural analysis (HHpred and InterPro) the remaining seven antiphage systems (out of the twenty identified) did not display significant homology to any previously described antiphage system, thus rendering them novel antiphage systems (Table 1). These systems were named after cheese, cattle or fermentation related deities (Rhea, Aristaios, Kamadhenu, Fliodhais, Audmula, Rugutis and Hesat)",
                "notes": "Grafakou et al. named Fliodhais as one of the novel lactococcal antiphage systems."
              },
              {
                "reference": "DOI:10.1093/nar/gkae671",
                "snippet": "All discovered systems, except Fliodhais, are single gene antiphage systems. Both genetic components are necessary for Fliodhais activity; the described antiphage activity (see below) was not observed when the two components were cloned and tested separately.",
                "notes": "Grafakou et al. report that both cloned Fliodhais components were necessary for activity."
              },
              {
                "reference": "DOI:10.1093/nar/gkae671",
                "snippet": "Fliodhais was associated with smaller c2 plaques surrounded by a halo (<1 mm clear-centred plaques with a faint ring), a phenotype that was not observed when phage c2 was plated on the wild type strain (up to 4 mm clear-centred plaques without a halo).",
                "notes": "Grafakou et al. report Fliodhais-associated c2 plaque-size reduction."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Fliodhais | 10\\.1093/nar/gkae671 | Discovery of antiphage systems in the lactococcal plasmidome",
                "notes": "The DefenseFinder article registry maps the named Fliodhais system to the Grafakou et al. lactococcal antiphage-system discovery paper."
              }
            ]
          },
          {
            "subject": "restricted_phage_propagation",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "fliodhais_system_trait",
            "description": "Fliodhais-mediated phage restriction realizes the Fliodhais system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1093/nar/gkae671",
                "snippet": "Fliodhais was associated with smaller c2 plaques surrounded by a halo (<1 mm clear-centred plaques with a faint ring), a phenotype that was not observed when phage c2 was plated on the wild type strain (up to 4 mm clear-centred plaques without a halo).",
                "notes": "Grafakou et al. report a Fliodhais-linked change in c2 plaque development."
              }
            ]
          },
          {
            "subject": "fliodhais_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Fliodhais system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Fliodhais | 10\\.1093/nar/gkae671 | Discovery of antiphage systems in the lactococcal plasmidome",
                "notes": "The DefenseFinder article registry maps the named Fliodhais system to the Grafakou et al. lactococcal antiphage-system discovery paper."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "fliodhais-mechanism-gap",
        "prompt": "Resolve Fliodhais phage triggers and effector outputs before minting narrower Fliodhais mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Grafakou et al. and DefenseFinder support Fliodhais as a named two-component anti-phage system, but the direct trigger, molecular substrate, antiviral effector output, natural locus breadth, and profile-to-component model are not resolved enough here to assert a narrower mechanistic child trait.",
        "attaches_to": [
          "causal_graphs#fliodhais_locus_restricts_phage"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-21"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-21T04:17:19Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Fliodhais system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v203.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000346",
    "label": "FS-GIY-YIG system",
    "definition": "A phage defense system in which an organism possesses an FS_GIY_YIG locus represented by DefenseFinder as a single-profile model requiring FS_GIY_YIG__GIY_YIG.",
    "definition_source": "DOI:10.1016/j.cell.2022.07.014",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "FS_GIY_YIG",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      },
      {
        "synonym_text": "FS_GIY_YIG__GIY_YIG",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "PMID:35985290",
        "snippet": "the phage-inducible chromosomal islands (PICIs), carry an impressive arsenal of defense mechanisms",
        "notes": "Fillol-Salom et al. support phage-inducible chromosomal islands as carriers of mobile-element defense mechanisms."
      },
      {
        "reference": "PMID:35985290",
        "snippet": "These defense systems provide broad immunity, blocking not only phage reproduction, but also plasmid and non-cognate PICI transfer.",
        "notes": "Fillol-Salom et al. support PICI-encoded defense systems as broad immunity determinants against phage reproduction and other mobile genetic element transfer."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "FS_GIY_YIG | 10\\.1016/j\\.cell\\.2022\\.07\\.014 | Bacteriophages benefit from mobilizing pathogenicity islands encoding immune systems against competitors",
        "notes": "The DefenseFinder article registry maps the named FS_GIY_YIG system to the Fillol-Salom et al. PICI defense-system paper."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "FS_GIY_YIG\tFS_GIY_YIG\t1\t1\tFS_GIY_YIG__GIY_YIG",
        "notes": "The DefenseFinder rules table models FS_GIY_YIG as a single-profile system requiring the FS_GIY_YIG__GIY_YIG profile."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| FS_GIY_YIG__GIY_YIG                              | FS_GIY_YIG__GIY_YIG                              | FS_GIY_YIG             | Custom                  | 100    |",
        "notes": "The DefenseFinder HMM inventory records FS_GIY_YIG__GIY_YIG under FS_GIY_YIG."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "fs_giy_yig_locus_restricts_phage",
        "title": "FS-GIY-YIG loci confer bacterial phage defense",
        "description": "Conservative system-level sketch linking possession of an FS_GIY_YIG locus to broad mobile-element defense without asserting the unresolved phage trigger or molecular output.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures FS-GIY-YIG as a named DefenseFinder single-profile system in the Fillol-Salom PICI defense family while leaving its natural host breadth, helper-phage trigger, GIY-YIG substrate, and direct effector activity unresolved.",
        "nodes": [
          {
            "node_id": "fs_giy_yig_locus",
            "label": "FS_GIY_YIG locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A DefenseFinder FS_GIY_YIG phage-defense locus represented by a GIY-YIG nuclease-like profile."
          },
          {
            "node_id": "pici_encoded_mobile_element_defense",
            "label": "PICI-encoded mobile-element defense",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Defense by phage-inducible chromosomal island loci against phage reproduction, plasmid transfer, or non-cognate PICI transfer."
          },
          {
            "node_id": "fs_giy_yig_system_trait",
            "label": "FS-GIY-YIG system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000346",
            "description": "Possession of a genome-encoded FS-GIY-YIG phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "fs_giy_yig_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "pici_encoded_mobile_element_defense",
            "description": "DefenseFinder maps FS_GIY_YIG to the Fillol-Salom et al. PICI-encoded immunity study and models it as a single-profile system requiring a GIY-YIG nuclease-like profile.",
            "evidence": [
              {
                "reference": "PMID:35985290",
                "snippet": "the phage-inducible chromosomal islands (PICIs), carry an impressive arsenal of defense mechanisms",
                "notes": "Fillol-Salom et al. support PICI loci as carriers of phage and mobile-element defense mechanisms."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "FS_GIY_YIG | 10\\.1016/j\\.cell\\.2022\\.07\\.014 | Bacteriophages benefit from mobilizing pathogenicity islands encoding immune systems against competitors",
                "notes": "The DefenseFinder article registry maps the named FS_GIY_YIG system to the Fillol-Salom et al. PICI defense-system paper."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "FS_GIY_YIG\tFS_GIY_YIG\t1\t1\tFS_GIY_YIG__GIY_YIG",
                "notes": "The DefenseFinder rules table models FS_GIY_YIG as a single-profile system requiring the FS_GIY_YIG__GIY_YIG profile."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| FS_GIY_YIG__GIY_YIG                              | FS_GIY_YIG__GIY_YIG                              | FS_GIY_YIG             | Custom                  | 100    |",
                "notes": "The DefenseFinder HMM inventory records FS_GIY_YIG__GIY_YIG under FS_GIY_YIG."
              }
            ]
          },
          {
            "subject": "pici_encoded_mobile_element_defense",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "fs_giy_yig_system_trait",
            "description": "FS_GIY_YIG-associated mobile-element defense realizes the FS-GIY-YIG system trait.",
            "evidence": [
              {
                "reference": "PMID:35985290",
                "snippet": "These defense systems provide broad immunity, blocking not only phage reproduction, but also plasmid and non-cognate PICI transfer.",
                "notes": "Fillol-Salom et al. support PICI-encoded defense systems as broad mobile-element immunity determinants."
              }
            ]
          },
          {
            "subject": "fs_giy_yig_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "FS-GIY-YIG system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "FS_GIY_YIG | 10\\.1016/j\\.cell\\.2022\\.07\\.014 | Bacteriophages benefit from mobilizing pathogenicity islands encoding immune systems against competitors",
                "notes": "The DefenseFinder article registry maps the named FS_GIY_YIG system to the Fillol-Salom et al. PICI defense-system paper."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "FS_GIY_YIG\tFS_GIY_YIG\t1\t1\tFS_GIY_YIG__GIY_YIG",
                "notes": "The DefenseFinder rules table models FS_GIY_YIG as a single-profile system requiring the FS_GIY_YIG__GIY_YIG profile."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "fs-giy-yig-mechanism-gap",
        "prompt": "Resolve FS_GIY_YIG natural hosts, helper-phage triggers, GIY-YIG substrates, and effector activity before minting narrower FS_GIY_YIG mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Fillol-Salom et al. support phage-inducible chromosomal islands as carriers of defense systems that provide broad immunity, and DefenseFinder models FS_GIY_YIG as a single-profile system. Its exact natural host breadth, helper-phage trigger, nuclease substrate, and profile-to-activity mapping remain unresolved.",
        "attaches_to": [
          "causal_graphs#fs_giy_yig_locus_restricts_phage"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-21"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-21T21:36:57Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted FS-GIY-YIG system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v223.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000347",
    "label": "FS-HEPN-TM system",
    "definition": "A phage defense system in which an organism possesses an FS_HEPN_TM locus represented by DefenseFinder as a two-profile model requiring FS_HEPN_TM__HEPN and FS_HEPN_TM__TM.",
    "definition_source": "DOI:10.1016/j.cell.2022.07.014",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "FS_HEPN_TM",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      },
      {
        "synonym_text": "FS_HEPN_TM__HEPN",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "FS_HEPN_TM__TM",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "PMID:35985290",
        "snippet": "the phage-inducible chromosomal islands (PICIs), carry an impressive arsenal of defense mechanisms",
        "notes": "Fillol-Salom et al. support phage-inducible chromosomal islands as carriers of mobile-element defense mechanisms."
      },
      {
        "reference": "PMID:35985290",
        "snippet": "These defense systems provide broad immunity, blocking not only phage reproduction, but also plasmid and non-cognate PICI transfer.",
        "notes": "Fillol-Salom et al. support PICI-encoded defense systems as broad immunity determinants against phage reproduction and other mobile genetic element transfer."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "FS_HEPN_TM | 10\\.1016/j\\.cell\\.2022\\.07\\.014 | Bacteriophages benefit from mobilizing pathogenicity islands encoding immune systems against competitors",
        "notes": "The DefenseFinder article registry maps the named FS_HEPN_TM system to the Fillol-Salom et al. PICI defense-system paper."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "FS_HEPN_TM\tFS_HEPN_TM\t2\t2\tFS_HEPN_TM__HEPN, FS_HEPN_TM__TM",
        "notes": "The DefenseFinder rules table models FS_HEPN_TM as a two-profile system requiring the FS_HEPN_TM__HEPN and FS_HEPN_TM__TM profiles."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| FS_HEPN_TM__HEPN                                 | FS_HEPN_TM__HEPN                                 | FS_HEPN_TM             | PF05168.15              | 20     |",
        "notes": "The DefenseFinder HMM inventory records FS_HEPN_TM__HEPN under FS_HEPN_TM."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| FS_HEPN_TM__TM                                   | FS_HEPN_TM__TM                                   | FS_HEPN_TM             | Custom                  | 20     |",
        "notes": "The DefenseFinder HMM inventory records FS_HEPN_TM__TM under FS_HEPN_TM."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "fs_hepn_tm_locus_restricts_phage",
        "title": "FS-HEPN-TM loci confer bacterial phage defense",
        "description": "Conservative system-level sketch linking possession of an FS_HEPN_TM locus to broad mobile-element defense without asserting the unresolved phage trigger or molecular output.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures FS-HEPN-TM as a named DefenseFinder two-profile system in the Fillol-Salom PICI defense family while leaving its natural host breadth, helper-phage trigger, HEPN-family substrate, and transmembrane partner function unresolved.",
        "nodes": [
          {
            "node_id": "fs_hepn_tm_locus",
            "label": "FS_HEPN_TM locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A DefenseFinder FS_HEPN_TM phage-defense locus represented by HEPN-family and transmembrane profiles."
          },
          {
            "node_id": "pici_encoded_mobile_element_defense",
            "label": "PICI-encoded mobile-element defense",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Defense by phage-inducible chromosomal island loci against phage reproduction, plasmid transfer, or non-cognate PICI transfer."
          },
          {
            "node_id": "fs_hepn_tm_system_trait",
            "label": "FS-HEPN-TM system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000347",
            "description": "Possession of a genome-encoded FS-HEPN-TM phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "fs_hepn_tm_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "pici_encoded_mobile_element_defense",
            "description": "DefenseFinder maps FS_HEPN_TM to the Fillol-Salom et al. PICI-encoded immunity study and models it as a two-profile system requiring HEPN-family and transmembrane profiles.",
            "evidence": [
              {
                "reference": "PMID:35985290",
                "snippet": "the phage-inducible chromosomal islands (PICIs), carry an impressive arsenal of defense mechanisms",
                "notes": "Fillol-Salom et al. support PICI loci as carriers of phage and mobile-element defense mechanisms."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "FS_HEPN_TM | 10\\.1016/j\\.cell\\.2022\\.07\\.014 | Bacteriophages benefit from mobilizing pathogenicity islands encoding immune systems against competitors",
                "notes": "The DefenseFinder article registry maps the named FS_HEPN_TM system to the Fillol-Salom et al. PICI defense-system paper."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "FS_HEPN_TM\tFS_HEPN_TM\t2\t2\tFS_HEPN_TM__HEPN, FS_HEPN_TM__TM",
                "notes": "The DefenseFinder rules table models FS_HEPN_TM as a two-profile system requiring the FS_HEPN_TM__HEPN and FS_HEPN_TM__TM profiles."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| FS_HEPN_TM__HEPN                                 | FS_HEPN_TM__HEPN                                 | FS_HEPN_TM             | PF05168.15              | 20     |",
                "notes": "The DefenseFinder HMM inventory records FS_HEPN_TM__HEPN under FS_HEPN_TM."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| FS_HEPN_TM__TM                                   | FS_HEPN_TM__TM                                   | FS_HEPN_TM             | Custom                  | 20     |",
                "notes": "The DefenseFinder HMM inventory records FS_HEPN_TM__TM under FS_HEPN_TM."
              }
            ]
          },
          {
            "subject": "pici_encoded_mobile_element_defense",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "fs_hepn_tm_system_trait",
            "description": "FS_HEPN_TM-associated mobile-element defense realizes the FS-HEPN-TM system trait.",
            "evidence": [
              {
                "reference": "PMID:35985290",
                "snippet": "These defense systems provide broad immunity, blocking not only phage reproduction, but also plasmid and non-cognate PICI transfer.",
                "notes": "Fillol-Salom et al. support PICI-encoded defense systems as broad mobile-element immunity determinants."
              }
            ]
          },
          {
            "subject": "fs_hepn_tm_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "FS-HEPN-TM system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "FS_HEPN_TM | 10\\.1016/j\\.cell\\.2022\\.07\\.014 | Bacteriophages benefit from mobilizing pathogenicity islands encoding immune systems against competitors",
                "notes": "The DefenseFinder article registry maps the named FS_HEPN_TM system to the Fillol-Salom et al. PICI defense-system paper."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "FS_HEPN_TM\tFS_HEPN_TM\t2\t2\tFS_HEPN_TM__HEPN, FS_HEPN_TM__TM",
                "notes": "The DefenseFinder rules table models FS_HEPN_TM as a two-profile system requiring the FS_HEPN_TM__HEPN and FS_HEPN_TM__TM profiles."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "fs-hepn-tm-mechanism-gap",
        "prompt": "Resolve FS_HEPN_TM natural hosts, helper-phage triggers, HEPN-family substrates, and transmembrane partner activity before minting narrower FS_HEPN_TM mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Fillol-Salom et al. support phage-inducible chromosomal islands as carriers of defense systems that provide broad immunity, and DefenseFinder models FS_HEPN_TM as a two-profile HEPN/transmembrane system. Its exact natural host breadth, helper-phage trigger, substrate, and profile-to-activity mapping remain unresolved.",
        "attaches_to": [
          "causal_graphs#fs_hepn_tm_locus_restricts_phage"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-21"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-21T22:22:47Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted FS-HEPN-TM system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v224.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000349",
    "label": "FS-HP-SDH-sah system",
    "definition": "A phage defense system in which an organism possesses an FS_HP_SDH_sah locus represented by DefenseFinder as a two-profile model requiring FS_HP_SDH_sah__HP and FS_HP_SDH_sah__SDH_sah.",
    "definition_source": "DOI:10.1016/j.cell.2022.07.014",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "FS_HP_SDH_sah",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      },
      {
        "synonym_text": "FS_HP_SDH_sah__HP",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "FS_HP_SDH_sah__SDH_sah",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "PMID:35985290",
        "snippet": "the phage-inducible chromosomal islands (PICIs), carry an impressive arsenal of defense mechanisms",
        "notes": "Fillol-Salom et al. support phage-inducible chromosomal islands as carriers of mobile-element defense mechanisms."
      },
      {
        "reference": "PMID:35985290",
        "snippet": "These defense systems provide broad immunity, blocking not only phage reproduction, but also plasmid and non-cognate PICI transfer.",
        "notes": "Fillol-Salom et al. support PICI-encoded defense systems as broad immunity determinants against phage reproduction and other mobile genetic element transfer."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "FS_HP_SDH_sah | 10\\.1016/j\\.cell\\.2022\\.07\\.014 | Bacteriophages benefit from mobilizing pathogenicity islands encoding immune systems against competitors",
        "notes": "The DefenseFinder article registry maps the named FS_HP_SDH_sah system to the Fillol-Salom et al. PICI defense-system paper."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "FS_HP_SDH_sah\tFS_HP_SDH_sah\t2\t2\tFS_HP_SDH_sah__HP, FS_HP_SDH_sah__SDH_sah",
        "notes": "The DefenseFinder rules table models FS_HP_SDH_sah as a two-profile system requiring the FS_HP_SDH_sah__HP and FS_HP_SDH_sah__SDH_sah profiles."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| FS_HP_SDH_sah__HP                                | FS_HP_SDH_sah__HP                                | FS_HP_SDH_sah          | Custom                  | 20     |",
        "notes": "The DefenseFinder HMM inventory records FS_HP_SDH_sah__HP under FS_HP_SDH_sah."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| FS_HP_SDH_sah__SDH_sah                           | FS_HP_SDH_sah__SDH_sah                           | FS_HP_SDH_sah          | Custom                  | 20     |",
        "notes": "The DefenseFinder HMM inventory records FS_HP_SDH_sah__SDH_sah under FS_HP_SDH_sah."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "fs_hp_sdh_sah_locus_restricts_phage",
        "title": "FS-HP-SDH-sah loci confer bacterial phage defense",
        "description": "Conservative system-level sketch linking possession of an FS_HP_SDH_sah locus to broad mobile-element defense without asserting the unresolved phage trigger or molecular output.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures FS-HP-SDH-sah as a named DefenseFinder two-profile system in the Fillol-Salom PICI defense family while leaving its natural host breadth, helper-phage trigger, HP component identity, SDH_sah partner function, and profile-to-activity mapping unresolved.",
        "nodes": [
          {
            "node_id": "fs_hp_sdh_sah_locus",
            "label": "FS_HP_SDH_sah locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A DefenseFinder FS_HP_SDH_sah phage-defense locus represented by custom FS_HP_SDH_sah__HP and FS_HP_SDH_sah__SDH_sah profiles."
          },
          {
            "node_id": "pici_encoded_mobile_element_defense",
            "label": "PICI-encoded mobile-element defense",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Defense by phage-inducible chromosomal island loci against phage reproduction, plasmid transfer, or non-cognate PICI transfer."
          },
          {
            "node_id": "fs_hp_sdh_sah_system_trait",
            "label": "FS-HP-SDH-sah system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000349",
            "description": "Possession of a genome-encoded FS-HP-SDH-sah phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "fs_hp_sdh_sah_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "pici_encoded_mobile_element_defense",
            "description": "DefenseFinder maps FS_HP_SDH_sah to the Fillol-Salom et al. PICI-encoded immunity study and models it as a two-profile system requiring custom HP and SDH_sah profiles.",
            "evidence": [
              {
                "reference": "PMID:35985290",
                "snippet": "the phage-inducible chromosomal islands (PICIs), carry an impressive arsenal of defense mechanisms",
                "notes": "Fillol-Salom et al. support PICI loci as carriers of phage and mobile-element defense mechanisms."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "FS_HP_SDH_sah | 10\\.1016/j\\.cell\\.2022\\.07\\.014 | Bacteriophages benefit from mobilizing pathogenicity islands encoding immune systems against competitors",
                "notes": "The DefenseFinder article registry maps the named FS_HP_SDH_sah system to the Fillol-Salom et al. PICI defense-system paper."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "FS_HP_SDH_sah\tFS_HP_SDH_sah\t2\t2\tFS_HP_SDH_sah__HP, FS_HP_SDH_sah__SDH_sah",
                "notes": "The DefenseFinder rules table models FS_HP_SDH_sah as a two-profile system requiring the FS_HP_SDH_sah__HP and FS_HP_SDH_sah__SDH_sah profiles."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| FS_HP_SDH_sah__HP                                | FS_HP_SDH_sah__HP                                | FS_HP_SDH_sah          | Custom                  | 20     |",
                "notes": "The DefenseFinder HMM inventory records FS_HP_SDH_sah__HP under FS_HP_SDH_sah."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| FS_HP_SDH_sah__SDH_sah                           | FS_HP_SDH_sah__SDH_sah                           | FS_HP_SDH_sah          | Custom                  | 20     |",
                "notes": "The DefenseFinder HMM inventory records FS_HP_SDH_sah__SDH_sah under FS_HP_SDH_sah."
              }
            ]
          },
          {
            "subject": "pici_encoded_mobile_element_defense",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "fs_hp_sdh_sah_system_trait",
            "description": "FS_HP_SDH_sah-associated mobile-element defense realizes the FS-HP-SDH-sah system trait.",
            "evidence": [
              {
                "reference": "PMID:35985290",
                "snippet": "These defense systems provide broad immunity, blocking not only phage reproduction, but also plasmid and non-cognate PICI transfer.",
                "notes": "Fillol-Salom et al. support PICI-encoded defense systems as broad mobile-element immunity determinants."
              }
            ]
          },
          {
            "subject": "fs_hp_sdh_sah_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "FS-HP-SDH-sah system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "FS_HP_SDH_sah | 10\\.1016/j\\.cell\\.2022\\.07\\.014 | Bacteriophages benefit from mobilizing pathogenicity islands encoding immune systems against competitors",
                "notes": "The DefenseFinder article registry maps the named FS_HP_SDH_sah system to the Fillol-Salom et al. PICI defense-system paper."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "FS_HP_SDH_sah\tFS_HP_SDH_sah\t2\t2\tFS_HP_SDH_sah__HP, FS_HP_SDH_sah__SDH_sah",
                "notes": "The DefenseFinder rules table models FS_HP_SDH_sah as a two-profile system requiring the FS_HP_SDH_sah__HP and FS_HP_SDH_sah__SDH_sah profiles."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "fs-hp-sdh-sah-mechanism-gap",
        "prompt": "Resolve FS_HP_SDH_sah natural hosts, helper-phage triggers, HP component identity, and SDH_sah partner activity before minting narrower FS_HP_SDH_sah mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Fillol-Salom et al. support phage-inducible chromosomal islands as carriers of defense systems that provide broad immunity, and DefenseFinder models FS_HP_SDH_sah as a two-profile system. Its exact natural host breadth, helper-phage trigger, HP component identity, SDH_sah partner activity, and profile-to-activity mapping remain unresolved.",
        "attaches_to": [
          "causal_graphs#fs_hp_sdh_sah_locus_restricts_phage"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-21"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-21T23:29:51Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted FS-HP-SDH-sah system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v226.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000348",
    "label": "FS-HP system",
    "definition": "A phage defense system in which an organism possesses an FS_HP locus represented by DefenseFinder as a single-profile model requiring FS_HP__HP.",
    "definition_source": "DOI:10.1016/j.cell.2022.07.014",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "FS_HP",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      },
      {
        "synonym_text": "FS_HP__HP",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "PMID:35985290",
        "snippet": "the phage-inducible chromosomal islands (PICIs), carry an impressive arsenal of defense mechanisms",
        "notes": "Fillol-Salom et al. support phage-inducible chromosomal islands as carriers of mobile-element defense mechanisms."
      },
      {
        "reference": "PMID:35985290",
        "snippet": "These defense systems provide broad immunity, blocking not only phage reproduction, but also plasmid and non-cognate PICI transfer.",
        "notes": "Fillol-Salom et al. support PICI-encoded defense systems as broad immunity determinants against phage reproduction and other mobile genetic element transfer."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "FS_HP | 10\\.1016/j\\.cell\\.2022\\.07\\.014 | Bacteriophages benefit from mobilizing pathogenicity islands encoding immune systems against competitors",
        "notes": "The DefenseFinder article registry maps the named FS_HP system to the Fillol-Salom et al. PICI defense-system paper."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "FS_HP\tFS_HP\t1\t1\tFS_HP__HP",
        "notes": "The DefenseFinder rules table models FS_HP as a single-profile system requiring the FS_HP__HP profile."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| FS_HP__HP                                        | FS_HP__HP                                        | FS_HP                  | Custom                  | 100    |",
        "notes": "The DefenseFinder HMM inventory records FS_HP__HP under FS_HP."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "fs_hp_locus_restricts_phage",
        "title": "FS-HP loci confer bacterial phage defense",
        "description": "Conservative system-level sketch linking possession of an FS_HP locus to broad mobile-element defense without asserting the unresolved phage trigger or molecular output.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures FS-HP as a named DefenseFinder single-profile system in the Fillol-Salom PICI defense family while leaving its natural host breadth, helper-phage trigger, HP component identity, and direct effector activity unresolved.",
        "nodes": [
          {
            "node_id": "fs_hp_locus",
            "label": "FS_HP locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A DefenseFinder FS_HP phage-defense locus represented by a custom FS_HP__HP profile."
          },
          {
            "node_id": "pici_encoded_mobile_element_defense",
            "label": "PICI-encoded mobile-element defense",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Defense by phage-inducible chromosomal island loci against phage reproduction, plasmid transfer, or non-cognate PICI transfer."
          },
          {
            "node_id": "fs_hp_system_trait",
            "label": "FS-HP system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000348",
            "description": "Possession of a genome-encoded FS-HP phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "fs_hp_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "pici_encoded_mobile_element_defense",
            "description": "DefenseFinder maps FS_HP to the Fillol-Salom et al. PICI-encoded immunity study and models it as a single-profile system requiring a custom FS_HP__HP profile.",
            "evidence": [
              {
                "reference": "PMID:35985290",
                "snippet": "the phage-inducible chromosomal islands (PICIs), carry an impressive arsenal of defense mechanisms",
                "notes": "Fillol-Salom et al. support PICI loci as carriers of phage and mobile-element defense mechanisms."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "FS_HP | 10\\.1016/j\\.cell\\.2022\\.07\\.014 | Bacteriophages benefit from mobilizing pathogenicity islands encoding immune systems against competitors",
                "notes": "The DefenseFinder article registry maps the named FS_HP system to the Fillol-Salom et al. PICI defense-system paper."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "FS_HP\tFS_HP\t1\t1\tFS_HP__HP",
                "notes": "The DefenseFinder rules table models FS_HP as a single-profile system requiring the FS_HP__HP profile."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| FS_HP__HP                                        | FS_HP__HP                                        | FS_HP                  | Custom                  | 100    |",
                "notes": "The DefenseFinder HMM inventory records FS_HP__HP under FS_HP."
              }
            ]
          },
          {
            "subject": "pici_encoded_mobile_element_defense",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "fs_hp_system_trait",
            "description": "FS_HP-associated mobile-element defense realizes the FS-HP system trait.",
            "evidence": [
              {
                "reference": "PMID:35985290",
                "snippet": "These defense systems provide broad immunity, blocking not only phage reproduction, but also plasmid and non-cognate PICI transfer.",
                "notes": "Fillol-Salom et al. support PICI-encoded defense systems as broad mobile-element immunity determinants."
              }
            ]
          },
          {
            "subject": "fs_hp_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "FS-HP system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "FS_HP | 10\\.1016/j\\.cell\\.2022\\.07\\.014 | Bacteriophages benefit from mobilizing pathogenicity islands encoding immune systems against competitors",
                "notes": "The DefenseFinder article registry maps the named FS_HP system to the Fillol-Salom et al. PICI defense-system paper."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "FS_HP\tFS_HP\t1\t1\tFS_HP__HP",
                "notes": "The DefenseFinder rules table models FS_HP as a single-profile system requiring the FS_HP__HP profile."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "fs-hp-mechanism-gap",
        "prompt": "Resolve FS_HP natural hosts, helper-phage triggers, HP component identity, and effector activity before minting narrower FS_HP mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Fillol-Salom et al. support phage-inducible chromosomal islands as carriers of defense systems that provide broad immunity, and DefenseFinder models FS_HP as a single-profile system. Its exact natural host breadth, helper-phage trigger, component identity, and profile-to-activity mapping remain unresolved.",
        "attaches_to": [
          "causal_graphs#fs_hp_locus_restricts_phage"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-21"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-21T22:51:56Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted FS-HP system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v225.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000350",
    "label": "FS-HsdR-like system",
    "definition": "A phage defense system in which an organism possesses an FS_HsdR_like locus represented by DefenseFinder as a two-gene model drawing from custom FS_HsdR_like__DUF6731, FS_HsdR_like__HP, and FS_HsdR_like__HdrR profiles.",
    "definition_source": "DOI:10.1016/j.cell.2022.07.014",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "FS_HsdR_like",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      },
      {
        "synonym_text": "FS_HsdR_like__DUF6731",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "FS_HsdR_like__HdrR",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "FS_HsdR_like__HP",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "PMID:35985290",
        "snippet": "the phage-inducible chromosomal islands (PICIs), carry an impressive arsenal of defense mechanisms",
        "notes": "Fillol-Salom et al. support phage-inducible chromosomal islands as carriers of mobile-element defense mechanisms."
      },
      {
        "reference": "PMID:35985290",
        "snippet": "These defense systems provide broad immunity, blocking not only phage reproduction, but also plasmid and non-cognate PICI transfer.",
        "notes": "Fillol-Salom et al. support PICI-encoded defense systems as broad immunity determinants against phage reproduction and other mobile genetic element transfer."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "FS_HsdR_like | 10\\.1016/j\\.cell\\.2022\\.07\\.014 | Bacteriophages benefit from mobilizing pathogenicity islands encoding immune systems against competitors",
        "notes": "The DefenseFinder article registry maps the named FS_HsdR_like system to the Fillol-Salom et al. PICI defense-system paper."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "FS_HsdR_like\tFS_HsdR_like\t2\t2\tFS_HsdR_like__DUF6731, FS_HsdR_like__HP, FS_HsdR_like__HdrR",
        "notes": "The DefenseFinder rules table models FS_HsdR_like with two mandatory profiles selected from three custom DUF6731, HP, and HdrR profile keys."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| FS_HsdR_like__DUF6731                            | FS_HsdR_like__DUF6731                            | FS_HsdR_like           | Custom                  | 20     |",
        "notes": "The DefenseFinder HMM inventory records FS_HsdR_like__DUF6731 under FS_HsdR_like."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| FS_HsdR_like__HdrR                               | FS_HsdR_like__HdrR                               | FS_HsdR_like           | Custom                  | 20     |",
        "notes": "The DefenseFinder HMM inventory records FS_HsdR_like__HdrR under FS_HsdR_like."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| FS_HsdR_like__HP                                 | FS_HsdR_like__HP                                 | FS_HsdR_like           | Custom                  | 20     |",
        "notes": "The DefenseFinder HMM inventory records FS_HsdR_like__HP under FS_HsdR_like."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "fs_hsdr_like_locus_restricts_phage",
        "title": "FS-HsdR-like loci confer bacterial phage defense",
        "description": "Conservative system-level sketch linking possession of an FS_HsdR_like locus to broad mobile-element defense without asserting the unresolved phage trigger or molecular output.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures FS-HsdR-like as a named DefenseFinder two-gene system in the Fillol-Salom PICI defense family while leaving its natural host breadth, helper-phage trigger, DUF6731 component activity, HP component identity, HdrR component activity, and profile-to-activity mapping unresolved.",
        "nodes": [
          {
            "node_id": "fs_hsdr_like_locus",
            "label": "FS_HsdR_like locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A DefenseFinder FS_HsdR_like phage-defense locus represented by custom FS_HsdR_like__DUF6731, FS_HsdR_like__HP, and FS_HsdR_like__HdrR profiles."
          },
          {
            "node_id": "pici_encoded_mobile_element_defense",
            "label": "PICI-encoded mobile-element defense",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Defense by phage-inducible chromosomal island loci against phage reproduction, plasmid transfer, or non-cognate PICI transfer."
          },
          {
            "node_id": "fs_hsdr_like_system_trait",
            "label": "FS-HsdR-like system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000350",
            "description": "Possession of a genome-encoded FS-HsdR-like phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "fs_hsdr_like_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "pici_encoded_mobile_element_defense",
            "description": "DefenseFinder maps FS_HsdR_like to the Fillol-Salom et al. PICI-encoded immunity study and models it as a two-gene system selecting from custom DUF6731, HP, and HdrR profiles.",
            "evidence": [
              {
                "reference": "PMID:35985290",
                "snippet": "the phage-inducible chromosomal islands (PICIs), carry an impressive arsenal of defense mechanisms",
                "notes": "Fillol-Salom et al. support PICI loci as carriers of phage and mobile-element defense mechanisms."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "FS_HsdR_like | 10\\.1016/j\\.cell\\.2022\\.07\\.014 | Bacteriophages benefit from mobilizing pathogenicity islands encoding immune systems against competitors",
                "notes": "The DefenseFinder article registry maps the named FS_HsdR_like system to the Fillol-Salom et al. PICI defense-system paper."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "FS_HsdR_like\tFS_HsdR_like\t2\t2\tFS_HsdR_like__DUF6731, FS_HsdR_like__HP, FS_HsdR_like__HdrR",
                "notes": "The DefenseFinder rules table models FS_HsdR_like with two mandatory profiles selected from three custom DUF6731, HP, and HdrR profile keys."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| FS_HsdR_like__DUF6731                            | FS_HsdR_like__DUF6731                            | FS_HsdR_like           | Custom                  | 20     |",
                "notes": "The DefenseFinder HMM inventory records FS_HsdR_like__DUF6731 under FS_HsdR_like."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| FS_HsdR_like__HdrR                               | FS_HsdR_like__HdrR                               | FS_HsdR_like           | Custom                  | 20     |",
                "notes": "The DefenseFinder HMM inventory records FS_HsdR_like__HdrR under FS_HsdR_like."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| FS_HsdR_like__HP                                 | FS_HsdR_like__HP                                 | FS_HsdR_like           | Custom                  | 20     |",
                "notes": "The DefenseFinder HMM inventory records FS_HsdR_like__HP under FS_HsdR_like."
              }
            ]
          },
          {
            "subject": "pici_encoded_mobile_element_defense",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "fs_hsdr_like_system_trait",
            "description": "FS_HsdR_like-associated mobile-element defense realizes the FS-HsdR-like system trait.",
            "evidence": [
              {
                "reference": "PMID:35985290",
                "snippet": "These defense systems provide broad immunity, blocking not only phage reproduction, but also plasmid and non-cognate PICI transfer.",
                "notes": "Fillol-Salom et al. support PICI-encoded defense systems as broad mobile-element immunity determinants."
              }
            ]
          },
          {
            "subject": "fs_hsdr_like_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "FS-HsdR-like system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "FS_HsdR_like | 10\\.1016/j\\.cell\\.2022\\.07\\.014 | Bacteriophages benefit from mobilizing pathogenicity islands encoding immune systems against competitors",
                "notes": "The DefenseFinder article registry maps the named FS_HsdR_like system to the Fillol-Salom et al. PICI defense-system paper."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "FS_HsdR_like\tFS_HsdR_like\t2\t2\tFS_HsdR_like__DUF6731, FS_HsdR_like__HP, FS_HsdR_like__HdrR",
                "notes": "The DefenseFinder rules table models FS_HsdR_like with two mandatory profiles selected from three custom DUF6731, HP, and HdrR profile keys."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "fs-hsdr-like-mechanism-gap",
        "prompt": "Resolve FS_HsdR_like natural hosts, helper-phage triggers, DUF6731 activity, HP component identity, HdrR activity, and the profile-to-activity mapping before minting narrower FS_HsdR_like mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Fillol-Salom et al. support phage-inducible chromosomal islands as carriers of defense systems that provide broad immunity, and DefenseFinder models FS_HsdR_like as a two-gene system drawing from three custom profile keys. Its exact natural host breadth, helper-phage trigger, component activities, and profile-to-activity mapping remain unresolved.",
        "attaches_to": [
          "causal_graphs#fs_hsdr_like_locus_restricts_phage"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-22"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-22T00:00:42Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted FS-HsdR-like system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v227.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000351",
    "label": "FS-Sma system",
    "definition": "A phage defense system in which an organism possesses an FS_Sma locus represented by DefenseFinder as a single-profile model requiring FS_Sma__Sma.",
    "definition_source": "DOI:10.1016/j.cell.2022.07.014",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "FS_Sma",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      },
      {
        "synonym_text": "FS_Sma__Sma",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "PMID:35985290",
        "snippet": "the phage-inducible chromosomal islands (PICIs), carry an impressive arsenal of defense mechanisms",
        "notes": "Fillol-Salom et al. support phage-inducible chromosomal islands as carriers of mobile-element defense mechanisms."
      },
      {
        "reference": "PMID:35985290",
        "snippet": "These defense systems provide broad immunity, blocking not only phage reproduction, but also plasmid and non-cognate PICI transfer.",
        "notes": "Fillol-Salom et al. support PICI-encoded defense systems as broad immunity determinants against phage reproduction and other mobile genetic element transfer."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "FS_Sma | 10\\.1016/j\\.cell\\.2022\\.07\\.014 | Bacteriophages benefit from mobilizing pathogenicity islands encoding immune systems against competitors",
        "notes": "The DefenseFinder article registry maps the named FS_Sma system to the Fillol-Salom et al. PICI defense-system paper."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "FS_Sma\tFS_Sma\t1\t1\tFS_Sma__Sma",
        "notes": "The DefenseFinder rules table models FS_Sma as a single-profile system requiring the FS_Sma__Sma profile."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| FS_Sma__Sma                                      | FS_Sma__Sma                                      | FS_Sma                 | Custom                  | 100    |",
        "notes": "The DefenseFinder HMM inventory records FS_Sma__Sma under FS_Sma."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "fs_sma_locus_restricts_phage",
        "title": "FS-Sma loci confer bacterial phage defense",
        "description": "Conservative system-level sketch linking possession of an FS_Sma locus to broad mobile-element defense without asserting the unresolved phage trigger or molecular output.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures FS-Sma as a named DefenseFinder single-profile system in the Fillol-Salom PICI defense family while leaving its natural host breadth, helper-phage trigger, Sma component identity, and direct effector activity unresolved.",
        "nodes": [
          {
            "node_id": "fs_sma_locus",
            "label": "FS_Sma locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A DefenseFinder FS_Sma phage-defense locus represented by a custom FS_Sma__Sma profile."
          },
          {
            "node_id": "pici_encoded_mobile_element_defense",
            "label": "PICI-encoded mobile-element defense",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Defense by phage-inducible chromosomal island loci against phage reproduction, plasmid transfer, or non-cognate PICI transfer."
          },
          {
            "node_id": "fs_sma_system_trait",
            "label": "FS-Sma system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000351",
            "description": "Possession of a genome-encoded FS-Sma phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "fs_sma_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "pici_encoded_mobile_element_defense",
            "description": "DefenseFinder maps FS_Sma to the Fillol-Salom et al. PICI-encoded immunity study and models it as a single-profile system requiring a custom FS_Sma__Sma profile.",
            "evidence": [
              {
                "reference": "PMID:35985290",
                "snippet": "the phage-inducible chromosomal islands (PICIs), carry an impressive arsenal of defense mechanisms",
                "notes": "Fillol-Salom et al. support PICI loci as carriers of phage and mobile-element defense mechanisms."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "FS_Sma | 10\\.1016/j\\.cell\\.2022\\.07\\.014 | Bacteriophages benefit from mobilizing pathogenicity islands encoding immune systems against competitors",
                "notes": "The DefenseFinder article registry maps the named FS_Sma system to the Fillol-Salom et al. PICI defense-system paper."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "FS_Sma\tFS_Sma\t1\t1\tFS_Sma__Sma",
                "notes": "The DefenseFinder rules table models FS_Sma as a single-profile system requiring the FS_Sma__Sma profile."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| FS_Sma__Sma                                      | FS_Sma__Sma                                      | FS_Sma                 | Custom                  | 100    |",
                "notes": "The DefenseFinder HMM inventory records FS_Sma__Sma under FS_Sma."
              }
            ]
          },
          {
            "subject": "pici_encoded_mobile_element_defense",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "fs_sma_system_trait",
            "description": "FS_Sma-associated mobile-element defense realizes the FS-Sma system trait.",
            "evidence": [
              {
                "reference": "PMID:35985290",
                "snippet": "These defense systems provide broad immunity, blocking not only phage reproduction, but also plasmid and non-cognate PICI transfer.",
                "notes": "Fillol-Salom et al. support PICI-encoded defense systems as broad mobile-element immunity determinants."
              }
            ]
          },
          {
            "subject": "fs_sma_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "FS-Sma system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "FS_Sma | 10\\.1016/j\\.cell\\.2022\\.07\\.014 | Bacteriophages benefit from mobilizing pathogenicity islands encoding immune systems against competitors",
                "notes": "The DefenseFinder article registry maps the named FS_Sma system to the Fillol-Salom et al. PICI defense-system paper."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "FS_Sma\tFS_Sma\t1\t1\tFS_Sma__Sma",
                "notes": "The DefenseFinder rules table models FS_Sma as a single-profile system requiring the FS_Sma__Sma profile."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "fs-sma-mechanism-gap",
        "prompt": "Resolve FS_Sma natural hosts, helper-phage triggers, Sma component identity, and effector activity before minting narrower FS_Sma mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Fillol-Salom et al. support phage-inducible chromosomal islands as carriers of defense systems that provide broad immunity, and DefenseFinder models FS_Sma as a single-profile system. Its exact natural host breadth, helper-phage trigger, component identity, and profile-to-activity mapping remain unresolved.",
        "attaches_to": [
          "causal_graphs#fs_sma_locus_restricts_phage"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-22"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-22T00:54:34Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted FS-Sma system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v228.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000215",
    "label": "Gabija system",
    "definition": "A genomics trait describing possession of a Gabija antiphage defense locus whose GajA and GajB proteins assemble into a complex that inhibits bacteriophage replication.",
    "definition_source": "DOI:10.1093/nar/gkad951",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "Gabija anti-phage defense system",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1093/nar/gkad951"
      },
      {
        "synonym_text": "Gabija anti-phage defence system",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1038/s41586-023-06855-2"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1093/nar/gkad951",
        "snippet": "Gabija is one of the most abundant prokaryotic antiviral systems and consists of two proteins, GajA and GajB",
        "notes": "Oh et al. support defining Gabija at the two-component antiviral-system level."
      },
      {
        "reference": "DOI:10.1093/nar/gkad951",
        "snippet": "The Gabija anti-phage defense system was first identified in Bacillus cereus and is present in >4000 prokaryotic genomes",
        "notes": "Oh et al. support B. cereus as the source organism for the Gabija system and support broad prokaryotic distribution."
      },
      {
        "reference": "DOI:10.1016/j.chom.2023.06.014",
        "snippet": "synergy between GajA-mediated DNA cleavage and nucleotide hydrolysis by GajB initiates efficient abortive infection defense against virulent bacteriophages",
        "notes": "Cheng et al. support the combined DNA-cleavage and nucleotide-depletion output of the Gabija complex."
      },
      {
        "reference": "DOI:10.1038/s41586-023-06855-2",
        "snippet": "Two sets of Gabija protein B (GajB) dimers dock at opposite sides of the complex and create a 4:4 GajA-GajB assembly (hereafter, GajAB) that is essential for phage resistance in vivo",
        "notes": "Antine et al. support the GajAB complex as essential for Gabija-mediated phage resistance."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1396",
        "taxon_label": "Bacillus cereus",
        "note": "Oh et al. report that the Gabija anti-phage defense system was first identified in Bacillus cereus and characterize GajB from the B. cereus VD045 Gabija system.",
        "reference": "DOI:10.1093/nar/gkad951"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "gabija_gajab_complex_antiphage_defense",
        "title": "Gabija GajAB complexes deplete nucleotides and cleave DNA",
        "description": "Evidence-backed process sketch linking a Gabija gajA-gajB operon to GajAB complex assembly, nucleotide depletion, DNA cleavage, and inhibition of bacteriophage replication.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures the characterized Gabija GajA/GajB outputs without asserting one universal phage sensor, DNA substrate, GajA:GajB stoichiometry, host death trigger, or anti-Gabija evasion mechanism across all Gabija loci.",
        "nodes": [
          {
            "node_id": "gabija_operon",
            "label": "Gabija gajA-gajB operon",
            "node_type": "GENETIC_ELEMENT",
            "description": "A Gabija defense locus encoding GajA and GajB proteins."
          },
          {
            "node_id": "gajab_complex_assembly",
            "label": "GajAB complex assembly",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Assembly of GajA and GajB proteins into the antiphage Gabija complex."
          },
          {
            "node_id": "gabija_nucleotide_depletion",
            "label": "Gabija nucleotide depletion",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "GajB-dependent hydrolysis of host dATP, dGTP, ATP, or GTP nucleotide pools."
          },
          {
            "node_id": "gabija_dna_cleavage",
            "label": "Gabija DNA cleavage",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "GajA-dependent cleavage of DNA during Gabija antiviral defense."
          },
          {
            "node_id": "phage_replication",
            "label": "phage replication",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Replication of invading bacteriophage DNA after host-cell entry."
          },
          {
            "node_id": "gabija_system_trait",
            "label": "Gabija system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000215",
            "description": "Possession of a genome-encoded Gabija antiphage defense locus."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "gabija_operon",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "gajab_complex_assembly",
            "description": "The gajA and gajB genes encode proteins that assemble into the Gabija GajAB antiphage complex.",
            "evidence": [
              {
                "reference": "DOI:10.1093/nar/gkad951",
                "snippet": "GajB interacts with GajA to form a heterooctameric Gabija complex",
                "notes": "Oh et al. support assembly of B. cereus VD045 GajA and GajB into a stable complex."
              },
              {
                "reference": "DOI:10.1038/s41586-023-06855-2",
                "snippet": "create a 4:4 GajA-GajB assembly (hereafter, GajAB) that is essential for phage resistance in vivo",
                "notes": "Antine et al. support the GajAB assembly as required for phage resistance."
              }
            ]
          },
          {
            "subject": "gajab_complex_assembly",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "gabija_nucleotide_depletion",
            "description": "The Gabija complex enables GajB-mediated nucleotide hydrolysis and nucleotide-pool depletion.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.chom.2023.06.014",
                "snippet": "GajA requires GajB, which senses DNA termini produced by GajA to hydrolyze (d)A/(d)GTP, depleting essential nucleotides",
                "notes": "Cheng et al. connect the GajA/GajB complex with depletion of adenine and guanine nucleotide pools."
              }
            ]
          },
          {
            "subject": "gajab_complex_assembly",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "gabija_dna_cleavage",
            "description": "The Gabija GajAB complex catalyzes GajA-mediated DNA cleavage during antiviral defense.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.chom.2023.06.014",
                "snippet": "synergy between GajA-mediated DNA cleavage and nucleotide hydrolysis by GajB initiates efficient abortive infection defense",
                "notes": "Cheng et al. support DNA cleavage as a GajA-dependent component of Gabija defense."
              }
            ]
          },
          {
            "subject": "gabija_nucleotide_depletion",
            "predicate": "mitigates",
            "predicate_id": "METPO:2007407",
            "object": "phage_replication",
            "description": "Gabija nucleotide depletion helps inhibit bacteriophage replication.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.chom.2023.06.014",
                "snippet": "depleting essential nucleotides. This ATPase activity of Gabija complex is only activated upon DNA binding",
                "notes": "Cheng et al. connect GajB ATPase activity to depletion of nucleotide pools required for phage replication."
              }
            ]
          },
          {
            "subject": "gabija_dna_cleavage",
            "predicate": "mitigates",
            "predicate_id": "METPO:2007407",
            "object": "phage_replication",
            "description": "Gabija DNA cleavage helps inhibit bacteriophage replication.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41586-023-06855-2",
                "snippet": "Gabija proteins assemble into a supramolecular complex of around 500 kDa that degrades phage DNA",
                "notes": "Antine et al. support phage-DNA degradation as an output of the GajAB complex."
              }
            ]
          },
          {
            "subject": "gabija_dna_cleavage",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "gabija_system_trait",
            "description": "GajAB DNA cleavage is part of the antiviral output that realizes the Gabija system defense phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.chom.2023.06.014",
                "snippet": "synergy between GajA-mediated DNA cleavage and nucleotide hydrolysis by GajB initiates efficient abortive infection defense",
                "notes": "Cheng et al. support GajA-mediated DNA cleavage as part of the Gabija defense phenotype."
              }
            ]
          },
          {
            "subject": "gabija_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Gabija system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1093/nar/gkad951",
                "snippet": "Gabija is one of the most abundant prokaryotic antiviral systems",
                "notes": "Oh et al. place Gabija among prokaryotic antiviral systems."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "gabija-activation-and-antidefense-gap",
        "prompt": "Resolve Gabija activation, stoichiometry, cell-outcome, and phage anti-defense breadth before minting narrower Gabija mechanistic children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Cheng et al. support nucleotide depletion and DNA cleavage as Gabija outputs, and Antine et al. support GajAB complex assembly plus Gad1-mediated inhibition, but Gabija family members need separate review before TraitMech asserts one universal trigger, exact GajA:GajB stoichiometry, host death program, DNA substrate, or anti-Gabija phage inhibitor.",
        "posed_by": "codex",
        "posed_date": "2026-09-15"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-15T12:36:55Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Gabija system as a DOI-backed GENOMICS TraitRecord under the phage defense system parent after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v92.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000334",
    "label": "ApeA system",
    "definition": "A phage defense system in which an organism possesses a single-component ApeA locus represented by the DefenseFinder Gao_Ape__ApeA profile, encoding an oligomeric HEPN-domain antiviral ribonuclease whose activation can cleave RNA substrates to restrict bacteriophage infection.",
    "definition_source": "DOI:10.64898/2026.01.26.701840",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "ApeA",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.64898/2026.01.26.701840"
      },
      {
        "synonym_text": "Gao_Ape",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.64898/2026.01.26.701840",
        "snippet": "Here, we focus on ApeA, a HEPN-domain antiviral protein that confers immunity through cleavage of host tRNAs within their anticodon loops.",
        "notes": "Juozapaitis et al. describe ApeA as a HEPN-domain antiviral protein that cleaves host tRNAs within their anticodon loops."
      },
      {
        "reference": "DOI:10.64898/2026.01.26.701840",
        "snippet": "Both ApeA homologs confer protection at low MOI but not at high MOI, when most cells are infected",
        "notes": "Juozapaitis et al. show that Ec1ApeA and Ec2ApeA protect at low multiplicity of infection but not high multiplicity, supporting abortive-infection behavior."
      },
      {
        "reference": "DOI:10.64898/2026.01.26.701840",
        "snippet": "activity of Ec1ApeA and Ec2ApeA proteins was abrogated by HEPN active site R521A and R502A mutations respectively",
        "notes": "HEPN active-site mutations abrogated antiviral activity in the tested Ec1ApeA and Ec2ApeA proteins."
      },
      {
        "reference": "DOI:10.64898/2026.01.26.701840",
        "snippet": "Together, these results demonstrate that Ec1ApeA exhibits endoribonuclease activity targeting the tRNA anticodon loop, which is specifically activated during bacteriophage infection.",
        "notes": "Ec1ApeA exhibits infection-activated endoribonuclease activity targeting the tRNA anticodon loop."
      },
      {
        "reference": "DOI:10.64898/2026.01.26.701840",
        "snippet": "In vitro ribonuclease assays showed that under our experimental conditions tRNA cleavage by wild-type Ec2ApeA was activated by dpCG",
        "notes": "Ec2ApeA tRNA cleavage can be activated by deoxydinucleotides in vitro, supporting ligand-stimulated ApeA RNase activity for one ApeA variant."
      },
      {
        "reference": "DOI:10.64898/2026.03.20.713152",
        "snippet": "We show that two ApeA homologs, Ec1ApeA and Ps2ApeA, protect against a variety of single-stranded RNA phages.",
        "notes": "Drobysheva et al. show that Ec1ApeA and Ps2ApeA protect against single-stranded RNA phages."
      },
      {
        "reference": "DOI:10.64898/2026.03.20.713152",
        "snippet": "results show that ApeA stops RNA phage replication by directly cleaving the phage genome.",
        "notes": "Drobysheva et al. support direct phage-genome cleavage as an ApeA RNA-phage defense output."
      },
      {
        "reference": "DOI:10.64898/2026.03.20.713152",
        "snippet": "In the case of infection with RNA phages, we did not see evidence for induced cell death by Ec1ApeA",
        "notes": "Drobysheva et al. distinguish Ec1ApeA RNA-phage defense from cell-death abortive infection."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "Gao_Ape | 10\\.1126/science\\.aba0372 | Diverse enzymatic activities mediate antiviral immunity in prokaryotes",
        "notes": "The DefenseFinder article registry maps the named Gao_Ape system to the Gao et al. prokaryotic antiviral-immunity paper."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "Gao_Ape\tGao_Ape\t1\t1\tGao_Ape__ApeA\t\t\t",
        "notes": "The DefenseFinder rules table models Gao_Ape as a single-mandatory-profile system with the Gao_Ape__ApeA profile."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| Gao_Ape__ApeA                                    | Gao_Ape__ApeA                                    | Gao_Ape                | Custom                  | 18     |",
        "notes": "The DefenseFinder HMM inventory records ApeA under the Gao_Ape model namespace."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "gao_ape_hepn_rnase_restricts_phage",
        "title": "ApeA loci activate HEPN RNase antiphage outputs",
        "description": "Conservative system-level sketch linking a Gao_Ape/ApeA locus to HEPN RNase activation, host tRNA anticodon-loop cleavage during DNA-phage abortive infection, phage genomic RNA cleavage during non-abortive RNA-phage defense, and the ApeA system trait.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures ApeA as a named DefenseFinder single-component system with alternate HEPN RNase outputs while leaving natural-host accession breadth, homolog- and phage-class-specific trigger differences, direct RNA-loop sensing by Ec1ApeA, the exact DNA-phage nuclease inputs to Ec2ApeA deoxydinucleotide signaling, and activity of additional homologs unresolved.",
        "nodes": [
          {
            "node_id": "gao_ape_locus",
            "label": "Gao_Ape locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A single-component ApeA antiphage locus represented by the DefenseFinder Gao_Ape__ApeA profile."
          },
          {
            "node_id": "apea_hepn_rnase_activity",
            "label": "ApeA HEPN RNase activity",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "Triggered ApeA ribonuclease activity dependent on HEPN active-site residues."
          },
          {
            "node_id": "trna_anticodon_loop_cleavage",
            "label": "tRNA anticodon-loop cleavage",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Cleavage of host tRNAs within their anticodon loops by activated ApeA HEPN RNase."
          },
          {
            "node_id": "abortive_phage_restriction",
            "label": "abortive phage restriction",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Abortive-infection defense in which ApeA-mediated translation arrest restricts bacteriophage propagation."
          },
          {
            "node_id": "phage_genomic_rna_cleavage",
            "label": "phage genomic RNA cleavage",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Direct ApeA-dependent cleavage of an RNA-phage genome by activated HEPN RNase."
          },
          {
            "node_id": "non_abortive_rna_phage_restriction",
            "label": "non-abortive RNA-phage restriction",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Restriction of single-stranded RNA-phage replication without inducing ApeA-dependent host-cell death."
          },
          {
            "node_id": "apea_system_trait",
            "label": "ApeA system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000334",
            "description": "Possession of a genome-encoded ApeA phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "gao_ape_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "apea_hepn_rnase_activity",
            "description": "ApeA loci encode a HEPN-domain antiviral RNase, and DefenseFinder models Gao_Ape as a single-profile ApeA system.",
            "evidence": [
              {
                "reference": "DOI:10.64898/2026.01.26.701840",
                "snippet": "Here, we focus on ApeA, a HEPN-domain antiviral protein that confers immunity through cleavage of host tRNAs within their anticodon loops.",
                "notes": "Juozapaitis et al. connect ApeA to HEPN-domain antiviral RNase activity."
              },
              {
                "reference": "DOI:10.64898/2026.01.26.701840",
                "snippet": "activity of Ec1ApeA and Ec2ApeA proteins was abrogated by HEPN active site R521A and R502A mutations respectively",
                "notes": "HEPN active-site mutations eliminated activity in Ec1ApeA and Ec2ApeA."
              },
              {
                "reference": "DOI:10.64898/2026.03.20.713152",
                "snippet": "We show that two ApeA homologs, Ec1ApeA and Ps2ApeA, protect against a variety of single-stranded RNA phages.",
                "notes": "Drobysheva et al. support HEPN-dependent Ec1ApeA and Ps2ApeA RNA-phage defense."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "Gao_Ape\tGao_Ape\t1\t1\tGao_Ape__ApeA\t\t\t",
                "notes": "The DefenseFinder rules table models Gao_Ape as a single-mandatory-profile system with the Gao_Ape__ApeA profile."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| Gao_Ape__ApeA                                    | Gao_Ape__ApeA                                    | Gao_Ape                | Custom                  | 18     |",
                "notes": "The DefenseFinder HMM inventory records ApeA under the Gao_Ape model namespace."
              }
            ]
          },
          {
            "subject": "apea_hepn_rnase_activity",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "trna_anticodon_loop_cleavage",
            "description": "Activated ApeA HEPN RNase cleaves host tRNAs within their anticodon loops.",
            "evidence": [
              {
                "reference": "DOI:10.64898/2026.01.26.701840",
                "snippet": "Together, these results demonstrate that Ec1ApeA exhibits endoribonuclease activity targeting the tRNA anticodon loop, which is specifically activated during bacteriophage infection.",
                "notes": "Ec1ApeA endoribonuclease activity targets the tRNA anticodon loop during phage infection."
              },
              {
                "reference": "DOI:10.64898/2026.01.26.701840",
                "snippet": "In vitro ribonuclease assays showed that under our experimental conditions tRNA cleavage by wild-type Ec2ApeA was activated by dpCG",
                "notes": "Ec2ApeA tRNA-cleavage activity can be reconstituted in vitro with deoxydinucleotide ligands."
              }
            ]
          },
          {
            "subject": "trna_anticodon_loop_cleavage",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "abortive_phage_restriction",
            "description": "ApeA-mediated host tRNA cleavage arrests translation during abortive phage defense.",
            "evidence": [
              {
                "reference": "DOI:10.64898/2026.01.26.701840",
                "snippet": "We further demonstrate that ApeA functions as an abortive infection system by cleaving host tRNAs within their anticodon loops to arrest translation",
                "notes": "Juozapaitis et al. link ApeA tRNA anticodon-loop cleavage to translation arrest during abortive infection."
              }
            ]
          },
          {
            "subject": "abortive_phage_restriction",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "apea_system_trait",
            "description": "ApeA low-MOI protection and abortive infection realize the ApeA system possession trait.",
            "evidence": [
              {
                "reference": "DOI:10.64898/2026.01.26.701840",
                "snippet": "Both ApeA homologs confer protection at low MOI but not at high MOI, when most cells are infected",
                "notes": "Ec1ApeA and Ec2ApeA low-MOI protection supports ApeA as an abortive infection system."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Gao_Ape | 10\\.1126/science\\.aba0372 | Diverse enzymatic activities mediate antiviral immunity in prokaryotes",
                "notes": "The DefenseFinder article registry maps the named Gao_Ape system to the Gao et al. prokaryotic antiviral-immunity paper."
              }
            ]
          },
          {
            "subject": "apea_hepn_rnase_activity",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "phage_genomic_rna_cleavage",
            "description": "Ec1ApeA HEPN RNase activity cleaves infecting RNA-phage genomes.",
            "evidence": [
              {
                "reference": "DOI:10.64898/2026.03.20.713152",
                "snippet": "results show that ApeA stops RNA phage replication by directly cleaving the phage genome.",
                "notes": "Drobysheva et al. show that ApeA can stop RNA-phage replication by direct phage-genome cleavage."
              }
            ]
          },
          {
            "subject": "phage_genomic_rna_cleavage",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "non_abortive_rna_phage_restriction",
            "description": "ApeA-dependent cleavage of the phage genome restricts RNA-phage replication without host-cell death.",
            "evidence": [
              {
                "reference": "DOI:10.64898/2026.03.20.713152",
                "snippet": "results show that ApeA stops RNA phage replication by directly cleaving the phage genome.",
                "notes": "Direct phage-genome cleavage is the main ApeA output in the assayed RNA-phage infection model."
              },
              {
                "reference": "DOI:10.64898/2026.03.20.713152",
                "snippet": "In the case of infection with RNA phages, we did not see evidence for induced cell death by Ec1ApeA",
                "notes": "Drobysheva et al. found no evidence for Ec1ApeA-induced cell death during RNA-phage infection."
              }
            ]
          },
          {
            "subject": "non_abortive_rna_phage_restriction",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "apea_system_trait",
            "description": "Non-abortive RNA-phage restriction realizes one ApeA system defense output.",
            "evidence": [
              {
                "reference": "DOI:10.64898/2026.03.20.713152",
                "snippet": "We show that two ApeA homologs, Ec1ApeA and Ps2ApeA, protect against a variety of single-stranded RNA phages.",
                "notes": "Drobysheva et al. show that ApeA homologs can protect against single-stranded RNA phages."
              }
            ]
          },
          {
            "subject": "apea_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "ApeA system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Gao_Ape | 10\\.1126/science\\.aba0372 | Diverse enzymatic activities mediate antiviral immunity in prokaryotes",
                "notes": "The DefenseFinder article registry maps the named Gao_Ape system to the Gao et al. prokaryotic antiviral-immunity paper."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "apea-trigger-and-homolog-scope-gap",
        "prompt": "Resolve ApeA natural-host loci, homolog-specific DNA-phage versus RNA-phage triggers, phage nuclease inputs, phage genomic RNA targets, abortive versus non-abortive outputs, and subtype activity before minting narrower ApeA mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Juozapaitis et al. support DNA-phage ApeA abortive infection through host tRNA anticodon-loop cleavage, Drobysheva et al. support non-abortive RNA-phage defense through phage-genomic-RNA cleavage, and DefenseFinder models Gao_Ape with the Gao_Ape__ApeA profile. This first record stays at system level because the curated evidence leaves homolog- and phage-class-specific trigger logic, the full DNA-versus-RNA substrate split, activity of additional homologs, and accession-level natural-host breadth unresolved.",
        "attaches_to": [
          "causal_graphs#gao_ape_hepn_rnase_restricts_phage"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-21"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-21T11:03:58Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted ApeA system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v211.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-21T11:04:58Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed the ApeA canonical_examples gap and left canonical_examples empty: the current evidence supports a named single-component phage-defense system, DefenseFinder Gao_Ape/ApeA profiles, and heterologously assayed ApeA homologs, but does not yet cite a directly observed natural microbial taxon with a source-backed Gao_Ape/ApeA locus. No paid research was used.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-21T11:20:58Z",
        "curator": "codex",
        "action": "ADDRESS_PR_REVIEW",
        "changes": "Broadened the ApeA root definition, graph, evidence, and discussion after the PR 1190 adversarial review filed issue 1191, adding the March 2026 RNA-phage ApeA preprint and separating Juozapaitis host-tRNA abortive infection from Drobysheva phage-genomic-RNA non-abortive restriction.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000361",
    "label": "Gao-Her-DUF system",
    "definition": "A phage defense system in which an organism possesses a Gao_Her_DUF locus represented by DefenseFinder as a two-profile model requiring Gao_Her_DUF__DUF4297 and Gao_Her_DUF__HerA_DUF.",
    "definition_source": "DOI:10.1126/science.aba0372",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000409"
    ],
    "synonyms": [
      {
        "synonym_text": "Gao_Her_DUF",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv"
      },
      {
        "synonym_text": "Gao_Her_DUF__DUF4297",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "Gao_Her_DUF__HerA_DUF",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "PMID:32855333",
        "snippet": "By systematic defense gene prediction and heterologous reconstitution, here we discover 29 widespread antiviral gene cassettes, collectively present in 32% of all sequenced bacterial and archaeal genomes, that mediate protection against specific bacteriophages.",
        "notes": "Gao et al. support a systematic defense-gene prediction and heterologous reconstitution campaign that discovered widespread antiviral gene cassettes."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "Gao_Her | 10\\.1126/science\\.aba0372 | Diverse enzymatic activities mediate antiviral immunity in prokaryotes",
        "notes": "The DefenseFinder article registry maps the broader Gao_Her family key to the Gao et al. prokaryotic antiviral-immunity paper."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "Gao_Her\tGao_Her_DUF\t2\t2\tGao_Her_DUF__DUF4297, Gao_Her_DUF__HerA_DUF",
        "notes": "The DefenseFinder rules table models Gao_Her_DUF as a two-profile system requiring Gao_Her_DUF__DUF4297 and Gao_Her_DUF__HerA_DUF."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| Gao_Her_DUF__DUF4297                             | Gao_Her_DUF__DUF4297                             | Gao_Her_DUF            | Custom                  | 20     |",
        "notes": "The DefenseFinder HMM inventory records Gao_Her_DUF__DUF4297 under Gao_Her_DUF."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| Gao_Her_DUF__HerA_DUF                            | Gao_Her_DUF__HerA_DUF                            | Gao_Her_DUF            | Custom                  | 20     |",
        "notes": "The DefenseFinder HMM inventory records Gao_Her_DUF__HerA_DUF under Gao_Her_DUF."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "gao_her_duf_locus_restricts_phage",
        "title": "Gao-Her-DUF loci confer bacterial phage defense",
        "description": "Conservative system-level sketch linking possession of a Gao_Her_DUF locus to Gao et al. antiviral cassette defense without asserting the unresolved Her-DUF component activities.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Gao-Her-DUF as a named DefenseFinder two-profile Gao-family system while leaving natural hosts, DUF4297/HerA_DUF protein functions, phage triggers, and direct effector activity unresolved.",
        "nodes": [
          {
            "node_id": "gao_her_duf_locus",
            "label": "Gao_Her_DUF locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A DefenseFinder Gao_Her_DUF phage-defense locus represented by custom DUF4297 and HerA_DUF profiles."
          },
          {
            "node_id": "gao_2020_antiviral_cassette_defense",
            "label": "Gao 2020 antiviral cassette defense",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Bacteriophage protection by one of the antiviral gene cassettes described in the Gao et al. systematic defense-gene discovery campaign."
          },
          {
            "node_id": "gao_her_duf_system_trait",
            "label": "Gao-Her-DUF system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000361",
            "description": "Possession of a genome-encoded Gao-Her-DUF phage-defense system."
          },
          {
            "node_id": "gao_her_system",
            "label": "Gao-Her system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000409",
            "description": "Possession of a genome-encoded Gao-Her phage-defense system."
          }
        ],
        "edges": [
          {
            "subject": "gao_her_duf_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "gao_2020_antiviral_cassette_defense",
            "description": "DefenseFinder maps the broader Gao_Her family key to the Gao et al. systematic antiphage-system discovery paper and models Gao_Her_DUF as a two-profile system requiring DUF4297 and HerA_DUF.",
            "evidence": [
              {
                "reference": "PMID:32855333",
                "snippet": "By systematic defense gene prediction and heterologous reconstitution, here we discover 29 widespread antiviral gene cassettes, collectively present in 32% of all sequenced bacterial and archaeal genomes, that mediate protection against specific bacteriophages.",
                "notes": "Gao et al. support bacteriophage protection by widespread antiviral gene cassettes."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Gao_Her | 10\\.1126/science\\.aba0372 | Diverse enzymatic activities mediate antiviral immunity in prokaryotes",
                "notes": "The DefenseFinder article registry maps the broader Gao_Her family key to the Gao et al. prokaryotic antiviral-immunity paper."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "Gao_Her\tGao_Her_DUF\t2\t2\tGao_Her_DUF__DUF4297, Gao_Her_DUF__HerA_DUF",
                "notes": "The DefenseFinder rules table models Gao_Her_DUF as a two-profile system requiring Gao_Her_DUF__DUF4297 and Gao_Her_DUF__HerA_DUF."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| Gao_Her_DUF__DUF4297                             | Gao_Her_DUF__DUF4297                             | Gao_Her_DUF            | Custom                  | 20     |",
                "notes": "The DefenseFinder HMM inventory records Gao_Her_DUF__DUF4297 under Gao_Her_DUF."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| Gao_Her_DUF__HerA_DUF                            | Gao_Her_DUF__HerA_DUF                            | Gao_Her_DUF            | Custom                  | 20     |",
                "notes": "The DefenseFinder HMM inventory records Gao_Her_DUF__HerA_DUF under Gao_Her_DUF."
              }
            ]
          },
          {
            "subject": "gao_2020_antiviral_cassette_defense",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "gao_her_duf_system_trait",
            "description": "Gao_Her_DUF-associated antiviral cassette defense realizes the Gao-Her-DUF system trait.",
            "evidence": [
              {
                "reference": "PMID:32855333",
                "snippet": "By systematic defense gene prediction and heterologous reconstitution, here we discover 29 widespread antiviral gene cassettes, collectively present in 32% of all sequenced bacterial and archaeal genomes, that mediate protection against specific bacteriophages.",
                "notes": "Gao et al. support bacteriophage protection by widespread antiviral gene cassettes."
              }
            ]
          },
          {
            "subject": "gao_her_duf_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "gao_her_system",
            "description": "Gao-Her-DUF system possession is a Gao-Her family phage-defense-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "Gao_Her\tGao_Her_DUF\t2\t2\tGao_Her_DUF__DUF4297, Gao_Her_DUF__HerA_DUF",
                "notes": "The DefenseFinder rules table models Gao_Her_DUF as a two-profile Gao_Her subsystem requiring Gao_Her_DUF__DUF4297 and Gao_Her_DUF__HerA_DUF."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "gao-her-duf-mechanism-gap",
        "prompt": "Resolve Gao_Her_DUF natural hosts, DUF4297/HerA_DUF component functions, phage triggers, and effector activity before minting narrower Gao_Her_DUF mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Gao et al. support widespread antiviral gene cassettes that mediate protection against specific bacteriophages, and DefenseFinder models Gao_Her_DUF as a two-profile system under the Gao_Her family key. The exact natural host breadth, DUF4297/HerA_DUF component identities, phage trigger, and profile-to-activity mapping remain unresolved.",
        "attaches_to": [
          "causal_graphs#gao_her_duf_locus_restricts_phage"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-22"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-22T09:33:34Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Gao-Her-DUF system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v238.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-27T13:51:19Z",
        "curator": "codex",
        "action": "EDIT",
        "changes": "Reparented the record under traitmech:000409 Gao-Her system and added a Gao-Her parent node plus subclass edge to the causal graph.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-27T13:56:56Z",
        "curator": "codex",
        "action": "EDIT",
        "changes": "Removed the redundant Gao-Her-to-phage subclass edge from the child graph; the Gao-Her parent record now carries that edge.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000362",
    "label": "Gao-Her-SIR system",
    "definition": "A phage defense system in which an organism possesses a Gao_Her_SIR locus represented by DefenseFinder as a two-profile model requiring Gao_Her_SIR__HerA_SIR2 and Gao_Her_SIR__SIR2.",
    "definition_source": "DOI:10.1126/science.aba0372",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000409"
    ],
    "synonyms": [
      {
        "synonym_text": "Gao_Her_SIR",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv"
      },
      {
        "synonym_text": "Gao_Her_SIR__HerA_SIR2",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "Gao_Her_SIR__SIR2",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "PMID:32855333",
        "snippet": "By systematic defense gene prediction and heterologous reconstitution, here we discover 29 widespread antiviral gene cassettes, collectively present in 32% of all sequenced bacterial and archaeal genomes, that mediate protection against specific bacteriophages.",
        "notes": "Gao et al. support a systematic defense-gene prediction and heterologous reconstitution campaign that discovered widespread antiviral gene cassettes."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "Gao_Her | 10\\.1126/science\\.aba0372 | Diverse enzymatic activities mediate antiviral immunity in prokaryotes",
        "notes": "The DefenseFinder article registry maps the broader Gao_Her family key to the Gao et al. prokaryotic antiviral-immunity paper."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "Gao_Her\tGao_Her_SIR\t2\t2\tGao_Her_SIR__HerA_SIR2, Gao_Her_SIR__SIR2",
        "notes": "The DefenseFinder rules table models Gao_Her_SIR as a two-profile system requiring Gao_Her_SIR__HerA_SIR2 and Gao_Her_SIR__SIR2."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| Gao_Her_SIR__HerA_SIR2                           | Gao_Her_SIR__HerA_SIR2                           | Gao_Her_SIR            | Custom                  | 43     |",
        "notes": "The DefenseFinder HMM inventory records Gao_Her_SIR__HerA_SIR2 under Gao_Her_SIR."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| Gao_Her_SIR__SIR2                                | Gao_Her_SIR__SIR2                                | Gao_Her_SIR            | Custom                  | 34     |",
        "notes": "The DefenseFinder HMM inventory records Gao_Her_SIR__SIR2 under Gao_Her_SIR."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "gao_her_sir_locus_restricts_phage",
        "title": "Gao-Her-SIR loci confer bacterial phage defense",
        "description": "Conservative system-level sketch linking possession of a Gao_Her_SIR locus to Gao et al. antiviral cassette defense without asserting the unresolved Her-SIR component activities.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Gao-Her-SIR as a named DefenseFinder two-profile Gao-family system while leaving natural hosts, HerA_SIR2/SIR2 protein functions, phage triggers, and direct effector activity unresolved.",
        "nodes": [
          {
            "node_id": "gao_her_sir_locus",
            "label": "Gao_Her_SIR locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A DefenseFinder Gao_Her_SIR phage-defense locus represented by custom HerA_SIR2 and SIR2 profiles."
          },
          {
            "node_id": "gao_2020_antiviral_cassette_defense",
            "label": "Gao 2020 antiviral cassette defense",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Bacteriophage protection by one of the antiviral gene cassettes described in the Gao et al. systematic defense-gene discovery campaign."
          },
          {
            "node_id": "gao_her_sir_system_trait",
            "label": "Gao-Her-SIR system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000362",
            "description": "Possession of a genome-encoded Gao-Her-SIR phage-defense system."
          },
          {
            "node_id": "gao_her_system",
            "label": "Gao-Her system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000409",
            "description": "Possession of a genome-encoded Gao-Her phage-defense system."
          }
        ],
        "edges": [
          {
            "subject": "gao_her_sir_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "gao_2020_antiviral_cassette_defense",
            "description": "DefenseFinder maps the broader Gao_Her family key to the Gao et al. systematic antiphage-system discovery paper and models Gao_Her_SIR as a two-profile system requiring HerA_SIR2 and SIR2.",
            "evidence": [
              {
                "reference": "PMID:32855333",
                "snippet": "By systematic defense gene prediction and heterologous reconstitution, here we discover 29 widespread antiviral gene cassettes, collectively present in 32% of all sequenced bacterial and archaeal genomes, that mediate protection against specific bacteriophages.",
                "notes": "Gao et al. support bacteriophage protection by widespread antiviral gene cassettes."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Gao_Her | 10\\.1126/science\\.aba0372 | Diverse enzymatic activities mediate antiviral immunity in prokaryotes",
                "notes": "The DefenseFinder article registry maps the broader Gao_Her family key to the Gao et al. prokaryotic antiviral-immunity paper."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "Gao_Her\tGao_Her_SIR\t2\t2\tGao_Her_SIR__HerA_SIR2, Gao_Her_SIR__SIR2",
                "notes": "The DefenseFinder rules table models Gao_Her_SIR as a two-profile system requiring Gao_Her_SIR__HerA_SIR2 and Gao_Her_SIR__SIR2."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| Gao_Her_SIR__HerA_SIR2                           | Gao_Her_SIR__HerA_SIR2                           | Gao_Her_SIR            | Custom                  | 43     |",
                "notes": "The DefenseFinder HMM inventory records Gao_Her_SIR__HerA_SIR2 under Gao_Her_SIR."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| Gao_Her_SIR__SIR2                                | Gao_Her_SIR__SIR2                                | Gao_Her_SIR            | Custom                  | 34     |",
                "notes": "The DefenseFinder HMM inventory records Gao_Her_SIR__SIR2 under Gao_Her_SIR."
              }
            ]
          },
          {
            "subject": "gao_2020_antiviral_cassette_defense",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "gao_her_sir_system_trait",
            "description": "Gao_Her_SIR-associated antiviral cassette defense realizes the Gao-Her-SIR system trait.",
            "evidence": [
              {
                "reference": "PMID:32855333",
                "snippet": "By systematic defense gene prediction and heterologous reconstitution, here we discover 29 widespread antiviral gene cassettes, collectively present in 32% of all sequenced bacterial and archaeal genomes, that mediate protection against specific bacteriophages.",
                "notes": "Gao et al. support bacteriophage protection by widespread antiviral gene cassettes."
              }
            ]
          },
          {
            "subject": "gao_her_sir_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "gao_her_system",
            "description": "Gao-Her-SIR system possession is a Gao-Her family phage-defense-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "Gao_Her\tGao_Her_SIR\t2\t2\tGao_Her_SIR__HerA_SIR2, Gao_Her_SIR__SIR2",
                "notes": "The DefenseFinder rules table models Gao_Her_SIR as a two-profile Gao_Her subsystem requiring Gao_Her_SIR__HerA_SIR2 and Gao_Her_SIR__SIR2."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "gao-her-sir-mechanism-gap",
        "prompt": "Resolve Gao_Her_SIR natural hosts, HerA_SIR2/SIR2 component functions, phage triggers, and effector activity before minting narrower Gao_Her_SIR mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Gao et al. support widespread antiviral gene cassettes that mediate protection against specific bacteriophages, and DefenseFinder models Gao_Her_SIR as a two-profile system under the Gao_Her family key. The exact natural host breadth, HerA_SIR2/SIR2 component identities, phage trigger, and profile-to-activity mapping remain unresolved.",
        "attaches_to": [
          "causal_graphs#gao_her_sir_locus_restricts_phage"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-22"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-22T10:04:44Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Gao-Her-SIR system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v239.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-27T13:51:19Z",
        "curator": "codex",
        "action": "EDIT",
        "changes": "Reparented the record under traitmech:000409 Gao-Her system and added a Gao-Her parent node plus subclass edge to the causal graph.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-27T13:56:56Z",
        "curator": "codex",
        "action": "EDIT",
        "changes": "Removed the redundant Gao-Her-to-phage subclass edge from the child graph; the Gao-Her parent record now carries that edge.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000409",
    "label": "Gao-Her system",
    "definition": "A phage defense system in which an organism possesses a Gao_Her locus represented by DefenseFinder as either a Gao_Her_DUF or Gao_Her_SIR two-profile subsystem.",
    "definition_source": "DOI:10.1126/science.aba0372",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "Gao_Her",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      }
    ],
    "evidence": [
      {
        "reference": "PMID:32855333",
        "snippet": "By systematic defense gene prediction and heterologous reconstitution, here we discover 29 widespread antiviral gene cassettes, collectively present in 32% of all sequenced bacterial and archaeal genomes, that mediate protection against specific bacteriophages.",
        "notes": "Gao et al. support a systematic defense-gene prediction and heterologous reconstitution campaign that discovered widespread antiviral gene cassettes."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "Gao_Her | 10\\.1126/science\\.aba0372 | Diverse enzymatic activities mediate antiviral immunity in prokaryotes",
        "notes": "The DefenseFinder article registry maps Gao_Her to the Gao et al. prokaryotic antiviral-immunity paper."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "Gao_Her\tGao_Her_DUF\t2\t2\tGao_Her_DUF__DUF4297, Gao_Her_DUF__HerA_DUF",
        "notes": "The DefenseFinder rules table models Gao_Her_DUF as a two-profile Gao_Her subsystem requiring Gao_Her_DUF__DUF4297 and Gao_Her_DUF__HerA_DUF."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "Gao_Her\tGao_Her_SIR\t2\t2\tGao_Her_SIR__HerA_SIR2, Gao_Her_SIR__SIR2",
        "notes": "The DefenseFinder rules table models Gao_Her_SIR as a two-profile Gao_Her subsystem requiring Gao_Her_SIR__HerA_SIR2 and Gao_Her_SIR__SIR2."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "gao_her_locus_restricts_phage",
        "title": "Gao-Her loci confer bacterial phage defense",
        "description": "Conservative family-level sketch linking Gao_Her loci to Gao et al. antiviral cassette defense without asserting the unresolved Her-DUF or Her-SIR component activities.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Gao-Her as the DefenseFinder Gao_Her family containing Gao_Her_DUF and Gao_Her_SIR subsystems while leaving natural hosts, subtype-specific phage triggers, and DUF4297, HerA_DUF, HerA_SIR2, and SIR2 molecular functions unresolved.",
        "nodes": [
          {
            "node_id": "gao_her_locus",
            "label": "Gao_Her locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A DefenseFinder Gao_Her phage-defense locus represented as a Gao_Her_DUF or Gao_Her_SIR two-profile subsystem."
          },
          {
            "node_id": "gao_2020_antiviral_cassette_defense",
            "label": "Gao 2020 antiviral cassette defense",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Bacteriophage protection by one of the antiviral gene cassettes described in the Gao et al. systematic defense-gene discovery campaign."
          },
          {
            "node_id": "gao_her_system_trait",
            "label": "Gao-Her system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000409",
            "description": "Possession of a genome-encoded Gao-Her phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "gao_her_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "gao_2020_antiviral_cassette_defense",
            "description": "DefenseFinder maps Gao_Her to the Gao et al. systematic antiphage-system discovery paper and models two Gao_Her subsystems, Gao_Her_DUF and Gao_Her_SIR.",
            "evidence": [
              {
                "reference": "PMID:32855333",
                "snippet": "By systematic defense gene prediction and heterologous reconstitution, here we discover 29 widespread antiviral gene cassettes, collectively present in 32% of all sequenced bacterial and archaeal genomes, that mediate protection against specific bacteriophages.",
                "notes": "Gao et al. support a systematic defense-gene prediction and heterologous reconstitution campaign that discovered widespread antiviral gene cassettes."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Gao_Her | 10\\.1126/science\\.aba0372 | Diverse enzymatic activities mediate antiviral immunity in prokaryotes",
                "notes": "The DefenseFinder article registry maps Gao_Her to the Gao et al. prokaryotic antiviral-immunity paper."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "Gao_Her\tGao_Her_DUF\t2\t2\tGao_Her_DUF__DUF4297, Gao_Her_DUF__HerA_DUF",
                "notes": "The DefenseFinder rules table models Gao_Her_DUF as a two-profile Gao_Her subsystem requiring Gao_Her_DUF__DUF4297 and Gao_Her_DUF__HerA_DUF."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "Gao_Her\tGao_Her_SIR\t2\t2\tGao_Her_SIR__HerA_SIR2, Gao_Her_SIR__SIR2",
                "notes": "The DefenseFinder rules table models Gao_Her_SIR as a two-profile Gao_Her subsystem requiring Gao_Her_SIR__HerA_SIR2 and Gao_Her_SIR__SIR2."
              }
            ]
          },
          {
            "subject": "gao_2020_antiviral_cassette_defense",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "gao_her_system_trait",
            "description": "Gao_Her-associated antiviral cassette defense realizes the Gao-Her system trait.",
            "evidence": [
              {
                "reference": "PMID:32855333",
                "snippet": "By systematic defense gene prediction and heterologous reconstitution, here we discover 29 widespread antiviral gene cassettes, collectively present in 32% of all sequenced bacterial and archaeal genomes, that mediate protection against specific bacteriophages.",
                "notes": "Gao et al. support a systematic defense-gene prediction and heterologous reconstitution campaign that discovered widespread antiviral gene cassettes."
              }
            ]
          },
          {
            "subject": "gao_her_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Gao-Her system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Gao_Her | 10\\.1126/science\\.aba0372 | Diverse enzymatic activities mediate antiviral immunity in prokaryotes",
                "notes": "The DefenseFinder article registry maps Gao_Her to the Gao et al. prokaryotic antiviral-immunity paper."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "Gao_Her\tGao_Her_DUF\t2\t2\tGao_Her_DUF__DUF4297, Gao_Her_DUF__HerA_DUF",
                "notes": "The DefenseFinder rules table models Gao_Her_DUF as a two-profile Gao_Her subsystem requiring Gao_Her_DUF__DUF4297 and Gao_Her_DUF__HerA_DUF."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "Gao_Her\tGao_Her_SIR\t2\t2\tGao_Her_SIR__HerA_SIR2, Gao_Her_SIR__SIR2",
                "notes": "The DefenseFinder rules table models Gao_Her_SIR as a two-profile Gao_Her subsystem requiring Gao_Her_SIR__HerA_SIR2 and Gao_Her_SIR__SIR2."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "gao-her-family-mechanism-gap",
        "prompt": "Resolve Gao_Her natural host breadth, subtype boundaries, phage triggers, and the effector outputs of Gao_Her_DUF and Gao_Her_SIR before minting narrower Gao-Her mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Gao et al. support bacteriophage protection by widespread antiviral gene cassettes, and DefenseFinder models Gao_Her_DUF and Gao_Her_SIR as two-profile subsystems under the Gao_Her family key. This first parent record captures the Gao_Her family while leaving subtype-specific triggers, natural host breadth, and direct effector activities unresolved.",
        "attaches_to": [
          "causal_graphs#gao_her_locus_restricts_phage"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-27"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-27T13:51:19Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Gao-Her system as a DOI- and DefenseFinder-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v286.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-27T13:56:56Z",
        "curator": "codex",
        "action": "EDIT",
        "changes": "Removed a repeated DefenseFinder article-row citation from the Gao-Her confers edge so no graph reuses the same snippet more than twice.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000353",
    "label": "Gao-Hhe system",
    "definition": "A phage defense system in which an organism possesses a Gao_Hhe locus represented by DefenseFinder as a single-profile model requiring Gao_Hhe__HheA.",
    "definition_source": "DOI:10.1126/science.aba0372",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "Gao_Hhe",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      },
      {
        "synonym_text": "Gao_Hhe__HheA",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "PMID:32855333",
        "snippet": "By systematic defense gene prediction and heterologous reconstitution, here we discover 29 widespread antiviral gene cassettes, collectively present in 32% of all sequenced bacterial and archaeal genomes, that mediate protection against specific bacteriophages.",
        "notes": "Gao et al. support a systematic defense-gene prediction and heterologous reconstitution campaign that discovered widespread antiviral gene cassettes."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "Gao_Hhe | 10\\.1126/science\\.aba0372 | Diverse enzymatic activities mediate antiviral immunity in prokaryotes",
        "notes": "The DefenseFinder article registry maps the named Gao_Hhe system to the Gao et al. prokaryotic antiviral-immunity paper."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "Gao_Hhe\tGao_Hhe\t1\t1\tGao_Hhe__HheA",
        "notes": "The DefenseFinder rules table models Gao_Hhe as a single-mandatory-profile system with the Gao_Hhe__HheA profile."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| Gao_Hhe__HheA                                    | Gao_Hhe__HheA                                    | Gao_Hhe                | Custom                  | 750    |",
        "notes": "The DefenseFinder HMM inventory records Gao_Hhe__HheA under Gao_Hhe."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "gao_hhe_locus_restricts_phage",
        "title": "Gao-Hhe loci confer bacterial phage defense",
        "description": "Conservative system-level sketch linking possession of a Gao_Hhe locus to Gao et al. antiviral cassette defense without asserting the unresolved HheA component activity.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Gao-Hhe as a named DefenseFinder single-profile Gao-family system while leaving natural hosts, HheA protein function, phage triggers, and direct effector activity unresolved.",
        "nodes": [
          {
            "node_id": "gao_hhe_locus",
            "label": "Gao_Hhe locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A DefenseFinder Gao_Hhe phage-defense locus represented by a custom HheA profile."
          },
          {
            "node_id": "gao_2020_antiviral_cassette_defense",
            "label": "Gao 2020 antiviral cassette defense",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Bacteriophage protection by one of the antiviral gene cassettes described in the Gao et al. systematic defense-gene discovery campaign."
          },
          {
            "node_id": "gao_hhe_system_trait",
            "label": "Gao-Hhe system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000353",
            "description": "Possession of a genome-encoded Gao-Hhe phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "gao_hhe_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "gao_2020_antiviral_cassette_defense",
            "description": "DefenseFinder maps Gao_Hhe to the Gao et al. systematic antiphage-system discovery paper and models it as a single-profile system requiring HheA.",
            "evidence": [
              {
                "reference": "PMID:32855333",
                "snippet": "By systematic defense gene prediction and heterologous reconstitution, here we discover 29 widespread antiviral gene cassettes, collectively present in 32% of all sequenced bacterial and archaeal genomes, that mediate protection against specific bacteriophages.",
                "notes": "Gao et al. support bacteriophage protection by widespread antiviral gene cassettes."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Gao_Hhe | 10\\.1126/science\\.aba0372 | Diverse enzymatic activities mediate antiviral immunity in prokaryotes",
                "notes": "The DefenseFinder article registry maps the named Gao_Hhe system to the Gao et al. prokaryotic antiviral-immunity paper."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "Gao_Hhe\tGao_Hhe\t1\t1\tGao_Hhe__HheA",
                "notes": "The DefenseFinder rules table models Gao_Hhe as a single-mandatory-profile system with the Gao_Hhe__HheA profile."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| Gao_Hhe__HheA                                    | Gao_Hhe__HheA                                    | Gao_Hhe                | Custom                  | 750    |",
                "notes": "The DefenseFinder HMM inventory records Gao_Hhe__HheA under Gao_Hhe."
              }
            ]
          },
          {
            "subject": "gao_2020_antiviral_cassette_defense",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "gao_hhe_system_trait",
            "description": "Gao_Hhe-associated antiviral cassette defense realizes the Gao-Hhe system trait.",
            "evidence": [
              {
                "reference": "PMID:32855333",
                "snippet": "By systematic defense gene prediction and heterologous reconstitution, here we discover 29 widespread antiviral gene cassettes, collectively present in 32% of all sequenced bacterial and archaeal genomes, that mediate protection against specific bacteriophages.",
                "notes": "Gao et al. support bacteriophage protection by widespread antiviral gene cassettes."
              }
            ]
          },
          {
            "subject": "gao_hhe_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Gao-Hhe system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Gao_Hhe | 10\\.1126/science\\.aba0372 | Diverse enzymatic activities mediate antiviral immunity in prokaryotes",
                "notes": "The DefenseFinder article registry maps the named Gao_Hhe system to the Gao et al. prokaryotic antiviral-immunity paper."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "Gao_Hhe\tGao_Hhe\t1\t1\tGao_Hhe__HheA",
                "notes": "The DefenseFinder rules table models Gao_Hhe as a single-mandatory-profile system with the Gao_Hhe__HheA profile."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "gao-hhe-mechanism-gap",
        "prompt": "Resolve Gao_Hhe natural hosts, HheA component function, phage triggers, and effector activity before minting narrower Gao_Hhe mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Gao et al. support widespread antiviral gene cassettes that mediate protection against specific bacteriophages, and DefenseFinder models Gao_Hhe as a single-profile system. The exact natural host breadth, HheA component identity, phage trigger, and profile-to-activity mapping remain unresolved.",
        "attaches_to": [
          "causal_graphs#gao_hhe_locus_restricts_phage"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-22"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-22T02:45:35Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Gao-Hhe system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v230.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000354",
    "label": "Gao-Iet system",
    "definition": "A phage defense system in which an organism possesses a Gao_Iet locus represented by DefenseFinder as a two-profile model requiring Gao_Iet__IetA and Gao_Iet__IetS.",
    "definition_source": "DOI:10.1126/science.aba0372",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "Gao_Iet",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      },
      {
        "synonym_text": "Gao_Iet__IetA",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "Gao_Iet__IetS",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "PMID:32855333",
        "snippet": "By systematic defense gene prediction and heterologous reconstitution, here we discover 29 widespread antiviral gene cassettes, collectively present in 32% of all sequenced bacterial and archaeal genomes, that mediate protection against specific bacteriophages.",
        "notes": "Gao et al. support a systematic defense-gene prediction and heterologous reconstitution campaign that discovered widespread antiviral gene cassettes."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "Gao_Iet | 10\\.1126/science\\.aba0372 | Diverse enzymatic activities mediate antiviral immunity in prokaryotes",
        "notes": "The DefenseFinder article registry maps the named Gao_Iet system to the Gao et al. prokaryotic antiviral-immunity paper."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "Gao_Iet\tGao_Iet\t2\t2\tGao_Iet__IetA, Gao_Iet__IetS",
        "notes": "The DefenseFinder rules table models Gao_Iet as a two-profile system requiring the Gao_Iet__IetA and Gao_Iet__IetS profiles."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| Gao_Iet__IetA                                    | Gao_Iet__IetA                                    | Gao_Iet                | Custom                  | 100    |",
        "notes": "The DefenseFinder HMM inventory records Gao_Iet__IetA under Gao_Iet."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| Gao_Iet__IetS                                    | Gao_Iet__IetS                                    | Gao_Iet                | Custom                  | 50     |",
        "notes": "The DefenseFinder HMM inventory records Gao_Iet__IetS under Gao_Iet."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "gao_iet_locus_restricts_phage",
        "title": "Gao-Iet loci confer bacterial phage defense",
        "description": "Conservative system-level sketch linking possession of a Gao_Iet locus to Gao et al. antiviral cassette defense without asserting the unresolved IetA or IetS component activities.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Gao-Iet as a named DefenseFinder two-profile Gao-family system while leaving natural hosts, IetA/IetS protein functions, phage triggers, and direct effector activity unresolved.",
        "nodes": [
          {
            "node_id": "gao_iet_locus",
            "label": "Gao_Iet locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A DefenseFinder Gao_Iet phage-defense locus represented by custom IetA and IetS profiles."
          },
          {
            "node_id": "gao_2020_antiviral_cassette_defense",
            "label": "Gao 2020 antiviral cassette defense",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Bacteriophage protection by one of the antiviral gene cassettes described in the Gao et al. systematic defense-gene discovery campaign."
          },
          {
            "node_id": "gao_iet_system_trait",
            "label": "Gao-Iet system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000354",
            "description": "Possession of a genome-encoded Gao-Iet phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "gao_iet_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "gao_2020_antiviral_cassette_defense",
            "description": "DefenseFinder maps Gao_Iet to the Gao et al. systematic antiphage-system discovery paper and models it as a two-profile system requiring IetA and IetS.",
            "evidence": [
              {
                "reference": "PMID:32855333",
                "snippet": "By systematic defense gene prediction and heterologous reconstitution, here we discover 29 widespread antiviral gene cassettes, collectively present in 32% of all sequenced bacterial and archaeal genomes, that mediate protection against specific bacteriophages.",
                "notes": "Gao et al. support bacteriophage protection by widespread antiviral gene cassettes."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Gao_Iet | 10\\.1126/science\\.aba0372 | Diverse enzymatic activities mediate antiviral immunity in prokaryotes",
                "notes": "The DefenseFinder article registry maps the named Gao_Iet system to the Gao et al. prokaryotic antiviral-immunity paper."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "Gao_Iet\tGao_Iet\t2\t2\tGao_Iet__IetA, Gao_Iet__IetS",
                "notes": "The DefenseFinder rules table models Gao_Iet as a two-profile system requiring the Gao_Iet__IetA and Gao_Iet__IetS profiles."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| Gao_Iet__IetA                                    | Gao_Iet__IetA                                    | Gao_Iet                | Custom                  | 100    |",
                "notes": "The DefenseFinder HMM inventory records Gao_Iet__IetA under Gao_Iet."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| Gao_Iet__IetS                                    | Gao_Iet__IetS                                    | Gao_Iet                | Custom                  | 50     |",
                "notes": "The DefenseFinder HMM inventory records Gao_Iet__IetS under Gao_Iet."
              }
            ]
          },
          {
            "subject": "gao_2020_antiviral_cassette_defense",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "gao_iet_system_trait",
            "description": "Gao_Iet-associated antiviral cassette defense realizes the Gao-Iet system trait.",
            "evidence": [
              {
                "reference": "PMID:32855333",
                "snippet": "By systematic defense gene prediction and heterologous reconstitution, here we discover 29 widespread antiviral gene cassettes, collectively present in 32% of all sequenced bacterial and archaeal genomes, that mediate protection against specific bacteriophages.",
                "notes": "Gao et al. support bacteriophage protection by widespread antiviral gene cassettes."
              }
            ]
          },
          {
            "subject": "gao_iet_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Gao-Iet system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Gao_Iet | 10\\.1126/science\\.aba0372 | Diverse enzymatic activities mediate antiviral immunity in prokaryotes",
                "notes": "The DefenseFinder article registry maps the named Gao_Iet system to the Gao et al. prokaryotic antiviral-immunity paper."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "Gao_Iet\tGao_Iet\t2\t2\tGao_Iet__IetA, Gao_Iet__IetS",
                "notes": "The DefenseFinder rules table models Gao_Iet as a two-profile system requiring the Gao_Iet__IetA and Gao_Iet__IetS profiles."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "gao-iet-mechanism-gap",
        "prompt": "Resolve Gao_Iet natural hosts, IetA/IetS component functions, phage triggers, and effector activity before minting narrower Gao_Iet mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Gao et al. support widespread antiviral gene cassettes that mediate protection against specific bacteriophages, and DefenseFinder models Gao_Iet as a two-profile system. The exact natural host breadth, Iet component identities, phage trigger, and profile-to-activity mapping remain unresolved.",
        "attaches_to": [
          "causal_graphs#gao_iet_locus_restricts_phage"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-22"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-22T03:34:26Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Gao-Iet system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v231.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000355",
    "label": "Gao-Mza system",
    "definition": "A phage defense system in which an organism possesses a Gao_Mza locus represented by DefenseFinder as a five-profile model requiring Gao_Mza__MzaA, Gao_Mza__MzaB, Gao_Mza__MzaC, Gao_Mza__MzaD, and Gao_Mza__MzaE.",
    "definition_source": "DOI:10.1126/science.aba0372",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "Gao_Mza",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      },
      {
        "synonym_text": "Gao_Mza__MzaA",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "Gao_Mza__MzaB",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "Gao_Mza__MzaC",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "Gao_Mza__MzaD",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "Gao_Mza__MzaE",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "PMID:32855333",
        "snippet": "By systematic defense gene prediction and heterologous reconstitution, here we discover 29 widespread antiviral gene cassettes, collectively present in 32% of all sequenced bacterial and archaeal genomes, that mediate protection against specific bacteriophages.",
        "notes": "Gao et al. support a systematic defense-gene prediction and heterologous reconstitution campaign that discovered widespread antiviral gene cassettes."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "Gao_Mza | 10\\.1126/science\\.aba0372 | Diverse enzymatic activities mediate antiviral immunity in prokaryotes",
        "notes": "The DefenseFinder article registry maps the named Gao_Mza system to the Gao et al. prokaryotic antiviral-immunity paper."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "Gao_Mza\tGao_Mza\t5\t5\tGao_Mza__MzaA, Gao_Mza__MzaB, Gao_Mza__MzaC, Gao_Mza__MzaD, Gao_Mza__MzaE",
        "notes": "The DefenseFinder rules table models Gao_Mza as a five-profile system requiring the Gao_Mza__MzaA through Gao_Mza__MzaE profiles."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| Gao_Mza__MzaA                                    | Gao_Mza__MzaA                                    | Gao_Mza                | Custom                  | 100    |",
        "notes": "The DefenseFinder HMM inventory records Gao_Mza__MzaA under Gao_Mza."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| Gao_Mza__MzaB                                    | Gao_Mza__MzaB                                    | Gao_Mza                | Custom                  | 400    |",
        "notes": "The DefenseFinder HMM inventory records Gao_Mza__MzaB under Gao_Mza."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| Gao_Mza__MzaC                                    | Gao_Mza__MzaC                                    | Gao_Mza                | Custom                  | 650    |",
        "notes": "The DefenseFinder HMM inventory records Gao_Mza__MzaC under Gao_Mza."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| Gao_Mza__MzaD                                    | Gao_Mza__MzaD                                    | Gao_Mza                | Custom                  | 100    |",
        "notes": "The DefenseFinder HMM inventory records Gao_Mza__MzaD under Gao_Mza."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| Gao_Mza__MzaE                                    | Gao_Mza__MzaE                                    | Gao_Mza                | Custom                  | 20     |",
        "notes": "The DefenseFinder HMM inventory records Gao_Mza__MzaE under Gao_Mza."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "gao_mza_locus_restricts_phage",
        "title": "Gao-Mza loci confer bacterial phage defense",
        "description": "Conservative system-level sketch linking possession of a Gao_Mza locus to Gao et al. antiviral cassette defense without asserting the unresolved MzaA, MzaB, MzaC, MzaD, or MzaE component activities.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Gao-Mza as a named DefenseFinder five-profile Gao-family system while leaving natural hosts, MzaA/MzaB/MzaC/MzaD/MzaE protein functions, phage triggers, and direct effector activity unresolved.",
        "nodes": [
          {
            "node_id": "gao_mza_locus",
            "label": "Gao_Mza locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A DefenseFinder Gao_Mza phage-defense locus represented by custom MzaA through MzaE profiles."
          },
          {
            "node_id": "gao_2020_antiviral_cassette_defense",
            "label": "Gao 2020 antiviral cassette defense",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Bacteriophage protection by one of the antiviral gene cassettes described in the Gao et al. systematic defense-gene discovery campaign."
          },
          {
            "node_id": "gao_mza_system_trait",
            "label": "Gao-Mza system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000355",
            "description": "Possession of a genome-encoded Gao-Mza phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "gao_mza_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "gao_2020_antiviral_cassette_defense",
            "description": "DefenseFinder maps Gao_Mza to the Gao et al. systematic antiphage-system discovery paper and models it as a five-profile system requiring MzaA through MzaE.",
            "evidence": [
              {
                "reference": "PMID:32855333",
                "snippet": "By systematic defense gene prediction and heterologous reconstitution, here we discover 29 widespread antiviral gene cassettes, collectively present in 32% of all sequenced bacterial and archaeal genomes, that mediate protection against specific bacteriophages.",
                "notes": "Gao et al. support bacteriophage protection by widespread antiviral gene cassettes."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Gao_Mza | 10\\.1126/science\\.aba0372 | Diverse enzymatic activities mediate antiviral immunity in prokaryotes",
                "notes": "The DefenseFinder article registry maps the named Gao_Mza system to the Gao et al. prokaryotic antiviral-immunity paper."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "Gao_Mza\tGao_Mza\t5\t5\tGao_Mza__MzaA, Gao_Mza__MzaB, Gao_Mza__MzaC, Gao_Mza__MzaD, Gao_Mza__MzaE",
                "notes": "The DefenseFinder rules table models Gao_Mza as a five-profile system requiring the Gao_Mza__MzaA through Gao_Mza__MzaE profiles."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| Gao_Mza__MzaA                                    | Gao_Mza__MzaA                                    | Gao_Mza                | Custom                  | 100    |",
                "notes": "The DefenseFinder HMM inventory records Gao_Mza__MzaA under Gao_Mza."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| Gao_Mza__MzaB                                    | Gao_Mza__MzaB                                    | Gao_Mza                | Custom                  | 400    |",
                "notes": "The DefenseFinder HMM inventory records Gao_Mza__MzaB under Gao_Mza."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| Gao_Mza__MzaC                                    | Gao_Mza__MzaC                                    | Gao_Mza                | Custom                  | 650    |",
                "notes": "The DefenseFinder HMM inventory records Gao_Mza__MzaC under Gao_Mza."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| Gao_Mza__MzaD                                    | Gao_Mza__MzaD                                    | Gao_Mza                | Custom                  | 100    |",
                "notes": "The DefenseFinder HMM inventory records Gao_Mza__MzaD under Gao_Mza."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| Gao_Mza__MzaE                                    | Gao_Mza__MzaE                                    | Gao_Mza                | Custom                  | 20     |",
                "notes": "The DefenseFinder HMM inventory records Gao_Mza__MzaE under Gao_Mza."
              }
            ]
          },
          {
            "subject": "gao_2020_antiviral_cassette_defense",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "gao_mza_system_trait",
            "description": "Gao_Mza-associated antiviral cassette defense realizes the Gao-Mza system trait.",
            "evidence": [
              {
                "reference": "PMID:32855333",
                "snippet": "By systematic defense gene prediction and heterologous reconstitution, here we discover 29 widespread antiviral gene cassettes, collectively present in 32% of all sequenced bacterial and archaeal genomes, that mediate protection against specific bacteriophages.",
                "notes": "Gao et al. support bacteriophage protection by widespread antiviral gene cassettes."
              }
            ]
          },
          {
            "subject": "gao_mza_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Gao-Mza system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Gao_Mza | 10\\.1126/science\\.aba0372 | Diverse enzymatic activities mediate antiviral immunity in prokaryotes",
                "notes": "The DefenseFinder article registry maps the named Gao_Mza system to the Gao et al. prokaryotic antiviral-immunity paper."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "Gao_Mza\tGao_Mza\t5\t5\tGao_Mza__MzaA, Gao_Mza__MzaB, Gao_Mza__MzaC, Gao_Mza__MzaD, Gao_Mza__MzaE",
                "notes": "The DefenseFinder rules table models Gao_Mza as a five-profile system requiring the Gao_Mza__MzaA through Gao_Mza__MzaE profiles."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "gao-mza-mechanism-gap",
        "prompt": "Resolve Gao_Mza natural hosts, MzaA/MzaB/MzaC/MzaD/MzaE component functions, phage triggers, and effector activity before minting narrower Gao_Mza mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Gao et al. support widespread antiviral gene cassettes that mediate protection against specific bacteriophages, and DefenseFinder models Gao_Mza as a five-profile system. The exact natural host breadth, Mza component identities, phage trigger, and profile-to-activity mapping remain unresolved.",
        "attaches_to": [
          "causal_graphs#gao_mza_locus_restricts_phage"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-22"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-22T04:08:35Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Gao-Mza system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v232.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000356",
    "label": "Gao-Ppl system",
    "definition": "A phage defense system in which an organism possesses a Gao_Ppl locus represented by DefenseFinder as a single-profile model requiring Gao_Ppl__PplA.",
    "definition_source": "DOI:10.1126/science.aba0372",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "Gao_Ppl",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      },
      {
        "synonym_text": "Gao_Ppl__PplA",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "PMID:32855333",
        "snippet": "By systematic defense gene prediction and heterologous reconstitution, here we discover 29 widespread antiviral gene cassettes, collectively present in 32% of all sequenced bacterial and archaeal genomes, that mediate protection against specific bacteriophages.",
        "notes": "Gao et al. support a systematic defense-gene prediction and heterologous reconstitution campaign that discovered widespread antiviral gene cassettes."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "Gao_Ppl | 10\\.1126/science\\.aba0372 | Diverse enzymatic activities mediate antiviral immunity in prokaryotes",
        "notes": "The DefenseFinder article registry maps the named Gao_Ppl system to the Gao et al. prokaryotic antiviral-immunity paper."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "Gao_Ppl\tGao_Ppl\t1\t1\tGao_Ppl__PplA",
        "notes": "The DefenseFinder rules table models Gao_Ppl as a single-mandatory-profile system with the Gao_Ppl__PplA profile."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| Gao_Ppl__PplA                                    | Gao_Ppl__PplA                                    | Gao_Ppl                | Custom                  | 100    |",
        "notes": "The DefenseFinder HMM inventory records Gao_Ppl__PplA under Gao_Ppl."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "gao_ppl_locus_restricts_phage",
        "title": "Gao-Ppl loci confer bacterial phage defense",
        "description": "Conservative system-level sketch linking possession of a Gao_Ppl locus to Gao et al. antiviral cassette defense without asserting the unresolved PplA component activity.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Gao-Ppl as a named DefenseFinder single-profile Gao-family system while leaving natural hosts, PplA protein function, phage triggers, and direct effector activity unresolved.",
        "nodes": [
          {
            "node_id": "gao_ppl_locus",
            "label": "Gao_Ppl locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A DefenseFinder Gao_Ppl phage-defense locus represented by a custom PplA profile."
          },
          {
            "node_id": "gao_2020_antiviral_cassette_defense",
            "label": "Gao 2020 antiviral cassette defense",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Bacteriophage protection by one of the antiviral gene cassettes described in the Gao et al. systematic defense-gene discovery campaign."
          },
          {
            "node_id": "gao_ppl_system_trait",
            "label": "Gao-Ppl system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000356",
            "description": "Possession of a genome-encoded Gao-Ppl phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "gao_ppl_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "gao_2020_antiviral_cassette_defense",
            "description": "DefenseFinder maps Gao_Ppl to the Gao et al. systematic antiphage-system discovery paper and models it as a single-profile system requiring PplA.",
            "evidence": [
              {
                "reference": "PMID:32855333",
                "snippet": "By systematic defense gene prediction and heterologous reconstitution, here we discover 29 widespread antiviral gene cassettes, collectively present in 32% of all sequenced bacterial and archaeal genomes, that mediate protection against specific bacteriophages.",
                "notes": "Gao et al. support bacteriophage protection by widespread antiviral gene cassettes."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Gao_Ppl | 10\\.1126/science\\.aba0372 | Diverse enzymatic activities mediate antiviral immunity in prokaryotes",
                "notes": "The DefenseFinder article registry maps the named Gao_Ppl system to the Gao et al. prokaryotic antiviral-immunity paper."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "Gao_Ppl\tGao_Ppl\t1\t1\tGao_Ppl__PplA",
                "notes": "The DefenseFinder rules table models Gao_Ppl as a single-mandatory-profile system with the Gao_Ppl__PplA profile."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| Gao_Ppl__PplA                                    | Gao_Ppl__PplA                                    | Gao_Ppl                | Custom                  | 100    |",
                "notes": "The DefenseFinder HMM inventory records Gao_Ppl__PplA under Gao_Ppl."
              }
            ]
          },
          {
            "subject": "gao_2020_antiviral_cassette_defense",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "gao_ppl_system_trait",
            "description": "Gao_Ppl-associated antiviral cassette defense realizes the Gao-Ppl system trait.",
            "evidence": [
              {
                "reference": "PMID:32855333",
                "snippet": "By systematic defense gene prediction and heterologous reconstitution, here we discover 29 widespread antiviral gene cassettes, collectively present in 32% of all sequenced bacterial and archaeal genomes, that mediate protection against specific bacteriophages.",
                "notes": "Gao et al. support bacteriophage protection by widespread antiviral gene cassettes."
              }
            ]
          },
          {
            "subject": "gao_ppl_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Gao-Ppl system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Gao_Ppl | 10\\.1126/science\\.aba0372 | Diverse enzymatic activities mediate antiviral immunity in prokaryotes",
                "notes": "The DefenseFinder article registry maps the named Gao_Ppl system to the Gao et al. prokaryotic antiviral-immunity paper."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "Gao_Ppl\tGao_Ppl\t1\t1\tGao_Ppl__PplA",
                "notes": "The DefenseFinder rules table models Gao_Ppl as a single-mandatory-profile system with the Gao_Ppl__PplA profile."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "gao-ppl-mechanism-gap",
        "prompt": "Resolve Gao_Ppl natural hosts, PplA component function, phage triggers, and effector activity before minting narrower Gao_Ppl mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Gao et al. support widespread antiviral gene cassettes that mediate protection against specific bacteriophages, and DefenseFinder models Gao_Ppl as a single-profile system. The exact natural host breadth, PplA component identity, phage trigger, and profile-to-activity mapping remain unresolved.",
        "attaches_to": [
          "causal_graphs#gao_ppl_locus_restricts_phage"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-22"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-22T06:23:08Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Gao-Ppl system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v233.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000359",
    "label": "Gao-Qat system",
    "definition": "A phage defense system in which an organism possesses a Gao_Qat locus represented by DefenseFinder as a four-profile model requiring Gao_Qat__QatA, Gao_Qat__QatB, Gao_Qat__QatC, and Gao_Qat__QatD.",
    "definition_source": "DOI:10.1126/science.aba0372",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "Gao_Qat",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      },
      {
        "synonym_text": "Gao_Qat__QatA",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "Gao_Qat__QatB",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "Gao_Qat__QatC",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "Gao_Qat__QatD",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "PMID:32855333",
        "snippet": "By systematic defense gene prediction and heterologous reconstitution, here we discover 29 widespread antiviral gene cassettes, collectively present in 32% of all sequenced bacterial and archaeal genomes, that mediate protection against specific bacteriophages.",
        "notes": "Gao et al. support a systematic defense-gene prediction and heterologous reconstitution campaign that discovered widespread antiviral gene cassettes."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "Gao_Qat | 10\\.1126/science\\.aba0372 | Diverse enzymatic activities mediate antiviral immunity in prokaryotes",
        "notes": "The DefenseFinder article registry maps the named Gao_Qat system to the Gao et al. prokaryotic antiviral-immunity paper."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "Gao_Qat\tGao_Qat\t4\t4\tGao_Qat__QatA, Gao_Qat__QatB, Gao_Qat__QatC, Gao_Qat__QatD",
        "notes": "The DefenseFinder rules table models Gao_Qat as a four-profile system requiring the Gao_Qat__QatA through Gao_Qat__QatD profiles."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| Gao_Qat__QatA                                    | Gao_Qat__QatA                                    | Gao_Qat                | Custom                  | 20     |",
        "notes": "The DefenseFinder HMM inventory records Gao_Qat__QatA under Gao_Qat."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| Gao_Qat__QatB                                    | Gao_Qat__QatB                                    | Gao_Qat                | Custom                  | 20     |",
        "notes": "The DefenseFinder HMM inventory records Gao_Qat__QatB under Gao_Qat."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| Gao_Qat__QatC                                    | Gao_Qat__QatC                                    | Gao_Qat                | Custom                  | 20     |",
        "notes": "The DefenseFinder HMM inventory records Gao_Qat__QatC under Gao_Qat."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| Gao_Qat__QatD                                    | Gao_Qat__QatD                                    | Gao_Qat                | Custom                  | 20     |",
        "notes": "The DefenseFinder HMM inventory records Gao_Qat__QatD under Gao_Qat."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "gao_qat_locus_restricts_phage",
        "title": "Gao-Qat loci confer bacterial phage defense",
        "description": "Conservative system-level sketch linking possession of a Gao_Qat locus to Gao et al. antiviral cassette defense without asserting the unresolved Qat component activities.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Gao-Qat as a named DefenseFinder four-profile Gao-family system while leaving natural hosts, QatA/QatB/QatC/QatD protein functions, phage triggers, and direct effector activity unresolved.",
        "nodes": [
          {
            "node_id": "gao_qat_locus",
            "label": "Gao_Qat locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A DefenseFinder Gao_Qat phage-defense locus represented by custom QatA through QatD profiles."
          },
          {
            "node_id": "gao_2020_antiviral_cassette_defense",
            "label": "Gao 2020 antiviral cassette defense",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Bacteriophage protection by one of the antiviral gene cassettes described in the Gao et al. systematic defense-gene discovery campaign."
          },
          {
            "node_id": "gao_qat_system_trait",
            "label": "Gao-Qat system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000359",
            "description": "Possession of a genome-encoded Gao-Qat phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "gao_qat_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "gao_2020_antiviral_cassette_defense",
            "description": "DefenseFinder maps Gao_Qat to the Gao et al. systematic antiphage-system discovery paper and models it as a four-profile system requiring QatA through QatD.",
            "evidence": [
              {
                "reference": "PMID:32855333",
                "snippet": "By systematic defense gene prediction and heterologous reconstitution, here we discover 29 widespread antiviral gene cassettes, collectively present in 32% of all sequenced bacterial and archaeal genomes, that mediate protection against specific bacteriophages.",
                "notes": "Gao et al. support bacteriophage protection by widespread antiviral gene cassettes."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Gao_Qat | 10\\.1126/science\\.aba0372 | Diverse enzymatic activities mediate antiviral immunity in prokaryotes",
                "notes": "The DefenseFinder article registry maps the named Gao_Qat system to the Gao et al. prokaryotic antiviral-immunity paper."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "Gao_Qat\tGao_Qat\t4\t4\tGao_Qat__QatA, Gao_Qat__QatB, Gao_Qat__QatC, Gao_Qat__QatD",
                "notes": "The DefenseFinder rules table models Gao_Qat as a four-profile system requiring the Gao_Qat__QatA through Gao_Qat__QatD profiles."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| Gao_Qat__QatA                                    | Gao_Qat__QatA                                    | Gao_Qat                | Custom                  | 20     |",
                "notes": "The DefenseFinder HMM inventory records Gao_Qat__QatA under Gao_Qat."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| Gao_Qat__QatB                                    | Gao_Qat__QatB                                    | Gao_Qat                | Custom                  | 20     |",
                "notes": "The DefenseFinder HMM inventory records Gao_Qat__QatB under Gao_Qat."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| Gao_Qat__QatC                                    | Gao_Qat__QatC                                    | Gao_Qat                | Custom                  | 20     |",
                "notes": "The DefenseFinder HMM inventory records Gao_Qat__QatC under Gao_Qat."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| Gao_Qat__QatD                                    | Gao_Qat__QatD                                    | Gao_Qat                | Custom                  | 20     |",
                "notes": "The DefenseFinder HMM inventory records Gao_Qat__QatD under Gao_Qat."
              }
            ]
          },
          {
            "subject": "gao_2020_antiviral_cassette_defense",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "gao_qat_system_trait",
            "description": "Gao_Qat-associated antiviral cassette defense realizes the Gao-Qat system trait.",
            "evidence": [
              {
                "reference": "PMID:32855333",
                "snippet": "By systematic defense gene prediction and heterologous reconstitution, here we discover 29 widespread antiviral gene cassettes, collectively present in 32% of all sequenced bacterial and archaeal genomes, that mediate protection against specific bacteriophages.",
                "notes": "Gao et al. support bacteriophage protection by widespread antiviral gene cassettes."
              }
            ]
          },
          {
            "subject": "gao_qat_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Gao-Qat system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Gao_Qat | 10\\.1126/science\\.aba0372 | Diverse enzymatic activities mediate antiviral immunity in prokaryotes",
                "notes": "The DefenseFinder article registry maps the named Gao_Qat system to the Gao et al. prokaryotic antiviral-immunity paper."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "Gao_Qat\tGao_Qat\t4\t4\tGao_Qat__QatA, Gao_Qat__QatB, Gao_Qat__QatC, Gao_Qat__QatD",
                "notes": "The DefenseFinder rules table models Gao_Qat as a four-profile system requiring the Gao_Qat__QatA through Gao_Qat__QatD profiles."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "gao-qat-mechanism-gap",
        "prompt": "Resolve Gao_Qat natural hosts, Qat component functions, phage triggers, and effector activity before minting narrower Gao_Qat mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Gao et al. support widespread antiviral gene cassettes that mediate protection against specific bacteriophages, and DefenseFinder models Gao_Qat as a four-profile system. The exact natural host breadth, QatA/QatB/QatC/QatD component identities, phage trigger, and profile-to-activity mapping remain unresolved.",
        "attaches_to": [
          "causal_graphs#gao_qat_locus_restricts_phage"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-22"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-22T08:09:38Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Gao-Qat system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v236.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000352",
    "label": "Gao-RL system",
    "definition": "A phage defense system in which an organism possesses a Gao_RL locus represented by DefenseFinder as a four-profile model requiring Gao_RL__RL_A, Gao_RL__RL_B, Gao_RL__RL_C, and Gao_RL__RL_D.",
    "definition_source": "DOI:10.1126/science.aba0372",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "Gao_RL",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      },
      {
        "synonym_text": "Gao_RL__RL_A",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "Gao_RL__RL_B",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "Gao_RL__RL_C",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "Gao_RL__RL_D",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "PMID:32855333",
        "snippet": "By systematic defense gene prediction and heterologous reconstitution, here we discover 29 widespread antiviral gene cassettes, collectively present in 32% of all sequenced bacterial and archaeal genomes, that mediate protection against specific bacteriophages.",
        "notes": "Gao et al. support a systematic defense-gene prediction and heterologous reconstitution campaign that discovered widespread antiviral gene cassettes."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "Gao_RL | 10\\.1126/science\\.aba0372 | Diverse enzymatic activities mediate antiviral immunity in prokaryotes",
        "notes": "The DefenseFinder article registry maps the named Gao_RL system to the Gao et al. prokaryotic antiviral-immunity paper."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "Gao_RL\tGao_RL\t4\t4\tGao_RL__RL_A, Gao_RL__RL_B, Gao_RL__RL_C, Gao_RL__RL_D",
        "notes": "The DefenseFinder rules table models Gao_RL as a four-profile system requiring RL_A through RL_D profiles."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| Gao_RL__RL_A                                     | Gao_RL__RL_A                                     | Gao_RL                 | Custom                  | 20     |",
        "notes": "The DefenseFinder HMM inventory records Gao_RL__RL_A under Gao_RL."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| Gao_RL__RL_B                                     | Gao_RL__RL_B                                     | Gao_RL                 | Custom                  | 20     |",
        "notes": "The DefenseFinder HMM inventory records Gao_RL__RL_B under Gao_RL."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| Gao_RL__RL_C                                     | Gao_RL__RL_C                                     | Gao_RL                 | Custom                  | 20     |",
        "notes": "The DefenseFinder HMM inventory records Gao_RL__RL_C under Gao_RL."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| Gao_RL__RL_D                                     | Gao_RL__RL_D                                     | Gao_RL                 | Custom                  | 100    |",
        "notes": "The DefenseFinder HMM inventory records Gao_RL__RL_D under Gao_RL."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "gao_rl_locus_restricts_phage",
        "title": "Gao-RL loci confer bacterial phage defense",
        "description": "Conservative system-level sketch linking possession of a Gao_RL locus to Gao et al. antiviral cassette defense without asserting the unresolved RL component activities.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Gao-RL as a named DefenseFinder four-profile Gao-family system while leaving natural hosts, RL_A/RL_B/RL_C/RL_D protein functions, phage triggers, and direct effector activity unresolved.",
        "nodes": [
          {
            "node_id": "gao_rl_locus",
            "label": "Gao_RL locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A DefenseFinder Gao_RL phage-defense locus represented by custom RL_A through RL_D profiles."
          },
          {
            "node_id": "gao_2020_antiviral_cassette_defense",
            "label": "Gao 2020 antiviral cassette defense",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Bacteriophage protection by one of the antiviral gene cassettes described in the Gao et al. systematic defense-gene discovery campaign."
          },
          {
            "node_id": "gao_rl_system_trait",
            "label": "Gao-RL system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000352",
            "description": "Possession of a genome-encoded Gao-RL phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "gao_rl_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "gao_2020_antiviral_cassette_defense",
            "description": "DefenseFinder maps Gao_RL to the Gao et al. systematic antiphage-system discovery paper and models it as a four-profile system requiring RL_A through RL_D.",
            "evidence": [
              {
                "reference": "PMID:32855333",
                "snippet": "By systematic defense gene prediction and heterologous reconstitution, here we discover 29 widespread antiviral gene cassettes, collectively present in 32% of all sequenced bacterial and archaeal genomes, that mediate protection against specific bacteriophages.",
                "notes": "Gao et al. support bacteriophage protection by widespread antiviral gene cassettes."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Gao_RL | 10\\.1126/science\\.aba0372 | Diverse enzymatic activities mediate antiviral immunity in prokaryotes",
                "notes": "The DefenseFinder article registry maps the named Gao_RL system to the Gao et al. prokaryotic antiviral-immunity paper."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "Gao_RL\tGao_RL\t4\t4\tGao_RL__RL_A, Gao_RL__RL_B, Gao_RL__RL_C, Gao_RL__RL_D",
                "notes": "The DefenseFinder rules table models Gao_RL as a four-profile system requiring RL_A through RL_D profiles."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| Gao_RL__RL_A                                     | Gao_RL__RL_A                                     | Gao_RL                 | Custom                  | 20     |",
                "notes": "The DefenseFinder HMM inventory records Gao_RL__RL_A under Gao_RL."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| Gao_RL__RL_B                                     | Gao_RL__RL_B                                     | Gao_RL                 | Custom                  | 20     |",
                "notes": "The DefenseFinder HMM inventory records Gao_RL__RL_B under Gao_RL."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| Gao_RL__RL_C                                     | Gao_RL__RL_C                                     | Gao_RL                 | Custom                  | 20     |",
                "notes": "The DefenseFinder HMM inventory records Gao_RL__RL_C under Gao_RL."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| Gao_RL__RL_D                                     | Gao_RL__RL_D                                     | Gao_RL                 | Custom                  | 100    |",
                "notes": "The DefenseFinder HMM inventory records Gao_RL__RL_D under Gao_RL."
              }
            ]
          },
          {
            "subject": "gao_2020_antiviral_cassette_defense",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "gao_rl_system_trait",
            "description": "Gao_RL-associated antiviral cassette defense realizes the Gao-RL system trait.",
            "evidence": [
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                "notes": "Gao et al. support bacteriophage protection by widespread antiviral gene cassettes."
              }
            ]
          },
          {
            "subject": "gao_rl_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Gao-RL system possession is a phage-defense-system trait.",
            "evidence": [
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                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Gao_RL | 10\\.1126/science\\.aba0372 | Diverse enzymatic activities mediate antiviral immunity in prokaryotes",
                "notes": "The DefenseFinder article registry maps the named Gao_RL system to the Gao et al. prokaryotic antiviral-immunity paper."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "Gao_RL\tGao_RL\t4\t4\tGao_RL__RL_A, Gao_RL__RL_B, Gao_RL__RL_C, Gao_RL__RL_D",
                "notes": "The DefenseFinder rules table models Gao_RL as a four-profile system requiring RL_A through RL_D profiles."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "gao-rl-mechanism-gap",
        "prompt": "Resolve Gao_RL natural hosts, RL_A/RL_B/RL_C/RL_D component functions, phage triggers, and effector activity before minting narrower Gao_RL mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Gao et al. support widespread antiviral gene cassettes that mediate protection against specific bacteriophages, and DefenseFinder models Gao_RL as a four-profile system. The exact natural host breadth, RL component identities, phage trigger, and profile-to-activity mapping remain unresolved.",
        "attaches_to": [
          "causal_graphs#gao_rl_locus_restricts_phage"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-22"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-22T01:39:05Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Gao-RL system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v229.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000360",
    "label": "Gao-TerY system",
    "definition": "A phage defense system in which an organism possesses a Gao_TerY locus represented by DefenseFinder as a three-profile model requiring Gao_TerY__TerYA, Gao_TerY__TerYB, and Gao_TerY__TerYC.",
    "definition_source": "DOI:10.1126/science.aba0372",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "Gao_TerY",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      },
      {
        "synonym_text": "Gao_TerY__TerYA",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "Gao_TerY__TerYB",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "Gao_TerY__TerYC",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "PMID:32855333",
        "snippet": "By systematic defense gene prediction and heterologous reconstitution, here we discover 29 widespread antiviral gene cassettes, collectively present in 32% of all sequenced bacterial and archaeal genomes, that mediate protection against specific bacteriophages.",
        "notes": "Gao et al. support a systematic defense-gene prediction and heterologous reconstitution campaign that discovered widespread antiviral gene cassettes."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "Gao_TerY | 10\\.1126/science\\.aba0372 | Diverse enzymatic activities mediate antiviral immunity in prokaryotes",
        "notes": "The DefenseFinder article registry maps the named Gao_TerY system to the Gao et al. prokaryotic antiviral-immunity paper."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "Gao_TerY\tGao_TerY\t3\t3\tGao_TerY__TerYA, Gao_TerY__TerYB, Gao_TerY__TerYC",
        "notes": "The DefenseFinder rules table models Gao_TerY as a three-profile system requiring the Gao_TerY__TerYA through Gao_TerY__TerYC profiles."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| Gao_TerY__TerYA                                  | Gao_TerY__TerYA                                  | Gao_TerY               | Custom                  | 100    |",
        "notes": "The DefenseFinder HMM inventory records Gao_TerY__TerYA under Gao_TerY."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| Gao_TerY__TerYB                                  | Gao_TerY__TerYB                                  | Gao_TerY               | Custom                  | 38     |",
        "notes": "The DefenseFinder HMM inventory records Gao_TerY__TerYB under Gao_TerY."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| Gao_TerY__TerYC                                  | Gao_TerY__TerYC                                  | Gao_TerY               | Custom                  | 200    |",
        "notes": "The DefenseFinder HMM inventory records Gao_TerY__TerYC under Gao_TerY."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "gao_tery_locus_restricts_phage",
        "title": "Gao-TerY loci confer bacterial phage defense",
        "description": "Conservative system-level sketch linking possession of a Gao_TerY locus to Gao et al. antiviral cassette defense without asserting the unresolved TerY component activities.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Gao-TerY as a named DefenseFinder three-profile Gao-family system while leaving natural hosts, TerYA/TerYB/TerYC protein functions, phage triggers, and direct effector activity unresolved.",
        "nodes": [
          {
            "node_id": "gao_tery_locus",
            "label": "Gao_TerY locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A DefenseFinder Gao_TerY phage-defense locus represented by custom TerYA through TerYC profiles."
          },
          {
            "node_id": "gao_2020_antiviral_cassette_defense",
            "label": "Gao 2020 antiviral cassette defense",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Bacteriophage protection by one of the antiviral gene cassettes described in the Gao et al. systematic defense-gene discovery campaign."
          },
          {
            "node_id": "gao_tery_system_trait",
            "label": "Gao-TerY system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000360",
            "description": "Possession of a genome-encoded Gao-TerY phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "gao_tery_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "gao_2020_antiviral_cassette_defense",
            "description": "DefenseFinder maps Gao_TerY to the Gao et al. systematic antiphage-system discovery paper and models it as a three-profile system requiring TerYA through TerYC.",
            "evidence": [
              {
                "reference": "PMID:32855333",
                "snippet": "By systematic defense gene prediction and heterologous reconstitution, here we discover 29 widespread antiviral gene cassettes, collectively present in 32% of all sequenced bacterial and archaeal genomes, that mediate protection against specific bacteriophages.",
                "notes": "Gao et al. support bacteriophage protection by widespread antiviral gene cassettes."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Gao_TerY | 10\\.1126/science\\.aba0372 | Diverse enzymatic activities mediate antiviral immunity in prokaryotes",
                "notes": "The DefenseFinder article registry maps the named Gao_TerY system to the Gao et al. prokaryotic antiviral-immunity paper."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "Gao_TerY\tGao_TerY\t3\t3\tGao_TerY__TerYA, Gao_TerY__TerYB, Gao_TerY__TerYC",
                "notes": "The DefenseFinder rules table models Gao_TerY as a three-profile system requiring the Gao_TerY__TerYA through Gao_TerY__TerYC profiles."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| Gao_TerY__TerYA                                  | Gao_TerY__TerYA                                  | Gao_TerY               | Custom                  | 100    |",
                "notes": "The DefenseFinder HMM inventory records Gao_TerY__TerYA under Gao_TerY."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| Gao_TerY__TerYB                                  | Gao_TerY__TerYB                                  | Gao_TerY               | Custom                  | 38     |",
                "notes": "The DefenseFinder HMM inventory records Gao_TerY__TerYB under Gao_TerY."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| Gao_TerY__TerYC                                  | Gao_TerY__TerYC                                  | Gao_TerY               | Custom                  | 200    |",
                "notes": "The DefenseFinder HMM inventory records Gao_TerY__TerYC under Gao_TerY."
              }
            ]
          },
          {
            "subject": "gao_2020_antiviral_cassette_defense",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "gao_tery_system_trait",
            "description": "Gao_TerY-associated antiviral cassette defense realizes the Gao-TerY system trait.",
            "evidence": [
              {
                "reference": "PMID:32855333",
                "snippet": "By systematic defense gene prediction and heterologous reconstitution, here we discover 29 widespread antiviral gene cassettes, collectively present in 32% of all sequenced bacterial and archaeal genomes, that mediate protection against specific bacteriophages.",
                "notes": "Gao et al. support bacteriophage protection by widespread antiviral gene cassettes."
              }
            ]
          },
          {
            "subject": "gao_tery_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Gao-TerY system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Gao_TerY | 10\\.1126/science\\.aba0372 | Diverse enzymatic activities mediate antiviral immunity in prokaryotes",
                "notes": "The DefenseFinder article registry maps the named Gao_TerY system to the Gao et al. prokaryotic antiviral-immunity paper."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "Gao_TerY\tGao_TerY\t3\t3\tGao_TerY__TerYA, Gao_TerY__TerYB, Gao_TerY__TerYC",
                "notes": "The DefenseFinder rules table models Gao_TerY as a three-profile system requiring the Gao_TerY__TerYA through Gao_TerY__TerYC profiles."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "gao-tery-mechanism-gap",
        "prompt": "Resolve Gao_TerY natural hosts, TerY component functions, phage triggers, and effector activity before minting narrower Gao_TerY mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Gao et al. support widespread antiviral gene cassettes that mediate protection against specific bacteriophages, and DefenseFinder models Gao_TerY as a three-profile system. The exact natural host breadth, TerYA/TerYB/TerYC component identities, phage trigger, and profile-to-activity mapping remain unresolved.",
        "attaches_to": [
          "causal_graphs#gao_tery_locus_restricts_phage"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-22"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-22T09:00:56Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Gao-TerY system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v237.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000357",
    "label": "Gao-Tmn system",
    "definition": "A phage defense system in which an organism possesses a Gao_Tmn locus represented by DefenseFinder as a single-profile model requiring Gao_Tmn__TmnA.",
    "definition_source": "DOI:10.1126/science.aba0372",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "Gao_Tmn",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      },
      {
        "synonym_text": "Gao_Tmn__TmnA",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "PMID:32855333",
        "snippet": "By systematic defense gene prediction and heterologous reconstitution, here we discover 29 widespread antiviral gene cassettes, collectively present in 32% of all sequenced bacterial and archaeal genomes, that mediate protection against specific bacteriophages.",
        "notes": "Gao et al. support a systematic defense-gene prediction and heterologous reconstitution campaign that discovered widespread antiviral gene cassettes."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "Gao_Tmn | 10\\.1126/science\\.aba0372 | Diverse enzymatic activities mediate antiviral immunity in prokaryotes",
        "notes": "The DefenseFinder article registry maps the named Gao_Tmn system to the Gao et al. prokaryotic antiviral-immunity paper."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "Gao_Tmn\tGao_Tmn\t1\t1\tGao_Tmn__TmnA",
        "notes": "The DefenseFinder rules table models Gao_Tmn as a single-mandatory-profile system with the Gao_Tmn__TmnA profile."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| Gao_Tmn__TmnA                                    | Gao_Tmn__TmnA                                    | Gao_Tmn                | Custom                  | 200    |",
        "notes": "The DefenseFinder HMM inventory records Gao_Tmn__TmnA under Gao_Tmn."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "gao_tmn_locus_restricts_phage",
        "title": "Gao-Tmn loci confer bacterial phage defense",
        "description": "Conservative system-level sketch linking possession of a Gao_Tmn locus to Gao et al. antiviral cassette defense without asserting the unresolved TmnA component activity.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Gao-Tmn as a named DefenseFinder single-profile Gao-family system while leaving natural hosts, TmnA protein function, phage triggers, and direct effector activity unresolved.",
        "nodes": [
          {
            "node_id": "gao_tmn_locus",
            "label": "Gao_Tmn locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A DefenseFinder Gao_Tmn phage-defense locus represented by a custom TmnA profile."
          },
          {
            "node_id": "gao_2020_antiviral_cassette_defense",
            "label": "Gao 2020 antiviral cassette defense",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Bacteriophage protection by one of the antiviral gene cassettes described in the Gao et al. systematic defense-gene discovery campaign."
          },
          {
            "node_id": "gao_tmn_system_trait",
            "label": "Gao-Tmn system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000357",
            "description": "Possession of a genome-encoded Gao-Tmn phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
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          {
            "subject": "gao_tmn_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "gao_2020_antiviral_cassette_defense",
            "description": "DefenseFinder maps Gao_Tmn to the Gao et al. systematic antiphage-system discovery paper and models it as a single-profile system requiring TmnA.",
            "evidence": [
              {
                "reference": "PMID:32855333",
                "snippet": "By systematic defense gene prediction and heterologous reconstitution, here we discover 29 widespread antiviral gene cassettes, collectively present in 32% of all sequenced bacterial and archaeal genomes, that mediate protection against specific bacteriophages.",
                "notes": "Gao et al. support bacteriophage protection by widespread antiviral gene cassettes."
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              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Gao_Tmn | 10\\.1126/science\\.aba0372 | Diverse enzymatic activities mediate antiviral immunity in prokaryotes",
                "notes": "The DefenseFinder article registry maps the named Gao_Tmn system to the Gao et al. prokaryotic antiviral-immunity paper."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "Gao_Tmn\tGao_Tmn\t1\t1\tGao_Tmn__TmnA",
                "notes": "The DefenseFinder rules table models Gao_Tmn as a single-mandatory-profile system with the Gao_Tmn__TmnA profile."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| Gao_Tmn__TmnA                                    | Gao_Tmn__TmnA                                    | Gao_Tmn                | Custom                  | 200    |",
                "notes": "The DefenseFinder HMM inventory records Gao_Tmn__TmnA under Gao_Tmn."
              }
            ]
          },
          {
            "subject": "gao_2020_antiviral_cassette_defense",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "gao_tmn_system_trait",
            "description": "Gao_Tmn-associated antiviral cassette defense realizes the Gao-Tmn system trait.",
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              {
                "reference": "PMID:32855333",
                "snippet": "By systematic defense gene prediction and heterologous reconstitution, here we discover 29 widespread antiviral gene cassettes, collectively present in 32% of all sequenced bacterial and archaeal genomes, that mediate protection against specific bacteriophages.",
                "notes": "Gao et al. support bacteriophage protection by widespread antiviral gene cassettes."
              }
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            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Gao-Tmn system possession is a phage-defense-system trait.",
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                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Gao_Tmn | 10\\.1126/science\\.aba0372 | Diverse enzymatic activities mediate antiviral immunity in prokaryotes",
                "notes": "The DefenseFinder article registry maps the named Gao_Tmn system to the Gao et al. prokaryotic antiviral-immunity paper."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "Gao_Tmn\tGao_Tmn\t1\t1\tGao_Tmn__TmnA",
                "notes": "The DefenseFinder rules table models Gao_Tmn as a single-mandatory-profile system with the Gao_Tmn__TmnA profile."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "gao-tmn-mechanism-gap",
        "prompt": "Resolve Gao_Tmn natural hosts, TmnA component function, phage triggers, and effector activity before minting narrower Gao_Tmn mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Gao et al. support widespread antiviral gene cassettes that mediate protection against specific bacteriophages, and DefenseFinder models Gao_Tmn as a single-profile system. The exact natural host breadth, TmnA component identity, phage trigger, and profile-to-activity mapping remain unresolved.",
        "attaches_to": [
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        ],
        "posed_by": "codex",
        "posed_date": "2026-09-22"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-22T07:00:35Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Gao-Tmn system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v234.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000358",
    "label": "Gao-Upx system",
    "definition": "A phage defense system in which an organism possesses a Gao_Upx locus represented by DefenseFinder as a single-profile model requiring Gao_Upx__UpxA.",
    "definition_source": "DOI:10.1126/science.aba0372",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
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    "synonyms": [
      {
        "synonym_text": "Gao_Upx",
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        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      },
      {
        "synonym_text": "Gao_Upx__UpxA",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
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        "reference": "PMID:32855333",
        "snippet": "By systematic defense gene prediction and heterologous reconstitution, here we discover 29 widespread antiviral gene cassettes, collectively present in 32% of all sequenced bacterial and archaeal genomes, that mediate protection against specific bacteriophages.",
        "notes": "Gao et al. support a systematic defense-gene prediction and heterologous reconstitution campaign that discovered widespread antiviral gene cassettes."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "Gao_Upx | 10\\.1126/science\\.aba0372 | Diverse enzymatic activities mediate antiviral immunity in prokaryotes",
        "notes": "The DefenseFinder article registry maps the named Gao_Upx system to the Gao et al. prokaryotic antiviral-immunity paper."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "Gao_Upx\tGao_Upx\t1\t1\tGao_Upx__UpxA",
        "notes": "The DefenseFinder rules table models Gao_Upx as a single-mandatory-profile system with the Gao_Upx__UpxA profile."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| Gao_Upx__UpxA                                    | Gao_Upx__UpxA                                    | Gao_Upx                | Custom                  | 250    |",
        "notes": "The DefenseFinder HMM inventory records Gao_Upx__UpxA under Gao_Upx."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "gao_upx_locus_restricts_phage",
        "title": "Gao-Upx loci confer bacterial phage defense",
        "description": "Conservative system-level sketch linking possession of a Gao_Upx locus to Gao et al. antiviral cassette defense without asserting the unresolved UpxA component activity.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Gao-Upx as a named DefenseFinder single-profile Gao-family system while leaving natural hosts, UpxA protein function, phage triggers, and direct effector activity unresolved.",
        "nodes": [
          {
            "node_id": "gao_upx_locus",
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            "description": "A DefenseFinder Gao_Upx phage-defense locus represented by a custom UpxA profile."
          },
          {
            "node_id": "gao_2020_antiviral_cassette_defense",
            "label": "Gao 2020 antiviral cassette defense",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Bacteriophage protection by one of the antiviral gene cassettes described in the Gao et al. systematic defense-gene discovery campaign."
          },
          {
            "node_id": "gao_upx_system_trait",
            "label": "Gao-Upx system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000358",
            "description": "Possession of a genome-encoded Gao-Upx phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
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            "subject": "gao_upx_locus",
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            "description": "DefenseFinder maps Gao_Upx to the Gao et al. systematic antiphage-system discovery paper and models it as a single-profile system requiring UpxA.",
            "evidence": [
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                "notes": "Gao et al. support bacteriophage protection by widespread antiviral gene cassettes."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Gao_Upx | 10\\.1126/science\\.aba0372 | Diverse enzymatic activities mediate antiviral immunity in prokaryotes",
                "notes": "The DefenseFinder article registry maps the named Gao_Upx system to the Gao et al. prokaryotic antiviral-immunity paper."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "Gao_Upx\tGao_Upx\t1\t1\tGao_Upx__UpxA",
                "notes": "The DefenseFinder rules table models Gao_Upx as a single-mandatory-profile system with the Gao_Upx__UpxA profile."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| Gao_Upx__UpxA                                    | Gao_Upx__UpxA                                    | Gao_Upx                | Custom                  | 250    |",
                "notes": "The DefenseFinder HMM inventory records Gao_Upx__UpxA under Gao_Upx."
              }
            ]
          },
          {
            "subject": "gao_2020_antiviral_cassette_defense",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "gao_upx_system_trait",
            "description": "Gao_Upx-associated antiviral cassette defense realizes the Gao-Upx system trait.",
            "evidence": [
              {
                "reference": "PMID:32855333",
                "snippet": "By systematic defense gene prediction and heterologous reconstitution, here we discover 29 widespread antiviral gene cassettes, collectively present in 32% of all sequenced bacterial and archaeal genomes, that mediate protection against specific bacteriophages.",
                "notes": "Gao et al. support bacteriophage protection by widespread antiviral gene cassettes."
              }
            ]
          },
          {
            "subject": "gao_upx_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Gao-Upx system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Gao_Upx | 10\\.1126/science\\.aba0372 | Diverse enzymatic activities mediate antiviral immunity in prokaryotes",
                "notes": "The DefenseFinder article registry maps the named Gao_Upx system to the Gao et al. prokaryotic antiviral-immunity paper."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "Gao_Upx\tGao_Upx\t1\t1\tGao_Upx__UpxA",
                "notes": "The DefenseFinder rules table models Gao_Upx as a single-mandatory-profile system with the Gao_Upx__UpxA profile."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "gao-upx-mechanism-gap",
        "prompt": "Resolve Gao_Upx natural hosts, UpxA component function, phage triggers, and effector activity before minting narrower Gao_Upx mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Gao et al. support widespread antiviral gene cassettes that mediate protection against specific bacteriophages, and DefenseFinder models Gao_Upx as a single-profile system. The exact natural host breadth, UpxA component identity, phage trigger, and profile-to-activity mapping remain unresolved.",
        "attaches_to": [
          "causal_graphs#gao_upx_locus_restricts_phage"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-22"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-22T07:33:14Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Gao-Upx system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v235.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000371",
    "label": "GAPS1 system",
    "definition": "A phage defense system in which an organism possesses a Gamma-Mobile-Trio island-associated GAPS1 locus that can be triggered by a phage capsid protein to induce cell dormancy.",
    "definition_source": "DOI:10.1038/s41564-024-01840-5",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "GAPS1",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1038/s41564-024-01840-5"
      },
      {
        "synonym_text": "GAPS1__GAPS1",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/s41564-024-01840-5",
        "snippet": "GMT islands' cargoes contain various anti-phage defence systems",
        "notes": "Mahata et al. identify GMT islands as carriers of anti-phage defense-system cargo."
      },
      {
        "reference": "DOI:10.1038/s41564-024-01840-5",
        "snippet": "We reveal four anti-phage defence systems encoded within GMT islands and further characterize one system, GAPS1, showing it is triggered by a phage capsid protein to induce cell dormancy",
        "notes": "Mahata et al. identify GAPS1 as one of four GMT-island anti-phage defense systems and connect GAPS1 activation to phage-capsid-protein-triggered cell dormancy."
      },
      {
        "reference": "DOI:10.1101/2023.03.28.534373",
        "snippet": "Gamma-Mobile-Trio systems define a new class of mobile elements rich in bacterial defensive and offensive tools",
        "notes": "The bioRxiv version of Mahata et al. is the DOI cited in DefenseFinder's GAPS1 article-registry row."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "GAPS1 | 10\\.1101/2023\\.03\\.28\\.534373 | Gamma-Mobile-Trio systems define a new class of mobile elements rich in bacterial defensive and offensive tools",
        "notes": "The DefenseFinder article registry maps the named GAPS1 system to the Mahata et al. preprint."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "GAPS1\tGAPS1\t1\t1\tGAPS1__GAPS1\t\t\t",
        "notes": "The DefenseFinder rules table models GAPS1 as a single-profile system requiring GAPS1__GAPS1."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| GAPS1__GAPS1                                     | GAPS1__GAPS1                                     | GAPS1                  | Custom                  | 100    |",
        "notes": "The DefenseFinder HMM inventory records GAPS1__GAPS1 under the GAPS1 model namespace."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "gaps1_capsid_triggered_dormancy",
        "title": "GAPS1 loci induce cell dormancy during phage defense",
        "description": "Conservative system-level sketch connecting the named GAPS1 locus model and the phage-capsid-protein-triggered dormancy phenotype to the GAPS1 system trait.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures GAPS1 as a named GMT-island anti-phage defense system represented in DefenseFinder by a single GAPS1__GAPS1 profile while leaving its universal host range, the molecular activity of the GAPS1 component, and the exact capsid-protein trigger unresolved.",
        "nodes": [
          {
            "node_id": "gaps1_locus",
            "label": "GAPS1 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A GMT-island-associated GAPS1 phage-defense locus represented by the custom DefenseFinder GAPS1__GAPS1 profile."
          },
          {
            "node_id": "gaps1_cell_dormancy",
            "label": "GAPS1-induced cell dormancy",
            "node_type": "STATE",
            "description": "Cellular dormancy induced by a GAPS1 system after recognition of a phage capsid-protein trigger."
          },
          {
            "node_id": "gaps1_system_trait",
            "label": "GAPS1 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000371",
            "description": "Possession of a genome-encoded GAPS1 phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "gaps1_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "gaps1_system_trait",
            "description": "DefenseFinder records GAPS1 as a named system and models it as a single-profile GAPS1__GAPS1 rule.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "GAPS1 | 10\\.1101/2023\\.03\\.28\\.534373 | Gamma-Mobile-Trio systems define a new class of mobile elements rich in bacterial defensive and offensive tools",
                "notes": "The DefenseFinder article registry maps the named GAPS1 system to the Mahata et al. preprint."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "GAPS1\tGAPS1\t1\t1\tGAPS1__GAPS1\t\t\t",
                "notes": "The DefenseFinder rules table models GAPS1 as a single-profile system requiring GAPS1__GAPS1."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| GAPS1__GAPS1                                     | GAPS1__GAPS1                                     | GAPS1                  | Custom                  | 100    |",
                "notes": "The DefenseFinder HMM inventory records GAPS1__GAPS1 under the GAPS1 model namespace."
              }
            ]
          },
          {
            "subject": "gaps1_cell_dormancy",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "gaps1_system_trait",
            "description": "Phage-capsid-protein-triggered cell dormancy is the characterized output that realizes the GAPS1 system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-024-01840-5",
                "snippet": "We reveal four anti-phage defence systems encoded within GMT islands and further characterize one system, GAPS1, showing it is triggered by a phage capsid protein to induce cell dormancy",
                "notes": "Mahata et al. identify GAPS1 as one of four GMT-island anti-phage defense systems and connect GAPS1 activation to phage-capsid-protein-triggered cell dormancy."
              }
            ]
          },
          {
            "subject": "gaps1_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "GAPS1 system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-024-01840-5",
                "snippet": "We reveal four anti-phage defence systems encoded within GMT islands and further characterize one system, GAPS1, showing it is triggered by a phage capsid protein to induce cell dormancy",
                "notes": "Mahata et al. identify GAPS1 as one of four GMT-island anti-phage defense systems and connect GAPS1 activation to phage-capsid-protein-triggered cell dormancy."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "GAPS1 | 10\\.1101/2023\\.03\\.28\\.534373 | Gamma-Mobile-Trio systems define a new class of mobile elements rich in bacterial defensive and offensive tools",
                "notes": "The DefenseFinder article registry maps the named GAPS1 system to the Mahata et al. preprint."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "gaps1-trigger-sibling-gap",
        "prompt": "Resolve GAPS1 component activity and natural-host exemplars before minting narrower GAPS traits.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Mahata et al. support GAPS1 as one GMT-island anti-phage defense system triggered by a phage capsid protein to induce cell dormancy, and DefenseFinder represents GAPS1 as one GAPS1__GAPS1 profile. This first system-level record does not assert the GAPS1 component's molecular activity, the capsid trigger identity, or a universal GAPS1 host range.",
        "evidence": [
          {
            "reference": "DOI:10.1038/s41564-024-01840-5",
            "snippet": "We reveal four anti-phage defence systems encoded within GMT islands and further characterize one system, GAPS1, showing it is triggered by a phage capsid protein to induce cell dormancy",
            "notes": "Mahata et al. identify GAPS1 as one of four GMT-island anti-phage defense systems and connect GAPS1 activation to phage-capsid-protein-triggered cell dormancy."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "snippet": "GAPS1\tGAPS1\t1\t1\tGAPS1__GAPS1\t\t\t",
            "notes": "The DefenseFinder rules table models GAPS1 as a single-profile system requiring GAPS1__GAPS1."
          }
        ],
        "attaches_to": [
          "causal_graphs#gaps1_capsid_triggered_dormancy"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-24"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-25T04:19:09Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted GAPS1 system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v248.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-26T11:02:35Z",
        "curator": "codex",
        "action": "UPDATED_DISCUSSION",
        "changes": "Resolved GitHub issue #1274 by narrowing stale GAPS1 sibling-boundary references to GAPS2/GAPS6 after GAPS4 was split into its own TraitRecord.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-26T11:26:43Z",
        "curator": "codex",
        "action": "UPDATED_DISCUSSION",
        "changes": "Narrowed stale GAPS1 sibling-boundary references to GAPS6 after GAPS2 was split into its own TraitRecord.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-26T11:58:15Z",
        "curator": "codex",
        "action": "UPDATED_DISCUSSION",
        "changes": "Resolved the remaining stale GAPS1 sibling-boundary reference after GAPS6 was split into its own TraitRecord.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000380",
    "label": "GAPS2 system",
    "definition": "A phage defense system in which an organism possesses a GMT-encoded GAPS2 locus represented by DefenseFinder as a single-profile model, GAPS2__GAPS2, and experimentally linked to P1-vir and lambda-vir protection when expressed in E. coli.",
    "definition_source": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps2.md",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "GAPS2",
        "synonym_type": "EXACT_SYNONYM",
        "source": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps2.md"
      },
      {
        "synonym_text": "GAPS2__GAPS2",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/s41564-024-01840-5",
        "snippet": "We reveal four anti-phage defence systems encoded within GMT islands and further characterize one system, GAPS1, showing it is triggered by a phage capsid protein to induce cell dormancy",
        "notes": "Mahata et al. identify four anti-phage defense systems in Gamma-Mobile-Trio islands."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps2.md",
        "snippet": "The GAPS2 system is composed of a single protein. It was found in Gamma-Mobile-Trio (GMT) protein containing genomic island in Vibrio, and cloned into E. coli K-12 :ref{doi=10.1101/2023.03.28.534373}. The name GAPS derives from the \"GMT-encoded Anti-Phage System\" acronym.",
        "notes": "The DefenseFinder wiki describes GAPS2 as a single-protein GMT-encoded system cloned from Vibrio into E. coli K-12."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps2.md",
        "snippet": "GAPS2 is composed of a single protein with a DNA BRCT domains :ref{doi=10.4161/cc.10.15.16312}.",
        "notes": "The DefenseFinder wiki reports a DNA BRCT domain in the single GAPS2 protein."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps2.md",
        "snippet": "As far as we are aware, the molecular mechanism is unknown.",
        "notes": "The DefenseFinder wiki records the GAPS2 mechanism as unknown."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps2.md",
        "snippet": "The GAPS2 system in *Mannheimia sp. USDA-ARS-USMARC-1261* (GCF_000521605.1, NZ_CP006942) is composed of 1 protein: GAPS2 (WP_025236539.1)",
        "notes": "The DefenseFinder wiki illustrates a predicted single-protein GAPS2 locus in RefSeq assembly GCF_000521605.1 on NZ_CP006942."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps2.md",
        "snippet": "Mahata_2023[<a href='https://doi.org/10.1101/2023.03.28.534373'>Mahata et al., 2023</a>] --> Origin_0\n    Origin_0[Vibrio parahaemolyticus \n<a href='https://ncbi.nlm.nih.gov/protein/WP_174208646.1'>WP_174208646.1</a>] --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> P1-vir & Lambda-vir",
        "notes": "The DefenseFinder experimental-validation diagram links Mahata et al. to a Vibrio parahaemolyticus GAPS2 source locus expressed in E. coli against P1-vir and Lambda-vir."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps2.md",
        "snippet": "subgraph Title4[Protects against]\n        P1-vir\n        Lambda-vir",
        "notes": "The DefenseFinder experimental-validation diagram lists P1-vir and Lambda-vir in the GAPS2 protects-against subgraph."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "GAPS2 | 10\\.1101/2023\\.03\\.28\\.534373 | Gamma-Mobile-Trio systems define a new class of mobile elements rich in bacterial defensive and offensive tools",
        "notes": "The DefenseFinder article registry maps the named GAPS2 system to the Mahata et al. preprint."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "GAPS2\tGAPS2\t1\t1\tGAPS2__GAPS2\t\t\t",
        "notes": "The DefenseFinder rules table models GAPS2 as a single-profile system requiring GAPS2__GAPS2."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| GAPS2__GAPS2                                     | GAPS2__GAPS2                                     | GAPS2                  | Custom                  | 100    |",
        "notes": "The DefenseFinder HMM inventory records GAPS2__GAPS2 under the GAPS2 system namespace."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "gaps2_locus_restricts_phages",
        "title": "GAPS2 loci protect against P1-vir and lambda-vir",
        "description": "Conservative system-level sketch linking GAPS2 locus possession to protection against P1-vir and lambda-vir.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures GAPS2 as a named single-profile DefenseFinder phage-defense system while leaving natural host breadth, the molecular activity of the BRCT-domain GAPS2 component, the phage trigger, and exact GAPS2__GAPS2 profile-to-protein correspondence unresolved.",
        "nodes": [
          {
            "node_id": "gaps2_locus",
            "label": "GAPS2 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A GMT-encoded phage-defense locus represented by the GAPS2__GAPS2 DefenseFinder profile."
          },
          {
            "node_id": "gaps2_listed_phage_protection",
            "label": "P1-vir and lambda-vir protection",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Protection against P1-vir and lambda-vir by GAPS2."
          },
          {
            "node_id": "gaps2_system_trait",
            "label": "GAPS2 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000380",
            "description": "Possession of a genome-encoded GAPS2 phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "gaps2_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "gaps2_listed_phage_protection",
            "description": "The DefenseFinder wiki links a Vibrio parahaemolyticus GAPS2 locus from Mahata et al. to protection against P1-vir and lambda-vir, and DefenseFinder models GAPS2 through the GAPS2__GAPS2 profile.",
            "evidence": [
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps2.md",
                "snippet": "The GAPS2 system is composed of a single protein. It was found in Gamma-Mobile-Trio (GMT) protein containing genomic island in Vibrio, and cloned into E. coli K-12 :ref{doi=10.1101/2023.03.28.534373}. The name GAPS derives from the \"GMT-encoded Anti-Phage System\" acronym.",
                "notes": "The DefenseFinder wiki describes GAPS2 as a single-protein GMT-encoded system cloned from Vibrio into E. coli K-12."
              },
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps2.md",
                "snippet": "Mahata_2023[<a href='https://doi.org/10.1101/2023.03.28.534373'>Mahata et al., 2023</a>] --> Origin_0\n    Origin_0[Vibrio parahaemolyticus \n<a href='https://ncbi.nlm.nih.gov/protein/WP_174208646.1'>WP_174208646.1</a>] --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> P1-vir & Lambda-vir",
                "notes": "The DefenseFinder experimental-validation diagram links Mahata et al. to a Vibrio parahaemolyticus GAPS2 source locus expressed in E. coli against P1-vir and Lambda-vir."
              },
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps2.md",
                "snippet": "subgraph Title4[Protects against]\n        P1-vir\n        Lambda-vir",
                "notes": "The DefenseFinder experimental-validation diagram lists P1-vir and Lambda-vir in the GAPS2 protects-against subgraph."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "GAPS2\tGAPS2\t1\t1\tGAPS2__GAPS2\t\t\t",
                "notes": "The DefenseFinder rules table models GAPS2 as a single-profile system requiring GAPS2__GAPS2."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| GAPS2__GAPS2                                     | GAPS2__GAPS2                                     | GAPS2                  | Custom                  | 100    |",
                "notes": "The DefenseFinder HMM inventory records GAPS2__GAPS2 under the GAPS2 system namespace."
              }
            ]
          },
          {
            "subject": "gaps2_listed_phage_protection",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "gaps2_system_trait",
            "description": "Protection against P1-vir and lambda-vir realizes the GAPS2 system trait.",
            "evidence": [
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps2.md",
                "snippet": "Mahata_2023[<a href='https://doi.org/10.1101/2023.03.28.534373'>Mahata et al., 2023</a>] --> Origin_0\n    Origin_0[Vibrio parahaemolyticus \n<a href='https://ncbi.nlm.nih.gov/protein/WP_174208646.1'>WP_174208646.1</a>] --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> P1-vir & Lambda-vir",
                "notes": "The DefenseFinder experimental-validation diagram links Mahata et al. to a Vibrio parahaemolyticus GAPS2 source locus expressed in E. coli against P1-vir and Lambda-vir."
              },
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps2.md",
                "snippet": "subgraph Title4[Protects against]\n        P1-vir\n        Lambda-vir",
                "notes": "The DefenseFinder experimental-validation diagram lists P1-vir and Lambda-vir in the GAPS2 protects-against subgraph."
              }
            ]
          },
          {
            "subject": "gaps2_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "GAPS2 system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-024-01840-5",
                "snippet": "We reveal four anti-phage defence systems encoded within GMT islands and further characterize one system, GAPS1, showing it is triggered by a phage capsid protein to induce cell dormancy",
                "notes": "Mahata et al. identify four anti-phage defense systems in Gamma-Mobile-Trio islands."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "GAPS2 | 10\\.1101/2023\\.03\\.28\\.534373 | Gamma-Mobile-Trio systems define a new class of mobile elements rich in bacterial defensive and offensive tools",
                "notes": "The DefenseFinder article registry maps the named GAPS2 system to the Mahata et al. preprint."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "GAPS2\tGAPS2\t1\t1\tGAPS2__GAPS2\t\t\t",
                "notes": "The DefenseFinder rules table models GAPS2 as a single-profile system requiring GAPS2__GAPS2."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "gaps2-mechanism-gap",
        "prompt": "Resolve GAPS2 natural host breadth, BRCT-domain activity, phage trigger specificity, and exact GAPS2__GAPS2 profile-to-protein correspondence before minting narrower GAPS2 mechanism traits.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Mahata et al. support GAPS2 as a GMT-encoded anti-phage defense system that protects E. coli against P1-vir and lambda-vir when expressed from a Vibrio parahaemolyticus locus, and DefenseFinder represents GAPS2 as a single-profile system. Natural host breadth, BRCT-domain activity, the phage trigger, and exact profile-to-protein correspondence remain unresolved.",
        "evidence": [
          {
            "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps2.md",
            "snippet": "The GAPS2 system is composed of a single protein. It was found in Gamma-Mobile-Trio (GMT) protein containing genomic island in Vibrio, and cloned into E. coli K-12 :ref{doi=10.1101/2023.03.28.534373}. The name GAPS derives from the \"GMT-encoded Anti-Phage System\" acronym.",
            "notes": "The DefenseFinder wiki describes GAPS2 as a single-protein GMT-encoded system cloned from Vibrio into E. coli K-12."
          },
          {
            "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps2.md",
            "snippet": "GAPS2 is composed of a single protein with a DNA BRCT domains :ref{doi=10.4161/cc.10.15.16312}.",
            "notes": "The DefenseFinder wiki reports a DNA BRCT domain in the single GAPS2 protein."
          },
          {
            "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps2.md",
            "snippet": "As far as we are aware, the molecular mechanism is unknown.",
            "notes": "The DefenseFinder wiki records the GAPS2 mechanism as unknown."
          },
          {
            "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps2.md",
            "snippet": "Mahata_2023[<a href='https://doi.org/10.1101/2023.03.28.534373'>Mahata et al., 2023</a>] --> Origin_0\n    Origin_0[Vibrio parahaemolyticus \n<a href='https://ncbi.nlm.nih.gov/protein/WP_174208646.1'>WP_174208646.1</a>] --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> P1-vir & Lambda-vir",
            "notes": "The DefenseFinder experimental-validation diagram links Mahata et al. to a Vibrio parahaemolyticus GAPS2 source locus expressed in E. coli against P1-vir and Lambda-vir."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "snippet": "GAPS2\tGAPS2\t1\t1\tGAPS2__GAPS2\t\t\t",
            "notes": "The DefenseFinder rules table models GAPS2 as a single-profile system requiring GAPS2__GAPS2."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| GAPS2__GAPS2                                     | GAPS2__GAPS2                                     | GAPS2                  | Custom                  | 100    |",
            "notes": "The DefenseFinder HMM inventory records GAPS2__GAPS2 under the GAPS2 system namespace."
          }
        ],
        "attaches_to": [
          "causal_graphs#gaps2_locus_restricts_phages"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-26"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-26T11:26:41Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted GAPS2 system as a DOI- and DefenseFinder-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v257.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-26T11:26:42Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed GAPS2 system canonical_examples and left them empty because the current sources support a Vibrio parahaemolyticus accession-level experimental validation graph, a DefenseFinder system model, and a RefSeq Mannheimia sp. example, but not a direct native microbial isolate exemplar with experimentally verified endogenous GAPS2 activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000379",
    "label": "GAPS4 system",
    "definition": "A phage defense system in which an organism possesses a GMT-encoded GAPS4 locus represented by DefenseFinder as a two-profile model, GAPS4__GAPS4a and GAPS4__GAPS4b, and experimentally linked to T7, T4, P1-vir, and lambda-vir protection when expressed in E. coli.",
    "definition_source": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps4.md",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "GAPS4",
        "synonym_type": "EXACT_SYNONYM",
        "source": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps4.md"
      },
      {
        "synonym_text": "GAPS4__GAPS4a",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "GAPS4__GAPS4b",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/s41564-024-01840-5",
        "snippet": "We reveal four anti-phage defence systems encoded within GMT islands and further characterize one system, GAPS1, showing it is triggered by a phage capsid protein to induce cell dormancy",
        "notes": "Mahata et al. identify four anti-phage defense systems in Gamma-Mobile-Trio islands."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps4.md",
        "snippet": "GAPS4 is a two genes system (GAPS4a and GAPS4b). GAPS stands for GMT-encoded Anti-Phage System.",
        "notes": "The DefenseFinder wiki describes GAPS4 as a two-gene GMT-encoded anti-phage system."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps4.md",
        "snippet": "GAPS4 is present in both Gram-positive and Gram-negative GAPS4 activity was assessed in *E. coli* and was shown to be active against T4, P1-vir and lambda-vir and to reduce lysis plaque size of T7 :ref{doi=10.1101/2023.03.28.534373}.",
        "notes": "The DefenseFinder wiki summarizes GAPS4 activity against T4, P1-vir, lambda-vir, and T7 plaque lysis in an E. coli assay."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps4.md",
        "snippet": "GAPS4a is a nuclease containing a domain from the PDDEXK clan (CL0236) suggesting that the GAPS4 defense system is acting via DNA degradation. Both genes are required for phage defense and were predicted to form a heterodimer. It was shown that the system causes host DNA degradation upon infection by lambda-vir only, which would suggest that GAPS4 is an abortive infection system :ref{doi=10.1101/2023.03.28.534373}.",
        "notes": "The DefenseFinder wiki summarizes evidence for PDDEXK-domain GAPS4a, dual-gene requirement, and lambda-vir-associated host DNA degradation."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps4.md",
        "snippet": "The GAPS4 system in *Hafnia alvei* (GCF_902387815.1, NZ_LR699008) is composed of 2 proteins GAPS4a (WP_111329122.1) GAPS4b (WP_111329123.1)",
        "notes": "The DefenseFinder wiki illustrates a predicted two-protein GAPS4 locus in RefSeq assembly GCF_902387815.1 on NZ_LR699008."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps4.md",
        "snippet": "Mahata_2023[<a href='https://doi.org/10.1101/2023.03.28.534373'>Mahata et al., 2023</a>] --> Origin_0\n    Origin_0[Vibrio parahaemolyticus \n<a href='https://ncbi.nlm.nih.gov/protein/WP_055466293.1'>WP_055466293.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_055466294.1'>WP_055466294.1</a>] --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> T7 & T4 & P1-vir & Lambda-vir",
        "notes": "The DefenseFinder experimental-validation diagram links Mahata et al. to a Vibrio parahaemolyticus GAPS4 source locus expressed in E. coli against T7, T4, P1-vir, and Lambda-vir."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps4.md",
        "snippet": "subgraph Title4[Protects against]\n        T7\n        T4\n        P1-vir\n        Lambda-vir",
        "notes": "The DefenseFinder experimental-validation diagram lists T7, T4, P1-vir, and Lambda-vir in the GAPS4 protects-against subgraph."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "GAPS4 | 10\\.1101/2023\\.03\\.28\\.534373 | Gamma-Mobile-Trio systems define a new class of mobile elements rich in bacterial defensive and offensive tools",
        "notes": "The DefenseFinder article registry maps the named GAPS4 system to the Mahata et al. preprint."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "GAPS4\tGAPS4\t2\t2\tGAPS4__GAPS4a, GAPS4__GAPS4b\t\t\t",
        "notes": "The DefenseFinder rules table models GAPS4 as a two-profile system requiring GAPS4__GAPS4a and GAPS4__GAPS4b."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| GAPS4__GAPS4a                                    | GAPS4__GAPS4a                                    | GAPS4                  | Custom                  | 20     |",
        "notes": "The DefenseFinder HMM inventory records GAPS4__GAPS4a under the GAPS4 system namespace."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| GAPS4__GAPS4b                                    | GAPS4__GAPS4b                                    | GAPS4                  | Custom                  | 20     |",
        "notes": "The DefenseFinder HMM inventory records GAPS4__GAPS4b under the GAPS4 system namespace."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "gaps4_locus_restricts_phages",
        "title": "GAPS4 loci protect against T7, T4, P1-vir, and lambda-vir",
        "description": "Conservative system-level sketch linking GAPS4 locus possession to protection against T7, T4, P1-vir, and lambda-vir.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures GAPS4 as a named two-profile DefenseFinder phage-defense system while leaving natural host breadth, the lambda-vir trigger of host DNA degradation, the abortive-infection mechanism, and exact GAPS4a/GAPS4b profile-to-protein correspondence unresolved.",
        "nodes": [
          {
            "node_id": "gaps4_locus",
            "label": "GAPS4 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A GMT-encoded phage-defense locus represented by the GAPS4a and GAPS4b DefenseFinder profiles."
          },
          {
            "node_id": "gaps4_listed_phage_protection",
            "label": "T7, T4, P1-vir, and lambda-vir protection",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Protection against T7, T4, P1-vir, and lambda-vir by GAPS4."
          },
          {
            "node_id": "gaps4_system_trait",
            "label": "GAPS4 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000379",
            "description": "Possession of a genome-encoded GAPS4 phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "gaps4_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "gaps4_listed_phage_protection",
            "description": "The DefenseFinder wiki links a Vibrio parahaemolyticus GAPS4 locus from Mahata et al. to protection against T7, T4, P1-vir, and lambda-vir, and DefenseFinder models GAPS4 through GAPS4a and GAPS4b profiles.",
            "evidence": [
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps4.md",
                "snippet": "GAPS4 is a two genes system (GAPS4a and GAPS4b). GAPS stands for GMT-encoded Anti-Phage System.",
                "notes": "The DefenseFinder wiki describes GAPS4 as a two-gene GMT-encoded anti-phage system."
              },
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps4.md",
                "snippet": "GAPS4 is present in both Gram-positive and Gram-negative GAPS4 activity was assessed in *E. coli* and was shown to be active against T4, P1-vir and lambda-vir and to reduce lysis plaque size of T7 :ref{doi=10.1101/2023.03.28.534373}.",
                "notes": "The DefenseFinder wiki summarizes GAPS4 activity against T4, P1-vir, lambda-vir, and T7 plaque lysis in an E. coli assay."
              },
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps4.md",
                "snippet": "Mahata_2023[<a href='https://doi.org/10.1101/2023.03.28.534373'>Mahata et al., 2023</a>] --> Origin_0\n    Origin_0[Vibrio parahaemolyticus \n<a href='https://ncbi.nlm.nih.gov/protein/WP_055466293.1'>WP_055466293.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_055466294.1'>WP_055466294.1</a>] --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> T7 & T4 & P1-vir & Lambda-vir",
                "notes": "The DefenseFinder experimental-validation diagram links Mahata et al. to a Vibrio parahaemolyticus GAPS4 source locus expressed in E. coli against T7, T4, P1-vir, and Lambda-vir."
              },
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps4.md",
                "snippet": "subgraph Title4[Protects against]\n        T7\n        T4\n        P1-vir\n        Lambda-vir",
                "notes": "The DefenseFinder experimental-validation diagram lists T7, T4, P1-vir, and Lambda-vir in the GAPS4 protects-against subgraph."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "GAPS4\tGAPS4\t2\t2\tGAPS4__GAPS4a, GAPS4__GAPS4b\t\t\t",
                "notes": "The DefenseFinder rules table models GAPS4 as a two-profile system requiring GAPS4__GAPS4a and GAPS4__GAPS4b."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| GAPS4__GAPS4a                                    | GAPS4__GAPS4a                                    | GAPS4                  | Custom                  | 20     |",
                "notes": "The DefenseFinder HMM inventory records GAPS4__GAPS4a under the GAPS4 system namespace."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| GAPS4__GAPS4b                                    | GAPS4__GAPS4b                                    | GAPS4                  | Custom                  | 20     |",
                "notes": "The DefenseFinder HMM inventory records GAPS4__GAPS4b under the GAPS4 system namespace."
              }
            ]
          },
          {
            "subject": "gaps4_listed_phage_protection",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "gaps4_system_trait",
            "description": "Protection against T7, T4, P1-vir, and lambda-vir realizes the GAPS4 system trait.",
            "evidence": [
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps4.md",
                "snippet": "GAPS4 is present in both Gram-positive and Gram-negative GAPS4 activity was assessed in *E. coli* and was shown to be active against T4, P1-vir and lambda-vir and to reduce lysis plaque size of T7 :ref{doi=10.1101/2023.03.28.534373}.",
                "notes": "The DefenseFinder wiki summarizes GAPS4 activity against T4, P1-vir, lambda-vir, and T7 plaque lysis in an E. coli assay."
              },
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps4.md",
                "snippet": "Mahata_2023[<a href='https://doi.org/10.1101/2023.03.28.534373'>Mahata et al., 2023</a>] --> Origin_0\n    Origin_0[Vibrio parahaemolyticus \n<a href='https://ncbi.nlm.nih.gov/protein/WP_055466293.1'>WP_055466293.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_055466294.1'>WP_055466294.1</a>] --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> T7 & T4 & P1-vir & Lambda-vir",
                "notes": "The DefenseFinder experimental-validation diagram links Mahata et al. to a Vibrio parahaemolyticus GAPS4 source locus expressed in E. coli against T7, T4, P1-vir, and Lambda-vir."
              },
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps4.md",
                "snippet": "subgraph Title4[Protects against]\n        T7\n        T4\n        P1-vir\n        Lambda-vir",
                "notes": "The DefenseFinder experimental-validation diagram lists T7, T4, P1-vir, and Lambda-vir in the GAPS4 protects-against subgraph."
              }
            ]
          },
          {
            "subject": "gaps4_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "GAPS4 system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-024-01840-5",
                "snippet": "We reveal four anti-phage defence systems encoded within GMT islands and further characterize one system, GAPS1, showing it is triggered by a phage capsid protein to induce cell dormancy",
                "notes": "Mahata et al. identify four anti-phage defense systems in Gamma-Mobile-Trio islands."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "GAPS4 | 10\\.1101/2023\\.03\\.28\\.534373 | Gamma-Mobile-Trio systems define a new class of mobile elements rich in bacterial defensive and offensive tools",
                "notes": "The DefenseFinder article registry maps the named GAPS4 system to the Mahata et al. preprint."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "GAPS4\tGAPS4\t2\t2\tGAPS4__GAPS4a, GAPS4__GAPS4b\t\t\t",
                "notes": "The DefenseFinder rules table models GAPS4 as a two-profile system requiring GAPS4__GAPS4a and GAPS4__GAPS4b."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "gaps4-mechanism-gap",
        "prompt": "Resolve GAPS4 natural host breadth, lambda-vir host-DNA-degradation triggers, abortive-infection mechanism, and exact GAPS4a/GAPS4b profile-to-protein correspondence before minting narrower GAPS4 mechanism traits.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Mahata et al. support GAPS4 as a GMT-encoded anti-phage defense system that protects E. coli against T7, T4, P1-vir, and lambda-vir when expressed from a Vibrio parahaemolyticus locus, and DefenseFinder represents GAPS4 as a two-profile system. Natural host breadth, the lambda-vir-specific trigger of host DNA degradation, the abortive-infection mechanism, and exact profile-to-protein correspondence remain unresolved.",
        "evidence": [
          {
            "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps4.md",
            "snippet": "GAPS4 is present in both Gram-positive and Gram-negative GAPS4 activity was assessed in *E. coli* and was shown to be active against T4, P1-vir and lambda-vir and to reduce lysis plaque size of T7 :ref{doi=10.1101/2023.03.28.534373}.",
            "notes": "The DefenseFinder wiki summarizes GAPS4 activity against T4, P1-vir, lambda-vir, and T7 plaque lysis in an E. coli assay."
          },
          {
            "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps4.md",
            "snippet": "GAPS4a is a nuclease containing a domain from the PDDEXK clan (CL0236) suggesting that the GAPS4 defense system is acting via DNA degradation. Both genes are required for phage defense and were predicted to form a heterodimer. It was shown that the system causes host DNA degradation upon infection by lambda-vir only, which would suggest that GAPS4 is an abortive infection system :ref{doi=10.1101/2023.03.28.534373}.",
            "notes": "The DefenseFinder wiki summarizes evidence for PDDEXK-domain GAPS4a, dual-gene requirement, and lambda-vir-associated host DNA degradation."
          },
          {
            "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps4.md",
            "snippet": "Mahata_2023[<a href='https://doi.org/10.1101/2023.03.28.534373'>Mahata et al., 2023</a>] --> Origin_0\n    Origin_0[Vibrio parahaemolyticus \n<a href='https://ncbi.nlm.nih.gov/protein/WP_055466293.1'>WP_055466293.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_055466294.1'>WP_055466294.1</a>] --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> T7 & T4 & P1-vir & Lambda-vir",
            "notes": "The DefenseFinder experimental-validation diagram links Mahata et al. to a Vibrio parahaemolyticus GAPS4 source locus expressed in E. coli against T7, T4, P1-vir, and Lambda-vir."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "snippet": "GAPS4\tGAPS4\t2\t2\tGAPS4__GAPS4a, GAPS4__GAPS4b\t\t\t",
            "notes": "The DefenseFinder rules table models GAPS4 as a two-profile system requiring GAPS4__GAPS4a and GAPS4__GAPS4b."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| GAPS4__GAPS4a                                    | GAPS4__GAPS4a                                    | GAPS4                  | Custom                  | 20     |",
            "notes": "The DefenseFinder HMM inventory records GAPS4__GAPS4a under the GAPS4 system namespace."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| GAPS4__GAPS4b                                    | GAPS4__GAPS4b                                    | GAPS4                  | Custom                  | 20     |",
            "notes": "The DefenseFinder HMM inventory records GAPS4__GAPS4b under the GAPS4 system namespace."
          }
        ],
        "attaches_to": [
          "causal_graphs#gaps4_locus_restricts_phages"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-26"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-26T10:47:13Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted GAPS4 system as a DOI- and DefenseFinder-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v256.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-26T10:47:14Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed GAPS4 system canonical_examples and left them empty because the current sources support a Vibrio parahaemolyticus accession-level experimental validation graph, a DefenseFinder system model, and a RefSeq Hafnia alvei example, but not a direct native microbial isolate exemplar with experimentally verified endogenous GAPS4 activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000381",
    "label": "GAPS6 system",
    "definition": "A phage defense system in which an organism possesses a GMT-encoded GAPS6 locus represented by DefenseFinder as a two-profile model, GAPS6__GAPS6a and GAPS6__GAPS6b, and experimentally linked to T7, T4, P1-vir, and lambda-vir protection when expressed in E. coli.",
    "definition_source": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps6.md",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "GAPS6",
        "synonym_type": "EXACT_SYNONYM",
        "source": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps6.md"
      },
      {
        "synonym_text": "GAPS6__GAPS6a",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "GAPS6__GAPS6b",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/s41564-024-01840-5",
        "snippet": "We reveal four anti-phage defence systems encoded within GMT islands and further characterize one system, GAPS1, showing it is triggered by a phage capsid protein to induce cell dormancy",
        "notes": "Mahata et al. identify four anti-phage defense systems in Gamma-Mobile-Trio islands."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps6.md",
        "snippet": "GAPS6 is composed of two proteins, [GAPS6a](https://www.ncbi.nlm.nih.gov/protein/WP_248387294.1/) and [GAPS6b](https://www.ncbi.nlm.nih.gov/protein/WP_248387295.1/). These two proteins are encoded together in diverse Gram-negative bacteria.",
        "notes": "The DefenseFinder wiki describes GAPS6 as a two-protein system with GAPS6a and GAPS6b encoded together."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps6.md",
        "snippet": "GAPS6b is essential for the defense phenotype, however it is not known whether GAPS6b could be sufficient.",
        "notes": "The DefenseFinder wiki reports that GAPS6b is essential for GAPS6 defense but leaves GAPS6b sufficiency unresolved."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps6.md",
        "snippet": "GAPS6b is composed of TPR repeats at the N-terminus, possibly allowing ligand binding and a predicted RNAse domain (PINc, PF08745.14) at the C-terminus. PINc domains have been implicated as toxins in bacterial toxin-antitoxin modules :ref{doi=10.1093/protein/gzq081}. The PINc domain is required for the anti-phage defense activity of GAPS6.",
        "notes": "The DefenseFinder wiki reports that GAPS6b carries TPR repeats and a PINc domain required for GAPS6 anti-phage activity."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps6.md",
        "snippet": "The GAPS6 system in *Escherichia coli* (GCF_013372365.1, NZ_CP054227) is composed of 2 proteins GAPS6b (WP_096985931.1) GAPS6a (WP_000346990.1)",
        "notes": "The DefenseFinder wiki illustrates a predicted two-protein GAPS6 locus in RefSeq assembly GCF_013372365.1 on NZ_CP054227."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps6.md",
        "snippet": "Mahata_2023[<a href='https://doi.org/10.1101/2023.03.28.534373'>Mahata et al., 2023</a>] --> Origin_0\n    Origin_0[Vibrio parahaemolyticus \n<a href='https://ncbi.nlm.nih.gov/protein/WP_248387294.1'>WP_248387294.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_248387295.1'>WP_248387295.1</a>] --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> T7 & T4 & P1-vir & Lambda-vir",
        "notes": "The DefenseFinder experimental-validation diagram links Mahata et al. to a Vibrio parahaemolyticus GAPS6 source locus expressed in E. coli against T7, T4, P1-vir, and Lambda-vir."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "GAPS6 | 10\\.1101/2023\\.03\\.28\\.534373 | Gamma-Mobile-Trio systems define a new class of mobile elements rich in bacterial defensive and offensive tools",
        "notes": "The DefenseFinder article registry maps the named GAPS6 system to the Mahata et al. preprint."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "GAPS6\tGAPS6\t2\t2\tGAPS6__GAPS6a, GAPS6__GAPS6b\t\t\t",
        "notes": "The DefenseFinder rules table models GAPS6 as a two-profile system requiring GAPS6__GAPS6a and GAPS6__GAPS6b."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| GAPS6__GAPS6a                                    | GAPS6__GAPS6a                                    | GAPS6                  | Custom                  | 20     |",
        "notes": "The DefenseFinder HMM inventory records GAPS6__GAPS6a under the GAPS6 system namespace."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| GAPS6__GAPS6b                                    | GAPS6__GAPS6b                                    | GAPS6                  | Custom                  | 20     |",
        "notes": "The DefenseFinder HMM inventory records GAPS6__GAPS6b under the GAPS6 system namespace."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "gaps6_locus_restricts_phages",
        "title": "GAPS6 loci protect against T7, T4, P1-vir, and lambda-vir",
        "description": "Conservative system-level sketch linking GAPS6 locus possession to protection against T7, T4, P1-vir, and lambda-vir.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures GAPS6 as a named two-profile DefenseFinder phage-defense system while leaving natural host breadth, the activity of GAPS6a, GAPS6b sufficiency and trigger specificity, and exact GAPS6a/GAPS6b profile-to-protein correspondence unresolved.",
        "nodes": [
          {
            "node_id": "gaps6_locus",
            "label": "GAPS6 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A GMT-encoded phage-defense locus represented by the GAPS6__GAPS6a and GAPS6__GAPS6b DefenseFinder profiles."
          },
          {
            "node_id": "gaps6_listed_phage_protection",
            "label": "T7, T4, P1-vir, and lambda-vir protection",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Protection against T7, T4, P1-vir, and lambda-vir by GAPS6."
          },
          {
            "node_id": "gaps6_system_trait",
            "label": "GAPS6 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000381",
            "description": "Possession of a genome-encoded GAPS6 phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "gaps6_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "gaps6_listed_phage_protection",
            "description": "The DefenseFinder wiki links a Vibrio parahaemolyticus GAPS6 locus from Mahata et al. to protection against T7, T4, P1-vir, and lambda-vir, and DefenseFinder models GAPS6 through two mandatory profiles.",
            "evidence": [
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps6.md",
                "snippet": "GAPS6 is composed of two proteins, [GAPS6a](https://www.ncbi.nlm.nih.gov/protein/WP_248387294.1/) and [GAPS6b](https://www.ncbi.nlm.nih.gov/protein/WP_248387295.1/). These two proteins are encoded together in diverse Gram-negative bacteria.",
                "notes": "The DefenseFinder wiki describes GAPS6 as a two-protein system with GAPS6a and GAPS6b encoded together."
              },
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps6.md",
                "snippet": "Mahata_2023[<a href='https://doi.org/10.1101/2023.03.28.534373'>Mahata et al., 2023</a>] --> Origin_0\n    Origin_0[Vibrio parahaemolyticus \n<a href='https://ncbi.nlm.nih.gov/protein/WP_248387294.1'>WP_248387294.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_248387295.1'>WP_248387295.1</a>] --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> T7 & T4 & P1-vir & Lambda-vir",
                "notes": "The DefenseFinder experimental-validation diagram links Mahata et al. to a Vibrio parahaemolyticus GAPS6 source locus expressed in E. coli against T7, T4, P1-vir, and Lambda-vir."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "GAPS6\tGAPS6\t2\t2\tGAPS6__GAPS6a, GAPS6__GAPS6b\t\t\t",
                "notes": "The DefenseFinder rules table models GAPS6 as a two-profile system requiring GAPS6__GAPS6a and GAPS6__GAPS6b."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| GAPS6__GAPS6a                                    | GAPS6__GAPS6a                                    | GAPS6                  | Custom                  | 20     |",
                "notes": "The DefenseFinder HMM inventory records GAPS6__GAPS6a under the GAPS6 system namespace."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| GAPS6__GAPS6b                                    | GAPS6__GAPS6b                                    | GAPS6                  | Custom                  | 20     |",
                "notes": "The DefenseFinder HMM inventory records GAPS6__GAPS6b under the GAPS6 system namespace."
              }
            ]
          },
          {
            "subject": "gaps6_listed_phage_protection",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "gaps6_system_trait",
            "description": "Protection against T7, T4, P1-vir, and lambda-vir realizes the GAPS6 system trait.",
            "evidence": [
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps6.md",
                "snippet": "Mahata_2023[<a href='https://doi.org/10.1101/2023.03.28.534373'>Mahata et al., 2023</a>] --> Origin_0\n    Origin_0[Vibrio parahaemolyticus \n<a href='https://ncbi.nlm.nih.gov/protein/WP_248387294.1'>WP_248387294.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_248387295.1'>WP_248387295.1</a>] --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> T7 & T4 & P1-vir & Lambda-vir",
                "notes": "The DefenseFinder experimental-validation diagram links Mahata et al. to a Vibrio parahaemolyticus GAPS6 source locus expressed in E. coli against T7, T4, P1-vir, and Lambda-vir."
              }
            ]
          },
          {
            "subject": "gaps6_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "GAPS6 system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-024-01840-5",
                "snippet": "We reveal four anti-phage defence systems encoded within GMT islands and further characterize one system, GAPS1, showing it is triggered by a phage capsid protein to induce cell dormancy",
                "notes": "Mahata et al. identify four anti-phage defense systems in Gamma-Mobile-Trio islands."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "GAPS6 | 10\\.1101/2023\\.03\\.28\\.534373 | Gamma-Mobile-Trio systems define a new class of mobile elements rich in bacterial defensive and offensive tools",
                "notes": "The DefenseFinder article registry maps the named GAPS6 system to the Mahata et al. preprint."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "GAPS6\tGAPS6\t2\t2\tGAPS6__GAPS6a, GAPS6__GAPS6b\t\t\t",
                "notes": "The DefenseFinder rules table models GAPS6 as a two-profile system requiring GAPS6__GAPS6a and GAPS6__GAPS6b."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "gaps6-mechanism-gap",
        "prompt": "Resolve GAPS6 natural host breadth, GAPS6a activity, GAPS6b sufficiency and trigger specificity, and exact GAPS6a/GAPS6b profile-to-protein correspondence before minting narrower GAPS6 mechanism traits.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Mahata et al. support GAPS6 as a GMT-encoded anti-phage defense system that protects E. coli against T7, T4, P1-vir, and lambda-vir when expressed from a Vibrio parahaemolyticus locus, and DefenseFinder represents GAPS6 as a two-profile system. Natural host breadth, GAPS6a activity, GAPS6b sufficiency, the phage trigger, and exact profile-to-protein correspondence remain unresolved.",
        "evidence": [
          {
            "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps6.md",
            "snippet": "GAPS6 is composed of two proteins, [GAPS6a](https://www.ncbi.nlm.nih.gov/protein/WP_248387294.1/) and [GAPS6b](https://www.ncbi.nlm.nih.gov/protein/WP_248387295.1/). These two proteins are encoded together in diverse Gram-negative bacteria.",
            "notes": "The DefenseFinder wiki describes GAPS6 as a two-protein system with GAPS6a and GAPS6b encoded together."
          },
          {
            "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps6.md",
            "snippet": "GAPS6b is essential for the defense phenotype, however it is not known whether GAPS6b could be sufficient.",
            "notes": "The DefenseFinder wiki reports that GAPS6b is essential for GAPS6 defense but leaves GAPS6b sufficiency unresolved."
          },
          {
            "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps6.md",
            "snippet": "GAPS6b is composed of TPR repeats at the N-terminus, possibly allowing ligand binding and a predicted RNAse domain (PINc, PF08745.14) at the C-terminus. PINc domains have been implicated as toxins in bacterial toxin-antitoxin modules :ref{doi=10.1093/protein/gzq081}. The PINc domain is required for the anti-phage defense activity of GAPS6.",
            "notes": "The DefenseFinder wiki reports that GAPS6b carries TPR repeats and a PINc domain required for GAPS6 anti-phage activity."
          },
          {
            "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps6.md",
            "snippet": "Mahata_2023[<a href='https://doi.org/10.1101/2023.03.28.534373'>Mahata et al., 2023</a>] --> Origin_0\n    Origin_0[Vibrio parahaemolyticus \n<a href='https://ncbi.nlm.nih.gov/protein/WP_248387294.1'>WP_248387294.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_248387295.1'>WP_248387295.1</a>] --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> T7 & T4 & P1-vir & Lambda-vir",
            "notes": "The DefenseFinder experimental-validation diagram links Mahata et al. to a Vibrio parahaemolyticus GAPS6 source locus expressed in E. coli against T7, T4, P1-vir, and Lambda-vir."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "snippet": "GAPS6\tGAPS6\t2\t2\tGAPS6__GAPS6a, GAPS6__GAPS6b\t\t\t",
            "notes": "The DefenseFinder rules table models GAPS6 as a two-profile system requiring GAPS6__GAPS6a and GAPS6__GAPS6b."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| GAPS6__GAPS6a                                    | GAPS6__GAPS6a                                    | GAPS6                  | Custom                  | 20     |",
            "notes": "The DefenseFinder HMM inventory records GAPS6__GAPS6a under the GAPS6 system namespace."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| GAPS6__GAPS6b                                    | GAPS6__GAPS6b                                    | GAPS6                  | Custom                  | 20     |",
            "notes": "The DefenseFinder HMM inventory records GAPS6__GAPS6b under the GAPS6 system namespace."
          }
        ],
        "attaches_to": [
          "causal_graphs#gaps6_locus_restricts_phages"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-26"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-26T11:58:13Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted GAPS6 system as a DOI- and DefenseFinder-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v258.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-26T11:58:14Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed GAPS6 system canonical_examples and left them empty because the current sources support a Vibrio parahaemolyticus accession-level experimental validation graph, a DefenseFinder system model, and a RefSeq Escherichia coli example, but not a direct native microbial isolate exemplar with experimentally verified endogenous GAPS6 activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000336",
    "label": "GasderMIN system",
    "definition": "A phage defense system in which an organism possesses a bacterial gasdermin locus represented by the DefenseFinder GasderMIN__bGSDM profile, whose bGSDM effectors are associated with bacteriophage defense and can be proteolytically activated in characterized bGSDM-protease systems to assemble membrane pores, disrupt membrane integrity, and execute cell death.",
    "definition_source": "DOI:10.1126/science.abj8432",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "GasderMIN",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      },
      {
        "synonym_text": "GasderMIN__bGSDM",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1126/science.abj8432",
        "snippet": "We discovered gasdermin homologs encoded in bacteria that defended against phages and executed cell death.",
        "notes": "Johnson et al. support bacterial gasdermin homologs as phage-defense proteins that execute cell death."
      },
      {
        "reference": "https://pmc.ncbi.nlm.nih.gov/articles/PMC9134750/",
        "snippet": "bGSDM-protease systems are found in diverse bacteria and archaea, as well as in metagenomic samples of prokaryotic origin",
        "notes": "Johnson et al. report bGSDM-protease systems across bacteria, archaea, and prokaryotic metagenomic samples, supporting curation above one engineered locus."
      },
      {
        "reference": "https://pmc.ncbi.nlm.nih.gov/articles/PMC9134750/",
        "snippet": "a four gene operon from Lysobacter enzymogenes exhibited robust defense against coliphages T4, T5, and T6",
        "notes": "Johnson et al. experimentally tested a Lysobacter enzymogenes bGSDM-containing operon that defended against coliphages T4, T5, and T6."
      },
      {
        "reference": "https://pmc.ncbi.nlm.nih.gov/articles/PMC9134750/",
        "snippet": "Deletion of the bGSDM gene from the Lysobacter operon abolished protection",
        "notes": "Deletion of the bGSDM gene from the Lysobacter operon abolished the observed phage protection."
      },
      {
        "reference": "DOI:10.1126/science.abj8432",
        "snippet": "Bacterial gasdermins were activated by dedicated caspase-like proteases that catalyzed site-specific cleavage and the removal of an inhibitory C-terminal peptide.",
        "notes": "Johnson et al. connect bacterial gasdermin activation to dedicated caspase-like proteases that remove an inhibitory C-terminal peptide."
      },
      {
        "reference": "DOI:10.1126/science.abj8432",
        "snippet": "Release of autoinhibition induced the assembly of large and heterogeneous pores that disrupted membrane integrity.",
        "notes": "Johnson et al. support pore assembly and membrane disruption as outputs of bacterial gasdermin autoinhibition release."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "GasderMIN | 10\\.1101/2021\\.06\\.07\\.447441 | Bacterial gasdermins reveal an ancient mechanism of cell death",
        "notes": "The DefenseFinder article registry maps the GasderMIN model namespace to the Johnson et al. bacterial gasdermin preprint, later published under DOI:10.1126/science.abj8432."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| GasderMIN__bGSDM                                 | GasderMIN__bGSDM___bGSDM                         | GasderMIN              | Custom                  | 50     |",
        "notes": "The DefenseFinder HMM inventory records the bGSDM profile under the GasderMIN model namespace."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "GasderMIN\tGasderMIN\t1\t1\tGasderMIN__bGSDM\t\t\t",
        "notes": "The DefenseFinder rules table models GasderMIN as a one-mandatory-profile system requiring GasderMIN__bGSDM."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "CARD_NLR\tCARD_NLR_GasderMIN\t1\t3\tGasderMIN__bGSDM\tCARD_NLR__CARD_Protease, CARD_NLR__NLR_new, CARD_NLR__Trypsin\tCARD_NLR__Endonuclease, CARD_NLR__Endonuclease_new, CARD_NLR__Phospho, CARD_NLR__Phospho_Trypsin, CARD_NLR__Subtilase, CARD_NLR__Subtilase_long_new, CARD_NLR__Subtilase_small_new, CARD_NLR__Trypsin_Phospho, CARD_NLR__Trypsine_Endonuclease_new\t",
        "notes": "The DefenseFinder rules table also models a CARD_NLR_GasderMIN subtype with GasderMIN__bGSDM as its mandatory profile."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:69",
        "taxon_label": "Lysobacter enzymogenes",
        "note": "Johnson et al. showed that a Lysobacter enzymogenes bGSDM-containing operon provided robust defense against coliphages T4, T5, and T6 in an Escherichia coli heterologous assay, and that deleting the bGSDM gene abolished protection.",
        "reference": "DOI:10.1126/science.abj8432"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "gasdermin_proteolysis_triggers_pore_cell_death",
        "title": "GasderMIN activation forms lethal membrane pores",
        "description": "System-level sketch linking a bacterial gasdermin locus to phage defense-system possession and linking characterized bGSDM-protease systems to caspase-like proteolytic activation, gasdermin pore assembly, membrane disruption, and cell death.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures GasderMIN as a named DefenseFinder single-mandatory-profile system supported by Johnson et al. bacterial gasdermin experiments while leaving the natural phage trigger, the universality of adjacent protease activation, the full family breadth, and CARD-NLR-associated gasdermin variants unresolved.",
        "nodes": [
          {
            "node_id": "gasdermin_locus",
            "label": "bacterial gasdermin locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A bacterial gasdermin phage-defense locus cataloged in DefenseFinder with the GasderMIN__bGSDM profile."
          },
          {
            "node_id": "caspase_like_bgsdm_cleavage",
            "label": "caspase-like bGSDM cleavage",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Site-specific bacterial gasdermin cleavage by a dedicated caspase-like protease."
          },
          {
            "node_id": "gasdermin_pore_assembly",
            "label": "bacterial gasdermin pore assembly",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Assembly of activated bacterial gasdermins into large membrane pores."
          },
          {
            "node_id": "membrane_integrity_disruption",
            "label": "membrane integrity disruption",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Loss of bacterial membrane integrity after gasdermin pore formation."
          },
          {
            "node_id": "gasdermin_cell_death",
            "label": "gasdermin-dependent cell death",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Host cell death executed by activated bacterial gasdermin pores."
          },
          {
            "node_id": "gasdermin_system_trait",
            "label": "GasderMIN system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000336",
            "description": "Possession of a genome-encoded GasderMIN phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "gasdermin_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "caspase_like_bgsdm_cleavage",
            "description": "Characterized bacterial gasdermin-protease loci can encode dedicated caspase-like proteases that cleave bGSDM effectors and remove their inhibitory C-terminal peptide.",
            "evidence": [
              {
                "reference": "https://pmc.ncbi.nlm.nih.gov/articles/PMC9134750/",
                "snippet": "bGSDM-protease systems are found in diverse bacteria and archaea, as well as in metagenomic samples of prokaryotic origin",
                "notes": "Johnson et al. describe bGSDM-protease systems across prokaryotic genomes and metagenomes."
              },
              {
                "reference": "DOI:10.1126/science.abj8432",
                "snippet": "Bacterial gasdermins were activated by dedicated caspase-like proteases that catalyzed site-specific cleavage and the removal of an inhibitory C-terminal peptide.",
                "notes": "Johnson et al. support caspase-like proteases as direct activators of bacterial gasdermins."
              }
            ]
          },
          {
            "subject": "caspase_like_bgsdm_cleavage",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "gasdermin_pore_assembly",
            "description": "Proteolytic release of the inhibitory bacterial gasdermin peptide induces large pore assembly.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.abj8432",
                "snippet": "Release of autoinhibition induced the assembly of large and heterogeneous pores that disrupted membrane integrity.",
                "notes": "Johnson et al. connect release of autoinhibition to gasdermin pore assembly."
              },
              {
                "reference": "https://pmc.ncbi.nlm.nih.gov/articles/PMC9134750/",
                "snippet": "The Runella bGSDM and protease only induced cellular toxicity when expressed together",
                "notes": "The Runella bGSDM system required both bGSDM and its protease to trigger cellular toxicity."
              }
            ]
          },
          {
            "subject": "gasdermin_pore_assembly",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "membrane_integrity_disruption",
            "description": "Activated bacterial gasdermins assemble pores that disrupt membrane integrity.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.abj8432",
                "snippet": "Release of autoinhibition induced the assembly of large and heterogeneous pores that disrupted membrane integrity.",
                "notes": "Johnson et al. link bacterial gasdermin pore assembly to disrupted membrane integrity."
              }
            ]
          },
          {
            "subject": "membrane_integrity_disruption",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "gasdermin_cell_death",
            "description": "Bacterial gasdermin activation can execute cell death through loss of membrane integrity.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.abj8432",
                "snippet": "We discovered gasdermin homologs encoded in bacteria that defended against phages and executed cell death.",
                "notes": "Johnson et al. identify bacterial gasdermins as phage-defense homologs that execute cell death."
              }
            ]
          },
          {
            "subject": "gasdermin_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "gasdermin_system_trait",
            "description": "The GasderMIN DefenseFinder model identifies a GasderMIN__bGSDM profile, and Johnson et al. show that deleting a bGSDM gene can abolish phage protection by a gasdermin operon.",
            "evidence": [
              {
                "reference": "https://pmc.ncbi.nlm.nih.gov/articles/PMC9134750/",
                "snippet": "a four gene operon from Lysobacter enzymogenes exhibited robust defense against coliphages T4, T5, and T6",
                "notes": "The tested Lysobacter enzymogenes bGSDM-containing operon protected cells from coliphage challenge."
              },
              {
                "reference": "https://pmc.ncbi.nlm.nih.gov/articles/PMC9134750/",
                "snippet": "Deletion of the bGSDM gene from the Lysobacter operon abolished protection",
                "notes": "The bGSDM gene was essential for the Lysobacter operon's observed phage protection."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| GasderMIN__bGSDM                                 | GasderMIN__bGSDM___bGSDM                         | GasderMIN              | Custom                  | 50     |",
                "notes": "The DefenseFinder HMM inventory records the bGSDM profile under the GasderMIN model namespace."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "GasderMIN\tGasderMIN\t1\t1\tGasderMIN__bGSDM\t\t\t",
                "notes": "The DefenseFinder rules table models GasderMIN as a one-mandatory-profile system requiring GasderMIN__bGSDM."
              }
            ]
          },
          {
            "subject": "gasdermin_cell_death",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "gasdermin_system_trait",
            "description": "Bacterial gasdermin-mediated cell death realizes the GasderMIN phage-defense-system output in tested bGSDM-protease systems.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.abj8432",
                "snippet": "We discovered gasdermin homologs encoded in bacteria that defended against phages and executed cell death.",
                "notes": "Johnson et al. connect bacterial gasdermin phage defense with cell death."
              }
            ]
          },
          {
            "subject": "gasdermin_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "GasderMIN system possession is a bacterial gasdermin phage-defense-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "GasderMIN | 10\\.1101/2021\\.06\\.07\\.447441 | Bacterial gasdermins reveal an ancient mechanism of cell death",
                "notes": "The DefenseFinder article registry maps the GasderMIN model namespace to the Johnson et al. bacterial gasdermin preprint, later published under DOI:10.1126/science.abj8432."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "GasderMIN\tGasderMIN\t1\t1\tGasderMIN__bGSDM\t\t\t",
                "notes": "The DefenseFinder rules table models GasderMIN as a one-mandatory-profile system requiring GasderMIN__bGSDM."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "gasdermin-family-breadth-and-card-nlr-scope-gap",
        "prompt": "Resolve natural GasderMIN family breadth and CARD-NLR gasdermin context before minting narrower gasdermin subfamily traits.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Johnson et al. experimentally tested a Lysobacter bGSDM-containing operon and mechanistically dissected Runella bGSDM protease-triggered toxicity, while some bacterial gasdermins showed no discernible phage restriction in Escherichia coli and the GasderMIN__bGSDM profile is also used in CARD-NLR detector contexts in the pinned DefenseFinder rules table. This record captures the standalone GasderMIN detector namespace and leaves CARD-NLR-associated gasdermins, natural phage triggers, and broader family boundaries unresolved.",
        "attaches_to": [
          "causal_graphs#gasdermin_proteolysis_triggers_pore_cell_death"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-21"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-21T13:10:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted GasderMIN system as a DOI-backed GENOMICS TraitRecord under the phage defense system parent after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v213.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000127",
    "label": "GC content",
    "definition": "A quality that is describing the percentage of guanine and cytosine nucleotides in genomic DNA, calculated as the ratio of GC base pairs to total base pairs.",
    "definition_source": "DOI:10.1038/nrg2358",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000188"
    ],
    "created_by": "Luke Wang",
    "evidence": [
      {
        "reference": "DOI:10.1038/nrg2358",
        "snippet": "GC content",
        "notes": "Bacterial-genome review supports GC content as a fundamental genome-composition descriptor varying widely across prokaryotic lineages."
      },
      {
        "reference": "DOI:10.1186/1471-2148-10-374",
        "snippet": "GC-biased gene conversion",
        "notes": "Bacterial-GC-content evolution review supports GC-biased gene conversion and mutation bias as the mechanistic drivers of genomic GC composition."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:562",
        "taxon_label": "Escherichia coli",
        "reference": "PMID:9278503",
        "note": "The complete E. coli K-12 genome provides a source-backed whole-genome GC-composition measurement and is used here as a family-level exemplar, distinct from the bin-specific taxa below."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "gc_content_composition_drivers",
        "title": "GC content composition drivers",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This genomics record is a measurement, genomic-element classification, or population-level descriptor rather than one taxon-specific protein mechanism; contextual protein nodes do not receive token UniProt examples.",
        "description": "DOI-backed graph linking mutation bias, GC-biased gene conversion, and selection on codon usage to the genome-wide GC content phenotype, with `is a` edges to the four METPO GC-content bins.",
        "nodes": [
          {
            "node_id": "gc_content_trait",
            "label": "GC content",
            "node_type": "TRAIT",
            "grounding": "METPO:1000127",
            "description": "Percentage of guanine and cytosine nucleotides in genomic DNA."
          },
          {
            "node_id": "genomic_dna",
            "label": "genomic DNA",
            "node_type": "CELLULAR_LOCALIZATION",
            "description": "Bacterial or archaeal chromosomal DNA on which GC composition is measured."
          },
          {
            "node_id": "mutation_bias",
            "label": "GC/AT mutation bias",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Asymmetric substitution rates between GC and AT base pairs across the genome."
          },
          {
            "node_id": "gc_biased_gene_conversion",
            "label": "GC-biased gene conversion",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Recombination-associated process favoring fixation of GC alleles at heterozygous sites."
          },
          {
            "node_id": "codon_usage_selection",
            "label": "selection on codon usage",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Translational and gene-expression selection shaping synonymous-codon GC content."
          },
          {
            "node_id": "gc_high_bin",
            "label": "GC high",
            "node_type": "TRAIT",
            "grounding": "METPO:1000432",
            "description": "METPO GC-high bin (synonym GC_<=42.65; see record)."
          },
          {
            "node_id": "gc_low_bin",
            "label": "GC low",
            "node_type": "TRAIT",
            "grounding": "METPO:1000429",
            "description": "METPO GC-low bin (synonym GC_42.65_57.0; see record)."
          },
          {
            "node_id": "gc_mid1_bin",
            "label": "GC mid1",
            "node_type": "TRAIT",
            "grounding": "METPO:1000430",
            "description": "METPO GC-mid1 bin (synonym GC_>66.3; see record)."
          },
          {
            "node_id": "gc_mid2_bin",
            "label": "GC mid2",
            "node_type": "TRAIT",
            "grounding": "METPO:1000431",
            "description": "METPO GC-mid2 bin (synonym GC_57.0_66.3; see record)."
          },
          {
            "node_id": "cytosine_deamination",
            "label": "cytosine deamination",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Hydrolytic deamination of cytosine to uracil/thymine, a GC-to-AT mutational lesion."
          },
          {
            "node_id": "guanine_oxidation",
            "label": "guanine oxidation (8-oxoG)",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Oxidative damage forming 8-oxoguanine that mispairs and biases the mutational spectrum toward AT."
          },
          {
            "node_id": "dna_repair_replication_system",
            "label": "DNA replication and repair (DRR) system change",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Evolutionary change in DNA replication/repair machinery producing mutational biases that shape GC composition."
          },
          {
            "node_id": "translesion_synthesis",
            "label": "error-prone translesion synthesis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Error-prone DNA synthesis past lesions by specialized polymerases, causally linked to increased genomic GC.",
            "grounding": "GO:0042276"
          }
        ],
        "edges": [
          {
            "subject": "genomic_dna",
            "predicate": "carries",
            "object": "gc_content_trait",
            "description": "Genomic DNA is the substrate on which the GC content phenotype is measured.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrg2358",
                "snippet": "GC content",
                "notes": "Supports GC content as a property of the genomic DNA sequence."
              }
            ]
          },
          {
            "subject": "mutation_bias",
            "predicate": "causes",
            "object": "gc_content_trait",
            "description": "Asymmetric GC/AT mutation bias shapes the equilibrium genome-wide GC content.",
            "evidence": [
              {
                "reference": "DOI:10.1186/1471-2148-10-374",
                "snippet": "mutation bias",
                "notes": "Supports mutation bias as a primary driver of bacterial GC content."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "gc_biased_gene_conversion",
            "predicate": "causes",
            "object": "gc_content_trait",
            "description": "GC-biased gene conversion elevates GC content at recombination hotspots and across the genome.",
            "evidence": [
              {
                "reference": "DOI:10.1186/1471-2148-10-374",
                "snippet": "GC-biased gene conversion",
                "notes": "Supports GC-biased gene conversion as a recombination-driven contributor to GC content."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "codon_usage_selection",
            "predicate": "contributes to",
            "object": "gc_content_trait",
            "description": "Selection on synonymous codon usage contributes to genome-wide GC content patterns.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrg2358",
                "snippet": "codon usage",
                "notes": "Supports translational selection on codon usage as a contributor to GC composition."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "gc_high_bin",
            "predicate": "is a",
            "object": "gc_content_trait",
            "description": "GC high is a quantitative bin of the GC-content phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrg2358",
                "snippet": "GC content",
                "notes": "Supports the binned phenotype as a value within the GC-content distribution."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "gc_low_bin",
            "predicate": "is a",
            "object": "gc_content_trait",
            "description": "GC low is a quantitative bin of the GC-content phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrg2358",
                "snippet": "GC content",
                "notes": "Supports the binned phenotype as a value within the GC-content distribution."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "gc_mid1_bin",
            "predicate": "is a",
            "object": "gc_content_trait",
            "description": "GC mid1 is a quantitative bin of the GC-content phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrg2358",
                "snippet": "GC content",
                "notes": "Supports the binned phenotype as a value within the GC-content distribution."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "gc_mid2_bin",
            "predicate": "is a",
            "object": "gc_content_trait",
            "description": "GC mid2 is a quantitative bin of the GC-content phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrg2358",
                "snippet": "GC content",
                "notes": "Supports the binned phenotype as a value within the GC-content distribution."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "cytosine_deamination",
            "predicate": "decreases",
            "object": "gc_content_trait",
            "description": "Cytosine deamination introduces GC-to-AT changes, reducing genome-wide GC content.",
            "evidence": [
              {
                "reference": "DOI:10.1128/spectrum.02145-22",
                "snippet": "cytosine deamination reduces the GC content",
                "notes": "Strong mechanistic statement from bacterial comparative study; general mutation-bias edge."
              }
            ],
            "predicate_id": "RO:0002212"
          },
          {
            "subject": "guanine_oxidation",
            "predicate": "decreases",
            "object": "gc_content_trait",
            "description": "Guanine oxidation (8-oxoG) promotes G:C to A:T mispairing, biasing composition toward lower GC.",
            "evidence": [
              {
                "reference": "DOI:10.1128/spectrum.02145-22",
                "snippet": "guanine oxidation (8OG) causes A mis-pairing",
                "notes": "Source-backed oxidative-damage mechanism shifting the mutational spectrum toward AT."
              }
            ],
            "predicate_id": "RO:0002212"
          },
          {
            "subject": "dna_repair_replication_system",
            "predicate": "causes",
            "object": "gc_content_trait",
            "description": "Changes in the DNA replication and repair system drive mutational biases that shape GC-content evolution.",
            "evidence": [
              {
                "reference": "DOI:10.1128/spectrum.02145-22",
                "snippet": "ancient adaptations transformed the DRR system, producing mutational biases that shaped GC-content evolution",
                "notes": "Core, directly stated high-level mechanistic edge for the mutation-bias module."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "translesion_synthesis",
            "predicate": "increases",
            "object": "gc_content_trait",
            "description": "Error-prone translesion synthesis polymerases are causally linked to increases in genomic GC content.",
            "evidence": [
              {
                "reference": "DOI:10.1128/spectrum.02145-22",
                "snippet": "Error-prone polymerases are causally linked to increases in genomic GC",
                "notes": "Direction explicit in comparative study; complements existing mutation-bias drivers."
              }
            ],
            "predicate_id": "RO:0002213"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.811180+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-13T13:00:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed causal graph linking mutation bias, GC-biased gene conversion, and codon-usage selection to the GC-content phenotype, with is-a edges to the four METPO GC-content bins.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:30Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 5 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (rdfs:subClassOf\u00d74, RO:0002326\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:18Z",
        "curator": "claude",
        "action": "RENAME_PREDICATE_LABELS",
        "changes": "Renamed 2 causal-edge predicate label(s) to align with existing groundings: shapes \u2192 causes \u00d72.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:21Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:causes\u00d72).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 4 evidence-backed generic edges (4 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:11Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 4 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002212\u00d72, biolink:causes\u00d71, RO:0002213\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:32Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0042276\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope gc_content_composition_drivers=NONMECHANISTIC with scope_notes.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T04:43:24Z",
        "curator": "codex",
        "action": "ADD_CANONICAL_EXAMPLES",
        "changes": "Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Escherichia coli (NCBITaxon:562; PMID:9278503). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000432",
    "label": "GC high",
    "definition": "A GC-content phenotype with genome-wide GC composition at or below approximately 42.65% (the METPO `GC_<=42.65` bin; note that the upstream label 'high' does not match this numeric threshold, but the synonym is preserved as the authoritative bin definition).",
    "definition_source": "DOI:10.1038/nrg2358",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000127"
    ],
    "synonyms": [
      {
        "synonym_text": "GC_<=42.65",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/nrg2358",
        "snippet": "GC content",
        "notes": "Bacterial-genome review supports the lower end of GC content as a distinct genomic-composition phenotype."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:243273",
        "taxon_label": "Mycoplasmoides genitalium G37",
        "reference": "DOI:10.1126/science.270.5235.397",
        "note": "The complete Mycoplasmoides genitalium G37 genome is approximately 31.7% GC, wholly below this record's authoritative 42.65% threshold."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "gc_high_low_gc_bin",
        "title": "GC-high (METPO \u226442.65%) low-GC bin",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This genomics record is a measurement, genomic-element classification, or population-level descriptor rather than one taxon-specific protein mechanism; contextual protein nodes do not receive token UniProt examples.",
        "description": "DOI-backed graph linking AT-biased mutation pressure to a GC content at or below ~42.65% (the threshold encoded by the METPO synonym GC_<=42.65 on this record).",
        "nodes": [
          {
            "node_id": "gc_high_trait",
            "label": "GC high",
            "node_type": "TRAIT",
            "grounding": "METPO:1000432",
            "description": "GC content at or below ~42.65% (per METPO synonym GC_<=42.65)."
          },
          {
            "node_id": "gc_content",
            "label": "GC content",
            "node_type": "TRAIT",
            "grounding": "METPO:1000127",
            "description": "Percentage of guanine and cytosine nucleotides in genomic DNA."
          },
          {
            "node_id": "at_mutation_bias",
            "label": "AT-biased mutation pressure",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Mutational bias favoring AT base pairs that lowers genome-wide GC content."
          },
          {
            "node_id": "cytosine_deamination",
            "label": "Cytosine deamination",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Spontaneous conversion of cytosine to uracil, read as thymine at replication, causing GC-eroding G->A transitions."
          },
          {
            "node_id": "udg_loss",
            "label": "Loss of uracil-DNA glycosylase (UDG family)",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Loss of UDG-family base-excision repair activity, leaving deaminated cytosine (uracil) unrepaired."
          },
          {
            "node_id": "ber_glycosylase_loss",
            "label": "Loss of BER glycosylases (Tag/AlkA/MPG/Nei)",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Concerted loss of base-excision-repair glycosylases removing defenses against GC-eroding small-base lesions."
          },
          {
            "node_id": "mutt_loss",
            "label": "Loss of MutT nucleotide-pool sanitization",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Loss of MutT-family dNTP-pool sanitizing activity, contributing to mutational dysregulation."
          },
          {
            "node_id": "hypermutator_state",
            "label": "Hypermutator phenotype",
            "node_type": "STATE",
            "description": "Elevated genome-wide mutation rate with GC-eroding mutation spectra arising from repair-gene loss."
          },
          {
            "node_id": "gc3_at_enrichment",
            "label": "Third-codon-position AT enrichment",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Preferential substitution of synonymous third codon positions toward AT-rich nucleotides."
          },
          {
            "node_id": "purifying_selection_bgc",
            "label": "Purifying selection and biased gene conversion",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Selection and GC-biased gene conversion that counteract AT mutation bias and resist GC decline."
          }
        ],
        "edges": [
          {
            "subject": "at_mutation_bias",
            "predicate": "confers",
            "object": "gc_high_trait",
            "description": "AT-biased mutation pressure produces low genome-wide GC composition.",
            "evidence": [
              {
                "reference": "DOI:10.1186/1471-2148-10-374",
                "snippet": "mutation bias",
                "notes": "Supports mutation bias as the primary driver of low-GC composition."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "gc_high_trait",
            "predicate": "is a",
            "object": "gc_content",
            "description": "GC high is a quantitative bin of the GC-content phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrg2358",
                "snippet": "GC content",
                "notes": "Supports the \u226442.65% bin as a value within the GC-content distribution."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "cytosine_deamination",
            "predicate": "contributes to",
            "object": "gc_high_trait",
            "description": "Cytosine deamination drives AT-enriching G->A transitions lowering genome-wide GC.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-026-71228-y",
                "notes": "Spontaneous cytosine deamination produces unrepaired uracil read as thymine, causing G->A transitions (pages 6-7)."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "udg_loss",
            "predicate": "causally promotes",
            "object": "gc_high_trait",
            "description": "Loss of UDG repair leaves deaminated cytosine unrepaired, promoting GC erosion.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-026-71228-y",
                "notes": "Absence of DNA glycosylases compromises repair of deaminated cytosine (uracil), causing G->A transitions (pages 6-7)."
              }
            ]
          },
          {
            "subject": "ber_glycosylase_loss",
            "predicate": "causally promotes",
            "object": "gc_high_trait",
            "description": "Concerted loss of BER glycosylases biases mutation spectra toward GC-eroding changes.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-026-71228-y",
                "notes": "Concerted loss of Tag/AlkA/MPG, UDG, Nei, MutT removed defenses against small-base lesions; mutation spectra biased toward GC-eroding changes (pages 8-9)."
              }
            ]
          },
          {
            "subject": "mutt_loss",
            "predicate": "causally promotes",
            "object": "gc_high_trait",
            "description": "Loss of MutT nucleotide-pool sanitization contributes to GC-eroding mutational dysregulation.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-026-71228-y",
                "notes": "Concerted loss of sanitizing enzymes including MutT removed defenses; analogues showed mutation spectra biased toward GC-eroding changes (pages 8-9)."
              }
            ]
          },
          {
            "subject": "hypermutator_state",
            "predicate": "causally promotes",
            "object": "gc_high_trait",
            "description": "Hypermutator state provides a mechanistic path to genome-wide AT enrichment.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-026-71228-y",
                "notes": "Mutator phenotypes (10- to 1e4-fold) with GC-eroding mutation spectra provide a mechanistic path to AT-enrichment (pages 8-9)."
              }
            ]
          },
          {
            "subject": "gc3_at_enrichment",
            "predicate": "contributes to",
            "object": "gc_high_trait",
            "description": "AT-rich substitution at third codon positions is a principal driver of decreased GC.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-026-71228-y",
                "notes": "Substitution of third codon positions with AT-rich nucleotides identified as a principal driver of decreased GC (pages 9-10)."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "purifying_selection_bgc",
            "predicate": "opposes",
            "object": "gc_high_trait",
            "description": "Purifying selection and biased gene conversion counteract AT bias, resisting GC decline.",
            "evidence": [
              {
                "reference": "DOI:10.63635/mrj.v1i4.188",
                "notes": "Purifying selection and biased gene conversion can counteract AT bias (pages 3-5)."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.818260+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-13T13:00:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed definition (derived from METPO synonym GC_<=42.65) and causal graph linking AT-biased mutation pressure to this GC bin. Documented the upstream label-vs-threshold inconsistency.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:30Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d71, rdfs:subClassOf\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 7 evidence-backed generic edges (7 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:11Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002326\u00d72).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates (1 to confers), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope gc_high_low_gc_bin=NONMECHANISTIC with scope_notes.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T04:43:24Z",
        "curator": "codex",
        "action": "ADD_CANONICAL_EXAMPLES",
        "changes": "Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Mycoplasmoides genitalium G37 (NCBITaxon:243273; DOI:10.1126/science.270.5235.397). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000429",
    "label": "GC low",
    "definition": "A GC-content phenotype with genome-wide GC composition between approximately 42.65% and 57.0% (the METPO `GC_42.65_57.0` bin; note that the upstream label 'low' does not match this mid-range numeric threshold, but the synonym is preserved as the authoritative bin definition).",
    "definition_source": "DOI:10.1038/nrg2358",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000127"
    ],
    "synonyms": [
      {
        "synonym_text": "GC_42.65_57.0",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1371/journal.pgen.1001107",
        "snippet": "The genomic GC-content of bacteria varies dramatically, from less than 20% to more than 70%",
        "notes": "Verified against the open Hildebrand et al. abstract; bacterial genome-wide GC content spans the METPO 42.65-57.0% bin, whose cutpoints come from this record's METPO synonym."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1793963",
        "taxon_label": "Bacillus nakamurai",
        "reference": "DOI:10.1099/ijsem.0.001135",
        "note": "Bacillus nakamurai NRRL B-41091T has 43.8 mol% genomic GC in its primary species description, wholly inside this record's authoritative 42.65-57.0% interval."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "gc_low_mid_low_gc_bin",
        "title": "GC-low METPO 42.65-57.0% genome-composition context",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This genomics record is a measurement, genomic-element classification, or population-level descriptor rather than one taxon-specific protein mechanism; contextual protein nodes do not receive token UniProt examples.",
        "description": "DOI-backed nonmechanistic graph connecting DNA-repair defects, mutational spectra, cytosine-deamination context, AT-enriching spectrum context, replication/repair enzyme bias, and moderate mutation bias to continuous genome-wide GC content and the METPO GC_42.65_57.0 bin.",
        "nodes": [
          {
            "node_id": "gc_low_trait",
            "label": "GC low",
            "node_type": "TRAIT",
            "grounding": "METPO:1000429",
            "description": "GC content ~42.65\u201357.0% (per METPO synonym GC_42.65_57.0)."
          },
          {
            "node_id": "gc_content",
            "label": "GC content",
            "node_type": "TRAIT",
            "grounding": "METPO:1000127",
            "description": "Percentage of guanine and cytosine nucleotides in genomic DNA."
          },
          {
            "node_id": "moderate_mutation_bias",
            "label": "moderate mutation bias",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Modest mutation-bias balance between AT- and GC-favoring pressures yielding mid-range GC composition."
          },
          {
            "node_id": "dna_repair_defect",
            "label": "DNA repair defect",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Loss/impairment of DNA repair pathways (MMR, BER, HR) altering mutation accumulation."
          },
          {
            "node_id": "mutational_spectrum",
            "label": "mutational spectrum",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Distribution of mutation types (substitution classes) characterizing a genome."
          },
          {
            "node_id": "cytosine_deamination",
            "label": "cytosine deamination / C>T bias",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Spontaneous cytosine deamination driving C>T transitions, the most common mutation type."
          },
          {
            "node_id": "at_enriching_spectrum",
            "label": "AT-enriching mutation spectrum",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Mutation spectrum biased toward AT-increasing substitutions (C>A/T enriched, C>G depleted)."
          },
          {
            "node_id": "repair_enzyme_bias",
            "label": "DNA replication/repair enzyme bias",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Nucleotide biases of DNA replication and repair enzymes contributing to genome base composition."
          }
        ],
        "edges": [
          {
            "subject": "moderate_mutation_bias",
            "predicate": "contributes to",
            "object": "gc_content",
            "description": "Moderate mutation-bias balance contributes to continuous genome-wide GC composition.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2024.1412318",
                "snippet": "The GC% of genomes depends in part on the mutation rates between each nucleotide",
                "notes": "Verified against the open Delgado et al. introduction; mutation rates are described as one component of genome GC percent, with selection pressures and codon-usage effects also contributing."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "gc_low_trait",
            "predicate": "is a",
            "object": "gc_content",
            "description": "GC low is a quantitative bin of the GC-content phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1371/journal.pgen.1001107",
                "snippet": "The genomic GC-content of bacteria varies dramatically, from less than 20% to more than 70%",
                "notes": "Verified against the open Hildebrand et al. abstract; the public source supports genome-wide GC content as a continuous bacterial genome-composition measurement, while the METPO synonym supplies this bin's cutpoints."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "dna_repair_defect",
            "predicate": "causes",
            "object": "mutational_spectrum",
            "description": "Defects in DNA repair genes (MMR, BER, HR) create distinctive bacterial mutational signatures.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-023-42916-w",
                "snippet": "defects in DNA repair create distinctive mutational signatures",
                "notes": "Verified against the open Ruis et al. abstract and results; hypermutator lineages with mutations in MMR, BER, or HR DNA-repair genes were used to extract pathway-specific bacterial signatures."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "cytosine_deamination",
            "predicate": "contributes to",
            "object": "at_enriching_spectrum",
            "description": "Cytosine deamination and the resulting C>T transitions contribute to an AT-enriching bacterial mutation spectrum.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-023-42916-w",
                "snippet": "cytosine to thymine (C\u2009>\u2009T) was typically the most common mutation type identified",
                "notes": "Verified against the open Ruis et al. results; C>T was the most common mutation type in 69 of 84 bacterial single-base-substitution spectra and is discussed as potentially arising from cytosine deamination."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "at_enriching_spectrum",
            "predicate": "associated with",
            "object": "gc_content",
            "description": "AT-enriching C>A/T and depleted C>G mutation spectra are associated with continuous genome-wide G+C content.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-023-42916-w",
                "snippet": "Genomic G\u2009+\u2009C content exhibited a negative correlation with proportion of C\u2009>\u2009A/T mutations",
                "notes": "Verified against the open Ruis et al. results; the spectrum-to-composition association is left on the continuous GC-content node rather than asserted as specific causation of this METPO numeric bin."
              }
            ],
            "predicate_id": "biolink:associated_with"
          },
          {
            "subject": "repair_enzyme_bias",
            "predicate": "contributes to",
            "object": "gc_content",
            "description": "Biases of DNA replication/repair enzymes and inter-nucleotide mutation rates contribute to genomic GC percent.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2024.1412318",
                "snippet": "enzymes involved in DNA replication and/or repair are known to present biases",
                "notes": "Verified against the open Delgado et al. introduction; DNA replication and repair enzyme biases are framed as mutation-rate effects that help determine genome GC percent."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "at_enriching_spectrum",
            "predicate": "is a",
            "object": "mutational_spectrum",
            "description": "The AT-enriching C>A/T spectrum is a mutational-spectrum context connecting cytosine-deamination bias to bacterial DNA-repair mutational signatures.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-023-42916-w",
                "snippet": "context-dependent patterns of base substitutions termed mutational signatures, which combine to form a mutational spectrum",
                "notes": "Verified against the open Ruis et al. results; this connector identifies the AT-enriching C>A/T pattern as a specific bacterial mutational-spectrum context rather than a direct cause of the METPO GC_42.65_57.0 bin."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.816924+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-13T13:00:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed definition (derived from METPO synonym GC_42.65_57.0) and causal graph linking moderate mutation bias to this GC bin. Documented the upstream label-vs-threshold inconsistency.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:30Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d71, rdfs:subClassOf\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 4 evidence-backed generic edges (5 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:11Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:causes\u00d71, biolink:associated_with\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates (1 to confers), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope gc_low_mid_low_gc_bin=NONMECHANISTIC with scope_notes.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T04:43:24Z",
        "curator": "codex",
        "action": "ADD_CANONICAL_EXAMPLES",
        "changes": "Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Bacillus nakamurai (NCBITaxon:1793963; DOI:10.1099/ijsem.0.001135). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-04T05:00:00Z",
        "curator": "codex",
        "action": "REVIEW_CAUSAL_EVIDENCE",
        "changes": "Reviewed the gc_low_mid_low_gc_bin graph for issue #183: added exact snippets to GC-low evidence and 6 causal-edge evidence items, grounded 2 residual predicates, and preserved the METPO GC_42.65_57.0 interval as a nonmechanistic whole-genome GC-content classification. No paid research service was called.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-04T23:40:00Z",
        "curator": "codex",
        "action": "CONNECT_CAUSAL_GRAPH_COMPONENTS",
        "changes": "Resolved issue #183 graph fragmentation (2 components to 1) by adding 1 source-backed is-a connector from the AT-enriching mutation spectrum to the broader mutational-spectrum node. No paid research service was called.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-06T13:30:00Z",
        "curator": "codex",
        "action": "ADVERSARIAL_REVIEW_REPAIR",
        "changes": "Addressed PR #664 adversarial review issue #666: replaced the borrowed GC-content snippet on the AT-enriching-spectrum is-a connector with a direct SBS-spectrum snippet from the same source.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-06T17:10:00Z",
        "curator": "codex",
        "action": "ADVERSARIAL_REVIEW_REPAIR",
        "changes": "Addressed PR #664 adversarial review: replaced the copied GC-low connector snippet with exact Ruis et al. wording defining a mutational spectrum as combined context-dependent substitution signatures.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000430",
    "label": "GC mid1",
    "definition": "A GC-content phenotype with genome-wide GC composition above approximately 66.3% (the METPO `GC_>66.3` bin; note that the upstream label 'mid1' does not match this high-end numeric threshold, but the synonym is preserved as the authoritative bin definition).",
    "definition_source": "DOI:10.1038/nrg2358",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000127"
    ],
    "synonyms": [
      {
        "synonym_text": "GC_>66.3",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1186/1471-2148-10-374",
        "snippet": "GC-biased gene conversion",
        "notes": "Bacterial-GC-content evolution review supports GC-biased gene conversion as the mechanism elevating GC content into the high range."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:100226",
        "taxon_label": "Streptomyces coelicolor A3(2)",
        "reference": "DOI:10.1038/417141a",
        "note": "The complete Streptomyces coelicolor A3(2) genome is approximately 72.1% GC, wholly above this record's authoritative 66.3% threshold."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "gc_mid1_high_gc_bin",
        "title": "GC-mid1 (METPO >66.3%) high-GC bin",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This genomics record is a measurement, genomic-element classification, or population-level descriptor rather than one taxon-specific protein mechanism; contextual protein nodes do not receive token UniProt examples.",
        "description": "DOI-backed graph linking strong GC-biased gene conversion to a GC content above ~66.3% (the threshold encoded by the METPO synonym GC_>66.3 on this record).",
        "nodes": [
          {
            "node_id": "gc_mid1_trait",
            "label": "GC mid1",
            "node_type": "TRAIT",
            "grounding": "METPO:1000430",
            "description": "GC content above ~66.3% (per METPO synonym GC_>66.3)."
          },
          {
            "node_id": "gc_content",
            "label": "GC content",
            "node_type": "TRAIT",
            "grounding": "METPO:1000127",
            "description": "Percentage of guanine and cytosine nucleotides in genomic DNA."
          },
          {
            "node_id": "strong_gbgc",
            "label": "strong GC-biased gene conversion",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Recombination-associated process strongly favoring GC alleles that elevates genome-wide GC content into the high range."
          },
          {
            "node_id": "nhej_pathway",
            "label": "NHEJ pathway (Ku, LigD)",
            "node_type": "PATHWAY",
            "description": "Non-homologous end joining double-strand-break repair pathway (Ku, LigD); KEGG ko03450."
          },
          {
            "node_id": "high_dsb_rate",
            "label": "high double-strand break rate",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Elevated rate of DNA double-strand break formation that may select for increased GC content."
          },
          {
            "node_id": "drr_system_composition",
            "label": "DNA replication and repair (DRR) system composition",
            "node_type": "PATHWAY",
            "description": "Composition of DRR pathways (BER/NER/MMR/HR/NHEJ/TLS) whose KEGG-ortholog profile correlates with genomic GC."
          },
          {
            "node_id": "nhej_end_joining_efficiency",
            "label": "NHEJ end-joining efficiency",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "Efficiency of NHEJ end-joining via stabilized short overhang / microhomology pairing."
          }
        ],
        "edges": [
          {
            "subject": "strong_gbgc",
            "predicate": "confers",
            "object": "gc_mid1_trait",
            "description": "Strong GC-biased gene conversion yields high genome-wide GC composition.",
            "evidence": [
              {
                "reference": "DOI:10.1186/1471-2148-10-374",
                "snippet": "GC-biased gene conversion",
                "notes": "Supports GC-biased gene conversion as the driver of high-GC composition."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "gc_mid1_trait",
            "predicate": "is a",
            "object": "gc_content",
            "description": "GC mid1 is a quantitative bin of the GC-content phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrg2358",
                "snippet": "GC content",
                "notes": "Supports the >66.3% bin as a value within the GC-content distribution."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "nhej_pathway",
            "predicate": "positively correlated with",
            "object": "gc_mid1_trait",
            "description": "Ku/NHEJ presence is strongly associated with elevated genomic GC content.",
            "evidence": [
              {
                "reference": "DOI:10.1371/journal.pgen.1008493",
                "notes": "Strong association between Ku presence and elevated GC content; Pearson r=0.54 (p<2.2e-16). Correlational across prokaryotes."
              }
            ]
          },
          {
            "subject": "high_dsb_rate",
            "predicate": "selects for",
            "object": "gc_mid1_trait",
            "description": "Higher DSB formation rate selects for increased GC content relative to genomic background.",
            "evidence": [
              {
                "reference": "DOI:10.1371/journal.pgen.1008493",
                "notes": "Sites with higher DSB rates are under selection for increased GC content; proposed unifying driver of GC content across prokaryotes."
              }
            ],
            "predicate_id": "METPO:2007401"
          },
          {
            "subject": "drr_system_composition",
            "predicate": "strongly correlated with",
            "object": "gc_mid1_trait",
            "description": "DRR-system KEGG-ortholog composition explains a large fraction of genomic GC variance.",
            "evidence": [
              {
                "reference": "DOI:10.1128/spectrum.02145-22",
                "notes": "Linear model using 217 DRR-related KEGG orthologs explains up to 88% of variance in genomic GC (multiple correlation 0.94)."
              }
            ]
          },
          {
            "subject": "gc_mid1_trait",
            "predicate": "may increase",
            "object": "nhej_end_joining_efficiency",
            "description": "High GC may increase NHEJ repair efficiency by stabilizing short overhangs/microhomologies via extra hydrogen bonds.",
            "evidence": [
              {
                "reference": "DOI:10.1371/journal.pgen.1008493",
                "notes": "High GC via increased hydrogen bonds may stabilize short overhang/microhomology pairing and increase NHEJ efficiency."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.817373+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-13T13:00:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed definition (derived from METPO synonym GC_>66.3) and causal graph linking strong GC-biased gene conversion to this GC bin. Documented the upstream label-vs-threshold inconsistency.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:30Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d71, rdfs:subClassOf\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 4 evidence-backed generic edges (4 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:11Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007401\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates (1 to confers), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope gc_mid1_high_gc_bin=NONMECHANISTIC with scope_notes.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T04:43:24Z",
        "curator": "codex",
        "action": "ADD_CANONICAL_EXAMPLES",
        "changes": "Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Streptomyces coelicolor A3(2) (NCBITaxon:100226; DOI:10.1038/417141a). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000431",
    "label": "GC mid2",
    "definition": "A GC-content phenotype with genome-wide GC composition between approximately 57.0% and 66.3% (the METPO `GC_57.0_66.3` bin).",
    "definition_source": "DOI:10.1038/nrg2358",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000127"
    ],
    "synonyms": [
      {
        "synonym_text": "GC_57.0_66.3",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1186/1471-2148-10-374",
        "snippet": "GC-biased gene conversion",
        "notes": "Bacterial-GC-content evolution review supports moderate GC-biased gene conversion as the mechanism producing mid-high GC content."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:3028314",
        "taxon_label": "Oceanimonas pelagia",
        "reference": "DOI:10.1007/s10482-024-01948-y",
        "note": "The Oceanimonas pelagia NTOU-MSR1T genome has 61.0 mol% GC, wholly inside this record's authoritative 57.0-66.3% interval."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "gc_mid2_mid_high_gc_bin",
        "title": "GC-mid2 (METPO 57.0\u201366.3%) mid-high GC bin",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This genomics record is a measurement, genomic-element classification, or population-level descriptor rather than one taxon-specific protein mechanism; contextual protein nodes do not receive token UniProt examples.",
        "description": "DOI-backed graph linking moderate GC-biased gene conversion to a GC content of ~57.0\u201366.3% (the threshold encoded by the METPO synonym GC_57.0_66.3 on this record).",
        "nodes": [
          {
            "node_id": "gc_mid2_trait",
            "label": "GC mid2",
            "node_type": "TRAIT",
            "grounding": "METPO:1000431",
            "description": "GC content ~57.0\u201366.3% (per METPO synonym GC_57.0_66.3)."
          },
          {
            "node_id": "gc_content",
            "label": "GC content",
            "node_type": "TRAIT",
            "grounding": "METPO:1000127",
            "description": "Percentage of guanine and cytosine nucleotides in genomic DNA."
          },
          {
            "node_id": "moderate_gbgc",
            "label": "moderate GC-biased gene conversion",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Recombination-associated GC-favoring activity sufficient to elevate GC content into the mid-high range."
          },
          {
            "node_id": "homologous_recombination",
            "label": "homologous recombination",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Template-directed exchange/repair pathway that drives GC-biased gene conversion.",
            "grounding": "GO:0035825"
          },
          {
            "node_id": "mutation_bias_at",
            "label": "mutation bias toward AT",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Universal excess of G/C->A/T mutations in bacteria opposing high genomic GC."
          },
          {
            "node_id": "cytosine_deamination",
            "label": "cytosine deamination",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Spontaneous/chemically promoted C->T transition source contributing to AT enrichment."
          },
          {
            "node_id": "guanine_oxidation",
            "label": "guanine oxidation / 8-oxoG damage",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Oxidative lesion process yielding G->T/C->A transversions and compositional bias."
          },
          {
            "node_id": "dna_repair_efficiency",
            "label": "DNA repair efficiency",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Efficiency/specificity of repair pathways affecting which mutational biases are fixed."
          },
          {
            "node_id": "assembly_gc_bias",
            "label": "sequencing/assembly GC bias",
            "node_type": "EXPERIMENTAL_FACTOR",
            "description": "Technical bias where observed assembly GC shifts with true GC%, depth, and error rate."
          }
        ],
        "edges": [
          {
            "subject": "moderate_gbgc",
            "predicate": "confers",
            "object": "gc_mid2_trait",
            "description": "Moderate GC-biased gene conversion yields mid-high genome-wide GC composition.",
            "evidence": [
              {
                "reference": "DOI:10.1186/1471-2148-10-374",
                "snippet": "GC-biased gene conversion",
                "notes": "Supports GC-biased gene conversion as the driver of mid-high GC bins."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "gc_mid2_trait",
            "predicate": "is a",
            "object": "gc_content",
            "description": "GC mid2 is a quantitative bin of the GC-content phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrg2358",
                "snippet": "GC content",
                "notes": "Supports the 57.0\u201366.3% bin as a value within the GC-content distribution."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "homologous_recombination",
            "predicate": "positively influences",
            "object": "moderate_gbgc",
            "description": "Recombination increases fixation of AT->GC mutations via GC-biased gene conversion.",
            "evidence": [
              {
                "reference": "DOI:10.1101/011023",
                "notes": "gBGC: recombination tends to increase fixation of AT->GC mutations."
              }
            ]
          },
          {
            "subject": "mutation_bias_at",
            "predicate": "negatively influences",
            "object": "gc_mid2_trait",
            "description": "Universal AT-biased mutation opposes maintenance of mid-high genomic GC.",
            "evidence": [
              {
                "reference": "DOI:10.1101/011023",
                "notes": "Universal excess of G/C->A/T mutations; mutation universally biased towards AT."
              }
            ]
          },
          {
            "subject": "cytosine_deamination",
            "predicate": "positively influences",
            "object": "mutation_bias_at",
            "description": "Cytosine deamination (C->T) drives A+T enrichment.",
            "evidence": [
              {
                "reference": "DOI:10.63635/mrj.v1i4.188",
                "notes": "Cytosine deamination (C->T) drives A+T enrichment."
              }
            ]
          },
          {
            "subject": "guanine_oxidation",
            "predicate": "positively influences",
            "object": "mutation_bias_at",
            "description": "Guanine oxidation to 8-oxo-guanine (G->T) contributes to AT-biased composition.",
            "evidence": [
              {
                "reference": "DOI:10.63635/mrj.v1i4.188",
                "notes": "Guanine oxidation to 8-oxo-guanine (G->T)."
              }
            ]
          },
          {
            "subject": "dna_repair_efficiency",
            "predicate": "influences",
            "object": "gc_mid2_trait",
            "description": "Variation in repair efficiency affects fixation of changes and long-term G+C content.",
            "evidence": [
              {
                "reference": "DOI:10.63635/mrj.v1i4.188",
                "notes": "Variations in DNA repair efficiency influence fixation and thus long-term G+C content."
              }
            ]
          },
          {
            "subject": "assembly_gc_bias",
            "predicate": "can distort measurement of",
            "object": "gc_mid2_trait",
            "description": "Assembly conditions can bias observed GC% in a direction dependent on true GC%.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s12864-023-09910-4",
                "notes": "In low-GC genomes factors inflate assembly GC; in high-GC genomes they decrease it."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.817814+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-13T13:00:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed definition (derived from METPO synonym GC_57.0_66.3) and causal graph linking moderate GC-biased gene conversion to this GC bin.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:30Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d71, rdfs:subClassOf\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 6 evidence-backed generic edges (6 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:32Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0035825\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates (1 to confers), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope gc_mid2_mid_high_gc_bin=NONMECHANISTIC with scope_notes.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T04:43:24Z",
        "curator": "codex",
        "action": "ADD_CANONICAL_EXAMPLES",
        "changes": "Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Oceanimonas pelagia (NCBITaxon:3028314; DOI:10.1007/s10482-024-01948-y). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000097",
    "label": "GC skew",
    "definition": "A genome-sequence property describing strand asymmetry in guanine versus cytosine content between the leading and lagging replication strands, commonly used to locate the replication origin and terminus.",
    "definition_source": "DOI:10.1093/oxfordjournals.molbev.a025626",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000188"
    ],
    "synonyms": [
      {
        "synonym_text": "strand compositional asymmetry",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1016/S0378-1119(99)00297-8"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1093/oxfordjournals.molbev.a025626",
        "notes": "Lobry first described asymmetric substitution patterns between the two DNA strands of bacteria, the basis of GC skew that marks replication boundaries."
      },
      {
        "reference": "DOI:10.1016/S0378-1119(99)00297-8",
        "notes": "Frank & Lobry review the mutational and selective mechanisms underlying strand compositional asymmetry."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:562",
        "taxon_label": "Escherichia coli",
        "reference": "PMID:9278503",
        "note": "The complete circular E. coli K-12 chromosome is a source-backed model for leading/lagging-strand GC asymmetry and replication-origin inference."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "gc_skew_replication_strand_asymmetry",
        "title": "GC skew arises from replication-strand mutational asymmetry",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This genomics record is a measurement, genomic-element classification, or population-level descriptor rather than one taxon-specific protein mechanism; contextual protein nodes do not receive token UniProt examples.",
        "description": "Evidence-backed causal sketch linking DNA replication to leading-versus-lagging strand compositional asymmetry that marks the replication origin and terminus.",
        "nodes": [
          {
            "node_id": "gc_skew_trait",
            "label": "GC skew",
            "node_type": "TRAIT",
            "grounding": "traitmech:000097",
            "description": "Strand asymmetry in guanine versus cytosine content along the replichores."
          },
          {
            "node_id": "dna_replication",
            "label": "DNA replication",
            "node_type": "BIOLOGICAL_PROCESS",
            "grounding": "GO:0006260",
            "description": "Semiconservative duplication of the chromosome."
          },
          {
            "node_id": "replication_boundary",
            "label": "replication origin / terminus",
            "node_type": "QUALITY",
            "description": "Genomic position where leading/lagging strand identity switches."
          },
          {
            "node_id": "lagging_strand_ssdna",
            "label": "lagging-strand single-stranded DNA exposure",
            "node_type": "STATE",
            "description": "Transient ssDNA exposure of the lagging strand during replication."
          },
          {
            "node_id": "cytosine_deamination",
            "label": "cytosine deamination at replication forks",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Cytosine-to-thymine conversion favored on transiently single-stranded DNA at forks."
          },
          {
            "node_id": "gene_strand_bias",
            "label": "leading-strand gene density / gene strand bias",
            "node_type": "QUALITY",
            "description": "Biased distribution of genes toward the leading strand of replichores."
          },
          {
            "node_id": "translational_selection",
            "label": "translational selection and genetic code constraints",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Codon usage and genetic-code constraints shaping asymmetric base composition."
          },
          {
            "node_id": "third_codon_mutational_bias",
            "label": "third-codon-position mutational bias",
            "node_type": "QUALITY",
            "description": "Mutational bias detectable at the degenerate third codon position."
          },
          {
            "node_id": "strand_specific_repair",
            "label": "strand-specific DNA repair",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "MutSL-dependent mismatch repair and transcription-coupled NER acting asymmetrically on strands."
          }
        ],
        "edges": [
          {
            "subject": "dna_replication",
            "predicate": "causes",
            "object": "gc_skew_trait",
            "description": "Asymmetric mutation between leading and lagging strands during replication produces strand-specific G/C bias.",
            "evidence": [
              {
                "reference": "DOI:10.1093/oxfordjournals.molbev.a025626",
                "notes": "Lobry first described replication-linked asymmetric substitution patterns between the two DNA strands."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "gc_skew_trait",
            "predicate": "associated with",
            "object": "replication_boundary",
            "description": "GC skew inversions mark the replication origin and terminus.",
            "evidence": [
              {
                "reference": "DOI:10.1016/S0378-1119(99)00297-8",
                "notes": "Frank & Lobry review strand-asymmetry signatures used to locate replication boundaries."
              }
            ],
            "predicate_id": "biolink:associated_with"
          },
          {
            "subject": "lagging_strand_ssdna",
            "predicate": "increases",
            "object": "cytosine_deamination",
            "description": "Single-stranded exposure of the lagging strand increases cytosine deamination.",
            "evidence": [
              {
                "reference": "DOI:10.1101/2023.11.15.567178",
                "notes": "Lagging strand exposed as ssDNA, increasing cytosine-to-thymine mutations and thus contributing to GC skew."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "cytosine_deamination",
            "predicate": "contributes to",
            "object": "gc_skew_trait",
            "description": "Cytosine deamination at the replication fork generates strand-specific G/C bias.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2026.1727296",
                "notes": "Cytosine deamination at the replication fork is explicitly implicated in generating GC skew."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "gene_strand_bias",
            "predicate": "contributes to",
            "object": "gc_skew_trait",
            "description": "Biased gene density on leading versus lagging strands contributes to skew.",
            "evidence": [
              {
                "reference": "DOI:10.1101/2023.11.15.567178",
                "notes": "Biased gene density on leading vs lagging strands is highlighted as a major contributor to skew."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "translational_selection",
            "predicate": "contributes to",
            "object": "gc_skew_trait",
            "description": "Translational selection and genetic-code constraints shape asymmetric G/C distributions.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2026.1727296",
                "notes": "Translational selection and the nature of the genetic code are universal determinants of asymmetric G/C distributions."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "third_codon_mutational_bias",
            "predicate": "contributes to",
            "object": "gc_skew_trait",
            "description": "Mutational bias at the degenerate third codon position contributes to strand compositional asymmetry.",
            "evidence": [
              {
                "reference": "DOI:10.1007/pl00006428",
                "notes": "Third-position skews probably reflect mutational biases, separating mutational from protein-coding constraints."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "strand_specific_repair",
            "predicate": "contributes to",
            "object": "gc_skew_trait",
            "description": "Strand-specific MMR and transcription-coupled NER contribute to strand compositional asymmetry.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2026.1727296",
                "notes": "Strand-specific DNA repair pathways (MutSL-dependent MMR, transcription-coupled NER) contribute to asymmetry."
              }
            ],
            "predicate_id": "RO:0002326"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-06-05T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate GENOMICS trait (GC skew) from literature research; distinct from the existing GC-content composition bins.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-08T14:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (GC skew / replication strand asymmetry) with GO node grounding and biolink predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 6 evidence-backed generic edges (6 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:11Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 6 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002326\u00d75, RO:0002213\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope gc_skew_replication_strand_asymmetry=NONMECHANISTIC with scope_notes.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T04:43:24Z",
        "curator": "codex",
        "action": "ADD_CANONICAL_EXAMPLES",
        "changes": "Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Escherichia coli (NCBITaxon:562; PMID:9278503). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000287",
    "label": "Geb system",
    "definition": "A phage defense system in which an organism possesses a Geb locus that can protect bacteria from bacteriophage infection.",
    "definition_source": "DOI:10.1101/2025.01.08.631966",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "Geb",
        "synonym_type": "EXACT_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      },
      {
        "synonym_text": "GebA1",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "GebA2",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1101/2025.01.08.631966",
        "snippet": "Among the remaining eight systems, six demonstrated increased resistance to at least one phage with more than 100 fold reduction in plaque forming units (PFU) (Figure 3a, Supplementary Figure 5). As Streptomyces are mostly soil dwelling bacteria, we named these systems after deities of the soil and earth (Ceres, Geb, Veles, Prithvi, Ukko and Oshun).",
        "notes": "Mordret et al. directly name Geb among six Streptomyces systems that increased resistance to at least one phage."
      },
      {
        "reference": "DOI:10.1101/2025.01.08.631966",
        "snippet": "The bacterial pangenome encodes an immense array of antiphage systems, yet much of their diversity remains uncharted",
        "notes": "Mordret et al. motivate a conservative system-level record that does not assert a resolved Geb trigger, effector output, or universal pathway."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "Geb | 10\\.1101/2025\\.01\\.08\\.631966 | Protein and genomic language models chart a vast landscape of antiphage defenses",
        "notes": "The DefenseFinder model registry maps the named Geb system to the Mordret et al. antiphage-system discovery preprint."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "Geb__GebA1                                       |                                                  | Geb",
        "notes": "The DefenseFinder HMM inventory records GebA1 in the Geb model namespace."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "Geb__GebA2                                       |                                                  | Geb",
        "notes": "The DefenseFinder HMM inventory records GebA2 in the Geb model namespace."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "geb_locus_restricts_phage",
        "title": "Geb loci confer bacterial phage defense",
        "description": "Conservative system-level sketch linking possession of a Geb locus to restricted bacteriophage propagation without asserting the unresolved phage trigger or molecular output.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Geb as a named anti-phage system with GebA1 and GebA2 DefenseFinder HMM profile entries while leaving its phage trigger, molecular substrate, antiviral effector output, and subtype breadth unresolved.",
        "nodes": [
          {
            "node_id": "geb_locus",
            "label": "Geb locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A Geb anti-phage defense locus cataloged in DefenseFinder with GebA1 and GebA2 HMM profile entries."
          },
          {
            "node_id": "restricted_phage_propagation",
            "label": "restricted phage propagation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced propagation of bacteriophage in cells carrying the Geb system."
          },
          {
            "node_id": "geb_system_trait",
            "label": "Geb system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000287",
            "description": "Possession of a genome-encoded Geb phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "geb_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "restricted_phage_propagation",
            "description": "DefenseFinder maps Geb to a protein- and genomic-language-model antiphage-system discovery preprint and catalogs GebA1 and GebA2 HMM profile entries in the Geb model namespace.",
            "evidence": [
              {
                "reference": "DOI:10.1101/2025.01.08.631966",
                "snippet": "Among the remaining eight systems, six demonstrated increased resistance to at least one phage with more than 100 fold reduction in plaque forming units (PFU) (Figure 3a, Supplementary Figure 5). As Streptomyces are mostly soil dwelling bacteria, we named these systems after deities of the soil and earth (Ceres, Geb, Veles, Prithvi, Ukko and Oshun).",
                "notes": "Mordret et al. directly name Geb among six Streptomyces systems that restricted at least one phage."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Geb | 10\\.1101/2025\\.01\\.08\\.631966 | Protein and genomic language models chart a vast landscape of antiphage defenses",
                "notes": "The DefenseFinder registry maps Geb itself to the Mordret et al. bacterial antiphage-system discovery preprint."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "Geb__GebA1                                       |                                                  | Geb",
                "notes": "The DefenseFinder HMM inventory records GebA1 in the Geb model namespace."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "Geb__GebA2                                       |                                                  | Geb",
                "notes": "The DefenseFinder HMM inventory records GebA2 in the Geb model namespace."
              }
            ]
          },
          {
            "subject": "restricted_phage_propagation",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "geb_system_trait",
            "description": "Geb-mediated phage restriction realizes the Geb system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1101/2025.01.08.631966",
                "snippet": "Among the remaining eight systems, six demonstrated increased resistance to at least one phage with more than 100 fold reduction in plaque forming units (PFU) (Figure 3a, Supplementary Figure 5). As Streptomyces are mostly soil dwelling bacteria, we named these systems after deities of the soil and earth (Ceres, Geb, Veles, Prithvi, Ukko and Oshun).",
                "notes": "Mordret et al. directly name Geb among six systems that increased resistance to at least one phage."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Geb | 10\\.1101/2025\\.01\\.08\\.631966 | Protein and genomic language models chart a vast landscape of antiphage defenses",
                "notes": "DefenseFinder records Geb as a named system from the Mordret et al. antiphage discovery preprint."
              }
            ]
          },
          {
            "subject": "geb_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Geb system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| Geb | 10\\.1101/2025\\.01\\.08\\.631966 | Protein and genomic language models chart a vast landscape of antiphage defenses |",
                "notes": "DefenseFinder associates Geb with the Mordret et al. bacterial antiphage-system discovery preprint."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "geb-mechanism-gap",
        "prompt": "Resolve Geb phage triggers and effector outputs before minting narrower Geb mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Mordret et al. and DefenseFinder support Geb as a named anti-phage system with GebA1 and GebA2 HMM profile entries, but the trigger, molecular substrate, antiviral effector output, and subtype-specific mechanism are not resolved enough here to assert a narrower mechanistic child trait.",
        "attaches_to": [
          "causal_graphs#geb_locus_restricts_phage"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-19"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-19T17:00:41Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Geb system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v164.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-19T17:39:40Z",
        "curator": "codex",
        "action": "ADDRESSED_PR_REVIEW",
        "changes": "Resolved PR #1073 review issues #1074 and #1075 by making the Geb subclass evidence snippet self-supporting and replacing unsupported GebA1-or-GebA2 profile-choice wording with wording limited to the DefenseFinder HMM inventory.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-19T18:00:25Z",
        "curator": "codex",
        "action": "ADDRESSED_PR_REVIEW",
        "changes": "Resolved PR #1073 review issue #1076 by replacing abstract-only Geb validation support with Mordret full-text snippets that directly name Geb among the six phage-restricting systems.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000098",
    "label": "genome size",
    "definition": "A quantitative genomics property describing the total length of an organism's genome (typically expressed in megabase pairs), which varies widely across prokaryotes and reflects lifestyle and evolutionary forces.",
    "definition_source": "DOI:10.1038/nrmicro3331",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000188"
    ],
    "synonyms": [
      {
        "synonym_text": "genome length",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1038/nrmicro3331"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/nrmicro3331",
        "notes": "Batut et al. review reductive genome evolution, linking genome size to population size and lifestyle across prokaryotes."
      },
      {
        "reference": "DOI:10.1038/ismej.2014.60",
        "notes": "Giovannoni et al. discuss streamlining theory and the small genomes of abundant free-living microbes."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:243273",
        "taxon_label": "Mycoplasmoides genitalium G37",
        "reference": "DOI:10.1126/science.270.5235.397",
        "note": "The complete Mycoplasmoides genitalium G37 genome contains 580,070 base pairs, a directly sequenced compact-genome example."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "genome_size_population_lifestyle",
        "title": "Genome size reflects effective population size and lifestyle",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This genomics record is a measurement, genomic-element classification, or population-level descriptor rather than one taxon-specific protein mechanism; contextual protein nodes do not receive token UniProt examples.",
        "description": "Evidence-backed causal sketch linking effective population size and lifestyle to reductive evolution shaping prokaryotic genome length.",
        "nodes": [
          {
            "node_id": "genome_size_trait",
            "label": "genome size",
            "node_type": "TRAIT",
            "grounding": "traitmech:000098",
            "description": "Total genomic length of an organism."
          },
          {
            "node_id": "effective_population_size",
            "label": "effective population size",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Long-term breeding population size shaping selection efficiency."
          },
          {
            "node_id": "reductive_genome_evolution",
            "label": "reductive genome evolution",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Selective and drift-driven loss of genomic content.",
            "grounding": "METPO:1007721"
          },
          {
            "node_id": "ocean_depth",
            "label": "ocean depth",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Depth layer in the marine water column (epipelagic to bathypelagic)."
          },
          {
            "node_id": "soil_ph",
            "label": "soil pH",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Acidity/alkalinity of soil habitat.",
            "grounding": "ENVO:09200010"
          },
          {
            "node_id": "horizontal_gene_transfer",
            "label": "horizontal gene transfer",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Acquisition of genetic material between organisms, expanding gene content.",
            "grounding": "GO:0009292"
          },
          {
            "node_id": "mobile_genetic_elements",
            "label": "mobile genetic elements",
            "node_type": "CHEMICAL",
            "description": "Plasmids, phages, ICEs, transposons and insertion sequences that move DNA between genomes."
          },
          {
            "node_id": "gene_loss",
            "label": "gene loss",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Loss of protein-coding genes leading to genome reduction."
          },
          {
            "node_id": "metabolic_versatility",
            "label": "metabolic versatility",
            "node_type": "CAPACITY",
            "description": "Breadth of metabolic functions encoded by a genome."
          }
        ],
        "edges": [
          {
            "subject": "effective_population_size",
            "predicate": "regulates",
            "object": "reductive_genome_evolution",
            "description": "Large Ne strengthens selection against superfluous DNA; small Ne permits drift-driven loss in symbionts.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro3331",
                "notes": "Batut et al. compare reductive genome evolution at both ends of the population-size spectrum."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "reductive_genome_evolution",
            "predicate": "causes",
            "object": "genome_size_trait",
            "description": "Reductive evolution sets the observed genome length.",
            "evidence": [
              {
                "reference": "DOI:10.1038/ismej.2014.60",
                "notes": "Giovannoni et al. link streamlining theory to small genomes in abundant free-living microbes."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "ocean_depth",
            "predicate": "positively associated with",
            "object": "genome_size_trait",
            "description": "Average genome size of marine communities increases with ocean depth.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-023-36988-x",
                "notes": "Ngugi 2023: AGS increases with depth across epipelagic, mesopelagic and bathypelagic metagenomes."
              }
            ]
          },
          {
            "subject": "soil_ph",
            "predicate": "negatively associated with",
            "object": "genome_size_trait",
            "description": "Low-pH soils host communities with larger average genomes.",
            "evidence": [
              {
                "reference": "DOI:10.1101/2021.11.17.469016",
                "notes": "Chuckran 2023: negative AGS-pH relationship in soil; strengthened after microbial-DNA correction (R2 0.32->0.57)."
              }
            ]
          },
          {
            "subject": "horizontal_gene_transfer",
            "predicate": "increases",
            "object": "genome_size_trait",
            "description": "HGT is a driving force behind genome expansion, adding accessory gene content.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41559-024-02357-0",
                "notes": "Dmitrijeva 2024: HGT described as driving force behind genome expansion; ~42.5% of genes affected by HGT per species."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "mobile_genetic_elements",
            "predicate": "mediates",
            "object": "horizontal_gene_transfer",
            "description": "MGEs (plasmids, phages, ICEs, transposons, insertion sequences) carry out HGT.",
            "evidence": [
              {
                "reference": "DOI:10.1111/1462-2920.16630",
                "notes": "Kogay 2024: MGEs crucial for horizontal gene transfer, including plasmids, ICEs, transposons, IS and phages."
              }
            ]
          },
          {
            "subject": "gene_loss",
            "predicate": "decreases",
            "object": "genome_size_trait",
            "description": "Loss of protein-coding genes reduces genome length.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-024-50368-z",
                "notes": "Dong 2024: KO-abundance changes track genome size, indicating protein-coding gene loss and genome reduction."
              }
            ],
            "predicate_id": "RO:0002212"
          },
          {
            "subject": "metabolic_versatility",
            "predicate": "positively associated with",
            "object": "genome_size_trait",
            "description": "Greater metabolic versatility is correlated with larger genomes.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-023-01465-0",
                "notes": "Piton 2023: soil bacterial trait axis of metabolic versatility strongly positively correlated with genome size (R2=0.64)."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-06-05T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate GENOMICS trait (genome size) from literature research.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-08T14:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (genome size / population-size and lifestyle) with RO/biolink predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-16T06:54:40Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (METPO:1007721\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 6 evidence-backed generic edges (6 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:11Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002213\u00d71, RO:0002212\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:18Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0009292\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:32Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (ENVO:09200010\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope genome_size_population_lifestyle=NONMECHANISTIC with scope_notes.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T04:43:24Z",
        "curator": "codex",
        "action": "ADD_CANONICAL_EXAMPLES",
        "changes": "Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Mycoplasmoides genitalium G37 (NCBITaxon:243273; DOI:10.1126/science.270.5235.397). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000099",
    "label": "genome streamlining",
    "definition": "A genomics trait describing selective reduction of genome size and gene content in free-living microbes with very large effective population sizes, minimizing the cellular cost of replication and biosynthesis.",
    "definition_source": "DOI:10.1038/ismej.2014.60",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000188"
    ],
    "synonyms": [
      {
        "synonym_text": "streamlined genome",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1038/ismej.2014.60"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/ismej.2014.60",
        "notes": "Giovannoni et al. set out streamlining theory, explaining small streamlined genomes of abundant oligotrophic microbes."
      },
      {
        "reference": "DOI:10.1038/nrmicro3331",
        "notes": "Batut et al. compare reductive genome evolution at both ends of the bacterial population-size spectrum."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1219",
        "taxon_label": "Prochlorococcus marinus",
        "note": "Paradigm of genome streamlining: the most abundant photoautotroph, with one of the smallest genomes of any free-living phototroph.",
        "reference": "PMID:12917486"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "streamlining_oligotrophic_selection",
        "title": "Oligotrophic environments select for streamlined genomes",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This genomics record is a measurement, genomic-element classification, or population-level descriptor rather than one taxon-specific protein mechanism; contextual protein nodes do not receive token UniProt examples.",
        "description": "Evidence-backed causal sketch linking oligotrophic, high-Ne lifestyles to selective reduction of genome content.",
        "nodes": [
          {
            "node_id": "streamlining_trait",
            "label": "genome streamlining",
            "node_type": "TRAIT",
            "grounding": "traitmech:000099",
            "description": "Selective reduction of genome size and gene content."
          },
          {
            "node_id": "oligotrophic_environment",
            "label": "oligotrophic environment",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Low-nutrient habitat supporting large free-living populations."
          },
          {
            "node_id": "reductive_genome_evolution",
            "label": "reductive genome evolution",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Selective and drift-driven loss of genomic content.",
            "grounding": "METPO:1007721"
          },
          {
            "node_id": "smaller_microbial_genome",
            "label": "smaller microbial genome size",
            "node_type": "QUALITY",
            "description": "Reduced genome size in free-living microbes."
          },
          {
            "node_id": "depletion_metabolic_genes",
            "label": "depletion of metabolic genes",
            "node_type": "QUALITY",
            "description": "Generalizable signature: loss of metabolic gene content in streamlined genomes."
          },
          {
            "node_id": "metabolic_cross_feeding",
            "label": "metabolic cross-feeding",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Community-level exchange of metabolites among auxotrophic members."
          },
          {
            "node_id": "reduced_cofactor_biosynthesis",
            "label": "reduced cofactor/vitamin biosynthesis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Loss of cofactor and vitamin biosynthetic capacity."
          },
          {
            "node_id": "exogenous_bvitamin_dependence",
            "label": "dependence on exogenous B-vitamin precursors",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reliance on externally supplied B1/B12 precursors and products."
          }
        ],
        "edges": [
          {
            "subject": "oligotrophic_environment",
            "predicate": "selects for",
            "object": "streamlining_trait",
            "description": "Resource limitation and large Ne favor minimizing cellular cost via genome reduction.",
            "evidence": [
              {
                "reference": "DOI:10.1038/ismej.2014.60",
                "notes": "Giovannoni et al. articulate streamlining theory for abundant oligotrophic microbes."
              }
            ],
            "predicate_id": "METPO:2007401"
          },
          {
            "subject": "reductive_genome_evolution",
            "predicate": "causes",
            "object": "streamlining_trait",
            "description": "Reductive evolution is the population-genetic process realizing the streamlined-genome phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro3331",
                "notes": "Batut et al. compare reductive genome evolution across the bacterial population-size spectrum."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "oligotrophic_environment",
            "predicate": "selects for",
            "object": "smaller_microbial_genome",
            "description": "Resource-poor oligotrophic waters select for smaller microbial genomes across free-living marine microbes.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-023-36988-x",
                "notes": "Ngugi 2023: \"small microbial genomes in the resource-poor photic ocean\"; broad comparative support across 364 marine metagenomes."
              }
            ],
            "predicate_id": "METPO:2007401"
          },
          {
            "subject": "streamlining_trait",
            "predicate": "associated with",
            "object": "depletion_metabolic_genes",
            "description": "Streamlined genomes show a generalizable depletion of metabolic genes.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-024-50368-z",
                "notes": "Dong 2024: \"reduced genome sizes associated with a depletion of metabolic genes\"; generalizable signature of streamlined genomes under stress."
              }
            ],
            "predicate_id": "biolink:associated_with"
          },
          {
            "subject": "streamlining_trait",
            "predicate": "promotes",
            "object": "metabolic_cross_feeding",
            "description": "Streamlining and resulting auxotrophies promote metabolic cross-feeding in bacterioplankton communities.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-024-46374-w",
                "notes": "Giordano 2024: \"genome streamlining and metabolic auxotrophies as central joint mechanisms shaping bacterioplankton community assembly\"."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "reduced_cofactor_biosynthesis",
            "predicate": "increases dependence on",
            "object": "exogenous_bvitamin_dependence",
            "description": "Loss of cofactor/vitamin biosynthesis increases reliance on exogenous B-vitamin precursors and products.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-024-46374-w",
                "notes": "Giordano 2024: \"reliance ... on exogenous B1 and B12 precursors/products\"; Black Queen-like public-goods dependency."
              }
            ]
          },
          {
            "subject": "streamlining_trait",
            "predicate": "associated with",
            "object": "exogenous_bvitamin_dependence",
            "description": "Community metabolic modelling associates genome streamlining and auxotrophy with predicted exchange of B vitamins; this is a model-supported association, not a universal causal consequence of streamlining.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-024-46374-w",
                "snippet": "genome streamlining and metabolic auxotrophies may act as joint mechanisms",
                "notes": "The authors explicitly frame the streamlining-auxotrophy relationship as a model-supported possibility."
              },
              {
                "reference": "DOI:10.1038/s41467-024-46374-w",
                "snippet": "conserved metabolic cross-feedings, in particular of specific amino acids and group B vitamins",
                "notes": "The same community models predict B-vitamin exchange among co-active bacterioplankton communities."
              }
            ],
            "predicate_id": "biolink:associated_with"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-06-05T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate GENOMICS trait (genome streamlining) from literature research.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-08T14:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (oligotrophic selection / reductive evolution) with METPO/biolink predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-16T06:54:40Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (METPO:1007721\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 5 evidence-backed generic edges (6 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:11Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007401\u00d71, biolink:associated_with\u00d71, RO:0002213\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope streamlining_oligotrophic_selection=NONMECHANISTIC with scope_notes; removed 1 node(s) and 1 edge(s) together with their evidence (marginal_fitness_genes).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T09:27:10Z",
        "curator": "codex",
        "action": "CONNECT_CAUSAL_GRAPH",
        "changes": "Connected the vitamin-dependence branch to the genome-streamlining graph with a deliberately noncausal, model-qualified association backed by two source-verified snippets (issues 426 and 183).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000093",
    "label": "genomic island",
    "definition": "A genomics trait describing possession of a genomic island \u2014 a horizontally acquired chromosomal region (e.g. a pathogenicity, symbiosis, or metabolic island) that often retains mobility signatures such as flanking repeats and atypical nucleotide composition.",
    "definition_source": "DOI:10.1038/nrmicro884",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "traitmech:000089"
    ],
    "synonyms": [
      {
        "synonym_text": "pathogenicity island",
        "synonym_type": "NARROW_SYNONYM",
        "source": "DOI:10.1038/nrmicro884"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/nrmicro884",
        "snippet": "widely distributed in pathogenic, non-pathogenic and environmental microorganisms",
        "notes": "Verified against the Nature Reviews Microbiology publisher abstract; Dobrindt et al. frame genomic islands across pathogenic, non-pathogenic, and environmental microorganisms."
      },
      {
        "reference": "DOI:10.1111/j.1574-6976.2008.00136.x",
        "snippet": "horizontal gene transfer is or has been facilitated by genomic islands",
        "notes": "Verified against the open Juhas et al. abstract; the review summarizes genomic islands as mediators of bacterial horizontal gene transfer and evolution."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:28901",
        "taxon_label": "Salmonella enterica",
        "note": "Salmonella pathogenicity islands (SPI)",
        "reference": "PMID:17715824"
      },
      {
        "taxon_id": "NCBITaxon:666",
        "taxon_label": "Vibrio cholerae",
        "note": "Vibrio pathogenicity island (VPI)",
        "reference": "PMID:33123494"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "gi_hgt_accessory_function",
        "title": "Genomic islands acquired by HGT carry accessory functions",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This genomics record is a measurement, genomic-element classification, or population-level descriptor rather than one taxon-specific protein mechanism; contextual protein nodes do not receive token UniProt examples.",
        "description": "Evidence-backed causal sketch linking horizontal gene transfer to acquisition of genomic islands that confer accessory phenotypes (pathogenicity, symbiosis, metabolism).",
        "nodes": [
          {
            "node_id": "gi_trait",
            "label": "genomic island",
            "node_type": "TRAIT",
            "grounding": "traitmech:000093",
            "description": "Possession of a horizontally acquired chromosomal island."
          },
          {
            "node_id": "horizontal_gene_transfer",
            "label": "horizontal gene transfer",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Transfer of genetic material between organisms outside vertical descent.",
            "grounding": "GO:0009292"
          },
          {
            "node_id": "accessory_function",
            "label": "accessory function",
            "node_type": "QUALITY",
            "description": "Pathogenicity, symbiosis, or metabolic capability encoded by the island."
          },
          {
            "node_id": "mobility_module",
            "label": "integrase/recombinase/transposase mobility module",
            "node_type": "GENE_OR_PROTEIN",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed as a contextual protein or protein-complex label in a nonmechanistic genomics classification; no exact semantic family term was established for this aggregate use.",
            "description": "DDE transposases or tyrosine/serine recombinases that mediate island integration and mobility."
          },
          {
            "node_id": "integrative_conjugative_element",
            "label": "integrative conjugative element",
            "node_type": "TRAIT",
            "description": "Possession of a self-transmissible integrative and conjugative genomic island.",
            "grounding": "traitmech:000410"
          },
          {
            "node_id": "conjugation",
            "label": "conjugation",
            "node_type": "BIOLOGICAL_PROCESS",
            "grounding": "GO:0009291",
            "description": "Contact-dependent transfer of DNA between cells."
          },
          {
            "node_id": "type_iv_secretion_system",
            "label": "type IV secretion system (T4SS)",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Secretion apparatus that mediates conjugative DNA transfer.",
            "grounding": "GO:0043684"
          },
          {
            "node_id": "integrative_mobilizable_element",
            "label": "integrative mobilizable element (IME)",
            "node_type": "GENETIC_ELEMENT",
            "description": "Genomic island subclass that lacks its own conjugation apparatus and spreads using a helper ICE or conjugative plasmid."
          }
        ],
        "edges": [
          {
            "subject": "horizontal_gene_transfer",
            "predicate": "causes",
            "object": "gi_trait",
            "description": "Genomic islands are integrated into host chromosomes via HGT.",
            "evidence": [
              {
                "reference": "DOI:10.1111/j.1574-6976.2008.00136.x",
                "snippet": "acquisition by horizontal gene transfer; (2) integration into the host's chromosome",
                "notes": "Verified against the open Juhas et al. full text; the review's mobile-genomic-island life cycle places HGT acquisition before chromosomal integration."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "gi_trait",
            "predicate": "contributes to",
            "object": "accessory_function",
            "description": "Genomic islands deliver pathogenicity, symbiosis, or metabolic modules to the host.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro884",
                "snippet": "GEIs contribute to fitness and adaptation",
                "notes": "Verified against the Nature Reviews Microbiology publisher abstract; Dobrindt et al. describe genomic islands as gain-of-function elements affecting ecological and pathogenic traits."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "gi_trait",
            "predicate": "includes",
            "object": "mobility_module",
            "description": "Genomic islands often include integration modules made up of DDE transposases or tyrosine/serine recombinases.",
            "evidence": [
              {
                "reference": "DOI:10.1093/nar/gkad644",
                "snippet": "tyrosine (INT_Tyr) and serine (large unidirectional type, INT_Ser) recombinases, as well as DDE transposases",
                "notes": "Verified against the open Bioteau et al. methods; the AtollGenDB integrase module tracks the same DDE transposase, serine recombinase, and tyrosine recombinase families used for genomic-island mobility classification."
              }
            ],
            "predicate_id": "biolink:has_part"
          },
          {
            "subject": "integrative_conjugative_element",
            "predicate": "enables",
            "object": "conjugation",
            "description": "Self-transmissible ICE-type genomic islands disseminate by conjugation.",
            "evidence": [
              {
                "reference": "DOI:10.1093/nar/gkad644",
                "snippet": "ICEs disseminate by conjugation, a mechanism involving the secretion of DNA from the donor cell",
                "notes": "Verified against the open Bioteau et al. introduction; ICEs are presented as self-transmissible genomic islands that disseminate DNA by conjugation."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "type_iv_secretion_system",
            "predicate": "enables",
            "object": "conjugation",
            "description": "ICE-encoded type IV secretion systems translocate DNA between mating cells in direct contact.",
            "evidence": [
              {
                "reference": "DOI:10.1093/nar/gkad644",
                "snippet": "the DNA is translocated between mating cells in direct contact by a type IV secretion system",
                "notes": "Verified against the open Bioteau et al. introduction; the paper describes ICE conjugation as direct-contact DNA translocation mediated by a T4SS."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "integrative_mobilizable_element",
            "predicate": "depends on",
            "object": "conjugation",
            "description": "IME-type genomic islands depend on helper ICE or conjugative-plasmid transfer machinery for conjugative mobilization.",
            "evidence": [
              {
                "reference": "DOI:10.1093/nar/gkad644",
                "snippet": "spread via the conjugative apparatus encoded by a helper ICE or conjugative plasmid",
                "notes": "Verified against the open Bioteau et al. introduction; IMEs are framed as mobilizable genomic islands that rely on helper ICE or conjugative-plasmid apparatus."
              }
            ],
            "predicate_id": "RO:0002502"
          },
          {
            "subject": "integrative_conjugative_element",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "gi_trait",
            "description": "Integrative-conjugative-element possession is a genomic-island possession trait.",
            "evidence": [
              {
                "reference": "DOI:10.1093/nar/gkad644",
                "snippet": "The term \u2018genomic island\u2019 encompasses diverse types of mobile genetic elements that exhibit various structures and gene contents, including prophages, transposons, integrated plasmids, integrative and mobilizable elements (IMEs), and integrative and conjugative elements (ICEs)",
                "notes": "Bioteau et al. place integrative and conjugative elements among the mobile-genetic-element subclasses encompassed by genomic islands."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-06-05T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate GENOMICS trait (genomic island); sub-variant of mobile genetic element.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-08T14:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (HGT-acquired genomic island accessory function) with RO/biolink predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-14T06:55:38Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0009292\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 4 evidence-backed generic edges (5 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:23:53Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0043684\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope gi_hgt_accessory_function=NONMECHANISTIC with scope_notes; marked 1 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (mobility_module).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-04T05:20:00Z",
        "curator": "codex",
        "action": "REVIEW_CAUSAL_EVIDENCE",
        "changes": "Reviewed the gi_hgt_accessory_function graph for issue #183: added exact snippets to 8 genomic-island evidence items, grounded 4 residual predicates, retyped ICE/IME nodes as GENETIC_ELEMENT, and grounded the conjugation process. No paid research service was called.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-07T02:20:00Z",
        "curator": "codex",
        "action": "ADVERSARIAL_REVIEW_REPAIR",
        "changes": "Addressed PR #664 adversarial review issue #681: replaced generic Dobrindt article-preview notes with Nature Reviews Microbiology publisher-abstract verification notes.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-07T03:40:00Z",
        "curator": "codex",
        "action": "ADVERSARIAL_REVIEW_REPAIR",
        "changes": "Addressed PR #664 adversarial review issue #684: added a Bioteau-backed ICE subclass edge to reconnect the ICE/IME/T4SS/conjugation branch to the genomic island trait.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-08T03:05:00Z",
        "curator": "codex",
        "action": "ADVERSARIAL_REVIEW_REPAIR",
        "changes": "Addressed PR #664 adversarial review issue #701: removed the ICE rdfs:subClassOf genomic-island-trait edge because the source supports ICE as a genomic-island genetic element, not a subclass of the possession trait.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-27T14:42:32Z",
        "curator": "codex",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Resolved the exact ICE causal node by grounding it to traitmech:000410 and reintroducing an rdfs:subClassOf edge only after the node was retyped from a raw genetic element to the possession trait.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000506",
    "label": "GmrSD system",
    "definition": "A type IV modification-dependent restriction system in which an organism possesses a GmrSD locus encoding either separate GmrS and GmrD proteins or a fused double-domain GmrSD-family protein, that targets glucosylated hydroxymethylcytosine-containing DNA.",
    "definition_source": "DOI:10.1016/j.jmb.2006.11.051",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000496"
    ],
    "synonyms": [
      {
        "synonym_text": "GmrSD",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1016/j.jmb.2006.11.051"
      },
      {
        "synonym_text": "GmrSD_RM_Type_IV",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1016/j.jmb.2006.11.051",
        "snippet": "The Escherichia coli CT596 prophage exclusion genes gmrS and gmrD were found to encode a novel type IV modification-dependent restriction nuclease that targets and digests glucosylated (glc)-hydroxymethylcytosine (HMC) DNAs.",
        "notes": "Bair and Black experimentally support split gmrS and gmrD genes as a GmrSD Type IV modification-dependent restriction nuclease targeting glucosylated hydroxymethylcytosine DNA."
      },
      {
        "reference": "DOI:10.1016/j.jmb.2006.11.051",
        "snippet": "Nuclease activity is dependent upon the presence of both the GmrS and the GmrD proteins.",
        "notes": "Bair and Black support both split GmrS and GmrD proteins as required for the characterized CT596 GmrSD restriction activity."
      },
      {
        "reference": "DOI:10.1186/s12859-015-0773-z",
        "snippet": "GmrSD is a modification-dependent restriction endonuclease that specifically targets and cleaves glucosylated hydroxymethylcytosine (glc-HMC) modified DNA.",
        "notes": "Machnicka et al. support GmrSD as a glucosylated-hydroxymethylcytosine-targeting modification-dependent restriction endonuclease."
      },
      {
        "reference": "DOI:10.1186/s12859-015-0773-z",
        "snippet": "It is encoded either as two separate single-domain GmrS and GmrD proteins or as a single protein carrying both domains.",
        "notes": "Machnicka et al. support treating split GmrS/GmrD loci and fused double-domain GmrSD homologs within the same first-pass system family."
      },
      {
        "reference": "DOI:10.1186/s12859-015-0773-z",
        "snippet": "Moreover, we found that GmrSD systems exist predominantly as a fused, double-domain form rather than as a heterodimer and that their homologs are often encoded in regions enriched in defense and gene mobility-related elements.",
        "notes": "Machnicka et al. report that fused double-domain GmrSD systems are common and are often found near defense- and mobility-linked features."
      },
      {
        "reference": "DOI:10.1093/nar/gkt747",
        "snippet": "The new class of modification-dependent restriction enzymes was named Type IV, as distinct from the familiar modification-blocked Types I-III.",
        "notes": "Loenen and Raleigh define the Type IV class as modification-dependent restriction enzymes."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| GmrSD_RM_Type_IV | 10\\.1016/j\\.jmb\\.2006\\.11\\.051 | A type IV modification dependent restriction nuclease that targets glucosylated hydroxymethyl cytosine modified DNAs | ",
        "notes": "The pinned DefenseFinder article registry maps the GmrSD_RM_Type_IV source key to Bair and Black."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "gmrsd_restricts_glucosylated_hmc_dna",
        "title": "GmrSD restricts glucosylated HMC DNA",
        "description": "Conservative system-level sketch linking a GmrSD locus to modification-dependent restriction of glucosylated hydroxymethylcytosine DNA and to the Type IV restriction parent trait.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures GmrSD as a named Type IV modification-dependent restriction system while leaving GmrS/GmrD domain activities, complete sugar-HMC substrate breadth, split-versus-fused host breadth, IPI inhibition, and DefenseFinder RM_Type_IV HMM/rules mapping unresolved.",
        "nodes": [
          {
            "node_id": "gmrsd_locus",
            "label": "GmrSD locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A locus encoding split GmrS and GmrD proteins or a fused double-domain GmrSD-family protein."
          },
          {
            "node_id": "glucosylated_hmc_dna",
            "label": "glucosylated HMC DNA",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "DNA containing glucosylated hydroxymethylcytosine base modifications."
          },
          {
            "node_id": "gmrsd_dependent_type_iv_restriction",
            "label": "GmrSD-dependent Type IV restriction",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Modification-dependent restriction of glucosylated-hydroxymethylcytosine DNA by GmrSD."
          },
          {
            "node_id": "gmrsd_system_trait",
            "label": "GmrSD system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000506",
            "description": "Possession of a genome-encoded GmrSD modification-dependent restriction system."
          },
          {
            "node_id": "type_iv_modification_dependent_restriction",
            "label": "type IV modification-dependent restriction system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000496",
            "description": "Possession of a genome-encoded Type IV modification-dependent restriction system."
          }
        ],
        "edges": [
          {
            "subject": "gmrsd_locus",
            "predicate": "enables",
            "predicate_id": "RO:0002327",
            "object": "gmrsd_dependent_type_iv_restriction",
            "description": "The GmrSD locus encodes the proteins that cleave glucosylated hydroxymethylcytosine DNA.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.jmb.2006.11.051",
                "snippet": "Nuclease activity is dependent upon the presence of both the GmrS and the GmrD proteins.",
                "notes": "Bair and Black support both split GmrS and GmrD proteins as required for the characterized CT596 GmrSD restriction activity."
              },
              {
                "reference": "DOI:10.1186/s12859-015-0773-z",
                "snippet": "It is encoded either as two separate single-domain GmrS and GmrD proteins or as a single protein carrying both domains.",
                "notes": "Machnicka et al. support treating split GmrS/GmrD loci and fused double-domain GmrSD homologs within the same first-pass system family."
              }
            ]
          },
          {
            "subject": "gmrsd_dependent_type_iv_restriction",
            "predicate": "mitigates",
            "predicate_id": "METPO:2007407",
            "object": "glucosylated_hmc_dna",
            "description": "GmrSD-dependent Type IV restriction targets glucosylated hydroxymethylcytosine DNA.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.jmb.2006.11.051",
                "snippet": "The Escherichia coli CT596 prophage exclusion genes gmrS and gmrD were found to encode a novel type IV modification-dependent restriction nuclease that targets and digests glucosylated (glc)-hydroxymethylcytosine (HMC) DNAs.",
                "notes": "Bair and Black experimentally support split gmrS and gmrD genes as a GmrSD Type IV modification-dependent restriction nuclease targeting glucosylated hydroxymethylcytosine DNA."
              },
              {
                "reference": "DOI:10.1186/s12859-015-0773-z",
                "snippet": "GmrSD is a modification-dependent restriction endonuclease that specifically targets and cleaves glucosylated hydroxymethylcytosine (glc-HMC) modified DNA.",
                "notes": "Machnicka et al. support GmrSD as a glucosylated-hydroxymethylcytosine-targeting modification-dependent restriction endonuclease."
              }
            ]
          },
          {
            "subject": "gmrsd_dependent_type_iv_restriction",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "gmrsd_system_trait",
            "description": "GmrSD-dependent Type IV restriction realizes the organism-level GmrSD system possession trait.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s12859-015-0773-z",
                "snippet": "GmrSD is a modification-dependent restriction endonuclease that specifically targets and cleaves glucosylated hydroxymethylcytosine (glc-HMC) modified DNA.",
                "notes": "Machnicka et al. support GmrSD as a glucosylated-hydroxymethylcytosine-targeting modification-dependent restriction endonuclease."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| GmrSD_RM_Type_IV | 10\\.1016/j\\.jmb\\.2006\\.11\\.051 | A type IV modification dependent restriction nuclease that targets glucosylated hydroxymethyl cytosine modified DNAs | ",
                "notes": "The pinned DefenseFinder article registry maps the GmrSD_RM_Type_IV source key to Bair and Black."
              }
            ]
          },
          {
            "subject": "gmrsd_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "type_iv_modification_dependent_restriction",
            "description": "GmrSD system possession is a Type IV modification-dependent restriction system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.jmb.2006.11.051",
                "snippet": "The Escherichia coli CT596 prophage exclusion genes gmrS and gmrD were found to encode a novel type IV modification-dependent restriction nuclease that targets and digests glucosylated (glc)-hydroxymethylcytosine (HMC) DNAs.",
                "notes": "Bair and Black experimentally support split gmrS and gmrD genes as a GmrSD Type IV modification-dependent restriction nuclease targeting glucosylated hydroxymethylcytosine DNA."
              },
              {
                "reference": "DOI:10.1093/nar/gkt747",
                "snippet": "The new class of modification-dependent restriction enzymes was named Type IV, as distinct from the familiar modification-blocked Types I-III.",
                "notes": "Loenen and Raleigh define the Type IV class as modification-dependent restriction enzymes."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "gmrsd-defensefinder-model-gap",
        "prompt": "Resolve exact GmrS/GmrD domain activities, complete sugar-modified HMC substrate breadth, split-versus-fused host breadth, phage IPI inhibition, and DefenseFinder RM_Type_IV HMM/rules mapping before minting narrower GmrSD mechanism or component traits.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Bair and Black support split GmrS/GmrD as a Type IV modification-dependent restriction nuclease that targets glucosylated hydroxymethylcytosine DNA, Machnicka et al. support GmrSD homologs as either split or fused double-domain systems, and the pinned DefenseFinder article registry maps GmrSD_RM_Type_IV to Bair and Black. The pinned HMM inventory and rules table have no exact GmrSD or GmrSD_RM_Type_IV rows. This first-pass record therefore does not resolve a reusable DefenseFinder profile model, exact split-versus-fused prevalence across natural hosts, the complete set of sugar-modified HMC targets, the exact domain contributions of GmrS and GmrD, or the relationship between phage IPI inhibition and the organism-level GmrSD system trait.",
        "evidence": [
          {
            "reference": "DOI:10.1016/j.jmb.2006.11.051",
            "snippet": "The Escherichia coli CT596 prophage exclusion genes gmrS and gmrD were found to encode a novel type IV modification-dependent restriction nuclease that targets and digests glucosylated (glc)-hydroxymethylcytosine (HMC) DNAs.",
            "notes": "Bair and Black experimentally support split gmrS and gmrD genes as a GmrSD Type IV modification-dependent restriction nuclease targeting glucosylated hydroxymethylcytosine DNA."
          },
          {
            "reference": "DOI:10.1016/j.jmb.2006.11.051",
            "snippet": "Nuclease activity is dependent upon the presence of both the GmrS and the GmrD proteins.",
            "notes": "Bair and Black support both split GmrS and GmrD proteins as required for the characterized CT596 GmrSD restriction activity."
          },
          {
            "reference": "DOI:10.1186/s12859-015-0773-z",
            "snippet": "GmrSD is a modification-dependent restriction endonuclease that specifically targets and cleaves glucosylated hydroxymethylcytosine (glc-HMC) modified DNA.",
            "notes": "Machnicka et al. support GmrSD as a glucosylated-hydroxymethylcytosine-targeting modification-dependent restriction endonuclease."
          },
          {
            "reference": "DOI:10.1186/s12859-015-0773-z",
            "snippet": "It is encoded either as two separate single-domain GmrS and GmrD proteins or as a single protein carrying both domains.",
            "notes": "Machnicka et al. support treating split GmrS/GmrD loci and fused double-domain GmrSD homologs within the same first-pass system family."
          },
          {
            "reference": "DOI:10.1186/s12859-015-0773-z",
            "snippet": "Moreover, we found that GmrSD systems exist predominantly as a fused, double-domain form rather than as a heterodimer and that their homologs are often encoded in regions enriched in defense and gene mobility-related elements.",
            "notes": "Machnicka et al. report that fused double-domain GmrSD systems are common and are often found near defense- and mobility-linked features."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
            "snippet": "| GmrSD_RM_Type_IV | 10\\.1016/j\\.jmb\\.2006\\.11\\.051 | A type IV modification dependent restriction nuclease that targets glucosylated hydroxymethyl cytosine modified DNAs | ",
            "notes": "The pinned DefenseFinder article registry maps the GmrSD_RM_Type_IV source key to Bair and Black."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "notes": "A structured first-pass search of the pinned DefenseFinder HMM inventory found no exact GmrSD or GmrSD_RM_Type_IV row."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "A structured first-pass search of the pinned DefenseFinder rules table found no exact GmrSD or GmrSD_RM_Type_IV system row."
          }
        ],
        "attaches_to": [
          "causal_graphs#gmrsd_restricts_glucosylated_hmc_dna"
        ],
        "posed_by": "codex",
        "posed_date": "2026-10-01"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-01T04:21:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted GmrSD system as a DOI- and DefenseFinder-backed GENOMICS TraitRecord under the type IV modification-dependent restriction system parent after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v383.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-01T04:21:02Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed GmrSD system during initial curation and left canonical_examples empty because the Bair and Black and Machnicka et al. sources support the split CT596 GmrSD enzyme and broader split-or-fused GmrSD family, but not a single stable NCBITaxon strain exemplar for the organism-level GmrSD system trait. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000219",
    "label": "Hachiman system",
    "definition": "A phage defense system in which an organism possesses a Hachiman antiphage locus encoding a HamA/HamB core.",
    "definition_source": "DOI:10.1016/j.cell.2024.09.020",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "Hachiman antiphage defense system",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1016/j.cell.2024.09.020"
      },
      {
        "synonym_text": "Hachiman defense system",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1038/s41467-025-57851-1"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1016/j.cell.2024.09.020",
        "snippet": "Hachiman is a broad-spectrum antiphage defense system of unknown function",
        "notes": "Tuck et al. support Hachiman as a named broad-spectrum antiphage system."
      },
      {
        "reference": "DOI:10.1016/j.cell.2024.09.020",
        "snippet": "Hachiman is a heterodimeric nuclease-helicase complex, HamAB",
        "notes": "Tuck et al. support the HamA/HamB nuclease-helicase core of characterized Hachiman systems."
      },
      {
        "reference": "DOI:10.1016/j.cell.2024.09.020",
        "snippet": "When the HamAB complex detects DNA damage, HamB helicase activity activates HamA, unleashing nuclease activity",
        "notes": "Tuck et al. connect HamB helicase activity with HamA nuclease activation after DNA-damage detection."
      },
      {
        "reference": "DOI:10.1016/j.cell.2024.09.020",
        "snippet": "Hachiman activation degrades all DNA in the cell, creating \"phantom\" cells devoid of both phage and host DNA",
        "notes": "Tuck et al. support nonspecific DNA degradation as the type I-A Hachiman antiviral output."
      },
      {
        "reference": "DOI:10.1038/s41467-025-57851-1",
        "snippet": "The Hachiman system is a novel prokaryotic antiphage defense system comprising HamA and HamB proteins",
        "notes": "Cui et al. support the recurring Hachiman system name and its HamA/HamB composition."
      },
      {
        "reference": "DOI:10.1038/s41467-025-57851-1",
        "snippet": "HamA interacts with HamB to form a heterodimer HamAB to mediate ATP hydrolysis and execute DNA cleavage, thus implementing antiphage defense",
        "notes": "Cui et al. support a type I-B HamAB heterodimer that couples ATP hydrolysis to antiphage DNA cleavage."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:562",
        "taxon_label": "Escherichia coli",
        "note": "Tuck et al. identified Hachiman loci in E. coli ECOR04, ECOR28, and ECOR31, and showed that ECOR31 HamAB reduced plaquing by diverse double-stranded DNA phages.",
        "reference": "DOI:10.1016/j.cell.2024.09.020"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "hachiman_hamab_dna_cleavage",
        "title": "Hachiman HamAB complexes cleave DNA during antiphage defense",
        "description": "Evidence-backed process sketch linking a Hachiman locus to HamAB nuclease-helicase activity, cellular DNA degradation, and inhibition of bacteriophage progeny production.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures characterized type I-A and type I-B Hachiman nuclease-helicase outputs without asserting one universal DNA-damage trigger, DNA substrate, active nuclease domain, HamC accessory role, Cap4 architecture, phage breadth, or abortive-infection pathway across all Hachiman loci.",
        "nodes": [
          {
            "node_id": "hachiman_locus",
            "label": "Hachiman locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A Hachiman antiphage locus encoding a HamA/HamB core. This graph describes characterized type-I systems, not the HamC-containing type-II architecture represented by traitmech:000574."
          },
          {
            "node_id": "hamab_complex_assembly",
            "label": "HamAB complex assembly",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Formation of a Hachiman HamA/HamB nuclease-helicase complex capable of ATP-dependent DNA processing."
          },
          {
            "node_id": "hachiman_dna_cleavage",
            "label": "Hachiman DNA cleavage",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "HamAB-mediated cleavage or degradation of DNA during Hachiman activation."
          },
          {
            "node_id": "phage_particle_production",
            "label": "phage particle production",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Production of new infectious bacteriophage particles inside an infected bacterial host."
          },
          {
            "node_id": "hachiman_system_trait",
            "label": "Hachiman system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000219",
            "description": "Possession of a genome-encoded Hachiman antiphage defense locus."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "hachiman_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "hamab_complex_assembly",
            "description": "Hachiman loci encode HamA and HamB components that assemble into HamAB nuclease-helicase complexes.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.cell.2024.09.020",
                "snippet": "One such system is Hachiman, a two-gene locus encoding HamA",
                "notes": "Tuck et al. support HamA/HamB as the two-gene Hachiman locus core."
              },
              {
                "reference": "DOI:10.1038/s41467-025-57851-1",
                "snippet": "The Hachiman system is a novel prokaryotic antiphage defense system comprising HamA and HamB proteins",
                "notes": "Cui et al. also support HamA/HamB as the core Hachiman components."
              }
            ]
          },
          {
            "subject": "hamab_complex_assembly",
            "predicate": "enables",
            "predicate_id": "RO:0002327",
            "object": "hachiman_dna_cleavage",
            "description": "HamA/HamB complexation enables ATP-dependent DNA cleavage by Hachiman systems.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.cell.2024.09.020",
                "snippet": "When the HamAB complex detects DNA damage, HamB helicase activity activates HamA, unleashing nuclease activity",
                "notes": "Tuck et al. connect HamAB activation with HamA nuclease activity."
              },
              {
                "reference": "DOI:10.1038/s41467-025-57851-1",
                "snippet": "HamA interacts with HamB to form a heterodimer HamAB to mediate ATP hydrolysis and execute DNA cleavage",
                "notes": "Cui et al. support ATP-hydrolysis-coupled DNA cleavage by a type I-B HamAB heterodimer."
              }
            ]
          },
          {
            "subject": "hachiman_dna_cleavage",
            "predicate": "mitigates",
            "predicate_id": "METPO:2007407",
            "object": "phage_particle_production",
            "description": "Hachiman-mediated DNA degradation inhibits the generation of new phage particles.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.cell.2024.09.020",
                "snippet": "Hachiman activation degrades all DNA in the cell",
                "notes": "Tuck et al. support DNA degradation as the activated Hachiman output."
              },
              {
                "reference": "DOI:10.1016/j.cell.2024.09.020",
                "snippet": "We confirmed that Hachiman limits the production of new phage particles",
                "notes": "Tuck et al. connect Hachiman activity to restriction of phage progeny production."
              }
            ]
          },
          {
            "subject": "hachiman_dna_cleavage",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "hachiman_system_trait",
            "description": "HamAB-mediated DNA cleavage is the antiviral output that realizes the Hachiman system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-025-57851-1",
                "snippet": "execute DNA cleavage, thus implementing antiphage defense",
                "notes": "Cui et al. support DNA cleavage as an antiphage output of the Hachiman complex."
              }
            ]
          },
          {
            "subject": "hachiman_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Hachiman system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-025-57851-1",
                "snippet": "The Hachiman system is a novel prokaryotic antiphage defense system",
                "notes": "Cui et al. place Hachiman in the antiphage-defense-system family."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "hachiman-subtype-and-trigger-gap",
        "prompt": "Resolve Hachiman subtype effectors, DNA substrates, and activation triggers before minting narrower Hachiman mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Tuck et al. support DNA-damage-triggered type I-A HamAB activation and Cui et al. support type I-B HamAB ATPase and DNA-cleavage activity, but Hachiman variants need separate review before TraitMech asserts one universal triggering DNA substrate, HamA catalytic domain, HamC accessory role, Cap4 fusion architecture, phage range, or abortive-infection output. Hachiman type II system (traitmech:000574) now resolves the HamABC architecture defined by Payne et al. (DOI:10.1093/nar/gkab883) and retained by Cui et al. The DSM 14551 locus has heterologous antiphage evidence, but HamC function and type-II mechanism remain open. The family definition no longer requires universal DNA cleavage; this graph and its evidence remain restricted to characterized type-I systems. Proposal v451 replaces v96's overgeneralized family definition while preserving the stable local family identifier. Type I remains a separate architecture-class discovery lead. That architecture-class lead is now represented by traitmech:000575 Hachiman type I system for HamAB loci without HamC. The component definition follows Payne and Cui, not a failed detector hit or a type-II knockout. The existing graph still describes characterized I-A/I-B mechanisms, not all type-I subtypes. Subtype-specific mechanisms and native-locus activity remain open; no graph, example or hierarchy is changed.",
        "posed_by": "codex",
        "posed_date": "2026-09-15"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-15T14:47:54Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Hachiman system as a DOI-backed GENOMICS TraitRecord under the phage defense system parent after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v96.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-03T18:08:00Z",
        "curator": "codex",
        "action": "SCOPE_HACHIMAN_FAMILY_AND_TYPE_II",
        "changes": "Addressed #1630: removed the unsupported universal DNA-cleavage condition from the family definition while retaining the type-I mechanism evidence and graph scope. Linked the new HamABC child traitmech:000574; HamC chemistry remains an open question. Proposal v451 supersedes v96 without editing the old TSV.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-03T18:37:00Z",
        "curator": "codex",
        "action": "TRACK_HACHIMAN_TYPE_I_CLASS",
        "changes": "Linked traitmech:000575 Hachiman type I system using the component classification in DOI:10.1093/nar/gkab883 and DOI:10.1038/s41467-025-57851-1. Kept definitions, hierarchy, examples, evidence and graphs unchanged; mechanism questions remain open. No absence assertion is inferred from detector output.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000575",
    "label": "Hachiman type I system",
    "definition": "A Hachiman system in which an organism possesses a HamA/HamB locus without a HamC component.",
    "definition_source": "DOI:10.1038/s41467-025-57851-1",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000219"
    ],
    "synonyms": [
      {
        "synonym_text": "Hachiman type I",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1093/nar/gkab883"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1093/nar/gkab883",
        "snippet": "We refer to the new Hachiman systems as type II, and the original Hachiman systems as type I.",
        "notes": "Results, new-subtype classification: Payne et al. distinguish the original HamAB architecture from the newly identified HamC-associated systems. Figure 2C depicts the component contrast. These names classify system architecture, not individual proteins or organism-level disjoint classes."
      },
      {
        "reference": "DOI:10.1038/s41467-025-57851-1",
        "snippet": "Payne et al. classified the Hachiman systems that contain only HamA and HamB as type I",
        "notes": "Introduction: Cui et al. explicitly retain the HamAB-only classification, citing Payne rather than independently originating the name. Their own experiments characterize type I-A and I-B. Methods identify the type-I-B source as K-12, U00096.3 positions 2761204-2765368. Defense assays used plasmid-borne HamAB in a hamAB-deleted MG1655 host; these are not measurements of unmodified native-locus activity. The subtype results do not establish a universal type-I effector domain, activation trigger or phage spectrum."
      },
      {
        "reference": "https://raw.githubusercontent.com/padlocbio/padloc-db/9e380165633a8d6aef93b5a164cea0f3359bd33f/sys/hachiman_type_I.yaml",
        "snippet": "prohibited_genes:\n  - HamC2",
        "notes": "Pinned PADLOC rule, retrieved 2026-10-03: the core is HamA1 plus HamB1, minimum_core and minimum_total are 2, maximum_separation is 0, and force_strand is FALSE. HamC2 is prohibited in the detected system. This is a profile constraint, not proof that a biological locus lacks every divergent HamC homolog or that the whole genome lacks HamC."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/definitions/DefenseFinder/Hachiman/Hachiman.xml",
        "snippet": "<gene name=\"Hachiman__HamB\" presence=\"mandatory\"/>",
        "notes": "Pinned DefenseFinder XML, retrieved 2026-10-03: HamA_1 (exchangeable with HamA_2) and HamB are mandatory, both minimum counts are 2, and inter_gene_max_space is 5. The model has no forbidden HamC component. A raw Hachiman call therefore does not establish the type-I absence condition; complete biological locus context must be reviewed. The model name is not added as a type-I exact synonym."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:511145",
        "taxon_label": "Escherichia coli str. K-12 substr. MG1655",
        "reference": "DOI:10.1038/s41467-025-57851-1",
        "note": "Cui et al. identify the type-I-B source locus at U00096.3 positions 2761204-2765368. NCBI independently resolves that accession to K-12 MG1655, taxon 511145; the source region contains abpA (HamA) and abpB (HamB). This example denotes natural source-strain possession, not all E. coli strains or native-locus protection measured without manipulation. Their defense assays complemented a hamAB-deleted MG1655 host with plasmid-borne HamAB, and protein expression used BL21(DE3). The type-I assignment comes from the paper, not an inference of HamC absence from the retrieved sequence interval alone."
      }
    ],
    "discussions": [
      {
        "discussion_id": "hachiman-type-i-absence-and-subtype-scope",
        "prompt": "Resolve type-I subtype mechanisms without equating missing hits with component absence.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Type I denotes the literature-defined HamAB architecture without HamC, not an isolated HamA/HamB hit, an incomplete assembly, a purified-complex omission or automatic reclassification of a type-II HamC knockout. A genome may possess both type-I and type-II loci, so these possession traits are not disjoint. Cui et al. separate four HamA-domain subtypes within type I; experimental support for I-A/I-B does not validate every predicted subtype or establish one universal nuclease domain, DNA substrate, trigger or antiviral spectrum. Subtype classes remain discovery leads requiring separate source review. The broader Hachiman record already retains source-qualified I-A/I-B mechanism evidence; no duplicate or universal causal graph is added here. Native-locus activity and broader accession-resolved functional generalization remain open.",
        "posed_by": "codex",
        "posed_date": "2026-10-03"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-03T18:37:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added the literature-defined HamC-lacking HamAB possession class with two DOI sources, exact snippets, pinned detector constraints and an NCBI-resolved MG1655 source-locus example. Novelty and allocation searches included ignored and hidden files; the fresh METPO seed has no exact class. Reserved METPO:1052900 in v452. Kept natural source, engineered assays and subtype chemistry distinct.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000574",
    "label": "Hachiman type II system",
    "definition": "A Hachiman system in which an organism possesses a locus encoding HamA and HamB together with an additional HamC (DUF3223) component.",
    "definition_source": "DOI:10.1093/nar/gkab883",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000219"
    ],
    "synonyms": [
      {
        "synonym_text": "Hachiman type II",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1093/nar/gkab883"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1093/nar/gkab883",
        "snippet": "a gene encoding a DUF3223 protein (HamC) either upstream or downstream of hamAB",
        "notes": "Results, new-subtype classification: Payne et al. name this HamC-associated Hachiman architecture type II. Methods and Figure 3 identify the DSM 14551 source locus and show antiphage activity after expression in E. coli BL21-AI. The natural source and engineered assay host are distinct. The paper does not establish native-host resistance, a universal phage spectrum, HamC essentiality or HamC chemistry."
      },
      {
        "reference": "DOI:10.1038/s41467-025-57851-1",
        "snippet": "Hachiman systems that include HamA, HamB, and HamC (DUF3223) were referred to as type II",
        "notes": "Introduction: Cui et al. retain the HamABC classification and attribute it to Payne et al.; this is corroborating terminology, not an independent type-II experiment. Their biochemical experiments on type I-A/I-B do not establish DNA-damage sensing, DNA cleavage or HamC function in type II."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/definitions/DefenseFinder/Hachiman/Hachiman_II.xml",
        "snippet": "<gene name=\"Hachiman_II__HamC\" presence=\"mandatory\"/>",
        "notes": "Pinned DefenseFinder XML, retrieved 2026-10-03: HamA (HamA_1 with HamA_2 exchangeable), HamB and HamC are marked mandatory, but both minimum gene counts are 2 and the inter-gene maximum space is 5. Thus the model does not require all three marked components in every accepted call; a raw Hachiman_II call alone is insufficient to establish the complete biological architecture. This is a detector constraint, not an experiment or a trait synonym."
      },
      {
        "reference": "https://raw.githubusercontent.com/padlocbio/padloc-db/9e380165633a8d6aef93b5a164cea0f3359bd33f/sys/hachiman_type_II.yaml",
        "snippet": "minimum_core: 3\nminimum_total: 3\ncore_genes:\n  - HamA2\n  - HamB2\n  - HamC2",
        "notes": "Pinned PADLOC rule, retrieved 2026-10-03: all three core components are required, maximum_separation is 0 and force_strand is FALSE. This differs from DefenseFinder's two-gene minimum; neither detector proves functional defense or experimental necessity of each component."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:173675",
        "taxon_label": "Sphingopyxis witflariensis",
        "reference": "DOI:10.1093/nar/gkab883",
        "note": "DSM 14551 is the natural source of the type-II locus amplified from genomic DNA by Payne et al. (NZ_NISJ01000011.1). The NCBI GenBank source feature independently identifies DSM 14551 and taxon 173675. This example denotes possession in this source strain, not all members of the species or native-host resistance. The reported defense assays used engineered E. coli BL21-AI."
      }
    ],
    "discussions": [
      {
        "discussion_id": "hachiman-type-ii-component-and-mechanism-scope",
        "prompt": "Resolve HamC function and type-II mechanisms beyond heterologous defense assays.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Type II denotes the HamABC locus architecture, not a HamC hit alone, a source database row or a fixed phage-protection phenotype. Type-I DNA-damage sensing and DNA-cleavage mechanisms are not generalized to this class; HamC's biochemical role and necessity remain unresolved by these sources. No causal mechanism graph or unverified protein accession is asserted. Native-host assays and accession-resolved functional evidence remain desirable. DefenseFinder and PADLOC have different component-count rules; inspect complete locus context before converting calls into trait assertions. Component absence cannot be inferred from a failed hit or incomplete assembly. Type I remains a separate discovery lead, and coexisting loci would not make organism-level type-I and type-II possession traits disjoint. The type-I lead is now represented by traitmech:000575 Hachiman type I system for the literature-defined HamC-lacking HamAB architecture. This does not imply organism-level disjointness, turn missing detector hits into absence evidence, or transfer type-I chemistry to type II. HamC function and type-II mechanisms remain unresolved.",
        "posed_by": "codex",
        "posed_date": "2026-10-03"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-03T18:08:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added the literature-defined HamABC possession class with two DOI sources, exact snippets, pinned detector rules and the NCBI-resolved DSM 14551 example. Searches included ignored and hidden files and found no exact live record or METPO class. Reserved METPO:1052801 in v451; METPO:1052800 replaces the broad parent's v96 proposal. Kept natural source, heterologous activity and type-I chemistry distinct.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-03T18:37:00Z",
        "curator": "codex",
        "action": "TRACK_HACHIMAN_TYPE_I_CLASS",
        "changes": "Linked traitmech:000575 Hachiman type I system using the component classification in DOI:10.1093/nar/gkab883 and DOI:10.1038/s41467-025-57851-1. Kept definitions, hierarchy, examples, evidence and graphs unchanged; mechanism questions remain open. No absence assertion is inferred from detector output.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000242",
    "label": "Hailong system",
    "definition": "A phage defense system in which an organism possesses a Hailong locus encoding a HalB NTase DNA-signal enzyme and a HalA membrane effector complex that can be held inactive by HalB-derived oligodeoxyadenylate until viral DNA exonucleases release the primed HalA complex and induce protective host cell growth arrest.",
    "definition_source": "DOI:10.1038/s41586-025-09058-z",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "Hailong anti-phage system",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1016/j.molcel.2025.06.011"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/s41586-025-09058-z",
        "snippet": "Here we discover a family of bacterial defence systems, which we name Hailong, that use NTase enzymes to constitutively synthesize DNA signals and guard against phage infection",
        "notes": "Tan et al. support Hailong as a named NTase-linked bacterial phage-defense family."
      },
      {
        "reference": "DOI:10.1038/s41586-025-09058-z",
        "snippet": "Hailong is a two-gene operon that encodes Hailong protein A (HalA), a transmembrane protein of unknown function, and Hailong protein B (HalB), the predicted NTase enzyme",
        "notes": "Tan et al. support curating the two core Hailong genes as a complete locus rather than as separate HalA or HalB protein traits."
      },
      {
        "reference": "DOI:10.1038/s41586-025-09058-z",
        "snippet": "Hailong operons are widely conserved in defence islands across >70 genera of gram-positive and gram-negative bacteria",
        "notes": "Tan et al. support placing Hailong at a bacterial system level rather than curating only the assayed plasmid or species instances."
      },
      {
        "reference": "DOI:10.1038/s41586-025-09058-z",
        "snippet": "Hailong protein B (HalB) is an NTase that converts deoxy-ATP into single-stranded DNA oligomers",
        "notes": "Tan et al. identify the HalB NTase signal-synthesis reaction inside the Hailong system."
      },
      {
        "reference": "DOI:10.1038/s41586-025-09058-z",
        "snippet": "We show that HalB DNA signals bind to and repress activation of a partnering Hailong protein A (HalA) effector complex",
        "notes": "Tan et al. support repression of the HalA effector complex by HalB-derived DNA signals."
      },
      {
        "reference": "DOI:10.1038/s41586-025-09058-z",
        "snippet": "viral DNA exonucleases required for phage replication trigger release of the primed HalA complex and induce protective host cell growth arrest",
        "notes": "Tan et al. support the phage-exonuclease trigger and growth-arrest output captured in the Hailong graph."
      },
      {
        "reference": "DOI:10.1016/j.molcel.2025.06.011",
        "snippet": "the bacterial Hailong anti-phage system, in which constitutively synthesized DNA oligonucleotides inhibit a toxic ion channel-a molecular booby trap primed for activation by phage exonucleases",
        "notes": "Kuehn and Pinilla-Redondo summarize Hailong as a bacterial anti-phage system gated by constitutive inhibitory DNA oligonucleotide signals."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:562",
        "taxon_label": "Escherichia coli",
        "note": "Tan et al. showed that an Escherichia coli STEC 1178 Hailong system gave more than 10,000-fold protection against dsDNA phages in E. coli challenge assays.",
        "reference": "DOI:10.1038/s41586-025-09058-z"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "hailong_dna_gated_growth_arrest",
        "title": "Hailong DNA-signal gating couples phage exonuclease challenge to growth arrest",
        "description": "Evidence-backed process sketch linking a Hailong locus to HalB oligodeoxyadenylate signal synthesis, HalA effector repression, viral DNA exonuclease challenge, HalA channel activation, and host cell growth arrest.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Tan et al. Hailong oligodeoxyadenylate-gated phage-exonuclease-response evidence without asserting one universal ODA-transfer mechanism, phage trigger, HalA ion specificity, ancillary gene architecture, or host-processing factor across all Hailong homologs.",
        "nodes": [
          {
            "node_id": "hailong_locus",
            "label": "Hailong locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A Hailong phage-defense locus encoding a HalA membrane effector and a HalB NTase signal enzyme."
          },
          {
            "node_id": "oda_signal_synthesis",
            "label": "oligodeoxyadenylate signal synthesis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Constitutive synthesis of single-stranded DNA oligodeoxyadenylate signals by the Hailong HalB NTase."
          },
          {
            "node_id": "hala_oda_repressed_complex",
            "label": "HalA-oligodeoxyadenylate repressed complex",
            "node_type": "STATE",
            "description": "A primed, repressed HalA effector complex bound to HalB-derived oligodeoxyadenylate."
          },
          {
            "node_id": "phage_exonuclease_challenge",
            "label": "phage exonuclease challenge",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Viral DNA exonuclease activity encountered during phage replication that degrades the Hailong inhibitory DNA signal."
          },
          {
            "node_id": "hala_channel_activation",
            "label": "HalA channel activation",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "Release of Hailong HalA ion-channel effector function after inhibitory oligodeoxyadenylate is removed."
          },
          {
            "node_id": "host_cell_growth_arrest",
            "label": "host cell growth arrest",
            "node_type": "STATE",
            "description": "Protective arrest of host-cell growth downstream of Hailong HalA effector activation."
          },
          {
            "node_id": "hailong_system_trait",
            "label": "Hailong system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000242",
            "description": "Possession of a genome-encoded Hailong phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "hailong_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "oda_signal_synthesis",
            "description": "The Hailong locus encodes HalB, an NTase that constitutively synthesizes oligodeoxyadenylate DNA signals.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41586-025-09058-z",
                "snippet": "Hailong protein B (HalB) is an NTase that converts deoxy-ATP into single-stranded DNA oligomers",
                "notes": "Tan et al. identify HalB as the DNA-signal-synthesizing Hailong NTase."
              }
            ]
          },
          {
            "subject": "oda_signal_synthesis",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "hala_oda_repressed_complex",
            "description": "HalB-derived DNA signals bind the HalA effector complex and hold the complex in a primed, repressed state before phage infection.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41586-025-09058-z",
                "snippet": "We show that HalB DNA signals bind to and repress activation of a partnering Hailong protein A (HalA) effector complex",
                "notes": "Tan et al. support formation of a repressed HalA effector complex by HalB-derived DNA signals."
              }
            ]
          },
          {
            "subject": "hala_oda_repressed_complex",
            "predicate": "negatively regulates",
            "predicate_id": "RO:0002212",
            "object": "hala_channel_activation",
            "description": "Oligodeoxyadenylate binding negatively regulates HalA channel function by locking the membrane effector in an inactive state.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41586-025-09058-z",
                "snippet": "These results support that ODA-binding negatively regulates HalA channel function",
                "notes": "Tan et al. directly support negative regulation of HalA channel function by ODA binding."
              }
            ]
          },
          {
            "subject": "phage_exonuclease_challenge",
            "predicate": "activates",
            "predicate_id": "RO:0002213",
            "object": "hala_channel_activation",
            "description": "Viral DNA exonucleases degrade the inhibitory Hailong signal and trigger release of the primed HalA effector complex.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41586-025-09058-z",
                "snippet": "viral DNA exonucleases required for phage replication trigger release of the primed HalA complex",
                "notes": "Tan et al. support viral DNA exonucleases as triggers for release of primed HalA."
              }
            ]
          },
          {
            "subject": "hala_channel_activation",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "host_cell_growth_arrest",
            "description": "Release of HalA channel effector function links phage exonuclease sensing to protective host cell growth arrest.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41586-025-09058-z",
                "snippet": "viral DNA replication enzymes that degrade ODA and trigger release of HalA ion channel effector function",
                "notes": "Tan et al. connect ODA degradation to release of HalA ion-channel effector function."
              },
              {
                "reference": "DOI:10.1038/s41586-025-09058-z",
                "snippet": "viral DNA exonucleases required for phage replication trigger release of the primed HalA complex and induce protective host cell growth arrest",
                "notes": "Tan et al. support host cell growth arrest as a protective Hailong output after phage-exonuclease challenge."
              }
            ]
          },
          {
            "subject": "host_cell_growth_arrest",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "hailong_system_trait",
            "description": "Hailong-mediated host growth arrest is the phage-defense output that realizes the Hailong system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41586-025-09058-z",
                "snippet": "Hailong from the bacterium E. coli STEC 1178 providing >10,000-fold protection against dsDNA phages",
                "notes": "Tan et al. support Hailong-mediated growth arrest as part of a plasmid-borne system that protects E. coli against phage infection."
              }
            ]
          },
          {
            "subject": "hailong_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Hailong system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41586-025-09058-z",
                "snippet": "Here we discover a family of bacterial defence systems, which we name Hailong",
                "notes": "Tan et al. place Hailong in the bacterial phage-defense system family."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "hailong-mechanism-and-family-breadth-gap",
        "prompt": "Resolve Hailong ODA transfer, phage-trigger breadth, HalA ion specificity, and family architecture before minting narrower Hailong mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Tan et al. support HalB oligodeoxyadenylate synthesis, HalA repression by inhibitory DNA signals, and viral DNA-exonuclease-triggered release of HalA effector function, but Hailong homologs need separate review before TraitMech asserts one complete ODA-transfer pathway, phage nuclease trigger, HalA ion selectivity, host-processing factor, or ancillary-gene architecture across the full Hailong family.",
        "posed_by": "codex",
        "posed_date": "2026-09-18"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-18T13:27:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Hailong system as a DOI-backed GENOMICS TraitRecord under the phage defense system parent after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v119.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000417",
    "label": "HEC-02 system",
    "definition": "A phage defense system in which an organism possesses the two-gene HEC-02 Hma-embedded candidate locus, encoding an ABC ATPase and an associated nuclease-related domain protein, that can reduce bacteriophage plaquing.",
    "definition_source": "DOI:10.1101/2024.01.29.577857",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "HEC-02",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1101/2024.01.29.577857"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1101/2024.01.29.577857",
        "snippet": "The candidate systems encoded diverse protein families, including three ATPases associated with either a topoisomerase-primase (TOPRIM) (HEC-01), nuclease-related (NERD) (HEC-02), or PilT N-terminal (PIN) (HEC-03) domain-containing protein",
        "notes": "Payne et al. identify HEC-02 as a candidate two-gene Hma-embedded antiviral system pairing an ATPase with a nuclease-related-domain protein."
      },
      {
        "reference": "DOI:10.1101/2024.01.29.577857",
        "snippet": "A quantitative assessment of the remaining systems showed that these were able to reduce the EOP of at least two phages by several orders of magnitude compared to the control",
        "notes": "Payne et al. support reduced plaquing for the active Hma-embedded candidate systems after excluding inactive HEC-01 and HEC-09 candidates."
      },
      {
        "reference": "DOI:10.1101/2024.01.29.577857",
        "snippet": "For the two-gene systems HEC-02 and HEC-03, both genes were required for defence",
        "notes": "Payne et al. show that both genes in the two-gene HEC-02 candidate system were required for defense."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| HEC-02 | 10\\.1101/2024\\.01\\.29\\.577857 | New antiviral defences are genetically embedded within prokaryotic immune systems |",
        "notes": "The pinned DefenseFinder article registry maps the HEC-02 source key to the Payne et al. Hma-embedded-candidate preprint."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| HEC-02__HEC-02A                                  |                                                  | HEC-02                 | Custom                  | 100    |",
        "notes": "The pinned DefenseFinder HMM inventory records HEC-02__HEC-02A as a custom HEC-02 profile."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| HEC-02__HEC-02B                                  |                                                  | HEC-02                 | Custom                  | 20     |",
        "notes": "The pinned DefenseFinder HMM inventory records HEC-02__HEC-02B as a custom HEC-02 profile."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "hec_02_locus_reduces_phage_plaquing",
        "title": "HEC-02 loci reduce bacteriophage plaquing",
        "description": "Conservative system-level sketch linking the two-gene HEC-02 locus to reduced bacteriophage plaquing and HEC-02 system possession.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures HEC-02 at candidate locus and anti-phage-output level without asserting native host breadth, exact profile-to-component mapping, the direct viral trigger or substrate, exact molecular output, or a DefenseFinder detection rule absent from the pinned rules table.",
        "nodes": [
          {
            "node_id": "hec_02_locus",
            "label": "HEC-02 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A two-gene Hma-embedded candidate locus represented in the pinned DefenseFinder HMM inventory by HEC-02A and HEC-02B custom profiles."
          },
          {
            "node_id": "reduced_phage_plaquing",
            "label": "reduced bacteriophage plaquing",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced efficiency of plaquing by bacteriophages in cells carrying a complete HEC-02 candidate system."
          },
          {
            "node_id": "hec_02_system_trait",
            "label": "HEC-02 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000417",
            "description": "Possession of a genome-encoded HEC-02 phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "hec_02_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "reduced_phage_plaquing",
            "description": "The two-gene HEC-02 locus contributes to reduced bacteriophage plaquing when both HEC-02 genes are present.",
            "evidence": [
              {
                "reference": "DOI:10.1101/2024.01.29.577857",
                "snippet": "The candidate systems encoded diverse protein families, including three ATPases associated with either a topoisomerase-primase (TOPRIM) (HEC-01), nuclease-related (NERD) (HEC-02), or PilT N-terminal (PIN) (HEC-03) domain-containing protein",
                "notes": "Payne et al. identify HEC-02 as pairing an ATPase with a nuclease-related-domain protein."
              },
              {
                "reference": "DOI:10.1101/2024.01.29.577857",
                "snippet": "For the two-gene systems HEC-02 and HEC-03, both genes were required for defence",
                "notes": "Payne et al. show that HEC-02 requires both genes for defense."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| HEC-02__HEC-02A                                  |                                                  | HEC-02                 | Custom                  | 100    |",
                "notes": "The pinned DefenseFinder HMM inventory records HEC-02__HEC-02A as a custom HEC-02 profile."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| HEC-02__HEC-02B                                  |                                                  | HEC-02                 | Custom                  | 20     |",
                "notes": "The pinned DefenseFinder HMM inventory records HEC-02__HEC-02B as a custom HEC-02 profile."
              }
            ]
          },
          {
            "subject": "reduced_phage_plaquing",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "hec_02_system_trait",
            "description": "HEC-02-mediated plaquing reduction realizes the HEC-02 system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1101/2024.01.29.577857",
                "snippet": "A quantitative assessment of the remaining systems showed that these were able to reduce the EOP of at least two phages by several orders of magnitude compared to the control",
                "notes": "Payne et al. support reduced efficiency of plaquing for the active HEC systems."
              },
              {
                "reference": "DOI:10.1101/2024.01.29.577857",
                "snippet": "For the two-gene systems HEC-02 and HEC-03, both genes were required for defence",
                "notes": "Payne et al. show that complete HEC-02 requires both genes for defense."
              }
            ]
          },
          {
            "subject": "hec_02_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "HEC-02 system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| HEC-02 | 10\\.1101/2024\\.01\\.29\\.577857 | New antiviral defences are genetically embedded within prokaryotic immune systems |",
                "notes": "The pinned DefenseFinder article registry maps the HEC-02 source key to the Payne et al. Hma-embedded-candidate preprint."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "hec-02-defensefinder-model-gap",
        "prompt": "Resolve HEC-02 native host breadth, exact HEC-02A/HEC-02B component functions, sensitive-phage breadth, molecular output, and rule-level detection criteria before minting narrower HEC-02 mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Payne et al. support HEC-02 as an Hma-embedded candidate anti-phage system whose two genes are both required for defense, and the pinned DefenseFinder HMM inventory records HEC-02A and HEC-02B profile rows. The pinned rules table has no HEC-02 row, and the first-pass record does not yet resolve natural host breadth, HEC-02 profile-to-component mapping, phage target breadth, or the direct molecular output.",
        "evidence": [
          {
            "reference": "DOI:10.1101/2024.01.29.577857",
            "snippet": "The candidate systems encoded diverse protein families, including three ATPases associated with either a topoisomerase-primase (TOPRIM) (HEC-01), nuclease-related (NERD) (HEC-02), or PilT N-terminal (PIN) (HEC-03) domain-containing protein",
            "notes": "Payne et al. identify HEC-02 as one of the ATPase-associated Hma-embedded candidate systems."
          },
          {
            "reference": "DOI:10.1101/2024.01.29.577857",
            "snippet": "For the two-gene systems HEC-02 and HEC-03, both genes were required for defence",
            "notes": "Payne et al. support two-gene requirement for HEC-02-mediated defense."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
            "snippet": "| HEC-02 | 10\\.1101/2024\\.01\\.29\\.577857 | New antiviral defences are genetically embedded within prokaryotic immune systems |",
            "notes": "The pinned DefenseFinder article registry maps the HEC-02 source key to the Payne et al. Hma-embedded-candidate preprint."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| HEC-02__HEC-02A                                  |                                                  | HEC-02                 | Custom                  | 100    |",
            "notes": "The pinned DefenseFinder HMM inventory records HEC-02__HEC-02A as a custom HEC-02 profile."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| HEC-02__HEC-02B                                  |                                                  | HEC-02                 | Custom                  | 20     |",
            "notes": "The pinned DefenseFinder HMM inventory records HEC-02__HEC-02B as a custom HEC-02 profile."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "The pinned DefenseFinder rules table does not list HEC-02, leaving rule-level detection criteria unresolved."
          }
        ],
        "attaches_to": [
          "causal_graphs#hec_02_locus_reduces_phage_plaquing"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-27"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-27T20:52:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted HEC-02 system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; kept the graph at two-gene candidate-locus level because the pinned DefenseFinder HEC-02 HMM rows are not backed by pinned rules rows; the replacement placeholder is reserved in proposals/metpo_traitmech_v294.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-27T20:52:01Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed HEC-02 system during canonical-example issue 444 enforcement and left canonical_examples empty because the sources support heterologous efficiency-of-plaquing assays and DefenseFinder HEC-02 HMM rows, but not a direct named native microbial isolate exemplar with experimentally verified endogenous HEC-02 activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000418",
    "label": "HEC-03 system",
    "definition": "A phage defense system in which an organism possesses the two-gene HEC-03 Hma-embedded candidate locus, encoding an ABC ATPase and an associated PilT N-terminal domain protein, that can reduce bacteriophage plaquing.",
    "definition_source": "DOI:10.1101/2024.01.29.577857",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "HEC-03",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1101/2024.01.29.577857"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1101/2024.01.29.577857",
        "snippet": "The candidate systems encoded diverse protein families, including three ATPases associated with either a topoisomerase-primase (TOPRIM) (HEC-01), nuclease-related (NERD) (HEC-02), or PilT N-terminal (PIN) (HEC-03) domain-containing protein",
        "notes": "Payne et al. identify HEC-03 as a candidate two-gene Hma-embedded antiviral system pairing an ATPase with a PilT N-terminal-domain protein."
      },
      {
        "reference": "DOI:10.1101/2024.01.29.577857",
        "snippet": "A quantitative assessment of the remaining systems showed that these were able to reduce the EOP of at least two phages by several orders of magnitude compared to the control",
        "notes": "Payne et al. support reduced plaquing for the active Hma-embedded candidate systems after excluding inactive HEC-01 and HEC-09 candidates."
      },
      {
        "reference": "DOI:10.1101/2024.01.29.577857",
        "snippet": "For the two-gene systems HEC-02 and HEC-03, both genes were required for defence",
        "notes": "Payne et al. show that both genes in the two-gene HEC-03 candidate system were required for defense."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| HEC-03 | 10\\.1101/2024\\.01\\.29\\.577857 | New antiviral defences are genetically embedded within prokaryotic immune systems |",
        "notes": "The pinned DefenseFinder article registry maps the HEC-03 source key to the Payne et al. Hma-embedded-candidate preprint."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| HEC-03__HEC-03A                                  |                                                  | HEC-03                 | Custom                  | 50     |",
        "notes": "The pinned DefenseFinder HMM inventory records HEC-03__HEC-03A as a custom HEC-03 profile."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| HEC-03__HEC-03B                                  |                                                  | HEC-03                 | Custom                  | 150    |",
        "notes": "The pinned DefenseFinder HMM inventory records HEC-03__HEC-03B as a custom HEC-03 profile."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "hec_03_locus_reduces_phage_plaquing",
        "title": "HEC-03 loci reduce bacteriophage plaquing",
        "description": "Conservative system-level sketch linking the two-gene HEC-03 locus to reduced bacteriophage plaquing and HEC-03 system possession.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures HEC-03 at candidate locus and anti-phage-output level without asserting native host breadth, exact profile-to-component mapping, the direct viral trigger or substrate, exact molecular output, or a DefenseFinder detection rule absent from the pinned rules table.",
        "nodes": [
          {
            "node_id": "hec_03_locus",
            "label": "HEC-03 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A two-gene Hma-embedded candidate locus represented in the pinned DefenseFinder HMM inventory by HEC-03A and HEC-03B custom profiles."
          },
          {
            "node_id": "reduced_phage_plaquing",
            "label": "reduced bacteriophage plaquing",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced efficiency of plaquing by bacteriophages in cells carrying a complete HEC-03 candidate system."
          },
          {
            "node_id": "hec_03_system_trait",
            "label": "HEC-03 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000418",
            "description": "Possession of a genome-encoded HEC-03 phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "hec_03_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "reduced_phage_plaquing",
            "description": "The two-gene HEC-03 locus contributes to reduced bacteriophage plaquing when both HEC-03 genes are present.",
            "evidence": [
              {
                "reference": "DOI:10.1101/2024.01.29.577857",
                "snippet": "The candidate systems encoded diverse protein families, including three ATPases associated with either a topoisomerase-primase (TOPRIM) (HEC-01), nuclease-related (NERD) (HEC-02), or PilT N-terminal (PIN) (HEC-03) domain-containing protein",
                "notes": "Payne et al. identify HEC-03 as pairing an ATPase with a PilT N-terminal-domain protein."
              },
              {
                "reference": "DOI:10.1101/2024.01.29.577857",
                "snippet": "For the two-gene systems HEC-02 and HEC-03, both genes were required for defence",
                "notes": "Payne et al. show that HEC-03 requires both genes for defense."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| HEC-03__HEC-03A                                  |                                                  | HEC-03                 | Custom                  | 50     |",
                "notes": "The pinned DefenseFinder HMM inventory records HEC-03__HEC-03A as a custom HEC-03 profile."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| HEC-03__HEC-03B                                  |                                                  | HEC-03                 | Custom                  | 150    |",
                "notes": "The pinned DefenseFinder HMM inventory records HEC-03__HEC-03B as a custom HEC-03 profile."
              }
            ]
          },
          {
            "subject": "reduced_phage_plaquing",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "hec_03_system_trait",
            "description": "HEC-03-mediated plaquing reduction realizes the HEC-03 system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1101/2024.01.29.577857",
                "snippet": "A quantitative assessment of the remaining systems showed that these were able to reduce the EOP of at least two phages by several orders of magnitude compared to the control",
                "notes": "Payne et al. support reduced efficiency of plaquing for the active HEC systems."
              },
              {
                "reference": "DOI:10.1101/2024.01.29.577857",
                "snippet": "For the two-gene systems HEC-02 and HEC-03, both genes were required for defence",
                "notes": "Payne et al. show that complete HEC-03 requires both genes for defense."
              }
            ]
          },
          {
            "subject": "hec_03_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "HEC-03 system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| HEC-03 | 10\\.1101/2024\\.01\\.29\\.577857 | New antiviral defences are genetically embedded within prokaryotic immune systems |",
                "notes": "The pinned DefenseFinder article registry maps the HEC-03 source key to the Payne et al. Hma-embedded-candidate preprint."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "hec-03-defensefinder-model-gap",
        "prompt": "Resolve HEC-03 native host breadth, exact HEC-03A/HEC-03B component functions, sensitive-phage breadth, molecular output, and rule-level detection criteria before minting narrower HEC-03 mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Payne et al. support HEC-03 as an Hma-embedded candidate anti-phage system whose two genes are both required for defense, and the pinned DefenseFinder HMM inventory records HEC-03A and HEC-03B profile rows. The pinned rules table has no HEC-03 row, and the first-pass record does not yet resolve natural host breadth, HEC-03 profile-to-component mapping, phage target breadth, or the direct molecular output.",
        "evidence": [
          {
            "reference": "DOI:10.1101/2024.01.29.577857",
            "snippet": "The candidate systems encoded diverse protein families, including three ATPases associated with either a topoisomerase-primase (TOPRIM) (HEC-01), nuclease-related (NERD) (HEC-02), or PilT N-terminal (PIN) (HEC-03) domain-containing protein",
            "notes": "Payne et al. identify HEC-03 as one of the ATPase-associated Hma-embedded candidate systems."
          },
          {
            "reference": "DOI:10.1101/2024.01.29.577857",
            "snippet": "For the two-gene systems HEC-02 and HEC-03, both genes were required for defence",
            "notes": "Payne et al. support two-gene requirement for HEC-03-mediated defense."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
            "snippet": "| HEC-03 | 10\\.1101/2024\\.01\\.29\\.577857 | New antiviral defences are genetically embedded within prokaryotic immune systems |",
            "notes": "The pinned DefenseFinder article registry maps the HEC-03 source key to the Payne et al. Hma-embedded-candidate preprint."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| HEC-03__HEC-03A                                  |                                                  | HEC-03                 | Custom                  | 50     |",
            "notes": "The pinned DefenseFinder HMM inventory records HEC-03__HEC-03A as a custom HEC-03 profile."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| HEC-03__HEC-03B                                  |                                                  | HEC-03                 | Custom                  | 150    |",
            "notes": "The pinned DefenseFinder HMM inventory records HEC-03__HEC-03B as a custom HEC-03 profile."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "The pinned DefenseFinder rules table does not list HEC-03, leaving rule-level detection criteria unresolved."
          }
        ],
        "attaches_to": [
          "causal_graphs#hec_03_locus_reduces_phage_plaquing"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-27"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-27T21:21:54Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted HEC-03 system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; kept the graph at two-gene candidate-locus level because the pinned DefenseFinder HEC-03 HMM rows are not backed by pinned rules rows; the replacement placeholder is reserved in proposals/metpo_traitmech_v295.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-27T21:21:55Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed HEC-03 system during canonical-example issue 444 enforcement and left canonical_examples empty because the sources support heterologous efficiency-of-plaquing assays and DefenseFinder HEC-03 HMM rows, but not a direct named native microbial isolate exemplar with experimentally verified endogenous HEC-03 activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000465",
    "label": "HEC-04 system",
    "definition": "A phage defense system in which an organism possesses the single-gene HEC-04 Hma-embedded candidate locus, encoding an ABC ATPase fused to a TOPRIM-family nuclease domain, that can reduce bacteriophage plaquing.",
    "definition_source": "DOI:10.1101/2024.01.29.577857",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "HEC-04",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1101/2024.01.29.577857"
      },
      {
        "synonym_text": "HEC-04__HEC-04",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1101/2024.01.29.577857",
        "snippet": "an ATPase fused to a TOPRIM domain (HEC-04)",
        "notes": "Payne et al. identify HEC-04 as a Hma-embedded antiviral candidate encoding an ATPase fused to a TOPRIM domain."
      },
      {
        "reference": "DOI:10.1101/2024.01.29.577857",
        "snippet": "A quantitative assessment of the remaining systems showed that these were able to reduce the EOP of at least two phages by several orders of magnitude compared to the control",
        "notes": "Payne et al. support reduced plaquing for the active Hma-embedded candidate systems after excluding inactive HEC-01 and HEC-09 candidates."
      },
      {
        "reference": "DOI:10.1101/2024.01.29.577857",
        "snippet": "For HEC-04, mutation of key active site residues in either the ABC ATPase or nuclease domains demonstrated their essential roles in defence",
        "notes": "Payne et al. show that HEC-04 defense requires intact ABC ATPase and nuclease active-site residues."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| HEC-04 | 10\\.1101/2024\\.01\\.29\\.577857 | New antiviral defences are genetically embedded within prokaryotic immune systems |",
        "notes": "The pinned DefenseFinder article registry maps the HEC-04 source key to the Payne et al. Hma-embedded-candidate preprint."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| HEC-04__HEC-04                                   |                                                  | HEC-04                 | Custom                  | 200    |",
        "notes": "The pinned DefenseFinder HMM inventory records HEC-04__HEC-04 as a custom HEC-04 profile."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "hec_04_locus_reduces_phage_plaquing",
        "title": "HEC-04 loci reduce bacteriophage plaquing",
        "description": "Conservative system-level sketch linking the single-gene HEC-04 locus to reduced bacteriophage plaquing and HEC-04 system possession.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures HEC-04 at candidate locus and anti-phage-output level without asserting native host breadth, the direct viral trigger or substrate, exact molecular output, or a DefenseFinder detection rule absent from the pinned rules table.",
        "nodes": [
          {
            "node_id": "hec_04_locus",
            "label": "HEC-04 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A single-gene Hma-embedded candidate locus represented in the pinned DefenseFinder HMM inventory by a HEC-04 custom profile."
          },
          {
            "node_id": "reduced_phage_plaquing",
            "label": "reduced bacteriophage plaquing",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced efficiency of plaquing by bacteriophages in cells carrying a complete HEC-04 candidate system."
          },
          {
            "node_id": "hec_04_system_trait",
            "label": "HEC-04 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000465",
            "description": "Possession of a genome-encoded HEC-04 phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "hec_04_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "reduced_phage_plaquing",
            "description": "The HEC-04 locus contributes to reduced bacteriophage plaquing when ABC ATPase and nuclease active-site residues are intact.",
            "evidence": [
              {
                "reference": "DOI:10.1101/2024.01.29.577857",
                "snippet": "an ATPase fused to a TOPRIM domain (HEC-04)",
                "notes": "Payne et al. identify HEC-04 as encoding an ATPase-TOPRIM fused protein."
              },
              {
                "reference": "DOI:10.1101/2024.01.29.577857",
                "snippet": "For HEC-04, mutation of key active site residues in either the ABC ATPase or nuclease domains demonstrated their essential roles in defence",
                "notes": "Payne et al. show that HEC-04 requires intact ATPase and nuclease domains for defense."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| HEC-04__HEC-04                                   |                                                  | HEC-04                 | Custom                  | 200    |",
                "notes": "The pinned DefenseFinder HMM inventory records HEC-04__HEC-04 as a custom HEC-04 profile."
              }
            ]
          },
          {
            "subject": "reduced_phage_plaquing",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "hec_04_system_trait",
            "description": "HEC-04-mediated plaquing reduction realizes the HEC-04 system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1101/2024.01.29.577857",
                "snippet": "A quantitative assessment of the remaining systems showed that these were able to reduce the EOP of at least two phages by several orders of magnitude compared to the control",
                "notes": "Payne et al. support reduced efficiency of plaquing for the active HEC systems."
              },
              {
                "reference": "DOI:10.1101/2024.01.29.577857",
                "snippet": "For HEC-04, mutation of key active site residues in either the ABC ATPase or nuclease domains demonstrated their essential roles in defence",
                "notes": "Payne et al. support ABC ATPase and nuclease active-site requirements for HEC-04-mediated defense."
              }
            ]
          },
          {
            "subject": "hec_04_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "HEC-04 system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| HEC-04 | 10\\.1101/2024\\.01\\.29\\.577857 | New antiviral defences are genetically embedded within prokaryotic immune systems |",
                "notes": "The pinned DefenseFinder article registry maps the HEC-04 source key to the Payne et al. Hma-embedded-candidate preprint."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "hec-04-defensefinder-model-gap",
        "prompt": "Resolve HEC-04 native host breadth, sensitive-phage breadth, ATPase-TOPRIM molecular output, and rule-level detection criteria before minting narrower HEC-04 mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Payne et al. support HEC-04 as a single-gene Hma-embedded candidate anti-phage system whose ABC ATPase and nuclease domains are both required for defense, and the pinned DefenseFinder HMM inventory records one HEC-04 profile row. The pinned rules table has no HEC-04 row, and the first-pass record does not yet resolve natural host breadth, phage target breadth, or the direct molecular output.",
        "evidence": [
          {
            "reference": "DOI:10.1101/2024.01.29.577857",
            "snippet": "an ATPase fused to a TOPRIM domain (HEC-04)",
            "notes": "Payne et al. identify HEC-04 as the ATPase-TOPRIM Hma-embedded candidate system."
          },
          {
            "reference": "DOI:10.1101/2024.01.29.577857",
            "snippet": "For HEC-04, mutation of key active site residues in either the ABC ATPase or nuclease domains demonstrated their essential roles in defence",
            "notes": "Payne et al. support HEC-04 domain requirements for defense."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
            "snippet": "| HEC-04 | 10\\.1101/2024\\.01\\.29\\.577857 | New antiviral defences are genetically embedded within prokaryotic immune systems |",
            "notes": "The pinned DefenseFinder article registry maps the HEC-04 source key to the Payne et al. Hma-embedded-candidate preprint."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| HEC-04__HEC-04                                   |                                                  | HEC-04                 | Custom                  | 200    |",
            "notes": "The pinned DefenseFinder HMM inventory records HEC-04__HEC-04 as a custom HEC-04 profile."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "The pinned DefenseFinder rules table does not list HEC-04, leaving rule-level detection criteria unresolved."
          }
        ],
        "attaches_to": [
          "causal_graphs#hec_04_locus_reduces_phage_plaquing"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-29"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-29T14:17:47Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted HEC-04 system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; kept the graph at single-gene candidate-locus level because the pinned DefenseFinder HEC-04 HMM row is not backed by a pinned rules row; the replacement placeholder is reserved in proposals/metpo_traitmech_v342.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-29T14:17:48Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed HEC-04 system during canonical-example issue 444 enforcement and left canonical_examples empty because the sources support heterologous efficiency-of-plaquing assays and a DefenseFinder HEC-04 HMM row, but not a direct named native microbial isolate exemplar with experimentally verified endogenous HEC-04 activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000466",
    "label": "HEC-05 system",
    "definition": "A phage defense system in which an organism possesses the single-gene HEC-05 Hma-embedded candidate locus, encoding a GmrSD-like protein closely matching BrxU, that can reduce bacteriophage plaquing.",
    "definition_source": "DOI:10.1101/2024.01.29.577857",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "HEC-05",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1101/2024.01.29.577857"
      },
      {
        "synonym_text": "HEC-05__HEC-05",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1101/2024.01.29.577857",
        "snippet": "two GmrSD-like proteins (HEC-05 and HEC-06)",
        "notes": "Payne et al. identify HEC-05 as one of the Hma-embedded GmrSD-like candidate systems."
      },
      {
        "reference": "DOI:10.1101/2024.01.29.577857",
        "snippet": "chosen HEC-05 homolog shares 99.2% amino acid identity",
        "notes": "Payne et al. report that the selected HEC-05 homolog closely matches the independently characterized BrxU phage-defense protein."
      },
      {
        "reference": "DOI:10.1101/2024.01.29.577857",
        "snippet": "these were able to reduce the EOP of at least two phages",
        "notes": "Payne et al. support reduced plaquing for the active Hma-embedded candidate systems after excluding inactive HEC-01 and HEC-09 candidates."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| HEC-05 | 10\\.1101/2024\\.01\\.29\\.577857 | New antiviral defences are genetically embedded within prokaryotic immune systems |",
        "notes": "The pinned DefenseFinder article registry maps the HEC-05 source key to the Payne et al. Hma-embedded-candidate preprint."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| HEC-05__HEC-05                                   |                                                  | HEC-05                 | Custom                  | 150    |",
        "notes": "The pinned DefenseFinder HMM inventory records HEC-05__HEC-05 as a custom HEC-05 profile."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "hec_05_locus_reduces_phage_plaquing",
        "title": "HEC-05 loci reduce bacteriophage plaquing",
        "description": "Conservative system-level sketch linking the single-gene HEC-05 locus to reduced bacteriophage plaquing and HEC-05 system possession.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures HEC-05 at candidate locus and anti-phage-output level without asserting native host breadth, the direct viral trigger or substrate, exact GmrSD-like molecular output, or a DefenseFinder detection rule absent from the pinned rules table.",
        "nodes": [
          {
            "node_id": "hec_05_locus",
            "label": "HEC-05 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A single-gene Hma-embedded candidate locus represented in the pinned DefenseFinder HMM inventory by a HEC-05 custom profile."
          },
          {
            "node_id": "reduced_phage_plaquing",
            "label": "reduced bacteriophage plaquing",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced efficiency of plaquing by bacteriophages in cells carrying a complete HEC-05 candidate system."
          },
          {
            "node_id": "hec_05_system_trait",
            "label": "HEC-05 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000466",
            "description": "Possession of a genome-encoded HEC-05 phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "hec_05_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "reduced_phage_plaquing",
            "description": "The HEC-05 locus contributes to reduced bacteriophage plaquing as a GmrSD-like Hma-embedded candidate.",
            "evidence": [
              {
                "reference": "DOI:10.1101/2024.01.29.577857",
                "snippet": "two GmrSD-like proteins (HEC-05 and HEC-06)",
                "notes": "Payne et al. identify HEC-05 among the GmrSD-like Hma-embedded candidates."
              },
              {
                "reference": "DOI:10.1101/2024.01.29.577857",
                "snippet": "chosen HEC-05 homolog shares 99.2% amino acid identity",
                "notes": "Payne et al. tie the selected HEC-05 homolog to a close BrxU-like GmrSD-family architecture."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| HEC-05__HEC-05                                   |                                                  | HEC-05                 | Custom                  | 150    |",
                "notes": "The pinned DefenseFinder HMM inventory records HEC-05__HEC-05 as a custom HEC-05 profile."
              }
            ]
          },
          {
            "subject": "reduced_phage_plaquing",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "hec_05_system_trait",
            "description": "HEC-05-mediated plaquing reduction realizes the HEC-05 system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1101/2024.01.29.577857",
                "snippet": "these were able to reduce the EOP of at least two phages",
                "notes": "Payne et al. support reduced efficiency of plaquing for the active HEC systems."
              }
            ]
          },
          {
            "subject": "hec_05_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "HEC-05 system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| HEC-05 | 10\\.1101/2024\\.01\\.29\\.577857 | New antiviral defences are genetically embedded within prokaryotic immune systems |",
                "notes": "The pinned DefenseFinder article registry maps the HEC-05 source key to the Payne et al. Hma-embedded-candidate preprint."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "hec-05-defensefinder-model-gap",
        "prompt": "Resolve HEC-05 native host breadth, sensitive-phage breadth, BrxU synonymy, GmrSD-like molecular output, and rule-level detection criteria before minting narrower HEC-05 mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Payne et al. support HEC-05 as a single-gene Hma-embedded candidate anti-phage system closely matching BrxU, and the pinned DefenseFinder HMM inventory records one HEC-05 profile row. The pinned rules table has no HEC-05 row, and the first-pass record does not yet resolve natural host breadth, phage target breadth, or the direct molecular output.",
        "evidence": [
          {
            "reference": "DOI:10.1101/2024.01.29.577857",
            "snippet": "two GmrSD-like proteins (HEC-05 and HEC-06)",
            "notes": "Payne et al. identify HEC-05 as one of the GmrSD-like Hma-embedded candidate systems."
          },
          {
            "reference": "DOI:10.1101/2024.01.29.577857",
            "snippet": "chosen HEC-05 homolog shares 99.2% amino acid identity",
            "notes": "Payne et al. report that the selected HEC-05 homolog closely matches BrxU."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
            "snippet": "| HEC-05 | 10\\.1101/2024\\.01\\.29\\.577857 | New antiviral defences are genetically embedded within prokaryotic immune systems |",
            "notes": "The pinned DefenseFinder article registry maps the HEC-05 source key to the Payne et al. Hma-embedded-candidate preprint."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| HEC-05__HEC-05                                   |                                                  | HEC-05                 | Custom                  | 150    |",
            "notes": "The pinned DefenseFinder HMM inventory records HEC-05__HEC-05 as a custom HEC-05 profile."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "The pinned DefenseFinder rules table does not list HEC-05, leaving rule-level detection criteria unresolved."
          }
        ],
        "attaches_to": [
          "causal_graphs#hec_05_locus_reduces_phage_plaquing"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-29"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-29T16:05:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted HEC-05 system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; kept the graph at single-gene candidate-locus level because the pinned DefenseFinder HEC-05 HMM row is not backed by a pinned rules row; the replacement placeholder is reserved in proposals/metpo_traitmech_v343.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-29T16:05:01Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed HEC-05 system during canonical-example issue 444 enforcement and left canonical_examples empty because the sources support heterologous efficiency-of-plaquing assays and a DefenseFinder HEC-05 HMM row, but not a direct named native microbial isolate exemplar with experimentally verified endogenous HEC-05 activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000467",
    "label": "HEC-06 system",
    "definition": "A phage defense system in which an organism possesses the single-gene HEC-06 Hma-embedded candidate locus, encoding a GmrSD-like protein, that can reduce bacteriophage plaquing.",
    "definition_source": "DOI:10.1101/2024.01.29.577857",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "HEC-06",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1101/2024.01.29.577857"
      },
      {
        "synonym_text": "HEC-06__HEC-06",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1101/2024.01.29.577857",
        "snippet": "two GmrSD-like proteins (HEC-05 and HEC-06)",
        "notes": "Payne et al. identify HEC-06 as one of the Hma-embedded GmrSD-like candidate systems."
      },
      {
        "reference": "DOI:10.1101/2024.01.29.577857",
        "snippet": "these were able to reduce the EOP of at least two phages",
        "notes": "Payne et al. support reduced plaquing for the active Hma-embedded candidate systems after excluding inactive HEC-01 and HEC-09 candidates."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| HEC-06 | 10\\.1101/2024\\.01\\.29\\.577857 | New antiviral defences are genetically embedded within prokaryotic immune systems |",
        "notes": "The pinned DefenseFinder article registry maps the HEC-06 source key to the Payne et al. Hma-embedded-candidate preprint."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| HEC-06__HEC-06                                   |                                                  | HEC-06                 | Custom                  | 450    |",
        "notes": "The pinned DefenseFinder HMM inventory records HEC-06__HEC-06 as a custom HEC-06 profile."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "hec_06_locus_reduces_phage_plaquing",
        "title": "HEC-06 loci reduce bacteriophage plaquing",
        "description": "Conservative system-level sketch linking the single-gene HEC-06 locus to reduced bacteriophage plaquing and HEC-06 system possession.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures HEC-06 at candidate locus and anti-phage-output level without asserting native host breadth, the direct viral trigger or substrate, exact GmrSD-like molecular output, or a DefenseFinder detection rule absent from the pinned rules table.",
        "nodes": [
          {
            "node_id": "hec_06_locus",
            "label": "HEC-06 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A single-gene Hma-embedded candidate locus represented in the pinned DefenseFinder HMM inventory by a HEC-06 custom profile."
          },
          {
            "node_id": "reduced_phage_plaquing",
            "label": "reduced bacteriophage plaquing",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced efficiency of plaquing by bacteriophages in cells carrying a complete HEC-06 candidate system."
          },
          {
            "node_id": "hec_06_system_trait",
            "label": "HEC-06 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000467",
            "description": "Possession of a genome-encoded HEC-06 phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "hec_06_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "reduced_phage_plaquing",
            "description": "The HEC-06 locus contributes to reduced bacteriophage plaquing as a GmrSD-like Hma-embedded candidate.",
            "evidence": [
              {
                "reference": "DOI:10.1101/2024.01.29.577857",
                "snippet": "two GmrSD-like proteins (HEC-05 and HEC-06)",
                "notes": "Payne et al. identify HEC-06 among the GmrSD-like Hma-embedded candidates."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| HEC-06__HEC-06                                   |                                                  | HEC-06                 | Custom                  | 450    |",
                "notes": "The pinned DefenseFinder HMM inventory records HEC-06__HEC-06 as a custom HEC-06 profile."
              }
            ]
          },
          {
            "subject": "reduced_phage_plaquing",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "hec_06_system_trait",
            "description": "HEC-06-mediated plaquing reduction realizes the HEC-06 system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1101/2024.01.29.577857",
                "snippet": "these were able to reduce the EOP of at least two phages",
                "notes": "Payne et al. support reduced efficiency of plaquing for the active HEC systems."
              }
            ]
          },
          {
            "subject": "hec_06_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "HEC-06 system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| HEC-06 | 10\\.1101/2024\\.01\\.29\\.577857 | New antiviral defences are genetically embedded within prokaryotic immune systems |",
                "notes": "The pinned DefenseFinder article registry maps the HEC-06 source key to the Payne et al. Hma-embedded-candidate preprint."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "hec-06-defensefinder-model-gap",
        "prompt": "Resolve HEC-06 native host breadth, sensitive-phage breadth, GmrSD-like molecular output, and rule-level detection criteria before minting narrower HEC-06 mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Payne et al. support HEC-06 as a single-gene Hma-embedded candidate anti-phage system encoding a GmrSD-like protein, and the pinned DefenseFinder HMM inventory records one HEC-06 profile row. The pinned rules table has no HEC-06 row, and the first-pass record does not yet resolve natural host breadth, phage target breadth, or the direct molecular output.",
        "evidence": [
          {
            "reference": "DOI:10.1101/2024.01.29.577857",
            "snippet": "two GmrSD-like proteins (HEC-05 and HEC-06)",
            "notes": "Payne et al. identify HEC-06 as one of the GmrSD-like Hma-embedded candidate systems."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
            "snippet": "| HEC-06 | 10\\.1101/2024\\.01\\.29\\.577857 | New antiviral defences are genetically embedded within prokaryotic immune systems |",
            "notes": "The pinned DefenseFinder article registry maps the HEC-06 source key to the Payne et al. Hma-embedded-candidate preprint."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| HEC-06__HEC-06                                   |                                                  | HEC-06                 | Custom                  | 450    |",
            "notes": "The pinned DefenseFinder HMM inventory records HEC-06__HEC-06 as a custom HEC-06 profile."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "The pinned DefenseFinder rules table does not list HEC-06, leaving rule-level detection criteria unresolved."
          }
        ],
        "attaches_to": [
          "causal_graphs#hec_06_locus_reduces_phage_plaquing"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-29"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-29T15:27:24Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted HEC-06 system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; kept the graph at single-gene candidate-locus level because the pinned DefenseFinder HEC-06 HMM row is not backed by a pinned rules row; the replacement placeholder is reserved in proposals/metpo_traitmech_v344.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-29T15:27:25Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed HEC-06 system during canonical-example issue 444 enforcement and left canonical_examples empty because the sources support heterologous efficiency-of-plaquing assays and a DefenseFinder HEC-06 HMM row, but not a direct named native microbial isolate exemplar with experimentally verified endogenous HEC-06 activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000478",
    "label": "HEC-07 system",
    "definition": "A phage defense system in which an organism possesses the single-gene HEC-07 Hma-embedded candidate locus, encoding a RelE domain-containing protein, that can reduce bacteriophage plaquing.",
    "definition_source": "DOI:10.1101/2024.01.29.577857",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "HEC-07",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1101/2024.01.29.577857"
      },
      {
        "synonym_text": "HEC-07__HEC-07",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1101/2024.01.29.577857",
        "snippet": "RelE (HEC-07), higher eukaryotes and prokaryotes nucleotide-binding (HEPN) (HEC-08) and Nedd4-BP1/YacP nuclease (NYN) (HEC-09) domain-containing proteins",
        "notes": "Payne et al. identify HEC-07 as a RelE-domain Hma-embedded candidate system."
      },
      {
        "reference": "DOI:10.1101/2024.01.29.577857",
        "snippet": "these were able to reduce the EOP of at least two phages",
        "notes": "Payne et al. support reduced plaquing for the active Hma-embedded candidate systems after excluding inactive HEC-01 and HEC-09 candidates."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| HEC-07 | 10\\.1101/2024\\.01\\.29\\.577857 | New antiviral defences are genetically embedded within prokaryotic immune systems |",
        "notes": "The pinned DefenseFinder article registry maps the HEC-07 source key to the Payne et al. Hma-embedded-candidate preprint."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| HEC-07__HEC-07                                   |                                                  | HEC-07                 | Custom                  | 200    |",
        "notes": "The pinned DefenseFinder HMM inventory records HEC-07__HEC-07 as a custom HEC-07 profile."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "hec_07_locus_reduces_phage_plaquing",
        "title": "HEC-07 loci reduce bacteriophage plaquing",
        "description": "Conservative system-level sketch linking the single-gene HEC-07 locus to reduced bacteriophage plaquing and HEC-07 system possession.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures HEC-07 at candidate locus and anti-phage-output level without asserting native host breadth, the direct viral trigger or substrate, exact RelE-domain molecular output, or a DefenseFinder detection rule absent from the pinned rules table.",
        "nodes": [
          {
            "node_id": "hec_07_locus",
            "label": "HEC-07 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A single-gene Hma-embedded candidate locus represented in the pinned DefenseFinder HMM inventory by a HEC-07 custom profile."
          },
          {
            "node_id": "reduced_phage_plaquing",
            "label": "reduced bacteriophage plaquing",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced efficiency of plaquing by bacteriophages in cells carrying a complete HEC-07 candidate system."
          },
          {
            "node_id": "hec_07_system_trait",
            "label": "HEC-07 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000478",
            "description": "Possession of a genome-encoded HEC-07 phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "hec_07_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "reduced_phage_plaquing",
            "description": "The HEC-07 locus contributes to reduced bacteriophage plaquing as a RelE-domain Hma-embedded candidate.",
            "evidence": [
              {
                "reference": "DOI:10.1101/2024.01.29.577857",
                "snippet": "RelE (HEC-07), higher eukaryotes and prokaryotes nucleotide-binding (HEPN) (HEC-08) and Nedd4-BP1/YacP nuclease (NYN) (HEC-09) domain-containing proteins",
                "notes": "Payne et al. identify HEC-07 among the RelE-domain Hma-embedded candidates."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| HEC-07__HEC-07                                   |                                                  | HEC-07                 | Custom                  | 200    |",
                "notes": "The pinned DefenseFinder HMM inventory records HEC-07__HEC-07 as a custom HEC-07 profile."
              }
            ]
          },
          {
            "subject": "reduced_phage_plaquing",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "hec_07_system_trait",
            "description": "HEC-07-mediated plaquing reduction realizes the HEC-07 system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1101/2024.01.29.577857",
                "snippet": "these were able to reduce the EOP of at least two phages",
                "notes": "Payne et al. support reduced efficiency of plaquing for the active HEC systems."
              }
            ]
          },
          {
            "subject": "hec_07_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "HEC-07 system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| HEC-07 | 10\\.1101/2024\\.01\\.29\\.577857 | New antiviral defences are genetically embedded within prokaryotic immune systems |",
                "notes": "The pinned DefenseFinder article registry maps the HEC-07 source key to the Payne et al. Hma-embedded-candidate preprint."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "hec-07-defensefinder-model-gap",
        "prompt": "Resolve HEC-07 native host breadth, sensitive-phage breadth, RelE-domain molecular output, and rule-level detection criteria before minting narrower HEC-07 mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Payne et al. support HEC-07 as a single-gene Hma-embedded candidate anti-phage system encoding a RelE-domain protein, and the pinned DefenseFinder HMM inventory records one HEC-07 profile row. The pinned rules table has no HEC-07 row, and the first-pass record does not yet resolve natural host breadth, phage target breadth, or the direct molecular output.",
        "evidence": [
          {
            "reference": "DOI:10.1101/2024.01.29.577857",
            "snippet": "RelE (HEC-07), higher eukaryotes and prokaryotes nucleotide-binding (HEPN) (HEC-08) and Nedd4-BP1/YacP nuclease (NYN) (HEC-09) domain-containing proteins",
            "notes": "Payne et al. identify HEC-07 as a RelE-domain Hma-embedded candidate system."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
            "snippet": "| HEC-07 | 10\\.1101/2024\\.01\\.29\\.577857 | New antiviral defences are genetically embedded within prokaryotic immune systems |",
            "notes": "The pinned DefenseFinder article registry maps the HEC-07 source key to the Payne et al. Hma-embedded-candidate preprint."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| HEC-07__HEC-07                                   |                                                  | HEC-07                 | Custom                  | 200    |",
            "notes": "The pinned DefenseFinder HMM inventory records HEC-07__HEC-07 as a custom HEC-07 profile."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "The pinned DefenseFinder rules table does not list HEC-07, leaving rule-level detection criteria unresolved."
          }
        ],
        "attaches_to": [
          "causal_graphs#hec_07_locus_reduces_phage_plaquing"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-30"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-30T00:50:18Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted HEC-07 system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; kept the graph at single-gene candidate-locus level because the pinned DefenseFinder HEC-07 HMM row is not backed by a pinned rules row; the replacement placeholder is reserved in proposals/metpo_traitmech_v355.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-30T00:50:19Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed HEC-07 system during canonical-example issue 444 enforcement and left canonical_examples empty because the sources support heterologous efficiency-of-plaquing assays and a DefenseFinder HEC-07 HMM row, but not a direct named native microbial isolate exemplar with experimentally verified endogenous HEC-07 activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000479",
    "label": "HEC-08 system",
    "definition": "A phage defense system in which an organism possesses the single-gene HEC-08 Hma-embedded candidate locus, encoding a higher eukaryotes and prokaryotes nucleotide-binding domain-containing protein, that can reduce bacteriophage plaquing.",
    "definition_source": "DOI:10.1101/2024.01.29.577857",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "HEC-08",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1101/2024.01.29.577857"
      },
      {
        "synonym_text": "HEC-08__HEC-08",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1101/2024.01.29.577857",
        "snippet": "RelE (HEC-07), higher eukaryotes and prokaryotes nucleotide-binding (HEPN) (HEC-08) and Nedd4-BP1/YacP nuclease (NYN) (HEC-09) domain-containing proteins",
        "notes": "Payne et al. identify HEC-08 as a HEPN-domain Hma-embedded candidate system."
      },
      {
        "reference": "DOI:10.1101/2024.01.29.577857",
        "snippet": "these were able to reduce the EOP of at least two phages",
        "notes": "Payne et al. support reduced plaquing for the active Hma-embedded candidate systems after excluding inactive HEC-01 and HEC-09 candidates."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| HEC-08 | 10\\.1101/2024\\.01\\.29\\.577857 | New antiviral defences are genetically embedded within prokaryotic immune systems |",
        "notes": "The pinned DefenseFinder article registry maps the HEC-08 source key to the Payne et al. Hma-embedded-candidate preprint."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| HEC-08__HEC-08                                   |                                                  | HEC-08                 | Custom                  | 200    |",
        "notes": "The pinned DefenseFinder HMM inventory records HEC-08__HEC-08 as a custom HEC-08 profile."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "hec_08_locus_reduces_phage_plaquing",
        "title": "HEC-08 loci reduce bacteriophage plaquing",
        "description": "Conservative system-level sketch linking the single-gene HEC-08 locus to reduced bacteriophage plaquing and HEC-08 system possession.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures HEC-08 at candidate locus and anti-phage-output level without asserting native host breadth, the direct viral trigger or substrate, exact HEPN-domain molecular output, or a DefenseFinder detection rule absent from the pinned rules table.",
        "nodes": [
          {
            "node_id": "hec_08_locus",
            "label": "HEC-08 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A single-gene Hma-embedded candidate locus represented in the pinned DefenseFinder HMM inventory by a HEC-08 custom profile."
          },
          {
            "node_id": "reduced_phage_plaquing",
            "label": "reduced bacteriophage plaquing",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced efficiency of plaquing by bacteriophages in cells carrying a complete HEC-08 candidate system."
          },
          {
            "node_id": "hec_08_system_trait",
            "label": "HEC-08 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000479",
            "description": "Possession of a genome-encoded HEC-08 phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "hec_08_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "reduced_phage_plaquing",
            "description": "The HEC-08 locus contributes to reduced bacteriophage plaquing as a HEPN-domain Hma-embedded candidate.",
            "evidence": [
              {
                "reference": "DOI:10.1101/2024.01.29.577857",
                "snippet": "RelE (HEC-07), higher eukaryotes and prokaryotes nucleotide-binding (HEPN) (HEC-08) and Nedd4-BP1/YacP nuclease (NYN) (HEC-09) domain-containing proteins",
                "notes": "Payne et al. identify HEC-08 among the HEPN-domain Hma-embedded candidates."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| HEC-08__HEC-08                                   |                                                  | HEC-08                 | Custom                  | 200    |",
                "notes": "The pinned DefenseFinder HMM inventory records HEC-08__HEC-08 as a custom HEC-08 profile."
              }
            ]
          },
          {
            "subject": "reduced_phage_plaquing",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "hec_08_system_trait",
            "description": "HEC-08-mediated plaquing reduction realizes the HEC-08 system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1101/2024.01.29.577857",
                "snippet": "these were able to reduce the EOP of at least two phages",
                "notes": "Payne et al. support reduced efficiency of plaquing for the active HEC systems."
              }
            ]
          },
          {
            "subject": "hec_08_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "HEC-08 system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| HEC-08 | 10\\.1101/2024\\.01\\.29\\.577857 | New antiviral defences are genetically embedded within prokaryotic immune systems |",
                "notes": "The pinned DefenseFinder article registry maps the HEC-08 source key to the Payne et al. Hma-embedded-candidate preprint."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "hec-08-defensefinder-model-gap",
        "prompt": "Resolve HEC-08 native host breadth, sensitive-phage breadth, HEPN-domain molecular output, and rule-level detection criteria before minting narrower HEC-08 mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Payne et al. support HEC-08 as a single-gene Hma-embedded candidate anti-phage system encoding a HEPN-domain protein, and the pinned DefenseFinder HMM inventory records one HEC-08 profile row. The pinned rules table has no HEC-08 row, and the first-pass record does not yet resolve natural host breadth, phage target breadth, or the direct molecular output.",
        "evidence": [
          {
            "reference": "DOI:10.1101/2024.01.29.577857",
            "snippet": "RelE (HEC-07), higher eukaryotes and prokaryotes nucleotide-binding (HEPN) (HEC-08) and Nedd4-BP1/YacP nuclease (NYN) (HEC-09) domain-containing proteins",
            "notes": "Payne et al. identify HEC-08 as a HEPN-domain Hma-embedded candidate system."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
            "snippet": "| HEC-08 | 10\\.1101/2024\\.01\\.29\\.577857 | New antiviral defences are genetically embedded within prokaryotic immune systems |",
            "notes": "The pinned DefenseFinder article registry maps the HEC-08 source key to the Payne et al. Hma-embedded-candidate preprint."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| HEC-08__HEC-08                                   |                                                  | HEC-08                 | Custom                  | 200    |",
            "notes": "The pinned DefenseFinder HMM inventory records HEC-08__HEC-08 as a custom HEC-08 profile."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "The pinned DefenseFinder rules table does not list HEC-08, leaving rule-level detection criteria unresolved."
          }
        ],
        "attaches_to": [
          "causal_graphs#hec_08_locus_reduces_phage_plaquing"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-30"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-30T01:34:07Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted HEC-08 system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; kept the graph at single-gene candidate-locus level because the pinned DefenseFinder HEC-08 HMM row is not backed by a pinned rules row; the replacement placeholder is reserved in proposals/metpo_traitmech_v356.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-30T01:34:08Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed HEC-08 system during canonical-example issue 444 enforcement and left canonical_examples empty because the sources support heterologous efficiency-of-plaquing assays and a DefenseFinder HEC-08 HMM row, but not a direct named native microbial isolate exemplar with experimentally verified endogenous HEC-08 activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000327",
    "label": "Hesat system",
    "definition": "A phage defense system in which an organism possesses a Hesat locus that can restrict bacteriophage infection.",
    "definition_source": "DOI:10.1093/nar/gkae671",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "Hesat",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1093/nar/gkae671"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1093/nar/gkae671",
        "snippet": "Based on comparative sequence analysis (BLASTN and BLASTP) and on functional and structural analysis (HHpred and InterPro) the remaining seven antiphage systems (out of the twenty identified) did not display significant homology to any previously described antiphage system, thus rendering them novel antiphage systems (Table 1). These systems were named after cheese, cattle or fermentation related deities (Rhea, Aristaios, Kamadhenu, Fliodhais, Audmula, Rugutis and Hesat)",
        "notes": "Grafakou et al. named Hesat among seven not previously described lactococcal antiphage systems."
      },
      {
        "reference": "DOI:10.1093/nar/gkae671",
        "snippet": "Except for Hesat, which was cloned in pPTPi with the addition of its native signals, all novel systems were cloned in the high-copy number vector pNZ44 (Supplementary Table S2). All discovered systems, except Fliodhais, are single gene antiphage systems.",
        "notes": "Grafakou et al. identify Hesat as a single-gene novel antiphage system cloned with native signals in pPTPi."
      },
      {
        "reference": "DOI:10.1093/nar/gkae671",
        "snippet": "For Hesat, no domain was predicted by HHpred and InterPro. Dali analysis reports significant hits with the colicin-D toxic domain (PDB ID 1V74; Figure 4N, O), which specifically cleaves the anticodon loop of all four tRNA(Arg) iso-acceptors, thereby resulting in cell death (68). Therefore, it is proposed that Hesat upon phage infection is activated to block translation, which is in accordance with its abortive infection phenotype.",
        "notes": "Grafakou et al. report that Hesat had no HHpred or InterPro domain prediction, and they propose a colicin-D-like translation-blocking activity upon phage infection."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "Hesat | 10\\.1093/nar/gkae671 | Discovery of antiphage systems in the lactococcal plasmidome",
        "notes": "The DefenseFinder article registry maps the named Hesat system to the Grafakou et al. lactococcal antiphage-system discovery paper."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "hesat_locus_restricts_phage",
        "title": "Hesat loci confer bacterial phage defense",
        "description": "Conservative system-level sketch linking possession of a Hesat locus to restricted bacteriophage propagation without asserting the unresolved phage trigger or molecular output.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Hesat as a named single-gene lactococcal anti-phage system while leaving its direct phage trigger, molecular substrate, experimentally validated antiviral effector output, natural locus breadth, and the absence of pinned DefenseFinder HMM or rule rows unresolved.",
        "nodes": [
          {
            "node_id": "hesat_locus",
            "label": "Hesat locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A single-gene Hesat anti-phage defense locus described among lactococcal plasmid-encoded phage-resistance systems."
          },
          {
            "node_id": "restricted_phage_propagation",
            "label": "restricted phage propagation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced propagation of bacteriophage in cells carrying the Hesat system."
          },
          {
            "node_id": "hesat_system_trait",
            "label": "Hesat system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000327",
            "description": "Possession of a genome-encoded Hesat phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "hesat_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "restricted_phage_propagation",
            "description": "The lactococcal plasmidome screen discovered Hesat as a named single-gene antiphage system, and the DefenseFinder article registry maps the Hesat system to that discovery paper.",
            "evidence": [
              {
                "reference": "DOI:10.1093/nar/gkae671",
                "snippet": "Based on comparative sequence analysis (BLASTN and BLASTP) and on functional and structural analysis (HHpred and InterPro) the remaining seven antiphage systems (out of the twenty identified) did not display significant homology to any previously described antiphage system, thus rendering them novel antiphage systems (Table 1). These systems were named after cheese, cattle or fermentation related deities (Rhea, Aristaios, Kamadhenu, Fliodhais, Audmula, Rugutis and Hesat)",
                "notes": "Grafakou et al. named Hesat as one of the novel lactococcal antiphage systems."
              },
              {
                "reference": "DOI:10.1093/nar/gkae671",
                "snippet": "Except for Hesat, which was cloned in pPTPi with the addition of its native signals, all novel systems were cloned in the high-copy number vector pNZ44 (Supplementary Table S2). All discovered systems, except Fliodhais, are single gene antiphage systems.",
                "notes": "Grafakou et al. identify Hesat as a single-gene antiphage system."
              },
              {
                "reference": "DOI:10.1093/nar/gkae671",
                "snippet": "For Hesat, no domain was predicted by HHpred and InterPro. Dali analysis reports significant hits with the colicin-D toxic domain (PDB ID 1V74; Figure 4N, O), which specifically cleaves the anticodon loop of all four tRNA(Arg) iso-acceptors, thereby resulting in cell death (68). Therefore, it is proposed that Hesat upon phage infection is activated to block translation, which is in accordance with its abortive infection phenotype.",
                "notes": "Grafakou et al. propose that Hesat blocks translation after phage infection while leaving that molecular output unresolved."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Hesat | 10\\.1093/nar/gkae671 | Discovery of antiphage systems in the lactococcal plasmidome",
                "notes": "The DefenseFinder article registry maps the named Hesat system to the Grafakou et al. lactococcal antiphage-system discovery paper."
              }
            ]
          },
          {
            "subject": "restricted_phage_propagation",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "hesat_system_trait",
            "description": "Hesat-mediated phage restriction realizes the Hesat system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1093/nar/gkae671",
                "snippet": "For Hesat, no domain was predicted by HHpred and InterPro. Dali analysis reports significant hits with the colicin-D toxic domain (PDB ID 1V74; Figure 4N, O), which specifically cleaves the anticodon loop of all four tRNA(Arg) iso-acceptors, thereby resulting in cell death (68). Therefore, it is proposed that Hesat upon phage infection is activated to block translation, which is in accordance with its abortive infection phenotype.",
                "notes": "Grafakou et al. treat Hesat as having an abortive infection phenotype and propose a translation-blocking mechanism upon phage infection."
              }
            ]
          },
          {
            "subject": "hesat_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Hesat system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Hesat | 10\\.1093/nar/gkae671 | Discovery of antiphage systems in the lactococcal plasmidome",
                "notes": "The DefenseFinder article registry maps the named Hesat system to the Grafakou et al. lactococcal antiphage-system discovery paper."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "hesat-mechanism-gap",
        "prompt": "Resolve Hesat phage triggers and effector outputs before minting narrower Hesat mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Grafakou et al. and DefenseFinder support Hesat as a named single-gene anti-phage system, but the direct trigger, experimentally validated molecular substrate, antiviral effector output, natural locus breadth, and profile-to-component model are not resolved enough here to assert a narrower mechanistic child trait.",
        "attaches_to": [
          "causal_graphs#hesat_locus_restricts_phage"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-21"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-21T04:55:54Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Hesat system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v204.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000608",
    "label": "heterokaryosis",
    "definition": "A fungal phenotype characterized by the coexistence of genetically distinct nuclei within a shared cytoplasm.",
    "definition_source": "DOI:10.1098/rspb.2022.0971",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1098/rspb.2022.0971",
        "snippet": "Heterokaryosis is a system in which genetically distinct nuclei coexist within the same cytoplasm.",
        "notes": "2022 primary study, PMID:35946150. Exact span of the directly retrieved Europe PMC abstract. Introduction, Methods, Results and Discussion were read in the PMC9363985 full-text XML; actual figures and supplements were not inspected. Neurospora tetrasperma lineages L1, L6 and L10 were reconstituted from homokaryotic components, with DNA-ratio validation. Developmental stage and lineage affect expression; global transcription does not diagnose heterokaryosis by itself. L10 heterokaryons can remain largely sterile despite containing both mating types. Expression correlations do not establish a protein-resolved regulatory mechanism."
      },
      {
        "reference": "DOI:10.1098/rspb.2014.0084",
        "snippet": "A heterokaryon is a tissue type composed of cells containing genetically different nuclei.",
        "notes": "Samils et al. (2014), PMID:24850920. Exact span of the directly retrieved Europe PMC abstract. Main-text Methods, Results and Discussion were read at PMC4046401; actual figures and supplements were not visually inspected. The study assays natural N. tetrasperma heterokaryons from lineages L1, L6 and L7 with multiple mating-type-linked SNPs. Bulk DNA ratios and RNA expression are different readouts; they do not count nuclei in every cell. The snippet names the tissue, whereas this record denotes the phenotype."
      },
      {
        "reference": "DOI:10.1016/j.fgb.2018.01.005",
        "snippet": "Shifts in fungicide sensitivity and microsatellite genotypes indicated that heterokaryons could adapt to changes in fungicide pressure.",
        "notes": "Kessler et al. (2018), PMID:29331685. Exact span of the directly retrieved Europe PMC abstract. Methods and relevant Results and Discussion were read in the author-hosted PDF at https://researchmap.jp/umassturfpathology/published_papers/2317022/attachment_file.pdf; actual Figures 5-6 were inspected, but other figures and supplements remain uninspected. Sclerotinia homoeocarpa field isolates were paired in vitro; fluorescent nuclear imaging used engineered derivatives. Tagged histones can move through shared cytoplasm into other nuclei, so dual fluorescence alone does not establish nuclear fusion or genotype. Microsatellite and SNP assays provide complementary evidence, with detection-limit qualifications. Fungicide responses are condition-specific, not defining properties of every heterokaryon; parasexuality was suspected, not demonstrated."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:40127",
        "taxon_label": "Neurospora tetrasperma",
        "reference": "DOI:10.1098/rspb.2014.0084",
        "note": "Qualified example: natural heterokaryon P581 (lineage L6), Lihue, Hawaii. Primary provenance is Methods 2a and Table 1 at https://pmc.ncbi.nlm.nih.gov/articles/PMC4046401/. FGSC 2508 and 2509 are its homokaryotic components, not identifiers for the heterokaryon. The study measures cultured mycelial and sexual tissues at 25 C, not an in-situ nuclear census. This does not assert that all isolates or life stages are heterokaryotic. NCBI taxonomy 40127 resolves to the active species name on 2026-10-04."
      }
    ],
    "discussions": [
      {
        "discussion_id": "heterokaryosis-trait-scope",
        "prompt": "Keep nuclear coexistence distinct from copy number and reproductive processes.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "This is a reusable genomic phenotype, not a locus or sequence feature. GENOMICS is a filesystem category, not an ontology parent. Genetically distinct nuclei sharing cytoplasm differ from genome-copy number, multinucleation alone, hyphal fusion, postfusion incompatibility and a complete parasexual cycle. Those traits are not is-a parents. Do not require exactly two nuclei, diploidy, a fixed nuclear ratio, universal self-fertility or fungicide resistance. Heterokaryon names a structure, not an automatically exact phenotype synonym. The fungal scope reflects the cited studies; broader terminology and external mappings require authority-level interpretation before adding synonyms or xrefs.",
        "posed_by": "codex",
        "posed_date": "2026-10-04"
      },
      {
        "discussion_id": "heterokaryosis-mechanism-and-readouts",
        "prompt": "Resolve molecular mechanisms and nuclear identity with independent readouts.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Complete unread figures and supplements before extending quantitative or causal claims. Fluorescent protein localization, DNA genotype and RNA expression are different readouts; label exchange must not be interpreted as nuclear fusion. Negative allele detection does not by itself prove biological absence. Resolve native protein identities and experimentally supported edges before adding a mechanistic graph; do not use NONMECHANISTIC to bypass missing grounding. Keep the 2014 natural P581 example separate from reconstituted 2022 cultures and engineered 2018 imaging strains. Verify current taxonomic placement and strain provenance before adding further taxa.",
        "posed_by": "codex",
        "posed_date": "2026-10-04"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-05T00:29:53Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added heterokaryosis with three primary DOI-backed references and exact abstract snippets. Separated nuclear coexistence from ploidy, fusion, incompatibility and parasexual reproduction. Added a qualified natural P581 Neurospora tetrasperma example after primary strain-provenance and NCBI taxonomy checks. Ignored-and-hidden repository searches and structured METPO review found no exact record. Reserved METPO:1056200 in v485 under released phenotype. Retained source-access and experimental-readout limits; external mappings and protein-resolved mechanisms remain unresolved.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000533",
    "label": "Hma system",
    "definition": "A phage defense system in which an organism possesses a genome-encoded Hma locus with predicted HmaA helicase, HmaB m5c methyltransferase, and HmaC ATPase components.",
    "definition_source": "DOI:10.1093/nar/gkab883",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "Hma",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1093/nar/gkab883"
      },
      {
        "synonym_text": "Hma__HmaA",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "Hma__HmaB",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "Hma__HmaC",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1093/nar/gkab883",
        "snippet": "We designated this as a new candidate defence system named Hma, as it encodes three proteins with predicted helicase (HmaA), m5c methyltransferase (HmaB) and ATPase (HmaC) domains.",
        "notes": "Payne et al. define Hma as a predicted three-gene antiviral defense system with HmaA, HmaB, and HmaC components."
      },
      {
        "reference": "DOI:10.1093/nar/gkab883",
        "snippet": "The putative Hma system was very widespread, present in 26 phyla, surpassed only by CBASS type I, Gabija and Septu type I.",
        "notes": "Payne et al. report that the predicted Hma system occurs across many bacterial and archaeal phyla."
      },
      {
        "reference": "DOI:10.1111/1751-7915.14524",
        "snippet": "we characterized a new defence system, Hma",
        "notes": "Liu et al. experimentally studied Hma in coral-associated Halomonas meridiana."
      },
      {
        "reference": "DOI:10.1111/1751-7915.14524",
        "snippet": "Mutation analysis revealed the nickase activity of the nuclease domain (belonging to PDD/EXK superfamily) of HmaA is essential in phage defence.",
        "notes": "Liu et al. connect HmaA nuclease activity to anti-phage defense against Escherichia phage T4."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| Hma | 10\\.1093/nar/gkac400 | PADLOC: a web server for the identification of antiviral defence systems in microbial genomes | ",
        "notes": "The pinned DefenseFinder article registry maps the Hma source key to the PADLOC web-server paper."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| Hma__HmaA                                        |                                                  | Hma                    | Custom                  | 400    |",
        "notes": "The pinned DefenseFinder HMM inventory records Hma__HmaA under the Hma model namespace."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| Hma__HmaB                                        |                                                  | Hma                    | Custom                  | 20     |",
        "notes": "The pinned DefenseFinder HMM inventory records Hma__HmaB under the Hma model namespace."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| Hma__HmaC                                        |                                                  | Hma                    | Custom                  | 20     |",
        "notes": "The pinned DefenseFinder HMM inventory records Hma__HmaC under the Hma model namespace."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "hma_locus_phage_defense",
        "title": "Hma loci support helicase-associated phage defense",
        "description": "Conservative system-level sketch linking a three-gene Hma locus to HmaA-dependent phage defense and Hma system possession.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Hma at locus and HmaA antiviral-output level without asserting HmaB or HmaC regulation, HmaB/HmaC effector activity, complete HmaABC phage breadth, natural host activity, accessory systems inserted in the hma region, or rule-level DefenseFinder detection criteria.",
        "nodes": [
          {
            "node_id": "hma_locus",
            "label": "Hma locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A candidate antiviral Hma locus encoding HmaA, HmaB, and HmaC components."
          },
          {
            "node_id": "hmaA_phage_defense",
            "label": "HmaA phage defense",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "HmaA helicase/nickase-associated inhibition of bacteriophage infection."
          },
          {
            "node_id": "hma_system_trait",
            "label": "Hma system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000533",
            "description": "Possession of a genome-encoded Hma phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "hma_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "hmaA_phage_defense",
            "description": "Hma loci encode HmaA, and HmaA nickase activity is required for the characterized anti-phage activity.",
            "evidence": [
              {
                "reference": "DOI:10.1093/nar/gkab883",
                "snippet": "We designated this as a new candidate defence system named Hma, as it encodes three proteins with predicted helicase (HmaA), m5c methyltransferase (HmaB) and ATPase (HmaC) domains.",
                "notes": "Payne et al. define Hma as a predicted three-gene antiviral defense system with HmaA, HmaB, and HmaC components."
              },
              {
                "reference": "DOI:10.1111/1751-7915.14524",
                "snippet": "Mutation analysis revealed the nickase activity of the nuclease domain (belonging to PDD/EXK superfamily) of HmaA is essential in phage defence.",
                "notes": "Liu et al. connect HmaA nuclease activity to anti-phage defense against Escherichia phage T4."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| Hma__HmaA                                        |                                                  | Hma                    | Custom                  | 400    |",
                "notes": "The pinned DefenseFinder HMM inventory records Hma__HmaA under the Hma model namespace."
              }
            ]
          },
          {
            "subject": "hmaA_phage_defense",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "hma_system_trait",
            "description": "HmaA-dependent anti-phage activity realizes the first-pass organism-level Hma system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1111/1751-7915.14524",
                "snippet": "we characterized a new defence system, Hma",
                "notes": "Liu et al. experimentally studied Hma in coral-associated Halomonas meridiana."
              },
              {
                "reference": "DOI:10.1111/1751-7915.14524",
                "snippet": "Mutation analysis revealed the nickase activity of the nuclease domain (belonging to PDD/EXK superfamily) of HmaA is essential in phage defence.",
                "notes": "Liu et al. connect HmaA nuclease activity to anti-phage defense against Escherichia phage T4."
              }
            ]
          },
          {
            "subject": "hma_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Hma system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1093/nar/gkab883",
                "snippet": "We designated this as a new candidate defence system named Hma, as it encodes three proteins with predicted helicase (HmaA), m5c methyltransferase (HmaB) and ATPase (HmaC) domains.",
                "notes": "Payne et al. define Hma as a predicted three-gene antiviral defense system with HmaA, HmaB, and HmaC components."
              },
              {
                "reference": "DOI:10.1093/nar/gkab883",
                "snippet": "The putative Hma system was very widespread, present in 26 phyla, surpassed only by CBASS type I, Gabija and Septu type I.",
                "notes": "Payne et al. report that the predicted Hma system occurs across many bacterial and archaeal phyla."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| Hma | 10\\.1093/nar/gkac400 | PADLOC: a web server for the identification of antiviral defence systems in microbial genomes | ",
                "notes": "The pinned DefenseFinder article registry maps the Hma source key to the PADLOC web-server paper."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "hma-defensefinder-rule-and-component-gap",
        "prompt": "Resolve HmaB/HmaC contributions, complete HmaABC system requirements, hma-region accessory systems, sensitive-phage breadth, native host breadth, and DefenseFinder rule-level criteria before minting Hma mechanism or component children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Payne et al. predicted Hma as a three-gene candidate defense system, Liu et al. showed that the HmaA nuclease domain is essential for T4 phage defense, and the pinned DefenseFinder HMM inventory records HmaA, HmaB, and HmaC profiles. However, Liu et al. state that HmaB/HmaC regulation of HmaA was not known, and the pinned DefenseFinder rules table lacks an Hma row. This first-pass record therefore does not resolve exact HmaB or HmaC activities, complete-system genetic requirements, accessory defense systems inserted near hma, full sensitive-phage breadth, endogenous native-host activity, or reusable rule-level detection criteria.",
        "evidence": [
          {
            "reference": "DOI:10.1093/nar/gkab883",
            "snippet": "We designated this as a new candidate defence system named Hma, as it encodes three proteins with predicted helicase (HmaA), m5c methyltransferase (HmaB) and ATPase (HmaC) domains.",
            "notes": "Payne et al. define Hma as a predicted three-gene antiviral defense system with HmaA, HmaB, and HmaC components."
          },
          {
            "reference": "DOI:10.1111/1751-7915.14524",
            "snippet": "we characterized a new defence system, Hma",
            "notes": "Liu et al. experimentally studied Hma in coral-associated Halomonas meridiana."
          },
          {
            "reference": "DOI:10.1111/1751-7915.14524",
            "snippet": "Mutation analysis revealed the nickase activity of the nuclease domain (belonging to PDD/EXK superfamily) of HmaA is essential in phage defence.",
            "notes": "Liu et al. connect HmaA nuclease activity to anti-phage defense against Escherichia phage T4."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| Hma__HmaA                                        |                                                  | Hma                    | Custom                  | 400    |",
            "notes": "The pinned DefenseFinder HMM inventory records Hma__HmaA under the Hma model namespace."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| Hma__HmaB                                        |                                                  | Hma                    | Custom                  | 20     |",
            "notes": "The pinned DefenseFinder HMM inventory records Hma__HmaB under the Hma model namespace."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| Hma__HmaC                                        |                                                  | Hma                    | Custom                  | 20     |",
            "notes": "The pinned DefenseFinder HMM inventory records Hma__HmaC under the Hma model namespace."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "A structured first-pass search of the pinned DefenseFinder rules table found no exact Hma system row."
          }
        ],
        "attaches_to": [
          "causal_graphs#hma_locus_phage_defense"
        ],
        "posed_by": "codex",
        "posed_date": "2026-10-02"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-02T03:38:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Hma system as a DOI- and DefenseFinder-backed GENOMICS TraitRecord under the phage defense system parent after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v410.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-02T03:38:01Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed Hma system during initial curation and left canonical_examples empty because the sources support the three-gene Hma system namespace, Hma HMM profiles, and HmaA-dependent activity but not an accession-backed native microbial taxon exemplar with experimentally verified endogenous HmaABC activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000241",
    "label": "Hna system",
    "definition": "A phage defense system in which an organism possesses an Hna locus encoding a single SF2 helicase/nuclease effector that protects cells from bacteriophage infection by responding to phage single-stranded DNA-binding protein challenge, shifting toward dysregulated nuclease activation, and triggering abortive infection.",
    "definition_source": "DOI:10.1016/j.chom.2023.01.010",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "Hna anti-phage defense system",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1038/s41467-026-73157-2"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1016/j.chom.2023.01.010",
        "snippet": "single phage defense protein, Hna, that provides protection against diverse phages in Sinorhizobium meliloti",
        "notes": "Sather et al. support Hna as a single-protein phage-defense determinant in S. meliloti."
      },
      {
        "reference": "DOI:10.1016/j.chom.2023.01.010",
        "snippet": "Homologs of Hna are distributed widely across bacterial lineages",
        "notes": "Sather et al. support placing Hna at a bacterial family level rather than curating only the S. meliloti instance."
      },
      {
        "reference": "DOI:10.1016/j.chom.2023.01.010",
        "snippet": "Hna contains superfamily II helicase motifs at its N terminus and a nuclease motif at its C terminus, with mutagenesis of these motifs inactivating viral defense",
        "notes": "Sather et al. connect the predicted helicase/nuclease domain architecture to Hna antiphage activity."
      },
      {
        "reference": "DOI:10.1038/s41467-026-73157-2",
        "snippet": "Hna is a broadly distributed anti-phage immune system that confers resistance against diverse phage by eliciting an abortive infection response",
        "notes": "Hooper et al. independently support Hna as a named anti-phage immune system with abortive-infection output."
      },
      {
        "reference": "DOI:10.1038/s41467-026-73157-2",
        "snippet": "shifts catalytic partitioning toward dysregulated nuclease activation",
        "notes": "Hooper et al. support phage single-stranded DNA-binding protein as a direct stimulus for Hna nuclease activation."
      },
      {
        "reference": "DOI:10.1016/j.chom.2023.01.010",
        "snippet": "Hna limits phage spread by initiating abortive infection in response to a phage protein",
        "notes": "Sather et al. support abortive infection in response to a phage-encoded protein as the Hna phage-defense output."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:382",
        "taxon_label": "Sinorhizobium meliloti",
        "note": "Sather et al. showed that Sinorhizobium meliloti Hna provides protection against diverse bacteriophages and triggers abortive infection in phage-infected cells.",
        "reference": "DOI:10.1016/j.chom.2023.01.010"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "hna_ssb_triggered_abortive_infection",
        "title": "Hna nuclease activation couples phage SSB challenge to abortive infection",
        "description": "Evidence-backed process sketch linking an Hna locus to phage single-stranded DNA-binding protein challenge, dysregulated helicase/nuclease activity, abortive infection, and inhibition of phage spread.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Sather et al. and Hooper et al. Hna phage-SSB-triggered abortive infection evidence without asserting one universal phage trigger, escape route, DNA substrate, ATP-concentration gate, or host-cell-death timing across all Hna homologs.",
        "nodes": [
          {
            "node_id": "hna_locus",
            "label": "Hna locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A single-effector Hna phage-defense locus encoding an SF2 helicase/nuclease immune protein."
          },
          {
            "node_id": "phage_ssb_stimulation",
            "label": "phage SSB stimulation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Stimulation of Hna by a phage-encoded single-stranded DNA-binding protein."
          },
          {
            "node_id": "hna_nuclease_activation",
            "label": "Hna nuclease activation",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "Dysregulated activation of Hna nuclease activity after phage single-stranded DNA-binding protein challenge."
          },
          {
            "node_id": "abortive_infection_response",
            "label": "abortive infection response",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Host cell death after infection that prevents release of bacteriophage progeny."
          },
          {
            "node_id": "hna_system_trait",
            "label": "Hna system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000241",
            "description": "Possession of a genome-encoded Hna phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "hna_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "hna_nuclease_activation",
            "description": "Hna loci encode SF2 helicase/nuclease proteins whose conserved helicase and nuclease motifs are required for viral defense.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.chom.2023.01.010",
                "snippet": "mutagenesis of these motifs inactivating viral defense",
                "notes": "Sather et al. connect Hna helicase and nuclease motifs to antiphage activity."
              }
            ]
          },
          {
            "subject": "phage_ssb_stimulation",
            "predicate": "activates",
            "predicate_id": "RO:0002213",
            "object": "hna_nuclease_activation",
            "description": "A phage-encoded single-stranded DNA-binding protein stimulates Hna and shifts it toward dysregulated nuclease activation.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.chom.2023.01.010",
                "snippet": "A similar host cell response is triggered in cells containing Hna upon expression of a phage-encoded single-stranded DNA binding protein (SSB)",
                "notes": "Sather et al. support Hna response to a phage SSB independently of whole-phage infection."
              },
              {
                "reference": "DOI:10.1038/s41467-026-73157-2",
                "snippet": "shifts catalytic partitioning toward dysregulated nuclease activation",
                "notes": "Hooper et al. directly connect phage SSB stimulation to Hna nuclease activation."
              }
            ]
          },
          {
            "subject": "hna_nuclease_activation",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "abortive_infection_response",
            "description": "Dysregulated Hna nuclease activation damages DNA, causes cellular toxicity, and contributes to the abortive infection response.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-026-73157-2",
                "snippet": "Disruption of this balance enhances DNA cleavage and causes cellular toxicity",
                "notes": "Hooper et al. support Hna nuclease dysregulation as a toxic DNA-cleavage output."
              },
              {
                "reference": "DOI:10.1016/j.chom.2023.01.010",
                "snippet": "infected cells carrying the system die but do not release phage progeny",
                "notes": "Sather et al. support the abortive infection host-cell fate of Hna-containing cells."
              }
            ]
          },
          {
            "subject": "abortive_infection_response",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "hna_system_trait",
            "description": "Hna-mediated abortive infection is the phage-defense output that realizes the Hna system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.chom.2023.01.010",
                "snippet": "Hna limits phage spread by initiating abortive infection in response to a phage protein",
                "notes": "Sather et al. support abortive infection as the Hna antiviral output."
              }
            ]
          },
          {
            "subject": "hna_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Hna system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-026-73157-2",
                "snippet": "Hna is a broadly distributed anti-phage immune system",
                "notes": "Hooper et al. place Hna in the anti-phage immune-system family."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "hna-trigger-and-family-breadth-gap",
        "prompt": "Resolve Hna trigger breadth, phage escape routes, and family architecture before minting narrower Hna mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Sather et al. support Sinorhizobium Hna abortive infection after phage infection or phage SSB expression, and Hooper et al. support 5A SSB stimulation of nuclease activation, but Hna homologs need separate review before TraitMech asserts one universal phage trigger, ATP-dependent activation gate, DNA substrate, escape route, or host death timing across the full Hna family.",
        "posed_by": "codex",
        "posed_date": "2026-09-18"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-18T12:46:11Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Hna system as a DOI-backed GENOMICS TraitRecord under the phage defense system parent after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v118.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000309",
    "label": "Hypnos system",
    "definition": "A phage defense system in which an organism possesses a Hypnos locus that can protect bacteria from bacteriophage infection.",
    "definition_source": "DOI:10.1016/j.chom.2024.07.007",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "Hypnos",
        "synonym_type": "EXACT_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      },
      {
        "synonym_text": "HyoA",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1016/j.chom.2024.07.007",
        "snippet": "We validated six of these phage defense systems, including factors preventing viral attachment, R-loop-acting enzymes, the inflammasome, ubiquitin pathway, and pathogen recognition signaling.",
        "notes": "van den Berg et al. validated six phage defense systems related to eukaryotic innate antiviral responses."
      },
      {
        "reference": "DOI:10.1016/j.chom.2024.07.007",
        "snippet": "Searching for phage defense systems related to innate antiviral genes from vertebrates and plants, we uncovered over 450 candidates.",
        "notes": "van den Berg et al. motivate a conservative system-level record that does not assert a resolved Hypnos trigger, effector output, or universal pathway."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "Hypnos | 10\\.1016/j\\.chom\\.2024\\.07\\.007 | Bacterial homologs of innate eukaryotic antiviral defenses with anti-phage activity highlight shared evolutionary roots of viral defenses",
        "notes": "The DefenseFinder model registry maps the named Hypnos system to the van den Berg et al. antiphage-system discovery paper."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "Hypnos__HyoA                                     |                                                  | Hypnos",
        "notes": "The DefenseFinder HMM inventory records Hypnos__HyoA in the Hypnos model namespace."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "hypnos_locus_restricts_phage",
        "title": "Hypnos loci confer bacterial phage defense",
        "description": "Conservative system-level sketch linking possession of a Hypnos locus to restricted bacteriophage propagation without asserting the unresolved phage trigger or molecular output.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Hypnos as a named anti-phage system with a Hypnos__HyoA DefenseFinder HMM profile entry while leaving its phage trigger, molecular substrate, antiviral effector output, and subtype breadth unresolved.",
        "nodes": [
          {
            "node_id": "hypnos_locus",
            "label": "Hypnos locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A Hypnos anti-phage defense locus cataloged in DefenseFinder with a Hypnos__HyoA HMM profile entry."
          },
          {
            "node_id": "restricted_phage_propagation",
            "label": "restricted phage propagation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced propagation of bacteriophage in cells carrying the Hypnos system."
          },
          {
            "node_id": "hypnos_system_trait",
            "label": "Hypnos system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000309",
            "description": "Possession of a genome-encoded Hypnos phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "hypnos_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "restricted_phage_propagation",
            "description": "DefenseFinder maps Hypnos to a eukaryotic-antiviral-homolog antiphage-system discovery paper and catalogs a Hypnos__HyoA HMM profile entry in the Hypnos model namespace.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.chom.2024.07.007",
                "snippet": "We validated six of these phage defense systems, including factors preventing viral attachment, R-loop-acting enzymes, the inflammasome, ubiquitin pathway, and pathogen recognition signaling.",
                "notes": "van den Berg et al. validated six phage defense systems related to eukaryotic innate antiviral responses."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Hypnos | 10\\.1016/j\\.chom\\.2024\\.07\\.007 | Bacterial homologs of innate eukaryotic antiviral defenses with anti-phage activity highlight shared evolutionary roots of viral defenses",
                "notes": "The DefenseFinder model registry maps the named Hypnos system to the van den Berg et al. antiphage-system discovery paper."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "Hypnos__HyoA                                     |                                                  | Hypnos",
                "notes": "The DefenseFinder HMM inventory records Hypnos__HyoA in the Hypnos model namespace."
              }
            ]
          },
          {
            "subject": "restricted_phage_propagation",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "hypnos_system_trait",
            "description": "Hypnos-mediated phage restriction realizes the Hypnos system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.chom.2024.07.007",
                "snippet": "We validated six of these phage defense systems, including factors preventing viral attachment, R-loop-acting enzymes, the inflammasome, ubiquitin pathway, and pathogen recognition signaling.",
                "notes": "van den Berg et al. validated six phage defense systems related to eukaryotic antiviral responses."
              }
            ]
          },
          {
            "subject": "hypnos_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Hypnos system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Hypnos | 10\\.1016/j\\.chom\\.2024\\.07\\.007 | Bacterial homologs of innate eukaryotic antiviral defenses with anti-phage activity highlight shared evolutionary roots of viral defenses",
                "notes": "The DefenseFinder model registry maps the named Hypnos system to the van den Berg et al. antiphage-system discovery paper."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "hypnos-mechanism-gap",
        "prompt": "Resolve Hypnos phage triggers and effector outputs before minting narrower Hypnos mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "van den Berg et al. and DefenseFinder support Hypnos as a named anti-phage system with a Hypnos__HyoA HMM profile entry, but the trigger, molecular substrate, antiviral effector output, and subtype-specific mechanism are not resolved enough here to assert a narrower mechanistic child trait.",
        "attaches_to": [
          "causal_graphs#hypnos_locus_restricts_phage"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-20"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-20T13:10:22Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Hypnos system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v186.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000508",
    "label": "Ig-like Schlafen system",
    "definition": "A phage defense system in which an organism possesses a genome-encoded prokaryotic Schlafen nuclease fused to an immunoglobulin-like sensor domain that recognizes T5-like phage tail assembly chaperones and activates Schlafen tRNase defense.",
    "definition_source": "DOI:10.1038/s41564-026-02277-8",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "Shlafen_Ig-like",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      },
      {
        "synonym_text": "pSlfn5",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1038/s41564-026-02277-8"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/s41564-026-02277-8",
        "snippet": "prokaryotic Schlafen nucleases are widespread antiviral effectors that protect bacteria from bacteriophages and are fused to a diverse array of phage-sensing domains.",
        "notes": "Perez Taboada et al. support bacterial prokaryotic Schlafen nucleases as antiviral effectors fused to phage-sensing domains."
      },
      {
        "reference": "DOI:10.1038/s41564-026-02277-8",
        "snippet": "Schlafen nuclease is fused to a previously unknown immunoglobulin-like sensor domain and demonstrated that it recognizes tail assembly chaperones of T5-like phages.",
        "notes": "Perez Taboada et al. support Ig-like domain fusion and T5-like tail assembly chaperone recognition by an Ig-like prokaryotic Schlafen system."
      },
      {
        "reference": "DOI:10.1038/s41564-026-02277-8",
        "snippet": "We expressed seven Enterobacterales Schlafen systems in Escherichia coli, identifying two that confer defence against coliphages.",
        "notes": "Perez Taboada et al. cloned candidate Enterobacterales Schlafen systems into E. coli and observed coliphage defense for two of them."
      },
      {
        "reference": "DOI:10.1038/s41564-026-02277-8",
        "snippet": "Upon activation, the Schlafen nuclease cleaves both E. coli and phage-encoded tRNAs and restricts T5 phage by reducing its burst size.",
        "notes": "Perez Taboada et al. connect activation of an Ig-like RorSlfn5 nuclease to bacterial and phage tRNA cleavage and T5 burst-size reduction."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| Shlafen_Ig-like | 10\\.1038/s41564-026-02277-8 | Bacterial Schlafen proteins mediate phage defence | ",
        "notes": "The pinned DefenseFinder article registry maps the Shlafen_Ig-like source key to the Perez Taboada et al. Schlafen phage-defense paper."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "ig_like_schlafen_trna_cleavage",
        "title": "Ig-like Schlafen systems cleave tRNAs after phage sensing",
        "description": "Conservative system-level sketch linking an Ig-like prokaryotic Schlafen locus to T5-like tail assembly chaperone sensing, Schlafen nuclease-dependent tRNA cleavage, and the Ig-like Schlafen phage-defense trait.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures the Ig-like prokaryotic Schlafen DefenseFinder article namespace at system level and deliberately defers a protein-resolved RorSlfn5 mechanism. Perez Taboada et al. support an Ig-like Schlafen nuclease system that recognizes T5-like phage tail assembly chaperones and cleaves bacterial and phage tRNAs, but exact profile boundaries, natural host exemplars, phage trigger breadth, and DefenseFinder HMM/rules profiles are unresolved.",
        "nodes": [
          {
            "node_id": "ig_like_schlafen_locus",
            "label": "Ig-like Schlafen locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A locus encoding a prokaryotic Schlafen nuclease fused to an Ig-like sensor domain."
          },
          {
            "node_id": "t5_like_tail_chaperone_sensing",
            "label": "T5-like tail chaperone sensing",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Recognition of T5-like phage tail assembly chaperones by an Ig-like prokaryotic Schlafen sensor domain."
          },
          {
            "node_id": "schlafen_trna_cleavage",
            "label": "Schlafen tRNA cleavage",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Cleavage of bacterial and phage tRNAs by an activated Schlafen nuclease."
          },
          {
            "node_id": "ig_like_schlafen_system_trait",
            "label": "Ig-like Schlafen system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000508",
            "description": "Possession of a genome-encoded Ig-like prokaryotic Schlafen phage-defense system."
          },
          {
            "node_id": "phage_defense_system_trait",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "ig_like_schlafen_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "t5_like_tail_chaperone_sensing",
            "description": "Ig-like Schlafen loci encode a Schlafen nuclease fused to an Ig-like sensor domain that recognizes T5-like phage tail assembly chaperones.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-026-02277-8",
                "snippet": "Schlafen nuclease is fused to a previously unknown immunoglobulin-like sensor domain and demonstrated that it recognizes tail assembly chaperones of T5-like phages.",
                "notes": "Perez Taboada et al. support Ig-like domain fusion and T5-like tail assembly chaperone recognition by an Ig-like prokaryotic Schlafen system."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| Shlafen_Ig-like | 10\\.1038/s41564-026-02277-8 | Bacterial Schlafen proteins mediate phage defence | ",
                "notes": "The pinned DefenseFinder article registry maps the Shlafen_Ig-like source key to the Perez Taboada et al. Schlafen phage-defense paper."
              }
            ]
          },
          {
            "subject": "t5_like_tail_chaperone_sensing",
            "predicate": "activates",
            "predicate_id": "RO:0002213",
            "object": "schlafen_trna_cleavage",
            "description": "Phage-triggered activation of the Ig-like Schlafen nuclease leads to bacterial and phage tRNA cleavage.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-026-02277-8",
                "snippet": "Schlafen nuclease is fused to a previously unknown immunoglobulin-like sensor domain and demonstrated that it recognizes tail assembly chaperones of T5-like phages.",
                "notes": "Perez Taboada et al. support Ig-like domain fusion and T5-like tail assembly chaperone recognition by an Ig-like prokaryotic Schlafen system."
              },
              {
                "reference": "DOI:10.1038/s41564-026-02277-8",
                "snippet": "Upon activation, the Schlafen nuclease cleaves both E. coli and phage-encoded tRNAs and restricts T5 phage by reducing its burst size.",
                "notes": "Perez Taboada et al. connect activation of an Ig-like RorSlfn5 nuclease to bacterial and phage tRNA cleavage and T5 burst-size reduction."
              }
            ]
          },
          {
            "subject": "schlafen_trna_cleavage",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "ig_like_schlafen_system_trait",
            "description": "Schlafen tRNase activity restricts T5 phage and realizes the organism-level Ig-like Schlafen system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-026-02277-8",
                "snippet": "prokaryotic Schlafen nucleases are widespread antiviral effectors that protect bacteria from bacteriophages and are fused to a diverse array of phage-sensing domains.",
                "notes": "Perez Taboada et al. support bacterial prokaryotic Schlafen nucleases as antiviral effectors fused to phage-sensing domains."
              },
              {
                "reference": "DOI:10.1038/s41564-026-02277-8",
                "snippet": "Upon activation, the Schlafen nuclease cleaves both E. coli and phage-encoded tRNAs and restricts T5 phage by reducing its burst size.",
                "notes": "Perez Taboada et al. connect activation of an Ig-like RorSlfn5 nuclease to bacterial and phage tRNA cleavage and T5 burst-size reduction."
              }
            ]
          },
          {
            "subject": "ig_like_schlafen_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system_trait",
            "description": "Ig-like Schlafen system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-026-02277-8",
                "snippet": "prokaryotic Schlafen nucleases are widespread antiviral effectors that protect bacteria from bacteriophages and are fused to a diverse array of phage-sensing domains.",
                "notes": "Perez Taboada et al. support bacterial prokaryotic Schlafen nucleases as antiviral effectors fused to phage-sensing domains."
              },
              {
                "reference": "DOI:10.1038/s41564-026-02277-8",
                "snippet": "We expressed seven Enterobacterales Schlafen systems in Escherichia coli, identifying two that confer defence against coliphages.",
                "notes": "Perez Taboada et al. cloned candidate Enterobacterales Schlafen systems into E. coli and observed coliphage defense for two of them."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "ig-like-schlafen-defensefinder-profile-gap",
        "prompt": "Resolve exact pSlfn5 family boundaries, natural host exemplars, T5-like tail chaperone trigger breadth, and DefenseFinder HMM/rules coverage before minting narrower Ig-like Schlafen mechanism or component traits.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Perez Taboada et al. support prokaryotic Schlafen nucleases as widespread antiviral effectors and experimentally characterize the Ig-like RorSlfn5 nuclease as a T5-like tail chaperone-triggered tRNase, and the pinned DefenseFinder article registry maps the Shlafen_Ig-like key to the same article. The pinned HMM inventory and rules table have no exact Schlafen rows. This first-pass record therefore does not resolve exact pSlfn5 family boundaries, natural host exemplars, accession-level Schlafen proteins, full phage trigger breadth, or a reusable DefenseFinder profile model.",
        "evidence": [
          {
            "reference": "DOI:10.1038/s41564-026-02277-8",
            "snippet": "prokaryotic Schlafen nucleases are widespread antiviral effectors that protect bacteria from bacteriophages and are fused to a diverse array of phage-sensing domains.",
            "notes": "Perez Taboada et al. support bacterial prokaryotic Schlafen nucleases as antiviral effectors fused to phage-sensing domains."
          },
          {
            "reference": "DOI:10.1038/s41564-026-02277-8",
            "snippet": "Schlafen nuclease is fused to a previously unknown immunoglobulin-like sensor domain and demonstrated that it recognizes tail assembly chaperones of T5-like phages.",
            "notes": "Perez Taboada et al. support Ig-like domain fusion and T5-like tail assembly chaperone recognition by an Ig-like prokaryotic Schlafen system."
          },
          {
            "reference": "DOI:10.1038/s41564-026-02277-8",
            "snippet": "Upon activation, the Schlafen nuclease cleaves both E. coli and phage-encoded tRNAs and restricts T5 phage by reducing its burst size.",
            "notes": "Perez Taboada et al. connect activation of an Ig-like RorSlfn5 nuclease to bacterial and phage tRNA cleavage and T5 burst-size reduction."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
            "snippet": "| Shlafen_Ig-like | 10\\.1038/s41564-026-02277-8 | Bacterial Schlafen proteins mediate phage defence | ",
            "notes": "The pinned DefenseFinder article registry maps the Shlafen_Ig-like source key to the Perez Taboada et al. Schlafen phage-defense paper."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "notes": "A structured first-pass search of the pinned DefenseFinder HMM inventory found no exact Shlafen_Ig-like, Schlafen, or pSlfn5 row."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "A structured first-pass search of the pinned DefenseFinder rules table found no exact Shlafen_Ig-like, Schlafen, or pSlfn5 system row."
          }
        ],
        "attaches_to": [
          "causal_graphs#ig_like_schlafen_trna_cleavage"
        ],
        "posed_by": "codex",
        "posed_date": "2026-10-01"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-01T06:21:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Ig-like Schlafen system as a DOI- and DefenseFinder-backed GENOMICS TraitRecord under the phage defense system parent after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v385.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-01T06:21:01Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed Ig-like Schlafen system during initial curation and left canonical_examples empty because Perez Taboada et al. support RorSlfn5 from Raoultella ornithinolytica, but an NCBI Taxonomy lookup for that current name did not resolve during first-pass curation. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000410",
    "label": "integrative conjugative element",
    "definition": "A genomic island trait in which an organism possesses an integrative and conjugative element, a self-transmissible mobile genetic element that integrates into host DNA, excises under induced expression, and encodes type IV secretion machinery for conjugative transfer to recipient cells.",
    "definition_source": "DOI:10.1146/annurev-genet-112414-055018",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000093"
    ],
    "synonyms": [
      {
        "synonym_text": "ICE",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1146/annurev-genet-112414-055018"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev-genet-112414-055018",
        "snippet": "There are two defining features of ICEs: (a) They are found integrated in a host genome; and (b) they encode a functional conjugation system, a type IV secretion system",
        "notes": "Johnson and Grossman define integrative and conjugative elements as host-integrated mobile genetic elements that encode a functional type IV secretion conjugation system."
      },
      {
        "reference": "DOI:10.1093/nar/gkad644",
        "snippet": "The term \u2018genomic island\u2019 encompasses diverse types of mobile genetic elements that exhibit various structures and gene contents, including prophages, transposons, integrated plasmids, integrative and mobilizable elements (IMEs), and integrative and conjugative elements (ICEs)",
        "notes": "Bioteau et al. place integrative and conjugative elements among the mobile-genetic-element subclasses encompassed by genomic islands."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1423",
        "taxon_label": "Bacillus subtilis",
        "note": "ICEBs1",
        "reference": "DOI:10.1146/annurev-genet-112414-055018"
      },
      {
        "taxon_id": "NCBITaxon:1351",
        "taxon_label": "Enterococcus faecalis",
        "note": "Tn916",
        "reference": "DOI:10.1146/annurev-genet-112414-055018"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "ice_excision_conjugation_integration",
        "title": "ICEs excise, transfer by conjugation, and reintegrate",
        "description": "Conservative ICE life-cycle sketch linking an integrated ICE locus to circularization, oriT processing, T4SS-mediated conjugative transfer, recipient integration, and the genomic-island possession trait.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This genomics graph summarizes the shared ICE life cycle at the mobile-element level. It does not assert exact protein-family groundings for heterogeneous ICE integrases, relaxases, type IV coupling proteins, or T4SS subunits.",
        "nodes": [
          {
            "node_id": "integrated_ice_locus",
            "label": "integrated ICE locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "An integrative and conjugative element integrated into a host replicon."
          },
          {
            "node_id": "ice_excision_circularization",
            "label": "ICE excision and circularization",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Induction-associated excision of an integrated ICE to a circular double-stranded DNA intermediate."
          },
          {
            "node_id": "orit_processing",
            "label": "oriT processing",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Processing at the ICE origin of transfer to generate the linear transfer-DNA complex."
          },
          {
            "node_id": "conjugation",
            "label": "conjugation",
            "node_type": "BIOLOGICAL_PROCESS",
            "grounding": "GO:0009291",
            "description": "Contact-dependent transfer of ICE DNA into a recipient cell through the conjugation machinery."
          },
          {
            "node_id": "ice_integration",
            "label": "ICE integration",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Recombination of circular ICE DNA into the recipient host chromosome."
          },
          {
            "node_id": "integrative_conjugative_element",
            "label": "integrative conjugative element",
            "node_type": "TRAIT",
            "grounding": "traitmech:000410",
            "description": "Possession of a genome-encoded integrative and conjugative element."
          },
          {
            "node_id": "genomic_island",
            "label": "genomic island",
            "node_type": "TRAIT",
            "grounding": "traitmech:000093",
            "description": "Possession of a horizontally acquired chromosomal island."
          }
        ],
        "edges": [
          {
            "subject": "integrated_ice_locus",
            "predicate": "enables",
            "predicate_id": "RO:0002327",
            "object": "ice_excision_circularization",
            "description": "Upon induction, an integrated ICE excises from the chromosome and forms a circular dsDNA intermediate.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-genet-112414-055018",
                "snippet": "When ICE gene expression is induced, by specific cellular conditions or perhaps stochastically, the ICE excises from the chromosome and forms a circular dsDNA molecule",
                "notes": "Johnson and Grossman summarize induction-linked ICE excision and circular double-stranded DNA intermediate formation."
              }
            ]
          },
          {
            "subject": "ice_excision_circularization",
            "predicate": "enables",
            "predicate_id": "RO:0002327",
            "object": "orit_processing",
            "description": "The circular ICE is processed at oriT to generate the linear ssDNA-protein transfer complex.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-genet-112414-055018",
                "snippet": "Other host and ICE-encoded proteins recognize the origin of transfer (oriT) and process the ICE DNA to generate a linear ssDNA-protein complex",
                "notes": "Johnson and Grossman describe oriT recognition and ICE DNA processing that produces the linear transfer-DNA complex."
              }
            ]
          },
          {
            "subject": "orit_processing",
            "predicate": "enables",
            "predicate_id": "RO:0002327",
            "object": "conjugation",
            "description": "The mating machinery transports the processed transfer DNA into a recipient cell.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-genet-112414-055018",
                "snippet": "The mating machinery pumps the T-DNA into the recipient",
                "notes": "The Johnson and Grossman life-cycle summary places mating-machinery transport after transfer-DNA generation."
              }
            ]
          },
          {
            "subject": "conjugation",
            "predicate": "enables",
            "predicate_id": "RO:0002327",
            "object": "ice_integration",
            "description": "Transferred ICE DNA recircularizes and becomes a double-stranded integration substrate in the recipient.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-genet-112414-055018",
                "snippet": "In both the donor and recipient, the circular dsDNA ICE integrates into the host chromosome.",
                "notes": "Johnson and Grossman's ICE life-cycle figure caption states that the circular double-stranded ICE reintegrates in donor and recipient cells."
              }
            ]
          },
          {
            "subject": "ice_integration",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "integrative_conjugative_element",
            "description": "Recipient-chromosome integration completes possession of an integrated conjugative element.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-genet-112414-055018",
                "snippet": "There are two defining features of ICEs: (a) They are found integrated in a host genome; and (b) they encode a functional conjugation system, a type IV secretion system",
                "notes": "Johnson and Grossman define integrative and conjugative elements as host-integrated mobile genetic elements that encode a functional type IV secretion conjugation system."
              }
            ]
          },
          {
            "subject": "integrative_conjugative_element",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "genomic_island",
            "description": "Integrative-conjugative-element possession is a genomic-island possession trait.",
            "evidence": [
              {
                "reference": "DOI:10.1093/nar/gkad644",
                "snippet": "The term \u2018genomic island\u2019 encompasses diverse types of mobile genetic elements that exhibit various structures and gene contents, including prophages, transposons, integrated plasmids, integrative and mobilizable elements (IMEs), and integrative and conjugative elements (ICEs)",
                "notes": "Bioteau et al. place integrative and conjugative elements among the mobile-genetic-element subclasses encompassed by genomic islands."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "ice-family-resolution-gap",
        "prompt": "Resolve bacterial ICE subfamilies, Actinomycete ICE boundaries, integrase/relaxase/T4SS signatures, and cargo-phenotype scope before minting narrower ICE mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Johnson and Grossman define ICEs by host-genome integration and a functional type IV secretion conjugation system, while Bioteau et al. classify ICEs as self-transmissible genomic islands. This first record captures the genome-level possession trait without claiming exact molecular groundings for heterogeneous integrases, relaxases, T4SS variants, Actinomycete ICE machinery, or adaptive cargo phenotypes.",
        "attaches_to": [
          "causal_graphs#ice_excision_conjugation_integration"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-27"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-27T14:42:32Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted integrative conjugative element as a DOI-backed GENOMICS TraitRecord under genomic island with ICEBs1 and Tn916 canonical examples after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v287.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000305",
    "label": "JukAB system",
    "definition": "A phage defense system in which an organism possesses a two-gene jukAB locus encoding a JukA sensor that binds a PhiKZ-like gp241 early phage protein at the EPI vesicle and directly recruits the pore-forming-toxin-like JukB effector to destabilize the vesicle, suppress early phage gene expression, and prevent phage DNA replication and nucleus assembly.",
    "definition_source": "DOI:10.1016/j.cell.2025.02.016",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "JukAB",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      },
      {
        "synonym_text": "jumbo phage killer",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1016/j.cell.2025.02.016"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1016/j.cell.2025.02.016",
        "snippet": "a two-component immune system that terminates infection of \u03c6KZ-like phages",
        "notes": "Li et al. define Juk as a two-component immune system that terminates PhiKZ-like jumbo-phage infection."
      },
      {
        "reference": "DOI:10.1101/2022.09.17.508391",
        "snippet": "jukA and jukB together, but not either gene alone, conferred resistance against",
        "notes": "Li et al. show that the JukA sensor and JukB effector are jointly required for heterologous PhiKZ resistance."
      },
      {
        "reference": "DOI:10.1016/j.cell.2025.02.016",
        "snippet": "JukA (formerly YaaW) rapidly senses the EPI vesicle by binding to an early-expressed phage protein, gp241, and then directly recruits JukB",
        "notes": "Li et al. identify JukA binding to the PhiKZ-like early phage protein gp241 at the EPI vesicle as the JukAB input that recruits JukB."
      },
      {
        "reference": "DOI:10.1016/j.cell.2025.02.016",
        "snippet": "The JukB effector structurally resembles a pore-forming toxin and destabilizes the EPI vesicle",
        "notes": "Li et al. connect the recruited JukB effector to destabilization of the early phage infection vesicle."
      },
      {
        "reference": "DOI:10.1016/j.cell.2025.02.016",
        "snippet": "suppressing the expression of early phage genes and preventing phage DNA replication and phage nucleus assembly while saving the cell",
        "notes": "Li et al. describe the downstream anti-phage outcome of two-component Juk immunity."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "JukAB | 10\\.1101/2022\\.09\\.17\\.508391 | A family of novel immune systems targets early infection of nucleus-forming jumbo phages",
        "notes": "The DefenseFinder article registry maps the named JukAB system to the Li et al. Juk immune-system preprint."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "JukAB\tJukAB\t2\t2\tJukAB__JukA, JukAB__JukB",
        "notes": "The DefenseFinder rules table models JukAB as a two-component system requiring JukAB__JukA and JukAB__JukB profiles."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| JukAB__JukA                                      | JukAB__JukA                                      | JukAB                  | Custom                  | 20     |",
        "notes": "The DefenseFinder HMM inventory records JukAB__JukA under the JukAB model namespace."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| JukAB__JukB                                      | JukAB__JukB                                      | JukAB                  | Custom                  | 20     |",
        "notes": "The DefenseFinder HMM inventory records JukAB__JukB under the JukAB model namespace."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:287",
        "taxon_label": "Pseudomonas aeruginosa",
        "note": "Li et al. discovered the native jukA-jukB operon in Pseudomonas aeruginosa PA14 and showed that the two-gene Juk locus provides immunity against PhiKZ-related nucleus-forming jumbo phages.",
        "reference": "DOI:10.1101/2022.09.17.508391"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "jukab_recruits_effector_to_block_jumbo_phage",
        "title": "JukAB blocks early jumbo-phage infection",
        "description": "Conservative system-level sketch linking a jukAB locus to gp241/EPI-vesicle sensing by JukA, JukB recruitment, JukB-mediated EPI-vesicle destabilization, suppression of early PhiKZ-like jumbo-phage development, and JukAB system possession.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures JukAB as a named DefenseFinder two-profile system in which JukA binds the PhiKZ gp241 early phage protein at the EPI vesicle and recruits JukB to destabilize that vesicle. It summarizes the direct two-component system without minting separate sequence feature traits for jukA, jukB, gp241, or other JukA-associated effector families.",
        "nodes": [
          {
            "node_id": "jukab_locus",
            "label": "jukAB locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A two-gene locus encoding JukA and JukB and represented by the DefenseFinder JukAB rule."
          },
          {
            "node_id": "jukA_phage_ejected_factor_sensing",
            "label": "JukA gp241 EPI-vesicle sensing",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Binding of the JukA sensor to PhiKZ-like gp241 at the early phage infection vesicle."
          },
          {
            "node_id": "jukB_effector_recruitment",
            "label": "JukB effector recruitment",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "JukA-dependent recruitment of the JukB effector to the phage infection site."
          },
          {
            "node_id": "early_jumbo_phage_progression",
            "label": "early jumbo-phage progression",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Early phage transcription, DNA replication, and nucleus assembly during infection by a nucleus-forming jumbo phage."
          },
          {
            "node_id": "epi_vesicle_destabilization",
            "label": "EPI vesicle destabilization",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "JukB-associated destabilization of the lipid-based early phage infection vesicle."
          },
          {
            "node_id": "jukab_system_trait",
            "label": "JukAB system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000305",
            "description": "Possession of a genome-encoded JukAB phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "jukab_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "jukA_phage_ejected_factor_sensing",
            "description": "The JukAB locus encodes JukA, the sensor that binds the early phage protein gp241 at the EPI vesicle.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.cell.2025.02.016",
                "snippet": "JukA (formerly YaaW) rapidly senses the EPI vesicle by binding to an early-expressed phage protein, gp241",
                "notes": "Li et al. identify gp241/EPI-vesicle binding by JukA as the characterized JukAB sensor input."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "JukAB\tJukAB\t2\t2\tJukAB__JukA, JukAB__JukB",
                "notes": "DefenseFinder requires the JukA profile in its JukAB system rule."
              }
            ]
          },
          {
            "subject": "jukA_phage_ejected_factor_sensing",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "jukB_effector_recruitment",
            "description": "JukA sensing of gp241 at the EPI vesicle directly recruits the JukB effector.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.cell.2025.02.016",
                "snippet": "JukA (formerly YaaW) rapidly senses the EPI vesicle by binding to an early-expressed phage protein, gp241, and then directly recruits JukB",
                "notes": "Li et al. place direct JukB recruitment downstream of JukA-gp241 binding at the EPI vesicle."
              }
            ]
          },
          {
            "subject": "jukB_effector_recruitment",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "epi_vesicle_destabilization",
            "description": "Recruited JukB is a pore-forming-toxin-like effector that destabilizes the EPI vesicle.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.cell.2025.02.016",
                "snippet": "The JukB effector structurally resembles a pore-forming toxin and destabilizes the EPI vesicle",
                "notes": "Li et al. connect JukB to the vesicle destabilization step of JukAB immunity."
              }
            ]
          },
          {
            "subject": "epi_vesicle_destabilization",
            "predicate": "mitigates",
            "predicate_id": "METPO:2007407",
            "object": "early_jumbo_phage_progression",
            "description": "EPI-vesicle destabilization by the JukAB response blocks early jumbo-phage gene expression, DNA replication, and nucleus assembly.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.cell.2025.02.016",
                "snippet": "suppressing the expression of early phage genes and preventing phage DNA replication and phage nucleus assembly while saving the cell",
                "notes": "Li et al. define the anti-phage output of the two-component Juk system."
              }
            ]
          },
          {
            "subject": "epi_vesicle_destabilization",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "jukab_system_trait",
            "description": "JukB-associated EPI-vesicle destabilization realizes the JukAB defense trait.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.cell.2025.02.016",
                "snippet": "a two-component immune system that terminates infection of \u03c6KZ-like phages",
                "notes": "Li et al. frame two-component Juk as an immune system that terminates PhiKZ-like phage infection."
              }
            ]
          },
          {
            "subject": "jukab_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "JukAB system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "JukAB | 10\\.1101/2022\\.09\\.17\\.508391 | A family of novel immune systems targets early infection of nucleus-forming jumbo phages",
                "notes": "DefenseFinder associates JukAB with the Li et al. nucleus-forming-jumbo-phage immune system paper."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "jukab-vesicle-effector-family-gap",
        "prompt": "Resolve JukB vesicle-destabilization chemistry and the boundaries of other JukA-containing systems before minting narrower mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Li et al. resolve gp241/EPI-vesicle sensing by JukA and direct recruitment of JukB as a two-component JukAB strategy, but the exact chemistry of JukB-mediated vesicle destabilization and the relationship between canonical JukAB and JukA homologs paired with diverse other putative effectors still need narrower review.",
        "attaches_to": [
          "causal_graphs#jukab_recruits_effector_to_block_jumbo_phage"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-20"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-20T08:47:10Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted JukAB system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v182.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000310",
    "label": "Kamadhenu system",
    "definition": "A phage defense system in which an organism possesses a Kamadhenu locus that can restrict bacteriophage infection.",
    "definition_source": "DOI:10.1093/nar/gkae671",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "Kamadhenu",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1093/nar/gkae671"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1093/nar/gkae671",
        "snippet": "These systems were named after cheese, cattle or fermentation related deities (Rhea, Aristaios, Kamadhenu, Fliodhais, Audmula, Rugutis and Hesat)",
        "notes": "Grafakou et al. named Kamadhenu among seven not previously described lactococcal antiphage systems."
      },
      {
        "reference": "DOI:10.1073/pnas.2426508122",
        "snippet": "we isolated 66 phage escape mutants which had become insensitive to 13 distinct, plasmid-encoded lactococcal phage resistance systems (i.e. Rhea, Kamadhenu, Rugutis, Audmula, PARIS, type II CBASS, Septu, AbiA, AbiB, AbiD/F, AbiG, AbiJ, AbiP)",
        "notes": "Mosterd et al. later included Kamadhenu among the distinct plasmid-encoded lactococcal phage-resistance systems investigated by phage escape-mutant isolation."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "Kamadhenu | 10\\.1093/nar/gkae671 | Discovery of antiphage systems in the lactococcal plasmidome",
        "notes": "The DefenseFinder article registry maps the named Kamadhenu system to the Grafakou et al. lactococcal antiphage-system discovery paper."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "kamadhenu_locus_restricts_phage",
        "title": "Kamadhenu loci confer bacterial phage defense",
        "description": "Conservative system-level sketch linking possession of a Kamadhenu locus to restricted bacteriophage propagation without asserting the unresolved phage trigger or molecular output.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Kamadhenu as a named lactococcal anti-phage system while leaving its direct phage trigger, molecular substrate, antiviral effector output, natural locus breadth, and the absence of pinned DefenseFinder HMM or rule rows unresolved.",
        "nodes": [
          {
            "node_id": "kamadhenu_locus",
            "label": "Kamadhenu locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A Kamadhenu anti-phage defense locus described among lactococcal plasmid-encoded phage-resistance systems."
          },
          {
            "node_id": "restricted_phage_propagation",
            "label": "restricted phage propagation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced propagation of bacteriophage in cells carrying the Kamadhenu system."
          },
          {
            "node_id": "kamadhenu_system_trait",
            "label": "Kamadhenu system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000310",
            "description": "Possession of a genome-encoded Kamadhenu phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "kamadhenu_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "restricted_phage_propagation",
            "description": "The lactococcal plasmidome screen discovered Kamadhenu as a named antiphage system, and the DefenseFinder article registry maps the Kamadhenu system to that discovery paper.",
            "evidence": [
              {
                "reference": "DOI:10.1093/nar/gkae671",
                "snippet": "These systems were named after cheese, cattle or fermentation related deities (Rhea, Aristaios, Kamadhenu, Fliodhais, Audmula, Rugutis and Hesat)",
                "notes": "Grafakou et al. named Kamadhenu as one of the novel lactococcal antiphage systems."
              },
              {
                "reference": "DOI:10.1073/pnas.2426508122",
                "snippet": "we isolated 66 phage escape mutants which had become insensitive to 13 distinct, plasmid-encoded lactococcal phage resistance systems (i.e. Rhea, Kamadhenu, Rugutis, Audmula, PARIS, type II CBASS, Septu, AbiA, AbiB, AbiD/F, AbiG, AbiJ, AbiP)",
                "notes": "Mosterd et al. treat Kamadhenu as a plasmid-encoded lactococcal phage-resistance system in their escape-mutant screen."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Kamadhenu | 10\\.1093/nar/gkae671 | Discovery of antiphage systems in the lactococcal plasmidome",
                "notes": "The DefenseFinder article registry maps the named Kamadhenu system to the Grafakou et al. lactococcal antiphage-system discovery paper."
              }
            ]
          },
          {
            "subject": "restricted_phage_propagation",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "kamadhenu_system_trait",
            "description": "Kamadhenu-mediated phage restriction realizes the Kamadhenu system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1073/pnas.2426508122",
                "snippet": "we isolated 66 phage escape mutants which had become insensitive to 13 distinct, plasmid-encoded lactococcal phage resistance systems (i.e. Rhea, Kamadhenu, Rugutis, Audmula, PARIS, type II CBASS, Septu, AbiA, AbiB, AbiD/F, AbiG, AbiJ, AbiP)",
                "notes": "Mosterd et al. treat Kamadhenu as a plasmid-encoded lactococcal phage-resistance system in their escape-mutant screen."
              }
            ]
          },
          {
            "subject": "kamadhenu_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Kamadhenu system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Kamadhenu | 10\\.1093/nar/gkae671 | Discovery of antiphage systems in the lactococcal plasmidome",
                "notes": "The DefenseFinder article registry maps the named Kamadhenu system to the Grafakou et al. lactococcal antiphage-system discovery paper."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "kamadhenu-mechanism-gap",
        "prompt": "Resolve Kamadhenu phage triggers and effector outputs before minting narrower Kamadhenu mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Grafakou et al., Mosterd et al., and DefenseFinder support Kamadhenu as a named anti-phage system, but the direct trigger, molecular substrate, antiviral effector output, natural locus breadth, and profile-to-component model are not resolved enough here to assert a narrower mechanistic child trait.",
        "attaches_to": [
          "causal_graphs#kamadhenu_locus_restricts_phage"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-20"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-20T13:47:53Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Kamadhenu system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v187.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-20T14:22:36Z",
        "curator": "codex",
        "action": "UPDATED_EVIDENCE",
        "changes": "Added direct Mosterd et al. phage-resistance evidence to the Kamadhenu locus edge in response to PR #1140 review issue #1141.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000231",
    "label": "Kiwa system",
    "definition": "A phage defense system in which an organism possesses a two-component Kiwa locus encoding the transmembrane sensor KwaA and DNA-binding effector KwaB that assemble into a membrane-associated supercomplex and coordinate phage-attachment sensing with inhibition of phage DNA replication and late transcription.",
    "definition_source": "DOI:10.1016/j.cell.2025.07.002",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "Kiwa",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1016/j.cell.2025.07.002"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1126/science.aar4120",
        "snippet": "Kiwa KwaAB pfam16162 No annotated domain 934 924 (1.8%) Membrane associated",
        "notes": "Doron et al. reported Kiwa/KwaAB as a membrane-associated defense system in their pangenome-scale antiphage-system discovery screen."
      },
      {
        "reference": "DOI:10.1016/j.cell.2025.07.002",
        "snippet": "Kiwa, a widespread two-component system composed of the transmembrane sensor KwaA and the DNA-binding effector KwaB",
        "notes": "Zhang et al. support defining Kiwa as a recurring two-component KwaA/KwaB antiviral system."
      },
      {
        "reference": "DOI:10.1016/j.cell.2025.07.002",
        "snippet": "KwaA and KwaB assemble into a large, membrane-associated supercomplex",
        "notes": "Zhang et al. connect the KwaA and KwaB components to membrane-associated supercomplex assembly."
      },
      {
        "reference": "DOI:10.1016/j.cell.2025.07.002",
        "snippet": "Upon phage binding, KwaA senses infection at the membrane, leading to KwaB binding of ejected phage DNA and inhibition of replication and late transcription, without inducing host cell death",
        "notes": "Zhang et al. connect phage binding to KwaA-dependent membrane sensing, KwaB binding of phage DNA, and inhibition of phage replication and late transcription."
      },
      {
        "reference": "DOI:10.1016/j.cell.2025.07.002",
        "snippet": "its antiviral activity requires association with KwaA, suggesting spatial or conformational regulation",
        "notes": "Zhang et al. support KwaA-KwaB association as required for Kiwa antiviral activity."
      },
      {
        "reference": "DOI:10.1016/j.cell.2025.07.002",
        "snippet": "Kiwa coordinates membrane-associated detection of phage infection with downstream DNA binding by its effector, forming a spatially coordinated antiviral mechanism",
        "notes": "Zhang et al. summarize the Kiwa system-level mechanism as membrane-associated phage-infection detection coordinated with effector DNA binding."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:562",
        "taxon_label": "Escherichia coli",
        "note": "Zhang et al. characterized the Escherichia coli O55:H7 Kiwa system and showed that its KwaA/KwaB pair assembles into a membrane-associated supercomplex that inhibits phage DNA replication and late transcription.",
        "reference": "DOI:10.1016/j.cell.2025.07.002"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "kiwa_membrane_sensing_dna_binding",
        "title": "Kiwa coordinates membrane sensing with phage DNA binding",
        "description": "Evidence-backed process sketch linking a Kiwa kwaAB locus to KwaA-KwaB supercomplex assembly, membrane-associated phage-infection sensing, binding of ejected phage DNA, and inhibition of phage DNA replication and late transcription.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures the characterized two-component Kiwa mechanism without asserting one exact phage receptor, the precise KwaA conformational change, the structural basis of KwaB DNA binding, Gam-mediated counter-defense, or RecBCD rescue as universal across all Kiwa loci.",
        "nodes": [
          {
            "node_id": "kiwa_locus",
            "label": "Kiwa locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A two-component phage-defense locus encoding the transmembrane sensor KwaA and DNA-binding effector KwaB."
          },
          {
            "node_id": "kwaab_supercomplex_assembly",
            "label": "KwaA-KwaB supercomplex assembly",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Assembly of KwaA and KwaB into a large membrane-associated Kiwa supercomplex."
          },
          {
            "node_id": "membrane_phage_sensing_and_dna_binding",
            "label": "membrane phage sensing and DNA binding",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "KwaA-mediated membrane sensing of phage binding coordinated with KwaB binding to ejected phage DNA."
          },
          {
            "node_id": "phage_replication_and_late_transcription",
            "label": "phage replication and late transcription",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Phage DNA replication and late phage transcription inside an infected bacterial host."
          },
          {
            "node_id": "kiwa_system_trait",
            "label": "Kiwa system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000231",
            "description": "Possession of a genome-encoded Kiwa phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "kiwa_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "kwaab_supercomplex_assembly",
            "description": "The Kiwa kwaAB locus encodes KwaA and KwaB components that assemble into a membrane-associated supercomplex.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.cell.2025.07.002",
                "snippet": "KwaA and KwaB assemble into a large, membrane-associated supercomplex",
                "notes": "Zhang et al. support KwaA/KwaB supercomplex assembly."
              }
            ]
          },
          {
            "subject": "kwaab_supercomplex_assembly",
            "predicate": "enables",
            "predicate_id": "RO:0002327",
            "object": "membrane_phage_sensing_and_dna_binding",
            "description": "Association with KwaA is required for Kiwa antiviral activity despite independent KwaB DNA binding.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.cell.2025.07.002",
                "snippet": "its antiviral activity requires association with KwaA, suggesting spatial or conformational regulation",
                "notes": "Zhang et al. support KwaA association as required for KwaB antiviral activity."
              }
            ]
          },
          {
            "subject": "membrane_phage_sensing_and_dna_binding",
            "predicate": "mitigates",
            "predicate_id": "METPO:2007407",
            "object": "phage_replication_and_late_transcription",
            "description": "KwaA sensing of phage binding coordinates with KwaB binding of ejected phage DNA to inhibit phage replication and late transcription.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.cell.2025.07.002",
                "snippet": "Upon phage binding, KwaA senses infection at the membrane, leading to KwaB binding of ejected phage DNA and inhibition of replication and late transcription",
                "notes": "Zhang et al. connect Kiwa membrane sensing and KwaB DNA binding to inhibition of phage replication and late transcription."
              }
            ]
          },
          {
            "subject": "membrane_phage_sensing_and_dna_binding",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "kiwa_system_trait",
            "description": "Spatially coordinated membrane-associated phage sensing and effector DNA binding realizes the Kiwa antiphage-defense phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.cell.2025.07.002",
                "snippet": "Kiwa coordinates membrane-associated detection of phage infection with downstream DNA binding by its effector",
                "notes": "Zhang et al. summarize the system-level Kiwa antiviral mechanism."
              }
            ]
          },
          {
            "subject": "kiwa_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Kiwa system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.cell.2025.07.002",
                "snippet": "Our findings support a model in which Kiwa coordinates membrane-associated detection of phage infection",
                "notes": "Zhang et al. support Kiwa as an antiviral phage-defense system."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "kiwa-activation-and-counterdefense-gap",
        "prompt": "Resolve Kiwa activation, phage counter-defense, and RecBCD-rescue details before minting narrower Kiwa mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Zhang et al. support a KwaA/KwaB membrane-associated antiviral supercomplex and also describe the phage Gam DNA-mimic counter-defense and RecBCD-dependent restoration of Kiwa protection, but the first TraitRecord stays at the system level until separate review resolves the activation conformational change, exact DNA-binding state, phage counter-defense breadth, and RecBCD connection.",
        "posed_by": "codex",
        "posed_date": "2026-09-15"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-15T22:47:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Kiwa system as a DOI-backed GENOMICS TraitRecord under the phage defense system parent after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v108.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000501",
    "label": "Kongming system",
    "definition": "A phage defense system in which an organism possesses a Kongming locus that uses phage-triggered deoxyinosine triphosphate signaling to activate a KomBC effector complex and mediate NAD depletion-linked death of infected cells.",
    "definition_source": "DOI:10.1126/science.ads6055",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "Kongming",
        "synonym_type": "EXACT_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      },
      {
        "synonym_text": "Kongming system",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1038/s41467-026-74710-9"
      },
      {
        "synonym_text": "Kongming immune system",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1038/s41467-026-74710-9"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1126/science.ads6055",
        "snippet": "In this study, we reveal a bacterial antiphage system that mediates immune signaling through nucleobase modification.",
        "notes": "Zeng et al. describe the Science Kongming paper's antiphage system as a nucleobase-modification immune-signaling pathway."
      },
      {
        "reference": "DOI:10.1126/science.ads6055",
        "snippet": "Immunity is triggered by phage nucleotide kinases, which, combined with the system-encoded adenosine deaminase, produce deoxyinosine triphosphates (dITPs) as immune messengers.",
        "notes": "Zeng et al. connect phage-triggered Kongming immunity to system-dependent production of dITP immune messengers."
      },
      {
        "reference": "DOI:10.1126/science.ads6055",
        "snippet": "The dITP signal activates a downstream effector to mediate depletion of cellular nicotinamide adenine dinucleotide (oxidized form), resulting in population-level defense through the death of infected cells.",
        "notes": "Zeng et al. place dITP upstream of an effector that depletes NAD and drives infected-cell death."
      },
      {
        "reference": "DOI:10.1038/s41467-026-74710-9",
        "snippet": "One of them is the Kongming system, which includes an effector complex (KomBC), composed of a non-canonical purine NTP pyrophosphatase (KomB) and a SIR2 domain-containing protein (KomC).",
        "notes": "Li et al. name the Kongming effector complex and its KomB and KomC components."
      },
      {
        "reference": "DOI:10.1038/s41467-026-74710-9",
        "snippet": "The Kongming system is activated by an atypical signaling nucleotide, dITP, generated upon phage infection.",
        "notes": "Li et al. describe dITP as a phage-infection-generated Kongming activation signal."
      },
      {
        "reference": "DOI:10.1038/s41467-026-74710-9",
        "snippet": "Binding of dITP to KomB initiates progressive conformational rearrangements within the filament, ultimately remodeling the filament into a distinct architecture in which KomC adopts an active conformation with NADase activity.",
        "notes": "Li et al. connect dITP-bound KomB to activation of KomC NADase activity within the Kongming KomBC effector complex."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| Kongming | 10\\.1126/science\\.ads6055 | Base-modified nucleotides mediate immune signaling in bacteria | ",
        "notes": "The pinned DefenseFinder article registry maps the named Kongming system to the Zeng et al. Science paper."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "kongming_ditp_nadase_defense",
        "title": "Kongming loci activate dITP-linked NADase defense",
        "description": "Conservative system-level sketch linking a Kongming locus to phage-triggered dITP signaling, KomBC activation, NAD depletion, infected-cell death, and Kongming system possession.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Kongming as a named dITP-signaling phage-defense system while leaving exact locus breadth, natural host breadth, phage nucleotide-kinase inputs, profile-to-component mapping, and DefenseFinder HMM/rules detection criteria unresolved.",
        "nodes": [
          {
            "node_id": "kongming_locus",
            "label": "Kongming locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A Kongming anti-phage locus encoding dITP immune-signaling and KomBC effector functions."
          },
          {
            "node_id": "ditp_immune_signaling",
            "label": "dITP immune signaling",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Production of deoxyinosine triphosphate immune messengers after phage infection."
          },
          {
            "node_id": "komc_nadase_activation",
            "label": "KomC NADase activation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Activation of KomC NADase activity in the KomBC effector complex after dITP binding to KomB."
          },
          {
            "node_id": "nad_depletion_cell_death",
            "label": "NAD depletion-linked infected-cell death",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Depletion of cellular NAD followed by death of infected cells during population-level defense."
          },
          {
            "node_id": "kongming_system_trait",
            "label": "Kongming system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000501",
            "description": "Possession of a genome-encoded Kongming phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "kongming_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "ditp_immune_signaling",
            "description": "Kongming loci mediate phage-triggered production of dITP immune messengers.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.ads6055",
                "snippet": "In this study, we reveal a bacterial antiphage system that mediates immune signaling through nucleobase modification.",
                "notes": "Zeng et al. describe the Science Kongming paper's antiphage system as a nucleobase-modification immune-signaling pathway."
              },
              {
                "reference": "DOI:10.1126/science.ads6055",
                "snippet": "Immunity is triggered by phage nucleotide kinases, which, combined with the system-encoded adenosine deaminase, produce deoxyinosine triphosphates (dITPs) as immune messengers.",
                "notes": "Zeng et al. connect phage-triggered Kongming immunity to system-dependent production of dITP immune messengers."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| Kongming | 10\\.1126/science\\.ads6055 | Base-modified nucleotides mediate immune signaling in bacteria | ",
                "notes": "The pinned DefenseFinder article registry maps the named Kongming system to the Zeng et al. Science paper."
              }
            ]
          },
          {
            "subject": "ditp_immune_signaling",
            "predicate": "activates",
            "predicate_id": "RO:0002213",
            "object": "komc_nadase_activation",
            "description": "dITP binding activates KomC NADase activity in the Kongming KomBC effector complex.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-026-74710-9",
                "snippet": "The Kongming system is activated by an atypical signaling nucleotide, dITP, generated upon phage infection.",
                "notes": "Li et al. describe dITP as a phage-infection-generated Kongming activation signal."
              },
              {
                "reference": "DOI:10.1038/s41467-026-74710-9",
                "snippet": "Binding of dITP to KomB initiates progressive conformational rearrangements within the filament, ultimately remodeling the filament into a distinct architecture in which KomC adopts an active conformation with NADase activity.",
                "notes": "Li et al. connect dITP-bound KomB to activation of KomC NADase activity within the Kongming KomBC effector complex."
              }
            ]
          },
          {
            "subject": "komc_nadase_activation",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "nad_depletion_cell_death",
            "description": "KomBC effector activation mediates NAD depletion that can kill phage-infected cells.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.ads6055",
                "snippet": "The dITP signal activates a downstream effector to mediate depletion of cellular nicotinamide adenine dinucleotide (oxidized form), resulting in population-level defense through the death of infected cells.",
                "notes": "Zeng et al. place dITP upstream of an effector that depletes NAD and drives infected-cell death."
              },
              {
                "reference": "DOI:10.1038/s41467-026-74710-9",
                "snippet": "One of them is the Kongming system, which includes an effector complex (KomBC), composed of a non-canonical purine NTP pyrophosphatase (KomB) and a SIR2 domain-containing protein (KomC).",
                "notes": "Li et al. name the Kongming effector complex and its KomB and KomC components."
              },
              {
                "reference": "DOI:10.1038/s41467-026-74710-9",
                "snippet": "Binding of dITP to KomB initiates progressive conformational rearrangements within the filament, ultimately remodeling the filament into a distinct architecture in which KomC adopts an active conformation with NADase activity.",
                "notes": "Li et al. connect dITP-bound KomB to activation of KomC NADase activity within the Kongming KomBC effector complex."
              }
            ]
          },
          {
            "subject": "nad_depletion_cell_death",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "kongming_system_trait",
            "description": "dITP-triggered NAD depletion and infected-cell death realize the Kongming system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.ads6055",
                "snippet": "The dITP signal activates a downstream effector to mediate depletion of cellular nicotinamide adenine dinucleotide (oxidized form), resulting in population-level defense through the death of infected cells.",
                "notes": "Zeng et al. place dITP upstream of an effector that depletes NAD and drives infected-cell death."
              }
            ]
          },
          {
            "subject": "kongming_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Kongming system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.ads6055",
                "snippet": "In this study, we reveal a bacterial antiphage system that mediates immune signaling through nucleobase modification.",
                "notes": "Zeng et al. describe the Science Kongming paper's antiphage system as a nucleobase-modification immune-signaling pathway."
              },
              {
                "reference": "DOI:10.1038/s41467-026-74710-9",
                "snippet": "The Kongming system is activated by an atypical signaling nucleotide, dITP, generated upon phage infection.",
                "notes": "Li et al. describe dITP as a phage-infection-generated Kongming activation signal."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| Kongming | 10\\.1126/science\\.ads6055 | Base-modified nucleotides mediate immune signaling in bacteria | ",
                "notes": "The pinned DefenseFinder article registry maps the named Kongming system to the Zeng et al. Science paper."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "kongming-profile-host-and-component-gap",
        "prompt": "Resolve Kongming natural host breadth, exact locus composition, phage nucleotide-kinase inputs, KomA/KomB/KomC profile boundaries, and DefenseFinder HMM/rule coverage before minting narrower Kongming mechanism or component traits.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Zeng et al. support a bacterial antiphage system that uses system-encoded adenosine deaminase and phage nucleotide kinases to produce dITP messengers, and Li et al. connect the named Kongming system to dITP-driven activation of the KomBC NADase effector. The pinned DefenseFinder article registry maps the Kongming source key to the Zeng et al. Science paper, but the pinned HMM inventory and rules table have no exact Kongming rows. This first-pass record therefore does not resolve the complete locus model, direct HMM/profile mapping, or native host breadth.",
        "evidence": [
          {
            "reference": "DOI:10.1126/science.ads6055",
            "snippet": "Immunity is triggered by phage nucleotide kinases, which, combined with the system-encoded adenosine deaminase, produce deoxyinosine triphosphates (dITPs) as immune messengers.",
            "notes": "Zeng et al. connect phage-triggered Kongming immunity to system-dependent production of dITP immune messengers."
          },
          {
            "reference": "DOI:10.1038/s41467-026-74710-9",
            "snippet": "One of them is the Kongming system, which includes an effector complex (KomBC), composed of a non-canonical purine NTP pyrophosphatase (KomB) and a SIR2 domain-containing protein (KomC).",
            "notes": "Li et al. name the Kongming effector complex and its KomB and KomC components."
          },
          {
            "reference": "DOI:10.1038/s41467-026-74710-9",
            "snippet": "Binding of dITP to KomB initiates progressive conformational rearrangements within the filament, ultimately remodeling the filament into a distinct architecture in which KomC adopts an active conformation with NADase activity.",
            "notes": "Li et al. connect dITP-bound KomB to activation of KomC NADase activity within the Kongming KomBC effector complex."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
            "snippet": "| Kongming | 10\\.1126/science\\.ads6055 | Base-modified nucleotides mediate immune signaling in bacteria | ",
            "notes": "The pinned DefenseFinder article registry maps the named Kongming system to the Zeng et al. Science paper."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "notes": "A structured first-pass search of the pinned DefenseFinder HMM inventory found no exact Kongming row."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "A structured first-pass search of the pinned DefenseFinder rules table found no exact Kongming system row."
          }
        ],
        "attaches_to": [
          "causal_graphs#kongming_ditp_nadase_defense"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-30"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-30T22:04:45Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Kongming system as a Science-, Nature-, and DefenseFinder-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v378.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-30T22:04:46Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed Kongming system canonical_examples and left them empty because public Science, Nature, and DefenseFinder evidence supports the named phage-defense system but not a direct named native microbial isolate exemplar with experimentally verified endogenous Kongming activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000556",
    "label": "Lamassu-Amidase system",
    "definition": "A Lamassu system in which an organism possesses a genome-encoded DefenseFinder Lamassu-Amidase subtype locus represented by the Lamassu-Amidase rule row requiring the Lamassu-Fam__LmuA_effector_Amidase and Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II profiles.",
    "definition_source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000232"
    ],
    "synonyms": [
      {
        "synonym_text": "Lamassu-Amidase",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv"
      },
      {
        "synonym_text": "Lamassu-Fam__LmuA_effector_Amidase",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "Lamassu-Fam__LmuC_acc_Lipase",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1073/pnas.2519643122",
        "snippet": "a bacterial immune system family featuring diverse effectors but a core conserved SMC-like sensor",
        "notes": "Haudiquet et al. support placing Lamassu subtypes under a Lamassu family with diverse LmuA effectors and a conserved SMC-like sensor."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| Lamassu-Fam | 10\\.1101/2022\\.05\\.11\\.491447 | An expanding arsenal of immune systems that protect bacteria from phages | ",
        "notes": "The pinned DefenseFinder article registry maps the Lamassu-Fam model namespace to a bacterial immune-systems preprint."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| Lamassu-Fam__LmuA_effector_Amidase               | Lamassu-Fam__LmuA_effector_Amidase               | Lamassu-Fam            | Custom                  | 20     |",
        "notes": "The pinned DefenseFinder HMM inventory records the Lamassu-Fam__LmuA_effector_Amidase custom profile listed as mandatory by the Lamassu-Amidase rule row."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II           | Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II           | Lamassu-Fam            | Custom                  | 20     |",
        "notes": "The pinned DefenseFinder HMM inventory records the Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II custom profile listed as mandatory by the Lamassu-Amidase rule row."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| Lamassu-Fam__LmuC_acc_Lipase                     | Lamassu-Fam__LmuC_acc_Lipase                     | Lamassu-Fam            | Custom                  | 20     |",
        "notes": "The pinned DefenseFinder HMM inventory records the Lamassu-Fam__LmuC_acc_Lipase custom profile listed as accessory by the Lamassu-Amidase rule row."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "Lamassu-Fam\tLamassu-Amidase\t2\t2\tLamassu-Fam__LmuA_effector_Amidase, Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II\tLamassu-Fam__LmuC_acc_Lipase\tLamassu-Fam__LmuA_effector_Cap4_nuclease, Lamassu-Fam__LmuA_effector_Cap4_nuclease_II, Lamassu-Fam__LmuA_effector_FMO, Lamassu-Fam__LmuA_effector_Hydrolase, Lamassu-Fam__LmuA_effector_Lipase, Lamassu-Fam__LmuA_effector_Mrr, Lamassu-Fam__LmuA_effector_PDDEXK, Lamassu-Fam__LmuA_effector_Protease, Lamassu-Fam__LmuA_effector_Sir2, Lamassu-Fam__LmuA_effector_hypothetical\t",
        "notes": "The pinned DefenseFinder rules table models Lamassu-Amidase as a Lamassu-Fam subsystem requiring Lamassu-Fam__LmuA_effector_Amidase and Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II, with Lamassu-Fam__LmuC_acc_Lipase as an accessory profile."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "lamassu_amidase_locus_subtype_defense",
        "title": "Lamassu-Amidase loci mark a Lamassu antiphage subtype",
        "description": "Conservative subtype-level sketch linking a DefenseFinder Lamassu-Amidase locus to Lamassu antiphage activity and Lamassu-Amidase system possession.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures the Lamassu-Amidase subtype at DefenseFinder rule-row level without asserting the exact amidase substrate, viral-DNA trigger, LmuC requirement, native host breadth, cell-death output, or whether every DefenseFinder Lamassu-Amidase prediction is a complete experimentally active locus.",
        "nodes": [
          {
            "node_id": "lamassu_amidase_locus",
            "label": "Lamassu-Amidase locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A DefenseFinder Lamassu-Amidase subtype locus represented by LmuA amidase and LmuB SMC mandatory profiles."
          },
          {
            "node_id": "lamassu_subtype_antiphage_activity",
            "label": "Lamassu subtype antiphage activity",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Antiphage activity of a Lamassu-Fam subtype locus with a specific LmuA effector profile."
          },
          {
            "node_id": "lamassu_amidase_system_trait",
            "label": "Lamassu-Amidase system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000556",
            "description": "Possession of a genome-encoded Lamassu-Amidase phage-defense system."
          },
          {
            "node_id": "lamassu_system_trait",
            "label": "Lamassu system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000232",
            "description": "Possession of a genome-encoded Lamassu phage-defense system."
          }
        ],
        "edges": [
          {
            "subject": "lamassu_amidase_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "lamassu_subtype_antiphage_activity",
            "description": "Lamassu-Amidase loci are modeled in DefenseFinder by LmuA amidase and LmuB SMC mandatory profiles plus an LmuC accessory profile.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| Lamassu-Fam__LmuA_effector_Amidase               | Lamassu-Fam__LmuA_effector_Amidase               | Lamassu-Fam            | Custom                  | 20     |",
                "notes": "The pinned DefenseFinder HMM inventory records the Lamassu-Fam__LmuA_effector_Amidase custom profile listed as mandatory by the Lamassu-Amidase rule row."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II           | Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II           | Lamassu-Fam            | Custom                  | 20     |",
                "notes": "The pinned DefenseFinder HMM inventory records the Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II custom profile listed as mandatory by the Lamassu-Amidase rule row."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| Lamassu-Fam__LmuC_acc_Lipase                     | Lamassu-Fam__LmuC_acc_Lipase                     | Lamassu-Fam            | Custom                  | 20     |",
                "notes": "The pinned DefenseFinder HMM inventory records the Lamassu-Fam__LmuC_acc_Lipase custom profile listed as accessory by the Lamassu-Amidase rule row."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "Lamassu-Fam\tLamassu-Amidase\t2\t2\tLamassu-Fam__LmuA_effector_Amidase, Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II\tLamassu-Fam__LmuC_acc_Lipase\tLamassu-Fam__LmuA_effector_Cap4_nuclease, Lamassu-Fam__LmuA_effector_Cap4_nuclease_II, Lamassu-Fam__LmuA_effector_FMO, Lamassu-Fam__LmuA_effector_Hydrolase, Lamassu-Fam__LmuA_effector_Lipase, Lamassu-Fam__LmuA_effector_Mrr, Lamassu-Fam__LmuA_effector_PDDEXK, Lamassu-Fam__LmuA_effector_Protease, Lamassu-Fam__LmuA_effector_Sir2, Lamassu-Fam__LmuA_effector_hypothetical\t",
                "notes": "The pinned DefenseFinder rules table models Lamassu-Amidase as a Lamassu-Fam subsystem requiring Lamassu-Fam__LmuA_effector_Amidase and Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II, with Lamassu-Fam__LmuC_acc_Lipase as an accessory profile."
              }
            ]
          },
          {
            "subject": "lamassu_subtype_antiphage_activity",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "lamassu_amidase_system_trait",
            "description": "The first-pass Lamassu-Amidase system trait is realized by a DefenseFinder Lamassu-Amidase subtype locus.",
            "evidence": [
              {
                "reference": "DOI:10.1073/pnas.2519643122",
                "snippet": "a bacterial immune system family featuring diverse effectors but a core conserved SMC-like sensor",
                "notes": "Haudiquet et al. support placing Lamassu subtypes under a Lamassu family with diverse LmuA effectors and a conserved SMC-like sensor."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "Lamassu-Amidase\t2\t2\tLamassu-Fam__LmuA_effector_Amidase, Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II\tLamassu-Fam__LmuC_acc_Lipase",
                "notes": "The pinned DefenseFinder rules table models Lamassu-Amidase as requiring LmuA amidase and LmuB SMC profiles with LmuC as an accessory profile."
              }
            ]
          },
          {
            "subject": "lamassu_amidase_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "lamassu_system_trait",
            "description": "Lamassu-Amidase system possession is a Lamassu-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| Lamassu-Fam | 10\\.1101/2022\\.05\\.11\\.491447 | An expanding arsenal of immune systems that protect bacteria from phages | ",
                "notes": "The pinned DefenseFinder article registry maps the Lamassu-Fam model namespace to a bacterial immune-systems preprint."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "Lamassu-Fam\tLamassu-Amidase\t2\t2",
                "notes": "The pinned DefenseFinder rules table places the Lamassu-Amidase subsystem under the Lamassu-Fam system key with 2 mandatory matches and 2 genes required."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "lamassu-amidase-activity-gap",
        "prompt": "Resolve Lamassu-Amidase phage triggers, native hosts, amidase effector substrates, LmuC usage, and profile-to-activity criteria before minting enzyme, trigger, or component children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Haudiquet et al. support a Lamassu family with diverse LmuA effectors and a conserved SMC-like sensor, and the pinned DefenseFinder HMM inventory and rules table support Lamassu-Amidase as a Lamassu-Fam subtype whose rule row requires Lamassu-Fam__LmuA_effector_Amidase and Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II. This first-pass record leaves exact amidase substrate, LmuC requirement, native hosts, phage triggers, cell-death output, and profile-to-activity criteria unresolved.",
        "evidence": [
          {
            "reference": "DOI:10.1073/pnas.2519643122",
            "snippet": "a bacterial immune system family featuring diverse effectors but a core conserved SMC-like sensor",
            "notes": "Haudiquet et al. support placing Lamassu subtypes under a Lamassu family with diverse LmuA effectors and a conserved SMC-like sensor."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| Lamassu-Fam__LmuA_effector_Amidase               | Lamassu-Fam__LmuA_effector_Amidase               | Lamassu-Fam            | Custom                  | 20     |",
            "notes": "The pinned DefenseFinder HMM inventory records the Lamassu-Fam__LmuA_effector_Amidase custom profile listed as mandatory by the Lamassu-Amidase rule row."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "snippet": "Lamassu-Fam\tLamassu-Amidase\t2\t2\tLamassu-Fam__LmuA_effector_Amidase, Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II\tLamassu-Fam__LmuC_acc_Lipase\tLamassu-Fam__LmuA_effector_Cap4_nuclease, Lamassu-Fam__LmuA_effector_Cap4_nuclease_II, Lamassu-Fam__LmuA_effector_FMO, Lamassu-Fam__LmuA_effector_Hydrolase, Lamassu-Fam__LmuA_effector_Lipase, Lamassu-Fam__LmuA_effector_Mrr, Lamassu-Fam__LmuA_effector_PDDEXK, Lamassu-Fam__LmuA_effector_Protease, Lamassu-Fam__LmuA_effector_Sir2, Lamassu-Fam__LmuA_effector_hypothetical\t",
            "notes": "The pinned DefenseFinder rules table models Lamassu-Amidase as a Lamassu-Fam subsystem requiring Lamassu-Fam__LmuA_effector_Amidase and Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II, with Lamassu-Fam__LmuC_acc_Lipase as an accessory profile."
          }
        ],
        "attaches_to": [
          "causal_graphs#lamassu_amidase_locus_subtype_defense"
        ],
        "posed_by": "codex",
        "posed_date": "2026-10-02"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-02T21:43:24Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Lamassu-Amidase system as a DefenseFinder-backed GENOMICS TraitRecord under the Lamassu system parent after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record for the target local ID, placeholder METPO ID, proposal cohort, record slug, human label, DefenseFinder subsystem, or LmuA amidase profile string; the replacement placeholder is reserved in proposals/metpo_traitmech_v433.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-02T21:43:26Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed Lamassu-Amidase system during initial curation and left canonical_examples empty because the pinned DefenseFinder tables support a rule-row subtype but not an accession-backed native microbial taxon exemplar tied to the Lamassu-Amidase profiles and experimentally verified endogenous activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000557",
    "label": "Lamassu-Cap4 nuclease system",
    "definition": "A Lamassu system in which an organism possesses a genome-encoded DefenseFinder Lamassu-Cap4_nuclease subtype locus represented by the Lamassu-Cap4_nuclease rule row requiring the Lamassu-Fam__LmuA_effector_Cap4_nuclease_II and Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II profiles.",
    "definition_source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000232"
    ],
    "synonyms": [
      {
        "synonym_text": "Lamassu-Cap4_nuclease",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv"
      },
      {
        "synonym_text": "Lamassu-Fam__LmuA_effector_Cap4_nuclease_II",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "Lamassu-Fam__LmuC_acc_Lipase",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1073/pnas.2519643122",
        "snippet": "a bacterial immune system family featuring diverse effectors but a core conserved SMC-like sensor",
        "notes": "Haudiquet et al. support placing Lamassu subtypes under a Lamassu family with diverse LmuA effectors and a conserved SMC-like sensor."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| Lamassu-Fam | 10\\.1101/2022\\.05\\.11\\.491447 | An expanding arsenal of immune systems that protect bacteria from phages | ",
        "notes": "The pinned DefenseFinder article registry maps the Lamassu-Fam model namespace to a bacterial immune-systems preprint."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| Lamassu-Fam__LmuA_effector_Cap4_nuclease_II      | Lamassu-Fam__LmuA_effector_Cap4_nuclease_II      | Lamassu-Fam            | Custom                  | 20     |",
        "notes": "The pinned DefenseFinder HMM inventory records the Lamassu-Fam__LmuA_effector_Cap4_nuclease_II custom profile listed as mandatory by the Lamassu-Cap4_nuclease rule row."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II           | Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II           | Lamassu-Fam            | Custom                  | 20     |",
        "notes": "The pinned DefenseFinder HMM inventory records the Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II custom profile listed as mandatory by the Lamassu-Cap4_nuclease rule row."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| Lamassu-Fam__LmuC_acc_Lipase                     | Lamassu-Fam__LmuC_acc_Lipase                     | Lamassu-Fam            | Custom                  | 20     |",
        "notes": "The pinned DefenseFinder HMM inventory records the Lamassu-Fam__LmuC_acc_Lipase custom profile listed as accessory by the Lamassu-Cap4_nuclease rule row."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "Lamassu-Fam\tLamassu-Cap4_nuclease\t2\t2\tLamassu-Fam__LmuA_effector_Cap4_nuclease_II, Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II\tLamassu-Fam__LmuC_acc_Lipase\tLamassu-Fam__LmuA_effector_Amidase, Lamassu-Fam__LmuA_effector_FMO, Lamassu-Fam__LmuA_effector_Hydrolase, Lamassu-Fam__LmuA_effector_Lipase, Lamassu-Fam__LmuA_effector_Mrr, Lamassu-Fam__LmuA_effector_PDDEXK, Lamassu-Fam__LmuA_effector_Protease, Lamassu-Fam__LmuA_effector_Sir2, Lamassu-Fam__LmuA_effector_hypothetical\t",
        "notes": "The pinned DefenseFinder rules table models Lamassu-Cap4_nuclease as a Lamassu-Fam subsystem requiring Lamassu-Fam__LmuA_effector_Cap4_nuclease_II and Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II, with Lamassu-Fam__LmuC_acc_Lipase as an accessory profile."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "lamassu_cap4_nuclease_locus_subtype_defense",
        "title": "Lamassu-Cap4 nuclease loci mark a Lamassu antiphage subtype",
        "description": "Conservative subtype-level sketch linking a DefenseFinder Lamassu-Cap4_nuclease locus to Lamassu antiphage activity and Lamassu-Cap4 nuclease system possession.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures the Lamassu-Cap4_nuclease subtype at DefenseFinder rule-row level without asserting exact phage-triggered substrate chemistry, viral-DNA trigger, LmuC requirement, native host breadth, cell-death output, or whether every DefenseFinder Lamassu-Cap4_nuclease prediction is a complete experimentally active locus.",
        "nodes": [
          {
            "node_id": "lamassu_cap4_nuclease_locus",
            "label": "Lamassu-Cap4 nuclease locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A DefenseFinder Lamassu-Cap4_nuclease subtype locus represented by LmuA Cap4 nuclease and LmuB SMC mandatory profiles."
          },
          {
            "node_id": "lamassu_subtype_antiphage_activity",
            "label": "Lamassu subtype antiphage activity",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Antiphage activity of a Lamassu-Fam subtype locus with a specific LmuA effector profile."
          },
          {
            "node_id": "lamassu_cap4_nuclease_system_trait",
            "label": "Lamassu-Cap4 nuclease system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000557",
            "description": "Possession of a genome-encoded Lamassu-Cap4 nuclease phage-defense system."
          },
          {
            "node_id": "lamassu_system_trait",
            "label": "Lamassu system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000232",
            "description": "Possession of a genome-encoded Lamassu phage-defense system."
          }
        ],
        "edges": [
          {
            "subject": "lamassu_cap4_nuclease_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "lamassu_subtype_antiphage_activity",
            "description": "Lamassu-Cap4 nuclease loci are modeled in DefenseFinder by LmuA Cap4 nuclease and LmuB SMC mandatory profiles plus an LmuC accessory profile.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| Lamassu-Fam__LmuA_effector_Cap4_nuclease_II      | Lamassu-Fam__LmuA_effector_Cap4_nuclease_II      | Lamassu-Fam            | Custom                  | 20     |",
                "notes": "The pinned DefenseFinder HMM inventory records the Lamassu-Fam__LmuA_effector_Cap4_nuclease_II custom profile listed as mandatory by the Lamassu-Cap4_nuclease rule row."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II           | Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II           | Lamassu-Fam            | Custom                  | 20     |",
                "notes": "The pinned DefenseFinder HMM inventory records the Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II custom profile listed as mandatory by the Lamassu-Cap4_nuclease rule row."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| Lamassu-Fam__LmuC_acc_Lipase                     | Lamassu-Fam__LmuC_acc_Lipase                     | Lamassu-Fam            | Custom                  | 20     |",
                "notes": "The pinned DefenseFinder HMM inventory records the Lamassu-Fam__LmuC_acc_Lipase custom profile listed as accessory by the Lamassu-Cap4_nuclease rule row."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "Lamassu-Fam\tLamassu-Cap4_nuclease\t2\t2\tLamassu-Fam__LmuA_effector_Cap4_nuclease_II, Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II\tLamassu-Fam__LmuC_acc_Lipase\tLamassu-Fam__LmuA_effector_Amidase, Lamassu-Fam__LmuA_effector_FMO, Lamassu-Fam__LmuA_effector_Hydrolase, Lamassu-Fam__LmuA_effector_Lipase, Lamassu-Fam__LmuA_effector_Mrr, Lamassu-Fam__LmuA_effector_PDDEXK, Lamassu-Fam__LmuA_effector_Protease, Lamassu-Fam__LmuA_effector_Sir2, Lamassu-Fam__LmuA_effector_hypothetical\t",
                "notes": "The pinned DefenseFinder rules table models Lamassu-Cap4_nuclease as a Lamassu-Fam subsystem requiring Lamassu-Fam__LmuA_effector_Cap4_nuclease_II and Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II, with Lamassu-Fam__LmuC_acc_Lipase as an accessory profile."
              }
            ]
          },
          {
            "subject": "lamassu_subtype_antiphage_activity",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "lamassu_cap4_nuclease_system_trait",
            "description": "The first-pass Lamassu-Cap4 nuclease system trait is realized by a DefenseFinder Lamassu-Cap4_nuclease subtype locus.",
            "evidence": [
              {
                "reference": "DOI:10.1073/pnas.2519643122",
                "snippet": "a bacterial immune system family featuring diverse effectors but a core conserved SMC-like sensor",
                "notes": "Haudiquet et al. support placing Lamassu subtypes under a Lamassu family with diverse LmuA effectors and a conserved SMC-like sensor."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "Lamassu-Cap4_nuclease\t2\t2\tLamassu-Fam__LmuA_effector_Cap4_nuclease_II, Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II\tLamassu-Fam__LmuC_acc_Lipase",
                "notes": "The pinned DefenseFinder rules table models Lamassu-Cap4_nuclease as requiring LmuA Cap4 nuclease and LmuB SMC profiles with LmuC as an accessory profile."
              }
            ]
          },
          {
            "subject": "lamassu_cap4_nuclease_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "lamassu_system_trait",
            "description": "Lamassu-Cap4 nuclease system possession is a Lamassu-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| Lamassu-Fam | 10\\.1101/2022\\.05\\.11\\.491447 | An expanding arsenal of immune systems that protect bacteria from phages | ",
                "notes": "The pinned DefenseFinder article registry maps the Lamassu-Fam model namespace to a bacterial immune-systems preprint."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "Lamassu-Fam\tLamassu-Cap4_nuclease\t2\t2",
                "notes": "The pinned DefenseFinder rules table places the Lamassu-Cap4_nuclease subsystem under the Lamassu-Fam system key with 2 mandatory matches and 2 genes required."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "lamassu-cap4-nuclease-activity-gap",
        "prompt": "Resolve Lamassu-Cap4 nuclease phage triggers, native hosts, Cap4 nuclease substrates, LmuC usage, and profile-to-activity criteria before minting enzyme, trigger, or component children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Haudiquet et al. support a Lamassu family with diverse LmuA effectors and a conserved SMC-like sensor, and the pinned DefenseFinder HMM inventory and rules table support Lamassu-Cap4_nuclease as a Lamassu-Fam subtype whose rule row requires Lamassu-Fam__LmuA_effector_Cap4_nuclease_II and Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II. This first-pass record leaves exact Cap4 nuclease substrates, LmuC requirement, native hosts, phage triggers, cell-death output, profile-to-activity criteria, and the relationship between the DefenseFinder _II row and the structurally characterized Lamassu Vc-Cap4 branch unresolved.",
        "evidence": [
          {
            "reference": "DOI:10.1073/pnas.2519643122",
            "snippet": "a bacterial immune system family featuring diverse effectors but a core conserved SMC-like sensor",
            "notes": "Haudiquet et al. support placing Lamassu subtypes under a Lamassu family with diverse LmuA effectors and a conserved SMC-like sensor."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| Lamassu-Fam__LmuA_effector_Cap4_nuclease_II      | Lamassu-Fam__LmuA_effector_Cap4_nuclease_II      | Lamassu-Fam            | Custom                  | 20     |",
            "notes": "The pinned DefenseFinder HMM inventory records the Lamassu-Fam__LmuA_effector_Cap4_nuclease_II custom profile listed as mandatory by the Lamassu-Cap4_nuclease rule row."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "snippet": "Lamassu-Fam\tLamassu-Cap4_nuclease\t2\t2\tLamassu-Fam__LmuA_effector_Cap4_nuclease_II, Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II\tLamassu-Fam__LmuC_acc_Lipase\tLamassu-Fam__LmuA_effector_Amidase, Lamassu-Fam__LmuA_effector_FMO, Lamassu-Fam__LmuA_effector_Hydrolase, Lamassu-Fam__LmuA_effector_Lipase, Lamassu-Fam__LmuA_effector_Mrr, Lamassu-Fam__LmuA_effector_PDDEXK, Lamassu-Fam__LmuA_effector_Protease, Lamassu-Fam__LmuA_effector_Sir2, Lamassu-Fam__LmuA_effector_hypothetical\t",
            "notes": "The pinned DefenseFinder rules table models Lamassu-Cap4_nuclease as a Lamassu-Fam subsystem requiring Lamassu-Fam__LmuA_effector_Cap4_nuclease_II and Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II, with Lamassu-Fam__LmuC_acc_Lipase as an accessory profile."
          }
        ],
        "attaches_to": [
          "causal_graphs#lamassu_cap4_nuclease_locus_subtype_defense"
        ],
        "posed_by": "codex",
        "posed_date": "2026-10-02"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-02T22:16:24Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Lamassu-Cap4 nuclease system as a DefenseFinder-backed GENOMICS TraitRecord under the Lamassu system parent after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record for the target local ID, placeholder METPO ID, proposal cohort, record slug, human label, or DefenseFinder subsystem; the replacement placeholder is reserved in proposals/metpo_traitmech_v434. Exact Cap4 effector profile hits were limited to evidence and forbidden-profile strings on the neighboring Lamassu-Amidase record.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-02T22:16:26Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed Lamassu-Cap4 nuclease system during initial curation and left canonical_examples empty because the pinned DefenseFinder tables support a rule-row subtype but not an accession-backed native microbial taxon exemplar tied to the Lamassu-Cap4_nuclease profiles and experimentally verified endogenous activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000558",
    "label": "Lamassu-FMO system",
    "definition": "A Lamassu system in which an organism possesses a genome-encoded DefenseFinder Lamassu-FMO subtype locus represented by the Lamassu-FMO rule row requiring the Lamassu-Fam__LmuA_effector_FMO and Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II profiles.",
    "definition_source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000232"
    ],
    "synonyms": [
      {
        "synonym_text": "Lamassu-FMO",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv"
      },
      {
        "synonym_text": "Lamassu-Fam__LmuA_effector_FMO",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1073/pnas.2519643122",
        "snippet": "a bacterial immune system family featuring diverse effectors but a core conserved SMC-like sensor",
        "notes": "Haudiquet et al. support placing Lamassu subtypes under a Lamassu family with diverse LmuA effectors and a conserved SMC-like sensor."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| Lamassu-Fam | 10\\.1101/2022\\.05\\.11\\.491447 | An expanding arsenal of immune systems that protect bacteria from phages | ",
        "notes": "The pinned DefenseFinder article registry maps the Lamassu-Fam model namespace to a bacterial immune-systems preprint."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| Lamassu-Fam__LmuA_effector_FMO                   | Lamassu-Fam__LmuA_effector_FMO                   | Lamassu-Fam            | Custom                  | 20     |",
        "notes": "The pinned DefenseFinder HMM inventory records the Lamassu-Fam__LmuA_effector_FMO custom profile listed as mandatory by the Lamassu-FMO rule row."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II           | Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II           | Lamassu-Fam            | Custom                  | 20     |",
        "notes": "The pinned DefenseFinder HMM inventory records the Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II custom profile, which the Lamassu-FMO rule row lists as mandatory despite the HMM inventory also carrying an FMO-scoped LmuB SMC profile."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| Lamassu-Fam__LmuC_acc_Lipase                     | Lamassu-Fam__LmuC_acc_Lipase                     | Lamassu-Fam            | Custom                  | 20     |",
        "notes": "The pinned DefenseFinder HMM inventory records the Lamassu-Fam__LmuC_acc_Lipase custom profile, which the Lamassu-FMO rule row lists as accessory despite the HMM inventory also carrying an FMO-scoped LmuC accessory profile."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| Lamassu-Fam__LmuB_SMC_FMO                        | Lamassu-Fam__LmuB_SMC_FMO                        | Lamassu-Fam            | Custom                  | 20     |",
        "notes": "The pinned DefenseFinder HMM inventory records a Lamassu-Fam__LmuB_SMC_FMO custom profile that is not the LmuB SMC profile named by the pinned Lamassu-FMO rule row."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| Lamassu-Fam__LmuC_acc_FMO                        | Lamassu-Fam__LmuC_acc_FMO                        | Lamassu-Fam            | Custom                  | 20     |",
        "notes": "The pinned DefenseFinder HMM inventory records a Lamassu-Fam__LmuC_acc_FMO custom profile that is not the LmuC accessory profile named by the pinned Lamassu-FMO rule row."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "Lamassu-Fam\tLamassu-FMO\t2\t2\tLamassu-Fam__LmuA_effector_FMO, Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II\tLamassu-Fam__LmuC_acc_Lipase\tLamassu-Fam__LmuA_effector_Amidase, Lamassu-Fam__LmuA_effector_Cap4_nuclease, Lamassu-Fam__LmuA_effector_Cap4_nuclease_II, Lamassu-Fam__LmuA_effector_Hydrolase, Lamassu-Fam__LmuA_effector_Lipase, Lamassu-Fam__LmuA_effector_Mrr, Lamassu-Fam__LmuA_effector_PDDEXK, Lamassu-Fam__LmuA_effector_Protease, Lamassu-Fam__LmuA_effector_Sir2, Lamassu-Fam__LmuA_effector_hypothetical\t",
        "notes": "The pinned DefenseFinder rules table models Lamassu-FMO as a Lamassu-Fam subsystem requiring Lamassu-Fam__LmuA_effector_FMO and Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II, with Lamassu-Fam__LmuC_acc_Lipase as an accessory profile."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "lamassu_fmo_locus_subtype_defense",
        "title": "Lamassu-FMO is a DefenseFinder Lamassu subtype",
        "description": "Conservative subtype-level classification linking the DefenseFinder Lamassu-FMO rule-row definition to Lamassu-FMO system possession and its Lamassu parent.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Lamassu-FMO as a DefenseFinder rule-row subtype of Lamassu system possession without asserting a Lamassu-FMO-specific antiphage process, expanding the FMO profile name, selecting between the rule-row LmuB/LmuC profiles and the FMO-scoped HMM rows, or resolving exact phage-triggered substrate chemistry, viral-DNA trigger, LmuC requirement, native host breadth, cell-death output, or whether every DefenseFinder Lamassu-FMO prediction is a complete experimentally active locus.",
        "nodes": [
          {
            "node_id": "lamassu_fmo_system_trait",
            "label": "Lamassu-FMO system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000558",
            "description": "Possession of a genome-encoded Lamassu-FMO phage-defense system."
          },
          {
            "node_id": "lamassu_system_trait",
            "label": "Lamassu system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000232",
            "description": "Possession of a genome-encoded Lamassu phage-defense system."
          }
        ],
        "edges": [
          {
            "subject": "lamassu_fmo_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "lamassu_system_trait",
            "description": "Lamassu-FMO system possession is a Lamassu-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| Lamassu-Fam | 10\\.1101/2022\\.05\\.11\\.491447 | An expanding arsenal of immune systems that protect bacteria from phages | ",
                "notes": "The pinned DefenseFinder article registry maps the Lamassu-Fam model namespace to a bacterial immune-systems preprint."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "Lamassu-Fam\tLamassu-FMO\t2\t2",
                "notes": "The pinned DefenseFinder rules table places the Lamassu-FMO subsystem under the Lamassu-Fam system key with 2 mandatory matches and 2 genes required."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "lamassu-fmo-activity-gap",
        "prompt": "Resolve Lamassu-FMO phage triggers, native hosts, FMO effector meaning, LmuB/LmuC model rows, LmuC usage, and profile-to-activity criteria before minting enzyme, trigger, or component children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Haudiquet et al. support a Lamassu family with diverse LmuA effectors and a conserved SMC-like sensor, and the pinned DefenseFinder HMM inventory and rules table support Lamassu-FMO as a Lamassu-Fam subtype whose rule row requires Lamassu-Fam__LmuA_effector_FMO and Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II. This first-pass record follows the rule row but leaves the relationship between its LmuB/LmuC Cap4-nuclease/Lipase profile names and the FMO-scoped Lamassu-Fam__LmuB_SMC_FMO and Lamassu-Fam__LmuC_acc_FMO HMM rows unresolved, along with exact FMO expansion and substrate chemistry, LmuC requirement, native hosts, phage triggers, cell-death output, and profile-to-activity criteria.",
        "evidence": [
          {
            "reference": "DOI:10.1073/pnas.2519643122",
            "snippet": "a bacterial immune system family featuring diverse effectors but a core conserved SMC-like sensor",
            "notes": "Haudiquet et al. support placing Lamassu subtypes under a Lamassu family with diverse LmuA effectors and a conserved SMC-like sensor."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| Lamassu-Fam__LmuA_effector_FMO                   | Lamassu-Fam__LmuA_effector_FMO                   | Lamassu-Fam            | Custom                  | 20     |",
            "notes": "The pinned DefenseFinder HMM inventory records the Lamassu-Fam__LmuA_effector_FMO custom profile listed as mandatory by the Lamassu-FMO rule row."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| Lamassu-Fam__LmuB_SMC_FMO                        | Lamassu-Fam__LmuB_SMC_FMO                        | Lamassu-Fam            | Custom                  | 20     |",
            "notes": "The pinned DefenseFinder HMM inventory records a Lamassu-Fam__LmuB_SMC_FMO custom profile that is not the LmuB SMC profile named by the pinned Lamassu-FMO rule row."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| Lamassu-Fam__LmuC_acc_FMO                        | Lamassu-Fam__LmuC_acc_FMO                        | Lamassu-Fam            | Custom                  | 20     |",
            "notes": "The pinned DefenseFinder HMM inventory records a Lamassu-Fam__LmuC_acc_FMO custom profile that is not the LmuC accessory profile named by the pinned Lamassu-FMO rule row."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "snippet": "Lamassu-Fam\tLamassu-FMO\t2\t2\tLamassu-Fam__LmuA_effector_FMO, Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II\tLamassu-Fam__LmuC_acc_Lipase\tLamassu-Fam__LmuA_effector_Amidase, Lamassu-Fam__LmuA_effector_Cap4_nuclease, Lamassu-Fam__LmuA_effector_Cap4_nuclease_II, Lamassu-Fam__LmuA_effector_Hydrolase, Lamassu-Fam__LmuA_effector_Lipase, Lamassu-Fam__LmuA_effector_Mrr, Lamassu-Fam__LmuA_effector_PDDEXK, Lamassu-Fam__LmuA_effector_Protease, Lamassu-Fam__LmuA_effector_Sir2, Lamassu-Fam__LmuA_effector_hypothetical\t",
            "notes": "The pinned DefenseFinder rules table models Lamassu-FMO as a Lamassu-Fam subsystem requiring Lamassu-Fam__LmuA_effector_FMO and Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II, with Lamassu-Fam__LmuC_acc_Lipase as an accessory profile."
          }
        ],
        "attaches_to": [
          "causal_graphs#lamassu_fmo_locus_subtype_defense"
        ],
        "posed_by": "codex",
        "posed_date": "2026-10-02"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-02T23:11:37Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Lamassu-FMO system as a DefenseFinder-backed GENOMICS TraitRecord under the Lamassu system parent after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record for the target local ID, placeholder METPO ID, proposal cohort, record slug, human label, DefenseFinder subsystem, or LmuA FMO profile string; the replacement placeholder is reserved in proposals/metpo_traitmech_v435.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-02T23:11:39Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed Lamassu-FMO system during initial curation and left canonical_examples empty because the pinned DefenseFinder tables support a rule-row subtype but not an accession-backed native microbial taxon exemplar tied to the Lamassu-FMO profiles and experimentally verified endogenous activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000568",
    "label": "Lamassu-HNH system",
    "definition": "A Lamassu system in which an organism possesses a locus encoding an HNH-domain LmuA effector, a short-form SMC-like LmuB sensor, and LmuC.",
    "definition_source": "DOI:10.1073/pnas.2519643122",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000570",
      "traitmech:000572"
    ],
    "synonyms": [
      {
        "synonym_text": "Lamassu_HNH",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/definitions/DefenseFinder/Lamassu-Fam/Lamassu_HNH.xml"
      },
      {
        "synonym_text": "Lamassu/Lamassu/Lamassu_HNH",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://pmc-oa-opendata.s3.amazonaws.com/PMC12663957.1/pnas.2519643122.sd01.xlsx"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1073/pnas.2519643122",
        "snippet": "others are type-specific like the flavin-containing monooxygenase (FMO) for long Lamassu, and HNH, SMEK, and Lipase for short Lamassu.",
        "notes": "Results, effector-diversity paragraph: 'others' refers to LmuA effector types. Figure 1A depicts HNH-domain LmuA with short LmuB and LmuC. This establishes a recognized architecture, not HNH-specific biochemical or infection-assay validation."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/definitions/DefenseFinder/Lamassu-Fam/Lamassu_HNH.xml",
        "snippet": "<model inter_gene_max_space=\"1\" min_mandatory_genes_required=\"3\" min_genes_required=\"3\" vers=\"2.0\">",
        "notes": "The executable model requires three mandatory components and permits at most one intervening gene between components."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/definitions/DefenseFinder/Lamassu-Fam/Lamassu_HNH.xml",
        "snippet": "<gene name=\"Lamassu__LmuA_HNH\" presence=\"mandatory\"/>",
        "notes": "HNH-bearing LmuA is mandatory. Other named LmuA effector profiles are forbidden by separate blocks; an isolated HNH-profile hit does not establish possession of the complete system."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/definitions/DefenseFinder/Lamassu-Fam/Lamassu_HNH.xml",
        "snippet": "<gene name=\"Lamassu__LmuB_Long\" presence=\"mandatory\">\n<exchangeables>\n<gene name=\"Lamassu__LmuB_Short\"/>\n</exchangeables>\n</gene>",
        "notes": "The detector accepts either long or short LmuB. Its software scope is broader than this record's literature-supported short-LmuB architecture, so the model key is only a related synonym."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/definitions/DefenseFinder/Lamassu-Fam/Lamassu_HNH.xml",
        "snippet": "<gene name=\"Lamassu__LmuC_Clade_I\" presence=\"mandatory\">",
        "notes": "LmuC is mandatory, with Clade II-VII and MC1-MC8 profiles in the exchangeables block. There are no accessory components in this XML."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC12663957.1/pnas.2519643122.sd01.xlsx",
        "snippet": "ACHA001.0722.00006.C001\tACHA001.0722.00006.C001_03320\tLamassu__LmuB_Short\nACHA001.0722.00006.C001\tACHA001.0722.00006.C001_03321\tLamassu__LmuC_MC7\nACHA001.0722.00006.C001\tACHA001.0722.00006.C001_03322\tLamassu__LmuA_HNH",
        "notes": "Dataset S1, S3_Lamassu_Detection!A121:C123, raw cells in column order. Columns E, F, I and M identify one Lamassu/Lamassu/Lamassu_HNH call, ACHA001.0722.00006.C001_Lamassu_HNH_807, with sys_wholeness 1.0 and three mandatory hits. The full sheet has 281 unique HNH system IDs, each with short LmuB. These are computational genome annotations, not experimental antiviral phenotypes."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC12663957.1/pnas.2519643122.sd01.xlsx",
        "snippet": "ACHA001.0722.00006.C001\tGCF_009892245.1\tBacteria\tProteobacteria\tAcinetobacter haemolyticus\tNZ_CP031972",
        "notes": "Dataset S1, S2_Genomes!A1159:F1159, raw cells linking the HNH-bearing replicon to assembly GCF_009892245.1 and its species. The historical phylum label is quoted as source data, not adopted as a taxonomic assertion. This supports a genome-qualified possession example."
      },
      {
        "reference": "https://api.ncbi.nlm.nih.gov/datasets/v2/genome/accession/GCF_009892245.1/dataset_report",
        "snippet": "\"tax_id\":29430,\"organism_name\":\"Acinetobacter haemolyticus\",\"infraspecific_names\":{\"strain\":\"AN59\"}",
        "notes": "NCBI Datasets assembly report, verified 2026-10-03: resolves the study's assembly to species taxon 29430 and strain AN59. This source verifies identity only; the published dataset supports the computational system-possession annotation."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:29430",
        "taxon_label": "Acinetobacter haemolyticus",
        "note": "Computational genomic example: strain AN59, assembly GCF_009892245.1, study replicon ACHA001.0722.00006.C001, has a complete three-component HNH-system call in Dataset S1 (S3_Lamassu_Detection rows 121-123; S2_Genomes row 1159). NCBI Datasets resolves the assembly to this species and strain. This does not establish experimentally measured antiviral activity in AN59 or species-wide possession.",
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC12663957.1/pnas.2519643122.sd01.xlsx"
      }
    ],
    "discussions": [
      {
        "discussion_id": "lamassu-hnh-function-and-model-scope",
        "prompt": "Validate HNH-system function and reconcile detector scope.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "The paper identifies HNH as a short-Lamassu effector type, and all 281 HNH calls in Dataset S1 contain short LmuB. The pinned executable XML nevertheless permits long LmuB, so the detector name is not an exact biological equivalence. At the same commit, the legacy DefenseFinder_rules.tsv and Liste_hmm_system.md lack an HNH-system entry even though the executable XML and HNH profile exist. Summary-table absence is not model absence. HNH-specific experimental antiviral validation, exact substrates, activation order, and accession-level protein anchors remain unresolved. Cap4 and Lipase experiments do not establish HNH chemistry or its phage spectrum. No protein-resolved causal graph or functional equivalence to standalone HNH proteins is asserted. The direct parent is now traitmech:000570 short Lamassu system, matching the short-form LmuB restriction already present in this record's definition. This hierarchy refinement does not narrow the executable detector, resolve the functional gaps, or reinterpret computational calls as measured antiviral phenotypes. A second direct parent, traitmech:000572 Lamassu type II system, now captures the LmuC component already required by this definition. The short-family parent is retained because component presence and LmuB-length family are separate axes. Neither hierarchy relation experimentally validates HNH antiviral activity or narrows the detector's broader scope.",
        "posed_by": "codex",
        "posed_date": "2026-10-03"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-03T10:35:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added the literature-supported short-Lamassu HNH architecture with DOI, executable-model, published dataset and NCBI identity evidence and exact snippets. Restricted the AN59 example to computational genomic possession. Ignored-and-hidden searches found no exact record or METPO term. Reserved METPO:1052200 in proposals/metpo_traitmech_v445; retained the detector-scope and HNH-specific functional-validation gaps.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-03T12:33:00Z",
        "curator": "codex",
        "action": "REPARENT_TO_SHORT_LAMASSU",
        "changes": "Placed the existing short-LmuB HNH architecture below traitmech:000570 short Lamassu system without changing its definition, evidence, model-scope qualifications or example. The v445 broader Lamassu proposal axiom remains true; v447 documents the added immediate-parent relation for upstream minting.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-03T15:14:27Z",
        "curator": "codex",
        "action": "ADD_TYPE_II_PARENT",
        "changes": "Linked traitmech:000572 Lamassu type II system using the LmuC-containing classification in DOI:10.1093/nar/gkab883. Preserved biological definitions, evidence, examples and length-family distinctions. Historical proposal parent axioms remain true; v449 documents the additional subclass relations for upstream minting. This is not new experimental validation.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000567",
    "label": "Lamassu Hydrolase-Protease system",
    "definition": "A Lamassu system in which an organism possesses a defense locus encoding a protease-domain LmuA effector together with a hydrolase-like protein, an SMC-like LmuB sensor, and LmuC.",
    "definition_source": "DOI:10.1073/pnas.2519643122",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000572"
    ],
    "synonyms": [
      {
        "synonym_text": "Lamassu-Hydrolase_Protease",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv"
      },
      {
        "synonym_text": "Lamassu_Hydrolase-Protease",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/definitions/DefenseFinder/Lamassu-Fam/Lamassu_Hydrolase-Protease.xml"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1073/pnas.2519643122",
        "snippet": "Protease (accompanied by a hydrolase-like protein)",
        "notes": "Results, effector-diversity paragraph: the protease branch is paired with a hydrolase-like protein in both long and short Lamassu. Figure 1A shows the paired architecture with LmuB and LmuC. These annotations do not establish exact effector substrates."
      },
      {
        "reference": "DOI:10.1073/pnas.2519643122",
        "snippet": "one system from Bacillus cereus B4077, encoding Hydrolase-Protease effectors",
        "notes": "Results, LmuB phylogeny paragraph: identifies B4077 as the source of a previously validated long-Lamassu system, citing Millman et al. (2022). This supports a strain-qualified possession example, not species-wide prevalence or a native-host infection assay."
      },
      {
        "reference": "DOI:10.1016/j.chom.2022.09.017",
        "snippet": "Mutation in the effector domains of these systems also abolished defense, as well as the deletion of lmuC",
        "notes": "Figure 2C and its Results paragraph report loss of defense after effector mutations or lmuC deletion in tested Lamassu systems, including the hydrolase/protease construct. The functional tests used heterologous hosts. This does not establish a substrate or the biochemical order of activation for the paired proteins."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/definitions/DefenseFinder/Lamassu-Fam/Lamassu_Hydrolase-Protease.xml",
        "snippet": "<model inter_gene_max_space=\"1\" min_mandatory_genes_required=\"4\" min_genes_required=\"4\" vers=\"2.0\">",
        "notes": "The executable model requires four mandatory components, with at most one intervening gene between components."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/definitions/DefenseFinder/Lamassu-Fam/Lamassu_Hydrolase-Protease.xml",
        "snippet": "<gene name=\"Lamassu__LmuA_Protease\" presence=\"mandatory\">\n<exchangeables>\n<gene name=\"Lamassu__LmuA_Protease_II\"/>\n</exchangeables>\n</gene>\n\n<gene name=\"Lamassu__LmuA_Hydrolase\" presence=\"mandatory\"/>",
        "notes": "The model requires both protease and hydrolase components; Protease_II can substitute for the primary protease profile. Separate mandatory blocks also require LmuB_Long (exchangeable with LmuB_Short) and LmuC_Clade_I (with listed alternatives)."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/definitions/DefenseFinder/Lamassu-Fam/Lamassu_Hydrolase-Protease.xml",
        "snippet": "<gene name=\"Lamassu__LmuC_Clade_I\" presence=\"mandatory\">",
        "notes": "LmuC is mandatory in this executable model, with alternative LmuC profiles listed in its exchangeables block."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "Lamassu-Fam\tLamassu-Hydrolase_Protease\t3\t3",
        "notes": "The summary TSV places the paired subtype within Lamassu-Fam but gives three mandatory matches and three genes. Its mandatory column lists the legacy Hydrolase, Protease and Cap4_nuclease_II SMC profiles, and its accessory column lists the Lipase LmuC profile. This summary disagrees with the executable XML at the same commit and is retained only as provenance for the older label."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1396",
        "taxon_label": "Bacillus cereus",
        "note": "Strain B4077 is the source of the experimentally validated long-Lamassu Hydrolase-Protease system identified by Haudiquet et al. with reference to Millman et al. (2022). The species identifier anchors this strain-qualified example; it does not imply that all B. cereus strains possess it.",
        "reference": "DOI:10.1073/pnas.2519643122"
      }
    ],
    "discussions": [
      {
        "discussion_id": "lamassu-hydrolase-protease-model-and-mechanism",
        "prompt": "Reconcile model-summary drift and resolve paired effector chemistry.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "The pinned XML uses four mandatory components and newer Lamassu__ profile names, but its companion TSV uses three mandatory legacy profiles and accessory LmuC. The inventory's Hydrolase_protease LmuB and hydrolase_protease LmuC rows also differ from both representations. Model-summary reconciliation is required before using that TSV for genotype calls. The definition follows the biological paired architecture and executable model, not the table's thresholds. Exact substrates, activation order, native-host activity, and accession-level protein examples remain unresolved. No causal mechanism graph is asserted without those molecular anchors. The single-effector table-defined siblings are not asserted to be parents or equivalents of this paired system. The direct parent is now traitmech:000572 Lamassu type II system because the biological definition already includes LmuC. The paired effector architecture illustrates why type II is not restricted to exactly three genes. This refinement does not resolve the legacy detector-summary drift or assign the whole trait to one LmuB-length family.",
        "posed_by": "codex",
        "posed_date": "2026-10-03"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-03T09:29:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added the literature-supported paired Lamassu architecture with DOI and pinned executable-model evidence, exact snippets, and a B4077 canonical example. Ignored-and-hidden searches found only pending parent mentions, not an exact existing record or METPO term. Reserved METPO:1052100 in proposals/metpo_traitmech_v444. Recorded summary-table drift rather than adopting its constraints.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-03T15:14:27Z",
        "curator": "codex",
        "action": "ADD_TYPE_II_PARENT",
        "changes": "Linked traitmech:000572 Lamassu type II system using the LmuC-containing classification in DOI:10.1093/nar/gkab883. Preserved biological definitions, evidence, examples and length-family distinctions. Historical proposal parent axioms remain true; v449 documents the additional subclass relations for upstream minting. This is not new experimental validation.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000561",
    "label": "Lamassu-Hydrolase system",
    "definition": "A Lamassu system in which an organism possesses a genome-encoded DefenseFinder Lamassu-Hydrolase subtype locus represented by the Lamassu-Hydrolase rule row requiring the Lamassu-Fam__LmuA_effector_Hydrolase and Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II profiles.",
    "definition_source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000232"
    ],
    "synonyms": [
      {
        "synonym_text": "Lamassu-Hydrolase",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv"
      },
      {
        "synonym_text": "Lamassu-Fam__LmuA_effector_Hydrolase",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1073/pnas.2519643122",
        "snippet": "a bacterial immune system family featuring diverse effectors but a core conserved SMC-like sensor",
        "notes": "Haudiquet et al. support placing Lamassu subtypes under a Lamassu family with diverse LmuA effectors and a conserved SMC-like sensor."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| Lamassu-Fam | 10\\.1101/2022\\.05\\.11\\.491447 | An expanding arsenal of immune systems that protect bacteria from phages | ",
        "notes": "The pinned DefenseFinder article registry maps the Lamassu-Fam model namespace to a bacterial immune-systems preprint."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| Lamassu-Fam__LmuA_effector_Hydrolase             | Lamassu-Fam__LmuA_effector_Hydrolase             | Lamassu-Fam            | Custom                  | 20     |",
        "notes": "The pinned DefenseFinder HMM inventory records the Lamassu-Fam__LmuA_effector_Hydrolase custom profile listed as mandatory by the Lamassu-Hydrolase rule row."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II           | Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II           | Lamassu-Fam            | Custom                  | 20     |",
        "notes": "The pinned DefenseFinder HMM inventory records the Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II custom profile listed as mandatory by the Lamassu-Hydrolase rule row."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| Lamassu-Fam__LmuC_acc_Lipase                     | Lamassu-Fam__LmuC_acc_Lipase                     | Lamassu-Fam            | Custom                  | 20     |",
        "notes": "The pinned DefenseFinder HMM inventory records the Lamassu-Fam__LmuC_acc_Lipase custom profile listed as accessory by the Lamassu-Hydrolase rule row."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "Lamassu-Fam\tLamassu-Hydrolase\t2\t2\tLamassu-Fam__LmuA_effector_Hydrolase, Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II\tLamassu-Fam__LmuC_acc_Lipase\tLamassu-Fam__LmuA_effector_Amidase, Lamassu-Fam__LmuA_effector_Cap4_nuclease, Lamassu-Fam__LmuA_effector_Cap4_nuclease_II, Lamassu-Fam__LmuA_effector_FMO, Lamassu-Fam__LmuA_effector_Lipase, Lamassu-Fam__LmuA_effector_Mrr, Lamassu-Fam__LmuA_effector_PDDEXK, Lamassu-Fam__LmuA_effector_Protease, Lamassu-Fam__LmuA_effector_Sir2, Lamassu-Fam__LmuA_effector_hypothetical\t",
        "notes": "The pinned DefenseFinder rules table models Lamassu-Hydrolase as a Lamassu-Fam subsystem requiring Lamassu-Fam__LmuA_effector_Hydrolase and Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II, with Lamassu-Fam__LmuC_acc_Lipase as an accessory profile."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "lamassu_hydrolase_locus_subtype_defense",
        "title": "Lamassu-Hydrolase is a DefenseFinder Lamassu subtype",
        "description": "Conservative subtype-level classification linking the DefenseFinder Lamassu-Hydrolase rule-row definition to Lamassu-Hydrolase system possession and its Lamassu parent.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Lamassu-Hydrolase as a DefenseFinder rule-row subtype of Lamassu system possession without asserting a Lamassu-Hydrolase-specific antiphage process, exact phage-triggered substrate chemistry, viral-DNA trigger, LmuC requirement, native host breadth, cell-death output, or whether every DefenseFinder Lamassu-Hydrolase prediction is a complete experimentally active locus.",
        "nodes": [
          {
            "node_id": "lamassu_hydrolase_system_trait",
            "label": "Lamassu-Hydrolase system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000561",
            "description": "Possession of a genome-encoded Lamassu-Hydrolase phage-defense system."
          },
          {
            "node_id": "lamassu_system_trait",
            "label": "Lamassu system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000232",
            "description": "Possession of a genome-encoded Lamassu phage-defense system."
          }
        ],
        "edges": [
          {
            "subject": "lamassu_hydrolase_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "lamassu_system_trait",
            "description": "Lamassu-Hydrolase system possession is a Lamassu-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| Lamassu-Fam | 10\\.1101/2022\\.05\\.11\\.491447 | An expanding arsenal of immune systems that protect bacteria from phages | ",
                "notes": "The pinned DefenseFinder article registry maps the Lamassu-Fam model namespace to a bacterial immune-systems preprint."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "Lamassu-Fam\tLamassu-Hydrolase\t2\t2",
                "notes": "The pinned DefenseFinder rules table places the Lamassu-Hydrolase subsystem under the Lamassu-Fam system key with 2 mandatory matches and 2 genes required."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "lamassu-hydrolase-activity-gap",
        "prompt": "Resolve Lamassu-Hydrolase phage triggers, native hosts, hydrolase effector substrates, LmuC usage, and profile-to-activity criteria before minting enzyme, trigger, or component children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Haudiquet et al. support a Lamassu family with diverse LmuA effectors and a conserved SMC-like sensor, and the pinned DefenseFinder HMM inventory and rules table support Lamassu-Hydrolase as a Lamassu-Fam subtype whose rule row requires Lamassu-Fam__LmuA_effector_Hydrolase and Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II. This first-pass record follows the rule row but leaves exact hydrolase substrates, LmuC requirement, native hosts, phage triggers, cell-death output, and profile-to-activity criteria unresolved.",
        "evidence": [
          {
            "reference": "DOI:10.1073/pnas.2519643122",
            "snippet": "a bacterial immune system family featuring diverse effectors but a core conserved SMC-like sensor",
            "notes": "Haudiquet et al. support placing Lamassu subtypes under a Lamassu family with diverse LmuA effectors and a conserved SMC-like sensor."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| Lamassu-Fam__LmuA_effector_Hydrolase             | Lamassu-Fam__LmuA_effector_Hydrolase             | Lamassu-Fam            | Custom                  | 20     |",
            "notes": "The pinned DefenseFinder HMM inventory records the Lamassu-Fam__LmuA_effector_Hydrolase custom profile listed as mandatory by the Lamassu-Hydrolase rule row."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| Lamassu-Fam__LmuC_acc_Lipase                     | Lamassu-Fam__LmuC_acc_Lipase                     | Lamassu-Fam            | Custom                  | 20     |",
            "notes": "The pinned DefenseFinder HMM inventory records the Lamassu-Fam__LmuC_acc_Lipase custom profile listed as accessory by the Lamassu-Hydrolase rule row."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "snippet": "Lamassu-Fam\tLamassu-Hydrolase\t2\t2\tLamassu-Fam__LmuA_effector_Hydrolase, Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II\tLamassu-Fam__LmuC_acc_Lipase\tLamassu-Fam__LmuA_effector_Amidase, Lamassu-Fam__LmuA_effector_Cap4_nuclease, Lamassu-Fam__LmuA_effector_Cap4_nuclease_II, Lamassu-Fam__LmuA_effector_FMO, Lamassu-Fam__LmuA_effector_Lipase, Lamassu-Fam__LmuA_effector_Mrr, Lamassu-Fam__LmuA_effector_PDDEXK, Lamassu-Fam__LmuA_effector_Protease, Lamassu-Fam__LmuA_effector_Sir2, Lamassu-Fam__LmuA_effector_hypothetical\t",
            "notes": "The pinned DefenseFinder rules table models Lamassu-Hydrolase as a Lamassu-Fam subsystem requiring Lamassu-Fam__LmuA_effector_Hydrolase and Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II, with Lamassu-Fam__LmuC_acc_Lipase as an accessory profile."
          }
        ],
        "attaches_to": [
          "causal_graphs#lamassu_hydrolase_locus_subtype_defense"
        ],
        "posed_by": "codex",
        "posed_date": "2026-10-03"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-03T03:10:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Lamassu-Hydrolase system as a DefenseFinder-backed GENOMICS TraitRecord under the Lamassu system parent after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record for the target local ID, placeholder METPO ID, proposal cohort, record slug, human label, or DefenseFinder subsystem; existing Lamassu-Fam__LmuA_effector_Hydrolase mentions were limited to forbidden-profile evidence on neighboring Lamassu-Fam subtypes, and the replacement placeholder is reserved in proposals/metpo_traitmech_v438.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-03T03:10:02Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed Lamassu-Hydrolase system during initial curation and left canonical_examples empty because the pinned DefenseFinder tables support a rule-row subtype but not an accession-backed native microbial taxon exemplar tied to the Lamassu-Hydrolase profiles and experimentally verified endogenous activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000562",
    "label": "Lamassu-Lipase system",
    "definition": "A Lamassu system in which an organism possesses a genome-encoded DefenseFinder Lamassu-Lipase subtype locus represented by the Lamassu-Lipase rule row requiring the Lamassu-Fam__LmuA_effector_Lipase and Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II profiles.",
    "definition_source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000232"
    ],
    "synonyms": [
      {
        "synonym_text": "Lamassu-Lipase",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv"
      },
      {
        "synonym_text": "Lamassu-Fam__LmuA_effector_Lipase",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1073/pnas.2519643122",
        "snippet": "a bacterial immune system family featuring diverse effectors but a core conserved SMC-like sensor",
        "notes": "Haudiquet et al. support placing Lamassu subtypes under a Lamassu family with diverse LmuA effectors and a conserved SMC-like sensor."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| Lamassu-Fam | 10\\.1101/2022\\.05\\.11\\.491447 | An expanding arsenal of immune systems that protect bacteria from phages | ",
        "notes": "The pinned DefenseFinder article registry maps the Lamassu-Fam model namespace to a bacterial immune-systems preprint."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| Lamassu-Fam__LmuA_effector_Lipase                | Lamassu-Fam__LmuA_effector_Lipase                | Lamassu-Fam            | Custom                  | 20     |",
        "notes": "The pinned DefenseFinder HMM inventory records the Lamassu-Fam__LmuA_effector_Lipase custom profile listed as mandatory by the Lamassu-Lipase rule row."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II           | Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II           | Lamassu-Fam            | Custom                  | 20     |",
        "notes": "The pinned DefenseFinder HMM inventory records the Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II custom profile, which the Lamassu-Lipase rule row lists as mandatory despite the HMM inventory also carrying a Lipase-scoped LmuB SMC profile."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| Lamassu-Fam__LmuB_SMC_Lipase                     | Lamassu-Fam__LmuB_SMC_Lipase                     | Lamassu-Fam            | Custom                  | 20     |",
        "notes": "The pinned DefenseFinder HMM inventory records a Lamassu-Fam__LmuB_SMC_Lipase custom profile that is not the LmuB SMC profile named by the pinned Lamassu-Lipase rule row."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| Lamassu-Fam__LmuC_acc_Lipase                     | Lamassu-Fam__LmuC_acc_Lipase                     | Lamassu-Fam            | Custom                  | 20     |",
        "notes": "The pinned DefenseFinder HMM inventory records the Lamassu-Fam__LmuC_acc_Lipase custom profile listed as accessory by the Lamassu-Lipase rule row."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "Lamassu-Fam\tLamassu-Lipase\t2\t2\tLamassu-Fam__LmuA_effector_Lipase, Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II\tLamassu-Fam__LmuC_acc_Lipase\tLamassu-Fam__LmuA_effector_Amidase, Lamassu-Fam__LmuA_effector_Cap4_nuclease, Lamassu-Fam__LmuA_effector_Cap4_nuclease_II, Lamassu-Fam__LmuA_effector_FMO, Lamassu-Fam__LmuA_effector_Hydrolase, Lamassu-Fam__LmuA_effector_Mrr, Lamassu-Fam__LmuA_effector_PDDEXK, Lamassu-Fam__LmuA_effector_Protease, Lamassu-Fam__LmuA_effector_Sir2, Lamassu-Fam__LmuA_effector_hypothetical\t",
        "notes": "The pinned DefenseFinder rules table models Lamassu-Lipase as a Lamassu-Fam subsystem requiring Lamassu-Fam__LmuA_effector_Lipase and Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II, with Lamassu-Fam__LmuC_acc_Lipase as an accessory profile."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "lamassu_lipase_locus_subtype_defense",
        "title": "Lamassu-Lipase is a DefenseFinder Lamassu subtype",
        "description": "Conservative subtype-level classification linking the DefenseFinder Lamassu-Lipase rule-row definition to Lamassu-Lipase system possession and its Lamassu parent.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Lamassu-Lipase as a DefenseFinder rule-row subtype of Lamassu system possession without asserting a Lamassu-Lipase-specific antiphage process, selecting between the rule-row LmuB profile and the Lipase-scoped LmuB HMM row, or resolving exact phage-triggered substrate chemistry, viral-DNA trigger, LmuC requirement, native host breadth, cell-death output, or whether every DefenseFinder Lamassu-Lipase prediction is a complete experimentally active locus.",
        "nodes": [
          {
            "node_id": "lamassu_lipase_system_trait",
            "label": "Lamassu-Lipase system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000562",
            "description": "Possession of a genome-encoded Lamassu-Lipase phage-defense system."
          },
          {
            "node_id": "lamassu_system_trait",
            "label": "Lamassu system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000232",
            "description": "Possession of a genome-encoded Lamassu phage-defense system."
          }
        ],
        "edges": [
          {
            "subject": "lamassu_lipase_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "lamassu_system_trait",
            "description": "Lamassu-Lipase system possession is a Lamassu-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| Lamassu-Fam | 10\\.1101/2022\\.05\\.11\\.491447 | An expanding arsenal of immune systems that protect bacteria from phages | ",
                "notes": "The pinned DefenseFinder article registry maps the Lamassu-Fam model namespace to a bacterial immune-systems preprint."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "Lamassu-Fam\tLamassu-Lipase\t2\t2",
                "notes": "The pinned DefenseFinder rules table places the Lamassu-Lipase subsystem under the Lamassu-Fam system key with 2 mandatory matches and 2 genes required."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "lamassu-lipase-activity-gap",
        "prompt": "Resolve Lamassu-Lipase phage triggers, native hosts, lipase effector substrates, LmuB/LmuC model rows, LmuC usage, and profile-to-activity criteria before minting enzyme, trigger, or component children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Haudiquet et al. support a Lamassu family with diverse LmuA effectors and a conserved SMC-like sensor, and the pinned DefenseFinder HMM inventory and rules table support Lamassu-Lipase as a Lamassu-Fam subtype whose rule row requires Lamassu-Fam__LmuA_effector_Lipase and Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II. This first-pass record follows the rule row but leaves the relationship between its LmuB Cap4-nuclease profile name and the Lipase-scoped Lamassu-Fam__LmuB_SMC_Lipase HMM row unresolved, along with exact lipase substrates, LmuC requirement, native hosts, phage triggers, cell-death output, and profile-to-activity criteria.",
        "evidence": [
          {
            "reference": "DOI:10.1073/pnas.2519643122",
            "snippet": "a bacterial immune system family featuring diverse effectors but a core conserved SMC-like sensor",
            "notes": "Haudiquet et al. support placing Lamassu subtypes under a Lamassu family with diverse LmuA effectors and a conserved SMC-like sensor."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| Lamassu-Fam__LmuA_effector_Lipase                | Lamassu-Fam__LmuA_effector_Lipase                | Lamassu-Fam            | Custom                  | 20     |",
            "notes": "The pinned DefenseFinder HMM inventory records the Lamassu-Fam__LmuA_effector_Lipase custom profile listed as mandatory by the Lamassu-Lipase rule row."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| Lamassu-Fam__LmuB_SMC_Lipase                     | Lamassu-Fam__LmuB_SMC_Lipase                     | Lamassu-Fam            | Custom                  | 20     |",
            "notes": "The pinned DefenseFinder HMM inventory records a Lamassu-Fam__LmuB_SMC_Lipase custom profile that is not the LmuB SMC profile named by the pinned Lamassu-Lipase rule row."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| Lamassu-Fam__LmuC_acc_Lipase                     | Lamassu-Fam__LmuC_acc_Lipase                     | Lamassu-Fam            | Custom                  | 20     |",
            "notes": "The pinned DefenseFinder HMM inventory records the Lamassu-Fam__LmuC_acc_Lipase custom profile listed as accessory by the Lamassu-Lipase rule row."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "snippet": "Lamassu-Fam\tLamassu-Lipase\t2\t2\tLamassu-Fam__LmuA_effector_Lipase, Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II\tLamassu-Fam__LmuC_acc_Lipase\tLamassu-Fam__LmuA_effector_Amidase, Lamassu-Fam__LmuA_effector_Cap4_nuclease, Lamassu-Fam__LmuA_effector_Cap4_nuclease_II, Lamassu-Fam__LmuA_effector_FMO, Lamassu-Fam__LmuA_effector_Hydrolase, Lamassu-Fam__LmuA_effector_Mrr, Lamassu-Fam__LmuA_effector_PDDEXK, Lamassu-Fam__LmuA_effector_Protease, Lamassu-Fam__LmuA_effector_Sir2, Lamassu-Fam__LmuA_effector_hypothetical\t",
            "notes": "The pinned DefenseFinder rules table models Lamassu-Lipase as a Lamassu-Fam subsystem requiring Lamassu-Fam__LmuA_effector_Lipase and Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II, with Lamassu-Fam__LmuC_acc_Lipase as an accessory profile."
          }
        ],
        "attaches_to": [
          "causal_graphs#lamassu_lipase_locus_subtype_defense"
        ],
        "posed_by": "codex",
        "posed_date": "2026-10-03"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-03T03:48:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Lamassu-Lipase system as a DefenseFinder-backed GENOMICS TraitRecord under the Lamassu system parent after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record for the target local ID, placeholder METPO ID, proposal cohort, record slug, human label, or DefenseFinder subsystem; existing Lamassu-Fam__LmuA_effector_Lipase mentions were limited to forbidden-profile evidence on neighboring Lamassu-Fam subtypes, and the replacement placeholder is reserved in proposals/metpo_traitmech_v439.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-03T03:48:02Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed Lamassu-Lipase system during initial curation and left canonical_examples empty because the pinned DefenseFinder tables support a rule-row subtype but not an accession-backed native microbial taxon exemplar tied to the Lamassu-Lipase profiles and experimentally verified endogenous activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000563",
    "label": "Lamassu-Mrr system",
    "definition": "A Lamassu system in which an organism possesses a genome-encoded DefenseFinder Lamassu-Mrr subtype locus represented by the Lamassu-Mrr rule row requiring the Lamassu-Fam__LmuA_effector_Mrr and Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II profiles.",
    "definition_source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000232"
    ],
    "synonyms": [
      {
        "synonym_text": "Lamassu-Mrr",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv"
      },
      {
        "synonym_text": "Lamassu-Fam__LmuA_effector_Mrr",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1073/pnas.2519643122",
        "snippet": "a bacterial immune system family featuring diverse effectors but a core conserved SMC-like sensor",
        "notes": "Haudiquet et al. support placing Lamassu subtypes under a Lamassu family with diverse LmuA effectors and a conserved SMC-like sensor."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| Lamassu-Fam | 10\\.1101/2022\\.05\\.11\\.491447 | An expanding arsenal of immune systems that protect bacteria from phages | ",
        "notes": "The pinned DefenseFinder article registry maps the Lamassu-Fam model namespace to a bacterial immune-systems preprint."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| Lamassu-Fam__LmuA_effector_Mrr                   | Lamassu-Fam__LmuA_effector_Mrr                   | Lamassu-Fam            | Custom                  | 20     |",
        "notes": "The pinned DefenseFinder HMM inventory records the Lamassu-Fam__LmuA_effector_Mrr custom profile listed as mandatory by the Lamassu-Mrr rule row."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II           | Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II           | Lamassu-Fam            | Custom                  | 20     |",
        "notes": "The pinned DefenseFinder HMM inventory records the Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II custom profile, which the Lamassu-Mrr rule row lists as mandatory despite the HMM inventory also carrying an Mrr-scoped LmuB SMC profile."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| Lamassu-Fam__LmuB_SMC_Mrr                        | Lamassu-Fam__LmuB_SMC_Mrr                        | Lamassu-Fam            | Custom                  | 20     |",
        "notes": "The pinned DefenseFinder HMM inventory records a Lamassu-Fam__LmuB_SMC_Mrr custom profile that is not the LmuB SMC profile named by the pinned Lamassu-Mrr rule row."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| Lamassu-Fam__LmuC_acc_Lipase                     | Lamassu-Fam__LmuC_acc_Lipase                     | Lamassu-Fam            | Custom                  | 20     |",
        "notes": "The pinned DefenseFinder HMM inventory records the Lamassu-Fam__LmuC_acc_Lipase custom profile listed as accessory by the Lamassu-Mrr rule row."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| Lamassu-Fam__LmuC_acc_Mrr                        | Lamassu-Fam__LmuC_acc_Mrr                        | Lamassu-Fam            | Custom                  | 20     |",
        "notes": "The pinned DefenseFinder HMM inventory records a Lamassu-Fam__LmuC_acc_Mrr custom profile that is not the LmuC accessory profile named by the pinned Lamassu-Mrr rule row."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "Lamassu-Fam\tLamassu-Mrr\t2\t2\tLamassu-Fam__LmuA_effector_Mrr, Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II\tLamassu-Fam__LmuC_acc_Lipase\tLamassu-Fam__LmuA_effector_Amidase, Lamassu-Fam__LmuA_effector_Cap4_nuclease, Lamassu-Fam__LmuA_effector_Cap4_nuclease_II, Lamassu-Fam__LmuA_effector_FMO, Lamassu-Fam__LmuA_effector_Hydrolase, Lamassu-Fam__LmuA_effector_Lipase, Lamassu-Fam__LmuA_effector_PDDEXK, Lamassu-Fam__LmuA_effector_Protease, Lamassu-Fam__LmuA_effector_Sir2, Lamassu-Fam__LmuA_effector_hypothetical\t",
        "notes": "The pinned DefenseFinder rules table models Lamassu-Mrr as a Lamassu-Fam subsystem requiring Lamassu-Fam__LmuA_effector_Mrr and Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II, with Lamassu-Fam__LmuC_acc_Lipase as an accessory profile."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "lamassu_mrr_locus_subtype_defense",
        "title": "Lamassu-Mrr is a DefenseFinder Lamassu subtype",
        "description": "Conservative subtype-level classification linking the DefenseFinder Lamassu-Mrr rule-row definition to Lamassu-Mrr system possession and its Lamassu parent.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Lamassu-Mrr as a DefenseFinder rule-row subtype of Lamassu system possession without asserting a Lamassu-Mrr-specific antiphage process, selecting between the rule-row LmuB/LmuC profile names and the Mrr-scoped LmuB/LmuC HMM rows, or resolving exact phage-triggered Mrr effector activity, viral-DNA trigger, LmuC requirement, native host breadth, cell-death output, or whether every DefenseFinder Lamassu-Mrr prediction is a complete experimentally active locus.",
        "nodes": [
          {
            "node_id": "lamassu_mrr_system_trait",
            "label": "Lamassu-Mrr system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000563",
            "description": "Possession of a genome-encoded Lamassu-Mrr phage-defense system."
          },
          {
            "node_id": "lamassu_system_trait",
            "label": "Lamassu system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000232",
            "description": "Possession of a genome-encoded Lamassu phage-defense system."
          }
        ],
        "edges": [
          {
            "subject": "lamassu_mrr_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "lamassu_system_trait",
            "description": "Lamassu-Mrr system possession is a Lamassu-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| Lamassu-Fam | 10\\.1101/2022\\.05\\.11\\.491447 | An expanding arsenal of immune systems that protect bacteria from phages | ",
                "notes": "The pinned DefenseFinder article registry maps the Lamassu-Fam model namespace to a bacterial immune-systems preprint."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "Lamassu-Fam\tLamassu-Mrr\t2\t2",
                "notes": "The pinned DefenseFinder rules table places the Lamassu-Mrr subsystem under the Lamassu-Fam system key with 2 mandatory matches and 2 genes required."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "lamassu-mrr-activity-gap",
        "prompt": "Resolve Lamassu-Mrr phage triggers, native hosts, Mrr effector activity, LmuB/LmuC model rows, LmuC usage, and profile-to-activity criteria before minting enzyme, trigger, or component children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Haudiquet et al. support a Lamassu family with diverse LmuA effectors and a conserved SMC-like sensor, and the pinned DefenseFinder HMM inventory and rules table support Lamassu-Mrr as a Lamassu-Fam subtype whose rule row requires Lamassu-Fam__LmuA_effector_Mrr and Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II. This first-pass record follows the rule row but leaves the relationship between its LmuB Cap4-nuclease and LmuC Lipase profile names and the Mrr-scoped Lamassu-Fam__LmuB_SMC_Mrr and Lamassu-Fam__LmuC_acc_Mrr HMM rows unresolved, along with exact Mrr effector activity, LmuC requirement, native hosts, phage triggers, cell-death output, and profile-to-activity criteria.",
        "evidence": [
          {
            "reference": "DOI:10.1073/pnas.2519643122",
            "snippet": "a bacterial immune system family featuring diverse effectors but a core conserved SMC-like sensor",
            "notes": "Haudiquet et al. support placing Lamassu subtypes under a Lamassu family with diverse LmuA effectors and a conserved SMC-like sensor."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| Lamassu-Fam__LmuA_effector_Mrr                   | Lamassu-Fam__LmuA_effector_Mrr                   | Lamassu-Fam            | Custom                  | 20     |",
            "notes": "The pinned DefenseFinder HMM inventory records the Lamassu-Fam__LmuA_effector_Mrr custom profile listed as mandatory by the Lamassu-Mrr rule row."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| Lamassu-Fam__LmuB_SMC_Mrr                        | Lamassu-Fam__LmuB_SMC_Mrr                        | Lamassu-Fam            | Custom                  | 20     |",
            "notes": "The pinned DefenseFinder HMM inventory records a Lamassu-Fam__LmuB_SMC_Mrr custom profile that is not the LmuB SMC profile named by the pinned Lamassu-Mrr rule row."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| Lamassu-Fam__LmuC_acc_Mrr                        | Lamassu-Fam__LmuC_acc_Mrr                        | Lamassu-Fam            | Custom                  | 20     |",
            "notes": "The pinned DefenseFinder HMM inventory records a Lamassu-Fam__LmuC_acc_Mrr custom profile that is not the LmuC accessory profile named by the pinned Lamassu-Mrr rule row."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "snippet": "Lamassu-Fam\tLamassu-Mrr\t2\t2\tLamassu-Fam__LmuA_effector_Mrr, Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II\tLamassu-Fam__LmuC_acc_Lipase\tLamassu-Fam__LmuA_effector_Amidase, Lamassu-Fam__LmuA_effector_Cap4_nuclease, Lamassu-Fam__LmuA_effector_Cap4_nuclease_II, Lamassu-Fam__LmuA_effector_FMO, Lamassu-Fam__LmuA_effector_Hydrolase, Lamassu-Fam__LmuA_effector_Lipase, Lamassu-Fam__LmuA_effector_PDDEXK, Lamassu-Fam__LmuA_effector_Protease, Lamassu-Fam__LmuA_effector_Sir2, Lamassu-Fam__LmuA_effector_hypothetical\t",
            "notes": "The pinned DefenseFinder rules table models Lamassu-Mrr as a Lamassu-Fam subsystem requiring Lamassu-Fam__LmuA_effector_Mrr and Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II, with Lamassu-Fam__LmuC_acc_Lipase as an accessory profile."
          }
        ],
        "attaches_to": [
          "causal_graphs#lamassu_mrr_locus_subtype_defense"
        ],
        "posed_by": "codex",
        "posed_date": "2026-10-03"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-03T04:26:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Lamassu-Mrr system as a DefenseFinder-backed GENOMICS TraitRecord under the Lamassu system parent after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record for the target local ID, placeholder METPO ID, proposal cohort, record slug, human label, or DefenseFinder subsystem; existing Lamassu-Fam__LmuA_effector_Mrr mentions were limited to forbidden-profile evidence on neighboring Lamassu-Fam subtypes, and the replacement placeholder is reserved in proposals/metpo_traitmech_v440.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-03T04:26:02Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed Lamassu-Mrr system during initial curation and left canonical_examples empty because the pinned DefenseFinder tables support a rule-row subtype but not an accession-backed native microbial taxon exemplar tied to the Lamassu-Mrr profiles and experimentally verified endogenous activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000564",
    "label": "Lamassu-PDDEXK system",
    "definition": "A Lamassu system in which an organism possesses a genome-encoded DefenseFinder Lamassu-PDDEXK subtype locus represented by the Lamassu-PDDEXK rule row requiring the Lamassu-Fam__LmuA_effector_PDDEXK and Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II profiles.",
    "definition_source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000232"
    ],
    "synonyms": [
      {
        "synonym_text": "Lamassu-PDDEXK",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv"
      },
      {
        "synonym_text": "Lamassu-Fam__LmuA_effector_PDDEXK",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1073/pnas.2519643122",
        "snippet": "a bacterial immune system family featuring diverse effectors but a core conserved SMC-like sensor",
        "notes": "Haudiquet et al. support placing Lamassu subtypes under a Lamassu family with diverse LmuA effectors and a conserved SMC-like sensor."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| Lamassu-Fam | 10\\.1101/2022\\.05\\.11\\.491447 | An expanding arsenal of immune systems that protect bacteria from phages | ",
        "notes": "The pinned DefenseFinder article registry maps the Lamassu-Fam model namespace to a bacterial immune-systems preprint."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| Lamassu-Fam__LmuA_effector_PDDEXK                | Lamassu-Fam__LmuA_effector_PDDEXK                | Lamassu-Fam            | Custom                  | 20     |",
        "notes": "The pinned DefenseFinder HMM inventory records the Lamassu-Fam__LmuA_effector_PDDEXK custom profile listed as mandatory by the Lamassu-PDDEXK rule row."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II           | Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II           | Lamassu-Fam            | Custom                  | 20     |",
        "notes": "The pinned DefenseFinder HMM inventory records the Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II custom profile, which the Lamassu-PDDEXK rule row lists as mandatory despite the HMM inventory also carrying a PDDEXK-scoped LmuB SMC profile."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| Lamassu-Fam__LmuB_SMC_PDDEXK                     | Lamassu-Fam__LmuB_SMC_PDDEXK                     | Lamassu-Fam            | Custom                  | 20     |",
        "notes": "The pinned DefenseFinder HMM inventory records a Lamassu-Fam__LmuB_SMC_PDDEXK custom profile that is not the LmuB SMC profile named by the pinned Lamassu-PDDEXK rule row."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| Lamassu-Fam__LmuC_acc_Lipase                     | Lamassu-Fam__LmuC_acc_Lipase                     | Lamassu-Fam            | Custom                  | 20     |",
        "notes": "The pinned DefenseFinder HMM inventory records the Lamassu-Fam__LmuC_acc_Lipase custom profile listed as accessory by the Lamassu-PDDEXK rule row."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| Lamassu-Fam__LmuC_acc_PDDEXK                     | Lamassu-Fam__LmuC_acc_PDDEXK                     | Lamassu-Fam            | Custom                  | 20     |",
        "notes": "The pinned DefenseFinder HMM inventory records a Lamassu-Fam__LmuC_acc_PDDEXK custom profile that is not the LmuC accessory profile named by the pinned Lamassu-PDDEXK rule row."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "Lamassu-Fam\tLamassu-PDDEXK\t2\t2\tLamassu-Fam__LmuA_effector_PDDEXK, Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II\tLamassu-Fam__LmuC_acc_Lipase\tLamassu-Fam__LmuA_effector_Amidase, Lamassu-Fam__LmuA_effector_Cap4_nuclease, Lamassu-Fam__LmuA_effector_Cap4_nuclease_II, Lamassu-Fam__LmuA_effector_FMO, Lamassu-Fam__LmuA_effector_Hydrolase, Lamassu-Fam__LmuA_effector_Lipase, Lamassu-Fam__LmuA_effector_Mrr, Lamassu-Fam__LmuA_effector_Protease, Lamassu-Fam__LmuA_effector_Sir2, Lamassu-Fam__LmuA_effector_hypothetical\t",
        "notes": "The pinned DefenseFinder rules table models Lamassu-PDDEXK as a Lamassu-Fam subsystem requiring Lamassu-Fam__LmuA_effector_PDDEXK and Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II, with Lamassu-Fam__LmuC_acc_Lipase as an accessory profile."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "lamassu_pddexk_locus_subtype_defense",
        "title": "Lamassu-PDDEXK is a DefenseFinder Lamassu subtype",
        "description": "Conservative subtype-level classification linking the DefenseFinder Lamassu-PDDEXK rule-row definition to Lamassu-PDDEXK system possession and its Lamassu parent.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Lamassu-PDDEXK as a DefenseFinder rule-row subtype of Lamassu system possession without asserting a Lamassu-PDDEXK-specific antiphage process, selecting between the rule-row LmuB/LmuC profile names and the PDDEXK-scoped LmuB/LmuC HMM rows, or resolving exact phage-triggered PDDEXK effector activity, viral-DNA trigger, LmuC requirement, native host breadth, cell-death output, or whether every DefenseFinder Lamassu-PDDEXK prediction is a complete experimentally active locus.",
        "nodes": [
          {
            "node_id": "lamassu_pddexk_system_trait",
            "label": "Lamassu-PDDEXK system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000564",
            "description": "Possession of a genome-encoded Lamassu-PDDEXK phage-defense system."
          },
          {
            "node_id": "lamassu_system_trait",
            "label": "Lamassu system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000232",
            "description": "Possession of a genome-encoded Lamassu phage-defense system."
          }
        ],
        "edges": [
          {
            "subject": "lamassu_pddexk_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "lamassu_system_trait",
            "description": "Lamassu-PDDEXK system possession is a Lamassu-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| Lamassu-Fam | 10\\.1101/2022\\.05\\.11\\.491447 | An expanding arsenal of immune systems that protect bacteria from phages | ",
                "notes": "The pinned DefenseFinder article registry maps the Lamassu-Fam model namespace to a bacterial immune-systems preprint."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "Lamassu-Fam\tLamassu-PDDEXK\t2\t2",
                "notes": "The pinned DefenseFinder rules table places the Lamassu-PDDEXK subsystem under the Lamassu-Fam system key with 2 mandatory matches and 2 genes required."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "lamassu-pddexk-activity-gap",
        "prompt": "Resolve Lamassu-PDDEXK phage triggers, native hosts, PDDEXK effector activity, LmuB/LmuC model rows, LmuC usage, and profile-to-activity criteria before minting enzyme, trigger, or component children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Haudiquet et al. support a Lamassu family with diverse LmuA effectors and a conserved SMC-like sensor, and the pinned DefenseFinder HMM inventory and rules table support Lamassu-PDDEXK as a Lamassu-Fam subtype whose rule row requires Lamassu-Fam__LmuA_effector_PDDEXK and Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II. This first-pass record follows the rule row but leaves the relationship between its LmuB Cap4-nuclease and LmuC Lipase profile names and the PDDEXK-scoped Lamassu-Fam__LmuB_SMC_PDDEXK and Lamassu-Fam__LmuC_acc_PDDEXK HMM rows unresolved, along with exact PDDEXK effector activity, LmuC requirement, native hosts, phage triggers, cell-death output, and profile-to-activity criteria.",
        "evidence": [
          {
            "reference": "DOI:10.1073/pnas.2519643122",
            "snippet": "a bacterial immune system family featuring diverse effectors but a core conserved SMC-like sensor",
            "notes": "Haudiquet et al. support placing Lamassu subtypes under a Lamassu family with diverse LmuA effectors and a conserved SMC-like sensor."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| Lamassu-Fam__LmuA_effector_PDDEXK                | Lamassu-Fam__LmuA_effector_PDDEXK                | Lamassu-Fam            | Custom                  | 20     |",
            "notes": "The pinned DefenseFinder HMM inventory records the Lamassu-Fam__LmuA_effector_PDDEXK custom profile listed as mandatory by the Lamassu-PDDEXK rule row."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| Lamassu-Fam__LmuB_SMC_PDDEXK                     | Lamassu-Fam__LmuB_SMC_PDDEXK                     | Lamassu-Fam            | Custom                  | 20     |",
            "notes": "The pinned DefenseFinder HMM inventory records a Lamassu-Fam__LmuB_SMC_PDDEXK custom profile that is not the LmuB SMC profile named by the pinned Lamassu-PDDEXK rule row."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| Lamassu-Fam__LmuC_acc_PDDEXK                     | Lamassu-Fam__LmuC_acc_PDDEXK                     | Lamassu-Fam            | Custom                  | 20     |",
            "notes": "The pinned DefenseFinder HMM inventory records a Lamassu-Fam__LmuC_acc_PDDEXK custom profile that is not the LmuC accessory profile named by the pinned Lamassu-PDDEXK rule row."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "snippet": "Lamassu-Fam\tLamassu-PDDEXK\t2\t2\tLamassu-Fam__LmuA_effector_PDDEXK, Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II\tLamassu-Fam__LmuC_acc_Lipase\tLamassu-Fam__LmuA_effector_Amidase, Lamassu-Fam__LmuA_effector_Cap4_nuclease, Lamassu-Fam__LmuA_effector_Cap4_nuclease_II, Lamassu-Fam__LmuA_effector_FMO, Lamassu-Fam__LmuA_effector_Hydrolase, Lamassu-Fam__LmuA_effector_Lipase, Lamassu-Fam__LmuA_effector_Mrr, Lamassu-Fam__LmuA_effector_Protease, Lamassu-Fam__LmuA_effector_Sir2, Lamassu-Fam__LmuA_effector_hypothetical\t",
            "notes": "The pinned DefenseFinder rules table models Lamassu-PDDEXK as a Lamassu-Fam subsystem requiring Lamassu-Fam__LmuA_effector_PDDEXK and Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II, with Lamassu-Fam__LmuC_acc_Lipase as an accessory profile."
          }
        ],
        "attaches_to": [
          "causal_graphs#lamassu_pddexk_locus_subtype_defense"
        ],
        "posed_by": "codex",
        "posed_date": "2026-10-03"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-03T05:05:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Lamassu-PDDEXK system as a DefenseFinder-backed GENOMICS TraitRecord under the Lamassu system parent after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record for the target local ID, placeholder METPO ID, proposal cohort, record slug, human label, or DefenseFinder subsystem; existing Lamassu-Fam__LmuA_effector_PDDEXK mentions were limited to forbidden-profile evidence on neighboring Lamassu-Fam subtypes, their earlier writer scripts, and rendered pages, and the replacement placeholder is reserved in proposals/metpo_traitmech_v441.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-03T05:05:02Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed Lamassu-PDDEXK system during initial curation and left canonical_examples empty because the pinned DefenseFinder tables support a rule-row subtype but not an accession-backed native microbial taxon exemplar tied to the Lamassu-PDDEXK profiles and experimentally verified endogenous activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000565",
    "label": "Lamassu-Protease system",
    "definition": "A Lamassu system in which an organism possesses a genome-encoded DefenseFinder Lamassu-Protease subtype locus represented by the Lamassu-Protease rule row requiring the Lamassu-Fam__LmuA_effector_Protease and Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II profiles.",
    "definition_source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000232"
    ],
    "synonyms": [
      {
        "synonym_text": "Lamassu-Protease",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv"
      },
      {
        "synonym_text": "Lamassu-Fam__LmuA_effector_Protease",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1073/pnas.2519643122",
        "snippet": "a bacterial immune system family featuring diverse effectors but a core conserved SMC-like sensor",
        "notes": "Haudiquet et al. support placing Lamassu subtypes under a Lamassu family with diverse LmuA effectors and a conserved SMC-like sensor."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| Lamassu-Fam | 10\\.1101/2022\\.05\\.11\\.491447 | An expanding arsenal of immune systems that protect bacteria from phages | ",
        "notes": "The pinned DefenseFinder article registry maps the Lamassu-Fam model namespace to a bacterial immune-systems preprint."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| Lamassu-Fam__LmuA_effector_Protease              | Lamassu-Fam__LmuA_effector_Protease              | Lamassu-Fam            | Custom                  | 20     |",
        "notes": "The pinned DefenseFinder HMM inventory records the Lamassu-Fam__LmuA_effector_Protease custom profile listed as mandatory by the Lamassu-Protease rule row."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II           | Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II           | Lamassu-Fam            | Custom                  | 20     |",
        "notes": "The pinned DefenseFinder HMM inventory records the Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II custom profile listed as mandatory by the Lamassu-Protease rule row."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| Lamassu-Fam__LmuC_acc_Lipase                     | Lamassu-Fam__LmuC_acc_Lipase                     | Lamassu-Fam            | Custom                  | 20     |",
        "notes": "The pinned DefenseFinder HMM inventory records the Lamassu-Fam__LmuC_acc_Lipase custom profile listed as accessory by the Lamassu-Protease rule row."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "Lamassu-Fam\tLamassu-Protease\t2\t2\tLamassu-Fam__LmuA_effector_Protease, Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II\tLamassu-Fam__LmuC_acc_Lipase\tLamassu-Fam__LmuA_effector_Amidase, Lamassu-Fam__LmuA_effector_Cap4_nuclease, Lamassu-Fam__LmuA_effector_Cap4_nuclease_II, Lamassu-Fam__LmuA_effector_FMO, Lamassu-Fam__LmuA_effector_Hydrolase, Lamassu-Fam__LmuA_effector_Lipase, Lamassu-Fam__LmuA_effector_Mrr, Lamassu-Fam__LmuA_effector_PDDEXK, Lamassu-Fam__LmuA_effector_Sir2, Lamassu-Fam__LmuA_effector_hypothetical\t",
        "notes": "The pinned DefenseFinder rules table models Lamassu-Protease as a Lamassu-Fam subsystem requiring Lamassu-Fam__LmuA_effector_Protease and Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II, with Lamassu-Fam__LmuC_acc_Lipase as an accessory profile."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "lamassu_protease_locus_subtype_defense",
        "title": "Lamassu-Protease is a DefenseFinder Lamassu subtype",
        "description": "Conservative subtype-level classification linking the DefenseFinder Lamassu-Protease rule-row definition to Lamassu-Protease system possession and its Lamassu parent.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Lamassu-Protease as a DefenseFinder rule-row subtype of Lamassu system possession without asserting a Lamassu-Protease-specific antiphage process, exact phage-triggered protease effector activity, viral-DNA trigger, LmuC requirement, native host breadth, cell-death output, or whether every DefenseFinder Lamassu-Protease prediction is a complete experimentally active locus.",
        "nodes": [
          {
            "node_id": "lamassu_protease_system_trait",
            "label": "Lamassu-Protease system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000565",
            "description": "Possession of a genome-encoded Lamassu-Protease phage-defense system."
          },
          {
            "node_id": "lamassu_system_trait",
            "label": "Lamassu system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000232",
            "description": "Possession of a genome-encoded Lamassu phage-defense system."
          }
        ],
        "edges": [
          {
            "subject": "lamassu_protease_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "lamassu_system_trait",
            "description": "Lamassu-Protease system possession is a Lamassu-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| Lamassu-Fam | 10\\.1101/2022\\.05\\.11\\.491447 | An expanding arsenal of immune systems that protect bacteria from phages | ",
                "notes": "The pinned DefenseFinder article registry maps the Lamassu-Fam model namespace to a bacterial immune-systems preprint."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "Lamassu-Fam\tLamassu-Protease\t2\t2",
                "notes": "The pinned DefenseFinder rules table places the Lamassu-Protease subsystem under the Lamassu-Fam system key with 2 mandatory matches and 2 genes required."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "lamassu-protease-activity-gap",
        "prompt": "Resolve Lamassu-Protease phage triggers, native hosts, protease effector activity, LmuC usage, and profile-to-activity criteria before minting enzyme, trigger, or component children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Haudiquet et al. support a Lamassu family with diverse LmuA effectors and a conserved SMC-like sensor, and the pinned DefenseFinder HMM inventory and rules table support Lamassu-Protease as a Lamassu-Fam subtype whose rule row requires Lamassu-Fam__LmuA_effector_Protease and Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II. This first-pass record follows the rule row but leaves exact protease effector activity, LmuC requirement, native hosts, phage triggers, cell-death output, and profile-to-activity criteria unresolved.",
        "evidence": [
          {
            "reference": "DOI:10.1073/pnas.2519643122",
            "snippet": "a bacterial immune system family featuring diverse effectors but a core conserved SMC-like sensor",
            "notes": "Haudiquet et al. support placing Lamassu subtypes under a Lamassu family with diverse LmuA effectors and a conserved SMC-like sensor."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| Lamassu-Fam__LmuA_effector_Protease              | Lamassu-Fam__LmuA_effector_Protease              | Lamassu-Fam            | Custom                  | 20     |",
            "notes": "The pinned DefenseFinder HMM inventory records the Lamassu-Fam__LmuA_effector_Protease custom profile listed as mandatory by the Lamassu-Protease rule row."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "snippet": "Lamassu-Fam\tLamassu-Protease\t2\t2\tLamassu-Fam__LmuA_effector_Protease, Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II\tLamassu-Fam__LmuC_acc_Lipase\tLamassu-Fam__LmuA_effector_Amidase, Lamassu-Fam__LmuA_effector_Cap4_nuclease, Lamassu-Fam__LmuA_effector_Cap4_nuclease_II, Lamassu-Fam__LmuA_effector_FMO, Lamassu-Fam__LmuA_effector_Hydrolase, Lamassu-Fam__LmuA_effector_Lipase, Lamassu-Fam__LmuA_effector_Mrr, Lamassu-Fam__LmuA_effector_PDDEXK, Lamassu-Fam__LmuA_effector_Sir2, Lamassu-Fam__LmuA_effector_hypothetical\t",
            "notes": "The pinned DefenseFinder rules table models Lamassu-Protease as a Lamassu-Fam subsystem requiring Lamassu-Fam__LmuA_effector_Protease and Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II, with Lamassu-Fam__LmuC_acc_Lipase as an accessory profile."
          }
        ],
        "attaches_to": [
          "causal_graphs#lamassu_protease_locus_subtype_defense"
        ],
        "posed_by": "codex",
        "posed_date": "2026-10-03"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-03T05:46:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Lamassu-Protease system as a DefenseFinder-backed GENOMICS TraitRecord under the Lamassu system parent after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record for the target local ID, placeholder METPO ID, proposal cohort, record slug, human label, or DefenseFinder subsystem; existing Lamassu-Fam__LmuA_effector_Protease mentions were limited to forbidden-profile evidence on neighboring Lamassu-Fam subtypes, their earlier writer scripts, and rendered pages, and the replacement placeholder is reserved in proposals/metpo_traitmech_v442.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-03T05:46:02Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed Lamassu-Protease system during initial curation and left canonical_examples empty because the pinned DefenseFinder tables support a rule-row subtype but not an accession-backed native microbial taxon exemplar tied to the Lamassu-Protease profiles and experimentally verified endogenous activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000566",
    "label": "Lamassu-Sir2 system",
    "definition": "A Lamassu system in which an organism possesses a genome-encoded DefenseFinder Lamassu-Sir2 subtype locus represented by the Lamassu-Sir2 rule row requiring the Lamassu-Fam__LmuA_effector_Sir2 and Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II profiles.",
    "definition_source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000232"
    ],
    "synonyms": [
      {
        "synonym_text": "Lamassu-Sir2",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv"
      },
      {
        "synonym_text": "Lamassu-Fam__LmuA_effector_Sir2",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1073/pnas.2519643122",
        "snippet": "a bacterial immune system family featuring diverse effectors but a core conserved SMC-like sensor",
        "notes": "Haudiquet et al. support placing Lamassu subtypes under a Lamassu family with diverse LmuA effectors and a conserved SMC-like sensor."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| Lamassu-Fam | 10\\.1101/2022\\.05\\.11\\.491447 | An expanding arsenal of immune systems that protect bacteria from phages | ",
        "notes": "The pinned DefenseFinder article registry maps the Lamassu-Fam model namespace to a bacterial immune-systems preprint."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| Lamassu-Fam__LmuA_effector_Sir2                  | Lamassu-Fam__LmuA_effector_Sir2                  | Lamassu-Fam            | Custom                  | 20     |",
        "notes": "The pinned DefenseFinder HMM inventory records the Lamassu-Fam__LmuA_effector_Sir2 custom profile listed as mandatory by the Lamassu-Sir2 rule row."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II           | Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II           | Lamassu-Fam            | Custom                  | 20     |",
        "notes": "The pinned DefenseFinder HMM inventory records the Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II custom profile listed as mandatory by the Lamassu-Sir2 rule row."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| Lamassu-Fam__LmuC_acc_Lipase                     | Lamassu-Fam__LmuC_acc_Lipase                     | Lamassu-Fam            | Custom                  | 20     |",
        "notes": "The pinned DefenseFinder HMM inventory records the Lamassu-Fam__LmuC_acc_Lipase custom profile listed as accessory by the Lamassu-Sir2 rule row."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| Lamassu-Fam__LmuB_SMC_Sir2                       | Lamassu-Fam__LmuB_SMC_Sir2                       | Lamassu-Fam            | Custom                  | 20     |",
        "notes": "The pinned DefenseFinder HMM inventory records a Lamassu-Fam__LmuB_SMC_Sir2 custom profile that is not the LmuB SMC profile named by the pinned Lamassu-Sir2 rule row."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| Lamassu-Fam__LmuC_acc_Sir2                       | Lamassu-Fam__LmuC_acc_Sir2                       | Lamassu-Fam            | Custom                  | 20     |",
        "notes": "The pinned DefenseFinder HMM inventory records a Lamassu-Fam__LmuC_acc_Sir2 custom profile that is not the LmuC accessory profile named by the pinned Lamassu-Sir2 rule row."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "Lamassu-Fam\tLamassu-Sir2\t2\t2\tLamassu-Fam__LmuA_effector_Sir2, Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II\tLamassu-Fam__LmuC_acc_Lipase\tLamassu-Fam__LmuA_effector_Amidase, Lamassu-Fam__LmuA_effector_Cap4_nuclease, Lamassu-Fam__LmuA_effector_Cap4_nuclease_II, Lamassu-Fam__LmuA_effector_FMO, Lamassu-Fam__LmuA_effector_Hydrolase, Lamassu-Fam__LmuA_effector_Lipase, Lamassu-Fam__LmuA_effector_Mrr, Lamassu-Fam__LmuA_effector_PDDEXK, Lamassu-Fam__LmuA_effector_Protease, Lamassu-Fam__LmuA_effector_hypothetical\t",
        "notes": "The pinned DefenseFinder rules table models Lamassu-Sir2 as a Lamassu-Fam subsystem requiring Lamassu-Fam__LmuA_effector_Sir2 and Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II, with Lamassu-Fam__LmuC_acc_Lipase as an accessory profile."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "lamassu_sir2_locus_subtype_defense",
        "title": "Lamassu-Sir2 is a DefenseFinder Lamassu subtype",
        "description": "Conservative subtype-level classification linking the DefenseFinder Lamassu-Sir2 rule-row definition to Lamassu-Sir2 system possession and its Lamassu parent.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Lamassu-Sir2 as a DefenseFinder rule-row subtype of Lamassu system possession without asserting a Lamassu-Sir2-specific antiphage process, exact phage-triggered Sir2 effector activity, viral-DNA trigger, LmuC requirement, native host breadth, cell-death output, or whether every DefenseFinder Lamassu-Sir2 prediction is a complete experimentally active locus.",
        "nodes": [
          {
            "node_id": "lamassu_sir2_system_trait",
            "label": "Lamassu-Sir2 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000566",
            "description": "Possession of a genome-encoded Lamassu-Sir2 phage-defense system."
          },
          {
            "node_id": "lamassu_system_trait",
            "label": "Lamassu system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000232",
            "description": "Possession of a genome-encoded Lamassu phage-defense system."
          }
        ],
        "edges": [
          {
            "subject": "lamassu_sir2_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "lamassu_system_trait",
            "description": "Lamassu-Sir2 system possession is a Lamassu-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| Lamassu-Fam | 10\\.1101/2022\\.05\\.11\\.491447 | An expanding arsenal of immune systems that protect bacteria from phages | ",
                "notes": "The pinned DefenseFinder article registry maps the Lamassu-Fam model namespace to a bacterial immune-systems preprint."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "Lamassu-Fam\tLamassu-Sir2\t2\t2",
                "notes": "The pinned DefenseFinder rules table places the Lamassu-Sir2 subsystem under the Lamassu-Fam system key with 2 mandatory matches and 2 genes required."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "lamassu-sir2-activity-gap",
        "prompt": "Resolve Lamassu-Sir2 phage triggers, native hosts, Sir2 effector activity, LmuC usage, and profile-to-activity criteria before minting enzyme, trigger, or component children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Haudiquet et al. support a Lamassu family with diverse LmuA effectors and a conserved SMC-like sensor, and the pinned DefenseFinder HMM inventory and rules table support Lamassu-Sir2 as a Lamassu-Fam subtype whose rule row requires Lamassu-Fam__LmuA_effector_Sir2 and Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II. This first-pass record follows the rule row but leaves exact Sir2 effector activity, the rule row's relationship to Sir2-scoped LmuB/LmuC HMM rows, LmuC requirement, native hosts, phage triggers, cell-death output, and profile-to-activity criteria unresolved.",
        "evidence": [
          {
            "reference": "DOI:10.1073/pnas.2519643122",
            "snippet": "a bacterial immune system family featuring diverse effectors but a core conserved SMC-like sensor",
            "notes": "Haudiquet et al. support placing Lamassu subtypes under a Lamassu family with diverse LmuA effectors and a conserved SMC-like sensor."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| Lamassu-Fam__LmuA_effector_Sir2                  | Lamassu-Fam__LmuA_effector_Sir2                  | Lamassu-Fam            | Custom                  | 20     |",
            "notes": "The pinned DefenseFinder HMM inventory records the Lamassu-Fam__LmuA_effector_Sir2 custom profile listed as mandatory by the Lamassu-Sir2 rule row."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| Lamassu-Fam__LmuB_SMC_Sir2                       | Lamassu-Fam__LmuB_SMC_Sir2                       | Lamassu-Fam            | Custom                  | 20     |",
            "notes": "The pinned DefenseFinder HMM inventory records a Lamassu-Fam__LmuB_SMC_Sir2 custom profile that is not the LmuB SMC profile named by the pinned Lamassu-Sir2 rule row."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| Lamassu-Fam__LmuC_acc_Sir2                       | Lamassu-Fam__LmuC_acc_Sir2                       | Lamassu-Fam            | Custom                  | 20     |",
            "notes": "The pinned DefenseFinder HMM inventory records a Lamassu-Fam__LmuC_acc_Sir2 custom profile that is not the LmuC accessory profile named by the pinned Lamassu-Sir2 rule row."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "snippet": "Lamassu-Fam\tLamassu-Sir2\t2\t2\tLamassu-Fam__LmuA_effector_Sir2, Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II\tLamassu-Fam__LmuC_acc_Lipase\tLamassu-Fam__LmuA_effector_Amidase, Lamassu-Fam__LmuA_effector_Cap4_nuclease, Lamassu-Fam__LmuA_effector_Cap4_nuclease_II, Lamassu-Fam__LmuA_effector_FMO, Lamassu-Fam__LmuA_effector_Hydrolase, Lamassu-Fam__LmuA_effector_Lipase, Lamassu-Fam__LmuA_effector_Mrr, Lamassu-Fam__LmuA_effector_PDDEXK, Lamassu-Fam__LmuA_effector_Protease, Lamassu-Fam__LmuA_effector_hypothetical\t",
            "notes": "The pinned DefenseFinder rules table models Lamassu-Sir2 as a Lamassu-Fam subsystem requiring Lamassu-Fam__LmuA_effector_Sir2 and Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II, with Lamassu-Fam__LmuC_acc_Lipase as an accessory profile."
          }
        ],
        "attaches_to": [
          "causal_graphs#lamassu_sir2_locus_subtype_defense"
        ],
        "posed_by": "codex",
        "posed_date": "2026-10-03"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-03T06:34:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Lamassu-Sir2 system as a DefenseFinder-backed GENOMICS TraitRecord under the Lamassu system parent after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record for the target local ID, placeholder METPO ID, proposal cohort, record slug, human label, or DefenseFinder subsystem; existing Lamassu-Fam__LmuA_effector_Sir2 mentions were limited to forbidden-profile evidence on neighboring Lamassu-Fam subtypes, their earlier writer scripts, and rendered pages, and the replacement placeholder is reserved in proposals/metpo_traitmech_v443.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-03T06:34:02Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed Lamassu-Sir2 system during initial curation and left canonical_examples empty because the pinned DefenseFinder tables support a rule-row subtype but not an accession-backed native microbial taxon exemplar tied to the Lamassu-Sir2 profiles and experimentally verified endogenous activity. No paid research was used.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-03T06:56:28Z",
        "curator": "codex",
        "action": "EXPANDED_EVIDENCE",
        "changes": "Addressed adversarial review issue #1604 by adding exact evidence for the Sir2-scoped Lamassu-Fam__LmuB_SMC_Sir2 and Lamassu-Fam__LmuC_acc_Sir2 HMM rows so the unresolved relationship between those rows and the generic LmuB/LmuC rows named by the Lamassu-Sir2 rule is auditable on the Lamassu-Sir2 record itself.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000569",
    "label": "Lamassu-SMEK system",
    "definition": "A Lamassu system in which an organism possesses a locus encoding an LmuA effector with a SMEK domain, an SMC-like LmuB sensor, and LmuC.",
    "definition_source": "DOI:10.1073/pnas.2519643122",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000572"
    ],
    "synonyms": [
      {
        "synonym_text": "Lamassu_SMEK",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/definitions/DefenseFinder/Lamassu-Fam/Lamassu_SMEK.xml"
      },
      {
        "synonym_text": "Lamassu/Lamassu/Lamassu_SMEK",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://pmc-oa-opendata.s3.amazonaws.com/PMC12663957.1/pnas.2519643122.sd01.xlsx"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1073/pnas.2519643122",
        "snippet": "others are type-specific like the flavin-containing monooxygenase (FMO) for long Lamassu, and HNH, SMEK, and Lipase for short Lamassu.",
        "notes": "Results, effector-diversity paragraph: 'others' refers to LmuA effector types. The paper recognizes SMEK-bearing Lamassu and describes it as short-specific. Dataset S1 nevertheless contains one long-profile SMEK-system call; that annotation discrepancy is not resolved by treating the detector as experimental evidence."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/definitions/DefenseFinder/Lamassu-Fam/Lamassu_SMEK.xml",
        "snippet": "<model inter_gene_max_space=\"1\" min_mandatory_genes_required=\"3\" min_genes_required=\"3\" vers=\"2.0\">",
        "notes": "The executable model requires three mandatory components and permits at most one intervening gene between components."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/definitions/DefenseFinder/Lamassu-Fam/Lamassu_SMEK.xml",
        "snippet": "<gene name=\"Lamassu__LmuA_SMEK\" presence=\"mandatory\"/>",
        "notes": "SMEK-bearing LmuA is mandatory, without an exchangeable effector. Other named LmuA effector profiles are forbidden by separate blocks. An isolated SMEK-domain or profile hit does not establish this trait."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/definitions/DefenseFinder/Lamassu-Fam/Lamassu_SMEK.xml",
        "snippet": "<gene name=\"Lamassu__LmuB_Long\" presence=\"mandatory\">\n<exchangeables>\n<gene name=\"Lamassu__LmuB_Short\"/>\n</exchangeables>\n</gene>",
        "notes": "The detector accepts either long or short LmuB. This permissiveness does not prove biological function in either clade. The trait definition follows the shared architecture without a length restriction."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/definitions/DefenseFinder/Lamassu-Fam/Lamassu_SMEK.xml",
        "snippet": "<gene name=\"Lamassu__LmuC_Clade_I\" presence=\"mandatory\">",
        "notes": "LmuC is mandatory, with Clade II-VII and MC1-MC8 exchangeable profiles. There are no accessory components in this executable XML."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC12663957.1/pnas.2519643122.sd01.xlsx",
        "snippet": "ACJU001.0722.00009.C001\tACJU001.0722.00009.C001_01299\tLamassu__LmuB_Short\nACJU001.0722.00009.C001\tACJU001.0722.00009.C001_01300\tLamassu__LmuC_Clade_VI\nACJU001.0722.00009.C001\tACJU001.0722.00009.C001_01301\tLamassu__LmuA_SMEK",
        "notes": "Dataset S1, S3_Lamassu_Detection!A165:C167, raw cells in column order. Columns E, F, I and M identify one Lamassu/Lamassu/Lamassu_SMEK call, ACJU001.0722.00009.C001_Lamassu_SMEK_36, with sys_wholeness 1.0 and three mandatory hits. This is computational evidence of the complete architecture, not experimental antiviral activity."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC12663957.1/pnas.2519643122.sd01.xlsx",
        "snippet": "ACJU001.0722.00009.C001\tGCF_021491935.1\tBacteria\tProteobacteria\tAcinetobacter junii\tNZ_CP090890",
        "notes": "Dataset S1, S2_Genomes!A1383:F1383, raw cells linking the SMEK-system replicon to assembly GCF_021491935.1 and its species. The historical phylum name is retained only inside this source quote."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC12663957.1/pnas.2519643122.sd01.xlsx",
        "snippet": "Lamassu__LmuB_Long\nLamassu__LmuC_Clade_VII\nLamassu__LmuA_SMEK\nLamassu__LmuB_Long",
        "notes": "Dataset S1, S3_Lamassu_Detection!C6042:C6045, raw cells for HAAN001.0722.00001.C001_Lamassu_SMEK_499. Column F assigns these four rows to one call, including two distinct long-profile LmuB hits. Across the sheet, 125 unique SMEK system IDs comprise 124 calls with short LmuB and this one call with long LmuB; these sets do not overlap. Component-row counts are not system counts. The long-profile call is an annotation exception needing review, not a validated biological long-Lamassu SMEK subtype."
      },
      {
        "reference": "https://api.ncbi.nlm.nih.gov/datasets/v2/genome/accession/GCF_021491935.1/dataset_report",
        "snippet": "\"tax_id\":40215,\"organism_name\":\"Acinetobacter junii\",\"infraspecific_names\":{\"strain\":\"WCO-9\"}",
        "notes": "NCBI Datasets assembly report, verified 2026-10-03: resolves GCF_021491935.1 to taxon 40215 and strain WCO-9. This source verifies identity only; Dataset S1 supports system possession."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:40215",
        "taxon_label": "Acinetobacter junii",
        "note": "Computational genomic example: strain WCO-9, assembly GCF_021491935.1, study replicon ACJU001.0722.00009.C001. Dataset S1 S3_Lamassu_Detection rows 165-167 record a complete short-LmuB, LmuC and SMEK-LmuA call; S2_Genomes row 1383 links it to the assembly. NCBI resolves the strain and taxon. This does not establish experimentally measured antiviral activity in WCO-9 or species-wide possession.",
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC12663957.1/pnas.2519643122.sd01.xlsx"
      }
    ],
    "discussions": [
      {
        "discussion_id": "lamassu-smek-function-and-annotation-scope",
        "prompt": "Resolve the long-profile exception and validate SMEK-system function.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "The paper describes SMEK as short-Lamassu-specific, while Dataset S1 has 124 short-profile calls and one long-profile call with two distinct LmuB hits. The pinned model accepts both lengths. Reconcile that exceptional call with phylogeny and locus context before claiming a biological long-LmuB subtype or short-only distribution. The definition therefore captures architecture without a length restriction. The pinned legacy summary TSV and HMM inventory lack SMEK entries although the executable model and SMEK profile exist. This whole-system trait is not equivalent to DS-27 (traitmech:000451), whose existing definition denotes a single-gene transcriptional unit with the working label SMEK. No DS-27 assay phenotype or exact synonym is transferred. SMEK-specific Lamassu antiviral validation, substrates, activation order, domain-name expansion and accession-level protein mechanisms remain unresolved. Cap4 and Lipase experiments do not establish SMEK chemistry. No causal graph is asserted from these computational architecture calls alone. The direct parent is now traitmech:000572 Lamassu type II system because this definition already includes LmuC. This component-based refinement neither resolves the long-profile exception nor restricts the trait to short Lamassu, and does not confer experimental validation on the computational calls.",
        "posed_by": "codex",
        "posed_date": "2026-10-03"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-03T11:15:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added the literature-recognized Lamassu-SMEK architecture using DOI, pinned executable-model, Dataset S1 and NCBI identity evidence with exact snippets. Distinguished 125 system calls from 377 component rows and recorded the long-profile exception. Kept the WCO-9 example computational and rejected equivalence to DS-27. Ignored-and-hidden searches found no exact record or METPO term. Reserved METPO:1052300 in proposals/metpo_traitmech_v446.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-03T15:14:27Z",
        "curator": "codex",
        "action": "ADD_TYPE_II_PARENT",
        "changes": "Linked traitmech:000572 Lamassu type II system using the LmuC-containing classification in DOI:10.1093/nar/gkab883. Preserved biological definitions, evidence, examples and length-family distinctions. Historical proposal parent axioms remain true; v449 documents the additional subclass relations for upstream minting. This is not new experimental validation.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000232",
    "label": "Lamassu system",
    "definition": "A phage defense system in which an organism possesses a Lamassu locus built around a conserved SMC-like LmuB sensor paired with a modular LmuA effector and subfamily-specific partner architecture, enabling viral-DNA sensing and effector-mediated antiviral activity.",
    "definition_source": "DOI:10.1073/pnas.2519643122",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "Lamassu",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1073/pnas.2519643122"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1126/science.aar4120",
        "snippet": "Lamassu LmuAB pfam14130, pfam02463 SMC ATPase N-terminal domain 697 682 (1.3%)",
        "notes": "Doron et al. reported Lamassu/LmuAB as an SMC-ATPase-linked system in their pangenome-scale antiphage-system discovery screen."
      },
      {
        "reference": "DOI:10.1073/pnas.2519643122",
        "snippet": "Lamassu is a widespread antiviral system in bacteria that uses structural maintenance of chromosomes-like proteins",
        "notes": "Haudiquet et al. support defining Lamassu as a recurring bacterial antiviral system with an SMC-like component."
      },
      {
        "reference": "DOI:10.1073/pnas.2519643122",
        "snippet": "a bacterial immune system family featuring diverse effectors but a core conserved SMC-like sensor",
        "notes": "Haudiquet et al. support placing Lamassu at the family level rather than defining a single effector subtype."
      },
      {
        "reference": "DOI:10.1073/pnas.2519643122",
        "snippet": "It comprises LmuB, an SMC-like protein, LmuC, a small protein with a domain of unknown function, and LmuA",
        "notes": "Haudiquet et al. support the LmuA/LmuB/LmuC composition of the structurally characterized Lamassu Vc-Cap4 branch."
      },
      {
        "reference": "DOI:10.1073/pnas.2519643122",
        "snippet": "Lamassu specifically senses dsDNA ends in vitro and phage replication origins in vivo",
        "notes": "Haudiquet et al. connect Lamassu to direct DNA-end and phage replication origin sensing."
      },
      {
        "reference": "DOI:10.1073/pnas.2519643122",
        "snippet": "triggering the formation of LmuA tetramers that activate its Cap4 nuclease domain",
        "notes": "Haudiquet et al. connect viral-DNA sensing to LmuA tetramer formation and Cap4 nuclease-domain activation in Lamassu Vc-Cap4."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:666",
        "taxon_label": "Vibrio cholerae",
        "note": "Haudiquet et al. structurally characterized the Vibrio cholerae Lamassu Vc-Cap4 system and connected its LmuABC complex to dsDNA-end sensing and LmuA Cap4 nuclease-domain activation.",
        "reference": "DOI:10.1073/pnas.2519643122"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "lamassu_smc_dna_sensing_nuclease_activation",
        "title": "Lamassu SMC-like complexes activate LmuA antiviral effectors",
        "description": "Evidence-backed process sketch linking a Lamassu locus to LmuABC complex formation, viral DNA sensing, LmuA effector activation, and inhibition of bacteriophage infection.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures the structurally characterized Lamassu Vc-Cap4 system without asserting one exact effector domain, LmuC requirement, LmuB clade, zinc-hook architecture, viral DNA cue, cell-death output, or phage breadth across all Lamassu loci.",
        "nodes": [
          {
            "node_id": "lamassu_locus",
            "label": "Lamassu locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A Lamassu antiviral locus built around an SMC-like LmuB core and a cognate LmuA effector."
          },
          {
            "node_id": "lmuabc_complex_assembly",
            "label": "LmuABC complex assembly",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Assembly of LmuA, SMC-like LmuB, and LmuC into a Lamassu Vc-Cap4 complex."
          },
          {
            "node_id": "lamassu_viral_dna_sensing",
            "label": "Lamassu viral DNA sensing",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Lamassu-mediated sensing of viral double-stranded DNA ends or phage replication origins."
          },
          {
            "node_id": "lmuA_effector_activation",
            "label": "LmuA effector activation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Oligomerization-dependent activation of a LmuA effector nuclease domain."
          },
          {
            "node_id": "phage_infection",
            "label": "phage infection",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Bacteriophage infection and propagation inside a bacterial host cell."
          },
          {
            "node_id": "lamassu_system_trait",
            "label": "Lamassu system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000232",
            "description": "Possession of a genome-encoded Lamassu phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "lamassu_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "lmuabc_complex_assembly",
            "description": "The characterized Lamassu Vc-Cap4 locus encodes LmuA, SMC-like LmuB, and LmuC components.",
            "evidence": [
              {
                "reference": "DOI:10.1073/pnas.2519643122",
                "snippet": "It comprises LmuB, an SMC-like protein, LmuC, a small protein with a domain of unknown function, and LmuA",
                "notes": "Haudiquet et al. support the LmuABC composition of the Lamassu Vc-Cap4 branch."
              }
            ]
          },
          {
            "subject": "lmuabc_complex_assembly",
            "predicate": "enables",
            "predicate_id": "RO:0002327",
            "object": "lamassu_viral_dna_sensing",
            "description": "Lamassu complexes bind double-stranded DNA and sense DNA ends or phage replication origins.",
            "evidence": [
              {
                "reference": "DOI:10.1073/pnas.2519643122",
                "snippet": "Lamassu specifically senses dsDNA ends in vitro and phage replication origins in vivo",
                "notes": "Haudiquet et al. connect Lamassu to direct viral-DNA-associated sensing."
              }
            ]
          },
          {
            "subject": "lamassu_viral_dna_sensing",
            "predicate": "activates",
            "predicate_id": "RO:0002213",
            "object": "lmuA_effector_activation",
            "description": "Lamassu viral-DNA sensing triggers LmuA tetramer formation and Cap4 nuclease-domain activation.",
            "evidence": [
              {
                "reference": "DOI:10.1073/pnas.2519643122",
                "snippet": "triggering the formation of LmuA tetramers that activate its Cap4 nuclease domain",
                "notes": "Haudiquet et al. connect Lamassu DNA sensing to LmuA Cap4 nuclease-domain activation."
              }
            ]
          },
          {
            "subject": "lmuA_effector_activation",
            "predicate": "mitigates",
            "predicate_id": "METPO:2007407",
            "object": "phage_infection",
            "description": "Lamassu effector activation helps halt phage infection in the bacterial host.",
            "evidence": [
              {
                "reference": "DOI:10.1073/pnas.2519643122",
                "snippet": "Lamassu is a widespread antiviral system in bacteria that uses structural maintenance of chromosomes-like proteins, typically associated with chromosome maintenance, to detect and halt phage infection",
                "notes": "Haudiquet et al. support coupling Lamassu SMC-like detection to inhibition of phage infection."
              }
            ]
          },
          {
            "subject": "lmuA_effector_activation",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "lamassu_system_trait",
            "description": "Viral-DNA-triggered LmuA effector activation realizes the Lamassu system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1073/pnas.2519643122",
                "snippet": "a bacterial immune system family featuring diverse effectors but a core conserved SMC-like sensor",
                "notes": "Haudiquet et al. support the shared SMC-like sensor and diverse effector logic of Lamassu immunity."
              }
            ]
          },
          {
            "subject": "lamassu_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Lamassu system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.aar4120",
                "snippet": "Lamassu LmuAB pfam14130, pfam02463 SMC ATPase N-terminal domain 697 682 (1.3%)",
                "notes": "Doron et al. reported Lamassu in a table of candidate antiphage defense systems."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "lamassu-subtype-and-effector-gap",
        "prompt": "Resolve Lamassu subtype architecture, effector diversity, and viral-DNA trigger specificity before minting narrower Lamassu mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Haudiquet et al. support a structurally characterized Vibrio cholerae Lamassu Vc-Cap4 system with LmuABC DNA-end sensing and LmuA Cap4 nuclease activation, and the pinned DefenseFinder tables model Lamassu-Amidase, Lamassu-Cap4_nuclease, Lamassu-FMO, Lamassu-Hydrolase, Lamassu-Lipase, Lamassu-Mrr, Lamassu-PDDEXK, Lamassu-Protease, Lamassu-Sir2, and other Lamassu-Fam subtypes as rule-row variants. Lamassu-Amidase, Lamassu-Cap4 nuclease, Lamassu-FMO, Lamassu-Hydrolase, Lamassu-Lipase, Lamassu-Mrr, Lamassu-PDDEXK, Lamassu-Protease, and Lamassu-Sir2 now capture nine DefenseFinder rule-row subtypes, but long-versus-short LmuB clades, LmuC-independent subfamilies, the Lamassu-Fam base, Lamassu-Hydrolase_Protease, and Lamassu-Hypothetical rule rows, viral-DNA triggers, exact LmuA effector substrates, FMO acronym expansion, the Lamassu-FMO rule row's relationship to FMO-scoped LmuB/LmuC HMM rows, the Lamassu-Lipase rule row's relationship to its Lipase-scoped LmuB HMM row, the Lamassu-Mrr rule row's relationship to Mrr-scoped LmuB/LmuC HMM rows, the Lamassu-PDDEXK rule row's relationship to PDDEXK-scoped LmuB/LmuC HMM rows, the Lamassu-Sir2 rule row's relationship to Sir2-scoped LmuB/LmuC HMM rows, and cell-death outputs across Lamassu loci remain unresolved. Lamassu Hydrolase-Protease system (traitmech:000567) now captures the literature-supported paired architecture with LmuB and LmuC. Its pinned executable XML requires four components, whereas the summary TSV requires three matches and calls LmuC accessory. The existing table-defined Lamassu-Hydrolase and Lamassu-Protease siblings each forbid the other's effector profile and are not exact matches to this paired architecture. Reconciling the legacy table-based sibling definitions with executable models remains open; do not interpret the summary's profile labels as current executable model requirements. Lamassu-HNH system (traitmech:000568) now captures the literature-supported short-LmuB architecture with HNH-domain LmuA and LmuC. The published dataset supplies complete computational genome calls, not HNH-specific functional validation. The pinned executable HNH model accepts either long or short LmuB, whereas all HNH calls in that dataset use short LmuB; its software key is therefore not an exact synonym for this biological scope. HNH-specific activity, substrates, and activation remain unresolved. Lamassu-SMEK system (traitmech:000569) now captures a locus with SMEK-domain LmuA, LmuB, and LmuC. The paper describes SMEK as short-specific, but its dataset contains 124 short-profile system calls and one long-profile call; the latter requires reconciliation before asserting a biological long-LmuB subtype. The definition therefore does not impose a LmuB-length restriction. The three-component architecture is not equivalent to the single-gene DS-27 system that also uses SMEK as a working label. SMEK-specific functional validation and chemistry remain unresolved. Short Lamassu system (traitmech:000570) now captures the short-LmuB phylogenetic and structural family, not a fixed protein-length bin or an effector-specific detector. Lamassu-HNH is placed below it because its existing definition explicitly requires short-form LmuB. SMEK remains directly under the broader Lamassu parent because of its unresolved long-profile exception. The short family permits the reported LmuC-loss and effector-domain-loss architectures; type I is not an exact synonym for the whole short family. The Lamassu-Hypothetical registry label is not accepted as a separate biological trait here: unknown annotation does not establish effector-domain loss, and its relationship to the paper's clade O still needs explicit mapping. The long family and component-number subtypes remain separate discovery leads. Long Lamassu system (traitmech:000571) now captures the complementary long-LmuB phylogenetic and structural family, not an 800-residue cutoff or a particular effector model. The paper assigns the B. cereus B4077 Hydrolase-Protease system to this family, but that effector architecture also occurs in short Lamassu, so the whole Hydrolase-Protease trait is not reparented. The legacy table-defined FMO trait still needs model and biological-scope reconciliation before assigning the entire record to the long family. SMEK's exception remains unresolved. Raw detection gene_name hits must not be confused with exchangeable hit_gene_ref model slots, and ambiguous loci need phylogenetic classification. Component-number type I/II traits remain separate discovery leads. Lamassu type II system (traitmech:000572) now captures the LmuC-containing component architecture defined by Payne et al. (DOI:10.1093/nar/gkab883) and independently used by Li et al. (DOI:10.1038/s41589-025-02102-z). HNH, SMEK and Hydrolase-Protease already require LmuC in their definitions and now have this parent; HNH retains its short-family parent too. This does not assert a three-gene count, universal LmuC essentiality, or new antiviral validation of those children. Long/short families and legacy detector rows are not equivalent to this component class. Type I and family-wide mechanisms remain open discovery and curation questions. Lamassu type I system (traitmech:000573) now resolves the component-class discovery lead: Haudiquet et al. explicitly identify the LmuC-loss architecture as type I, and Li et al. independently study a type-I LmuA/LmuB complex. This is not equivalent to all short Lamassu or proof that every failed LmuC hit is biological absence. No existing effector-defined child is reparented. Family-wide mechanisms, legacy model reconciliation and native-host activity remain open.",
        "posed_by": "codex",
        "posed_date": "2026-09-15"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-15T23:14:40Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Lamassu system as a DOI-backed GENOMICS TraitRecord under the phage defense system parent after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v109.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-02T21:43:25Z",
        "curator": "codex",
        "action": "TRACK_NARROWER_RECORD",
        "changes": "Documented Lamassu-Amidase as split out in the open Lamassu subtype-effector discussion after minting traitmech:000556 for the DefenseFinder-backed Lamassu-Amidase child; remaining Lamassu-Fam subtypes and finer Lamassu activation mechanisms remain open.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-02T22:16:25Z",
        "curator": "codex",
        "action": "TRACK_NARROWER_RECORD",
        "changes": "Documented Lamassu-Cap4 nuclease as split out in the open Lamassu subtype-effector discussion after minting traitmech:000557 for the DefenseFinder-backed Lamassu-Cap4_nuclease child; remaining Lamassu-Fam subtypes and finer Lamassu activation mechanisms remain open.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-02T23:11:38Z",
        "curator": "codex",
        "action": "TRACK_NARROWER_RECORD",
        "changes": "Documented Lamassu-FMO as split out in the open Lamassu subtype-effector discussion after minting traitmech:000558 for the DefenseFinder-backed Lamassu-FMO child; the first-pass record follows the pinned rule row while tracking its non-FMO-specific LmuB/LmuC profile names as unresolved; remaining Lamassu-Fam subtypes and finer Lamassu activation mechanisms remain open.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-03T03:10:01Z",
        "curator": "codex",
        "action": "TRACK_NARROWER_RECORD",
        "changes": "Documented Lamassu-Hydrolase as split out in the open Lamassu subtype-effector discussion after minting traitmech:000561 for the DefenseFinder-backed Lamassu-Hydrolase child; remaining Lamassu-Fam subtypes and finer Lamassu activation mechanisms remain open.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-03T03:48:01Z",
        "curator": "codex",
        "action": "TRACK_NARROWER_RECORD",
        "changes": "Documented Lamassu-Lipase as split out in the open Lamassu subtype-effector discussion after minting traitmech:000562 for the DefenseFinder-backed Lamassu-Lipase child; the first-pass record follows the pinned rule row while tracking its non-Lipase-specific LmuB profile name as unresolved; remaining Lamassu-Fam subtypes and finer Lamassu activation mechanisms remain open.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-03T04:26:01Z",
        "curator": "codex",
        "action": "TRACK_NARROWER_RECORD",
        "changes": "Documented Lamassu-Mrr as split out in the open Lamassu subtype-effector discussion after minting traitmech:000563 for the DefenseFinder-backed Lamassu-Mrr child; the first-pass record follows the pinned rule row while tracking its non-Mrr-specific LmuB/LmuC profile names as unresolved; remaining Lamassu-Fam subtypes and finer Lamassu activation mechanisms remain open.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-03T05:05:01Z",
        "curator": "codex",
        "action": "TRACK_NARROWER_RECORD",
        "changes": "Documented Lamassu-PDDEXK as split out in the open Lamassu subtype-effector discussion after minting traitmech:000564 for the DefenseFinder-backed Lamassu-PDDEXK child; the first-pass record follows the pinned rule row while tracking its non-PDDEXK-specific LmuB/LmuC profile names as unresolved; remaining Lamassu-Fam subtypes and finer Lamassu activation mechanisms remain open.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-03T05:46:01Z",
        "curator": "codex",
        "action": "TRACK_NARROWER_RECORD",
        "changes": "Documented Lamassu-Protease as split out in the open Lamassu subtype-effector discussion after minting traitmech:000565 for the DefenseFinder-backed Lamassu-Protease child; remaining Lamassu-Fam rule rows and finer Lamassu activation mechanisms remain open.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-03T06:34:01Z",
        "curator": "codex",
        "action": "TRACK_NARROWER_RECORD",
        "changes": "Documented Lamassu-Sir2 as split out in the open Lamassu subtype-effector discussion after minting traitmech:000566 for the DefenseFinder-backed Lamassu-Sir2 child; remaining Lamassu-Fam rule rows and finer Lamassu activation mechanisms remain open.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-03T09:29:00Z",
        "curator": "codex",
        "action": "TRACK_NARROWER_RECORD",
        "changes": "Linked traitmech:000567 Lamassu Hydrolase-Protease system and documented disagreement between executable models and legacy tables; retained remaining subtype and mechanism gaps.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-03T10:35:00Z",
        "curator": "codex",
        "action": "TRACK_NARROWER_RECORD",
        "changes": "Linked traitmech:000568 Lamassu-HNH system and distinguished its short-LmuB genomic architecture from the broader executable detector. Retained HNH-specific functional-validation gaps.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-03T11:15:00Z",
        "curator": "codex",
        "action": "TRACK_NARROWER_RECORD",
        "changes": "Linked traitmech:000569 Lamassu-SMEK system; documented the long-profile dataset exception and distinction from the single-gene DS-27 SMEK working label. Retained function gaps.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-03T12:33:00Z",
        "curator": "codex",
        "action": "TRACK_NARROWER_RECORD",
        "changes": "Linked traitmech:000570 short Lamassu system and the HNH parent refinement; retained the SMEK length exception and rejected unproven equivalence of a Hypothetical label to effector-domain loss.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-03T14:29:24Z",
        "curator": "codex",
        "action": "TRACK_NARROWER_RECORD",
        "changes": "Linked traitmech:000571 long Lamassu system and recorded why Hydrolase-Protease, FMO and SMEK are not automatically reparented. Retained component-classification and family-mechanism gaps.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-03T15:14:27Z",
        "curator": "codex",
        "action": "TRACK_TYPE_II_CLASS",
        "changes": "Linked traitmech:000572 Lamassu type II system using the LmuC-containing classification in DOI:10.1093/nar/gkab883. Preserved biological definitions, evidence, examples and length-family distinctions. Historical proposal parent axioms remain true; v449 documents the additional subclass relations for upstream minting. This is not new experimental validation.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-03T15:57:07Z",
        "curator": "codex",
        "action": "TRACK_TYPE_I_CLASS",
        "changes": "Linked traitmech:000573 Lamassu type I system to the existing component-architecture discussion using DOI:10.1073/pnas.2519643122 and DOI:10.1038/s41589-025-02102-z. Preserved all definitions, parents, evidence, examples and prior history. Component absence, LmuB-length family and experimental activity remain separate claims.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000573",
    "label": "Lamassu type I system",
    "definition": "A Lamassu system in which an organism possesses a locus encoding the LmuA effector and SMC-like LmuB sensor but no LmuC component.",
    "definition_source": "DOI:10.1073/pnas.2519643122",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000232"
    ],
    "synonyms": [
      {
        "synonym_text": "type I Lamassu",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1073/pnas.2519643122"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1073/pnas.2519643122",
        "snippet": "We observed loss of LmuC in a specific clade (Clade S, Fig. 1B), an architecture previously called type I Lamassu shown to be antiphage",
        "notes": "Results, effector-diversity paragraph: Haudiquet et al. explicitly identify the LmuC-loss architecture as type I. Clade S occurs in their short-Lamassu phylogeny, but this does not make type I equivalent to the whole short family or establish a universal protein-length cutoff. Clade O's LmuA effector-domain loss is a different observation."
      },
      {
        "reference": "DOI:10.1038/s41589-025-02102-z",
        "snippet": "the type-I Lamassu complex from Bacillus cellulasensis and the type-II Lamassu complex from Vibrio cholerae",
        "notes": "Abstract: Li et al. independently distinguish the two source-qualified complexes. The associated 9UX7 deposition identifies the type-I source as Bacillus sp. nio-1130, NCBITaxon:1761765. Retain the issuing authority's current label rather than asserting species-name equivalence from the abstract. One studied nuclease mechanism is not a universal mechanism for every type-I effector."
      },
      {
        "reference": "https://rest.uniprot.org/uniprotkb/P0DW44.json",
        "snippet": "Component of antiviral defense system Lamassu type I, composed of LmuA and LmuB.",
        "notes": "Reviewed P0DW44, entry version 8, retrieved 2026-10-03: the FUNCTION annotation identifies the LmuA/LmuB system in the NIO-1130 source strain (taxon 1761765), citing PMID:29371424. Its protection assays were heterologous expression in B. subtilis BEST7003, not native-host assays. The source organism and expression host are not interchangeable."
      },
      {
        "reference": "https://data.rcsb.org/rest/v1/core/polymer_entity/9UX7/1",
        "snippet": "\"pdbx_gene_src_ncbi_taxonomy_id\":\"1761765\",\"pdbx_gene_src_scientific_name\":\"Bacillus sp. nio-1130\"",
        "notes": "PDB 9UX7 entity 1 independently records the LmuB source taxon and maps the sequence to P0DW44. The separate expression host is E. coli. The deposited 562-residue length is not a type-I membership threshold; absence of a component from a purified structure alone would not establish genomic absence."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1761765",
        "taxon_label": "Bacillus sp. nio-1130",
        "reference": "https://rest.uniprot.org/uniprotkb/P0DW44.json",
        "note": "NIO-1130 is the source strain of the reviewed LmuB entry P0DW44 explicitly annotated as part of Lamassu type I. PDB 9UX7 entity 1 independently identifies the same source taxon; NCBI confirms this exact current label. The example denotes source-strain possession, not native-host resistance. The cited defense assays used B. subtilis BEST7003 and structural expression used E. coli. The paper's B. cellulasensis name is not asserted as a taxonomic synonym or species-wide trait."
      }
    ],
    "discussions": [
      {
        "discussion_id": "lamassu-type-i-absence-and-mechanism-scope",
        "prompt": "Resolve type-I architecture and mechanism without inferring absence from missing hits.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Type I denotes the literature-supported LmuA/LmuB architecture without LmuC, not an isolated LmuB hit, a failed LmuC detector call, an incomplete assembly or a knockout of a type-II locus. Component absence must be established in the biological locus; absence from a purified complex alone is insufficient. The reported clade S is in the short family, but the component definition is not equated with that whole family or a protein length bin. Keep the broad Lamassu parent until wider phylogenetic scope is established; no existing detector-defined effector subtype is reparented from an optional LmuC rule. Type-II loci can coexist in the same genome, so these organism-level possession traits are not asserted disjoint. Source-specific nuclease activity is not generalized to all type-I effectors. A family-wide mechanism, native-host activity and the paper's B. cellulasensis nomenclature relative to current NCBI naming remain unresolved. No causal mechanism graph is asserted.",
        "posed_by": "codex",
        "posed_date": "2026-10-03"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-03T15:57:07Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added the LmuC-lacking Lamassu type-I possession class with two independent primary DOI sources, exact snippets, reviewed UniProt and PDB source metadata, and the NCBI-resolved NIO-1130 example. Ignored-and-hidden searches found no exact record or METPO class. Reserved METPO:1052700 in proposals/metpo_traitmech_v450. Linked existing parent, short-family and type-II discussions without changing their biological definitions or hierarchy.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000572",
    "label": "Lamassu type II system",
    "definition": "A Lamassu system in which an organism possesses a locus with an additional LmuC component alongside the LmuA effector module and SMC-like LmuB sensor.",
    "definition_source": "DOI:10.1093/nar/gkab883",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000232"
    ],
    "synonyms": [
      {
        "synonym_text": "Lamassu type II",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1093/nar/gkab883"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1093/nar/gkab883",
        "snippet": "Similarly, an additional hypothetical protein (LmuC) was identified in about 10.2% of the Lamassu systems detected (371 systems) (Lamassu type II).",
        "notes": "Results: Payne et al. name the LmuC-containing subtype. The quoted frequency belongs to their RefSeq v201 analysis, not universal prevalence. Methods and Figure 3 identify the DSM 9628 source locus and its heterologous phage-protection assays; these do not establish native-host resistance or universal LmuC essentiality."
      },
      {
        "reference": "DOI:10.1038/s41589-025-02102-z",
        "snippet": "the type-I Lamassu complex from Bacillus cellulasensis and the type-II Lamassu complex from Vibrio cholerae",
        "notes": "Abstract: Li et al. report cryo-EM structures for these two source-qualified complexes. This independently supports the type-II category, not species-wide possession, equivalence to a long/short family, or transfer of one nuclease mechanism to all LmuC-containing effector architectures."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1349767",
        "taxon_label": "Janthinobacterium agaricidamnosum NBRC 102515 = DSM 9628",
        "reference": "DOI:10.1093/nar/gkab883",
        "note": "Payne et al. amplified the type-II locus from DSM 9628 genomic DNA (source accession NZ_HG322949.1) and tested it in Escherichia coli BL21-AI. NCBI independently resolves that accession and this strain taxon. The example denotes source-strain possession, not native-host antiviral activity or possession by every member of the species."
      }
    ],
    "discussions": [
      {
        "discussion_id": "lamassu-type-ii-component-and-mechanism-scope",
        "prompt": "Resolve type-II effector diversity and LmuC function without conflating axes.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Type II classifies LmuC-containing Lamassu architecture, not an isolated LmuC hit, a fixed three-gene count, a long-LmuB clade, or a universal LmuC-dependence phenotype. The effector module can include more than one gene. Existing HNH, SMEK and Hydrolase-Protease definitions require LmuC and therefore fall below this class; HNH also retains its short-family parent. This is a definition-based hierarchy inference, not new experimental validation of those children. Legacy detector-defined effector records and the complete long/short families are not reparented merely from model labels or optional LmuC calls. The V. cholerae nuclease mechanism does not establish chemistry for every effector module. Native-host activity, protein accessions and broader mechanistic generalization remain unresolved; no causal mechanism graph is asserted. Type I remains a separate discovery lead. That discovery lead is now represented by traitmech:000573 Lamassu type I system for LmuA/LmuB loci without LmuC. The two component architectures do not establish disjoint organism-level possession classes: one genome could encode both. LmuC absence is not inferred from a missing model hit or a type-II knockout. This record's definition, child classification and unresolved mechanism questions are unchanged.",
        "posed_by": "codex",
        "posed_date": "2026-10-03"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-03T15:14:27Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added the literature-defined LmuC-containing Lamassu class with two independent DOI sources, exact snippets and an NCBI-resolved DSM 9628 possession example. Kept type II distinct from a length family, fixed gene count and universal biochemical mechanism. Ignored-and-hidden searches found no exact record or METPO term. Reserved METPO:1052600 in proposals/metpo_traitmech_v449 and refined three existing LmuC-containing child definitions' hierarchy.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-03T15:57:07Z",
        "curator": "codex",
        "action": "TRACK_TYPE_I_CLASS",
        "changes": "Linked traitmech:000573 Lamassu type I system to the existing component-architecture discussion using DOI:10.1073/pnas.2519643122 and DOI:10.1038/s41589-025-02102-z. Preserved all definitions, parents, evidence, examples and prior history. Component absence, LmuB-length family and experimental activity remain separate claims.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000416",
    "label": "lanthivirin system",
    "definition": "A phage defense system in which an organism possesses a lanthivirin lanthipeptide biosynthetic gene cluster that can confer anti-phage activity in a native Streptomyces context and after heterologous expression of complete lanthivirin systems.",
    "definition_source": "DOI:10.1016/j.chom.2026.06.017",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "lanthivirin BGC",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1016/j.chom.2026.06.017"
      },
      {
        "synonym_text": "Lanthiphage",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1016/j.chom.2026.06.017",
        "snippet": "We demonstrate anti-phage activity both in a native Streptomyces context and through heterologous expression of six distinct lanthivirin systems.",
        "notes": "Serra et al. support native Streptomyces anti-phage activity and activity from multiple heterologously expressed lanthivirin systems."
      },
      {
        "reference": "DOI:10.1016/j.chom.2026.06.017",
        "snippet": "lanthivirin maturation is required for anti-phage activity",
        "notes": "Serra et al. support the requirement for lanthivirin maturation in anti-phage activity."
      },
      {
        "reference": "DOI:10.1016/j.chom.2026.06.017",
        "snippet": "phage-protein-dependent inhibition of phage DNA replication",
        "notes": "Serra et al. link lanthivirins to inhibition of phage DNA replication."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| Lanthiphage | 10\\.1101/2024\\.06\\.26\\.600839 | A family of lanthipeptides with anti-phage function |",
        "notes": "The pinned DefenseFinder article registry maps the Lanthiphage source key to the lanthipeptide anti-phage preprint."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| Lanthiphage__LphA                                |",
        "notes": "The pinned DefenseFinder HMM inventory records Lanthiphage__LphA as a custom Lanthiphage profile."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| Lanthiphage__LphB1                               |",
        "notes": "The pinned DefenseFinder HMM inventory records Lanthiphage__LphB1 as a custom Lanthiphage profile."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "lanthivirin_bgc_inhibits_phage_dna_replication",
        "title": "Lanthivirin BGCs mediate anti-phage activity",
        "description": "Conservative system-level sketch linking possession of a lanthivirin biosynthetic gene cluster to anti-phage activity and lanthivirin system possession.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures lanthivirins at the biosynthetic gene cluster and anti-phage-output level without asserting the full native host range, exact Lanthiphage profile-to-component model, complete phage target breadth, or a DefenseFinder detection rule absent from the pinned rules table.",
        "nodes": [
          {
            "node_id": "lanthivirin_bgc",
            "label": "lanthivirin biosynthetic gene cluster",
            "node_type": "GENETIC_ELEMENT",
            "description": "A lanthivirin biosynthetic gene cluster represented in the pinned DefenseFinder HMM inventory by Lanthiphage custom profiles."
          },
          {
            "node_id": "lanthivirin_maturation",
            "label": "lanthivirin maturation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Maturation of a lanthivirin lanthipeptide by its biosynthetic gene cluster."
          },
          {
            "node_id": "phage_dna_replication",
            "label": "phage DNA replication",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Replication of infecting bacteriophage DNA."
          },
          {
            "node_id": "lanthivirin_system_trait",
            "label": "lanthivirin system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000416",
            "description": "Possession of a genome-encoded lanthivirin anti-phage system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "lanthivirin_bgc",
            "predicate": "enables",
            "predicate_id": "RO:0002327",
            "object": "lanthivirin_maturation",
            "description": "A lanthivirin biosynthetic gene cluster encodes the machinery required for lanthivirin maturation.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.chom.2026.06.017",
                "snippet": "lanthivirin maturation is required for anti-phage activity",
                "notes": "Serra et al. support the requirement for lanthivirin maturation in anti-phage activity."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| Lanthiphage__LphA                                |",
                "notes": "The pinned DefenseFinder HMM inventory records Lanthiphage__LphA as a custom Lanthiphage profile."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| Lanthiphage__LphB1                               |",
                "notes": "The pinned DefenseFinder HMM inventory records Lanthiphage__LphB1 as a custom Lanthiphage profile."
              }
            ]
          },
          {
            "subject": "lanthivirin_maturation",
            "predicate": "mitigates",
            "predicate_id": "METPO:2007407",
            "object": "phage_dna_replication",
            "description": "Mature lanthivirins are associated with a phage-protein-dependent inhibition of phage DNA replication.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.chom.2026.06.017",
                "snippet": "phage-protein-dependent inhibition of phage DNA replication",
                "notes": "Serra et al. link lanthivirins to inhibition of phage DNA replication."
              }
            ]
          },
          {
            "subject": "lanthivirin_maturation",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "lanthivirin_system_trait",
            "description": "Lanthivirin maturation realizes the anti-phage activity of the lanthivirin system.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.chom.2026.06.017",
                "snippet": "We demonstrate anti-phage activity both in a native Streptomyces context and through heterologous expression of six distinct lanthivirin systems.",
                "notes": "Serra et al. support native Streptomyces anti-phage activity and activity from multiple heterologously expressed lanthivirin systems."
              }
            ]
          },
          {
            "subject": "lanthivirin_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Lanthivirin system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| Lanthiphage | 10\\.1101/2024\\.06\\.26\\.600839 | A family of lanthipeptides with anti-phage function |",
                "notes": "The pinned DefenseFinder article registry maps the Lanthiphage source key to the lanthipeptide anti-phage preprint."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "lanthivirin-defensefinder-model-gap",
        "prompt": "Resolve Lanthiphage HMM-to-component coverage, rule-level detection criteria, sensitive-phage breadth, and exact lanthivirin effector identity before minting narrower lanthivirin mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Serra et al. support lanthivirin biosynthetic gene clusters as anti-phage systems, and the pinned DefenseFinder HMM inventory records Lanthiphage profile rows. The pinned rules table has no Lanthiphage row, and the first-pass record does not yet resolve exact profile-to-component mapping, full native host breadth, phage target breadth, or the direct mature lanthivirin effector.",
        "evidence": [
          {
            "reference": "DOI:10.1016/j.chom.2026.06.017",
            "snippet": "We demonstrate anti-phage activity both in a native Streptomyces context and through heterologous expression of six distinct lanthivirin systems.",
            "notes": "Serra et al. support native Streptomyces anti-phage activity and activity from multiple heterologously expressed lanthivirin systems."
          },
          {
            "reference": "DOI:10.1016/j.chom.2026.06.017",
            "snippet": "lanthivirin maturation is required for anti-phage activity",
            "notes": "Serra et al. support the requirement for lanthivirin maturation in anti-phage activity."
          },
          {
            "reference": "DOI:10.1016/j.chom.2026.06.017",
            "snippet": "phage-protein-dependent inhibition of phage DNA replication",
            "notes": "Serra et al. link lanthivirins to inhibition of phage DNA replication."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
            "snippet": "| Lanthiphage | 10\\.1101/2024\\.06\\.26\\.600839 | A family of lanthipeptides with anti-phage function |",
            "notes": "The pinned DefenseFinder article registry maps the Lanthiphage source key to the lanthipeptide anti-phage preprint."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| Lanthiphage__LphA                                |",
            "notes": "The pinned DefenseFinder HMM inventory records Lanthiphage__LphA as a custom Lanthiphage profile."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| Lanthiphage__LphB1                               |",
            "notes": "The pinned DefenseFinder HMM inventory records Lanthiphage__LphB1 as a custom Lanthiphage profile."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "The pinned DefenseFinder rules table does not list Lanthiphage, leaving rule-level detection criteria unresolved."
          }
        ],
        "attaches_to": [
          "causal_graphs#lanthivirin_bgc_inhibits_phage_dna_replication"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-27"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-27T20:02:44Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted lanthivirin system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; kept the graph at lanthipeptide biosynthetic-gene-cluster level because the pinned DefenseFinder HMM rows are not backed by pinned rules rows; the replacement placeholder is reserved in proposals/metpo_traitmech_v293.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-27T20:02:45Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed lanthivirin system during canonical-example issue 444 enforcement and left canonical_examples empty because the sources support Streptomyces-context and heterologous expression assays, plus DefenseFinder Lanthiphage HMM rows, but not a direct named native microbial isolate exemplar with experimentally verified endogenous lanthivirin activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000363",
    "label": "Lit system",
    "definition": "A phage defense system in which an organism possesses a Lit locus represented by DefenseFinder as a single-profile model requiring Lit__Lit.",
    "definition_source": "DOI:10.1021/bi0495026",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "Lit",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      },
      {
        "synonym_text": "Gol-Lit",
        "synonym_type": "RELATED_SYNONYM",
        "source": "PMID:21129205"
      },
      {
        "synonym_text": "Lit__Lit",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "PMID:15196039",
        "snippet": "Bacteriophage exclusion is a suicide response to viral infection. In strains of Escherichia coli K-12 infected with T4 phage this process is mediated by the host-encoded Lit peptidase. Lit is activated by a unique sequence in the major head protein of the T4 phage (the Gol sequence) which then cleaves site-specifically the host translation factor EF-Tu, ultimately leading to cell death.",
        "notes": "Copeland et al. support host Lit as a T4-activated bacteriophage-exclusion peptidase that cleaves EF-Tu and leads to cell death."
      },
      {
        "reference": "PMID:21129205",
        "snippet": "phage exclusion systems that involve T4-mediated activation of a latent endoribonuclease (PrrC) and cofactor-assisted activation of EF-Tu proteolysis (Gol-Lit)",
        "notes": "Uzan et al. name Gol-Lit as a T4 phage-exclusion system whose output is cofactor-assisted activation of EF-Tu proteolysis."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "Lit | 10\\.1186/1743-422X-7-360 | Post-transcriptional control by bacteriophage T4: mRNA decay and inhibition of translation initiation",
        "notes": "The DefenseFinder article registry maps the named Lit system to the Uzan et al. T4 post-transcriptional-control review."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "Lit\tLit\t1\t1\tLit__Lit",
        "notes": "The DefenseFinder rules table models Lit as a single-mandatory-profile system with the Lit__Lit profile."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| Lit__Lit                                         | Lit__Lit                                         | Lit                    | Custom                  | 20     |",
        "notes": "The DefenseFinder HMM inventory records Lit__Lit under Lit."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "lit_locus_restricts_t4_phage",
        "title": "Lit loci confer T4 phage exclusion",
        "description": "Conservative system-level sketch linking possession of a Lit locus to T4 Gol-Lit phage exclusion without asserting a protein-resolved Lit mechanism node.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Lit as a named DefenseFinder single-profile phage-exclusion system while leaving natural host breadth, non-e14 Lit loci, and the exact DefenseFinder profile-to-activity mapping unresolved.",
        "nodes": [
          {
            "node_id": "lit_locus",
            "label": "Lit locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A DefenseFinder Lit phage-defense locus represented by the Lit__Lit profile."
          },
          {
            "node_id": "t4_gol_lit_phage_exclusion",
            "label": "T4 Gol-Lit phage exclusion",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Bacteriophage T4 exclusion mediated by Gol-activated Lit proteolysis of the host translation factor EF-Tu."
          },
          {
            "node_id": "lit_system_trait",
            "label": "Lit system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000363",
            "description": "Possession of a genome-encoded Lit phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "lit_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "t4_gol_lit_phage_exclusion",
            "description": "Lit phage-defense loci can mediate T4 bacteriophage exclusion through Gol-activated EF-Tu proteolysis, and DefenseFinder models Lit as a single-profile system.",
            "evidence": [
              {
                "reference": "PMID:15196039",
                "snippet": "Bacteriophage exclusion is a suicide response to viral infection. In strains of Escherichia coli K-12 infected with T4 phage this process is mediated by the host-encoded Lit peptidase. Lit is activated by a unique sequence in the major head protein of the T4 phage (the Gol sequence) which then cleaves site-specifically the host translation factor EF-Tu, ultimately leading to cell death.",
                "notes": "Copeland et al. support Lit-mediated bacteriophage exclusion and EF-Tu cleavage."
              },
              {
                "reference": "PMID:21129205",
                "snippet": "phage exclusion systems that involve T4-mediated activation of a latent endoribonuclease (PrrC) and cofactor-assisted activation of EF-Tu proteolysis (Gol-Lit)",
                "notes": "Uzan et al. identify Gol-Lit as a phage-exclusion system mediated by EF-Tu proteolysis."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Lit | 10\\.1186/1743-422X-7-360 | Post-transcriptional control by bacteriophage T4: mRNA decay and inhibition of translation initiation",
                "notes": "The DefenseFinder article registry maps the named Lit system to the Uzan et al. T4 post-transcriptional-control review."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "Lit\tLit\t1\t1\tLit__Lit",
                "notes": "The DefenseFinder rules table models Lit as a single-mandatory-profile system with the Lit__Lit profile."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| Lit__Lit                                         | Lit__Lit                                         | Lit                    | Custom                  | 20     |",
                "notes": "The DefenseFinder HMM inventory records Lit__Lit under Lit."
              }
            ]
          },
          {
            "subject": "t4_gol_lit_phage_exclusion",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "lit_system_trait",
            "description": "T4 Gol-Lit phage exclusion realizes the Lit system trait.",
            "evidence": [
              {
                "reference": "PMID:15196039",
                "snippet": "Bacteriophage exclusion is a suicide response to viral infection. In strains of Escherichia coli K-12 infected with T4 phage this process is mediated by the host-encoded Lit peptidase. Lit is activated by a unique sequence in the major head protein of the T4 phage (the Gol sequence) which then cleaves site-specifically the host translation factor EF-Tu, ultimately leading to cell death.",
                "notes": "Copeland et al. connect host-encoded Lit to T4 bacteriophage exclusion."
              }
            ]
          },
          {
            "subject": "lit_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Lit system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Lit | 10\\.1186/1743-422X-7-360 | Post-transcriptional control by bacteriophage T4: mRNA decay and inhibition of translation initiation",
                "notes": "The DefenseFinder article registry maps the named Lit system to the Uzan et al. T4 post-transcriptional-control review."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "Lit\tLit\t1\t1\tLit__Lit",
                "notes": "The DefenseFinder rules table models Lit as a single-mandatory-profile system with the Lit__Lit profile."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "lit-mechanism-gap",
        "prompt": "Resolve natural Lit loci, host breadth beyond Escherichia coli K-12 e14, Gol-activation contexts, and Lit__Lit profile-to-activity mapping before minting narrower Lit mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Copeland et al. support the T4-triggered e14 Lit peptidase as a bacteriophage-exclusion determinant, Uzan et al. summarize Gol-Lit as a T4 phage-exclusion system, and DefenseFinder models Lit as a single-profile system. The natural host breadth and profile-to-activity mapping remain unresolved.",
        "attaches_to": [
          "causal_graphs#lit_locus_restricts_t4_phage"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-22"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-22T10:38:17Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Lit system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v240.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000571",
    "label": "long Lamassu system",
    "definition": "A Lamassu system in which an organism possesses a locus from the long-LmuB family, characterized by longer coiled-coil regions in its SMC-like LmuB sensor than in short Lamassu systems.",
    "definition_source": "DOI:10.1073/pnas.2519643122",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000232"
    ],
    "synonyms": [
      {
        "synonym_text": "long Lamassu",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1073/pnas.2519643122"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1073/pnas.2519643122",
        "snippet": "two major clades, which were mainly distinguished by the length of coiled-coil regions",
        "notes": "Results, LmuB phylogeny paragraph and Figure 1: the long family is distinguished from short Lamassu by phylogeny and structure. The approximate 800-residue total LmuB length is descriptive, not a membership cutoff."
      },
      {
        "reference": "DOI:10.1073/pnas.2519643122",
        "snippet": "one system from Bacillus cereus B4077, encoding Hydrolase-Protease effectors",
        "notes": "The same paragraph explicitly identifies B4077 as the long-clade exception among previously validated systems. This supports strain-qualified possession, not species-wide distribution or a native-host phage-resistance measurement."
      },
      {
        "reference": "https://pmc-oa-opendata.s3.amazonaws.com/PMC12663957.1/pnas.2519643122.sd01.xlsx",
        "snippet": "ACCA003.0722.00003.C001\tACCA003.0722.00003.C001_02431\tLamassu__LmuB_Long\nACCA003.0722.00003.C001\tACCA003.0722.00003.C001_02432\tLamassu__LmuC_Clade_VII\nACCA003.0722.00003.C001\tACCA003.0722.00003.C001_02433\tLamassu__LmuA_Cap4_III",
        "notes": "Dataset S1, S3_Lamassu_Detection!A58:C60, raw cells in column order. Column F assigns these rows to one ACCA003.0722.00003.C001_Lamassu_Cap4_321 call; column I reports sys_wholeness 1.0. Column C (gene_name) identifies the actual long-LmuB hit, unlike column L (hit_gene_ref), which can name the long model slot for short hits. These are computational locus observations, not an experimental antiviral phenotype or a family-membership rule."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1396",
        "taxon_label": "Bacillus cereus",
        "reference": "DOI:10.1073/pnas.2519643122",
        "note": "Strain B4077 is the source of the Hydrolase-Protease system assigned to the long family by Haudiquet et al. The species identifier anchors this strain-qualified example; no genome assembly, universal species possession, or native-host phage-resistance phenotype is inferred."
      }
    ],
    "discussions": [
      {
        "discussion_id": "long-lamassu-classification-and-mechanism-scope",
        "prompt": "Resolve borderline loci and long-family activation mechanisms.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Long denotes a phylogenetic and structural family, not an isolated protein, a fixed amino-acid threshold, an effector name, or the component-number type II category. A raw long-profile hit alone does not settle membership of an ambiguous locus. The published detection sheet uses gene_name for actual hits and hit_gene_ref for potentially exchangeable model slots; these fields must not be conflated. Hydrolase-Protease spans both length families; the legacy FMO record's detector-defined scope and SMEK's long-profile exception need separate reconciliation before reparenting. No universal effector chemistry, LmuC requirement, zinc-hook count, or stoichiometry is imposed. The experimentally resolved short Vc-Cap4 activation mechanism is not transferred to this family. Native-host activity, accession-level protein anchors and family-wide activation remain open, so no causal mechanism graph is asserted.",
        "posed_by": "codex",
        "posed_date": "2026-10-03"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-03T14:29:24Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added the literature-defined long Lamassu family with exact primary paper and dataset snippets and a strain-qualified B4077 example. Distinguished actual profile hits from model slots without adopting a length cutoff or transferring short-family mechanisms. Ignored-and-hidden searches found no exact record or METPO term. Reserved METPO:1052500 in proposals/metpo_traitmech_v448; left sibling hierarchies unchanged pending their own scope reconciliation.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000283",
    "label": "Lugos system",
    "definition": "A phage defense system in which an organism possesses a Lugos locus represented by a VCA0409 profile that can protect bacteria from bacteriophage infection.",
    "definition_source": "DOI:10.1126/science.ads0768",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "Lugos",
        "synonym_type": "EXACT_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      },
      {
        "synonym_text": "VCA0409",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1126/science.ads0768",
        "snippet": "nearly 10% of the integron cassettes in the pandemic Vibrio cholerae strain encode novel antiphage functions",
        "notes": "Darracq et al. support treating the newly discovered Vibrio cholerae SCI antiphage cassettes as bacterial anti-phage systems."
      },
      {
        "reference": "DOI:10.1126/science.ads0768",
        "snippet": "Most of these novel systems have little or no similarity to previously known ones, with several providing defense through cell lysis or growth arrest",
        "notes": "Darracq et al. support a conservative system record that does not assert a resolved Lugos trigger, effector output, or universal pathway."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "Lugos | 10\\.1126/science\\.ads0768 | Sedentary chromosomal integrons as biobanks of bacterial antiphage defense systems",
        "notes": "The DefenseFinder model registry maps the named Lugos system to the Darracq et al. SCI antiphage-system paper."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "Lugos__VCA0409                                   |                                                  | Lugos",
        "notes": "The DefenseFinder HMM inventory records VCA0409 in the Lugos model namespace."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "lugos_locus_restricts_phage",
        "title": "Lugos loci confer bacterial phage defense",
        "description": "Conservative system-level sketch linking possession of a Lugos locus to restricted bacteriophage propagation without asserting the unresolved phage trigger or molecular output.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Lugos as a named SCI-derived anti-phage system with a VCA0409 DefenseFinder profile while leaving its phage trigger, molecular substrate, antiviral effector output, and subtype breadth unresolved.",
        "nodes": [
          {
            "node_id": "lugos_locus",
            "label": "Lugos locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A Lugos anti-phage defense locus represented in DefenseFinder by a VCA0409 profile."
          },
          {
            "node_id": "restricted_phage_propagation",
            "label": "restricted phage propagation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced propagation of bacteriophage in cells carrying the Lugos system."
          },
          {
            "node_id": "lugos_system_trait",
            "label": "Lugos system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000283",
            "description": "Possession of a genome-encoded Lugos phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "lugos_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "restricted_phage_propagation",
            "description": "DefenseFinder maps Lugos to an SCI anti-phage-system discovery paper and represents Lugos loci through the VCA0409 component profile.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.ads0768",
                "snippet": "nearly 10% of the integron cassettes in the pandemic Vibrio cholerae strain encode novel antiphage functions",
                "notes": "Darracq et al. describe the newly discovered antiphage-system cohort that the DefenseFinder Lugos registry row maps to the Lugos system."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "Lugos__VCA0409                                   |                                                  | Lugos",
                "notes": "The DefenseFinder HMM inventory supports VCA0409 as the Lugos component profile."
              }
            ]
          },
          {
            "subject": "restricted_phage_propagation",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "lugos_system_trait",
            "description": "Lugos-mediated phage restriction realizes the Lugos system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.ads0768",
                "snippet": "Most of these novel systems have little or no similarity to previously known ones",
                "notes": "Darracq et al. place the Lugos discovery cohort in a set of novel bacterial systems that protect against phages."
              }
            ]
          },
          {
            "subject": "lugos_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Lugos system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Lugos | 10\\.1126/science\\.ads0768 | Sedentary chromosomal integrons as biobanks of bacterial antiphage defense systems",
                "notes": "DefenseFinder associates Lugos with the Darracq et al. bacterial antiphage-system paper."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "lugos-mechanism-gap",
        "prompt": "Resolve Lugos phage triggers and effector outputs before minting narrower Lugos mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Darracq et al. and DefenseFinder support Lugos as a named anti-phage system with a VCA0409 profile, but the trigger, molecular substrate, antiviral effector output, and subtype-specific mechanism are not resolved enough here to assert a narrower mechanistic child trait.",
        "attaches_to": [
          "causal_graphs#lugos_locus_restricts_phage"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-19"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-19T15:04:20Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Lugos system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v160.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000370",
    "label": "MADS system",
    "definition": "A phage defense system in which an organism possesses a methylation-associated defense system locus whose canonical architecture has mad1 through mad8 genes and whose methylation-coupled self/non-self discrimination can restrict bacteriophage infection.",
    "definition_source": "DOI:10.1016/j.chom.2024.07.005",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "MADS",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1016/j.chom.2024.07.005"
      },
      {
        "synonym_text": "methylation-associated defense system",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1016/j.chom.2024.07.005"
      },
      {
        "synonym_text": "MADS__mad1",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "MADS__mad2",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "MADS__mad3",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "MADS__mad4",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "MADS__mad5",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "MADS__mad6",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "MADS__mad7",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "MADS__mad8",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1016/j.chom.2024.07.005",
        "snippet": "coined methylation-associated defense system (MADS)",
        "notes": "Maestri et al. coin methylation-associated defense system (MADS) for the newly discovered phage-defense locus."
      },
      {
        "reference": "DOI:10.1016/j.chom.2024.07.005",
        "snippet": "MADS interacts with a CRISPR-Cas system in its native host to provide robust and durable resistance against phages",
        "notes": "Maestri et al. show that native-host MADS and CRISPR-Cas cooperate to provide robust phage resistance."
      },
      {
        "reference": "DOI:10.1016/j.chom.2024.07.005",
        "snippet": "MADS encodes a defense system that is active against at least 4 different DNA phages",
        "notes": "Maestri et al. support MADS activity against DMS3vir and three additional DNA phages."
      },
      {
        "reference": "DOI:10.1016/j.chom.2024.07.005",
        "snippet": "MADS uses a methylation-based self/non-self discrimination mechanism",
        "notes": "Maestri et al. connect MADS to methylation-based self/non-self discrimination."
      },
      {
        "reference": "DOI:10.1101/2023.03.30.534895",
        "snippet": "Bacterial defences interact synergistically by disrupting phage cooperation",
        "notes": "The bioRxiv version of Maestri et al. is the DOI cited in DefenseFinder's MADS article-registry row."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "MADS | 10\\.1101/2023\\.03\\.30\\.534895 | Bacterial defences interact synergistically by disrupting phage cooperation",
        "notes": "The DefenseFinder article registry maps the named MADS system to the Maestri et al. preprint."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "MADS\tMADS\t3\t3\tMADS__mad1, MADS__mad2, MADS__mad3, MADS__mad4, MADS__mad5, MADS__mad6, MADS__mad7, MADS__mad8\t\t\t",
        "notes": "The DefenseFinder rules table models MADS with MADS__mad1 through MADS__mad8 profiles and a minimum of three mandatory matches."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| MADS__mad1                                       | MADS__mad1                                       | MADS                   | Custom                  | 20     |",
        "notes": "The DefenseFinder HMM inventory records MADS__mad1 under the MADS model namespace."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| MADS__mad2                                       | MADS__mad2                                       | MADS                   | Custom                  | 150    |",
        "notes": "The DefenseFinder HMM inventory records MADS__mad2 under the MADS model namespace."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| MADS__mad3                                       | MADS__mad3                                       | MADS                   | Custom                  | 200    |",
        "notes": "The DefenseFinder HMM inventory records MADS__mad3 under the MADS model namespace."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| MADS__mad4                                       | MADS__mad4                                       | MADS                   | Custom                  | 50     |",
        "notes": "The DefenseFinder HMM inventory records MADS__mad4 under the MADS model namespace."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| MADS__mad5                                       | MADS__mad5                                       | MADS                   | Custom                  | 50     |",
        "notes": "The DefenseFinder HMM inventory records MADS__mad5 under the MADS model namespace."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| MADS__mad6                                       | MADS__mad6                                       | MADS                   | Custom                  | 150    |",
        "notes": "The DefenseFinder HMM inventory records MADS__mad6 under the MADS model namespace."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| MADS__mad7                                       | MADS__mad7                                       | MADS                   | Custom                  | 100    |",
        "notes": "The DefenseFinder HMM inventory records MADS__mad7 under the MADS model namespace."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| MADS__mad8                                       | MADS__mad8                                       | MADS                   | Custom                  | 100    |",
        "notes": "The DefenseFinder HMM inventory records MADS__mad8 under the MADS model namespace."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:287",
        "taxon_label": "Pseudomonas aeruginosa",
        "note": "Maestri et al. discovered MADS in the native Pseudomonas aeruginosa SMC4386 locus and showed that deleting the locus reduced resistance to phage DMS3vir.",
        "reference": "DOI:10.1016/j.chom.2024.07.005"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "mads_methylation_restricts_phage",
        "title": "MADS loci confer methylation-associated phage defense",
        "description": "Conservative system-level sketch linking possession of a MADS locus to methylation-based self/non-self discrimination, restriction of DNA phages, and the MADS system trait.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures MADS as a named eight-gene DefenseFinder profile set whose activity is associated with methylation and DNA restriction while leaving the exact mapping from the MADS__mad profiles to nuclease, ATPase, kinase, specificity, and methyltransferase activities unresolved.",
        "nodes": [
          {
            "node_id": "mads_locus",
            "label": "MADS locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A methylation-associated phage-defense locus in the MADS family."
          },
          {
            "node_id": "mads_self_nonself_discrimination",
            "label": "MADS self/non-self discrimination",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Methylation-based discrimination between host DNA and unmethylated mobile genetic element DNA by MADS."
          },
          {
            "node_id": "dna_phage_restriction",
            "label": "DNA phage restriction",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Restriction of infecting DNA bacteriophages by the MADS locus."
          },
          {
            "node_id": "mads_system_trait",
            "label": "MADS system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000370",
            "description": "Possession of a genome-encoded MADS phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "mads_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "mads_self_nonself_discrimination",
            "description": "MADS loci encode an eight-gene methylation-associated defense system, and DefenseFinder models MADS as an eight-profile rule with at least three mandatory matches.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.chom.2024.07.005",
                "snippet": "coined methylation-associated defense system (MADS)",
                "notes": "Maestri et al. coin methylation-associated defense system (MADS) for the newly discovered phage-defense locus."
              },
              {
                "reference": "DOI:10.1016/j.chom.2024.07.005",
                "snippet": "MADS uses a methylation-based self/non-self discrimination mechanism",
                "notes": "Maestri et al. connect MADS to methylation-based self/non-self discrimination."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "MADS | 10\\.1101/2023\\.03\\.30\\.534895 | Bacterial defences interact synergistically by disrupting phage cooperation",
                "notes": "The DefenseFinder article registry maps the named MADS system to the Maestri et al. preprint."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "MADS\tMADS\t3\t3\tMADS__mad1, MADS__mad2, MADS__mad3, MADS__mad4, MADS__mad5, MADS__mad6, MADS__mad7, MADS__mad8\t\t\t",
                "notes": "The DefenseFinder rules table models MADS with MADS__mad1 through MADS__mad8 profiles and a minimum of three mandatory matches."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| MADS__mad1                                       | MADS__mad1                                       | MADS                   | Custom                  | 20     |",
                "notes": "The DefenseFinder HMM inventory records MADS__mad1 under the MADS model namespace."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| MADS__mad2                                       | MADS__mad2                                       | MADS                   | Custom                  | 150    |",
                "notes": "The DefenseFinder HMM inventory records MADS__mad2 under the MADS model namespace."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| MADS__mad3                                       | MADS__mad3                                       | MADS                   | Custom                  | 200    |",
                "notes": "The DefenseFinder HMM inventory records MADS__mad3 under the MADS model namespace."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| MADS__mad4                                       | MADS__mad4                                       | MADS                   | Custom                  | 50     |",
                "notes": "The DefenseFinder HMM inventory records MADS__mad4 under the MADS model namespace."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| MADS__mad5                                       | MADS__mad5                                       | MADS                   | Custom                  | 50     |",
                "notes": "The DefenseFinder HMM inventory records MADS__mad5 under the MADS model namespace."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| MADS__mad6                                       | MADS__mad6                                       | MADS                   | Custom                  | 150    |",
                "notes": "The DefenseFinder HMM inventory records MADS__mad6 under the MADS model namespace."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| MADS__mad7                                       | MADS__mad7                                       | MADS                   | Custom                  | 100    |",
                "notes": "The DefenseFinder HMM inventory records MADS__mad7 under the MADS model namespace."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| MADS__mad8                                       | MADS__mad8                                       | MADS                   | Custom                  | 100    |",
                "notes": "The DefenseFinder HMM inventory records MADS__mad8 under the MADS model namespace."
              }
            ]
          },
          {
            "subject": "mads_self_nonself_discrimination",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "dna_phage_restriction",
            "description": "MADS-associated methylation-based self/non-self discrimination contributes to DNA-phage restriction.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.chom.2024.07.005",
                "snippet": "MADS uses a methylation-based self/non-self discrimination mechanism",
                "notes": "Maestri et al. connect MADS to methylation-based self/non-self discrimination."
              },
              {
                "reference": "DOI:10.1016/j.chom.2024.07.005",
                "snippet": "MADS encodes a defense system that is active against at least 4 different DNA phages",
                "notes": "Maestri et al. support MADS activity against DMS3vir and three additional DNA phages."
              }
            ]
          },
          {
            "subject": "dna_phage_restriction",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "mads_system_trait",
            "description": "MADS-mediated DNA-phage restriction realizes the MADS system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.chom.2024.07.005",
                "snippet": "MADS encodes a defense system that is active against at least 4 different DNA phages",
                "notes": "Maestri et al. support MADS activity against DMS3vir and three additional DNA phages."
              }
            ]
          },
          {
            "subject": "mads_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "MADS system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.chom.2024.07.005",
                "snippet": "coined methylation-associated defense system (MADS)",
                "notes": "Maestri et al. coin methylation-associated defense system (MADS) for the newly discovered phage-defense locus."
              },
              {
                "reference": "DOI:10.1016/j.chom.2024.07.005",
                "snippet": "MADS interacts with a CRISPR-Cas system in its native host to provide robust and durable resistance against phages",
                "notes": "Maestri et al. show that native-host MADS and CRISPR-Cas cooperate to provide robust phage resistance."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "MADS | 10\\.1101/2023\\.03\\.30\\.534895 | Bacterial defences interact synergistically by disrupting phage cooperation",
                "notes": "The DefenseFinder article registry maps the named MADS system to the Maestri et al. preprint."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "mads-profile-activity-gap",
        "prompt": "Resolve MADS subtype boundaries, MADS3-4 relationships, and Mad1-Mad8 profile-to-activity mappings before minting narrower MADS mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Maestri et al. support MADS as a methylation-associated defense system active against DNA phages, and DefenseFinder models MADS as an eight-profile rule. The pinned model does not resolve which combinations of MADS__mad profiles correspond to methylation, specificity, nuclease, ATPase, or kinase activities, so this first record stays at system level.",
        "evidence": [
          {
            "reference": "DOI:10.1016/j.chom.2024.07.005",
            "snippet": "MADS encodes a defense system that is active against at least 4 different DNA phages",
            "notes": "Maestri et al. support MADS activity against DMS3vir and three additional DNA phages."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "snippet": "MADS\tMADS\t3\t3\tMADS__mad1, MADS__mad2, MADS__mad3, MADS__mad4, MADS__mad5, MADS__mad6, MADS__mad7, MADS__mad8\t\t\t",
            "notes": "The DefenseFinder rules table models MADS with MADS__mad1 through MADS__mad8 profiles and a minimum of three mandatory matches."
          }
        ],
        "attaches_to": [
          "causal_graphs#mads_methylation_restricts_phage"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-24"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-25T03:36:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted MADS system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v247.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000345",
    "label": "MazEF system",
    "definition": "A phage defense system in which an organism possesses a two-component MazEF toxin-antitoxin locus whose MazE antitoxin and MazF endoribonuclease can protect Escherichia coli against RNA phages and that DefenseFinder represents with mandatory MazEF__MazE and MazEF__MazF profiles.",
    "definition_source": "DOI:10.1098/rsbl.2025.0080",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "MazEF",
        "synonym_type": "EXACT_SYNONYM",
        "source": "PMID:40494395"
      },
      {
        "synonym_text": "mazEF",
        "synonym_type": "RELATED_SYNONYM",
        "source": "PMID:40494395"
      },
      {
        "synonym_text": "MazEF__MazE",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "MazEF__MazF",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "PMID:40494395",
        "snippet": "we investigated the role of a model toxin-antitoxin system, MazEF, in protecting Escherichia coli against two RNA phage species",
        "notes": "Nikolic et al. directly tested MazEF as an Escherichia coli toxin-antitoxin module protecting against RNA phages."
      },
      {
        "reference": "PMID:40494395",
        "snippet": "the native presence of mazEF moderately reduced population susceptibility and increased the survival of individual E. coli cells",
        "notes": "Nikolic et al. support native mazEF as a moderate RNA phage defense determinant in Escherichia coli."
      },
      {
        "reference": "PMID:40494395",
        "snippet": "Genomic analysis further revealed an underrepresentation of the MazF cleavage site in genomes of RNA phages infecting E. coli",
        "notes": "Nikolic et al. support selection against MazF ACA cleavage sites in RNA phages that infect E. coli."
      },
      {
        "reference": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12151602/",
        "snippet": "MazEF interferes with RNA phage replication within already infected cells",
        "notes": "Nikolic et al. interpret the mazEF deletion phenotype as intracellular interference with RNA phage replication, not an adsorption defect."
      },
      {
        "reference": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12151602/",
        "snippet": "direct interference, rather than abortive infection, plays the predominant role in the case of MazEF",
        "notes": "Nikolic et al. caution that the main MazEF effect in their RNA phage assays appears to be direct interference rather than abortive infection."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "MazEF | 10\\.1098/rsbl\\.2025\\.0080 | A bacterial toxin-antitoxin system as a native defence element against RNA phages",
        "notes": "The DefenseFinder article registry maps the named MazEF system to the Nikolic et al. RNA-phage defense paper."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "MazEF\tMazEF\t2\t2\tMazEF__MazE, MazEF__MazF",
        "notes": "The DefenseFinder rules table models MazEF as a two-profile system requiring MazE and MazF profiles."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| MazEF__MazE                                      | MazEF__MazE                                      | MazEF                  | Custom                  | 20     |",
        "notes": "The DefenseFinder HMM inventory records the MazE profile in the MazEF model namespace."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| MazEF__MazF                                      | MazEF__MazF                                      | MazEF                  | Custom                  | 20     |",
        "notes": "The DefenseFinder HMM inventory records the MazF profile in the MazEF model namespace."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:562",
        "taxon_label": "Escherichia coli",
        "note": "Nikolic et al. compared Escherichia coli K-12 MG1655 derivatives carrying or lacking the native mazEF locus and found moderate but measurable native mazEF protection against the MS2 and Qbeta RNA phages.",
        "reference": "DOI:10.1098/rsbl.2025.0080"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "mazef_rna_phage_defense",
        "title": "MazEF loci reduce RNA phage susceptibility",
        "description": "Conservative system-level sketch linking a MazEF locus to native RNA phage defense and the MazEF system possession trait.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures native MazEF protection against RNA phages without asserting a phage-triggered MazF activation route, a resolved direct phage-RNA cleavage event, MazEF-mediated DNA-phage defense breadth, or a generic abortive-infection output.",
        "nodes": [
          {
            "node_id": "mazef_locus",
            "label": "MazEF locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A two-component toxin-antitoxin locus represented by MazE and MazF profiles."
          },
          {
            "node_id": "rna_phage_replication_interference",
            "label": "RNA phage replication interference",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced RNA phage replication or survival of RNA phage-infected cells associated with native mazEF."
          },
          {
            "node_id": "mazef_system_trait",
            "label": "MazEF system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000345",
            "description": "Possession of a genome-encoded MazEF toxin-antitoxin phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "mazef_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "rna_phage_replication_interference",
            "description": "Native mazEF contributes to reduced Escherichia coli susceptibility to the MS2 and Qbeta RNA phages.",
            "evidence": [
              {
                "reference": "PMID:40494395",
                "snippet": "the native presence of mazEF moderately reduced population susceptibility",
                "notes": "Nikolic et al. connect native mazEF presence to reduced RNA phage susceptibility."
              },
              {
                "reference": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12151602/",
                "snippet": "MazEF interferes with RNA phage replication within already infected cells",
                "notes": "Nikolic et al. distinguish MazEF-mediated intracellular interference from blocked RNA phage adsorption."
              }
            ]
          },
          {
            "subject": "rna_phage_replication_interference",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "mazef_system_trait",
            "description": "MazEF-associated reduction of RNA phage susceptibility realizes the MazEF system trait.",
            "evidence": [
              {
                "reference": "PMID:40494395",
                "snippet": "RNA-degrading toxin-antitoxin systems may also help defend against RNA phages",
                "notes": "Nikolic et al. frame the MazEF result as support for RNA-degrading toxin-antitoxin systems as RNA phage defense elements."
              }
            ]
          },
          {
            "subject": "mazef_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "MazEF system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "MazEF | 10\\.1098/rsbl\\.2025\\.0080 | A bacterial toxin-antitoxin system as a native defence element against RNA phages",
                "notes": "DefenseFinder associates MazEF with the Nikolic et al. RNA-phage defense paper."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "MazEF\tMazEF\t2\t2\tMazEF__MazE, MazEF__MazF",
                "notes": "The DefenseFinder rules table models MazEF as a two-profile system requiring MazE and MazF profiles."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "mazef-activation-breadth-gap",
        "prompt": "Resolve MazEF activation, direct MazF RNA targets, and RNA- versus DNA-phage breadth before minting narrower MazEF mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Nikolic et al. support native MazEF protection against RNA phages and argue that direct interference predominates in those assays, but the phage-induced route to active MazF, the relative contributions of phage-RNA cleavage and host-RNA degradation, the breadth of MazEF DNA-phage defense, and the DefenseFinder MazEF model boundaries remain unresolved.",
        "attaches_to": [
          "causal_graphs#mazef_rna_phage_defense"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-21"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-21T21:03:46Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted MazEF system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v222.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000505",
    "label": "McrBC system",
    "definition": "A type IV modification-dependent restriction system in which an organism possesses an mcrBC locus encoding McrB DNA-binding and McrC cleavage-associated subunits that assemble into an McrBC restriction endonuclease complex targeting methylated cytosine-containing DNA.",
    "definition_source": "DOI:10.1093/emboj/20.12.3210",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000496"
    ],
    "synonyms": [
      {
        "synonym_text": "McrBC",
        "synonym_type": "EXACT_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      },
      {
        "synonym_text": "McrBC restriction endonuclease",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1093/emboj/20.12.3210"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1093/emboj/20.12.3210",
        "snippet": "McrBC from Escherichia coli K-12 is a restriction enzyme that belongs to the family of AAA(+) proteins and cuts DNA containing modified cytosines.",
        "notes": "Panne et al. identify McrBC from Escherichia coli K-12 as a restriction enzyme that attacks modified-cytosine DNA."
      },
      {
        "reference": "DOI:10.1093/emboj/20.12.3210",
        "snippet": "McrB(L) binds specifically to the methylated recognition site and is, therefore, the DNA-binding moiety of the McrBC endonuclease.",
        "notes": "Panne et al. support methylated-site DNA binding by McrB(L), one of the products of the E. coli K-12 mcrB gene."
      },
      {
        "reference": "DOI:10.1093/emboj/20.12.3210",
        "snippet": "In the presence of McrC, a subunit that is essential for DNA cleavage, the tetradecameric species was the major form of the endonuclease.",
        "notes": "Panne et al. support McrC as the cleavage-associated subunit of the McrBC endonuclease complex."
      },
      {
        "reference": "DOI:10.1093/nar/gkt747",
        "snippet": "The rgl genes were renamed mcrA and mcrBC (modified cytosine restriction).",
        "notes": "Loenen and Raleigh place mcrBC in the modified-cytosine restriction branch that helped define Type IV restriction."
      },
      {
        "reference": "DOI:10.1093/nar/gkt747",
        "snippet": "The new class of modification-dependent restriction enzymes was named Type IV, as distinct from the familiar modification-blocked Types I-III.",
        "notes": "Loenen and Raleigh define the Type IV class as modification-dependent restriction enzymes."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| McrBC | 10\\.1093/emboj/20\\.12\\.3210 | The McrBC restriction endonuclease assembles into a ring structure in the presence of G nucleotides | ",
        "notes": "The pinned DefenseFinder article registry maps the McrBC source key to Panne et al."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:83333",
        "taxon_label": "Escherichia coli K-12",
        "note": "Panne et al. characterized the McrBC endonuclease from Escherichia coli K-12.",
        "reference": "DOI:10.1093/emboj/20.12.3210"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "mcrbc_restricts_methylated_cytosine_dna",
        "title": "McrBC restricts methylated-cytosine DNA",
        "description": "Conservative system-level sketch linking an mcrBC locus to modification-dependent restriction of methylated-cytosine DNA and to the Type IV restriction parent trait.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures McrBC as a named, E. coli K-12-derived Type IV modification-dependent restriction system while leaving exact McrB/McrC protein activities, complete modified-cytosine target breadth, natural host breadth, and DefenseFinder RM_Type_IV HMM/rules mapping unresolved.",
        "nodes": [
          {
            "node_id": "mcrbc_locus",
            "label": "mcrBC locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A locus encoding the McrB and McrC subunits of the McrBC modification-dependent restriction endonuclease."
          },
          {
            "node_id": "mcrbc_methylated_dna_restriction",
            "label": "McrBC methylated-DNA restriction",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "McrBC endonuclease restriction of DNA containing modified cytosines."
          },
          {
            "node_id": "mcrbc_system_trait",
            "label": "McrBC system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000505",
            "description": "Possession of a genome-encoded McrBC modification-dependent restriction system."
          },
          {
            "node_id": "type_iv_modification_dependent_restriction",
            "label": "type IV modification-dependent restriction system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000496",
            "description": "Possession of a genome-encoded Type IV modification-dependent restriction system."
          }
        ],
        "edges": [
          {
            "subject": "mcrbc_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "mcrbc_methylated_dna_restriction",
            "description": "The mcrBC locus encodes the McrBC endonuclease subunits that bind and cleave modified-cytosine DNA.",
            "evidence": [
              {
                "reference": "DOI:10.1093/emboj/20.12.3210",
                "snippet": "McrBC from Escherichia coli K-12 is a restriction enzyme that belongs to the family of AAA(+) proteins and cuts DNA containing modified cytosines.",
                "notes": "Panne et al. identify McrBC from Escherichia coli K-12 as a restriction enzyme that attacks modified-cytosine DNA."
              },
              {
                "reference": "DOI:10.1093/emboj/20.12.3210",
                "snippet": "McrB(L) binds specifically to the methylated recognition site and is, therefore, the DNA-binding moiety of the McrBC endonuclease.",
                "notes": "Panne et al. support methylated-site DNA binding by McrB(L), one of the products of the E. coli K-12 mcrB gene."
              },
              {
                "reference": "DOI:10.1093/emboj/20.12.3210",
                "snippet": "In the presence of McrC, a subunit that is essential for DNA cleavage, the tetradecameric species was the major form of the endonuclease.",
                "notes": "Panne et al. support McrC as the cleavage-associated subunit of the McrBC endonuclease complex."
              }
            ]
          },
          {
            "subject": "mcrbc_methylated_dna_restriction",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "mcrbc_system_trait",
            "description": "McrBC methylated-DNA restriction realizes the organism-level McrBC system possession trait.",
            "evidence": [
              {
                "reference": "DOI:10.1093/emboj/20.12.3210",
                "snippet": "McrBC from Escherichia coli K-12 is a restriction enzyme that belongs to the family of AAA(+) proteins and cuts DNA containing modified cytosines.",
                "notes": "Panne et al. identify McrBC from Escherichia coli K-12 as a restriction enzyme that attacks modified-cytosine DNA."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| McrBC | 10\\.1093/emboj/20\\.12\\.3210 | The McrBC restriction endonuclease assembles into a ring structure in the presence of G nucleotides | ",
                "notes": "The pinned DefenseFinder article registry maps the McrBC source key to Panne et al."
              }
            ]
          },
          {
            "subject": "mcrbc_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "type_iv_modification_dependent_restriction",
            "description": "McrBC system possession is a Type IV modification-dependent restriction system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1093/nar/gkt747",
                "snippet": "The rgl genes were renamed mcrA and mcrBC (modified cytosine restriction).",
                "notes": "Loenen and Raleigh place mcrBC in the modified-cytosine restriction branch that helped define Type IV restriction."
              },
              {
                "reference": "DOI:10.1093/nar/gkt747",
                "snippet": "The new class of modification-dependent restriction enzymes was named Type IV, as distinct from the familiar modification-blocked Types I-III.",
                "notes": "Loenen and Raleigh define the Type IV class as modification-dependent restriction enzymes."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "mcrbc-defensefinder-model-gap",
        "prompt": "Resolve exact McrB/McrC component activities, complete modified-cytosine target breadth, natural host breadth, and DefenseFinder RM_Type_IV HMM/rules mapping before minting narrower McrBC mechanism or component traits.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Panne et al. support McrBC from Escherichia coli K-12 as a restriction endonuclease complex that cuts DNA containing modified cytosines, and Loenen and Raleigh place mcrBC in the modified-cytosine restriction branch of Type IV modification-dependent restriction systems. The pinned DefenseFinder article registry maps the McrBC source key to Panne et al., but the pinned HMM inventory and rules table have no exact McrBC rows. This first-pass record therefore does not resolve a reusable DefenseFinder profile model, the exact relationship between individual McrB and McrC molecular functions and organism-level McrBC possession, the complete set of modified-cytosine targets, or the natural host breadth of McrBC systems.",
        "evidence": [
          {
            "reference": "DOI:10.1093/emboj/20.12.3210",
            "snippet": "McrBC from Escherichia coli K-12 is a restriction enzyme that belongs to the family of AAA(+) proteins and cuts DNA containing modified cytosines.",
            "notes": "Panne et al. identify McrBC from Escherichia coli K-12 as a restriction enzyme that attacks modified-cytosine DNA."
          },
          {
            "reference": "DOI:10.1093/emboj/20.12.3210",
            "snippet": "McrB(L) binds specifically to the methylated recognition site and is, therefore, the DNA-binding moiety of the McrBC endonuclease.",
            "notes": "Panne et al. support methylated-site DNA binding by McrB(L), one of the products of the E. coli K-12 mcrB gene."
          },
          {
            "reference": "DOI:10.1093/emboj/20.12.3210",
            "snippet": "In the presence of McrC, a subunit that is essential for DNA cleavage, the tetradecameric species was the major form of the endonuclease.",
            "notes": "Panne et al. support McrC as the cleavage-associated subunit of the McrBC endonuclease complex."
          },
          {
            "reference": "DOI:10.1093/nar/gkt747",
            "snippet": "The rgl genes were renamed mcrA and mcrBC (modified cytosine restriction).",
            "notes": "Loenen and Raleigh place mcrBC in the modified-cytosine restriction branch that helped define Type IV restriction."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
            "snippet": "| McrBC | 10\\.1093/emboj/20\\.12\\.3210 | The McrBC restriction endonuclease assembles into a ring structure in the presence of G nucleotides | ",
            "notes": "The pinned DefenseFinder article registry maps the McrBC source key to Panne et al."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "notes": "A structured first-pass search of the pinned DefenseFinder HMM inventory found no exact McrBC row."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "A structured first-pass search of the pinned DefenseFinder rules table found no exact McrBC system row."
          }
        ],
        "attaches_to": [
          "causal_graphs#mcrbc_restricts_methylated_cytosine_dna"
        ],
        "posed_by": "codex",
        "posed_date": "2026-10-01"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-01T03:37:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted McrBC system as a DOI- and DefenseFinder-backed GENOMICS TraitRecord under the type IV modification-dependent restriction system parent after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v382.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000253",
    "label": "Menshen system",
    "definition": "A phage defense system in which an organism possesses a Menshen locus represented by NsnA, NsnB, and NsnC profile choices that can protect bacteria from bacteriophage infection.",
    "definition_source": "DOI:10.1016/j.chom.2022.09.017",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "Menshen",
        "synonym_type": "EXACT_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1016/j.chom.2022.09.017",
        "snippet": "discovery of 21 defense systems that protect bacteria from phages, based on computational genomic analyses and phage-infection experiments",
        "notes": "Millman et al. report the computational and experimental cohort that DefenseFinder cites for Menshen as a bacterial anti-phage system."
      },
      {
        "reference": "DOI:10.1101/2022.05.11.491447",
        "snippet": "discovery of 21 new defense systems that protect bacteria from phages, based on computational genomic analyses and phage infection experiments",
        "notes": "The bioRxiv version of Millman et al. independently carries the 21-system discovery claim linked from DefenseFinder's Menshen article registry."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "Menshen | 10\\.1101/2022\\.05\\.11\\.491447 | An expanding arsenal of immune systems that protect bacteria from phages",
        "notes": "The DefenseFinder model registry maps the named Menshen system to the Millman et al. antiphage-system discovery preprint."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "Menshen\tMenshen\t2\t2\tMenshen__NsnA, Menshen__NsnB, Menshen__NsnC_2507451963",
        "notes": "The DefenseFinder rules table models Menshen with NsnA, NsnB, and NsnC profile choices."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "Menshen__NsnA                                     | Menshen__NsnA                                     | Menshen",
        "notes": "The DefenseFinder HMM inventory records NsnA as a Menshen profile."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "Menshen__NsnB                                     | Menshen__NsnB                                     | Menshen",
        "notes": "The DefenseFinder HMM inventory records NsnB as a Menshen profile."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "Menshen__NsnC_2507451963                          | Menshen__NsnC_2507451963                          | Menshen",
        "notes": "The DefenseFinder HMM inventory records NsnC as a Menshen profile."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "menshen_locus_restricts_phage",
        "title": "Menshen loci confer bacterial phage defense",
        "description": "Conservative system-level sketch linking possession of a Menshen locus to restricted bacteriophage propagation without asserting the unresolved phage trigger or molecular output.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Menshen as a named anti-phage system with DefenseFinder NsnA, NsnB, and NsnC profile choices while leaving its phage trigger, molecular substrate, antiviral effector output, and subtype breadth unresolved.",
        "nodes": [
          {
            "node_id": "menshen_locus",
            "label": "Menshen locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A Menshen anti-phage defense locus satisfying a DefenseFinder rule over NsnA, NsnB, and NsnC profiles."
          },
          {
            "node_id": "restricted_phage_propagation",
            "label": "restricted phage propagation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced propagation of bacteriophage in cells carrying the Menshen system."
          },
          {
            "node_id": "menshen_system_trait",
            "label": "Menshen system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000253",
            "description": "Possession of a genome-encoded Menshen phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "menshen_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "restricted_phage_propagation",
            "description": "DefenseFinder maps Menshen to a bacterial anti-phage-system discovery preprint and represents Menshen loci through NsnA, NsnB, and NsnC component profiles.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.chom.2022.09.017",
                "snippet": "discovery of 21 defense systems that protect bacteria from phages",
                "notes": "Millman et al. describe the anti-phage discovery cohort that the DefenseFinder Menshen registry row maps to the Menshen system."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Menshen | 10\\.1101/2022\\.05\\.11\\.491447 | An expanding arsenal of immune systems that protect bacteria from phages",
                "notes": "The DefenseFinder registry maps Menshen itself to the Millman et al. bacterial antiphage-system discovery preprint."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "Menshen\tMenshen\t2\t2\tMenshen__NsnA, Menshen__NsnB, Menshen__NsnC_2507451963",
                "notes": "The DefenseFinder rules table supports NsnA, NsnB, and NsnC as Menshen system profile choices."
              }
            ]
          },
          {
            "subject": "restricted_phage_propagation",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "menshen_system_trait",
            "description": "Menshen-mediated phage restriction realizes the Menshen system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.chom.2022.09.017",
                "snippet": "discovery of 21 defense systems that protect bacteria from phages",
                "notes": "Millman et al. place the Menshen discovery cohort in the set of bacterial systems that protect against phages."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Menshen | 10\\.1101/2022\\.05\\.11\\.491447 | An expanding arsenal of immune systems that protect bacteria from phages",
                "notes": "DefenseFinder records Menshen as a named system from the Millman et al. antiphage discovery preprint."
              }
            ]
          },
          {
            "subject": "menshen_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Menshen system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "An expanding arsenal of immune systems that protect bacteria from phages",
                "notes": "DefenseFinder associates Menshen with the Millman et al. bacterial antiphage-system discovery paper."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "menshen-mechanism-gap",
        "prompt": "Resolve Menshen phage triggers and effector outputs before minting narrower Menshen mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Millman et al. and DefenseFinder support Menshen as a named anti-phage system with NsnA, NsnB, and NsnC profile choices, but the trigger, molecular substrate, antiviral effector output, and subtype-specific mechanism are not resolved enough here to assert a narrower mechanistic child trait.",
        "attaches_to": [
          "causal_graphs#menshen_locus_restricts_phage"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-18"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-18T22:20:11Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Menshen system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v130.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000502",
    "label": "Metis system",
    "definition": "A phage defense system in which an organism possesses a Metis locus that senses phage-mediated host-genome degradation through N6-methyl-deoxyadenosine monophosphate and activates a type-specific toxic effector.",
    "definition_source": "DOI:10.1126/science.aed6782",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "Metis",
        "synonym_type": "EXACT_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1126/science.aed6782",
        "snippet": "In this work, we describe Metis, a bacterial defense system that directly senses phage-mediated host genome degradation.",
        "notes": "Osterman et al. directly name Metis as a bacterial system sensing host-genome degradation during phage infection."
      },
      {
        "reference": "DOI:10.1126/science.aed6782",
        "snippet": "Metis aborts phage infection once it detects the modified mononucleotide N6-methyl-deoxyadenosine monophosphate (m6dAMP).",
        "notes": "Osterman et al. identify m6dAMP as the modified mononucleotide cue detected by Metis."
      },
      {
        "reference": "DOI:10.1126/science.aed6782",
        "snippet": "As methylation of deoxyadenosines usually occurs on the DNA polymer, accumulation of m6dAMP signals that the host genome has been degraded.",
        "notes": "Osterman et al. explain why free m6dAMP reports host-genome degradation."
      },
      {
        "reference": "DOI:10.1126/science.aed6782",
        "snippet": "In type I Metis, sensing of m6dAMP activates a nicotinamide adenine dinucleotide (NAD+) diphosphatase, leading to NAD+ depletion and cessation of the infection process, whereas the effector in type II Metis is a membrane-spanning protein whose toxicity is triggered in response to the modified mononucleotide.",
        "notes": "Osterman et al. distinguish type I and type II Metis effectors without resolving a DefenseFinder rule-level model in the pinned registry."
      },
      {
        "reference": "DOI:10.1126/science.aed6782",
        "snippet": "We further show that Metis defense depends on endogenous DNA methylases and that phages can escape Metis through mutations that inactivate host genome degradation.",
        "notes": "Osterman et al. link Metis immunity to endogenous DNA methylases and to phage genome-degradation activity."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| Metis | 10\\.1101/2025\\.11\\.05\\.686725 | Bacteria sense virus-induced genome degradation via methylated mononucleotides | ",
        "notes": "The pinned DefenseFinder article registry maps the named Metis system to the Osterman et al. preprint."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "metis_m6damp_toxic_effector_defense",
        "title": "Metis systems detect methylated mononucleotides",
        "description": "Conservative system-level sketch linking a Metis locus to phage-mediated host-genome degradation, modified mononucleotide sensing, toxic effector activation, and Metis system possession.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Metis as a named m6dAMP-sensing phage-defense system while leaving exact type I and type II locus composition, native host breadth, subtype distribution, effector biochemistry, and DefenseFinder HMM/rules detection criteria unresolved.",
        "nodes": [
          {
            "node_id": "metis_locus",
            "label": "Metis locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A Metis anti-phage locus encoding m6dAMP sensing and type-specific toxic effector functions."
          },
          {
            "node_id": "phage_mediated_host_genome_degradation",
            "label": "phage-mediated host genome degradation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Degradation of bacterial host genomic DNA to individual nucleotides during phage infection."
          },
          {
            "node_id": "modified_mononucleotide_sensing",
            "label": "modified mononucleotide sensing",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Detection of the modified mononucleotide m6dAMP as a signal of phage-mediated host-genome degradation."
          },
          {
            "node_id": "type_specific_toxic_effector_activation",
            "label": "type-specific toxic effector activation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Activation of a Metis effector that depletes NAD in type I systems or triggers membrane-linked toxicity in type II systems."
          },
          {
            "node_id": "metis_system_trait",
            "label": "Metis system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000502",
            "description": "Possession of a genome-encoded Metis phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "metis_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "modified_mononucleotide_sensing",
            "description": "Metis loci directly sense m6dAMP after phage-mediated host-genome degradation.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.aed6782",
                "snippet": "In this work, we describe Metis, a bacterial defense system that directly senses phage-mediated host genome degradation.",
                "notes": "Osterman et al. directly name Metis as a bacterial system sensing host-genome degradation during phage infection."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| Metis | 10\\.1101/2025\\.11\\.05\\.686725 | Bacteria sense virus-induced genome degradation via methylated mononucleotides | ",
                "notes": "The pinned DefenseFinder article registry maps the named Metis system to the Osterman et al. preprint."
              }
            ]
          },
          {
            "subject": "phage_mediated_host_genome_degradation",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "modified_mononucleotide_sensing",
            "description": "Accumulation of free m6dAMP after host-genome degradation provides the modified mononucleotide signal detected by Metis.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.aed6782",
                "snippet": "Metis aborts phage infection once it detects the modified mononucleotide N6-methyl-deoxyadenosine monophosphate (m6dAMP). As methylation of deoxyadenosines usually occurs on the DNA polymer, accumulation of m6dAMP signals that the host genome has been degraded.",
                "notes": "Osterman et al. connect Metis detection of m6dAMP to the accumulation of that nucleotide after host-genome degradation."
              },
              {
                "reference": "DOI:10.1126/science.aed6782",
                "snippet": "We further show that Metis defense depends on endogenous DNA methylases and that phages can escape Metis through mutations that inactivate host genome degradation.",
                "notes": "Osterman et al. link Metis immunity to endogenous DNA methylases and to phage genome-degradation activity."
              }
            ]
          },
          {
            "subject": "modified_mononucleotide_sensing",
            "predicate": "activates",
            "predicate_id": "RO:0002213",
            "object": "type_specific_toxic_effector_activation",
            "description": "m6dAMP sensing activates a Metis type-specific toxic effector.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.aed6782",
                "snippet": "In type I Metis, sensing of m6dAMP activates a nicotinamide adenine dinucleotide (NAD+) diphosphatase, leading to NAD+ depletion and cessation of the infection process, whereas the effector in type II Metis is a membrane-spanning protein whose toxicity is triggered in response to the modified mononucleotide.",
                "notes": "Osterman et al. distinguish type I and type II Metis effectors without resolving a DefenseFinder rule-level model in the pinned registry."
              }
            ]
          },
          {
            "subject": "type_specific_toxic_effector_activation",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "metis_system_trait",
            "description": "Triggered Metis effector toxicity realizes the Metis system trait by aborting phage infection.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.aed6782",
                "snippet": "Metis aborts phage infection once it detects the modified mononucleotide N6-methyl-deoxyadenosine monophosphate (m6dAMP).",
                "notes": "Osterman et al. connect m6dAMP sensing to type-specific effector toxicity and abortion of the phage infection process."
              }
            ]
          },
          {
            "subject": "metis_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Metis system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.aed6782",
                "snippet": "In this work, we describe Metis, a bacterial defense system that directly senses phage-mediated host genome degradation. Metis aborts phage infection once it detects the modified mononucleotide N6-methyl-deoxyadenosine monophosphate (m6dAMP).",
                "notes": "Osterman et al. identify Metis as a bacterial defense system that aborts phage infection after sensing m6dAMP."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "metis-subtype-and-model-coverage-gap",
        "prompt": "Resolve Metis type I and type II locus composition, native host breadth, profile-to-component mapping, subtype-specific effector biochemistry, and DefenseFinder HMM/rule coverage before minting narrower Metis mechanism or component traits.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Osterman et al. support Metis as a bacterial defense system that senses m6dAMP from phage-mediated host-genome degradation and activates type-specific toxic effectors. The pinned DefenseFinder article registry maps the Metis source key to the Osterman et al. preprint, but the pinned HMM inventory and rules table have no exact Metis rows. This first-pass record therefore does not resolve the complete locus model, subtype component boundaries, direct HMM/profile mapping, or native host breadth.",
        "evidence": [
          {
            "reference": "DOI:10.1126/science.aed6782",
            "snippet": "In this work, we describe Metis, a bacterial defense system that directly senses phage-mediated host genome degradation.",
            "notes": "Osterman et al. directly name Metis as a bacterial system sensing host-genome degradation during phage infection."
          },
          {
            "reference": "DOI:10.1126/science.aed6782",
            "snippet": "In type I Metis, sensing of m6dAMP activates a nicotinamide adenine dinucleotide (NAD+) diphosphatase, leading to NAD+ depletion and cessation of the infection process, whereas the effector in type II Metis is a membrane-spanning protein whose toxicity is triggered in response to the modified mononucleotide.",
            "notes": "Osterman et al. distinguish type I and type II Metis effectors without resolving a DefenseFinder rule-level model in the pinned registry."
          },
          {
            "reference": "DOI:10.1126/science.aed6782",
            "snippet": "We further show that Metis defense depends on endogenous DNA methylases and that phages can escape Metis through mutations that inactivate host genome degradation.",
            "notes": "Osterman et al. link Metis immunity to endogenous DNA methylases and to phage genome-degradation activity."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
            "snippet": "| Metis | 10\\.1101/2025\\.11\\.05\\.686725 | Bacteria sense virus-induced genome degradation via methylated mononucleotides | ",
            "notes": "The pinned DefenseFinder article registry maps the named Metis system to the Osterman et al. preprint."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "notes": "A structured first-pass search of the pinned DefenseFinder HMM inventory found no exact Metis row."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "A structured first-pass search of the pinned DefenseFinder rules table found no exact Metis system row."
          }
        ],
        "attaches_to": [
          "causal_graphs#metis_m6damp_toxic_effector_defense"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-30"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-30T22:51:08Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Metis system as a Science-, PubMed-, and DefenseFinder-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, research, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v379.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-30T22:51:09Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed Metis system canonical_examples and left them empty because public PubMed and DefenseFinder evidence supports the named phage-defense system but not a direct named native microbial isolate exemplar with experimentally verified endogenous Metis activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000526",
    "label": "MksBEFG system",
    "definition": "A Wadjet system in which an organism possesses an MksBEFG derivative SMC locus encoding an MksBEF ATPase core and an MksG nuclease that degrades plasmid DNA.",
    "definition_source": "DOI:10.1093/nar/gkad130",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000218"
    ],
    "synonyms": [
      {
        "synonym_text": "MksBEFG",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1093/nar/gkad130"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1093/nar/gkad130",
        "snippet": "The MksG nuclease is the executing part of the bacterial plasmid defense system MksBEFG",
        "notes": "Weiss et al. describe MksBEFG as a bacterial plasmid-defense system and identify MksG as its executing nuclease component."
      },
      {
        "reference": "DOI:10.1093/nar/gkad130",
        "snippet": "MksG is a nuclease that degrades plasmid DNA",
        "notes": "Weiss et al. support plasmid-DNA degradation by the MksG nuclease of the MksBEFG system."
      },
      {
        "reference": "DOI:10.1093/nar/gkad130",
        "snippet": "Introduction of plasmids results in an increase in DNA bound MksG, indicating an activation of the system in vivo",
        "notes": "Weiss et al. support plasmid-responsive activation of the Corynebacterium glutamicum MksBEFG system in vivo."
      },
      {
        "reference": "DOI:10.1093/nar/gkad130",
        "snippet": "The MksBEF subunits exhibit an ATPase cycle in vitro",
        "notes": "Weiss et al. support ATPase cycling by the C. glutamicum MksBEF core."
      },
      {
        "reference": "DOI:10.1016/j.molcel.2022.11.015",
        "snippet": "Wadjet systems (JetABCD/MksBEFG/EptABCD) are derivative SMC complexes with roles in bacterial immunity against selfish DNA",
        "notes": "Liu et al. support MksBEFG as a Wadjet-family derivative SMC complex related to JetABCD and EptABCD."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1718",
        "taxon_label": "Corynebacterium glutamicum",
        "note": "Weiss et al. investigated the Corynebacterium glutamicum MksBEFG complex and showed that plasmid introduction increased DNA-bound MksG in vivo.",
        "reference": "DOI:10.1093/nar/gkad130"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "mksbefg_degrades_plasmid_dna",
        "title": "MksBEFG systems degrade plasmid DNA",
        "description": "Conservative system-level sketch linking MksBEFG loci to MksG-dependent plasmid DNA degradation and Wadjet system possession.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures the MksBEFG subfamily at locus and plasmid-degradation-output level without asserting the exact MksBEF ATPase-to-MksG coupling step, plasmid substrate breadth, cellular MksG loading path, or accession-level protein examples.",
        "nodes": [
          {
            "node_id": "mksbefg_locus",
            "label": "MksBEFG locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A Wadjet-family plasmid-defense locus encoding MksB, MksE, MksF, and MksG components."
          },
          {
            "node_id": "mksbef_atpase_cycle",
            "label": "MksBEF ATPase cycle",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "ATPase cycling by the MksB, MksE, and MksF subunits of the MksBEFG complex."
          },
          {
            "node_id": "mksg_plasmid_dna_degradation",
            "label": "MksG plasmid DNA degradation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Degradation of plasmid DNA by the MksG nuclease component of the MksBEFG system."
          },
          {
            "node_id": "plasmid_transformation",
            "label": "plasmid transformation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Introduction and establishment of exogenous plasmid DNA in a bacterial cell."
          },
          {
            "node_id": "mksbefg_system_trait",
            "label": "MksBEFG system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000526",
            "description": "Possession of a genome-encoded MksBEFG anti-plasmid defense system."
          },
          {
            "node_id": "wadjet_system_trait",
            "label": "Wadjet system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000218",
            "description": "Possession of a genome-encoded Wadjet anti-plasmid defense locus."
          }
        ],
        "edges": [
          {
            "subject": "mksbefg_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "mksbef_atpase_cycle",
            "description": "MksBEFG loci encode the MksBEF ATPase core.",
            "evidence": [
              {
                "reference": "DOI:10.1093/nar/gkad130",
                "snippet": "The MksBEF subunits exhibit an ATPase cycle in vitro",
                "notes": "Weiss et al. support ATPase cycling by the C. glutamicum MksBEF core."
              }
            ]
          },
          {
            "subject": "mksbefg_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "mksg_plasmid_dna_degradation",
            "description": "MksBEFG loci encode the MksG nuclease that degrades plasmid DNA.",
            "evidence": [
              {
                "reference": "DOI:10.1093/nar/gkad130",
                "snippet": "The MksG nuclease is the executing part of the bacterial plasmid defense system MksBEFG",
                "notes": "Weiss et al. describe MksBEFG as a bacterial plasmid-defense system and identify MksG as its executing nuclease component."
              },
              {
                "reference": "DOI:10.1093/nar/gkad130",
                "snippet": "MksG is a nuclease that degrades plasmid DNA",
                "notes": "Weiss et al. support plasmid-DNA degradation by the MksG nuclease of the MksBEFG system."
              }
            ]
          },
          {
            "subject": "mksg_plasmid_dna_degradation",
            "predicate": "mitigates",
            "predicate_id": "METPO:2007407",
            "object": "plasmid_transformation",
            "description": "MksG-dependent plasmid DNA degradation restricts incoming plasmid DNA.",
            "evidence": [
              {
                "reference": "DOI:10.1093/nar/gkad130",
                "snippet": "MksG is a nuclease that degrades plasmid DNA",
                "notes": "Weiss et al. support plasmid-DNA degradation by the MksG nuclease of the MksBEFG system."
              },
              {
                "reference": "DOI:10.1093/nar/gkad130",
                "snippet": "Introduction of plasmids results in an increase in DNA bound MksG, indicating an activation of the system in vivo",
                "notes": "Weiss et al. support plasmid-responsive activation of the Corynebacterium glutamicum MksBEFG system in vivo."
              }
            ]
          },
          {
            "subject": "mksg_plasmid_dna_degradation",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "mksbefg_system_trait",
            "description": "Plasmid DNA degradation realizes the MksBEFG anti-plasmid defense trait.",
            "evidence": [
              {
                "reference": "DOI:10.1093/nar/gkad130",
                "snippet": "The MksG nuclease is the executing part of the bacterial plasmid defense system MksBEFG",
                "notes": "Weiss et al. describe MksBEFG as a bacterial plasmid-defense system and identify MksG as its executing nuclease component."
              }
            ]
          },
          {
            "subject": "mksbefg_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "wadjet_system_trait",
            "description": "MksBEFG system possession is a Wadjet system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.molcel.2022.11.015",
                "snippet": "Wadjet systems (JetABCD/MksBEFG/EptABCD) are derivative SMC complexes with roles in bacterial immunity against selfish DNA",
                "notes": "Liu et al. support MksBEFG as a Wadjet-family derivative SMC complex related to JetABCD and EptABCD."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "mksbefg-activation-and-substrate-gap",
        "prompt": "Resolve MksBEFG plasmid substrate breadth, MksBEF ATPase-to-MksG coupling, MksG activation state, and accession-level protein examples before minting narrower MksBEFG mechanism or component traits.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Weiss et al. support MksBEFG as a bacterial plasmid-defense system with an MksBEF ATPase core and MksG plasmid-DNA-degradation nuclease, and Liu et al. place MksBEFG in the broader Wadjet derivative-SMC family. This first-pass record leaves exact plasmid substrate breadth, MksBEF-to-MksG coupling, cellular MksG loading, and accession-level component examples unresolved.",
        "evidence": [
          {
            "reference": "DOI:10.1093/nar/gkad130",
            "snippet": "The MksG nuclease is the executing part of the bacterial plasmid defense system MksBEFG",
            "notes": "Weiss et al. describe MksBEFG as a bacterial plasmid-defense system and identify MksG as its executing nuclease component."
          },
          {
            "reference": "DOI:10.1093/nar/gkad130",
            "snippet": "MksG is a nuclease that degrades plasmid DNA",
            "notes": "Weiss et al. support plasmid-DNA degradation by the MksG nuclease of the MksBEFG system."
          },
          {
            "reference": "DOI:10.1093/nar/gkad130",
            "snippet": "Introduction of plasmids results in an increase in DNA bound MksG, indicating an activation of the system in vivo",
            "notes": "Weiss et al. support plasmid-responsive activation of the Corynebacterium glutamicum MksBEFG system in vivo."
          },
          {
            "reference": "DOI:10.1093/nar/gkad130",
            "snippet": "The MksBEF subunits exhibit an ATPase cycle in vitro",
            "notes": "Weiss et al. support ATPase cycling by the C. glutamicum MksBEF core."
          },
          {
            "reference": "DOI:10.1016/j.molcel.2022.11.015",
            "snippet": "Wadjet systems (JetABCD/MksBEFG/EptABCD) are derivative SMC complexes with roles in bacterial immunity against selfish DNA",
            "notes": "Liu et al. support MksBEFG as a Wadjet-family derivative SMC complex related to JetABCD and EptABCD."
          }
        ],
        "attaches_to": [
          "causal_graphs#mksbefg_degrades_plasmid_dna"
        ],
        "posed_by": "codex",
        "posed_date": "2026-10-01"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-01T21:15:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted MksBEFG system as a DOI-backed GENOMICS TraitRecord under the Wadjet system parent after an ignored-and-hidden duplicate review found no exact same-scope live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v403.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000297",
    "label": "MMB gp29-gp30 system",
    "definition": "A phage defense system in which an organism possesses an MMB gp29-gp30 locus that can protect bacteria from bacteriophage infection.",
    "definition_source": "DOI:10.1038/nmicrobiol.2016.251",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "MMB_gp29_gp30",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/nmicrobiol.2016.251",
        "snippet": "at least five distinct prophage-expressed viral defense systems that interfere with infection",
        "notes": "The PMC author manuscript for Dedrick et al. places the Cluster N MMB gp29-gp30 system in a cohort of prophage-expressed defenses against lytic and temperate mycobacteriophages."
      },
      {
        "reference": "DOI:10.1038/nmicrobiol.2016.251",
        "snippet": "Tweety (F1) is targeted by Xerxes, MMB, Phrann and Panchino",
        "notes": "The PMC author manuscript for Dedrick et al. identifies Tweety as one phage targeted by the MichelleMyBell prophage defense profile."
      },
      {
        "reference": "DOI:10.1038/nmicrobiol.2016.251",
        "snippet": "Phages MMB, Xerxes, and Pipsqueaks are closely-related in the lysis-immunity region (Fig. 4a) and MMB and Xerxes have almost identical patterns of defense against eleven individual phages",
        "notes": "The PMC author manuscript for Dedrick et al. connects the MichelleMyBell and Xerxes defense spectra to their shared lysis-immunity-region context."
      },
      {
        "reference": "DOI:10.1038/nmicrobiol.2016.251",
        "snippet": "we constructed a MMB mutant in which genes 29 and 30 are removed (deletions of individual genes appear to generate non-viable mutants; Supplementary Table 3) and showed that prophage-mediated defense is lost",
        "notes": "The PMC author manuscript for Dedrick et al. deletes the MMB 29-30 interval when testing whether gp29 and gp30 contribute to MMB defense."
      },
      {
        "reference": "DOI:10.1038/nmicrobiol.2016.251",
        "snippet": "expressing MMB 29 and 30 confers the same pattern of defense as the MMB lysogen",
        "notes": "The PMC author manuscript for Dedrick et al. shows that recombinant MMB genes 29 and 30 reproduce the MMB prophage-mediated defense pattern."
      },
      {
        "reference": "DOI:10.1038/nmicrobiol.2016.251",
        "snippet": "MMB 29-30 and Phrann 29-30 also confer survival to infection by a lytic Tweety derivative",
        "notes": "The PMC author manuscript for Dedrick et al. shows that the MMB gp29-gp30 system can protect bacteria from a lytic Tweety derivative in addition to wild-type Tweety."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "MMB_gp29_gp30 | 10\\.1038/nmicrobiol\\.2016\\.251 | Prophage-mediated defence against viral attack and viral counter-defence",
        "notes": "The DefenseFinder model registry maps the named MMB_gp29_gp30 system to the Dedrick et al. prophage-mediated viral-defense paper."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "MMB_gp29_gp30__gp29                              | MMB_gp29_gp30__gp29                              | MMB_gp29_gp30",
        "notes": "The DefenseFinder HMM inventory records an MMB gp29-gp30 profile for MMB_gp29_gp30__gp29 in the MMB_gp29_gp30 model namespace."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "MMB_gp29_gp30__gp30                              | MMB_gp29_gp30__gp30                              | MMB_gp29_gp30",
        "notes": "The DefenseFinder HMM inventory records an MMB gp29-gp30 profile for MMB_gp29_gp30__gp30 in the MMB_gp29_gp30 model namespace."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "MMB_gp29_gp30\tMMB_gp29_gp30\t2\t2\tMMB_gp29_gp30__gp29, MMB_gp29_gp30__gp30",
        "notes": "The DefenseFinder rules table models MMB_gp29_gp30 as a two-component system requiring gp29 and gp30 profiles."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "mmb_gp29_gp30_locus_restricts_phage",
        "title": "MMB gp29-gp30 loci confer heterotypic phage defense",
        "description": "Conservative system-level sketch linking possession of an MMB gp29-gp30 locus to restricted bacteriophage propagation without asserting the unresolved lytic trigger, gp29-gp30 interaction, or downstream arrest mechanism.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures MMB gp29-gp30 as a named anti-phage system with DefenseFinder gp29 and gp30 profiles while leaving the direct lytic trigger, MMB gp30 regulatory role, MMB gp29 biochemical activity, and exact downstream arrest mechanism unresolved.",
        "nodes": [
          {
            "node_id": "mmb_gp29_gp30_locus",
            "label": "MMB gp29-gp30 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "An MMB gp29-gp30 anti-phage defense locus cataloged in DefenseFinder with gp29 and gp30 HMM profiles."
          },
          {
            "node_id": "restricted_phage_propagation",
            "label": "restricted phage propagation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced propagation of bacteriophage in cells carrying the MMB gp29-gp30 system."
          },
          {
            "node_id": "mmb_gp29_gp30_system_trait",
            "label": "MMB gp29-gp30 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000297",
            "description": "Possession of a genome-encoded MMB gp29-gp30 phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "mmb_gp29_gp30_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "restricted_phage_propagation",
            "description": "Dedrick et al. show that MMB genes 29 and 30 are necessary and sufficient for the tested MMB defense profile, and DefenseFinder catalogs gp29 and gp30 profiles in the MMB_gp29_gp30 model namespace.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nmicrobiol.2016.251",
                "snippet": "we constructed a MMB mutant in which genes 29 and 30 are removed (deletions of individual genes appear to generate non-viable mutants; Supplementary Table 3) and showed that prophage-mediated defense is lost",
                "notes": "The PMC author manuscript for Dedrick et al. shows that deleting the MMB 29-30 interval abolishes MMB prophage-mediated defense."
              },
              {
                "reference": "DOI:10.1038/nmicrobiol.2016.251",
                "snippet": "expressing MMB 29 and 30 confers the same pattern of defense as the MMB lysogen",
                "notes": "The PMC author manuscript for Dedrick et al. shows that MMB genes 29 and 30 are sufficient to reproduce the MMB defense pattern."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "MMB_gp29_gp30__gp29                              | MMB_gp29_gp30__gp29                              | MMB_gp29_gp30",
                "notes": "The DefenseFinder HMM inventory records an MMB gp29-gp30 profile for MMB_gp29_gp30__gp29 in the MMB_gp29_gp30 model namespace."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "MMB_gp29_gp30__gp30                              | MMB_gp29_gp30__gp30                              | MMB_gp29_gp30",
                "notes": "The DefenseFinder HMM inventory records an MMB gp29-gp30 profile for MMB_gp29_gp30__gp30 in the MMB_gp29_gp30 model namespace."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "MMB_gp29_gp30\tMMB_gp29_gp30\t2\t2\tMMB_gp29_gp30__gp29, MMB_gp29_gp30__gp30",
                "notes": "The DefenseFinder rules table models MMB_gp29_gp30 as a two-component system requiring gp29 and gp30 profiles."
              }
            ]
          },
          {
            "subject": "restricted_phage_propagation",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "mmb_gp29_gp30_system_trait",
            "description": "MMB-gp29-gp30-mediated restriction of phage propagation realizes the MMB gp29-gp30 system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nmicrobiol.2016.251",
                "snippet": "expressing MMB 29 and 30 confers the same pattern of defense as the MMB lysogen",
                "notes": "The PMC author manuscript for Dedrick et al. shows that MMB genes 29 and 30 reproduce the MMB defense pattern."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "MMB_gp29_gp30 | 10\\.1038/nmicrobiol\\.2016\\.251 | Prophage-mediated defence against viral attack and viral counter-defence",
                "notes": "DefenseFinder records MMB_gp29_gp30 as a named system from the Dedrick et al. prophage-defense paper."
              }
            ]
          },
          {
            "subject": "mmb_gp29_gp30_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "MMB gp29-gp30 system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| MMB_gp29_gp30 | 10\\.1038/nmicrobiol\\.2016\\.251 | Prophage-mediated defence against viral attack and viral counter-defence |",
                "notes": "DefenseFinder associates MMB_gp29_gp30 with the Dedrick et al. prophage-mediated viral-defense paper."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "mmb_gp29_gp30-mechanism-gap",
        "prompt": "Resolve the MMB gp29 biochemical activity, MMB gp30 regulatory role, lytic trigger, gp29-gp30 interaction, counter-defense specificity, and homolog breadth before minting narrower MMB gp29-gp30 mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Dedrick et al. and DefenseFinder support MMB gp29-gp30 as a named anti-phage system with gp29 and gp30 profiles, but the MMB gp29 biochemical activity, direct gp29-gp30 interaction, triggering Tweety early lytic gene or genes, MMB-specific counter-defense tuning, and relationship to Squirty homologs are not resolved enough here to assert a narrower mechanistic child trait.",
        "attaches_to": [
          "causal_graphs#mmb_gp29_gp30_locus_restricts_phage"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-20"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-20T00:13:48Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted MMB gp29-gp30 system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v174.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000089",
    "label": "mobile genetic element",
    "definition": "A genomics trait describing possession of DNA segments that can move within or between genomes and mediate horizontal gene transfer, including plasmids, prophages, transposable elements, and genomic islands.",
    "definition_source": "DOI:10.1038/nrmicro1235",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000188"
    ],
    "synonyms": [
      {
        "synonym_text": "MGE",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1038/nrmicro1235"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/nrmicro1235",
        "notes": "Frost et al. review mobile genetic elements as the agents of horizontal gene transfer and genome plasticity; parent of the plasmid, prophage, transposable- element, and genomic-island sub-variants."
      },
      {
        "reference": "DOI:10.1111/1574-6976.12067",
        "notes": "Siguier, Gourbeyre & Chandler review insertion sequences as a major class of mobile genetic elements shaping bacterial genomes."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:562",
        "taxon_label": "Escherichia coli",
        "note": "plasmids, IS elements, integrons",
        "reference": "PMID:32807088"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "mge_horizontal_gene_transfer",
        "title": "Mobile genetic elements mediate horizontal gene transfer",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This genomics record is a measurement, genomic-element classification, or population-level descriptor rather than one taxon-specific protein mechanism; contextual protein nodes do not receive token UniProt examples.",
        "description": "Evidence-backed causal sketch linking MGE possession to horizontal gene transfer and resulting genome plasticity.",
        "nodes": [
          {
            "node_id": "mge_trait",
            "label": "mobile genetic element",
            "node_type": "TRAIT",
            "grounding": "traitmech:000089",
            "description": "Possession of DNA segments that move within or between genomes."
          },
          {
            "node_id": "horizontal_gene_transfer",
            "label": "horizontal gene transfer",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Transfer of genetic material between organisms outside vertical descent.",
            "grounding": "GO:0009292"
          },
          {
            "node_id": "genome_plasticity",
            "label": "genome plasticity",
            "node_type": "QUALITY",
            "description": "Capacity of a genome for rearrangement and gene gain/loss."
          },
          {
            "node_id": "relaxase",
            "label": "relaxase",
            "node_type": "GENE_OR_PROTEIN",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed as a contextual protein or protein-complex label in a nonmechanistic genomics classification; no exact semantic family term was established for this aggregate use.",
            "description": "Conjugation enzyme that nicks and unwinds DNA at oriT and covalently attaches to the 5-prime end."
          },
          {
            "node_id": "orit",
            "label": "origin of transfer (oriT)",
            "node_type": "CELLULAR_LOCALIZATION",
            "description": "DNA site where the relaxase nicks to initiate rolling-circle conjugative transfer."
          },
          {
            "node_id": "coupling_protein",
            "label": "type IV coupling protein",
            "node_type": "GENE_OR_PROTEIN",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed as a contextual protein or protein-complex label in a nonmechanistic genomics classification; no exact semantic family term was established for this aggregate use.",
            "description": "VirD4/TraD-like ATPase that recruits the relaxase-DNA substrate to the T4SS."
          },
          {
            "node_id": "t4ss",
            "label": "type IV secretion system",
            "node_type": "GENE_OR_PROTEIN",
            "description": "VirB4/VirD4-containing macromolecular machine that mediates conjugative DNA transfer.",
            "grounding": "GO:0043684"
          },
          {
            "node_id": "conjugative_dna_transfer",
            "label": "conjugative DNA transfer",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Cell-to-cell transfer of single-stranded DNA through the mating apparatus."
          },
          {
            "node_id": "integrase_excisionase",
            "label": "integrase and excisionase",
            "node_type": "GENE_OR_PROTEIN",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed as a contextual protein or protein-complex label in a nonmechanistic genomics classification; no exact semantic family term was established for this aggregate use.",
            "description": "Recombinase plus recombination directionality factor that mediate ICE/IME excision."
          },
          {
            "node_id": "ice_excision",
            "label": "ICE excision and circularization",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Excision of an integrated conjugative element to form a circular dsDNA transfer intermediate."
          },
          {
            "node_id": "integron_integrase",
            "label": "integron integrase (IntI)",
            "node_type": "GENE_OR_PROTEIN",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed as a contextual protein or protein-complex label in a nonmechanistic genomics classification; no exact semantic family term was established for this aggregate use.",
            "description": "Site-specific recombinase that captures and excises gene cassettes at attI/attC sites."
          },
          {
            "node_id": "cassette_recombination",
            "label": "attI/attC cassette recombination",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Site-specific recombination inserting or excising integron gene cassettes."
          },
          {
            "node_id": "transposition",
            "label": "transposition",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Movement of insertion sequences and transposons within or between replicons.",
            "grounding": "GO:0032196"
          },
          {
            "node_id": "transduction",
            "label": "transduction of host DNA",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Phage-mediated packaging and transfer of host DNA during prophage induction or lytic infection."
          },
          {
            "node_id": "antibiotic_selection",
            "label": "antibiotic selective pressure",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Selective pressure from antibiotics that enriches resistance gene cargo on mobile elements."
          },
          {
            "node_id": "amr_cargo",
            "label": "antimicrobial resistance gene cargo",
            "node_type": "QUALITY",
            "description": "Accumulation of antimicrobial resistance genes carried on self-transmissible ICEs and genomic islands."
          }
        ],
        "edges": [
          {
            "subject": "mge_trait",
            "predicate": "enables",
            "object": "horizontal_gene_transfer",
            "description": "MGEs serve as the vehicles of horizontal gene transfer.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro1235",
                "notes": "Frost et al. frame MGEs as the agents of horizontal gene transfer."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "horizontal_gene_transfer",
            "predicate": "contributes to",
            "object": "genome_plasticity",
            "description": "HGT mediated by MGEs drives gene gain/loss and rearrangement.",
            "evidence": [
              {
                "reference": "DOI:10.1111/1574-6976.12067",
                "notes": "Siguier et al. review insertion-sequence-driven genome plasticity."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "relaxase",
            "predicate": "nicks/unwinds at",
            "object": "orit",
            "description": "Relaxase nicks and unwinds DNA at oriT, covalently attaching to the 5-prime end to initiate transfer.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.01360-24",
                "notes": "nicking/unwinding by a relaxase at oriT, covalent attachment of relaxase to the 5-prime end."
              }
            ]
          },
          {
            "subject": "coupling_protein",
            "predicate": "recruits substrate to",
            "object": "t4ss",
            "description": "The cognate coupling protein recruits the relaxase-DNA substrate to the secretion apparatus.",
            "evidence": [
              {
                "reference": "DOI:10.1093/nar/gkac1079",
                "notes": "the secretion apparatus by the cognate coupling protein TraD; type IV coupling proteins (T4CPs)."
              }
            ]
          },
          {
            "subject": "t4ss",
            "predicate": "mediates",
            "object": "conjugative_dna_transfer",
            "description": "VirB4/VirD4-containing T4SS mediates conjugative DNA transfer between donor and recipient.",
            "evidence": [
              {
                "reference": "DOI:10.1093/nar/gkad024",
                "notes": "VirB4 and VirD4 ATPases of the Type IV secretion system (T4SS) mediate conjugative transfer."
              }
            ]
          },
          {
            "subject": "conjugative_dna_transfer",
            "predicate": "enables",
            "object": "horizontal_gene_transfer",
            "description": "Conjugative DNA transfer is a major route of MGE-mediated horizontal gene transfer.",
            "evidence": [
              {
                "reference": "DOI:10.1111/1751-7915.14408",
                "notes": "transfer of a single-stranded DNA molecule, followed by integration into the recipient chromosome."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "integrase_excisionase",
            "predicate": "enables",
            "object": "ice_excision",
            "description": "Integrase and excisionase mediate ICE excision and circular dsDNA intermediate formation.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.01360-24",
                "notes": "excision mediated by an integrase (recombinase) and an excisionase, formation of a circular dsDNA intermediate."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "ice_excision",
            "predicate": "enables",
            "object": "conjugative_dna_transfer",
            "description": "Excision and circularization produce the transferable form required for conjugative transfer.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.01360-24",
                "notes": "Circular dsDNA intermediate is the transferable form prior to conjugation."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "integron_integrase",
            "predicate": "catalyzes",
            "object": "cassette_recombination",
            "description": "Integron integrase catalyzes site-specific recombination at attI/attC to capture or excise cassettes.",
            "evidence": [
              {
                "reference": "DOI:10.1111/1751-7915.14408",
                "notes": "IntI recognises attI/attC and catalyses site-specific recombination inserting cassettes."
              }
            ],
            "predicate_id": "biolink:catalyzes"
          },
          {
            "subject": "mge_trait",
            "predicate": "enables",
            "object": "transposition",
            "description": "Insertion sequences and transposons excise and move within or between regions of the genome.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-micro-032521-022006",
                "notes": "transposons and insertion sequences excise and move or transpose between regions of the genome."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "transposition",
            "predicate": "contributes to",
            "object": "genome_plasticity",
            "description": "Transposition drives genome rearrangement and gene gain/loss.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-micro-032521-022006",
                "notes": "IS/transposon mobility reshapes replicons, contributing to genome plasticity."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "transduction",
            "predicate": "contributes to",
            "object": "horizontal_gene_transfer",
            "description": "Prophage induction and lytic infection package and transduce host DNA, a route of HGT.",
            "evidence": [
              {
                "reference": "DOI:10.1093/nar/gkae489",
                "notes": "host DNA packaged and transduced during both prophage induction and lytic infection."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "antibiotic_selection",
            "predicate": "enriches",
            "object": "amr_cargo",
            "description": "Antibiotic selective pressure enriches AMR genes on self-transmissible ICEs and genomic islands.",
            "evidence": [
              {
                "reference": "DOI:10.1093/nar/gkad644",
                "notes": "antibiotic selective pressure tied to the accumulation and spread of resistance on self-transmissible ICEs."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-06-05T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate GENOMICS axis class (mobile genetic element) to parent plasmid carriage, prophage, transposable element, and genomic island.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-08T14:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (MGE-mediated horizontal gene transfer) with RO/biolink predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-14T06:55:38Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0009292\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 11 evidence-backed generic edges (13 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:11Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 7 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d74, RO:0002326\u00d72, biolink:catalyzes\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:32Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0032196\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-26T07:15:18Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A015YCT3\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:21:11Z",
        "curator": "claude",
        "action": "RETRACT_DEAD_UNIPROT_GROUNDINGS",
        "changes": "Retracted 1 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:23:53Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0043684\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope mge_horizontal_gene_transfer=NONMECHANISTIC with scope_notes; marked 4 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (relaxase, coupling_protein, integrase_excisionase, integron_integrase).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000372",
    "label": "Mok-Hok-Sok system",
    "definition": "A phage defense system in which an organism possesses a hok/sok toxin-antitoxin locus represented by DefenseFinder as the two-profile Mok_Hok_Sok model and experimentally linked to bacteriophage T4 exclusion by the plasmid R1 hok/sok locus.",
    "definition_source": "DOI:10.1128/jb.178.7.2044-2050.1996",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "Mok_Hok_Sok",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      },
      {
        "synonym_text": "hok/sok",
        "synonym_type": "RELATED_SYNONYM",
        "source": "PMID:8606182"
      },
      {
        "synonym_text": "Mok_Hok_Sok__Hok",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "Mok_Hok_Sok__Mok",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "PMID:8606182",
        "snippet": "To investigate whether the hok/sok locus evolved as a phage-exclusion mechanism, Escherichia coli cells that contain hok/sok on a pBR322-based plasmid were challenged with T1, T4, T5, T7, and lambda phage.",
        "notes": "Pecota and Wood tested whether a plasmid-carried hok/sok locus can act as a phage-exclusion mechanism."
      },
      {
        "reference": "PMID:8606182",
        "snippet": "The presence of hok/sok reduced the efficiency of plating of T4 by 42% and decreased the plaque size by approximately 85%.",
        "notes": "Pecota and Wood show that hok/sok reduced bacteriophage T4 plating efficiency and plaque size."
      },
      {
        "reference": "PMID:8606182",
        "snippet": "Single-step growth experiments demonstrated that hok/sok decreased the T4 burst size by 40%, increased the time to form mature phage (eclipse time) from 22 to 30 min, and increased the time to cell lysis (latent period) from 30 to 60 min.",
        "notes": "Pecota and Wood support delayed T4 development and a lower T4 burst size in the presence of hok/sok."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "Mok_Hok_Sok | 10\\.1128/jb\\.178\\.7\\.2044-2050\\.1996 | Exclusion of T4 phage by the hok/sok killer locus from plasmid R1",
        "notes": "The DefenseFinder article registry maps the named Mok_Hok_Sok system to the Pecota and Wood plasmid R1 hok/sok phage-exclusion paper."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "Mok_Hok_Sok\tMok_Hok_Sok\t1\t1\tMok_Hok_Sok__Hok, Mok_Hok_Sok__Mok\t\t\t",
        "notes": "The DefenseFinder rules table models Mok_Hok_Sok as a single system listing Hok and Mok profiles with 1/1 thresholds."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| Mok_Hok_Sok__Hok                                 | Mok_Hok_Sok__Hok                                 | Mok_Hok_Sok            | Custom                  | 90     |",
        "notes": "The DefenseFinder HMM inventory records Mok_Hok_Sok__Hok under Mok_Hok_Sok."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| Mok_Hok_Sok__Mok                                 | Mok_Hok_Sok__Mok                                 | Mok_Hok_Sok            | Custom                  | 20     |",
        "notes": "The DefenseFinder HMM inventory records Mok_Hok_Sok__Mok under Mok_Hok_Sok."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "mok_hok_sok_locus_restricts_t4_phage",
        "title": "Mok-Hok-Sok loci exclude T4 phage",
        "description": "Conservative system-level sketch linking a DefenseFinder Mok_Hok_Sok locus to bacteriophage T4 exclusion and the Mok-Hok-Sok system trait.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Mok_Hok_Sok as a named DefenseFinder two-profile model tied to plasmid R1 hok/sok T4 exclusion while leaving natural host breadth, Sok antisense-RNA representation, Hok toxin activation, and the exact DefenseFinder Hok/Mok profile-to-activity mapping unresolved.",
        "nodes": [
          {
            "node_id": "mok_hok_sok_locus",
            "label": "Mok_Hok_Sok locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A hok/sok toxin-antitoxin phage-defense locus represented by the DefenseFinder Mok_Hok_Sok Hok and Mok profiles."
          },
          {
            "node_id": "t4_phage_exclusion",
            "label": "T4 phage exclusion",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Restriction of bacteriophage T4 plaque formation, burst size, and lysis timing in a host carrying hok/sok."
          },
          {
            "node_id": "mok_hok_sok_system_trait",
            "label": "Mok-Hok-Sok system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000372",
            "description": "Possession of a genome-encoded Mok-Hok-Sok phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "mok_hok_sok_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "t4_phage_exclusion",
            "description": "The plasmid R1 hok/sok locus can mediate T4 phage exclusion, and DefenseFinder models Mok_Hok_Sok as a Hok/Mok two-profile system.",
            "evidence": [
              {
                "reference": "PMID:8606182",
                "snippet": "The presence of hok/sok reduced the efficiency of plating of T4 by 42% and decreased the plaque size by approximately 85%.",
                "notes": "Pecota and Wood connect hok/sok possession to bacteriophage T4 restriction."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "Mok_Hok_Sok\tMok_Hok_Sok\t1\t1\tMok_Hok_Sok__Hok, Mok_Hok_Sok__Mok\t\t\t",
                "notes": "The DefenseFinder rules table models Mok_Hok_Sok as a single system listing Hok and Mok profiles with 1/1 thresholds."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| Mok_Hok_Sok__Hok                                 | Mok_Hok_Sok__Hok                                 | Mok_Hok_Sok            | Custom                  | 90     |",
                "notes": "The DefenseFinder HMM inventory records Mok_Hok_Sok__Hok under Mok_Hok_Sok."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| Mok_Hok_Sok__Mok                                 | Mok_Hok_Sok__Mok                                 | Mok_Hok_Sok            | Custom                  | 20     |",
                "notes": "The DefenseFinder HMM inventory records Mok_Hok_Sok__Mok under Mok_Hok_Sok."
              }
            ]
          },
          {
            "subject": "t4_phage_exclusion",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "mok_hok_sok_system_trait",
            "description": "T4 phage exclusion realizes the Mok-Hok-Sok system trait.",
            "evidence": [
              {
                "reference": "PMID:8606182",
                "snippet": "Single-step growth experiments demonstrated that hok/sok decreased the T4 burst size by 40%, increased the time to form mature phage (eclipse time) from 22 to 30 min, and increased the time to cell lysis (latent period) from 30 to 60 min.",
                "notes": "Pecota and Wood show lower burst size and delayed T4 development when hok/sok is present."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Mok_Hok_Sok | 10\\.1128/jb\\.178\\.7\\.2044-2050\\.1996 | Exclusion of T4 phage by the hok/sok killer locus from plasmid R1",
                "notes": "The DefenseFinder article registry maps the named Mok_Hok_Sok system to the Pecota and Wood plasmid R1 hok/sok phage-exclusion paper."
              }
            ]
          },
          {
            "subject": "mok_hok_sok_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Mok-Hok-Sok system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Mok_Hok_Sok | 10\\.1128/jb\\.178\\.7\\.2044-2050\\.1996 | Exclusion of T4 phage by the hok/sok killer locus from plasmid R1",
                "notes": "The DefenseFinder article registry maps the named Mok_Hok_Sok system to the Pecota and Wood plasmid R1 hok/sok phage-exclusion paper."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "Mok_Hok_Sok\tMok_Hok_Sok\t1\t1\tMok_Hok_Sok__Hok, Mok_Hok_Sok__Mok\t\t\t",
                "notes": "The DefenseFinder rules table models Mok_Hok_Sok as a single system listing Hok and Mok profiles with 1/1 thresholds."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "mok-hok-sok-natural-context-gap",
        "prompt": "Resolve the natural host range, Sok antisense-RNA representation, Hok toxin activation, and Hok/Mok profile-to-activity mapping before minting narrower Mok-Hok-Sok mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Pecota and Wood support T4 exclusion by the plasmid R1 hok/sok locus carried on a pBR322-based plasmid, and DefenseFinder models Mok_Hok_Sok with Hok and Mok protein profiles. This first record leaves the native biological breadth, RNA antitoxin representation, Hok triggering, and profile-to-activity mapping unresolved.",
        "attaches_to": [
          "causal_graphs#mok_hok_sok_locus_restricts_t4_phage"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-25"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-25T05:02:42Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Mok-Hok-Sok system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v249.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000246",
    "label": "Mokosh system",
    "definition": "A phage defense system in which an organism possesses a Mokosh locus represented by MkoA/MkoB type I or MkoC type II components that can protect bacteria from bacteriophage infection.",
    "definition_source": "DOI:10.1016/j.chom.2022.09.017",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "Mokosh",
        "synonym_type": "EXACT_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1016/j.chom.2022.09.017",
        "snippet": "discovery of 21 defense systems that protect bacteria from phages, based on computational genomic analyses and phage-infection experiments",
        "notes": "Millman et al. report the computational and experimental cohort that DefenseFinder cites for Mokosh as a bacterial anti-phage system."
      },
      {
        "reference": "DOI:10.1101/2022.05.11.491447",
        "snippet": "discovery of 21 new defense systems that protect bacteria from phages, based on computational genomic analyses and phage infection experiments",
        "notes": "The bioRxiv version of Millman et al. independently carries the 21-system discovery claim linked from DefenseFinder's Mokosh article registry."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "Mokosh | 10\\.1101/2022\\.05\\.11\\.491447 | An expanding arsenal of immune systems that protect bacteria from phages",
        "notes": "The DefenseFinder model registry maps the named Mokosh system to the Millman et al. antiphage-system discovery preprint."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "Mokosh_type_I__MkoA_A, Mokosh_type_I__MkoB_A",
        "notes": "The DefenseFinder rules table models one type I Mokosh subtype with MkoA and MkoB profiles."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "Mokosh_TypeII__MkoC",
        "notes": "The DefenseFinder rules table models type II Mokosh systems around an MkoC profile."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "Mokosh_type_I__MkoA_A",
        "notes": "The DefenseFinder HMM inventory records MkoA as a Mokosh type I profile."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "Mokosh_type_I__MkoB_A",
        "notes": "The DefenseFinder HMM inventory records MkoB as a Mokosh type I profile."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "Mokosh_TypeII__MkoC",
        "notes": "The DefenseFinder HMM inventory records MkoC as a Mokosh type II profile."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "mokosh_locus_restricts_phage",
        "title": "Mokosh loci confer bacterial phage defense",
        "description": "Conservative system-level sketch linking possession of a Mokosh locus to restricted bacteriophage propagation without asserting the unresolved phage trigger or molecular output.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Mokosh as a named anti-phage system with type I MkoA/MkoB and type II MkoC DefenseFinder profiles while leaving its phage trigger, molecular substrate, antiviral effector output, and subtype breadth unresolved.",
        "nodes": [
          {
            "node_id": "mokosh_locus",
            "label": "Mokosh locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A Mokosh anti-phage defense locus containing type I MkoA/MkoB or type II MkoC components."
          },
          {
            "node_id": "restricted_phage_propagation",
            "label": "restricted phage propagation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced propagation of bacteriophage in cells carrying the Mokosh system."
          },
          {
            "node_id": "mokosh_system_trait",
            "label": "Mokosh system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000246",
            "description": "Possession of a genome-encoded Mokosh phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "mokosh_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "restricted_phage_propagation",
            "description": "DefenseFinder maps Mokosh to a bacterial anti-phage-system discovery preprint and represents Mokosh loci through type I MkoA/MkoB and type II MkoC component profiles.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.chom.2022.09.017",
                "snippet": "discovery of 21 defense systems that protect bacteria from phages",
                "notes": "Millman et al. describe the anti-phage discovery cohort that the DefenseFinder Mokosh registry row maps to the Mokosh system."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Mokosh | 10\\.1101/2022\\.05\\.11\\.491447 | An expanding arsenal of immune systems that protect bacteria from phages",
                "notes": "The DefenseFinder registry maps Mokosh itself to the Millman et al. bacterial antiphage-system discovery preprint."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "Mokosh_type_I__MkoA_A, Mokosh_type_I__MkoB_A",
                "notes": "The DefenseFinder rules table supports MkoA and MkoB as Mokosh type I profiles."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "Mokosh_TypeII__MkoC",
                "notes": "The DefenseFinder rules table supports MkoC as a Mokosh type II profile."
              }
            ]
          },
          {
            "subject": "restricted_phage_propagation",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "mokosh_system_trait",
            "description": "Mokosh-mediated phage restriction realizes the Mokosh system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.chom.2022.09.017",
                "snippet": "discovery of 21 defense systems that protect bacteria from phages",
                "notes": "Millman et al. place the Mokosh discovery cohort in the set of bacterial systems that protect against phages."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Mokosh | 10\\.1101/2022\\.05\\.11\\.491447 | An expanding arsenal of immune systems that protect bacteria from phages",
                "notes": "DefenseFinder records Mokosh as a named system from the Millman et al. antiphage discovery preprint."
              }
            ]
          },
          {
            "subject": "mokosh_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Mokosh system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "An expanding arsenal of immune systems that protect bacteria from phages",
                "notes": "DefenseFinder associates Mokosh with the Millman et al. bacterial antiphage-system discovery paper."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "mokosh-mechanism-gap",
        "prompt": "Resolve Mokosh phage triggers and effector outputs before minting narrower Mokosh mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Millman et al. and DefenseFinder support Mokosh as a named anti-phage system with type I and type II profiles, but the trigger, molecular substrate, antiviral effector output, and subtype-specific mechanism are not resolved enough here to assert a narrower mechanistic child trait.",
        "attaches_to": [
          "causal_graphs#mokosh_locus_restricts_phage"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-18"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-18T16:50:59Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Mokosh system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v123.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000368",
    "label": "MqsRAC system",
    "definition": "A phage defense system in which an organism possesses a tripartite MqsRAC toxin-antitoxin-chaperone locus represented by DefenseFinder as a two-profile model requiring MqsRAC__mqsC and MqsRAC__mqsR.",
    "definition_source": "DOI:10.1128/spectrum.03388-23",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "MqsRAC",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1128/spectrum.03388-23"
      },
      {
        "synonym_text": "MqsR/MqsA/MqsC",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1128/spectrum.03388-23"
      },
      {
        "synonym_text": "MqsRAC__mqsC",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "MqsRAC__mqsR",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "PMID:38054715",
        "snippet": "Therefore, our results are important since we show for the first time that a phage-defense system, the MqsRAC toxin/antitoxin system, allows the host to survive infection by forming persister cells, rather than inducing cell suicide.",
        "notes": "Fernandez-Garcia et al. support MqsRAC as a phage-defense system whose outcome is host survival through persister-cell formation rather than cell suicide."
      },
      {
        "reference": "PMID:38054715",
        "snippet": "Moreover, we demonstrate that the MqsRAC system works in concert with restriction/modification systems.",
        "notes": "Fernandez-Garcia et al. connect the MqsRAC system to restriction/modification systems during phage inhibition."
      },
      {
        "reference": "DOI:10.1128/spectrum.03388-23",
        "snippet": "the tripartite system MqsR (RNase toxin)/MqsA (antitoxin)/MqsC (SecB-type chaperone)",
        "notes": "Fernandez-Garcia et al. describe MqsR/MqsA/MqsC as a tripartite toxin-antitoxin-chaperone phage-exclusion system from Escherichia coli C496_10."
      },
      {
        "reference": "DOI:10.1128/spectrum.03388-23",
        "snippet": "We found there was a 2,100 to a 5,000-fold reduction in the EOP with phage T2 when the cells produced MqsR/MqsA/MqsC",
        "notes": "Fernandez-Garcia et al. support MqsRAC-mediated reduction of T2 efficiency of plating."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "MqsRAC | 10\\.1101/2022\\.05\\.12\\.491691 | Mapping the landscape of anti-phage defense mechanisms in the E\\. coli pangenome",
        "notes": "The DefenseFinder article registry maps the named MqsRAC system to Vassallo et al.'s E. coli pangenome phage-defense screen."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "MqsRAC\tMqsRAC\t2\t2\tMqsRAC__mqsC, MqsRAC__mqsR\t\t\t",
        "notes": "The DefenseFinder rules table models MqsRAC as a two-profile system requiring the MqsRAC__mqsC and MqsRAC__mqsR profiles."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| MqsRAC__mqsC                                     | MqsRAC__mqsC                                     | MqsRAC                 | Custom                  | 20     |",
        "notes": "The DefenseFinder HMM inventory records MqsRAC__mqsC under MqsRAC."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| MqsRAC__mqsR                                     | MqsRAC__mqsR                                     | MqsRAC                 | Custom                  | 20     |",
        "notes": "The DefenseFinder HMM inventory records MqsRAC__mqsR under MqsRAC."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "mqsrac_locus_promotes_persister_phage_defense",
        "title": "MqsRAC loci support T2 phage inhibition",
        "description": "Conservative system-level sketch linking possession of an MqsRAC locus to persister-cell formation and T2 inhibition without asserting a universal phage trigger, lethal abortive-infection route, or exact MqsRAC profile-to-activity mapping.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures MqsRAC as a named DefenseFinder two-profile phage-defense system while leaving natural phage breadth, upstream MqsRAC activation logic, the exact relationship between the two DefenseFinder profiles and the tripartite MqsR/MqsA/MqsC locus, and cooperating restriction/modification contexts unresolved.",
        "nodes": [
          {
            "node_id": "mqsrac_locus",
            "label": "MqsRAC locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A toxin-antitoxin-chaperone locus represented by DefenseFinder MqsRAC__mqsC and MqsRAC__mqsR profiles."
          },
          {
            "node_id": "mqsrac_persister_formation",
            "label": "MqsRAC-dependent persister cell formation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Formation of persister cells during T2 phage attack in cells producing MqsR/MqsA/MqsC."
          },
          {
            "node_id": "rm_assisted_t2_inhibition",
            "label": "restriction/modification-assisted T2 inhibition",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Inhibition of T2 phage by MqsR/MqsA/MqsC in concert with restriction/modification systems."
          },
          {
            "node_id": "mqsrac_system_trait",
            "label": "MqsRAC system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000368",
            "description": "Possession of a genome-encoded MqsRAC toxin-antitoxin-chaperone phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "mqsrac_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "mqsrac_persister_formation",
            "description": "Fernandez-Garcia et al. show that the MqsR/MqsA/MqsC toxin-antitoxin-chaperone system can promote persister-cell formation during T2 attack, and DefenseFinder models MqsRAC as a two-profile system.",
            "evidence": [
              {
                "reference": "PMID:38054715",
                "snippet": "Therefore, our results are important since we show for the first time that a phage-defense system, the MqsRAC toxin/antitoxin system, allows the host to survive infection by forming persister cells, rather than inducing cell suicide.",
                "notes": "Fernandez-Garcia et al. connect the MqsRAC system to persister-cell formation."
              },
              {
                "reference": "DOI:10.1128/spectrum.03388-23",
                "snippet": "the tripartite system MqsR (RNase toxin)/MqsA (antitoxin)/MqsC (SecB-type chaperone)",
                "notes": "Fernandez-Garcia et al. identify the system components as MqsR, MqsA, and MqsC."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "MqsRAC | 10\\.1101/2022\\.05\\.12\\.491691 | Mapping the landscape of anti-phage defense mechanisms in the E\\. coli pangenome",
                "notes": "The DefenseFinder article registry maps the named MqsRAC system to Vassallo et al.'s E. coli pangenome phage-defense screen."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "MqsRAC\tMqsRAC\t2\t2\tMqsRAC__mqsC, MqsRAC__mqsR\t\t\t",
                "notes": "The DefenseFinder rules table models MqsRAC as a two-profile system requiring the MqsRAC__mqsC and MqsRAC__mqsR profiles."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| MqsRAC__mqsC                                     | MqsRAC__mqsC                                     | MqsRAC                 | Custom                  | 20     |",
                "notes": "The DefenseFinder HMM inventory records MqsRAC__mqsC under MqsRAC."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| MqsRAC__mqsR                                     | MqsRAC__mqsR                                     | MqsRAC                 | Custom                  | 20     |",
                "notes": "The DefenseFinder HMM inventory records MqsRAC__mqsR under MqsRAC."
              }
            ]
          },
          {
            "subject": "mqsrac_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "rm_assisted_t2_inhibition",
            "description": "Fernandez-Garcia et al. report that the MqsR/MqsA/MqsC toxin-antitoxin-chaperone system works in concert with restriction/modification systems during T2 inhibition.",
            "evidence": [
              {
                "reference": "DOI:10.1128/spectrum.03388-23",
                "snippet": "Therefore, MqsR/MqsA/MqsC works in concert with restriction/modification systems to inhibit T2 phage.",
                "notes": "Fernandez-Garcia et al. connect the MqsRAC system to restriction/modification activity during T2 inhibition."
              }
            ]
          },
          {
            "subject": "mqsrac_persister_formation",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "mqsrac_system_trait",
            "description": "MqsRAC-dependent survival through persister-cell formation realizes the MqsRAC system trait.",
            "evidence": [
              {
                "reference": "PMID:38054715",
                "snippet": "Therefore, our results are important since we show for the first time that a phage-defense system, the MqsRAC toxin/antitoxin system, allows the host to survive infection by forming persister cells, rather than inducing cell suicide.",
                "notes": "Fernandez-Garcia et al. report MqsRAC-dependent host survival through persister-cell formation rather than cell suicide."
              }
            ]
          },
          {
            "subject": "rm_assisted_t2_inhibition",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "mqsrac_system_trait",
            "description": "MqsR/MqsA/MqsC-mediated T2 inhibition realizes the MqsRAC system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1128/spectrum.03388-23",
                "snippet": "We found there was a 2,100 to a 5,000-fold reduction in the EOP with phage T2 when the cells produced MqsR/MqsA/MqsC",
                "notes": "Fernandez-Garcia et al. report reduced T2 efficiency of plating in cells producing MqsR/MqsA/MqsC."
              }
            ]
          },
          {
            "subject": "mqsrac_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "MqsRAC system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "MqsRAC | 10\\.1101/2022\\.05\\.12\\.491691 | Mapping the landscape of anti-phage defense mechanisms in the E\\. coli pangenome",
                "notes": "The DefenseFinder article registry maps the named MqsRAC system to Vassallo et al.'s E. coli pangenome phage-defense screen."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "MqsRAC\tMqsRAC\t2\t2\tMqsRAC__mqsC, MqsRAC__mqsR\t\t\t",
                "notes": "The DefenseFinder rules table models MqsRAC as a two-profile system requiring the MqsRAC__mqsC and MqsRAC__mqsR profiles."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "mqsrac-breadth-and-profile-gap",
        "prompt": "Resolve MqsRAC natural phage breadth, phage-activation signals, the exact DefenseFinder profile-to-MqsR/MqsA/MqsC relationship, and cooperating restriction/modification contexts before minting narrower MqsRAC mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Fernandez-Garcia et al. support MqsR/MqsA/MqsC as an Escherichia coli C496_10 toxin-antitoxin-chaperone system that inhibits T2 phage through persister-cell formation and in concert with restriction/modification systems, while DefenseFinder models MqsRAC through MqsRAC__mqsC and MqsRAC__mqsR markers. Natural phage breadth, the phage signal that activates MqsRAC, MqsA coverage in the DefenseFinder model, and cooperating restriction/modification contexts remain unresolved.",
        "evidence": [
          {
            "reference": "PMID:38054715",
            "snippet": "Moreover, we demonstrate that the MqsRAC system works in concert with restriction/modification systems.",
            "notes": "Fernandez-Garcia et al. leave the MqsRAC and restriction/modification connection at system-level resolution."
          }
        ],
        "attaches_to": [
          "causal_graphs#mqsrac_locus_promotes_persister_phage_defense"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-22"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-22T15:02:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted MqsRAC system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v245.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-22T15:03:00Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed the MqsRAC canonical_examples gap and left canonical_examples empty: the current evidence supports a MqsR/MqsA/MqsC system from Escherichia coli C496_10 expressed from its natural promoter in a K-12 host, but it does not cite a directly observed natural microbial taxon broad enough for a canonical example of endogenous MqsRAC system possession. No paid research was used.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-22T15:15:00Z",
        "curator": "codex",
        "action": "GRAPH_EDGE_DIRECTION_REVIEW",
        "changes": "Addressed issue #1258 by replacing the unsupported MqsRAC persister-cell formation to restriction/modification-assisted T2 inhibition edge with independent MqsRAC locus to restriction/modification-assisted T2 inhibition and MqsRAC-dependent persister formation to MqsRAC system trait edges.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-22T15:18:00Z",
        "curator": "codex",
        "action": "REVIEW_RESTRICTION_MODIFICATION_SPECIFICITY",
        "changes": "Addressed issue #1259 by generalizing unsupported McrBC-specific wording to restriction/modification-assisted T2 inhibition throughout the MqsRAC graph and discussion.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000510",
    "label": "MspJI system",
    "definition": "A type IV modification-dependent restriction system in which an organism possesses an MspJI-family Mrr-like locus encoding a restriction endonuclease that recognizes methylcytosine- or hydroxymethylcytosine-modified DNA and cleaves both strands at a fixed distance from the modified cytosine.",
    "definition_source": "DOI:10.1073/pnas.1018448108",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000496"
    ],
    "synonyms": [
      {
        "synonym_text": "MspJI",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1073/pnas.1018448108",
        "snippet": "MspJI is a novel modification-dependent restriction endonuclease that cleaves at a fixed distance away from the modification site.",
        "notes": "Cohen-Karni et al. support MspJI as a modification-dependent restriction endonuclease with distance-defined cleavage relative to its modified target."
      },
      {
        "reference": "DOI:10.1073/pnas.1018448108",
        "snippet": "All of the enzymes specifically recognize cytosine C5 modification (methylation or hydroxymethylation) in DNA and cleave at a constant distance (N(12)/N(16)) away from the modified cytosine.",
        "notes": "Cohen-Karni et al. biochemically characterized MspJI homologs and support the MspJI family as C5-modified-cytosine-dependent restriction endonucleases."
      },
      {
        "reference": "DOI:10.1093/nar/gkq327",
        "snippet": "Besides 5-methylcytosine, MspJI also recognizes 5-hydroxymethylcytosine but is blocked by 5-glucosylhydroxymethylcytosine.",
        "notes": "Zheng et al. support MspJI restriction of both methylcytosine- and hydroxymethylcytosine-containing DNA while leaving glucosylated hydroxymethylcytosine DNA uncleaved."
      },
      {
        "reference": "DOI:10.1093/nar/gkt747",
        "snippet": "The new class of modification-dependent restriction enzymes was named Type IV, as distinct from the familiar modification-blocked Types I-III.",
        "notes": "Loenen and Raleigh define the Type IV class as modification-dependent restriction enzymes."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| MspJI | 10\\.1073/pnas\\.1018448108 | The MspJI family of modification-dependent restriction endonucleases for epigenetic studies | ",
        "notes": "The pinned DefenseFinder article registry maps the MspJI source key to the Cohen-Karni et al. MspJI-family paper."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "mspji_restricts_modified_cytosine_dna",
        "title": "MspJI restricts modified-cytosine DNA",
        "description": "Conservative system-level sketch linking an MspJI-family locus to modified-cytosine DNA restriction and to the Type IV restriction parent trait.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures MspJI as a named Mrr-like Type IV modification-dependent restriction family while leaving natural host breadth, exact sequence-context specificity across characterized homologs, accession-level protein examples, and DefenseFinder RM_Type_IV HMM/rules mapping unresolved.",
        "nodes": [
          {
            "node_id": "mspji_family_locus",
            "label": "MspJI-family locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A locus encoding an MspJI-family modification-dependent restriction endonuclease."
          },
          {
            "node_id": "mspji_modified_cytosine_dna",
            "label": "MspJI-targeted modified-cytosine DNA",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "DNA containing methylcytosine or hydroxymethylcytosine in an MspJI-family sequence context."
          },
          {
            "node_id": "mspji_modified_cytosine_restriction",
            "label": "MspJI modified-cytosine restriction",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Modification-dependent restriction of C5-modified-cytosine DNA by an MspJI-family endonuclease."
          },
          {
            "node_id": "mspji_system_trait",
            "label": "MspJI system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000510",
            "description": "Possession of a genome-encoded MspJI-family modification-dependent restriction system."
          },
          {
            "node_id": "type_iv_modification_dependent_restriction",
            "label": "type IV modification-dependent restriction system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000496",
            "description": "Possession of a genome-encoded Type IV modification-dependent restriction system."
          }
        ],
        "edges": [
          {
            "subject": "mspji_family_locus",
            "predicate": "enables",
            "predicate_id": "RO:0002327",
            "object": "mspji_modified_cytosine_restriction",
            "description": "MspJI-family loci encode Mrr-like modification-dependent restriction endonucleases.",
            "evidence": [
              {
                "reference": "DOI:10.1073/pnas.1018448108",
                "snippet": "MspJI is a novel modification-dependent restriction endonuclease that cleaves at a fixed distance away from the modification site.",
                "notes": "Cohen-Karni et al. support MspJI as a modification-dependent restriction endonuclease with distance-defined cleavage relative to its modified target."
              },
              {
                "reference": "DOI:10.1073/pnas.1018448108",
                "snippet": "All of the enzymes specifically recognize cytosine C5 modification (methylation or hydroxymethylation) in DNA and cleave at a constant distance (N(12)/N(16)) away from the modified cytosine.",
                "notes": "Cohen-Karni et al. biochemically characterized MspJI homologs and support the MspJI family as C5-modified-cytosine-dependent restriction endonucleases."
              }
            ]
          },
          {
            "subject": "mspji_modified_cytosine_restriction",
            "predicate": "mitigates",
            "predicate_id": "METPO:2007407",
            "object": "mspji_modified_cytosine_dna",
            "description": "MspJI-family restriction targets methylcytosine- or hydroxymethylcytosine-containing DNA.",
            "evidence": [
              {
                "reference": "DOI:10.1073/pnas.1018448108",
                "snippet": "All of the enzymes specifically recognize cytosine C5 modification (methylation or hydroxymethylation) in DNA and cleave at a constant distance (N(12)/N(16)) away from the modified cytosine.",
                "notes": "Cohen-Karni et al. biochemically characterized MspJI homologs and support the MspJI family as C5-modified-cytosine-dependent restriction endonucleases."
              },
              {
                "reference": "DOI:10.1093/nar/gkq327",
                "snippet": "Besides 5-methylcytosine, MspJI also recognizes 5-hydroxymethylcytosine but is blocked by 5-glucosylhydroxymethylcytosine.",
                "notes": "Zheng et al. support MspJI restriction of both methylcytosine- and hydroxymethylcytosine-containing DNA while leaving glucosylated hydroxymethylcytosine DNA uncleaved."
              }
            ]
          },
          {
            "subject": "mspji_modified_cytosine_restriction",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "mspji_system_trait",
            "description": "MspJI-family modified-cytosine restriction realizes the organism-level MspJI system possession trait.",
            "evidence": [
              {
                "reference": "DOI:10.1093/nar/gkq327",
                "snippet": "Besides 5-methylcytosine, MspJI also recognizes 5-hydroxymethylcytosine but is blocked by 5-glucosylhydroxymethylcytosine.",
                "notes": "Zheng et al. support MspJI restriction of both methylcytosine- and hydroxymethylcytosine-containing DNA while leaving glucosylated hydroxymethylcytosine DNA uncleaved."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| MspJI | 10\\.1073/pnas\\.1018448108 | The MspJI family of modification-dependent restriction endonucleases for epigenetic studies | ",
                "notes": "The pinned DefenseFinder article registry maps the MspJI source key to the Cohen-Karni et al. MspJI-family paper."
              }
            ]
          },
          {
            "subject": "mspji_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "type_iv_modification_dependent_restriction",
            "description": "MspJI system possession is a Type IV modification-dependent restriction system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1073/pnas.1018448108",
                "snippet": "MspJI is a novel modification-dependent restriction endonuclease that cleaves at a fixed distance away from the modification site.",
                "notes": "Cohen-Karni et al. support MspJI as a modification-dependent restriction endonuclease with distance-defined cleavage relative to its modified target."
              },
              {
                "reference": "DOI:10.1093/nar/gkt747",
                "snippet": "The new class of modification-dependent restriction enzymes was named Type IV, as distinct from the familiar modification-blocked Types I-III.",
                "notes": "Loenen and Raleigh define the Type IV class as modification-dependent restriction enzymes."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "mspji-defensefinder-model-gap",
        "prompt": "Resolve MspJI-family breadth, methylcytosine and hydroxymethylcytosine sequence-context specificity across natural hosts, accession-level protein examples, and DefenseFinder RM_Type_IV HMM/rules mapping before minting narrower MspJI mechanism or component traits.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Zheng et al. support MspJI as a methylcytosine- and hydroxymethylcytosine-dependent restriction endonuclease, Cohen-Karni et al. support MspJI homologs as a family of C5-modified-cytosine-dependent restriction endonucleases, and the pinned DefenseFinder article registry maps MspJI to the Cohen-Karni et al. paper. The pinned HMM inventory and rules table have no exact MspJI rows. This first-pass record therefore does not resolve a reusable DefenseFinder profile model, exact accession-level protein examples, the breadth of MspJI-like systems across natural hosts, or the complete set of natural methylcytosine and hydroxymethylcytosine sequence contexts.",
        "evidence": [
          {
            "reference": "DOI:10.1073/pnas.1018448108",
            "snippet": "MspJI is a novel modification-dependent restriction endonuclease that cleaves at a fixed distance away from the modification site.",
            "notes": "Cohen-Karni et al. support MspJI as a modification-dependent restriction endonuclease with distance-defined cleavage relative to its modified target."
          },
          {
            "reference": "DOI:10.1073/pnas.1018448108",
            "snippet": "All of the enzymes specifically recognize cytosine C5 modification (methylation or hydroxymethylation) in DNA and cleave at a constant distance (N(12)/N(16)) away from the modified cytosine.",
            "notes": "Cohen-Karni et al. biochemically characterized MspJI homologs and support the MspJI family as C5-modified-cytosine-dependent restriction endonucleases."
          },
          {
            "reference": "DOI:10.1093/nar/gkq327",
            "snippet": "Besides 5-methylcytosine, MspJI also recognizes 5-hydroxymethylcytosine but is blocked by 5-glucosylhydroxymethylcytosine.",
            "notes": "Zheng et al. support MspJI restriction of both methylcytosine- and hydroxymethylcytosine-containing DNA while leaving glucosylated hydroxymethylcytosine DNA uncleaved."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
            "snippet": "| MspJI | 10\\.1073/pnas\\.1018448108 | The MspJI family of modification-dependent restriction endonucleases for epigenetic studies | ",
            "notes": "The pinned DefenseFinder article registry maps the MspJI source key to the Cohen-Karni et al. MspJI-family paper."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "notes": "A structured first-pass search of the pinned DefenseFinder HMM inventory found no exact MspJI row."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "A structured first-pass search of the pinned DefenseFinder rules table found no exact MspJI system row."
          }
        ],
        "attaches_to": [
          "causal_graphs#mspji_restricts_modified_cytosine_dna"
        ],
        "posed_by": "codex",
        "posed_date": "2026-10-01"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-01T08:04:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted MspJI system as a DOI- and DefenseFinder-backed GENOMICS TraitRecord under the type IV modification-dependent restriction system parent after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v387.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-01T08:04:02Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed MspJI system during initial curation and left canonical_examples empty because Zheng et al. and Cohen-Karni et al. support MspJI and MspJI-family enzymes, but not a single stable NCBITaxon strain exemplar or accession-level protein example for the organism-level MspJI system trait. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000284",
    "label": "Nantosuelta system",
    "definition": "A phage defense system in which an organism possesses a Nantosuelta locus represented by a VCA0322 profile that can protect bacteria from bacteriophage infection.",
    "definition_source": "DOI:10.1126/science.ads0768",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "Nantosuelta",
        "synonym_type": "EXACT_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      },
      {
        "synonym_text": "VCA0322",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1126/science.ads0768",
        "snippet": "nearly 10% of the integron cassettes in the pandemic Vibrio cholerae strain encode novel antiphage functions",
        "notes": "Darracq et al. support treating the newly discovered Vibrio cholerae SCI antiphage cassettes as bacterial anti-phage systems."
      },
      {
        "reference": "DOI:10.1126/science.ads0768",
        "snippet": "Most of these novel systems have little or no similarity to previously known ones, with several providing defense through cell lysis or growth arrest",
        "notes": "Darracq et al. support a conservative system record that does not assert a resolved Nantosuelta trigger, effector output, or universal pathway."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "Nantosuelta | 10\\.1126/science\\.ads0768 | Sedentary chromosomal integrons as biobanks of bacterial antiphage defense systems",
        "notes": "The DefenseFinder model registry maps the named Nantosuelta system to the Darracq et al. SCI antiphage-system paper."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "Nantosuelta__VCA0322                             |                                                  | Nantosuelta",
        "notes": "The DefenseFinder HMM inventory records VCA0322 in the Nantosuelta model namespace."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "nantosuelta_locus_restricts_phage",
        "title": "Nantosuelta loci confer bacterial phage defense",
        "description": "Conservative system-level sketch linking possession of a Nantosuelta locus to restricted bacteriophage propagation without asserting the unresolved phage trigger or molecular output.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Nantosuelta as a named SCI-derived anti-phage system with a VCA0322 DefenseFinder profile while leaving its phage trigger, molecular substrate, antiviral effector output, and subtype breadth unresolved.",
        "nodes": [
          {
            "node_id": "nantosuelta_locus",
            "label": "Nantosuelta locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A Nantosuelta anti-phage defense locus represented in DefenseFinder by a VCA0322 profile."
          },
          {
            "node_id": "restricted_phage_propagation",
            "label": "restricted phage propagation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced propagation of bacteriophage in cells carrying the Nantosuelta system."
          },
          {
            "node_id": "nantosuelta_system_trait",
            "label": "Nantosuelta system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000284",
            "description": "Possession of a genome-encoded Nantosuelta phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "nantosuelta_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "restricted_phage_propagation",
            "description": "DefenseFinder maps Nantosuelta to an SCI anti-phage-system discovery paper and represents Nantosuelta loci through the VCA0322 component profile.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.ads0768",
                "snippet": "nearly 10% of the integron cassettes in the pandemic Vibrio cholerae strain encode novel antiphage functions",
                "notes": "Darracq et al. describe the newly discovered antiphage-system cohort that the DefenseFinder Nantosuelta registry row maps to the Nantosuelta system."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "Nantosuelta__VCA0322                             |                                                  | Nantosuelta",
                "notes": "The DefenseFinder HMM inventory supports VCA0322 as the Nantosuelta component profile."
              }
            ]
          },
          {
            "subject": "restricted_phage_propagation",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "nantosuelta_system_trait",
            "description": "Nantosuelta-mediated phage restriction realizes the Nantosuelta system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.ads0768",
                "snippet": "Most of these novel systems have little or no similarity to previously known ones, with several providing defense through cell lysis or growth arrest",
                "notes": "Darracq et al. place the Nantosuelta discovery cohort in a set of novel bacterial systems that protect against phages."
              }
            ]
          },
          {
            "subject": "nantosuelta_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Nantosuelta system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Nantosuelta | 10\\.1126/science\\.ads0768 | Sedentary chromosomal integrons as biobanks of bacterial antiphage defense systems",
                "notes": "DefenseFinder associates Nantosuelta with the Darracq et al. bacterial antiphage-system paper."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "nantosuelta-mechanism-gap",
        "prompt": "Resolve Nantosuelta phage triggers and effector outputs before minting narrower Nantosuelta mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Darracq et al. and DefenseFinder support Nantosuelta as a named anti-phage system with a VCA0322 profile, but the trigger, molecular substrate, antiviral effector output, and subtype-specific mechanism are not resolved enough here to assert a narrower mechanistic child trait.",
        "attaches_to": [
          "causal_graphs#nantosuelta_locus_restricts_phage"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-19"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-19T15:29:21Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Nantosuelta system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v161.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-19T15:47:16Z",
        "curator": "codex",
        "action": "EDIT",
        "changes": "Expanded the Nantosuelta confers-edge Darracq snippet so the stored quote includes the phage-defense clause flagged in issue #1070.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000285",
    "label": "Nemetona system",
    "definition": "A phage defense system in which an organism possesses a Nemetona locus represented by a VCA0441 profile that can protect bacteria from bacteriophage infection.",
    "definition_source": "DOI:10.1126/science.ads0768",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "Nemetona",
        "synonym_type": "EXACT_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      },
      {
        "synonym_text": "VCA0441",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1126/science.ads0768",
        "snippet": "nearly 10% of the integron cassettes in the pandemic Vibrio cholerae strain encode novel antiphage functions",
        "notes": "Darracq et al. support treating the newly discovered Vibrio cholerae SCI antiphage cassettes as bacterial anti-phage systems."
      },
      {
        "reference": "DOI:10.1126/science.ads0768",
        "snippet": "Most of these novel systems have little or no similarity to previously known ones, with several providing defense through cell lysis or growth arrest",
        "notes": "Darracq et al. support a conservative system record that does not assert a resolved Nemetona trigger, effector output, or universal pathway."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "Nemetona | 10\\.1126/science\\.ads0768 | Sedentary chromosomal integrons as biobanks of bacterial antiphage defense systems",
        "notes": "The DefenseFinder model registry maps the named Nemetona system to the Darracq et al. SCI antiphage-system paper."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "Nemetona__VCA0441                                |                                                  | Nemetona",
        "notes": "The DefenseFinder HMM inventory records VCA0441 in the Nemetona model namespace."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "nemetona_locus_restricts_phage",
        "title": "Nemetona loci confer bacterial phage defense",
        "description": "Conservative system-level sketch linking possession of a Nemetona locus to restricted bacteriophage propagation without asserting the unresolved phage trigger or molecular output.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Nemetona as a named SCI-derived anti-phage system with a VCA0441 DefenseFinder profile while leaving its phage trigger, molecular substrate, antiviral effector output, and subtype breadth unresolved.",
        "nodes": [
          {
            "node_id": "nemetona_locus",
            "label": "Nemetona locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A Nemetona anti-phage defense locus represented in DefenseFinder by a VCA0441 profile."
          },
          {
            "node_id": "restricted_phage_propagation",
            "label": "restricted phage propagation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced propagation of bacteriophage in cells carrying the Nemetona system."
          },
          {
            "node_id": "nemetona_system_trait",
            "label": "Nemetona system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000285",
            "description": "Possession of a genome-encoded Nemetona phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "nemetona_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "restricted_phage_propagation",
            "description": "DefenseFinder maps Nemetona to an SCI anti-phage-system discovery paper and represents Nemetona loci through the VCA0441 component profile.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.ads0768",
                "snippet": "nearly 10% of the integron cassettes in the pandemic Vibrio cholerae strain encode novel antiphage functions",
                "notes": "Darracq et al. describe the newly discovered antiphage-system cohort that the DefenseFinder Nemetona registry row maps to the Nemetona system."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "Nemetona__VCA0441                                |                                                  | Nemetona",
                "notes": "The DefenseFinder HMM inventory supports VCA0441 as the Nemetona component profile."
              }
            ]
          },
          {
            "subject": "restricted_phage_propagation",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "nemetona_system_trait",
            "description": "Nemetona-mediated phage restriction realizes the Nemetona system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.ads0768",
                "snippet": "Most of these novel systems have little or no similarity to previously known ones, with several providing defense through cell lysis or growth arrest",
                "notes": "Darracq et al. place the Nemetona discovery cohort in a set of novel bacterial systems that protect against phages."
              }
            ]
          },
          {
            "subject": "nemetona_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Nemetona system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Nemetona | 10\\.1126/science\\.ads0768 | Sedentary chromosomal integrons as biobanks of bacterial antiphage defense systems",
                "notes": "DefenseFinder associates Nemetona with the Darracq et al. bacterial antiphage-system paper."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "nemetona-mechanism-gap",
        "prompt": "Resolve Nemetona phage triggers and effector outputs before minting narrower Nemetona mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Darracq et al. and DefenseFinder support Nemetona as a named anti-phage system with a VCA0441 profile, but the trigger, molecular substrate, antiviral effector output, and subtype-specific mechanism are not resolved enough here to assert a narrower mechanistic child trait.",
        "attaches_to": [
          "causal_graphs#nemetona_locus_restricts_phage"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-19"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-19T16:03:52Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Nemetona system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v162.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000332",
    "label": "Nhi system",
    "definition": "A phage defense system in which an organism possesses an Nhi-family locus represented by the DefenseFinder Nhi__Nhi profile and exemplified by a single enzyme with nuclease and helicase activities that protects against diverse staphylococcal phages, prevents phage DNA accumulation, and is inferred to target and degrade phage-specific replication intermediates.",
    "definition_source": "DOI:10.1016/j.chom.2022.03.001",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "Nhi",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1016/j.chom.2022.03.001",
        "snippet": "Here, we describe a unique mode of nucleic acid immunity mediated by a single enzyme with nuclease and helicase activities, herein referred to as Nhi (nuclease-helicase immunity)",
        "notes": "Bari et al. define Nhi as nuclease-helicase immunity mediated by one enzyme with nuclease and helicase activities."
      },
      {
        "reference": "DOI:10.1016/j.chom.2022.03.001",
        "snippet": "This enzyme provides robust protection against diverse staphylococcal phages and prevents phage DNA accumulation in cells stripped of all other known defenses",
        "notes": "Bari et al. support Nhi as a system that protects against diverse staphylococcal phages and prevents phage DNA accumulation even without other known defenses."
      },
      {
        "reference": "DOI:10.1016/j.chom.2022.03.001",
        "snippet": "Our observations support a model in which Nhi targets and degrades phage-specific replication intermediates",
        "notes": "Bari et al. infer that Nhi targets and degrades phage-specific replication intermediates."
      },
      {
        "reference": "DOI:10.1016/j.chom.2022.03.001",
        "snippet": "Nhi homologs are distributed in diverse bacteria and exhibit functional conservation",
        "notes": "Bari et al. support functional conservation of Nhi homologs across diverse bacteria."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "Nhi | 10\\.1101/776245 | A unique mode of nucleic acid immunity performed by a single multifunctional enzyme",
        "notes": "The DefenseFinder article registry maps the named Nhi model namespace to the Bari et al. nuclease-helicase immunity preprint."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "Nhi\tNhi\t1\t1\tNhi__Nhi",
        "notes": "The DefenseFinder rules table models Nhi as a one-component system requiring the Nhi__Nhi profile."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| Nhi__Nhi                                         | Nhi__Nhi                                         | Nhi                    | Custom                  | 100    |",
        "notes": "The DefenseFinder HMM inventory records Nhi__Nhi under the Nhi model namespace."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1282",
        "taxon_label": "Staphylococcus epidermidis",
        "note": "Bari et al. characterized Nhi from the Staphylococcus epidermidis RP62a locus and showed that this single nuclease-helicase enzyme protects against diverse staphylococcal phages.",
        "reference": "DOI:10.1016/j.chom.2022.03.001"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "nhi_locus_restricts_staphylococcal_phages",
        "title": "Nhi loci provide nuclease-helicase phage defense",
        "description": "Conservative system-level sketch linking an Nhi locus to nuclease-helicase immunity, phage-replication-intermediate degradation, prevention of phage DNA accumulation, and the Nhi system trait.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Nhi as a named single-profile phage defense system without asserting the direct phage trigger, the exact nuclease-helicase substrate, an accession-level natural host protein, or the full taxonomic breadth of functional homologs.",
        "nodes": [
          {
            "node_id": "nhi_locus",
            "label": "Nhi locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "An Nhi-family anti-phage defense locus represented by the DefenseFinder Nhi__Nhi profile."
          },
          {
            "node_id": "nhi_nuclease_helicase_immunity",
            "label": "Nhi nuclease-helicase immunity",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Nucleic acid immunity mediated by one enzyme with nuclease and helicase activities."
          },
          {
            "node_id": "phage_specific_replication_intermediate_degradation",
            "label": "phage-specific replication intermediate degradation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Targeting and degradation of phage-specific replication intermediates by Nhi."
          },
          {
            "node_id": "phage_dna_accumulation_prevention",
            "label": "phage DNA accumulation prevention",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Prevention of phage DNA accumulation during Nhi anti-phage activity."
          },
          {
            "node_id": "nhi_system_trait",
            "label": "Nhi system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000332",
            "description": "Possession of a genome-encoded Nhi nuclease-helicase phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "nhi_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "nhi_nuclease_helicase_immunity",
            "description": "The Nhi locus encodes a single-enzyme nuclease-helicase immunity system, and DefenseFinder models Nhi as a one-profile system.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.chom.2022.03.001",
                "snippet": "Here, we describe a unique mode of nucleic acid immunity mediated by a single enzyme with nuclease and helicase activities, herein referred to as Nhi (nuclease-helicase immunity)",
                "notes": "Bari et al. describe Nhi as immunity mediated by one enzyme with nuclease and helicase activities."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "Nhi\tNhi\t1\t1\tNhi__Nhi",
                "notes": "The DefenseFinder rules table models Nhi as a one-component system requiring the Nhi__Nhi profile."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| Nhi__Nhi                                         | Nhi__Nhi                                         | Nhi                    | Custom                  | 100    |",
                "notes": "The DefenseFinder HMM inventory records Nhi__Nhi under the Nhi model namespace."
              }
            ]
          },
          {
            "subject": "nhi_nuclease_helicase_immunity",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "phage_specific_replication_intermediate_degradation",
            "description": "Nhi nuclease-helicase immunity is inferred to target and degrade phage-specific replication intermediates.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.chom.2022.03.001",
                "snippet": "Our observations support a model in which Nhi targets and degrades phage-specific replication intermediates",
                "notes": "Bari et al. support this as a model for Nhi rather than as a completely resolved direct-substrate assignment."
              }
            ]
          },
          {
            "subject": "phage_specific_replication_intermediate_degradation",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "phage_dna_accumulation_prevention",
            "description": "Degradation of phage-specific replication intermediates explains Nhi-dependent prevention of phage DNA accumulation.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.chom.2022.03.001",
                "snippet": "This enzyme provides robust protection against diverse staphylococcal phages and prevents phage DNA accumulation in cells stripped of all other known defenses",
                "notes": "Bari et al. directly observed prevention of phage DNA accumulation in Nhi-containing cells; the replication-intermediate target is recorded as the authors' model."
              },
              {
                "reference": "DOI:10.1016/j.chom.2022.03.001",
                "snippet": "Our observations support a model in which Nhi targets and degrades phage-specific replication intermediates",
                "notes": "Bari et al. model Nhi as targeting and degrading phage-specific replication intermediates."
              }
            ]
          },
          {
            "subject": "phage_dna_accumulation_prevention",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "nhi_system_trait",
            "description": "Preventing phage DNA accumulation realizes the Nhi phage-defense trait.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.chom.2022.03.001",
                "snippet": "This enzyme provides robust protection against diverse staphylococcal phages and prevents phage DNA accumulation in cells stripped of all other known defenses",
                "notes": "Bari et al. connect Nhi to protection against staphylococcal phages and to prevention of phage DNA accumulation."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Nhi | 10\\.1101/776245 | A unique mode of nucleic acid immunity performed by a single multifunctional enzyme",
                "notes": "The DefenseFinder article registry maps the named Nhi model namespace to the Bari et al. nuclease-helicase immunity preprint."
              }
            ]
          },
          {
            "subject": "nhi_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Nhi system possession is a bacterial phage-defense system.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.chom.2022.03.001",
                "snippet": "highlighting the versatility of such compact weapons as major players in antiphage defense",
                "notes": "Bari et al. place Nhi among compact anti-phage defense systems."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "nhi-trigger-and-substrate-gap",
        "prompt": "Resolve the Nhi phage trigger, exact replication-intermediate substrate, accession-level natural host protein, and homolog breadth before minting narrower mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Bari et al. support Nhi as a compact single-enzyme nuclease-helicase immunity system that prevents phage DNA accumulation and is inferred to target and degrade phage-specific replication intermediates. DefenseFinder models Nhi with a one-profile rule, but this first system-level record leaves the direct phage trigger, exact substrate, natural-host accession, and full taxonomic breadth of functional homologs unresolved.",
        "attaches_to": [
          "causal_graphs#nhi_locus_restricts_staphylococcal_phages"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-21"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-21T16:05:11Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Nhi system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v209.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000333",
    "label": "NixI system",
    "definition": "A phage defense system in which an organism possesses a NixI-family phage-satellite locus represented by the DefenseFinder NixI__NixI profile and exemplified by a PLE-encoded nicking endonuclease that cleaves ICP1 bacteriophage DNA, inhibits ICP1 genome replication, and reduces progeny production in Vibrio cholerae.",
    "definition_source": "DOI:10.1093/nar/gkac002",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "NixI",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1093/nar/gkac002",
        "snippet": "Here, we characterize a PLE-encoded nuclease, NixI, that blocks phage development likely by nicking ICP1\u2019s genome as it transitions to RCR",
        "notes": "LeGault et al. characterize NixI as a PLE-encoded nuclease that likely blocks ICP1 development by nicking the ICP1 genome as it transitions to rolling-circle replication."
      },
      {
        "reference": "DOI:10.1093/nar/gkac002",
        "snippet": "Together, these data show that PLE encodes a nicking endonuclease, NixI, that is necessary for cleavage of ICP1\u2019s genome in vivo and that shows in vitro specificity for sequences found in ICP1\u2019s genome",
        "notes": "LeGault et al. show that NixI is a PLE-encoded nicking endonuclease necessary for in vivo ICP1 cleavage and specific for ICP1-derived sequences in vitro."
      },
      {
        "reference": "DOI:10.1093/nar/gkac002",
        "snippet": "NixI, however, is sufficient to limit ICP1 progeny production in a single round of infection",
        "notes": "LeGault et al. support NixI as a PLE-encoded product sufficient to limit ICP1 progeny production in a single infection round."
      },
      {
        "reference": "DOI:10.1093/nar/gkac002",
        "snippet": "Together, these data demonstrate that nixI is a potent inhibitor of ICP1 replication, resulting in decreased virion production.",
        "notes": "LeGault et al. support NixI as a potent inhibitor of ICP1 genome replication, resulting in decreased virion production."
      },
      {
        "reference": "DOI:10.1093/nar/gkac002",
        "snippet": "Phage parasites can be considered host defense systems, as the parasite inhibits production of its viral host, benefiting the bacterial population",
        "notes": "LeGault et al. explicitly frame PLE-like phage parasites as host defense systems because they inhibit production of their viral hosts."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "NixI | 10\\.1101/2021\\.07\\.12\\.452122 | A phage parasite deploys a nicking nuclease effector to inhibit replication of its viral host",
        "notes": "The DefenseFinder article registry maps the named NixI model namespace to the LeGault et al. PLE-encoded nicking-nuclease preprint, later published under DOI:10.1093/nar/gkac002."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "NixI\tNixI\t1\t1\tNixI__NixI\tNixI__Stix\t\t",
        "notes": "The DefenseFinder rules table models NixI with the NixI__NixI profile as its mandatory component and an optional NixI__Stix profile."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| NixI__NixI                                       | NixI__NixI                                       | NixI                   | Custom                  | 20     |",
        "notes": "The DefenseFinder HMM inventory records NixI__NixI under the NixI model namespace."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:666",
        "taxon_label": "Vibrio cholerae",
        "note": "LeGault et al. used PLE-positive Vibrio cholerae to show that NixI-dependent cleavage sites appear in ICP1 during infection and that nixI inhibits ICP1 replication and progeny production.",
        "reference": "DOI:10.1093/nar/gkac002"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "nixi_locus_inhibits_icp1_replication",
        "title": "NixI loci inhibit ICP1 replication",
        "description": "Conservative system-level sketch linking a NixI-family phage-satellite locus to ICP1 genome cleavage, ICP1 replication inhibition, and the NixI system trait.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures NixI as a named DefenseFinder single-mandatory-profile system without asserting the exact satellite self-protection mechanism, the complete set of PLE-encoded anti-ICP1 mechanisms, the accession-level natural-host protein, the full functional breadth of divergent NixI homologs, or the experimental scope of the optional NixI__Stix profile.",
        "nodes": [
          {
            "node_id": "nixi_locus",
            "label": "NixI locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A NixI-family phage-satellite locus represented by the DefenseFinder NixI__NixI profile."
          },
          {
            "node_id": "icp1_genome_cleavage",
            "label": "ICP1 genome cleavage",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "NixI-dependent cleavage of the ICP1 bacteriophage genome in PLE-positive Vibrio cholerae."
          },
          {
            "node_id": "icp1_replication_inhibition",
            "label": "ICP1 replication inhibition",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Inhibition of ICP1 genome replication and progeny production by NixI."
          },
          {
            "node_id": "nixi_system_trait",
            "label": "NixI system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000333",
            "description": "Possession of a genome-encoded NixI phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "nixi_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "icp1_genome_cleavage",
            "description": "The PLE-encoded NixI nicking endonuclease is necessary for cleavage of ICP1 DNA in vivo, and DefenseFinder models NixI with the mandatory NixI__NixI profile.",
            "evidence": [
              {
                "reference": "DOI:10.1093/nar/gkac002",
                "snippet": "Together, these data show that PLE encodes a nicking endonuclease, NixI, that is necessary for cleavage of ICP1\u2019s genome in vivo and that shows in vitro specificity for sequences found in ICP1\u2019s genome",
                "notes": "LeGault et al. support NixI as the PLE-encoded nicking endonuclease responsible for ICP1 genome cleavage."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "NixI\tNixI\t1\t1\tNixI__NixI\tNixI__Stix\t\t",
                "notes": "The DefenseFinder rules table models NixI with the NixI__NixI profile as its mandatory component and an optional NixI__Stix profile."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| NixI__NixI                                       | NixI__NixI                                       | NixI                   | Custom                  | 20     |",
                "notes": "The DefenseFinder HMM inventory records NixI__NixI under the NixI model namespace."
              }
            ]
          },
          {
            "subject": "nixi_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "icp1_replication_inhibition",
            "description": "NixI inhibits ICP1 replication and decreases ICP1 virion production.",
            "evidence": [
              {
                "reference": "DOI:10.1093/nar/gkac002",
                "snippet": "Together, these data demonstrate that nixI is a potent inhibitor of ICP1 replication, resulting in decreased virion production.",
                "notes": "LeGault et al. show that NixI is a potent inhibitor of ICP1 replication."
              },
              {
                "reference": "DOI:10.1093/nar/gkac002",
                "snippet": "NixI, however, is sufficient to limit ICP1 progeny production in a single round of infection",
                "notes": "LeGault et al. show that NixI is sufficient to limit ICP1 progeny production."
              }
            ]
          },
          {
            "subject": "icp1_genome_cleavage",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "icp1_replication_inhibition",
            "description": "NixI-dependent cleavage of the ICP1 genome contributes to inhibition of ICP1 replication.",
            "evidence": [
              {
                "reference": "DOI:10.1093/nar/gkac002",
                "snippet": "Here, we characterize a PLE-encoded nuclease, NixI, that blocks phage development likely by nicking ICP1\u2019s genome as it transitions to RCR",
                "notes": "LeGault et al. connect NixI's nicking of ICP1 DNA to blocked phage development during the transition to rolling-circle replication."
              },
              {
                "reference": "DOI:10.1093/nar/gkac002",
                "snippet": "Together, these data show that PLE encodes a nicking endonuclease, NixI, that is necessary for cleavage of ICP1\u2019s genome in vivo and that shows in vitro specificity for sequences found in ICP1\u2019s genome",
                "notes": "LeGault et al. support NixI as the PLE-encoded nicking endonuclease responsible for ICP1 genome cleavage."
              }
            ]
          },
          {
            "subject": "icp1_replication_inhibition",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "nixi_system_trait",
            "description": "NixI-dependent ICP1 replication inhibition realizes the NixI system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1093/nar/gkac002",
                "snippet": "Here, we characterize a PLE-encoded nuclease, NixI, that blocks phage development likely by nicking ICP1\u2019s genome as it transitions to RCR",
                "notes": "LeGault et al. characterize NixI as a PLE-encoded nuclease blocking ICP1 phage development."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "NixI | 10\\.1101/2021\\.07\\.12\\.452122 | A phage parasite deploys a nicking nuclease effector to inhibit replication of its viral host",
                "notes": "The DefenseFinder article registry maps the named NixI model namespace to the LeGault et al. PLE-encoded nicking-nuclease preprint, later published under DOI:10.1093/nar/gkac002."
              }
            ]
          },
          {
            "subject": "nixi_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "NixI system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1093/nar/gkac002",
                "snippet": "Phage parasites can be considered host defense systems, as the parasite inhibits production of its viral host, benefiting the bacterial population",
                "notes": "LeGault et al. place phage parasites such as NixI-encoding PLE among host defense systems because they inhibit their viral hosts."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "nixi-stix-and-satellite-scope-gap",
        "prompt": "Resolve NixI satellite self-protection, optional Stix profile scope, natural-host protein accessions, and divergent-homolog activity before minting narrower NixI mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "LeGault et al. support NixI as a PLE-encoded nicking endonuclease that cleaves ICP1 DNA and inhibits ICP1 genome replication, and DefenseFinder models NixI with a required NixI__NixI profile plus optional NixI__Stix. This first system-level record leaves the exact PLE self-protection mechanism, the optional Stix profile's experimental scope, the accession-level PLE1 NixI protein, the breadth of divergent homolog activity, and additional PLE anti-ICP1 mechanisms unresolved.",
        "attaches_to": [
          "causal_graphs#nixi_locus_inhibits_icp1_replication"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-21"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-21T10:01:24Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted NixI system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v210.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-21T10:30:48Z",
        "curator": "codex",
        "action": "UPDATED_CAUSAL_GRAPH",
        "changes": "Connected ICP1 genome cleavage to ICP1 replication inhibition in the NixI graph so nuclease-mediated DNA cleavage lies on the path from NixI locus to NixI system, addressing issue #1189.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000408",
    "label": "NLR-like bNACHT system",
    "definition": "A phage defense system in which an organism possesses an NLR-related bacterial NACHT locus represented by DefenseFinder as an NLR_like_bNACHT01 or NLR_like_bNACHT09 single-profile model, encoding a NACHT-module STAND-family protein that can restrict bacteriophage production.",
    "definition_source": "DOI:10.1016/j.cell.2023.04.015",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "NLR",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      },
      {
        "synonym_text": "bNACHT",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1016/j.cell.2023.04.015"
      },
      {
        "synonym_text": "NLR_like_bNACHT01",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv"
      },
      {
        "synonym_text": "NLR_like_bNACHT09",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv"
      }
    ],
    "evidence": [
      {
        "reference": "https://pmc.ncbi.nlm.nih.gov/articles/PMC10294775/",
        "snippet": "Here we show that proteins containing a NACHT module, the central feature of the animal nucleotide-binding domain and leucine-rich repeat-containing gene family (NLRs), are found in bacteria and defend against phages.",
        "notes": "Kibby et al. support NACHT-module proteins as bacterial NLR-related proteins that defend against phages."
      },
      {
        "reference": "https://pmc.ncbi.nlm.nih.gov/articles/PMC10294775/",
        "snippet": "Genome context of bNACHT01, which is located near a CBASS system in Klebsiella pneumoniae MGH 35.",
        "notes": "Kibby et al. identified a NACHT-module gene in Klebsiella pneumoniae MGH 35 before naming it bNACHT01."
      },
      {
        "reference": "https://pmc.ncbi.nlm.nih.gov/articles/PMC10294775/",
        "snippet": "We named this gene bacterial NACHT module-containing protein 1 (bNACHT01), and it did not appear to be in an operon with any other genes.",
        "notes": "Kibby et al. named the selected NACHT-module gene bNACHT01."
      },
      {
        "reference": "https://pmc.ncbi.nlm.nih.gov/articles/PMC10294775/",
        "snippet": "bNACHT01 conferred over a 100-fold increase in protection against phage T4 and over a 1000-fold increase in protection against phages T5 and T6",
        "notes": "bNACHT01 protected against phages T4, T5, and T6 in the E. coli heterologous assay."
      },
      {
        "reference": "https://pmc.ncbi.nlm.nih.gov/articles/PMC10294775/",
        "snippet": "bacteria expressing bNACHT01 restricted phage virion production and continued growing",
        "notes": "Kibby et al. observed restricted phage virion production in bacteria expressing bNACHT01."
      },
      {
        "reference": "https://pmc.ncbi.nlm.nih.gov/articles/PMC10294775/",
        "snippet": "Mutation of R214 to alanine maintained expression of the protein but abrogated phage defense",
        "notes": "An R214A mutation preserved bNACHT01 expression but abrogated defense, supporting a NACHT-dependent output."
      },
      {
        "reference": "https://pmc.ncbi.nlm.nih.gov/articles/PMC10294775/",
        "snippet": "Diverse bacterial NACHT proteins from different clades exhibited robust antiphage activity across a wide range of phages",
        "notes": "Kibby et al. observed antiphage activity across diverse bacterial NACHT proteins."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "NLR | 10\\.1101/2022\\.07\\.19\\.500537 | Bacterial NLR-related proteins protect against phage",
        "notes": "The DefenseFinder article registry maps the NLR family key to the Kibby et al. bNACHT preprint."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "NLR\tNLR_like_bNACHT01\t1\t1\tNLR_like_bNACHT01__NLR_like_bNACHT01\t\t\t",
        "notes": "The DefenseFinder rules table models NLR_like_bNACHT01 as a one-profile NLR-family subsystem."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "NLR\tNLR_like_bNACHT09\t1\t1\tNLR_like_bNACHT09__NLR_like_bNACHT09\t\t\t",
        "notes": "The DefenseFinder rules table models NLR_like_bNACHT09 as a one-profile NLR-family subsystem."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| NLR_like_bNACHT01__NLR_like_bNACHT01             | NLR_like_bNACHT01__NLR_like_bNACHT01             | NLR_like_bNACHT01      | Custom                  | 250    |",
        "notes": "The DefenseFinder HMM inventory records the NLR_like_bNACHT01 profile under the same-named model namespace."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| NLR_like_bNACHT09__NLR_like_bNACHT09             | NLR_like_bNACHT09__NLR_like_bNACHT09             | NLR_like_bNACHT09      | Custom                  | 400    |",
        "notes": "The DefenseFinder HMM inventory records the NLR_like_bNACHT09 profile under the same-named model namespace."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:573",
        "taxon_label": "Klebsiella pneumoniae",
        "note": "Kibby et al. identified the bNACHT01 locus in Klebsiella pneumoniae MGH 35 and found that bNACHT01 expressed from its endogenous promoter in Escherichia coli protected against phages T4, T5, and T6.",
        "reference": "DOI:10.1016/j.cell.2023.04.015"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "nlr_like_bnacht_loci_restrict_phage",
        "title": "NLR-like bNACHT loci restrict phage production",
        "description": "Conservative system-level sketch linking NLR-like bNACHT loci to bacteriophage restriction while leaving subtype triggers and effector outputs unresolved.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures DefenseFinder NLR_like_bNACHT01 and NLR_like_bNACHT09 as named bNACHT phage-defense models supported by Kibby et al. bacterial NLR-related protein experiments while leaving natural host breadth, phage triggers, the exact profile-to-bNACHT01 or profile-to-bNACHT09 correspondences, and subtype-specific effector mechanisms unresolved.",
        "nodes": [
          {
            "node_id": "nlr_like_bnacht_locus",
            "label": "NLR-like bNACHT locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A bacterial NLR-related phage-defense locus cataloged in DefenseFinder with a bNACHT profile."
          },
          {
            "node_id": "bnacht_phage_restriction",
            "label": "bNACHT phage restriction",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Restriction of phage production by a bacterial NACHT-module antiviral protein."
          },
          {
            "node_id": "nlr_like_bnacht_system_trait",
            "label": "NLR-like bNACHT system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000408",
            "description": "Possession of a genome-encoded NLR-like bNACHT phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "nlr_like_bnacht_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "bnacht_phage_restriction",
            "description": "Kibby et al. showed that bacterial NACHT proteins can restrict bacteriophages, and DefenseFinder models two NLR_like_bNACHT subtypes.",
            "evidence": [
              {
                "reference": "https://pmc.ncbi.nlm.nih.gov/articles/PMC10294775/",
                "snippet": "Here we show that proteins containing a NACHT module, the central feature of the animal nucleotide-binding domain and leucine-rich repeat-containing gene family (NLRs), are found in bacteria and defend against phages.",
                "notes": "Kibby et al. support NACHT-module proteins as bacterial NLR-related proteins that defend against phages."
              },
              {
                "reference": "https://pmc.ncbi.nlm.nih.gov/articles/PMC10294775/",
                "snippet": "bNACHT01 conferred over a 100-fold increase in protection against phage T4 and over a 1000-fold increase in protection against phages T5 and T6",
                "notes": "bNACHT01 protected against phages T4, T5, and T6 in the E. coli heterologous assay."
              },
              {
                "reference": "https://pmc.ncbi.nlm.nih.gov/articles/PMC10294775/",
                "snippet": "bacteria expressing bNACHT01 restricted phage virion production and continued growing",
                "notes": "Kibby et al. observed restricted phage virion production in bacteria expressing bNACHT01."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "NLR\tNLR_like_bNACHT01\t1\t1\tNLR_like_bNACHT01__NLR_like_bNACHT01\t\t\t",
                "notes": "The DefenseFinder rules table models NLR_like_bNACHT01 as a one-profile NLR-family subsystem."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "NLR\tNLR_like_bNACHT09\t1\t1\tNLR_like_bNACHT09__NLR_like_bNACHT09\t\t\t",
                "notes": "The DefenseFinder rules table models NLR_like_bNACHT09 as a one-profile NLR-family subsystem."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| NLR_like_bNACHT01__NLR_like_bNACHT01             | NLR_like_bNACHT01__NLR_like_bNACHT01             | NLR_like_bNACHT01      | Custom                  | 250    |",
                "notes": "The DefenseFinder HMM inventory records the NLR_like_bNACHT01 profile under the same-named model namespace."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| NLR_like_bNACHT09__NLR_like_bNACHT09             | NLR_like_bNACHT09__NLR_like_bNACHT09             | NLR_like_bNACHT09      | Custom                  | 400    |",
                "notes": "The DefenseFinder HMM inventory records the NLR_like_bNACHT09 profile under the same-named model namespace."
              }
            ]
          },
          {
            "subject": "bnacht_phage_restriction",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "nlr_like_bnacht_system_trait",
            "description": "NACHT-module-dependent phage restriction realizes the NLR-like bNACHT system trait.",
            "evidence": [
              {
                "reference": "https://pmc.ncbi.nlm.nih.gov/articles/PMC10294775/",
                "snippet": "bacteria expressing bNACHT01 restricted phage virion production and continued growing",
                "notes": "Kibby et al. observed restricted phage virion production in bacteria expressing bNACHT01."
              },
              {
                "reference": "https://pmc.ncbi.nlm.nih.gov/articles/PMC10294775/",
                "snippet": "Mutation of R214 to alanine maintained expression of the protein but abrogated phage defense",
                "notes": "An R214A mutation preserved bNACHT01 expression but abrogated defense, supporting a NACHT-dependent output."
              }
            ]
          },
          {
            "subject": "nlr_like_bnacht_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "NLR-like bNACHT system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "https://pmc.ncbi.nlm.nih.gov/articles/PMC10294775/",
                "snippet": "Here we show that proteins containing a NACHT module, the central feature of the animal nucleotide-binding domain and leucine-rich repeat-containing gene family (NLRs), are found in bacteria and defend against phages.",
                "notes": "Kibby et al. support NACHT-module proteins as bacterial NLR-related proteins that defend against phages."
              },
              {
                "reference": "https://pmc.ncbi.nlm.nih.gov/articles/PMC10294775/",
                "snippet": "Diverse bacterial NACHT proteins from different clades exhibited robust antiphage activity across a wide range of phages",
                "notes": "Kibby et al. observed antiphage activity across diverse bacterial NACHT proteins."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "NLR | 10\\.1101/2022\\.07\\.19\\.500537 | Bacterial NLR-related proteins protect against phage",
                "notes": "The DefenseFinder article registry maps the NLR family key to the Kibby et al. bNACHT preprint."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "nlr-like-bnacht-mechanism-gap",
        "prompt": "Resolve the exact mapping between DefenseFinder NLR_like_bNACHT01 and NLR_like_bNACHT09 profiles and the experimentally tested bNACHT proteins, natural host breadth, phage triggers, and bNACHT effector mechanisms before minting narrower bNACHT subtype traits.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Kibby et al. support bacterial NACHT proteins as NLR-related phage-defense proteins and DefenseFinder models NLR_like_bNACHT01 and NLR_like_bNACHT09 as single-profile NLR-family subsystems. This first system-level record leaves profile-to-assayed-protein correspondence and subtype-specific trigger and effector mechanisms unresolved.",
        "evidence": [
          {
            "reference": "https://pmc.ncbi.nlm.nih.gov/articles/PMC10294775/",
            "snippet": "Here we show that proteins containing a NACHT module, the central feature of the animal nucleotide-binding domain and leucine-rich repeat-containing gene family (NLRs), are found in bacteria and defend against phages.",
            "notes": "Kibby et al. support NACHT-module proteins as bacterial NLR-related proteins that defend against phages."
          },
          {
            "reference": "https://pmc.ncbi.nlm.nih.gov/articles/PMC10294775/",
            "snippet": "bNACHT01 conferred over a 100-fold increase in protection against phage T4 and over a 1000-fold increase in protection against phages T5 and T6",
            "notes": "bNACHT01 protected against phages T4, T5, and T6 in the E. coli heterologous assay."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "snippet": "NLR\tNLR_like_bNACHT01\t1\t1\tNLR_like_bNACHT01__NLR_like_bNACHT01\t\t\t",
            "notes": "The DefenseFinder rules table models NLR_like_bNACHT01 as a one-profile NLR-family subsystem."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "snippet": "NLR\tNLR_like_bNACHT09\t1\t1\tNLR_like_bNACHT09__NLR_like_bNACHT09\t\t\t",
            "notes": "The DefenseFinder rules table models NLR_like_bNACHT09 as a one-profile NLR-family subsystem."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| NLR_like_bNACHT01__NLR_like_bNACHT01             | NLR_like_bNACHT01__NLR_like_bNACHT01             | NLR_like_bNACHT01      | Custom                  | 250    |",
            "notes": "The DefenseFinder HMM inventory records the NLR_like_bNACHT01 profile under the same-named model namespace."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| NLR_like_bNACHT09__NLR_like_bNACHT09             | NLR_like_bNACHT09__NLR_like_bNACHT09             | NLR_like_bNACHT09      | Custom                  | 400    |",
            "notes": "The DefenseFinder HMM inventory records the NLR_like_bNACHT09 profile under the same-named model namespace."
          }
        ],
        "attaches_to": [
          "causal_graphs#nlr_like_bnacht_loci_restrict_phage"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-27"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-27T12:41:08Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted NLR-like bNACHT system as a DOI-, PMID-, and stable-URL-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v285.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-27T12:41:09Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed NLR-like bNACHT system canonical-example evidence and kept the example at the Klebsiella pneumoniae species level because Kibby et al. identified the tested bNACHT01 locus from K. pneumoniae MGH 35 but assayed the endogenous-promoter construct heterologously in Escherichia coli. No paid research was used.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-27T13:11:20Z",
        "curator": "codex",
        "action": "ADDRESS_REVIEW_FINDINGS",
        "changes": "Corrected the Cell paper attribution from Ofir et al. to Kibby et al. and narrowed the R214A evidence note so it no longer places the residue inside the NACHT module beyond the curated snippet.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-27T13:27:10Z",
        "curator": "codex",
        "action": "ADD_BNACHT01_SOURCE_STRAIN_SNIPPET",
        "changes": "Added verbatim Kibby et al. evidence that the NACHT-module gene later named bNACHT01 was identified in Klebsiella pneumoniae MGH 35, directly supporting the canonical example taxon.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000286",
    "label": "Ogmios system",
    "definition": "A phage defense system in which an organism possesses an Ogmios locus represented by a VCA0308 profile that can protect bacteria from bacteriophage infection.",
    "definition_source": "DOI:10.1126/science.ads0768",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "Ogmios",
        "synonym_type": "EXACT_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      },
      {
        "synonym_text": "VCA0308",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1126/science.ads0768",
        "snippet": "nearly 10% of the integron cassettes in the pandemic Vibrio cholerae strain encode novel antiphage functions",
        "notes": "Darracq et al. support treating the newly discovered Vibrio cholerae SCI antiphage cassettes as bacterial anti-phage systems."
      },
      {
        "reference": "DOI:10.1126/science.ads0768",
        "snippet": "Most of these novel systems have little or no similarity to previously known ones, with several providing defense through cell lysis or growth arrest",
        "notes": "Darracq et al. support a conservative system record that does not assert a resolved Ogmios trigger, effector output, or universal pathway."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "Ogmios | 10\\.1126/science\\.ads0768 | Sedentary chromosomal integrons as biobanks of bacterial antiphage defense systems",
        "notes": "The DefenseFinder model registry maps the named Ogmios system to the Darracq et al. SCI antiphage-system paper."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "Ogmios__VCA0308                                  |                                                  | Ogmios",
        "notes": "The DefenseFinder HMM inventory records VCA0308 in the Ogmios model namespace."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "ogmios_locus_restricts_phage",
        "title": "Ogmios loci confer bacterial phage defense",
        "description": "Conservative system-level sketch linking possession of an Ogmios locus to restricted bacteriophage propagation without asserting the unresolved phage trigger or molecular output.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Ogmios as a named SCI-derived anti-phage system with a VCA0308 DefenseFinder profile while leaving its phage trigger, molecular substrate, antiviral effector output, and subtype breadth unresolved.",
        "nodes": [
          {
            "node_id": "ogmios_locus",
            "label": "Ogmios locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "An Ogmios anti-phage defense locus represented in DefenseFinder by a VCA0308 profile."
          },
          {
            "node_id": "restricted_phage_propagation",
            "label": "restricted phage propagation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced propagation of bacteriophage in cells carrying the Ogmios system."
          },
          {
            "node_id": "ogmios_system_trait",
            "label": "Ogmios system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000286",
            "description": "Possession of a genome-encoded Ogmios phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "ogmios_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "restricted_phage_propagation",
            "description": "DefenseFinder maps Ogmios to an SCI anti-phage-system discovery paper and represents Ogmios loci through the VCA0308 component profile.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.ads0768",
                "snippet": "nearly 10% of the integron cassettes in the pandemic Vibrio cholerae strain encode novel antiphage functions",
                "notes": "Darracq et al. describe the newly discovered antiphage-system cohort that the DefenseFinder Ogmios registry row maps to the Ogmios system."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "Ogmios__VCA0308                                  |                                                  | Ogmios",
                "notes": "The DefenseFinder HMM inventory supports VCA0308 as the Ogmios component profile."
              }
            ]
          },
          {
            "subject": "restricted_phage_propagation",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "ogmios_system_trait",
            "description": "Ogmios-mediated phage restriction realizes the Ogmios system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.ads0768",
                "snippet": "Most of these novel systems have little or no similarity to previously known ones, with several providing defense through cell lysis or growth arrest",
                "notes": "Darracq et al. place the Ogmios discovery cohort in a set of novel bacterial systems that protect against phages."
              }
            ]
          },
          {
            "subject": "ogmios_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Ogmios system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Ogmios | 10\\.1126/science\\.ads0768 | Sedentary chromosomal integrons as biobanks of bacterial antiphage defense systems",
                "notes": "DefenseFinder associates Ogmios with the Darracq et al. bacterial antiphage-system paper."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "ogmios-mechanism-gap",
        "prompt": "Resolve Ogmios phage triggers and effector outputs before minting narrower Ogmios mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Darracq et al. and DefenseFinder support Ogmios as a named anti-phage system with a VCA0308 profile, but the trigger, molecular substrate, antiviral effector output, and subtype-specific mechanism are not resolved enough here to assert a narrower mechanistic child trait.",
        "attaches_to": [
          "causal_graphs#ogmios_locus_restricts_phage"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-19"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-19T16:33:14Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Ogmios system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v163.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000399",
    "label": "Old exonuclease system",
    "definition": "A phage defense system in which an organism possesses an Old exonuclease locus represented by DefenseFinder as a single-profile model, Old_exonuclease__Old_exonuclease, and experimentally linked to interference with phage lambda by the bacteriophage P2 Old protein.",
    "definition_source": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/old_exonuclease.md",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "Old_exonuclease",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      },
      {
        "synonym_text": "Old_exonuclease__Old_exonuclease",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1128/jb.177.3.497-501.1995",
        "snippet": "The Old protein of bacteriophage P2 is responsible for interference with the growth of phage lambda and for killing of recBC mutant Escherichia coli.",
        "notes": "The 1995 Old nuclease study identifies the P2 Old protein as responsible for phage-lambda interference."
      },
      {
        "reference": "DOI:10.1128/jb.177.3.497-501.1995",
        "snippet": "The Old protein fused to maltose-binding protein has exonuclease activity on double-stranded DNA as well as nuclease activity on single-stranded DNA and RNA.",
        "notes": "The 1995 biochemical study shows Old has nuclease activity on double-stranded DNA, single-stranded DNA, and RNA."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/old_exonuclease.md",
        "snippet": "It's been shown to protect against phage lambda :ref{doi=10.1128/jb.177.3.497-501.1995}, and when cloned with the P2 Tin accessory gene, it was shown to protect against other *E. coli* phages :ref{doi=10.1016/j.chom.2022.02.018}.",
        "notes": "The pinned DefenseFinder wiki page links Old_exonuclease to lambda protection and to broader P2 Old plus Tin protection."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/old_exonuclease.md",
        "snippet": "The old_exonuclease is dsDNA exonuclease that digests in the 5' to 3' direction :ref{doi=10.1128/jb.177.3.497-501.1995}. To our knowledge, other aspects of the molecular mechanisms remain unknown.",
        "notes": "The pinned DefenseFinder wiki page supports Old dsDNA exonuclease activity while leaving the remaining molecular mechanism unresolved."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/old_exonuclease.md",
        "snippet": "The Old_exonuclease is composed of 1 protein: Old_exonuclease.",
        "notes": "The pinned DefenseFinder wiki page describes Old_exonuclease as a one-protein system."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/old_exonuclease.md",
        "snippet": "The Old_exonuclease system in *Shewanella xiamenensis* (GCF_022453805.1, NZ_CP092630) is composed of 1 protein: Old_exonuclease (WP_240293412.1)",
        "notes": "The pinned DefenseFinder wiki page illustrates a predicted Old_exonuclease locus in RefSeq assembly GCF_022453805.1 on NZ_CP092630."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/old_exonuclease.md",
        "snippet": "Rousset_2022[<a href='https://doi.org/10.1016/j.chom.2022.02.018'>Rousset et al., 2022</a>] --> Origin_0\n    Origin_0[Enterobacteria phage P2 \n<a href='https://ncbi.nlm.nih.gov/protein/NP_046798.1'>NP_046798.1</a>] --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> Lambda & T4 & LF82_P8 & Al505_P2",
        "notes": "The DefenseFinder experimental-validation diagram links Rousset et al. to Enterobacteria phage P2 Old expressed in Escherichia coli against lambda, T4, LF82_P8, and Al505_P2."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/old_exonuclease.md",
        "snippet": "subgraph Title4[Protects against]\n        Lambda\n        T4\n        LF82_P8\n        Al505_P2",
        "notes": "The DefenseFinder experimental-validation diagram lists lambda, T4, LF82_P8, and Al505_P2 in the Old_exonuclease protects-against subgraph."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "Old_exonuclease | 10\\.1101/2021\\.01\\.21\\.427644 | Prophage-encoded hotspots of bacterial immune systems",
        "notes": "The DefenseFinder article registry maps the named Old_exonuclease system to the Rousset et al. preprint."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "Old_exonuclease\tOld_exonuclease\t1\t1\tOld_exonuclease__Old_exonuclease\t\t\t",
        "notes": "The DefenseFinder rules table models Old_exonuclease as a single-profile system requiring Old_exonuclease__Old_exonuclease."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| Old_exonuclease__Old_exonuclease                 | Old_exonuclease__Old_exonuclease                 | Old_exonuclease        | Custom                  | 200    |",
        "notes": "The DefenseFinder HMM inventory records Old_exonuclease__Old_exonuclease under the Old_exonuclease system namespace."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "old_exonuclease_locus_interferes_with_lambda",
        "title": "Old exonuclease loci interfere with phage lambda",
        "description": "Conservative system-level sketch linking a named Old_exonuclease one-profile model to phage-lambda interference.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Old_exonuclease as a named DefenseFinder single-profile phage-defense system while leaving natural host breadth, Tin accessory dependence, RecBCD-triggered activation, profile-to-protein mapping, and the lambda interference mechanism unresolved.",
        "nodes": [
          {
            "node_id": "old_exonuclease_locus",
            "label": "Old exonuclease locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A single-profile Old-exonuclease phage-defense locus represented by the custom DefenseFinder Old_exonuclease profile."
          },
          {
            "node_id": "lambda_phage_interference",
            "label": "lambda phage interference",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Interference with growth of phage lambda in a host expressing bacteriophage P2 Old."
          },
          {
            "node_id": "old_exonuclease_system_trait",
            "label": "Old exonuclease system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000399",
            "description": "Possession of a genome-encoded Old exonuclease phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "old_exonuclease_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "lambda_phage_interference",
            "description": "The P2 Old protein is linked to phage-lambda interference, and DefenseFinder models Old_exonuclease as a single-profile system.",
            "evidence": [
              {
                "reference": "DOI:10.1128/jb.177.3.497-501.1995",
                "snippet": "The Old protein of bacteriophage P2 is responsible for interference with the growth of phage lambda and for killing of recBC mutant Escherichia coli.",
                "notes": "The 1995 Old nuclease study identifies the P2 Old protein as responsible for phage-lambda interference."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "Old_exonuclease\tOld_exonuclease\t1\t1\tOld_exonuclease__Old_exonuclease\t\t\t",
                "notes": "The DefenseFinder rules table models Old_exonuclease as a single-profile system requiring Old_exonuclease__Old_exonuclease."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| Old_exonuclease__Old_exonuclease                 | Old_exonuclease__Old_exonuclease                 | Old_exonuclease        | Custom                  | 200    |",
                "notes": "The DefenseFinder HMM inventory records Old_exonuclease__Old_exonuclease under the Old_exonuclease system namespace."
              }
            ]
          },
          {
            "subject": "lambda_phage_interference",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "old_exonuclease_system_trait",
            "description": "Old-mediated phage-lambda interference realizes the Old exonuclease system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1128/jb.177.3.497-501.1995",
                "snippet": "The Old protein of bacteriophage P2 is responsible for interference with the growth of phage lambda and for killing of recBC mutant Escherichia coli.",
                "notes": "The 1995 Old nuclease study identifies the P2 Old protein as responsible for phage-lambda interference."
              },
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/old_exonuclease.md",
                "snippet": "Rousset_2022[<a href='https://doi.org/10.1016/j.chom.2022.02.018'>Rousset et al., 2022</a>] --> Origin_0\n    Origin_0[Enterobacteria phage P2 \n<a href='https://ncbi.nlm.nih.gov/protein/NP_046798.1'>NP_046798.1</a>] --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> Lambda & T4 & LF82_P8 & Al505_P2",
                "notes": "The DefenseFinder experimental-validation diagram links Rousset et al. to Enterobacteria phage P2 Old expressed in Escherichia coli against lambda, T4, LF82_P8, and Al505_P2."
              },
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/old_exonuclease.md",
                "snippet": "subgraph Title4[Protects against]\n        Lambda\n        T4\n        LF82_P8\n        Al505_P2",
                "notes": "The DefenseFinder experimental-validation diagram lists lambda, T4, LF82_P8, and Al505_P2 in the Old_exonuclease protects-against subgraph."
              }
            ]
          },
          {
            "subject": "old_exonuclease_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Old exonuclease system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/old_exonuclease.md",
                "snippet": "It's been shown to protect against phage lambda :ref{doi=10.1128/jb.177.3.497-501.1995}, and when cloned with the P2 Tin accessory gene, it was shown to protect against other *E. coli* phages :ref{doi=10.1016/j.chom.2022.02.018}.",
                "notes": "The pinned DefenseFinder wiki page links Old_exonuclease to lambda protection and to broader P2 Old plus Tin protection."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Old_exonuclease | 10\\.1101/2021\\.01\\.21\\.427644 | Prophage-encoded hotspots of bacterial immune systems",
                "notes": "The DefenseFinder article registry maps the named Old_exonuclease system to the Rousset et al. preprint."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "Old_exonuclease\tOld_exonuclease\t1\t1\tOld_exonuclease__Old_exonuclease\t\t\t",
                "notes": "The DefenseFinder rules table models Old_exonuclease as a single-profile system requiring Old_exonuclease__Old_exonuclease."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "old-exonuclease-tin-trigger-mechanism-gap",
        "prompt": "Resolve Old_exonuclease natural host breadth, Tin accessory dependence, RecBCD-triggered activation, profile-to-protein mapping, and lambda interference mechanism before minting narrower Old nuclease mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "The 1995 P2 Old paper supports Old nuclease activity and phage-lambda interference, and DefenseFinder represents Old_exonuclease as a required single-profile model. This first system-level record leaves Tin dependence in the Rousset et al. assay, natural host breadth, RecBCD-linked activation, profile-to-protein mapping, and the exact phage-interference mechanism unresolved.",
        "evidence": [
          {
            "reference": "DOI:10.1128/jb.177.3.497-501.1995",
            "snippet": "The Old protein of bacteriophage P2 is responsible for interference with the growth of phage lambda and for killing of recBC mutant Escherichia coli.",
            "notes": "The 1995 Old nuclease study identifies the P2 Old protein as responsible for phage-lambda interference."
          },
          {
            "reference": "DOI:10.1128/jb.177.3.497-501.1995",
            "snippet": "The Old protein fused to maltose-binding protein has exonuclease activity on double-stranded DNA as well as nuclease activity on single-stranded DNA and RNA.",
            "notes": "The 1995 biochemical study shows Old has nuclease activity on double-stranded DNA, single-stranded DNA, and RNA."
          },
          {
            "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/old_exonuclease.md",
            "snippet": "The old_exonuclease is dsDNA exonuclease that digests in the 5' to 3' direction :ref{doi=10.1128/jb.177.3.497-501.1995}. To our knowledge, other aspects of the molecular mechanisms remain unknown.",
            "notes": "The pinned DefenseFinder wiki page supports Old dsDNA exonuclease activity while leaving the remaining molecular mechanism unresolved."
          },
          {
            "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/old_exonuclease.md",
            "snippet": "The Old_exonuclease is composed of 1 protein: Old_exonuclease.",
            "notes": "The pinned DefenseFinder wiki page describes Old_exonuclease as a one-protein system."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "snippet": "Old_exonuclease\tOld_exonuclease\t1\t1\tOld_exonuclease__Old_exonuclease\t\t\t",
            "notes": "The DefenseFinder rules table models Old_exonuclease as a single-profile system requiring Old_exonuclease__Old_exonuclease."
          }
        ],
        "attaches_to": [
          "causal_graphs#old_exonuclease_locus_interferes_with_lambda"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-27"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-27T01:44:29Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Old exonuclease system as a DOI- and DefenseFinder-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v276.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-27T01:44:30Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed Old exonuclease system during canonical-example issue 444 enforcement and left canonical_examples empty because the sources support a bacteriophage P2 Old protein, a heterologous Old plus Tin protection assay in Escherichia coli, and a DefenseFinder RefSeq model example, but not a direct native microbial isolate exemplar with experimentally verified Old_exonuclease activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000254",
    "label": "Olokun system",
    "definition": "A phage defense system in which an organism possesses a two-component Olokun locus represented by OloA and OloB profiles that can protect bacteria from bacteriophage infection.",
    "definition_source": "DOI:10.1016/j.chom.2022.09.017",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "Olokun",
        "synonym_type": "EXACT_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1016/j.chom.2022.09.017",
        "snippet": "discovery of 21 defense systems that protect bacteria from phages, based on computational genomic analyses and phage-infection experiments",
        "notes": "Millman et al. report the computational and experimental cohort that DefenseFinder cites for Olokun as a bacterial anti-phage system."
      },
      {
        "reference": "DOI:10.1101/2022.05.11.491447",
        "snippet": "discovery of 21 new defense systems that protect bacteria from phages, based on computational genomic analyses and phage infection experiments",
        "notes": "The bioRxiv version of Millman et al. independently carries the 21-system discovery claim linked from DefenseFinder's Olokun article registry."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "Olokun | 10\\.1101/2022\\.05\\.11\\.491447 | An expanding arsenal of immune systems that protect bacteria from phages",
        "notes": "The DefenseFinder model registry maps the named Olokun system to the Millman et al. antiphage-system discovery preprint."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "Olokun\tOlokun\t2\t2\tOlokun__OloA, Olokun__OloB",
        "notes": "The DefenseFinder rules table models Olokun with OloA and OloB profiles."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "Olokun__OloA                                      | Olokun__OloA                                      | Olokun",
        "notes": "The DefenseFinder HMM inventory records OloA as an Olokun profile."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "Olokun__OloB                                      | Olokun__OloB                                      | Olokun",
        "notes": "The DefenseFinder HMM inventory records OloB as an Olokun profile."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "olokun_locus_restricts_phage",
        "title": "Olokun loci confer bacterial phage defense",
        "description": "Conservative system-level sketch linking possession of an Olokun locus to restricted bacteriophage propagation without asserting the unresolved phage trigger or molecular output.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Olokun as a named anti-phage system with DefenseFinder OloA and OloB profile choices while leaving its phage trigger, molecular substrate, antiviral effector output, and subtype breadth unresolved.",
        "nodes": [
          {
            "node_id": "olokun_locus",
            "label": "Olokun locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "An Olokun anti-phage defense locus satisfying a DefenseFinder rule over OloA and OloB profiles."
          },
          {
            "node_id": "restricted_phage_propagation",
            "label": "restricted phage propagation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced propagation of bacteriophage in cells carrying the Olokun system."
          },
          {
            "node_id": "olokun_system_trait",
            "label": "Olokun system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000254",
            "description": "Possession of a genome-encoded Olokun phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "olokun_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "restricted_phage_propagation",
            "description": "DefenseFinder maps Olokun to a bacterial anti-phage-system discovery preprint and represents Olokun loci through OloA and OloB component profiles.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.chom.2022.09.017",
                "snippet": "discovery of 21 defense systems that protect bacteria from phages",
                "notes": "Millman et al. describe the anti-phage discovery cohort that the DefenseFinder Olokun registry row maps to the Olokun system."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Olokun | 10\\.1101/2022\\.05\\.11\\.491447 | An expanding arsenal of immune systems that protect bacteria from phages",
                "notes": "The DefenseFinder registry maps Olokun itself to the Millman et al. bacterial antiphage-system discovery preprint."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "Olokun\tOlokun\t2\t2\tOlokun__OloA, Olokun__OloB",
                "notes": "The DefenseFinder rules table supports OloA and OloB as Olokun system profile choices."
              }
            ]
          },
          {
            "subject": "restricted_phage_propagation",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "olokun_system_trait",
            "description": "Olokun-mediated phage restriction realizes the Olokun system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.chom.2022.09.017",
                "snippet": "discovery of 21 defense systems that protect bacteria from phages",
                "notes": "Millman et al. place the Olokun discovery cohort in the set of bacterial systems that protect against phages."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Olokun | 10\\.1101/2022\\.05\\.11\\.491447 | An expanding arsenal of immune systems that protect bacteria from phages",
                "notes": "DefenseFinder records Olokun as a named system from the Millman et al. antiphage discovery preprint."
              }
            ]
          },
          {
            "subject": "olokun_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Olokun system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "An expanding arsenal of immune systems that protect bacteria from phages",
                "notes": "DefenseFinder associates Olokun with the Millman et al. bacterial antiphage-system discovery paper."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "olokun-mechanism-gap",
        "prompt": "Resolve Olokun phage triggers and effector outputs before minting narrower Olokun mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Millman et al. and DefenseFinder support Olokun as a named anti-phage system with OloA and OloB profile choices, but the trigger, molecular substrate, antiviral effector output, and subtype-specific mechanism are not resolved enough here to assert a narrower mechanistic child trait.",
        "attaches_to": [
          "causal_graphs#olokun_locus_restricts_phage"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-18"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-18T22:52:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Olokun system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v131.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000331",
    "label": "Ophion system",
    "definition": "A phage defense system in which an organism possesses a three-gene Ophion locus encoding OpnA, OpnB, and OpnC components that can block jumbo-phage infection before phage-nucleus formation.",
    "definition_source": "DOI:10.1101/2025.09.30.679545",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "Ophion",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1101/2025.09.30.679545"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1101/2025.09.30.679545",
        "snippet": "From over 500 candidate defense systems, we selected nine for experimental testing and validated three: Dionysus, a TerB-encoding system that disrupts early phage infection vesicle formation by Jumbo phages; Ophion, a Radical SAM-containing system that prevents the formation of the Jumbo phage nucleus; and Ambrosia, a tightly regulated RM-like system.",
        "notes": "Keesman et al. named Ophion among three modular phage-defense candidates validated experimentally from an initial pool of more than 500 candidates."
      },
      {
        "reference": "DOI:10.1101/2025.09.30.679545",
        "snippet": "Ophion, named after a primordial serpent from Greek mythology, is a three gene system encoding a radical S-adenosyl-L-methionine (rSAM) enzyme (OpnA), a polymerase-and histidinol-phosphatase (PHP, OpnB), and a phosphoribosyl transferase (PRTase, OpnC)",
        "notes": "Keesman et al. support Ophion as a three-gene system encoding OpnA, OpnB, and OpnC components with Radical SAM, PHP, and phosphoribosyl-transferase domains."
      },
      {
        "reference": "DOI:10.1101/2025.09.30.679545",
        "snippet": "Ophion shows strong protection against jumbo phages",
        "notes": "Keesman et al. support Ophion as a system that strongly protects against jumbo phages."
      },
      {
        "reference": "DOI:10.1101/2025.09.30.679545",
        "snippet": "Mutating conserved residues of the rSAM and PRTase domains revealed these to be essential for protection, with partial dependence on the PHP domain",
        "notes": "Keesman et al. support the OpnA Radical SAM and OpnC phosphoribosyl-transferase domains as essential in the tested Ophion system, with partial dependence on OpnB PHP."
      },
      {
        "reference": "DOI:10.1101/2025.09.30.679545",
        "snippet": "Ophion provides potent and specific defense against jumbo phages by blocking progression from the EPI vesicle to the nucleus stage, possibly by halting the transcription of the nucleus forming genes",
        "notes": "Keesman et al. connect Ophion-mediated defense to arrest of jumbo phages as they progress from the early phage infection vesicle stage to nucleus formation."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "Ophion | 10\\.1101/2025\\.09\\.30\\.679545 | Discovery of phage defense systems through component modularity networks",
        "notes": "The DefenseFinder article registry maps the named Ophion system to the Keesman et al. modular phage-defense discovery preprint; the pinned DefenseFinder HMM inventory and rules table do not list Ophion, so this row is name-to-paper evidence rather than model-component evidence."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "ophion_locus_restricts_phage",
        "title": "Ophion loci confer bacterial phage defense",
        "description": "Conservative system-level sketch linking possession of an Ophion locus to restricted jumbo-phage propagation without asserting the direct phage trigger, modified nucleotide product, or early-transcription target.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Ophion as a named three-gene anti-jumbo-phage system while leaving its direct phage trigger, the OpnA/OpnB/OpnC interaction sequence, the nucleotide-modification product, the natural locus breadth, and the absence of pinned DefenseFinder HMM or rule rows unresolved.",
        "nodes": [
          {
            "node_id": "ophion_locus",
            "label": "Ophion locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A three-gene Ophion anti-jumbo-phage defense locus encoding OpnA, OpnB, and OpnC components."
          },
          {
            "node_id": "restricted_phage_propagation",
            "label": "restricted phage propagation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced propagation of jumbo bacteriophages in cells carrying the Ophion system."
          },
          {
            "node_id": "ophion_system_trait",
            "label": "Ophion system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000331",
            "description": "Possession of a genome-encoded Ophion phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "ophion_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "restricted_phage_propagation",
            "description": "The three-gene Ophion locus restricts infection by jumbo phages.",
            "evidence": [
              {
                "reference": "DOI:10.1101/2025.09.30.679545",
                "snippet": "Ophion shows strong protection against jumbo phages",
                "notes": "Keesman et al. report that Ophion protects against jumbo phages."
              },
              {
                "reference": "DOI:10.1101/2025.09.30.679545",
                "snippet": "Mutating conserved residues of the rSAM and PRTase domains revealed these to be essential for protection, with partial dependence on the PHP domain",
                "notes": "Keesman et al. report that conserved-residue mutations establish the OpnA Radical SAM and OpnC phosphoribosyl-transferase domains as essential, with partial dependence on OpnB PHP."
              }
            ]
          },
          {
            "subject": "restricted_phage_propagation",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "ophion_system_trait",
            "description": "Ophion-mediated phage restriction realizes the Ophion system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1101/2025.09.30.679545",
                "snippet": "Ophion provides potent and specific defense against jumbo phages by blocking progression from the EPI vesicle to the nucleus stage, possibly by halting the transcription of the nucleus forming genes",
                "notes": "Keesman et al. connect Ophion activity to blocking progression from the jumbo-phage early phage infection vesicle stage to the nucleus stage."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Ophion | 10\\.1101/2025\\.09\\.30\\.679545 | Discovery of phage defense systems through component modularity networks",
                "notes": "The DefenseFinder article registry maps the named Ophion system to the Keesman et al. modular phage-defense discovery preprint; the pinned DefenseFinder HMM inventory and rules table do not list Ophion, so this row is name-to-paper evidence rather than model-component evidence."
              }
            ]
          },
          {
            "subject": "ophion_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Ophion system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1101/2025.09.30.679545",
                "snippet": "From over 500 candidate defense systems, we selected nine for experimental testing and validated three: Dionysus, a TerB-encoding system that disrupts early phage infection vesicle formation by Jumbo phages; Ophion, a Radical SAM-containing system that prevents the formation of the Jumbo phage nucleus; and Ambrosia, a tightly regulated RM-like system.",
                "notes": "Keesman et al. list Ophion among experimentally validated phage-defense systems."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Ophion | 10\\.1101/2025\\.09\\.30\\.679545 | Discovery of phage defense systems through component modularity networks",
                "notes": "The DefenseFinder article registry maps the named Ophion system to the Keesman et al. modular phage-defense discovery preprint; the pinned DefenseFinder HMM inventory and rules table do not list Ophion, so this row is name-to-paper evidence rather than model-component evidence."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "ophion-jumbo-phage-mechanism-gap",
        "prompt": "Resolve Ophion phage triggers, nucleotide-modification products, and model coverage before minting narrower Ophion mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Keesman et al. support Ophion as a three-gene anti-jumbo-phage system that blocks progression from the early phage infection vesicle to the phage nucleus, but the direct phage trigger, exact OpnA/OpnB/OpnC interaction sequence, modified nucleotide product, natural locus breadth, and profile-to-component model are not resolved enough here to assert a narrower mechanistic child trait.",
        "attaches_to": [
          "causal_graphs#ophion_locus_restricts_phage"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-21"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-21T08:20:12Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Ophion system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v208.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-21T08:47:47Z",
        "curator": "codex",
        "action": "ADDRESS_PR_REVIEW",
        "changes": "Tightened the Ophion conserved-residue evidence note after the PR 1183 adversarial review filed issue 1184, narrowing the claim to essential OpnA Radical SAM and OpnC phosphoribosyl-transferase domains plus partial OpnB PHP dependence.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000293",
    "label": "Oshun system",
    "definition": "A phage defense system in which an organism possesses an Oshun locus that can protect bacteria from bacteriophage infection.",
    "definition_source": "DOI:10.1101/2025.01.08.631966",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "Oshun",
        "synonym_type": "EXACT_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      },
      {
        "synonym_text": "OsnA2",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1101/2025.01.08.631966",
        "snippet": "Among the remaining eight systems, six demonstrated increased resistance to at least one phage with more than 100 fold reduction in plaque forming units (PFU) (Figure 3a, Supplementary Figure 5). As Streptomyces are mostly soil dwelling bacteria, we named these systems after deities of the soil and earth (Ceres, Geb, Veles, Prithvi, Ukko and Oshun).",
        "notes": "Mordret et al. directly name Oshun among six Streptomyces systems that increased resistance to at least one phage."
      },
      {
        "reference": "DOI:10.1101/2025.01.08.631966",
        "snippet": "The bacterial pangenome encodes an immense array of antiphage systems, yet much of their diversity remains uncharted",
        "notes": "Mordret et al. motivate a conservative system-level record that does not assert a resolved Oshun trigger, effector output, or universal pathway."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "Oshun | 10\\.1101/2025\\.01\\.08\\.631966 | Protein and genomic language models chart a vast landscape of antiphage defenses",
        "notes": "The DefenseFinder model registry maps the named Oshun system to the Mordret et al. antiphage-system discovery preprint."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "Oshun__OsnA2                                     |                                                  | Oshun",
        "notes": "The DefenseFinder HMM inventory records OsnA2 in the Oshun model namespace."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "oshun_locus_restricts_phage",
        "title": "Oshun loci confer bacterial phage defense",
        "description": "Conservative system-level sketch linking possession of an Oshun locus to restricted bacteriophage propagation without asserting the unresolved phage trigger or molecular output.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Oshun as a named anti-phage system with an OsnA2 HMM profile entry while leaving its phage trigger, molecular substrate, antiviral effector output, and subtype breadth unresolved.",
        "nodes": [
          {
            "node_id": "oshun_locus",
            "label": "Oshun locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "An Oshun anti-phage defense locus cataloged in DefenseFinder with an OsnA2 HMM profile entry."
          },
          {
            "node_id": "restricted_phage_propagation",
            "label": "restricted phage propagation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced propagation of bacteriophage in cells carrying the Oshun system."
          },
          {
            "node_id": "oshun_system_trait",
            "label": "Oshun system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000293",
            "description": "Possession of a genome-encoded Oshun phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "oshun_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "restricted_phage_propagation",
            "description": "DefenseFinder maps Oshun to a protein- and genomic-language-model antiphage-system discovery preprint and catalogs an OsnA2 HMM profile entry in the Oshun model namespace.",
            "evidence": [
              {
                "reference": "DOI:10.1101/2025.01.08.631966",
                "snippet": "Among the remaining eight systems, six demonstrated increased resistance to at least one phage with more than 100 fold reduction in plaque forming units (PFU) (Figure 3a, Supplementary Figure 5). As Streptomyces are mostly soil dwelling bacteria, we named these systems after deities of the soil and earth (Ceres, Geb, Veles, Prithvi, Ukko and Oshun).",
                "notes": "Mordret et al. directly name Oshun among six Streptomyces systems that restricted at least one phage."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Oshun | 10\\.1101/2025\\.01\\.08\\.631966 | Protein and genomic language models chart a vast landscape of antiphage defenses",
                "notes": "The DefenseFinder registry maps Oshun itself to the Mordret et al. bacterial antiphage-system discovery preprint."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "Oshun__OsnA2                                     |                                                  | Oshun",
                "notes": "The DefenseFinder HMM inventory records OsnA2 in the Oshun model namespace."
              }
            ]
          },
          {
            "subject": "restricted_phage_propagation",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "oshun_system_trait",
            "description": "Oshun-mediated phage restriction realizes the Oshun system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1101/2025.01.08.631966",
                "snippet": "Among the remaining eight systems, six demonstrated increased resistance to at least one phage with more than 100 fold reduction in plaque forming units (PFU) (Figure 3a, Supplementary Figure 5). As Streptomyces are mostly soil dwelling bacteria, we named these systems after deities of the soil and earth (Ceres, Geb, Veles, Prithvi, Ukko and Oshun).",
                "notes": "Mordret et al. directly name Oshun among six systems that increased resistance to at least one phage."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Oshun | 10\\.1101/2025\\.01\\.08\\.631966 | Protein and genomic language models chart a vast landscape of antiphage defenses",
                "notes": "DefenseFinder records Oshun as a named system from the Mordret et al. antiphage discovery preprint."
              }
            ]
          },
          {
            "subject": "oshun_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Oshun system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| Oshun | 10\\.1101/2025\\.01\\.08\\.631966 | Protein and genomic language models chart a vast landscape of antiphage defenses |",
                "notes": "DefenseFinder associates Oshun with the Mordret et al. bacterial antiphage-system discovery preprint."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "oshun-mechanism-gap",
        "prompt": "Resolve Oshun phage triggers and effector outputs before minting narrower Oshun mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Mordret et al. and DefenseFinder support Oshun as a named anti-phage system with an OsnA2 HMM profile entry, but the trigger, molecular substrate, antiviral effector output, and subtype-specific mechanism are not resolved enough here to assert a narrower mechanistic child trait.",
        "attaches_to": [
          "causal_graphs#oshun_locus_restricts_phage"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-19"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-19T21:03:41Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Oshun system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v170.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000419",
    "label": "prokaryotic Argonaute defense system",
    "definition": "A genomics trait describing possession of a prokaryotic Argonaute-centered defense locus that uses a pAgo protein, alone or with cognate accessory proteins, to defend against plasmids, bacteriophages, or other mobile genetic elements.",
    "definition_source": "DOI:10.1186/1745-6150-4-29",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000188"
    ],
    "synonyms": [
      {
        "synonym_text": "pAgo",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1186/1745-6150-4-29",
        "snippet": "The hypothesis that pAgos are key components of a novel prokaryotic immune system that employs guide RNA or DNA molecules to degrade nucleic acids of invading mobile elements",
        "notes": "Makarova et al. link prokaryotic Argonaute homologs to a predicted defense system against mobile genetic elements; later SPARTA and DdmDE experiments support two branches of this family."
      },
      {
        "reference": "DOI:10.1016/j.cell.2022.03.012",
        "snippet": "short prokaryotic Argonaute and the associated TIR-APAZ (SPARTA) proteins form heterodimeric complexes",
        "notes": "Koopal et al. support SPARTA as one experimentally resolved short pAgo and TIR-APAZ defense system."
      },
      {
        "reference": "DOI:10.1038/s41586-022-04546-y",
        "snippet": "These systems, termed DdmABC and DdmDE",
        "notes": "Jaskolska et al. support DdmDE as another prokaryotic Argonaute defense system in Vibrio cholerae."
      },
      {
        "reference": "DOI:10.1038/s41586-024-07515-9",
        "snippet": "DdmE is a catalytically inactive, DNA-guided, DNA-targeting pAgo",
        "notes": "Bravo et al. directly identify DdmE as the DNA-targeting prokaryotic Argonaute component of DdmDE."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| pAgo | 10\\.1186/1745-6150-4-29 | Prokaryotic homologs of Argonaute proteins are predicted to function as key components of a novel system of defense against mobile genetic elements |",
        "notes": "The pinned DefenseFinder article registry maps the pAgo model namespace to the Makarova et al. prokaryotic Argonaute mobile genetic element defense paper."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "pAgo\tpAgo\t1\t3\tpAgo__pAgo_LongA, pAgo__pAgo_LongB, pAgo__pAgo_S1A, pAgo__pAgo_S2B, pAgo__pAgo_SPARTA\tpAgo__EabAgaM, pAgo__EcAgaN, pAgo__GbbAgaS, pAgo__SIR2APAZ, pAgo__TIRAPAZ, pAgo__XAPAZ\t\t",
        "notes": "The pinned DefenseFinder rules table models pAgo as a system namespace with long pAgo, SPARTA, and optional APAZ-associated profile groups."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| pAgo__pAgo_SPARTA                                | pAgo__pAgo_SPARTA                                | pAgo                   | Custom                  | 20     |",
        "notes": "The pinned DefenseFinder HMM inventory records pAgo__pAgo_SPARTA under the pAgo model namespace."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| pAgo__TIRAPAZ                                    | pAgo__TIRAPAZ                                    | pAgo                   | Custom                  | 20     |",
        "notes": "The pinned DefenseFinder HMM inventory records pAgo__TIRAPAZ under the pAgo model namespace."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:666",
        "taxon_label": "Vibrio cholerae",
        "note": "V. cholerae seventh pandemic strains carry the prokaryotic-Argonaute DdmDE plasmid defense system.",
        "reference": "DOI:10.1038/s41586-022-04546-y"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "pago_system_family_hierarchy",
        "title": "Prokaryotic Argonaute systems include SPARTA and DdmDE defense loci",
        "description": "Nonmechanistic family sketch linking the pAgo possession trait to experimentally curated SPARTA and DdmDE child systems.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph is deliberately limited to family hierarchy because long pAgo, SPARTA, DdmDE, SIR2-APAZ, TIR-APAZ, and other APAZ-associated pAgo systems can differ in effector chemistry, guide origin, accessory proteins, and plasmid or phage target breadth.",
        "nodes": [
          {
            "node_id": "sparta_system",
            "label": "SPARTA system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000240",
            "description": "Possession of a short prokaryotic Argonaute TIR-APAZ defense system."
          },
          {
            "node_id": "ddmde_system",
            "label": "DdmDE system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000275",
            "description": "Possession of a DNA-guided prokaryotic Argonaute DdmDE defense system."
          },
          {
            "node_id": "pago_system_trait",
            "label": "prokaryotic Argonaute defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000419",
            "description": "Possession of a genome-encoded prokaryotic Argonaute-centered defense system."
          }
        ],
        "edges": [
          {
            "subject": "sparta_system",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "pago_system_trait",
            "description": "SPARTA is a short-pAgo TIR-APAZ system within the broader prokaryotic Argonaute defense family.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.cell.2022.03.012",
                "snippet": "short prokaryotic Argonaute and the associated TIR-APAZ (SPARTA) proteins form heterodimeric complexes",
                "notes": "Koopal et al. define SPARTA around a short pAgo and TIR-APAZ protein pair."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "pAgo\tpAgo\t1\t3\tpAgo__pAgo_LongA, pAgo__pAgo_LongB, pAgo__pAgo_S1A, pAgo__pAgo_S2B, pAgo__pAgo_SPARTA\tpAgo__EabAgaM, pAgo__EcAgaN, pAgo__GbbAgaS, pAgo__SIR2APAZ, pAgo__TIRAPAZ, pAgo__XAPAZ\t\t",
                "notes": "The pinned DefenseFinder rules table models pAgo as a system namespace with long pAgo, SPARTA, and optional APAZ-associated profile groups."
              }
            ]
          },
          {
            "subject": "ddmde_system",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "pago_system_trait",
            "description": "DdmDE is an anti-plasmid defense system with a DNA-guided pAgo component.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41586-024-07515-9",
                "snippet": "DdmE is a catalytically inactive, DNA-guided, DNA-targeting pAgo",
                "notes": "Bravo et al. identify DdmE as the pAgo component of DdmDE."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "pago-subfamily-boundary-gap",
        "prompt": "Resolve pAgo subfamily boundaries, accessory-protein requirements, and substrate breadth before minting narrower long-pAgo or APAZ-associated defense children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "SPARTA and DdmDE support prokaryotic Argonaute defense systems as a reusable genomics family, and DefenseFinder models a pAgo namespace with long pAgo, SPARTA, and optional APAZ-associated profiles. This parent does not yet resolve whether every DefenseFinder pAgo submodel has the same plasmid or phage substrate range, whether standalone APAZ-associated profiles are exact children, or which native-host examples support each subfamily.",
        "evidence": [
          {
            "reference": "DOI:10.1016/j.cell.2022.03.012",
            "snippet": "short prokaryotic Argonaute and the associated TIR-APAZ (SPARTA) proteins form heterodimeric complexes",
            "notes": "Koopal et al. support one short-pAgo branch as a paired SPARTA system."
          },
          {
            "reference": "DOI:10.1038/s41586-024-07515-9",
            "snippet": "DdmE is a catalytically inactive, DNA-guided, DNA-targeting pAgo",
            "notes": "Bravo et al. support one DdmDE branch with DdmE as a DNA-guided pAgo."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "snippet": "pAgo\tpAgo\t1\t3\tpAgo__pAgo_LongA, pAgo__pAgo_LongB, pAgo__pAgo_S1A, pAgo__pAgo_S2B, pAgo__pAgo_SPARTA\tpAgo__EabAgaM, pAgo__EcAgaN, pAgo__GbbAgaS, pAgo__SIR2APAZ, pAgo__TIRAPAZ, pAgo__XAPAZ\t\t",
            "notes": "The pinned DefenseFinder rules table models pAgo as a system namespace with long pAgo, SPARTA, and optional APAZ-associated profile groups."
          }
        ],
        "attaches_to": [
          "causal_graphs#pago_system_family_hierarchy"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-27"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-27T22:11:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted prokaryotic Argonaute defense system as a DOI-backed GENOMICS TraitRecord under the quality root after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; scoped the graph to SPARTA and DdmDE family hierarchy and reserved the replacement placeholder in proposals/metpo_traitmech_v296.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-27T22:20:00Z",
        "curator": "codex",
        "action": "LOCAL_VALIDATION_REPAIR",
        "changes": "Added a contiguous Makarova et al. abstract snippet after the evidence snippet audit flagged the prokaryotic Argonaute defense system record as a new MISSING_SNIPPET finding.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000294",
    "label": "Panchino gp28 system",
    "definition": "A phage defense system in which an organism possesses a Panchino gp28 locus that can protect bacteria from bacteriophage infection.",
    "definition_source": "DOI:10.1038/nmicrobiol.2016.251",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "Panchino_gp28",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/nmicrobiol.2016.251",
        "snippet": "at least five distinct prophage-expressed viral defense systems that interfere with infection",
        "notes": "Dedrick et al. place the Cluster N Panchino gp28 system in a cohort of prophage-expressed defenses against lytic and temperate mycobacteriophages."
      },
      {
        "reference": "DOI:10.1038/nmicrobiol.2016.251",
        "snippet": "The Panchino restriction system (gp28) is a strong candidate for conferring this defense",
        "notes": "Dedrick et al. identify Panchino gp28 as the candidate restriction system responsible for a heterotypic viral-defense phenotype."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "Panchino_gp28 | 10\\.1038/nmicrobiol\\.2016\\.251 | Prophage-mediated defence against viral attack and viral counter-defence",
        "notes": "The DefenseFinder model registry maps the named Panchino_gp28 system to the Dedrick et al. prophage-mediated viral-defense paper."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "Panchino_gp28__gp28                              | Panchino_gp28__gp28                              | Panchino_gp28",
        "notes": "The DefenseFinder HMM inventory records gp28 in the Panchino_gp28 model namespace."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "panchino_gp28_locus_restricts_phage",
        "title": "Panchino gp28 loci confer bacterial phage defense",
        "description": "Conservative system-level sketch linking possession of a Panchino gp28 locus to restricted bacteriophage propagation without asserting the unresolved restriction target, methylation context, or target-phage breadth.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Panchino gp28 as a named anti-phage system with a DefenseFinder gp28 profile while leaving its restriction target, methylation requirements, and target-phage breadth unresolved.",
        "nodes": [
          {
            "node_id": "panchino_gp28_locus",
            "label": "Panchino gp28 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A Panchino gp28 anti-phage defense locus cataloged in DefenseFinder with a gp28 HMM profile."
          },
          {
            "node_id": "restricted_phage_propagation",
            "label": "restricted phage propagation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced propagation of bacteriophage in cells carrying the Panchino gp28 system."
          },
          {
            "node_id": "panchino_gp28_system_trait",
            "label": "Panchino gp28 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000294",
            "description": "Possession of a genome-encoded Panchino gp28 phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "panchino_gp28_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "restricted_phage_propagation",
            "description": "Dedrick et al. identify Panchino gp28 as a prophage-expressed viral-defense candidate, and DefenseFinder catalogs a gp28 profile in the Panchino_gp28 model namespace.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nmicrobiol.2016.251",
                "snippet": "The Panchino restriction system (gp28) is a strong candidate for conferring this defense",
                "notes": "Dedrick et al. support Panchino gp28 as the candidate system that confers a Panchino defense profile."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "Panchino_gp28__gp28                              | Panchino_gp28__gp28                              | Panchino_gp28",
                "notes": "The DefenseFinder HMM inventory records gp28 in the Panchino_gp28 model namespace."
              }
            ]
          },
          {
            "subject": "restricted_phage_propagation",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "panchino_gp28_system_trait",
            "description": "Panchino-gp28-mediated phage restriction realizes the Panchino gp28 system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nmicrobiol.2016.251",
                "snippet": "at least five distinct prophage-expressed viral defense systems that interfere with infection",
                "notes": "Dedrick et al. place Panchino gp28 among Cluster N prophage systems that defend against phage infection."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Panchino_gp28 | 10\\.1038/nmicrobiol\\.2016\\.251 | Prophage-mediated defence against viral attack and viral counter-defence",
                "notes": "DefenseFinder records Panchino_gp28 as a named system from the Dedrick et al. prophage-defense paper."
              }
            ]
          },
          {
            "subject": "panchino_gp28_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Panchino gp28 system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| Panchino_gp28 | 10\\.1038/nmicrobiol\\.2016\\.251 | Prophage-mediated defence against viral attack and viral counter-defence |",
                "notes": "DefenseFinder associates Panchino_gp28 with the Dedrick et al. prophage-mediated viral-defense paper."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "panchino_gp28-mechanism-gap",
        "prompt": "Resolve the Panchino gp28 restriction target, methylation requirements, and homolog breadth before minting narrower Panchino gp28 mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Dedrick et al. and DefenseFinder support Panchino gp28 as a named anti-phage system with a gp28 profile, but the restriction target, methylation context, and full target-phage breadth are not resolved enough here to assert a narrower mechanistic child trait.",
        "attaches_to": [
          "causal_graphs#panchino_gp28_locus_restricts_phage"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-19"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-19T21:37:34Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Panchino gp28 system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v171.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-19T22:03:20Z",
        "curator": "codex",
        "action": "DEMOTED_SOURCE_KEY_SYNONYM",
        "changes": "Resolved PR #1085 review issue #1086 by demoting the DefenseFinder source key Panchino_gp28 from exact synonym to related synonym scope.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-19T22:07:53Z",
        "curator": "codex",
        "action": "FIXED_FIXED_WIDTH_SNIPPET",
        "changes": "Resolved PR #1085 review issue #1087 by removing an extra separator space from the two fixed-width DefenseFinder Panchino_gp28__gp28 HMM snippets.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-19T22:13:50Z",
        "curator": "codex",
        "action": "REMOVED_AMBIGUOUS_SYNONYM",
        "changes": "Resolved PR #1085 review issue #1088 by dropping the ambiguous bare gp28 related synonym while retaining the pinned Panchino_gp28__gp28 HMM profile as evidence.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000102",
    "label": "pangenome openness",
    "definition": "A genomics trait describing the structure of a species' pangenome \u2014 the balance of core versus accessory genes and whether the pangenome is open (continually acquiring new genes across genomes) or closed.",
    "definition_source": "DOI:10.1073/pnas.0506758102",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000188"
    ],
    "synonyms": [
      {
        "synonym_text": "open pangenome",
        "synonym_type": "NARROW_SYNONYM",
        "source": "DOI:10.1073/pnas.0506758102"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1073/pnas.0506758102",
        "notes": "Tettelin et al. introduced the microbial pan-genome concept, distinguishing core and dispensable genes and open versus closed pangenomes."
      },
      {
        "reference": "DOI:10.1038/nmicrobiol.2017.40",
        "notes": "McInerney, McNally & O'Connell review why prokaryotes have pangenomes and what drives their openness."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:562",
        "taxon_label": "Escherichia coli",
        "note": "Textbook open pan-genome: enormous accessory-genome diversity across strains relative to the core genome.",
        "reference": "PMID:20623278"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "pangenome_openness_hgt",
        "title": "Horizontal gene transfer drives open pangenomes",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This genomics record is a measurement, genomic-element classification, or population-level descriptor rather than one taxon-specific protein mechanism; contextual protein nodes do not receive token UniProt examples.",
        "description": "Evidence-backed causal sketch linking HGT and ecological breadth to open versus closed pangenome structure.",
        "nodes": [
          {
            "node_id": "pangenome_openness_trait",
            "label": "pangenome openness",
            "node_type": "TRAIT",
            "grounding": "traitmech:000102",
            "description": "Open versus closed structure of a species' pangenome."
          },
          {
            "node_id": "horizontal_gene_transfer",
            "label": "horizontal gene transfer",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Acquisition of genes between lineages outside vertical descent.",
            "grounding": "GO:0009292"
          },
          {
            "node_id": "accessory_gene_pool",
            "label": "accessory gene pool",
            "node_type": "QUALITY",
            "description": "Strain-variable genes outside the species core."
          },
          {
            "node_id": "plasmid",
            "label": "plasmid",
            "node_type": "GENETIC_ELEMENT",
            "description": "Mobile genetic element acting as a vehicle for accessory genes."
          },
          {
            "node_id": "prophage",
            "label": "prophage",
            "node_type": "GENETIC_ELEMENT",
            "description": "Integrated bacteriophage genome contributing to gene flux."
          },
          {
            "node_id": "gene_gain_loss_dynamics",
            "label": "gene gain and loss dynamics",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Ongoing acquisition and loss of genes across sampled lineages."
          },
          {
            "node_id": "core_gene_fraction",
            "label": "core gene fraction",
            "node_type": "QUALITY",
            "description": "Proportion of genes conserved across all genomes in the species."
          },
          {
            "node_id": "rare_gene_fraction",
            "label": "rare gene fraction",
            "node_type": "QUALITY",
            "description": "Proportion of genes present in only a few genomes."
          },
          {
            "node_id": "sampling_bias",
            "label": "sampling bias",
            "node_type": "EXPERIMENTAL_FACTOR",
            "description": "Bias in which genomes are sampled, distorting openness estimates."
          },
          {
            "node_id": "annotation_error",
            "label": "annotation error",
            "node_type": "EXPERIMENTAL_FACTOR",
            "description": "Misannotation of genes that distorts presence/absence calls."
          },
          {
            "node_id": "apparent_pangenome_openness",
            "label": "apparent pangenome openness",
            "node_type": "QUALITY",
            "description": "Estimated openness that may reflect artifacts rather than true HGT dynamics."
          }
        ],
        "edges": [
          {
            "subject": "horizontal_gene_transfer",
            "predicate": "causes",
            "object": "pangenome_openness_trait",
            "description": "HGT continually adds new accessory genes, keeping the pangenome open.",
            "evidence": [
              {
                "reference": "DOI:10.1073/pnas.0506758102",
                "notes": "Tettelin et al. introduce the pan-genome concept distinguishing open vs closed pangenomes."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "pangenome_openness_trait",
            "predicate": "associated with",
            "object": "accessory_gene_pool",
            "description": "Open pangenomes accumulate large accessory gene pools across strains.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nmicrobiol.2017.40",
                "notes": "McInerney et al. review the ecological and population drivers of pangenome openness."
              }
            ],
            "predicate_id": "biolink:associated_with"
          },
          {
            "subject": "plasmid",
            "predicate": "enables",
            "object": "horizontal_gene_transfer",
            "description": "Plasmids are mobile vehicles for accessory genes, increasing opportunity for gene acquisition.",
            "evidence": [
              {
                "reference": "DOI:10.1099/mgen.0.001021",
                "notes": "Gene gain and loss mediated by mobile genetic elements including plasmids."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "prophage",
            "predicate": "promotes",
            "object": "pangenome_openness_trait",
            "description": "Prophage-associated gene flux contributes to recent gain/loss and accessory genome expansion.",
            "evidence": [
              {
                "reference": "DOI:10.3390/microorganisms12050986",
                "notes": "Prophages, integrases, and transfer/mobile elements identified as main drivers of pangenome openness."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "gene_gain_loss_dynamics",
            "predicate": "shapes",
            "object": "pangenome_openness_trait",
            "description": "Open/closed behavior reflects balance of ongoing gene gain versus loss across sampled lineages.",
            "evidence": [
              {
                "reference": "DOI:10.1101/2022.04.23.489244",
                "notes": "HGT and resultant gene gain and loss dynamics are central drivers of pangenome composition."
              }
            ]
          },
          {
            "subject": "core_gene_fraction",
            "predicate": "negatively associated with",
            "object": "pangenome_openness_trait",
            "description": "A larger conserved core leaves less flexible accessory fraction; empirically anticorrelated with openness.",
            "evidence": [
              {
                "reference": "DOI:10.3390/microorganisms12050986",
                "notes": "Strong inverse correlation between core gene percentage and openness coefficient (corr = -0.910)."
              }
            ]
          },
          {
            "subject": "rare_gene_fraction",
            "predicate": "positively associated with",
            "object": "pangenome_openness_trait",
            "description": "A higher proportion of rare genes indicates continued acquisition and non-saturation of the pangenome.",
            "evidence": [
              {
                "reference": "DOI:10.3390/microorganisms12050986",
                "notes": "Positive correlation between rare gene percentage and openness coefficient (corr = 0.742)."
              }
            ]
          },
          {
            "subject": "sampling_bias",
            "predicate": "biases estimate of",
            "object": "apparent_pangenome_openness",
            "description": "Apparent openness can reflect which genomes were sampled rather than true HGT dynamics.",
            "evidence": [
              {
                "reference": "DOI:10.1101/2022.04.23.489244",
                "notes": "Gene accumulation curves can be misleading because they may reflect sampling temporal/diversity bias."
              }
            ]
          },
          {
            "subject": "annotation_error",
            "predicate": "biases estimate of",
            "object": "apparent_pangenome_openness",
            "description": "Misannotation inflates or deflates presence/absence calls and can misclassify open/closed status.",
            "evidence": [
              {
                "reference": "DOI:10.1101/2022.04.23.489244",
                "notes": "Higher rates of annotation error can lead to incorrect estimates of whether a pangenome is open or closed."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-06-05T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate GENOMICS trait (pangenome openness) from literature research.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-08T14:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (HGT-driven open pangenome) with biolink predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-14T06:55:38Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0009292\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 7 evidence-backed generic edges (8 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:11Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d71, RO:0002213\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope pangenome_openness_hgt=NONMECHANISTIC with scope_notes; retyped 2 node(s) (plasmid->GENETIC_ELEMENT, prophage->GENETIC_ELEMENT).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000407",
    "label": "Panoptes system",
    "definition": "A phage defense system in which an organism possesses a two-gene optSE locus encoding an OptS protein that constitutively produces cyclic dinucleotides and an OptE transmembrane effector that is released from cyclic-dinucleotide repression when phage Acb2-like proteins sequester those signals, leading to inner-membrane disruption.",
    "definition_source": "DOI:10.1038/s41586-025-09557-z",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "Panoptes antiphage system",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1038/s41586-025-09557-z"
      },
      {
        "synonym_text": "optSE",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1038/s41586-025-09557-z"
      },
      {
        "synonym_text": "OptSE",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1038/s41586-025-09557-z"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/s41586-025-09557-z",
        "snippet": "Panoptes is a two-gene operon, optSE, wherein OptS is predicted to synthesize a nucleotide-derived second messenger and OptE is predicted to bind that signal and drive effector-mediated defence.",
        "notes": "Sullivan et al. define Panoptes as the two-gene optSE system encoding OptS and OptE."
      },
      {
        "reference": "DOI:10.1038/s41586-025-09557-z",
        "snippet": "We named OptSE the Panoptes antiphage system for Argus Panoptes, the all-seeing, many-eyed giant in Greek mythology who was a faithful watchman to Hera.",
        "notes": "Sullivan et al. name OptSE as the Panoptes antiphage system."
      },
      {
        "reference": "DOI:10.1038/s41586-025-09557-z",
        "snippet": "OptS orthologues from two distinct Panoptes systems generated cyclic dinucleotide products, including 2\u2032,3\u2032-cyclic diadenosine monophosphate (2\u2032,3\u2032-c-di-AMP), which we showed were able to bind the soluble domain of the OptE transmembrane effector.",
        "notes": "OptS orthologues produce cyclic dinucleotides, including 2\u2032,3\u2032-c-di-AMP, that can bind the soluble domain of the OptE transmembrane effector."
      },
      {
        "reference": "DOI:10.1038/s41586-025-09557-z",
        "snippet": "Panoptes potently restricted phage replication, but phages that had loss-of-function mutations in anti-cyclic oligonucleotide-based antiphage signalling system (CBASS) protein 2 (Acb2) escaped defence.",
        "notes": "Phage replication was restricted by Panoptes, while Acb2 loss-of-function mutations escaped defense."
      },
      {
        "reference": "DOI:10.1038/s41586-025-09557-z",
        "snippet": "Our data support the idea that cyclic nucleotide sequestration by Acb2 releases OptE toxicity, thereby initiating inner membrane disruption, leading to phage defence.",
        "notes": "Acb2 cyclic-nucleotide sequestration releases OptE toxicity and leads to inner-membrane disruption."
      },
      {
        "reference": "DOI:10.1038/s41586-025-09557-z",
        "snippet": "We investigated a candidate two-gene Panoptes operon from Vibrio navarrensis.",
        "notes": "Sullivan et al. used a Vibrio navarrensis optSE locus for direct Panoptes defense assays."
      },
      {
        "reference": "DOI:10.1038/s41586-025-09557-z",
        "snippet": "We expressed the operon from its endogenous promoter in Escherichia coli MG1655 and challenged these bacteria with a panel of diverse phages. The VnOptSE operon specifically defended against phages from the Straboviridae family",
        "notes": "The V. navarrensis operon was expressed from its endogenous promoter in E. coli MG1655 and protected the heterologous host against Straboviridae phages."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| Panoptes | 10\\.1038/s41586-025-09557-z | The Panoptes system uses decoy cyclic nucleotides to defend against phage |",
        "notes": "The pinned DefenseFinder article registry maps the Panoptes key to Sullivan et al.; the same pinned rules and HMM inventory omit a Panoptes model."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:29495",
        "taxon_label": "Vibrio navarrensis",
        "note": "Species carrying the assayed VnOptSE Panoptes system; defense activity was tested heterologously from the endogenous V. navarrensis promoter in E. coli MG1655.",
        "reference": "DOI:10.1038/s41586-025-09557-z"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "panoptes_decoy_cyclic_nucleotide_defense",
        "title": "Panoptes loci couple cyclic-nucleotide sequestration to OptE membrane disruption",
        "description": "Evidence-backed process sketch linking an optSE locus to OptS cyclic-dinucleotide synthesis, OptE repression, Acb2-like sequestration of the OptS-derived signal, inner-membrane disruption, and phage restriction.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "The graph captures OptS/OptE/Acb2 coupling from Sullivan et al. while leaving cyclic-dinucleotide identity, anti-defense breadth, phage breadth, and OptE oligomerization unspecified for untested optSE homologs.",
        "nodes": [
          {
            "node_id": "optse_locus",
            "label": "optSE locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A two-gene Panoptes locus encoding OptS and OptE."
          },
          {
            "node_id": "opts_cyclic_dinucleotide_synthase",
            "label": "OptS cyclic-dinucleotide synthase",
            "node_type": "GENE_OR_PROTEIN",
            "grounding": "InterPro:IPR040942",
            "grounding_notes": "InterPro:IPR040942 is a Minimal_Cpol polymerase domain present in VnOptS; it is broader than Panoptes-specific OptS and is retained as a domain-level grounding because no narrower taxon-agnostic OptS family identifier is available.",
            "description": "Minimal CRISPR polymerase domain protein that synthesizes cyclic dinucleotides in Panoptes operons.",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:A0A099LXT1",
                "protein_label": "Minimal CRISPR polymerase domain-containing protein",
                "gene_symbol": "optS",
                "taxon_id": "NCBITaxon:29495",
                "taxon_label": "Vibrio navarrensis",
                "proteome_id": "UP000029994",
                "entry_status": "UNREVIEWED",
                "retrieved_on": "2026-09-27",
                "entry_version": 30,
                "sequence_version": 1,
                "role": "VnOptS is the OptS synthase encoded by the V. navarrensis optSE Panoptes operon.",
                "evidence": [
                  {
                    "reference": "DOI:10.1038/s41586-025-09557-z",
                    "snippet": "We investigated a candidate two-gene Panoptes operon from Vibrio navarrensis.",
                    "notes": "Sullivan et al. used a Vibrio navarrensis optSE locus for direct Panoptes defense assays."
                  },
                  {
                    "reference": "DOI:10.1038/s41586-025-09557-z",
                    "snippet": "OptS orthologues from two distinct Panoptes systems generated cyclic dinucleotide products, including 2\u2032,3\u2032-cyclic diadenosine monophosphate (2\u2032,3\u2032-c-di-AMP), which we showed were able to bind the soluble domain of the OptE transmembrane effector.",
                    "notes": "OptS orthologues produce cyclic dinucleotides, including 2\u2032,3\u2032-c-di-AMP, that can bind the soluble domain of the OptE transmembrane effector."
                  }
                ]
              }
            ]
          },
          {
            "node_id": "opte_transmembrane_effector",
            "label": "OptE transmembrane effector",
            "node_type": "GENE_OR_PROTEIN",
            "grounding": "InterPro:IPR041208",
            "grounding_notes": "InterPro:IPR041208 is the Cap15 family carried by VnOptE and retained as the closest taxon-agnostic grounding for the OptE transmembrane effector pending a narrower Panoptes-specific profile.",
            "description": "OptE-family transmembrane effector encoded by Panoptes operons.",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:A0A099LW44",
                "protein_label": "CD-NTase-associated protein 15 domain-containing protein",
                "gene_symbol": "optE",
                "taxon_id": "NCBITaxon:29495",
                "taxon_label": "Vibrio navarrensis",
                "proteome_id": "UP000029994",
                "entry_status": "UNREVIEWED",
                "retrieved_on": "2026-09-27",
                "entry_version": 37,
                "sequence_version": 1,
                "role": "VnOptE is the OptE transmembrane effector encoded by the V. navarrensis optSE Panoptes operon.",
                "evidence": [
                  {
                    "reference": "DOI:10.1038/s41586-025-09557-z",
                    "snippet": "Panoptes is a two-gene operon, optSE, wherein OptS is predicted to synthesize a nucleotide-derived second messenger and OptE is predicted to bind that signal and drive effector-mediated defence.",
                    "notes": "Sullivan et al. define Panoptes as the two-gene optSE system encoding OptS and OptE."
                  },
                  {
                    "reference": "DOI:10.1038/s41586-025-09557-z",
                    "snippet": "OptS orthologues from two distinct Panoptes systems generated cyclic dinucleotide products, including 2\u2032,3\u2032-cyclic diadenosine monophosphate (2\u2032,3\u2032-c-di-AMP), which we showed were able to bind the soluble domain of the OptE transmembrane effector.",
                    "notes": "OptS orthologues produce cyclic dinucleotides, including 2\u2032,3\u2032-c-di-AMP, that can bind the soluble domain of the OptE transmembrane effector."
                  },
                  {
                    "reference": "DOI:10.1038/s41586-025-09557-z",
                    "snippet": "We expressed the operon from its endogenous promoter in Escherichia coli MG1655 and challenged these bacteria with a panel of diverse phages. The VnOptSE operon specifically defended against phages from the Straboviridae family",
                    "notes": "The V. navarrensis operon was expressed from its endogenous promoter in E. coli MG1655 and protected the heterologous host against Straboviridae phages."
                  }
                ]
              }
            ]
          },
          {
            "node_id": "opts_cyclic_dinucleotide_synthesis",
            "label": "OptS cyclic dinucleotide synthesis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Constitutive OptS-dependent production of 2\u2032,3\u2032-c-di-AMP and other cyclic dinucleotides."
          },
          {
            "node_id": "opte_cyclic_dinucleotide_repression",
            "label": "OptE cyclic dinucleotide repression",
            "node_type": "STATE",
            "description": "Inactive-state repression of OptE by OptS-derived cyclic dinucleotides."
          },
          {
            "node_id": "acb2_like_signal_sequestration",
            "label": "Acb2-like signal sequestration",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Sequestration or depletion of OptS-derived cyclic nucleotides by phage Acb2 or similar immune-evasion proteins."
          },
          {
            "node_id": "phage_infection",
            "label": "phage infection",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Infection by a bacteriophage that expresses Acb2 or similar cyclic-nucleotide sequestration proteins."
          },
          {
            "node_id": "opte_inner_membrane_disruption",
            "label": "OptE inner membrane disruption",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "OptE effector toxicity that disrupts the bacterial inner membrane during Panoptes defense."
          },
          {
            "node_id": "phage_replication",
            "label": "phage replication",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Replication of bacteriophages that would proceed in a susceptible host."
          },
          {
            "node_id": "panoptes_system_trait",
            "label": "Panoptes system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000407",
            "description": "Possession of a genome-encoded Panoptes phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "optse_locus",
            "predicate": "encodes",
            "object": "opts_cyclic_dinucleotide_synthase",
            "description": "Panoptes optSE loci encode OptS cyclic-dinucleotide synthases.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41586-025-09557-z",
                "snippet": "Panoptes is a two-gene operon, optSE, wherein OptS is predicted to synthesize a nucleotide-derived second messenger and OptE is predicted to bind that signal and drive effector-mediated defence.",
                "notes": "Sullivan et al. define Panoptes as the two-gene optSE system encoding OptS and OptE."
              },
              {
                "reference": "DOI:10.1038/s41586-025-09557-z",
                "snippet": "We investigated a candidate two-gene Panoptes operon from Vibrio navarrensis.",
                "notes": "Sullivan et al. used a Vibrio navarrensis optSE locus for direct Panoptes defense assays."
              }
            ]
          },
          {
            "subject": "optse_locus",
            "predicate": "encodes",
            "object": "opte_transmembrane_effector",
            "description": "Panoptes optSE loci encode OptE transmembrane effectors.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41586-025-09557-z",
                "snippet": "Panoptes is a two-gene operon, optSE, wherein OptS is predicted to synthesize a nucleotide-derived second messenger and OptE is predicted to bind that signal and drive effector-mediated defence.",
                "notes": "Sullivan et al. define Panoptes as the two-gene optSE system encoding OptS and OptE."
              },
              {
                "reference": "DOI:10.1038/s41586-025-09557-z",
                "snippet": "We investigated a candidate two-gene Panoptes operon from Vibrio navarrensis.",
                "notes": "Sullivan et al. used a Vibrio navarrensis optSE locus for direct Panoptes defense assays."
              }
            ]
          },
          {
            "subject": "opts_cyclic_dinucleotide_synthase",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "opts_cyclic_dinucleotide_synthesis",
            "description": "OptS is the Panoptes synthase that generates OptE-binding cyclic dinucleotides.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41586-025-09557-z",
                "snippet": "OptS orthologues from two distinct Panoptes systems generated cyclic dinucleotide products, including 2\u2032,3\u2032-cyclic diadenosine monophosphate (2\u2032,3\u2032-c-di-AMP), which we showed were able to bind the soluble domain of the OptE transmembrane effector.",
                "notes": "OptS orthologues produce cyclic dinucleotides, including 2\u2032,3\u2032-c-di-AMP, that can bind the soluble domain of the OptE transmembrane effector."
              }
            ]
          },
          {
            "subject": "opts_cyclic_dinucleotide_synthesis",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "opte_cyclic_dinucleotide_repression",
            "description": "OptS-derived cyclic dinucleotides bind OptE and hold the effector in an inactive state before phage counter-defense challenge.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41586-025-09557-z",
                "snippet": "OptS orthologues from two distinct Panoptes systems generated cyclic dinucleotide products, including 2\u2032,3\u2032-cyclic diadenosine monophosphate (2\u2032,3\u2032-c-di-AMP), which we showed were able to bind the soluble domain of the OptE transmembrane effector.",
                "notes": "OptS orthologues produce cyclic dinucleotides, including 2\u2032,3\u2032-c-di-AMP, that can bind the soluble domain of the OptE transmembrane effector."
              },
              {
                "reference": "DOI:10.1038/s41586-025-09557-z",
                "snippet": "we found that OptS constitutively produced signalling nucleotides to repress OptE-mediated growth inhibition.",
                "notes": "OptS constitutive signalling nucleotide production represses OptE-mediated growth inhibition."
              }
            ]
          },
          {
            "subject": "opte_cyclic_dinucleotide_repression",
            "predicate": "negatively regulates",
            "predicate_id": "RO:0002212",
            "object": "opte_inner_membrane_disruption",
            "description": "Cyclic-dinucleotide binding restrains OptE-mediated toxicity and inner-membrane disruption.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41586-025-09557-z",
                "snippet": "we found that OptS constitutively produced signalling nucleotides to repress OptE-mediated growth inhibition.",
                "notes": "OptS constitutive signalling nucleotide production represses OptE-mediated growth inhibition."
              }
            ]
          },
          {
            "subject": "opte_transmembrane_effector",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "opte_inner_membrane_disruption",
            "description": "OptE is the Panoptes effector whose released toxicity disrupts the inner membrane.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41586-025-09557-z",
                "snippet": "Our data support the idea that cyclic nucleotide sequestration by Acb2 releases OptE toxicity, thereby initiating inner membrane disruption, leading to phage defence.",
                "notes": "Acb2 cyclic-nucleotide sequestration releases OptE toxicity and leads to inner-membrane disruption."
              }
            ]
          },
          {
            "subject": "phage_infection",
            "predicate": "activates",
            "predicate_id": "RO:0002213",
            "object": "acb2_like_signal_sequestration",
            "description": "Phage infection produces Acb2 or similar immune-evasion proteins that sequester OptS-derived cyclic nucleotide signals.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41586-025-09557-z",
                "snippet": "During phage infection, Acb2 or similar immune evasion proteins are produced that sequester the OptS-derived signalling molecule, leading to a population of OptE that is no longer bound to cyclic dinucleotide and is free to become activated, in turn disrupting the bacterial membrane and resulting in phage defence",
                "notes": "The Panoptes model links Acb2-like signal sequestration to OptE activation, bacterial membrane disruption, and phage defense."
              }
            ]
          },
          {
            "subject": "acb2_like_signal_sequestration",
            "predicate": "activates",
            "predicate_id": "RO:0002213",
            "object": "opte_inner_membrane_disruption",
            "description": "Acb2 or similar immune-evasion proteins sequester the OptS-derived signal and release OptE-mediated membrane disruption.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41586-025-09557-z",
                "snippet": "Our data support the idea that cyclic nucleotide sequestration by Acb2 releases OptE toxicity, thereby initiating inner membrane disruption, leading to phage defence.",
                "notes": "Acb2 cyclic-nucleotide sequestration releases OptE toxicity and leads to inner-membrane disruption."
              }
            ]
          },
          {
            "subject": "opte_inner_membrane_disruption",
            "predicate": "mitigates",
            "predicate_id": "METPO:2007407",
            "object": "phage_replication",
            "description": "Panoptes-associated OptE membrane disruption restricts bacteriophage replication.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41586-025-09557-z",
                "snippet": "Panoptes potently restricted phage replication, but phages that had loss-of-function mutations in anti-cyclic oligonucleotide-based antiphage signalling system (CBASS) protein 2 (Acb2) escaped defence.",
                "notes": "Phage replication was restricted by Panoptes, while Acb2 loss-of-function mutations escaped defense."
              }
            ]
          },
          {
            "subject": "opte_inner_membrane_disruption",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "panoptes_system_trait",
            "description": "OptE-mediated inner-membrane disruption is the phage-defense output that realizes the Panoptes system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41586-025-09557-z",
                "snippet": "During phage infection, Acb2 or similar immune evasion proteins are produced that sequester the OptS-derived signalling molecule, leading to a population of OptE that is no longer bound to cyclic dinucleotide and is free to become activated, in turn disrupting the bacterial membrane and resulting in phage defence",
                "notes": "The Panoptes model links Acb2-like signal sequestration to OptE activation, bacterial membrane disruption, and phage defense."
              }
            ]
          },
          {
            "subject": "panoptes_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Panoptes system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41586-025-09557-z",
                "snippet": "We named OptSE the Panoptes antiphage system for Argus Panoptes, the all-seeing, many-eyed giant in Greek mythology who was a faithful watchman to Hera.",
                "notes": "Sullivan et al. name OptSE as the Panoptes antiphage system."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "panoptes-defensefinder-model-gap",
        "prompt": "Recheck DefenseFinder Panoptes rules and HMM profiles before using DefenseFinder model rows as optSE profile evidence.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "The pinned DefenseFinder article registry maps Panoptes to Sullivan et al. and the Nature article title, but the pinned DefenseFinder rules and HMM inventories do not include Panoptes rows. This record therefore cites the DOI-backed article and treats the article registry as name-to-paper evidence rather than as profile support.",
        "evidence": [
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
            "snippet": "| Panoptes | 10\\.1038/s41586-025-09557-z | The Panoptes system uses decoy cyclic nucleotides to defend against phage |",
            "notes": "The pinned DefenseFinder article registry maps the Panoptes key to Sullivan et al.; the same pinned rules and HMM inventory omit a Panoptes model."
          }
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-27"
      },
      {
        "discussion_id": "panoptes-natural-host-gap",
        "prompt": "Find a native endogenous microbial isolate with direct chromosomal Panoptes antiphage validation beyond the heterologous VnOptSE source-species exemplar.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Sullivan et al. investigated a candidate Vibrio navarrensis optSE operon and showed that VnOptSE defended against Straboviridae phages when expressed in E. coli MG1655 from its endogenous promoter. V. navarrensis is retained as the operon source for mechanistic protein examples, but that heterologous challenge assay does not establish a direct endogenous V. navarrensis chromosomal Panoptes assay.",
        "evidence": [
          {
            "reference": "DOI:10.1038/s41586-025-09557-z",
            "snippet": "We investigated a candidate two-gene Panoptes operon from Vibrio navarrensis.",
            "notes": "Sullivan et al. used a Vibrio navarrensis optSE locus for direct Panoptes defense assays."
          },
          {
            "reference": "DOI:10.1038/s41586-025-09557-z",
            "snippet": "We expressed the operon from its endogenous promoter in Escherichia coli MG1655 and challenged these bacteria with a panel of diverse phages. The VnOptSE operon specifically defended against phages from the Straboviridae family",
            "notes": "The V. navarrensis operon was expressed from its endogenous promoter in E. coli MG1655 and protected the heterologous host against Straboviridae phages."
          }
        ],
        "attaches_to": [
          "causal_graphs#panoptes_decoy_cyclic_nucleotide_defense"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-27"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-27T09:24:21Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Panoptes system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v284.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-27T09:24:22Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed Panoptes system canonical_examples and added V. navarrensis as the VnOptSE operon source for the mechanistic protein examples; direct native chromosomal Panoptes activity remains open because the current challenge assay used heterologous E. coli MG1655. No paid research was used.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-27T11:38:27Z",
        "curator": "codex",
        "action": "VERIFY_PANOPTES_PROTEIN_GROUNDINGS",
        "changes": "Verified the Panoptes UniProt protein examples with audit_uniprot_grounding.py: UniProtKB:A0A099LXT1 is a current unreviewed V. navarrensis UP000029994 primary accession at entry version 30 / sequence version 1, UniProtKB:A0A099LW44 is a current unreviewed V. navarrensis UP000029994 primary accession at entry version 37 / sequence version 1, and UniProt cross-references link them to InterPro:IPR040942 (Minimal_Cpol) and InterPro:IPR041208 (Cap15).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-27T11:59:19Z",
        "curator": "codex",
        "action": "DOCUMENT_PANOPTES_INTERPRO_SCOPE",
        "changes": "Added grounding notes for the new Panoptes InterPro CURIEs: InterPro:IPR040942 is a broader Minimal_Cpol domain present in VnOptS rather than an OptS-only family, and InterPro:IPR041208 is the Cap15 family carried by VnOptE.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000237",
    "label": "PARIS system",
    "definition": "An abortive infection system in which an organism possesses a phage anti-restriction-induced system locus encoding an AriA ABC ATPase sensor and an AriB TOPRIM-family nuclease whose activation by phage anti-restriction or other foreign proteins releases AriB to inhibit translation through lysine tRNA cleavage and block bacteriophage propagation.",
    "definition_source": "DOI:10.1016/j.chom.2022.02.018",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000214"
    ],
    "synonyms": [
      {
        "synonym_text": "phage anti-restriction-induced system",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1016/j.chom.2022.02.018"
      },
      {
        "synonym_text": "phage antirestriction induced system",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1038/s41586-024-07874-3"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1016/j.chom.2022.02.018",
        "snippet": "We validate the activity of diverse systems and describe PARIS, an abortive infection system triggered by a phage-encoded anti-restriction protein",
        "notes": "Rousset et al. support PARIS as a named abortive infection system activated by a phage anti-restriction protein."
      },
      {
        "reference": "DOI:10.1016/j.chom.2022.02.018",
        "snippet": "phage anti-restriction-induced system (PARIS), an abortive infection system that triggers growth arrest upon sensing an anti-restriction protein",
        "notes": "Rousset et al. support the PARIS long-form name and the growth-arrest output of the system."
      },
      {
        "reference": "DOI:10.1038/s41586-024-07772-8",
        "snippet": "operates as a toxin-antitoxin system, in which the antitoxin AriA sequesters and inactivates the toxin AriB until triggered by the T7 phage counterdefence protein Ocr",
        "notes": "Deep et al. support defining the Ocr-triggered PARIS mechanism around the AriA antitoxin and AriB toxin."
      },
      {
        "reference": "DOI:10.1038/s41586-024-07772-8",
        "snippet": "AriB is a toprim/OLD-family nuclease, the activation of which arrests cell growth and inhibits phage propagation by globally inhibiting protein translation through specific cleavage of a lysine tRNA",
        "notes": "Deep et al. support the AriB nuclease, lysine-tRNA cleavage, translational-inhibition, growth-arrest, and phage-propagation outputs."
      },
      {
        "reference": "DOI:10.1038/s41586-024-07874-3",
        "snippet": "The phage antirestriction induced system (PARIS) is a defence system, often encoded in viral genomes, that is composed of a 55 kDa ABC ATPase (AriA) and a 35 kDa TOPRIM nuclease (AriB)",
        "notes": "Burman et al. independently support the AriA ABC ATPase and AriB TOPRIM nuclease components."
      },
      {
        "reference": "DOI:10.1038/s41586-024-07874-3",
        "snippet": "ATP-dependent detection of foreign proteins triggers the release of AriB, which assembles into a homodimeric nuclease that blocks infection by cleaving host lysine transfer RNA",
        "notes": "Burman et al. support an activation model in which foreign-protein detection releases AriB to cleave host lysine tRNA."
      },
      {
        "reference": "DOI:10.1038/s41586-024-07874-3",
        "snippet": "Phage T5 subverts PARIS immunity through expression of a lysine transfer RNA variant that is not cleaved by PARIS, thereby restoring viral infection",
        "notes": "Burman et al. support recording T5 lysine tRNA anti-defense as a reviewed counter-defense gap before minting narrower PARIS subtype children."
      },
      {
        "reference": "DOI:10.1016/j.chom.2022.02.018",
        "snippet": "While the system from E. coli B185 provided robust defense when expressed from its natural promoter",
        "notes": "Rousset et al. support E. coli as a canonical organism by cloning the E. coli B185 PARIS system with its native promoter and observing robust antiphage defense."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:562",
        "taxon_label": "Escherichia coli",
        "note": "Rousset et al. cloned the native-promoter PARIS locus from E. coli B185 and showed that it provided robust defense.",
        "reference": "DOI:10.1016/j.chom.2022.02.018"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "paris_ariab_trna_cleavage_abortive_defense",
        "title": "PARIS loci couple phage anti-restriction sensing to AriB tRNA cleavage",
        "description": "Evidence-backed process sketch linking a complete PARIS locus to AriA/AriB immune-complex assembly, foreign-protein sensing, AriB activation, host lysine tRNA cleavage, translational inhibition, and inhibition of phage propagation.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph stays at the PARIS-family level and uses characterized E. coli B185 AriA/AriB examples without asserting one universal phage trigger, Ocr response, Ptr1/Ptr2 response, T5 lysine tRNA suppressor, exact AriA/AriB stoichiometry, or anti-anti-restriction context across all PARIS loci.",
        "nodes": [
          {
            "node_id": "paris_locus",
            "label": "PARIS locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A complete phage anti-restriction-induced system locus encoding the AriA ABC ATPase sensor and AriB TOPRIM-family nuclease effector."
          },
          {
            "node_id": "aria_arib_complex_assembly",
            "label": "AriA/AriB immune complex assembly",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Assembly of an AriA scaffold that sequesters and inactivates AriB nuclease subunits before PARIS activation."
          },
          {
            "node_id": "foreign_protein_sensing",
            "label": "foreign protein sensing",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "AriA-dependent detection of activating phage proteins such as the T7 Ocr anti-restriction protein."
          },
          {
            "node_id": "arib_nuclease_activation",
            "label": "AriB nuclease activation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Release and dimerization of the AriB TOPRIM-family nuclease effector from the AriA scaffold."
          },
          {
            "node_id": "lysine_trna_cleavage",
            "label": "lysine tRNA cleavage",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "AriB-dependent cleavage of host lysine transfer RNA after PARIS activation."
          },
          {
            "node_id": "translation_inhibition",
            "label": "translation inhibition",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Global protein-translation inhibition and growth arrest following host lysine tRNA cleavage."
          },
          {
            "node_id": "phage_propagation",
            "label": "phage propagation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Completion of bacteriophage replication and spread in a susceptible bacterial population."
          },
          {
            "node_id": "paris_system_trait",
            "label": "PARIS system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000237",
            "description": "Possession of a genome-encoded PARIS abortive-infection defense system."
          },
          {
            "node_id": "abortive_infection_system_trait",
            "label": "abortive infection system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000214",
            "description": "Possession of a genome-encoded abortive-infection phage defense system."
          }
        ],
        "edges": [
          {
            "subject": "paris_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "aria_arib_complex_assembly",
            "description": "PARIS loci encode AriA and AriB components that assemble into an immune complex.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41586-024-07874-3",
                "snippet": "Here we show that AriA and AriB assemble into a 425 kDa supramolecular immune complex",
                "notes": "Burman et al. support AriA/AriB complex assembly as a direct PARIS system activity."
              }
            ]
          },
          {
            "subject": "aria_arib_complex_assembly",
            "predicate": "enables",
            "predicate_id": "RO:0002327",
            "object": "foreign_protein_sensing",
            "description": "The AriA/AriB immune complex detects foreign proteins in an ATP-dependent way.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41586-024-07874-3",
                "snippet": "ATP-dependent detection of foreign proteins triggers the release of AriB",
                "notes": "Burman et al. support AriA-dependent foreign protein detection as the triggering event for PARIS activation."
              }
            ]
          },
          {
            "subject": "foreign_protein_sensing",
            "predicate": "activates",
            "predicate_id": "RO:0002213",
            "object": "arib_nuclease_activation",
            "description": "T7 Ocr or other foreign-protein detection releases AriB from AriA and activates the AriB nuclease.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41586-024-07772-8",
                "snippet": "After Ocr binding, the AriA hexamer undergoes a structural rearrangement, releasing AriB and allowing it to dimerize and activate",
                "notes": "Deep et al. support Ocr-triggered AriB release and dimerization in the E. coli B185 PARIS system."
              }
            ]
          },
          {
            "subject": "arib_nuclease_activation",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "lysine_trna_cleavage",
            "description": "Activated AriB cleaves host lysine transfer RNA.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41586-024-07874-3",
                "snippet": "AriB, which assembles into a homodimeric nuclease that blocks infection by cleaving host lysine transfer RNA",
                "notes": "Burman et al. support host lysine-tRNA cleavage by activated AriB."
              }
            ]
          },
          {
            "subject": "lysine_trna_cleavage",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "translation_inhibition",
            "description": "AriB-mediated lysine tRNA cleavage inhibits host-cell translation.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41586-024-07772-8",
                "snippet": "globally inhibiting protein translation through specific cleavage of a lysine tRNA",
                "notes": "Deep et al. connect AriB lysine-tRNA cleavage to global inhibition of protein translation."
              }
            ]
          },
          {
            "subject": "translation_inhibition",
            "predicate": "mitigates",
            "predicate_id": "METPO:2007407",
            "object": "phage_propagation",
            "description": "PARIS-associated translational arrest blocks phage infection.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41586-024-07772-8",
                "snippet": "arrests cell growth and inhibits phage propagation by globally inhibiting protein translation",
                "notes": "Deep et al. support the growth-arrest and phage-inhibition output of AriB activation."
              }
            ]
          },
          {
            "subject": "translation_inhibition",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "paris_system_trait",
            "description": "AriB-dependent translational inhibition realizes the PARIS abortive-infection phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.chom.2022.02.018",
                "snippet": "Therefore, ariAB seem to halt growth in infected cells, preventing the completion of the phage cycle, a typical feature of abortive infection systems",
                "notes": "Rousset et al. connect AriA/AriB to growth arrest, phage-cycle inhibition, and abortive infection."
              }
            ]
          },
          {
            "subject": "paris_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "abortive_infection_system_trait",
            "description": "PARIS system possession is an abortive-infection system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.chom.2022.02.018",
                "snippet": "describe PARIS, an abortive infection system triggered by a phage-encoded anti-restriction protein",
                "notes": "Rousset et al. explicitly describe PARIS as an abortive infection system."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "paris-trigger-and-counterdefense-gap",
        "prompt": "Resolve PARIS trigger specificity, AriA/AriB stoichiometry, phage T5 lysine-tRNA suppression, and non-Ocr phage triggers before minting narrower PARIS subtype children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Rousset et al. discovered PARIS as an abortive infection system triggered by T7 Ocr; Deep et al. resolved Ocr-dependent AriA release of AriB for the E. coli B185 system; and Burman et al. showed that T5 Ptr1 and Ptr2 can activate PARIS while a phage T5 lysine tRNA variant can evade AriB cleavage. The first TraitRecord therefore stays at the broad PARIS-system level until separate subtype review resolves which foreign-protein triggers, AriB activities, and anti-defense suppressors apply across each PARIS family.",
        "posed_by": "codex",
        "posed_date": "2026-09-18"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-18T08:27:56Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted PARIS system as a DOI-backed GENOMICS TraitRecord under the abortive infection system parent after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v114.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-18T09:16:05Z",
        "curator": "codex",
        "action": "ADVERSARIAL_REVIEW_REPAIR",
        "changes": "Resolved PR #976 review issue #977 by scoping the PARIS canonical example note to the Rousset et al. E. coli B185 evidence cited by that example.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000404",
    "label": "PD-Lambda-1 system",
    "definition": "A phage defense system in which an organism possesses a PD-Lambda-1 locus represented by DefenseFinder as a single-profile model, PD-Lambda-1__PD-Lambda-1, and experimentally linked to LambdaVir protection when expressed in E. coli.",
    "definition_source": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-1.md",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "PD-Lambda-1",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-1.md"
      },
      {
        "synonym_text": "PD-Lambda-1__PD-Lambda-1",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/s41564-022-01219-4",
        "snippet": "Here we developed an experimental selection scheme agnostic to genomic context to identify defence systems in 71 diverse E. coli strains. Our results unveil 21 conserved defence systems, none of which were previously detected as enriched in defence islands.",
        "notes": "Vassallo et al. developed the agnostic E. coli pangenome selection that uncovered PD-Lambda-1 and related conserved phage-defense systems."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-1.md",
        "snippet": "The PD-Lambda-1 system is composed of one protein, PD-Lambda-1, and confers resistance to LambdaVir :ref{doi=10.1038/s41564-022-01219-4}.",
        "notes": "The DefenseFinder wiki describes PD-Lambda-1 as a one-protein system that can confer LambdaVir resistance."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-1.md",
        "snippet": "As far as we are aware, the molecular mechanism is unknown.",
        "notes": "The DefenseFinder wiki records the PD-Lambda-1 molecular mechanism as unresolved."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-1.md",
        "snippet": "The PD-Lambda-1 is composed of 1 protein: PD-Lambda-1.",
        "notes": "The DefenseFinder wiki names PD-Lambda-1 as a single-protein system."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-1.md",
        "snippet": "The PD-Lambda-1 system in *Gemmata massiliana* (GCF_901538265.1, NZ_LR593886) is composed of 1 protein: PD-Lambda-1 (WP_197909633.1)",
        "notes": "The DefenseFinder wiki illustrates a predicted one-protein PD-Lambda-1 locus in RefSeq assembly GCF_901538265.1 on NZ_LR593886."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-1.md",
        "snippet": "Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0\n    Origin_0[Escherichia coli \n<a href='https://ncbi.nlm.nih.gov/protein/RCP76574.1'>RCP76574.1</a>] --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> LambdaVir",
        "notes": "The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-Lambda-1 source locus expressed in E. coli against LambdaVir."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-1.md",
        "snippet": "subgraph Title4[Protects against]\n        LambdaVir",
        "notes": "The DefenseFinder experimental-validation diagram lists LambdaVir in the PD-Lambda-1 protects-against subgraph."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "PD-Lambda-1\tPD-Lambda-1\t1\t1\tPD-Lambda-1__PD-Lambda-1\t\t\t",
        "notes": "The DefenseFinder rules table models PD-Lambda-1 as a single-profile system requiring PD-Lambda-1__PD-Lambda-1."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| PD-Lambda-1__PD-Lambda-1                         | PD-Lambda-1__PD-Lambda-1                         | PD-Lambda-1            | Custom                  | 200    |",
        "notes": "The DefenseFinder HMM inventory records PD-Lambda-1__PD-Lambda-1 under the PD-Lambda-1 system namespace."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "pd_lambda_1_locus_restricts_lambda_vir",
        "title": "PD-Lambda-1 loci restrict LambdaVir",
        "description": "Conservative system-level sketch linking possession of a PD-Lambda-1 locus to LambdaVir protection.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures PD-Lambda-1 as a named DefenseFinder phage-defense system while leaving natural host breadth, the direct phage trigger, and the effector mechanism unresolved.",
        "nodes": [
          {
            "node_id": "pd_lambda_1_locus",
            "label": "PD-Lambda-1 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A phage-defense locus represented by the PD-Lambda-1 DefenseFinder profile."
          },
          {
            "node_id": "pd_lambda_1_listed_phage_protection",
            "label": "LambdaVir protection",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Protection against LambdaVir by PD-Lambda-1."
          },
          {
            "node_id": "pd_lambda_1_system_trait",
            "label": "PD-Lambda-1 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000404",
            "description": "Possession of a genome-encoded PD-Lambda-1 phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "pd_lambda_1_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "pd_lambda_1_listed_phage_protection",
            "description": "The DefenseFinder wiki links a PD-Lambda-1 locus from Vassallo et al. to LambdaVir protection, and DefenseFinder models PD-Lambda-1 through one mandatory profile.",
            "evidence": [
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-1.md",
                "snippet": "The PD-Lambda-1 system is composed of one protein, PD-Lambda-1, and confers resistance to LambdaVir :ref{doi=10.1038/s41564-022-01219-4}.",
                "notes": "The DefenseFinder wiki describes PD-Lambda-1 as a one-protein system that can confer LambdaVir resistance."
              },
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-1.md",
                "snippet": "The PD-Lambda-1 is composed of 1 protein: PD-Lambda-1.",
                "notes": "The DefenseFinder wiki names PD-Lambda-1 as a single-protein system."
              },
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-1.md",
                "snippet": "Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0\n    Origin_0[Escherichia coli \n<a href='https://ncbi.nlm.nih.gov/protein/RCP76574.1'>RCP76574.1</a>] --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> LambdaVir",
                "notes": "The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-Lambda-1 source locus expressed in E. coli against LambdaVir."
              },
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-1.md",
                "snippet": "subgraph Title4[Protects against]\n        LambdaVir",
                "notes": "The DefenseFinder experimental-validation diagram lists LambdaVir in the PD-Lambda-1 protects-against subgraph."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "PD-Lambda-1\tPD-Lambda-1\t1\t1\tPD-Lambda-1__PD-Lambda-1\t\t\t",
                "notes": "The DefenseFinder rules table models PD-Lambda-1 as a single-profile system requiring PD-Lambda-1__PD-Lambda-1."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| PD-Lambda-1__PD-Lambda-1                         | PD-Lambda-1__PD-Lambda-1                         | PD-Lambda-1            | Custom                  | 200    |",
                "notes": "The DefenseFinder HMM inventory records PD-Lambda-1__PD-Lambda-1 under the PD-Lambda-1 system namespace."
              }
            ]
          },
          {
            "subject": "pd_lambda_1_listed_phage_protection",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "pd_lambda_1_system_trait",
            "description": "Protection against LambdaVir realizes the PD-Lambda-1 system trait.",
            "evidence": [
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-1.md",
                "snippet": "The PD-Lambda-1 system is composed of one protein, PD-Lambda-1, and confers resistance to LambdaVir :ref{doi=10.1038/s41564-022-01219-4}.",
                "notes": "The DefenseFinder wiki describes PD-Lambda-1 as a one-protein system that can confer LambdaVir resistance."
              },
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-1.md",
                "snippet": "Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0\n    Origin_0[Escherichia coli \n<a href='https://ncbi.nlm.nih.gov/protein/RCP76574.1'>RCP76574.1</a>] --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> LambdaVir",
                "notes": "The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-Lambda-1 source locus expressed in E. coli against LambdaVir."
              },
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-1.md",
                "snippet": "subgraph Title4[Protects against]\n        LambdaVir",
                "notes": "The DefenseFinder experimental-validation diagram lists LambdaVir in the PD-Lambda-1 protects-against subgraph."
              }
            ]
          },
          {
            "subject": "pd_lambda_1_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "PD-Lambda-1 system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-022-01219-4",
                "snippet": "Here we developed an experimental selection scheme agnostic to genomic context to identify defence systems in 71 diverse E. coli strains. Our results unveil 21 conserved defence systems, none of which were previously detected as enriched in defence islands.",
                "notes": "Vassallo et al. developed the agnostic E. coli pangenome selection that uncovered PD-Lambda-1 and related conserved phage-defense systems."
              },
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-1.md",
                "snippet": "The PD-Lambda-1 is composed of 1 protein: PD-Lambda-1.",
                "notes": "The DefenseFinder wiki names PD-Lambda-1 as a single-protein system."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "PD-Lambda-1\tPD-Lambda-1\t1\t1\tPD-Lambda-1__PD-Lambda-1\t\t\t",
                "notes": "The DefenseFinder rules table models PD-Lambda-1 as a single-profile system requiring PD-Lambda-1__PD-Lambda-1."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "pd-lambda-1-mechanism-gap",
        "prompt": "Resolve PD-Lambda-1 natural host breadth, direct phage trigger, and effector mechanism before minting narrower PD-Lambda-1 mechanism traits.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Vassallo et al. support PD-Lambda-1 as one of the conserved systems from an E. coli pangenome phage-defense selection, the DefenseFinder wiki maps the source locus to LambdaVir protection, and DefenseFinder represents the system with one profile. Natural host breadth, the direct phage trigger, and effector logic remain unresolved.",
        "evidence": [
          {
            "reference": "DOI:10.1038/s41564-022-01219-4",
            "snippet": "Here we developed an experimental selection scheme agnostic to genomic context to identify defence systems in 71 diverse E. coli strains. Our results unveil 21 conserved defence systems, none of which were previously detected as enriched in defence islands.",
            "notes": "Vassallo et al. developed the agnostic E. coli pangenome selection that uncovered PD-Lambda-1 and related conserved phage-defense systems."
          },
          {
            "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-1.md",
            "snippet": "The PD-Lambda-1 system is composed of one protein, PD-Lambda-1, and confers resistance to LambdaVir :ref{doi=10.1038/s41564-022-01219-4}.",
            "notes": "The DefenseFinder wiki describes PD-Lambda-1 as a one-protein system that can confer LambdaVir resistance."
          },
          {
            "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-1.md",
            "snippet": "As far as we are aware, the molecular mechanism is unknown.",
            "notes": "The DefenseFinder wiki records the PD-Lambda-1 molecular mechanism as unresolved."
          },
          {
            "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-1.md",
            "snippet": "Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0\n    Origin_0[Escherichia coli \n<a href='https://ncbi.nlm.nih.gov/protein/RCP76574.1'>RCP76574.1</a>] --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> LambdaVir",
            "notes": "The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-Lambda-1 source locus expressed in E. coli against LambdaVir."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "snippet": "PD-Lambda-1\tPD-Lambda-1\t1\t1\tPD-Lambda-1__PD-Lambda-1\t\t\t",
            "notes": "The DefenseFinder rules table models PD-Lambda-1 as a single-profile system requiring PD-Lambda-1__PD-Lambda-1."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| PD-Lambda-1__PD-Lambda-1                         | PD-Lambda-1__PD-Lambda-1                         | PD-Lambda-1            | Custom                  | 200    |",
            "notes": "The DefenseFinder HMM inventory records PD-Lambda-1__PD-Lambda-1 under the PD-Lambda-1 system namespace."
          }
        ],
        "attaches_to": [
          "causal_graphs#pd_lambda_1_locus_restricts_lambda_vir"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-27"
      },
      {
        "discussion_id": "pd-lambda-1-defensefinder-article-registry-gap",
        "prompt": "Recheck whether DefenseFinder adds a PD-Lambda-1 List_system_article.md row before using the article registry as direct PD-Lambda-1 model-to-paper evidence.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "The pinned DefenseFinder wiki, rules table, and HMM inventory all represent PD-Lambda-1, but the pinned List_system_article.md registry omits a PD-Lambda-1 row. The PD-Lambda-1 record therefore cites the pinned wiki plus the DOI-backed Vassallo et al. screen instead of inventing a missing article-registry entry.",
        "evidence": [
          {
            "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-1.md",
            "snippet": "The PD-Lambda-1 system is composed of one protein, PD-Lambda-1, and confers resistance to LambdaVir :ref{doi=10.1038/s41564-022-01219-4}.",
            "notes": "The DefenseFinder wiki describes PD-Lambda-1 as a one-protein system that can confer LambdaVir resistance."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "snippet": "PD-Lambda-1\tPD-Lambda-1\t1\t1\tPD-Lambda-1__PD-Lambda-1\t\t\t",
            "notes": "The DefenseFinder rules table models PD-Lambda-1 as a single-profile system requiring PD-Lambda-1__PD-Lambda-1."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| PD-Lambda-1__PD-Lambda-1                         | PD-Lambda-1__PD-Lambda-1                         | PD-Lambda-1            | Custom                  | 200    |",
            "notes": "The DefenseFinder HMM inventory records PD-Lambda-1__PD-Lambda-1 under the PD-Lambda-1 system namespace."
          }
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-27"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-27T07:17:46Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted PD-Lambda-1 system as a DOI- and DefenseFinder-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v281.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-27T07:17:47Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed PD-Lambda-1 system canonical_examples and left them empty because the current sources support an E. coli accession-level experimental validation graph, a DefenseFinder system model, and a RefSeq Gemmata massiliana example, but not a direct native microbial isolate exemplar with experimentally verified endogenous PD-Lambda-1 activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000378",
    "label": "PD-Lambda-2 system",
    "definition": "A phage defense system in which an organism possesses a PD-Lambda-2 locus represented by DefenseFinder as a model with two mandatory profiles, PD-Lambda-2__PD-Lambda-2_A and PD-Lambda-2__PD-Lambda-2_B, plus the accessory PD-Lambda-2__PD-Lambda-2_C profile.",
    "definition_source": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-2.md",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "PD-Lambda-2",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-2.md"
      },
      {
        "synonym_text": "PD-Lambda-2__PD-Lambda-2_A",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "PD-Lambda-2__PD-Lambda-2_B",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "PD-Lambda-2__PD-Lambda-2_C",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/s41564-022-01219-4",
        "snippet": "Here we developed an experimental selection scheme agnostic to genomic context to identify defence systems in 71 diverse E. coli strains. Our results unveil 21 conserved defence systems, none of which were previously detected as enriched in defence islands.",
        "notes": "Vassallo et al. developed the agnostic E. coli pangenome selection that uncovered PD-Lambda-2 and related conserved phage-defense systems."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-2.md",
        "snippet": "The PD-Lambda-2 is composed of 3 proteins: PD-Lambda-2_A, PD-Lambda-2_B and PD-Lambda-2_C.",
        "notes": "The DefenseFinder wiki names PD-Lambda-2 as a three-protein system."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-2.md",
        "snippet": "The PD-Lambda-2 system in *Vibrio parahaemolyticus* (GCF_013393845.1, NZ_CP040100) is composed of 3 proteins PD-Lambda-2_C (WP_116869984.1) PD-Lambda-2_B (WP_029809306.1) PD-Lambda-2_A (WP_029809305.1)",
        "notes": "The DefenseFinder wiki illustrates a predicted PD-Lambda-2 locus in RefSeq assembly GCF_013393845.1 on NZ_CP040100."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-2.md",
        "snippet": "Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0\n    Origin_0[Escherichia coli \n<a href='https://ncbi.nlm.nih.gov/protein/RCO93357.1'>RCO93357.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/RCO93356.1'>RCO93356.1</a>,\n<a href='https://ncbi.nlm.nih.gov/protein/RCO93355.1'>RCO93355.1</a>] --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> LambdaVir & SECphi17 & SECphi18 & SECphi27 & T3",
        "notes": "The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-Lambda-2 source locus and testing in E. coli against LambdaVir, SECphi17, SECphi18, SECphi27, and T3."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-2.md",
        "snippet": "subgraph Title4[Protects against]\n        LambdaVir\n        SECphi17\n        SECphi18\n        SECphi27\n        T3",
        "notes": "The DefenseFinder experimental-validation diagram lists LambdaVir, SECphi17, SECphi18, SECphi27, and T3 in the PD-Lambda-2 protects-against subgraph."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "PD-Lambda-2 | 10\\.1101/2022\\.05\\.12\\.491691 | Mapping the landscape of anti-phage defense mechanisms in the E\\. coli pangenome",
        "notes": "The DefenseFinder article registry maps the named PD-Lambda-2 system to the Vassallo et al. E. coli pangenome phage-defense preprint."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "PD-Lambda-2\tPD-Lambda-2\t2\t2\tPD-Lambda-2__PD-Lambda-2_A, PD-Lambda-2__PD-Lambda-2_B\tPD-Lambda-2__PD-Lambda-2_C\t\t",
        "notes": "The DefenseFinder rules table models PD-Lambda-2 with PD-Lambda-2__PD-Lambda-2_A and PD-Lambda-2__PD-Lambda-2_B as mandatory profiles and PD-Lambda-2__PD-Lambda-2_C as an accessory profile."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| PD-Lambda-2__PD-Lambda-2_A                       | PD-Lambda-2__PD-Lambda-2_A                       | PD-Lambda-2            | Custom                  | 60     |",
        "notes": "The DefenseFinder HMM inventory records PD-Lambda-2__PD-Lambda-2_A under the PD-Lambda-2 system namespace."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| PD-Lambda-2__PD-Lambda-2_B                       | PD-Lambda-2__PD-Lambda-2_B                       | PD-Lambda-2            | Custom                  | 100    |",
        "notes": "The DefenseFinder HMM inventory records PD-Lambda-2__PD-Lambda-2_B under the PD-Lambda-2 system namespace."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| PD-Lambda-2__PD-Lambda-2_C                       | PD-Lambda-2__PD-Lambda-2_C                       | PD-Lambda-2            | Custom                  | 20     |",
        "notes": "The DefenseFinder HMM inventory records PD-Lambda-2__PD-Lambda-2_C under the PD-Lambda-2 system namespace."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "pd_lambda_2_locus_restricts_phages",
        "title": "PD-Lambda-2 loci restrict LambdaVir, SECphi17, SECphi18, SECphi27, and T3",
        "description": "Conservative system-level sketch linking possession of a PD-Lambda-2 locus to protection against LambdaVir, SECphi17, SECphi18, SECphi27, and T3.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures PD-Lambda-2 as a named DefenseFinder phage-defense system while leaving natural host breadth, the direct phage trigger, the effector mechanism, and exact PD-Lambda-2 profile-to-protein correspondence unresolved.",
        "nodes": [
          {
            "node_id": "pd_lambda_2_locus",
            "label": "PD-Lambda-2 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A phage-defense locus represented by the PD-Lambda-2 DefenseFinder profiles."
          },
          {
            "node_id": "pd_lambda_2_listed_phage_protection",
            "label": "LambdaVir, SECphi17, SECphi18, SECphi27, and T3 protection",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Protection against LambdaVir, SECphi17, SECphi18, SECphi27, and T3 by PD-Lambda-2."
          },
          {
            "node_id": "pd_lambda_2_system_trait",
            "label": "PD-Lambda-2 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000378",
            "description": "Possession of a genome-encoded PD-Lambda-2 phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "pd_lambda_2_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "pd_lambda_2_listed_phage_protection",
            "description": "The DefenseFinder wiki links a PD-Lambda-2 locus from Vassallo et al. to protection against LambdaVir, SECphi17, SECphi18, SECphi27, and T3, and DefenseFinder models PD-Lambda-2 through A, B, and C profiles.",
            "evidence": [
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-2.md",
                "snippet": "The PD-Lambda-2 is composed of 3 proteins: PD-Lambda-2_A, PD-Lambda-2_B and PD-Lambda-2_C.",
                "notes": "The DefenseFinder wiki names PD-Lambda-2 as a three-protein system."
              },
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-2.md",
                "snippet": "Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0\n    Origin_0[Escherichia coli \n<a href='https://ncbi.nlm.nih.gov/protein/RCO93357.1'>RCO93357.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/RCO93356.1'>RCO93356.1</a>,\n<a href='https://ncbi.nlm.nih.gov/protein/RCO93355.1'>RCO93355.1</a>] --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> LambdaVir & SECphi17 & SECphi18 & SECphi27 & T3",
                "notes": "The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-Lambda-2 source locus and testing in E. coli against LambdaVir, SECphi17, SECphi18, SECphi27, and T3."
              },
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-2.md",
                "snippet": "subgraph Title4[Protects against]\n        LambdaVir\n        SECphi17\n        SECphi18\n        SECphi27\n        T3",
                "notes": "The DefenseFinder experimental-validation diagram lists LambdaVir, SECphi17, SECphi18, SECphi27, and T3 in the PD-Lambda-2 protects-against subgraph."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "PD-Lambda-2\tPD-Lambda-2\t2\t2\tPD-Lambda-2__PD-Lambda-2_A, PD-Lambda-2__PD-Lambda-2_B\tPD-Lambda-2__PD-Lambda-2_C\t\t",
                "notes": "The DefenseFinder rules table models PD-Lambda-2 with PD-Lambda-2__PD-Lambda-2_A and PD-Lambda-2__PD-Lambda-2_B as mandatory profiles and PD-Lambda-2__PD-Lambda-2_C as an accessory profile."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| PD-Lambda-2__PD-Lambda-2_A                       | PD-Lambda-2__PD-Lambda-2_A                       | PD-Lambda-2            | Custom                  | 60     |",
                "notes": "The DefenseFinder HMM inventory records PD-Lambda-2__PD-Lambda-2_A under the PD-Lambda-2 system namespace."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| PD-Lambda-2__PD-Lambda-2_B                       | PD-Lambda-2__PD-Lambda-2_B                       | PD-Lambda-2            | Custom                  | 100    |",
                "notes": "The DefenseFinder HMM inventory records PD-Lambda-2__PD-Lambda-2_B under the PD-Lambda-2 system namespace."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| PD-Lambda-2__PD-Lambda-2_C                       | PD-Lambda-2__PD-Lambda-2_C                       | PD-Lambda-2            | Custom                  | 20     |",
                "notes": "The DefenseFinder HMM inventory records PD-Lambda-2__PD-Lambda-2_C under the PD-Lambda-2 system namespace."
              }
            ]
          },
          {
            "subject": "pd_lambda_2_listed_phage_protection",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "pd_lambda_2_system_trait",
            "description": "Protection against LambdaVir, SECphi17, SECphi18, SECphi27, and T3 realizes the PD-Lambda-2 system trait.",
            "evidence": [
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-2.md",
                "snippet": "Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0\n    Origin_0[Escherichia coli \n<a href='https://ncbi.nlm.nih.gov/protein/RCO93357.1'>RCO93357.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/RCO93356.1'>RCO93356.1</a>,\n<a href='https://ncbi.nlm.nih.gov/protein/RCO93355.1'>RCO93355.1</a>] --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> LambdaVir & SECphi17 & SECphi18 & SECphi27 & T3",
                "notes": "The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-Lambda-2 source locus and testing in E. coli against LambdaVir, SECphi17, SECphi18, SECphi27, and T3."
              },
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-2.md",
                "snippet": "subgraph Title4[Protects against]\n        LambdaVir\n        SECphi17\n        SECphi18\n        SECphi27\n        T3",
                "notes": "The DefenseFinder experimental-validation diagram lists LambdaVir, SECphi17, SECphi18, SECphi27, and T3 in the PD-Lambda-2 protects-against subgraph."
              }
            ]
          },
          {
            "subject": "pd_lambda_2_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "PD-Lambda-2 system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-022-01219-4",
                "snippet": "Here we developed an experimental selection scheme agnostic to genomic context to identify defence systems in 71 diverse E. coli strains. Our results unveil 21 conserved defence systems, none of which were previously detected as enriched in defence islands.",
                "notes": "Vassallo et al. developed the agnostic E. coli pangenome selection that uncovered PD-Lambda-2 and related conserved phage-defense systems."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "PD-Lambda-2 | 10\\.1101/2022\\.05\\.12\\.491691 | Mapping the landscape of anti-phage defense mechanisms in the E\\. coli pangenome",
                "notes": "The DefenseFinder article registry maps the named PD-Lambda-2 system to the Vassallo et al. E. coli pangenome phage-defense preprint."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "PD-Lambda-2\tPD-Lambda-2\t2\t2\tPD-Lambda-2__PD-Lambda-2_A, PD-Lambda-2__PD-Lambda-2_B\tPD-Lambda-2__PD-Lambda-2_C\t\t",
                "notes": "The DefenseFinder rules table models PD-Lambda-2 with PD-Lambda-2__PD-Lambda-2_A and PD-Lambda-2__PD-Lambda-2_B as mandatory profiles and PD-Lambda-2__PD-Lambda-2_C as an accessory profile."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "pd-lambda-2-mechanism-gap",
        "prompt": "Resolve PD-Lambda-2 natural host breadth, direct phage trigger, effector mechanism, and exact profile-to-protein correspondence before minting narrower PD-Lambda-2 mechanism traits.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Vassallo et al. support PD-Lambda-2 as one of the conserved systems from an E. coli pangenome phage-defense selection, the DefenseFinder wiki maps the source locus to protection against LambdaVir, SECphi17, SECphi18, SECphi27, and T3, and DefenseFinder represents the system with A, B, and C profiles. Natural host breadth, the direct phage trigger, effector logic, and exact profile-to-protein correspondence remain unresolved.",
        "evidence": [
          {
            "reference": "DOI:10.1038/s41564-022-01219-4",
            "snippet": "Here we developed an experimental selection scheme agnostic to genomic context to identify defence systems in 71 diverse E. coli strains. Our results unveil 21 conserved defence systems, none of which were previously detected as enriched in defence islands.",
            "notes": "Vassallo et al. developed the agnostic E. coli pangenome selection that uncovered PD-Lambda-2 and related conserved phage-defense systems."
          },
          {
            "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-2.md",
            "snippet": "The PD-Lambda-2 is composed of 3 proteins: PD-Lambda-2_A, PD-Lambda-2_B and PD-Lambda-2_C.",
            "notes": "The DefenseFinder wiki names PD-Lambda-2 as a three-protein system."
          },
          {
            "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-2.md",
            "snippet": "Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0\n    Origin_0[Escherichia coli \n<a href='https://ncbi.nlm.nih.gov/protein/RCO93357.1'>RCO93357.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/RCO93356.1'>RCO93356.1</a>,\n<a href='https://ncbi.nlm.nih.gov/protein/RCO93355.1'>RCO93355.1</a>] --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> LambdaVir & SECphi17 & SECphi18 & SECphi27 & T3",
            "notes": "The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-Lambda-2 source locus and testing in E. coli against LambdaVir, SECphi17, SECphi18, SECphi27, and T3."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "snippet": "PD-Lambda-2\tPD-Lambda-2\t2\t2\tPD-Lambda-2__PD-Lambda-2_A, PD-Lambda-2__PD-Lambda-2_B\tPD-Lambda-2__PD-Lambda-2_C\t\t",
            "notes": "The DefenseFinder rules table models PD-Lambda-2 with PD-Lambda-2__PD-Lambda-2_A and PD-Lambda-2__PD-Lambda-2_B as mandatory profiles and PD-Lambda-2__PD-Lambda-2_C as an accessory profile."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| PD-Lambda-2__PD-Lambda-2_A                       | PD-Lambda-2__PD-Lambda-2_A                       | PD-Lambda-2            | Custom                  | 60     |",
            "notes": "The DefenseFinder HMM inventory records PD-Lambda-2__PD-Lambda-2_A under the PD-Lambda-2 system namespace."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| PD-Lambda-2__PD-Lambda-2_B                       | PD-Lambda-2__PD-Lambda-2_B                       | PD-Lambda-2            | Custom                  | 100    |",
            "notes": "The DefenseFinder HMM inventory records PD-Lambda-2__PD-Lambda-2_B under the PD-Lambda-2 system namespace."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| PD-Lambda-2__PD-Lambda-2_C                       | PD-Lambda-2__PD-Lambda-2_C                       | PD-Lambda-2            | Custom                  | 20     |",
            "notes": "The DefenseFinder HMM inventory records PD-Lambda-2__PD-Lambda-2_C under the PD-Lambda-2 system namespace."
          }
        ],
        "attaches_to": [
          "causal_graphs#pd_lambda_2_locus_restricts_phages"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-26"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-26T09:48:10Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted PD-Lambda-2 system as a DOI- and DefenseFinder-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v255.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-26T09:48:11Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed PD-Lambda-2 system canonical_examples and left them empty because the current sources support an E. coli accession-level experimental validation graph, a DefenseFinder system model, and a RefSeq Vibrio parahaemolyticus example, but not a direct native microbial isolate exemplar with experimentally verified endogenous PD-Lambda-2 activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000382",
    "label": "PD-Lambda-3 system",
    "definition": "A phage defense system in which an organism possesses a PD-Lambda-3 locus represented by DefenseFinder as a two-profile model, PD-Lambda-3__PD-Lambda-3_A and PD-Lambda-3__PD-Lambda-3_B, and experimentally linked to LambdaVir protection when expressed in E. coli.",
    "definition_source": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-3.md",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "PD-Lambda-3",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-3.md"
      },
      {
        "synonym_text": "PD-Lambda-3__PD-Lambda-3_A",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "PD-Lambda-3__PD-Lambda-3_B",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/s41564-022-01219-4",
        "snippet": "Here we developed an experimental selection scheme agnostic to genomic context to identify defence systems in 71 diverse E. coli strains. Our results unveil 21 conserved defence systems, none of which were previously detected as enriched in defence islands.",
        "notes": "Vassallo et al. developed the agnostic E. coli pangenome selection that uncovered PD-Lambda-3 and related conserved phage-defense systems."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-3.md",
        "snippet": "The PD-Lambda-3 is composed of 2 proteins: PD-Lambda-3_A and PD-Lambda-3_B.",
        "notes": "The DefenseFinder wiki names PD-Lambda-3 as a two-protein system with PD-Lambda-3_A and PD-Lambda-3_B."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-3.md",
        "snippet": "The PD-Lambda-3 system in *Enterobacter sp. CRENT-193* (GCF_002787395.1, NZ_CP024812) is composed of 2 proteins PD-Lambda-3_A (WP_001542736.1) PD-Lambda-3_B (WP_039268887.1)",
        "notes": "The DefenseFinder wiki illustrates a predicted two-protein PD-Lambda-3 locus in RefSeq assembly GCF_002787395.1 on NZ_CP024812."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-3.md",
        "snippet": "As far as we are aware, the molecular mechanism is unknown.",
        "notes": "The DefenseFinder wiki records the PD-Lambda-3 mechanism as unknown."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-3.md",
        "snippet": "Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0\n    Origin_0[Escherichia coli \n<a href='https://ncbi.nlm.nih.gov/protein/RCP74640.1'>RCP74640.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/RCP74641.1'>RCP74641.1</a>,\n<a href='https://ncbi.nlm.nih.gov/protein/RCP74642.1'>RCP74642.1</a>] --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> LambdaVir",
        "notes": "The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-Lambda-3 source locus expressed in E. coli against LambdaVir."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-3.md",
        "snippet": "subgraph Title4[Protects against]\n        LambdaVir",
        "notes": "The DefenseFinder experimental-validation diagram lists LambdaVir in the PD-Lambda-3 protects-against subgraph."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "PD-Lambda-3 | 10\\.1101/2022\\.05\\.12\\.491691 | Mapping the landscape of anti-phage defense mechanisms in the E\\. coli pangenome",
        "notes": "The DefenseFinder article registry maps the named PD-Lambda-3 system to the Vassallo et al. E. coli pangenome phage-defense preprint."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "PD-Lambda-3\tPD-Lambda-3\t2\t2\tPD-Lambda-3__PD-Lambda-3_A, PD-Lambda-3__PD-Lambda-3_B\t\t\t",
        "notes": "The DefenseFinder rules table models PD-Lambda-3 as a two-profile system requiring PD-Lambda-3__PD-Lambda-3_A and PD-Lambda-3__PD-Lambda-3_B."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| PD-Lambda-3__PD-Lambda-3_A                       | PD-Lambda-3__PD-Lambda-3_A                       | PD-Lambda-3            | Custom                  | 20     |",
        "notes": "The DefenseFinder HMM inventory records PD-Lambda-3__PD-Lambda-3_A under the PD-Lambda-3 system namespace."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| PD-Lambda-3__PD-Lambda-3_B                       | PD-Lambda-3__PD-Lambda-3_B                       | PD-Lambda-3            | Custom                  | 75     |",
        "notes": "The DefenseFinder HMM inventory records PD-Lambda-3__PD-Lambda-3_B under the PD-Lambda-3 system namespace."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "pd_lambda_3_locus_restricts_lambda_vir",
        "title": "PD-Lambda-3 loci restrict LambdaVir",
        "description": "Conservative system-level sketch linking possession of a PD-Lambda-3 locus to protection against LambdaVir.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures PD-Lambda-3 as a named DefenseFinder phage-defense system while leaving natural host breadth, the direct phage trigger, the effector mechanism, the third protein in the experimental source locus, and exact PD-Lambda-3 profile-to-protein correspondence unresolved.",
        "nodes": [
          {
            "node_id": "pd_lambda_3_locus",
            "label": "PD-Lambda-3 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A phage-defense locus represented by the PD-Lambda-3 DefenseFinder profiles."
          },
          {
            "node_id": "pd_lambda_3_listed_phage_protection",
            "label": "LambdaVir protection",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Protection against LambdaVir by PD-Lambda-3."
          },
          {
            "node_id": "pd_lambda_3_system_trait",
            "label": "PD-Lambda-3 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000382",
            "description": "Possession of a genome-encoded PD-Lambda-3 phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "pd_lambda_3_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "pd_lambda_3_listed_phage_protection",
            "description": "The DefenseFinder wiki links a PD-Lambda-3 locus from Vassallo et al. to protection against LambdaVir, and DefenseFinder models PD-Lambda-3 through two mandatory profiles.",
            "evidence": [
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-3.md",
                "snippet": "The PD-Lambda-3 is composed of 2 proteins: PD-Lambda-3_A and PD-Lambda-3_B.",
                "notes": "The DefenseFinder wiki names PD-Lambda-3 as a two-protein system with PD-Lambda-3_A and PD-Lambda-3_B."
              },
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-3.md",
                "snippet": "Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0\n    Origin_0[Escherichia coli \n<a href='https://ncbi.nlm.nih.gov/protein/RCP74640.1'>RCP74640.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/RCP74641.1'>RCP74641.1</a>,\n<a href='https://ncbi.nlm.nih.gov/protein/RCP74642.1'>RCP74642.1</a>] --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> LambdaVir",
                "notes": "The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-Lambda-3 source locus expressed in E. coli against LambdaVir."
              },
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-3.md",
                "snippet": "subgraph Title4[Protects against]\n        LambdaVir",
                "notes": "The DefenseFinder experimental-validation diagram lists LambdaVir in the PD-Lambda-3 protects-against subgraph."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "PD-Lambda-3\tPD-Lambda-3\t2\t2\tPD-Lambda-3__PD-Lambda-3_A, PD-Lambda-3__PD-Lambda-3_B\t\t\t",
                "notes": "The DefenseFinder rules table models PD-Lambda-3 as a two-profile system requiring PD-Lambda-3__PD-Lambda-3_A and PD-Lambda-3__PD-Lambda-3_B."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| PD-Lambda-3__PD-Lambda-3_A                       | PD-Lambda-3__PD-Lambda-3_A                       | PD-Lambda-3            | Custom                  | 20     |",
                "notes": "The DefenseFinder HMM inventory records PD-Lambda-3__PD-Lambda-3_A under the PD-Lambda-3 system namespace."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| PD-Lambda-3__PD-Lambda-3_B                       | PD-Lambda-3__PD-Lambda-3_B                       | PD-Lambda-3            | Custom                  | 75     |",
                "notes": "The DefenseFinder HMM inventory records PD-Lambda-3__PD-Lambda-3_B under the PD-Lambda-3 system namespace."
              }
            ]
          },
          {
            "subject": "pd_lambda_3_listed_phage_protection",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "pd_lambda_3_system_trait",
            "description": "Protection against LambdaVir realizes the PD-Lambda-3 system trait.",
            "evidence": [
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-3.md",
                "snippet": "Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0\n    Origin_0[Escherichia coli \n<a href='https://ncbi.nlm.nih.gov/protein/RCP74640.1'>RCP74640.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/RCP74641.1'>RCP74641.1</a>,\n<a href='https://ncbi.nlm.nih.gov/protein/RCP74642.1'>RCP74642.1</a>] --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> LambdaVir",
                "notes": "The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-Lambda-3 source locus expressed in E. coli against LambdaVir."
              },
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-3.md",
                "snippet": "subgraph Title4[Protects against]\n        LambdaVir",
                "notes": "The DefenseFinder experimental-validation diagram lists LambdaVir in the PD-Lambda-3 protects-against subgraph."
              }
            ]
          },
          {
            "subject": "pd_lambda_3_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "PD-Lambda-3 system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-022-01219-4",
                "snippet": "Here we developed an experimental selection scheme agnostic to genomic context to identify defence systems in 71 diverse E. coli strains. Our results unveil 21 conserved defence systems, none of which were previously detected as enriched in defence islands.",
                "notes": "Vassallo et al. developed the agnostic E. coli pangenome selection that uncovered PD-Lambda-3 and related conserved phage-defense systems."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "PD-Lambda-3 | 10\\.1101/2022\\.05\\.12\\.491691 | Mapping the landscape of anti-phage defense mechanisms in the E\\. coli pangenome",
                "notes": "The DefenseFinder article registry maps the named PD-Lambda-3 system to the Vassallo et al. E. coli pangenome phage-defense preprint."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "PD-Lambda-3\tPD-Lambda-3\t2\t2\tPD-Lambda-3__PD-Lambda-3_A, PD-Lambda-3__PD-Lambda-3_B\t\t\t",
                "notes": "The DefenseFinder rules table models PD-Lambda-3 as a two-profile system requiring PD-Lambda-3__PD-Lambda-3_A and PD-Lambda-3__PD-Lambda-3_B."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "pd-lambda-3-mechanism-gap",
        "prompt": "Resolve PD-Lambda-3 natural host breadth, direct phage trigger, effector mechanism, the third protein in the experimental source locus, and exact profile-to-protein correspondence before minting narrower PD-Lambda-3 mechanism traits.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Vassallo et al. support PD-Lambda-3 as one of the conserved systems from an E. coli pangenome phage-defense selection, the DefenseFinder wiki maps the source locus to protection against LambdaVir, and DefenseFinder represents the system with A and B profiles. Natural host breadth, the direct phage trigger, effector logic, the third protein in the experimental source locus, and exact profile-to-protein correspondence remain unresolved.",
        "evidence": [
          {
            "reference": "DOI:10.1038/s41564-022-01219-4",
            "snippet": "Here we developed an experimental selection scheme agnostic to genomic context to identify defence systems in 71 diverse E. coli strains. Our results unveil 21 conserved defence systems, none of which were previously detected as enriched in defence islands.",
            "notes": "Vassallo et al. developed the agnostic E. coli pangenome selection that uncovered PD-Lambda-3 and related conserved phage-defense systems."
          },
          {
            "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-3.md",
            "snippet": "The PD-Lambda-3 is composed of 2 proteins: PD-Lambda-3_A and PD-Lambda-3_B.",
            "notes": "The DefenseFinder wiki names PD-Lambda-3 as a two-protein system with PD-Lambda-3_A and PD-Lambda-3_B."
          },
          {
            "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-3.md",
            "snippet": "As far as we are aware, the molecular mechanism is unknown.",
            "notes": "The DefenseFinder wiki records the PD-Lambda-3 mechanism as unknown."
          },
          {
            "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-3.md",
            "snippet": "Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0\n    Origin_0[Escherichia coli \n<a href='https://ncbi.nlm.nih.gov/protein/RCP74640.1'>RCP74640.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/RCP74641.1'>RCP74641.1</a>,\n<a href='https://ncbi.nlm.nih.gov/protein/RCP74642.1'>RCP74642.1</a>] --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> LambdaVir",
            "notes": "The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-Lambda-3 source locus expressed in E. coli against LambdaVir."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "snippet": "PD-Lambda-3\tPD-Lambda-3\t2\t2\tPD-Lambda-3__PD-Lambda-3_A, PD-Lambda-3__PD-Lambda-3_B\t\t\t",
            "notes": "The DefenseFinder rules table models PD-Lambda-3 as a two-profile system requiring PD-Lambda-3__PD-Lambda-3_A and PD-Lambda-3__PD-Lambda-3_B."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| PD-Lambda-3__PD-Lambda-3_A                       | PD-Lambda-3__PD-Lambda-3_A                       | PD-Lambda-3            | Custom                  | 20     |",
            "notes": "The DefenseFinder HMM inventory records PD-Lambda-3__PD-Lambda-3_A under the PD-Lambda-3 system namespace."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| PD-Lambda-3__PD-Lambda-3_B                       | PD-Lambda-3__PD-Lambda-3_B                       | PD-Lambda-3            | Custom                  | 75     |",
            "notes": "The DefenseFinder HMM inventory records PD-Lambda-3__PD-Lambda-3_B under the PD-Lambda-3 system namespace."
          }
        ],
        "attaches_to": [
          "causal_graphs#pd_lambda_3_locus_restricts_lambda_vir"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-26"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-26T12:32:10Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted PD-Lambda-3 system as a DOI- and DefenseFinder-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v259.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-26T12:32:11Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed PD-Lambda-3 system canonical_examples and left them empty because the current sources support an E. coli accession-level experimental validation graph, a DefenseFinder system model, and a RefSeq Enterobacter sp. example, but not a direct native microbial isolate exemplar with experimentally verified endogenous PD-Lambda-3 activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000384",
    "label": "PD-Lambda-4 system",
    "definition": "A phage defense system in which an organism possesses a PD-Lambda-4 locus represented by DefenseFinder as a two-profile model, PD-Lambda-4__PD-Lambda-4_A and PD-Lambda-4__PD-Lambda-4_B, and experimentally linked to T4, LambdaVir, SECphi27, and T7 protection when expressed in E. coli.",
    "definition_source": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-4.md",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "PD-Lambda-4",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-4.md"
      },
      {
        "synonym_text": "PD-Lambda-4__PD-Lambda-4_A",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "PD-Lambda-4__PD-Lambda-4_B",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/s41564-022-01219-4",
        "snippet": "Here we developed an experimental selection scheme agnostic to genomic context to identify defence systems in 71 diverse E. coli strains. Our results unveil 21 conserved defence systems, none of which were previously detected as enriched in defence islands.",
        "notes": "Vassallo et al. developed the agnostic E. coli pangenome selection that uncovered PD-Lambda-4 and related conserved phage-defense systems."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-4.md",
        "snippet": "The PD-Lambda-4 is composed of 2 proteins: PD-Lambda-4_A and PD-Lambda-4_B.",
        "notes": "The DefenseFinder wiki names PD-Lambda-4 as a two-protein system with PD-Lambda-4_A and PD-Lambda-4_B."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-4.md",
        "snippet": "The PD-Lambda-4 system in *Serratia sp. LS-1* (GCF_003719595.1, NZ_CP033504) is composed of 2 proteins PD-Lambda-4_B (WP_123061920.1) PD-Lambda-4_A (WP_123061921.1)",
        "notes": "The DefenseFinder wiki illustrates a predicted two-protein PD-Lambda-4 locus in RefSeq assembly GCF_003719595.1 on NZ_CP033504."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-4.md",
        "snippet": "Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0\n    Origin_0[Escherichia coli \n<a href='https://ncbi.nlm.nih.gov/protein/RCP47953.1'>RCP47953.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/RCP47952.1'>RCP47952.1</a>] --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> T4 & LambdaVir & SECphi27 & T7",
        "notes": "The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-Lambda-4 source locus expressed in E. coli against T4, LambdaVir, SECphi27, and T7."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-4.md",
        "snippet": "subgraph Title4[Protects against]\n        T4\n        LambdaVir\n        SECphi27\n        T7",
        "notes": "The DefenseFinder experimental-validation diagram lists T4, LambdaVir, SECphi27, and T7 in the PD-Lambda-4 protects-against subgraph."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "PD-Lambda-4 | 10\\.1101/2022\\.05\\.12\\.491691 | Mapping the landscape of anti-phage defense mechanisms in the E\\. coli pangenome",
        "notes": "The DefenseFinder article registry maps the named PD-Lambda-4 system to the Vassallo et al. E. coli pangenome phage-defense preprint."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "PD-Lambda-4\tPD-Lambda-4\t2\t2\tPD-Lambda-4__PD-Lambda-4_A, PD-Lambda-4__PD-Lambda-4_B\t\t\t",
        "notes": "The DefenseFinder rules table models PD-Lambda-4 as a two-profile system requiring PD-Lambda-4__PD-Lambda-4_A and PD-Lambda-4__PD-Lambda-4_B."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| PD-Lambda-4__PD-Lambda-4_A                       | PD-Lambda-4__PD-Lambda-4_A                       | PD-Lambda-4            | Custom                  | 400    |",
        "notes": "The DefenseFinder HMM inventory records PD-Lambda-4__PD-Lambda-4_A under the PD-Lambda-4 system namespace."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| PD-Lambda-4__PD-Lambda-4_B                       | PD-Lambda-4__PD-Lambda-4_B                       | PD-Lambda-4            | Custom                  | 20     |",
        "notes": "The DefenseFinder HMM inventory records PD-Lambda-4__PD-Lambda-4_B under the PD-Lambda-4 system namespace."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "pd_lambda_4_locus_restricts_phages",
        "title": "PD-Lambda-4 loci restrict T4, LambdaVir, SECphi27, and T7",
        "description": "Conservative system-level sketch linking possession of a PD-Lambda-4 locus to protection against T4, LambdaVir, SECphi27, and T7.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures PD-Lambda-4 as a named DefenseFinder phage-defense system while leaving natural host breadth, the direct phage trigger, the effector mechanism, and exact PD-Lambda-4 profile-to-protein correspondence unresolved.",
        "nodes": [
          {
            "node_id": "pd_lambda_4_locus",
            "label": "PD-Lambda-4 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A phage-defense locus represented by the PD-Lambda-4 DefenseFinder profiles."
          },
          {
            "node_id": "pd_lambda_4_listed_phage_protection",
            "label": "T4, LambdaVir, SECphi27, and T7 protection",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Protection against T4, LambdaVir, SECphi27, and T7 by PD-Lambda-4."
          },
          {
            "node_id": "pd_lambda_4_system_trait",
            "label": "PD-Lambda-4 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000384",
            "description": "Possession of a genome-encoded PD-Lambda-4 phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "pd_lambda_4_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "pd_lambda_4_listed_phage_protection",
            "description": "The DefenseFinder wiki links a PD-Lambda-4 locus from Vassallo et al. to protection against T4, LambdaVir, SECphi27, and T7, and DefenseFinder models PD-Lambda-4 through two mandatory profiles.",
            "evidence": [
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-4.md",
                "snippet": "The PD-Lambda-4 is composed of 2 proteins: PD-Lambda-4_A and PD-Lambda-4_B.",
                "notes": "The DefenseFinder wiki names PD-Lambda-4 as a two-protein system with PD-Lambda-4_A and PD-Lambda-4_B."
              },
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-4.md",
                "snippet": "Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0\n    Origin_0[Escherichia coli \n<a href='https://ncbi.nlm.nih.gov/protein/RCP47953.1'>RCP47953.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/RCP47952.1'>RCP47952.1</a>] --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> T4 & LambdaVir & SECphi27 & T7",
                "notes": "The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-Lambda-4 source locus expressed in E. coli against T4, LambdaVir, SECphi27, and T7."
              },
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-4.md",
                "snippet": "subgraph Title4[Protects against]\n        T4\n        LambdaVir\n        SECphi27\n        T7",
                "notes": "The DefenseFinder experimental-validation diagram lists T4, LambdaVir, SECphi27, and T7 in the PD-Lambda-4 protects-against subgraph."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "PD-Lambda-4\tPD-Lambda-4\t2\t2\tPD-Lambda-4__PD-Lambda-4_A, PD-Lambda-4__PD-Lambda-4_B\t\t\t",
                "notes": "The DefenseFinder rules table models PD-Lambda-4 as a two-profile system requiring PD-Lambda-4__PD-Lambda-4_A and PD-Lambda-4__PD-Lambda-4_B."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| PD-Lambda-4__PD-Lambda-4_A                       | PD-Lambda-4__PD-Lambda-4_A                       | PD-Lambda-4            | Custom                  | 400    |",
                "notes": "The DefenseFinder HMM inventory records PD-Lambda-4__PD-Lambda-4_A under the PD-Lambda-4 system namespace."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| PD-Lambda-4__PD-Lambda-4_B                       | PD-Lambda-4__PD-Lambda-4_B                       | PD-Lambda-4            | Custom                  | 20     |",
                "notes": "The DefenseFinder HMM inventory records PD-Lambda-4__PD-Lambda-4_B under the PD-Lambda-4 system namespace."
              }
            ]
          },
          {
            "subject": "pd_lambda_4_listed_phage_protection",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "pd_lambda_4_system_trait",
            "description": "Protection against T4, LambdaVir, SECphi27, and T7 realizes the PD-Lambda-4 system trait.",
            "evidence": [
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-4.md",
                "snippet": "Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0\n    Origin_0[Escherichia coli \n<a href='https://ncbi.nlm.nih.gov/protein/RCP47953.1'>RCP47953.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/RCP47952.1'>RCP47952.1</a>] --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> T4 & LambdaVir & SECphi27 & T7",
                "notes": "The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-Lambda-4 source locus expressed in E. coli against T4, LambdaVir, SECphi27, and T7."
              },
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-4.md",
                "snippet": "subgraph Title4[Protects against]\n        T4\n        LambdaVir\n        SECphi27\n        T7",
                "notes": "The DefenseFinder experimental-validation diagram lists T4, LambdaVir, SECphi27, and T7 in the PD-Lambda-4 protects-against subgraph."
              }
            ]
          },
          {
            "subject": "pd_lambda_4_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "PD-Lambda-4 system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-022-01219-4",
                "snippet": "Here we developed an experimental selection scheme agnostic to genomic context to identify defence systems in 71 diverse E. coli strains. Our results unveil 21 conserved defence systems, none of which were previously detected as enriched in defence islands.",
                "notes": "Vassallo et al. developed the agnostic E. coli pangenome selection that uncovered PD-Lambda-4 and related conserved phage-defense systems."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "PD-Lambda-4 | 10\\.1101/2022\\.05\\.12\\.491691 | Mapping the landscape of anti-phage defense mechanisms in the E\\. coli pangenome",
                "notes": "The DefenseFinder article registry maps the named PD-Lambda-4 system to the Vassallo et al. E. coli pangenome phage-defense preprint."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "PD-Lambda-4\tPD-Lambda-4\t2\t2\tPD-Lambda-4__PD-Lambda-4_A, PD-Lambda-4__PD-Lambda-4_B\t\t\t",
                "notes": "The DefenseFinder rules table models PD-Lambda-4 as a two-profile system requiring PD-Lambda-4__PD-Lambda-4_A and PD-Lambda-4__PD-Lambda-4_B."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "pd-lambda-4-mechanism-gap",
        "prompt": "Resolve PD-Lambda-4 natural host breadth, direct phage trigger, effector mechanism, and profile-to-protein correspondence before minting narrower PD-Lambda-4 mechanism traits.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Vassallo et al. support PD-Lambda-4 as one of the conserved systems from an E. coli pangenome phage-defense selection, the DefenseFinder wiki maps the source locus to protection against T4, LambdaVir, SECphi27, and T7, and DefenseFinder represents the system with two mandatory profiles. Natural host breadth, the direct phage trigger, effector logic, and exact profile-to-protein correspondence remain unresolved.",
        "evidence": [
          {
            "reference": "DOI:10.1038/s41564-022-01219-4",
            "snippet": "Here we developed an experimental selection scheme agnostic to genomic context to identify defence systems in 71 diverse E. coli strains. Our results unveil 21 conserved defence systems, none of which were previously detected as enriched in defence islands.",
            "notes": "Vassallo et al. developed the agnostic E. coli pangenome selection that uncovered PD-Lambda-4 and related conserved phage-defense systems."
          },
          {
            "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-4.md",
            "snippet": "The PD-Lambda-4 is composed of 2 proteins: PD-Lambda-4_A and PD-Lambda-4_B.",
            "notes": "The DefenseFinder wiki names PD-Lambda-4 as a two-protein system with PD-Lambda-4_A and PD-Lambda-4_B."
          },
          {
            "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-4.md",
            "snippet": "Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0\n    Origin_0[Escherichia coli \n<a href='https://ncbi.nlm.nih.gov/protein/RCP47953.1'>RCP47953.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/RCP47952.1'>RCP47952.1</a>] --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> T4 & LambdaVir & SECphi27 & T7",
            "notes": "The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-Lambda-4 source locus expressed in E. coli against T4, LambdaVir, SECphi27, and T7."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "snippet": "PD-Lambda-4\tPD-Lambda-4\t2\t2\tPD-Lambda-4__PD-Lambda-4_A, PD-Lambda-4__PD-Lambda-4_B\t\t\t",
            "notes": "The DefenseFinder rules table models PD-Lambda-4 as a two-profile system requiring PD-Lambda-4__PD-Lambda-4_A and PD-Lambda-4__PD-Lambda-4_B."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| PD-Lambda-4__PD-Lambda-4_A                       | PD-Lambda-4__PD-Lambda-4_A                       | PD-Lambda-4            | Custom                  | 400    |",
            "notes": "The DefenseFinder HMM inventory records PD-Lambda-4__PD-Lambda-4_A under the PD-Lambda-4 system namespace."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| PD-Lambda-4__PD-Lambda-4_B                       | PD-Lambda-4__PD-Lambda-4_B                       | PD-Lambda-4            | Custom                  | 20     |",
            "notes": "The DefenseFinder HMM inventory records PD-Lambda-4__PD-Lambda-4_B under the PD-Lambda-4 system namespace."
          }
        ],
        "attaches_to": [
          "causal_graphs#pd_lambda_4_locus_restricts_phages"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-26"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-26T13:35:40Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted PD-Lambda-4 system as a DOI- and DefenseFinder-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v261.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-26T13:35:41Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed PD-Lambda-4 system canonical_examples and left them empty because the current sources support an E. coli accession-level experimental validation graph, a DefenseFinder system model, and a RefSeq Serratia sp. LS-1 example, but not a direct native microbial isolate exemplar with experimentally verified endogenous PD-Lambda-4 activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000385",
    "label": "PD-Lambda-5 system",
    "definition": "A phage defense system in which an organism possesses a PD-Lambda-5 locus represented by DefenseFinder as a two-profile model, PD-Lambda-5__PD-Lambda-5_A and PD-Lambda-5__PD-Lambda-5_B, and experimentally linked to T2, T4, T6, LambdaVir, SECphi17, SECphi18, SECphi27, T3, and T7 protection when expressed in E. coli.",
    "definition_source": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-5.md",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "PD-Lambda-5",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-5.md"
      },
      {
        "synonym_text": "PD-Lambda-5__PD-Lambda-5_A",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "PD-Lambda-5__PD-Lambda-5_B",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/s41564-022-01219-4",
        "snippet": "Here we developed an experimental selection scheme agnostic to genomic context to identify defence systems in 71 diverse E. coli strains. Our results unveil 21 conserved defence systems, none of which were previously detected as enriched in defence islands.",
        "notes": "Vassallo et al. developed the agnostic E. coli pangenome selection that uncovered PD-Lambda-5 and related conserved phage-defense systems."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-5.md",
        "snippet": "PD-lambda-5 is a two-gene system identified in a P2-like prophage. It encodes a protein with a nuclease and a HEPN domain, and a predicted methyltransferase. It confers broad anti-phage defense and does not seem to mediate abortive infection.",
        "notes": "The DefenseFinder wiki describes PD-Lambda-5 as a two-gene system from a P2-like prophage that can confer broad anti-phage defense."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-5.md",
        "snippet": "PD-lambda-5 molecular mechanism has not been described to date.",
        "notes": "The DefenseFinder wiki records the PD-Lambda-5 molecular mechanism as not yet described."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-5.md",
        "snippet": "The PD-Lambda-5 is composed of 2 proteins: PD-Lambda-5_A and PD-Lambda-5_B.",
        "notes": "The DefenseFinder wiki names PD-Lambda-5 as a two-protein system with PD-Lambda-5_A and PD-Lambda-5_B."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-5.md",
        "snippet": "The PD-Lambda-5 system in *Plantactinospora sp. BB1* (GCF_003030385.1, NZ_CP028159) is composed of 2 proteins PD-Lambda-5_A (WP_159104731.1) PD-Lambda-5_B (WP_199853739.1)",
        "notes": "The DefenseFinder wiki illustrates a predicted two-protein PD-Lambda-5 locus in RefSeq assembly GCF_003030385.1 on NZ_CP028159."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-5.md",
        "snippet": "Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0\n    Origin_0[Escherichia coli \n<a href='https://ncbi.nlm.nih.gov/protein/RCQ13837.1'>RCQ13837.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/RCQ13838.1'>RCQ13838.1</a>] --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> T2 & T4 & T6 & LambdaVir & SECphi17 & SECphi18 & SECphi27 & T3 & T7",
        "notes": "The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-Lambda-5 source locus expressed in E. coli against T2, T4, T6, LambdaVir, SECphi17, SECphi18, SECphi27, T3, and T7."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-5.md",
        "snippet": "subgraph Title4[Protects against]\n        T2\n        T4\n        T6\n        LambdaVir\n        SECphi17\n        SECphi18\n        SECphi27\n        T3\n        T7",
        "notes": "The DefenseFinder experimental-validation diagram lists T2, T4, T6, LambdaVir, SECphi17, SECphi18, SECphi27, T3, and T7 in the PD-Lambda-5 protects-against subgraph."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "PD-Lambda-5 | 10\\.1101/2022\\.05\\.12\\.491691 | Mapping the landscape of anti-phage defense mechanisms in the E\\. coli pangenome",
        "notes": "The DefenseFinder article registry maps the named PD-Lambda-5 system to the Vassallo et al. E. coli pangenome phage-defense preprint."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "PD-Lambda-5\tPD-Lambda-5\t2\t2\tPD-Lambda-5__PD-Lambda-5_A, PD-Lambda-5__PD-Lambda-5_B\t\t\t",
        "notes": "The DefenseFinder rules table models PD-Lambda-5 as a two-profile system requiring PD-Lambda-5__PD-Lambda-5_A and PD-Lambda-5__PD-Lambda-5_B."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| PD-Lambda-5__PD-Lambda-5_A                       | PD-Lambda-5__PD-Lambda-5_A                       | PD-Lambda-5            | Custom                  | 20     |",
        "notes": "The DefenseFinder HMM inventory records PD-Lambda-5__PD-Lambda-5_A under the PD-Lambda-5 system namespace."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| PD-Lambda-5__PD-Lambda-5_B                       | PD-Lambda-5__PD-Lambda-5_B                       | PD-Lambda-5            | Custom                  | 20     |",
        "notes": "The DefenseFinder HMM inventory records PD-Lambda-5__PD-Lambda-5_B under the PD-Lambda-5 system namespace."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "pd_lambda_5_locus_restricts_phages",
        "title": "PD-Lambda-5 loci restrict T2, T4, T6, LambdaVir, SECphi17, SECphi18, SECphi27, T3, and T7",
        "description": "Conservative system-level sketch linking possession of a PD-Lambda-5 locus to protection against T2, T4, T6, LambdaVir, SECphi17, SECphi18, SECphi27, T3, and T7.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures PD-Lambda-5 as a named DefenseFinder phage-defense system while leaving natural host breadth, the direct phage trigger, the effector mechanism, and exact PD-Lambda-5 profile-to-protein correspondence unresolved.",
        "nodes": [
          {
            "node_id": "pd_lambda_5_locus",
            "label": "PD-Lambda-5 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A phage-defense locus represented by the PD-Lambda-5 DefenseFinder profiles."
          },
          {
            "node_id": "pd_lambda_5_listed_phage_protection",
            "label": "T2, T4, T6, LambdaVir, SECphi17, SECphi18, SECphi27, T3, and T7 protection",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Protection against T2, T4, T6, LambdaVir, SECphi17, SECphi18, SECphi27, T3, and T7 by PD-Lambda-5."
          },
          {
            "node_id": "pd_lambda_5_system_trait",
            "label": "PD-Lambda-5 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000385",
            "description": "Possession of a genome-encoded PD-Lambda-5 phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "pd_lambda_5_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "pd_lambda_5_listed_phage_protection",
            "description": "The DefenseFinder wiki links a PD-Lambda-5 locus from Vassallo et al. to protection against T2, T4, T6, LambdaVir, SECphi17, SECphi18, SECphi27, T3, and T7, and DefenseFinder models PD-Lambda-5 through two mandatory profiles.",
            "evidence": [
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-5.md",
                "snippet": "PD-lambda-5 is a two-gene system identified in a P2-like prophage. It encodes a protein with a nuclease and a HEPN domain, and a predicted methyltransferase. It confers broad anti-phage defense and does not seem to mediate abortive infection.",
                "notes": "The DefenseFinder wiki describes PD-Lambda-5 as a two-gene system from a P2-like prophage that can confer broad anti-phage defense."
              },
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-5.md",
                "snippet": "The PD-Lambda-5 is composed of 2 proteins: PD-Lambda-5_A and PD-Lambda-5_B.",
                "notes": "The DefenseFinder wiki names PD-Lambda-5 as a two-protein system with PD-Lambda-5_A and PD-Lambda-5_B."
              },
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-5.md",
                "snippet": "Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0\n    Origin_0[Escherichia coli \n<a href='https://ncbi.nlm.nih.gov/protein/RCQ13837.1'>RCQ13837.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/RCQ13838.1'>RCQ13838.1</a>] --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> T2 & T4 & T6 & LambdaVir & SECphi17 & SECphi18 & SECphi27 & T3 & T7",
                "notes": "The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-Lambda-5 source locus expressed in E. coli against T2, T4, T6, LambdaVir, SECphi17, SECphi18, SECphi27, T3, and T7."
              },
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-5.md",
                "snippet": "subgraph Title4[Protects against]\n        T2\n        T4\n        T6\n        LambdaVir\n        SECphi17\n        SECphi18\n        SECphi27\n        T3\n        T7",
                "notes": "The DefenseFinder experimental-validation diagram lists T2, T4, T6, LambdaVir, SECphi17, SECphi18, SECphi27, T3, and T7 in the PD-Lambda-5 protects-against subgraph."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "PD-Lambda-5\tPD-Lambda-5\t2\t2\tPD-Lambda-5__PD-Lambda-5_A, PD-Lambda-5__PD-Lambda-5_B\t\t\t",
                "notes": "The DefenseFinder rules table models PD-Lambda-5 as a two-profile system requiring PD-Lambda-5__PD-Lambda-5_A and PD-Lambda-5__PD-Lambda-5_B."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| PD-Lambda-5__PD-Lambda-5_A                       | PD-Lambda-5__PD-Lambda-5_A                       | PD-Lambda-5            | Custom                  | 20     |",
                "notes": "The DefenseFinder HMM inventory records PD-Lambda-5__PD-Lambda-5_A under the PD-Lambda-5 system namespace."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| PD-Lambda-5__PD-Lambda-5_B                       | PD-Lambda-5__PD-Lambda-5_B                       | PD-Lambda-5            | Custom                  | 20     |",
                "notes": "The DefenseFinder HMM inventory records PD-Lambda-5__PD-Lambda-5_B under the PD-Lambda-5 system namespace."
              }
            ]
          },
          {
            "subject": "pd_lambda_5_listed_phage_protection",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "pd_lambda_5_system_trait",
            "description": "Protection against T2, T4, T6, LambdaVir, SECphi17, SECphi18, SECphi27, T3, and T7 realizes the PD-Lambda-5 system trait.",
            "evidence": [
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-5.md",
                "snippet": "Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0\n    Origin_0[Escherichia coli \n<a href='https://ncbi.nlm.nih.gov/protein/RCQ13837.1'>RCQ13837.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/RCQ13838.1'>RCQ13838.1</a>] --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> T2 & T4 & T6 & LambdaVir & SECphi17 & SECphi18 & SECphi27 & T3 & T7",
                "notes": "The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-Lambda-5 source locus expressed in E. coli against T2, T4, T6, LambdaVir, SECphi17, SECphi18, SECphi27, T3, and T7."
              },
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-5.md",
                "snippet": "subgraph Title4[Protects against]\n        T2\n        T4\n        T6\n        LambdaVir\n        SECphi17\n        SECphi18\n        SECphi27\n        T3\n        T7",
                "notes": "The DefenseFinder experimental-validation diagram lists T2, T4, T6, LambdaVir, SECphi17, SECphi18, SECphi27, T3, and T7 in the PD-Lambda-5 protects-against subgraph."
              }
            ]
          },
          {
            "subject": "pd_lambda_5_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "PD-Lambda-5 system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-022-01219-4",
                "snippet": "Here we developed an experimental selection scheme agnostic to genomic context to identify defence systems in 71 diverse E. coli strains. Our results unveil 21 conserved defence systems, none of which were previously detected as enriched in defence islands.",
                "notes": "Vassallo et al. developed the agnostic E. coli pangenome selection that uncovered PD-Lambda-5 and related conserved phage-defense systems."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "PD-Lambda-5 | 10\\.1101/2022\\.05\\.12\\.491691 | Mapping the landscape of anti-phage defense mechanisms in the E\\. coli pangenome",
                "notes": "The DefenseFinder article registry maps the named PD-Lambda-5 system to the Vassallo et al. E. coli pangenome phage-defense preprint."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "PD-Lambda-5\tPD-Lambda-5\t2\t2\tPD-Lambda-5__PD-Lambda-5_A, PD-Lambda-5__PD-Lambda-5_B\t\t\t",
                "notes": "The DefenseFinder rules table models PD-Lambda-5 as a two-profile system requiring PD-Lambda-5__PD-Lambda-5_A and PD-Lambda-5__PD-Lambda-5_B."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "pd-lambda-5-mechanism-gap",
        "prompt": "Resolve PD-Lambda-5 natural host breadth, direct phage trigger, effector mechanism, and profile-to-protein correspondence before minting narrower PD-Lambda-5 mechanism traits.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Vassallo et al. support PD-Lambda-5 as one of the conserved systems from an E. coli pangenome phage-defense selection, the DefenseFinder wiki maps the source locus to protection against T2, T4, T6, LambdaVir, SECphi17, SECphi18, SECphi27, T3, and T7, and DefenseFinder represents the system with two mandatory profiles. Natural host breadth, the direct phage trigger, effector logic, and exact profile-to-protein correspondence remain unresolved.",
        "evidence": [
          {
            "reference": "DOI:10.1038/s41564-022-01219-4",
            "snippet": "Here we developed an experimental selection scheme agnostic to genomic context to identify defence systems in 71 diverse E. coli strains. Our results unveil 21 conserved defence systems, none of which were previously detected as enriched in defence islands.",
            "notes": "Vassallo et al. developed the agnostic E. coli pangenome selection that uncovered PD-Lambda-5 and related conserved phage-defense systems."
          },
          {
            "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-5.md",
            "snippet": "PD-lambda-5 is a two-gene system identified in a P2-like prophage. It encodes a protein with a nuclease and a HEPN domain, and a predicted methyltransferase. It confers broad anti-phage defense and does not seem to mediate abortive infection.",
            "notes": "The DefenseFinder wiki describes PD-Lambda-5 as a two-gene system from a P2-like prophage that can confer broad anti-phage defense."
          },
          {
            "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-5.md",
            "snippet": "PD-lambda-5 molecular mechanism has not been described to date.",
            "notes": "The DefenseFinder wiki records the PD-Lambda-5 molecular mechanism as not yet described."
          },
          {
            "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-5.md",
            "snippet": "The PD-Lambda-5 is composed of 2 proteins: PD-Lambda-5_A and PD-Lambda-5_B.",
            "notes": "The DefenseFinder wiki names PD-Lambda-5 as a two-protein system with PD-Lambda-5_A and PD-Lambda-5_B."
          },
          {
            "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-5.md",
            "snippet": "Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0\n    Origin_0[Escherichia coli \n<a href='https://ncbi.nlm.nih.gov/protein/RCQ13837.1'>RCQ13837.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/RCQ13838.1'>RCQ13838.1</a>] --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> T2 & T4 & T6 & LambdaVir & SECphi17 & SECphi18 & SECphi27 & T3 & T7",
            "notes": "The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-Lambda-5 source locus expressed in E. coli against T2, T4, T6, LambdaVir, SECphi17, SECphi18, SECphi27, T3, and T7."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "snippet": "PD-Lambda-5\tPD-Lambda-5\t2\t2\tPD-Lambda-5__PD-Lambda-5_A, PD-Lambda-5__PD-Lambda-5_B\t\t\t",
            "notes": "The DefenseFinder rules table models PD-Lambda-5 as a two-profile system requiring PD-Lambda-5__PD-Lambda-5_A and PD-Lambda-5__PD-Lambda-5_B."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| PD-Lambda-5__PD-Lambda-5_A                       | PD-Lambda-5__PD-Lambda-5_A                       | PD-Lambda-5            | Custom                  | 20     |",
            "notes": "The DefenseFinder HMM inventory records PD-Lambda-5__PD-Lambda-5_A under the PD-Lambda-5 system namespace."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| PD-Lambda-5__PD-Lambda-5_B                       | PD-Lambda-5__PD-Lambda-5_B                       | PD-Lambda-5            | Custom                  | 20     |",
            "notes": "The DefenseFinder HMM inventory records PD-Lambda-5__PD-Lambda-5_B under the PD-Lambda-5 system namespace."
          }
        ],
        "attaches_to": [
          "causal_graphs#pd_lambda_5_locus_restricts_phages"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-26"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-26T14:07:45Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted PD-Lambda-5 system as a DOI- and DefenseFinder-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v262.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-26T14:07:46Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed PD-Lambda-5 system canonical_examples and left them empty because the current sources support an E. coli accession-level experimental validation graph, a DefenseFinder system model, and a RefSeq Plantactinospora sp. BB1 example, but not a direct native microbial isolate exemplar with experimentally verified endogenous PD-Lambda-5 activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000383",
    "label": "PD-Lambda-6 system",
    "definition": "A phage defense system in which an organism possesses a PD-Lambda-6 locus represented by DefenseFinder as a single-profile model, PD-Lambda-6__PD-Lambda-6, and experimentally linked to LambdaVir and T5 protection when expressed in E. coli.",
    "definition_source": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-6.md",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "PD-Lambda-6",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-6.md"
      },
      {
        "synonym_text": "PD-Lambda-6__PD-Lambda-6",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/s41564-022-01219-4",
        "snippet": "Here we developed an experimental selection scheme agnostic to genomic context to identify defence systems in 71 diverse E. coli strains. Our results unveil 21 conserved defence systems, none of which were previously detected as enriched in defence islands.",
        "notes": "Vassallo et al. developed the agnostic E. coli pangenome selection that uncovered PD-Lambda-6 and related conserved phage-defense systems."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-6.md",
        "snippet": "The PD-Lambda-6 is composed of 1 protein: PD-Lambda-6.",
        "notes": "The DefenseFinder wiki names PD-Lambda-6 as a single-protein system."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-6.md",
        "snippet": "The PD-Lambda-6 system in *Enterobacter asburiae* (GCF_013782005.1, NZ_CP056126) is composed of 1 protein: PD-Lambda-6 (WP_181599444.1)",
        "notes": "The DefenseFinder wiki illustrates a predicted one-protein PD-Lambda-6 locus in RefSeq assembly GCF_013782005.1 on NZ_CP056126."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-6.md",
        "snippet": "Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0\n    Origin_0[Escherichia coli \n<a href='https://ncbi.nlm.nih.gov/protein/RRK48647.1'>RRK48647.1</a>] --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> LambdaVir & T5",
        "notes": "The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-Lambda-6 source locus expressed in E. coli against LambdaVir and T5."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-6.md",
        "snippet": "subgraph Title4[Protects against]\n        LambdaVir\n        T5",
        "notes": "The DefenseFinder experimental-validation diagram lists LambdaVir and T5 in the PD-Lambda-6 protects-against subgraph."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "PD-Lambda-6 | 10\\.1101/2022\\.05\\.12\\.491691 | Mapping the landscape of anti-phage defense mechanisms in the E\\. coli pangenome",
        "notes": "The DefenseFinder article registry maps the named PD-Lambda-6 system to the Vassallo et al. E. coli pangenome phage-defense preprint."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "PD-Lambda-6\tPD-Lambda-6\t1\t1\tPD-Lambda-6__PD-Lambda-6\t\t\t",
        "notes": "The DefenseFinder rules table models PD-Lambda-6 as a single-profile system requiring PD-Lambda-6__PD-Lambda-6."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| PD-Lambda-6__PD-Lambda-6                         | PD-Lambda-6__PD-Lambda-6                         | PD-Lambda-6            | Custom                  | 20     |",
        "notes": "The DefenseFinder HMM inventory records PD-Lambda-6__PD-Lambda-6 under the PD-Lambda-6 system namespace."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "pd_lambda_6_locus_restricts_lambda_vir_and_t5",
        "title": "PD-Lambda-6 loci restrict LambdaVir and T5",
        "description": "Conservative system-level sketch linking possession of a PD-Lambda-6 locus to protection against LambdaVir and T5.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures PD-Lambda-6 as a named DefenseFinder phage-defense system while leaving natural host breadth, the direct phage trigger, and the effector mechanism unresolved.",
        "nodes": [
          {
            "node_id": "pd_lambda_6_locus",
            "label": "PD-Lambda-6 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A phage-defense locus represented by the PD-Lambda-6 DefenseFinder profile."
          },
          {
            "node_id": "pd_lambda_6_listed_phage_protection",
            "label": "LambdaVir and T5 protection",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Protection against LambdaVir and T5 by PD-Lambda-6."
          },
          {
            "node_id": "pd_lambda_6_system_trait",
            "label": "PD-Lambda-6 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000383",
            "description": "Possession of a genome-encoded PD-Lambda-6 phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "pd_lambda_6_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "pd_lambda_6_listed_phage_protection",
            "description": "The DefenseFinder wiki links a PD-Lambda-6 locus from Vassallo et al. to protection against LambdaVir and T5, and DefenseFinder models PD-Lambda-6 through one mandatory profile.",
            "evidence": [
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-6.md",
                "snippet": "The PD-Lambda-6 is composed of 1 protein: PD-Lambda-6.",
                "notes": "The DefenseFinder wiki names PD-Lambda-6 as a single-protein system."
              },
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-6.md",
                "snippet": "Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0\n    Origin_0[Escherichia coli \n<a href='https://ncbi.nlm.nih.gov/protein/RRK48647.1'>RRK48647.1</a>] --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> LambdaVir & T5",
                "notes": "The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-Lambda-6 source locus expressed in E. coli against LambdaVir and T5."
              },
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-6.md",
                "snippet": "subgraph Title4[Protects against]\n        LambdaVir\n        T5",
                "notes": "The DefenseFinder experimental-validation diagram lists LambdaVir and T5 in the PD-Lambda-6 protects-against subgraph."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "PD-Lambda-6\tPD-Lambda-6\t1\t1\tPD-Lambda-6__PD-Lambda-6\t\t\t",
                "notes": "The DefenseFinder rules table models PD-Lambda-6 as a single-profile system requiring PD-Lambda-6__PD-Lambda-6."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| PD-Lambda-6__PD-Lambda-6                         | PD-Lambda-6__PD-Lambda-6                         | PD-Lambda-6            | Custom                  | 20     |",
                "notes": "The DefenseFinder HMM inventory records PD-Lambda-6__PD-Lambda-6 under the PD-Lambda-6 system namespace."
              }
            ]
          },
          {
            "subject": "pd_lambda_6_listed_phage_protection",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "pd_lambda_6_system_trait",
            "description": "Protection against LambdaVir and T5 realizes the PD-Lambda-6 system trait.",
            "evidence": [
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-6.md",
                "snippet": "Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0\n    Origin_0[Escherichia coli \n<a href='https://ncbi.nlm.nih.gov/protein/RRK48647.1'>RRK48647.1</a>] --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> LambdaVir & T5",
                "notes": "The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-Lambda-6 source locus expressed in E. coli against LambdaVir and T5."
              },
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-6.md",
                "snippet": "subgraph Title4[Protects against]\n        LambdaVir\n        T5",
                "notes": "The DefenseFinder experimental-validation diagram lists LambdaVir and T5 in the PD-Lambda-6 protects-against subgraph."
              }
            ]
          },
          {
            "subject": "pd_lambda_6_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "PD-Lambda-6 system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-022-01219-4",
                "snippet": "Here we developed an experimental selection scheme agnostic to genomic context to identify defence systems in 71 diverse E. coli strains. Our results unveil 21 conserved defence systems, none of which were previously detected as enriched in defence islands.",
                "notes": "Vassallo et al. developed the agnostic E. coli pangenome selection that uncovered PD-Lambda-6 and related conserved phage-defense systems."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "PD-Lambda-6 | 10\\.1101/2022\\.05\\.12\\.491691 | Mapping the landscape of anti-phage defense mechanisms in the E\\. coli pangenome",
                "notes": "The DefenseFinder article registry maps the named PD-Lambda-6 system to the Vassallo et al. E. coli pangenome phage-defense preprint."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "PD-Lambda-6\tPD-Lambda-6\t1\t1\tPD-Lambda-6__PD-Lambda-6\t\t\t",
                "notes": "The DefenseFinder rules table models PD-Lambda-6 as a single-profile system requiring PD-Lambda-6__PD-Lambda-6."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "pd-lambda-6-mechanism-gap",
        "prompt": "Resolve PD-Lambda-6 natural host breadth, direct phage trigger, and effector mechanism before minting narrower PD-Lambda-6 mechanism traits.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Vassallo et al. support PD-Lambda-6 as one of the conserved systems from an E. coli pangenome phage-defense selection, the DefenseFinder wiki maps the source locus to protection against LambdaVir and T5, and DefenseFinder represents the system with one profile. Natural host breadth, the direct phage trigger, and effector logic remain unresolved.",
        "evidence": [
          {
            "reference": "DOI:10.1038/s41564-022-01219-4",
            "snippet": "Here we developed an experimental selection scheme agnostic to genomic context to identify defence systems in 71 diverse E. coli strains. Our results unveil 21 conserved defence systems, none of which were previously detected as enriched in defence islands.",
            "notes": "Vassallo et al. developed the agnostic E. coli pangenome selection that uncovered PD-Lambda-6 and related conserved phage-defense systems."
          },
          {
            "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-6.md",
            "snippet": "The PD-Lambda-6 is composed of 1 protein: PD-Lambda-6.",
            "notes": "The DefenseFinder wiki names PD-Lambda-6 as a single-protein system."
          },
          {
            "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-6.md",
            "snippet": "Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0\n    Origin_0[Escherichia coli \n<a href='https://ncbi.nlm.nih.gov/protein/RRK48647.1'>RRK48647.1</a>] --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> LambdaVir & T5",
            "notes": "The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-Lambda-6 source locus expressed in E. coli against LambdaVir and T5."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "snippet": "PD-Lambda-6\tPD-Lambda-6\t1\t1\tPD-Lambda-6__PD-Lambda-6\t\t\t",
            "notes": "The DefenseFinder rules table models PD-Lambda-6 as a single-profile system requiring PD-Lambda-6__PD-Lambda-6."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| PD-Lambda-6__PD-Lambda-6                         | PD-Lambda-6__PD-Lambda-6                         | PD-Lambda-6            | Custom                  | 20     |",
            "notes": "The DefenseFinder HMM inventory records PD-Lambda-6__PD-Lambda-6 under the PD-Lambda-6 system namespace."
          }
        ],
        "attaches_to": [
          "causal_graphs#pd_lambda_6_locus_restricts_lambda_vir_and_t5"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-26"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-26T13:07:26Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted PD-Lambda-6 system as a DOI- and DefenseFinder-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v260.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-26T13:07:27Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed PD-Lambda-6 system canonical_examples and left them empty because the current sources support an E. coli accession-level experimental validation graph, a DefenseFinder system model, and a RefSeq Enterobacter asburiae example, but not a direct native microbial isolate exemplar with experimentally verified endogenous PD-Lambda-6 activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000476",
    "label": "PD-T2-1 system",
    "definition": "A phage defense system in which an organism possesses a two-gene PD-T2-1 operon whose expression was experimentally linked to protection against T2, T6, Bas18, T4, and T5 phages.",
    "definition_source": "DOI:10.1038/s41564-025-02239-6",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "PD-T2-1",
        "synonym_type": "EXACT_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      },
      {
        "synonym_text": "PD-T2\u20131",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1038/s41564-025-02239-6"
      },
      {
        "synonym_text": "geneAB operon",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12875140/"
      }
    ],
    "evidence": [
      {
        "reference": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12875140/",
        "snippet": "Two phage proteins were further investigated, revealing T7 gp17 and additional tail fiber proteins activated the undescribed antiphage system PD-T2\u20131 and identifying \u03bb gpE major capsid protein activated the antiphage system Avs8.",
        "notes": "Goedecke et al. report that T7 gp17 and additional tail fiber proteins activated the previously undescribed PD-T2-1 antiphage system."
      },
      {
        "reference": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12875140/",
        "snippet": "Sequencing the transposon insertion site of mutants that did grow revealed 28 out of 48 mutants contained transposons that disrupted a two-gene operon of unknown function",
        "notes": "ECOR03 transposon mutants that escaped T7 gp17-mediated growth inhibition were enriched for insertions disrupting the same unknown two-gene operon."
      },
      {
        "reference": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12875140/",
        "snippet": "Operon structure of phage defense against T2 system 1 (PD-T2\u20131). Transposon insertions identified in mutant ECOR03 expressing T7 gp17 are indicated with triangles. A predicted transmembrane domain (TM) for PD-T2\u20131A, accession numbers, and the length of each protein in amino acids (aa) are shown.",
        "notes": "The PD-T2-1 operon figure identifies transposon insertions, the predicted transmembrane domain in PD-T2-1A, and the protein accessions used in the study."
      },
      {
        "reference": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12875140/",
        "snippet": "GeneAB conferred >100-fold protection against phages T2, T6, and Bas18, and approximately 10-fold protection against phages T4 and T5",
        "notes": "Expression of the operon in MG1655 protected against T2, T6, Bas18, T4, and T5 in phage-challenge assays."
      },
      {
        "reference": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12875140/",
        "snippet": "These findings led us to rename the geneAB operon phage defense against T2 system 1 (PD-T2\u20131)",
        "notes": "Goedecke et al. renamed the placeholder geneAB operon phage defense against T2 system 1."
      },
      {
        "reference": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12875140/",
        "snippet": "Transformation efficiency assays revealed that PD-T2\u20131 also selectively inhibited bacterial growth when T2 gp37, T2 gp34, and T2 gp12 were co-expressed",
        "notes": "PD-T2-1 also selectively inhibited growth when the T2 tail-fiber genes gp37, gp34, and gp12 were expressed."
      },
      {
        "reference": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12875140/",
        "snippet": "These results indicate PD-T2\u20131 does not function as a canonical toxin-antitoxin system.",
        "notes": "Single-gene expression experiments argue against PD-T2-1 as a canonical toxin-antitoxin system."
      },
      {
        "reference": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12875140/",
        "snippet": "ECOR03 PD-T2\u20131A: RCR47252.1; WP_075861856.1",
        "notes": "The Methods section reports the ECOR03 PD-T2-1A RefSeq and nonredundant protein accessions used in the article."
      },
      {
        "reference": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12875140/",
        "snippet": "Nucleotide coordinates for PD-T2\u20131 in ECOR03 (accession QOWO01000016): 10,064\u201311,256",
        "notes": "The extended-data figure caption places the ECOR03 PD-T2-1 locus on nucleotide record QOWO01000016."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "PD-T2-1 | 10\\.1101/2025\\.07\\.02\\.662641 | Identifying phage proteins that activate the bacterial innate immune system",
        "notes": "The pinned DefenseFinder article registry maps the named PD-T2-1 system to the Goedecke et al. preprint."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "pd_t2_1_locus_phage_protection",
        "title": "PD-T2-1 loci protect against multiple phages",
        "description": "Conservative system-level sketch linking a PD-T2-1 locus to experimentally measured T2, T6, Bas18, T4, and T5 protection.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures PD-T2-1 as a named phage-defense system in the final Goedecke et al. article and pinned DefenseFinder article registry while leaving the direct sensor or output mechanism, native host breadth, accession-level protein examples, profile-to-protein mapping, and exact DefenseFinder HMM/rules detection criteria unresolved.",
        "nodes": [
          {
            "node_id": "pd_t2_1_locus",
            "label": "PD-T2-1 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A two-gene phage-defense locus corresponding to the ECOR03 operon renamed PD-T2-1."
          },
          {
            "node_id": "pd_t2_1_listed_phage_protection",
            "label": "T2, T6, Bas18, T4, and T5 protection",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Protection against T2, T6, Bas18, T4, and T5 after PD-T2-1 expression in MG1655."
          },
          {
            "node_id": "pd_t2_1_system_trait",
            "label": "PD-T2-1 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000476",
            "description": "Possession of a genome-encoded PD-T2-1 phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "pd_t2_1_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "pd_t2_1_listed_phage_protection",
            "description": "Expression of the PD-T2-1 operon in MG1655 protected against phages T2, T6, Bas18, T4, and T5.",
            "evidence": [
              {
                "reference": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12875140/",
                "snippet": "GeneAB conferred >100-fold protection against phages T2, T6, and Bas18, and approximately 10-fold protection against phages T4 and T5",
                "notes": "Goedecke et al. challenged MG1655 expressing the PD-T2-1 operon with diverse phages and measured protection."
              },
              {
                "reference": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12875140/",
                "snippet": "These findings led us to rename the geneAB operon phage defense against T2 system 1 (PD-T2\u20131)",
                "notes": "Goedecke et al. renamed the two-gene geneAB operon PD-T2-1."
              }
            ]
          },
          {
            "subject": "pd_t2_1_listed_phage_protection",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "pd_t2_1_system_trait",
            "description": "Protection against T2, T6, Bas18, T4, and T5 realizes the PD-T2-1 phage-defense-system trait.",
            "evidence": [
              {
                "reference": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12875140/",
                "snippet": "GeneAB conferred >100-fold protection against phages T2, T6, and Bas18, and approximately 10-fold protection against phages T4 and T5",
                "notes": "The PD-T2-1 operon conferred phage protection when expressed in MG1655."
              }
            ]
          },
          {
            "subject": "pd_t2_1_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "PD-T2-1 system possession is a phage-defense system trait.",
            "evidence": [
              {
                "reference": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12875140/",
                "snippet": "Two phage proteins were further investigated, revealing T7 gp17 and additional tail fiber proteins activated the undescribed antiphage system PD-T2\u20131 and identifying \u03bb gpE major capsid protein activated the antiphage system Avs8.",
                "notes": "Goedecke et al. identify PD-T2-1 as an undescribed antiphage system."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "PD-T2-1 | 10\\.1101/2025\\.07\\.02\\.662641 | Identifying phage proteins that activate the bacterial innate immune system",
                "notes": "The pinned DefenseFinder article registry maps the named PD-T2-1 system to the Goedecke et al. preprint."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "pd-t2-1-mechanism-and-model-coverage-gap",
        "prompt": "Resolve the PD-T2-1 direct sensor, effector output, native host breadth, and DefenseFinder HMM/rules model coverage before minting narrower PD-T2-1 mechanism or protein-component traits.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "The final Goedecke et al. article supports PD-T2-1 as a two-gene operon activated by multiple phage tail-fiber proteins, links heterologous expression to protection against T2, T6, Bas18, T4, and T5, and argues that the system is not a canonical toxin-antitoxin system. The pinned DefenseFinder article registry names PD-T2-1 and maps it to the Goedecke et al. preprint, but the pinned HMM inventory and rules table do not contain PD-T2-1 rows, leaving profile coverage and detection criteria unresolved.",
        "evidence": [
          {
            "reference": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12875140/",
            "snippet": "Transformation efficiency assays revealed that PD-T2\u20131 also selectively inhibited bacterial growth when T2 gp37, T2 gp34, and T2 gp12 were co-expressed",
            "notes": "PD-T2-1 responded to multiple T2 tail-fiber proteins in transformation-efficiency assays."
          },
          {
            "reference": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12875140/",
            "snippet": "These results indicate PD-T2\u20131 does not function as a canonical toxin-antitoxin system.",
            "notes": "The PD-T2-1A/PD-T2-1B single-gene assays argue against a canonical toxin-antitoxin mechanism."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
            "snippet": "PD-T2-1 | 10\\.1101/2025\\.07\\.02\\.662641 | Identifying phage proteins that activate the bacterial innate immune system",
            "notes": "The pinned DefenseFinder article registry maps the named PD-T2-1 system to the Goedecke et al. preprint."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "notes": "No PD-T2-1 or PD-T2-1-prefixed HMM inventory row was present in the pinned DefenseFinder model file."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "No PD-T2-1 rule row was present in the pinned DefenseFinder rules table."
          }
        ],
        "attaches_to": [
          "causal_graphs#pd_t2_1_locus_phage_protection"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-29"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-29T22:58:06Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted PD-T2-1 system as a DOI- and DefenseFinder-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record. The proposals/metpo_traitmech_v353 cohort reserves the replacement placeholder.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-29T22:58:07Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed PD-T2-1 canonical_examples and left them empty because ECOR03 supports native discovery and locus coordinates without a verified NCBITaxon strain CURIE, while heterologous MG1655 phage-challenge assays do not by themselves support an endogenous named isolate exemplar. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000394",
    "label": "PD-T4-10 system",
    "definition": "An abortive infection system in which an organism possesses a PD-T4-10 locus represented by DefenseFinder as a two-profile model, PD-T4-10__PD-T4-10_A and PD-T4-10__PD-T4-10_B, and experimentally linked to T2, T4, T6, T5, and SECphi27 protection when expressed in E. coli.",
    "definition_source": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-10.md",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000214"
    ],
    "synonyms": [
      {
        "synonym_text": "PD-T4-10",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-10.md"
      },
      {
        "synonym_text": "PD-T4-10__PD-T4-10_A",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "PD-T4-10__PD-T4-10_B",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/s41564-022-01219-4",
        "snippet": "Here we developed an experimental selection scheme agnostic to genomic context to identify defence systems in 71 diverse E. coli strains. Our results unveil 21 conserved defence systems, none of which were previously detected as enriched in defence islands.",
        "notes": "Vassallo et al. developed the agnostic E. coli pangenome selection that uncovered PD-T4-10 and related conserved phage-defense systems."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-10.md",
        "snippet": "The PD-T4-10 system is composed of 2 proteins: PD-T4-10_B and, PD-T4-10_A. These ORFs are overlapping and PD-T4-10_B is toxic while PD-T4-10_A neutralizes its toxicity, hinting at a toxin-antitoxin (TA) mechanism. It confers resitance to T2, T4, T6 and SECphi27 through an Abi defense mechanism :ref{doi=10.1038/s41564-022-01219-4}.",
        "notes": "The DefenseFinder wiki describes PD-T4-10 as a two-protein Abi system whose overlapping ORFs include a toxic PD-T4-10_B and neutralizing PD-T4-10_A."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-10.md",
        "snippet": "The PD-T4-10 is composed of 2 proteins: PD-T4-10_A and PD-T4-10_B.",
        "notes": "The DefenseFinder wiki names PD-T4-10_A and PD-T4-10_B as the two components of the PD-T4-10 system."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-10.md",
        "snippet": "The PD-T4-10 system in *Escherichia fergusonii* (GCF_019047545.1, NZ_CP077242) is composed of 2 proteins PD-T4-10_A (WP_032236482.1) PD-T4-10_B (WP_032236481.1)",
        "notes": "The DefenseFinder wiki illustrates a predicted PD-T4-10 locus in RefSeq assembly GCF_019047545.1 on NZ_CP077242."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-10.md",
        "snippet": "Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0\n    Origin_0[Escherichia coli \n<a href='https://ncbi.nlm.nih.gov/protein/RCO36089.1'>RCO36089.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/RCO36088.1'>RCO36088.1</a>] --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> T2 & T4 & T6 & T5 & SECphi27",
        "notes": "The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-T4-10 source locus expressed in E. coli against T2, T4, T6, T5, and SECphi27."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-10.md",
        "snippet": "subgraph Title4[Protects against]\n        T2\n        T4\n        T6\n        T5\n        SECphi27",
        "notes": "The DefenseFinder experimental-validation diagram lists T2, T4, T6, T5, and SECphi27 in the PD-T4-10 protects-against subgraph."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "PD-T4-10 | 10\\.1101/2022\\.05\\.12\\.491691 | Mapping the landscape of anti-phage defense mechanisms in the E\\. coli pangenome",
        "notes": "The DefenseFinder article registry maps the named PD-T4-10 system to the Vassallo et al. E. coli pangenome phage-defense preprint."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "PD-T4-10\tPD-T4-10\t2\t2\tPD-T4-10__PD-T4-10_A, PD-T4-10__PD-T4-10_B\t\t\t",
        "notes": "The DefenseFinder rules table models PD-T4-10 as a two-profile system requiring PD-T4-10__PD-T4-10_A and PD-T4-10__PD-T4-10_B."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| PD-T4-10__PD-T4-10_A                             | PD-T4-10__PD-T4-10_A                             | PD-T4-10               | Custom                  | 20     |\n| PD-T4-10__PD-T4-10_B                             | PD-T4-10__PD-T4-10_B                             | PD-T4-10               | Custom                  | 20     |",
        "notes": "The DefenseFinder HMM inventory records PD-T4-10__PD-T4-10_A and PD-T4-10__PD-T4-10_B under the PD-T4-10 system namespace."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "pd_t4_10_locus_restricts_t2_t4_t6_t5_and_secphi27",
        "title": "PD-T4-10 loci restrict T2, T4, T6, T5, and SECphi27",
        "description": "Conservative system-level sketch linking possession of a PD-T4-10 locus to protection against T2, T4, T6, T5, and SECphi27.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures PD-T4-10 as a named DefenseFinder abortive-infection system while leaving natural host breadth, the direct phage trigger, the toxic PD-T4-10_B target, and the PD-T4-10_A neutralization logic unresolved.",
        "nodes": [
          {
            "node_id": "pd_t4_10_locus",
            "label": "PD-T4-10 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A two-profile abortive-infection locus represented by the DefenseFinder PD-T4-10_A and PD-T4-10_B profiles."
          },
          {
            "node_id": "pd_t4_10_listed_phage_protection",
            "label": "T2, T4, T6, T5, and SECphi27 protection",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Protection against T2, T4, T6, T5, and SECphi27 by PD-T4-10."
          },
          {
            "node_id": "pd_t4_10_system_trait",
            "label": "PD-T4-10 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000394",
            "description": "Possession of a genome-encoded PD-T4-10 abortive-infection phage-defense system."
          },
          {
            "node_id": "abortive_infection_system",
            "label": "abortive infection system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000214",
            "description": "Possession of a genome-encoded abortive-infection phage-defense system."
          }
        ],
        "edges": [
          {
            "subject": "pd_t4_10_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "pd_t4_10_listed_phage_protection",
            "description": "The DefenseFinder wiki links a PD-T4-10 locus from Vassallo et al. to protection against T2, T4, T6, T5, and SECphi27, and DefenseFinder models PD-T4-10 through two mandatory profiles.",
            "evidence": [
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-10.md",
                "snippet": "The PD-T4-10 system is composed of 2 proteins: PD-T4-10_B and, PD-T4-10_A. These ORFs are overlapping and PD-T4-10_B is toxic while PD-T4-10_A neutralizes its toxicity, hinting at a toxin-antitoxin (TA) mechanism. It confers resitance to T2, T4, T6 and SECphi27 through an Abi defense mechanism :ref{doi=10.1038/s41564-022-01219-4}.",
                "notes": "The DefenseFinder wiki describes PD-T4-10 as a two-protein Abi system whose overlapping ORFs include a toxic PD-T4-10_B and neutralizing PD-T4-10_A."
              },
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-10.md",
                "snippet": "The PD-T4-10 is composed of 2 proteins: PD-T4-10_A and PD-T4-10_B.",
                "notes": "The DefenseFinder wiki names PD-T4-10_A and PD-T4-10_B as the two components of the PD-T4-10 system."
              },
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-10.md",
                "snippet": "Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0\n    Origin_0[Escherichia coli \n<a href='https://ncbi.nlm.nih.gov/protein/RCO36089.1'>RCO36089.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/RCO36088.1'>RCO36088.1</a>] --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> T2 & T4 & T6 & T5 & SECphi27",
                "notes": "The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-T4-10 source locus expressed in E. coli against T2, T4, T6, T5, and SECphi27."
              },
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-10.md",
                "snippet": "subgraph Title4[Protects against]\n        T2\n        T4\n        T6\n        T5\n        SECphi27",
                "notes": "The DefenseFinder experimental-validation diagram lists T2, T4, T6, T5, and SECphi27 in the PD-T4-10 protects-against subgraph."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "PD-T4-10\tPD-T4-10\t2\t2\tPD-T4-10__PD-T4-10_A, PD-T4-10__PD-T4-10_B\t\t\t",
                "notes": "The DefenseFinder rules table models PD-T4-10 as a two-profile system requiring PD-T4-10__PD-T4-10_A and PD-T4-10__PD-T4-10_B."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| PD-T4-10__PD-T4-10_A                             | PD-T4-10__PD-T4-10_A                             | PD-T4-10               | Custom                  | 20     |\n| PD-T4-10__PD-T4-10_B                             | PD-T4-10__PD-T4-10_B                             | PD-T4-10               | Custom                  | 20     |",
                "notes": "The DefenseFinder HMM inventory records PD-T4-10__PD-T4-10_A and PD-T4-10__PD-T4-10_B under the PD-T4-10 system namespace."
              }
            ]
          },
          {
            "subject": "pd_t4_10_listed_phage_protection",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "pd_t4_10_system_trait",
            "description": "Protection against T2, T4, T6, T5, and SECphi27 realizes the PD-T4-10 system trait.",
            "evidence": [
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-10.md",
                "snippet": "Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0\n    Origin_0[Escherichia coli \n<a href='https://ncbi.nlm.nih.gov/protein/RCO36089.1'>RCO36089.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/RCO36088.1'>RCO36088.1</a>] --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> T2 & T4 & T6 & T5 & SECphi27",
                "notes": "The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-T4-10 source locus expressed in E. coli against T2, T4, T6, T5, and SECphi27."
              },
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-10.md",
                "snippet": "subgraph Title4[Protects against]\n        T2\n        T4\n        T6\n        T5\n        SECphi27",
                "notes": "The DefenseFinder experimental-validation diagram lists T2, T4, T6, T5, and SECphi27 in the PD-T4-10 protects-against subgraph."
              }
            ]
          },
          {
            "subject": "pd_t4_10_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "abortive_infection_system",
            "description": "PD-T4-10 system possession is an abortive-infection-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-022-01219-4",
                "snippet": "Here we developed an experimental selection scheme agnostic to genomic context to identify defence systems in 71 diverse E. coli strains. Our results unveil 21 conserved defence systems, none of which were previously detected as enriched in defence islands.",
                "notes": "Vassallo et al. developed the agnostic E. coli pangenome selection that uncovered PD-T4-10 and related conserved phage-defense systems."
              },
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-10.md",
                "snippet": "The PD-T4-10 system is composed of 2 proteins: PD-T4-10_B and, PD-T4-10_A. These ORFs are overlapping and PD-T4-10_B is toxic while PD-T4-10_A neutralizes its toxicity, hinting at a toxin-antitoxin (TA) mechanism. It confers resitance to T2, T4, T6 and SECphi27 through an Abi defense mechanism :ref{doi=10.1038/s41564-022-01219-4}.",
                "notes": "The DefenseFinder wiki describes PD-T4-10 as a two-protein Abi system whose overlapping ORFs include a toxic PD-T4-10_B and neutralizing PD-T4-10_A."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "PD-T4-10 | 10\\.1101/2022\\.05\\.12\\.491691 | Mapping the landscape of anti-phage defense mechanisms in the E\\. coli pangenome",
                "notes": "The DefenseFinder article registry maps the named PD-T4-10 system to the Vassallo et al. E. coli pangenome phage-defense preprint."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "PD-T4-10\tPD-T4-10\t2\t2\tPD-T4-10__PD-T4-10_A, PD-T4-10__PD-T4-10_B\t\t\t",
                "notes": "The DefenseFinder rules table models PD-T4-10 as a two-profile system requiring PD-T4-10__PD-T4-10_A and PD-T4-10__PD-T4-10_B."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "pd-t4-10-mechanism-gap",
        "prompt": "Resolve PD-T4-10 natural host breadth, direct phage trigger, the toxic PD-T4-10_B target, and PD-T4-10_A neutralization logic before minting narrower PD-T4-10 mechanism traits.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Vassallo et al. support PD-T4-10 as one of the conserved systems from an E. coli pangenome phage-defense selection, the DefenseFinder wiki maps the source locus to protection against T2, T4, T6, T5, and SECphi27, and DefenseFinder represents the system with two mandatory profiles and an abortive-infection mechanism assignment. Natural host breadth, the direct phage trigger, the toxic PD-T4-10_B target, and the PD-T4-10_A neutralization logic remain unresolved.",
        "evidence": [
          {
            "reference": "DOI:10.1038/s41564-022-01219-4",
            "snippet": "Here we developed an experimental selection scheme agnostic to genomic context to identify defence systems in 71 diverse E. coli strains. Our results unveil 21 conserved defence systems, none of which were previously detected as enriched in defence islands.",
            "notes": "Vassallo et al. developed the agnostic E. coli pangenome selection that uncovered PD-T4-10 and related conserved phage-defense systems."
          },
          {
            "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-10.md",
            "snippet": "The PD-T4-10 system is composed of 2 proteins: PD-T4-10_B and, PD-T4-10_A. These ORFs are overlapping and PD-T4-10_B is toxic while PD-T4-10_A neutralizes its toxicity, hinting at a toxin-antitoxin (TA) mechanism. It confers resitance to T2, T4, T6 and SECphi27 through an Abi defense mechanism :ref{doi=10.1038/s41564-022-01219-4}.",
            "notes": "The DefenseFinder wiki describes PD-T4-10 as a two-protein Abi system whose overlapping ORFs include a toxic PD-T4-10_B and neutralizing PD-T4-10_A."
          },
          {
            "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-10.md",
            "snippet": "The PD-T4-10 is composed of 2 proteins: PD-T4-10_A and PD-T4-10_B.",
            "notes": "The DefenseFinder wiki names PD-T4-10_A and PD-T4-10_B as the two components of the PD-T4-10 system."
          },
          {
            "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-10.md",
            "snippet": "Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0\n    Origin_0[Escherichia coli \n<a href='https://ncbi.nlm.nih.gov/protein/RCO36089.1'>RCO36089.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/RCO36088.1'>RCO36088.1</a>] --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> T2 & T4 & T6 & T5 & SECphi27",
            "notes": "The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-T4-10 source locus expressed in E. coli against T2, T4, T6, T5, and SECphi27."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "snippet": "PD-T4-10\tPD-T4-10\t2\t2\tPD-T4-10__PD-T4-10_A, PD-T4-10__PD-T4-10_B\t\t\t",
            "notes": "The DefenseFinder rules table models PD-T4-10 as a two-profile system requiring PD-T4-10__PD-T4-10_A and PD-T4-10__PD-T4-10_B."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| PD-T4-10__PD-T4-10_A                             | PD-T4-10__PD-T4-10_A                             | PD-T4-10               | Custom                  | 20     |\n| PD-T4-10__PD-T4-10_B                             | PD-T4-10__PD-T4-10_B                             | PD-T4-10               | Custom                  | 20     |",
            "notes": "The DefenseFinder HMM inventory records PD-T4-10__PD-T4-10_A and PD-T4-10__PD-T4-10_B under the PD-T4-10 system namespace."
          }
        ],
        "attaches_to": [
          "causal_graphs#pd_t4_10_locus_restricts_t2_t4_t6_t5_and_secphi27"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-26"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-26T20:56:41Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted PD-T4-10 system as a DOI- and DefenseFinder-backed GENOMICS TraitRecord under abortive infection system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v271.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-26T20:56:42Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed PD-T4-10 system canonical_examples and left them empty because the current sources support an E. coli accession-level experimental validation graph, a DefenseFinder two-profile system model, and a RefSeq Escherichia fergusonii example, but not a direct native microbial isolate exemplar with experimentally verified endogenous PD-T4-10 activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000386",
    "label": "PD-T4-1 system",
    "definition": "A phage defense system in which an organism possesses a PD-T4-1 locus represented by DefenseFinder as a single-profile model, PD-T4-1__PD-T4-1, and experimentally linked to T2, T4, and T6 protection when expressed in E. coli.",
    "definition_source": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-1.md",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "PD-T4-1",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-1.md"
      },
      {
        "synonym_text": "PD-T4-1__PD-T4-1",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/s41564-022-01219-4",
        "snippet": "Here we developed an experimental selection scheme agnostic to genomic context to identify defence systems in 71 diverse E. coli strains. Our results unveil 21 conserved defence systems, none of which were previously detected as enriched in defence islands.",
        "notes": "Vassallo et al. developed the agnostic E. coli pangenome selection that uncovered PD-T4-1 and related conserved phage-defense systems."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-1.md",
        "snippet": "The PD-T4-1 is composed of 1 protein: PD-T4-1.",
        "notes": "The DefenseFinder wiki names PD-T4-1 as a single-protein system."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-1.md",
        "snippet": "The PD-T4-1 system in *Macrococcus armenti* (GCF_020097055.1, NZ_CP083595) is composed of 1 protein: PD-T4-1 (WP_224185715.1)",
        "notes": "The DefenseFinder wiki illustrates a predicted one-protein PD-T4-1 locus in RefSeq assembly GCF_020097055.1 on NZ_CP083595."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-1.md",
        "snippet": "Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0\n    Origin_0[Escherichia coli \n<a href='https://ncbi.nlm.nih.gov/protein/RRM93940.1'>RRM93940.1</a>] --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> T2 & T4 & T6",
        "notes": "The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-T4-1 source locus expressed in E. coli against T2, T4, and T6."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-1.md",
        "snippet": "subgraph Title4[Protects against]\n        T2\n        T4\n        T6",
        "notes": "The DefenseFinder experimental-validation diagram lists T2, T4, and T6 in the PD-T4-1 protects-against subgraph."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "PD-T4-1 | 10\\.1101/2022\\.05\\.12\\.491691 | Mapping the landscape of anti-phage defense mechanisms in the E\\. coli pangenome",
        "notes": "The DefenseFinder article registry maps the named PD-T4-1 system to the Vassallo et al. E. coli pangenome phage-defense preprint."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "PD-T4-1\tPD-T4-1\t1\t1\tPD-T4-1__PD-T4-1\t\t\t",
        "notes": "The DefenseFinder rules table models PD-T4-1 as a single-profile system requiring PD-T4-1__PD-T4-1."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| PD-T4-1__PD-T4-1                                 | PD-T4-1__PD-T4-1                                 | PD-T4-1                | Custom                  | 120    |",
        "notes": "The DefenseFinder HMM inventory records PD-T4-1__PD-T4-1 under the PD-T4-1 system namespace."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "pd_t4_1_locus_restricts_t2_t4_and_t6",
        "title": "PD-T4-1 loci restrict T2, T4, and T6",
        "description": "Conservative system-level sketch linking possession of a PD-T4-1 locus to protection against T2, T4, and T6.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures PD-T4-1 as a named DefenseFinder phage-defense system while leaving natural host breadth, the direct phage trigger, and the effector mechanism unresolved.",
        "nodes": [
          {
            "node_id": "pd_t4_1_locus",
            "label": "PD-T4-1 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A phage-defense locus represented by the PD-T4-1 DefenseFinder profile."
          },
          {
            "node_id": "pd_t4_1_listed_phage_protection",
            "label": "T2, T4, and T6 protection",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Protection against T2, T4, and T6 by PD-T4-1."
          },
          {
            "node_id": "pd_t4_1_system_trait",
            "label": "PD-T4-1 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000386",
            "description": "Possession of a genome-encoded PD-T4-1 phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "pd_t4_1_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "pd_t4_1_listed_phage_protection",
            "description": "The DefenseFinder wiki links a PD-T4-1 locus from Vassallo et al. to protection against T2, T4, and T6, and DefenseFinder models PD-T4-1 through one mandatory profile.",
            "evidence": [
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-1.md",
                "snippet": "The PD-T4-1 is composed of 1 protein: PD-T4-1.",
                "notes": "The DefenseFinder wiki names PD-T4-1 as a single-protein system."
              },
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-1.md",
                "snippet": "Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0\n    Origin_0[Escherichia coli \n<a href='https://ncbi.nlm.nih.gov/protein/RRM93940.1'>RRM93940.1</a>] --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> T2 & T4 & T6",
                "notes": "The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-T4-1 source locus expressed in E. coli against T2, T4, and T6."
              },
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-1.md",
                "snippet": "subgraph Title4[Protects against]\n        T2\n        T4\n        T6",
                "notes": "The DefenseFinder experimental-validation diagram lists T2, T4, and T6 in the PD-T4-1 protects-against subgraph."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "PD-T4-1\tPD-T4-1\t1\t1\tPD-T4-1__PD-T4-1\t\t\t",
                "notes": "The DefenseFinder rules table models PD-T4-1 as a single-profile system requiring PD-T4-1__PD-T4-1."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| PD-T4-1__PD-T4-1                                 | PD-T4-1__PD-T4-1                                 | PD-T4-1                | Custom                  | 120    |",
                "notes": "The DefenseFinder HMM inventory records PD-T4-1__PD-T4-1 under the PD-T4-1 system namespace."
              }
            ]
          },
          {
            "subject": "pd_t4_1_listed_phage_protection",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "pd_t4_1_system_trait",
            "description": "Protection against T2, T4, and T6 realizes the PD-T4-1 system trait.",
            "evidence": [
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-1.md",
                "snippet": "Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0\n    Origin_0[Escherichia coli \n<a href='https://ncbi.nlm.nih.gov/protein/RRM93940.1'>RRM93940.1</a>] --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> T2 & T4 & T6",
                "notes": "The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-T4-1 source locus expressed in E. coli against T2, T4, and T6."
              },
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-1.md",
                "snippet": "subgraph Title4[Protects against]\n        T2\n        T4\n        T6",
                "notes": "The DefenseFinder experimental-validation diagram lists T2, T4, and T6 in the PD-T4-1 protects-against subgraph."
              }
            ]
          },
          {
            "subject": "pd_t4_1_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "PD-T4-1 system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-022-01219-4",
                "snippet": "Here we developed an experimental selection scheme agnostic to genomic context to identify defence systems in 71 diverse E. coli strains. Our results unveil 21 conserved defence systems, none of which were previously detected as enriched in defence islands.",
                "notes": "Vassallo et al. developed the agnostic E. coli pangenome selection that uncovered PD-T4-1 and related conserved phage-defense systems."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "PD-T4-1 | 10\\.1101/2022\\.05\\.12\\.491691 | Mapping the landscape of anti-phage defense mechanisms in the E\\. coli pangenome",
                "notes": "The DefenseFinder article registry maps the named PD-T4-1 system to the Vassallo et al. E. coli pangenome phage-defense preprint."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "PD-T4-1\tPD-T4-1\t1\t1\tPD-T4-1__PD-T4-1\t\t\t",
                "notes": "The DefenseFinder rules table models PD-T4-1 as a single-profile system requiring PD-T4-1__PD-T4-1."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "pd-t4-1-mechanism-gap",
        "prompt": "Resolve PD-T4-1 natural host breadth, direct phage trigger, and effector mechanism before minting narrower PD-T4-1 mechanism traits.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Vassallo et al. support PD-T4-1 as one of the conserved systems from an E. coli pangenome phage-defense selection, the DefenseFinder wiki maps the source locus to protection against T2, T4, and T6, and DefenseFinder represents the system with one profile. Natural host breadth, the direct phage trigger, and effector logic remain unresolved.",
        "evidence": [
          {
            "reference": "DOI:10.1038/s41564-022-01219-4",
            "snippet": "Here we developed an experimental selection scheme agnostic to genomic context to identify defence systems in 71 diverse E. coli strains. Our results unveil 21 conserved defence systems, none of which were previously detected as enriched in defence islands.",
            "notes": "Vassallo et al. developed the agnostic E. coli pangenome selection that uncovered PD-T4-1 and related conserved phage-defense systems."
          },
          {
            "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-1.md",
            "snippet": "The PD-T4-1 is composed of 1 protein: PD-T4-1.",
            "notes": "The DefenseFinder wiki names PD-T4-1 as a single-protein system."
          },
          {
            "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-1.md",
            "snippet": "Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0\n    Origin_0[Escherichia coli \n<a href='https://ncbi.nlm.nih.gov/protein/RRM93940.1'>RRM93940.1</a>] --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> T2 & T4 & T6",
            "notes": "The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-T4-1 source locus expressed in E. coli against T2, T4, and T6."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "snippet": "PD-T4-1\tPD-T4-1\t1\t1\tPD-T4-1__PD-T4-1\t\t\t",
            "notes": "The DefenseFinder rules table models PD-T4-1 as a single-profile system requiring PD-T4-1__PD-T4-1."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| PD-T4-1__PD-T4-1                                 | PD-T4-1__PD-T4-1                                 | PD-T4-1                | Custom                  | 120    |",
            "notes": "The DefenseFinder HMM inventory records PD-T4-1__PD-T4-1 under the PD-T4-1 system namespace."
          }
        ],
        "attaches_to": [
          "causal_graphs#pd_t4_1_locus_restricts_t2_t4_and_t6"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-26"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-26T15:03:18Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted PD-T4-1 system as a DOI- and DefenseFinder-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v263.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-26T15:03:19Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed PD-T4-1 system canonical_examples and left them empty because the current sources support an E. coli accession-level experimental validation graph, a DefenseFinder system model, and a RefSeq Macrococcus armenti example, but not a direct native microbial isolate exemplar with experimentally verified endogenous PD-T4-1 activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000387",
    "label": "PD-T4-2 system",
    "definition": "A phage defense system in which an organism possesses a PD-T4-2 locus represented by DefenseFinder as a two-profile model requiring PD-T4-2__PD-T4-2_A and PD-T4-2__PD-T4-2_B, and experimentally linked to T2, T4, T6, T5, and SECphi27 protection when expressed in E. coli.",
    "definition_source": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-2.md",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "PD-T4-2",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-2.md"
      },
      {
        "synonym_text": "PD-T4-2__PD-T4-2_A",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "PD-T4-2__PD-T4-2_B",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/s41564-022-01219-4",
        "snippet": "Here we developed an experimental selection scheme agnostic to genomic context to identify defence systems in 71 diverse E. coli strains. Our results unveil 21 conserved defence systems, none of which were previously detected as enriched in defence islands.",
        "notes": "Vassallo et al. developed the agnostic E. coli pangenome selection that uncovered PD-T4-2 and related conserved phage-defense systems."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-2.md",
        "snippet": "The PD-T4-2 is composed of 2 proteins: PD-T4-2_A and PD-T4-2_B.",
        "notes": "The DefenseFinder wiki names PD-T4-2 as a two-protein system."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-2.md",
        "snippet": "The PD-T4-2 system in *Jeotgalibaca sp. PTS2502* (GCF_001975685.1, NZ_CP019433) is composed of 2 proteins PD-T4-2_A (WP_083686895.1) PD-T4-2_B (WP_076765701.1)",
        "notes": "The DefenseFinder wiki illustrates a predicted two-protein PD-T4-2 locus in RefSeq assembly GCF_001975685.1 on NZ_CP019433."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-2.md",
        "snippet": "Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0\n    Origin_0[Escherichia coli] --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> T2 & T4 & T6 & T5 & SECphi27",
        "notes": "The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-T4-2 source locus expressed in E. coli against T2, T4, T6, T5, and SECphi27."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-2.md",
        "snippet": "subgraph Title4[Protects against]\n        T2\n        T4\n        T6\n        T5\n        SECphi27",
        "notes": "The DefenseFinder experimental-validation diagram lists T2, T4, T6, T5, and SECphi27 in the PD-T4-2 protects-against subgraph."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "PD-T4-2 | 10\\.1101/2022\\.05\\.12\\.491691 | Mapping the landscape of anti-phage defense mechanisms in the E\\. coli pangenome",
        "notes": "The DefenseFinder article registry maps the named PD-T4-2 system to the Vassallo et al. E. coli pangenome phage-defense preprint."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "PD-T4-2\tPD-T4-2\t2\t2\tPD-T4-2__PD-T4-2_A, PD-T4-2__PD-T4-2_B\t\t\t",
        "notes": "The DefenseFinder rules table models PD-T4-2 as a two-profile system requiring PD-T4-2__PD-T4-2_A and PD-T4-2__PD-T4-2_B."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| PD-T4-2__PD-T4-2_A                               | PD-T4-2__PD-T4-2_A                               | PD-T4-2                | Custom                  | 150    |",
        "notes": "The DefenseFinder HMM inventory records PD-T4-2__PD-T4-2_A under the PD-T4-2 system namespace."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| PD-T4-2__PD-T4-2_B                               | PD-T4-2__PD-T4-2_B                               | PD-T4-2                | Custom                  | 20     |",
        "notes": "The DefenseFinder HMM inventory records PD-T4-2__PD-T4-2_B under the PD-T4-2 system namespace."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "pd_t4_2_locus_restricts_phages",
        "title": "PD-T4-2 loci restrict T2, T4, T6, T5, and SECphi27",
        "description": "Conservative system-level sketch linking possession of a PD-T4-2 locus to protection against T2, T4, T6, T5, and SECphi27.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures PD-T4-2 as a named DefenseFinder phage-defense system while leaving natural host breadth, the direct phage trigger, and the effector mechanism unresolved.",
        "nodes": [
          {
            "node_id": "pd_t4_2_locus",
            "label": "PD-T4-2 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A phage-defense locus represented by the PD-T4-2 DefenseFinder profiles."
          },
          {
            "node_id": "pd_t4_2_listed_phage_protection",
            "label": "T2, T4, T6, T5, and SECphi27 protection",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Protection against T2, T4, T6, T5, and SECphi27 by PD-T4-2."
          },
          {
            "node_id": "pd_t4_2_system_trait",
            "label": "PD-T4-2 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000387",
            "description": "Possession of a genome-encoded PD-T4-2 phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "pd_t4_2_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "pd_t4_2_listed_phage_protection",
            "description": "The DefenseFinder wiki links a PD-T4-2 locus from Vassallo et al. to protection against T2, T4, T6, T5, and SECphi27, and DefenseFinder models PD-T4-2 through two mandatory profiles.",
            "evidence": [
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-2.md",
                "snippet": "The PD-T4-2 is composed of 2 proteins: PD-T4-2_A and PD-T4-2_B.",
                "notes": "The DefenseFinder wiki names PD-T4-2 as a two-protein system."
              },
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-2.md",
                "snippet": "Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0\n    Origin_0[Escherichia coli] --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> T2 & T4 & T6 & T5 & SECphi27",
                "notes": "The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-T4-2 source locus expressed in E. coli against T2, T4, T6, T5, and SECphi27."
              },
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-2.md",
                "snippet": "subgraph Title4[Protects against]\n        T2\n        T4\n        T6\n        T5\n        SECphi27",
                "notes": "The DefenseFinder experimental-validation diagram lists T2, T4, T6, T5, and SECphi27 in the PD-T4-2 protects-against subgraph."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "PD-T4-2\tPD-T4-2\t2\t2\tPD-T4-2__PD-T4-2_A, PD-T4-2__PD-T4-2_B\t\t\t",
                "notes": "The DefenseFinder rules table models PD-T4-2 as a two-profile system requiring PD-T4-2__PD-T4-2_A and PD-T4-2__PD-T4-2_B."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| PD-T4-2__PD-T4-2_A                               | PD-T4-2__PD-T4-2_A                               | PD-T4-2                | Custom                  | 150    |",
                "notes": "The DefenseFinder HMM inventory records PD-T4-2__PD-T4-2_A under the PD-T4-2 system namespace."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| PD-T4-2__PD-T4-2_B                               | PD-T4-2__PD-T4-2_B                               | PD-T4-2                | Custom                  | 20     |",
                "notes": "The DefenseFinder HMM inventory records PD-T4-2__PD-T4-2_B under the PD-T4-2 system namespace."
              }
            ]
          },
          {
            "subject": "pd_t4_2_listed_phage_protection",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "pd_t4_2_system_trait",
            "description": "Protection against T2, T4, T6, T5, and SECphi27 realizes the PD-T4-2 system trait.",
            "evidence": [
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-2.md",
                "snippet": "Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0\n    Origin_0[Escherichia coli] --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> T2 & T4 & T6 & T5 & SECphi27",
                "notes": "The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-T4-2 source locus expressed in E. coli against T2, T4, T6, T5, and SECphi27."
              },
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-2.md",
                "snippet": "subgraph Title4[Protects against]\n        T2\n        T4\n        T6\n        T5\n        SECphi27",
                "notes": "The DefenseFinder experimental-validation diagram lists T2, T4, T6, T5, and SECphi27 in the PD-T4-2 protects-against subgraph."
              }
            ]
          },
          {
            "subject": "pd_t4_2_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "PD-T4-2 system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-022-01219-4",
                "snippet": "Here we developed an experimental selection scheme agnostic to genomic context to identify defence systems in 71 diverse E. coli strains. Our results unveil 21 conserved defence systems, none of which were previously detected as enriched in defence islands.",
                "notes": "Vassallo et al. developed the agnostic E. coli pangenome selection that uncovered PD-T4-2 and related conserved phage-defense systems."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "PD-T4-2 | 10\\.1101/2022\\.05\\.12\\.491691 | Mapping the landscape of anti-phage defense mechanisms in the E\\. coli pangenome",
                "notes": "The DefenseFinder article registry maps the named PD-T4-2 system to the Vassallo et al. E. coli pangenome phage-defense preprint."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "PD-T4-2\tPD-T4-2\t2\t2\tPD-T4-2__PD-T4-2_A, PD-T4-2__PD-T4-2_B\t\t\t",
                "notes": "The DefenseFinder rules table models PD-T4-2 as a two-profile system requiring PD-T4-2__PD-T4-2_A and PD-T4-2__PD-T4-2_B."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "pd-t4-2-mechanism-gap",
        "prompt": "Resolve PD-T4-2 natural host breadth, direct phage trigger, and effector mechanism before minting narrower PD-T4-2 mechanism traits.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Vassallo et al. support PD-T4-2 as one of the conserved systems from an E. coli pangenome phage-defense selection, the DefenseFinder wiki maps the source locus to protection against T2, T4, T6, T5, and SECphi27, and DefenseFinder represents the system with two mandatory profiles. Natural host breadth, the direct phage trigger, and effector logic remain unresolved.",
        "evidence": [
          {
            "reference": "DOI:10.1038/s41564-022-01219-4",
            "snippet": "Here we developed an experimental selection scheme agnostic to genomic context to identify defence systems in 71 diverse E. coli strains. Our results unveil 21 conserved defence systems, none of which were previously detected as enriched in defence islands.",
            "notes": "Vassallo et al. developed the agnostic E. coli pangenome selection that uncovered PD-T4-2 and related conserved phage-defense systems."
          },
          {
            "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-2.md",
            "snippet": "The PD-T4-2 is composed of 2 proteins: PD-T4-2_A and PD-T4-2_B.",
            "notes": "The DefenseFinder wiki names PD-T4-2 as a two-protein system."
          },
          {
            "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-2.md",
            "snippet": "Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0\n    Origin_0[Escherichia coli] --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> T2 & T4 & T6 & T5 & SECphi27",
            "notes": "The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-T4-2 source locus expressed in E. coli against T2, T4, T6, T5, and SECphi27."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "snippet": "PD-T4-2\tPD-T4-2\t2\t2\tPD-T4-2__PD-T4-2_A, PD-T4-2__PD-T4-2_B\t\t\t",
            "notes": "The DefenseFinder rules table models PD-T4-2 as a two-profile system requiring PD-T4-2__PD-T4-2_A and PD-T4-2__PD-T4-2_B."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| PD-T4-2__PD-T4-2_A                               | PD-T4-2__PD-T4-2_A                               | PD-T4-2                | Custom                  | 150    |",
            "notes": "The DefenseFinder HMM inventory records PD-T4-2__PD-T4-2_A under the PD-T4-2 system namespace."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| PD-T4-2__PD-T4-2_B                               | PD-T4-2__PD-T4-2_B                               | PD-T4-2                | Custom                  | 20     |",
            "notes": "The DefenseFinder HMM inventory records PD-T4-2__PD-T4-2_B under the PD-T4-2 system namespace."
          }
        ],
        "attaches_to": [
          "causal_graphs#pd_t4_2_locus_restricts_phages"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-26"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-26T15:35:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted PD-T4-2 system as a DOI- and DefenseFinder-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v264.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-26T15:35:01Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed PD-T4-2 system canonical_examples and left them empty because the current sources support an E. coli species-level experimental validation graph, a DefenseFinder system model, and a RefSeq Jeotgalibaca sp. PTS2502 example, but not a direct native microbial isolate exemplar with experimentally verified endogenous PD-T4-2 activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000388",
    "label": "PD-T4-3 system",
    "definition": "A phage defense system in which an organism possesses a PD-T4-3 locus represented by DefenseFinder as a single-profile model, PD-T4-3__PD-T4-3, and experimentally linked to T2, T4, and T6 protection when expressed in E. coli.",
    "definition_source": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-3.md",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "PD-T4-3",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-3.md"
      },
      {
        "synonym_text": "PD-T4-3__PD-T4-3",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/s41564-022-01219-4",
        "snippet": "Here we developed an experimental selection scheme agnostic to genomic context to identify defence systems in 71 diverse E. coli strains. Our results unveil 21 conserved defence systems, none of which were previously detected as enriched in defence islands.",
        "notes": "Vassallo et al. developed the agnostic E. coli pangenome selection that uncovered PD-T4-3 and related conserved phage-defense systems."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-3.md",
        "snippet": "PD-T4-3 is a single gene system isolated during an experimental screen of fosmids derived from 71 strains of diverse *E.coli*, and cloned back in a derivative of K12.",
        "notes": "The DefenseFinder wiki describes PD-T4-3 as a single-gene system isolated from the Vassallo et al. fosmid screen."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-3.md",
        "snippet": "The PD-T4-3 is composed of 1 protein: PD-T4-3.",
        "notes": "The DefenseFinder wiki names PD-T4-3 as a single-protein system."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-3.md",
        "snippet": "The PD-T4-3 system in *Morganella morganii* (GCF_018802485.1, NZ_CP064826) is composed of 1 protein: PD-T4-3 (WP_214179544.1)",
        "notes": "The DefenseFinder wiki illustrates a predicted PD-T4-3 locus in RefSeq assembly GCF_018802485.1 on NZ_CP064826."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-3.md",
        "snippet": "Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0\n    Origin_0[Escherichia coli \n<a href='https://ncbi.nlm.nih.gov/protein/RCO27183.1'>RCO27183.1</a>] --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> T2 & T4 & T6",
        "notes": "The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-T4-3 source locus expressed in E. coli against T2, T4, and T6."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-3.md",
        "snippet": "subgraph Title4[Protects against]\n        T2\n        T4\n        T6",
        "notes": "The DefenseFinder experimental-validation diagram lists T2, T4, and T6 in the PD-T4-3 protects-against subgraph."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "PD-T4-3 | 10\\.1101/2022\\.05\\.12\\.491691 | Mapping the landscape of anti-phage defense mechanisms in the E\\. coli pangenome",
        "notes": "The DefenseFinder article registry maps the named PD-T4-3 system to the Vassallo et al. E. coli pangenome phage-defense preprint."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "PD-T4-3\tPD-T4-3\t1\t1\tPD-T4-3__PD-T4-3\t\t\t",
        "notes": "The DefenseFinder rules table models PD-T4-3 as a single-profile system requiring PD-T4-3__PD-T4-3."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| PD-T4-3__PD-T4-3                                 | PD-T4-3__PD-T4-3                                 | PD-T4-3                | Custom                  | 150    |",
        "notes": "The DefenseFinder HMM inventory records PD-T4-3__PD-T4-3 under the PD-T4-3 system namespace."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "pd_t4_3_locus_restricts_t2_t4_and_t6",
        "title": "PD-T4-3 loci restrict T2, T4, and T6",
        "description": "Conservative system-level sketch linking possession of a PD-T4-3 locus to protection against T2, T4, and T6.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures PD-T4-3 as a named DefenseFinder phage-defense system while leaving natural host breadth, the direct phage trigger, and the effector mechanism unresolved.",
        "nodes": [
          {
            "node_id": "pd_t4_3_locus",
            "label": "PD-T4-3 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A phage-defense locus represented by the PD-T4-3 DefenseFinder profile."
          },
          {
            "node_id": "pd_t4_3_listed_phage_protection",
            "label": "T2, T4, and T6 protection",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Protection against T2, T4, and T6 by PD-T4-3."
          },
          {
            "node_id": "pd_t4_3_system_trait",
            "label": "PD-T4-3 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000388",
            "description": "Possession of a genome-encoded PD-T4-3 phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "pd_t4_3_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "pd_t4_3_listed_phage_protection",
            "description": "The DefenseFinder wiki links a PD-T4-3 locus from Vassallo et al. to protection against T2, T4, and T6, and DefenseFinder models PD-T4-3 through one mandatory profile.",
            "evidence": [
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-3.md",
                "snippet": "PD-T4-3 is a single gene system isolated during an experimental screen of fosmids derived from 71 strains of diverse *E.coli*, and cloned back in a derivative of K12.",
                "notes": "The DefenseFinder wiki describes PD-T4-3 as a single-gene system isolated from the Vassallo et al. fosmid screen."
              },
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-3.md",
                "snippet": "The PD-T4-3 is composed of 1 protein: PD-T4-3.",
                "notes": "The DefenseFinder wiki names PD-T4-3 as a single-protein system."
              },
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-3.md",
                "snippet": "Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0\n    Origin_0[Escherichia coli \n<a href='https://ncbi.nlm.nih.gov/protein/RCO27183.1'>RCO27183.1</a>] --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> T2 & T4 & T6",
                "notes": "The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-T4-3 source locus expressed in E. coli against T2, T4, and T6."
              },
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-3.md",
                "snippet": "subgraph Title4[Protects against]\n        T2\n        T4\n        T6",
                "notes": "The DefenseFinder experimental-validation diagram lists T2, T4, and T6 in the PD-T4-3 protects-against subgraph."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "PD-T4-3\tPD-T4-3\t1\t1\tPD-T4-3__PD-T4-3\t\t\t",
                "notes": "The DefenseFinder rules table models PD-T4-3 as a single-profile system requiring PD-T4-3__PD-T4-3."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| PD-T4-3__PD-T4-3                                 | PD-T4-3__PD-T4-3                                 | PD-T4-3                | Custom                  | 150    |",
                "notes": "The DefenseFinder HMM inventory records PD-T4-3__PD-T4-3 under the PD-T4-3 system namespace."
              }
            ]
          },
          {
            "subject": "pd_t4_3_listed_phage_protection",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "pd_t4_3_system_trait",
            "description": "Protection against T2, T4, and T6 realizes the PD-T4-3 system trait.",
            "evidence": [
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-3.md",
                "snippet": "Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0\n    Origin_0[Escherichia coli \n<a href='https://ncbi.nlm.nih.gov/protein/RCO27183.1'>RCO27183.1</a>] --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> T2 & T4 & T6",
                "notes": "The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-T4-3 source locus expressed in E. coli against T2, T4, and T6."
              },
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-3.md",
                "snippet": "subgraph Title4[Protects against]\n        T2\n        T4\n        T6",
                "notes": "The DefenseFinder experimental-validation diagram lists T2, T4, and T6 in the PD-T4-3 protects-against subgraph."
              }
            ]
          },
          {
            "subject": "pd_t4_3_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "PD-T4-3 system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-022-01219-4",
                "snippet": "Here we developed an experimental selection scheme agnostic to genomic context to identify defence systems in 71 diverse E. coli strains. Our results unveil 21 conserved defence systems, none of which were previously detected as enriched in defence islands.",
                "notes": "Vassallo et al. developed the agnostic E. coli pangenome selection that uncovered PD-T4-3 and related conserved phage-defense systems."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "PD-T4-3 | 10\\.1101/2022\\.05\\.12\\.491691 | Mapping the landscape of anti-phage defense mechanisms in the E\\. coli pangenome",
                "notes": "The DefenseFinder article registry maps the named PD-T4-3 system to the Vassallo et al. E. coli pangenome phage-defense preprint."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "PD-T4-3\tPD-T4-3\t1\t1\tPD-T4-3__PD-T4-3\t\t\t",
                "notes": "The DefenseFinder rules table models PD-T4-3 as a single-profile system requiring PD-T4-3__PD-T4-3."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "pd-t4-3-mechanism-gap",
        "prompt": "Resolve PD-T4-3 natural host breadth, direct phage trigger, and effector mechanism before minting narrower PD-T4-3 mechanism traits.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Vassallo et al. support PD-T4-3 as one of the conserved systems from an E. coli pangenome phage-defense selection, the DefenseFinder wiki maps the source locus to protection against T2, T4, and T6, and DefenseFinder represents the system with one mandatory profile. Natural host breadth, the direct phage trigger, and effector logic remain unresolved.",
        "evidence": [
          {
            "reference": "DOI:10.1038/s41564-022-01219-4",
            "snippet": "Here we developed an experimental selection scheme agnostic to genomic context to identify defence systems in 71 diverse E. coli strains. Our results unveil 21 conserved defence systems, none of which were previously detected as enriched in defence islands.",
            "notes": "Vassallo et al. developed the agnostic E. coli pangenome selection that uncovered PD-T4-3 and related conserved phage-defense systems."
          },
          {
            "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-3.md",
            "snippet": "PD-T4-3 is a single gene system isolated during an experimental screen of fosmids derived from 71 strains of diverse *E.coli*, and cloned back in a derivative of K12.",
            "notes": "The DefenseFinder wiki describes PD-T4-3 as a single-gene system isolated from the Vassallo et al. fosmid screen."
          },
          {
            "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-3.md",
            "snippet": "The PD-T4-3 is composed of 1 protein: PD-T4-3.",
            "notes": "The DefenseFinder wiki names PD-T4-3 as a single-protein system."
          },
          {
            "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-3.md",
            "snippet": "Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0\n    Origin_0[Escherichia coli \n<a href='https://ncbi.nlm.nih.gov/protein/RCO27183.1'>RCO27183.1</a>] --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> T2 & T4 & T6",
            "notes": "The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-T4-3 source locus expressed in E. coli against T2, T4, and T6."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "snippet": "PD-T4-3\tPD-T4-3\t1\t1\tPD-T4-3__PD-T4-3\t\t\t",
            "notes": "The DefenseFinder rules table models PD-T4-3 as a single-profile system requiring PD-T4-3__PD-T4-3."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| PD-T4-3__PD-T4-3                                 | PD-T4-3__PD-T4-3                                 | PD-T4-3                | Custom                  | 150    |",
            "notes": "The DefenseFinder HMM inventory records PD-T4-3__PD-T4-3 under the PD-T4-3 system namespace."
          }
        ],
        "attaches_to": [
          "causal_graphs#pd_t4_3_locus_restricts_t2_t4_and_t6"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-26"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-26T16:05:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted PD-T4-3 system as a DOI- and DefenseFinder-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v265.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-26T16:05:01Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed PD-T4-3 system canonical_examples and left them empty because the current sources support an E. coli accession-level experimental validation graph, a DefenseFinder system model, and a RefSeq Morganella morganii example, but not a direct native microbial isolate exemplar with experimentally verified endogenous PD-T4-3 activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000389",
    "label": "PD-T4-4 system",
    "definition": "A phage defense system in which an organism possesses a PD-T4-4 locus represented by DefenseFinder as a two-profile model requiring PD-T4-4__PD-T4-4_A and PD-T4-4__PD-T4-4_B, and experimentally linked to T2, T4, T6, and SECphi17 protection when expressed in E. coli.",
    "definition_source": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-4.md",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "PD-T4-4",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-4.md"
      },
      {
        "synonym_text": "PD-T4-4__PD-T4-4_A",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "PD-T4-4__PD-T4-4_B",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/s41564-022-01219-4",
        "snippet": "Here we developed an experimental selection scheme agnostic to genomic context to identify defence systems in 71 diverse E. coli strains. Our results unveil 21 conserved defence systems, none of which were previously detected as enriched in defence islands.",
        "notes": "Vassallo et al. developed the agnostic E. coli pangenome selection that uncovered PD-T4-4 and related conserved phage-defense systems."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-4.md",
        "snippet": "PD-T4-4 is a defense system composed of two proteins, a P-loop NTPase and a nuclease, that is most likely protecting the bacterial population through abortive infection. It was identified from an ICE in an *E. coli* genome.",
        "notes": "The DefenseFinder wiki describes PD-T4-4 as a two-protein system from an E. coli integrative and conjugative element."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-4.md",
        "snippet": "The PD-T4-4 is composed of 2 proteins: PD-T4-4_A and PD-T4-4_B.",
        "notes": "The DefenseFinder wiki names PD-T4-4 as a two-protein system with PD-T4-4_A and PD-T4-4_B components."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-4.md",
        "snippet": "The PD-T4-4 system in *Thiothrix subterranea* (GCF_016772315.1, NZ_CP053482) is composed of 2 proteins PD-T4-4_A (WP_202716711.1) PD-T4-4_B (WP_202716712.1)",
        "notes": "The DefenseFinder wiki illustrates a predicted two-protein PD-T4-4 locus in RefSeq assembly GCF_016772315.1 on NZ_CP053482."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-4.md",
        "snippet": "Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0\n    Origin_0[Escherichia coli \n<a href='https://ncbi.nlm.nih.gov/protein/RCO57999.1'>RCO57999.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/RCO57988.1'>RCO57988.1</a>] --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> T2 & T4 & T6 & SECphi17",
        "notes": "The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-T4-4 source locus expressed in E. coli against T2, T4, T6, and SECphi17."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-4.md",
        "snippet": "subgraph Title4[Protects against]\n        T2\n        T4\n        T6\n        SECphi17",
        "notes": "The DefenseFinder experimental-validation diagram lists T2, T4, T6, and SECphi17 in the PD-T4-4 protects-against subgraph."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "PD-T4-4 | 10\\.1101/2022\\.05\\.12\\.491691 | Mapping the landscape of anti-phage defense mechanisms in the E\\. coli pangenome",
        "notes": "The DefenseFinder article registry maps the named PD-T4-4 system to the Vassallo et al. E. coli pangenome phage-defense preprint."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "PD-T4-4\tPD-T4-4\t2\t2\tPD-T4-4__PD-T4-4_A, PD-T4-4__PD-T4-4_B\t\t\t",
        "notes": "The DefenseFinder rules table models PD-T4-4 as a two-profile system requiring PD-T4-4__PD-T4-4_A and PD-T4-4__PD-T4-4_B."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| PD-T4-4__PD-T4-4_A                               | PD-T4-4__PD-T4-4_A                               | PD-T4-4                | Custom                  | 75     |",
        "notes": "The DefenseFinder HMM inventory records PD-T4-4__PD-T4-4_A under the PD-T4-4 system namespace."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| PD-T4-4__PD-T4-4_B                               | PD-T4-4__PD-T4-4_B                               | PD-T4-4                | Custom                  | 25     |",
        "notes": "The DefenseFinder HMM inventory records PD-T4-4__PD-T4-4_B under the PD-T4-4 system namespace."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "pd_t4_4_locus_restricts_t2_t4_t6_and_secphi17",
        "title": "PD-T4-4 loci restrict T2, T4, T6, and SECphi17",
        "description": "Conservative system-level sketch linking possession of a PD-T4-4 locus to protection against T2, T4, T6, and SECphi17.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures PD-T4-4 as a named DefenseFinder phage-defense system while leaving natural host breadth, the direct phage trigger, and the hinted abortive-infection effector mechanism unmodeled until direct mechanism evidence is available.",
        "nodes": [
          {
            "node_id": "pd_t4_4_locus",
            "label": "PD-T4-4 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A phage-defense locus represented by the two PD-T4-4 DefenseFinder profiles."
          },
          {
            "node_id": "pd_t4_4_listed_phage_protection",
            "label": "T2, T4, T6, and SECphi17 protection",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Protection against T2, T4, T6, and SECphi17 by PD-T4-4."
          },
          {
            "node_id": "pd_t4_4_system_trait",
            "label": "PD-T4-4 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000389",
            "description": "Possession of a genome-encoded PD-T4-4 phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "pd_t4_4_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "pd_t4_4_listed_phage_protection",
            "description": "The DefenseFinder wiki links a PD-T4-4 locus from Vassallo et al. to protection against T2, T4, T6, and SECphi17, and DefenseFinder models PD-T4-4 through two mandatory profiles.",
            "evidence": [
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-4.md",
                "snippet": "PD-T4-4 is a defense system composed of two proteins, a P-loop NTPase and a nuclease, that is most likely protecting the bacterial population through abortive infection. It was identified from an ICE in an *E. coli* genome.",
                "notes": "The DefenseFinder wiki describes PD-T4-4 as a two-protein system from an E. coli integrative and conjugative element."
              },
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-4.md",
                "snippet": "The PD-T4-4 is composed of 2 proteins: PD-T4-4_A and PD-T4-4_B.",
                "notes": "The DefenseFinder wiki names PD-T4-4 as a two-protein system with PD-T4-4_A and PD-T4-4_B components."
              },
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-4.md",
                "snippet": "Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0\n    Origin_0[Escherichia coli \n<a href='https://ncbi.nlm.nih.gov/protein/RCO57999.1'>RCO57999.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/RCO57988.1'>RCO57988.1</a>] --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> T2 & T4 & T6 & SECphi17",
                "notes": "The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-T4-4 source locus expressed in E. coli against T2, T4, T6, and SECphi17."
              },
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-4.md",
                "snippet": "subgraph Title4[Protects against]\n        T2\n        T4\n        T6\n        SECphi17",
                "notes": "The DefenseFinder experimental-validation diagram lists T2, T4, T6, and SECphi17 in the PD-T4-4 protects-against subgraph."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "PD-T4-4\tPD-T4-4\t2\t2\tPD-T4-4__PD-T4-4_A, PD-T4-4__PD-T4-4_B\t\t\t",
                "notes": "The DefenseFinder rules table models PD-T4-4 as a two-profile system requiring PD-T4-4__PD-T4-4_A and PD-T4-4__PD-T4-4_B."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| PD-T4-4__PD-T4-4_A                               | PD-T4-4__PD-T4-4_A                               | PD-T4-4                | Custom                  | 75     |",
                "notes": "The DefenseFinder HMM inventory records PD-T4-4__PD-T4-4_A under the PD-T4-4 system namespace."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| PD-T4-4__PD-T4-4_B                               | PD-T4-4__PD-T4-4_B                               | PD-T4-4                | Custom                  | 25     |",
                "notes": "The DefenseFinder HMM inventory records PD-T4-4__PD-T4-4_B under the PD-T4-4 system namespace."
              }
            ]
          },
          {
            "subject": "pd_t4_4_listed_phage_protection",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "pd_t4_4_system_trait",
            "description": "Protection against T2, T4, T6, and SECphi17 realizes the PD-T4-4 system trait.",
            "evidence": [
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-4.md",
                "snippet": "Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0\n    Origin_0[Escherichia coli \n<a href='https://ncbi.nlm.nih.gov/protein/RCO57999.1'>RCO57999.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/RCO57988.1'>RCO57988.1</a>] --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> T2 & T4 & T6 & SECphi17",
                "notes": "The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-T4-4 source locus expressed in E. coli against T2, T4, T6, and SECphi17."
              },
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-4.md",
                "snippet": "subgraph Title4[Protects against]\n        T2\n        T4\n        T6\n        SECphi17",
                "notes": "The DefenseFinder experimental-validation diagram lists T2, T4, T6, and SECphi17 in the PD-T4-4 protects-against subgraph."
              }
            ]
          },
          {
            "subject": "pd_t4_4_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "PD-T4-4 system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-022-01219-4",
                "snippet": "Here we developed an experimental selection scheme agnostic to genomic context to identify defence systems in 71 diverse E. coli strains. Our results unveil 21 conserved defence systems, none of which were previously detected as enriched in defence islands.",
                "notes": "Vassallo et al. developed the agnostic E. coli pangenome selection that uncovered PD-T4-4 and related conserved phage-defense systems."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "PD-T4-4 | 10\\.1101/2022\\.05\\.12\\.491691 | Mapping the landscape of anti-phage defense mechanisms in the E\\. coli pangenome",
                "notes": "The DefenseFinder article registry maps the named PD-T4-4 system to the Vassallo et al. E. coli pangenome phage-defense preprint."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "PD-T4-4\tPD-T4-4\t2\t2\tPD-T4-4__PD-T4-4_A, PD-T4-4__PD-T4-4_B\t\t\t",
                "notes": "The DefenseFinder rules table models PD-T4-4 as a two-profile system requiring PD-T4-4__PD-T4-4_A and PD-T4-4__PD-T4-4_B."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "pd-t4-4-mechanism-gap",
        "prompt": "Resolve PD-T4-4 natural host breadth, direct phage trigger, and effector mechanism before minting narrower PD-T4-4 mechanism traits.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Vassallo et al. support PD-T4-4 as one of the conserved systems from an E. coli pangenome phage-defense selection, the DefenseFinder wiki maps the source locus to protection against T2, T4, T6, and SECphi17, and DefenseFinder represents the system with two mandatory profiles. Natural host breadth, the direct phage trigger, and direct effector logic remain unresolved, so the likely abortive-infection hypothesis is left unmodeled.",
        "evidence": [
          {
            "reference": "DOI:10.1038/s41564-022-01219-4",
            "snippet": "Here we developed an experimental selection scheme agnostic to genomic context to identify defence systems in 71 diverse E. coli strains. Our results unveil 21 conserved defence systems, none of which were previously detected as enriched in defence islands.",
            "notes": "Vassallo et al. developed the agnostic E. coli pangenome selection that uncovered PD-T4-4 and related conserved phage-defense systems."
          },
          {
            "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-4.md",
            "snippet": "PD-T4-4 is a defense system composed of two proteins, a P-loop NTPase and a nuclease, that is most likely protecting the bacterial population through abortive infection. It was identified from an ICE in an *E. coli* genome.",
            "notes": "The DefenseFinder wiki describes PD-T4-4 as a two-protein system from an E. coli integrative and conjugative element."
          },
          {
            "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-4.md",
            "snippet": "The PD-T4-4 is composed of 2 proteins: PD-T4-4_A and PD-T4-4_B.",
            "notes": "The DefenseFinder wiki names PD-T4-4 as a two-protein system with PD-T4-4_A and PD-T4-4_B components."
          },
          {
            "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-4.md",
            "snippet": "Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0\n    Origin_0[Escherichia coli \n<a href='https://ncbi.nlm.nih.gov/protein/RCO57999.1'>RCO57999.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/RCO57988.1'>RCO57988.1</a>] --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> T2 & T4 & T6 & SECphi17",
            "notes": "The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-T4-4 source locus expressed in E. coli against T2, T4, T6, and SECphi17."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "snippet": "PD-T4-4\tPD-T4-4\t2\t2\tPD-T4-4__PD-T4-4_A, PD-T4-4__PD-T4-4_B\t\t\t",
            "notes": "The DefenseFinder rules table models PD-T4-4 as a two-profile system requiring PD-T4-4__PD-T4-4_A and PD-T4-4__PD-T4-4_B."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| PD-T4-4__PD-T4-4_A                               | PD-T4-4__PD-T4-4_A                               | PD-T4-4                | Custom                  | 75     |",
            "notes": "The DefenseFinder HMM inventory records PD-T4-4__PD-T4-4_A under the PD-T4-4 system namespace."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| PD-T4-4__PD-T4-4_B                               | PD-T4-4__PD-T4-4_B                               | PD-T4-4                | Custom                  | 25     |",
            "notes": "The DefenseFinder HMM inventory records PD-T4-4__PD-T4-4_B under the PD-T4-4 system namespace."
          }
        ],
        "attaches_to": [
          "causal_graphs#pd_t4_4_locus_restricts_t2_t4_t6_and_secphi17"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-26"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-26T16:51:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted PD-T4-4 system as a DOI- and DefenseFinder-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v266.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-26T16:51:01Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed PD-T4-4 system canonical_examples and left them empty because the current sources support an E. coli accession-level experimental validation graph, a DefenseFinder system model, and a RefSeq Thiothrix subterranea example, but not a direct native microbial isolate exemplar with experimentally verified endogenous PD-T4-4 activity. No paid research was used.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-26T17:24:43Z",
        "curator": "codex",
        "action": "ADDRESS_SCOPE_NOTE_REVIEW",
        "changes": "Clarified after Claude Code Review issue 1288 that the DefenseFinder wiki names abortive infection as the likely PD-T4-4 population-level protection route, but the graph leaves that hypothesis unmodeled until direct mechanism evidence is available.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000390",
    "label": "PD-T4-5 system",
    "definition": "A phage defense system in which an organism possesses a PD-T4-5 locus represented by DefenseFinder as a single-profile model, PD-T4-5__PD-T4-5, and experimentally linked to T4, T6, LambdaVir, and T5 protection when expressed in E. coli.",
    "definition_source": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-5.md",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "PD-T4-5",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-5.md"
      },
      {
        "synonym_text": "PD-T4-5__PD-T4-5",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/s41564-022-01219-4",
        "snippet": "Here we developed an experimental selection scheme agnostic to genomic context to identify defence systems in 71 diverse E. coli strains. Our results unveil 21 conserved defence systems, none of which were previously detected as enriched in defence islands.",
        "notes": "Vassallo et al. developed the agnostic E. coli pangenome selection that uncovered PD-T4-5 and related conserved phage-defense systems."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-5.md",
        "snippet": "The PD-T4-5 is composed of 1 protein: PD-T4-5.",
        "notes": "The DefenseFinder wiki names PD-T4-5 as a single-protein system."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-5.md",
        "snippet": "The PD-T4-5 system in *Grimontia hollisae* (GCF_009665295.1, NZ_CP035690) is composed of 1 protein: PD-T4-5 (WP_154124046.1)",
        "notes": "The DefenseFinder wiki illustrates a predicted PD-T4-5 locus in RefSeq assembly GCF_009665295.1 on NZ_CP035690."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-5.md",
        "snippet": "Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0\n    Origin_0[Escherichia coli \n<a href='https://ncbi.nlm.nih.gov/protein/RCQ99930.1'>RCQ99930.1</a>] --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> T4 & T6 & LambdaVir & T5",
        "notes": "The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-T4-5 source locus expressed in E. coli against T4, T6, LambdaVir, and T5."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-5.md",
        "snippet": "subgraph Title4[Protects against]\n        T4\n        T6\n        LambdaVir\n        T5",
        "notes": "The DefenseFinder experimental-validation diagram lists T4, T6, LambdaVir, and T5 in the PD-T4-5 protects-against subgraph."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "PD-T4-5 | 10\\.1101/2022\\.05\\.12\\.491691 | Mapping the landscape of anti-phage defense mechanisms in the E\\. coli pangenome",
        "notes": "The DefenseFinder article registry maps the named PD-T4-5 system to the Vassallo et al. E. coli pangenome phage-defense preprint."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "PD-T4-5\tPD-T4-5\t1\t1\tPD-T4-5__PD-T4-5\t\t\t",
        "notes": "The DefenseFinder rules table models PD-T4-5 as a single-profile system requiring PD-T4-5__PD-T4-5."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| PD-T4-5__PD-T4-5                                 | PD-T4-5__PD-T4-5                                 | PD-T4-5                | Custom                  | 120    |",
        "notes": "The DefenseFinder HMM inventory records PD-T4-5__PD-T4-5 under the PD-T4-5 system namespace."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "pd_t4_5_locus_restricts_t4_t6_lambdavir_and_t5",
        "title": "PD-T4-5 loci restrict T4, T6, LambdaVir, and T5",
        "description": "Conservative system-level sketch linking possession of a PD-T4-5 locus to protection against T4, T6, LambdaVir, and T5.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures PD-T4-5 as a named DefenseFinder phage-defense system while leaving natural host breadth, the direct phage trigger, and the effector mechanism unresolved.",
        "nodes": [
          {
            "node_id": "pd_t4_5_locus",
            "label": "PD-T4-5 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A phage-defense locus represented by the PD-T4-5 DefenseFinder profile."
          },
          {
            "node_id": "pd_t4_5_listed_phage_protection",
            "label": "T4, T6, LambdaVir, and T5 protection",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Protection against T4, T6, LambdaVir, and T5 by PD-T4-5."
          },
          {
            "node_id": "pd_t4_5_system_trait",
            "label": "PD-T4-5 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000390",
            "description": "Possession of a genome-encoded PD-T4-5 phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "pd_t4_5_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "pd_t4_5_listed_phage_protection",
            "description": "The DefenseFinder wiki links a PD-T4-5 locus from Vassallo et al. to protection against T4, T6, LambdaVir, and T5, and DefenseFinder models PD-T4-5 through one mandatory profile.",
            "evidence": [
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-5.md",
                "snippet": "The PD-T4-5 is composed of 1 protein: PD-T4-5.",
                "notes": "The DefenseFinder wiki names PD-T4-5 as a single-protein system."
              },
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-5.md",
                "snippet": "Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0\n    Origin_0[Escherichia coli \n<a href='https://ncbi.nlm.nih.gov/protein/RCQ99930.1'>RCQ99930.1</a>] --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> T4 & T6 & LambdaVir & T5",
                "notes": "The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-T4-5 source locus expressed in E. coli against T4, T6, LambdaVir, and T5."
              },
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-5.md",
                "snippet": "subgraph Title4[Protects against]\n        T4\n        T6\n        LambdaVir\n        T5",
                "notes": "The DefenseFinder experimental-validation diagram lists T4, T6, LambdaVir, and T5 in the PD-T4-5 protects-against subgraph."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "PD-T4-5\tPD-T4-5\t1\t1\tPD-T4-5__PD-T4-5\t\t\t",
                "notes": "The DefenseFinder rules table models PD-T4-5 as a single-profile system requiring PD-T4-5__PD-T4-5."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| PD-T4-5__PD-T4-5                                 | PD-T4-5__PD-T4-5                                 | PD-T4-5                | Custom                  | 120    |",
                "notes": "The DefenseFinder HMM inventory records PD-T4-5__PD-T4-5 under the PD-T4-5 system namespace."
              }
            ]
          },
          {
            "subject": "pd_t4_5_listed_phage_protection",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "pd_t4_5_system_trait",
            "description": "Protection against T4, T6, LambdaVir, and T5 realizes the PD-T4-5 system trait.",
            "evidence": [
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-5.md",
                "snippet": "Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0\n    Origin_0[Escherichia coli \n<a href='https://ncbi.nlm.nih.gov/protein/RCQ99930.1'>RCQ99930.1</a>] --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> T4 & T6 & LambdaVir & T5",
                "notes": "The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-T4-5 source locus expressed in E. coli against T4, T6, LambdaVir, and T5."
              },
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-5.md",
                "snippet": "subgraph Title4[Protects against]\n        T4\n        T6\n        LambdaVir\n        T5",
                "notes": "The DefenseFinder experimental-validation diagram lists T4, T6, LambdaVir, and T5 in the PD-T4-5 protects-against subgraph."
              }
            ]
          },
          {
            "subject": "pd_t4_5_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "PD-T4-5 system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-022-01219-4",
                "snippet": "Here we developed an experimental selection scheme agnostic to genomic context to identify defence systems in 71 diverse E. coli strains. Our results unveil 21 conserved defence systems, none of which were previously detected as enriched in defence islands.",
                "notes": "Vassallo et al. developed the agnostic E. coli pangenome selection that uncovered PD-T4-5 and related conserved phage-defense systems."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "PD-T4-5 | 10\\.1101/2022\\.05\\.12\\.491691 | Mapping the landscape of anti-phage defense mechanisms in the E\\. coli pangenome",
                "notes": "The DefenseFinder article registry maps the named PD-T4-5 system to the Vassallo et al. E. coli pangenome phage-defense preprint."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "PD-T4-5\tPD-T4-5\t1\t1\tPD-T4-5__PD-T4-5\t\t\t",
                "notes": "The DefenseFinder rules table models PD-T4-5 as a single-profile system requiring PD-T4-5__PD-T4-5."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "pd-t4-5-mechanism-gap",
        "prompt": "Resolve PD-T4-5 natural host breadth, direct phage trigger, and effector mechanism before minting narrower PD-T4-5 mechanism traits.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Vassallo et al. support PD-T4-5 as one of the conserved systems from an E. coli pangenome phage-defense selection, the DefenseFinder wiki maps the source locus to protection against T4, T6, LambdaVir, and T5, and DefenseFinder represents the system with one mandatory profile. Natural host breadth, the direct phage trigger, and effector logic remain unresolved.",
        "evidence": [
          {
            "reference": "DOI:10.1038/s41564-022-01219-4",
            "snippet": "Here we developed an experimental selection scheme agnostic to genomic context to identify defence systems in 71 diverse E. coli strains. Our results unveil 21 conserved defence systems, none of which were previously detected as enriched in defence islands.",
            "notes": "Vassallo et al. developed the agnostic E. coli pangenome selection that uncovered PD-T4-5 and related conserved phage-defense systems."
          },
          {
            "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-5.md",
            "snippet": "The PD-T4-5 is composed of 1 protein: PD-T4-5.",
            "notes": "The DefenseFinder wiki names PD-T4-5 as a single-protein system."
          },
          {
            "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-5.md",
            "snippet": "Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0\n    Origin_0[Escherichia coli \n<a href='https://ncbi.nlm.nih.gov/protein/RCQ99930.1'>RCQ99930.1</a>] --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> T4 & T6 & LambdaVir & T5",
            "notes": "The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-T4-5 source locus expressed in E. coli against T4, T6, LambdaVir, and T5."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "snippet": "PD-T4-5\tPD-T4-5\t1\t1\tPD-T4-5__PD-T4-5\t\t\t",
            "notes": "The DefenseFinder rules table models PD-T4-5 as a single-profile system requiring PD-T4-5__PD-T4-5."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| PD-T4-5__PD-T4-5                                 | PD-T4-5__PD-T4-5                                 | PD-T4-5                | Custom                  | 120    |",
            "notes": "The DefenseFinder HMM inventory records PD-T4-5__PD-T4-5 under the PD-T4-5 system namespace."
          }
        ],
        "attaches_to": [
          "causal_graphs#pd_t4_5_locus_restricts_t4_t6_lambdavir_and_t5"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-26"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-26T17:56:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted PD-T4-5 system as a DOI- and DefenseFinder-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v267.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-26T17:56:01Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed PD-T4-5 system canonical_examples and left them empty because the current sources support an E. coli accession-level experimental validation graph, a DefenseFinder system model, and a RefSeq Grimontia hollisae example, but not a direct native microbial isolate exemplar with experimentally verified endogenous PD-T4-5 activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000391",
    "label": "PD-T4-6 system",
    "definition": "A phage defense system in which an organism possesses a PD-T4-6 locus represented by DefenseFinder as a single-profile model, PD-T4-6__PD-T4-6, and experimentally linked to T2, T4, and T6 protection when expressed in E. coli.",
    "definition_source": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-6.md",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "PD-T4-6",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-6.md"
      },
      {
        "synonym_text": "PD-T4-6__PD-T4-6",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/s41564-022-01219-4",
        "snippet": "Here we developed an experimental selection scheme agnostic to genomic context to identify defence systems in 71 diverse E. coli strains. Our results unveil 21 conserved defence systems, none of which were previously detected as enriched in defence islands.",
        "notes": "Vassallo et al. developed the agnostic E. coli pangenome selection that uncovered PD-T4-6 and related conserved phage-defense systems."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-6.md",
        "snippet": "The PD-T4-6 is composed of 1 protein: PD-T4-6.",
        "notes": "The DefenseFinder wiki names PD-T4-6 as a single-protein system."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-6.md",
        "snippet": "The PD-T4-6 system in *Streptococcus ruminantium* (GCF_021654555.1, NZ_AP025333) is composed of 1 protein: PD-T4-6 (WP_024532776.1)",
        "notes": "The DefenseFinder wiki illustrates a predicted PD-T4-6 locus in RefSeq assembly GCF_021654555.1 on NZ_AP025333."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-6.md",
        "snippet": "Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0\n    Origin_0[Escherichia coli \n<a href='https://ncbi.nlm.nih.gov/protein/RRM76169.1'>RRM76169.1</a>] --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> T2 & T4 & T6",
        "notes": "The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-T4-6 source locus expressed in E. coli against T2, T4, and T6."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-6.md",
        "snippet": "subgraph Title4[Protects against]\n        T2\n        T4\n        T6",
        "notes": "The DefenseFinder experimental-validation diagram lists T2, T4, and T6 in the PD-T4-6 protects-against subgraph."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "PD-T4-6 | 10\\.1101/2022\\.05\\.12\\.491691 | Mapping the landscape of anti-phage defense mechanisms in the E\\. coli pangenome",
        "notes": "The DefenseFinder article registry maps the named PD-T4-6 system to the Vassallo et al. E. coli pangenome phage-defense preprint."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "PD-T4-6\tPD-T4-6\t1\t1\tPD-T4-6__PD-T4-6\t\t\t",
        "notes": "The DefenseFinder rules table models PD-T4-6 as a single-profile system requiring PD-T4-6__PD-T4-6."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| PD-T4-6__PD-T4-6                                 | PD-T4-6__PD-T4-6                                 | PD-T4-6                | Custom                  | 350    |",
        "notes": "The DefenseFinder HMM inventory records PD-T4-6__PD-T4-6 under the PD-T4-6 system namespace."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "pd_t4_6_locus_restricts_t2_t4_and_t6",
        "title": "PD-T4-6 loci restrict T2, T4, and T6",
        "description": "Conservative system-level sketch linking possession of a PD-T4-6 locus to protection against T2, T4, and T6.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures PD-T4-6 as a named DefenseFinder phage-defense system while leaving natural host breadth, the direct phage trigger, and the effector mechanism unresolved.",
        "nodes": [
          {
            "node_id": "pd_t4_6_locus",
            "label": "PD-T4-6 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A phage-defense locus represented by the PD-T4-6 DefenseFinder profile."
          },
          {
            "node_id": "pd_t4_6_listed_phage_protection",
            "label": "T2, T4, and T6 protection",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Protection against T2, T4, and T6 by PD-T4-6."
          },
          {
            "node_id": "pd_t4_6_system_trait",
            "label": "PD-T4-6 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000391",
            "description": "Possession of a genome-encoded PD-T4-6 phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "pd_t4_6_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "pd_t4_6_listed_phage_protection",
            "description": "The DefenseFinder wiki links a PD-T4-6 locus from Vassallo et al. to protection against T2, T4, and T6, and DefenseFinder models PD-T4-6 through one mandatory profile.",
            "evidence": [
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-6.md",
                "snippet": "The PD-T4-6 is composed of 1 protein: PD-T4-6.",
                "notes": "The DefenseFinder wiki names PD-T4-6 as a single-protein system."
              },
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-6.md",
                "snippet": "Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0\n    Origin_0[Escherichia coli \n<a href='https://ncbi.nlm.nih.gov/protein/RRM76169.1'>RRM76169.1</a>] --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> T2 & T4 & T6",
                "notes": "The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-T4-6 source locus expressed in E. coli against T2, T4, and T6."
              },
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-6.md",
                "snippet": "subgraph Title4[Protects against]\n        T2\n        T4\n        T6",
                "notes": "The DefenseFinder experimental-validation diagram lists T2, T4, and T6 in the PD-T4-6 protects-against subgraph."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "PD-T4-6\tPD-T4-6\t1\t1\tPD-T4-6__PD-T4-6\t\t\t",
                "notes": "The DefenseFinder rules table models PD-T4-6 as a single-profile system requiring PD-T4-6__PD-T4-6."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| PD-T4-6__PD-T4-6                                 | PD-T4-6__PD-T4-6                                 | PD-T4-6                | Custom                  | 350    |",
                "notes": "The DefenseFinder HMM inventory records PD-T4-6__PD-T4-6 under the PD-T4-6 system namespace."
              }
            ]
          },
          {
            "subject": "pd_t4_6_listed_phage_protection",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "pd_t4_6_system_trait",
            "description": "Protection against T2, T4, and T6 realizes the PD-T4-6 system trait.",
            "evidence": [
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-6.md",
                "snippet": "Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0\n    Origin_0[Escherichia coli \n<a href='https://ncbi.nlm.nih.gov/protein/RRM76169.1'>RRM76169.1</a>] --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> T2 & T4 & T6",
                "notes": "The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-T4-6 source locus expressed in E. coli against T2, T4, and T6."
              },
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-6.md",
                "snippet": "subgraph Title4[Protects against]\n        T2\n        T4\n        T6",
                "notes": "The DefenseFinder experimental-validation diagram lists T2, T4, and T6 in the PD-T4-6 protects-against subgraph."
              }
            ]
          },
          {
            "subject": "pd_t4_6_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "PD-T4-6 system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-022-01219-4",
                "snippet": "Here we developed an experimental selection scheme agnostic to genomic context to identify defence systems in 71 diverse E. coli strains. Our results unveil 21 conserved defence systems, none of which were previously detected as enriched in defence islands.",
                "notes": "Vassallo et al. developed the agnostic E. coli pangenome selection that uncovered PD-T4-6 and related conserved phage-defense systems."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "PD-T4-6 | 10\\.1101/2022\\.05\\.12\\.491691 | Mapping the landscape of anti-phage defense mechanisms in the E\\. coli pangenome",
                "notes": "The DefenseFinder article registry maps the named PD-T4-6 system to the Vassallo et al. E. coli pangenome phage-defense preprint."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "PD-T4-6\tPD-T4-6\t1\t1\tPD-T4-6__PD-T4-6\t\t\t",
                "notes": "The DefenseFinder rules table models PD-T4-6 as a single-profile system requiring PD-T4-6__PD-T4-6."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "pd-t4-6-mechanism-gap",
        "prompt": "Resolve PD-T4-6 natural host breadth, direct phage trigger, and effector mechanism before minting narrower PD-T4-6 mechanism traits.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Vassallo et al. support PD-T4-6 as one of the conserved systems from an E. coli pangenome phage-defense selection, the DefenseFinder wiki maps the source locus to protection against T2, T4, and T6, and DefenseFinder represents the system with one mandatory profile. Natural host breadth, the direct phage trigger, and effector logic remain unresolved.",
        "evidence": [
          {
            "reference": "DOI:10.1038/s41564-022-01219-4",
            "snippet": "Here we developed an experimental selection scheme agnostic to genomic context to identify defence systems in 71 diverse E. coli strains. Our results unveil 21 conserved defence systems, none of which were previously detected as enriched in defence islands.",
            "notes": "Vassallo et al. developed the agnostic E. coli pangenome selection that uncovered PD-T4-6 and related conserved phage-defense systems."
          },
          {
            "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-6.md",
            "snippet": "The PD-T4-6 is composed of 1 protein: PD-T4-6.",
            "notes": "The DefenseFinder wiki names PD-T4-6 as a single-protein system."
          },
          {
            "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-6.md",
            "snippet": "Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0\n    Origin_0[Escherichia coli \n<a href='https://ncbi.nlm.nih.gov/protein/RRM76169.1'>RRM76169.1</a>] --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> T2 & T4 & T6",
            "notes": "The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-T4-6 source locus expressed in E. coli against T2, T4, and T6."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "snippet": "PD-T4-6\tPD-T4-6\t1\t1\tPD-T4-6__PD-T4-6\t\t\t",
            "notes": "The DefenseFinder rules table models PD-T4-6 as a single-profile system requiring PD-T4-6__PD-T4-6."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| PD-T4-6__PD-T4-6                                 | PD-T4-6__PD-T4-6                                 | PD-T4-6                | Custom                  | 350    |",
            "notes": "The DefenseFinder HMM inventory records PD-T4-6__PD-T4-6 under the PD-T4-6 system namespace."
          }
        ],
        "attaches_to": [
          "causal_graphs#pd_t4_6_locus_restricts_t2_t4_and_t6"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-26"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-26T18:33:49Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted PD-T4-6 system as a DOI- and DefenseFinder-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v268.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-26T18:33:50Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed PD-T4-6 system canonical_examples and left them empty because the current sources support an E. coli accession-level experimental validation graph, a DefenseFinder system model, and a RefSeq Streptococcus ruminantium example, but not a direct native microbial isolate exemplar with experimentally verified endogenous PD-T4-6 activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000392",
    "label": "PD-T4-7 system",
    "definition": "An abortive infection system in which an organism possesses a PD-T4-7 locus represented by DefenseFinder as a single-profile model, PD-T4-7__PD-T4-7, and experimentally linked to T2, T4, and T6 protection when expressed in E. coli.",
    "definition_source": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-7.md",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000214"
    ],
    "synonyms": [
      {
        "synonym_text": "PD-T4-7",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-7.md"
      },
      {
        "synonym_text": "PD-T4-7__PD-T4-7",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/s41564-022-01219-4",
        "snippet": "Here we developed an experimental selection scheme agnostic to genomic context to identify defence systems in 71 diverse E. coli strains. Our results unveil 21 conserved defence systems, none of which were previously detected as enriched in defence islands.",
        "notes": "Vassallo et al. developed the agnostic E. coli pangenome selection that uncovered PD-T4-7 and related conserved phage-defense systems."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-7.md",
        "snippet": "The PD-T4-7 is composed of 1 protein: PD-T4-7.",
        "notes": "The DefenseFinder wiki names PD-T4-7 as a single-protein system."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-7.md",
        "snippet": "Vassalo et al. :ref{doi=10.1038/s41564-022-01219-4} state that PD-T4-7 functions through an abortive infection mechanism.",
        "notes": "The DefenseFinder wiki reports an abortive-infection mechanism assignment for PD-T4-7 while leaving the direct substrate and effector logic unresolved."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-7.md",
        "snippet": "The PD-T4-7 system in *Thalassospira sp. B30-1* (GCF_015767575.1, NZ_CP065232) is composed of 1 protein: PD-T4-7 (WP_139190007.1)",
        "notes": "The DefenseFinder wiki illustrates a predicted PD-T4-7 locus in RefSeq assembly GCF_015767575.1 on NZ_CP065232."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-7.md",
        "snippet": "Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0\n    Origin_0[Escherichia coli \n<a href='https://ncbi.nlm.nih.gov/protein/RRN43039.1'>RRN43039.1</a>] --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> T2 & T4 & T6",
        "notes": "The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-T4-7 source locus expressed in E. coli against T2, T4, and T6."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-7.md",
        "snippet": "subgraph Title4[Protects against]\n        T2\n        T4\n        T6",
        "notes": "The DefenseFinder experimental-validation diagram lists T2, T4, and T6 in the PD-T4-7 protects-against subgraph."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "PD-T4-7 | 10\\.1101/2022\\.05\\.12\\.491691 | Mapping the landscape of anti-phage defense mechanisms in the E\\. coli pangenome",
        "notes": "The DefenseFinder article registry maps the named PD-T4-7 system to the Vassallo et al. E. coli pangenome phage-defense preprint."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "PD-T4-7\tPD-T4-7\t1\t1\tPD-T4-7__PD-T4-7\t\t\t",
        "notes": "The DefenseFinder rules table models PD-T4-7 as a single-profile system requiring PD-T4-7__PD-T4-7."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| PD-T4-7__PD-T4-7                                 | PD-T4-7__PD-T4-7                                 | PD-T4-7                | Custom                  | 80     |",
        "notes": "The DefenseFinder HMM inventory records PD-T4-7__PD-T4-7 under the PD-T4-7 system namespace."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "pd_t4_7_locus_restricts_t2_t4_and_t6",
        "title": "PD-T4-7 loci restrict T2, T4, and T6",
        "description": "Conservative system-level sketch linking possession of a PD-T4-7 locus to protection against T2, T4, and T6.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures PD-T4-7 as a named DefenseFinder abortive-infection system while leaving natural host breadth, the direct phage trigger, and the direct effector logic unresolved.",
        "nodes": [
          {
            "node_id": "pd_t4_7_locus",
            "label": "PD-T4-7 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A phage-defense locus represented by the PD-T4-7 DefenseFinder profile."
          },
          {
            "node_id": "pd_t4_7_listed_phage_protection",
            "label": "T2, T4, and T6 protection",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Protection against T2, T4, and T6 by PD-T4-7."
          },
          {
            "node_id": "pd_t4_7_system_trait",
            "label": "PD-T4-7 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000392",
            "description": "Possession of a genome-encoded PD-T4-7 phage-defense system."
          },
          {
            "node_id": "abortive_infection_system",
            "label": "abortive infection system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000214",
            "description": "Possession of a genome-encoded abortive-infection phage defense system."
          }
        ],
        "edges": [
          {
            "subject": "pd_t4_7_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "pd_t4_7_listed_phage_protection",
            "description": "The DefenseFinder wiki links a PD-T4-7 locus from Vassallo et al. to protection against T2, T4, and T6, and DefenseFinder models PD-T4-7 through one mandatory profile.",
            "evidence": [
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-7.md",
                "snippet": "The PD-T4-7 is composed of 1 protein: PD-T4-7.",
                "notes": "The DefenseFinder wiki names PD-T4-7 as a single-protein system."
              },
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-7.md",
                "snippet": "Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0\n    Origin_0[Escherichia coli \n<a href='https://ncbi.nlm.nih.gov/protein/RRN43039.1'>RRN43039.1</a>] --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> T2 & T4 & T6",
                "notes": "The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-T4-7 source locus expressed in E. coli against T2, T4, and T6."
              },
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-7.md",
                "snippet": "subgraph Title4[Protects against]\n        T2\n        T4\n        T6",
                "notes": "The DefenseFinder experimental-validation diagram lists T2, T4, and T6 in the PD-T4-7 protects-against subgraph."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "PD-T4-7\tPD-T4-7\t1\t1\tPD-T4-7__PD-T4-7\t\t\t",
                "notes": "The DefenseFinder rules table models PD-T4-7 as a single-profile system requiring PD-T4-7__PD-T4-7."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| PD-T4-7__PD-T4-7                                 | PD-T4-7__PD-T4-7                                 | PD-T4-7                | Custom                  | 80     |",
                "notes": "The DefenseFinder HMM inventory records PD-T4-7__PD-T4-7 under the PD-T4-7 system namespace."
              }
            ]
          },
          {
            "subject": "pd_t4_7_listed_phage_protection",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "pd_t4_7_system_trait",
            "description": "Protection against T2, T4, and T6 realizes the PD-T4-7 system trait.",
            "evidence": [
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-7.md",
                "snippet": "Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0\n    Origin_0[Escherichia coli \n<a href='https://ncbi.nlm.nih.gov/protein/RRN43039.1'>RRN43039.1</a>] --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> T2 & T4 & T6",
                "notes": "The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-T4-7 source locus expressed in E. coli against T2, T4, and T6."
              },
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-7.md",
                "snippet": "subgraph Title4[Protects against]\n        T2\n        T4\n        T6",
                "notes": "The DefenseFinder experimental-validation diagram lists T2, T4, and T6 in the PD-T4-7 protects-against subgraph."
              }
            ]
          },
          {
            "subject": "pd_t4_7_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "abortive_infection_system",
            "description": "PD-T4-7 system possession is an abortive-infection-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-022-01219-4",
                "snippet": "Here we developed an experimental selection scheme agnostic to genomic context to identify defence systems in 71 diverse E. coli strains. Our results unveil 21 conserved defence systems, none of which were previously detected as enriched in defence islands.",
                "notes": "Vassallo et al. developed the agnostic E. coli pangenome selection that uncovered PD-T4-7 and related conserved phage-defense systems."
              },
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-7.md",
                "snippet": "Vassalo et al. :ref{doi=10.1038/s41564-022-01219-4} state that PD-T4-7 functions through an abortive infection mechanism.",
                "notes": "The DefenseFinder wiki reports an abortive-infection mechanism assignment for PD-T4-7 while leaving the direct substrate and effector logic unresolved."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "PD-T4-7 | 10\\.1101/2022\\.05\\.12\\.491691 | Mapping the landscape of anti-phage defense mechanisms in the E\\. coli pangenome",
                "notes": "The DefenseFinder article registry maps the named PD-T4-7 system to the Vassallo et al. E. coli pangenome phage-defense preprint."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "PD-T4-7\tPD-T4-7\t1\t1\tPD-T4-7__PD-T4-7\t\t\t",
                "notes": "The DefenseFinder rules table models PD-T4-7 as a single-profile system requiring PD-T4-7__PD-T4-7."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "pd-t4-7-mechanism-gap",
        "prompt": "Resolve PD-T4-7 natural host breadth, direct phage trigger, and direct abortive-infection effector logic before minting narrower PD-T4-7 mechanism traits.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Vassallo et al. support PD-T4-7 as one of the conserved systems from an E. coli pangenome phage-defense selection, the DefenseFinder wiki maps the source locus to protection against T2, T4, and T6, and DefenseFinder represents the system with one mandatory profile and an abortive-infection mechanism assignment. Natural host breadth, the direct phage trigger, and direct effector logic remain unresolved.",
        "evidence": [
          {
            "reference": "DOI:10.1038/s41564-022-01219-4",
            "snippet": "Here we developed an experimental selection scheme agnostic to genomic context to identify defence systems in 71 diverse E. coli strains. Our results unveil 21 conserved defence systems, none of which were previously detected as enriched in defence islands.",
            "notes": "Vassallo et al. developed the agnostic E. coli pangenome selection that uncovered PD-T4-7 and related conserved phage-defense systems."
          },
          {
            "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-7.md",
            "snippet": "The PD-T4-7 is composed of 1 protein: PD-T4-7.",
            "notes": "The DefenseFinder wiki names PD-T4-7 as a single-protein system."
          },
          {
            "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-7.md",
            "snippet": "Vassalo et al. :ref{doi=10.1038/s41564-022-01219-4} state that PD-T4-7 functions through an abortive infection mechanism.",
            "notes": "The DefenseFinder wiki reports an abortive-infection mechanism assignment for PD-T4-7 while leaving the direct substrate and effector logic unresolved."
          },
          {
            "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-7.md",
            "snippet": "Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0\n    Origin_0[Escherichia coli \n<a href='https://ncbi.nlm.nih.gov/protein/RRN43039.1'>RRN43039.1</a>] --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> T2 & T4 & T6",
            "notes": "The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-T4-7 source locus expressed in E. coli against T2, T4, and T6."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "snippet": "PD-T4-7\tPD-T4-7\t1\t1\tPD-T4-7__PD-T4-7\t\t\t",
            "notes": "The DefenseFinder rules table models PD-T4-7 as a single-profile system requiring PD-T4-7__PD-T4-7."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| PD-T4-7__PD-T4-7                                 | PD-T4-7__PD-T4-7                                 | PD-T4-7                | Custom                  | 80     |",
            "notes": "The DefenseFinder HMM inventory records PD-T4-7__PD-T4-7 under the PD-T4-7 system namespace."
          }
        ],
        "attaches_to": [
          "causal_graphs#pd_t4_7_locus_restricts_t2_t4_and_t6"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-26"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-26T19:13:36Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted PD-T4-7 system as a DOI- and DefenseFinder-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v269.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-26T19:13:37Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed PD-T4-7 system canonical_examples and left them empty because the current sources support an E. coli accession-level experimental validation graph, a DefenseFinder system model, and a RefSeq Thalassospira example, but not a direct native microbial isolate exemplar with experimentally verified endogenous PD-T4-7 activity. No paid research was used.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-26T19:42:30Z",
        "curator": "codex",
        "action": "ADDRESS_SCOPE_NOTE_REVIEW",
        "changes": "Addressed PR 1292 review issue 1293 by reparenting PD-T4-7 under abortive infection system, updating the subclass graph node, and naming the DefenseFinder abortive-infection assignment while leaving natural host breadth, the direct phage trigger, and direct effector logic unresolved.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-26T19:55:00Z",
        "curator": "codex",
        "action": "RESTORE_MINT_EVENT_PROVENANCE",
        "changes": "Addressed PR 1292 review issue 1294 by restoring the original mint event to say PD-T4-7 was minted under phage defense system; the later ADDRESS_SCOPE_NOTE_REVIEW event records the abortive-infection reparenting.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000393",
    "label": "PD-T4-8 system",
    "definition": "A phage defense system in which an organism possesses a PD-T4-8 locus represented by DefenseFinder as a single-profile model, PD-T4-8__PD-T4-8, and experimentally linked to T2, T4, T6, SECphi18, and SECphi27 protection when expressed in E. coli.",
    "definition_source": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-8.md",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "PD-T4-8",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-8.md"
      },
      {
        "synonym_text": "PD-T4-8__PD-T4-8",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/s41564-022-01219-4",
        "snippet": "Here we developed an experimental selection scheme agnostic to genomic context to identify defence systems in 71 diverse E. coli strains. Our results unveil 21 conserved defence systems, none of which were previously detected as enriched in defence islands.",
        "notes": "Vassallo et al. developed the agnostic E. coli pangenome selection that uncovered PD-T4-8 and related conserved phage-defense systems."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-8.md",
        "snippet": "PD-T4-8 is composed of a single protein that contains a DUF4263 domain found in the [Shedu](/defense-systems/shedu) defense system :ref{doi=10.1038/s41564-022-01219-4}. PD-T4-8 from *Escherichia coli* RCP52534.1 confers resistance against T2, T4, T6, SECphi18 and SECphi27.",
        "notes": "The DefenseFinder wiki reports that PD-T4-8 contains a DUF4263 domain and that the E. coli RCP52534.1 locus confers resistance against T2, T4, T6, SECphi18, and SECphi27."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-8.md",
        "snippet": "The PD-T4-8 is composed of 1 protein: PD-T4-8.",
        "notes": "The DefenseFinder wiki names PD-T4-8 as a single-protein system."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-8.md",
        "snippet": "The PD-T4-8 system in *Algoriphagus sp. Y33* (GCF_014838715.1, NZ_CP061947) is composed of 1 protein: PD-T4-8 (WP_144603961.1)",
        "notes": "The DefenseFinder wiki illustrates a predicted PD-T4-8 locus in RefSeq assembly GCF_014838715.1 on NZ_CP061947."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-8.md",
        "snippet": "Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0\n    Origin_0[Escherichia coli \n<a href='https://ncbi.nlm.nih.gov/protein/RCP52534.1'>RCP52534.1</a>] --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> T2 & T4 & T6 & SECphi18 & SECphi27",
        "notes": "The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-T4-8 source locus expressed in E. coli against T2, T4, T6, SECphi18, and SECphi27."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-8.md",
        "snippet": "subgraph Title4[Protects against]\n        T2\n        T4\n        T6\n        SECphi18\n        SECphi27",
        "notes": "The DefenseFinder experimental-validation diagram lists T2, T4, T6, SECphi18, and SECphi27 in the PD-T4-8 protects-against subgraph."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "PD-T4-8 | 10\\.1101/2022\\.05\\.12\\.491691 | Mapping the landscape of anti-phage defense mechanisms in the E\\. coli pangenome",
        "notes": "The DefenseFinder article registry maps the named PD-T4-8 system to the Vassallo et al. E. coli pangenome phage-defense preprint."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "PD-T4-8\tPD-T4-8\t1\t1\tPD-T4-8__PD-T4-8\t\t\t",
        "notes": "The DefenseFinder rules table models PD-T4-8 as a single-profile system requiring PD-T4-8__PD-T4-8."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| PD-T4-8__PD-T4-8                                 | PD-T4-8__PD-T4-8                                 | PD-T4-8                | Custom                  | 80     |",
        "notes": "The DefenseFinder HMM inventory records PD-T4-8__PD-T4-8 under the PD-T4-8 system namespace."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "pd_t4_8_locus_restricts_t2_t4_t6_secphi18_and_secphi27",
        "title": "PD-T4-8 loci restrict T2, T4, T6, SECphi18, and SECphi27",
        "description": "Conservative system-level sketch linking possession of a PD-T4-8 locus to protection against T2, T4, T6, SECphi18, and SECphi27.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures PD-T4-8 as a named DefenseFinder phage-defense system while leaving natural host breadth, the direct phage trigger, and effector logic unresolved.",
        "nodes": [
          {
            "node_id": "pd_t4_8_locus",
            "label": "PD-T4-8 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A phage-defense locus represented by the PD-T4-8 DefenseFinder profile."
          },
          {
            "node_id": "pd_t4_8_listed_phage_protection",
            "label": "T2, T4, T6, SECphi18, and SECphi27 protection",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Protection against T2, T4, T6, SECphi18, and SECphi27 by PD-T4-8."
          },
          {
            "node_id": "pd_t4_8_system_trait",
            "label": "PD-T4-8 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000393",
            "description": "Possession of a genome-encoded PD-T4-8 phage-defense system."
          }
        ],
        "edges": [
          {
            "subject": "pd_t4_8_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "pd_t4_8_listed_phage_protection",
            "description": "The DefenseFinder wiki links a PD-T4-8 locus from Vassallo et al. to protection against T2, T4, T6, SECphi18, and SECphi27, and DefenseFinder models PD-T4-8 through one mandatory profile.",
            "evidence": [
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-8.md",
                "snippet": "PD-T4-8 is composed of a single protein that contains a DUF4263 domain found in the [Shedu](/defense-systems/shedu) defense system :ref{doi=10.1038/s41564-022-01219-4}. PD-T4-8 from *Escherichia coli* RCP52534.1 confers resistance against T2, T4, T6, SECphi18 and SECphi27.",
                "notes": "The DefenseFinder wiki reports that PD-T4-8 contains a DUF4263 domain and that the E. coli RCP52534.1 locus confers resistance against T2, T4, T6, SECphi18, and SECphi27."
              },
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-8.md",
                "snippet": "The PD-T4-8 is composed of 1 protein: PD-T4-8.",
                "notes": "The DefenseFinder wiki names PD-T4-8 as a single-protein system."
              },
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-8.md",
                "snippet": "Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0\n    Origin_0[Escherichia coli \n<a href='https://ncbi.nlm.nih.gov/protein/RCP52534.1'>RCP52534.1</a>] --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> T2 & T4 & T6 & SECphi18 & SECphi27",
                "notes": "The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-T4-8 source locus expressed in E. coli against T2, T4, T6, SECphi18, and SECphi27."
              },
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-8.md",
                "snippet": "subgraph Title4[Protects against]\n        T2\n        T4\n        T6\n        SECphi18\n        SECphi27",
                "notes": "The DefenseFinder experimental-validation diagram lists T2, T4, T6, SECphi18, and SECphi27 in the PD-T4-8 protects-against subgraph."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "PD-T4-8\tPD-T4-8\t1\t1\tPD-T4-8__PD-T4-8\t\t\t",
                "notes": "The DefenseFinder rules table models PD-T4-8 as a single-profile system requiring PD-T4-8__PD-T4-8."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| PD-T4-8__PD-T4-8                                 | PD-T4-8__PD-T4-8                                 | PD-T4-8                | Custom                  | 80     |",
                "notes": "The DefenseFinder HMM inventory records PD-T4-8__PD-T4-8 under the PD-T4-8 system namespace."
              }
            ]
          },
          {
            "subject": "pd_t4_8_listed_phage_protection",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "pd_t4_8_system_trait",
            "description": "Protection against T2, T4, T6, SECphi18, and SECphi27 realizes the PD-T4-8 system trait.",
            "evidence": [
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-8.md",
                "snippet": "PD-T4-8 is composed of a single protein that contains a DUF4263 domain found in the [Shedu](/defense-systems/shedu) defense system :ref{doi=10.1038/s41564-022-01219-4}. PD-T4-8 from *Escherichia coli* RCP52534.1 confers resistance against T2, T4, T6, SECphi18 and SECphi27.",
                "notes": "The DefenseFinder wiki reports that PD-T4-8 contains a DUF4263 domain and that the E. coli RCP52534.1 locus confers resistance against T2, T4, T6, SECphi18, and SECphi27."
              },
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-8.md",
                "snippet": "Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0\n    Origin_0[Escherichia coli \n<a href='https://ncbi.nlm.nih.gov/protein/RCP52534.1'>RCP52534.1</a>] --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> T2 & T4 & T6 & SECphi18 & SECphi27",
                "notes": "The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-T4-8 source locus expressed in E. coli against T2, T4, T6, SECphi18, and SECphi27."
              },
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-8.md",
                "snippet": "subgraph Title4[Protects against]\n        T2\n        T4\n        T6\n        SECphi18\n        SECphi27",
                "notes": "The DefenseFinder experimental-validation diagram lists T2, T4, T6, SECphi18, and SECphi27 in the PD-T4-8 protects-against subgraph."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "pd-t4-8-mechanism-gap",
        "prompt": "Resolve PD-T4-8 natural host breadth, direct phage trigger, and effector logic before minting narrower PD-T4-8 mechanism traits.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Vassallo et al. support PD-T4-8 as one of the conserved systems from an E. coli pangenome phage-defense selection, the DefenseFinder wiki maps the source locus to protection against T2, T4, T6, SECphi18, and SECphi27, and DefenseFinder represents the system with one mandatory profile. Natural host breadth, the direct phage trigger, and effector logic remain unresolved.",
        "evidence": [
          {
            "reference": "DOI:10.1038/s41564-022-01219-4",
            "snippet": "Here we developed an experimental selection scheme agnostic to genomic context to identify defence systems in 71 diverse E. coli strains. Our results unveil 21 conserved defence systems, none of which were previously detected as enriched in defence islands.",
            "notes": "Vassallo et al. developed the agnostic E. coli pangenome selection that uncovered PD-T4-8 and related conserved phage-defense systems."
          },
          {
            "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-8.md",
            "snippet": "PD-T4-8 is composed of a single protein that contains a DUF4263 domain found in the [Shedu](/defense-systems/shedu) defense system :ref{doi=10.1038/s41564-022-01219-4}. PD-T4-8 from *Escherichia coli* RCP52534.1 confers resistance against T2, T4, T6, SECphi18 and SECphi27.",
            "notes": "The DefenseFinder wiki reports that PD-T4-8 contains a DUF4263 domain and that the E. coli RCP52534.1 locus confers resistance against T2, T4, T6, SECphi18, and SECphi27."
          },
          {
            "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-8.md",
            "snippet": "The PD-T4-8 is composed of 1 protein: PD-T4-8.",
            "notes": "The DefenseFinder wiki names PD-T4-8 as a single-protein system."
          },
          {
            "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-8.md",
            "snippet": "Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0\n    Origin_0[Escherichia coli \n<a href='https://ncbi.nlm.nih.gov/protein/RCP52534.1'>RCP52534.1</a>] --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> T2 & T4 & T6 & SECphi18 & SECphi27",
            "notes": "The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-T4-8 source locus expressed in E. coli against T2, T4, T6, SECphi18, and SECphi27."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "snippet": "PD-T4-8\tPD-T4-8\t1\t1\tPD-T4-8__PD-T4-8\t\t\t",
            "notes": "The DefenseFinder rules table models PD-T4-8 as a single-profile system requiring PD-T4-8__PD-T4-8."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| PD-T4-8__PD-T4-8                                 | PD-T4-8__PD-T4-8                                 | PD-T4-8                | Custom                  | 80     |",
            "notes": "The DefenseFinder HMM inventory records PD-T4-8__PD-T4-8 under the PD-T4-8 system namespace."
          }
        ],
        "attaches_to": [
          "causal_graphs#pd_t4_8_locus_restricts_t2_t4_t6_secphi18_and_secphi27"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-26"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-26T20:08:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted PD-T4-8 system as a DOI- and DefenseFinder-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v270.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-26T20:08:01Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed PD-T4-8 system canonical_examples and left them empty because the current sources support an E. coli accession-level experimental validation graph, a DefenseFinder system model, and a RefSeq Algoriphagus example, but not a direct native microbial isolate exemplar with experimentally verified endogenous PD-T4-8 activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000395",
    "label": "PD-T7-1 system",
    "definition": "A phage defense system in which an organism possesses a PD-T7-1 locus represented by DefenseFinder as a single-profile model, PD-T7-1__PD-T7-1, and experimentally linked to T7 protection when expressed in E. coli.",
    "definition_source": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-1.md",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "PD-T7-1",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-1.md"
      },
      {
        "synonym_text": "PD-T7-1__PD-T7-1",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/s41564-022-01219-4",
        "snippet": "Here we developed an experimental selection scheme agnostic to genomic context to identify defence systems in 71 diverse E. coli strains. Our results unveil 21 conserved defence systems, none of which were previously detected as enriched in defence islands.",
        "notes": "Vassallo et al. developed the agnostic E. coli pangenome selection that uncovered PD-T7-1 and related conserved phage-defense systems."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-1.md",
        "snippet": "PD-T7-1 is a single gene defense system that was discovered in :ref{doi=10.1038/s41564-022-01219-4}. Its antiphage activity was assessed in *E. coli* and it was shown to be active against T7.",
        "notes": "The DefenseFinder wiki describes PD-T7-1 as a single-gene system and names T7 as its experimentally assessed activity."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-1.md",
        "snippet": "The PD-T7-1 is composed of 1 protein: PD-T7-1.",
        "notes": "The DefenseFinder wiki names PD-T7-1 as a single-protein system."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-1.md",
        "snippet": "The PD-T7-1 system in *Klebsiella sp. P1927* (GCF_018204675.1, NZ_CP073377) is composed of 1 protein: PD-T7-1 (WP_004150873.1)",
        "notes": "The DefenseFinder wiki illustrates a predicted one-protein PD-T7-1 locus in RefSeq assembly GCF_018204675.1 on NZ_CP073377."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-1.md",
        "snippet": "Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0\n    Origin_0[Escherichia coli \n<a href='https://ncbi.nlm.nih.gov/protein/RCQ85672.1'>RCQ85672.1</a>] --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> T7",
        "notes": "The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-T7-1 source locus expressed in E. coli against T7."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-1.md",
        "snippet": "subgraph Title4[Protects against]\n        T7",
        "notes": "The DefenseFinder experimental-validation diagram lists T7 in the PD-T7-1 protects-against subgraph."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "PD-T7-1 | 10\\.1101/2022\\.05\\.12\\.491691 | Mapping the landscape of anti-phage defense mechanisms in the E\\. coli pangenome",
        "notes": "The DefenseFinder article registry maps the named PD-T7-1 system to the Vassallo et al. E. coli pangenome phage-defense preprint."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "PD-T7-1\tPD-T7-1\t1\t1\tPD-T7-1__PD-T7-1\t\t\t",
        "notes": "The DefenseFinder rules table models PD-T7-1 as a single-profile system requiring PD-T7-1__PD-T7-1."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| PD-T7-1__PD-T7-1                                 | PD-T7-1__PD-T7-1                                 | PD-T7-1                | Custom                  | 100    |",
        "notes": "The DefenseFinder HMM inventory records PD-T7-1__PD-T7-1 under the PD-T7-1 system namespace."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "pd_t7_1_locus_restricts_t7",
        "title": "PD-T7-1 loci restrict T7",
        "description": "Conservative system-level sketch linking possession of a PD-T7-1 locus to protection against T7.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures PD-T7-1 as a named DefenseFinder phage-defense system while leaving natural host breadth, the direct phage trigger, and the effector mechanism unresolved.",
        "nodes": [
          {
            "node_id": "pd_t7_1_locus",
            "label": "PD-T7-1 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A phage-defense locus represented by the PD-T7-1 DefenseFinder profile."
          },
          {
            "node_id": "pd_t7_1_listed_phage_protection",
            "label": "T7 protection",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Protection against T7 by PD-T7-1."
          },
          {
            "node_id": "pd_t7_1_system_trait",
            "label": "PD-T7-1 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000395",
            "description": "Possession of a genome-encoded PD-T7-1 phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "pd_t7_1_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "pd_t7_1_listed_phage_protection",
            "description": "The DefenseFinder wiki links a PD-T7-1 locus from Vassallo et al. to protection against T7, and DefenseFinder models PD-T7-1 through one mandatory profile.",
            "evidence": [
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-1.md",
                "snippet": "PD-T7-1 is a single gene defense system that was discovered in :ref{doi=10.1038/s41564-022-01219-4}. Its antiphage activity was assessed in *E. coli* and it was shown to be active against T7.",
                "notes": "The DefenseFinder wiki describes PD-T7-1 as a single-gene system and names T7 as its experimentally assessed activity."
              },
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-1.md",
                "snippet": "The PD-T7-1 is composed of 1 protein: PD-T7-1.",
                "notes": "The DefenseFinder wiki names PD-T7-1 as a single-protein system."
              },
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-1.md",
                "snippet": "Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0\n    Origin_0[Escherichia coli \n<a href='https://ncbi.nlm.nih.gov/protein/RCQ85672.1'>RCQ85672.1</a>] --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> T7",
                "notes": "The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-T7-1 source locus expressed in E. coli against T7."
              },
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-1.md",
                "snippet": "subgraph Title4[Protects against]\n        T7",
                "notes": "The DefenseFinder experimental-validation diagram lists T7 in the PD-T7-1 protects-against subgraph."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "PD-T7-1\tPD-T7-1\t1\t1\tPD-T7-1__PD-T7-1\t\t\t",
                "notes": "The DefenseFinder rules table models PD-T7-1 as a single-profile system requiring PD-T7-1__PD-T7-1."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| PD-T7-1__PD-T7-1                                 | PD-T7-1__PD-T7-1                                 | PD-T7-1                | Custom                  | 100    |",
                "notes": "The DefenseFinder HMM inventory records PD-T7-1__PD-T7-1 under the PD-T7-1 system namespace."
              }
            ]
          },
          {
            "subject": "pd_t7_1_listed_phage_protection",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "pd_t7_1_system_trait",
            "description": "Protection against T7 realizes the PD-T7-1 system trait.",
            "evidence": [
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-1.md",
                "snippet": "PD-T7-1 is a single gene defense system that was discovered in :ref{doi=10.1038/s41564-022-01219-4}. Its antiphage activity was assessed in *E. coli* and it was shown to be active against T7.",
                "notes": "The DefenseFinder wiki describes PD-T7-1 as a single-gene system and names T7 as its experimentally assessed activity."
              },
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-1.md",
                "snippet": "Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0\n    Origin_0[Escherichia coli \n<a href='https://ncbi.nlm.nih.gov/protein/RCQ85672.1'>RCQ85672.1</a>] --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> T7",
                "notes": "The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-T7-1 source locus expressed in E. coli against T7."
              },
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-1.md",
                "snippet": "subgraph Title4[Protects against]\n        T7",
                "notes": "The DefenseFinder experimental-validation diagram lists T7 in the PD-T7-1 protects-against subgraph."
              }
            ]
          },
          {
            "subject": "pd_t7_1_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "PD-T7-1 system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-022-01219-4",
                "snippet": "Here we developed an experimental selection scheme agnostic to genomic context to identify defence systems in 71 diverse E. coli strains. Our results unveil 21 conserved defence systems, none of which were previously detected as enriched in defence islands.",
                "notes": "Vassallo et al. developed the agnostic E. coli pangenome selection that uncovered PD-T7-1 and related conserved phage-defense systems."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "PD-T7-1 | 10\\.1101/2022\\.05\\.12\\.491691 | Mapping the landscape of anti-phage defense mechanisms in the E\\. coli pangenome",
                "notes": "The DefenseFinder article registry maps the named PD-T7-1 system to the Vassallo et al. E. coli pangenome phage-defense preprint."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "PD-T7-1\tPD-T7-1\t1\t1\tPD-T7-1__PD-T7-1\t\t\t",
                "notes": "The DefenseFinder rules table models PD-T7-1 as a single-profile system requiring PD-T7-1__PD-T7-1."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "pd-t7-1-mechanism-gap",
        "prompt": "Resolve PD-T7-1 natural host breadth, direct phage trigger, and effector mechanism before minting narrower PD-T7-1 mechanism traits.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Vassallo et al. support PD-T7-1 as one of the conserved systems from an E. coli pangenome phage-defense selection, the DefenseFinder wiki maps the source locus to protection against T7, and DefenseFinder represents the system with one profile. Natural host breadth, the direct phage trigger, and effector logic remain unresolved.",
        "evidence": [
          {
            "reference": "DOI:10.1038/s41564-022-01219-4",
            "snippet": "Here we developed an experimental selection scheme agnostic to genomic context to identify defence systems in 71 diverse E. coli strains. Our results unveil 21 conserved defence systems, none of which were previously detected as enriched in defence islands.",
            "notes": "Vassallo et al. developed the agnostic E. coli pangenome selection that uncovered PD-T7-1 and related conserved phage-defense systems."
          },
          {
            "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-1.md",
            "snippet": "PD-T7-1 is a single gene defense system that was discovered in :ref{doi=10.1038/s41564-022-01219-4}. Its antiphage activity was assessed in *E. coli* and it was shown to be active against T7.",
            "notes": "The DefenseFinder wiki describes PD-T7-1 as a single-gene system and names T7 as its experimentally assessed activity."
          },
          {
            "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-1.md",
            "snippet": "The PD-T7-1 is composed of 1 protein: PD-T7-1.",
            "notes": "The DefenseFinder wiki names PD-T7-1 as a single-protein system."
          },
          {
            "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-1.md",
            "snippet": "Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0\n    Origin_0[Escherichia coli \n<a href='https://ncbi.nlm.nih.gov/protein/RCQ85672.1'>RCQ85672.1</a>] --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> T7",
            "notes": "The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-T7-1 source locus expressed in E. coli against T7."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "snippet": "PD-T7-1\tPD-T7-1\t1\t1\tPD-T7-1__PD-T7-1\t\t\t",
            "notes": "The DefenseFinder rules table models PD-T7-1 as a single-profile system requiring PD-T7-1__PD-T7-1."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| PD-T7-1__PD-T7-1                                 | PD-T7-1__PD-T7-1                                 | PD-T7-1                | Custom                  | 100    |",
            "notes": "The DefenseFinder HMM inventory records PD-T7-1__PD-T7-1 under the PD-T7-1 system namespace."
          }
        ],
        "attaches_to": [
          "causal_graphs#pd_t7_1_locus_restricts_t7"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-26"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-26T23:12:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted PD-T7-1 system as a DOI- and DefenseFinder-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v272.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-26T23:12:01Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed PD-T7-1 system canonical_examples and left them empty because the current sources support an E. coli accession-level experimental validation graph, a DefenseFinder system model, and a RefSeq Klebsiella sp. P1927 example, but not a direct native microbial isolate exemplar with experimentally verified endogenous PD-T7-1 activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000396",
    "label": "PD-T7-2 system",
    "definition": "A phage defense system in which an organism possesses a PD-T7-2 locus represented by DefenseFinder as a two-profile model, PD-T7-2__PD-T7-2_A and PD-T7-2__PD-T7-2_B, and experimentally linked to T2, T4, T6, LambdaVir, T5, SECphi18, SECphi27, T3, and T7 protection when expressed in E. coli.",
    "definition_source": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-2.md",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "PD-T7-2",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-2.md"
      },
      {
        "synonym_text": "PD-T7-2__PD-T7-2_A",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "PD-T7-2__PD-T7-2_B",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/s41564-022-01219-4",
        "snippet": "Here we developed an experimental selection scheme agnostic to genomic context to identify defence systems in 71 diverse E. coli strains. Our results unveil 21 conserved defence systems, none of which were previously detected as enriched in defence islands.",
        "notes": "Vassallo et al. developed the agnostic E. coli pangenome selection that uncovered PD-T7-2 and related conserved phage-defense systems."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-2.md",
        "snippet": "The PD-T7-2 is composed of 2 proteins: PD-T7-2_A and PD-T7-2_B.",
        "notes": "The DefenseFinder wiki names PD-T7-2 as a two-protein system with PD-T7-2_A and PD-T7-2_B."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-2.md",
        "snippet": "The PD-T7-2 system in *Lederbergia lenta* (GCF_900478165.1, NZ_LS483476) is composed of 2 proteins PD-T7-2_A (WP_066145327.1) PD-T7-2_B (WP_066145329.1)",
        "notes": "The DefenseFinder wiki illustrates a predicted two-protein PD-T7-2 locus in RefSeq assembly GCF_900478165.1 on NZ_LS483476."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-2.md",
        "snippet": "Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0\n    Origin_0[Escherichia coli \n<a href='https://ncbi.nlm.nih.gov/protein/RRM73498.1'>RRM73498.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/RRM73410.1'>RRM73410.1</a>] --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> T2 & T4 & T6 & LambdaVir & T5 & SECphi18 & SECphi27 & T3 & T7",
        "notes": "The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-T7-2 source locus expressed in E. coli against T2, T4, T6, LambdaVir, T5, SECphi18, SECphi27, T3, and T7."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-2.md",
        "snippet": "subgraph Title4[Protects against]\n        T2\n        T4\n        T6\n        LambdaVir\n        T5\n        SECphi18\n        SECphi27\n        T3\n        T7",
        "notes": "The DefenseFinder experimental-validation diagram lists T2, T4, T6, LambdaVir, T5, SECphi18, SECphi27, T3, and T7 in the PD-T7-2 protects-against subgraph."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "PD-T7-2 | 10\\.1101/2022\\.05\\.12\\.491691 | Mapping the landscape of anti-phage defense mechanisms in the E\\. coli pangenome",
        "notes": "The DefenseFinder article registry maps the named PD-T7-2 system to the Vassallo et al. E. coli pangenome phage-defense preprint."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "PD-T7-2\tPD-T7-2\t2\t2\tPD-T7-2__PD-T7-2_A, PD-T7-2__PD-T7-2_B\t\t\t",
        "notes": "The DefenseFinder rules table models PD-T7-2 as a two-profile system requiring PD-T7-2__PD-T7-2_A and PD-T7-2__PD-T7-2_B."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| PD-T7-2__PD-T7-2_A                               | PD-T7-2__PD-T7-2_A                               | PD-T7-2                | Custom                  | 50     |",
        "notes": "The DefenseFinder HMM inventory records PD-T7-2__PD-T7-2_A under the PD-T7-2 system namespace."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| PD-T7-2__PD-T7-2_B                               | PD-T7-2__PD-T7-2_B                               | PD-T7-2                | Custom                  | 100    |",
        "notes": "The DefenseFinder HMM inventory records PD-T7-2__PD-T7-2_B under the PD-T7-2 system namespace."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "pd_t7_2_locus_restricts_phages",
        "title": "PD-T7-2 loci restrict T2, T4, T6, LambdaVir, T5, SECphi18, SECphi27, T3, and T7",
        "description": "Conservative system-level sketch linking possession of a PD-T7-2 locus to protection against T2, T4, T6, LambdaVir, T5, SECphi18, SECphi27, T3, and T7.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures PD-T7-2 as a named DefenseFinder phage-defense system while leaving natural host breadth, the direct phage trigger, the effector mechanism, and exact profile-to-protein correspondence unresolved.",
        "nodes": [
          {
            "node_id": "pd_t7_2_locus",
            "label": "PD-T7-2 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A phage-defense locus represented by the PD-T7-2_A and PD-T7-2_B DefenseFinder profiles."
          },
          {
            "node_id": "pd_t7_2_listed_phage_protection",
            "label": "T2, T4, T6, LambdaVir, T5, SECphi18, SECphi27, T3, and T7 protection",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Protection against T2, T4, T6, LambdaVir, T5, SECphi18, SECphi27, T3, and T7 by PD-T7-2."
          },
          {
            "node_id": "pd_t7_2_system_trait",
            "label": "PD-T7-2 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000396",
            "description": "Possession of a genome-encoded PD-T7-2 phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "pd_t7_2_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "pd_t7_2_listed_phage_protection",
            "description": "The DefenseFinder wiki links a PD-T7-2 locus from Vassallo et al. to broad phage protection, and DefenseFinder models PD-T7-2 through two mandatory profiles.",
            "evidence": [
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-2.md",
                "snippet": "The PD-T7-2 is composed of 2 proteins: PD-T7-2_A and PD-T7-2_B.",
                "notes": "The DefenseFinder wiki names PD-T7-2 as a two-protein system with PD-T7-2_A and PD-T7-2_B."
              },
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-2.md",
                "snippet": "Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0\n    Origin_0[Escherichia coli \n<a href='https://ncbi.nlm.nih.gov/protein/RRM73498.1'>RRM73498.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/RRM73410.1'>RRM73410.1</a>] --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> T2 & T4 & T6 & LambdaVir & T5 & SECphi18 & SECphi27 & T3 & T7",
                "notes": "The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-T7-2 source locus expressed in E. coli against T2, T4, T6, LambdaVir, T5, SECphi18, SECphi27, T3, and T7."
              },
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-2.md",
                "snippet": "subgraph Title4[Protects against]\n        T2\n        T4\n        T6\n        LambdaVir\n        T5\n        SECphi18\n        SECphi27\n        T3\n        T7",
                "notes": "The DefenseFinder experimental-validation diagram lists T2, T4, T6, LambdaVir, T5, SECphi18, SECphi27, T3, and T7 in the PD-T7-2 protects-against subgraph."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "PD-T7-2\tPD-T7-2\t2\t2\tPD-T7-2__PD-T7-2_A, PD-T7-2__PD-T7-2_B\t\t\t",
                "notes": "The DefenseFinder rules table models PD-T7-2 as a two-profile system requiring PD-T7-2__PD-T7-2_A and PD-T7-2__PD-T7-2_B."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| PD-T7-2__PD-T7-2_A                               | PD-T7-2__PD-T7-2_A                               | PD-T7-2                | Custom                  | 50     |",
                "notes": "The DefenseFinder HMM inventory records PD-T7-2__PD-T7-2_A under the PD-T7-2 system namespace."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| PD-T7-2__PD-T7-2_B                               | PD-T7-2__PD-T7-2_B                               | PD-T7-2                | Custom                  | 100    |",
                "notes": "The DefenseFinder HMM inventory records PD-T7-2__PD-T7-2_B under the PD-T7-2 system namespace."
              }
            ]
          },
          {
            "subject": "pd_t7_2_listed_phage_protection",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "pd_t7_2_system_trait",
            "description": "Protection against the listed phages realizes the PD-T7-2 system trait.",
            "evidence": [
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-2.md",
                "snippet": "Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0\n    Origin_0[Escherichia coli \n<a href='https://ncbi.nlm.nih.gov/protein/RRM73498.1'>RRM73498.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/RRM73410.1'>RRM73410.1</a>] --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> T2 & T4 & T6 & LambdaVir & T5 & SECphi18 & SECphi27 & T3 & T7",
                "notes": "The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-T7-2 source locus expressed in E. coli against T2, T4, T6, LambdaVir, T5, SECphi18, SECphi27, T3, and T7."
              },
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-2.md",
                "snippet": "subgraph Title4[Protects against]\n        T2\n        T4\n        T6\n        LambdaVir\n        T5\n        SECphi18\n        SECphi27\n        T3\n        T7",
                "notes": "The DefenseFinder experimental-validation diagram lists T2, T4, T6, LambdaVir, T5, SECphi18, SECphi27, T3, and T7 in the PD-T7-2 protects-against subgraph."
              }
            ]
          },
          {
            "subject": "pd_t7_2_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "PD-T7-2 system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-022-01219-4",
                "snippet": "Here we developed an experimental selection scheme agnostic to genomic context to identify defence systems in 71 diverse E. coli strains. Our results unveil 21 conserved defence systems, none of which were previously detected as enriched in defence islands.",
                "notes": "Vassallo et al. developed the agnostic E. coli pangenome selection that uncovered PD-T7-2 and related conserved phage-defense systems."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "PD-T7-2 | 10\\.1101/2022\\.05\\.12\\.491691 | Mapping the landscape of anti-phage defense mechanisms in the E\\. coli pangenome",
                "notes": "The DefenseFinder article registry maps the named PD-T7-2 system to the Vassallo et al. E. coli pangenome phage-defense preprint."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "PD-T7-2\tPD-T7-2\t2\t2\tPD-T7-2__PD-T7-2_A, PD-T7-2__PD-T7-2_B\t\t\t",
                "notes": "The DefenseFinder rules table models PD-T7-2 as a two-profile system requiring PD-T7-2__PD-T7-2_A and PD-T7-2__PD-T7-2_B."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "pd-t7-2-mechanism-gap",
        "prompt": "Resolve PD-T7-2 natural host breadth, direct phage trigger, effector mechanism, and profile-to-protein correspondence before minting narrower PD-T7-2 mechanism traits.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Vassallo et al. support PD-T7-2 as one of the conserved systems from an E. coli pangenome phage-defense selection, the DefenseFinder wiki maps the source locus to broad phage protection, and DefenseFinder represents the system with two profiles. Natural host breadth, the direct phage trigger, exact effector logic, and the exact correspondence between the two profiles and proteins remain unresolved.",
        "evidence": [
          {
            "reference": "DOI:10.1038/s41564-022-01219-4",
            "snippet": "Here we developed an experimental selection scheme agnostic to genomic context to identify defence systems in 71 diverse E. coli strains. Our results unveil 21 conserved defence systems, none of which were previously detected as enriched in defence islands.",
            "notes": "Vassallo et al. developed the agnostic E. coli pangenome selection that uncovered PD-T7-2 and related conserved phage-defense systems."
          },
          {
            "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-2.md",
            "snippet": "The PD-T7-2 is composed of 2 proteins: PD-T7-2_A and PD-T7-2_B.",
            "notes": "The DefenseFinder wiki names PD-T7-2 as a two-protein system with PD-T7-2_A and PD-T7-2_B."
          },
          {
            "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-2.md",
            "snippet": "Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0\n    Origin_0[Escherichia coli \n<a href='https://ncbi.nlm.nih.gov/protein/RRM73498.1'>RRM73498.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/RRM73410.1'>RRM73410.1</a>] --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> T2 & T4 & T6 & LambdaVir & T5 & SECphi18 & SECphi27 & T3 & T7",
            "notes": "The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-T7-2 source locus expressed in E. coli against T2, T4, T6, LambdaVir, T5, SECphi18, SECphi27, T3, and T7."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "snippet": "PD-T7-2\tPD-T7-2\t2\t2\tPD-T7-2__PD-T7-2_A, PD-T7-2__PD-T7-2_B\t\t\t",
            "notes": "The DefenseFinder rules table models PD-T7-2 as a two-profile system requiring PD-T7-2__PD-T7-2_A and PD-T7-2__PD-T7-2_B."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| PD-T7-2__PD-T7-2_A                               | PD-T7-2__PD-T7-2_A                               | PD-T7-2                | Custom                  | 50     |",
            "notes": "The DefenseFinder HMM inventory records PD-T7-2__PD-T7-2_A under the PD-T7-2 system namespace."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| PD-T7-2__PD-T7-2_B                               | PD-T7-2__PD-T7-2_B                               | PD-T7-2                | Custom                  | 100    |",
            "notes": "The DefenseFinder HMM inventory records PD-T7-2__PD-T7-2_B under the PD-T7-2 system namespace."
          }
        ],
        "attaches_to": [
          "causal_graphs#pd_t7_2_locus_restricts_phages"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-26"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-26T23:48:04Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted PD-T7-2 system as a DOI- and DefenseFinder-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v273.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-26T23:48:05Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed PD-T7-2 system canonical_examples and left them empty because the current sources support an E. coli accession-level experimental validation graph, a DefenseFinder system model, and a RefSeq Lederbergia lenta example, but not a direct native microbial isolate exemplar with experimentally verified endogenous PD-T7-2 activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000405",
    "label": "PD-T7-3 system",
    "definition": "A phage defense system in which an organism possesses a PD-T7-3 locus represented by DefenseFinder as a single-profile model, PD-T7-3__PD-T7-3, and experimentally linked to protection against T2, T4, T6, T5, SECphi17, T3, and T7 when expressed in E. coli.",
    "definition_source": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-3.md",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "PD-T7-3",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-3.md"
      },
      {
        "synonym_text": "PD-T7-3__PD-T7-3",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/s41564-022-01219-4",
        "snippet": "Here we developed an experimental selection scheme agnostic to genomic context to identify defence systems in 71 diverse E. coli strains. Our results unveil 21 conserved defence systems, none of which were previously detected as enriched in defence islands.",
        "notes": "Vassallo et al. developed the agnostic E. coli pangenome selection that uncovered PD-T7-3 and related conserved phage-defense systems."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-3.md",
        "snippet": "PD-T7-3 systems were discovered to be anti-phage systems during an experimental screen performed on *E. coli* strains :ref{doi=10.1038/s41564-022-01219-4}",
        "notes": "The DefenseFinder wiki describes PD-T7-3 as a phage-defense system discovered in an E. coli experimental screen."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-3.md",
        "snippet": "As far as we are aware, the molecular mechanism of PD-T7-3 is unknown.",
        "notes": "The DefenseFinder wiki records the PD-T7-3 molecular mechanism as unresolved."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-3.md",
        "snippet": "The PD-T7-3 is composed of 1 protein: PD-T7-3.",
        "notes": "The DefenseFinder wiki names PD-T7-3 as a single-protein system."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-3.md",
        "snippet": "The PD-T7-3 system in *Paraglaciecola psychrophila* (GCF_000347635.1, NC_020514) is composed of 1 protein: PD-T7-3 (WP_007636449.1)",
        "notes": "The DefenseFinder wiki illustrates a predicted one-protein PD-T7-3 locus in RefSeq assembly GCF_000347635.1 on NC_020514."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-3.md",
        "snippet": "Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0\n    Origin_0[Escherichia coli \n<a href='https://ncbi.nlm.nih.gov/protein/RCP48690.1'>RCP48690.1</a>] --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> T2 & T4 & T6 & T5 & SECphi17 & T3 & T7",
        "notes": "The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-T7-3 source locus expressed in E. coli against T2, T4, T6, T5, SECphi17, T3, and T7."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-3.md",
        "snippet": "subgraph Title4[Protects against]\n        T2\n        T4\n        T6\n        T5\n        SECphi17\n        T3\n        T7",
        "notes": "The DefenseFinder experimental-validation diagram lists T2, T4, T6, T5, SECphi17, T3, and T7 in the PD-T7-3 protects-against subgraph."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "PD-T7-3\tPD-T7-3\t1\t1\tPD-T7-3__PD-T7-3\t\t\t",
        "notes": "The DefenseFinder rules table models PD-T7-3 as a single-profile system requiring PD-T7-3__PD-T7-3."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| PD-T7-3__PD-T7-3                                 | PD-T7-3__PD-T7-3                                 | PD-T7-3                | Custom                  | 100    |",
        "notes": "The DefenseFinder HMM inventory records PD-T7-3__PD-T7-3 under the PD-T7-3 system namespace."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "pd_t7_3_locus_restricts_phages",
        "title": "PD-T7-3 loci restrict T2, T4, T6, T5, SECphi17, T3, and T7",
        "description": "Conservative system-level sketch linking possession of a PD-T7-3 locus to protection against T2, T4, T6, T5, SECphi17, T3, and T7.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures PD-T7-3 as a named DefenseFinder phage-defense system while leaving natural host breadth, the direct phage trigger, and the effector mechanism unresolved.",
        "nodes": [
          {
            "node_id": "pd_t7_3_locus",
            "label": "PD-T7-3 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A phage-defense locus represented by the PD-T7-3 DefenseFinder profile."
          },
          {
            "node_id": "pd_t7_3_listed_phage_protection",
            "label": "T2, T4, T6, T5, SECphi17, T3, and T7 protection",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Protection against T2, T4, T6, T5, SECphi17, T3, and T7 by PD-T7-3."
          },
          {
            "node_id": "pd_t7_3_system_trait",
            "label": "PD-T7-3 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000405",
            "description": "Possession of a genome-encoded PD-T7-3 phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "pd_t7_3_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "pd_t7_3_listed_phage_protection",
            "description": "The DefenseFinder wiki links a PD-T7-3 locus from Vassallo et al. to protection against T2, T4, T6, T5, SECphi17, T3, and T7, and DefenseFinder models PD-T7-3 through one mandatory profile.",
            "evidence": [
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-3.md",
                "snippet": "PD-T7-3 systems were discovered to be anti-phage systems during an experimental screen performed on *E. coli* strains :ref{doi=10.1038/s41564-022-01219-4}",
                "notes": "The DefenseFinder wiki describes PD-T7-3 as a phage-defense system discovered in an E. coli experimental screen."
              },
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-3.md",
                "snippet": "As far as we are aware, the molecular mechanism of PD-T7-3 is unknown.",
                "notes": "The DefenseFinder wiki records the PD-T7-3 molecular mechanism as unresolved."
              },
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-3.md",
                "snippet": "The PD-T7-3 is composed of 1 protein: PD-T7-3.",
                "notes": "The DefenseFinder wiki names PD-T7-3 as a single-protein system."
              },
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-3.md",
                "snippet": "Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0\n    Origin_0[Escherichia coli \n<a href='https://ncbi.nlm.nih.gov/protein/RCP48690.1'>RCP48690.1</a>] --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> T2 & T4 & T6 & T5 & SECphi17 & T3 & T7",
                "notes": "The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-T7-3 source locus expressed in E. coli against T2, T4, T6, T5, SECphi17, T3, and T7."
              },
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-3.md",
                "snippet": "subgraph Title4[Protects against]\n        T2\n        T4\n        T6\n        T5\n        SECphi17\n        T3\n        T7",
                "notes": "The DefenseFinder experimental-validation diagram lists T2, T4, T6, T5, SECphi17, T3, and T7 in the PD-T7-3 protects-against subgraph."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "PD-T7-3\tPD-T7-3\t1\t1\tPD-T7-3__PD-T7-3\t\t\t",
                "notes": "The DefenseFinder rules table models PD-T7-3 as a single-profile system requiring PD-T7-3__PD-T7-3."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| PD-T7-3__PD-T7-3                                 | PD-T7-3__PD-T7-3                                 | PD-T7-3                | Custom                  | 100    |",
                "notes": "The DefenseFinder HMM inventory records PD-T7-3__PD-T7-3 under the PD-T7-3 system namespace."
              }
            ]
          },
          {
            "subject": "pd_t7_3_listed_phage_protection",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "pd_t7_3_system_trait",
            "description": "Protection against T2, T4, T6, T5, SECphi17, T3, and T7 realizes the PD-T7-3 system trait.",
            "evidence": [
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-3.md",
                "snippet": "Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0\n    Origin_0[Escherichia coli \n<a href='https://ncbi.nlm.nih.gov/protein/RCP48690.1'>RCP48690.1</a>] --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> T2 & T4 & T6 & T5 & SECphi17 & T3 & T7",
                "notes": "The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-T7-3 source locus expressed in E. coli against T2, T4, T6, T5, SECphi17, T3, and T7."
              },
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-3.md",
                "snippet": "subgraph Title4[Protects against]\n        T2\n        T4\n        T6\n        T5\n        SECphi17\n        T3\n        T7",
                "notes": "The DefenseFinder experimental-validation diagram lists T2, T4, T6, T5, SECphi17, T3, and T7 in the PD-T7-3 protects-against subgraph."
              }
            ]
          },
          {
            "subject": "pd_t7_3_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "PD-T7-3 system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-022-01219-4",
                "snippet": "Here we developed an experimental selection scheme agnostic to genomic context to identify defence systems in 71 diverse E. coli strains. Our results unveil 21 conserved defence systems, none of which were previously detected as enriched in defence islands.",
                "notes": "Vassallo et al. developed the agnostic E. coli pangenome selection that uncovered PD-T7-3 and related conserved phage-defense systems."
              },
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-3.md",
                "snippet": "The PD-T7-3 is composed of 1 protein: PD-T7-3.",
                "notes": "The DefenseFinder wiki names PD-T7-3 as a single-protein system."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "PD-T7-3\tPD-T7-3\t1\t1\tPD-T7-3__PD-T7-3\t\t\t",
                "notes": "The DefenseFinder rules table models PD-T7-3 as a single-profile system requiring PD-T7-3__PD-T7-3."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "pd-t7-3-mechanism-gap",
        "prompt": "Resolve PD-T7-3 natural host breadth, direct phage trigger, and effector mechanism before minting narrower PD-T7-3 mechanism traits.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Vassallo et al. support PD-T7-3 as one of the conserved systems from an E. coli pangenome phage-defense selection, the DefenseFinder wiki maps the source locus to protection against T2, T4, T6, T5, SECphi17, T3, and T7, and DefenseFinder represents the system with one profile. Natural host breadth, the direct phage trigger, and effector logic remain unresolved.",
        "evidence": [
          {
            "reference": "DOI:10.1038/s41564-022-01219-4",
            "snippet": "Here we developed an experimental selection scheme agnostic to genomic context to identify defence systems in 71 diverse E. coli strains. Our results unveil 21 conserved defence systems, none of which were previously detected as enriched in defence islands.",
            "notes": "Vassallo et al. developed the agnostic E. coli pangenome selection that uncovered PD-T7-3 and related conserved phage-defense systems."
          },
          {
            "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-3.md",
            "snippet": "PD-T7-3 systems were discovered to be anti-phage systems during an experimental screen performed on *E. coli* strains :ref{doi=10.1038/s41564-022-01219-4}",
            "notes": "The DefenseFinder wiki describes PD-T7-3 as a phage-defense system discovered in an E. coli experimental screen."
          },
          {
            "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-3.md",
            "snippet": "As far as we are aware, the molecular mechanism of PD-T7-3 is unknown.",
            "notes": "The DefenseFinder wiki records the PD-T7-3 molecular mechanism as unresolved."
          },
          {
            "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-3.md",
            "snippet": "Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0\n    Origin_0[Escherichia coli \n<a href='https://ncbi.nlm.nih.gov/protein/RCP48690.1'>RCP48690.1</a>] --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> T2 & T4 & T6 & T5 & SECphi17 & T3 & T7",
            "notes": "The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-T7-3 source locus expressed in E. coli against T2, T4, T6, T5, SECphi17, T3, and T7."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "snippet": "PD-T7-3\tPD-T7-3\t1\t1\tPD-T7-3__PD-T7-3\t\t\t",
            "notes": "The DefenseFinder rules table models PD-T7-3 as a single-profile system requiring PD-T7-3__PD-T7-3."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| PD-T7-3__PD-T7-3                                 | PD-T7-3__PD-T7-3                                 | PD-T7-3                | Custom                  | 100    |",
            "notes": "The DefenseFinder HMM inventory records PD-T7-3__PD-T7-3 under the PD-T7-3 system namespace."
          }
        ],
        "attaches_to": [
          "causal_graphs#pd_t7_3_locus_restricts_phages"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-27"
      },
      {
        "discussion_id": "pd-t7-3-defensefinder-article-registry-gap",
        "prompt": "Recheck whether DefenseFinder adds a PD-T7-3 List_system_article.md row before using the article registry as direct PD-T7-3 model-to-paper evidence.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "The pinned DefenseFinder wiki, rules table, and HMM inventory all represent PD-T7-3, but the pinned List_system_article.md registry omits a PD-T7-3 row. The PD-T7-3 record therefore cites the pinned wiki plus the DOI-backed Vassallo et al. screen instead of inventing a missing article-registry entry.",
        "evidence": [
          {
            "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-3.md",
            "snippet": "PD-T7-3 systems were discovered to be anti-phage systems during an experimental screen performed on *E. coli* strains :ref{doi=10.1038/s41564-022-01219-4}",
            "notes": "The DefenseFinder wiki describes PD-T7-3 as a phage-defense system discovered in an E. coli experimental screen."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "snippet": "PD-T7-3\tPD-T7-3\t1\t1\tPD-T7-3__PD-T7-3\t\t\t",
            "notes": "The DefenseFinder rules table models PD-T7-3 as a single-profile system requiring PD-T7-3__PD-T7-3."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| PD-T7-3__PD-T7-3                                 | PD-T7-3__PD-T7-3                                 | PD-T7-3                | Custom                  | 100    |",
            "notes": "The DefenseFinder HMM inventory records PD-T7-3__PD-T7-3 under the PD-T7-3 system namespace."
          }
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-27"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-27T08:02:09Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted PD-T7-3 system as a DOI- and DefenseFinder-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v282.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-27T08:02:10Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed PD-T7-3 system canonical_examples and left them empty because the current sources support an E. coli accession-level experimental validation graph, a DefenseFinder system model, and a RefSeq Paraglaciecola psychrophila example, but not a direct native microbial isolate exemplar with experimentally verified endogenous PD-T7-3 activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000406",
    "label": "PD-T7-4 system",
    "definition": "A phage defense system in which an organism possesses a PD-T7-4 locus represented by DefenseFinder as a single-profile model, PD-T7-4__PD-T7-4, and experimentally linked to protection against SECphi18, SECphi27, T3, and T7 when expressed in E. coli.",
    "definition_source": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-4.md",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "PD-T7-4",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-4.md"
      },
      {
        "synonym_text": "PD-T7-4__PD-T7-4",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/s41564-022-01219-4",
        "snippet": "Here we developed an experimental selection scheme agnostic to genomic context to identify defence systems in 71 diverse E. coli strains. Our results unveil 21 conserved defence systems, none of which were previously detected as enriched in defence islands.",
        "notes": "Vassallo et al. developed the agnostic E. coli pangenome selection that uncovered PD-T7-4 and related conserved phage-defense systems."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-4.md",
        "snippet": "Sensor: Unknown\n    Activator: Unknown\n    Effector: Unknown\n    PFAM: PF13643",
        "notes": "The pinned DefenseFinder PD-T7-4 page has no sensor, activator, or effector annotation for PD-T7-4 and lists PF13643 as the associated Pfam profile."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-4.md",
        "snippet": "The PD-T7-4 is composed of 1 protein: PD-T7-4.",
        "notes": "The DefenseFinder wiki names PD-T7-4 as a single-protein system."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-4.md",
        "snippet": "The PD-T7-4 system in *Salinibacterium hongtaonis* (GCF_003065485.1, NZ_CP026951) is composed of 1 protein: PD-T7-4 (WP_108515598.1)",
        "notes": "The DefenseFinder wiki illustrates a predicted one-protein PD-T7-4 locus in RefSeq assembly GCF_003065485.1 on NZ_CP026951."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-4.md",
        "snippet": "Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0\n    Origin_0[Escherichia coli \n<a href='https://ncbi.nlm.nih.gov/protein/RRL46918.1'>RRL46918.1</a>] --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> SECphi18 & SECphi27 & T3 & T7",
        "notes": "The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-T7-4 source locus expressed in E. coli against SECphi18, SECphi27, T3, and T7."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-4.md",
        "snippet": "subgraph Title4[Protects against]\n        SECphi18\n        SECphi27\n        T3\n        T7",
        "notes": "The DefenseFinder experimental-validation diagram lists SECphi18, SECphi27, T3, and T7 in the PD-T7-4 protects-against subgraph."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "PD-T7-4\tPD-T7-4\t1\t1\tPD-T7-4__PD-T7-4\t\t\t",
        "notes": "The DefenseFinder rules table models PD-T7-4 as a single-profile system requiring PD-T7-4__PD-T7-4."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| PD-T7-4__PD-T7-4                                 | PD-T7-4__PD-T7-4                                 | PD-T7-4                | Custom                  | 100    |",
        "notes": "The DefenseFinder HMM inventory records PD-T7-4__PD-T7-4 under the PD-T7-4 system namespace."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "pd_t7_4_locus_restricts_phages",
        "title": "PD-T7-4 loci restrict SECphi18, SECphi27, T3, and T7",
        "description": "Conservative system-level sketch linking possession of a PD-T7-4 locus to protection against SECphi18, SECphi27, T3, and T7.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures PD-T7-4 as a named DefenseFinder phage-defense system while leaving natural host breadth, the direct phage trigger, and the PF13643-associated effector mechanism unresolved.",
        "nodes": [
          {
            "node_id": "pd_t7_4_locus",
            "label": "PD-T7-4 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A phage-defense locus represented by the PD-T7-4 DefenseFinder profile."
          },
          {
            "node_id": "pd_t7_4_listed_phage_protection",
            "label": "SECphi18, SECphi27, T3, and T7 protection",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Protection against SECphi18, SECphi27, T3, and T7 by PD-T7-4."
          },
          {
            "node_id": "pd_t7_4_system_trait",
            "label": "PD-T7-4 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000406",
            "description": "Possession of a genome-encoded PD-T7-4 phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "pd_t7_4_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "pd_t7_4_listed_phage_protection",
            "description": "The DefenseFinder wiki links a PD-T7-4 locus from Vassallo et al. to protection against SECphi18, SECphi27, T3, and T7, and DefenseFinder models PD-T7-4 through one mandatory profile.",
            "evidence": [
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-4.md",
                "snippet": "Sensor: Unknown\n    Activator: Unknown\n    Effector: Unknown\n    PFAM: PF13643",
                "notes": "The pinned DefenseFinder PD-T7-4 page has no sensor, activator, or effector annotation for PD-T7-4 and lists PF13643 as the associated Pfam profile."
              },
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-4.md",
                "snippet": "The PD-T7-4 is composed of 1 protein: PD-T7-4.",
                "notes": "The DefenseFinder wiki names PD-T7-4 as a single-protein system."
              },
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-4.md",
                "snippet": "Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0\n    Origin_0[Escherichia coli \n<a href='https://ncbi.nlm.nih.gov/protein/RRL46918.1'>RRL46918.1</a>] --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> SECphi18 & SECphi27 & T3 & T7",
                "notes": "The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-T7-4 source locus expressed in E. coli against SECphi18, SECphi27, T3, and T7."
              },
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-4.md",
                "snippet": "subgraph Title4[Protects against]\n        SECphi18\n        SECphi27\n        T3\n        T7",
                "notes": "The DefenseFinder experimental-validation diagram lists SECphi18, SECphi27, T3, and T7 in the PD-T7-4 protects-against subgraph."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "PD-T7-4\tPD-T7-4\t1\t1\tPD-T7-4__PD-T7-4\t\t\t",
                "notes": "The DefenseFinder rules table models PD-T7-4 as a single-profile system requiring PD-T7-4__PD-T7-4."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| PD-T7-4__PD-T7-4                                 | PD-T7-4__PD-T7-4                                 | PD-T7-4                | Custom                  | 100    |",
                "notes": "The DefenseFinder HMM inventory records PD-T7-4__PD-T7-4 under the PD-T7-4 system namespace."
              }
            ]
          },
          {
            "subject": "pd_t7_4_listed_phage_protection",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "pd_t7_4_system_trait",
            "description": "Protection against SECphi18, SECphi27, T3, and T7 realizes the PD-T7-4 system trait.",
            "evidence": [
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-4.md",
                "snippet": "Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0\n    Origin_0[Escherichia coli \n<a href='https://ncbi.nlm.nih.gov/protein/RRL46918.1'>RRL46918.1</a>] --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> SECphi18 & SECphi27 & T3 & T7",
                "notes": "The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-T7-4 source locus expressed in E. coli against SECphi18, SECphi27, T3, and T7."
              },
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-4.md",
                "snippet": "subgraph Title4[Protects against]\n        SECphi18\n        SECphi27\n        T3\n        T7",
                "notes": "The DefenseFinder experimental-validation diagram lists SECphi18, SECphi27, T3, and T7 in the PD-T7-4 protects-against subgraph."
              }
            ]
          },
          {
            "subject": "pd_t7_4_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "PD-T7-4 system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-022-01219-4",
                "snippet": "Here we developed an experimental selection scheme agnostic to genomic context to identify defence systems in 71 diverse E. coli strains. Our results unveil 21 conserved defence systems, none of which were previously detected as enriched in defence islands.",
                "notes": "Vassallo et al. developed the agnostic E. coli pangenome selection that uncovered PD-T7-4 and related conserved phage-defense systems."
              },
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-4.md",
                "snippet": "The PD-T7-4 is composed of 1 protein: PD-T7-4.",
                "notes": "The DefenseFinder wiki names PD-T7-4 as a single-protein system."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "PD-T7-4\tPD-T7-4\t1\t1\tPD-T7-4__PD-T7-4\t\t\t",
                "notes": "The DefenseFinder rules table models PD-T7-4 as a single-profile system requiring PD-T7-4__PD-T7-4."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "pd-t7-4-mechanism-gap",
        "prompt": "Resolve PD-T7-4 natural host breadth, direct phage trigger, and PF13643-associated effector mechanism before minting narrower PD-T7-4 mechanism traits.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Vassallo et al. support PD-T7-4 as one of the conserved systems from an E. coli pangenome phage-defense selection, the DefenseFinder wiki maps the source locus to protection against SECphi18, SECphi27, T3, and T7, and DefenseFinder represents the system with one profile. Natural host breadth, the direct phage trigger, and effector logic remain unresolved.",
        "evidence": [
          {
            "reference": "DOI:10.1038/s41564-022-01219-4",
            "snippet": "Here we developed an experimental selection scheme agnostic to genomic context to identify defence systems in 71 diverse E. coli strains. Our results unveil 21 conserved defence systems, none of which were previously detected as enriched in defence islands.",
            "notes": "Vassallo et al. developed the agnostic E. coli pangenome selection that uncovered PD-T7-4 and related conserved phage-defense systems."
          },
          {
            "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-4.md",
            "snippet": "Sensor: Unknown\n    Activator: Unknown\n    Effector: Unknown\n    PFAM: PF13643",
            "notes": "The pinned DefenseFinder PD-T7-4 page has no sensor, activator, or effector annotation for PD-T7-4 and lists PF13643 as the associated Pfam profile."
          },
          {
            "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-4.md",
            "snippet": "Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0\n    Origin_0[Escherichia coli \n<a href='https://ncbi.nlm.nih.gov/protein/RRL46918.1'>RRL46918.1</a>] --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> SECphi18 & SECphi27 & T3 & T7",
            "notes": "The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-T7-4 source locus expressed in E. coli against SECphi18, SECphi27, T3, and T7."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "snippet": "PD-T7-4\tPD-T7-4\t1\t1\tPD-T7-4__PD-T7-4\t\t\t",
            "notes": "The DefenseFinder rules table models PD-T7-4 as a single-profile system requiring PD-T7-4__PD-T7-4."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| PD-T7-4__PD-T7-4                                 | PD-T7-4__PD-T7-4                                 | PD-T7-4                | Custom                  | 100    |",
            "notes": "The DefenseFinder HMM inventory records PD-T7-4__PD-T7-4 under the PD-T7-4 system namespace."
          }
        ],
        "attaches_to": [
          "causal_graphs#pd_t7_4_locus_restricts_phages"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-27"
      },
      {
        "discussion_id": "pd-t7-4-defensefinder-article-registry-gap",
        "prompt": "Recheck whether DefenseFinder adds a PD-T7-4 List_system_article.md row before using the article registry as direct PD-T7-4 model-to-paper evidence.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "The pinned DefenseFinder wiki, rules table, and HMM inventory all represent PD-T7-4, but the pinned List_system_article.md registry omits a PD-T7-4 row. The PD-T7-4 record therefore cites the pinned wiki plus the DOI-backed Vassallo et al. screen instead of inventing a missing article-registry entry.",
        "evidence": [
          {
            "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-4.md",
            "snippet": "The PD-T7-4 is composed of 1 protein: PD-T7-4.",
            "notes": "The DefenseFinder wiki names PD-T7-4 as a single-protein system."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "snippet": "PD-T7-4\tPD-T7-4\t1\t1\tPD-T7-4__PD-T7-4\t\t\t",
            "notes": "The DefenseFinder rules table models PD-T7-4 as a single-profile system requiring PD-T7-4__PD-T7-4."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| PD-T7-4__PD-T7-4                                 | PD-T7-4__PD-T7-4                                 | PD-T7-4                | Custom                  | 100    |",
            "notes": "The DefenseFinder HMM inventory records PD-T7-4__PD-T7-4 under the PD-T7-4 system namespace."
          }
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-27"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-27T08:45:27Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted PD-T7-4 system as a DOI- and DefenseFinder-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v283.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-27T08:45:28Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed PD-T7-4 system canonical_examples and left them empty because the current sources support an E. coli accession-level experimental validation graph, a DefenseFinder system model, and a RefSeq Salinibacterium hongtaonis example, but not a direct native microbial isolate exemplar with experimentally verified endogenous PD-T7-4 activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000397",
    "label": "PD-T7-5 system",
    "definition": "A phage defense system in which an organism possesses a PD-T7-5 locus represented by DefenseFinder as a single-profile model, PD-T7-5__PD-T7-5, and experimentally linked to SECphi17, T3, and T7 protection when expressed in E. coli.",
    "definition_source": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-5.md",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "PD-T7-5",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-5.md"
      },
      {
        "synonym_text": "PD-T7-5__PD-T7-5",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/s41564-022-01219-4",
        "snippet": "Here we developed an experimental selection scheme agnostic to genomic context to identify defence systems in 71 diverse E. coli strains. Our results unveil 21 conserved defence systems, none of which were previously detected as enriched in defence islands.",
        "notes": "Vassallo et al. developed the agnostic E. coli pangenome selection that uncovered PD-T7-5 and related conserved phage-defense systems."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-5.md",
        "snippet": "PD-T7-5 is a defense system composed of a single protein which was discovered in :ref{doi=10.1038/s41564-022-01219-4}. Its antiphage activity was assessed by heterologous expression in *E. coli* against T7 and to reduce the size of lysis plaques of T3 :ref{doi=10.1038/s41564-022-01219-4}. PD-T7-5 contains a PD(D/E)XK nuclease domain like [PD-T7-1](/defense-systems/pd-t7-1).",
        "notes": "The DefenseFinder wiki describes PD-T7-5 as a single-protein defense system with heterologous E. coli antiphage activity against T7 and T3 plaque-size reduction."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-5.md",
        "snippet": "As far as we are aware, the molecular mechanism is unknown. However, the presence of a PD(D/E)XK domain in PD-T7-5 suggests a mechanism of action via DNA degradation :ref{doi=10.1038/s41564-022-01219-4}.",
        "notes": "The DefenseFinder wiki states that PD-T7-5 molecular mechanism is unresolved and leaves the PD(D/E)XK-mediated DNA degradation interpretation as a hypothesis."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-5.md",
        "snippet": "The PD-T7-5 system is composed of one protein: PD-T7-5.",
        "notes": "The DefenseFinder wiki names PD-T7-5 as a single-protein system."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-5.md",
        "snippet": "The PD-T7-5 system in *Shewanella putrefaciens* (GCF_019599085.1, NZ_CP080633) is composed of 1 protein: PD-T7-5 (WP_220590848.1)",
        "notes": "The DefenseFinder wiki illustrates a predicted one-protein PD-T7-5 locus in RefSeq assembly GCF_019599085.1 on NZ_CP080633."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-5.md",
        "snippet": "Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0\n    Origin_0[Escherichia coli \n<a href='https://ncbi.nlm.nih.gov/protein/RRM82777.1'>RRM82777.1</a>] --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> SECphi17 & T3 & T7",
        "notes": "The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-T7-5 source locus expressed in E. coli against SECphi17, T3, and T7."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-5.md",
        "snippet": "subgraph Title4[Protects against]\n        SECphi17\n        T3\n        T7",
        "notes": "The DefenseFinder experimental-validation diagram lists SECphi17, T3, and T7 in the PD-T7-5 protects-against subgraph."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "PD-T7-5 | 10\\.1101/2022\\.05\\.12\\.491691 | Mapping the landscape of anti-phage defense mechanisms in the E\\. coli pangenome",
        "notes": "The DefenseFinder article registry maps the named PD-T7-5 system to the Vassallo et al. E. coli pangenome phage-defense preprint."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "PD-T7-5\tPD-T7-5\t1\t1\tPD-T7-5__PD-T7-5\t\t\t",
        "notes": "The DefenseFinder rules table models PD-T7-5 as a single-profile system requiring PD-T7-5__PD-T7-5."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| PD-T7-5__PD-T7-5                                 | PD-T7-5__PD-T7-5                                 | PD-T7-5                | Custom                  | 90     |",
        "notes": "The DefenseFinder HMM inventory records PD-T7-5__PD-T7-5 under the PD-T7-5 system namespace."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "pd_t7_5_locus_restricts_phages",
        "title": "PD-T7-5 loci restrict SECphi17, T3, and T7",
        "description": "Conservative system-level sketch linking possession of a PD-T7-5 locus to protection against SECphi17, T3, and T7.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures PD-T7-5 as a named DefenseFinder phage-defense system while leaving natural host breadth, the direct phage trigger, and the PD(D/E)XK effector mechanism unresolved.",
        "nodes": [
          {
            "node_id": "pd_t7_5_locus",
            "label": "PD-T7-5 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A phage-defense locus represented by the PD-T7-5 DefenseFinder profile."
          },
          {
            "node_id": "pd_t7_5_listed_phage_protection",
            "label": "SECphi17, T3, and T7 protection",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Protection against SECphi17, T3, and T7 by PD-T7-5."
          },
          {
            "node_id": "pd_t7_5_system_trait",
            "label": "PD-T7-5 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000397",
            "description": "Possession of a genome-encoded PD-T7-5 phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "pd_t7_5_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "pd_t7_5_listed_phage_protection",
            "description": "The DefenseFinder wiki links a PD-T7-5 locus from Vassallo et al. to protection against SECphi17, T3, and T7, and DefenseFinder models PD-T7-5 through one mandatory profile.",
            "evidence": [
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-5.md",
                "snippet": "PD-T7-5 is a defense system composed of a single protein which was discovered in :ref{doi=10.1038/s41564-022-01219-4}. Its antiphage activity was assessed by heterologous expression in *E. coli* against T7 and to reduce the size of lysis plaques of T3 :ref{doi=10.1038/s41564-022-01219-4}. PD-T7-5 contains a PD(D/E)XK nuclease domain like [PD-T7-1](/defense-systems/pd-t7-1).",
                "notes": "The DefenseFinder wiki describes PD-T7-5 as a single-protein defense system with heterologous E. coli antiphage activity against T7 and T3 plaque-size reduction."
              },
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-5.md",
                "snippet": "As far as we are aware, the molecular mechanism is unknown. However, the presence of a PD(D/E)XK domain in PD-T7-5 suggests a mechanism of action via DNA degradation :ref{doi=10.1038/s41564-022-01219-4}.",
                "notes": "The DefenseFinder wiki states that PD-T7-5 molecular mechanism is unresolved and leaves the PD(D/E)XK-mediated DNA degradation interpretation as a hypothesis."
              },
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-5.md",
                "snippet": "The PD-T7-5 system is composed of one protein: PD-T7-5.",
                "notes": "The DefenseFinder wiki names PD-T7-5 as a single-protein system."
              },
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-5.md",
                "snippet": "Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0\n    Origin_0[Escherichia coli \n<a href='https://ncbi.nlm.nih.gov/protein/RRM82777.1'>RRM82777.1</a>] --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> SECphi17 & T3 & T7",
                "notes": "The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-T7-5 source locus expressed in E. coli against SECphi17, T3, and T7."
              },
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-5.md",
                "snippet": "subgraph Title4[Protects against]\n        SECphi17\n        T3\n        T7",
                "notes": "The DefenseFinder experimental-validation diagram lists SECphi17, T3, and T7 in the PD-T7-5 protects-against subgraph."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "PD-T7-5\tPD-T7-5\t1\t1\tPD-T7-5__PD-T7-5\t\t\t",
                "notes": "The DefenseFinder rules table models PD-T7-5 as a single-profile system requiring PD-T7-5__PD-T7-5."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| PD-T7-5__PD-T7-5                                 | PD-T7-5__PD-T7-5                                 | PD-T7-5                | Custom                  | 90     |",
                "notes": "The DefenseFinder HMM inventory records PD-T7-5__PD-T7-5 under the PD-T7-5 system namespace."
              }
            ]
          },
          {
            "subject": "pd_t7_5_listed_phage_protection",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "pd_t7_5_system_trait",
            "description": "Protection against SECphi17, T3, and T7 realizes the PD-T7-5 system trait.",
            "evidence": [
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-5.md",
                "snippet": "Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0\n    Origin_0[Escherichia coli \n<a href='https://ncbi.nlm.nih.gov/protein/RRM82777.1'>RRM82777.1</a>] --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> SECphi17 & T3 & T7",
                "notes": "The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-T7-5 source locus expressed in E. coli against SECphi17, T3, and T7."
              },
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-5.md",
                "snippet": "subgraph Title4[Protects against]\n        SECphi17\n        T3\n        T7",
                "notes": "The DefenseFinder experimental-validation diagram lists SECphi17, T3, and T7 in the PD-T7-5 protects-against subgraph."
              }
            ]
          },
          {
            "subject": "pd_t7_5_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "PD-T7-5 system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-022-01219-4",
                "snippet": "Here we developed an experimental selection scheme agnostic to genomic context to identify defence systems in 71 diverse E. coli strains. Our results unveil 21 conserved defence systems, none of which were previously detected as enriched in defence islands.",
                "notes": "Vassallo et al. developed the agnostic E. coli pangenome selection that uncovered PD-T7-5 and related conserved phage-defense systems."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "PD-T7-5 | 10\\.1101/2022\\.05\\.12\\.491691 | Mapping the landscape of anti-phage defense mechanisms in the E\\. coli pangenome",
                "notes": "The DefenseFinder article registry maps the named PD-T7-5 system to the Vassallo et al. E. coli pangenome phage-defense preprint."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "PD-T7-5\tPD-T7-5\t1\t1\tPD-T7-5__PD-T7-5\t\t\t",
                "notes": "The DefenseFinder rules table models PD-T7-5 as a single-profile system requiring PD-T7-5__PD-T7-5."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "pd-t7-5-mechanism-gap",
        "prompt": "Resolve PD-T7-5 natural host breadth, direct phage trigger, and PD(D/E)XK effector mechanism before minting narrower PD-T7-5 mechanism traits.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Vassallo et al. support PD-T7-5 as one of the conserved systems from an E. coli pangenome phage-defense selection, the DefenseFinder wiki maps the source locus to protection against SECphi17, T3, and T7, and DefenseFinder represents the system with one profile. Natural host breadth, the direct phage trigger, and the PD(D/E)XK effector mechanism remain unresolved.",
        "evidence": [
          {
            "reference": "DOI:10.1038/s41564-022-01219-4",
            "snippet": "Here we developed an experimental selection scheme agnostic to genomic context to identify defence systems in 71 diverse E. coli strains. Our results unveil 21 conserved defence systems, none of which were previously detected as enriched in defence islands.",
            "notes": "Vassallo et al. developed the agnostic E. coli pangenome selection that uncovered PD-T7-5 and related conserved phage-defense systems."
          },
          {
            "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-5.md",
            "snippet": "PD-T7-5 is a defense system composed of a single protein which was discovered in :ref{doi=10.1038/s41564-022-01219-4}. Its antiphage activity was assessed by heterologous expression in *E. coli* against T7 and to reduce the size of lysis plaques of T3 :ref{doi=10.1038/s41564-022-01219-4}. PD-T7-5 contains a PD(D/E)XK nuclease domain like [PD-T7-1](/defense-systems/pd-t7-1).",
            "notes": "The DefenseFinder wiki describes PD-T7-5 as a single-protein defense system with heterologous E. coli antiphage activity against T7 and T3 plaque-size reduction."
          },
          {
            "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-5.md",
            "snippet": "As far as we are aware, the molecular mechanism is unknown. However, the presence of a PD(D/E)XK domain in PD-T7-5 suggests a mechanism of action via DNA degradation :ref{doi=10.1038/s41564-022-01219-4}.",
            "notes": "The DefenseFinder wiki states that PD-T7-5 molecular mechanism is unresolved and leaves the PD(D/E)XK-mediated DNA degradation interpretation as a hypothesis."
          },
          {
            "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-5.md",
            "snippet": "The PD-T7-5 system is composed of one protein: PD-T7-5.",
            "notes": "The DefenseFinder wiki names PD-T7-5 as a single-protein system."
          },
          {
            "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-5.md",
            "snippet": "Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0\n    Origin_0[Escherichia coli \n<a href='https://ncbi.nlm.nih.gov/protein/RRM82777.1'>RRM82777.1</a>] --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> SECphi17 & T3 & T7",
            "notes": "The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-T7-5 source locus expressed in E. coli against SECphi17, T3, and T7."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "snippet": "PD-T7-5\tPD-T7-5\t1\t1\tPD-T7-5__PD-T7-5\t\t\t",
            "notes": "The DefenseFinder rules table models PD-T7-5 as a single-profile system requiring PD-T7-5__PD-T7-5."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| PD-T7-5__PD-T7-5                                 | PD-T7-5__PD-T7-5                                 | PD-T7-5                | Custom                  | 90     |",
            "notes": "The DefenseFinder HMM inventory records PD-T7-5__PD-T7-5 under the PD-T7-5 system namespace."
          }
        ],
        "attaches_to": [
          "causal_graphs#pd_t7_5_locus_restricts_phages"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-27"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-27T00:29:55Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted PD-T7-5 system as a DOI- and DefenseFinder-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v274.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-27T00:29:56Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed PD-T7-5 system canonical_examples and left them empty because the current sources support an E. coli accession-level experimental validation graph, a DefenseFinder system model, and a RefSeq Shewanella putrefaciens example, but not a direct native microbial isolate exemplar with experimentally verified endogenous PD-T7-5 activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000365",
    "label": "PfiAT system",
    "definition": "A phage defense system in which an organism possesses a Pf4 prophage-encoded PfiAT toxin-antitoxin locus represented by DefenseFinder as a two-profile model requiring PfiAT__PfiA and PfiAT__PfiT.",
    "definition_source": "DOI:10.1111/1751-7915.13570",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "PfiAT",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      },
      {
        "synonym_text": "PfiAT__PfiA",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "PfiAT__PfiT",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "PMID:32246813",
        "snippet": "we provided experimental evidence to demonstrate that PA0729 and the upstream ORF Rorf0727 near the right attachment site of Pf4 form a type II toxin/antitoxin (TA) pair.",
        "notes": "Li et al. experimentally identify PA0729 and Rorf0727 in the Pf4 prophage as a PfiT/PfiA type II toxin-antitoxin pair."
      },
      {
        "reference": "PMID:32246813",
        "snippet": "Importantly, we found that the deletion of the toxin gene PA0729 greatly increased Pf4 phage production.",
        "notes": "Li et al. show that deleting pfiT increases Pf4 phage production."
      },
      {
        "reference": "PMID:32246813",
        "snippet": "We thus suggest the toxin PA0729 be named PfiT for Pf4 inhibition toxin and Rorf0727 be named PfiA for PfiT antitoxin.",
        "notes": "Li et al. name PA0729 as PfiT and Rorf0727 as PfiA."
      },
      {
        "reference": "PMID:32246813",
        "snippet": "Therefore, this study reveals that the TA systems in Pf prophages can regulate phage production and phage immunity, providing new insights into the function of TAs in mobile genetic elements.",
        "notes": "Li et al. frame Pf prophage toxin-antitoxin systems as regulators of phage production and phage immunity."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "PfiAT | 10\\.1111/1751-7915\\.13570 | Prophage encoding toxin/antitoxin system PfiT/PfiA inhibits Pf4 production in Pseudomonas aeruginosa",
        "notes": "The DefenseFinder article registry maps the named PfiAT system to Li et al.'s Pf4 prophage PfiT/PfiA paper."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "PfiAT\tPfiAT\t2\t2\tPfiAT__PfiA, PfiAT__PfiT\t\t\t",
        "notes": "The DefenseFinder rules table models PfiAT as a two-profile system requiring the PfiAT__PfiA and PfiAT__PfiT profiles."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| PfiAT__PfiA                                      | PfiAT__PfiA                                      | PfiAT                  | Custom                  | 20     |",
        "notes": "The DefenseFinder HMM inventory records PfiAT__PfiA under PfiAT."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| PfiAT__PfiT                                      | PfiAT__PfiT                                      | PfiAT                  | Custom                  | 20     |",
        "notes": "The DefenseFinder HMM inventory records PfiAT__PfiT under PfiAT."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "pfiat_locus_regulates_pf4_phage",
        "title": "PfiAT loci regulate Pf4 prophage production",
        "description": "Conservative system-level sketch linking possession of a PfiAT locus to PfiT/PfiA-dependent regulation of Pf4 phage production and immunity without asserting the cellular PfiT toxin target or natural host breadth.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures PfiAT as a named DefenseFinder two-profile Pf prophage system while leaving natural host breadth, the cellular target of PfiT in Pseudomonas, Pf4 phage-immunity coupling, and PfiAT profile-to-activity mapping unresolved.",
        "nodes": [
          {
            "node_id": "pfiat_locus",
            "label": "PfiAT locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A Pf prophage-encoded PfiAT toxin-antitoxin locus represented by PfiAT__PfiA and PfiAT__PfiT profiles."
          },
          {
            "node_id": "pf4_phage_production_regulation",
            "label": "Pf4 phage production regulation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Regulation of Pf4 phage production and Pf4 phage immunity by a prophage-encoded PfiT/PfiA toxin-antitoxin pair."
          },
          {
            "node_id": "pfiat_system_trait",
            "label": "PfiAT system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000365",
            "description": "Possession of a genome-encoded PfiAT phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "pfiat_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "pf4_phage_production_regulation",
            "description": "Li et al. identify the Pf4 PA0729 and Rorf0727 locus as a PfiT/PfiA toxin-antitoxin pair whose pfiT toxin gene inhibits Pf4 production, and DefenseFinder models PfiAT as a two-profile system.",
            "evidence": [
              {
                "reference": "PMID:32246813",
                "snippet": "we provided experimental evidence to demonstrate that PA0729 and the upstream ORF Rorf0727 near the right attachment site of Pf4 form a type II toxin/antitoxin (TA) pair.",
                "notes": "Li et al. experimentally identify PA0729 and Rorf0727 as a PfiT/PfiA toxin-antitoxin pair near the right attachment site of Pf4."
              },
              {
                "reference": "PMID:32246813",
                "snippet": "Importantly, we found that the deletion of the toxin gene PA0729 greatly increased Pf4 phage production.",
                "notes": "Li et al. show that pfiT inhibits Pf4 phage production."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "PfiAT | 10\\.1111/1751-7915\\.13570 | Prophage encoding toxin/antitoxin system PfiT/PfiA inhibits Pf4 production in Pseudomonas aeruginosa",
                "notes": "The DefenseFinder article registry maps the named PfiAT system to Li et al.'s Pf4 prophage PfiT/PfiA paper."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "PfiAT\tPfiAT\t2\t2\tPfiAT__PfiA, PfiAT__PfiT\t\t\t",
                "notes": "The DefenseFinder rules table models PfiAT as a two-profile system requiring the PfiAT__PfiA and PfiAT__PfiT profiles."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| PfiAT__PfiA                                      | PfiAT__PfiA                                      | PfiAT                  | Custom                  | 20     |",
                "notes": "The DefenseFinder HMM inventory records PfiAT__PfiA under PfiAT."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| PfiAT__PfiT                                      | PfiAT__PfiT                                      | PfiAT                  | Custom                  | 20     |",
                "notes": "The DefenseFinder HMM inventory records PfiAT__PfiT under PfiAT."
              }
            ]
          },
          {
            "subject": "pf4_phage_production_regulation",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "pfiat_system_trait",
            "description": "PfiT/PfiA-dependent regulation of Pf4 phage production and immunity realizes the PfiAT system trait.",
            "evidence": [
              {
                "reference": "PMID:32246813",
                "snippet": "Therefore, this study reveals that the TA systems in Pf prophages can regulate phage production and phage immunity, providing new insights into the function of TAs in mobile genetic elements.",
                "notes": "Li et al. support Pf prophage toxin-antitoxin systems as regulators of phage production and phage immunity."
              }
            ]
          },
          {
            "subject": "pfiat_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "PfiAT system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "PfiAT | 10\\.1111/1751-7915\\.13570 | Prophage encoding toxin/antitoxin system PfiT/PfiA inhibits Pf4 production in Pseudomonas aeruginosa",
                "notes": "The DefenseFinder article registry maps the named PfiAT system to Li et al.'s Pf4 prophage PfiT/PfiA paper."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "PfiAT\tPfiAT\t2\t2\tPfiAT__PfiA, PfiAT__PfiT\t\t\t",
                "notes": "The DefenseFinder rules table models PfiAT as a two-profile system requiring the PfiAT__PfiA and PfiAT__PfiT profiles."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "pfiat-mechanism-gap",
        "prompt": "Resolve natural PfiAT host breadth, the PfiT cellular target in Pseudomonas, Pf prophage production and immunity coupling, and PfiAT profile-to-activity mapping before minting narrower PfiAT mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Li et al. support PA0729/PfiT and Rorf0727/PfiA in the Pf4 prophage as a type II toxin-antitoxin pair that regulates Pf4 production and phage immunity, and DefenseFinder models PfiAT as a two-profile system with PfiAT__PfiA and PfiAT__PfiT markers. Natural host breadth, the cellular target of PfiT, Pf4 immunity coupling, and profile-to-activity mapping remain unresolved.",
        "evidence": [
          {
            "reference": "PMID:32246813",
            "snippet": "Homologs of PfiT are also found in other Pseudomonas strains, and the cellular target of PfiT in Pseudomonas will be investigated in future studies.",
            "notes": "Li et al. explicitly leave the PfiT cellular target unresolved."
          }
        ],
        "attaches_to": [
          "causal_graphs#pfiat_locus_regulates_pf4_phage"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-22"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-22T12:25:36Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted PfiAT system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v242.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-22T12:25:37Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed the PfiAT canonical_examples gap and left canonical_examples empty: the current evidence supports the Pf4 prophage PfiT/PfiA toxin-antitoxin pair, its control of Pf4 phage production and immunity, and the pinned DefenseFinder PfiAT profiles, but does not cite a directly observed natural microbial taxon with a source-backed PfiAT locus broad enough for a canonical example. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000209",
    "label": "phage defense system",
    "definition": "A genomics trait describing possession of one or more bacterial or archaeal immune systems that inhibit bacteriophage infection.",
    "definition_source": "DOI:10.1038/s41579-019-0278-2",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000188"
    ],
    "synonyms": [
      {
        "synonym_text": "antiphage defense system",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1126/science.aar4120"
      },
      {
        "synonym_text": "anti-phage system",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1038/s41586-019-1894-8"
      },
      {
        "synonym_text": "pan-immune system",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1038/s41579-019-0278-2"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/s41579-019-0278-2",
        "snippet": "Viruses and their hosts are engaged in a constant arms race leading to the evolution of antiviral defence mechanisms",
        "notes": "Bernheim and Sorek define the bacterial bacteriophage-defense context and review the pan-genomic diversity and cost of antiviral defense systems."
      },
      {
        "reference": "DOI:10.1038/s41579-019-0278-2",
        "snippet": "individual microorganisms often encode multiple distinct defence systems",
        "notes": "The pan-immune-system model supports treating possession of one or more defense systems as a strain-level genomics trait rather than a single protein, locus, or pathway."
      },
      {
        "reference": "DOI:10.1038/s41586-019-1894-8",
        "snippet": "Bacteria have evolved numerous immune mechanisms, both innate and adaptive",
        "notes": "Hampton et al. review innate and adaptive anti-phage systems and the phage counter-defense mechanisms that evade them."
      },
      {
        "reference": "DOI:10.1038/s41586-019-1894-8",
        "snippet": "Here we review the spectrum of anti-phage systems and highlight their evasion by bacteriophages",
        "notes": "This supports the umbrella scope spanning diverse CRISPR-Cas, restriction-modification, BREX, DISARM, abortive-infection, and related anti-phage defenses."
      },
      {
        "reference": "DOI:10.1126/science.aar4120",
        "snippet": "Candidate immune systems were then experimentally validated for their activities",
        "notes": "The Science article summary for Doron et al. supports genomic discovery and experimental validation of antiphage defense systems from microbial pangenomes."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1308",
        "taxon_label": "Streptococcus thermophilus",
        "note": "S. thermophilus is the organism in which CRISPR-Cas adaptive immunity was experimentally shown to provide phage resistance.",
        "reference": "DOI:10.1126/science.1138140"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "phage_defense_system_hierarchy",
        "title": "Antiphage defense systems resist viral challenge",
        "description": "Evidence-backed ontology sketch linking phage pressure to the umbrella phage-defense-system trait and its reviewed CRISPR-Cas and restriction-modification children.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This parent trait groups independently reviewed genome-level anti-phage defense systems without claiming that CRISPR-Cas, restriction-modification, BREX, DISARM, abortive infection, or other defense families share one universal molecular mechanism.",
        "nodes": [
          {
            "node_id": "bacteriophage_pressure",
            "label": "bacteriophage pressure",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Selective pressure imposed by bacteriophage infection."
          },
          {
            "node_id": "phage_defense_system_trait",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          },
          {
            "node_id": "crispr_cas_system",
            "label": "CRISPR-Cas system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000094",
            "description": "Adaptive immune system using CRISPR arrays and Cas proteins to recognize invading nucleic acids."
          },
          {
            "node_id": "restriction_modification_system",
            "label": "restriction-modification system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000095",
            "description": "Paired methyltransferase and restriction-endonuclease system for self/non-self DNA discrimination."
          }
        ],
        "edges": [
          {
            "subject": "bacteriophage_pressure",
            "predicate": "selects for",
            "predicate_id": "METPO:2007401",
            "object": "phage_defense_system_trait",
            "description": "Virus-host arms races select for microbial antiviral defense mechanisms.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41579-019-0278-2",
                "snippet": "constant arms race leading to the evolution of antiviral defence mechanisms",
                "notes": "Bernheim and Sorek frame bacteriophages and bacterial hosts as engaged in an evolutionary arms race."
              }
            ]
          },
          {
            "subject": "crispr_cas_system",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system_trait",
            "description": "CRISPR-Cas possession is an adaptive phage-defense system.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.aar4120",
                "snippet": "well-known defense arsenals such as restriction-modification and CRISPR systems",
                "notes": "The Science article summary for Doron et al. places CRISPR systems among the recognized microbial defense arsenals."
              }
            ]
          },
          {
            "subject": "restriction_modification_system",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system_trait",
            "description": "Restriction-modification possession is an innate phage-defense system.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.aar4120",
                "snippet": "well-known defense arsenals such as restriction-modification and CRISPR systems",
                "notes": "The Science article summary for Doron et al. places restriction-modification systems among the recognized microbial defense arsenals."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "phage-defense-system-xref-gap",
        "prompt": "Resolve exact ontology xrefs for organism-level phage defense system possession before adding TraitRecord xrefs.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "The pinned METPO snapshot retains only obsolete phage defense, and GO:0051607 defense response to virus is a biological process rather than this GENOMICS possession trait. CRISPR-Cas, restriction-modification, BREX, DISARM, abortive-infection, and other mechanism terms are narrower than the umbrella parent curated here.",
        "posed_by": "codex",
        "posed_date": "2026-09-15"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-15T07:55:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted phage defense system as a DOI-backed GENOMICS TraitRecord after an ignored-and-hidden duplicate review found only obsolete METPO phage defense and future-gap mentions; the replacement placeholder is reserved in proposals/metpo_traitmech_v86.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000213",
    "label": "phosphorothioate defense system",
    "definition": "A genomics trait describing possession of a DNA phosphorothioation-dependent antiviral locus in which host DNA phosphorothioate modification is paired with a Dnd-, Ssp-, or Pbe-family effector module to restrict invading viral DNA.",
    "definition_source": "DOI:10.1038/s41564-020-0700-6",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "PT-associated R-M system",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1128/mbio.00933-23"
      },
      {
        "synonym_text": "PT-related R-M system",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1128/mbio.00933-23"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/s41564-020-0700-6",
        "snippet": "We previously identified the Dnd system, which uses DndABCDE to insert sulfur into the DNA backbone as a double-stranded phosphorothioate (PT) modification, and DndFGH, a restriction component",
        "notes": "Xiong et al. summarize the Dnd modification and restriction modules as a DNA phosphorothioation defense system."
      },
      {
        "reference": "DOI:10.1038/s41564-020-0700-6",
        "snippet": "SspABCD coupled with SspE provides protection against phages",
        "notes": "Xiong et al. support SspABCD-SspE as a bacterial phosphorothioation-sensing antiphage defense system."
      },
      {
        "reference": "DOI:10.1128/mbio.00933-23",
        "snippet": "Usually, this modification gene cluster is paired with a restriction module consisting of DndF, DndG, and DndH",
        "notes": "Jiang et al. support the paired modification-plus-restriction architecture of Dnd-related phosphorothioate R-M systems."
      },
      {
        "reference": "DOI:10.1128/mbio.00933-23",
        "snippet": "the host could benefit from the protection provided by Dnd-related R-M systems against infection by various lytic phages as well as temperate phages",
        "notes": "Jiang et al. experimentally demonstrated broad antiphage protection by Dnd-related phosphorothioate R-M systems."
      },
      {
        "reference": "DOI:10.1038/s41467-019-09390-9",
        "snippet": "DndCDEA-specific DNA phosphorothioate (PT) modification and the PbeABCD-mediated halt of virus propagation",
        "notes": "Xiong et al. support DndCDEA-PbeABCD as an archaeal phosphorothioation-dependent antiviral branch distinct from bacterial DndFGH and Ssp systems."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:340184",
        "taxon_label": "Escherichia coli B7A",
        "note": "Jiang et al. cloned the native E. coli B7A dndBCDE-FGH module into E. coli DH10B and measured strong DndB7A R-M protection against multiple lytic phages.",
        "reference": "DOI:10.1128/mbio.00933-23"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "phosphorothioate_dna_restriction_antiviral_defense",
        "title": "Phosphorothioate restriction modules target invading viral DNA",
        "description": "Evidence-backed process sketch linking host DNA phosphorothioate modification to PT-dependent self/non-self discrimination, restriction of invading viral DNA, and impaired viral DNA replication.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures system-level logic shared by phosphorothioate-based Dnd, Ssp, and Pbe antiviral systems without claiming that DndFGH, SspE, SspFGH, and PbeABCD sense PT marks, damage foreign DNA, or inhibit viral replication by one exact protein mechanism.",
        "nodes": [
          {
            "node_id": "phosphorothioate_modification_module",
            "label": "phosphorothioate modification module",
            "node_type": "GENETIC_ELEMENT",
            "description": "A Dnd-, Ssp-, or Pbe-paired gene module that installs sequence-specific phosphorothioate modifications on host DNA."
          },
          {
            "node_id": "dna_phosphorothioation",
            "label": "DNA phosphorothioation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Replacement of a nonbridging oxygen in the DNA phosphate backbone with sulfur."
          },
          {
            "node_id": "pt_dependent_foreign_dna_targeting",
            "label": "PT-dependent foreign DNA targeting",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Phosphorothioate-dependent self/non-self discrimination that targets invading DNA for restriction."
          },
          {
            "node_id": "viral_dna_restriction",
            "label": "viral DNA restriction",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Restriction of invading viral DNA by a PT-associated Dnd, Ssp, or Pbe effector module."
          },
          {
            "node_id": "viral_dna_replication",
            "label": "viral DNA replication",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Replication of invading viral DNA after host cell entry."
          },
          {
            "node_id": "phosphorothioate_defense_system_trait",
            "label": "phosphorothioate defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000213",
            "description": "Possession of a genome-encoded phosphorothioate-based antiviral defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit viral infection."
          }
        ],
        "edges": [
          {
            "subject": "phosphorothioate_modification_module",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "dna_phosphorothioation",
            "description": "DndABCDE or SspABCD modification modules install sequence-specific phosphorothioate marks on host DNA.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-020-0700-6",
                "snippet": "uses DndABCDE to insert sulfur into the DNA backbone as a double-stranded phosphorothioate (PT) modification",
                "notes": "Xiong et al. support DndABCDE-dependent host DNA phosphorothioation."
              },
              {
                "reference": "DOI:10.1038/s41564-020-0700-6",
                "snippet": "SspABCD confers single-stranded and high-frequency PTs with SspB acting as a nickase",
                "notes": "Xiong et al. support SspABCD-dependent host DNA phosphorothioation."
              }
            ]
          },
          {
            "subject": "dna_phosphorothioation",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "pt_dependent_foreign_dna_targeting",
            "description": "Sequence-specific PT marks couple host DNA modification to PT-dependent self/non-self restriction by Dnd-, Ssp-, and Pbe-family effector modules.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-020-0700-6",
                "snippet": "SspE senses sequence-specific PTs by virtue of its PT-stimulated NTPase activity to exert its anti-phage activity",
                "notes": "Xiong et al. support direct coupling between sequence-specific PT marks and SspE restriction activity."
              }
            ]
          },
          {
            "subject": "pt_dependent_foreign_dna_targeting",
            "predicate": "activates",
            "predicate_id": "RO:0002213",
            "object": "viral_dna_restriction",
            "description": "Dnd, Ssp, and Pbe phosphorothioation-dependent systems converge on restriction of viral DNA lacking host PT marks.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-020-0700-6",
                "snippet": "SspE inhibits phage propagation by introducing nicking damage to impair phage DNA replication",
                "notes": "Xiong et al. support SspE-linked nicking damage as a second PT-dependent route to restricted phage replication."
              },
              {
                "reference": "DOI:10.1128/mbio.00933-23",
                "snippet": "DndF, DndG, and DndH undergoes conformational changes to perform DNA binding, translocation, and DNA nicking activities and scavenge the foreign DNA",
                "notes": "Jiang et al. summarize DndFGH-mediated DNA binding, translocation, and nicking of foreign DNA that lacks PT modification."
              },
              {
                "reference": "DOI:10.1038/s41467-019-09390-9",
                "snippet": "PbeABCD exerted antiviral activity depending on the presence of PT modifications",
                "notes": "Xiong et al. support PT-dependent PbeABCD antiviral activity."
              }
            ]
          },
          {
            "subject": "viral_dna_restriction",
            "predicate": "mitigates",
            "predicate_id": "METPO:2007407",
            "object": "viral_dna_replication",
            "description": "PT-dependent effector activity inhibits replication of invading viral DNA.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-020-0700-6",
                "snippet": "SspE inhibits phage propagation by introducing nicking damage to impair phage DNA replication",
                "notes": "Xiong et al. directly connect SspE DNA nicking to impaired phage replication."
              },
              {
                "reference": "DOI:10.1038/s41467-019-09390-9",
                "snippet": "PbeABCD-mediated halt of virus propagation via inhibition of DNA replication",
                "notes": "Xiong et al. connect PbeABCD-dependent PT restriction to inhibited archaeal viral DNA replication."
              }
            ]
          },
          {
            "subject": "viral_dna_restriction",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "phosphorothioate_defense_system_trait",
            "description": "Restriction of invading viral DNA realizes phosphorothioate-based antiviral defense.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mbio.00933-23",
                "snippet": "the host could benefit from Dnd-related R-M systems for a broad range of antiphage activities",
                "notes": "Jiang et al. support Dnd-mediated phosphorothioate restriction as an antiphage defense output."
              },
              {
                "reference": "DOI:10.1038/s41467-019-09390-9",
                "snippet": "a new type of PT-based virus resistance system",
                "notes": "Xiong et al. place DndCDEA-PbeABCD in the PT antiviral defense family."
              }
            ]
          },
          {
            "subject": "phosphorothioate_defense_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Phosphorothioate restriction-system possession is an antiviral defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-020-0700-6",
                "snippet": "provides protection against phages",
                "notes": "Xiong et al. place PT-dependent SspABCD-SspE in the antiphage defense family."
              },
              {
                "reference": "DOI:10.1038/s41467-019-09390-9",
                "snippet": "a new type of PT-based virus resistance system",
                "notes": "Xiong et al. place DndCDEA-PbeABCD in the PT antiviral defense family."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "phosphorothioate-subfamily-split-gap",
        "prompt": "Resolve archaeal phosphorothioate-based antiviral systems before minting additional narrower children under the phosphorothioate defense parent.",
        "kind": "KNOWLEDGE_GAP",
        "status": "RESOLVED",
        "rationale": "Dnd, SspABCD-SspE, SspABCD-SspFGH, and archaeal DndCDEA-PbeABCD PT antiviral architectures have all been split out as narrower phosphorothioate defense system children.",
        "posed_by": "codex",
        "posed_date": "2026-09-15"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-15T10:54:22Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted phosphorothioate defense system as a DOI-backed GENOMICS TraitRecord under the phage defense system parent after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v90.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-15T16:03:59Z",
        "curator": "codex",
        "action": "RESOLVE_DISCUSSION_SCOPE",
        "changes": "Removed Dnd from the open phosphorothioate subfamily split-gap discussion after minting traitmech:000221 for the Dnd system; SspE, SspFGH, and archaeal phosphorothioate-based antiviral systems remain open.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-15T16:38:07Z",
        "curator": "codex",
        "action": "RESOLVE_DISCUSSION_SCOPE",
        "changes": "Removed SspBCD-E from the open phosphorothioate subfamily split-gap discussion after minting traitmech:000222 for the SspABCD-SspE system; SspFGH and archaeal phosphorothioate-based antiviral systems remain open.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-15T17:06:07Z",
        "curator": "codex",
        "action": "RESOLVE_DISCUSSION_SCOPE",
        "changes": "Removed SspFGH from the open phosphorothioate subfamily split-gap discussion after minting traitmech:000223 for the SspABCD-SspFGH system; archaeal phosphorothioate-based antiviral systems remain open.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-15T17:36:17Z",
        "curator": "codex",
        "action": "RESOLVE_DISCUSSION_SCOPE",
        "changes": "Minted traitmech:000224 for the archaeal DndCDEA-PbeABCD system, broadened the phosphorothioate defense system parent from bacteriophage-only Dnd/Ssp wording to Dnd/Ssp/Pbe viral-DNA restriction wording, and marked the phosphorothioate subfamily split-gap discussion resolved.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000296",
    "label": "Phrann gp29-gp30 system",
    "definition": "A phage defense system in which an organism possesses a Phrann gp29-gp30 locus that can protect bacteria from bacteriophage infection.",
    "definition_source": "DOI:10.1038/nmicrobiol.2016.251",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "Phrann_gp29_gp30",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/nmicrobiol.2016.251",
        "snippet": "at least five distinct prophage-expressed viral defense systems that interfere with infection",
        "notes": "Dedrick et al. place the Cluster N Phrann gp29-gp30 system in a cohort of prophage-expressed defenses against lytic and temperate mycobacteriophages."
      },
      {
        "reference": "DOI:10.1038/nmicrobiol.2016.251",
        "snippet": "Phrann genes 29 and/or 30 are involved in defense against Tweety and Gaia, as a mutant lysogen lacking Phrann 29 loses defense against these phages",
        "notes": "Dedrick et al. localize part of the Phrann prophage-mediated heterotypic defense phenotype to genes 29 and 30."
      },
      {
        "reference": "DOI:10.1038/nmicrobiol.2016.251",
        "snippet": "expressing Phrann genes 29 and 30 reproduce the Phrann defense against Tweety and Gaia",
        "notes": "Dedrick et al. show that recombinant Phrann genes 29 and 30 are sufficient to reproduce Phrann defense against Tweety and Gaia."
      },
      {
        "reference": "DOI:10.1038/nmicrobiol.2016.251",
        "snippet": "Phrann prophage-mediated defense is strictly heterotypic, and Phrann gp29/gp30 does not defend against Phrann or other Cluster N phages",
        "notes": "Dedrick et al. delimit the Phrann gp29-gp30 defense profile as heterotypic rather than Cluster N superinfection exclusion."
      },
      {
        "reference": "DOI:10.1038/nmicrobiol.2016.251",
        "snippet": "Prophage-mediated defense by (p)ppGpp synthetases is a new and intriguing system for defense against viral attack",
        "notes": "Dedrick et al. interpret Phrann gp29 as a putative (p)ppGpp synthetase in a prophage-mediated viral-defense system."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "Phrann_gp29_gp30 | 10\\.1038/nmicrobiol\\.2016\\.251 | Prophage-mediated defence against viral attack and viral counter-defence",
        "notes": "The DefenseFinder model registry maps the named Phrann_gp29_gp30 system to the Dedrick et al. prophage-mediated viral-defense paper."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "Phrann_gp29_gp30__gp29                           | Phrann_gp29_gp30__gp29                           | Phrann_gp29_gp30",
        "notes": "The DefenseFinder HMM inventory records a Phrann gp29-gp30 profile for Phrann_gp29_gp30__gp29 in the Phrann_gp29_gp30 model namespace."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "Phrann_gp29_gp30__gp30                           | Phrann_gp29_gp30__gp30                           | Phrann_gp29_gp30",
        "notes": "The DefenseFinder HMM inventory records a Phrann gp29-gp30 profile for Phrann_gp29_gp30__gp30 in the Phrann_gp29_gp30 model namespace."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "Phrann_gp29_gp30\tPhrann_gp29_gp30\t2\t2\tPhrann_gp29_gp30__gp29, Phrann_gp29_gp30__gp30",
        "notes": "The DefenseFinder rules table models Phrann_gp29_gp30 as a two-component system requiring gp29 and gp30 profiles."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "phrann_gp29_gp30_locus_restricts_phage",
        "title": "Phrann gp29-gp30 loci confer heterotypic phage defense",
        "description": "Conservative system-level sketch linking possession of a Phrann gp29-gp30 locus to restricted bacteriophage propagation without asserting the unresolved lytic trigger, gp29-gp30 interaction, or downstream arrest mechanism.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Phrann gp29-gp30 as a named anti-phage system with DefenseFinder gp29 and gp30 profiles while leaving the direct lytic trigger, Phrann gp30 regulatory role, and exact (p)ppGpp-linked arrest mechanism unresolved.",
        "nodes": [
          {
            "node_id": "phrann_gp29_gp30_locus",
            "label": "Phrann gp29-gp30 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A Phrann gp29-gp30 anti-phage defense locus cataloged in DefenseFinder with gp29 and gp30 HMM profiles."
          },
          {
            "node_id": "restricted_phage_propagation",
            "label": "restricted phage propagation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced propagation of bacteriophage in cells carrying the Phrann gp29-gp30 system."
          },
          {
            "node_id": "phrann_gp29_gp30_system_trait",
            "label": "Phrann gp29-gp30 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000296",
            "description": "Possession of a genome-encoded Phrann gp29-gp30 phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "phrann_gp29_gp30_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "restricted_phage_propagation",
            "description": "Dedrick et al. support Phrann genes 29 and 30 in heterotypic phage defense, and DefenseFinder catalogs gp29 and gp30 profiles in the Phrann_gp29_gp30 model namespace.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nmicrobiol.2016.251",
                "snippet": "Phrann genes 29 and/or 30 are involved in defense against Tweety and Gaia, as a mutant lysogen lacking Phrann 29 loses defense against these phages",
                "notes": "Dedrick et al. connect Phrann genes 29 and 30 to Phrann defense against Tweety and Gaia."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "Phrann_gp29_gp30__gp29                           | Phrann_gp29_gp30__gp29                           | Phrann_gp29_gp30",
                "notes": "The DefenseFinder HMM inventory records a Phrann gp29-gp30 profile for Phrann_gp29_gp30__gp29 in the Phrann_gp29_gp30 model namespace."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "Phrann_gp29_gp30__gp30                           | Phrann_gp29_gp30__gp30                           | Phrann_gp29_gp30",
                "notes": "The DefenseFinder HMM inventory records a Phrann gp29-gp30 profile for Phrann_gp29_gp30__gp30 in the Phrann_gp29_gp30 model namespace."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "Phrann_gp29_gp30\tPhrann_gp29_gp30\t2\t2\tPhrann_gp29_gp30__gp29, Phrann_gp29_gp30__gp30",
                "notes": "The DefenseFinder rules table models Phrann_gp29_gp30 as a two-component system requiring gp29 and gp30 profiles."
              }
            ]
          },
          {
            "subject": "restricted_phage_propagation",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "phrann_gp29_gp30_system_trait",
            "description": "Phrann-gp29-gp30-mediated defense against Tweety and Gaia realizes the Phrann gp29-gp30 system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nmicrobiol.2016.251",
                "snippet": "expressing Phrann genes 29 and 30 reproduce the Phrann defense against Tweety and Gaia",
                "notes": "Dedrick et al. show that genes 29 and 30 are sufficient to reproduce Phrann defense against Tweety and Gaia."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Phrann_gp29_gp30 | 10\\.1038/nmicrobiol\\.2016\\.251 | Prophage-mediated defence against viral attack and viral counter-defence",
                "notes": "DefenseFinder records Phrann_gp29_gp30 as a named system from the Dedrick et al. prophage-defense paper."
              }
            ]
          },
          {
            "subject": "phrann_gp29_gp30_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Phrann gp29-gp30 system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| Phrann_gp29_gp30 | 10\\.1038/nmicrobiol\\.2016\\.251 | Prophage-mediated defence against viral attack and viral counter-defence |",
                "notes": "DefenseFinder associates Phrann_gp29_gp30 with the Dedrick et al. prophage-mediated viral-defense paper."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "phrann_gp29_gp30-mechanism-gap",
        "prompt": "Resolve the Phrann gp29-gp30 contribution to TM4 defense, Phrann gp30 regulator role, lytic trigger, (p)ppGpp synthetase activity, and remaining target-phage breadth before minting narrower Phrann gp29-gp30 mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Dedrick et al. and DefenseFinder support Phrann gp29-gp30 as a named anti-phage system with gp29 and gp30 profiles, but the Phrann gp30 regulatory role, lytic-phage trigger, direct (p)ppGpp activation mechanism, relative contribution to TM4 defense, and remaining target breadth are not resolved enough here to assert a narrower mechanistic child trait.",
        "attaches_to": [
          "causal_graphs#phrann_gp29_gp30_locus_restricts_phage"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-19"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-19T23:37:58Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Phrann gp29-gp30 system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v173.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-19T23:47:14Z",
        "curator": "codex",
        "action": "CURATION_REVIEW_REVISION",
        "changes": "Resolved PR #1092 review issues #1093 and #1094 by replacing a restriction-implying Phrann gp29-gp30 edge description with generic defense wording and narrowing the breadth knowledge gap to the unresolved TM4 contribution and remaining target-phage breadth.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-19T23:56:21Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed the PR #1092 canonical_examples gap and left canonical_examples empty: the current Phrann gp29-gp30 evidence supports a named phage-defense system and DefenseFinder profiles, but the curated record does not yet cite a source-backed bacterial taxon with a directly observed Phrann gp29-gp30 locus. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000323",
    "label": "Pif system",
    "definition": "An abortive infection system in which an organism possesses an F-plasmid pif-family locus represented by the DefenseFinder Pif__PifA and Pif__PifC profiles and exemplified by the pif region that specifies abortive infection of T7 phage.",
    "definition_source": "DOI:10.1007/BF00327934",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000214"
    ],
    "synonyms": [
      {
        "synonym_text": "Pif",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      }
    ],
    "evidence": [
      {
        "reference": "PMID:6096670",
        "snippet": "Molecular analysis of F plasmid pif region specifying abortive infection of T7 phage.",
        "notes": "Cram et al. title the paper around F-plasmid pif-region specification of the T7 abortive-infection phenotype."
      },
      {
        "reference": "DOI:10.1007/BF00327934",
        "snippet": "We report the molecular cloning of the pif region of the F plasmid and its physical dissection by subcloning and deletion analysis.",
        "notes": "Cram et al. cloned and deletion-mapped the F-plasmid pif region."
      },
      {
        "reference": "DOI:10.1007/BF00327934",
        "snippet": "Examination of the polypeptide products synthesized in maxicells by plasmids carrying defined pif sequences has shown that the region specifies at least two proteins of molecular weights 80,000 and 40,000, the genes for which appear to lie in the same transcriptional unit.",
        "notes": "Cram et al. support a multigene pif region without resolving a direct PifA or PifC molecular function."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "Pif | 10\\.1007/BF00327934 | Molecular analysis of F plasmid pif region specifying abortive infection of T7 phage",
        "notes": "The DefenseFinder article registry maps the named Pif model namespace to the F-plasmid pif-region molecular analysis paper."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "Pif\tPif\t2\t2\tPif__PifA, Pif__PifC",
        "notes": "The DefenseFinder rules table models Pif as a two-component system requiring both the Pif__PifA and Pif__PifC profiles."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| Pif__PifA                                        | Pif__PifA                                        | Pif                    | Custom                  | 20     |",
        "notes": "The DefenseFinder HMM inventory records Pif__PifA under Pif."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| Pif__PifC                                        | Pif__PifC                                        | Pif                    | Custom                  | 20     |",
        "notes": "The DefenseFinder HMM inventory records Pif__PifC under Pif."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "pif_locus_specifies_t7_abortive_infection",
        "title": "Pif locus specifies T7 abortive infection",
        "description": "Conservative system-level sketch linking an F-plasmid pif-family locus to T7 abortive infection and Pif-system possession without asserting the direct phage trigger, host-cell output, or PifA/PifC molecular targets.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Pif as a named DefenseFinder two-profile abortive-infection system whose F-plasmid prototype specifies T7 abortive infection. It leaves the direct T7 trigger, PifA and PifC molecular functions, host-cell output, and phage escape route unresolved.",
        "nodes": [
          {
            "node_id": "pif_locus",
            "label": "pif locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "An F-plasmid pif-family abortive-infection locus represented by the DefenseFinder Pif__PifA and Pif__PifC profiles."
          },
          {
            "node_id": "t7_abortive_infection",
            "label": "T7 abortive infection",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Abortive infection of T7 phage specified by an F-plasmid pif region."
          },
          {
            "node_id": "pif_system_trait",
            "label": "Pif system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000323",
            "description": "Possession of a genome-encoded Pif abortive-infection phage-defense system."
          }
        ],
        "edges": [
          {
            "subject": "pif_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "t7_abortive_infection",
            "description": "The F-plasmid pif region specifies T7 abortive infection, and DefenseFinder represents Pif with required PifA and PifC profiles.",
            "evidence": [
              {
                "reference": "PMID:6096670",
                "snippet": "Molecular analysis of F plasmid pif region specifying abortive infection of T7 phage.",
                "notes": "Cram et al. frame the F-plasmid pif region as specifying T7 abortive infection."
              },
              {
                "reference": "DOI:10.1007/BF00327934",
                "snippet": "the region specifies at least two proteins of molecular weights 80,000 and 40,000",
                "notes": "Cram et al. observed two pif-region polypeptides in maxicells."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "Pif\tPif\t2\t2\tPif__PifA, Pif__PifC",
                "notes": "The DefenseFinder rules table models Pif as a two-component system requiring both the Pif__PifA and Pif__PifC profiles."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| Pif__PifA                                        | Pif__PifA                                        | Pif                    | Custom                  | 20     |",
                "notes": "The DefenseFinder HMM inventory records Pif__PifA under Pif."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| Pif__PifC                                        | Pif__PifC                                        | Pif                    | Custom                  | 20     |",
                "notes": "The DefenseFinder HMM inventory records Pif__PifC under Pif."
              }
            ]
          },
          {
            "subject": "t7_abortive_infection",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "pif_system_trait",
            "description": "F-plasmid-pif-specified T7 abortive infection realizes the Pif system trait.",
            "evidence": [
              {
                "reference": "PMID:6096670",
                "snippet": "Molecular analysis of F plasmid pif region specifying abortive infection of T7 phage.",
                "notes": "Cram et al. support T7 abortive infection as the pif-region output."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Pif | 10\\.1007/BF00327934 | Molecular analysis of F plasmid pif region specifying abortive infection of T7 phage",
                "notes": "The DefenseFinder article registry maps the named Pif model namespace to the F-plasmid pif-region molecular analysis paper."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "pif-output-gap",
        "prompt": "Resolve the direct T7 trigger, PifA and PifC molecular functions, host-cell output, and phage escape routes before minting narrower Pif mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Cram et al. support an F-plasmid pif-region abortive-infection system that maps to a two-profile DefenseFinder model, but the direct T7 trigger, the molecular functions of PifA and PifC, the host-cell growth-arrest or cell-death output, and phage escape routes remain unresolved.",
        "attaches_to": [
          "causal_graphs#pif_locus_specifies_t7_abortive_infection"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-21"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-21T01:30:12Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Pif system as a DOI-backed GENOMICS TraitRecord under the abortive infection system parent after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v200.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-21T01:30:13Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed canonical example evidence while minting Pif system and left canonical_examples empty: the Cram et al. prototype supports an F-plasmid pif region that specifies T7 abortive infection and the pinned DefenseFinder registry maps a two-profile Pif namespace, but the available curation sources do not identify a natural organism instance with a directly observed Pif locus. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000090",
    "label": "plasmid carriage",
    "definition": "A genomics trait describing possession of one or more plasmids \u2014 extrachromosomal, typically circular DNA replicons that carry accessory genes such as resistance, virulence, or metabolic functions and can transfer by conjugation.",
    "definition_source": "DOI:10.1128/MMBR.00020-10",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "traitmech:000089"
    ],
    "synonyms": [
      {
        "synonym_text": "plasmid-bearing",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1128/MMBR.00020-10"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1128/MMBR.00020-10",
        "notes": "Smillie et al. review plasmid mobility, classifying conjugative and mobilizable plasmids as key vectors of horizontal gene transfer."
      },
      {
        "reference": "DOI:10.1038/nrmicro1235",
        "notes": "Frost et al. include plasmids among the principal mobile genetic elements."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:562",
        "taxon_label": "Escherichia coli",
        "note": "F/R plasmid carriage",
        "reference": "PMID:36409140"
      },
      {
        "taxon_id": "NCBITaxon:139",
        "taxon_label": "Borreliella burgdorferi",
        "note": "numerous linear/circular plasmids",
        "reference": "PMID:9403685"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "plasmid_conjugation_hgt",
        "title": "Plasmid carriage drives conjugative horizontal gene transfer",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This genomics record is a measurement, genomic-element classification, or population-level descriptor rather than one taxon-specific protein mechanism; contextual protein nodes do not receive token UniProt examples.",
        "description": "Evidence-backed causal sketch linking plasmid possession to conjugation and accessory-function delivery.",
        "nodes": [
          {
            "node_id": "plasmid_carriage_trait",
            "label": "plasmid carriage",
            "node_type": "TRAIT",
            "grounding": "traitmech:000090",
            "description": "Possession of extrachromosomal plasmid replicons."
          },
          {
            "node_id": "conjugation",
            "label": "conjugation",
            "node_type": "BIOLOGICAL_PROCESS",
            "grounding": "GO:0009291",
            "description": "Cell-to-cell transfer of genetic material via direct contact."
          },
          {
            "node_id": "accessory_function",
            "label": "accessory function",
            "node_type": "QUALITY",
            "description": "Plasmid-encoded resistance, virulence, or metabolic capability."
          },
          {
            "node_id": "ta_system",
            "label": "toxin-antitoxin system",
            "node_type": "GENE_OR_PROTEIN",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed as a contextual protein or protein-complex label in a nonmechanistic genomics classification; no exact semantic family term was established for this aggregate use.",
            "description": "Selfish genetic module mediating plasmid addiction / post-segregational killing."
          },
          {
            "node_id": "plasmid_vertical_inheritance",
            "label": "plasmid vertical inheritance",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Stable transmission of a plasmid to daughter cells across generations."
          },
          {
            "node_id": "plasmid_methylase",
            "label": "plasmid-encoded methylase",
            "node_type": "GENE_OR_PROTEIN",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed as a contextual protein or protein-complex label in a nonmechanistic genomics classification; no exact semantic family term was established for this aggregate use.",
            "description": "Plasmid-borne methyltransferase shielding plasmid DNA from restriction."
          },
          {
            "node_id": "restriction_of_plasmid_dna",
            "label": "restriction of incoming plasmid DNA",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Cleavage of unmethylated incoming plasmid DNA by restriction-modification systems."
          },
          {
            "node_id": "anti_restriction_proteins",
            "label": "plasmid-encoded anti-restriction proteins",
            "node_type": "GENE_OR_PROTEIN",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed as a contextual protein or protein-complex label in a nonmechanistic genomics classification; no exact semantic family term was established for this aggregate use.",
            "description": "Plasmid-encoded proteins that inhibit host restriction-modification defence; their encoding genes remain record-level metadata rather than nodes."
          },
          {
            "node_id": "antibiotic_selective_pressure",
            "label": "antibiotic selective pressure",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Antibiotic exposure selecting for retention of resistance plasmids."
          },
          {
            "node_id": "fitness_cost",
            "label": "plasmid fitness cost",
            "node_type": "QUALITY",
            "description": "Reduced host fitness from additional material and energy consumption of plasmid carriage."
          },
          {
            "node_id": "compensatory_mutation",
            "label": "compensatory mutation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Chromosomal or plasmid mutation that ameliorates plasmid-imposed fitness cost."
          }
        ],
        "edges": [
          {
            "subject": "plasmid_carriage_trait",
            "predicate": "enables",
            "object": "conjugation",
            "description": "Conjugative plasmids encode the machinery for cell-to-cell transfer.",
            "evidence": [
              {
                "reference": "DOI:10.1128/MMBR.00020-10",
                "notes": "Smillie et al. classify conjugative and mobilizable plasmids."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "plasmid_carriage_trait",
            "predicate": "contributes to",
            "object": "accessory_function",
            "description": "Plasmids carry accessory genes that extend host phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro1235",
                "notes": "Frost et al. include plasmids among the principal MGEs delivering accessory functions."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "ta_system",
            "predicate": "stabilizes",
            "object": "plasmid_vertical_inheritance",
            "description": "Toxin-antitoxin systems increase vertical stability of their replicons.",
            "evidence": [
              {
                "reference": "DOI:10.1093/nar/gkae018",
                "notes": "TA systems are small selfish genetic modules that increase vertical stability of their replicons."
              }
            ]
          },
          {
            "subject": "plasmid_methylase",
            "predicate": "protects against",
            "object": "restriction_of_plasmid_dna",
            "description": "Plasmid-encoded methylases protect plasmid DNA from host restriction.",
            "evidence": [
              {
                "reference": "DOI:10.1093/nar/gkae896",
                "notes": "plasmid-encoded methylases that protect plasmids from restriction."
              }
            ]
          },
          {
            "subject": "anti_restriction_proteins",
            "predicate": "protects against",
            "object": "restriction_of_plasmid_dna",
            "description": "Plasmid-encoded anti-restriction proteins counter multiple RM system types.",
            "evidence": [
              {
                "reference": "DOI:10.1093/nar/gkae896",
                "notes": "plasmid-encoded anti-restriction proteins that protect against multiple RM types."
              }
            ]
          },
          {
            "subject": "antibiotic_selective_pressure",
            "predicate": "promotes retention of",
            "object": "plasmid_carriage_trait",
            "description": "Without selection plasmids tend to be lost; antibiotic pressure promotes retention.",
            "evidence": [
              {
                "reference": "DOI:10.1080/22221751.2024.2352432",
                "notes": "without selection plasmids tend to be lost, whereas antibiotic (or metal) selective pressure promotes retention."
              }
            ]
          },
          {
            "subject": "plasmid_carriage_trait",
            "predicate": "imposes",
            "object": "fitness_cost",
            "description": "Plasmid carriage imposes a fitness cost from additional material and energy consumption.",
            "evidence": [
              {
                "reference": "DOI:10.1080/22221751.2024.2352432",
                "notes": "Plasmid carriage imposes fitness costs (additional material and energy consumption)."
              }
            ]
          },
          {
            "subject": "compensatory_mutation",
            "predicate": "decreases",
            "object": "fitness_cost",
            "description": "Compensatory evolution of chromosomes and plasmids counteracts plasmid fitness cost.",
            "evidence": [
              {
                "reference": "DOI:10.1002/ece3.70121",
                "notes": "Compensatory evolution of chromosomes and plasmids counteracts the plasmid fitness cost."
              }
            ],
            "predicate_id": "RO:0002212"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-08-25T00:00:00-07:00",
        "curator": "codex",
        "action": "REVIEW_ONTOLOGY_GROUNDINGS",
        "changes": "Replaced obsolete GO:0000746 conjugation with GO:0009291 unidirectional conjugation, whose definition specifically covers contact-dependent donor-to-recipient transfer of genetic material described by this plasmid graph.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-05T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate GENOMICS trait (plasmid carriage); sub-variant of mobile genetic element.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-08T14:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (plasmid conjugation / HGT) with GO node grounding and RO predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 6 evidence-backed generic edges (8 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:11Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000017\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T02:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES_PART2",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates onto their causal-graph counterparts (1 to reduces), issue 301 part 2. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Each replacement is a 1:1 mirror of its source predicate that changes only the domain, so the claim each edge makes is unchanged and directions are unchanged. The replacements are proposed in proposals/metpo_traitmech_v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T06:00:00Z",
        "curator": "claude",
        "action": "REGROUND_CAUSAL_EDGE",
        "changes": "Relabelled 1 causal edge from `reduces` to `decreases` and re-grounded it from METPO:2007802 to RO:0002212 (negatively regulates), issue 330. The corpus wrote two senses under the single label `reduces` - genuine electron donation, and a lessens/decreases sense - and METPO:2007802 is defined as donating electrons to the object and lowering its oxidation state, which this edge does not assert. The two senses could not be separated mechanically because the label was identical, so they migrated together in issue 329 and were split here by reading each edge. RO:0002212 declares no rdfs:domain or rdfs:range, so this introduces no entailment of the kind issue 301 removed.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-15T06:00:00Z",
        "curator": "claude",
        "action": "SPLIT_PROTEIN_FROM_ACTIVITY",
        "changes": "Separated the protein sense from the activity sense so one node_id means one thing (issue 356): retyped plasmid_methylase: MOLECULAR_FUNCTION -> GENE_OR_PROTEIN. The exception in this tranche. Both occurrences describe the ENZYME -- 'Methyltransferase encoded by a mobile element that pre-methylates its DNA' (GENE_OR_PROTEIN) and 'Plasmid-borne methyltransferase shielding plasmid DNA from restriction' (MOLECULAR_FUNCTION). Neither names an activity, so there is one concept here and it is a protein. A rename would have invented a distinction the corpus does not draw.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope plasmid_conjugation_hgt=NONMECHANISTIC with scope_notes; marked 3 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (ta_system, plasmid_methylase, anti_restriction_proteins); added 1 node(s) and 1 edge(s) (anti_restriction_proteins); removed 1 node(s) and 1 edge(s) together with their evidence (anti_restriction_genes).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000100",
    "label": "ploidy",
    "definition": "A genomics trait describing the number of complete genome copies per cell; many bacteria and archaea are polyploid, maintaining many chromosome copies that support survival, repair, and large cell size.",
    "definition_source": "DOI:10.1159/000368855",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000188"
    ],
    "synonyms": [
      {
        "synonym_text": "polyploidy",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1159/000368855"
      }
    ],
    "xrefs": [
      "PATO:0001374"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1159/000368855",
        "notes": "Soppa reviews polyploidy in archaea and bacteria and its links to desiccation resistance, giant cell size, and long-term survival."
      },
      {
        "reference": "DOI:10.1073/pnas.0707522105",
        "notes": "Mendell et al. document extreme polyploidy (tens of thousands of genome copies) in the large bacterium Epulopiscium."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:354",
        "taxon_label": "Azotobacter vinelandii",
        "note": "Model of bacterial polyploidy (accumulates up to ~100 genome copies per cell in stationary phase).",
        "reference": "PMID:8021173"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "ploidy_repair_survival",
        "title": "Polyploidy supports DNA repair and long-term survival",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This genomics record is a measurement, genomic-element classification, or population-level descriptor rather than one taxon-specific protein mechanism; contextual protein nodes do not receive token UniProt examples.",
        "description": "Evidence-backed causal sketch linking multiple genome copies to homologous-recombination repair templates and survival under desiccation and starvation.",
        "nodes": [
          {
            "node_id": "ploidy_trait",
            "label": "ploidy",
            "node_type": "TRAIT",
            "grounding": "traitmech:000100",
            "description": "Number of complete genome copies per cell."
          },
          {
            "node_id": "dna_recombinational_repair",
            "label": "recombinational repair of damaged DNA",
            "node_type": "BIOLOGICAL_PROCESS",
            "grounding": "GO:0000725",
            "description": "Homologous recombination using sister chromosome as repair template."
          },
          {
            "node_id": "long_term_survival",
            "label": "long-term survival",
            "node_type": "QUALITY",
            "description": "Persistence under desiccation, starvation, and damage."
          },
          {
            "node_id": "phosphate_starvation",
            "label": "phosphate starvation",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Absence or limitation of environmental phosphate."
          },
          {
            "node_id": "genome_copy_number",
            "label": "genome copy number per cell",
            "node_type": "QUALITY",
            "description": "Number of chromosomal genome copies maintained per cell."
          },
          {
            "node_id": "dna_phosphate_storage",
            "label": "genomic DNA as phosphate storage polymer",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "Use of genomic DNA copies as an intracellular phosphate reservoir."
          },
          {
            "node_id": "growth_without_phosphate",
            "label": "growth in absence of environmental phosphate",
            "node_type": "TRAIT",
            "description": "Ability to grow when external phosphate is unavailable."
          },
          {
            "node_id": "segregational_drift",
            "label": "segregational drift",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Stochastic segregation of alleles on polyploid replicons during cell division."
          },
          {
            "node_id": "beneficial_allele_loss",
            "label": "loss of beneficial resistance alleles",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Stochastic loss of beneficial alleles carried on multicopy replicons."
          }
        ],
        "edges": [
          {
            "subject": "ploidy_trait",
            "predicate": "enables",
            "object": "dna_recombinational_repair",
            "description": "Extra genome copies provide templates for recombinational repair of DNA damage.",
            "evidence": [
              {
                "reference": "DOI:10.1159/000368855",
                "notes": "Soppa reviews polyploidy supporting damage tolerance via redundant chromosomes."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "ploidy_trait",
            "predicate": "contributes to",
            "object": "long_term_survival",
            "description": "Polyploidy underpins desiccation resistance and large cell sizes observed in extreme polyploid lineages.",
            "evidence": [
              {
                "reference": "DOI:10.1073/pnas.0707522105",
                "notes": "Mendell et al. document extreme polyploidy in Epulopiscium supporting giant cell size."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "phosphate_starvation",
            "predicate": "decreases",
            "object": "genome_copy_number",
            "description": "Polyploid prokaryotes reduce chromosomal copy number under phosphate starvation.",
            "evidence": [
              {
                "reference": "DOI:10.3390/microorganisms11092267",
                "notes": "All five characterized polyploid prokaryotic species grow without environmental phosphate by reducing genome copy numbers."
              }
            ],
            "predicate_id": "RO:0002212"
          },
          {
            "subject": "genome_copy_number",
            "predicate": "confers",
            "object": "growth_without_phosphate",
            "description": "Consuming extra genome copies as a phosphate source confers growth in the absence of external phosphate; monoploid E. coli cannot.",
            "evidence": [
              {
                "reference": "DOI:10.3390/microorganisms11092267",
                "notes": "Multiple polyploid prokaryotes grow without external phosphate by reducing intracellular genome copy number; monoploid E. coli showed no growth without phosphate."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "genome_copy_number",
            "predicate": "has function",
            "object": "dna_phosphate_storage",
            "description": "Genomic DNA copies act as a phosphate storage polymer that can be consumed under starvation.",
            "evidence": [
              {
                "reference": "DOI:10.3390/microorganisms11092267",
                "notes": "Genomic DNA acts as a phosphate storage polymer in polyploid prokaryotes."
              }
            ],
            "predicate_id": "RO:0000085"
          },
          {
            "subject": "ploidy_trait",
            "predicate": "increases",
            "object": "segregational_drift",
            "description": "Higher ploidy increases stochastic segregation of alleles on polyploid replicons during division.",
            "evidence": [
              {
                "reference": "DOI:10.1371/journal.pgen.1010829",
                "notes": "Alleles on polyploid replicons segregate stochastically during cell division, termed segregational drift; shown with experiments and modeling."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "segregational_drift",
            "predicate": "causes",
            "object": "beneficial_allele_loss",
            "description": "Segregational drift drives frequent loss of beneficial resistance alleles on multicopy replicons.",
            "evidence": [
              {
                "reference": "DOI:10.1371/journal.pgen.1010829",
                "notes": "Resistance alleles in polyploid elements are lost frequently versus monoploid elements due to segregational drift."
              }
            ],
            "predicate_id": "biolink:causes"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-06-05T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate GENOMICS trait (ploidy / polyploidy) from literature research.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-08T14:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (ploidy / repair / survival) with GO node grounding and RO predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 5 evidence-backed generic edges (6 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:11Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 5 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002212\u00d71, RO:0002327\u00d71, RO:0000085\u00d71, RO:0002213\u00d71, biolink:causes\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-07T05:00:00Z",
        "curator": "claude",
        "action": "RETYPE_CAUSAL_NODE",
        "changes": "Retyped the object node from STATE/CAPACITY to TRAIT and re-grounded its in-edge from enables/RO:0002327 to METPO:2007700 (confers), issue 334. biolink declares enables range 'biological process or activity', which only BIOLOGICAL_PROCESS, PATHWAY and MOLECULAR_FUNCTION satisfy. The node's own description gives it away as a disposition rather than a state - phrasings like \"Capacity of an organism to grow and survive under...\", \"Ability to grow when...\" and \"tolerance of...\" describe what an organism CAN do, which is what a TRAIT is. So the defect was the node type, not the predicate, which is the third time in this issue's neighbourhood that has been true (compare issue 331's acetate kinase step and issue 330's negated node name). With the object correctly a TRAIT, confers applies unchanged.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope ploidy_repair_survival=NONMECHANISTIC with scope_notes.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T06:15:38Z",
        "curator": "codex",
        "action": "ADD_EXACT_ONTOLOGY_MATCH",
        "changes": "Ontology exact-match review (2026-08-25): approved exact xref(s): PATO:0001374. Evidence is predicate-scoped in the versioned ontology snapshots; OAK cross-checked direct data, and OLS4 spot-checked release deltas and disputed hits.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000290",
    "label": "Prithvi system",
    "definition": "A phage defense system in which an organism possesses a Prithvi locus that can protect bacteria from bacteriophage infection.",
    "definition_source": "DOI:10.1101/2025.01.08.631966",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "Prithvi",
        "synonym_type": "EXACT_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      },
      {
        "synonym_text": "PtvA",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1101/2025.01.08.631966",
        "snippet": "Among the remaining eight systems, six demonstrated increased resistance to at least one phage with more than 100 fold reduction in plaque forming units (PFU) (Figure 3a, Supplementary Figure 5). As Streptomyces are mostly soil dwelling bacteria, we named these systems after deities of the soil and earth (Ceres, Geb, Veles, Prithvi, Ukko and Oshun).",
        "notes": "Mordret et al. directly name Prithvi among six Streptomyces systems that increased resistance to at least one phage."
      },
      {
        "reference": "DOI:10.1101/2025.01.08.631966",
        "snippet": "The bacterial pangenome encodes an immense array of antiphage systems, yet much of their diversity remains uncharted",
        "notes": "Mordret et al. motivate a conservative system-level record that does not assert a resolved Prithvi trigger, effector output, or universal pathway."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "Prithvi | 10\\.1101/2025\\.01\\.08\\.631966 | Protein and genomic language models chart a vast landscape of antiphage defenses",
        "notes": "The DefenseFinder model registry maps the named Prithvi system to the Mordret et al. antiphage-system discovery preprint."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "Prithvi__PtvA                                    |                                                  | Prithvi",
        "notes": "The DefenseFinder HMM inventory records PtvA in the Prithvi model namespace."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "prithvi_locus_restricts_phage",
        "title": "Prithvi loci confer bacterial phage defense",
        "description": "Conservative system-level sketch linking possession of a Prithvi locus to restricted bacteriophage propagation without asserting the unresolved phage trigger or molecular output.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Prithvi as a named anti-phage system with a PtvA DefenseFinder HMM profile entry while leaving its phage trigger, molecular substrate, antiviral effector output, and subtype breadth unresolved.",
        "nodes": [
          {
            "node_id": "prithvi_locus",
            "label": "Prithvi locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A Prithvi anti-phage defense locus cataloged in DefenseFinder with a PtvA HMM profile entry."
          },
          {
            "node_id": "restricted_phage_propagation",
            "label": "restricted phage propagation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced propagation of bacteriophage in cells carrying the Prithvi system."
          },
          {
            "node_id": "prithvi_system_trait",
            "label": "Prithvi system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000290",
            "description": "Possession of a genome-encoded Prithvi phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "prithvi_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "restricted_phage_propagation",
            "description": "DefenseFinder maps Prithvi to a protein- and genomic-language-model antiphage-system discovery preprint and catalogs a PtvA HMM profile entry in the Prithvi model namespace.",
            "evidence": [
              {
                "reference": "DOI:10.1101/2025.01.08.631966",
                "snippet": "Among the remaining eight systems, six demonstrated increased resistance to at least one phage with more than 100 fold reduction in plaque forming units (PFU) (Figure 3a, Supplementary Figure 5). As Streptomyces are mostly soil dwelling bacteria, we named these systems after deities of the soil and earth (Ceres, Geb, Veles, Prithvi, Ukko and Oshun).",
                "notes": "Mordret et al. directly name Prithvi among six Streptomyces systems that restricted at least one phage."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Prithvi | 10\\.1101/2025\\.01\\.08\\.631966 | Protein and genomic language models chart a vast landscape of antiphage defenses",
                "notes": "The DefenseFinder registry maps Prithvi itself to the Mordret et al. bacterial antiphage-system discovery preprint."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "Prithvi__PtvA                                    |                                                  | Prithvi",
                "notes": "The DefenseFinder HMM inventory records PtvA in the Prithvi model namespace."
              }
            ]
          },
          {
            "subject": "restricted_phage_propagation",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "prithvi_system_trait",
            "description": "Prithvi-mediated phage restriction realizes the Prithvi system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1101/2025.01.08.631966",
                "snippet": "Among the remaining eight systems, six demonstrated increased resistance to at least one phage with more than 100 fold reduction in plaque forming units (PFU) (Figure 3a, Supplementary Figure 5). As Streptomyces are mostly soil dwelling bacteria, we named these systems after deities of the soil and earth (Ceres, Geb, Veles, Prithvi, Ukko and Oshun).",
                "notes": "Mordret et al. directly name Prithvi among six systems that increased resistance to at least one phage."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Prithvi | 10\\.1101/2025\\.01\\.08\\.631966 | Protein and genomic language models chart a vast landscape of antiphage defenses",
                "notes": "DefenseFinder records Prithvi as a named system from the Mordret et al. antiphage discovery preprint."
              }
            ]
          },
          {
            "subject": "prithvi_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Prithvi system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| Prithvi | 10\\.1101/2025\\.01\\.08\\.631966 | Protein and genomic language models chart a vast landscape of antiphage defenses |",
                "notes": "DefenseFinder associates Prithvi with the Mordret et al. bacterial antiphage-system discovery preprint."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "prithvi-mechanism-gap",
        "prompt": "Resolve Prithvi phage triggers and effector outputs before minting narrower Prithvi mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Mordret et al. and DefenseFinder support Prithvi as a named anti-phage system with a PtvA HMM profile entry, but the trigger, molecular substrate, antiviral effector output, and subtype-specific mechanism are not resolved enough here to assert a narrower mechanistic child trait.",
        "attaches_to": [
          "causal_graphs#prithvi_locus_restricts_phage"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-19"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-19T19:16:49Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Prithvi system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v167.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000291",
    "label": "Prometheus system",
    "definition": "A phage defense system in which an organism possesses a Prometheus locus that can protect bacteria from bacteriophage infection.",
    "definition_source": "DOI:10.1016/j.chom.2024.07.007",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "Prometheus",
        "synonym_type": "EXACT_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1016/j.chom.2024.07.007",
        "snippet": "We validated six of these phage defense systems, including factors preventing viral attachment, R-loop-acting enzymes, the inflammasome, ubiquitin pathway, and pathogen recognition signaling.",
        "notes": "van den Berg et al. validated six phage defense systems related to eukaryotic innate antiviral responses."
      },
      {
        "reference": "DOI:10.1016/j.chom.2024.07.007",
        "snippet": "Searching for phage defense systems related to innate antiviral genes from vertebrates and plants, we uncovered over 450 candidates.",
        "notes": "van den Berg et al. motivate a conservative system-level record that does not assert a resolved Prometheus trigger, effector output, or universal pathway."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "Prometheus | 10\\.1016/j\\.chom\\.2024\\.07\\.007 | Bacterial homologs of innate eukaryotic antiviral defenses with anti-phage activity highlight shared evolutionary roots of viral defenses",
        "notes": "The DefenseFinder model registry maps the named Prometheus system to the van den Berg et al. antiphage-system discovery paper."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "Prometheus__ProA                                 |                                                  | Prometheus",
        "notes": "The DefenseFinder HMM inventory records Prometheus__ProA in the Prometheus model namespace."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "prometheus_locus_restricts_phage",
        "title": "Prometheus loci confer bacterial phage defense",
        "description": "Conservative system-level sketch linking possession of a Prometheus locus to restricted bacteriophage propagation without asserting the unresolved phage trigger or molecular output.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Prometheus as a named anti-phage system with a Prometheus__ProA DefenseFinder HMM profile entry while leaving its phage trigger, molecular substrate, antiviral effector output, and subtype breadth unresolved.",
        "nodes": [
          {
            "node_id": "prometheus_locus",
            "label": "Prometheus locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A Prometheus anti-phage defense locus cataloged in DefenseFinder with a Prometheus__ProA HMM profile entry."
          },
          {
            "node_id": "restricted_phage_propagation",
            "label": "restricted phage propagation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced propagation of bacteriophage in cells carrying the Prometheus system."
          },
          {
            "node_id": "prometheus_system_trait",
            "label": "Prometheus system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000291",
            "description": "Possession of a genome-encoded Prometheus phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "prometheus_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "restricted_phage_propagation",
            "description": "DefenseFinder maps Prometheus to a eukaryotic-antiviral-homolog antiphage-system discovery paper and catalogs a Prometheus__ProA HMM profile entry in the Prometheus model namespace.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.chom.2024.07.007",
                "snippet": "We validated six of these phage defense systems, including factors preventing viral attachment, R-loop-acting enzymes, the inflammasome, ubiquitin pathway, and pathogen recognition signaling.",
                "notes": "van den Berg et al. validated six phage defense systems related to eukaryotic innate antiviral responses."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Prometheus | 10\\.1016/j\\.chom\\.2024\\.07\\.007 | Bacterial homologs of innate eukaryotic antiviral defenses with anti-phage activity highlight shared evolutionary roots of viral defenses",
                "notes": "The DefenseFinder registry maps Prometheus itself to the van den Berg et al. bacterial antiphage-system discovery paper."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "Prometheus__ProA                                 |                                                  | Prometheus",
                "notes": "The DefenseFinder HMM inventory records Prometheus__ProA in the Prometheus model namespace."
              }
            ]
          },
          {
            "subject": "restricted_phage_propagation",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "prometheus_system_trait",
            "description": "Prometheus-mediated phage restriction realizes the Prometheus system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.chom.2024.07.007",
                "snippet": "We validated six of these phage defense systems, including factors preventing viral attachment, R-loop-acting enzymes, the inflammasome, ubiquitin pathway, and pathogen recognition signaling.",
                "notes": "van den Berg et al. validated six phage defense systems related to eukaryotic antiviral responses."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Prometheus | 10\\.1016/j\\.chom\\.2024\\.07\\.007 | Bacterial homologs of innate eukaryotic antiviral defenses with anti-phage activity highlight shared evolutionary roots of viral defenses",
                "notes": "DefenseFinder records Prometheus as a named system from the van den Berg et al. antiphage discovery paper."
              }
            ]
          },
          {
            "subject": "prometheus_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Prometheus system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| Prometheus | 10\\.1016/j\\.chom\\.2024\\.07\\.007 | Bacterial homologs of innate eukaryotic antiviral defenses with anti-phage activity highlight shared evolutionary roots of viral defenses |",
                "notes": "DefenseFinder associates Prometheus with the van den Berg et al. bacterial antiphage-system discovery paper."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "prometheus-mechanism-gap",
        "prompt": "Resolve Prometheus phage triggers and effector outputs before minting narrower Prometheus mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "van den Berg et al. and DefenseFinder support Prometheus as a named anti-phage system with a Prometheus__ProA HMM profile entry, but the trigger, molecular substrate, antiviral effector output, and subtype-specific mechanism are not resolved enough here to assert a narrower mechanistic child trait.",
        "attaches_to": [
          "causal_graphs#prometheus_locus_restricts_phage"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-19"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-19T20:12:30Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Prometheus system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v168.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000091",
    "label": "prophage",
    "definition": "A genomics trait describing possession of an integrated (or extrachromosomal) temperate bacteriophage genome (a prophage) maintained in the host during lysogeny, often contributing genes that alter host phenotype.",
    "definition_source": "DOI:10.1128/MMBR.67.2.238-276.2003",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "traitmech:000089"
    ],
    "synonyms": [
      {
        "synonym_text": "lysogen",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1038/ismej.2017.16"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1128/MMBR.67.2.238-276.2003",
        "notes": "Canchaya et al. review prophage genomics, showing most sequenced bacterial genomes carry prophage sequences."
      },
      {
        "reference": "DOI:10.1038/ismej.2017.16",
        "notes": "Howard-Varona et al. review lysogeny in nature, the maintenance of temperate phage genomes within hosts."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:562",
        "taxon_label": "Escherichia coli",
        "note": "lambda and other integrated prophages",
        "reference": "PMID:21266997"
      },
      {
        "taxon_id": "NCBITaxon:28901",
        "taxon_label": "Salmonella enterica",
        "note": "Gifsy/Fels prophages",
        "reference": "PMID:29780368"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "prophage_lysogeny",
        "title": "Prophage maintenance during lysogeny alters host phenotype",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This genomics record is a measurement, genomic-element classification, or population-level descriptor rather than one taxon-specific protein mechanism; contextual protein nodes do not receive token UniProt examples.",
        "description": "Evidence-backed causal sketch linking prophage carriage to lysogenic maintenance and lysogenic conversion of the host.",
        "nodes": [
          {
            "node_id": "prophage_trait",
            "label": "prophage",
            "node_type": "TRAIT",
            "grounding": "traitmech:000091",
            "description": "Possession of an integrated or maintained temperate phage genome."
          },
          {
            "node_id": "lysogeny",
            "label": "lysogeny",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Maintenance of a temperate phage genome within the host without lysis."
          },
          {
            "node_id": "host_phenotype",
            "label": "host phenotype",
            "node_type": "QUALITY",
            "description": "Phage-encoded gene functions expressed in the lysogen."
          },
          {
            "node_id": "host_chromosome",
            "label": "bacterial chromosome",
            "node_type": "CELLULAR_LOCALIZATION",
            "description": "Host genomic DNA into which a temperate prophage integrates."
          },
          {
            "node_id": "ci_repressor",
            "label": "CI master repressor",
            "node_type": "GENE_OR_PROTEIN",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed as a contextual protein or protein-complex label in a nonmechanistic genomics classification; no exact semantic family term was established for this aggregate use.",
            "description": "Phage-encoded cI-family repressor that maintains lysogeny by blocking lytic gene expression."
          },
          {
            "node_id": "lytic_gene_expression",
            "label": "lytic gene expression",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Expression of phage lytic genes (from promoter PR) leading to the lytic cycle."
          },
          {
            "node_id": "dna_damage",
            "label": "DNA damage / replication stress",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Genotoxic stress or replication inhibition that generates ssDNA and triggers the SOS response."
          },
          {
            "node_id": "sos_response",
            "label": "RecA-LexA SOS response",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Bacterial DNA-damage-inducible SOS response mediated by RecA and LexA.",
            "grounding": "GO:0009432"
          },
          {
            "node_id": "reca_filament",
            "label": "RecA* nucleoprotein filament",
            "node_type": "GENE_OR_PROTEIN",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed as a contextual protein or protein-complex label in a nonmechanistic genomics classification; no exact semantic family term was established for this aggregate use.",
            "description": "Activated RecA nucleoprotein filament that promotes autocleavage of LexA and phage repressors."
          },
          {
            "node_id": "lexa_repressor",
            "label": "LexA repressor",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Host SOS master repressor inactivated by RecA*-stimulated autoproteolysis.",
            "grounding": "InterPro:IPR050077"
          },
          {
            "node_id": "prophage_induction",
            "label": "prophage induction",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Switch from lysogeny to the lytic cycle following derepression of phage lytic genes.",
            "grounding": "GO:0098689"
          },
          {
            "node_id": "phage_plasmid",
            "label": "phage-plasmid",
            "node_type": "GENETIC_ELEMENT",
            "description": "Hybrid mobile genetic element; a temperate phage maintained extrachromosomally as a plasmid."
          },
          {
            "node_id": "extrachromosomal_maintenance",
            "label": "extrachromosomal prophage maintenance",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Maintenance of a temperate phage genome episomally rather than integrated in the chromosome."
          }
        ],
        "edges": [
          {
            "subject": "prophage_trait",
            "predicate": "enables",
            "object": "lysogeny",
            "description": "Prophage carriage is the genomic state realized during lysogeny.",
            "evidence": [
              {
                "reference": "DOI:10.1128/MMBR.67.2.238-276.2003",
                "notes": "Canchaya et al. document widespread prophage maintenance in sequenced bacterial genomes."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "prophage_trait",
            "predicate": "contributes to",
            "object": "host_phenotype",
            "description": "Prophage-encoded genes can alter host virulence or fitness (lysogenic conversion).",
            "evidence": [
              {
                "reference": "DOI:10.1038/ismej.2017.16",
                "notes": "Howard-Varona et al. review host-phenotype effects of lysogeny in nature."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "prophage_trait",
            "predicate": "integrates into",
            "object": "host_chromosome",
            "description": "Temperate prophages canonically integrate into the host chromosome (though some persist extrachromosomally).",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41586-023-06376-y",
                "notes": "Temperate phages remain dormant as prophages integrated into the host genome and passed to host progeny."
              }
            ]
          },
          {
            "subject": "ci_repressor",
            "predicate": "represses",
            "object": "lytic_gene_expression",
            "description": "Lysogeny is maintained by a phage-encoded CI repressor that binds the lysis promoter PR to block lytic gene expression.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41586-023-06376-y",
                "notes": "cI repressor binds the lysis promoter (PR) to block lytic gene expression."
              }
            ]
          },
          {
            "subject": "dna_damage",
            "predicate": "activates",
            "object": "sos_response",
            "description": "DNA damage / replication stress generates ssDNA that triggers the RecA-LexA SOS response.",
            "evidence": [
              {
                "reference": "DOI:10.1073/pnas.2407832121",
                "notes": "Replication inhibition creates ssDNA gaps that trigger the classical SOS response."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "reca_filament",
            "predicate": "promotes autocleavage of",
            "object": "lexa_repressor",
            "description": "Activated RecA* promotes LexA autoproteolysis, de-repressing the SOS regulon.",
            "evidence": [
              {
                "reference": "DOI:10.1128/aem.01716-22",
                "notes": "RecA* activation induces LexA autoproteolysis; SOS response is mediated by RecA and LexA."
              }
            ]
          },
          {
            "subject": "reca_filament",
            "predicate": "promotes autocleavage of",
            "object": "ci_repressor",
            "description": "RecA* stimulates self-cleavage/inactivation of the phage CI repressor, de-repressing lysis and triggering induction.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41586-023-06376-y",
                "notes": "Host RecA activation leads to autoproteolysis and inactivation of cI, de-repressing lysis."
              }
            ]
          },
          {
            "subject": "ci_repressor",
            "predicate": "prevents",
            "object": "prophage_induction",
            "description": "While intact, the CI repressor maintains lysogeny and prevents prophage induction; its inactivation triggers induction.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41586-023-06376-y",
                "notes": "CI repression must be relieved (cI inactivation) to de-repress lysis and drive prophage induction."
              }
            ],
            "predicate_id": "RO:0002212"
          },
          {
            "subject": "phage_plasmid",
            "predicate": "enables",
            "object": "extrachromosomal_maintenance",
            "description": "Phage-plasmids are temperate phages maintained extrachromosomally, so prophages need not be integrated.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-024-45757-3",
                "notes": "Phage-plasmids are temperate phages maintained extrachromosomally as low-copy-number episomal forms."
              }
            ],
            "predicate_id": "RO:0002327"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-06-05T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate GENOMICS trait (prophage / lysogeny); sub-variant of mobile genetic element.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-08T14:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (prophage lysogeny) with RO predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 7 evidence-backed generic edges (10 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:11Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002213\u00d71, RO:0002212\u00d71, RO:0002327\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:32Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0098689\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-26T07:15:18Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A016XIE2\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:21:11Z",
        "curator": "claude",
        "action": "RETRACT_DEAD_UNIPROT_GROUNDINGS",
        "changes": "Retracted 1 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:23:53Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (InterPro:IPR050077\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope prophage_lysogeny=NONMECHANISTIC with scope_notes; marked 2 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (ci_repressor, reca_filament); retyped 1 node(s) (phage_plasmid->GENETIC_ELEMENT).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-15T06:22:00Z",
        "curator": "codex",
        "action": "GROUND_CAUSAL_NODE",
        "changes": "Grounded the RecA-LexA SOS-response biological-process node to GO:0009432 while adding the organism-level traitmech:000207 SOS response record.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000364",
    "label": "PrrC system",
    "definition": "A phage defense system in which an organism possesses a PrrC locus represented by DefenseFinder as a two-profile model requiring PrrC__EcoprrI and PrrC__PrrC, with type I restriction-modification components accepted as accessory markers.",
    "definition_source": "DOI:10.1186/1743-422X-7-360",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "PrrC",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      },
      {
        "synonym_text": "PrrC__EcoprrI",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "PrrC__PrrC",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "PMID:21129205",
        "snippet": "phage exclusion systems that involve T4-mediated activation of a latent endoribonuclease (PrrC) and cofactor-assisted activation of EF-Tu proteolysis (Gol-Lit)",
        "notes": "Uzan et al. name PrrC as a T4-mediated phage-exclusion system that activates a latent endoribonuclease."
      },
      {
        "reference": "PMID:16790566",
        "snippet": "The tRNA(Lys) anticodon nuclease PrrC is associated in latent form with the type Ic DNA restriction endonuclease EcoprrI and activated by a phage T4-encoded inhibitor of EcoprrI.",
        "notes": "Blanga-Kanfi et al. support latent PrrC association with the EcoprrI restriction endonuclease and activation by a T4-encoded EcoprrI inhibitor."
      },
      {
        "reference": "PMID:16790566",
        "snippet": "This triad exists in all the known PrrC homologs but only some of them feature residues needed for tRNA(Lys) recognition by the Escherichia coli prototype.",
        "notes": "Blanga-Kanfi et al. support a family of PrrC homologs whose substrate-recognition residues can differ from the Escherichia coli prototype."
      },
      {
        "reference": "PMID:16790566",
        "snippet": "The differential conservation and consistent genetic linkage of the PrrC proteins with EcoprrI homologs portray them as a family of restriction RNases of diverse substrate specificities that are mobilized when an associated DNA restriction nuclease is compromised.",
        "notes": "Blanga-Kanfi et al. support genetic linkage between PrrC proteins and EcoprrI homologs as a restriction-RNase family mobilized when an associated restriction nuclease is compromised."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "PrrC | 10\\.1186/1743-422X-7-360 | Post-transcriptional control by bacteriophage T4: mRNA decay and inhibition of translation initiation",
        "notes": "The DefenseFinder article registry maps the named PrrC system to the Uzan et al. T4 post-transcriptional-control review."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "PrrC\tPrrC\t2\t2\tPrrC__EcoprrI, PrrC__PrrC\tRM__Type_I_REases, RM__Type_I_S",
        "notes": "The DefenseFinder rules table models PrrC as a two-profile system requiring the PrrC__EcoprrI and PrrC__PrrC profiles, with type I restriction-modification components as accessory markers."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| PrrC__EcoprrI                                    | PrrC__EcoprrI                                    | PrrC                   | Custom                  | 20     |",
        "notes": "The DefenseFinder HMM inventory records PrrC__EcoprrI under PrrC."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| PrrC__PrrC                                       | PrrC__PrrC                                       | PrrC                   | Custom                  | 100    |",
        "notes": "The DefenseFinder HMM inventory records PrrC__PrrC under PrrC."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "prrc_locus_restricts_t4_phage",
        "title": "PrrC loci confer T4 phage exclusion",
        "description": "Conservative system-level sketch linking possession of a PrrC locus to T4-induced PrrC restriction-RNase defense without asserting the exact T4 trigger, natural substrate, or accessory component logic.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures PrrC as a named DefenseFinder two-profile phage-exclusion system while leaving natural homolog substrate specificity, the exact EcoprrI accessory composition and profile matching, the phage trigger logic, and PrrC profile-to-activity mapping unresolved.",
        "nodes": [
          {
            "node_id": "prrc_locus",
            "label": "PrrC locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A DefenseFinder PrrC phage-defense locus represented by PrrC__EcoprrI and PrrC__PrrC profiles."
          },
          {
            "node_id": "t4_induced_prrc_rnase_defense",
            "label": "T4-induced PrrC RNase defense",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Mobilization of a PrrC-family restriction RNase during bacteriophage T4 interference with the associated EcoprrI restriction nuclease."
          },
          {
            "node_id": "prrc_system_trait",
            "label": "PrrC system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000364",
            "description": "Possession of a genome-encoded PrrC phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "prrc_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "t4_induced_prrc_rnase_defense",
            "description": "PrrC proteins are genetically linked with EcoprrI homologs and can be mobilized when associated DNA restriction nucleases are compromised, and DefenseFinder models PrrC as a two-profile system.",
            "evidence": [
              {
                "reference": "PMID:21129205",
                "snippet": "phage exclusion systems that involve T4-mediated activation of a latent endoribonuclease (PrrC) and cofactor-assisted activation of EF-Tu proteolysis (Gol-Lit)",
                "notes": "Uzan et al. identify PrrC as a latent endonuclease participating in T4-mediated phage exclusion."
              },
              {
                "reference": "PMID:16790566",
                "snippet": "The tRNA(Lys) anticodon nuclease PrrC is associated in latent form with the type Ic DNA restriction endonuclease EcoprrI and activated by a phage T4-encoded inhibitor of EcoprrI.",
                "notes": "Blanga-Kanfi et al. connect PrrC to EcoprrI and T4 inhibitor-triggered activation."
              },
              {
                "reference": "PMID:16790566",
                "snippet": "The differential conservation and consistent genetic linkage of the PrrC proteins with EcoprrI homologs portray them as a family of restriction RNases of diverse substrate specificities that are mobilized when an associated DNA restriction nuclease is compromised.",
                "notes": "Blanga-Kanfi et al. generalize PrrC homologs as EcoprrI-linked restriction RNases."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "PrrC | 10\\.1186/1743-422X-7-360 | Post-transcriptional control by bacteriophage T4: mRNA decay and inhibition of translation initiation",
                "notes": "The DefenseFinder article registry maps the named PrrC system to the Uzan et al. T4 post-transcriptional-control review."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "PrrC\tPrrC\t2\t2\tPrrC__EcoprrI, PrrC__PrrC\tRM__Type_I_REases, RM__Type_I_S",
                "notes": "The DefenseFinder rules table models PrrC as a two-profile system requiring the PrrC__EcoprrI and PrrC__PrrC profiles, with type I restriction-modification components as accessory markers."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| PrrC__EcoprrI                                    | PrrC__EcoprrI                                    | PrrC                   | Custom                  | 20     |",
                "notes": "The DefenseFinder HMM inventory records PrrC__EcoprrI under PrrC."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| PrrC__PrrC                                       | PrrC__PrrC                                       | PrrC                   | Custom                  | 100    |",
                "notes": "The DefenseFinder HMM inventory records PrrC__PrrC under PrrC."
              }
            ]
          },
          {
            "subject": "t4_induced_prrc_rnase_defense",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "prrc_system_trait",
            "description": "T4-induced PrrC RNase defense realizes the PrrC system trait.",
            "evidence": [
              {
                "reference": "PMID:16790566",
                "snippet": "The tRNA(Lys) anticodon nuclease PrrC is associated in latent form with the type Ic DNA restriction endonuclease EcoprrI and activated by a phage T4-encoded inhibitor of EcoprrI.",
                "notes": "Blanga-Kanfi et al. support latent PrrC activation by a T4-encoded inhibitor of EcoprrI."
              },
              {
                "reference": "PMID:16790566",
                "snippet": "The differential conservation and consistent genetic linkage of the PrrC proteins with EcoprrI homologs portray them as a family of restriction RNases of diverse substrate specificities that are mobilized when an associated DNA restriction nuclease is compromised.",
                "notes": "Blanga-Kanfi et al. support broader mobilization of EcoprrI-linked PrrC-family restriction RNases."
              }
            ]
          },
          {
            "subject": "prrc_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "PrrC system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "PrrC | 10\\.1186/1743-422X-7-360 | Post-transcriptional control by bacteriophage T4: mRNA decay and inhibition of translation initiation",
                "notes": "The DefenseFinder article registry maps the named PrrC system to the Uzan et al. T4 post-transcriptional-control review."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "PrrC\tPrrC\t2\t2\tPrrC__EcoprrI, PrrC__PrrC\tRM__Type_I_REases, RM__Type_I_S",
                "notes": "The DefenseFinder rules table models PrrC as a two-profile system requiring the PrrC__EcoprrI and PrrC__PrrC profiles, with type I restriction-modification components as accessory markers."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "prrc-mechanism-gap",
        "prompt": "Resolve natural PrrC homolog substrate specificity, exact EcoprrI accessory composition and profile matching, and phage trigger logic before minting narrower PrrC mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Uzan et al. summarize PrrC as a T4 phage-exclusion system, Blanga-Kanfi et al. support PrrC and EcoprrI homologs as genetically linked restriction RNases, and DefenseFinder models PrrC as a two-profile system with EcoprrI and PrrC markers plus type I restriction-modification accessories. The natural substrates, accessory composition, and phage trigger logic remain unresolved.",
        "attaches_to": [
          "causal_graphs#prrc_locus_restricts_t4_phage"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-22"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-22T11:25:19Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted PrrC system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v241.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-22T11:39:03Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed the PrrC canonical_examples gap and left canonical_examples empty: the current evidence supports a named PrrC phage-exclusion system, the pinned DefenseFinder PrrC profiles, and EcoprrI-linked PrrC homologs, but does not cite a directly observed natural microbial taxon with a source-backed PrrC locus. No paid research was used. Fixes #1247.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-22T11:42:52Z",
        "curator": "codex",
        "action": "ADDRESS_PR_REVIEW",
        "changes": "Resolved PR #1245 review issue #1249 by removing the bare EcoprrI component name from PrrC system related synonyms while retaining the DefenseFinder PrrC__EcoprrI profile name and Blanga-Kanfi evidence for EcoprrI-linked PrrC homologs.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000257",
    "label": "PsyrTA system",
    "definition": "A phage defense system in which an organism possesses a two-component PsyrTA locus represented by PsyrA and PsyrT profiles that can protect bacteria from bacteriophage infection.",
    "definition_source": "DOI:10.1016/j.chom.2022.09.017",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "PsyrTA",
        "synonym_type": "EXACT_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1016/j.chom.2022.09.017",
        "snippet": "discovery of 21 defense systems that protect bacteria from phages, based on computational genomic analyses and phage-infection experiments",
        "notes": "Millman et al. report the computational and experimental cohort that DefenseFinder cites for PsyrTA as a bacterial anti-phage system."
      },
      {
        "reference": "DOI:10.1101/2022.05.11.491447",
        "snippet": "discovery of 21 new defense systems that protect bacteria from phages, based on computational genomic analyses and phage infection experiments",
        "notes": "The bioRxiv version of Millman et al. independently carries the 21-system discovery claim linked from DefenseFinder's PsyrTA article registry."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "PsyrTA | 10\\.1101/2022\\.05\\.11\\.491447 | An expanding arsenal of immune systems that protect bacteria from phages",
        "notes": "The DefenseFinder model registry maps the named PsyrTA system to the Millman et al. antiphage-system discovery preprint."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "PsyrTA\tPsyrTA\t2\t2\tPsyrTA__PsyrA, PsyrTA__PsyrT",
        "notes": "The DefenseFinder rules table models PsyrTA with PsyrA and PsyrT profiles."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "PsyrTA__PsyrA                                    | PsyrTA__PsyrA                                    | PsyrTA",
        "notes": "The DefenseFinder HMM inventory records PsyrA as a PsyrTA profile."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "PsyrTA__PsyrT                                    | PsyrTA__PsyrT                                    | PsyrTA",
        "notes": "The DefenseFinder HMM inventory records PsyrT as a PsyrTA profile."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "psyrta_locus_restricts_phage",
        "title": "PsyrTA loci confer bacterial phage defense",
        "description": "Conservative system-level sketch linking possession of a PsyrTA locus to restricted bacteriophage propagation without asserting the unresolved phage trigger or molecular output.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures PsyrTA as a named anti-phage system with the required DefenseFinder PsyrA and PsyrT profiles while leaving its phage trigger, molecular substrate, antiviral effector output, and subtype breadth unresolved.",
        "nodes": [
          {
            "node_id": "psyrta_locus",
            "label": "PsyrTA locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A PsyrTA anti-phage defense locus satisfying a DefenseFinder rule over PsyrA and PsyrT profiles."
          },
          {
            "node_id": "restricted_phage_propagation",
            "label": "restricted phage propagation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced propagation of bacteriophage in cells carrying the PsyrTA system."
          },
          {
            "node_id": "psyrta_system_trait",
            "label": "PsyrTA system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000257",
            "description": "Possession of a genome-encoded PsyrTA phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "psyrta_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "restricted_phage_propagation",
            "description": "DefenseFinder maps PsyrTA to a bacterial anti-phage-system discovery preprint and represents PsyrTA loci through PsyrA and PsyrT component profiles.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.chom.2022.09.017",
                "snippet": "discovery of 21 defense systems that protect bacteria from phages",
                "notes": "Millman et al. describe the anti-phage discovery cohort that the DefenseFinder PsyrTA registry row maps to the PsyrTA system."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "PsyrTA | 10\\.1101/2022\\.05\\.11\\.491447 | An expanding arsenal of immune systems that protect bacteria from phages",
                "notes": "The DefenseFinder registry maps PsyrTA itself to the Millman et al. bacterial antiphage-system discovery preprint."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "PsyrTA\tPsyrTA\t2\t2\tPsyrTA__PsyrA, PsyrTA__PsyrT",
                "notes": "The DefenseFinder rules table supports both PsyrA and PsyrT as required PsyrTA system profiles."
              }
            ]
          },
          {
            "subject": "restricted_phage_propagation",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "psyrta_system_trait",
            "description": "PsyrTA-mediated phage restriction realizes the PsyrTA system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.chom.2022.09.017",
                "snippet": "discovery of 21 defense systems that protect bacteria from phages",
                "notes": "Millman et al. place the PsyrTA discovery cohort in the set of bacterial systems that protect against phages."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "PsyrTA | 10\\.1101/2022\\.05\\.11\\.491447 | An expanding arsenal of immune systems that protect bacteria from phages",
                "notes": "DefenseFinder records PsyrTA as a named system from the Millman et al. antiphage discovery preprint."
              }
            ]
          },
          {
            "subject": "psyrta_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "PsyrTA system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "An expanding arsenal of immune systems that protect bacteria from phages",
                "notes": "DefenseFinder associates PsyrTA with the Millman et al. bacterial antiphage-system discovery paper."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "psyrta-mechanism-gap",
        "prompt": "Resolve PsyrTA phage triggers and effector outputs before minting narrower PsyrTA mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Millman et al. and DefenseFinder support PsyrTA as a named anti-phage system with required PsyrA and PsyrT profiles, but the trigger, molecular substrate, antiviral effector output, and subtype-specific mechanism are not resolved enough here to assert a narrower mechanistic child trait.",
        "attaches_to": [
          "causal_graphs#psyrta_locus_restricts_phage"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-19"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-19T00:47:28Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted PsyrTA system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v134.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000511",
    "label": "PvuRts1I system",
    "definition": "A type IV modification-dependent restriction system in which an organism possesses a PvuRts1I-family locus encoding a restriction endonuclease that recognizes 5-hydroxymethylcytosine or 5-glucosylhydroxymethylcytosine in double-stranded DNA and cleaves both strands on the 3'-side away from the recognized modified cytosine.",
    "definition_source": "DOI:10.1093/nar/gkr607",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000496"
    ],
    "synonyms": [
      {
        "synonym_text": "PvuRts1I",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1093/nar/gkr607",
        "snippet": "Using PvuRts1I as the founding member, we define a family of homologous proteins with similar DNA modification-dependent recognition properties.",
        "notes": "Wang et al. support PvuRts1I as the founding member of a family of modification-dependent restriction enzymes."
      },
      {
        "reference": "DOI:10.1093/nar/gkr607",
        "snippet": "PvuRts1I is a modification-dependent restriction endonuclease that recognizes 5-hydroxymethylcytosine (5hmC) as well as 5-glucosylhydroxymethylcytosine (5ghmC) in double-stranded DNA.",
        "notes": "Wang et al. support PvuRts1I recognition of 5hmC- and 5ghmC-containing double-stranded DNA."
      },
      {
        "reference": "DOI:10.1093/nar/gkr607",
        "snippet": "We show that these enzymes introduce a double-stranded cleavage at the 3'-side away from the recognized modified cytosine.",
        "notes": "Wang et al. support PvuRts1I-family enzymes as modification-dependent restriction endonucleases that cleave both DNA strands at a defined offset from the modified cytosine."
      },
      {
        "reference": "DOI:10.1093/nar/gkt747",
        "snippet": "The new class of modification-dependent restriction enzymes was named Type IV, as distinct from the familiar modification-blocked Types I-III.",
        "notes": "Loenen and Raleigh define the Type IV class as modification-dependent restriction enzymes."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| PvuRts1I | 10\\.1093/nar/gkr607 | Comparative characterization of the PvuRts1I family of restriction enzymes and their application in mapping genomic 5-hydroxymethylcytosine | ",
        "notes": "The pinned DefenseFinder article registry maps the PvuRts1I source key to the Wang et al. PvuRts1I-family paper."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "pvurts1i_restricts_modified_hmc_dna",
        "title": "PvuRts1I restricts modified-HMC DNA",
        "description": "Conservative system-level sketch linking a PvuRts1I-family locus to modified-hydroxymethylcytosine DNA restriction and to the Type IV restriction parent trait.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures PvuRts1I as a named Type IV modification-dependent restriction family while leaving natural host breadth, exact target selectivity across characterized homologs, accession-level protein examples, and DefenseFinder RM_Type_IV HMM/rules mapping unresolved.",
        "nodes": [
          {
            "node_id": "pvurts1i_family_locus",
            "label": "PvuRts1I-family locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A locus encoding a PvuRts1I-family modification-dependent restriction endonuclease."
          },
          {
            "node_id": "pvurts1i_modified_hmc_dna",
            "label": "PvuRts1I-targeted modified-HMC DNA",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Double-stranded DNA containing 5hmC or 5ghmC in a PvuRts1I-family recognition context."
          },
          {
            "node_id": "pvurts1i_modified_hmc_restriction",
            "label": "PvuRts1I modified-HMC restriction",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Modification-dependent restriction of 5hmC- or 5ghmC-containing DNA by a PvuRts1I-family endonuclease."
          },
          {
            "node_id": "pvurts1i_system_trait",
            "label": "PvuRts1I system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000511",
            "description": "Possession of a genome-encoded PvuRts1I-family modification-dependent restriction system."
          },
          {
            "node_id": "type_iv_modification_dependent_restriction",
            "label": "type IV modification-dependent restriction system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000496",
            "description": "Possession of a genome-encoded Type IV modification-dependent restriction system."
          }
        ],
        "edges": [
          {
            "subject": "pvurts1i_family_locus",
            "predicate": "enables",
            "predicate_id": "RO:0002327",
            "object": "pvurts1i_modified_hmc_restriction",
            "description": "PvuRts1I-family loci encode modification-dependent restriction endonucleases.",
            "evidence": [
              {
                "reference": "DOI:10.1093/nar/gkr607",
                "snippet": "Using PvuRts1I as the founding member, we define a family of homologous proteins with similar DNA modification-dependent recognition properties.",
                "notes": "Wang et al. support PvuRts1I as the founding member of a family of modification-dependent restriction enzymes."
              },
              {
                "reference": "DOI:10.1093/nar/gkr607",
                "snippet": "We show that these enzymes introduce a double-stranded cleavage at the 3'-side away from the recognized modified cytosine.",
                "notes": "Wang et al. support PvuRts1I-family enzymes as modification-dependent restriction endonucleases that cleave both DNA strands at a defined offset from the modified cytosine."
              }
            ]
          },
          {
            "subject": "pvurts1i_modified_hmc_restriction",
            "predicate": "mitigates",
            "predicate_id": "METPO:2007407",
            "object": "pvurts1i_modified_hmc_dna",
            "description": "PvuRts1I-family restriction targets DNA with 5hmC or 5ghmC modifications.",
            "evidence": [
              {
                "reference": "DOI:10.1093/nar/gkr607",
                "snippet": "PvuRts1I is a modification-dependent restriction endonuclease that recognizes 5-hydroxymethylcytosine (5hmC) as well as 5-glucosylhydroxymethylcytosine (5ghmC) in double-stranded DNA.",
                "notes": "Wang et al. support PvuRts1I recognition of 5hmC- and 5ghmC-containing double-stranded DNA."
              },
              {
                "reference": "DOI:10.1093/nar/gkr607",
                "snippet": "We show that these enzymes introduce a double-stranded cleavage at the 3'-side away from the recognized modified cytosine.",
                "notes": "Wang et al. support PvuRts1I-family enzymes as modification-dependent restriction endonucleases that cleave both DNA strands at a defined offset from the modified cytosine."
              }
            ]
          },
          {
            "subject": "pvurts1i_modified_hmc_restriction",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "pvurts1i_system_trait",
            "description": "PvuRts1I-family modified-HMC restriction realizes the organism-level PvuRts1I system possession trait.",
            "evidence": [
              {
                "reference": "DOI:10.1093/nar/gkr607",
                "snippet": "PvuRts1I is a modification-dependent restriction endonuclease that recognizes 5-hydroxymethylcytosine (5hmC) as well as 5-glucosylhydroxymethylcytosine (5ghmC) in double-stranded DNA.",
                "notes": "Wang et al. support PvuRts1I recognition of 5hmC- and 5ghmC-containing double-stranded DNA."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| PvuRts1I | 10\\.1093/nar/gkr607 | Comparative characterization of the PvuRts1I family of restriction enzymes and their application in mapping genomic 5-hydroxymethylcytosine | ",
                "notes": "The pinned DefenseFinder article registry maps the PvuRts1I source key to the Wang et al. PvuRts1I-family paper."
              }
            ]
          },
          {
            "subject": "pvurts1i_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "type_iv_modification_dependent_restriction",
            "description": "PvuRts1I system possession is a Type IV modification-dependent restriction system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1093/nar/gkr607",
                "snippet": "Using PvuRts1I as the founding member, we define a family of homologous proteins with similar DNA modification-dependent recognition properties.",
                "notes": "Wang et al. support PvuRts1I as the founding member of a family of modification-dependent restriction enzymes."
              },
              {
                "reference": "DOI:10.1093/nar/gkt747",
                "snippet": "The new class of modification-dependent restriction enzymes was named Type IV, as distinct from the familiar modification-blocked Types I-III.",
                "notes": "Loenen and Raleigh define the Type IV class as modification-dependent restriction enzymes."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "pvurts1i-defensefinder-model-gap",
        "prompt": "Resolve PvuRts1I-family breadth, 5hmC and 5ghmC target selectivity across natural hosts, accession-level protein examples, and DefenseFinder RM_Type_IV HMM/rules mapping before minting narrower PvuRts1I mechanism or component traits.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Wang et al. support PvuRts1I as the founding member of a family of 5hmC- and 5ghmC-recognizing modification-dependent restriction endonucleases, and the pinned DefenseFinder article registry maps PvuRts1I to the Wang et al. paper. The pinned HMM inventory and rules table have no exact PvuRts1I rows. This first-pass record therefore does not resolve a reusable DefenseFinder profile model, exact accession-level protein examples, the breadth of PvuRts1I-like systems across natural hosts, or the complete set of natural 5hmC and 5ghmC target contexts.",
        "evidence": [
          {
            "reference": "DOI:10.1093/nar/gkr607",
            "snippet": "Using PvuRts1I as the founding member, we define a family of homologous proteins with similar DNA modification-dependent recognition properties.",
            "notes": "Wang et al. support PvuRts1I as the founding member of a family of modification-dependent restriction enzymes."
          },
          {
            "reference": "DOI:10.1093/nar/gkr607",
            "snippet": "PvuRts1I is a modification-dependent restriction endonuclease that recognizes 5-hydroxymethylcytosine (5hmC) as well as 5-glucosylhydroxymethylcytosine (5ghmC) in double-stranded DNA.",
            "notes": "Wang et al. support PvuRts1I recognition of 5hmC- and 5ghmC-containing double-stranded DNA."
          },
          {
            "reference": "DOI:10.1093/nar/gkr607",
            "snippet": "We show that these enzymes introduce a double-stranded cleavage at the 3'-side away from the recognized modified cytosine.",
            "notes": "Wang et al. support PvuRts1I-family enzymes as modification-dependent restriction endonucleases that cleave both DNA strands at a defined offset from the modified cytosine."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
            "snippet": "| PvuRts1I | 10\\.1093/nar/gkr607 | Comparative characterization of the PvuRts1I family of restriction enzymes and their application in mapping genomic 5-hydroxymethylcytosine | ",
            "notes": "The pinned DefenseFinder article registry maps the PvuRts1I source key to the Wang et al. PvuRts1I-family paper."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "notes": "A structured first-pass search of the pinned DefenseFinder HMM inventory found no exact PvuRts1I row."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "A structured first-pass search of the pinned DefenseFinder rules table found no exact PvuRts1I system row."
          }
        ],
        "attaches_to": [
          "causal_graphs#pvurts1i_restricts_modified_hmc_dna"
        ],
        "posed_by": "codex",
        "posed_date": "2026-10-01"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-01T09:01:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted PvuRts1I system as a DOI- and DefenseFinder-backed GENOMICS TraitRecord under the type IV modification-dependent restriction system parent after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v388.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-01T09:01:02Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed PvuRts1I system during initial curation and left canonical_examples empty because Wang et al. support PvuRts1I and PvuRts1I-family enzymes, but not a single stable NCBITaxon strain exemplar or accession-level protein example for the organism-level PvuRts1I system trait. No paid research was used.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-01T09:28:12Z",
        "curator": "codex",
        "action": "ADVERSARIAL_REVIEW_REPAIR",
        "changes": "Addressed PR #1514 adversarial review issue #1515 by tightening the PvuRts1I system definition to match the Wang et al. 3'-side cleavage evidence without claiming a fixed cleavage distance.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000236",
    "label": "Pycsar system",
    "definition": "A phage defense system in which an organism possesses a Pycsar locus encoding a PycC pyrimidine cyclase and a cognate cyclic-pyrimidine receptor effector whose phage-induced cyclic CMP or cyclic UMP signaling activates antiviral effector outputs that inhibit bacteriophage propagation.",
    "definition_source": "DOI:10.1016/j.cell.2021.09.031",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "Pyrimidine Cyclase System for Antiphage Resistance",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1016/j.cell.2021.09.031"
      },
      {
        "synonym_text": "pyrimidine cyclase system for anti-phage resistance",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1038/s41467-024-49861-2"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1016/j.cell.2021.09.031",
        "snippet": "We discovered a family of bacterial pyrimidine cyclase enzymes that specifically synthesize cCMP and cUMP following phage infection",
        "notes": "Tal et al. support Pycsar-associated pyrimidine cyclases as phage-induced producers of cyclic CMP and cyclic UMP."
      },
      {
        "reference": "DOI:10.1016/j.cell.2021.09.031",
        "snippet": "The cCMP and cUMP molecules then activate effector proteins",
        "notes": "Tal et al. connect cyclic pyrimidine second messengers to activation of Pycsar effector proteins."
      },
      {
        "reference": "DOI:10.1016/j.cell.2021.09.031",
        "snippet": "The predicted cyclase genes are usually found in an operon together with an additional gene, and we therefore cloned such two-gene operons, one from Escherichia coli 303145 and the other from E. coli E831, into the laboratory E. coli strain MG1655. Challenging the transformed bacteria with a panel of 12 phages showed that both operons provided substantial defense against multiple phages",
        "notes": "Tal et al. support a canonical Escherichia coli example by showing that two E. coli Pycsar loci conferred antiphage defense after cloning into E. coli MG1655."
      },
      {
        "reference": "DOI:10.1016/j.cell.2021.09.031",
        "snippet": "Mutation in the predicted active site of the cyclase domain abolished defense",
        "notes": "Tal et al. support the functional importance of the PycC cyclase domain for the antiphage phenotype."
      },
      {
        "reference": "DOI:10.1038/s41467-024-49861-2",
        "snippet": "This system consists of a pyrimidine cyclase and a cyclic pyrimidine receptor protein",
        "notes": "Hou et al. support defining Pycsar systems around a pyrimidine cyclase plus a cognate cyclic-pyrimidine receptor rather than a bare pycC gene."
      },
      {
        "reference": "DOI:10.1038/s41467-024-49861-2",
        "snippet": "a distinct zinc-finger motif of the uridylate cyclase is identified to confer substantial resistance against phage infections",
        "notes": "Hou et al. support the uridylate-cyclase branch while the broad TraitRecord leaves cCMP-producing and cUMP-producing Pycsar clades unresolved as children."
      },
      {
        "reference": "DOI:10.1038/s41467-024-49861-2",
        "snippet": "structural characterization of cUMP receptor protein PycTIR provides clear picture of specific cUMP recognition and identifies a conserved N-terminal extension that mediates PycTIR oligomerization and activation",
        "notes": "Hou et al. support cyclic UMP recognition by the PycTIR cyclic-pyrimidine receptor as one resolved Pycsar effector-activation mechanism."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:562",
        "taxon_label": "Escherichia coli",
        "note": "Tal et al. cloned native Pycsar two-gene operons from E. coli 303145 and E. coli E831 into E. coli MG1655 and showed that both operons provided substantial defense against multiple phages.",
        "reference": "DOI:10.1016/j.cell.2021.09.031"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "pycsar_cyclic_pyrimidine_phage_defense",
        "title": "Pycsar loci couple cyclic-pyrimidine signaling to phage defense",
        "description": "Evidence-backed process sketch linking a complete Pycsar locus to phage-induced PycC pyrimidine cyclase activity, cyclic CMP or cyclic UMP signaling, cyclic-pyrimidine receptor activation, antiviral effector output, and inhibition of phage propagation.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph stays at the Pycsar-family level and uses characterized cytidylate-cyclase and uridylate-cyclase examples without asserting one universal cyclase clade, cCMP-versus-cUMP product, PycTIR-versus-PycTM effector fold, AGS-C role, zinc-finger role, activating phage trigger, membrane impairment, or NAD-depletion output across all Pycsar antiphage loci.",
        "nodes": [
          {
            "node_id": "pycsar_locus",
            "label": "Pycsar locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A complete Pycsar antiphage locus encoding a PycC pyrimidine cyclase and a cognate cyclic-pyrimidine receptor effector."
          },
          {
            "node_id": "phage_induced_pycC_cyclase_activity",
            "label": "phage-induced PycC cyclase activity",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Activation of a PycC pyrimidine cyclase during phage infection."
          },
          {
            "node_id": "cyclic_pyrimidine_synthesis",
            "label": "cyclic pyrimidine second messenger synthesis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "PycC-catalyzed production of cyclic CMP or cyclic UMP second messengers."
          },
          {
            "node_id": "cyclic_pyrimidine_receptor_activation",
            "label": "cyclic pyrimidine receptor activation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Activation of a Pycsar cyclic-pyrimidine receptor effector by cyclic CMP or cyclic UMP."
          },
          {
            "node_id": "pycsar_antiviral_output",
            "label": "Pycsar antiviral output",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Execution of a Pycsar effector output that arrests infected host cells or otherwise limits bacteriophage amplification."
          },
          {
            "node_id": "phage_propagation",
            "label": "phage propagation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Completion of bacteriophage replication and spread in a susceptible bacterial population."
          },
          {
            "node_id": "pycsar_system_trait",
            "label": "Pycsar system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000236",
            "description": "Possession of a genome-encoded Pycsar cyclic-pyrimidine phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "pycsar_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "phage_induced_pycC_cyclase_activity",
            "description": "Pycsar loci encode a PycC pyrimidine cyclase whose catalytic activity is required for the antiphage phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.cell.2021.09.031",
                "snippet": "Mutation in the predicted active site of the cyclase domain abolished defense",
                "notes": "Tal et al. show that the PycC active site is required for defense in an E. coli Pycsar locus."
              }
            ]
          },
          {
            "subject": "pycsar_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "cyclic_pyrimidine_receptor_activation",
            "description": "Complete Pycsar systems pair the PycC cyclase with a cyclic-pyrimidine receptor effector.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-024-49861-2",
                "snippet": "This system consists of a pyrimidine cyclase and a cyclic pyrimidine receptor protein",
                "notes": "Hou et al. support a two-part system definition rather than a cyclase-only sequence feature."
              }
            ]
          },
          {
            "subject": "phage_induced_pycC_cyclase_activity",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "cyclic_pyrimidine_synthesis",
            "description": "PycC pyrimidine cyclases synthesize cyclic CMP or cyclic UMP after phage infection.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.cell.2021.09.031",
                "snippet": "We discovered a family of bacterial pyrimidine cyclase enzymes that specifically synthesize cCMP and cUMP following phage infection",
                "notes": "Tal et al. link PycC cyclase activity to phage-induced cyclic CMP and cyclic UMP production."
              }
            ]
          },
          {
            "subject": "cyclic_pyrimidine_synthesis",
            "predicate": "activates",
            "predicate_id": "RO:0002213",
            "object": "cyclic_pyrimidine_receptor_activation",
            "description": "Cyclic CMP and cyclic UMP second messengers can activate Pycsar effector proteins.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.cell.2021.09.031",
                "snippet": "The cCMP and cUMP molecules then activate effector proteins",
                "notes": "Tal et al. support cyclic-pyrimidine second messengers as direct activators of Pycsar effector proteins."
              }
            ]
          },
          {
            "subject": "cyclic_pyrimidine_receptor_activation",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "pycsar_antiviral_output",
            "description": "Pycsar receptor activation stimulates an immune-effector state that antagonizes phage infection.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.cell.2021.09.031",
                "snippet": "We discovered a family of bacterial pyrimidine cyclase enzymes that specifically synthesize cCMP and cUMP following phage infection and demonstrate that these molecules activate immune effectors that execute an antiviral response",
                "notes": "Tal et al. connect cCMP and cUMP to immune-effector activation and antiviral output."
              }
            ]
          },
          {
            "subject": "pycsar_antiviral_output",
            "predicate": "mitigates",
            "predicate_id": "METPO:2007407",
            "object": "phage_propagation",
            "description": "Native E. coli Pycsar systems substantially defend against multiple bacteriophages.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.cell.2021.09.031",
                "snippet": "The predicted cyclase genes are usually found in an operon together with an additional gene, and we therefore cloned such two-gene operons, one from Escherichia coli 303145 and the other from E. coli E831, into the laboratory E. coli strain MG1655. Challenging the transformed bacteria with a panel of 12 phages showed that both operons provided substantial defense against multiple phages",
                "notes": "Tal et al. demonstrated substantial antiphage defense by two native E. coli Pycsar operons cloned into E. coli MG1655."
              }
            ]
          },
          {
            "subject": "pycsar_antiviral_output",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "pycsar_system_trait",
            "description": "Cyclic-pyrimidine signaling through a Pycsar receptor realizes the Pycsar antiphage trait.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-024-49861-2",
                "snippet": "named pyrimidine cyclase system for anti-phage resistance (Pycsar)",
                "notes": "Hou et al. connect the Pycsar name to the cyclic-pyrimidine signaling system's antiphage-resistance phenotype."
              }
            ]
          },
          {
            "subject": "pycsar_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Pycsar system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.cell.2021.09.031",
                "snippet": "cCMP/cUMP cyclases function as part of a family of bacterial anti-phage defense systems",
                "notes": "Tal et al. support Pycsar system as a child of phage defense system."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "pycsar-signal-and-effector-gap",
        "prompt": "Resolve Pycsar cyclase clades, cyclic pyrimidine specificity, receptor-effector folds, activating phage triggers, and effector outputs before minting narrower Pycsar subtype children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Tal et al. support Pycsar systems as widespread PycC-containing antiphage systems whose phage-induced cyclic CMP or cyclic UMP second messengers activate immune effectors, and Hou et al. resolve a uridylate-cyclase/PycTIR branch with zinc-finger and cUMP-recognition determinants. The first TraitRecord therefore stays at the broad Pycsar-system level until separate subtype review resolves which cyclase clades, second messengers, receptor folds, phage triggers, and outputs apply across each family.",
        "posed_by": "codex",
        "posed_date": "2026-09-18"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-18T07:33:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Pycsar system as a DOI-backed GENOMICS TraitRecord under the phage defense system parent after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v113.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000238",
    "label": "RADAR system",
    "definition": "A phage defense system in which an organism possesses a restriction by an adenosine deaminase acting on RNA locus encoding an RdrA AAA+ ATPase and an RdrB adenosine deaminase that assemble into a supramolecular defense complex to modify adenosine-containing substrates and inhibit bacteriophage replication.",
    "definition_source": "DOI:10.1016/j.cell.2023.01.012",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "restriction by an adenosine deaminase acting on RNA",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1016/j.cell.2023.01.012"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1016/j.cell.2023.01.012",
        "snippet": "RADAR is a two-protein bacterial defense system that was reported to defend against phage",
        "notes": "Duncan-Lowey et al. support RADAR as a named bacterial phage-defense system."
      },
      {
        "reference": "DOI:10.1016/j.cell.2023.01.012",
        "snippet": "revealing RdrA as a heptameric, two-layered AAA+ ATPase and RdrB as a dodecameric, hollow complex with twelve surface-exposed deaminase active sites",
        "notes": "Duncan-Lowey et al. support the RdrA AAA+ ATPase and RdrB adenosine-deaminase complex components."
      },
      {
        "reference": "DOI:10.1016/j.cell.2023.01.012",
        "snippet": "RdrB catalyzes ATP-to-ITP conversion in vitro and induces the massive accumulation of inosine mononucleotides during phage infection in vivo, limiting phage replication",
        "notes": "Duncan-Lowey et al. support ATP-to-ITP deamination and inosine-mononucleotide accumulation as RADAR antiphage outputs."
      },
      {
        "reference": "DOI:10.1016/j.cell.2023.01.012",
        "snippet": "When heterologously expressed in E. coli MG1655, all RADAR systems conferred defense against the closely related T-even phages T2, T4, and T6",
        "notes": "Duncan-Lowey et al. support the E. coli P0304799.3 RADAR locus as experimentally investigated and antiphage-active when cloned into E. coli MG1655."
      },
      {
        "reference": "DOI:10.1016/j.cell.2023.01.026",
        "snippet": "RADAR contains an adenosine triphosphatase (RdrA) and an adenosine deaminase (RdrB)",
        "notes": "Gao et al. independently support defining RADAR around the RdrA ATPase and RdrB deaminase components."
      },
      {
        "reference": "DOI:10.1016/j.cell.2023.01.026",
        "snippet": "up to twelve RdrA rings can dock one RdrB cage with precise alignments between deaminase catalytic pockets and RNA-translocation channels",
        "notes": "Gao et al. independently resolve RADAR RdrA/RdrB supramolecular assemblies while supporting an RNA-translocation interpretation of the deaminase substrate."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:562",
        "taxon_label": "Escherichia coli",
        "note": "Duncan-Lowey et al. selected the RADAR system from E. coli P0304799.3 for experimental investigation and reported that it conferred defense against T-even phages when heterologously expressed in E. coli MG1655.",
        "reference": "DOI:10.1016/j.cell.2023.01.012"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "radar_rdrab_deamination_antiphage_defense",
        "title": "RADAR RdrA/RdrB complexes couple deamination to phage defense",
        "description": "Evidence-backed process sketch covering RADAR locus assembly, infection-associated adenosine-substrate deamination, inosine nucleotide accumulation, and inhibition of phage replication without asserting the unresolved exact coupling step.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph stays at the RADAR-family level and uses the mononucleotide-deamination mechanism from Duncan-Lowey et al. without asserting that the exact RdrA activation trigger, ATP-versus-RNA substrate, inosine toxicity route, or abortive-infection output is resolved across all RADAR loci.",
        "nodes": [
          {
            "node_id": "radar_locus",
            "label": "RADAR locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A complete restriction by an adenosine deaminase acting on RNA locus encoding RdrA and RdrB components."
          },
          {
            "node_id": "rdra_rdrb_complex_assembly",
            "label": "RdrA/RdrB supramolecular complex assembly",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Assembly of the RdrA AAA+ ATPase and RdrB adenosine deaminase into a supramolecular RADAR defense complex."
          },
          {
            "node_id": "adenosine_substrate_deamination",
            "label": "RADAR adenosine-substrate deamination",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "RdrB-associated deamination of adenosine-containing substrates during RADAR activation."
          },
          {
            "node_id": "inosine_nucleotide_accumulation",
            "label": "inosine nucleotide accumulation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Accumulation of inosine nucleotides such as ITP and dITP in infected cells."
          },
          {
            "node_id": "phage_replication",
            "label": "phage replication",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Bacteriophage genome replication and production inside an infected bacterial host."
          },
          {
            "node_id": "radar_system_trait",
            "label": "RADAR system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000238",
            "description": "Possession of a genome-encoded RADAR phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "radar_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "rdra_rdrb_complex_assembly",
            "description": "RADAR loci encode RdrA and RdrB proteins that assemble into a supramolecular defense complex.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.cell.2023.01.012",
                "snippet": "RdrA and RdrB join to form a giant assembly up to 10 MDa",
                "notes": "Duncan-Lowey et al. support RdrA/RdrB RADAR complex assembly."
              }
            ]
          },
          {
            "subject": "adenosine_substrate_deamination",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "inosine_nucleotide_accumulation",
            "description": "RADAR-associated ATP-to-ITP deamination drives inosine-mononucleotide accumulation during phage infection.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.cell.2023.01.012",
                "snippet": "RdrB catalyzes ATP-to-ITP conversion in vitro and induces the massive accumulation of inosine mononucleotides during phage infection in vivo",
                "notes": "Duncan-Lowey et al. connect RdrB ATP-to-ITP catalysis to phage-infection-associated inosine mononucleotide accumulation."
              }
            ]
          },
          {
            "subject": "inosine_nucleotide_accumulation",
            "predicate": "mitigates",
            "predicate_id": "METPO:2007407",
            "object": "phage_replication",
            "description": "RADAR-induced inosine nucleotide accumulation limits phage replication.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.cell.2023.01.012",
                "snippet": "RdrB catalyzes ATP-to-ITP conversion in vitro and induces the massive accumulation of inosine mononucleotides during phage infection in vivo, limiting phage replication",
                "notes": "Duncan-Lowey et al. support inosine mononucleotide accumulation as a phage-limiting RADAR output."
              }
            ]
          },
          {
            "subject": "adenosine_substrate_deamination",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "radar_system_trait",
            "description": "RADAR-mediated adenosine-nucleotide deamination realizes the RADAR antiphage phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.cell.2023.01.012",
                "snippet": "rapid deamination of adenosine nucleotides is a key mediator of RADAR anti-phage defense",
                "notes": "Duncan-Lowey et al. connect rapid adenosine-nucleotide deamination, rather than downstream inosine accumulation alone, to RADAR antiphage defense."
              }
            ]
          },
          {
            "subject": "radar_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "RADAR system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.cell.2023.01.012",
                "snippet": "RADAR is a two-protein bacterial defense system that was reported to defend against phage",
                "notes": "Duncan-Lowey et al. support RADAR as a bacterial phage-defense system."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "radar-trigger-and-substrate-gap",
        "prompt": "Resolve RADAR phage triggers, RdrA activation, ATP-versus-RNA deamination, and inosine nucleotide toxicity before minting narrower RADAR mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Gao et al. support an RNA translocation and deamination model for RdrA/RdrB RADAR assemblies, whereas Duncan-Lowey et al. found that ATP and dATP mononucleotide deamination rather than robust RNA editing mediates RADAR immunity. The first TraitRecord therefore stays at the RADAR-system level until separate review resolves which activating phage cues, RdrA sensor states, deaminase substrates, and inosine toxicity routes generalize across RADAR loci.",
        "posed_by": "codex",
        "posed_date": "2026-09-18"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-18T09:55:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted RADAR system as a DOI-backed GENOMICS TraitRecord under the phage defense system parent after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v115.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-18T10:07:00Z",
        "curator": "codex",
        "action": "ADVERSARIAL_REVIEW_REPAIR",
        "changes": "Resolved PR #978 review follow-ups #979, #980, and #981 plus PR #982 review follow-ups #983, #984, and #985 by removing the unsupported RADAR-locus-to-deamination edge, rewiring the RADAR confers edge to adenosine-nucleotide deamination, and normalizing the initial per-record curation timestamp while leaving the append-only session history record intact.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000411",
    "label": "RAZR system",
    "definition": "A phage defense system in which an organism possesses a locus encoding a RAZR zinc-finger HEPN RNase that can form a phage-triggered higher-order ring complex, cleave RNA broadly, inhibit translation, and restrict phage propagation.",
    "definition_source": "DOI:10.1038/s41586-025-10060-8",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "RAZR",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1038/s41586-025-10060-8"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/s41586-025-10060-8",
        "snippet": "assembles into an active, 24-meric ring",
        "notes": "Zhang et al. define RAZR as a ring-activated zinc-finger RNase whose phage-triggered higher-order assembly generates an active 24-subunit ring."
      },
      {
        "reference": "DOI:10.1038/s41586-025-10060-8",
        "snippet": "cleave RNA nonspecifically to inhibit translation and restrict phage propagation",
        "notes": "Zhang et al. connect activated RAZR complexes to broad RNA cleavage, translational shutdown, and restriction of phage growth."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| RAZR | 10\\.1038/s41586-025-10060-8 | Bacterial immune activation via supramolecular assembly with phage triggers |",
        "notes": "The pinned DefenseFinder article registry maps the named RAZR system to the Zhang et al. Nature article; the pinned DefenseFinder HMM inventory (https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md) and rules table (https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv) do not list RAZR, so this row is name-to-paper evidence rather than model-component evidence."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "razr_ring_trigger_restricts_phage",
        "title": "RAZR ring assembly activates RNase defense",
        "description": "Conservative system-level sketch linking a RAZR locus and a phage ring trigger to RAZR oligomerization, nonspecific RNA cleavage, translation inhibition, phage-propagation restriction, and RAZR system possession.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures RAZR as a named phage-defense RNase activated by phage protein ring scaffolds while leaving natural hosts, the complete phage-trigger set, exact RNA-substrate preference, and profile-to-component DefenseFinder modeling unresolved.",
        "nodes": [
          {
            "node_id": "razr_locus",
            "label": "RAZR locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A bacterial locus encoding a ring-activated zinc-finger HEPN RNase."
          },
          {
            "node_id": "phage_ring_trigger",
            "label": "phage ring trigger",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Formation of a phage-encoded protein ring scaffold whose geometry can promote RAZR assembly."
          },
          {
            "node_id": "razr_oligomerization",
            "label": "RAZR oligomerization",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Assembly of RAZR into a higher-order active RNase ring around a phage protein ring scaffold."
          },
          {
            "node_id": "nonspecific_rna_cleavage",
            "label": "nonspecific RNA cleavage",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Broad RNA cleavage by activated RAZR ribonuclease complexes."
          },
          {
            "node_id": "translation_inhibition",
            "label": "translation inhibition",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Suppression of translation downstream of activated RAZR-mediated RNA cleavage."
          },
          {
            "node_id": "phage_propagation",
            "label": "phage propagation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Productive bacteriophage propagation."
          },
          {
            "node_id": "restricted_phage_propagation",
            "label": "restricted phage propagation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Restriction of productive phage propagation in bacteria carrying activated RAZR defense."
          },
          {
            "node_id": "razr_system_trait",
            "label": "RAZR system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000411",
            "description": "Possession of a genome-encoded RAZR phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "razr_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "razr_oligomerization",
            "description": "A RAZR locus encodes the RNase that assembles into an active phage-triggered ring complex.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41586-025-10060-8",
                "snippet": "assembles into an active, 24-meric ring",
                "notes": "Zhang et al. connect the RAZR bacterial immunity protein to phage-triggered active ring assembly."
              }
            ]
          },
          {
            "subject": "phage_ring_trigger",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "razr_oligomerization",
            "description": "Phage-encoded ring scaffolds provide the geometry that activates RAZR assembly.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41586-025-10060-8",
                "snippet": "formed by two unrelated phage proteins",
                "notes": "Zhang et al. show that RAZR activation can be triggered by ring scaffolds from unrelated phage proteins."
              }
            ]
          },
          {
            "subject": "razr_oligomerization",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "nonspecific_rna_cleavage",
            "description": "RAZR ring assembly activates broad RNase activity.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41586-025-10060-8",
                "snippet": "enables RAZR to cleave RNA nonspecifically",
                "notes": "Zhang et al. place nonspecific RNA cleavage downstream of RAZR complex formation."
              }
            ]
          },
          {
            "subject": "nonspecific_rna_cleavage",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "translation_inhibition",
            "description": "Broad RAZR-mediated RNA cleavage inhibits cellular translation during phage infection.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41586-025-10060-8",
                "snippet": "inhibit translation",
                "notes": "Zhang et al. identify translation inhibition as an output of activated RAZR-mediated RNA cleavage."
              }
            ]
          },
          {
            "subject": "translation_inhibition",
            "predicate": "mitigates",
            "predicate_id": "METPO:2007407",
            "object": "phage_propagation",
            "description": "Translation inhibition caused by RAZR activation restricts phage propagation.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41586-025-10060-8",
                "snippet": "restrict phage propagation",
                "notes": "Zhang et al. connect RAZR-dependent translation inhibition to restricted phage propagation."
              }
            ]
          },
          {
            "subject": "translation_inhibition",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "restricted_phage_propagation",
            "description": "RAZR-associated translation inhibition realizes restriction of phage propagation.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41586-025-10060-8",
                "snippet": "to inhibit translation and restrict phage propagation",
                "notes": "Zhang et al. report that the same activated RAZR RNase output inhibits translation and restricts phage propagation."
              }
            ]
          },
          {
            "subject": "restricted_phage_propagation",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "razr_system_trait",
            "description": "RAZR-mediated phage restriction realizes the RAZR system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41586-025-10060-8",
                "snippet": "cleave RNA nonspecifically to inhibit translation and restrict phage propagation",
                "notes": "Zhang et al. support restricted phage propagation as an output of active RAZR defense complexes."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| RAZR | 10\\.1038/s41586-025-10060-8 | Bacterial immune activation via supramolecular assembly with phage triggers |",
                "notes": "The pinned DefenseFinder article registry maps the named RAZR system to the Zhang et al. Nature article; the pinned DefenseFinder HMM inventory (https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md) and rules table (https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv) do not list RAZR, so this row is name-to-paper evidence rather than model-component evidence."
              }
            ]
          },
          {
            "subject": "razr_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "RAZR system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41586-025-10060-8",
                "snippet": "assembles into an active, 24-meric ring",
                "notes": "Zhang et al. frame RAZR as a bacterial immune RNase whose activated state restricts phage propagation."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| RAZR | 10\\.1038/s41586-025-10060-8 | Bacterial immune activation via supramolecular assembly with phage triggers |",
                "notes": "The pinned DefenseFinder article registry maps the named RAZR system to the Zhang et al. Nature article; the pinned DefenseFinder HMM inventory (https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md) and rules table (https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv) do not list RAZR, so this row is name-to-paper evidence rather than model-component evidence."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "razr-trigger-model-gap",
        "prompt": "Resolve RAZR natural hosts, phage ring triggers, RNA-substrate breadth, and model coverage before minting narrower RAZR mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Zhang et al. support RAZR as a ring-activated zinc-finger HEPN RNase that can oligomerize around unrelated phage ring scaffolds, but natural locus breadth, the full phage-trigger set, exact RNA-substrate preference, and absence from the pinned DefenseFinder HMM/rules rows need further review.",
        "attaches_to": [
          "causal_graphs#razr_ring_trigger_restricts_phage"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-27"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-27T15:45:19Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted RAZR system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; left canonical_examples empty until direct native-locus evidence supports a microbial exemplar; the replacement placeholder is reserved in proposals/metpo_traitmech_v288.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000531",
    "label": "Resolvase DUF5677 system",
    "definition": "A phage defense system in which an organism possesses a genome-encoded, resolvase- and DUF5677-associated prokaryotic Schlafen nuclease locus.",
    "definition_source": "DOI:10.1038/s41564-026-02277-8",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "Resolvase_DUF5677",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/s41564-026-02277-8",
        "snippet": "prokaryotic Schlafen nucleases are widespread antiviral effectors that protect bacteria from bacteriophages and are fused to a diverse array of phage-sensing domains.",
        "notes": "Perez Taboada et al. support bacterial prokaryotic Schlafen nucleases as antiviral effectors fused to phage-sensing domains."
      },
      {
        "reference": "DOI:10.1038/s41564-026-02277-8",
        "snippet": "We expressed seven Enterobacterales Schlafen systems in Escherichia coli, identifying two that confer defence against coliphages.",
        "notes": "Perez Taboada et al. cloned candidate Enterobacterales Schlafen systems into E. coli and observed coliphage defense for two of them."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| Resolvase_DUF5677 | 10\\.1038/s41564-026-02277-8 | Bacterial Schlafen proteins mediate phage defence | ",
        "notes": "The pinned DefenseFinder article registry maps the Resolvase_DUF5677 source key to the Perez Taboada et al. Schlafen phage-defense paper."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "resolvase_duf5677_phage_defense",
        "title": "Resolvase DUF5677 loci support Schlafen phage defense",
        "description": "Conservative system-level sketch linking a Resolvase_DUF5677 locus to prokaryotic Schlafen nuclease antiviral activity and the phage-defense parent.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures the DefenseFinder Resolvase_DUF5677 article namespace at system level and deliberately leaves the exact locus architecture, the DUF5677-associated domain boundary, accession-level protein examples, native host exemplars, phage trigger breadth, and DefenseFinder HMM/rules profiles unresolved.",
        "nodes": [
          {
            "node_id": "resolvase_duf5677_locus",
            "label": "Resolvase DUF5677 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A locus encoding a prokaryotic Schlafen nuclease in a Resolvase_DUF5677 anti-phage system."
          },
          {
            "node_id": "schlafen_antiviral_activity",
            "label": "Schlafen antiviral activity",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Anti-phage activity mediated by a prokaryotic Schlafen nuclease."
          },
          {
            "node_id": "resolvase_duf5677_system_trait",
            "label": "Resolvase DUF5677 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000531",
            "description": "Possession of a genome-encoded resolvase- and DUF5677-associated prokaryotic Schlafen phage-defense system."
          },
          {
            "node_id": "phage_defense_system_trait",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "resolvase_duf5677_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "schlafen_antiviral_activity",
            "description": "Resolvase_DUF5677 loci are part of the bacterial prokaryotic Schlafen nuclease phage-defense family.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-026-02277-8",
                "snippet": "prokaryotic Schlafen nucleases are widespread antiviral effectors that protect bacteria from bacteriophages and are fused to a diverse array of phage-sensing domains.",
                "notes": "Perez Taboada et al. support bacterial prokaryotic Schlafen nucleases as antiviral effectors fused to phage-sensing domains."
              }
            ]
          },
          {
            "subject": "schlafen_antiviral_activity",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "resolvase_duf5677_system_trait",
            "description": "Prokaryotic Schlafen antiviral effector activity realizes the organism-level Resolvase DUF5677 system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-026-02277-8",
                "snippet": "prokaryotic Schlafen nucleases are widespread antiviral effectors that protect bacteria from bacteriophages and are fused to a diverse array of phage-sensing domains.",
                "notes": "Perez Taboada et al. support bacterial prokaryotic Schlafen nucleases as antiviral effectors fused to phage-sensing domains."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| Resolvase_DUF5677 | 10\\.1038/s41564-026-02277-8 | Bacterial Schlafen proteins mediate phage defence | ",
                "notes": "The pinned DefenseFinder article registry maps the Resolvase_DUF5677 source key to the Perez Taboada et al. Schlafen phage-defense paper."
              }
            ]
          },
          {
            "subject": "resolvase_duf5677_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system_trait",
            "description": "Resolvase DUF5677 system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-026-02277-8",
                "snippet": "We expressed seven Enterobacterales Schlafen systems in Escherichia coli, identifying two that confer defence against coliphages.",
                "notes": "Perez Taboada et al. cloned candidate Enterobacterales Schlafen systems into E. coli and observed coliphage defense for two of them."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| Resolvase_DUF5677 | 10\\.1038/s41564-026-02277-8 | Bacterial Schlafen proteins mediate phage defence | ",
                "notes": "The pinned DefenseFinder article registry maps the Resolvase_DUF5677 source key to the Perez Taboada et al. Schlafen phage-defense paper."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "resolvase-duf5677-defensefinder-profile-gap",
        "prompt": "Resolve exact Resolvase_DUF5677 locus architecture, DUF5677-associated domain boundaries, natural host exemplars, phage trigger breadth, and DefenseFinder HMM/rules coverage before minting narrower Resolvase DUF5677 mechanism or component traits.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Perez Taboada et al. support prokaryotic Schlafen nucleases as widespread antiviral effectors fused to phage-sensing domains, and the pinned DefenseFinder article registry maps the Resolvase_DUF5677 key to the same article. The pinned HMM inventory and rules table have no exact Resolvase_DUF5677 or DUF5677 rows for this source key. This first-pass record therefore does not resolve whether the exact Resolvase_DUF5677 architecture is a single-protein fusion or multi-gene locus, its exact DUF5677-associated domain boundaries, natural host exemplars, accession-level Schlafen proteins, full phage trigger breadth, or a reusable DefenseFinder profile model.",
        "evidence": [
          {
            "reference": "DOI:10.1038/s41564-026-02277-8",
            "snippet": "prokaryotic Schlafen nucleases are widespread antiviral effectors that protect bacteria from bacteriophages and are fused to a diverse array of phage-sensing domains.",
            "notes": "Perez Taboada et al. support bacterial prokaryotic Schlafen nucleases as antiviral effectors fused to phage-sensing domains."
          },
          {
            "reference": "DOI:10.1038/s41564-026-02277-8",
            "snippet": "We expressed seven Enterobacterales Schlafen systems in Escherichia coli, identifying two that confer defence against coliphages.",
            "notes": "Perez Taboada et al. cloned candidate Enterobacterales Schlafen systems into E. coli and observed coliphage defense for two of them."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
            "snippet": "| Resolvase_DUF5677 | 10\\.1038/s41564-026-02277-8 | Bacterial Schlafen proteins mediate phage defence | ",
            "notes": "The pinned DefenseFinder article registry maps the Resolvase_DUF5677 source key to the Perez Taboada et al. Schlafen phage-defense paper."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "notes": "A structured first-pass search of the pinned DefenseFinder HMM inventory found no exact Resolvase_DUF5677, Schlafen, or DUF5677 row for this system."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "A structured first-pass search of the pinned DefenseFinder rules table found no exact Resolvase_DUF5677, Schlafen, or DUF5677 system row for this system."
          }
        ],
        "attaches_to": [
          "causal_graphs#resolvase_duf5677_phage_defense"
        ],
        "posed_by": "codex",
        "posed_date": "2026-10-02"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-02T01:50:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Resolvase DUF5677 system as a DOI- and DefenseFinder-backed GENOMICS TraitRecord under the phage defense system parent after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v408.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-02T01:50:01Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed Resolvase DUF5677 system during initial curation and left canonical_examples empty because Perez Taboada et al. and the pinned DefenseFinder article registry support the Resolvase_DUF5677 system namespace, but not an accession-backed native microbial taxon exemplar for the exact Resolvase_DUF5677 source key. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000532",
    "label": "Resolvase KAP NTPase system",
    "definition": "A phage defense system in which an organism possesses a genome-encoded, resolvase- and KAP NTPase-associated prokaryotic Schlafen nuclease locus.",
    "definition_source": "DOI:10.1038/s41564-026-02277-8",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "Resolvase_KAP_NTPase",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/s41564-026-02277-8",
        "snippet": "prokaryotic Schlafen nucleases are widespread antiviral effectors that protect bacteria from bacteriophages and are fused to a diverse array of phage-sensing domains.",
        "notes": "Perez Taboada et al. support bacterial prokaryotic Schlafen nucleases as antiviral effectors fused to phage-sensing domains."
      },
      {
        "reference": "DOI:10.1038/s41564-026-02277-8",
        "snippet": "We expressed seven Enterobacterales Schlafen systems in Escherichia coli, identifying two that confer defence against coliphages.",
        "notes": "Perez Taboada et al. cloned candidate Enterobacterales Schlafen systems into E. coli and observed coliphage defense for two of them."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| Resolvase_KAP_NTPase | 10\\.1038/s41564-026-02277-8 | Bacterial Schlafen proteins mediate phage defence | ",
        "notes": "The pinned DefenseFinder article registry maps the Resolvase_KAP_NTPase source key to the Perez Taboada et al. Schlafen phage-defense paper."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "resolvase_kap_ntpase_phage_defense",
        "title": "Resolvase KAP NTPase loci support Schlafen phage defense",
        "description": "Conservative system-level sketch linking a Resolvase_KAP_NTPase locus to prokaryotic Schlafen nuclease antiviral activity and the phage-defense parent.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures the DefenseFinder Resolvase_KAP_NTPase article namespace at system level and deliberately leaves the exact locus architecture, the KAP NTPase-associated domain boundary, accession-level protein examples, native host exemplars, phage trigger breadth, and DefenseFinder HMM/rules profiles unresolved.",
        "nodes": [
          {
            "node_id": "resolvase_kap_ntpase_locus",
            "label": "Resolvase KAP NTPase locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A locus encoding a prokaryotic Schlafen nuclease in a Resolvase_KAP_NTPase anti-phage system."
          },
          {
            "node_id": "schlafen_antiviral_activity",
            "label": "Schlafen antiviral activity",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Anti-phage activity mediated by a prokaryotic Schlafen nuclease."
          },
          {
            "node_id": "resolvase_kap_ntpase_system_trait",
            "label": "Resolvase KAP NTPase system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000532",
            "description": "Possession of a genome-encoded resolvase- and KAP NTPase-associated prokaryotic Schlafen phage-defense system."
          },
          {
            "node_id": "phage_defense_system_trait",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "resolvase_kap_ntpase_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "schlafen_antiviral_activity",
            "description": "Resolvase_KAP_NTPase loci are part of the bacterial prokaryotic Schlafen nuclease phage-defense family.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-026-02277-8",
                "snippet": "prokaryotic Schlafen nucleases are widespread antiviral effectors that protect bacteria from bacteriophages and are fused to a diverse array of phage-sensing domains.",
                "notes": "Perez Taboada et al. support bacterial prokaryotic Schlafen nucleases as antiviral effectors fused to phage-sensing domains."
              }
            ]
          },
          {
            "subject": "schlafen_antiviral_activity",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "resolvase_kap_ntpase_system_trait",
            "description": "Prokaryotic Schlafen antiviral effector activity realizes the organism-level Resolvase KAP NTPase system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-026-02277-8",
                "snippet": "prokaryotic Schlafen nucleases are widespread antiviral effectors that protect bacteria from bacteriophages and are fused to a diverse array of phage-sensing domains.",
                "notes": "Perez Taboada et al. support bacterial prokaryotic Schlafen nucleases as antiviral effectors fused to phage-sensing domains."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| Resolvase_KAP_NTPase | 10\\.1038/s41564-026-02277-8 | Bacterial Schlafen proteins mediate phage defence | ",
                "notes": "The pinned DefenseFinder article registry maps the Resolvase_KAP_NTPase source key to the Perez Taboada et al. Schlafen phage-defense paper."
              }
            ]
          },
          {
            "subject": "resolvase_kap_ntpase_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system_trait",
            "description": "Resolvase KAP NTPase system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-026-02277-8",
                "snippet": "We expressed seven Enterobacterales Schlafen systems in Escherichia coli, identifying two that confer defence against coliphages.",
                "notes": "Perez Taboada et al. cloned candidate Enterobacterales Schlafen systems into E. coli and observed coliphage defense for two of them."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| Resolvase_KAP_NTPase | 10\\.1038/s41564-026-02277-8 | Bacterial Schlafen proteins mediate phage defence | ",
                "notes": "The pinned DefenseFinder article registry maps the Resolvase_KAP_NTPase source key to the Perez Taboada et al. Schlafen phage-defense paper."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "resolvase-kap-ntpase-defensefinder-profile-gap",
        "prompt": "Resolve exact Resolvase_KAP_NTPase locus architecture, KAP NTPase-associated domain boundaries, natural host exemplars, phage trigger breadth, and DefenseFinder HMM/rules coverage before minting narrower Resolvase KAP NTPase mechanism or component traits.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Perez Taboada et al. support prokaryotic Schlafen nucleases as widespread antiviral effectors fused to phage-sensing domains, and the pinned DefenseFinder article registry maps the Resolvase_KAP_NTPase key to the same article. The pinned HMM inventory and rules table have no exact Resolvase_KAP_NTPase or KAP_NTPase rows for this source key. This first-pass record therefore does not resolve whether the exact Resolvase_KAP_NTPase architecture is a single-protein fusion or multi-gene locus, its exact KAP NTPase-associated domain boundaries, natural host exemplars, accession-level Schlafen proteins, full phage trigger breadth, or a reusable DefenseFinder profile model.",
        "evidence": [
          {
            "reference": "DOI:10.1038/s41564-026-02277-8",
            "snippet": "prokaryotic Schlafen nucleases are widespread antiviral effectors that protect bacteria from bacteriophages and are fused to a diverse array of phage-sensing domains.",
            "notes": "Perez Taboada et al. support bacterial prokaryotic Schlafen nucleases as antiviral effectors fused to phage-sensing domains."
          },
          {
            "reference": "DOI:10.1038/s41564-026-02277-8",
            "snippet": "We expressed seven Enterobacterales Schlafen systems in Escherichia coli, identifying two that confer defence against coliphages.",
            "notes": "Perez Taboada et al. cloned candidate Enterobacterales Schlafen systems into E. coli and observed coliphage defense for two of them."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
            "snippet": "| Resolvase_KAP_NTPase | 10\\.1038/s41564-026-02277-8 | Bacterial Schlafen proteins mediate phage defence | ",
            "notes": "The pinned DefenseFinder article registry maps the Resolvase_KAP_NTPase source key to the Perez Taboada et al. Schlafen phage-defense paper."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "notes": "A structured first-pass search of the pinned DefenseFinder HMM inventory found no exact Resolvase_KAP_NTPase, Schlafen, or KAP_NTPase row for this system."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "A structured first-pass search of the pinned DefenseFinder rules table found no exact Resolvase_KAP_NTPase, Schlafen, or KAP_NTPase system row for this system."
          }
        ],
        "attaches_to": [
          "causal_graphs#resolvase_kap_ntpase_phage_defense"
        ],
        "posed_by": "codex",
        "posed_date": "2026-10-02"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-02T02:32:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Resolvase KAP NTPase system as a DOI- and DefenseFinder-backed GENOMICS TraitRecord under the phage defense system parent after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v409.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-02T02:32:01Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed Resolvase KAP NTPase system during initial curation and left canonical_examples empty because Perez Taboada et al. and the pinned DefenseFinder article registry support the Resolvase_KAP_NTPase system namespace, but not an accession-backed native microbial taxon exemplar for the exact Resolvase_KAP_NTPase source key. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000529",
    "label": "Resolvase Schlafen system",
    "definition": "A phage defense system in which an organism possesses a genome-encoded, resolvase-associated prokaryotic Schlafen nuclease locus.",
    "definition_source": "DOI:10.1038/s41564-026-02277-8",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "Resolvase_Schlafen",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/s41564-026-02277-8",
        "snippet": "prokaryotic Schlafen nucleases are widespread antiviral effectors that protect bacteria from bacteriophages and are fused to a diverse array of phage-sensing domains.",
        "notes": "Perez Taboada et al. support bacterial prokaryotic Schlafen nucleases as antiviral effectors fused to phage-sensing domains."
      },
      {
        "reference": "DOI:10.1038/s41564-026-02277-8",
        "snippet": "We expressed seven Enterobacterales Schlafen systems in Escherichia coli, identifying two that confer defence against coliphages.",
        "notes": "Perez Taboada et al. cloned candidate Enterobacterales Schlafen systems into E. coli and observed coliphage defense for two of them."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| Resolvase_Schlafen | 10\\.1038/s41564-026-02277-8 | Bacterial Schlafen proteins mediate phage defence | ",
        "notes": "The pinned DefenseFinder article registry maps the Resolvase_Schlafen source key to the Perez Taboada et al. Schlafen phage-defense paper."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "resolvase_schlafen_phage_defense",
        "title": "Resolvase Schlafen loci support Schlafen phage defense",
        "description": "Conservative system-level sketch linking a Resolvase_Schlafen locus to prokaryotic Schlafen nuclease antiviral activity and the phage-defense parent.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures the DefenseFinder Resolvase_Schlafen article namespace at system level and deliberately leaves the exact locus architecture, the resolvase-associated domain boundary, accession-level protein examples, native host exemplars, phage trigger breadth, and DefenseFinder HMM/rules profiles unresolved.",
        "nodes": [
          {
            "node_id": "resolvase_schlafen_locus",
            "label": "Resolvase Schlafen locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A locus encoding a prokaryotic Schlafen nuclease in a resolvase-associated anti-phage system."
          },
          {
            "node_id": "schlafen_antiviral_activity",
            "label": "Schlafen antiviral activity",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Anti-phage activity mediated by a prokaryotic Schlafen nuclease."
          },
          {
            "node_id": "resolvase_schlafen_system_trait",
            "label": "Resolvase Schlafen system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000529",
            "description": "Possession of a genome-encoded resolvase-associated prokaryotic Schlafen phage-defense system."
          },
          {
            "node_id": "phage_defense_system_trait",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "resolvase_schlafen_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "schlafen_antiviral_activity",
            "description": "Resolvase_Schlafen loci are part of the bacterial prokaryotic Schlafen nuclease phage-defense family.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-026-02277-8",
                "snippet": "prokaryotic Schlafen nucleases are widespread antiviral effectors that protect bacteria from bacteriophages and are fused to a diverse array of phage-sensing domains.",
                "notes": "Perez Taboada et al. support bacterial prokaryotic Schlafen nucleases as antiviral effectors fused to phage-sensing domains."
              }
            ]
          },
          {
            "subject": "schlafen_antiviral_activity",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "resolvase_schlafen_system_trait",
            "description": "Prokaryotic Schlafen antiviral effector activity realizes the organism-level Resolvase Schlafen system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-026-02277-8",
                "snippet": "prokaryotic Schlafen nucleases are widespread antiviral effectors that protect bacteria from bacteriophages and are fused to a diverse array of phage-sensing domains.",
                "notes": "Perez Taboada et al. support bacterial prokaryotic Schlafen nucleases as antiviral effectors fused to phage-sensing domains."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| Resolvase_Schlafen | 10\\.1038/s41564-026-02277-8 | Bacterial Schlafen proteins mediate phage defence | ",
                "notes": "The pinned DefenseFinder article registry maps the Resolvase_Schlafen source key to the Perez Taboada et al. Schlafen phage-defense paper."
              }
            ]
          },
          {
            "subject": "resolvase_schlafen_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system_trait",
            "description": "Resolvase Schlafen system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-026-02277-8",
                "snippet": "We expressed seven Enterobacterales Schlafen systems in Escherichia coli, identifying two that confer defence against coliphages.",
                "notes": "Perez Taboada et al. cloned candidate Enterobacterales Schlafen systems into E. coli and observed coliphage defense for two of them."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| Resolvase_Schlafen | 10\\.1038/s41564-026-02277-8 | Bacterial Schlafen proteins mediate phage defence | ",
                "notes": "The pinned DefenseFinder article registry maps the Resolvase_Schlafen source key to the Perez Taboada et al. Schlafen phage-defense paper."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "resolvase-schlafen-defensefinder-profile-gap",
        "prompt": "Resolve exact Resolvase_Schlafen locus architecture, resolvase-associated domain boundaries, natural host exemplars, phage trigger breadth, and DefenseFinder HMM/rules coverage before minting narrower Resolvase Schlafen mechanism or component traits.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Perez Taboada et al. support prokaryotic Schlafen nucleases as widespread antiviral effectors fused to phage-sensing domains, and the pinned DefenseFinder article registry maps the Resolvase_Schlafen key to the same article. The pinned HMM inventory and rules table have no exact Schlafen rows. This first-pass record therefore does not resolve whether the exact Resolvase_Schlafen architecture is a single-protein fusion or multi-gene locus, its exact resolvase-associated domain boundaries, natural host exemplars, accession-level Schlafen proteins, full phage trigger breadth, or a reusable DefenseFinder profile model.",
        "evidence": [
          {
            "reference": "DOI:10.1038/s41564-026-02277-8",
            "snippet": "prokaryotic Schlafen nucleases are widespread antiviral effectors that protect bacteria from bacteriophages and are fused to a diverse array of phage-sensing domains.",
            "notes": "Perez Taboada et al. support bacterial prokaryotic Schlafen nucleases as antiviral effectors fused to phage-sensing domains."
          },
          {
            "reference": "DOI:10.1038/s41564-026-02277-8",
            "snippet": "We expressed seven Enterobacterales Schlafen systems in Escherichia coli, identifying two that confer defence against coliphages.",
            "notes": "Perez Taboada et al. cloned candidate Enterobacterales Schlafen systems into E. coli and observed coliphage defense for two of them."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
            "snippet": "| Resolvase_Schlafen | 10\\.1038/s41564-026-02277-8 | Bacterial Schlafen proteins mediate phage defence | ",
            "notes": "The pinned DefenseFinder article registry maps the Resolvase_Schlafen source key to the Perez Taboada et al. Schlafen phage-defense paper."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "notes": "A structured first-pass search of the pinned DefenseFinder HMM inventory found no exact Resolvase_Schlafen, Schlafen, or resolvase row for this system."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "A structured first-pass search of the pinned DefenseFinder rules table found no exact Resolvase_Schlafen, Schlafen, or resolvase system row for this system."
          }
        ],
        "attaches_to": [
          "causal_graphs#resolvase_schlafen_phage_defense"
        ],
        "posed_by": "codex",
        "posed_date": "2026-10-01"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-01T23:10:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Resolvase Schlafen system as a DOI- and DefenseFinder-backed GENOMICS TraitRecord under the phage defense system parent after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v406.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-01T23:10:01Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed Resolvase Schlafen system during initial curation and left canonical_examples empty because Perez Taboada et al. and the pinned DefenseFinder article registry support the Resolvase_Schlafen system namespace, but not an accession-backed native microbial taxon exemplar for the exact Resolvase_Schlafen source key. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000095",
    "label": "restriction-modification system",
    "definition": "A genomics trait describing possession of a restriction-modification system that distinguishes self from non-self DNA through sequence-specific methylation and cleavage of unmethylated DNA by a restriction endonuclease.",
    "definition_source": "DOI:10.1128/MMBR.00044-12",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "R-M system",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1128/MMBR.00044-12"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1128/MMBR.00044-12",
        "notes": "Vasu & Nagaraja review restriction-modification systems and their defense and additional cellular functions."
      },
      {
        "reference": "DOI:10.3389/fmicb.2015.00528",
        "notes": "Review of restriction-modification systems as engines of genomic diversity."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:727",
        "taxon_label": "Haemophilus influenzae",
        "note": "Source of HindII, the first type II restriction endonuclease characterized; classic restriction-modification model.",
        "reference": "PMID:5312500"
      },
      {
        "taxon_id": "NCBITaxon:71421",
        "taxon_label": "Haemophilus influenzae Rd KW20",
        "note": "Genome-strain exemplar paired to reviewed HindII, the historically characterized type II restriction endonuclease.",
        "reference": "PMID:5312500"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "rm_self_nonself_defense",
        "title": "Restriction-modification distinguishes self from non-self DNA",
        "description": "Evidence-backed causal sketch linking R-M system possession to sequence-specific cleavage of unmethylated foreign DNA.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "The HindII accession anchors the type II restriction-endonuclease branch in H. influenzae Rd. It is not presented as an example of the cognate methyltransferase, type IV enzymes, or mobile-element counterdefense proteins.",
        "nodes": [
          {
            "node_id": "rm_trait",
            "label": "restriction-modification system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000095",
            "description": "Possession of a paired methyltransferase / restriction endonuclease defense system."
          },
          {
            "node_id": "dna_restriction_modification",
            "label": "DNA restriction-modification system",
            "node_type": "BIOLOGICAL_PROCESS",
            "grounding": "GO:0009307",
            "description": "Sequence-specific methylation marking self DNA and cleavage of unmethylated foreign DNA."
          },
          {
            "node_id": "foreign_dna",
            "label": "foreign DNA",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Invading phage or plasmid DNA challenging the cell."
          },
          {
            "node_id": "cognate_mtase",
            "label": "cognate DNA methyltransferase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Methyltransferase that methylates the host recognition sites of an R-M system.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "This generic node spans unrelated cognate methyltransferase families across restriction-modification system types."
          },
          {
            "node_id": "host_site_methylation",
            "label": "host recognition site methylation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Methylation marking self DNA at R-M recognition sites."
          },
          {
            "node_id": "restriction_endonuclease",
            "label": "restriction endonuclease",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Endonuclease that cleaves unmethylated double-stranded DNA at recognition sites.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "This generic node spans multiple structurally unrelated restriction endonuclease families; the attached HindII accession is one explicit example.",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:P44413",
                "protein_label": "Type II restriction enzyme HindII",
                "gene_symbol": "hindIIR",
                "taxon_id": "NCBITaxon:71421",
                "taxon_label": "Haemophilus influenzae Rd KW20",
                "entry_status": "REVIEWED",
                "retrieved_on": "2026-10-22",
                "entry_version": 125,
                "sequence_version": 2,
                "role": "HindII recognizes its target sequence and cleaves foreign double-stranded DNA as the restriction component of the HindII system.",
                "evidence": [
                  {
                    "reference": "PMID:5312500",
                    "snippet": "restriction enzyme from Hemophilus influenzae",
                    "notes": "The original H. influenzae work characterized the sequence-specific restriction activity; UniProt verifies the reviewed Rd HindII protein."
                  }
                ]
              }
            ]
          },
          {
            "node_id": "endonuclease_cleavage",
            "label": "restriction endonuclease cleavage",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "Sequence-specific cleavage activity of the restriction endonuclease."
          },
          {
            "node_id": "plasmid_methylase",
            "label": "plasmid-encoded methylase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Methyltransferase encoded by a mobile element that pre-methylates its DNA to evade host restriction.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "This functional label spans unrelated plasmid-encoded methyltransferase families."
          },
          {
            "node_id": "phage_mtase",
            "label": "phage-encoded DNA methyltransferase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Phage methyltransferase that methylates the phage genome to counter host restriction.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "This functional label spans unrelated phage DNA-methyltransferase families."
          }
        ],
        "edges": [
          {
            "subject": "rm_trait",
            "predicate": "enables",
            "object": "dna_restriction_modification",
            "description": "R-M systems realize self-vs-non-self discrimination by paired methylation and restriction.",
            "evidence": [
              {
                "reference": "DOI:10.1128/MMBR.00044-12",
                "notes": "Vasu & Nagaraja review R-M systems and their defense functions."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "dna_restriction_modification",
            "predicate": "mitigates",
            "object": "foreign_dna",
            "description": "Restriction endonuclease cleavage destroys unmethylated foreign DNA before it can establish.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2015.00528",
                "notes": "R-M systems as engines of genomic diversity through differential cleavage of foreign DNA."
              }
            ],
            "predicate_id": "METPO:2007407"
          },
          {
            "subject": "cognate_mtase",
            "predicate": "methylates",
            "object": "host_site_methylation",
            "description": "The cognate methyltransferase methylates host recognition sites, marking self DNA.",
            "evidence": [
              {
                "reference": "DOI:10.1093/nar/gkad452",
                "notes": "A methyltransferase methylates those sites to protect host DNA (shaw2023)."
              }
            ]
          },
          {
            "subject": "host_site_methylation",
            "predicate": "protects against",
            "object": "endonuclease_cleavage",
            "description": "Methylation of host recognition sites protects self DNA from cognate restriction endonuclease cleavage.",
            "evidence": [
              {
                "reference": "DOI:10.1093/nar/gkad452",
                "notes": "Host DNA is protected while incoming foreign DNA lacking the same methylation is cleaved (shaw2023)."
              }
            ]
          },
          {
            "subject": "restriction_endonuclease",
            "predicate": "has function",
            "object": "endonuclease_cleavage",
            "description": "The restriction endonuclease cleaves unmethylated foreign double-stranded DNA.",
            "evidence": [
              {
                "reference": "DOI:10.1093/nar/gkad452",
                "notes": "A restriction endonuclease cuts double-stranded DNA; unmethylated foreign DNA is cleaved (shaw2023)."
              }
            ],
            "predicate_id": "RO:0000085"
          },
          {
            "subject": "endonuclease_cleavage",
            "predicate": "mitigates",
            "object": "foreign_dna",
            "description": "Restriction endonuclease cleavage destroys unmethylated foreign DNA.",
            "evidence": [
              {
                "reference": "DOI:10.1093/nar/gkad452",
                "notes": "Incoming foreign DNA lacking host methylation is cleaved (shaw2023)."
              }
            ],
            "predicate_id": "METPO:2007407"
          },
          {
            "subject": "plasmid_methylase",
            "predicate": "protects against",
            "object": "endonuclease_cleavage",
            "description": "Plasmid-encoded methylases pre-methylate plasmid DNA, protecting it from host restriction activity.",
            "evidence": [
              {
                "reference": "DOI:10.1093/nar/gkae896",
                "notes": "Some plasmids encode methylases that protect against restriction activity (dimitriu2024)."
              }
            ]
          },
          {
            "subject": "phage_mtase",
            "predicate": "protects against",
            "object": "endonuclease_cleavage",
            "description": "Phage-encoded DNA methyltransferases methylate the phage genome to reduce host RM restriction.",
            "evidence": [
              {
                "reference": "DOI:10.1128/MMBR.00044-12",
                "notes": "Phages encode DNA methyltransferases to protect their genomes from restriction (vasu2013)."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-06-05T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate GENOMICS trait (restriction-modification system) from literature research to fill the genome-defense-system gap.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-08T14:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (R-M self / non-self defense) with GO node grounding and RO/METPO predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 7 evidence-backed generic edges (8 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:11Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0000085\u00d71, METPO:2007407\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-26T07:15:18Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A015ZKG4\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:21:11Z",
        "curator": "claude",
        "action": "RETRACT_DEAD_UNIPROT_GROUNDINGS",
        "changes": "Retracted 1 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "CURATE_PROTEIN_TAXON_EXAMPLE",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope rm_self_nonself_defense=MECHANISTIC with scope_notes; marked 5 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (cognate_mtase, restriction_endonuclease, type_iv_restriction_enzyme, plasmid_methylase, phage_mtase); added taxon-paired protein example(s) UniProtKB:P44413 on restriction_endonuclease (NCBITaxon:71421); added canonical example(s) NCBITaxon:71421.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T05:40:00Z",
        "curator": "codex",
        "action": "CONNECT_CAUSAL_GRAPH_COMPONENTS",
        "changes": "Resolved issue #183 graph fragmentation (2 components to 1) using 0 snippet-backed connector(s) supported by source passages. Removed the explicitly out-of-scope Type IV subtype island; the tracked report identifies modification-dependent restriction as distinct from the canonical Types I-III self/non-self mechanism. No research service was called.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-15T07:55:00Z",
        "curator": "codex",
        "action": "REFINED_PARENT_TRAITS",
        "changes": "Reparented restriction-modification system from the broad genomics parent to the newly minted phage defense system parent.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-22T01:35:00Z",
        "curator": "claude",
        "action": "REFRESH_UNIPROT_ENTRY_VERSION",
        "changes": "Refreshed UniProtKB entry_version against live UniProt REST on 2026-10-22: UniProtKB:P44413 (124 -> 125 on restriction_endonuclease).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000235",
    "label": "Retron system",
    "definition": "A phage defense system in which an organism possesses a retron locus encoding a reverse transcriptase, an msr/msd non-coding RNA that yields multicopy single-stranded DNA, and an associated effector whose activation can inhibit bacteriophage propagation through abortive infection.",
    "definition_source": "DOI:10.1016/j.cell.2020.09.065",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1016/j.cell.2020.09.065",
        "snippet": "We report that retrons function as anti-phage defense systems",
        "notes": "Millman et al. support retrons as experimentally observed antiphage defense systems rather than only retroelement sequence features."
      },
      {
        "reference": "DOI:10.1016/j.cell.2020.09.065",
        "snippet": "The defensive unit is composed of three components: the RT, the ncRNA, and an effector protein",
        "notes": "Millman et al. support defining the broad record around a reverse transcriptase, non-coding RNA, and associated effector rather than a bare reverse-transcriptase gene."
      },
      {
        "reference": "DOI:10.1016/j.cell.2020.09.065",
        "snippet": "We examined multiple retron systems and show that they confer defense against a broad range of phages via abortive infection",
        "notes": "Millman et al. support treating Retron system as a family of organism-level antiphage traits, with abortive infection as a shared defense output."
      },
      {
        "reference": "DOI:10.1016/j.cell.2020.09.065",
        "snippet": "retrons, functioning together with their associated effector genes, form anti-phage defense systems",
        "notes": "Millman et al. connect associated effector genes to Retron antiphage function."
      },
      {
        "reference": "DOI:10.1038/s41586-022-05091-4",
        "snippet": "RcaT is neutralized by the reverse transcriptase\u2013msDNA antitoxin complex, and becomes active upon perturbation of msDNA biosynthesis",
        "notes": "Bobonis et al. support an RcaT-containing Retron-Sen2 example in which the reverse-transcriptase-msDNA complex controls effector activity."
      },
      {
        "reference": "DOI:10.1038/s41586-022-05091-4",
        "snippet": "we identified multiple trigger and blocker proteins of phage origin",
        "notes": "Bobonis et al. support phage-encoded trigger and blocker logic for the characterized Retron-Sen2 RcaT system."
      },
      {
        "reference": "DOI:10.1038/s41586-022-05091-4",
        "snippet": "phage-related triggers directly modify the msDNA, thereby activating RcaT and inhibiting bacterial growth",
        "notes": "Bobonis et al. connect phage-triggered msDNA modification to RcaT activation in Retron-Sen2 without making that trigger universal across all retrons."
      },
      {
        "reference": "DOI:10.1038/s41586-022-05091-4",
        "snippet": "retron toxin\u2013antitoxin systems act as abortive infection anti-phage defence systems",
        "notes": "Bobonis et al. support retron toxin-antitoxin systems as abortive-infection antiphage systems."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:562",
        "taxon_label": "Escherichia coli",
        "note": "Millman et al. cloned E. coli Ec48 and Ec73 retrons with their predicted effector genes into E. coli MG1655 and showed that both engineered E. coli systems had broad antiphage activity that depended on reverse-transcriptase catalytic-site residues.",
        "reference": "DOI:10.1016/j.cell.2020.09.065"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "retron_msdna_effector_abortive_defense",
        "title": "Retrons couple msDNA complexes to effector activation",
        "description": "Evidence-backed process sketch linking a complete retron locus to RT/ncRNA-dependent msDNA biosynthesis, control of associated effectors, abortive-infection outputs, and inhibition of phage growth.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph stays at the retron family level and uses the Ec48 RecBCD-guarding and Retron-Sen2 RcaT mechanisms as characterized examples without asserting one universal effector fold, phage trigger, direct msDNA-modification event, guarded host target, or Retron-Septu release architecture across all retron antiphage loci.",
        "nodes": [
          {
            "node_id": "retron_locus",
            "label": "retron locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A complete retron antiphage locus encoding a reverse transcriptase, msr/msd non-coding RNA, and an associated effector."
          },
          {
            "node_id": "retron_msdna_biosynthesis",
            "label": "retron msDNA biosynthesis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reverse-transcriptase-dependent production of multicopy single-stranded DNA from a retron non-coding RNA template."
          },
          {
            "node_id": "rt_msdna_effector_control",
            "label": "RT-msDNA effector control",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Regulation of retron effector activity by reverse-transcriptase-msDNA complexes."
          },
          {
            "node_id": "effector_dependent_abortive_infection",
            "label": "effector-dependent abortive infection",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Activation of a retron-associated effector output that arrests or kills infected host cells and limits phage amplification."
          },
          {
            "node_id": "phage_growth",
            "label": "phage growth",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Bacteriophage growth and amplification inside a bacterial host population."
          },
          {
            "node_id": "retron_system_trait",
            "label": "Retron system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000235",
            "description": "Possession of a genome-encoded Retron phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "retron_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "retron_msdna_biosynthesis",
            "description": "Retron loci encode the reverse transcriptase and non-coding RNA components that biosynthesize msDNA.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.cell.2020.09.065",
                "snippet": "Retrons encode a non-coding RNA (ncRNA) and a reverse transcriptase (RT)",
                "notes": "Millman et al. describe the RT and ncRNA parts of the retron msDNA-biosynthesis module."
              }
            ]
          },
          {
            "subject": "retron_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "rt_msdna_effector_control",
            "description": "Complete retron defensive units include an associated effector coupled to the RT/ncRNA core.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.cell.2020.09.065",
                "snippet": "The defensive unit is composed of three components: the RT, the ncRNA, and an effector protein",
                "notes": "Millman et al. support the effector as a required part of a complete retron defensive unit."
              }
            ]
          },
          {
            "subject": "retron_msdna_biosynthesis",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "rt_msdna_effector_control",
            "description": "The reverse-transcriptase-msDNA complex can control associated retron effector activity.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41586-022-05091-4",
                "snippet": "RcaT is neutralized by the reverse transcriptase\u2013msDNA antitoxin complex, and becomes active upon perturbation of msDNA biosynthesis",
                "notes": "Bobonis et al. connect msDNA biosynthesis and the RT-msDNA complex to RcaT toxin control in Retron-Sen2."
              }
            ]
          },
          {
            "subject": "rt_msdna_effector_control",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "effector_dependent_abortive_infection",
            "description": "Phage-triggered perturbation of retron effector control can activate an associated effector.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41586-022-05091-4",
                "snippet": "phage-related triggers directly modify the msDNA, thereby activating RcaT and inhibiting bacterial growth",
                "notes": "Bobonis et al. support phage-triggered activation of the RcaT effector in Retron-Sen2."
              }
            ]
          },
          {
            "subject": "effector_dependent_abortive_infection",
            "predicate": "mitigates",
            "predicate_id": "METPO:2007407",
            "object": "phage_growth",
            "description": "Retron effector activation can block phage amplification through abortive infection.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.cell.2020.09.065",
                "snippet": "We examined multiple retron systems and show that they confer defense against a broad range of phages via abortive infection",
                "notes": "Millman et al. link multiple retron systems to broad antiphage defense by abortive infection."
              }
            ]
          },
          {
            "subject": "effector_dependent_abortive_infection",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "retron_system_trait",
            "description": "Associated effector activity realizes the Retron system defense phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.cell.2020.09.065",
                "snippet": "retrons, functioning together with their associated effector genes, form anti-phage defense systems",
                "notes": "Millman et al. support complete retron systems in which the retron and associated effector genes together confer defense."
              }
            ]
          },
          {
            "subject": "retron_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Retron system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.cell.2020.09.065",
                "snippet": "We report that retrons function as anti-phage defense systems",
                "notes": "Millman et al. support Retron system as a child of phage defense system."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "retron-effector-trigger-gap",
        "prompt": "Resolve retron effector, phage-trigger, and hybrid-system diversity before minting narrower Retron-Sen2, Ec48, or Retron-Septu mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Millman et al. support multiple RT/ncRNA/effector retron systems as abortive-infection antiphage systems, and Bobonis et al. resolve the Retron-Sen2 RcaT example in which a reverse-transcriptase-msDNA antitoxin complex responds to phage-triggered msDNA modification. The first TraitRecord therefore stays at the broad retron-system level until separate subtype review resolves which effectors, guarded host targets, phage triggers, direct-msDNA modification steps, and Septu-coupled architectures apply across each retron family.",
        "posed_by": "codex",
        "posed_date": "2026-09-15"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-16T01:28:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Retron system as a DOI-backed GENOMICS TraitRecord under the phage defense system parent after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v112.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000499",
    "label": "Reve system",
    "definition": "A phage defense system in which an organism possesses a single-gene Reve antiviral locus that is encoded by P4-like phage satellites and can protect bacteria from bacteriophage infection.",
    "definition_source": "DOI:10.1093/nar/gkag898",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "Reve",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1093/nar/gkag898"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1093/nar/gkag898",
        "snippet": "The Reve system is another single-gene system, with ATPase and KAP family P-loop domains",
        "notes": "de Sousa et al. identify Reve as a single-gene P4 defense system with ATPase and KAP-family P-loop domain annotations."
      },
      {
        "reference": "DOI:10.1093/nar/gkag898",
        "snippet": "with most (e.g. Bandua, Aernus, Toga, and Reve) providing strong protection against phages of different families",
        "notes": "de Sousa et al. identify Reve among the novel P4-associated systems that provided strong protection against phage challenge."
      },
      {
        "reference": "DOI:10.1093/nar/gkag898",
        "snippet": "Our experimental validation of anti-phage activity for 13 novel systems encoded by P4 confirms",
        "notes": "de Sousa et al. summarize the validated P4-encoded novel-system cohort in their discussion."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| Reve | 10\\.64898/2026\\.02\\.27\\.708500 | Shuttling, swapping and mixing: the rapid modular evolution of antiviral repertoires in temperate phages and their satellites | ",
        "notes": "The pinned DefenseFinder article registry maps the Reve source key to the de Sousa et al. P4/P2 antiviral-repertoire paper preprint."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "reve_locus_restricts_phage",
        "title": "Reve loci confer bacterial phage defense",
        "description": "Conservative system-level sketch linking possession of a Reve locus to restricted bacteriophage propagation without asserting the unresolved trigger or molecular output.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Reve as a named single-gene P4 anti-phage system while leaving its phage trigger, molecular substrate, ATPase/P-loop role, antiviral effector output, source-locus breadth, and DefenseFinder HMM/rule model coverage unresolved.",
        "nodes": [
          {
            "node_id": "reve_locus",
            "label": "Reve locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A P4-associated Reve anti-phage defense locus."
          },
          {
            "node_id": "restricted_phage_propagation",
            "label": "restricted phage propagation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced propagation of bacteriophage in cells carrying the Reve system."
          },
          {
            "node_id": "reve_system_trait",
            "label": "Reve system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000499",
            "description": "Possession of a genome-encoded Reve phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "reve_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "restricted_phage_propagation",
            "description": "Reve loci are among the novel P4-encoded systems that reduced bacteriophage infection.",
            "evidence": [
              {
                "reference": "DOI:10.1093/nar/gkag898",
                "snippet": "with most (e.g. Bandua, Aernus, Toga, and Reve) providing strong protection against phages of different families",
                "notes": "de Sousa et al. name Reve among the novel P4 systems with antiviral phenotypes."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| Reve | 10\\.64898/2026\\.02\\.27\\.708500 | Shuttling, swapping and mixing: the rapid modular evolution of antiviral repertoires in temperate phages and their satellites | ",
                "notes": "The pinned DefenseFinder article registry maps the Reve source key to the de Sousa et al. P4/P2 antiviral-repertoire paper preprint."
              }
            ]
          },
          {
            "subject": "restricted_phage_propagation",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "reve_system_trait",
            "description": "Reve-mediated phage protection realizes the Reve system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1093/nar/gkag898",
                "snippet": "with most (e.g. Bandua, Aernus, Toga, and Reve) providing strong protection against phages of different families",
                "notes": "de Sousa et al. connect Reve to strong protection in the novel-system validation cohort."
              }
            ]
          },
          {
            "subject": "reve_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Reve system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1093/nar/gkag898",
                "snippet": "13 novel systems encoded by P4 confirms that the contribution of defence functions to the pangenomes of P4 and P2",
                "notes": "de Sousa et al. frame Reve and its cohort as newly validated P4-encoded anti-phage defense functions."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "reve-mechanism-and-modelling-gap",
        "prompt": "Resolve Reve locus breadth, exact phage triggers, ATPase/P-loop molecular roles, direct antiviral output, source-system table rows, and DefenseFinder HMM/rule coverage before minting narrower Reve mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "de Sousa et al. support Reve as one of the novel single-gene P4-encoded systems with experimental phage-protection activity, and the pinned DefenseFinder article registry maps the Reve source key to the corresponding preprint. The pinned HMM inventory and rules table have no exact Reve rows, and this first-pass record does not resolve the tested source locus, complete phage breadth, exact trigger, molecular output, or detection rule.",
        "evidence": [
          {
            "reference": "DOI:10.1093/nar/gkag898",
            "snippet": "The Reve system is another single-gene system, with ATPase and KAP family P-loop domains",
            "notes": "de Sousa et al. support Reve as a named single-gene defense system while leaving exact mechanism for separate review."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
            "snippet": "| Reve | 10\\.64898/2026\\.02\\.27\\.708500 | Shuttling, swapping and mixing: the rapid modular evolution of antiviral repertoires in temperate phages and their satellites | ",
            "notes": "The pinned DefenseFinder article registry maps the Reve source key to the de Sousa et al. P4/P2 antiviral-repertoire paper preprint."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "notes": "A structured first-pass search of the pinned DefenseFinder HMM inventory found no exact Reve row."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "A structured first-pass search of the pinned DefenseFinder rules table found no exact Reve system row."
          }
        ],
        "attaches_to": [
          "causal_graphs#reve_locus_restricts_phage"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-30"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-30T19:41:32Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Reve system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v376.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-30T19:41:33Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed Reve system canonical_examples and left them empty because de Sousa et al. support P4-encoded Reve phage protection and a DefenseFinder article-registry row, but not a direct named native microbial isolate exemplar with experimentally verified endogenous Reve activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000324",
    "label": "RexAB system",
    "definition": "An abortive infection system in which an organism possesses a bacteriophage-lambda Rex-family locus represented by the DefenseFinder RexAB__RexA and RexAB__RexB profiles and exemplified by the rexA and rexB two-component system that aborts lytic growth of bacterial viruses.",
    "definition_source": "DOI:10.1101/gad.6.3.497",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000214"
    ],
    "synonyms": [
      {
        "synonym_text": "RexAB",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1101/gad.6.3.497",
        "snippet": "The rexA and rexB genes of bacteriophage lambda encode a two-component system that aborts lytic growth of bacterial viruses.",
        "notes": "Parma et al. support RexA and RexB as a two-component Rex exclusion system."
      },
      {
        "reference": "DOI:10.1101/gad.6.3.497",
        "snippet": "Rex exclusion is characterized by termination of macromolecular synthesis, loss of active transport, the hydrolysis of ATP, and cell death.",
        "notes": "Parma et al. support Rex exclusion as an abortive-infection-like output with host-cell death."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "RexAB | 10\\.1101/gad\\.6\\.3\\.497 | The Rex system of bacteriophage lambda: tolerance and altruistic cell death",
        "notes": "The DefenseFinder article registry maps the named RexAB model namespace to the bacteriophage-lambda Rex system paper."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "RexAB\tRexAB\t2\t2\tRexAB__RexA, RexAB__RexB",
        "notes": "The DefenseFinder rules table models RexAB as a two-component system requiring the RexA and RexB profiles."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| RexAB__RexA                                      | RexAB__RexA                                      | RexAB                  | PF15969.7               | 25     |",
        "notes": "The DefenseFinder HMM inventory records RexAB__RexA under RexAB."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| RexAB__RexB                                      | RexAB__RexB                                      | RexAB                  | PF15968.7               | 27     |",
        "notes": "The DefenseFinder HMM inventory records RexAB__RexB under RexAB."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "rexab_locus_mediates_rex_exclusion",
        "title": "RexAB loci mediate abortive Rex exclusion",
        "description": "Conservative system-level sketch linking RexA/RexB locus possession to Rex exclusion and RexAB-system possession without asserting the direct phage trigger, RexA/RexB stoichiometry, membrane target, or bacteriophage-lambda self-protection route.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures RexAB as a named DefenseFinder two-profile abortive-infection system whose lambda prototype aborts lytic growth. It leaves the direct phage trigger, RexA/RexB molecular coupling, ion-channel activity, self-exclusion control, and phage escape routes unresolved.",
        "nodes": [
          {
            "node_id": "rexab_locus",
            "label": "RexAB locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A bacteriophage-lambda Rex-family abortive exclusion locus represented by the DefenseFinder RexAB__RexA and RexAB__RexB profiles."
          },
          {
            "node_id": "rex_exclusion",
            "label": "Rex exclusion",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Abortive exclusion of sensitive bacteriophages in cells carrying RexA and RexB."
          },
          {
            "node_id": "rexab_system_trait",
            "label": "RexAB system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000324",
            "description": "Possession of a genome-encoded RexAB abortive-infection phage-defense system."
          }
        ],
        "edges": [
          {
            "subject": "rexab_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "rex_exclusion",
            "description": "The bacteriophage-lambda RexA/RexB system aborts lytic growth of bacterial viruses, and DefenseFinder represents RexAB with required RexA and RexB profiles.",
            "evidence": [
              {
                "reference": "DOI:10.1101/gad.6.3.497",
                "snippet": "The rexA and rexB genes of bacteriophage lambda encode a two-component system that aborts lytic growth of bacterial viruses.",
                "notes": "Parma et al. support RexA and RexB as the core genetic components of Rex exclusion."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "RexAB\tRexAB\t2\t2\tRexAB__RexA, RexAB__RexB",
                "notes": "The DefenseFinder rules table models RexAB as a two-component system requiring the RexA and RexB profiles."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| RexAB__RexA                                      | RexAB__RexA                                      | RexAB                  | PF15969.7               | 25     |",
                "notes": "The DefenseFinder HMM inventory records RexAB__RexA under RexAB."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| RexAB__RexB                                      | RexAB__RexB                                      | RexAB                  | PF15968.7               | 27     |",
                "notes": "The DefenseFinder HMM inventory records RexAB__RexB under RexAB."
              }
            ]
          },
          {
            "subject": "rex_exclusion",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "rexab_system_trait",
            "description": "RexA/RexB-dependent abortive exclusion realizes the RexAB system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1101/gad.6.3.497",
                "snippet": "Rex exclusion is characterized by termination of macromolecular synthesis, loss of active transport, the hydrolysis of ATP, and cell death.",
                "notes": "Parma et al. connect Rex exclusion to host-cell shutdown and death."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "RexAB | 10\\.1101/gad\\.6\\.3\\.497 | The Rex system of bacteriophage lambda: tolerance and altruistic cell death",
                "notes": "The DefenseFinder article registry maps the named RexAB model namespace to the bacteriophage-lambda Rex system paper."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "rexab-mechanism-gap",
        "prompt": "Resolve the direct RexAB phage trigger, RexA and RexB molecular coupling, ion-channel activity, lambda self-exclusion control, and sensitive-phage escape routes before minting narrower RexAB mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Parma et al. support bacteriophage-lambda rexA and rexB as a two-component system that aborts lytic growth of bacterial viruses, and DefenseFinder maps RexAB to RexAB__RexA and RexAB__RexB profiles. The direct phage trigger, RexA/RexB molecular coupling, ion-channel output, lambda self-exclusion control, and sensitive-phage escape routes remain unresolved.",
        "attaches_to": [
          "causal_graphs#rexab_locus_mediates_rex_exclusion"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-21"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-21T02:17:07Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted RexAB system as a DOI-backed GENOMICS TraitRecord under the abortive infection system parent after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v201.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-21T02:17:08Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed canonical example evidence while minting RexAB system and left canonical_examples empty: the bacteriophage-lambda prototype supports a prophage-encoded rexA and rexB exclusion system and the pinned DefenseFinder registry maps a two-profile RexAB namespace, but the available curation sources do not identify a natural organism instance with a directly observed RexAB locus. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000311",
    "label": "Rhea system",
    "definition": "A phage defense system in which an organism possesses a Rhea locus that can restrict bacteriophage infection.",
    "definition_source": "DOI:10.1093/nar/gkae671",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "Rhea",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1093/nar/gkae671"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1093/nar/gkae671",
        "snippet": "These systems were named after cheese, cattle or fermentation related deities (Rhea, Aristaios, Kamadhenu, Fliodhais, Audmula, Rugutis and Hesat)",
        "notes": "Grafakou et al. named Rhea among seven not previously described lactococcal antiphage systems."
      },
      {
        "reference": "DOI:10.1073/pnas.2426508122",
        "snippet": "we isolated 66 phage escape mutants which had become insensitive to 13 distinct, plasmid-encoded lactococcal phage resistance systems (i.e. Rhea, Kamadhenu, Rugutis, Audmula, PARIS, type II CBASS, Septu, AbiA, AbiB, AbiD/F, AbiG, AbiJ, AbiP)",
        "notes": "Mosterd et al. later included Rhea among the distinct plasmid-encoded lactococcal phage-resistance systems investigated by phage escape-mutant isolation."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "Rhea | 10\\.1093/nar/gkae671 | Discovery of antiphage systems in the lactococcal plasmidome",
        "notes": "The DefenseFinder article registry maps the named Rhea system to the Grafakou et al. lactococcal antiphage-system discovery paper."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "rhea_locus_restricts_phage",
        "title": "Rhea loci confer bacterial phage defense",
        "description": "Conservative system-level sketch linking possession of a Rhea locus to restricted bacteriophage propagation without asserting the unresolved phage trigger or molecular output.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Rhea as a named lactococcal anti-phage system while leaving its direct phage trigger, molecular substrate, antiviral effector output, natural locus breadth, and the absence of pinned DefenseFinder HMM or rule rows unresolved.",
        "nodes": [
          {
            "node_id": "rhea_locus",
            "label": "Rhea locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A Rhea anti-phage defense locus described among lactococcal plasmid-encoded phage-resistance systems."
          },
          {
            "node_id": "restricted_phage_propagation",
            "label": "restricted phage propagation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced propagation of bacteriophage in cells carrying the Rhea system."
          },
          {
            "node_id": "rhea_system_trait",
            "label": "Rhea system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000311",
            "description": "Possession of a genome-encoded Rhea phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "rhea_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "restricted_phage_propagation",
            "description": "The lactococcal plasmidome screen discovered Rhea as a named antiphage system, and the DefenseFinder article registry maps the Rhea system to that discovery paper.",
            "evidence": [
              {
                "reference": "DOI:10.1093/nar/gkae671",
                "snippet": "These systems were named after cheese, cattle or fermentation related deities (Rhea, Aristaios, Kamadhenu, Fliodhais, Audmula, Rugutis and Hesat)",
                "notes": "Grafakou et al. named Rhea as one of the novel lactococcal antiphage systems."
              },
              {
                "reference": "DOI:10.1073/pnas.2426508122",
                "snippet": "we isolated 66 phage escape mutants which had become insensitive to 13 distinct, plasmid-encoded lactococcal phage resistance systems (i.e. Rhea, Kamadhenu, Rugutis, Audmula, PARIS, type II CBASS, Septu, AbiA, AbiB, AbiD/F, AbiG, AbiJ, AbiP)",
                "notes": "Mosterd et al. treat Rhea as a plasmid-encoded lactococcal phage-resistance system in their escape-mutant screen."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Rhea | 10\\.1093/nar/gkae671 | Discovery of antiphage systems in the lactococcal plasmidome",
                "notes": "The DefenseFinder article registry maps the named Rhea system to the Grafakou et al. lactococcal antiphage-system discovery paper."
              }
            ]
          },
          {
            "subject": "restricted_phage_propagation",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "rhea_system_trait",
            "description": "Rhea-mediated phage restriction realizes the Rhea system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1073/pnas.2426508122",
                "snippet": "we isolated 66 phage escape mutants which had become insensitive to 13 distinct, plasmid-encoded lactococcal phage resistance systems (i.e. Rhea, Kamadhenu, Rugutis, Audmula, PARIS, type II CBASS, Septu, AbiA, AbiB, AbiD/F, AbiG, AbiJ, AbiP)",
                "notes": "Mosterd et al. treat Rhea as a plasmid-encoded lactococcal phage-resistance system in their escape-mutant screen."
              }
            ]
          },
          {
            "subject": "rhea_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Rhea system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Rhea | 10\\.1093/nar/gkae671 | Discovery of antiphage systems in the lactococcal plasmidome",
                "notes": "The DefenseFinder article registry maps the named Rhea system to the Grafakou et al. lactococcal antiphage-system discovery paper."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "rhea-mechanism-gap",
        "prompt": "Resolve Rhea phage triggers and effector outputs before minting narrower Rhea mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Grafakou et al., Mosterd et al., and DefenseFinder support Rhea as a named anti-phage system, but the direct trigger, molecular substrate, antiviral effector output, natural locus breadth, and profile-to-component model are not resolved enough here to assert a narrower mechanistic child trait.",
        "attaches_to": [
          "causal_graphs#rhea_locus_restricts_phage"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-20"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-20T14:45:33Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Rhea system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v188.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000366",
    "label": "RloC system",
    "definition": "A phage defense system in which an organism possesses a genome-encoded RloC locus represented by DefenseFinder as a one-profile model requiring RloC__RloC.",
    "definition_source": "DOI:10.1111/j.1365-2958.2008.06387.x",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "RloC",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      },
      {
        "synonym_text": "RloC__RloC",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "PMID:18681940",
        "snippet": "The conserved bacterial protein RloC, a distant homologue of the tRNA(Lys) anticodon nuclease (ACNase) PrrC, is shown here to act as a wobble nucleotide-excising and Zn(++)-responsive tRNase.",
        "notes": "Davidov and Kaufmann identify RloC as a conserved bacterial wobble nucleotide-excising, zinc-responsive tRNase related to PrrC."
      },
      {
        "reference": "PMID:18681940",
        "snippet": "Geobacillus kaustophilus RloC expressed in Escherichia coli exhibited ACNase activity that differed from PrrC's in substrate preference and ability to excise the wobble nucleotide.",
        "notes": "Davidov and Kaufmann support wobble nucleotide excision by Geobacillus kaustophilus RloC expressed in Escherichia coli."
      },
      {
        "reference": "PMID:26031711",
        "snippet": "In contrast, RloC is rarely linked to an RM protein, and its ACNase is regulated by an internal switch responsive to double-stranded DNA breaks.",
        "notes": "Bitton et al. describe RloC ACNase regulation by an internal switch that responds to double-stranded DNA breaks."
      },
      {
        "reference": "PMID:26031711",
        "snippet": "Consistent with these predictions we show that Acinetobacter baylyi RloC expressed in Escherichia coli is activated by wild-type phage T4 but not by a mutant impaired in host DNA degradation.",
        "notes": "Bitton et al. show that Acinetobacter baylyi RloC expressed in Escherichia coli is activated by wild-type phage T4, but not by a host-DNA-degradation mutant."
      },
      {
        "reference": "PMID:26031711",
        "snippet": "Nonetheless, T4's plating efficiency was inefficiently impaired by AbaRloC, presumably due to a decoy function of the phage encoded tRNA target, the absence of which exacerbated the restriction.",
        "notes": "Bitton et al. report that Acinetobacter baylyi RloC inefficiently impairs wild-type T4 plating and more strongly restricts a phage mutant lacking the decoy tRNA target."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "RloC | 10\\.1111/j\\.1365-2958\\.2008\\.06387\\.x | RloC: a wobble nucleotide-excising and zinc-responsive bacterial tRNase",
        "notes": "The DefenseFinder article registry maps the named RloC system to Davidov and Kaufmann's wobble nucleotide-excising tRNase paper."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "RloC\tRloC\t1\t1\tRloC__RloC\t\t\t",
        "notes": "The DefenseFinder rules table models RloC as a one-profile system requiring the RloC__RloC profile."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| RloC__RloC                                       | RloC__RloC                                       | RloC                   | Custom                  | 120    |",
        "notes": "The DefenseFinder HMM inventory records RloC__RloC under RloC."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "rloc_locus_triggers_dna_break_responsive_activation",
        "title": "RloC loci encode DNA-break-responsive activation",
        "description": "Conservative system-level sketch linking possession of a DefenseFinder RloC locus to DNA-break-responsive RloC anticodon nuclease activation without asserting natural host breadth, the endogenous phage trigger, or exact RloC profile-to-activity mapping.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures RloC as a named DefenseFinder one-profile phage-defense system while leaving natural host breadth, the endogenous DNA-break trigger, phage restriction strength, and RloC profile-to-activity mapping unresolved.",
        "nodes": [
          {
            "node_id": "rloc_locus",
            "label": "RloC locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A DefenseFinder RloC phage-defense locus represented by the RloC__RloC profile."
          },
          {
            "node_id": "dna_break_responsive_rloc_activation",
            "label": "DNA-break-responsive RloC activation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Activation of RloC anticodon nuclease activity by double-stranded DNA breaks, causing wobble nucleotide excision from tRNA."
          },
          {
            "node_id": "rloc_system_trait",
            "label": "RloC system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000366",
            "description": "Possession of a genome-encoded RloC phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "rloc_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "dna_break_responsive_rloc_activation",
            "description": "RloC encodes a wobble nucleotide-excising anticodon nuclease, Acinetobacter baylyi RloC responds to T4 host DNA degradation when expressed in Escherichia coli, and DefenseFinder models RloC as a one-profile system.",
            "evidence": [
              {
                "reference": "PMID:18681940",
                "snippet": "The conserved bacterial protein RloC, a distant homologue of the tRNA(Lys) anticodon nuclease (ACNase) PrrC, is shown here to act as a wobble nucleotide-excising and Zn(++)-responsive tRNase.",
                "notes": "Davidov and Kaufmann identify RloC as a wobble nucleotide-excising and zinc-responsive tRNase."
              },
              {
                "reference": "PMID:26031711",
                "snippet": "In contrast, RloC is rarely linked to an RM protein, and its ACNase is regulated by an internal switch responsive to double-stranded DNA breaks.",
                "notes": "Bitton et al. support RloC ACNase regulation by an internal double-stranded-DNA-break switch."
              },
              {
                "reference": "PMID:26031711",
                "snippet": "Consistent with these predictions we show that Acinetobacter baylyi RloC expressed in Escherichia coli is activated by wild-type phage T4 but not by a mutant impaired in host DNA degradation.",
                "notes": "Bitton et al. show T4 host DNA degradation activates Acinetobacter baylyi RloC expressed in Escherichia coli."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "RloC | 10\\.1111/j\\.1365-2958\\.2008\\.06387\\.x | RloC: a wobble nucleotide-excising and zinc-responsive bacterial tRNase",
                "notes": "The DefenseFinder article registry maps the named RloC system to Davidov and Kaufmann's wobble nucleotide-excising tRNase paper."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "RloC\tRloC\t1\t1\tRloC__RloC\t\t\t",
                "notes": "The DefenseFinder rules table models RloC as a one-profile system requiring the RloC__RloC profile."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| RloC__RloC                                       | RloC__RloC                                       | RloC                   | Custom                  | 120    |",
                "notes": "The DefenseFinder HMM inventory records RloC__RloC under RloC."
              }
            ]
          },
          {
            "subject": "dna_break_responsive_rloc_activation",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "rloc_system_trait",
            "description": "DNA-break-responsive RloC anticodon nuclease activation realizes the RloC system trait.",
            "evidence": [
              {
                "reference": "PMID:26031711",
                "snippet": "Consistent with these predictions we show that Acinetobacter baylyi RloC expressed in Escherichia coli is activated by wild-type phage T4 but not by a mutant impaired in host DNA degradation.",
                "notes": "Bitton et al. show that wild-type phage T4 activates Acinetobacter baylyi RloC expressed in Escherichia coli."
              },
              {
                "reference": "PMID:26031711",
                "snippet": "Nonetheless, T4's plating efficiency was inefficiently impaired by AbaRloC, presumably due to a decoy function of the phage encoded tRNA target, the absence of which exacerbated the restriction.",
                "notes": "Bitton et al. report that Acinetobacter baylyi RloC inefficiently impairs wild-type T4 plating and more strongly restricts a phage mutant lacking the decoy tRNA target."
              }
            ]
          },
          {
            "subject": "rloc_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "RloC system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "RloC | 10\\.1111/j\\.1365-2958\\.2008\\.06387\\.x | RloC: a wobble nucleotide-excising and zinc-responsive bacterial tRNase",
                "notes": "The DefenseFinder article registry maps the named RloC system to Davidov and Kaufmann's wobble nucleotide-excising tRNase paper."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "RloC\tRloC\t1\t1\tRloC__RloC\t\t\t",
                "notes": "The DefenseFinder rules table models RloC as a one-profile system requiring the RloC__RloC profile."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "rloc-mechanism-gap",
        "prompt": "Resolve natural RloC host breadth, endogenous RloC activation triggers, phage restriction strength, and RloC profile-to-activity mapping before minting narrower RloC mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Davidov and Kaufmann support RloC as a bacterial wobble nucleotide-excising tRNase, Bitton et al. show that Acinetobacter baylyi RloC responds to phage T4 host DNA degradation in an Escherichia coli expression context, and DefenseFinder models RloC as a one-profile system with an RloC__RloC marker. Natural host breadth, native phage triggers, restriction strength, and profile-to-activity mapping remain unresolved.",
        "evidence": [
          {
            "reference": "PMID:26031711",
            "snippet": "The natural role of the conserved bacterial anticodon nuclease (ACNase) RloC is not known, but traits that set it apart from the homologous phage T4-excluding ACNase PrrC could provide relevant clues.",
            "notes": "Bitton et al. leave the natural role of conserved bacterial RloC unknown while comparing it to the phage T4-excluding PrrC ACNase."
          }
        ],
        "attaches_to": [
          "causal_graphs#rloc_locus_triggers_dna_break_responsive_activation"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-22"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-22T13:03:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted RloC system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v243.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-22T13:03:01Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed the RloC canonical_examples gap and left canonical_examples empty: the current evidence supports RloC as a wobble nucleotide-excising tRNase, T4 activation of Acinetobacter baylyi RloC expressed in Escherichia coli, and the pinned DefenseFinder RloC profile, but does not cite a directly observed natural microbial taxon with a source-backed RloC locus broad enough for a canonical example. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000367",
    "label": "RnlAB system",
    "definition": "A phage defense system in which an organism possesses a genome-encoded RnlAB toxin-antitoxin locus represented by DefenseFinder as a two-profile model requiring RnlAB__RnlA and RnlAB__RnlB.",
    "definition_source": "DOI:10.1534/genetics.110.121798",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "RnlAB",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      },
      {
        "synonym_text": "RnlAB__RnlA",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "RnlAB__RnlB",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "PMID:20980243",
        "snippet": "RNase LS was originally identified as a potential antagonist of bacteriophage T4 infection. When T4 dmd is defective, RNase LS activity rapidly increases after T4 infection and cleaves T4 mRNAs to antagonize T4 reproduction.",
        "notes": "Koga et al. frame RnlA-dependent RNase LS activity as a potential antagonist of bacteriophage T4 dmd mutants."
      },
      {
        "reference": "PMID:20980243",
        "snippet": "Here we show that rnlA, a structural gene of RNase LS, encodes a novel toxin, and that rnlB (formally yfjO), located immediately downstream of rnlA, encodes an antitoxin against RnlA.",
        "notes": "Koga et al. identify rnlA as the RNase LS toxin gene and rnlB as the neighboring cognate antitoxin gene."
      },
      {
        "reference": "PMID:20980243",
        "snippet": "Pull-down analysis showed a specific interaction between RnlA and RnlB.",
        "notes": "Koga et al. support direct RnlA/RnlB interaction by pull-down analysis."
      },
      {
        "reference": "PMID:20980243",
        "snippet": "All of these results suggested that rnlA-rnlB define a new toxin-antitoxin (TA) system.",
        "notes": "Koga et al. define rnlA-rnlB as a new toxin-antitoxin system."
      },
      {
        "reference": "PMID:22403819",
        "snippet": "Predicted proteins encoded by these two ORFs were found to share a weak homology with RnlA and RnlB, respectively, a toxin\u2013antitoxin system encoded on the E. coli K-12 chromosome.",
        "notes": "Otsuka and Yonesaki describe RnlA/RnlB as a toxin-antitoxin system encoded on the Escherichia coli K-12 chromosome."
      },
      {
        "reference": "PMID:22403819",
        "snippet": "T4 phage Dmd suppressed the toxicities of both RnlA and LsoA by direct interaction, the first example of a phage with an antitoxin against multiple toxins.",
        "notes": "Otsuka and Yonesaki support T4 Dmd as a phage antitoxin that suppresses RnlA toxicity by direct interaction."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "RnlAB | 10\\.1534/genetics\\.110\\.121798 | Escherichia coli rnlA and rnlB compose a novel toxin-antitoxin system",
        "notes": "The DefenseFinder article registry maps the named RnlAB system to Koga et al.'s rnlA-rnlB toxin-antitoxin paper."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "RnlAB\tRnlAB\t2\t2\tRnlAB__RnlA, RnlAB__RnlB\t\t\t",
        "notes": "The DefenseFinder rules table models RnlAB as a two-profile system requiring the RnlAB__RnlA and RnlAB__RnlB profiles."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| RnlAB__RnlA                                      | RnlAB__RnlA                                      | RnlAB                  | Custom                  | 20     |",
        "notes": "The DefenseFinder HMM inventory records RnlAB__RnlA under RnlAB."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| RnlAB__RnlB                                      | RnlAB__RnlB                                      | RnlAB                  | Custom                  | 20     |",
        "notes": "The DefenseFinder HMM inventory records RnlAB__RnlB under RnlAB."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:83333",
        "taxon_label": "Escherichia coli K-12",
        "note": "Otsuka and Yonesaki describe the RnlA/RnlB toxin-antitoxin system as encoded on the Escherichia coli K-12 chromosome.",
        "reference": "DOI:10.1111/j.1365-2958.2012.07975.x"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "rnlab_locus_antagonizes_t4_dmd_mutants",
        "title": "RnlAB loci support RnlA-dependent RNase LS activity",
        "description": "Conservative system-level sketch linking possession of an RnlAB locus to RnlA-dependent RNase LS activity against bacteriophage T4 dmd mutants without asserting a wild-type-phage trigger, broad phage host range, or exact RnlAB profile-to-activity mapping.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures RnlAB as a named DefenseFinder two-profile phage-defense system while leaving natural phage breadth, wild-type T4 evasion through Dmd, induction or activation routes in non-T4 contexts, and RnlAB profile-to-activity mapping unresolved.",
        "nodes": [
          {
            "node_id": "rnlab_locus",
            "label": "RnlAB locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A toxin-antitoxin locus represented by RnlAB__RnlA and RnlAB__RnlB profiles."
          },
          {
            "node_id": "rnla_dependent_rnase_ls_activity",
            "label": "RnlA-dependent RNase LS activity",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "RNase LS activity encoded by rnlA and controlled by rnlB, with RnlA capable of cleaving T4 mRNAs when phage Dmd is absent."
          },
          {
            "node_id": "rnlab_system_trait",
            "label": "RnlAB system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000367",
            "description": "Possession of a genome-encoded RnlAB toxin-antitoxin phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "rnlab_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "rnla_dependent_rnase_ls_activity",
            "description": "Koga et al. show that rnlA encodes the RNase LS toxin and rnlB encodes the cognate antitoxin; DefenseFinder models RnlAB as a two-profile system.",
            "evidence": [
              {
                "reference": "PMID:20980243",
                "snippet": "Here we show that rnlA, a structural gene of RNase LS, encodes a novel toxin, and that rnlB (formally yfjO), located immediately downstream of rnlA, encodes an antitoxin against RnlA.",
                "notes": "Koga et al. identify rnlA as the RNase LS toxin gene and rnlB as the antitoxin gene."
              },
              {
                "reference": "PMID:20980243",
                "snippet": "Pull-down analysis showed a specific interaction between RnlA and RnlB.",
                "notes": "Koga et al. show that RnlA and RnlB specifically interact."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "RnlAB | 10\\.1534/genetics\\.110\\.121798 | Escherichia coli rnlA and rnlB compose a novel toxin-antitoxin system",
                "notes": "The DefenseFinder article registry maps the named RnlAB system to Koga et al.'s rnlA-rnlB toxin-antitoxin paper."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "RnlAB\tRnlAB\t2\t2\tRnlAB__RnlA, RnlAB__RnlB\t\t\t",
                "notes": "The DefenseFinder rules table models RnlAB as a two-profile system requiring the RnlAB__RnlA and RnlAB__RnlB profiles."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| RnlAB__RnlA                                      | RnlAB__RnlA                                      | RnlAB                  | Custom                  | 20     |",
                "notes": "The DefenseFinder HMM inventory records RnlAB__RnlA under RnlAB."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| RnlAB__RnlB                                      | RnlAB__RnlB                                      | RnlAB                  | Custom                  | 20     |",
                "notes": "The DefenseFinder HMM inventory records RnlAB__RnlB under RnlAB."
              }
            ]
          },
          {
            "subject": "rnla_dependent_rnase_ls_activity",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "rnlab_system_trait",
            "description": "RnlA-dependent RNase LS activity against T4 dmd-mutant mRNAs realizes the RnlAB system trait.",
            "evidence": [
              {
                "reference": "PMID:20980243",
                "snippet": "RNase LS was originally identified as a potential antagonist of bacteriophage T4 infection. When T4 dmd is defective, RNase LS activity rapidly increases after T4 infection and cleaves T4 mRNAs to antagonize T4 reproduction.",
                "notes": "Koga et al. support RNase LS antagonism of T4 dmd-mutant reproduction."
              },
              {
                "reference": "PMID:22403819",
                "snippet": "T4 phage Dmd suppressed the toxicities of both RnlA and LsoA by direct interaction, the first example of a phage with an antitoxin against multiple toxins.",
                "notes": "Otsuka and Yonesaki show phage Dmd can suppress RnlA toxicity by direct interaction."
              }
            ]
          },
          {
            "subject": "rnlab_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "RnlAB system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "RnlAB | 10\\.1534/genetics\\.110\\.121798 | Escherichia coli rnlA and rnlB compose a novel toxin-antitoxin system",
                "notes": "The DefenseFinder article registry maps the named RnlAB system to Koga et al.'s rnlA-rnlB toxin-antitoxin paper."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "RnlAB\tRnlAB\t2\t2\tRnlAB__RnlA, RnlAB__RnlB\t\t\t",
                "notes": "The DefenseFinder rules table models RnlAB as a two-profile system requiring the RnlAB__RnlA and RnlAB__RnlB profiles."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "rnlab-phage-breadth-evasion-gap",
        "prompt": "Resolve natural RnlAB phage breadth, wild-type T4 evasion through Dmd, induction or activation routes in non-T4 contexts, and RnlAB profile-to-activity mapping before minting narrower RnlAB mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Koga et al. support RnlA/RnlB as an Escherichia coli K-12 toxin-antitoxin system whose RNase LS activity can antagonize T4 dmd mutants, Otsuka and Yonesaki show that T4 phage Dmd suppresses RnlA toxicity, and DefenseFinder models RnlAB as a two-profile system with RnlAB__RnlA and RnlAB__RnlB markers. Natural phage breadth, wild-type T4 evasion, non-T4 activation contexts, and profile-to-activity mapping remain unresolved.",
        "evidence": [
          {
            "reference": "PMID:22403819",
            "snippet": "T4 phage Dmd suppressed the toxicities of both RnlA and LsoA by direct interaction, the first example of a phage with an antitoxin against multiple toxins.",
            "notes": "Otsuka and Yonesaki show that T4 Dmd suppresses RnlA toxicity, marking phage evasion as a real boundary around RnlAB mechanism curation."
          }
        ],
        "attaches_to": [
          "causal_graphs#rnlab_locus_antagonizes_t4_dmd_mutants"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-22"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-22T13:54:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted RnlAB system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v244.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000256",
    "label": "RosmerTA system",
    "definition": "A phage defense system in which an organism possesses a two-component RosmerTA locus represented by RmrA and RmrT profiles that can protect bacteria from bacteriophage infection.",
    "definition_source": "DOI:10.1016/j.chom.2022.09.017",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "RosmerTA",
        "synonym_type": "EXACT_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1016/j.chom.2022.09.017",
        "snippet": "discovery of 21 defense systems that protect bacteria from phages, based on computational genomic analyses and phage-infection experiments",
        "notes": "Millman et al. report the computational and experimental cohort that DefenseFinder cites for RosmerTA as a bacterial anti-phage system."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "RosmerTA | 10\\.1016/j\\.chom\\.2022\\.09\\.017 | An expanded arsenal of immune systems that protect bacteria from phages",
        "notes": "The DefenseFinder model registry maps the named RosmerTA system to the Millman et al. Cell Host & Microbe article; the RosmerTA row in the pinned registry uses the final article DOI and title rather than the bioRxiv preprint DOI used by sibling Millman-system rows."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "RosmerTA\tRosmerTA\t2\t2\tRosmerTA__RmrA_2585209417, RosmerTA__RmrT_2585209417",
        "notes": "The DefenseFinder rules table models RosmerTA with RmrA and RmrT profiles."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "RosmerTA__RmrA_2585209417                         | RosmerTA__RmrA_2585209417                         | RosmerTA",
        "notes": "The DefenseFinder HMM inventory records RmrA as a RosmerTA profile."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "RosmerTA__RmrT_2585209417                         | RosmerTA__RmrT_2585209417                         | RosmerTA",
        "notes": "The DefenseFinder HMM inventory records RmrT as a RosmerTA profile."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "rosmerta_locus_restricts_phage",
        "title": "RosmerTA loci confer bacterial phage defense",
        "description": "Conservative system-level sketch linking possession of a RosmerTA locus to restricted bacteriophage propagation without asserting the unresolved phage trigger or molecular output.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures RosmerTA as a named anti-phage system with the required DefenseFinder RmrA and RmrT profiles while leaving its phage trigger, molecular substrate, antiviral effector output, and subtype breadth unresolved.",
        "nodes": [
          {
            "node_id": "rosmerta_locus",
            "label": "RosmerTA locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A RosmerTA anti-phage defense locus satisfying a DefenseFinder rule over RmrA and RmrT profiles."
          },
          {
            "node_id": "restricted_phage_propagation",
            "label": "restricted phage propagation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced propagation of bacteriophage in cells carrying the RosmerTA system."
          },
          {
            "node_id": "rosmerta_system_trait",
            "label": "RosmerTA system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000256",
            "description": "Possession of a genome-encoded RosmerTA phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "rosmerta_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "restricted_phage_propagation",
            "description": "DefenseFinder maps RosmerTA to a bacterial anti-phage-system discovery paper and represents RosmerTA loci through RmrA and RmrT component profiles.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.chom.2022.09.017",
                "snippet": "discovery of 21 defense systems that protect bacteria from phages",
                "notes": "Millman et al. describe the anti-phage discovery cohort that the DefenseFinder RosmerTA registry row maps to the RosmerTA system."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "RosmerTA | 10\\.1016/j\\.chom\\.2022\\.09\\.017 | An expanded arsenal of immune systems that protect bacteria from phages",
                "notes": "The DefenseFinder registry maps RosmerTA itself to the final Millman et al. bacterial antiphage-system paper, unlike sibling rows from the same discovery cohort that still point at the bioRxiv preprint."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "RosmerTA\tRosmerTA\t2\t2\tRosmerTA__RmrA_2585209417, RosmerTA__RmrT_2585209417",
                "notes": "The DefenseFinder rules table supports both RmrA and RmrT as required RosmerTA system profiles."
              }
            ]
          },
          {
            "subject": "restricted_phage_propagation",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "rosmerta_system_trait",
            "description": "RosmerTA-mediated phage restriction realizes the RosmerTA system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.chom.2022.09.017",
                "snippet": "discovery of 21 defense systems that protect bacteria from phages",
                "notes": "Millman et al. place the RosmerTA discovery cohort in the set of bacterial systems that protect against phages."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "RosmerTA | 10\\.1016/j\\.chom\\.2022\\.09\\.017 | An expanded arsenal of immune systems that protect bacteria from phages",
                "notes": "DefenseFinder records RosmerTA as a named system from the final Millman et al. antiphage-system paper rather than the bioRxiv preprint used by the neighboring Millman cohort rows."
              }
            ]
          },
          {
            "subject": "rosmerta_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "RosmerTA system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "An expanded arsenal of immune systems that protect bacteria from phages",
                "notes": "DefenseFinder associates RosmerTA with the final Cell Host & Microbe version of the Millman et al. bacterial antiphage-system discovery paper."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "rosmerta-mechanism-gap",
        "prompt": "Resolve RosmerTA phage triggers and effector outputs before minting narrower RosmerTA mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Millman et al. and DefenseFinder support RosmerTA as a named anti-phage system with required RmrA and RmrT profiles, but the trigger, molecular substrate, antiviral effector output, and subtype-specific mechanism are not resolved enough here to assert a narrower mechanistic child trait.",
        "attaches_to": [
          "causal_graphs#rosmerta_locus_restricts_phage"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-18"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-18T23:49:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted RosmerTA system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v133.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000101",
    "label": "rRNA operon copy number",
    "definition": "A quantitative genomics property describing the number of ribosomal RNA (rrn) operons encoded in a genome, which correlates with maximal growth rate and ecological strategy.",
    "definition_source": "DOI:10.1128/AEM.66.4.1328-1333.2000",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000188"
    ],
    "synonyms": [
      {
        "synonym_text": "rrn copy number",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1128/AEM.66.4.1328-1333.2000"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1128/AEM.66.4.1328-1333.2000",
        "notes": "Klappenbach, Dunbar & Schmidt show rRNA operon copy number reflects ecological strategies, with fast responders carrying more copies."
      },
      {
        "reference": "DOI:10.1038/nmicrobiol.2016.160",
        "notes": "Roller, Stoddard & Schmidt link rrn copy number to bacterial growth rate and growth efficiency."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:691",
        "taxon_label": "Vibrio natriegens",
        "note": "high rRNA-operon copy number (fast growth)",
        "reference": "PMID:23969053"
      },
      {
        "taxon_id": "NCBITaxon:562",
        "taxon_label": "Escherichia coli",
        "note": "seven rRNA operons",
        "reference": "PMID:15528533"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "rrn_copy_growth_rate",
        "title": "rRNA operon copy number sets ribosome biogenesis and growth rate",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This genomics record is a measurement, genomic-element classification, or population-level descriptor rather than one taxon-specific protein mechanism; contextual protein nodes do not receive token UniProt examples.",
        "description": "Evidence-backed causal sketch linking rrn copy number to ribosome biogenesis capacity and maximal growth rate.",
        "nodes": [
          {
            "node_id": "rrna_copy_trait",
            "label": "rRNA operon copy number",
            "node_type": "TRAIT",
            "grounding": "traitmech:000101",
            "description": "Number of rrn operons encoded per genome."
          },
          {
            "node_id": "ribosome_biogenesis",
            "label": "ribosome biogenesis",
            "node_type": "BIOLOGICAL_PROCESS",
            "grounding": "GO:0042254",
            "description": "Assembly of ribosomal RNA and proteins into functional ribosomes."
          },
          {
            "node_id": "maximal_growth_rate",
            "label": "maximal growth rate",
            "node_type": "QUALITY",
            "description": "Upper bound on per-cell exponential growth rate."
          },
          {
            "node_id": "rrna_transcription",
            "label": "rRNA transcription",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Synthesis of ribosomal RNA from rrn operons by RNA polymerase.",
            "grounding": "GO:0009303"
          },
          {
            "node_id": "growth_efficiency",
            "label": "growth efficiency",
            "node_type": "QUALITY",
            "description": "Carbon/substrate use efficiency of biomass production."
          },
          {
            "node_id": "chemotactic_motility",
            "label": "chemotactic motility",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Directed cell movement in response to chemical gradients."
          },
          {
            "node_id": "genome_size",
            "label": "genome size",
            "node_type": "QUALITY",
            "description": "Total genome length of an organism."
          }
        ],
        "edges": [
          {
            "subject": "rrna_copy_trait",
            "predicate": "enables",
            "object": "ribosome_biogenesis",
            "description": "Higher rrn copy number raises rRNA transcription capacity for ribosome assembly.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.66.4.1328-1333.2000",
                "notes": "Klappenbach et al. tie rrn copy number to copiotrophic strategies with fast ribosome assembly."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "rrna_copy_trait",
            "predicate": "associated with",
            "object": "maximal_growth_rate",
            "description": "rrn copy number correlates with maximal growth rate across bacteria.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nmicrobiol.2016.160",
                "notes": "Roller et al. link rrn copy number to bacterial growth rate and growth efficiency."
              }
            ],
            "predicate_id": "biolink:associated_with"
          },
          {
            "subject": "rrna_copy_trait",
            "predicate": "increases capacity for",
            "object": "rrna_transcription",
            "description": "Multiple rrn operons increase capacity to raise rRNA transcription and ribosome synthesis rapidly.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.66.4.1328-1333.2000",
                "notes": "rrn transcription can account for up to ~70% of cellular transcription during rapid growth; multiple operons increase ability to raise ribosome synthesis rapidly."
              }
            ]
          },
          {
            "subject": "rrna_copy_trait",
            "predicate": "decreases",
            "object": "growth_efficiency",
            "description": "Higher rrn copy number is associated with lower growth (carbon use) efficiency.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nmicrobiol.2016.160",
                "notes": "Roller et al.: growth efficiency is inversely related to maximal growth rate and rrn copy number."
              }
            ],
            "predicate_id": "RO:0002212"
          },
          {
            "subject": "rrna_copy_trait",
            "predicate": "positively associated with",
            "object": "chemotactic_motility",
            "description": "Higher rrn copy number is associated with greater probability of chemotactic motility across genomes.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nmicrobiol.2016.160",
                "notes": "Chemotactic motility shows a positive relationship with log2-rrn (up to +41.25% non-phylogenetic, +10.60% phylogenetic) across 1,167 genomes."
              }
            ]
          },
          {
            "subject": "rrna_copy_trait",
            "predicate": "positively correlates with",
            "object": "genome_size",
            "description": "rrn copy number positively correlates with genome size across bacteria.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nmicrobiol.2016.160",
                "notes": "Genome size and rrn copy number show a positive logarithmic relationship; ~+0.66 Mbp phylogenetically for 15 vs 1 rrn."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-06-05T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate GENOMICS trait (rRNA operon copy number) from literature research.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-08T14:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (rrn copy / ribosome biogenesis / growth rate) with GO node grounding and RO/biolink predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 4 evidence-backed generic edges (4 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:11Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002212\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:32Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0009303\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-21T08:00:00Z",
        "curator": "codex",
        "action": "NORMALISE_NODE_TYPE",
        "changes": "Tranche 5 of issue 356 settles the process/quality families and merges ids that meant the same sense: maximal_growth_rate is QUALITY. A maximal growth rate is a measured upper bound or peak specific rate. Its edges associate, enable, or manifest that value; none describe the process of cell growth itself. An edge cannot enable a QUALITY under RO:0002327's biological-process range, so edges that causally support the rate use promotes (RO:0002213) instead.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope rrn_copy_growth_rate=NONMECHANISTIC with scope_notes.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000400",
    "label": "Rst_2TM_1TM_TIR system",
    "definition": "A phage defense system in which an organism possesses a three-protein Rst_2TM_1TM_TIR locus represented by DefenseFinder as a three-profile model requiring Rst_2TM_1TM_TIR__Rst_1TM_TIR, Rst_2TM_1TM_TIR__Rst_2TM_TIR, and Rst_2TM_1TM_TIR__Rst_TIR_tm and experimentally linked to multi-phage protection when expressed in Escherichia coli C.",
    "definition_source": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/rst_2tm_1tm_tir.md",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "Rst_2TM_1TM_TIR",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      },
      {
        "synonym_text": "Rst_2TM_1TM_TIR__Rst_1TM_TIR",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "Rst_2TM_1TM_TIR__Rst_2TM_TIR",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "Rst_2TM_1TM_TIR__Rst_TIR_tm",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1016/j.chom.2022.02.018",
        "snippet": "Phage resistance heatmaps of the validated defense systems show the median fold resistance of three independent replicates against a panel of eight phages",
        "notes": "The Figure 5 legend frames the cloned Rst_2TM_1TM_TIR hit as one of the validated defense systems in a replicated phage-resistance heatmap."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/rst_2tm_1tm_tir.md",
        "snippet": "The Rst_2TM_1TM_TIR system is carried by the P2-like phage AC1 and protects *Escherichia coli* C against lambda, LF82_P8 and P2 phages. This system is composed of three proteins, Rst_TIR_tm, which contains a TIR (Toll/interleukin-1 receptor) domain, Rst_1TM_TIR, which contains a transmembrane helix (TM) and Rst_2TM_TIR, that contains two TMs :ref{doi=10.1016/j.chom.2022.02.018}.",
        "notes": "The pinned DefenseFinder wiki page names Rst_2TM_1TM_TIR as a three-protein system and links the AC1 locus to lambda, LF82_P8, and P2 protection in Escherichia coli C."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/rst_2tm_1tm_tir.md",
        "snippet": "Rousset et al. suggested that the TIR-containing protein could generate a nucleotide messenger that in turn could activate the associated transmembrane proteins.",
        "notes": "The pinned DefenseFinder wiki page records the unresolved Rousset et al. hypothesis that the TIR-containing protein could produce a nucleotide messenger that activates the transmembrane proteins."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/rst_2tm_1tm_tir.md",
        "snippet": "As far as we are aware, the molecular mechanism is unknown.",
        "notes": "The pinned DefenseFinder wiki page leaves the Rst_2TM_1TM_TIR molecular mechanism unresolved."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/rst_2tm_1tm_tir.md",
        "snippet": "The Rst_2TM_1TM_TIR is composed of 3 proteins: Rst_2TM_TIR, Rst_TIR_tm and Rst_1TM_TIR.",
        "notes": "The pinned DefenseFinder wiki page describes Rst_2TM_1TM_TIR as a three-component Rst_2TM_TIR/Rst_TIR_tm/Rst_1TM_TIR system."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/rst_2tm_1tm_tir.md",
        "snippet": "The Rst_2TM_1TM_TIR system in *Escherichia coli* (GCF_004006575.1, NZ_CP034787) is composed of 3 proteins Rst_TIR_tm (WP_023140578.1) Rst_1TM_TIR (WP_001534953.1) Rst_2TM_TIR (WP_023140577.1)",
        "notes": "The DefenseFinder wiki illustrates a predicted three-protein Rst_2TM_1TM_TIR locus in RefSeq assembly GCF_004006575.1 on NZ_CP034787."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/rst_2tm_1tm_tir.md",
        "snippet": "Rousset_2022[<a href='https://doi.org/10.1016/j.chom.2022.02.018'>Rousset et al., 2022</a>] --> Origin_0\n    Origin_0[Escherichia coli C\n<a href='https://ncbi.nlm.nih.gov/protein/WP_001534952.1'>WP_001534952.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_001534953.1'>WP_001534953.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_001534955.1'>WP_001534955.1</a>] --> Expressed_0[Escherichia coli C]\n    Expressed_0[Escherichia coli C] ----> Lambda & LF82_P8 & P2 & SIAC10 & SID07 & DC1 & AC1",
        "notes": "The DefenseFinder experimental-validation diagram links Rousset et al. to an Escherichia coli C source locus expressed in Escherichia coli C against seven phages."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/rst_2tm_1tm_tir.md",
        "snippet": "subgraph Title4[Protects against]\n        Lambda\n        LF82_P8\n        P2\n        SIAC10\n        SID07\n        DC1\n        AC1",
        "notes": "The DefenseFinder experimental-validation diagram lists lambda, LF82_P8, P2, SIAC10, SID07, DC1, and AC1 in the Rst_2TM_1TM_TIR protects-against subgraph."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "Rst_2TM_1TM_TIR | 10\\.1101/2021\\.01\\.21\\.427644 | Prophage-encoded hotspots of bacterial immune systems",
        "notes": "The DefenseFinder article registry maps the named Rst_2TM_1TM_TIR system to the Rousset et al. preprint."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "Rst_2TM_1TM_TIR\tRst_2TM_1TM_TIR\t3\t3\tRst_2TM_1TM_TIR__Rst_1TM_TIR, Rst_2TM_1TM_TIR__Rst_2TM_TIR, Rst_2TM_1TM_TIR__Rst_TIR_tm\t\t\t",
        "notes": "The DefenseFinder rules table models Rst_2TM_1TM_TIR as a three-profile system requiring Rst_2TM_1TM_TIR__Rst_1TM_TIR, Rst_2TM_1TM_TIR__Rst_2TM_TIR, and Rst_2TM_1TM_TIR__Rst_TIR_tm."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| Rst_2TM_1TM_TIR__Rst_1TM_TIR                     | Rst_2TM_1TM_TIR__Rst_1TM_TIR                     | Rst_2TM_1TM_TIR        | Custom                  | 20     |\n| Rst_2TM_1TM_TIR__Rst_2TM_TIR                     | Rst_2TM_1TM_TIR__Rst_2TM_TIR                     | Rst_2TM_1TM_TIR        | Custom                  | 20     |\n| Rst_2TM_1TM_TIR__Rst_TIR_tm                      | Rst_2TM_1TM_TIR__Rst_TIR_tm                      | Rst_2TM_1TM_TIR        | Custom                  | 20     |",
        "notes": "The DefenseFinder HMM inventory records the Rst_1TM_TIR, Rst_2TM_TIR, and Rst_TIR_tm profiles under Rst_2TM_1TM_TIR."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "rst_2tm_1tm_tir_locus_restricts_phages",
        "title": "Rst_2TM_1TM_TIR loci restrict phages",
        "description": "Conservative system-level sketch linking the named Rst_2TM_1TM_TIR three-gene locus model to multi-phage resistance.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Rst_2TM_1TM_TIR as a named DefenseFinder three-profile phage-defense system while leaving native host breadth, accession-level component grounding, the putative nucleotide messenger, and the mechanism of phage restriction unresolved.",
        "nodes": [
          {
            "node_id": "rst_2tm_1tm_tir_locus",
            "label": "Rst_2TM_1TM_TIR locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A three-gene Rst_TIR_tm/Rst_1TM_TIR/Rst_2TM_TIR phage-defense locus represented by the custom DefenseFinder Rst_2TM_1TM_TIR profiles."
          },
          {
            "node_id": "multi_phage_resistance",
            "label": "multi-phage resistance",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Resistance against multiple phages in a host expressing an Rst_2TM_1TM_TIR locus."
          },
          {
            "node_id": "rst_2tm_1tm_tir_system_trait",
            "label": "Rst_2TM_1TM_TIR system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000400",
            "description": "Possession of a genome-encoded Rst_2TM_1TM_TIR phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "rst_2tm_1tm_tir_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "multi_phage_resistance",
            "description": "The pinned DefenseFinder wiki links AC1 Rst_2TM_1TM_TIR to protection against multiple phages, and DefenseFinder models Rst_2TM_1TM_TIR as a three-profile system.",
            "evidence": [
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/rst_2tm_1tm_tir.md",
                "snippet": "The Rst_2TM_1TM_TIR system is carried by the P2-like phage AC1 and protects *Escherichia coli* C against lambda, LF82_P8 and P2 phages. This system is composed of three proteins, Rst_TIR_tm, which contains a TIR (Toll/interleukin-1 receptor) domain, Rst_1TM_TIR, which contains a transmembrane helix (TM) and Rst_2TM_TIR, that contains two TMs :ref{doi=10.1016/j.chom.2022.02.018}.",
                "notes": "The pinned DefenseFinder wiki page names Rst_2TM_1TM_TIR as a three-protein system and links the AC1 locus to lambda, LF82_P8, and P2 protection in Escherichia coli C."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "Rst_2TM_1TM_TIR\tRst_2TM_1TM_TIR\t3\t3\tRst_2TM_1TM_TIR__Rst_1TM_TIR, Rst_2TM_1TM_TIR__Rst_2TM_TIR, Rst_2TM_1TM_TIR__Rst_TIR_tm\t\t\t",
                "notes": "The DefenseFinder rules table models Rst_2TM_1TM_TIR as a three-profile system requiring Rst_2TM_1TM_TIR__Rst_1TM_TIR, Rst_2TM_1TM_TIR__Rst_2TM_TIR, and Rst_2TM_1TM_TIR__Rst_TIR_tm."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| Rst_2TM_1TM_TIR__Rst_1TM_TIR                     | Rst_2TM_1TM_TIR__Rst_1TM_TIR                     | Rst_2TM_1TM_TIR        | Custom                  | 20     |\n| Rst_2TM_1TM_TIR__Rst_2TM_TIR                     | Rst_2TM_1TM_TIR__Rst_2TM_TIR                     | Rst_2TM_1TM_TIR        | Custom                  | 20     |\n| Rst_2TM_1TM_TIR__Rst_TIR_tm                      | Rst_2TM_1TM_TIR__Rst_TIR_tm                      | Rst_2TM_1TM_TIR        | Custom                  | 20     |",
                "notes": "The DefenseFinder HMM inventory records the Rst_1TM_TIR, Rst_2TM_TIR, and Rst_TIR_tm profiles under Rst_2TM_1TM_TIR."
              }
            ]
          },
          {
            "subject": "multi_phage_resistance",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "rst_2tm_1tm_tir_system_trait",
            "description": "Rst_2TM_1TM_TIR-linked multi-phage resistance realizes the Rst_2TM_1TM_TIR system trait.",
            "evidence": [
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/rst_2tm_1tm_tir.md",
                "snippet": "Rousset_2022[<a href='https://doi.org/10.1016/j.chom.2022.02.018'>Rousset et al., 2022</a>] --> Origin_0\n    Origin_0[Escherichia coli C\n<a href='https://ncbi.nlm.nih.gov/protein/WP_001534952.1'>WP_001534952.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_001534953.1'>WP_001534953.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_001534955.1'>WP_001534955.1</a>] --> Expressed_0[Escherichia coli C]\n    Expressed_0[Escherichia coli C] ----> Lambda & LF82_P8 & P2 & SIAC10 & SID07 & DC1 & AC1",
                "notes": "The DefenseFinder experimental-validation diagram links Rousset et al. to an Escherichia coli C source locus expressed in Escherichia coli C against seven phages."
              },
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/rst_2tm_1tm_tir.md",
                "snippet": "subgraph Title4[Protects against]\n        Lambda\n        LF82_P8\n        P2\n        SIAC10\n        SID07\n        DC1\n        AC1",
                "notes": "The DefenseFinder experimental-validation diagram lists lambda, LF82_P8, P2, SIAC10, SID07, DC1, and AC1 in the Rst_2TM_1TM_TIR protects-against subgraph."
              }
            ]
          },
          {
            "subject": "rst_2tm_1tm_tir_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Rst_2TM_1TM_TIR system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.chom.2022.02.018",
                "snippet": "Phage resistance heatmaps of the validated defense systems show the median fold resistance of three independent replicates against a panel of eight phages",
                "notes": "The Figure 5 legend frames the cloned Rst_2TM_1TM_TIR hit as one of the validated defense systems in a replicated phage-resistance heatmap."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Rst_2TM_1TM_TIR | 10\\.1101/2021\\.01\\.21\\.427644 | Prophage-encoded hotspots of bacterial immune systems",
                "notes": "The DefenseFinder article registry maps the named Rst_2TM_1TM_TIR system to the Rousset et al. preprint."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "rst-2tm-1tm-tir-mechanism-gap",
        "prompt": "Resolve Rst_2TM_1TM_TIR native host breadth, accession-level components, the proposed TIR-derived nucleotide messenger, and the downstream transmembrane activation mechanism before minting narrower Rst_2TM_1TM_TIR mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "The pinned DefenseFinder wiki supports a three-component AC1 Rst_2TM_1TM_TIR system that protects Escherichia coli C against multiple phages, and DefenseFinder represents Rst_2TM_1TM_TIR as a required three-profile model. Rousset et al. proposed that the TIR-containing protein could generate a nucleotide messenger to activate associated transmembrane proteins, but the wiki still records the molecular mechanism as unknown.",
        "evidence": [
          {
            "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/rst_2tm_1tm_tir.md",
            "snippet": "Rousset et al. suggested that the TIR-containing protein could generate a nucleotide messenger that in turn could activate the associated transmembrane proteins.",
            "notes": "The pinned DefenseFinder wiki page records the unresolved Rousset et al. hypothesis that the TIR-containing protein could produce a nucleotide messenger that activates the transmembrane proteins."
          },
          {
            "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/rst_2tm_1tm_tir.md",
            "snippet": "As far as we are aware, the molecular mechanism is unknown.",
            "notes": "The pinned DefenseFinder wiki page leaves the Rst_2TM_1TM_TIR molecular mechanism unresolved."
          },
          {
            "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/rst_2tm_1tm_tir.md",
            "snippet": "The Rst_2TM_1TM_TIR is composed of 3 proteins: Rst_2TM_TIR, Rst_TIR_tm and Rst_1TM_TIR.",
            "notes": "The pinned DefenseFinder wiki page describes Rst_2TM_1TM_TIR as a three-component Rst_2TM_TIR/Rst_TIR_tm/Rst_1TM_TIR system."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "snippet": "Rst_2TM_1TM_TIR\tRst_2TM_1TM_TIR\t3\t3\tRst_2TM_1TM_TIR__Rst_1TM_TIR, Rst_2TM_1TM_TIR__Rst_2TM_TIR, Rst_2TM_1TM_TIR__Rst_TIR_tm\t\t\t",
            "notes": "The DefenseFinder rules table models Rst_2TM_1TM_TIR as a three-profile system requiring Rst_2TM_1TM_TIR__Rst_1TM_TIR, Rst_2TM_1TM_TIR__Rst_2TM_TIR, and Rst_2TM_1TM_TIR__Rst_TIR_tm."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| Rst_2TM_1TM_TIR__Rst_1TM_TIR                     | Rst_2TM_1TM_TIR__Rst_1TM_TIR                     | Rst_2TM_1TM_TIR        | Custom                  | 20     |\n| Rst_2TM_1TM_TIR__Rst_2TM_TIR                     | Rst_2TM_1TM_TIR__Rst_2TM_TIR                     | Rst_2TM_1TM_TIR        | Custom                  | 20     |\n| Rst_2TM_1TM_TIR__Rst_TIR_tm                      | Rst_2TM_1TM_TIR__Rst_TIR_tm                      | Rst_2TM_1TM_TIR        | Custom                  | 20     |",
            "notes": "The DefenseFinder HMM inventory records the Rst_1TM_TIR, Rst_2TM_TIR, and Rst_TIR_tm profiles under Rst_2TM_1TM_TIR."
          }
        ],
        "attaches_to": [
          "causal_graphs#rst_2tm_1tm_tir_locus_restricts_phages"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-27"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-27T02:40:20Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Rst_2TM_1TM_TIR system as a stable-URL-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v277.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-27T02:40:21Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed Rst_2TM_1TM_TIR during canonical-example issue 444 enforcement and left canonical_examples empty because the sources support a cloned P2-like-phage AC1 locus assayed in Escherichia coli C and a DefenseFinder RefSeq model example, but not a direct native microbial host exemplar with experimental Rst_2TM_1TM_TIR activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000398",
    "label": "Rst_3HP system",
    "definition": "A phage defense system in which an organism possesses a three-protein Rst_3HP locus represented by DefenseFinder as a three-profile model requiring Rst_3HP__Hp1, Rst_3HP__Hp2, and Rst_3HP__Hp3 and experimentally linked to P1 protection when expressed in Escherichia coli.",
    "definition_source": "DOI:10.1016/j.chom.2022.02.018",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "Rst_3HP",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      },
      {
        "synonym_text": "Rst_3HP__Hp1",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "Rst_3HP__Hp2",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "Rst_3HP__Hp3",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1016/j.chom.2022.02.018",
        "snippet": "The second system comprises three genes that have no clear predicted domain and protect against P1.",
        "notes": "Rousset et al. experimentally describe the unnamed three-gene P2-hotspot system that DefenseFinder tracks as Rst_3HP."
      },
      {
        "reference": "DOI:10.1016/j.chom.2022.02.018",
        "snippet": "Phage resistance heatmaps of the validated defense systems show the median fold resistance of three independent replicates against a panel of eight phages",
        "notes": "The Figure 5 legend frames the cloned P2-hotspot hits, including the three-gene P1-restricting system, as validated defense systems in a replicated phage-resistance heatmap."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/rst_3hp.md",
        "snippet": "The Rst_3HP system is composed of 3 proteins: Hp1, Hp2 and, Hp3. These proteins do not have clear predicted domains but they confer resistance against the phage P1 in *Escherichia coli* E1114 :ref{doi=10.1016/j.chom.2022.02.018}.",
        "notes": "The pinned DefenseFinder wiki page names Rst_3HP as a three-protein system and links Hp1, Hp2, and Hp3 to P1 resistance in Escherichia coli E1114."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/rst_3hp.md",
        "snippet": "As far as we are aware, the molecular mechanism is unknown.",
        "notes": "The pinned DefenseFinder wiki page leaves the Rst_3HP molecular mechanism unresolved."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/rst_3hp.md",
        "snippet": "The Rst_3HP is composed of 3 proteins: Hp1, Hp2 and Hp3.",
        "notes": "The pinned DefenseFinder wiki page describes Rst_3HP as a three-component Hp1/Hp2/Hp3 system."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/rst_3hp.md",
        "snippet": "The Rst_3HP system in *Aquitalea denitrificans* (GCF_009856625.1, NZ_CP047241) is composed of 3 proteins Hp1 (WP_159879082.1) Hp2 (WP_159879084.1) Hp3 (WP_159879086.1)",
        "notes": "The DefenseFinder wiki illustrates a predicted three-protein Rst_3HP locus in RefSeq assembly GCF_009856625.1 on NZ_CP047241."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/rst_3hp.md",
        "snippet": "Rousset_2022[<a href='https://doi.org/10.1016/j.chom.2022.02.018'>Rousset et al., 2022</a>] --> Origin_0\n    Origin_0[Escherichia coli P2 loci \n<a href='https://ncbi.nlm.nih.gov/protein/WP_000508501.1'>WP_000508501.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_112026686.1'>WP_112026686.1</a>,\n<a href='https://ncbi.nlm.nih.gov/protein/WP_000756244.1'>WP_000756244.1</a>] --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> P1",
        "notes": "The DefenseFinder experimental-validation diagram links Rousset et al. to an Escherichia coli P2-locus source expressed in Escherichia coli against P1."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/rst_3hp.md",
        "snippet": "subgraph Title4[Protects against]\n        P1",
        "notes": "The DefenseFinder experimental-validation diagram lists P1 in the Rst_3HP protects-against subgraph."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "Rst_3HP | 10\\.1101/2021\\.01\\.21\\.427644 | Prophage-encoded hotspots of bacterial immune systems",
        "notes": "The DefenseFinder article registry maps the named Rst_3HP system to the Rousset et al. preprint."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "Rst_3HP\tRst_3HP\t3\t3\tRst_3HP__Hp1, Rst_3HP__Hp2, Rst_3HP__Hp3\t\t\t",
        "notes": "The DefenseFinder rules table models Rst_3HP as a three-profile system requiring Rst_3HP__Hp1, Rst_3HP__Hp2, and Rst_3HP__Hp3."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| Rst_3HP__Hp1                                     | Rst_3HP__Hp1                                     | Rst_3HP                | Custom                  | 67     |\n| Rst_3HP__Hp2                                     | Rst_3HP__Hp2                                     | Rst_3HP                | Custom                  | 26     |\n| Rst_3HP__Hp3                                     | Rst_3HP__Hp3                                     | Rst_3HP                | Custom                  | 20     |",
        "notes": "The DefenseFinder HMM inventory records Hp1, Hp2, and Hp3 custom profiles under Rst_3HP."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "rst_3hp_locus_restricts_p1",
        "title": "Rst_3HP loci restrict P1 phage",
        "description": "Conservative system-level sketch linking a named Rst_3HP three-gene locus model to P1 phage resistance.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Rst_3HP as a named DefenseFinder three-profile phage-defense system while leaving native host breadth, Hp1/Hp2/Hp3 molecular activities, profile-to-gene mapping, the direct phage trigger, and the P1 restriction mechanism unresolved.",
        "nodes": [
          {
            "node_id": "rst_3hp_locus",
            "label": "Rst_3HP locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A three-gene Hp1/Hp2/Hp3 phage-defense locus represented by the custom DefenseFinder Rst_3HP profiles."
          },
          {
            "node_id": "p1_phage_resistance",
            "label": "P1 phage resistance",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Resistance against phage P1 in a host expressing an Rst_3HP locus."
          },
          {
            "node_id": "rst_3hp_system_trait",
            "label": "Rst_3HP system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000398",
            "description": "Possession of a genome-encoded Rst_3HP phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "rst_3hp_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "p1_phage_resistance",
            "description": "Rousset et al. linked a cloned three-gene P2-hotspot system to P1 protection, and DefenseFinder models Rst_3HP as a three-profile Hp1/Hp2/Hp3 system.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.chom.2022.02.018",
                "snippet": "The second system comprises three genes that have no clear predicted domain and protect against P1.",
                "notes": "Rousset et al. experimentally describe the unnamed three-gene P2-hotspot system that DefenseFinder tracks as Rst_3HP."
              },
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/rst_3hp.md",
                "snippet": "The Rst_3HP system is composed of 3 proteins: Hp1, Hp2 and, Hp3. These proteins do not have clear predicted domains but they confer resistance against the phage P1 in *Escherichia coli* E1114 :ref{doi=10.1016/j.chom.2022.02.018}.",
                "notes": "The pinned DefenseFinder wiki page names Rst_3HP as a three-protein system and links Hp1, Hp2, and Hp3 to P1 resistance in Escherichia coli E1114."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "Rst_3HP\tRst_3HP\t3\t3\tRst_3HP__Hp1, Rst_3HP__Hp2, Rst_3HP__Hp3\t\t\t",
                "notes": "The DefenseFinder rules table models Rst_3HP as a three-profile system requiring Rst_3HP__Hp1, Rst_3HP__Hp2, and Rst_3HP__Hp3."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| Rst_3HP__Hp1                                     | Rst_3HP__Hp1                                     | Rst_3HP                | Custom                  | 67     |\n| Rst_3HP__Hp2                                     | Rst_3HP__Hp2                                     | Rst_3HP                | Custom                  | 26     |\n| Rst_3HP__Hp3                                     | Rst_3HP__Hp3                                     | Rst_3HP                | Custom                  | 20     |",
                "notes": "The DefenseFinder HMM inventory records Hp1, Hp2, and Hp3 custom profiles under Rst_3HP."
              }
            ]
          },
          {
            "subject": "p1_phage_resistance",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "rst_3hp_system_trait",
            "description": "Rst_3HP-linked P1 resistance realizes the Rst_3HP system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.chom.2022.02.018",
                "snippet": "The second system comprises three genes that have no clear predicted domain and protect against P1.",
                "notes": "Rousset et al. experimentally describe the unnamed three-gene P2-hotspot system that DefenseFinder tracks as Rst_3HP."
              },
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/rst_3hp.md",
                "snippet": "Rousset_2022[<a href='https://doi.org/10.1016/j.chom.2022.02.018'>Rousset et al., 2022</a>] --> Origin_0\n    Origin_0[Escherichia coli P2 loci \n<a href='https://ncbi.nlm.nih.gov/protein/WP_000508501.1'>WP_000508501.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_112026686.1'>WP_112026686.1</a>,\n<a href='https://ncbi.nlm.nih.gov/protein/WP_000756244.1'>WP_000756244.1</a>] --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> P1",
                "notes": "The DefenseFinder experimental-validation diagram links Rousset et al. to an Escherichia coli P2-locus source expressed in Escherichia coli against P1."
              },
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/rst_3hp.md",
                "snippet": "subgraph Title4[Protects against]\n        P1",
                "notes": "The DefenseFinder experimental-validation diagram lists P1 in the Rst_3HP protects-against subgraph."
              }
            ]
          },
          {
            "subject": "rst_3hp_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Rst_3HP system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.chom.2022.02.018",
                "snippet": "Phage resistance heatmaps of the validated defense systems show the median fold resistance of three independent replicates against a panel of eight phages",
                "notes": "The Figure 5 legend frames the cloned P2-hotspot hits, including the three-gene P1-restricting system, as validated defense systems in a replicated phage-resistance heatmap."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Rst_3HP | 10\\.1101/2021\\.01\\.21\\.427644 | Prophage-encoded hotspots of bacterial immune systems",
                "notes": "The DefenseFinder article registry maps the named Rst_3HP system to the Rousset et al. preprint."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "rst-3hp-host-mechanism-gap",
        "prompt": "Resolve Rst_3HP native host breadth, Hp1/Hp2/Hp3 molecular activities, profile-to-gene mapping, and the mechanism of P1 restriction before minting narrower Rst_3HP mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Rousset et al. support a three-gene P2-hotspot system with no clear predicted domains that protects against P1, and DefenseFinder represents Rst_3HP as a required Hp1/Hp2/Hp3 three-profile model. This first system-level record leaves native host breadth, profile-to-gene mapping, the molecular activities of Hp1, Hp2, and Hp3, and the P1 restriction mechanism unresolved.",
        "evidence": [
          {
            "reference": "DOI:10.1016/j.chom.2022.02.018",
            "snippet": "The second system comprises three genes that have no clear predicted domain and protect against P1.",
            "notes": "Rousset et al. experimentally describe the unnamed three-gene P2-hotspot system that DefenseFinder tracks as Rst_3HP."
          },
          {
            "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/rst_3hp.md",
            "snippet": "As far as we are aware, the molecular mechanism is unknown.",
            "notes": "The pinned DefenseFinder wiki page leaves the Rst_3HP molecular mechanism unresolved."
          },
          {
            "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/rst_3hp.md",
            "snippet": "The Rst_3HP is composed of 3 proteins: Hp1, Hp2 and Hp3.",
            "notes": "The pinned DefenseFinder wiki page describes Rst_3HP as a three-component Hp1/Hp2/Hp3 system."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "snippet": "Rst_3HP\tRst_3HP\t3\t3\tRst_3HP__Hp1, Rst_3HP__Hp2, Rst_3HP__Hp3\t\t\t",
            "notes": "The DefenseFinder rules table models Rst_3HP as a three-profile system requiring Rst_3HP__Hp1, Rst_3HP__Hp2, and Rst_3HP__Hp3."
          }
        ],
        "attaches_to": [
          "causal_graphs#rst_3hp_locus_restricts_p1"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-27"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-27T01:03:20Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Rst_3HP system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v275.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-27T01:03:21Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed Rst_3HP during canonical-example issue 444 enforcement and left canonical_examples empty because the sources support a cloned P2-hotspot Hp1/Hp2/Hp3 locus assayed in Escherichia coli and a DefenseFinder RefSeq model example, but not a direct native microbial isolate exemplar with experimentally verified Rst_3HP activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000374",
    "label": "Rst_DUF4238 system",
    "definition": "A phage defense system in which an organism possesses a single-gene Rst_DUF4238 locus represented by DefenseFinder as an Rst_DUF4238__DUF4238_Pers single-profile model and experimentally linked to strong resistance against phage T7.",
    "definition_source": "DOI:10.1016/j.chom.2022.02.018",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "Rst_DUF4238",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      },
      {
        "synonym_text": "Rst_DUF4238__DUF4238_Pers",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "DUF4238_Pers",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/rst_duf4238.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1016/j.chom.2022.02.018",
        "snippet": "The first system consists of a single protein with a DUF4238 domain (whose molecular function is currently unknown) that provides strong resistance against T7.",
        "notes": "Rousset et al. describe the one-protein DUF4238 candidate from the P2-encoded hotspot and connect it to strong T7 resistance."
      },
      {
        "reference": "DOI:10.1016/j.chom.2022.02.018",
        "snippet": "Phage resistance heatmaps of the validated defense systems show the median fold resistance of three independent replicates against a panel of eight phages",
        "notes": "The Figure 5 legend frames the cloned P2-hotspot hits, including the DUF4238 system, as validated defense systems in a replicated phage-resistance heatmap."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/rst_duf4238.md",
        "snippet": "Rst_DUF4238 is a single gene system found in a screen of phage and phage-satellites antiviral hotspots :ref{doi=10.1016/j.chom.2022.02.018}. It was shown to provide *E.coli* with a strong resistance against phage T7.",
        "notes": "The pinned DefenseFinder wiki page names Rst_DUF4238 as a single-gene system and links it to strong T7 resistance."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/rst_duf4238.md",
        "snippet": "As far as we are aware, the molecular mechanism is unknown.",
        "notes": "The pinned DefenseFinder wiki page leaves the Rst_DUF4238 molecular mechanism unresolved."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/rst_duf4238.md",
        "snippet": "The Rst_DUF4238 is composed of 1 protein: DUF4238.",
        "notes": "The pinned DefenseFinder wiki page describes Rst_DUF4238 as a one-component DUF4238 system."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "Rst_DUF4238 | 10\\.1101/2021\\.01\\.21\\.427644 | Prophage-encoded hotspots of bacterial immune systems",
        "notes": "The DefenseFinder article registry maps the named Rst_DUF4238 system to the Rousset et al. preprint."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "Rst_DUF4238\tRst_DUF4238\t1\t1\tRst_DUF4238__DUF4238_Pers\t\t\t",
        "notes": "The DefenseFinder rules table models Rst_DUF4238 as a single-profile system requiring Rst_DUF4238__DUF4238_Pers."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| Rst_DUF4238__DUF4238_Pers                        | Rst_DUF4238__DUF4238_Pers                        | Rst_DUF4238            | Custom                  | 100    |",
        "notes": "The DefenseFinder HMM inventory records Rst_DUF4238__DUF4238_Pers under Rst_DUF4238."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "rst_duf4238_locus_restricts_t7",
        "title": "Rst_DUF4238 loci restrict T7 phage",
        "description": "Conservative system-level sketch linking the named Rst_DUF4238 single-gene locus model to strong T7 phage resistance.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Rst_DUF4238 as a named DefenseFinder single-profile phage-defense system while leaving native host breadth, the molecular activity of the DUF4238 component, exact DUF4238_Pers profile grounding, and the mechanism of T7 restriction unresolved.",
        "nodes": [
          {
            "node_id": "rst_duf4238_locus",
            "label": "Rst_DUF4238 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A single-gene DUF4238 phage-defense locus represented by the custom DefenseFinder Rst_DUF4238__DUF4238_Pers profile."
          },
          {
            "node_id": "t7_phage_resistance",
            "label": "T7 phage resistance",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Strong resistance against phage T7 in a host expressing an Rst_DUF4238 locus."
          },
          {
            "node_id": "rst_duf4238_system_trait",
            "label": "Rst_DUF4238 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000374",
            "description": "Possession of a genome-encoded Rst_DUF4238 phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "rst_duf4238_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "t7_phage_resistance",
            "description": "Rousset et al. linked a cloned one-protein DUF4238 locus to strong T7 resistance, and DefenseFinder models Rst_DUF4238 as a single-profile DUF4238_Pers system.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.chom.2022.02.018",
                "snippet": "The first system consists of a single protein with a DUF4238 domain (whose molecular function is currently unknown) that provides strong resistance against T7.",
                "notes": "Rousset et al. describe the one-protein DUF4238 candidate from the P2-encoded hotspot and connect it to strong T7 resistance."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "Rst_DUF4238\tRst_DUF4238\t1\t1\tRst_DUF4238__DUF4238_Pers\t\t\t",
                "notes": "The DefenseFinder rules table models Rst_DUF4238 as a single-profile system requiring Rst_DUF4238__DUF4238_Pers."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| Rst_DUF4238__DUF4238_Pers                        | Rst_DUF4238__DUF4238_Pers                        | Rst_DUF4238            | Custom                  | 100    |",
                "notes": "The DefenseFinder HMM inventory records Rst_DUF4238__DUF4238_Pers under Rst_DUF4238."
              }
            ]
          },
          {
            "subject": "t7_phage_resistance",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "rst_duf4238_system_trait",
            "description": "Strong T7 resistance realizes the Rst_DUF4238 system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.chom.2022.02.018",
                "snippet": "The first system consists of a single protein with a DUF4238 domain (whose molecular function is currently unknown) that provides strong resistance against T7.",
                "notes": "Rousset et al. describe the one-protein DUF4238 candidate from the P2-encoded hotspot and connect it to strong T7 resistance."
              },
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/rst_duf4238.md",
                "snippet": "Rst_DUF4238 is a single gene system found in a screen of phage and phage-satellites antiviral hotspots :ref{doi=10.1016/j.chom.2022.02.018}. It was shown to provide *E.coli* with a strong resistance against phage T7.",
                "notes": "The pinned DefenseFinder wiki page names Rst_DUF4238 as a single-gene system and links it to strong T7 resistance."
              }
            ]
          },
          {
            "subject": "rst_duf4238_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Rst_DUF4238 system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.chom.2022.02.018",
                "snippet": "Phage resistance heatmaps of the validated defense systems show the median fold resistance of three independent replicates against a panel of eight phages",
                "notes": "The Figure 5 legend frames the cloned P2-hotspot hits, including the DUF4238 system, as validated defense systems in a replicated phage-resistance heatmap."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Rst_DUF4238 | 10\\.1101/2021\\.01\\.21\\.427644 | Prophage-encoded hotspots of bacterial immune systems",
                "notes": "The DefenseFinder article registry maps the named Rst_DUF4238 system to the Rousset et al. preprint."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "rst-duf4238-host-mechanism-gap",
        "prompt": "Resolve Rst_DUF4238 native host breadth, accession-level DUF4238 proteins, and the molecular mechanism of T7 restriction before minting narrower Rst_DUF4238 mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Rousset et al. support a one-protein DUF4238 P2-hotspot system that provides strong T7 resistance when expressed in Escherichia coli, and DefenseFinder represents Rst_DUF4238 as a single-profile Rst_DUF4238__DUF4238_Pers model. This first system-level record leaves native host breadth, accession-level component grounding, the profile-to-activity mapping, and the T7 restriction mechanism unresolved.",
        "evidence": [
          {
            "reference": "DOI:10.1016/j.chom.2022.02.018",
            "snippet": "The first system consists of a single protein with a DUF4238 domain (whose molecular function is currently unknown) that provides strong resistance against T7.",
            "notes": "Rousset et al. describe the one-protein DUF4238 candidate from the P2-encoded hotspot and connect it to strong T7 resistance."
          },
          {
            "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/rst_duf4238.md",
            "snippet": "As far as we are aware, the molecular mechanism is unknown.",
            "notes": "The pinned DefenseFinder wiki page leaves the Rst_DUF4238 molecular mechanism unresolved."
          },
          {
            "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/rst_duf4238.md",
            "snippet": "The Rst_DUF4238 is composed of 1 protein: DUF4238.",
            "notes": "The pinned DefenseFinder wiki page describes Rst_DUF4238 as a one-component DUF4238 system."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "snippet": "Rst_DUF4238\tRst_DUF4238\t1\t1\tRst_DUF4238__DUF4238_Pers\t\t\t",
            "notes": "The DefenseFinder rules table models Rst_DUF4238 as a single-profile system requiring Rst_DUF4238__DUF4238_Pers."
          }
        ],
        "attaches_to": [
          "causal_graphs#rst_duf4238_locus_restricts_t7"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-26"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-26T07:22:10Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Rst_DUF4238 system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v251.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-26T07:32:10Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed Rst_DUF4238 during canonical-example issue 444 enforcement and left canonical_examples empty because the sources support a cloned P2-hotspot DUF4238 locus assayed in Escherichia coli and a DefenseFinder RefSeq model example, but not a direct native host exemplar with experimental Rst_DUF4238 activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000376",
    "label": "Rst gop-beta-cII system",
    "definition": "A phage defense system in which an organism possesses a P4-like gop-beta-cII locus represented by DefenseFinder as the Rst_gop_beta_cll model and experimentally linked to lambda and P1 phage restriction.",
    "definition_source": "DOI:10.1016/j.chom.2022.02.018",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "gop-\u03b2-cII",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1016/j.chom.2022.02.018"
      },
      {
        "synonym_text": "Rst_gop_beta_cll",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1016/j.chom.2022.02.018",
        "snippet": "The well-characterized P4 satellite (NC_001609) carries at this position the non-essential genes gop, \u03b2, and cII, with gop and \u03b2 likely acting as a toxin-antitoxin pair",
        "notes": "Rousset et al. describe the canonical P4 satellite gop, beta, and cII locus before testing it for anti-phage activity."
      },
      {
        "reference": "DOI:10.1016/j.chom.2022.02.018",
        "snippet": "We report that gop-\u03b2-cII forms an anti-phage system that protects against \u03bb and P1.",
        "notes": "Rousset et al. directly identify gop-beta-cII as an anti-phage system that protects against lambda and P1."
      },
      {
        "reference": "DOI:10.1016/j.chom.2022.02.018",
        "snippet": "When compared with a control vector encoding a green fluorescent protein (GFP), seven systems provided robust and reproducible resistance to at least one phage",
        "notes": "Rousset et al. cloned P4/P2 hotspot systems under native promoters and measured reproducible phage resistance against their coliphage panel."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "Rst_gop_beta_cll | 10\\.1101/2021\\.01\\.21\\.427644 | Prophage-encoded hotspots of bacterial immune systems",
        "notes": "The DefenseFinder article registry maps the named Rst_gop_beta_cll system to the Rousset et al. preprint."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "Rst_gop_beta_cll\tRst_gop_beta_cll\t3\t3\tRst_gop_beta_cll__beta, Rst_gop_beta_cll__cll, Rst_gop_beta_cll__gop\t\t\t",
        "notes": "The DefenseFinder rules table models Rst_gop_beta_cll as a three-profile system requiring beta, cll, and gop profiles."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| Rst_gop_beta_cll__beta                           | Rst_gop_beta_cll__beta                           | Rst_gop_beta_cll       | Custom                  | 20     |\n| Rst_gop_beta_cll__cll                            | Rst_gop_beta_cll__cll                            | Rst_gop_beta_cll       | Custom                  | 20     |\n| Rst_gop_beta_cll__gop                            | Rst_gop_beta_cll__gop                            | Rst_gop_beta_cll       | Custom                  | 20     |",
        "notes": "The DefenseFinder HMM inventory records custom beta, cll, and gop profiles under the Rst_gop_beta_cll system namespace."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "rst_gop_beta_cll_locus_restricts_lambda_p1",
        "title": "Rst gop-beta-cII loci restrict lambda and P1 phages",
        "description": "Conservative system-level sketch linking a P4 gop-beta-cII locus to lambda and P1 phage restriction.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures gop-beta-cII as a named DefenseFinder three-profile phage-defense system while leaving natural host breadth, the direct phage trigger, the gop and beta toxin-antitoxin interpretation, cII activity, and profile-to-gene mapping unresolved.",
        "nodes": [
          {
            "node_id": "rst_gop_beta_cll_locus",
            "label": "Rst gop-beta-cII locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A P4-like gop-beta-cII phage-defense locus represented by beta, cll, and gop DefenseFinder profiles."
          },
          {
            "node_id": "lambda_and_p1_phage_restriction",
            "label": "lambda and P1 phage restriction",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Restriction of bacteriophages lambda and P1 by the gop-beta-cII locus."
          },
          {
            "node_id": "rst_gop_beta_cll_system_trait",
            "label": "Rst gop-beta-cII system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000376",
            "description": "Possession of a genome-encoded gop-beta-cII phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "rst_gop_beta_cll_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "lambda_and_p1_phage_restriction",
            "description": "Rousset et al. linked gop-beta-cII to lambda and P1 phage protection, and DefenseFinder models Rst_gop_beta_cll as a three-profile system.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.chom.2022.02.018",
                "snippet": "The well-characterized P4 satellite (NC_001609) carries at this position the non-essential genes gop, \u03b2, and cII, with gop and \u03b2 likely acting as a toxin-antitoxin pair",
                "notes": "Rousset et al. describe the canonical P4 satellite gop, beta, and cII locus before testing it for anti-phage activity."
              },
              {
                "reference": "DOI:10.1016/j.chom.2022.02.018",
                "snippet": "When compared with a control vector encoding a green fluorescent protein (GFP), seven systems provided robust and reproducible resistance to at least one phage",
                "notes": "Rousset et al. cloned P4/P2 hotspot systems under native promoters and measured reproducible phage resistance against their coliphage panel."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "Rst_gop_beta_cll\tRst_gop_beta_cll\t3\t3\tRst_gop_beta_cll__beta, Rst_gop_beta_cll__cll, Rst_gop_beta_cll__gop\t\t\t",
                "notes": "The DefenseFinder rules table models Rst_gop_beta_cll as a three-profile system requiring beta, cll, and gop profiles."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| Rst_gop_beta_cll__beta                           | Rst_gop_beta_cll__beta                           | Rst_gop_beta_cll       | Custom                  | 20     |\n| Rst_gop_beta_cll__cll                            | Rst_gop_beta_cll__cll                            | Rst_gop_beta_cll       | Custom                  | 20     |\n| Rst_gop_beta_cll__gop                            | Rst_gop_beta_cll__gop                            | Rst_gop_beta_cll       | Custom                  | 20     |",
                "notes": "The DefenseFinder HMM inventory records custom beta, cll, and gop profiles under the Rst_gop_beta_cll system namespace."
              }
            ]
          },
          {
            "subject": "lambda_and_p1_phage_restriction",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "rst_gop_beta_cll_system_trait",
            "description": "Restriction of lambda and P1 phages realizes the Rst gop-beta-cII system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.chom.2022.02.018",
                "snippet": "We report that gop-\u03b2-cII forms an anti-phage system that protects against \u03bb and P1.",
                "notes": "Rousset et al. directly identify gop-beta-cII as an anti-phage system that protects against lambda and P1."
              },
              {
                "reference": "DOI:10.1016/j.chom.2022.02.018",
                "snippet": "When compared with a control vector encoding a green fluorescent protein (GFP), seven systems provided robust and reproducible resistance to at least one phage",
                "notes": "Rousset et al. cloned P4/P2 hotspot systems under native promoters and measured reproducible phage resistance against their coliphage panel."
              }
            ]
          },
          {
            "subject": "rst_gop_beta_cll_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Rst gop-beta-cII system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.chom.2022.02.018",
                "snippet": "P2-like phages and their parasitic P4-like satellites carry hotspots of genetic variation containing reservoirs of anti-phage systems",
                "notes": "Rousset et al. frame the P4-like satellite hotspot that contains gop-beta-cII as a reservoir of anti-phage systems."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Rst_gop_beta_cll | 10\\.1101/2021\\.01\\.21\\.427644 | Prophage-encoded hotspots of bacterial immune systems",
                "notes": "The DefenseFinder article registry maps the named Rst_gop_beta_cll system to the Rousset et al. preprint."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "rst-gop-beta-cll-mechanism-gap",
        "prompt": "Resolve Rst_gop_beta_cll natural host breadth, exact beta and cll gene correspondence, direct phage trigger, and Gop or beta toxin-antitoxin activities before minting narrower P4 gop-beta-cII mechanism traits.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Rousset et al. support a canonical P4 gop-beta-cII system that protects against lambda and P1, and DefenseFinder represents Rst_gop_beta_cll as a required beta/cll/gop three-profile model. This first system-level record leaves natural host breadth, profile-to-gene mapping, the direct phage trigger, and the gop, beta, or cII effector logic unresolved.",
        "evidence": [
          {
            "reference": "DOI:10.1016/j.chom.2022.02.018",
            "snippet": "The well-characterized P4 satellite (NC_001609) carries at this position the non-essential genes gop, \u03b2, and cII, with gop and \u03b2 likely acting as a toxin-antitoxin pair",
            "notes": "Rousset et al. describe the canonical P4 satellite gop, beta, and cII locus before testing it for anti-phage activity."
          },
          {
            "reference": "DOI:10.1016/j.chom.2022.02.018",
            "snippet": "We report that gop-\u03b2-cII forms an anti-phage system that protects against \u03bb and P1.",
            "notes": "Rousset et al. directly identify gop-beta-cII as an anti-phage system that protects against lambda and P1."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "snippet": "Rst_gop_beta_cll\tRst_gop_beta_cll\t3\t3\tRst_gop_beta_cll__beta, Rst_gop_beta_cll__cll, Rst_gop_beta_cll__gop\t\t\t",
            "notes": "The DefenseFinder rules table models Rst_gop_beta_cll as a three-profile system requiring beta, cll, and gop profiles."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| Rst_gop_beta_cll__beta                           | Rst_gop_beta_cll__beta                           | Rst_gop_beta_cll       | Custom                  | 20     |\n| Rst_gop_beta_cll__cll                            | Rst_gop_beta_cll__cll                            | Rst_gop_beta_cll       | Custom                  | 20     |\n| Rst_gop_beta_cll__gop                            | Rst_gop_beta_cll__gop                            | Rst_gop_beta_cll       | Custom                  | 20     |",
            "notes": "The DefenseFinder HMM inventory records custom beta, cll, and gop profiles under the Rst_gop_beta_cll system namespace."
          }
        ],
        "attaches_to": [
          "causal_graphs#rst_gop_beta_cll_locus_restricts_lambda_p1"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-26"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-26T08:43:24Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Rst gop-beta-cII system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v253.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-26T08:53:24Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed Rst gop-beta-cII system during canonical-example issue 444 enforcement and left canonical_examples empty because the sources support a cloned P4 gop-beta-cII locus tested in Escherichia coli and a DefenseFinder system model, but not a direct native microbial isolate exemplar with experimentally verified Rst_gop_beta_cll activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000401",
    "label": "Rst_HelicaseDUF2290 system",
    "definition": "A phage defense system in which an organism possesses a two-protein Rst_HelicaseDUF2290 locus represented by DefenseFinder as a two-profile model requiring Rst_HelicaseDUF2290__DUF2290 and Rst_HelicaseDUF2290__Helicase and experimentally linked to T7 protection when expressed in Escherichia coli.",
    "definition_source": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/223cf269/content/3.defense-systems/rst_helicaseduf2290.md",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "Rst_HelicaseDUF2290",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      },
      {
        "synonym_text": "Rst_HelicaseDUF2290__DUF2290",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "Rst_HelicaseDUF2290__DUF2290_Pers",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "Rst_HelicaseDUF2290__Helicase",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "DUF2290_Pers",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/223cf269/content/3.defense-systems/rst_helicaseduf2290.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1016/j.chom.2022.02.018",
        "snippet": "two systems that specifically inhibit the growth of phage T7: an ATP-dependent helicase associated with a DUF2290 protein and a HAD-like hydrolase associated with a transmembrane protein",
        "notes": "Rousset et al. experimentally linked an ATP-dependent helicase plus DUF2290 protein pair to specific inhibition of phage T7 growth."
      },
      {
        "reference": "DOI:10.1016/j.chom.2022.02.018",
        "snippet": "Phage resistance heatmap of the validated defense systems shows the mean fold resistance of three independent replicates against a panel of eight phages",
        "notes": "The Figure 2 legend frames the cloned P4-hotspot hits, including the ATP-dependent helicase plus DUF2290 system, as validated defense systems in a replicated phage-resistance heatmap."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/223cf269/content/3.defense-systems/rst_helicaseduf2290.md",
        "snippet": "The Rst_HelicaseDUF2290 system was discovered during a screen for defense systems targeted at hotspots of antiphage activity in phages and phage-satellites. It is composed of 2 proteins, a helicase and a protein with the domain DUF2290.",
        "notes": "The pinned DefenseFinder wiki page names Rst_HelicaseDUF2290 as a two-protein helicase/DUF2290 system found in antiviral hotspots of phages and phage satellites."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/223cf269/content/3.defense-systems/rst_helicaseduf2290.md",
        "snippet": "As far as we are aware, the molecular mechanism is unknown.",
        "notes": "The pinned DefenseFinder wiki page leaves the Rst_HelicaseDUF2290 molecular mechanism unresolved."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/223cf269/content/3.defense-systems/rst_helicaseduf2290.md",
        "snippet": "The Rst_HelicaseDUF2290 is composed of 2 proteins: Helicase and DUF2290.",
        "notes": "The pinned DefenseFinder wiki page describes Rst_HelicaseDUF2290 as a two-component Helicase/DUF2290 system."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/223cf269/content/3.defense-systems/rst_helicaseduf2290.md",
        "snippet": "The Rst_HelicaseDUF2290 system in *Klebsiella quasipneumoniae* (GCF_003020825.1, NZ_CP023478) is composed of 2 proteins Helicase (WP_046623504.1) DUF2290_Pers (WP_046623503.1)",
        "notes": "The DefenseFinder wiki illustrates a predicted two-protein Rst_HelicaseDUF2290 locus in RefSeq assembly GCF_003020825.1 on NZ_CP023478."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/223cf269/content/3.defense-systems/rst_helicaseduf2290.md",
        "snippet": "Rousset_2022[<a href='https://doi.org/10.1016/j.chom.2022.02.018'>Rousset et al., 2022</a>] --> Origin_0\n    Origin_0[Klebsiella pneumoniae P4 loci \n<a href='https://ncbi.nlm.nih.gov/protein/WP_046623503.1'>WP_046623503.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_046623504.1'>WP_046623504.1</a>] --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> T7",
        "notes": "The DefenseFinder experimental-validation diagram links Rousset et al. to a Klebsiella pneumoniae P4-locus source expressed in Escherichia coli against T7."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/223cf269/content/3.defense-systems/rst_helicaseduf2290.md",
        "snippet": "subgraph Title4[Protects against]\n        T7",
        "notes": "The DefenseFinder experimental-validation diagram lists T7 in the Rst_HelicaseDUF2290 protects-against subgraph."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "Rst_HelicaseDUF2290 | 10\\.1101/2021\\.01\\.21\\.427644 | Prophage-encoded hotspots of bacterial immune systems",
        "notes": "The DefenseFinder article registry maps the named Rst_HelicaseDUF2290 system to the Rousset et al. preprint."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "Rst_HelicaseDUF2290\tRst_HelicaseDUF2290\t2\t2\tRst_HelicaseDUF2290__DUF2290, Rst_HelicaseDUF2290__Helicase\t\t\t",
        "notes": "The DefenseFinder rules table models Rst_HelicaseDUF2290 as a two-profile system requiring Rst_HelicaseDUF2290__DUF2290 and Rst_HelicaseDUF2290__Helicase."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| Rst_HelicaseDUF2290__DUF2290                     | Rst_HelicaseDUF2290__DUF2290___DUF2290           | Rst_HelicaseDUF2290    | PF10053.11              | 25     |\n| Rst_HelicaseDUF2290__DUF2290_Pers                | Rst_HelicaseDUF2290__DUF2290_Pers___DUF2290_Pers | Rst_HelicaseDUF2290    | Custom                  | 20     |\n| Rst_HelicaseDUF2290__Helicase                    | Rst_HelicaseDUF2290__Helicase___Helicase         | Rst_HelicaseDUF2290    | Custom                  | 20     |",
        "notes": "The DefenseFinder HMM inventory records DUF2290, DUF2290_Pers, and Helicase profiles under Rst_HelicaseDUF2290."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "rst_helicaseduf2290_locus_restricts_t7",
        "title": "Rst_HelicaseDUF2290 loci restrict T7",
        "description": "Conservative system-level sketch linking the named Rst_HelicaseDUF2290 two-gene locus model to T7 phage resistance.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Rst_HelicaseDUF2290 as a named DefenseFinder two-profile phage-defense system while leaving native host breadth, accession-level DUF2290 and helicase roles, the extra DUF2290_Pers profile, and the mechanism of T7 restriction unresolved.",
        "nodes": [
          {
            "node_id": "rst_helicaseduf2290_locus",
            "label": "Rst_HelicaseDUF2290 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A two-gene helicase/DUF2290 phage-defense locus represented by the DefenseFinder Rst_HelicaseDUF2290 profiles."
          },
          {
            "node_id": "t7_phage_resistance",
            "label": "T7 phage resistance",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Resistance against phage T7 in a host expressing an Rst_HelicaseDUF2290 locus."
          },
          {
            "node_id": "rst_helicaseduf2290_system_trait",
            "label": "Rst_HelicaseDUF2290 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000401",
            "description": "Possession of a genome-encoded Rst_HelicaseDUF2290 phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "rst_helicaseduf2290_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "t7_phage_resistance",
            "description": "Rousset et al. linked an ATP-dependent helicase plus DUF2290 locus to T7 restriction, and DefenseFinder models Rst_HelicaseDUF2290 as a two-profile system.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.chom.2022.02.018",
                "snippet": "two systems that specifically inhibit the growth of phage T7: an ATP-dependent helicase associated with a DUF2290 protein and a HAD-like hydrolase associated with a transmembrane protein",
                "notes": "Rousset et al. experimentally linked an ATP-dependent helicase plus DUF2290 protein pair to specific inhibition of phage T7 growth."
              },
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/223cf269/content/3.defense-systems/rst_helicaseduf2290.md",
                "snippet": "The Rst_HelicaseDUF2290 system was discovered during a screen for defense systems targeted at hotspots of antiphage activity in phages and phage-satellites. It is composed of 2 proteins, a helicase and a protein with the domain DUF2290.",
                "notes": "The pinned DefenseFinder wiki page names Rst_HelicaseDUF2290 as a two-protein helicase/DUF2290 system found in antiviral hotspots of phages and phage satellites."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "Rst_HelicaseDUF2290\tRst_HelicaseDUF2290\t2\t2\tRst_HelicaseDUF2290__DUF2290, Rst_HelicaseDUF2290__Helicase\t\t\t",
                "notes": "The DefenseFinder rules table models Rst_HelicaseDUF2290 as a two-profile system requiring Rst_HelicaseDUF2290__DUF2290 and Rst_HelicaseDUF2290__Helicase."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| Rst_HelicaseDUF2290__DUF2290                     | Rst_HelicaseDUF2290__DUF2290___DUF2290           | Rst_HelicaseDUF2290    | PF10053.11              | 25     |\n| Rst_HelicaseDUF2290__DUF2290_Pers                | Rst_HelicaseDUF2290__DUF2290_Pers___DUF2290_Pers | Rst_HelicaseDUF2290    | Custom                  | 20     |\n| Rst_HelicaseDUF2290__Helicase                    | Rst_HelicaseDUF2290__Helicase___Helicase         | Rst_HelicaseDUF2290    | Custom                  | 20     |",
                "notes": "The DefenseFinder HMM inventory records DUF2290, DUF2290_Pers, and Helicase profiles under Rst_HelicaseDUF2290."
              }
            ]
          },
          {
            "subject": "t7_phage_resistance",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "rst_helicaseduf2290_system_trait",
            "description": "Rst_HelicaseDUF2290-linked T7 resistance realizes the Rst_HelicaseDUF2290 system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.chom.2022.02.018",
                "snippet": "two systems that specifically inhibit the growth of phage T7: an ATP-dependent helicase associated with a DUF2290 protein and a HAD-like hydrolase associated with a transmembrane protein",
                "notes": "Rousset et al. experimentally linked an ATP-dependent helicase plus DUF2290 protein pair to specific inhibition of phage T7 growth."
              },
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/223cf269/content/3.defense-systems/rst_helicaseduf2290.md",
                "snippet": "Rousset_2022[<a href='https://doi.org/10.1016/j.chom.2022.02.018'>Rousset et al., 2022</a>] --> Origin_0\n    Origin_0[Klebsiella pneumoniae P4 loci \n<a href='https://ncbi.nlm.nih.gov/protein/WP_046623503.1'>WP_046623503.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_046623504.1'>WP_046623504.1</a>] --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> T7",
                "notes": "The DefenseFinder experimental-validation diagram links Rousset et al. to a Klebsiella pneumoniae P4-locus source expressed in Escherichia coli against T7."
              },
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/223cf269/content/3.defense-systems/rst_helicaseduf2290.md",
                "snippet": "subgraph Title4[Protects against]\n        T7",
                "notes": "The DefenseFinder experimental-validation diagram lists T7 in the Rst_HelicaseDUF2290 protects-against subgraph."
              }
            ]
          },
          {
            "subject": "rst_helicaseduf2290_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Rst_HelicaseDUF2290 system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.chom.2022.02.018",
                "snippet": "Phage resistance heatmap of the validated defense systems shows the mean fold resistance of three independent replicates against a panel of eight phages",
                "notes": "The Figure 2 legend frames the cloned P4-hotspot hits, including the ATP-dependent helicase plus DUF2290 system, as validated defense systems in a replicated phage-resistance heatmap."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Rst_HelicaseDUF2290 | 10\\.1101/2021\\.01\\.21\\.427644 | Prophage-encoded hotspots of bacterial immune systems",
                "notes": "The DefenseFinder article registry maps the named Rst_HelicaseDUF2290 system to the Rousset et al. preprint."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "rst-helicaseduf2290-host-mechanism-gap",
        "prompt": "Resolve Rst_HelicaseDUF2290 native host breadth, accession-level DUF2290/helicase roles, the DUF2290_Pers profile relationship, and the mechanism of T7 restriction before minting narrower Rst_HelicaseDUF2290 mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Rousset et al. support a two-gene ATP-dependent helicase plus DUF2290 P4-hotspot system that inhibits T7 growth, and DefenseFinder represents Rst_HelicaseDUF2290 as a required two-profile model. This first system-level record leaves native host breadth, profile-to-gene mapping, the role of the extra DUF2290_Pers HMM profile, the molecular activities of the DUF2290 and helicase components, and the T7 restriction mechanism unresolved.",
        "evidence": [
          {
            "reference": "DOI:10.1016/j.chom.2022.02.018",
            "snippet": "two systems that specifically inhibit the growth of phage T7: an ATP-dependent helicase associated with a DUF2290 protein and a HAD-like hydrolase associated with a transmembrane protein",
            "notes": "Rousset et al. experimentally linked an ATP-dependent helicase plus DUF2290 protein pair to specific inhibition of phage T7 growth."
          },
          {
            "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/223cf269/content/3.defense-systems/rst_helicaseduf2290.md",
            "snippet": "As far as we are aware, the molecular mechanism is unknown.",
            "notes": "The pinned DefenseFinder wiki page leaves the Rst_HelicaseDUF2290 molecular mechanism unresolved."
          },
          {
            "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/223cf269/content/3.defense-systems/rst_helicaseduf2290.md",
            "snippet": "The Rst_HelicaseDUF2290 is composed of 2 proteins: Helicase and DUF2290.",
            "notes": "The pinned DefenseFinder wiki page describes Rst_HelicaseDUF2290 as a two-component Helicase/DUF2290 system."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "snippet": "Rst_HelicaseDUF2290\tRst_HelicaseDUF2290\t2\t2\tRst_HelicaseDUF2290__DUF2290, Rst_HelicaseDUF2290__Helicase\t\t\t",
            "notes": "The DefenseFinder rules table models Rst_HelicaseDUF2290 as a two-profile system requiring Rst_HelicaseDUF2290__DUF2290 and Rst_HelicaseDUF2290__Helicase."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| Rst_HelicaseDUF2290__DUF2290                     | Rst_HelicaseDUF2290__DUF2290___DUF2290           | Rst_HelicaseDUF2290    | PF10053.11              | 25     |\n| Rst_HelicaseDUF2290__DUF2290_Pers                | Rst_HelicaseDUF2290__DUF2290_Pers___DUF2290_Pers | Rst_HelicaseDUF2290    | Custom                  | 20     |\n| Rst_HelicaseDUF2290__Helicase                    | Rst_HelicaseDUF2290__Helicase___Helicase         | Rst_HelicaseDUF2290    | Custom                  | 20     |",
            "notes": "The DefenseFinder HMM inventory records DUF2290, DUF2290_Pers, and Helicase profiles under Rst_HelicaseDUF2290."
          }
        ],
        "attaches_to": [
          "causal_graphs#rst_helicaseduf2290_locus_restricts_t7"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-27"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-27T04:03:20Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Rst_HelicaseDUF2290 system as a DOI/stable-URL-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v278.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-27T04:03:21Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed Rst_HelicaseDUF2290 during canonical-example issue 444 enforcement and left canonical_examples empty because the sources support a cloned P4-hotspot helicase/DUF2290 locus assayed in Escherichia coli and a DefenseFinder RefSeq model example, but not a direct native microbial host exemplar with experimentally verified Rst_HelicaseDUF2290 activity. No paid research was used.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-27T06:09:38Z",
        "curator": "codex",
        "action": "EDIT",
        "changes": "Corrected the Rousset et al. replicated phage-resistance heatmap evidence for the P4-hotspot Rst_HelicaseDUF2290 system from the Figure 5 P2 median-fold-resistance legend to the Figure 2 P4 mean-fold-resistance legend.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000402",
    "label": "Rst_Hydrolase-3Tm system",
    "definition": "A phage defense system in which an organism possesses a two-protein Rst_Hydrolase-3Tm locus represented by DefenseFinder as a two-profile Rst_Hydrolase-Tm model requiring Rst_Hydrolase-Tm__Hydrolase and Rst_Hydrolase-Tm__Hydrolase-Tm and experimentally linked to T7 protection when expressed in Escherichia coli.",
    "definition_source": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/223cf269/content/3.defense-systems/rst_hydrolase-3tm.md",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "Rst_Hydrolase-3Tm",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      },
      {
        "synonym_text": "Rst_Hydrolase-Tm",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv"
      },
      {
        "synonym_text": "Rst_Hydrolase-Tm__Hydrolase",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "Rst_Hydrolase-Tm__Hydrolase-Tm",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "Hydrolase-Tm",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/223cf269/content/3.defense-systems/rst_hydrolase-3tm.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1016/j.chom.2022.02.018",
        "snippet": "two systems that specifically inhibit the growth of phage T7: an ATP-dependent helicase associated with a DUF2290 protein and a HAD-like hydrolase associated with a transmembrane protein",
        "notes": "Rousset et al. experimentally linked a HAD-like hydrolase plus transmembrane-protein pair to specific inhibition of phage T7 growth."
      },
      {
        "reference": "DOI:10.1016/j.chom.2022.02.018",
        "snippet": "Phage resistance heatmap of the validated defense systems shows the mean fold resistance of three independent replicates against a panel of eight phages",
        "notes": "The Figure 2 legend frames the cloned P4-hotspot hits, including the hydrolase plus transmembrane-protein system, as validated defense systems in a replicated phage-resistance heatmap."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/223cf269/content/3.defense-systems/rst_hydrolase-3tm.md",
        "snippet": "The Rst_Hydrolase-3Tm is composed of 2 proteins: Hydrolase and Hydrolase-Tm.",
        "notes": "The pinned DefenseFinder wiki page names Rst_Hydrolase-3Tm as a two-component Hydrolase/Hydrolase-Tm system."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/223cf269/content/3.defense-systems/rst_hydrolase-3tm.md",
        "snippet": "The Rst_Hydrolase-Tm system in *Pectobacterium versatile* (GCF_003031305.1, NZ_CP024842) is composed of 2 proteins Hydrolase (WP_107333258.1) Hydrolase-Tm (WP_107333259.1)",
        "notes": "The DefenseFinder wiki illustrates a predicted two-protein Rst_Hydrolase-Tm locus in RefSeq assembly GCF_003031305.1 on NZ_CP024842."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/223cf269/content/3.defense-systems/rst_hydrolase-3tm.md",
        "snippet": "Rousset_2022[<a href='https://doi.org/10.1016/j.chom.2022.02.018'>Rousset et al., 2022</a>] --> Origin_0\n    Origin_0[Escherichia coli P4 loci \n<a href='https://ncbi.nlm.nih.gov/protein/WP_000754434.1'>WP_000754434.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_001401335.1'>WP_001401335.1</a>] --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> T7",
        "notes": "The DefenseFinder experimental-validation diagram links Rousset et al. to an Escherichia coli P4-locus source expressed in Escherichia coli against T7."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/223cf269/content/3.defense-systems/rst_hydrolase-3tm.md",
        "snippet": "subgraph Title4[Protects against]\n        T7",
        "notes": "The DefenseFinder experimental-validation diagram lists T7 in the Rst_Hydrolase-3Tm protects-against subgraph."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "Rst_Hydrolase-3Tm | 10\\.1101/2021\\.01\\.21\\.427644 | Prophage-encoded hotspots of bacterial immune systems",
        "notes": "The DefenseFinder article registry maps the named Rst_Hydrolase-3Tm system to the Rousset et al. preprint."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "Rst_Hydrolase-3Tm\tRst_Hydrolase-Tm\t2\t2\tRst_Hydrolase-Tm__Hydrolase, Rst_Hydrolase-Tm__Hydrolase-Tm\t\t\t",
        "notes": "The DefenseFinder rules table maps Rst_Hydrolase-3Tm to a two-profile Rst_Hydrolase-Tm model requiring Hydrolase and Hydrolase-Tm profiles."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| Rst_Hydrolase-Tm__Hydrolase                      | Rst_Hydrolase-Tm__Hydrolase                      | Rst_Hydrolase-Tm       | Custom                  | 20     |\n| Rst_Hydrolase-Tm__Hydrolase-Tm                   | Rst_Hydrolase-Tm__Hydrolase-Tm                   | Rst_Hydrolase-Tm       | Custom                  | 20     |",
        "notes": "The DefenseFinder HMM inventory records Hydrolase and Hydrolase-Tm profiles under the normalized Rst_Hydrolase-Tm system namespace."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "rst_hydrolase_3tm_locus_restricts_t7",
        "title": "Rst_Hydrolase-3Tm loci restrict T7",
        "description": "Conservative system-level sketch linking a named Rst_Hydrolase-3Tm two-gene locus model to T7 phage resistance.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Rst_Hydrolase-3Tm as a named DefenseFinder two-profile phage-defense system while leaving native host breadth, the exact Rst_Hydrolase-3Tm-to-Rst_Hydrolase-Tm naming relationship, Hydrolase and Hydrolase-Tm molecular roles, and the mechanism of T7 restriction unresolved.",
        "nodes": [
          {
            "node_id": "rst_hydrolase_3tm_locus",
            "label": "Rst_Hydrolase-3Tm locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A two-gene hydrolase/transmembrane phage-defense locus represented by the DefenseFinder Rst_Hydrolase-Tm profiles."
          },
          {
            "node_id": "t7_phage_resistance",
            "label": "T7 phage resistance",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Resistance against phage T7 in a host expressing an Rst_Hydrolase-3Tm locus."
          },
          {
            "node_id": "rst_hydrolase_3tm_system_trait",
            "label": "Rst_Hydrolase-3Tm system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000402",
            "description": "Possession of a genome-encoded Rst_Hydrolase-3Tm phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "rst_hydrolase_3tm_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "t7_phage_resistance",
            "description": "Rousset et al. linked a HAD-like hydrolase plus transmembrane-protein locus to T7 restriction, and DefenseFinder models Rst_Hydrolase-3Tm as a two-profile Rst_Hydrolase-Tm system.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.chom.2022.02.018",
                "snippet": "two systems that specifically inhibit the growth of phage T7: an ATP-dependent helicase associated with a DUF2290 protein and a HAD-like hydrolase associated with a transmembrane protein",
                "notes": "Rousset et al. experimentally linked a HAD-like hydrolase plus transmembrane-protein pair to specific inhibition of phage T7 growth."
              },
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/223cf269/content/3.defense-systems/rst_hydrolase-3tm.md",
                "snippet": "The Rst_Hydrolase-3Tm is composed of 2 proteins: Hydrolase and Hydrolase-Tm.",
                "notes": "The pinned DefenseFinder wiki page names Rst_Hydrolase-3Tm as a two-component Hydrolase/Hydrolase-Tm system."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "Rst_Hydrolase-3Tm\tRst_Hydrolase-Tm\t2\t2\tRst_Hydrolase-Tm__Hydrolase, Rst_Hydrolase-Tm__Hydrolase-Tm\t\t\t",
                "notes": "The DefenseFinder rules table maps Rst_Hydrolase-3Tm to a two-profile Rst_Hydrolase-Tm model requiring Hydrolase and Hydrolase-Tm profiles."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| Rst_Hydrolase-Tm__Hydrolase                      | Rst_Hydrolase-Tm__Hydrolase                      | Rst_Hydrolase-Tm       | Custom                  | 20     |\n| Rst_Hydrolase-Tm__Hydrolase-Tm                   | Rst_Hydrolase-Tm__Hydrolase-Tm                   | Rst_Hydrolase-Tm       | Custom                  | 20     |",
                "notes": "The DefenseFinder HMM inventory records Hydrolase and Hydrolase-Tm profiles under the normalized Rst_Hydrolase-Tm system namespace."
              }
            ]
          },
          {
            "subject": "t7_phage_resistance",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "rst_hydrolase_3tm_system_trait",
            "description": "Rst_Hydrolase-3Tm-linked T7 resistance realizes the Rst_Hydrolase-3Tm system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.chom.2022.02.018",
                "snippet": "two systems that specifically inhibit the growth of phage T7: an ATP-dependent helicase associated with a DUF2290 protein and a HAD-like hydrolase associated with a transmembrane protein",
                "notes": "Rousset et al. experimentally linked a HAD-like hydrolase plus transmembrane-protein pair to specific inhibition of phage T7 growth."
              },
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/223cf269/content/3.defense-systems/rst_hydrolase-3tm.md",
                "snippet": "Rousset_2022[<a href='https://doi.org/10.1016/j.chom.2022.02.018'>Rousset et al., 2022</a>] --> Origin_0\n    Origin_0[Escherichia coli P4 loci \n<a href='https://ncbi.nlm.nih.gov/protein/WP_000754434.1'>WP_000754434.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_001401335.1'>WP_001401335.1</a>] --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> T7",
                "notes": "The DefenseFinder experimental-validation diagram links Rousset et al. to an Escherichia coli P4-locus source expressed in Escherichia coli against T7."
              },
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/223cf269/content/3.defense-systems/rst_hydrolase-3tm.md",
                "snippet": "subgraph Title4[Protects against]\n        T7",
                "notes": "The DefenseFinder experimental-validation diagram lists T7 in the Rst_Hydrolase-3Tm protects-against subgraph."
              }
            ]
          },
          {
            "subject": "rst_hydrolase_3tm_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Rst_Hydrolase-3Tm system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.chom.2022.02.018",
                "snippet": "Phage resistance heatmap of the validated defense systems shows the mean fold resistance of three independent replicates against a panel of eight phages",
                "notes": "The Figure 2 legend frames the cloned P4-hotspot hits, including the hydrolase plus transmembrane-protein system, as validated defense systems in a replicated phage-resistance heatmap."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Rst_Hydrolase-3Tm | 10\\.1101/2021\\.01\\.21\\.427644 | Prophage-encoded hotspots of bacterial immune systems",
                "notes": "The DefenseFinder article registry maps the named Rst_Hydrolase-3Tm system to the Rousset et al. preprint."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "rst-hydrolase-3tm-host-mechanism-gap",
        "prompt": "Resolve Rst_Hydrolase-3Tm native host breadth, the Rst_Hydrolase-3Tm and Rst_Hydrolase-Tm namespace relationship, accession-level Hydrolase/Hydrolase-Tm roles, and the mechanism of T7 restriction before minting narrower Rst_Hydrolase-3Tm mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Rousset et al. support a two-gene HAD-like hydrolase plus transmembrane-protein P4-hotspot system that inhibits T7 growth, and DefenseFinder maps Rst_Hydrolase-3Tm to a required two-profile Rst_Hydrolase-Tm model. This first system-level record leaves native host breadth, profile-to-gene mapping, the model-namespace mismatch, the molecular activities of the Hydrolase and Hydrolase-Tm components, and the T7 restriction mechanism unresolved.",
        "evidence": [
          {
            "reference": "DOI:10.1016/j.chom.2022.02.018",
            "snippet": "two systems that specifically inhibit the growth of phage T7: an ATP-dependent helicase associated with a DUF2290 protein and a HAD-like hydrolase associated with a transmembrane protein",
            "notes": "Rousset et al. experimentally linked a HAD-like hydrolase plus transmembrane-protein pair to specific inhibition of phage T7 growth."
          },
          {
            "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/223cf269/content/3.defense-systems/rst_hydrolase-3tm.md",
            "snippet": "The Rst_Hydrolase-3Tm is composed of 2 proteins: Hydrolase and Hydrolase-Tm.",
            "notes": "The pinned DefenseFinder wiki page names Rst_Hydrolase-3Tm as a two-component Hydrolase/Hydrolase-Tm system."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "snippet": "Rst_Hydrolase-3Tm\tRst_Hydrolase-Tm\t2\t2\tRst_Hydrolase-Tm__Hydrolase, Rst_Hydrolase-Tm__Hydrolase-Tm\t\t\t",
            "notes": "The DefenseFinder rules table maps Rst_Hydrolase-3Tm to a two-profile Rst_Hydrolase-Tm model requiring Hydrolase and Hydrolase-Tm profiles."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| Rst_Hydrolase-Tm__Hydrolase                      | Rst_Hydrolase-Tm__Hydrolase                      | Rst_Hydrolase-Tm       | Custom                  | 20     |\n| Rst_Hydrolase-Tm__Hydrolase-Tm                   | Rst_Hydrolase-Tm__Hydrolase-Tm                   | Rst_Hydrolase-Tm       | Custom                  | 20     |",
            "notes": "The DefenseFinder HMM inventory records Hydrolase and Hydrolase-Tm profiles under the normalized Rst_Hydrolase-Tm system namespace."
          }
        ],
        "attaches_to": [
          "causal_graphs#rst_hydrolase_3tm_locus_restricts_t7"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-27"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-27T05:04:25Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Rst_Hydrolase-3Tm system as a DOI/stable-URL-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v279.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-27T05:04:26Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed Rst_Hydrolase-3Tm during canonical-example issue 444 enforcement and left canonical_examples empty because the sources support a cloned P4-hotspot Hydrolase/Hydrolase-Tm locus assayed in Escherichia coli and a DefenseFinder RefSeq model example, but not a direct native microbial host exemplar with experimentally verified Rst_Hydrolase-3Tm activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000403",
    "label": "Rst_RT-nitrilase-Tm system",
    "definition": "A phage defense system in which an organism possesses a two-protein Rst_RT-nitrilase-Tm locus represented by DefenseFinder as a two-profile Rst_RT-Tm model requiring Rst_RT-Tm__RT and Rst_RT-Tm__RT-Tm and experimentally linked to AL505_P2 protection when expressed in Escherichia coli.",
    "definition_source": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/rst_rt-nitrilase-tm.md",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "Rst_RT-nitrilase-Tm",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      },
      {
        "synonym_text": "RT-nitrilase-Tm",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/rst_rt-nitrilase-tm.md"
      },
      {
        "synonym_text": "UG5-large",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/rst_rt-nitrilase-tm.md"
      },
      {
        "synonym_text": "Rst_RT-Tm",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv"
      },
      {
        "synonym_text": "Rst_RT-Tm__RT",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "Rst_RT-Tm__RT2",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "Rst_RT-Tm__RT-Tm",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "RT-Tm",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/rst_rt-nitrilase-tm.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1016/j.chom.2022.02.018",
        "snippet": "with a C-terminal nitrilase domain (Table S3) that is associated with a transmembrane effector",
        "notes": "Rousset et al. described a validated P4-hotspot system containing a group-5 reverse transcriptase with a C-terminal nitrilase domain associated with a transmembrane effector."
      },
      {
        "reference": "DOI:10.1016/j.chom.2022.02.018",
        "snippet": "Phage resistance heatmap of the validated defense systems shows the mean fold resistance of three independent replicates against a panel of eight phages",
        "notes": "The Figure 2 legend frames the cloned P4-hotspot hits, including the RT-nitrilase plus one-TM system, as validated defense systems in a replicated phage-resistance heatmap."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/rst_rt-nitrilase-tm.md",
        "snippet": "RT-nitrilase-Tm (also named UG5-large) is a two-gene defense system. It was discovered from P4-like satellites in *E. coli* genomes :ref{doi=10.1016/j.chom.2022.02.018} :ref{doi=10.1093/nar/gkac467}. Its antiphage activity was shown in *E. coli* against phage AL505_P2 (Myoviridae).",
        "notes": "The pinned DefenseFinder wiki page names RT-nitrilase-Tm, also called UG5-large, as a two-gene system and records AL505_P2 antiphage activity in Escherichia coli."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/rst_rt-nitrilase-tm.md",
        "snippet": "The first protein is a reverse transcriptase (RT) fussed with C-N hydrolase domain (nitrilase); the second protein is transmembrane protein :ref{doi=10.1093/nar/gkac467}.",
        "notes": "The pinned DefenseFinder wiki page describes the reverse-transcriptase/nitrilase plus transmembrane-protein architecture."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/rst_rt-nitrilase-tm.md",
        "snippet": "The Rst_RT-nitrilase-Tm is composed of 2 proteins: RT and RT-Tm.",
        "notes": "The pinned DefenseFinder wiki page maps the Rst-prefixed name to a two-component RT/RT-Tm structure."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/rst_rt-nitrilase-tm.md",
        "snippet": "The Rst_RT-Tm system in *Morganella morganii* (GCF_900478755.1, NZ_LS483498) is composed of 2 proteins RT (WP_061057569.1) RT-Tm (WP_004234654.1)",
        "notes": "The DefenseFinder wiki illustrates a predicted two-protein Rst_RT-Tm locus in RefSeq assembly GCF_900478755.1 on NZ_LS483498."
      },
      {
        "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/rst_rt-nitrilase-tm.md",
        "snippet": "Expressed_0[Escherichia coli] ----> Al505_P2",
        "notes": "The DefenseFinder experimental-validation diagram links Escherichia coli expression of the Rst_RT-nitrilase-Tm system to protection against AL505_P2."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "Rst_RT-nitrilase-Tm | 10\\.1101/2021\\.01\\.21\\.427644 | Prophage-encoded hotspots of bacterial immune systems",
        "notes": "The DefenseFinder article registry maps the named Rst_RT-nitrilase-Tm system to the Rousset et al. preprint."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "Rst_RT-nitrilase-Tm\tRst_RT-Tm\t2\t2\tRst_RT-Tm__RT, Rst_RT-Tm__RT-Tm\t\t\t",
        "notes": "The DefenseFinder rules table maps Rst_RT-nitrilase-Tm to a two-profile Rst_RT-Tm model requiring RT and RT-Tm profiles."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| Rst_RT-Tm__RT                                    | Rst_RT-Tm__RT                                    | Rst_RT-Tm              | Custom                  | 500    |\n| Rst_RT-Tm__RT2                                   |                                                  | Rst_RT-Tm              | Custom                  | 100    |\n| Rst_RT-Tm__RT-Tm                                 | Rst_RT-Tm__RT-Tm                                 | Rst_RT-Tm              | Custom                  | 100    |",
        "notes": "The DefenseFinder HMM inventory records the RT, alternate RT2, and RT-Tm profiles under the normalized Rst_RT-Tm system namespace."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "rst_rt_nitrilase_tm_locus_restricts_al505_p2",
        "title": "Rst_RT-nitrilase-Tm loci restrict AL505_P2",
        "description": "Conservative system-level sketch linking a named Rst_RT-nitrilase-Tm two-gene locus model to AL505_P2 phage resistance.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Rst_RT-nitrilase-Tm as a named DefenseFinder two-profile phage-defense system while leaving native host breadth, the exact Rst_RT-nitrilase-Tm-to-Rst_RT-Tm naming relationship, RT and RT-Tm molecular roles, the relationship to UG5-large systems, and the mechanism of AL505_P2 restriction unresolved.",
        "nodes": [
          {
            "node_id": "rst_rt_nitrilase_tm_locus",
            "label": "Rst_RT-nitrilase-Tm locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A two-gene reverse-transcriptase/nitrilase plus transmembrane-protein phage-defense locus represented by the DefenseFinder Rst_RT-Tm profiles."
          },
          {
            "node_id": "al505_p2_phage_resistance",
            "label": "AL505_P2 phage resistance",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Resistance against phage AL505_P2 in a host expressing an Rst_RT-nitrilase-Tm locus."
          },
          {
            "node_id": "rst_rt_nitrilase_tm_system_trait",
            "label": "Rst_RT-nitrilase-Tm system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000403",
            "description": "Possession of a genome-encoded Rst_RT-nitrilase-Tm phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "rst_rt_nitrilase_tm_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "al505_p2_phage_resistance",
            "description": "Rousset et al. linked a group-5 reverse transcriptase/nitrilase plus transmembrane effector locus to phage resistance, and DefenseFinder models Rst_RT-nitrilase-Tm as a two-profile Rst_RT-Tm system.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.chom.2022.02.018",
                "snippet": "with a C-terminal nitrilase domain (Table S3) that is associated with a transmembrane effector",
                "notes": "Rousset et al. described a validated P4-hotspot system containing a group-5 reverse transcriptase with a C-terminal nitrilase domain associated with a transmembrane effector."
              },
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/rst_rt-nitrilase-tm.md",
                "snippet": "The first protein is a reverse transcriptase (RT) fussed with C-N hydrolase domain (nitrilase); the second protein is transmembrane protein :ref{doi=10.1093/nar/gkac467}.",
                "notes": "The pinned DefenseFinder wiki page describes the reverse-transcriptase/nitrilase plus transmembrane-protein architecture."
              },
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/rst_rt-nitrilase-tm.md",
                "snippet": "The Rst_RT-nitrilase-Tm is composed of 2 proteins: RT and RT-Tm.",
                "notes": "The pinned DefenseFinder wiki page maps the Rst-prefixed name to a two-component RT/RT-Tm structure."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "Rst_RT-nitrilase-Tm\tRst_RT-Tm\t2\t2\tRst_RT-Tm__RT, Rst_RT-Tm__RT-Tm\t\t\t",
                "notes": "The DefenseFinder rules table maps Rst_RT-nitrilase-Tm to a two-profile Rst_RT-Tm model requiring RT and RT-Tm profiles."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| Rst_RT-Tm__RT                                    | Rst_RT-Tm__RT                                    | Rst_RT-Tm              | Custom                  | 500    |\n| Rst_RT-Tm__RT2                                   |                                                  | Rst_RT-Tm              | Custom                  | 100    |\n| Rst_RT-Tm__RT-Tm                                 | Rst_RT-Tm__RT-Tm                                 | Rst_RT-Tm              | Custom                  | 100    |",
                "notes": "The DefenseFinder HMM inventory records the RT, alternate RT2, and RT-Tm profiles under the normalized Rst_RT-Tm system namespace."
              }
            ]
          },
          {
            "subject": "al505_p2_phage_resistance",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "rst_rt_nitrilase_tm_system_trait",
            "description": "Rst_RT-nitrilase-Tm-linked AL505_P2 resistance realizes the Rst_RT-nitrilase-Tm system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.chom.2022.02.018",
                "snippet": "Phage resistance heatmap of the validated defense systems shows the mean fold resistance of three independent replicates against a panel of eight phages",
                "notes": "The Figure 2 legend frames the cloned P4-hotspot hits, including the RT-nitrilase plus one-TM system, as validated defense systems in a replicated phage-resistance heatmap."
              },
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/rst_rt-nitrilase-tm.md",
                "snippet": "RT-nitrilase-Tm (also named UG5-large) is a two-gene defense system. It was discovered from P4-like satellites in *E. coli* genomes :ref{doi=10.1016/j.chom.2022.02.018} :ref{doi=10.1093/nar/gkac467}. Its antiphage activity was shown in *E. coli* against phage AL505_P2 (Myoviridae).",
                "notes": "The pinned DefenseFinder wiki page names RT-nitrilase-Tm, also called UG5-large, as a two-gene system and records AL505_P2 antiphage activity in Escherichia coli."
              },
              {
                "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/rst_rt-nitrilase-tm.md",
                "snippet": "Expressed_0[Escherichia coli] ----> Al505_P2",
                "notes": "The DefenseFinder experimental-validation diagram links Escherichia coli expression of the Rst_RT-nitrilase-Tm system to protection against AL505_P2."
              }
            ]
          },
          {
            "subject": "rst_rt_nitrilase_tm_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Rst_RT-nitrilase-Tm system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.chom.2022.02.018",
                "snippet": "Phage resistance heatmap of the validated defense systems shows the mean fold resistance of three independent replicates against a panel of eight phages",
                "notes": "The Figure 2 legend frames the cloned P4-hotspot hits, including the RT-nitrilase plus one-TM system, as validated defense systems in a replicated phage-resistance heatmap."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Rst_RT-nitrilase-Tm | 10\\.1101/2021\\.01\\.21\\.427644 | Prophage-encoded hotspots of bacterial immune systems",
                "notes": "The DefenseFinder article registry maps the named Rst_RT-nitrilase-Tm system to the Rousset et al. preprint."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "rst-rt-nitrilase-tm-host-mechanism-gap",
        "prompt": "Resolve Rst_RT-nitrilase-Tm native host breadth, the Rst_RT-nitrilase-Tm and Rst_RT-Tm namespace relationship, accession-level RT/RT-Tm roles, the relationship to UG5-large source naming, and the mechanism of AL505_P2 restriction before minting narrower Rst_RT-nitrilase-Tm mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Rousset et al. support a two-gene P4-hotspot system that combines a group-5 reverse transcriptase with a C-terminal nitrilase domain and a transmembrane effector, and DefenseFinder maps Rst_RT-nitrilase-Tm to a required two-profile Rst_RT-Tm model. This first system-level record leaves native host breadth, exact profile-to-gene mapping, the model-namespace mismatch, the relationship to UG5-large source naming, the molecular activities of the RT and RT-Tm components, and the AL505_P2 restriction mechanism unresolved.",
        "evidence": [
          {
            "reference": "DOI:10.1016/j.chom.2022.02.018",
            "snippet": "with a C-terminal nitrilase domain (Table S3) that is associated with a transmembrane effector",
            "notes": "Rousset et al. described a validated P4-hotspot system containing a group-5 reverse transcriptase with a C-terminal nitrilase domain associated with a transmembrane effector."
          },
          {
            "reference": "https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/rst_rt-nitrilase-tm.md",
            "snippet": "RT-nitrilase-Tm (also named UG5-large) is a two-gene defense system. It was discovered from P4-like satellites in *E. coli* genomes :ref{doi=10.1016/j.chom.2022.02.018} :ref{doi=10.1093/nar/gkac467}. Its antiphage activity was shown in *E. coli* against phage AL505_P2 (Myoviridae).",
            "notes": "The pinned DefenseFinder wiki page names RT-nitrilase-Tm, also called UG5-large, as a two-gene system and records AL505_P2 antiphage activity in Escherichia coli."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "snippet": "Rst_RT-nitrilase-Tm\tRst_RT-Tm\t2\t2\tRst_RT-Tm__RT, Rst_RT-Tm__RT-Tm\t\t\t",
            "notes": "The DefenseFinder rules table maps Rst_RT-nitrilase-Tm to a two-profile Rst_RT-Tm model requiring RT and RT-Tm profiles."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| Rst_RT-Tm__RT                                    | Rst_RT-Tm__RT                                    | Rst_RT-Tm              | Custom                  | 500    |\n| Rst_RT-Tm__RT2                                   |                                                  | Rst_RT-Tm              | Custom                  | 100    |\n| Rst_RT-Tm__RT-Tm                                 | Rst_RT-Tm__RT-Tm                                 | Rst_RT-Tm              | Custom                  | 100    |",
            "notes": "The DefenseFinder HMM inventory records the RT, alternate RT2, and RT-Tm profiles under the normalized Rst_RT-Tm system namespace."
          }
        ],
        "attaches_to": [
          "causal_graphs#rst_rt_nitrilase_tm_locus_restricts_al505_p2"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-27"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-27T06:35:23Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Rst_RT-nitrilase-Tm system as a DOI/stable-URL-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v280.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-27T06:35:24Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed Rst_RT-nitrilase-Tm during canonical-example issue 444 enforcement and left canonical_examples empty because the sources support a cloned P4-hotspot RT/RT-Tm locus assayed in Escherichia coli and a DefenseFinder RefSeq model example, but not a direct native microbial host exemplar with experimentally verified Rst_RT-nitrilase-Tm activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000377",
    "label": "Rst TIR-NLR system",
    "definition": "A phage defense system in which an organism possesses a P4-like TIR-NLR locus represented by DefenseFinder as the Rst_TIR-NLR single-profile model and experimentally linked to broad virulent-phage and P2-like phage restriction.",
    "definition_source": "DOI:10.1016/j.chom.2022.02.018",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "TIR-NLR system",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1016/j.chom.2022.02.018"
      },
      {
        "synonym_text": "Rst_TIR-NLR",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      },
      {
        "synonym_text": "Rst_TIR-NLR__TIR",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1016/j.chom.2022.02.018",
        "snippet": "Here, we show that hotspots of genetic diversity within the P2-like phage and P4-like satellite families constitute large reservoirs of anti-phage systems.",
        "notes": "Rousset et al. establish that P2-like phage and P4-like satellite hotspots are large reservoirs of anti-phage systems."
      },
      {
        "reference": "DOI:10.1016/j.chom.2022.02.018",
        "snippet": "Validated systems also include a single-gene system with a TIR (toll/interleukin-1-receptor-like) domain protein.",
        "notes": "Rousset et al. describe one validated P4 hotspot system as a single-gene TIR-domain system."
      },
      {
        "reference": "DOI:10.1016/j.chom.2022.02.018",
        "snippet": "Out of the 18 tested systems, only the TIR-NLR system provided protection",
        "notes": "Rousset et al. report that TIR-NLR was the only P4 system in their tested cohort that protected against P2-like phages."
      },
      {
        "reference": "DOI:10.1016/j.chom.2022.02.018",
        "snippet": "This shows that while the TIR-NLR system protects against a broad range of virulent phages, this comes at the cost of limiting the transduction of P4 by P2.",
        "notes": "Rousset et al. summarize broad virulent-phage protection by the TIR-NLR system in the context of P4 transduction costs."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "Rst_TIR-NLR | 10\\.1101/2021\\.01\\.21\\.427644 | Prophage-encoded hotspots of bacterial immune systems",
        "notes": "The DefenseFinder article registry maps the named Rst_TIR-NLR system to the Rousset et al. preprint."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "Rst_TIR-NLR\tRst_TIR-NLR\t1\t1\tRst_TIR-NLR__TIR\t\t\t",
        "notes": "The DefenseFinder rules table models Rst_TIR-NLR as a single-profile system requiring the Rst_TIR-NLR__TIR profile."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| Rst_TIR-NLR__TIR                                 | Rst_TIR-NLR__TIR                                 | Rst_TIR-NLR            | Custom                  | 70     |",
        "notes": "The DefenseFinder HMM inventory records Rst_TIR-NLR__TIR under the Rst_TIR-NLR system namespace."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "rst_tir_nlr_locus_restricts_phages",
        "title": "Rst TIR-NLR loci restrict virulent and P2-like phages",
        "description": "Conservative system-level sketch linking a P4-like Rst TIR-NLR locus to phage restriction.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Rst_TIR-NLR as a named DefenseFinder single-profile phage-defense system while leaving source locus breadth, the phage trigger, TIR/STAND activation, and exact Rst_TIR-NLR__TIR profile-to-gene correspondence unresolved.",
        "nodes": [
          {
            "node_id": "rst_tir_nlr_locus",
            "label": "Rst TIR-NLR locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A P4-like TIR-NLR phage-defense locus represented by the Rst_TIR-NLR DefenseFinder profile."
          },
          {
            "node_id": "virulent_and_p2_like_phage_restriction",
            "label": "virulent and P2-like phage restriction",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Restriction of broad virulent phages and P2-like phages by the TIR-NLR locus."
          },
          {
            "node_id": "rst_tir_nlr_system_trait",
            "label": "Rst TIR-NLR system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000377",
            "description": "Possession of a genome-encoded TIR-NLR phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "rst_tir_nlr_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "virulent_and_p2_like_phage_restriction",
            "description": "Rousset et al. linked the TIR-NLR system to virulent and P2-like phage protection, and DefenseFinder models Rst_TIR-NLR as a single-profile system.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.chom.2022.02.018",
                "snippet": "Validated systems also include a single-gene system with a TIR (toll/interleukin-1-receptor-like) domain protein.",
                "notes": "Rousset et al. describe one validated P4 hotspot system as a single-gene TIR-domain system."
              },
              {
                "reference": "DOI:10.1016/j.chom.2022.02.018",
                "snippet": "Out of the 18 tested systems, only the TIR-NLR system provided protection",
                "notes": "Rousset et al. report that TIR-NLR was the only P4 system in their tested cohort that protected against P2-like phages."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "Rst_TIR-NLR\tRst_TIR-NLR\t1\t1\tRst_TIR-NLR__TIR\t\t\t",
                "notes": "The DefenseFinder rules table models Rst_TIR-NLR as a single-profile system requiring the Rst_TIR-NLR__TIR profile."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| Rst_TIR-NLR__TIR                                 | Rst_TIR-NLR__TIR                                 | Rst_TIR-NLR            | Custom                  | 70     |",
                "notes": "The DefenseFinder HMM inventory records Rst_TIR-NLR__TIR under the Rst_TIR-NLR system namespace."
              }
            ]
          },
          {
            "subject": "virulent_and_p2_like_phage_restriction",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "rst_tir_nlr_system_trait",
            "description": "Restriction of virulent and P2-like phages realizes the Rst TIR-NLR system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.chom.2022.02.018",
                "snippet": "This shows that while the TIR-NLR system protects against a broad range of virulent phages, this comes at the cost of limiting the transduction of P4 by P2.",
                "notes": "Rousset et al. summarize broad virulent-phage protection by the TIR-NLR system in the context of P4 transduction costs."
              },
              {
                "reference": "DOI:10.1016/j.chom.2022.02.018",
                "snippet": "Out of the 18 tested systems, only the TIR-NLR system provided protection",
                "notes": "Rousset et al. report that TIR-NLR was the only P4 system in their tested cohort that protected against P2-like phages."
              }
            ]
          },
          {
            "subject": "rst_tir_nlr_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Rst TIR-NLR system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.chom.2022.02.018",
                "snippet": "Here, we show that hotspots of genetic diversity within the P2-like phage and P4-like satellite families constitute large reservoirs of anti-phage systems.",
                "notes": "Rousset et al. establish that P2-like phage and P4-like satellite hotspots are large reservoirs of anti-phage systems."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Rst_TIR-NLR | 10\\.1101/2021\\.01\\.21\\.427644 | Prophage-encoded hotspots of bacterial immune systems",
                "notes": "The DefenseFinder article registry maps the named Rst_TIR-NLR system to the Rousset et al. preprint."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "rst-tir-nlr-mechanism-gap",
        "prompt": "Resolve Rst_TIR-NLR natural host breadth, exact profile-to-gene correspondence, direct phage trigger, and TIR/STAND activation before minting narrower Rst TIR-NLR mechanism traits.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Rousset et al. support a P4-like TIR-NLR system that protects against virulent and P2-like phages, and DefenseFinder represents Rst_TIR-NLR as a single-profile model. This first system-level record leaves natural host breadth, profile-to-gene mapping, the direct phage trigger, and TIR/STAND effector logic unresolved.",
        "evidence": [
          {
            "reference": "DOI:10.1016/j.chom.2022.02.018",
            "snippet": "Validated systems also include a single-gene system with a TIR (toll/interleukin-1-receptor-like) domain protein.",
            "notes": "Rousset et al. describe one validated P4 hotspot system as a single-gene TIR-domain system."
          },
          {
            "reference": "DOI:10.1016/j.chom.2022.02.018",
            "snippet": "Out of the 18 tested systems, only the TIR-NLR system provided protection",
            "notes": "Rousset et al. report that TIR-NLR was the only P4 system in their tested cohort that protected against P2-like phages."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "snippet": "Rst_TIR-NLR\tRst_TIR-NLR\t1\t1\tRst_TIR-NLR__TIR\t\t\t",
            "notes": "The DefenseFinder rules table models Rst_TIR-NLR as a single-profile system requiring the Rst_TIR-NLR__TIR profile."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| Rst_TIR-NLR__TIR                                 | Rst_TIR-NLR__TIR                                 | Rst_TIR-NLR            | Custom                  | 70     |",
            "notes": "The DefenseFinder HMM inventory records Rst_TIR-NLR__TIR under the Rst_TIR-NLR system namespace."
          }
        ],
        "attaches_to": [
          "causal_graphs#rst_tir_nlr_locus_restricts_phages"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-26"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-26T09:17:05Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Rst TIR-NLR system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v254.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-26T09:17:06Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed Rst TIR-NLR system during canonical-example issue 444 enforcement and left canonical_examples empty because the sources support cloned P4-like TIR-NLR system assays and a DefenseFinder system model, but not a direct native microbial isolate exemplar with experimentally verified Rst_TIR-NLR activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000315",
    "label": "Rugutis system",
    "definition": "A phage defense system in which an organism possesses a Rugutis locus that can restrict bacteriophage infection.",
    "definition_source": "DOI:10.1093/nar/gkae671",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "Rugutis",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1093/nar/gkae671"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1093/nar/gkae671",
        "snippet": "These systems were named after cheese, cattle or fermentation related deities (Rhea, Aristaios, Kamadhenu, Fliodhais, Audmula, Rugutis and Hesat)",
        "notes": "Grafakou et al. named Rugutis among seven not previously described lactococcal antiphage systems."
      },
      {
        "reference": "DOI:10.1073/pnas.2426508122",
        "snippet": "we isolated 66 phage escape mutants which had become insensitive to 13 distinct, plasmid-encoded lactococcal phage resistance systems (i.e. Rhea, Kamadhenu, Rugutis, Audmula, PARIS, type II CBASS, Septu, AbiA, AbiB, AbiD/F, AbiG, AbiJ, AbiP)",
        "notes": "Mosterd et al. later included Rugutis among the distinct plasmid-encoded lactococcal phage-resistance systems investigated by phage escape-mutant isolation."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "Rugutis | 10\\.1093/nar/gkae671 | Discovery of antiphage systems in the lactococcal plasmidome",
        "notes": "The DefenseFinder article registry maps the named Rugutis system to the Grafakou et al. lactococcal antiphage-system discovery paper."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "rugutis_locus_restricts_phage",
        "title": "Rugutis loci confer bacterial phage defense",
        "description": "Conservative system-level sketch linking possession of a Rugutis locus to restricted bacteriophage propagation without asserting the unresolved phage trigger or molecular output.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Rugutis as a named lactococcal anti-phage system while leaving its direct phage trigger, molecular substrate, antiviral effector output, natural locus breadth, and the absence of pinned DefenseFinder HMM or rule rows unresolved.",
        "nodes": [
          {
            "node_id": "rugutis_locus",
            "label": "Rugutis locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A Rugutis anti-phage defense locus described among lactococcal plasmid-encoded phage-resistance systems."
          },
          {
            "node_id": "restricted_phage_propagation",
            "label": "restricted phage propagation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced propagation of bacteriophage in cells carrying the Rugutis system."
          },
          {
            "node_id": "rugutis_system_trait",
            "label": "Rugutis system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000315",
            "description": "Possession of a genome-encoded Rugutis phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "rugutis_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "restricted_phage_propagation",
            "description": "The lactococcal plasmidome screen discovered Rugutis as a named antiphage system, and the DefenseFinder article registry maps the Rugutis system to that discovery paper.",
            "evidence": [
              {
                "reference": "DOI:10.1093/nar/gkae671",
                "snippet": "These systems were named after cheese, cattle or fermentation related deities (Rhea, Aristaios, Kamadhenu, Fliodhais, Audmula, Rugutis and Hesat)",
                "notes": "Grafakou et al. named Rugutis as one of the novel lactococcal antiphage systems."
              },
              {
                "reference": "DOI:10.1073/pnas.2426508122",
                "snippet": "we isolated 66 phage escape mutants which had become insensitive to 13 distinct, plasmid-encoded lactococcal phage resistance systems (i.e. Rhea, Kamadhenu, Rugutis, Audmula, PARIS, type II CBASS, Septu, AbiA, AbiB, AbiD/F, AbiG, AbiJ, AbiP)",
                "notes": "Mosterd et al. treat Rugutis as a plasmid-encoded lactococcal phage-resistance system in their escape-mutant screen."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Rugutis | 10\\.1093/nar/gkae671 | Discovery of antiphage systems in the lactococcal plasmidome",
                "notes": "The DefenseFinder article registry maps the named Rugutis system to the Grafakou et al. lactococcal antiphage-system discovery paper."
              }
            ]
          },
          {
            "subject": "restricted_phage_propagation",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "rugutis_system_trait",
            "description": "Rugutis-mediated phage restriction realizes the Rugutis system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1073/pnas.2426508122",
                "snippet": "we isolated 66 phage escape mutants which had become insensitive to 13 distinct, plasmid-encoded lactococcal phage resistance systems (i.e. Rhea, Kamadhenu, Rugutis, Audmula, PARIS, type II CBASS, Septu, AbiA, AbiB, AbiD/F, AbiG, AbiJ, AbiP)",
                "notes": "Mosterd et al. treat Rugutis as a plasmid-encoded lactococcal phage-resistance system in their escape-mutant screen."
              }
            ]
          },
          {
            "subject": "rugutis_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Rugutis system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Rugutis | 10\\.1093/nar/gkae671 | Discovery of antiphage systems in the lactococcal plasmidome",
                "notes": "The DefenseFinder article registry maps the named Rugutis system to the Grafakou et al. lactococcal antiphage-system discovery paper."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "rugutis-mechanism-gap",
        "prompt": "Resolve Rugutis phage triggers and effector outputs before minting narrower Rugutis mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Grafakou et al., Mosterd et al., and DefenseFinder support Rugutis as a named anti-phage system, but the direct trigger, molecular substrate, antiviral effector output, natural locus breadth, and profile-to-component model are not resolved enough here to assert a narrower mechanistic child trait.",
        "attaches_to": [
          "causal_graphs#rugutis_locus_restricts_phage"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-20"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-20T17:37:28Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Rugutis system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v192.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000373",
    "label": "SanaTA system",
    "definition": "A phage defense system in which an organism possesses a sanaTA toxin-antitoxin locus represented by DefenseFinder as a SanaA/SanaT two-profile model and experimentally linked to resistance against T7 phage mutants lacking gene 4.5 anti-defense activity.",
    "definition_source": "DOI:10.1016/j.molcel.2013.02.002",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "sanaTA",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1016/j.molcel.2013.02.002"
      },
      {
        "synonym_text": "SanaTA",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      },
      {
        "synonym_text": "SanaTA__SanaA",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "SanaTA__SanaT",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "PMID:23478446",
        "snippet": "In all six tested pairs, induction of toxin expression inhibited bacterial growth, while co-induction of the toxin and antitoxin resulted in bacterial survival",
        "notes": "Sberro et al. experimentally validated the sanaTA family as one of six new toxin-antitoxin systems."
      },
      {
        "reference": "PMID:23478446",
        "snippet": "One of the tested systems, sanaTA, was found to provide E. coli with resistance against T7\u03944.5 and T7\u03944.3\u03944.5\u03944.7, reducing sensitivity to these phage strains by about 3 orders of magnitude",
        "notes": "Sberro et al. connect the sanaTA system to lower sensitivity to T7 phages lacking gene 4.5."
      },
      {
        "reference": "PMID:23478446",
        "snippet": "Since the sanaTA system provides resistance to the T7\u03944.5 mutant phage but not to the WT T7 phage, we hypothesized that the 4.5 gene codes for an anti-defense mechanism that overcomes the abortive infection imposed by the TA system.",
        "notes": "Sberro et al. show that SanaTA resists a T7 gene 4.5 mutant and leave the phage-encoded anti-Abi interaction as part of the system context."
      },
      {
        "reference": "DOI:10.1016/j.molcel.2013.02.002",
        "snippet": "Infection experiments with T7 phage showed that two of the new modules can provide resistance against phage.",
        "notes": "Sberro et al. summarize that infection experiments found phage resistance in two of the newly identified modules."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "SanaTA | 10\\.1016/j\\.molcel\\.2013\\.02\\.002 | Discovery of functional toxin/antitoxin systems in bacteria by shotgun cloning",
        "notes": "The DefenseFinder article registry maps the named SanaTA system to the Sberro et al. toxin/antitoxin shotgun-cloning paper."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "SanaTA\tSanaTA\t2\t2\tSanaTA__SanaA, SanaTA__SanaT\t\t\t",
        "notes": "The DefenseFinder rules table models SanaTA as a two-profile system requiring SanaTA__SanaA and SanaTA__SanaT."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| SanaTA__SanaA                                    | SanaTA__SanaA                                    | SanaTA                 | Custom                  | 20     |",
        "notes": "The DefenseFinder HMM inventory records SanaTA__SanaA under SanaTA."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| SanaTA__SanaT                                    | SanaTA__SanaT                                    | SanaTA                 | Custom                  | 20     |",
        "notes": "The DefenseFinder HMM inventory records SanaTA__SanaT under SanaTA."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "sanata_locus_restricts_t7_mutants",
        "title": "SanaTA loci restrict T7 gene 4.5 mutants",
        "description": "Conservative system-level sketch linking a DefenseFinder SanaTA locus to resistance against T7 phages lacking gene 4.5 anti-defense activity.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures SanaTA as a named two-profile toxin-antitoxin phage-defense system while leaving native host breadth, SanaA and SanaT molecular activities, the exact T7 Gp4.5/Lon interaction sequence, and the extra pinned SanaTA__SanaT_1 HMM row unresolved.",
        "nodes": [
          {
            "node_id": "sanata_locus",
            "label": "SanaTA locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A sanaTA toxin-antitoxin phage-defense locus represented by the DefenseFinder SanaTA__SanaA and SanaTA__SanaT profiles."
          },
          {
            "node_id": "t7_gene_45_mutant_resistance",
            "label": "T7 gene 4.5 mutant resistance",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Restriction of T7 phage mutants that lack the gene 4.5 anti-defense activity in a host expressing SanaTA."
          },
          {
            "node_id": "sanata_system_trait",
            "label": "SanaTA system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000373",
            "description": "Possession of a genome-encoded SanaTA phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "sanata_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "t7_gene_45_mutant_resistance",
            "description": "A cloned sanaTA toxin-antitoxin system can reduce sensitivity to T7 phages lacking gene 4.5, and DefenseFinder models SanaTA as a two-profile SanaA/SanaT system.",
            "evidence": [
              {
                "reference": "PMID:23478446",
                "snippet": "One of the tested systems, sanaTA, was found to provide E. coli with resistance against T7\u03944.5 and T7\u03944.3\u03944.5\u03944.7, reducing sensitivity to these phage strains by about 3 orders of magnitude",
                "notes": "Sberro et al. show that SanaTA reduced sensitivity to T7 mutants lacking gene 4.5."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "SanaTA\tSanaTA\t2\t2\tSanaTA__SanaA, SanaTA__SanaT\t\t\t",
                "notes": "The DefenseFinder rules table models SanaTA as a two-profile system requiring SanaTA__SanaA and SanaTA__SanaT."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| SanaTA__SanaA                                    | SanaTA__SanaA                                    | SanaTA                 | Custom                  | 20     |",
                "notes": "The DefenseFinder HMM inventory records SanaTA__SanaA under SanaTA."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| SanaTA__SanaT                                    | SanaTA__SanaT                                    | SanaTA                 | Custom                  | 20     |",
                "notes": "The DefenseFinder HMM inventory records SanaTA__SanaT under SanaTA."
              }
            ]
          },
          {
            "subject": "t7_gene_45_mutant_resistance",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "sanata_system_trait",
            "description": "SanaTA-mediated resistance to T7 gene 4.5 mutants realizes the SanaTA system trait.",
            "evidence": [
              {
                "reference": "PMID:23478446",
                "snippet": "Since the sanaTA system provides resistance to the T7\u03944.5 mutant phage but not to the WT T7 phage, we hypothesized that the 4.5 gene codes for an anti-defense mechanism that overcomes the abortive infection imposed by the TA system.",
                "notes": "Sberro et al. frame T7 gene 4.5 as the anti-defense context for SanaTA-mediated abortive infection."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "SanaTA | 10\\.1016/j\\.molcel\\.2013\\.02\\.002 | Discovery of functional toxin/antitoxin systems in bacteria by shotgun cloning",
                "notes": "The DefenseFinder article registry maps the named SanaTA system to the Sberro et al. toxin/antitoxin shotgun-cloning paper."
              }
            ]
          },
          {
            "subject": "sanata_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "SanaTA system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.molcel.2013.02.002",
                "snippet": "Infection experiments with T7 phage showed that two of the new modules can provide resistance against phage.",
                "notes": "Sberro et al. connect newly discovered toxin-antitoxin modules to phage resistance in T7 infection experiments."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "SanaTA | 10\\.1016/j\\.molcel\\.2013\\.02\\.002 | Discovery of functional toxin/antitoxin systems in bacteria by shotgun cloning",
                "notes": "The DefenseFinder article registry maps the named SanaTA system to the Sberro et al. toxin/antitoxin shotgun-cloning paper."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "sanata-host-trigger-profile-gap",
        "prompt": "Resolve SanaTA native host breadth, SanaA/SanaT molecular activities, T7 Gp4.5/Lon anti-defense logic, and the SanaTA__SanaT_1 profile before minting narrower SanaTA mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Sberro et al. support sanaTA as a Shewanella sp. ANA-3 two-gene toxin-antitoxin family that confers resistance to T7 phage mutants lacking gene 4.5 when expressed in Escherichia coli, and DefenseFinder models SanaTA with SanaTA__SanaA and SanaTA__SanaT. This first system-level record leaves the natural host range, SanaA/SanaT activities, T7 Gp4.5/Lon counter-defense sequence, and the extra non-rule SanaTA__SanaT_1 HMM unresolved.",
        "evidence": [
          {
            "reference": "PMID:23478446",
            "snippet": "Since the sanaTA system provides resistance to the T7\u03944.5 mutant phage but not to the WT T7 phage, we hypothesized that the 4.5 gene codes for an anti-defense mechanism that overcomes the abortive infection imposed by the TA system.",
            "notes": "Sberro et al. connect T7 gene 4.5 to SanaTA anti-Abi escape but leave the locus-level SanaTA mechanism only partly resolved."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "snippet": "SanaTA\tSanaTA\t2\t2\tSanaTA__SanaA, SanaTA__SanaT\t\t\t",
            "notes": "The DefenseFinder rules table models SanaTA as a two-profile system requiring SanaTA__SanaA and SanaTA__SanaT."
          }
        ],
        "attaches_to": [
          "causal_graphs#sanata_locus_restricts_t7_mutants"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-25"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-25T06:02:46Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted SanaTA system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v250.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-25T06:20:44Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed SanaTA during canonical-example issue 444 enforcement and left canonical_examples empty because the source validates a broad DefenseFinder toxin-antitoxin family in an Escherichia coli expression assay and does not establish a direct native host exemplar. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000512",
    "label": "ScoMcrA system",
    "definition": "A type IV modification-dependent restriction system in which an organism possesses a ScoMcrA-family locus encoding a sulfur-binding-domain phosphorothioated-DNA restriction endonuclease.",
    "definition_source": "DOI:10.1038/s41467-018-07093-1",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000496"
    ],
    "synonyms": [
      {
        "synonym_text": "ScoMcrA",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1371/journal.pgen.1001253",
        "snippet": "A His-tagged derivative of ScoA3McrA cleaved S-modified DNA and also Dcm-methylated DNA in vitro near the respective modification sites.",
        "notes": "Liu et al. support ScoA3McrA cleavage of phosphorothioated DNA and Dcm-methylated DNA."
      },
      {
        "reference": "DOI:10.1371/journal.pgen.1001253",
        "snippet": "Double-strand cleavage occurred 16-28 nucleotides away from the phosphorothioate links.",
        "notes": "Liu et al. support double-strand ScoA3McrA cleavage near DNA phosphorothioate linkages."
      },
      {
        "reference": "DOI:10.1371/journal.pgen.1001253",
        "snippet": "This is the first report of in vitro endonuclease activity of a McrA homologue and also the first demonstration of an enzyme that specifically cleaves S-modified DNA.",
        "notes": "Liu et al. frame ScoA3McrA as a McrA homolog with phosphorothioated-DNA-specific cleavage activity."
      },
      {
        "reference": "DOI:10.1038/s41467-018-07093-1",
        "snippet": "Here we present the crystal structure of the sulfur-binding domain (SBD) from the DNA phosphorothioation (PT)-dependent restriction endonuclease ScoMcrA.",
        "notes": "Liu et al. support ScoMcrA as a phosphorothioated-DNA-dependent restriction endonuclease with a sulfur-binding domain."
      },
      {
        "reference": "DOI:10.1038/s41467-018-07093-1",
        "snippet": "We show that three of these homologs bind PT-DNA in vitro and restrict PT-DNA gene transfer in vivo.",
        "notes": "Liu et al. support SBD homologs as phosphorothioated-DNA readers with in vivo PT-DNA restriction activity."
      },
      {
        "reference": "DOI:10.1093/nar/gkt747",
        "snippet": "The new class of modification-dependent restriction enzymes was named Type IV, as distinct from the familiar modification-blocked Types I-III.",
        "notes": "Loenen and Raleigh define the Type IV class as modification-dependent restriction enzymes."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| ScoMcrA | 10\\.1038/s41467-018-07093-1 | Structural basis for the recognition of sulfur in phosphorothioated DNA | ",
        "notes": "The pinned DefenseFinder article registry maps the ScoMcrA source key to the Liu et al. sulfur-recognition paper."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "scomcra_restricts_phosphorothioated_dna",
        "title": "ScoMcrA restricts phosphorothioated DNA",
        "description": "Conservative system-level sketch linking a ScoMcrA-family locus to phosphorothioated-DNA restriction and to the Type IV restriction parent trait.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures ScoMcrA as a named Type IV modification-dependent restriction family while leaving natural host breadth, exact PT-DNA sequence-context specificity across characterized homologs, Dcm-methylated DNA target breadth, accession-level protein examples, and DefenseFinder RM_Type_IV HMM/rules mapping unresolved.",
        "nodes": [
          {
            "node_id": "scomcra_family_locus",
            "label": "ScoMcrA-family locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A locus encoding a ScoMcrA-family phosphorothioated-DNA restriction endonuclease."
          },
          {
            "node_id": "scomcra_phosphorothioated_dna",
            "label": "ScoMcrA-targeted phosphorothioated DNA",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "DNA containing phosphorothioate linkages in a ScoMcrA-family recognition context."
          },
          {
            "node_id": "scomcra_phosphorothioated_dna_restriction",
            "label": "ScoMcrA phosphorothioated-DNA restriction",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Modification-dependent restriction of phosphorothioated DNA by a ScoMcrA-family endonuclease."
          },
          {
            "node_id": "scomcra_system_trait",
            "label": "ScoMcrA system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000512",
            "description": "Possession of a genome-encoded ScoMcrA-family modification-dependent restriction system."
          },
          {
            "node_id": "type_iv_modification_dependent_restriction",
            "label": "type IV modification-dependent restriction system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000496",
            "description": "Possession of a genome-encoded Type IV modification-dependent restriction system."
          }
        ],
        "edges": [
          {
            "subject": "scomcra_family_locus",
            "predicate": "enables",
            "predicate_id": "RO:0002327",
            "object": "scomcra_phosphorothioated_dna_restriction",
            "description": "ScoMcrA-family loci encode PT-DNA readers that restrict phosphorothioated DNA.",
            "evidence": [
              {
                "reference": "DOI:10.1371/journal.pgen.1001253",
                "snippet": "A His-tagged derivative of ScoA3McrA cleaved S-modified DNA and also Dcm-methylated DNA in vitro near the respective modification sites.",
                "notes": "Liu et al. support ScoA3McrA cleavage of phosphorothioated DNA and Dcm-methylated DNA."
              },
              {
                "reference": "DOI:10.1038/s41467-018-07093-1",
                "snippet": "Here we present the crystal structure of the sulfur-binding domain (SBD) from the DNA phosphorothioation (PT)-dependent restriction endonuclease ScoMcrA.",
                "notes": "Liu et al. support ScoMcrA as a phosphorothioated-DNA-dependent restriction endonuclease with a sulfur-binding domain."
              },
              {
                "reference": "DOI:10.1038/s41467-018-07093-1",
                "snippet": "We show that three of these homologs bind PT-DNA in vitro and restrict PT-DNA gene transfer in vivo.",
                "notes": "Liu et al. support SBD homologs as phosphorothioated-DNA readers with in vivo PT-DNA restriction activity."
              }
            ]
          },
          {
            "subject": "scomcra_phosphorothioated_dna_restriction",
            "predicate": "mitigates",
            "predicate_id": "METPO:2007407",
            "object": "scomcra_phosphorothioated_dna",
            "description": "ScoMcrA-family restriction targets phosphorothioated DNA.",
            "evidence": [
              {
                "reference": "DOI:10.1371/journal.pgen.1001253",
                "snippet": "A His-tagged derivative of ScoA3McrA cleaved S-modified DNA and also Dcm-methylated DNA in vitro near the respective modification sites.",
                "notes": "Liu et al. support ScoA3McrA cleavage of phosphorothioated DNA and Dcm-methylated DNA."
              },
              {
                "reference": "DOI:10.1371/journal.pgen.1001253",
                "snippet": "Double-strand cleavage occurred 16-28 nucleotides away from the phosphorothioate links.",
                "notes": "Liu et al. support double-strand ScoA3McrA cleavage near DNA phosphorothioate linkages."
              },
              {
                "reference": "DOI:10.1038/s41467-018-07093-1",
                "snippet": "We show that three of these homologs bind PT-DNA in vitro and restrict PT-DNA gene transfer in vivo.",
                "notes": "Liu et al. support SBD homologs as phosphorothioated-DNA readers with in vivo PT-DNA restriction activity."
              }
            ]
          },
          {
            "subject": "scomcra_phosphorothioated_dna_restriction",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "scomcra_system_trait",
            "description": "ScoMcrA-family phosphorothioated-DNA restriction realizes the organism-level ScoMcrA system possession trait.",
            "evidence": [
              {
                "reference": "DOI:10.1371/journal.pgen.1001253",
                "snippet": "This is the first report of in vitro endonuclease activity of a McrA homologue and also the first demonstration of an enzyme that specifically cleaves S-modified DNA.",
                "notes": "Liu et al. frame ScoA3McrA as a McrA homolog with phosphorothioated-DNA-specific cleavage activity."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| ScoMcrA | 10\\.1038/s41467-018-07093-1 | Structural basis for the recognition of sulfur in phosphorothioated DNA | ",
                "notes": "The pinned DefenseFinder article registry maps the ScoMcrA source key to the Liu et al. sulfur-recognition paper."
              }
            ]
          },
          {
            "subject": "scomcra_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "type_iv_modification_dependent_restriction",
            "description": "ScoMcrA system possession is a Type IV modification-dependent restriction system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1371/journal.pgen.1001253",
                "snippet": "This is the first report of in vitro endonuclease activity of a McrA homologue and also the first demonstration of an enzyme that specifically cleaves S-modified DNA.",
                "notes": "Liu et al. frame ScoA3McrA as a McrA homolog with phosphorothioated-DNA-specific cleavage activity."
              },
              {
                "reference": "DOI:10.1093/nar/gkt747",
                "snippet": "The new class of modification-dependent restriction enzymes was named Type IV, as distinct from the familiar modification-blocked Types I-III.",
                "notes": "Loenen and Raleigh define the Type IV class as modification-dependent restriction enzymes."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "scomcra-defensefinder-model-gap",
        "prompt": "Resolve ScoMcrA-family breadth, phosphorothioated-DNA sequence-context specificity across natural hosts, methylated-DNA target breadth, accession-level protein examples, and DefenseFinder RM_Type_IV HMM/rules mapping before minting narrower ScoMcrA mechanism or component traits.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Liu et al. support ScoA3McrA as a Type IV McrA homolog that cleaves S-modified DNA in vitro and support ScoMcrA as a PT-dependent endonuclease with a sulfur-binding domain. The pinned DefenseFinder article registry maps ScoMcrA to the sulfur-recognition paper, but the pinned HMM inventory and rules table have no exact ScoMcrA rows. This first-pass record therefore does not resolve a reusable DefenseFinder profile model, exact accession-level protein examples, the breadth of ScoMcrA-like systems across natural hosts, the complete set of natural phosphorothioated-DNA contexts, or the breadth of methylated-DNA target contexts.",
        "evidence": [
          {
            "reference": "DOI:10.1371/journal.pgen.1001253",
            "snippet": "A His-tagged derivative of ScoA3McrA cleaved S-modified DNA and also Dcm-methylated DNA in vitro near the respective modification sites.",
            "notes": "Liu et al. support ScoA3McrA cleavage of phosphorothioated DNA and Dcm-methylated DNA."
          },
          {
            "reference": "DOI:10.1371/journal.pgen.1001253",
            "snippet": "Double-strand cleavage occurred 16-28 nucleotides away from the phosphorothioate links.",
            "notes": "Liu et al. support double-strand ScoA3McrA cleavage near DNA phosphorothioate linkages."
          },
          {
            "reference": "DOI:10.1371/journal.pgen.1001253",
            "snippet": "This is the first report of in vitro endonuclease activity of a McrA homologue and also the first demonstration of an enzyme that specifically cleaves S-modified DNA.",
            "notes": "Liu et al. frame ScoA3McrA as a McrA homolog with phosphorothioated-DNA-specific cleavage activity."
          },
          {
            "reference": "DOI:10.1038/s41467-018-07093-1",
            "snippet": "Here we present the crystal structure of the sulfur-binding domain (SBD) from the DNA phosphorothioation (PT)-dependent restriction endonuclease ScoMcrA.",
            "notes": "Liu et al. support ScoMcrA as a phosphorothioated-DNA-dependent restriction endonuclease with a sulfur-binding domain."
          },
          {
            "reference": "DOI:10.1038/s41467-018-07093-1",
            "snippet": "We show that three of these homologs bind PT-DNA in vitro and restrict PT-DNA gene transfer in vivo.",
            "notes": "Liu et al. support SBD homologs as phosphorothioated-DNA readers with in vivo PT-DNA restriction activity."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
            "snippet": "| ScoMcrA | 10\\.1038/s41467-018-07093-1 | Structural basis for the recognition of sulfur in phosphorothioated DNA | ",
            "notes": "The pinned DefenseFinder article registry maps the ScoMcrA source key to the Liu et al. sulfur-recognition paper."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "notes": "A structured first-pass search of the pinned DefenseFinder HMM inventory found no exact ScoMcrA row."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "A structured first-pass search of the pinned DefenseFinder rules table found no exact ScoMcrA system row."
          }
        ],
        "attaches_to": [
          "causal_graphs#scomcra_restricts_phosphorothioated_dna"
        ],
        "posed_by": "codex",
        "posed_date": "2026-10-01"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-01T10:14:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted ScoMcrA system as a DOI- and DefenseFinder-backed GENOMICS TraitRecord under the type IV modification-dependent restriction system parent after an ignored-and-hidden duplicate review found no exact same-scope live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v389.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-01T10:14:02Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed ScoMcrA system during initial curation and left canonical_examples empty because Liu et al. support ScoA3McrA and sulfur-binding-domain homologs, but not a single stable NCBITaxon strain exemplar or accession-level protein example for the organism-level ScoMcrA system trait. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000420",
    "label": "SDIC1 system",
    "definition": "A phage defense system in which an organism possesses an SDIC1 locus encoding a TIR-domain SDIC1A component and a ubiquitin-ligase-like SDIC1B component that can provide population-wide immunity against bacteriophages.",
    "definition_source": "DOI:10.1016/j.celrep.2024.115055",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "SDIC1",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1016/j.celrep.2024.115055"
      },
      {
        "synonym_text": "SDIC1__SDIC1A",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "SDIC1__SDIC1B",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1016/j.celrep.2024.115055",
        "snippet": "four newly identified anti-phage systems",
        "notes": "Cummins et al. identify SDIC1 in a cohort of Serratia defense-island candidate systems with anti-phage activity."
      },
      {
        "reference": "DOI:10.1016/j.celrep.2024.115055",
        "snippet": "previously unreported Toll/interleukin (IL)-1 receptor (TIR)-domain-containing system with population-wide immunity",
        "notes": "Cummins et al. support SDIC1 as a TIR-domain-containing phage-defense system with a population-wide immunity phenotype."
      },
      {
        "reference": "DOI:10.1016/j.celrep.2024.115055",
        "snippet": "SDIC1 combines TIR and ubiquitin ligase",
        "notes": "Cummins et al. connect the SDIC1 system with TIR and ubiquitin-ligase-like components."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "SDIC1 | 10\\.1016/j\\.celrep\\.2024\\.115055 | Multi-conflict islands are a widespread trend within Serratia spp",
        "notes": "The pinned DefenseFinder article registry maps the SDIC1 source key to the Cummins et al. Serratia multi-conflict-island paper."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| SDIC1__SDIC1A                                    |                                                  | SDIC1                  | Custom                  | 350    |",
        "notes": "The pinned DefenseFinder HMM inventory records SDIC1__SDIC1A as a custom SDIC1 profile."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| SDIC1__SDIC1B                                    |                                                  | SDIC1                  | Custom                  | 130    |",
        "notes": "The pinned DefenseFinder HMM inventory records SDIC1__SDIC1B as a custom SDIC1 profile."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "sdic1_locus_restricts_phage",
        "title": "SDIC1 loci confer bacterial phage defense",
        "description": "Conservative system-level sketch linking the SDIC1 locus to population-wide immunity against bacteriophages.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures SDIC1 as a named anti-phage system with SDIC1A and SDIC1B DefenseFinder profiles while leaving natural host breadth, sensitive-phage breadth, the exact SDIC1A/SDIC1B profile-to-protein correspondence, the direct trigger, the ubiquitination substrate, and rule-level detection criteria unresolved.",
        "nodes": [
          {
            "node_id": "sdic1_locus",
            "label": "SDIC1 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "An SDIC1 anti-phage defense locus represented in the pinned DefenseFinder HMM inventory by SDIC1A and SDIC1B custom profiles."
          },
          {
            "node_id": "population_wide_antiphage_immunity",
            "label": "population-wide anti-phage immunity",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Protection of a bacterial population against bacteriophage infection by SDIC1 activity."
          },
          {
            "node_id": "sdic1_system_trait",
            "label": "SDIC1 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000420",
            "description": "Possession of a genome-encoded SDIC1 phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "sdic1_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "population_wide_antiphage_immunity",
            "description": "The SDIC1 locus contributes to population-wide immunity against bacteriophages.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.celrep.2024.115055",
                "snippet": "previously unreported Toll/interleukin (IL)-1 receptor (TIR)-domain-containing system with population-wide immunity",
                "notes": "Cummins et al. report population-wide immunity for the SDIC1 TIR-domain system."
              },
              {
                "reference": "DOI:10.1016/j.celrep.2024.115055",
                "snippet": "SDIC1 combines TIR and ubiquitin ligase",
                "notes": "Cummins et al. place TIR and ubiquitin-ligase-like activities in the SDIC1 system."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| SDIC1__SDIC1A                                    |                                                  | SDIC1                  | Custom                  | 350    |",
                "notes": "The pinned DefenseFinder HMM inventory records SDIC1__SDIC1A as a custom SDIC1 profile."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| SDIC1__SDIC1B                                    |                                                  | SDIC1                  | Custom                  | 130    |",
                "notes": "The pinned DefenseFinder HMM inventory records SDIC1__SDIC1B as a custom SDIC1 profile."
              }
            ]
          },
          {
            "subject": "population_wide_antiphage_immunity",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "sdic1_system_trait",
            "description": "SDIC1-mediated anti-phage immunity realizes the SDIC1 system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.celrep.2024.115055",
                "snippet": "four newly identified anti-phage systems",
                "notes": "Cummins et al. identify SDIC1 in the newly reported anti-phage system cohort."
              }
            ]
          },
          {
            "subject": "sdic1_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "SDIC1 system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.celrep.2024.115055",
                "snippet": "four newly identified anti-phage systems",
                "notes": "Cummins et al. identify SDIC1 among anti-phage systems."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "SDIC1 | 10\\.1016/j\\.celrep\\.2024\\.115055 | Multi-conflict islands are a widespread trend within Serratia spp",
                "notes": "The pinned DefenseFinder article registry maps the SDIC1 source key to the Cummins et al. Serratia multi-conflict-island paper."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "sdic1-defensefinder-model-gap",
        "prompt": "Resolve SDIC1 natural host breadth, SDIC1A/SDIC1B component functions, phage triggers, ubiquitination substrates, population-immunity mechanism, and rule-level detection criteria before minting narrower SDIC1 mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Cummins et al. support SDIC1 as a TIR-domain-containing anti-phage system with a ubiquitin-ligase-like component, and the pinned DefenseFinder HMM inventory records SDIC1A and SDIC1B profile rows. The pinned rules table has no SDIC1 row, and the first-pass record does not resolve natural host breadth, sensitive-phage breadth, the exact profile-to-component mapping, phage triggers, the direct TIR-dependent output, or the ubiquitination substrate.",
        "evidence": [
          {
            "reference": "DOI:10.1016/j.celrep.2024.115055",
            "snippet": "previously unreported Toll/interleukin (IL)-1 receptor (TIR)-domain-containing system with population-wide immunity",
            "notes": "Cummins et al. support SDIC1 as a TIR-domain anti-phage system with a population-level output."
          },
          {
            "reference": "DOI:10.1016/j.celrep.2024.115055",
            "snippet": "SDIC1 combines TIR and ubiquitin ligase",
            "notes": "Cummins et al. connect SDIC1 with a TIR domain and a ubiquitin-ligase-like component."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
            "snippet": "SDIC1 | 10\\.1016/j\\.celrep\\.2024\\.115055 | Multi-conflict islands are a widespread trend within Serratia spp",
            "notes": "The pinned DefenseFinder article registry maps the SDIC1 source key to the Cummins et al. Serratia multi-conflict-island paper."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| SDIC1__SDIC1A                                    |                                                  | SDIC1                  | Custom                  | 350    |",
            "notes": "The pinned DefenseFinder HMM inventory records SDIC1__SDIC1A as a custom SDIC1 profile."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| SDIC1__SDIC1B                                    |                                                  | SDIC1                  | Custom                  | 130    |",
            "notes": "The pinned DefenseFinder HMM inventory records SDIC1__SDIC1B as a custom SDIC1 profile."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "The pinned DefenseFinder rules table does not list SDIC1, leaving rule-level detection criteria unresolved."
          }
        ],
        "attaches_to": [
          "causal_graphs#sdic1_locus_restricts_phage"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-27"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-27T22:49:28Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted SDIC1 system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; kept the graph at candidate-locus level because the pinned DefenseFinder SDIC1 HMM rows are not backed by a rules row; proposals/metpo_traitmech_v297 reserves the replacement placeholder.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000423",
    "label": "SDIC3 system",
    "definition": "A phage defense system in which an organism possesses an SDIC3 Serratia defense-island candidate locus that can confer strong protection against several bacteriophages when plasmid expressed.",
    "definition_source": "DOI:10.1016/j.celrep.2024.115055",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "SDIC3",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1016/j.celrep.2024.115055"
      },
      {
        "synonym_text": "SDIC3__SDIC3B",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "SDIC3__SDIC3C",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "SDIC3__SDIC3D",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "SDIC3__SDIC3E",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "SDIC3__SDIC3F",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1016/j.celrep.2024.115055",
        "snippet": "Using this approach, we identified three candidate anti-phage systems/subtypes, which were renamed SDIC1\u20133",
        "notes": "Cummins et al. identify SDIC3 as one of three Serratia defense-island candidate anti-phage systems or subtypes."
      },
      {
        "reference": "DOI:10.1016/j.celrep.2024.115055",
        "snippet": "In E. coli, SDIC1, SDIC2, and SDIC3 confer strong protection against several phages (R1,000-fold), including those from the Durham collection",
        "notes": "Cummins et al. show that plasmid-expressed SDIC3 can strongly protect E. coli against several bacteriophages."
      },
      {
        "reference": "DOI:10.1016/j.celrep.2024.115055",
        "snippet": "The four candidates were cloned into a low-copy plasmid under the control of a constitutive promoter compatible with expression in E. coli and S. marcescens",
        "notes": "Cummins et al. assayed the four SDIC candidates from low-copy plasmids under a constitutive promoter."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| SDIC3 | 10\\.1016/j\\.celrep\\.2024\\.115055 | Multi-conflict islands are a widespread trend within Serratia spp |",
        "notes": "The pinned DefenseFinder article registry maps the SDIC3 source key to the Cummins et al. Serratia multi-conflict-island paper."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| SDIC3__SDIC3B                                    |                                                  | SDIC3                  | Custom                  | 20     |",
        "notes": "The pinned DefenseFinder HMM inventory records SDIC3__SDIC3B as a custom SDIC3 profile."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| SDIC3__SDIC3C                                    |                                                  | SDIC3                  | Custom                  | 220    |",
        "notes": "The pinned DefenseFinder HMM inventory records SDIC3__SDIC3C as a custom SDIC3 profile."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| SDIC3__SDIC3D                                    |                                                  | SDIC3                  | Custom                  | 40     |",
        "notes": "The pinned DefenseFinder HMM inventory records SDIC3__SDIC3D as a custom SDIC3 profile."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| SDIC3__SDIC3E                                    |                                                  | SDIC3                  | Custom                  | 80     |",
        "notes": "The pinned DefenseFinder HMM inventory records SDIC3__SDIC3E as a custom SDIC3 profile."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| SDIC3__SDIC3F                                    |                                                  | SDIC3                  | Custom                  | 600    |",
        "notes": "The pinned DefenseFinder HMM inventory records SDIC3__SDIC3F as a custom SDIC3 profile."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "sdic3_locus_restricts_phage",
        "title": "SDIC3 loci confer bacterial phage defense",
        "description": "Conservative system-level sketch linking an SDIC3 locus to reduced bacteriophage propagation without resolving exact SDIC3 components or effector activity.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures SDIC3 as a named anti-phage system with DefenseFinder SDIC3B, SDIC3C, SDIC3D, SDIC3E, and SDIC3F profile rows. It does not assert native host breadth, SDIC3A status, exact profile-to-protein correspondence, whether SDIC3 is a distinct ECOR61-system subtype, sensitive-phage breadth, the direct trigger, the molecular output, or DefenseFinder rule-level detection criteria.",
        "nodes": [
          {
            "node_id": "sdic3_locus",
            "label": "SDIC3 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "An SDIC3 candidate anti-phage locus represented in the pinned DefenseFinder HMM inventory by custom SDIC3B, SDIC3C, SDIC3D, SDIC3E, and SDIC3F profiles."
          },
          {
            "node_id": "restricted_phage_propagation",
            "label": "restricted phage propagation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced bacteriophage propagation in cells carrying a plasmid-expressed SDIC3 candidate anti-phage system."
          },
          {
            "node_id": "sdic3_system_trait",
            "label": "SDIC3 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000423",
            "description": "Possession of a genome-encoded SDIC3 phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "sdic3_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "restricted_phage_propagation",
            "description": "The SDIC3 candidate locus contributes to strong restriction of bacteriophage propagation when plasmid expressed.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.celrep.2024.115055",
                "snippet": "Using this approach, we identified three candidate anti-phage systems/subtypes, which were renamed SDIC1\u20133",
                "notes": "Cummins et al. identify SDIC3 as an anti-phage candidate found in Serratia defense islands."
              },
              {
                "reference": "DOI:10.1016/j.celrep.2024.115055",
                "snippet": "In E. coli, SDIC1, SDIC2, and SDIC3 confer strong protection against several phages (R1,000-fold), including those from the Durham collection",
                "notes": "Cummins et al. report strong SDIC3-mediated protection against multiple phages."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| SDIC3__SDIC3B                                    |                                                  | SDIC3                  | Custom                  | 20     |",
                "notes": "The pinned DefenseFinder HMM inventory records SDIC3__SDIC3B as a custom SDIC3 profile."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| SDIC3__SDIC3C                                    |                                                  | SDIC3                  | Custom                  | 220    |",
                "notes": "The pinned DefenseFinder HMM inventory records SDIC3__SDIC3C as a custom SDIC3 profile."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| SDIC3__SDIC3D                                    |                                                  | SDIC3                  | Custom                  | 40     |",
                "notes": "The pinned DefenseFinder HMM inventory records SDIC3__SDIC3D as a custom SDIC3 profile."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| SDIC3__SDIC3E                                    |                                                  | SDIC3                  | Custom                  | 80     |",
                "notes": "The pinned DefenseFinder HMM inventory records SDIC3__SDIC3E as a custom SDIC3 profile."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| SDIC3__SDIC3F                                    |                                                  | SDIC3                  | Custom                  | 600    |",
                "notes": "The pinned DefenseFinder HMM inventory records SDIC3__SDIC3F as a custom SDIC3 profile."
              }
            ]
          },
          {
            "subject": "restricted_phage_propagation",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "sdic3_system_trait",
            "description": "SDIC3-mediated phage restriction realizes the SDIC3 system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.celrep.2024.115055",
                "snippet": "In E. coli, SDIC1, SDIC2, and SDIC3 confer strong protection against several phages (R1,000-fold), including those from the Durham collection",
                "notes": "Cummins et al. connect SDIC3 with strong phage protection."
              }
            ]
          },
          {
            "subject": "sdic3_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "SDIC3 system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.celrep.2024.115055",
                "snippet": "Using this approach, we identified three candidate anti-phage systems/subtypes, which were renamed SDIC1\u20133",
                "notes": "Cummins et al. identify SDIC3 as an anti-phage candidate found in Serratia defense islands."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| SDIC3 | 10\\.1016/j\\.celrep\\.2024\\.115055 | Multi-conflict islands are a widespread trend within Serratia spp |",
                "notes": "The pinned DefenseFinder article registry maps the SDIC3 source key to the Cummins et al. Serratia multi-conflict-island paper."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "sdic3-defensefinder-model-gap",
        "prompt": "Resolve SDIC3 natural host breadth, SDIC3A status, exact SDIC3B/SDIC3C/SDIC3D/SDIC3E/SDIC3F component functions, sensitive-phage breadth, ECOR61-system subtype scope, the direct trigger and molecular output, and rule-level detection criteria before minting narrower SDIC3 mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Cummins et al. support SDIC3 as a Serratia defense-island candidate anti-phage system that can strongly protect E. coli when plasmid expressed, and the pinned DefenseFinder HMM inventory records SDIC3B, SDIC3C, SDIC3D, SDIC3E, and SDIC3F profile rows. The pinned rules table has no SDIC3 row, and the first-pass record does not resolve natural host breadth, whether SDIC3A is part of the DefenseFinder-detectable system, phage target breadth, ECOR61 anti-phage-system boundaries, or the direct molecular output.",
        "evidence": [
          {
            "reference": "DOI:10.1016/j.celrep.2024.115055",
            "snippet": "Using this approach, we identified three candidate anti-phage systems/subtypes, which were renamed SDIC1\u20133",
            "notes": "Cummins et al. identify SDIC3 as a Serratia defense-island candidate."
          },
          {
            "reference": "DOI:10.1016/j.celrep.2024.115055",
            "snippet": "In E. coli, SDIC1, SDIC2, and SDIC3 confer strong protection against several phages (R1,000-fold), including those from the Durham collection",
            "notes": "Cummins et al. report strong phage protection in E. coli."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
            "snippet": "| SDIC3 | 10\\.1016/j\\.celrep\\.2024\\.115055 | Multi-conflict islands are a widespread trend within Serratia spp |",
            "notes": "The pinned DefenseFinder article registry maps the SDIC3 source key to the Cummins et al. Serratia multi-conflict-island paper."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| SDIC3__SDIC3B                                    |                                                  | SDIC3                  | Custom                  | 20     |",
            "notes": "The pinned DefenseFinder HMM inventory records SDIC3__SDIC3B as a custom SDIC3 profile."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| SDIC3__SDIC3C                                    |                                                  | SDIC3                  | Custom                  | 220    |",
            "notes": "The pinned DefenseFinder HMM inventory records SDIC3__SDIC3C as a custom SDIC3 profile."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| SDIC3__SDIC3D                                    |                                                  | SDIC3                  | Custom                  | 40     |",
            "notes": "The pinned DefenseFinder HMM inventory records SDIC3__SDIC3D as a custom SDIC3 profile."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| SDIC3__SDIC3E                                    |                                                  | SDIC3                  | Custom                  | 80     |",
            "notes": "The pinned DefenseFinder HMM inventory records SDIC3__SDIC3E as a custom SDIC3 profile."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| SDIC3__SDIC3F                                    |                                                  | SDIC3                  | Custom                  | 600    |",
            "notes": "The pinned DefenseFinder HMM inventory records SDIC3__SDIC3F as a custom SDIC3 profile."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "The pinned DefenseFinder rules table does not list SDIC3, leaving rule-level detection criteria unresolved."
          }
        ],
        "attaches_to": [
          "causal_graphs#sdic3_locus_restricts_phage"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-28"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-28T01:42:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted SDIC3 system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; kept the graph at candidate-locus level because the pinned DefenseFinder SDIC3 HMM rows are not backed by a rules row; proposals/metpo_traitmech_v300 reserves the replacement placeholder.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-28T01:42:01Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed SDIC3 system canonical_examples and left them empty because Cummins et al. support plasmid-expressed E. coli and S. marcescens phage-challenge assays plus a DefenseFinder SDIC3 system model, but not a direct native microbial isolate exemplar with experimentally verified endogenous SDIC3 activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000421",
    "label": "SDIC4 system",
    "definition": "A phage defense system in which an organism possesses an SDIC4 locus encoding an SDIC4A component and a VasI-like SDIC4B component that can reduce adsorption of invading bacteriophages.",
    "definition_source": "DOI:10.1016/j.celrep.2024.115055",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "SDIC4",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1016/j.celrep.2024.115055"
      },
      {
        "synonym_text": "SDIC4__SDIC4A",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "SDIC4__SDIC4B",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1016/j.celrep.2024.115055",
        "snippet": "SDIC4 comprises SDIC4A, a protein of unknown function, and SDIC4B, harboring the VasI-like domain",
        "notes": "Cummins et al. describe the SDIC4 locus as encoding an SDIC4A component of unknown function and a VasI-like SDIC4B component."
      },
      {
        "reference": "DOI:10.1016/j.celrep.2024.115055",
        "snippet": "SDIC4-mediated anti-phage activity is more modest (R10- to 200-fold) but still significant",
        "notes": "Cummins et al. report significant SDIC4-mediated anti-phage activity when SDIC4 was expressed in E. coli."
      },
      {
        "reference": "DOI:10.1016/j.celrep.2024.115055",
        "snippet": "In the presence of full-length SDIC4 or SDIC4B, we observed a decrease in the adsorption rate",
        "notes": "Cummins et al. connect full-length SDIC4 and SDIC4B with a decreased bacteriophage adsorption rate."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "SDIC4 | 10\\.1016/j\\.celrep\\.2024\\.115055 | Multi-conflict islands are a widespread trend within Serratia spp",
        "notes": "The pinned DefenseFinder article registry maps the SDIC4 source key to the Cummins et al. Serratia multi-conflict-island paper."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| SDIC4__SDIC4A                                    |                                                  | SDIC4                  | Custom                  | 100    |",
        "notes": "The pinned DefenseFinder HMM inventory records SDIC4__SDIC4A as a custom SDIC4 profile."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| SDIC4__SDIC4B                                    |                                                  | SDIC4                  | Custom                  | 100    |",
        "notes": "The pinned DefenseFinder HMM inventory records SDIC4__SDIC4B as a custom SDIC4 profile."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "sdic4_locus_reduces_phage_adsorption",
        "title": "SDIC4 loci reduce bacterial phage adsorption",
        "description": "Conservative system-level sketch linking the SDIC4 locus to reduced adsorption of invading bacteriophages.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures SDIC4 as a named anti-phage system with SDIC4A and SDIC4B DefenseFinder profiles while leaving natural host breadth, sensitive-phage breadth, the SDIC4 type I versus type II boundary, the exact SDIC4A/SDIC4B profile-to-protein correspondence, the receptor or phage target, and rule-level detection criteria unresolved.",
        "nodes": [
          {
            "node_id": "sdic4_locus",
            "label": "SDIC4 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "An SDIC4 anti-phage defense locus represented in the pinned DefenseFinder HMM inventory by SDIC4A and SDIC4B custom profiles."
          },
          {
            "node_id": "phage_adsorption_reduction",
            "label": "reduced phage adsorption rate",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduction of the rate at which invading bacteriophages adsorb to bacterial cells."
          },
          {
            "node_id": "sdic4_system_trait",
            "label": "SDIC4 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000421",
            "description": "Possession of a genome-encoded SDIC4 phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "sdic4_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "phage_adsorption_reduction",
            "description": "The SDIC4 locus contributes to reduced adsorption of invading bacteriophages.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.celrep.2024.115055",
                "snippet": "In the presence of full-length SDIC4 or SDIC4B, we observed a decrease in the adsorption rate",
                "notes": "Cummins et al. report decreased phage adsorption for full-length SDIC4 and SDIC4B."
              },
              {
                "reference": "DOI:10.1016/j.celrep.2024.115055",
                "snippet": "SDIC4 type I and type II elicit protection against phage infection by reducing the adsorption rate of invading phages",
                "notes": "Cummins et al. connect both tested SDIC4 subtypes with reduced phage adsorption."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| SDIC4__SDIC4A                                    |                                                  | SDIC4                  | Custom                  | 100    |",
                "notes": "The pinned DefenseFinder HMM inventory records SDIC4__SDIC4A as a custom SDIC4 profile."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| SDIC4__SDIC4B                                    |                                                  | SDIC4                  | Custom                  | 100    |",
                "notes": "The pinned DefenseFinder HMM inventory records SDIC4__SDIC4B as a custom SDIC4 profile."
              }
            ]
          },
          {
            "subject": "phage_adsorption_reduction",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "sdic4_system_trait",
            "description": "Reduced phage adsorption realizes the SDIC4 system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.celrep.2024.115055",
                "snippet": "SDIC4-mediated anti-phage activity is more modest (R10- to 200-fold) but still significant",
                "notes": "Cummins et al. report significant SDIC4-mediated anti-phage activity."
              }
            ]
          },
          {
            "subject": "sdic4_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "SDIC4 system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.celrep.2024.115055",
                "snippet": "SDIC4-mediated anti-phage activity is more modest (R10- to 200-fold) but still significant",
                "notes": "Cummins et al. report SDIC4-mediated anti-phage activity."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "SDIC4 | 10\\.1016/j\\.celrep\\.2024\\.115055 | Multi-conflict islands are a widespread trend within Serratia spp",
                "notes": "The pinned DefenseFinder article registry maps the SDIC4 source key to the Cummins et al. Serratia multi-conflict-island paper."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "sdic4-defensefinder-model-gap",
        "prompt": "Resolve SDIC4 natural host breadth, sensitive-phage breadth, type I versus type II component scope, SDIC4A/SDIC4B component functions, receptor or phage target, and rule-level detection criteria before minting narrower SDIC4 mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Cummins et al. support SDIC4 as a VasI-like anti-phage system that reduces phage adsorption, and the pinned DefenseFinder HMM inventory records SDIC4A and SDIC4B profile rows. The pinned rules table has no SDIC4 row, and the first-pass record does not resolve natural host breadth, sensitive-phage breadth, type I versus type II system boundaries, the exact profile-to-component mapping, the SDIC4A/SDIC4B relationship, or the phage-adsorption target.",
        "evidence": [
          {
            "reference": "DOI:10.1016/j.celrep.2024.115055",
            "snippet": "SDIC4 comprises SDIC4A, a protein of unknown function, and SDIC4B, harboring the VasI-like domain",
            "notes": "Cummins et al. describe the initially named SDIC4 candidate as an SDIC4A/SDIC4B system."
          },
          {
            "reference": "DOI:10.1016/j.celrep.2024.115055",
            "snippet": "SDIC4 type I and type II elicit protection against phage infection by reducing the adsorption rate of invading phages",
            "notes": "Cummins et al. later add a second SDIC4 subtype and connect both tested types with reduced adsorption."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
            "snippet": "SDIC4 | 10\\.1016/j\\.celrep\\.2024\\.115055 | Multi-conflict islands are a widespread trend within Serratia spp",
            "notes": "The pinned DefenseFinder article registry maps the SDIC4 source key to the Cummins et al. Serratia multi-conflict-island paper."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| SDIC4__SDIC4A                                    |                                                  | SDIC4                  | Custom                  | 100    |",
            "notes": "The pinned DefenseFinder HMM inventory records SDIC4__SDIC4A as a custom SDIC4 profile."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| SDIC4__SDIC4B                                    |                                                  | SDIC4                  | Custom                  | 100    |",
            "notes": "The pinned DefenseFinder HMM inventory records SDIC4__SDIC4B as a custom SDIC4 profile."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "The pinned DefenseFinder rules table does not list SDIC4, leaving rule-level detection criteria unresolved."
          }
        ],
        "attaches_to": [
          "causal_graphs#sdic4_locus_reduces_phage_adsorption"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-27"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-27T23:47:56Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted SDIC4 system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; kept the graph at candidate-locus level because the pinned DefenseFinder SDIC4 HMM rows are not backed by a rules row; proposals/metpo_traitmech_v298 reserves the replacement placeholder.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-27T23:47:57Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed SDIC4 system canonical_examples and left them empty because Cummins et al. support plasmid-expressed E. coli and S. marcescens phage-challenge and phage-adsorption assays plus a DefenseFinder SDIC4 system model, but not a direct native microbial isolate exemplar with experimentally verified endogenous SDIC4 activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000259",
    "label": "SEFIR system",
    "definition": "A phage defense system in which an organism possesses a SEFIR locus represented by a bSEFIR profile that can protect bacteria from bacteriophage infection.",
    "definition_source": "DOI:10.1016/j.chom.2022.09.017",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "SEFIR",
        "synonym_type": "EXACT_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1016/j.chom.2022.09.017",
        "snippet": "discovery of 21 defense systems that protect bacteria from phages, based on computational genomic analyses and phage-infection experiments",
        "notes": "Millman et al. report the computational and experimental cohort that DefenseFinder cites for SEFIR as a bacterial anti-phage system."
      },
      {
        "reference": "DOI:10.1101/2022.05.11.491447",
        "snippet": "discovery of 21 new defense systems that protect bacteria from phages, based on computational genomic analyses and phage infection experiments",
        "notes": "The bioRxiv version of Millman et al. independently carries the 21-system discovery claim linked from DefenseFinder's SEFIR article registry."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "SEFIR | 10\\.1101/2022\\.05\\.11\\.491447 | An expanding arsenal of immune systems that protect bacteria from phages",
        "notes": "The DefenseFinder model registry maps the named SEFIR system to the Millman et al. antiphage-system discovery preprint."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "SEFIR\tSEFIR\t1\t1\tSEFIR__bSEFIR",
        "notes": "The DefenseFinder rules table models SEFIR with a bSEFIR profile."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "SEFIR__bSEFIR                                    | SEFIR__bSEFIR                                    | SEFIR",
        "notes": "The DefenseFinder HMM inventory records bSEFIR as a SEFIR profile."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "sefir_locus_restricts_phage",
        "title": "SEFIR loci confer bacterial phage defense",
        "description": "Conservative system-level sketch linking possession of a SEFIR locus to restricted bacteriophage propagation without asserting the unresolved phage trigger or molecular output.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures SEFIR as a named anti-phage system with the required DefenseFinder bSEFIR profile while leaving its phage trigger, molecular substrate, antiviral effector output, and subtype breadth unresolved.",
        "nodes": [
          {
            "node_id": "sefir_locus",
            "label": "SEFIR locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A SEFIR anti-phage defense locus satisfying a DefenseFinder rule over the bSEFIR profile."
          },
          {
            "node_id": "restricted_phage_propagation",
            "label": "restricted phage propagation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced propagation of bacteriophage in cells carrying the SEFIR system."
          },
          {
            "node_id": "sefir_system_trait",
            "label": "SEFIR system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000259",
            "description": "Possession of a genome-encoded SEFIR phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "sefir_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "restricted_phage_propagation",
            "description": "DefenseFinder maps SEFIR to a bacterial anti-phage-system discovery preprint and represents SEFIR loci through the bSEFIR component profile.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.chom.2022.09.017",
                "snippet": "discovery of 21 defense systems that protect bacteria from phages",
                "notes": "Millman et al. describe the anti-phage discovery cohort that the DefenseFinder SEFIR registry row maps to the SEFIR system."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "SEFIR | 10\\.1101/2022\\.05\\.11\\.491447 | An expanding arsenal of immune systems that protect bacteria from phages",
                "notes": "The DefenseFinder registry maps SEFIR itself to the Millman et al. bacterial antiphage-system discovery preprint."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "SEFIR\tSEFIR\t1\t1\tSEFIR__bSEFIR",
                "notes": "The DefenseFinder rules table supports bSEFIR as the required SEFIR system profile."
              }
            ]
          },
          {
            "subject": "restricted_phage_propagation",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "sefir_system_trait",
            "description": "SEFIR-mediated phage restriction realizes the SEFIR system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.chom.2022.09.017",
                "snippet": "discovery of 21 defense systems that protect bacteria from phages",
                "notes": "Millman et al. place the SEFIR discovery cohort in the set of bacterial systems that protect against phages."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "SEFIR | 10\\.1101/2022\\.05\\.11\\.491447 | An expanding arsenal of immune systems that protect bacteria from phages",
                "notes": "DefenseFinder records SEFIR as a named system from the Millman et al. antiphage discovery preprint."
              }
            ]
          },
          {
            "subject": "sefir_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "SEFIR system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "An expanding arsenal of immune systems that protect bacteria from phages",
                "notes": "DefenseFinder associates SEFIR with the Millman et al. bacterial antiphage-system discovery paper."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "sefir-mechanism-gap",
        "prompt": "Resolve SEFIR phage triggers and effector outputs before minting narrower SEFIR mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Millman et al. and DefenseFinder support SEFIR as a named anti-phage system with a bSEFIR profile, but the trigger, molecular substrate, antiviral effector output, and subtype-specific mechanism are not resolved enough here to assert a narrower mechanistic child trait.",
        "attaches_to": [
          "causal_graphs#sefir_locus_restricts_phage"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-19"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-19T01:51:02Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted SEFIR system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v136.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000233",
    "label": "Septu system",
    "definition": "A phage defense system in which an organism possesses a Septu locus encoding PtuA and the HNH endonuclease PtuB, whose PtuAB oligomer confers antiphage immunity through nuclease-mediated phage genome cleavage in standalone systems and can be regulated by retron RT-msDNA complexes in Retron-Septu loci.",
    "definition_source": "DOI:10.1038/s41594-023-01172-8",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "Septu",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1126/science.aar4120"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1126/science.aar4120",
        "snippet": "Septu PtuAB pfam13304, COG3950, pfam13395, pfam01844 ATPase, HNH nuclease 2,506 2,117 (4.1%)",
        "notes": "Doron et al. reported Septu/PtuAB as an ATPase- and HNH-nuclease-linked system in their pangenome-scale antiphage-system discovery screen."
      },
      {
        "reference": "DOI:10.1038/s41594-023-01172-8",
        "snippet": "E. coli Septu system, an anti-phage defense system, comprises two components: PtuA and PtuB",
        "notes": "Yang et al. support defining Septu as a two-component PtuA/PtuB antiphage system."
      },
      {
        "reference": "DOI:10.1038/s41594-023-01172-8",
        "snippet": "PtuA contains an ATPase domain while PtuB is a nuclease that belongs to the His-Asn-His (HNH) family",
        "notes": "Yang et al. support the ATPase and HNH endonuclease component classes that distinguish the PtuAB system."
      },
      {
        "reference": "DOI:10.1038/s41594-023-01172-8",
        "snippet": "PtuAB restricts phage growth by cleaving phage genomic DNA",
        "notes": "Yang et al. connect the PtuAB complex to nuclease-mediated restriction of phage growth in cells."
      },
      {
        "reference": "DOI:10.1126/science.adv3344",
        "snippet": "The Retron-Septu system uniquely integrates retron and Septu antiphage defenses",
        "notes": "Wang et al. support recognizing Retron-Septu as a Septu architecture with coupled retron regulation, not as a separate exact replacement for the broader Septu class."
      },
      {
        "reference": "DOI:10.1126/science.adv3344",
        "snippet": "Activation occurs upon disassembly, releasing PtuAB, which degrades single-stranded DNA to restrict phage replication",
        "notes": "Wang et al. connect Retron-Septu activation to release of PtuAB and DNA degradation that restricts phage replication."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:562",
        "taxon_label": "Escherichia coli",
        "note": "Yang et al. structurally and functionally characterized an Escherichia coli Septu system in which PtuA and PtuB assemble into a 6:2 oligomer that restricts phage growth by cleaving phage genomic DNA.",
        "reference": "DOI:10.1038/s41594-023-01172-8"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "septu_ptuab_oligomer_nuclease_defense",
        "title": "Septu PtuAB oligomers cleave phage genomic DNA",
        "description": "Evidence-backed process sketch linking a Septu locus to PtuAB oligomer assembly, PtuB-dependent nuclease activity, cleavage of phage genomic DNA, and inhibition of phage replication.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures the shared PtuA/PtuB nuclease logic without asserting one exact activation trigger, ATP regulatory state, phage cue, target DNA modification, standalone-versus-retron architecture, or ssDNA-versus-genomic-DNA substrate across all Septu and Retron-Septu loci.",
        "nodes": [
          {
            "node_id": "septu_locus",
            "label": "Septu locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A Septu antiphage locus encoding a PtuA ATPase and cognate PtuB HNH nuclease."
          },
          {
            "node_id": "ptuab_oligomer_assembly",
            "label": "PtuAB oligomer assembly",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Assembly of PtuA and PtuB into a higher-order antiphage complex."
          },
          {
            "node_id": "ptuab_antiphage_activity",
            "label": "PtuAB antiphage activity",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "PtuAB complex activity, dependent on PtuB nuclease activity, that restricts phage growth."
          },
          {
            "node_id": "phage_genomic_dna_cleavage",
            "label": "phage genomic DNA cleavage",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Cleavage or degradation of phage genomic DNA by an activated PtuAB complex."
          },
          {
            "node_id": "phage_growth",
            "label": "phage growth",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Bacteriophage growth and amplification inside a bacterial host population."
          },
          {
            "node_id": "septu_system_trait",
            "label": "Septu system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000233",
            "description": "Possession of a genome-encoded Septu phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "septu_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "ptuab_oligomer_assembly",
            "description": "The Septu locus encodes PtuA and PtuB components that assemble into a higher-order PtuAB complex.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41594-023-01172-8",
                "snippet": "PtuA and PtuB form a stable complex with a 6:2 stoichiometry",
                "notes": "Yang et al. support assembly of the PtuA and PtuB Septu components."
              }
            ]
          },
          {
            "subject": "ptuab_oligomer_assembly",
            "predicate": "enables",
            "predicate_id": "RO:0002327",
            "object": "ptuab_antiphage_activity",
            "description": "PtuAB assembly is critical for antiphage activity.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41594-023-01172-8",
                "snippet": "the assembly of PtuAB is critical for its anti-phage activity",
                "notes": "Yang et al. support a functional connection between PtuAB assembly and antiphage activity."
              }
            ]
          },
          {
            "subject": "ptuab_antiphage_activity",
            "predicate": "enables",
            "predicate_id": "RO:0002327",
            "object": "phage_genomic_dna_cleavage",
            "description": "The PtuAB complex restricts phage growth by cleaving phage genomic DNA.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41594-023-01172-8",
                "snippet": "E. coli anti-phage defense mediated by PtuAB via degrading the phage genomic DNA",
                "notes": "Yang et al. connect PtuAB activity to cleavage of phage genomic DNA."
              }
            ]
          },
          {
            "subject": "phage_genomic_dna_cleavage",
            "predicate": "mitigates",
            "predicate_id": "METPO:2007407",
            "object": "phage_growth",
            "description": "PtuAB-mediated cleavage of phage genomic DNA restricts phage growth.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41594-023-01172-8",
                "snippet": "PtuAB restricts phage growth by cleaving phage genomic DNA",
                "notes": "Yang et al. connect PtuAB nuclease activity to reduced phage growth."
              }
            ]
          },
          {
            "subject": "phage_genomic_dna_cleavage",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "septu_system_trait",
            "description": "PtuAB-mediated phage genomic DNA cleavage realizes the Septu system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41594-023-01172-8",
                "snippet": "PtuAB can confer bacteria immune defense against phage infection by digesting phage genomic DNA in a species-dependent way",
                "notes": "Yang et al. support the DNA-digestion logic of PtuAB antiphage defense."
              }
            ]
          },
          {
            "subject": "septu_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Septu system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.aar4120",
                "snippet": "Septu PtuAB pfam13304, COG3950, pfam13395, pfam01844 ATPase, HNH nuclease 2,506 2,117 (4.1%)",
                "notes": "Doron et al. reported Septu in a table of candidate antiphage defense systems."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "septu-standalone-retron-regulation-gap",
        "prompt": "Resolve standalone Septu activation, Retron-Septu release, and DNA-substrate specificity before minting narrower Septu mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Yang et al. support a standalone Escherichia coli PtuAB system in which ATP modulates PtuA/PtuB nuclease activity through an incompletely resolved phage trigger, and Wang et al. support Retron-Septu Ec83/Ec78 complexes in which retron RT-msDNA association keeps PtuAB inactive until disassembly. The first TraitRecord therefore stays at the PtuA/PtuB system level until separate review resolves standalone activation, retron-dependent release, target DNA classes, and phage-specific activity across Septu loci.",
        "posed_by": "codex",
        "posed_date": "2026-09-15"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-15T23:58:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Septu system as a DOI-backed GENOMICS TraitRecord under the phage defense system parent after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v110.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000255",
    "label": "Shango system",
    "definition": "A phage defense system in which an organism possesses a Shango locus represented by a mandatory SngA profile and an SngB or SngC profile that can protect bacteria from bacteriophage infection.",
    "definition_source": "DOI:10.1016/j.chom.2022.09.017",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "Shango",
        "synonym_type": "EXACT_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1016/j.chom.2022.09.017",
        "snippet": "discovery of 21 defense systems that protect bacteria from phages, based on computational genomic analyses and phage-infection experiments",
        "notes": "Millman et al. report the computational and experimental cohort that DefenseFinder cites for Shango as a bacterial anti-phage system."
      },
      {
        "reference": "DOI:10.1101/2022.05.11.491447",
        "snippet": "discovery of 21 new defense systems that protect bacteria from phages, based on computational genomic analyses and phage infection experiments",
        "notes": "The bioRxiv version of Millman et al. independently carries the 21-system discovery claim linked from DefenseFinder's Shango article registry."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "Shango | 10\\.1101/2022\\.05\\.11\\.491447 | An expanding arsenal of immune systems that protect bacteria from phages",
        "notes": "The DefenseFinder model registry maps the named Shango system to the Millman et al. antiphage-system discovery preprint."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "Shango\tShango\t1\t2\tShango__SngA\tShango__SngB, Shango__SngC",
        "notes": "The DefenseFinder rules table models Shango with mandatory SngA plus SngB or SngC accessory profiles."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "Shango__SngA                                      | Shango__SngA                                      | Shango",
        "notes": "The DefenseFinder HMM inventory records SngA as a Shango profile."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "Shango__SngB                                      | Shango__SngB                                      | Shango",
        "notes": "The DefenseFinder HMM inventory records SngB as a Shango profile."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "Shango__SngC                                      | Shango__SngC                                      | Shango",
        "notes": "The DefenseFinder HMM inventory records SngC as a Shango profile."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "shango_locus_restricts_phage",
        "title": "Shango loci confer bacterial phage defense",
        "description": "Conservative system-level sketch linking possession of a Shango locus to restricted bacteriophage propagation without asserting the unresolved phage trigger or molecular output.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Shango as a named anti-phage system with DefenseFinder SngA, SngB, and SngC profile choices while leaving its phage trigger, molecular substrate, antiviral effector output, and subtype breadth unresolved.",
        "nodes": [
          {
            "node_id": "shango_locus",
            "label": "Shango locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A Shango anti-phage defense locus satisfying a DefenseFinder rule over SngA and SngB/SngC profiles."
          },
          {
            "node_id": "restricted_phage_propagation",
            "label": "restricted phage propagation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced propagation of bacteriophage in cells carrying the Shango system."
          },
          {
            "node_id": "shango_system_trait",
            "label": "Shango system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000255",
            "description": "Possession of a genome-encoded Shango phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "shango_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "restricted_phage_propagation",
            "description": "DefenseFinder maps Shango to a bacterial anti-phage-system discovery preprint and represents Shango loci through SngA, SngB, and SngC component profiles.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.chom.2022.09.017",
                "snippet": "discovery of 21 defense systems that protect bacteria from phages",
                "notes": "Millman et al. describe the anti-phage discovery cohort that the DefenseFinder Shango registry row maps to the Shango system."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Shango | 10\\.1101/2022\\.05\\.11\\.491447 | An expanding arsenal of immune systems that protect bacteria from phages",
                "notes": "The DefenseFinder registry maps Shango itself to the Millman et al. bacterial antiphage-system discovery preprint."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "Shango\tShango\t1\t2\tShango__SngA\tShango__SngB, Shango__SngC",
                "notes": "The DefenseFinder rules table supports SngA as a mandatory Shango profile and SngB or SngC as accessory Shango profiles."
              }
            ]
          },
          {
            "subject": "restricted_phage_propagation",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "shango_system_trait",
            "description": "Shango-mediated phage restriction realizes the Shango system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.chom.2022.09.017",
                "snippet": "discovery of 21 defense systems that protect bacteria from phages",
                "notes": "Millman et al. place the Shango discovery cohort in the set of bacterial systems that protect against phages."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Shango | 10\\.1101/2022\\.05\\.11\\.491447 | An expanding arsenal of immune systems that protect bacteria from phages",
                "notes": "DefenseFinder records Shango as a named system from the Millman et al. antiphage discovery preprint."
              }
            ]
          },
          {
            "subject": "shango_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Shango system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "An expanding arsenal of immune systems that protect bacteria from phages",
                "notes": "DefenseFinder associates Shango with the Millman et al. bacterial antiphage-system discovery paper."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "shango-mechanism-gap",
        "prompt": "Resolve Shango phage triggers and effector outputs before minting narrower Shango mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Millman et al. and DefenseFinder support Shango as a named anti-phage system with SngA, SngB, and SngC profile choices, but the trigger, molecular substrate, antiviral effector output, and subtype-specific mechanism are not resolved enough here to assert a narrower mechanistic child trait.",
        "attaches_to": [
          "causal_graphs#shango_locus_restricts_phage"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-18"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-18T23:31:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Shango system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v132.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000220",
    "label": "Shedu system",
    "definition": "A genomics trait describing possession of a Shedu antiphage defense system encoding a single-protein immune nuclease with a conserved nuclease core and regulated sensor domain architecture.",
    "definition_source": "DOI:10.1016/j.cell.2024.11.030",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "Shedu anti-phage defense system",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1016/j.cell.2024.11.030"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1016/j.cell.2024.11.030",
        "snippet": "Shedu is a single-component defense system comprising a putative nuclease SduA",
        "notes": "Loeff et al. support Shedu as a named, single-component antiphage defense system centered on SduA."
      },
      {
        "reference": "DOI:10.1016/j.cell.2024.11.030",
        "snippet": "End binding positions the DNA over the PD-(D/E)XK nuclease domain, resulting in dsDNA nicking at a fixed distance from the 5' end",
        "notes": "Loeff et al. connect Shedu DNA-end recognition to positioned double-stranded DNA nicking."
      },
      {
        "reference": "DOI:10.1016/j.cell.2024.11.030",
        "snippet": "The end-directed DNA nicking activity of Shedu prevents propagation of linear DNA",
        "notes": "Loeff et al. support DNA-end-directed nicking as an antiviral Shedu output that blocks linear DNA propagation."
      },
      {
        "reference": "DOI:10.1016/j.molcel.2024.12.004",
        "snippet": "Prokaryotes possess diverse anti-bacteriophage immune systems, including the single-protein Shedu nuclease",
        "notes": "Gu et al. also place Shedu among prokaryotic antiphage immune systems and support its single-protein nuclease architecture."
      },
      {
        "reference": "DOI:10.1016/j.molcel.2024.12.004",
        "snippet": "we reveal the structural basis for activation of Bacillus cereus Shedu",
        "notes": "Gu et al. support Bacillus cereus Shedu as a structurally characterized representative."
      },
      {
        "reference": "DOI:10.1016/j.molcel.2024.12.004",
        "snippet": "these data reveal Shedu as a broad family of immune nucleases with a common nuclease core regulated by diverse NTDs",
        "notes": "Gu et al. support defining Shedu at the immune-nuclease family level while leaving N-terminal domain diversity for narrower subtype review."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1396",
        "taxon_label": "Bacillus cereus",
        "note": "Gu et al. structurally characterized Bacillus cereus Shedu and reported that this nuclease cleaves near DNA ends with a 3' single-stranded overhang.",
        "reference": "DOI:10.1016/j.molcel.2024.12.004"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "shedu_dna_end_nicking",
        "title": "Shedu immune nucleases nick DNA ends during antiphage defense",
        "description": "Evidence-backed process sketch linking a Shedu locus to SduA-like sensor-dependent nuclease activation, DNA-end nicking, and inhibition of bacteriophage DNA propagation.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures SduA/Shedu immune-nuclease outputs without asserting one universal N-terminal sensor class, DNA-end substrate, overhang preference, phage target, activation signal, escape strategy, or Bacillus-specific mechanism across all Shedu homologs.",
        "nodes": [
          {
            "node_id": "shedu_locus",
            "label": "Shedu locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A Shedu antiphage defense locus encoding a single-protein SduA-like immune nuclease."
          },
          {
            "node_id": "sdua_immune_nuclease",
            "label": "SduA immune nuclease",
            "node_type": "GENE_OR_PROTEIN",
            "description": "The single-protein Shedu immune nuclease, comprising a conserved nuclease core and an N-terminal regulatory/sensor domain.",
            "gene_symbols": [
              "sduA"
            ],
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "No family-level term covers SduA. A bounded search of all InterPro member databases and of GO via OLS4 for 'Shedu' on 2026-10-08 returned only two domain entries plus their InterPro integrations: IPR025359 (Shedu protein SduA, C-terminal; Pfam PF14082, whose InterPro name history is DUF4263 then SduA_C) and IPR048396 (Shedu protein SduA, N-terminal; Pfam PF21407). Neither denotes the whole protein: InterPro reports PF14082 in 1304 UniProt proteins across 2464 taxa with 18 domain architectures, so grounding this whole-protein node to the C-terminal domain would sweep in carriers whose partner domains differ from SduA's. UniProt lists no NCBIfam cross-reference for B7HFR2, and OLS4 returns no GO term for Shedu. The node therefore stays reviewed label-only rather than taking a domain term as a family grounding.",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:B7HFR2",
                "protein_label": "Shedu protein SduA",
                "gene_symbol": "sduA",
                "taxon_id": "NCBITaxon:405532",
                "taxon_label": "Bacillus cereus (strain B4264)",
                "entry_status": "REVIEWED",
                "retrieved_on": "2026-10-08",
                "entry_version": 58,
                "sequence_version": 1,
                "role": "Bacillus cereus B4264 SduA switches between inactive and active states through conformational changes affecting active-site architecture, which Gu et al. report are controlled by its N-terminal domain. UniProt annotates this entry as the only component of its Shedu system; the attached snippets do not establish that single-component architecture.",
                "evidence": [
                  {
                    "reference": "DOI:10.1016/j.molcel.2024.12.004",
                    "snippet": "we reveal the structural basis for activation of Bacillus cereus Shedu",
                    "notes": "Gu et al. determined cryo-EM structures of Bacillus cereus Shedu; PDBe maps their entries 8TI8, 8TI9 and 8TIA to UniProtKB:B7HFR2 (Bacillus cereus B4264), so the structurally characterized protein is this accession. Snippet verified verbatim in the Europe PMC abstract of PMID:39742666."
                  },
                  {
                    "reference": "DOI:10.1016/j.molcel.2024.12.004",
                    "snippet": "Two cryoelectron microscopy structures of Shedu show that it switches between inactive and active states through conformational changes affecting active-site architecture, which are controlled by the protein's N-terminal domain (NTD)",
                    "notes": "Gu et al. establish the N-terminal domain as the regulator of the nuclease active site in this B. cereus protein. The role statement is scoped to the tested protein; the paper's survey of 79 N-terminal domain types is explicitly about homologs, not about this accession. Snippet verified verbatim in the Europe PMC abstract of PMID:39742666."
                  }
                ]
              }
            ]
          },
          {
            "node_id": "shedu_nuclease_activation",
            "label": "Shedu nuclease activation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Sensor-dependent activation of the Shedu nuclease core."
          },
          {
            "node_id": "shedu_dna_end_nicking",
            "label": "Shedu DNA end nicking",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Shedu-mediated recognition and nicking of DNA near free or structured ends."
          },
          {
            "node_id": "phage_dna_propagation",
            "label": "phage DNA propagation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Propagation of bacteriophage DNA inside an infected bacterial host."
          },
          {
            "node_id": "shedu_system_trait",
            "label": "Shedu system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000220",
            "description": "Possession of a genome-encoded Shedu antiphage defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "sdua_immune_nuclease",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "shedu_nuclease_activation",
            "description": "In Bacillus cereus SduA, the N-terminal domain controls switching of the nuclease core between inactive and active states. Scoped to that protein: the graph's scope_notes leave the sensor class open across Shedu homologs, and the Loeff edge gives the N-terminal domain a DNA-end clamp role in a different homolog.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.molcel.2024.12.004",
                "snippet": "Two cryoelectron microscopy structures of Shedu show that it switches between inactive and active states through conformational changes affecting active-site architecture, which are controlled by the protein's N-terminal domain (NTD)",
                "notes": "Gu et al. support N-terminal-domain-controlled activation of the B. cereus Shedu nuclease active site."
              }
            ]
          },
          {
            "subject": "shedu_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "shedu_nuclease_activation",
            "description": "Shedu loci encode SduA-like single-protein immune nucleases whose sensor domains regulate a common nuclease core.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.cell.2024.11.030",
                "snippet": "Shedu is a single-component defense system comprising a putative nuclease SduA",
                "notes": "Loeff et al. support the single-component SduA-centered Shedu architecture."
              },
              {
                "reference": "DOI:10.1016/j.molcel.2024.12.004",
                "snippet": "these data reveal Shedu as a broad family of immune nucleases with a common nuclease core regulated by diverse NTDs",
                "notes": "Gu et al. support Shedu as a broader family of sensor-regulated immune nucleases."
              }
            ]
          },
          {
            "subject": "shedu_nuclease_activation",
            "predicate": "enables",
            "predicate_id": "RO:0002327",
            "object": "shedu_dna_end_nicking",
            "description": "Shedu sensor-domain activation enables PD-(D/E)XK nuclease-domain nicking of DNA near DNA ends.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.cell.2024.11.030",
                "snippet": "the N-terminal domains of SduA form a clamp that recognizes free DNA ends",
                "notes": "Loeff et al. support free DNA-end recognition by the N-terminal SduA clamp."
              },
              {
                "reference": "DOI:10.1016/j.cell.2024.11.030",
                "snippet": "End binding positions the DNA over the PD-(D/E)XK nuclease domain, resulting in dsDNA nicking at a fixed distance from the 5' end",
                "notes": "Loeff et al. connect DNA-end binding to SduA nuclease-domain positioning and double-stranded DNA nicking."
              }
            ]
          },
          {
            "subject": "shedu_dna_end_nicking",
            "predicate": "mitigates",
            "predicate_id": "METPO:2007407",
            "object": "phage_dna_propagation",
            "description": "Shedu-mediated nicking or degradation of phage DNA ends inhibits bacteriophage DNA propagation.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.cell.2024.11.030",
                "snippet": "The end-directed DNA nicking activity of Shedu prevents propagation of linear DNA",
                "notes": "Loeff et al. support Shedu DNA nicking as a barrier to linear DNA propagation."
              },
              {
                "reference": "DOI:10.1016/j.molcel.2024.12.004",
                "snippet": "Shedu cleaves near DNA ends with a 3' single-stranded overhang, likely enabling it to specifically degrade the DNA injected by certain bacteriophages",
                "notes": "Gu et al. connect B. cereus Shedu DNA-end cleavage to likely degradation of injected phage DNA."
              }
            ]
          },
          {
            "subject": "shedu_dna_end_nicking",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "shedu_system_trait",
            "description": "DNA-end nicking is a characterized antiviral output that realizes the Shedu system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.cell.2024.11.030",
                "snippet": "Taken together, these results define the antiviral mechanism of Shedu systems",
                "notes": "Loeff et al. connect DNA-end sensing and cleavage to the Shedu antiviral mechanism."
              }
            ]
          },
          {
            "subject": "shedu_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Shedu system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.molcel.2024.12.004",
                "snippet": "Prokaryotes possess diverse anti-bacteriophage immune systems, including the single-protein Shedu nuclease",
                "notes": "Gu et al. place Shedu in the family of prokaryotic antiphage immune systems."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "shedu-sensor-and-substrate-gap",
        "prompt": "Resolve Shedu sensor classes and DNA substrate preferences before minting narrower Shedu subtype or mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Loeff et al. support free-DNA-end recognition and end-directed DNA nicking by SduA, and Gu et al. support a common Shedu nuclease core regulated by diverse N-terminal domains, but Shedu homologs need separate review before TraitMech asserts one universal N-terminal sensor class, activating DNA substrate, overhang preference, phage target, or escape strategy.",
        "posed_by": "codex",
        "posed_date": "2026-09-15"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-15T15:25:04Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Shedu system as a DOI-backed GENOMICS TraitRecord under the phage defense system parent after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v97.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-08T04:22:03Z",
        "curator": "claude",
        "action": "ADD_SDUA_PROTEIN_EXAMPLE",
        "changes": "Added a GENE_OR_PROTEIN node for the single-protein Shedu immune nuclease with UniProtKB:B7HFR2 (Shedu protein SduA, Bacillus cereus B4264, NCBITaxon:405532) as a taxon-paired protein example, plus one contributes-to edge to Shedu nuclease activation. UniProt REST verified the accession anonymously on 2026-10-08 as a current reviewed (Swiss-Prot) primary accession with no secondary accessions, entry version 58 and sequence version 1, organism Bacillus cereus strain B4264 (taxon 405532), cross-referenced to Pfam PF14082 (SduA_C, whose InterPro name history is DUF4263 then SduA_C) and PF21407. Evidence is Gu et al. 2024 Mol Cell (PMID:39742666, DOI:10.1016/j.molcel.2024.12.004), whose cryo-EM entries 8TI8/8TI9/8TIA PDBe maps to this exact accession; both snippets were verified verbatim against the Europe PMC abstract. The node is REVIEWED_LABEL_ONLY because no family-level InterPro, NCBIfam or GO term covers SduA: only the two domain entries IPR025359 and IPR048396 exist, and PF14082 spans 1304 UniProt proteins with 18 domain architectures. Graph scope_status, mapping_status, definition, hierarchy and existing evidence are unchanged.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000570",
    "label": "short Lamassu system",
    "definition": "A Lamassu system in which an organism possesses a locus from the short-LmuB family, characterized by shorter coiled-coil regions in its SMC-like LmuB sensor than in long Lamassu systems.",
    "definition_source": "DOI:10.1073/pnas.2519643122",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000232"
    ],
    "synonyms": [
      {
        "synonym_text": "short Lamassu",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1073/pnas.2519643122"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1073/pnas.2519643122",
        "snippet": "two major clades, which were mainly distinguished by the length of coiled-coil regions",
        "notes": "Results, LmuB phylogeny paragraph and Figure 1: the authors distinguish short and long families using phylogeny and structure. Their approximate 600-residue short-family average is not a membership cutoff."
      },
      {
        "reference": "DOI:10.1073/pnas.2519643122",
        "snippet": "short Lamassus, selecting the experimentally validated Cap4 system from V. cholerae",
        "notes": "Results, paragraph introducing structural work: identifies Vc-Cap4 as a short-family exemplar. Figure 2A shows its 653-residue LmuB. Antiphage assays here used the natural operon expressed in E. coli, not a species-wide native-host assay."
      },
      {
        "reference": "https://data.rcsb.org/rest/v1/core/polymer_entity/9NY5/3",
        "snippet": "\"rcsb_sample_sequence_length\":653",
        "notes": "PDB 9NY5, entity 3, entity_poly: deposited LmuB sequence length, consistent with paper Figure 2A. This is not the number of modeled residues or a length threshold for the family."
      },
      {
        "reference": "https://data.rcsb.org/rest/v1/core/polymer_entity/9NY5/3",
        "snippet": "\"pdbx_gene_src_ncbi_taxonomy_id\":\"666\",\"pdbx_gene_src_scientific_name\":\"Vibrio cholerae\"",
        "notes": "PDB entity_src_gen: source organism of the deposited LmuB, not the recombinant expression host. No strain or genome assembly is inferred from the species-level deposition."
      },
      {
        "reference": "https://data.rcsb.org/rest/v1/core/polymer_entity/9NY5/3",
        "snippet": "\"pdbx_host_org_ncbi_taxonomy_id\":\"562\",\"pdbx_host_org_scientific_name\":\"Escherichia coli\"",
        "notes": "PDB entity_src_gen explicitly identifies the separate expression host. This does not establish natural E. coli possession of the Vc-Cap4 locus."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:666",
        "taxon_label": "Vibrio cholerae",
        "reference": "DOI:10.1073/pnas.2519643122",
        "note": "The source organism of the Vc-Cap4 system explicitly selected as a short-Lamassu exemplar. PDB 9NY5 entity 3 independently records a 653-residue LmuB from taxon 666, expressed in E. coli. The cited antiphage assays use a heterologous E. coli host. This does not assert species-wide possession, a specific strain or assembly, or native V. cholerae phage resistance."
      }
    ],
    "discussions": [
      {
        "discussion_id": "short-lamassu-classification-and-mechanism-scope",
        "prompt": "Resolve family-wide mechanisms and classify borderline loci.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Short denotes the phylogenetic and structural LmuB family, not an arbitrary amino-acid cutoff or an isolated short protein. LmuC-loss clade S and effector-domain-loss clade O preclude requiring one universal three-component effector architecture. Type I/II component classifications and effector names are not exact synonyms for this family. HNH's explicitly short-form definition supports its new parent; SMEK's unresolved long-profile call prevents the same inference. Other table-defined subtypes require their own scope review before reparenting. The Vc-Cap4 mechanism already described on the Lamassu parent is not assumed universal across short-family effectors, so no duplicate or universal mechanism graph is asserted here. A registry Hypothetical label must not be equated with clade O's effector-domain loss without explicit evidence. The LmuC-loss architecture is now represented separately by traitmech:000573 Lamassu type I system. The paper identifies clade S as type I; clade O's effector-domain loss remains a distinct question. The new component class is not treated as a synonym for this whole length family, and its broader phylogenetic distribution is left open rather than inferred from one clade. Existing hierarchy and mechanism scope are unchanged.",
        "posed_by": "codex",
        "posed_date": "2026-10-03"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-03T12:33:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added the literature-defined short Lamassu family with exact paper, PDB and NCBI snippets, a qualified Vc-Cap4 source-organism example, and no artificial protein-length cutoff. Ignored-and-hidden searches found no exact record or METPO term. Reserved METPO:1052400 in proposals/metpo_traitmech_v447 and refined the HNH child's parent.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-03T13:17:37Z",
        "curator": "codex",
        "action": "STRENGTHEN_TAXON_IDENTITY_SNIPPET",
        "changes": "Replaced the verbatim ID-only NCBI snippet with a contiguous species-name-and-ID span supporting the identity notes (#1617). Fresh source checks confirmed the earlier citation form was also verbatim; this change improves claim support, not taxon grounding.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-03T13:41:34Z",
        "curator": "codex",
        "action": "REFINE_SYNONYM_AND_EVIDENCE_SCOPE",
        "changes": "Used the source-attested family name as the exact synonym and aligned the v447 template (#1618). Removed the redundant NCBI evidence row to avoid a quote spanning HTML blocks (#1619). The paper, five exact paper/PDB snippets, PDB source metadata and verified canonical-example taxon retain the substantive support. Earlier curation history is preserved.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-03T13:57:07Z",
        "curator": "codex",
        "action": "CLARIFY_HISTORICAL_SNIPPET_VERIFICATION",
        "changes": "Correction to the 13:17:37Z event (#1620): withdraw the description of the removed species-name-and-ID quote as contiguous. That check joined text across HTML blocks and did not establish a contiguous source span. The distinct earlier citation-form verification is supported by these exact inline raw HTML bytes from https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=666&mode=Info: Taxonomy ID: 666 <small>(for references in articles please use ncbitaxon:666)</small><br>. The lowercase form is quoted source text, not a curated CURIE. Current evidence and taxon grounding are unchanged; earlier events remain preserved.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-03T15:57:07Z",
        "curator": "codex",
        "action": "TRACK_TYPE_I_CLASS",
        "changes": "Linked traitmech:000573 Lamassu type I system to the existing component-architecture discussion using DOI:10.1073/pnas.2519643122 and DOI:10.1038/s41589-025-02102-z. Preserved all definitions, parents, evidence, examples and prior history. Component absence, LmuB-length family and experimental activity remain separate claims.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000258",
    "label": "ShosTA system",
    "definition": "A phage defense system in which an organism possesses a two-component ShosTA locus represented by ShosA and ShosT profiles that can protect bacteria from bacteriophage infection.",
    "definition_source": "DOI:10.1016/j.chom.2022.09.017",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "ShosTA",
        "synonym_type": "EXACT_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1016/j.chom.2022.09.017",
        "snippet": "discovery of 21 defense systems that protect bacteria from phages, based on computational genomic analyses and phage-infection experiments",
        "notes": "Millman et al. report the computational and experimental cohort that DefenseFinder cites for ShosTA as a bacterial anti-phage system."
      },
      {
        "reference": "DOI:10.1101/2022.05.11.491447",
        "snippet": "discovery of 21 new defense systems that protect bacteria from phages, based on computational genomic analyses and phage infection experiments",
        "notes": "The bioRxiv version of Millman et al. independently carries the 21-system discovery claim linked from DefenseFinder's ShosTA article registry."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "ShosTA | 10\\.1101/2022\\.05\\.11\\.491447 | An expanding arsenal of immune systems that protect bacteria from phages",
        "notes": "The DefenseFinder model registry maps the named ShosTA system to the Millman et al. antiphage-system discovery preprint."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "ShosTA\tShosTA\t2\t2\tShosTA__ShosA, ShosTA__ShosT",
        "notes": "The DefenseFinder rules table models ShosTA with ShosA and ShosT profiles."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "ShosTA__ShosA                                    | ShosTA__ShosA                                    | ShosTA",
        "notes": "The DefenseFinder HMM inventory records ShosA as a ShosTA profile."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "ShosTA__ShosT                                    | ShosTA__ShosT                                    | ShosTA",
        "notes": "The DefenseFinder HMM inventory records ShosT as a ShosTA profile."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "shosta_locus_restricts_phage",
        "title": "ShosTA loci confer bacterial phage defense",
        "description": "Conservative system-level sketch linking possession of a ShosTA locus to restricted bacteriophage propagation without asserting the unresolved phage trigger or molecular output.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures ShosTA as a named anti-phage system with the required DefenseFinder ShosA and ShosT profiles while leaving its phage trigger, molecular substrate, antiviral effector output, and subtype breadth unresolved.",
        "nodes": [
          {
            "node_id": "shosta_locus",
            "label": "ShosTA locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A ShosTA anti-phage defense locus satisfying a DefenseFinder rule over ShosA and ShosT profiles."
          },
          {
            "node_id": "restricted_phage_propagation",
            "label": "restricted phage propagation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced propagation of bacteriophage in cells carrying the ShosTA system."
          },
          {
            "node_id": "shosta_system_trait",
            "label": "ShosTA system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000258",
            "description": "Possession of a genome-encoded ShosTA phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "shosta_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "restricted_phage_propagation",
            "description": "DefenseFinder maps ShosTA to a bacterial anti-phage-system discovery preprint and represents ShosTA loci through ShosA and ShosT component profiles.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.chom.2022.09.017",
                "snippet": "discovery of 21 defense systems that protect bacteria from phages",
                "notes": "Millman et al. describe the anti-phage discovery cohort that the DefenseFinder ShosTA registry row maps to the ShosTA system."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "ShosTA | 10\\.1101/2022\\.05\\.11\\.491447 | An expanding arsenal of immune systems that protect bacteria from phages",
                "notes": "The DefenseFinder registry maps ShosTA itself to the Millman et al. bacterial antiphage-system discovery preprint."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "ShosTA\tShosTA\t2\t2\tShosTA__ShosA, ShosTA__ShosT",
                "notes": "The DefenseFinder rules table supports both ShosA and ShosT as required ShosTA system profiles."
              }
            ]
          },
          {
            "subject": "restricted_phage_propagation",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "shosta_system_trait",
            "description": "ShosTA-mediated phage restriction realizes the ShosTA system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.chom.2022.09.017",
                "snippet": "discovery of 21 defense systems that protect bacteria from phages",
                "notes": "Millman et al. place the ShosTA discovery cohort in the set of bacterial systems that protect against phages."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "ShosTA | 10\\.1101/2022\\.05\\.11\\.491447 | An expanding arsenal of immune systems that protect bacteria from phages",
                "notes": "DefenseFinder records ShosTA as a named system from the Millman et al. antiphage discovery preprint."
              }
            ]
          },
          {
            "subject": "shosta_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "ShosTA system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "An expanding arsenal of immune systems that protect bacteria from phages",
                "notes": "DefenseFinder associates ShosTA with the Millman et al. bacterial antiphage-system discovery paper."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "shosta-mechanism-gap",
        "prompt": "Resolve ShosTA phage triggers and effector outputs before minting narrower ShosTA mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Millman et al. and DefenseFinder support ShosTA as a named anti-phage system with required ShosA and ShosT profiles, but the trigger, molecular substrate, antiviral effector output, and subtype-specific mechanism are not resolved enough here to assert a narrower mechanistic child trait.",
        "attaches_to": [
          "causal_graphs#shosta_locus_restricts_phage"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-19"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-19T01:24:12Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted ShosTA system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v135.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000264",
    "label": "Sirona system",
    "definition": "A phage defense system in which an organism possesses a Sirona locus represented by a VCA0356 profile that can protect bacteria from bacteriophage infection.",
    "definition_source": "DOI:10.1126/science.ads0768",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "Sirona",
        "synonym_type": "EXACT_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      },
      {
        "synonym_text": "VCA0356",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1126/science.ads0768",
        "snippet": "nearly 10% of the integron cassettes in the pandemic Vibrio cholerae strain encode novel antiphage functions",
        "notes": "Darracq et al. support treating the newly discovered Vibrio cholerae SCI antiphage cassettes as bacterial anti-phage systems."
      },
      {
        "reference": "DOI:10.1126/science.ads0768",
        "snippet": "Most of these novel systems have little or no similarity to previously known ones, with several providing defense through cell lysis or growth arrest",
        "notes": "Darracq et al. support a nonmechanistic system record that does not assert a resolved Sirona trigger, effector output, or pathway."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "Sirona | 10\\.1126/science\\.ads0768 | Sedentary chromosomal integrons as biobanks of bacterial antiphage defense systems",
        "notes": "The DefenseFinder model registry maps the named Sirona system to the Darracq et al. SCI antiphage-system paper."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "Sirona__VCA0356                                  |                                                  | Sirona",
        "notes": "The DefenseFinder HMM inventory records VCA0356 in the Sirona model namespace."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "sirona_locus_restricts_phage",
        "title": "Sirona loci confer bacterial phage defense",
        "description": "Conservative system-level sketch linking possession of a Sirona locus to restricted bacteriophage propagation without asserting the unresolved phage trigger or molecular output.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Sirona as a named SCI-derived anti-phage system with a VCA0356 DefenseFinder profile while leaving its phage trigger, molecular substrate, antiviral effector output, and subtype breadth unresolved.",
        "nodes": [
          {
            "node_id": "sirona_locus",
            "label": "Sirona locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A Sirona anti-phage defense locus represented in DefenseFinder by a VCA0356 profile."
          },
          {
            "node_id": "restricted_phage_propagation",
            "label": "restricted phage propagation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced propagation of bacteriophage in cells carrying the Sirona system."
          },
          {
            "node_id": "sirona_system_trait",
            "label": "Sirona system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000264",
            "description": "Possession of a genome-encoded Sirona phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "sirona_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "restricted_phage_propagation",
            "description": "DefenseFinder maps Sirona to an SCI anti-phage-system discovery paper and represents Sirona loci through the VCA0356 component profile.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.ads0768",
                "snippet": "nearly 10% of the integron cassettes in the pandemic Vibrio cholerae strain encode novel antiphage functions",
                "notes": "Darracq et al. describe the newly discovered antiphage-system cohort that the DefenseFinder Sirona registry row maps to the Sirona system."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "Sirona__VCA0356                                  |                                                  | Sirona",
                "notes": "The DefenseFinder HMM inventory supports VCA0356 as the Sirona component profile."
              }
            ]
          },
          {
            "subject": "restricted_phage_propagation",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "sirona_system_trait",
            "description": "Sirona-mediated phage restriction realizes the Sirona system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.ads0768",
                "snippet": "Most of these novel systems have little or no similarity to previously known ones",
                "notes": "Darracq et al. place the Sirona discovery cohort in a set of novel bacterial systems that protect against phages."
              }
            ]
          },
          {
            "subject": "sirona_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Sirona system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.ads0768",
                "snippet": "We also demonstrate that nearly 10% of the integron cassettes in the pandemic Vibrio cholerae strain encode novel antiphage functions",
                "notes": "Darracq et al. support treating the Sirona source cohort as novel bacterial anti-phage systems."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Sirona | 10\\.1126/science\\.ads0768 | Sedentary chromosomal integrons as biobanks of bacterial antiphage defense systems",
                "notes": "DefenseFinder associates Sirona with the Darracq et al. bacterial antiphage-system paper."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "sirona-mechanism-gap",
        "prompt": "Resolve Sirona phage triggers and effector outputs before minting narrower Sirona mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Darracq et al. and DefenseFinder support Sirona as a named anti-phage system with a VCA0356 profile, but the trigger, molecular substrate, antiviral effector output, and subtype-specific mechanism are not resolved enough here to assert a narrower mechanistic child trait.",
        "attaches_to": [
          "causal_graphs#sirona_locus_restricts_phage"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-19"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-19T04:27:15Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Sirona system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v141.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-19T04:32:33Z",
        "curator": "codex",
        "action": "EDIT",
        "changes": "Reduced repeated DefenseFinder registry snippets in the Sirona causal graph after the evidence snippet audit flagged the same registry row on three edges.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000314",
    "label": "6A-MBL system",
    "definition": "A phage defense system in which an organism possesses a 6A-MBL locus that can protect bacteria from bacteriophage infection.",
    "definition_source": "DOI:10.1016/j.chom.2024.07.007",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "6A-MBL",
        "synonym_type": "EXACT_SYNONYM",
        "source": "https://zenodo.org/records/11209165"
      },
      {
        "synonym_text": "6A_MBL",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      },
      {
        "synonym_text": "cap2_3",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "MblB",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1016/j.chom.2024.07.007",
        "snippet": "We validated six of these phage defense systems, including factors preventing viral attachment, R-loop-acting enzymes, the inflammasome, ubiquitin pathway, and pathogen recognition signaling.",
        "notes": "van den Berg et al. validated six phage defense systems related to eukaryotic innate antiviral responses."
      },
      {
        "reference": "DOI:10.1016/j.chom.2024.07.007",
        "snippet": "Searching for phage defense systems related to innate antiviral genes from vertebrates and plants, we uncovered over 450 candidates.",
        "notes": "van den Berg et al. motivate a conservative system-level record that does not assert a resolved 6A-MBL trigger, effector output, or universal pathway."
      },
      {
        "reference": "https://zenodo.org/records/11209165",
        "snippet": "In addition, a fused ubiquitin-like E1-E2-JAB protein combined with a putative MBL nuclease (6A-MBL) was found",
        "notes": "The Zenodo manuscript/supplementary-data record from van den Berg et al. names 6A-MBL as a putative MBL-nuclease system candidate."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "6A_MBL | 10\\.1016/j\\.chom\\.2024\\.07\\.007 | Bacterial homologs of innate eukaryotic antiviral defenses with anti-phage activity highlight shared evolutionary roots of viral defenses",
        "notes": "The DefenseFinder article registry maps the named 6A-MBL system to the van den Berg et al. antiphage-system discovery paper."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "6A_MBL__cap2_3                                   |                                                  | 6A_MBL",
        "notes": "The DefenseFinder HMM inventory records 6A_MBL__cap2_3 as a cap2_3 profile in the 6A_MBL model namespace."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "6A_MBL__MblB                                     |                                                  | 6A_MBL",
        "notes": "The DefenseFinder HMM inventory records 6A_MBL__MblB as a MblB profile in the 6A_MBL model namespace."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "six_a_mbl_locus_restricts_phage",
        "title": "6A-MBL loci confer bacterial phage defense",
        "description": "Conservative system-level sketch linking possession of a 6A-MBL locus to restricted bacteriophage propagation without asserting the unresolved phage trigger or molecular output.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures 6A-MBL as a named anti-phage system with 6A_MBL__cap2_3 and 6A_MBL__MblB DefenseFinder HMM profile entries while leaving its phage trigger, molecular substrate, antiviral effector output, and subtype breadth unresolved.",
        "nodes": [
          {
            "node_id": "six_a_mbl_locus",
            "label": "6A-MBL locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A 6A-MBL anti-phage defense locus cataloged in DefenseFinder with cap2_3 and MblB HMM profile entries."
          },
          {
            "node_id": "restricted_phage_propagation",
            "label": "restricted phage propagation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced propagation of bacteriophage in cells carrying the 6A-MBL system."
          },
          {
            "node_id": "six_a_mbl_system_trait",
            "label": "6A-MBL system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000314",
            "description": "Possession of a genome-encoded 6A-MBL phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "six_a_mbl_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "restricted_phage_propagation",
            "description": "DefenseFinder maps 6A_MBL to a eukaryotic-antiviral-homolog antiphage-system discovery paper and catalogs cap2_3 and MblB HMM profile entries in the 6A_MBL model namespace.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.chom.2024.07.007",
                "snippet": "We validated six of these phage defense systems, including factors preventing viral attachment, R-loop-acting enzymes, the inflammasome, ubiquitin pathway, and pathogen recognition signaling.",
                "notes": "van den Berg et al. validated six phage defense systems related to eukaryotic innate antiviral responses."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "6A_MBL | 10\\.1016/j\\.chom\\.2024\\.07\\.007 | Bacterial homologs of innate eukaryotic antiviral defenses with anti-phage activity highlight shared evolutionary roots of viral defenses",
                "notes": "The DefenseFinder article registry maps the named 6A-MBL system to the van den Berg et al. antiphage-system discovery paper."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "6A_MBL__cap2_3                                   |                                                  | 6A_MBL",
                "notes": "The DefenseFinder HMM inventory records 6A_MBL__cap2_3 as a cap2_3 profile in the 6A_MBL model namespace."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "6A_MBL__MblB                                     |                                                  | 6A_MBL",
                "notes": "The DefenseFinder HMM inventory records 6A_MBL__MblB as a MblB profile in the 6A_MBL model namespace."
              }
            ]
          },
          {
            "subject": "restricted_phage_propagation",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "six_a_mbl_system_trait",
            "description": "6A-MBL-mediated phage restriction realizes the 6A-MBL system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.chom.2024.07.007",
                "snippet": "We validated six of these phage defense systems, including factors preventing viral attachment, R-loop-acting enzymes, the inflammasome, ubiquitin pathway, and pathogen recognition signaling.",
                "notes": "van den Berg et al. validated six phage defense systems related to eukaryotic innate antiviral responses."
              }
            ]
          },
          {
            "subject": "six_a_mbl_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "6A-MBL system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "6A_MBL | 10\\.1016/j\\.chom\\.2024\\.07\\.007 | Bacterial homologs of innate eukaryotic antiviral defenses with anti-phage activity highlight shared evolutionary roots of viral defenses",
                "notes": "The DefenseFinder article registry maps the named 6A-MBL system to the van den Berg et al. antiphage-system discovery paper."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "six-a-mbl-mechanism-gap",
        "prompt": "Resolve 6A-MBL phage triggers and effector outputs before minting narrower 6A-MBL mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "van den Berg et al. and DefenseFinder support 6A-MBL as a named anti-phage system with 6A_MBL__cap2_3 and 6A_MBL__MblB HMM profile entries, but the trigger, molecular substrate, antiviral effector output, and subtype-specific mechanism are not resolved enough here to assert a narrower mechanistic child trait.",
        "attaches_to": [
          "causal_graphs#six_a_mbl_locus_restricts_phage"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-20"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-20T16:42:08Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted 6A-MBL system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v191.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-20T16:43:08Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed the 6A-MBL canonical_examples gap and left canonical_examples empty: the current evidence supports a named phage-defense system and DefenseFinder profiles, but the curated record does not yet cite a source-backed bacterial taxon with a directly observed 6A-MBL locus. No paid research was used.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-20T17:16:31Z",
        "curator": "codex",
        "action": "CURATION_REVIEW_REVISION",
        "changes": "Resolved issue #1148 by sourcing the exact 6A-MBL synonym from the stable van den Berg Zenodo record that names 6A-MBL verbatim, leaving DefenseFinder model and component labels as related synonyms.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000414",
    "label": "SNIPE system",
    "definition": "A phage defense system in which an organism possesses a SNIPE anti-bacteriophage system that localizes to the bacterial membrane, exploits the spatial organization of phage genome injection, and directly cleaves incoming phage DNA to block siphovirus infection.",
    "definition_source": "DOI:10.1038/s41586-026-10207-1",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "SNIPE",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1038/s41586-026-10207-1"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/s41586-026-10207-1",
        "snippet": "Here, we characterize SNIPE, an anti-bacteriophage defence system that constitutively localizes to the bacterial cell membrane in Escherichia coli",
        "notes": "Saxton et al. define SNIPE as an anti-bacteriophage defence system and localize it to the bacterial cell membrane in Escherichia coli."
      },
      {
        "reference": "DOI:10.1038/s41586-026-10207-1",
        "snippet": "Using radiolabelled phage DNA and time-lapse microscopy to track phage genomes, we demonstrate that SNIPE directly cleaves phage DNA during genome injection.",
        "notes": "Saxton et al. show that SNIPE directly cleaves phage DNA while the phage genome is being injected."
      },
      {
        "reference": "DOI:10.1038/s41586-026-10207-1",
        "snippet": "SNIPE also defends against diverse siphoviruses",
        "notes": "Saxton et al. support SNIPE defence against diverse siphoviruses."
      },
      {
        "reference": "DOI:10.1038/s41586-026-10207-1",
        "snippet": "Our findings establish SNIPE as a widespread bacterial defence system that exploits the spatial organization of phage genome injection to specifically target viral DNA",
        "notes": "Saxton et al. frame SNIPE as a widespread defence system that exploits phage genome-injection geometry to target viral DNA."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| SNIPE | 10\\.1038/s41586-026-10207-1 | A membrane-bound nuclease directly cleaves phage DNA during genome injection |",
        "notes": "The pinned DefenseFinder article registry maps the named SNIPE system to the Saxton et al. phage-genome-injection cleavage paper. The pinned HMM inventory and rules table do not list SNIPE, so this row is name-to-paper evidence rather than model-component evidence."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "snipe_cleaves_injected_phage_dna",
        "title": "SNIPE cleaves phage DNA during genome injection",
        "description": "Conservative system-level sketch linking a SNIPE locus to direct phage DNA cleavage during genome injection, inhibition of siphovirus infection, and SNIPE system possession.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures SNIPE at membrane-localized phage-genome-injection targeting level without asserting the exact direct viral sensor, the full host or phage range, or any DefenseFinder HMM-to-component mapping.",
        "nodes": [
          {
            "node_id": "snipe_locus",
            "label": "SNIPE locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A SNIPE anti-bacteriophage locus encoding the membrane-localized SNIPE defense activity."
          },
          {
            "node_id": "snipe_direct_phage_dna_cleavage",
            "label": "SNIPE direct phage DNA cleavage",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Direct cleavage of phage DNA by SNIPE as the viral genome is injected."
          },
          {
            "node_id": "phage_genome_injection",
            "label": "phage genome injection",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Injection of a siphovirus genome into the bacterial cell."
          },
          {
            "node_id": "siphovirus_infection",
            "label": "siphovirus infection",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Productive infection by bacteriophages with siphovirus morphology."
          },
          {
            "node_id": "snipe_system_trait",
            "label": "SNIPE system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000414",
            "description": "Possession of a genome-encoded SNIPE phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "snipe_locus",
            "predicate": "enables",
            "predicate_id": "RO:0002327",
            "object": "snipe_direct_phage_dna_cleavage",
            "description": "A SNIPE locus enables direct cleavage of phage DNA during genome injection.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41586-026-10207-1",
                "snippet": "Using radiolabelled phage DNA and time-lapse microscopy to track phage genomes, we demonstrate that SNIPE directly cleaves phage DNA during genome injection.",
                "notes": "Saxton et al. directly connect SNIPE to phage DNA cleavage during genome injection."
              }
            ]
          },
          {
            "subject": "snipe_direct_phage_dna_cleavage",
            "predicate": "mitigates",
            "predicate_id": "METPO:2007407",
            "object": "phage_genome_injection",
            "description": "SNIPE targets viral DNA during the genome-injection stage of phage infection.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41586-026-10207-1",
                "snippet": "Our findings establish SNIPE as a widespread bacterial defence system that exploits the spatial organization of phage genome injection to specifically target viral DNA",
                "notes": "Saxton et al. frame SNIPE cleavage as exploitation of the spatial organization of phage genome injection."
              }
            ]
          },
          {
            "subject": "snipe_direct_phage_dna_cleavage",
            "predicate": "mitigates",
            "predicate_id": "METPO:2007407",
            "object": "siphovirus_infection",
            "description": "By targeting injected viral DNA, SNIPE restricts siphovirus infection.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41586-026-10207-1",
                "snippet": "SNIPE also defends against diverse siphoviruses",
                "notes": "Saxton et al. support SNIPE-mediated defence against diverse siphoviruses."
              }
            ]
          },
          {
            "subject": "snipe_direct_phage_dna_cleavage",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "snipe_system_trait",
            "description": "Direct cleavage of injected phage DNA realizes the SNIPE system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41586-026-10207-1",
                "snippet": "Using radiolabelled phage DNA and time-lapse microscopy to track phage genomes, we demonstrate that SNIPE directly cleaves phage DNA during genome injection.",
                "notes": "Saxton et al. show the SNIPE phage-defense output as direct phage DNA cleavage during genome injection."
              }
            ]
          },
          {
            "subject": "snipe_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "SNIPE system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41586-026-10207-1",
                "snippet": "Here, we characterize SNIPE, an anti-bacteriophage defence system that constitutively localizes to the bacterial cell membrane in Escherichia coli",
                "notes": "Saxton et al. define SNIPE as an anti-bacteriophage defence system."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| SNIPE | 10\\.1038/s41586-026-10207-1 | A membrane-bound nuclease directly cleaves phage DNA during genome injection |",
                "notes": "The pinned DefenseFinder article registry maps the named SNIPE system to the Saxton et al. phage-genome-injection cleavage paper. The pinned HMM inventory and rules table do not list SNIPE, so this row is name-to-paper evidence rather than model-component evidence."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "snipe-defensefinder-model-gap",
        "prompt": "Resolve SNIPE host breadth, sensitive-phage breadth, direct tape-measure interaction specificity, and DefenseFinder HMM/rules coverage before minting narrower SNIPE mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Saxton et al. support SNIPE as a membrane-localized anti-bacteriophage system that directly cleaves phage DNA during genome injection, while the pinned DefenseFinder article registry names a SNIPE system. The pinned DefenseFinder HMM inventory and rules table have no SNIPE rows, and the evidence does not yet resolve full host breadth, full target-phage breadth, direct tape-measure protein specificity, or profile-to-activity modeling.",
        "evidence": [
          {
            "reference": "DOI:10.1038/s41586-026-10207-1",
            "snippet": "Our findings establish SNIPE as a widespread bacterial defence system that exploits the spatial organization of phage genome injection to specifically target viral DNA",
            "notes": "Saxton et al. support SNIPE as a widespread phage-defense system targeting viral DNA during phage genome injection."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
            "snippet": "| SNIPE | 10\\.1038/s41586-026-10207-1 | A membrane-bound nuclease directly cleaves phage DNA during genome injection |",
            "notes": "The pinned DefenseFinder article registry maps the named SNIPE system to the Saxton et al. phage-genome-injection cleavage paper. The pinned HMM inventory and rules table do not list SNIPE, so this row is name-to-paper evidence rather than model-component evidence."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "notes": "The pinned DefenseFinder HMM inventory does not list SNIPE, leaving profile-level components unresolved."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "The pinned DefenseFinder rules table does not list SNIPE, leaving rule-level detection criteria unresolved."
          }
        ],
        "attaches_to": [
          "causal_graphs#snipe_cleaves_injected_phage_dna"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-27"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-27T18:23:52Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted SNIPE system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; kept the graph at membrane-localized phage-genome-injection cleavage level because the pinned DefenseFinder article row is not backed by pinned HMM or rules rows; the replacement placeholder is reserved in proposals/metpo_traitmech_v291.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-27T18:23:53Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed SNIPE system during canonical-example issue 444 enforcement and left canonical_examples empty because the sources support E. coli expression and phage-challenge assays plus a DefenseFinder article-registry system name, but not a direct native microbial isolate exemplar with experimentally verified SNIPE activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000260",
    "label": "SoFIC system",
    "definition": "A phage defense system in which an organism possesses a SoFIC locus represented by a SoFic profile that can protect bacteria from bacteriophage infection.",
    "definition_source": "DOI:10.1016/j.chom.2022.09.017",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "SoFIC",
        "synonym_type": "EXACT_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1016/j.chom.2022.09.017",
        "snippet": "discovery of 21 defense systems that protect bacteria from phages, based on computational genomic analyses and phage-infection experiments",
        "notes": "Millman et al. report the computational and experimental cohort that DefenseFinder cites for SoFIC as a bacterial anti-phage system."
      },
      {
        "reference": "DOI:10.1101/2022.05.11.491447",
        "snippet": "discovery of 21 new defense systems that protect bacteria from phages, based on computational genomic analyses and phage infection experiments",
        "notes": "The bioRxiv version of Millman et al. independently carries the 21-system discovery claim linked from DefenseFinder's SoFIC article registry."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "SoFIC | 10\\.1101/2022\\.05\\.11\\.491447 | An expanding arsenal of immune systems that protect bacteria from phages",
        "notes": "The DefenseFinder model registry maps the named SoFIC system to the Millman et al. antiphage-system discovery preprint."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "SoFIC\tSoFic\t1\t1\tSoFic__SoFic",
        "notes": "The DefenseFinder rules table models SoFIC with a SoFic profile."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "SoFic__SoFic                                     | SoFic__SoFic                                     | SoFic",
        "notes": "The DefenseFinder HMM inventory records SoFic in the SoFic model namespace for the SoFIC system."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "sofic_locus_restricts_phage",
        "title": "SoFIC loci confer bacterial phage defense",
        "description": "Conservative system-level sketch linking possession of a SoFIC locus to restricted bacteriophage propagation without asserting the unresolved phage trigger or molecular output.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures SoFIC as a named anti-phage system with the required DefenseFinder SoFic profile while leaving its phage trigger, molecular substrate, antiviral effector output, and subtype breadth unresolved.",
        "nodes": [
          {
            "node_id": "sofic_locus",
            "label": "SoFIC locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A SoFIC anti-phage defense locus satisfying a DefenseFinder rule over the SoFic profile."
          },
          {
            "node_id": "restricted_phage_propagation",
            "label": "restricted phage propagation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced propagation of bacteriophage in cells carrying the SoFIC system."
          },
          {
            "node_id": "sofic_system_trait",
            "label": "SoFIC system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000260",
            "description": "Possession of a genome-encoded SoFIC phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "sofic_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "restricted_phage_propagation",
            "description": "DefenseFinder maps SoFIC to a bacterial anti-phage-system discovery preprint and represents SoFIC loci through the SoFic component profile.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.chom.2022.09.017",
                "snippet": "discovery of 21 defense systems that protect bacteria from phages",
                "notes": "Millman et al. describe the anti-phage discovery cohort that the DefenseFinder SoFIC registry row maps to the SoFIC system."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "SoFIC | 10\\.1101/2022\\.05\\.11\\.491447 | An expanding arsenal of immune systems that protect bacteria from phages",
                "notes": "The DefenseFinder registry maps SoFIC itself to the Millman et al. bacterial antiphage-system discovery preprint."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "SoFIC\tSoFic\t1\t1\tSoFic__SoFic",
                "notes": "The DefenseFinder rules table supports SoFic as the required SoFIC system profile."
              }
            ]
          },
          {
            "subject": "restricted_phage_propagation",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "sofic_system_trait",
            "description": "SoFIC-mediated phage restriction realizes the SoFIC system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.chom.2022.09.017",
                "snippet": "discovery of 21 defense systems that protect bacteria from phages",
                "notes": "Millman et al. place the SoFIC discovery cohort in the set of bacterial systems that protect against phages."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "SoFIC | 10\\.1101/2022\\.05\\.11\\.491447 | An expanding arsenal of immune systems that protect bacteria from phages",
                "notes": "DefenseFinder records SoFIC as a named system from the Millman et al. antiphage discovery preprint."
              }
            ]
          },
          {
            "subject": "sofic_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "SoFIC system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "An expanding arsenal of immune systems that protect bacteria from phages",
                "notes": "DefenseFinder associates SoFIC with the Millman et al. bacterial antiphage-system discovery paper."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "sofic-mechanism-gap",
        "prompt": "Resolve SoFIC phage triggers and effector outputs before minting narrower SoFIC mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Millman et al. and DefenseFinder support SoFIC as a named anti-phage system with a SoFic profile, but the trigger, molecular substrate, antiviral effector output, and subtype-specific mechanism are not resolved enough here to assert a narrower mechanistic child trait.",
        "attaches_to": [
          "causal_graphs#sofic_locus_restricts_phage"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-19"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-19T02:18:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted SoFIC system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v137.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000240",
    "label": "SPARTA system",
    "definition": "A genomics trait describing possession of a short prokaryotic Argonaute TIR-APAZ (SPARTA) locus whose short pAgo and TIR-APAZ proteins form heterodimeric complexes that oligomerize after guide RNA-mediated target DNA binding and unleash TIR domain-mediated NAD(P)ase activity that depletes NAD(P)+ to remove plasmid-invaded cells.",
    "definition_source": "DOI:10.1016/j.cell.2022.03.012",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000419"
    ],
    "synonyms": [
      {
        "synonym_text": "short prokaryotic Argonaute TIR-APAZ system",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1016/j.cell.2022.03.012"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1016/j.cell.2022.03.012",
        "snippet": "short prokaryotic Argonaute and the associated TIR-APAZ (SPARTA) proteins form heterodimeric complexes",
        "notes": "Koopal et al. define SPARTA as a short pAgo plus TIR-APAZ system rather than an individual gene or single protein."
      },
      {
        "reference": "DOI:10.1016/j.cell.2022.03.012",
        "snippet": "Upon guide RNA-mediated target DNA binding, four SPARTA heterodimers form oligomers in which TIR domain-mediated NAD(P)ase activity is unleashed",
        "notes": "Koopal et al. support the guide RNA and target DNA-triggered oligomerization mechanism that activates SPARTA NAD(P)ase activity."
      },
      {
        "reference": "DOI:10.1016/j.cell.2022.03.012",
        "snippet": "SPARTA is activated in the presence of highly transcribed multicopy plasmid DNA, which causes cell death through NAD(P)+ depletion",
        "notes": "Koopal et al. support plasmid-challenge activation and NAD(P)+ depletion as experimentally demonstrated SPARTA outcomes."
      },
      {
        "reference": "DOI:10.1038/s41467-024-49271-4",
        "snippet": "cryo-EM structure of the SPARTA oligomer (tetramer of heterodimers) bound to guide-RNA/target-ssDNA",
        "notes": "Kottur et al. independently support the RNA/target-DNA activated oligomeric state of a SPARTA complex."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "sparta_pago_tir_apaz_nadase_cell_death",
        "title": "SPARTA complexes couple guide RNA target binding to NAD(P)ase-triggered cell death",
        "description": "Evidence-backed process sketch linking a SPARTA locus to short-pAgo/TIR-APAZ heterodimer assembly, guide RNA-target DNA activation, oligomerization, TIR-domain NAD(P)ase activity, NAD(P)+ depletion, and removal of plasmid-invaded cells.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph stays at the SPARTA-family level and models the high-copy plasmid activation route from Koopal et al. without asserting that phage defense, SIR2-APAZ systems, nuclease-APAZ systems, or every other short-pAgo family uses the same enzymatic output.",
        "nodes": [
          {
            "node_id": "sparta_locus",
            "label": "SPARTA locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A short prokaryotic Argonaute TIR-APAZ locus encoding short pAgo and TIR-APAZ proteins."
          },
          {
            "node_id": "sparta_heterodimer_assembly",
            "label": "SPARTA heterodimer assembly",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Assembly of short pAgo and TIR-APAZ proteins into SPARTA heterodimeric complexes."
          },
          {
            "node_id": "guide_target_binding",
            "label": "guide RNA-mediated target DNA binding",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Recognition of target DNA by a SPARTA complex through a bound guide RNA."
          },
          {
            "node_id": "sparta_oligomerization",
            "label": "SPARTA oligomerization",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Formation of a target-DNA-bound SPARTA oligomer from four guide-loaded heterodimers."
          },
          {
            "node_id": "tir_nadpase_activity",
            "label": "SPARTA TIR-domain NAD(P)ase activity",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "NAD(P)+ hydrolysis by TIR domains assembled in an active SPARTA oligomer."
          },
          {
            "node_id": "nadp_depletion",
            "label": "NAD(P)+ depletion",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Loss of cellular NAD(P)+ downstream of activated SPARTA TIR-domain NAD(P)ase activity."
          },
          {
            "node_id": "invaded_cell_death",
            "label": "plasmid-invaded cell death",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Cell death triggered in host cells carrying highly transcribed multicopy plasmid DNA detected by SPARTA."
          },
          {
            "node_id": "sparta_system_trait",
            "label": "SPARTA system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000240",
            "description": "Possession of a genome-encoded short prokaryotic Argonaute TIR-APAZ defense system."
          }
        ],
        "edges": [
          {
            "subject": "sparta_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "sparta_heterodimer_assembly",
            "description": "SPARTA loci encode short pAgo and TIR-APAZ proteins that assemble into heterodimeric complexes.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.cell.2022.03.012",
                "snippet": "SPARTA proteins form heterodimeric complexes",
                "notes": "Koopal et al. support the paired-protein complex architecture of SPARTA."
              }
            ]
          },
          {
            "subject": "sparta_heterodimer_assembly",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "sparta_oligomerization",
            "description": "SPARTA heterodimers are the building blocks of the target-DNA-bound SPARTA oligomer.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.cell.2022.03.012",
                "snippet": "four SPARTA heterodimers form oligomers",
                "notes": "Koopal et al. support oligomer formation from SPARTA heterodimers."
              }
            ]
          },
          {
            "subject": "guide_target_binding",
            "predicate": "activates",
            "predicate_id": "RO:0002213",
            "object": "sparta_oligomerization",
            "description": "Guide RNA-mediated target DNA binding triggers SPARTA tetramer-of-heterodimers oligomerization.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.cell.2022.03.012",
                "snippet": "Upon guide RNA-mediated target DNA binding, four SPARTA heterodimers form oligomers",
                "notes": "Koopal et al. connect target recognition to SPARTA oligomer formation."
              }
            ]
          },
          {
            "subject": "sparta_oligomerization",
            "predicate": "activates",
            "predicate_id": "RO:0002213",
            "object": "tir_nadpase_activity",
            "description": "SPARTA oligomerization aligns TIR domains and activates NAD(P)+ hydrolysis.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.cell.2022.03.012",
                "snippet": "oligomers in which TIR domain-mediated NAD(P)ase activity is unleashed",
                "notes": "Koopal et al. link oligomer formation to activation of TIR-domain NAD(P)ase activity."
              },
              {
                "reference": "DOI:10.1038/s41467-024-49271-4",
                "snippet": "The TIR domains amass in a parallel-strands arrangement for catalysis",
                "notes": "Kottur et al. structurally support TIR-domain arrangement in the active SPARTA assembly."
              }
            ]
          },
          {
            "subject": "tir_nadpase_activity",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "nadp_depletion",
            "description": "Activated SPARTA TIR domains hydrolyze NAD(P)+, depleting the cellular NAD(P)+ pool.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-024-49271-4",
                "snippet": "activated by invading DNA to unleash its TIR domain for NAD(P)+ hydrolysis",
                "notes": "Kottur et al. describe DNA-triggered release of SPARTA TIR-domain NAD(P)+ hydrolysis."
              }
            ]
          },
          {
            "subject": "nadp_depletion",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "invaded_cell_death",
            "description": "SPARTA-associated NAD(P)+ depletion contributes to death of plasmid-invaded host cells.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.cell.2022.03.012",
                "snippet": "causes cell death through NAD(P)+ depletion",
                "notes": "Koopal et al. connect SPARTA-driven NAD(P)+ depletion to cell death."
              }
            ]
          },
          {
            "subject": "invaded_cell_death",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "sparta_system_trait",
            "description": "Removal of plasmid-invaded cells is the cellular outcome of the SPARTA possession trait.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.cell.2022.03.012",
                "snippet": "This results in the removal of plasmid-invaded cells from bacterial cultures",
                "notes": "Koopal et al. support SPARTA-mediated removal of plasmid-invaded cells."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "sparta-native-host-and-substrate-gap",
        "prompt": "Resolve SPARTA natural-host substrates before adding canonical examples or narrower short-pAgo defense children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Koopal et al. support strong high-copy plasmid activation and only limited, NADase-independent phage effects; Kottur et al. support C. thermophila SPARTA structural activation. This first record therefore stays broad until natural-host activity, phage scope, and whether SIR2-APAZ or nuclease-APAZ relatives should be separate children are resolved.",
        "posed_by": "codex",
        "posed_date": "2026-09-18"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-18T11:59:02Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted SPARTA system as a DOI-backed GENOMICS TraitRecord under the quality root after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v117.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-27T22:11:00Z",
        "curator": "codex",
        "action": "REPAIRED_PARENT_TRAIT",
        "changes": "Reparented SPARTA system from the generic quality root to the newly minted prokaryotic Argonaute defense system parent without changing SPARTA-specific evidence or mechanism claims.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000325",
    "label": "SpbK system",
    "definition": "An abortive infection system in which an organism possesses a SpbK-family locus represented by the DefenseFinder SpbK__SpbK profile and exemplified by the ICEBs1 spbK gene whose SP\u03b2-YonE-dependent activity inhibits SP\u03b2 production and kills infected cells.",
    "definition_source": "DOI:10.1371/journal.pgen.1010065",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000214"
    ],
    "synonyms": [
      {
        "synonym_text": "SpbK",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1371/journal.pgen.1010065",
        "snippet": "The ICEBs1 gene spbK, although dispensable for conjugation, was necessary and sufficient for the inhibition of SP\u00df.",
        "notes": "Johnson et al. support spbK as the ICEBs1 locus sufficient for SP\u03b2 inhibition."
      },
      {
        "reference": "DOI:10.1371/journal.pgen.1010065",
        "snippet": "The anti-SP\u00df phenotype (abortive infection) caused by spbK was dependent on the SP\u00df gene yonE.",
        "notes": "Johnson et al. support yonE-dependent abortive infection as the phage-specific SpbK output."
      },
      {
        "reference": "DOI:10.1371/journal.pgen.1010065",
        "snippet": "Co-expression of spbK and yonE inhibited host cell growth and caused a drop in cell viability, even in the absence of any other ICEBs1 or SP\u00df genes.",
        "notes": "Johnson et al. support SpbK/YonE-associated host growth inhibition and cell death."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "SpbK | 10\\.1371/journal\\.pgen\\.1010065 | Interactions between mobile genetic elements: An anti-phage gene in an integrative and conjugative element protects host cells from predation by a temperate bacteriophage",
        "notes": "The DefenseFinder article registry maps the named SpbK model namespace to the ICEBs1 SpbK anti-phage paper."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "SpbK\tSpbK\t1\t1\tSpbK__SpbK",
        "notes": "The DefenseFinder rules table models SpbK as a single-profile system requiring the SpbK__SpbK profile."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| SpbK__SpbK                                       | SpbK__SpbK                                       | SpbK                   | Custom                  | 80     |",
        "notes": "The DefenseFinder HMM inventory records SpbK__SpbK under SpbK."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1423",
        "taxon_label": "Bacillus subtilis",
        "note": "Johnson et al. showed that ICEBs1 encodes an SpbK-dependent abortive infection system that protects B. subtilis host populations from SP\u03b2.",
        "reference": "DOI:10.1371/journal.pgen.1010065"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "spbk_locus_mediates_spb_defense",
        "title": "SpbK loci mediate SP\u03b2 abortive defense",
        "description": "Conservative system-level sketch linking SpbK-family locus possession to SP\u03b2 YonE-dependent abortive infection and the SpbK system trait without asserting the direct SpbK-YonE coupling event or TIR-domain effector chemistry.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures SpbK as a named DefenseFinder single-profile abortive-infection system whose Bacillus ICEBs1 prototype requires the SP\u03b2 YonE trigger. It leaves the direct SpbK-YonE coupling, TIR-domain output, essential host target, and homolog breadth unresolved.",
        "nodes": [
          {
            "node_id": "spbk_locus",
            "label": "SpbK locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "An ICEBs1-like abortive-infection locus represented by the DefenseFinder SpbK__SpbK profile."
          },
          {
            "node_id": "spbk_yone_abortive_infection",
            "label": "SpbK/YonE-dependent abortive infection",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Abortive infection in which SpbK activity depends on the SP\u03b2 YonE gene and causes host growth inhibition and cell death."
          },
          {
            "node_id": "spbk_system_trait",
            "label": "SpbK system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000325",
            "description": "Possession of a genome-encoded SpbK abortive-infection phage-defense system."
          }
        ],
        "edges": [
          {
            "subject": "spbk_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "spbk_yone_abortive_infection",
            "description": "The ICEBs1 spbK locus is necessary and sufficient for YonE-dependent SP\u03b2 abortive infection, and DefenseFinder represents SpbK with a required SpbK profile.",
            "evidence": [
              {
                "reference": "DOI:10.1371/journal.pgen.1010065",
                "snippet": "The ICEBs1 gene spbK, although dispensable for conjugation, was necessary and sufficient for the inhibition of SP\u00df.",
                "notes": "Johnson et al. connect the ICEBs1 spbK gene to SP\u03b2 inhibition."
              },
              {
                "reference": "DOI:10.1371/journal.pgen.1010065",
                "snippet": "The anti-SP\u00df phenotype (abortive infection) caused by spbK was dependent on the SP\u00df gene yonE.",
                "notes": "Johnson et al. support YonE dependence of SpbK-mediated abortive infection."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "SpbK\tSpbK\t1\t1\tSpbK__SpbK",
                "notes": "The DefenseFinder rules table models SpbK as a single-profile system requiring the SpbK__SpbK profile."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| SpbK__SpbK                                       | SpbK__SpbK                                       | SpbK                   | Custom                  | 80     |",
                "notes": "The DefenseFinder HMM inventory records SpbK__SpbK under SpbK."
              }
            ]
          },
          {
            "subject": "spbk_yone_abortive_infection",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "spbk_system_trait",
            "description": "SpbK/YonE-dependent abortive infection realizes the SpbK system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1371/journal.pgen.1010065",
                "snippet": "Whatever the mechanism, we conclude that ICEBs1 encodes an abortive infection system that protects its host from predation by SP\u00df.",
                "notes": "Johnson et al. classify ICEBs1 spbK activity as an abortive infection system that protects its host from SP\u03b2 predation."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "SpbK | 10\\.1371/journal\\.pgen\\.1010065 | Interactions between mobile genetic elements: An anti-phage gene in an integrative and conjugative element protects host cells from predation by a temperate bacteriophage",
                "notes": "The DefenseFinder article registry maps the named SpbK model namespace to the ICEBs1 SpbK anti-phage paper."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "spbk-mechanism-gap",
        "prompt": "Resolve the direct SP\u03b2 YonE trigger, SpbK TIR-domain output, essential host target, and broader SpbK homolog scope before minting narrower SpbK mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Johnson et al. support ICEBs1 spbK as a YonE-dependent abortive infection gene that inhibits SP\u03b2 and causes cell death, and DefenseFinder maps SpbK to the SpbK__SpbK profile. The direct SpbK-YonE coupling event, TIR-domain output, essential host target, and homolog breadth remain unresolved.",
        "attaches_to": [
          "causal_graphs#spbk_locus_mediates_spb_defense"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-21"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-21T03:22:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted SpbK system as a DOI-backed GENOMICS TraitRecord under the abortive infection system parent after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v202.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-21T03:45:00Z",
        "curator": "codex",
        "action": "REVISED_TEXT",
        "changes": "Standardized curator-written SP\u03b2 phage mentions to the canonical Greek beta spelling while preserving Johnson et al. evidence snippets exactly as exposed by the PLOS XML.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000222",
    "label": "SspABCD-SspE system",
    "definition": "A phosphorothioate defense system in which an organism possesses an SspABCD-SspE locus that pairs an SspABCD single-stranded DNA phosphorothioation module with the SspE restriction enzyme to sense host phosphorothioate marks and nick invading DNA.",
    "definition_source": "DOI:10.1038/s41564-020-0700-6",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000213"
    ],
    "synonyms": [
      {
        "synonym_text": "SspABCD-SspE PT system",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1038/s41564-020-0700-6"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/s41564-020-0700-6",
        "snippet": "Here, we describe an unusual SspABCD-SspE PT system in Vibrio cyclitrophicus, Escherichia coli and Streptomyces yokosukanensis",
        "notes": "Xiong et al. name SspABCD-SspE as a bacterial phosphorothioation system distinct from Dnd."
      },
      {
        "reference": "DOI:10.1038/s41564-020-0700-6",
        "snippet": "SspABCD confers single-stranded and high-frequency PTs with SspB acting as a nickase",
        "notes": "Xiong et al. support the SspABCD modification module and its single-stranded high-frequency PT output."
      },
      {
        "reference": "DOI:10.1038/s41564-020-0700-6",
        "snippet": "SspABCD coupled with SspE provides protection against phages",
        "notes": "Xiong et al. support the modification-plus-restriction architecture and the antiphage output of SspABCD-SspE."
      },
      {
        "reference": "DOI:10.1038/s41467-022-34505-0",
        "snippet": "In the PT-based defense system Ssp, SspABCD confers a single-stranded PT modification of host DNA",
        "notes": "Gao et al. support Ssp as a PT-based defense system with host-DNA phosphorothioation by SspABCD."
      },
      {
        "reference": "DOI:10.1038/s41467-022-34505-0",
        "snippet": "SspE relies on PT modification in host DNA to exert antiphage activity",
        "notes": "Gao et al. connect host PT modification to SspE-mediated antiphage activity."
      },
      {
        "reference": "DOI:10.1128/mbio.00933-23",
        "snippet": "a novel PT-related R-M system, composed of the modification module SspABCD paired with a single restriction enzyme, SspE",
        "notes": "Jiang et al. support defining this child by the SspABCD modification module paired with single-enzyme SspE restriction, separate from DndFGH and SspFGH systems."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:47951",
        "taxon_label": "Vibrio cyclitrophicus",
        "note": "Xiong et al. describe an SspABCD-SspE PT system in Vibrio cyclitrophicus and analyze its SspABCD-dependent single-stranded PTs plus SspE-dependent antiphage activity.",
        "reference": "DOI:10.1038/s41564-020-0700-6"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "sspabcd_sspe_pt_site_dependent_dna_nicking",
        "title": "SspABCD-SspE systems couple Ssp PT marks to DNA nicking",
        "description": "Evidence-backed process sketch linking an SspABCD-SspE locus to single-stranded host DNA phosphorothioation, SspE PT-site recognition, SspE GTPase-linked nuclease activation, and reduced phage DNA replication.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures SspABCD-SspE restriction at the system level without asserting one universal host taxon, PT frequency, DNA motif outside 5'-CPSCA-3'-characterized systems, full SspE conformational cycle, or relationship to SspFGH and archaeal PT antiviral systems.",
        "nodes": [
          {
            "node_id": "sspabcd_sspe_locus",
            "label": "SspABCD-SspE locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "An Ssp phosphorothioation-dependent restriction locus pairing the SspABCD DNA modification module with SspE restriction activity."
          },
          {
            "node_id": "ssp_single_stranded_dna_phosphorothioation",
            "label": "Ssp single-stranded DNA phosphorothioation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "SspABCD-mediated installation of single-stranded phosphorothioate marks on host DNA."
          },
          {
            "node_id": "sspe_pt_site_recruitment",
            "label": "SspE PT-site recruitment",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Preferential recruitment of SspE to phosphorothioate-marked DNA sites."
          },
          {
            "node_id": "sspe_gtpase_activation",
            "label": "SspE GTPase activation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "PT-dependent enlargement of the SspE GTP-binding pocket and stimulation of GTP hydrolysis."
          },
          {
            "node_id": "sspe_dna_nicking",
            "label": "SspE DNA nicking",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "SspE nuclease activation and DNA nicking during phosphorothioate-dependent self/nonself discrimination."
          },
          {
            "node_id": "phage_dna_replication",
            "label": "phage DNA replication",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Replication of invading bacteriophage DNA after host cell entry."
          },
          {
            "node_id": "sspabcd_sspe_system_trait",
            "label": "SspABCD-SspE system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000222",
            "description": "Possession of a genome-encoded SspABCD-SspE restriction-modification defense system."
          },
          {
            "node_id": "phosphorothioate_defense_system_trait",
            "label": "phosphorothioate defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000213",
            "description": "Possession of a genome-encoded phosphorothioate-based phage defense system."
          }
        ],
        "edges": [
          {
            "subject": "sspabcd_sspe_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "ssp_single_stranded_dna_phosphorothioation",
            "description": "The SspABCD modification module installs single-stranded, high-frequency PT marks on host DNA.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-020-0700-6",
                "snippet": "SspABCD confers single-stranded and high-frequency PTs with SspB acting as a nickase",
                "notes": "Xiong et al. support SspABCD-dependent host DNA phosphorothioation."
              }
            ]
          },
          {
            "subject": "sspabcd_sspe_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "sspe_pt_site_recruitment",
            "description": "SspABCD-SspE loci pair SspABCD host-DNA phosphorothioation with single-enzyme SspE restriction activity.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mbio.00933-23",
                "snippet": "the modification module SspABCD paired with a single restriction enzyme, SspE",
                "notes": "Jiang et al. support the paired SspABCD modification and SspE restriction architecture."
              }
            ]
          },
          {
            "subject": "ssp_single_stranded_dna_phosphorothioation",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "sspe_pt_site_recruitment",
            "description": "SspE relies on host DNA PT marks and is preferentially recruited to PT sites.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-022-34505-0",
                "snippet": "SspE relies on PT modification in host DNA to exert antiphage activity",
                "notes": "Gao et al. support PT-dependent SspE activity."
              }
            ]
          },
          {
            "subject": "sspe_pt_site_recruitment",
            "predicate": "activates",
            "predicate_id": "RO:0002213",
            "object": "sspe_gtpase_activation",
            "description": "PT-site recognition stimulates the SspE GTPase cycle.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-022-34505-0",
                "snippet": "PT recognition enlarges the GTP-binding pocket, thereby increasing GTP hydrolysis activity",
                "notes": "Gao et al. support PT-induced SspE GTPase activation."
              }
            ]
          },
          {
            "subject": "sspe_gtpase_activation",
            "predicate": "activates",
            "predicate_id": "RO:0002213",
            "object": "sspe_dna_nicking",
            "description": "GTPase-linked conformational switching activates SspE nuclease nicking activity.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-022-34505-0",
                "snippet": "turns on the DNA nicking nuclease activity of CTD",
                "notes": "Gao et al. support activation of SspE DNA-nicking nuclease activity."
              }
            ]
          },
          {
            "subject": "sspe_dna_nicking",
            "predicate": "mitigates",
            "predicate_id": "METPO:2007407",
            "object": "phage_dna_replication",
            "description": "SspE-linked DNA nicking inhibits phage propagation by impairing phage DNA replication.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-020-0700-6",
                "snippet": "SspE inhibits phage propagation by introducing nicking damage to impair phage DNA replication",
                "notes": "Xiong et al. directly connect SspE DNA-nicking damage to impaired phage DNA replication."
              }
            ]
          },
          {
            "subject": "sspe_dna_nicking",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "sspabcd_sspe_system_trait",
            "description": "SspE DNA nicking realizes the SspABCD-SspE antiphage defense trait.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-022-34505-0",
                "snippet": "enabling SspE to accomplish self-nonself discrimination and limit phage predation",
                "notes": "Gao et al. support SspE self/nonself discrimination as the Ssp antiphage output."
              }
            ]
          },
          {
            "subject": "sspabcd_sspe_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phosphorothioate_defense_system_trait",
            "description": "SspABCD-SspE possession is a phosphorothioate-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-020-0700-6",
                "snippet": "SspABCD coupled with SspE provides protection against phages",
                "notes": "Xiong et al. place SspABCD-SspE within phosphorothioation-dependent antiphage defense systems."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-15T16:38:06Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted SspABCD-SspE system as a DOI-backed GENOMICS TraitRecord under the phosphorothioate defense system parent after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v99.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000223",
    "label": "SspABCD-SspFGH system",
    "definition": "A phosphorothioate defense system in which an organism possesses an SspABCD-SspFGH locus that pairs an SspABCD-family single-stranded DNA phosphorothioation module with an SspFGH restriction module to damage non-phosphorothioated phage DNA and suppress phage DNA replication.",
    "definition_source": "DOI:10.1128/mbio.00613-21",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000213"
    ],
    "synonyms": [
      {
        "synonym_text": "SspABCD-SspFGH defense system",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1128/mbio.00613-21"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1128/mbio.00613-21",
        "snippet": "new type of ssDNA PT-based SspABCD-SspFGH defense system capable of providing protection against phages",
        "notes": "Wang et al. name SspABCD-SspFGH as a single-stranded DNA phosphorothioation-based bacterial phage-defense system."
      },
      {
        "reference": "DOI:10.1128/mbio.00613-21",
        "snippet": "PT-modifying genes sspBCD and iscS in Vibrio anguillarum strain FF-93 can provide protection against a range of phages in combination with sspFGH",
        "notes": "Wang et al. support a native Vibrio anguillarum FF-93 Ssp system whose IscS-SspBCD phosphorothioation module works with the sspFGH cassette."
      },
      {
        "reference": "DOI:10.1128/mbio.00613-21",
        "snippet": "SspFGH coupled with IscS-SspBCD behaves as a new type of ssDNA PT modification-based defense barrier to fend off phage invasion",
        "notes": "Wang et al. support the modification-plus-restriction architecture and antiphage output."
      },
      {
        "reference": "DOI:10.1128/mbio.00613-21",
        "snippet": "SspFGH damages non-PT-modified DNA and exerts antiphage activity by suppressing phage DNA replication",
        "notes": "Wang et al. connect SspFGH-dependent DNA damage to the observed block in phage DNA replication."
      },
      {
        "reference": "DOI:10.1038/s41564-020-0700-6",
        "snippet": "SspABCD confers single-stranded and high-frequency PTs with SspB acting as a nickase",
        "notes": "Xiong et al. independently support SspABCD-family single-stranded host-DNA phosphorothioation."
      },
      {
        "reference": "DOI:10.3390/ijms252413316",
        "snippet": "could also be coupled to SspFGH for anti-phage activity",
        "notes": "Xu and Gu summarize SspFGH as an SspABCD-coupled phosphorothioate antiphage restriction module."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:55601",
        "taxon_label": "Vibrio anguillarum",
        "note": "Wang et al. identified an sspFGH cassette adjacent to the sspBCD cluster in Vibrio anguillarum FF-93 and showed that its SspFGH module couples to IscS-SspBCD phosphorothioation for phage defense.",
        "reference": "DOI:10.1128/mbio.00613-21"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "sspabcd_sspfgh_non_pt_dna_damage",
        "title": "SspABCD-SspFGH systems couple Ssp PT marks to foreign-DNA damage",
        "description": "Evidence-backed process sketch linking an SspABCD-SspFGH locus to single-stranded host DNA phosphorothioation, SspFGH-dependent damage of non-phosphorothioated phage DNA, and reduced phage DNA replication.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures SspABCD-SspFGH restriction at the system level without asserting one universal host taxon, PT frequency, a DNA-damage chemistry, a complete SspFGH subunit cycle, or relationship to SspE and archaeal PT antiviral systems.",
        "nodes": [
          {
            "node_id": "sspabcd_sspfgh_locus",
            "label": "SspABCD-SspFGH locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "An Ssp phosphorothioation-dependent restriction locus pairing an SspABCD-family DNA modification module with SspFGH restriction activity."
          },
          {
            "node_id": "ssp_single_stranded_dna_phosphorothioation",
            "label": "Ssp single-stranded DNA phosphorothioation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "SspABCD-family installation of single-stranded phosphorothioate marks on host DNA."
          },
          {
            "node_id": "ssp_pt_self_nonself_discrimination",
            "label": "Ssp PT self/nonself discrimination",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Use of Ssp phosphorothioate marks to distinguish phosphorothioated host DNA from invading DNA that lacks host phosphorothioate marks."
          },
          {
            "node_id": "sspfgh_non_pt_dna_damage",
            "label": "SspFGH-dependent non-PT DNA damage",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "SspFGH-dependent damage of DNA molecules that lack host single-stranded phosphorothioate marks."
          },
          {
            "node_id": "phage_dna_replication",
            "label": "phage DNA replication",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Replication of invading bacteriophage DNA after host cell entry."
          },
          {
            "node_id": "sspabcd_sspfgh_system_trait",
            "label": "SspABCD-SspFGH system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000223",
            "description": "Possession of a genome-encoded SspABCD-SspFGH restriction-modification defense system."
          },
          {
            "node_id": "phosphorothioate_defense_system_trait",
            "label": "phosphorothioate defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000213",
            "description": "Possession of a genome-encoded phosphorothioate-based phage defense system."
          }
        ],
        "edges": [
          {
            "subject": "sspabcd_sspfgh_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "ssp_single_stranded_dna_phosphorothioation",
            "description": "The SspABCD-family modification module installs single-stranded PT marks on host DNA.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mbio.00613-21",
                "snippet": "IscS and SspBCD in FF-93 also confer DNA PT modification at 5'-CPSCA-3' consensus sequences",
                "notes": "Wang et al. support single-stranded host-DNA phosphorothioation by the FF-93 IscS-SspBCD module."
              }
            ]
          },
          {
            "subject": "sspabcd_sspfgh_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "sspfgh_non_pt_dna_damage",
            "description": "SspABCD-SspFGH loci pair the Ssp modification module with SspFGH-dependent restriction activity against DNA lacking PT marks.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mbio.00613-21",
                "snippet": "SspFGH coupled with IscS-SspBCD behaves as a new type of ssDNA PT modification-based defense barrier",
                "notes": "Wang et al. support the paired Ssp phosphorothioation and SspFGH restriction architecture."
              }
            ]
          },
          {
            "subject": "ssp_single_stranded_dna_phosphorothioation",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "ssp_pt_self_nonself_discrimination",
            "description": "SspFGH uses Ssp phosphorothioate marks as a recognition tag to discriminate self DNA from invading non-PT DNA.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mbio.00613-21",
                "snippet": "SspFGH employs ssDNA PT modification as a recognition tag to introduce damage to non-PT-modified phage genomes",
                "notes": "Wang et al. support PT-dependent self/nonself discrimination by the SspFGH barrier."
              }
            ]
          },
          {
            "subject": "ssp_pt_self_nonself_discrimination",
            "predicate": "activates",
            "predicate_id": "RO:0002213",
            "object": "sspfgh_non_pt_dna_damage",
            "description": "Ssp PT self/nonself discrimination leads to SspFGH-dependent damage of non-PT phage DNA.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mbio.00613-21",
                "snippet": "SspFGH introduces damage to non-PT DNA and consequently impairs phage DNA replication",
                "notes": "Wang et al. connect SspFGH non-PT DNA damage to the restriction output."
              }
            ]
          },
          {
            "subject": "sspfgh_non_pt_dna_damage",
            "predicate": "mitigates",
            "predicate_id": "METPO:2007407",
            "object": "phage_dna_replication",
            "description": "SspFGH-dependent damage of phage DNA suppresses phage DNA replication.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mbio.00613-21",
                "snippet": "its DNA replication was markedly suppressed in the presence of IscS-SspBCD-SspFGH",
                "notes": "Wang et al. directly connect the SspFGH barrier to impaired phage DNA replication."
              }
            ]
          },
          {
            "subject": "sspfgh_non_pt_dna_damage",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "sspabcd_sspfgh_system_trait",
            "description": "SspFGH-dependent non-PT DNA damage realizes the SspABCD-SspFGH antiphage defense trait.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mbio.00613-21",
                "snippet": "SspFGH provided moderate levels of protection against phages",
                "notes": "Wang et al. support phage restriction as the SspFGH system output."
              }
            ]
          },
          {
            "subject": "sspabcd_sspfgh_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phosphorothioate_defense_system_trait",
            "description": "SspABCD-SspFGH possession is a phosphorothioate-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mbio.00613-21",
                "snippet": "new type of ssDNA PT-based SspABCD-SspFGH defense system",
                "notes": "Wang et al. place SspABCD-SspFGH among single-stranded DNA phosphorothioation-based defense systems."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-15T17:06:06Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted SspABCD-SspFGH system as a DOI-backed GENOMICS TraitRecord under the phosphorothioate defense system parent after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v100.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000303",
    "label": "Stk2 system",
    "definition": "An abortive infection system in which an organism possesses a phage-defense locus encoding the Stk2 serine/threonine kinase, which can be activated by a phage protein to phosphorylate host proteins and induce host-cell death that prevents bacteriophage propagation.",
    "definition_source": "DOI:10.1016/j.chom.2016.08.010",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000214"
    ],
    "synonyms": [
      {
        "synonym_text": "Stk2",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1016/j.chom.2016.08.010",
        "snippet": "Here we identify Stk2, a staphylococcal serine/threonine kinase that provides efficient immunity against bacteriophages by inducing abortive infection",
        "notes": "Depardieu et al. identify Stk2 as a staphylococcal serine/threonine kinase that provides bacteriophage immunity through abortive infection."
      },
      {
        "reference": "DOI:10.1016/j.chom.2016.08.010",
        "snippet": "A phage protein of unknown function activates the Stk2 kinase",
        "notes": "Depardieu et al. connect an unidentified phage protein to Stk2 kinase activation."
      },
      {
        "reference": "DOI:10.1016/j.chom.2016.08.010",
        "snippet": "This leads to the Stk2-dependent phosphorylation of several proteins involved in translation, global transcription control, cell-cycle control, stress response, DNA topology, DNA repair, and central metabolism",
        "notes": "Depardieu et al. describe Stk2-dependent phosphorylation of multiple host-protein targets after Stk2 activation."
      },
      {
        "reference": "DOI:10.1016/j.chom.2016.08.010",
        "snippet": "Bacterial host cells die as a consequence of Stk2 activation, thereby preventing propagation of the phage to the rest of the bacterial population",
        "notes": "Depardieu et al. connect Stk2 activation to host-cell death and the resulting block of phage propagation."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "Stk2 | 10\\.1016/j\\.chom\\.2016\\.08\\.010 | A eukaryotic-like Serine/threonine kinase protects staphylococci against phages",
        "notes": "The DefenseFinder article registry maps the named Stk2 system to the Depardieu et al. final article."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "Stk2\tStk2\t1\t1\tStk2__Stk2",
        "notes": "The DefenseFinder rules table models Stk2 as a one-component system requiring the Stk2__Stk2 profile."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| Stk2__Stk2                                       | Stk2__Stk2                                       | Stk2                   | Custom                  | 150    |",
        "notes": "The DefenseFinder HMM inventory records the Stk2__Stk2 profile under the Stk2 model namespace."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "stk2_activation_aborts_phage_infection",
        "title": "Stk2 kinase activation aborts phage infection",
        "description": "Conservative system-level sketch linking possession of a Stk2 phage-defense locus to phage-protein-triggered kinase activation, host protein phosphorylation, host-cell death, and the Stk2 abortive-infection trait without asserting the unresolved direct phage activator or lethal phosphorylation target.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Stk2 as a named DefenseFinder single-profile abortive-infection system with a phage-activated serine/threonine kinase output while leaving the activating phage protein, the direct lethal phosphorylation event, target conservation, and phage-specific escape routes unresolved.",
        "nodes": [
          {
            "node_id": "stk2_locus",
            "label": "Stk2 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A Stk2 abortive-infection phage-defense locus represented by the DefenseFinder Stk2__Stk2 profile."
          },
          {
            "node_id": "stk2_kinase_activation",
            "label": "Stk2 kinase activation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Activation of the Stk2 serine/threonine kinase by a phage protein of unknown function."
          },
          {
            "node_id": "host_protein_phosphorylation",
            "label": "host protein phosphorylation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Stk2-dependent phosphorylation of host proteins after Stk2 kinase activation."
          },
          {
            "node_id": "host_cell_death",
            "label": "host cell death",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Stk2-activation-dependent death of infected bacterial host cells."
          },
          {
            "node_id": "phage_propagation",
            "label": "phage propagation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Propagation of bacteriophage through a bacterial host population."
          },
          {
            "node_id": "stk2_system_trait",
            "label": "Stk2 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000303",
            "description": "Possession of a genome-encoded Stk2 abortive-infection phage-defense system."
          },
          {
            "node_id": "abortive_infection_system",
            "label": "abortive infection system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000214",
            "description": "Possession of a bacteriophage abortive-infection defense system."
          }
        ],
        "edges": [
          {
            "subject": "stk2_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "stk2_kinase_activation",
            "description": "Depardieu et al. identify the Stk2 serine/threonine kinase as a phage-immunity factor, and DefenseFinder models Stk2 as a single-profile system.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.chom.2016.08.010",
                "snippet": "Here we identify Stk2, a staphylococcal serine/threonine kinase that provides efficient immunity against bacteriophages",
                "notes": "Depardieu et al. identify Stk2 as a bacteriophage-immunity factor."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "Stk2\tStk2\t1\t1\tStk2__Stk2",
                "notes": "The DefenseFinder rules table models Stk2 as a one-component system requiring the Stk2__Stk2 profile."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| Stk2__Stk2                                       | Stk2__Stk2                                       | Stk2                   | Custom                  | 150    |",
                "notes": "The DefenseFinder HMM inventory records the Stk2__Stk2 profile under the Stk2 model namespace."
              }
            ]
          },
          {
            "subject": "stk2_kinase_activation",
            "predicate": "enables",
            "predicate_id": "RO:0002327",
            "object": "host_protein_phosphorylation",
            "description": "Phage-protein activation of Stk2 leads to Stk2-dependent phosphorylation of several host proteins.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.chom.2016.08.010",
                "snippet": "A phage protein of unknown function activates the Stk2 kinase",
                "notes": "Depardieu et al. show phage-protein activation of Stk2."
              },
              {
                "reference": "DOI:10.1016/j.chom.2016.08.010",
                "snippet": "This leads to the Stk2-dependent phosphorylation of several proteins",
                "notes": "Depardieu et al. connect Stk2 activation to host-protein phosphorylation."
              }
            ]
          },
          {
            "subject": "stk2_kinase_activation",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "host_cell_death",
            "description": "Stk2 activation is followed by death of infected bacterial host cells.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.chom.2016.08.010",
                "snippet": "Bacterial host cells die as a consequence of Stk2 activation",
                "notes": "Depardieu et al. connect Stk2 activation to host-cell death."
              }
            ]
          },
          {
            "subject": "host_cell_death",
            "predicate": "mitigates",
            "predicate_id": "METPO:2007407",
            "object": "phage_propagation",
            "description": "Stk2-triggered host-cell death prevents propagation of the phage through the rest of the bacterial population.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.chom.2016.08.010",
                "snippet": "Bacterial host cells die as a consequence of Stk2 activation, thereby preventing propagation of the phage to the rest of the bacterial population",
                "notes": "Depardieu et al. connect Stk2-dependent host-cell death to phage-propagation prevention."
              }
            ]
          },
          {
            "subject": "host_cell_death",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "stk2_system_trait",
            "description": "Stk2-triggered host-cell death realizes the Stk2 abortive-infection trait.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.chom.2016.08.010",
                "snippet": "provides efficient immunity against bacteriophages by inducing abortive infection",
                "notes": "Depardieu et al. classify the Stk2-dependent immunity mechanism as abortive infection."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Stk2 | 10\\.1016/j\\.chom\\.2016\\.08\\.010 | A eukaryotic-like Serine/threonine kinase protects staphylococci against phages",
                "notes": "The DefenseFinder article registry maps the named Stk2 system to the Depardieu et al. final article."
              }
            ]
          },
          {
            "subject": "stk2_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "abortive_infection_system",
            "description": "Stk2 system possession is an abortive-infection system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.chom.2016.08.010",
                "snippet": "provides efficient immunity against bacteriophages by inducing abortive infection",
                "notes": "Depardieu et al. support Stk2 as an abortive-infection system."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "stk2-activator-and-death-target-gap",
        "prompt": "Resolve the Stk2-activating phage protein and lethal host-phosphorylation target before minting narrower Stk2 mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Depardieu et al. support Stk2 as a named phage-activated serine/threonine kinase system whose activation causes host-protein phosphorylation, bacterial host-cell death, and abortive infection, and DefenseFinder represents Stk2 with a one-profile model. This system-level record leaves the direct phage activator, the lethal Stk2 phosphorylation target, target conservation across Stk2 loci, and phage escape routes unresolved.",
        "attaches_to": [
          "causal_graphs#stk2_activation_aborts_phage_infection"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-20"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-20T07:41:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Stk2 system as a DOI-backed GENOMICS TraitRecord under the abortive infection system parent after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v180.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000266",
    "label": "Sucellos system",
    "definition": "A phage defense system in which an organism possesses a Sucellos locus represented by SclA_VCA0367 and SclB_VCA0368 profiles that can protect bacteria from bacteriophage infection.",
    "definition_source": "DOI:10.1126/science.ads0768",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "Sucellos",
        "synonym_type": "EXACT_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      },
      {
        "synonym_text": "SclA_VCA0367",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "SclB_VCA0368",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1126/science.ads0768",
        "snippet": "nearly 10% of the integron cassettes in the pandemic Vibrio cholerae strain encode novel antiphage functions",
        "notes": "Darracq et al. support treating the newly discovered Vibrio cholerae SCI antiphage cassettes as bacterial anti-phage systems."
      },
      {
        "reference": "DOI:10.1126/science.ads0768",
        "snippet": "Most of these novel systems have little or no similarity to previously known ones, with several providing defense through cell lysis or growth arrest",
        "notes": "Darracq et al. support a conservative system record that does not assert a resolved Sucellos trigger, effector output, or universal pathway."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "Sucellos | 10\\.1126/science\\.ads0768 | Sedentary chromosomal integrons as biobanks of bacterial antiphage defense systems",
        "notes": "The DefenseFinder model registry maps the named Sucellos system to the Darracq et al. SCI antiphage-system paper."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "Sucellos__SclA_VCA0367                           |                                                  | Sucellos",
        "notes": "The DefenseFinder HMM inventory records SclA_VCA0367 in the Sucellos model namespace."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "Sucellos__SclB_VCA0368                           |                                                  | Sucellos",
        "notes": "The DefenseFinder HMM inventory records SclB_VCA0368 in the Sucellos model namespace."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "sucellos_locus_restricts_phage",
        "title": "Sucellos loci confer bacterial phage defense",
        "description": "Conservative system-level sketch linking possession of a Sucellos locus to restricted bacteriophage propagation without asserting the unresolved phage trigger or molecular output.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Sucellos as a named SCI-derived anti-phage system with SclA_VCA0367 and SclB_VCA0368 DefenseFinder profiles while leaving its phage trigger, molecular substrate, antiviral effector output, and subtype breadth unresolved.",
        "nodes": [
          {
            "node_id": "sucellos_locus",
            "label": "Sucellos locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A Sucellos anti-phage defense locus represented in DefenseFinder by SclA_VCA0367 and SclB_VCA0368 profiles."
          },
          {
            "node_id": "restricted_phage_propagation",
            "label": "restricted phage propagation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced propagation of bacteriophage in cells carrying the Sucellos system."
          },
          {
            "node_id": "sucellos_system_trait",
            "label": "Sucellos system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000266",
            "description": "Possession of a genome-encoded Sucellos phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "sucellos_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "restricted_phage_propagation",
            "description": "DefenseFinder maps Sucellos to an SCI anti-phage-system discovery paper and represents Sucellos loci through the SclA_VCA0367 and SclB_VCA0368 component profiles.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.ads0768",
                "snippet": "nearly 10% of the integron cassettes in the pandemic Vibrio cholerae strain encode novel antiphage functions",
                "notes": "Darracq et al. describe the newly discovered antiphage-system cohort that the DefenseFinder Sucellos registry row maps to the Sucellos system."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "Sucellos__SclA_VCA0367                           |                                                  | Sucellos",
                "notes": "The DefenseFinder HMM inventory supports SclA_VCA0367 as one Sucellos component profile."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "Sucellos__SclB_VCA0368                           |                                                  | Sucellos",
                "notes": "The DefenseFinder HMM inventory supports SclB_VCA0368 as one Sucellos component profile."
              }
            ]
          },
          {
            "subject": "restricted_phage_propagation",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "sucellos_system_trait",
            "description": "Sucellos-mediated phage restriction realizes the Sucellos system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.ads0768",
                "snippet": "Most of these novel systems have little or no similarity to previously known ones",
                "notes": "Darracq et al. place the Sucellos discovery cohort in a set of novel bacterial systems that protect against phages."
              }
            ]
          },
          {
            "subject": "sucellos_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Sucellos system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Sucellos | 10\\.1126/science\\.ads0768 | Sedentary chromosomal integrons as biobanks of bacterial antiphage defense systems",
                "notes": "DefenseFinder associates Sucellos with the Darracq et al. bacterial antiphage-system paper."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "sucellos-mechanism-gap",
        "prompt": "Resolve Sucellos phage triggers and effector outputs before minting narrower Sucellos mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Darracq et al. and DefenseFinder support Sucellos as a named anti-phage system with SclA_VCA0367 and SclB_VCA0368 profiles, but the trigger, molecular substrate, antiviral effector output, and subtype-specific mechanism are not resolved enough here to assert a narrower mechanistic child trait.",
        "attaches_to": [
          "causal_graphs#sucellos_locus_restricts_phage"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-19"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-19T05:32:39Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Sucellos system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v143.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000413",
    "label": "Tab system",
    "definition": "A phage defense system in which an organism or resident prophage possesses a Tab virion-assembly-inhibition locus that expresses the Tab tail-assembly-blocking protein, blocks assembly of invading phage tails, prevents infectious virion formation, and protects the bacterial community from phage spread.",
    "definition_source": "DOI:10.1038/s41467-024-45892-x",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "Tab",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1038/s41467-024-45892-x"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/s41467-024-45892-x",
        "snippet": "a type of anti-phage defence that interferes with the virion assembly pathway of invading phages",
        "notes": "Patel et al. define the Tab-associated anti-phage defence as interference with the virion assembly pathway of invading phages."
      },
      {
        "reference": "DOI:10.1038/s41467-024-45892-x",
        "snippet": "The protein that mediates this defence, which we call Tab",
        "notes": "Patel et al. name the protein mediating this prophage defence Tab."
      },
      {
        "reference": "DOI:10.1038/s41467-024-45892-x",
        "snippet": "blocks assembly of the phage tail, thus preventing formation of infectious virions",
        "notes": "Patel et al. show that Tab blocks phage-tail assembly and thereby prevents production of infectious virions."
      },
      {
        "reference": "DOI:10.1038/s41467-024-45892-x",
        "snippet": "there is no release of infectious phage progeny, and the bacterial community is thereby protected from a phage epidemic",
        "notes": "Patel et al. connect Tab-mediated inhibition of infectious phage release to protection of the bacterial community from a phage epidemic."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| Tab | 10\\.1038/s41467-024-45892-x | Anti-phage defence through inhibition of virion assembly |",
        "notes": "The pinned DefenseFinder article registry maps the named Tab system to the Patel et al. virion-assembly-inhibition paper. The pinned HMM inventory (https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md) and pinned rules table (https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv) do not list Tab, so this row is name-to-paper evidence rather than model-component evidence."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "tab_blocks_virion_assembly",
        "title": "Tab blocks phage virion assembly",
        "description": "Conservative system-level sketch linking a Tab prophage-associated locus to inhibition of invading phage tail assembly, blocked infectious virion formation, and Tab system possession.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Tab as a prophage-encoded virion-assembly-inhibition system without asserting the full host range, full sensitive-phage range, Tab counter-defence specificity, or profile-to-component DefenseFinder modeling.",
        "nodes": [
          {
            "node_id": "tab_locus",
            "label": "Tab prophage locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A prophage locus expressing Tab, a phage tail assembly blocker."
          },
          {
            "node_id": "tab_virion_assembly_inhibition",
            "label": "Tab-mediated virion assembly inhibition",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Tab-mediated interference with the virion assembly pathway of invading phages."
          },
          {
            "node_id": "phage_tail_assembly",
            "label": "phage tail assembly",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Assembly of the phage tail during productive virion morphogenesis."
          },
          {
            "node_id": "infectious_virion_formation",
            "label": "infectious virion formation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Formation and release of infectious phage progeny."
          },
          {
            "node_id": "tab_system_trait",
            "label": "Tab system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000413",
            "description": "Possession of a genome-encoded Tab phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "tab_locus",
            "predicate": "enables",
            "predicate_id": "RO:0002327",
            "object": "tab_virion_assembly_inhibition",
            "description": "A prophage-associated tab locus expresses the Tab protein that mediates virion-assembly inhibition.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-024-45892-x",
                "snippet": "The protein that mediates this defence, which we call Tab",
                "notes": "Patel et al. name Tab as the protein mediating this prophage anti-phage defence."
              }
            ]
          },
          {
            "subject": "tab_virion_assembly_inhibition",
            "predicate": "mitigates",
            "predicate_id": "METPO:2007407",
            "object": "phage_tail_assembly",
            "description": "Tab-mediated virion assembly inhibition blocks assembly of invading phage tails.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-024-45892-x",
                "snippet": "blocks assembly of the phage tail, thus preventing formation of infectious virions",
                "notes": "Patel et al. connect Tab to blockade of phage-tail assembly."
              }
            ]
          },
          {
            "subject": "tab_virion_assembly_inhibition",
            "predicate": "mitigates",
            "predicate_id": "METPO:2007407",
            "object": "infectious_virion_formation",
            "description": "By blocking tail assembly, Tab-mediated defence prevents formation and release of infectious phage progeny.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-024-45892-x",
                "snippet": "there is no release of infectious phage progeny, and the bacterial community is thereby protected from a phage epidemic",
                "notes": "Patel et al. report no infectious phage progeny release under Tab-mediated defence."
              }
            ]
          },
          {
            "subject": "tab_virion_assembly_inhibition",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "tab_system_trait",
            "description": "Virion assembly inhibition realizes the Tab system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-024-45892-x",
                "snippet": "Tab-mediated inhibition of virion assembly provides a new type of anti-phage defence",
                "notes": "Patel et al. frame Tab-mediated virion assembly inhibition as a new anti-phage defence type."
              }
            ]
          },
          {
            "subject": "tab_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Tab system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-024-45892-x",
                "snippet": "a type of anti-phage defence that interferes with the virion assembly pathway of invading phages",
                "notes": "Patel et al. place Tab in anti-phage defence by virion assembly pathway interference."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "tab-defensefinder-model-gap",
        "prompt": "Resolve Tab host breadth, sensitive-phage breadth, counter-defence specificity, and DefenseFinder HMM/rules coverage before minting narrower Tab mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Patel et al. support Tab as a prophage-encoded anti-phage defence protein that blocks invading phage-tail assembly and prevents release of infectious phage progeny, while the pinned DefenseFinder article registry names a Tab system. The pinned DefenseFinder HMM inventory and rules table have no Tab rows, and the evidence does not yet resolve host breadth, target-phage breadth, counter-defence specificity, or profile-to-activity modeling.",
        "evidence": [
          {
            "reference": "DOI:10.1038/s41467-024-45892-x",
            "snippet": "blocks assembly of the phage tail, thus preventing formation of infectious virions",
            "notes": "Patel et al. support Tab blockade of phage-tail assembly."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
            "snippet": "| Tab | 10\\.1038/s41467-024-45892-x | Anti-phage defence through inhibition of virion assembly |",
            "notes": "The pinned DefenseFinder article registry maps the named Tab system to the Patel et al. virion-assembly-inhibition paper. The pinned HMM inventory (https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md) and pinned rules table (https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv) do not list Tab, so this row is name-to-paper evidence rather than model-component evidence."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "notes": "The pinned DefenseFinder HMM inventory does not list Tab, leaving profile-level components unresolved."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "The pinned DefenseFinder rules table does not list Tab, leaving rule-level detection criteria unresolved."
          }
        ],
        "attaches_to": [
          "causal_graphs#tab_blocks_virion_assembly"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-27"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-27T17:41:07Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Tab system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; kept the graph at prophage-locus and virion-assembly-inhibition level because the pinned DefenseFinder article row is not backed by pinned HMM or rules rows; the replacement placeholder is reserved in proposals/metpo_traitmech_v290.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000513",
    "label": "TagI system",
    "definition": "A type IV modification-dependent restriction system in which an organism possesses a TagI-family locus encoding an SRA-HNH restriction endonuclease that recognizes 5-methylcytosine- or 5-hydroxymethylcytosine-modified DNA.",
    "definition_source": "DOI:10.1093/nar/gky781",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000496"
    ],
    "synonyms": [
      {
        "synonym_text": "TagI",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      }
    ],
    "evidence": [
      {
        "reference": "PMID:30202937",
        "snippet": "TagI belongs to the recently characterized SRA-HNH family of modification-dependent restriction endonucleases (REases) that also includes ScoA3IV (Sco5333) and TbiR51I (Tbis1).",
        "notes": "Kisiala et al. support TagI as a member of an SRA-HNH modification-dependent restriction endonuclease family."
      },
      {
        "reference": "PMID:30202937",
        "snippet": "Here, we present a crystal structure of dimeric TagI, which exhibits a DNA binding site formed jointly by the nuclease domains, and separate binding sites for modified DNA bases in the two protomers.",
        "notes": "Kisiala et al. support dimeric TagI structure with nuclease and modified-base-binding sites."
      },
      {
        "reference": "PMID:30202937",
        "snippet": "Their pockets for the flipped bases are spacious enough to accommodate 5-methylcytosine (5mC) or 5-hydroxymethylcytosine (5hmC), but not glucosyl-5-hydroxymethylcytosine (g5hmC).",
        "notes": "Kisiala et al. support TagI recognition of flipped 5mC and 5hmC bases."
      },
      {
        "reference": "PMID:30202937",
        "snippet": "Such preference is in agreement with the biochemical determination of the TagI modification dependence and the results of phage restriction assays.",
        "notes": "Kisiala et al. support TagI modification dependence and phage restriction activity."
      },
      {
        "reference": "PMID:30202937",
        "snippet": "The ability of TagI to digest plasmids methylated by Dcm (C5mCWGG), M.Fnu4HI (G5mCNGC) or M.HpyCH4IV (A5mCGT) suggests that the SRA domains of the enzyme are tolerant to different sequence contexts of the modified base.",
        "notes": "Kisiala et al. support TagI digestion of multiple 5mC-modified plasmid sequence contexts."
      },
      {
        "reference": "DOI:10.1093/nar/gkt747",
        "snippet": "The new class of modification-dependent restriction enzymes was named Type IV, as distinct from the familiar modification-blocked Types I-III.",
        "notes": "Loenen and Raleigh define the Type IV class as modification-dependent restriction enzymes."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| TagI | 10\\.1093/nar/gky781 | Crystal structure of the modification-dependent SRA-HNH endonuclease TagI | ",
        "notes": "The pinned DefenseFinder article registry maps the TagI source key to the Kisiala et al. structural paper."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "tagi_restricts_modified_cytosine_dna",
        "title": "TagI restricts modified-cytosine DNA",
        "description": "Conservative system-level sketch linking a TagI-family locus to 5mC/5hmC-dependent DNA restriction and to the Type IV restriction parent trait.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures TagI as a named Type IV modification-dependent restriction family while leaving natural host breadth, exact modified-DNA sequence-context specificity across SRA-HNH homologs, accession-level protein examples, and DefenseFinder RM_Type_IV HMM/rules mapping unresolved.",
        "nodes": [
          {
            "node_id": "tagi_family_locus",
            "label": "TagI-family locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A locus encoding a TagI-family SRA-HNH modification-dependent restriction endonuclease."
          },
          {
            "node_id": "tagi_modified_cytosine_dna",
            "label": "TagI-targeted modified-cytosine DNA",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "DNA containing 5-methylcytosine or 5-hydroxymethylcytosine in a TagI-family recognition context."
          },
          {
            "node_id": "tagi_modified_cytosine_restriction",
            "label": "TagI modified-cytosine DNA restriction",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Modification-dependent restriction of 5mC/5hmC-modified DNA by a TagI-family endonuclease."
          },
          {
            "node_id": "tagi_system_trait",
            "label": "TagI system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000513",
            "description": "Possession of a genome-encoded TagI-family modification-dependent restriction system."
          },
          {
            "node_id": "type_iv_modification_dependent_restriction",
            "label": "type IV modification-dependent restriction system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000496",
            "description": "Possession of a genome-encoded Type IV modification-dependent restriction system."
          }
        ],
        "edges": [
          {
            "subject": "tagi_family_locus",
            "predicate": "enables",
            "predicate_id": "RO:0002327",
            "object": "tagi_modified_cytosine_restriction",
            "description": "TagI-family loci encode SRA-HNH endonucleases that restrict 5mC/5hmC-modified DNA.",
            "evidence": [
              {
                "reference": "PMID:30202937",
                "snippet": "Here, we present a crystal structure of dimeric TagI, which exhibits a DNA binding site formed jointly by the nuclease domains, and separate binding sites for modified DNA bases in the two protomers.",
                "notes": "Kisiala et al. support dimeric TagI structure with nuclease and modified-base-binding sites."
              },
              {
                "reference": "PMID:30202937",
                "snippet": "Their pockets for the flipped bases are spacious enough to accommodate 5-methylcytosine (5mC) or 5-hydroxymethylcytosine (5hmC), but not glucosyl-5-hydroxymethylcytosine (g5hmC).",
                "notes": "Kisiala et al. support TagI recognition of flipped 5mC and 5hmC bases."
              }
            ]
          },
          {
            "subject": "tagi_modified_cytosine_restriction",
            "predicate": "mitigates",
            "predicate_id": "METPO:2007407",
            "object": "tagi_modified_cytosine_dna",
            "description": "TagI-family restriction targets 5mC- or 5hmC-modified DNA.",
            "evidence": [
              {
                "reference": "PMID:30202937",
                "snippet": "Their pockets for the flipped bases are spacious enough to accommodate 5-methylcytosine (5mC) or 5-hydroxymethylcytosine (5hmC), but not glucosyl-5-hydroxymethylcytosine (g5hmC).",
                "notes": "Kisiala et al. support TagI recognition of flipped 5mC and 5hmC bases."
              },
              {
                "reference": "PMID:30202937",
                "snippet": "Such preference is in agreement with the biochemical determination of the TagI modification dependence and the results of phage restriction assays.",
                "notes": "Kisiala et al. support TagI modification dependence and phage restriction activity."
              },
              {
                "reference": "PMID:30202937",
                "snippet": "The ability of TagI to digest plasmids methylated by Dcm (C5mCWGG), M.Fnu4HI (G5mCNGC) or M.HpyCH4IV (A5mCGT) suggests that the SRA domains of the enzyme are tolerant to different sequence contexts of the modified base.",
                "notes": "Kisiala et al. support TagI digestion of multiple 5mC-modified plasmid sequence contexts."
              }
            ]
          },
          {
            "subject": "tagi_modified_cytosine_restriction",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "tagi_system_trait",
            "description": "TagI-family modified-cytosine DNA restriction realizes the organism-level TagI system possession trait.",
            "evidence": [
              {
                "reference": "PMID:30202937",
                "snippet": "TagI belongs to the recently characterized SRA-HNH family of modification-dependent restriction endonucleases (REases) that also includes ScoA3IV (Sco5333) and TbiR51I (Tbis1).",
                "notes": "Kisiala et al. support TagI as a member of an SRA-HNH modification-dependent restriction endonuclease family."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| TagI | 10\\.1093/nar/gky781 | Crystal structure of the modification-dependent SRA-HNH endonuclease TagI | ",
                "notes": "The pinned DefenseFinder article registry maps the TagI source key to the Kisiala et al. structural paper."
              }
            ]
          },
          {
            "subject": "tagi_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "type_iv_modification_dependent_restriction",
            "description": "TagI system possession is a Type IV modification-dependent restriction system trait.",
            "evidence": [
              {
                "reference": "PMID:30202937",
                "snippet": "TagI belongs to the recently characterized SRA-HNH family of modification-dependent restriction endonucleases (REases) that also includes ScoA3IV (Sco5333) and TbiR51I (Tbis1).",
                "notes": "Kisiala et al. support TagI as a member of an SRA-HNH modification-dependent restriction endonuclease family."
              },
              {
                "reference": "DOI:10.1093/nar/gkt747",
                "snippet": "The new class of modification-dependent restriction enzymes was named Type IV, as distinct from the familiar modification-blocked Types I-III.",
                "notes": "Loenen and Raleigh define the Type IV class as modification-dependent restriction enzymes."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "tagi-defensefinder-model-gap",
        "prompt": "Resolve TagI-family breadth, modified-cytosine sequence-context specificity across natural hosts, accession-level protein examples, and DefenseFinder RM_Type_IV HMM/rules mapping before minting narrower TagI mechanism or component traits.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Kisiala et al. support TagI as an SRA-HNH modification-dependent restriction endonuclease that recognizes 5mC/5hmC bases and restricts phage in assays. The pinned DefenseFinder article registry maps TagI to that paper, but the pinned HMM inventory and rules table have no exact TagI rows. This first-pass record therefore does not resolve a reusable DefenseFinder profile model, exact accession-level protein examples, the breadth of TagI-like systems across natural hosts, or the complete set of natural modified-cytosine sequence contexts.",
        "evidence": [
          {
            "reference": "PMID:30202937",
            "snippet": "TagI belongs to the recently characterized SRA-HNH family of modification-dependent restriction endonucleases (REases) that also includes ScoA3IV (Sco5333) and TbiR51I (Tbis1).",
            "notes": "Kisiala et al. support TagI as a member of an SRA-HNH modification-dependent restriction endonuclease family."
          },
          {
            "reference": "PMID:30202937",
            "snippet": "Here, we present a crystal structure of dimeric TagI, which exhibits a DNA binding site formed jointly by the nuclease domains, and separate binding sites for modified DNA bases in the two protomers.",
            "notes": "Kisiala et al. support dimeric TagI structure with nuclease and modified-base-binding sites."
          },
          {
            "reference": "PMID:30202937",
            "snippet": "Their pockets for the flipped bases are spacious enough to accommodate 5-methylcytosine (5mC) or 5-hydroxymethylcytosine (5hmC), but not glucosyl-5-hydroxymethylcytosine (g5hmC).",
            "notes": "Kisiala et al. support TagI recognition of flipped 5mC and 5hmC bases."
          },
          {
            "reference": "PMID:30202937",
            "snippet": "Such preference is in agreement with the biochemical determination of the TagI modification dependence and the results of phage restriction assays.",
            "notes": "Kisiala et al. support TagI modification dependence and phage restriction activity."
          },
          {
            "reference": "PMID:30202937",
            "snippet": "The ability of TagI to digest plasmids methylated by Dcm (C5mCWGG), M.Fnu4HI (G5mCNGC) or M.HpyCH4IV (A5mCGT) suggests that the SRA domains of the enzyme are tolerant to different sequence contexts of the modified base.",
            "notes": "Kisiala et al. support TagI digestion of multiple 5mC-modified plasmid sequence contexts."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
            "snippet": "| TagI | 10\\.1093/nar/gky781 | Crystal structure of the modification-dependent SRA-HNH endonuclease TagI | ",
            "notes": "The pinned DefenseFinder article registry maps the TagI source key to the Kisiala et al. structural paper."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "notes": "A structured first-pass search of the pinned DefenseFinder HMM inventory found no exact TagI row."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "A structured first-pass search of the pinned DefenseFinder rules table found no exact TagI system row."
          }
        ],
        "attaches_to": [
          "causal_graphs#tagi_restricts_modified_cytosine_dna"
        ],
        "posed_by": "codex",
        "posed_date": "2026-10-01"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-01T11:10:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted TagI system as a DOI/PMID- and DefenseFinder-backed GENOMICS TraitRecord under the type IV modification-dependent restriction system parent after an ignored-and-hidden duplicate review found no exact same-scope live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v390.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-01T11:10:02Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed TagI system during initial curation and left canonical_examples empty because Kisiala et al. support the purified TagI enzyme, structure, and phage restriction assays, but not a single stable NCBITaxon strain exemplar or accession-level protein example for the organism-level TagI system trait. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000265",
    "label": "Taranis system",
    "definition": "A phage defense system in which an organism possesses a Taranis locus represented by a VCA0396 profile that can protect bacteria from bacteriophage infection.",
    "definition_source": "DOI:10.1126/science.ads0768",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "Taranis",
        "synonym_type": "EXACT_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      },
      {
        "synonym_text": "VCA0396",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1126/science.ads0768",
        "snippet": "nearly 10% of the integron cassettes in the pandemic Vibrio cholerae strain encode novel antiphage functions",
        "notes": "Darracq et al. support treating the newly discovered Vibrio cholerae SCI antiphage cassettes as bacterial anti-phage systems."
      },
      {
        "reference": "DOI:10.1126/science.ads0768",
        "snippet": "Most of these novel systems have little or no similarity to previously known ones, with several providing defense through cell lysis or growth arrest",
        "notes": "Darracq et al. support a conservative system record that does not assert a resolved Taranis trigger, effector output, or universal pathway."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "Taranis | 10\\.1126/science\\.ads0768 | Sedentary chromosomal integrons as biobanks of bacterial antiphage defense systems",
        "notes": "The DefenseFinder model registry maps the named Taranis system to the Darracq et al. SCI antiphage-system paper."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "Taranis__VCA0396                                 |                                                  | Taranis",
        "notes": "The DefenseFinder HMM inventory records VCA0396 in the Taranis model namespace."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "taranis_locus_restricts_phage",
        "title": "Taranis loci confer bacterial phage defense",
        "description": "Conservative system-level sketch linking possession of a Taranis locus to restricted bacteriophage propagation without asserting the unresolved phage trigger or molecular output.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Taranis as a named SCI-derived anti-phage system with a VCA0396 DefenseFinder profile while leaving its phage trigger, molecular substrate, antiviral effector output, and subtype breadth unresolved.",
        "nodes": [
          {
            "node_id": "taranis_locus",
            "label": "Taranis locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A Taranis anti-phage defense locus represented in DefenseFinder by a VCA0396 profile."
          },
          {
            "node_id": "restricted_phage_propagation",
            "label": "restricted phage propagation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced propagation of bacteriophage in cells carrying the Taranis system."
          },
          {
            "node_id": "taranis_system_trait",
            "label": "Taranis system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000265",
            "description": "Possession of a genome-encoded Taranis phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "taranis_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "restricted_phage_propagation",
            "description": "DefenseFinder maps Taranis to an SCI anti-phage-system discovery paper and represents Taranis loci through the VCA0396 component profile.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.ads0768",
                "snippet": "nearly 10% of the integron cassettes in the pandemic Vibrio cholerae strain encode novel antiphage functions",
                "notes": "Darracq et al. describe the newly discovered antiphage-system cohort that the DefenseFinder Taranis registry row maps to the Taranis system."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "Taranis__VCA0396                                 |                                                  | Taranis",
                "notes": "The DefenseFinder HMM inventory supports VCA0396 as the Taranis component profile."
              }
            ]
          },
          {
            "subject": "restricted_phage_propagation",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "taranis_system_trait",
            "description": "Taranis-mediated phage restriction realizes the Taranis system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.ads0768",
                "snippet": "Most of these novel systems have little or no similarity to previously known ones",
                "notes": "Darracq et al. place the Taranis discovery cohort in a set of novel bacterial systems that protect against phages."
              }
            ]
          },
          {
            "subject": "taranis_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Taranis system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Taranis | 10\\.1126/science\\.ads0768 | Sedentary chromosomal integrons as biobanks of bacterial antiphage defense systems",
                "notes": "DefenseFinder associates Taranis with the Darracq et al. bacterial antiphage-system paper."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "taranis-mechanism-gap",
        "prompt": "Resolve Taranis phage triggers and effector outputs before minting narrower Taranis mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Darracq et al. and DefenseFinder support Taranis as a named anti-phage system with a VCA0396 profile, but the trigger, molecular substrate, antiviral effector output, and subtype-specific mechanism are not resolved enough here to assert a narrower mechanistic child trait.",
        "attaches_to": [
          "causal_graphs#taranis_locus_restricts_phage"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-19"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-19T05:02:55Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Taranis system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v142.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000412",
    "label": "TgvAB system",
    "definition": "A restriction-modification system in which an organism possesses a two-gene TgvAB locus embedded in the Vibrio cholerae VPI-2 type I R-M cluster, encoding TgvA and TgvB modification-dependent restriction proteins related to GmrSD type IV restriction enzymes that restrict glucosylated hmC-containing T-even-like phage DNA.",
    "definition_source": "DOI:10.1128/jb.00145-24",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000095"
    ],
    "synonyms": [
      {
        "synonym_text": "TgvAB",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1128/jb.00145-24"
      },
      {
        "synonym_text": "TgvAB__TgvA",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "TgvAB__TgvB",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1128/jb.00145-24",
        "snippet": "the two genes embedded within the T1RM system encode a novel two-protein modification-dependent restriction system related to the GmrSD family of type IV restriction enzymes",
        "notes": "Vizzarro et al. define TgvAB as a modification-dependent restriction system related to GmrSD-family type IV restriction enzymes."
      },
      {
        "reference": "DOI:10.1128/jb.00145-24",
        "snippet": "potent anti-phage activity against diverse members of the Tevenvirinae",
        "notes": "Vizzarro et al. support TgvAB anti-phage activity against phages with hypermodified genomes."
      },
      {
        "reference": "DOI:10.1128/jb.00143-24",
        "snippet": "both TgvA and TgvB are required for defense against T2, T4, and T6",
        "notes": "Gomez and Waters independently report that both TgvA and TgvB are required for TgvAB-mediated anti-phage activity."
      },
      {
        "reference": "DOI:10.1128/jb.00143-24",
        "snippet": "TgvAB targets phage DNA with glucosylated 5-hydroxymethylcytosine (5hmC) bases",
        "notes": "Gomez and Waters support TgvAB as a type IV restriction system targeting glucosylated 5-hydroxymethylcytosine in T-even phage genomes."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| TgvAB | 10\\.1128/jb\\.00145-24 | Vibrio cholerae pathogenicity island 2 encodes two distinct types of restriction systems |",
        "notes": "The pinned DefenseFinder article registry maps the named TgvAB system to the Vizzarro et al. VPI-2 restriction-systems paper. The pinned rules table (https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv) does not list TgvAB, so the registry and HMM rows support a named system-possession trait rather than complete DefenseFinder detection criteria."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| TgvAB__TgvA                                      |                                                   | TgvAB                  | Custom                  | 200    |",
        "notes": "The pinned DefenseFinder HMM inventory records TgvAB__TgvA as a custom TgvAB profile."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| TgvAB__TgvB                                      |                                                   | TgvAB                  | Custom                  | 400    |",
        "notes": "The pinned DefenseFinder HMM inventory records TgvAB__TgvB as a custom TgvAB profile."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "tgvab_type_iv_restriction",
        "title": "TgvAB restricts glucosylated T-even-like phage DNA",
        "description": "Conservative system-level sketch linking a two-gene TgvAB locus to modification-dependent type IV restriction of glucosylated hmC-containing T-even-like phage DNA and TgvAB system possession.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures TgvAB at VPI-2, T-even-like-phage, and type-IV-restriction level without asserting complete native host breadth, exact TgvA/TgvB subunit stoichiometry, or a DefenseFinder rule-level profile combination.",
        "nodes": [
          {
            "node_id": "tgvab_locus",
            "label": "TgvAB locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A two-gene locus encoding TgvA and TgvB GmrSD-related modification-dependent restriction proteins."
          },
          {
            "node_id": "glucosylated_hmc_phage_dna",
            "label": "glucosylated hmC phage DNA",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "T-even-like bacteriophage DNA carrying glucosylated 5-hydroxymethylcytosine modifications."
          },
          {
            "node_id": "tgvab_dependent_type_iv_restriction",
            "label": "TgvAB-dependent type IV restriction",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Modification-dependent restriction of hypermodified phage DNA by TgvAB."
          },
          {
            "node_id": "t_even_like_phage_propagation",
            "label": "T-even-like phage propagation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Productive propagation of T-even-like phages whose genomes carry glucosylated hmC."
          },
          {
            "node_id": "tgvab_system_trait",
            "label": "TgvAB system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000412",
            "description": "Possession of a genome-encoded TgvAB modification-dependent restriction system."
          },
          {
            "node_id": "restriction_modification_system",
            "label": "restriction-modification system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000095",
            "description": "Possession of a methyltransferase and restriction endonuclease system for self/non-self DNA discrimination."
          }
        ],
        "edges": [
          {
            "subject": "tgvab_locus",
            "predicate": "enables",
            "predicate_id": "RO:0002327",
            "object": "tgvab_dependent_type_iv_restriction",
            "description": "A TgvAB locus encodes both proteins required for modification-dependent restriction of T-even phage DNA.",
            "evidence": [
              {
                "reference": "DOI:10.1128/jb.00145-24",
                "snippet": "the two genes embedded within the T1RM system encode a novel two-protein modification-dependent restriction system related to the GmrSD family of type IV restriction enzymes",
                "notes": "Vizzarro et al. define the embedded VPI-2 TgvAB locus as a GmrSD-related type IV restriction system."
              },
              {
                "reference": "DOI:10.1128/jb.00143-24",
                "snippet": "both TgvA and TgvB are required for defense against T2, T4, and T6",
                "notes": "Gomez and Waters show that anti-phage activity requires both TgvA and TgvB."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| TgvAB | 10\\.1128/jb\\.00145-24 | Vibrio cholerae pathogenicity island 2 encodes two distinct types of restriction systems |",
                "notes": "The pinned DefenseFinder article registry maps the named TgvAB system to the Vizzarro et al. VPI-2 restriction-systems paper. The pinned rules table (https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv) does not list TgvAB, so the registry and HMM rows support a named system-possession trait rather than complete DefenseFinder detection criteria."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| TgvAB__TgvA                                      |                                                   | TgvAB                  | Custom                  | 200    |",
                "notes": "The pinned DefenseFinder HMM inventory records TgvAB__TgvA as a custom TgvAB profile."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| TgvAB__TgvB                                      |                                                   | TgvAB                  | Custom                  | 400    |",
                "notes": "The pinned DefenseFinder HMM inventory records TgvAB__TgvB as a custom TgvAB profile."
              }
            ]
          },
          {
            "subject": "tgvab_dependent_type_iv_restriction",
            "predicate": "mitigates",
            "predicate_id": "METPO:2007407",
            "object": "glucosylated_hmc_phage_dna",
            "description": "TgvAB-dependent type IV restriction targets T-even-like phage DNA bearing glucosylated 5-hydroxymethylcytosine.",
            "evidence": [
              {
                "reference": "DOI:10.1128/jb.00143-24",
                "snippet": "TgvAB targets phage DNA with glucosylated 5-hydroxymethylcytosine (5hmC) bases",
                "notes": "Gomez and Waters directly connect the TgvAB system to targeting glucosylated 5-hydroxymethylcytosine during phage defense."
              }
            ]
          },
          {
            "subject": "tgvab_dependent_type_iv_restriction",
            "predicate": "mitigates",
            "predicate_id": "METPO:2007407",
            "object": "t_even_like_phage_propagation",
            "description": "Restriction of hypermodified T-even-like phage DNA inhibits productive phage propagation.",
            "evidence": [
              {
                "reference": "DOI:10.1128/jb.00145-24",
                "snippet": "potent anti-phage activity against diverse members of the Tevenvirinae",
                "notes": "Vizzarro et al. support TgvAB anti-phage activity against hypermodified phages."
              },
              {
                "reference": "DOI:10.1128/jb.00143-24",
                "snippet": "TgvAB targets phage DNA with glucosylated 5-hydroxymethylcytosine (5hmC) bases",
                "notes": "Gomez and Waters identify glucosylated 5-hydroxymethylcytosine as the phage-DNA modification targeted by TgvAB."
              }
            ]
          },
          {
            "subject": "tgvab_dependent_type_iv_restriction",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "tgvab_system_trait",
            "description": "TgvAB-dependent type IV restriction realizes the TgvAB system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1128/jb.00145-24",
                "snippet": "novel modification-dependent type IV restriction system that recognizes hypermodified cytosines",
                "notes": "Vizzarro et al. frame TgvAB as a type IV restriction system recognizing hypermodified cytosines."
              },
              {
                "reference": "DOI:10.1128/jb.00143-24",
                "snippet": "both TgvA and TgvB are required for defense against T2, T4, and T6",
                "notes": "Gomez and Waters report that both encoded TgvAB components are required for anti-phage activity."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| TgvAB | 10\\.1128/jb\\.00145-24 | Vibrio cholerae pathogenicity island 2 encodes two distinct types of restriction systems |",
                "notes": "The pinned DefenseFinder article registry maps the named TgvAB system to the Vizzarro et al. VPI-2 restriction-systems paper. The pinned rules table (https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv) does not list TgvAB, so the registry and HMM rows support a named system-possession trait rather than complete DefenseFinder detection criteria."
              }
            ]
          },
          {
            "subject": "tgvab_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "restriction_modification_system",
            "description": "TgvAB is a GmrSD-related type IV restriction system in the broader restriction-modification family.",
            "evidence": [
              {
                "reference": "DOI:10.1128/jb.00145-24",
                "snippet": "the two genes embedded within the T1RM system encode a novel two-protein modification-dependent restriction system related to the GmrSD family of type IV restriction enzymes",
                "notes": "Vizzarro et al. place TgvAB among GmrSD-family type IV restriction enzymes."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "tgvab-defensefinder-rule-gap",
        "prompt": "Resolve TgvAB native host breadth, TgvA/TgvB biochemical roles, phage substrate breadth, and DefenseFinder rule or model coverage before minting narrower TgvAB mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Vizzarro et al. and Gomez and Waters support TgvAB as a two-component VPI-2 type IV restriction system that restricts glucosylated hmC-containing T-even phage DNA, and the pinned DefenseFinder HMM inventory carries TgvA and TgvB custom profiles. The pinned DefenseFinder rules table has no TgvAB row, and the evidence does not yet resolve native host breadth, the individual TgvA versus TgvB biochemical roles, full phage substrate breadth, or a rule-level profile combination.",
        "evidence": [
          {
            "reference": "DOI:10.1128/jb.00145-24",
            "snippet": "the two genes embedded within the T1RM system encode a novel two-protein modification-dependent restriction system related to the GmrSD family of type IV restriction enzymes",
            "notes": "Vizzarro et al. name TgvAB as the GmrSD-related modification-dependent restriction system."
          },
          {
            "reference": "DOI:10.1128/jb.00143-24",
            "snippet": "TgvAB targets phage DNA with glucosylated 5-hydroxymethylcytosine (5hmC) bases",
            "notes": "Gomez and Waters support the glucosylated hmC substrate class while leaving broader phage substrate limits open."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| TgvAB__TgvA                                      |                                                   | TgvAB                  | Custom                  | 200    |",
            "notes": "The pinned DefenseFinder HMM inventory records TgvAB__TgvA as a custom TgvAB profile."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| TgvAB__TgvB                                      |                                                   | TgvAB                  | Custom                  | 400    |",
            "notes": "The pinned DefenseFinder HMM inventory records TgvAB__TgvB as a custom TgvAB profile."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "The pinned DefenseFinder rules table does not list a TgvAB row, leaving rule-level detection criteria unresolved."
          }
        ],
        "attaches_to": [
          "causal_graphs#tgvab_type_iv_restriction"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-27"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-27T16:50:26Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted TgvAB system as a DOI-backed GENOMICS TraitRecord under restriction-modification system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; kept the graph at two-component TgvAB/type-IV-restriction level because the pinned DefenseFinder HMM rows are not backed by a pinned rules row; the replacement placeholder is reserved in proposals/metpo_traitmech_v289.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000497",
    "label": "Tha system",
    "definition": "A phage defense system in which an organism possesses a Tha tail-activated HEPN anti-phage locus that can be activated by incoming-phage minor tail proteins to mediate nonspecific RNase-linked defense.",
    "definition_source": "DOI:10.1038/s41564-024-01661-6",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "Tha",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1038/s41564-024-01661-6"
      },
      {
        "synonym_text": "tail-activated, HEPN domain-containing anti-phage system",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1038/s41564-024-01661-6"
      },
      {
        "synonym_text": "Tha__Tha",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/s41564-024-01661-6",
        "snippet": "multiple Staphylococcus aureus prophages encode Tha (tail-activated, HEPN (higher eukaryotes and prokaryotes nucleotide-binding) domain-containing anti-phage system)",
        "notes": "Rostol et al. define Tha as a tail-activated HEPN anti-phage system encoded by multiple S. aureus prophages."
      },
      {
        "reference": "DOI:10.1038/s41564-024-01661-6",
        "snippet": "We demonstrate the function of two Tha systems, Tha-1 and Tha-2, activated by distinct tail proteins",
        "notes": "Rostol et al. support multiple experimentally tested Tha variants that are activated by different phage tail proteins."
      },
      {
        "reference": "DOI:10.1038/s41564-024-01661-6",
        "snippet": "Tha is a non-specific RNase that is activated by conserved minor tail proteins from temperate phages",
        "notes": "Rostol et al. connect the Tha anti-phage system to minor-tail-protein activation and nonspecific RNase activity."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| Tha | 10\\.1038/s41564-024-01661-6 | Bacteriophages avoid autoimmunity from cognate immune systems as an intrinsic part of their life cycles | ",
        "notes": "The pinned DefenseFinder article registry maps the Tha source key to the primary Nat Microbiol Tha paper."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| Tha__Tha                                         |                                                  | Tha                    | Custom                  | 20     |",
        "notes": "The pinned DefenseFinder HMM inventory lists one Tha__Tha custom HMM row under the Tha system namespace."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1280",
        "taxon_label": "Staphylococcus aureus",
        "note": "Rostol et al. report that multiple Staphylococcus aureus prophages encode Tha and experimentally test Tha-1 and Tha-2 antiphage defense in S. aureus RN4220.",
        "reference": "DOI:10.1038/s41564-024-01661-6"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "tha_tail_activated_hepn_rnase_defense",
        "title": "Tha systems activate HEPN RNase defense after tail cues",
        "description": "Conservative system-level sketch linking a Tha locus to incoming-phage minor-tail-protein activation, Tha HEPN RNase activity, and phage-defense-system possession.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures the Tha system at family scope without asserting that all Tha variants sense the same minor tail protein, have the same cognate Ith inhibitor, block the same phages, share the same native prophage organization, or map to a DefenseFinder rules row.",
        "nodes": [
          {
            "node_id": "tha_locus",
            "label": "Tha locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A phage-encoded Tha locus encoding a tail-activated HEPN anti-phage system."
          },
          {
            "node_id": "minor_tail_protein_activation",
            "label": "minor-tail-protein activation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Activation of Tha by incoming-phage minor tail proteins during bacteriophage infection."
          },
          {
            "node_id": "tha_hepn_rnase_activity",
            "label": "Tha HEPN RNase activity",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "Nonspecific RNase activity mediated by a Tha HEPN domain after activation by a cognate minor tail protein."
          },
          {
            "node_id": "tha_system_trait",
            "label": "Tha system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000497",
            "description": "Possession of a genome-encoded Tha phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "tha_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "minor_tail_protein_activation",
            "description": "Tha loci encode HEPN anti-phage proteins that can be activated by structural tail proteins of incoming phages.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-024-01661-6",
                "snippet": "a defence system activated by structural tail proteins of incoming phages",
                "notes": "Rostol et al. define Tha as a defense system activated by incoming-phage structural tail proteins."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| Tha | 10\\.1038/s41564-024-01661-6 | Bacteriophages avoid autoimmunity from cognate immune systems as an intrinsic part of their life cycles | ",
                "notes": "The pinned DefenseFinder article registry maps the Tha source key to the primary Nat Microbiol Tha paper."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| Tha__Tha                                         |                                                  | Tha                    | Custom                  | 20     |",
                "notes": "The pinned DefenseFinder HMM inventory lists one Tha__Tha custom HMM row under the Tha system namespace."
              }
            ]
          },
          {
            "subject": "minor_tail_protein_activation",
            "predicate": "activates",
            "predicate_id": "RO:0002213",
            "object": "tha_hepn_rnase_activity",
            "description": "Incoming-phage minor tail proteins activate Tha HEPN-domain RNase activity.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-024-01661-6",
                "snippet": "Tha is a non-specific RNase that is activated by conserved minor tail proteins from temperate phages",
                "notes": "Rostol et al. connect conserved minor tail proteins to Tha RNase activation."
              }
            ]
          },
          {
            "subject": "tha_hepn_rnase_activity",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "tha_system_trait",
            "description": "Tha-mediated nonspecific RNase activity realizes the Tha system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-024-01661-6",
                "snippet": "confirming that Tha-1 is a non-specific RNase",
                "notes": "Rostol et al. validate Tha-1 nonspecific RNase activity."
              }
            ]
          },
          {
            "subject": "tha_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Tha system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-024-01661-6",
                "snippet": "Tha-1 is an anti-phage system that causes autoimmunity when improperly regulated",
                "notes": "Rostol et al. experimentally tested the anti-phage properties of Tha-1."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "tha-variant-profile-rule-gap",
        "prompt": "Resolve Tha variant boundaries, exact minor-tail-protein triggers, Ith inhibitor relationships, native host breadth, and DefenseFinder rule/profile coverage before minting narrower Tha mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Rostol et al. support Tha-1 and Tha-2 as S. aureus prophage-encoded Tha systems activated by distinct incoming-phage minor tail proteins. The pinned DefenseFinder registries map the Tha source key to the same primary paper and list one Tha__Tha custom HMM row, but no exact Tha system rule row was present in the pinned rules table. The first TraitRecord therefore stays at Tha-system scope until separate review resolves variant boundaries, exact activators, Ith inhibitor relationships, native host breadth, and model coverage.",
        "evidence": [
          {
            "reference": "DOI:10.1038/s41564-024-01661-6",
            "snippet": "Tha systems can also block reproduction of the induced tha-positive prophages",
            "notes": "Rostol et al. report Tha autoimmunity and inhibition by cognate overlapping antisense Ith proteins."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
            "snippet": "| Tha | 10\\.1038/s41564-024-01661-6 | Bacteriophages avoid autoimmunity from cognate immune systems as an intrinsic part of their life cycles | ",
            "notes": "The pinned DefenseFinder article registry maps the Tha source key to the primary Nat Microbiol Tha paper."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| Tha__Tha                                         |                                                  | Tha                    | Custom                  | 20     |",
            "notes": "The pinned DefenseFinder HMM inventory lists one Tha__Tha custom HMM row under the Tha system namespace."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "A structured first-pass search of the pinned DefenseFinder rules table found no exact Tha system row."
          }
        ],
        "attaches_to": [
          "causal_graphs#tha_tail_activated_hepn_rnase_defense"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-30"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-30T17:20:02Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Tha system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v374.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-30T17:20:03Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE",
        "changes": "Reviewed Tha system canonical_examples and kept Staphylococcus aureus because Rostol et al. report that multiple S. aureus prophages encode Tha and experimentally test plasmid-carried Tha-1 and Tha-2 in S. aureus RN4220 phage-challenge assays. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000216",
    "label": "Thoeris system",
    "definition": "A genomics trait describing possession of a Thoeris antiphage defense locus in which phage-triggered TIR-domain proteins generate a cyclic-ADP-ribose-like signal that activates a ThsA NADase effector to deplete NAD and inhibit bacteriophage replication.",
    "definition_source": "DOI:10.1038/s41586-021-04098-7",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "Thoeris defense system",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1038/s41467-020-16703-w"
      },
      {
        "synonym_text": "Thoeris defence system",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1038/s41586-021-04098-7"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/s41467-020-16703-w",
        "snippet": "One such system is the Thoeris defense system, which consists of two genes, thsA and thsB",
        "notes": "Ka et al. support the two-component B. cereus Thoeris system architecture and its standard US-English name."
      },
      {
        "reference": "DOI:10.1038/s41467-020-16703-w",
        "snippet": "Mutation analysis suggests that NAD+ cleavage is linked to the antiphage function of Thoeris",
        "notes": "Ka et al. support the relationship between ThsA NADase activity and Thoeris antiphage function."
      },
      {
        "reference": "DOI:10.1038/s41586-021-04098-7",
        "snippet": "phage infection triggers Thoeris TIR-domain proteins to produce an isomer of cyclic ADP-ribose",
        "notes": "Ofir et al. support the phage-triggered TIR-domain signal production that activates the ThsA effector."
      },
      {
        "reference": "DOI:10.1038/s41586-021-04098-7",
        "snippet": "This molecular signal activates a second protein, ThsA, which then depletes the cell of the essential molecule nicotinamide adenine dinucleotide (NAD)",
        "notes": "Ofir et al. connect the Thoeris TIR-domain signal to ThsA NAD depletion."
      },
      {
        "reference": "DOI:10.1038/s41467-020-16703-w",
        "snippet": "One is from Bacillus cereus MSX-D12. The thsA gene and its downstream thsB gene conferred resistance against myophage infection when engineered into the model bacterium Bacillus subtilis BEST7003",
        "notes": "Ka et al. summarize experimental validation of the native Bacillus cereus MSX-D12 Thoeris thsA-thsB locus."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1396",
        "taxon_label": "Bacillus cereus",
        "note": "Ka et al. describe the Bacillus cereus MSX-D12 thsA-thsB Thoeris system that conferred resistance to myophage infection when engineered into a Thoeris-lacking Bacillus subtilis host.",
        "reference": "DOI:10.1038/s41467-020-16703-w"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "thoeris_tir_signal_nad_depletion_defense",
        "title": "Thoeris TIR signalling activates ThsA NAD depletion",
        "description": "Evidence-backed process sketch linking a Thoeris locus to phage-triggered TIR-domain signalling, ThsA-dependent NAD depletion, and inhibition of bacteriophage replication.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures the characterized Thoeris TIR-signal and ThsA NADase outputs without asserting one universal number of TIR-domain proteins, exact cADPR isomer structure, ThsA oligomeric state, cell-death pathway, or phage trigger across all Thoeris loci.",
        "nodes": [
          {
            "node_id": "phage_infection",
            "label": "phage infection",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Entry and replication attempt by a bacteriophage inside a bacterial host."
          },
          {
            "node_id": "thoeris_locus",
            "label": "Thoeris locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A Thoeris antiphage defense locus encoding a ThsA NADase effector and one or more Thoeris TIR-domain sensor proteins."
          },
          {
            "node_id": "thoeris_tir_signal_production",
            "label": "Thoeris TIR cADPR-isomer production",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Phage-triggered production of a cyclic-ADP-ribose isomer by Thoeris TIR-domain proteins."
          },
          {
            "node_id": "thsa_nad_depletion",
            "label": "ThsA NAD depletion",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Thoeris signal-activated ThsA NADase activity that depletes intracellular nicotinamide adenine dinucleotide."
          },
          {
            "node_id": "phage_replication",
            "label": "phage replication",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Replication of invading bacteriophage DNA after host-cell entry."
          },
          {
            "node_id": "thoeris_system_trait",
            "label": "Thoeris system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000216",
            "description": "Possession of a genome-encoded Thoeris antiphage defense locus."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "thoeris_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "thoeris_tir_signal_production",
            "description": "The Thoeris locus encodes TIR-domain proteins that produce a cADPR-like signal during phage infection.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41586-021-04098-7",
                "snippet": "phage infection triggers Thoeris TIR-domain proteins to produce an isomer of cyclic ADP-ribose",
                "notes": "Ofir et al. support Thoeris TIR-domain proteins as phage-triggered cADPR-isomer producers."
              }
            ]
          },
          {
            "subject": "phage_infection",
            "predicate": "activates",
            "predicate_id": "RO:0002213",
            "object": "thoeris_tir_signal_production",
            "description": "Phage infection activates production of the Thoeris TIR-domain cADPR-like signal.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41586-021-04098-7",
                "snippet": "phage infection triggers Thoeris TIR-domain proteins to produce an isomer of cyclic ADP-ribose",
                "notes": "Ofir et al. support phage-triggered Thoeris signal production."
              }
            ]
          },
          {
            "subject": "thoeris_tir_signal_production",
            "predicate": "activates",
            "predicate_id": "RO:0002213",
            "object": "thsa_nad_depletion",
            "description": "The Thoeris cADPR-like signal activates ThsA, which then depletes cellular NAD.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41586-021-04098-7",
                "snippet": "This molecular signal activates a second protein, ThsA, which then depletes the cell of the essential molecule nicotinamide adenine dinucleotide (NAD)",
                "notes": "Ofir et al. connect the TIR-derived signal to ThsA-mediated NAD depletion."
              }
            ]
          },
          {
            "subject": "thsa_nad_depletion",
            "predicate": "mitigates",
            "predicate_id": "METPO:2007407",
            "object": "phage_replication",
            "description": "ThsA NAD depletion helps inhibit bacteriophage replication.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-020-16703-w",
                "snippet": "highlighting a unique strategy for bacterial antiphage resistance via NAD+ degradation",
                "notes": "Ka et al. place ThsA-linked NAD degradation in Thoeris antiphage resistance."
              }
            ]
          },
          {
            "subject": "thsa_nad_depletion",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "thoeris_system_trait",
            "description": "ThsA NAD depletion is the antiviral output that realizes the Thoeris system defense phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41586-021-04098-7",
                "snippet": "depletes the cell of the essential molecule nicotinamide adenine dinucleotide (NAD) and leads to abortive infection and cell death",
                "notes": "Ofir et al. support NAD depletion as the Thoeris output that drives abortive infection."
              }
            ]
          },
          {
            "subject": "thoeris_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Thoeris system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41586-021-04098-7",
                "snippet": "bacterial anti-phage defence system called Thoeris",
                "notes": "Ofir et al. place Thoeris in the bacterial antiphage-defense-system family."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "thoeris-family-signal-and-trigger-gap",
        "prompt": "Resolve Thoeris family architecture, signal chemistry, and phage triggering before minting narrower Thoeris mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Ka et al. support the B. cereus ThsA/ThsB two-gene system and Ofir et al. support the TIR-produced cADPR-like signal that activates ThsA NAD depletion, but Thoeris variants need separate review before TraitMech asserts one exact number of TIR-domain proteins, cADPR-isomer chemistry, TIR target, ThsA activation state, cell-death pathway, or phage-triggering mechanism.",
        "posed_by": "codex",
        "posed_date": "2026-09-15"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-15T13:11:03Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Thoeris system as a DOI-backed GENOMICS TraitRecord under the phage defense system parent after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v93.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000261",
    "label": "Tiamat system",
    "definition": "A phage defense system in which an organism possesses a Tiamat locus represented by a TmtA profile that can protect bacteria from bacteriophage infection.",
    "definition_source": "DOI:10.1016/j.chom.2022.09.017",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "Tiamat",
        "synonym_type": "EXACT_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1016/j.chom.2022.09.017",
        "snippet": "discovery of 21 defense systems that protect bacteria from phages, based on computational genomic analyses and phage-infection experiments",
        "notes": "Millman et al. report the computational and experimental cohort that DefenseFinder cites for Tiamat as a bacterial anti-phage system."
      },
      {
        "reference": "DOI:10.1101/2022.05.11.491447",
        "snippet": "discovery of 21 new defense systems that protect bacteria from phages, based on computational genomic analyses and phage infection experiments",
        "notes": "The bioRxiv version of Millman et al. independently carries the 21-system discovery claim linked from DefenseFinder's Tiamat article registry."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "Tiamat | 10\\.1101/2022\\.05\\.11\\.491447 | An expanding arsenal of immune systems that protect bacteria from phages",
        "notes": "The DefenseFinder model registry maps the named Tiamat system to the Millman et al. antiphage-system discovery preprint."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "Tiamat\tTiamat\t1\t1\tTiamat__TmtA",
        "notes": "The DefenseFinder rules table models Tiamat with a TmtA profile."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "Tiamat__TmtA                                     | Tiamat__TmtA                                     | Tiamat",
        "notes": "The DefenseFinder HMM inventory records TmtA in the Tiamat model namespace."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "tiamat_locus_restricts_phage",
        "title": "Tiamat loci confer bacterial phage defense",
        "description": "Conservative system-level sketch linking possession of a Tiamat locus to restricted bacteriophage propagation without asserting the unresolved phage trigger or molecular output.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Tiamat as a named anti-phage system with the required DefenseFinder TmtA profile while leaving its phage trigger, molecular substrate, antiviral effector output, and subtype breadth unresolved.",
        "nodes": [
          {
            "node_id": "tiamat_locus",
            "label": "Tiamat locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A Tiamat anti-phage defense locus satisfying a DefenseFinder rule over the TmtA profile."
          },
          {
            "node_id": "restricted_phage_propagation",
            "label": "restricted phage propagation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced propagation of bacteriophage in cells carrying the Tiamat system."
          },
          {
            "node_id": "tiamat_system_trait",
            "label": "Tiamat system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000261",
            "description": "Possession of a genome-encoded Tiamat phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "tiamat_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "restricted_phage_propagation",
            "description": "DefenseFinder maps Tiamat to a bacterial anti-phage-system discovery preprint and represents Tiamat loci through the TmtA component profile.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.chom.2022.09.017",
                "snippet": "discovery of 21 defense systems that protect bacteria from phages",
                "notes": "Millman et al. describe the anti-phage discovery cohort that the DefenseFinder Tiamat registry row maps to the Tiamat system."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Tiamat | 10\\.1101/2022\\.05\\.11\\.491447 | An expanding arsenal of immune systems that protect bacteria from phages",
                "notes": "The DefenseFinder registry maps Tiamat itself to the Millman et al. bacterial antiphage-system discovery preprint."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "Tiamat\tTiamat\t1\t1\tTiamat__TmtA",
                "notes": "The DefenseFinder rules table supports TmtA as the required Tiamat system profile."
              }
            ]
          },
          {
            "subject": "restricted_phage_propagation",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "tiamat_system_trait",
            "description": "Tiamat-mediated phage restriction realizes the Tiamat system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.chom.2022.09.017",
                "snippet": "discovery of 21 defense systems that protect bacteria from phages",
                "notes": "Millman et al. place the Tiamat discovery cohort in the set of bacterial systems that protect against phages."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Tiamat | 10\\.1101/2022\\.05\\.11\\.491447 | An expanding arsenal of immune systems that protect bacteria from phages",
                "notes": "DefenseFinder records Tiamat as a named system from the Millman et al. antiphage discovery preprint."
              }
            ]
          },
          {
            "subject": "tiamat_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Tiamat system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "An expanding arsenal of immune systems that protect bacteria from phages",
                "notes": "DefenseFinder associates Tiamat with the Millman et al. bacterial antiphage-system discovery paper."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "tiamat-mechanism-gap",
        "prompt": "Resolve Tiamat phage triggers and effector outputs before minting narrower Tiamat mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Millman et al. and DefenseFinder support Tiamat as a named anti-phage system with a TmtA profile, but the trigger, molecular substrate, antiviral effector output, and subtype-specific mechanism are not resolved enough here to assert a narrower mechanistic child trait.",
        "attaches_to": [
          "causal_graphs#tiamat_locus_restricts_phage"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-19"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-19T02:44:11Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Tiamat system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v138.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000480",
    "label": "TIR-I system",
    "definition": "A phage defense system in which an organism possesses a TIR-I locus, represented in the pinned DefenseFinder HMM inventory by TIR-I__TIR-I_A and TIR-I__TIR-I_B custom profiles, that can inhibit bacteriophage plaquing.",
    "definition_source": "DOI:10.1038/s41467-024-51738-3",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "TIR-I",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1038/s41467-024-51738-3"
      },
      {
        "synonym_text": "TIR-I__TIR-I_A",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "TIR-I__TIR-I_B",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/s41467-024-51738-3",
        "snippet": "Twelve systems have defense activities against a variable number of phages, and 9 of them are new defense systems and named TIR-I to IX",
        "notes": "Wang et al. report that TIR-I belongs to nine newly named TIR-domain anti-phage defense systems with activity against variable phage subsets."
      },
      {
        "reference": "DOI:10.1038/s41467-024-51738-3",
        "snippet": "The defense activity of the TIR systems against each phage was determined based on their ability to inhibit plaque formation compared to the pSEC1 empty vector control",
        "notes": "Wang et al. assayed cloned Escherichia coli TIR systems by efficiency-of-plating reduction against a phage panel."
      },
      {
        "reference": "DOI:10.1038/s41467-024-51738-3",
        "snippet": "TIR-I, TIR-III, and TIR-IV systems appear in diverse domains contexts, whereas the TIR-VII and TIR-VIII systems were found in a single form",
        "notes": "Wang et al. found that TIR-I, TIR-III, and TIR-IV systems occur in diverse domain contexts, while TIR-VII and TIR-VIII systems were recovered in a single form."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| TIR-I | 10\\.1038/s41467-024-51738-3 | The role of TIR domain-containing proteins in bacterial defense against phages |",
        "notes": "The pinned DefenseFinder article registry maps the named TIR-I system to the Wang et al. TIR-domain anti-phage system paper."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| TIR-I__TIR-I_A                                   |                                                  | TIR-I                  | Custom                  | 300    |\n| TIR-I__TIR-I_B                                   |                                                  | TIR-I                  | Custom                  | 500    |",
        "notes": "The pinned DefenseFinder HMM inventory records TIR-I__TIR-I_A and TIR-I__TIR-I_B custom profiles under the TIR-I system namespace."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "tir_i_locus_inhibits_phage_plaquing",
        "title": "TIR-I loci inhibit bacteriophage plaquing",
        "description": "Conservative system-level sketch linking a TIR-I locus to inhibited bacteriophage plaquing and TIR-I system possession.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures TIR-I at TIR-system and anti-phage assay level without asserting exact native-host breadth, one universal domain architecture, a direct phage trigger, TIR-domain catalytic output, accession-level components, or a DefenseFinder detection rule absent from the pinned rules table.",
        "nodes": [
          {
            "node_id": "tir_i_locus",
            "label": "TIR-I locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A TIR-I phage-defense locus represented in the pinned DefenseFinder HMM inventory by TIR-I__TIR-I_A and TIR-I__TIR-I_B custom profiles."
          },
          {
            "node_id": "inhibited_phage_plaquing",
            "label": "inhibited bacteriophage plaquing",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced efficiency of plaquing by bacteriophages in cells carrying a complete TIR-I system."
          },
          {
            "node_id": "tir_i_system_trait",
            "label": "TIR-I system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000480",
            "description": "Possession of a genome-encoded TIR-I phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "tir_i_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "inhibited_phage_plaquing",
            "description": "Wang et al. linked TIR-I to anti-phage activity, and DefenseFinder records two custom TIR-I system profiles.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-024-51738-3",
                "snippet": "Twelve systems have defense activities against a variable number of phages, and 9 of them are new defense systems and named TIR-I to IX",
                "notes": "Wang et al. report that TIR-I belongs to nine newly named TIR-domain anti-phage defense systems with activity against variable phage subsets."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| TIR-I__TIR-I_A                                   |                                                  | TIR-I                  | Custom                  | 300    |\n| TIR-I__TIR-I_B                                   |                                                  | TIR-I                  | Custom                  | 500    |",
                "notes": "The pinned DefenseFinder HMM inventory records TIR-I__TIR-I_A and TIR-I__TIR-I_B custom profiles under the TIR-I system namespace."
              }
            ]
          },
          {
            "subject": "inhibited_phage_plaquing",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "tir_i_system_trait",
            "description": "TIR-I-mediated inhibition of bacteriophage plaquing realizes the TIR-I system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-024-51738-3",
                "snippet": "The defense activity of the TIR systems against each phage was determined based on their ability to inhibit plaque formation compared to the pSEC1 empty vector control",
                "notes": "Wang et al. measured cloned TIR-system activity by inhibited plaque formation relative to an empty-vector control."
              }
            ]
          },
          {
            "subject": "tir_i_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "TIR-I system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| TIR-I | 10\\.1038/s41467-024-51738-3 | The role of TIR domain-containing proteins in bacterial defense against phages |",
                "notes": "The pinned DefenseFinder article registry maps the named TIR-I system to the Wang et al. TIR-domain anti-phage system paper."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "tir-i-detection-trigger-gap",
        "prompt": "Resolve TIR-I native host breadth, the TIR-I__TIR-I_A and TIR-I__TIR-I_B profile-to-component mapping, phage-trigger specificity, TIR-domain output chemistry, and rule-level DefenseFinder detection criteria before minting narrower TIR-I mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Wang et al. support TIR-I as one of nine newly named TIR-domain anti-phage defense systems and note that TIR-I occurs in diverse domain contexts. The pinned DefenseFinder HMM inventory records TIR-I__TIR-I_A and TIR-I__TIR-I_B custom profile rows, but the pinned DefenseFinder rules table has no TIR-I row. This first record therefore does not assert profile requirement logic, accession-level components, a universal domain architecture, or a direct phage trigger.",
        "evidence": [
          {
            "reference": "DOI:10.1038/s41467-024-51738-3",
            "snippet": "Twelve systems have defense activities against a variable number of phages, and 9 of them are new defense systems and named TIR-I to IX",
            "notes": "Wang et al. report that TIR-I belongs to nine newly named TIR-domain anti-phage defense systems with activity against variable phage subsets."
          },
          {
            "reference": "DOI:10.1038/s41467-024-51738-3",
            "snippet": "TIR-I, TIR-III, and TIR-IV systems appear in diverse domains contexts, whereas the TIR-VII and TIR-VIII systems were found in a single form",
            "notes": "Wang et al. support unresolved TIR-I domain architecture breadth."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| TIR-I__TIR-I_A                                   |                                                  | TIR-I                  | Custom                  | 300    |\n| TIR-I__TIR-I_B                                   |                                                  | TIR-I                  | Custom                  | 500    |",
            "notes": "The pinned DefenseFinder HMM inventory records TIR-I__TIR-I_A and TIR-I__TIR-I_B custom profiles under the TIR-I system namespace."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "The pinned DefenseFinder rules table does not list TIR-I, leaving rule-level detection criteria unresolved."
          }
        ],
        "attaches_to": [
          "causal_graphs#tir_i_locus_inhibits_phage_plaquing"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-30"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-30T02:41:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted TIR-I system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; kept the graph at TIR-system and phage-plaquing level because TIR-I direct triggers, profile-to-component mapping, and rule-level DefenseFinder criteria remain unresolved; the replacement placeholder is reserved in proposals/metpo_traitmech_v357.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-30T02:41:01Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed TIR-I system during canonical-example issue 444 enforcement and left canonical_examples empty because Wang et al. support heterologous E. coli MG1655 plaque assays and DefenseFinder TIR-I HMM rows, but the first-pass curation did not recover a direct named native microbial isolate exemplar with experimentally verified endogenous TIR-I activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000481",
    "label": "TIR-III system",
    "definition": "A phage defense system in which an organism possesses a TIR-III locus, represented in the pinned DefenseFinder HMM inventory by TIR-III__TIR-III_A and TIR-III__TIR-III_B custom profiles, that can inhibit bacteriophage plaquing.",
    "definition_source": "DOI:10.1038/s41467-024-51738-3",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "TIR-III",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1038/s41467-024-51738-3"
      },
      {
        "synonym_text": "TIR-III__TIR-III_A",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "TIR-III__TIR-III_B",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/s41467-024-51738-3",
        "snippet": "Twelve systems have defense activities against a variable number of phages, and 9 of them are new defense systems and named TIR-I to IX",
        "notes": "Wang et al. report that TIR-III belongs to nine newly named TIR-domain anti-phage defense systems with activity against variable phage subsets."
      },
      {
        "reference": "DOI:10.1038/s41467-024-51738-3",
        "snippet": "The defense activity of the TIR systems against each phage was determined based on their ability to inhibit plaque formation compared to the pSEC1 empty vector control",
        "notes": "Wang et al. assayed cloned Escherichia coli TIR systems by efficiency-of-plating reduction against a phage panel."
      },
      {
        "reference": "DOI:10.1038/s41467-024-51738-3",
        "snippet": "TIR-I, TIR-III, and TIR-IV systems appear in diverse domains contexts, whereas the TIR-VII and TIR-VIII systems were found in a single form",
        "notes": "Wang et al. found that TIR-I, TIR-III, and TIR-IV systems occur in diverse domain contexts, while TIR-VII and TIR-VIII systems were recovered in a single form."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| TIR-III | 10\\.1038/s41467-024-51738-3 | The role of TIR domain-containing proteins in bacterial defense against phages |",
        "notes": "The pinned DefenseFinder article registry maps the named TIR-III system to the Wang et al. TIR-domain anti-phage system paper."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| TIR-III__TIR-III_A                               |                                                  | TIR-III                | Custom                  | 100    |\n| TIR-III__TIR-III_B                               |                                                  | TIR-III                | Custom                  | 300    |",
        "notes": "The pinned DefenseFinder HMM inventory records TIR-III__TIR-III_A and TIR-III__TIR-III_B custom profiles under the TIR-III system namespace."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "tir_iii_locus_inhibits_phage_plaquing",
        "title": "TIR-III loci inhibit bacteriophage plaquing",
        "description": "Conservative system-level sketch linking a TIR-III locus to inhibited bacteriophage plaquing and TIR-III system possession.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures TIR-III at TIR-system and anti-phage assay level without asserting exact native-host breadth, one universal domain architecture, a direct phage trigger, TIR-domain catalytic output, accession-level components, or a DefenseFinder detection rule absent from the pinned rules table.",
        "nodes": [
          {
            "node_id": "tir_iii_locus",
            "label": "TIR-III locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A TIR-III phage-defense locus represented in the pinned DefenseFinder HMM inventory by TIR-III__TIR-III_A and TIR-III__TIR-III_B custom profiles."
          },
          {
            "node_id": "inhibited_phage_plaquing",
            "label": "inhibited bacteriophage plaquing",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced efficiency of plaquing by bacteriophages in cells carrying a complete TIR-III system."
          },
          {
            "node_id": "tir_iii_system_trait",
            "label": "TIR-III system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000481",
            "description": "Possession of a genome-encoded TIR-III phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "tir_iii_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "inhibited_phage_plaquing",
            "description": "Wang et al. linked TIR-III to anti-phage activity, and DefenseFinder records two custom TIR-III system profiles.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-024-51738-3",
                "snippet": "Twelve systems have defense activities against a variable number of phages, and 9 of them are new defense systems and named TIR-I to IX",
                "notes": "Wang et al. report that TIR-III belongs to nine newly named TIR-domain anti-phage defense systems with activity against variable phage subsets."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| TIR-III__TIR-III_A                               |                                                  | TIR-III                | Custom                  | 100    |\n| TIR-III__TIR-III_B                               |                                                  | TIR-III                | Custom                  | 300    |",
                "notes": "The pinned DefenseFinder HMM inventory records TIR-III__TIR-III_A and TIR-III__TIR-III_B custom profiles under the TIR-III system namespace."
              }
            ]
          },
          {
            "subject": "inhibited_phage_plaquing",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "tir_iii_system_trait",
            "description": "TIR-III-mediated inhibition of bacteriophage plaquing realizes the TIR-III system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-024-51738-3",
                "snippet": "The defense activity of the TIR systems against each phage was determined based on their ability to inhibit plaque formation compared to the pSEC1 empty vector control",
                "notes": "Wang et al. measured cloned TIR-system activity by inhibited plaque formation relative to an empty-vector control."
              }
            ]
          },
          {
            "subject": "tir_iii_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "TIR-III system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| TIR-III | 10\\.1038/s41467-024-51738-3 | The role of TIR domain-containing proteins in bacterial defense against phages |",
                "notes": "The pinned DefenseFinder article registry maps the named TIR-III system to the Wang et al. TIR-domain anti-phage system paper."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "tir-iii-detection-trigger-gap",
        "prompt": "Resolve TIR-III native host breadth, the TIR-III__TIR-III_A and TIR-III__TIR-III_B profile-to-component mapping, phage-trigger specificity, TIR-domain output chemistry, and rule-level DefenseFinder detection criteria before minting narrower TIR-III mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Wang et al. support TIR-III as one of nine newly named TIR-domain anti-phage defense systems and note that TIR-III occurs in diverse domain contexts. The pinned DefenseFinder HMM inventory records TIR-III__TIR-III_A and TIR-III__TIR-III_B custom profile rows, but the pinned DefenseFinder rules table has no TIR-III row. This first record therefore does not assert profile requirement logic, accession-level components, a universal domain architecture, or a direct phage trigger.",
        "evidence": [
          {
            "reference": "DOI:10.1038/s41467-024-51738-3",
            "snippet": "Twelve systems have defense activities against a variable number of phages, and 9 of them are new defense systems and named TIR-I to IX",
            "notes": "Wang et al. report that TIR-III belongs to nine newly named TIR-domain anti-phage defense systems with activity against variable phage subsets."
          },
          {
            "reference": "DOI:10.1038/s41467-024-51738-3",
            "snippet": "TIR-I, TIR-III, and TIR-IV systems appear in diverse domains contexts, whereas the TIR-VII and TIR-VIII systems were found in a single form",
            "notes": "Wang et al. support unresolved TIR-III domain architecture breadth."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| TIR-III__TIR-III_A                               |                                                  | TIR-III                | Custom                  | 100    |\n| TIR-III__TIR-III_B                               |                                                  | TIR-III                | Custom                  | 300    |",
            "notes": "The pinned DefenseFinder HMM inventory records TIR-III__TIR-III_A and TIR-III__TIR-III_B custom profiles under the TIR-III system namespace."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "The pinned DefenseFinder rules table does not list TIR-III, leaving rule-level detection criteria unresolved."
          }
        ],
        "attaches_to": [
          "causal_graphs#tir_iii_locus_inhibits_phage_plaquing"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-30"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-30T03:32:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted TIR-III system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact same-scope live TraitMech, METPO, history, or prior proposal record; kept the graph at TIR-system and phage-plaquing level because TIR-III direct triggers, profile-to-component mapping, and rule-level DefenseFinder criteria remain unresolved; the replacement placeholder is reserved in proposals/metpo_traitmech_v358.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-30T03:32:01Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed TIR-III system during canonical-example issue 444 enforcement and left canonical_examples empty because Wang et al. support heterologous E. coli MG1655 plaque assays and DefenseFinder TIR-III HMM rows, but the first-pass curation did not recover a direct named native microbial isolate exemplar with experimentally verified endogenous TIR-III activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000482",
    "label": "TIR-IV system",
    "definition": "A phage defense system in which an organism possesses a TIR-IV locus, represented in the pinned DefenseFinder HMM inventory by TIR-IV__TIR-IV_A and TIR-IV__TIR-IV_B custom profiles, that can inhibit bacteriophage plaquing.",
    "definition_source": "DOI:10.1038/s41467-024-51738-3",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "TIR-IV",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1038/s41467-024-51738-3"
      },
      {
        "synonym_text": "TIR-IV__TIR-IV_A",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "TIR-IV__TIR-IV_B",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/s41467-024-51738-3",
        "snippet": "Twelve systems have defense activities against a variable number of phages, and 9 of them are new defense systems and named TIR-I to IX",
        "notes": "Wang et al. report that TIR-IV belongs to nine newly named TIR-domain anti-phage defense systems with activity against variable phage subsets."
      },
      {
        "reference": "DOI:10.1038/s41467-024-51738-3",
        "snippet": "The defense activity of the TIR systems against each phage was determined based on their ability to inhibit plaque formation compared to the pSEC1 empty vector control",
        "notes": "Wang et al. assayed cloned Escherichia coli TIR systems by efficiency-of-plating reduction against a phage panel."
      },
      {
        "reference": "DOI:10.1038/s41467-024-51738-3",
        "snippet": "TIR-I, TIR-III, and TIR-IV systems appear in diverse domains contexts, whereas the TIR-VII and TIR-VIII systems were found in a single form",
        "notes": "Wang et al. found that TIR-IV, like TIR-I and TIR-III, occurs in diverse domain contexts."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| TIR-IV | 10\\.1038/s41467-024-51738-3 | The role of TIR domain-containing proteins in bacterial defense against phages |",
        "notes": "The pinned DefenseFinder article registry maps the named TIR-IV system to the Wang et al. TIR-domain anti-phage system paper."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| TIR-IV__TIR-IV_A                                 |                                                  | TIR-IV                 | Custom                  | 100    |\n| TIR-IV__TIR-IV_B                                 |                                                  | TIR-IV                 | Custom                  | 100    |",
        "notes": "The pinned DefenseFinder HMM inventory records TIR-IV__TIR-IV_A and TIR-IV__TIR-IV_B custom profiles under the TIR-IV system namespace."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "tir_iv_locus_inhibits_phage_plaquing",
        "title": "TIR-IV loci inhibit bacteriophage plaquing",
        "description": "Conservative system-level sketch linking a TIR-IV locus to inhibited bacteriophage plaquing and TIR-IV system possession.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures TIR-IV at TIR-system and anti-phage assay level without asserting exact native-host breadth, one universal domain architecture, a direct phage trigger, TIR-domain catalytic output, accession-level components, or a DefenseFinder detection rule absent from the pinned rules table.",
        "nodes": [
          {
            "node_id": "tir_iv_locus",
            "label": "TIR-IV locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A TIR-IV phage-defense locus represented in the pinned DefenseFinder HMM inventory by TIR-IV__TIR-IV_A and TIR-IV__TIR-IV_B custom profiles."
          },
          {
            "node_id": "inhibited_phage_plaquing",
            "label": "inhibited bacteriophage plaquing",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced efficiency of plaquing by bacteriophages in cells carrying a complete TIR-IV system."
          },
          {
            "node_id": "tir_iv_system_trait",
            "label": "TIR-IV system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000482",
            "description": "Possession of a genome-encoded TIR-IV phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "tir_iv_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "inhibited_phage_plaquing",
            "description": "Wang et al. linked TIR-IV to anti-phage activity, and DefenseFinder records two custom TIR-IV system profiles.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-024-51738-3",
                "snippet": "Twelve systems have defense activities against a variable number of phages, and 9 of them are new defense systems and named TIR-I to IX",
                "notes": "Wang et al. report that TIR-IV belongs to nine newly named TIR-domain anti-phage defense systems with activity against variable phage subsets."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| TIR-IV__TIR-IV_A                                 |                                                  | TIR-IV                 | Custom                  | 100    |\n| TIR-IV__TIR-IV_B                                 |                                                  | TIR-IV                 | Custom                  | 100    |",
                "notes": "The pinned DefenseFinder HMM inventory records TIR-IV__TIR-IV_A and TIR-IV__TIR-IV_B custom profiles under the TIR-IV system namespace."
              }
            ]
          },
          {
            "subject": "inhibited_phage_plaquing",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "tir_iv_system_trait",
            "description": "TIR-IV-mediated inhibition of bacteriophage plaquing realizes the TIR-IV system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-024-51738-3",
                "snippet": "The defense activity of the TIR systems against each phage was determined based on their ability to inhibit plaque formation compared to the pSEC1 empty vector control",
                "notes": "Wang et al. measured cloned TIR-system activity by inhibited plaque formation relative to an empty-vector control."
              }
            ]
          },
          {
            "subject": "tir_iv_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "TIR-IV system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| TIR-IV | 10\\.1038/s41467-024-51738-3 | The role of TIR domain-containing proteins in bacterial defense against phages |",
                "notes": "The pinned DefenseFinder article registry maps the named TIR-IV system to the Wang et al. TIR-domain anti-phage system paper."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "tir-iv-detection-trigger-gap",
        "prompt": "Resolve TIR-IV native host breadth, the TIR-IV__TIR-IV_A and TIR-IV__TIR-IV_B profile-to-component mapping, phage-trigger specificity, TIR-domain output chemistry, and rule-level DefenseFinder detection criteria before minting narrower TIR-IV mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Wang et al. support TIR-IV as one of nine newly named TIR-domain anti-phage defense systems and note that TIR-IV occurs in diverse domain contexts. The pinned DefenseFinder HMM inventory records TIR-IV__TIR-IV_A and TIR-IV__TIR-IV_B custom profile rows, but the pinned DefenseFinder rules table has no TIR-IV row. This first record therefore does not assert profile requirement logic, accession-level components, a universal domain architecture, or a direct phage trigger.",
        "evidence": [
          {
            "reference": "DOI:10.1038/s41467-024-51738-3",
            "snippet": "Twelve systems have defense activities against a variable number of phages, and 9 of them are new defense systems and named TIR-I to IX",
            "notes": "Wang et al. report that TIR-IV belongs to nine newly named TIR-domain anti-phage defense systems with activity against variable phage subsets."
          },
          {
            "reference": "DOI:10.1038/s41467-024-51738-3",
            "snippet": "TIR-I, TIR-III, and TIR-IV systems appear in diverse domains contexts, whereas the TIR-VII and TIR-VIII systems were found in a single form",
            "notes": "Wang et al. support unresolved TIR-IV domain architecture breadth."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| TIR-IV__TIR-IV_A                                 |                                                  | TIR-IV                 | Custom                  | 100    |\n| TIR-IV__TIR-IV_B                                 |                                                  | TIR-IV                 | Custom                  | 100    |",
            "notes": "The pinned DefenseFinder HMM inventory records TIR-IV__TIR-IV_A and TIR-IV__TIR-IV_B custom profiles under the TIR-IV system namespace."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "The pinned DefenseFinder rules table does not list TIR-IV, leaving rule-level detection criteria unresolved."
          }
        ],
        "attaches_to": [
          "causal_graphs#tir_iv_locus_inhibits_phage_plaquing"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-30"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-30T04:28:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted TIR-IV system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact same-scope live TraitMech, METPO, history, or prior proposal record; kept the graph at TIR-system and phage-plaquing level because TIR-IV direct triggers, profile-to-component mapping, and rule-level DefenseFinder criteria remain unresolved; the replacement placeholder is reserved in proposals/metpo_traitmech_v359.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-30T04:28:01Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed TIR-IV system during canonical-example issue 444 enforcement and left canonical_examples empty because Wang et al. support heterologous E. coli MG1655 plaque assays and DefenseFinder TIR-IV HMM rows, but the first-pass curation did not recover a direct named native microbial isolate exemplar with experimentally verified endogenous TIR-IV activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000483",
    "label": "TIR-VII system",
    "definition": "A phage defense system in which an organism possesses a TIR-VII locus, represented in the pinned DefenseFinder HMM inventory by TIR-VII__TIR-VII_A and TIR-VII__TIR-VII_B custom profiles, that can inhibit bacteriophage plaquing.",
    "definition_source": "DOI:10.1038/s41467-024-51738-3",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "TIR-VII",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1038/s41467-024-51738-3"
      },
      {
        "synonym_text": "TIR-VII__TIR-VII_A",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "TIR-VII__TIR-VII_B",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/s41467-024-51738-3",
        "snippet": "Twelve systems have defense activities against a variable number of phages, and 9 of them are new defense systems and named TIR-I to IX",
        "notes": "Wang et al. report that TIR-VII belongs to nine newly named TIR-domain anti-phage defense systems with activity against variable phage subsets."
      },
      {
        "reference": "DOI:10.1038/s41467-024-51738-3",
        "snippet": "The defense activity of the TIR systems against each phage was determined based on their ability to inhibit plaque formation compared to the pSEC1 empty vector control",
        "notes": "Wang et al. assayed cloned Escherichia coli TIR systems by efficiency-of-plating reduction against a phage panel."
      },
      {
        "reference": "DOI:10.1038/s41467-024-51738-3",
        "snippet": "TIR-I, TIR-III, and TIR-IV systems appear in diverse domains contexts, whereas the TIR-VII and TIR-VIII systems were found in a single form",
        "notes": "Wang et al. found that TIR-VII and TIR-VIII systems were recovered in a single form, while TIR-I, TIR-III, and TIR-IV systems occur in diverse domain contexts."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| TIR-VII | 10\\.1038/s41467-024-51738-3 | The role of TIR domain-containing proteins in bacterial defense against phages |",
        "notes": "The pinned DefenseFinder article registry maps the named TIR-VII system to the Wang et al. TIR-domain anti-phage system paper."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| TIR-VII__TIR-VII_A                               |                                                  | TIR-VII                | Custom                  | 50     |\n| TIR-VII__TIR-VII_B                               |                                                  | TIR-VII                | Custom                  | 500    |",
        "notes": "The pinned DefenseFinder HMM inventory records TIR-VII__TIR-VII_A and TIR-VII__TIR-VII_B custom profiles under the TIR-VII system namespace."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "tir_vii_locus_inhibits_phage_plaquing",
        "title": "TIR-VII loci inhibit bacteriophage plaquing",
        "description": "Conservative system-level sketch linking a TIR-VII locus to inhibited bacteriophage plaquing and TIR-VII system possession.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures TIR-VII at TIR-system and anti-phage assay level without asserting exact native-host breadth, profile-to-component mapping, a direct phage trigger, TIR-domain catalytic output, accession-level components, or a DefenseFinder detection rule absent from the pinned rules table.",
        "nodes": [
          {
            "node_id": "tir_vii_locus",
            "label": "TIR-VII locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A TIR-VII phage-defense locus represented in the pinned DefenseFinder HMM inventory by TIR-VII__TIR-VII_A and TIR-VII__TIR-VII_B custom profiles."
          },
          {
            "node_id": "inhibited_phage_plaquing",
            "label": "inhibited bacteriophage plaquing",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced efficiency of plaquing by bacteriophages in cells carrying a complete TIR-VII system."
          },
          {
            "node_id": "tir_vii_system_trait",
            "label": "TIR-VII system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000483",
            "description": "Possession of a genome-encoded TIR-VII phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "tir_vii_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "inhibited_phage_plaquing",
            "description": "Wang et al. linked TIR-VII to anti-phage activity, and DefenseFinder records two custom TIR-VII system profiles.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-024-51738-3",
                "snippet": "Twelve systems have defense activities against a variable number of phages, and 9 of them are new defense systems and named TIR-I to IX",
                "notes": "Wang et al. report that TIR-VII belongs to nine newly named TIR-domain anti-phage defense systems with activity against variable phage subsets."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| TIR-VII__TIR-VII_A                               |                                                  | TIR-VII                | Custom                  | 50     |\n| TIR-VII__TIR-VII_B                               |                                                  | TIR-VII                | Custom                  | 500    |",
                "notes": "The pinned DefenseFinder HMM inventory records TIR-VII__TIR-VII_A and TIR-VII__TIR-VII_B custom profiles under the TIR-VII system namespace."
              }
            ]
          },
          {
            "subject": "inhibited_phage_plaquing",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "tir_vii_system_trait",
            "description": "TIR-VII-mediated inhibition of bacteriophage plaquing realizes the TIR-VII system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-024-51738-3",
                "snippet": "The defense activity of the TIR systems against each phage was determined based on their ability to inhibit plaque formation compared to the pSEC1 empty vector control",
                "notes": "Wang et al. measured cloned TIR-system activity by inhibited plaque formation relative to an empty-vector control."
              }
            ]
          },
          {
            "subject": "tir_vii_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "TIR-VII system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| TIR-VII | 10\\.1038/s41467-024-51738-3 | The role of TIR domain-containing proteins in bacterial defense against phages |",
                "notes": "The pinned DefenseFinder article registry maps the named TIR-VII system to the Wang et al. TIR-domain anti-phage system paper."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "tir-vii-detection-trigger-gap",
        "prompt": "Resolve TIR-VII native host breadth, the TIR-VII__TIR-VII_A and TIR-VII__TIR-VII_B profile-to-component mapping, phage-trigger specificity, TIR-domain output chemistry, and rule-level DefenseFinder detection criteria before minting narrower TIR-VII mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Wang et al. support TIR-VII as one of nine newly named TIR-domain anti-phage defense systems and note that TIR-VII was recovered in a single form with TIR-VIII. The pinned DefenseFinder HMM inventory records TIR-VII__TIR-VII_A and TIR-VII__TIR-VII_B custom profile rows, but the pinned DefenseFinder rules table has no TIR-VII row. This first record therefore does not assert profile requirement logic, accession-level components, a direct phage trigger, or TIR-domain output chemistry.",
        "evidence": [
          {
            "reference": "DOI:10.1038/s41467-024-51738-3",
            "snippet": "Twelve systems have defense activities against a variable number of phages, and 9 of them are new defense systems and named TIR-I to IX",
            "notes": "Wang et al. report that TIR-VII belongs to nine newly named TIR-domain anti-phage defense systems with activity against variable phage subsets."
          },
          {
            "reference": "DOI:10.1038/s41467-024-51738-3",
            "snippet": "TIR-I, TIR-III, and TIR-IV systems appear in diverse domains contexts, whereas the TIR-VII and TIR-VIII systems were found in a single form",
            "notes": "Wang et al. report that TIR-VII and TIR-VIII were found in a single form."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| TIR-VII__TIR-VII_A                               |                                                  | TIR-VII                | Custom                  | 50     |\n| TIR-VII__TIR-VII_B                               |                                                  | TIR-VII                | Custom                  | 500    |",
            "notes": "The pinned DefenseFinder HMM inventory records TIR-VII__TIR-VII_A and TIR-VII__TIR-VII_B custom profiles under the TIR-VII system namespace."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "The pinned DefenseFinder rules table does not list TIR-VII, leaving rule-level detection criteria unresolved."
          }
        ],
        "attaches_to": [
          "causal_graphs#tir_vii_locus_inhibits_phage_plaquing"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-30"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-30T05:13:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted TIR-VII system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact same-scope live TraitMech, METPO, history, or prior proposal record; kept the graph at TIR-system and phage-plaquing level because TIR-VII direct triggers, profile-to-component mapping, and rule-level DefenseFinder criteria remain unresolved; the replacement placeholder is reserved in proposals/metpo_traitmech_v360.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-30T05:13:01Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed TIR-VII system during canonical-example issue 444 enforcement and left canonical_examples empty because Wang et al. support heterologous E. coli MG1655 plaque assays and DefenseFinder TIR-VII HMM rows, but the first-pass curation did not recover a direct named native microbial isolate exemplar with experimentally verified endogenous TIR-VII activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000484",
    "label": "TIR-VIII system",
    "definition": "A phage defense system in which an organism possesses a TIR-VIII locus, represented in the pinned DefenseFinder HMM inventory by TIR-VIII__TIR-VIII_A and TIR-VIII__TIR-VIII_B custom profiles, that can inhibit bacteriophage plaquing.",
    "definition_source": "DOI:10.1038/s41467-024-51738-3",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "TIR-VIII",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1038/s41467-024-51738-3"
      },
      {
        "synonym_text": "TIR-VIII__TIR-VIII_A",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "TIR-VIII__TIR-VIII_B",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/s41467-024-51738-3",
        "snippet": "Twelve systems have defense activities against a variable number of phages, and 9 of them are new defense systems and named TIR-I to IX",
        "notes": "Wang et al. report that TIR-VIII belongs to nine newly named TIR-domain anti-phage defense systems with activity against variable phage subsets."
      },
      {
        "reference": "DOI:10.1038/s41467-024-51738-3",
        "snippet": "The defense activity of the TIR systems against each phage was determined based on their ability to inhibit plaque formation compared to the pSEC1 empty vector control",
        "notes": "Wang et al. assayed cloned Escherichia coli TIR systems by efficiency-of-plaquing reduction against a phage panel."
      },
      {
        "reference": "DOI:10.1038/s41467-024-51738-3",
        "snippet": "TIR-I, TIR-III, and TIR-IV systems appear in diverse domains contexts, whereas the TIR-VII and TIR-VIII systems were found in a single form",
        "notes": "Wang et al. found that TIR-VII and TIR-VIII systems were recovered in a single form, while TIR-I, TIR-III, and TIR-IV systems occur in diverse domain contexts."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| TIR-VIII | 10\\.1038/s41467-024-51738-3 | The role of TIR domain-containing proteins in bacterial defense against phages |",
        "notes": "The pinned DefenseFinder article registry maps the named TIR-VIII system to the Wang et al. TIR-domain anti-phage system paper."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| TIR-VIII__TIR-VIII_A                             |                                                  | TIR-VIII               | Custom                  | 100    |\n| TIR-VIII__TIR-VIII_B                             |                                                  | TIR-VIII               | Custom                  | 400    |",
        "notes": "The pinned DefenseFinder HMM inventory records TIR-VIII__TIR-VIII_A and TIR-VIII__TIR-VIII_B custom profiles under the TIR-VIII system namespace."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "tir_viii_locus_inhibits_phage_plaquing",
        "title": "TIR-VIII loci inhibit bacteriophage plaquing",
        "description": "Conservative system-level sketch linking a TIR-VIII locus to inhibited bacteriophage plaquing and TIR-VIII system possession.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures TIR-VIII at TIR-system and anti-phage assay level without asserting exact native-host breadth, profile-to-component mapping, a direct phage trigger, TIR-domain catalytic output, accession-level components, or a DefenseFinder detection rule absent from the pinned rules table.",
        "nodes": [
          {
            "node_id": "tir_viii_locus",
            "label": "TIR-VIII locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A TIR-VIII phage-defense locus represented in the pinned DefenseFinder HMM inventory by TIR-VIII__TIR-VIII_A and TIR-VIII__TIR-VIII_B custom profiles."
          },
          {
            "node_id": "inhibited_phage_plaquing",
            "label": "inhibited bacteriophage plaquing",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced efficiency of plaquing by bacteriophages in cells carrying a complete TIR-VIII system."
          },
          {
            "node_id": "tir_viii_system_trait",
            "label": "TIR-VIII system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000484",
            "description": "Possession of a genome-encoded TIR-VIII phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "tir_viii_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "inhibited_phage_plaquing",
            "description": "Wang et al. linked TIR-VIII to anti-phage activity, and DefenseFinder records two custom TIR-VIII system profiles.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-024-51738-3",
                "snippet": "Twelve systems have defense activities against a variable number of phages, and 9 of them are new defense systems and named TIR-I to IX",
                "notes": "Wang et al. report that TIR-VIII belongs to nine newly named TIR-domain anti-phage defense systems with activity against variable phage subsets."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| TIR-VIII__TIR-VIII_A                             |                                                  | TIR-VIII               | Custom                  | 100    |\n| TIR-VIII__TIR-VIII_B                             |                                                  | TIR-VIII               | Custom                  | 400    |",
                "notes": "The pinned DefenseFinder HMM inventory records TIR-VIII__TIR-VIII_A and TIR-VIII__TIR-VIII_B custom profiles under the TIR-VIII system namespace."
              }
            ]
          },
          {
            "subject": "inhibited_phage_plaquing",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "tir_viii_system_trait",
            "description": "TIR-VIII-mediated inhibition of bacteriophage plaquing realizes the TIR-VIII system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-024-51738-3",
                "snippet": "The defense activity of the TIR systems against each phage was determined based on their ability to inhibit plaque formation compared to the pSEC1 empty vector control",
                "notes": "Wang et al. measured cloned TIR-system activity by inhibited plaque formation relative to an empty-vector control."
              }
            ]
          },
          {
            "subject": "tir_viii_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "TIR-VIII system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| TIR-VIII | 10\\.1038/s41467-024-51738-3 | The role of TIR domain-containing proteins in bacterial defense against phages |",
                "notes": "The pinned DefenseFinder article registry maps the named TIR-VIII system to the Wang et al. TIR-domain anti-phage system paper."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "tir-viii-detection-trigger-gap",
        "prompt": "Resolve TIR-VIII native host breadth, the TIR-VIII__TIR-VIII_A and TIR-VIII__TIR-VIII_B profile-to-component mapping, phage-trigger specificity, TIR-domain output chemistry, and rule-level DefenseFinder detection criteria before minting narrower TIR-VIII mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Wang et al. support TIR-VIII as one of nine newly named TIR-domain anti-phage defense systems and note that TIR-VIII was recovered in a single form with TIR-VII. The pinned DefenseFinder HMM inventory records TIR-VIII__TIR-VIII_A and TIR-VIII__TIR-VIII_B custom profile rows, but the pinned DefenseFinder rules table has no TIR-VIII row. This first record therefore does not assert profile requirement logic, accession-level components, a direct phage trigger, or TIR-domain output chemistry.",
        "evidence": [
          {
            "reference": "DOI:10.1038/s41467-024-51738-3",
            "snippet": "Twelve systems have defense activities against a variable number of phages, and 9 of them are new defense systems and named TIR-I to IX",
            "notes": "Wang et al. report that TIR-VIII belongs to nine newly named TIR-domain anti-phage defense systems with activity against variable phage subsets."
          },
          {
            "reference": "DOI:10.1038/s41467-024-51738-3",
            "snippet": "TIR-I, TIR-III, and TIR-IV systems appear in diverse domains contexts, whereas the TIR-VII and TIR-VIII systems were found in a single form",
            "notes": "Wang et al. report that TIR-VII and TIR-VIII were found in a single form."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| TIR-VIII__TIR-VIII_A                             |                                                  | TIR-VIII               | Custom                  | 100    |\n| TIR-VIII__TIR-VIII_B                             |                                                  | TIR-VIII               | Custom                  | 400    |",
            "notes": "The pinned DefenseFinder HMM inventory records TIR-VIII__TIR-VIII_A and TIR-VIII__TIR-VIII_B custom profiles under the TIR-VIII system namespace."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "The pinned DefenseFinder rules table does not list TIR-VIII, leaving rule-level detection criteria unresolved."
          }
        ],
        "attaches_to": [
          "causal_graphs#tir_viii_locus_inhibits_phage_plaquing"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-30"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-30T06:03:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted TIR-VIII system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact same-scope live TraitMech, METPO, history, or prior proposal record; kept the graph at TIR-system and phage-plaquing level because TIR-VIII direct triggers, profile-to-component mapping, and rule-level DefenseFinder criteria remain unresolved; the replacement placeholder is reserved in proposals/metpo_traitmech_v361.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-30T06:03:01Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed TIR-VIII system during canonical-example issue 444 enforcement and left canonical_examples empty because Wang et al. support heterologous E. coli MG1655 plaque assays and DefenseFinder TIR-VIII HMM rows, but the first-pass curation did not recover a direct named native microbial isolate exemplar with experimentally verified endogenous TIR-VIII activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000498",
    "label": "Toga system",
    "definition": "A phage defense system in which an organism possesses a single-protein Toga antiviral locus that is encoded by P4-like phage satellites and can protect bacteria from bacteriophage infection.",
    "definition_source": "DOI:10.1093/nar/gkag898",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "Toga",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1093/nar/gkag898"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1093/nar/gkag898",
        "snippet": "The single protein in the Toga system has several hits with protein domains associated (through FoldSeek) with the Gao_Ppl",
        "notes": "de Sousa et al. identify Toga as a single-protein defense system with detectable defense-domain similarity."
      },
      {
        "reference": "DOI:10.1093/nar/gkag898",
        "snippet": "with most (e.g. Bandua, Aernus, Toga, and Reve) providing strong protection against phages of different families",
        "notes": "de Sousa et al. identify Toga among the novel P4-associated systems that provided strong protection against phage challenge."
      },
      {
        "reference": "DOI:10.1093/nar/gkag898",
        "snippet": "Our experimental validation of anti-phage activity for 13 novel systems encoded by P4 confirms",
        "notes": "de Sousa et al. summarize the validated P4-encoded novel-system cohort in their discussion."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| Toga | 10\\.64898/2026\\.02\\.27\\.708500 | Shuttling, swapping and mixing: the rapid modular evolution of antiviral repertoires in temperate phages and their satellites | ",
        "notes": "The pinned DefenseFinder article registry maps the Toga source key to the de Sousa et al. P4/P2 antiviral-repertoire paper preprint."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "toga_locus_restricts_phage",
        "title": "Toga loci confer bacterial phage defense",
        "description": "Conservative system-level sketch linking possession of a Toga locus to restricted bacteriophage propagation without asserting the unresolved trigger or molecular output.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Toga as a named single-protein P4 anti-phage system while leaving its phage trigger, molecular substrate, antiviral effector output, source-locus breadth, and DefenseFinder HMM/rule model coverage unresolved.",
        "nodes": [
          {
            "node_id": "toga_locus",
            "label": "Toga locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A P4-associated Toga anti-phage defense locus."
          },
          {
            "node_id": "restricted_phage_propagation",
            "label": "restricted phage propagation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced propagation of bacteriophage in cells carrying the Toga system."
          },
          {
            "node_id": "toga_system_trait",
            "label": "Toga system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000498",
            "description": "Possession of a genome-encoded Toga phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "toga_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "restricted_phage_propagation",
            "description": "Toga loci are among the novel P4-encoded systems that reduced bacteriophage infection.",
            "evidence": [
              {
                "reference": "DOI:10.1093/nar/gkag898",
                "snippet": "with most (e.g. Bandua, Aernus, Toga, and Reve) providing strong protection against phages of different families",
                "notes": "de Sousa et al. name Toga among the novel P4 systems with antiviral phenotypes."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| Toga | 10\\.64898/2026\\.02\\.27\\.708500 | Shuttling, swapping and mixing: the rapid modular evolution of antiviral repertoires in temperate phages and their satellites | ",
                "notes": "The pinned DefenseFinder article registry maps the Toga source key to the de Sousa et al. P4/P2 antiviral-repertoire paper preprint."
              }
            ]
          },
          {
            "subject": "restricted_phage_propagation",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "toga_system_trait",
            "description": "Toga-mediated phage protection realizes the Toga system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1093/nar/gkag898",
                "snippet": "with most (e.g. Bandua, Aernus, Toga, and Reve) providing strong protection against phages of different families",
                "notes": "de Sousa et al. connect Toga to strong protection in the novel-system validation cohort."
              }
            ]
          },
          {
            "subject": "toga_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Toga system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1093/nar/gkag898",
                "snippet": "13 novel systems encoded by P4 confirms that the contribution of defence functions to the pangenomes of P4 and P2",
                "notes": "de Sousa et al. frame Toga and its cohort as newly validated P4-encoded anti-phage defense functions."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "toga-mechanism-and-modelling-gap",
        "prompt": "Resolve Toga locus breadth, exact phage triggers, direct molecular output, source-system table rows, and DefenseFinder HMM/rule coverage before minting narrower Toga mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "de Sousa et al. support Toga as one of the novel P4-encoded systems with experimental phage-protection activity, and the pinned DefenseFinder article registry maps the Toga source key to the corresponding preprint. The pinned HMM inventory and rules table have no exact Toga rows, and this first-pass record does not resolve the tested source locus, complete phage breadth, exact trigger, molecular output, or detection rule.",
        "evidence": [
          {
            "reference": "DOI:10.1093/nar/gkag898",
            "snippet": "The single protein in the Toga system has several hits with protein domains associated (through FoldSeek) with the Gao_Ppl",
            "notes": "de Sousa et al. support Toga as a named single-protein defense system while leaving exact mechanism for separate review."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
            "snippet": "| Toga | 10\\.64898/2026\\.02\\.27\\.708500 | Shuttling, swapping and mixing: the rapid modular evolution of antiviral repertoires in temperate phages and their satellites | ",
            "notes": "The pinned DefenseFinder article registry maps the Toga source key to the de Sousa et al. P4/P2 antiviral-repertoire paper preprint."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "notes": "A structured first-pass search of the pinned DefenseFinder HMM inventory found no exact Toga row."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "A structured first-pass search of the pinned DefenseFinder rules table found no exact Toga system row."
          }
        ],
        "attaches_to": [
          "causal_graphs#toga_locus_restricts_phage"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-30"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-30T18:12:22Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Toga system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v375.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-30T18:12:23Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE",
        "changes": "Reviewed Toga system canonical_examples and left them empty because de Sousa et al. support P4-encoded Toga phage protection and a DefenseFinder article-registry row, but not a direct named native microbial isolate exemplar with experimentally verified endogenous Toga activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000267",
    "label": "Toutatis system",
    "definition": "A phage defense system in which an organism possesses a Toutatis locus represented by TutA_VCA0446 and TutB_VCA0447 profiles that can protect bacteria from bacteriophage infection.",
    "definition_source": "DOI:10.1126/science.ads0768",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "Toutatis",
        "synonym_type": "EXACT_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      },
      {
        "synonym_text": "TutA_VCA0446",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "TutB_VCA0447",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1126/science.ads0768",
        "snippet": "nearly 10% of the integron cassettes in the pandemic Vibrio cholerae strain encode novel antiphage functions",
        "notes": "Darracq et al. support treating the newly discovered Vibrio cholerae SCI antiphage cassettes as bacterial anti-phage systems."
      },
      {
        "reference": "DOI:10.1126/science.ads0768",
        "snippet": "Most of these novel systems have little or no similarity to previously known ones, with several providing defense through cell lysis or growth arrest",
        "notes": "Darracq et al. support a conservative system record that does not assert a resolved Toutatis trigger, effector output, or universal pathway."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "Toutatis | 10\\.1126/science\\.ads0768 | Sedentary chromosomal integrons as biobanks of bacterial antiphage defense systems",
        "notes": "The DefenseFinder model registry maps the named Toutatis system to the Darracq et al. SCI antiphage-system paper."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "Toutatis__TutA_VCA0446                           |                                                  | Toutatis",
        "notes": "The DefenseFinder HMM inventory records TutA_VCA0446 in the Toutatis model namespace."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "Toutatis__TutB_VCA0447                           |                                                  | Toutatis",
        "notes": "The DefenseFinder HMM inventory records TutB_VCA0447 in the Toutatis model namespace."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "toutatis_locus_restricts_phage",
        "title": "Toutatis loci confer bacterial phage defense",
        "description": "Conservative system-level sketch linking possession of a Toutatis locus to restricted bacteriophage propagation without asserting the unresolved phage trigger or molecular output.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Toutatis as a named SCI-derived anti-phage system with TutA_VCA0446 and TutB_VCA0447 DefenseFinder profiles while leaving its phage trigger, molecular substrate, antiviral effector output, and subtype breadth unresolved.",
        "nodes": [
          {
            "node_id": "toutatis_locus",
            "label": "Toutatis locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A Toutatis anti-phage defense locus represented in DefenseFinder by TutA_VCA0446 and TutB_VCA0447 profiles."
          },
          {
            "node_id": "restricted_phage_propagation",
            "label": "restricted phage propagation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced propagation of bacteriophage in cells carrying the Toutatis system."
          },
          {
            "node_id": "toutatis_system_trait",
            "label": "Toutatis system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000267",
            "description": "Possession of a genome-encoded Toutatis phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "toutatis_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "restricted_phage_propagation",
            "description": "DefenseFinder maps Toutatis to an SCI anti-phage-system discovery paper and represents Toutatis loci through the TutA_VCA0446 and TutB_VCA0447 component profiles.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.ads0768",
                "snippet": "nearly 10% of the integron cassettes in the pandemic Vibrio cholerae strain encode novel antiphage functions",
                "notes": "Darracq et al. describe the newly discovered antiphage-system cohort that the DefenseFinder Toutatis registry row maps to the Toutatis system."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "Toutatis__TutA_VCA0446                           |                                                  | Toutatis",
                "notes": "The DefenseFinder HMM inventory supports TutA_VCA0446 as one Toutatis component profile."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "Toutatis__TutB_VCA0447                           |                                                  | Toutatis",
                "notes": "The DefenseFinder HMM inventory supports TutB_VCA0447 as one Toutatis component profile."
              }
            ]
          },
          {
            "subject": "restricted_phage_propagation",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "toutatis_system_trait",
            "description": "Toutatis-mediated phage restriction realizes the Toutatis system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.ads0768",
                "snippet": "Most of these novel systems have little or no similarity to previously known ones",
                "notes": "Darracq et al. place the Toutatis discovery cohort in a set of novel bacterial systems that protect against phages."
              }
            ]
          },
          {
            "subject": "toutatis_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Toutatis system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Toutatis | 10\\.1126/science\\.ads0768 | Sedentary chromosomal integrons as biobanks of bacterial antiphage defense systems",
                "notes": "DefenseFinder associates Toutatis with the Darracq et al. bacterial antiphage-system paper."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "toutatis-mechanism-gap",
        "prompt": "Resolve Toutatis phage triggers and effector outputs before minting narrower Toutatis mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Darracq et al. and DefenseFinder support Toutatis as a named anti-phage system with TutA_VCA0446 and TutB_VCA0447 profiles, but the trigger, molecular substrate, antiviral effector output, and subtype-specific mechanism are not resolved enough here to assert a narrower mechanistic child trait.",
        "attaches_to": [
          "causal_graphs#toutatis_locus_restricts_phage"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-19"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-19T06:05:05Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Toutatis system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v144.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000226",
    "label": "ToxIN system",
    "definition": "An abortive infection system in which an organism possesses a toxIN type III protein-RNA toxin-antitoxin locus whose ToxN toxin and tandem ToxI RNA antitoxins constitute a two-component Abi module that inhibits bacterial growth and restricts phage propagation.",
    "definition_source": "DOI:10.1073/pnas.0808832106",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000214"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1073/pnas.0808832106",
        "snippet": "A highly effective 2-gene Abi system from the phytopathogen Erwinia carotovora subspecies atroseptica, designated ToxIN, is described",
        "notes": "Fineran et al. define ToxIN as a two-gene abortive infection system from the native pECA1039 plasmid."
      },
      {
        "reference": "DOI:10.1073/pnas.0808832106",
        "snippet": "ToxN inhibiting bacterial growth and the tandemly repeated ToxI RNA antitoxin counteracting the toxicity",
        "notes": "Fineran et al. connect the ToxN protein toxin and tandem ToxI RNA repeats to the toxin-antitoxin behavior of ToxIN."
      },
      {
        "reference": "DOI:10.1073/pnas.0808832106",
        "snippet": "ToxIN defines an entirely new TA class that functions via a novel protein-RNA mechanism",
        "notes": "Fineran et al. support ToxIN as the defining member of the type III protein-RNA toxin-antitoxin class."
      },
      {
        "reference": "DOI:10.1073/pnas.0808832106",
        "snippet": "All of our data are consistent with ToxIN functioning as a phage Abi system",
        "notes": "Fineran et al. ruled out adsorption blockade and a restriction-modification explanation before classifying ToxIN as abortive infection."
      },
      {
        "reference": "DOI:10.1073/pnas.0808832106",
        "snippet": "ToxN functions through a reversible growth-inhibiting (bacteriostatic) mechanism",
        "notes": "Fineran et al. support host growth inhibition as the ToxN toxin output."
      },
      {
        "reference": "DOI:10.1128/JB.00720-09",
        "snippet": "Designated ToxIN, this two-component abortive infection system acts as a toxin-antitoxin module",
        "notes": "Blower et al. place the two-component ToxIN module in the abortive infection class."
      },
      {
        "reference": "DOI:10.1128/JB.00720-09",
        "snippet": "We determined the minimal ToxI RNA sequence in the native operon that is both necessary and sufficient for abortive infection and to counteract the toxicity of ToxN",
        "notes": "Blower et al. connect ToxI RNA repeat dosage to both ToxN neutralization and the native abortive-infection phenotype."
      },
      {
        "reference": "DOI:10.1128/JB.00720-09",
        "snippet": "this two-component Abi system operates as a novel protein-RNA toxin-antitoxin (TA) system to abort phage infection in multiple gram-negative bacteria",
        "notes": "Blower et al. support the ToxIN system as an Abi trait that can operate beyond the source Erwinia strain."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:29471",
        "taxon_label": "Pectobacterium atrosepticum",
        "note": "Fineran et al. isolated pECA1039 from Erwinia carotovora subsp. atroseptica 1039, designated its two-gene Abi system ToxIN, and showed that the native toxIN locus conferred phage resistance in strain SCRI 1043.",
        "reference": "DOI:10.1073/pnas.0808832106"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "toxin_type_iii_ta_antiphage_activity",
        "title": "ToxIN type III toxin-antitoxin activity restricts phage propagation",
        "description": "Evidence-backed process sketch linking a toxIN locus to type III toxin-antitoxin activity, ToxN-dependent growth inhibition, restricted phage propagation, and abortive-infection system possession.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures ToxIN at the system level without asserting a universal phage activator, an exact molecular target for ToxN, or the stoichiometry of ToxI neutralization.",
        "nodes": [
          {
            "node_id": "toxin_locus",
            "label": "toxIN locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A type III protein-RNA toxin-antitoxin abortive-infection locus encoding the ToxN toxin and tandem ToxI RNA antitoxins."
          },
          {
            "node_id": "toxin_type_iii_toxin_antitoxin_activity",
            "label": "ToxIN type III toxin-antitoxin activity",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Protein-RNA toxin-antitoxin activity of ToxIN, in which tandem ToxI RNA repeats counteract ToxN toxicity."
          },
          {
            "node_id": "toxn_growth_inhibition",
            "label": "ToxN-dependent growth inhibition",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reversible bacterial growth inhibition caused by ToxN toxin activity."
          },
          {
            "node_id": "restricted_phage_propagation",
            "label": "restricted phage propagation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced completion of phage propagation in a ToxIN-containing infected host cell."
          },
          {
            "node_id": "toxin_system_trait",
            "label": "ToxIN system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000226",
            "description": "Possession of a genome-encoded toxIN type III toxin-antitoxin abortive-infection system."
          },
          {
            "node_id": "abortive_infection_system_trait",
            "label": "abortive infection system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000214",
            "description": "Possession of a genome-encoded abortive-infection phage defense system."
          }
        ],
        "edges": [
          {
            "subject": "toxin_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "toxin_type_iii_toxin_antitoxin_activity",
            "description": "The toxIN locus encodes the defining type III protein-RNA toxin-antitoxin module.",
            "evidence": [
              {
                "reference": "DOI:10.1073/pnas.0808832106",
                "snippet": "ToxIN defines an entirely new TA class that functions via a novel protein-RNA mechanism",
                "notes": "Fineran et al. show that ToxIN constitutes a protein-RNA toxin-antitoxin system."
              }
            ]
          },
          {
            "subject": "toxin_type_iii_toxin_antitoxin_activity",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "toxn_growth_inhibition",
            "description": "The ToxIN toxin-antitoxin module couples ToxN growth inhibition to ToxI RNA antitoxin counteraction.",
            "evidence": [
              {
                "reference": "DOI:10.1073/pnas.0808832106",
                "snippet": "ToxN inhibiting bacterial growth and the tandemly repeated ToxI RNA antitoxin counteracting the toxicity",
                "notes": "Fineran et al. identify ToxN as the toxic component and ToxI repeats as RNA antitoxins."
              }
            ]
          },
          {
            "subject": "toxin_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "restricted_phage_propagation",
            "description": "The native toxIN locus contributes to abortive restriction of phage propagation.",
            "evidence": [
              {
                "reference": "DOI:10.1073/pnas.0808832106",
                "snippet": "All of our data are consistent with ToxIN functioning as a phage Abi system",
                "notes": "Fineran et al. connect the toxIN locus to the abortive-infection phage resistance output."
              }
            ]
          },
          {
            "subject": "restricted_phage_propagation",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "toxin_system_trait",
            "description": "Restriction of phage propagation realizes the ToxIN abortive-infection defense trait.",
            "evidence": [
              {
                "reference": "DOI:10.1128/JB.00720-09",
                "snippet": "this two-component Abi system operates as a novel protein-RNA toxin-antitoxin (TA) system to abort phage infection in multiple gram-negative bacteria",
                "notes": "Blower et al. describe ToxIN as a two-component Abi system that aborts phage infection."
              }
            ]
          },
          {
            "subject": "toxin_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "abortive_infection_system_trait",
            "description": "ToxIN system possession is an abortive-infection-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1128/JB.00720-09",
                "snippet": "Designated ToxIN, this two-component abortive infection system acts as a toxin-antitoxin module",
                "notes": "Blower et al. place ToxIN in the abortive infection class of phage defense."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-15T19:25:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted ToxIN system as a DOI-backed GENOMICS TraitRecord under the abortive infection system parent after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v103.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000092",
    "label": "transposable element",
    "definition": "A genomics trait describing possession of transposable elements \u2014 such as insertion sequences and transposons \u2014 that move within the genome and drive genome rearrangement, gene inactivation, and plasticity.",
    "definition_source": "DOI:10.1111/1574-6976.12067",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "traitmech:000089"
    ],
    "synonyms": [
      {
        "synonym_text": "insertion sequence",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1111/1574-6976.12067"
      },
      {
        "synonym_text": "transposon",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1111/1574-6976.12067"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1111/1574-6976.12067",
        "notes": "Siguier, Gourbeyre & Chandler review bacterial insertion sequences and their genomic impact and diversity."
      },
      {
        "reference": "DOI:10.1038/nrmicro1235",
        "notes": "Frost et al. include transposons among the mobile genetic elements driving genome evolution."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:562",
        "taxon_label": "Escherichia coli",
        "note": "insertion sequences and Tn transposons",
        "reference": "PMID:21224843"
      },
      {
        "taxon_id": "NCBITaxon:303",
        "taxon_label": "Pseudomonas putida",
        "note": "catabolic transposons",
        "reference": "PMID:16352819"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "te_transposition_rearrangement",
        "title": "Transposable elements drive DNA transposition and genome rearrangement",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This genomics record is a measurement, genomic-element classification, or population-level descriptor rather than one taxon-specific protein mechanism; contextual protein nodes do not receive token UniProt examples.",
        "description": "Evidence-backed causal sketch linking TE possession to DNA transposition activity and resulting genome rearrangement and plasticity.",
        "nodes": [
          {
            "node_id": "te_trait",
            "label": "transposable element",
            "node_type": "TRAIT",
            "grounding": "traitmech:000092",
            "description": "Possession of insertion sequences or transposons."
          },
          {
            "node_id": "dna_transposition",
            "label": "DNA transposition",
            "node_type": "BIOLOGICAL_PROCESS",
            "grounding": "GO:0006313",
            "description": "Movement of a DNA segment to a new genomic location."
          },
          {
            "node_id": "genome_rearrangement",
            "label": "genome rearrangement",
            "node_type": "QUALITY",
            "description": "Insertions, deletions, and inversions of chromosomal segments."
          },
          {
            "node_id": "transposase",
            "label": "transposase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "DDE-family enzyme encoded by the element that catalyzes its movement.",
            "grounding": "GO:0004803"
          },
          {
            "node_id": "te_insertion",
            "label": "transposable element insertion",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Integration of a transposable element at a target genomic site."
          },
          {
            "node_id": "target_site_duplication",
            "label": "target site duplication",
            "node_type": "QUALITY",
            "description": "Short direct repeats flanking the element created upon insertion."
          },
          {
            "node_id": "gene_disruption",
            "label": "gene disruption",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Inactivation of a gene by insertion of a transposable element into it."
          },
          {
            "node_id": "homologous_recombination_is",
            "label": "homologous recombination between IS copies",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Recombination between identical IS copies at distinct loci."
          }
        ],
        "edges": [
          {
            "subject": "te_trait",
            "predicate": "enables",
            "object": "dna_transposition",
            "description": "TEs encode transposases that catalyze transposition.",
            "evidence": [
              {
                "reference": "DOI:10.1111/1574-6976.12067",
                "notes": "Siguier et al. review insertion-sequence transposase machinery and activity."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "dna_transposition",
            "predicate": "causes",
            "object": "genome_rearrangement",
            "description": "Transposition events generate insertions and rearrangements.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro1235",
                "notes": "Frost et al. cite transposons among MGEs driving genome evolution."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "te_trait",
            "predicate": "has participant",
            "object": "transposase",
            "description": "The defining effector of a TE is a transposase required for movement.",
            "evidence": [
              {
                "reference": "DOI:10.1128/MMBR.00119-22",
                "notes": "IS element encodes a single ORF, a DDE-family transposase required for movement (Harmer & Hall 2024)."
              }
            ]
          },
          {
            "subject": "transposase",
            "predicate": "enables",
            "object": "dna_transposition",
            "description": "Transposase activity is causal for element movement/transposition.",
            "evidence": [
              {
                "reference": "DOI:10.1128/MMBR.00119-22",
                "notes": "tnp26 encodes a transposase required for movement (Harmer & Hall 2024)."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "te_insertion",
            "predicate": "causes",
            "object": "target_site_duplication",
            "description": "Element insertion typically generates short flanking target site duplications.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-023-39964-7",
                "notes": "Insertion sequences typically create target site duplications (TSDs) upon insertion (Sheng et al. 2023)."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "te_insertion",
            "predicate": "causes",
            "object": "gene_disruption",
            "description": "Insertion into a coding region disrupts gene function.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-023-39964-7",
                "notes": "Element movement causes gene disruption (Sheng et al. 2023)."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "homologous_recombination_is",
            "predicate": "causes",
            "object": "genome_rearrangement",
            "description": "Recombination between identical IS copies produces genome rearrangements.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-023-39964-7",
                "notes": "Homologous recombination between identical IS copies can produce genome rearrangements (Sheng et al. 2023)."
              }
            ],
            "predicate_id": "biolink:causes"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-06-05T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate GENOMICS trait (transposable element); sub-variant of mobile genetic element.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-08T14:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (transposition / genome rearrangement) with GO node grounding and RO/biolink predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 5 evidence-backed generic edges (5 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:11Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 4 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:causes\u00d73, RO:0002327\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-26T07:15:18Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A023WVD3\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:21:11Z",
        "curator": "claude",
        "action": "RETRACT_DEAD_UNIPROT_GROUNDINGS",
        "changes": "Retracted 1 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:23:53Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0004803\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope te_transposition_rearrangement=NONMECHANISTIC with scope_notes.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000494",
    "label": "type I restriction-modification system",
    "definition": "A restriction-modification system in which an organism possesses a Type I R-M locus encoding a pentameric enzyme with HsdR-like restriction, HsdM-like methylation, and HsdS-like DNA sequence-recognition subunits, including RM_Type_I loci represented by DefenseFinder.",
    "definition_source": "DOI:10.1093/nar/gkt847",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000095"
    ],
    "synonyms": [
      {
        "synonym_text": "RM_Type_I",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      },
      {
        "synonym_text": "RM__Type_I_MTases",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv"
      },
      {
        "synonym_text": "RM__Type_I_REases",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv"
      },
      {
        "synonym_text": "RM__Type_I_S",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1093/nar/gkt847",
        "snippet": "Type I restriction enzymes (REases) are large pentameric proteins with separate restriction (R), methylation (M) and DNA sequence-recognition (S) subunits.",
        "notes": "Loenen et al. define Type I restriction enzymes as pentameric systems with distinct restriction, methylation, and sequence-recognition subunits."
      },
      {
        "reference": "DOI:10.1093/nar/gkt847",
        "snippet": "Type I R\u2013M enzymes are pentameric proteins of composition 2R+2M+S.",
        "notes": "Loenen et al. describe the Type I R-M enzyme complex as a 2R+2M+S pentamer with both restriction-endonuclease and methyltransferase activities."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "RM_Type_I | 10\\.1093/nar/gkac975 | REBASE: a database for DNA restriction and modification: enzymes, genes and genomes",
        "notes": "The pinned DefenseFinder article registry maps the RM_Type_I model namespace to the REBASE update."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "RM\tRM_Type_I\t2\t2\tRM__Type_I_MTases, RM__Type_I_REases\tRM__Type_I_S\t\t",
        "notes": "The DefenseFinder rules table models RM_Type_I as an RM subsystem requiring Type_I_MTases and Type_I_REases profile groups with Type_I_S as an accessory specificity-subunit group."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| RM__Type_I_MTases_FAM_0                          |                                                  | RM                     | Custom                  | 150    |",
        "notes": "The pinned DefenseFinder HMM inventory lists custom Type I methyltransferase profiles under the broad RM system namespace."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| RM__Type_I_REases_FAM_0.einsi_trimmed            |                                                  | RM                     | Custom                  | 34     |",
        "notes": "The pinned DefenseFinder HMM inventory lists custom Type I restriction-endonuclease profiles under the broad RM system namespace."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| RM__Type_I_S_01                                  |                                                  | RM                     | Custom                  | 75     |",
        "notes": "The pinned DefenseFinder HMM inventory lists custom Type I specificity-subunit profiles under the broad RM system namespace."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "type_i_rm_locus_restricts_foreign_dna",
        "title": "Type I R-M loci mark self and restrict foreign DNA",
        "description": "Conservative system-level sketch linking Type I restriction-modification loci to restriction-modification-mediated foreign DNA cleavage.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures a reusable Type I R-M locus architecture and the DefenseFinder RM_Type_I system namespace without asserting an accession-level mapping between any custom HMM row and characterized HsdR, HsdM, or HsdS families.",
        "nodes": [
          {
            "node_id": "type_i_rm_locus",
            "label": "type I restriction-modification locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A Type I R-M locus encoding restriction, methylation, and sequence-recognition subunits."
          },
          {
            "node_id": "foreign_unmethylated_dna_cleavage",
            "label": "foreign unmethylated DNA cleavage",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Restriction of invading DNA that has not been protected by cognate methylation."
          },
          {
            "node_id": "type_i_restriction_modification_system_trait",
            "label": "type I restriction-modification system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000494",
            "description": "Possession of a genome-encoded type I restriction-modification system."
          },
          {
            "node_id": "restriction_modification_system",
            "label": "restriction-modification system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000095",
            "description": "Possession of a methyltransferase and restriction endonuclease system for self/non-self DNA discrimination."
          }
        ],
        "edges": [
          {
            "subject": "type_i_rm_locus",
            "predicate": "enables",
            "predicate_id": "RO:0002327",
            "object": "foreign_unmethylated_dna_cleavage",
            "description": "Type I R-M loci encode the restriction, methylation, and specificity functions needed to recognize and cleave unprotected foreign DNA.",
            "evidence": [
              {
                "reference": "DOI:10.1093/nar/gkt847",
                "snippet": "Type I R\u2013M enzymes are pentameric proteins of composition 2R+2M+S.",
                "notes": "Loenen et al. describe the Type I R-M enzyme complex as a 2R+2M+S pentamer with both restriction-endonuclease and methyltransferase activities."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "RM\tRM_Type_I\t2\t2\tRM__Type_I_MTases, RM__Type_I_REases\tRM__Type_I_S\t\t",
                "notes": "The DefenseFinder rules table models RM_Type_I as an RM subsystem requiring Type_I_MTases and Type_I_REases profile groups with Type_I_S as an accessory specificity-subunit group."
              }
            ]
          },
          {
            "subject": "foreign_unmethylated_dna_cleavage",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "type_i_restriction_modification_system_trait",
            "description": "Type I restriction-modification activity realizes the organism-level Type I R-M system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "RM_Type_I | 10\\.1093/nar/gkac975 | REBASE: a database for DNA restriction and modification: enzymes, genes and genomes",
                "notes": "The pinned DefenseFinder article registry maps the RM_Type_I model namespace to the REBASE update."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| RM__Type_I_MTases_FAM_0                          |                                                  | RM                     | Custom                  | 150    |",
                "notes": "The pinned DefenseFinder HMM inventory lists custom Type I methyltransferase profiles under the broad RM system namespace."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| RM__Type_I_REases_FAM_0.einsi_trimmed            |                                                  | RM                     | Custom                  | 34     |",
                "notes": "The pinned DefenseFinder HMM inventory lists custom Type I restriction-endonuclease profiles under the broad RM system namespace."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| RM__Type_I_S_01                                  |                                                  | RM                     | Custom                  | 75     |",
                "notes": "The pinned DefenseFinder HMM inventory lists custom Type I specificity-subunit profiles under the broad RM system namespace."
              }
            ]
          },
          {
            "subject": "type_i_restriction_modification_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "restriction_modification_system",
            "description": "A Type I R-M system is a subtype of broader restriction-modification system possession.",
            "evidence": [
              {
                "reference": "DOI:10.1093/nar/gkt847",
                "snippet": "Type I restriction enzymes (REases) are large pentameric proteins with separate restriction (R), methylation (M) and DNA sequence-recognition (S) subunits.",
                "notes": "Loenen et al. define Type I restriction enzymes as pentameric systems with distinct restriction, methylation, and sequence-recognition subunits."
              },
              {
                "reference": "DOI:10.1093/nar/gkt847",
                "snippet": "Type I R\u2013M enzymes are pentameric proteins of composition 2R+2M+S.",
                "notes": "Loenen et al. describe the Type I R-M enzyme complex as a 2R+2M+S pentamer with both restriction-endonuclease and methyltransferase activities."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "type-i-rm-profile-interpretation-gap",
        "prompt": "Resolve the accession-level relationships between DefenseFinder RM Type I custom methyltransferase, restriction-endonuclease, and specificity-subunit profiles and characterized HsdR, HsdM, and HsdS families before minting narrower Type I protein or custom-profile traits.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Loenen et al. support Type I R-M system architecture and restriction/modification activity, while the pinned DefenseFinder registry supports an RM_Type_I namespace with broad Type_I_MTases, Type_I_REases, and Type_I_S custom profile groups. The evidence does not yet map individual custom profile rows to exact characterized Hsd families or resolve whether each source-model boundary corresponds to a reusable organism-level trait below this class.",
        "evidence": [
          {
            "reference": "DOI:10.1093/nar/gkt847",
            "snippet": "Type I restriction enzymes (REases) are large pentameric proteins with separate restriction (R), methylation (M) and DNA sequence-recognition (S) subunits.",
            "notes": "Loenen et al. define Type I restriction enzymes as pentameric systems with distinct restriction, methylation, and sequence-recognition subunits."
          },
          {
            "reference": "DOI:10.1093/nar/gkt847",
            "snippet": "Type I R\u2013M enzymes are pentameric proteins of composition 2R+2M+S.",
            "notes": "Loenen et al. describe the Type I R-M enzyme complex as a 2R+2M+S pentamer with both restriction-endonuclease and methyltransferase activities."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "snippet": "RM\tRM_Type_I\t2\t2\tRM__Type_I_MTases, RM__Type_I_REases\tRM__Type_I_S\t\t",
            "notes": "The DefenseFinder rules table models RM_Type_I as an RM subsystem requiring Type_I_MTases and Type_I_REases profile groups with Type_I_S as an accessory specificity-subunit group."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| RM__Type_I_MTases_FAM_0                          |                                                  | RM                     | Custom                  | 150    |",
            "notes": "The pinned DefenseFinder HMM inventory lists custom Type I methyltransferase profiles under the broad RM system namespace."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| RM__Type_I_REases_FAM_0.einsi_trimmed            |                                                  | RM                     | Custom                  | 34     |",
            "notes": "The pinned DefenseFinder HMM inventory lists custom Type I restriction-endonuclease profiles under the broad RM system namespace."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| RM__Type_I_S_01                                  |                                                  | RM                     | Custom                  | 75     |",
            "notes": "The pinned DefenseFinder HMM inventory lists custom Type I specificity-subunit profiles under the broad RM system namespace."
          }
        ],
        "attaches_to": [
          "causal_graphs#type_i_rm_locus_restricts_foreign_dna"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-30"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-30T14:49:40Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted type I restriction-modification system as a DOI-backed GENOMICS TraitRecord under restriction-modification system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v371.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-30T14:49:41Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed type I restriction-modification system during initial curation and left canonical_examples empty because the sources support a broad Type I R-M class, a DefenseFinder system model, and multiple biochemical enzyme examples, but not a single stable NCBITaxon strain exemplar for the whole broad Type I branch. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000493",
    "label": "type II restriction-modification system",
    "definition": "A restriction-modification system in which an organism possesses a Type II restriction endonuclease activity paired with cognate methyltransferase self-protection, including conventional RM_Type_II loci represented by DefenseFinder.",
    "definition_source": "DOI:10.1093/nar/gkac1124",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000095"
    ],
    "synonyms": [
      {
        "synonym_text": "RM_Type_II",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      },
      {
        "synonym_text": "RM_Type_II__Type_II_MTases",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv"
      },
      {
        "synonym_text": "RM_Type_II__Type_II_REases",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1093/nar/gkac1124",
        "snippet": "The action of Type II restriction-modification (RM) systems depends on restriction endonuclease (REase), which cleaves foreign DNA at specific sites, and methyltransferase (MTase), which protects host genome from restriction by methylating the same sites.",
        "notes": "Kirillov et al. describe Type II restriction-modification systems as requiring a restriction endonuclease that cleaves foreign DNA and a methyltransferase that protects host DNA by methylating the same sites."
      },
      {
        "reference": "DOI:10.1093/nar/gku447",
        "snippet": "Type II REases are produced by prokaryotes to combat bacteriophages. With extreme accuracy, each recognizes a particular sequence in double-stranded DNA and cleaves at a fixed position within or nearby.",
        "notes": "Pingoud et al. review Type II restriction endonucleases as prokaryotic phage-defense enzymes that recognize specific double-stranded DNA sequences and cleave at fixed positions within or near those sequences."
      },
      {
        "reference": "DOI:10.1093/nar/gku447",
        "snippet": "REBASE (rebase.neb.com/rebase/rebase.html), the definitive source for information on REases and their companion proteins",
        "notes": "Pingoud et al. point to REBASE as the source for restriction endonucleases and companion proteins; DefenseFinder links its RM_Type_II model namespace to the 2023 REBASE update."
      },
      {
        "reference": "DOI:10.1038/srep03838",
        "snippet": "Type IIG (symmetric or asymmetric target sites; endonuclease activity affected by AdoMet (SAM))",
        "notes": "Zhu et al. place Type IIG enzymes in the Type II restriction enzyme classification, supporting the Type IIG child record's reparenting beneath this Type II R-M parent."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "RM_Type_II | 10\\.1093/nar/gkac975 | REBASE: a database for DNA restriction and modification: enzymes, genes and genomes",
        "notes": "The pinned DefenseFinder article registry maps the RM_Type_II model namespace to the REBASE update."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "RM\tRM_Type_II\t2\t2\tRM_Type_II__Type_II_MTases, RM_Type_II__Type_II_REases\t\t\t",
        "notes": "The DefenseFinder rules table models RM_Type_II as an RM subsystem requiring Type_II_MTases and Type_II_REases profile groups."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| RM_Type_II__Type_II_MTases_FAM_0                 |                                                  | RM_Type_II             | Custom                  | 20     |",
        "notes": "The pinned DefenseFinder HMM inventory lists custom methyltransferase profiles under the RM_Type_II system namespace."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| RM_Type_II__Type_II_REase01                      |                                                  | RM_Type_II             | Custom                  | 20     |",
        "notes": "The pinned DefenseFinder HMM inventory lists custom restriction endonuclease profiles under the RM_Type_II system namespace."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "type_ii_rm_locus_restricts_foreign_dna",
        "title": "Type II R-M loci mark self and restrict foreign DNA",
        "description": "Conservative system-level sketch linking Type II restriction-modification loci to restriction-modification-mediated foreign DNA cleavage.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures a reusable Type II R-M locus architecture and the DefenseFinder RM_Type_II custom-profile namespace without asserting an accession-level mapping between any custom HMM row and characterized Type II restriction endonucleases or methyltransferases.",
        "nodes": [
          {
            "node_id": "type_ii_rm_locus",
            "label": "type II restriction-modification locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A Type II R-M locus encoding restriction endonuclease activity and cognate DNA methyltransferase activity."
          },
          {
            "node_id": "foreign_unmethylated_dna_cleavage",
            "label": "foreign unmethylated DNA cleavage",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Restriction of invading DNA that has not been protected by cognate methylation."
          },
          {
            "node_id": "type_ii_restriction_modification_system_trait",
            "label": "type II restriction-modification system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000493",
            "description": "Possession of a genome-encoded type II restriction-modification system."
          },
          {
            "node_id": "restriction_modification_system",
            "label": "restriction-modification system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000095",
            "description": "Possession of a methyltransferase and restriction endonuclease system for self/non-self DNA discrimination."
          }
        ],
        "edges": [
          {
            "subject": "type_ii_rm_locus",
            "predicate": "enables",
            "predicate_id": "RO:0002327",
            "object": "foreign_unmethylated_dna_cleavage",
            "description": "Type II R-M loci encode the paired restriction and methylation functions needed to cleave unprotected foreign DNA.",
            "evidence": [
              {
                "reference": "DOI:10.1093/nar/gku447",
                "snippet": "Type II REases are produced by prokaryotes to combat bacteriophages. With extreme accuracy, each recognizes a particular sequence in double-stranded DNA and cleaves at a fixed position within or nearby.",
                "notes": "Pingoud et al. review Type II restriction endonucleases as prokaryotic phage-defense enzymes that recognize specific double-stranded DNA sequences and cleave at fixed positions within or near those sequences."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "RM\tRM_Type_II\t2\t2\tRM_Type_II__Type_II_MTases, RM_Type_II__Type_II_REases\t\t\t",
                "notes": "The DefenseFinder rules table models RM_Type_II as an RM subsystem requiring Type_II_MTases and Type_II_REases profile groups."
              }
            ]
          },
          {
            "subject": "foreign_unmethylated_dna_cleavage",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "type_ii_restriction_modification_system_trait",
            "description": "Type II restriction-modification activity realizes the organism-level Type II R-M system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "RM_Type_II | 10\\.1093/nar/gkac975 | REBASE: a database for DNA restriction and modification: enzymes, genes and genomes",
                "notes": "The pinned DefenseFinder article registry maps the RM_Type_II model namespace to the REBASE update."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| RM_Type_II__Type_II_MTases_FAM_0                 |                                                  | RM_Type_II             | Custom                  | 20     |",
                "notes": "The pinned DefenseFinder HMM inventory lists custom methyltransferase profiles under the RM_Type_II system namespace."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| RM_Type_II__Type_II_REase01                      |                                                  | RM_Type_II             | Custom                  | 20     |",
                "notes": "The pinned DefenseFinder HMM inventory lists custom restriction endonuclease profiles under the RM_Type_II system namespace."
              }
            ]
          },
          {
            "subject": "type_ii_restriction_modification_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "restriction_modification_system",
            "description": "A Type II R-M system is a subtype of broader restriction-modification system possession.",
            "evidence": [
              {
                "reference": "DOI:10.1093/nar/gkac1124",
                "snippet": "The action of Type II restriction-modification (RM) systems depends on restriction endonuclease (REase), which cleaves foreign DNA at specific sites, and methyltransferase (MTase), which protects host genome from restriction by methylating the same sites.",
                "notes": "Kirillov et al. describe Type II restriction-modification systems as requiring a restriction endonuclease that cleaves foreign DNA and a methyltransferase that protects host DNA by methylating the same sites."
              },
              {
                "reference": "DOI:10.1093/nar/gku447",
                "snippet": "REBASE (rebase.neb.com/rebase/rebase.html), the definitive source for information on REases and their companion proteins",
                "notes": "Pingoud et al. point to REBASE as the source for restriction endonucleases and companion proteins; DefenseFinder links its RM_Type_II model namespace to the 2023 REBASE update."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "type-ii-rm-profile-interpretation-gap",
        "prompt": "Resolve the accession-level relationships between DefenseFinder RM_Type_II custom methyltransferase and restriction-endonuclease profiles, characterized Type II enzyme families, and Type IIG subclass boundaries before minting narrower Type II protein or custom-profile traits.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Kirillov et al. and Pingoud et al. support Type II R-M system architecture and Type II restriction-endonuclease activity, while the pinned DefenseFinder registry supports an RM_Type_II namespace with broad custom MTase and REase profile groups. The evidence does not yet map individual custom profile rows to exact characterized enzyme families or resolve whether each source-model boundary corresponds to a reusable organism-level trait below this class.",
        "evidence": [
          {
            "reference": "DOI:10.1093/nar/gkac1124",
            "snippet": "The action of Type II restriction-modification (RM) systems depends on restriction endonuclease (REase), which cleaves foreign DNA at specific sites, and methyltransferase (MTase), which protects host genome from restriction by methylating the same sites.",
            "notes": "Kirillov et al. describe Type II restriction-modification systems as requiring a restriction endonuclease that cleaves foreign DNA and a methyltransferase that protects host DNA by methylating the same sites."
          },
          {
            "reference": "DOI:10.1093/nar/gku447",
            "snippet": "Type II REases are produced by prokaryotes to combat bacteriophages. With extreme accuracy, each recognizes a particular sequence in double-stranded DNA and cleaves at a fixed position within or nearby.",
            "notes": "Pingoud et al. review Type II restriction endonucleases as prokaryotic phage-defense enzymes that recognize specific double-stranded DNA sequences and cleave at fixed positions within or near those sequences."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "snippet": "RM\tRM_Type_II\t2\t2\tRM_Type_II__Type_II_MTases, RM_Type_II__Type_II_REases\t\t\t",
            "notes": "The DefenseFinder rules table models RM_Type_II as an RM subsystem requiring Type_II_MTases and Type_II_REases profile groups."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| RM_Type_II__Type_II_MTases_FAM_0                 |                                                  | RM_Type_II             | Custom                  | 20     |",
            "notes": "The pinned DefenseFinder HMM inventory lists custom methyltransferase profiles under the RM_Type_II system namespace."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| RM_Type_II__Type_II_REase01                      |                                                  | RM_Type_II             | Custom                  | 20     |",
            "notes": "The pinned DefenseFinder HMM inventory lists custom restriction endonuclease profiles under the RM_Type_II system namespace."
          }
        ],
        "attaches_to": [
          "causal_graphs#type_ii_rm_locus_restricts_foreign_dna"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-30"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-30T13:40:53Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted type II restriction-modification system as a DOI-backed GENOMICS TraitRecord under restriction-modification system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v370.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-30T13:40:55Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed type II restriction-modification system during initial curation and left canonical_examples empty because the sources support a broad Type II R-M class, a DefenseFinder system model, and many biochemical enzyme examples, but not a single stable NCBITaxon strain exemplar for the whole broad Type II branch. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000375",
    "label": "type IIG restriction-modification system",
    "definition": "A restriction-modification system in which an organism possesses a Type IIG locus centered on a restriction-methyltransferase-specificity fusion gene represented by DefenseFinder as the RM_Type_IIG subsystem.",
    "definition_source": "DOI:10.1093/nar/gkr543",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000493"
    ],
    "synonyms": [
      {
        "synonym_text": "RM_Type_IIG",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      },
      {
        "synonym_text": "RM_Type_IIG__Type_IIG",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1093/nar/gkr543",
        "snippet": "Type IIG R\u2013M systems also follow this general strategy for target recognition, but instead of encoding separate REase, MTase and specificity subunits, they have evolved to combine them within a single uninterrupted protein chain.",
        "notes": "Shen et al. define Type IIG restriction-modification systems as systems that combine restriction, methyltransferase, and specificity subunits in one uninterrupted protein chain."
      },
      {
        "reference": "DOI:10.1093/nar/gkr543",
        "snippet": "The entire BpuSI R\u2013M system consists of two MTase genes (M1 and M2) and the R\u2013M fusion gene.",
        "notes": "The characterized BpuSI Type IIG example carries two companion methyltransferase genes and an R-M fusion gene, supporting a locus-level system trait rather than a single protein trait."
      },
      {
        "reference": "DOI:10.1038/srep03838",
        "snippet": "Type IIG (symmetric or asymmetric target sites; endonuclease activity affected by AdoMet (SAM))",
        "notes": "Zhu et al. place Type IIG in the Type II restriction enzyme classification and describe variable target symmetry plus AdoMet/SAM-sensitive endonuclease activity."
      },
      {
        "reference": "DOI:10.1038/srep03838",
        "snippet": "Tth111II contains both endonuclease (R) and methylase (M) domains and a shared specificity domain (S).",
        "notes": "The cloned Tth111II Type IIGS enzyme has endonuclease, methylase, and specificity domains in one polypeptide."
      },
      {
        "reference": "DOI:10.1038/srep03838",
        "snippet": "The biological function of restriction-modification systems is to restrict/cleave foreign invading DNA",
        "notes": "Zhu et al. frame the Type IIGS decision between cleaving and modifying unmodified DNA in the broader restriction-modification role of cleaving foreign invading DNA."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "RM_Type_IIG | 10\\.1093/nar/gkac975 | REBASE: a database for DNA restriction and modification: enzymes, genes and genomes",
        "notes": "The pinned DefenseFinder article registry maps the named RM_Type_IIG model to the REBASE update."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "RM\tRM_Type_IIG\t1\t1\tRM_Type_IIG__Type_IIG\t\tBREX__pglZB, DISARM__drmB\t",
        "notes": "The DefenseFinder rules table models RM_Type_IIG as an RM subsystem that requires the RM_Type_IIG__Type_IIG profile group and excludes two non-RM profiles."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| RM_Type_IIG__Type_IIG_1                          |                                                  | RM_Type_IIG            | Custom                  | 300    |\n| RM_Type_IIG__Type_IIG_2                          |                                                  | RM_Type_IIG            | Custom                  | 300    |\n| RM_Type_IIG__Type_IIG_3                          |                                                  | RM_Type_IIG            | Custom                  | 300    |\n| RM_Type_IIG__Type_IIG_4                          |                                                  | RM_Type_IIG            | Custom                  | 300    |\n| RM_Type_IIG__Type_IIG_5                          |                                                  | RM_Type_IIG            | Custom                  | 300    |\n| RM_Type_IIG__Type_IIG_FAM_0.einsi_trimmed        |                                                  | RM_Type_IIG            | Custom                  | 300    |\n| RM_Type_IIG__Type_IIG_FAM_1.einsi_trimmed        |                                                  | RM_Type_IIG            | Custom                  | 300    |\n| RM_Type_IIG__Type_IIG_FAM_2.einsi_trimmed        |                                                  | RM_Type_IIG            | Custom                  | 300    |",
        "notes": "The DefenseFinder HMM inventory lists eight custom profiles under the RM_Type_IIG system namespace."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "type_iig_rm_locus_restricts_foreign_dna",
        "title": "Type IIG R-M loci mark self and restrict foreign DNA",
        "description": "Conservative system-level sketch linking Type IIG restriction-methyltransferase-specificity fusion loci to restriction-modification-mediated foreign DNA cleavage.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures the reusable Type IIG locus architecture and the DefenseFinder RM_Type_IIG custom-profile namespace without asserting an accession-level mapping between each custom HMM, BpuSI, Tth111II, or companion methyltransferases.",
        "nodes": [
          {
            "node_id": "type_iig_rm_locus",
            "label": "type IIG restriction-modification locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A Type IIG R-M locus centered on a single restriction-methyltransferase-specificity fusion gene and, in some systems, one or more companion methyltransferase genes."
          },
          {
            "node_id": "foreign_unmethylated_dna_cleavage",
            "label": "foreign unmethylated DNA cleavage",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Restriction of invading DNA that has not been protected by cognate methylation."
          },
          {
            "node_id": "type_iig_restriction_modification_system_trait",
            "label": "type IIG restriction-modification system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000375",
            "description": "Possession of a genome-encoded type IIG restriction-modification system."
          },
          {
            "node_id": "restriction_modification_system",
            "label": "restriction-modification system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000095",
            "description": "Possession of a methyltransferase and restriction endonuclease system for self/non-self DNA discrimination."
          }
        ],
        "edges": [
          {
            "subject": "type_iig_rm_locus",
            "predicate": "enables",
            "predicate_id": "RO:0002327",
            "object": "foreign_unmethylated_dna_cleavage",
            "description": "Type IIG loci encode the fusion architecture and methyltransferase context needed to cleave unprotected foreign DNA.",
            "evidence": [
              {
                "reference": "DOI:10.1093/nar/gkr543",
                "snippet": "Type IIG R\u2013M systems also follow this general strategy for target recognition, but instead of encoding separate REase, MTase and specificity subunits, they have evolved to combine them within a single uninterrupted protein chain.",
                "notes": "Shen et al. define Type IIG restriction-modification systems as systems that combine restriction, methyltransferase, and specificity subunits in one uninterrupted protein chain."
              },
              {
                "reference": "DOI:10.1093/nar/gkr543",
                "snippet": "The entire BpuSI R\u2013M system consists of two MTase genes (M1 and M2) and the R\u2013M fusion gene.",
                "notes": "The characterized BpuSI Type IIG example carries two companion methyltransferase genes and an R-M fusion gene, supporting a locus-level system trait rather than a single protein trait."
              },
              {
                "reference": "DOI:10.1038/srep03838",
                "snippet": "Tth111II contains both endonuclease (R) and methylase (M) domains and a shared specificity domain (S).",
                "notes": "The cloned Tth111II Type IIGS enzyme has endonuclease, methylase, and specificity domains in one polypeptide."
              }
            ]
          },
          {
            "subject": "foreign_unmethylated_dna_cleavage",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "type_iig_restriction_modification_system_trait",
            "description": "Type IIG restriction-modification activity realizes the organism-level Type IIG R-M system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1038/srep03838",
                "snippet": "Type IIG (symmetric or asymmetric target sites; endonuclease activity affected by AdoMet (SAM))",
                "notes": "Zhu et al. place Type IIG in the Type II restriction enzyme classification and describe variable target symmetry plus AdoMet/SAM-sensitive endonuclease activity."
              },
              {
                "reference": "DOI:10.1038/srep03838",
                "snippet": "The biological function of restriction-modification systems is to restrict/cleave foreign invading DNA",
                "notes": "Zhu et al. frame the Type IIGS decision between cleaving and modifying unmodified DNA in the broader restriction-modification role of cleaving foreign invading DNA."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "RM\tRM_Type_IIG\t1\t1\tRM_Type_IIG__Type_IIG\t\tBREX__pglZB, DISARM__drmB\t",
                "notes": "The DefenseFinder rules table models RM_Type_IIG as an RM subsystem that requires the RM_Type_IIG__Type_IIG profile group and excludes two non-RM profiles."
              }
            ]
          },
          {
            "subject": "type_iig_restriction_modification_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "restriction_modification_system",
            "description": "A Type IIG R-M system is a subtype of broader restriction-modification system possession.",
            "evidence": [
              {
                "reference": "DOI:10.1093/nar/gkr543",
                "snippet": "Type IIG R\u2013M systems also follow this general strategy for target recognition, but instead of encoding separate REase, MTase and specificity subunits, they have evolved to combine them within a single uninterrupted protein chain.",
                "notes": "Shen et al. define Type IIG restriction-modification systems as systems that combine restriction, methyltransferase, and specificity subunits in one uninterrupted protein chain."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "RM_Type_IIG | 10\\.1093/nar/gkac975 | REBASE: a database for DNA restriction and modification: enzymes, genes and genomes",
                "notes": "The pinned DefenseFinder article registry maps the named RM_Type_IIG model to the REBASE update."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| RM_Type_IIG__Type_IIG_1                          |                                                  | RM_Type_IIG            | Custom                  | 300    |\n| RM_Type_IIG__Type_IIG_2                          |                                                  | RM_Type_IIG            | Custom                  | 300    |\n| RM_Type_IIG__Type_IIG_3                          |                                                  | RM_Type_IIG            | Custom                  | 300    |\n| RM_Type_IIG__Type_IIG_4                          |                                                  | RM_Type_IIG            | Custom                  | 300    |\n| RM_Type_IIG__Type_IIG_5                          |                                                  | RM_Type_IIG            | Custom                  | 300    |\n| RM_Type_IIG__Type_IIG_FAM_0.einsi_trimmed        |                                                  | RM_Type_IIG            | Custom                  | 300    |\n| RM_Type_IIG__Type_IIG_FAM_1.einsi_trimmed        |                                                  | RM_Type_IIG            | Custom                  | 300    |\n| RM_Type_IIG__Type_IIG_FAM_2.einsi_trimmed        |                                                  | RM_Type_IIG            | Custom                  | 300    |",
                "notes": "The DefenseFinder HMM inventory lists eight custom profiles under the RM_Type_IIG system namespace."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "type-iig-rm-profile-interpretation-gap",
        "prompt": "Resolve the accession-level relationships between DefenseFinder RM_Type_IIG custom profiles, characterized BpuSI- or Tth111II-like enzymes, and companion methyltransferases before minting narrower Type IIG protein or subfamily traits.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Shen et al. and Zhu et al. support Type IIG R-M system architecture and experimentally characterized BpuSI and Tth111II examples, while the pinned DefenseFinder registry supports an RM_Type_IIG system-level namespace with eight custom HMM rows. The evidence does not yet map each custom profile row to exact characterized enzyme families or resolve companion methyltransferase requirements.",
        "evidence": [
          {
            "reference": "DOI:10.1093/nar/gkr543",
            "snippet": "Type IIG R\u2013M systems also follow this general strategy for target recognition, but instead of encoding separate REase, MTase and specificity subunits, they have evolved to combine them within a single uninterrupted protein chain.",
            "notes": "Shen et al. define Type IIG restriction-modification systems as systems that combine restriction, methyltransferase, and specificity subunits in one uninterrupted protein chain."
          },
          {
            "reference": "DOI:10.1038/srep03838",
            "snippet": "Tth111II contains both endonuclease (R) and methylase (M) domains and a shared specificity domain (S).",
            "notes": "The cloned Tth111II Type IIGS enzyme has endonuclease, methylase, and specificity domains in one polypeptide."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "snippet": "RM\tRM_Type_IIG\t1\t1\tRM_Type_IIG__Type_IIG\t\tBREX__pglZB, DISARM__drmB\t",
            "notes": "The DefenseFinder rules table models RM_Type_IIG as an RM subsystem that requires the RM_Type_IIG__Type_IIG profile group and excludes two non-RM profiles."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| RM_Type_IIG__Type_IIG_1                          |                                                  | RM_Type_IIG            | Custom                  | 300    |\n| RM_Type_IIG__Type_IIG_2                          |                                                  | RM_Type_IIG            | Custom                  | 300    |\n| RM_Type_IIG__Type_IIG_3                          |                                                  | RM_Type_IIG            | Custom                  | 300    |\n| RM_Type_IIG__Type_IIG_4                          |                                                  | RM_Type_IIG            | Custom                  | 300    |\n| RM_Type_IIG__Type_IIG_5                          |                                                  | RM_Type_IIG            | Custom                  | 300    |\n| RM_Type_IIG__Type_IIG_FAM_0.einsi_trimmed        |                                                  | RM_Type_IIG            | Custom                  | 300    |\n| RM_Type_IIG__Type_IIG_FAM_1.einsi_trimmed        |                                                  | RM_Type_IIG            | Custom                  | 300    |\n| RM_Type_IIG__Type_IIG_FAM_2.einsi_trimmed        |                                                  | RM_Type_IIG            | Custom                  | 300    |",
            "notes": "The DefenseFinder HMM inventory lists eight custom profiles under the RM_Type_IIG system namespace."
          }
        ],
        "attaches_to": [
          "causal_graphs#type_iig_rm_locus_restricts_foreign_dna"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-26"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-26T08:04:20Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted type IIG restriction-modification system as a DOI-backed GENOMICS TraitRecord under restriction-modification system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v252.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-26T08:14:20Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed type IIG restriction-modification system during canonical-example issue 444 enforcement and left canonical_examples empty because the sources support biochemically characterized BpuSI and Tth111II natural isolates plus a DefenseFinder system model, but not a direct stable NCBITaxon strain exemplar with whole-system Type IIG activity. No paid research was used.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-30T13:40:54Z",
        "curator": "codex",
        "action": "REPARENT_TO_TYPE_II_RM",
        "changes": "Reparented type IIG restriction-modification system from the broad restriction-modification system to the newly minted type II restriction-modification system parent, preserving Type IIG as a narrower Type II R-M architecture while keeping unresolved DefenseFinder profile interpretations in an open knowledge gap.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000495",
    "label": "type III restriction-modification system",
    "definition": "A restriction-modification system in which an organism possesses a Type III R-M locus encoding Mod-like DNA methyltransferase and Res-like ATP-dependent restriction subunits, including RM_Type_III loci represented by DefenseFinder.",
    "definition_source": "DOI:10.1093/nar/gku122",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000095"
    ],
    "synonyms": [
      {
        "synonym_text": "RM_Type_III",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      },
      {
        "synonym_text": "RM_Type_III__Type_III_MTases",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv"
      },
      {
        "synonym_text": "RM_Type_III__Type_III_REases",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1093/nar/gku122",
        "snippet": "The Type III REs are hetero-oligomeric assemblies, comprising polypeptides encoded by the res (restriction) and mod (modification) genes (4).",
        "notes": "Butterer et al. describe Type III restriction endonucleases as hetero-oligomeric assemblies encoded by res restriction and mod modification genes."
      },
      {
        "reference": "DOI:10.1093/nar/gku122",
        "snippet": "In this study, we present a series of results obtained by native mass spectrometry and size exclusion chromatography with multi-angle light scattering consistent with a 1:2 ratio of Res to Mod subunits in the EcoP15I, EcoPI and PstII complexes as the main holoenzyme species and a 1:1 stoichiometry of specific DNA (sDNA) binding by EcoP15I and EcoPI.",
        "notes": "Butterer et al. support a Type III R-M holoenzyme model with one Res subunit and two Mod subunits for characterized EcoP15I, EcoPI, and PstII complexes."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "RM_Type_III | 10\\.1093/nar/gkac975 | REBASE: a database for DNA restriction and modification: enzymes, genes and genomes",
        "notes": "The pinned DefenseFinder article registry maps the RM_Type_III model namespace to the REBASE update."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "RM\tRM_Type_III\t2\t2\tRM_Type_III__Type_III_MTases, RM_Type_III__Type_III_REases\t\t\t",
        "notes": "The DefenseFinder rules table models RM_Type_III as an RM subsystem requiring Type_III_MTases and Type_III_REases profile groups."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| RM_Type_III__Type_III_MTases_FAM_0               |                                                  | RM_Type_III            | Custom                  | 100    |\n| RM_Type_III__Type_III_MTases_FAM_1               |                                                  | RM_Type_III            | Custom                  | 100    |",
        "notes": "The pinned DefenseFinder HMM inventory lists custom Type III methyltransferase profiles under the RM_Type_III system namespace."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| RM_Type_III__Type_III_REases_FAM_0.einsi_trimmed |                                                  | RM_Type_III            | Custom                  | 22     |\n| RM_Type_III__Type_III_REases_FAM_1.einsi_trimmed |                                                  | RM_Type_III            | Custom                  | 22     |",
        "notes": "The pinned DefenseFinder HMM inventory lists custom Type III restriction-endonuclease profiles under the RM_Type_III system namespace."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "type_iii_rm_locus_restricts_foreign_dna",
        "title": "Type III R-M loci mark self and restrict foreign DNA",
        "description": "Conservative system-level sketch linking Type III restriction-modification loci to restriction-modification-mediated foreign DNA cleavage.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures a reusable Type III R-M locus architecture and the DefenseFinder RM_Type_III custom-profile namespace without asserting an accession-level mapping between any custom HMM row and characterized Res or Mod families.",
        "nodes": [
          {
            "node_id": "type_iii_rm_locus",
            "label": "type III restriction-modification locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A Type III R-M locus encoding Mod-like and Res-like subunits."
          },
          {
            "node_id": "foreign_unmethylated_dna_cleavage",
            "label": "foreign unmethylated DNA cleavage",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Restriction of invading DNA that has not been protected by cognate methylation."
          },
          {
            "node_id": "type_iii_restriction_modification_system_trait",
            "label": "type III restriction-modification system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000495",
            "description": "Possession of a genome-encoded type III restriction-modification system."
          },
          {
            "node_id": "restriction_modification_system",
            "label": "restriction-modification system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000095",
            "description": "Possession of a methyltransferase and restriction endonuclease system for self/non-self DNA discrimination."
          }
        ],
        "edges": [
          {
            "subject": "type_iii_rm_locus",
            "predicate": "enables",
            "predicate_id": "RO:0002327",
            "object": "foreign_unmethylated_dna_cleavage",
            "description": "Type III R-M loci encode the Mod and Res functions needed to recognize, methylate, and cleave DNA at Type III recognition sites.",
            "evidence": [
              {
                "reference": "DOI:10.1093/nar/gku122",
                "snippet": "The Type III REs are hetero-oligomeric assemblies, comprising polypeptides encoded by the res (restriction) and mod (modification) genes (4).",
                "notes": "Butterer et al. describe Type III restriction endonucleases as hetero-oligomeric assemblies encoded by res restriction and mod modification genes."
              },
              {
                "reference": "DOI:10.1093/nar/gku122",
                "snippet": "In this study, we present a series of results obtained by native mass spectrometry and size exclusion chromatography with multi-angle light scattering consistent with a 1:2 ratio of Res to Mod subunits in the EcoP15I, EcoPI and PstII complexes as the main holoenzyme species and a 1:1 stoichiometry of specific DNA (sDNA) binding by EcoP15I and EcoPI.",
                "notes": "Butterer et al. support a Type III R-M holoenzyme model with one Res subunit and two Mod subunits for characterized EcoP15I, EcoPI, and PstII complexes."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "RM\tRM_Type_III\t2\t2\tRM_Type_III__Type_III_MTases, RM_Type_III__Type_III_REases\t\t\t",
                "notes": "The DefenseFinder rules table models RM_Type_III as an RM subsystem requiring Type_III_MTases and Type_III_REases profile groups."
              }
            ]
          },
          {
            "subject": "foreign_unmethylated_dna_cleavage",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "type_iii_restriction_modification_system_trait",
            "description": "Type III restriction-modification activity realizes the organism-level Type III R-M system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "RM_Type_III | 10\\.1093/nar/gkac975 | REBASE: a database for DNA restriction and modification: enzymes, genes and genomes",
                "notes": "The pinned DefenseFinder article registry maps the RM_Type_III model namespace to the REBASE update."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| RM_Type_III__Type_III_MTases_FAM_0               |                                                  | RM_Type_III            | Custom                  | 100    |\n| RM_Type_III__Type_III_MTases_FAM_1               |                                                  | RM_Type_III            | Custom                  | 100    |",
                "notes": "The pinned DefenseFinder HMM inventory lists custom Type III methyltransferase profiles under the RM_Type_III system namespace."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| RM_Type_III__Type_III_REases_FAM_0.einsi_trimmed |                                                  | RM_Type_III            | Custom                  | 22     |\n| RM_Type_III__Type_III_REases_FAM_1.einsi_trimmed |                                                  | RM_Type_III            | Custom                  | 22     |",
                "notes": "The pinned DefenseFinder HMM inventory lists custom Type III restriction-endonuclease profiles under the RM_Type_III system namespace."
              }
            ]
          },
          {
            "subject": "type_iii_restriction_modification_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "restriction_modification_system",
            "description": "A Type III R-M system is a subtype of broader restriction-modification system possession.",
            "evidence": [
              {
                "reference": "DOI:10.1093/nar/gku122",
                "snippet": "The Type III REs are hetero-oligomeric assemblies, comprising polypeptides encoded by the res (restriction) and mod (modification) genes (4).",
                "notes": "Butterer et al. describe Type III restriction endonucleases as hetero-oligomeric assemblies encoded by res restriction and mod modification genes."
              },
              {
                "reference": "DOI:10.1093/nar/gku122",
                "snippet": "In this study, we present a series of results obtained by native mass spectrometry and size exclusion chromatography with multi-angle light scattering consistent with a 1:2 ratio of Res to Mod subunits in the EcoP15I, EcoPI and PstII complexes as the main holoenzyme species and a 1:1 stoichiometry of specific DNA (sDNA) binding by EcoP15I and EcoPI.",
                "notes": "Butterer et al. support a Type III R-M holoenzyme model with one Res subunit and two Mod subunits for characterized EcoP15I, EcoPI, and PstII complexes."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "type-iii-rm-profile-interpretation-gap",
        "prompt": "Resolve the accession-level relationships between DefenseFinder RM_Type_III custom methyltransferase and restriction-endonuclease profiles and characterized Mod and Res families before minting narrower Type III protein or custom-profile traits.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Butterer et al. support Type III R-M Res/Mod architecture, while the pinned DefenseFinder registry supports an RM_Type_III namespace with broad Type_III_MTases and Type_III_REases custom profile groups. The evidence does not yet map individual custom profile rows to exact characterized Res or Mod families or resolve whether each source-model boundary corresponds to a reusable organism-level trait below this class.",
        "evidence": [
          {
            "reference": "DOI:10.1093/nar/gku122",
            "snippet": "The Type III REs are hetero-oligomeric assemblies, comprising polypeptides encoded by the res (restriction) and mod (modification) genes (4).",
            "notes": "Butterer et al. describe Type III restriction endonucleases as hetero-oligomeric assemblies encoded by res restriction and mod modification genes."
          },
          {
            "reference": "DOI:10.1093/nar/gku122",
            "snippet": "In this study, we present a series of results obtained by native mass spectrometry and size exclusion chromatography with multi-angle light scattering consistent with a 1:2 ratio of Res to Mod subunits in the EcoP15I, EcoPI and PstII complexes as the main holoenzyme species and a 1:1 stoichiometry of specific DNA (sDNA) binding by EcoP15I and EcoPI.",
            "notes": "Butterer et al. support a Type III R-M holoenzyme model with one Res subunit and two Mod subunits for characterized EcoP15I, EcoPI, and PstII complexes."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "snippet": "RM\tRM_Type_III\t2\t2\tRM_Type_III__Type_III_MTases, RM_Type_III__Type_III_REases\t\t\t",
            "notes": "The DefenseFinder rules table models RM_Type_III as an RM subsystem requiring Type_III_MTases and Type_III_REases profile groups."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| RM_Type_III__Type_III_MTases_FAM_0               |                                                  | RM_Type_III            | Custom                  | 100    |\n| RM_Type_III__Type_III_MTases_FAM_1               |                                                  | RM_Type_III            | Custom                  | 100    |",
            "notes": "The pinned DefenseFinder HMM inventory lists custom Type III methyltransferase profiles under the RM_Type_III system namespace."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| RM_Type_III__Type_III_REases_FAM_0.einsi_trimmed |                                                  | RM_Type_III            | Custom                  | 22     |\n| RM_Type_III__Type_III_REases_FAM_1.einsi_trimmed |                                                  | RM_Type_III            | Custom                  | 22     |",
            "notes": "The pinned DefenseFinder HMM inventory lists custom Type III restriction-endonuclease profiles under the RM_Type_III system namespace."
          }
        ],
        "attaches_to": [
          "causal_graphs#type_iii_rm_locus_restricts_foreign_dna"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-30"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-30T15:29:46Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted type III restriction-modification system as a DOI-backed GENOMICS TraitRecord under restriction-modification system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v372.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-30T15:29:47Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed type III restriction-modification system during initial curation and left canonical_examples empty because the sources support a broad Type III R-M class, a DefenseFinder system model, and multiple biochemical enzyme examples, but not a single stable NCBITaxon strain exemplar for the whole broad Type III branch. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000496",
    "label": "type IV modification-dependent restriction system",
    "definition": "A phage defense system in which an organism possesses a Type IV modification-dependent restriction locus, including DefenseFinder RM_Type_IV loci, whose restriction-enzyme activity cleaves foreign DNA carrying recognized base or backbone modifications rather than the unmodified targets of canonical Type I-III restriction-modification systems.",
    "definition_source": "DOI:10.1093/nar/gkt747",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "RM_Type_IV",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv"
      },
      {
        "synonym_text": "RM_Type_IV__Type_IV_REases",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv"
      },
      {
        "synonym_text": "Other_Type_IV",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1093/nar/gkt747",
        "snippet": "The new class of modification-dependent restriction enzymes was named Type IV, as distinct from the familiar modification-blocked Types I\u2013III.",
        "notes": "Loenen and Raleigh define Type IV as modification-dependent restriction, distinct from modification-blocked Types I-III."
      },
      {
        "reference": "DOI:10.1093/nar/gkt747",
        "snippet": "Type IV enzymes recognize modified DNA with low sequence selectivity and have emerged many times independently during evolution.",
        "notes": "Loenen and Raleigh support the broad Type IV class as enzymes that recognize modified DNA with limited sequence specificity."
      },
      {
        "reference": "DOI:10.1093/nar/gkt747",
        "snippet": "there are enzymes that attack DNA only when the modification is present",
        "notes": "Loenen and Raleigh contrast modification-dependent restriction with protective modification by describing enzymes that attack DNA only when a modification is present."
      },
      {
        "reference": "DOI:10.1016/j.jmb.2006.11.051",
        "snippet": "The Escherichia coli CT596 prophage exclusion genes gmrS and gmrD were found to encode a novel type IV modification-dependent restriction nuclease that targets and digests glucosylated (glc)-hydroxymethylcytosine (HMC) DNAs.",
        "notes": "Bair and Black experimentally support GmrSD as a Type IV modification-dependent restriction nuclease targeting glucosylated hydroxymethylcytosine DNA."
      },
      {
        "reference": "DOI:10.1016/j.jmb.2006.11.051",
        "snippet": "Overall activities of the purified GmrSD enzyme are in good agreement with the properties of the cloned gmr genes in vivo and suggest a restriction enzyme specific for sugar modified HMC DNAs.",
        "notes": "Bair and Black verify purified GmrSD restriction activity against sugar-modified hydroxymethylcytosine DNA, one concrete activity within the Type IV branch."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| Other_Type_IV | 10\\.1093/nar/gkac975 | REBASE: a database for DNA restriction and modification: enzymes, genes and genomes | ",
        "notes": "The pinned DefenseFinder article registry maps the Other_Type_IV source key to the REBASE update, while RM_Type_IV itself is represented in the pinned rule and HMM registries."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "RM\tRM_Type_IV\t1\t1\tRM_Type_IV__Type_IV_REases\t\t\t",
        "notes": "The pinned DefenseFinder rules table models RM_Type_IV as an RM subsystem requiring the Type_IV_REases profile group."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| RM_Type_IV__FAM_0                                |                                                  | RM_Type_IV             | Custom                  | 100    |\n| RM_Type_IV__FAM_1                                |                                                  | RM_Type_IV             | Custom                  | 100    |\n| RM_Type_IV__FAM_2                                |                                                  | RM_Type_IV             | Custom                  | 100    |\n| RM_Type_IV__Type_IV_01                           |                                                  | RM_Type_IV             | Custom                  | 100    |\n| RM_Type_IV__Type_IV_03                           |                                                  | RM_Type_IV             | Custom                  | 60     |\n| RM_Type_IV__Type_IV_05                           |                                                  | RM_Type_IV             | Custom                  | 70     |\n| RM_Type_IV__Type_IV_21                           |                                                  | RM_Type_IV             | Custom                  | 175    |\n| RM_Type_IV__Type_IV_22                           |                                                  | RM_Type_IV             | Custom                  | 150    |",
        "notes": "The pinned DefenseFinder HMM inventory lists eight custom HMM rows under the RM_Type_IV system namespace."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "type_iv_modification_dependent_restriction",
        "title": "Type IV restriction loci attack modified foreign DNA",
        "description": "Conservative system-level sketch linking Type IV modification-dependent restriction loci to the broad phage-defense parent without resolving individual enzyme families or DefenseFinder profile rows.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures the broad Type IV modification-dependent restriction class and the DefenseFinder RM_Type_IV custom-profile namespace without asserting accession-level mappings between HMM rows and McrA, McrBC, GmrSD, MspJI, PvuRts1I, EcoKMcrA, ScoMcrA, TagI, or VcaM4I subfamilies.",
        "nodes": [
          {
            "node_id": "type_iv_rease_locus",
            "label": "type IV restriction-enzyme locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A locus encoding one or more Type IV modification-dependent restriction enzymes."
          },
          {
            "node_id": "modified_foreign_dna",
            "label": "modified foreign DNA",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Incoming bacteriophage or other foreign DNA bearing modified bases or phosphorothioated backbone positions."
          },
          {
            "node_id": "modification_dependent_restriction",
            "label": "modification-dependent DNA restriction",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Restriction activity that cleaves DNA only when the target DNA carries a recognized modification."
          },
          {
            "node_id": "type_iv_modification_dependent_restriction_system_trait",
            "label": "type IV modification-dependent restriction system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000496",
            "description": "Possession of a genome-encoded Type IV modification-dependent restriction system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "type_iv_rease_locus",
            "predicate": "enables",
            "predicate_id": "RO:0002327",
            "object": "modification_dependent_restriction",
            "description": "Type IV restriction loci encode restriction enzymes that recognize and cleave modified DNA.",
            "evidence": [
              {
                "reference": "DOI:10.1093/nar/gkt747",
                "snippet": "Type IV enzymes recognize modified DNA with low sequence selectivity and have emerged many times independently during evolution.",
                "notes": "Loenen and Raleigh support the broad Type IV class as enzymes that recognize modified DNA with limited sequence specificity."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "RM\tRM_Type_IV\t1\t1\tRM_Type_IV__Type_IV_REases\t\t\t",
                "notes": "The pinned DefenseFinder rules table models RM_Type_IV as an RM subsystem requiring the Type_IV_REases profile group."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| RM_Type_IV__FAM_0                                |                                                  | RM_Type_IV             | Custom                  | 100    |\n| RM_Type_IV__FAM_1                                |                                                  | RM_Type_IV             | Custom                  | 100    |\n| RM_Type_IV__FAM_2                                |                                                  | RM_Type_IV             | Custom                  | 100    |\n| RM_Type_IV__Type_IV_01                           |                                                  | RM_Type_IV             | Custom                  | 100    |\n| RM_Type_IV__Type_IV_03                           |                                                  | RM_Type_IV             | Custom                  | 60     |\n| RM_Type_IV__Type_IV_05                           |                                                  | RM_Type_IV             | Custom                  | 70     |\n| RM_Type_IV__Type_IV_21                           |                                                  | RM_Type_IV             | Custom                  | 175    |\n| RM_Type_IV__Type_IV_22                           |                                                  | RM_Type_IV             | Custom                  | 150    |",
                "notes": "The pinned DefenseFinder HMM inventory lists eight custom HMM rows under the RM_Type_IV system namespace."
              }
            ]
          },
          {
            "subject": "modification_dependent_restriction",
            "predicate": "mitigates",
            "predicate_id": "METPO:2007407",
            "object": "modified_foreign_dna",
            "description": "Modification-dependent restriction attacks DNA only when a recognized DNA modification is present.",
            "evidence": [
              {
                "reference": "DOI:10.1093/nar/gkt747",
                "snippet": "there are enzymes that attack DNA only when the modification is present",
                "notes": "Loenen and Raleigh contrast modification-dependent restriction with protective modification by describing enzymes that attack DNA only when a modification is present."
              },
              {
                "reference": "DOI:10.1093/nar/gkt747",
                "snippet": "Type IV enzymes recognize modified DNA with low sequence selectivity and have emerged many times independently during evolution.",
                "notes": "Loenen and Raleigh support the broad Type IV class as enzymes that recognize modified DNA with limited sequence specificity."
              },
              {
                "reference": "DOI:10.1016/j.jmb.2006.11.051",
                "snippet": "The Escherichia coli CT596 prophage exclusion genes gmrS and gmrD were found to encode a novel type IV modification-dependent restriction nuclease that targets and digests glucosylated (glc)-hydroxymethylcytosine (HMC) DNAs.",
                "notes": "Bair and Black experimentally support GmrSD as a Type IV modification-dependent restriction nuclease targeting glucosylated hydroxymethylcytosine DNA."
              }
            ]
          },
          {
            "subject": "modification_dependent_restriction",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "type_iv_modification_dependent_restriction_system_trait",
            "description": "Type IV modification-dependent restriction realizes the organism-level Type IV system-possession trait.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.jmb.2006.11.051",
                "snippet": "Overall activities of the purified GmrSD enzyme are in good agreement with the properties of the cloned gmr genes in vivo and suggest a restriction enzyme specific for sugar modified HMC DNAs.",
                "notes": "Bair and Black verify purified GmrSD restriction activity against sugar-modified hydroxymethylcytosine DNA, one concrete activity within the Type IV branch."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "RM\tRM_Type_IV\t1\t1\tRM_Type_IV__Type_IV_REases\t\t\t",
                "notes": "The pinned DefenseFinder rules table models RM_Type_IV as an RM subsystem requiring the Type_IV_REases profile group."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| RM_Type_IV__FAM_0                                |                                                  | RM_Type_IV             | Custom                  | 100    |\n| RM_Type_IV__FAM_1                                |                                                  | RM_Type_IV             | Custom                  | 100    |\n| RM_Type_IV__FAM_2                                |                                                  | RM_Type_IV             | Custom                  | 100    |\n| RM_Type_IV__Type_IV_01                           |                                                  | RM_Type_IV             | Custom                  | 100    |\n| RM_Type_IV__Type_IV_03                           |                                                  | RM_Type_IV             | Custom                  | 60     |\n| RM_Type_IV__Type_IV_05                           |                                                  | RM_Type_IV             | Custom                  | 70     |\n| RM_Type_IV__Type_IV_21                           |                                                  | RM_Type_IV             | Custom                  | 175    |\n| RM_Type_IV__Type_IV_22                           |                                                  | RM_Type_IV             | Custom                  | 150    |",
                "notes": "The pinned DefenseFinder HMM inventory lists eight custom HMM rows under the RM_Type_IV system namespace."
              }
            ]
          },
          {
            "subject": "type_iv_modification_dependent_restriction_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Type IV modification-dependent restriction system possession is curated as a genome-encoded phage-defense trait.",
            "evidence": [
              {
                "reference": "DOI:10.1093/nar/gkt747",
                "snippet": "there are enzymes that attack DNA only when the modification is present",
                "notes": "Loenen and Raleigh contrast modification-dependent restriction with protective modification by describing enzymes that attack DNA only when a modification is present."
              },
              {
                "reference": "DOI:10.1016/j.jmb.2006.11.051",
                "snippet": "The Escherichia coli CT596 prophage exclusion genes gmrS and gmrD were found to encode a novel type IV modification-dependent restriction nuclease that targets and digests glucosylated (glc)-hydroxymethylcytosine (HMC) DNAs.",
                "notes": "Bair and Black experimentally support GmrSD as a Type IV modification-dependent restriction nuclease targeting glucosylated hydroxymethylcytosine DNA."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| Other_Type_IV | 10\\.1093/nar/gkac975 | REBASE: a database for DNA restriction and modification: enzymes, genes and genomes | ",
                "notes": "The pinned DefenseFinder article registry maps the Other_Type_IV source key to the REBASE update, while RM_Type_IV itself is represented in the pinned rule and HMM registries."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "type-iv-rm-profile-interpretation-gap",
        "prompt": "Resolve the accession-level relationships between DefenseFinder RM_Type_IV custom Type_IV_REases profiles and the characterized McrA family before minting narrower Type IV custom-profile traits.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Loenen and Raleigh support the broad Type IV modification-dependent restriction class, and the pinned DefenseFinder registries support an RM_Type_IV namespace with a broad Type_IV_REases custom profile group. The evidence does not yet map any of the eight pinned RM_Type_IV HMM rows to the characterized McrA family or resolve whether the Other_Type_IV article-registry row corresponds to a reusable organism-level trait below this class.",
        "evidence": [
          {
            "reference": "DOI:10.1093/nar/gkt747",
            "snippet": "The new class of modification-dependent restriction enzymes was named Type IV, as distinct from the familiar modification-blocked Types I\u2013III.",
            "notes": "Loenen and Raleigh define Type IV as modification-dependent restriction, distinct from modification-blocked Types I-III."
          },
          {
            "reference": "DOI:10.1093/nar/gkt747",
            "snippet": "Type IV enzymes recognize modified DNA with low sequence selectivity and have emerged many times independently during evolution.",
            "notes": "Loenen and Raleigh support the broad Type IV class as enzymes that recognize modified DNA with limited sequence specificity."
          },
          {
            "reference": "DOI:10.1016/j.jmb.2006.11.051",
            "snippet": "The Escherichia coli CT596 prophage exclusion genes gmrS and gmrD were found to encode a novel type IV modification-dependent restriction nuclease that targets and digests glucosylated (glc)-hydroxymethylcytosine (HMC) DNAs.",
            "notes": "Bair and Black experimentally support GmrSD as a Type IV modification-dependent restriction nuclease targeting glucosylated hydroxymethylcytosine DNA."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
            "snippet": "| Other_Type_IV | 10\\.1093/nar/gkac975 | REBASE: a database for DNA restriction and modification: enzymes, genes and genomes | ",
            "notes": "The pinned DefenseFinder article registry maps the Other_Type_IV source key to the REBASE update, while RM_Type_IV itself is represented in the pinned rule and HMM registries."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "snippet": "RM\tRM_Type_IV\t1\t1\tRM_Type_IV__Type_IV_REases\t\t\t",
            "notes": "The pinned DefenseFinder rules table models RM_Type_IV as an RM subsystem requiring the Type_IV_REases profile group."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| RM_Type_IV__FAM_0                                |                                                  | RM_Type_IV             | Custom                  | 100    |\n| RM_Type_IV__FAM_1                                |                                                  | RM_Type_IV             | Custom                  | 100    |\n| RM_Type_IV__FAM_2                                |                                                  | RM_Type_IV             | Custom                  | 100    |\n| RM_Type_IV__Type_IV_01                           |                                                  | RM_Type_IV             | Custom                  | 100    |\n| RM_Type_IV__Type_IV_03                           |                                                  | RM_Type_IV             | Custom                  | 60     |\n| RM_Type_IV__Type_IV_05                           |                                                  | RM_Type_IV             | Custom                  | 70     |\n| RM_Type_IV__Type_IV_21                           |                                                  | RM_Type_IV             | Custom                  | 175    |\n| RM_Type_IV__Type_IV_22                           |                                                  | RM_Type_IV             | Custom                  | 150    |",
            "notes": "The pinned DefenseFinder HMM inventory lists eight custom HMM rows under the RM_Type_IV system namespace."
          }
        ],
        "attaches_to": [
          "causal_graphs#type_iv_modification_dependent_restriction"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-30"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-30T16:21:47Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted type IV modification-dependent restriction system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v373.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-30T16:21:48Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed type IV modification-dependent restriction system during initial curation and left canonical_examples empty because the sources support a broad Type IV modification-dependent restriction class, a GmrSD enzyme example, and a DefenseFinder system model, but not a single stable NCBITaxon strain exemplar for the whole broad Type IV branch. No paid research was used.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-30T16:57:37Z",
        "curator": "codex",
        "action": "REVISED_DEFINITION",
        "changes": "Broadened the Type IV modification-dependent restriction system definition from modified bases to recognized base or backbone DNA modifications after PR #1488 local review found the original definition excluded phosphorothioated backbone targets; fixes #1489.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-01T03:37:01Z",
        "curator": "codex",
        "action": "RESOLVE_DISCUSSION_SCOPE",
        "changes": "Documented McrBC as split out in the open Type IV modification-dependent restriction profile-interpretation discussion after minting traitmech:000505 for the McrBC system; other RM_Type_IV custom HMM and article-registry families remain open.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-01T04:21:01Z",
        "curator": "codex",
        "action": "RESOLVE_DISCUSSION_SCOPE",
        "changes": "Documented GmrSD as split out in the open Type IV modification-dependent restriction profile-interpretation discussion after minting traitmech:000506 for the GmrSD system; other RM_Type_IV custom HMM and article-registry families remain open.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-01T07:10:01Z",
        "curator": "codex",
        "action": "RESOLVE_DISCUSSION_SCOPE",
        "changes": "Documented EcoKMcrA as split out in the open Type IV modification-dependent restriction profile-interpretation discussion after minting traitmech:000509 for the EcoKMcrA system; other RM_Type_IV custom HMM and article-registry families remain open.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-01T08:04:01Z",
        "curator": "codex",
        "action": "RESOLVE_DISCUSSION_SCOPE",
        "changes": "Documented MspJI as split out in the open Type IV modification-dependent restriction profile-interpretation discussion after minting traitmech:000510 for the MspJI system; other RM_Type_IV custom HMM and article-registry families remain open.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-01T09:01:01Z",
        "curator": "codex",
        "action": "RESOLVE_DISCUSSION_SCOPE",
        "changes": "Documented PvuRts1I as split out in the open Type IV modification-dependent restriction profile-interpretation discussion after minting traitmech:000511 for the PvuRts1I system; other RM_Type_IV custom HMM and article-registry families remain open.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-01T10:14:01Z",
        "curator": "codex",
        "action": "RESOLVE_DISCUSSION_SCOPE",
        "changes": "Documented ScoMcrA as split out in the open Type IV modification-dependent restriction profile-interpretation discussion after minting traitmech:000512 for the ScoMcrA system; other RM_Type_IV custom HMM and article-registry families remain open.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-01T11:10:01Z",
        "curator": "codex",
        "action": "RESOLVE_DISCUSSION_SCOPE",
        "changes": "Documented TagI as split out in the open Type IV modification-dependent restriction profile-interpretation discussion after minting traitmech:000513 for the TagI system; other RM_Type_IV custom HMM and article-registry families remain open.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-01T11:48:01Z",
        "curator": "codex",
        "action": "RESOLVE_DISCUSSION_SCOPE",
        "changes": "Documented VcaM4I as split out in the open Type IV modification-dependent restriction profile-interpretation discussion after minting traitmech:000514 for the VcaM4I system; McrA and Other_Type_IV remain open.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000292",
    "label": "Ukko system",
    "definition": "A phage defense system in which an organism possesses a Ukko locus that can protect bacteria from bacteriophage infection.",
    "definition_source": "DOI:10.1101/2025.01.08.631966",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "Ukko",
        "synonym_type": "EXACT_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      },
      {
        "synonym_text": "UkkA1",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "UkkA2",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "UkkB1",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "UkkB2",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "UkkC1",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "UkkC2",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "UkkD1",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "UkkD2",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1101/2025.01.08.631966",
        "snippet": "Among the remaining eight systems, six demonstrated increased resistance to at least one phage with more than 100 fold reduction in plaque forming units (PFU) (Figure 3a, Supplementary Figure 5). As Streptomyces are mostly soil dwelling bacteria, we named these systems after deities of the soil and earth (Ceres, Geb, Veles, Prithvi, Ukko and Oshun).",
        "notes": "Mordret et al. directly name Ukko among six Streptomyces systems that increased resistance to at least one phage."
      },
      {
        "reference": "DOI:10.1101/2025.01.08.631966",
        "snippet": "The bacterial pangenome encodes an immense array of antiphage systems, yet much of their diversity remains uncharted",
        "notes": "Mordret et al. motivate a conservative system-level record that does not assert a resolved Ukko trigger, effector output, or universal pathway."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "Ukko | 10\\.1101/2025\\.01\\.08\\.631966 | Protein and genomic language models chart a vast landscape of antiphage defenses",
        "notes": "The DefenseFinder model registry maps the named Ukko system to the Mordret et al. antiphage-system discovery preprint."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "Ukko__UkkA1                                      |                                                  | Ukko",
        "notes": "The DefenseFinder HMM inventory records UkkA1 in the Ukko model namespace."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "Ukko__UkkA2                                      |                                                  | Ukko",
        "notes": "The DefenseFinder HMM inventory records UkkA2 in the Ukko model namespace."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "Ukko__UkkB1                                      |                                                  | Ukko",
        "notes": "The DefenseFinder HMM inventory records UkkB1 in the Ukko model namespace."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "Ukko__UkkB2                                      |                                                  | Ukko",
        "notes": "The DefenseFinder HMM inventory records UkkB2 in the Ukko model namespace."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "Ukko__UkkC1                                      |                                                  | Ukko",
        "notes": "The DefenseFinder HMM inventory records UkkC1 in the Ukko model namespace."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "Ukko__UkkC2                                      |                                                  | Ukko",
        "notes": "The DefenseFinder HMM inventory records UkkC2 in the Ukko model namespace."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "Ukko__UkkD1                                      |                                                  | Ukko",
        "notes": "The DefenseFinder HMM inventory records UkkD1 in the Ukko model namespace."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "Ukko__UkkD2                                      |                                                  | Ukko",
        "notes": "The DefenseFinder HMM inventory records UkkD2 in the Ukko model namespace."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "ukko_locus_restricts_phage",
        "title": "Ukko loci confer bacterial phage defense",
        "description": "Conservative system-level sketch linking possession of a Ukko locus to restricted bacteriophage propagation without asserting the unresolved phage trigger or molecular output.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Ukko as a named anti-phage system with UkkA1, UkkA2, UkkB1, UkkB2, UkkC1, UkkC2, UkkD1, and UkkD2 DefenseFinder HMM profile entries while leaving its phage trigger, molecular substrate, antiviral effector output, and subtype breadth unresolved.",
        "nodes": [
          {
            "node_id": "ukko_locus",
            "label": "Ukko locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A Ukko anti-phage defense locus cataloged in DefenseFinder with UkkA1, UkkA2, UkkB1, UkkB2, UkkC1, UkkC2, UkkD1, and UkkD2 HMM profile entries."
          },
          {
            "node_id": "restricted_phage_propagation",
            "label": "restricted phage propagation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced propagation of bacteriophage in cells carrying the Ukko system."
          },
          {
            "node_id": "ukko_system_trait",
            "label": "Ukko system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000292",
            "description": "Possession of a genome-encoded Ukko phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "ukko_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "restricted_phage_propagation",
            "description": "DefenseFinder maps Ukko to a protein- and genomic-language-model antiphage-system discovery preprint and catalogs UkkA1, UkkA2, UkkB1, UkkB2, UkkC1, UkkC2, UkkD1, and UkkD2 HMM profile entries in the Ukko model namespace.",
            "evidence": [
              {
                "reference": "DOI:10.1101/2025.01.08.631966",
                "snippet": "Among the remaining eight systems, six demonstrated increased resistance to at least one phage with more than 100 fold reduction in plaque forming units (PFU) (Figure 3a, Supplementary Figure 5). As Streptomyces are mostly soil dwelling bacteria, we named these systems after deities of the soil and earth (Ceres, Geb, Veles, Prithvi, Ukko and Oshun).",
                "notes": "Mordret et al. directly name Ukko among six Streptomyces systems that restricted at least one phage."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Ukko | 10\\.1101/2025\\.01\\.08\\.631966 | Protein and genomic language models chart a vast landscape of antiphage defenses",
                "notes": "The DefenseFinder registry maps Ukko itself to the Mordret et al. bacterial antiphage-system discovery preprint."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "Ukko__UkkA1                                      |                                                  | Ukko",
                "notes": "The DefenseFinder HMM inventory records UkkA1 in the Ukko model namespace."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "Ukko__UkkA2                                      |                                                  | Ukko",
                "notes": "The DefenseFinder HMM inventory records UkkA2 in the Ukko model namespace."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "Ukko__UkkB1                                      |                                                  | Ukko",
                "notes": "The DefenseFinder HMM inventory records UkkB1 in the Ukko model namespace."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "Ukko__UkkB2                                      |                                                  | Ukko",
                "notes": "The DefenseFinder HMM inventory records UkkB2 in the Ukko model namespace."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "Ukko__UkkC1                                      |                                                  | Ukko",
                "notes": "The DefenseFinder HMM inventory records UkkC1 in the Ukko model namespace."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "Ukko__UkkC2                                      |                                                  | Ukko",
                "notes": "The DefenseFinder HMM inventory records UkkC2 in the Ukko model namespace."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "Ukko__UkkD1                                      |                                                  | Ukko",
                "notes": "The DefenseFinder HMM inventory records UkkD1 in the Ukko model namespace."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "Ukko__UkkD2                                      |                                                  | Ukko",
                "notes": "The DefenseFinder HMM inventory records UkkD2 in the Ukko model namespace."
              }
            ]
          },
          {
            "subject": "restricted_phage_propagation",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "ukko_system_trait",
            "description": "Ukko-mediated phage restriction realizes the Ukko system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1101/2025.01.08.631966",
                "snippet": "Among the remaining eight systems, six demonstrated increased resistance to at least one phage with more than 100 fold reduction in plaque forming units (PFU) (Figure 3a, Supplementary Figure 5). As Streptomyces are mostly soil dwelling bacteria, we named these systems after deities of the soil and earth (Ceres, Geb, Veles, Prithvi, Ukko and Oshun).",
                "notes": "Mordret et al. directly name Ukko among six systems that increased resistance to at least one phage."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Ukko | 10\\.1101/2025\\.01\\.08\\.631966 | Protein and genomic language models chart a vast landscape of antiphage defenses",
                "notes": "DefenseFinder records Ukko as a named system from the Mordret et al. antiphage discovery preprint."
              }
            ]
          },
          {
            "subject": "ukko_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Ukko system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| Ukko | 10\\.1101/2025\\.01\\.08\\.631966 | Protein and genomic language models chart a vast landscape of antiphage defenses |",
                "notes": "DefenseFinder associates Ukko with the Mordret et al. bacterial antiphage-system discovery preprint."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "ukko-mechanism-gap",
        "prompt": "Resolve Ukko phage triggers and effector outputs before minting narrower Ukko mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Mordret et al. and DefenseFinder support Ukko as a named anti-phage system with UkkA1, UkkA2, UkkB1, UkkB2, UkkC1, UkkC2, UkkD1, and UkkD2 HMM profile entries, but the trigger, molecular substrate, antiviral effector output, and subtype-specific mechanism are not resolved enough here to assert a narrower mechanistic child trait.",
        "attaches_to": [
          "causal_graphs#ukko_locus_restricts_phage"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-19"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-19T20:26:31Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Ukko system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v169.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000262",
    "label": "Uzume system",
    "definition": "A phage defense system in which an organism possesses an Uzume locus represented by a UzuA profile that can protect bacteria from bacteriophage infection.",
    "definition_source": "DOI:10.1016/j.chom.2022.09.017",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "Uzume",
        "synonym_type": "EXACT_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1016/j.chom.2022.09.017",
        "snippet": "discovery of 21 defense systems that protect bacteria from phages, based on computational genomic analyses and phage-infection experiments",
        "notes": "Millman et al. report the computational and experimental cohort that DefenseFinder cites for Uzume as a bacterial anti-phage system."
      },
      {
        "reference": "DOI:10.1101/2022.05.11.491447",
        "snippet": "discovery of 21 new defense systems that protect bacteria from phages, based on computational genomic analyses and phage infection experiments",
        "notes": "The bioRxiv version of Millman et al. independently carries the 21-system discovery claim linked from DefenseFinder's Uzume article registry."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "Uzume | 10\\.1101/2022\\.05\\.11\\.491447 | An expanding arsenal of immune systems that protect bacteria from phages",
        "notes": "The DefenseFinder model registry maps the named Uzume system to the Millman et al. antiphage-system discovery preprint."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "Uzume\tUzume\t1\t1\tUzume__UzuA",
        "notes": "The DefenseFinder rules table models Uzume with a UzuA profile."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "Uzume__UzuA                                      | Uzume__UzuA                                      | Uzume",
        "notes": "The DefenseFinder HMM inventory records UzuA in the Uzume model namespace."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "uzume_locus_restricts_phage",
        "title": "Uzume loci confer bacterial phage defense",
        "description": "Conservative system-level sketch linking possession of an Uzume locus to restricted bacteriophage propagation without asserting the unresolved phage trigger or molecular output.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Uzume as a named anti-phage system with the required DefenseFinder UzuA profile while leaving its phage trigger, molecular substrate, antiviral effector output, and subtype breadth unresolved.",
        "nodes": [
          {
            "node_id": "uzume_locus",
            "label": "Uzume locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "An Uzume anti-phage defense locus satisfying a DefenseFinder rule over the UzuA profile."
          },
          {
            "node_id": "restricted_phage_propagation",
            "label": "restricted phage propagation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced propagation of bacteriophage in cells carrying the Uzume system."
          },
          {
            "node_id": "uzume_system_trait",
            "label": "Uzume system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000262",
            "description": "Possession of a genome-encoded Uzume phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "uzume_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "restricted_phage_propagation",
            "description": "DefenseFinder maps Uzume to a bacterial anti-phage-system discovery preprint and represents Uzume loci through the UzuA component profile.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.chom.2022.09.017",
                "snippet": "discovery of 21 defense systems that protect bacteria from phages",
                "notes": "Millman et al. describe the anti-phage discovery cohort that the DefenseFinder Uzume registry row maps to the Uzume system."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Uzume | 10\\.1101/2022\\.05\\.11\\.491447 | An expanding arsenal of immune systems that protect bacteria from phages",
                "notes": "The DefenseFinder registry maps Uzume itself to the Millman et al. bacterial antiphage-system discovery preprint."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "Uzume\tUzume\t1\t1\tUzume__UzuA",
                "notes": "The DefenseFinder rules table supports UzuA as the required Uzume system profile."
              }
            ]
          },
          {
            "subject": "restricted_phage_propagation",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "uzume_system_trait",
            "description": "Uzume-mediated phage restriction realizes the Uzume system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.chom.2022.09.017",
                "snippet": "discovery of 21 defense systems that protect bacteria from phages",
                "notes": "Millman et al. place the Uzume discovery cohort in the set of bacterial systems that protect against phages."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Uzume | 10\\.1101/2022\\.05\\.11\\.491447 | An expanding arsenal of immune systems that protect bacteria from phages",
                "notes": "DefenseFinder records Uzume as a named system from the Millman et al. antiphage discovery preprint."
              }
            ]
          },
          {
            "subject": "uzume_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Uzume system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "An expanding arsenal of immune systems that protect bacteria from phages",
                "notes": "DefenseFinder associates Uzume with the Millman et al. bacterial antiphage-system discovery paper."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "uzume-mechanism-gap",
        "prompt": "Resolve Uzume phage triggers and effector outputs before minting narrower Uzume mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Millman et al. and DefenseFinder support Uzume as a named anti-phage system with a UzuA profile, but the trigger, molecular substrate, antiviral effector output, and subtype-specific mechanism are not resolved enough here to assert a narrower mechanistic child trait.",
        "attaches_to": [
          "causal_graphs#uzume_locus_restricts_phage"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-19"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-19T03:14:32Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Uzume system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v139.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000514",
    "label": "VcaM4I system",
    "definition": "A type IV modification-dependent restriction system in which an organism possesses a VcaM4I-family locus encoding an EVE-HNH restriction endonuclease that recognizes 5-methylcytosine- or 5-hydroxymethylcytosine-modified DNA.",
    "definition_source": "DOI:10.1093/nar/gkaa1218",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000496"
    ],
    "synonyms": [
      {
        "synonym_text": "VcaM4I",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1093/nar/gkaa1218",
        "snippet": "EVE domains belong to the PUA superfamily, and are present in MDREs in combination with HNH nuclease domains.",
        "notes": "Mierzejewska et al. support the EVE-HNH architecture of VcaM4I-family modification-dependent restriction endonucleases."
      },
      {
        "reference": "DOI:10.1093/nar/gkaa1218",
        "snippet": "Here, we present a biochemical characterization of the EVE-HNH endonuclease VcaM4I and crystal structures of the protein alone, with EVE domain bound to either 5mC modified dsDNA or to 5mC/5hmC containing ssDNA.",
        "notes": "Mierzejewska et al. biochemically characterized VcaM4I and solved structures of apo and modified-DNA-bound enzyme."
      },
      {
        "reference": "DOI:10.1093/nar/gkaa1218",
        "snippet": "The EVE domain is moderately specific for 5mC/5hmC containing DNA according to EMSA experiments.",
        "notes": "Mierzejewska et al. support VcaM4I EVE-domain recognition of 5mC/5hmC-containing DNA."
      },
      {
        "reference": "DOI:10.1093/nar/gkaa1218",
        "snippet": "Removal of the EVE domain and inter-domain linker, but not of the EVE domain alone converts VcaM4I into a non-specific toxic nuclease.",
        "notes": "Mierzejewska et al. support VcaM4I as a nuclease whose domain organization modulates toxic DNA cleavage."
      },
      {
        "reference": "DOI:10.1093/nar/gkaa1218",
        "snippet": "The role of the key residues in the EVE and HNH domains of VcaM4I is confirmed by digestion and restriction assays with the enzyme variants that differ from the wild-type by changes to the base binding pocket or to the catalytic residues.",
        "notes": "Mierzejewska et al. support the VcaM4I EVE base-binding pocket and HNH catalytic residues by digestion and restriction assays."
      },
      {
        "reference": "DOI:10.1093/nar/gkt747",
        "snippet": "The new class of modification-dependent restriction enzymes was named Type IV, as distinct from the familiar modification-blocked Types I-III.",
        "notes": "Loenen and Raleigh define the Type IV class as modification-dependent restriction enzymes."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| VcaM4I | 10\\.1093/nar/gkaa1218 | Crystal structures of the EVE-HNH endonuclease VcaM4I in the presence and absence of DNA | ",
        "notes": "The pinned DefenseFinder article registry maps the VcaM4I source key to the Mierzejewska et al. structural paper."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "vcam4i_restricts_modified_cytosine_dna",
        "title": "VcaM4I restricts modified-cytosine DNA",
        "description": "Conservative system-level sketch linking a VcaM4I-family locus to EVE-HNH 5mC/5hmC-dependent DNA restriction and to the Type IV restriction parent trait.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures VcaM4I as a named Type IV modification-dependent restriction family while leaving natural host breadth, exact modified-DNA sequence-context specificity across EVE-HNH homologs, accession-level protein examples, and DefenseFinder RM_Type_IV HMM/rules mapping unresolved.",
        "nodes": [
          {
            "node_id": "vcam4i_family_locus",
            "label": "VcaM4I-family locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A locus encoding a VcaM4I-family EVE-HNH modification-dependent restriction endonuclease."
          },
          {
            "node_id": "vcam4i_modified_cytosine_dna",
            "label": "VcaM4I-targeted modified-cytosine DNA",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "DNA containing 5-methylcytosine or 5-hydroxymethylcytosine in a VcaM4I-family recognition context."
          },
          {
            "node_id": "vcam4i_eve_hnh_restriction",
            "label": "VcaM4I EVE-HNH DNA restriction",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Modification-dependent restriction of 5mC/5hmC-modified DNA by a VcaM4I-family EVE-HNH endonuclease."
          },
          {
            "node_id": "vcam4i_system_trait",
            "label": "VcaM4I system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000514",
            "description": "Possession of a genome-encoded VcaM4I-family modification-dependent restriction system."
          },
          {
            "node_id": "type_iv_modification_dependent_restriction",
            "label": "type IV modification-dependent restriction system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000496",
            "description": "Possession of a genome-encoded Type IV modification-dependent restriction system."
          }
        ],
        "edges": [
          {
            "subject": "vcam4i_family_locus",
            "predicate": "enables",
            "predicate_id": "RO:0002327",
            "object": "vcam4i_eve_hnh_restriction",
            "description": "VcaM4I-family loci encode EVE-HNH endonucleases that restrict 5mC/5hmC-modified DNA.",
            "evidence": [
              {
                "reference": "DOI:10.1093/nar/gkaa1218",
                "snippet": "EVE domains belong to the PUA superfamily, and are present in MDREs in combination with HNH nuclease domains.",
                "notes": "Mierzejewska et al. support the EVE-HNH architecture of VcaM4I-family modification-dependent restriction endonucleases."
              },
              {
                "reference": "DOI:10.1093/nar/gkaa1218",
                "snippet": "Here, we present a biochemical characterization of the EVE-HNH endonuclease VcaM4I and crystal structures of the protein alone, with EVE domain bound to either 5mC modified dsDNA or to 5mC/5hmC containing ssDNA.",
                "notes": "Mierzejewska et al. biochemically characterized VcaM4I and solved structures of apo and modified-DNA-bound enzyme."
              }
            ]
          },
          {
            "subject": "vcam4i_eve_hnh_restriction",
            "predicate": "mitigates",
            "predicate_id": "METPO:2007407",
            "object": "vcam4i_modified_cytosine_dna",
            "description": "VcaM4I-family EVE-HNH restriction targets 5mC- or 5hmC-modified DNA.",
            "evidence": [
              {
                "reference": "DOI:10.1093/nar/gkaa1218",
                "snippet": "The EVE domain is moderately specific for 5mC/5hmC containing DNA according to EMSA experiments.",
                "notes": "Mierzejewska et al. support VcaM4I EVE-domain recognition of 5mC/5hmC-containing DNA."
              },
              {
                "reference": "DOI:10.1093/nar/gkaa1218",
                "snippet": "The role of the key residues in the EVE and HNH domains of VcaM4I is confirmed by digestion and restriction assays with the enzyme variants that differ from the wild-type by changes to the base binding pocket or to the catalytic residues.",
                "notes": "Mierzejewska et al. support the VcaM4I EVE base-binding pocket and HNH catalytic residues by digestion and restriction assays."
              }
            ]
          },
          {
            "subject": "vcam4i_eve_hnh_restriction",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "vcam4i_system_trait",
            "description": "VcaM4I-family EVE-HNH DNA restriction realizes the organism-level VcaM4I system possession trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| VcaM4I | 10\\.1093/nar/gkaa1218 | Crystal structures of the EVE-HNH endonuclease VcaM4I in the presence and absence of DNA | ",
                "notes": "The pinned DefenseFinder article registry maps the VcaM4I source key to the Mierzejewska et al. structural paper."
              }
            ]
          },
          {
            "subject": "vcam4i_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "type_iv_modification_dependent_restriction",
            "description": "VcaM4I system possession is a Type IV modification-dependent restriction system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1093/nar/gkaa1218",
                "snippet": "Removal of the EVE domain and inter-domain linker, but not of the EVE domain alone converts VcaM4I into a non-specific toxic nuclease.",
                "notes": "Mierzejewska et al. support VcaM4I as a nuclease whose domain organization modulates toxic DNA cleavage."
              },
              {
                "reference": "DOI:10.1093/nar/gkt747",
                "snippet": "The new class of modification-dependent restriction enzymes was named Type IV, as distinct from the familiar modification-blocked Types I-III.",
                "notes": "Loenen and Raleigh define the Type IV class as modification-dependent restriction enzymes."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "vcam4i-defensefinder-model-gap",
        "prompt": "Resolve VcaM4I-family breadth, modified-cytosine sequence-context specificity across natural hosts, accession-level protein examples, and DefenseFinder RM_Type_IV HMM/rules mapping before minting narrower VcaM4I mechanism or component traits.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Mierzejewska et al. support VcaM4I as an EVE-HNH modification-dependent restriction endonuclease that recognizes 5mC/5hmC DNA and validate EVE-domain modified-base binding plus HNH catalytic residues by digestion and restriction assays. The pinned DefenseFinder article registry maps VcaM4I to that paper, but the pinned HMM inventory and rules table have no exact VcaM4I rows. This first-pass record therefore does not resolve a reusable DefenseFinder profile model, exact accession-level protein examples, the breadth of VcaM4I-like systems across natural hosts, or the complete set of natural modified-cytosine sequence contexts.",
        "evidence": [
          {
            "reference": "DOI:10.1093/nar/gkaa1218",
            "snippet": "EVE domains belong to the PUA superfamily, and are present in MDREs in combination with HNH nuclease domains.",
            "notes": "Mierzejewska et al. support the EVE-HNH architecture of VcaM4I-family modification-dependent restriction endonucleases."
          },
          {
            "reference": "DOI:10.1093/nar/gkaa1218",
            "snippet": "Here, we present a biochemical characterization of the EVE-HNH endonuclease VcaM4I and crystal structures of the protein alone, with EVE domain bound to either 5mC modified dsDNA or to 5mC/5hmC containing ssDNA.",
            "notes": "Mierzejewska et al. biochemically characterized VcaM4I and solved structures of apo and modified-DNA-bound enzyme."
          },
          {
            "reference": "DOI:10.1093/nar/gkaa1218",
            "snippet": "The EVE domain is moderately specific for 5mC/5hmC containing DNA according to EMSA experiments.",
            "notes": "Mierzejewska et al. support VcaM4I EVE-domain recognition of 5mC/5hmC-containing DNA."
          },
          {
            "reference": "DOI:10.1093/nar/gkaa1218",
            "snippet": "The role of the key residues in the EVE and HNH domains of VcaM4I is confirmed by digestion and restriction assays with the enzyme variants that differ from the wild-type by changes to the base binding pocket or to the catalytic residues.",
            "notes": "Mierzejewska et al. support the VcaM4I EVE base-binding pocket and HNH catalytic residues by digestion and restriction assays."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
            "snippet": "| VcaM4I | 10\\.1093/nar/gkaa1218 | Crystal structures of the EVE-HNH endonuclease VcaM4I in the presence and absence of DNA | ",
            "notes": "The pinned DefenseFinder article registry maps the VcaM4I source key to the Mierzejewska et al. structural paper."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "notes": "A structured first-pass search of the pinned DefenseFinder HMM inventory found no exact VcaM4I row."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "A structured first-pass search of the pinned DefenseFinder rules table found no exact VcaM4I system row."
          }
        ],
        "attaches_to": [
          "causal_graphs#vcam4i_restricts_modified_cytosine_dna"
        ],
        "posed_by": "codex",
        "posed_date": "2026-10-01"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-01T11:48:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted VcaM4I system as a DOI- and DefenseFinder-backed GENOMICS TraitRecord under the type IV modification-dependent restriction system parent after an ignored-and-hidden duplicate review found no exact same-scope live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v391.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-01T11:48:02Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed VcaM4I system during initial curation and left canonical_examples empty because Mierzejewska et al. support the purified VcaM4I enzyme, structures, and restriction assays, but not a single stable NCBITaxon strain exemplar or accession-level protein example for the organism-level VcaM4I system trait. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000289",
    "label": "Veles system",
    "definition": "A phage defense system in which an organism possesses a Veles locus that can protect bacteria from bacteriophage infection.",
    "definition_source": "DOI:10.1101/2025.01.08.631966",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "Veles",
        "synonym_type": "EXACT_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      },
      {
        "synonym_text": "VlsA1",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "VlsA2",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "VlsB1",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "VlsB2",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "VlsC1",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "VlsC2",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1101/2025.01.08.631966",
        "snippet": "Among the remaining eight systems, six demonstrated increased resistance to at least one phage with more than 100 fold reduction in plaque forming units (PFU) (Figure 3a, Supplementary Figure 5). As Streptomyces are mostly soil dwelling bacteria, we named these systems after deities of the soil and earth (Ceres, Geb, Veles, Prithvi, Ukko and Oshun).",
        "notes": "Mordret et al. directly name Veles among six Streptomyces systems that increased resistance to at least one phage."
      },
      {
        "reference": "DOI:10.1101/2025.01.08.631966",
        "snippet": "The bacterial pangenome encodes an immense array of antiphage systems, yet much of their diversity remains uncharted",
        "notes": "Mordret et al. motivate a conservative system-level record that does not assert a resolved Veles trigger, effector output, or universal pathway."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "Veles | 10\\.1101/2025\\.01\\.08\\.631966 | Protein and genomic language models chart a vast landscape of antiphage defenses",
        "notes": "The DefenseFinder model registry maps the named Veles system to the Mordret et al. antiphage-system discovery preprint."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "Veles__VlsA1                                     |                                                  | Veles",
        "notes": "The DefenseFinder HMM inventory records VlsA1 in the Veles model namespace."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "Veles__VlsA2                                     |                                                  | Veles",
        "notes": "The DefenseFinder HMM inventory records VlsA2 in the Veles model namespace."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "Veles__VlsB1                                     |                                                  | Veles",
        "notes": "The DefenseFinder HMM inventory records VlsB1 in the Veles model namespace."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "Veles__VlsB2                                     |                                                  | Veles",
        "notes": "The DefenseFinder HMM inventory records VlsB2 in the Veles model namespace."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "Veles__VlsC1                                     |                                                  | Veles",
        "notes": "The DefenseFinder HMM inventory records VlsC1 in the Veles model namespace."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "Veles__VlsC2                                     |                                                  | Veles",
        "notes": "The DefenseFinder HMM inventory records VlsC2 in the Veles model namespace."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "veles_locus_restricts_phage",
        "title": "Veles loci confer bacterial phage defense",
        "description": "Conservative system-level sketch linking possession of a Veles locus to restricted bacteriophage propagation without asserting the unresolved phage trigger or molecular output.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures Veles as a named anti-phage system with VlsA1, VlsA2, VlsB1, VlsB2, VlsC1, and VlsC2 DefenseFinder HMM profile entries while leaving its phage trigger, molecular substrate, antiviral effector output, and subtype breadth unresolved.",
        "nodes": [
          {
            "node_id": "veles_locus",
            "label": "Veles locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A Veles anti-phage defense locus cataloged in DefenseFinder with VlsA1, VlsA2, VlsB1, VlsB2, VlsC1, and VlsC2 HMM profile entries."
          },
          {
            "node_id": "restricted_phage_propagation",
            "label": "restricted phage propagation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced propagation of bacteriophage in cells carrying the Veles system."
          },
          {
            "node_id": "veles_system_trait",
            "label": "Veles system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000289",
            "description": "Possession of a genome-encoded Veles phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "veles_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "restricted_phage_propagation",
            "description": "DefenseFinder maps Veles to a protein- and genomic-language-model antiphage-system discovery preprint and catalogs VlsA1, VlsA2, VlsB1, VlsB2, VlsC1, and VlsC2 HMM profile entries in the Veles model namespace.",
            "evidence": [
              {
                "reference": "DOI:10.1101/2025.01.08.631966",
                "snippet": "Among the remaining eight systems, six demonstrated increased resistance to at least one phage with more than 100 fold reduction in plaque forming units (PFU) (Figure 3a, Supplementary Figure 5). As Streptomyces are mostly soil dwelling bacteria, we named these systems after deities of the soil and earth (Ceres, Geb, Veles, Prithvi, Ukko and Oshun).",
                "notes": "Mordret et al. directly name Veles among six Streptomyces systems that restricted at least one phage."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Veles | 10\\.1101/2025\\.01\\.08\\.631966 | Protein and genomic language models chart a vast landscape of antiphage defenses",
                "notes": "The DefenseFinder registry maps Veles itself to the Mordret et al. bacterial antiphage-system discovery preprint."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "Veles__VlsA1                                     |                                                  | Veles",
                "notes": "The DefenseFinder HMM inventory records VlsA1 in the Veles model namespace."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "Veles__VlsA2                                     |                                                  | Veles",
                "notes": "The DefenseFinder HMM inventory records VlsA2 in the Veles model namespace."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "Veles__VlsB1                                     |                                                  | Veles",
                "notes": "The DefenseFinder HMM inventory records VlsB1 in the Veles model namespace."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "Veles__VlsB2                                     |                                                  | Veles",
                "notes": "The DefenseFinder HMM inventory records VlsB2 in the Veles model namespace."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "Veles__VlsC1                                     |                                                  | Veles",
                "notes": "The DefenseFinder HMM inventory records VlsC1 in the Veles model namespace."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "Veles__VlsC2                                     |                                                  | Veles",
                "notes": "The DefenseFinder HMM inventory records VlsC2 in the Veles model namespace."
              }
            ]
          },
          {
            "subject": "restricted_phage_propagation",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "veles_system_trait",
            "description": "Veles-mediated phage restriction realizes the Veles system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1101/2025.01.08.631966",
                "snippet": "Among the remaining eight systems, six demonstrated increased resistance to at least one phage with more than 100 fold reduction in plaque forming units (PFU) (Figure 3a, Supplementary Figure 5). As Streptomyces are mostly soil dwelling bacteria, we named these systems after deities of the soil and earth (Ceres, Geb, Veles, Prithvi, Ukko and Oshun).",
                "notes": "Mordret et al. directly name Veles among six systems that increased resistance to at least one phage."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "Veles | 10\\.1101/2025\\.01\\.08\\.631966 | Protein and genomic language models chart a vast landscape of antiphage defenses",
                "notes": "DefenseFinder records Veles as a named system from the Mordret et al. antiphage discovery preprint."
              }
            ]
          },
          {
            "subject": "veles_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Veles system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| Veles | 10\\.1101/2025\\.01\\.08\\.631966 | Protein and genomic language models chart a vast landscape of antiphage defenses |",
                "notes": "DefenseFinder associates Veles with the Mordret et al. bacterial antiphage-system discovery preprint."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "veles-mechanism-gap",
        "prompt": "Resolve Veles phage triggers and effector outputs before minting narrower Veles mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Mordret et al. and DefenseFinder support Veles as a named anti-phage system with VlsA1, VlsA2, VlsB1, VlsB2, VlsC1, and VlsC2 HMM profile entries, but the trigger, molecular substrate, antiviral effector output, and subtype-specific mechanism are not resolved enough here to assert a narrower mechanistic child trait.",
        "attaches_to": [
          "causal_graphs#veles_locus_restricts_phage"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-19"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-19T18:44:49Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Veles system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v166.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000263",
    "label": "Viperin system",
    "definition": "A phage defense system in which an organism possesses a prokaryotic viperin locus represented by a pVip profile that can produce antiviral modified ribonucleotides and protect against phage infection.",
    "definition_source": "DOI:10.1038/s41586-020-2762-2",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "Viperin",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      },
      {
        "synonym_text": "pVip",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1038/s41586-020-2762-2"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/s41586-020-2762-2",
        "snippet": "Here we show that eukaryotic viperin originated from a clade of bacterial and archaeal proteins that protect against phage infection",
        "notes": "Bernheim et al. support treating prokaryotic viperins as bacterial and archaeal phage-protective proteins rather than only as an animal antiviral factor."
      },
      {
        "reference": "DOI:10.1038/s41586-020-2762-2",
        "snippet": "Prokaryotic viperins produce a set of modified ribonucleotides",
        "notes": "Bernheim et al. support modified ribonucleotide synthesis as a recurring output of prokaryotic viperin proteins."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "Viperin | 10\\.1038/s41586-020-2762-2 | Prokaryotic viperins produce diverse antiviral molecules",
        "notes": "The DefenseFinder model registry maps the named Viperin system to the Bernheim et al. prokaryotic viperin paper."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "Viperin\tViperin\t1\t1\tViperin__pVip",
        "notes": "The DefenseFinder rules table models Viperin with a pVip profile."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "Viperin__pVip                                    | Viperin__pVip                                    | Viperin",
        "notes": "The DefenseFinder HMM inventory records pVip in the Viperin model namespace."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "viperin_modified_ribonucleotides_restrict_phage",
        "title": "Prokaryotic viperins produce antiviral ribonucleotides",
        "description": "Conservative system-level sketch linking possession of a prokaryotic viperin locus to modified ribonucleotide production and inhibited phage transcription.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures characterized pVip-mediated modified ribonucleotide production and T7 transcription inhibition without asserting one universal nucleotide product, viral polymerase target, accessory-gene architecture, or phage range across all Viperin loci.",
        "nodes": [
          {
            "node_id": "viperin_locus",
            "label": "Viperin locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A prokaryotic viperin phage-defense locus satisfying a DefenseFinder rule over the pVip profile."
          },
          {
            "node_id": "modified_ribonucleotide_production",
            "label": "modified ribonucleotide production",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Production of modified ribonucleotides by prokaryotic viperin enzymes."
          },
          {
            "node_id": "t7_phage_transcription_inhibition",
            "label": "T7 phage transcription inhibition",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Inhibition of T7 phage polymerase-dependent transcription."
          },
          {
            "node_id": "viperin_system_trait",
            "label": "Viperin system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000263",
            "description": "Possession of a genome-encoded prokaryotic viperin phage-defense locus."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "viperin_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "modified_ribonucleotide_production",
            "description": "The Viperin locus encodes a pVip-class radical-SAM enzyme that produces modified ribonucleotides.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41586-020-2762-2",
                "snippet": "Prokaryotic viperins produce a set of modified ribonucleotides",
                "notes": "Bernheim et al. support modified ribonucleotide production as a pVip output."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "Viperin\tViperin\t1\t1\tViperin__pVip",
                "notes": "The DefenseFinder rules table supports pVip as the required Viperin system profile."
              }
            ]
          },
          {
            "subject": "modified_ribonucleotide_production",
            "predicate": "enables",
            "predicate_id": "RO:0002327",
            "object": "t7_phage_transcription_inhibition",
            "description": "Prokaryotic viperin products can inhibit T7 phage polymerase-dependent transcription.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41586-020-2762-2",
                "snippet": "prokaryotic viperins protect against T7 phage infection by inhibiting viral polymerase-dependent transcription",
                "notes": "Bernheim et al. connect prokaryotic viperin activity to inhibition of T7 transcription."
              }
            ]
          },
          {
            "subject": "t7_phage_transcription_inhibition",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "viperin_system_trait",
            "description": "Inhibition of phage transcription is a source-backed antiviral output that realizes the Viperin system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41586-020-2762-2",
                "snippet": "prokaryotic viperins protect against T7 phage infection by inhibiting viral polymerase-dependent transcription",
                "notes": "Bernheim et al. support pVip-mediated protection from T7 phage infection."
              }
            ]
          },
          {
            "subject": "viperin_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Viperin system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41586-020-2762-2",
                "snippet": "Here we show that eukaryotic viperin originated from a clade of bacterial and archaeal proteins that protect against phage infection",
                "notes": "Bernheim et al. support Viperin as a prokaryotic phage-defense system."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "viperin-product-and-subtype-gap",
        "prompt": "Resolve Viperin nucleotide products, accessory genes, and phage-target breadth before minting narrower Viperin mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Bernheim et al. support prokaryotic viperins as phage-protective producers of modified ribonucleotides, and DefenseFinder models Viperin through the pVip profile, but Viperin-family loci need separate review before TraitMech asserts one universal antiviral nucleotide, polymerase target, or accessory-gene architecture.",
        "attaches_to": [
          "causal_graphs#viperin_modified_ribonucleotides_restrict_phage"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-19"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-19T03:43:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Viperin system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v140.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-19T03:58:00Z",
        "curator": "codex",
        "action": "EDIT",
        "changes": "Replaced the Viperin phage-defense-system subclass edge snippet with a Bernheim et al. phage-protection abstract span found by local adversarial review in issue #1037.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-19T04:06:03Z",
        "curator": "codex",
        "action": "EDIT",
        "changes": "Aligned the Viperin definition with the bacterial and archaeal prokaryotic scope identified in Claude review issue #1038.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000486",
    "label": "VP1796 system",
    "definition": "A phage defense system in which an organism possesses a VP1796-family locus represented by the DefenseFinder VP1796__VP1796 custom HMM profile and experimentally linked to reduced bacteriophage plaquing when the cloned Vibrio parahaemolyticus RIMD 2210633 vp1796 cassette is expressed from a VSV105 plasmid.",
    "definition_source": "DOI:10.1038/s41564-025-01927-7",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "VP1796",
        "synonym_type": "EXACT_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      },
      {
        "synonym_text": "Vp1796",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx"
      },
      {
        "synonym_text": "VP1796__VP1796",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/s41564-025-01927-7",
        "snippet": "Intrigued by this discovery, we cloned 57 integron gene cassettes and identified 9 previously unrecognized systems that mediate defence.",
        "notes": "Getz et al. identify nine previously unrecognized Vibrio parahaemolyticus integron cassettes as anti-phage defense systems."
      },
      {
        "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
        "snippet": "VP_RS08620\tVp1796\tY\tWP_005477844.1 \tHypothetical Protein",
        "notes": "Supplementary Table 8 lists VP_RS08620/Vp1796 as a cloned RIMD 2210633 integron cassette with protein accession WP_005477844.1."
      },
      {
        "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
        "snippet": "VSV105-vp1796\tVSV105 carrying gene vp1796 behind the lac promoter, cloned into KpnI by In-Fusion\tThis Study",
        "notes": "Supplementary Table 12 records the VSV105-vp1796 lac-expression plasmid used to express vp1796 behind the lac promoter."
      },
      {
        "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
        "snippet": "VP1796\tLL1\t0",
        "notes": "Supplementary Table 9 identifies the VP1796/LL1 phage-plating readout as a Fold Change value of 0."
      },
      {
        "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
        "snippet": "VP1796\tVp1\t3.33e-09",
        "notes": "Supplementary Table 9 identifies the VP1796/Vp1 phage-plating readout as a Fold Change value of 3.33e-09."
      },
      {
        "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM3_ESM.xlsx",
        "snippet": ">WP_005477844.1 hypothetical protein [Vibrio parahaemolyticus]",
        "notes": "Supplementary Data 1's VP1796 worksheet labels WP_005477844.1 from Vibrio parahaemolyticus as the PSI-BLAST query protein."
      },
      {
        "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM3_ESM.xlsx",
        "snippet": "Scientific Name\tQuery Cover\tE value\tPer. ident\tAcc. Len\tAccession  \nVibrio parahaemolyticus\t1\t6e-141\t100\t283\tWP_257878370.1",
        "notes": "Supplementary Data 1's VP1796 worksheet records a full-length 100% PSI-BLAST hit from the WP_005477844.1 query to the separate Vibrio parahaemolyticus homolog WP_257878370.1."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| VP1796 | 10\\.1038/s41564-025-01927-7 | Integrons are anti-phage defence libraries in Vibrio parahaemolyticus | ",
        "notes": "The pinned DefenseFinder article registry maps the VP1796 model namespace to the Getz et al. Vibrio parahaemolyticus integron-defense paper."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| VP1796__VP1796                                   |                                                  | VP1796                 | Custom                  | 50     |",
        "notes": "The pinned DefenseFinder HMM inventory records VP1796__VP1796 as a custom VP1796 profile."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "vp1796_locus_reduces_bacteriophage_plaquing",
        "title": "VP1796 loci reduce bacteriophage plaquing",
        "description": "Conservative system-level sketch linking VP1796-family locus possession to reduced bacteriophage plaquing without resolving VP1796 component function or molecular output.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures VP1796 as a RIMD 2210633 integron cassette with cloned phage-plating readouts, a PSI-BLAST homolog lead, one pinned DefenseFinder custom HMM-profile row, and no pinned DefenseFinder rule row. It does not assert native host breadth, exact profile-to-protein correspondence, molecular activity, phage trigger, substrate, complete homolog boundary, endogenous activity, or rule-level DefenseFinder detection criteria.",
        "nodes": [
          {
            "node_id": "vp1796_locus",
            "label": "VP1796 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A VP1796-like integron cassette locus represented in the pinned DefenseFinder HMM inventory by the VP1796__VP1796 custom profile."
          },
          {
            "node_id": "reduced_bacteriophage_plaquing",
            "label": "reduced bacteriophage plaquing",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced plaquing of bacteriophages in cells expressing cloned vp1796."
          },
          {
            "node_id": "vp1796_system_trait",
            "label": "VP1796 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000486",
            "description": "Possession of a genome-encoded VP1796 phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "vp1796_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "reduced_bacteriophage_plaquing",
            "description": "The cloned V. parahaemolyticus vp1796 integron cassette contributes to reduced bacteriophage plaquing in VSV105 plasmid-expression assays, and DefenseFinder represents the VP1796 family with one custom HMM profile.",
            "evidence": [
              {
                "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
                "snippet": "VP_RS08620\tVp1796\tY\tWP_005477844.1 \tHypothetical Protein",
                "notes": "Supplementary Table 8 lists VP_RS08620/Vp1796 as a cloned RIMD 2210633 integron cassette with protein accession WP_005477844.1."
              },
              {
                "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
                "snippet": "VSV105-vp1796\tVSV105 carrying gene vp1796 behind the lac promoter, cloned into KpnI by In-Fusion\tThis Study",
                "notes": "Supplementary Table 12 records the VSV105-vp1796 lac-expression plasmid used to express vp1796 behind the lac promoter."
              },
              {
                "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
                "snippet": "VP1796\tLL1\t0",
                "notes": "Supplementary Table 9 identifies the VP1796/LL1 phage-plating readout as a Fold Change value of 0."
              },
              {
                "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
                "snippet": "VP1796\tVp1\t3.33e-09",
                "notes": "Supplementary Table 9 identifies the VP1796/Vp1 phage-plating readout as a Fold Change value of 3.33e-09."
              },
              {
                "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM3_ESM.xlsx",
                "snippet": ">WP_005477844.1 hypothetical protein [Vibrio parahaemolyticus]",
                "notes": "Supplementary Data 1's VP1796 worksheet labels WP_005477844.1 from Vibrio parahaemolyticus as the PSI-BLAST query protein."
              },
              {
                "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM3_ESM.xlsx",
                "snippet": "Scientific Name\tQuery Cover\tE value\tPer. ident\tAcc. Len\tAccession  \nVibrio parahaemolyticus\t1\t6e-141\t100\t283\tWP_257878370.1",
                "notes": "Supplementary Data 1's VP1796 worksheet records a full-length 100% PSI-BLAST hit from the WP_005477844.1 query to the separate Vibrio parahaemolyticus homolog WP_257878370.1."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| VP1796__VP1796                                   |                                                  | VP1796                 | Custom                  | 50     |",
                "notes": "The pinned DefenseFinder HMM inventory records VP1796__VP1796 as a custom VP1796 profile."
              }
            ]
          },
          {
            "subject": "reduced_bacteriophage_plaquing",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "vp1796_system_trait",
            "description": "VP1796-mediated bacteriophage plaquing reduction realizes the VP1796 system trait.",
            "evidence": [
              {
                "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
                "snippet": "VP1796\tLL1\t0",
                "notes": "Supplementary Table 9 identifies the VP1796/LL1 phage-plating readout as a Fold Change value of 0."
              },
              {
                "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
                "snippet": "VP1796\tVp1\t3.33e-09",
                "notes": "Supplementary Table 9 identifies the VP1796/Vp1 phage-plating readout as a Fold Change value of 3.33e-09."
              }
            ]
          },
          {
            "subject": "vp1796_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "VP1796 system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-025-01927-7",
                "snippet": "Intrigued by this discovery, we cloned 57 integron gene cassettes and identified 9 previously unrecognized systems that mediate defence.",
                "notes": "Getz et al. identify nine previously unrecognized Vibrio parahaemolyticus integron cassettes as anti-phage defense systems."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| VP1796 | 10\\.1038/s41564-025-01927-7 | Integrons are anti-phage defence libraries in Vibrio parahaemolyticus | ",
                "notes": "The pinned DefenseFinder article registry maps the VP1796 model namespace to the Getz et al. Vibrio parahaemolyticus integron-defense paper."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "vp1796-defensefinder-model-gap",
        "prompt": "Resolve VP1796 native host breadth, exact single-component activity, profile-to-protein mapping, homolog boundary, full phage breadth, molecular output, and rule-level DefenseFinder criteria before minting narrower VP1796 mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Getz et al. support VP1796 as one of nine RIMD 2210633 integron-encoded cassettes whose cloned expression reduced phage plaquing, Supplementary Tables 8, 9, and 12 map VP1796 to VP_RS08620/Vp1796, WP_005477844.1, VSV105-vp1796, and phage-plating fold changes, and Supplementary Data 1 reports PSI-BLAST homologs. The pinned DefenseFinder HMM inventory records one VP1796 custom profile row. The pinned rules table has no VP1796 row, and the first-pass record does not resolve native host breadth, complete phage breadth, direct profile-to-protein correspondence, molecular output, or endogenous activity.",
        "evidence": [
          {
            "reference": "DOI:10.1038/s41564-025-01927-7",
            "snippet": "Intrigued by this discovery, we cloned 57 integron gene cassettes and identified 9 previously unrecognized systems that mediate defence.",
            "notes": "Getz et al. identify nine previously unrecognized Vibrio parahaemolyticus integron cassettes as anti-phage defense systems."
          },
          {
            "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
            "snippet": "VP_RS08620\tVp1796\tY\tWP_005477844.1 \tHypothetical Protein",
            "notes": "Supplementary Table 8 lists VP_RS08620/Vp1796 as a cloned RIMD 2210633 integron cassette with protein accession WP_005477844.1."
          },
          {
            "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
            "snippet": "VSV105-vp1796\tVSV105 carrying gene vp1796 behind the lac promoter, cloned into KpnI by In-Fusion\tThis Study",
            "notes": "Supplementary Table 12 records the VSV105-vp1796 lac-expression plasmid used to express vp1796 behind the lac promoter."
          },
          {
            "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
            "snippet": "VP1796\tLL1\t0",
            "notes": "Supplementary Table 9 identifies the VP1796/LL1 phage-plating readout as a Fold Change value of 0."
          },
          {
            "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM3_ESM.xlsx",
            "snippet": ">WP_005477844.1 hypothetical protein [Vibrio parahaemolyticus]",
            "notes": "Supplementary Data 1's VP1796 worksheet labels WP_005477844.1 from Vibrio parahaemolyticus as the PSI-BLAST query protein."
          },
          {
            "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM3_ESM.xlsx",
            "snippet": "Scientific Name\tQuery Cover\tE value\tPer. ident\tAcc. Len\tAccession  \nVibrio parahaemolyticus\t1\t6e-141\t100\t283\tWP_257878370.1",
            "notes": "Supplementary Data 1's VP1796 worksheet records a full-length 100% PSI-BLAST hit from the WP_005477844.1 query to the separate Vibrio parahaemolyticus homolog WP_257878370.1."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
            "snippet": "| VP1796 | 10\\.1038/s41564-025-01927-7 | Integrons are anti-phage defence libraries in Vibrio parahaemolyticus | ",
            "notes": "The pinned DefenseFinder article registry maps the VP1796 model namespace to the Getz et al. Vibrio parahaemolyticus integron-defense paper."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| VP1796__VP1796                                   |                                                  | VP1796                 | Custom                  | 50     |",
            "notes": "The pinned DefenseFinder HMM inventory records VP1796__VP1796 as a custom VP1796 profile."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "The pinned DefenseFinder rules table does not list VP1796, leaving rule-level detection criteria unresolved."
          }
        ],
        "attaches_to": [
          "causal_graphs#vp1796_locus_reduces_bacteriophage_plaquing"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-30"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-30T07:47:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted VP1796 system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact same-scope live TraitMech, METPO, history, or prior proposal record; kept the graph at cloned integron-cassette level because molecular output, native activity, and rule rows remain unresolved; proposals/metpo_traitmech_v363 reserves the replacement placeholder.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-30T07:47:01Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed VP1796 system canonical_examples and left them empty because Getz et al. directly support cloned VP1796 VSV105-plasmid assays, PSI-BLAST homologs, and a DefenseFinder VP1796 model, but not a direct named native microbial isolate exemplar with experimentally verified endogenous VP1796 activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000487",
    "label": "VP1817 system",
    "definition": "A phage defense system in which an organism possesses a VP1817-family locus represented by the DefenseFinder VP1817__VP1817 custom HMM profile and experimentally linked to reduced bacteriophage plaquing when the cloned Vibrio parahaemolyticus RIMD 2210633 vp1817 cassette is expressed from a VSV105 plasmid.",
    "definition_source": "DOI:10.1038/s41564-025-01927-7",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "VP1817",
        "synonym_type": "EXACT_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      },
      {
        "synonym_text": "VP1817__VP1817",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/s41564-025-01927-7",
        "snippet": "Intrigued by this discovery, we cloned 57 integron gene cassettes and identified 9 previously unrecognized systems that mediate defence.",
        "notes": "Getz et al. identify nine previously unrecognized Vibrio parahaemolyticus integron cassettes as anti-phage defense systems."
      },
      {
        "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
        "snippet": "VP_RS08765\tVP1817\tY\tWP_024699215.1\tHypothetical Protein",
        "notes": "Supplementary Table 8 lists VP_RS08765/VP1817 as a cloned RIMD 2210633 integron cassette with protein accession WP_024699215.1."
      },
      {
        "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
        "snippet": "VSV105-vp1817\tVSV105 carrying gene vp1817 behind the lac promoter, cloned into KpnI by In-Fusion\tThis Study",
        "notes": "Supplementary Table 12 records the VSV105-vp1817 lac-expression plasmid used to express vp1817 behind the lac promoter."
      },
      {
        "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
        "snippet": "VP1817\tBas27\t0.01",
        "notes": "Supplementary Table 9 identifies the VP1817/Bas27 phage-plating readout as a Fold Change value of 0.01."
      },
      {
        "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
        "snippet": "VP1817\tBas37\t0.03125",
        "notes": "Supplementary Table 9 identifies the VP1817/Bas37 phage-plating readout as a Fold Change value of 0.03125."
      },
      {
        "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM3_ESM.xlsx",
        "snippet": ">BAC60080.1 hypothetical protein [Vibrio parahaemolyticus RIMD 2210633]",
        "notes": "Supplementary Data 1's VP1817 worksheet labels BAC60080.1 from Vibrio parahaemolyticus RIMD 2210633 as the PSI-BLAST query protein."
      },
      {
        "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM3_ESM.xlsx",
        "snippet": "Scientific Name\tQuery Cover\tE value\tPer. ident\tAccession  \nVibrio parahaemolyticus\t1\t8e-56\t100\tARC19819.1",
        "notes": "Supplementary Data 1's VP1817 worksheet records a full-length 100% PSI-BLAST hit from the BAC60080.1 query to the separate Vibrio parahaemolyticus homolog ARC19819.1."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| VP1817 | 10\\.1038/s41564-025-01927-7 | Integrons are anti-phage defence libraries in Vibrio parahaemolyticus | ",
        "notes": "The pinned DefenseFinder article registry maps the VP1817 model namespace to the Getz et al. Vibrio parahaemolyticus integron-defense paper."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| VP1817__VP1817                                   |                                                  | VP1817                 | Custom                  | 30     |",
        "notes": "The pinned DefenseFinder HMM inventory records VP1817__VP1817 as a custom VP1817 profile."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "vp1817_locus_reduces_bacteriophage_plaquing",
        "title": "VP1817 loci reduce bacteriophage plaquing",
        "description": "Conservative system-level sketch linking VP1817-family locus possession to reduced bacteriophage plaquing without resolving VP1817 component function or molecular output.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures VP1817 as a RIMD 2210633 integron cassette with cloned phage-plating readouts, a PSI-BLAST homolog lead, one pinned DefenseFinder custom HMM-profile row, and no pinned DefenseFinder rule row. It does not assert native host breadth, exact profile-to-protein correspondence, molecular activity, phage trigger, substrate, complete homolog boundary, endogenous activity, or rule-level DefenseFinder detection criteria.",
        "nodes": [
          {
            "node_id": "vp1817_locus",
            "label": "VP1817 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A VP1817-like integron cassette locus represented in the pinned DefenseFinder HMM inventory by the VP1817__VP1817 custom profile."
          },
          {
            "node_id": "reduced_bacteriophage_plaquing",
            "label": "reduced bacteriophage plaquing",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced plaquing of bacteriophages in cells expressing cloned vp1817."
          },
          {
            "node_id": "vp1817_system_trait",
            "label": "VP1817 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000487",
            "description": "Possession of a genome-encoded VP1817 phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "vp1817_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "reduced_bacteriophage_plaquing",
            "description": "The cloned V. parahaemolyticus vp1817 integron cassette contributes to reduced bacteriophage plaquing in VSV105 plasmid-expression assays, and DefenseFinder represents the VP1817 family with one custom HMM profile.",
            "evidence": [
              {
                "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
                "snippet": "VP_RS08765\tVP1817\tY\tWP_024699215.1\tHypothetical Protein",
                "notes": "Supplementary Table 8 lists VP_RS08765/VP1817 as a cloned RIMD 2210633 integron cassette with protein accession WP_024699215.1."
              },
              {
                "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
                "snippet": "VSV105-vp1817\tVSV105 carrying gene vp1817 behind the lac promoter, cloned into KpnI by In-Fusion\tThis Study",
                "notes": "Supplementary Table 12 records the VSV105-vp1817 lac-expression plasmid used to express vp1817 behind the lac promoter."
              },
              {
                "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
                "snippet": "VP1817\tBas27\t0.01",
                "notes": "Supplementary Table 9 identifies the VP1817/Bas27 phage-plating readout as a Fold Change value of 0.01."
              },
              {
                "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
                "snippet": "VP1817\tBas37\t0.03125",
                "notes": "Supplementary Table 9 identifies the VP1817/Bas37 phage-plating readout as a Fold Change value of 0.03125."
              },
              {
                "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM3_ESM.xlsx",
                "snippet": ">BAC60080.1 hypothetical protein [Vibrio parahaemolyticus RIMD 2210633]",
                "notes": "Supplementary Data 1's VP1817 worksheet labels BAC60080.1 from Vibrio parahaemolyticus RIMD 2210633 as the PSI-BLAST query protein."
              },
              {
                "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM3_ESM.xlsx",
                "snippet": "Scientific Name\tQuery Cover\tE value\tPer. ident\tAccession  \nVibrio parahaemolyticus\t1\t8e-56\t100\tARC19819.1",
                "notes": "Supplementary Data 1's VP1817 worksheet records a full-length 100% PSI-BLAST hit from the BAC60080.1 query to the separate Vibrio parahaemolyticus homolog ARC19819.1."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| VP1817__VP1817                                   |                                                  | VP1817                 | Custom                  | 30     |",
                "notes": "The pinned DefenseFinder HMM inventory records VP1817__VP1817 as a custom VP1817 profile."
              }
            ]
          },
          {
            "subject": "reduced_bacteriophage_plaquing",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "vp1817_system_trait",
            "description": "VP1817-mediated bacteriophage plaquing reduction realizes the VP1817 system trait.",
            "evidence": [
              {
                "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
                "snippet": "VP1817\tBas27\t0.01",
                "notes": "Supplementary Table 9 identifies the VP1817/Bas27 phage-plating readout as a Fold Change value of 0.01."
              },
              {
                "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
                "snippet": "VP1817\tBas37\t0.03125",
                "notes": "Supplementary Table 9 identifies the VP1817/Bas37 phage-plating readout as a Fold Change value of 0.03125."
              }
            ]
          },
          {
            "subject": "vp1817_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "VP1817 system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-025-01927-7",
                "snippet": "Intrigued by this discovery, we cloned 57 integron gene cassettes and identified 9 previously unrecognized systems that mediate defence.",
                "notes": "Getz et al. identify nine previously unrecognized Vibrio parahaemolyticus integron cassettes as anti-phage defense systems."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| VP1817 | 10\\.1038/s41564-025-01927-7 | Integrons are anti-phage defence libraries in Vibrio parahaemolyticus | ",
                "notes": "The pinned DefenseFinder article registry maps the VP1817 model namespace to the Getz et al. Vibrio parahaemolyticus integron-defense paper."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "vp1817-defensefinder-model-gap",
        "prompt": "Resolve VP1817 native host breadth, exact single-component activity, profile-to-protein mapping, homolog boundary, full phage breadth, molecular output, and rule-level DefenseFinder criteria before minting narrower VP1817 mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Getz et al. support VP1817 as one of nine RIMD 2210633 integron-encoded cassettes whose cloned expression reduced phage plaquing, Supplementary Tables 8, 9, and 12 map VP1817 to VP_RS08765/VP1817, WP_024699215.1, VSV105-vp1817, and phage-plating fold changes, and Supplementary Data 1 reports PSI-BLAST homologs. The pinned DefenseFinder HMM inventory records one VP1817 custom profile row. The pinned rules table has no VP1817 row, and the first-pass record does not resolve native host breadth, complete phage breadth, direct profile-to-protein correspondence, molecular output, or endogenous activity.",
        "evidence": [
          {
            "reference": "DOI:10.1038/s41564-025-01927-7",
            "snippet": "Intrigued by this discovery, we cloned 57 integron gene cassettes and identified 9 previously unrecognized systems that mediate defence.",
            "notes": "Getz et al. identify nine previously unrecognized Vibrio parahaemolyticus integron cassettes as anti-phage defense systems."
          },
          {
            "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
            "snippet": "VP_RS08765\tVP1817\tY\tWP_024699215.1\tHypothetical Protein",
            "notes": "Supplementary Table 8 lists VP_RS08765/VP1817 as a cloned RIMD 2210633 integron cassette with protein accession WP_024699215.1."
          },
          {
            "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
            "snippet": "VSV105-vp1817\tVSV105 carrying gene vp1817 behind the lac promoter, cloned into KpnI by In-Fusion\tThis Study",
            "notes": "Supplementary Table 12 records the VSV105-vp1817 lac-expression plasmid used to express vp1817 behind the lac promoter."
          },
          {
            "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
            "snippet": "VP1817\tBas27\t0.01",
            "notes": "Supplementary Table 9 identifies the VP1817/Bas27 phage-plating readout as a Fold Change value of 0.01."
          },
          {
            "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
            "snippet": "VP1817\tBas37\t0.03125",
            "notes": "Supplementary Table 9 identifies the VP1817/Bas37 phage-plating readout as a Fold Change value of 0.03125."
          },
          {
            "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM3_ESM.xlsx",
            "snippet": ">BAC60080.1 hypothetical protein [Vibrio parahaemolyticus RIMD 2210633]",
            "notes": "Supplementary Data 1's VP1817 worksheet labels BAC60080.1 from Vibrio parahaemolyticus RIMD 2210633 as the PSI-BLAST query protein."
          },
          {
            "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM3_ESM.xlsx",
            "snippet": "Scientific Name\tQuery Cover\tE value\tPer. ident\tAccession  \nVibrio parahaemolyticus\t1\t8e-56\t100\tARC19819.1",
            "notes": "Supplementary Data 1's VP1817 worksheet records a full-length 100% PSI-BLAST hit from the BAC60080.1 query to the separate Vibrio parahaemolyticus homolog ARC19819.1."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
            "snippet": "| VP1817 | 10\\.1038/s41564-025-01927-7 | Integrons are anti-phage defence libraries in Vibrio parahaemolyticus | ",
            "notes": "The pinned DefenseFinder article registry maps the VP1817 model namespace to the Getz et al. Vibrio parahaemolyticus integron-defense paper."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| VP1817__VP1817                                   |                                                  | VP1817                 | Custom                  | 30     |",
            "notes": "The pinned DefenseFinder HMM inventory records VP1817__VP1817 as a custom VP1817 profile."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "The pinned DefenseFinder rules table does not list VP1817, leaving rule-level detection criteria unresolved."
          }
        ],
        "attaches_to": [
          "causal_graphs#vp1817_locus_reduces_bacteriophage_plaquing"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-30"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-30T08:41:53Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted VP1817 system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact same-scope live TraitMech, METPO, history, or prior proposal record; kept the graph at cloned integron-cassette level because molecular output, native activity, and rule rows remain unresolved; proposals/metpo_traitmech_v364 reserves the replacement placeholder.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-30T08:41:54Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed VP1817 system canonical_examples and left them empty because Getz et al. directly support cloned VP1817 VSV105-plasmid assays, PSI-BLAST homologs, and a DefenseFinder VP1817 model, but not a direct named native microbial isolate exemplar with experimentally verified endogenous VP1817 activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000485",
    "label": "VP1823 system",
    "definition": "A phage defense system in which an organism possesses a VP1823-family locus represented by the DefenseFinder VP1823__VP1823 custom HMM profile and experimentally linked to reduced bacteriophage plaquing when the cloned Vibrio parahaemolyticus RIMD 2210633 vp1823 cassette is expressed from a VSV105 plasmid.",
    "definition_source": "DOI:10.1038/s41564-025-01927-7",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "VP1823",
        "synonym_type": "EXACT_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      },
      {
        "synonym_text": "VP1823__VP1823",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/s41564-025-01927-7",
        "snippet": "Intrigued by this discovery, we cloned 57 integron gene cassettes and identified 9 previously unrecognized systems that mediate defence.",
        "notes": "Getz et al. identify nine previously unrecognized Vibrio parahaemolyticus integron cassettes as anti-phage defense systems."
      },
      {
        "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
        "snippet": "VP_RS08795\tVP1823\tY\tWP_079749463.1 \tHypothetical Protein",
        "notes": "Supplementary Table 8 lists VP_RS08795/VP1823 as a cloned RIMD 2210633 integron cassette with protein accession WP_079749463.1."
      },
      {
        "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
        "snippet": "VSV105-vp1823\tVSV105 carrying gene vp1823 behind the lac promoter, cloned into KpnI by In-Fusion\tThis Study",
        "notes": "Supplementary Table 12 records the VSV105-vp1823 lac-expression plasmid used to express vp1823 behind the lac promoter."
      },
      {
        "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
        "snippet": "VP1823\tBas30\t0.0003",
        "notes": "Supplementary Table 9 identifies the VP1823/Bas30 phage-plating readout as a Fold Change value of 0.0003."
      },
      {
        "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
        "snippet": "VP1823\tT4\t1e-05",
        "notes": "Supplementary Table 9 identifies the VP1823/T4 phage-plating readout as a Fold Change value of 1e-05."
      },
      {
        "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM3_ESM.xlsx",
        "snippet": ">BAC60086.1 hypothetical protein [Vibrio parahaemolyticus RIMD 2210633]",
        "notes": "Supplementary Data 1's VP1823 worksheet labels BAC60086.1 from Vibrio parahaemolyticus RIMD 2210633 as the PSI-BLAST query protein."
      },
      {
        "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM3_ESM.xlsx",
        "snippet": "Scientific Name\tQuery Cover\tE value\tPer. ident\tAccession  \nVibrio parahaemolyticus\t1\t2e-166\t100\tWP_237666972.1",
        "notes": "Supplementary Data 1's VP1823 worksheet records a full-length 100% PSI-BLAST hit from the BAC60086.1 query to the separate Vibrio parahaemolyticus homolog WP_237666972.1."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| VP1823 | 10\\.1038/s41564-025-01927-7 | Integrons are anti-phage defence libraries in Vibrio parahaemolyticus | ",
        "notes": "The pinned DefenseFinder article registry maps the VP1823 model namespace to the Getz et al. Vibrio parahaemolyticus integron-defense paper."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| VP1823__VP1823                                   |                                                  | VP1823                 | Custom                  | 200    |",
        "notes": "The pinned DefenseFinder HMM inventory records VP1823__VP1823 as a custom VP1823 profile."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "vp1823_locus_reduces_bacteriophage_plaquing",
        "title": "VP1823 loci reduce bacteriophage plaquing",
        "description": "Conservative system-level sketch linking VP1823-family locus possession to reduced bacteriophage plaquing without resolving VP1823 component function or molecular output.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures VP1823 as a RIMD 2210633 integron cassette with cloned phage-plating readouts, a PSI-BLAST homolog lead, one pinned DefenseFinder custom HMM-profile row, and no pinned DefenseFinder rule row. It does not assert native host breadth, exact profile-to-protein correspondence, molecular activity, phage trigger, substrate, complete homolog boundary, endogenous activity, or rule-level DefenseFinder detection criteria.",
        "nodes": [
          {
            "node_id": "vp1823_locus",
            "label": "VP1823 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A VP1823-like integron cassette locus represented in the pinned DefenseFinder HMM inventory by the VP1823__VP1823 custom profile."
          },
          {
            "node_id": "reduced_bacteriophage_plaquing",
            "label": "reduced bacteriophage plaquing",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced plaquing of bacteriophages in cells expressing cloned vp1823."
          },
          {
            "node_id": "vp1823_system_trait",
            "label": "VP1823 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000485",
            "description": "Possession of a genome-encoded VP1823 phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "vp1823_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "reduced_bacteriophage_plaquing",
            "description": "The cloned V. parahaemolyticus vp1823 integron cassette contributes to reduced bacteriophage plaquing in VSV105 plasmid-expression assays, and DefenseFinder represents the VP1823 family with one custom HMM profile.",
            "evidence": [
              {
                "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
                "snippet": "VP_RS08795\tVP1823\tY\tWP_079749463.1 \tHypothetical Protein",
                "notes": "Supplementary Table 8 lists VP_RS08795/VP1823 as a cloned RIMD 2210633 integron cassette with protein accession WP_079749463.1."
              },
              {
                "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
                "snippet": "VSV105-vp1823\tVSV105 carrying gene vp1823 behind the lac promoter, cloned into KpnI by In-Fusion\tThis Study",
                "notes": "Supplementary Table 12 records the VSV105-vp1823 lac-expression plasmid used to express vp1823 behind the lac promoter."
              },
              {
                "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
                "snippet": "VP1823\tBas30\t0.0003",
                "notes": "Supplementary Table 9 identifies the VP1823/Bas30 phage-plating readout as a Fold Change value of 0.0003."
              },
              {
                "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
                "snippet": "VP1823\tT4\t1e-05",
                "notes": "Supplementary Table 9 identifies the VP1823/T4 phage-plating readout as a Fold Change value of 1e-05."
              },
              {
                "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM3_ESM.xlsx",
                "snippet": ">BAC60086.1 hypothetical protein [Vibrio parahaemolyticus RIMD 2210633]",
                "notes": "Supplementary Data 1's VP1823 worksheet labels BAC60086.1 from Vibrio parahaemolyticus RIMD 2210633 as the PSI-BLAST query protein."
              },
              {
                "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM3_ESM.xlsx",
                "snippet": "Scientific Name\tQuery Cover\tE value\tPer. ident\tAccession  \nVibrio parahaemolyticus\t1\t2e-166\t100\tWP_237666972.1",
                "notes": "Supplementary Data 1's VP1823 worksheet records a full-length 100% PSI-BLAST hit from the BAC60086.1 query to the separate Vibrio parahaemolyticus homolog WP_237666972.1."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| VP1823__VP1823                                   |                                                  | VP1823                 | Custom                  | 200    |",
                "notes": "The pinned DefenseFinder HMM inventory records VP1823__VP1823 as a custom VP1823 profile."
              }
            ]
          },
          {
            "subject": "reduced_bacteriophage_plaquing",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "vp1823_system_trait",
            "description": "VP1823-mediated bacteriophage plaquing reduction realizes the VP1823 system trait.",
            "evidence": [
              {
                "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
                "snippet": "VP1823\tBas30\t0.0003",
                "notes": "Supplementary Table 9 identifies the VP1823/Bas30 phage-plating readout as a Fold Change value of 0.0003."
              },
              {
                "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
                "snippet": "VP1823\tT4\t1e-05",
                "notes": "Supplementary Table 9 identifies the VP1823/T4 phage-plating readout as a Fold Change value of 1e-05."
              }
            ]
          },
          {
            "subject": "vp1823_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "VP1823 system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-025-01927-7",
                "snippet": "Intrigued by this discovery, we cloned 57 integron gene cassettes and identified 9 previously unrecognized systems that mediate defence.",
                "notes": "Getz et al. identify nine previously unrecognized Vibrio parahaemolyticus integron cassettes as anti-phage defense systems."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| VP1823 | 10\\.1038/s41564-025-01927-7 | Integrons are anti-phage defence libraries in Vibrio parahaemolyticus | ",
                "notes": "The pinned DefenseFinder article registry maps the VP1823 model namespace to the Getz et al. Vibrio parahaemolyticus integron-defense paper."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "vp1823-defensefinder-model-gap",
        "prompt": "Resolve VP1823 native host breadth, exact single-component activity, profile-to-protein mapping, homolog boundary, full phage breadth, molecular output, and rule-level DefenseFinder criteria before minting narrower VP1823 mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Getz et al. support VP1823 as one of nine RIMD 2210633 integron-encoded cassettes whose cloned expression reduced phage plaquing, Supplementary Tables 8, 9, and 12 map VP1823 to VP_RS08795/VP1823, WP_079749463.1, VSV105-vp1823, and phage-plating fold changes, and Supplementary Data 1 reports PSI-BLAST homologs. The pinned DefenseFinder HMM inventory records one VP1823 custom profile row. The pinned rules table has no VP1823 row, and the first-pass record does not resolve native host breadth, complete phage breadth, direct profile-to-protein correspondence, molecular output, or endogenous activity.",
        "evidence": [
          {
            "reference": "DOI:10.1038/s41564-025-01927-7",
            "snippet": "Intrigued by this discovery, we cloned 57 integron gene cassettes and identified 9 previously unrecognized systems that mediate defence.",
            "notes": "Getz et al. identify nine previously unrecognized Vibrio parahaemolyticus integron cassettes as anti-phage defense systems."
          },
          {
            "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
            "snippet": "VP_RS08795\tVP1823\tY\tWP_079749463.1 \tHypothetical Protein",
            "notes": "Supplementary Table 8 lists VP_RS08795/VP1823 as a cloned RIMD 2210633 integron cassette with protein accession WP_079749463.1."
          },
          {
            "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
            "snippet": "VSV105-vp1823\tVSV105 carrying gene vp1823 behind the lac promoter, cloned into KpnI by In-Fusion\tThis Study",
            "notes": "Supplementary Table 12 records the VSV105-vp1823 lac-expression plasmid used to express vp1823 behind the lac promoter."
          },
          {
            "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
            "snippet": "VP1823\tBas30\t0.0003",
            "notes": "Supplementary Table 9 identifies the VP1823/Bas30 phage-plating readout as a Fold Change value of 0.0003."
          },
          {
            "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM3_ESM.xlsx",
            "snippet": ">BAC60086.1 hypothetical protein [Vibrio parahaemolyticus RIMD 2210633]",
            "notes": "Supplementary Data 1's VP1823 worksheet labels BAC60086.1 from Vibrio parahaemolyticus RIMD 2210633 as the PSI-BLAST query protein."
          },
          {
            "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM3_ESM.xlsx",
            "snippet": "Scientific Name\tQuery Cover\tE value\tPer. ident\tAccession  \nVibrio parahaemolyticus\t1\t2e-166\t100\tWP_237666972.1",
            "notes": "Supplementary Data 1's VP1823 worksheet records a full-length 100% PSI-BLAST hit from the BAC60086.1 query to the separate Vibrio parahaemolyticus homolog WP_237666972.1."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
            "snippet": "| VP1823 | 10\\.1038/s41564-025-01927-7 | Integrons are anti-phage defence libraries in Vibrio parahaemolyticus | ",
            "notes": "The pinned DefenseFinder article registry maps the VP1823 model namespace to the Getz et al. Vibrio parahaemolyticus integron-defense paper."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| VP1823__VP1823                                   |                                                  | VP1823                 | Custom                  | 200    |",
            "notes": "The pinned DefenseFinder HMM inventory records VP1823__VP1823 as a custom VP1823 profile."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "The pinned DefenseFinder rules table does not list VP1823, leaving rule-level detection criteria unresolved."
          }
        ],
        "attaches_to": [
          "causal_graphs#vp1823_locus_reduces_bacteriophage_plaquing"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-30"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-30T06:58:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted VP1823 system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact same-scope live TraitMech, METPO, history, or prior proposal record; kept the graph at cloned integron-cassette level because molecular output, native activity, and rule rows remain unresolved; proposals/metpo_traitmech_v362 reserves the replacement placeholder.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-30T06:58:01Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed VP1823 system canonical_examples and left them empty because Getz et al. directly support cloned VP1823 VSV105-plasmid assays, PSI-BLAST homologs, and a DefenseFinder VP1823 model, but not a direct named native microbial isolate exemplar with experimentally verified endogenous VP1823 activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000488",
    "label": "VP1826 system",
    "definition": "A phage defense system in which an organism possesses a VP1826-family locus represented by the DefenseFinder VP1826__VP1826 custom HMM profile and experimentally linked to reduced bacteriophage plaquing when the cloned Vibrio parahaemolyticus RIMD 2210633 vp1826 cassette is expressed from a VSV105 plasmid.",
    "definition_source": "DOI:10.1038/s41564-025-01927-7",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "VP1826",
        "synonym_type": "EXACT_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      },
      {
        "synonym_text": "Vp1826",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx"
      },
      {
        "synonym_text": "VP1826__VP1826",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/s41564-025-01927-7",
        "snippet": "Intrigued by this discovery, we cloned 57 integron gene cassettes and identified 9 previously unrecognized systems that mediate defence.",
        "notes": "Getz et al. identify nine previously unrecognized Vibrio parahaemolyticus integron cassettes as anti-phage defense systems."
      },
      {
        "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
        "snippet": "VP_RS08820\tVp1826\tY\tWP_005464673.1\tphospholipase D-like domain-containing protein",
        "notes": "Supplementary Table 8 lists VP_RS08820/Vp1826 as a cloned RIMD 2210633 integron cassette with protein accession WP_005464673.1."
      },
      {
        "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
        "snippet": "VSV105-vp1826\tVSV105 carrying gene vp1826 behind the lac promoter, cloned into KpnI by In-Fusion\tThis Study",
        "notes": "Supplementary Table 12 records the VSV105-vp1826 lac-expression plasmid used to express vp1826 behind the lac promoter."
      },
      {
        "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
        "snippet": "VP1826\tBas4\t0.02",
        "notes": "Supplementary Table 9 identifies the VP1826/Bas4 phage-plating readout as a Fold Change value of 0.02."
      },
      {
        "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
        "snippet": "VP1826\tBas6\t0.18",
        "notes": "Supplementary Table 9 identifies the VP1826/Bas6 phage-plating readout as a Fold Change value of 0.18."
      },
      {
        "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
        "snippet": "VP1826\tBas9\t2.5e-06",
        "notes": "Supplementary Table 9 identifies the VP1826/Bas9 phage-plating readout as a Fold Change value of 2.5e-06."
      },
      {
        "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM3_ESM.xlsx",
        "snippet": ">BAC60089.1 hypothetical protein [Vibrio parahaemolyticus RIMD 2210633]",
        "notes": "Supplementary Data 1's VP1826 worksheet labels BAC60089.1 from Vibrio parahaemolyticus RIMD 2210633 as the PSI-BLAST query protein."
      },
      {
        "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM3_ESM.xlsx",
        "snippet": "Scientific Name\tQuery Cover\tE value\tPer. ident\tAccession  \nVibrio parahaemolyticus\t1\t9e-157\t100\tWP_005464673.1",
        "notes": "Supplementary Data 1's VP1826 worksheet records a full-length 100% PSI-BLAST hit from the BAC60089.1 query to WP_005464673.1."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| VP1826 | 10\\.1038/s41564-025-01927-7 | Integrons are anti-phage defence libraries in Vibrio parahaemolyticus | ",
        "notes": "The pinned DefenseFinder article registry maps the VP1826 model namespace to the Getz et al. Vibrio parahaemolyticus integron-defense paper."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| VP1826__VP1826                                   |                                                  | VP1826                 | Custom                  | 175    |",
        "notes": "The pinned DefenseFinder HMM inventory records VP1826__VP1826 as a custom VP1826 profile."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "vp1826_locus_reduces_bacteriophage_plaquing",
        "title": "VP1826 loci reduce bacteriophage plaquing",
        "description": "Conservative system-level sketch linking VP1826-family locus possession to reduced bacteriophage plaquing without resolving VP1826 component function or molecular output.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures VP1826 as a RIMD 2210633 integron cassette with cloned phage-plating readouts, a PSI-BLAST homolog lead, one pinned DefenseFinder custom HMM-profile row, and no pinned DefenseFinder rule row. It does not assert native host breadth, exact profile-to-protein correspondence, molecular activity, phage trigger, substrate, complete homolog boundary, endogenous activity, or rule-level DefenseFinder detection criteria.",
        "nodes": [
          {
            "node_id": "vp1826_locus",
            "label": "VP1826 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A VP1826-like integron cassette locus represented in the pinned DefenseFinder HMM inventory by the VP1826__VP1826 custom profile."
          },
          {
            "node_id": "reduced_bacteriophage_plaquing",
            "label": "reduced bacteriophage plaquing",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced plaquing of bacteriophages in cells expressing cloned vp1826."
          },
          {
            "node_id": "vp1826_system_trait",
            "label": "VP1826 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000488",
            "description": "Possession of a genome-encoded VP1826 phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "vp1826_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "reduced_bacteriophage_plaquing",
            "description": "The cloned V. parahaemolyticus vp1826 integron cassette contributes to reduced bacteriophage plaquing in VSV105 plasmid-expression assays, and DefenseFinder represents the VP1826 family with one custom HMM profile.",
            "evidence": [
              {
                "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
                "snippet": "VP_RS08820\tVp1826\tY\tWP_005464673.1\tphospholipase D-like domain-containing protein",
                "notes": "Supplementary Table 8 lists VP_RS08820/Vp1826 as a cloned RIMD 2210633 integron cassette with protein accession WP_005464673.1."
              },
              {
                "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
                "snippet": "VSV105-vp1826\tVSV105 carrying gene vp1826 behind the lac promoter, cloned into KpnI by In-Fusion\tThis Study",
                "notes": "Supplementary Table 12 records the VSV105-vp1826 lac-expression plasmid used to express vp1826 behind the lac promoter."
              },
              {
                "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
                "snippet": "VP1826\tBas4\t0.02",
                "notes": "Supplementary Table 9 identifies the VP1826/Bas4 phage-plating readout as a Fold Change value of 0.02."
              },
              {
                "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
                "snippet": "VP1826\tBas6\t0.18",
                "notes": "Supplementary Table 9 identifies the VP1826/Bas6 phage-plating readout as a Fold Change value of 0.18."
              },
              {
                "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
                "snippet": "VP1826\tBas9\t2.5e-06",
                "notes": "Supplementary Table 9 identifies the VP1826/Bas9 phage-plating readout as a Fold Change value of 2.5e-06."
              },
              {
                "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM3_ESM.xlsx",
                "snippet": ">BAC60089.1 hypothetical protein [Vibrio parahaemolyticus RIMD 2210633]",
                "notes": "Supplementary Data 1's VP1826 worksheet labels BAC60089.1 from Vibrio parahaemolyticus RIMD 2210633 as the PSI-BLAST query protein."
              },
              {
                "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM3_ESM.xlsx",
                "snippet": "Scientific Name\tQuery Cover\tE value\tPer. ident\tAccession  \nVibrio parahaemolyticus\t1\t9e-157\t100\tWP_005464673.1",
                "notes": "Supplementary Data 1's VP1826 worksheet records a full-length 100% PSI-BLAST hit from the BAC60089.1 query to WP_005464673.1."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| VP1826__VP1826                                   |                                                  | VP1826                 | Custom                  | 175    |",
                "notes": "The pinned DefenseFinder HMM inventory records VP1826__VP1826 as a custom VP1826 profile."
              }
            ]
          },
          {
            "subject": "reduced_bacteriophage_plaquing",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "vp1826_system_trait",
            "description": "VP1826-mediated bacteriophage plaquing reduction realizes the VP1826 system trait.",
            "evidence": [
              {
                "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
                "snippet": "VP1826\tBas4\t0.02",
                "notes": "Supplementary Table 9 identifies the VP1826/Bas4 phage-plating readout as a Fold Change value of 0.02."
              },
              {
                "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
                "snippet": "VP1826\tBas6\t0.18",
                "notes": "Supplementary Table 9 identifies the VP1826/Bas6 phage-plating readout as a Fold Change value of 0.18."
              },
              {
                "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
                "snippet": "VP1826\tBas9\t2.5e-06",
                "notes": "Supplementary Table 9 identifies the VP1826/Bas9 phage-plating readout as a Fold Change value of 2.5e-06."
              }
            ]
          },
          {
            "subject": "vp1826_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "VP1826 system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-025-01927-7",
                "snippet": "Intrigued by this discovery, we cloned 57 integron gene cassettes and identified 9 previously unrecognized systems that mediate defence.",
                "notes": "Getz et al. identify nine previously unrecognized Vibrio parahaemolyticus integron cassettes as anti-phage defense systems."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| VP1826 | 10\\.1038/s41564-025-01927-7 | Integrons are anti-phage defence libraries in Vibrio parahaemolyticus | ",
                "notes": "The pinned DefenseFinder article registry maps the VP1826 model namespace to the Getz et al. Vibrio parahaemolyticus integron-defense paper."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "vp1826-defensefinder-model-gap",
        "prompt": "Resolve VP1826 native host breadth, exact single-component activity, profile-to-protein mapping, homolog boundary, full phage breadth, molecular output, and rule-level DefenseFinder criteria before minting narrower VP1826 mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Getz et al. support VP1826 as one of nine RIMD 2210633 integron-encoded cassettes whose cloned expression reduced phage plaquing, Supplementary Tables 8, 9, and 12 map VP1826 to VP_RS08820/Vp1826, WP_005464673.1, VSV105-vp1826, and phage-plating fold changes, and Supplementary Data 1 reports PSI-BLAST homologs. The pinned DefenseFinder HMM inventory records one VP1826 custom profile row. The pinned rules table has no VP1826 row, and the first-pass record does not resolve native host breadth, complete phage breadth, direct profile-to-protein correspondence, molecular output, or endogenous activity.",
        "evidence": [
          {
            "reference": "DOI:10.1038/s41564-025-01927-7",
            "snippet": "Intrigued by this discovery, we cloned 57 integron gene cassettes and identified 9 previously unrecognized systems that mediate defence.",
            "notes": "Getz et al. identify nine previously unrecognized Vibrio parahaemolyticus integron cassettes as anti-phage defense systems."
          },
          {
            "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
            "snippet": "VP_RS08820\tVp1826\tY\tWP_005464673.1\tphospholipase D-like domain-containing protein",
            "notes": "Supplementary Table 8 lists VP_RS08820/Vp1826 as a cloned RIMD 2210633 integron cassette with protein accession WP_005464673.1."
          },
          {
            "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
            "snippet": "VSV105-vp1826\tVSV105 carrying gene vp1826 behind the lac promoter, cloned into KpnI by In-Fusion\tThis Study",
            "notes": "Supplementary Table 12 records the VSV105-vp1826 lac-expression plasmid used to express vp1826 behind the lac promoter."
          },
          {
            "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
            "snippet": "VP1826\tBas4\t0.02",
            "notes": "Supplementary Table 9 identifies the VP1826/Bas4 phage-plating readout as a Fold Change value of 0.02."
          },
          {
            "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
            "snippet": "VP1826\tBas6\t0.18",
            "notes": "Supplementary Table 9 identifies the VP1826/Bas6 phage-plating readout as a Fold Change value of 0.18."
          },
          {
            "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
            "snippet": "VP1826\tBas9\t2.5e-06",
            "notes": "Supplementary Table 9 identifies the VP1826/Bas9 phage-plating readout as a Fold Change value of 2.5e-06."
          },
          {
            "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM3_ESM.xlsx",
            "snippet": ">BAC60089.1 hypothetical protein [Vibrio parahaemolyticus RIMD 2210633]",
            "notes": "Supplementary Data 1's VP1826 worksheet labels BAC60089.1 from Vibrio parahaemolyticus RIMD 2210633 as the PSI-BLAST query protein."
          },
          {
            "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM3_ESM.xlsx",
            "snippet": "Scientific Name\tQuery Cover\tE value\tPer. ident\tAccession  \nVibrio parahaemolyticus\t1\t9e-157\t100\tWP_005464673.1",
            "notes": "Supplementary Data 1's VP1826 worksheet records a full-length 100% PSI-BLAST hit from the BAC60089.1 query to WP_005464673.1."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
            "snippet": "| VP1826 | 10\\.1038/s41564-025-01927-7 | Integrons are anti-phage defence libraries in Vibrio parahaemolyticus | ",
            "notes": "The pinned DefenseFinder article registry maps the VP1826 model namespace to the Getz et al. Vibrio parahaemolyticus integron-defense paper."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| VP1826__VP1826                                   |                                                  | VP1826                 | Custom                  | 175    |",
            "notes": "The pinned DefenseFinder HMM inventory records VP1826__VP1826 as a custom VP1826 profile."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "The pinned DefenseFinder rules table does not list VP1826, leaving rule-level detection criteria unresolved."
          }
        ],
        "attaches_to": [
          "causal_graphs#vp1826_locus_reduces_bacteriophage_plaquing"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-30"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-30T09:51:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted VP1826 system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact same-scope live TraitMech, METPO, history, or prior proposal record; kept the graph at cloned integron-cassette level because molecular output, native activity, and rule rows remain unresolved; proposals/metpo_traitmech_v365 reserves the replacement placeholder.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-30T09:51:01Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed VP1826 system canonical_examples and left them empty because Getz et al. directly support cloned VP1826 VSV105-plasmid assays, PSI-BLAST homologs, and a DefenseFinder VP1826 model, but not a direct named native microbial isolate exemplar with experimentally verified endogenous VP1826 activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000489",
    "label": "VP1839 system",
    "definition": "A phage defense system in which an organism possesses a VP1839-family locus represented by the DefenseFinder VP1839__VP1839 custom HMM profile and experimentally linked to reduced bacteriophage plaquing when the cloned Vibrio parahaemolyticus RIMD 2210633 vp1839 cassette is expressed from a VSV105 plasmid.",
    "definition_source": "DOI:10.1038/s41564-025-01927-7",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "VP1839",
        "synonym_type": "EXACT_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      },
      {
        "synonym_text": "Vp1839",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx"
      },
      {
        "synonym_text": "VP1839__VP1839",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/s41564-025-01927-7",
        "snippet": "Intrigued by this discovery, we cloned 57 integron gene cassettes and identified 9 previously unrecognized systems that mediate defence.",
        "notes": "Getz et al. identify nine previously unrecognized Vibrio parahaemolyticus integron cassettes as anti-phage defense systems."
      },
      {
        "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
        "snippet": "VP_RS08915\tVp1839\tY\tWP_024699234.1\tHypothetical Protein",
        "notes": "Supplementary Table 8 lists VP_RS08915/Vp1839 as a cloned RIMD 2210633 integron cassette with protein accession WP_024699234.1."
      },
      {
        "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
        "snippet": "VSV105-vp1839\tVSV105 carrying gene vp1839 behind the lac promoter, cloned into KpnI by In-Fusion\tThis Study",
        "notes": "Supplementary Table 12 records the VSV105-vp1839 lac-expression plasmid used to express vp1839 behind the lac promoter."
      },
      {
        "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
        "snippet": "VP1839\tBas60\t0.002",
        "notes": "Supplementary Table 9 identifies the VP1839/Bas60 phage-plating readout as a Fold Change value of 0.002."
      },
      {
        "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
        "snippet": "VP1839\tBas61\t0.166666666666667",
        "notes": "Supplementary Table 9 identifies the VP1839/Bas61 phage-plating readout as a Fold Change value of 0.166666666666667."
      },
      {
        "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
        "snippet": "VP1839\tBas62\t0.0727272727272727",
        "notes": "Supplementary Table 9 identifies the VP1839/Bas62 phage-plating readout as a Fold Change value of 0.0727272727272727."
      },
      {
        "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM3_ESM.xlsx",
        "snippet": ">BAC60102.1 hypothetical protein [Vibrio parahaemolyticus RIMD 2210633]",
        "notes": "Supplementary Data 1's VP1839 worksheet labels BAC60102.1 from Vibrio parahaemolyticus RIMD 2210633 as the PSI-BLAST query protein."
      },
      {
        "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM3_ESM.xlsx",
        "snippet": "Scientific Name\tQuery Cover\tE value\tPer. ident\tAccession  \nVibrio parahaemolyticus\t1\t5e-113\t100\tARC19797.1",
        "notes": "Supplementary Data 1's VP1839 worksheet records a full-length 100% PSI-BLAST hit from the BAC60102.1 query to ARC19797.1."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| VP1839 | 10\\.1038/s41564-025-01927-7 | Integrons are anti-phage defence libraries in Vibrio parahaemolyticus | ",
        "notes": "The pinned DefenseFinder article registry maps the VP1839 model namespace to the Getz et al. Vibrio parahaemolyticus integron-defense paper."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| VP1839__VP1839                                   |                                                  | VP1839                 | Custom                  | 25     |",
        "notes": "The pinned DefenseFinder HMM inventory records VP1839__VP1839 as a custom VP1839 profile."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "vp1839_locus_reduces_bacteriophage_plaquing",
        "title": "VP1839 loci reduce bacteriophage plaquing",
        "description": "Conservative system-level sketch linking VP1839-family locus possession to reduced bacteriophage plaquing without resolving VP1839 component function or molecular output.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures VP1839 as a RIMD 2210633 integron cassette with cloned phage-plating readouts, a PSI-BLAST homolog lead, one pinned DefenseFinder custom HMM-profile row, and no pinned DefenseFinder rule row. It does not assert native host breadth, exact profile-to-protein correspondence, molecular activity, phage trigger, substrate, complete homolog boundary, endogenous activity, or rule-level DefenseFinder detection criteria.",
        "nodes": [
          {
            "node_id": "vp1839_locus",
            "label": "VP1839 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A Vp1839-like integron cassette locus represented in the pinned DefenseFinder HMM inventory by the VP1839__VP1839 custom profile."
          },
          {
            "node_id": "reduced_bacteriophage_plaquing",
            "label": "reduced bacteriophage plaquing",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced plaquing of bacteriophages in cells expressing cloned vp1839."
          },
          {
            "node_id": "vp1839_system_trait",
            "label": "VP1839 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000489",
            "description": "Possession of a genome-encoded VP1839 phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "vp1839_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "reduced_bacteriophage_plaquing",
            "description": "The cloned V. parahaemolyticus vp1839 integron cassette contributes to reduced bacteriophage plaquing in VSV105 plasmid-expression assays, and DefenseFinder represents the VP1839 family with one custom HMM profile.",
            "evidence": [
              {
                "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
                "snippet": "VP_RS08915\tVp1839\tY\tWP_024699234.1\tHypothetical Protein",
                "notes": "Supplementary Table 8 lists VP_RS08915/Vp1839 as a cloned RIMD 2210633 integron cassette with protein accession WP_024699234.1."
              },
              {
                "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
                "snippet": "VSV105-vp1839\tVSV105 carrying gene vp1839 behind the lac promoter, cloned into KpnI by In-Fusion\tThis Study",
                "notes": "Supplementary Table 12 records the VSV105-vp1839 lac-expression plasmid used to express vp1839 behind the lac promoter."
              },
              {
                "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
                "snippet": "VP1839\tBas60\t0.002",
                "notes": "Supplementary Table 9 identifies the VP1839/Bas60 phage-plating readout as a Fold Change value of 0.002."
              },
              {
                "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
                "snippet": "VP1839\tBas61\t0.166666666666667",
                "notes": "Supplementary Table 9 identifies the VP1839/Bas61 phage-plating readout as a Fold Change value of 0.166666666666667."
              },
              {
                "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
                "snippet": "VP1839\tBas62\t0.0727272727272727",
                "notes": "Supplementary Table 9 identifies the VP1839/Bas62 phage-plating readout as a Fold Change value of 0.0727272727272727."
              },
              {
                "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM3_ESM.xlsx",
                "snippet": ">BAC60102.1 hypothetical protein [Vibrio parahaemolyticus RIMD 2210633]",
                "notes": "Supplementary Data 1's VP1839 worksheet labels BAC60102.1 from Vibrio parahaemolyticus RIMD 2210633 as the PSI-BLAST query protein."
              },
              {
                "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM3_ESM.xlsx",
                "snippet": "Scientific Name\tQuery Cover\tE value\tPer. ident\tAccession  \nVibrio parahaemolyticus\t1\t5e-113\t100\tARC19797.1",
                "notes": "Supplementary Data 1's VP1839 worksheet records a full-length 100% PSI-BLAST hit from the BAC60102.1 query to ARC19797.1."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| VP1839__VP1839                                   |                                                  | VP1839                 | Custom                  | 25     |",
                "notes": "The pinned DefenseFinder HMM inventory records VP1839__VP1839 as a custom VP1839 profile."
              }
            ]
          },
          {
            "subject": "reduced_bacteriophage_plaquing",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "vp1839_system_trait",
            "description": "VP1839-mediated bacteriophage plaquing reduction realizes the VP1839 system trait.",
            "evidence": [
              {
                "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
                "snippet": "VP1839\tBas60\t0.002",
                "notes": "Supplementary Table 9 identifies the VP1839/Bas60 phage-plating readout as a Fold Change value of 0.002."
              },
              {
                "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
                "snippet": "VP1839\tBas61\t0.166666666666667",
                "notes": "Supplementary Table 9 identifies the VP1839/Bas61 phage-plating readout as a Fold Change value of 0.166666666666667."
              },
              {
                "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
                "snippet": "VP1839\tBas62\t0.0727272727272727",
                "notes": "Supplementary Table 9 identifies the VP1839/Bas62 phage-plating readout as a Fold Change value of 0.0727272727272727."
              }
            ]
          },
          {
            "subject": "vp1839_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "VP1839 system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-025-01927-7",
                "snippet": "Intrigued by this discovery, we cloned 57 integron gene cassettes and identified 9 previously unrecognized systems that mediate defence.",
                "notes": "Getz et al. identify nine previously unrecognized Vibrio parahaemolyticus integron cassettes as anti-phage defense systems."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| VP1839 | 10\\.1038/s41564-025-01927-7 | Integrons are anti-phage defence libraries in Vibrio parahaemolyticus | ",
                "notes": "The pinned DefenseFinder article registry maps the VP1839 model namespace to the Getz et al. Vibrio parahaemolyticus integron-defense paper."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "vp1839-defensefinder-model-gap",
        "prompt": "Resolve VP1839 native host breadth, exact single-component activity, profile-to-protein mapping, homolog boundary, full phage breadth, molecular output, and rule-level DefenseFinder criteria before minting narrower VP1839 mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Getz et al. support VP1839 as one of nine RIMD 2210633 integron-encoded cassettes whose cloned expression reduced phage plaquing, Supplementary Tables 8, 9, and 12 map VP1839 to VP_RS08915/Vp1839, WP_024699234.1, VSV105-vp1839, and phage-plating fold changes, and Supplementary Data 1 reports PSI-BLAST homologs. The pinned DefenseFinder HMM inventory records one VP1839 custom profile row. The pinned rules table has no VP1839 row, and the first-pass record does not resolve native host breadth, complete phage breadth, direct profile-to-protein correspondence, molecular output, or endogenous activity.",
        "evidence": [
          {
            "reference": "DOI:10.1038/s41564-025-01927-7",
            "snippet": "Intrigued by this discovery, we cloned 57 integron gene cassettes and identified 9 previously unrecognized systems that mediate defence.",
            "notes": "Getz et al. identify nine previously unrecognized Vibrio parahaemolyticus integron cassettes as anti-phage defense systems."
          },
          {
            "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
            "snippet": "VP_RS08915\tVp1839\tY\tWP_024699234.1\tHypothetical Protein",
            "notes": "Supplementary Table 8 lists VP_RS08915/Vp1839 as a cloned RIMD 2210633 integron cassette with protein accession WP_024699234.1."
          },
          {
            "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
            "snippet": "VSV105-vp1839\tVSV105 carrying gene vp1839 behind the lac promoter, cloned into KpnI by In-Fusion\tThis Study",
            "notes": "Supplementary Table 12 records the VSV105-vp1839 lac-expression plasmid used to express vp1839 behind the lac promoter."
          },
          {
            "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
            "snippet": "VP1839\tBas60\t0.002",
            "notes": "Supplementary Table 9 identifies the VP1839/Bas60 phage-plating readout as a Fold Change value of 0.002."
          },
          {
            "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
            "snippet": "VP1839\tBas61\t0.166666666666667",
            "notes": "Supplementary Table 9 identifies the VP1839/Bas61 phage-plating readout as a Fold Change value of 0.166666666666667."
          },
          {
            "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
            "snippet": "VP1839\tBas62\t0.0727272727272727",
            "notes": "Supplementary Table 9 identifies the VP1839/Bas62 phage-plating readout as a Fold Change value of 0.0727272727272727."
          },
          {
            "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM3_ESM.xlsx",
            "snippet": ">BAC60102.1 hypothetical protein [Vibrio parahaemolyticus RIMD 2210633]",
            "notes": "Supplementary Data 1's VP1839 worksheet labels BAC60102.1 from Vibrio parahaemolyticus RIMD 2210633 as the PSI-BLAST query protein."
          },
          {
            "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM3_ESM.xlsx",
            "snippet": "Scientific Name\tQuery Cover\tE value\tPer. ident\tAccession  \nVibrio parahaemolyticus\t1\t5e-113\t100\tARC19797.1",
            "notes": "Supplementary Data 1's VP1839 worksheet records a full-length 100% PSI-BLAST hit from the BAC60102.1 query to ARC19797.1."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
            "snippet": "| VP1839 | 10\\.1038/s41564-025-01927-7 | Integrons are anti-phage defence libraries in Vibrio parahaemolyticus | ",
            "notes": "The pinned DefenseFinder article registry maps the VP1839 model namespace to the Getz et al. Vibrio parahaemolyticus integron-defense paper."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| VP1839__VP1839                                   |                                                  | VP1839                 | Custom                  | 25     |",
            "notes": "The pinned DefenseFinder HMM inventory records VP1839__VP1839 as a custom VP1839 profile."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "The pinned DefenseFinder rules table does not list VP1839, leaving rule-level detection criteria unresolved."
          }
        ],
        "attaches_to": [
          "causal_graphs#vp1839_locus_reduces_bacteriophage_plaquing"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-30"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-30T10:36:56Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted VP1839 system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact same-scope live TraitMech, METPO, history, or prior proposal record; kept the graph at cloned integron-cassette level because molecular output, native activity, and rule rows remain unresolved; proposals/metpo_traitmech_v366 reserves the replacement placeholder.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-30T10:36:57Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed VP1839 system canonical_examples and left them empty because Getz et al. directly support cloned VP1839 VSV105-plasmid assays, PSI-BLAST homologs, and a DefenseFinder VP1839 model, but not a direct named native microbial isolate exemplar with experimentally verified endogenous VP1839 activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000450",
    "label": "VP1840 system",
    "definition": "A phage defense system in which an organism possesses a VP1840-family locus represented by the DefenseFinder VP1840__VP1840 custom HMM profile and experimentally linked to reduced bacteriophage plaquing when the cloned Vibrio parahaemolyticus RIMD 2210633 vp1840 cassette is expressed from a VSV105 plasmid.",
    "definition_source": "DOI:10.1038/s41564-025-01927-7",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "VP1840",
        "synonym_type": "EXACT_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      },
      {
        "synonym_text": "Vp1840",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx"
      },
      {
        "synonym_text": "VP1840__VP1840",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/s41564-025-01927-7",
        "snippet": "Intrigued by this discovery, we cloned 57 integron gene cassettes and identified 9 previously unrecognized systems that mediate defence.",
        "notes": "Getz et al. identify nine previously unrecognized Vibrio parahaemolyticus integron cassettes as anti-phage defense systems."
      },
      {
        "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
        "snippet": "VP_RS08920\tVp1840\tY\tWP_005483293.1 \tHypothetical Protein",
        "notes": "Supplementary Table 8 lists VP_RS08920/Vp1840 as a cloned RIMD 2210633 integron cassette with protein accession WP_005483293.1."
      },
      {
        "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
        "snippet": "VSV105-vp1840\tVSV105 carrying gene vp1840 behind the lac promoter, cloned into KpnI by In-Fusion\tThis Study",
        "notes": "Supplementary Table 12 records the VSV105-vp1840 lac-expression plasmid used to express vp1840 behind the lac promoter."
      },
      {
        "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
        "snippet": "VP1840\tBas21\t2e-09",
        "notes": "Supplementary Table 9 identifies the VP1840/Bas21 phage-plating readout as a Fold Change value of 2e-09."
      },
      {
        "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
        "snippet": "VP1840\tLL1\t0",
        "notes": "Supplementary Table 9 identifies the VP1840/LL1 phage-plating readout as a Fold Change value of 0."
      },
      {
        "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM3_ESM.xlsx",
        "snippet": ">BAC60103.1 hypothetical protein [Vibrio parahaemolyticus RIMD 2210633]",
        "notes": "Supplementary Data 1's VP1840 worksheet labels BAC60103.1 from Vibrio parahaemolyticus RIMD 2210633 as the PSI-BLAST query protein."
      },
      {
        "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM3_ESM.xlsx",
        "snippet": "Scientific Name\tQuery Cover\tE value\tPer. ident\tAccession  \nVibrio parahaemolyticus\t1\t3e-121\t100\tWP_229652597.1",
        "notes": "Supplementary Data 1's VP1840 worksheet records a full-length 100% PSI-BLAST hit from the BAC60103.1 query to the separate Vibrio parahaemolyticus homolog WP_229652597.1."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| VP1840 | 10\\.1038/s41564-025-01927-7 | Integrons are anti-phage defence libraries in Vibrio parahaemolyticus | ",
        "notes": "The pinned DefenseFinder article registry maps the VP1840 model namespace to the Getz et al. Vibrio parahaemolyticus integron-defense paper."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| VP1840__VP1840                                   |                                                  | VP1840                 | Custom                  | 75     |",
        "notes": "The pinned DefenseFinder HMM inventory records VP1840__VP1840 as a custom VP1840 profile."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "vp1840_locus_reduces_bacteriophage_plaquing",
        "title": "VP1840 loci reduce bacteriophage plaquing",
        "description": "Conservative system-level sketch linking VP1840-family locus possession to reduced bacteriophage plaquing without resolving VP1840 component function or molecular output.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures VP1840 as a RIMD 2210633 integron cassette with cloned phage-plating readouts, a PSI-BLAST homolog lead, one pinned DefenseFinder custom HMM-profile row, and no pinned DefenseFinder rule row. It does not assert native host breadth, exact profile-to-protein correspondence, molecular activity, phage trigger, substrate, complete homolog boundary, endogenous activity, or rule-level DefenseFinder detection criteria.",
        "nodes": [
          {
            "node_id": "vp1840_locus",
            "label": "VP1840 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A Vp1840-like integron cassette locus represented in the pinned DefenseFinder HMM inventory by the VP1840__VP1840 custom profile."
          },
          {
            "node_id": "reduced_bacteriophage_plaquing",
            "label": "reduced bacteriophage plaquing",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced plaquing of bacteriophages in cells expressing cloned vp1840."
          },
          {
            "node_id": "vp1840_system_trait",
            "label": "VP1840 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000450",
            "description": "Possession of a genome-encoded VP1840 phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "vp1840_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "reduced_bacteriophage_plaquing",
            "description": "The cloned V. parahaemolyticus vp1840 integron cassette contributes to reduced bacteriophage plaquing in VSV105 plasmid-expression assays, and DefenseFinder represents the VP1840 family with one custom HMM profile.",
            "evidence": [
              {
                "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
                "snippet": "VP_RS08920\tVp1840\tY\tWP_005483293.1 \tHypothetical Protein",
                "notes": "Supplementary Table 8 lists VP_RS08920/Vp1840 as a cloned RIMD 2210633 integron cassette with protein accession WP_005483293.1."
              },
              {
                "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
                "snippet": "VSV105-vp1840\tVSV105 carrying gene vp1840 behind the lac promoter, cloned into KpnI by In-Fusion\tThis Study",
                "notes": "Supplementary Table 12 records the VSV105-vp1840 lac-expression plasmid used to express vp1840 behind the lac promoter."
              },
              {
                "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
                "snippet": "VP1840\tBas21\t2e-09",
                "notes": "Supplementary Table 9 identifies the VP1840/Bas21 phage-plating readout as a Fold Change value of 2e-09."
              },
              {
                "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
                "snippet": "VP1840\tLL1\t0",
                "notes": "Supplementary Table 9 identifies the VP1840/LL1 phage-plating readout as a Fold Change value of 0."
              },
              {
                "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM3_ESM.xlsx",
                "snippet": ">BAC60103.1 hypothetical protein [Vibrio parahaemolyticus RIMD 2210633]",
                "notes": "Supplementary Data 1's VP1840 worksheet labels BAC60103.1 from Vibrio parahaemolyticus RIMD 2210633 as the PSI-BLAST query protein."
              },
              {
                "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM3_ESM.xlsx",
                "snippet": "Scientific Name\tQuery Cover\tE value\tPer. ident\tAccession  \nVibrio parahaemolyticus\t1\t3e-121\t100\tWP_229652597.1",
                "notes": "Supplementary Data 1's VP1840 worksheet records a full-length 100% PSI-BLAST hit from the BAC60103.1 query to the separate Vibrio parahaemolyticus homolog WP_229652597.1."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| VP1840__VP1840                                   |                                                  | VP1840                 | Custom                  | 75     |",
                "notes": "The pinned DefenseFinder HMM inventory records VP1840__VP1840 as a custom VP1840 profile."
              }
            ]
          },
          {
            "subject": "reduced_bacteriophage_plaquing",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "vp1840_system_trait",
            "description": "VP1840-mediated bacteriophage plaquing reduction realizes the VP1840 system trait.",
            "evidence": [
              {
                "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
                "snippet": "VP1840\tBas21\t2e-09",
                "notes": "Supplementary Table 9 identifies the VP1840/Bas21 phage-plating readout as a Fold Change value of 2e-09."
              },
              {
                "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
                "snippet": "VP1840\tLL1\t0",
                "notes": "Supplementary Table 9 identifies the VP1840/LL1 phage-plating readout as a Fold Change value of 0."
              }
            ]
          },
          {
            "subject": "vp1840_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "VP1840 system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-025-01927-7",
                "snippet": "Intrigued by this discovery, we cloned 57 integron gene cassettes and identified 9 previously unrecognized systems that mediate defence.",
                "notes": "Getz et al. identify nine previously unrecognized Vibrio parahaemolyticus integron cassettes as anti-phage defense systems."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| VP1840 | 10\\.1038/s41564-025-01927-7 | Integrons are anti-phage defence libraries in Vibrio parahaemolyticus | ",
                "notes": "The pinned DefenseFinder article registry maps the VP1840 model namespace to the Getz et al. Vibrio parahaemolyticus integron-defense paper."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "vp1840-defensefinder-model-gap",
        "prompt": "Resolve VP1840 native host breadth, exact single-component activity, profile-to-protein mapping, homolog boundary, full phage breadth, molecular output, and rule-level DefenseFinder criteria before minting narrower VP1840 mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Getz et al. support VP1840 as one of nine RIMD 2210633 integron-encoded cassettes whose cloned expression reduced phage plaquing, Supplementary Tables 8, 9, and 12 map VP1840 to VP_RS08920/Vp1840, WP_005483293.1, VSV105-vp1840, and phage-plating fold changes, and Supplementary Data 1 reports PSI-BLAST homologs. The pinned DefenseFinder HMM inventory records one VP1840 custom profile row. The pinned rules table has no VP1840 row, and the first-pass record does not resolve native host breadth, complete phage breadth, direct profile-to-protein correspondence, molecular output, or endogenous activity.",
        "evidence": [
          {
            "reference": "DOI:10.1038/s41564-025-01927-7",
            "snippet": "Intrigued by this discovery, we cloned 57 integron gene cassettes and identified 9 previously unrecognized systems that mediate defence.",
            "notes": "Getz et al. identify nine previously unrecognized Vibrio parahaemolyticus integron cassettes as anti-phage defense systems."
          },
          {
            "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
            "snippet": "VP_RS08920\tVp1840\tY\tWP_005483293.1 \tHypothetical Protein",
            "notes": "Supplementary Table 8 lists VP_RS08920/Vp1840 as a cloned RIMD 2210633 integron cassette with protein accession WP_005483293.1."
          },
          {
            "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
            "snippet": "VSV105-vp1840\tVSV105 carrying gene vp1840 behind the lac promoter, cloned into KpnI by In-Fusion\tThis Study",
            "notes": "Supplementary Table 12 records the VSV105-vp1840 lac-expression plasmid used to express vp1840 behind the lac promoter."
          },
          {
            "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
            "snippet": "VP1840\tBas21\t2e-09",
            "notes": "Supplementary Table 9 identifies the VP1840/Bas21 phage-plating readout as a Fold Change value of 2e-09."
          },
          {
            "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM3_ESM.xlsx",
            "snippet": ">BAC60103.1 hypothetical protein [Vibrio parahaemolyticus RIMD 2210633]",
            "notes": "Supplementary Data 1's VP1840 worksheet labels BAC60103.1 from Vibrio parahaemolyticus RIMD 2210633 as the PSI-BLAST query protein."
          },
          {
            "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM3_ESM.xlsx",
            "snippet": "Scientific Name\tQuery Cover\tE value\tPer. ident\tAccession  \nVibrio parahaemolyticus\t1\t3e-121\t100\tWP_229652597.1",
            "notes": "Supplementary Data 1's VP1840 worksheet records a full-length 100% PSI-BLAST hit from the BAC60103.1 query to the separate Vibrio parahaemolyticus homolog WP_229652597.1."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
            "snippet": "| VP1840 | 10\\.1038/s41564-025-01927-7 | Integrons are anti-phage defence libraries in Vibrio parahaemolyticus | ",
            "notes": "The pinned DefenseFinder article registry maps the VP1840 model namespace to the Getz et al. Vibrio parahaemolyticus integron-defense paper."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| VP1840__VP1840                                   |                                                  | VP1840                 | Custom                  | 75     |",
            "notes": "The pinned DefenseFinder HMM inventory records VP1840__VP1840 as a custom VP1840 profile."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "The pinned DefenseFinder rules table does not list VP1840, leaving rule-level detection criteria unresolved."
          }
        ],
        "attaches_to": [
          "causal_graphs#vp1840_locus_reduces_bacteriophage_plaquing"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-29"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-29T02:26:23Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted VP1840 system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; kept the graph at cloned integron-cassette level because the molecular output and rule rows remain unresolved, and proposals/metpo_traitmech_v327 reserves the replacement placeholder.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-29T02:26:24Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed VP1840 system canonical_examples and left them empty because Getz et al. directly support cloned Vp1840 VSV105-plasmid assays, PSI-BLAST homologs, and a DefenseFinder VP1840 model, but not a direct named native microbial isolate exemplar with experimentally verified endogenous VP1840 activity. No paid research was used.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-29T02:51:42Z",
        "curator": "codex",
        "action": "CLARIFIED_EVIDENCE_SNIPPETS",
        "changes": "Clarified Supplementary Table 9 VP1840 phage-plating notes to name the paper's Fold Change column and expanded the Supplementary Data 1 VP1840 PSI-BLAST snippet with its column header so the WP_229652597.1 hit is self-identifying.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-29T03:13:39Z",
        "curator": "codex",
        "action": "GROUNDED_PSIBLAST_QUERY_ACCESSION",
        "changes": "Quoted the Supplementary Data 1 VP1840 worksheet query row so the BAC60103.1 PSI-BLAST query named in the WP_229652597.1 homolog-hit note is directly evidenced.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-29T03:27:44Z",
        "curator": "codex",
        "action": "CLARIFIED_PHAGE_PLATING_SCOPE",
        "changes": "Quoted the Supplementary Table 9 Fold Change header in the Bas21 and LL1 snippets and neutralized unsupported VP1840 host-clade phrasing to bacteriophage wording.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-29T03:45:05Z",
        "curator": "codex",
        "action": "UNSTITCHED_PHAGE_PLATING_SNIPPETS",
        "changes": "Removed the non-contiguous Supplementary Table 9 Fold Change header prefix from the Bas21 and LL1 snippets so each phage-plating snippet quotes only a contiguous data row.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000490",
    "label": "VP1848 system",
    "definition": "A phage defense system in which an organism possesses a VP1848-family locus represented by the DefenseFinder VP1848__VP1848 custom HMM profile and experimentally linked to reduced bacteriophage plaquing when the cloned Vibrio parahaemolyticus RIMD 2210633 vp1848 cassette is expressed from a VSV105 plasmid.",
    "definition_source": "DOI:10.1038/s41564-025-01927-7",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "VP1848",
        "synonym_type": "EXACT_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      },
      {
        "synonym_text": "Vp1848",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx"
      },
      {
        "synonym_text": "VP1848__VP1848",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/s41564-025-01927-7",
        "snippet": "Intrigued by this discovery, we cloned 57 integron gene cassettes and identified 9 previously unrecognized systems that mediate defence.",
        "notes": "Getz et al. identify nine previously unrecognized Vibrio parahaemolyticus integron cassettes as anti-phage defense systems."
      },
      {
        "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
        "snippet": "VP_RS08970\tVp1848\tY\tWP_005483286.1 \tHypothetical Protein",
        "notes": "Supplementary Table 8 lists VP_RS08970/Vp1848 as a cloned RIMD 2210633 integron cassette with protein accession WP_005483286.1."
      },
      {
        "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
        "snippet": "VSV105-vp1848\tVSV105 carrying gene vp1848 behind the lac promoter, cloned into KpnI by In-Fusion\tThis Study",
        "notes": "Supplementary Table 12 records the VSV105-vp1848 lac-expression plasmid used to express vp1848 behind the lac promoter."
      },
      {
        "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
        "snippet": "VP1848\tBas64\t0.07\tSmall",
        "notes": "Supplementary Table 9 identifies the VP1848/Bas64 phage-plating readout as a Fold Change value of 0.07 with a Small Plaque Size comment."
      },
      {
        "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
        "snippet": "VP1848\tBas65\t0.00266666666666667\tSmall",
        "notes": "Supplementary Table 9 identifies the VP1848/Bas65 phage-plating readout as a Fold Change value of 0.00266666666666667 with a Small Plaque Size comment."
      },
      {
        "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM3_ESM.xlsx",
        "snippet": ">BAC60111.1 hypothetical protein [Vibrio parahaemolyticus RIMD 2210633]",
        "notes": "Supplementary Data 1's VP1848 worksheet labels BAC60111.1 from Vibrio parahaemolyticus RIMD 2210633 as the PSI-BLAST query protein."
      },
      {
        "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM3_ESM.xlsx",
        "snippet": "Scientific Name\tQuery Cover\tE value\tPer. ident\tAccession  \nVibrio parahaemolyticus\t1\t9e-95\t100\tWP_203479114.1",
        "notes": "Supplementary Data 1's VP1848 worksheet records a full-length 100% PSI-BLAST hit from the BAC60111.1 query to WP_203479114.1."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| VP1848 | 10\\.1038/s41564-025-01927-7 | Integrons are anti-phage defence libraries in Vibrio parahaemolyticus | ",
        "notes": "The pinned DefenseFinder article registry maps the VP1848 model namespace to the Getz et al. Vibrio parahaemolyticus integron-defense paper."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| VP1848__VP1848                                   |                                                  | VP1848                 | Custom                  | 100    |",
        "notes": "The pinned DefenseFinder HMM inventory records VP1848__VP1848 as a custom VP1848 profile."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "vp1848_locus_reduces_bacteriophage_plaquing",
        "title": "VP1848 loci reduce bacteriophage plaquing",
        "description": "Conservative system-level sketch linking VP1848-family locus possession to reduced bacteriophage plaquing without resolving VP1848 component function or molecular output.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures VP1848 as a RIMD 2210633 integron cassette with cloned phage-plating readouts, a PSI-BLAST homolog lead, one pinned DefenseFinder custom HMM-profile row, and no pinned DefenseFinder rule row. It does not assert native host breadth, exact profile-to-protein correspondence, molecular activity, phage trigger, substrate, complete homolog boundary, endogenous activity, or rule-level DefenseFinder detection criteria.",
        "nodes": [
          {
            "node_id": "vp1848_locus",
            "label": "VP1848 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A Vp1848-like integron cassette locus represented in the pinned DefenseFinder HMM inventory by the VP1848__VP1848 custom profile."
          },
          {
            "node_id": "reduced_bacteriophage_plaquing",
            "label": "reduced bacteriophage plaquing",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced plaquing of bacteriophages in cells expressing cloned vp1848."
          },
          {
            "node_id": "vp1848_system_trait",
            "label": "VP1848 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000490",
            "description": "Possession of a genome-encoded VP1848 phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "vp1848_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "reduced_bacteriophage_plaquing",
            "description": "The cloned V. parahaemolyticus vp1848 integron cassette contributes to reduced bacteriophage plaquing in VSV105 plasmid-expression assays, and DefenseFinder represents the VP1848 family with one custom HMM profile.",
            "evidence": [
              {
                "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
                "snippet": "VP_RS08970\tVp1848\tY\tWP_005483286.1 \tHypothetical Protein",
                "notes": "Supplementary Table 8 lists VP_RS08970/Vp1848 as a cloned RIMD 2210633 integron cassette with protein accession WP_005483286.1."
              },
              {
                "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
                "snippet": "VSV105-vp1848\tVSV105 carrying gene vp1848 behind the lac promoter, cloned into KpnI by In-Fusion\tThis Study",
                "notes": "Supplementary Table 12 records the VSV105-vp1848 lac-expression plasmid used to express vp1848 behind the lac promoter."
              },
              {
                "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
                "snippet": "VP1848\tBas64\t0.07\tSmall",
                "notes": "Supplementary Table 9 identifies the VP1848/Bas64 phage-plating readout as a Fold Change value of 0.07 with a Small Plaque Size comment."
              },
              {
                "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
                "snippet": "VP1848\tBas65\t0.00266666666666667\tSmall",
                "notes": "Supplementary Table 9 identifies the VP1848/Bas65 phage-plating readout as a Fold Change value of 0.00266666666666667 with a Small Plaque Size comment."
              },
              {
                "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM3_ESM.xlsx",
                "snippet": ">BAC60111.1 hypothetical protein [Vibrio parahaemolyticus RIMD 2210633]",
                "notes": "Supplementary Data 1's VP1848 worksheet labels BAC60111.1 from Vibrio parahaemolyticus RIMD 2210633 as the PSI-BLAST query protein."
              },
              {
                "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM3_ESM.xlsx",
                "snippet": "Scientific Name\tQuery Cover\tE value\tPer. ident\tAccession  \nVibrio parahaemolyticus\t1\t9e-95\t100\tWP_203479114.1",
                "notes": "Supplementary Data 1's VP1848 worksheet records a full-length 100% PSI-BLAST hit from the BAC60111.1 query to WP_203479114.1."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| VP1848__VP1848                                   |                                                  | VP1848                 | Custom                  | 100    |",
                "notes": "The pinned DefenseFinder HMM inventory records VP1848__VP1848 as a custom VP1848 profile."
              }
            ]
          },
          {
            "subject": "reduced_bacteriophage_plaquing",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "vp1848_system_trait",
            "description": "VP1848-mediated bacteriophage plaquing reduction realizes the VP1848 system trait.",
            "evidence": [
              {
                "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
                "snippet": "VP1848\tBas64\t0.07\tSmall",
                "notes": "Supplementary Table 9 identifies the VP1848/Bas64 phage-plating readout as a Fold Change value of 0.07 with a Small Plaque Size comment."
              },
              {
                "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
                "snippet": "VP1848\tBas65\t0.00266666666666667\tSmall",
                "notes": "Supplementary Table 9 identifies the VP1848/Bas65 phage-plating readout as a Fold Change value of 0.00266666666666667 with a Small Plaque Size comment."
              }
            ]
          },
          {
            "subject": "vp1848_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "VP1848 system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-025-01927-7",
                "snippet": "Intrigued by this discovery, we cloned 57 integron gene cassettes and identified 9 previously unrecognized systems that mediate defence.",
                "notes": "Getz et al. identify nine previously unrecognized Vibrio parahaemolyticus integron cassettes as anti-phage defense systems."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| VP1848 | 10\\.1038/s41564-025-01927-7 | Integrons are anti-phage defence libraries in Vibrio parahaemolyticus | ",
                "notes": "The pinned DefenseFinder article registry maps the VP1848 model namespace to the Getz et al. Vibrio parahaemolyticus integron-defense paper."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "vp1848-defensefinder-model-gap",
        "prompt": "Resolve VP1848 native host breadth, exact single-component activity, profile-to-protein mapping, homolog boundary, full phage breadth, molecular output, and rule-level DefenseFinder criteria before minting narrower VP1848 mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Getz et al. support VP1848 as one of nine RIMD 2210633 integron-encoded cassettes whose cloned expression reduced phage plaquing, Supplementary Tables 8, 9, and 12 map VP1848 to VP_RS08970/Vp1848, WP_005483286.1, VSV105-vp1848, and phage-plating fold changes, and Supplementary Data 1 reports PSI-BLAST homologs. The pinned DefenseFinder HMM inventory records one VP1848 custom profile row. The pinned rules table has no VP1848 row, and the first-pass record does not resolve native host breadth, complete phage breadth, direct profile-to-protein correspondence, molecular output, or endogenous activity.",
        "evidence": [
          {
            "reference": "DOI:10.1038/s41564-025-01927-7",
            "snippet": "Intrigued by this discovery, we cloned 57 integron gene cassettes and identified 9 previously unrecognized systems that mediate defence.",
            "notes": "Getz et al. identify nine previously unrecognized Vibrio parahaemolyticus integron cassettes as anti-phage defense systems."
          },
          {
            "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
            "snippet": "VP_RS08970\tVp1848\tY\tWP_005483286.1 \tHypothetical Protein",
            "notes": "Supplementary Table 8 lists VP_RS08970/Vp1848 as a cloned RIMD 2210633 integron cassette with protein accession WP_005483286.1."
          },
          {
            "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
            "snippet": "VSV105-vp1848\tVSV105 carrying gene vp1848 behind the lac promoter, cloned into KpnI by In-Fusion\tThis Study",
            "notes": "Supplementary Table 12 records the VSV105-vp1848 lac-expression plasmid used to express vp1848 behind the lac promoter."
          },
          {
            "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
            "snippet": "VP1848\tBas64\t0.07\tSmall",
            "notes": "Supplementary Table 9 identifies the VP1848/Bas64 phage-plating readout as a Fold Change value of 0.07 with a Small Plaque Size comment."
          },
          {
            "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
            "snippet": "VP1848\tBas65\t0.00266666666666667\tSmall",
            "notes": "Supplementary Table 9 identifies the VP1848/Bas65 phage-plating readout as a Fold Change value of 0.00266666666666667 with a Small Plaque Size comment."
          },
          {
            "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM3_ESM.xlsx",
            "snippet": ">BAC60111.1 hypothetical protein [Vibrio parahaemolyticus RIMD 2210633]",
            "notes": "Supplementary Data 1's VP1848 worksheet labels BAC60111.1 from Vibrio parahaemolyticus RIMD 2210633 as the PSI-BLAST query protein."
          },
          {
            "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM3_ESM.xlsx",
            "snippet": "Scientific Name\tQuery Cover\tE value\tPer. ident\tAccession  \nVibrio parahaemolyticus\t1\t9e-95\t100\tWP_203479114.1",
            "notes": "Supplementary Data 1's VP1848 worksheet records a full-length 100% PSI-BLAST hit from the BAC60111.1 query to WP_203479114.1."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
            "snippet": "| VP1848 | 10\\.1038/s41564-025-01927-7 | Integrons are anti-phage defence libraries in Vibrio parahaemolyticus | ",
            "notes": "The pinned DefenseFinder article registry maps the VP1848 model namespace to the Getz et al. Vibrio parahaemolyticus integron-defense paper."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| VP1848__VP1848                                   |                                                  | VP1848                 | Custom                  | 100    |",
            "notes": "The pinned DefenseFinder HMM inventory records VP1848__VP1848 as a custom VP1848 profile."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "The pinned DefenseFinder rules table does not list VP1848, leaving rule-level detection criteria unresolved."
          }
        ],
        "attaches_to": [
          "causal_graphs#vp1848_locus_reduces_bacteriophage_plaquing"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-30"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-30T11:32:10Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted VP1848 system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact same-scope live TraitMech, METPO, history, or prior proposal record; kept the graph at cloned integron-cassette level because molecular output, native activity, and rule rows remain unresolved; proposals/metpo_traitmech_v367 reserves the replacement placeholder.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-30T11:32:11Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed VP1848 system canonical_examples and left them empty because Getz et al. directly support cloned VP1848 VSV105-plasmid assays, PSI-BLAST homologs, and a DefenseFinder VP1848 model, but not a direct named native microbial isolate exemplar with experimentally verified endogenous VP1848 activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000491",
    "label": "VP1851 system",
    "definition": "A phage defense system in which an organism possesses a VP1851-family locus represented by the DefenseFinder VP1851__VP1851 custom HMM profile and experimentally linked to reduced bacteriophage plaquing when the cloned Vibrio parahaemolyticus RIMD 2210633 vp1851 cassette is expressed from a VSV105 plasmid.",
    "definition_source": "DOI:10.1038/s41564-025-01927-7",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "VP1851",
        "synonym_type": "EXACT_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      },
      {
        "synonym_text": "Vp1851",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx"
      },
      {
        "synonym_text": "VP1851__VP1851",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/s41564-025-01927-7",
        "snippet": "Intrigued by this discovery, we cloned 57 integron gene cassettes and identified 9 previously unrecognized systems that mediate defence.",
        "notes": "Getz et al. identify nine previously unrecognized Vibrio parahaemolyticus integron cassettes as anti-phage defense systems."
      },
      {
        "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
        "snippet": "VP_RS09000\tVp1851\tY\tWP_005483174.1 \tEcsC family protein",
        "notes": "Supplementary Table 8 lists VP_RS09000/Vp1851 as a cloned RIMD 2210633 integron cassette with protein accession WP_005483174.1."
      },
      {
        "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
        "snippet": "VSV105-vp1851\tVSV105 carrying gene vp1851 behind the lac promoter, cloned into KpnI by In-Fusion\tThis Study",
        "notes": "Supplementary Table 12 records the VSV105-vp1851 lac-expression plasmid used to express vp1851 behind the lac promoter."
      },
      {
        "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
        "snippet": "VP1851\tLL1\t0",
        "notes": "Supplementary Table 9 identifies the VP1851/LL1 phage-plating readout as a Fold Change value of 0."
      },
      {
        "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
        "snippet": "VP1851\tVL1\t1.54e-07",
        "notes": "Supplementary Table 9 identifies the VP1851/VL1 phage-plating readout as a Fold Change value of 1.54e-07."
      },
      {
        "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM3_ESM.xlsx",
        "snippet": ">WP_005483174.1 MULTISPECIES: EcsC family protein [Vibrio harveyi group]",
        "notes": "Supplementary Data 1's VP1851 worksheet labels WP_005483174.1 from the Vibrio harveyi group as the PSI-BLAST query protein."
      },
      {
        "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM3_ESM.xlsx",
        "snippet": "Scientific Name\tQuery Cover\tE value\tPer. ident\tAccession  \nVibrio harveyi group\t1\t2e-144\t100\tWP_005483174.1\nVibrio parahaemolyticus\t0.99\t2e-143\t100\tARC19782.1",
        "notes": "Supplementary Data 1's VP1851 worksheet records a full-length 100% PSI-BLAST row for WP_005483174.1 and a 99% query-coverage 100% identity hit to Vibrio parahaemolyticus ARC19782.1."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| VP1851 | 10\\.1038/s41564-025-01927-7 | Integrons are anti-phage defence libraries in Vibrio parahaemolyticus | ",
        "notes": "The pinned DefenseFinder article registry maps the VP1851 model namespace to the Getz et al. Vibrio parahaemolyticus integron-defense paper."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| VP1851__VP1851                                   |                                                  | VP1851                 | Custom                  | 125    |",
        "notes": "The pinned DefenseFinder HMM inventory records VP1851__VP1851 as a custom VP1851 profile."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "vp1851_locus_reduces_bacteriophage_plaquing",
        "title": "VP1851 loci reduce bacteriophage plaquing",
        "description": "Conservative system-level sketch linking VP1851-family locus possession to reduced bacteriophage plaquing without resolving VP1851 component function or molecular output.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures VP1851 as a RIMD 2210633 integron cassette with cloned phage-plating readouts, a PSI-BLAST homolog lead, one pinned DefenseFinder custom HMM-profile row, and no pinned DefenseFinder rule row. It does not assert native host breadth, exact profile-to-protein correspondence, molecular activity, phage trigger, substrate, complete homolog boundary, endogenous activity, or rule-level DefenseFinder detection criteria.",
        "nodes": [
          {
            "node_id": "vp1851_locus",
            "label": "VP1851 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A Vp1851-like integron cassette locus represented in the pinned DefenseFinder HMM inventory by the VP1851__VP1851 custom profile."
          },
          {
            "node_id": "reduced_bacteriophage_plaquing",
            "label": "reduced bacteriophage plaquing",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced plaquing of bacteriophages in cells expressing cloned vp1851."
          },
          {
            "node_id": "vp1851_system_trait",
            "label": "VP1851 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000491",
            "description": "Possession of a genome-encoded VP1851 phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "vp1851_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "reduced_bacteriophage_plaquing",
            "description": "The cloned V. parahaemolyticus vp1851 integron cassette contributes to reduced bacteriophage plaquing in VSV105 plasmid-expression assays, and DefenseFinder represents the VP1851 family with one custom HMM profile.",
            "evidence": [
              {
                "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
                "snippet": "VP_RS09000\tVp1851\tY\tWP_005483174.1 \tEcsC family protein",
                "notes": "Supplementary Table 8 lists VP_RS09000/Vp1851 as a cloned RIMD 2210633 integron cassette with protein accession WP_005483174.1."
              },
              {
                "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
                "snippet": "VSV105-vp1851\tVSV105 carrying gene vp1851 behind the lac promoter, cloned into KpnI by In-Fusion\tThis Study",
                "notes": "Supplementary Table 12 records the VSV105-vp1851 lac-expression plasmid used to express vp1851 behind the lac promoter."
              },
              {
                "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
                "snippet": "VP1851\tLL1\t0",
                "notes": "Supplementary Table 9 identifies the VP1851/LL1 phage-plating readout as a Fold Change value of 0."
              },
              {
                "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
                "snippet": "VP1851\tVL1\t1.54e-07",
                "notes": "Supplementary Table 9 identifies the VP1851/VL1 phage-plating readout as a Fold Change value of 1.54e-07."
              },
              {
                "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM3_ESM.xlsx",
                "snippet": ">WP_005483174.1 MULTISPECIES: EcsC family protein [Vibrio harveyi group]",
                "notes": "Supplementary Data 1's VP1851 worksheet labels WP_005483174.1 from the Vibrio harveyi group as the PSI-BLAST query protein."
              },
              {
                "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM3_ESM.xlsx",
                "snippet": "Scientific Name\tQuery Cover\tE value\tPer. ident\tAccession  \nVibrio harveyi group\t1\t2e-144\t100\tWP_005483174.1\nVibrio parahaemolyticus\t0.99\t2e-143\t100\tARC19782.1",
                "notes": "Supplementary Data 1's VP1851 worksheet records a full-length 100% PSI-BLAST row for WP_005483174.1 and a 99% query-coverage 100% identity hit to Vibrio parahaemolyticus ARC19782.1."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| VP1851__VP1851                                   |                                                  | VP1851                 | Custom                  | 125    |",
                "notes": "The pinned DefenseFinder HMM inventory records VP1851__VP1851 as a custom VP1851 profile."
              }
            ]
          },
          {
            "subject": "reduced_bacteriophage_plaquing",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "vp1851_system_trait",
            "description": "VP1851-mediated bacteriophage plaquing reduction realizes the VP1851 system trait.",
            "evidence": [
              {
                "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
                "snippet": "VP1851\tLL1\t0",
                "notes": "Supplementary Table 9 identifies the VP1851/LL1 phage-plating readout as a Fold Change value of 0."
              },
              {
                "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
                "snippet": "VP1851\tVL1\t1.54e-07",
                "notes": "Supplementary Table 9 identifies the VP1851/VL1 phage-plating readout as a Fold Change value of 1.54e-07."
              }
            ]
          },
          {
            "subject": "vp1851_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "VP1851 system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-025-01927-7",
                "snippet": "Intrigued by this discovery, we cloned 57 integron gene cassettes and identified 9 previously unrecognized systems that mediate defence.",
                "notes": "Getz et al. identify nine previously unrecognized Vibrio parahaemolyticus integron cassettes as anti-phage defense systems."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| VP1851 | 10\\.1038/s41564-025-01927-7 | Integrons are anti-phage defence libraries in Vibrio parahaemolyticus | ",
                "notes": "The pinned DefenseFinder article registry maps the VP1851 model namespace to the Getz et al. Vibrio parahaemolyticus integron-defense paper."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "vp1851-defensefinder-model-gap",
        "prompt": "Resolve VP1851 native host breadth, exact single-component activity, profile-to-protein mapping, homolog boundary, full phage breadth, molecular output, and rule-level DefenseFinder criteria before minting narrower VP1851 mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Getz et al. support VP1851 as one of nine RIMD 2210633 integron-encoded cassettes whose cloned expression reduced phage plaquing, Supplementary Tables 8, 9, and 12 map VP1851 to VP_RS09000/Vp1851, WP_005483174.1, VSV105-vp1851, and phage-plating fold changes, and Supplementary Data 1 reports PSI-BLAST homologs. The pinned DefenseFinder HMM inventory records one VP1851 custom profile row. The pinned rules table has no VP1851 row, and the first-pass record does not resolve native host breadth, complete phage breadth, direct profile-to-protein correspondence, molecular output, or endogenous activity.",
        "evidence": [
          {
            "reference": "DOI:10.1038/s41564-025-01927-7",
            "snippet": "Intrigued by this discovery, we cloned 57 integron gene cassettes and identified 9 previously unrecognized systems that mediate defence.",
            "notes": "Getz et al. identify nine previously unrecognized Vibrio parahaemolyticus integron cassettes as anti-phage defense systems."
          },
          {
            "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
            "snippet": "VP_RS09000\tVp1851\tY\tWP_005483174.1 \tEcsC family protein",
            "notes": "Supplementary Table 8 lists VP_RS09000/Vp1851 as a cloned RIMD 2210633 integron cassette with protein accession WP_005483174.1."
          },
          {
            "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
            "snippet": "VSV105-vp1851\tVSV105 carrying gene vp1851 behind the lac promoter, cloned into KpnI by In-Fusion\tThis Study",
            "notes": "Supplementary Table 12 records the VSV105-vp1851 lac-expression plasmid used to express vp1851 behind the lac promoter."
          },
          {
            "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
            "snippet": "VP1851\tLL1\t0",
            "notes": "Supplementary Table 9 identifies the VP1851/LL1 phage-plating readout as a Fold Change value of 0."
          },
          {
            "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
            "snippet": "VP1851\tVL1\t1.54e-07",
            "notes": "Supplementary Table 9 identifies the VP1851/VL1 phage-plating readout as a Fold Change value of 1.54e-07."
          },
          {
            "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM3_ESM.xlsx",
            "snippet": ">WP_005483174.1 MULTISPECIES: EcsC family protein [Vibrio harveyi group]",
            "notes": "Supplementary Data 1's VP1851 worksheet labels WP_005483174.1 from the Vibrio harveyi group as the PSI-BLAST query protein."
          },
          {
            "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM3_ESM.xlsx",
            "snippet": "Scientific Name\tQuery Cover\tE value\tPer. ident\tAccession  \nVibrio harveyi group\t1\t2e-144\t100\tWP_005483174.1\nVibrio parahaemolyticus\t0.99\t2e-143\t100\tARC19782.1",
            "notes": "Supplementary Data 1's VP1851 worksheet records a full-length 100% PSI-BLAST row for WP_005483174.1 and a 99% query-coverage 100% identity hit to Vibrio parahaemolyticus ARC19782.1."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
            "snippet": "| VP1851 | 10\\.1038/s41564-025-01927-7 | Integrons are anti-phage defence libraries in Vibrio parahaemolyticus | ",
            "notes": "The pinned DefenseFinder article registry maps the VP1851 model namespace to the Getz et al. Vibrio parahaemolyticus integron-defense paper."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| VP1851__VP1851                                   |                                                  | VP1851                 | Custom                  | 125    |",
            "notes": "The pinned DefenseFinder HMM inventory records VP1851__VP1851 as a custom VP1851 profile."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "The pinned DefenseFinder rules table does not list VP1851, leaving rule-level detection criteria unresolved."
          }
        ],
        "attaches_to": [
          "causal_graphs#vp1851_locus_reduces_bacteriophage_plaquing"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-30"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-30T12:15:25Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted VP1851 system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact same-scope live TraitMech, METPO, history, or prior proposal record; kept the graph at cloned integron-cassette level because molecular output, native activity, and rule rows remain unresolved; proposals/metpo_traitmech_v368 reserves the replacement placeholder.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-30T12:15:26Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed VP1851 system canonical_examples and left them empty because Getz et al. directly support cloned VP1851 VSV105-plasmid assays, PSI-BLAST homologs, and a DefenseFinder VP1851 model, but not a direct named native microbial isolate exemplar with experimentally verified endogenous VP1851 activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000492",
    "label": "VP1853 system",
    "definition": "A phage defense system in which an organism possesses a VP1853-family locus represented by the DefenseFinder VP1853__VP1853 custom HMM profile and experimentally linked to reduced bacteriophage plaquing when the cloned Vibrio parahaemolyticus RIMD 2210633 vp1853 cassette is expressed from a VSV105 plasmid.",
    "definition_source": "DOI:10.1038/s41564-025-01927-7",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "VP1853",
        "synonym_type": "EXACT_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md"
      },
      {
        "synonym_text": "Vp1853",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx"
      },
      {
        "synonym_text": "VP1853__VP1853",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/s41564-025-01927-7",
        "snippet": "Intrigued by this discovery, we cloned 57 integron gene cassettes and identified 9 previously unrecognized systems that mediate defence.",
        "notes": "Getz et al. identify nine previously unrecognized Vibrio parahaemolyticus integron cassettes as anti-phage defense systems."
      },
      {
        "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
        "snippet": "VP_RS09025\tVp1853\tY\tWP_005483178.1\tTIGR02391 family protein",
        "notes": "Supplementary Table 8 lists VP_RS09025/Vp1853 as a cloned RIMD 2210633 integron cassette with protein accession WP_005483178.1."
      },
      {
        "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
        "snippet": "VSV105-vp1853\tVSV105 carrying gene vp1853 behind the lac promoter, cloned into KpnI by In-Fusion\tThis Study",
        "notes": "Supplementary Table 12 records the VSV105-vp1853 lac-expression plasmid used to express vp1853 behind the lac promoter."
      },
      {
        "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
        "snippet": "VP1853\t\u03bb\t0.001\tSmall",
        "notes": "Supplementary Table 9 identifies the VP1853/lambda phage-plating readout as a Fold Change value of 0.001 with a Small Plaque Size comment."
      },
      {
        "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM3_ESM.xlsx",
        "snippet": ">WP_005483178.1 TIGR02391 family protein [Vibrio parahaemolyticus]",
        "notes": "Supplementary Data 1's VP1853 worksheet labels WP_005483178.1 from Vibrio parahaemolyticus as the PSI-BLAST query protein."
      },
      {
        "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM3_ESM.xlsx",
        "snippet": "Scientific Name\tQuery Cover\tE value\tPer. ident\tAccession  \nVibrio parahaemolyticus\t1\t0\t100\tWP_005483178.1\nVibrio parahaemolyticus\t1\t0\t100\tWP_049875404.1",
        "notes": "Supplementary Data 1's VP1853 worksheet records full-length 100% PSI-BLAST rows for WP_005483178.1 and WP_049875404.1."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| VP1853 | 10\\.1038/s41564-025-01927-7 | Integrons are anti-phage defence libraries in Vibrio parahaemolyticus | ",
        "notes": "The pinned DefenseFinder article registry maps the VP1853 model namespace to the Getz et al. Vibrio parahaemolyticus integron-defense paper."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| VP1853__VP1853                                   |                                                  | VP1853                 | Custom                  | 150    |",
        "notes": "The pinned DefenseFinder HMM inventory records VP1853__VP1853 as a custom VP1853 profile."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "vp1853_locus_reduces_bacteriophage_plaquing",
        "title": "VP1853 loci reduce bacteriophage plaquing",
        "description": "Conservative system-level sketch linking VP1853-family locus possession to reduced bacteriophage plaquing without resolving VP1853 component function or molecular output.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures VP1853 as a RIMD 2210633 integron cassette with cloned phage-plating readouts, a PSI-BLAST homolog lead, one pinned DefenseFinder custom HMM-profile row, and no pinned DefenseFinder rule row. It does not assert native host breadth, exact profile-to-protein correspondence, molecular activity, phage trigger, substrate, complete homolog boundary, endogenous activity, or rule-level DefenseFinder detection criteria.",
        "nodes": [
          {
            "node_id": "vp1853_locus",
            "label": "VP1853 locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A Vp1853-like integron cassette locus represented in the pinned DefenseFinder HMM inventory by the VP1853__VP1853 custom profile."
          },
          {
            "node_id": "reduced_bacteriophage_plaquing",
            "label": "reduced bacteriophage plaquing",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced plaquing of bacteriophages in cells expressing cloned vp1853."
          },
          {
            "node_id": "vp1853_system_trait",
            "label": "VP1853 system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000492",
            "description": "Possession of a genome-encoded VP1853 phage-defense system."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "vp1853_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "reduced_bacteriophage_plaquing",
            "description": "The cloned V. parahaemolyticus vp1853 integron cassette contributes to reduced bacteriophage plaquing in VSV105 plasmid-expression assays, and DefenseFinder represents the VP1853 family with one custom HMM profile.",
            "evidence": [
              {
                "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
                "snippet": "VP_RS09025\tVp1853\tY\tWP_005483178.1\tTIGR02391 family protein",
                "notes": "Supplementary Table 8 lists VP_RS09025/Vp1853 as a cloned RIMD 2210633 integron cassette with protein accession WP_005483178.1."
              },
              {
                "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
                "snippet": "VSV105-vp1853\tVSV105 carrying gene vp1853 behind the lac promoter, cloned into KpnI by In-Fusion\tThis Study",
                "notes": "Supplementary Table 12 records the VSV105-vp1853 lac-expression plasmid used to express vp1853 behind the lac promoter."
              },
              {
                "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
                "snippet": "VP1853\t\u03bb\t0.001\tSmall",
                "notes": "Supplementary Table 9 identifies the VP1853/lambda phage-plating readout as a Fold Change value of 0.001 with a Small Plaque Size comment."
              },
              {
                "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM3_ESM.xlsx",
                "snippet": ">WP_005483178.1 TIGR02391 family protein [Vibrio parahaemolyticus]",
                "notes": "Supplementary Data 1's VP1853 worksheet labels WP_005483178.1 from Vibrio parahaemolyticus as the PSI-BLAST query protein."
              },
              {
                "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM3_ESM.xlsx",
                "snippet": "Scientific Name\tQuery Cover\tE value\tPer. ident\tAccession  \nVibrio parahaemolyticus\t1\t0\t100\tWP_005483178.1\nVibrio parahaemolyticus\t1\t0\t100\tWP_049875404.1",
                "notes": "Supplementary Data 1's VP1853 worksheet records full-length 100% PSI-BLAST rows for WP_005483178.1 and WP_049875404.1."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| VP1853__VP1853                                   |                                                  | VP1853                 | Custom                  | 150    |",
                "notes": "The pinned DefenseFinder HMM inventory records VP1853__VP1853 as a custom VP1853 profile."
              }
            ]
          },
          {
            "subject": "reduced_bacteriophage_plaquing",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "vp1853_system_trait",
            "description": "VP1853-mediated bacteriophage plaquing reduction realizes the VP1853 system trait.",
            "evidence": [
              {
                "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
                "snippet": "VP1853\t\u03bb\t0.001\tSmall",
                "notes": "Supplementary Table 9 identifies the VP1853/lambda phage-plating readout as a Fold Change value of 0.001 with a Small Plaque Size comment."
              }
            ]
          },
          {
            "subject": "vp1853_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "VP1853 system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-025-01927-7",
                "snippet": "Intrigued by this discovery, we cloned 57 integron gene cassettes and identified 9 previously unrecognized systems that mediate defence.",
                "notes": "Getz et al. identify nine previously unrecognized Vibrio parahaemolyticus integron cassettes as anti-phage defense systems."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| VP1853 | 10\\.1038/s41564-025-01927-7 | Integrons are anti-phage defence libraries in Vibrio parahaemolyticus | ",
                "notes": "The pinned DefenseFinder article registry maps the VP1853 model namespace to the Getz et al. Vibrio parahaemolyticus integron-defense paper."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "vp1853-defensefinder-model-gap",
        "prompt": "Resolve VP1853 native host breadth, exact single-component activity, profile-to-protein mapping, homolog boundary, full phage breadth, molecular output, and rule-level DefenseFinder criteria before minting narrower VP1853 mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Getz et al. support VP1853 as one of nine RIMD 2210633 integron-encoded cassettes whose cloned expression reduced phage plaquing, Supplementary Tables 8, 9, and 12 map VP1853 to VP_RS09025/Vp1853, WP_005483178.1, VSV105-vp1853, and a phage-plating fold change, and Supplementary Data 1 reports PSI-BLAST homologs. The pinned DefenseFinder HMM inventory records one VP1853 custom profile row. The pinned rules table has no VP1853 row, and the first-pass record does not resolve native host breadth, complete phage breadth, direct profile-to-protein correspondence, molecular output, or endogenous activity.",
        "evidence": [
          {
            "reference": "DOI:10.1038/s41564-025-01927-7",
            "snippet": "Intrigued by this discovery, we cloned 57 integron gene cassettes and identified 9 previously unrecognized systems that mediate defence.",
            "notes": "Getz et al. identify nine previously unrecognized Vibrio parahaemolyticus integron cassettes as anti-phage defense systems."
          },
          {
            "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
            "snippet": "VP_RS09025\tVp1853\tY\tWP_005483178.1\tTIGR02391 family protein",
            "notes": "Supplementary Table 8 lists VP_RS09025/Vp1853 as a cloned RIMD 2210633 integron cassette with protein accession WP_005483178.1."
          },
          {
            "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
            "snippet": "VSV105-vp1853\tVSV105 carrying gene vp1853 behind the lac promoter, cloned into KpnI by In-Fusion\tThis Study",
            "notes": "Supplementary Table 12 records the VSV105-vp1853 lac-expression plasmid used to express vp1853 behind the lac promoter."
          },
          {
            "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx",
            "snippet": "VP1853\t\u03bb\t0.001\tSmall",
            "notes": "Supplementary Table 9 identifies the VP1853/lambda phage-plating readout as a Fold Change value of 0.001 with a Small Plaque Size comment."
          },
          {
            "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM3_ESM.xlsx",
            "snippet": ">WP_005483178.1 TIGR02391 family protein [Vibrio parahaemolyticus]",
            "notes": "Supplementary Data 1's VP1853 worksheet labels WP_005483178.1 from Vibrio parahaemolyticus as the PSI-BLAST query protein."
          },
          {
            "reference": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM3_ESM.xlsx",
            "snippet": "Scientific Name\tQuery Cover\tE value\tPer. ident\tAccession  \nVibrio parahaemolyticus\t1\t0\t100\tWP_005483178.1\nVibrio parahaemolyticus\t1\t0\t100\tWP_049875404.1",
            "notes": "Supplementary Data 1's VP1853 worksheet records full-length 100% PSI-BLAST rows for WP_005483178.1 and WP_049875404.1."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
            "snippet": "| VP1853 | 10\\.1038/s41564-025-01927-7 | Integrons are anti-phage defence libraries in Vibrio parahaemolyticus | ",
            "notes": "The pinned DefenseFinder article registry maps the VP1853 model namespace to the Getz et al. Vibrio parahaemolyticus integron-defense paper."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| VP1853__VP1853                                   |                                                  | VP1853                 | Custom                  | 150    |",
            "notes": "The pinned DefenseFinder HMM inventory records VP1853__VP1853 as a custom VP1853 profile."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "notes": "The pinned DefenseFinder rules table does not list VP1853, leaving rule-level detection criteria unresolved."
          }
        ],
        "attaches_to": [
          "causal_graphs#vp1853_locus_reduces_bacteriophage_plaquing"
        ],
        "posed_by": "codex",
        "posed_date": "2026-09-30"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-30T12:56:22Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted VP1853 system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact same-scope live TraitMech, METPO, history, or prior proposal record; kept the graph at cloned integron-cassette level because molecular output, native activity, and rule rows remain unresolved; proposals/metpo_traitmech_v369 reserves the replacement placeholder.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-30T12:56:23Z",
        "curator": "codex",
        "action": "REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP",
        "changes": "Reviewed VP1853 system canonical_examples and left them empty because Getz et al. directly support cloned VP1853 VSV105-plasmid assays, PSI-BLAST homologs, and a DefenseFinder VP1853 model, but not a direct named native microbial isolate exemplar with experimentally verified endogenous VP1853 activity. No paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000218",
    "label": "Wadjet system",
    "definition": "A genomics trait describing possession of a Wadjet anti-plasmid defense locus encoding a derivative SMC complex such as JetABCD, MksBEFG, or EptABCD that restricts circular plasmids by ATPase-dependent DNA cleavage.",
    "definition_source": "DOI:10.1016/j.molcel.2022.11.015",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000188"
    ],
    "synonyms": [
      {
        "synonym_text": "Wadjet defense system",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1016/j.molcel.2022.09.008"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1016/j.molcel.2022.11.015",
        "snippet": "Wadjet systems (JetABCD/MksBEFG/EptABCD) are derivative SMC complexes with roles in bacterial immunity against selfish DNA",
        "notes": "Liu et al. support defining Wadjet as a recurring SMC-derived bacterial immune system spanning JetABCD, MksBEFG, and EptABCD subfamilies."
      },
      {
        "reference": "DOI:10.1016/j.molcel.2022.09.008",
        "snippet": "the Wadjet defense system recognizes DNA topology to protect its host against plasmid transformation",
        "notes": "Deep et al. support the standard Wadjet defense system name and connect the system to anti-plasmid immunity."
      },
      {
        "reference": "DOI:10.1016/j.molcel.2022.09.008",
        "snippet": "Wadjet forms a complex similar to the bacterial condensin complex MukBEF, with a novel nuclease subunit similar to a type II DNA topoisomerase",
        "notes": "Deep et al. support the SMC-family complex architecture and JetD-like nuclease component."
      },
      {
        "reference": "DOI:10.1016/j.molcel.2022.11.015",
        "snippet": "Purified JetABCD complexes cleave circular DNA molecules, regardless of the DNA helical topology; cleavage is DNA sequence nonspecific and depends on the SMC ATPase",
        "notes": "Liu et al. connect JetABCD SMC ATPase activity to sequence-independent cleavage of circular plasmid DNA."
      },
      {
        "reference": "DOI:10.1093/nar/gkad130",
        "snippet": "MksG is a nuclease that degrades plasmid DNA",
        "notes": "Weiss et al. support the MksG nuclease as the executing plasmid-DNA-degradation component of MksBEFG."
      },
      {
        "reference": "DOI:10.1093/nar/gkad130",
        "snippet": "Introduction of plasmids results in an increase in DNA bound MksG, indicating an activation of the system in vivo",
        "notes": "Weiss et al. support plasmid-responsive activation of the Corynebacterium glutamicum MksBEFG system in vivo."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1718",
        "taxon_label": "Corynebacterium glutamicum",
        "note": "Weiss et al. investigated the Corynebacterium glutamicum MksBEFG complex and showed that plasmid introduction increased DNA-bound MksG in vivo.",
        "reference": "DOI:10.1093/nar/gkad130"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "wadjet_smc_plasmid_restriction",
        "title": "Wadjet SMC complexes cleave circular plasmid DNA",
        "description": "Evidence-backed process sketch linking a Wadjet locus to SMC ATPase cycling, Wadjet nuclease-mediated circular plasmid cleavage, and restriction of plasmid transformation.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures JetABCD and MksBEFG family-level anti-plasmid outputs without asserting one universal subfamily architecture, plasmid size threshold, linear plasmid escape rule, polar scaffold, DNA-loop-extrusion state, or activation cue across all Wadjet loci.",
        "nodes": [
          {
            "node_id": "wadjet_locus",
            "label": "Wadjet locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A Wadjet anti-plasmid defense locus encoding JetABCD, MksBEFG, EptABCD, or related SMC-family components."
          },
          {
            "node_id": "wadjet_smc_atpase_cycle",
            "label": "Wadjet SMC ATPase cycle",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "ATPase cycling by the Wadjet SMC core complex during circular DNA restriction."
          },
          {
            "node_id": "wadjet_plasmid_dna_cleavage",
            "label": "Wadjet plasmid DNA cleavage",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Cleavage or processive degradation of circular plasmid DNA by a Wadjet-associated nuclease."
          },
          {
            "node_id": "plasmid_transformation",
            "label": "plasmid transformation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Introduction and establishment of exogenous plasmid DNA in a bacterial cell."
          },
          {
            "node_id": "wadjet_system_trait",
            "label": "Wadjet system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000218",
            "description": "Possession of a genome-encoded Wadjet anti-plasmid defense locus."
          }
        ],
        "edges": [
          {
            "subject": "wadjet_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "wadjet_smc_atpase_cycle",
            "description": "Wadjet loci encode derivative SMC complexes with Jet, Mks, or Ept ATPase cores.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.molcel.2022.11.015",
                "snippet": "Wadjet systems (JetABCD/MksBEFG/EptABCD) are derivative SMC complexes with roles in bacterial immunity against selfish DNA",
                "notes": "Liu et al. support JetABCD, MksBEFG, and EptABCD as Wadjet-family SMC complexes."
              }
            ]
          },
          {
            "subject": "wadjet_smc_atpase_cycle",
            "predicate": "enables",
            "predicate_id": "RO:0002327",
            "object": "wadjet_plasmid_dna_cleavage",
            "description": "The Wadjet SMC ATPase cycle enables nuclease-driven cleavage of circular plasmid DNA.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.molcel.2022.11.015",
                "snippet": "Purified JetABCD complexes cleave circular DNA molecules, regardless of the DNA helical topology; cleavage is DNA sequence nonspecific and depends on the SMC ATPase",
                "notes": "Liu et al. support SMC-ATPase-dependent cleavage by purified JetABCD."
              },
              {
                "reference": "DOI:10.1093/nar/gkad130",
                "snippet": "The MksBEF subunits exhibit an ATPase cycle in vitro",
                "notes": "Weiss et al. support ATPase cycling by the C. glutamicum MksBEF core."
              }
            ]
          },
          {
            "subject": "wadjet_plasmid_dna_cleavage",
            "predicate": "mitigates",
            "predicate_id": "METPO:2007407",
            "object": "plasmid_transformation",
            "description": "Wadjet-mediated plasmid DNA cleavage restricts incoming circular plasmids.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.molcel.2022.09.008",
                "snippet": "the Wadjet defense system recognizes DNA topology to protect its host against plasmid transformation",
                "notes": "Deep et al. support Wadjet-mediated protection against plasmid transformation."
              }
            ]
          },
          {
            "subject": "wadjet_plasmid_dna_cleavage",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "wadjet_system_trait",
            "description": "Wadjet nuclease-mediated plasmid DNA cleavage is the anti-plasmid output that realizes the Wadjet system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1093/nar/gkad130",
                "snippet": "MksG is a nuclease that degrades plasmid DNA",
                "notes": "Weiss et al. support MksG nuclease activity as a Wadjet/MksBEFG plasmid-degradation output."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "wadjet-subfamily-and-substrate-gap",
        "prompt": "Resolve JetABCD, EptABCD, DefenseFinder Wadjet subtype boundaries, plasmid substrate specificity, and activation cues before minting additional narrower Wadjet mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Deep et al. and Liu et al. support JetABCD-mediated topology- or shape-biased circular plasmid cleavage and the broad JetABCD/MksBEFG/EptABCD Wadjet family, while the MksBEFG child now captures the Weiss et al. plasmid-degradation branch. The parent still leaves JetABCD, EptABCD, DefenseFinder Wadjet I-III boundaries, exact target size threshold, linear-plasmid escape rule, loop-extrusion endpoint, polar localization pattern, and nuclease activation models for additional Wadjet variants unresolved.",
        "posed_by": "codex",
        "posed_date": "2026-09-15"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-15T14:19:20Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Wadjet system as a DOI-backed GENOMICS TraitRecord after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v95.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-01T21:15:01Z",
        "curator": "codex",
        "action": "RESOLVE_DISCUSSION_SCOPE",
        "changes": "Documented MksBEFG as split out in the open Wadjet subfamily and substrate discussion after minting traitmech:000526 for the MksBEFG system; JetABCD, EptABCD, and DefenseFinder Wadjet subtype boundaries remain open.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000217",
    "label": "Zorya system",
    "definition": "A genomics trait describing possession of a Zorya antiphage defense locus in which conserved ZorA/ZorB membrane-motor core proteins and subtype-specific effector proteins inhibit bacteriophage propagation.",
    "definition_source": "DOI:10.1038/s41586-024-08493-8",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000209"
    ],
    "synonyms": [
      {
        "synonym_text": "Zorya anti-phage defence system",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1038/s41586-024-08493-8"
      },
      {
        "synonym_text": "Zorya phage defense system",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1038/s41467-025-57397-2"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/s41586-024-08493-8",
        "snippet": "Zorya is a recently identified and widely distributed bacterial immune system that protects bacteria from viral (phage) infections",
        "notes": "Hu et al. support Zorya as a bacterial antiviral immune system."
      },
      {
        "reference": "DOI:10.1038/s41467-025-57397-2",
        "snippet": "The Zorya phage defense system was first discovered in 2018",
        "notes": "Mariano et al. support the standard US-English family name for the Zorya system."
      },
      {
        "reference": "DOI:10.1038/s41467-025-57397-2",
        "snippet": "all Zorya systems share two components, ZorA and ZorB, containing domains distantly related, respectively, to the MotA and MotB subunits of the bacterial flagellar motor",
        "notes": "Mariano et al. support the conserved ZorA/ZorB motor-core architecture shared by Zorya systems."
      },
      {
        "reference": "DOI:10.1038/s41586-024-08493-8",
        "snippet": "ZorAB transfers the phage invasion signal through the ZorA cytoplasmic tail to recruit and activate the soluble ZorC and ZorD effectors",
        "notes": "Hu et al. support the Type I ZorAB-dependent effector recruitment and activation step."
      },
      {
        "reference": "DOI:10.1038/s41467-025-57397-2",
        "snippet": "For Zorya II, anti-phage activity requires the presence of the ZorE effector, which we show is recruited by ZorAB",
        "notes": "Mariano et al. support Type II ZorE as a ZorAB-recruited effector."
      },
      {
        "reference": "DOI:10.1038/s41467-025-57397-2",
        "snippet": "We observed that homologs of Zorya I from Serratia marcescens ATCC 274 and Zorya II from E. coli ATCC 8739 provide protection against several phages from the Durham collection",
        "notes": "Mariano et al. support experimentally validated Zorya phage protection from native Serratia marcescens and E. coli loci."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:562",
        "taxon_label": "Escherichia coli",
        "note": "Mariano et al. report that a Zorya II locus from E. coli ATCC 8739 protected E. coli MT56 against several tested coliphages.",
        "reference": "DOI:10.1038/s41467-025-57397-2"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "zorya_zorab_effector_antiphage_defense",
        "title": "Zorya ZorAB motors recruit antiphage effectors",
        "description": "Evidence-backed process sketch linking a Zorya locus to phage-triggered ZorAB ion-motor activation, effector recruitment, and inhibition of bacteriophage replication.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures characterized Type I ZorC/ZorD and Type II ZorE outputs without asserting one universal ZorAB-coupled effector, ion substrate, DNA target, cell-death pathway, Type III mechanism, or anti-Zorya-evasion mechanism across all Zorya loci.",
        "nodes": [
          {
            "node_id": "phage_invasion",
            "label": "phage invasion",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Entry of a bacteriophage and its nucleic acid into a bacterial host cell."
          },
          {
            "node_id": "zorya_locus",
            "label": "Zorya locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A Zorya antiphage defense locus encoding conserved ZorA/ZorB membrane core proteins and subtype-specific effector proteins."
          },
          {
            "node_id": "zorab_ion_motor_activation",
            "label": "ZorAB ion-motor activation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Activation of a membrane-anchored ZorA/ZorB ion-driven motor after detection of phage invasion."
          },
          {
            "node_id": "zorya_effector_activity",
            "label": "Zorya effector activity",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Activity of ZorAB-coupled Zorya effector proteins such as Type I ZorC/ZorD or Type II ZorE."
          },
          {
            "node_id": "phage_replication",
            "label": "phage replication",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Replication of invading bacteriophage DNA after host-cell entry."
          },
          {
            "node_id": "zorya_system_trait",
            "label": "Zorya system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000217",
            "description": "Possession of a genome-encoded Zorya antiphage defense locus."
          },
          {
            "node_id": "phage_defense_system",
            "label": "phage defense system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000209",
            "description": "Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection."
          }
        ],
        "edges": [
          {
            "subject": "zorya_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "zorab_ion_motor_activation",
            "description": "Zorya loci encode the conserved ZorA and ZorB membrane core proteins that form the ZorAB motor.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-025-57397-2",
                "snippet": "all Zorya systems share two components, ZorA and ZorB, containing domains distantly related, respectively, to the MotA and MotB subunits of the bacterial flagellar motor",
                "notes": "Mariano et al. support ZorA/ZorB as the conserved Zorya core proteins."
              }
            ]
          },
          {
            "subject": "phage_invasion",
            "predicate": "activates",
            "predicate_id": "RO:0002213",
            "object": "zorab_ion_motor_activation",
            "description": "Phage invasion activates the ZorAB ion motor after Zorya senses bacteriophage challenge.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41586-024-08493-8",
                "snippet": "ZorAB operates as a proton-driven motor that becomes activated after sensing of phage invasion",
                "notes": "Hu et al. support phage-invasion-dependent ZorAB activation."
              }
            ]
          },
          {
            "subject": "zorab_ion_motor_activation",
            "predicate": "activates",
            "predicate_id": "RO:0002213",
            "object": "zorya_effector_activity",
            "description": "ZorAB motor activation recruits and activates subtype-specific Zorya effector proteins.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41586-024-08493-8",
                "snippet": "ZorAB transfers the phage invasion signal through the ZorA cytoplasmic tail to recruit and activate the soluble ZorC and ZorD effectors",
                "notes": "Hu et al. support ZorAB-mediated Type I ZorC/ZorD activation."
              },
              {
                "reference": "DOI:10.1038/s41467-025-57397-2",
                "snippet": "For Zorya II, anti-phage activity requires the presence of the ZorE effector, which we show is recruited by ZorAB",
                "notes": "Mariano et al. support ZorAB-mediated recruitment of the Type II ZorE effector."
              }
            ]
          },
          {
            "subject": "zorya_effector_activity",
            "predicate": "mitigates",
            "predicate_id": "METPO:2007407",
            "object": "phage_replication",
            "description": "Zorya effector activity helps inhibit invading bacteriophages.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41586-024-08493-8",
                "snippet": "soluble ZorC and ZorD effectors, which facilitate the degradation of the phage DNA",
                "notes": "Hu et al. support Type I ZorC/ZorD effectors as phage-DNA-degradation outputs."
              }
            ]
          },
          {
            "subject": "zorya_effector_activity",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "zorya_system_trait",
            "description": "Zorya effector activity is the antiviral output that realizes the Zorya system defense phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-025-57397-2",
                "snippet": "Our work reveals the molecular basis of the activity of Zorya systems and highlights the ZorE nickase as crucial for population-wide immunity in the type II system",
                "notes": "Mariano et al. support ZorE nickase activity as a Type II Zorya effector output."
              }
            ]
          },
          {
            "subject": "zorya_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "phage_defense_system",
            "description": "Zorya system possession is a phage-defense-system trait.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-025-57397-2",
                "snippet": "The Zorya phage defense system was first discovered in 2018",
                "notes": "Mariano et al. place Zorya in the phage-defense-system family."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "zorya-subtype-effector-and-trigger-gap",
        "prompt": "Resolve Zorya subtype effectors, ion usage, and phage triggers before minting narrower Zorya mechanism children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Hu et al. support Type I ZorAB activation and ZorC/ZorD-mediated phage-DNA degradation, Mariano et al. support Type I/II ZorAB architecture plus a recruited Type II ZorE nickase, and the pinned DefenseFinder rules table supports distinct Zorya_TypeI and Zorya_TypeII subtype rows. Zorya type I and type II TraitRecords now capture those DefenseFinder subtypes, but Zorya variants still need separate review before TraitMech asserts one universal ion substrate, effector composition, nuclease target, cell-death pathway, Type III mechanism, or anti-defense breadth. The type-III architecture is now represented by traitmech:000576 Zorya type III system for ZorA/ZorB/ZorF/ZorG loci. Payne Figure 2C and Discussion plus Mariano's Introduction support that composition despite the conflicting zorBC wording in Payne's Results. DefenseFinder's three-match threshold is not a complete four-component biological definition. Type-III component roles and native-host mechanisms remain open; the family definition, graph and type-I/II records are unchanged.",
        "posed_by": "codex",
        "posed_date": "2026-09-15"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-15T13:45:12Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Zorya system as a DOI-backed GENOMICS TraitRecord under the phage defense system parent after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v94.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-02T18:08:01Z",
        "curator": "codex",
        "action": "TRACK_NARROWER_RECORD",
        "changes": "Documented Zorya type II as split out in the open Zorya subtype-effector discussion after minting traitmech:000552 for the DefenseFinder-backed Zorya_TypeII child; Type I, Type III, and finer Zorya subtype mechanisms remain open.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-02T20:10:34Z",
        "curator": "codex",
        "action": "TRACK_NARROWER_RECORD",
        "changes": "Documented Zorya type I as split out in the open Zorya subtype-effector discussion after minting traitmech:000554 for the DefenseFinder-backed Zorya_TypeI child; Type III and finer Zorya subtype mechanisms remain open.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-03T19:16:00Z",
        "curator": "codex",
        "action": "TRACK_ZORYA_TYPE_III_CLASS",
        "changes": "Linked traitmech:000576 using DOI:10.1093/nar/gkab883 and DOI:10.1038/s41467-025-57397-2. Kept the family definition, hierarchy, graph, evidence and example unchanged; type-III component functions remain open rather than inheriting type-I/II chemistry.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000554",
    "label": "Zorya type I system",
    "definition": "A Zorya system in which an organism possesses a genome-encoded DefenseFinder Zorya_TypeI subtype locus whose rule row lists Zorya_TypeI__ZorC, Zorya_TypeI__ZorD, Zorya__ZorA, and Zorya__ZorB in its mandatory profile set with 3 mandatory matches and 3 genes required.",
    "definition_source": "DOI:10.1038/s41586-024-08493-8",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000217"
    ],
    "synonyms": [
      {
        "synonym_text": "Zorya_TypeI",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv"
      },
      {
        "synonym_text": "Zorya_TypeI__ZorC",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "Zorya_TypeI__ZorD",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "Zorya__ZorA",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "Zorya__ZorB",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/s41586-024-08493-8",
        "snippet": "ZorAB transfers the phage invasion signal through the ZorA cytoplasmic tail to recruit and activate the soluble ZorC and ZorD effectors",
        "notes": "Hu et al. support ZorAB-mediated recruitment and activation of the soluble ZorC and ZorD Type I effectors."
      },
      {
        "reference": "DOI:10.1038/s41586-024-08493-8",
        "snippet": "soluble ZorC and ZorD effectors, which facilitate the degradation of the phage DNA",
        "notes": "Hu et al. support Type I ZorC/ZorD effectors as phage-DNA degradation outputs."
      },
      {
        "reference": "DOI:10.1038/s41467-025-57397-2",
        "snippet": "We observed that homologs of Zorya I from Serratia marcescens ATCC 274 and Zorya II from E. coli ATCC 8739 provide protection against several phages from the Durham collection",
        "notes": "Mariano et al. support experimentally validated phage protection by a Zorya I homolog set from Serratia marcescens ATCC 274."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| Zorya | 10\\.1126/science\\.aar4120 | Systematic discovery of antiphage defense systems in the microbial pangenome |",
        "notes": "The pinned DefenseFinder article registry maps the Zorya source key to the Doron et al. microbial-pangenome antiphage-system discovery paper."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| Zorya__ZorA                                      | Zorya__ZorA                                      | Zorya                  | Custom                  | 20     |",
        "notes": "The pinned DefenseFinder HMM inventory records the Zorya__ZorA custom profile listed by the Zorya_TypeI rule."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| Zorya__ZorB                                      | Zorya__ZorB                                      | Zorya                  | Custom                  | 20     |",
        "notes": "The pinned DefenseFinder HMM inventory records the Zorya__ZorB custom profile listed by the Zorya_TypeI rule."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| Zorya_TypeI__ZorC                                | Zorya_TypeI__ZorC                                | Zorya_TypeI            | Custom                  | 20     |\n| Zorya_TypeI__ZorD                                | Zorya_TypeI__ZorD                                | Zorya_TypeI            | Custom                  | 20     |",
        "notes": "The pinned DefenseFinder HMM inventory records Zorya_TypeI__ZorC and Zorya_TypeI__ZorD under the Zorya_TypeI model namespace."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "Zorya\tZorya_TypeI\t3\t3\tZorya_TypeI__ZorC, Zorya_TypeI__ZorD, Zorya__ZorA, Zorya__ZorB\t\t\t",
        "notes": "The pinned DefenseFinder rules table models Zorya_TypeI as a Zorya subsystem with Zorya_TypeI__ZorC, Zorya_TypeI__ZorD, Zorya__ZorA, and Zorya__ZorB in its mandatory profile set and 3 mandatory matches / 3 genes required."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:615",
        "taxon_label": "Serratia marcescens",
        "note": "Mariano et al. report that a Zorya I homolog set from Serratia marcescens ATCC 274 protected against several tested Durham-collection phages.",
        "reference": "DOI:10.1038/s41467-025-57397-2"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "zorya_type_i_locus_subtype_defense",
        "title": "Zorya type I loci mark a ZorC/ZorD-dependent Zorya subtype",
        "description": "Conservative subtype-level sketch linking a DefenseFinder Zorya_TypeI locus to ZorC/ZorD-dependent type I antiphage activity and Zorya type I system possession.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures the Zorya_TypeI subtype at DefenseFinder rule-row level without asserting the exact phage trigger, ion substrate, ZorC/ZorD nuclease target, anti-defense escape breadth, or whether every DefenseFinder Zorya_TypeI prediction is a complete experimentally active locus.",
        "nodes": [
          {
            "node_id": "zorya_type_i_locus",
            "label": "Zorya type I locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A DefenseFinder Zorya_TypeI subtype locus whose rule row lists Zorya_TypeI__ZorC, Zorya_TypeI__ZorD, Zorya__ZorA, and Zorya__ZorB in its mandatory profile set with 3 mandatory matches and 3 genes required."
          },
          {
            "node_id": "zorya_type_i_antiphage_activity",
            "label": "Zorya type I antiphage activity",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Antiphage activity of a ZorC/ZorD-dependent type I Zorya locus."
          },
          {
            "node_id": "zorya_type_i_system_trait",
            "label": "Zorya type I system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000554",
            "description": "Possession of a genome-encoded Zorya type I phage-defense system."
          },
          {
            "node_id": "zorya_system_trait",
            "label": "Zorya system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000217",
            "description": "Possession of a genome-encoded Zorya phage-defense system."
          }
        ],
        "edges": [
          {
            "subject": "zorya_type_i_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "zorya_type_i_antiphage_activity",
            "description": "Zorya_TypeI loci are modeled in DefenseFinder by a rule row listing Zorya_TypeI__ZorC, Zorya_TypeI__ZorD, Zorya__ZorA, and Zorya__ZorB in its mandatory profile set with 3 mandatory matches and 3 genes required, and the characterized Zorya type I branch recruits ZorC and ZorD effectors.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41586-024-08493-8",
                "snippet": "ZorAB transfers the phage invasion signal through the ZorA cytoplasmic tail to recruit and activate the soluble ZorC and ZorD effectors",
                "notes": "Hu et al. support ZorAB-mediated recruitment and activation of the soluble ZorC and ZorD Type I effectors."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| Zorya__ZorA                                      | Zorya__ZorA                                      | Zorya                  | Custom                  | 20     |",
                "notes": "The pinned DefenseFinder HMM inventory records the Zorya__ZorA custom profile listed by the Zorya_TypeI rule."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| Zorya__ZorB                                      | Zorya__ZorB                                      | Zorya                  | Custom                  | 20     |",
                "notes": "The pinned DefenseFinder HMM inventory records the Zorya__ZorB custom profile listed by the Zorya_TypeI rule."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| Zorya_TypeI__ZorC                                | Zorya_TypeI__ZorC                                | Zorya_TypeI            | Custom                  | 20     |\n| Zorya_TypeI__ZorD                                | Zorya_TypeI__ZorD                                | Zorya_TypeI            | Custom                  | 20     |",
                "notes": "The pinned DefenseFinder HMM inventory records Zorya_TypeI__ZorC and Zorya_TypeI__ZorD under the Zorya_TypeI model namespace."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "Zorya\tZorya_TypeI\t3\t3\tZorya_TypeI__ZorC, Zorya_TypeI__ZorD, Zorya__ZorA, Zorya__ZorB\t\t\t",
                "notes": "The pinned DefenseFinder rules table models Zorya_TypeI as a Zorya subsystem with Zorya_TypeI__ZorC, Zorya_TypeI__ZorD, Zorya__ZorA, and Zorya__ZorB in its mandatory profile set and 3 mandatory matches / 3 genes required."
              }
            ]
          },
          {
            "subject": "zorya_type_i_antiphage_activity",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "zorya_type_i_system_trait",
            "description": "The first-pass Zorya type I system trait is realized by a DefenseFinder Zorya_TypeI subtype locus.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41586-024-08493-8",
                "snippet": "ZorAB transfers the phage invasion signal through the ZorA cytoplasmic tail to recruit and activate the soluble ZorC and ZorD effectors",
                "notes": "Hu et al. support ZorAB-mediated recruitment and activation of the soluble ZorC and ZorD Type I effectors."
              },
              {
                "reference": "DOI:10.1038/s41586-024-08493-8",
                "snippet": "soluble ZorC and ZorD effectors, which facilitate the degradation of the phage DNA",
                "notes": "Hu et al. support Type I ZorC/ZorD effectors as phage-DNA degradation outputs."
              },
              {
                "reference": "DOI:10.1038/s41467-025-57397-2",
                "snippet": "We observed that homologs of Zorya I from Serratia marcescens ATCC 274 and Zorya II from E. coli ATCC 8739 provide protection against several phages from the Durham collection",
                "notes": "Mariano et al. support experimentally validated phage protection by a Zorya I homolog set from Serratia marcescens ATCC 274."
              }
            ]
          },
          {
            "subject": "zorya_type_i_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "zorya_system_trait",
            "description": "Zorya type I system possession is a Zorya-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| Zorya | 10\\.1126/science\\.aar4120 | Systematic discovery of antiphage defense systems in the microbial pangenome |",
                "notes": "The pinned DefenseFinder article registry maps the Zorya source key to the Doron et al. microbial-pangenome antiphage-system discovery paper."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "Zorya\tZorya_TypeI\t3\t3\tZorya_TypeI__ZorC, Zorya_TypeI__ZorD, Zorya__ZorA, Zorya__ZorB\t\t\t",
                "notes": "The pinned DefenseFinder rules table models Zorya_TypeI as a Zorya subsystem with Zorya_TypeI__ZorC, Zorya_TypeI__ZorD, Zorya__ZorA, and Zorya__ZorB in its mandatory profile set and 3 mandatory matches / 3 genes required."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "zorya-type-i-activity-gap",
        "prompt": "Resolve Zorya_TypeI phage triggers, native host breadth, ZorC/ZorD nuclease targets, ZorAB-to-ZorC/ZorD activation, and profile-to-activity criteria before minting enzyme, trigger, or component children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Hu et al. support ZorAB activation and phage-DNA degradation by type I Zorya ZorC/ZorD effectors, Mariano et al. support Zorya I phage protection from a Serratia marcescens locus, and the pinned DefenseFinder HMM inventory and rules table support Zorya_TypeI as a subtype whose rule row lists Zorya_TypeI__ZorC, Zorya_TypeI__ZorD, Zorya__ZorA, and Zorya__ZorB with 3 mandatory matches and 3 genes required. This first-pass record leaves exact phage triggers, native hosts, profile-to-component correspondence, ion usage, anti-defense escape, and ZorC/ZorD nuclease outputs unresolved.",
        "evidence": [
          {
            "reference": "DOI:10.1038/s41586-024-08493-8",
            "snippet": "ZorAB transfers the phage invasion signal through the ZorA cytoplasmic tail to recruit and activate the soluble ZorC and ZorD effectors",
            "notes": "Hu et al. support ZorAB-mediated recruitment and activation of the soluble ZorC and ZorD Type I effectors."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| Zorya_TypeI__ZorC                                | Zorya_TypeI__ZorC                                | Zorya_TypeI            | Custom                  | 20     |\n| Zorya_TypeI__ZorD                                | Zorya_TypeI__ZorD                                | Zorya_TypeI            | Custom                  | 20     |",
            "notes": "The pinned DefenseFinder HMM inventory records Zorya_TypeI__ZorC and Zorya_TypeI__ZorD under the Zorya_TypeI model namespace."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "snippet": "Zorya\tZorya_TypeI\t3\t3\tZorya_TypeI__ZorC, Zorya_TypeI__ZorD, Zorya__ZorA, Zorya__ZorB\t\t\t",
            "notes": "The pinned DefenseFinder rules table models Zorya_TypeI as a Zorya subsystem with Zorya_TypeI__ZorC, Zorya_TypeI__ZorD, Zorya__ZorA, and Zorya__ZorB in its mandatory profile set and 3 mandatory matches / 3 genes required."
          }
        ],
        "attaches_to": [
          "causal_graphs#zorya_type_i_locus_subtype_defense"
        ],
        "posed_by": "codex",
        "posed_date": "2026-10-02"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-02T20:10:33Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Zorya type I system as a DOI- and DefenseFinder-backed GENOMICS TraitRecord under the Zorya system parent after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record for the target local ID, placeholder METPO ID, proposal cohort, record slug, or human label; the replacement placeholder is reserved in proposals/metpo_traitmech_v431.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000552",
    "label": "Zorya type II system",
    "definition": "A Zorya system in which an organism possesses a genome-encoded DefenseFinder Zorya_TypeII subtype locus represented by Zorya_TypeII__ZorE, Zorya__ZorA2, and Zorya__ZorB rule profiles.",
    "definition_source": "DOI:10.1038/s41467-025-57397-2",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000217"
    ],
    "synonyms": [
      {
        "synonym_text": "Zorya_TypeII",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv"
      },
      {
        "synonym_text": "Zorya_TypeII__ZorE",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "Zorya__ZorA2",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      },
      {
        "synonym_text": "Zorya__ZorB",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/s41467-025-57397-2",
        "snippet": "For Zorya II, anti-phage activity requires the presence of the ZorE effector, which we show is recruited by ZorAB",
        "notes": "Mariano et al. support the dependence of Zorya type II phage defense on a ZorAB-recruited ZorE effector."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
        "snippet": "| Zorya | 10\\.1126/science\\.aar4120 | Systematic discovery of antiphage defense systems in the microbial pangenome |",
        "notes": "The pinned DefenseFinder article registry maps the Zorya source key to the Doron et al. microbial-pangenome antiphage-system discovery paper."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| Zorya__ZorA2                                     | Zorya__ZorA2                                     | Zorya                  | Custom                  | 20     |\n| Zorya__ZorB                                      | Zorya__ZorB                                      | Zorya                  | Custom                  | 20     |",
        "notes": "The pinned DefenseFinder HMM inventory records the Zorya__ZorA2 and Zorya__ZorB custom profiles used by the Zorya_TypeII rule."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
        "snippet": "| Zorya_TypeII__ZorE                               | Zorya_TypeII__ZorE                               | Zorya_TypeII           | Custom                  | 20     |",
        "notes": "The pinned DefenseFinder HMM inventory records Zorya_TypeII__ZorE under the Zorya_TypeII model namespace."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
        "snippet": "Zorya\tZorya_TypeII\t3\t3\tZorya_TypeII__ZorE, Zorya__ZorA2, Zorya__ZorB\t\t\t",
        "notes": "The pinned DefenseFinder rules table models Zorya_TypeII as a Zorya subsystem requiring Zorya_TypeII__ZorE plus shared Zorya__ZorA2 and Zorya__ZorB profiles."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:562",
        "taxon_label": "Escherichia coli",
        "note": "Mariano et al. report that a Zorya II locus from E. coli ATCC 8739 protected E. coli MT56 against several tested coliphages.",
        "reference": "DOI:10.1038/s41467-025-57397-2"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "zorya_type_ii_locus_subtype_defense",
        "title": "Zorya type II loci mark a ZorE-dependent Zorya subtype",
        "description": "Conservative subtype-level sketch linking a DefenseFinder Zorya_TypeII locus to ZorE-dependent type II antiphage activity and Zorya type II system possession.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures the Zorya_TypeII subtype at DefenseFinder rule-row level without asserting the exact phage trigger, ion substrate, ZorE nuclease target, anti-defense escape breadth, or whether every DefenseFinder Zorya_TypeII prediction is a complete experimentally active locus.",
        "nodes": [
          {
            "node_id": "zorya_type_ii_locus",
            "label": "Zorya type II locus",
            "node_type": "GENETIC_ELEMENT",
            "description": "A DefenseFinder Zorya_TypeII subtype locus represented by Zorya_TypeII__ZorE, Zorya__ZorA2, and Zorya__ZorB profiles."
          },
          {
            "node_id": "zorya_type_ii_antiphage_activity",
            "label": "Zorya type II antiphage activity",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Antiphage activity of a ZorE-dependent type II Zorya locus."
          },
          {
            "node_id": "zorya_type_ii_system_trait",
            "label": "Zorya type II system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000552",
            "description": "Possession of a genome-encoded Zorya type II phage-defense system."
          },
          {
            "node_id": "zorya_system_trait",
            "label": "Zorya system",
            "node_type": "TRAIT",
            "grounding": "traitmech:000217",
            "description": "Possession of a genome-encoded Zorya phage-defense system."
          }
        ],
        "edges": [
          {
            "subject": "zorya_type_ii_locus",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "zorya_type_ii_antiphage_activity",
            "description": "Zorya_TypeII loci are represented in DefenseFinder by Zorya_TypeII__ZorE, Zorya__ZorA2, and Zorya__ZorB rule profiles and the characterized Zorya II branch requires ZorE for anti-phage activity.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-025-57397-2",
                "snippet": "For Zorya II, anti-phage activity requires the presence of the ZorE effector, which we show is recruited by ZorAB",
                "notes": "Mariano et al. support the dependence of Zorya type II phage defense on a ZorAB-recruited ZorE effector."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| Zorya__ZorA2                                     | Zorya__ZorA2                                     | Zorya                  | Custom                  | 20     |\n| Zorya__ZorB                                      | Zorya__ZorB                                      | Zorya                  | Custom                  | 20     |",
                "notes": "The pinned DefenseFinder HMM inventory records the Zorya__ZorA2 and Zorya__ZorB custom profiles used by the Zorya_TypeII rule."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
                "snippet": "| Zorya_TypeII__ZorE                               | Zorya_TypeII__ZorE                               | Zorya_TypeII           | Custom                  | 20     |",
                "notes": "The pinned DefenseFinder HMM inventory records Zorya_TypeII__ZorE under the Zorya_TypeII model namespace."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "Zorya\tZorya_TypeII\t3\t3\tZorya_TypeII__ZorE, Zorya__ZorA2, Zorya__ZorB\t\t\t",
                "notes": "The pinned DefenseFinder rules table models Zorya_TypeII as a Zorya subsystem requiring Zorya_TypeII__ZorE plus shared Zorya__ZorA2 and Zorya__ZorB profiles."
              }
            ]
          },
          {
            "subject": "zorya_type_ii_antiphage_activity",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "zorya_type_ii_system_trait",
            "description": "The first-pass Zorya type II system trait is realized by a DefenseFinder Zorya_TypeII subtype locus.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-025-57397-2",
                "snippet": "For Zorya II, anti-phage activity requires the presence of the ZorE effector, which we show is recruited by ZorAB",
                "notes": "Mariano et al. support the dependence of Zorya type II phage defense on a ZorAB-recruited ZorE effector."
              }
            ]
          },
          {
            "subject": "zorya_type_ii_system_trait",
            "predicate": "is a",
            "predicate_id": "rdfs:subClassOf",
            "object": "zorya_system_trait",
            "description": "Zorya type II system possession is a Zorya-system trait.",
            "evidence": [
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md",
                "snippet": "| Zorya | 10\\.1126/science\\.aar4120 | Systematic discovery of antiphage defense systems in the microbial pangenome |",
                "notes": "The pinned DefenseFinder article registry maps the Zorya source key to the Doron et al. microbial-pangenome antiphage-system discovery paper."
              },
              {
                "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
                "snippet": "Zorya\tZorya_TypeII\t3\t3\tZorya_TypeII__ZorE, Zorya__ZorA2, Zorya__ZorB\t\t\t",
                "notes": "The pinned DefenseFinder rules table models Zorya_TypeII as a Zorya subsystem requiring Zorya_TypeII__ZorE plus shared Zorya__ZorA2 and Zorya__ZorB profiles."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "zorya-type-ii-activity-gap",
        "prompt": "Resolve Zorya_TypeII phage triggers, native host breadth, ZorE nuclease targets, ZorAB-to-ZorE activation, and profile-to-activity criteria before minting enzyme, trigger, or component children.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Mariano et al. support ZorE dependence for type II Zorya anti-phage activity, and the pinned DefenseFinder HMM inventory and rules table support Zorya_TypeII as a subtype with Zorya_TypeII__ZorE, Zorya__ZorA2, and Zorya__ZorB profiles. This first-pass record leaves exact phage triggers, native hosts, profile-to-component correspondence, ion usage, anti-defense escape, and ZorE nuclease outputs unresolved.",
        "evidence": [
          {
            "reference": "DOI:10.1038/s41467-025-57397-2",
            "snippet": "For Zorya II, anti-phage activity requires the presence of the ZorE effector, which we show is recruited by ZorAB",
            "notes": "Mariano et al. support the dependence of Zorya type II phage defense on a ZorAB-recruited ZorE effector."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md",
            "snippet": "| Zorya_TypeII__ZorE                               | Zorya_TypeII__ZorE                               | Zorya_TypeII           | Custom                  | 20     |",
            "notes": "The pinned DefenseFinder HMM inventory records Zorya_TypeII__ZorE under the Zorya_TypeII model namespace."
          },
          {
            "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv",
            "snippet": "Zorya\tZorya_TypeII\t3\t3\tZorya_TypeII__ZorE, Zorya__ZorA2, Zorya__ZorB\t\t\t",
            "notes": "The pinned DefenseFinder rules table models Zorya_TypeII as a Zorya subsystem requiring Zorya_TypeII__ZorE plus shared Zorya__ZorA2 and Zorya__ZorB profiles."
          }
        ],
        "attaches_to": [
          "causal_graphs#zorya_type_ii_locus_subtype_defense"
        ],
        "posed_by": "codex",
        "posed_date": "2026-10-02"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-02T18:08:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted Zorya type II system as a DOI- and DefenseFinder-backed GENOMICS TraitRecord under the Zorya system parent after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record for the target local ID, placeholder METPO ID, proposal cohort, record slug, or human label; the replacement placeholder is reserved in proposals/metpo_traitmech_v429.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000576",
    "label": "Zorya type III system",
    "definition": "A Zorya system in which an organism possesses a locus encoding ZorA and ZorB together with ZorF and ZorG.",
    "definition_source": "DOI:10.1093/nar/gkab883",
    "trait_category": "GENOMICS",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000217"
    ],
    "synonyms": [
      {
        "synonym_text": "Zorya type III",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1093/nar/gkab883"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1093/nar/gkab883",
        "snippet": "our data demonstrate activity of the Zorya type III system comprised of ZorA, ZorB, ZorF and ZorG",
        "notes": "Payne et al., Discussion and Figure 2C: the four-component architecture is ZorF/ZorA/ZorB/ZorG. The Results paragraph instead says zorBC; that wording conflicts with the figure and Discussion and is not used as the component definition. Methods identify the natural source as Stenotrophomonas nitritireducens DSM 12575, NZ_LDJG01000021.1. Figure 3 assays tested the cloned system in E. coli BL21-AI, not native defense in DSM 12575. The proposed regulatory roles of ZorF/ZorG are hypotheses, not demonstrated chemistry."
      },
      {
        "reference": "DOI:10.1038/s41467-025-57397-2",
        "snippet": "Zorya III instead encodes a DUF3348 domain protein (ZorF) and a DUF2894 domain protein (ZorG)",
        "notes": "Mariano et al., Introduction and Figure 1a/b, independently retain ZorA/ZorB as the shared core and ZorF/ZorG as the type-III distinguishing components, citing Payne for the classification. Their mechanistic experiments concern types I and II; these do not demonstrate a type-III ion substrate, nuclease activity, phage trigger or death pathway."
      },
      {
        "reference": "https://raw.githubusercontent.com/padlocbio/padloc-db/9e380165633a8d6aef93b5a164cea0f3359bd33f/sys/zorya_type_III.yaml",
        "snippet": "core_genes:\n  - ZorA3\n  - ZorB3\n  - ZorF3\n  - ZorG3",
        "notes": "Pinned executable PADLOC rule, retrieved 2026-10-03: minimum_core and minimum_total are both 4, maximum_separation is 0, and force_strand is FALSE. There are no additional secondary, neutral or prohibited profiles. These are detection constraints, not evidence for biological essentiality or activity of every predicted locus."
      },
      {
        "reference": "https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/definitions/DefenseFinder/Zorya/Zorya_TypeIII.xml",
        "snippet": "<model inter_gene_max_space=\"5\" min_mandatory_genes_required=\"3\" min_genes_required=\"3\" vers=\"2.0\">",
        "notes": "Pinned executable DefenseFinder model, retrieved 2026-10-03: four mandatory slots are Zorya__ZorA2 (exchangeable with Zorya__ZorA), Zorya__ZorB, Zorya_III__ZorG3 and Zorya_III__ZorF3, but the minimum counts are only 3. A detector call therefore does not by itself establish all four biological components; inspect the complete locus. The raw detector key is not an exact trait synonym."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:83617",
        "taxon_label": "Stenotrophomonas nitritireducens",
        "reference": "DOI:10.1093/nar/gkab883",
        "note": "Payne et al. amplified the type-III system from DSM 12575 genomic DNA, accession NZ_LDJG01000021.1. NCBI independently resolves that accession to this species, taxon 83617, and strain DSM 12575. This example is limited to natural possession by the named strain, not species-wide possession or a native-host protection assay. The paper tested a plasmid-borne construct in E. coli BL21-AI, which naturally lacked the system."
      }
    ],
    "discussions": [
      {
        "discussion_id": "zorya-type-iii-component-and-mechanism-scope",
        "prompt": "Resolve type-III component roles without transferring type-I/II mechanisms.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "The accepted architecture follows Payne Figure 2C and Discussion plus Mariano Figure 1 and Introduction, not Payne's conflicting Results wording or a detector key alone. ZorF/ZorG regulation of ZorAB is a proposal; no direct component-resolved mechanism is asserted here. Neither type-I phage-DNA degradation nor type-II ZorE nickase activity is assigned to type III. The ion substrate, activation trigger, native-host activity, individual component dependence and antiviral breadth remain open. The four-component definition is not weakened to match DefenseFinder's three-match threshold, and a missing hit or incomplete assembly is not proof of biological component absence. Multiple subtype loci may coexist in a genome; no organism-level disjointness is asserted. No mechanistic graph or protein examples are added without accession-resolved functional evidence.",
        "posed_by": "codex",
        "posed_date": "2026-10-03"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-03T19:16:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added the literature-defined ZorA/B/F/G possession class with two DOI sources, four exact snippets, pinned executable detection rules and the NCBI-resolved DSM 12575 source-strain example. Ignored-and-hidden novelty and allocation searches found no exact record or METPO term; reserved METPO:1053000 in v453. Kept source strain, heterologous assay, predicted regulation and detector thresholds distinct.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:2000210",
    "label": "accumulates",
    "definition": "An OBJECT_PROPERTY relating an organism to a chemical entity that the organism intracellularly accumulates above environmental concentration.",
    "definition_source": "DOI:10.1146/annurev.micro.55.1.485",
    "trait_category": "METABOLISM",
    "term_kind": "OBJECT_PROPERTY",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:2000001"
    ],
    "domain": "https://w3id.org/metpo/1000525",
    "range_": "http://purl.obolibrary.org/obo/CHEBI_24431",
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev.micro.55.1.485",
        "snippet": "accumulation",
        "notes": "Microbial-physiology reference supports 'accumulates' as a canonical predicate composed with a CHEBI-class chemical object at assertion time."
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.985274+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (OBJECT_PROPERTY)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic transport or storage relation carrier; later replacement should use more specific trait records that combine the relation with the transported, imported, exported, accumulated, or sequestered entity, cellular location or compartment, and positive or negative context.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-16T08:50:00-07:00",
        "curator": "claude",
        "action": "UNDEPRECATED_AS_COMPOSITION_PRIMITIVE",
        "changes": "Restored from DEPRECATED to REVIEWED under the predicate+class composition pattern (intended use: <organism> + this predicate + CHEBI chemical class). Added DOI/PMID-backed definition, evidence, and explicit domain/range slots.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000191",
    "label": "acetoclastic methanogenesis",
    "definition": "A methanogenesis in which acetate is split into methane and carbon dioxide.",
    "definition_source": "DOI:10.1007/s00253-023-12700-3",
    "trait_category": "METABOLISM",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000844"
    ],
    "synonyms": [
      {
        "synonym_text": "methanogenesis using acetate",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.3389/fmicb.2017.01198"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1007/s00253-023-12700-3",
        "snippet": "the acetoclastic methanogens split acetate to CH4 and CO2",
        "notes": "Szuhaj et al. distinguish acetoclastic methanogens by their acetate-to-methane-and-carbon-dioxide branch of methanogenesis."
      },
      {
        "reference": "DOI:10.3389/fmicb.2017.01198",
        "snippet": "acetoclastic methanogenesis using acetate",
        "notes": "Evans et al. describe acetoclastic methanogenesis as the acetate-using branch among major methanogenic carbon-source pathways."
      }
    ],
    "discussions": [
      {
        "discussion_id": "acetoclastic-methanogenesis-xref-gap",
        "prompt": "Resolve an exact external ontology xref for acetate-splitting methanogenesis before adding a TraitRecord xref.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "The pinned METPO snapshot contains only obsolete METPO:1000865 Acetoclastic methanogenesis. GO:0015948 methane biosynthetic process is exact only for the broader methanogenesis parent, and no exact active external class has yet been resolved for the acetate-splitting branch.",
        "posed_by": "codex",
        "posed_date": "2026-09-14"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-14T21:20:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted acetoclastic methanogenesis as a DOI-backed child of methanogenesis after a repository-wide duplicate review covering ignored and hidden files; the pinned METPO snapshot has only an obsolete Acetoclastic methanogenesis class.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000845",
    "label": "Acetogenesis",
    "definition": "A metabolism that produces acetate as the primary end product through the reduction of carbon dioxide or other carbon compounds using the Wood-Ljungdahl pathway, typically performed by acetogenic bacteria under anaerobic conditions.",
    "definition_source": "DOI:10.1016/j.bbapap.2008.08.012",
    "trait_category": "METABOLISM",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000060"
    ],
    "synonyms": [
      {
        "synonym_text": "Acetate fermentation",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "created_by": "Jed Dongjin Kim-Ozaeta",
    "evidence": [
      {
        "reference": "DOI:10.1016/j.bbapap.2008.08.012",
        "snippet": "Acetogenesis and the Wood-Ljungdahl Pathway of CO2 Fixation",
        "notes": "Review supports acetogenesis via the Wood-Ljungdahl CO2-fixation pathway."
      },
      {
        "reference": "DOI:10.1196/annals.1419.015",
        "snippet": "convert carbon dioxide and CO into acetyl-CoA",
        "notes": "Supports acetyl-CoA formation from CO2 and CO in acetogens."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1525",
        "taxon_label": "Neomoorella thermoacetica",
        "note": "THE model acetogen used to elucidate the Wood-Ljungdahl pathway (formerly Moorella/Clostridium thermoaceticum). Acetobacterium woodii is the modern bioenergetics model.",
        "reference": "DOI:10.1073/pnas.220404397"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "acetogenesis_wood_ljungdahl",
        "title": "Acetogenesis Wood-Ljungdahl mechanism",
        "description": "Evidence-backed causal sketch linking anaerobic carbon fixation through the Wood-Ljungdahl pathway to acetate production.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "The graph represents canonical Wood-Ljungdahl acetogenesis. The AcsB example is one component of the CODH/ACS complex and supports acetyl-CoA formation; it is not presented as a marker sufficient by itself to infer acetogenesis.",
        "nodes": [
          {
            "node_id": "acetogenesis_trait",
            "label": "Acetogenesis",
            "node_type": "TRAIT",
            "grounding": "METPO:1000845",
            "description": "Acetate-producing anaerobic metabolism."
          },
          {
            "node_id": "anaerobic_condition",
            "label": "anaerobic condition",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Oxygen-free condition required for many acetogenic enzymes.",
            "grounding": "PATO:0001456"
          },
          {
            "node_id": "wood_ljungdahl_pathway",
            "label": "Wood-Ljungdahl pathway",
            "node_type": "PATHWAY",
            "description": "Reductive acetyl-CoA pathway used by acetogens.",
            "grounding": "GO:0030634",
            "related_records": [
              {
                "corpus": "PathwayMech",
                "identifier": "WikiPathways:WP5019",
                "relation": "PATHWAY_CONTEXT",
                "basis": "PathwayMech context: Acetogenesis in Acetobacterium woodii (NCBITaxon:33952). The shared reductive acetyl-CoA route combines methyl and carbonyl branches for acetogenesis; the bacterial exemplar does not establish archaeal variants. No exact equivalence or transfer of organism scope is asserted.",
                "source_version": "aa305727458c44ab05614901334540e2c87a9f3a"
              }
            ]
          },
          {
            "node_id": "acetyl_coa_synthase",
            "label": "acetyl-CoA synthase (ACS)",
            "node_type": "GENE_OR_PROTEIN",
            "description": "AcsB component of CODH/ACS that forms acetyl-CoA where the carbonyl and methyl branches converge.",
            "grounding": "GO:0043884",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:P27988",
                "protein_label": "Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit alpha",
                "gene_symbol": "acsB",
                "taxon_id": "NCBITaxon:1525",
                "taxon_label": "Neomoorella thermoacetica",
                "entry_status": "REVIEWED",
                "retrieved_on": "2026-10-22",
                "entry_version": 126,
                "sequence_version": 1,
                "role": "AcsB alpha component that combines CO, CoA, and the CoFeSP-borne methyl group to form acetyl-CoA; this accession is not the complete CODH/ACS complex.",
                "evidence": [
                  {
                    "reference": "DOI:10.1073/pnas.220404397",
                    "snippet": "Genes acsA and acsB encode the beta and alpha subunits",
                    "notes": "The primary cloning and reconstitution study identifies acsB as the alpha component of active CODH/ACS from C. thermoaceticum; UniProtKB P27988 verifies the reviewed current N. thermoacetica taxon mapping."
                  }
                ]
              }
            ]
          },
          {
            "node_id": "carbon_dioxide",
            "label": "carbon dioxide",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:16526",
            "description": "Carbon substrate fixed by the Wood-Ljungdahl pathway."
          },
          {
            "node_id": "carbon_monoxide",
            "label": "carbon monoxide",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:17245",
            "description": "Carbon substrate or intermediate in acetyl-CoA synthesis."
          },
          {
            "node_id": "acetyl_coa",
            "label": "acetyl-CoA",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:15351",
            "description": "Central product of Wood-Ljungdahl carbon fixation."
          },
          {
            "node_id": "acetate",
            "label": "acetate",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:30089",
            "description": "Primary end product of acetogenesis."
          },
          {
            "node_id": "formate",
            "label": "formate",
            "node_type": "CHEMICAL",
            "description": "Methyl-branch intermediate from CO2 reduction."
          },
          {
            "node_id": "formyl_thf",
            "label": "10-formyl-tetrahydrofolate",
            "node_type": "CHEMICAL",
            "description": "Methyl-branch folate-bound formyl intermediate."
          },
          {
            "node_id": "methylene_thf",
            "label": "5,10-methylene-tetrahydrofolate",
            "node_type": "CHEMICAL",
            "description": "Methyl-branch folate-bound methylene intermediate."
          },
          {
            "node_id": "methyl_thf",
            "label": "5-methyl-tetrahydrofolate",
            "node_type": "CHEMICAL",
            "description": "Methyl-branch folate-bound methyl carrier feeding methyl transfer."
          },
          {
            "node_id": "acetyl_phosphate",
            "label": "acetyl phosphate",
            "node_type": "CHEMICAL",
            "description": "Activated acetyl intermediate from phosphotransacetylase.",
            "grounding": "CHEBI:15350"
          },
          {
            "node_id": "acetate_kinase_step",
            "label": "acetate kinase step",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Substrate-level phosphorylation step in which acetate kinase converts acetyl phosphate to acetate, yielding ATP."
          },
          {
            "node_id": "atp",
            "label": "ATP",
            "node_type": "CHEMICAL",
            "description": "Energy currency generated by substrate-level phosphorylation at acetate kinase."
          }
        ],
        "edges": [
          {
            "subject": "acetogenesis_trait",
            "predicate": "occurs in",
            "object": "anaerobic_condition",
            "description": "Acetogenesis is typically an anaerobic metabolism.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.bbapap.2008.08.012",
                "snippet": "grow organisms and work with enzymes under strictly oxygen-free conditions",
                "notes": "Review emphasizes oxygen-free handling for acetogenic enzymes and organisms."
              }
            ],
            "predicate_id": "biolink:occurs_in"
          },
          {
            "subject": "acetogenesis_trait",
            "predicate": "has mechanistic pathway",
            "object": "wood_ljungdahl_pathway",
            "description": "The Wood-Ljungdahl pathway is the central acetogenic carbon-fixation route.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.bbapap.2008.08.012",
                "snippet": "Wood-Ljungdahl Pathway of CO2 Fixation",
                "notes": "Review title and scope support pathway assignment."
              }
            ]
          },
          {
            "subject": "carbon_dioxide",
            "predicate": "participates in",
            "object": "wood_ljungdahl_pathway",
            "description": "Carbon dioxide is fixed through the Wood-Ljungdahl pathway.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.bbapap.2008.08.012",
                "snippet": "CO2 Fixation",
                "notes": "Supports CO2 as a pathway substrate."
              }
            ],
            "predicate_id": "biolink:participates_in"
          },
          {
            "subject": "carbon_monoxide",
            "predicate": "participates in",
            "object": "wood_ljungdahl_pathway",
            "description": "Carbon monoxide can be converted through the acetogenic pathway.",
            "evidence": [
              {
                "reference": "DOI:10.1196/annals.1419.015",
                "snippet": "convert carbon dioxide and CO into acetyl-CoA",
                "notes": "Supports CO as a substrate for acetogenic acetyl-CoA synthesis."
              }
            ],
            "predicate_id": "biolink:participates_in"
          },
          {
            "subject": "acetyl_coa_synthase",
            "predicate": "catalyzes formation of",
            "object": "acetyl_coa",
            "description": "The AcsB component of CODH/ACS catalyzes acetyl-CoA formation at convergence of the Wood-Ljungdahl pathway branches.",
            "evidence": [
              {
                "reference": "DOI:10.1073/pnas.220404397",
                "snippet": "Genes acsA and acsB encode the beta and alpha subunits",
                "notes": "Active AcsAB was reconstituted in the primary study; the edge is scoped to AcsB acting as a component of CODH/ACS, not as a standalone complete complex."
              }
            ],
            "predicate_id": "biolink:catalyzes"
          },
          {
            "subject": "wood_ljungdahl_pathway",
            "predicate": "has output",
            "object": "acetyl_coa",
            "description": "The Wood-Ljungdahl pathway synthesizes acetyl-CoA.",
            "evidence": [
              {
                "reference": "DOI:10.1196/annals.1419.015",
                "snippet": "convert carbon dioxide and CO into acetyl-CoA",
                "notes": "Supports acetyl-CoA as pathway product."
              }
            ],
            "predicate_id": "RO:0002234"
          },
          {
            "subject": "acetyl_coa",
            "predicate": "precursor of",
            "object": "acetate",
            "description": "Acetyl-CoA is converted onward to acetate in acetogenesis.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.bbapap.2008.08.012",
                "snippet": "Energy metabolism associated with acetogenesis",
                "notes": "Review discusses acetogenic energy metabolism downstream of acetyl-CoA synthesis."
              }
            ]
          },
          {
            "subject": "carbon_dioxide",
            "predicate": "is converted to",
            "object": "formate",
            "description": "CO2 is reduced to formate by formate dehydrogenase / HDCR, the first methyl-branch step.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fbioe.2024.1395540",
                "notes": "FDH reduces CO2 to formate; HDCR catalyzes hydrogen-dependent CO2 reduction to formate (methyl-branch core step)."
              }
            ]
          },
          {
            "subject": "formate",
            "predicate": "is converted to",
            "object": "formyl_thf",
            "description": "Formate is condensed onto tetrahydrofolate by formyl-THF synthetase (Fhs).",
            "evidence": [
              {
                "reference": "DOI:10.3389/fbioe.2024.1395540",
                "notes": "FTS (formyl-THF synthetase) converts formate to formyl-THF consuming 1 ATP; canonical WLP methyl-branch step."
              }
            ]
          },
          {
            "subject": "formyl_thf",
            "predicate": "is converted to",
            "object": "methylene_thf",
            "description": "Formyl-THF is processed by cyclohydrolase and methylene-THF dehydrogenase (FolD) to methylene-THF.",
            "evidence": [
              {
                "reference": "DOI:10.34726/hss.2024.114566",
                "notes": "5,10-methenyl-THF cyclohydrolase and NAD-dependent 5,10-methylene-THF dehydrogenase convert formyl-THF to methylene-THF."
              }
            ]
          },
          {
            "subject": "methylene_thf",
            "predicate": "is converted to",
            "object": "methyl_thf",
            "description": "Methylene-THF is reduced to methyl-THF by methylene-THF reductase (MTHFR).",
            "evidence": [
              {
                "reference": "DOI:10.3389/fbioe.2024.1395540",
                "notes": "MTHFR reduces methenyl-THF to methylene-THF to methyl-THF; common acetogen methyl-branch step."
              }
            ]
          },
          {
            "subject": "carbon_dioxide",
            "predicate": "is converted to",
            "object": "carbon_monoxide",
            "description": "CO2 is reduced to CO by carbon monoxide dehydrogenase (CODH) in the carbonyl branch.",
            "evidence": [
              {
                "reference": "DOI:10.34726/hss.2024.114566",
                "notes": "In the carbonyl branch CODH reduces CO2 to CO; central carbonyl-branch step."
              }
            ]
          },
          {
            "subject": "acetyl_coa",
            "predicate": "is converted to",
            "object": "acetyl_phosphate",
            "description": "Acetyl-CoA is converted to acetyl phosphate by phosphotransacetylase (PTA).",
            "evidence": [
              {
                "reference": "DOI:10.3389/fbioe.2024.1395540",
                "notes": "PTA and ACK convert acetyl-CoA to acetate; PTA yields acetyl phosphate."
              }
            ]
          },
          {
            "subject": "acetyl_phosphate",
            "predicate": "is converted to",
            "object": "acetate",
            "description": "Acetyl phosphate is converted to acetate by acetate kinase (ACK), yielding ATP by substrate-level phosphorylation.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fbioe.2024.1395540",
                "notes": "ACK (acetate kinase) converts acetyl-phosphate to acetate, yielding ATP via SLP; trait-defining end-product step."
              }
            ]
          },
          {
            "subject": "acetate_kinase_step",
            "predicate": "has input",
            "object": "acetyl_phosphate",
            "description": "Acetate kinase consumes acetyl phosphate in the substrate-level phosphorylation step.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fbioe.2024.1395540",
                "notes": "ACK convert acetyl-phosphate to acetate, yielding ATP via SLP."
              }
            ],
            "predicate_id": "RO:0002233"
          },
          {
            "subject": "acetate_kinase_step",
            "predicate": "has output",
            "object": "atp",
            "description": "The acetate kinase step generates ATP via substrate-level phosphorylation.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fbioe.2024.1395540",
                "notes": "ACK convert acetyl-phosphate to acetate, yielding ATP via SLP."
              }
            ],
            "predicate_id": "RO:0002234"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.915402+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-07T00:00:00-07:00",
        "curator": "codex",
        "action": "ADDED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed causal graph for anaerobic Wood-Ljungdahl carbon fixation and acetate production.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:30Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:38:00Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (ENVO:01001057\u00d71, GO:0046358\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-26T05:00:47Z",
        "curator": "claude",
        "action": "RENAME_PREDICATE_LABELS",
        "changes": "Renamed 3 causal-edge predicate label(s) to align with existing groundings: input to \u2192 participates in \u00d72; occurs under \u2192 occurs in \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-26T05:00:50Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:participates_in\u00d72, biolink:occurs_in\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-15T07:19:08Z",
        "curator": "claude",
        "action": "FIX_NODE_GROUNDING_CURIE",
        "changes": "Overwrote 1 causal-node grounding(s) to corrected CURIEs (phase-2 id-label fix; verified vs OAK).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-15T07:20:37Z",
        "curator": "claude",
        "action": "FIX_NODE_GROUNDING_CURIE",
        "changes": "Overwrote 1 causal-node grounding(s) (obsolete/wrong GO -> corrected, verified vs OAK).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-17T04:09:44Z",
        "curator": "claude",
        "action": "REMOVE_REDUNDANT_SYNONYM",
        "changes": "Removed 1 synonym(s) whose text duplicated the label (seeder redundancy; no information lost).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 8 evidence-backed generic edges (6 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:11Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:18Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:15350\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates (1 to has output), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T02:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES_PART2",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates onto their causal-graph counterparts (1 to produces), issue 301 part 2. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Each replacement is a 1:1 mirror of its source predicate that changes only the domain, so the claim each edge makes is unchanged and directions are unchanged. The replacements are proposed in proposals/metpo_traitmech_v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T07:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Modelled the acetate kinase step as an explicit BIOLOGICAL_PROCESS node and split `acetyl_phosphate produces atp` into `acetate_kinase_step has input acetyl_phosphate` (RO:0002233) and `acetate_kinase_step has output atp` (RO:0002234), issue 331. The old edge had a CHEMICAL subject on METPO:2007800, whose definition is that the activity or state of the subject brings the object into existence - a chemical has neither in that sense. RO:0001001 (derives into) did not fit either, because ATP's matter comes mostly from ADP and only the phosphoryl group transfers, failing that relation's inherits-the-significant-portion-of-the-matter test. The process the edge description already named was simply not in the graph; both new edges are range-correct and the step is wired on both sides so nothing is orphaned. This was the last CHEMICAL-subject produces edge, which let METPO:2007800's subject_types gate drop CHEMICAL. Two modelling choices are recorded here as decisions rather than left as omissions (issue 331 review). The node is typed BIOLOGICAL_PROCESS rather than MOLECULAR_FUNCTION, which would have grounded to GO:0008776 (acetate kinase activity) via mappings/node_grounding.tsv - this trait's own research report asks for a process label plus explicit reaction edges for the substrate-level phosphorylation step, and that is what this is. And the step carries has-output atp but deliberately not has-output acetate, because the existing acetyl_phosphate is-converted-to acetate edge already states that half of the reaction on the chemical chain; asserting it again at the process level is the duplication at two levels of description that issue 303 criticised in dissimilatory_iron_reduction.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-24T10:00:00Z",
        "curator": "codex",
        "action": "CURATE_PROTEIN_TAXON_EXAMPLE",
        "changes": "Scoped the acetogenesis graph, replaced the model-organism URL with a primary DOI, and added DOI-backed reviewed AcsB as an explicit N. thermoacetica component example with a supported acetyl-CoA-formation edge.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T06:33:02Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:catalyzes\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-05T17:46:22Z",
        "curator": "codex",
        "action": "ADD_PATHWAY_CONTEXT",
        "changes": "Added pinned PathwayMech context on reviewed causal nodes with explicit route and organism limitations; retained existing groundings and exact xrefs.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-22T01:35:00Z",
        "curator": "claude",
        "action": "REFRESH_UNIPROT_ENTRY_VERSION",
        "changes": "Refreshed UniProtKB entry_version against live UniProt REST on 2026-10-22: UniProtKB:P27988 (125 -> 126 on acetyl_coa_synthase).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000180",
    "label": "acetone-butanol-ethanol fermentation",
    "definition": "A fermentation in which solventogenic bacteria convert organic carbon sources to organic acids and then reassimilate those acids to produce acetone, butanol, and ethanol solvents.",
    "definition_source": "DOI:10.1073/pnas.1423143112",
    "trait_category": "METABOLISM",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1002005"
    ],
    "synonyms": [
      {
        "synonym_text": "ABE fermentation",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1073/pnas.1423143112"
      },
      {
        "synonym_text": "acetone-butanol fermentation",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1128/mr.50.4.484-524.1986"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1073/pnas.1423143112",
        "snippet": "One canonical example of such processes is acetone-butanol-ethanol (ABE) fermentation by Clostridium acetobutylicum, during which cells convert carbon sources to organic acids that are later reassimilated to produce solvents as a strategy for cellular survival.",
        "notes": "Liao et al. use the exact acetone-butanol-ethanol (ABE) fermentation name and describe the acidogenic-to-solventogenic conversion of carbon sources into solvent end products."
      },
      {
        "reference": "DOI:10.1002/bit.22003",
        "snippet": "Biological production of butanol (with acetone and ethanol) was one of the largest industrial fermentation processes early in the 20th century.",
        "notes": "Lee et al. independently review fermentative butanol production with acetone and ethanol by Clostridia."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:272562",
        "taxon_label": "Clostridium acetobutylicum ATCC 824",
        "note": "Wild-type ATCC 824 strain whose ABE fermentations were experimentally reproduced by Liao et al.'s integrated model.",
        "reference": "DOI:10.1073/pnas.1423143112"
      }
    ],
    "discussions": [
      {
        "discussion_id": "acetone-butanol-ethanol-fermentation-xref-gap",
        "prompt": "Resolve an exact external ontology class for acetone-butanol-ethanol fermentation before adding a TraitRecord xref.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "No exact GO or external metabolism class was resolved for the organism-level ABE fermentation phenotype; broader fermentation classes and individual solvent-production reactions are shifted relative to this product-specific fermentation class.",
        "posed_by": "codex",
        "posed_date": "2026-09-14"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-14T02:40:39Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted acetone-butanol-ethanol fermentation as a DOI-backed solventogenic fermentation TraitRecord after a repository-wide duplicate review covering ignored and hidden files; METPO has no exact acetone-butanol-ethanol fermentation class yet and the placeholder is reserved in proposals/metpo_traitmech_v57.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000801",
    "label": "Aerobic respiration",
    "definition": "A respiration in which molecular oxygen serves as the terminal electron acceptor in the electron transport chain, generating ATP through oxidative phosphorylation with water as the final product.",
    "definition_source": "DOI:10.1146/annurev.biophys.27.1.329",
    "trait_category": "METABOLISM",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000800"
    ],
    "synonyms": [
      {
        "synonym_text": "Oxic respiration",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "Oxygen respiration",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "created_by": "Jed Dongjin Kim-Ozaeta",
    "xrefs": [
      "GO:0009060"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev.biophys.27.1.329",
        "snippet": "terminal enzyme of respiratory chains",
        "notes": "Review supports cytochrome c oxidase reducing molecular oxygen to water in aerobic respiratory chains."
      },
      {
        "reference": "DOI:10.1016/j.bbabio.2008.09.008",
        "snippet": "membrane-bound electron transport chain",
        "notes": "Review supports proton-gradient energy conservation by prokaryotic respiratory chains."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:562",
        "taxon_label": "Escherichia coli",
        "note": "aerobic respiratory chain",
        "reference": "PMID:31669488"
      },
      {
        "taxon_id": "NCBITaxon:266",
        "taxon_label": "Paracoccus denitrificans",
        "note": "mitochondrion-like respiratory chain",
        "reference": "PMID:9841665"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "aerobic_respiration_terminal_oxidase",
        "title": "Aerobic respiration terminal oxidase mechanism",
        "description": "DOI-backed graph linking oxygen reduction, respiratory electron transport, proton motive force, and ATP synthesis.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "Represents the cytochrome-c-oxidase branch of aerobic respiration through proton-motive-force-coupled ATP synthesis; it does not assert that this terminal oxidase family is universal across aerobes.",
        "nodes": [
          {
            "node_id": "aerobic_respiration_trait",
            "label": "Aerobic respiration",
            "node_type": "TRAIT",
            "grounding": "METPO:1000801",
            "description": "Oxygen-dependent respiratory energy metabolism."
          },
          {
            "node_id": "electron_transport_chain",
            "label": "electron transport chain",
            "node_type": "PATHWAY",
            "grounding": "GO:0022900",
            "description": "Membrane-associated redox chain coupling electron flow to ion translocation."
          },
          {
            "node_id": "cytochrome_c_oxidase",
            "label": "cytochrome c oxidase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Terminal oxidase that transfers electrons to molecular oxygen.",
            "grounding": "GO:0004129",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:P08306",
                "protein_label": "Cytochrome c oxidase subunit 2",
                "gene_symbol": "ctaC",
                "taxon_id": "NCBITaxon:266",
                "taxon_label": "Paracoccus denitrificans",
                "entry_status": "REVIEWED",
                "retrieved_on": "2026-10-22",
                "entry_version": 168,
                "sequence_version": 1,
                "role": "Subunit II component of the purified P. denitrificans cytochrome c oxidase; this accession is not presented as the complete terminal-oxidase complex.",
                "evidence": [
                  {
                    "reference": "DOI:10.1016/S0005-2728(98)00092-9",
                    "snippet": "enzyme containing polypeptides I-IV",
                    "notes": "The primary purification study compares P. denitrificans oxidase complexes and establishes subunit II as a component; UniProtKB P08306 verifies the reviewed protein and taxon."
                  }
                ]
              }
            ]
          },
          {
            "node_id": "molecular_oxygen",
            "label": "molecular oxygen",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:15379",
            "description": "Terminal electron acceptor in aerobic respiration."
          },
          {
            "node_id": "water",
            "label": "water",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:15377",
            "description": "Reduced product of oxygen reduction."
          },
          {
            "node_id": "proton_motive_force",
            "label": "proton motive force",
            "node_type": "STATE",
            "description": "Electrochemical ion gradient generated across the coupling membrane.",
            "grounding": "METPO:1007500"
          },
          {
            "node_id": "atp_synthase",
            "label": "ATP synthase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Enzyme complex that uses proton motive force to synthesize ATP.",
            "grounding": "GO:0045259"
          },
          {
            "node_id": "atp",
            "label": "ATP",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:30616",
            "description": "Energy carrier produced by oxidative phosphorylation."
          }
        ],
        "edges": [
          {
            "subject": "aerobic_respiration_trait",
            "predicate": "has mechanistic pathway",
            "object": "electron_transport_chain",
            "description": "Aerobic respiration uses a membrane-bound respiratory electron transport chain.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.bbabio.2008.09.008",
                "snippet": "membrane-bound electron transport chain",
                "notes": "Review describes respiration as redox reactions catalyzed by membrane-bound electron transport chains."
              }
            ]
          },
          {
            "subject": "cytochrome_c_oxidase",
            "predicate": "reduces",
            "object": "molecular_oxygen",
            "description": "Terminal oxidase transfers electrons to molecular oxygen.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev.biophys.27.1.329",
                "snippet": "electron transfer from cytochrome c to molecular oxygen",
                "notes": "Supports oxygen as terminal electron acceptor for cytochrome c oxidase."
              }
            ],
            "predicate_id": "METPO:2007802"
          },
          {
            "subject": "molecular_oxygen",
            "predicate": "reduced to",
            "object": "water",
            "description": "Oxygen reduction forms water at the terminal oxidase.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev.biophys.27.1.329",
                "snippet": "reducing the latter to water",
                "notes": "Supports water as the product of terminal oxygen reduction."
              }
            ]
          },
          {
            "subject": "electron_transport_chain",
            "predicate": "generates",
            "object": "proton_motive_force",
            "description": "Respiratory redox energy is conserved as an ion gradient.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.bbabio.2008.09.008",
                "snippet": "generation of an electrochemical ion gradient",
                "notes": "Supports proton motive force generation by respiratory chains."
              }
            ],
            "predicate_id": "biolink:produces"
          },
          {
            "subject": "proton_motive_force",
            "predicate": "regulates",
            "object": "atp_synthase",
            "description": "The proton motive force powers ATP synthase.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev.biophys.27.1.329",
                "snippet": "employed by the F0F1-ATPase",
                "notes": "Supports ATP synthase use of the respiratory proton gradient."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "atp_synthase",
            "predicate": "produces",
            "object": "atp",
            "description": "ATP synthase produces ATP during oxidative phosphorylation.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.bbabio.2008.09.008",
                "snippet": "gradient across a coupling membrane that drives ATP synthesis",
                "notes": "Supports ATP synthesis driven by the respiratory ion gradient."
              }
            ],
            "predicate_id": "METPO:2007800"
          },
          {
            "subject": "cytochrome_c_oxidase",
            "predicate": "part of",
            "object": "electron_transport_chain",
            "description": "Cytochrome c oxidase is the terminal enzyme of the graph's represented aerobic respiratory-chain branch.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev.biophys.27.1.329",
                "snippet": "terminal enzyme of respiratory chains",
                "notes": "Connects the documented cytochrome-c-oxidase branch to the respiratory electron-transport pathway without asserting that this oxidase family is universal across aerobes."
              }
            ],
            "predicate_id": "biolink:part_of"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-08-23T09:08:00Z",
        "curator": "codex",
        "action": "CURATE_PROTEIN_TAXON_EXAMPLE",
        "changes": "Reviewed the graph as mechanistic, grounded ATP synthase as a complex, and added DOI-backed UniProtKB P08306 as an explicit P. denitrificans cytochrome-c-oxidase subunit-II exemplar.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-05T01:35:46.911295+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-08T00:00:00-07:00",
        "curator": "codex",
        "action": "ADDED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed causal graph for oxygen reduction, proton motive force, and ATP synthesis in aerobic respiration.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:30Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T08:21:49Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:produces\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:19Z",
        "curator": "claude",
        "action": "RENAME_PREDICATE_LABELS",
        "changes": "Renamed 1 causal-edge predicate label(s) to align with existing groundings: drives \u2192 regulates \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:21Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002211\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:41:03Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (METPO:1007500\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T05:05:14Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A075NZN5\u00d71, UniProtKB:A0A415TT77\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-26T02:30:13Z",
        "curator": "claude",
        "action": "RETYPE_CAUSAL_NODES",
        "changes": "Re-typed 1 causal-node node_type field(s) to align with CausalNodeTypeEnum semantics: proton motive force: BIOLOGICAL_PROCESS \u2192 STATE \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-16T06:30:56Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000017\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:21:11Z",
        "curator": "claude",
        "action": "RETRACT_DEAD_UNIPROT_GROUNDINGS",
        "changes": "Retracted 1 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T02:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES_PART2",
        "changes": "Re-grounded 2 causal edge(s) off microbe-domain METPO predicates onto their causal-graph counterparts (1 to produces, 1 to reduces), issue 301 part 2. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Each replacement is a 1:1 mirror of its source predicate that changes only the domain, so the claim each edge makes is unchanged and directions are unchanged. The replacements are proposed in proposals/metpo_traitmech_v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-16T02:00:00Z",
        "curator": "claude",
        "action": "NORMALISE_NODE_TYPE",
        "changes": "Under the PATHWAY-vs-BIOLOGICAL_PROCESS rule, one node_id means one thing corpus-wide (issue 356): electron_transport_chain is typed PATHWAY. PATHWAY is a named, conventionally enumerable multi-step route; BIOLOGICAL_PROCESS is everything else. A named route through enumerable complexes. Was 4 PATHWAY to 2 before this tranche.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-22T04:26:15Z",
        "curator": "codex",
        "action": "REVIEW_UNIPROT_INSTANCE_GROUNDINGS",
        "changes": "Reviewed 1 organism-specific UniProtKB grounding(s): replaced 1 with taxon-agnostic GO/InterPro terms and retracted 0 to label-only where no exact semantic term was supported (docs/GROUNDING_POLICY.md).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T01:14:57Z",
        "curator": "codex",
        "action": "ADD_EXACT_ONTOLOGY_MATCH",
        "changes": "Ontology exact-match review (2026-08-25): approved exact xref(s): GO:0009060. Evidence is predicate-scoped in the versioned ontology snapshots; OAK cross-checked direct data, and OLS4 spot-checked release deltas and disputed hits.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T10:25:59Z",
        "curator": "codex",
        "action": "CONNECT_CAUSAL_GRAPH",
        "changes": "Connected cytochrome c oxidase to the represented electron-transport-chain branch with one source-supported part-of edge, joining both graph components. The protein remains a supporting YAML graph field and the existing scope note continues to reject a universal terminal-oxidase-family claim. Addresses issues 426 and 183.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-22T01:35:00Z",
        "curator": "claude",
        "action": "REFRESH_UNIPROT_ENTRY_VERSION",
        "changes": "Refreshed UniProtKB entry_version against live UniProt REST on 2026-10-22: UniProtKB:P08306 (167 -> 168 on cytochrome_c_oxidase).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000188",
    "label": "anaerobic ammonium oxidation",
    "definition": "An anaerobic nitrogen metabolism in which ammonium is oxidized with nitrite as the electron acceptor to form dinitrogen.",
    "definition_source": "DOI:10.1038/22749",
    "trait_category": "METABOLISM",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000121"
    ],
    "synonyms": [
      {
        "synonym_text": "anammox",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1038/22749"
      },
      {
        "synonym_text": "anaerobic ammonia oxidation",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1038/22749"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/22749",
        "snippet": "This new process combines ammonia and nitrite directly into dinitrogen gas",
        "notes": "Strous et al. identified the anaerobic ammonia oxidation process and linked ammonia plus nitrite conversion to dinitrogen formation."
      },
      {
        "reference": "DOI:10.1128/AEM.65.7.3248-3250.1999",
        "snippet": "The affinity constants for the substrates ammonium and nitrite were each less than 0.1 mg of nitrogen per liter.",
        "notes": "Strous et al. measured ammonium and nitrite as high-affinity anammox substrates."
      },
      {
        "reference": "DOI:10.1038/nature10453",
        "snippet": "anammox converts ammonia and nitrite into dinitrogen (N2) gas",
        "notes": "Kartal et al. review the pathway scope and support anammox as the established exact synonym."
      }
    ],
    "discussions": [
      {
        "discussion_id": "anaerobic-ammonium-oxidation-xref-gap",
        "prompt": "Resolve an exact external ontology class for anaerobic ammonium oxidation before adding a TraitRecord xref.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "The pinned METPO snapshot contains only METPO:1000812 obsolete Anaerobic ammonium oxidation. Candidate GO classes should be checked against the primary Gene Ontology release before adding an exact xref because component ammonium- or nitrite-oxidation processes are narrower than the whole anammox metabolism.",
        "posed_by": "codex",
        "posed_date": "2026-09-14"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-14T20:06:42Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted anaerobic ammonium oxidation as a DOI-backed nitrogen respiration TraitRecord after a repository-wide duplicate review covering ignored and hidden files; the local METPO snapshot has only obsolete anammox classes and the replacement placeholder is reserved in proposals/metpo_traitmech_v65.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000033",
    "label": "anaerobic oxidation of methane",
    "definition": "A metabolism in which methane is oxidized under anoxic conditions, classically coupled to sulfate reduction and mediated by consortia of anaerobic methanotrophic archaea (ANME) and sulfate-reducing bacteria. It is a major sink for methane in marine sediments.",
    "definition_source": "DOI:10.1038/35036572",
    "trait_category": "METABOLISM",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000802"
    ],
    "synonyms": [
      {
        "synonym_text": "AOM",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1038/35036572"
      },
      {
        "synonym_text": "anaerobic methanotrophy",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.3389/fmars.2025.1609892"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/35036572",
        "notes": "Boetius et al. described the marine microbial consortium of ANME archaea and sulfate-reducing bacteria mediating anaerobic oxidation of methane."
      },
      {
        "reference": "DOI:10.3389/fmars.2025.1609892",
        "notes": "Review of AOM in marine sediments supports sulfate- and metal-coupled anaerobic methane oxidation as a major methane sink."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1392998",
        "taxon_label": "Candidatus Methanoperedens nitratireducens",
        "note": "Canonical nitrate-dependent ANME archaeon performing anaerobic oxidation of methane (ANME-2d). Candidatus taxon (no validly published name).",
        "reference": "DOI:10.1038/s41564-022-01292-9"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "aom_anme_sulfate_consortium",
        "title": "AOM couples methane oxidation to sulfate reduction in ANME-SRB consortia",
        "description": "Evidence-backed causal sketch linking anaerobic methanotrophic archaea (ANME) and sulfate-reducing bacteria to coupled methane oxidation and sulfate reduction.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "This is a composite AOM graph spanning sulfate-coupled ANME-SRB consortia and nitrate-dependent Ca. Methanoperedens. The mcrA example supports methane activation in the nitrate-dependent branch; MCR occurrence alone does not establish reaction direction or the AOM phenotype.",
        "nodes": [
          {
            "node_id": "aom_trait",
            "label": "anaerobic oxidation of methane",
            "node_type": "TRAIT",
            "grounding": "traitmech:000033",
            "description": "Anaerobic methane oxidation, classically coupled to sulfate reduction."
          },
          {
            "node_id": "methane",
            "label": "methane",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:16183",
            "description": "Substrate oxidized under anoxic conditions."
          },
          {
            "node_id": "sulfate",
            "label": "sulfate",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:16189",
            "description": "Terminal electron acceptor for AOM."
          },
          {
            "node_id": "reverse_methanogenesis",
            "label": "reverse methanogenesis",
            "node_type": "PATHWAY",
            "description": "Core pathway by which methane is activated and oxidized to CO2 during AOM."
          },
          {
            "node_id": "mcr",
            "label": "methyl-coenzyme M reductase (MCR)",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Enzyme that activates methane (to methyl-S-CoM) as the initial step of AOM.",
            "grounding": "GO:0044674",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:A0A284VQI9",
                "protein_label": "coenzyme-B sulfoethylthiotransferase",
                "gene_symbol": "mcrA",
                "taxon_id": "NCBITaxon:1392998",
                "taxon_label": "Candidatus Methanoperedens nitratireducens",
                "entry_status": "UNREVIEWED",
                "proteome_id": "UP000218615",
                "retrieved_on": "2026-10-22",
                "entry_version": 22,
                "sequence_version": 1,
                "role": "McrA alpha component of methyl-coenzyme M reductase in nitrate-dependent reverse methanogenesis; this accession is not the complete MCR complex and is not a directionality marker by itself.",
                "evidence": [
                  {
                    "reference": "DOI:10.1038/nature12375",
                    "snippet": "independent AOM through reverse methanogenesis using nitrate as the terminal electron acceptor",
                    "notes": "The primary isotope, genome, and transcript study establishes nitrate-dependent AOM by Ca. M. nitroreducens through reverse methanogenesis."
                  },
                  {
                    "reference": "DOI:10.1007/s00253-016-8065-8",
                    "snippet": "complete reverse methanogenesis pathway including the mcrABCDG genes was identified",
                    "notes": "The taxon-specific study verifies mcrA in Ca. M. nitroreducens; UniProtKB maps A0A284VQI9 to mcrA in its reference proteome."
                  }
                ]
              }
            ]
          },
          {
            "node_id": "diet",
            "label": "direct interspecies electron transfer (DIET)",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Electron transfer from ANME to sulfate-reducing bacteria via conserved outer-membrane complexes in sulfate-AOM syntrophy."
          },
          {
            "node_id": "nitrate",
            "label": "nitrate",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:17632",
            "description": "Terminal electron acceptor for nitrate-dependent AOM."
          },
          {
            "node_id": "nitrite",
            "label": "nitrite",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:16301",
            "description": "Terminal electron acceptor for nitrite-dependent AOM."
          }
        ],
        "edges": [
          {
            "subject": "methane",
            "predicate": "oxidized to",
            "object": "sulfate",
            "description": "Methane oxidation is coupled to sulfate reduction in the ANME-SRB consortium.",
            "evidence": [
              {
                "reference": "DOI:10.1038/35036572",
                "notes": "Boetius et al. described the marine ANME-SRB consortium mediating AOM."
              }
            ],
            "predicate_id": "METPO:2007405"
          },
          {
            "subject": "aom_trait",
            "predicate": "associated with",
            "object": "methane",
            "description": "AOM is a major biological sink for methane in anoxic sediments.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmars.2025.1609892",
                "notes": "AOM review supports sulfate- and metal-coupled methane oxidation as a major methane sink."
              }
            ],
            "predicate_id": "biolink:associated_with"
          },
          {
            "subject": "aom_trait",
            "predicate": "has core pathway",
            "object": "reverse_methanogenesis",
            "description": "AOM proceeds via the reverse methanogenesis pathway, oxidizing methane to CO2.",
            "evidence": [
              {
                "reference": "DOI:10.3390/fermentation9070645",
                "notes": "AOM proceeds via the reverse methanogenesis pathway: CH4 is converted to methyl-S-CoM by Mcr then oxidized to CO2."
              }
            ]
          },
          {
            "subject": "mcr",
            "predicate": "catalyzes initial step of",
            "object": "aom_trait",
            "description": "MCR activates methane as the initial step of AOM (reverse methanogenesis).",
            "evidence": [
              {
                "reference": "DOI:10.1021/acs.est.3c07197",
                "notes": "Methane activation by methyl-coenzyme M reductase (MCR) is the methane-activation step in reverse methanogenesis."
              }
            ]
          },
          {
            "subject": "sulfate",
            "predicate": "serves as terminal electron acceptor for",
            "object": "aom_trait",
            "description": "Sulfate is the terminal electron acceptor in sulfate-coupled AOM.",
            "evidence": [
              {
                "reference": "DOI:10.1371/journal.pbio.3002292",
                "notes": "Sulfate-coupled AOM is performed by consortia of ANME in obligate syntrophic partnership with sulfate-reducing bacteria."
              }
            ]
          },
          {
            "subject": "diet",
            "predicate": "confers",
            "object": "aom_trait",
            "description": "DIET via conserved ANME-to-SRB outer-membrane complexes enables sulfate-coupled AOM syntrophy.",
            "evidence": [
              {
                "reference": "DOI:10.1371/journal.pbio.3002292",
                "notes": "Protein complexes involved in direct interspecies electron transfer (DIET) from ANME to the SRB outer membrane are conserved."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "nitrate",
            "predicate": "serves as terminal electron acceptor for",
            "object": "aom_trait",
            "description": "Nitrate serves as terminal electron acceptor in nitrate-dependent AOM via reverse methanogenesis.",
            "evidence": [
              {
                "reference": "DOI:10.1021/acs.est.3c07197",
                "notes": "Methane oxidation via a reverse methanogenesis pathway coupled to nitrate reduction to nitrite."
              }
            ]
          },
          {
            "subject": "nitrite",
            "predicate": "serves as terminal electron acceptor for",
            "object": "aom_trait",
            "description": "Nitrite serves as terminal electron acceptor in nitrite-dependent AOM (n-DAMO).",
            "evidence": [
              {
                "reference": "DOI:10.1021/acs.est.3c07197",
                "notes": "Nitrite-dependent methane oxidation reduces nitrite to nitric oxide in an intra-aerobic pathway."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-30T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate METABOLISM trait (anaerobic oxidation of methane) from literature research; complements the existing methanogenesis class (the reverse process).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-10T14:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (ANME-SRB AOM consortium) with CHEBI node groundings and METPO/biolink predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 6 evidence-backed generic edges (5 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:12Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:23:53Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0044674\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 1 causal edge(s) off enables/RO:0002327 with a TRAIT object (1 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-24T10:05:00Z",
        "curator": "codex",
        "action": "CURATE_PROTEIN_TAXON_EXAMPLE",
        "changes": "Scoped the composite AOM graph, converted the canonical example to its DOI, and added a taxon-matched Ca. M. nitroreducens mcrA example with explicit complex-component and directionality caveats.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-22T01:35:00Z",
        "curator": "claude",
        "action": "REFRESH_UNIPROT_ENTRY_VERSION",
        "changes": "Refreshed UniProtKB entry_version against live UniProt REST on 2026-10-22: UniProtKB:A0A284VQI9 (21 -> 22 on mcr).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000802",
    "label": "Anaerobic respiration",
    "definition": "A respiration in which an organism uses electron acceptors other than oxygen for energy production.",
    "definition_source": "DOI:10.1128/mmbr.61.4.533-616.1997",
    "trait_category": "METABOLISM",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000800"
    ],
    "synonyms": [
      {
        "synonym_text": "Anoxic respiration",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "Dissimilatory respiration (non-O\u2082)",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "xrefs": [
      "GO:0009061"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1128/mmbr.61.4.533-616.1997",
        "snippet": "N oxides as terminal electron acceptors",
        "notes": "Denitrification review supports anaerobic respiration using non-oxygen terminal electron acceptors."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:70863",
        "taxon_label": "Shewanella oneidensis",
        "note": "respires metals/alternative acceptors",
        "reference": "DOI:10.1038/nbt749"
      },
      {
        "taxon_id": "NCBITaxon:562",
        "taxon_label": "Escherichia coli",
        "note": "nitrate/fumarate anaerobic respiration",
        "reference": "PMID:9230919"
      },
      {
        "taxon_id": "NCBITaxon:266",
        "taxon_label": "Paracoccus denitrificans",
        "note": "Complete denitrifier paired to the reviewed NosZ example for the representative nitrogen-oxide respiration branch.",
        "reference": "DOI:10.1042/BJ20020782"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "anaerobic_respiration_denitrification",
        "title": "Anaerobic respiration with nitrogen oxide acceptors",
        "description": "Evidence-backed causal sketch using denitrification as a representative anaerobic respiratory process.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "This graph uses complete denitrification as one representative branch of anaerobic respiration. The P. denitrificans NosZ example supports only its terminal N2O-reduction step; metal, fumarate, sulfate, and other acceptor routes use different reductases.",
        "nodes": [
          {
            "node_id": "anaerobic_respiration_trait",
            "label": "Anaerobic respiration",
            "node_type": "TRAIT",
            "grounding": "METPO:1000802",
            "description": "Respiration using terminal electron acceptors other than oxygen."
          },
          {
            "node_id": "low_oxygen_condition",
            "label": "anaerobic or microaerophilic condition",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Low-oxygen condition permissive for denitrifying respiration."
          },
          {
            "node_id": "denitrification",
            "label": "denitrification",
            "node_type": "BIOLOGICAL_PROCESS",
            "grounding": "GO:0019333",
            "description": "Respiratory reduction of nitrogen oxides."
          },
          {
            "node_id": "nitrogen_oxides",
            "label": "nitrogen oxides",
            "node_type": "CHEMICAL",
            "description": "Non-oxygen terminal electron acceptors used in denitrification.",
            "grounding": "CHEBI:35196"
          },
          {
            "node_id": "terminal_electron_acceptor",
            "label": "terminal electron acceptor",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "Electron-accepting role in respiratory bioenergetics.",
            "grounding": "METPO:1007504"
          },
          {
            "node_id": "energy_conservation",
            "label": "cellular energy conservation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Bioenergetic output of respiratory electron transport."
          },
          {
            "node_id": "oxygen_limitation",
            "label": "oxygen limitation / anoxic transition",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Onset of low-oxygen / anoxic conditions that triggers expression and activity of anaerobic respiratory reductases."
          },
          {
            "node_id": "denitrification_reductases",
            "label": "denitrification reductases",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Respiratory reductases (e.g., Nar, Nos) that catalyze stepwise reduction of nitrogen oxides during denitrification.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "This plural umbrella node groups unrelated Nar, Nir, Nor, and Nos enzyme families, so no single protein-family, activity, or complex term exactly represents it."
          },
          {
            "node_id": "nitrate_reductase",
            "label": "respiratory nitrate reductase (NarGHI)",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Membrane-bound respiratory nitrate reductase complex that reduces nitrate to nitrite.",
            "grounding": "GO:0009325"
          },
          {
            "node_id": "nitrate",
            "label": "nitrate",
            "node_type": "CHEMICAL",
            "description": "Oxidized nitrogen oxyanion reduced to nitrite during nitrate respiration.",
            "grounding": "CHEBI:17632"
          },
          {
            "node_id": "nitrite",
            "label": "nitrite",
            "node_type": "CHEMICAL",
            "description": "Reduced product of nitrate reduction and substrate for subsequent denitrification or DNRA.",
            "grounding": "CHEBI:16301"
          },
          {
            "node_id": "nitrous_oxide_reductase",
            "label": "nitrous oxide reductase (NosZ)",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Terminal reductase of denitrification reducing nitrous oxide to dinitrogen.",
            "grounding": "GO:0050304",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:Q51705",
                "protein_label": "Nitrous-oxide reductase",
                "gene_symbol": "nosZ",
                "taxon_id": "NCBITaxon:266",
                "taxon_label": "Paracoccus denitrificans",
                "entry_status": "REVIEWED",
                "retrieved_on": "2026-08-24",
                "entry_version": 135,
                "sequence_version": 1,
                "role": "NosZ enzyme catalyzing the terminal N2O-to-dinitrogen step in P. denitrificans.",
                "evidence": [
                  {
                    "reference": "DOI:10.1042/BJ20020782",
                    "snippet": "N2OR is a multicopper protein which converts N2O into dinitrogen and water.",
                    "notes": "The primary structural study purified and characterized N2O reductase from P. denitrificans; UniProtKB Q51705 verifies the reviewed NosZ protein and matching taxon."
                  }
                ]
              }
            ]
          },
          {
            "node_id": "nitrous_oxide",
            "label": "nitrous oxide",
            "node_type": "CHEMICAL",
            "description": "Denitrification intermediate reduced to dinitrogen by NosZ.",
            "grounding": "CHEBI:17045"
          },
          {
            "node_id": "dinitrogen",
            "label": "dinitrogen",
            "node_type": "CHEMICAL",
            "description": "Gaseous end product of complete denitrification.",
            "grounding": "CHEBI:17997"
          }
        ],
        "edges": [
          {
            "subject": "denitrification",
            "predicate": "occurs in",
            "object": "low_oxygen_condition",
            "description": "Denitrification can occur under anaerobic and microaerophilic conditions.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mmbr.61.4.533-616.1997",
                "snippet": "under anaerobic, microaerophilic, and occasionally aerobic conditions",
                "notes": "Supports low-oxygen context for denitrification."
              }
            ],
            "predicate_id": "biolink:occurs_in"
          },
          {
            "subject": "nitrogen_oxides",
            "predicate": "acts as",
            "object": "terminal_electron_acceptor",
            "description": "Nitrogen oxides serve as terminal electron acceptors.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mmbr.61.4.533-616.1997",
                "snippet": "N oxides as terminal electron acceptors",
                "notes": "Supports the terminal electron acceptor role."
              }
            ]
          },
          {
            "subject": "denitrification",
            "predicate": "uses",
            "object": "nitrogen_oxides",
            "description": "Denitrification uses nitrogen oxides in respiratory bioenergetics.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mmbr.61.4.533-616.1997",
                "snippet": "making use of N oxides",
                "notes": "Supports nitrogen oxides as denitrification substrates."
              }
            ]
          },
          {
            "subject": "denitrification",
            "predicate": "conserves",
            "object": "energy_conservation",
            "description": "Denitrification is a respiratory route for energy conservation.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mmbr.61.4.533-616.1997",
                "snippet": "distinct means of energy conservation",
                "notes": "Supports energy conservation via denitrification."
              }
            ]
          },
          {
            "subject": "anaerobic_respiration_trait",
            "predicate": "exemplified by",
            "object": "denitrification",
            "description": "Denitrification is a representative anaerobic respiratory process.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mmbr.61.4.533-616.1997",
                "snippet": "terminal electron acceptors for cellular bioenergetics",
                "notes": "Supports denitrification as non-oxygen respiratory bioenergetics."
              }
            ]
          },
          {
            "subject": "oxygen_limitation",
            "predicate": "increases activity of",
            "object": "denitrification_reductases",
            "description": "Onset of anoxia drives early transcription and activity of denitrification reductases.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-024-51688-w",
                "notes": "early transcription of NAR (and sometimes NOS) at the cusp of anoxia; environmental driver activating denitrification reductases."
              }
            ]
          },
          {
            "subject": "nitrate_reductase",
            "predicate": "catalyzes reduction of",
            "object": "nitrate",
            "description": "Respiratory nitrate reductase NarGHI catalyzes the reduction of nitrate to nitrite.",
            "evidence": [
              {
                "reference": "DOI:10.1128/msystems.00967-23",
                "notes": "the narGHI nitrate reductase cluster; NarGHI catalyzes nitrate reduction to nitrite, the canonical first step of nitrate respiration."
              }
            ]
          },
          {
            "subject": "nitrate_reductase",
            "predicate": "produces",
            "object": "nitrite",
            "description": "Reduction of nitrate by NarGHI yields nitrite.",
            "evidence": [
              {
                "reference": "DOI:10.1128/msystems.00967-23",
                "notes": "NarGHI nitrate reductase produces nitrite from nitrate."
              }
            ],
            "predicate_id": "METPO:2007800"
          },
          {
            "subject": "nitrous_oxide_reductase",
            "predicate": "reduces",
            "object": "nitrous_oxide",
            "description": "NosZ reduces nitrous oxide to dinitrogen, the terminal step of complete denitrification.",
            "evidence": [
              {
                "reference": "DOI:10.1128/msystems.00967-23",
                "notes": "NosZ reduces N2O to N2; canonical terminal denitrification step."
              }
            ],
            "predicate_id": "METPO:2007802"
          },
          {
            "subject": "nitrous_oxide_reductase",
            "predicate": "produces",
            "object": "dinitrogen",
            "description": "NosZ-catalyzed reduction of nitrous oxide produces dinitrogen.",
            "evidence": [
              {
                "reference": "DOI:10.1128/msystems.00967-23",
                "notes": "NosZ reduces N2O to N2; produces dinitrogen as denitrification end product."
              }
            ],
            "predicate_id": "METPO:2007800"
          },
          {
            "subject": "nitrate_reductase",
            "predicate": "example of",
            "object": "denitrification_reductases",
            "description": "Respiratory NarGHI is one of the reductase systems used in denitrifying respiration.",
            "evidence": [
              {
                "reference": "DOI:10.1128/msystems.00967-23",
                "snippet": "the narGHI nitrate reductase cluster; NarGHI catalyzes nitrate reduction to nitrite, the canonical first step of nitrate respiration.",
                "notes": "Verified against the free public article text."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "nitrous_oxide_reductase",
            "predicate": "example of",
            "object": "denitrification_reductases",
            "description": "NosZ is the terminal member of the denitrification-reductase set.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mmbr.61.4.533-616.1997",
                "snippet": "the isolation of the novel enzymes nitric oxide reductase and nitrous oxide reductase",
                "notes": "Verified against the free public article text."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "denitrification_reductases",
            "predicate": "contributes to",
            "object": "denitrification",
            "description": "The respiratory reductase ensemble executes the sequential reductions of denitrification.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mmbr.61.4.533-616.1997",
                "snippet": "unexpected relationships among denitrification enzymes and respiratory oxygen reductases",
                "notes": "Verified against the free public article text."
              }
            ],
            "predicate_id": "RO:0002326"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.912036+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-07T00:00:00-07:00",
        "curator": "codex",
        "action": "ADDED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed causal graph for anaerobic respiration using denitrification and nitrogen oxide terminal electron acceptors.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:41:03Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (METPO:1007504\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-26T05:00:47Z",
        "curator": "claude",
        "action": "RENAME_PREDICATE_LABELS",
        "changes": "Renamed 1 causal-edge predicate label(s) to align with existing groundings: occurs under \u2192 occurs in \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-26T05:00:50Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:occurs_in\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-14T05:51:45Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:35196\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 5 evidence-backed generic edges (8 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:12Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d72, METPO:2000017\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:18Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:17632\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:32Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 3 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:16301\u00d71, CHEBI:17045\u00d71, CHEBI:17997\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:23:53Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0050304\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T02:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES_PART2",
        "changes": "Re-grounded 3 causal edge(s) off microbe-domain METPO predicates onto their causal-graph counterparts (2 to produces, 1 to reduces), issue 301 part 2. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Each replacement is a 1:1 mirror of its source predicate that changes only the domain, so the claim each edge makes is unchanged and directions are unchanged. The replacements are proposed in proposals/metpo_traitmech_v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-24T08:20:00Z",
        "curator": "codex",
        "action": "CURATE_PROTEIN_TAXON_EXAMPLE",
        "changes": "Added a DOI-backed P. denitrificans NosZ example for the representative denitrification branch, grounded NarGHI to its current GO complex term, explicitly reviewed the plural reductase umbrella as label-only, and documented graph scope.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T06:15:39Z",
        "curator": "codex",
        "action": "ADD_EXACT_ONTOLOGY_MATCH",
        "changes": "Ontology exact-match review (2026-08-25): approved exact xref(s): GO:0009061. Evidence is predicate-scoped in the versioned ontology snapshots; OAK cross-checked direct data, and OLS4 spot-checked release deltas and disputed hits.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T12:15:00Z",
        "curator": "codex",
        "action": "CONNECT_CAUSAL_GRAPH_COMPONENTS",
        "changes": "Resolved issue #183 graph fragmentation (4 components to 1) with 3 public-source connector(s). No paid research service was called.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000035",
    "label": "anoxygenic photosynthesis",
    "definition": "A phototrophic metabolism that uses light energy with a single photosystem and bacteriochlorophyll, using electron donors other than water (e.g. H2S, H2, Fe(II), organics) and therefore not evolving oxygen. Characteristic of purple and green sulfur bacteria, Chloroflexi, and heliobacteria.",
    "definition_source": "DOI:10.1016/j.tim.2006.09.001",
    "trait_category": "METABOLISM",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "traitmech:000038"
    ],
    "synonyms": [
      {
        "synonym_text": "bacterial photosynthesis",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1016/j.tim.2006.09.001"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1016/j.tim.2006.09.001",
        "notes": "Bryant & Frigaard describe anoxygenic photosynthesis across five prokaryotic phyla using bacteriochlorophyll and a single photosystem without O2 evolution."
      },
      {
        "reference": "DOI:10.3389/fmicb.2024.1417714",
        "notes": "Review of anoxygenic photosynthesis in green sulfur bacteria supports sulfide as electron donor and the absence of oxygen production."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1063",
        "taxon_label": "Cereibacter sphaeroides",
        "note": "Textbook purple-bacterial (Type II) anoxygenic phototroph (formerly Rhodobacter sphaeroides). Chlorobaculum tepidum is the green-sulfur (Type I) model.",
        "reference": "DOI:10.1023/A:1006350405674"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "anoxygenic_photosynthesis_sulfide_donor",
        "title": "Anoxygenic photosynthesis uses non-water electron donors",
        "description": "Evidence-backed causal sketch linking a single bacteriochlorophyll photosystem and non-water electron donors (sulfide, H2, Fe(II), organics) to photosynthetic electron flow without O2 evolution.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "The graph combines a sulfide-donor branch documented in sulfur phototrophs with the type II reaction-center branch illustrated by Cereibacter sphaeroides; it does not imply that every anoxygenic phototroph uses sulfide or a type II center.",
        "nodes": [
          {
            "node_id": "anoxygenic_photosynthesis_trait",
            "label": "anoxygenic photosynthesis",
            "node_type": "TRAIT",
            "grounding": "traitmech:000035",
            "description": "Bacteriochlorophyll-based photosynthesis using non-water electron donors."
          },
          {
            "node_id": "sulfide",
            "label": "sulfide",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:15138",
            "description": "Reduced sulfur electron donor (representative anoxygenic donor)."
          },
          {
            "node_id": "photosynthetic_etc",
            "label": "photosynthetic electron transport",
            "node_type": "PATHWAY",
            "grounding": "GO:0009767",
            "description": "Single-photosystem electron transport powering anoxygenic photosynthesis."
          },
          {
            "node_id": "bacteriochlorophyll",
            "label": "bacteriochlorophyll",
            "node_type": "CHEMICAL",
            "description": "Light-harvesting pigment of anoxygenic phototrophs.",
            "grounding": "CHEBI:38201"
          },
          {
            "node_id": "light_energy",
            "label": "light energy",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Light input driving photochemistry in anoxygenic photosynthesis."
          },
          {
            "node_id": "type_ii_reaction_center_m",
            "label": "type II photosynthetic reaction center M subunit",
            "node_type": "GENE_OR_PROTEIN",
            "grounding": "InterPro:IPR005781",
            "description": "PufM component of the heterodimeric type II reaction center in purple phototrophic bacteria.",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:P0C0Y9",
                "protein_label": "Reaction center protein M chain",
                "gene_symbol": "pufM",
                "taxon_id": "NCBITaxon:1063",
                "taxon_label": "Cereibacter sphaeroides",
                "entry_status": "REVIEWED",
                "retrieved_on": "2026-10-22",
                "entry_version": 109,
                "sequence_version": 2,
                "role": "M-chain component of the type II photosynthetic reaction center; this accession is not presented as the complete reaction-center complex.",
                "evidence": [
                  {
                    "reference": "DOI:10.1016/j.bbabio.2003.08.008",
                    "snippet": "Strains of Rb. sphaeroides containing the AM260W reaction centre are incapable of growth under anaerobic conditions in the light.",
                    "notes": "A primary pufM mutagenesis study links the M chain to photosynthetic growth in R. sphaeroides; UniProtKB P0C0Y9 verifies the reviewed Cereibacter sphaeroides protein and InterPro IPR005781 verifies the M-subunit family."
                  }
                ]
              }
            ]
          },
          {
            "node_id": "elemental_sulfur",
            "label": "elemental sulfur (S0)",
            "node_type": "CHEMICAL",
            "description": "Oxidized sulfur product from sulfide oxidation during anoxygenic photosynthesis."
          }
        ],
        "edges": [
          {
            "subject": "sulfide",
            "predicate": "feeds electrons into",
            "object": "photosynthetic_etc",
            "description": "Sulfide and other non-water donors feed electrons into the single photosystem.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2024.1417714",
                "notes": "Review of green sulfur bacteria supports sulfide as electron donor and the absence of oxygen production."
              }
            ],
            "predicate_id": "METPO:2007402"
          },
          {
            "subject": "photosynthetic_etc",
            "predicate": "confers",
            "object": "anoxygenic_photosynthesis_trait",
            "description": "Bacteriochlorophyll-based electron flow realizes anoxygenic photosynthesis.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.tim.2006.09.001",
                "notes": "Bryant & Frigaard describe anoxygenic photosynthesis across five prokaryotic phyla using bacteriochlorophyll and a single photosystem."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "bacteriochlorophyll",
            "predicate": "absorbs",
            "object": "light_energy",
            "description": "Bacteriochlorophyll harvests light energy to drive single-photosystem photochemistry.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.tim.2006.09.001",
                "notes": "Bryant & Frigaard: anoxygenic photosynthesis uses bacteriochlorophyll and a single photosystem to capture light energy."
              }
            ]
          },
          {
            "subject": "light_energy",
            "predicate": "powers",
            "object": "photosynthetic_etc",
            "description": "Absorbed light energy drives photosynthetic electron transport through the single photosystem.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.tim.2006.09.001",
                "notes": "Light energy captured by bacteriochlorophyll powers single-photosystem electron flow in anoxygenic phototrophs."
              }
            ]
          },
          {
            "subject": "type_ii_reaction_center_m",
            "predicate": "confers",
            "object": "anoxygenic_photosynthesis_trait",
            "description": "The PufM-containing type II reaction center is required for photosynthetic growth in the purple bacterium Cereibacter sphaeroides.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.bbabio.2003.08.008",
                "snippet": "Strains of Rb. sphaeroides containing the AM260W reaction centre are incapable of growth under anaerobic conditions in the light.",
                "notes": "The M-polypeptide perturbation directly impaired photosynthetic growth; the claim is restricted to the type II reaction-center branch represented by C. sphaeroides."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "type_ii_reaction_center_m",
            "predicate": "part of",
            "object": "photosynthetic_etc",
            "description": "PufM is a component of the reaction center that drives cyclic electron transfer in purple bacterial photosynthesis.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.bbabio.2003.08.008",
                "snippet": "light energy is used to power a cycle of electron transfer reactions",
                "notes": "The primary study describes the R. sphaeroides reaction center within cyclic photosynthetic electron transfer and experimentally perturbs its M polypeptide."
              }
            ],
            "predicate_id": "biolink:part_of"
          },
          {
            "subject": "sulfide",
            "predicate": "oxidized to",
            "object": "elemental_sulfur",
            "description": "Sulfide donated to the photosystem is oxidized to elemental sulfur (S0) during anoxygenic photosynthesis.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2024.1417714",
                "notes": "Kushkevych et al.: H2S serves as electron donor and is oxidized to S0 in green/purple sulfur bacteria anoxygenic photosynthesis."
              }
            ],
            "predicate_id": "METPO:2007405"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-30T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate METABOLISM trait (anoxygenic photosynthesis) from literature research to fill the phototrophy gap.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-10T14:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (sulfide-driven anoxygenic photosynthesis) with CHEBI/GO node groundings and RO/METPO predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 5 evidence-backed generic edges (4 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:12Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d71, biolink:part_of\u00d71, METPO:2007405\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:18Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:38201\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 2 causal edge(s) off enables/RO:0002327 with a TRAIT object (2 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-24T00:00:00Z",
        "curator": "codex",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Corrected the canonical C. sphaeroides branch from a Type I center to the PufM component of a type II reaction center, added InterPro grounding and a DOI-backed taxon-matched UniProt example, and documented the graph's composite scope.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-22T01:35:00Z",
        "curator": "claude",
        "action": "REFRESH_UNIPROT_ENTRY_VERSION",
        "changes": "Refreshed UniProtKB entry_version against live UniProt REST on 2026-10-22: UniProtKB:P0C0Y9 (108 -> 109 on type_ii_reaction_center_m).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000130",
    "label": "aromatic compound degradation",
    "definition": "A metabolism in which an organism catabolizes an aromatic compound, whether or not that compound is a hydrocarbon.",
    "definition_source": "DOI:10.1126/science.aaf4507",
    "trait_category": "METABOLISM",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000060"
    ],
    "synonyms": [
      {
        "synonym_text": "aromatic_compound_degradation",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1126/science.aaf4507"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.3390/ijerph6010278",
        "snippet": "bacterial degradation pathways of selected aromatic compounds",
        "notes": "Seo et al. review bacterial pathways for degradation of aromatic compounds."
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-08T00:00:00Z",
        "curator": "codex",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed a DOI-backed FAPROTAX metabolic capability from proposals/metpo_traitmech_v11 after repository-wide duplicate review.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-21T20:01:04Z",
        "curator": "claude",
        "action": "RECORD_MECHANISM_KNOWLEDGE_GAP",
        "changes": "Recorded OPEN KNOWLEDGE_GAP discussion (aromatic-compound-degradation-causal-graph-source-gap) documenting the source-limited mechanism gap for causal_graphs.",
        "llm_assisted": true
      }
    ],
    "discussions": [
      {
        "discussion_id": "aromatic-compound-degradation-causal-graph-source-gap",
        "prompt": "Add multi-step ring-cleavage pathway evidence (e.g. catechol or protocatechuate dioxygenase enzymes, substrates, and products) and a strain-matched canonical example before constructing causal_graphs.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "The current record carries a single broad FAPROTAX review snippet (DOI:10.3390/ijerph6010278) naming bacterial degradation pathways of aromatic compounds without specific enzyme or intermediate claims; constructing a multi-edge causal graph from that single 60-character phrase would require clause-splitting or unsupported edges.",
        "posed_by": "claude",
        "posed_date": "2026-10-21",
        "evidence": [
          {
            "reference": "DOI:10.3390/ijerph6010278",
            "supports": "PARTIAL",
            "snippet": "bacterial degradation pathways of selected aromatic compounds",
            "explanation": "Existing record-level evidence supports the high-level metabolic trait definition but does not provide multi-step enzymatic mechanism quotes for a connected causal graph."
          }
        ]
      }
    ]
  },
  {
    "identifier": "traitmech:000129",
    "label": "aromatic hydrocarbon degradation",
    "definition": "A hydrocarbon degradation in which the substrate carries at least one aromatic ring.",
    "definition_source": "DOI:10.1126/science.aaf4507",
    "trait_category": "METABOLISM",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000128",
      "traitmech:000130"
    ],
    "synonyms": [
      {
        "synonym_text": "aromatic_hydrocarbon_degradation",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1126/science.aaf4507"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1007/BF00058836",
        "snippet": "benzene, certain arenes, biphenyl and selected fused aromatic hydrocarbons",
        "notes": "Smith reviews bacterial biodegradation of aromatic hydrocarbons as a distinct hydrocarbon-degradation branch."
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-08T00:00:00Z",
        "curator": "codex",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed a DOI-backed FAPROTAX metabolic capability from proposals/metpo_traitmech_v11 after repository-wide duplicate review.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-21T20:01:04Z",
        "curator": "claude",
        "action": "RECORD_MECHANISM_KNOWLEDGE_GAP",
        "changes": "Recorded OPEN KNOWLEDGE_GAP discussion (aromatic-hydrocarbon-degradation-causal-graph-source-gap) documenting the source-limited mechanism gap for causal_graphs.",
        "llm_assisted": true
      }
    ],
    "discussions": [
      {
        "discussion_id": "aromatic-hydrocarbon-degradation-causal-graph-source-gap",
        "prompt": "Add primary literature evidence for aromatic-ring hydroxylation and cleavage enzymes (e.g. benzene/biphenyl dioxygenase) and a strain-matched canonical example before constructing causal_graphs.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "The current record carries a single substrate-list snippet (DOI:10.1007/BF00058836) enumerating benzene, arenes, biphenyl, and fused aromatic hydrocarbons without catalytic or pathway-step assertions.",
        "posed_by": "claude",
        "posed_date": "2026-10-21",
        "evidence": [
          {
            "reference": "DOI:10.1007/BF00058836",
            "supports": "PARTIAL",
            "snippet": "benzene, certain arenes, biphenyl and selected fused aromatic hydrocarbons",
            "explanation": "Existing record-level evidence supports the high-level metabolic trait definition but does not provide multi-step enzymatic mechanism quotes for a connected causal graph."
          }
        ]
      }
    ]
  },
  {
    "identifier": "traitmech:000195",
    "label": "arsenate respiration",
    "definition": "An anaerobic respiration in which an organism uses arsenate as the terminal electron acceptor and reduces it to arsenite for energy conservation.",
    "definition_source": "DOI:10.1073/pnas.1834303100",
    "trait_category": "METABOLISM",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000802"
    ],
    "synonyms": [
      {
        "synonym_text": "As(V) respiration",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1073/pnas.1834303100"
      },
      {
        "synonym_text": "respiratory As(V) reduction",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1073/pnas.1834303100"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1073/pnas.1834303100",
        "snippet": "can be used by microorganisms as a terminal electron acceptor in anaerobic respiration",
        "notes": "Saltikov and Newman define the organism-level scope as microbial anaerobic respiration using arsenate, As(V), as a terminal electron acceptor."
      },
      {
        "reference": "DOI:10.1128/AEM.69.5.2800-2809.2003",
        "snippet": "This gram-negative strain stoichiometrically couples the oxidation of lactate to acetate with the reduction of As(V) to arsenite",
        "notes": "Saltikov et al. isolated and characterized ANA-3 as a facultatively anaerobic As(V)-respiring Shewanella strain."
      },
      {
        "reference": "DOI:10.1128/JB.01110-07",
        "snippet": "the Shewanella sp. strain ANA-3 arsenate respiratory reductase (ARR), the key enzyme involved in this metabolism",
        "notes": "Malasarn et al. biochemically characterize ARR as the arsenate respiratory reductase for ANA-3 arsenate respiration."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:94122",
        "taxon_label": "Shewanella sp. ANA-3",
        "note": "Facultatively anaerobic Shewanella isolate characterized for arsenate-respiration studies.",
        "reference": "DOI:10.1128/AEM.69.5.2800-2809.2003"
      }
    ],
    "discussions": [
      {
        "discussion_id": "arsenate-respiration-xref-gap",
        "prompt": "Resolve an exact external ontology class for organism-level arsenate respiration before adding a TraitRecord xref.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "The pinned METPO snapshot contains obsolete arsenate reduction and arsenate-reducing classes but no active organism-level arsenate respiration class. Potential GO, Rhea, EC, and protein-family terms for respiratory arsenate reductase are narrower than the whole-organism anaerobic respiration phenotype, and future groundings must keep ArrAB respiratory reduction separate from ArsC cytosolic detoxification.",
        "posed_by": "codex",
        "posed_date": "2026-09-14"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-14T23:52:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted arsenate respiration as a DOI-backed anaerobic respiration TraitRecord after a repository-wide duplicate review covering ignored and hidden files; the local METPO snapshot has only obsolete arsenate-reduction classes and the replacement placeholder is reserved in proposals/metpo_traitmech_v72.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-15T00:08:31Z",
        "curator": "codex",
        "action": "TIGHTENED_CANONICAL_EXAMPLE",
        "changes": "Tightened the ANA-3 canonical example note to the DOI-backed isolation and facultative arsenate-respiration evidence without making a broader genetic-tractability claim.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000189",
    "label": "arsenite oxidation",
    "definition": "A metabolism in which an organism enzymatically oxidizes arsenite to arsenate as an energy-generating electron donor or detoxification substrate.",
    "definition_source": "DOI:10.3389/fmicb.2020.569282",
    "trait_category": "METABOLISM",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000060"
    ],
    "synonyms": [
      {
        "synonym_text": "As(III) oxidation",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.3389/fmicb.2020.569282"
      },
      {
        "synonym_text": "microbial arsenite oxidation",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.3389/fmicb.2020.569282"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.3389/fmicb.2020.569282",
        "snippet": "The biological oxidation of arsenite [As(III)] to arsenate [As(V)] is considered a strategy to reduce arsenic toxicity and provide energy",
        "notes": "Shi et al. review biological As(III)-to-As(V) oxidation as a microbial detoxification and energy-generating metabolism."
      },
      {
        "reference": "DOI:10.1128/AEM.66.1.92-97.2000",
        "snippet": "A facultatively chemolithoautotrophic arsenite oxidizer (strain NT-26) was isolated from the arsenopyrite-containing gold mine at Pine Creek, Northern Territory, Australia.",
        "notes": "Santini et al. isolated the aerobic chemolithoautotrophic arsenite-oxidizing strain NT-26."
      },
      {
        "reference": "DOI:10.1186/s12866-024-03676-9",
        "snippet": "Both BAW48 and BAS32 isolates demonstrated As(III) oxidation",
        "notes": "Hoque et al. report As(III)-oxidizing Achromobacter aegrifaciens isolates from arsenic-contaminated tubewell water and soil."
      }
    ],
    "discussions": [
      {
        "discussion_id": "arsenite-oxidation-xref-gap",
        "prompt": "Resolve an exact external ontology class for organism-level arsenite oxidation before adding a TraitRecord xref.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "The pinned METPO snapshot contains only METPO:1000840 obsolete Arsenite oxidation. Potential external molecular function terms for arsenite oxidase activity are narrower than the organism-level As(III)-to-As(V) metabolism, and a future mechanism graph should distinguish aerobic AioBA oxidation from anaerobic ArxAB-mediated arsenite oxidation.",
        "posed_by": "codex",
        "posed_date": "2026-09-14"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-14T20:30:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted arsenite oxidation as a DOI-backed arsenic metabolism TraitRecord after a repository-wide duplicate review covering ignored and hidden files; the local METPO snapshot has only an obsolete Arsenite oxidation class and the replacement placeholder is reserved in proposals/metpo_traitmech_v66.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:2000002",
    "label": "assimilates",
    "definition": "An OBJECT_PROPERTY relating an organism to a chemical entity that the organism takes up and incorporates into cellular biomass.",
    "definition_source": "DOI:10.1146/annurev.micro.55.1.485",
    "trait_category": "METABOLISM",
    "term_kind": "OBJECT_PROPERTY",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:2000001"
    ],
    "synonyms": [
      {
        "synonym_text": "assimilation",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "domain": "https://w3id.org/metpo/1000525",
    "range_": "http://purl.obolibrary.org/obo/CHEBI_24431",
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev.micro.55.1.485",
        "snippet": "assimilation",
        "notes": "Microbial-physiology reference supports 'assimilates' as a canonical predicate composed with a CHEBI-class chemical object at assertion time."
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.950665+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (OBJECT_PROPERTY)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic biochemical conversion or activity relation carrier; later replacement should use more specific trait records that combine the relation with the substrate, product, enzyme or activity target, assay context, growth condition, or other entity.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-16T08:50:00-07:00",
        "curator": "claude",
        "action": "UNDEPRECATED_AS_COMPOSITION_PRIMITIVE",
        "changes": "Restored from DEPRECATED to REVIEWED under the predicate+class composition pattern (intended use: <organism> + this predicate + CHEBI chemical class). Added DOI/PMID-backed definition, evidence, and explicit domain/range slots.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000110",
    "label": "biopolymer degradation",
    "definition": "A metabolism in which an organism secretes enzymes to depolymerize recalcitrant biopolymers (such as cellulose, hemicellulose, chitin, and lignin) into assimilable units for growth.",
    "definition_source": "DOI:10.1016/j.cbpa.2015.10.018",
    "trait_category": "METABOLISM",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000060"
    ],
    "synonyms": [
      {
        "synonym_text": "biomass degradation",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1016/j.cbpa.2015.10.018"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1016/j.cbpa.2015.10.018",
        "notes": "Cragg et al. review lignocellulose degradation mechanisms across the tree of life, using complementary enzymes to deconstruct plant biopolymers; parent of the polymer-specific sub-variants."
      },
      {
        "reference": "DOI:10.1128/MMBR.66.3.506-577.2002",
        "notes": "Lynd et al. review microbial utilization of cellulose, the archetypal biopolymer-degradation process."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1423",
        "taxon_label": "Bacillus subtilis",
        "note": "secreted polymer hydrolases",
        "reference": "PMID:35893563"
      },
      {
        "taxon_id": "NCBITaxon:1708",
        "taxon_label": "Cellulomonas fimi",
        "note": "cellulose/biopolymer degrader",
        "reference": "PMID:23342046"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "biopolymer_degradation_extracellular_hydrolysis",
        "title": "Biopolymer degradation depolymerizes recalcitrant biomass extracellularly",
        "description": "Evidence-backed causal sketch linking secreted depolymerizing enzymes to liberation of assimilable units from recalcitrant biopolymers.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "This is a composite umbrella graph spanning cellulose, chitin, polysaccharide-import, and lignin branches. The C. fimi CenA example supports the cellulose branch only; it is not presented as a protein that realizes every branch.",
        "nodes": [
          {
            "node_id": "biopolymer_degradation_trait",
            "label": "biopolymer degradation",
            "node_type": "TRAIT",
            "grounding": "traitmech:000110",
            "description": "Secreted enzymatic depolymerization of biopolymers (cellulose, chitin, lignin, etc.)."
          },
          {
            "node_id": "extracellular_enzymes",
            "label": "secreted depolymerizing enzymes",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Extracellular hydrolases / oxidoreductases acting on biopolymers.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "This umbrella node combines unrelated hydrolase and oxidoreductase families, so no single GO or InterPro term denotes the represented set."
          },
          {
            "node_id": "assimilable_units",
            "label": "assimilable mono- and oligosaccharides",
            "node_type": "CHEMICAL",
            "description": "Sugars, peptides, and oligomers released for uptake."
          },
          {
            "node_id": "endoglucanase",
            "label": "endoglucanase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Glycoside hydrolase cleaving internal beta-1,4 linkages in cellulose.",
            "grounding": "GO:0008810",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:P07984",
                "protein_label": "Endoglucanase A",
                "gene_symbol": "cenA",
                "taxon_id": "NCBITaxon:1708",
                "taxon_label": "Cellulomonas fimi",
                "entry_status": "REVIEWED",
                "retrieved_on": "2026-10-22",
                "entry_version": 123,
                "sequence_version": 1,
                "role": "Secreted CenA endoglucanase representing the cellulose-hydrolysis branch of this composite biopolymer-degradation graph.",
                "evidence": [
                  {
                    "reference": "DOI:10.1016/0378-1119(86)90196-4",
                    "snippet": "they expressed carboxymethylcellulase activity in Escherichia coli",
                    "notes": "The primary cloning and deletion study identifies active C. fimi CenA. UniProtKB P07984 is the reviewed CenA entry from the same species."
                  }
                ]
              }
            ]
          },
          {
            "node_id": "cello_oligosaccharides",
            "label": "cello-oligosaccharides",
            "node_type": "CHEMICAL",
            "description": "Soluble cellulose-derived oligomers produced by endoglucanase action."
          },
          {
            "node_id": "beta_glucosidase",
            "label": "beta-glucosidase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Hydrolase converting cellobiose/oligosaccharides to glucose.",
            "grounding": "GO:0008422"
          },
          {
            "node_id": "glucose",
            "label": "glucose",
            "node_type": "CHEMICAL",
            "description": "Assimilable monosaccharide released by terminal saccharification.",
            "grounding": "CHEBI:17234"
          },
          {
            "node_id": "susc_transporter",
            "label": "SusC-like TonB-dependent transporter",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Outer-membrane TonB-dependent transporter importing oligosaccharides into the periplasm.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "SusC-like transporters are substrate-diverse; the cited starch-utilization example does not establish one exact family term for every oligosaccharide transporter represented by this broad node."
          },
          {
            "node_id": "oligosaccharides",
            "label": "oligosaccharides",
            "node_type": "CHEMICAL",
            "description": "Oligomeric breakdown products captured at the cell surface and imported.",
            "grounding": "CHEBI:50699"
          },
          {
            "node_id": "periplasmic_gh3",
            "label": "periplasmic GH3 hydrolase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Periplasmic glycosyl hydrolase converting imported oligomers to monosaccharides.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "GH3 is a functionally diverse glycoside-hydrolase family, while this node additionally asserts localization and substrate context not captured by a single reviewed semantic term."
          },
          {
            "node_id": "endochitinase",
            "label": "endo-chitinase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Enzyme cleaving internally within the beta-1,4-GlcNAc chitin polymer.",
            "grounding": "GO:0008843"
          },
          {
            "node_id": "chitooligosaccharides",
            "label": "chitooligosaccharides",
            "node_type": "CHEMICAL",
            "description": "Chitin-derived oligomers produced by endo-chitinase action."
          },
          {
            "node_id": "lignin_oxidative_enzymes",
            "label": "lignin-oxidizing redox enzymes (LiP/MnP/VP/laccase/DyP)",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Secreted oxidoreductases that oxidatively attack lignin.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "This combined label spans LiP, MnP, versatile peroxidase, laccase, and DyP families; no one protein-family term is valid for the full set."
          },
          {
            "node_id": "lignin",
            "label": "lignin",
            "node_type": "CHEMICAL",
            "description": "Recalcitrant aromatic plant biopolymer.",
            "grounding": "CHEBI:6457"
          }
        ],
        "edges": [
          {
            "subject": "extracellular_enzymes",
            "predicate": "confers",
            "object": "biopolymer_degradation_trait",
            "description": "Secreted enzymes drive extracellular biopolymer breakdown.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.cbpa.2015.10.018",
                "notes": "Cragg et al. review the complementary enzymes used to deconstruct plant biopolymers across the tree of life."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "biopolymer_degradation_trait",
            "predicate": "produces",
            "object": "assimilable_units",
            "description": "Depolymerization releases assimilable units for cellular uptake.",
            "evidence": [
              {
                "reference": "DOI:10.1128/MMBR.66.3.506-577.2002",
                "notes": "Lynd et al. review microbial cellulose utilization as the archetypal biopolymer-degradation process."
              }
            ],
            "predicate_id": "METPO:2007800"
          },
          {
            "subject": "endoglucanase",
            "predicate": "cleaves",
            "object": "cello_oligosaccharides",
            "description": "Endoglucanases hydrolyze internal beta-1,4 bonds in cellulose to release cello-oligosaccharides.",
            "evidence": [
              {
                "reference": "DOI:10.1101/2024.11.06.622210",
                "notes": "Hsin 2024: \"Endoglucanases ... cleave internal beta-1,4 linkages\" (strong, general)."
              }
            ]
          },
          {
            "subject": "endoglucanase",
            "predicate": "contributes to",
            "object": "biopolymer_degradation_trait",
            "description": "Endoglucanase contributes the internal-chain-cleavage step of the cellulose-specific branch of biopolymer degradation.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.heliyon.2024.e24022",
                "snippet": "Endo-1,4-beta-glucanase randomly cleave and attack the amorphous part",
                "notes": "Datta reviews endoglucanase as one component of the synergistic cellulase system; this edge is restricted to the cellulose branch of the umbrella trait."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "beta_glucosidase",
            "predicate": "converts",
            "object": "glucose",
            "description": "Beta-glucosidases convert cellobiose/oligosaccharides to glucose (terminal saccharification).",
            "evidence": [
              {
                "reference": "DOI:10.1101/2024.11.06.622210",
                "notes": "Hsin 2024: \"beta-glucosidases ... convert cellobiose/oligosaccharides to glucose\" (strong, general)."
              }
            ]
          },
          {
            "subject": "beta_glucosidase",
            "predicate": "contributes to",
            "object": "biopolymer_degradation_trait",
            "description": "Beta-glucosidase contributes terminal saccharification of cellulose-derived oligomers to glucose.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.heliyon.2024.e24022",
                "snippet": "with the release of glucose molecules",
                "notes": "Datta places beta-glucosidase in the synergistic cellulase system and describes glucose release from endo- and exoglucanase products."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "susc_transporter",
            "predicate": "imports",
            "object": "oligosaccharides",
            "description": "SusC-like TonB-dependent transporter imports oligosaccharides across the outer membrane into the periplasm.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mbio.02599-23",
                "notes": "Wong 2024: \"SusC is a TonB-dependent transporter that imports maltooligosaccharides into the periplasm\" (strong)."
              }
            ],
            "predicate_id": "METPO:2007805"
          },
          {
            "subject": "susc_transporter",
            "predicate": "contributes to",
            "object": "biopolymer_degradation_trait",
            "description": "SusC-like uptake contributes the transport stage of a polysaccharide-utilization branch after extracellular or surface depolymerization.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mbio.02599-23",
                "snippet": "activity of Sus-like systems depends on polysaccharide size, ultimately impacting bacterial growth",
                "notes": "Wong et al. directly connect a Sus-like polysaccharide-utilization system to size-dependent metabolism and growth; this is a Bacteroides branch, not a universal transporter claim."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "periplasmic_gh3",
            "predicate": "converts",
            "object": "glucose",
            "description": "Periplasmic GH3 hydrolases depolymerize imported oligomers to glucose after uptake.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2024.1393588",
                "notes": "Kalenborn 2024: \"conversion of oligomeric laminarin to glucose in the periplasm can be catalyzed by ... glycosyl hydrolases\" (strong)."
              }
            ]
          },
          {
            "subject": "endochitinase",
            "predicate": "depolymerizes",
            "object": "chitooligosaccharides",
            "description": "Endo-chitinases cleave internally within chitin to produce chitooligosaccharides.",
            "evidence": [
              {
                "reference": "DOI:10.1128/spectrum.00886-24",
                "notes": "Meunier 2024: \"endo-chitinases EC 3.2.1.14 cleaving internally to produce multimers\" (strong)."
              }
            ]
          },
          {
            "subject": "endochitinase",
            "predicate": "contributes to",
            "object": "biopolymer_degradation_trait",
            "description": "Endo-chitinase contributes the internal-cleavage step of the chitin-specific branch of biopolymer degradation.",
            "evidence": [
              {
                "reference": "DOI:10.1128/spectrum.00886-24",
                "snippet": "endo-chitinases EC 3.2.1.14 cleaving internally to produce multimers",
                "notes": "Meunier et al. distinguish the endo-cleavage step in chitin degradation; the edge does not assert that chitinolysis always supplies growth carbon."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "lignin_oxidative_enzymes",
            "predicate": "depolymerizes",
            "object": "lignin",
            "description": "Secreted oxidative redox enzymes (LiP/MnP/VP/laccase/DyP) depolymerize lignin.",
            "evidence": [
              {
                "reference": "DOI:10.1101/2024.11.06.622210",
                "notes": "Hsin 2024: \"white-rot species deploy multiple oxidative enzymes (DyPs, LCMOs, LiP, MnP, LaC, VP)\"."
              }
            ]
          },
          {
            "subject": "lignin_oxidative_enzymes",
            "predicate": "contributes to",
            "object": "biopolymer_degradation_trait",
            "description": "Secreted lignin peroxidases and related oxidoreductases contribute the extracellular oxidative branch of biopolymer degradation.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s00253-024-13371-4",
                "snippet": "target and break down carbon-carbon and ether linkages in lignin",
                "notes": "Kato et al. describe secreted LiP, MnP, and versatile peroxidases producing lignin-derived aromatics in white-rot fungi; the edge is branch-specific."
              }
            ],
            "predicate_id": "RO:0002326"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-06-08T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate METABOLISM axis class (biopolymer degradation) to parent cellulolysis, chitinolysis, xylan degradation, and lignin degradation.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-10T14:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (biopolymer-degradation axis) with RO/METPO predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 6 evidence-backed generic edges (11 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:12Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000208\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:18Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:17234\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:32Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:50699\u00d71, CHEBI:6457\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-26T07:15:18Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 3 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A060H8L4\u00d71, UniProtKB:A0A031JNC1\u00d71, UniProtKB:Q693B6\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:21:11Z",
        "curator": "claude",
        "action": "RETRACT_DEAD_UNIPROT_GROUNDINGS",
        "changes": "Retracted 3 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:23:53Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0008422\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 1 causal edge(s) off enables/RO:0002327 with a TRAIT object (1 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T02:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES_PART2",
        "changes": "Re-grounded 2 causal edge(s) off microbe-domain METPO predicates onto their causal-graph counterparts (1 to imports, 1 to produces), issue 301 part 2. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Each replacement is a 1:1 mirror of its source predicate that changes only the domain, so the claim each edge makes is unchanged and directions are unchanged. The replacements are proposed in proposals/metpo_traitmech_v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-24T09:05:00Z",
        "curator": "codex",
        "action": "CURATE_PROTEIN_TAXON_EXAMPLE",
        "changes": "Scoped the composite mechanism, added a DOI-backed C. fimi CenA example, grounded endoglucanase and endochitinase activities, and recorded explicit reviewed label-only dispositions for the broad multi-family protein nodes.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:24:00Z",
        "curator": "claude",
        "action": "RESTORE_CANONICAL_CITATION",
        "changes": "Restored the canonical-example citation for NCBITaxon:1708 from DOI:10.1016/0378-1119(86)90196-4 back to PMID:23342046 (review issue 519). The tranche event described the change as a PMID-to-DOI upgrade, but the DOI resolves to a different paper than the PMID, so this was a replacement rather than an identifier normalisation. The pre-tranche citation is restored; a deliberate replacement can be made in a new event that says so.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T09:54:20Z",
        "curator": "codex",
        "action": "CONNECT_CAUSAL_GRAPH",
        "changes": "Connected the cellulose-cleavage, Sus-like uptake, chitin-cleavage, and lignin-oxidation branches to the umbrella biopolymer-degradation trait with five branch-qualified, source-supported contributes-to edges; gene and enzyme concepts remain supporting YAML graph fields rather than primary records (issues 426 and 183).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-22T01:35:00Z",
        "curator": "claude",
        "action": "REFRESH_UNIPROT_ENTRY_VERSION",
        "changes": "Refreshed UniProtKB entry_version against live UniProt REST on 2026-10-22: UniProtKB:P07984 (122 -> 123 on endoglucanase).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:2000003",
    "label": "builds acid from",
    "definition": "An OBJECT_PROPERTY relating an organism to a chemical substrate from which the organism produces an acidic metabolite, lowering medium pH.",
    "definition_source": "PMID:21413255",
    "trait_category": "METABOLISM",
    "term_kind": "OBJECT_PROPERTY",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:2000001"
    ],
    "domain": "https://w3id.org/metpo/1000525",
    "range_": "http://purl.obolibrary.org/obo/CHEBI_24431",
    "evidence": [
      {
        "reference": "PMID:21413255",
        "snippet": "acid production",
        "notes": "Microbial-physiology reference supports 'builds acid from' as a canonical predicate composed with a CHEBI-class chemical object at assertion time."
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.951125+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (OBJECT_PROPERTY)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic biochemical conversion or activity relation carrier; later replacement should use more specific trait records that combine the relation with the substrate, product, enzyme or activity target, assay context, growth condition, or other entity.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-16T08:50:00-07:00",
        "curator": "claude",
        "action": "UNDEPRECATED_AS_COMPOSITION_PRIMITIVE",
        "changes": "Restored from DEPRECATED to REVIEWED under the predicate+class composition pattern (intended use: <organism> + this predicate + CHEBI chemical class). Added DOI/PMID-backed definition, evidence, and explicit domain/range slots.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-17T04:09:44Z",
        "curator": "claude",
        "action": "REMOVE_REDUNDANT_SYNONYM",
        "changes": "Removed 1 synonym(s) whose text duplicated the label (seeder redundancy; no information lost).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:2000004",
    "label": "builds base from",
    "definition": "An OBJECT_PROPERTY relating an organism to a chemical substrate from which the organism produces an alkaline metabolite, raising medium pH.",
    "definition_source": "PMID:21413255",
    "trait_category": "METABOLISM",
    "term_kind": "OBJECT_PROPERTY",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:2000001"
    ],
    "domain": "https://w3id.org/metpo/1000525",
    "range_": "http://purl.obolibrary.org/obo/CHEBI_24431",
    "evidence": [
      {
        "reference": "PMID:21413255",
        "snippet": "alkaline",
        "notes": "Microbial-physiology reference supports 'builds base from' as a canonical predicate composed with a CHEBI-class chemical object at assertion time."
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.951600+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (OBJECT_PROPERTY)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic biochemical conversion or activity relation carrier; later replacement should use more specific trait records that combine the relation with the substrate, product, enzyme or activity target, assay context, growth condition, or other entity.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-16T08:50:00-07:00",
        "curator": "claude",
        "action": "UNDEPRECATED_AS_COMPOSITION_PRIMITIVE",
        "changes": "Restored from DEPRECATED to REVIEWED under the predicate+class composition pattern (intended use: <organism> + this predicate + CHEBI chemical class). Added DOI/PMID-backed definition, evidence, and explicit domain/range slots.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-17T04:09:44Z",
        "curator": "claude",
        "action": "REMOVE_REDUNDANT_SYNONYM",
        "changes": "Removed 1 synonym(s) whose text duplicated the label (seeder redundancy; no information lost).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:2000005",
    "label": "builds gas from",
    "definition": "An OBJECT_PROPERTY relating an organism to a chemical substrate from which the organism produces a gaseous metabolite (e.g. CO2, H2, N2, H2S, CH4).",
    "definition_source": "PMID:21413255",
    "trait_category": "METABOLISM",
    "term_kind": "OBJECT_PROPERTY",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:2000001"
    ],
    "domain": "https://w3id.org/metpo/1000525",
    "range_": "http://purl.obolibrary.org/obo/CHEBI_24431",
    "evidence": [
      {
        "reference": "PMID:21413255",
        "snippet": "gas production",
        "notes": "Microbial-physiology reference supports 'builds gas from' as a canonical predicate composed with a CHEBI-class chemical object at assertion time."
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.952082+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (OBJECT_PROPERTY)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic biochemical conversion or activity relation carrier; later replacement should use more specific trait records that combine the relation with the substrate, product, enzyme or activity target, assay context, growth condition, or other entity.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-16T08:50:00-07:00",
        "curator": "claude",
        "action": "UNDEPRECATED_AS_COMPOSITION_PRIMITIVE",
        "changes": "Restored from DEPRECATED to REVIEWED under the predicate+class composition pattern (intended use: <organism> + this predicate + CHEBI chemical class). Added DOI/PMID-backed definition, evidence, and explicit domain/range slots.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-17T04:09:44Z",
        "curator": "claude",
        "action": "REMOVE_REDUNDANT_SYNONYM",
        "changes": "Removed 1 synonym(s) whose text duplicated the label (seeder redundancy; no information lost).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000181",
    "label": "2,3-butanediol fermentation",
    "definition": "A fermentation in which microorganisms convert sugars to acetoin and 2,3-butanediol neutral end products through the butanediol pathway.",
    "definition_source": "DOI:10.1186/s12934-023-02163-6",
    "trait_category": "METABOLISM",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1002005"
    ],
    "synonyms": [
      {
        "synonym_text": "butanediol fermentation",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://asm.org/getmedia/40946f85-9357-4563-aa8a-994427efa825/Methyl-Red-and-Voges-Proskauer-Test-Protocols.pdf"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1186/s12934-023-02163-6",
        "snippet": "3-Hydroxybutanone (Acetoin, AC) and 2,3-butanediol (BD) are two essential four-carbon platform compounds with numerous pharmaceutical and chemical synthesis applications. AC and BD have two and three stereoisomers, respectively, while the application of the single isomer product in chemical synthesis is superior. AC and BD are glucose overflow metabolites produced by biological fermentation from a variety of microorganisms.",
        "notes": "Li et al. define acetoin and 2,3-butanediol as microbial glucose-overflow fermentation products and review the enzymology of their stereoisomer formation."
      },
      {
        "reference": "https://asm.org/getmedia/40946f85-9357-4563-aa8a-994427efa825/Methyl-Red-and-Voges-Proskauer-Test-Protocols.pdf",
        "snippet": "Bacteria fermenting sugars via the butanediol pathway produce acetoin (i.e., acetyl methyl carbinol or 3-hydroxybutanone) as an intermediate which can be further reduced to 2,3-butanediol.",
        "notes": "The ASM methyl-red/Voges-Proskauer protocol distinguishes the butanediol fermentation pathway by acetoin formation with further reduction to 2,3-butanediol."
      },
      {
        "reference": "DOI:10.1007/s00253-014-5526-9",
        "snippet": "Klebsiella pneumoniae is known to produce meso-2,3-butanediol and 2S,3S-butanediol, whereas 2R,3R-butanediol was detected in the culture broth of K. pneumoniae CGMCC 1.6366.",
        "notes": "Chen et al. directly studied 2,3-butanediol stereoisomer formation by K. pneumoniae, supporting this species as a canonical 2,3-butanediol fermenter."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:573",
        "taxon_label": "Klebsiella pneumoniae",
        "note": "K. pneumoniae CGMCC 1.6366 produced multiple 2,3-butanediol stereoisomers in culture.",
        "reference": "DOI:10.1007/s00253-014-5526-9"
      }
    ],
    "discussions": [
      {
        "discussion_id": "butanediol-fermentation-xref-gap",
        "prompt": "Resolve an exact external ontology class for 2,3-butanediol fermentation before adding a TraitRecord xref.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "No exact GO or external metabolism class was resolved for the organism-level 2,3-butanediol fermentation phenotype; Voges-Proskauer assay terms, acetoin or butanediol chemical production reactions, and individual dehydrogenase molecular functions are shifted relative to this product-specific fermentation class.",
        "posed_by": "codex",
        "posed_date": "2026-09-14"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-14T03:36:23Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted 2,3-butanediol fermentation as a DOI- and stable-URL-backed product-specific fermentation TraitRecord after a repository-wide duplicate review covering ignored and hidden files; METPO has no exact 2,3-butanediol fermentation class yet and the placeholder is reserved in proposals/metpo_traitmech_v58.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000179",
    "label": "butyric acid fermentation",
    "definition": "A fermentation in which anaerobic bacteria convert organic substrates to butyrate as a major reduced end product while conserving energy by substrate-level phosphorylation or ion-gradient generation.",
    "definition_source": "DOI:10.1111/j.1574-6968.2009.01514.x",
    "trait_category": "METABOLISM",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1002005"
    ],
    "synonyms": [
      {
        "synonym_text": "butyrate fermentation",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1111/j.1574-6968.2009.01514.x"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.3389/fmicb.2021.703525",
        "snippet": "Until about 10 years ago, anaerobes were thought to exclusively use substrate level phosphorylation (SLP), by which only part of the available energy could be conserved. Therefore, anaerobes were regarded as unproductive and inefficient energy conservers. The discovery of electrochemical Na+ gradients generated by biotin-dependent decarboxylations or by reduction of NAD+ with ferredoxin changed this view.",
        "notes": "Buckel supplies anaerobic-fermentation energy-conservation context, including substrate-level phosphorylation and ferredoxin-linked ion-gradient generation."
      },
      {
        "reference": "DOI:10.1111/j.1574-6968.2009.01514.x",
        "snippet": "Five different arrangements have been identified for the genes of the central pathway involved in butyrate synthesis, while in most cases butyryl-CoA : acetate CoA-transferase, rather than butyrate kinase, appears to perform the final step in butyrate synthesis. Mechanisms have been proposed recently in non-gut Clostridium spp. whereby butyrate synthesis can result in energy generation via both substrate-level phosphorylation and proton gradients.",
        "notes": "Louis and Flint connect butyrate synthesis to energy generation through substrate-level phosphorylation and proton gradients while reviewing the butyryl-CoA : acetate CoA-transferase terminal route."
      },
      {
        "reference": "DOI:10.1111/1751-7915.12304",
        "snippet": "the adapted C. tyrobutyricum strain was characterized by a high yield and selectivity to butyric acid",
        "notes": "Baroi et al. directly studied butyric acid fermentation from pretreated and hydrolysed wheat straw by an adapted Clostridium tyrobutyricum strain."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1519",
        "taxon_label": "Clostridium tyrobutyricum",
        "note": "Butyric-acid fermenter used by Baroi et al. for fermentative conversion of wheat-straw hydrolysate to butyric acid.",
        "reference": "DOI:10.1111/1751-7915.12304"
      }
    ],
    "discussions": [
      {
        "discussion_id": "butyric-acid-fermentation-xref-gap",
        "prompt": "Resolve an exact external ontology class for butyric acid fermentation before adding a TraitRecord xref.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "No exact GO or external metabolism class was resolved for the organism-level butyrate-producing fermentation phenotype; butyrate-synthesis enzyme molecular functions and chemical production relations are shifted relative to this product-specific fermentation class.",
        "posed_by": "codex",
        "posed_date": "2026-09-14"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-14T01:34:38Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted butyric acid fermentation as a DOI-backed product-specific fermentation TraitRecord after a repository-wide duplicate review covering ignored and hidden files; METPO has no exact butyric acid fermentation class yet and the placeholder is reserved in proposals/metpo_traitmech_v56.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1002003",
    "label": "Cable bacteria metabolism",
    "definition": "A metabolism in which electrons are transferred over centimeter-scale distances through multicellular filaments.",
    "definition_source": "DOI:10.1073/pnas.1800367115",
    "trait_category": "METABOLISM",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000060"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1073/pnas.1800367115",
        "snippet": "Long-distance electron transport in individual, living cable bacteria",
        "notes": "Study directly demonstrates long-distance electron transport in cable bacteria."
      },
      {
        "reference": "DOI:10.3389/fmars.2017.00028",
        "snippet": "oxidize sulfide in deeper sediments",
        "notes": "Study supports electrogenic sulfur oxidation with sulfide oxidation and oxygen reduction zones."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1859128",
        "taxon_label": "Candidatus Electrothrix",
        "note": "Marine cable bacteria conducting electrons over centimetre distances along filaments (long-distance electron transport).",
        "reference": "DOI:10.1016/j.syapm.2016.05.006"
      },
      {
        "taxon_id": "NCBITaxon:2005002",
        "taxon_label": "Candidatus Electronema aureum",
        "note": "Freshwater cable bacterium strain GS with a closed genome, electrogenic sulfur oxidation physiology, and expressed dissimilatory sulfur-metabolism machinery.",
        "reference": "DOI:10.1016/j.syapm.2021.126236"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "cable_bacteria_long_distance_electron_transport",
        "title": "Cable bacteria long-distance electron transport",
        "description": "DOI-backed graph linking sulfide oxidation, conductive multicellular filaments, centimeter-scale electron transport, and oxygen reduction.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "The long-distance electron-transport mechanism is experimentally established. DsrAB is included as an expressed E. aureum sulfur-metabolism complex, but its precise reaction direction and causal position in electrogenic sulfur oxidation remain genomic/transcriptomic inferences. No protein identity is assigned to the conductive fibers.",
        "nodes": [
          {
            "node_id": "cable_bacteria_trait",
            "label": "Cable bacteria metabolism",
            "node_type": "TRAIT",
            "grounding": "METPO:1002003",
            "description": "Multicellular filament metabolism involving long-distance electron transport."
          },
          {
            "node_id": "sulfidic_sediment_zone",
            "label": "sulfidic sediment zone",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Anoxic sediment layer containing sulfide."
          },
          {
            "node_id": "oxic_sediment_zone",
            "label": "oxic sediment zone",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Surface sediment layer containing oxygen."
          },
          {
            "node_id": "sulfide",
            "label": "sulfide",
            "node_type": "CHEMICAL",
            "description": "Electron donor oxidized by anodic cable bacteria cells.",
            "grounding": "CHEBI:15138"
          },
          {
            "node_id": "molecular_oxygen",
            "label": "molecular oxygen",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:15379",
            "description": "Electron acceptor reduced by cathodic cable bacteria cells."
          },
          {
            "node_id": "multicellular_filament",
            "label": "multicellular filament",
            "node_type": "CELLULAR_LOCALIZATION",
            "description": "Chain of cable bacteria cells spanning redox-separated zones."
          },
          {
            "node_id": "conductive_fiber_network",
            "label": "conductive fiber network",
            "node_type": "CELLULAR_LOCALIZATION",
            "description": "Conductive cell-envelope structure supporting long-distance electron transport."
          },
          {
            "node_id": "long_distance_electron_transport",
            "label": "long-distance electron transport",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Electron transport across millimeter-to-centimeter distances."
          },
          {
            "node_id": "electrogenic_sulfur_oxidation",
            "label": "electrogenic sulfur oxidation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Spatially separated sulfide oxidation and oxygen reduction connected by electrical current."
          },
          {
            "node_id": "sulfate",
            "label": "sulfate",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:16189",
            "description": "Oxidized sulfur product."
          },
          {
            "node_id": "cell_envelope",
            "label": "cell envelope",
            "node_type": "CELLULAR_LOCALIZATION",
            "description": "Outer cell-envelope structure in which conductive fibers are embedded.",
            "grounding": "GO:0030313"
          },
          {
            "node_id": "nickel_cofactor",
            "label": "sulfur-ligated nickel cofactor",
            "node_type": "CHEMICAL",
            "description": "Novel nickel-containing cofactor (NiBiD) associated with the conductive fibers."
          },
          {
            "node_id": "cytochrome_redox_gradient",
            "label": "cytochrome redox gradient",
            "node_type": "STATE",
            "description": "Redox state gradient of cytochromes maintained along the conductive filament."
          },
          {
            "node_id": "sulfur_oxidation_pathway",
            "label": "Dsr-Apr-Qmo-Sqr-Psr/Phs sulfur oxidation pathway",
            "node_type": "PATHWAY",
            "description": "Genomically predicted dissimilatory sulfur oxidation pathway supporting sulfide oxidation."
          },
          {
            "node_id": "dsrab_complex",
            "label": "DsrAB dissimilatory sulfite reductase complex",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Expressed alpha/beta dissimilatory sulfite-reductase complex implicated in the cable-bacterium sulfur-metabolism repertoire.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "This node denotes the DsrA-DsrB heteromeric complex and its unresolved direction in cable bacteria; no one verified family or activity term captures that complete, direction-neutral entity.",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:A0A521G5H7",
                "protein_label": "Dissimilatory sulfite reductase alpha subunit",
                "gene_symbol": "CDV28_10159",
                "taxon_id": "NCBITaxon:2005002",
                "taxon_label": "Candidatus Electronema aureum",
                "entry_status": "UNREVIEWED",
                "proteome_id": "UP000316238",
                "retrieved_on": "2026-10-22",
                "entry_version": 25,
                "sequence_version": 1,
                "role": "DsrA alpha component of the E. aureum DsrAB complex; this accession is not the complete complex and does not by itself establish pathway direction.",
                "evidence": [
                  {
                    "reference": "DOI:10.1186/s12864-026-12675-1",
                    "snippet": "They encode a complete reductive-type Dsr pathway",
                    "notes": "Comparative genomics plus transcriptomic/proteomic reanalysis supports expression of the Dsr repertoire in cable bacteria; UniProtKB maps this reference-proteome entry to the E. aureum DsrA locus."
                  }
                ]
              },
              {
                "uniprot_id": "UniProtKB:A0A521G566",
                "protein_label": "Dissimilatory sulfite reductase beta subunit",
                "gene_symbol": "CDV28_10160",
                "taxon_id": "NCBITaxon:2005002",
                "taxon_label": "Candidatus Electronema aureum",
                "entry_status": "UNREVIEWED",
                "proteome_id": "UP000316238",
                "retrieved_on": "2026-10-22",
                "entry_version": 25,
                "sequence_version": 1,
                "role": "DsrB beta component of the E. aureum DsrAB complex; this accession is not the complete complex and does not by itself establish pathway direction.",
                "evidence": [
                  {
                    "reference": "DOI:10.1186/s12864-026-12675-1",
                    "snippet": "They encode a complete reductive-type Dsr pathway",
                    "notes": "Comparative genomics plus transcriptomic/proteomic reanalysis supports expression of the Dsr repertoire in cable bacteria; UniProtKB maps this reference-proteome entry to the E. aureum DsrB locus."
                  }
                ]
              }
            ]
          }
        ],
        "edges": [
          {
            "subject": "cable_bacteria_trait",
            "predicate": "occurs in",
            "object": "multicellular_filament",
            "description": "Cable bacteria metabolism is performed by long multicellular filaments.",
            "evidence": [
              {
                "reference": "DOI:10.1073/pnas.1800367115",
                "snippet": "centimeter-long, multicellular filamentous bacteria",
                "notes": "Supports multicellular filament organization."
              }
            ],
            "predicate_id": "biolink:occurs_in"
          },
          {
            "subject": "sulfidic_sediment_zone",
            "predicate": "provides electron donor",
            "object": "sulfide",
            "description": "Deeper sulfidic sediment provides sulfide for oxidation.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmars.2017.00028",
                "snippet": "oxidize sulfide in deeper sediments",
                "notes": "Supports sulfide oxidation in deeper sediment."
              }
            ]
          },
          {
            "subject": "oxic_sediment_zone",
            "predicate": "provides electron acceptor",
            "object": "molecular_oxygen",
            "description": "The oxic sediment zone provides oxygen for electron acceptance.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmars.2017.00028",
                "snippet": "oxic zone",
                "notes": "Supports electron transfer from deeper sediments to oxic zones."
              }
            ]
          },
          {
            "subject": "conductive_fiber_network",
            "predicate": "located in",
            "object": "multicellular_filament",
            "description": "Conductive fibers run along the cable bacteria filament.",
            "evidence": [
              {
                "reference": "DOI:10.1073/pnas.1800367115",
                "snippet": "conductive fibers",
                "notes": "Supports conductive filament structures."
              }
            ],
            "predicate_id": "biolink:located_in"
          },
          {
            "subject": "sulfide",
            "predicate": "oxidized during",
            "object": "electrogenic_sulfur_oxidation",
            "description": "Sulfide oxidation supplies electrons to the cable.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmars.2017.00028",
                "snippet": "Electrogenic Sulfur Oxidation",
                "notes": "Supports sulfide oxidation as the anodic process."
              }
            ]
          },
          {
            "subject": "electrogenic_sulfur_oxidation",
            "predicate": "has output",
            "object": "sulfate",
            "description": "Sulfide oxidation can yield sulfate.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmars.2017.00028",
                "snippet": "sulfide",
                "notes": "Source supports electrogenic sulfide oxidation; sulfate is the oxidized sulfur end product in the modeled sulfur oxidation route."
              }
            ],
            "predicate_id": "RO:0002234"
          },
          {
            "subject": "conductive_fiber_network",
            "predicate": "mediates",
            "object": "long_distance_electron_transport",
            "description": "Conductive fibers mediate long-distance electron transport.",
            "evidence": [
              {
                "reference": "DOI:10.1073/pnas.1800367115",
                "snippet": "long-distance electron transport",
                "notes": "Supports electron transport over millimeter-to-centimeter distances."
              }
            ]
          },
          {
            "subject": "long_distance_electron_transport",
            "predicate": "transfers electrons to",
            "object": "molecular_oxygen",
            "description": "Long-distance electron transport connects sulfide oxidation to oxygen reduction.",
            "evidence": [
              {
                "reference": "DOI:10.1073/pnas.1800367115",
                "snippet": "sulfide as an electron source at one end and oxygen as an electron acceptor at the other",
                "notes": "Supports redox-separated sulfide-to-oxygen electron flow."
              }
            ],
            "predicate_id": "METPO:2007403"
          },
          {
            "subject": "molecular_oxygen",
            "predicate": "reduced during",
            "object": "electrogenic_sulfur_oxidation",
            "description": "Oxygen reduction is the cathodic half reaction in many cable bacteria systems.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmars.2017.00028",
                "snippet": "reduction of oxygen",
                "notes": "Supports oxygen reduction coupled to sulfide oxidation."
              }
            ]
          },
          {
            "subject": "conductive_fiber_network",
            "predicate": "part of",
            "object": "cell_envelope",
            "description": "Conductive fibers are embedded in and run along the cell envelope.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s12864-024-10594-7",
                "notes": "Fibers are \"embedded in the cell envelope\" and run along filament length."
              }
            ],
            "predicate_id": "biolink:part_of"
          },
          {
            "subject": "nickel_cofactor",
            "predicate": "component of",
            "object": "conductive_fiber_network",
            "description": "A sulfur-ligated nickel cofactor is a component of the conductive fibers.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s12864-024-10594-7",
                "notes": "Conductive fibers \"harbour a novel nickel-containing cofactor\"; Raman/extraction data show Ni-cofactor-associated modes."
              }
            ]
          },
          {
            "subject": "nickel_cofactor",
            "predicate": "mediates",
            "object": "long_distance_electron_transport",
            "description": "The nickel cofactor supports/mediates long-range electron transport.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2024.1208033",
                "notes": "Authors link a \"Ni-based, long-range electron transport pathway\" to the cofactor; orientation-dependent Raman aligns cofactor with electron path."
              }
            ]
          },
          {
            "subject": "long_distance_electron_transport",
            "predicate": "maintains",
            "object": "cytochrome_redox_gradient",
            "description": "An intact electrical connection along the filament maintains the cytochrome redox gradient.",
            "evidence": [
              {
                "reference": "DOI:10.1073/pnas.1800367115",
                "notes": "A redox gradient along filaments immediately broke down upon removal of oxygen or laser cutting, showing dependence on intact long-distance transport."
              }
            ]
          },
          {
            "subject": "dsrab_complex",
            "predicate": "part of",
            "object": "sulfur_oxidation_pathway",
            "description": "DsrAB is an expressed component of the predicted sulfur-metabolism repertoire associated with electrogenic sulfur oxidation in cable bacteria.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s12864-026-12675-1",
                "snippet": "Transcriptomic and proteomic reanalyses confirm expression of this full repertoire",
                "notes": "This edge records complex membership and expression, not a proven reaction direction; the source explicitly leaves central aspects of cable-bacterium sulfur metabolism unresolved."
              }
            ],
            "predicate_id": "biolink:part_of"
          },
          {
            "subject": "sulfur_oxidation_pathway",
            "predicate": "supports",
            "object": "electrogenic_sulfur_oxidation",
            "description": "The Dsr-Apr-Qmo-Sqr-Psr/Phs pathway supports sulfide oxidation metabolism.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s12864-024-10594-7",
                "notes": "Comparative genomics predicts sulfur oxidation through a Dsr-Apr-Qmo-Sqr-Psr/Phs pathway with DsrMKJOPG across closed genomes."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.935199+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-08T00:00:00-07:00",
        "curator": "codex",
        "action": "ADDED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed causal graph for multicellular cable filaments, conductive fibers, redox-separated sulfide oxidation and oxygen reduction, and long-distance electron transport.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:30Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T05:49:24Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:occurs_in\u00d71, biolink:located_in\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T21:30:06Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007403\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:38:00Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:15138\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 5 evidence-backed generic edges (4 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:12Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:part_of\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:32Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0030313\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates (1 to has output), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-17T02:00:00Z",
        "curator": "claude",
        "action": "NORMALISE_NODE_SENSE",
        "changes": "One node_id per SENSE (issues 356, 384): molecular_oxygen is the chemical sense here. The molecule, not the condition \u2014 the dioxygen participating in the reaction the graph describes. Normalised onto molecular_oxygen, the id 20 other chemical occurrences already use, so one id means one sense corpus-wide (issues 356, 384).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-24T10:10:00Z",
        "curator": "codex",
        "action": "CURATE_PROTEIN_TAXON_EXAMPLE",
        "changes": "Scoped the cable-bacterium mechanism, added E. aureum as a DOI-backed canonical species, and represented both DsrAB components as taxon-paired examples while preserving uncertainty about pathway direction and conductive-fiber identity.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-22T01:35:00Z",
        "curator": "claude",
        "action": "REFRESH_UNIPROT_ENTRY_VERSION",
        "changes": "Refreshed UniProtKB entry_version against live UniProt REST on 2026-10-22: UniProtKB:A0A521G566 (24 -> 25 on dsrab_complex), UniProtKB:A0A521G5H7 (24 -> 25 on dsrab_complex).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000020",
    "label": "Calvin-Benson-Bassham cycle",
    "definition": "An autotrophic carbon-fixation pathway (the reductive pentose phosphate cycle) that fixes CO2 using ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO). It is the most widespread CO2-fixation pathway, used by plants, algae, cyanobacteria, and many proteobacteria.",
    "definition_source": "DOI:10.1128/AEM.02473-10",
    "trait_category": "METABOLISM",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "traitmech:000019"
    ],
    "synonyms": [
      {
        "synonym_text": "Calvin cycle",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1128/AEM.02473-10"
      },
      {
        "synonym_text": "reductive pentose phosphate cycle",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1128/AEM.02473-10"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1128/AEM.02473-10",
        "notes": "Berg review identifies the Calvin-Benson-Bassham (reductive pentose phosphate) cycle as the reference autotrophic pathway against which the other five are distinguished."
      },
      {
        "reference": "DOI:10.1146/annurev-marine-120709-142712",
        "notes": "H\u00fcgler & Sievert support the Calvin cycle as the most common/widespread CO2-fixation pathway, including among marine cyanobacteria and proteobacteria."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:106590",
        "taxon_label": "Cupriavidus necator",
        "note": "Model chemolithoautotroph fixing CO2 via the Calvin-Benson-Bassham cycle on H2+CO2 (strain H16).",
        "reference": "DOI:10.1038/nbt1244"
      },
      {
        "taxon_id": "NCBITaxon:381666",
        "taxon_label": "Cupriavidus necator H16",
        "note": "Strain-level model whose two CBB operons are active during autotrophic carbon fixation; paired here to the reviewed plasmid cbbL2 protein example.",
        "reference": "DOI:10.1186/s12934-020-01494-y"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "cbb_rubisco_co2_fixation",
        "title": "Calvin-Benson-Bassham cycle fixes CO2 via RuBisCO",
        "description": "Evidence-backed causal sketch linking RuBisCO-catalyzed CO2 carboxylation of RuBP to the reductive pentose phosphate cycle.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "This is a composite bacterial CBB graph. The Cupriavidus example grounds the RuBisCO and cbb-regulatory branch, whereas carboxysome and carbonic-anhydrase edges describe source-backed cyanobacterial or other bacterial CO2-concentrating modules that are not asserted to occur in C. necator H16.",
        "nodes": [
          {
            "node_id": "cbb_trait",
            "label": "Calvin-Benson-Bassham cycle",
            "node_type": "TRAIT",
            "grounding": "traitmech:000020",
            "description": "Reductive pentose phosphate cycle that fixes CO2."
          },
          {
            "node_id": "cbb_pathway",
            "label": "Calvin-Benson cycle",
            "node_type": "PATHWAY",
            "grounding": "GO:0019253",
            "description": "Reductive pentose phosphate (Calvin-Benson-Bassham) cycle."
          },
          {
            "node_id": "rubisco",
            "label": "RuBisCO",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Ribulose-1,5-bisphosphate carboxylase/oxygenase.",
            "grounding": "InterPro:IPR033966",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:P42721",
                "protein_label": "Ribulose bisphosphate carboxylase large chain, plasmid",
                "gene_symbol": "cbbL2",
                "taxon_id": "NCBITaxon:381666",
                "taxon_label": "Cupriavidus necator H16",
                "entry_status": "REVIEWED",
                "retrieved_on": "2026-10-22",
                "entry_version": 154,
                "sequence_version": 3,
                "role": "Large-chain component of the plasmid-encoded RuBisCO in one of the two active CBB operons of C. necator H16.",
                "evidence": [
                  {
                    "reference": "DOI:10.1186/s12934-020-01494-y",
                    "snippet": "both CBB operons were active and contributed almost equally to the carbon fixation process",
                    "notes": "The strain-level perturbation study supports activity of both H16 CBB operons; UniProtKB P42721 identifies the reviewed plasmid cbbL2 large chain in that strain."
                  }
                ]
              }
            ]
          },
          {
            "node_id": "carbon_dioxide",
            "label": "carbon dioxide",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:16526",
            "description": "Substrate fixed by RuBisCO."
          },
          {
            "node_id": "rubp",
            "label": "ribulose-1,5-bisphosphate",
            "node_type": "CHEMICAL",
            "description": "CO2 acceptor substrate carboxylated by RuBisCO in the CBB cycle."
          },
          {
            "node_id": "three_pga",
            "label": "3-phospho-D-glycerate",
            "node_type": "CHEMICAL",
            "description": "Product of RuBisCO carboxylation of RuBP; first stable CBB intermediate.",
            "grounding": "CHEBI:17794"
          },
          {
            "node_id": "carboxysome",
            "label": "carboxysome",
            "node_type": "ORGANELLE",
            "description": "Bacterial microcompartment that encapsulates RuBisCO and carbonic anhydrase as part of the CO2-concentrating mechanism.",
            "grounding": "GO:0031470"
          },
          {
            "node_id": "bicarbonate",
            "label": "bicarbonate",
            "node_type": "CHEMICAL",
            "description": "HCO3-, inorganic carbon species converted to CO2 by carbonic anhydrase near RuBisCO.",
            "grounding": "CHEBI:17544"
          },
          {
            "node_id": "carboxysomal_ca",
            "label": "carboxysomal carbonic anhydrase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Carbonic anhydrase within the carboxysome that converts HCO3- to CO2 to supply RuBisCO.",
            "grounding": "GO:0004089"
          },
          {
            "node_id": "cbbr",
            "label": "CbbR transcriptional regulator",
            "node_type": "GENE_OR_PROTEIN",
            "description": "LysR-type master transcriptional activator of bacterial cbb CO2-fixation operons.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "CbbR is a mechanism-specific LysR regulator label; a generic LysR-family term would be broader than the protein role supported by the cited cbb-operon evidence."
          },
          {
            "node_id": "cbb_operon",
            "label": "cbb operon transcription",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Transcription of an operon encoding CBB-cycle CO2-fixation enzymes."
          },
          {
            "node_id": "cytoplasmic_ca",
            "label": "cytoplasmic carbonic anhydrase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Non-vectorial cytosolic carbonic anhydrase whose activity can dissipate the CO2-concentrating mechanism.",
            "grounding": "GO:0004089"
          },
          {
            "node_id": "co2_leakage",
            "label": "CO2 leakage",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Dissipation of concentrated CO2 from the CCM, reducing carbon-fixation efficiency."
          }
        ],
        "edges": [
          {
            "subject": "rubisco",
            "predicate": "enables",
            "object": "cbb_pathway",
            "description": "RuBisCO catalyzes the CO2-fixing carboxylation step of the cycle.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.02473-10",
                "notes": "Berg identifies the CBB cycle as the reference autotrophic pathway."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "cbb_pathway",
            "predicate": "confers",
            "object": "cbb_trait",
            "description": "The reductive pentose phosphate cycle realizes the trait.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-marine-120709-142712",
                "notes": "H\u00fcgler & Sievert support the Calvin cycle as the most widespread CO2-fixation pathway."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "carbon_dioxide",
            "predicate": "fixed by",
            "object": "cbb_trait",
            "description": "CO2 is the substrate fixed by the CBB cycle.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.02473-10",
                "notes": "Berg identifies the CBB cycle as a CO2-fixing pathway."
              }
            ],
            "predicate_id": "METPO:2007404"
          },
          {
            "subject": "rubisco",
            "predicate": "converts",
            "object": "three_pga",
            "description": "RuBisCO catalyzes the first CBB reaction, carboxylating RuBP with CO2 to yield 3-phosphoglycerate.",
            "evidence": [
              {
                "reference": "DOI:10.1111/ppl.14140",
                "notes": "Kurkela 2024: \"RubisCo... catalyses the first CBB reaction (RuBP + CO2 -> 3-PGA).\""
              }
            ]
          },
          {
            "subject": "rubp",
            "predicate": "substrate of",
            "object": "rubisco",
            "description": "RuBP is the CO2-acceptor substrate carboxylated by RuBisCO.",
            "evidence": [
              {
                "reference": "DOI:10.1111/ppl.14140",
                "notes": "Kurkela 2024: RuBP + CO2 -> 3-PGA is the first CBB reaction catalysed by RubisCo."
              }
            ]
          },
          {
            "subject": "carboxysome",
            "predicate": "contains",
            "object": "rubisco",
            "description": "Carboxysomes encapsulate RuBisCO as part of the CO2-concentrating mechanism.",
            "evidence": [
              {
                "reference": "DOI:10.1111/ppl.14140",
                "notes": "Kurkela 2024: \"carboxysomes that encapsulate RuBisCo and carbonic anhydrase.\""
              }
            ]
          },
          {
            "subject": "carboxysome",
            "predicate": "concentrates",
            "object": "carbon_dioxide",
            "description": "Carboxysomes concentrate CO2 near RuBisCO, bridging environmental DIC supply to enzymatic demand.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.01557-23",
                "notes": "Scott 2024: \"carboxysomes... concentrate CO2 near Rubisco to bridge environmental DIC supply to enzymatic demand.\""
              }
            ]
          },
          {
            "subject": "carboxysomal_ca",
            "predicate": "converts",
            "object": "carbon_dioxide",
            "description": "Carboxysomal carbonic anhydrase converts HCO3- to CO2 to elevate luminal CO2 and promote RuBisCO fixation.",
            "evidence": [
              {
                "reference": "DOI:10.1126/sciadv.adk7283",
                "notes": "Pulsford 2024: within carboxysomes, CA converts HCO3- to CO2 to elevate luminal CO2 and promote Rubisco-catalyzed CO2 fixation."
              }
            ]
          },
          {
            "subject": "bicarbonate",
            "predicate": "substrate of",
            "object": "carboxysomal_ca",
            "description": "Bicarbonate is dehydrated by carboxysomal carbonic anhydrase to supply CO2 to RuBisCO.",
            "evidence": [
              {
                "reference": "DOI:10.1126/sciadv.adk7283",
                "notes": "Pulsford 2024: carboxysomal CA converts HCO3- to CO2 to promote Rubisco-catalyzed CO2 fixation."
              }
            ]
          },
          {
            "subject": "cbbr",
            "predicate": "activates transcription of",
            "object": "cbb_operon",
            "description": "CbbR is the master transcriptional activator that elevates expression of bacterial cbb CO2-fixation operons.",
            "evidence": [
              {
                "reference": "DOI:10.1128/JB.00442-15",
                "notes": "Dangel 2015: \"CbbR, the Master Regulator for Microbial Carbon Dioxide Fixation\"; elevates expression of the cbb CO2 fixation operons. Broad evidence across bacteria."
              }
            ]
          },
          {
            "subject": "cytoplasmic_ca",
            "predicate": "can cause",
            "object": "co2_leakage",
            "description": "Cytosolic (non-vectorial) carbonic anhydrase activity can dissipate the CCM by causing CO2 leakage.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.01557-23",
                "notes": "Scott 2024: \"cytosolic (non-vectoral) CA activity can dissipate the CCM by causing CO2 leakage.\""
              }
            ]
          },
          {
            "subject": "cbb_operon",
            "predicate": "part of",
            "object": "cbb_pathway",
            "description": "The cbb operon specifies enzymes of the CBB pathway.",
            "evidence": [
              {
                "reference": "DOI:10.1128/JB.00442-15",
                "snippet": "cbb operons that specify enzymes of the Calvin-Bassham-Benson (CBB) pathway",
                "notes": "Verified against the public PMC full text."
              }
            ],
            "predicate_id": "biolink:part_of"
          },
          {
            "subject": "co2_leakage",
            "predicate": "negatively regulates",
            "object": "cbb_pathway",
            "description": "CO2 leakage opposes the carboxysome concentration mechanism that supplies Rubisco for the CBB pathway.",
            "evidence": [
              {
                "reference": "DOI:10.1371/journal.pone.0007521",
                "snippet": "the carboxysome shell constitutes a diffusional barrier for CO2, thereby preventing leakage of this Ci species out of the microcompartment",
                "notes": "Verified against the public PMC full text; the same introduction identifies Rubisco as catalyzing the first CBB-cycle step."
              }
            ],
            "predicate_id": "RO:0002212"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-30T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate METABOLISM trait (Calvin-Benson-Bassham carbon-fixation cycle); sub-variant of carbon fixation.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-10T14:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (CBB / RuBisCO CO2 fixation) with CHEBI/GO node groundings and RO/METPO predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-14T05:51:45Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A075WF79\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 8 evidence-backed generic edges (9 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:32Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 3 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:17794\u00d71, GO:0031470\u00d71, CHEBI:17544\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:21:11Z",
        "curator": "claude",
        "action": "RETRACT_DEAD_UNIPROT_GROUNDINGS",
        "changes": "Retracted 1 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:23:53Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (InterPro:IPR033966\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 1 causal edge(s) off enables/RO:0002327 with a TRAIT object (1 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-24T00:00:00Z",
        "curator": "codex",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Added a strain-matched C. necator H16 RuBisCO example, grounded both carbonic-anhydrase nodes, retyped the cbb operon carrier as transcription, retained CbbR as reviewed label-only, and documented the composite graph scope.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T09:00:00Z",
        "curator": "codex",
        "action": "CONNECT_CAUSAL_GRAPH_COMPONENTS",
        "changes": "Resolved issue #183 graph fragmentation (3 components to 1) using 2 public-source, verbatim-snippet-backed connector(s). No paid research service was called.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-22T01:35:00Z",
        "curator": "claude",
        "action": "REFRESH_UNIPROT_ENTRY_VERSION",
        "changes": "Refreshed UniProtKB entry_version against live UniProt REST on 2026-10-22: UniProtKB:P42721 (153 -> 154 on rubisco).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:2000103",
    "label": "capable of",
    "definition": "A general OBJECT_PROPERTY relating an organism to a biological process or metabolic capability the organism is capable of. Intended use is predicate + class composition at assertion time, with a METPO biological-process (or GO biological-process) class as the object.",
    "definition_source": "DOI:10.1146/annurev.micro.55.1.485",
    "trait_category": "METABOLISM",
    "term_kind": "OBJECT_PROPERTY",
    "mapping_status": "REVIEWED",
    "domain": "https://w3id.org/metpo/1000525",
    "range_": "https://w3id.org/metpo/1000630",
    "xrefs": [
      "RO:0002215"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev.micro.55.1.485",
        "snippet": "capability",
        "notes": "Microbial-physiology reference supports 'capable of' as a canonical predicate relating an organism to a biological-process class (the capability), composed at assertion time."
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.982473+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (OBJECT_PROPERTY)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic metabolism relation carrier; later replacement should use more specific trait records that combine the relation with the chemical, phenotype, quality, compartment, enzyme or activity target, growth context, measurement, or other entity.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-16T08:50:00-07:00",
        "curator": "claude",
        "action": "UNDEPRECATED_AS_COMPOSITION_PRIMITIVE",
        "changes": "Restored from DEPRECATED to REVIEWED under the predicate+class composition pattern (intended use: <organism> + this predicate + CHEBI chemical class). Added DOI/PMID-backed definition, evidence, and explicit domain/range slots.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-17T10:00:00-07:00",
        "curator": "claude",
        "action": "ADDED_EXTERNAL_PREDICATE_XREF",
        "changes": "Added xrefs ['RO:0002215'] to record an external equivalence predicate (RO:0002215 'capable of'). RO:0002215 'capable of' is the exact equivalent (organism/material capable of a biological process; matches METPO's biological-process range). Source: OLS4 property search.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000019",
    "label": "carbon fixation",
    "definition": "A metabolic process in which an organism assimilates inorganic carbon (CO2 or bicarbonate) into organic compounds (autotrophy). Six distinct natural autotrophic carbon-fixation pathways are currently recognized.",
    "definition_source": "DOI:10.1128/AEM.02473-10",
    "trait_category": "METABOLISM",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000060"
    ],
    "synonyms": [
      {
        "synonym_text": "CO2 fixation",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1128/AEM.02473-10"
      },
      {
        "synonym_text": "autotrophic carbon assimilation",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1146/annurev-marine-120709-142712"
      },
      {
        "synonym_text": "autotrophic CO2 fixation",
        "synonym_type": "EXACT_SYNONYM",
        "source": "http://purl.obolibrary.org/obo/go/releases/2026-07-26/go-basic.obo"
      },
      {
        "synonym_text": "autotrophic CO2 fixation pathway",
        "synonym_type": "EXACT_SYNONYM",
        "source": "http://purl.obolibrary.org/obo/go/releases/2026-07-26/go-basic.obo"
      },
      {
        "synonym_text": "autotrophy",
        "synonym_type": "EXACT_SYNONYM",
        "source": "http://purl.obolibrary.org/obo/go/releases/2026-07-26/go-basic.obo"
      }
    ],
    "xrefs": [
      "GO:0015977"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1128/AEM.02473-10",
        "notes": "Berg review of the distribution of autotrophic CO2-fixation pathways establishes that, besides the Calvin-Benson-Bassham cycle, five further autotrophic carbon-fixation pathways are known, parent of the six pathway sub-variants proposed here."
      },
      {
        "reference": "DOI:10.1146/annurev-marine-120709-142712",
        "notes": "H\u00fcgler & Sievert, \"Beyond the Calvin cycle\", supports multiple autotrophic carbon-fixation pathways operating among ocean microorganisms."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:106590",
        "taxon_label": "Cupriavidus necator",
        "note": "Model chemolithoautotroph fixing CO2 via the Calvin-Benson-Bassham cycle on H2+CO2 (strain H16).",
        "reference": "DOI:10.1038/nbt1244"
      },
      {
        "taxon_id": "NCBITaxon:381666",
        "taxon_label": "Cupriavidus necator H16",
        "note": "Strain-level CBB model paired to the reviewed plasmid cbbL2 RuBisCO large-chain example.",
        "reference": "DOI:10.1186/s12934-020-01494-y"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "carbon_fixation_co2_assimilation",
        "title": "Autotrophic carbon fixation assimilates CO2 into organic carbon",
        "description": "Evidence-backed causal sketch linking inorganic CO2 to organic carbon via six recognized autotrophic carbon-fixation pathways.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "This composite graph spans multiple independent carbon-fixation pathways. The C. necator H16 RuBisCO example supports the CBB branch only; the rTCA, 3HP/4HB, and Wood-Ljungdahl branches require different pathway-specific proteins.",
        "nodes": [
          {
            "node_id": "carbon_fixation_trait",
            "label": "carbon fixation",
            "node_type": "TRAIT",
            "grounding": "traitmech:000019",
            "description": "Assimilation of inorganic carbon into organic compounds (autotrophy)."
          },
          {
            "node_id": "carbon_dioxide",
            "label": "carbon dioxide",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:16526",
            "description": "Inorganic carbon substrate fixed into biomass."
          },
          {
            "node_id": "carbon_fixation_process",
            "label": "carbon fixation",
            "node_type": "BIOLOGICAL_PROCESS",
            "grounding": "GO:0015977",
            "description": "Conversion of inorganic CO2/bicarbonate into organic compounds."
          },
          {
            "node_id": "bicarbonate",
            "label": "bicarbonate",
            "node_type": "CHEMICAL",
            "description": "Dissolved inorganic carbon species; substrate/intermediate in carbon fixation.",
            "grounding": "CHEBI:17544"
          },
          {
            "node_id": "carbonic_anhydrase",
            "label": "carbonic anhydrase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Enzyme accelerating interconversion of CO2 and bicarbonate.",
            "grounding": "InterPro:IPR001765"
          },
          {
            "node_id": "rubisco",
            "label": "ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO)",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Carboxylating enzyme of the Calvin-Benson-Bassham cycle that fixes CO2.",
            "grounding": "InterPro:IPR033966",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:P42721",
                "protein_label": "Ribulose bisphosphate carboxylase large chain, plasmid",
                "gene_symbol": "cbbL2",
                "taxon_id": "NCBITaxon:381666",
                "taxon_label": "Cupriavidus necator H16",
                "entry_status": "REVIEWED",
                "retrieved_on": "2026-10-22",
                "entry_version": 154,
                "sequence_version": 3,
                "role": "Large-chain component of the plasmid-encoded RuBisCO in one of the two active CBB operons of C. necator H16.",
                "evidence": [
                  {
                    "reference": "DOI:10.1186/s12934-020-01494-y",
                    "snippet": "both CBB operons were active and contributed almost equally to the carbon fixation process",
                    "notes": "The strain-level perturbation study supports activity of both H16 CBB operons; UniProtKB P42721 identifies the reviewed plasmid cbbL2 large chain in that strain."
                  }
                ]
              }
            ]
          },
          {
            "node_id": "cbb_cycle",
            "label": "Calvin-Benson-Bassham cycle",
            "node_type": "PATHWAY",
            "description": "Canonical autotrophic carbon-fixation pathway."
          },
          {
            "node_id": "rtca_cycle",
            "label": "reverse (reductive) tricarboxylic acid cycle",
            "node_type": "PATHWAY",
            "description": "Reductive TCA autotrophic carbon-fixation pathway."
          },
          {
            "node_id": "hp_hb_cycle",
            "label": "3-hydroxypropionate/4-hydroxybutyrate cycle",
            "node_type": "PATHWAY",
            "description": "Autotrophic carbon-fixation pathway in some archaea."
          },
          {
            "node_id": "wood_ljungdahl_pathway",
            "label": "Wood-Ljungdahl pathway",
            "node_type": "PATHWAY",
            "description": "Reductive acetyl-CoA autotrophic carbon-fixation pathway.",
            "grounding": "GO:0030634",
            "related_records": [
              {
                "corpus": "PathwayMech",
                "identifier": "WikiPathways:WP5019",
                "relation": "PATHWAY_CONTEXT",
                "basis": "PathwayMech context: Acetogenesis in Acetobacterium woodii (NCBITaxon:33952). The shared reductive acetyl-CoA route combines methyl and carbonyl branches for acetogenesis; the bacterial exemplar does not establish archaeal variants. No exact equivalence or transfer of organism scope is asserted.",
                "source_version": "aa305727458c44ab05614901334540e2c87a9f3a"
              }
            ]
          },
          {
            "node_id": "acetyl_coa",
            "label": "acetyl-CoA",
            "node_type": "CHEMICAL",
            "description": "Product of CO2 fixation via the Wood-Ljungdahl pathway."
          },
          {
            "node_id": "atp",
            "label": "ATP",
            "node_type": "CHEMICAL",
            "description": "Energy cofactor consumed by carbon-fixation pathways."
          },
          {
            "node_id": "nadph",
            "label": "NADPH",
            "node_type": "CHEMICAL",
            "description": "Reducing-equivalent cofactor consumed by carbon-fixation pathways.",
            "grounding": "CHEBI:16474"
          },
          {
            "node_id": "reduced_ferredoxin",
            "label": "reduced ferredoxin",
            "node_type": "CHEMICAL",
            "description": "Low-potential electron carrier required by the reverse TCA cycle.",
            "grounding": "CHEBI:17513"
          },
          {
            "node_id": "atp_citrate_lyase",
            "label": "ATP citrate lyase (aclAB)",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Key marker enzyme enabling the reverse TCA carbon-fixation cycle.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "This node denotes the two-subunit AclAB ATP citrate lyase complex; verified family terms describe individual AclA or AclB chains rather than the complete complex represented here."
          }
        ],
        "edges": [
          {
            "subject": "carbon_dioxide",
            "predicate": "fixed by",
            "object": "carbon_fixation_trait",
            "description": "CO2 is the substrate fixed by autotrophic carbon-fixation pathways.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.02473-10",
                "notes": "Berg reviews the distribution of autotrophic CO2-fixation pathways."
              }
            ],
            "predicate_id": "METPO:2007404"
          },
          {
            "subject": "carbon_fixation_process",
            "predicate": "confers",
            "object": "carbon_fixation_trait",
            "description": "The autotrophic carbon-fixation process realizes the trait.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-marine-120709-142712",
                "notes": "H\u00fcgler & Sievert support multiple autotrophic carbon-fixation pathways operating among ocean microorganisms."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "carbonic_anhydrase",
            "predicate": "accelerates interconversion of",
            "object": "carbon_dioxide",
            "description": "Carbonic anhydrase speeds interconversion of CO2 and bicarbonate, bridging DIC supply to demand.",
            "evidence": [
              {
                "reference": "DOI:10.1128/aem.01557-23",
                "notes": "Scott 2024: CA activity speeds the interconversion of CO2 and HCO3-."
              }
            ]
          },
          {
            "subject": "rubisco",
            "predicate": "uses substrate",
            "object": "carbon_dioxide",
            "description": "RubisCO fixes CO2 as its carboxylation substrate in CBB-associated fixation.",
            "evidence": [
              {
                "reference": "DOI:10.1128/aem.01557-23",
                "notes": "Scott 2024: RubisCO substrate is CO2; applies broadly to CBB-associated fixation."
              }
            ]
          },
          {
            "subject": "cbb_cycle",
            "predicate": "consumes",
            "object": "atp",
            "description": "CBB carbon fixation consumes ATP (nine ATP per three CO2 fixed to one GAP).",
            "evidence": [
              {
                "reference": "DOI:10.1186/s40643-023-00705-9",
                "notes": "Bahrle 2023: three CO2 to one GAP at the cost of nine ATP and six NADPH."
              }
            ],
            "predicate_id": "biolink:consumes"
          },
          {
            "subject": "cbb_cycle",
            "predicate": "consumes",
            "object": "nadph",
            "description": "CBB carbon fixation consumes NADPH (six NADPH per three CO2 fixed).",
            "evidence": [
              {
                "reference": "DOI:10.1186/s40643-023-00705-9",
                "notes": "Bahrle 2023: three CO2 to one GAP at the cost of nine ATP and six NADPH."
              }
            ],
            "predicate_id": "biolink:consumes"
          },
          {
            "subject": "rtca_cycle",
            "predicate": "requires",
            "object": "reduced_ferredoxin",
            "description": "The reverse TCA carbon-fixation cycle requires reduced ferredoxin as a cofactor.",
            "evidence": [
              {
                "reference": "DOI:10.4014/jmb.2306.06005",
                "notes": "Kang 2023: rTCA cycle cofactors include NAD(P)H, ATP, Fdred, FADH."
              }
            ]
          },
          {
            "subject": "hp_hb_cycle",
            "predicate": "requires",
            "object": "nadph",
            "description": "The 3HP/4HB carbon-fixation cycle requires NADPH and ATP.",
            "evidence": [
              {
                "reference": "DOI:10.4014/jmb.2306.06005",
                "notes": "Kang 2023: 3-HP/4-HB cycle NADPH and ATP required."
              }
            ]
          },
          {
            "subject": "wood_ljungdahl_pathway",
            "predicate": "fixes CO2 to produce",
            "object": "acetyl_coa",
            "description": "The Wood-Ljungdahl pathway fixes CO2 to produce acetyl-CoA.",
            "evidence": [
              {
                "reference": "DOI:10.3390/bioengineering10121357",
                "notes": "Kurt 2023: WLP is employed for CO2 fixation and acetyl-CoA production."
              }
            ]
          },
          {
            "subject": "atp_citrate_lyase",
            "predicate": "enables",
            "object": "rtca_cycle",
            "description": "ATP citrate lyase (aclAB) is a key enzyme enabling the reverse TCA carbon-fixation cycle.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-024-01704-y",
                "notes": "Mitchell 2024: aclAB ATP citrate lyase is one of four key enzymes to run the TCA cycle in reverse."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "carbonic_anhydrase",
            "predicate": "produces",
            "object": "bicarbonate",
            "description": "Carbonic anhydrase interconverts CO2 and bicarbonate, supplying inorganic carbon to fixation.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.02473-10",
                "notes": "Connecting edge wiring the enrichment node into the graph."
              }
            ],
            "predicate_id": "METPO:2007800"
          },
          {
            "subject": "cbb_cycle",
            "predicate": "contributes to",
            "object": "carbon_fixation_process",
            "description": "The Calvin-Benson cycle is an autotrophic carbon-dioxide-fixation mechanism.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.02473-10",
                "snippet": "The reductive pentose phosphate cycle is the quantitatively most important mechanism of autotrophic CO2 fixation in nature.",
                "notes": "Verified against the free public article text."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "rtca_cycle",
            "predicate": "contributes to",
            "object": "carbon_fixation_process",
            "description": "The reductive TCA cycle is an autotrophic carbon-dioxide-fixation route.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.02473-10",
                "snippet": "the second autotrophic CO2 fixation cycle (the reductive citric acid cycle) had been discovered",
                "notes": "Verified against the free public article text."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "wood_ljungdahl_pathway",
            "predicate": "contributes to",
            "object": "carbon_fixation_process",
            "description": "The Wood-Ljungdahl pathway fixes carbon dioxide into acetyl-CoA.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.02473-10",
                "snippet": "The Wood-Ljungdahl pathway is a noncyclic pathway that results in the fixation of two CO2 molecules to form acetyl-CoA",
                "notes": "Verified against the free public article text."
              }
            ],
            "predicate_id": "RO:0002326"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-30T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate METABOLISM trait (autotrophic carbon fixation) from literature research to fill the carbon-fixation-pathway coverage gap. Parent of the six pathway-specific sub-variants.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-10T14:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (CO2 assimilation axis) with CHEBI/GO node groundings and RO/METPO predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 8 evidence-backed generic edges (12 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "FIX_ORPHAN_NODE",
        "changes": "Connected orphaned node 'bicarbonate' via carbonic_anhydrase -[produces]-> bicarbonate.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:12Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 4 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:consumes\u00d72, RO:0002327\u00d71, METPO:2000202\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:18Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0030634\u00d71, CHEBI:16474\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:32Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:17544\u00d71, CHEBI:17513\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-26T07:15:18Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A009PMS8\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:21:11Z",
        "curator": "claude",
        "action": "RETRACT_DEAD_UNIPROT_GROUNDINGS",
        "changes": "Retracted 1 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:23:53Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (InterPro:IPR001765\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 1 causal edge(s) off enables/RO:0002327 with a TRAIT object (1 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T02:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES_PART2",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates onto their causal-graph counterparts (1 to produces), issue 301 part 2. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Each replacement is a 1:1 mirror of its source predicate that changes only the domain, so the claim each edge makes is unchanged and directions are unchanged. The replacements are proposed in proposals/metpo_traitmech_v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-24T08:25:00Z",
        "curator": "codex",
        "action": "CURATE_PROTEIN_TAXON_EXAMPLE",
        "changes": "Added a DOI-backed C. necator H16 cbbL2/RuBisCO example, grounded the generic RuBisCO node to InterPro, recorded the AclAB complex as reviewed label-only, and scoped the example to the CBB branch of this multi-pathway graph.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T06:15:39Z",
        "curator": "codex",
        "action": "ADD_EXACT_ONTOLOGY_MATCH",
        "changes": "Ontology exact-match review (2026-08-25): approved exact xref(s): GO:0015977; declared exact synonym(s): 'autotrophic CO2 fixation', 'autotrophic CO2 fixation pathway', 'autotrophy'. Evidence is predicate-scoped in the versioned ontology snapshots; OAK cross-checked direct data, and OLS4 spot-checked release deltas and disputed hits.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T12:15:00Z",
        "curator": "codex",
        "action": "CONNECT_CAUSAL_GRAPH_COMPONENTS",
        "changes": "Resolved issue #183 graph fragmentation (4 components to 1) with 3 public-source connector(s). No paid research service was called.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-05T17:46:22Z",
        "curator": "codex",
        "action": "ADD_PATHWAY_CONTEXT",
        "changes": "Added pinned PathwayMech context on reviewed causal nodes with explicit route and organism limitations; retained existing groundings and exact xrefs.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-22T01:35:00Z",
        "curator": "claude",
        "action": "REFRESH_UNIPROT_ENTRY_VERSION",
        "changes": "Refreshed UniProtKB entry_version against live UniProt REST on 2026-10-22: UniProtKB:P42721 (153 -> 154 on rubisco).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000111",
    "label": "cellulolysis",
    "definition": "A biopolymer-degradation metabolism in which an organism hydrolyzes cellulose to cellodextrins and glucose using cellulase systems, sometimes organized into cellulosomes.",
    "definition_source": "DOI:10.1128/MMBR.66.3.506-577.2002",
    "trait_category": "METABOLISM",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "traitmech:000110"
    ],
    "synonyms": [
      {
        "synonym_text": "cellulolytic",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1128/MMBR.66.3.506-577.2002"
      },
      {
        "synonym_text": "cellulose degradation",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1128/MMBR.66.3.506-577.2002"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1128/MMBR.66.3.506-577.2002",
        "notes": "Lynd et al. review microbial cellulose utilization, its enzymology, and cellulosome systems."
      },
      {
        "reference": "DOI:10.1016/j.cbpa.2015.10.018",
        "notes": "Cragg et al. place cellulose deconstruction within lignocellulose degradation across diverse organisms."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1515",
        "taxon_label": "Acetivibrio thermocellus",
        "note": "Thermophilic anaerobe secreting the paradigm cellulosome (formerly Clostridium thermocellum). Ruminococcus is the mesophilic rumen model.",
        "reference": "DOI:10.1016/S0022-2836(02)00497-7"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "cellulolysis_cellulase_systems",
        "title": "Cellulolysis hydrolyzes cellulose to glucose",
        "description": "Evidence-backed causal sketch linking cellulase systems (cellulosomes / free enzymes) to cellulose hydrolysis into cellodextrins and glucose.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "The graph combines free cellulases and cellulosome organization. The A. thermocellus CelS example supports the cellobiohydrolase and cellulosome branch, not every cellulase or regulatory component in the graph.",
        "nodes": [
          {
            "node_id": "cellulolysis_trait",
            "label": "cellulolysis",
            "node_type": "TRAIT",
            "grounding": "traitmech:000111",
            "description": "Hydrolysis of cellulose to assimilable sugars."
          },
          {
            "node_id": "cellulase",
            "label": "cellulase systems",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Endoglucanases, exoglucanases, and beta-glucosidases (sometimes cellulosomal).",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "This system-level node combines multiple catalytic families and free-enzyme versus cellulosomal architectures, so no single protein-family term denotes it."
          },
          {
            "node_id": "glucose",
            "label": "glucose",
            "node_type": "CHEMICAL",
            "description": "Monomeric assimilable sugar released from cellulose.",
            "grounding": "CHEBI:17234"
          },
          {
            "node_id": "cellulose",
            "label": "cellulose",
            "node_type": "CHEMICAL",
            "description": "Beta-1,4-linked glucose polymer substrate.",
            "grounding": "CHEBI:18246"
          },
          {
            "node_id": "endoglucanase",
            "label": "endoglucanase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Cellulase that cleaves internal bonds of cellulose chains.",
            "grounding": "GO:0008810"
          },
          {
            "node_id": "cellobiohydrolase",
            "label": "cellobiohydrolase / exoglucanase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Cellulase that processively releases cellobiose from chain ends.",
            "grounding": "GO:0102252",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:P0C2S5",
                "protein_label": "Cellulose 1,4-beta-cellobiosidase (reducing end) CelS",
                "gene_symbol": "celS",
                "taxon_id": "NCBITaxon:1515",
                "taxon_label": "Acetivibrio thermocellus",
                "entry_status": "REVIEWED",
                "retrieved_on": "2026-10-22",
                "entry_version": 81,
                "sequence_version": 1,
                "role": "Catalytic CelS component of the A. thermocellus cellulosome; this accession denotes the cellobiohydrolase component, not the complete cellulosome.",
                "evidence": [
                  {
                    "reference": "DOI:10.1016/S0022-2836(02)00497-7",
                    "snippet": "Cellobiohydrolase CelS plays an important role in the cellulosome",
                    "notes": "The primary structural and catalytic study identifies CelS as the major enzymatic component of the A. thermocellus cellulosome. UniProtKB P0C2S5 is the reviewed CelS entry from that species."
                  }
                ]
              }
            ]
          },
          {
            "node_id": "beta_glucosidase",
            "label": "beta-glucosidase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Enzyme hydrolyzing cellobiose to glucose.",
            "grounding": "GO:0008422"
          },
          {
            "node_id": "cellobiose",
            "label": "cellobiose",
            "node_type": "CHEMICAL",
            "description": "Glucose disaccharide intermediate of cellulose hydrolysis.",
            "grounding": "CHEBI:17057"
          },
          {
            "node_id": "cellulosome",
            "label": "cellulosome",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Multienzyme complex built on scaffoldins for cellulose degradation.",
            "grounding": "GO:0043263"
          },
          {
            "node_id": "scaffoldin",
            "label": "scaffoldin",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Non-catalytic backbone protein of the cellulosome.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Scaffoldins are modular proteins with varying cohesin, carbohydrate-binding, dockerin, and anchoring architectures; verified terms describe their modules rather than the complete scaffoldin class."
          },
          {
            "node_id": "cohesin_domain",
            "label": "cohesin domain",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Scaffoldin module that binds dockerin domains.",
            "grounding": "InterPro:IPR002102"
          },
          {
            "node_id": "dockerin_domain",
            "label": "dockerin domain",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Enzyme-borne module that binds scaffoldin cohesin domains.",
            "grounding": "InterPro:IPR002105"
          },
          {
            "node_id": "ccr",
            "label": "carbon catabolite repression",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Glucose-signal-driven repression of catabolic gene transcription."
          }
        ],
        "edges": [
          {
            "subject": "cellulase",
            "predicate": "confers",
            "object": "cellulolysis_trait",
            "description": "Cellulase systems hydrolyze cellulose extracellularly.",
            "evidence": [
              {
                "reference": "DOI:10.1128/MMBR.66.3.506-577.2002",
                "notes": "Lynd et al. review microbial cellulose utilization and the cellulase systems involved."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "cellulolysis_trait",
            "predicate": "produces",
            "object": "glucose",
            "description": "Cellulose hydrolysis yields cellodextrins and glucose.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.cbpa.2015.10.018",
                "notes": "Cragg et al. place cellulose deconstruction within lignocellulose degradation."
              }
            ],
            "predicate_id": "METPO:2007800"
          },
          {
            "subject": "endoglucanase",
            "predicate": "degrades",
            "object": "cellulose",
            "description": "Endoglucanase participates in concerted hydrolysis of cellulose.",
            "evidence": [
              {
                "reference": "DOI:10.1093/jambio/lxac002",
                "notes": "Complete degradation of cellulose to glucose requires concerted action of cellobiohydrolases, endoglucanases and beta-glucosidases."
              }
            ],
            "predicate_id": "METPO:2007809"
          },
          {
            "subject": "cellobiohydrolase",
            "predicate": "degrades",
            "object": "cellulose",
            "description": "Cellobiohydrolase/exoglucanase participates in concerted hydrolysis of cellulose.",
            "evidence": [
              {
                "reference": "DOI:10.1093/jambio/lxac002",
                "notes": "Complete degradation of cellulose to glucose requires concerted action of cellobiohydrolases, endoglucanases and beta-glucosidases."
              }
            ],
            "predicate_id": "METPO:2007809"
          },
          {
            "subject": "beta_glucosidase",
            "predicate": "hydrolyzes",
            "object": "cellobiose",
            "description": "Beta-glucosidase hydrolyzes cellobiose in the downstream saccharification step.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s13568-023-01658-0",
                "notes": "Beta-glucosidase activity converting cellobiose into glucose."
              }
            ],
            "predicate_id": "METPO:2007808"
          },
          {
            "subject": "beta_glucosidase",
            "predicate": "produces",
            "object": "glucose",
            "description": "Beta-glucosidase releases glucose from cellobiose.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s13568-023-01658-0",
                "notes": "Beta-glucosidase activity converting cellobiose into glucose; product edge directly stated."
              }
            ],
            "predicate_id": "METPO:2007800"
          },
          {
            "subject": "cellulosome",
            "predicate": "has backbone component",
            "object": "scaffoldin",
            "description": "Cellulosomes are multienzyme complexes built on scaffoldins.",
            "evidence": [
              {
                "reference": "DOI:10.1093/jambio/lxac002",
                "notes": "They are multienzyme complexes built on scaffoldins."
              }
            ]
          },
          {
            "subject": "scaffoldin",
            "predicate": "contains",
            "object": "cohesin_domain",
            "description": "Scaffoldins bear cohesin modules.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2023.1288286",
                "notes": "Scaffoldins are the non-catalytic backbone and bear modules called cohesin."
              }
            ]
          },
          {
            "subject": "dockerin_domain",
            "predicate": "binds to",
            "object": "cohesin_domain",
            "description": "Dockerin-cohesin interaction assembles enzymes onto the scaffoldin.",
            "evidence": [
              {
                "reference": "DOI:10.1093/jambio/lxac002",
                "notes": "Dockerin modules interacting with scaffoldin cohesin modules; canonical assembly interaction."
              }
            ]
          },
          {
            "subject": "ccr",
            "predicate": "represses production of",
            "object": "cellulase",
            "description": "Carbon catabolite repression lowers production of the cellulase machinery when glucose signals are high.",
            "evidence": [
              {
                "reference": "DOI:10.1093/jambio/lxac002",
                "snippet": "transcription of lignocellulose-catabolic genes",
                "notes": "CcpA recognition of CRE sites represses transcription of the genes encoding lignocellulose-catabolic proteins; the genes are metadata rather than graph nodes."
              }
            ]
          },
          {
            "subject": "cellulose",
            "predicate": "is hydrolyzed to",
            "object": "cellobiose",
            "description": "Cellulose depolymerization yields cellobiose as the principal soluble disaccharide product, completing the substrate-to-product cascade.",
            "evidence": [
              {
                "reference": "DOI:10.1111/j.1742-4658.2010.07585.x",
                "snippet": "cleave off cellobiose",
                "notes": "Substrate-product step of the catalytic cascade; cellobiose is the dominant but not the only soluble product (cellodextrins of higher DP also occur)."
              }
            ],
            "predicate_id": "RO:0001001"
          },
          {
            "subject": "cellobiohydrolase",
            "predicate": "produces",
            "object": "cellobiose",
            "description": "Cellobiohydrolase processively releases cellobiose from cellulose chain ends.",
            "evidence": [
              {
                "reference": "DOI:10.1128/aem.01742-24",
                "snippet": "GH48, GH6 with CBM2 domains \u2026 release glucose and cellobiose from chain ends",
                "notes": "Enzyme-product edge that links the chain-end-acting cellulases to the downstream beta-glucosidase step. Exact product ratio is enzyme-dependent."
              }
            ],
            "predicate_id": "METPO:2007800"
          },
          {
            "subject": "endoglucanase",
            "predicate": "part of",
            "object": "cellulase",
            "description": "Endoglucanase is a component activity of the concerted cellulase system.",
            "evidence": [
              {
                "reference": "DOI:10.1093/jambio/lxac002",
                "snippet": "Complete degradation of cellulose to glucose requires concerted action of cellobiohydrolases, endoglucanases and beta-glucosidases.",
                "notes": "Establishes the three component activities as members of one cellulase system rather than independent actors."
              }
            ],
            "predicate_id": "biolink:part_of"
          },
          {
            "subject": "cellobiohydrolase",
            "predicate": "part of",
            "object": "cellulase",
            "description": "Cellobiohydrolase/exoglucanase is a component activity of the concerted cellulase system.",
            "evidence": [
              {
                "reference": "DOI:10.1093/jambio/lxac002",
                "snippet": "Complete degradation of cellulose to glucose requires concerted action of cellobiohydrolases, endoglucanases and beta-glucosidases.",
                "notes": "Establishes the three component activities as members of one cellulase system rather than independent actors."
              }
            ],
            "predicate_id": "biolink:part_of"
          },
          {
            "subject": "beta_glucosidase",
            "predicate": "part of",
            "object": "cellulase",
            "description": "Beta-glucosidase is a component activity of the concerted cellulase system.",
            "evidence": [
              {
                "reference": "DOI:10.1093/jambio/lxac002",
                "snippet": "Complete degradation of cellulose to glucose requires concerted action of cellobiohydrolases, endoglucanases and beta-glucosidases.",
                "notes": "Establishes the three component activities as members of one cellulase system rather than independent actors."
              }
            ],
            "predicate_id": "biolink:part_of"
          },
          {
            "subject": "cellulosome",
            "predicate": "confers",
            "object": "cellulolysis_trait",
            "description": "Cellulosomes are one of the alternative cellulase-system architectures that confer cellulolysis; they are taxonomically restricted, not universal.",
            "evidence": [
              {
                "reference": "DOI:10.1128/MMBR.66.3.506-577.2002",
                "snippet": "complexed cellulase systems",
                "notes": "Lynd et al. distinguish noncomplexed (free-enzyme) from complexed (cellulosomal) systems as alternative implementations of cellulose utilization. Cellulosomes occur only in restricted lineages; this edge must not be read as a requirement."
              }
            ],
            "predicate_id": "METPO:2007700"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-06-08T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate METABOLISM trait (cellulolysis); sub-variant of biopolymer degradation.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-10T14:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (cellulase hydrolysis of cellulose) with RO/METPO predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-14T06:55:38Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:17234\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 8 evidence-backed generic edges (11 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:12Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:32Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:18246\u00d71, GO:0043263\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:38Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000007\u00d72, METPO:2000013\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-26T07:15:18Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 3 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A060H8L4\u00d71, UniProtKB:A0A031JNC1\u00d71, UniProtKB:A0A174EJP3\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:21:11Z",
        "curator": "claude",
        "action": "RETRACT_DEAD_UNIPROT_GROUNDINGS",
        "changes": "Retracted 3 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:23:53Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0008422\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-30T00:00:00Z",
        "curator": "claude",
        "action": "CONNECT_CAUSAL_GRAPH",
        "changes": "Deep-research audit (Edison/PaperQA3 + Codex) found the graph split into 4 disconnected components with 9 of 14 nodes unreachable from the trait node. Added 7 evidence-backed edges to merge them into one connected graph: cellulose\u2192cellobiose, cellobiohydrolase\u2192cellobiose, endoglucanase/cellobiohydrolase/beta_glucosidase part_of cellulase, cellulosome\u2192enables\u2192trait, cellulolytic_genes\u2192encodes\u2192cellulase. Grounded cellobiose (CHEBI:17057). Retyped cellulosome CELLULAR_LOCALIZATION\u2192GENE_OR_PROTEIN (a complex, not a location; GO:0043263 grounding retained). Deferred to a follow-up pass: LPMO/CBM/transport/phosphorolysis branches, splitting cellobiohydrolase by chain end, and replacing the generic CCR edge with taxon-specific cip-cel evidence.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 2 causal edge(s) off enables/RO:0002327 with a TRAIT object (2 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T02:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES_PART2",
        "changes": "Re-grounded 6 causal edge(s) off microbe-domain METPO predicates onto their causal-graph counterparts (2 to degrades, 1 to hydrolyzes, 3 to produces), issue 301 part 2. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Each replacement is a 1:1 mirror of its source predicate that changes only the domain, so the claim each edge makes is unchanged and directions are unchanged. The replacements are proposed in proposals/metpo_traitmech_v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T05:00:00Z",
        "curator": "claude",
        "action": "REGROUND_CAUSAL_EDGE",
        "changes": "Re-grounded the cellulose is-hydrolyzed-to cellobiose edge from METPO:2000013 to RO:0001001 (derives into), issue 327. METPO:2000013 reads agent-to-substrate, so grounding a substrate-to-product edge to it asserted that cellulose hydrolyses cellobiose; it also inherits rdfs:domain METPO:1000525 (microbe) via METPO:2000001, which no causal node type can satisfy (issue 301). RO:0001001 holds between an old and a new material entity where the new inherits the significant portion of the old's matter, which is exactly what depolymerisation does, and it declares no domain. The label is kept because it names the mechanism, which the general relation does not. This was the last of the 366 edges in issue 301.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-07T04:00:00Z",
        "curator": "claude",
        "action": "REGROUND_CAUSAL_EDGE",
        "changes": "Re-grounded the `encodes` edge(s) from biolink:encodes to METPO:2007813, issue 342. biolink:encodes is NOT a slot in the pinned biolink 4.4.0 model, so the CURIE resolved to nothing upstream while looking like an upstream term to anyone reading this record -- the disclaimer saying otherwise lived in mappings/predicate_grounding.tsv, which is not read at the point of use. RO:0002205 (has gene product) is the nearest real term but relates a GENE to a gene product, whereas these edges relate a gene cluster or operon to a protein complex or a biosynthetic process, which its range does not admit; that mismatch is why the coinage existed. METPO:2007813 is proposed in proposals/metpo_traitmech_v9 and is a placeholder id until METPO mints it, which puts it in the same state as the rest of that cohort rather than in a category of its own.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-24T09:10:00Z",
        "curator": "codex",
        "action": "CURATE_PROTEIN_TAXON_EXAMPLE",
        "changes": "Scoped the cellulase-system graph, added a DOI-backed A. thermocellus CelS example, grounded cellulase activities and cohesin/dockerin modules, and documented the remaining system-level labels as reviewed label-only.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-22T01:35:00Z",
        "curator": "claude",
        "action": "REFRESH_UNIPROT_ENTRY_VERSION",
        "changes": "Refreshed UniProtKB entry_version against live UniProt REST on 2026-10-22: UniProtKB:P0C2S5 (80 -> 81 on cellobiohydrolase).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000112",
    "label": "chitinolysis",
    "definition": "A biopolymer-degradation metabolism in which an organism hydrolyzes chitin to N-acetylglucosamine oligomers and monomers using secreted chitinases.",
    "definition_source": "DOI:10.3389/fmicb.2013.00149",
    "trait_category": "METABOLISM",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "traitmech:000110"
    ],
    "synonyms": [
      {
        "synonym_text": "chitinolytic",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.3389/fmicb.2013.00149"
      },
      {
        "synonym_text": "chitin degradation",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.3389/fmicb.2013.00149"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.3389/fmicb.2013.00149",
        "notes": "Beier & Bertilsson review bacterial chitin degradation mechanisms and ecophysiological strategies."
      },
      {
        "reference": "DOI:10.1080/07388550601168223",
        "notes": "Bhattacharya et al. review the properties and potential of bacterial chitinases."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:615",
        "taxon_label": "Serratia marcescens",
        "note": "Textbook chitinolytic system (ChiA/ChiB/ChiC1 plus the CBP21 LPMO that founded the lytic polysaccharide monooxygenase field).",
        "reference": "PMID:23398882"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "chitinolysis_chitinase",
        "title": "Chitinolysis hydrolyzes chitin to N-acetylglucosamine",
        "description": "Evidence-backed causal sketch linking secreted chitinases to chitin hydrolysis into N-acetylglucosamine oligomers and monomers.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "The graph represents the experimentally characterized S. marcescens chitinolytic system. ChiA and CBP21 examples support complementary hydrolytic and oxidative branches, respectively.",
        "nodes": [
          {
            "node_id": "chitinolysis_trait",
            "label": "chitinolysis",
            "node_type": "TRAIT",
            "grounding": "traitmech:000112",
            "description": "Hydrolysis of chitin to assimilable sugars/oligomers."
          },
          {
            "node_id": "chitinase",
            "label": "chitinases",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Secreted bacterial chitinases acting on chitin polymer.",
            "grounding": "GO:0004568",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:P07254",
                "protein_label": "Chitinase A",
                "gene_symbol": "chiA",
                "taxon_id": "NCBITaxon:615",
                "taxon_label": "Serratia marcescens",
                "entry_status": "REVIEWED",
                "retrieved_on": "2026-10-22",
                "entry_version": 159,
                "sequence_version": 3,
                "role": "Secreted GH18 ChiA component of the S. marcescens chitinolytic system.",
                "evidence": [
                  {
                    "reference": "DOI:10.1002/j.1460-2075.1986.tb04235.x",
                    "snippet": "chiA and chiB, which encode distinct secreted forms of the enzyme chitinase",
                    "notes": "The primary cloning study identifies secreted S. marcescens ChiA and ChiB genes. UniProtKB P07254 is the reviewed ChiA entry from that species."
                  }
                ]
              }
            ]
          },
          {
            "node_id": "n_acetylglucosamine",
            "label": "N-acetylglucosamine",
            "node_type": "CHEMICAL",
            "description": "Monomer released from chitin hydrolysis."
          },
          {
            "node_id": "chitin",
            "label": "chitin",
            "node_type": "CHEMICAL",
            "description": "Insoluble beta-1,4-linked N-acetyl-D-glucosamine polymer; primary substrate.",
            "grounding": "CHEBI:17029"
          },
          {
            "node_id": "chitooligosaccharides",
            "label": "chitooligosaccharides ((GlcNAc)n)",
            "node_type": "CHEMICAL",
            "description": "Soluble oligomeric hydrolysis products of chitin."
          },
          {
            "node_id": "diacetylchitobiose",
            "label": "diacetylchitobiose ((GlcNAc)2)",
            "node_type": "CHEMICAL",
            "description": "Disaccharide released by exo-chitinases/chitobiosidases from chitin chain ends."
          },
          {
            "node_id": "exochitinase",
            "label": "exochitinase / chitobiosidase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Processive chain-end hydrolase releasing mainly (GlcNAc)2.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "The combined label conflates exo-action, processivity, and chitobiosidase product preference; available GO terms do not encode this complete mechanistic combination."
          },
          {
            "node_id": "n_acetylglucosaminidase",
            "label": "beta-N-acetylglucosaminidase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Hydrolyzes chitooligosaccharides/chitobiose to GlcNAc monomers.",
            "grounding": "GO:0016231"
          },
          {
            "node_id": "lpmo",
            "label": "lytic polysaccharide monooxygenase (LPMO; AA10)",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Oxidatively cleaves crystalline chitin, accelerating hydrolytic depolymerization.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Current InterPro matches for CBP21 describe a binding domain or a broad family containing both catalytic and non-catalytic proteins, not the exact AA10 chitin-active LPMO class asserted here.",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:P9WEM3",
                "protein_label": "AA10 family lytic polysaccharide monooxygenase CBP21",
                "gene_symbol": "CBP21",
                "taxon_id": "NCBITaxon:615",
                "taxon_label": "Serratia marcescens",
                "entry_status": "REVIEWED",
                "retrieved_on": "2026-10-22",
                "entry_version": 9,
                "sequence_version": 1,
                "role": "Chitin-active CBP21/SmLPMO10A that oxidatively opens crystalline chitin for the hydrolytic enzymes in the same S. marcescens system.",
                "evidence": [
                  {
                    "reference": "DOI:10.1126/science.1193369",
                    "snippet": "CBP21 catalyzes cleavage of glycosidic bonds in crystalline chitin",
                    "notes": "The primary biochemical study established oxidative cleavage by S. marcescens CBP21. UniProtKB P9WEM3 is the reviewed CBP21 entry from that species."
                  }
                ]
              }
            ]
          }
        ],
        "edges": [
          {
            "subject": "chitinase",
            "predicate": "confers",
            "object": "chitinolysis_trait",
            "description": "Secreted chitinases drive chitin depolymerization.",
            "evidence": [
              {
                "reference": "DOI:10.1080/07388550601168223",
                "notes": "Bhattacharya et al. review the properties and applications of bacterial chitinases."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "chitinolysis_trait",
            "predicate": "produces",
            "object": "n_acetylglucosamine",
            "description": "Chitin hydrolysis yields N-acetylglucosamine.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2013.00149",
                "notes": "Beier & Bertilsson review bacterial chitin degradation strategies."
              }
            ],
            "predicate_id": "METPO:2007800"
          },
          {
            "subject": "chitinase",
            "predicate": "hydrolyzes to",
            "object": "chitooligosaccharides",
            "description": "Chitinases cleave beta-1,4 bonds of insoluble chitin to soluble chitooligosaccharides.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2013.00149",
                "notes": "Extracellular cleavage of insoluble chitin into soluble oligomers; broad taxonomic support."
              },
              {
                "reference": "DOI:10.1007/s11356-024-33728-6",
                "notes": "Chitinases cleave the beta-1,4-glycosidic bonds of chitin to produce chitooligosaccharides."
              }
            ]
          },
          {
            "subject": "exochitinase",
            "predicate": "hydrolyzes to",
            "object": "diacetylchitobiose",
            "description": "Processive exo-chitinases/chitobiosidases release diacetylchitobiose from chitin chain ends.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2013.00149",
                "notes": "Processive exoenzymes release disaccharides from chain ends."
              },
              {
                "reference": "DOI:10.3390/toxins16010026",
                "notes": "Chitobiosidases release di-acetylchitobiose from chain ends."
              }
            ]
          },
          {
            "subject": "n_acetylglucosaminidase",
            "predicate": "hydrolyzes to",
            "object": "n_acetylglucosamine",
            "description": "beta-N-acetylglucosaminidases hydrolyze chitooligomers/chitobiose to GlcNAc monomers.",
            "evidence": [
              {
                "reference": "DOI:10.3390/toxins16010026",
                "notes": "beta-N-acetylglucosaminidases hydrolyze oligomers ((GlcNAc)2-(GlcNAc)4) to GlcNAc monomers."
              }
            ]
          },
          {
            "subject": "lpmo",
            "predicate": "oxidatively cleaves",
            "object": "chitin",
            "description": "LPMOs (AA10) oxidatively cleave the chitin polymer and accelerate hydrolytic depolymerization.",
            "evidence": [
              {
                "reference": "DOI:10.15407/microbiolj86.04.053",
                "notes": "Polysaccharide monooxygenases (LPMOs) oxidatively cleave the polymer and accelerate hydrolysis."
              }
            ]
          },
          {
            "subject": "chitinase",
            "predicate": "hydrolyzes",
            "object": "chitin",
            "description": "Chitinases hydrolyze the beta-1,4 glycosidic bonds of polymeric chitin, connecting the enzyme-driven trait to its substrate.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2013.00149",
                "snippet": "initial hydrolysis of the (1\u21924)-\u03b2-glycoside bond, as seen for chitinase-catalyzed chitin degradation",
                "notes": "The foundational bacterial chitin-degradation review defines chitinolysis by chitinase-catalyzed hydrolysis of the polymer bond."
              }
            ],
            "predicate_id": "METPO:2007808"
          },
          {
            "subject": "exochitinase",
            "predicate": "hydrolyzes",
            "object": "chitin",
            "description": "Processive exochitinases hydrolyze chitin from chain ends while releasing diacetylchitobiose.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2013.00149",
                "snippet": "ChiA and ChiB are processive enzymes cleaving off disaccharides while sliding along the chitin polymer",
                "notes": "The review directly supports the substrate, processive action, and disaccharide product represented by this branch."
              }
            ],
            "predicate_id": "METPO:2007808"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-06-08T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate METABOLISM trait (chitinolysis); sub-variant of biopolymer degradation.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-10T14:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (chitinase hydrolysis of chitin) with RO/METPO predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 4 evidence-backed generic edges (6 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:32Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:17029\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-26T07:15:18Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A086GXI9\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:21:11Z",
        "curator": "claude",
        "action": "RETRACT_DEAD_UNIPROT_GROUNDINGS",
        "changes": "Retracted 1 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:23:53Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0016231\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 1 causal edge(s) off enables/RO:0002327 with a TRAIT object (1 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T02:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES_PART2",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates onto their causal-graph counterparts (1 to produces), issue 301 part 2. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Each replacement is a 1:1 mirror of its source predicate that changes only the domain, so the claim each edge makes is unchanged and directions are unchanged. The replacements are proposed in proposals/metpo_traitmech_v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-24T09:15:00Z",
        "curator": "codex",
        "action": "CURATE_PROTEIN_TAXON_EXAMPLE",
        "changes": "Scoped the S. marcescens mechanism, added DOI-backed ChiA and CBP21 protein examples, grounded the generic chitinase activity, and documented why the combined exochitinase and AA10 labels remain reviewed label-only.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:24:00Z",
        "curator": "claude",
        "action": "RESTORE_CANONICAL_CITATION",
        "changes": "Restored the canonical-example citation for NCBITaxon:615 from DOI:10.1002/j.1460-2075.1986.tb04235.x back to PMID:23398882 (review issue 519). The tranche event described the change as a PMID-to-DOI upgrade, but the DOI resolves to a different paper than the PMID, so this was a replacement rather than an identifier normalisation. The pre-tranche citation is restored; a deliberate replacement can be made in a new event that says so.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T09:02:18Z",
        "curator": "codex",
        "action": "CONNECT_CAUSAL_GRAPH",
        "changes": "Added two directly supported chitinase-to-chitin substrate edges, connecting the generic hydrolytic core and the exochitinase branch to the LPMO/chitin branch. The graph now has one component without adding genes or operons as primary records or importing downstream utilization as proof of chitinolysis. Issues 183 and 426.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-22T01:35:00Z",
        "curator": "claude",
        "action": "REFRESH_UNIPROT_ENTRY_VERSION",
        "changes": "Refreshed UniProtKB entry_version against live UniProt REST on 2026-10-22: UniProtKB:P07254 (158 -> 159 on chitinase), UniProtKB:P9WEM3 (8 -> 9 on lpmo).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000198",
    "label": "chlorate respiration",
    "definition": "An anaerobic respiration in which an organism uses chlorate as the terminal electron acceptor and reduces it to chloride for energy conservation.",
    "definition_source": "DOI:10.1128/AEM.69.9.5585-5592.2003",
    "trait_category": "METABOLISM",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000802"
    ],
    "synonyms": [
      {
        "synonym_text": "dissimilatory chlorate reduction",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1128/AEM.07303-11"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1128/AEM.69.9.5585-5592.2003",
        "snippet": "chlorate ion as the sole electron acceptor for oxidation of organic matter in a previously unknown mode of respiration",
        "notes": "Danielsson Thorell et al. support the organism-level respiratory use of chlorate as the electron acceptor."
      },
      {
        "reference": "DOI:10.1128/AEM.69.9.5585-5592.2003",
        "snippet": "reduction of chlorate occurs in a two-step reaction: chlorate reduction followed by chlorite decomposition",
        "notes": "The Ideonella dechloratans chlorate pathway reduces chlorate and then decomposes the chlorite intermediate."
      },
      {
        "reference": "DOI:10.1128/AEM.07303-11",
        "snippet": "Perchlorate-respiring bacteria (PRB) can use both perchlorate and chlorate as terminal electron acceptors, whereas chlorate-respiring bacteria (CRB) use only chlorate",
        "notes": "Hellberg Lindqvist et al. separate chlorate-respiring bacteria from broader perchlorate reducers."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:36863",
        "taxon_label": "Ideonella dechloratans",
        "note": "Chlorate-respiring bacterium assayed anaerobically with acetate as electron donor and sodium chlorate as electron acceptor.",
        "reference": "DOI:10.1128/AEM.07303-11"
      }
    ],
    "discussions": [
      {
        "discussion_id": "chlorate-respiration-xref-gap",
        "prompt": "Resolve an exact external ontology class for organism-level chlorate respiration before adding a TraitRecord xref.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "The pinned METPO snapshot contains only the obsolete broad (Per)chlorate respiration class and no active exact organism-level chlorate respiration class. Candidate EC, Rhea, and protein-family terms for chlorate reductase or chlorite dismutase are narrower than the whole-organism anaerobic respiration phenotype.",
        "posed_by": "codex",
        "posed_date": "2026-09-15"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-15T01:28:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted chlorate respiration as a DOI-backed anaerobic respiration TraitRecord with a related synonym after a repository-wide duplicate review covering ignored and hidden files; the local METPO snapshot has only an obsolete broad (Per)chlorate respiration class and the replacement placeholder is reserved in proposals/metpo_traitmech_v75.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000182",
    "label": "citrate fermentation",
    "definition": "A fermentation in which citrate is the primary fermentable substrate.",
    "definition_source": "DOI:10.1128/JB.183.18.5248-5256.2001",
    "trait_category": "METABOLISM",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1002005"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1128/JB.183.18.5248-5256.2001",
        "snippet": "Klebsiella pneumoniae is able to grow anaerobically with citrate as a sole carbon and energy source by a fermentative pathway",
        "notes": "Meyer et al. provide direct Klebsiella pneumoniae evidence for anaerobic growth on citrate through a fermentative pathway."
      },
      {
        "reference": "DOI:10.1186/1471-2180-9-168",
        "snippet": "Not all, but nearly half of the K. pneumoniae clinical isolates carry the genes responsible for anaerobic growth on citrate.",
        "notes": "Chen et al. found citrate-growth gene clusters in clinical K. pneumoniae isolates, supporting K. pneumoniae as a canonical citrate fermenter with strain-level variation."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:573",
        "taxon_label": "Klebsiella pneumoniae",
        "note": "Chen et al. and Meyer et al. both studied anaerobic citrate fermentation in K. pneumoniae strains.",
        "reference": "DOI:10.1186/1471-2180-9-168"
      }
    ],
    "discussions": [
      {
        "discussion_id": "citrate-fermentation-xref-gap",
        "prompt": "Resolve an exact external ontology class for citrate fermentation before adding a TraitRecord xref.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "No exact GO or external metabolism class was resolved for anaerobic citrate fermentation; generic citrate metabolic process terms, citrate lyase or transporter molecular functions, and citrate-test assay terms are shifted relative to this pathway-scoped fermentation class.",
        "posed_by": "codex",
        "posed_date": "2026-09-14"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-14T04:09:24Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted citrate fermentation as a DOI-backed TraitRecord after a repository-wide duplicate review covering ignored and hidden files; METPO has no exact anaerobic citrate fermentation class yet and the placeholder is reserved in proposals/metpo_traitmech_v59.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-14T04:38:10Z",
        "curator": "codex",
        "action": "CURATION_REVIEW_REVISION",
        "changes": "Resolved PR #894 review issue #897 by narrowing the minted record from citrate utilization to pathway-scoped citrate fermentation.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:2000212",
    "label": "compartmentalizes",
    "definition": "An OBJECT_PROPERTY relating an organism to a chemical that the organism sequesters into a specific subcellular compartment or specialised organelle.",
    "definition_source": "DOI:10.1146/annurev.micro.55.1.485",
    "trait_category": "METABOLISM",
    "term_kind": "OBJECT_PROPERTY",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:2000210"
    ],
    "domain": "https://w3id.org/metpo/1000525",
    "range_": "http://purl.obolibrary.org/obo/CHEBI_24431",
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev.micro.55.1.485",
        "snippet": "compartment",
        "notes": "Microbial-physiology reference supports 'compartmentalizes' as a canonical predicate composed with a CHEBI-class chemical object at assertion time."
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.986147+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (OBJECT_PROPERTY)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic metabolism relation carrier; later replacement should use more specific trait records that combine the relation with the chemical, phenotype, quality, compartment, enzyme or activity target, growth context, measurement, or other entity.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-16T08:50:00-07:00",
        "curator": "claude",
        "action": "UNDEPRECATED_AS_COMPOSITION_PRIMITIVE",
        "changes": "Restored from DEPRECATED to REVIEWED under the predicate+class composition pattern (intended use: <organism> + this predicate + CHEBI chemical class). Added DOI/PMID-backed definition, evidence, and explicit domain/range slots.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000187",
    "label": "complete ammonia oxidation",
    "definition": "A nitrification metabolism in which a single organism oxidizes ammonia via nitrite to nitrate.",
    "definition_source": "DOI:10.1038/nature16459",
    "trait_category": "METABOLISM",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1005001"
    ],
    "synonyms": [
      {
        "synonym_text": "comammox",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1038/nature16459"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/nature16459",
        "snippet": "Complete oxidation of ammonia to nitrate in one organism (complete ammonia oxidation; comammox) is energetically feasible",
        "notes": "van Kessel et al. define complete ammonia oxidation, or comammox, as oxidation of ammonia to nitrate in a single organism."
      },
      {
        "reference": "DOI:10.1038/nature16461",
        "snippet": "Here we report on the discovery and cultivation of a completely nitrifying bacterium from the genus Nitrospira, a globally distributed group of nitrite oxidizers.",
        "notes": "Daims et al. independently demonstrated complete nitrification in a single Nitrospira organism."
      },
      {
        "reference": "DOI:10.1128/aem.01698-23",
        "snippet": "The dominance of Nitrospira sp. BO4 could be explained by the ability of comammox to generate more energy through the complete oxidation of ammonia to nitrate",
        "notes": "Ghimire-Kafle et al. support the same ammonia-to-nitrate scope in a freshwater complete-ammonia-oxidizing Nitrospira enrichment."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1715989",
        "taxon_label": "Candidatus Nitrospira inopinata",
        "note": "Daims et al. cultivated and physiologically characterized Candidatus Nitrospira inopinata as a complete nitrifier.",
        "reference": "DOI:10.1038/nature16461"
      }
    ],
    "discussions": [
      {
        "discussion_id": "complete-ammonia-oxidation-xref-gap",
        "prompt": "Resolve an exact external ontology class for one-organism complete ammonia oxidation before adding a TraitRecord xref.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "The pinned METPO snapshot contains only METPO:1000862 obsolete Complete ammonia oxidation. METPO:1005001 denotes nitrification without requiring both oxidation steps to occur in one organism, while GO:0019329 ammonia oxidation and GO:0019332 nitrite oxidation each cover only one component of the comammox phenotype.",
        "posed_by": "codex",
        "posed_date": "2026-09-14"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-14T19:03:57Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted complete ammonia oxidation as a DOI-backed nitrification TraitRecord after a repository-wide duplicate review covering ignored and hidden files; METPO has only an obsolete Complete ammonia oxidation class in the local snapshot and the replacement placeholder is reserved in proposals/metpo_traitmech_v64.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000131",
    "label": "dark hydrogen oxidation",
    "definition": "A metabolism in which an organism oxidizes molecular hydrogen as an electron donor for energy conservation independently of light.",
    "definition_source": "DOI:10.1126/science.aaf4507",
    "trait_category": "METABOLISM",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000060"
    ],
    "synonyms": [
      {
        "synonym_text": "dark_hydrogen_oxidation",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1126/science.aaf4507"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.3389/fmicb.2018.02873",
        "snippet": "hydrogen-oxidizing organisms play a key role in deep-sea hydrothermal vent ecosystems as they can be considerably involved in light-independent primary biomass production",
        "notes": "Adam and Perner review hydrogen oxidation in deep-sea hydrothermal vents as a light-independent microbial energy metabolism."
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-08T00:00:00Z",
        "curator": "codex",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed a DOI-backed FAPROTAX metabolic capability from proposals/metpo_traitmech_v11 after repository-wide duplicate review.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-21T20:01:04Z",
        "curator": "claude",
        "action": "RECORD_MECHANISM_KNOWLEDGE_GAP",
        "changes": "Recorded OPEN KNOWLEDGE_GAP discussion (dark-hydrogen-oxidation-causal-graph-source-gap) documenting the source-limited mechanism gap for causal_graphs.",
        "llm_assisted": true
      }
    ],
    "discussions": [
      {
        "discussion_id": "dark-hydrogen-oxidation-causal-graph-source-gap",
        "prompt": "Add primary literature evidence for uptake [NiFe]-hydrogenase catalysis, terminal electron-acceptor coupling, and a strain-matched canonical example before constructing causal_graphs.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "The current record carries a single ecological review snippet (DOI:10.3389/fmicb.2018.02873) describing hydrothermal-vent biomass production by hydrogen-oxidizing organisms without enzyme-level or electron-transport claims.",
        "posed_by": "claude",
        "posed_date": "2026-10-21",
        "evidence": [
          {
            "reference": "DOI:10.3389/fmicb.2018.02873",
            "supports": "PARTIAL",
            "snippet": "hydrogen-oxidizing organisms play a key role in deep-sea hydrothermal vent ecosystems as they can be considerably involved in light-independent primary biomass production",
            "explanation": "Existing record-level evidence supports the high-level metabolic trait definition but does not provide multi-step enzymatic mechanism quotes for a connected causal graph."
          }
        ]
      }
    ]
  },
  {
    "identifier": "traitmech:000132",
    "label": "dark oxidation of sulfur compounds",
    "definition": "A sulfur oxidation in which an organism oxidizes a reduced inorganic sulfur compound as an electron donor for energy conservation independently of light.",
    "definition_source": "DOI:10.1126/science.aaf4507",
    "trait_category": "METABOLISM",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000106"
    ],
    "synonyms": [
      {
        "synonym_text": "dark_oxidation_of_sulfur_compounds",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1126/science.aaf4507"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1111/1462-2920.14543",
        "snippet": "dark sulfide oxidation was coupled to high oxygen consumption rates",
        "notes": "Berg et al. experimentally couple dark aerobic sulfide oxidation to oxygen consumption in anoxygenic phototrophs."
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-08T00:00:00Z",
        "curator": "codex",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed a DOI-backed FAPROTAX metabolic capability from proposals/metpo_traitmech_v11 after repository-wide duplicate review.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-21T20:01:04Z",
        "curator": "claude",
        "action": "RECORD_MECHANISM_KNOWLEDGE_GAP",
        "changes": "Recorded OPEN KNOWLEDGE_GAP discussion (dark-oxidation-of-sulfur-compounds-causal-graph-source-gap) documenting the source-limited mechanism gap for causal_graphs.",
        "llm_assisted": true
      }
    ],
    "discussions": [
      {
        "discussion_id": "dark-oxidation-of-sulfur-compounds-causal-graph-source-gap",
        "prompt": "Add primary literature evidence for sulfur-oxidizing enzyme complexes (e.g. Sox, Sqr, or Dsr pathways) and a strain-matched canonical example before constructing causal_graphs.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "The current record carries a single physiological rate snippet (DOI:10.1111/1462-2920.14543) coupling dark sulfide oxidation to oxygen consumption without enzyme or intermediate assertions.",
        "posed_by": "claude",
        "posed_date": "2026-10-21",
        "evidence": [
          {
            "reference": "DOI:10.1111/1462-2920.14543",
            "supports": "PARTIAL",
            "snippet": "dark sulfide oxidation was coupled to high oxygen consumption rates",
            "explanation": "Existing record-level evidence supports the high-level metabolic trait definition but does not provide multi-step enzymatic mechanism quotes for a connected causal graph."
          }
        ]
      }
    ]
  },
  {
    "identifier": "METPO:2000007",
    "label": "degrades",
    "definition": "An OBJECT_PROPERTY relating an organism to a chemical substrate that the organism enzymatically breaks down.",
    "definition_source": "DOI:10.1146/annurev.micro.55.1.485",
    "trait_category": "METABOLISM",
    "term_kind": "OBJECT_PROPERTY",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:2000001"
    ],
    "synonyms": [
      {
        "synonym_text": "degradation",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "domain": "https://w3id.org/metpo/1000525",
    "range_": "http://purl.obolibrary.org/obo/CHEBI_24431",
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev.micro.55.1.485",
        "snippet": "degradation",
        "notes": "Microbial-physiology reference supports 'degrades' as a canonical predicate composed with a CHEBI-class chemical object at assertion time."
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.953008+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (OBJECT_PROPERTY)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic biochemical conversion or activity relation carrier; later replacement should use more specific trait records that combine the relation with the substrate, product, enzyme or activity target, assay context, growth condition, or other entity.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-16T08:50:00-07:00",
        "curator": "claude",
        "action": "UNDEPRECATED_AS_COMPOSITION_PRIMITIVE",
        "changes": "Restored from DEPRECATED to REVIEWED under the predicate+class composition pattern (intended use: <organism> + this predicate + CHEBI chemical class). Added DOI/PMID-backed definition, evidence, and explicit domain/range slots.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000104",
    "label": "denitrification",
    "definition": "An anaerobic respiratory metabolism in which nitrate is reduced stepwise to gaseous dinitrogen via nitrite, nitric oxide, and nitrous oxide, removing fixed nitrogen from the system as gas.",
    "definition_source": "DOI:10.1128/mmbr.61.4.533-616.1997",
    "trait_category": "METABOLISM",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "traitmech:000122"
    ],
    "synonyms": [
      {
        "synonym_text": "denitrifying",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1128/mmbr.61.4.533-616.1997"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1128/mmbr.61.4.533-616.1997",
        "notes": "Zumft reviews the cell biology and molecular basis of denitrification, the stepwise respiratory reduction of nitrate to dinitrogen."
      },
      {
        "reference": "DOI:10.1038/nrmicro.2018.9",
        "notes": "Kuypers et al. place denitrification as a nitrogen-loss branch of the microbial nitrogen-cycling network."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:266",
        "taxon_label": "Paracoccus denitrificans",
        "note": "Classic complete denitrifier (NO3->NO2->NO->N2O->N2 via nar/nir/nor/nos); free-living model of the respiratory chain.",
        "reference": "DOI:10.1128/mmbr.61.4.533-616.1997"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "denitrification_stepwise_nitrate_to_n2",
        "title": "Denitrification reduces nitrate stepwise to N2",
        "description": "Evidence-backed causal sketch linking nitrate reduction via nitrite, NO, and N2O to gaseous N2 in anaerobic respiration.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "Represents complete canonical denitrification and uses Paracoccus denitrificans NosZ as the taxon-paired protein example. Individual denitrifiers may lack one or more modules, as captured by the graph's modularity branch.",
        "nodes": [
          {
            "node_id": "denitrification_trait",
            "label": "denitrification",
            "node_type": "TRAIT",
            "grounding": "traitmech:000104",
            "description": "Anaerobic respiratory reduction of nitrate to N2."
          },
          {
            "node_id": "nitrate",
            "label": "nitrate",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:17632",
            "description": "Terminal electron acceptor reduced in denitrification."
          },
          {
            "node_id": "dinitrogen",
            "label": "dinitrogen",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:17997",
            "description": "Final gaseous product released to the atmosphere."
          },
          {
            "node_id": "anaerobic_respiration",
            "label": "anaerobic respiration",
            "node_type": "BIOLOGICAL_PROCESS",
            "grounding": "GO:0009061",
            "description": "Energy-conserving respiration with a non-O2 terminal acceptor."
          },
          {
            "node_id": "narghi",
            "label": "respiratory nitrate reductase NarGHI",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Membrane-bound respiratory nitrate reductase catalyzing NO3- to NO2-.",
            "grounding": "GO:0009325"
          },
          {
            "node_id": "nitrate_reduction_to_nitrite",
            "label": "nitrate reduction to nitrite",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "First step of denitrification: reduction of nitrate to nitrite."
          },
          {
            "node_id": "nirs",
            "label": "cytochrome cd1 nitrite reductase NirS",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Cytochrome cd1 nitrite reductase reducing nitrite to nitric oxide.",
            "grounding": "GO:0050421"
          },
          {
            "node_id": "nitrite_reduction_to_no",
            "label": "nitrite reduction to nitric oxide",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduction of nitrite to nitric oxide, the committed denitrification step."
          },
          {
            "node_id": "nor",
            "label": "nitric oxide reductase Nor",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Nitric oxide reductase (norB) reducing NO to N2O.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "The cited graph evidence supports a NorB-containing nitric-oxide reductase but does not distinguish cNor, qNor, or another exact complex family."
          },
          {
            "node_id": "no_reduction_to_n2o",
            "label": "nitric oxide reduction to nitrous oxide",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduction of nitric oxide to nitrous oxide."
          },
          {
            "node_id": "nosz",
            "label": "nitrous oxide reductase NosZ",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Nitrous oxide reductase (nosZ) reducing N2O to N2, terminal step.",
            "grounding": "GO:0050304",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:Q51705",
                "protein_label": "Nitrous-oxide reductase",
                "gene_symbol": "nosZ",
                "taxon_id": "NCBITaxon:266",
                "taxon_label": "Paracoccus denitrificans",
                "entry_status": "REVIEWED",
                "retrieved_on": "2026-08-24",
                "entry_version": 135,
                "sequence_version": 1,
                "role": "NosZ enzyme catalyzing the terminal N2O-to-dinitrogen step in P. denitrificans.",
                "evidence": [
                  {
                    "reference": "DOI:10.1042/BJ20020782",
                    "snippet": "N2OR is a multicopper protein which converts N2O into dinitrogen and water.",
                    "notes": "The primary structural study purified and characterized N2O reductase from P. denitrificans; UniProtKB Q51705 verifies the reviewed NosZ protein and matching taxon."
                  }
                ]
              }
            ]
          },
          {
            "node_id": "n2o_reduction_to_n2",
            "label": "nitrous oxide reduction to dinitrogen",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Terminal step: reduction of N2O to N2."
          },
          {
            "node_id": "molecular_oxygen",
            "label": "oxygen (O2)",
            "node_type": "CHEMICAL",
            "description": "Molecular oxygen, superordinate repressor of denitrification."
          },
          {
            "node_id": "denitrification_modularity",
            "label": "denitrification pathway modularity",
            "node_type": "QUALITY",
            "description": "Modular organization of denitrification enzyme steps across organisms."
          },
          {
            "node_id": "transient_intermediate_accumulation",
            "label": "transient accumulation of intermediates",
            "node_type": "STATE",
            "description": "Transient build-up of denitrification intermediates (NO2-, NO, N2O)."
          }
        ],
        "edges": [
          {
            "subject": "nitrate",
            "predicate": "oxidized to",
            "object": "dinitrogen",
            "description": "Nitrate is reduced stepwise via NO2-, NO, N2O to N2.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mmbr.61.4.533-616.1997",
                "notes": "Zumft reviews the stepwise respiratory reduction of nitrate to N2."
              }
            ],
            "predicate_id": "METPO:2007405"
          },
          {
            "subject": "denitrification_trait",
            "predicate": "participates in",
            "object": "anaerobic_respiration",
            "description": "Denitrification is a nitrate-respiring form of anaerobic respiration.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro.2018.9",
                "notes": "Kuypers et al. place denitrification within the microbial nitrogen-cycling network."
              }
            ],
            "predicate_id": "biolink:participates_in"
          },
          {
            "subject": "narghi",
            "predicate": "enables",
            "object": "nitrate_reduction_to_nitrite",
            "description": "Respiratory nitrate reductase NarGHI catalyzes the first denitrification step.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s40793-024-00643-9",
                "notes": "narG (NO3- reductase) supports the canonical first step of denitrification."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "nirs",
            "predicate": "enables",
            "object": "nitrite_reduction_to_no",
            "description": "Cytochrome cd1 nitrite reductase NirS reduces nitrite to nitric oxide.",
            "evidence": [
              {
                "reference": "DOI:10.1093/ismeco/ycae020",
                "notes": "Nitrite is reduced to gaseous NO by nitrite reductases including cytochrome cd1 NirS; strong general mechanistic support."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "nor",
            "predicate": "enables",
            "object": "no_reduction_to_n2o",
            "description": "Nitric oxide reductase Nor reduces NO to N2O.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2023.1218207",
                "notes": "NO reductase (NOR), encoded by norB, reduces NO to N2O; canonical N2O-producing step."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "nosz",
            "predicate": "enables",
            "object": "n2o_reduction_to_n2",
            "description": "Nitrous oxide reductase NosZ reduces N2O to N2, the terminal step.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2023.1218207",
                "notes": "N2O reductase (NOS) catalyzes reduction of N2O to N2; canonical terminal step."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "nosz",
            "predicate": "part_of",
            "object": "denitrification_trait",
            "description": "NosZ is the final-step component of complete denitrification.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2024.1407573",
                "notes": "Reduction of N2O to N2 requires nitrous oxide reductase encoded by nosZ."
              }
            ]
          },
          {
            "subject": "molecular_oxygen",
            "predicate": "negatively regulates",
            "object": "denitrification_trait",
            "description": "Oxygen acts as a superordinate repressor of denitrification.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-024-51688-w",
                "notes": "O2 acts as a superordinate repressor of denitrification."
              }
            ],
            "predicate_id": "RO:0002212"
          },
          {
            "subject": "denitrification_modularity",
            "predicate": "causes",
            "object": "transient_intermediate_accumulation",
            "description": "Modularity of the denitrification pathway drives transient accumulation of intermediates.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-024-51688-w",
                "notes": "The modular nature of the denitrification pathway affects phenotypes and transient accumulation of intermediates."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "nitrate_reduction_to_nitrite",
            "predicate": "has input",
            "object": "nitrate",
            "description": "The first canonical denitrification step takes nitrate as its substrate.",
            "evidence": [
              {
                "reference": "DOI:10.1128/msystems.00742-23",
                "snippet": "nitrate reductase which reduces nitrate to nitrite",
                "notes": "Supports nitrate as the input to the Nar-catalyzed first step of the canonical pathway."
              }
            ],
            "predicate_id": "RO:0002233"
          },
          {
            "subject": "nitrate_reduction_to_nitrite",
            "predicate": "causally upstream of",
            "object": "nitrite_reduction_to_no",
            "description": "Formation of nitrite precedes its reduction to nitric oxide in the canonical pathway.",
            "evidence": [
              {
                "reference": "DOI:10.1128/msystems.00742-23",
                "snippet": "the nitrite is further reduced to nitric oxide",
                "notes": "Supports the order of the nitrate-to-nitrite and nitrite-to-NO process modules."
              }
            ],
            "predicate_id": "RO:0002411"
          },
          {
            "subject": "nitrite_reduction_to_no",
            "predicate": "causally upstream of",
            "object": "no_reduction_to_n2o",
            "description": "Formation of nitric oxide precedes its reduction to nitrous oxide in the canonical pathway.",
            "evidence": [
              {
                "reference": "DOI:10.1128/msystems.00742-23",
                "snippet": "nitric oxide to nitrous oxide",
                "notes": "Supports the order of the nitrite-to-NO and NO-to-N2O process modules."
              }
            ],
            "predicate_id": "RO:0002411"
          },
          {
            "subject": "no_reduction_to_n2o",
            "predicate": "causally upstream of",
            "object": "n2o_reduction_to_n2",
            "description": "Formation of nitrous oxide precedes its terminal reduction to dinitrogen in complete denitrification.",
            "evidence": [
              {
                "reference": "DOI:10.1128/msystems.00742-23",
                "snippet": "nitrous oxide to N2",
                "notes": "Supports the order of the NO-to-N2O and N2O-to-N2 process modules."
              }
            ],
            "predicate_id": "RO:0002411"
          },
          {
            "subject": "n2o_reduction_to_n2",
            "predicate": "has output",
            "object": "dinitrogen",
            "description": "The terminal canonical denitrification step produces dinitrogen.",
            "evidence": [
              {
                "reference": "DOI:10.1042/BJ20020782",
                "snippet": "N2OR is a multicopper protein which converts N2O into dinitrogen and water.",
                "notes": "Supports dinitrogen as the output of the NosZ-catalyzed terminal step."
              }
            ],
            "predicate_id": "RO:0002234"
          },
          {
            "subject": "denitrification_modularity",
            "predicate": "associated with",
            "object": "denitrification_trait",
            "description": "Complete and partial denitrification phenotypes reflect the pathway's modular distribution across organisms.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41396-021-01045-2",
                "snippet": "The denitrification pathway is modular",
                "notes": "Uses the weakest grounded association predicate to connect this documented pathway quality without implying that modularity defines complete denitrification."
              }
            ],
            "predicate_id": "biolink:associated_with"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-06-08T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate METABOLISM trait (denitrification); round 2, parented to anaerobic respiration (METPO:1000802). Complements round-1 DNRA.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-10T14:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (nitrate \u2192 N2 denitrification) with CHEBI/GO node groundings and METPO/biolink predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 7 evidence-backed generic edges (11 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:12Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 5 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d74, biolink:causes\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-26T07:15:18Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:I0HLW6\u00d71, UniProtKB:Q30PN7\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-04T03:08:14Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002212\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-17T02:00:00Z",
        "curator": "claude",
        "action": "NORMALISE_NODE_SENSE",
        "changes": "One node_id per SENSE (issues 356, 384): molecular_oxygen is the chemical sense here. The molecule, not the condition \u2014 the dioxygen participating in the reaction the graph describes. Normalised onto molecular_oxygen, the id 20 other chemical occurrences already use, so one id means one sense corpus-wide (issues 356, 384).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-22T04:26:15Z",
        "curator": "codex",
        "action": "REVIEW_UNIPROT_INSTANCE_GROUNDINGS",
        "changes": "Reviewed 2 organism-specific UniProtKB grounding(s): replaced 2 with taxon-agnostic GO/InterPro terms and retracted 0 to label-only where no exact semantic term was supported (docs/GROUNDING_POLICY.md).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-24T00:00:00Z",
        "curator": "codex",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Added a DOI-backed P. denitrificans NosZ example, grounded the NarGHI complex, retained unresolved Nor family specificity as reviewed label-only, and documented complete-pathway scope and modularity.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T10:19:19Z",
        "curator": "codex",
        "action": "CONNECT_CAUSAL_GRAPH",
        "changes": "Connected the four existing reductase-process modules from nitrate input through dinitrogen output and associated the documented modularity branch with the trait, joining all six graph components. Genes and protein complexes remain supporting YAML graph fields rather than primary TraitRecord entries. Addresses issues 426 and 183.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-08T00:00:00Z",
        "curator": "codex",
        "action": "REFINE_PARENT_TRAIT",
        "changes": "Narrowed parent from anaerobic respiration to nitrate respiration.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000025",
    "label": "dicarboxylate/4-hydroxybutyrate cycle",
    "definition": "An autotrophic carbon-fixation pathway that fixes one molecule of CO2 and one of bicarbonate per turn via a dicarboxylate stage and a 4-hydroxybutyrate stage. It operates in anaerobic and microaerophilic Crenarchaeota such as Ignicoccus and Thermoproteales.",
    "definition_source": "DOI:10.1126/science.1149976",
    "trait_category": "METABOLISM",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "traitmech:000019"
    ],
    "synonyms": [
      {
        "synonym_text": "DC/4HB cycle",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1128/AEM.02473-10"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1128/AEM.02473-10",
        "notes": "Berg review describes the dicarboxylate/4-hydroxybutyrate cycle as the anaerobic archaeal counterpart of the 3HP/4HB cycle."
      },
      {
        "reference": "DOI:10.1126/science.1149976",
        "notes": "Berg et al.'s archaeal carbon-fixation work establishes the 4-hydroxybutyrate chemistry shared by this cycle in Crenarchaeota."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:160233",
        "taxon_label": "Ignicoccus hospitalis",
        "note": "Hyperthermophilic crenarchaeon in which the dicarboxylate/4-hydroxybutyrate autotrophic CO2-fixation cycle was discovered.",
        "reference": "DOI:10.1073/pnas.0801043105"
      },
      {
        "taxon_id": "NCBITaxon:453591",
        "taxon_label": "Ignicoccus hospitalis KIN4/I",
        "note": "Strain-level DC/4HB model paired to the Igni_0341 PEP-carboxylase example.",
        "reference": "DOI:10.1073/pnas.2022114118"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "dc_four_hb_anaerobic_archaeal_co2_fixation",
        "title": "DC/4HB cycle fixes CO2 in anaerobic Crenarchaeota",
        "description": "Evidence-backed causal sketch linking dicarboxylate and 4-hydroxybutyrate intermediates to CO2 fixation in anaerobic / microaerophilic Crenarchaeota.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "The graph represents the experimentally reconstructed I. hospitalis DC/4HB cycle. The Igni_0341 PEP-carboxylase example supports one of its two carbon-fixing reactions; its recombinant protein was insoluble, so the source treats gene identity as unambiguous but does not report purified-enzyme activity for that locus.",
        "nodes": [
          {
            "node_id": "dc_four_hb_trait",
            "label": "dicarboxylate/4-hydroxybutyrate cycle",
            "node_type": "TRAIT",
            "grounding": "traitmech:000025",
            "description": "Anaerobic archaeal autotrophic carbon-fixation cycle."
          },
          {
            "node_id": "carbon_dioxide",
            "label": "carbon dioxide",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:16526",
            "description": "One CO2 and one bicarbonate fixed per cycle turn."
          },
          {
            "node_id": "carbon_fixation_process",
            "label": "carbon fixation",
            "node_type": "BIOLOGICAL_PROCESS",
            "grounding": "GO:0015977",
            "description": "Conversion of inorganic carbon into organic compounds."
          },
          {
            "node_id": "molecular_oxygen",
            "label": "molecular oxygen",
            "node_type": "CHEMICAL",
            "description": "O2; inactivates O2-sensitive enzymes and electron carriers of the cycle.",
            "grounding": "CHEBI:15379"
          },
          {
            "node_id": "bicarbonate",
            "label": "bicarbonate",
            "node_type": "CHEMICAL",
            "description": "HCO3-; inorganic carbon species used as a carboxylation cosubstrate.",
            "grounding": "CHEBI:17544"
          },
          {
            "node_id": "pyruvate_synthase",
            "label": "pyruvate synthase (pyruvate:ferredoxin oxidoreductase)",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Reductively carboxylates acetyl-CoA to pyruvate using CO2.",
            "grounding": "GO:0019164"
          },
          {
            "node_id": "pep_carboxylase",
            "label": "phosphoenolpyruvate carboxylase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Carboxylates PEP to oxaloacetate using bicarbonate.",
            "grounding": "GO:0008964",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:A8A9C2",
                "protein_label": "Phosphoenolpyruvate carboxylase",
                "taxon_id": "NCBITaxon:453591",
                "taxon_label": "Ignicoccus hospitalis KIN4/I",
                "entry_status": "UNREVIEWED",
                "proteome_id": "UP000000262",
                "retrieved_on": "2026-10-22",
                "entry_version": 71,
                "sequence_version": 1,
                "role": "Igni_0341 PEP carboxylase assigned to the bicarbonate-fixing reaction of the I. hospitalis DC/4HB cycle.",
                "evidence": [
                  {
                    "reference": "DOI:10.1073/pnas.2022114118",
                    "snippet": "the identity of the PEP carboxylase gene was unambiguous",
                    "notes": "The primary localization study explicitly maps PEP carboxylase to Igni_0341 while disclosing failed recovery of active recombinant protein. UniProtKB A8A9C2 is the exact unreviewed Igni_0341 entry in reference proteome UP000000262."
                  }
                ]
              }
            ]
          },
          {
            "node_id": "acetyl_coa",
            "label": "acetyl-CoA",
            "node_type": "CHEMICAL",
            "description": "Starting and regenerated C2 acceptor of the cycle."
          },
          {
            "node_id": "pyruvate",
            "label": "pyruvate",
            "node_type": "CHEMICAL",
            "description": "Product of reductive carboxylation of acetyl-CoA.",
            "grounding": "CHEBI:15361"
          },
          {
            "node_id": "phosphoenolpyruvate",
            "label": "phosphoenolpyruvate",
            "node_type": "CHEMICAL",
            "description": "Substrate for carboxylation to oxaloacetate."
          },
          {
            "node_id": "oxaloacetate",
            "label": "oxaloacetate",
            "node_type": "CHEMICAL",
            "description": "C4 product of PEP carboxylation in the dicarboxylate stage.",
            "grounding": "CHEBI:16452"
          },
          {
            "node_id": "four_hydroxybutyryl_coa",
            "label": "4-hydroxybutyryl-CoA",
            "node_type": "CHEMICAL",
            "description": "Substrate of the hallmark radical dehydratase in the 4HB branch.",
            "grounding": "CHEBI:28522"
          },
          {
            "node_id": "four_hydroxybutyryl_coa_dehydratase",
            "label": "4-hydroxybutyryl-CoA dehydratase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Hallmark radical enzyme dehydrating 4-hydroxybutyryl-CoA to crotonyl-CoA.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Available family signatures cover domains shared with related HpaB/PvcC/vinylacetyl-CoA isomerase proteins rather than an exact reviewed whole-protein family for the historical 4-hydroxybutyryl-CoA dehydratase label."
          },
          {
            "node_id": "crotonyl_coa",
            "label": "crotonyl-CoA",
            "node_type": "CHEMICAL",
            "description": "Product of the radical dehydratase; cleaved via beta-oxidation to two acetyl-CoA."
          }
        ],
        "edges": [
          {
            "subject": "carbon_dioxide",
            "predicate": "fixed by",
            "object": "dc_four_hb_trait",
            "description": "CO2 is fixed by the anaerobic archaeal DC/4HB cycle.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.02473-10",
                "notes": "Berg describes the DC/4HB cycle as the anaerobic counterpart of the 3HP/4HB cycle."
              }
            ],
            "predicate_id": "METPO:2007404"
          },
          {
            "subject": "dc_four_hb_trait",
            "predicate": "contributes to",
            "object": "carbon_fixation_process",
            "description": "The DC/4HB cycle is one of the recognized autotrophic CO2 pathways.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.1149976",
                "notes": "Berg et al. establish 4-hydroxybutyrate chemistry shared by the cycle in Crenarchaeota."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "molecular_oxygen",
            "predicate": "negatively regulates",
            "object": "dc_four_hb_trait",
            "description": "O2 constrains the cycle because key enzymes and electron carriers are oxygen-sensitive, restricting it to anoxic conditions.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.02473-10",
                "notes": "Restricted to organisms growing under anoxic conditions due to oxygen sensitivity of key enzymes and electron carriers."
              }
            ],
            "predicate_id": "RO:0002212"
          },
          {
            "subject": "carbon_dioxide",
            "predicate": "is cosubstrate for",
            "object": "pyruvate_synthase",
            "description": "CO2 serves as the carboxylation cosubstrate for pyruvate synthase in the cycle.",
            "evidence": [
              {
                "reference": "DOI:10.1002/9783527629916",
                "notes": "CO2 as cosubstrate for pyruvate synthase."
              }
            ]
          },
          {
            "subject": "bicarbonate",
            "predicate": "is cosubstrate for",
            "object": "pep_carboxylase",
            "description": "Bicarbonate is the inorganic carbon cosubstrate for PEP carboxylase, supporting mixed CO2/HCO3- usage.",
            "evidence": [
              {
                "reference": "DOI:10.1002/9783527629916",
                "notes": "Bicarbonate as cosubstrate for PEP carboxylase."
              }
            ]
          },
          {
            "subject": "pyruvate_synthase",
            "predicate": "catalyzes conversion of",
            "object": "acetyl_coa",
            "description": "Pyruvate synthase reductively carboxylates acetyl-CoA to pyruvate, the first fixation step.",
            "evidence": [
              {
                "reference": "DOI:10.1002/9783527629916",
                "notes": "Starts from acetyl-CoA, which is reductively carboxylated to pyruvate."
              }
            ]
          },
          {
            "subject": "pyruvate_synthase",
            "predicate": "produces",
            "object": "pyruvate",
            "description": "Reductive carboxylation of acetyl-CoA by pyruvate synthase yields pyruvate.",
            "evidence": [
              {
                "reference": "DOI:10.1002/9783527629916",
                "notes": "Acetyl-CoA is reductively carboxylated to pyruvate."
              }
            ],
            "predicate_id": "METPO:2007800"
          },
          {
            "subject": "pep_carboxylase",
            "predicate": "catalyzes conversion of",
            "object": "phosphoenolpyruvate",
            "description": "PEP carboxylase carboxylates phosphoenolpyruvate to oxaloacetate in the dicarboxylate stage.",
            "evidence": [
              {
                "reference": "DOI:10.1002/9783527629916",
                "notes": "Pyruvate is converted to PEP and then carboxylated to oxaloacetate."
              }
            ]
          },
          {
            "subject": "pep_carboxylase",
            "predicate": "produces",
            "object": "oxaloacetate",
            "description": "Carboxylation of PEP by PEP carboxylase yields oxaloacetate.",
            "evidence": [
              {
                "reference": "DOI:10.1002/9783527629916",
                "notes": "PEP is carboxylated to oxaloacetate."
              }
            ],
            "predicate_id": "METPO:2007800"
          },
          {
            "subject": "four_hydroxybutyryl_coa_dehydratase",
            "predicate": "catalyzes conversion of",
            "object": "four_hydroxybutyryl_coa",
            "description": "Hallmark radical 4-hydroxybutyryl-CoA dehydratase dehydrates 4-hydroxybutyryl-CoA to crotonyl-CoA.",
            "evidence": [
              {
                "reference": "DOI:10.1073/pnas.0801043105",
                "notes": "Dehydrated by a radical 4-hydroxybutyryl-CoA dehydratase to crotonyl-CoA; core hallmark enzyme of the 4HB branch."
              }
            ]
          },
          {
            "subject": "four_hydroxybutyryl_coa_dehydratase",
            "predicate": "produces",
            "object": "crotonyl_coa",
            "description": "The radical dehydratase yields crotonyl-CoA in the 4-hydroxybutyrate branch.",
            "evidence": [
              {
                "reference": "DOI:10.1073/pnas.0801043105",
                "notes": "Dehydrated to crotonyl-CoA."
              }
            ],
            "predicate_id": "METPO:2007800"
          },
          {
            "subject": "crotonyl_coa",
            "predicate": "is converted via beta-oxidation to",
            "object": "acetyl_coa",
            "description": "Crotonyl-CoA is cleaved via beta-oxidation to regenerate two acetyl-CoA, closing the cycle.",
            "evidence": [
              {
                "reference": "DOI:10.1073/pnas.0801043105",
                "notes": "Via beta-oxidation yields two acetyl-CoA."
              }
            ]
          },
          {
            "subject": "pep_carboxylase",
            "predicate": "contributes to",
            "object": "dc_four_hb_trait",
            "description": "PEP carboxylase performs one of the two carboxylating reactions that constitute the DC/4HB carbon-fixation cycle.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.02473-10",
                "snippet": "In the DC/HB cycle, pyruvate synthase and PEP carboxylase are the two carboxylating enzymes",
                "notes": "Verified against the public PMC full text; contributes-to does not claim that PEP carboxylase alone is sufficient for the cycle."
              }
            ],
            "predicate_id": "RO:0002326"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-30T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate METABOLISM trait (dicarboxylate/4-hydroxybutyrate cycle); archaeal sub-variant of carbon fixation.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-10T14:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (DC/4HB anaerobic archaeal CO2 fixation) with CHEBI/GO node groundings and RO/METPO predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 10 evidence-backed generic edges (11 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:12Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d73).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:18Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:15379\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:32Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 4 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:17544\u00d71, CHEBI:15361\u00d71, CHEBI:16452\u00d71, CHEBI:28522\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-26T07:15:18Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A031JWX5\u00d71, UniProtKB:A0A017H5F8\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:21:11Z",
        "curator": "claude",
        "action": "RETRACT_DEAD_UNIPROT_GROUNDINGS",
        "changes": "Retracted 2 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:23:53Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0019164\u00d71, GO:0008964\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-04T03:08:14Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002212\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T02:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES_PART2",
        "changes": "Re-grounded 3 causal edge(s) off microbe-domain METPO predicates onto their causal-graph counterparts (3 to produces), issue 301 part 2. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Each replacement is a 1:1 mirror of its source predicate that changes only the domain, so the claim each edge makes is unchanged and directions are unchanged. The replacements are proposed in proposals/metpo_traitmech_v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-24T09:35:00Z",
        "curator": "codex",
        "action": "CURATE_PROTEIN_TAXON_EXAMPLE",
        "changes": "Scoped the I. hospitalis DC/4HB mechanism, added a DOI-backed strain-level Igni_0341 PEP-carboxylase example with its experimental limitation, and recorded the historical 4-hydroxybutyryl-CoA-dehydratase node as reviewed label-only.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T08:20:00Z",
        "curator": "codex",
        "action": "CONNECT_CAUSAL_GRAPH_COMPONENTS",
        "changes": "Resolved issue #183 graph fragmentation (2 components to 1) using 1 public-source, verbatim-snippet-backed connector(s). No paid research service was called.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-22T01:35:00Z",
        "curator": "claude",
        "action": "REFRESH_UNIPROT_ENTRY_VERSION",
        "changes": "Refreshed UniProtKB entry_version against live UniProt REST on 2026-10-22: UniProtKB:A8A9C2 (70 -> 71 on pep_carboxylase).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000201",
    "label": "dimethyl sulfoxide respiration",
    "definition": "An anaerobic respiration in which an organism uses dimethyl sulfoxide as the terminal electron acceptor for energy conservation.",
    "definition_source": "DOI:10.1073/pnas.0505959103",
    "trait_category": "METABOLISM",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000802"
    ],
    "synonyms": [
      {
        "synonym_text": "DMSO respiration",
        "synonym_type": "EXACT_SYNONYM"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1073/pnas.0505959103",
        "snippet": "one (SO1427-SO1432) is required for anaerobic respiration of DMSO",
        "notes": "Gralnick et al. identify the SO1427-SO1432 gene cluster required for Shewanella oneidensis MR-1 anaerobic respiration of dimethyl sulfoxide."
      },
      {
        "reference": "DOI:10.1073/pnas.0505959103",
        "snippet": "DMSO respiration is an extracellular respiratory process",
        "notes": "Gralnick et al. support DMSO respiration as a bona fide respiratory process rather than an isolated reductase assay."
      },
      {
        "reference": "DOI:10.1111/1462-2920.15971",
        "snippet": "M. thermoacetica can also use dimethyl sulfoxide as terminal electron acceptor",
        "notes": "Rosenbaum et al. support organism-level use of dimethyl sulfoxide as an anaerobic terminal electron acceptor."
      },
      {
        "reference": "DOI:10.1111/1462-2920.15971",
        "snippet": "Membranes showed a DMSO reductase activity",
        "notes": "Rosenbaum et al. biochemically support an induced DMSO reductase activity in Moorella thermoacetica membranes."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:211586",
        "taxon_label": "Shewanella oneidensis MR-1",
        "note": "Gralnick et al. showed that the SO1427-SO1432 gene cluster is required for anaerobic DMSO respiration in Shewanella oneidensis MR-1.",
        "reference": "DOI:10.1073/pnas.0505959103"
      }
    ],
    "discussions": [
      {
        "discussion_id": "dimethyl-sulfoxide-respiration-xref-gap",
        "prompt": "Resolve an exact external ontology class for organism-level dimethyl sulfoxide respiration before adding a TraitRecord xref.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "The pinned METPO snapshot has only an obsolete dimethyl sulfoxide respiration class. Candidate EC, Rhea, KEGG, and protein-family terms for DMSO reductase or DmsABC are narrower than the whole-organism anaerobic respiration phenotype.",
        "posed_by": "codex",
        "posed_date": "2026-09-15"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-15T02:53:12Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted dimethyl sulfoxide respiration as a DOI-backed anaerobic respiration TraitRecord after a repository-wide duplicate review covering ignored and hidden files; the local METPO snapshot has only obsolete sulfoxide respiration classes and the replacement placeholder is reserved in proposals/metpo_traitmech_v78.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:2000200",
    "label": "disproportionates",
    "definition": "An OBJECT_PROPERTY relating an organism to a chemical substrate that the organism simultaneously oxidises and reduces (disproportionation), yielding both higher- and lower-oxidation-state products.",
    "definition_source": "DOI:10.1146/annurev.micro.55.1.485",
    "trait_category": "METABOLISM",
    "term_kind": "OBJECT_PROPERTY",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:2000001"
    ],
    "synonyms": [
      {
        "synonym_text": "dismutates",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "domain": "https://w3id.org/metpo/1000525",
    "range_": "http://purl.obolibrary.org/obo/CHEBI_24431",
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev.micro.55.1.485",
        "snippet": "disproportionation",
        "notes": "Microbial-physiology reference supports 'disproportionates' as a canonical predicate composed with a CHEBI-class chemical object at assertion time."
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.982903+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (OBJECT_PROPERTY)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic biochemical conversion or activity relation carrier; later replacement should use more specific trait records that combine the relation with the substrate, product, enzyme or activity target, assay context, growth condition, or other entity.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-16T08:50:00-07:00",
        "curator": "claude",
        "action": "UNDEPRECATED_AS_COMPOSITION_PRIMITIVE",
        "changes": "Restored from DEPRECATED to REVIEWED under the predicate+class composition pattern (intended use: <organism> + this predicate + CHEBI chemical class). Added DOI/PMID-backed definition, evidence, and explicit domain/range slots.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000806",
    "label": "Disproportionation",
    "definition": "A metabolism in which a single substrate simultaneously undergoes both oxidation and reduction reactions, with part of the substrate serving as the electron donor and another part serving as the electron acceptor.",
    "definition_source": "DOI:10.1080/17415990802105770",
    "trait_category": "METABOLISM",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000060"
    ],
    "created_by": "Jed Dongjin Kim-Ozaeta",
    "evidence": [
      {
        "reference": "DOI:10.1080/17415990802105770",
        "snippet": "serve as both electron donor and acceptor",
        "notes": "Review supports inorganic sulfur disproportionation as one substrate serving both donor and acceptor roles."
      },
      {
        "reference": "DOI:10.1016/j.gca.2013.03.013",
        "snippet": "elemental sulfur disproportionation",
        "notes": "Study supports elemental sulfur disproportionation in acidophilic microbial metabolism."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:65555",
        "taxon_label": "Desulfocapsa sulfexigens",
        "note": "Model for inorganic-sulfur disproportionation (S0/thiosulfate/sulfite to sulfate + sulfide as sole energy source).",
        "reference": "DOI:10.4056/sigs.3777412"
      },
      {
        "taxon_id": "NCBITaxon:2283",
        "taxon_label": "Acidianus ambivalens",
        "note": "Thermoacidophilic archaeon whose purified SOR catalyzes oxygen-dependent elemental-sulfur disproportionation; this is distinct from the canonical anaerobic growth mechanism of D. sulfexigens.",
        "reference": "DOI:10.1126/science.1120306"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "sulfur_disproportionation_redox_split",
        "title": "Sulfur disproportionation redox split",
        "description": "DOI-backed graph linking a single sulfur intermediate to simultaneous oxidation and reduction products under anoxic conditions.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "This cross-taxon graph combines the canonical anaerobic phenotype with chemically explicit TsdA/TetH and oxygen-dependent SOR branches. SOR supports an enzymatic sulfur-disproportionation reaction but is not asserted as the mechanism of anaerobic D. sulfexigens growth; TsdA and TetH occurrence alone is not diagnostic.",
        "nodes": [
          {
            "node_id": "disproportionation_trait",
            "label": "Disproportionation",
            "node_type": "TRAIT",
            "grounding": "METPO:1000806",
            "description": "Metabolism in which one substrate is both oxidized and reduced."
          },
          {
            "node_id": "anoxic_condition",
            "label": "anoxic condition",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Oxygen-free condition for many microbial sulfur disproportionation processes.",
            "grounding": "PATO:0001456"
          },
          {
            "node_id": "inorganic_sulfur_intermediate",
            "label": "inorganic sulfur intermediate",
            "node_type": "CHEMICAL",
            "description": "Sulfur compound that can act as both electron donor and acceptor."
          },
          {
            "node_id": "elemental_sulfur",
            "label": "elemental sulfur",
            "node_type": "CHEMICAL",
            "description": "Representative sulfur disproportionation substrate.",
            "grounding": "CHEBI:26833"
          },
          {
            "node_id": "thiosulfate",
            "label": "thiosulfate",
            "node_type": "CHEMICAL",
            "description": "Representative sulfur disproportionation substrate.",
            "grounding": "CHEBI:16094"
          },
          {
            "node_id": "sulfide",
            "label": "sulfide",
            "node_type": "CHEMICAL",
            "description": "Reduced sulfur product.",
            "grounding": "CHEBI:15138"
          },
          {
            "node_id": "sulfate",
            "label": "sulfate",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:16189",
            "description": "Oxidized sulfur product."
          },
          {
            "node_id": "reverse_sulfate_reduction_pathway",
            "label": "reverse sulfate reduction pathway",
            "node_type": "PATHWAY",
            "description": "Enzymatic route proposed for some sulfur disproportionators."
          },
          {
            "node_id": "tetrathionate",
            "label": "tetrathionate",
            "node_type": "CHEMICAL",
            "description": "S4-intermediate (S4O6 2-) produced from thiosulfate oxidation in the S4I pathway."
          },
          {
            "node_id": "sulfite",
            "label": "sulfite",
            "node_type": "CHEMICAL",
            "description": "Sulfur oxyanion product of elemental sulfur disproportionation by SOR."
          },
          {
            "node_id": "tsda_thiosulfate_dehydrogenase",
            "label": "TsdA thiosulfate dehydrogenase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Enzyme oxidizing thiosulfate to tetrathionate, entry step of the S4 intermediate pathway.",
            "grounding": "GO:0050338"
          },
          {
            "node_id": "teth_tetrathionate_hydrolase",
            "label": "TetH tetrathionate hydrolase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Enzyme that hydrolyzes/disproportionates tetrathionate to elemental sulfur, thiosulfate, and sulfate.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "TetH proteins are taxon- and acidophile-specific members of broader hydrolase families; no exact verified GO or InterPro term was assigned to this generic pathway label."
          },
          {
            "node_id": "sor_sulfur_oxygenase_reductase",
            "label": "SOR sulfur oxygenase reductase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Enzyme catalyzing O2-dependent disproportionation of elemental sulfur into sulfite and sulfide.",
            "grounding": "GO:0033755",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:P29082",
                "protein_label": "Sulfur oxygenase/reductase",
                "gene_symbol": "sor",
                "taxon_id": "NCBITaxon:2283",
                "taxon_label": "Acidianus ambivalens",
                "entry_status": "REVIEWED",
                "retrieved_on": "2026-10-22",
                "entry_version": 102,
                "sequence_version": 3,
                "role": "Catalytic subunit forming the homo-24-mer SOR that performs oxygen-dependent elemental-sulfur disproportionation in A. ambivalens.",
                "evidence": [
                  {
                    "reference": "DOI:10.1126/science.1120306",
                    "snippet": "catalyzes an oxygen-dependent disproportionation of elemental sulfur",
                    "notes": "The primary structural and biochemical study establishes the reaction and self-compartmentalized SOR assembly; UniProtKB P29082 is the reviewed A. ambivalens sor product."
                  }
                ]
              }
            ]
          },
          {
            "node_id": "iron_sulfide_mineral",
            "label": "iron-sulfide mineral formation",
            "node_type": "CHEMICAL",
            "description": "Fe-sulfide mineral (e.g., FeSx) formed when produced sulfide is scavenged, removing inhibitory sulfide."
          }
        ],
        "edges": [
          {
            "subject": "disproportionation_trait",
            "predicate": "occurs in",
            "object": "anoxic_condition",
            "description": "Sulfur disproportionation is commonly observed as anaerobic microbial metabolism.",
            "evidence": [
              {
                "reference": "DOI:10.1080/17415990802105770",
                "snippet": "microbiologically catalyzed chemolithotrophic process",
                "notes": "Supports microbial sulfur disproportionation under non-oxygenated sulfur cycling contexts."
              }
            ],
            "predicate_id": "biolink:occurs_in"
          },
          {
            "subject": "inorganic_sulfur_intermediate",
            "predicate": "serves as electron donor and acceptor",
            "object": "disproportionation_trait",
            "description": "A single sulfur intermediate provides both donor and acceptor halves.",
            "evidence": [
              {
                "reference": "DOI:10.1080/17415990802105770",
                "snippet": "serve as both electron donor and acceptor",
                "notes": "Directly supports the defining redox split."
              }
            ],
            "predicate_id": "METPO:2007603"
          },
          {
            "subject": "elemental_sulfur",
            "predicate": "example of",
            "object": "inorganic_sulfur_intermediate",
            "description": "Elemental sulfur is a disproportionation substrate.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.gca.2013.03.013",
                "snippet": "elemental sulfur disproportionation",
                "notes": "Supports elemental sulfur as a substrate."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "thiosulfate",
            "predicate": "example of",
            "object": "inorganic_sulfur_intermediate",
            "description": "Thiosulfate is a disproportionation substrate.",
            "evidence": [
              {
                "reference": "DOI:10.1080/17415990802105770",
                "snippet": "elemental sulfur, thiosulfate, and sulfite",
                "notes": "Supports thiosulfate among disproportionated sulfur intermediates."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "inorganic_sulfur_intermediate",
            "predicate": "reduced to",
            "object": "sulfide",
            "description": "One fraction of the substrate is reduced to sulfide.",
            "evidence": [
              {
                "reference": "DOI:10.1080/17415990802105770",
                "snippet": "generate hydrogen sulfide and sulfate",
                "notes": "Supports sulfide as reduced product."
              }
            ]
          },
          {
            "subject": "inorganic_sulfur_intermediate",
            "predicate": "oxidized to",
            "object": "sulfate",
            "description": "One fraction of the substrate is oxidized to sulfate.",
            "evidence": [
              {
                "reference": "DOI:10.1080/17415990802105770",
                "snippet": "generate hydrogen sulfide and sulfate",
                "notes": "Supports sulfate as oxidized product."
              }
            ],
            "predicate_id": "METPO:2007405"
          },
          {
            "subject": "reverse_sulfate_reduction_pathway",
            "predicate": "participates in",
            "object": "disproportionation_trait",
            "description": "Some disproportionating microbes use reversed sulfate-reduction enzymes.",
            "evidence": [
              {
                "reference": "DOI:10.1080/17415990802105770",
                "snippet": "reverse the sulfate reduction pathway",
                "notes": "Supports the proposed pathway mechanism for some isolates."
              }
            ],
            "predicate_id": "biolink:participates_in"
          },
          {
            "subject": "thiosulfate",
            "predicate": "derives into",
            "object": "sulfate",
            "description": "Thiosulfate disproportionation yields sulfate as the oxidized product.",
            "evidence": [
              {
                "reference": "DOI:10.1128/msystems.00954-22",
                "notes": "Thiosulfate disproportionation follows the stoichiometry S2O3(2-) + H2O -> SO4(2-) + HS- + H+."
              }
            ],
            "predicate_id": "RO:0001001"
          },
          {
            "subject": "thiosulfate",
            "predicate": "derives into",
            "object": "sulfide",
            "description": "Thiosulfate disproportionation yields sulfide as the reduced product.",
            "evidence": [
              {
                "reference": "DOI:10.1128/msystems.00954-22",
                "notes": "Thiosulfate disproportionation follows the stoichiometry S2O3(2-) + H2O -> SO4(2-) + HS- + H+."
              }
            ],
            "predicate_id": "RO:0001001"
          },
          {
            "subject": "tsda_thiosulfate_dehydrogenase",
            "predicate": "catalyzes oxidation of",
            "object": "thiosulfate",
            "description": "TsdA oxidizes thiosulfate to tetrathionate, the entry step of the S4 intermediate pathway.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2024.1426584",
                "notes": "tsdA (and doxDA) catalyze conversion of thiosulfate (S2O3 2-) to tetrathionate (S4O6 2-)."
              }
            ]
          },
          {
            "subject": "tsda_thiosulfate_dehydrogenase",
            "predicate": "produces",
            "object": "tetrathionate",
            "description": "Product of TsdA-catalyzed thiosulfate oxidation is tetrathionate.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2024.1426584",
                "notes": "tsdA catalyzes conversion of thiosulfate to tetrathionate (S4O6 2-)."
              }
            ],
            "predicate_id": "METPO:2007800"
          },
          {
            "subject": "teth_tetrathionate_hydrolase",
            "predicate": "disproportionates",
            "object": "tetrathionate",
            "description": "TetH hydrolyzes/disproportionates tetrathionate into elemental sulfur, thiosulfate, and sulfate.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2024.1426584",
                "notes": "Tetrathionate can be subsequently disproportionated via tetH to form S0, S2O3 2-, and SO4 2-."
              }
            ],
            "predicate_id": "METPO:2007811"
          },
          {
            "subject": "sor_sulfur_oxygenase_reductase",
            "predicate": "disproportionates",
            "object": "elemental_sulfur",
            "description": "SOR catalyzes disproportionation of elemental sulfur, releasing sulfite and sulfide.",
            "evidence": [
              {
                "reference": "DOI:10.1007/978-3-031-54306-7_15",
                "notes": "The SOR catalyzes an O2-dependent S0 disproportionation releasing SO3 2- and HS-."
              }
            ],
            "predicate_id": "METPO:2007811"
          },
          {
            "subject": "sor_sulfur_oxygenase_reductase",
            "predicate": "produces",
            "object": "sulfite",
            "description": "Sulfite is the oxidized product of SOR-catalyzed elemental sulfur disproportionation.",
            "evidence": [
              {
                "reference": "DOI:10.1007/978-3-031-54306-7_15",
                "notes": "SOR catalyzes an O2-dependent S0 disproportionation releasing SO3 2- and HS-."
              }
            ],
            "predicate_id": "METPO:2007800"
          },
          {
            "subject": "iron_sulfide_mineral",
            "predicate": "scavenges",
            "object": "sulfide",
            "description": "Formation of Fe-sulfide minerals scavenges produced sulfide, relieving product inhibition of sulfur disproportionation.",
            "evidence": [
              {
                "reference": "DOI:10.1128/msystems.00954-22",
                "notes": "Ferrihydrite scavenges produced sulfide as Fe-sulfide."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.914112+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-08T00:00:00-07:00",
        "curator": "codex",
        "action": "ADDED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed causal graph for sulfur disproportionation substrates, donor/acceptor redox split, sulfide and sulfate products, and reverse sulfate-reduction pathway involvement.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T05:49:24Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:participates_in\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T08:21:49Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (rdfs:subClassOf\u00d72).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T21:30:06Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007405\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:38:00Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (ENVO:01001057\u00d71, CHEBI:15138\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T08:14:32Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:33542\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-26T05:00:47Z",
        "curator": "claude",
        "action": "RENAME_PREDICATE_LABELS",
        "changes": "Renamed 1 causal-edge predicate label(s) to align with existing groundings: occurs under \u2192 occurs in \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-26T05:00:50Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:occurs_in\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-14T05:51:46Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:26833\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-14T07:26:19Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007603\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-15T07:19:08Z",
        "curator": "claude",
        "action": "FIX_NODE_GROUNDING_CURIE",
        "changes": "Overwrote 2 causal-node grounding(s) to corrected CURIEs (phase-2 id-label fix; verified vs OAK).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 8 evidence-backed generic edges (6 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:12Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 4 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d74).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:38Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000200\u00d72).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T02:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES_PART2",
        "changes": "Re-grounded 6 causal edge(s) off microbe-domain METPO predicates onto their causal-graph counterparts (2 to disproportionates, 4 to produces), issue 301 part 2. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Each replacement is a 1:1 mirror of its source predicate that changes only the domain, so the claim each edge makes is unchanged and directions are unchanged. The replacements are proposed in proposals/metpo_traitmech_v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T05:00:00Z",
        "curator": "claude",
        "action": "REGROUND_CAUSAL_EDGE",
        "changes": "Relabelled the two thiosulfate edges from produces to derives into and re-grounded them from METPO:2007800 to RO:0001001, issue 327. Both have a CHEMICAL subject, and a chemical does not bring another chemical into existence the way an agent does; RO:0001001 is the substrate-to-product relation and fits disproportionation directly. METPO:2007405 (oxidized to, proposals v2) was considered for the sulfate half and rejected because it fits only the oxidised half, which would split a matched pair from one reaction, and because it is an unminted placeholder where RO:0001001 is real.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-24T10:15:00Z",
        "curator": "codex",
        "action": "CURATE_PROTEIN_TAXON_EXAMPLE",
        "changes": "Scoped the cross-taxon disproportionation graph, grounded TsdA and SOR, added a DOI-backed reviewed A. ambivalens SOR example, and documented TetH plus the distinction between aerobic SOR chemistry and anaerobic disproportionating growth.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-22T01:35:00Z",
        "curator": "claude",
        "action": "REFRESH_UNIPROT_ENTRY_VERSION",
        "changes": "Refreshed UniProtKB entry_version against live UniProt REST on 2026-10-22: UniProtKB:P29082 (101 -> 102 on sor_sulfur_oxygenase_reductase).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000031",
    "label": "dissimilatory iron reduction",
    "definition": "An anaerobic respiratory metabolism in which an organism conserves energy for growth by coupling the oxidation of organic matter or hydrogen to the reduction of Fe(III) as a terminal electron acceptor. Characteristic of Geobacter and Shewanella, often via extracellular electron transfer.",
    "definition_source": "DOI:10.1128/mr.55.2.259-287.1991",
    "trait_category": "METABOLISM",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "traitmech:000039"
    ],
    "synonyms": [
      {
        "synonym_text": "ferric iron respiration",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1128/mr.55.2.259-287.1991"
      },
      {
        "synonym_text": "dissimilatory Fe(III) reduction",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1128/mr.55.2.259-287.1991"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1128/mr.55.2.259-287.1991",
        "snippet": "The oxidation of organic matter coupled to the reduction of Fe(III) or Mn(IV) is one of the most important biogeochemical reactions in aquatic sediments, soils, and groundwater",
        "notes": "Lovley review establishes dissimilatory Fe(III)/Mn(IV) reduction as energy-conserving anaerobic respiration coupling organic-matter oxidation to metal reduction."
      },
      {
        "reference": "PMID:7826009",
        "notes": "Nealson & Saffarini, \"Iron and manganese in anaerobic respiration\", supports Fe(III) and Mn(IV) as terminal electron acceptors competitive with nitrate."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:35554",
        "taxon_label": "Geobacter sulfurreducens",
        "note": "Textbook Fe(III)-reducer; oxidizes acetate coupled to metal reduction (type strain PCA).",
        "reference": "https://pmc.ncbi.nlm.nih.gov/articles/PMC201883/"
      },
      {
        "taxon_id": "NCBITaxon:211586",
        "taxon_label": "Shewanella oneidensis MR-1",
        "note": "Strain-level dissimilatory metal reducer paired to the MtrC surface decaheme cytochrome example supporting the Fe(III)-reduction branch.",
        "reference": "DOI:10.1073/pnas.0604517103"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "dir_ferric_iron_respiration",
        "title": "Dissimilatory iron reduction respires Fe(III) to Fe(II)",
        "description": "Evidence-backed causal sketch linking ferric iron as terminal electron acceptor to anaerobic respiration in Geobacter and Shewanella.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "The graph combines Geobacter and Shewanella routes. The taxon-paired MtrC example supports the extracellular Fe(III)-reduction branch in S. oneidensis MR-1 and is not asserted as a universal component of all iron reducers.",
        "nodes": [
          {
            "node_id": "dir_trait",
            "label": "dissimilatory iron reduction",
            "node_type": "TRAIT",
            "grounding": "traitmech:000031",
            "description": "Anaerobic respiration on Fe(III) as terminal electron acceptor."
          },
          {
            "node_id": "ferric_iron",
            "label": "iron(3+)",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:29034",
            "description": "Terminal electron acceptor reduced in DIR."
          },
          {
            "node_id": "ferrous_iron",
            "label": "iron(2+)",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:29033",
            "description": "Soluble product released after Fe(III) reduction."
          },
          {
            "node_id": "anaerobic_respiration",
            "label": "energy-conserving anaerobic respiration",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Anaerobic respiratory metabolism conserving energy via a terminal electron acceptor."
          },
          {
            "node_id": "organic_matter_oxidation",
            "label": "oxidation of organic matter",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Oxidation of organic carbon serving as the electron donor in DIR."
          },
          {
            "node_id": "hydrogen_oxidation",
            "label": "H2 oxidation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Oxidation of molecular hydrogen as an electron donor coupled to Fe(III) reduction."
          },
          {
            "node_id": "dissolved_fe3_om_complex",
            "label": "dissolved Fe(III)-organic-matter complex",
            "node_type": "CHEMICAL",
            "description": "Soluble Fe(III) bound to organic matter; reduced faster than solid Fe(III) minerals."
          },
          {
            "node_id": "solid_fe3_mineral",
            "label": "solid Fe(III) mineral",
            "node_type": "CHEMICAL",
            "description": "Insoluble Fe(III) oxide mineral phase serving as terminal electron acceptor."
          },
          {
            "node_id": "mtrc",
            "label": "MtrC-family surface decaheme c-type cytochrome",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Cell-surface decaheme cytochrome supporting extracellular reduction of ferric iron in Shewanella.",
            "grounding": "InterPro:IPR020014",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:Q8EG34",
                "protein_label": "Extracellular iron oxide respiratory system surface decaheme cytochrome c component MtrC",
                "gene_symbol": "mtrC",
                "taxon_id": "NCBITaxon:211586",
                "taxon_label": "Shewanella oneidensis MR-1",
                "entry_status": "UNREVIEWED",
                "proteome_id": "UP000008186",
                "retrieved_on": "2026-10-22",
                "entry_version": 126,
                "sequence_version": 1,
                "role": "MtrC cell-surface component implicated in efficient Fe(III) reduction; this accession is not presented as the complete MtrCAB conduit.",
                "evidence": [
                  {
                    "reference": "DOI:10.1073/pnas.0604517103",
                    "snippet": "The decaheme c-type cytochrome MtrC (SO1778) had been implicated in efficient reduction of Fe(III) and Mn(IV) by MR-1.",
                    "notes": "The primary S. oneidensis MR-1 study supports the MtrC role in metal reduction. UniProtKB Q8EG34 is the exact unreviewed MtrC entry from reference proteome UP000008186 and verifies the strain taxon."
                  }
                ]
              }
            ]
          }
        ],
        "edges": [
          {
            "subject": "ferric_iron",
            "predicate": "oxidized to",
            "object": "ferrous_iron",
            "description": "Fe(III) is reduced to Fe(II) as DIR terminal-acceptor chemistry.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mr.55.2.259-287.1991",
                "notes": "Lovley establishes Fe(III) reduction coupled to organic-matter oxidation as energy-conserving anaerobic respiration."
              }
            ],
            "predicate_id": "METPO:2007405"
          },
          {
            "subject": "dir_trait",
            "predicate": "has electron acceptor",
            "object": "ferric_iron",
            "description": "Fe(III) acts as terminal electron acceptor enabling DIR.",
            "evidence": [
              {
                "reference": "PMID:7826009",
                "notes": "Nealson & Saffarini support Fe(III) as a terminal electron acceptor competitive with nitrate."
              }
            ],
            "predicate_id": "METPO:2007702"
          },
          {
            "subject": "dir_trait",
            "predicate": "is a",
            "object": "anaerobic_respiration",
            "description": "DIR is a form of energy-conserving anaerobic respiration.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mr.55.2.259-287.1991",
                "notes": "Organisms can obtain energy by completely oxidizing organic compounds to CO2 with Fe(III) or Mn(IV) as the sole acceptor."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "organic_matter_oxidation",
            "predicate": "coupled to",
            "object": "ferric_iron",
            "description": "Oxidation of organic matter is coupled to Fe(III) reduction in DIR.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mr.55.2.259-287.1991",
                "notes": "The oxidation of organic matter coupled to the reduction of Fe(III) or Mn(IV) is the direct result of enzymatic activity of specialized microorganisms."
              }
            ]
          },
          {
            "subject": "hydrogen_oxidation",
            "predicate": "coupled to",
            "object": "ferric_iron",
            "description": "H2 oxidation can serve as the electron donor coupled to Fe(III) reduction.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mr.55.2.259-287.1991",
                "notes": "Abundant evidence that H2 oxidation can be coupled to Fe(III)/Mn(IV) reduction in sediments."
              }
            ]
          },
          {
            "subject": "dissolved_fe3_om_complex",
            "predicate": "reduced faster than",
            "object": "solid_fe3_mineral",
            "description": "Dissolved Fe(III)-OM complexes are reduced at significantly higher rates than solid Fe(III) minerals.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s10533-024-01186-4",
                "notes": "The reduction rates of dissolved Fe(III)-OM complexes are significantly higher than those observed for solid Fe(III) minerals."
              }
            ]
          },
          {
            "subject": "dir_trait",
            "predicate": "has electron acceptor",
            "object": "solid_fe3_mineral",
            "description": "Insoluble Fe(III) oxides are the environmentally dominant terminal electron acceptor for DIR, which is why the trait requires extracellular electron transfer.",
            "evidence": [
              {
                "reference": "PMID:15518832",
                "snippet": "Unlike other commonly considered electron acceptors, Fe(III) and Mn(IV) oxides, the most prevalent form of Fe(III) and Mn(IV) in most environments, are insoluble.",
                "notes": "Lovley et al. identify insoluble Fe(III)/Mn(IV) oxides as the prevalent environmental form of the acceptor, which is what ties the solid-mineral pool to the trait rather than leaving it a free-standing geochemical observation."
              }
            ],
            "predicate_id": "METPO:2007702"
          },
          {
            "subject": "dir_trait",
            "predicate": "has electron acceptor",
            "object": "dissolved_fe3_om_complex",
            "description": "Solubilised Fe(III) is a second terminal electron acceptor pool, reachable without direct contact with the mineral surface.",
            "evidence": [
              {
                "reference": "PMID:15518832",
                "snippet": "In contrast, Shewanella and Geothrix species produce chelators that solubilize Fe(III) and release electron-shuttling compounds that transfer electrons from the cell surface to the surface of Fe(III) oxides not in direct contact with the cells.",
                "notes": "Establishes that a solubilised, non-contact Fe(III) pool is respired, which is what attaches the dissolved-vs-solid rate comparison to the trait. Scope caveat kept explicit (issue 297) - the quote is about chelators the organism itself secretes, whereas this node is ambient Fe(III)-organic-matter complex, so it supports the existence of the pool rather than its origin."
              }
            ],
            "predicate_id": "METPO:2007702"
          },
          {
            "subject": "mtrc",
            "predicate": "enables reduction of",
            "object": "solid_fe3_mineral",
            "description": "Cell-surface MtrC supports efficient extracellular reduction of insoluble Fe(III) acceptors in S. oneidensis MR-1.",
            "evidence": [
              {
                "reference": "DOI:10.1073/pnas.0604517103",
                "snippet": "The decaheme c-type cytochrome MtrC (SO1778) had been implicated in efficient reduction of Fe(III) and Mn(IV) by MR-1.",
                "notes": "This primary-source edge is restricted to the Shewanella MR-1 branch; Geobacter and other iron reducers can use different extracellular electron-transfer machinery."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-30T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate METABOLISM trait (dissimilatory iron reduction) from literature research to fill the metal-redox metabolism gap.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-10T14:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (Fe(III) \u2192 Fe(II) respiration) with CHEBI node groundings and RO/METPO predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 4 evidence-backed generic edges (5 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:12Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (rdfs:subClassOf\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-05T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 2 evidence-backed edges connecting the stranded Fe(III)-pool component to the trait (issue 183): dir_trait uses electron acceptor solid_fe3_mineral, and dir_trait uses electron acceptor dissolved_fe3_om_complex, both grounded METPO:2000008 to match the established uses-electron-donor convention. Both carry verbatim snippets from PMID:15518832, checked character-for-character against the PubMed abstract rather than lifted from the deep-research report, whose evidence text is paraphrase (issue 247). Resolves this graph's FRAGMENTED_GRAPH and its 2 UNREACHABLE_FROM_TRAIT findings.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-05T12:00:00Z",
        "curator": "claude",
        "action": "REVERSE_CAUSAL_EDGE_DIRECTION",
        "changes": "Reversed 2 causal edges from dir_trait uses electron acceptor <chemical> to <chemical> enables dir_trait (predicate_id METPO:2000008 -> RO:0002327), issue 295. This supersedes the 2026-08-05T00:00:00Z ENRICH_CAUSAL_GRAPH entry above, which describes those two edges in their original direction and grounding: METPO:2000008 is rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so the trait-subject form entailed that dir_trait is a microbe. Graph connectivity from issue 183 is preserved - the edges still join the Fe(III)-pool component to the trait, just in the other direction. Evidence unchanged. Note RO:0002327 has range 'biological process or activity', so the new form is not fully range-correct either, and both acceptor edges now share a predicate with the donor convention - tracked in issues 302 and 303.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 3 causal edge(s) off enables/RO:0002327 with a TRAIT object (3 to has electron acceptor), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them. 3 electron edge(s) were also reversed back to trait -> chemical, restoring the donor/acceptor role that PR 300 collapsed onto enables (issue 303); the organism-subject problem that forced that collapse does not arise here because these predicates take a causal-node domain rather than METPO:2000001's microbe domain (issue 301).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-24T08:00:00Z",
        "curator": "codex",
        "action": "CURATE_PROTEIN_TAXON_EXAMPLE",
        "changes": "Added a DOI-backed S. oneidensis MR-1 MtrC example, an InterPro family grounding, an explicitly strain-scoped MtrC-to-Fe(III) edge, and mechanistic scope notes. The unreviewed accession is retained only as an exact component from reference proteome UP000008186.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-22T01:35:00Z",
        "curator": "claude",
        "action": "REFRESH_UNIPROT_ENTRY_VERSION",
        "changes": "Refreshed UniProtKB entry_version against live UniProt REST on 2026-10-22: UniProtKB:Q8EG34 (125 -> 126 on mtrc).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000108",
    "label": "dissimilatory manganese reduction",
    "definition": "An anaerobic respiratory metabolism in which an organism conserves energy by reducing Mn(IV) oxides to soluble Mn(II) as a terminal electron acceptor while oxidizing organic matter or hydrogen.",
    "definition_source": "DOI:10.1128/mr.55.2.259-287.1991",
    "trait_category": "METABOLISM",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "traitmech:000039"
    ],
    "synonyms": [
      {
        "synonym_text": "Mn(IV) reduction",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1128/mr.55.2.259-287.1991"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1128/mr.55.2.259-287.1991",
        "notes": "Lovley establishes dissimilatory Fe(III)/Mn(IV) reduction as energy-conserving anaerobic respiration on metal-oxide acceptors."
      },
      {
        "reference": "PMID:7826009",
        "notes": "Nealson & Saffarini review iron and manganese in anaerobic respiration as terminal electron acceptors."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:70863",
        "taxon_label": "Shewanella oneidensis",
        "note": "Model dissimilatory metal reducer (strain MR-1 = Manganese Reducer 1); respires Mn(IV)/Fe(III) via extracellular electron transfer.",
        "reference": "DOI:10.1038/nbt749"
      },
      {
        "taxon_id": "NCBITaxon:211586",
        "taxon_label": "Shewanella oneidensis MR-1",
        "note": "Strain-level metal reducer paired to the MtrC surface decaheme cytochrome example supporting efficient Mn(IV) reduction.",
        "reference": "DOI:10.1073/pnas.0604517103"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "dmr_mn_oxide_respiration",
        "title": "Dissimilatory manganese reduction respires Mn(IV) to Mn(II)",
        "description": "Evidence-backed causal sketch linking Mn(IV) oxide as terminal electron acceptor to soluble Mn(II) and anaerobic respiration.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "The MtrC protein example and protein-to-Mn(IV) edge are specific to the extracellular metal-reduction route characterized in S. oneidensis MR-1; they are not asserted as universal across manganese reducers.",
        "nodes": [
          {
            "node_id": "dmr_trait",
            "label": "dissimilatory manganese reduction",
            "node_type": "TRAIT",
            "grounding": "traitmech:000108",
            "description": "Anaerobic respiration on Mn(IV) oxide as terminal acceptor."
          },
          {
            "node_id": "mn_iv_oxide",
            "label": "Mn(IV) oxide",
            "node_type": "CHEMICAL",
            "description": "Insoluble Mn(IV) oxide used as terminal electron acceptor."
          },
          {
            "node_id": "mn_ii",
            "label": "manganese(2+)",
            "node_type": "CHEMICAL",
            "description": "Soluble Mn(II) released after reduction.",
            "grounding": "CHEBI:29035"
          },
          {
            "node_id": "organic_matter",
            "label": "organic matter",
            "node_type": "CHEMICAL",
            "description": "Organic carbon electron donor oxidized during Mn(IV) respiration."
          },
          {
            "node_id": "hydrogen",
            "label": "dihydrogen",
            "node_type": "CHEMICAL",
            "description": "H2 used as electron donor for dissimilatory manganese reduction.",
            "grounding": "CHEBI:18276"
          },
          {
            "node_id": "anoxia",
            "label": "anoxic conditions",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Absence of oxygen permitting anaerobic Mn(IV) respiration."
          },
          {
            "node_id": "methane_oxidation",
            "label": "anaerobic methane oxidation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Anaerobic oxidation of methane (AOM) coupled to metal-oxide reduction."
          },
          {
            "node_id": "mtrc",
            "label": "MtrC-family surface decaheme c-type cytochrome",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Cell-surface decaheme cytochrome supporting extracellular reduction of manganese oxide in Shewanella.",
            "grounding": "InterPro:IPR020014",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:Q8EG34",
                "protein_label": "Extracellular iron oxide respiratory system surface decaheme cytochrome c component MtrC",
                "gene_symbol": "mtrC",
                "taxon_id": "NCBITaxon:211586",
                "taxon_label": "Shewanella oneidensis MR-1",
                "entry_status": "UNREVIEWED",
                "proteome_id": "UP000008186",
                "retrieved_on": "2026-10-22",
                "entry_version": 126,
                "sequence_version": 1,
                "role": "MtrC cell-surface component implicated in efficient Mn(IV) reduction; this accession is not presented as the complete MtrCAB conduit.",
                "evidence": [
                  {
                    "reference": "DOI:10.1073/pnas.0604517103",
                    "snippet": "The decaheme c-type cytochrome MtrC (SO1778) had been implicated in efficient reduction of Fe(III) and Mn(IV) by MR-1.",
                    "notes": "The primary S. oneidensis MR-1 study supports the MtrC role in metal reduction. UniProtKB Q8EG34 is the exact unreviewed MtrC entry from reference proteome UP000008186 and verifies the strain taxon."
                  }
                ]
              }
            ]
          }
        ],
        "edges": [
          {
            "subject": "mn_iv_oxide",
            "predicate": "oxidized to",
            "object": "mn_ii",
            "description": "Mn(IV) oxide is reduced to soluble Mn(II).",
            "evidence": [
              {
                "reference": "DOI:10.1128/mr.55.2.259-287.1991",
                "notes": "Lovley establishes Mn(IV) reduction coupled to organic-matter oxidation as energy-conserving anaerobic respiration."
              }
            ],
            "predicate_id": "METPO:2007405"
          },
          {
            "subject": "dmr_trait",
            "predicate": "has electron acceptor",
            "object": "mn_iv_oxide",
            "description": "Mn(IV) acts as terminal electron acceptor enabling DMR.",
            "evidence": [
              {
                "reference": "PMID:7826009",
                "notes": "Nealson & Saffarini place Mn(IV) as a terminal electron acceptor in anaerobic respiration."
              }
            ],
            "predicate_id": "METPO:2007702"
          },
          {
            "subject": "organic_matter",
            "predicate": "is oxidized coupled to",
            "object": "dmr_trait",
            "description": "Oxidation of organic matter is coupled to Mn(IV) reduction.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mr.55.2.259-287.1991",
                "notes": "Lovley: oxidation of organic matter coupled to reduction of Fe(III) or Mn(IV); fatty acids and aromatics fully oxidized with Mn(IV) as sole acceptor."
              }
            ]
          },
          {
            "subject": "hydrogen",
            "predicate": "donates electrons to",
            "object": "dmr_trait",
            "description": "H2 serves as electron donor for dissimilatory manganese reduction.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mr.55.2.259-287.1991",
                "notes": "Lovley: organisms with Mn(IV) as sole electron acceptor can completely oxidize hydrogen."
              }
            ],
            "predicate_id": "METPO:2007403"
          },
          {
            "subject": "anoxia",
            "predicate": "confers",
            "object": "dmr_trait",
            "description": "Anoxic conditions enable anaerobic Mn(IV) respiration.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mr.55.2.259-287.1991",
                "notes": "Lovley frames Mn(IV) reduction as anaerobic respiration in aquatic sediments, soils, and groundwater under anaerobic conditions."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "methane_oxidation",
            "predicate": "is coupled to",
            "object": "dmr_trait",
            "description": "Anaerobic methane oxidation can be coupled to Mn reduction (Fe-Mn-AOM).",
            "evidence": [
              {
                "reference": "DOI:10.5194/egusphere-2024-1829",
                "notes": "Sivan: AOM coupled with Fe-Mn reduction (Fe-Mn-AOM) is a globally important biogeochemical process with MnO2-coupled AOM reactions."
              }
            ]
          },
          {
            "subject": "mtrc",
            "predicate": "enables reduction of",
            "object": "mn_iv_oxide",
            "description": "Cell-surface MtrC supports efficient extracellular reduction of Mn(IV) acceptors in S. oneidensis MR-1.",
            "evidence": [
              {
                "reference": "DOI:10.1073/pnas.0604517103",
                "snippet": "The decaheme c-type cytochrome MtrC (SO1778) had been implicated in efficient reduction of Fe(III) and Mn(IV) by MR-1.",
                "notes": "This primary-source edge is restricted to the S. oneidensis MR-1 route; methane-coupled and other manganese-reduction mechanisms may use different proteins."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-06-08T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate METABOLISM trait (dissimilatory manganese reduction); round 2, parented to the existing dissimilatory metal reduction axis (traitmech:000039) alongside round-1 iron reduction.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-10T14:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (Mn(IV) \u2192 Mn(II) respiration) with RO/METPO predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-14T06:55:38Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:29035\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 4 evidence-backed generic edges (4 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:12Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007403\u00d71, RO:0002327\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:32Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:18276\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 2 causal edge(s) off enables/RO:0002327 with a TRAIT object (1 to has electron acceptor, 1 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them. 1 electron edge(s) were also reversed back to trait -> chemical, restoring the donor/acceptor role that PR 300 collapsed onto enables (issue 303); the organism-subject problem that forced that collapse does not arise here because these predicates take a causal-node domain rather than METPO:2000001's microbe domain (issue 301).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-24T08:05:00Z",
        "curator": "codex",
        "action": "CURATE_PROTEIN_TAXON_EXAMPLE",
        "changes": "Added a DOI-backed S. oneidensis MR-1 MtrC example, an InterPro family grounding, an explicitly strain-scoped MtrC-to-Mn(IV) edge, and mechanistic scope notes. The unreviewed accession is retained only as an exact component from reference proteome UP000008186.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-22T01:35:00Z",
        "curator": "claude",
        "action": "REFRESH_UNIPROT_ENTRY_VERSION",
        "changes": "Refreshed UniProtKB entry_version against live UniProt REST on 2026-10-22: UniProtKB:Q8EG34 (125 -> 126 on mtrc).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000039",
    "label": "dissimilatory metal reduction",
    "definition": "An anaerobic respiratory metabolism in which an organism conserves energy for growth by coupling the oxidation of organic matter or hydrogen to the reduction of a metal (e.g. Fe(III), Mn(IV)) as a terminal electron acceptor.",
    "definition_source": "DOI:10.1128/mr.55.2.259-287.1991",
    "trait_category": "METABOLISM",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000802"
    ],
    "synonyms": [
      {
        "synonym_text": "dissimilatory metal-ion reduction",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1128/mr.55.2.259-287.1991"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1128/mr.55.2.259-287.1991",
        "snippet": "The oxidation of organic matter coupled to the reduction of Fe(III) or Mn(IV) is one of the most important biogeochemical reactions in aquatic sediments, soils, and groundwater",
        "notes": "Lovley review establishes dissimilatory metal (Fe(III)/Mn(IV)) reduction as energy-conserving anaerobic respiration; parent of the metal-specific reduction sub-variants."
      },
      {
        "reference": "PMID:7826009",
        "notes": "Nealson & Saffarini, \"Iron and manganese in anaerobic respiration\", supports metals as terminal electron acceptors in anaerobic respiration."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:35554",
        "taxon_label": "Geobacter sulfurreducens",
        "note": "Model dissimilatory metal reducer; respires Fe(III)/Mn(IV) via extracellular electron transfer and conductive pili (type strain PCA).",
        "reference": "DOI:10.1126/science.1088727"
      },
      {
        "taxon_id": "NCBITaxon:211586",
        "taxon_label": "Shewanella oneidensis MR-1",
        "note": "Strain-level metal reducer paired to the MtrC surface component of the MtrCAB extracellular electron-transfer conduit.",
        "reference": "DOI:10.1073/pnas.0604517103"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "metal_reduction_anaerobic_respiration",
        "title": "Dissimilatory metal reduction couples organic oxidation to metal respiration",
        "description": "Evidence-backed causal sketch linking oxidation of organic matter or hydrogen to reduction of metal terminal electron acceptors.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "The graph combines broad metal respiration with a Shewanella MtrCAB branch and other extracellular-transfer routes. The MtrC protein example supports only the S. oneidensis MR-1 branch and does not imply that all metal reducers encode MtrCAB.",
        "nodes": [
          {
            "node_id": "metal_reduction_trait",
            "label": "dissimilatory metal reduction",
            "node_type": "TRAIT",
            "grounding": "traitmech:000039",
            "description": "Energy-conserving anaerobic respiration with a metal acceptor."
          },
          {
            "node_id": "metal_terminal_acceptor",
            "label": "terminal electron acceptor",
            "node_type": "CHEMICAL",
            "grounding": "METPO:1007504",
            "description": "Fe(III) or Mn(IV) oxide acting as terminal electron acceptor."
          },
          {
            "node_id": "anaerobic_respiration",
            "label": "anaerobic respiration",
            "node_type": "BIOLOGICAL_PROCESS",
            "grounding": "GO:0009061",
            "description": "Energy-conserving respiration with non-O2 acceptor."
          },
          {
            "node_id": "organic_matter_oxidation",
            "label": "organic compound oxidation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Oxidation of organic compounds providing electrons for metal reduction."
          },
          {
            "node_id": "fe3_reduction",
            "label": "Fe(III) reduction",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduction of ferric iron to ferrous iron."
          },
          {
            "node_id": "mtrcab_complex",
            "label": "MtrCAB outer-membrane complex",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Outer-membrane porin-cytochrome complex forming an electron-transfer conduit.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "MtrCAB is a multisubunit porin-cytochrome conduit; the verified MtrC family term denotes one surface component rather than the complete complex represented by this node.",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:Q8EG34",
                "protein_label": "Extracellular iron oxide respiratory system surface decaheme cytochrome c component MtrC",
                "gene_symbol": "mtrC",
                "taxon_id": "NCBITaxon:211586",
                "taxon_label": "Shewanella oneidensis MR-1",
                "entry_status": "UNREVIEWED",
                "proteome_id": "UP000008186",
                "retrieved_on": "2026-10-22",
                "entry_version": 126,
                "sequence_version": 1,
                "role": "Cell-surface MtrC component of the MtrCAB conduit; this accession is not presented as the complete three-component complex.",
                "evidence": [
                  {
                    "reference": "DOI:10.1073/pnas.0604517103",
                    "snippet": "The decaheme c-type cytochrome MtrC (SO1778) had been implicated in efficient reduction of Fe(III) and Mn(IV) by MR-1.",
                    "notes": "The primary S. oneidensis MR-1 study supports MtrC in metal reduction. UniProtKB Q8EG34 is the exact unreviewed MtrC entry from reference proteome UP000008186 and verifies the strain taxon."
                  }
                ]
              }
            ]
          },
          {
            "node_id": "extracellular_acceptor",
            "label": "extracellular electron acceptor",
            "node_type": "CHEMICAL",
            "description": "Insoluble or extracellular acceptor receiving respiratory electrons."
          },
          {
            "node_id": "flavin_shuttle",
            "label": "flavin electron shuttle",
            "node_type": "CHEMICAL",
            "description": "Redox-active flavin mediating electron transfer to distant substrates."
          },
          {
            "node_id": "insoluble_metal_substrate",
            "label": "oxidized insoluble metal",
            "node_type": "CHEMICAL",
            "description": "Oxidized insoluble/crystalline metal serving as respiratory substrate."
          },
          {
            "node_id": "anaerobic_subsurface_env",
            "label": "anaerobic subsurface environment",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Anaerobic subsurface where Fe(III) is present as insoluble/crystalline forms."
          }
        ],
        "edges": [
          {
            "subject": "metal_reduction_trait",
            "predicate": "has electron acceptor",
            "object": "metal_terminal_acceptor",
            "description": "Metal-ion acceptors enable energy-conserving anaerobic respiration on metals.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mr.55.2.259-287.1991",
                "notes": "Lovley establishes dissimilatory metal (Fe(III)/Mn(IV)) reduction as energy-conserving anaerobic respiration."
              }
            ],
            "predicate_id": "METPO:2007702"
          },
          {
            "subject": "metal_reduction_trait",
            "predicate": "participates in",
            "object": "anaerobic_respiration",
            "description": "Metal reduction is a class of anaerobic respiration.",
            "evidence": [
              {
                "reference": "PMID:7826009",
                "notes": "Nealson & Saffarini place iron and manganese as terminal electron acceptors within anaerobic respiration."
              }
            ],
            "predicate_id": "biolink:participates_in"
          },
          {
            "subject": "organic_matter_oxidation",
            "predicate": "donates electrons to",
            "object": "fe3_reduction",
            "description": "Oxidation of organic compounds donates electrons to Fe(III) reduction in metal-reducing bacteria.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s11783-019-1173-9",
                "notes": "FeRB transfers electrons to Fe(III), Fe(III) is reduced to Fe(II), and organic compounds are mineralized (Jiang et al., 2019); general respiratory coupling."
              }
            ],
            "predicate_id": "METPO:2007403"
          },
          {
            "subject": "mtrcab_complex",
            "predicate": "transfers electrons to",
            "object": "extracellular_acceptor",
            "description": "The MtrCAB outer-membrane complex creates a pathway transferring electrons to an extracellular acceptor.",
            "evidence": [
              {
                "reference": "DOI:10.1128/aem.00044-24",
                "notes": "The outer membrane complex MtrCAB creates a pathway that transfers electrons to an extracellular acceptor (Hsu et al., 2024); generalized EET conduit role."
              }
            ],
            "predicate_id": "METPO:2007403"
          },
          {
            "subject": "flavin_shuttle",
            "predicate": "facilitates electron transfer to",
            "object": "extracellular_acceptor",
            "description": "Flavin shuttles facilitate electron transfer to substrates distant from the cell surface.",
            "evidence": [
              {
                "reference": "DOI:10.3390/fermentation11070381",
                "notes": "Redox-active small molecules (flavins) facilitate electron transfer to substrates distant from the cell surface (Soares et al., 2025); mediated EET especially where metal oxides are spatially inaccessible."
              }
            ]
          },
          {
            "subject": "insoluble_metal_substrate",
            "predicate": "serves as respiratory substrate for",
            "object": "metal_reduction_trait",
            "description": "Oxidized insoluble metals serve as an abundant respiratory substrate for metal reduction.",
            "evidence": [
              {
                "reference": "DOI:10.1128/aem.00044-24",
                "notes": "Oxidized, insoluble metals are an abundant electron acceptor that microbes could utilize as a respiratory substrate (Hsu et al., 2024); trait-defining."
              }
            ]
          },
          {
            "subject": "anaerobic_subsurface_env",
            "predicate": "provides condition for",
            "object": "fe3_reduction",
            "description": "Fe(III) reduction occurs under anaerobic subsurface conditions where Fe(III) is insoluble/crystalline.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s11783-019-1173-9",
                "notes": "Fe(III) has solubility ~10^-9 M at neutral pH and is generally present as insoluble or crystalline forms under anaerobic subsurface environments (Jiang et al., 2019); environmental/chemical constraint."
              }
            ]
          },
          {
            "subject": "fe3_reduction",
            "predicate": "contributes to",
            "object": "metal_reduction_trait",
            "description": "Ferric-iron reduction is a defining process within dissimilatory metal reduction.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s11783-019-1173-9",
                "snippet": "FeRB transfers electrons to Fe(III), Fe(III) is reduced to Fe(II), and organic compounds are mineralized",
                "notes": "Verified against the free public article text."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "insoluble_metal_substrate",
            "predicate": "example of",
            "object": "extracellular_acceptor",
            "description": "Oxidized insoluble metals are extracellular respiratory electron acceptors.",
            "evidence": [
              {
                "reference": "DOI:10.1128/aem.00044-24",
                "snippet": "oxidized, insoluble metals are an abundant electron acceptor that microbes could potentially utilize as a respiratory substrate",
                "notes": "Verified against the free public article text."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-31T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Minted intermediate axis class (dissimilatory metal reduction) under anaerobic respiration (METPO:1000802) to parent dissimilatory iron reduction.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-10T14:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (metal-acceptor anaerobic respiration) with METPO/GO node groundings and RO/biolink predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 5 evidence-backed generic edges (7 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:12Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007403\u00d72).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 1 causal edge(s) off enables/RO:0002327 with a TRAIT object (1 to has electron acceptor), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them. 1 electron edge(s) were also reversed back to trait -> chemical, restoring the donor/acceptor role that PR 300 collapsed onto enables (issue 303); the organism-subject problem that forced that collapse does not arise here because these predicates take a causal-node domain rather than METPO:2000001's microbe domain (issue 301).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-24T08:10:00Z",
        "curator": "codex",
        "action": "CURATE_PROTEIN_TAXON_EXAMPLE",
        "changes": "Added a DOI-backed S. oneidensis MR-1 MtrC component example, documented why the whole MtrCAB complex remains reviewed label-only, and scoped the graph's mixed extracellular metal-reduction routes. The unreviewed accession is retained only as an exact reference-proteome component.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T12:15:00Z",
        "curator": "codex",
        "action": "CONNECT_CAUSAL_GRAPH_COMPONENTS",
        "changes": "Resolved issue #183 graph fragmentation (3 components to 1) with 2 public-source connector(s). No paid research service was called.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-22T01:35:00Z",
        "curator": "claude",
        "action": "REFRESH_UNIPROT_ENTRY_VERSION",
        "changes": "Refreshed UniProtKB entry_version against live UniProt REST on 2026-10-22: UniProtKB:Q8EG34 (125 -> 126 on mtrcab_complex).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000030",
    "label": "dissimilatory nitrate reduction to ammonium",
    "definition": "An anaerobic respiratory metabolism in which nitrate is reduced via nitrite to ammonium (rather than to N2), conserving fixed nitrogen within the ecosystem. It is favored over denitrification under nitrate-limited, high-electron-donor conditions.",
    "definition_source": "DOI:10.1126/science.1254070",
    "trait_category": "METABOLISM",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "traitmech:000122"
    ],
    "synonyms": [
      {
        "synonym_text": "DNRA",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1126/science.1254070"
      },
      {
        "synonym_text": "nitrate ammonification",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1007/s11157-025-09719-5"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1126/science.1254070",
        "notes": "Kraft et al. show the donor-to-acceptor ratio governs whether nitrate respiration ends in ammonium (DNRA) or N2 (denitrification)."
      },
      {
        "reference": "DOI:10.1007/s11157-025-09719-5",
        "notes": "Review of DNRA vs denitrification supports DNRA's competitive advantage and nitrogen-retaining role under nitrate-limited conditions."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:844",
        "taxon_label": "Wolinella succinogenes",
        "note": "Model organism for respiratory dissimilatory nitrate/nitrite reduction to ammonium (DNRA).",
        "reference": "DOI:10.1073/pnas.1932838100"
      },
      {
        "taxon_id": "NCBITaxon:273121",
        "taxon_label": "Wolinella succinogenes ATCC 29543",
        "note": "Strain-level source of the structurally characterized NrfA cytochrome c nitrite reductase and the matching reviewed UniProt example.",
        "reference": "DOI:10.1074/jbc.M006188200"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "dnra_nitrate_to_ammonium",
        "title": "DNRA reduces nitrate to ammonium, conserving fixed nitrogen",
        "description": "Evidence-backed causal sketch linking nitrate respiration ending in ammonium to nitrogen retention under high donor-to-acceptor ratios.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "Represents the canonical Nar/Nrf DNRA route and illustrates its nitrite-to-ammonium step with W. succinogenes NrfA. Regulatory details are broader bacterial modules and are not asserted to be identical in every DNRA organism.",
        "nodes": [
          {
            "node_id": "dnra_trait",
            "label": "dissimilatory nitrate reduction to ammonium",
            "node_type": "TRAIT",
            "grounding": "traitmech:000030",
            "description": "Anaerobic respiratory reduction of nitrate to ammonium."
          },
          {
            "node_id": "nitrate",
            "label": "nitrate",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:17632",
            "description": "Terminal electron acceptor reduced in DNRA."
          },
          {
            "node_id": "ammonium",
            "label": "ammonium",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:28938",
            "description": "Final reduction product retained in the ecosystem."
          },
          {
            "node_id": "donor_acceptor_ratio",
            "label": "high donor-to-acceptor ratio",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Nitrate-limited, high-electron-donor environment selecting for DNRA over denitrification."
          },
          {
            "node_id": "nitrite",
            "label": "nitrite",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:16301",
            "description": "Intermediate reduced from nitrate and then to ammonium in DNRA."
          },
          {
            "node_id": "narghi",
            "label": "NarGHI nitrate reductase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Membrane-bound nitrate reductase catalyzing the first DNRA step (nitrate to nitrite).",
            "grounding": "GO:0009325"
          },
          {
            "node_id": "nrfa",
            "label": "NrfA cytochrome c nitrite reductase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Cytochrome c nitrite reductase catalyzing the canonical second DNRA step (nitrite to ammonium).",
            "grounding": "GO:0042279",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:Q9S1E5",
                "protein_label": "Cytochrome c-552",
                "gene_symbol": "nrfA",
                "taxon_id": "NCBITaxon:273121",
                "taxon_label": "Wolinella succinogenes ATCC 29543",
                "entry_status": "REVIEWED",
                "retrieved_on": "2026-10-22",
                "entry_version": 164,
                "sequence_version": 2,
                "role": "Ammonia-forming cytochrome c nitrite reductase catalyzing the six-electron nitrite reduction step in W. succinogenes.",
                "evidence": [
                  {
                    "reference": "DOI:10.1074/jbc.M006188200",
                    "snippet": "Cytochrome c nitrite reductase catalyzes the 6-electron reduction of nitrite to ammonia.",
                    "notes": "The primary structural and mechanistic study is from W. succinogenes; UniProtKB Q9S1E5 verifies the reviewed NrfA protein and strain taxon."
                  }
                ]
              }
            ]
          },
          {
            "node_id": "narx_narl",
            "label": "NarX-NarL two-component system",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Nitrate/nitrite-sensing two-component regulatory system activating DNRA operon transcription.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "This node combines the NarX sensor kinase and NarL response regulator; an exact semantic grounding requires splitting the two components."
          },
          {
            "node_id": "fnr",
            "label": "FNR regulator",
            "node_type": "GENE_OR_PROTEIN",
            "description": "O2/NO-sensing global regulator activating nitrate respiration operons under anaerobic conditions.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "FNR-family regulators vary in sensor chemistry and target scope; the cited evidence does not establish an exact family term for this generic node."
          },
          {
            "node_id": "nrf_operon",
            "label": "nrf operon transcription",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Transcription of the operon encoding NrfA and accessory DNRA proteins."
          },
          {
            "node_id": "anaerobic_conditions",
            "label": "anaerobic conditions",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Oxygen-depleted environment permissive for DNRA respiration."
          }
        ],
        "edges": [
          {
            "subject": "nitrate",
            "predicate": "oxidized to",
            "object": "ammonium",
            "description": "Nitrate is reduced via nitrite to ammonium, retaining N in the cell/system.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.1254070",
                "notes": "Kraft et al. show DNRA produces ammonium from nitrate under nitrate-limited conditions."
              }
            ],
            "predicate_id": "METPO:2007405"
          },
          {
            "subject": "donor_acceptor_ratio",
            "predicate": "selects for",
            "object": "dnra_trait",
            "description": "High donor-to-acceptor ratio favors DNRA over denitrification.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s11157-025-09719-5",
                "notes": "DNRA review supports its competitive advantage and N-retaining role under nitrate-limited conditions."
              }
            ],
            "predicate_id": "METPO:2007401"
          },
          {
            "subject": "nitrate",
            "predicate": "reduced to",
            "object": "nitrite",
            "description": "NarGHI nitrate reductase catalyzes the canonical first DNRA step, reducing nitrate to nitrite.",
            "evidence": [
              {
                "reference": "DOI:10.1128/msystems.00967-23",
                "notes": "Nitrate is reduced via nitrite; known nitrate reductases include cytoplasmic NarGHI (egas2024)."
              }
            ]
          },
          {
            "subject": "narghi",
            "predicate": "catalyzes",
            "object": "nitrite",
            "description": "NarGHI nitrate reductase catalyzes production of nitrite from nitrate.",
            "evidence": [
              {
                "reference": "DOI:10.1128/msystems.00967-23",
                "notes": "Known nitrate reductases include periplasmic NapAB and cytoplasmic NarGHI catalyzing the first step."
              }
            ],
            "predicate_id": "biolink:catalyzes"
          },
          {
            "subject": "nitrite",
            "predicate": "reduced to",
            "object": "ammonium",
            "description": "NrfA cytochrome c nitrite reductase catalyzes the canonical second DNRA step, reducing nitrite to ammonium.",
            "evidence": [
              {
                "reference": "DOI:10.1128/aem.00292-25",
                "notes": "Second step performed by cytochrome c nitrite reductase (NrfA): reduction of nitrite to ammonium (hird2025)."
              }
            ]
          },
          {
            "subject": "nrfa",
            "predicate": "catalyzes",
            "object": "ammonium",
            "description": "NrfA reduces nitrite to ammonium, the final DNRA product.",
            "evidence": [
              {
                "reference": "DOI:10.1128/aem.00292-25",
                "notes": "Cytochrome c nitrite reductase (NrfA) performs the canonical reduction of nitrite to ammonium."
              }
            ],
            "predicate_id": "biolink:catalyzes"
          },
          {
            "subject": "narx_narl",
            "predicate": "activates expression of",
            "object": "nrf_operon",
            "description": "NarX-NarL nitrate/nitrite sensing activates transcription of the nrf operon.",
            "evidence": [
              {
                "reference": "DOI:10.1128/aem.00292-25",
                "notes": "Expression of nap and nrf operons is tightly regulated by NarX-NarL and NarQ-NarP, activating transcription under appropriate conditions (hird2025)."
              }
            ]
          },
          {
            "subject": "fnr",
            "predicate": "activates expression of",
            "object": "nrf_operon",
            "description": "FNR activates nrf operon transcription under anaerobic conditions.",
            "evidence": [
              {
                "reference": "DOI:10.1128/aem.00292-25",
                "notes": "FNR (O2/NO sensing) activates transcription under anaerobic and nitrate/nitrite-rich conditions (hird2025)."
              }
            ]
          },
          {
            "subject": "anaerobic_conditions",
            "predicate": "permits",
            "object": "dnra_trait",
            "description": "Anaerobic conditions, sensed via FNR, permit DNRA respiration.",
            "evidence": [
              {
                "reference": "DOI:10.1128/aem.00292-25",
                "notes": "nap/nrf operon expression activated under anaerobic conditions; DNRA proceeds under oxygen-depleted conditions (hird2025)."
              }
            ]
          },
          {
            "subject": "nrfa",
            "predicate": "contributes to",
            "object": "dnra_trait",
            "description": "NrfA executes the canonical nitrite-to-ammonium step of DNRA.",
            "evidence": [
              {
                "reference": "DOI:10.1128/aem.00292-25",
                "snippet": "The second step of the pathway is performed by cytochrome c nitrite reductase (NrfA)",
                "notes": "Verified against the free public article text."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "nrf_operon",
            "predicate": "contributes to",
            "object": "dnra_trait",
            "description": "Regulated expression of the nrf operon supplies the Nrf machinery for DNRA.",
            "evidence": [
              {
                "reference": "DOI:10.1128/aem.00292-25",
                "snippet": "The regulation of nrf operons is a complex and finely tuned process involving multiple layers of control",
                "notes": "Verified against the free public article text."
              }
            ],
            "predicate_id": "RO:0002326"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-30T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate METABOLISM trait (dissimilatory nitrate reduction to ammonium) from literature research to fill the nitrogen-cycling gap.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-10T14:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (DNRA nitrate \u2192 ammonium retention) with CHEBI node groundings and METPO predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 7 evidence-backed generic edges (7 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:12Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:catalyzes\u00d72).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-24T00:00:00Z",
        "curator": "codex",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Added a strain-matched W. succinogenes NrfA example and exact GO activity, grounded NarGHI, retyped the nrf operon carrier as transcription, and retained combined NarX-NarL and broad FNR labels with explicit review rationales.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T12:15:00Z",
        "curator": "codex",
        "action": "CONNECT_CAUSAL_GRAPH_COMPONENTS",
        "changes": "Resolved issue #183 graph fragmentation (3 components to 1) with 2 public-source connector(s). No paid research service was called.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-08T00:00:00Z",
        "curator": "codex",
        "action": "REFINE_PARENT_TRAIT",
        "changes": "Narrowed parent from anaerobic respiration to nitrate respiration.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-22T01:35:00Z",
        "curator": "claude",
        "action": "REFRESH_UNIPROT_ENTRY_VERSION",
        "changes": "Refreshed UniProtKB entry_version against live UniProt REST on 2026-10-22: UniProtKB:Q9S1E5 (163 -> 164 on nrfa).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000105",
    "label": "dissimilatory sulfate reduction",
    "definition": "An anaerobic respiratory metabolism in which an organism uses sulfate as the terminal electron acceptor, reducing it to hydrogen sulfide while oxidizing organic matter or hydrogen for energy.",
    "definition_source": "DOI:10.1038/nrmicro1892",
    "trait_category": "METABOLISM",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "traitmech:000124"
    ],
    "synonyms": [
      {
        "synonym_text": "sulfate respiration",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1038/nrmicro1892"
      },
      {
        "synonym_text": "dissimilatory sulphate reduction",
        "synonym_type": "EXACT_SYNONYM",
        "source": "http://purl.obolibrary.org/obo/go/releases/2026-07-26/go-basic.obo"
      }
    ],
    "xrefs": [
      "GO:0019420"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/nrmicro1892",
        "notes": "Muyzer & Stams review sulfate-reducing bacteria, which respire sulfate to sulfide in anoxic habitats."
      },
      {
        "reference": "DOI:10.3389/fmicb.2011.00081",
        "notes": "Plugge et al. review the metabolic flexibility of sulfate-reducing bacteria."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:882",
        "taxon_label": "Nitratidesulfovibrio vulgaris str. Hildenborough",
        "note": "Model dissimilatory sulfate reducer (formerly Desulfovibrio vulgaris Hildenborough).",
        "reference": "DOI:10.1038/nbt959"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "sulfate_reduction_to_sulfide",
        "title": "Dissimilatory sulfate reduction respires sulfate to sulfide",
        "description": "Evidence-backed causal sketch linking sulfate as terminal electron acceptor to sulfide production in anoxic anaerobic respiration.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "Represents the canonical Sat-Apr-Dsr route and uses explicit DsrA and DsrC components from N. vulgaris Hildenborough. One accession is not treated as denoting the DsrAB-DsrC assembly or the separate DsrMKJOP membrane complex.",
        "nodes": [
          {
            "node_id": "sulfate_reduction_trait",
            "label": "dissimilatory sulfate reduction",
            "node_type": "TRAIT",
            "grounding": "traitmech:000105",
            "description": "Anaerobic respiration on sulfate as terminal electron acceptor."
          },
          {
            "node_id": "sulfate",
            "label": "sulfate",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:16189",
            "description": "Terminal electron acceptor reduced in this respiration."
          },
          {
            "node_id": "sulfide",
            "label": "sulfide",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:15138",
            "description": "Final reduction product released to anoxic habitats."
          },
          {
            "node_id": "anaerobic_respiration",
            "label": "anaerobic respiration",
            "node_type": "BIOLOGICAL_PROCESS",
            "grounding": "GO:0009061",
            "description": "Energy-conserving respiration with non-O2 acceptor."
          },
          {
            "node_id": "sat_enzyme",
            "label": "ATP sulfurylase (Sat)",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Sulfate adenylyltransferase that activates sulfate to APS.",
            "grounding": "GO:0004781"
          },
          {
            "node_id": "aps",
            "label": "adenosine-5\u2032-phosphosulfate (APS)",
            "node_type": "CHEMICAL",
            "description": "Activated sulfate intermediate reduced to sulfite."
          },
          {
            "node_id": "sulfite",
            "label": "sulfite",
            "node_type": "CHEMICAL",
            "description": "Intermediate produced from APS, substrate of the Dsr cascade."
          },
          {
            "node_id": "aprab_complex",
            "label": "APS reductase AprAB",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Reduces APS to sulfite.",
            "grounding": "GO:0009973"
          },
          {
            "node_id": "dsrab_dsrc",
            "label": "DsrAB with DsrC",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Dissimilatory sulfite reductase DsrAB acting with DsrC protein.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "This node intentionally represents the DsrAB enzyme together with its DsrC partner; no one protein-family or complex term exactly denotes that combined mechanistic assembly.",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:P45574",
                "protein_label": "Sulfite reductase, dissimilatory-type subunit alpha",
                "gene_symbol": "dsrA",
                "taxon_id": "NCBITaxon:882",
                "taxon_label": "Nitratidesulfovibrio vulgaris str. Hildenborough",
                "entry_status": "REVIEWED",
                "retrieved_on": "2026-10-22",
                "entry_version": 147,
                "sequence_version": 3,
                "role": "DsrA alpha component of the DsrAB sulfite reductase bound to DsrC; this accession is not presented as the complete assembly.",
                "evidence": [
                  {
                    "reference": "DOI:10.1074/jbc.M805643200",
                    "snippet": "the dSiR DsrAB (sulfite reductase) subunits are bound to the DsrC protein",
                    "notes": "The primary structure is from D. vulgaris Hildenborough and identifies DsrA within the DsrAB-DsrC assembly; UniProtKB P45574 verifies the reviewed alpha subunit and current taxon."
                  }
                ]
              },
              {
                "uniprot_id": "UniProtKB:P45573",
                "protein_label": "Sulfite reductase, dissimilatory-type subunit gamma",
                "gene_symbol": "dsvC",
                "taxon_id": "NCBITaxon:882",
                "taxon_label": "Nitratidesulfovibrio vulgaris str. Hildenborough",
                "entry_status": "REVIEWED",
                "retrieved_on": "2026-08-24",
                "entry_version": 142,
                "sequence_version": 2,
                "role": "DsrC/gamma partner bound to DsrAB in the source-backed assembly; this accession is not presented as DsrAB itself.",
                "evidence": [
                  {
                    "reference": "DOI:10.1074/jbc.M805643200",
                    "snippet": "the dSiR DsrAB (sulfite reductase) subunits are bound to the DsrC protein",
                    "notes": "The primary structure resolves DsrC bound to DsrAB in D. vulgaris Hildenborough; UniProtKB P45573 verifies the reviewed gamma/DsrC protein and current taxon."
                  }
                ]
              }
            ]
          },
          {
            "node_id": "dsrc_trisulfide",
            "label": "DsrC-trisulfide",
            "node_type": "CHEMICAL",
            "description": "Protein-bound trisulfide intermediate from sulfite reduction."
          },
          {
            "node_id": "dsrmkjop_complex",
            "label": "DsrMK(JOP) membrane complex",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Reduces DsrC-trisulfide to sulfide, recycling DsrC and conserving energy.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "DsrMKJOP composition and nomenclature vary among sulfate reducers, and no exact complex term was verified for the generic parenthetical label."
          },
          {
            "node_id": "srm",
            "label": "sulfate/sulfite-reducing microorganisms",
            "node_type": "STATE",
            "description": "Microorganisms capable of dissimilatory sulfate/sulfite reduction."
          }
        ],
        "edges": [
          {
            "subject": "sulfate",
            "predicate": "oxidized to",
            "object": "sulfide",
            "description": "Sulfate is reduced stepwise to sulfide.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro1892",
                "notes": "Muyzer & Stams review sulfate-reducing bacteria respiring sulfate to sulfide."
              }
            ],
            "predicate_id": "METPO:2007405"
          },
          {
            "subject": "sulfate_reduction_trait",
            "predicate": "participates in",
            "object": "anaerobic_respiration",
            "description": "Sulfate respiration is a major form of anaerobic respiration.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2011.00081",
                "notes": "Plugge et al. review the metabolic flexibility of sulfate-reducing bacteria within anaerobic respiration."
              }
            ],
            "predicate_id": "biolink:participates_in"
          },
          {
            "subject": "sulfate",
            "predicate": "activated by",
            "object": "sat_enzyme",
            "description": "Sulfate is activated by ATP sulfurylase (Sat).",
            "evidence": [
              {
                "reference": "DOI:10.3390/antiox12030767",
                "notes": "Sulfate is taken up and activated by the enzyme ATP sulfurylase (Sat) to form APS."
              }
            ]
          },
          {
            "subject": "sat_enzyme",
            "predicate": "produces",
            "object": "aps",
            "description": "Sat activates sulfate to form APS.",
            "evidence": [
              {
                "reference": "DOI:10.3390/antiox12030767",
                "notes": "Activated by ATP sulfurylase (Sat) to form adenosine-5\u2032-phosphosulfate (APS)."
              }
            ],
            "predicate_id": "METPO:2007800"
          },
          {
            "subject": "aprab_complex",
            "predicate": "reduces",
            "object": "aps",
            "description": "APS reductase AprAB reduces APS to sulfite.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41396-023-01477-y",
                "notes": "The APS reductase AprAB reduces APS to sulfite, serving as substrate of the Dsr cascade."
              }
            ],
            "predicate_id": "METPO:2007802"
          },
          {
            "subject": "aprab_complex",
            "predicate": "produces",
            "object": "sulfite",
            "description": "AprAB reduction of APS yields sulfite.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41396-023-01477-y",
                "notes": "APS is reduced to sulfite serving as substrate of the Dsr cascade."
              }
            ],
            "predicate_id": "METPO:2007800"
          },
          {
            "subject": "dsrab_dsrc",
            "predicate": "produces",
            "object": "dsrc_trisulfide",
            "description": "DsrAB produces a DsrC-trisulfide from sulfite and DsrC.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41396-023-01477-y",
                "notes": "DsrAB produces a DsrC-trisulfide from sulfite and the DsrC protein."
              }
            ],
            "predicate_id": "METPO:2007800"
          },
          {
            "subject": "dsrmkjop_complex",
            "predicate": "reduces",
            "object": "dsrc_trisulfide",
            "description": "DsrMK(JOP) reduces the DsrC-trisulfide, recycling DsrC and releasing sulfide with energy conservation.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41396-023-01477-y",
                "notes": "DsrC-trisulfide is reduced by the DsrMK(JOP) membrane complex recycling DsrC and releasing sulfide while coupling to energy conservation."
              }
            ],
            "predicate_id": "METPO:2007802"
          },
          {
            "subject": "dsrmkjop_complex",
            "predicate": "produces",
            "object": "sulfide",
            "description": "Terminal reduction of the DsrC-trisulfide releases sulfide.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41396-023-01477-y",
                "notes": "DsrMK(JOP) reduction releases sulfide while coupling this reduction to energy conservation."
              }
            ],
            "predicate_id": "METPO:2007800"
          },
          {
            "subject": "dsrab_dsrc",
            "predicate": "marker for",
            "object": "srm",
            "description": "The dissimilatory sulfite reductase encoded by dsrAB is a hallmark of sulfate/sulfite-reducing microorganisms.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuad058",
                "notes": "A hallmark of SRM is the dissimilatory sulfite reductase encoded by the genes dsrAB."
              }
            ]
          },
          {
            "subject": "sulfate",
            "predicate": "participates in",
            "object": "sulfate_reduction_trait",
            "description": "Sulfate participates in dissimilatory sulfate reduction as the alternative terminal electron acceptor.",
            "evidence": [
              {
                "reference": "DOI:10.3390/antiox12030767",
                "snippet": "Sulfate can be used as an alternative terminal electron acceptor under anaerobic conditions",
                "notes": "Verified against the public PMC full text; this bridges the named respiratory trait to its existing Sat-Apr-Dsr pathway."
              }
            ],
            "predicate_id": "biolink:participates_in"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-06-08T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate METABOLISM trait (dissimilatory sulfate reduction); round 2, parented to anaerobic respiration (METPO:1000802).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-10T14:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (sulfate \u2192 sulfide respiration) with CHEBI/GO node groundings and METPO/biolink predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 8 evidence-backed generic edges (8 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:12Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 6 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d74, METPO:2000017\u00d72).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T02:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES_PART2",
        "changes": "Re-grounded 6 causal edge(s) off microbe-domain METPO predicates onto their causal-graph counterparts (4 to produces, 2 to reduces), issue 301 part 2. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Each replacement is a 1:1 mirror of its source predicate that changes only the domain, so the claim each edge makes is unchanged and directions are unchanged. The replacements are proposed in proposals/metpo_traitmech_v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-24T00:00:00Z",
        "curator": "codex",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Added explicit DsrA and DsrC UniProt components from N. vulgaris Hildenborough, grounded Sat and Apr activities, retained combined Dsr assemblies as reviewed label-only, and documented multisubunit scope.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T06:15:39Z",
        "curator": "codex",
        "action": "ADD_EXACT_ONTOLOGY_MATCH",
        "changes": "Ontology exact-match review (2026-08-25): approved exact xref(s): GO:0019420; declared exact synonym(s): 'dissimilatory sulphate reduction'. Evidence is predicate-scoped in the versioned ontology snapshots; OAK cross-checked direct data, and OLS4 spot-checked release deltas and disputed hits.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T08:20:00Z",
        "curator": "codex",
        "action": "CONNECT_CAUSAL_GRAPH_COMPONENTS",
        "changes": "Resolved issue #183 graph fragmentation (2 components to 1) using 1 public-source, verbatim-snippet-backed connector(s). No paid research service was called.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-08T00:00:00Z",
        "curator": "codex",
        "action": "REFINE_PARENT_TRAIT",
        "changes": "Narrowed parent from anaerobic respiration to respiration of sulfur compounds.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-22T01:35:00Z",
        "curator": "claude",
        "action": "REFRESH_UNIPROT_ENTRY_VERSION",
        "changes": "Refreshed UniProtKB entry_version against live UniProt REST on 2026-10-22: UniProtKB:P45574 (146 -> 147 on dsrab_dsrc).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:2000230",
    "label": "does not accumulate",
    "definition": "An OBJECT_PROPERTY asserting that an organism does NOT intracellularly accumulate a given chemical entity above environmental concentration. Negation companion of the positive 'accumulates' predicate. The intended use is predicate + class composition at assertion time, e.g. `<organism> <this property> <CHEBI class>`.",
    "definition_source": "DOI:10.1146/annurev.micro.55.1.485",
    "trait_category": "METABOLISM",
    "term_kind": "OBJECT_PROPERTY",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:2000001"
    ],
    "domain": "https://w3id.org/metpo/1000525",
    "range_": "http://purl.obolibrary.org/obo/CHEBI_24431",
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev.micro.55.1.485",
        "snippet": "accumulation",
        "notes": "Microbial-physiology reference supports 'does not accumulate' as a canonical predicate composed with a CHEBI-class chemical object at assertion time."
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.988799+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (OBJECT_PROPERTY)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic transport or storage relation carrier; later replacement should use more specific trait records that combine the relation with the transported, imported, exported, accumulated, or sequestered entity, cellular location or compartment, and positive or negative context.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-16T08:50:00-07:00",
        "curator": "claude",
        "action": "UNDEPRECATED_AS_COMPOSITION_PRIMITIVE",
        "changes": "Restored from DEPRECATED to REVIEWED under the predicate+class composition pattern (intended use: <organism> + this predicate + CHEBI chemical class). Added DOI/PMID-backed definition, evidence, and explicit domain/range slots.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:2000027",
    "label": "does not assimilate",
    "definition": "An OBJECT_PROPERTY asserting that an organism does NOT take up and incorporate a given chemical entity into cellular biomass. Negation companion of the positive 'assimilates' predicate.",
    "definition_source": "DOI:10.1146/annurev.micro.55.1.485",
    "trait_category": "METABOLISM",
    "term_kind": "OBJECT_PROPERTY",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:2000001"
    ],
    "synonyms": [
      {
        "synonym_text": "assimilation",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "domain": "https://w3id.org/metpo/1000525",
    "range_": "http://purl.obolibrary.org/obo/CHEBI_24431",
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev.micro.55.1.485",
        "snippet": "assimilation",
        "notes": "Microbial-physiology reference supports 'does not assimilate' as a canonical predicate composed with a CHEBI-class chemical object at assertion time."
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.963086+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (OBJECT_PROPERTY)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic negative biochemical conversion or activity relation carrier; later replacement should use more specific trait records that combine the relation with the substrate, product, enzyme or activity target, assay context, growth condition, and negative evidence.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-16T08:50:00-07:00",
        "curator": "claude",
        "action": "UNDEPRECATED_AS_COMPOSITION_PRIMITIVE",
        "changes": "Restored from DEPRECATED to REVIEWED under the predicate+class composition pattern (intended use: <organism> + this predicate + CHEBI chemical class). Added DOI/PMID-backed definition, evidence, and explicit domain/range slots.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:2000028",
    "label": "does not build acid from",
    "definition": "An OBJECT_PROPERTY asserting that an organism does NOT produce an acidic metabolite from a given chemical substrate (no medium acidification observed). Negation companion of 'builds acid from'.",
    "definition_source": "PMID:21413255",
    "trait_category": "METABOLISM",
    "term_kind": "OBJECT_PROPERTY",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:2000001"
    ],
    "synonyms": [
      {
        "synonym_text": "builds acid from",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "domain": "https://w3id.org/metpo/1000525",
    "range_": "http://purl.obolibrary.org/obo/CHEBI_24431",
    "evidence": [
      {
        "reference": "PMID:21413255",
        "snippet": "acid production",
        "notes": "Microbial-physiology reference supports 'does not build acid from' as a canonical predicate composed with a CHEBI-class chemical object at assertion time."
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.963575+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (OBJECT_PROPERTY)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic negative biochemical conversion or activity relation carrier; later replacement should use more specific trait records that combine the relation with the substrate, product, enzyme or activity target, assay context, growth condition, and negative evidence.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-16T08:50:00-07:00",
        "curator": "claude",
        "action": "UNDEPRECATED_AS_COMPOSITION_PRIMITIVE",
        "changes": "Restored from DEPRECATED to REVIEWED under the predicate+class composition pattern (intended use: <organism> + this predicate + CHEBI chemical class). Added DOI/PMID-backed definition, evidence, and explicit domain/range slots.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:2000029",
    "label": "does not build base from",
    "definition": "An OBJECT_PROPERTY asserting that an organism does NOT produce an alkaline metabolite from a given chemical substrate (no medium alkalinisation observed). Negation companion of 'builds base from'.",
    "definition_source": "PMID:21413255",
    "trait_category": "METABOLISM",
    "term_kind": "OBJECT_PROPERTY",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:2000001"
    ],
    "synonyms": [
      {
        "synonym_text": "builds base from",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "domain": "https://w3id.org/metpo/1000525",
    "range_": "http://purl.obolibrary.org/obo/CHEBI_24431",
    "evidence": [
      {
        "reference": "PMID:21413255",
        "snippet": "alkaline",
        "notes": "Microbial-physiology reference supports 'does not build base from' as a canonical predicate composed with a CHEBI-class chemical object at assertion time."
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.964097+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (OBJECT_PROPERTY)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic negative biochemical conversion or activity relation carrier; later replacement should use more specific trait records that combine the relation with the substrate, product, enzyme or activity target, assay context, growth condition, and negative evidence.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-16T08:50:00-07:00",
        "curator": "claude",
        "action": "UNDEPRECATED_AS_COMPOSITION_PRIMITIVE",
        "changes": "Restored from DEPRECATED to REVIEWED under the predicate+class composition pattern (intended use: <organism> + this predicate + CHEBI chemical class). Added DOI/PMID-backed definition, evidence, and explicit domain/range slots.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:2000030",
    "label": "does not build gas from",
    "definition": "An OBJECT_PROPERTY asserting that an organism does NOT produce a gaseous metabolite from a given chemical substrate. Negation companion of 'builds gas from'.",
    "definition_source": "PMID:21413255",
    "trait_category": "METABOLISM",
    "term_kind": "OBJECT_PROPERTY",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:2000001"
    ],
    "synonyms": [
      {
        "synonym_text": "builds gas from",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "domain": "https://w3id.org/metpo/1000525",
    "range_": "http://purl.obolibrary.org/obo/CHEBI_24431",
    "evidence": [
      {
        "reference": "PMID:21413255",
        "snippet": "gas production",
        "notes": "Microbial-physiology reference supports 'does not build gas from' as a canonical predicate composed with a CHEBI-class chemical object at assertion time."
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.964909+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (OBJECT_PROPERTY)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic negative biochemical conversion or activity relation carrier; later replacement should use more specific trait records that combine the relation with the substrate, product, enzyme or activity target, assay context, growth condition, and negative evidence.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-16T08:50:00-07:00",
        "curator": "claude",
        "action": "UNDEPRECATED_AS_COMPOSITION_PRIMITIVE",
        "changes": "Restored from DEPRECATED to REVIEWED under the predicate+class composition pattern (intended use: <organism> + this predicate + CHEBI chemical class). Added DOI/PMID-backed definition, evidence, and explicit domain/range slots.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:2000232",
    "label": "does not compartmentalize",
    "definition": "An OBJECT_PROPERTY asserting that an organism does NOT sequester a given chemical into a specific subcellular compartment. Negation companion of 'compartmentalizes'.",
    "definition_source": "DOI:10.1146/annurev.micro.55.1.485",
    "trait_category": "METABOLISM",
    "term_kind": "OBJECT_PROPERTY",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:2000230"
    ],
    "domain": "https://w3id.org/metpo/1000525",
    "range_": "http://purl.obolibrary.org/obo/CHEBI_24431",
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev.micro.55.1.485",
        "snippet": "compartment",
        "notes": "Microbial-physiology reference supports 'does not compartmentalize' as a canonical predicate composed with a CHEBI-class chemical object at assertion time."
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.989648+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (OBJECT_PROPERTY)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic metabolism relation carrier; later replacement should use more specific trait records that combine the relation with the chemical, phenotype, quality, compartment, enzyme or activity target, growth context, measurement, or other entity.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-16T08:50:00-07:00",
        "curator": "claude",
        "action": "UNDEPRECATED_AS_COMPOSITION_PRIMITIVE",
        "changes": "Restored from DEPRECATED to REVIEWED under the predicate+class composition pattern (intended use: <organism> + this predicate + CHEBI chemical class). Added DOI/PMID-backed definition, evidence, and explicit domain/range slots.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:2000033",
    "label": "does not degrade",
    "definition": "An OBJECT_PROPERTY asserting that an organism does NOT enzymatically break down a given chemical substrate. Negation companion of 'degrades'.",
    "definition_source": "DOI:10.1146/annurev.micro.55.1.485",
    "trait_category": "METABOLISM",
    "term_kind": "OBJECT_PROPERTY",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:2000001"
    ],
    "synonyms": [
      {
        "synonym_text": "degradation",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "domain": "https://w3id.org/metpo/1000525",
    "range_": "http://purl.obolibrary.org/obo/CHEBI_24431",
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev.micro.55.1.485",
        "snippet": "degradation",
        "notes": "Microbial-physiology reference supports 'does not degrade' as a canonical predicate composed with a CHEBI-class chemical object at assertion time."
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.966460+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (OBJECT_PROPERTY)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic negative biochemical conversion or activity relation carrier; later replacement should use more specific trait records that combine the relation with the substrate, product, enzyme or activity target, assay context, growth condition, and negative evidence.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-16T08:50:00-07:00",
        "curator": "claude",
        "action": "UNDEPRECATED_AS_COMPOSITION_PRIMITIVE",
        "changes": "Restored from DEPRECATED to REVIEWED under the predicate+class composition pattern (intended use: <organism> + this predicate + CHEBI chemical class). Added DOI/PMID-backed definition, evidence, and explicit domain/range slots.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:2000220",
    "label": "does not disproportionate",
    "definition": "An OBJECT_PROPERTY asserting that an organism does NOT carry out a disproportionation reaction on a given chemical substrate. Negation companion of 'disproportionates'.",
    "definition_source": "DOI:10.1146/annurev.micro.55.1.485",
    "trait_category": "METABOLISM",
    "term_kind": "OBJECT_PROPERTY",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:2000001"
    ],
    "synonyms": [
      {
        "synonym_text": "dismutates",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "domain": "https://w3id.org/metpo/1000525",
    "range_": "http://purl.obolibrary.org/obo/CHEBI_24431",
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev.micro.55.1.485",
        "snippet": "disproportionation",
        "notes": "Microbial-physiology reference supports 'does not disproportionate' as a canonical predicate composed with a CHEBI-class chemical object at assertion time."
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.986630+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (OBJECT_PROPERTY)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic negative biochemical conversion or activity relation carrier; later replacement should use more specific trait records that combine the relation with the substrate, product, enzyme or activity target, assay context, growth condition, and negative evidence.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-16T08:50:00-07:00",
        "curator": "claude",
        "action": "UNDEPRECATED_AS_COMPOSITION_PRIMITIVE",
        "changes": "Restored from DEPRECATED to REVIEWED under the predicate+class composition pattern (intended use: <organism> + this predicate + CHEBI chemical class). Added DOI/PMID-backed definition, evidence, and explicit domain/range slots.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:2000229",
    "label": "does not export",
    "definition": "An OBJECT_PROPERTY asserting that an organism does NOT export a given chemical from the cytoplasm. Negation companion of 'exports'.",
    "definition_source": "DOI:10.1146/annurev.micro.55.1.485",
    "trait_category": "METABOLISM",
    "term_kind": "OBJECT_PROPERTY",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:2000227"
    ],
    "domain": "https://w3id.org/metpo/1000525",
    "range_": "http://purl.obolibrary.org/obo/CHEBI_24431",
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev.micro.55.1.485",
        "snippet": "export",
        "notes": "Microbial-physiology reference supports 'does not export' as a canonical predicate composed with a CHEBI-class chemical object at assertion time."
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.988364+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (OBJECT_PROPERTY)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic transport or storage relation carrier; later replacement should use more specific trait records that combine the relation with the transported, imported, exported, accumulated, or sequestered entity, cellular location or compartment, and positive or negative context.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-16T08:50:00-07:00",
        "curator": "claude",
        "action": "UNDEPRECATED_AS_COMPOSITION_PRIMITIVE",
        "changes": "Restored from DEPRECATED to REVIEWED under the predicate+class composition pattern (intended use: <organism> + this predicate + CHEBI chemical class). Added DOI/PMID-backed definition, evidence, and explicit domain/range slots.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:2000037",
    "label": "does not ferment",
    "definition": "An OBJECT_PROPERTY asserting that an organism does NOT ferment a given chemical substrate. Negation companion of 'ferments'.",
    "definition_source": "DOI:10.1146/annurev.micro.55.1.485",
    "trait_category": "METABOLISM",
    "term_kind": "OBJECT_PROPERTY",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:2000001"
    ],
    "synonyms": [
      {
        "synonym_text": "fermentation",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "domain": "https://w3id.org/metpo/1000525",
    "range_": "http://purl.obolibrary.org/obo/CHEBI_24431",
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev.micro.55.1.485",
        "snippet": "fermentation",
        "notes": "Microbial-physiology reference supports 'does not ferment' as a canonical predicate composed with a CHEBI-class chemical object at assertion time."
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.968440+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (OBJECT_PROPERTY)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic negative biochemical conversion or activity relation carrier; later replacement should use more specific trait records that combine the relation with the substrate, product, enzyme or activity target, assay context, growth condition, and negative evidence.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-16T08:50:00-07:00",
        "curator": "claude",
        "action": "UNDEPRECATED_AS_COMPOSITION_PRIMITIVE",
        "changes": "Restored from DEPRECATED to REVIEWED under the predicate+class composition pattern (intended use: <organism> + this predicate + CHEBI chemical class). Added DOI/PMID-backed definition, evidence, and explicit domain/range slots.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:2000039",
    "label": "does not hydrolyze",
    "definition": "An OBJECT_PROPERTY asserting that an organism does NOT hydrolyse a given chemical substrate. Negation companion of 'hydrolyzes'.",
    "definition_source": "DOI:10.1146/annurev.micro.55.1.485",
    "trait_category": "METABOLISM",
    "term_kind": "OBJECT_PROPERTY",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:2000001"
    ],
    "synonyms": [
      {
        "synonym_text": "hydrolysis",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "domain": "https://w3id.org/metpo/1000525",
    "range_": "http://purl.obolibrary.org/obo/CHEBI_24431",
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev.micro.55.1.485",
        "snippet": "hydrolysis",
        "notes": "Microbial-physiology reference supports 'does not hydrolyze' as a canonical predicate composed with a CHEBI-class chemical object at assertion time."
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.969397+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (OBJECT_PROPERTY)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic negative biochemical conversion or activity relation carrier; later replacement should use more specific trait records that combine the relation with the substrate, product, enzyme or activity target, assay context, growth condition, and negative evidence.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-16T08:50:00-07:00",
        "curator": "claude",
        "action": "UNDEPRECATED_AS_COMPOSITION_PRIMITIVE",
        "changes": "Restored from DEPRECATED to REVIEWED under the predicate+class composition pattern (intended use: <organism> + this predicate + CHEBI chemical class). Added DOI/PMID-backed definition, evidence, and explicit domain/range slots.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:2000228",
    "label": "does not import",
    "definition": "An OBJECT_PROPERTY asserting that an organism does NOT import a given chemical from the extracellular environment. Negation companion of 'imports'.",
    "definition_source": "DOI:10.1146/annurev.micro.55.1.485",
    "trait_category": "METABOLISM",
    "term_kind": "OBJECT_PROPERTY",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:2000227"
    ],
    "domain": "https://w3id.org/metpo/1000525",
    "range_": "http://purl.obolibrary.org/obo/CHEBI_24431",
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev.micro.55.1.485",
        "snippet": "import",
        "notes": "Microbial-physiology reference supports 'does not import' as a canonical predicate composed with a CHEBI-class chemical object at assertion time."
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.987935+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (OBJECT_PROPERTY)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic transport or storage relation carrier; later replacement should use more specific trait records that combine the relation with the transported, imported, exported, accumulated, or sequestered entity, cellular location or compartment, and positive or negative context.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-16T08:50:00-07:00",
        "curator": "claude",
        "action": "UNDEPRECATED_AS_COMPOSITION_PRIMITIVE",
        "changes": "Restored from DEPRECATED to REVIEWED under the predicate+class composition pattern (intended use: <organism> + this predicate + CHEBI chemical class). Added DOI/PMID-backed definition, evidence, and explicit domain/range slots.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:2000042",
    "label": "does not oxidize",
    "definition": "An OBJECT_PROPERTY asserting that an organism does NOT oxidise a given chemical substrate. Negation companion of 'oxidizes'.",
    "definition_source": "DOI:10.1146/annurev.micro.55.1.485",
    "trait_category": "METABOLISM",
    "term_kind": "OBJECT_PROPERTY",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:2000001"
    ],
    "synonyms": [
      {
        "synonym_text": "oxidation",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "domain": "https://w3id.org/metpo/1000525",
    "range_": "http://purl.obolibrary.org/obo/CHEBI_24431",
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev.micro.55.1.485",
        "snippet": "oxidation",
        "notes": "Microbial-physiology reference supports 'does not oxidize' as a canonical predicate composed with a CHEBI-class chemical object at assertion time."
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.970872+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (OBJECT_PROPERTY)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic negative biochemical conversion or activity relation carrier; later replacement should use more specific trait records that combine the relation with the substrate, product, enzyme or activity target, assay context, growth condition, and negative evidence.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-16T08:50:00-07:00",
        "curator": "claude",
        "action": "UNDEPRECATED_AS_COMPOSITION_PRIMITIVE",
        "changes": "Restored from DEPRECATED to REVIEWED under the predicate+class composition pattern (intended use: <organism> + this predicate + CHEBI chemical class). Added DOI/PMID-backed definition, evidence, and explicit domain/range slots.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:2000222",
    "label": "does not produce",
    "definition": "An OBJECT_PROPERTY asserting that an organism does NOT produce a given chemical as a metabolic product. Negation companion of 'produces'.",
    "definition_source": "DOI:10.1146/annurev.micro.55.1.485",
    "trait_category": "METABOLISM",
    "term_kind": "OBJECT_PROPERTY",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:2000001"
    ],
    "synonyms": [
      {
        "synonym_text": "produces",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "domain": "https://w3id.org/metpo/1000525",
    "range_": "http://purl.obolibrary.org/obo/CHEBI_24431",
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev.micro.55.1.485",
        "snippet": "production",
        "notes": "Microbial-physiology reference supports 'does not produce' as a canonical predicate composed with a CHEBI-class chemical object at assertion time."
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.987105+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (OBJECT_PROPERTY)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic negative biochemical conversion or activity relation carrier; later replacement should use more specific trait records that combine the relation with the substrate, product, enzyme or activity target, assay context, growth condition, and negative evidence.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-16T08:50:00-07:00",
        "curator": "claude",
        "action": "UNDEPRECATED_AS_COMPOSITION_PRIMITIVE",
        "changes": "Restored from DEPRECATED to REVIEWED under the predicate+class composition pattern (intended use: <organism> + this predicate + CHEBI chemical class). Added DOI/PMID-backed definition, evidence, and explicit domain/range slots.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:2000044",
    "label": "does not reduce",
    "definition": "An OBJECT_PROPERTY asserting that an organism does NOT reduce a given chemical substrate. Negation companion of 'reduces'.",
    "definition_source": "DOI:10.1146/annurev.micro.55.1.485",
    "trait_category": "METABOLISM",
    "term_kind": "OBJECT_PROPERTY",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:2000001"
    ],
    "synonyms": [
      {
        "synonym_text": "reduction",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "domain": "https://w3id.org/metpo/1000525",
    "range_": "http://purl.obolibrary.org/obo/CHEBI_24431",
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev.micro.55.1.485",
        "snippet": "reduction",
        "notes": "Microbial-physiology reference supports 'does not reduce' as a canonical predicate composed with a CHEBI-class chemical object at assertion time."
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.971836+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (OBJECT_PROPERTY)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic negative biochemical conversion or activity relation carrier; later replacement should use more specific trait records that combine the relation with the substrate, product, enzyme or activity target, assay context, growth condition, and negative evidence.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-16T08:50:00-07:00",
        "curator": "claude",
        "action": "UNDEPRECATED_AS_COMPOSITION_PRIMITIVE",
        "changes": "Restored from DEPRECATED to REVIEWED under the predicate+class composition pattern (intended use: <organism> + this predicate + CHEBI chemical class). Added DOI/PMID-backed definition, evidence, and explicit domain/range slots.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:2000231",
    "label": "does not sequester",
    "definition": "An OBJECT_PROPERTY asserting that an organism does NOT sequester or chelate a given chemical. Negation companion of 'sequesters'.",
    "definition_source": "DOI:10.1146/annurev.micro.55.1.485",
    "trait_category": "METABOLISM",
    "term_kind": "OBJECT_PROPERTY",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:2000230"
    ],
    "domain": "https://w3id.org/metpo/1000525",
    "range_": "http://purl.obolibrary.org/obo/CHEBI_24431",
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev.micro.55.1.485",
        "snippet": "sequestration",
        "notes": "Microbial-physiology reference supports 'does not sequester' as a canonical predicate composed with a CHEBI-class chemical object at assertion time."
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.989191+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (OBJECT_PROPERTY)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic transport or storage relation carrier; later replacement should use more specific trait records that combine the relation with the transported, imported, exported, accumulated, or sequestered entity, cellular location or compartment, and positive or negative context.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-16T08:50:00-07:00",
        "curator": "claude",
        "action": "UNDEPRECATED_AS_COMPOSITION_PRIMITIVE",
        "changes": "Restored from DEPRECATED to REVIEWED under the predicate+class composition pattern (intended use: <organism> + this predicate + CHEBI chemical class). Added DOI/PMID-backed definition, evidence, and explicit domain/range slots.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:2000303",
    "label": "does not show activity of",
    "definition": "An OBJECT_PROPERTY asserting that an organism does NOT show the catalytic activity of a given enzyme (material entity) class. Negation companion of 'shows activity of'. Intended use is predicate + class composition at assertion time with a METPO enzyme class (METPO:1000527 or its subclass) as the object.",
    "definition_source": "PMID:21413255",
    "trait_category": "METABOLISM",
    "term_kind": "OBJECT_PROPERTY",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:2000301"
    ],
    "synonyms": [
      {
        "synonym_text": "Physiology and metabolism.enzymes.[].activity",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "domain": "https://w3id.org/metpo/1000525",
    "range_": "https://w3id.org/metpo/1000527",
    "evidence": [
      {
        "reference": "PMID:21413255",
        "snippet": "activity",
        "notes": "Microbial-physiology reference supports 'does not show activity of' as a canonical predicate relating an organism to an enzyme/activity class (asserted negatively), composed at assertion time."
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.991570+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (OBJECT_PROPERTY)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic negative biochemical conversion or activity relation carrier; later replacement should use more specific trait records that combine the relation with the substrate, product, enzyme or activity target, assay context, growth condition, and negative evidence.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-16T08:50:00-07:00",
        "curator": "claude",
        "action": "UNDEPRECATED_AS_COMPOSITION_PRIMITIVE",
        "changes": "Restored from DEPRECATED to REVIEWED under the predicate+class composition pattern (intended use: <organism> + this predicate + CHEBI chemical class). Added DOI/PMID-backed definition, evidence, and explicit domain/range slots.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:2000227",
    "label": "does not transport",
    "definition": "An OBJECT_PROPERTY asserting that an organism does NOT transport a given chemical across its membranes. Negation companion of 'transports'.",
    "definition_source": "DOI:10.1146/annurev.micro.55.1.485",
    "trait_category": "METABOLISM",
    "term_kind": "OBJECT_PROPERTY",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:2000001"
    ],
    "domain": "https://w3id.org/metpo/1000525",
    "range_": "http://purl.obolibrary.org/obo/CHEBI_24431",
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev.micro.55.1.485",
        "snippet": "transport",
        "notes": "Microbial-physiology reference supports 'does not transport' as a canonical predicate composed with a CHEBI-class chemical object at assertion time."
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.987559+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (OBJECT_PROPERTY)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic transport or storage relation carrier; later replacement should use more specific trait records that combine the relation with the transported, imported, exported, accumulated, or sequestered entity, cellular location or compartment, and positive or negative context.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-16T08:50:00-07:00",
        "curator": "claude",
        "action": "UNDEPRECATED_AS_COMPOSITION_PRIMITIVE",
        "changes": "Restored from DEPRECATED to REVIEWED under the predicate+class composition pattern (intended use: <organism> + this predicate + CHEBI chemical class). Added DOI/PMID-backed definition, evidence, and explicit domain/range slots.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:2000031",
    "label": "does not use as carbon source",
    "definition": "An OBJECT_PROPERTY asserting that an organism does *not* use a given chemical entity as a source of carbon for biosynthesis. The intended use is predicate + class composition at assertion time, e.g. `<organism> METPO:2000031 CHEBI:17234` (\"organism does not use glucose as carbon source\"). Negation companion to METPO:2000006.",
    "definition_source": "PMID:21413255",
    "trait_category": "METABOLISM",
    "term_kind": "OBJECT_PROPERTY",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:2000001"
    ],
    "synonyms": [
      {
        "synonym_text": "carbon source",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "domain": "https://w3id.org/metpo/1000525",
    "range_": "http://purl.obolibrary.org/obo/CHEBI_24431",
    "evidence": [
      {
        "reference": "PMID:21413255",
        "snippet": "carbon source",
        "notes": "Microbial-physiology reference supports the positive form of this relation; the negation companion uses the same domain/range with the assertion negated at use-site."
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.965443+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (OBJECT_PROPERTY)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic chemical-use relation carrier; later replacement should use more specific trait records that combine the relation with the chemical, metabolic role, growth condition, and positive or negative usage context.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-16T08:50:00-07:00",
        "curator": "claude",
        "action": "UNDEPRECATED_AS_COMPOSITION_PRIMITIVE",
        "changes": "Restored from DEPRECATED to REVIEWED under the predicate+class composition pattern (intended use: <organism> + this predicate + CHEBI chemical class). Added DOI/PMID-backed definition, evidence, and explicit domain/range slots.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:2000034",
    "label": "does not use as electron acceptor",
    "definition": "An OBJECT_PROPERTY asserting that an organism does *not* use a given chemical entity as a terminal electron acceptor in respiration. The intended use is predicate + class composition at assertion time, e.g. `<organism> METPO:X CHEBI:17632` (\"organism does not use nitrate as electron acceptor\"). Negation companion to METPO:2000008.",
    "definition_source": "DOI:10.1146/annurev.micro.61.080706.093130",
    "trait_category": "METABOLISM",
    "term_kind": "OBJECT_PROPERTY",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:2000001"
    ],
    "synonyms": [
      {
        "synonym_text": "electron acceptor",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "domain": "https://w3id.org/metpo/1000525",
    "range_": "http://purl.obolibrary.org/obo/CHEBI_24431",
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev.micro.61.080706.093130",
        "snippet": "electron acceptor",
        "notes": "Microbial-physiology reference supports the positive form of this relation; the negation companion uses the same domain/range with the assertion negated at use-site."
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.966955+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (OBJECT_PROPERTY)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic chemical-use relation carrier; later replacement should use more specific trait records that combine the relation with the chemical, metabolic role, growth condition, and positive or negative usage context.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-16T08:50:00-07:00",
        "curator": "claude",
        "action": "UNDEPRECATED_AS_COMPOSITION_PRIMITIVE",
        "changes": "Restored from DEPRECATED to REVIEWED under the predicate+class composition pattern (intended use: <organism> + this predicate + CHEBI chemical class). Added DOI/PMID-backed definition, evidence, and explicit domain/range slots.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:2000035",
    "label": "does not use as electron donor",
    "definition": "An OBJECT_PROPERTY asserting that an organism does *not* use a given chemical entity as an electron donor. The intended use is predicate + class composition at assertion time, e.g. `<organism> METPO:X CHEBI:18276` (\"organism does not use H2 as electron donor\"). Negation companion to METPO:2000009.",
    "definition_source": "DOI:10.1146/annurev.micro.61.080706.093130",
    "trait_category": "METABOLISM",
    "term_kind": "OBJECT_PROPERTY",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:2000001"
    ],
    "synonyms": [
      {
        "synonym_text": "electron donor",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "domain": "https://w3id.org/metpo/1000525",
    "range_": "http://purl.obolibrary.org/obo/CHEBI_24431",
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev.micro.61.080706.093130",
        "snippet": "electron donor",
        "notes": "Microbial-physiology reference supports the positive form of this relation; the negation companion uses the same domain/range with the assertion negated at use-site."
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.967448+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (OBJECT_PROPERTY)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic chemical-use relation carrier; later replacement should use more specific trait records that combine the relation with the chemical, metabolic role, growth condition, and positive or negative usage context.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-16T08:50:00-07:00",
        "curator": "claude",
        "action": "UNDEPRECATED_AS_COMPOSITION_PRIMITIVE",
        "changes": "Restored from DEPRECATED to REVIEWED under the predicate+class composition pattern (intended use: <organism> + this predicate + CHEBI chemical class). Added DOI/PMID-backed definition, evidence, and explicit domain/range slots.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:2000036",
    "label": "does not use as energy source",
    "definition": "An OBJECT_PROPERTY asserting that an organism does NOT use a given chemical as a source of energy for metabolism. Negation companion of 'uses as energy source'.",
    "definition_source": "DOI:10.1146/annurev.micro.55.1.485",
    "trait_category": "METABOLISM",
    "term_kind": "OBJECT_PROPERTY",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:2000001"
    ],
    "synonyms": [
      {
        "synonym_text": "energy source",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "domain": "https://w3id.org/metpo/1000525",
    "range_": "http://purl.obolibrary.org/obo/CHEBI_24431",
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev.micro.55.1.485",
        "snippet": "energy source",
        "notes": "Microbial-physiology reference supports 'does not use as energy source' as a canonical predicate composed with a CHEBI-class chemical object at assertion time."
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.967940+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (OBJECT_PROPERTY)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic chemical-use relation carrier; later replacement should use more specific trait records that combine the relation with the chemical, metabolic role, growth condition, and positive or negative usage context.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-16T08:50:00-07:00",
        "curator": "claude",
        "action": "UNDEPRECATED_AS_COMPOSITION_PRIMITIVE",
        "changes": "Restored from DEPRECATED to REVIEWED under the predicate+class composition pattern (intended use: <organism> + this predicate + CHEBI chemical class). Added DOI/PMID-backed definition, evidence, and explicit domain/range slots.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:2000040",
    "label": "does not use as nitrogen source",
    "definition": "An OBJECT_PROPERTY asserting that an organism does NOT use a given chemical as a source of nitrogen for biosynthesis. Negation companion of 'uses as nitrogen source'.",
    "definition_source": "PMID:21413255",
    "trait_category": "METABOLISM",
    "term_kind": "OBJECT_PROPERTY",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:2000001"
    ],
    "synonyms": [
      {
        "synonym_text": "nitrogen source",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "domain": "https://w3id.org/metpo/1000525",
    "range_": "http://purl.obolibrary.org/obo/CHEBI_51143",
    "evidence": [
      {
        "reference": "PMID:21413255",
        "snippet": "nitrogen source",
        "notes": "Microbial-physiology reference supports 'does not use as nitrogen source' as a canonical predicate composed with a CHEBI-class chemical object at assertion time."
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.969885+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (OBJECT_PROPERTY)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic chemical-use relation carrier; later replacement should use more specific trait records that combine the relation with the chemical, metabolic role, growth condition, and positive or negative usage context.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-16T08:50:00-07:00",
        "curator": "claude",
        "action": "UNDEPRECATED_AS_COMPOSITION_PRIMITIVE",
        "changes": "Restored from DEPRECATED to REVIEWED under the predicate+class composition pattern (intended use: <organism> + this predicate + CHEBI chemical class). Added DOI/PMID-backed definition, evidence, and explicit domain/range slots.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-16T09:35:00-07:00",
        "curator": "claude",
        "action": "TIGHTENED_RANGE_TO_CHEBI_SUBCLASS",
        "changes": "Narrowed range_ from http://purl.obolibrary.org/obo/CHEBI_24431 to http://purl.obolibrary.org/obo/CHEBI_51143 ('nitrogen molecular entity'). The earlier CHEBI:24431 root was used as a safe default during bulk un-deprecation (PR #54); the more specific CHEBI subclass better reflects the predicate's intended substrates.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:2000047",
    "label": "does not use as sulfur source",
    "definition": "An OBJECT_PROPERTY asserting that an organism does NOT use a given chemical as a source of sulfur for biosynthesis. Negation companion of 'uses as sulfur source'.",
    "definition_source": "PMID:21413255",
    "trait_category": "METABOLISM",
    "term_kind": "OBJECT_PROPERTY",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:2000001"
    ],
    "synonyms": [
      {
        "synonym_text": "sulfur source",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "domain": "https://w3id.org/metpo/1000525",
    "range_": "http://purl.obolibrary.org/obo/CHEBI_26835",
    "evidence": [
      {
        "reference": "PMID:21413255",
        "snippet": "sulfur source",
        "notes": "Microbial-physiology reference supports 'does not use as sulfur source' as a canonical predicate composed with a CHEBI-class chemical object at assertion time."
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.973242+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (OBJECT_PROPERTY)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic chemical-use relation carrier; later replacement should use more specific trait records that combine the relation with the chemical, metabolic role, growth condition, and positive or negative usage context.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-16T08:50:00-07:00",
        "curator": "claude",
        "action": "UNDEPRECATED_AS_COMPOSITION_PRIMITIVE",
        "changes": "Restored from DEPRECATED to REVIEWED under the predicate+class composition pattern (intended use: <organism> + this predicate + CHEBI chemical class). Added DOI/PMID-backed definition, evidence, and explicit domain/range slots.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-16T09:35:00-07:00",
        "curator": "claude",
        "action": "TIGHTENED_RANGE_TO_CHEBI_SUBCLASS",
        "changes": "Narrowed range_ from http://purl.obolibrary.org/obo/CHEBI_24431 to http://purl.obolibrary.org/obo/CHEBI_26835 ('sulfur molecular entity'). The earlier CHEBI:24431 root was used as a safe default during bulk un-deprecation (PR #54); the more specific CHEBI subclass better reflects the predicate's intended substrates.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:2000021",
    "label": "does not use for aerobic catabolization",
    "definition": "An OBJECT_PROPERTY asserting that an organism does NOT catabolise a given substrate under aerobic conditions. Negation companion of 'uses for aerobic catabolization'.",
    "definition_source": "DOI:10.1146/annurev.micro.55.1.485",
    "trait_category": "METABOLISM",
    "term_kind": "OBJECT_PROPERTY",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:2000001"
    ],
    "synonyms": [
      {
        "synonym_text": "aerobic catabolization",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "domain": "https://w3id.org/metpo/1000525",
    "range_": "http://purl.obolibrary.org/obo/CHEBI_24431",
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev.micro.55.1.485",
        "snippet": "aerobic catabolism",
        "notes": "Microbial-physiology reference supports 'does not use for aerobic catabolization' as a canonical predicate composed with a CHEBI-class chemical object at assertion time."
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.959733+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (OBJECT_PROPERTY)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic negative use-context relation carrier; later replacement should use more specific trait records that combine the relation with the chemical, growth or respiration context, experimental condition, and negative usage evidence.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-16T08:50:00-07:00",
        "curator": "claude",
        "action": "UNDEPRECATED_AS_COMPOSITION_PRIMITIVE",
        "changes": "Restored from DEPRECATED to REVIEWED under the predicate+class composition pattern (intended use: <organism> + this predicate + CHEBI chemical class). Added DOI/PMID-backed definition, evidence, and explicit domain/range slots.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:2000022",
    "label": "does not use for aerobic growth",
    "definition": "An OBJECT_PROPERTY asserting that an organism does NOT grow under aerobic conditions using a given chemical. Negation companion of 'uses for aerobic growth'.",
    "definition_source": "DOI:10.1146/annurev.micro.55.1.485",
    "trait_category": "METABOLISM",
    "term_kind": "OBJECT_PROPERTY",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:2000001"
    ],
    "synonyms": [
      {
        "synonym_text": "aerobic growth",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "domain": "https://w3id.org/metpo/1000525",
    "range_": "http://purl.obolibrary.org/obo/CHEBI_24431",
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev.micro.55.1.485",
        "snippet": "aerobic growth",
        "notes": "Microbial-physiology reference supports 'does not use for aerobic growth' as a canonical predicate composed with a CHEBI-class chemical object at assertion time."
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.960272+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (OBJECT_PROPERTY)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic negative use-context relation carrier; later replacement should use more specific trait records that combine the relation with the chemical, growth or respiration context, experimental condition, and negative usage evidence.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-16T08:50:00-07:00",
        "curator": "claude",
        "action": "UNDEPRECATED_AS_COMPOSITION_PRIMITIVE",
        "changes": "Restored from DEPRECATED to REVIEWED under the predicate+class composition pattern (intended use: <organism> + this predicate + CHEBI chemical class). Added DOI/PMID-backed definition, evidence, and explicit domain/range slots.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:2000023",
    "label": "does not use for anaerobic catabolization",
    "definition": "An OBJECT_PROPERTY asserting that an organism does NOT catabolise a given substrate under anaerobic conditions. Negation companion of 'uses for anaerobic catabolization'.",
    "definition_source": "DOI:10.1146/annurev.micro.55.1.485",
    "trait_category": "METABOLISM",
    "term_kind": "OBJECT_PROPERTY",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:2000001"
    ],
    "synonyms": [
      {
        "synonym_text": "anaerobic catabolization",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "domain": "https://w3id.org/metpo/1000525",
    "range_": "http://purl.obolibrary.org/obo/CHEBI_24431",
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev.micro.55.1.485",
        "snippet": "anaerobic catabolism",
        "notes": "Microbial-physiology reference supports 'does not use for anaerobic catabolization' as a canonical predicate composed with a CHEBI-class chemical object at assertion time."
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.960797+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (OBJECT_PROPERTY)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic negative use-context relation carrier; later replacement should use more specific trait records that combine the relation with the chemical, growth or respiration context, experimental condition, and negative usage evidence.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-16T08:50:00-07:00",
        "curator": "claude",
        "action": "UNDEPRECATED_AS_COMPOSITION_PRIMITIVE",
        "changes": "Restored from DEPRECATED to REVIEWED under the predicate+class composition pattern (intended use: <organism> + this predicate + CHEBI chemical class). Added DOI/PMID-backed definition, evidence, and explicit domain/range slots.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:2000024",
    "label": "does not use for anaerobic growth",
    "definition": "An OBJECT_PROPERTY asserting that an organism does NOT grow under anaerobic conditions using a given chemical. Negation companion of 'uses for anaerobic growth'.",
    "definition_source": "DOI:10.1146/annurev.micro.55.1.485",
    "trait_category": "METABOLISM",
    "term_kind": "OBJECT_PROPERTY",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:2000001"
    ],
    "synonyms": [
      {
        "synonym_text": "anaerobic growth",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "domain": "https://w3id.org/metpo/1000525",
    "range_": "http://purl.obolibrary.org/obo/CHEBI_24431",
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev.micro.55.1.485",
        "snippet": "anaerobic growth",
        "notes": "Microbial-physiology reference supports 'does not use for anaerobic growth' as a canonical predicate composed with a CHEBI-class chemical object at assertion time."
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.961343+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (OBJECT_PROPERTY)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic negative use-context relation carrier; later replacement should use more specific trait records that combine the relation with the chemical, growth or respiration context, experimental condition, and negative usage evidence.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-16T08:50:00-07:00",
        "curator": "claude",
        "action": "UNDEPRECATED_AS_COMPOSITION_PRIMITIVE",
        "changes": "Restored from DEPRECATED to REVIEWED under the predicate+class composition pattern (intended use: <organism> + this predicate + CHEBI chemical class). Added DOI/PMID-backed definition, evidence, and explicit domain/range slots.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:2000025",
    "label": "does not use for anaerobic growth in the dark",
    "definition": "An OBJECT_PROPERTY asserting that an organism does NOT grow under anaerobic conditions without illumination using a given chemical. Negation companion of 'uses for anaerobic growth in the dark'.",
    "definition_source": "DOI:10.1146/annurev.micro.55.1.485",
    "trait_category": "METABOLISM",
    "term_kind": "OBJECT_PROPERTY",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:2000001"
    ],
    "synonyms": [
      {
        "synonym_text": "anaerobic growth in the dark",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "domain": "https://w3id.org/metpo/1000525",
    "range_": "http://purl.obolibrary.org/obo/CHEBI_24431",
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev.micro.55.1.485",
        "snippet": "anaerobic",
        "notes": "Microbial-physiology reference supports 'does not use for anaerobic growth in the dark' as a canonical predicate composed with a CHEBI-class chemical object at assertion time."
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.962053+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (OBJECT_PROPERTY)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic negative use-context relation carrier; later replacement should use more specific trait records that combine the relation with the chemical, growth or respiration context, experimental condition, and negative usage evidence.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-16T08:50:00-07:00",
        "curator": "claude",
        "action": "UNDEPRECATED_AS_COMPOSITION_PRIMITIVE",
        "changes": "Restored from DEPRECATED to REVIEWED under the predicate+class composition pattern (intended use: <organism> + this predicate + CHEBI chemical class). Added DOI/PMID-backed definition, evidence, and explicit domain/range slots.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:2000026",
    "label": "does not use for anaerobic growth with light",
    "definition": "An OBJECT_PROPERTY asserting that an organism does NOT grow under anaerobic conditions with illumination using a given chemical. Negation companion of 'uses for anaerobic growth with light'.",
    "definition_source": "DOI:10.1146/annurev.micro.55.1.485",
    "trait_category": "METABOLISM",
    "term_kind": "OBJECT_PROPERTY",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:2000001"
    ],
    "synonyms": [
      {
        "synonym_text": "anaerobic growth with light",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "domain": "https://w3id.org/metpo/1000525",
    "range_": "http://purl.obolibrary.org/obo/CHEBI_24431",
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev.micro.55.1.485",
        "snippet": "phototrophic",
        "notes": "Microbial-physiology reference supports 'does not use for anaerobic growth with light' as a canonical predicate composed with a CHEBI-class chemical object at assertion time."
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.962572+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (OBJECT_PROPERTY)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic negative use-context relation carrier; later replacement should use more specific trait records that combine the relation with the chemical, growth or respiration context, experimental condition, and negative usage evidence.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-16T08:50:00-07:00",
        "curator": "claude",
        "action": "UNDEPRECATED_AS_COMPOSITION_PRIMITIVE",
        "changes": "Restored from DEPRECATED to REVIEWED under the predicate+class composition pattern (intended use: <organism> + this predicate + CHEBI chemical class). Added DOI/PMID-backed definition, evidence, and explicit domain/range slots.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:2000038",
    "label": "does not use for growth",
    "definition": "An OBJECT_PROPERTY asserting that an organism does NOT grow on a given chemical. Negation companion of 'uses for growth'.",
    "definition_source": "PMID:21413255",
    "trait_category": "METABOLISM",
    "term_kind": "OBJECT_PROPERTY",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:2000001"
    ],
    "synonyms": [
      {
        "synonym_text": "growth",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "domain": "https://w3id.org/metpo/1000525",
    "range_": "http://purl.obolibrary.org/obo/CHEBI_24431",
    "evidence": [
      {
        "reference": "PMID:21413255",
        "snippet": "growth",
        "notes": "Microbial-physiology reference supports 'does not use for growth' as a canonical predicate composed with a CHEBI-class chemical object at assertion time."
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.968917+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (OBJECT_PROPERTY)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic negative use-context relation carrier; later replacement should use more specific trait records that combine the relation with the chemical, growth or respiration context, experimental condition, and negative usage evidence.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-16T08:50:00-07:00",
        "curator": "claude",
        "action": "UNDEPRECATED_AS_COMPOSITION_PRIMITIVE",
        "changes": "Restored from DEPRECATED to REVIEWED under the predicate+class composition pattern (intended use: <organism> + this predicate + CHEBI chemical class). Added DOI/PMID-backed definition, evidence, and explicit domain/range slots.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:2000046",
    "label": "does not use for respiration",
    "definition": "An OBJECT_PROPERTY asserting that an organism does NOT use a given chemical in respiratory metabolism. Negation companion of 'uses for respiration'.",
    "definition_source": "DOI:10.1146/annurev.micro.55.1.485",
    "trait_category": "METABOLISM",
    "term_kind": "OBJECT_PROPERTY",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:2000001"
    ],
    "synonyms": [
      {
        "synonym_text": "respiration",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "domain": "https://w3id.org/metpo/1000525",
    "range_": "http://purl.obolibrary.org/obo/CHEBI_24431",
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev.micro.55.1.485",
        "snippet": "respiration",
        "notes": "Microbial-physiology reference supports 'does not use for respiration' as a canonical predicate composed with a CHEBI-class chemical object at assertion time."
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.972783+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (OBJECT_PROPERTY)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic negative use-context relation carrier; later replacement should use more specific trait records that combine the relation with the chemical, growth or respiration context, experimental condition, and negative usage evidence.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-16T08:50:00-07:00",
        "curator": "claude",
        "action": "UNDEPRECATED_AS_COMPOSITION_PRIMITIVE",
        "changes": "Restored from DEPRECATED to REVIEWED under the predicate+class composition pattern (intended use: <organism> + this predicate + CHEBI chemical class). Added DOI/PMID-backed definition, evidence, and explicit domain/range slots.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:2000041",
    "label": "does not use in other way",
    "definition": "Catch-all negation OBJECT_PROPERTY asserting that an organism does NOT use a given chemical in any way not covered by the more specific predicates. Negation companion of 'uses in other way'.",
    "definition_source": "DOI:10.1146/annurev.micro.55.1.485",
    "trait_category": "METABOLISM",
    "term_kind": "OBJECT_PROPERTY",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:2000001"
    ],
    "synonyms": [
      {
        "synonym_text": "other",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "domain": "https://w3id.org/metpo/1000525",
    "range_": "http://purl.obolibrary.org/obo/CHEBI_24431",
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev.micro.55.1.485",
        "snippet": "chemical use",
        "notes": "Microbial-physiology reference supports 'does not use in other way' as a canonical predicate composed with a CHEBI-class chemical object at assertion time."
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.970382+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (OBJECT_PROPERTY)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic negative biochemical conversion or activity relation carrier; later replacement should use more specific trait records that combine the relation with the substrate, product, enzyme or activity target, assay context, growth condition, and negative evidence.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-16T08:50:00-07:00",
        "curator": "claude",
        "action": "UNDEPRECATED_AS_COMPOSITION_PRIMITIVE",
        "changes": "Restored from DEPRECATED to REVIEWED under the predicate+class composition pattern (intended use: <organism> + this predicate + CHEBI chemical class). Added DOI/PMID-backed definition, evidence, and explicit domain/range slots.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000805",
    "label": "Electron transfer",
    "definition": "A metabolism in which electrons are transferred from an electron donor to an electron acceptor.",
    "definition_source": "DOI:10.1016/j.bbabio.2008.09.008",
    "trait_category": "METABOLISM",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000060"
    ],
    "created_by": "Jed Dongjin Kim-Ozaeta",
    "evidence": [
      {
        "reference": "DOI:10.1016/j.bbabio.2008.09.008",
        "snippet": "electron transfer process",
        "notes": "Review supports electron donor-to-acceptor flow in membrane respiratory chains."
      },
      {
        "reference": "DOI:10.1038/nrmicro.2016.93",
        "snippet": "c-type cytochromes and microbial nanowires",
        "notes": "Review supports extracellular electron-transfer mechanisms."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:35554",
        "taxon_label": "Geobacter sulfurreducens",
        "note": "extracellular electron transfer via pili/cytochromes",
        "reference": "DOI:10.1126/science.1088727"
      },
      {
        "taxon_id": "NCBITaxon:70863",
        "taxon_label": "Shewanella oneidensis",
        "note": "extracellular electron transfer to metals",
        "reference": "DOI:10.1038/nbt749"
      },
      {
        "taxon_id": "NCBITaxon:211586",
        "taxon_label": "Shewanella oneidensis MR-1",
        "note": "Strain-level extracellular electron-transfer model paired to its MtrC surface decaheme cytochrome.",
        "reference": "DOI:10.1073/pnas.0604517103"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "electron_transfer_redox_carriers",
        "title": "Electron transfer redox carrier mechanism",
        "description": "DOI-backed graph for electron donor/acceptor chemistry, redox proteins, membrane electron transport, and extracellular electron-transfer structures.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "This is a composite graph spanning respiratory-chain and extracellular electron-transfer modules. The MtrC example supports the S. oneidensis MR-1 extracellular branch only; it does not ground the generic respiratory complexes or imply that MtrC participates in all electron-transfer traits.",
        "nodes": [
          {
            "node_id": "electron_transfer_trait",
            "label": "Electron transfer",
            "node_type": "TRAIT",
            "grounding": "METPO:1000805",
            "description": "Metabolic electron movement from donor to acceptor."
          },
          {
            "node_id": "electron_donor",
            "label": "electron donor",
            "node_type": "CHEMICAL",
            "description": "Reduced substrate or carrier supplying electrons.",
            "grounding": "CHEBI:15022"
          },
          {
            "node_id": "electron_acceptor",
            "label": "electron acceptor",
            "node_type": "CHEMICAL",
            "description": "Oxidized substrate or carrier receiving electrons."
          },
          {
            "node_id": "redox_protein",
            "label": "redox protein",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Protein carrier mediating electron transfer.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Redox protein is an umbrella label spanning unrelated carrier families and activities, so no single exact GO or InterPro term represents this generic node."
          },
          {
            "node_id": "cytochrome",
            "label": "c-type cytochrome",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Heme-containing electron-transfer protein.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "The broad c-type cytochrome label spans many monoheme and multiheme families; the MtrC example illustrates one source-backed extracellular branch without narrowing the generic node to that family.",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:Q8EG34",
                "protein_label": "Extracellular iron oxide respiratory system surface decaheme cytochrome c component MtrC",
                "gene_symbol": "mtrC",
                "taxon_id": "NCBITaxon:211586",
                "taxon_label": "Shewanella oneidensis MR-1",
                "entry_status": "UNREVIEWED",
                "proteome_id": "UP000008186",
                "retrieved_on": "2026-10-22",
                "entry_version": 126,
                "sequence_version": 1,
                "role": "MtrC-family c-type cytochrome mediating extracellular electron transfer to Fe(III) and Mn(IV) acceptors in S. oneidensis MR-1.",
                "evidence": [
                  {
                    "reference": "DOI:10.1073/pnas.0604517103",
                    "snippet": "The decaheme c-type cytochrome MtrC (SO1778) had been implicated in efficient reduction of Fe(III) and Mn(IV) by MR-1.",
                    "notes": "The primary study supports the extracellular electron-transfer role. UniProtKB Q8EG34 is the exact unreviewed MtrC entry from reference proteome UP000008186 and verifies the strain taxon."
                  }
                ]
              }
            ]
          },
          {
            "node_id": "membrane_electron_transport_chain",
            "label": "membrane electron transport chain",
            "node_type": "PATHWAY",
            "description": "Ordered redox chain in a biological membrane.",
            "grounding": "GO:0022900"
          },
          {
            "node_id": "extracellular_electron_transfer",
            "label": "extracellular electron transfer",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Electron exchange between cells and extracellular minerals, electrodes, or cells."
          },
          {
            "node_id": "microbial_nanowire",
            "label": "microbial nanowire",
            "node_type": "CELLULAR_LOCALIZATION",
            "description": "Conductive extracellular structure implicated in long-range electron transfer."
          },
          {
            "node_id": "terminal_acceptor_reduction",
            "label": "terminal acceptor reduction",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "Reduction of the final electron acceptor."
          },
          {
            "node_id": "complex_i",
            "label": "NADH dehydrogenase (Complex I)",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Proton-translocating NADH:ubiquinone oxidoreductase entry point of the respiratory chain.",
            "grounding": "GO:0030964"
          },
          {
            "node_id": "ubiquinone",
            "label": "ubiquinone",
            "node_type": "CHEMICAL",
            "description": "Membrane quinone electron carrier reduced to ubiquinol in the respiratory chain."
          },
          {
            "node_id": "ubiquinol",
            "label": "ubiquinol",
            "node_type": "CHEMICAL",
            "description": "Reduced form of ubiquinone that donates electrons to the cytochrome bc1 complex.",
            "grounding": "CHEBI:17976"
          },
          {
            "node_id": "cytochrome_bc1",
            "label": "cytochrome bc1 complex",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Ubiquinol:cytochrome c oxidoreductase (Complex III) of the respiratory chain.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "The graph uses a bacterial respiratory bc1-complex label, while the reviewed candidate terms were either molecular-function activities or compartment-specific complexes rather than an exact taxon-agnostic complex."
          },
          {
            "node_id": "cytochrome_c",
            "label": "cytochrome c",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Mobile electron carrier shuttling electrons from bc1 to the terminal oxidase.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Cytochrome c is a broad protein class containing multiple families; this graph does not identify one exact family or chain architecture."
          },
          {
            "node_id": "terminal_oxidase",
            "label": "terminal oxidase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Terminal respiratory oxidase (Complex IV) that reduces the final acceptor.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Terminal oxidase is deliberately broad across heme-copper and quinol oxidase families; the cited graph does not identify one exact family or multisubunit complex term."
          },
          {
            "node_id": "molecular_oxygen",
            "label": "oxygen",
            "node_type": "CHEMICAL",
            "description": "Molecular oxygen, terminal electron acceptor in aerobic respiration."
          },
          {
            "node_id": "proton_motive_force",
            "label": "proton motive force",
            "node_type": "STATE",
            "description": "Transmembrane electrochemical proton gradient generated by respiratory electron transfer.",
            "grounding": "METPO:1007500"
          }
        ],
        "edges": [
          {
            "subject": "electron_transfer_trait",
            "predicate": "transfers electrons from",
            "object": "electron_donor",
            "description": "Electron transfer starts from an electron donor.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.bbabio.2008.09.008",
                "snippet": "free energy of a redox reaction",
                "notes": "Supports donor-side redox chemistry."
              }
            ]
          },
          {
            "subject": "electron_donor",
            "predicate": "transfers electrons to",
            "object": "electron_acceptor",
            "description": "Electron transfer moves reducing equivalents from donor to acceptor.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.bbabio.2008.09.008",
                "snippet": "electron transfer process",
                "notes": "Supports donor-to-acceptor electron flow."
              }
            ],
            "predicate_id": "METPO:2007403"
          },
          {
            "subject": "redox_protein",
            "predicate": "mediates transfer between",
            "object": "electron_donor",
            "description": "Redox proteins mediate biological electron-transfer steps.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro.2016.93",
                "snippet": "molecular mechanisms ... exchange electrons",
                "notes": "Supports protein-mediated microbial electron exchange."
              }
            ]
          },
          {
            "subject": "cytochrome",
            "predicate": "example of",
            "object": "redox_protein",
            "description": "c-type cytochromes are electron-transfer proteins.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro.2016.93",
                "snippet": "c-type cytochromes",
                "notes": "Supports c-type cytochromes as electron-transfer components."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "membrane_electron_transport_chain",
            "predicate": "performs",
            "object": "terminal_acceptor_reduction",
            "description": "Electron transport chains deliver electrons to terminal acceptors.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.bbabio.2008.09.008",
                "snippet": "membrane-bound electron transport chain",
                "notes": "Supports membrane redox chains as electron-transfer machinery."
              }
            ]
          },
          {
            "subject": "extracellular_electron_transfer",
            "predicate": "uses structure",
            "object": "microbial_nanowire",
            "description": "Some microbes use conductive appendages or nanowires for extracellular electron transfer.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro.2016.93",
                "snippet": "microbial nanowires",
                "notes": "Supports nanowires as an extracellular electron-transfer mechanism."
              }
            ]
          },
          {
            "subject": "extracellular_electron_transfer",
            "predicate": "uses protein",
            "object": "cytochrome",
            "description": "Extracellular electron transfer can use c-type cytochromes.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro.2016.93",
                "snippet": "c-Type cytochromes",
                "notes": "Supports c-type cytochromes in extracellular electron exchange."
              }
            ]
          },
          {
            "subject": "complex_i",
            "predicate": "reduces",
            "object": "ubiquinone",
            "description": "Complex I oxidizes NADH and reduces ubiquinone in the respiratory chain.",
            "evidence": [
              {
                "reference": "DOI:10.3390/ijms252413421",
                "notes": "Complex I oxidizes NADH using ubiquinone (broad bacterial respiratory ETC)."
              }
            ],
            "predicate_id": "METPO:2007802"
          },
          {
            "subject": "complex_i",
            "predicate": "translocates",
            "object": "proton_motive_force",
            "description": "Complex I couples NADH:ubiquinone oxidoreduction to transmembrane proton translocation, generating the PMF.",
            "evidence": [
              {
                "reference": "DOI:10.3390/ijms252413421",
                "notes": "Coupling of redox reaction to vectorial translocation of four protons to generate proton motive force."
              }
            ]
          },
          {
            "subject": "ubiquinol",
            "predicate": "donates electrons to",
            "object": "cytochrome_bc1",
            "description": "Ubiquinol delivers electrons from the quinone pool to the cytochrome bc1 complex.",
            "evidence": [
              {
                "reference": "DOI:10.1073/pnas.2307093120",
                "notes": "UQH2:cyt c oxidoreductase (Complex III); electrons flow from quinone pool to the bc1 complex."
              }
            ],
            "predicate_id": "METPO:2007403"
          },
          {
            "subject": "cytochrome_bc1",
            "predicate": "transfers electrons to",
            "object": "cytochrome_c",
            "description": "The bc1 complex passes electrons onward to mobile cytochrome c.",
            "evidence": [
              {
                "reference": "DOI:10.1073/pnas.2307093120",
                "notes": "Electrons flow to the bc1 complex and onward via cytochrome c."
              }
            ],
            "predicate_id": "METPO:2007403"
          },
          {
            "subject": "cytochrome_c",
            "predicate": "transfers electrons to",
            "object": "terminal_oxidase",
            "description": "Cytochrome c delivers electrons to the terminal oxidase (Complex IV).",
            "evidence": [
              {
                "reference": "DOI:10.1073/pnas.2307093120",
                "notes": "Onward via cytochrome c to terminal oxidases (Complex IV) that reduce O2 to H2O."
              }
            ],
            "predicate_id": "METPO:2007403"
          },
          {
            "subject": "terminal_oxidase",
            "predicate": "reduces",
            "object": "molecular_oxygen",
            "description": "The terminal oxidase reduces molecular oxygen to water in aerobic respiration.",
            "evidence": [
              {
                "reference": "DOI:10.1073/pnas.2307093120",
                "notes": "Terminal oxidases (Complex IV) reduce O2 to H2O (broad aerobic respiration edge)."
              }
            ],
            "predicate_id": "METPO:2007802"
          },
          {
            "subject": "membrane_electron_transport_chain",
            "predicate": "contributes to",
            "object": "electron_transfer_trait",
            "description": "A membrane electron-transport chain is a principal cellular electron-transfer system.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.bbabio.2008.09.008",
                "snippet": "membrane-bound electron transport chain",
                "notes": "Verified against the free public article text."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "complex_i",
            "predicate": "participates in",
            "object": "membrane_electron_transport_chain",
            "description": "Complex I is an entry enzyme of the membrane respiratory electron-transport chain.",
            "evidence": [
              {
                "reference": "DOI:10.3390/ijms252413421",
                "snippet": "Complex I oxidizes NADH using ubiquinone",
                "notes": "Verified against the free public article text."
              }
            ],
            "predicate_id": "biolink:participates_in"
          },
          {
            "subject": "cytochrome_c",
            "predicate": "example of",
            "object": "cytochrome",
            "description": "Cytochrome c is a mobile member of the cytochrome electron-carrier class.",
            "evidence": [
              {
                "reference": "DOI:10.1073/pnas.2307093120",
                "snippet": "electrons flow to the bc1 complex and onward via cytochrome c",
                "notes": "Verified against the free public article text."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.913647+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-08T00:00:00-07:00",
        "curator": "codex",
        "action": "ADDED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed causal graph for donor-to-acceptor electron transfer, redox proteins, cytochromes, membrane chains, and extracellular nanowire-associated transfer.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T08:21:49Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (rdfs:subClassOf\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T21:30:06Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007403\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T05:05:14Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A076EJF0\u00d71, UniProtKB:A0A072TMC1\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T08:14:32Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:17499\u00d71, GO:0022900\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-15T07:19:08Z",
        "curator": "claude",
        "action": "FIX_NODE_GROUNDING_CURIE",
        "changes": "Overwrote 1 causal-node grounding(s) to corrected CURIEs (phase-2 id-label fix; verified vs OAK).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 6 evidence-backed generic edges (8 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:12Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 5 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007403\u00d73, METPO:2000017\u00d72).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:32Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:17976\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-26T07:15:18Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A061JR98\u00d71, UniProtKB:A0A2U9ILE5\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:21:11Z",
        "curator": "claude",
        "action": "RETRACT_DEAD_UNIPROT_GROUNDINGS",
        "changes": "Retracted 3 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T02:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES_PART2",
        "changes": "Re-grounded 2 causal edge(s) off microbe-domain METPO predicates onto their causal-graph counterparts (2 to reduces), issue 301 part 2. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Each replacement is a 1:1 mirror of its source predicate that changes only the domain, so the claim each edge makes is unchanged and directions are unchanged. The replacements are proposed in proposals/metpo_traitmech_v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-15T02:00:00Z",
        "curator": "claude",
        "action": "NORMALISE_NODE_TYPE",
        "changes": "Normalised causal-node type(s) so one node_id means one thing corpus-wide (issue 356): proton_motive_force: BIOLOGICAL_PROCESS -> STATE. The schema's OWN example of STATE: 'a bioenergetic or molecular state of the cell (e.g. proton motive force ...) ... the state is the gradient / steady-value, not its establishment'. All 35 occurrences describe the gradient -- every description across all four types reads 'electrochemical proton gradient', including the 13 typed BIOLOGICAL_PROCESS ('Transmembrane electrochemical gradient generated by respiration'), which name the gradient and its provenance rather than the generating process. Nothing here means the establishment, so this is a retype and not a rename; records that DO mean the process already use a separate id (proton_motive_force_generation in ph_delta.yaml). Also settles the one edge #356 was filed for: phototrophic.yaml's CAPACITY typing was blocking `powers` (METPO:2007900), which is gated to BIOLOGICAL_PROCESS|STATE.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-17T02:00:00Z",
        "curator": "claude",
        "action": "NORMALISE_NODE_SENSE",
        "changes": "One node_id per SENSE (issues 356, 384): molecular_oxygen is the chemical sense here. The molecule, not the condition \u2014 the dioxygen participating in the reaction the graph describes. Normalised onto molecular_oxygen, the id 20 other chemical occurrences already use, so one id means one sense corpus-wide (issues 356, 384).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-20T07:10:35Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (METPO:1007500\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-22T04:26:15Z",
        "curator": "codex",
        "action": "REVIEW_UNIPROT_INSTANCE_GROUNDINGS",
        "changes": "Reviewed 1 organism-specific UniProtKB grounding(s): replaced 0 with taxon-agnostic GO/InterPro terms and retracted 1 to label-only where no exact semantic term was supported (docs/GROUNDING_POLICY.md).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-24T08:15:00Z",
        "curator": "codex",
        "action": "CURATE_PROTEIN_TAXON_EXAMPLE",
        "changes": "Added a DOI-backed S. oneidensis MR-1 MtrC example, grounded Complex I to the current GO complex term, recorded explicit reviewed label-only dispositions for the remaining broad protein labels, and documented the graph's composite respiratory/EET scope.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T12:15:00Z",
        "curator": "codex",
        "action": "CONNECT_CAUSAL_GRAPH_COMPONENTS",
        "changes": "Resolved issue #183 graph fragmentation (4 components to 1) with 3 public-source connector(s). No paid research service was called.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-22T01:35:00Z",
        "curator": "claude",
        "action": "REFRESH_UNIPROT_ENTRY_VERSION",
        "changes": "Refreshed UniProtKB entry_version against live UniProt REST on 2026-10-22: UniProtKB:Q8EG34 (125 -> 126 on cytochrome).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:2000301",
    "label": "enzyme activity analyzed",
    "definition": "An OBJECT_PROPERTY relating an organism to an enzyme (material entity) whose catalytic activity has been experimentally assayed for that organism. Intended use is predicate + class composition at assertion time with a METPO enzyme class (METPO:1000527 or its subclass) as the object.",
    "definition_source": "PMID:21413255",
    "trait_category": "METABOLISM",
    "term_kind": "OBJECT_PROPERTY",
    "mapping_status": "REVIEWED",
    "synonyms": [
      {
        "synonym_text": "Physiology and metabolism.enzymes.[].activity",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "domain": "https://w3id.org/metpo/1000525",
    "range_": "https://w3id.org/metpo/1000527",
    "evidence": [
      {
        "reference": "PMID:21413255",
        "snippet": "enzyme activity",
        "notes": "Microbial-physiology reference supports 'enzyme activity analyzed' as a canonical predicate relating an organism to an enzyme/activity class, composed at assertion time."
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.990561+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (OBJECT_PROPERTY)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic metabolism relation carrier; later replacement should use more specific trait records that combine the relation with the chemical, phenotype, quality, compartment, enzyme or activity target, growth context, measurement, or other entity.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-16T08:50:00-07:00",
        "curator": "claude",
        "action": "UNDEPRECATED_AS_COMPOSITION_PRIMITIVE",
        "changes": "Restored from DEPRECATED to REVIEWED under the predicate+class composition pattern (intended use: <organism> + this predicate + CHEBI chemical class). Added DOI/PMID-backed definition, evidence, and explicit domain/range slots.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000028",
    "label": "ethanol fermentation",
    "definition": "A fermentation in which pyruvate is decarboxylated to acetaldehyde (releasing CO2) and then reduced by NADH to ethanol, regenerating NAD+ for glycolysis. Characteristic of yeasts and the bacterium Zymomonas mobilis.",
    "definition_source": "DOI:10.3389/fmicb.2021.703525",
    "trait_category": "METABOLISM",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1002005"
    ],
    "synonyms": [
      {
        "synonym_text": "alcoholic fermentation",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.3390/molecules31020333"
      },
      {
        "synonym_text": "glucose fermentation to ethanol",
        "synonym_type": "EXACT_SYNONYM",
        "source": "http://purl.obolibrary.org/obo/go/releases/2026-07-26/go-basic.obo"
      }
    ],
    "xrefs": [
      "GO:0019655"
    ],
    "evidence": [
      {
        "reference": "DOI:10.3390/molecules31020333",
        "notes": "Review of classical fermentations describes the alcoholic (ethanol) pathway in which pyruvate is decarboxylated and reduced to ethanol."
      },
      {
        "reference": "DOI:10.3389/fmicb.2021.703525",
        "notes": "Review of fermentative energy conservation supports ethanol as an NADH-reoxidizing fermentation end product."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:542",
        "taxon_label": "Zymomonas mobilis",
        "note": "Canonical bacterial ethanologen (Entner-Doudoroff route to ethanol).",
        "reference": "PMID:27629544"
      },
      {
        "taxon_id": "NCBITaxon:264203",
        "taxon_label": "Zymomonas mobilis subsp. mobilis ZM4",
        "note": "Strain-level exemplar used to establish the role of its pyruvate decarboxylase in directing pyruvate into ethanol production.",
        "reference": "DOI:10.1186/s12934-024-02419-9"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "ethanol_fermentation_pyruvate_to_ethanol",
        "title": "Ethanol (alcoholic) fermentation converts pyruvate to ethanol + CO2",
        "description": "Evidence-backed causal sketch linking pyruvate decarboxylation and NADH-driven ethanol production to NAD+ regeneration.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "Retains the two directly catalyzed steps from pyruvate to ethanol and their redox consequence; the protein exemplar is restricted to the PDC step demonstrated in Z. mobilis ZM4.",
        "nodes": [
          {
            "node_id": "ethanol_fermentation_trait",
            "label": "ethanol fermentation",
            "node_type": "TRAIT",
            "grounding": "traitmech:000028",
            "description": "Alcoholic fermentation producing ethanol and CO2."
          },
          {
            "node_id": "fermentation_process",
            "label": "fermentation",
            "node_type": "BIOLOGICAL_PROCESS",
            "grounding": "GO:0006113",
            "description": "ATP-yielding catabolism with organic terminal acceptors."
          },
          {
            "node_id": "ethanol",
            "label": "ethanol",
            "node_type": "CHEMICAL",
            "description": "Reduced end product regenerating NAD+ from NADH.",
            "grounding": "CHEBI:16236"
          },
          {
            "node_id": "pyruvate",
            "label": "pyruvate",
            "node_type": "CHEMICAL",
            "description": "Glycolytic end product decarboxylated in ethanol fermentation.",
            "grounding": "CHEBI:15361"
          },
          {
            "node_id": "pyruvate_decarboxylase",
            "label": "pyruvate decarboxylase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Enzyme (EC 4.1.1.1) decarboxylating pyruvate to acetaldehyde and CO2.",
            "grounding": "GO:0004737",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:P06672",
                "protein_label": "Pyruvate decarboxylase",
                "gene_symbol": "pdc",
                "taxon_id": "NCBITaxon:264203",
                "taxon_label": "Zymomonas mobilis subsp. mobilis ZM4",
                "entry_status": "REVIEWED",
                "proteome_id": "UP000001173",
                "retrieved_on": "2026-10-22",
                "entry_version": 174,
                "sequence_version": 1,
                "role": "Catalyzes the gateway decarboxylation of pyruvate to acetaldehyde in the ethanol-production pathway; this accession is a protein instance, not the taxon-agnostic grounding for the node.",
                "evidence": [
                  {
                    "reference": "DOI:10.1186/s12934-024-02419-9",
                    "snippet": "The key enzyme in the ethanol production pathway is the pyruvate decarboxylase",
                    "notes": "The study used Z. mobilis ZM4 and experimentally controlled the native pdc gateway; UniProtKB P06672 verifies the protein identity and strain taxonomy."
                  }
                ]
              }
            ]
          },
          {
            "node_id": "acetaldehyde",
            "label": "acetaldehyde",
            "node_type": "CHEMICAL",
            "description": "Intermediate produced from pyruvate and reduced to ethanol.",
            "grounding": "CHEBI:15343"
          },
          {
            "node_id": "carbon_dioxide",
            "label": "carbon dioxide",
            "node_type": "CHEMICAL",
            "description": "CO2 released during pyruvate decarboxylation.",
            "grounding": "CHEBI:16526"
          },
          {
            "node_id": "alcohol_dehydrogenase",
            "label": "alcohol dehydrogenase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Enzyme (EC 1.1.1.1) reducing acetaldehyde to ethanol using NADH.",
            "grounding": "GO:0004022"
          },
          {
            "node_id": "nadh",
            "label": "NADH",
            "node_type": "CHEMICAL",
            "description": "Reduced cofactor reoxidized during ethanol formation."
          },
          {
            "node_id": "nad_plus",
            "label": "NAD+",
            "node_type": "CHEMICAL",
            "description": "Oxidized cofactor regenerated to sustain glycolysis.",
            "grounding": "CHEBI:15846"
          }
        ],
        "edges": [
          {
            "subject": "ethanol_fermentation_trait",
            "predicate": "participates in",
            "object": "fermentation_process",
            "description": "Alcoholic fermentation is a class of fermentation metabolism.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2021.703525",
                "snippet": "fermentation is defined as an anaerobic bacterial redox process of an organic substrate leading to different products",
                "notes": "Energy-conservation review supports ethanol as an NADH-reoxidizing fermentation end product."
              }
            ],
            "predicate_id": "biolink:participates_in"
          },
          {
            "subject": "ethanol_fermentation_trait",
            "predicate": "produces",
            "object": "ethanol",
            "description": "Ethanol is the characteristic end product of the pathway.",
            "evidence": [
              {
                "reference": "DOI:10.3390/molecules31020333",
                "snippet": "sugars such as glucose, fructose, and sucrose are converted into ethyl alcohol (ethanol) and carbon dioxide",
                "notes": "Classical-fermentation review describes pyruvate decarboxylation and reduction to ethanol."
              }
            ],
            "predicate_id": "METPO:2007800"
          },
          {
            "subject": "pyruvate",
            "predicate": "is substrate for",
            "object": "pyruvate_decarboxylase",
            "description": "Pyruvate is decarboxylated by pyruvate decarboxylase to acetaldehyde + CO2.",
            "evidence": [
              {
                "reference": "DOI:10.5376/be.2024.14.0025",
                "snippet": "The decarboxylation of pyruvate to acetaldehyde is catalyzed by the enzyme pyruvate decarboxylase (PDC)",
                "notes": "Pyruvate is decarboxylated to acetaldehyde by pyruvate decarboxylase (PDC), releasing CO2."
              }
            ]
          },
          {
            "subject": "pyruvate_decarboxylase",
            "predicate": "produces",
            "object": "acetaldehyde",
            "description": "Pyruvate decarboxylase yields acetaldehyde from pyruvate.",
            "evidence": [
              {
                "reference": "DOI:10.5376/be.2024.14.0025",
                "snippet": "converts pyruvate into acetaldehyde",
                "notes": "Pyruvate is decarboxylated to acetaldehyde by pyruvate decarboxylase (PDC)."
              }
            ],
            "predicate_id": "METPO:2007800"
          },
          {
            "subject": "pyruvate_decarboxylase",
            "predicate": "produces",
            "object": "carbon_dioxide",
            "description": "Decarboxylation of pyruvate releases CO2.",
            "evidence": [
              {
                "reference": "DOI:10.5376/be.2024.14.0025",
                "snippet": "This reaction releases one molecule of CO2",
                "notes": "Pyruvate is decarboxylated to acetaldehyde by pyruvate decarboxylase (PDC), releasing CO2."
              }
            ],
            "predicate_id": "METPO:2007800"
          },
          {
            "subject": "acetaldehyde",
            "predicate": "is substrate for",
            "object": "alcohol_dehydrogenase",
            "description": "Acetaldehyde is reduced to ethanol by alcohol dehydrogenase.",
            "evidence": [
              {
                "reference": "DOI:10.5376/be.2024.14.0025",
                "snippet": "reduction of acetaldehyde to ethanol, a reaction catalyzed by alcohol dehydrogenase (ADH)",
                "notes": "Acetaldehyde is reduced to ethanol by alcohol dehydrogenase (ADH)."
              }
            ]
          },
          {
            "subject": "alcohol_dehydrogenase",
            "predicate": "produces",
            "object": "ethanol",
            "description": "Alcohol dehydrogenase produces ethanol from acetaldehyde.",
            "evidence": [
              {
                "reference": "DOI:10.5376/be.2024.14.0025",
                "snippet": "The final step in ethanol fermentation involves the reduction of acetaldehyde to ethanol",
                "notes": "Acetaldehyde is reduced to ethanol by alcohol dehydrogenase (ADH)."
              }
            ],
            "predicate_id": "METPO:2007800"
          },
          {
            "subject": "alcohol_dehydrogenase",
            "predicate": "consumes",
            "object": "nadh",
            "description": "The ADH reduction step oxidizes NADH.",
            "evidence": [
              {
                "reference": "DOI:10.5376/be.2024.14.0025",
                "snippet": "regenerates NAD+ from NADH",
                "notes": "ADH reaction reoxidizes NADH, regenerating NAD+ to sustain glycolysis."
              }
            ],
            "predicate_id": "biolink:consumes"
          },
          {
            "subject": "alcohol_dehydrogenase",
            "predicate": "produces",
            "object": "nad_plus",
            "description": "NAD+ is regenerated from NADH during ethanol formation, sustaining glycolysis.",
            "evidence": [
              {
                "reference": "DOI:10.5376/be.2024.14.0025",
                "snippet": "This step also regenerates NAD+ from NADH",
                "notes": "Regenerating NAD+ from NADH to sustain glycolysis."
              }
            ],
            "predicate_id": "METPO:2007800"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-30T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate METABOLISM trait (ethanol/alcoholic fermentation); product-specific sub-variant of the existing Fermentation class (METPO:1002005).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-10T14:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (alcoholic fermentation / ethanol production) with GO node grounding and METPO/biolink predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-14T06:55:38Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:16236\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 7 evidence-backed generic edges (7 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:12Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 5 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d74, biolink:consumes\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:18Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:16526\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:32Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 3 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:15361\u00d71, CHEBI:15343\u00d71, CHEBI:15846\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-26T07:15:18Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A067Z5Y9\u00d71, UniProtKB:A0A022L3Z7\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:21:11Z",
        "curator": "claude",
        "action": "RETRACT_DEAD_UNIPROT_GROUNDINGS",
        "changes": "Retracted 2 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:23:54Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0004737\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T02:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES_PART2",
        "changes": "Re-grounded 5 causal edge(s) off microbe-domain METPO predicates onto their causal-graph counterparts (5 to produces), issue 301 part 2. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Each replacement is a 1:1 mirror of its source predicate that changes only the domain, so the claim each edge makes is unchanged and directions are unchanged. The replacements are proposed in proposals/metpo_traitmech_v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-20T07:10:35Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0004022\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-23T09:00:00Z",
        "curator": "codex",
        "action": "CURATE_PROTEIN_TAXON_EXAMPLE",
        "changes": "Reviewed the graph as mechanistic and added DOI-backed, taxon-paired UniProtKB P06672 as the Z. mobilis ZM4 pyruvate-decarboxylase exemplar.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T06:15:39Z",
        "curator": "codex",
        "action": "ADD_EXACT_ONTOLOGY_MATCH",
        "changes": "Ontology exact-match review (2026-08-25): approved exact xref(s): GO:0019655; declared exact synonym(s): 'glucose fermentation to ethanol'. Evidence is predicate-scoped in the versioned ontology snapshots; OAK cross-checked direct data, and OLS4 spot-checked release deltas and disputed hits.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-22T01:35:00Z",
        "curator": "claude",
        "action": "REFRESH_UNIPROT_ENTRY_VERSION",
        "changes": "Refreshed UniProtKB entry_version against live UniProt REST on 2026-10-22: UniProtKB:P06672 (173 -> 174 on pyruvate_decarboxylase).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:2000209",
    "label": "exports",
    "definition": "An OBJECT_PROPERTY relating an organism to a chemical that the organism exports from the cytoplasm to the periplasm or extracellular environment.",
    "definition_source": "DOI:10.1146/annurev.micro.55.1.485",
    "trait_category": "METABOLISM",
    "term_kind": "OBJECT_PROPERTY",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:2000207"
    ],
    "domain": "https://w3id.org/metpo/1000525",
    "range_": "http://purl.obolibrary.org/obo/CHEBI_24431",
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev.micro.55.1.485",
        "snippet": "export",
        "notes": "Microbial-physiology reference supports 'exports' as a canonical predicate composed with a CHEBI-class chemical object at assertion time."
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.984796+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (OBJECT_PROPERTY)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic transport or storage relation carrier; later replacement should use more specific trait records that combine the relation with the transported, imported, exported, accumulated, or sequestered entity, cellular location or compartment, and positive or negative context.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-16T08:50:00-07:00",
        "curator": "claude",
        "action": "UNDEPRECATED_AS_COMPOSITION_PRIMITIVE",
        "changes": "Restored from DEPRECATED to REVIEWED under the predicate+class composition pattern (intended use: <organism> + this predicate + CHEBI chemical class). Added DOI/PMID-backed definition, evidence, and explicit domain/range slots.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1002005",
    "label": "Fermentation",
    "definition": "A respiration that generates energy through the oxidation of organic compounds without using an external electron acceptor, using organic molecules as both electron donors and final electron acceptors.",
    "definition_source": "DOI:10.3389/fmicb.2021.703525",
    "trait_category": "METABOLISM",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000800"
    ],
    "created_by": "Luke Wang",
    "xrefs": [
      "GO:0006113"
    ],
    "evidence": [
      {
        "reference": "DOI:10.3389/fmicb.2021.703525",
        "snippet": "substrate of a fermentation has to serve as electron donor as well as acceptor",
        "notes": "Supports donor/acceptor definition of anaerobic bacterial fermentation."
      },
      {
        "reference": "DOI:10.1111/1751-7915.13746",
        "snippet": "Substrate-level phosphorylation is one of the main sources of energy",
        "notes": "Supports substrate-level phosphorylation as a major fermentative energy-conservation mechanism."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:562",
        "taxon_label": "Escherichia coli",
        "note": "mixed-acid fermentation",
        "reference": "DOI:10.3389/fbioe.2014.00016"
      },
      {
        "taxon_id": "NCBITaxon:1358",
        "taxon_label": "Lactococcus lactis",
        "note": "homolactic fermentation",
        "reference": "DOI:10.1093/femsre/fuaa033"
      },
      {
        "taxon_id": "NCBITaxon:1488",
        "taxon_label": "Clostridium acetobutylicum",
        "note": "ABE fermentation",
        "reference": "DOI:10.1128/jb.183.16.4823-4838.2001"
      },
      {
        "taxon_id": "NCBITaxon:272562",
        "taxon_label": "Clostridium acetobutylicum ATCC 824",
        "note": "Strain-level ABE fermenter paired to the experimentally expressed PFOR locus CA_C2229.",
        "reference": "DOI:10.1128/mbio.01808-15"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "fermentation_redox_energy",
        "title": "Fermentation redox and substrate-level phosphorylation",
        "description": "Evidence-backed causal sketch linking organic substrate redox balancing to fermentative ATP generation.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "This composite graph combines substrate-level phosphorylation with ferredoxin-linked and ion-gradient modules found in subsets of fermenters. The C. acetobutylicum ATCC 824 PFOR example supports the pyruvate-to-reduced-ferredoxin branch and is not a universal fermentation marker.",
        "nodes": [
          {
            "node_id": "fermentation_trait",
            "label": "Fermentation",
            "node_type": "TRAIT",
            "grounding": "METPO:1002005",
            "description": "Anaerobic redox metabolism using organic substrates and products."
          },
          {
            "node_id": "organic_substrate",
            "label": "organic substrate",
            "node_type": "CHEMICAL",
            "description": "Fermented carbon and energy source."
          },
          {
            "node_id": "reduced_redox_cofactors",
            "label": "reduced redox cofactors",
            "node_type": "CHEMICAL",
            "description": "Reduced cofactors generated during substrate oxidation."
          },
          {
            "node_id": "fermentation_products",
            "label": "fermentation products",
            "node_type": "CHEMICAL",
            "description": "Reduced products that restore cofactor redox balance."
          },
          {
            "node_id": "substrate_level_phosphorylation",
            "label": "substrate-level phosphorylation",
            "node_type": "BIOLOGICAL_PROCESS",
            "grounding": "METPO:1000804",
            "description": "Direct ATP formation by phosphoryl transfer from metabolic intermediates."
          },
          {
            "node_id": "atp",
            "label": "ATP",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:30616",
            "description": "Cellular energy currency generated by fermentation."
          },
          {
            "node_id": "external_inorganic_acceptor",
            "label": "external inorganic terminal electron acceptor",
            "node_type": "CHEMICAL",
            "description": "External inorganic acceptors (e.g. nitrate, sulfur compounds) used in anaerobic respiration but excluded by fermentation."
          },
          {
            "node_id": "glycolysis_emp",
            "label": "glycolysis (Embden-Meyerhof-Parnas pathway)",
            "node_type": "PATHWAY",
            "description": "Central catabolic pathway oxidizing glucose to pyruvate, feeding fermentation branches."
          },
          {
            "node_id": "pyruvate",
            "label": "pyruvate",
            "node_type": "CHEMICAL",
            "description": "Central branch-point metabolite feeding fermentation product pathways.",
            "grounding": "CHEBI:15361"
          },
          {
            "node_id": "pfor",
            "label": "pyruvate:ferredoxin oxidoreductase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Enzyme (EC 1.2.7.1) oxidatively decarboxylating pyruvate and reducing ferredoxin.",
            "grounding": "InterPro:IPR011895",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:Q97GY6",
                "protein_label": "Pyruvate:ferredoxin oxidoreductase",
                "taxon_id": "NCBITaxon:272562",
                "taxon_label": "Clostridium acetobutylicum ATCC 824",
                "entry_status": "UNREVIEWED",
                "proteome_id": "UP000000814",
                "retrieved_on": "2026-10-22",
                "entry_version": 153,
                "sequence_version": 1,
                "role": "PFOR encoded by locus CA_C2229, the expressed enzyme linking pyruvate oxidation to reduced ferredoxin in fermentative C. acetobutylicum ATCC 824.",
                "evidence": [
                  {
                    "reference": "DOI:10.1128/mbio.01808-15",
                    "snippet": "Under all conditions, only CA_C2229 was transcribed and translated.",
                    "notes": "The primary fluxomic, transcriptomic, and proteomic study identifies CA_C2229 as the expressed PFOR locus and describes production of reduced ferredoxin, CO2, and acetyl-CoA. UniProtKB Q97GY6 is its exact unreviewed entry in reference proteome UP000000814."
                  }
                ]
              }
            ]
          },
          {
            "node_id": "reduced_ferredoxin",
            "label": "reduced ferredoxin",
            "node_type": "CHEMICAL",
            "description": "Low-potential electron carrier central to anaerobic redox balancing.",
            "grounding": "CHEBI:17513"
          },
          {
            "node_id": "fnor",
            "label": "ferredoxin:NAD+ oxidoreductase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Enzyme (EC 1.18.1.3) transferring electrons from reduced ferredoxin to NAD+.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "The cited C. acetobutylicum study reports that the corresponding ferredoxin-NAD+ reductase gene is unknown, and the graph does not identify an exact protein family or multisubunit complex."
          },
          {
            "node_id": "nad_plus",
            "label": "NAD+",
            "node_type": "CHEMICAL",
            "description": "Oxidized nicotinamide cofactor regenerated during fermentative redox balancing.",
            "grounding": "CHEBI:15846"
          },
          {
            "node_id": "flavin_based_electron_bifurcation",
            "label": "flavin-based electron bifurcation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Mechanism coupling an exergonic and an endergonic redox reaction within a single enzyme complex."
          },
          {
            "node_id": "ion_motive_force",
            "label": "ion-motive force",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Transmembrane ion gradient generated by ferredoxin-oxidizing complexes."
          },
          {
            "node_id": "atp_synthase",
            "label": "ATP synthase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Membrane complex synthesizing ATP from an ion-motive force.",
            "grounding": "GO:0045259"
          }
        ],
        "edges": [
          {
            "subject": "fermentation_trait",
            "predicate": "uses",
            "object": "organic_substrate",
            "description": "Fermentation uses an organic substrate as both electron donor and acceptor source.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2021.703525",
                "snippet": "substrate of a fermentation has to serve as electron donor as well as acceptor",
                "notes": "Supports organic substrate donor/acceptor role."
              }
            ]
          },
          {
            "subject": "organic_substrate",
            "predicate": "oxidation reduces",
            "object": "reduced_redox_cofactors",
            "description": "Substrate oxidation generates reduced redox cofactors.",
            "evidence": [
              {
                "reference": "DOI:10.1111/1751-7915.13746",
                "snippet": "a substrate is oxidized to an intermediate",
                "notes": "Review describes substrate oxidation with cofactor reduction in fermentation."
              }
            ]
          },
          {
            "subject": "reduced_redox_cofactors",
            "predicate": "reoxidized by",
            "object": "fermentation_products",
            "description": "Product-forming reductions regenerate oxidized cofactors.",
            "evidence": [
              {
                "reference": "DOI:10.1111/1751-7915.13746",
                "snippet": "after which the intermediate is reduced",
                "notes": "Supports product-side reduction and redox cofactor regeneration."
              }
            ]
          },
          {
            "subject": "fermentation_trait",
            "predicate": "conserves energy by",
            "object": "substrate_level_phosphorylation",
            "description": "Substrate-level phosphorylation is a major fermentative energy-conservation route.",
            "evidence": [
              {
                "reference": "DOI:10.1111/1751-7915.13746",
                "snippet": "main sources of energy under fermentative conditions",
                "notes": "Supports SLP as a fermentative energy mechanism."
              }
            ]
          },
          {
            "subject": "substrate_level_phosphorylation",
            "predicate": "has output",
            "object": "atp",
            "description": "Substrate-level phosphorylation directly forms ATP.",
            "evidence": [
              {
                "reference": "DOI:10.1111/1751-7915.13746",
                "snippet": "energy-rich bonds (for example via substrate-level phosphorylation)",
                "notes": "Supports SLP as ATP-linked energy conservation."
              }
            ],
            "predicate_id": "RO:0002234"
          },
          {
            "subject": "fermentation_trait",
            "predicate": "excludes",
            "object": "external_inorganic_acceptor",
            "description": "Fermentation excludes use of external inorganic terminal electron acceptors, distinguishing it from anaerobic respiration.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuae016",
                "notes": "Excludes processes that use external inorganic terminal acceptors, explicitly naming nitrate and sulfur respiration."
              }
            ]
          },
          {
            "subject": "glycolysis_emp",
            "predicate": "feeds into",
            "object": "pyruvate",
            "description": "Glycolysis (EMP) feeds carbon flux to pyruvate, the entry point for fermentation branches.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuae016",
                "notes": "Glycolysis (EMP) and the pentose phosphate pathway feed to pyruvate."
              }
            ]
          },
          {
            "subject": "pfor",
            "predicate": "produces",
            "object": "reduced_ferredoxin",
            "description": "Pyruvate:ferredoxin oxidoreductase oxidizes pyruvate and produces reduced ferredoxin.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuae016",
                "notes": "Pyruvate:ferredoxin oxidoreductase produces reduced ferredoxin; central to redox balancing."
              }
            ],
            "predicate_id": "METPO:2007800"
          },
          {
            "subject": "fnor",
            "predicate": "transfers electrons from reduced ferredoxin to",
            "object": "nad_plus",
            "description": "Ferredoxin:NAD+ oxidoreductase reoxidizes reduced ferredoxin by transferring electrons to NAD+.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuae016",
                "notes": "Ferredoxin-NAD+ reductase transfers electrons from reduced ferredoxin to NAD+; strong redox-balancing edge."
              }
            ]
          },
          {
            "subject": "flavin_based_electron_bifurcation",
            "predicate": "reduces",
            "object": "reduced_ferredoxin",
            "description": "Flavin-based electron bifurcation couples exergonic and endergonic redox reactions, reducing low-potential ferredoxin.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-023-41212-x",
                "notes": "Couples an exergonic and an endergonic redox reaction within a single soluble enzyme complex, typically reducing low-potential ferredoxin."
              }
            ],
            "predicate_id": "METPO:2007802"
          },
          {
            "subject": "ion_motive_force",
            "predicate": "drives",
            "object": "atp_synthase",
            "description": "Ion-motive force generated during fermentation drives ATP synthase-mediated ATP formation.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuae016",
                "notes": "Ion gradients drive ATP synthesis via ATP synthases; links fermentation to chemiosmotic ATP conservation."
              }
            ]
          },
          {
            "subject": "atp_synthase",
            "predicate": "produces",
            "object": "atp",
            "description": "ATP synthase forms ATP using the ion-motive force.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuae016",
                "notes": "ATP synthesis via ATP synthases driven by ion gradients during fermentation."
              }
            ],
            "predicate_id": "METPO:2007800"
          },
          {
            "subject": "glycolysis_emp",
            "predicate": "contributes to",
            "object": "fermentation_trait",
            "description": "EMP glycolysis supplies pyruvate to downstream fermentation branches.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuae016",
                "snippet": "Glycolysis (EMP) and the pentose phosphate pathway feed to pyruvate.",
                "notes": "Verified against the free public article text."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "pfor",
            "predicate": "oxidizes",
            "object": "pyruvate",
            "description": "Pyruvate:ferredoxin oxidoreductase oxidizes pyruvate while reducing ferredoxin.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuae016",
                "snippet": "Pyruvate:ferredoxin oxidoreductase produces reduced ferredoxin; central to redox balancing.",
                "notes": "Verified against the free public article text."
              }
            ],
            "predicate_id": "METPO:2007803"
          },
          {
            "subject": "fnor",
            "predicate": "oxidizes",
            "object": "reduced_ferredoxin",
            "description": "Ferredoxin-NAD+ reductase oxidizes reduced ferredoxin while reducing NAD+.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuae016",
                "snippet": "Ferredoxin-NAD+ reductase transfers electrons from reduced ferredoxin to NAD+; strong redox-balancing edge.",
                "notes": "Verified against the free public article text."
              }
            ],
            "predicate_id": "METPO:2007803"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.935638+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-07T00:00:00-07:00",
        "curator": "codex",
        "action": "ADDED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed causal graph for fermentation redox balancing and substrate-level phosphorylation.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:30Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-17T04:09:44Z",
        "curator": "claude",
        "action": "REMOVE_REDUNDANT_SYNONYM",
        "changes": "Removed 1 synonym(s) whose text duplicated the label (seeder redundancy; no information lost).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 7 evidence-backed generic edges (10 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:12Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d72, METPO:2000017\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:18Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A415TT77\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:32Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 3 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:15361\u00d71, CHEBI:17513\u00d71, CHEBI:15846\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-26T07:15:18Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A075WCC3\u00d71, UniProtKB:I3R731\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:21:11Z",
        "curator": "claude",
        "action": "RETRACT_DEAD_UNIPROT_GROUNDINGS",
        "changes": "Retracted 2 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates (1 to has output), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T02:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES_PART2",
        "changes": "Re-grounded 3 causal edge(s) off microbe-domain METPO predicates onto their causal-graph counterparts (2 to produces, 1 to reduces), issue 301 part 2. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Each replacement is a 1:1 mirror of its source predicate that changes only the domain, so the claim each edge makes is unchanged and directions are unchanged. The replacements are proposed in proposals/metpo_traitmech_v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-22T04:26:15Z",
        "curator": "codex",
        "action": "REVIEW_UNIPROT_INSTANCE_GROUNDINGS",
        "changes": "Reviewed 1 organism-specific UniProtKB grounding(s): replaced 0 with taxon-agnostic GO/InterPro terms and retracted 1 to label-only where no exact semantic term was supported (docs/GROUNDING_POLICY.md).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-24T08:30:00Z",
        "curator": "codex",
        "action": "CURATE_PROTEIN_TAXON_EXAMPLE",
        "changes": "Added a DOI-backed C. acetobutylicum ATCC 824 PFOR example from the experimentally expressed CA_C2229 locus, grounded PFOR and ATP synthase to current semantic terms, retained unresolved FNOR as explicitly reviewed label-only, and documented the graph's branch-specific scope.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T06:15:39Z",
        "curator": "codex",
        "action": "ADD_EXACT_ONTOLOGY_MATCH",
        "changes": "Ontology exact-match review (2026-08-25): approved exact xref(s): GO:0006113. Evidence is predicate-scoped in the versioned ontology snapshots; OAK cross-checked direct data, and OLS4 spot-checked release deltas and disputed hits.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T12:15:00Z",
        "curator": "codex",
        "action": "CONNECT_CAUSAL_GRAPH_COMPONENTS",
        "changes": "Resolved issue #183 graph fragmentation (4 components to 1) with 3 public-source connector(s). No paid research service was called.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-22T01:35:00Z",
        "curator": "claude",
        "action": "REFRESH_UNIPROT_ENTRY_VERSION",
        "changes": "Refreshed UniProtKB entry_version against live UniProt REST on 2026-10-22: UniProtKB:Q97GY6 (152 -> 153 on pfor).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000109",
    "label": "fermentative hydrogen production",
    "definition": "A fermentation in which an organism disposes of excess reducing equivalents by producing molecular hydrogen (H2), typically via hydrogenases acting on reduced ferredoxin or formate.",
    "definition_source": "DOI:10.3389/fmicb.2021.703525",
    "trait_category": "METABOLISM",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1002005"
    ],
    "synonyms": [
      {
        "synonym_text": "biohydrogen production",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1016/S0360-3199(02)00131-3"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.3389/fmicb.2021.703525",
        "notes": "Review of fermentative energy conservation supports H2 production as a redox-balancing fermentation output via hydrogenases."
      },
      {
        "reference": "DOI:10.1016/S0360-3199(02)00131-3",
        "notes": "Hallenbeck & Benemann review biological hydrogen production, including dark fermentative H2 generation."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:2336",
        "taxon_label": "Thermotoga maritima",
        "note": "Model dark-fermentative hydrogen producer (near-theoretical 4 H2 per glucose); hyperthermophilic anaerobe.",
        "reference": "DOI:10.1128/JB.01582-08"
      },
      {
        "taxon_id": "NCBITaxon:243274",
        "taxon_label": "Thermotoga maritima MSB8",
        "note": "Strain-level source of the characterized bifurcating HydABC hydrogenase and its reviewed HydA protein example.",
        "reference": "DOI:10.1128/JB.01582-08"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "fermentative_h2_production",
        "title": "Fermentative H2 production disposes of excess reducing equivalents",
        "description": "Evidence-backed causal sketch linking hydrogenase activity on reduced ferredoxin or formate to molecular hydrogen production as a redox-balancing fermentation output.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "The protein example and protein-to-H2 edge are restricted to the bifurcating HydABC branch characterized in T. maritima, which requires both NADH and reduced ferredoxin. Other fermenters can use distinct hydrogenase or formate-hydrogenlyase routes.",
        "nodes": [
          {
            "node_id": "fermentative_h2_trait",
            "label": "fermentative hydrogen production",
            "node_type": "TRAIT",
            "grounding": "traitmech:000109",
            "description": "Fermentation that yields H2 to dispose of excess electrons."
          },
          {
            "node_id": "fermentation_process",
            "label": "fermentation",
            "node_type": "BIOLOGICAL_PROCESS",
            "grounding": "GO:0006113",
            "description": "ATP-yielding catabolism with organic terminal acceptors."
          },
          {
            "node_id": "molecular_hydrogen",
            "label": "molecular hydrogen",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:18276",
            "description": "H2 produced by hydrogenases."
          },
          {
            "node_id": "fefe_hydrogenase",
            "label": "bifurcating [FeFe] hydrogenase HydABC",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Trimeric electron-bifurcating hydrogenase that couples oxidation of NADH and reduced ferredoxin to H2 production.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "HydABC is a multisubunit electron-bifurcating complex; the verified HydA family terms describe one component rather than the complete complex represented by this node.",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:O52683",
                "protein_label": "Bifurcating [FeFe] hydrogenase alpha subunit",
                "gene_symbol": "hydA",
                "taxon_id": "NCBITaxon:243274",
                "taxon_label": "Thermotoga maritima MSB8",
                "entry_status": "REVIEWED",
                "retrieved_on": "2026-10-22",
                "entry_version": 158,
                "sequence_version": 1,
                "role": "HydA alpha component of the trimeric bifurcating hydrogenase; this accession is not presented as the complete HydABC complex.",
                "evidence": [
                  {
                    "reference": "DOI:10.1128/JB.01582-08",
                    "snippet": "The enzyme oxidizes NADH and ferredoxin simultaneously in an approximately 1:1 ratio and in a synergistic fashion to produce H2.",
                    "notes": "The primary biochemical study characterizes the trimeric T. maritima hydrogenase; UniProtKB O52683 verifies its reviewed HydA alpha component and strain taxon."
                  }
                ]
              }
            ]
          },
          {
            "node_id": "low_h2_partial_pressure",
            "label": "low H2 partial pressure",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Low ambient hydrogen partial pressure in the environment."
          },
          {
            "node_id": "high_h2_partial_pressure",
            "label": "high H2 partial pressure",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "High ambient hydrogen partial pressure in the environment."
          },
          {
            "node_id": "environmental_ph",
            "label": "pH",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Environmental pH affecting hydrogenase activity and fermentative H2 yield.",
            "grounding": "PATO:0001842"
          }
        ],
        "edges": [
          {
            "subject": "fermentative_h2_trait",
            "predicate": "participates in",
            "object": "fermentation_process",
            "description": "Fermentative H2 production is a class of fermentation metabolism.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2021.703525",
                "notes": "Energy-conservation review supports H2 production as a redox-balancing fermentation output via hydrogenases."
              }
            ],
            "predicate_id": "biolink:participates_in"
          },
          {
            "subject": "fermentative_h2_trait",
            "predicate": "produces",
            "object": "molecular_hydrogen",
            "description": "Hydrogenases produce H2 to regenerate oxidized cofactors.",
            "evidence": [
              {
                "reference": "DOI:10.1016/S0360-3199(02)00131-3",
                "notes": "Hallenbeck & Benemann review biological hydrogen production, including dark fermentative H2 generation."
              }
            ],
            "predicate_id": "METPO:2007800"
          },
          {
            "subject": "fefe_hydrogenase",
            "predicate": "produces",
            "object": "molecular_hydrogen",
            "description": "The T. maritima bifurcating HydABC hydrogenase oxidizes NADH and ferredoxin synergistically to produce H2.",
            "evidence": [
              {
                "reference": "DOI:10.1128/JB.01582-08",
                "snippet": "The enzyme oxidizes NADH and ferredoxin simultaneously in an approximately 1:1 ratio and in a synergistic fashion to produce H2.",
                "notes": "Direct biochemical evidence for H2 production by the bifurcating hydrogenase purified from T. maritima; the edge is not generalized to all [FeFe] hydrogenases."
              }
            ],
            "predicate_id": "METPO:2007800"
          },
          {
            "subject": "low_h2_partial_pressure",
            "predicate": "stimulates",
            "object": "fermentative_h2_trait",
            "description": "Low ambient H2 partial pressure stimulates H2 formation.",
            "evidence": [
              {
                "reference": "DOI:10.1128/aem.00634-23",
                "notes": "Low ambient H2 stimulated hydrogen (H2) formation; likely broadly relevant across fermenters."
              }
            ]
          },
          {
            "subject": "high_h2_partial_pressure",
            "predicate": "inhibits",
            "object": "fermentative_h2_trait",
            "description": "High ambient H2 partial pressure inhibits H2 formation (product feedback).",
            "evidence": [
              {
                "reference": "DOI:10.1128/aem.00634-23",
                "notes": "High H2 inhibited H2 formation."
              }
            ],
            "predicate_id": "RO:0002212"
          },
          {
            "subject": "environmental_ph",
            "predicate": "affects",
            "object": "fermentative_h2_trait",
            "description": "pH affects the activity of hydrogenase enzymes and thus dark fermentative H2 yield.",
            "evidence": [
              {
                "reference": "DOI:10.3390/en16083321",
                "notes": "pH affects the activity of hydrogenase enzymes and dark fermentative H2 yield."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-06-08T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate METABOLISM trait (fermentative hydrogen production); round 2, sub-variant of the existing Fermentation class (METPO:1002005).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-10T14:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (fermentative H2 production) with GO/CHEBI node groundings and METPO/biolink predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 4 evidence-backed generic edges (4 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:12Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d71, RO:0002212\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:32Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (PATO:0001842\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T02:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES_PART2",
        "changes": "Re-grounded 2 causal edge(s) off microbe-domain METPO predicates onto their causal-graph counterparts (2 to produces), issue 301 part 2. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Each replacement is a 1:1 mirror of its source predicate that changes only the domain, so the claim each edge makes is unchanged and directions are unchanged. The replacements are proposed in proposals/metpo_traitmech_v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-24T00:00:00Z",
        "curator": "codex",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Refined the broad hydrogenase node to the T. maritima bifurcating HydABC mechanism, added a DOI-backed HydA component example and strain taxon, and kept the complex reviewed label-only pending an exact complex term.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-30T19:21:37Z",
        "curator": "codex",
        "action": "REVIEW_EVIDENCE_REFERENCE_CHURN",
        "changes": "Offline review for issue 520 retained 1 evidence-reference replacement(s) that PR 511 made on surviving causal edges outside its stated protein-taxon scope. The pre-tranche evidence entries had references but no snippets; the retained entries supply edge-specific snippets and explanatory notes. Reverting would discard that claim-level provenance, so the scope defect is resolved by documenting the decision instead. This audit changed no causal claim or evidence field. Reviewed replacements: DOI:10.3390/en16083321 -> DOI:10.1128/JB.01582-08 (1 edge).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-22T01:35:00Z",
        "curator": "claude",
        "action": "REFRESH_UNIPROT_ENTRY_VERSION",
        "changes": "Refreshed UniProtKB entry_version against live UniProt REST on 2026-10-22: UniProtKB:O52683 (157 -> 158 on fefe_hydrogenase).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:2000011",
    "label": "ferments",
    "definition": "An OBJECT_PROPERTY relating an organism to a chemical substrate that the organism ferments \u2014 using organic compounds as both electron donors and acceptors with substrate-level phosphorylation for ATP.",
    "definition_source": "DOI:10.1146/annurev.micro.55.1.485",
    "trait_category": "METABOLISM",
    "term_kind": "OBJECT_PROPERTY",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:2000001"
    ],
    "synonyms": [
      {
        "synonym_text": "fermentation",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "domain": "https://w3id.org/metpo/1000525",
    "range_": "http://purl.obolibrary.org/obo/CHEBI_24431",
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev.micro.55.1.485",
        "snippet": "fermentation",
        "notes": "Microbial-physiology reference supports 'ferments' as a canonical predicate composed with a CHEBI-class chemical object at assertion time."
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.954932+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (OBJECT_PROPERTY)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic biochemical conversion or activity relation carrier; later replacement should use more specific trait records that combine the relation with the substrate, product, enzyme or activity target, assay context, growth condition, or other entity.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-16T08:50:00-07:00",
        "curator": "claude",
        "action": "UNDEPRECATED_AS_COMPOSITION_PRIMITIVE",
        "changes": "Restored from DEPRECATED to REVIEWED under the predicate+class composition pattern (intended use: <organism> + this predicate + CHEBI chemical class). Added DOI/PMID-backed definition, evidence, and explicit domain/range slots.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000196",
    "label": "fumarate respiration",
    "definition": "An anaerobic respiration in which an organism uses fumarate as the terminal electron acceptor and reduces it to succinate for energy conservation.",
    "definition_source": "DOI:10.1128/mBio.03238-19",
    "trait_category": "METABOLISM",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000802"
    ],
    "synonyms": [
      {
        "synonym_text": "anaerobic respiration on fumarate",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1128/JB.00389-22"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1128/mBio.03238-19",
        "snippet": "under anaerobic conditions, fumarate can serve as a terminal electron acceptor, with fumarate reductase (FRD) transferring electrons from the reduced quinone, producing succinate",
        "notes": "Ito et al. summarize Bacteroides anaerobic respiration as quinone-linked transfer to fumarate through fumarate reductase, producing succinate."
      },
      {
        "reference": "DOI:10.1128/JB.00389-22",
        "snippet": "The respiratory chain responsible for anaerobic respiration (NADH to fumarate) involves two NADH dehydrogenases",
        "notes": "Butler et al. describe the B. fragilis anaerobic respiratory chain as an NADH-to-fumarate route."
      },
      {
        "reference": "DOI:10.1128/JB.00389-22",
        "snippet": "Analysis of fumarate reductase showed that it is synthesized and active under anaerobic and nanaerobic conditions",
        "notes": "The 2023 biochemical assay shows fumarate reductase remains synthesized and active in B. fragilis membranes under strictly anaerobic growth and under low-oxygen growth."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:817",
        "taxon_label": "Bacteroides fragilis",
        "note": "Gut anaerobe with fumarate-linked anaerobic respiration characterized in membrane and mutant assays.",
        "reference": "DOI:10.1128/mBio.03238-19"
      }
    ],
    "discussions": [
      {
        "discussion_id": "fumarate-respiration-xref-gap",
        "prompt": "Resolve an exact external ontology class for organism-level fumarate respiration before adding a TraitRecord xref.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "The pinned METPO snapshot contains only obsolete Fumarate respiration and no active organism-level class for anaerobic respiration using fumarate as the terminal electron acceptor. Potential GO, Rhea, EC, and protein-family terms for fumarate reductase or the fumarate-to-succinate reaction are narrower than the whole-organism anaerobic respiration phenotype and should be checked separately before grounding FrdABCD-level causal nodes.",
        "posed_by": "codex",
        "posed_date": "2026-09-15"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-15T00:25:53Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted fumarate respiration as a DOI-backed anaerobic respiration TraitRecord after a repository-wide duplicate review covering ignored and hidden files; the local METPO snapshot has only obsolete Fumarate respiration and the replacement placeholder is reserved in proposals/metpo_traitmech_v73.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:2000508",
    "label": "has growth NaCl observation",
    "definition": "Relates a microbe to a growth NaCl observation.",
    "trait_category": "METABOLISM",
    "term_kind": "OBJECT_PROPERTY",
    "mapping_status": "DEPRECATED",
    "parent_traits": [
      "METPO:2000506"
    ],
    "domain": "https://w3id.org/metpo/1000525",
    "range_": "https://w3id.org/metpo/1001007",
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.994931+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (OBJECT_PROPERTY)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic observation relation carrier; later replacement should use more specific trait records that combine the relation with measured quantity, growth context, chemical, value bounds, or other entity.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-17T15:30:00-07:00",
        "curator": "claude",
        "action": "DEPRECATION_CONFIRMED_AS_OUT_OF_SCOPE",
        "changes": "DEPRECATED status confirmed as final after the predicate+class composition\npivot (#54/#55/#56). This record's observation-shape modelling is out of\nscope for TraitMech; the trait vocabulary + mechanism need is met by the un-\ndeprecated METPO predicates, and per-organism numeric observations belong\ndownstream (KG-Microbe / BacDive). See\ndocs/DEPRECATED_REPLACEMENT_PROPOSAL.md, section 'Observation-value records\nstay deprecated', for the rationale.\n",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:2000514",
    "label": "has growth oxygen observation",
    "definition": "Relates a microbe to a growth oxygen observation.",
    "trait_category": "METABOLISM",
    "term_kind": "OBJECT_PROPERTY",
    "mapping_status": "DEPRECATED",
    "parent_traits": [
      "METPO:2000512"
    ],
    "domain": "https://w3id.org/metpo/1000525",
    "range_": "https://w3id.org/metpo/1001017",
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.998135+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (OBJECT_PROPERTY)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic observation relation carrier; later replacement should use more specific trait records that combine the relation with measured quantity, growth context, chemical, value bounds, or other entity.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-17T15:30:00-07:00",
        "curator": "claude",
        "action": "DEPRECATION_CONFIRMED_AS_OUT_OF_SCOPE",
        "changes": "DEPRECATED status confirmed as final after the predicate+class composition\npivot (#54/#55/#56). This record's observation-shape modelling is out of\nscope for TraitMech; the trait vocabulary + mechanism need is met by the un-\ndeprecated METPO predicates, and per-organism numeric observations belong\ndownstream (KG-Microbe / BacDive). See\ndocs/DEPRECATED_REPLACEMENT_PROPOSAL.md, section 'Observation-value records\nstay deprecated', for the rationale.\n",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:2000502",
    "label": "has growth pH observation",
    "definition": "Relates a microbe to a growth pH observation.",
    "trait_category": "METABOLISM",
    "term_kind": "OBJECT_PROPERTY",
    "mapping_status": "DEPRECATED",
    "parent_traits": [
      "METPO:2000239"
    ],
    "domain": "https://w3id.org/metpo/1000525",
    "range_": "https://w3id.org/metpo/1001012",
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.992553+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (OBJECT_PROPERTY)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic observation relation carrier; later replacement should use more specific trait records that combine the relation with measured quantity, growth context, chemical, value bounds, or other entity.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-17T15:30:00-07:00",
        "curator": "claude",
        "action": "DEPRECATION_CONFIRMED_AS_OUT_OF_SCOPE",
        "changes": "DEPRECATED status confirmed as final after the predicate+class composition\npivot (#54/#55/#56). This record's observation-shape modelling is out of\nscope for TraitMech; the trait vocabulary + mechanism need is met by the un-\ndeprecated METPO predicates, and per-organism numeric observations belong\ndownstream (KG-Microbe / BacDive). See\ndocs/DEPRECATED_REPLACEMENT_PROPOSAL.md, section 'Observation-value records\nstay deprecated', for the rationale.\n",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:2000054",
    "label": "has growth temperature observation",
    "definition": "Relates a microbe to a growth temperature observation.",
    "trait_category": "METABOLISM",
    "term_kind": "OBJECT_PROPERTY",
    "mapping_status": "DEPRECATED",
    "parent_traits": [
      "METPO:2000052"
    ],
    "domain": "https://w3id.org/metpo/1000525",
    "range_": "https://w3id.org/metpo/1001002",
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.976577+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (OBJECT_PROPERTY)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic observation relation carrier; later replacement should use more specific trait records that combine the relation with measured quantity, growth context, chemical, value bounds, or other entity.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-17T15:30:00-07:00",
        "curator": "claude",
        "action": "DEPRECATION_CONFIRMED_AS_OUT_OF_SCOPE",
        "changes": "DEPRECATED status confirmed as final after the predicate+class composition\npivot (#54/#55/#56). This record's observation-shape modelling is out of\nscope for TraitMech; the trait vocabulary + mechanism need is met by the un-\ndeprecated METPO predicates, and per-organism numeric observations belong\ndownstream (KG-Microbe / BacDive). See\ndocs/DEPRECATED_REPLACEMENT_PROPOSAL.md, section 'Observation-value records\nstay deprecated', for the rationale.\n",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:2000510",
    "label": "has NaCl delta observation",
    "definition": "Relates a microbe to a NaCl tolerance breadth (delta) observation.",
    "trait_category": "METABOLISM",
    "term_kind": "OBJECT_PROPERTY",
    "mapping_status": "DEPRECATED",
    "parent_traits": [
      "METPO:2000506"
    ],
    "domain": "https://w3id.org/metpo/1000525",
    "range_": "https://w3id.org/metpo/1001008",
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.995842+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (OBJECT_PROPERTY)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic observation relation carrier; later replacement should use more specific trait records that combine the relation with measured quantity, growth context, chemical, value bounds, or other entity.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-17T15:30:00-07:00",
        "curator": "claude",
        "action": "DEPRECATION_CONFIRMED_AS_OUT_OF_SCOPE",
        "changes": "DEPRECATED status confirmed as final after the predicate+class composition\npivot (#54/#55/#56). This record's observation-shape modelling is out of\nscope for TraitMech; the trait vocabulary + mechanism need is met by the un-\ndeprecated METPO predicates, and per-organism numeric observations belong\ndownstream (KG-Microbe / BacDive). See\ndocs/DEPRECATED_REPLACEMENT_PROPOSAL.md, section 'Observation-value records\nstay deprecated', for the rationale.\n",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:2000506",
    "label": "has NaCl observation",
    "definition": "Relates a microbe to a NaCl observation.",
    "trait_category": "METABOLISM",
    "term_kind": "OBJECT_PROPERTY",
    "mapping_status": "DEPRECATED",
    "parent_traits": [
      "METPO:2000511"
    ],
    "domain": "https://w3id.org/metpo/1000525",
    "range_": "https://w3id.org/metpo/1001022",
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.993979+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (OBJECT_PROPERTY)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic observation relation carrier; later replacement should use more specific trait records that combine the relation with measured quantity, growth context, chemical, value bounds, or other entity.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-17T15:30:00-07:00",
        "curator": "claude",
        "action": "DEPRECATION_CONFIRMED_AS_OUT_OF_SCOPE",
        "changes": "DEPRECATED status confirmed as final after the predicate+class composition\npivot (#54/#55/#56). This record's observation-shape modelling is out of\nscope for TraitMech; the trait vocabulary + mechanism need is met by the un-\ndeprecated METPO predicates, and per-organism numeric observations belong\ndownstream (KG-Microbe / BacDive). See\ndocs/DEPRECATED_REPLACEMENT_PROPOSAL.md, section 'Observation-value records\nstay deprecated', for the rationale.\n",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:2000511",
    "label": "has observation",
    "trait_category": "METABOLISM",
    "term_kind": "OBJECT_PROPERTY",
    "mapping_status": "DEPRECATED",
    "domain": "https://w3id.org/metpo/1000525",
    "range_": "https://w3id.org/metpo/1001000",
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.996310+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (OBJECT_PROPERTY)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic observation relation carrier; later replacement should use more specific trait records that combine the relation with measured quantity, growth context, chemical, value bounds, or other entity.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-17T15:30:00-07:00",
        "curator": "claude",
        "action": "DEPRECATION_CONFIRMED_AS_OUT_OF_SCOPE",
        "changes": "DEPRECATED status confirmed as final after the predicate+class composition\npivot (#54/#55/#56). This record's observation-shape modelling is out of\nscope for TraitMech; the trait vocabulary + mechanism need is met by the un-\ndeprecated METPO predicates, and per-organism numeric observations belong\ndownstream (KG-Microbe / BacDive). See\ndocs/DEPRECATED_REPLACEMENT_PROPOSAL.md, section 'Observation-value records\nstay deprecated', for the rationale.\n",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:2000507",
    "label": "has optimum NaCl observation",
    "definition": "Relates a microbe to an optimum NaCl observation.",
    "trait_category": "METABOLISM",
    "term_kind": "OBJECT_PROPERTY",
    "mapping_status": "DEPRECATED",
    "parent_traits": [
      "METPO:2000506"
    ],
    "domain": "https://w3id.org/metpo/1000525",
    "range_": "https://w3id.org/metpo/1001010",
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.994465+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (OBJECT_PROPERTY)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic observation relation carrier; later replacement should use more specific trait records that combine the relation with measured quantity, growth context, chemical, value bounds, or other entity.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-17T15:30:00-07:00",
        "curator": "claude",
        "action": "DEPRECATION_CONFIRMED_AS_OUT_OF_SCOPE",
        "changes": "DEPRECATED status confirmed as final after the predicate+class composition\npivot (#54/#55/#56). This record's observation-shape modelling is out of\nscope for TraitMech; the trait vocabulary + mechanism need is met by the un-\ndeprecated METPO predicates, and per-organism numeric observations belong\ndownstream (KG-Microbe / BacDive). See\ndocs/DEPRECATED_REPLACEMENT_PROPOSAL.md, section 'Observation-value records\nstay deprecated', for the rationale.\n",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:2000513",
    "label": "has optimum oxygen observation",
    "definition": "Relates a microbe to an optimum oxygen observation.",
    "trait_category": "METABOLISM",
    "term_kind": "OBJECT_PROPERTY",
    "mapping_status": "DEPRECATED",
    "parent_traits": [
      "METPO:2000512"
    ],
    "domain": "https://w3id.org/metpo/1000525",
    "range_": "https://w3id.org/metpo/1001016",
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.997546+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (OBJECT_PROPERTY)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic observation relation carrier; later replacement should use more specific trait records that combine the relation with measured quantity, growth context, chemical, value bounds, or other entity.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-17T15:30:00-07:00",
        "curator": "claude",
        "action": "DEPRECATION_CONFIRMED_AS_OUT_OF_SCOPE",
        "changes": "DEPRECATED status confirmed as final after the predicate+class composition\npivot (#54/#55/#56). This record's observation-shape modelling is out of\nscope for TraitMech; the trait vocabulary + mechanism need is met by the un-\ndeprecated METPO predicates, and per-organism numeric observations belong\ndownstream (KG-Microbe / BacDive). See\ndocs/DEPRECATED_REPLACEMENT_PROPOSAL.md, section 'Observation-value records\nstay deprecated', for the rationale.\n",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:2000501",
    "label": "has optimum pH observation",
    "definition": "Relates a microbe to an optimum pH observation.",
    "trait_category": "METABOLISM",
    "term_kind": "OBJECT_PROPERTY",
    "mapping_status": "DEPRECATED",
    "parent_traits": [
      "METPO:2000239"
    ],
    "domain": "https://w3id.org/metpo/1000525",
    "range_": "https://w3id.org/metpo/1001013",
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.992087+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (OBJECT_PROPERTY)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic observation relation carrier; later replacement should use more specific trait records that combine the relation with measured quantity, growth context, chemical, value bounds, or other entity.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-17T15:30:00-07:00",
        "curator": "claude",
        "action": "DEPRECATION_CONFIRMED_AS_OUT_OF_SCOPE",
        "changes": "DEPRECATED status confirmed as final after the predicate+class composition\npivot (#54/#55/#56). This record's observation-shape modelling is out of\nscope for TraitMech; the trait vocabulary + mechanism need is met by the un-\ndeprecated METPO predicates, and per-organism numeric observations belong\ndownstream (KG-Microbe / BacDive). See\ndocs/DEPRECATED_REPLACEMENT_PROPOSAL.md, section 'Observation-value records\nstay deprecated', for the rationale.\n",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:2000053",
    "label": "has optimum temperature observation",
    "definition": "Relates a microbe to an optimum temperature observation.",
    "trait_category": "METABOLISM",
    "term_kind": "OBJECT_PROPERTY",
    "mapping_status": "DEPRECATED",
    "parent_traits": [
      "METPO:2000052"
    ],
    "domain": "https://w3id.org/metpo/1000525",
    "range_": "https://w3id.org/metpo/1001001",
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.976091+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (OBJECT_PROPERTY)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic observation relation carrier; later replacement should use more specific trait records that combine the relation with measured quantity, growth context, chemical, value bounds, or other entity.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-17T15:30:00-07:00",
        "curator": "claude",
        "action": "DEPRECATION_CONFIRMED_AS_OUT_OF_SCOPE",
        "changes": "DEPRECATED status confirmed as final after the predicate+class composition\npivot (#54/#55/#56). This record's observation-shape modelling is out of\nscope for TraitMech; the trait vocabulary + mechanism need is met by the un-\ndeprecated METPO predicates, and per-organism numeric observations belong\ndownstream (KG-Microbe / BacDive). See\ndocs/DEPRECATED_REPLACEMENT_PROPOSAL.md, section 'Observation-value records\nstay deprecated', for the rationale.\n",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:2000516",
    "label": "has oxygen delta observation",
    "definition": "Relates a microbe to a oxygen tolerance breadth (delta) observation.",
    "trait_category": "METABOLISM",
    "term_kind": "OBJECT_PROPERTY",
    "mapping_status": "DEPRECATED",
    "parent_traits": [
      "METPO:2000512"
    ],
    "domain": "https://w3id.org/metpo/1000525",
    "range_": "https://w3id.org/metpo/1001019",
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.999265+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (OBJECT_PROPERTY)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic observation relation carrier; later replacement should use more specific trait records that combine the relation with measured quantity, growth context, chemical, value bounds, or other entity.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-17T15:30:00-07:00",
        "curator": "claude",
        "action": "DEPRECATION_CONFIRMED_AS_OUT_OF_SCOPE",
        "changes": "DEPRECATED status confirmed as final after the predicate+class composition\npivot (#54/#55/#56). This record's observation-shape modelling is out of\nscope for TraitMech; the trait vocabulary + mechanism need is met by the un-\ndeprecated METPO predicates, and per-organism numeric observations belong\ndownstream (KG-Microbe / BacDive). See\ndocs/DEPRECATED_REPLACEMENT_PROPOSAL.md, section 'Observation-value records\nstay deprecated', for the rationale.\n",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:2000512",
    "label": "has oxygen observation",
    "definition": "Relates a microbe to an oxygen observation.",
    "trait_category": "METABOLISM",
    "term_kind": "OBJECT_PROPERTY",
    "mapping_status": "DEPRECATED",
    "parent_traits": [
      "METPO:2000511"
    ],
    "domain": "https://w3id.org/metpo/1000525",
    "range_": "https://w3id.org/metpo/1001020",
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.996749+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (OBJECT_PROPERTY)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic observation relation carrier; later replacement should use more specific trait records that combine the relation with measured quantity, growth context, chemical, value bounds, or other entity.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-17T15:30:00-07:00",
        "curator": "claude",
        "action": "DEPRECATION_CONFIRMED_AS_OUT_OF_SCOPE",
        "changes": "DEPRECATED status confirmed as final after the predicate+class composition\npivot (#54/#55/#56). This record's observation-shape modelling is out of\nscope for TraitMech; the trait vocabulary + mechanism need is met by the un-\ndeprecated METPO predicates, and per-organism numeric observations belong\ndownstream (KG-Microbe / BacDive). See\ndocs/DEPRECATED_REPLACEMENT_PROPOSAL.md, section 'Observation-value records\nstay deprecated', for the rationale.\n",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:2000504",
    "label": "has pH delta observation",
    "definition": "Relates a microbe to a pH tolerance breadth (delta) observation.",
    "trait_category": "METABOLISM",
    "term_kind": "OBJECT_PROPERTY",
    "mapping_status": "DEPRECATED",
    "parent_traits": [
      "METPO:2000239"
    ],
    "domain": "https://w3id.org/metpo/1000525",
    "range_": "https://w3id.org/metpo/1001014",
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.993485+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (OBJECT_PROPERTY)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic observation relation carrier; later replacement should use more specific trait records that combine the relation with measured quantity, growth context, chemical, value bounds, or other entity.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-17T15:30:00-07:00",
        "curator": "claude",
        "action": "DEPRECATION_CONFIRMED_AS_OUT_OF_SCOPE",
        "changes": "DEPRECATED status confirmed as final after the predicate+class composition\npivot (#54/#55/#56). This record's observation-shape modelling is out of\nscope for TraitMech; the trait vocabulary + mechanism need is met by the un-\ndeprecated METPO predicates, and per-organism numeric observations belong\ndownstream (KG-Microbe / BacDive). See\ndocs/DEPRECATED_REPLACEMENT_PROPOSAL.md, section 'Observation-value records\nstay deprecated', for the rationale.\n",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:2000239",
    "label": "has pH observation",
    "definition": "Relates a microbe to a pH observation.",
    "trait_category": "METABOLISM",
    "term_kind": "OBJECT_PROPERTY",
    "mapping_status": "DEPRECATED",
    "parent_traits": [
      "METPO:2000511"
    ],
    "domain": "https://w3id.org/metpo/1000525",
    "range_": "https://w3id.org/metpo/1001023",
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.990099+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (OBJECT_PROPERTY)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic observation relation carrier; later replacement should use more specific trait records that combine the relation with measured quantity, growth context, chemical, value bounds, or other entity.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-17T15:30:00-07:00",
        "curator": "claude",
        "action": "DEPRECATION_CONFIRMED_AS_OUT_OF_SCOPE",
        "changes": "DEPRECATED status confirmed as final after the predicate+class composition\npivot (#54/#55/#56). This record's observation-shape modelling is out of\nscope for TraitMech; the trait vocabulary + mechanism need is met by the un-\ndeprecated METPO predicates, and per-organism numeric observations belong\ndownstream (KG-Microbe / BacDive). See\ndocs/DEPRECATED_REPLACEMENT_PROPOSAL.md, section 'Observation-value records\nstay deprecated', for the rationale.\n",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:2000102",
    "label": "has phenotype",
    "trait_category": "METABOLISM",
    "term_kind": "OBJECT_PROPERTY",
    "mapping_status": "DEPRECATED",
    "parent_traits": [
      "METPO:2000101"
    ],
    "domain": "https://w3id.org/metpo/1000525",
    "range_": "https://w3id.org/metpo/1000059",
    "xrefs": [
      "RO:0002200"
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.982025+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (OBJECT_PROPERTY)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic metabolism relation carrier; later replacement should use more specific trait records that combine the relation with the chemical, phenotype, quality, compartment, enzyme or activity target, growth context, measurement, or other entity.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-17T15:30:00-07:00",
        "curator": "claude",
        "action": "DEPRECATION_CONFIRMED_AS_OUT_OF_SCOPE",
        "changes": "DEPRECATED status confirmed as final after the predicate+class composition\npivot (#54/#55/#56). This record's observation-shape modelling is out of\nscope for TraitMech; the trait vocabulary + mechanism need is met by the un-\ndeprecated METPO predicates, and per-organism numeric observations belong\ndownstream (KG-Microbe / BacDive). See\ndocs/DEPRECATED_REPLACEMENT_PROPOSAL.md, section 'Observation-value records\nstay deprecated', for the rationale.\n",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T01:14:58Z",
        "curator": "codex",
        "action": "ADD_EXACT_ONTOLOGY_MATCH",
        "changes": "Ontology exact-match review (2026-08-25): approved exact xref(s): RO:0002200. Evidence is predicate-scoped in the versioned ontology snapshots; OAK cross-checked direct data, and OLS4 spot-checked release deltas and disputed hits.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:2000101",
    "label": "has quality",
    "trait_category": "METABOLISM",
    "term_kind": "OBJECT_PROPERTY",
    "mapping_status": "DEPRECATED",
    "domain": "https://w3id.org/metpo/1000525",
    "range_": "https://w3id.org/metpo/1000188",
    "xrefs": [
      "RO:0000086"
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.981609+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (OBJECT_PROPERTY)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic metabolism relation carrier; later replacement should use more specific trait records that combine the relation with the chemical, phenotype, quality, compartment, enzyme or activity target, growth context, measurement, or other entity.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-17T15:30:00-07:00",
        "curator": "claude",
        "action": "DEPRECATION_CONFIRMED_AS_OUT_OF_SCOPE",
        "changes": "DEPRECATED status confirmed as final after the predicate+class composition\npivot (#54/#55/#56). This record's observation-shape modelling is out of\nscope for TraitMech; the trait vocabulary + mechanism need is met by the un-\ndeprecated METPO predicates, and per-organism numeric observations belong\ndownstream (KG-Microbe / BacDive). See\ndocs/DEPRECATED_REPLACEMENT_PROPOSAL.md, section 'Observation-value records\nstay deprecated', for the rationale.\n",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T01:14:58Z",
        "curator": "codex",
        "action": "ADD_EXACT_ONTOLOGY_MATCH",
        "changes": "Ontology exact-match review (2026-08-25): approved exact xref(s): RO:0000086. Evidence is predicate-scoped in the versioned ontology snapshots; OAK cross-checked direct data, and OLS4 spot-checked release deltas and disputed hits.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:2000509",
    "label": "has range NaCl observation",
    "definition": "Relates a microbe to a growth NaCl range observation.",
    "trait_category": "METABOLISM",
    "term_kind": "OBJECT_PROPERTY",
    "mapping_status": "DEPRECATED",
    "parent_traits": [
      "METPO:2000506"
    ],
    "domain": "https://w3id.org/metpo/1000525",
    "range_": "https://w3id.org/metpo/1001009",
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.995382+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (OBJECT_PROPERTY)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic observation relation carrier; later replacement should use more specific trait records that combine the relation with measured quantity, growth context, chemical, value bounds, or other entity.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-17T15:30:00-07:00",
        "curator": "claude",
        "action": "DEPRECATION_CONFIRMED_AS_OUT_OF_SCOPE",
        "changes": "DEPRECATED status confirmed as final after the predicate+class composition\npivot (#54/#55/#56). This record's observation-shape modelling is out of\nscope for TraitMech; the trait vocabulary + mechanism need is met by the un-\ndeprecated METPO predicates, and per-organism numeric observations belong\ndownstream (KG-Microbe / BacDive). See\ndocs/DEPRECATED_REPLACEMENT_PROPOSAL.md, section 'Observation-value records\nstay deprecated', for the rationale.\n",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:2000515",
    "label": "has range oxygen observation",
    "definition": "Relates a microbe to a growth oxygen range observation.",
    "trait_category": "METABOLISM",
    "term_kind": "OBJECT_PROPERTY",
    "mapping_status": "DEPRECATED",
    "parent_traits": [
      "METPO:2000512"
    ],
    "domain": "https://w3id.org/metpo/1000525",
    "range_": "https://w3id.org/metpo/1001018",
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.998642+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (OBJECT_PROPERTY)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic observation relation carrier; later replacement should use more specific trait records that combine the relation with measured quantity, growth context, chemical, value bounds, or other entity.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-17T15:30:00-07:00",
        "curator": "claude",
        "action": "DEPRECATION_CONFIRMED_AS_OUT_OF_SCOPE",
        "changes": "DEPRECATED status confirmed as final after the predicate+class composition\npivot (#54/#55/#56). This record's observation-shape modelling is out of\nscope for TraitMech; the trait vocabulary + mechanism need is met by the un-\ndeprecated METPO predicates, and per-organism numeric observations belong\ndownstream (KG-Microbe / BacDive). See\ndocs/DEPRECATED_REPLACEMENT_PROPOSAL.md, section 'Observation-value records\nstay deprecated', for the rationale.\n",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:2000503",
    "label": "has range pH observation",
    "definition": "Relates a microbe to a growth pH range observation.",
    "trait_category": "METABOLISM",
    "term_kind": "OBJECT_PROPERTY",
    "mapping_status": "DEPRECATED",
    "parent_traits": [
      "METPO:2000239"
    ],
    "domain": "https://w3id.org/metpo/1000525",
    "range_": "https://w3id.org/metpo/1001015",
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.993027+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (OBJECT_PROPERTY)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic observation relation carrier; later replacement should use more specific trait records that combine the relation with measured quantity, growth context, chemical, value bounds, or other entity.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-17T15:30:00-07:00",
        "curator": "claude",
        "action": "DEPRECATION_CONFIRMED_AS_OUT_OF_SCOPE",
        "changes": "DEPRECATED status confirmed as final after the predicate+class composition\npivot (#54/#55/#56). This record's observation-shape modelling is out of\nscope for TraitMech; the trait vocabulary + mechanism need is met by the un-\ndeprecated METPO predicates, and per-organism numeric observations belong\ndownstream (KG-Microbe / BacDive). See\ndocs/DEPRECATED_REPLACEMENT_PROPOSAL.md, section 'Observation-value records\nstay deprecated', for the rationale.\n",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:2000055",
    "label": "has range temperature observation",
    "definition": "Relates a microbe to a growth temperature range observation.",
    "trait_category": "METABOLISM",
    "term_kind": "OBJECT_PROPERTY",
    "mapping_status": "DEPRECATED",
    "parent_traits": [
      "METPO:2000052"
    ],
    "domain": "https://w3id.org/metpo/1000525",
    "range_": "https://w3id.org/metpo/1001003",
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.977049+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (OBJECT_PROPERTY)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic observation relation carrier; later replacement should use more specific trait records that combine the relation with measured quantity, growth context, chemical, value bounds, or other entity.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-17T15:30:00-07:00",
        "curator": "claude",
        "action": "DEPRECATION_CONFIRMED_AS_OUT_OF_SCOPE",
        "changes": "DEPRECATED status confirmed as final after the predicate+class composition\npivot (#54/#55/#56). This record's observation-shape modelling is out of\nscope for TraitMech; the trait vocabulary + mechanism need is met by the un-\ndeprecated METPO predicates, and per-organism numeric observations belong\ndownstream (KG-Microbe / BacDive). See\ndocs/DEPRECATED_REPLACEMENT_PROPOSAL.md, section 'Observation-value records\nstay deprecated', for the rationale.\n",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:2000056",
    "label": "has temperature delta observation",
    "definition": "Relates a microbe to a temperature tolerance breadth (delta) observation.",
    "trait_category": "METABOLISM",
    "term_kind": "OBJECT_PROPERTY",
    "mapping_status": "DEPRECATED",
    "parent_traits": [
      "METPO:2000052"
    ],
    "domain": "https://w3id.org/metpo/1000525",
    "range_": "https://w3id.org/metpo/1001004",
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.977523+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (OBJECT_PROPERTY)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic observation relation carrier; later replacement should use more specific trait records that combine the relation with measured quantity, growth context, chemical, value bounds, or other entity.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-17T15:30:00-07:00",
        "curator": "claude",
        "action": "DEPRECATION_CONFIRMED_AS_OUT_OF_SCOPE",
        "changes": "DEPRECATED status confirmed as final after the predicate+class composition\npivot (#54/#55/#56). This record's observation-shape modelling is out of\nscope for TraitMech; the trait vocabulary + mechanism need is met by the un-\ndeprecated METPO predicates, and per-organism numeric observations belong\ndownstream (KG-Microbe / BacDive). See\ndocs/DEPRECATED_REPLACEMENT_PROPOSAL.md, section 'Observation-value records\nstay deprecated', for the rationale.\n",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:2000052",
    "label": "has temperature observation",
    "definition": "Relates a microbe to a temperature observation.",
    "trait_category": "METABOLISM",
    "term_kind": "OBJECT_PROPERTY",
    "mapping_status": "DEPRECATED",
    "parent_traits": [
      "METPO:2000511"
    ],
    "domain": "https://w3id.org/metpo/1000525",
    "range_": "https://w3id.org/metpo/1001021",
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.975608+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (OBJECT_PROPERTY)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic observation relation carrier; later replacement should use more specific trait records that combine the relation with measured quantity, growth context, chemical, value bounds, or other entity.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-17T15:30:00-07:00",
        "curator": "claude",
        "action": "DEPRECATION_CONFIRMED_AS_OUT_OF_SCOPE",
        "changes": "DEPRECATED status confirmed as final after the predicate+class composition\npivot (#54/#55/#56). This record's observation-shape modelling is out of\nscope for TraitMech; the trait vocabulary + mechanism need is met by the un-\ndeprecated METPO predicates, and per-organism numeric observations belong\ndownstream (KG-Microbe / BacDive). See\ndocs/DEPRECATED_REPLACEMENT_PROPOSAL.md, section 'Observation-value records\nstay deprecated', for the rationale.\n",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000846",
    "label": "Homoacetogenesis",
    "definition": "A metabolism in which acetate is produced as the sole reduced end product from reduction of CO2 via the acetyl-CoA pathway.",
    "definition_source": "DOI:10.1016/j.tibtech.2019.05.008",
    "trait_category": "METABOLISM",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000060"
    ],
    "synonyms": [
      {
        "synonym_text": "Reductive acetyl-CoA pathway",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "Wood-Ljungdahl pathway",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1016/j.tibtech.2019.05.008",
        "snippet": "two mol of carbon dioxide are reduced to one mol of acetyl-CoA",
        "notes": "Review supports Wood-Ljungdahl reduction of CO2 to acetyl-CoA and acetate."
      },
      {
        "reference": "DOI:10.1016/j.bbapap.2008.08.012",
        "snippet": "Wood-Ljungdahl Pathway of CO2 Fixation",
        "notes": "Review supports acetogens using the Wood-Ljungdahl pathway for CO2 fixation."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:33952",
        "taxon_label": "Acetobacterium woodii",
        "note": "Model homoacetogen; reduces CO2 to acetate via the Wood-Ljungdahl pathway (Rnf bioenergetics model).",
        "reference": "PMID:22479398"
      },
      {
        "taxon_id": "NCBITaxon:1525",
        "taxon_label": "Neomoorella thermoacetica",
        "note": "Model homoacetogen used for biochemical reconstruction of the CODH/ACS convergence step in the Wood-Ljungdahl pathway.",
        "reference": "DOI:10.1073/pnas.220404397"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "homoacetogenesis_wood_ljungdahl_acetate",
        "title": "Homoacetogenesis Wood-Ljungdahl acetate mechanism",
        "description": "DOI-backed graph linking anaerobic CO2 reduction, hydrogen/CO inputs, acetyl-CoA synthesis, and acetate as the sole reduced product.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "The graph represents the conserved Wood-Ljungdahl core plus taxon-dependent energy-conservation alternatives. The N. thermoacetica AcsB example supports the CODH/ACS convergence step, while the A. woodii canonical example anchors an Rnf-type implementation; Rnf and Ech are not asserted to be simultaneously universal.",
        "nodes": [
          {
            "node_id": "homoacetogenesis_trait",
            "label": "Homoacetogenesis",
            "node_type": "TRAIT",
            "grounding": "METPO:1000846",
            "description": "Acetate-producing metabolism through the reductive acetyl-CoA pathway."
          },
          {
            "node_id": "anaerobic_condition",
            "label": "anaerobic condition",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Oxygen-free condition associated with acetogens.",
            "grounding": "PATO:0001456"
          },
          {
            "node_id": "wood_ljungdahl_pathway",
            "label": "Wood-Ljungdahl pathway",
            "node_type": "PATHWAY",
            "description": "Reductive acetyl-CoA pathway used for CO2 fixation.",
            "grounding": "GO:0030634",
            "related_records": [
              {
                "corpus": "PathwayMech",
                "identifier": "WikiPathways:WP5019",
                "relation": "PATHWAY_CONTEXT",
                "basis": "PathwayMech context: Acetogenesis in Acetobacterium woodii (NCBITaxon:33952). The shared reductive acetyl-CoA route combines methyl and carbonyl branches for acetogenesis; the bacterial exemplar does not establish archaeal variants. No exact equivalence or transfer of organism scope is asserted.",
                "source_version": "aa305727458c44ab05614901334540e2c87a9f3a"
              }
            ]
          },
          {
            "node_id": "carbon_dioxide",
            "label": "carbon dioxide",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:16526",
            "description": "C1 carbon input reduced during homoacetogenesis."
          },
          {
            "node_id": "molecular_hydrogen",
            "label": "molecular hydrogen",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:18276",
            "description": "Electron donor for CO2 reduction in many homoacetogens."
          },
          {
            "node_id": "carbon_monoxide",
            "label": "carbon monoxide",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:17245",
            "description": "C1 substrate or intermediate in acetyl-CoA synthesis."
          },
          {
            "node_id": "acetyl_coa",
            "label": "acetyl-CoA",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:15351",
            "description": "Central product of Wood-Ljungdahl carbon fixation."
          },
          {
            "node_id": "acetate",
            "label": "acetate",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:30089",
            "description": "Sole reduced end product in homoacetogenesis."
          },
          {
            "node_id": "atp",
            "label": "ATP",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:30616",
            "description": "Energy carrier conserved during acetate formation."
          },
          {
            "node_id": "formate",
            "label": "formate",
            "node_type": "CHEMICAL",
            "description": "C1 intermediate in the methyl branch of the Wood-Ljungdahl pathway."
          },
          {
            "node_id": "formate_dehydrogenase",
            "label": "formate dehydrogenase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Enzyme reducing CO2 to formate in the methyl branch.",
            "grounding": "GO:0009326"
          },
          {
            "node_id": "formyl_thf",
            "label": "formyl-tetrahydrofolate",
            "node_type": "CHEMICAL",
            "description": "Formyl-THF, the C1-loaded folate intermediate of the methyl branch."
          },
          {
            "node_id": "formyl_thf_synthetase",
            "label": "formyl-THF synthetase (Fhs)",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Formate--tetrahydrofolate ligase converting formate to formyl-THF.",
            "grounding": "GO:0004329"
          },
          {
            "node_id": "methyl_branch",
            "label": "methyl branch of WLP",
            "node_type": "PATHWAY",
            "description": "Eastern/methyl branch generating the methyl group of acetyl-CoA."
          },
          {
            "node_id": "carbonyl_branch",
            "label": "carbonyl branch of WLP",
            "node_type": "PATHWAY",
            "description": "Western/carbonyl branch generating the carbonyl group via CO."
          },
          {
            "node_id": "acs_codh_complex",
            "label": "ACS/CODH complex",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Acetyl-CoA synthase / CO dehydrogenase complex where the two WLP branches converge.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "This node denotes the complete multisubunit ACS/CODH assembly; no single GO or InterPro term exactly represents the combined complex.",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:P27988",
                "protein_label": "Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit alpha",
                "gene_symbol": "acsB",
                "taxon_id": "NCBITaxon:1525",
                "taxon_label": "Neomoorella thermoacetica",
                "entry_status": "REVIEWED",
                "retrieved_on": "2026-10-22",
                "entry_version": 126,
                "sequence_version": 1,
                "role": "AcsB alpha component of CODH/ACS that forms acetyl-CoA; this accession is not presented as the complete complex.",
                "evidence": [
                  {
                    "reference": "DOI:10.1073/pnas.220404397",
                    "snippet": "Genes acsA and acsB encode the beta and alpha subunits",
                    "notes": "The primary cloning and reconstitution study identifies acsB as the alpha component of active AcsAB from C. thermoaceticum; UniProtKB P27988 verifies the reviewed current N. thermoacetica mapping."
                  }
                ]
              }
            ]
          },
          {
            "node_id": "acetate_kinase",
            "label": "acetate kinase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Enzyme generating ATP by substrate-level phosphorylation during acetate formation.",
            "grounding": "GO:0008776"
          },
          {
            "node_id": "substrate_level_phosphorylation",
            "label": "substrate-level phosphorylation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "ATP-generating phosphoryl transfer at acetate kinase in the WLP."
          },
          {
            "node_id": "energy_conservation_module",
            "label": "membrane energy-conservation module (Rnf/Ech)",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Membrane-associated Rnf or Ech complex translocating ions to build the transmembrane gradient.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Rnf and Ech are distinct, taxon-dependent multisubunit alternatives; no one complex or family term can ground this deliberately disjunctive node."
          },
          {
            "node_id": "transmembrane_ion_gradient",
            "label": "transmembrane ion gradient",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Na+/H+ electrochemical gradient driving ATP synthase during acetogenesis."
          },
          {
            "node_id": "atp_synthase",
            "label": "ATP synthase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Membrane enzyme using the ion gradient to synthesize ATP.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "The node is intentionally broad across proton- and sodium-coupled F/V-type ATP synthases; an exact complex term requires a taxon-specific architecture."
          }
        ],
        "edges": [
          {
            "subject": "homoacetogenesis_trait",
            "predicate": "occurs in",
            "object": "anaerobic_condition",
            "description": "Homoacetogenesis is an anaerobic acetogenic metabolism.",
            "evidence": [
              {
                "reference": "DOI:10.1023/A:1020514617738",
                "snippet": "obligately anaerobic bacteria",
                "notes": "Supports anaerobic context for acetogens."
              }
            ],
            "predicate_id": "biolink:occurs_in"
          },
          {
            "subject": "homoacetogenesis_trait",
            "predicate": "has mechanistic pathway",
            "object": "wood_ljungdahl_pathway",
            "description": "Homoacetogenesis proceeds through the Wood-Ljungdahl pathway.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.tibtech.2019.05.008",
                "snippet": "Wood-Ljungdahl pathway",
                "notes": "Supports pathway assignment for acetogens."
              }
            ]
          },
          {
            "subject": "carbon_dioxide",
            "predicate": "participates in",
            "object": "wood_ljungdahl_pathway",
            "description": "CO2 is reduced through the Wood-Ljungdahl pathway.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.tibtech.2019.05.008",
                "snippet": "carbon dioxide are reduced",
                "notes": "Supports CO2 as substrate."
              }
            ],
            "predicate_id": "biolink:participates_in"
          },
          {
            "subject": "molecular_hydrogen",
            "predicate": "provides electrons for",
            "object": "wood_ljungdahl_pathway",
            "description": "Hydrogen can provide reducing equivalents for CO2 reduction.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.bbapap.2008.08.012",
                "snippet": "acetyl-CoA from CO or CO2 + H2",
                "notes": "Supports H2 as an electron donor with CO2."
              }
            ],
            "predicate_id": "METPO:2007402"
          },
          {
            "subject": "carbon_monoxide",
            "predicate": "participates in",
            "object": "wood_ljungdahl_pathway",
            "description": "CO can serve as a C1 input or intermediate for acetyl-CoA synthesis.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.bbapap.2008.08.012",
                "snippet": "acetyl-CoA from CO or CO2 + H2",
                "notes": "Supports CO as substrate or intermediate."
              }
            ],
            "predicate_id": "biolink:participates_in"
          },
          {
            "subject": "wood_ljungdahl_pathway",
            "predicate": "has output",
            "object": "acetyl_coa",
            "description": "Wood-Ljungdahl carbon fixation produces acetyl-CoA.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.tibtech.2019.05.008",
                "snippet": "reduced to one mol of acetyl-CoA",
                "notes": "Supports acetyl-CoA synthesis from CO2."
              }
            ],
            "predicate_id": "RO:0002234"
          },
          {
            "subject": "acetyl_coa",
            "predicate": "converted to",
            "object": "acetate",
            "description": "Acetyl-CoA is converted to acetate as the reduced product.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.tibtech.2019.05.008",
                "snippet": "further to acetate",
                "notes": "Supports acetate formation downstream of acetyl-CoA."
              }
            ]
          },
          {
            "subject": "homoacetogenesis_trait",
            "predicate": "produces",
            "object": "acetate",
            "description": "Homoacetogenesis produces acetate as the sole reduced end product.",
            "evidence": [
              {
                "reference": "DOI:10.1023/A:1020514617738",
                "snippet": "reduce CO2 to acetate",
                "notes": "Supports acetate as the defining acetogenic product."
              }
            ],
            "predicate_id": "METPO:2007800"
          },
          {
            "subject": "acetyl_coa",
            "predicate": "supports formation of",
            "object": "atp",
            "description": "Conversion to acetate can conserve energy as ATP.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.tibtech.2019.05.008",
                "snippet": "further to acetate",
                "notes": "Review discusses acetate formation as the energy-conserving product branch."
              }
            ]
          },
          {
            "subject": "carbon_dioxide",
            "predicate": "reduced by enzyme to",
            "object": "formate",
            "description": "CO2 is reduced to formate by formate dehydrogenase in the methyl branch.",
            "evidence": [
              {
                "reference": "DOI:10.1039/d4cb00099d",
                "notes": "CO2 to formate catalyzed by formate dehydrogenase (Fdh); core WLP methyl-branch step."
              }
            ]
          },
          {
            "subject": "formate_dehydrogenase",
            "predicate": "catalyzes",
            "object": "formate",
            "description": "Formate dehydrogenase produces formate from CO2.",
            "evidence": [
              {
                "reference": "DOI:10.1039/d4cb00099d",
                "notes": "CO2 -> formate catalyzed by formate dehydrogenase (Fdh)."
              }
            ],
            "predicate_id": "biolink:catalyzes"
          },
          {
            "subject": "formate",
            "predicate": "converted by enzyme to",
            "object": "formyl_thf",
            "description": "Formate is converted to formyl-THF by formyl-THF synthetase.",
            "evidence": [
              {
                "reference": "DOI:10.1039/d4cb00099d",
                "notes": "formate -> formyl-THF by formyl-THF synthetase (Fhs); methyl-branch step."
              }
            ]
          },
          {
            "subject": "formyl_thf_synthetase",
            "predicate": "catalyzes",
            "object": "formyl_thf",
            "description": "Formyl-THF synthetase (Fhs) forms formyl-THF from formate.",
            "evidence": [
              {
                "reference": "DOI:10.1039/d4cb00099d",
                "notes": "formate -> formyl-THF by formyl-THF synthetase (Fhs)."
              }
            ],
            "predicate_id": "biolink:catalyzes"
          },
          {
            "subject": "methyl_branch",
            "predicate": "converges with",
            "object": "carbonyl_branch",
            "description": "The methyl and carbonyl branches of the WLP converge at the ACS/CODH complex.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s13068-024-02554-w",
                "notes": "eastern/methyl branch and carbonyl/western branch meet at the acetyl-CoA synthase/carbon monoxide dehydrogenase complex (ACS/CODH); canonical WLP architecture."
              }
            ]
          },
          {
            "subject": "acs_codh_complex",
            "predicate": "produces",
            "object": "acetyl_coa",
            "description": "The ACS/CODH complex condenses the methyl and carbonyl groups into acetyl-CoA.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s13068-024-02554-w",
                "notes": "the two WLP branches meet at the ACS/CODH complex to form acetyl-CoA."
              }
            ],
            "predicate_id": "METPO:2007800"
          },
          {
            "subject": "acetate_kinase",
            "predicate": "generates",
            "object": "atp",
            "description": "Acetate kinase generates ATP by substrate-level phosphorylation during acetate formation, the only WLP ATP-yielding step.",
            "evidence": [
              {
                "reference": "DOI:10.1039/d4cb00099d",
                "notes": "acetyl-CoA -> acetate via acetyl-phosphate with ATP from substrate-level phosphorylation (acetate kinase); WLP is otherwise net-zero ATP."
              }
            ],
            "predicate_id": "biolink:produces"
          },
          {
            "subject": "acetate_kinase",
            "predicate": "participates in",
            "object": "substrate_level_phosphorylation",
            "description": "Acetate kinase mediates substrate-level phosphorylation in the acetate branch.",
            "evidence": [
              {
                "reference": "DOI:10.1039/d4cb00099d",
                "notes": "ATP from substrate-level phosphorylation at acetate kinase."
              }
            ],
            "predicate_id": "biolink:participates_in"
          },
          {
            "subject": "energy_conservation_module",
            "predicate": "generates",
            "object": "transmembrane_ion_gradient",
            "description": "The membrane Rnf or Ech module translocates Na+/H+ to generate the transmembrane ion gradient.",
            "evidence": [
              {
                "reference": "DOI:10.1039/d4cb00099d",
                "notes": "Rnf transfers electrons from Fdred to NAD+ while translocating Na+/H+; Ech acts as Fd:H+ oxidoreductase."
              },
              {
                "reference": "DOI:10.3389/fmicb.2023.1185739",
                "notes": "membrane-associated energy-conservation module involving Rnf or Ech plus ATP synthase."
              }
            ],
            "predicate_id": "biolink:produces"
          },
          {
            "subject": "transmembrane_ion_gradient",
            "predicate": "drives",
            "object": "atp_synthase",
            "description": "The transmembrane ion gradient drives ATP synthase to conserve energy during acetogenesis.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2023.1185739",
                "notes": "membrane-associated energy-conservation module ... plus ATP synthase."
              }
            ]
          },
          {
            "subject": "atp_synthase",
            "predicate": "produces",
            "object": "atp",
            "description": "ATP synthase produces ATP from the ion gradient, conserving energy in the near-thermodynamic-limit acetogenic metabolism.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2023.1185739",
                "notes": "ATP synthase couples the ion gradient to ATP synthesis in acetogens."
              }
            ],
            "predicate_id": "METPO:2007800"
          },
          {
            "subject": "methyl_branch",
            "predicate": "part of",
            "object": "wood_ljungdahl_pathway",
            "description": "The methyl branch is one of the two converging branches of the Wood-Ljungdahl pathway.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s13068-024-02554-w",
                "snippet": "The WLP, which was elucidated over decades, proceeds through two branches",
                "notes": "Verified against the public PMC full text; the existing edge between methyl and carbonyl branches keeps both branches connected."
              }
            ],
            "predicate_id": "biolink:part_of"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.916045+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-08T00:00:00-07:00",
        "curator": "codex",
        "action": "ADDED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed causal graph for anaerobic Wood-Ljungdahl CO2 reduction, H2/CO inputs, acetyl-CoA formation, acetate product formation, and ATP conservation.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:30Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d72).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:38:00Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (ENVO:01001057\u00d71, GO:0046358\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-26T05:00:47Z",
        "curator": "claude",
        "action": "RENAME_PREDICATE_LABELS",
        "changes": "Renamed 3 causal-edge predicate label(s) to align with existing groundings: input to \u2192 participates in \u00d72; occurs under \u2192 occurs in \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-26T05:00:50Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:participates_in\u00d72, biolink:occurs_in\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-14T07:26:19Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007402\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-15T07:19:08Z",
        "curator": "claude",
        "action": "FIX_NODE_GROUNDING_CURIE",
        "changes": "Overwrote 1 causal-node grounding(s) to corrected CURIEs (phase-2 id-label fix; verified vs OAK).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-15T07:20:37Z",
        "curator": "claude",
        "action": "FIX_NODE_GROUNDING_CURIE",
        "changes": "Overwrote 1 causal-node grounding(s) (obsolete/wrong GO -> corrected, verified vs OAK).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 11 evidence-backed generic edges (12 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:12Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 7 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:catalyzes\u00d72, METPO:2000202\u00d72, biolink:produces\u00d72, biolink:participates_in\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:18Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A081KVG3\u00d71, UniProtKB:A0A415TT77\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-26T07:15:18Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A016XII7\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:21:11Z",
        "curator": "claude",
        "action": "RETRACT_DEAD_UNIPROT_GROUNDINGS",
        "changes": "Retracted 3 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:23:54Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0009326\u00d71, GO:0008776\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates (1 to has output), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T02:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES_PART2",
        "changes": "Re-grounded 3 causal edge(s) off microbe-domain METPO predicates onto their causal-graph counterparts (3 to produces), issue 301 part 2. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Each replacement is a 1:1 mirror of its source predicate that changes only the domain, so the claim each edge makes is unchanged and directions are unchanged. The replacements are proposed in proposals/metpo_traitmech_v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-24T10:20:00Z",
        "curator": "codex",
        "action": "CURATE_PROTEIN_TAXON_EXAMPLE",
        "changes": "Scoped the homoacetogenesis mechanism, grounded Fhs, added DOI-backed N. thermoacetica AcsB as an explicit CODH/ACS component, and documented the combined CODH/ACS, Rnf/Ech, and ATP-synthase labels without over-generalizing architecture.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:24:00Z",
        "curator": "claude",
        "action": "RESTORE_CANONICAL_CITATION",
        "changes": "Restored the canonical-example citation for NCBITaxon:33952 from DOI:10.1128/JB.00357-18 back to PMID:22479398 (review issue 519). The tranche event described the change as a PMID-to-DOI upgrade, but the DOI resolves to a different paper than the PMID, so this was a replacement rather than an identifier normalisation. The pre-tranche citation is restored; a deliberate replacement can be made in a new event that says so.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T08:20:00Z",
        "curator": "codex",
        "action": "CONNECT_CAUSAL_GRAPH_COMPONENTS",
        "changes": "Resolved issue #183 graph fragmentation (2 components to 1) using 1 public-source, verbatim-snippet-backed connector(s). No paid research service was called.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-05T17:46:22Z",
        "curator": "codex",
        "action": "ADD_PATHWAY_CONTEXT",
        "changes": "Added pinned PathwayMech context on reviewed causal nodes with explicit route and organism limitations; retained existing groundings and exact xrefs.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-22T01:35:00Z",
        "curator": "claude",
        "action": "REFRESH_UNIPROT_ENTRY_VERSION",
        "changes": "Refreshed UniProtKB entry_version against live UniProt REST on 2026-10-22: UniProtKB:P27988 (125 -> 126 on acs_codh_complex).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000128",
    "label": "hydrocarbon degradation",
    "definition": "A metabolism in which an organism catabolizes a hydrocarbon, using it as a carbon and energy source.",
    "definition_source": "DOI:10.1126/science.aaf4507",
    "trait_category": "METABOLISM",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000060"
    ],
    "synonyms": [
      {
        "synonym_text": "hydrocarbon_degradation",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1126/science.aaf4507"
      }
    ],
    "xrefs": [
      "GO:0120253"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1128/MR.54.3.305-315.1990",
        "snippet": "Hydrocarbons are degraded primarily by bacteria and fungi",
        "notes": "Leahy and Colwell review microbial hydrocarbon degradation across environmental microorganisms."
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-08T00:00:00Z",
        "curator": "codex",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed a DOI-backed FAPROTAX metabolic capability from proposals/metpo_traitmech_v11 after repository-wide duplicate review.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-21T20:01:04Z",
        "curator": "claude",
        "action": "RECORD_MECHANISM_KNOWLEDGE_GAP",
        "changes": "Recorded OPEN KNOWLEDGE_GAP discussion (hydrocarbon-degradation-causal-graph-source-gap) documenting the source-limited mechanism gap for causal_graphs.",
        "llm_assisted": true
      }
    ],
    "discussions": [
      {
        "discussion_id": "hydrocarbon-degradation-causal-graph-source-gap",
        "prompt": "Add primary literature evidence for alkane monooxygenase or anaerobic hydrocarbon-activating enzymes and a strain-matched canonical example before constructing causal_graphs.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "The current record carries a single high-level review snippet (DOI:10.1128/MR.54.3.305-315.1990) stating that hydrocarbons are degraded primarily by bacteria and fungi, which is insufficient to ground a multi-edge mechanism graph without inventing unsupported edges.",
        "posed_by": "claude",
        "posed_date": "2026-10-21",
        "evidence": [
          {
            "reference": "DOI:10.1128/MR.54.3.305-315.1990",
            "supports": "PARTIAL",
            "snippet": "Hydrocarbons are degraded primarily by bacteria and fungi",
            "explanation": "Existing record-level evidence supports the high-level metabolic trait definition but does not provide multi-step enzymatic mechanism quotes for a connected causal graph."
          }
        ]
      }
    ]
  },
  {
    "identifier": "traitmech:000127",
    "label": "hydrogenotrophic methanogenesis",
    "definition": "A methanogenesis in which carbon dioxide is reduced to methane using molecular hydrogen as the electron donor.",
    "definition_source": "DOI:10.1126/science.aaf4507",
    "trait_category": "METABOLISM",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000844"
    ],
    "synonyms": [
      {
        "synonym_text": "hydrogenotrophic_methanogenesis",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1126/science.aaf4507"
      },
      {
        "synonym_text": "methanogenesis_by_CO2_reduction_with_H2",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1126/science.aaf4507"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev-micro-011720-122807",
        "snippet": "from CO2 and H2 to methane",
        "notes": "Shima et al. support the H2/CO2 branch of archaeal methane production."
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-08T00:00:00Z",
        "curator": "codex",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed a DOI-backed FAPROTAX metabolic capability from proposals/metpo_traitmech_v11 after repository-wide duplicate review.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-21T20:01:04Z",
        "curator": "claude",
        "action": "RECORD_MECHANISM_KNOWLEDGE_GAP",
        "changes": "Recorded OPEN KNOWLEDGE_GAP discussion (hydrogenotrophic-methanogenesis-causal-graph-source-gap) documenting the source-limited mechanism gap for causal_graphs.",
        "llm_assisted": true
      }
    ],
    "discussions": [
      {
        "discussion_id": "hydrogenotrophic-methanogenesis-causal-graph-source-gap",
        "prompt": "Add primary literature evidence for the H2/CO2 methanogenesis pathway steps (e.g. Fmd/Fwd, Mch, Mtd, Mer, Mtr, Mcr, and energy-converting hydrogenases) and a strain-matched canonical example before constructing causal_graphs.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "The current record carries a single 26-character phrase ('from CO2 and H2 to methane' in DOI:10.1146/annurev-micro-011720-122807); building a multi-edge graph from one short phrase would violate the snippet-diversity and anti-clause-splitting rules.",
        "posed_by": "claude",
        "posed_date": "2026-10-21",
        "evidence": [
          {
            "reference": "DOI:10.1146/annurev-micro-011720-122807",
            "supports": "PARTIAL",
            "snippet": "from CO2 and H2 to methane",
            "explanation": "Existing record-level evidence supports the high-level metabolic trait definition but does not provide multi-step enzymatic mechanism quotes for a connected causal graph."
          }
        ]
      }
    ]
  },
  {
    "identifier": "METPO:2000013",
    "label": "hydrolyzes",
    "definition": "An OBJECT_PROPERTY relating an organism to a chemical substrate that the organism hydrolyses (cleaves by addition of water).",
    "definition_source": "DOI:10.1146/annurev.micro.55.1.485",
    "trait_category": "METABOLISM",
    "term_kind": "OBJECT_PROPERTY",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:2000001"
    ],
    "synonyms": [
      {
        "synonym_text": "hydrolysis",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "domain": "https://w3id.org/metpo/1000525",
    "range_": "http://purl.obolibrary.org/obo/CHEBI_24431",
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev.micro.55.1.485",
        "snippet": "hydrolysis",
        "notes": "Microbial-physiology reference supports 'hydrolyzes' as a canonical predicate composed with a CHEBI-class chemical object at assertion time."
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.955855+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (OBJECT_PROPERTY)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic biochemical conversion or activity relation carrier; later replacement should use more specific trait records that combine the relation with the substrate, product, enzyme or activity target, assay context, growth condition, or other entity.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-16T08:50:00-07:00",
        "curator": "claude",
        "action": "UNDEPRECATED_AS_COMPOSITION_PRIMITIVE",
        "changes": "Restored from DEPRECATED to REVIEWED under the predicate+class composition pattern (intended use: <organism> + this predicate + CHEBI chemical class). Added DOI/PMID-backed definition, evidence, and explicit domain/range slots.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:2000208",
    "label": "imports",
    "definition": "An OBJECT_PROPERTY relating an organism to a chemical that the organism imports from the extracellular environment into the cytoplasm.",
    "definition_source": "DOI:10.1146/annurev.micro.55.1.485",
    "trait_category": "METABOLISM",
    "term_kind": "OBJECT_PROPERTY",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:2000207"
    ],
    "domain": "https://w3id.org/metpo/1000525",
    "range_": "http://purl.obolibrary.org/obo/CHEBI_24431",
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev.micro.55.1.485",
        "snippet": "import",
        "notes": "Microbial-physiology reference supports 'imports' as a canonical predicate composed with a CHEBI-class chemical object at assertion time."
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.984336+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (OBJECT_PROPERTY)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic transport or storage relation carrier; later replacement should use more specific trait records that combine the relation with the transported, imported, exported, accumulated, or sequestered entity, cellular location or compartment, and positive or negative context.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-16T08:50:00-07:00",
        "curator": "claude",
        "action": "UNDEPRECATED_AS_COMPOSITION_PRIMITIVE",
        "changes": "Restored from DEPRECATED to REVIEWED under the predicate+class composition pattern (intended use: <organism> + this predicate + CHEBI chemical class). Added DOI/PMID-backed definition, evidence, and explicit domain/range slots.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000203",
    "label": "iodate respiration",
    "definition": "An anaerobic respiration in which an organism uses iodate as the terminal electron acceptor for energy conservation.",
    "definition_source": "DOI:10.1128/AEM.00241-07",
    "trait_category": "METABOLISM",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000802"
    ],
    "synonyms": [
      {
        "synonym_text": "dissimilatory iodate reduction",
        "synonym_type": "EXACT_SYNONYM"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1128/AEM.00241-07",
        "snippet": "SCT was capable of anaerobic growth with 3 mM iodate as the sole electron acceptor",
        "notes": "Amachi et al. isolated Pseudomonas sp. strain SCT from marine sediment slurry and showed anaerobic growth with iodate as sole electron acceptor."
      },
      {
        "reference": "DOI:10.1128/AEM.00241-07",
        "snippet": "SCT is a dissimilatory iodate-reducing bacterium",
        "notes": "Amachi et al. support the dissimilatory iodate reduction synonym and organism-level phenotype scope."
      },
      {
        "reference": "DOI:10.1038/s41396-021-01034-5",
        "snippet": "dissimilatory IO3\u2212 reduction to iodide (I\u2212) by a novel estuarine bacterium, Denitromonas sp. IR-12",
        "notes": "Reyes-Umana et al. show that iodate respiration recurs in an estuarine Denitromonas isolate."
      },
      {
        "reference": "DOI:10.3389/fmicb.2021.804181",
        "snippet": "A. toluclasticum sp. TC-10 couples acetate oxidation to iodate reduction with a concomitant increase in the OD600.",
        "notes": "Reyes-Umana et al. extend the dissimilatory iodate-reducing phenotype to the freshwater isolate Aromatoleum toluclasticum sp. TC-10."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:412955",
        "taxon_label": "Pseudomonas sp. SCT",
        "note": "Amachi et al. isolated Pseudomonas sp. strain SCT from marine sediment slurry and showed anaerobic growth with iodate as the sole electron acceptor.",
        "reference": "DOI:10.1128/AEM.00241-07"
      }
    ],
    "discussions": [
      {
        "discussion_id": "iodate-respiration-xref-gap",
        "prompt": "Resolve an exact external ontology class for organism-level iodate respiration before adding a TraitRecord xref.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Candidate Idr, DmsAB, EC, Rhea, and protein-family terms describe narrower iodate reductase activities, reactions, or enzymes rather than the whole-organism anaerobic respiration phenotype.",
        "posed_by": "codex",
        "posed_date": "2026-09-15"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-15T03:53:45Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted iodate respiration as a DOI-backed anaerobic respiration TraitRecord after a repository-wide duplicate review covering ignored and hidden files; the local METPO snapshot has no exact iodate respiration class and the replacement placeholder is reserved in proposals/metpo_traitmech_v80.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000107",
    "label": "iron oxidation",
    "definition": "A metabolism in which an organism oxidizes ferrous iron (Fe2+) to ferric iron (Fe3+) to conserve energy, at acidic or circumneutral pH and under aerobic or anaerobic conditions.",
    "definition_source": "DOI:10.1146/annurev.micro.112408.134208",
    "trait_category": "METABOLISM",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000060"
    ],
    "synonyms": [
      {
        "synonym_text": "ferrous iron oxidation",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1146/annurev.micro.112408.134208"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev.micro.112408.134208",
        "notes": "Emerson, Fleming & McBeth review iron-oxidizing bacteria from an environmental and genomic perspective."
      },
      {
        "reference": "DOI:10.1099/mic.0.045344-0",
        "notes": "Hedrich, Schlomann & Johnson review the iron-oxidizing proteobacteria and their energy metabolism."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:180",
        "taxon_label": "Leptospirillum ferrooxidans",
        "note": "Acidophilic Fe(II) oxidiser (bioleaching/AMD). Gallionella ferruginea is the neutrophilic stalk-forming Fe oxidiser.",
        "reference": "PMID:22815442"
      },
      {
        "taxon_id": "NCBITaxon:243159",
        "taxon_label": "Acidithiobacillus ferrooxidans ATCC 23270",
        "note": "Reference acidophilic iron oxidizer in which the Cyc2-containing trans-envelope supercomplex was purified and shown to carry iron-oxidase activity.",
        "reference": "DOI:10.1074/jbc.M802496200"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "iron_oxidation_ferrous_to_ferric",
        "title": "Ferrous iron oxidation for energy",
        "description": "Evidence-backed causal sketch linking the iron-oxidation trait to oxidation of ferrous iron to ferric iron for energy conservation.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "This is a cross-taxon iron-oxidation graph. The A. ferrooxidans Cyc2 example supports the acidophilic Cyc2 branch; cbb3, bd, and multiheme proteins represent lineage- and condition-specific alternatives and are not universal markers.",
        "nodes": [
          {
            "node_id": "iron_oxidation_trait",
            "label": "iron oxidation",
            "node_type": "TRAIT",
            "grounding": "traitmech:000107",
            "description": "Capacity to oxidize Fe(II) to Fe(III) for energy."
          },
          {
            "node_id": "ferrous_iron",
            "label": "ferrous iron",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:29033",
            "description": "Fe(2+) electron-donor substrate."
          },
          {
            "node_id": "ferric_iron",
            "label": "ferric iron",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:29034",
            "description": "Fe(3+) oxidized product."
          },
          {
            "node_id": "cyc2",
            "label": "Cyc2",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Outer-membrane cytochrome c that extracts electrons from extracellular Fe(II); the central iron oxidase across many FeOB.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Cyc2 homologs fall into functionally heterogeneous phylogenetic clusters, and no exact checked GO or InterPro term distinguishes the experimentally supported iron-oxidase class represented here.",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:B7JAQ7",
                "protein_label": "Cytochrome c",
                "gene_symbol": "cyc2",
                "taxon_id": "NCBITaxon:243159",
                "taxon_label": "Acidithiobacillus ferrooxidans ATCC 23270",
                "entry_status": "UNREVIEWED",
                "proteome_id": "UP000001362",
                "retrieved_on": "2026-08-24",
                "entry_version": 60,
                "sequence_version": 1,
                "role": "Outer-membrane Cyc2 component of the iron-oxidizing/O2-reducing supercomplex in A. ferrooxidans ATCC 23270.",
                "evidence": [
                  {
                    "reference": "DOI:10.1074/jbc.M802496200",
                    "snippet": "outer membrane-bound cytochrome c Cyc2 was purified",
                    "notes": "The primary biochemical study reports iron-oxidase activity and electron transfer through Cyc2 in the isolated trans-envelope supercomplex; UniProtKB B7JAQ7 is the strain's cyc2 reference-proteome entry."
                  }
                ]
              }
            ]
          },
          {
            "node_id": "cbb3_oxidase",
            "label": "cbb3-type terminal oxidase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "High-oxygen-affinity terminal oxidase used by FeOB.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "This label denotes a multisubunit cbb3 terminal-oxidase complex across FeOB lineages; exact subunit composition and taxon are not fixed here."
          },
          {
            "node_id": "bd_oxidase",
            "label": "cytochrome bd-type terminal oxidase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "High-oxygen-affinity terminal oxidase used by FeOB.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "This label denotes a multisubunit cytochrome-bd terminal oxidase across lineages; the graph does not identify a specific complex composition."
          },
          {
            "node_id": "microaerobic_conditions",
            "label": "microaerobic conditions",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Low-oxygen environmental niche favored by FeOB."
          },
          {
            "node_id": "low_oxygen_organic_rich",
            "label": "low-oxygen organic-rich niche",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Low-O2, organic-rich environmental niche."
          },
          {
            "node_id": "nitrite_no",
            "label": "nitrite and nitric oxide",
            "node_type": "CHEMICAL",
            "description": "Reactive nitrogen species that bind hemes and abiotically oxidize Fe(II)."
          },
          {
            "node_id": "enzymatic_iron_oxidation",
            "label": "enzymatic iron oxidation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Biological Fe(II) oxidation catalyzed by cytochromes."
          },
          {
            "node_id": "multiheme_cytochromes",
            "label": "multiheme c-type cytochromes",
            "node_type": "GENE_OR_PROTEIN",
            "description": "FeOB-enriched multiheme cytochromes conducting electrons across long distances and wide redox-potential ranges.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Multiheme c-type cytochromes comprise many non-equivalent families and heme architectures; the cited graph claim does not resolve one exact family."
          },
          {
            "node_id": "extracellular_electron_transfer",
            "label": "extracellular electron transfer",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Electron transfer across minerals and long distances, expanding usable iron substrates."
          }
        ],
        "edges": [
          {
            "subject": "iron_oxidation_trait",
            "predicate": "oxidizes",
            "object": "ferrous_iron",
            "description": "Iron oxidizers oxidize ferrous iron as an electron donor.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev.micro.112408.134208",
                "notes": "Emerson et al. review iron-oxidizing bacteria that use Fe(II) for energy."
              }
            ],
            "predicate_id": "METPO:2007803"
          },
          {
            "subject": "iron_oxidation_trait",
            "predicate": "produces",
            "object": "ferric_iron",
            "description": "Ferrous-iron oxidation yields ferric iron.",
            "evidence": [
              {
                "reference": "DOI:10.1099/mic.0.045344-0",
                "notes": "Hedrich et al. describe Fe(II) to Fe(III) oxidation by iron-oxidizing proteobacteria."
              }
            ],
            "predicate_id": "METPO:2007800"
          },
          {
            "subject": "cyc2",
            "predicate": "oxidizes",
            "object": "ferrous_iron",
            "description": "The outer-membrane cytochrome Cyc2 extracts electrons from extracellular Fe(II).",
            "evidence": [
              {
                "reference": "DOI:10.1128/mSystems.00720-23",
                "notes": "\"electrons are initially extracted from extracellular Fe(II) by the outer membrane cytochrome c Cyc2\"; Cyc2 also validated in neutrophiles."
              }
            ],
            "predicate_id": "METPO:2007803"
          },
          {
            "subject": "cbb3_oxidase",
            "predicate": "supports growth in",
            "object": "microaerobic_conditions",
            "description": "High-O2-affinity cbb3 oxidase enables FeOB growth under microaerobic conditions.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.00599-24",
                "notes": "\"These terminal oxidases have high affinity for oxygen and therefore are widely understood to be used under microaerobic conditions\"; consistent with FeOB ecology."
              }
            ]
          },
          {
            "subject": "bd_oxidase",
            "predicate": "supports growth in",
            "object": "low_oxygen_organic_rich",
            "description": "High-O2-affinity cytochrome bd oxidase supports FeOB growth in low-oxygen, organic-rich niches.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mSystems.00038-23",
                "notes": "\"cytochrome bd-type oxidases have a high affinity for oxygen ... can be more highly expressed ... under low-oxygen, organic-rich conditions\"."
              }
            ]
          },
          {
            "subject": "nitrite_no",
            "predicate": "negatively regulates",
            "object": "enzymatic_iron_oxidation",
            "description": "Nitrite and NO bind hemes inhibiting cytochromes and abiotically oxidize Fe(II), competing with enzymatic iron oxidation.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mSystems.00038-23",
                "notes": "\"they bind to hemes, inhibiting the activity of cytochromes, and also directly oxidize Fe(II), thus competing with enzymatic iron oxidation\"."
              }
            ],
            "predicate_id": "RO:0002212"
          },
          {
            "subject": "multiheme_cytochromes",
            "predicate": "enables",
            "object": "extracellular_electron_transfer",
            "description": "FeOB multiheme cytochromes conduct electrons across long distances and broad redox potentials, enabling extracellular electron transfer.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mSystems.00038-23",
                "notes": "\"MHCs efficiently conduct electrons across longer distances and function across a wide range of redox potentials ... which can expand the range of usable iron substrates\"."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "cbb3_oxidase",
            "predicate": "contributes to",
            "object": "iron_oxidation_trait",
            "description": "High-affinity terminal oxidation supports iron-oxidizer respiration in microaerobic niches.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.00599-24",
                "snippet": "These terminal oxidases have high affinity for oxygen and therefore are widely understood to be used under microaerobic conditions",
                "notes": "Verified against the free public article text."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "low_oxygen_organic_rich",
            "predicate": "example of",
            "object": "microaerobic_conditions",
            "description": "A low-oxygen, organic-rich setting is a specific microaerobic condition.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mSystems.00038-23",
                "snippet": "bd-type oxidases have a high affinity for oxygen, and recent studies show they can be more highly expressed than cbb3-type oxidases under low-oxygen, organic-rich conditions",
                "notes": "Verified against the free public article text."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "enzymatic_iron_oxidation",
            "predicate": "contributes to",
            "object": "iron_oxidation_trait",
            "description": "Enzymatic Fe(II) oxidation realizes the biological iron-oxidation capacity.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mSystems.00038-23",
                "snippet": "they bind to hemes, inhibiting the activity of cytochromes, and also directly oxidize Fe(II), thus competing with enzymatic iron oxidation",
                "notes": "Verified against the free public article text."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "extracellular_electron_transfer",
            "predicate": "contributes to",
            "object": "iron_oxidation_trait",
            "description": "Extracellular electron uptake extends iron oxidation across mineral substrates.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mSystems.00038-23",
                "snippet": "multiheme cytochromes (MHCs) in Gallionellaceae FeOB, which may facilitate extracellular electron uptake and the oxidation of different iron substrates",
                "notes": "Verified against the free public article text."
              }
            ],
            "predicate_id": "RO:0002326"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-06-08T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate METABOLISM trait (iron oxidation); round 2, metal-cycle gap. Complements round-1 dissimilatory iron reduction.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-08T12:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (Fe(II) to Fe(III) oxidation) with CHEBI node groundings and METPO predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 5 evidence-backed generic edges (9 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:12Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000016\u00d71, RO:0002327\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-04T03:08:14Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002212\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T02:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES_PART2",
        "changes": "Re-grounded 3 causal edge(s) off microbe-domain METPO predicates onto their causal-graph counterparts (2 to oxidizes, 1 to produces), issue 301 part 2. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Each replacement is a 1:1 mirror of its source predicate that changes only the domain, so the claim each edge makes is unchanged and directions are unchanged. The replacements are proposed in proposals/metpo_traitmech_v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-24T10:25:00Z",
        "curator": "codex",
        "action": "CURATE_PROTEIN_TAXON_EXAMPLE",
        "changes": "Scoped the cross-taxon iron-oxidation graph, added a DOI-backed A. ferrooxidans Cyc2 example, and documented Cyc2 cluster ambiguity plus the lineage-specific cbb3, bd, and multiheme labels.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T12:15:00Z",
        "curator": "codex",
        "action": "CONNECT_CAUSAL_GRAPH_COMPONENTS",
        "changes": "Resolved issue #183 graph fragmentation (5 components to 1) with 4 public-source connector(s). No paid research service was called.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:2000045",
    "label": "is not required for growth",
    "definition": "An OBJECT_PROPERTY relating an organism to a chemical entity that is *not* required for that organism's growth (positive assertion of non-requirement). Functions as the negation companion of 'requires for growth'.",
    "definition_source": "PMID:21413255",
    "trait_category": "METABOLISM",
    "term_kind": "OBJECT_PROPERTY",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:2000001"
    ],
    "synonyms": [
      {
        "synonym_text": "required for growth",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "domain": "https://w3id.org/metpo/1000525",
    "range_": "http://purl.obolibrary.org/obo/CHEBI_24431",
    "evidence": [
      {
        "reference": "PMID:21413255",
        "snippet": "growth",
        "notes": "Microbial-physiology reference supports 'is not required for growth' as a canonical predicate composed with a CHEBI-class chemical object at assertion time."
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.972308+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (OBJECT_PROPERTY)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic metabolism relation carrier; later replacement should use more specific trait records that combine the relation with the chemical, phenotype, quality, compartment, enzyme or activity target, growth context, measurement, or other entity.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-16T08:50:00-07:00",
        "curator": "claude",
        "action": "UNDEPRECATED_AS_COMPOSITION_PRIMITIVE",
        "changes": "Restored from DEPRECATED to REVIEWED under the predicate+class composition pattern (intended use: <organism> + this predicate + CHEBI chemical class). Added DOI/PMID-backed definition, evidence, and explicit domain/range slots.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000026",
    "label": "lactic acid fermentation",
    "definition": "A fermentation in which sugars are converted mainly to lactate, with ATP generated by substrate-level phosphorylation. Homolactic fermentation yields ~2 lactate per glucose via glycolysis; heterolactic fermentation also yields ethanol/acetate and CO2. Characteristic of lactic acid bacteria (e.g. Lactobacillus, Lactococcus).",
    "definition_source": "DOI:10.3389/fmicb.2021.703525",
    "trait_category": "METABOLISM",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1002005"
    ],
    "synonyms": [
      {
        "synonym_text": "lactate fermentation",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.3389/fmicb.2021.703525"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.3389/fmicb.2021.703525",
        "notes": "Review of energy conservation in anaerobic fermentations supports lactate as a fermentation end product generated with substrate-level phosphorylation."
      },
      {
        "reference": "DOI:10.3390/molecules31020333",
        "notes": "Review of classical food fermentations describes the lactic-acid pathway and lactic acid bacteria as its agents."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1358",
        "taxon_label": "Lactococcus lactis",
        "note": "Canonical homolactic fermenter and dairy model organism.",
        "reference": "PMID:17307855"
      },
      {
        "taxon_id": "NCBITaxon:272623",
        "taxon_label": "Lactococcus lactis subsp. lactis IL1403",
        "note": "Strain-level homolactic-fermentation exemplar paired to a reviewed lactate dehydrogenase protein instance.",
        "reference": "DOI:10.1128/JB.183.13.3817-3824.2001"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "lactic_acid_fermentation_lactate",
        "title": "Lactic acid fermentation converts sugars to lactate",
        "description": "Evidence-backed causal sketch linking glycolysis-coupled lactate production to substrate-level ATP generation in lactic acid bacteria.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "Represents pyruvate reduction, NAD+ regeneration, ATP-producing glycolysis, and acidification effects; the protein exemplar supports the central LDH step in L. lactis IL1403.",
        "nodes": [
          {
            "node_id": "lactic_acid_fermentation_trait",
            "label": "lactic acid fermentation",
            "node_type": "TRAIT",
            "grounding": "traitmech:000026",
            "description": "Fermentation producing lactate as the principal end product."
          },
          {
            "node_id": "fermentation_process",
            "label": "fermentation",
            "node_type": "BIOLOGICAL_PROCESS",
            "grounding": "GO:0006113",
            "description": "ATP-yielding catabolism with organic terminal acceptors."
          },
          {
            "node_id": "lactate",
            "label": "lactate",
            "node_type": "CHEMICAL",
            "description": "Principal end product of homolactic fermentation.",
            "grounding": "CHEBI:24996"
          },
          {
            "node_id": "glucose",
            "label": "glucose",
            "node_type": "CHEMICAL",
            "description": "Hexose substrate fermented by lactic acid bacteria.",
            "grounding": "CHEBI:17234"
          },
          {
            "node_id": "glycolysis_emp",
            "label": "EMP/glycolysis pathway",
            "node_type": "PATHWAY",
            "description": "Embden-Meyerhof-Parnas glycolytic pathway used by homofermentative LAB."
          },
          {
            "node_id": "pyruvate",
            "label": "pyruvate",
            "node_type": "CHEMICAL",
            "description": "Glycolytic intermediate reduced to lactate.",
            "grounding": "CHEBI:15361"
          },
          {
            "node_id": "lactate_dehydrogenase",
            "label": "lactate dehydrogenase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Enzyme that reduces pyruvate to lactate (EC 1.1.1.27).",
            "grounding": "GO:0004457",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:Q01462",
                "protein_label": "L-lactate dehydrogenase 1",
                "gene_symbol": "ldh1",
                "taxon_id": "NCBITaxon:272623",
                "taxon_label": "Lactococcus lactis subsp. lactis IL1403",
                "entry_status": "REVIEWED",
                "proteome_id": "UP000002196",
                "retrieved_on": "2026-08-23",
                "entry_version": 182,
                "sequence_version": 3,
                "role": "Catalyzes reduction of pyruvate to L-lactate during homolactic fermentation in the canonical L. lactis strain.",
                "evidence": [
                  {
                    "reference": "DOI:10.1128/JB.183.13.3817-3824.2001",
                    "snippet": "high lactate dehydrogenase activity",
                    "notes": "The primary study measured LDH activity and homolactic physiology in L. lactis IL1403; UniProtKB Q01462 supplies the exact reviewed protein and strain pairing."
                  }
                ]
              }
            ]
          },
          {
            "node_id": "phosphoketolase_pathway",
            "label": "phosphoketolase pathway",
            "node_type": "PATHWAY",
            "description": "Pentose-phosphate/phosphoketolase route used by heterofermentative LAB."
          },
          {
            "node_id": "carbon_dioxide",
            "label": "carbon dioxide",
            "node_type": "CHEMICAL",
            "description": "Co-product of heterolactic fermentation.",
            "grounding": "CHEBI:16526"
          },
          {
            "node_id": "ethanol",
            "label": "ethanol",
            "node_type": "CHEMICAL",
            "description": "Co-product of heterolactic fermentation.",
            "grounding": "CHEBI:16236"
          },
          {
            "node_id": "decreased_ph",
            "label": "decreased pH",
            "node_type": "QUALITY",
            "description": "Acidification resulting from lactic acid accumulation."
          },
          {
            "node_id": "pathogenic_microbe",
            "label": "pathogenic/spoilage microbe",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Spoilage and pathogenic microbes inhibited by acidification."
          }
        ],
        "edges": [
          {
            "subject": "lactic_acid_fermentation_trait",
            "predicate": "participates in",
            "object": "fermentation_process",
            "description": "Lactic acid fermentation is a class of fermentation metabolism.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2021.703525",
                "snippet": "fermentation is defined as an anaerobic bacterial redox process of an organic substrate leading to different products",
                "notes": "Energy-conservation review supports lactate as a fermentation end product."
              }
            ],
            "predicate_id": "biolink:participates_in"
          },
          {
            "subject": "lactic_acid_fermentation_trait",
            "predicate": "produces",
            "object": "lactate",
            "description": "Lactate is the characteristic end product of the pathway.",
            "evidence": [
              {
                "reference": "DOI:10.3390/molecules31020333",
                "snippet": "lactic fermentation channels carbohydrate metabolism toward lactate formation",
                "notes": "Classical-fermentation review describes the lactic-acid pathway."
              }
            ],
            "predicate_id": "METPO:2007800"
          },
          {
            "subject": "glucose",
            "predicate": "is fermented via",
            "object": "glycolysis_emp",
            "description": "Homofermentative LAB ferment glucose mainly via the EMP/glycolysis pathway.",
            "evidence": [
              {
                "reference": "DOI:10.3390/molecules31020333",
                "snippet": "Homolactic LAB metabolize hexoses (primarily glucose) via the EMP pathway",
                "notes": "homofermentative LAB rely mainly on glycolysis (EMP)."
              }
            ]
          },
          {
            "subject": "glycolysis_emp",
            "predicate": "has output",
            "object": "pyruvate",
            "description": "Glycolysis yields pyruvate as the intermediate reduced to lactate.",
            "evidence": [
              {
                "reference": "DOI:10.3390/foods12152850",
                "snippet": "glucose acts as the carbon source to create pyruvate through the glycolysis process",
                "notes": "Glycolysis of glucose generates pyruvate, which lactate dehydrogenase reduces to lactate."
              }
            ],
            "predicate_id": "RO:0002234"
          },
          {
            "subject": "pyruvate",
            "predicate": "is converted by",
            "object": "lactate_dehydrogenase",
            "description": "Pyruvate is the substrate of lactate dehydrogenase.",
            "evidence": [
              {
                "reference": "DOI:10.3390/foods12152850",
                "snippet": "subsequently converted to lactic acid by lactate dehydrogenase",
                "notes": "Lactate dehydrogenase converts pyruvate to lactate."
              }
            ]
          },
          {
            "subject": "lactate_dehydrogenase",
            "predicate": "produces",
            "object": "lactate",
            "description": "Lactate dehydrogenase reduces pyruvate to lactate.",
            "evidence": [
              {
                "reference": "DOI:10.3390/foods12152850",
                "snippet": "Lactate dehydrogenase plays an important role in the production of lactic acid from pyruvate",
                "notes": "one mole of glucose produces two moles of lactic acid and two ATP molecules via LDH."
              }
            ],
            "predicate_id": "METPO:2007800"
          },
          {
            "subject": "phosphoketolase_pathway",
            "predicate": "yields",
            "object": "lactate",
            "description": "Heterofermentative phosphoketolase route yields lactate among its products.",
            "evidence": [
              {
                "reference": "DOI:10.3390/molecules31020333",
                "snippet": "This route typically yields equimolar lactate, ethanol (or acetate) and CO2",
                "notes": "products are lactate, carbon dioxide, and either ethanol or acetate (phosphoketolase route)."
              }
            ],
            "predicate_id": "biolink:produces"
          },
          {
            "subject": "phosphoketolase_pathway",
            "predicate": "yields",
            "object": "carbon_dioxide",
            "description": "Heterolactic phosphoketolase route co-produces CO2.",
            "evidence": [
              {
                "reference": "DOI:10.3390/molecules31020333",
                "snippet": "leading to the formation of lactate, ethanol or acetate, and CO2",
                "notes": "heterolactic products are lactate, carbon dioxide, and ethanol or acetate."
              }
            ],
            "predicate_id": "biolink:produces"
          },
          {
            "subject": "phosphoketolase_pathway",
            "predicate": "yields",
            "object": "ethanol",
            "description": "Heterolactic phosphoketolase route co-produces ethanol (or acetate).",
            "evidence": [
              {
                "reference": "DOI:10.3390/molecules31020333",
                "snippet": "glucose is processed through the 6-phosphogluconate/phosphoketolase pathway, leading to the formation of lactate, ethanol or acetate",
                "notes": "heterolactic products include ethanol or acetate."
              }
            ],
            "predicate_id": "biolink:produces"
          },
          {
            "subject": "lactate",
            "predicate": "causes",
            "object": "decreased_ph",
            "description": "Accumulation of lactic acid acidifies the medium.",
            "evidence": [
              {
                "reference": "DOI:10.3390/molecules31020333",
                "snippet": "lactic fermentation channels carbohydrate metabolism toward lactate formation and rapid acidification of the environment",
                "notes": "acidification from lactic acid exerts antagonistic effects on microbes."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "decreased_ph",
            "predicate": "inhibits",
            "object": "pathogenic_microbe",
            "description": "Lactate-driven acidification inhibits spoilage and pathogenic microbes (biopreservation).",
            "evidence": [
              {
                "reference": "DOI:10.3390/molecules31020333",
                "snippet": "lowering pH and inhibiting pathogenic and spoilage microorganisms",
                "notes": "higher lactic acid / lower pH increases inhibition of spoilage and pathogenic microbes."
              }
            ],
            "predicate_id": "RO:0002212"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-30T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate METABOLISM trait (lactic acid fermentation); product-specific sub-variant of the existing Fermentation class (METPO:1002005).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-23T09:01:00Z",
        "curator": "codex",
        "action": "CURATE_PROTEIN_TAXON_EXAMPLE",
        "changes": "Reviewed the graph as mechanistic and added DOI-backed, taxon-paired UniProtKB Q01462 as the L. lactis IL1403 lactate-dehydrogenase exemplar.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-10T14:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (lactic acid fermentation / lactate production) with GO node grounding and METPO/biolink predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-14T06:55:38Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:24996\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 9 evidence-backed generic edges (9 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:12Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 7 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:produces\u00d73, METPO:2000202\u00d72, biolink:causes\u00d71, RO:0002212\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:18Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 3 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:17234\u00d71, CHEBI:16526\u00d71, CHEBI:16236\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:32Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:15361\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-26T07:15:18Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A073JRC3\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:21:11Z",
        "curator": "claude",
        "action": "RETRACT_DEAD_UNIPROT_GROUNDINGS",
        "changes": "Retracted 1 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:23:54Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0004457\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates (1 to has output), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T02:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES_PART2",
        "changes": "Re-grounded 2 causal edge(s) off microbe-domain METPO predicates onto their causal-graph counterparts (2 to produces), issue 301 part 2. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Each replacement is a 1:1 mirror of its source predicate that changes only the domain, so the claim each edge makes is unchanged and directions are unchanged. The replacements are proposed in proposals/metpo_traitmech_v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-30T19:21:37Z",
        "curator": "codex",
        "action": "REVIEW_EVIDENCE_REFERENCE_CHURN",
        "changes": "Offline review for issue 520 retained 6 evidence-reference replacement(s) that PR 511 made on surviving causal edges outside its stated protein-taxon scope. The pre-tranche evidence entries had references but no snippets; the retained entries supply edge-specific snippets and explanatory notes. Reverting would discard that claim-level provenance, so the scope defect is resolved by documenting the decision instead. This audit changed no causal claim or evidence field. Reviewed replacements: DOI:10.3390/fermentation10030168 -> DOI:10.3390/molecules31020333 (6 edges).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000114",
    "label": "lignin degradation",
    "definition": "A biopolymer-degradation metabolism in which an organism breaks down lignin, the recalcitrant aromatic heteropolymer of plant cell walls, using oxidative enzymes such as peroxidases and laccases.",
    "definition_source": "DOI:10.1039/c1np00042j",
    "trait_category": "METABOLISM",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "traitmech:000110"
    ],
    "synonyms": [
      {
        "synonym_text": "ligninolytic",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1039/c1np00042j"
      },
      {
        "synonym_text": "lignin breakdown",
        "synonym_type": "EXACT_SYNONYM",
        "source": "http://purl.obolibrary.org/obo/go/releases/2026-07-26/go-basic.obo"
      },
      {
        "synonym_text": "lignin catabolism",
        "synonym_type": "EXACT_SYNONYM",
        "source": "http://purl.obolibrary.org/obo/go/releases/2026-07-26/go-basic.obo"
      }
    ],
    "xrefs": [
      "GO:0046274"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1039/c1np00042j",
        "notes": "Bugg et al. review pathways for degradation of lignin in bacteria and fungi."
      },
      {
        "reference": "DOI:10.1016/j.cbpa.2015.10.018",
        "notes": "Cragg et al. cover lignin breakdown as part of lignocellulose degradation across the tree of life."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:132919",
        "taxon_label": "Rhodococcus jostii",
        "note": "bacterial lignin degrader (DypB peroxidase)",
        "reference": "PMID:21534568"
      },
      {
        "taxon_id": "NCBITaxon:165695",
        "taxon_label": "Sphingobium",
        "note": "lignin-aromatic catabolism",
        "reference": "PMID:22207743"
      },
      {
        "taxon_id": "NCBITaxon:100226",
        "taxon_label": "Streptomyces coelicolor A3(2)",
        "note": "Strain-level laccase-loss model paired to the small laccase protein example.",
        "reference": "DOI:10.1021/bi500285t"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "lignin_degradation_peroxidase_laccase",
        "title": "Lignin degradation breaks down aromatic plant biopolymers via oxidative enzymes",
        "description": "Evidence-backed causal sketch linking peroxidases and laccases to oxidative cleavage of recalcitrant lignin aromatic heteropolymer.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "The graph combines fungal and bacterial oxidative-enzyme mechanisms. The S. coelicolor small-laccase example supports the laccase branch only; the peroxidase branches remain taxon-independent literature summaries.",
        "nodes": [
          {
            "node_id": "lignin_degradation_trait",
            "label": "lignin degradation",
            "node_type": "TRAIT",
            "grounding": "traitmech:000114",
            "description": "Oxidative breakdown of lignin in plant cell walls."
          },
          {
            "node_id": "oxidative_enzymes",
            "label": "peroxidases and laccases",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Secreted oxidative enzymes acting on the lignin aromatic framework.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "This umbrella node combines phylogenetically and catalytically distinct laccase, DyP, manganese-peroxidase, and lignin-peroxidase families."
          },
          {
            "node_id": "aromatic_monomers",
            "label": "aromatic monomers / oligomers",
            "node_type": "CHEMICAL",
            "description": "Aromatic compounds released from depolymerized lignin."
          },
          {
            "node_id": "laccase",
            "label": "laccase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Multi-copper oxidase (EC 1.10.3.2) acting on lignin and using mediators.",
            "grounding": "GO:0052716",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:Q9XAL8",
                "protein_label": "Copper oxidase",
                "taxon_id": "NCBITaxon:100226",
                "taxon_label": "Streptomyces coelicolor A3(2)",
                "entry_status": "UNREVIEWED",
                "proteome_id": "UP000001973",
                "retrieved_on": "2026-10-22",
                "entry_version": 132,
                "sequence_version": 1,
                "role": "SCO6712 small laccase (ScLAC) tested by a laccase-loss comparison; this accession denotes the laccase component, not all oxidative enzymes in the graph.",
                "evidence": [
                  {
                    "reference": "DOI:10.1021/bi500285t",
                    "snippet": "strain SCdeltaLAC was inefficient in degrading lignin compared to strain SCWT",
                    "notes": "The primary mutant and biochemical study supports a causal role for the S. coelicolor small laccase. UniProtKB Q9XAL8 is the exact unreviewed SCO6712 entry in reference proteome UP000001973."
                  }
                ]
              }
            ]
          },
          {
            "node_id": "dyp_peroxidase",
            "label": "DyP-type peroxidase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Dye-decolorizing peroxidase (EC 1.11.1.19) contributing to lignin depolymerization.",
            "grounding": "InterPro:IPR006314"
          },
          {
            "node_id": "manganese_peroxidase",
            "label": "manganese peroxidase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Manganese peroxidase (EC 1.11.1.13) oxidizing Mn2+ to Mn3+.",
            "grounding": "GO:0016689"
          },
          {
            "node_id": "lignin_peroxidase",
            "label": "lignin peroxidase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Lignin peroxidase (EC 1.11.1.14) cleaving lignin interunit bonds.",
            "grounding": "GO:0016690"
          },
          {
            "node_id": "lignin_depolymerization",
            "label": "lignin depolymerization",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Extracellular oxidative depolymerization of the lignin polymer."
          },
          {
            "node_id": "mn2_ion",
            "label": "Mn2+",
            "node_type": "CHEMICAL",
            "description": "Manganous ion, substrate of manganese peroxidase.",
            "grounding": "CHEBI:29035"
          },
          {
            "node_id": "mn3_oxidant",
            "label": "Mn3+ diffusible oxidant",
            "node_type": "CHEMICAL",
            "description": "Mn3+ generated by MnP that diffuses into lignin acting as oxidant/mediator."
          },
          {
            "node_id": "small_molecule_mediators",
            "label": "small-molecule mediators",
            "node_type": "CHEMICAL",
            "description": "Low-molecular-weight redox mediators extending laccase oxidative reach."
          },
          {
            "node_id": "beta_o4_bond",
            "label": "beta-O-4 aryl ether bond",
            "node_type": "CHEMICAL",
            "description": "Predominant beta-O-4 aryl-ether interunit linkage of lignin."
          },
          {
            "node_id": "ca_cb_bond",
            "label": "Calpha-Cbeta bond",
            "node_type": "CHEMICAL",
            "description": "Calpha-Cbeta carbon-carbon bond in lignin beta-O-4 units."
          }
        ],
        "edges": [
          {
            "subject": "oxidative_enzymes",
            "predicate": "confers",
            "object": "lignin_degradation_trait",
            "description": "Peroxidases and laccases drive oxidative lignin breakdown.",
            "evidence": [
              {
                "reference": "DOI:10.1039/c1np00042j",
                "notes": "Bugg et al. review pathways for degradation of lignin in bacteria and fungi."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "lignin_degradation_trait",
            "predicate": "produces",
            "object": "aromatic_monomers",
            "description": "Lignin oxidation releases aromatic monomers/oligomers.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.cbpa.2015.10.018",
                "notes": "Cragg et al. cover lignin breakdown as part of lignocellulose degradation."
              }
            ],
            "predicate_id": "METPO:2007800"
          },
          {
            "subject": "laccase",
            "predicate": "participates in",
            "object": "lignin_depolymerization",
            "description": "Laccase participates in extracellular lignin depolymerization.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s13068-024-02470-z",
                "notes": "LME including laccase (EC 1.10.3.2) participated in depolymerization of large lignin polymers; broad across taxa."
              }
            ],
            "predicate_id": "biolink:participates_in"
          },
          {
            "subject": "dyp_peroxidase",
            "predicate": "participates in",
            "object": "lignin_depolymerization",
            "description": "DyP-type peroxidase participates in lignin depolymerization.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s13068-024-02470-z",
                "notes": "DyP-decolorizing peroxidase (EC 1.11.1.19) participated in depolymerization of large lignin polymers."
              }
            ],
            "predicate_id": "biolink:participates_in"
          },
          {
            "subject": "manganese_peroxidase",
            "predicate": "oxidizes",
            "object": "mn2_ion",
            "description": "Manganese peroxidase oxidizes Mn2+ to Mn3+ (canonical MnP mechanism).",
            "evidence": [
              {
                "reference": "DOI:10.3390/polym16172388",
                "notes": "Manganese peroxidase oxidizes Mn2+ to Mn3+ (Pei et al. 2024)."
              }
            ],
            "predicate_id": "METPO:2007803"
          },
          {
            "subject": "mn3_oxidant",
            "predicate": "acts as oxidant for",
            "object": "lignin_depolymerization",
            "description": "Mn3+ diffuses into lignin acting as a diffusible oxidant/mediator driving depolymerization.",
            "evidence": [
              {
                "reference": "DOI:10.1039/d3cc05298b",
                "notes": "Mn3+ oxidation product diffuses into lignin structure, acting as a diffusible oxidant or mediator (Bugg 2024)."
              }
            ]
          },
          {
            "subject": "laccase",
            "predicate": "uses",
            "object": "small_molecule_mediators",
            "description": "Laccases can utilise small-molecule mediators to extend oxidative reach.",
            "evidence": [
              {
                "reference": "DOI:10.1039/d3cc05298b",
                "notes": "Laccases or multi-copper oxidases can also utilise small molecule mediators (Bugg 2024)."
              }
            ]
          },
          {
            "subject": "manganese_peroxidase",
            "predicate": "cleaves",
            "object": "beta_o4_bond",
            "description": "MnP cleaves the beta-O-4 bond in phenolic and non-phenolic lignin model dimers.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s13068-024-02583-5",
                "notes": "MnPs could cleave the beta-O-4 bond in phenolic and non-phenolic lignin model dimers (Zhou 2024)."
              }
            ]
          },
          {
            "subject": "lignin_peroxidase",
            "predicate": "cleaves",
            "object": "ca_cb_bond",
            "description": "Lignin peroxidase cleaves the Calpha-Cbeta bond of beta-O-4 model compounds.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s13068-023-02447-4",
                "notes": "ALiP-P3 breaks the Calpha-Cbeta bond of the beta-O-4 model compound (Gu 2024)."
              }
            ]
          },
          {
            "subject": "oxidative_enzymes",
            "predicate": "participates in",
            "object": "lignin_depolymerization",
            "description": "Oxidative lignin-modifying enzymes carry out lignin depolymerization.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s13068-024-02470-z",
                "snippet": "LME including laccase (EC 1.10.3.2) participated in depolymerization of large lignin polymers",
                "notes": "Verified against the free public article text."
              }
            ],
            "predicate_id": "biolink:participates_in"
          },
          {
            "subject": "manganese_peroxidase",
            "predicate": "example of",
            "object": "oxidative_enzymes",
            "description": "Manganese peroxidase is a lignin-modifying oxidative enzyme.",
            "evidence": [
              {
                "reference": "DOI:10.3390/polym16172388",
                "snippet": "Manganese peroxidase oxidizes Mn2+ to Mn3+",
                "notes": "Verified against the free public article text."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "lignin_peroxidase",
            "predicate": "example of",
            "object": "oxidative_enzymes",
            "description": "Lignin peroxidase is a lignin-modifying oxidative enzyme.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s13068-023-02447-4",
                "snippet": "ALiP-P3 breaks the Calpha-Cbeta bond of the beta-O-4 model compound",
                "notes": "Verified against the free public article text."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-06-08T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate METABOLISM trait (lignin degradation); sub-variant of biopolymer degradation.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-10T14:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (oxidative lignin degradation) with RO/METPO predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 7 evidence-backed generic edges (10 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:12Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:participates_in\u00d72, METPO:2000016\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:32Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:29035\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-26T07:15:18Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 3 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A072TFX8\u00d71, UniProtKB:A0A024E2S9\u00d71, UniProtKB:A0A0H3L9R0\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:21:11Z",
        "curator": "claude",
        "action": "RETRACT_DEAD_UNIPROT_GROUNDINGS",
        "changes": "Retracted 3 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:23:54Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (InterPro:IPR017761\u00d71, GO:0016689\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 1 causal edge(s) off enables/RO:0002327 with a TRAIT object (1 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T02:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES_PART2",
        "changes": "Re-grounded 2 causal edge(s) off microbe-domain METPO predicates onto their causal-graph counterparts (1 to oxidizes, 1 to produces), issue 301 part 2. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Each replacement is a 1:1 mirror of its source predicate that changes only the domain, so the claim each edge makes is unchanged and directions are unchanged. The replacements are proposed in proposals/metpo_traitmech_v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-24T09:20:00Z",
        "curator": "codex",
        "action": "CURATE_PROTEIN_TAXON_EXAMPLE",
        "changes": "Scoped the cross-taxon oxidative mechanism, added a DOI-backed S. coelicolor small-laccase example, replaced the generic laccase family grounding with its exact GO activity, and grounded DyP and lignin-peroxidase nodes.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T06:15:39Z",
        "curator": "codex",
        "action": "ADD_EXACT_ONTOLOGY_MATCH",
        "changes": "Ontology exact-match review (2026-08-25): approved exact xref(s): GO:0046274; declared exact synonym(s): 'lignin breakdown', 'lignin catabolism'. Evidence is predicate-scoped in the versioned ontology snapshots; OAK cross-checked direct data, and OLS4 spot-checked release deltas and disputed hits.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T12:15:00Z",
        "curator": "codex",
        "action": "CONNECT_CAUSAL_GRAPH_COMPONENTS",
        "changes": "Resolved issue #183 graph fragmentation (4 components to 1) with 3 public-source connector(s). No paid research service was called.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-22T01:35:00Z",
        "curator": "claude",
        "action": "REFRESH_UNIPROT_ENTRY_VERSION",
        "changes": "Refreshed UniProtKB entry_version against live UniProt REST on 2026-10-22: UniProtKB:Q9XAL8 (131 -> 132 on laccase).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000190",
    "label": "lipolysis",
    "definition": "A metabolism in which a microorganism hydrolyzes triacylglycerols into fatty acids and glycerol through lipase-catalyzed ester cleavage.",
    "definition_source": "DOI:10.1186/s12934-020-01428-8",
    "trait_category": "METABOLISM",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000060"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1186/s12934-020-01428-8",
        "snippet": "Microbial lipases (EC 3.1.1.3) catalyze the hydrolysis of long chain triglycerides",
        "notes": "Chandra et al. review microbial lipases and their use in long-chain triglyceride hydrolysis."
      },
      {
        "reference": "DOI:10.1007/s00253-004-1568-8",
        "snippet": "Lipases, triacylglycerol hydrolases, are an important group of biotechnologically relevant enzymes",
        "notes": "Gupta et al. review bacterial lipases as microbial enzymes for triacylglycerol hydrolysis."
      }
    ],
    "discussions": [
      {
        "discussion_id": "lipolysis-xref-gap",
        "prompt": "Resolve an exact external ontology xref for organism-level microbial lipolysis before adding a TraitRecord xref.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "The pinned METPO snapshot contains only obsolete METPO:1000175 lipolysis, and GO:0016298 denotes the lipase molecular function rather than the organism-level lipid-hydrolysis trait. GO lipid catabolic process classes also include downstream fatty-acid catabolism and are broader than lipase-driven triacylglycerol hydrolysis.",
        "posed_by": "codex",
        "posed_date": "2026-09-14"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-14T21:00:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted lipolysis as a DOI-backed metabolism TraitRecord after a repository-wide duplicate review covering ignored and hidden files; METPO has only an obsolete lipolysis class.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000032",
    "label": "manganese oxidation",
    "definition": "A metabolism in which microorganisms oxidize soluble Mn(II) to Mn(III) or Mn(IV) products through mechanisms including bacterial multicopper oxidases and fungal manganese peroxidases; many systems deposit insoluble manganese oxides.",
    "definition_source": "DOI:10.1016/j.tim.2005.07.009",
    "trait_category": "METABOLISM",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000060"
    ],
    "synonyms": [
      {
        "synonym_text": "Mn(II) oxidation",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1016/j.tim.2005.07.009"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1016/j.tim.2005.07.009",
        "notes": "Tebo et al., \"Geomicrobiology of manganese(II) oxidation\", supports bacterial Mn(II) oxidation to Mn oxides via a multicopper-oxidase mechanism."
      },
      {
        "reference": "DOI:10.1146/annurev.earth.32.101802.120213",
        "notes": "Tebo et al., \"Biogenic manganese oxides\", supports the formation and properties of bacterially produced Mn(III/IV) oxides."
      },
      {
        "reference": "DOI:10.1021/bi002104s",
        "snippet": "ability to bind and oxidize MnII",
        "notes": "Site-directed mutagenesis of manganese peroxidase isozyme 1 supports a distinct fungal enzymatic route from Mn(II) to Mn(III)."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:89",
        "taxon_label": "Leptothrix discophora",
        "note": "Classic Mn(II)-oxidising sheathed bacterium.",
        "reference": "PMID:25149187"
      },
      {
        "taxon_id": "NCBITaxon:2822231",
        "taxon_label": "Phanerodontia chrysosporium",
        "note": "White-rot fungal exemplar for direct Mn(II) oxidation by manganese peroxidase isozyme 1.",
        "reference": "DOI:10.1021/bi002104s"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "manganese_oxidation_multicopper_oxidase",
        "title": "Enzymatic manganese oxidation produces Mn(III/IV) products",
        "description": "Evidence-backed causal sketch retaining the bacterial multicopper-oxidase oxide-forming branch and a distinct fungal manganese-peroxidase Mn(II)-to-Mn(III) branch.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "Both branches describe directly investigated oxidation mechanisms. MofA is not assigned as an exemplar because its exact catalytic role remains uncertain; the reviewed MnP-1 example supports only the fungal peroxidase branch.",
        "nodes": [
          {
            "node_id": "manganese_oxidation_trait",
            "label": "manganese oxidation",
            "node_type": "TRAIT",
            "grounding": "traitmech:000032",
            "description": "Microbial enzymatic oxidation of Mn(II) to Mn(III) or Mn(IV) products."
          },
          {
            "node_id": "multicopper_oxidase",
            "label": "multicopper oxidase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Enzyme family catalyzing Mn(II) oxidation in bacteria.",
            "grounding": "InterPro:IPR045087"
          },
          {
            "node_id": "manganese_peroxidase",
            "label": "manganese peroxidase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Fungal heme peroxidase that uses hydrogen peroxide to oxidize Mn(II) to diffusible Mn(III).",
            "grounding": "GO:0016689",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:Q02567",
                "protein_label": "Manganese peroxidase 1",
                "gene_symbol": "MNP1",
                "taxon_id": "NCBITaxon:2822231",
                "taxon_label": "Phanerodontia chrysosporium",
                "entry_status": "REVIEWED",
                "retrieved_on": "2026-10-22",
                "entry_version": 151,
                "sequence_version": 1,
                "role": "MnP-1 directly oxidizes Mn(II) to Mn(III); it illustrates the fungal peroxidase branch and is not presented as a bacterial multicopper oxidase.",
                "evidence": [
                  {
                    "reference": "DOI:10.1021/bi002104s",
                    "snippet": "manganese peroxidase isozyme 1",
                    "notes": "The primary mutagenesis study tested Mn binding and oxidation by isozyme 1 from P. chrysosporium; UniProtKB Q02567 verifies the reviewed protein and current organism taxonomy."
                  }
                ]
              }
            ]
          },
          {
            "node_id": "manganese_ii",
            "label": "manganese(II)",
            "node_type": "CHEMICAL",
            "description": "Soluble reduced manganese substrate for enzymatic oxidation.",
            "grounding": "CHEBI:29035"
          },
          {
            "node_id": "manganese_iii",
            "label": "manganese(III)",
            "node_type": "CHEMICAL",
            "description": "Oxidized manganese product released by manganese peroxidase.",
            "grounding": "CHEBI:29041"
          },
          {
            "node_id": "mn_oxides",
            "label": "Mn(III/IV) oxides",
            "node_type": "CHEMICAL",
            "description": "Insoluble bacterially-produced manganese oxides."
          },
          {
            "node_id": "molecular_oxygen",
            "label": "molecular oxygen (O2)",
            "node_type": "CHEMICAL",
            "description": "O2 used directly as the terminal oxidant by multicopper-oxidase Mn(II)-oxidizing systems."
          },
          {
            "node_id": "mn_iii_oh_mn_iii_intermediate",
            "label": "Mn(III)(OH)Mn(III) intermediate",
            "node_type": "CHEMICAL",
            "description": "Binuclear Mn(III) intermediate formed during cooperative two-electron Mn(II) oxidation."
          },
          {
            "node_id": "mn_iv_o_mn_iv_intermediate",
            "label": "Mn(IV)(O)Mn(IV) intermediate",
            "node_type": "CHEMICAL",
            "description": "Binuclear Mn(IV) species formed by disproportionation of Mn(III)(OH)Mn(III), en route to MnO2."
          },
          {
            "node_id": "mno2_nanoparticles",
            "label": "MnO2 nanoparticles",
            "node_type": "CHEMICAL",
            "description": "Insoluble MnO2 nanoparticles released as the final biomineral product."
          }
        ],
        "edges": [
          {
            "subject": "manganese_ii",
            "predicate": "is substrate for",
            "object": "manganese_peroxidase",
            "description": "MnP-1 binds and oxidizes Mn(II).",
            "evidence": [
              {
                "reference": "DOI:10.1021/bi002104s",
                "snippet": "ability to bind and oxidize MnII",
                "notes": "Primary mutagenesis and kinetic measurements establish Mn(II) as the substrate of P. chrysosporium MnP-1."
              }
            ]
          },
          {
            "subject": "manganese_peroxidase",
            "predicate": "produces",
            "object": "manganese_iii",
            "description": "Manganese peroxidase oxidizes Mn(II) and releases Mn(III).",
            "evidence": [
              {
                "reference": "DOI:10.1021/bi002104s",
                "snippet": "efficiently release MnIII",
                "notes": "The source describes Mn(III) release as the direct product of the MnP-catalyzed oxidation."
              }
            ],
            "predicate_id": "METPO:2007800"
          },
          {
            "subject": "manganese_peroxidase",
            "predicate": "confers",
            "object": "manganese_oxidation_trait",
            "description": "MnP-1 confers the Mn(II)-oxidizing capacity represented by the fungal branch of this trait.",
            "evidence": [
              {
                "reference": "DOI:10.1021/bi002104s",
                "snippet": "ability to bind and oxidize MnII",
                "notes": "The primary mutagenesis study directly tests Mn(II) oxidation by P. chrysosporium MnP-1, linking the enzyme to the trait without extending the claim to the bacterial multicopper-oxidase branch."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "multicopper_oxidase",
            "predicate": "confers",
            "object": "manganese_oxidation_trait",
            "description": "Multicopper oxidases catalyze the Mn(II) \u2192 Mn(III/IV) oxidation step.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.tim.2005.07.009",
                "snippet": "the reaction might involve a unique multicopper oxidase system capable of a two-electron oxidation of the substrate",
                "notes": "Tebo et al. support bacterial Mn(II) oxidation via a multicopper- oxidase mechanism."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "manganese_oxidation_trait",
            "predicate": "produces",
            "object": "mn_oxides",
            "description": "The metabolism deposits biogenic Mn(III/IV) oxides.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev.earth.32.101802.120213",
                "snippet": "Manganese(IV) oxides produced through microbial activity",
                "notes": "Tebo et al. characterize the formation and properties of bacterially produced Mn(III/IV) oxides."
              }
            ],
            "predicate_id": "METPO:2007800"
          },
          {
            "subject": "manganese_oxidation_trait",
            "predicate": "has electron acceptor",
            "object": "molecular_oxygen",
            "description": "O2 serves as the direct oxidant enabling multicopper-oxidase-mediated Mn(II) oxidation.",
            "evidence": [
              {
                "reference": "DOI:10.1021/jacs.3c06537",
                "snippet": "others can use O2 directly, via multicopper oxidase enzymes.",
                "notes": "Some microbes can use O2 directly via multicopper oxidase (MCO) enzymes for Mn(II) oxidation."
              }
            ],
            "predicate_id": "METPO:2007702"
          },
          {
            "subject": "manganese_oxidation_trait",
            "predicate": "produces",
            "object": "mn_iii_oh_mn_iii_intermediate",
            "description": "A cooperative two-electron oxidation step produces a Mn(III)(OH)Mn(III) intermediate.",
            "evidence": [
              {
                "reference": "DOI:10.1021/jacs.3c06537",
                "snippet": "The second step in the Mnx mechanism is a cooperative two-electron transfer, forming the Mn(III)(OH)Mn(III) intermediate",
                "notes": "Cryo-EM mechanistic model: a cooperative two-electron step producing a Mn(III)(OH)Mn(III) intermediate."
              }
            ],
            "predicate_id": "METPO:2007800"
          },
          {
            "subject": "mn_iii_oh_mn_iii_intermediate",
            "predicate": "disproportionates to form",
            "object": "mn_iv_o_mn_iv_intermediate",
            "description": "Two Mn(III)(OH)Mn(III) species disproportionate to form Mn(IV)(O)Mn(IV).",
            "evidence": [
              {
                "reference": "DOI:10.1021/jacs.3c06537",
                "snippet": "two Mn(III)(OH)Mn(III) intermediates interact and disproportionate, to form the next intermediate, Mn(IV)(O)Mn(IV)",
                "notes": "Disproportionation of two Mn(III)(OH)Mn(III) species to form Mn(IV)(O)Mn(IV)."
              }
            ]
          },
          {
            "subject": "mn_iv_o_mn_iv_intermediate",
            "predicate": "condenses into",
            "object": "mno2_nanoparticles",
            "description": "Mn(IV)(O)Mn(IV) condenses en route to MnO2 nanoparticle release.",
            "evidence": [
              {
                "reference": "DOI:10.1021/jacs.3c06537",
                "snippet": "The Mn(IV)(O)Mn(IV) complex is at the final oxidation level of the MnO2 product, but it needs to lose protons and condense into nanoparticles.",
                "notes": "Mn(IV)(O)Mn(IV) is en route to MnO2, with release of MnO2 nanoparticles."
              }
            ]
          },
          {
            "subject": "mno2_nanoparticles",
            "predicate": "is a",
            "object": "mn_oxides",
            "description": "MnO2 nanoparticles are a form of the insoluble biogenic Mn(III/IV) oxide product.",
            "evidence": [
              {
                "reference": "DOI:10.1021/jacs.3c06537",
                "snippet": "oxidize soluble Mn(II) to insoluble Mn(IV) oxides.",
                "notes": "MnO2 nanoparticles are the final insoluble Mn(IV) oxide biomineral product of the oxidation cascade."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-08-23T09:05:00Z",
        "curator": "codex",
        "action": "CURATE_PROTEIN_TAXON_EXAMPLE",
        "changes": "Reviewed the graph as mechanistic, retained MofA as unresolved, broadened the trait to microorganisms, and added a DOI-backed fungal MnP-1 oxidation branch with taxon-paired UniProtKB Q02567 connected explicitly to the trait.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-30T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate METABOLISM trait (manganese oxidation) from literature research to fill the metal-redox metabolism gap.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-10T14:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (multicopper-oxidase Mn(II) \u2192 Mn(III/IV) oxidation) with RO/METPO predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-14T06:38:15Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A059ZYC2\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 5 evidence-backed generic edges (4 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:12Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d71, METPO:2000202\u00d71, rdfs:subClassOf\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 2 causal edge(s) off enables/RO:0002327 with a TRAIT object (1 to has electron acceptor, 1 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them. 1 electron edge(s) were also reversed back to trait -> chemical, restoring the donor/acceptor role that PR 300 collapsed onto enables (issue 303); the organism-subject problem that forced that collapse does not arise here because these predicates take a causal-node domain rather than METPO:2000001's microbe domain (issue 301). The O2 edge is in that group because the node describes O2 as the terminal oxidant, which names the terminal-electron-acceptor role; the first cut of the migration rule matched only the literal phrase \"electron acceptor\" and would have grounded it to the generic confers relation, dropping exactly the role issue 303 exists to preserve.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T02:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES_PART2",
        "changes": "Re-grounded 2 causal edge(s) off microbe-domain METPO predicates onto their causal-graph counterparts (2 to produces), issue 301 part 2. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Each replacement is a 1:1 mirror of its source predicate that changes only the domain, so the claim each edge makes is unchanged and directions are unchanged. The replacements are proposed in proposals/metpo_traitmech_v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-22T04:26:15Z",
        "curator": "codex",
        "action": "REVIEW_UNIPROT_INSTANCE_GROUNDINGS",
        "changes": "Reviewed 1 organism-specific UniProtKB grounding(s): replaced 1 with taxon-agnostic GO/InterPro terms and retracted 0 to label-only where no exact semantic term was supported (docs/GROUNDING_POLICY.md).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-22T01:35:00Z",
        "curator": "claude",
        "action": "REFRESH_UNIPROT_ENTRY_VERSION",
        "changes": "Refreshed UniProtKB entry_version against live UniProt REST on 2026-10-22: UniProtKB:Q02567 (150 -> 151 on manganese_peroxidase).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000060",
    "label": "metabolism",
    "definition": "A biological process that maintains life in an organism.",
    "definition_source": "DOI:10.1126/science.1238842",
    "trait_category": "METABOLISM",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000630"
    ],
    "created_by": "Anthea Guo",
    "xrefs": [
      "GO:0008152"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1126/science.1238842",
        "snippet": "energy and microbial life",
        "notes": "Microbial-energetics review supports metabolism as the energy and material-flow process maintaining microbial life."
      },
      {
        "reference": "DOI:10.1146/annurev.biochem.71.110601.135503",
        "snippet": "ATP synthesis",
        "notes": "ATP-energetics review supports energy conservation as the central output of catabolic metabolism."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:83333",
        "taxon_label": "Escherichia coli K-12",
        "note": "Strain-level model paired to the reviewed AtpD beta component of the respiratory F-type ATP synthase branch represented in this broad metabolism graph.",
        "reference": "DOI:10.7554/eLife.21598"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "metabolism_substrate_to_growth",
        "title": "Metabolism substrate-to-growth flow",
        "description": "DOI-backed graph linking substrate uptake, catabolism producing ATP and reducing power, biosynthesis, and growth as the core organization of cellular metabolism.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "This upper-level graph is a composite organization of metabolism, not a universal linear pathway. The E. coli AtpD example supports only the respiratory ATP-synthase branch; substrate uptake, biosynthesis, and nonrespiratory energy conservation involve many other proteins.",
        "nodes": [
          {
            "node_id": "metabolism_trait",
            "label": "metabolism",
            "node_type": "TRAIT",
            "grounding": "METPO:1000060",
            "description": "Integrated biological process of substrate, energy, and material flow maintaining cellular life."
          },
          {
            "node_id": "substrate_uptake",
            "label": "substrate uptake",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Transport of carbon, nitrogen, and other substrates into the cell."
          },
          {
            "node_id": "catabolism",
            "label": "catabolism",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Breakdown of substrates yielding ATP and reducing equivalents.",
            "grounding": "GO:0009056"
          },
          {
            "node_id": "atp_and_reducing_power",
            "label": "ATP and reducing power",
            "node_type": "CHEMICAL",
            "description": "Energy currency (ATP) and electron carriers (NAD(P)H, FADH2) produced by catabolism."
          },
          {
            "node_id": "biosynthesis",
            "label": "biosynthesis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Anabolic synthesis of cellular building blocks and macromolecules.",
            "grounding": "GO:0009058"
          },
          {
            "node_id": "cellular_growth",
            "label": "cellular growth",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Net accumulation of biomass enabling division and survival.",
            "grounding": "GO:0016049"
          },
          {
            "node_id": "respiratory_electron_transport",
            "label": "respiratory electron transport chain",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Membrane electron transfer through respiratory chains that translocates protons.",
            "grounding": "GO:0022904"
          },
          {
            "node_id": "proton_motive_force",
            "label": "proton motive force",
            "node_type": "STATE",
            "description": "Electrochemical proton gradient across the membrane storing potential energy.",
            "grounding": "METPO:1007500"
          },
          {
            "node_id": "atp_synthase",
            "label": "ATP synthase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Membrane-bound enzyme complex that phosphorylates ADP to ATP using the proton motive force.",
            "grounding": "GO:0045259",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:P0ABB4",
                "protein_label": "ATP synthase subunit beta",
                "gene_symbol": "atpD",
                "taxon_id": "NCBITaxon:83333",
                "taxon_label": "Escherichia coli K-12",
                "entry_status": "REVIEWED",
                "retrieved_on": "2026-10-22",
                "entry_version": 156,
                "sequence_version": 2,
                "role": "Beta component of the F1 catalytic head of the E. coli F1Fo ATP synthase; this accession is not presented as the complete rotary complex.",
                "evidence": [
                  {
                    "reference": "DOI:10.7554/eLife.21598",
                    "snippet": "the potential energy of the proton motive force into rotation of the central stalk that drives conformational changes in the F1 catalytic sites",
                    "notes": "The primary cryo-EM study resolves the E. coli F1Fo complex and its beta-containing catalytic head. UniProtKB P0ABB4 verifies the reviewed AtpD beta component and K-12 taxon."
                  }
                ]
              }
            ]
          },
          {
            "node_id": "atp_production",
            "label": "ATP production",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "ATP biosynthetic process generating the cellular energy currency."
          },
          {
            "node_id": "respiration_energy_cost",
            "label": "respiration energy demand",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Carbon diverted to respiration for energy generation, maintenance, and enzyme production."
          },
          {
            "node_id": "carbon_use_efficiency",
            "label": "carbon use efficiency",
            "node_type": "QUALITY",
            "description": "Fraction of assimilated carbon converted to biomass rather than respired or exuded."
          },
          {
            "node_id": "substrate_complexity",
            "label": "substrate complexity",
            "node_type": "QUALITY",
            "description": "Degree to which substrates require enzymatic degradation before uptake."
          },
          {
            "node_id": "metabolic_energy_cost",
            "label": "energetic cost of metabolism",
            "node_type": "QUALITY",
            "description": "Energy expenditure required to acquire and process substrates."
          }
        ],
        "edges": [
          {
            "subject": "substrate_uptake",
            "predicate": "feeds",
            "object": "catabolism",
            "description": "Imported substrates feed the catabolic reactions of the cell.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.1238842",
                "snippet": "energy and microbial life",
                "notes": "Supports substrate uptake as the input to catabolic energy flow."
              }
            ]
          },
          {
            "subject": "catabolism",
            "predicate": "has output",
            "object": "atp_and_reducing_power",
            "description": "Catabolic reactions generate ATP and reducing equivalents.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev.biochem.71.110601.135503",
                "snippet": "ATP synthesis",
                "notes": "Supports ATP and reducing power as canonical outputs of catabolism."
              }
            ],
            "predicate_id": "RO:0002234"
          },
          {
            "subject": "atp_and_reducing_power",
            "predicate": "enables",
            "object": "biosynthesis",
            "description": "ATP and reducing power fuel biosynthetic reactions.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev.biochem.71.110601.135503",
                "snippet": "ATP synthesis",
                "notes": "Supports ATP-driven biosynthesis as the central coupling of energy to anabolism."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "biosynthesis",
            "predicate": "enables",
            "object": "cellular_growth",
            "description": "Biosynthesis supports accumulation of biomass and growth.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.1238842",
                "snippet": "energy and microbial life",
                "notes": "Supports biosynthesis-driven growth as the goal of cellular metabolism."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "cellular_growth",
            "predicate": "realizes",
            "object": "metabolism_trait",
            "description": "The coordinated substrate-uptake / catabolism / biosynthesis / growth flow realizes the metabolism phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.1238842",
                "snippet": "energy and microbial life",
                "notes": "Supports metabolism as the integrated process maintaining microbial life."
              }
            ]
          },
          {
            "subject": "respiratory_electron_transport",
            "predicate": "generates",
            "object": "proton_motive_force",
            "description": "Electron transfer through respiratory chains translocates protons to create the gradient.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.heliyon.2023.e22459",
                "notes": "Proton movement driven by respiratory electron transfer creates the gradient that powers ATP synthesis."
              }
            ],
            "predicate_id": "biolink:produces"
          },
          {
            "subject": "atp_synthase",
            "predicate": "uses",
            "object": "proton_motive_force",
            "description": "ATP synthase consumes the electrochemical proton motive force to drive phosphorylation.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.heliyon.2023.e22459",
                "notes": "ATP synthase converts ADP + Pi to ATP using an electrochemical proton motive force generated by respiratory chains."
              }
            ]
          },
          {
            "subject": "atp_synthase",
            "predicate": "produces",
            "object": "atp_production",
            "description": "ATP synthase phosphorylates ADP to ATP, generating cellular energy currency.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.heliyon.2023.e22459",
                "notes": "Membrane-bound ATP synthase converts potential energy to ATP by phosphorylating ADP."
              }
            ],
            "predicate_id": "METPO:2007800"
          },
          {
            "subject": "respiration_energy_cost",
            "predicate": "decreases",
            "object": "carbon_use_efficiency",
            "description": "Diverting more carbon to respiration lowers the fraction converted to biomass.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-024-52160-5",
                "notes": "CUE declines when more carbon is diverted to respiration to generate energy for uptake, maintenance, and enzyme production."
              }
            ],
            "predicate_id": "RO:0002212"
          },
          {
            "subject": "substrate_complexity",
            "predicate": "increases",
            "object": "metabolic_energy_cost",
            "description": "Substrates needing enzymatic degradation raise the energetic cost of metabolism.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-024-52160-5",
                "notes": "Energy required depends on whether compounds are directly taken up or need enzymatic degradation."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "respiratory_electron_transport",
            "predicate": "contributes to",
            "object": "catabolism",
            "description": "Respiratory electron transport is an energy-conserving component of catabolism.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.heliyon.2023.e22459",
                "snippet": "The transfer of electrons through the respiratory chain is tied to proton movement",
                "notes": "Verified against the free public article text."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "carbon_use_efficiency",
            "predicate": "contributes to",
            "object": "cellular_growth",
            "description": "Carbon-use efficiency measures allocation of assimilated carbon to new biomass.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-024-52160-5",
                "snippet": "represents the fraction of C uptake allocated to the production of new microbial biomass",
                "notes": "Verified against the free public article text."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "substrate_uptake",
            "predicate": "contributes to",
            "object": "metabolic_energy_cost",
            "description": "The accessibility of substrates determines the energetic cost of uptake and processing.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-024-52160-5",
                "snippet": "Polymeric substrates like lignin and cellulose need depolymerization before cellular uptake, whereas smaller substrates readily diffuse across membranes",
                "notes": "Verified against the free public article text."
              }
            ],
            "predicate_id": "RO:0002326"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.810665+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-11T23:30:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed causal graph framing metabolism as the integrated substrate-uptake / catabolism / biosynthesis / growth flow that maintains cellular life.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:30Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:19Z",
        "curator": "claude",
        "action": "RENAME_PREDICATE_LABELS",
        "changes": "Renamed 1 causal-edge predicate label(s) to align with existing groundings: supports \u2192 enables \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:21Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-26T05:00:47Z",
        "curator": "claude",
        "action": "RENAME_PREDICATE_LABELS",
        "changes": "Renamed 1 causal-edge predicate label(s) to align with existing groundings: powers \u2192 enables \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-26T05:00:50Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-14T05:51:46Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0016049\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 5 evidence-backed generic edges (8 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:12Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 4 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:produces\u00d71, METPO:2000202\u00d71, RO:0002212\u00d71, RO:0002213\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:18Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A415TT77\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:32Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0022904\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:21:11Z",
        "curator": "claude",
        "action": "RETRACT_DEAD_UNIPROT_GROUNDINGS",
        "changes": "Retracted 1 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates (1 to has output), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T02:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES_PART2",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates onto their causal-graph counterparts (1 to produces), issue 301 part 2. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Each replacement is a 1:1 mirror of its source predicate that changes only the domain, so the claim each edge makes is unchanged and directions are unchanged. The replacements are proposed in proposals/metpo_traitmech_v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-15T02:00:00Z",
        "curator": "claude",
        "action": "NORMALISE_NODE_TYPE",
        "changes": "Normalised causal-node type(s) so one node_id means one thing corpus-wide (issue 356): proton_motive_force: CHEMICAL -> STATE. The schema's OWN example of STATE: 'a bioenergetic or molecular state of the cell (e.g. proton motive force ...) ... the state is the gradient / steady-value, not its establishment'. All 35 occurrences describe the gradient -- every description across all four types reads 'electrochemical proton gradient', including the 13 typed BIOLOGICAL_PROCESS ('Transmembrane electrochemical gradient generated by respiration'), which name the gradient and its provenance rather than the generating process. Nothing here means the establishment, so this is a retype and not a rename; records that DO mean the process already use a separate id (proton_motive_force_generation in ph_delta.yaml). Also settles the one edge #356 was filed for: phototrophic.yaml's CAPACITY typing was blocking `powers` (METPO:2007900), which is gated to BIOLOGICAL_PROCESS|STATE.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-20T07:10:36Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (METPO:1007500\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-24T08:45:00Z",
        "curator": "codex",
        "action": "CURATE_PROTEIN_TAXON_EXAMPLE",
        "changes": "Retained the upper metabolism graph with an explicit composite-mechanism scope, added a DOI-backed E. coli K-12 AtpD beta-subunit example, and grounded the ATP synthase node to the current GO complex term without treating one component as the whole complex.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T06:15:39Z",
        "curator": "codex",
        "action": "ADD_EXACT_ONTOLOGY_MATCH",
        "changes": "Ontology exact-match review (2026-08-25): approved exact xref(s): GO:0008152. Evidence is predicate-scoped in the versioned ontology snapshots; OAK cross-checked direct data, and OLS4 spot-checked release deltas and disputed hits.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T12:15:00Z",
        "curator": "codex",
        "action": "CONNECT_CAUSAL_GRAPH_COMPONENTS",
        "changes": "Resolved issue #183 graph fragmentation (4 components to 1) with 3 public-source connector(s). No paid research service was called.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-22T01:35:00Z",
        "curator": "claude",
        "action": "REFRESH_UNIPROT_ENTRY_VERSION",
        "changes": "Refreshed UniProtKB entry_version against live UniProt REST on 2026-10-22: UniProtKB:P0ABB4 (155 -> 156 on atp_synthase).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000844",
    "label": "Methanogenesis",
    "definition": "A metabolism in which methane is produced as the primary end product through the reduction of carbon-containing compounds, formate, methanol, or acetate, exclusively performed by methanogenic archaea under strictly anaerobic conditions.",
    "definition_source": "DOI:10.1146/annurev-micro-011720-122807",
    "trait_category": "METABOLISM",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000060"
    ],
    "synonyms": [
      {
        "synonym_text": "Biological methanation",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "Biomethanation",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "Carbonate respiration",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "methane biosynthesis",
        "synonym_type": "EXACT_SYNONYM",
        "source": "http://purl.obolibrary.org/obo/go/releases/2026-07-26/go-basic.obo"
      },
      {
        "synonym_text": "methane biosynthetic process",
        "synonym_type": "EXACT_SYNONYM",
        "source": "http://purl.obolibrary.org/obo/go/releases/2026-07-26/go-basic.obo"
      }
    ],
    "created_by": "Luke Wang",
    "xrefs": [
      "GO:0015948"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev-micro-011720-122807",
        "snippet": "from CO2 and H2 to methane",
        "notes": "Supports hydrogenotrophic methanogenesis as a methane-producing archaeal pathway."
      },
      {
        "reference": "DOI:10.1021/acs.biochem.9b00164",
        "snippet": "catalyzes the reversible reduction of methyl-coenzyme M",
        "notes": "Supports methyl-coenzyme M reductase as the terminal methane-forming enzyme."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:2190",
        "taxon_label": "Methanocaldococcus jannaschii",
        "note": "Archetypal hydrogenotrophic methanogen (4 H2 + CO2 -> CH4 + 2 H2O); first archaeal genome sequenced.",
        "reference": "https://pmc.ncbi.nlm.nih.gov/articles/PMC6616113/"
      },
      {
        "taxon_id": "NCBITaxon:243232",
        "taxon_label": "Methanocaldococcus jannaschii DSM 2661",
        "note": "Genome-strain exemplar paired to the experimentally characterized McrA component of methyl-coenzyme M reductase I.",
        "reference": "DOI:10.1074/jbc.M503492200"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "methanogenesis_c1_reduction",
        "title": "Methanogenesis C1 reduction mechanism",
        "description": "Evidence-backed causal sketch linking anoxic C1 reduction, methyl-coenzyme M reductase, and methane formation.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "Represents hydrogenotrophic C1 reduction and the terminal methyl-coenzyme M reductase reaction, with branch labels for alternative methanogenic substrates; the exemplar is explicitly the McrA component, not the entire complex.",
        "nodes": [
          {
            "node_id": "methanogenesis_trait",
            "label": "Methanogenesis",
            "node_type": "TRAIT",
            "grounding": "METPO:1000844",
            "description": "Methane-producing archaeal metabolism."
          },
          {
            "node_id": "anoxic_habitat",
            "label": "anoxic habitat",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Oxygen-depleted condition where hydrogenotrophic methanogenesis occurs."
          },
          {
            "node_id": "carbon_dioxide",
            "label": "carbon dioxide",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:16526",
            "description": "C1 substrate reduced during hydrogenotrophic methanogenesis."
          },
          {
            "node_id": "molecular_hydrogen",
            "label": "molecular hydrogen",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:18276",
            "description": "Electron donor for hydrogenotrophic methanogenesis."
          },
          {
            "node_id": "methyl_coenzyme_m_reductase",
            "label": "methyl-coenzyme M reductase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Nickel F430 enzyme catalyzing the terminal methane-forming step.",
            "grounding": "GO:0044674",
            "gene_symbols": [
              "mcrA",
              "mcrB",
              "mcrG"
            ],
            "operon": "mcrABG",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:Q58256",
                "protein_label": "Methyl-coenzyme M reductase I subunit alpha",
                "gene_symbol": "mcrA",
                "taxon_id": "NCBITaxon:243232",
                "taxon_label": "Methanocaldococcus jannaschii DSM 2661",
                "entry_status": "REVIEWED",
                "proteome_id": "UP000000805",
                "retrieved_on": "2026-10-22",
                "entry_version": 147,
                "sequence_version": 2,
                "role": "Alpha subunit of methyl-coenzyme M reductase I, the multisubunit enzyme catalyzing the terminal methane-forming step; this accession is not presented as the complete McrABG complex.",
                "evidence": [
                  {
                    "reference": "DOI:10.1074/jbc.M503492200",
                    "snippet": "MJ0846 (McrA, 61227 Da)",
                    "notes": "The primary M. jannaschii study identifies the exact McrA component used in its methyl-coenzyme M reductase preparation; UniProtKB Q58256 verifies the reviewed strain-level entry."
                  },
                  {
                    "reference": "DOI:10.1016/S0076-6879(05)97026-2",
                    "snippet": "catalyzes the last step in methanogenesis",
                    "notes": "The mechanistic methods paper establishes the terminal pathway role of methyl-coenzyme M reductase while the first citation establishes the exact M. jannaschii component identity."
                  }
                ]
              }
            ]
          },
          {
            "node_id": "coenzyme_f430",
            "label": "coenzyme F430",
            "node_type": "CHEMICAL",
            "description": "Nickel-containing prosthetic group of methyl-coenzyme M reductase.",
            "grounding": "CHEBI:28265"
          },
          {
            "node_id": "methane",
            "label": "methane",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:16183",
            "description": "Primary reduced carbon end product."
          },
          {
            "node_id": "acetoclastic_methanogenesis",
            "label": "acetoclastic methanogenesis",
            "node_type": "TRAIT",
            "grounding": "traitmech:000191",
            "description": "Acetate-using methanogenesis branch."
          },
          {
            "node_id": "acetate",
            "label": "acetate",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:30089",
            "description": "C2 substrate for acetoclastic methanogenesis."
          },
          {
            "node_id": "methyl_based_methanogenesis",
            "label": "methyl-based methanogenesis",
            "node_type": "TRAIT",
            "grounding": "traitmech:000192",
            "description": "Methyl-substrate methanogenesis branch."
          },
          {
            "node_id": "methylated_compounds",
            "label": "methylated compounds",
            "node_type": "CHEMICAL",
            "description": "Methyl-bearing substrates (e.g. methanol, methylamines) feeding methyl-based methanogenesis."
          },
          {
            "node_id": "coenzyme_b",
            "label": "coenzyme B",
            "node_type": "CHEMICAL",
            "description": "Thiol cofactor (CoB) required in the terminal methane-forming reaction."
          },
          {
            "node_id": "coenzyme_m",
            "label": "coenzyme M",
            "node_type": "CHEMICAL",
            "description": "Methyl-carrier cofactor (CoM) onto which methyl groups are transferred to form methyl-CoM."
          },
          {
            "node_id": "coenzyme_f420",
            "label": "coenzyme F420 (F420H2)",
            "node_type": "CHEMICAL",
            "description": "Reduced deazaflavin electron carrier donating electrons for C1 reduction steps."
          }
        ],
        "edges": [
          {
            "subject": "methanogenesis_trait",
            "predicate": "occurs in",
            "object": "anoxic_habitat",
            "description": "Hydrogenotrophic methanogenesis is associated with anoxic habitats.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-micro-011720-122807",
                "snippet": "terminal step of microbial biomass degradation in anoxic habitats",
                "notes": "Review places hydrogenotrophic methanogenesis in anoxic microbial biomass degradation."
              }
            ],
            "predicate_id": "biolink:occurs_in"
          },
          {
            "subject": "carbon_dioxide",
            "predicate": "reduced with electron donor",
            "object": "molecular_hydrogen",
            "description": "Carbon dioxide is reduced using electrons derived from hydrogen.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-micro-011720-122807",
                "snippet": "from CO2 and H2 to methane",
                "notes": "Supports the CO2 plus H2 substrate relationship."
              }
            ]
          },
          {
            "subject": "methyl_coenzyme_m_reductase",
            "predicate": "has prosthetic group",
            "object": "coenzyme_f430",
            "description": "Methyl-coenzyme M reductase contains nickel coenzyme F430.",
            "evidence": [
              {
                "reference": "DOI:10.1021/acs.biochem.9b00164",
                "snippet": "harbors the nickel(I) hydrocorphin coenzyme F-430",
                "notes": "Supports F430 as the prosthetic group of the enzyme."
              }
            ]
          },
          {
            "subject": "methyl_coenzyme_m_reductase",
            "predicate": "catalyzes formation of",
            "object": "methane",
            "description": "Methyl-coenzyme M reductase catalyzes the terminal methane-forming reaction.",
            "evidence": [
              {
                "reference": "DOI:10.1021/acs.biochem.9b00164",
                "snippet": "catalyzes the reversible reduction of methyl-coenzyme M",
                "notes": "Source describes methane formation by methyl-coenzyme M reductase."
              }
            ],
            "predicate_id": "biolink:catalyzes"
          },
          {
            "subject": "methanogenesis_trait",
            "predicate": "produces",
            "object": "methane",
            "description": "The defining output of methanogenesis is methane.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-micro-011720-122807",
                "snippet": "from CO2 and H2 to methane",
                "notes": "Supports methane as the reduced product of hydrogenotrophic methanogenesis."
              }
            ],
            "predicate_id": "METPO:2007800"
          },
          {
            "subject": "acetate",
            "predicate": "serves as substrate for",
            "object": "acetoclastic_methanogenesis",
            "description": "Acetate is the substrate split to methane and CO2 in acetoclastic methanogenesis.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2017.01198",
                "snippet": "acetoclastic methanogenesis using acetate",
                "notes": "acetoclastic (splitting acetate to CH4 and CO2)."
              }
            ]
          },
          {
            "subject": "methylated_compounds",
            "predicate": "serves as substrate for",
            "object": "methyl_based_methanogenesis",
            "description": "Methylated compounds are the substrates for methyl-based methanogenesis.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2017.01198",
                "snippet": "methylotrophic methanogenesis using methylated compounds",
                "notes": "methylotrophic (using methylated compounds)."
              }
            ]
          },
          {
            "subject": "coenzyme_b",
            "predicate": "is required for",
            "object": "methane",
            "description": "Coenzyme B reacts with methyl-CoM in the terminal step to yield methane.",
            "evidence": [
              {
                "reference": "DOI:10.1021/ja906367h",
                "snippet": "It converts the thioether methyl-coenzyme M and the thiol coenzyme B into methane and the heterodisulfide of coenzyme M and coenzyme B.",
                "notes": "methyl-CoM reacts with coenzyme B (CoB) to yield methane."
              }
            ]
          },
          {
            "subject": "coenzyme_m",
            "predicate": "carries methyl group in",
            "object": "methanogenesis_trait",
            "description": "Methyltransferases transfer methyl groups to coenzyme M to form methyl-CoM.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mmbr.00024-22",
                "snippet": "the methyl group first transferred to a substrate-specific corrinoid protein and then to coenzyme M (CoM) to produce methyl-CoM",
                "notes": "methyltransferases transfer methyl groups ultimately to CoM to form methyl-CoM."
              }
            ]
          },
          {
            "subject": "coenzyme_f420",
            "predicate": "donates electrons to",
            "object": "carbon_dioxide",
            "description": "Reduced coenzyme F420 donates electrons for reduction of C1 intermediates derived from CO2.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2023.1296008",
                "snippet": "Reduced coenzyme F420 (F420H2), generated by an F420-reducing [NiFe]-hydrogenase (Frh) with H2, serves as a direct electron donor for the reduction of methenyl and methylene forms.",
                "notes": "Reduced coenzyme F420 (F420H2) donates electrons for reductions of methenyl/methylene intermediates."
              }
            ],
            "predicate_id": "METPO:2007403"
          },
          {
            "subject": "carbon_dioxide",
            "predicate": "participates in",
            "object": "methanogenesis_trait",
            "description": "CO2 is the carbon substrate of hydrogenotrophic methanogenesis.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2017.01198",
                "snippet": "Three major methanogenic pathways are known based on the type of carbon sources catabolized, i.e., hydrogenotrophic methanogenesis using CO2 and H2",
                "notes": "Verified against the freely available article full text."
              }
            ],
            "predicate_id": "biolink:participates_in"
          },
          {
            "subject": "acetoclastic_methanogenesis",
            "predicate": "part of",
            "object": "methanogenesis_trait",
            "description": "Acetoclastic methanogenesis is an acetate-using branch.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2017.01198",
                "snippet": "hydrogenotrophic methanogenesis using CO2 and H2, acetoclastic methanogenesis using acetate",
                "notes": "Verified against the freely available article full text."
              }
            ],
            "predicate_id": "biolink:part_of"
          },
          {
            "subject": "methyl_based_methanogenesis",
            "predicate": "part of",
            "object": "methanogenesis_trait",
            "description": "Methyl-based methanogenesis is a methyl-substrate branch.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2017.01198",
                "snippet": "acetoclastic methanogenesis using acetate, and methylotrophic methanogenesis using methylated compounds, such as methanol, methylamines",
                "notes": "Verified against the freely available article full text."
              }
            ],
            "predicate_id": "biolink:part_of"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-08-23T09:07:00Z",
        "curator": "codex",
        "action": "CURATE_PROTEIN_TAXON_EXAMPLE",
        "changes": "Reviewed the graph as mechanistic, documented the mcrABG cluster as an exact reviewed label-only node, and added DOI-backed UniProtKB Q58256 as the M. jannaschii McrA component exemplar.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-05T01:35:46.914643+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-07T00:00:00-07:00",
        "curator": "codex",
        "action": "ADDED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed causal graph for anoxic C1 reduction to methane and the methyl-coenzyme M reductase terminal step.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:30Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T05:05:14Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A099T5Q9\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-26T05:00:48Z",
        "curator": "claude",
        "action": "RENAME_PREDICATE_LABELS",
        "changes": "Renamed 1 causal-edge predicate label(s) to align with existing groundings: occurs under \u2192 occurs in \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-26T05:00:50Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:occurs_in\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-13T21:03:26Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:catalyzes\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-14T05:51:46Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:28265\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-17T04:09:44Z",
        "curator": "claude",
        "action": "REMOVE_REDUNDANT_SYNONYM",
        "changes": "Removed 1 synonym(s) whose text duplicated the label (seeder redundancy; no information lost).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 6 evidence-backed generic edges (8 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:12Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d71, METPO:2007403\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T02:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES_PART2",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates onto their causal-graph counterparts (1 to produces), issue 301 part 2. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Each replacement is a 1:1 mirror of its source predicate that changes only the domain, so the claim each edge makes is unchanged and directions are unchanged. The replacements are proposed in proposals/metpo_traitmech_v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T08:00:00Z",
        "curator": "claude",
        "action": "REGROUND_CAUSAL_EDGE",
        "changes": "Re-grounded causal edge(s) off enables/RO:0002327 onto encodes (biolink:encodes), issue 334. biolink declares enables range 'biological process or activity', which only BIOLOGICAL_PROCESS, PATHWAY and MOLECULAR_FUNCTION satisfy, so an edge pointing at a GENE_OR_PROTEIN entailed a false type. The replacements are chosen per idiom rather than swept: a gene cluster ENCODES its product, a subunit is PART OF the complex it belongs to, and an energy source or acquired repertoire CONTRIBUTES TO the machine it powers or composes. All three declare no rdfs:domain or rdfs:range, so none can reintroduce the class of defect being removed.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T09:30:00Z",
        "curator": "claude",
        "action": "REGROUND_CAUSAL_EDGE",
        "changes": "Correction to the REGROUND_CAUSAL_EDGE event above, issue 334 review. That event claimed \"All three declare no rdfs:domain or rdfs:range, so none can reintroduce the class of defect being removed\". For biolink:encodes that justification was vacuous: the term is ABSENT from the pinned biolink 4.4.0 model, so it trivially declares nothing, and the check used could not distinguish absent from unconstrained. reports/biolink_coverage.tsv already recorded it as the only applied biolink: CURIE with no backing slot. The grounding is retained because a gene CLUSTER to protein COMPLEX edge does not fit `has gene product`'s range of gene product mixin, so repointing would trade a missing term for a wrong range; mappings/predicate_grounding.tsv now states plainly that it is a local coinage. Tracked in issue 342. The edge itself is unchanged and is still an improvement on enables, whose declared range it genuinely violated.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-07T04:00:00Z",
        "curator": "claude",
        "action": "REGROUND_CAUSAL_EDGE",
        "changes": "Re-grounded the `encodes` edge(s) from biolink:encodes to METPO:2007813, issue 342. biolink:encodes is NOT a slot in the pinned biolink 4.4.0 model, so the CURIE resolved to nothing upstream while looking like an upstream term to anyone reading this record -- the disclaimer saying otherwise lived in mappings/predicate_grounding.tsv, which is not read at the point of use. RO:0002205 (has gene product) is the nearest real term but relates a GENE to a gene product, whereas these edges relate a gene cluster or operon to a protein complex or a biosynthetic process, which its range does not admit; that mismatch is why the coinage existed. METPO:2007813 is proposed in proposals/metpo_traitmech_v9 and is a placeholder id until METPO mints it, which puts it in the same state as the rest of that cohort rather than in a category of its own.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-22T04:26:15Z",
        "curator": "codex",
        "action": "REVIEW_UNIPROT_INSTANCE_GROUNDINGS",
        "changes": "Reviewed 1 organism-specific UniProtKB grounding(s): replaced 1 with taxon-agnostic GO/InterPro terms and retracted 0 to label-only where no exact semantic term was supported (docs/GROUNDING_POLICY.md).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T01:14:58Z",
        "curator": "codex",
        "action": "ADD_EXACT_ONTOLOGY_MATCH",
        "changes": "Ontology exact-match review (2026-08-25): approved exact xref(s): GO:0015948; declared exact synonym(s): 'methane biosynthesis', 'methane biosynthetic process'. Evidence is predicate-scoped in the versioned ontology snapshots; OAK cross-checked direct data, and OLS4 spot-checked release deltas and disputed hits.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-30T19:21:37Z",
        "curator": "codex",
        "action": "REVIEW_EVIDENCE_REFERENCE_CHURN",
        "changes": "Offline review for issue 520 retained 3 evidence-reference replacement(s) that PR 511 made on surviving causal edges outside its stated protein-taxon scope. The pre-tranche evidence entries had references but no snippets; the retained entries supply edge-specific snippets and explanatory notes. Reverting would discard that claim-level provenance, so the scope defect is resolved by documenting the decision instead. This audit changed no causal claim or evidence field. Reviewed replacements: DOI:10.1007/s00253-023-12700-3 -> DOI:10.3389/fmicb.2017.01198 (2 edges); DOI:10.1128/mmbr.00024-22 -> DOI:10.1021/ja906367h (1 edge).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T09:00:00Z",
        "curator": "codex",
        "action": "CONNECT_CAUSAL_GRAPH_COMPONENTS",
        "changes": "Resolved issue #183 graph fragmentation (4 components to 1) using 3 public-source, verbatim-snippet-backed connector(s). No paid research service was called.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-14T21:20:00Z",
        "curator": "codex",
        "action": "GROUND_CAUSAL_NODE",
        "changes": "Grounded the acetoclastic methanogenesis causal node to traitmech:000191 after minting the same-scope acetate-using methanogenesis TraitRecord.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-14T21:27:00Z",
        "curator": "codex",
        "action": "GROUND_CAUSAL_NODE",
        "changes": "Grounded the methyl-based methanogenesis causal node to traitmech:000192 after minting the same-scope methyl-substrate methanogenesis TraitRecord.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-22T01:35:00Z",
        "curator": "claude",
        "action": "REFRESH_UNIPROT_ENTRY_VERSION",
        "changes": "Refreshed UniProtKB entry_version against live UniProt REST on 2026-10-22: UniProtKB:Q58256 (146 -> 147 on methyl_coenzyme_m_reductase).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000133",
    "label": "methanol oxidation",
    "definition": "A metabolism in which an organism oxidizes methanol, typically to formaldehyde, as a carbon and energy source.",
    "definition_source": "DOI:10.1126/science.aaf4507",
    "trait_category": "METABOLISM",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000060"
    ],
    "synonyms": [
      {
        "synonym_text": "methanol_oxidation",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1126/science.aaf4507"
      }
    ],
    "xrefs": [
      "GO:0015946"
    ],
    "evidence": [
      {
        "reference": "DOI:10.3389/fbioe.2021.787791",
        "snippet": "methanol utilization in methylotrophy",
        "notes": "Le et al. review methanol dehydrogenases as primary enzymes that convert methanol to formaldehyde during methylotrophy."
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-08T00:00:00Z",
        "curator": "codex",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed a DOI-backed FAPROTAX metabolic capability from proposals/metpo_traitmech_v11 after repository-wide duplicate review.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-21T20:01:04Z",
        "curator": "claude",
        "action": "RECORD_MECHANISM_KNOWLEDGE_GAP",
        "changes": "Recorded OPEN KNOWLEDGE_GAP discussion (methanol-oxidation-causal-graph-source-gap) documenting the source-limited mechanism gap for causal_graphs.",
        "llm_assisted": true
      }
    ],
    "discussions": [
      {
        "discussion_id": "methanol-oxidation-causal-graph-source-gap",
        "prompt": "Add primary literature evidence for PQQ- or NAD-dependent methanol dehydrogenase (MxaFI/XoxF/Mdh), formaldehyde oxidation, and a strain-matched canonical example before constructing causal_graphs.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "The current record carries a single 37-character phrase ('methanol utilization in methylotrophy' in DOI:10.3389/fbioe.2021.787791) without verbatim catalytic or electron-transfer quotes in the evidence block.",
        "posed_by": "claude",
        "posed_date": "2026-10-21",
        "evidence": [
          {
            "reference": "DOI:10.3389/fbioe.2021.787791",
            "supports": "PARTIAL",
            "snippet": "methanol utilization in methylotrophy",
            "explanation": "Existing record-level evidence supports the high-level metabolic trait definition but does not provide multi-step enzymatic mechanism quotes for a connected causal graph."
          }
        ]
      }
    ]
  },
  {
    "identifier": "traitmech:000192",
    "label": "methyl-based methanogenesis",
    "definition": "A methanogenesis in which methylated compounds donate methyl groups that are transferred to coenzyme M and reduced to methane.",
    "definition_source": "DOI:10.1128/mmbr.00024-22",
    "trait_category": "METABOLISM",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000844"
    ],
    "synonyms": [
      {
        "synonym_text": "methylotrophic methanogenesis",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.3389/fmicb.2017.01198"
      },
      {
        "synonym_text": "methanogenesis using methylated compounds",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.3389/fmicb.2017.01198"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1128/mmbr.00024-22",
        "snippet": "Methyl-based methanogenesis is one of three broad categories of archaeal anaerobic methanogenesis, including both the methyl dismutation (methylotrophic) pathway and the methyl-reducing (also known as hydrogen-dependent methylotrophic) pathway",
        "notes": "Bueno de Mesquita et al. define methyl-based methanogenesis as the methanogenesis branch covering methyl dismutation and hydrogen-dependent methyl-reducing pathways."
      },
      {
        "reference": "DOI:10.3389/fmicb.2017.01198",
        "snippet": "acetoclastic methanogenesis using acetate, and methylotrophic methanogenesis using methylated compounds, such as methanol, methylamines",
        "notes": "Evans et al. describe methylotrophic methanogenesis as the methylated-compound-using branch among major methanogenic carbon-source pathways."
      }
    ],
    "discussions": [
      {
        "discussion_id": "methyl-based-methanogenesis-xref-gap",
        "prompt": "Resolve an exact external ontology xref for methyl-substrate methanogenesis before adding a TraitRecord xref.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "The pinned METPO snapshot contains only obsolete METPO:1000866 Methylotrophic methanogenesis. The existing methylotrophic record is the broader reduced-one-carbon trophic type, and GO:0015948 methane biosynthetic process is exact only for the broader methanogenesis parent, so no exact active external class has yet been resolved for this methyl-substrate branch.",
        "posed_by": "codex",
        "posed_date": "2026-09-14"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-14T21:27:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted methyl-based methanogenesis as a DOI-backed child of methanogenesis after a repository-wide duplicate review covering ignored and hidden files; the pinned METPO snapshot has only an obsolete Methylotrophic methanogenesis class.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000027",
    "label": "mixed-acid fermentation",
    "definition": "A fermentation in which sugars are converted via the glycolytic pathway to a mixture of acids (lactic, acetic, formic, succinic) plus ethanol, CO2 and H2. Characteristic of enteric bacteria such as Escherichia coli.",
    "definition_source": "DOI:10.3389/fmicb.2021.703525",
    "trait_category": "METABOLISM",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1002005"
    ],
    "evidence": [
      {
        "reference": "DOI:10.3389/fmicb.2021.703525",
        "notes": "Review of fermentative energy conservation lists acetate, ethanol, lactate, succinate and formate as products of mixed-acid fermentation."
      },
      {
        "reference": "DOI:10.3390/molecules31020333",
        "notes": "Review of fermentation pathways describes mixed-acid fermentation by enterobacteria and its characteristic acid product spectrum."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:562",
        "taxon_label": "Escherichia coli",
        "note": "Textbook mixed-acid fermenter (lactate, acetate, succinate, formate, ethanol, H2/CO2).",
        "reference": "DOI:10.3389/fbioe.2014.00016"
      },
      {
        "taxon_id": "NCBITaxon:83333",
        "taxon_label": "Escherichia coli K-12",
        "note": "Strain-level source of the reviewed PflB example used for the pyruvate-to-formate and acetyl-CoA branch of mixed-acid fermentation.",
        "reference": "DOI:10.1016/S0969-2126(99)80098-7"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "mixed_acid_fermentation_enterobacterial",
        "title": "Mixed-acid fermentation yields a spectrum of acids plus ethanol and gases",
        "description": "Evidence-backed causal sketch linking glycolytic sugar catabolism to mixed acid + ethanol + CO2 + H2 production in enterobacteria.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "Represents the enterobacterial branch centered on E. coli. The taxon-paired protein example establishes PflB, while Pta/AckA and FHL remain combined module labels pending component-level curation.",
        "nodes": [
          {
            "node_id": "mixed_acid_fermentation_trait",
            "label": "mixed-acid fermentation",
            "node_type": "TRAIT",
            "grounding": "traitmech:000027",
            "description": "Fermentation producing a mixture of acids and gases."
          },
          {
            "node_id": "fermentation_process",
            "label": "fermentation",
            "node_type": "BIOLOGICAL_PROCESS",
            "grounding": "GO:0006113",
            "description": "ATP-yielding catabolism with organic terminal acceptors."
          },
          {
            "node_id": "mixed_acid_products",
            "label": "mixed acid + ethanol + CO2/H2 products",
            "node_type": "CHEMICAL",
            "description": "Lactate, acetate, formate, succinate, ethanol, CO2, H2."
          },
          {
            "node_id": "pyruvate",
            "label": "pyruvate",
            "node_type": "CHEMICAL",
            "description": "Central glycolytic intermediate feeding fermentation branches.",
            "grounding": "CHEBI:15361"
          },
          {
            "node_id": "pyruvate_formate_lyase",
            "label": "pyruvate formate lyase (PflB)",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Enzyme cleaving pyruvate to formate and acetyl-CoA under anaerobiosis.",
            "grounding": "GO:0008861",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:P09373",
                "protein_label": "Formate acetyltransferase 1",
                "gene_symbol": "pflB",
                "taxon_id": "NCBITaxon:83333",
                "taxon_label": "Escherichia coli K-12",
                "entry_status": "REVIEWED",
                "retrieved_on": "2026-10-22",
                "entry_version": 218,
                "sequence_version": 2,
                "role": "PflB enzyme generating formate and acetyl-CoA from pyruvate during anaerobic glycolysis in E. coli.",
                "evidence": [
                  {
                    "reference": "DOI:10.1016/S0969-2126(99)80098-7",
                    "snippet": "The dimeric pyruvate formate lyase is the final enzyme in anaerobic glycolysis in Escherichia coli.",
                    "notes": "The primary structural study establishes the E. coli PFL role; UniProtKB P09373 verifies the reviewed PflB protein and K-12 taxon."
                  }
                ]
              }
            ]
          },
          {
            "node_id": "formate",
            "label": "formate",
            "node_type": "CHEMICAL",
            "description": "Acid product and substrate for the formate hydrogenlyase complex."
          },
          {
            "node_id": "acetyl_coa",
            "label": "acetyl-CoA",
            "node_type": "CHEMICAL",
            "description": "Branch-point intermediate from pyruvate cleavage."
          },
          {
            "node_id": "pta_acka",
            "label": "phosphotransacetylase / acetate kinase (Pta/AckA)",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Enzyme pair converting acetyl-CoA to acetate with ATP generation.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "This node combines two distinct enzymes, phosphotransacetylase and acetate kinase; exact semantic grounding requires splitting Pta and AckA."
          },
          {
            "node_id": "acetate",
            "label": "acetate",
            "node_type": "CHEMICAL",
            "description": "Major mixed-acid fermentation end product."
          },
          {
            "node_id": "fhl_complex",
            "label": "formate hydrogenlyase complex (FHL)",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Membrane complex disproportionating formate into CO2 and H2.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Enterobacterial formate hydrogenlyase is multisubunit and occurs in distinct FHL assemblies; the current evidence does not justify one exact complex term for this generic node."
          },
          {
            "node_id": "co2",
            "label": "carbon dioxide",
            "node_type": "CHEMICAL",
            "description": "Gas product of formate disproportionation.",
            "grounding": "CHEBI:16526"
          },
          {
            "node_id": "hydrogen",
            "label": "molecular hydrogen",
            "node_type": "CHEMICAL",
            "description": "Gas product of formate disproportionation by FHL.",
            "grounding": "CHEBI:18276"
          },
          {
            "node_id": "acidic_conditions",
            "label": "acidic conditions",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Low-pH environment favoring formate cleavage by FHL."
          },
          {
            "node_id": "ambient_oxygen",
            "label": "ambient molecular oxygen",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Oxygen, which suppresses fermentative hydrogen production."
          },
          {
            "node_id": "cytoplasm_ph",
            "label": "cytoplasmic pH",
            "node_type": "QUALITY",
            "description": "Intracellular pH lowered by acid accumulation during fermentation."
          }
        ],
        "edges": [
          {
            "subject": "mixed_acid_fermentation_trait",
            "predicate": "participates in",
            "object": "fermentation_process",
            "description": "Mixed-acid fermentation is a class of fermentation metabolism.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2021.703525",
                "notes": "Energy-conservation review lists the mixed-acid product spectrum."
              }
            ],
            "predicate_id": "biolink:participates_in"
          },
          {
            "subject": "mixed_acid_fermentation_trait",
            "predicate": "produces",
            "object": "mixed_acid_products",
            "description": "The pathway yields the characteristic acid + ethanol + gas spectrum.",
            "evidence": [
              {
                "reference": "DOI:10.3390/molecules31020333",
                "notes": "Classical-fermentation review describes mixed-acid fermentation by enterobacteria."
              }
            ],
            "predicate_id": "METPO:2007800"
          },
          {
            "subject": "mixed_acid_fermentation_trait",
            "predicate": "has output",
            "object": "pyruvate",
            "description": "Glycolysis upstream of mixed-acid fermentation produces pyruvate.",
            "evidence": [
              {
                "reference": "DOI:10.35812/cellulosechemtechnol.2024.58.90",
                "notes": "Pyruvate, ATP, and NADH are produced when glucose or other carbon sources reach the primary glycolytic pathway."
              }
            ]
          },
          {
            "subject": "pyruvate_formate_lyase",
            "predicate": "catalyzes conversion of",
            "object": "pyruvate",
            "description": "PflB cleaves pyruvate into formate and acetyl-CoA.",
            "evidence": [
              {
                "reference": "DOI:10.1128/iai.00176-23",
                "notes": "Pyruvate formate lyase (PflB) catalyzes the conversion of pyruvate into formate and acetyl-CoA."
              }
            ]
          },
          {
            "subject": "pyruvate_formate_lyase",
            "predicate": "produces",
            "object": "formate",
            "description": "PflB cleavage of pyruvate yields formate.",
            "evidence": [
              {
                "reference": "DOI:10.1128/iai.00176-23",
                "notes": "Pyruvate formate lyase (PflB) catalyzes the conversion of pyruvate into formate and acetyl-CoA."
              }
            ],
            "predicate_id": "METPO:2007800"
          },
          {
            "subject": "pta_acka",
            "predicate": "converts",
            "object": "acetate",
            "description": "Pta and AckA convert acetyl-CoA to acetate (with ATP generation).",
            "evidence": [
              {
                "reference": "DOI:10.1128/iai.00176-23",
                "notes": "Acetyl-CoA is further metabolized by Pta and AckA to generate acetate."
              }
            ]
          },
          {
            "subject": "formate",
            "predicate": "induces synthesis of",
            "object": "fhl_complex",
            "description": "Formate induces synthesis of the membrane-bound FHL complex.",
            "evidence": [
              {
                "reference": "DOI:10.1128/aem.01472-24",
                "notes": "Formate induces the synthesis of the membrane-bound FHL complex that catalyzes formate disproportionation into CO2 and H2."
              }
            ]
          },
          {
            "subject": "fhl_complex",
            "predicate": "produces",
            "object": "hydrogen",
            "description": "FHL disproportionates formate into CO2 and H2.",
            "evidence": [
              {
                "reference": "DOI:10.1128/aem.01472-24",
                "notes": "Formate is disproportionated into CO2 and H2 by the formate hydrogenlyase complex via FdhF and hydrogenase 3 (HycE)."
              }
            ],
            "predicate_id": "METPO:2007800"
          },
          {
            "subject": "fhl_complex",
            "predicate": "produces",
            "object": "co2",
            "description": "FHL disproportionates formate into CO2 and H2.",
            "evidence": [
              {
                "reference": "DOI:10.1128/aem.01472-24",
                "notes": "Formate is disproportionated into CO2 and H2 by the formate hydrogenlyase complex."
              }
            ],
            "predicate_id": "METPO:2007800"
          },
          {
            "subject": "acidic_conditions",
            "predicate": "positively regulates",
            "object": "fhl_complex",
            "description": "Acidic conditions favor FHL-mediated formate cleavage.",
            "evidence": [
              {
                "reference": "DOI:10.35812/cellulosechemtechnol.2024.58.90",
                "notes": "The enzyme complex formate:hydrogen lyase (FHL) cleaves formate under acidic conditions into H2 and CO2."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "ambient_oxygen",
            "predicate": "inhibits",
            "object": "hydrogen",
            "description": "Oxygen prevents fermentative hydrogen generation.",
            "evidence": [
              {
                "reference": "DOI:10.35812/cellulosechemtechnol.2024.58.90",
                "notes": "The presence of oxygen prevents the generation of hydrogen."
              }
            ],
            "predicate_id": "RO:0002212"
          },
          {
            "subject": "mixed_acid_fermentation_trait",
            "predicate": "lowers",
            "object": "cytoplasm_ph",
            "description": "Acid generation by MAF lowers cytoplasmic pH.",
            "evidence": [
              {
                "reference": "DOI:10.1128/iai.00176-23",
                "notes": "MAF results in the generation of acid, which subsequently lowers the pH of the cytoplasm."
              }
            ]
          },
          {
            "subject": "pyruvate_formate_lyase",
            "predicate": "produces",
            "object": "acetyl_coa",
            "description": "Pyruvate formate-lyase cleaves pyruvate into acetyl-CoA and formate.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2021.703525",
                "notes": "Connecting edge wiring the enrichment node into the graph."
              }
            ],
            "predicate_id": "METPO:2007800"
          },
          {
            "subject": "acetyl_coa",
            "predicate": "is metabolized by",
            "object": "pta_acka",
            "description": "The Pta/AckA enzyme pair metabolizes acetyl-CoA through the acetate-producing branch of mixed-acid fermentation.",
            "evidence": [
              {
                "reference": "DOI:10.1128/iai.00176-23",
                "snippet": "Acetyl-CoA is further metabolized by Pta and AckA to generate acetate",
                "notes": "Verified against the public PMC full text."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-30T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate METABOLISM trait (mixed-acid fermentation); product-specific sub-variant of the existing Fermentation class (METPO:1002005).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-10T14:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (mixed-acid fermentation) with GO node grounding and METPO/biolink predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 10 evidence-backed generic edges (12 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "FIX_ORPHAN_NODE",
        "changes": "Connected orphaned node 'acetyl_coa' via pyruvate_formate_lyase -[produces]-> acetyl_coa.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:12Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 5 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d74, RO:0002212\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:18Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:16526\u00d71, CHEBI:18276\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:32Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:15361\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-04T03:08:14Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002213\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T02:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES_PART2",
        "changes": "Re-grounded 5 causal edge(s) off microbe-domain METPO predicates onto their causal-graph counterparts (5 to produces), issue 301 part 2. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Each replacement is a 1:1 mirror of its source predicate that changes only the domain, so the claim each edge makes is unchanged and directions are unchanged. The replacements are proposed in proposals/metpo_traitmech_v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-17T02:00:00Z",
        "curator": "claude",
        "action": "NORMALISE_NODE_SENSE",
        "changes": "One node_id per SENSE (issues 356, 384): ambient_oxygen is the chemical sense here. Already the ambient sense. Listed so a re-run still normalises the label and still retracts ENVO:01001495 if it has been re-applied \u2014 the grounder keys on (label, node_type), so an un-normalised label is what lets the retracted CURIE come back.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-24T00:00:00Z",
        "curator": "codex",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Added a DOI-backed E. coli K-12 PflB example and GO activity, converted the species citation to DOI, retained combined Pta/AckA and FHL labels with explicit review rationales, and documented enterobacterial scope.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T08:20:00Z",
        "curator": "codex",
        "action": "CONNECT_CAUSAL_GRAPH_COMPONENTS",
        "changes": "Resolved issue #183 graph fragmentation (2 components to 1) using 1 public-source, verbatim-snippet-backed connector(s). No paid research service was called.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-22T01:35:00Z",
        "curator": "claude",
        "action": "REFRESH_UNIPROT_ENTRY_VERSION",
        "changes": "Refreshed UniProtKB entry_version against live UniProt REST on 2026-10-22: UniProtKB:P09373 (217 -> 218 on pyruvate_formate_lyase).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000134",
    "label": "nitrate reduction",
    "definition": "A metabolism in which an organism reduces nitrate, whether for energy conservation or for assimilation into biomass.",
    "definition_source": "DOI:10.1126/science.aaf4507",
    "trait_category": "METABOLISM",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000060"
    ],
    "synonyms": [
      {
        "synonym_text": "nitrate_reduction",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1126/science.aaf4507"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1128/JB.181.21.6573-6584.1999",
        "snippet": "Nitrate reduction can be performed with three different purposes",
        "notes": "Moreno-Vivian et al. review prokaryotic nitrate reduction across nitrate assimilation, nitrate respiration, and nitrate dissimilation."
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-08T00:00:00Z",
        "curator": "codex",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed a DOI-backed FAPROTAX metabolic capability from proposals/metpo_traitmech_v11 after repository-wide duplicate review.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-21T20:01:04Z",
        "curator": "claude",
        "action": "RECORD_MECHANISM_KNOWLEDGE_GAP",
        "changes": "Recorded OPEN KNOWLEDGE_GAP discussion (nitrate-reduction-causal-graph-source-gap) documenting the source-limited mechanism gap for causal_graphs.",
        "llm_assisted": true
      }
    ],
    "discussions": [
      {
        "discussion_id": "nitrate-reduction-causal-graph-source-gap",
        "prompt": "Add primary literature evidence distinguishing assimilatory (Nas), respiratory (Nar), and dissimilatory/periplasmic (Nap) nitrate reductase reactions and a strain-matched canonical example before constructing causal_graphs.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "The current record carries a single overview snippet (DOI:10.1128/JB.181.21.6573-6584.1999) noting that nitrate reduction serves three purposes, without verbatim quotes for the individual reductase branches.",
        "posed_by": "claude",
        "posed_date": "2026-10-21",
        "evidence": [
          {
            "reference": "DOI:10.1128/JB.181.21.6573-6584.1999",
            "supports": "PARTIAL",
            "snippet": "Nitrate reduction can be performed with three different purposes",
            "explanation": "Existing record-level evidence supports the high-level metabolic trait definition but does not provide multi-step enzymatic mechanism quotes for a connected causal graph."
          }
        ]
      }
    ]
  },
  {
    "identifier": "traitmech:000122",
    "label": "nitrate respiration",
    "definition": "A nitrogen respiration in which nitrate is the terminal electron acceptor, reduced to nitrite or further reduced products.",
    "definition_source": "DOI:10.1126/science.aaf4507",
    "trait_category": "METABOLISM",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000121",
      "traitmech:000134"
    ],
    "synonyms": [
      {
        "synonym_text": "nitrate_respiration",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1126/science.aaf4507"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1126/science.1254070",
        "snippet": "Denitrification converts nitrate into nitrogenous gas and thus removes fixed nitrogen from the biosphere, whereas ammonification converts nitrate into ammonium",
        "notes": "Kraft et al. support nitrate respiration as a bacterial nitrogen-oxide respiration branch with denitrification or DNRA endpoints."
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-08T00:00:00Z",
        "curator": "codex",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed a DOI-backed FAPROTAX metabolic capability from proposals/metpo_traitmech_v11 after repository-wide duplicate review.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-21T20:01:04Z",
        "curator": "claude",
        "action": "RECORD_MECHANISM_KNOWLEDGE_GAP",
        "changes": "Recorded OPEN KNOWLEDGE_GAP discussion (nitrate-respiration-causal-graph-source-gap) documenting the source-limited mechanism gap for causal_graphs.",
        "llm_assisted": true
      }
    ],
    "discussions": [
      {
        "discussion_id": "nitrate-respiration-causal-graph-source-gap",
        "prompt": "Add primary literature evidence for respiratory nitrate reductase (NarGHI/NapAB), electron-transport phosphorylation, and a strain-matched canonical example before constructing causal_graphs.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "The current record carries a single snippet (DOI:10.1126/science.1254070) contrasting denitrification and ammonification endpoints without enzyme-level nitrate-to-nitrite respiratory mechanism quotes.",
        "posed_by": "claude",
        "posed_date": "2026-10-21",
        "evidence": [
          {
            "reference": "DOI:10.1126/science.1254070",
            "supports": "PARTIAL",
            "snippet": "Denitrification converts nitrate into nitrogenous gas and thus removes fixed nitrogen from the biosphere, whereas ammonification converts nitrate into ammonium",
            "explanation": "Existing record-level evidence supports the high-level metabolic trait definition but does not provide multi-step enzymatic mechanism quotes for a connected causal graph."
          }
        ]
      }
    ]
  },
  {
    "identifier": "METPO:1005001",
    "label": "nitrification",
    "definition": "A biological process in which ammonia is oxidized to nitrite (ammonia oxidation) and nitrite is oxidized to nitrate (nitrite oxidation), in two steps.",
    "trait_category": "METABOLISM",
    "term_kind": "CLASS",
    "mapping_status": "SEEDED",
    "parent_traits": [
      "METPO:1000630"
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-11T06:15:37Z",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)"
      },
      {
        "timestamp": "2026-09-11T06:20:00Z",
        "curator": "codex",
        "action": "ENRICHED_FROM_LITERATURE",
        "changes": "Enriched the active METPO nitrification class with DOI-backed two-step ammonia- and nitrite-oxidation evidence after a repository-wide duplicate review covering ignored and hidden files.",
        "llm_assisted": true
      }
    ],
    "definition_source": "DOI:10.3389/fmicb.2020.01900",
    "evidence": [
      {
        "reference": "DOI:10.3389/fmicb.2020.01900",
        "snippet": "nitrification proceeds as a two-step process, involving the oxidation of ammonia to nitrite and the oxidation of nitrite to nitrate",
        "notes": "Sedlacek et al. review the historical evidence that established nitrification as a microbially mediated, two-step ammonia- and nitrite-oxidation process."
      }
    ],
    "discussions": [
      {
        "discussion_id": "nitrification-component-go-xref-gap",
        "prompt": "Resolve an exact external ontology class for the complete nitrification process before adding a TraitRecord xref.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "METPO cites GO:0019329 ammonia oxidation and GO:0019332 nitrite oxidation as definition components, but each GO term covers only one half of the full two-step nitrification trait and is not exact enough for TraitRecord xrefs.",
        "posed_by": "codex",
        "posed_date": "2026-09-11"
      }
    ]
  },
  {
    "identifier": "traitmech:000123",
    "label": "nitrite respiration",
    "definition": "A nitrogen respiration in which nitrite is the terminal electron acceptor.",
    "definition_source": "DOI:10.1126/science.aaf4507",
    "trait_category": "METABOLISM",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000121"
    ],
    "synonyms": [
      {
        "synonym_text": "nitrite_respiration",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1126/science.aaf4507"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1074/jbc.M709090200",
        "snippet": "Cytochrome c nitrite reductase (NrfA) from Escherichia coli has a well established role in the respiratory reduction of nitrite to ammonium",
        "notes": "van Wonderen et al. describe NrfA-catalyzed respiratory reduction of nitrite to ammonium."
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-08T00:00:00Z",
        "curator": "codex",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed a DOI-backed FAPROTAX metabolic capability from proposals/metpo_traitmech_v11 after repository-wide duplicate review.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-21T20:01:04Z",
        "curator": "claude",
        "action": "RECORD_MECHANISM_KNOWLEDGE_GAP",
        "changes": "Recorded OPEN KNOWLEDGE_GAP discussion (nitrite-respiration-causal-graph-source-gap) documenting the source-limited mechanism gap for causal_graphs.",
        "llm_assisted": true
      }
    ],
    "discussions": [
      {
        "discussion_id": "nitrite-respiration-causal-graph-source-gap",
        "prompt": "Add a second independent evidence snippet covering electron donation or proton-motive-force coupling alongside NrfA/NirS/NirK nitrite reduction and a strain-matched canonical example before constructing causal_graphs.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "The current record carries a single evidence item (DOI:10.1074/jbc.M709090200) on Escherichia coli NrfA reduction of nitrite to ammonium; a connected multi-edge graph requires at least two independent verbatim snippets so no single quote is reused or clause-split across edges.",
        "posed_by": "claude",
        "posed_date": "2026-10-21",
        "evidence": [
          {
            "reference": "DOI:10.1074/jbc.M709090200",
            "supports": "PARTIAL",
            "snippet": "Cytochrome c nitrite reductase (NrfA) from Escherichia coli has a well established role in the respiratory reduction of nitrite to ammonium",
            "explanation": "Existing record-level evidence supports the high-level metabolic trait definition but does not provide multi-step enzymatic mechanism quotes for a connected causal graph."
          }
        ]
      }
    ]
  },
  {
    "identifier": "traitmech:000103",
    "label": "nitrogen fixation",
    "definition": "A metabolism in which an organism reduces atmospheric dinitrogen (N2) to ammonia using the nitrogenase enzyme complex, making fixed nitrogen biologically available (diazotrophy).",
    "definition_source": "DOI:10.1038/nrmicro.2018.9",
    "trait_category": "METABOLISM",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000060"
    ],
    "synonyms": [
      {
        "synonym_text": "diazotrophy",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1038/nrmicro954"
      }
    ],
    "xrefs": [
      "GO:0009399"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/nrmicro.2018.9",
        "notes": "Kuypers, Marchant & Kartal place nitrogen fixation as the reductive entry point of the microbial nitrogen-cycling network."
      },
      {
        "reference": "DOI:10.1038/nrmicro954",
        "notes": "Dixon & Kahn review the genetic regulation of biological nitrogen fixation and nitrogenase."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:354",
        "taxon_label": "Azotobacter vinelandii",
        "note": "Preferred model free-living aerobic diazotroph; fixes N2 at high O2 via respiratory protection.",
        "reference": "DOI:10.1128/mbio.02593-21"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "nitrogen_fixation_nitrogenase",
        "title": "Nitrogenase-catalyzed dinitrogen reduction",
        "description": "Evidence-backed causal sketch linking the nitrogenase complex to reduction of atmospheric dinitrogen to ammonia.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "Represents the canonical molybdenum-nitrogenase electron-transfer and catalytic sequence plus oxygen inhibition; alternative nitrogenases and lineage-specific protection systems are outside this graph.",
        "nodes": [
          {
            "node_id": "nitrogen_fixation_trait",
            "label": "nitrogen fixation",
            "node_type": "TRAIT",
            "grounding": "traitmech:000103",
            "description": "Capacity to reduce N2 to ammonia."
          },
          {
            "node_id": "nitrogenase",
            "label": "nitrogenase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Oxygen-sensitive enzyme complex that reduces dinitrogen.",
            "grounding": "GO:0016610"
          },
          {
            "node_id": "nitrogen_fixation_process",
            "label": "nitrogen fixation",
            "node_type": "BIOLOGICAL_PROCESS",
            "grounding": "GO:0009399",
            "description": "Reduction of dinitrogen to ammonia."
          },
          {
            "node_id": "dinitrogen",
            "label": "dinitrogen",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:17997",
            "description": "Atmospheric N2 substrate."
          },
          {
            "node_id": "ammonia",
            "label": "ammonia",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:16134",
            "description": "Fixed-nitrogen product."
          },
          {
            "node_id": "ferredoxin_flavodoxin",
            "label": "ferredoxin/flavodoxin",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Low-potential electron carriers that donate electrons to the nitrogenase Fe-protein (NifH).",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "The combined label intentionally denotes alternative ferredoxin and flavodoxin donors; no single exact family term covers both without overstating a taxon-specific carrier."
          },
          {
            "node_id": "nifh_fe_protein",
            "label": "NifH (Fe-protein)",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Nitrogenase iron protein; ATP-dependent electron donor to the MoFe protein.",
            "grounding": "InterPro:IPR005977",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:P00459",
                "protein_label": "Nitrogenase iron protein 1",
                "gene_symbol": "nifH1",
                "taxon_id": "NCBITaxon:354",
                "taxon_label": "Azotobacter vinelandii",
                "entry_status": "REVIEWED",
                "retrieved_on": "2026-10-22",
                "entry_version": 168,
                "sequence_version": 2,
                "role": "ATP-coupled Fe-protein component that transfers electrons to the catalytic MoFe protein in the A. vinelandii nitrogenase system.",
                "evidence": [
                  {
                    "reference": "DOI:10.1074/jbc.271.4.1884",
                    "snippet": "exclusively due to the substitution of the Fe protein residue serine 44",
                    "notes": "The A. vinelandii nifH Fe-protein mutant causally links this exact component to altered nitrogenase electron transfer; UniProtKB P00459 verifies the reviewed protein and taxon."
                  }
                ]
              }
            ]
          },
          {
            "node_id": "p_cluster",
            "label": "P-cluster",
            "node_type": "CHEMICAL",
            "description": "[8Fe-7S] metallocluster in NifDK that relays electrons to the FeMo-cofactor."
          },
          {
            "node_id": "femo_cofactor",
            "label": "FeMo-cofactor (M-cluster)",
            "node_type": "CHEMICAL",
            "description": "[7Fe-9S-Mo-C-homocitrate] active-site cofactor that binds and reduces N2."
          },
          {
            "node_id": "atp",
            "label": "ATP",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:30616",
            "description": "Mg-ATP hydrolyzed by NifH to drive electron transfer to the MoFe protein."
          },
          {
            "node_id": "molecular_oxygen",
            "label": "molecular oxygen",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:15379",
            "description": "O2, which irreversibly inactivates oxygen-sensitive nitrogenase."
          }
        ],
        "edges": [
          {
            "subject": "nitrogenase",
            "predicate": "enables",
            "object": "nitrogen_fixation_process",
            "description": "The nitrogenase complex carries out biological nitrogen fixation.",
            "evidence": [
              {
                "reference": "DOI:10.34133/bdr.0005",
                "snippet": "In the biological nitrogen fixation reaction, N2 is reduced to form NH3 under ambient conditions by the nitrogenase enzyme",
                "notes": "The DOI-backed nitrogenase review identifies the enzyme as the catalyst of biological nitrogen fixation."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "nitrogen_fixation_process",
            "predicate": "consumes",
            "object": "dinitrogen",
            "description": "Nitrogen fixation consumes atmospheric dinitrogen.",
            "evidence": [
              {
                "reference": "DOI:10.34133/bdr.0005",
                "snippet": "In the biological nitrogen fixation reaction, N2 is reduced to form NH3 under ambient conditions by the nitrogenase enzyme",
                "notes": "The same review explicitly identifies N2 as the substrate reduced by nitrogenase."
              }
            ],
            "predicate_id": "biolink:consumes"
          },
          {
            "subject": "nitrogen_fixation_process",
            "predicate": "has output",
            "object": "ammonia",
            "description": "Nitrogen fixation produces ammonia.",
            "evidence": [
              {
                "reference": "DOI:10.34133/bdr.0005",
                "snippet": "N2 is reduced to form NH3 under ambient conditions by the nitrogenase enzyme",
                "notes": "Supports ammonia as the product of nitrogenase-catalyzed N2 reduction."
              }
            ],
            "predicate_id": "RO:0002234"
          },
          {
            "subject": "nitrogen_fixation_trait",
            "predicate": "depends on",
            "object": "nitrogenase",
            "description": "The nitrogen-fixation trait depends on the nitrogenase complex.",
            "evidence": [
              {
                "reference": "DOI:10.34133/bdr.0005",
                "snippet": "enzymes capable of converting atmospheric nitrogen N2 to NH3 in ambient conditions",
                "notes": "Supports nitrogenase as required for the trait."
              }
            ],
            "predicate_id": "RO:0002502"
          },
          {
            "subject": "ferredoxin_flavodoxin",
            "predicate": "transfers electron to",
            "object": "nifh_fe_protein",
            "description": "Reduced ferredoxin/flavodoxin donate electrons to the [4Fe-4S] cluster of the NifH homodimer.",
            "evidence": [
              {
                "reference": "DOI:10.34133/bdr.0005",
                "snippet": "Reduced electron carriers donate electrons to the [4Fe-4S] cluster at the interface of the NifH homodimer.",
                "notes": "Reduced electron carriers donate electrons to the [4Fe-4S] cluster at the interface of the NifH homodimer; core Mo-nitrogenase mechanism."
              }
            ]
          },
          {
            "subject": "nifh_fe_protein",
            "predicate": "transfers electron to",
            "object": "p_cluster",
            "description": "The Fe-protein accepts electrons from Fd/Fld and reduces the P-cluster in the MoFe protein in an ATP-dependent step.",
            "evidence": [
              {
                "reference": "DOI:10.1128/aem.00378-23",
                "snippet": "The Fe-protein contains 1 FeS cluster that accepts electrons from Fd or Fld and reduces the P-cluster in the MoFe protein in an ATP-dependent electron transfer.",
                "notes": "The Fe-protein FeS cluster accepts electrons from Fd or Fld and reduces the P-cluster in the MoFe protein in an ATP-dependent electron transfer."
              }
            ]
          },
          {
            "subject": "p_cluster",
            "predicate": "transfers electron to",
            "object": "femo_cofactor",
            "description": "The P-cluster relays electrons to the FeMo-cofactor for N2 reduction.",
            "evidence": [
              {
                "reference": "DOI:10.1128/aem.00378-23",
                "snippet": "The P-cluster delivers electrons to the MoFe cofactor allowing electrons to be loaded for the reduction of N2.",
                "notes": "The P-cluster delivers electrons to the MoFe cofactor allowing electrons to be loaded for the reduction of N2; core electron relay."
              }
            ]
          },
          {
            "subject": "femo_cofactor",
            "predicate": "enables",
            "object": "nitrogen_fixation_process",
            "description": "The FeMo-cofactor binds and reduces N2 to ammonia.",
            "evidence": [
              {
                "reference": "DOI:10.34133/bdr.0005",
                "snippet": "Electrons are sequentially donated to the [8Fe-7S] cluster in the NifDK protein, then finally to FeMo-co, which binds and reduces N2 to form NH3 and H2",
                "notes": "FeMo-co binds and reduces N2 to form NH3 and H2 in the canonical Mo-dependent nitrogenase."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "nifh_fe_protein",
            "predicate": "requires",
            "object": "atp",
            "description": "NifH hydrolyzes Mg-ATP during each electron transfer to the MoFe protein.",
            "evidence": [
              {
                "reference": "DOI:10.34133/bdr.0005",
                "snippet": "NifH transiently binds and then dissociates from the NifDK complex, hydrolyzing 2 molecules of Mg-ATP per electron transfer.",
                "notes": "NifH transiently binds and dissociates from NifDK, hydrolyzing 2 Mg-ATP per electron transfer; supports per-electron ATP cost."
              }
            ]
          },
          {
            "subject": "molecular_oxygen",
            "predicate": "inhibits",
            "object": "nitrogenase",
            "description": "Molecular oxygen inactivates the oxygen-sensitive nitrogenase complex.",
            "evidence": [
              {
                "reference": "DOI:10.1128/aem.00378-23",
                "snippet": "Each metal cofactor is very sensitive to oxygen damage.",
                "notes": "Nitrogenase is an O2-sensitive enzyme; broad, well-supported claim across diazotrophs."
              }
            ],
            "predicate_id": "RO:0002212"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-08-23T09:06:00Z",
        "curator": "codex",
        "action": "CURATE_PROTEIN_TAXON_EXAMPLE",
        "changes": "Reviewed the graph as mechanistic, grounded NifH semantically, retyped the P-cluster and FeMo-cofactor as chemicals, documented the combined carrier label, and added DOI-backed UniProtKB P00459 for A. vinelandii.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-08T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate METABOLISM trait (nitrogen fixation / diazotrophy); round 2, nitrogen-cycle gap.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-08T12:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (nitrogenase-catalyzed N2 reduction) with CHEBI/GO node groundings and RO/METPO/biolink predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-14T06:38:15Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A089HR75\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 6 evidence-backed generic edges (6 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:12Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d71, RO:0002212\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-26T07:15:18Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A7Y9D8L6\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:21:11Z",
        "curator": "claude",
        "action": "RETRACT_DEAD_UNIPROT_GROUNDINGS",
        "changes": "Retracted 1 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates (1 to has output), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-17T02:00:00Z",
        "curator": "claude",
        "action": "NORMALISE_NODE_SENSE",
        "changes": "One node_id per SENSE (issues 356, 384): molecular_oxygen is the chemical sense here. The molecule, not the condition \u2014 the dioxygen participating in the reaction the graph describes. Normalised onto molecular_oxygen, the id 20 other chemical occurrences already use, so one id means one sense corpus-wide (issues 356, 384).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-22T04:26:15Z",
        "curator": "codex",
        "action": "REVIEW_UNIPROT_INSTANCE_GROUNDINGS",
        "changes": "Reviewed 1 organism-specific UniProtKB grounding(s): replaced 1 with taxon-agnostic GO/InterPro terms and retracted 0 to label-only where no exact semantic term was supported (docs/GROUNDING_POLICY.md).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T01:14:58Z",
        "curator": "codex",
        "action": "ADD_EXACT_ONTOLOGY_MATCH",
        "changes": "Ontology exact-match review (2026-08-25): approved exact xref(s): GO:0009399. Evidence is predicate-scoped in the versioned ontology snapshots; OAK cross-checked direct data, and OLS4 spot-checked release deltas and disputed hits.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-30T19:21:37Z",
        "curator": "codex",
        "action": "REVIEW_EVIDENCE_REFERENCE_CHURN",
        "changes": "Offline review for issue 520 retained 5 evidence-reference replacement(s) that PR 511 made on surviving causal edges outside its stated protein-taxon scope. The pre-tranche evidence entries had references but no snippets; the retained entries supply edge-specific snippets and explanatory notes. Reverting would discard that claim-level provenance, so the scope defect is resolved by documenting the decision instead. This audit changed no causal claim or evidence field. Reviewed replacements: DOI:10.1038/nrmicro.2018.9 -> DOI:10.34133/bdr.0005 (1 edge); DOI:10.1038/nrmicro954 -> DOI:10.34133/bdr.0005 (3 edges); DOI:10.1128/aem.00378-23 -> DOI:10.34133/bdr.0005 (1 edge).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-22T01:35:00Z",
        "curator": "claude",
        "action": "REFRESH_UNIPROT_ENTRY_VERSION",
        "changes": "Refreshed UniProtKB entry_version against live UniProt REST on 2026-10-22: UniProtKB:P00459 (167 -> 168 on nifh_fe_protein).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000121",
    "label": "nitrogen respiration",
    "definition": "An anaerobic respiration in which an organism conserves energy by transferring electrons to an oxidized nitrogen compound as the terminal electron acceptor.",
    "definition_source": "DOI:10.1126/science.aaf4507",
    "trait_category": "METABOLISM",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000802"
    ],
    "synonyms": [
      {
        "synonym_text": "nitrogen_respiration",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1126/science.aaf4507"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1128/mmbr.61.4.533-616.1997",
        "snippet": "N oxides as terminal electron acceptors",
        "notes": "Zumft reviews denitrification as anaerobic respiration with oxidized nitrogen compounds as electron acceptors."
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-08T00:00:00Z",
        "curator": "codex",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed a DOI-backed FAPROTAX metabolic capability from proposals/metpo_traitmech_v11 after repository-wide duplicate review.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-21T20:01:04Z",
        "curator": "claude",
        "action": "RECORD_MECHANISM_KNOWLEDGE_GAP",
        "changes": "Recorded OPEN KNOWLEDGE_GAP discussion (nitrogen-respiration-causal-graph-source-gap) documenting the source-limited mechanism gap for causal_graphs.",
        "llm_assisted": true
      }
    ],
    "discussions": [
      {
        "discussion_id": "nitrogen-respiration-causal-graph-source-gap",
        "prompt": "Add primary literature evidence for nitrogen-oxide respiratory reductases, electron-transport chains, and a strain-matched canonical example before constructing causal_graphs.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "The current record carries a single 38-character snippet ('N oxides as terminal electron acceptors' in DOI:10.1128/mmbr.61.4.533-616.1997), which supports the upper-level class definition but not a multi-edge mechanism graph.",
        "posed_by": "claude",
        "posed_date": "2026-10-21",
        "evidence": [
          {
            "reference": "DOI:10.1128/mmbr.61.4.533-616.1997",
            "supports": "PARTIAL",
            "snippet": "N oxides as terminal electron acceptors",
            "explanation": "Existing record-level evidence supports the high-level metabolic trait definition but does not provide multi-step enzymatic mechanism quotes for a connected causal graph."
          }
        ]
      }
    ]
  },
  {
    "identifier": "METPO:2000001",
    "label": "organism interacts with chemical",
    "definition": "The root OBJECT_PROPERTY for all organism-to-chemical interactions in the metabolism vocabulary; concrete uses (uses-as-X, ferments, produces, etc.) specialise this relation.",
    "definition_source": "DOI:10.1146/annurev.micro.55.1.485",
    "trait_category": "METABOLISM",
    "term_kind": "OBJECT_PROPERTY",
    "mapping_status": "REVIEWED",
    "domain": "https://w3id.org/metpo/1000525",
    "range_": "http://purl.obolibrary.org/obo/CHEBI_24431",
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev.micro.55.1.485",
        "snippet": "interaction",
        "notes": "Microbial-physiology reference supports 'organism interacts with chemical' as a canonical predicate composed with a CHEBI-class chemical object at assertion time."
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.950239+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (OBJECT_PROPERTY)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic metabolism relation carrier; later replacement should use more specific trait records that combine the relation with the chemical, phenotype, quality, compartment, enzyme or activity target, growth context, measurement, or other entity.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-16T08:50:00-07:00",
        "curator": "claude",
        "action": "UNDEPRECATED_AS_COMPOSITION_PRIMITIVE",
        "changes": "Restored from DEPRECATED to REVIEWED under the predicate+class composition pattern (intended use: <organism> + this predicate + CHEBI chemical class). Added DOI/PMID-backed definition, evidence, and explicit domain/range slots.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-17T10:00:00-07:00",
        "curator": "claude",
        "action": "ADDED_EXTERNAL_PREDICATE_XREF",
        "changes": "Added xrefs ['MICRO:0000975'] to record an external equivalence predicate.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-17T15:00:00-07:00",
        "curator": "claude",
        "action": "REVERTED_NON_EQUIVALENT_XREF",
        "changes": "Removed MICRO:0000975 xref per Copilot review of PR #56. This record is the root for ALL organism-to-chemical interactions (produces, uses-as-X, ferments, etc.), while MICRO:0000975 \"uses chemical entity\" is narrower (use relations only). Encoding it as an xrefs equivalence would mismap downstream consumers. No other ontology has a sufficiently broad organism-to-chemical root predicate, so xrefs left empty.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000204",
    "label": "organohalide respiration",
    "definition": "An anaerobic respiration in which an organism uses an organohalide as the terminal electron acceptor for energy conservation.",
    "definition_source": "DOI:10.1098/rstb.2012.0322",
    "trait_category": "METABOLISM",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000802"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1098/rstb.2012.0322",
        "snippet": "Organohalide respiration is an anaerobic bacterial respiratory process that uses halogenated hydrocarbons as terminal electron acceptors during electron transport-based energy conservation.",
        "notes": "Hug et al. define organohalide respiration as anaerobic electron-transport-based energy conservation with halogenated hydrocarbons as terminal electron acceptors."
      },
      {
        "reference": "DOI:10.1098/rstb.2012.0322",
        "snippet": "Organohalide-respiring bacteria have been identified from multiple bacterial phyla",
        "notes": "Hug et al. support the record as a reusable bacterial respiration phenotype rather than a single-strain label."
      },
      {
        "reference": "DOI:10.1126/science.276.5318.1568",
        "snippet": "Growth of strain 195 with H2 and tetrachloroethene as the electron donor and acceptor pair required extracts from mixed microbial cultures.",
        "notes": "Maymo-Gatell et al. support tetrachloroethene as a growth-coupled organohalide electron acceptor in Dehalococcoides mccartyi strain 195."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:243164",
        "taxon_label": "Dehalococcoides mccartyi 195",
        "note": "Strain 195 grows by coupling H2 oxidation to tetrachloroethene reduction, establishing growth-coupled organohalide respiration.",
        "reference": "DOI:10.1126/science.276.5318.1568"
      }
    ],
    "discussions": [
      {
        "discussion_id": "organohalide-respiration-xref-gap",
        "prompt": "Resolve an exact external ontology class for organism-level organohalide respiration before adding a TraitRecord xref.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "The pinned METPO snapshot contains only obsolete Halogenated compound respiration and Organohalide respiration classes. Candidate reductive dehalogenase protein-family and enzyme terms are narrower than the whole-organism anaerobic respiration phenotype.",
        "posed_by": "codex",
        "posed_date": "2026-09-15"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-15T04:25:36Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted organohalide respiration as a DOI-backed anaerobic respiration TraitRecord after a repository-wide duplicate review covering ignored and hidden files; the local METPO snapshot has only obsolete organohalide/halogenated-compound respiration classes and the replacement placeholder is reserved in proposals/metpo_traitmech_v81.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000803",
    "label": "Oxidative phosphorylation",
    "definition": "A metabolism that generates ATP through the transfer of electrons from electron donors to electron acceptors via redox reactions, coupled to the pumping of protons across a membrane to create an electrochemical gradient.",
    "definition_source": "DOI:10.1038/191144a0",
    "trait_category": "METABOLISM",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000060"
    ],
    "synonyms": [
      {
        "synonym_text": "respiratory-chain phosphorylation",
        "synonym_type": "EXACT_SYNONYM",
        "source": "http://purl.obolibrary.org/obo/go/releases/2026-07-26/go-basic.obo"
      }
    ],
    "created_by": "Anthea Guo",
    "xrefs": [
      "GO:0006119"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/191144a0",
        "snippet": "phosphorylation to electron and hydrogen transfer",
        "notes": "Mitchell's chemiosmotic proposal supports coupling electron transfer to phosphorylation."
      },
      {
        "reference": "DOI:10.1038/s41598-019-38564-0",
        "snippet": "energized by the proton motive force",
        "notes": "Supports proton motive force-driven ATP synthesis by F1Fo ATP synthase."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:266",
        "taxon_label": "Paracoccus denitrificans",
        "note": "Free-living model of the mitochondrial-type respiratory chain and oxidative phosphorylation (full set of bacterial respiratory complexes).",
        "reference": "PMID:30428155"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "oxidative_phosphorylation_chemiosmotic_coupling",
        "title": "Oxidative phosphorylation chemiosmotic coupling",
        "description": "Evidence-backed causal sketch linking respiratory electron transfer, proton motive force, ATP synthase, and ATP production.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "Represents a concrete aerobic heme-copper-oxidase branch of bacterial oxidative phosphorylation. The redundant family-unspecified terminal-oxidase node was removed rather than assigned an overbroad grounding.",
        "nodes": [
          {
            "node_id": "oxidative_phosphorylation_trait",
            "label": "Oxidative phosphorylation",
            "node_type": "TRAIT",
            "grounding": "METPO:1000803",
            "description": "ATP generation coupled to redox-driven ion gradients."
          },
          {
            "node_id": "electron_transport_chain",
            "label": "electron transport chain",
            "node_type": "PATHWAY",
            "grounding": "GO:0022900",
            "description": "Membrane-associated electron transfer pathway."
          },
          {
            "node_id": "cellular_membrane",
            "label": "cellular membrane",
            "node_type": "CELLULAR_LOCALIZATION",
            "grounding": "GO:0016020",
            "description": "Membrane across which ions are translocated."
          },
          {
            "node_id": "proton_motive_force",
            "label": "proton motive force",
            "node_type": "STATE",
            "description": "Transmembrane electrochemical proton gradient.",
            "grounding": "METPO:1007500"
          },
          {
            "node_id": "atp_synthase",
            "label": "F1Fo ATP synthase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Rotary enzyme complex that synthesizes ATP using ion motive force.",
            "grounding": "GO:0045259"
          },
          {
            "node_id": "atp",
            "label": "ATP",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:30616",
            "description": "Energy-rich nucleotide product."
          },
          {
            "node_id": "nadh",
            "label": "NADH",
            "node_type": "CHEMICAL",
            "description": "Reduced electron donor feeding the respiratory chain."
          },
          {
            "node_id": "complex_i",
            "label": "Complex I / NADH:quinone oxidoreductase (NDH-1)",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Proton-translocating NADH:quinone oxidoreductase entry complex.",
            "grounding": "GO:0045271"
          },
          {
            "node_id": "succinate",
            "label": "succinate",
            "node_type": "CHEMICAL",
            "description": "Electron donor oxidized by succinate dehydrogenase."
          },
          {
            "node_id": "succinate_dehydrogenase",
            "label": "succinate dehydrogenase / Complex II",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Complex II coupling succinate oxidation to quinone reduction.",
            "grounding": "GO:0045273"
          },
          {
            "node_id": "quinone_pool",
            "label": "quinone pool",
            "node_type": "CHEMICAL",
            "description": "Membrane quinone/quinol electron carrier pool (ubiquinone/menaquinone)."
          },
          {
            "node_id": "proton",
            "label": "proton",
            "node_type": "CHEMICAL",
            "description": "Translocated ion forming the transmembrane gradient.",
            "grounding": "CHEBI:24636"
          },
          {
            "node_id": "proton_translocation",
            "label": "proton translocation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Vectorial transmembrane transfer of protons by respiratory complexes."
          },
          {
            "node_id": "molecular_oxygen",
            "label": "oxygen",
            "node_type": "CHEMICAL",
            "description": "Terminal electron acceptor in aerobic respiration."
          },
          {
            "node_id": "heme_copper_oxidase",
            "label": "heme-copper oxidase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Proton-pumping terminal oxidase class.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Available InterPro entries describe catalytic subunit-I families, not the complete heme-copper oxidase class represented by this node; the exemplar is therefore explicitly one subunit of a purified complex.",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:P08306",
                "protein_label": "Cytochrome c oxidase subunit 2",
                "gene_symbol": "ctaC",
                "taxon_id": "NCBITaxon:266",
                "taxon_label": "Paracoccus denitrificans",
                "entry_status": "REVIEWED",
                "retrieved_on": "2026-10-22",
                "entry_version": 168,
                "sequence_version": 1,
                "role": "Subunit II component of purified P. denitrificans cytochrome c oxidase; this accession does not represent the complete heme-copper oxidase complex.",
                "evidence": [
                  {
                    "reference": "DOI:10.1016/S0005-2728(98)00092-9",
                    "snippet": "enzyme containing polypeptides I-IV",
                    "notes": "The primary purification study establishes the four-subunit P. denitrificans oxidase and its subunit-II component; UniProtKB P08306 verifies the reviewed protein and taxon."
                  }
                ]
              }
            ]
          }
        ],
        "edges": [
          {
            "subject": "oxidative_phosphorylation_trait",
            "predicate": "uses pathway",
            "object": "electron_transport_chain",
            "description": "Oxidative phosphorylation couples phosphorylation to respiratory electron transfer.",
            "evidence": [
              {
                "reference": "DOI:10.1038/191144a0",
                "snippet": "electron and hydrogen transfer",
                "notes": "Mitchell paper supports coupling electron/hydrogen transfer to phosphorylation."
              }
            ]
          },
          {
            "subject": "electron_transport_chain",
            "predicate": "localized to",
            "object": "cellular_membrane",
            "description": "Electron transfer and proton translocation are membrane-coupled.",
            "evidence": [
              {
                "reference": "DOI:10.1038/191144a0",
                "snippet": "Chemi-Osmotic Type of Mechanism",
                "notes": "Chemiosmotic mechanism requires a membrane-separated ion gradient."
              }
            ],
            "predicate_id": "biolink:located_in"
          },
          {
            "subject": "electron_transport_chain",
            "predicate": "generates",
            "object": "proton_motive_force",
            "description": "Respiratory electron transfer establishes a proton motive force.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41598-019-38564-0",
                "snippet": "proton motive force (pmf) established and maintained by respiratory chain enzymes",
                "notes": "Supports respiratory chain generation of pmf."
              }
            ],
            "predicate_id": "biolink:produces"
          },
          {
            "subject": "proton_motive_force",
            "predicate": "regulates",
            "object": "atp_synthase",
            "description": "Proton motive force energizes F1Fo ATP synthase.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41598-019-38564-0",
                "snippet": "energized by the proton motive force",
                "notes": "Supports pmf-driven ATP synthase."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "atp_synthase",
            "predicate": "produces",
            "object": "atp",
            "description": "ATP synthase synthesizes ATP from ADP and phosphate.",
            "evidence": [
              {
                "reference": "DOI:10.1007/BF01923429",
                "snippet": "synthesis of ATP is also driven by a proton motive force",
                "notes": "ATP synthase review supports pmf-driven ATP synthesis."
              }
            ],
            "predicate_id": "METPO:2007800"
          },
          {
            "subject": "nadh",
            "predicate": "is oxidized by",
            "object": "complex_i",
            "description": "Complex I oxidizes NADH at the respiratory chain entry point.",
            "evidence": [
              {
                "reference": "DOI:10.3390/ijms252413421",
                "snippet": "Proton-translocating NADH\u2013ubiquinone oxidoreductase (complex I) catalyzes the oxidation of NADH by ubiquinone accompanied by the transmembrane transfer of four protons",
                "notes": "complex I catalyzes the oxidation of NADH by ubiquinone (general prokaryotic claim)."
              }
            ]
          },
          {
            "subject": "complex_i",
            "predicate": "reduces",
            "object": "quinone_pool",
            "description": "Complex I transfers electrons from NADH to the quinone pool.",
            "evidence": [
              {
                "reference": "DOI:10.3390/ijms252413421",
                "snippet": "oxidation of NADH by ubiquinone",
                "notes": "oxidation of NADH by ubiquinone; reduces the membrane quinone pool."
              }
            ],
            "predicate_id": "METPO:2007802"
          },
          {
            "subject": "complex_i",
            "predicate": "translocates",
            "object": "proton",
            "description": "Complex I couples redox chemistry to transmembrane proton translocation.",
            "evidence": [
              {
                "reference": "DOI:10.3390/ijms252413421",
                "snippet": "accompanied by the transmembrane transfer of four protons",
                "notes": "coupled with the vectorial transmembrane transfer of four H+ ions."
              }
            ]
          },
          {
            "subject": "complex_i",
            "predicate": "generates",
            "object": "proton_motive_force",
            "description": "Complex I proton translocation contributes directly to formation of the proton motive force.",
            "evidence": [
              {
                "reference": "DOI:10.3390/ijms252413421",
                "snippet": "contributing to the formation of a proton motive force (pmf)",
                "notes": "The review directly links proton-translocating NADH-ubiquinone oxidoreductase to PMF formation across bacterial and mitochondrial coupling membranes."
              }
            ],
            "predicate_id": "biolink:produces"
          },
          {
            "subject": "succinate",
            "predicate": "is oxidized by",
            "object": "succinate_dehydrogenase",
            "description": "Succinate dehydrogenase oxidizes succinate, reducing quinone.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s10863-024-10041-y",
                "snippet": "catalyzes the two-electron reduction of quinone by succinate",
                "notes": "succinate dehydrogenase catalyzes the two-electron reduction of quinone by succinate."
              }
            ]
          },
          {
            "subject": "succinate_dehydrogenase",
            "predicate": "reduces",
            "object": "quinone_pool",
            "description": "Complex II transfers electrons from succinate to the membrane quinone pool.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s10863-024-10041-y",
                "snippet": "catalyzes the two-electron reduction of quinone by succinate",
                "notes": "The B. licheniformis respiratory-chain study identifies succinate dehydrogenase as succinate:quinone oxidoreductase, directly joining Complex II to the quinone pool."
              }
            ],
            "predicate_id": "METPO:2007802"
          },
          {
            "subject": "proton_translocation",
            "predicate": "generates",
            "object": "proton_motive_force",
            "description": "Vectorial proton translocation establishes the proton motive force.",
            "evidence": [
              {
                "reference": "DOI:10.3390/ijms252413421",
                "snippet": "contributing to the formation of a proton motive force (pmf)",
                "notes": "energy conservation in the form of an electrochemical gradient (proton motive force, pmf)."
              }
            ],
            "predicate_id": "biolink:produces"
          },
          {
            "subject": "heme_copper_oxidase",
            "predicate": "reduces",
            "object": "molecular_oxygen",
            "description": "Heme-copper terminal oxidases catalyze four-electron reduction of O2 to water in the concrete branch represented here.",
            "evidence": [
              {
                "reference": "DOI:10.3390/ijms25021277",
                "snippet": "catalyze the four-electron reduction of O2 to 2H2O",
                "notes": "The review identifies heme-copper oxidases as a bacterial terminal-oxidase class carrying out the oxygen-reduction reaction."
              }
            ],
            "predicate_id": "METPO:2007802"
          },
          {
            "subject": "heme_copper_oxidase",
            "predicate": "translocates",
            "object": "proton",
            "description": "Heme-copper oxidases act as proton pumps contributing to PMF.",
            "evidence": [
              {
                "reference": "DOI:10.3390/ijms25021277",
                "snippet": "Heme-copper oxidases are true proton pumps",
                "notes": "Heme-copper oxidases are true proton pumps (general claim)."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-08-23T09:14:00Z",
        "curator": "codex",
        "action": "CURATE_PROTEIN_TAXON_EXAMPLE",
        "changes": "Reviewed the graph as mechanistic, grounded complexes I, II, and ATP synthase, replaced the ambiguous terminal-oxidase node with the cited heme-copper branch, connected the respiratory entry branches, and added DOI-backed P. denitrificans subunit-II P08306.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-05T01:35:46.912667+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-07T00:00:00-07:00",
        "curator": "codex",
        "action": "ADDED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed causal graph for chemiosmotic coupling, proton motive force, ATP synthase, and ATP production.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:30Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T08:21:49Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:located_in\u00d71, biolink:produces\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:19Z",
        "curator": "claude",
        "action": "RENAME_PREDICATE_LABELS",
        "changes": "Renamed 1 causal-edge predicate label(s) to align with existing groundings: drives \u2192 regulates \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:21Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002211\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:41:04Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (METPO:1007500\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-26T02:30:13Z",
        "curator": "claude",
        "action": "RETYPE_CAUSAL_NODES",
        "changes": "Re-typed 1 causal-node node_type field(s) to align with CausalNodeTypeEnum semantics: proton motive force: BIOLOGICAL_PROCESS \u2192 STATE \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 7 evidence-backed generic edges (10 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:12Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000017\u00d72, biolink:produces\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:18Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:24636\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-26T07:15:18Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A2U9ILE5\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T02:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES_PART2",
        "changes": "Re-grounded 3 causal edge(s) off microbe-domain METPO predicates onto their causal-graph counterparts (1 to produces, 2 to reduces), issue 301 part 2. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Each replacement is a 1:1 mirror of its source predicate that changes only the domain, so the claim each edge makes is unchanged and directions are unchanged. The replacements are proposed in proposals/metpo_traitmech_v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-16T02:00:00Z",
        "curator": "claude",
        "action": "NORMALISE_NODE_TYPE",
        "changes": "Under the PATHWAY-vs-BIOLOGICAL_PROCESS rule, one node_id means one thing corpus-wide (issue 356): electron_transport_chain is typed PATHWAY. PATHWAY is a named, conventionally enumerable multi-step route; BIOLOGICAL_PROCESS is everything else. A named route through enumerable complexes. Was 4 PATHWAY to 2 before this tranche.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-17T02:00:00Z",
        "curator": "claude",
        "action": "NORMALISE_NODE_SENSE",
        "changes": "One node_id per SENSE (issues 356, 384): molecular_oxygen is the chemical sense here. The molecule, not the condition \u2014 the dioxygen participating in the reaction the graph describes. Normalised onto molecular_oxygen, the id 20 other chemical occurrences already use, so one id means one sense corpus-wide (issues 356, 384).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-22T04:26:15Z",
        "curator": "codex",
        "action": "REVIEW_UNIPROT_INSTANCE_GROUNDINGS",
        "changes": "Reviewed 1 organism-specific UniProtKB grounding(s): replaced 0 with taxon-agnostic GO/InterPro terms and retracted 1 to label-only where no exact semantic term was supported (docs/GROUNDING_POLICY.md).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:24:00Z",
        "curator": "claude",
        "action": "RESTORE_CANONICAL_CITATION",
        "changes": "Restored the canonical-example citation for NCBITaxon:266 from DOI:10.1016/S0005-2728(98)00092-9 back to PMID:30428155 (review issue 519). The tranche event described the change as a PMID-to-DOI upgrade, but the DOI resolves to a different paper than the PMID, so this was a replacement rather than an identifier normalisation. The pre-tranche citation is restored; a deliberate replacement can be made in a new event that says so.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T06:15:39Z",
        "curator": "codex",
        "action": "ADD_EXACT_ONTOLOGY_MATCH",
        "changes": "Ontology exact-match review (2026-08-25): approved exact xref(s): GO:0006119; declared exact synonym(s): 'respiratory-chain phosphorylation'. Evidence is predicate-scoped in the versioned ontology snapshots; OAK cross-checked direct data, and OLS4 spot-checked release deltas and disputed hits.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-22T01:35:00Z",
        "curator": "claude",
        "action": "REFRESH_UNIPROT_ENTRY_VERSION",
        "changes": "Refreshed UniProtKB entry_version against live UniProt REST on 2026-10-22: UniProtKB:P08306 (167 -> 168 on heme_copper_oxidase).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:2000016",
    "label": "oxidizes",
    "definition": "An OBJECT_PROPERTY relating an organism to a chemical substrate that the organism oxidises (removes electrons or hydrogens from).",
    "definition_source": "DOI:10.1146/annurev.micro.55.1.485",
    "trait_category": "METABOLISM",
    "term_kind": "OBJECT_PROPERTY",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:2000001"
    ],
    "synonyms": [
      {
        "synonym_text": "oxidation",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "domain": "https://w3id.org/metpo/1000525",
    "range_": "http://purl.obolibrary.org/obo/CHEBI_24431",
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev.micro.55.1.485",
        "snippet": "oxidation",
        "notes": "Microbial-physiology reference supports 'oxidizes' as a canonical predicate composed with a CHEBI-class chemical object at assertion time."
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.957250+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (OBJECT_PROPERTY)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic biochemical conversion or activity relation carrier; later replacement should use more specific trait records that combine the relation with the substrate, product, enzyme or activity target, assay context, growth condition, or other entity.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-16T08:50:00-07:00",
        "curator": "claude",
        "action": "UNDEPRECATED_AS_COMPOSITION_PRIMITIVE",
        "changes": "Restored from DEPRECATED to REVIEWED under the predicate+class composition pattern (intended use: <organism> + this predicate + CHEBI chemical class). Added DOI/PMID-backed definition, evidence, and explicit domain/range slots.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000034",
    "label": "oxygenic photosynthesis",
    "definition": "A phototrophic metabolism that uses light energy to fix CO2, oxidizing water as the electron donor and releasing molecular oxygen. It uses two linked photosystems and chlorophyll, and is characteristic of cyanobacteria (and plant chloroplasts).",
    "definition_source": "DOI:10.1016/j.tim.2006.09.001",
    "trait_category": "METABOLISM",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "traitmech:000038"
    ],
    "synonyms": [
      {
        "synonym_text": "oxygenic_photoautotrophy",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1126/science.aaf4507"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1016/j.tim.2006.09.001",
        "notes": "Bryant & Frigaard, \"Prokaryotic photosynthesis and phototrophy illuminated\", contrasts oxygenic photosynthesis (water-splitting, O2-evolving) in cyanobacteria with anoxygenic phototrophy."
      },
      {
        "reference": "DOI:10.1146/annurev-earth-060313-054810",
        "notes": "Fischer et al., \"Evolution of Oxygenic Photosynthesis\", supports water-oxidizing, oxygen-evolving photosynthesis as a distinct, cyanobacterial innovation."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1148",
        "taxon_label": "Synechocystis sp. PCC 6803",
        "note": "Default model unicellular cyanobacterium for oxygenic photosynthesis; first phototroph genome-sequenced.",
        "reference": "DOI:10.1023/A:1013887908680"
      },
      {
        "taxon_id": "NCBITaxon:1111708",
        "taxon_label": "Synechocystis sp. PCC 6803",
        "note": "Strain-level model paired to the reviewed PsbA2/D1 protein example in the photosystem II water-oxidation branch.",
        "reference": "DOI:10.1074/jbc.M806116200"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "oxygenic_photosynthesis_water_splitting",
        "title": "Oxygenic photosynthesis splits water and releases O2",
        "description": "Evidence-backed causal sketch linking two linked photosystems and water oxidation to CO2 fixation and oxygen evolution.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "Represents the canonical cyanobacterial linear electron-transfer route and uses the D1 component of photosystem II from Synechocystis PCC 6803 as its taxon-paired example; one D1 accession does not denote the complete PSII complex.",
        "nodes": [
          {
            "node_id": "oxygenic_photosynthesis_trait",
            "label": "oxygenic photosynthesis",
            "node_type": "TRAIT",
            "grounding": "traitmech:000034",
            "description": "Light-driven CO2 fixation that oxidizes water and evolves O2."
          },
          {
            "node_id": "water",
            "label": "water",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:15377",
            "description": "Electron donor for oxygenic photosynthesis."
          },
          {
            "node_id": "molecular_oxygen",
            "label": "molecular oxygen",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:15379",
            "description": "O2 released by water oxidation."
          },
          {
            "node_id": "photosynthetic_etc",
            "label": "photosynthetic electron transport",
            "node_type": "PATHWAY",
            "grounding": "GO:0009767",
            "description": "Linked-photosystem electron transport powering CO2 fixation."
          },
          {
            "node_id": "photosystem_ii",
            "label": "photosystem II",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Pigment-protein complex that catalyzes light-driven water oxidation.",
            "grounding": "GO:0009523",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:P16033",
                "protein_label": "Photosystem II protein D1 2",
                "gene_symbol": "psbA2",
                "taxon_id": "NCBITaxon:1111708",
                "taxon_label": "Synechocystis sp. PCC 6803",
                "entry_status": "REVIEWED",
                "retrieved_on": "2026-10-22",
                "entry_version": 187,
                "sequence_version": 1,
                "role": "D1 reaction-center component of photosystem II; this accession is not presented as the complete water-oxidizing complex.",
                "evidence": [
                  {
                    "reference": "DOI:10.1074/jbc.M806116200",
                    "snippet": "the PsbA (D1) subunit of photosystem II (PSII)",
                    "notes": "A primary Synechocystis PCC 6803 study identifies PsbA/D1 as a PSII subunit and studies its biogenesis; UniProtKB P16033 verifies the reviewed PsbA2 protein and strain taxon."
                  }
                ]
              }
            ]
          },
          {
            "node_id": "plastoquinone_pool",
            "label": "plastoquinone/plastoquinol pool",
            "node_type": "CHEMICAL",
            "description": "Mobile quinone electron carrier reduced by PSII (PQ -> PQH2)."
          },
          {
            "node_id": "cytochrome_b6f",
            "label": "cytochrome b6f complex",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Electron transfer complex linking PSII/plastoquinol to PSI.",
            "grounding": "GO:0009512"
          },
          {
            "node_id": "photosystem_i",
            "label": "photosystem I",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Pigment-protein complex that oxidizes plastocyanin/cyt c6 and reduces ferredoxin.",
            "grounding": "GO:0009522"
          },
          {
            "node_id": "ferredoxin",
            "label": "ferredoxin",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Iron-sulfur electron carrier reduced by PSI.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Ferredoxin is an umbrella label spanning multiple iron-sulfur protein families; the cited pathway evidence does not identify one exact family."
          },
          {
            "node_id": "fnr",
            "label": "ferredoxin-NADP+ reductase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Enzyme reducing NADP+ to NADPH using ferredoxin-derived electrons.",
            "grounding": "GO:0004324"
          },
          {
            "node_id": "nadph",
            "label": "NADPH",
            "node_type": "CHEMICAL",
            "description": "Reducing equivalent generated by the light reactions.",
            "grounding": "CHEBI:16474"
          },
          {
            "node_id": "proton_motive_force",
            "label": "proton motive force",
            "node_type": "STATE",
            "description": "Transthylakoid proton motive force generated by linear electron transport.",
            "grounding": "METPO:1007500"
          },
          {
            "node_id": "atp",
            "label": "ATP",
            "node_type": "CHEMICAL",
            "description": "Energy currency synthesized by ATP synthase driven by the pmf."
          }
        ],
        "edges": [
          {
            "subject": "water",
            "predicate": "oxidized to",
            "object": "molecular_oxygen",
            "description": "Water is the electron donor; its oxidation releases O2.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.tim.2006.09.001",
                "notes": "Bryant & Frigaard contrast oxygenic photosynthesis (water-splitting, O2-evolving) with anoxygenic phototrophy."
              }
            ],
            "predicate_id": "METPO:2007405"
          },
          {
            "subject": "photosynthetic_etc",
            "predicate": "confers",
            "object": "oxygenic_photosynthesis_trait",
            "description": "Two linked photosystems power electron flow from water to NADP+.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-earth-060313-054810",
                "notes": "Fischer et al. support water-oxidizing, O2-evolving photosynthesis as a cyanobacterial innovation."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "photosystem_ii",
            "predicate": "oxidizes",
            "object": "water",
            "description": "PSII is the primary catalyst of water oxidation in oxygenic photosynthesis.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s11120-022-00991-y",
                "notes": "Shevela et al. 2023: PSII is the primary catalyst of water oxidation in oxygenic photosynthesis."
              }
            ],
            "predicate_id": "METPO:2007803"
          },
          {
            "subject": "photosystem_ii",
            "predicate": "reduces",
            "object": "plastoquinone_pool",
            "description": "Electrons extracted from water reduce plastoquinone (PQ -> PQH2).",
            "evidence": [
              {
                "reference": "DOI:10.1007/s11120-022-00991-y",
                "notes": "Shevela et al. 2023: water oxidation extracts electrons that reduce plastoquinone (PQ -> PQH2)."
              }
            ],
            "predicate_id": "METPO:2007802"
          },
          {
            "subject": "plastoquinone_pool",
            "predicate": "donates electrons to",
            "object": "cytochrome_b6f",
            "description": "Plastoquinol diffuses to reduce the cytochrome b6f complex.",
            "evidence": [
              {
                "reference": "DOI:10.3390/plants13152103",
                "notes": "Milrad et al. 2024: PQH2 diffuses to reduce the cytochrome b6f complex."
              }
            ],
            "predicate_id": "METPO:2007403"
          },
          {
            "subject": "cytochrome_b6f",
            "predicate": "transfers electrons to",
            "object": "photosystem_i",
            "description": "Cyt b6f transfers electrons to PSI via soluble carriers (plastocyanin or cytochrome c6).",
            "evidence": [
              {
                "reference": "DOI:10.3390/plants13152103",
                "notes": "Milrad et al. 2024: electrons transferred from Cytb6f to PSI via plastocyanin or cytochrome c6."
              }
            ],
            "predicate_id": "METPO:2007403"
          },
          {
            "subject": "photosystem_i",
            "predicate": "reduces",
            "object": "ferredoxin",
            "description": "PSI oxidizes plastocyanin and reduces ferredoxin.",
            "evidence": [
              {
                "reference": "DOI:10.1111/1751-7915.14519",
                "notes": "Grettenberger et al. 2024: PSI oxidizes plastocyanin and reduces ferredoxin."
              }
            ],
            "predicate_id": "METPO:2007802"
          },
          {
            "subject": "fnr",
            "predicate": "reduces",
            "object": "nadph",
            "description": "Ferredoxin-NADP+ reductase reduces NADP+ to NADPH using ferredoxin electrons.",
            "evidence": [
              {
                "reference": "DOI:10.1111/1751-7915.14519",
                "notes": "Grettenberger et al. 2024: electrons via ferredoxin and FNR reduce NADP+ to NADPH."
              }
            ],
            "predicate_id": "METPO:2007802"
          },
          {
            "subject": "photosynthetic_etc",
            "predicate": "generates",
            "object": "proton_motive_force",
            "description": "Linear electron transport generates the transthylakoid proton motive force.",
            "evidence": [
              {
                "reference": "DOI:10.3390/plants13152103",
                "notes": "Milrad et al. 2024: membrane proton motive force produced by these transfers comprises dpH and dPsi."
              }
            ],
            "predicate_id": "biolink:produces"
          },
          {
            "subject": "proton_motive_force",
            "predicate": "drives",
            "object": "atp",
            "description": "The proton motive force drives ATP synthesis by ATP synthase.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s11120-022-00991-y",
                "notes": "Shevela et al. 2023: raised proton motive force drives ATP synthesis by ATP synthase."
              }
            ]
          },
          {
            "subject": "photosystem_ii",
            "predicate": "contributes to",
            "object": "oxygenic_photosynthesis_trait",
            "description": "PSII supplies the water-oxidation entry point.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s11120-019-00648-3",
                "snippet": "The electrons for this process originate from water oxidation that takes place in PS II",
                "notes": "Verified against the public PMC full text."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "ferredoxin",
            "predicate": "donates electrons to",
            "object": "fnr",
            "description": "Reduced ferredoxin transfers PSI electrons to FNR.",
            "evidence": [
              {
                "reference": "DOI:10.1039/D2SC01546C",
                "snippet": "Fd (or Fld) then shuttles the electrons from PSI to ferredoxin NADP+-reductase (FNR) for the reduction of NADP+ to NADPH that is used in carbon fixation",
                "notes": "Verified against the public PMC full text."
              }
            ],
            "predicate_id": "METPO:2007403"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-30T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate METABOLISM trait (oxygenic photosynthesis) from literature research to fill the phototrophy gap.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-10T14:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (water-splitting / O2 evolution) with CHEBI/GO node groundings and RO/METPO predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 8 evidence-backed generic edges (9 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:12Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 7 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000017\u00d73, METPO:2007403\u00d72, METPO:2000016\u00d71, biolink:produces\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:18Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:16474\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-26T07:15:18Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A009PCQ5\u00d71, UniProtKB:A0A0E2H5I8\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:21:11Z",
        "curator": "claude",
        "action": "RETRACT_DEAD_UNIPROT_GROUNDINGS",
        "changes": "Retracted 2 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:23:54Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 4 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0009523\u00d71, GO:0009512\u00d71, GO:0009522\u00d71, GO:0004324\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 1 causal edge(s) off enables/RO:0002327 with a TRAIT object (1 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T02:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES_PART2",
        "changes": "Re-grounded 4 causal edge(s) off microbe-domain METPO predicates onto their causal-graph counterparts (1 to oxidizes, 3 to reduces), issue 301 part 2. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Each replacement is a 1:1 mirror of its source predicate that changes only the domain, so the claim each edge makes is unchanged and directions are unchanged. The replacements are proposed in proposals/metpo_traitmech_v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-15T02:00:00Z",
        "curator": "claude",
        "action": "NORMALISE_NODE_TYPE",
        "changes": "Normalised causal-node type(s) so one node_id means one thing corpus-wide (issue 356): proton_motive_force: CHEMICAL -> STATE. The schema's OWN example of STATE: 'a bioenergetic or molecular state of the cell (e.g. proton motive force ...) ... the state is the gradient / steady-value, not its establishment'. All 35 occurrences describe the gradient -- every description across all four types reads 'electrochemical proton gradient', including the 13 typed BIOLOGICAL_PROCESS ('Transmembrane electrochemical gradient generated by respiration'), which name the gradient and its provenance rather than the generating process. Nothing here means the establishment, so this is a retype and not a rename; records that DO mean the process already use a separate id (proton_motive_force_generation in ph_delta.yaml). Also settles the one edge #356 was filed for: phototrophic.yaml's CAPACITY typing was blocking `powers` (METPO:2007900), which is gated to BIOLOGICAL_PROCESS|STATE.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-19T00:00:00+00:00",
        "curator": "add_faprotax_synonyms",
        "action": "ADDED_SYNONYM",
        "changes": "Added 'oxygenic_photoautotrophy' (5221 occurrences in microbedecoder's unmapped labels) as a RELATED_SYNONYM (#453). FAPROTAX's oxygenic_photoautotrophy is autotrophic growth driven by oxygenic photosynthesis \u2014 the record's own definition is 'uses light energy to fix CO2, oxidizing water as the electron donor and releasing molecular oxygen', which is that phenotype. Written with the source's underscores because that is the string a consumer must resolve.",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-08-20T07:10:36Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (METPO:1007500\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-24T00:00:00Z",
        "curator": "codex",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Added a strain-matched Synechocystis PsbA2/D1 example with an explicit PSII component role, converted the species citation to DOI, retained broad ferredoxin as reviewed label-only, and documented graph scope.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T09:00:00Z",
        "curator": "codex",
        "action": "CONNECT_CAUSAL_GRAPH_COMPONENTS",
        "changes": "Resolved issue #183 graph fragmentation (3 components to 1) using 2 public-source, verbatim-snippet-backed connector(s). No paid research service was called.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T07:25:07Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007403\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-22T01:35:00Z",
        "curator": "claude",
        "action": "REFRESH_UNIPROT_ENTRY_VERSION",
        "changes": "Refreshed UniProtKB entry_version against live UniProt REST on 2026-10-22: UniProtKB:P16033 (186 -> 187 on photosystem_ii).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000135",
    "label": "pectin degradation",
    "definition": "A biopolymer-degradation metabolism in which an organism depolymerizes pectin into oligogalacturonides and catabolizes the released pectin breakdown products using pectinolytic enzymes.",
    "definition_source": "DOI:10.1128/MMBR.00038-07",
    "trait_category": "METABOLISM",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000110"
    ],
    "synonyms": [
      {
        "synonym_text": "pectinolysis",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1146/annurev.micro.50.1.213"
      },
      {
        "synonym_text": "pectin breakdown",
        "synonym_type": "EXACT_SYNONYM",
        "source": "http://purl.obolibrary.org/obo/go/releases/2026-07-26/go-basic.obo"
      },
      {
        "synonym_text": "pectin catabolism",
        "synonym_type": "EXACT_SYNONYM",
        "source": "http://purl.obolibrary.org/obo/go/releases/2026-07-26/go-basic.obo"
      },
      {
        "synonym_text": "pectinolytic",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1128/MMBR.00038-07"
      }
    ],
    "xrefs": [
      "GO:0045490"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1128/MMBR.00038-07",
        "snippet": "Catabolism of pectin and its breakdown products by pectinolytic bacteria occurs within distinct cellular environments",
        "notes": "Abbott and Boraston review pectin breakdown by pectinolytic Enterobacteriaceae as a multicomponent microbial catabolic pathway."
      },
      {
        "reference": "DOI:10.1146/annurev.micro.50.1.213",
        "snippet": "The extracellular degradation of the pectin leads to the formation of oligogalacturonides that are catabolized through an intracellular pathway",
        "notes": "Hugouvieux-Cotte-Pattat et al. review the pectinase system and pectin-catabolite pathway of Erwinia chrysanthemi strain 3937."
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-10T00:00:00Z",
        "curator": "codex",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed DOI-backed pectin degradation after a repository-wide duplicate review covering ignored and hidden files.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-21T21:12:25Z",
        "curator": "claude",
        "action": "ADD_CANONICAL_EXAMPLES",
        "changes": "Added source-backed canonical example Dickeya dadantii 3937 (NCBITaxon:198628; DOI:10.1146/annurev.micro.50.1.213) from existing record evidence on Erwinia chrysanthemi strain 3937.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-21T21:12:25Z",
        "curator": "claude",
        "action": "CURATE_CAUSAL_GRAPH",
        "changes": "Added MECHANISTIC causal_graphs entry (pectin_degradation_catabolic_sketch) anchored on existing verbatim record evidence snippets.",
        "llm_assisted": true
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:198628",
        "taxon_label": "Dickeya dadantii 3937",
        "note": "Hugouvieux-Cotte-Pattat et al. review extracellular pectin depolymerization and intracellular oligogalacturonide catabolism in Erwinia chrysanthemi strain 3937 (now Dickeya dadantii 3937).",
        "reference": "DOI:10.1146/annurev.micro.50.1.213"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "pectin_degradation_catabolic_sketch",
        "title": "Compartmentalized pectin depolymerization and oligogalacturonide catabolism",
        "description": "Evidence-backed pathway linking secreted pectate lyase depolymerization of pectin and compartmentalized oligogalacturonide catabolism to the pectin degradation phenotype.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "The taxon-matched protein example anchors the Dickeya dadantii 3937 (Erwinia chrysanthemi 3937) secreted pectate lyase PelA branch of extracellular pectin depolymerization.",
        "nodes": [
          {
            "node_id": "pectin_degradation_trait",
            "label": "pectin degradation",
            "node_type": "TRAIT",
            "grounding": "traitmech:000135",
            "description": "Biopolymer-degradation metabolism that depolymerizes pectin and catabolizes its breakdown products."
          },
          {
            "node_id": "pectin_degradation_catabolic_process",
            "label": "pectin catabolic process",
            "node_type": "BIOLOGICAL_PROCESS",
            "grounding": "GO:0045490",
            "description": "Compartmentalized extracellular depolymerization of pectin to oligogalacturonides and intracellular catabolism of breakdown products."
          },
          {
            "node_id": "pectin_degradation_pectate_lyase",
            "label": "pectate lyase",
            "node_type": "GENE_OR_PROTEIN",
            "grounding": "InterPro:IPR002022",
            "description": "Secreted pectate lyase (Pel) that cleaves extracellular pectin to oligogalacturonide intermediates.",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:P0C1A3",
                "protein_label": "Pectate lyase A",
                "gene_symbol": "pelA",
                "taxon_id": "NCBITaxon:198628",
                "taxon_label": "Dickeya dadantii (strain 3937)",
                "entry_status": "REVIEWED",
                "entry_version": 88,
                "sequence_version": 1,
                "proteome_id": "UP000006859",
                "retrieved_on": "2026-10-21",
                "role": "Secreted pectate lyase A (PelA) in Dickeya dadantii 3937 (Erwinia chrysanthemi 3937) that cleaves extracellular pectin to oligogalacturonides during pectin catabolism.",
                "evidence": [
                  {
                    "reference": "DOI:10.1146/annurev.micro.50.1.213",
                    "snippet": "The extracellular degradation of the pectin leads to the formation of oligogalacturonides that are catabolized through an intracellular pathway",
                    "notes": "Hugouvieux-Cotte-Pattat et al. review extracellular pectin degradation to oligogalacturonides in E. chrysanthemi 3937 (Dickeya dadantii 3937), exemplified by reviewed pectate lyase PelA (UniProtKB:P0C1A3)."
                  }
                ]
              }
            ]
          }
        ],
        "edges": [
          {
            "subject": "pectin_degradation_catabolic_process",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "pectin_degradation_trait",
            "description": "Compartmentalized catabolism of pectin and its breakdown products confers the pectin degradation trait.",
            "evidence": [
              {
                "reference": "DOI:10.1128/MMBR.00038-07",
                "snippet": "Catabolism of pectin and its breakdown products by pectinolytic bacteria occurs within distinct cellular environments",
                "notes": "Abbott and Boraston review compartmentalized catabolism of pectin and its breakdown products by pectinolytic bacteria."
              }
            ]
          },
          {
            "subject": "pectin_degradation_pectate_lyase",
            "predicate": "enables",
            "predicate_id": "RO:0002327",
            "object": "pectin_degradation_catabolic_process",
            "description": "Secreted pectate lyase mediates extracellular pectin depolymerization to oligogalacturonides during pectin catabolism.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev.micro.50.1.213",
                "snippet": "The extracellular degradation of the pectin leads to the formation of oligogalacturonides that are catabolized through an intracellular pathway",
                "notes": "Hugouvieux-Cotte-Pattat et al. describe extracellular pectin degradation forming oligogalacturonides for intracellular catabolism."
              }
            ]
          }
        ]
      }
    ]
  },
  {
    "identifier": "traitmech:000197",
    "label": "perchlorate respiration",
    "definition": "An anaerobic respiration in which an organism uses perchlorate as the terminal electron acceptor and reduces it to chloride for energy conservation.",
    "definition_source": "DOI:10.1038/nrmicro926",
    "trait_category": "METABOLISM",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000802"
    ],
    "synonyms": [
      {
        "synonym_text": "dissimilatory perchlorate reduction",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1186/s12864-015-2011-5"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1186/s12864-015-2011-5",
        "snippet": "reduction to chlorite (ClO2-) in the bacterial periplasm by perchlorate reductase, and the dismutation of chlorite to chloride and molecular oxygen",
        "notes": "Melnyk et al. describe the canonical perchlorate-to-chloride respiratory pathway through perchlorate reductase and chlorite dismutase."
      },
      {
        "reference": "DOI:10.1128/AEM.05758-11",
        "snippet": "perchlorate reductase and chlorite dismutase, which are encoded by the pcrABCD and cld genes",
        "notes": "Melnyk et al. support the PcrABCD and Cld gene modules as the two pathway-specific enzyme systems for perchlorate reduction to chloride."
      }
    ],
    "discussions": [
      {
        "discussion_id": "perchlorate-respiration-xref-gap",
        "prompt": "Resolve an exact external ontology class for organism-level perchlorate respiration before adding a TraitRecord xref.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "The pinned METPO snapshot contains only obsolete (Per)chlorate respiration, Perchlorate respiration, and Perchlorate-reducing classes. Candidate GO, EC, and protein-family terms for perchlorate reductase and chlorite dismutase are narrower than the whole-organism anaerobic respiration phenotype and should be checked separately before grounding PcrABCD- or Cld-level causal nodes.",
        "posed_by": "codex",
        "posed_date": "2026-09-15"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-15T00:56:27Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted perchlorate respiration as a DOI-backed anaerobic respiration TraitRecord after a repository-wide duplicate review covering ignored and hidden files; the local METPO snapshot has only obsolete perchlorate respiration classes and the replacement placeholder is reserved in proposals/metpo_traitmech_v74.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000193",
    "label": "photoferrotrophy",
    "definition": "A metabolism in which anoxygenic phototrophs use light energy to oxidize Fe(II) as an electron donor for carbon fixation and biomass formation.",
    "definition_source": "DOI:10.3389/fmicb.2014.00713",
    "trait_category": "METABOLISM",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000035",
      "traitmech:000107"
    ],
    "synonyms": [
      {
        "synonym_text": "phototrophic Fe(II) oxidation",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.3389/fmicb.2014.00713"
      },
      {
        "synonym_text": "anoxygenic phototrophic Fe(II) oxidation",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.3389/fmicb.2017.00323"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.3389/fmicb.2014.00713",
        "snippet": "photoferrotrophic bacteria use light as energy and Fe(II) as an electron source for carbon fixation and biomass formation",
        "notes": "Walter et al. directly describe the defining light-powered Fe(II)-donor physiology of photoferrotrophic bacteria."
      },
      {
        "reference": "DOI:10.3389/fmicb.2017.00323",
        "snippet": "reduced iron [Fe(II)] as an electron donor",
        "notes": "Camacho et al. review Fe(II) as the inorganic electron donor used by photoferrotrophs during anoxygenic photosynthesis."
      },
      {
        "reference": "DOI:10.1128/JB.00776-06",
        "snippet": "that is necessary for phototrophic Fe(II) oxidation",
        "notes": "Jiao & Newman discovered the R. palustris TIE-1 pio operon and showed that it is necessary for phototrophic Fe(II) oxidation."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:395960",
        "taxon_label": "Rhodopseudomonas palustris TIE-1",
        "note": "PioABC-model purple nonsulfur photoferrotroph.",
        "reference": "DOI:10.1128/JB.00776-06"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "photoferrotrophy_light_feii_oxidation",
        "title": "Photoferrotrophy couples light to Fe(II) oxidation",
        "description": "Evidence-backed causal sketch linking light, Fe(II) oxidation, photosynthetic electron transport, and carbon fixation in photoferrotrophic metabolism.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures the shared light, Fe(II)-donor, Fe(III) product, and carbon-fixation processes. It stays process-level because lineage-specific PioABC, FoxEYZ, and Cyc2 branches do not yet have a reviewed or audit-verifiable exact UniProt protein example for this TraitRecord.",
        "nodes": [
          {
            "node_id": "photoferrotrophy_trait",
            "label": "photoferrotrophy",
            "node_type": "TRAIT",
            "grounding": "traitmech:000193",
            "description": "Anoxygenic photosynthetic Fe(II)-oxidizing metabolism."
          },
          {
            "node_id": "light",
            "label": "light",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "grounding": "PATO:0001717",
            "description": "Energy source for anoxygenic phototrophic Fe(II) oxidation."
          },
          {
            "node_id": "ferrous_iron",
            "label": "ferrous iron",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:29033",
            "description": "Fe(II), the electron-donor substrate."
          },
          {
            "node_id": "ferric_iron",
            "label": "ferric iron",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:29034",
            "description": "Fe(III), the oxidized iron product."
          },
          {
            "node_id": "photosynthetic_electron_transport",
            "label": "photosynthetic electron transport",
            "node_type": "PATHWAY",
            "grounding": "GO:0009767",
            "description": "Light-driven electron-transport chain powered by photochemical reaction centers."
          },
          {
            "node_id": "carbon_fixation",
            "label": "carbon fixation",
            "node_type": "BIOLOGICAL_PROCESS",
            "grounding": "GO:0015977",
            "description": "Inorganic carbon assimilation into organic compounds."
          },
          {
            "node_id": "carbon_dioxide",
            "label": "carbon dioxide",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:16526",
            "description": "Inorganic carbon source fixed by photoferrotrophs."
          },
          {
            "node_id": "biomass",
            "label": "biomass",
            "node_type": "CHEMICAL",
            "grounding": "METPO:1007501",
            "description": "Cell material formed from fixed carbon."
          }
        ],
        "edges": [
          {
            "subject": "photoferrotrophy_trait",
            "predicate": "has energy source",
            "object": "light",
            "description": "Photoferrotrophy uses light as the metabolism's energy source.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2014.00713",
                "snippet": "photoferrotrophic bacteria use light as energy",
                "notes": "Verified against the open Frontiers primary article full text."
              }
            ],
            "predicate_id": "METPO:2007807"
          },
          {
            "subject": "photoferrotrophy_trait",
            "predicate": "has electron donor",
            "object": "ferrous_iron",
            "description": "Fe(II) is the electron donor for photoferrotrophy.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2017.00323",
                "snippet": "reduced iron [Fe(II)] as an electron donor",
                "notes": "Supports Fe(II) as the inorganic electron donor for anoxygenic photoferrotrophy."
              }
            ],
            "predicate_id": "METPO:2007701"
          },
          {
            "subject": "light",
            "predicate": "enables",
            "object": "photosynthetic_electron_transport",
            "description": "Light powers the photosynthetic electron flow in photoferrotrophic metabolism.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2014.00713",
                "snippet": "photoferrotrophic bacteria use light as energy",
                "notes": "Supports light as the energetic input for the photoferrotrophic electron-transport chain."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "ferrous_iron",
            "predicate": "feeds electrons into",
            "object": "photosynthetic_electron_transport",
            "description": "Fe(II) supplies electrons to anoxygenic photosynthetic electron transport in photoferrotrophs.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2014.00713",
                "snippet": "Fe(II) as an electron source for carbon fixation and biomass formation",
                "notes": "Supports ferrous iron as the electron source feeding photoferrotrophic carbon fixation."
              }
            ],
            "predicate_id": "METPO:2007402"
          },
          {
            "subject": "ferrous_iron",
            "predicate": "oxidized to",
            "object": "ferric_iron",
            "description": "Photoferrotrophy oxidizes Fe(II) to Fe(III).",
            "evidence": [
              {
                "reference": "DOI:10.1128/JB.00776-06",
                "snippet": "phototrophic Fe(II) oxidation in Rhodopseudomonas palustris TIE-1",
                "notes": "Supports Fe(II) oxidation by the model R. palustris TIE-1 photoferrotrophy system."
              }
            ],
            "predicate_id": "METPO:2007405"
          },
          {
            "subject": "photosynthetic_electron_transport",
            "predicate": "enables",
            "object": "carbon_fixation",
            "description": "Light-driven electron transport supports carbon fixation in photoferrotrophic metabolism.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2014.00713",
                "snippet": "Fe(II) as an electron source for carbon fixation",
                "notes": "Supports electron flow from Fe(II) into photoferrotrophic carbon fixation."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "carbon_dioxide",
            "predicate": "fixed during",
            "object": "carbon_fixation",
            "description": "Photoferrotrophs assimilate inorganic carbon by carbon fixation.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2017.00323",
                "snippet": "inorganic carbon is fixed into organic matter",
                "notes": "Supports carbon fixation during photoferrotrophic anoxygenic photosynthesis."
              }
            ]
          },
          {
            "subject": "carbon_fixation",
            "predicate": "has output",
            "object": "biomass",
            "description": "Carbon fixed during photoferrotrophy supports biomass formation.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2014.00713",
                "snippet": "photoferrotrophic bacteria use light as energy and Fe(II) as an electron source for carbon fixation and biomass formation",
                "notes": "Supports biomass formation coupled to Fe(II)-fed photoferrotrophic metabolism."
              }
            ],
            "predicate_id": "RO:0002234"
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "photoferrotrophy-xref-gap",
        "prompt": "Resolve an exact external ontology class for photoferrotrophy before adding a TraitRecord xref.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "The pinned METPO snapshot has no active photoferrotrophy or anoxygenic phototrophic Fe(II) oxidation class. Candidate GO classes for photosynthesis, photosynthetic electron transport, and carbon fixation are broader than this Fe(II)-donor organismal metabolism, so no exact external class has yet been resolved.",
        "posed_by": "codex",
        "posed_date": "2026-09-14"
      },
      {
        "discussion_id": "photoferrotrophy-protein-example-gap",
        "prompt": "Resolve a live, audit-clean UniProt protein example for a taxon-specific photoferrotrophy branch.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "R. palustris TIE-1 PioA and R. ferrooxidans SW2 FoxE have DOI-backed primary evidence, but their current exact UniProtKB accessions are unreviewed entries without live Proteomes cross-references. The first graph therefore stays process-level until a reviewed or audit-verifiable exact entry is available.",
        "posed_by": "codex",
        "posed_date": "2026-09-14"
      }
    ]
  },
  {
    "identifier": "traitmech:000038",
    "label": "photosynthesis",
    "definition": "A phototrophic metabolism that uses light energy and chlorophyll- or bacteriochlorophyll-based photochemical reaction centers to drive electron flow, fixing CO2 and/or generating reducing power. Subdivided into oxygenic and anoxygenic photosynthesis.",
    "definition_source": "DOI:10.1016/j.tim.2006.09.001",
    "trait_category": "METABOLISM",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "traitmech:000037"
    ],
    "xrefs": [
      "GO:0015979"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1016/j.tim.2006.09.001",
        "notes": "Bryant & Frigaard treat prokaryotic photosynthesis (reaction-center based) as encompassing both oxygenic and anoxygenic forms across five phyla."
      },
      {
        "reference": "DOI:10.1146/annurev-earth-060313-054810",
        "notes": "Fischer et al., \"Evolution of Oxygenic Photosynthesis\", supports reaction-center photosynthesis as the chlorophyll-based, CO2-fixing branch of phototrophy distinct from rhodopsin-based light capture."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1148",
        "taxon_label": "Synechocystis sp. PCC 6803",
        "note": "oxygenic photosynthesis",
        "reference": "PMID:16228363"
      },
      {
        "taxon_id": "NCBITaxon:1063",
        "taxon_label": "Cereibacter sphaeroides",
        "note": "anoxygenic photosynthesis",
        "reference": "PMID:21777427"
      },
      {
        "taxon_id": "NCBITaxon:1111708",
        "taxon_label": "Synechocystis sp. PCC 6803",
        "note": "Strain-level oxygenic photosynthesis model paired to the reviewed PsbA2/D1 component of photosystem II.",
        "reference": "DOI:10.1074/jbc.M806116200"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "photosynthesis_chlorophyll_reaction_center",
        "title": "Chlorophyll-based photosynthesis drives electron flow and CO2 fixation",
        "description": "Evidence-backed causal sketch linking chlorophyll-based reaction centers to electron flow that powers CO2 fixation.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "The graph spans oxygenic and anoxygenic chlorophyll-based photosynthesis. The Synechocystis PsbA2 example supports the oxygenic photosystem II branch only; anoxygenic reaction centers use different protein families.",
        "nodes": [
          {
            "node_id": "photosynthesis_trait",
            "label": "photosynthesis",
            "node_type": "TRAIT",
            "grounding": "traitmech:000038",
            "description": "Chlorophyll/bacteriochlorophyll-based reaction-center metabolism."
          },
          {
            "node_id": "photosynthesis_process",
            "label": "photosynthesis",
            "node_type": "BIOLOGICAL_PROCESS",
            "grounding": "GO:0015979",
            "description": "Conversion of light energy to chemical energy via reaction centers."
          },
          {
            "node_id": "carbon_fixation",
            "label": "carbon fixation",
            "node_type": "BIOLOGICAL_PROCESS",
            "grounding": "GO:0015977",
            "description": "Assimilation of inorganic CO2 into organic carbon."
          },
          {
            "node_id": "light_energy",
            "label": "light energy",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Photon energy absorbed and channeled by photosynthetic pigments."
          },
          {
            "node_id": "light_harvesting",
            "label": "light harvesting / excitation transfer",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Absorption and transfer of excitation energy by antenna pigments to reaction centers."
          },
          {
            "node_id": "charge_separation",
            "label": "reaction-center charge separation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Light-driven primary charge separation in chlorophyll/bacteriochlorophyll reaction centers."
          },
          {
            "node_id": "electron_transport",
            "label": "photosynthetic electron transport",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Light-driven electron flow through the photosynthetic electron transport chain (linear or cyclic)."
          },
          {
            "node_id": "proton_gradient",
            "label": "transmembrane electrochemical proton gradient",
            "node_type": "STATE",
            "description": "Proton motive force generated across the membrane by photosynthetic electron transport."
          },
          {
            "node_id": "atp_synthesis",
            "label": "ATP synthesis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Chemiosmotic ATP generation coupled to the proton motive force.",
            "grounding": "GO:0006754"
          },
          {
            "node_id": "reducing_power",
            "label": "reducing power (NAD(P)H)",
            "node_type": "CAPACITY",
            "description": "NADPH/NAD(P)H reducing equivalents produced by the light reactions."
          },
          {
            "node_id": "photosystem_ii",
            "label": "photosystem II",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Multisubunit pigment-protein reaction-center complex initiating oxygenic photosynthetic charge separation and water oxidation.",
            "grounding": "GO:0009523",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:P16033",
                "protein_label": "Photosystem II protein D1 2",
                "gene_symbol": "psbA2",
                "taxon_id": "NCBITaxon:1111708",
                "taxon_label": "Synechocystis sp. PCC 6803",
                "entry_status": "REVIEWED",
                "retrieved_on": "2026-10-22",
                "entry_version": 187,
                "sequence_version": 1,
                "role": "D1 reaction-center component of photosystem II; this accession is not presented as the complete water-oxidizing complex.",
                "evidence": [
                  {
                    "reference": "DOI:10.1074/jbc.M806116200",
                    "snippet": "the PsbA (D1) subunit of photosystem II (PSII)",
                    "notes": "A primary Synechocystis PCC 6803 study identifies PsbA/D1 as a PSII subunit and studies its biogenesis; UniProtKB P16033 verifies the reviewed PsbA2 protein and strain taxon."
                  }
                ]
              }
            ]
          }
        ],
        "edges": [
          {
            "subject": "photosynthesis_process",
            "predicate": "confers",
            "object": "photosynthesis_trait",
            "description": "Reaction-center photochemistry underlies the photosynthetic trait.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.tim.2006.09.001",
                "notes": "Bryant & Frigaard treat reaction-center photosynthesis as encompassing both oxygenic and anoxygenic forms."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "photosynthesis_trait",
            "predicate": "contributes to",
            "object": "carbon_fixation",
            "description": "Photosynthetic electron flow powers autotrophic CO2 fixation.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-earth-060313-054810",
                "notes": "Fischer et al. frame reaction-center photosynthesis as the chlorophyll-based, CO2-fixing branch of phototrophy."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "light_energy",
            "predicate": "enables",
            "object": "light_harvesting",
            "description": "Light energy drives pigment absorption and excitation transfer to reaction-center antennae.",
            "evidence": [
              {
                "reference": "DOI:10.1111/1751-7915.14519",
                "notes": "Chlorophyll/antenna pigments absorb and transfer light energy to the photosystems (light harvesting)."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "light_harvesting",
            "predicate": "initiates",
            "object": "charge_separation",
            "description": "Transferred excitation energy drives primary charge separation at the reaction-center special pair.",
            "evidence": [
              {
                "reference": "DOI:10.3390/biom14030311",
                "notes": "Light-driven charge separation in reaction-center photosystems initiates downstream electron flow (generic to Type I/II RCs)."
              }
            ]
          },
          {
            "subject": "charge_separation",
            "predicate": "powers",
            "object": "electron_transport",
            "description": "Reaction-center charge separation drives photosynthetic electron transport (linear or cyclic).",
            "evidence": [
              {
                "reference": "DOI:10.3390/biom14030311",
                "notes": "Light-driven charge separation powers electron transfer pathways; generalization for reaction-center photosystems."
              }
            ]
          },
          {
            "subject": "electron_transport",
            "predicate": "generates",
            "object": "proton_gradient",
            "description": "Photosynthetic electron transport establishes a transmembrane electrochemical proton gradient.",
            "evidence": [
              {
                "reference": "DOI:10.3390/biom14030311",
                "notes": "Electron transfer creates a transmembrane electrochemical proton gradient (energy-conservation edge)."
              }
            ],
            "predicate_id": "biolink:produces"
          },
          {
            "subject": "proton_gradient",
            "predicate": "drives",
            "object": "atp_synthesis",
            "description": "The proton motive force is used to drive chemiosmotic ATP synthesis.",
            "evidence": [
              {
                "reference": "DOI:10.3390/biom14030311",
                "notes": "The electrochemical proton gradient drives ATP synthesis; canonical bioenergetic edge."
              }
            ]
          },
          {
            "subject": "photosynthesis_process",
            "predicate": "has output",
            "object": "reducing_power",
            "description": "Light-dependent reactions generate ATP and NAD(P)H reducing power.",
            "evidence": [
              {
                "reference": "DOI:10.5287/ora-8jgz2nrvd",
                "notes": "Light-dependent reactions generate ATP and NAD(P)H; broad linkage across chlorophyll-based photosynthetic systems."
              }
            ],
            "predicate_id": "RO:0002234"
          },
          {
            "subject": "reducing_power",
            "predicate": "used in",
            "object": "carbon_fixation",
            "description": "NADPH reducing power supplies electrons for autotrophic CO2 fixation.",
            "evidence": [
              {
                "reference": "DOI:10.1111/1751-7915.14519",
                "notes": "NADPH from the light reactions is used in biosynthesis, including carbon fixation."
              }
            ]
          },
          {
            "subject": "photosystem_ii",
            "predicate": "initiates",
            "object": "charge_separation",
            "description": "Photosystem II initiates oxygenic electron transfer through light-induced reaction-center charge separation.",
            "evidence": [
              {
                "reference": "DOI:10.1073/pnas.1520211113",
                "snippet": "PSII reactions are initiated by light-induced charge separation between a chlorophyll dimer and a pheophytin electron acceptor.",
                "notes": "The primary spectroelectrochemical study supports the generic PSII charge-separation edge; the PsbA2 accession separately grounds a Synechocystis complex component."
              }
            ]
          },
          {
            "subject": "electron_transport",
            "predicate": "contributes to",
            "object": "reducing_power",
            "description": "Photosynthetic electron-transfer reactions contribute the NADPH reducing power used by downstream carbon fixation.",
            "evidence": [
              {
                "reference": "DOI:10.1111/1751-7915.14519",
                "snippet": "NADPH and ATP are produced from a proton gradient formed coincident with the electron transfer reactions and fuel downstream processes, including carbon fixation",
                "notes": "Verified against the public PMC full text; the passage describes the oxygenic branch represented by the existing PSII node."
              }
            ],
            "predicate_id": "RO:0002326"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-31T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Minted intermediate axis class (photosynthesis) under phototrophy to parent the oxygenic- and anoxygenic-photosynthesis traits.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-10T14:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (reaction-center photosynthesis / CO2 fixation) with GO node groundings and RO predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 7 evidence-backed generic edges (7 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:12Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d71, biolink:produces\u00d71, METPO:2000202\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:33Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0006754\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 1 causal edge(s) off enables/RO:0002327 with a TRAIT object (1 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates (1 to has output), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-15T02:00:00Z",
        "curator": "claude",
        "action": "NORMALISE_NODE_TYPE",
        "changes": "Normalised causal-node type(s) so one node_id means one thing corpus-wide (issue 356): reducing_power: CHEMICAL -> CAPACITY. The schema's OWN example of CAPACITY: 'an electron-donating pool, ATP charge, or other reservoir-of-X notion ... Examples include reducing power (NADH/NADPH pool)'. The lone CHEMICAL occurrence (metabolism/photosynthesis.yaml) describes 'NADPH/NAD(P)H reducing equivalents', i.e. the pool, not a single species -- which is the very distinction CAPACITY exists to draw, and the one docs/CURATION_PLAYBOOK.md records as the reservoir sense that must NOT be retyped to TRAIT (#352).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-24T08:35:00Z",
        "curator": "codex",
        "action": "CURATE_PROTEIN_TAXON_EXAMPLE",
        "changes": "Added a DOI-backed Synechocystis PCC 6803 PsbA2 component example, a GO-grounded photosystem II node, a primary-source PSII charge-separation edge, and scope notes separating oxygenic from anoxygenic branches.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T06:15:39Z",
        "curator": "codex",
        "action": "ADD_EXACT_ONTOLOGY_MATCH",
        "changes": "Ontology exact-match review (2026-08-25): approved exact xref(s): GO:0015979. Evidence is predicate-scoped in the versioned ontology snapshots; OAK cross-checked direct data, and OLS4 spot-checked release deltas and disputed hits.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T08:20:00Z",
        "curator": "codex",
        "action": "CONNECT_CAUSAL_GRAPH_COMPONENTS",
        "changes": "Resolved issue #183 graph fragmentation (2 components to 1) using 1 public-source, verbatim-snippet-backed connector(s). No paid research service was called.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-22T01:35:00Z",
        "curator": "claude",
        "action": "REFRESH_UNIPROT_ENTRY_VERSION",
        "changes": "Refreshed UniProtKB entry_version against live UniProt REST on 2026-10-22: UniProtKB:P16033 (186 -> 187 on photosystem_ii).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000037",
    "label": "phototrophy",
    "definition": "A metabolism in which an organism captures light as its energy source. It encompasses chlorophyll-based photosynthesis (with photochemical reaction centers) and retinal-based (rhodopsin) light-driven ion pumping.",
    "definition_source": "DOI:10.1016/j.tim.2006.09.001",
    "trait_category": "METABOLISM",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000060"
    ],
    "synonyms": [
      {
        "synonym_text": "phototrophic metabolism",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1016/j.tim.2006.09.001"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1016/j.tim.2006.09.001",
        "notes": "Bryant & Frigaard, \"Prokaryotic photosynthesis and phototrophy illuminated\", frames phototrophy as the broad use of light for energy, spanning chlorophyll- and rhodopsin-based mechanisms; parent of the photosynthesis and proteorhodopsin phototrophy sub-variants."
      },
      {
        "reference": "DOI:10.1126/science.289.5486.1902",
        "notes": "B\u00e9j\u00e0 et al. established retinal-based proteorhodopsin phototrophy as a light-energy capture mechanism distinct from chlorophyll-based photosynthesis."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1148",
        "taxon_label": "Synechocystis sp. PCC 6803",
        "note": "photolithotroph",
        "reference": "DOI:10.3390/md11082894"
      },
      {
        "taxon_id": "NCBITaxon:1085",
        "taxon_label": "Rhodospirillum rubrum",
        "note": "photoorganotroph",
        "reference": "DOI:10.4056/sigs.1804360"
      },
      {
        "taxon_id": "NCBITaxon:1111708",
        "taxon_label": "Synechocystis sp. PCC 6803",
        "note": "Strain-level oxygenic phototroph paired to the reviewed PsbA2/D1 example in the photosystem II branch.",
        "reference": "DOI:10.1074/jbc.M806116200"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "phototrophy_light_energy_capture",
        "title": "Phototrophy captures light as cellular energy",
        "description": "Evidence-backed causal sketch linking light input to ATP/PMF generation across chlorophyll- and retinal-based phototrophic mechanisms.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "This parent-trait graph intentionally combines independent chlorophyll-based and microbial-rhodopsin branches. The Synechocystis protein example supports only the photosystem II branch; no rhodopsin protein is implied for the canonical taxa.",
        "nodes": [
          {
            "node_id": "phototrophy_trait",
            "label": "phototrophy",
            "node_type": "TRAIT",
            "grounding": "traitmech:000037",
            "description": "Use of light as cellular energy source."
          },
          {
            "node_id": "light",
            "label": "light",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "grounding": "PATO:0001717",
            "description": "Radiant energy captured for cellular use."
          },
          {
            "node_id": "proton_motive_force",
            "label": "proton motive force",
            "node_type": "STATE",
            "grounding": "METPO:1007500",
            "description": "Bioenergetic gradient driving ATP synthesis."
          },
          {
            "node_id": "microbial_rhodopsin",
            "label": "microbial rhodopsin",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Retinal-binding light-activated membrane protein driving the photocycle.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Microbial rhodopsin is an umbrella label spanning pumps, channels, and sensory receptors; the broad graph evidence does not identify one exact family."
          },
          {
            "node_id": "rhodopsin_photocycle",
            "label": "rhodopsin photocycle",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Light-driven cyclic conformational/photochemical cycle of microbial rhodopsins."
          },
          {
            "node_id": "atp_synthesis",
            "label": "ATP synthesis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Synthesis of ATP driven by the transmembrane proton gradient.",
            "grounding": "GO:0006754"
          },
          {
            "node_id": "photosystem_ii",
            "label": "photosystem II",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Light-driven water-oxidizing complex initiating photosynthetic electron transport.",
            "grounding": "GO:0009523",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:P16033",
                "protein_label": "Photosystem II protein D1 2",
                "gene_symbol": "psbA2",
                "taxon_id": "NCBITaxon:1111708",
                "taxon_label": "Synechocystis sp. PCC 6803",
                "entry_status": "REVIEWED",
                "retrieved_on": "2026-10-22",
                "entry_version": 187,
                "sequence_version": 1,
                "role": "D1 reaction-center component of photosystem II in the oxygenic phototrophy branch; this accession is not the complete PSII complex.",
                "evidence": [
                  {
                    "reference": "DOI:10.1074/jbc.M806116200",
                    "snippet": "the PsbA (D1) subunit of photosystem II (PSII)",
                    "notes": "A primary Synechocystis PCC 6803 study identifies PsbA/D1 as a PSII subunit and studies its biogenesis; UniProtKB P16033 verifies the reviewed PsbA2 protein and strain taxon."
                  }
                ]
              }
            ]
          },
          {
            "node_id": "photosynthetic_electron_transport",
            "label": "photosynthetic electron transport chain",
            "node_type": "PATHWAY",
            "description": "Electron flow from water through PSII, cytochrome b6f and PSI.",
            "grounding": "GO:0009767"
          },
          {
            "node_id": "nadph",
            "label": "NADPH",
            "node_type": "CHEMICAL",
            "description": "Reducing power produced by photosynthetic electron transport.",
            "grounding": "CHEBI:16474"
          },
          {
            "node_id": "atp",
            "label": "ATP",
            "node_type": "CHEMICAL",
            "description": "Cellular energy currency produced from the photosynthetic proton gradient."
          },
          {
            "node_id": "high_light",
            "label": "high light intensity",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Excess photon flux causing photodamage."
          }
        ],
        "edges": [
          {
            "subject": "light",
            "predicate": "causes",
            "object": "phototrophy_trait",
            "description": "Light availability is the input the phototrophic trait realizes.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.tim.2006.09.001",
                "notes": "Bryant & Frigaard frame phototrophy as the broad use of light for energy."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "phototrophy_trait",
            "predicate": "contributes to",
            "object": "proton_motive_force",
            "description": "Chlorophyll- and retinal-based phototrophy generate proton motive force from absorbed light.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.289.5486.1902",
                "notes": "B\u00e9j\u00e0 et al. established retinal-based proteorhodopsin phototrophy as a light-driven proton pump, complementing chlorophyll-based photosynthesis."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "light",
            "predicate": "activates",
            "object": "rhodopsin_photocycle",
            "description": "Visible light activates the microbial rhodopsin photocycle across taxa.",
            "evidence": [
              {
                "reference": "DOI:10.1093/ismejo/wrae175",
                "notes": "\"All rhodopsins are activated by visible light and return to their original state through a photocycle\"; broad rhodopsin mechanism, not limited to one taxon."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "microbial_rhodopsin",
            "predicate": "enables",
            "object": "rhodopsin_photocycle",
            "description": "During the photocycle, microbial rhodopsins exhibit ion-transport function.",
            "evidence": [
              {
                "reference": "DOI:10.1093/ismejo/wrae175",
                "notes": "\"During the photocycle, they exhibit their cognate protein functions such as ion transport\"; general mechanistic edge for rhodopsin phototrophy."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "proton_motive_force",
            "predicate": "drives",
            "object": "atp_synthesis",
            "description": "The proton gradient drives ATP synthesis, conserving light-derived energy.",
            "evidence": [
              {
                "reference": "DOI:10.1128/spectrum.02177-23",
                "notes": "\"creating a proton gradient to drive the synthesis of ATP\"; direct support for rhodopsin-based energy conservation."
              }
            ]
          },
          {
            "subject": "photosystem_ii",
            "predicate": "supplies electrons to",
            "object": "photosynthetic_electron_transport",
            "description": "PSII water oxidation supplies electrons to the photosynthetic electron transport chain.",
            "evidence": [
              {
                "reference": "DOI:10.1111/1751-7915.14519",
                "notes": "\"electrons from the photo-oxidation of water in PSII are transferred through plastoquinone to cytochrome b6f\"; canonical oxygenic phototrophy edge."
              }
            ]
          },
          {
            "subject": "photosynthetic_electron_transport",
            "predicate": "has output",
            "object": "nadph",
            "description": "Electron flow through cytochrome b6f and PSI reduces ferredoxin/NADP+ to NADPH.",
            "evidence": [
              {
                "reference": "DOI:10.1111/1751-7915.14519",
                "notes": "\"These electrons are eventually transferred to ferredoxin and NADP+ to form NADPH\"; canonical oxygenic phototrophy edge."
              }
            ],
            "predicate_id": "RO:0002234"
          },
          {
            "subject": "photosynthetic_electron_transport",
            "predicate": "has output",
            "object": "atp",
            "description": "Photosynthetic electron transfer establishes a proton gradient that produces ATP.",
            "evidence": [
              {
                "reference": "DOI:10.1111/1751-7915.14519",
                "notes": "\"NADPH and ATP are produced from a proton gradient\"; canonical oxygenic phototrophy edge."
              }
            ],
            "predicate_id": "RO:0002234"
          },
          {
            "subject": "high_light",
            "predicate": "damages",
            "object": "photosystem_ii",
            "description": "High light intensity and resulting free radicals damage PSII (photoinhibition).",
            "evidence": [
              {
                "reference": "DOI:10.1111/1751-7915.14519",
                "notes": "\"High-energy photons and the generation of free radicals damage PSII\"; strong environmental inhibitor edge."
              }
            ]
          },
          {
            "subject": "photosystem_ii",
            "predicate": "contributes to",
            "object": "phototrophy_trait",
            "description": "Photosystem II contributes the light-sensing and reaction-center machinery of the graph's oxygenic phototrophy branch.",
            "evidence": [
              {
                "reference": "DOI:10.1111/1751-7915.14519",
                "snippet": "Both photosystems bind chlorophylls to sense light, use chlorophylls and other pigments to transfer light to a photosynthetic reaction centre",
                "notes": "Verified against the public PMC full text; the description keeps this connector scoped to oxygenic phototrophy."
              }
            ],
            "predicate_id": "RO:0002326"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-31T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Minted intermediate axis class (phototrophy) to parent the photosynthesis and proteorhodopsin-phototrophy traits, replacing their direct attachment to METPO:1000060 (metabolism).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-10T14:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (phototrophy / light \u2192 PMF) with PATO/METPO node groundings and RO/biolink predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 7 evidence-backed generic edges (8 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:12Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 4 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d72, RO:0002213\u00d71, RO:0002327\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:18Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:16474\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:33Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0006754\u00d71, GO:0009767\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:23:54Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0009523\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 2 causal edge(s) off microbe-domain METPO predicates (2 to has output), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-07T05:00:00Z",
        "curator": "claude",
        "action": "REGROUND_CAUSAL_EDGE",
        "changes": "Re-grounded the edge from enables/RO:0002327 to RO:0002326 (contributes to), issue 334. biolink declares enables range 'biological process or activity' and the object is a STATE, which does not satisfy it. Unlike the tolerance/capacity nodes in this same pass, this object is a genuine state rather than a mis-typed disposition - a gradient, a community composition, an internal environment - so retyping it to TRAIT would be wrong. contributes to fits because the subject genuinely contributes to the OCCURRENCE OR GENERATION of the object, which is biolink's definition; that is the same test the motive-force edges FAILED in issue 341, where the subject powers a machine it does not generate. RO:0002326 declares no rdfs:domain or rdfs:range.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-16T02:00:00Z",
        "curator": "claude",
        "action": "NORMALISE_NODE_TYPE",
        "changes": "Under the PATHWAY-vs-BIOLOGICAL_PROCESS rule, one node_id means one thing corpus-wide (issue 356): photosynthetic_electron_transport is typed PATHWAY. PATHWAY is a named, conventionally enumerable multi-step route; BIOLOGICAL_PROCESS is everything else. A named route in every record that carries it, though NOT THE SAME ROUTE, which is why no single step list belongs in this rationale. metabolism/phototrophy.yaml enumerates the oxygenic form ('Electron flow from water through PSII, cytochrome b6f and PSI'); photoheterotrophic.yaml and photoorganoheterotrophic.yaml cover ANOXYGENIC phototrophy -- one reaction centre, cyclic flow, no water oxidation -- and say the neutral thing on purpose. Quoting the oxygenic steps at them would assert biology they specifically do not claim (#400 review). Both forms are named routes whose steps a curator could list, which is the test. Was 5 PATHWAY to 1 before this tranche.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-24T00:00:00Z",
        "curator": "codex",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Added a strain-matched Synechocystis PsbA2/D1 example, converted both existing canonical citations to DOI, retained microbial rhodopsin as reviewed label-only, and documented the parent graph's independent mechanism branches.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T08:20:00Z",
        "curator": "codex",
        "action": "CONNECT_CAUSAL_GRAPH_COMPONENTS",
        "changes": "Resolved issue #183 graph fragmentation (2 components to 1) using 1 public-source, verbatim-snippet-backed connector(s). No paid research service was called.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-22T01:35:00Z",
        "curator": "claude",
        "action": "REFRESH_UNIPROT_ENTRY_VERSION",
        "changes": "Refreshed UniProtKB entry_version against live UniProt REST on 2026-10-22: UniProtKB:P16033 (186 -> 187 on photosystem_ii).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:2000202",
    "label": "produces",
    "definition": "An OBJECT_PROPERTY relating an organism to a chemical that the organism produces and exports or accumulates as a metabolic product.",
    "definition_source": "DOI:10.1146/annurev.micro.55.1.485",
    "trait_category": "METABOLISM",
    "term_kind": "OBJECT_PROPERTY",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:2000001"
    ],
    "domain": "https://w3id.org/metpo/1000525",
    "range_": "http://purl.obolibrary.org/obo/CHEBI_24431",
    "xrefs": [
      "RO:0003000"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev.micro.55.1.485",
        "snippet": "production",
        "notes": "Microbial-physiology reference supports 'produces' as a canonical predicate composed with a CHEBI-class chemical object at assertion time."
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.983403+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (OBJECT_PROPERTY)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic biochemical conversion or activity relation carrier; later replacement should use more specific trait records that combine the relation with the substrate, product, enzyme or activity target, assay context, growth condition, or other entity.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-16T08:50:00-07:00",
        "curator": "claude",
        "action": "UNDEPRECATED_AS_COMPOSITION_PRIMITIVE",
        "changes": "Restored from DEPRECATED to REVIEWED under the predicate+class composition pattern (intended use: <organism> + this predicate + CHEBI chemical class). Added DOI/PMID-backed definition, evidence, and explicit domain/range slots.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-17T10:00:00-07:00",
        "curator": "claude",
        "action": "ADDED_EXTERNAL_PREDICATE_XREF",
        "changes": "Added xrefs ['RO:0003000'] to record an external equivalence predicate (RO:0003000 'produces'). RO:0003000 'produces' is the equivalent material-entity-to-material-entity production predicate. Source: OLS4 property search.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-17T04:09:44Z",
        "curator": "claude",
        "action": "REMOVE_REDUNDANT_SYNONYM",
        "changes": "Removed 1 synonym(s) whose text duplicated the label (seeder redundancy; no information lost).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000029",
    "label": "propionic acid fermentation",
    "definition": "A fermentation that produces propionate (with acetate and CO2) from sugars or lactate, typically via the Wood-Werkman (methylmalonyl-CoA) pathway. Characteristic of propionibacteria (e.g. Propionibacterium freudenreichii).",
    "definition_source": "DOI:10.3390/molecules31020333",
    "trait_category": "METABOLISM",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1002005"
    ],
    "synonyms": [
      {
        "synonym_text": "propionate fermentation",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.3390/molecules31020333"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.3390/molecules31020333",
        "notes": "Review of classical fermentations describes propionic acid fermentation (acetic acid, propionic acid, CO2) and propionibacteria as its agents, including the Wood-Werkman route."
      },
      {
        "reference": "DOI:10.3389/fmicb.2021.703525",
        "notes": "Review of fermentative energy conservation supports propionate formation as a redox-balancing, energy-conserving fermentation route."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1744",
        "taxon_label": "Propionibacterium freudenreichii",
        "note": "Canonical propionic-acid fermenter (Swiss-cheese eyes and flavour).",
        "reference": "PMID:21620505"
      },
      {
        "taxon_id": "NCBITaxon:1752",
        "taxon_label": "Propionibacterium freudenreichii subsp. shermanii",
        "note": "Source organism for structural and substrate-bound characterization of the methylmalonyl-CoA transcarboxylase 12S component.",
        "reference": "DOI:10.1093/emboj/cdg244"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "propionic_acid_fermentation_propionate",
        "title": "Propionic acid fermentation produces propionate via the Wood-Werkman pathway",
        "description": "Evidence-backed causal sketch linking methylmalonyl-CoA-pathway catabolism of sugars or lactate to propionate, acetate, and CO2.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "Represents the Wood-Werkman reaction sequence and its biotin-dependent transcarboxylation step; the exemplar is explicitly one component of the three-subunit transcarboxylase, not the complete complex.",
        "nodes": [
          {
            "node_id": "propionic_acid_fermentation_trait",
            "label": "propionic acid fermentation",
            "node_type": "TRAIT",
            "grounding": "traitmech:000029",
            "description": "Fermentation producing propionate via the Wood-Werkman pathway."
          },
          {
            "node_id": "fermentation_process",
            "label": "fermentation",
            "node_type": "BIOLOGICAL_PROCESS",
            "grounding": "GO:0006113",
            "description": "ATP-yielding catabolism with organic terminal acceptors."
          },
          {
            "node_id": "propionate",
            "label": "propionate",
            "node_type": "CHEMICAL",
            "description": "Reduced end product characteristic of propionibacteria.",
            "grounding": "CHEBI:17272"
          },
          {
            "node_id": "wood_werkman_cycle",
            "label": "Wood-Werkman cycle",
            "node_type": "PATHWAY",
            "description": "Methylmalonyl-CoA cycle; predominant propionate-forming route in propionibacteria."
          },
          {
            "node_id": "pyruvate",
            "label": "pyruvate",
            "node_type": "CHEMICAL",
            "description": "Central glycolytic intermediate feeding the Wood-Werkman cycle.",
            "grounding": "CHEBI:15361"
          },
          {
            "node_id": "oxaloacetate",
            "label": "oxaloacetate",
            "node_type": "CHEMICAL",
            "description": "Formed by biotin-dependent carboxylation of pyruvate.",
            "grounding": "CHEBI:16452"
          },
          {
            "node_id": "malate",
            "label": "malate",
            "node_type": "CHEMICAL",
            "description": "Reduction product of oxaloacetate in the reductive branch."
          },
          {
            "node_id": "fumarate",
            "label": "fumarate",
            "node_type": "CHEMICAL",
            "description": "Dehydration product of malate in the Wood-Werkman route.",
            "grounding": "CHEBI:29806"
          },
          {
            "node_id": "succinate",
            "label": "succinate",
            "node_type": "CHEMICAL",
            "description": "Reduction product of fumarate en route to propionate."
          },
          {
            "node_id": "succinyl_coa",
            "label": "succinyl-CoA",
            "node_type": "CHEMICAL",
            "description": "Intermediate formed from succinate before rearrangement."
          },
          {
            "node_id": "methylmalonyl_coa",
            "label": "methylmalonyl-CoA",
            "node_type": "CHEMICAL",
            "description": "Intermediate rearranged toward propionyl-CoA."
          },
          {
            "node_id": "propionyl_coa",
            "label": "propionyl-CoA",
            "node_type": "CHEMICAL",
            "description": "Immediate CoA-thioester precursor of propionate.",
            "grounding": "CHEBI:15539"
          },
          {
            "node_id": "mmc_carboxytransferase",
            "label": "methylmalonyl-CoA carboxytransferase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Biotin-dependent transcarboxylase converting pyruvate to oxaloacetate.",
            "grounding": "GO:0047154",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:Q8GBW6",
                "protein_label": "Methylmalonyl-CoA carboxyltransferase 12S subunit",
                "taxon_id": "NCBITaxon:1752",
                "taxon_label": "Propionibacterium freudenreichii subsp. shermanii",
                "entry_status": "REVIEWED",
                "retrieved_on": "2026-10-22",
                "entry_version": 98,
                "sequence_version": 4,
                "role": "Forms the substrate-binding 12S component of the three-subunit transcarboxylase that couples methylmalonyl-CoA decarboxylation to pyruvate carboxylation.",
                "evidence": [
                  {
                    "reference": "DOI:10.1093/emboj/cdg244",
                    "snippet": "TC 12S bound to its MMCoA substrate",
                    "notes": "The primary structural study used the P. shermanii 12S component and resolved methylmalonyl-CoA binding; UniProtKB Q8GBW6 verifies the reviewed component identity and source taxon."
                  }
                ]
              }
            ]
          },
          {
            "node_id": "biotin",
            "label": "biotin",
            "node_type": "CHEMICAL",
            "description": "Cofactor required by the carboxytransferase step."
          },
          {
            "node_id": "acetate",
            "label": "acetate",
            "node_type": "CHEMICAL",
            "description": "Co-product of propionic acid fermentation."
          }
        ],
        "edges": [
          {
            "subject": "propionic_acid_fermentation_trait",
            "predicate": "participates in",
            "object": "fermentation_process",
            "description": "Propionic acid fermentation is a class of fermentation metabolism.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2021.703525",
                "snippet": "fermentation is defined as an anaerobic bacterial redox process of an organic substrate leading to different products",
                "notes": "Energy-conservation review supports propionate formation as a redox-balancing fermentation route."
              }
            ],
            "predicate_id": "biolink:participates_in"
          },
          {
            "subject": "propionic_acid_fermentation_trait",
            "predicate": "produces",
            "object": "propionate",
            "description": "Propionate is the characteristic end product of the pathway.",
            "evidence": [
              {
                "reference": "DOI:10.3390/molecules31020333",
                "snippet": "substrates such as glucose, glycerol or lactic acid are converted into propionic acid",
                "notes": "Classical-fermentation review describes propionic acid fermentation via the Wood-Werkman pathway in propionibacteria."
              }
            ],
            "predicate_id": "METPO:2007800"
          },
          {
            "subject": "propionic_acid_fermentation_trait",
            "predicate": "has major pathway",
            "object": "wood_werkman_cycle",
            "description": "The Wood-Werkman methylmalonyl-CoA cycle is the predominant propionate-forming route.",
            "evidence": [
              {
                "reference": "DOI:10.3390/molecules31020333",
                "snippet": "In Propionibacterium spp., the predominant route is the Wood-Werkman pathway",
                "notes": "Wood-Werkman cycle described as the predominant propionate-forming route in Propionibacterium and Acidipropionibacterium."
              }
            ]
          },
          {
            "subject": "pyruvate",
            "predicate": "causally upstream of",
            "object": "oxaloacetate",
            "description": "Pyruvate is carboxylated to oxaloacetate in a biotin-dependent reaction.",
            "evidence": [
              {
                "reference": "DOI:10.3390/molecules31020333",
                "snippet": "pyruvate is converted to oxaloacetate in a biotin-dependent carboxyl transfer reaction",
                "notes": "Pyruvate is carboxylated to oxaloacetate by methylmalonyl-CoA carboxytransferase in a biotin-dependent reaction."
              }
            ]
          },
          {
            "subject": "biotin",
            "predicate": "cofactor for",
            "object": "mmc_carboxytransferase",
            "description": "The transcarboxylation step is biotin-dependent.",
            "evidence": [
              {
                "reference": "DOI:10.3390/molecules31020333",
                "snippet": "biotin-dependent carboxyl transfer reaction catalyzed by methylmalonyl-CoA carboxytransferase",
                "notes": "The transcarboxylation converting pyruvate to oxaloacetate is explicitly described as biotin-dependent."
              }
            ]
          },
          {
            "subject": "oxaloacetate",
            "predicate": "causally upstream of",
            "object": "malate",
            "description": "Oxaloacetate is reduced to malate in the reductive branch.",
            "evidence": [
              {
                "reference": "DOI:10.3390/molecules31020333",
                "snippet": "Oxaloacetate is then reduced to malate",
                "notes": "Oxaloacetate is reduced to malate in the reductive branch leading toward succinate."
              }
            ]
          },
          {
            "subject": "malate",
            "predicate": "causally upstream of",
            "object": "fumarate",
            "description": "Malate is dehydrated to fumarate.",
            "evidence": [
              {
                "reference": "DOI:10.3390/molecules31020333",
                "snippet": "reduced to malate, dehydrated to fumarate",
                "notes": "Malate is dehydrated to fumarate in the Wood-Werkman route."
              }
            ]
          },
          {
            "subject": "fumarate",
            "predicate": "causally upstream of",
            "object": "succinate",
            "description": "Fumarate is reduced to succinate.",
            "evidence": [
              {
                "reference": "DOI:10.3390/molecules31020333",
                "snippet": "dehydrated to fumarate and reduced to succinate",
                "notes": "Fumarate is reduced to succinate en route to propionate formation."
              }
            ]
          },
          {
            "subject": "succinyl_coa",
            "predicate": "causally upstream of",
            "object": "methylmalonyl_coa",
            "description": "The pathway proceeds through succinyl-CoA and methylmalonyl-CoA intermediates.",
            "evidence": [
              {
                "reference": "DOI:10.3390/molecules31020333",
                "snippet": "Succinate is converted to succinyl-CoA by succinyl-CoA synthetase and rearranged via a vitamin B12-dependent methylmalonyl-CoA mutase to methylmalonyl-CoA",
                "notes": "The pathway proceeds through succinyl-CoA and methylmalonyl-CoA intermediates during propionate formation."
              }
            ]
          },
          {
            "subject": "propionyl_coa",
            "predicate": "causally upstream of",
            "object": "propionate",
            "description": "Propionyl-CoA is converted to propionate by a CoA-transferase.",
            "evidence": [
              {
                "reference": "DOI:10.3390/molecules31020333",
                "snippet": "propionyl-CoA is converted to propionic acid with the release of CoA by a CoA-transferase",
                "notes": "Propionyl-CoA is finally converted to propionic acid or propionate by a CoA-transferase."
              }
            ]
          },
          {
            "subject": "propionic_acid_fermentation_trait",
            "predicate": "has byproduct",
            "object": "acetate",
            "description": "The fermentation produces propionate with acetate as a co-product.",
            "evidence": [
              {
                "reference": "DOI:10.3390/molecules31020333",
                "snippet": "accompanied by acetic acid and CO2 formation",
                "notes": "The fermentation is defined as producing propionic acid with acetate as a co-product."
              }
            ]
          },
          {
            "subject": "pyruvate",
            "predicate": "contributes to",
            "object": "wood_werkman_cycle",
            "description": "Pyruvate carboxylation initiates the Wood-Werkman cycle.",
            "evidence": [
              {
                "reference": "DOI:10.3390/molecules31020333",
                "snippet": "It starts from pyruvate, generated via glycolysis, which can follow two alternative routes: Carboxylation to oxaloacetate: this initiates the Wood\u2013Werkman cycle and leads to propionic acid",
                "notes": "Verified against the public PMC full text."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "succinate",
            "predicate": "causally upstream of",
            "object": "succinyl_coa",
            "description": "The propionate pathway converts succinate through succinyl-CoA.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s12864-016-3367-x",
                "snippet": "Succinate is then converted into succinyl-CoA, methyl malonyl CoA, propanoyl CoA and propionate by specific enzymes",
                "notes": "Verified against the open article full text."
              }
            ]
          },
          {
            "subject": "mmc_carboxytransferase",
            "predicate": "catalyzes conversion of",
            "object": "pyruvate",
            "description": "Methylmalonyl-CoA carboxytransferase catalyzes the pyruvate-to-oxaloacetate entry reaction.",
            "evidence": [
              {
                "reference": "DOI:10.3390/molecules31020333",
                "snippet": "pyruvate is converted to oxaloacetate in a biotin-dependent carboxyl transfer reaction catalyzed by methylmalonyl-CoA carboxytransferase",
                "notes": "Verified against the public PMC full text."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-08-23T09:02:00Z",
        "curator": "codex",
        "action": "CURATE_PROTEIN_TAXON_EXAMPLE",
        "changes": "Reviewed the graph as mechanistic and added DOI-backed, taxon-paired UniProtKB Q8GBW6 as the transcarboxylase 12S component exemplar.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-30T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate METABOLISM trait (propionic acid fermentation); product-specific sub-variant of the existing Fermentation class (METPO:1002005).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-10T14:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (propionic acid fermentation) with GO node grounding and METPO/biolink predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-14T06:55:38Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:17272\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 9 evidence-backed generic edges (12 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:18Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:29806\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:33Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 3 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:15361\u00d71, CHEBI:16452\u00d71, CHEBI:15539\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-26T07:15:19Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A3S9JES8\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:21:11Z",
        "curator": "claude",
        "action": "RETRACT_DEAD_UNIPROT_GROUNDINGS",
        "changes": "Retracted 1 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:23:54Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0047154\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T02:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES_PART2",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates onto their causal-graph counterparts (1 to produces), issue 301 part 2. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Each replacement is a 1:1 mirror of its source predicate that changes only the domain, so the claim each edge makes is unchanged and directions are unchanged. The replacements are proposed in proposals/metpo_traitmech_v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T09:00:00Z",
        "curator": "codex",
        "action": "CONNECT_CAUSAL_GRAPH_COMPONENTS",
        "changes": "Resolved issue #183 graph fragmentation (4 components to 1) using 3 public-source, verbatim-snippet-backed connector(s). No paid research service was called.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-22T01:35:00Z",
        "curator": "claude",
        "action": "REFRESH_UNIPROT_ENTRY_VERSION",
        "changes": "Refreshed UniProtKB entry_version against live UniProt REST on 2026-10-22: UniProtKB:Q8GBW6 (97 -> 98 on mmc_carboxytransferase).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000116",
    "label": "proteolysis",
    "definition": "A biopolymer-degradation metabolism in which an organism secretes proteases to hydrolyze extracellular proteins and peptides into amino acids and short peptides for nutrition.",
    "definition_source": "DOI:10.1128/mmbr.62.3.597-635.1998",
    "trait_category": "METABOLISM",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "traitmech:000110"
    ],
    "synonyms": [
      {
        "synonym_text": "proteolytic",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1128/mmbr.62.3.597-635.1998"
      },
      {
        "synonym_text": "protein degradation",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1128/mmbr.62.3.597-635.1998"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1128/mmbr.62.3.597-635.1998",
        "notes": "Rao et al. review microbial proteases, noting that secreted (extracellular) proteases play a major nutritional role through their depolymerizing activity."
      },
      {
        "reference": "DOI:10.1093/femsre/fuab046",
        "notes": "Review of Bacillus proteases covers extracellular protease activities and their functions."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1423",
        "taxon_label": "Bacillus subtilis",
        "note": "Model secretor of extracellular proteases (subtilisin); paradigm for bacterial proteolysis.",
        "reference": "PMID:34410368"
      },
      {
        "taxon_id": "NCBITaxon:224308",
        "taxon_label": "Bacillus subtilis 168",
        "note": "Strain-level AprE model paired to the reviewed subtilisin E protein example.",
        "reference": "DOI:10.1128/jb.158.2.411-418.1984"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "proteolysis_extracellular_protease",
        "title": "Proteolysis hydrolyzes extracellular proteins to amino acids",
        "description": "Evidence-backed causal sketch linking secreted bacterial proteases to extracellular hydrolysis of proteins/peptides into amino acids and short peptides.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "The graph summarizes extracellular protein hydrolysis, peptide uptake, and intracellular hydrolysis. AprE is one experimentally characterized extracellular protease component and is not presented as the complete proteolytic system.",
        "nodes": [
          {
            "node_id": "proteolysis_trait",
            "label": "proteolysis",
            "node_type": "TRAIT",
            "grounding": "traitmech:000116",
            "description": "Secreted-protease hydrolysis of extracellular proteins."
          },
          {
            "node_id": "extracellular_protease",
            "label": "secreted proteases",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Extracellular microbial proteases acting on protein substrates.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Secreted microbial proteases span serine, metallo-, cysteine, and other peptidase families; no single family or activity term denotes the full plural node.",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:P04189",
                "protein_label": "Subtilisin E",
                "gene_symbol": "aprE",
                "taxon_id": "NCBITaxon:224308",
                "taxon_label": "Bacillus subtilis 168",
                "entry_status": "REVIEWED",
                "retrieved_on": "2026-10-22",
                "entry_version": 190,
                "sequence_version": 3,
                "role": "Major extracellular alkaline serine protease AprE, representing one component of the broader secreted-protease node.",
                "evidence": [
                  {
                    "reference": "DOI:10.1128/jb.158.2.411-418.1984",
                    "snippet": "a fivefold increase in serine protease activity was observed",
                    "notes": "The primary cloning study identifies the B. subtilis I168 subtilisin structural gene and its expressed protease activity. UniProtKB P04189 is the reviewed AprE entry from strain 168."
                  }
                ]
              }
            ]
          },
          {
            "node_id": "amino_acids",
            "label": "amino acids / short peptides",
            "node_type": "CHEMICAL",
            "description": "Assimilable nutrients released from protein hydrolysis."
          },
          {
            "node_id": "peptides",
            "label": "peptides / oligopeptides",
            "node_type": "CHEMICAL",
            "description": "Oligopeptides (~4-30 aa) released by extracellular protease cleavage of proteins."
          },
          {
            "node_id": "peptide_transport_systems",
            "label": "peptide transport systems (Opp/DtpT/Dpp)",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Membrane transporters (oligopeptide permease Opp, DtpT, ABC transporter Dpp) importing peptides short enough for uptake.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Opp, DtpT, and Dpp are distinct transporter architectures and the node intentionally combines them as alternative uptake systems."
          },
          {
            "node_id": "intracellular_peptidases",
            "label": "intracellular peptidases",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Cytoplasmic exo-/endo-peptidases that further hydrolyze imported peptides to free amino acids.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "The node denotes an organism-dependent set of intracellular exo- and endopeptidases rather than one protein family or exact activity."
          },
          {
            "node_id": "large_proteins",
            "label": "large extracellular proteins",
            "node_type": "CHEMICAL",
            "description": "Intact extracellular proteins too large for direct uptake by prokaryotic transporters."
          },
          {
            "node_id": "substrate_stoichiometry",
            "label": "substrate source / concentration / C:N stoichiometry",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Environmental substrate characteristics that filter expression of secreted extracellular proteases."
          }
        ],
        "edges": [
          {
            "subject": "extracellular_protease",
            "predicate": "confers",
            "object": "proteolysis_trait",
            "description": "Secreted proteases drive extracellular protein hydrolysis.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mmbr.62.3.597-635.1998",
                "notes": "Rao et al. review microbial proteases and their depolymerizing nutritional role."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "proteolysis_trait",
            "predicate": "produces",
            "object": "amino_acids",
            "description": "Protein hydrolysis releases amino acids and short peptides.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuab046",
                "notes": "Bacillus protease review covers extracellular protease activities."
              }
            ],
            "predicate_id": "METPO:2007800"
          },
          {
            "subject": "proteolysis_trait",
            "predicate": "produces",
            "object": "peptides",
            "description": "Extracellular protein hydrolysis yields oligopeptides (~4-30 aa).",
            "evidence": [
              {
                "reference": "DOI:10.1186/s43014-023-00165-w",
                "notes": "\"protein to oligopeptides\" / \"producing peptides of roughly 4-30 amino acids\"; extracellular proteolytic enzymes produce peptides."
              }
            ],
            "predicate_id": "METPO:2007800"
          },
          {
            "subject": "peptide_transport_systems",
            "predicate": "imports",
            "object": "peptides",
            "description": "Peptide transporters import peptides short enough for uptake.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s43014-023-00165-w",
                "notes": "Peptides \"taken up by dedicated transporters: oligopeptide permease (Opp, an ATP-driven system)\", DtpT and ABC transporter Dpp."
              }
            ],
            "predicate_id": "METPO:2007805"
          },
          {
            "subject": "intracellular_peptidases",
            "predicate": "hydrolyzes",
            "object": "peptides",
            "description": "Intracellular peptidases further hydrolyze imported peptides.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s43014-023-00165-w",
                "notes": "\"Inside the cell, multiple peptidases... further hydrolyze peptides\"."
              }
            ],
            "predicate_id": "METPO:2007808"
          },
          {
            "subject": "intracellular_peptidases",
            "predicate": "produces",
            "object": "amino_acids",
            "description": "Intracellular peptidases produce free amino acids used for growth.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s43014-023-00165-w",
                "notes": "\"further hydrolyze peptides to free amino acids used for growth\"."
              }
            ],
            "predicate_id": "METPO:2007800"
          },
          {
            "subject": "large_proteins",
            "predicate": "necessitates",
            "object": "proteolysis_trait",
            "description": "Proteins too large for direct uptake necessitate extracellular hydrolysis.",
            "evidence": [
              {
                "reference": "DOI:10.1128/spectrum.03036-23",
                "notes": "\"proteins are too large for direct uptake by prokaryotic transporter systems... explaining the need for extracellular cleavage\"."
              }
            ]
          },
          {
            "subject": "substrate_stoichiometry",
            "predicate": "controls expression of",
            "object": "extracellular_protease",
            "description": "Substrate source/concentration/C:N stoichiometry filters expression of secreted proteases.",
            "evidence": [
              {
                "reference": "DOI:10.1128/spectrum.03036-23",
                "notes": "\"the substrate's source, concentration and stoichiometry impose strong filtering on the expression of extracellular enzymes\"."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-06-08T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate METABOLISM trait (proteolysis / extracellular protein degradation); leftover round, sub-variant of biopolymer degradation.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-10T14:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (extracellular protease / amino-acid release) with RO/METPO predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 6 evidence-backed generic edges (5 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:12Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d72, METPO:2000208\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:38Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000013\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 1 causal edge(s) off enables/RO:0002327 with a TRAIT object (1 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T02:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES_PART2",
        "changes": "Re-grounded 5 causal edge(s) off microbe-domain METPO predicates onto their causal-graph counterparts (1 to hydrolyzes, 1 to imports, 3 to produces), issue 301 part 2. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Each replacement is a 1:1 mirror of its source predicate that changes only the domain, so the claim each edge makes is unchanged and directions are unchanged. The replacements are proposed in proposals/metpo_traitmech_v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-24T09:25:00Z",
        "curator": "codex",
        "action": "CURATE_PROTEIN_TAXON_EXAMPLE",
        "changes": "Scoped the extracellular-proteolysis mechanism, added a DOI-backed B. subtilis 168 AprE example, and recorded reviewed label-only dispositions for the broad protease, peptide-transporter, and intracellular-peptidase sets.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-22T01:35:00Z",
        "curator": "claude",
        "action": "REFRESH_UNIPROT_ENTRY_VERSION",
        "changes": "Refreshed UniProtKB entry_version against live UniProt REST on 2026-10-22: UniProtKB:P04189 (189 -> 190 on extracellular_protease).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000036",
    "label": "proteorhodopsin phototrophy",
    "definition": "A light-harvesting metabolism in which a retinal-containing membrane protein (proteorhodopsin) acts as a light-driven proton pump, generating proton motive force without chlorophyll-based reaction centers. Widespread among marine bacterioplankton.",
    "definition_source": "DOI:10.1126/science.289.5486.1902",
    "trait_category": "METABOLISM",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "traitmech:000037"
    ],
    "synonyms": [
      {
        "synonym_text": "rhodopsin-based phototrophy",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1038/35081051"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1126/science.289.5486.1902",
        "notes": "B\u00e9j\u00e0 et al. identified proteorhodopsin, a retinal-binding light-driven proton pump in an uncultivated marine bacterium, as evidence for a new type of phototrophy in the sea."
      },
      {
        "reference": "DOI:10.1038/35081051",
        "notes": "B\u00e9j\u00e0 et al., \"Proteorhodopsin phototrophy in the ocean\", supports proteorhodopsin as a widespread, spectrally tuned light-energy capture system in marine bacteria."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:313590",
        "taxon_label": "Dokdonia sp. MED134",
        "note": "Canonical proteorhodopsin phototroph: light stimulates growth under oligotrophic conditions (retinal-inhibition causally proven). Ca. Pelagibacter ubique uses PR for starvation maintenance.",
        "reference": "PMID:17215843"
      },
      {
        "taxon_id": "NCBITaxon:133804",
        "taxon_label": "gamma proteobacterium EBAC31A08",
        "note": "Source organism for the first functionally characterized green-light-absorbing proteorhodopsin sequence.",
        "reference": "DOI:10.1126/science.289.5486.1902"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "proteorhodopsin_light_driven_proton_pump",
        "title": "Proteorhodopsin pumps protons under illumination, generating PMF",
        "description": "Evidence-backed causal sketch linking retinal-based proteorhodopsin light-driven proton pumping to proton motive force without chlorophyll-based reaction centers.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "Represents the directly demonstrated retinal-dependent light-driven proton pump and downstream proton-motive-force branch; the exemplar is the original EBAC31A08 proteorhodopsin.",
        "nodes": [
          {
            "node_id": "proteorhodopsin_trait",
            "label": "proteorhodopsin phototrophy",
            "node_type": "TRAIT",
            "grounding": "traitmech:000036",
            "description": "Retinal-based light-driven proton-pumping phototrophy."
          },
          {
            "node_id": "proteorhodopsin",
            "label": "proteorhodopsin",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Retinal-binding light-driven proton pump.",
            "grounding": "InterPro:IPR017402",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:Q9F7P4",
                "protein_label": "Green-light absorbing proteorhodopsin",
                "taxon_id": "NCBITaxon:133804",
                "taxon_label": "gamma proteobacterium EBAC31A08",
                "entry_status": "REVIEWED",
                "retrieved_on": "2026-10-22",
                "entry_version": 98,
                "sequence_version": 1,
                "role": "Retinal-binding light-driven proton pump that establishes the core energy-transduction mechanism represented in this graph.",
                "evidence": [
                  {
                    "reference": "DOI:10.1126/science.289.5486.1902",
                    "snippet": "primarily as a light-driven proton pump",
                    "notes": "The discovery study functionally characterized proteorhodopsin from environmental clone EBAC31A08; UniProtKB Q9F7P4 verifies the reviewed protein and source taxon."
                  }
                ]
              }
            ]
          },
          {
            "node_id": "proton_motive_force",
            "label": "proton motive force",
            "node_type": "STATE",
            "grounding": "METPO:1007500",
            "description": "Transmembrane proton gradient generated by light-driven pumping."
          },
          {
            "node_id": "proton_pumping",
            "label": "light-driven proton pumping",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Proteorhodopsin-mediated transmembrane proton transport driven by light."
          },
          {
            "node_id": "atp_production",
            "label": "ATP production",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "ATP biosynthesis driven by PMF generated by proteorhodopsin proton pumping."
          },
          {
            "node_id": "nadph",
            "label": "NAD(P)H",
            "node_type": "CHEMICAL",
            "description": "Reducing equivalents for anabolic metabolism, not generated by proteorhodopsin.",
            "grounding": "CHEBI:13392"
          },
          {
            "node_id": "all_trans_retinal",
            "label": "all-trans retinal",
            "node_type": "CHEMICAL",
            "description": "Chromophore cofactor that forms a Schiff base with a central lysine in proteorhodopsin."
          },
          {
            "node_id": "beta_carotene",
            "label": "beta-carotene",
            "node_type": "CHEMICAL",
            "description": "Carotenoid precursor cleaved by dioxygenase to yield retinal.",
            "grounding": "CHEBI:17579"
          }
        ],
        "edges": [
          {
            "subject": "proteorhodopsin",
            "predicate": "confers",
            "object": "proteorhodopsin_trait",
            "description": "The retinal-binding pump realizes proteorhodopsin phototrophy.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.289.5486.1902",
                "snippet": "bound retinal to form an active, light-driven proton pump",
                "notes": "B\u00e9j\u00e0 et al. identified proteorhodopsin as a retinal-binding light-driven proton pump."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "proteorhodopsin_trait",
            "predicate": "contributes to",
            "object": "proton_motive_force",
            "description": "Light-driven proton pumping by proteorhodopsin generates PMF.",
            "evidence": [
              {
                "reference": "DOI:10.1073/pnas.0611035104",
                "snippet": "Illumination of these cells with light coinciding with PR's absorption spectrum creates a proton motive force (pmf)",
                "notes": "A primary physiological study directly measured light-dependent PMF generation in proteorhodopsin-expressing cells."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "proton_pumping",
            "predicate": "generates",
            "object": "proton_motive_force",
            "description": "Light-driven proton pumping by proteorhodopsin drives PMF generation.",
            "evidence": [
              {
                "reference": "DOI:10.1073/pnas.0611035104",
                "snippet": "Illumination of these cells with light coinciding with PR's absorption spectrum creates a proton motive force (pmf)",
                "notes": "The measured light-dependent PMF is the direct output of the represented proton-pumping process."
              }
            ],
            "predicate_id": "biolink:produces"
          },
          {
            "subject": "proton_motive_force",
            "predicate": "enables",
            "object": "atp_production",
            "description": "PR-mediated proton transport generates a membrane potential sufficient for ATP production.",
            "evidence": [
              {
                "reference": "DOI:10.1073/pnas.0611035104",
                "snippet": "Sinks include rotation of the flagellar motor and ATP synthesis.",
                "notes": "The primary study's PMF model identifies ATP synthesis as a sink for the proteorhodopsin-generated motive force."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "proteorhodopsin_trait",
            "predicate": "does not produce",
            "object": "nadph",
            "description": "Proteorhodopsin phototrophy cannot generate NAD(P)H for anabolic metabolism; ATP-only energy module.",
            "evidence": [
              {
                "reference": "DOI:10.4014/jmb.2410.10034",
                "snippet": "the PR function of strain IMCC1322, which supplies only ATP.",
                "notes": "Oh 2024: \"PR can never be harnessed to generate NAD(P)H for anabolic metabolism\"."
              }
            ],
            "predicate_id": "METPO:2007801"
          },
          {
            "subject": "all_trans_retinal",
            "predicate": "required for",
            "object": "proteorhodopsin",
            "description": "Functional proteorhodopsin requires all-trans retinal bound via a Schiff base to a central lysine.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-024-50960-3",
                "snippet": "all-trans retinal needs to be incorporated by forming a Schiff base with a central lysine in the chromophore binding pocket.",
                "notes": "Hirschi 2024: \"Functional proteorhodopsin requires insertion of all-trans retinal by formation of a Schiff base with a central lysine\"."
              }
            ]
          },
          {
            "subject": "beta_carotene",
            "predicate": "cleaved to produce",
            "object": "all_trans_retinal",
            "description": "Beta-carotene is cleaved by dioxygenase into retinal, an essential element of functional PR.",
            "evidence": [
              {
                "reference": "DOI:10.1128/MMBR.69.1.51-78.2005",
                "snippet": "converts \u03b2,\u03b2-carotene into retinal",
                "notes": "Jing 2022: \"beta-carotene can be cleaved by dioxygenase into retinal, which is an important element in functional PR\"."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-08-23T09:04:00Z",
        "curator": "codex",
        "action": "CURATE_PROTEIN_TAXON_EXAMPLE",
        "changes": "Reviewed the graph as mechanistic and added DOI-backed, taxon-paired UniProtKB Q9F7P4 as the EBAC31A08 proteorhodopsin exemplar.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-30T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate METABOLISM trait (proteorhodopsin phototrophy) from literature research to fill the light-driven-energy gap.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-10T14:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (proteorhodopsin light-driven proton pump) with METPO node grounding and RO predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-14T06:38:15Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A1D7QWW9\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 5 evidence-backed generic edges (5 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:12Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:produces\u00d71, RO:0002327\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:33Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:13392\u00d71, CHEBI:17579\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:38Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000222\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 1 causal edge(s) off enables/RO:0002327 with a TRAIT object (1 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T02:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES_PART2",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates onto their causal-graph counterparts (1 to does not produce), issue 301 part 2. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Each replacement is a 1:1 mirror of its source predicate that changes only the domain, so the claim each edge makes is unchanged and directions are unchanged. The replacements are proposed in proposals/metpo_traitmech_v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-07T05:00:00Z",
        "curator": "claude",
        "action": "REGROUND_CAUSAL_EDGE",
        "changes": "Re-grounded the edge from enables/RO:0002327 to RO:0002326 (contributes to), issue 334. biolink declares enables range 'biological process or activity' and the object is a STATE, which does not satisfy it. Unlike the tolerance/capacity nodes in this same pass, this object is a genuine state rather than a mis-typed disposition - a gradient, a community composition, an internal environment - so retyping it to TRAIT would be wrong. contributes to fits because the subject genuinely contributes to the OCCURRENCE OR GENERATION of the object, which is biolink's definition; that is the same test the motive-force edges FAILED in issue 341, where the subject powers a machine it does not generate. RO:0002326 declares no rdfs:domain or rdfs:range.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-22T04:26:15Z",
        "curator": "codex",
        "action": "REVIEW_UNIPROT_INSTANCE_GROUNDINGS",
        "changes": "Reviewed 1 organism-specific UniProtKB grounding(s): replaced 1 with taxon-agnostic GO/InterPro terms and retracted 0 to label-only where no exact semantic term was supported (docs/GROUNDING_POLICY.md).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-30T19:21:37Z",
        "curator": "codex",
        "action": "REVIEW_EVIDENCE_REFERENCE_CHURN",
        "changes": "Offline review for issue 520 retained 4 evidence-reference replacement(s) that PR 511 made on surviving causal edges outside its stated protein-taxon scope. The pre-tranche evidence entries had references but no snippets; the retained entries supply edge-specific snippets and explanatory notes. Reverting would discard that claim-level provenance, so the scope defect is resolved by documenting the decision instead. This audit changed no causal claim or evidence field. Reviewed replacements: DOI:10.1007/s12275-024-00125-0 -> DOI:10.1073/pnas.0611035104 (1 edge); DOI:10.1038/35081051 -> DOI:10.1073/pnas.0611035104 (1 edge); DOI:10.34133/2022/9782712 -> DOI:10.1128/MMBR.69.1.51-78.2005 (1 edge); DOI:10.4014/jmb.2410.10034 -> DOI:10.1073/pnas.0611035104 (1 edge).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-22T01:35:00Z",
        "curator": "claude",
        "action": "REFRESH_UNIPROT_ENTRY_VERSION",
        "changes": "Refreshed UniProtKB entry_version against live UniProt REST on 2026-10-22: UniProtKB:Q9F7P4 (97 -> 98 on proteorhodopsin).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:2000017",
    "label": "reduces",
    "definition": "An OBJECT_PROPERTY relating an organism to a chemical substrate that the organism reduces (adds electrons or hydrogens to).",
    "definition_source": "DOI:10.1146/annurev.micro.55.1.485",
    "trait_category": "METABOLISM",
    "term_kind": "OBJECT_PROPERTY",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:2000001"
    ],
    "synonyms": [
      {
        "synonym_text": "reduction",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "domain": "https://w3id.org/metpo/1000525",
    "range_": "http://purl.obolibrary.org/obo/CHEBI_24431",
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev.micro.55.1.485",
        "snippet": "reduction",
        "notes": "Microbial-physiology reference supports 'reduces' as a canonical predicate composed with a CHEBI-class chemical object at assertion time."
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.957753+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (OBJECT_PROPERTY)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic biochemical conversion or activity relation carrier; later replacement should use more specific trait records that combine the relation with the substrate, product, enzyme or activity target, assay context, growth condition, or other entity.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-16T08:50:00-07:00",
        "curator": "claude",
        "action": "UNDEPRECATED_AS_COMPOSITION_PRIMITIVE",
        "changes": "Restored from DEPRECATED to REVIEWED under the predicate+class composition pattern (intended use: <organism> + this predicate + CHEBI chemical class). Added DOI/PMID-backed definition, evidence, and explicit domain/range slots.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000021",
    "label": "reductive tricarboxylic acid cycle",
    "definition": "An autotrophic carbon-fixation pathway (reductive citric acid / Arnon-Buchanan cycle) that runs the tricarboxylic acid cycle in reverse to fix CO2. It operates in anaerobic and microaerophilic bacteria such as green sulfur bacteria (Chlorobium) and Aquificales.",
    "definition_source": "DOI:10.1128/AEM.02473-10",
    "trait_category": "METABOLISM",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "traitmech:000019"
    ],
    "synonyms": [
      {
        "synonym_text": "reductive citric acid cycle",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1128/AEM.02473-10"
      },
      {
        "synonym_text": "rTCA cycle",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1128/AEM.02473-10"
      },
      {
        "synonym_text": "Arnon-Buchanan cycle",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1146/annurev-marine-120709-142712"
      },
      {
        "synonym_text": "reductive carboxylate cycle",
        "synonym_type": "EXACT_SYNONYM",
        "source": "http://purl.obolibrary.org/obo/go/releases/2026-07-26/go-basic.obo"
      },
      {
        "synonym_text": "reductive carboxylic acid cycle",
        "synonym_type": "EXACT_SYNONYM",
        "source": "http://purl.obolibrary.org/obo/go/releases/2026-07-26/go-basic.obo"
      },
      {
        "synonym_text": "reductive citric acid pathway",
        "synonym_type": "EXACT_SYNONYM",
        "source": "http://purl.obolibrary.org/obo/go/releases/2026-07-26/go-basic.obo"
      },
      {
        "synonym_text": "reductive Kreb's cycle",
        "synonym_type": "EXACT_SYNONYM",
        "source": "http://purl.obolibrary.org/obo/go/releases/2026-07-26/go-basic.obo"
      },
      {
        "synonym_text": "reductive TCA cycle",
        "synonym_type": "EXACT_SYNONYM",
        "source": "http://purl.obolibrary.org/obo/go/releases/2026-07-26/go-basic.obo"
      }
    ],
    "xrefs": [
      "GO:0019643"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1128/AEM.02473-10",
        "notes": "Berg review describes the reductive citric acid cycle as functional in anaerobic/microaerophilic autotrophs."
      },
      {
        "reference": "DOI:10.1146/annurev-marine-120709-142712",
        "notes": "H\u00fcgler & Sievert document the rTCA cycle in chemolithoautotrophs and green sulfur bacteria in marine systems."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1097",
        "taxon_label": "Chlorobaculum tepidum",
        "note": "Green sulfur bacterium fixing CO2 via the reductive TCA cycle (rTCA first shown in Chlorobia).",
        "reference": "DOI:10.1128/JB.00523-06"
      },
      {
        "taxon_id": "NCBITaxon:194439",
        "taxon_label": "Chlorobaculum tepidum TLS",
        "note": "Strain-level rTCA model paired to both experimentally reconstituted AclAB protein components.",
        "reference": "DOI:10.1128/JB.00523-06"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "rtca_reverse_tricarboxylic_acid_co2_fixation",
        "title": "Reductive TCA cycle runs the TCA cycle in reverse to fix CO2",
        "description": "Evidence-backed causal sketch linking reverse TCA cycle operation in anaerobic/microaerophilic autotrophs to CO2 fixation.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "The graph includes alternative citrate-cleavage routes and reductive 2-oxoacid oxidoreductases. The C. tepidum TLS examples explicitly represent both components of the AclAB route and do not stand for the alternative CCS/CCL system.",
        "nodes": [
          {
            "node_id": "rtca_trait",
            "label": "reductive tricarboxylic acid cycle",
            "node_type": "TRAIT",
            "grounding": "traitmech:000021",
            "description": "Autotrophic carbon-fixation pathway running TCA in reverse."
          },
          {
            "node_id": "carbon_dioxide",
            "label": "carbon dioxide",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:16526",
            "description": "Inorganic carbon substrate fixed by the cycle."
          },
          {
            "node_id": "citrate",
            "label": "citrate",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:16947",
            "description": "TCA-cycle intermediate that the reductive cycle generates from CO2."
          },
          {
            "node_id": "atp_citrate_lyase",
            "label": "ATP citrate lyase (aclAB)",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Enzyme (EC 2.3.3.8) cleaving citrate into oxaloacetate and acetyl-CoA in rTCA.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "The node denotes the complete two-subunit prokaryotic AclAB enzyme; verified family terms describe individual subunits rather than this assembled catalytic complex.",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:Q8KDG1",
                "protein_label": "Citrate lyase, subunit1",
                "taxon_id": "NCBITaxon:194439",
                "taxon_label": "Chlorobaculum tepidum TLS",
                "entry_status": "UNREVIEWED",
                "proteome_id": "UP000001007",
                "retrieved_on": "2026-10-22",
                "entry_version": 118,
                "sequence_version": 1,
                "role": "Subunit 1 component of the C. tepidum ATP citrate lyase; this accession is not presented as the complete AclAB enzyme.",
                "evidence": [
                  {
                    "reference": "DOI:10.1128/JB.00523-06",
                    "snippet": "significant ACL activity required both CLS and CLL",
                    "notes": "The primary reconstitution study shows that both C. tepidum subunits are required for activity. UniProtKB Q8KDG1 is the exact subunit 1 entry in reference proteome UP000001007."
                  }
                ]
              },
              {
                "uniprot_id": "UniProtKB:Q8KDG2",
                "protein_label": "Citrate lyase, subunit2",
                "taxon_id": "NCBITaxon:194439",
                "taxon_label": "Chlorobaculum tepidum TLS",
                "entry_status": "UNREVIEWED",
                "proteome_id": "UP000001007",
                "retrieved_on": "2026-10-22",
                "entry_version": 118,
                "sequence_version": 1,
                "role": "Subunit 2 component of the C. tepidum ATP citrate lyase; this accession is not presented as the complete AclAB enzyme.",
                "evidence": [
                  {
                    "reference": "DOI:10.1128/JB.00523-06",
                    "snippet": "Neither purified recombinant subunit preparation alone possessed any enzymatic activity.",
                    "notes": "The primary reconstitution study shows that neither component alone represents active AclAB. UniProtKB Q8KDG2 is the exact subunit 2 entry in reference proteome UP000001007."
                  }
                ]
              }
            ]
          },
          {
            "node_id": "citryl_coa_synthetase_lyase",
            "label": "citryl-CoA synthetase/lyase route",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Two-enzyme citrate-cleavage system (CCS EC 6.2.1.18 + CCL EC 4.1.3.34) alternative to ACL.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "This combined route node intentionally denotes two distinct enzymes; a single protein-family grounding would incorrectly collapse CCS and CCL."
          },
          {
            "node_id": "pfor",
            "label": "pyruvate:ferredoxin oxidoreductase (PFOR)",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Key rTCA enzyme (EC 1.2.7.1) catalyzing reductive carboxylation of acetyl-CoA to pyruvate.",
            "grounding": "GO:0019164"
          },
          {
            "node_id": "ogor",
            "label": "2-oxoglutarate:ferredoxin oxidoreductase (OGOR/KOR)",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Key rTCA enzyme (EC 1.2.7.3/1.2.7.11) for reductive carboxylation of succinyl-CoA to 2-oxoglutarate.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "The node combines OGOR/KOR enzyme forms and two EC assignments, often realized by multi-subunit complexes; no single verified family term covers that full scope."
          },
          {
            "node_id": "reduced_ferredoxin",
            "label": "reduced ferredoxin",
            "node_type": "CHEMICAL",
            "description": "Low-potential [4Fe-4S] electron carrier serving as electron donor for PFOR and OGOR.",
            "grounding": "CHEBI:17513"
          }
        ],
        "edges": [
          {
            "subject": "carbon_dioxide",
            "predicate": "fixed by",
            "object": "rtca_trait",
            "description": "CO2 is fixed by the reverse TCA cycle in anaerobic autotrophs.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.02473-10",
                "notes": "Berg describes the reductive citric acid cycle as functional in anaerobic/microaerophilic autotrophs."
              }
            ],
            "predicate_id": "METPO:2007404"
          },
          {
            "subject": "rtca_trait",
            "predicate": "produces",
            "object": "citrate",
            "description": "The reverse cycle assembles citrate from CO2.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-marine-120709-142712",
                "notes": "H\u00fcgler & Sievert document the rTCA cycle in chemolithoautotrophs and green sulfur bacteria."
              }
            ],
            "predicate_id": "METPO:2007800"
          },
          {
            "subject": "atp_citrate_lyase",
            "predicate": "confers",
            "object": "rtca_trait",
            "description": "ATP citrate lyase cleaves citrate into oxaloacetate and acetyl-CoA, enabling the rTCA cycle.",
            "evidence": [
              {
                "reference": "DOI:10.1101/2022.10.25.513756",
                "notes": "Citrate cleavage into oxaloacetate and acetyl-CoA can be performed by ATP-citrate lyase (ACL)."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "citryl_coa_synthetase_lyase",
            "predicate": "alternative to",
            "object": "atp_citrate_lyase",
            "description": "The two-enzyme CCS/CCL system is an alternative route to ACL for citrate cleavage in rTCA.",
            "evidence": [
              {
                "reference": "DOI:10.1101/2022.10.25.513756",
                "notes": "Citrate cleavage can be performed by either a two-enzyme system (CCS/CCL) or a single enzyme (ACL)."
              }
            ]
          },
          {
            "subject": "pfor",
            "predicate": "part of",
            "object": "rtca_trait",
            "description": "Pyruvate:ferredoxin oxidoreductase is a canonical key enzyme of the rTCA cycle.",
            "evidence": [
              {
                "reference": "DOI:10.3390/life13030627",
                "notes": "Key enzymes of this pathway are pyruvate:ferredoxin oxidoreductase (PFOR) and 2-oxoglutarate:ferredoxin oxidoreductase (OGOR)."
              }
            ],
            "predicate_id": "biolink:part_of"
          },
          {
            "subject": "ogor",
            "predicate": "part of",
            "object": "rtca_trait",
            "description": "2-oxoglutarate:ferredoxin oxidoreductase is a canonical key enzyme of the rTCA cycle.",
            "evidence": [
              {
                "reference": "DOI:10.3390/life13030627",
                "notes": "Key enzymes of this pathway are PFOR and 2-oxoglutarate:ferredoxin oxidoreductase (OGOR)."
              }
            ],
            "predicate_id": "biolink:part_of"
          },
          {
            "subject": "reduced_ferredoxin",
            "predicate": "electron donor for",
            "object": "pfor",
            "description": "Reduced low-potential ferredoxin provides electrons to PFOR for reductive carboxylation.",
            "evidence": [
              {
                "reference": "DOI:10.3390/life13030627",
                "notes": "PFOR and OGOR require a strong reduction potential; Fd6/Fd7 could be the physiological electron donors."
              }
            ]
          },
          {
            "subject": "reduced_ferredoxin",
            "predicate": "electron donor for",
            "object": "ogor",
            "description": "Reduced low-potential ferredoxin provides electrons to OGOR for reductive carboxylation.",
            "evidence": [
              {
                "reference": "DOI:10.3390/life13030627",
                "notes": "Fd6 and Fd7 can physically interact and exchange electrons with both PFOR and OGOR."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-30T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate METABOLISM trait (reductive TCA carbon-fixation cycle); sub-variant of carbon fixation.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-10T14:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (rTCA reverse TCA / CO2 fixation) with CHEBI node groundings and METPO predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 6 evidence-backed generic edges (5 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:12Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:part_of\u00d72, RO:0002327\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:33Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:17513\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 1 causal edge(s) off enables/RO:0002327 with a TRAIT object (1 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T02:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES_PART2",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates onto their causal-graph counterparts (1 to produces), issue 301 part 2. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Each replacement is a 1:1 mirror of its source predicate that changes only the domain, so the claim each edge makes is unchanged and directions are unchanged. The replacements are proposed in proposals/metpo_traitmech_v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-24T09:40:00Z",
        "curator": "codex",
        "action": "CURATE_PROTEIN_TAXON_EXAMPLE",
        "changes": "Scoped the alternative rTCA routes, added DOI-backed C. tepidum TLS examples for both required AclAB components, grounded PFOR activity, and documented the multi-enzyme and multi-subunit labels that remain reviewed label-only.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T06:15:39Z",
        "curator": "codex",
        "action": "ADD_EXACT_ONTOLOGY_MATCH",
        "changes": "Ontology exact-match review (2026-08-25): approved exact xref(s): GO:0019643; declared exact synonym(s): 'reductive carboxylate cycle', 'reductive carboxylic acid cycle', 'reductive citric acid pathway', \"reductive Kreb's cycle\", 'reductive TCA cycle'. Evidence is predicate-scoped in the versioned ontology snapshots; OAK cross-checked direct data, and OLS4 spot-checked release deltas and disputed hits.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-22T01:35:00Z",
        "curator": "claude",
        "action": "REFRESH_UNIPROT_ENTRY_VERSION",
        "changes": "Refreshed UniProtKB entry_version against live UniProt REST on 2026-10-22: UniProtKB:Q8KDG1 (117 -> 118 on atp_citrate_lyase), UniProtKB:Q8KDG2 (117 -> 118 on atp_citrate_lyase).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:2000018",
    "label": "requires for growth",
    "definition": "An OBJECT_PROPERTY relating an organism to a chemical entity that the organism requires for growth (essential nutrient, cofactor, or growth factor).",
    "definition_source": "PMID:21413255",
    "trait_category": "METABOLISM",
    "term_kind": "OBJECT_PROPERTY",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:2000001"
    ],
    "synonyms": [
      {
        "synonym_text": "required for growth",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "domain": "https://w3id.org/metpo/1000525",
    "range_": "http://purl.obolibrary.org/obo/CHEBI_24431",
    "evidence": [
      {
        "reference": "PMID:21413255",
        "snippet": "growth factor",
        "notes": "Microbial-physiology reference supports 'requires for growth' as a canonical predicate composed with a CHEBI-class chemical object at assertion time."
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.958234+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (OBJECT_PROPERTY)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic metabolism relation carrier; later replacement should use more specific trait records that combine the relation with the chemical, phenotype, quality, compartment, enzyme or activity target, growth context, measurement, or other entity.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-16T08:50:00-07:00",
        "curator": "claude",
        "action": "UNDEPRECATED_AS_COMPOSITION_PRIMITIVE",
        "changes": "Restored from DEPRECATED to REVIEWED under the predicate+class composition pattern (intended use: <organism> + this predicate + CHEBI chemical class). Added DOI/PMID-backed definition, evidence, and explicit domain/range slots.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000800",
    "label": "respiration",
    "definition": "A metabolism that is characterized by the method of performing cellular respiration, distinguished primarily by the specific terminal electron acceptor utilized for producing cellular energy.",
    "definition_source": "DOI:10.1016/j.bbabio.2008.09.008",
    "trait_category": "METABOLISM",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000060"
    ],
    "synonyms": [
      {
        "synonym_text": "pathways",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "created_by": "Anthea Guo",
    "evidence": [
      {
        "reference": "DOI:10.1016/j.bbabio.2008.09.008",
        "snippet": "membrane-bound electron transport chain",
        "notes": "Review supports respiratory redox chains producing ion gradients and ATP."
      },
      {
        "reference": "DOI:10.1128/mmbr.61.4.533-616.1997",
        "snippet": "oxygen as terminal electron acceptor",
        "notes": "Review contrasts aerobic respiration with anaerobic use of alternative acceptors."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:562",
        "taxon_label": "Escherichia coli",
        "note": "aerobic and anaerobic respiration",
        "reference": "PMID:25268772"
      },
      {
        "taxon_id": "NCBITaxon:266",
        "taxon_label": "Paracoccus denitrificans",
        "note": "respiratory model",
        "reference": "PMID:41591903"
      },
      {
        "taxon_id": "NCBITaxon:83333",
        "taxon_label": "Escherichia coli K-12",
        "note": "Strain-level respiratory model paired to the reviewed AtpD beta component of its F-type ATP synthase.",
        "reference": "DOI:10.7554/eLife.21598"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "respiration_electron_acceptor_energy_conservation",
        "title": "Respiration electron acceptor energy conservation",
        "description": "DOI-backed graph linking electron donors, terminal electron acceptors, membrane electron transport, proton motive force, and ATP synthesis.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "This graph combines aerobic and anaerobic respiratory branches. The E. coli K-12 AtpD example supports the shared F-type ATP-synthase energy-conservation module; one beta-subunit accession does not denote the complete complex or every respiratory terminal reductase.",
        "nodes": [
          {
            "node_id": "respiration_trait",
            "label": "respiration",
            "node_type": "TRAIT",
            "grounding": "METPO:1000800",
            "description": "Energy metabolism using electron transport to a terminal electron acceptor."
          },
          {
            "node_id": "electron_donor",
            "label": "electron donor",
            "node_type": "CHEMICAL",
            "description": "Reduced substrate supplying electrons.",
            "grounding": "CHEBI:15022"
          },
          {
            "node_id": "terminal_electron_acceptor",
            "label": "terminal electron acceptor",
            "node_type": "CHEMICAL",
            "description": "Oxidized substrate receiving electrons at the end of a respiratory chain.",
            "grounding": "METPO:1007504"
          },
          {
            "node_id": "molecular_oxygen",
            "label": "molecular oxygen",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:15379",
            "description": "Aerobic terminal electron acceptor."
          },
          {
            "node_id": "nitrate",
            "label": "nitrate",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:17632",
            "description": "Alternative anaerobic terminal electron acceptor."
          },
          {
            "node_id": "membrane_electron_transport_chain",
            "label": "membrane electron transport chain",
            "node_type": "PATHWAY",
            "description": "Membrane redox chain conserving energy from donor-to-acceptor electron flow.",
            "grounding": "GO:0022900"
          },
          {
            "node_id": "proton_motive_force",
            "label": "proton motive force",
            "node_type": "STATE",
            "description": "Electrochemical ion gradient generated across a coupling membrane.",
            "grounding": "METPO:1007500"
          },
          {
            "node_id": "atp_synthase",
            "label": "ATP synthase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Enzyme complex using proton motive force for ATP synthesis.",
            "grounding": "GO:0045259",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:P0ABB4",
                "protein_label": "ATP synthase subunit beta",
                "gene_symbol": "atpD",
                "taxon_id": "NCBITaxon:83333",
                "taxon_label": "Escherichia coli K-12",
                "entry_status": "REVIEWED",
                "retrieved_on": "2026-10-22",
                "entry_version": 156,
                "sequence_version": 2,
                "role": "Beta component of the F1 catalytic head of the E. coli F1Fo ATP synthase; this accession is not presented as the complete rotary complex.",
                "evidence": [
                  {
                    "reference": "DOI:10.7554/eLife.21598",
                    "snippet": "the potential energy of the proton motive force into rotation of the central stalk that drives conformational changes in the F1 catalytic sites",
                    "notes": "The primary cryo-EM study resolves the E. coli F1Fo complex and its beta-containing catalytic head. UniProtKB P0ABB4 verifies the reviewed AtpD beta component and K-12 taxon."
                  }
                ]
              }
            ]
          },
          {
            "node_id": "atp",
            "label": "ATP",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:30616",
            "description": "Energy carrier produced by respiration."
          },
          {
            "node_id": "complex_i",
            "label": "respiratory Complex I (NADH:quinone oxidoreductase)",
            "node_type": "GENE_OR_PROTEIN",
            "description": "NADH dehydrogenase that oxidizes NADH, reduces quinone, and pumps protons (~4 H+/2e-).",
            "grounding": "GO:0030964"
          },
          {
            "node_id": "anoxic_microsites",
            "label": "anoxic microsites",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Localized oxygen-depleted zones that constrain available terminal electron acceptors."
          },
          {
            "node_id": "oxygen_depletion",
            "label": "oxygen depletion",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Decline of O2 below physiological thresholds in a microenvironment."
          },
          {
            "node_id": "anaerobic_respiration",
            "label": "anaerobic respiration",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Respiration using alternative (non-oxygen) terminal electron acceptors.",
            "grounding": "GO:0009061"
          }
        ],
        "edges": [
          {
            "subject": "respiration_trait",
            "predicate": "uses electron flow from",
            "object": "electron_donor",
            "description": "Respiration begins with reduced electron donors.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.bbabio.2008.09.008",
                "snippet": "free energy of a redox reaction",
                "notes": "Supports respiratory energy conservation from redox reactions."
              }
            ]
          },
          {
            "subject": "electron_donor",
            "predicate": "transfers electrons to",
            "object": "terminal_electron_acceptor",
            "description": "Electrons move from donors to terminal acceptors.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.bbabio.2008.09.008",
                "snippet": "electron transfer process",
                "notes": "Supports donor-to-acceptor electron flow in respiratory chains."
              }
            ],
            "predicate_id": "METPO:2007403"
          },
          {
            "subject": "molecular_oxygen",
            "predicate": "example of",
            "object": "terminal_electron_acceptor",
            "description": "Oxygen is the terminal electron acceptor in aerobic respiration.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mmbr.61.4.533-616.1997",
                "snippet": "oxygen as terminal electron acceptor",
                "notes": "Supports oxygen as a respiratory terminal acceptor."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "nitrate",
            "predicate": "example of",
            "object": "terminal_electron_acceptor",
            "description": "Nitrate is a representative anaerobic terminal electron acceptor.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mmbr.61.4.533-616.1997",
                "snippet": "utilization of nitrate",
                "notes": "Supports nitrate use in anaerobic respiration."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "membrane_electron_transport_chain",
            "predicate": "couples electron flow to",
            "object": "proton_motive_force",
            "description": "Respiratory chains conserve redox energy as an ion gradient.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.bbabio.2008.09.008",
                "snippet": "generation of an electrochemical ion gradient",
                "notes": "Supports ion-gradient generation by membrane electron transport."
              }
            ],
            "predicate_id": "METPO:2007602"
          },
          {
            "subject": "proton_motive_force",
            "predicate": "regulates",
            "object": "atp_synthase",
            "description": "Proton motive force powers ATP synthase.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.bbabio.2008.09.008",
                "snippet": "drives ATP synthesis",
                "notes": "Supports ATP synthase as the downstream energy-conservation output."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "atp_synthase",
            "predicate": "produces",
            "object": "atp",
            "description": "ATP synthase produces ATP during respiration.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.bbabio.2008.09.008",
                "snippet": "ATP synthesis",
                "notes": "Supports ATP production from respiratory energy conservation."
              }
            ],
            "predicate_id": "METPO:2007800"
          },
          {
            "subject": "complex_i",
            "predicate": "contributes to",
            "object": "proton_motive_force",
            "description": "Complex I pumps protons during NADH oxidation/quinone reduction, building the proton motive force.",
            "evidence": [
              {
                "reference": "DOI:10.3390/ijms252413421",
                "notes": "Complex I pumps four protons per pair of electrons, contributing to the formation of a proton motive force."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "anoxic_microsites",
            "predicate": "controls",
            "object": "terminal_electron_acceptor",
            "description": "Anoxic microsites control the local availability and ordering of terminal electron acceptors.",
            "evidence": [
              {
                "reference": "DOI:10.1021/acsearthspacechem.3c00032",
                "notes": "Microsites control the local availability and ordering of terminal electron acceptors (O2, NO3-, Fe(III), Mn(IV), SO4 2-)."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "oxygen_depletion",
            "predicate": "enables",
            "object": "anaerobic_respiration",
            "description": "When O2 falls below physiological thresholds, cells shift to alternative acceptors and perform anaerobic respiration.",
            "evidence": [
              {
                "reference": "DOI:10.1021/acsearthspacechem.3c00032",
                "notes": "When O2 falls below physiological thresholds, microorganisms shift to alternative electron acceptors and carry out anaerobic respiration."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "anaerobic_respiration",
            "predicate": "subtype of",
            "object": "respiration_trait",
            "description": "Anaerobic respiration is a form of respiration distinguished by its terminal electron acceptor.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mmbr.61.4.533-616.1997",
                "notes": "Review contrasts aerobic respiration with anaerobic use of alternative acceptors."
              }
            ]
          },
          {
            "subject": "membrane_electron_transport_chain",
            "predicate": "contributes to",
            "object": "respiration_trait",
            "description": "The membrane respiratory chain contributes donor-to-acceptor electron flow to the respiration trait.",
            "evidence": [
              {
                "reference": "DOI:10.3390/ijms252413421",
                "snippet": "Ubiquinol, produced by complex I, passes those reducing equivalents down the respiratory chain to the terminal acceptor\u2014oxygen",
                "notes": "Verified against the public PMC full text; the connector represents the aerobic branch without excluding alternative acceptors."
              }
            ],
            "predicate_id": "RO:0002326"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.910466+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-08T00:00:00-07:00",
        "curator": "codex",
        "action": "ADDED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed causal graph for donor-to-acceptor respiratory electron flow, membrane ion-gradient generation, and ATP synthesis.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:30Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T08:21:49Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (rdfs:subClassOf\u00d72).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T21:30:07Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007403\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:19Z",
        "curator": "claude",
        "action": "RENAME_PREDICATE_LABELS",
        "changes": "Renamed 1 causal-edge predicate label(s) to align with existing groundings: drives \u2192 regulates \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:21Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002211\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:41:04Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (METPO:1007504\u00d71, METPO:1007500\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T05:05:14Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A415TT77\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T08:14:32Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:17499\u00d71, GO:0022900\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-26T02:30:13Z",
        "curator": "claude",
        "action": "RETYPE_CAUSAL_NODES",
        "changes": "Re-typed 1 causal-node node_type field(s) to align with CausalNodeTypeEnum semantics: proton motive force: BIOLOGICAL_PROCESS \u2192 STATE \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-14T07:26:19Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007602\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-15T07:19:08Z",
        "curator": "claude",
        "action": "FIX_NODE_GROUNDING_CURIE",
        "changes": "Overwrote 1 causal-node grounding(s) to corrected CURIEs (phase-2 id-label fix; verified vs OAK).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 4 evidence-backed generic edges (4 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:12Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002326\u00d71, RO:0002211\u00d71, RO:0002327\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:19Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0009061\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:21:11Z",
        "curator": "claude",
        "action": "RETRACT_DEAD_UNIPROT_GROUNDINGS",
        "changes": "Retracted 1 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T02:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES_PART2",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates onto their causal-graph counterparts (1 to produces), issue 301 part 2. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Each replacement is a 1:1 mirror of its source predicate that changes only the domain, so the claim each edge makes is unchanged and directions are unchanged. The replacements are proposed in proposals/metpo_traitmech_v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-17T02:00:00Z",
        "curator": "claude",
        "action": "NORMALISE_NODE_SENSE",
        "changes": "One node_id per SENSE (issues 356, 384): molecular_oxygen is the chemical sense here. The molecule, not the condition \u2014 the dioxygen participating in the reaction the graph describes. Normalised onto molecular_oxygen, the id 20 other chemical occurrences already use, so one id means one sense corpus-wide (issues 356, 384).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-24T08:40:00Z",
        "curator": "codex",
        "action": "CURATE_PROTEIN_TAXON_EXAMPLE",
        "changes": "Added a DOI-backed E. coli K-12 AtpD beta-subunit example, grounded the ATP synthase and Complex I nodes to current GO complex terms, and documented the graph's mixed aerobic/anaerobic scope and component-level interpretation.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T08:20:00Z",
        "curator": "codex",
        "action": "CONNECT_CAUSAL_GRAPH_COMPONENTS",
        "changes": "Resolved issue #183 graph fragmentation (2 components to 1) using 1 public-source, verbatim-snippet-backed connector(s). No paid research service was called.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-22T01:35:00Z",
        "curator": "claude",
        "action": "REFRESH_UNIPROT_ENTRY_VERSION",
        "changes": "Refreshed UniProtKB entry_version against live UniProt REST on 2026-10-22: UniProtKB:P0ABB4 (155 -> 156 on atp_synthase).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000124",
    "label": "respiration of sulfur compounds",
    "definition": "An anaerobic respiration in which an organism conserves energy by transferring electrons to an inorganic sulfur compound as the terminal electron acceptor.",
    "definition_source": "DOI:10.1126/science.aaf4507",
    "trait_category": "METABOLISM",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000802"
    ],
    "synonyms": [
      {
        "synonym_text": "respiration_of_sulfur_compounds",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1126/science.aaf4507"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.3389/fmicb.2023.1108245",
        "snippet": "sulfate, sulfur, or thiosulfate respiration",
        "notes": "Zavarzina et al. experimentally compare iron respiration with sulfur/thiosulfate respiration in Dethiobacter alkaliphilus."
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-08T00:00:00Z",
        "curator": "codex",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed a DOI-backed FAPROTAX metabolic capability from proposals/metpo_traitmech_v11 after repository-wide duplicate review.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-21T20:01:04Z",
        "curator": "claude",
        "action": "RECORD_MECHANISM_KNOWLEDGE_GAP",
        "changes": "Recorded OPEN KNOWLEDGE_GAP discussion (respiration-of-sulfur-compounds-causal-graph-source-gap) documenting the source-limited mechanism gap for causal_graphs.",
        "llm_assisted": true
      }
    ],
    "discussions": [
      {
        "discussion_id": "respiration-of-sulfur-compounds-causal-graph-source-gap",
        "prompt": "Add primary literature evidence for dissimilatory sulfur/sulfate/thiosulfate reductases (e.g. DsrAB, PsrABC, PhsABC) and a strain-matched canonical example before constructing causal_graphs.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "The current record carries a single 42-character snippet ('sulfate, sulfur, or thiosulfate respiration' in DOI:10.3389/fmicb.2023.1108245) enumerating the respiratory subclasses without enzymatic mechanism quotes.",
        "posed_by": "claude",
        "posed_date": "2026-10-21",
        "evidence": [
          {
            "reference": "DOI:10.3389/fmicb.2023.1108245",
            "supports": "PARTIAL",
            "snippet": "sulfate, sulfur, or thiosulfate respiration",
            "explanation": "Existing record-level evidence supports the high-level metabolic trait definition but does not provide multi-step enzymatic mechanism quotes for a connected causal graph."
          }
        ]
      }
    ]
  },
  {
    "identifier": "traitmech:000202",
    "label": "selenate respiration",
    "definition": "An anaerobic respiration in which an organism uses selenate as the terminal electron acceptor for energy conservation.",
    "definition_source": "DOI:10.1128/aem.60.8.3011-3019.1994",
    "trait_category": "METABOLISM",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000802"
    ],
    "synonyms": [
      {
        "synonym_text": "dissimilatory selenate reduction",
        "synonym_type": "EXACT_SYNONYM"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1128/aem.60.8.3011-3019.1994",
        "snippet": "A gram-negative, strictly anaerobic, motile vibrio was isolated from a selenate-respiring enrichment culture",
        "notes": "Oremland et al. isolated strain SES-3 from a selenate-respiring enrichment culture and showed anaerobic growth coupled to selenate reduction."
      },
      {
        "reference": "DOI:10.1128/AEM.02737-06",
        "snippet": "use selenate as a terminal electron acceptor",
        "notes": "Narasingarao and Haggblom define the phenotype as use of selenate as a terminal electron acceptor in dissimilatory selenate reduction."
      },
      {
        "reference": "DOI:10.1128/AEM.02737-06",
        "snippet": "four novel anaerobic dissimilatory selenate-respiring bacteria",
        "notes": "Narasingarao and Haggblom support selenate respiration as a repeatedly observed microbial trait across aquatic-sediment isolates rather than a single strain-specific anomaly."
      },
      {
        "reference": "DOI:10.1016/j.syapm.2005.12.011",
        "snippet": "Here we characterize a novel selenate-respiring bacterium, strain AK4OH1, isolated from an estuarine sediment enrichment culture",
        "notes": "Narasingarao and Haggblom described Sedimenticola selenatireducens AK4OH1 as an anaerobic selenate-respiring bacterium isolated from estuarine sediment."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1111735",
        "taxon_label": "Sedimenticola selenatireducens DSM 17993",
        "note": "Narasingarao and Haggblom isolated and described Sedimenticola selenatireducens strain AK4OH1 as an anaerobic selenate-respiring bacterium.",
        "reference": "DOI:10.1016/j.syapm.2005.12.011"
      }
    ],
    "discussions": [
      {
        "discussion_id": "selenate-respiration-xref-gap",
        "prompt": "Resolve an exact external ontology class for organism-level selenate respiration before adding a TraitRecord xref.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Candidate EC, Rhea, and protein-family terms for selenate reductase describe narrower molecular functions, reactions, or enzymes rather than the whole-organism anaerobic respiration phenotype.",
        "posed_by": "codex",
        "posed_date": "2026-09-15"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-15T03:22:39Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted selenate respiration as a DOI-backed anaerobic respiration TraitRecord after a repository-wide duplicate review covering ignored and hidden files; the local METPO snapshot has no exact selenate respiration class and the replacement placeholder is reserved in proposals/metpo_traitmech_v79.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:2000211",
    "label": "sequesters",
    "definition": "An OBJECT_PROPERTY relating an organism to a chemical that the organism specifically sequesters or chelates intracellularly or in specialised structures.",
    "definition_source": "DOI:10.1146/annurev.micro.55.1.485",
    "trait_category": "METABOLISM",
    "term_kind": "OBJECT_PROPERTY",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:2000210"
    ],
    "domain": "https://w3id.org/metpo/1000525",
    "range_": "http://purl.obolibrary.org/obo/CHEBI_24431",
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev.micro.55.1.485",
        "snippet": "sequestration",
        "notes": "Microbial-physiology reference supports 'sequesters' as a canonical predicate composed with a CHEBI-class chemical object at assertion time."
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.985696+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (OBJECT_PROPERTY)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic transport or storage relation carrier; later replacement should use more specific trait records that combine the relation with the transported, imported, exported, accumulated, or sequestered entity, cellular location or compartment, and positive or negative context.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-16T08:50:00-07:00",
        "curator": "claude",
        "action": "UNDEPRECATED_AS_COMPOSITION_PRIMITIVE",
        "changes": "Restored from DEPRECATED to REVIEWED under the predicate+class composition pattern (intended use: <organism> + this predicate + CHEBI chemical class). Added DOI/PMID-backed definition, evidence, and explicit domain/range slots.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:2000302",
    "label": "shows activity of",
    "definition": "An OBJECT_PROPERTY relating an organism to an enzyme (material entity) for which the organism shows the corresponding catalytic activity. Intended use is predicate + class composition at assertion time with a METPO enzyme class (METPO:1000527 or its subclass) as the object \u2014 the assertion reads \"<organism> expresses an enzyme of class <X>, evidenced by activity measurement\".",
    "definition_source": "PMID:21413255",
    "trait_category": "METABOLISM",
    "term_kind": "OBJECT_PROPERTY",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:2000301"
    ],
    "synonyms": [
      {
        "synonym_text": "Physiology and metabolism.enzymes.[].activity",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "domain": "https://w3id.org/metpo/1000525",
    "range_": "https://w3id.org/metpo/1000527",
    "evidence": [
      {
        "reference": "PMID:21413255",
        "snippet": "activity",
        "notes": "Microbial-physiology reference supports 'shows activity of' as a canonical predicate relating an organism to an enzyme/activity class, composed at assertion time."
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.991056+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (OBJECT_PROPERTY)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic biochemical conversion or activity relation carrier; later replacement should use more specific trait records that combine the relation with the substrate, product, enzyme or activity target, assay context, growth condition, or other entity.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-16T08:50:00-07:00",
        "curator": "claude",
        "action": "UNDEPRECATED_AS_COMPOSITION_PRIMITIVE",
        "changes": "Restored from DEPRECATED to REVIEWED under the predicate+class composition pattern (intended use: <organism> + this predicate + CHEBI chemical class). Added DOI/PMID-backed definition, evidence, and explicit domain/range slots.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000115",
    "label": "starch degradation",
    "definition": "A biopolymer-degradation metabolism in which an organism hydrolyzes starch (amylose and amylopectin) to maltooligosaccharides and glucose using amylases and related glycoside hydrolases.",
    "definition_source": "DOI:10.1016/S0168-1656(01)00407-2",
    "trait_category": "METABOLISM",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "traitmech:000110"
    ],
    "synonyms": [
      {
        "synonym_text": "amylolytic",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1016/S0168-1656(01)00407-2"
      },
      {
        "synonym_text": "starch breakdown",
        "synonym_type": "EXACT_SYNONYM",
        "source": "http://purl.obolibrary.org/obo/go/releases/2026-07-26/go-basic.obo"
      },
      {
        "synonym_text": "starch catabolism",
        "synonym_type": "EXACT_SYNONYM",
        "source": "http://purl.obolibrary.org/obo/go/releases/2026-07-26/go-basic.obo"
      }
    ],
    "xrefs": [
      "GO:0005983"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1016/S0168-1656(01)00407-2",
        "notes": "van der Maarel et al. review starch-converting enzymes of the alpha-amylase family that hydrolyze starch to oligosaccharides and glucose."
      },
      {
        "reference": "DOI:10.1093/nar/gkt1178",
        "notes": "The CAZy database review classifies the glycoside hydrolases (including amylases) that microorganisms use to degrade starch and other polysaccharides."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1402",
        "taxon_label": "Bacillus licheniformis",
        "note": "Industrial amylase producer; model for extracellular starch hydrolysis.",
        "reference": "DOI:10.1186/gb-2004-5-10-r77"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "starch_degradation_amylase",
        "title": "Starch degradation hydrolyzes amylose/amylopectin to glucose",
        "description": "Evidence-backed causal sketch linking amylase systems to hydrolysis of starch into maltooligosaccharides and glucose.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "Represents extracellular alpha-amylase initiation followed by a generic exo-hydrolase step. The B. licheniformis protein example supports the alpha-amylase branch; alpha-glucosidase and glucoamylase remain unresolved as a combined downstream label.",
        "nodes": [
          {
            "node_id": "starch_degradation_trait",
            "label": "starch degradation",
            "node_type": "TRAIT",
            "grounding": "traitmech:000115",
            "description": "Hydrolysis of starch to assimilable sugars."
          },
          {
            "node_id": "amylase",
            "label": "alpha-amylase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Endo-acting alpha-amylase hydrolyzing internal alpha-1,4-glucosidic linkages in starch.",
            "grounding": "GO:0004556",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:P06278",
                "protein_label": "Alpha-amylase",
                "gene_symbol": "amyS",
                "taxon_id": "NCBITaxon:1402",
                "taxon_label": "Bacillus licheniformis",
                "entry_status": "REVIEWED",
                "retrieved_on": "2026-10-22",
                "entry_version": 174,
                "sequence_version": 1,
                "role": "Secreted alpha-amylase that hydrolyzes soluble starch in the canonical B. licheniformis example.",
                "evidence": [
                  {
                    "reference": "DOI:10.1021/bp060057a",
                    "snippet": "The enzymatic hydrolysis of soluble starch with an alpha-amylase from Bacillus licheniformis",
                    "notes": "The primary enzymology study directly tests B. licheniformis alpha-amylase on soluble starch; UniProtKB P06278 verifies the reviewed AmyS protein and taxon."
                  }
                ]
              }
            ]
          },
          {
            "node_id": "glucose",
            "label": "glucose",
            "node_type": "CHEMICAL",
            "description": "Monomeric sugar released from starch hydrolysis.",
            "grounding": "CHEBI:17234"
          },
          {
            "node_id": "starch",
            "label": "starch (amylose/amylopectin)",
            "node_type": "CHEMICAL",
            "description": "Alpha-glucan polysaccharide substrate of amylolytic degradation."
          },
          {
            "node_id": "maltooligosaccharides",
            "label": "maltooligosaccharides",
            "node_type": "CHEMICAL",
            "description": "Short alpha-1,4-linked glucose oligomers released by endo-amylase cleavage of starch.",
            "grounding": "CHEBI:17593"
          },
          {
            "node_id": "alpha_glucosidase",
            "label": "alpha-glucosidase / glucoamylase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Exo-acting glycoside hydrolase that releases glucose from maltooligosaccharides.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Alpha-glucosidase and glucoamylase are distinct activities and families; this combined label must be split before assigning an exact term."
          }
        ],
        "edges": [
          {
            "subject": "amylase",
            "predicate": "confers",
            "object": "starch_degradation_trait",
            "description": "Alpha-amylase endo-hydrolyzes starch alpha-1,4 linkages and initiates production of shorter glucans.",
            "evidence": [
              {
                "reference": "DOI:10.1016/S0168-1656(01)00407-2",
                "snippet": "the use of starch-converting enzymes in the production of maltodextrin, modified starches, or glucose and fructose syrups",
                "notes": "The review supports alpha-amylase-family starch conversion; the edge no longer attributes alpha-1,6 hydrolysis to the refined alpha-amylase node."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "starch_degradation_trait",
            "predicate": "produces",
            "object": "glucose",
            "description": "Starch hydrolysis yields maltodextrins and glucose.",
            "evidence": [
              {
                "reference": "DOI:10.1093/nar/gkt1178",
                "notes": "CAZy review classifies glycoside hydrolases (including amylases) used to degrade starch and other polysaccharides."
              }
            ],
            "predicate_id": "METPO:2007800"
          },
          {
            "subject": "starch",
            "predicate": "is hydrolyzed to",
            "object": "maltooligosaccharides",
            "description": "Endo-amylolytic cleavage of starch yields maltooligosaccharides as the core trait-level intermediate.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s00018-023-04812-w",
                "notes": "Reports hydrolysis of starch into maltooligosaccharides; flagged as broad trait-level core edge across taxa."
              }
            ],
            "predicate_id": "RO:0001001"
          },
          {
            "subject": "amylase",
            "predicate": "hydrolyzes",
            "object": "starch",
            "description": "B. licheniformis alpha-amylase hydrolyzes starch; the adjacent starch-to-maltooligosaccharide edge records the product transition.",
            "evidence": [
              {
                "reference": "DOI:10.1021/bp060057a",
                "snippet": "The enzymatic hydrolysis of soluble starch with an alpha-amylase from Bacillus licheniformis",
                "notes": "Direct substrate-enzyme evidence from the canonical taxon; changing the object from the product node corrects the previous edge direction."
              }
            ],
            "predicate_id": "METPO:2007808"
          },
          {
            "subject": "alpha_glucosidase",
            "predicate": "degrades",
            "object": "maltooligosaccharides",
            "description": "Alpha-glucosidase/glucoamylase exo-acts on maltooligosaccharides to release glucose.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mbio.01506-24",
                "notes": "Alpha-glucosidase/glucoamylase degrades maltooligosaccharides to glucose; generic terminal exo-hydrolysis step."
              }
            ],
            "predicate_id": "METPO:2007809"
          },
          {
            "subject": "alpha_glucosidase",
            "predicate": "produces",
            "object": "glucose",
            "description": "Exo-amylolytic release of glucose monomers from maltooligosaccharides.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mbio.01506-24",
                "notes": "Alpha-glucosidase/glucoamylase degrades maltooligosaccharides to glucose, the terminal assimilable sugar."
              }
            ],
            "predicate_id": "METPO:2007800"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-06-08T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate METABOLISM trait (starch degradation / amylolysis); leftover round, sub-variant of biopolymer degradation.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-10T14:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (amylase hydrolysis of starch) with RO/METPO predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-14T06:55:38Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:17234\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 4 evidence-backed generic edges (3 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:12Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:33Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:17593\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:38Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000013\u00d71, METPO:2000007\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 1 causal edge(s) off enables/RO:0002327 with a TRAIT object (1 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T02:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES_PART2",
        "changes": "Re-grounded 4 causal edge(s) off microbe-domain METPO predicates onto their causal-graph counterparts (1 to degrades, 1 to hydrolyzes, 2 to produces), issue 301 part 2. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Each replacement is a 1:1 mirror of its source predicate that changes only the domain, so the claim each edge makes is unchanged and directions are unchanged. The replacements are proposed in proposals/metpo_traitmech_v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T06:15:13Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0001001\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-24T00:00:00Z",
        "curator": "codex",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Refined the broad amylase node to alpha-amylase with GO and a DOI-backed B. licheniformis AmyS example, corrected the enzyme-substrate edge, retained the combined downstream exo-hydrolase label with an explicit rationale, and documented graph scope.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T06:15:39Z",
        "curator": "codex",
        "action": "ADD_EXACT_ONTOLOGY_MATCH",
        "changes": "Ontology exact-match review (2026-08-25): approved exact xref(s): GO:0005983; declared exact synonym(s): 'starch breakdown', 'starch catabolism'. Evidence is predicate-scoped in the versioned ontology snapshots; OAK cross-checked direct data, and OLS4 spot-checked release deltas and disputed hits.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-22T01:35:00Z",
        "curator": "claude",
        "action": "REFRESH_UNIPROT_ENTRY_VERSION",
        "changes": "Refreshed UniProtKB entry_version against live UniProt REST on 2026-10-22: UniProtKB:P06278 (173 -> 174 on amylase).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000804",
    "label": "Substrate-level phosphorylation",
    "definition": "A metabolism in which ATP is formed directly by transfer of a phosphoryl group from a substrate to ADP.",
    "definition_source": "DOI:10.1111/1751-7915.13746",
    "trait_category": "METABOLISM",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000060"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1111/1751-7915.13746",
        "snippet": "Substrate-level phosphorylation is one of the main sources",
        "notes": "Review supports SLP as microbial energy conservation in fermentative metabolism."
      },
      {
        "reference": "DOI:10.1128/MMBR.69.1.12-50.2005",
        "snippet": "phosphotransacetylase [PTA], acetate kinase [ACK]",
        "notes": "Review supports acetate kinase and phosphotransacetylase as central acetate-switch enzymes."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1314",
        "taxon_label": "Streptococcus pyogenes",
        "note": "ATP via glycolytic substrate-level phosphorylation",
        "reference": "PMID:27442496"
      },
      {
        "taxon_id": "NCBITaxon:1488",
        "taxon_label": "Clostridium acetobutylicum",
        "note": "fermentative substrate-level phosphorylation",
        "reference": "PMID:11466286"
      },
      {
        "taxon_id": "NCBITaxon:301447",
        "taxon_label": "Streptococcus pyogenes serotype M1",
        "note": "Reference-proteome strain SF370 in which arcC was deleted in-frame to test the arginine-deiminase pathway.",
        "reference": "DOI:10.1128/IAI.00916-13"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "substrate_level_phosphorylation_direct_atp",
        "title": "Substrate-level phosphorylation direct ATP formation",
        "description": "DOI-backed graph connecting high-energy phosphorylated intermediates, kinase reactions, ADP phosphorylation, and ATP formation.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "Represents direct phosphoryl transfer to ADP and two concrete enzyme routes; the unreviewed ArcC exemplar is retained only because it is the exact SF370 reference-proteome sequence paired to a gene-deletion study.",
        "nodes": [
          {
            "node_id": "substrate_level_phosphorylation_trait",
            "label": "Substrate-level phosphorylation",
            "node_type": "TRAIT",
            "grounding": "METPO:1000804",
            "description": "ATP generation by direct phosphoryl transfer from a metabolic intermediate."
          },
          {
            "node_id": "fermentative_condition",
            "label": "fermentative condition",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Metabolic context where SLP is a major ATP source."
          },
          {
            "node_id": "high_energy_phosphorylated_intermediate",
            "label": "high-energy phosphorylated intermediate",
            "node_type": "CHEMICAL",
            "description": "Metabolite carrying a transferable phosphoryl group."
          },
          {
            "node_id": "adp",
            "label": "ADP",
            "node_type": "CHEMICAL",
            "description": "Phosphoryl acceptor converted to ATP.",
            "grounding": "CHEBI:16761"
          },
          {
            "node_id": "kinase_reaction",
            "label": "kinase reaction",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "Enzymatic phosphoryl transfer to ADP.",
            "grounding": "GO:0016301"
          },
          {
            "node_id": "atp",
            "label": "ATP",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:30616",
            "description": "Energy carrier produced by SLP."
          },
          {
            "node_id": "acetyl_phosphate",
            "label": "acetyl phosphate",
            "node_type": "CHEMICAL",
            "description": "High-energy intermediate in acetate dissimilation.",
            "grounding": "CHEBI:15350"
          },
          {
            "node_id": "acetate_kinase",
            "label": "acetate kinase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Enzyme that converts acetyl phosphate and ADP to acetate and ATP.",
            "grounding": "GO:0008776"
          },
          {
            "node_id": "acetate",
            "label": "acetate",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:30089",
            "description": "Product of the acetate kinase SLP reaction."
          },
          {
            "node_id": "anaerobiosis",
            "label": "anaerobiosis / low oxygen",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Absence of oxygen enabling anaerobic catabolism such as fermentation."
          },
          {
            "node_id": "fermentation",
            "label": "fermentation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Anaerobic catabolism in which ATP is produced by substrate-level phosphorylation.",
            "grounding": "GO:0006113"
          },
          {
            "node_id": "acka_pta_pathway",
            "label": "AckA-Pta pathway",
            "node_type": "PATHWAY",
            "description": "Phosphotransacetylase/acetate kinase reaction set that produces ATP via SLP.",
            "related_records": [
              {
                "corpus": "PathwayMech",
                "identifier": "MetaCyc:PWY0-1312",
                "relation": "PATHWAY_CONTEXT",
                "basis": "PathwayMech context: acetate and ATP formation from acetyl-CoA I in Thermotoga maritima (NCBITaxon:2336). The linked route explicitly contains phosphate acetyltransferase and acetate kinase and produces ATP through acetyl phosphate. No exact equivalence or transfer of organism scope is asserted.",
                "source_version": "aa305727458c44ab05614901334540e2c87a9f3a"
              }
            ]
          },
          {
            "node_id": "carbamate_kinase_arginine_deiminase",
            "label": "carbamate kinase (arginine deiminase pathway)",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Carbamate kinase of the arginine deiminase pathway that generates ATP by SLP.",
            "grounding": "GO:0008804",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:Q99YT9",
                "protein_label": "Carbamate kinase",
                "gene_symbol": "arcC",
                "taxon_id": "NCBITaxon:301447",
                "taxon_label": "Streptococcus pyogenes serotype M1",
                "entry_status": "UNREVIEWED",
                "proteome_id": "UP000000750",
                "retrieved_on": "2026-10-22",
                "entry_version": 147,
                "sequence_version": 1,
                "role": "ArcC of the arginine-deiminase pathway, which catalyzes the ATP-forming carbamate-kinase reaction represented by this node.",
                "evidence": [
                  {
                    "reference": "DOI:10.1128/IAI.00916-13",
                    "snippet": "individual in-frame deletion mutations were constructed in arcC (SPy_1541)",
                    "notes": "The primary study constructed the exact SF370 arcC deletion; UniProtKB Q99YT9 is the corresponding current unreviewed entry in reference proteome UP000000750."
                  }
                ]
              }
            ],
            "related_records": [
              {
                "corpus": "PathwayMech",
                "identifier": "MetaCyc:ARGDEGRAD-PWY",
                "relation": "PATHWAY_CONTEXT",
                "basis": "PathwayMech context: L-arginine degradation V (arginine deiminase pathway) in Halobacterium salinarum (NCBITaxon:2242). The linked arginine deiminase route contains the ATP-forming carbamate kinase step; it does not assert that the full pathway is equivalent to this enzyme node. No exact equivalence or transfer of organism scope is asserted.",
                "source_version": "aa305727458c44ab05614901334540e2c87a9f3a"
              }
            ]
          }
        ],
        "edges": [
          {
            "subject": "substrate_level_phosphorylation_trait",
            "predicate": "occurs in",
            "object": "fermentative_condition",
            "description": "SLP is a major ATP source in fermentative energy metabolism.",
            "evidence": [
              {
                "reference": "DOI:10.1111/1751-7915.13746",
                "snippet": "main sources of energy under fermentative conditions",
                "notes": "Supports fermentative context for SLP."
              }
            ],
            "predicate_id": "biolink:occurs_in"
          },
          {
            "subject": "high_energy_phosphorylated_intermediate",
            "predicate": "donates phosphoryl group to",
            "object": "adp",
            "description": "SLP transfers phosphoryl groups from metabolic intermediates to ADP.",
            "evidence": [
              {
                "reference": "DOI:10.1111/1751-7915.13746",
                "snippet": "transferring a phosphate group to ADP",
                "notes": "Supports direct phosphoryl transfer to ADP."
              }
            ]
          },
          {
            "subject": "kinase_reaction",
            "predicate": "has output",
            "object": "atp",
            "description": "Kinase reactions convert phosphorylated intermediates and ADP to ATP.",
            "evidence": [
              {
                "reference": "DOI:10.1111/1751-7915.13746",
                "snippet": "kinase-catalysed reactions can be applied for SLP",
                "notes": "Supports kinase-mediated ATP formation."
              }
            ],
            "predicate_id": "RO:0002234"
          },
          {
            "subject": "acetyl_phosphate",
            "predicate": "substrate for",
            "object": "acetate_kinase",
            "description": "Acetyl phosphate is converted by acetate kinase during acetate dissimilation.",
            "evidence": [
              {
                "reference": "DOI:10.1128/MMBR.69.1.12-50.2005",
                "snippet": "acetyl\u223cP, the high-energy intermediate of acetate dissimilation",
                "notes": "Supports acetyl phosphate as the high-energy acetate-switch intermediate."
              }
            ]
          },
          {
            "subject": "acetate_kinase",
            "predicate": "produces",
            "object": "acetate",
            "description": "Acetate kinase forms acetate from acetyl phosphate.",
            "evidence": [
              {
                "reference": "DOI:10.1128/MMBR.69.1.12-50.2005",
                "snippet": "phosphotransacetylase [PTA], acetate kinase [ACK]",
                "notes": "Supports acetate kinase as a central acetate-switch component."
              }
            ],
            "predicate_id": "METPO:2007800"
          },
          {
            "subject": "acetate_kinase",
            "predicate": "produces",
            "object": "atp",
            "description": "Acetate kinase contributes ATP formation through substrate-level phosphorylation.",
            "evidence": [
              {
                "reference": "DOI:10.1111/1751-7915.13746",
                "snippet": "acetyl-phosphate to acetate",
                "notes": "Review lists acetyl-phosphate to acetate among SLP energy-conserving reactions."
              }
            ],
            "predicate_id": "METPO:2007800"
          },
          {
            "subject": "anaerobiosis",
            "predicate": "enables",
            "object": "fermentation",
            "description": "Absence of oxygen enables fermentative metabolism.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuae016",
                "snippet": "Fermentation is a type of metabolism carried out by organisms in environments without oxygen.",
                "notes": "Fermentation is a type of metabolism carried out by organisms in environments without oxygen."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "fermentation",
            "predicate": "produces ATP via",
            "object": "substrate_level_phosphorylation_trait",
            "description": "In fermentation, ATP is produced by substrate-level phosphorylation.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuae016",
                "snippet": "ATP is produced by substrate-level phosphorylation.",
                "notes": "ATP is produced by substrate-level phosphorylation; strong definitional edge."
              }
            ]
          },
          {
            "subject": "acka_pta_pathway",
            "predicate": "allows ATP production via",
            "object": "substrate_level_phosphorylation_trait",
            "description": "The AckA-Pta reaction set allows ATP production via substrate-level phosphorylation.",
            "evidence": [
              {
                "reference": "DOI:10.1042/ETLS20220092",
                "snippet": "acetate kinase and phosphotransacetylase (AckA-Pta), a set of reactions that allows ATP production via substrate-level phosphorylation",
                "notes": "AckA-Pta, a set of reactions that allows ATP production via substrate-level phosphorylation."
              }
            ]
          },
          {
            "subject": "carbamate_kinase_arginine_deiminase",
            "predicate": "generates ATP via",
            "object": "substrate_level_phosphorylation_trait",
            "description": "Carbamate kinase in the arginine deiminase pathway is an additional SLP route for ATP production.",
            "evidence": [
              {
                "reference": "DOI:10.1039/d4cb00099d",
                "snippet": "As part of the arginine deiminase (ADI) pathway, carbamate kinase generates one ATP molecule",
                "notes": "The carbamate kinase reaction has been reported to be effective for ATP production in several acetogens."
              }
            ]
          },
          {
            "subject": "kinase_reaction",
            "predicate": "has input",
            "object": "high_energy_phosphorylated_intermediate",
            "description": "The kinase reaction accepts a phosphoryl group from a high-energy metabolic intermediate.",
            "evidence": [
              {
                "reference": "DOI:10.1111/1751-7915.13746",
                "snippet": "transferring a phosphate group to ADP",
                "notes": "Verified against the free public article text."
              }
            ],
            "predicate_id": "RO:0002233"
          },
          {
            "subject": "kinase_reaction",
            "predicate": "contributes to",
            "object": "substrate_level_phosphorylation_trait",
            "description": "Kinase-catalyzed direct phosphoryl transfer realizes substrate-level phosphorylation.",
            "evidence": [
              {
                "reference": "DOI:10.1111/1751-7915.13746",
                "snippet": "kinase-catalysed reactions can be applied for SLP",
                "notes": "Verified against the free public article text."
              }
            ],
            "predicate_id": "RO:0002326"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-08-23T09:03:00Z",
        "curator": "codex",
        "action": "CURATE_PROTEIN_TAXON_EXAMPLE",
        "changes": "Reviewed the graph as mechanistic and added the DOI-backed SF370 ArcC reference-proteome exemplar with an explicit unreviewed-entry exception.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-05T01:35:46.913184+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-08T00:00:00-07:00",
        "curator": "codex",
        "action": "ADDED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed causal graph for direct phosphoryl transfer to ADP and acetate kinase-linked ATP formation.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:30Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d73).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T05:49:24Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:occurs_in\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:38:00Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0016301\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T05:05:14Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A081KVG3\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-14T05:51:46Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:16761\u00d71, CHEBI:15350\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 4 evidence-backed generic edges (4 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:12Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:19Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0006113\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:21:11Z",
        "curator": "claude",
        "action": "RETRACT_DEAD_UNIPROT_GROUNDINGS",
        "changes": "Retracted 1 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:23:54Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0008776\u00d71, GO:0008804\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates (1 to has output), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T02:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES_PART2",
        "changes": "Re-grounded 2 causal edge(s) off microbe-domain METPO predicates onto their causal-graph counterparts (2 to produces), issue 301 part 2. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Each replacement is a 1:1 mirror of its source predicate that changes only the domain, so the claim each edge makes is unchanged and directions are unchanged. The replacements are proposed in proposals/metpo_traitmech_v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-16T02:00:00Z",
        "curator": "claude",
        "action": "NORMALISE_NODE_TYPE",
        "changes": "Under the PATHWAY-vs-BIOLOGICAL_PROCESS rule, one node_id means one thing corpus-wide (issue 356): fermentation is typed BIOLOGICAL_PROCESS. PATHWAY is a named, conventionally enumerable multi-step route; BIOLOGICAL_PROCESS is everything else. A CLASS of routes rather than one route -- fermentation names a mode of energy conservation with many distinct implementations, so its steps cannot be enumerated without picking one. Was 3 BIOLOGICAL_PROCESS to 2 before this tranche. NOTE its groundings disagree with each other (GO:0006113 x3, METPO:1002005, and METPO:1000845 which is ACETOGENESIS, a different concept) -- filed as #391 and deliberately NOT touched here, because retyping a node while carrying a wrong CURIE along unchanged would make it look reviewed.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T12:15:00Z",
        "curator": "codex",
        "action": "CONNECT_CAUSAL_GRAPH_COMPONENTS",
        "changes": "Resolved issue #183 graph fragmentation (3 components to 1) with 2 public-source connector(s). No paid research service was called.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-05T17:46:21Z",
        "curator": "codex",
        "action": "ADD_PATHWAY_CONTEXT",
        "changes": "Added pinned PathwayMech context on reviewed causal nodes with explicit route and organism limitations; retained existing groundings and exact xrefs.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-22T01:35:00Z",
        "curator": "claude",
        "action": "REFRESH_UNIPROT_ENTRY_VERSION",
        "changes": "Refreshed UniProtKB entry_version against live UniProt REST on 2026-10-22: UniProtKB:Q99YT9 (146 -> 147 on carbamate_kinase_arginine_deiminase).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000106",
    "label": "sulfur oxidation",
    "definition": "A metabolism in which an organism oxidizes reduced inorganic sulfur compounds (sulfide, elemental sulfur, thiosulfate) to sulfate, conserving energy and often supporting chemolithotrophic growth.",
    "definition_source": "DOI:10.1111/j.1574-6976.2009.00187.x",
    "trait_category": "METABOLISM",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000060"
    ],
    "synonyms": [
      {
        "synonym_text": "sulfide oxidation",
        "synonym_type": "NARROW_SYNONYM",
        "source": "DOI:10.1111/j.1574-6976.2009.00187.x"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1111/j.1574-6976.2009.00187.x",
        "notes": "Ghosh & Dam review the biochemistry and molecular biology of lithotrophic sulfur oxidation across bacteria and archaea."
      },
      {
        "reference": "DOI:10.1128/AEM.67.7.2873-2882.2001",
        "notes": "Friedrich et al. describe a common mechanism for bacterial oxidation of reduced inorganic sulfur compounds (the Sox system)."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:36861",
        "taxon_label": "Thiobacillus denitrificans",
        "note": "Obligately chemolithoautotrophic sulfur-compound oxidizer with a sequenced genome anchoring sulfur-oxidation pathways. Beggiatoa is a historic morphological exemplar.",
        "reference": "DOI:10.1128/JB.00568-06"
      },
      {
        "taxon_id": "NCBITaxon:292415",
        "taxon_label": "Thiobacillus denitrificans ATCC 25259",
        "note": "Reference strain used for whole-genome transcriptional analysis of sulfur oxidation under aerobic and denitrifying conditions.",
        "reference": "DOI:10.1128/JB.00568-06"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "sulfur_oxidation_sox",
        "title": "Lithotrophic sulfur oxidation to sulfate",
        "description": "Evidence-backed causal sketch linking sulfur-oxidizing enzyme systems to oxidation of reduced sulfur compounds to sulfate.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "This is a cross-taxon composite of Sox, SQR/PDO, and S4-intermediate sulfur-oxidation routes. The T. denitrificans SQR example supports its denitrifying branch; PDO, TsdA, and TetH branches are not asserted as universal or co-required.",
        "nodes": [
          {
            "node_id": "sulfur_oxidation_trait",
            "label": "sulfur oxidation",
            "node_type": "TRAIT",
            "grounding": "traitmech:000106",
            "description": "Capacity to oxidize reduced inorganic sulfur to sulfate."
          },
          {
            "node_id": "sox_system",
            "label": "Sox enzyme system",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Sulfur-oxidizing multienzyme system.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "The Sox system comprises multiple non-equivalent protein components; no single GO or InterPro term denotes the complete generic system represented here."
          },
          {
            "node_id": "hydrogen_sulfide",
            "label": "hydrogen sulfide",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:16136",
            "description": "Reduced inorganic sulfur substrate."
          },
          {
            "node_id": "sulfate",
            "label": "sulfate",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:16189",
            "description": "Oxidized sulfur end product."
          },
          {
            "node_id": "sqr_enzyme",
            "label": "sulfide:quinone oxidoreductase (SQR)",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Membrane flavoprotein oxidizing sulfide to sulfane sulfur/polysulfide.",
            "grounding": "GO:0070224",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:Q3SJ10",
                "protein_label": "Sulfide:quinone oxidoreductase",
                "gene_symbol": "Tbd_1407",
                "taxon_id": "NCBITaxon:292415",
                "taxon_label": "Thiobacillus denitrificans ATCC 25259",
                "entry_status": "UNREVIEWED",
                "proteome_id": "UP000008291",
                "retrieved_on": "2026-08-24",
                "entry_version": 92,
                "sequence_version": 1,
                "role": "SQR encoded by Tbd_1407 and strongly induced during denitrifying sulfur metabolism in T. denitrificans ATCC 25259.",
                "evidence": [
                  {
                    "reference": "DOI:10.1128/JB.00568-06",
                    "snippet": "two copies of sulfide:quinone oxidoreductase",
                    "notes": "Whole-genome transcriptional analysis found Tbd_1407 strongly upregulated under denitrifying conditions and associated it with sulfur-compound oxidation; UniProtKB Q3SJ10 is the exact reference-proteome locus."
                  }
                ]
              }
            ]
          },
          {
            "node_id": "sulfane_sulfur",
            "label": "sulfane sulfur",
            "node_type": "CHEMICAL",
            "description": "Sulfane sulfur / S0 / polysulfide intermediate."
          },
          {
            "node_id": "pdo_enzyme",
            "label": "persulfide dioxygenase (PDO)",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Oxidizes glutathione persulfide to sulfite using O2.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "The graph does not resolve a taxon-specific PDO family, fusion architecture, or glutathione dependence needed for an exact semantic grounding."
          },
          {
            "node_id": "glutathione_persulfide",
            "label": "glutathione persulfide (GSSH)",
            "node_type": "CHEMICAL",
            "description": "Persulfide substrate of persulfide dioxygenase."
          },
          {
            "node_id": "sulfite",
            "label": "sulfite",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:16526",
            "description": "Sulfite intermediate in sulfur oxidation."
          },
          {
            "node_id": "thiosulfate",
            "label": "thiosulfate",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:30087",
            "description": "Thiosulfate intermediate substrate of the Sox system."
          },
          {
            "node_id": "tsda_enzyme",
            "label": "thiosulfate dehydrogenase (TsdA)",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Oxidizes thiosulfate to tetrathionate.",
            "grounding": "GO:0050338"
          },
          {
            "node_id": "tetrathionate",
            "label": "tetrathionate",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:30926",
            "description": "Tetrathionate intermediate in the S4 intermediate pathway."
          },
          {
            "node_id": "teth_enzyme",
            "label": "tetrathionate hydrolase (TetH)",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Hydrolyzes/disproportionates tetrathionate to S0, thiosulfate and sulfate.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "TetH proteins are taxon- and acidophile-specific members of broader hydrolase families; no exact verified GO or InterPro term was assigned to this generic pathway label."
          }
        ],
        "edges": [
          {
            "subject": "sox_system",
            "predicate": "confers",
            "object": "sulfur_oxidation_trait",
            "description": "The Sox system enables lithotrophic sulfur oxidation.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.67.7.2873-2882.2001",
                "notes": "Friedrich et al. describe the Sox system as a common sulfur-oxidation mechanism."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "sulfur_oxidation_trait",
            "predicate": "oxidizes",
            "object": "hydrogen_sulfide",
            "description": "Sulfur oxidizers oxidize reduced sulfur compounds such as sulfide.",
            "evidence": [
              {
                "reference": "DOI:10.1111/j.1574-6976.2009.00187.x",
                "notes": "Ghosh & Dam review lithotrophic oxidation of reduced inorganic sulfur."
              }
            ],
            "predicate_id": "METPO:2007803"
          },
          {
            "subject": "sulfur_oxidation_trait",
            "predicate": "produces",
            "object": "sulfate",
            "description": "Complete sulfur oxidation produces sulfate.",
            "evidence": [
              {
                "reference": "DOI:10.1111/j.1574-6976.2009.00187.x",
                "notes": "Supports sulfate as the oxidized end product."
              }
            ],
            "predicate_id": "METPO:2007800"
          },
          {
            "subject": "sqr_enzyme",
            "predicate": "oxidizes",
            "object": "hydrogen_sulfide",
            "description": "SQR oxidizes sulfide to sulfane sulfur (S0/polysulfide).",
            "evidence": [
              {
                "reference": "DOI:10.3390/ijms252010962",
                "notes": "SQR oxidizing sulfide to sulfane sulfur (S0/polysulfide)."
              }
            ],
            "predicate_id": "METPO:2007803"
          },
          {
            "subject": "sqr_enzyme",
            "predicate": "produces",
            "object": "sulfane_sulfur",
            "description": "SQR produces sulfane sulfur/polysulfide from sulfide.",
            "evidence": [
              {
                "reference": "DOI:10.3390/ijms252010962",
                "notes": "SQR oxidizing sulfide to sulfane sulfur (S0/polysulfide)."
              }
            ],
            "predicate_id": "METPO:2007800"
          },
          {
            "subject": "pdo_enzyme",
            "predicate": "oxidizes",
            "object": "glutathione_persulfide",
            "description": "PDO oxidizes glutathione persulfide (GSSH).",
            "evidence": [
              {
                "reference": "DOI:10.3390/ijms252010962",
                "notes": "PDO oxidizes glutathione persulfide (GSSH); O2-dependent."
              }
            ],
            "predicate_id": "METPO:2007803"
          },
          {
            "subject": "pdo_enzyme",
            "predicate": "produces",
            "object": "sulfite",
            "description": "Persulfide dioxygenase produces sulfite (GSSH + O2 + H2O -> GSH + SO3(2-)).",
            "evidence": [
              {
                "reference": "DOI:10.3390/ijms252010962",
                "notes": "GSSH + O2 + H2O -> GSH + SO3(2-) + 2H+; oxygen-dependent."
              }
            ],
            "predicate_id": "METPO:2007800"
          },
          {
            "subject": "sulfite",
            "predicate": "reacts to form",
            "object": "thiosulfate",
            "description": "Sulfite reacts with sulfane sulfur to form thiosulfate (non-enzymatic).",
            "evidence": [
              {
                "reference": "DOI:10.3390/ijms252010962",
                "notes": "The generated sulfite can react with sulfane sulfur to form thiosulfate."
              }
            ]
          },
          {
            "subject": "sox_system",
            "predicate": "oxidizes",
            "object": "thiosulfate",
            "description": "Thiosulfate is oxidized to sulfate via the Sox system.",
            "evidence": [
              {
                "reference": "DOI:10.3390/ijms252010962",
                "notes": "Thiosulfate is then oxidized to sulfate via the Sox-system."
              }
            ],
            "predicate_id": "METPO:2007803"
          },
          {
            "subject": "tsda_enzyme",
            "predicate": "oxidizes",
            "object": "thiosulfate",
            "description": "TsdA oxidizes thiosulfate to tetrathionate (S2O32- to S4O62-).",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2024.1426584",
                "notes": "tsdA (S2O32- to S4O62-)."
              }
            ],
            "predicate_id": "METPO:2007803"
          },
          {
            "subject": "tsda_enzyme",
            "predicate": "produces",
            "object": "tetrathionate",
            "description": "TsdA produces tetrathionate from thiosulfate.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2024.1426584",
                "notes": "tsdA (S2O32- to S4O62-)."
              }
            ],
            "predicate_id": "METPO:2007800"
          },
          {
            "subject": "teth_enzyme",
            "predicate": "oxidizes",
            "object": "tetrathionate",
            "description": "TetH disproportionates/hydrolyzes tetrathionate to S0, thiosulfate and sulfate.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2024.1426584",
                "notes": "Tetrathionate generated by tsdA can be disproportionated by tetH to yield S0, thiosulfate and sulfate."
              }
            ],
            "predicate_id": "METPO:2007803"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-08-25T00:00:00-07:00",
        "curator": "codex",
        "action": "REVIEW_ONTOLOGY_GROUNDINGS",
        "changes": "Retracted CHEBI:15037 from sulfane sulfur because the identifier is absent from ChEBI release 254, does not resolve in OAK, and has no sulfane-sulfur replacement in OLS4. Retained the chemically meaningful label for future curation.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-08T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate METABOLISM trait (sulfur oxidation); round 2, sulfur-cycle gap.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-08T12:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (Sox-mediated sulfur oxidation to sulfate) with CHEBI node groundings and RO/METPO predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 9 evidence-backed generic edges (9 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:12Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 8 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000016\u00d75, METPO:2000202\u00d73).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:23:54Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0070224\u00d71, GO:0050338\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 1 causal edge(s) off enables/RO:0002327 with a TRAIT object (1 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T02:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES_PART2",
        "changes": "Re-grounded 10 causal edge(s) off microbe-domain METPO predicates onto their causal-graph counterparts (6 to oxidizes, 4 to produces), issue 301 part 2. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Each replacement is a 1:1 mirror of its source predicate that changes only the domain, so the claim each edge makes is unchanged and directions are unchanged. The replacements are proposed in proposals/metpo_traitmech_v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-24T10:30:00Z",
        "curator": "codex",
        "action": "CURATE_PROTEIN_TAXON_EXAMPLE",
        "changes": "Scoped the cross-taxon sulfur-oxidation mechanism, added a DOI-backed Thiobacillus denitrificans SQR protein example, and documented why the broad Sox, PDO, and TetH labels remain reviewed label-only nodes.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000125",
    "label": "sulfur respiration",
    "definition": "A respiration of sulfur compounds in which elemental sulfur is the terminal electron acceptor and is reduced to sulfide.",
    "definition_source": "DOI:10.1126/science.aaf4507",
    "trait_category": "METABOLISM",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000124"
    ],
    "synonyms": [
      {
        "synonym_text": "sulfur_respiration",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1126/science.aaf4507"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.3389/fmicb.2023.1108245",
        "snippet": "using sulfur as an alternative electron acceptor",
        "notes": "Zavarzina et al. analyze a natronophilic bacterium capable of reducing zero-valent sulfur during anaerobic respiration."
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-08T00:00:00Z",
        "curator": "codex",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed a DOI-backed FAPROTAX metabolic capability from proposals/metpo_traitmech_v11 after repository-wide duplicate review.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-21T20:01:04Z",
        "curator": "claude",
        "action": "RECORD_MECHANISM_KNOWLEDGE_GAP",
        "changes": "Recorded OPEN KNOWLEDGE_GAP discussion (sulfur-respiration-causal-graph-source-gap) documenting the source-limited mechanism gap for causal_graphs.",
        "llm_assisted": true
      }
    ],
    "discussions": [
      {
        "discussion_id": "sulfur-respiration-causal-graph-source-gap",
        "prompt": "Add primary literature evidence for polysulfide/elemental-sulfur reductase (PsrABC or SreABC), sulfide production, and a strain-matched canonical example before constructing causal_graphs.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "The current record carries a single 48-character snippet ('using sulfur as an alternative electron acceptor' in DOI:10.3389/fmicb.2023.1108245) without a second independent mechanistic quote to support a connected multi-edge graph.",
        "posed_by": "claude",
        "posed_date": "2026-10-21",
        "evidence": [
          {
            "reference": "DOI:10.3389/fmicb.2023.1108245",
            "supports": "PARTIAL",
            "snippet": "using sulfur as an alternative electron acceptor",
            "explanation": "Existing record-level evidence supports the high-level metabolic trait definition but does not provide multi-step enzymatic mechanism quotes for a connected causal graph."
          }
        ]
      }
    ]
  },
  {
    "identifier": "METPO:1002006",
    "label": "Syntrophy",
    "definition": "A metabolism in which the metabolism of one species is thermodynamically dependent on the removal of its products by another species.",
    "definition_source": "DOI:10.1038/nrmicro2166",
    "trait_category": "METABOLISM",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000060"
    ],
    "created_by": "Jed Dongjin Kim-Ozaeta",
    "evidence": [
      {
        "reference": "DOI:10.1038/nrmicro2166",
        "snippet": "Interspecies electron transfer is a key process",
        "notes": "Review supports hydrogen/formate-mediated electron transfer in syntrophic communities."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:863",
        "taxon_label": "Syntrophomonas wolfei",
        "note": "Type species of Syntrophomonas; original syntrophic fatty-acid oxidiser (coculture with Methanospirillum hungatei).",
        "reference": "DOI:10.1128/AEM.41.4.1029-1039.1981"
      },
      {
        "taxon_id": "NCBITaxon:335541",
        "taxon_label": "Syntrophomonas wolfei subsp. wolfei (strain DSM 2245B / Goettingen)",
        "note": "Reference-proteome strain in which Swol_1933 was identified as one of two butyryl-CoA dehydrogenases expressed during syntrophic growth on butyrate.",
        "reference": "DOI:10.1128/JB.01605-08"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "syntrophy_interspecies_electron_transfer",
        "title": "Syntrophy interspecies electron transfer mechanism",
        "description": "DOI-backed graph for product removal and electron transfer between fermenting syntrophs and methanogenic partners.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "This broad graph covers hydrogen-, formate-, and direct-electron-transfer branches that are not universal to every syntrophic partnership. The S. wolfei Swol_1933 example specifically supports syntrophic butyrate oxidation and does not establish the taxon-general DIET branch.",
        "nodes": [
          {
            "node_id": "syntrophy_trait",
            "label": "Syntrophy",
            "node_type": "TRAIT",
            "grounding": "METPO:1002006",
            "description": "Thermodynamically coupled metabolism between partner organisms."
          },
          {
            "node_id": "syntrophic_product_formation",
            "label": "syntrophic product formation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Product-forming metabolism that depends on product removal by a partner."
          },
          {
            "node_id": "methanogenic_product_consumption",
            "label": "methanogenic product consumption",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Hydrogen- or formate-consuming methanogenic partner metabolism."
          },
          {
            "node_id": "molecular_hydrogen",
            "label": "molecular hydrogen",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:18276",
            "description": "Diffusible interspecies electron carrier."
          },
          {
            "node_id": "formate",
            "label": "formate",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:15740",
            "description": "Diffusible interspecies electron carrier."
          },
          {
            "node_id": "low_hydrogen_condition",
            "label": "low hydrogen condition",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Product concentration state that permits otherwise unfavorable syntrophic metabolism."
          },
          {
            "node_id": "methanogenesis",
            "label": "methanogenesis",
            "node_type": "PATHWAY",
            "grounding": "METPO:1000844",
            "description": "Hydrogen- or formate-consuming methane-producing pathway."
          },
          {
            "node_id": "interspecies_hydrogen_transfer",
            "label": "interspecies hydrogen transfer",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "H2-mediated interspecies electron transfer (MIET) between syntrophic partners."
          },
          {
            "node_id": "interspecies_formate_transfer",
            "label": "interspecies formate transfer",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Formate-mediated interspecies electron transfer between syntrophic partners."
          },
          {
            "node_id": "low_hydrogen_partial_pressure",
            "label": "low hydrogen partial pressure",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Extremely low H2 partial pressure required for thermodynamic feasibility of MIET."
          },
          {
            "node_id": "butyryl_coa_dehydrogenase",
            "label": "butyryl-CoA dehydrogenase Swol_1933",
            "node_type": "GENE_OR_PROTEIN",
            "grounding": "GO:0004085",
            "description": "Flavoprotein that oxidizes butanoyl-CoA to crotonyl-CoA during the beta-oxidation branch of syntrophic butyrate metabolism.",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:Q0AVM4",
                "protein_label": "Butyryl-CoA dehydrogenase Swol_1933",
                "gene_symbol": "Swol_1933",
                "taxon_id": "NCBITaxon:335541",
                "taxon_label": "Syntrophomonas wolfei subsp. wolfei (strain DSM 2245B / Goettingen)",
                "entry_status": "REVIEWED",
                "proteome_id": "UP000001968",
                "retrieved_on": "2026-10-22",
                "entry_version": 95,
                "sequence_version": 1,
                "role": "One of the experimentally identified butyryl-CoA dehydrogenases active during syntrophic butyrate oxidation; this example is not a hydrogenase or a marker for every syntrophic metabolism.",
                "evidence": [
                  {
                    "reference": "DOI:10.1128/JB.01605-08",
                    "snippet": "peptide mass fingerprinting revealed two Bcd proteins",
                    "notes": "The primary study maps one purified approximately 65-kDa protein to Swol_1933 during syntrophic growth on butyrate; UniProtKB Q0AVM4 is the reviewed protein entry for that locus and strain."
                  }
                ]
              }
            ]
          },
          {
            "node_id": "formate_dehydrogenase_complex",
            "label": "formate dehydrogenase complex",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Enzyme complex producing/consuming formate in syntrophic formate transfer.",
            "grounding": "GO:0009326"
          },
          {
            "node_id": "hydrogenase_complex",
            "label": "hydrogenase complex",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Enzyme complex producing/consuming H2 in syntrophic hydrogen transfer.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Hydrogenases used in syntrophy span multiple unrelated enzyme families and multisubunit architectures; this cross-taxon node does not identify one exact complex or family."
          },
          {
            "node_id": "direct_interspecies_electron_transfer",
            "label": "direct interspecies electron transfer",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "DIET: electron transfer via conductive structures without soluble H2/formate intermediates."
          },
          {
            "node_id": "hydrogen_pressure_inhibition",
            "label": "hydrogen pressure inhibition",
            "node_type": "STATE",
            "description": "Thermodynamic inhibition of syntrophic oxidation by elevated H2 partial pressure."
          },
          {
            "node_id": "conductive_pili",
            "label": "conductive pili (e-pili)",
            "node_type": "CELLULAR_LOCALIZATION",
            "description": "Electrically conductive pili that serve as a DIET conduit."
          },
          {
            "node_id": "multiheme_cytochromes",
            "label": "multiheme c-type cytochromes",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Outer-surface multiheme c-type cytochromes mediating DIET.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Multiheme c-type cytochromes comprise many non-equivalent families, and this broad DIET claim does not resolve a taxon-specific protein family."
          }
        ],
        "edges": [
          {
            "subject": "syntrophy_trait",
            "predicate": "requires partner interaction",
            "object": "methanogenic_product_consumption",
            "description": "Syntrophic metabolism depends on a partner that consumes products.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2166",
                "snippet": "metabolic abilities of their syntrophic partner",
                "notes": "Supports partner dependence in syntrophic communities."
              }
            ]
          },
          {
            "subject": "syntrophic_product_formation",
            "predicate": "transfers electrons via",
            "object": "molecular_hydrogen",
            "description": "Hydrogen can carry reducing equivalents between syntrophic partners.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2166",
                "snippet": "Hydrogen and formate are key components",
                "notes": "Supports hydrogen as a key interspecies electron-transfer carrier."
              }
            ],
            "predicate_id": "METPO:2007600"
          },
          {
            "subject": "syntrophic_product_formation",
            "predicate": "transfers electrons via",
            "object": "formate",
            "description": "Formate can carry reducing equivalents between syntrophic partners.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2166",
                "snippet": "transfer of hydrogen and formate",
                "notes": "Supports formate-mediated interspecies electron transfer."
              }
            ],
            "predicate_id": "METPO:2007600"
          },
          {
            "subject": "methanogenic_product_consumption",
            "predicate": "consumes",
            "object": "molecular_hydrogen",
            "description": "Methanogens keep hydrogen concentrations low enough for syntrophic metabolism.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2166",
                "snippet": "low hydrogen concentrations, which are created by the methanogen",
                "notes": "Supports product removal by methanogens as a thermodynamic driver."
              }
            ],
            "predicate_id": "biolink:consumes"
          },
          {
            "subject": "methanogenic_product_consumption",
            "predicate": "creates",
            "object": "low_hydrogen_condition",
            "description": "Hydrogen consumption creates the product-removal condition needed by the syntroph.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2166",
                "snippet": "live at the limits of what is thermodynamically possible",
                "notes": "Supports the thermodynamic constraint that product removal relieves."
              }
            ],
            "predicate_id": "biolink:produces"
          },
          {
            "subject": "molecular_hydrogen",
            "predicate": "participates in",
            "object": "methanogenesis",
            "description": "Hydrogen can feed methanogenesis in syntrophic communities.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2166",
                "snippet": "syntrophic methanogenic communities",
                "notes": "Supports hydrogen-linked electron flow into methanogenic partners."
              }
            ],
            "predicate_id": "biolink:participates_in"
          },
          {
            "subject": "butyryl_coa_dehydrogenase",
            "predicate": "participates in",
            "object": "syntrophic_product_formation",
            "description": "Swol_1933 catalyzes the butyryl-CoA oxidation step of syntrophic butyrate degradation in S. wolfei.",
            "evidence": [
              {
                "reference": "DOI:10.1128/JB.01605-08",
                "snippet": "syntrophic oxidation of butyrate in S. wolfei involves butyryl-CoA dehydrogenases",
                "notes": "Purified Bcd activity and peptide mass fingerprinting identified Swol_1933 in butyrate-grown cells, directly supporting this strain-specific mechanistic edge."
              }
            ],
            "predicate_id": "biolink:participates_in"
          },
          {
            "subject": "low_hydrogen_partial_pressure",
            "predicate": "enables",
            "object": "interspecies_hydrogen_transfer",
            "description": "H2-mediated transfer is thermodynamically feasible only at extremely low H2 partial pressure.",
            "evidence": [
              {
                "reference": "DOI:10.3390/fermentation9050467",
                "notes": "H2-mediated transfer thermodynamically feasible only when H2 < 10^-4 atm."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "interspecies_hydrogen_transfer",
            "predicate": "mediates",
            "object": "syntrophy_trait",
            "description": "Interspecies hydrogen transfer is a core mechanistic sub-process of syntrophy.",
            "evidence": [
              {
                "reference": "DOI:10.3390/fermentation9050467",
                "notes": "H2-mediated MIET (IHT) is a main interspecies electron transfer mode relevant to syntrophy."
              }
            ]
          },
          {
            "subject": "interspecies_formate_transfer",
            "predicate": "mediates",
            "object": "syntrophy_trait",
            "description": "Interspecies formate transfer is a core mechanistic sub-process of syntrophy.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuab057",
                "notes": "Interspecies formate transfer is one of three IET mechanisms in syntrophic propionate oxidation."
              }
            ]
          },
          {
            "subject": "formate_dehydrogenase_complex",
            "predicate": "mediates",
            "object": "interspecies_formate_transfer",
            "description": "Formate dehydrogenases provide the enzymatic basis for formate production/consumption in syntrophy.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s40168-020-00885-y",
                "notes": "Formate dehydrogenases and formate transporters expressed by FA-degrading syntrophic species."
              }
            ]
          },
          {
            "subject": "hydrogenase_complex",
            "predicate": "mediates",
            "object": "interspecies_hydrogen_transfer",
            "description": "Hydrogenases provide the enzymatic basis for H2 production/consumption in syntrophy.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41396-023-01504-y",
                "notes": "Hydrogen-mediated transfer supported by expression of hydrogenases in syntrophic communities."
              }
            ]
          },
          {
            "subject": "direct_interspecies_electron_transfer",
            "predicate": "bypasses",
            "object": "hydrogen_pressure_inhibition",
            "description": "DIET can overcome inhibition by hydrogen pressure, enabling syntrophy without soluble carriers.",
            "evidence": [
              {
                "reference": "DOI:10.3390/fermentation9100884",
                "notes": "DIET can overcome the inhibition of hydrogen pressure and formate concentration."
              }
            ]
          },
          {
            "subject": "conductive_pili",
            "predicate": "mediates",
            "object": "direct_interspecies_electron_transfer",
            "description": "Conductive pili (e-pili) are a canonical DIET conduit.",
            "evidence": [
              {
                "reference": "DOI:10.1134/S0026261720020101",
                "notes": "DIET occurs via conductive pili (e-pili)."
              }
            ]
          },
          {
            "subject": "multiheme_cytochromes",
            "predicate": "mediates",
            "object": "direct_interspecies_electron_transfer",
            "description": "Outer-surface multiheme c-type cytochromes are a core DIET redox conduit.",
            "evidence": [
              {
                "reference": "DOI:10.3390/life14050591",
                "notes": "DIET operates via outer-surface c-type cytochromes."
              }
            ]
          },
          {
            "subject": "direct_interspecies_electron_transfer",
            "predicate": "mediates",
            "object": "syntrophy_trait",
            "description": "Direct interspecies electron transfer is one mechanism that can mediate syntrophic growth without diffusible hydrogen or formate.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2016.00236",
                "snippet": "Direct interspecies electron transfer (DIET) has been recognized as an alternative to interspecies H2 transfer as a mechanism for syntrophic growth",
                "notes": "Verified against the freely available primary-study abstract; the edge does not assert that DIET occurs in every syntrophic pair."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.936190+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-08T00:00:00-07:00",
        "curator": "codex",
        "action": "ADDED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed causal graph for hydrogen/formate interspecies electron transfer and methanogenic product removal in syntrophy.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T05:49:24Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:consumes\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-26T05:00:48Z",
        "curator": "claude",
        "action": "RENAME_PREDICATE_LABELS",
        "changes": "Renamed 1 causal-edge predicate label(s) to align with existing groundings: input to \u2192 participates in \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-26T05:00:50Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:participates_in\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-13T21:03:26Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:produces\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-14T07:26:19Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007600\u00d72).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 8 evidence-backed generic edges (9 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:12Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:23:54Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0009326\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-24T10:35:00Z",
        "curator": "codex",
        "action": "CURATE_PROTEIN_TAXON_EXAMPLE",
        "changes": "Scoped the cross-taxon syntrophy graph, replaced the canonical species URL with its DOI, added the S. wolfei DSM 2245B canonical strain and reviewed Swol_1933 protein example, added its evidence-backed butyrate-oxidation edge, and dispositioned broad hydrogenase and multiheme-cytochrome labels.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T08:20:00Z",
        "curator": "codex",
        "action": "CONNECT_CAUSAL_GRAPH_COMPONENTS",
        "changes": "Resolved issue #183 graph fragmentation (2 components to 1) using 1 public-source, verbatim-snippet-backed connector(s). No paid research service was called.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-22T01:35:00Z",
        "curator": "claude",
        "action": "REFRESH_UNIPROT_ENTRY_VERSION",
        "changes": "Refreshed UniProtKB entry_version against live UniProt REST on 2026-10-22: UniProtKB:Q0AVM4 (94 -> 95 on butyryl_coa_dehydrogenase).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000200",
    "label": "tetrathionate respiration",
    "definition": "An anaerobic respiration in which an organism uses tetrathionate as the terminal electron acceptor and reduces it to thiosulfate for energy conservation.",
    "definition_source": "DOI:10.1046/j.1365-2958.1999.01345.x",
    "trait_category": "METABOLISM",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000802"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1046/j.1365-2958.1999.01345.x",
        "snippet": "A range of bacteria are able to use tetrathionate as a terminal respiratory electron acceptor",
        "notes": "Hensel et al. support tetrathionate as an organism-level terminal electron acceptor for anaerobic respiration."
      },
      {
        "reference": "DOI:10.1046/j.1365-2958.1999.01345.x",
        "snippet": "ttrA, ttrB and ttrC are the tetrathionate reductase structural genes",
        "notes": "Hensel et al. identify the TtrA/TtrB/TtrC structural genes for Salmonella tetrathionate reductase."
      },
      {
        "reference": "DOI:10.1128/JB.183.8.2463-2475.2001",
        "snippet": "Salmonella reduces tetrathionate to thiosulfate",
        "notes": "Price-Carter et al. support thiosulfate as the reduction product of Salmonella tetrathionate respiration."
      },
      {
        "reference": "DOI:10.1128/JB.183.8.2463-2475.2001",
        "snippet": "the electron acceptor tetrathionate, which allows Salmonella to grow anaerobically on ethanolamine or 1,2-propanediol",
        "notes": "Price-Carter et al. support tetrathionate-dependent anaerobic growth in Salmonella enterica serovar Typhimurium LT2."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:99287",
        "taxon_label": "Salmonella enterica subsp. enterica serovar Typhimurium str. LT2",
        "note": "Price-Carter et al. showed that the electron acceptor tetrathionate supports anaerobic growth of Salmonella enterica serovar Typhimurium LT2 on ethanolamine or 1,2-propanediol.",
        "reference": "DOI:10.1128/JB.183.8.2463-2475.2001"
      }
    ],
    "discussions": [
      {
        "discussion_id": "tetrathionate-respiration-xref-gap",
        "prompt": "Resolve an exact external ontology class for organism-level tetrathionate respiration before adding a TraitRecord xref.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "The pinned METPO snapshot has no active organism-level class for tetrathionate respiration. Candidate EC, Rhea, and protein-family terms for tetrathionate reductase or the TtrA/TtrB/TtrC complex are narrower than the whole-organism anaerobic respiration phenotype.",
        "posed_by": "codex",
        "posed_date": "2026-09-15"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-15T02:26:41Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted tetrathionate respiration as a DOI-backed anaerobic respiration TraitRecord after a repository-wide duplicate review covering ignored and hidden files; the local METPO snapshot has no exact class and the replacement placeholder is reserved in proposals/metpo_traitmech_v77.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000126",
    "label": "thiosulfate respiration",
    "definition": "A respiration of sulfur compounds in which thiosulfate is the terminal electron acceptor.",
    "definition_source": "DOI:10.1126/science.aaf4507",
    "trait_category": "METABOLISM",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000124"
    ],
    "synonyms": [
      {
        "synonym_text": "thiosulfate_respiration",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1126/science.aaf4507"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.3389/fmicb.2023.1108245",
        "snippet": "sulfur- and thiosulfate reducing type strain",
        "notes": "Zavarzina et al. analyze thiosulfate respiration in Dethiobacter alkaliphilus as an anaerobic energy metabolism."
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-08T00:00:00Z",
        "curator": "codex",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed a DOI-backed FAPROTAX metabolic capability from proposals/metpo_traitmech_v11 after repository-wide duplicate review.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-21T20:01:04Z",
        "curator": "claude",
        "action": "RECORD_MECHANISM_KNOWLEDGE_GAP",
        "changes": "Recorded OPEN KNOWLEDGE_GAP discussion (thiosulfate-respiration-causal-graph-source-gap) documenting the source-limited mechanism gap for causal_graphs.",
        "llm_assisted": true
      }
    ],
    "discussions": [
      {
        "discussion_id": "thiosulfate-respiration-causal-graph-source-gap",
        "prompt": "Add primary literature evidence for thiosulfate reductase (PhsABC), sulfite/sulfide products, and a strain-matched canonical example before constructing causal_graphs.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "The current record carries a single 45-character snippet ('sulfur- and thiosulfate reducing type strain' in DOI:10.3389/fmicb.2023.1108245) without enzymatic or product-level quotes needed for a multi-edge causal graph.",
        "posed_by": "claude",
        "posed_date": "2026-10-21",
        "evidence": [
          {
            "reference": "DOI:10.3389/fmicb.2023.1108245",
            "supports": "PARTIAL",
            "snippet": "sulfur- and thiosulfate reducing type strain",
            "explanation": "Existing record-level evidence supports the high-level metabolic trait definition but does not provide multi-step enzymatic mechanism quotes for a connected causal graph."
          }
        ]
      }
    ]
  },
  {
    "identifier": "traitmech:000023",
    "label": "3-hydroxypropionate bicycle",
    "definition": "An autotrophic carbon-fixation pathway in which two molecules of bicarbonate are fixed via 3-hydroxypropionate and converted to glyoxylate and pyruvate. It is characteristic of the filamentous anoxygenic phototroph Chloroflexus aurantiacus.",
    "definition_source": "DOI:10.1128/AEM.02473-10",
    "trait_category": "METABOLISM",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "traitmech:000019"
    ],
    "synonyms": [
      {
        "synonym_text": "3-hydroxypropionate cycle",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1128/AEM.02473-10"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1128/AEM.02473-10",
        "notes": "Berg review describes the 3-hydroxypropionate bicycle and its association with Chloroflexus."
      },
      {
        "reference": "DOI:10.1146/annurev-marine-120709-142712",
        "notes": "H\u00fcgler & Sievert include the 3-hydroxypropionate pathway among autotrophic carbon-fixation strategies."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1108",
        "taxon_label": "Chloroflexus aurantiacus",
        "note": "Where the 3-hydroxypropionate bicycle of autotrophic CO2 fixation was discovered (filamentous anoxygenic phototroph).",
        "reference": "DOI:10.1073/pnas.0908356106"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "three_hp_bicycle_chloroflexus",
        "title": "3-hydroxypropionate bicycle fixes bicarbonate in Chloroflexus",
        "description": "Evidence-backed causal sketch linking bicarbonate fixation via 3-hydroxypropionate to glyoxylate and pyruvate in Chloroflexus aurantiacus.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "The graph represents the experimentally completed C. aurantiacus 3HP bicycle. The reviewed mcl/MMC-lyase example supports the terminal trifunctional cleavage node; the other diagnostic multifunctional enzymes remain separately scoped.",
        "nodes": [
          {
            "node_id": "three_hp_bicycle_trait",
            "label": "3-hydroxypropionate bicycle",
            "node_type": "TRAIT",
            "grounding": "traitmech:000023",
            "description": "Autotrophic carbon-fixation bicycle via 3-hydroxypropionate."
          },
          {
            "node_id": "bicarbonate",
            "label": "hydrogencarbonate",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:17544",
            "description": "Inorganic carbon substrate fixed by the bicycle."
          },
          {
            "node_id": "carbon_fixation_process",
            "label": "carbon fixation",
            "node_type": "BIOLOGICAL_PROCESS",
            "grounding": "GO:0015977",
            "description": "Conversion of inorganic carbon into organic compounds."
          },
          {
            "node_id": "acetyl_coa_carboxylase",
            "label": "acetyl-CoA carboxylase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "EC 6.4.1.2; carboxylates acetyl-CoA to malonyl-CoA using bicarbonate and ATP.",
            "grounding": "GO:0003989"
          },
          {
            "node_id": "malonyl_coa",
            "label": "malonyl-CoA",
            "node_type": "CHEMICAL",
            "description": "Product of acetyl-CoA carboxylation; substrate for malonyl-CoA reductase."
          },
          {
            "node_id": "propionyl_coa_carboxylase",
            "label": "propionyl-CoA carboxylase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "EC 6.4.1.3; carboxylates propionyl-CoA to (2S)-methylmalonyl-CoA using bicarbonate and ATP.",
            "grounding": "GO:0004658"
          },
          {
            "node_id": "methylmalonyl_coa",
            "label": "(2S)-methylmalonyl-CoA",
            "node_type": "CHEMICAL",
            "description": "Product of propionyl-CoA carboxylation in the second carboxylation step."
          },
          {
            "node_id": "malonyl_coa_reductase",
            "label": "malonyl-CoA reductase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "EC 1.2.1.75; diagnostic enzyme reducing malonyl-CoA to 3-hydroxypropionate.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "The Chloroflexus enzyme is a bifunctional fusion, while current GO and InterPro matches are broader oxidoreductase domains rather than an exact malonyl-CoA-reductase family term."
          },
          {
            "node_id": "three_hydroxypropionate",
            "label": "3-hydroxypropionate",
            "node_type": "CHEMICAL",
            "description": "Signature intermediate of the bicycle, produced by malonyl-CoA reductase.",
            "grounding": "CHEBI:16510"
          },
          {
            "node_id": "propionyl_coa_synthase",
            "label": "propionyl-CoA synthase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Multifunctional enzyme converting 3-hydroxypropionate to propionyl-CoA.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Propionyl-CoA synthase is a multifunctional enzyme containing several catalytic modules; no single verified GO or InterPro term denotes the complete fusion represented here."
          },
          {
            "node_id": "propionyl_coa",
            "label": "propionyl-CoA",
            "node_type": "CHEMICAL",
            "description": "Product of propionyl-CoA synthase; substrate for the second carboxylation.",
            "grounding": "CHEBI:15539"
          },
          {
            "node_id": "mmc_lyase",
            "label": "malyl-CoA/beta-methylmalyl-CoA/citramalyl-CoA lyase (MMC lyase)",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Multifunctional malyl-CoA/citramalyl-CoA lyase cleaving citramalyl-CoA to pyruvate and acetyl-CoA.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "The node denotes three activities of one multifunctional enzyme; available GO terms cover individual reactions and the InterPro family also contains narrower citrate-lyase-beta/Mcl proteins.",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:S5N020",
                "protein_label": "Malyl-CoA/beta-methylmalyl-CoA/citramalyl-CoA lyase",
                "gene_symbol": "mcl",
                "taxon_id": "NCBITaxon:1108",
                "taxon_label": "Chloroflexus aurantiacus",
                "entry_status": "REVIEWED",
                "retrieved_on": "2026-08-24",
                "entry_version": 45,
                "sequence_version": 1,
                "role": "Trifunctional MMC lyase catalyzing malyl-CoA cleavage, beta-methylmalyl-CoA formation, and citramalyl-CoA cleavage in the C. aurantiacus bicycle.",
                "evidence": [
                  {
                    "reference": "DOI:10.1073/pnas.0908356106",
                    "snippet": "(S)-Citramalyl-CoA is cleaved into acetyl-CoA and pyruvate by a tri-functional lyase",
                    "notes": "The primary pathway-completion study identifies mcl as the trifunctional MMC lyase. UniProtKB S5N020 is the reviewed mcl entry from C. aurantiacus."
                  }
                ]
              }
            ]
          },
          {
            "node_id": "pyruvate",
            "label": "pyruvate",
            "node_type": "CHEMICAL",
            "description": "Net organic carbon output of the bicycle.",
            "grounding": "CHEBI:15361"
          },
          {
            "node_id": "acetyl_coa",
            "label": "acetyl-CoA",
            "node_type": "CHEMICAL",
            "description": "Co-product released during the cycle and regenerated as starting carboxylation substrate."
          }
        ],
        "edges": [
          {
            "subject": "bicarbonate",
            "predicate": "fixed by",
            "object": "three_hp_bicycle_trait",
            "description": "Two molecules of bicarbonate are fixed per cycle turn.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.02473-10",
                "notes": "Berg describes the 3-hydroxypropionate bicycle in Chloroflexus."
              }
            ],
            "predicate_id": "METPO:2007404"
          },
          {
            "subject": "three_hp_bicycle_trait",
            "predicate": "contributes to",
            "object": "carbon_fixation_process",
            "description": "The bicycle is one of the recognized autotrophic CO2-fixation pathways.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-marine-120709-142712",
                "notes": "H\u00fcgler & Sievert include the 3-hydroxypropionate pathway among autotrophic carbon-fixation strategies."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "acetyl_coa_carboxylase",
            "predicate": "causally upstream of",
            "object": "malonyl_coa",
            "description": "Acetyl-CoA carboxylase converts acetyl-CoA and bicarbonate to malonyl-CoA at the expense of ATP.",
            "evidence": [
              {
                "reference": "DOI:10.17192/z2022.0467",
                "notes": "acetyl-CoA carboxylase (EC 6.4.1.2) converts acetyl-CoA and bicarbonate to malonyl-CoA."
              }
            ]
          },
          {
            "subject": "propionyl_coa_carboxylase",
            "predicate": "causally upstream of",
            "object": "methylmalonyl_coa",
            "description": "Propionyl-CoA carboxylase converts propionyl-CoA and bicarbonate to (2S)-methylmalonyl-CoA at the expense of ATP.",
            "evidence": [
              {
                "reference": "DOI:10.17192/z2022.0467",
                "notes": "propionyl-CoA carboxylase (EC 6.4.1.3) converts propionyl-CoA and bicarbonate to (2S)-methylmalonyl-CoA."
              }
            ]
          },
          {
            "subject": "malonyl_coa_reductase",
            "predicate": "causally upstream of",
            "object": "three_hydroxypropionate",
            "description": "Malonyl-CoA reductase reduces malonyl-CoA to 3-hydroxypropionate; central diagnostic enzyme.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-marine-120709-142712",
                "notes": "malonyl-CoA reductase reducing malonyl-CoA to 3-hydroxypropionate."
              }
            ]
          },
          {
            "subject": "propionyl_coa_synthase",
            "predicate": "causally upstream of",
            "object": "propionyl_coa",
            "description": "Propionyl-CoA synthase converts 3-hydroxypropionate to propionyl-CoA.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-marine-120709-142712",
                "notes": "propionyl-CoA synthase converting 3-hydroxypropionate to propionyl-CoA."
              }
            ]
          },
          {
            "subject": "mmc_lyase",
            "predicate": "causally upstream of",
            "object": "pyruvate",
            "description": "MMC lyase cleaves citramalyl-CoA to pyruvate and acetyl-CoA.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-marine-120709-142712",
                "notes": "cleavage of citramalyl-CoA to pyruvate and acetyl-CoA."
              }
            ]
          },
          {
            "subject": "mmc_lyase",
            "predicate": "causally upstream of",
            "object": "acetyl_coa",
            "description": "MMC lyase cleavage also yields acetyl-CoA alongside pyruvate.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-marine-120709-142712",
                "notes": "cleavage of citramalyl-CoA to pyruvate and acetyl-CoA."
              }
            ]
          },
          {
            "subject": "three_hp_bicycle_trait",
            "predicate": "has output",
            "object": "pyruvate",
            "description": "Overall the bicycle produces one pyruvate from three bicarbonates.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-marine-120709-142712",
                "notes": "producing one pyruvate from three bicarbonates."
              }
            ]
          },
          {
            "subject": "acetyl_coa_carboxylase",
            "predicate": "contributes to",
            "object": "three_hp_bicycle_trait",
            "description": "Acetyl-CoA carboxylase is an enzyme of the 3HP bicycle.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.02473-10",
                "snippet": "The 3-hydroxypropionate (Fuchs-Holo) bi-cycle. Enzymes: 1, acetyl-CoA carboxylase",
                "notes": "Verified against the public PMC figure caption."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "malonyl_coa_reductase",
            "predicate": "contributes to",
            "object": "three_hp_bicycle_trait",
            "description": "Malonyl-CoA reductase is an enzyme of the 3HP bicycle.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.02473-10",
                "snippet": "Enzymes: 1, acetyl-CoA carboxylase; 2, malonyl-CoA reductase",
                "notes": "Verified against the public PMC figure caption."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "propionyl_coa_synthase",
            "predicate": "contributes to",
            "object": "three_hp_bicycle_trait",
            "description": "Propionyl-CoA synthase is an enzyme of the 3HP bicycle.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.02473-10",
                "snippet": "Enzymes: 1, acetyl-CoA carboxylase; 2, malonyl-CoA reductase; 3, propionyl-CoA synthase",
                "notes": "Verified against the public PMC figure caption."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "propionyl_coa_carboxylase",
            "predicate": "contributes to",
            "object": "three_hp_bicycle_trait",
            "description": "Propionyl-CoA carboxylase is an enzyme of the 3HP bicycle.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.02473-10",
                "snippet": "malonyl-CoA reductase; 3, propionyl-CoA synthase; 4, propionyl-CoA carboxylase",
                "notes": "Verified against the public PMC figure caption."
              }
            ],
            "predicate_id": "RO:0002326"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-30T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate METABOLISM trait (3-hydroxypropionate bicycle); sub-variant of carbon fixation.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-10T14:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (3HP bicycle bicarbonate fixation) with CHEBI/GO node groundings and RO/METPO predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 7 evidence-backed generic edges (11 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:33Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 3 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:16510\u00d71, CHEBI:15539\u00d71, CHEBI:15361\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-26T07:15:19Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 3 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A059L760\u00d71, UniProtKB:A0A024E6S7\u00d71, UniProtKB:Q6QQP7\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:21:11Z",
        "curator": "claude",
        "action": "RETRACT_DEAD_UNIPROT_GROUNDINGS",
        "changes": "Retracted 2 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:23:54Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0003989\u00d71, GO:0004658\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-22T04:26:15Z",
        "curator": "codex",
        "action": "REVIEW_UNIPROT_INSTANCE_GROUNDINGS",
        "changes": "Reviewed 1 organism-specific UniProtKB grounding(s): replaced 0 with taxon-agnostic GO/InterPro terms and retracted 1 to label-only where no exact semantic term was supported (docs/GROUNDING_POLICY.md).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-24T09:45:00Z",
        "curator": "codex",
        "action": "CURATE_PROTEIN_TAXON_EXAMPLE",
        "changes": "Scoped the C. aurantiacus 3HP bicycle, added a DOI-backed reviewed mcl/MMC-lyase example, and documented the multifunctional MCR, PCS, and MMC-lyase nodes as reviewed label-only where no single exact semantic term represents each fusion.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T09:00:00Z",
        "curator": "codex",
        "action": "CONNECT_CAUSAL_GRAPH_COMPONENTS",
        "changes": "Resolved issue #183 graph fragmentation (5 components to 1) using 4 public-source, verbatim-snippet-backed connector(s). No paid research service was called.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000024",
    "label": "3-hydroxypropionate/4-hydroxybutyrate cycle",
    "definition": "An autotrophic carbon-fixation pathway that fixes two molecules of bicarbonate per turn via 3-hydroxypropionate and 4-hydroxybutyrate intermediates. It operates in aerobic and microaerophilic Crenarchaeota such as Sulfolobus and Metallosphaera.",
    "definition_source": "DOI:10.1126/science.1149976",
    "trait_category": "METABOLISM",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "traitmech:000019"
    ],
    "synonyms": [
      {
        "synonym_text": "3HP/4HB cycle",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1126/science.1149976"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1126/science.1149976",
        "notes": "Berg et al. described the 3-hydroxypropionate/4-hydroxybutyrate autotrophic CO2-assimilation pathway in Archaea (Sulfolobales)."
      },
      {
        "reference": "DOI:10.1128/AEM.02473-10",
        "notes": "Berg review situates the 3HP/4HB cycle among the six recognized autotrophic carbon-fixation pathways."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:43687",
        "taxon_label": "Metallosphaera sedula",
        "note": "Thermoacidophilic crenarchaeon where the 3-hydroxypropionate/4-hydroxybutyrate CO2-fixation cycle was characterized.",
        "reference": "DOI:10.1126/science.1149976"
      },
      {
        "taxon_id": "NCBITaxon:399549",
        "taxon_label": "Metallosphaera sedula DSM 5348",
        "note": "Reference strain used to map the three carboxylase components and Msed_1321 4-hydroxybutyryl-CoA dehydratase in biochemical reconstruction of the cycle.",
        "reference": "DOI:10.1128/AEM.04146-13"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "three_hp_four_hb_sulfolobales",
        "title": "3HP/4HB cycle fixes bicarbonate in aerobic Crenarchaeota",
        "description": "Evidence-backed causal sketch linking bicarbonate fixation via 3-hydroxypropionate and 4-hydroxybutyrate intermediates in Sulfolobales.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "The graph represents the experimentally characterized M. sedula 3HP/4HB cycle. Its bifunctional carboxylase is a three-component complex, so each component is recorded separately rather than treating one accession as the complete enzyme.",
        "nodes": [
          {
            "node_id": "three_hp_four_hb_trait",
            "label": "3-hydroxypropionate/4-hydroxybutyrate cycle",
            "node_type": "TRAIT",
            "grounding": "traitmech:000024",
            "description": "Archaeal autotrophic carbon-fixation cycle."
          },
          {
            "node_id": "bicarbonate",
            "label": "hydrogencarbonate",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:17544",
            "description": "Inorganic carbon substrate fixed by the cycle."
          },
          {
            "node_id": "carbon_fixation_process",
            "label": "carbon fixation",
            "node_type": "BIOLOGICAL_PROCESS",
            "grounding": "GO:0015977",
            "description": "Conversion of inorganic carbon into organic compounds."
          },
          {
            "node_id": "acetyl_coa",
            "label": "acetyl-CoA",
            "node_type": "CHEMICAL",
            "description": "Central product/regenerated CoA-thioester of the cycle."
          },
          {
            "node_id": "succinyl_coa",
            "label": "succinyl-CoA",
            "node_type": "CHEMICAL",
            "description": "Central CoA-thioester intermediate of the 3HP/4HB cycle."
          },
          {
            "node_id": "four_hydroxybutyrate",
            "label": "4-hydroxybutyrate",
            "node_type": "CHEMICAL",
            "description": "Defining 4-hydroxybutyrate intermediate of the cycle.",
            "grounding": "CHEBI:16724"
          },
          {
            "node_id": "crotonyl_coa",
            "label": "crotonyl-CoA",
            "node_type": "CHEMICAL",
            "description": "CoA-thioester intermediate formed by 4-hydroxybutyryl-CoA dehydration."
          },
          {
            "node_id": "four_hydroxybutyryl_coa",
            "label": "4-hydroxybutyryl-CoA",
            "node_type": "CHEMICAL",
            "description": "Activated CoA-thioester of 4-hydroxybutyrate.",
            "grounding": "CHEBI:28522"
          },
          {
            "node_id": "nadph",
            "label": "NADPH",
            "node_type": "CHEMICAL",
            "description": "Reducing cofactor consumed by reductive steps of the cycle.",
            "grounding": "CHEBI:16474"
          },
          {
            "node_id": "acetyl_propionyl_coa_carboxylase",
            "label": "acetyl-CoA/propionyl-CoA carboxylase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Primary carboxylase fixing inorganic carbon in the cycle.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "This node denotes the complete archaeal three-component bifunctional carboxylase; available GO terms describe catalytic activities or subunits rather than this exact complex.",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:A4YD22",
                "protein_label": "Biotin carboxylase",
                "gene_symbol": "Msed_0147",
                "taxon_id": "NCBITaxon:399549",
                "taxon_label": "Metallosphaera sedula DSM 5348",
                "entry_status": "UNREVIEWED",
                "proteome_id": "UP000000242",
                "retrieved_on": "2026-08-24",
                "entry_version": 93,
                "sequence_version": 1,
                "role": "Alpha component (biotin carboxylase) of the three-component acetyl-CoA/propionyl-CoA carboxylase; this accession is not the complete enzyme.",
                "evidence": [
                  {
                    "reference": "DOI:10.1128/AEM.04146-13",
                    "snippet": "Acetyl-CoA/propionyl-CoA carboxylase Msed_0147, Msed_0148, Msed_1375",
                    "notes": "The primary M. sedula pathway reconstruction maps all three loci to the bifunctional carboxylase. UniProtKB A4YD22 is the Msed_0147 component from the reference proteome."
                  }
                ]
              },
              {
                "uniprot_id": "UniProtKB:A4YD23",
                "protein_label": "Biotin carboxyl carrier protein",
                "gene_symbol": "Msed_0148",
                "taxon_id": "NCBITaxon:399549",
                "taxon_label": "Metallosphaera sedula DSM 5348",
                "entry_status": "UNREVIEWED",
                "proteome_id": "UP000000242",
                "retrieved_on": "2026-08-24",
                "entry_version": 75,
                "sequence_version": 1,
                "role": "Biotin-carboxyl-carrier component of the three-component acetyl-CoA/propionyl-CoA carboxylase; this accession is not the complete enzyme.",
                "evidence": [
                  {
                    "reference": "DOI:10.1128/AEM.04146-13",
                    "snippet": "Acetyl-CoA/propionyl-CoA carboxylase Msed_0147, Msed_0148, Msed_1375",
                    "notes": "The primary M. sedula pathway reconstruction maps all three loci to the bifunctional carboxylase. UniProtKB A4YD23 is the Msed_0148 component from the reference proteome."
                  }
                ]
              },
              {
                "uniprot_id": "UniProtKB:A4YGI1",
                "protein_label": "Propionyl-CoA carboxylase beta chain",
                "gene_symbol": "Msed_1375",
                "taxon_id": "NCBITaxon:399549",
                "taxon_label": "Metallosphaera sedula DSM 5348",
                "entry_status": "UNREVIEWED",
                "proteome_id": "UP000000242",
                "retrieved_on": "2026-10-22",
                "entry_version": 86,
                "sequence_version": 1,
                "role": "Gamma carboxyltransferase component of the three-component acetyl-CoA/propionyl-CoA carboxylase; this accession is not the complete enzyme.",
                "evidence": [
                  {
                    "reference": "DOI:10.1128/AEM.04146-13",
                    "snippet": "Acetyl-CoA/propionyl-CoA carboxylase Msed_0147, Msed_0148, Msed_1375",
                    "notes": "The primary M. sedula pathway reconstruction maps all three loci to the bifunctional carboxylase. UniProtKB A4YGI1 is the Msed_1375 component from the reference proteome."
                  }
                ]
              }
            ]
          },
          {
            "node_id": "four_hydroxybutyryl_coa_dehydratase",
            "label": "4-hydroxybutyryl-CoA dehydratase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Enzyme dehydrating 4-hydroxybutyryl-CoA to crotonyl-CoA.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Current resources use divergent functional names for this radical enzyme, including vinylacetyl-CoA Delta-isomerase; no exact verified GO or InterPro term was assigned to the historical pathway-level label.",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:A4YGC7",
                "protein_label": "Vinylacetyl-CoA Delta-isomerase",
                "gene_symbol": "Msed_1321",
                "taxon_id": "NCBITaxon:399549",
                "taxon_label": "Metallosphaera sedula DSM 5348",
                "entry_status": "UNREVIEWED",
                "proteome_id": "UP000000242",
                "retrieved_on": "2026-08-24",
                "entry_version": 82,
                "sequence_version": 1,
                "role": "Msed_1321 protein biochemically assigned as 4-hydroxybutyryl-CoA dehydratase in the M. sedula pathway; the current UniProt label reflects alternate nomenclature.",
                "evidence": [
                  {
                    "reference": "DOI:10.1128/AEM.04146-13",
                    "snippet": "4-hydroxybutyryl-CoA dehydratase (Msed_1321)",
                    "notes": "Recombinant Msed_1321 was assigned to the dehydration step in the primary pathway reconstruction. UniProtKB A4YGC7 is the corresponding reference-proteome entry."
                  }
                ]
              }
            ]
          }
        ],
        "edges": [
          {
            "subject": "bicarbonate",
            "predicate": "fixed by",
            "object": "three_hp_four_hb_trait",
            "description": "Two molecules of bicarbonate are fixed per cycle turn.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.1149976",
                "notes": "Berg et al. describe the 3HP/4HB cycle in Sulfolobales."
              }
            ],
            "predicate_id": "METPO:2007404"
          },
          {
            "subject": "three_hp_four_hb_trait",
            "predicate": "contributes to",
            "object": "carbon_fixation_process",
            "description": "The 3HP/4HB cycle is among the six recognized autotrophic pathways.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.02473-10",
                "notes": "Berg situates the 3HP/4HB cycle among recognized carbon-fixation pathways."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "three_hp_four_hb_trait",
            "predicate": "produces",
            "object": "acetyl_coa",
            "description": "A complete cycle turn fixes two bicarbonate to produce one acetyl-CoA.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s40643-023-00705-9",
                "notes": "A complete 3HP/4HB cycle fixes two HCO3- to produce one acetyl-CoA."
              }
            ],
            "predicate_id": "METPO:2007800"
          },
          {
            "subject": "three_hp_four_hb_trait",
            "predicate": "forms intermediate",
            "object": "succinyl_coa",
            "description": "Carboxylation of acetyl-CoA/propionyl-CoA yields succinyl-CoA from two bicarbonate.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s40643-023-00705-9",
                "notes": "The pathway carboxylates acetyl-CoA/propionyl-CoA to form succinyl-CoA from two HCO3-."
              }
            ]
          },
          {
            "subject": "succinyl_coa",
            "predicate": "is reduced to",
            "object": "four_hydroxybutyrate",
            "description": "Succinyl-CoA is reduced to 4-hydroxybutyrate.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s40643-023-00705-9",
                "notes": "Succinyl-CoA is reduced to 4-hydroxybutyrate."
              }
            ]
          },
          {
            "subject": "four_hydroxybutyryl_coa_dehydratase",
            "predicate": "dehydrates",
            "object": "four_hydroxybutyryl_coa",
            "description": "4-hydroxybutyryl-CoA is dehydrated to crotonyl-CoA.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s42003-024-06432-x",
                "notes": "The cycle dehydrates 4-hydroxybutyryl-CoA to crotonyl-CoA."
              }
            ]
          },
          {
            "subject": "four_hydroxybutyryl_coa_dehydratase",
            "predicate": "produces",
            "object": "crotonyl_coa",
            "description": "Dehydration of 4-hydroxybutyryl-CoA yields crotonyl-CoA.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s42003-024-06432-x",
                "notes": "The pathway diagram shows dehydration to crotonyl-CoA."
              }
            ],
            "predicate_id": "METPO:2007800"
          },
          {
            "subject": "crotonyl_coa",
            "predicate": "regenerates",
            "object": "acetyl_coa",
            "description": "Crotonyl-CoA is processed/cleaved to regenerate acetyl-CoA for further cycle turns.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s40643-023-00705-9",
                "notes": "The pathway finally cleaves to yield acetyl-CoA for further turns."
              }
            ]
          },
          {
            "subject": "nadph",
            "predicate": "is required by",
            "object": "three_hp_four_hb_trait",
            "description": "Reductive steps of the cycle consume NADPH (about four NADPH per turn).",
            "evidence": [
              {
                "reference": "DOI:10.1186/s40643-023-00705-9",
                "notes": "Five reactions in the cycle require oxidation of NADPH; full cycle consumes four NADPH."
              }
            ]
          },
          {
            "subject": "acetyl_propionyl_coa_carboxylase",
            "predicate": "mediates carboxylation in",
            "object": "three_hp_four_hb_trait",
            "description": "Acetyl-CoA/propionyl-CoA carboxylase is the primary carboxylase fixing inorganic carbon.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s42003-024-06432-x",
                "notes": "The cycle fixes CO2 onto acetyl-CoA via an acetyl-CoA/propionyl-CoA carboxylase, the primary carboxylase."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-30T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate METABOLISM trait (3-hydroxypropionate/4-hydroxybutyrate cycle); archaeal sub-variant of carbon fixation.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-10T14:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (3HP/4HB Sulfolobales bicarbonate fixation) with CHEBI/GO node groundings and RO/METPO predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 8 evidence-backed generic edges (8 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:12Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d72).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:19Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:16474\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:33Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:16724\u00d71, CHEBI:28522\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-26T07:15:19Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A650CEQ7\u00d71, UniProtKB:A0A017H5F8\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:21:11Z",
        "curator": "claude",
        "action": "RETRACT_DEAD_UNIPROT_GROUNDINGS",
        "changes": "Retracted 1 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T02:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES_PART2",
        "changes": "Re-grounded 2 causal edge(s) off microbe-domain METPO predicates onto their causal-graph counterparts (2 to produces), issue 301 part 2. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Each replacement is a 1:1 mirror of its source predicate that changes only the domain, so the claim each edge makes is unchanged and directions are unchanged. The replacements are proposed in proposals/metpo_traitmech_v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-22T04:26:15Z",
        "curator": "codex",
        "action": "REVIEW_UNIPROT_INSTANCE_GROUNDINGS",
        "changes": "Reviewed 1 organism-specific UniProtKB grounding(s): replaced 0 with taxon-agnostic GO/InterPro terms and retracted 1 to label-only where no exact semantic term was supported (docs/GROUNDING_POLICY.md).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-24T09:50:00Z",
        "curator": "codex",
        "action": "CURATE_PROTEIN_TAXON_EXAMPLE",
        "changes": "Scoped the M. sedula 3HP/4HB mechanism, added all three DOI-backed carboxylase components plus Msed_1321 as taxon-paired UniProt examples, and documented why the complex and historical dehydratase labels remain reviewed label-only.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-22T01:35:00Z",
        "curator": "claude",
        "action": "REFRESH_UNIPROT_ENTRY_VERSION",
        "changes": "Refreshed UniProtKB entry_version against live UniProt REST on 2026-10-22: UniProtKB:A4YGI1 (85 -> 86 on acetyl_propionyl_coa_carboxylase).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:2000207",
    "label": "transports",
    "definition": "An OBJECT_PROPERTY relating an organism to a chemical that the organism transports across its membranes (without specifying direction or coupling).",
    "definition_source": "DOI:10.1146/annurev.micro.55.1.485",
    "trait_category": "METABOLISM",
    "term_kind": "OBJECT_PROPERTY",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:2000001"
    ],
    "domain": "https://w3id.org/metpo/1000525",
    "range_": "http://purl.obolibrary.org/obo/CHEBI_24431",
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev.micro.55.1.485",
        "snippet": "transport",
        "notes": "Microbial-physiology reference supports 'transports' as a canonical predicate composed with a CHEBI-class chemical object at assertion time."
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.983901+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (OBJECT_PROPERTY)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic transport or storage relation carrier; later replacement should use more specific trait records that combine the relation with the transported, imported, exported, accumulated, or sequestered entity, cellular location or compartment, and positive or negative context.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-16T08:50:00-07:00",
        "curator": "claude",
        "action": "UNDEPRECATED_AS_COMPOSITION_PRIMITIVE",
        "changes": "Restored from DEPRECATED to REVIEWED under the predicate+class composition pattern (intended use: <organism> + this predicate + CHEBI chemical class). Added DOI/PMID-backed definition, evidence, and explicit domain/range slots.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000199",
    "label": "trimethylamine N-oxide respiration",
    "definition": "An anaerobic respiration in which an organism uses trimethylamine N-oxide as the terminal electron acceptor and reduces it to trimethylamine for energy conservation.",
    "definition_source": "DOI:10.1111/1462-2920.12726",
    "trait_category": "METABOLISM",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000802"
    ],
    "synonyms": [
      {
        "synonym_text": "TMAO respiration",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.3389/fmicb.2024.1467153"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1111/1462-2920.12726",
        "snippet": "anaerobic respiratory growth with trimethylamine-N-oxide (TMAO) as the terminal electron acceptor",
        "notes": "Denby et al. support TMAO as the organism-level terminal electron acceptor for anaerobic respiratory growth."
      },
      {
        "reference": "DOI:10.1111/1462-2920.12726",
        "snippet": "TMAO is reduced to TMA by the enzyme TMAO reductase, encoded by the torCAD operon",
        "notes": "Denby et al. describe reduction of trimethylamine N-oxide to trimethylamine by the TorCAD-linked TMAO reductase."
      },
      {
        "reference": "DOI:10.3389/fmicb.2024.1467153",
        "snippet": "switching from aerobic intracellular energy metabolism to trimethylamine N-oxide respiration",
        "notes": "Qiu and Tang use the unabbreviated respiration label while linking high-pressure survival in Shewanella eurypsychrophilus YLB-09 to TMAO respiration."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:83333",
        "taxon_label": "Escherichia coli K-12",
        "note": "Denby et al. characterized E. coli K-12 MG1655 adaptation from anaerobic fermentative growth to a TMAO-respiratory/fermentative steady state after TMAO addition.",
        "reference": "DOI:10.1111/1462-2920.12726"
      }
    ],
    "discussions": [
      {
        "discussion_id": "trimethylamine-n-oxide-respiration-xref-gap",
        "prompt": "Resolve an exact external ontology class for organism-level trimethylamine N-oxide respiration before adding a TraitRecord xref.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "The pinned METPO snapshot has no active organism-level class for trimethylamine N-oxide respiration. Candidate EC, Rhea, and protein-family terms for TorA or broader trimethylamine N-oxide reductases are narrower than the whole-organism anaerobic respiration phenotype.",
        "posed_by": "codex",
        "posed_date": "2026-09-15"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-15T02:00:15Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted trimethylamine N-oxide respiration as a DOI-backed anaerobic respiration TraitRecord with an exact TMAO respiration synonym after a repository-wide duplicate review covering ignored and hidden files; the local METPO snapshot has no exact class and the replacement placeholder is reserved in proposals/metpo_traitmech_v76.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:2000006",
    "label": "uses as carbon source",
    "definition": "An OBJECT_PROPERTY relating an organism to a chemical entity (e.g. a CHEBI class) that the organism uses as a source of carbon for biosynthesis. The intended use is predicate + class composition at assertion time, e.g. `<organism> METPO:2000006 CHEBI:17234` (\"organism uses glucose as carbon source\").",
    "definition_source": "PMID:21413255",
    "trait_category": "METABOLISM",
    "term_kind": "OBJECT_PROPERTY",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:2000001"
    ],
    "synonyms": [
      {
        "synonym_text": "carbon source",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "domain": "https://w3id.org/metpo/1000525",
    "range_": "http://purl.obolibrary.org/obo/CHEBI_24431",
    "xrefs": [
      "MICRO:0001460"
    ],
    "evidence": [
      {
        "reference": "PMID:21413255",
        "snippet": "carbon source",
        "notes": "Medical Microbiology chapter supports \"carbon source\" as a standard descriptor for organism-substrate utilisation, composed at assertion time with the specific carbon-bearing chemical."
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.952542+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (OBJECT_PROPERTY)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic chemical-use relation carrier; later replacement should use more specific trait records that combine the relation with the chemical, metabolic role, growth condition, and positive or negative usage context.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-16T08:00:00-07:00",
        "curator": "claude",
        "action": "UNDEPRECATED_AS_COMPOSITION_PRIMITIVE",
        "changes": "Restored from DEPRECATED to REVIEWED. METPO modeling uses the predicate + class composition pattern (this OBJECT_PROPERTY composed with a CHEBI carbon-bearing chemical at assertion time) rather than precomposed substrate-specific TraitRecords. Added DOI-backed definition, evidence, and the intended composition example.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-17T10:00:00-07:00",
        "curator": "claude",
        "action": "ADDED_EXTERNAL_PREDICATE_XREF",
        "changes": "Added xrefs ['MICRO:0001460'] to record an external equivalence predicate (MICRO:0001460 'uses carbon source'). MICRO:0001460 'uses carbon source' is the direct equivalent. Source: OLS4 property search.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:2000008",
    "label": "uses as electron acceptor",
    "definition": "An OBJECT_PROPERTY relating an organism to a chemical entity (e.g. a CHEBI class) that the organism uses as the terminal electron acceptor in respiration. The intended use is predicate + class composition at assertion time, e.g. `<organism> METPO:2000008 CHEBI:17632` (\"organism uses nitrate as electron acceptor\").",
    "definition_source": "DOI:10.1146/annurev.micro.61.080706.093130",
    "trait_category": "METABOLISM",
    "term_kind": "OBJECT_PROPERTY",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:2000001"
    ],
    "synonyms": [
      {
        "synonym_text": "electron acceptor",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "domain": "https://w3id.org/metpo/1000525",
    "range_": "http://purl.obolibrary.org/obo/CHEBI_24431",
    "xrefs": [
      "MICRO:0001463"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev.micro.61.080706.093130",
        "snippet": "terminal electron acceptor",
        "notes": "Microbial-physiology review supports the \"electron acceptor\" relation as the standard descriptor for the terminal-acceptor pole of respiration; composed at assertion time with the specific acceptor chemical (O2, nitrate, sulfate, Fe(III), CO2, etc.)."
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.953476+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (OBJECT_PROPERTY)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic chemical-use relation carrier; later replacement should use more specific trait records that combine the relation with the chemical, metabolic role, growth condition, and positive or negative usage context.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-16T08:00:00-07:00",
        "curator": "claude",
        "action": "UNDEPRECATED_AS_COMPOSITION_PRIMITIVE",
        "changes": "Restored from DEPRECATED to REVIEWED. METPO modeling uses the predicate + class composition pattern (this OBJECT_PROPERTY composed with a CHEBI electron-acceptor chemical at assertion time) rather than precomposed substrate-specific TraitRecords. Added DOI-backed definition and evidence.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-17T10:00:00-07:00",
        "curator": "claude",
        "action": "ADDED_EXTERNAL_PREDICATE_XREF",
        "changes": "Added xrefs ['MICRO:0001463'] to record an external equivalence predicate (MICRO:0001463 'uses electron acceptor'). MICRO:0001463 'uses electron acceptor' is the direct equivalent. Source: OLS4 property search.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:2000009",
    "label": "uses as electron donor",
    "definition": "An OBJECT_PROPERTY relating an organism to a chemical entity (e.g. a CHEBI class) that the organism oxidises as an electron donor for energy conservation or biosynthetic reductant. The intended use is predicate + class composition at assertion time, e.g. `<organism> METPO:2000009 CHEBI:18276` (\"organism uses molecular hydrogen as electron donor\").",
    "definition_source": "DOI:10.1146/annurev.micro.55.1.485",
    "trait_category": "METABOLISM",
    "term_kind": "OBJECT_PROPERTY",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:2000001"
    ],
    "synonyms": [
      {
        "synonym_text": "electron donor",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "domain": "https://w3id.org/metpo/1000525",
    "range_": "http://purl.obolibrary.org/obo/CHEBI_24431",
    "xrefs": [
      "MICRO:0001462"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev.micro.55.1.485",
        "snippet": "electron donor",
        "notes": "Chemolithotrophy review supports the \"electron donor\" relation as the central descriptor for chemolithotrophic and chemo-organotrophic energy conservation; the relation is composed at assertion time with the specific donor chemical (H2, NH3, Fe2+, S, organic acids, etc.)."
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.953972+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (OBJECT_PROPERTY)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic chemical-use relation carrier; later replacement should use more specific trait records that combine the relation with the chemical, metabolic role, growth condition, and positive or negative usage context.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-16T08:00:00-07:00",
        "curator": "claude",
        "action": "UNDEPRECATED_AS_COMPOSITION_PRIMITIVE",
        "changes": "Restored from DEPRECATED to REVIEWED. METPO modeling uses the predicate + class composition pattern (this OBJECT_PROPERTY composed with a CHEBI electron-donor chemical at assertion time) rather than precomposed substrate-specific TraitRecords. Added DOI-backed definition and evidence.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-17T10:00:00-07:00",
        "curator": "claude",
        "action": "ADDED_EXTERNAL_PREDICATE_XREF",
        "changes": "Added xrefs ['MICRO:0001462'] to record an external equivalence predicate (MICRO:0001462 'uses electron donor'). MICRO:0001462 'uses electron donor' is the direct equivalent. Source: OLS4 property search.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:2000010",
    "label": "uses as energy source",
    "definition": "An OBJECT_PROPERTY relating an organism to a chemical entity that the organism uses as a source of energy for metabolism.",
    "definition_source": "DOI:10.1146/annurev.micro.55.1.485",
    "trait_category": "METABOLISM",
    "term_kind": "OBJECT_PROPERTY",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:2000001"
    ],
    "synonyms": [
      {
        "synonym_text": "energy source",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "domain": "https://w3id.org/metpo/1000525",
    "range_": "http://purl.obolibrary.org/obo/CHEBI_24431",
    "xrefs": [
      "MICRO:0001461"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev.micro.55.1.485",
        "snippet": "energy source",
        "notes": "Microbial-physiology reference supports 'uses as energy source' as a canonical predicate composed with a CHEBI-class chemical object at assertion time."
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.954453+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (OBJECT_PROPERTY)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic chemical-use relation carrier; later replacement should use more specific trait records that combine the relation with the chemical, metabolic role, growth condition, and positive or negative usage context.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-16T08:50:00-07:00",
        "curator": "claude",
        "action": "UNDEPRECATED_AS_COMPOSITION_PRIMITIVE",
        "changes": "Restored from DEPRECATED to REVIEWED under the predicate+class composition pattern (intended use: <organism> + this predicate + CHEBI chemical class). Added DOI/PMID-backed definition, evidence, and explicit domain/range slots.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-17T10:00:00-07:00",
        "curator": "claude",
        "action": "ADDED_EXTERNAL_PREDICATE_XREF",
        "changes": "Added xrefs ['MICRO:0001461'] to record an external equivalence predicate (MICRO:0001461 'uses energy source'). MICRO:0001461 'uses energy source' is the direct equivalent. Source: OLS4 property search.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:2000014",
    "label": "uses as nitrogen source",
    "definition": "An OBJECT_PROPERTY relating an organism to a chemical entity that the organism uses as a source of nitrogen for biosynthesis.",
    "definition_source": "PMID:21413255",
    "trait_category": "METABOLISM",
    "term_kind": "OBJECT_PROPERTY",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:2000001"
    ],
    "synonyms": [
      {
        "synonym_text": "nitrogen source",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "domain": "https://w3id.org/metpo/1000525",
    "range_": "http://purl.obolibrary.org/obo/CHEBI_51143",
    "evidence": [
      {
        "reference": "PMID:21413255",
        "snippet": "nitrogen source",
        "notes": "Microbial-physiology reference supports 'uses as nitrogen source' as a canonical predicate composed with a CHEBI-class chemical object at assertion time."
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.956313+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (OBJECT_PROPERTY)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic chemical-use relation carrier; later replacement should use more specific trait records that combine the relation with the chemical, metabolic role, growth condition, and positive or negative usage context.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-16T08:50:00-07:00",
        "curator": "claude",
        "action": "UNDEPRECATED_AS_COMPOSITION_PRIMITIVE",
        "changes": "Restored from DEPRECATED to REVIEWED under the predicate+class composition pattern (intended use: <organism> + this predicate + CHEBI chemical class). Added DOI/PMID-backed definition, evidence, and explicit domain/range slots.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-16T09:35:00-07:00",
        "curator": "claude",
        "action": "TIGHTENED_RANGE_TO_CHEBI_SUBCLASS",
        "changes": "Narrowed range_ from http://purl.obolibrary.org/obo/CHEBI_24431 to http://purl.obolibrary.org/obo/CHEBI_51143 ('nitrogen molecular entity'). The earlier CHEBI:24431 root was used as a safe default during bulk un-deprecation (PR #54); the more specific CHEBI subclass better reflects the predicate's intended substrates.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:2000020",
    "label": "uses as sulfur source",
    "definition": "An OBJECT_PROPERTY relating an organism to a chemical entity that the organism uses as a source of sulfur for biosynthesis.",
    "definition_source": "PMID:21413255",
    "trait_category": "METABOLISM",
    "term_kind": "OBJECT_PROPERTY",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:2000001"
    ],
    "synonyms": [
      {
        "synonym_text": "sulfur source",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "domain": "https://w3id.org/metpo/1000525",
    "range_": "http://purl.obolibrary.org/obo/CHEBI_26835",
    "evidence": [
      {
        "reference": "PMID:21413255",
        "snippet": "sulfur source",
        "notes": "Microbial-physiology reference supports 'uses as sulfur source' as a canonical predicate composed with a CHEBI-class chemical object at assertion time."
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.959225+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (OBJECT_PROPERTY)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic chemical-use relation carrier; later replacement should use more specific trait records that combine the relation with the chemical, metabolic role, growth condition, and positive or negative usage context.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-16T08:50:00-07:00",
        "curator": "claude",
        "action": "UNDEPRECATED_AS_COMPOSITION_PRIMITIVE",
        "changes": "Restored from DEPRECATED to REVIEWED under the predicate+class composition pattern (intended use: <organism> + this predicate + CHEBI chemical class). Added DOI/PMID-backed definition, evidence, and explicit domain/range slots.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-16T09:35:00-07:00",
        "curator": "claude",
        "action": "TIGHTENED_RANGE_TO_CHEBI_SUBCLASS",
        "changes": "Narrowed range_ from http://purl.obolibrary.org/obo/CHEBI_24431 to http://purl.obolibrary.org/obo/CHEBI_26835 ('sulfur molecular entity'). The earlier CHEBI:24431 root was used as a safe default during bulk un-deprecation (PR #54); the more specific CHEBI subclass better reflects the predicate's intended substrates.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:2000032",
    "label": "uses for aerobic catabolization",
    "definition": "An OBJECT_PROPERTY relating an organism to a chemical substrate that the organism catabolises under aerobic (oxygen-respiring) conditions.",
    "definition_source": "DOI:10.1146/annurev.micro.55.1.485",
    "trait_category": "METABOLISM",
    "term_kind": "OBJECT_PROPERTY",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:2000001"
    ],
    "synonyms": [
      {
        "synonym_text": "aerobic catabolization",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "domain": "https://w3id.org/metpo/1000525",
    "range_": "http://purl.obolibrary.org/obo/CHEBI_24431",
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev.micro.55.1.485",
        "snippet": "aerobic catabolism",
        "notes": "Microbial-physiology reference supports 'uses for aerobic catabolization' as a canonical predicate composed with a CHEBI-class chemical object at assertion time."
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.965949+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (OBJECT_PROPERTY)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic use-context relation carrier; later replacement should use more specific trait records that combine the relation with the chemical, growth or respiration context, experimental condition, or other entity.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-16T08:50:00-07:00",
        "curator": "claude",
        "action": "UNDEPRECATED_AS_COMPOSITION_PRIMITIVE",
        "changes": "Restored from DEPRECATED to REVIEWED under the predicate+class composition pattern (intended use: <organism> + this predicate + CHEBI chemical class). Added DOI/PMID-backed definition, evidence, and explicit domain/range slots.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:2000043",
    "label": "uses for aerobic growth",
    "definition": "An OBJECT_PROPERTY relating an organism to a chemical that supports the organism's growth under aerobic conditions.",
    "definition_source": "DOI:10.1146/annurev.micro.55.1.485",
    "trait_category": "METABOLISM",
    "term_kind": "OBJECT_PROPERTY",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:2000001"
    ],
    "synonyms": [
      {
        "synonym_text": "aerobic growth",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "domain": "https://w3id.org/metpo/1000525",
    "range_": "http://purl.obolibrary.org/obo/CHEBI_24431",
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev.micro.55.1.485",
        "snippet": "aerobic growth",
        "notes": "Microbial-physiology reference supports 'uses for aerobic growth' as a canonical predicate composed with a CHEBI-class chemical object at assertion time."
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.971349+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (OBJECT_PROPERTY)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic use-context relation carrier; later replacement should use more specific trait records that combine the relation with the chemical, growth or respiration context, experimental condition, or other entity.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-16T08:50:00-07:00",
        "curator": "claude",
        "action": "UNDEPRECATED_AS_COMPOSITION_PRIMITIVE",
        "changes": "Restored from DEPRECATED to REVIEWED under the predicate+class composition pattern (intended use: <organism> + this predicate + CHEBI chemical class). Added DOI/PMID-backed definition, evidence, and explicit domain/range slots.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:2000048",
    "label": "uses for anaerobic catabolization",
    "definition": "An OBJECT_PROPERTY relating an organism to a chemical substrate that the organism catabolises under anaerobic conditions.",
    "definition_source": "DOI:10.1146/annurev.micro.55.1.485",
    "trait_category": "METABOLISM",
    "term_kind": "OBJECT_PROPERTY",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:2000001"
    ],
    "synonyms": [
      {
        "synonym_text": "anaerobic catabolization",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "domain": "https://w3id.org/metpo/1000525",
    "range_": "http://purl.obolibrary.org/obo/CHEBI_24431",
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev.micro.55.1.485",
        "snippet": "anaerobic catabolism",
        "notes": "Microbial-physiology reference supports 'uses for anaerobic catabolization' as a canonical predicate composed with a CHEBI-class chemical object at assertion time."
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.973706+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (OBJECT_PROPERTY)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic use-context relation carrier; later replacement should use more specific trait records that combine the relation with the chemical, growth or respiration context, experimental condition, or other entity.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-16T08:50:00-07:00",
        "curator": "claude",
        "action": "UNDEPRECATED_AS_COMPOSITION_PRIMITIVE",
        "changes": "Restored from DEPRECATED to REVIEWED under the predicate+class composition pattern (intended use: <organism> + this predicate + CHEBI chemical class). Added DOI/PMID-backed definition, evidence, and explicit domain/range slots.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:2000049",
    "label": "uses for anaerobic growth",
    "definition": "An OBJECT_PROPERTY relating an organism to a chemical that supports the organism's growth under anaerobic conditions.",
    "definition_source": "DOI:10.1146/annurev.micro.55.1.485",
    "trait_category": "METABOLISM",
    "term_kind": "OBJECT_PROPERTY",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:2000001"
    ],
    "synonyms": [
      {
        "synonym_text": "anaerobic growth",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "domain": "https://w3id.org/metpo/1000525",
    "range_": "http://purl.obolibrary.org/obo/CHEBI_24431",
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev.micro.55.1.485",
        "snippet": "anaerobic growth",
        "notes": "Microbial-physiology reference supports 'uses for anaerobic growth' as a canonical predicate composed with a CHEBI-class chemical object at assertion time."
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.974191+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (OBJECT_PROPERTY)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic use-context relation carrier; later replacement should use more specific trait records that combine the relation with the chemical, growth or respiration context, experimental condition, or other entity.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-16T08:50:00-07:00",
        "curator": "claude",
        "action": "UNDEPRECATED_AS_COMPOSITION_PRIMITIVE",
        "changes": "Restored from DEPRECATED to REVIEWED under the predicate+class composition pattern (intended use: <organism> + this predicate + CHEBI chemical class). Added DOI/PMID-backed definition, evidence, and explicit domain/range slots.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:2000050",
    "label": "uses for anaerobic growth in the dark",
    "definition": "An OBJECT_PROPERTY relating an organism to a chemical that supports the organism's growth under anaerobic conditions without illumination (i.e. excluding phototrophic anaerobic growth).",
    "definition_source": "DOI:10.1146/annurev.micro.55.1.485",
    "trait_category": "METABOLISM",
    "term_kind": "OBJECT_PROPERTY",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:2000001"
    ],
    "synonyms": [
      {
        "synonym_text": "anaerobic growth in the dark",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "domain": "https://w3id.org/metpo/1000525",
    "range_": "http://purl.obolibrary.org/obo/CHEBI_24431",
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev.micro.55.1.485",
        "snippet": "anaerobic",
        "notes": "Microbial-physiology reference supports 'uses for anaerobic growth in the dark' as a canonical predicate composed with a CHEBI-class chemical object at assertion time."
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.974663+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (OBJECT_PROPERTY)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic use-context relation carrier; later replacement should use more specific trait records that combine the relation with the chemical, growth or respiration context, experimental condition, or other entity.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-16T08:50:00-07:00",
        "curator": "claude",
        "action": "UNDEPRECATED_AS_COMPOSITION_PRIMITIVE",
        "changes": "Restored from DEPRECATED to REVIEWED under the predicate+class composition pattern (intended use: <organism> + this predicate + CHEBI chemical class). Added DOI/PMID-backed definition, evidence, and explicit domain/range slots.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:2000051",
    "label": "uses for anaerobic growth with light",
    "definition": "An OBJECT_PROPERTY relating an organism to a chemical that supports the organism's growth under anaerobic conditions with illumination (anoxygenic phototrophic growth).",
    "definition_source": "DOI:10.1146/annurev.micro.55.1.485",
    "trait_category": "METABOLISM",
    "term_kind": "OBJECT_PROPERTY",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:2000001"
    ],
    "synonyms": [
      {
        "synonym_text": "anaerobic growth with light",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "domain": "https://w3id.org/metpo/1000525",
    "range_": "http://purl.obolibrary.org/obo/CHEBI_24431",
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev.micro.55.1.485",
        "snippet": "phototrophic",
        "notes": "Microbial-physiology reference supports 'uses for anaerobic growth with light' as a canonical predicate composed with a CHEBI-class chemical object at assertion time."
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.975139+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (OBJECT_PROPERTY)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic use-context relation carrier; later replacement should use more specific trait records that combine the relation with the chemical, growth or respiration context, experimental condition, or other entity.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-16T08:50:00-07:00",
        "curator": "claude",
        "action": "UNDEPRECATED_AS_COMPOSITION_PRIMITIVE",
        "changes": "Restored from DEPRECATED to REVIEWED under the predicate+class composition pattern (intended use: <organism> + this predicate + CHEBI chemical class). Added DOI/PMID-backed definition, evidence, and explicit domain/range slots.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:2000012",
    "label": "uses for growth",
    "definition": "An OBJECT_PROPERTY relating an organism to a chemical that supports the organism's growth (without specifying aerobic or anaerobic mode).",
    "definition_source": "PMID:21413255",
    "trait_category": "METABOLISM",
    "term_kind": "OBJECT_PROPERTY",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:2000001"
    ],
    "synonyms": [
      {
        "synonym_text": "growth",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "domain": "https://w3id.org/metpo/1000525",
    "range_": "http://purl.obolibrary.org/obo/CHEBI_24431",
    "evidence": [
      {
        "reference": "PMID:21413255",
        "snippet": "growth",
        "notes": "Microbial-physiology reference supports 'uses for growth' as a canonical predicate composed with a CHEBI-class chemical object at assertion time."
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.955391+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (OBJECT_PROPERTY)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic use-context relation carrier; later replacement should use more specific trait records that combine the relation with the chemical, growth or respiration context, experimental condition, or other entity.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-16T08:50:00-07:00",
        "curator": "claude",
        "action": "UNDEPRECATED_AS_COMPOSITION_PRIMITIVE",
        "changes": "Restored from DEPRECATED to REVIEWED under the predicate+class composition pattern (intended use: <organism> + this predicate + CHEBI chemical class). Added DOI/PMID-backed definition, evidence, and explicit domain/range slots.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:2000019",
    "label": "uses for respiration",
    "definition": "An OBJECT_PROPERTY relating an organism to a chemical entity that the organism uses in respiratory metabolism (typically as electron donor or terminal electron acceptor).",
    "definition_source": "DOI:10.1146/annurev.micro.55.1.485",
    "trait_category": "METABOLISM",
    "term_kind": "OBJECT_PROPERTY",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:2000001"
    ],
    "synonyms": [
      {
        "synonym_text": "respiration",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "domain": "https://w3id.org/metpo/1000525",
    "range_": "http://purl.obolibrary.org/obo/CHEBI_24431",
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev.micro.55.1.485",
        "snippet": "respiration",
        "notes": "Microbial-physiology reference supports 'uses for respiration' as a canonical predicate composed with a CHEBI-class chemical object at assertion time."
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.958727+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (OBJECT_PROPERTY)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic use-context relation carrier; later replacement should use more specific trait records that combine the relation with the chemical, growth or respiration context, experimental condition, or other entity.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-16T08:50:00-07:00",
        "curator": "claude",
        "action": "UNDEPRECATED_AS_COMPOSITION_PRIMITIVE",
        "changes": "Restored from DEPRECATED to REVIEWED under the predicate+class composition pattern (intended use: <organism> + this predicate + CHEBI chemical class). Added DOI/PMID-backed definition, evidence, and explicit domain/range slots.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:2000015",
    "label": "uses in other way",
    "definition": "A catch-all OBJECT_PROPERTY relating an organism to a chemical the organism uses in some way not covered by the more specific predicates (uses_as_carbon_source, uses_as_electron_donor, etc.).",
    "definition_source": "DOI:10.1146/annurev.micro.55.1.485",
    "trait_category": "METABOLISM",
    "term_kind": "OBJECT_PROPERTY",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:2000001"
    ],
    "synonyms": [
      {
        "synonym_text": "other",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "domain": "https://w3id.org/metpo/1000525",
    "range_": "http://purl.obolibrary.org/obo/CHEBI_24431",
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev.micro.55.1.485",
        "snippet": "chemical use",
        "notes": "Microbial-physiology reference supports 'uses in other way' as a canonical predicate composed with a CHEBI-class chemical object at assertion time."
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.956781+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (OBJECT_PROPERTY)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic metabolism relation carrier; later replacement should use more specific trait records that combine the relation with the chemical, phenotype, quality, compartment, enzyme or activity target, growth context, measurement, or other entity.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-16T08:50:00-07:00",
        "curator": "claude",
        "action": "UNDEPRECATED_AS_COMPOSITION_PRIMITIVE",
        "changes": "Restored from DEPRECATED to REVIEWED under the predicate+class composition pattern (intended use: <organism> + this predicate + CHEBI chemical class). Added DOI/PMID-backed definition, evidence, and explicit domain/range slots.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000022",
    "label": "Wood-Ljungdahl pathway",
    "definition": "An autotrophic carbon-fixation pathway (the reductive acetyl-CoA pathway) in which two molecules of CO2 are reduced and combined into acetyl-CoA. It is energetically efficient and used by acetogenic bacteria, methanogenic archaea, and some sulfate-reducing bacteria.",
    "definition_source": "DOI:10.1016/j.bbapap.2008.08.012",
    "trait_category": "METABOLISM",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "traitmech:000019"
    ],
    "synonyms": [
      {
        "synonym_text": "reductive acetyl-CoA pathway",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1016/j.bbapap.2008.08.012"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1016/j.bbapap.2008.08.012",
        "notes": "Ragsdale & Pierce, \"Acetogenesis and the Wood-Ljungdahl pathway of CO2 fixation\", is the reference treatment of this reductive acetyl-CoA pathway."
      },
      {
        "reference": "DOI:10.1128/AEM.02473-10",
        "notes": "Berg review places the reductive acetyl-CoA (Wood-Ljungdahl) pathway among the recognized autotrophic carbon-fixation pathways."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1525",
        "taxon_label": "Neomoorella thermoacetica",
        "note": "Model acetogen used to elucidate the reductive acetyl-CoA / Wood-Ljungdahl pathway (formerly Moorella/Clostridium thermoaceticum).",
        "reference": "https://pmc.ncbi.nlm.nih.gov/articles/PMC2575129/"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "wood_ljungdahl_reductive_acetyl_coa",
        "title": "Wood-Ljungdahl pathway reduces 2 CO2 to acetyl-CoA",
        "description": "Evidence-backed causal sketch linking reduction of two CO2 molecules into acetyl-CoA via the reductive acetyl-CoA pathway.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "Represents the methyl and carbonyl branches through acetyl-CoA formation, with an explicit alpha-subunit protein exemplar for the CODH/ACS complex; energetic variants outside this canonical acetogen route are not generalized.",
        "nodes": [
          {
            "node_id": "wood_ljungdahl_trait",
            "label": "Wood-Ljungdahl pathway",
            "node_type": "TRAIT",
            "grounding": "traitmech:000022",
            "description": "Reductive acetyl-CoA pathway combining 2 CO2 into acetyl-CoA."
          },
          {
            "node_id": "wood_ljungdahl_pathway",
            "label": "Wood-Ljungdahl pathway",
            "node_type": "PATHWAY",
            "grounding": "GO:0030634",
            "description": "Acetyl-CoA biosynthetic process from carbon dioxide.",
            "related_records": [
              {
                "corpus": "PathwayMech",
                "identifier": "WikiPathways:WP5019",
                "relation": "PATHWAY_CONTEXT",
                "basis": "PathwayMech context: Acetogenesis in Acetobacterium woodii (NCBITaxon:33952). The shared reductive acetyl-CoA route combines methyl and carbonyl branches for acetogenesis; the bacterial exemplar does not establish archaeal variants. No exact equivalence or transfer of organism scope is asserted.",
                "source_version": "aa305727458c44ab05614901334540e2c87a9f3a"
              }
            ]
          },
          {
            "node_id": "carbon_dioxide",
            "label": "carbon dioxide",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:16526",
            "description": "Inorganic carbon substrate reduced to acetyl-CoA."
          },
          {
            "node_id": "methyl_branch",
            "label": "methyl branch",
            "node_type": "PATHWAY",
            "description": "Eastern branch of WLP reducing CO2 stepwise to methyl-tetrahydrofolate."
          },
          {
            "node_id": "carbonyl_branch",
            "label": "carbonyl branch",
            "node_type": "PATHWAY",
            "description": "Western branch of WLP reducing CO2 to CO at the CODH/ACS complex."
          },
          {
            "node_id": "formate_dehydrogenase",
            "label": "formate dehydrogenase (FDH)",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Enzyme reducing CO2 to formate, the first step of the WLP methyl branch.",
            "grounding": "GO:0009326"
          },
          {
            "node_id": "formate",
            "label": "formate",
            "node_type": "CHEMICAL",
            "description": "C1 intermediate produced by reduction of CO2 in the methyl branch."
          },
          {
            "node_id": "formyl_thf_synthetase",
            "label": "formyl-THF synthetase (FTS/Fhs)",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Enzyme forming formyl-THF from formate, consuming one ATP.",
            "grounding": "GO:0004329"
          },
          {
            "node_id": "atp",
            "label": "ATP",
            "node_type": "CHEMICAL",
            "description": "Adenosine triphosphate consumed during formate activation in the WLP."
          },
          {
            "node_id": "methyltransferase",
            "label": "methyltransferase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Enzyme transferring the methyl group onto the corrinoid iron-sulfur protein.",
            "grounding": "GO:0102036"
          },
          {
            "node_id": "cofesp",
            "label": "corrinoid iron-sulfur protein (CoFeSP)",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Corrinoid iron-sulfur protein carrying the methyl group to ACS.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "CoFeSP is a multisubunit corrinoid iron-sulfur carrier; no checked single semantic family or complex term exactly covers the combined carrier represented by this node."
          },
          {
            "node_id": "acetyl_coa_synthase",
            "label": "acetyl-CoA synthase (ACS)",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Enzyme condensing CO, methyl-CoFeSP and CoA into acetyl-CoA.",
            "grounding": "GO:0043884",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:P27988",
                "protein_label": "Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit alpha",
                "gene_symbol": "acsB",
                "taxon_id": "NCBITaxon:1525",
                "taxon_label": "Neomoorella thermoacetica",
                "entry_status": "REVIEWED",
                "retrieved_on": "2026-10-22",
                "entry_version": 126,
                "sequence_version": 1,
                "role": "Alpha subunit that combines CO, CoA, and the CoFeSP-borne methyl group to form acetyl-CoA; this accession is one component of the alpha2-beta2 CODH/ACS complex.",
                "evidence": [
                  {
                    "reference": "DOI:10.1073/pnas.220404397",
                    "snippet": "Genes acsA and acsB encode the beta and alpha subunits",
                    "notes": "The primary cloning and reconstitution study identifies acsB as the alpha component and tests active AcsAB from C. thermoaceticum; UniProtKB P27988 verifies the reviewed current taxon mapping."
                  }
                ]
              }
            ]
          },
          {
            "node_id": "acetyl_coa",
            "label": "acetyl-CoA",
            "node_type": "CHEMICAL",
            "description": "Central product of the WLP, the convergence point of both branches."
          },
          {
            "node_id": "tetrahydrofolate",
            "label": "tetrahydrofolate (THF)",
            "node_type": "CHEMICAL",
            "description": "C1 carrier cofactor of the WLP methyl branch."
          },
          {
            "node_id": "net_zero_atp_slp",
            "label": "zero net ATP from substrate-level phosphorylation",
            "node_type": "QUALITY",
            "description": "Energetic property: formate activation offsets SLP so the WLP nets zero ATP."
          }
        ],
        "edges": [
          {
            "subject": "wood_ljungdahl_pathway",
            "predicate": "confers",
            "object": "wood_ljungdahl_trait",
            "description": "The reductive acetyl-CoA pathway underlies the trait.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.bbapap.2008.08.012",
                "snippet": "use the reductive acetyl-CoA or Wood-Ljungdahl pathway as their main mechanism for energy conservation and for synthesis of acetyl-CoA and cell carbon from CO2",
                "notes": "Ragsdale & Pierce review the Wood-Ljungdahl pathway as the reference reductive acetyl-CoA pathway."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "carbon_dioxide",
            "predicate": "fixed by",
            "object": "wood_ljungdahl_trait",
            "description": "Two molecules of CO2 are fixed and combined into acetyl-CoA.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fbioe.2024.1395540",
                "snippet": "WLP is the key pathway for acetogens to fix CO2 and generate acetate",
                "notes": "Berg places Wood-Ljungdahl among the recognized autotrophic carbon-fixation pathways."
              }
            ],
            "predicate_id": "METPO:2007404"
          },
          {
            "subject": "wood_ljungdahl_pathway",
            "predicate": "has part",
            "object": "methyl_branch",
            "description": "The WLP comprises a methyl (eastern) branch.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fbioe.2024.1395540",
                "snippet": "WLP consists of two branches, the methyl branch and the carbonyl branch",
                "notes": "The Wood-Ljungdahl pathway is a two-branch autotrophic CO2 fixation pathway: a methyl branch and a carbonyl branch."
              }
            ]
          },
          {
            "subject": "wood_ljungdahl_pathway",
            "predicate": "has part",
            "object": "carbonyl_branch",
            "description": "The WLP comprises a carbonyl (western) branch.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fbioe.2024.1395540",
                "snippet": "The carbonyl-branch involves a single reaction facilitated by a multi-component enzyme complex",
                "notes": "The Wood-Ljungdahl pathway is a two-branch autotrophic CO2 fixation pathway with a carbonyl branch."
              }
            ]
          },
          {
            "subject": "formate_dehydrogenase",
            "predicate": "reduces",
            "object": "carbon_dioxide",
            "description": "FDH reduces CO2 to formate, the first methyl-branch step (product: formate node).",
            "evidence": [
              {
                "reference": "DOI:10.3389/fbioe.2024.1395540",
                "snippet": "reduction of CO2 to formate catalyzed by formate dehydrogenase (FDH)",
                "notes": "Formate dehydrogenase (FDH) reduces CO2 to formate; canonical bacterial WLP step."
              }
            ],
            "predicate_id": "METPO:2007802"
          },
          {
            "subject": "formate_dehydrogenase",
            "predicate": "produces",
            "object": "formate",
            "description": "FDH-catalyzed reduction of CO2 yields formate.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fbioe.2024.1395540",
                "snippet": "the first reaction of methyl branch is the reduction of CO2 to formate",
                "notes": "Formate dehydrogenase (FDH) reduces CO2 to formate."
              }
            ],
            "predicate_id": "METPO:2007800"
          },
          {
            "subject": "formyl_thf_synthetase",
            "predicate": "requires",
            "object": "atp",
            "description": "Formyl-THF synthetase consumes one ATP to activate formate.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fbioe.2024.1395540",
                "snippet": "catalyzed by formyl-THF synthetase (FTS) and consuming one ATP",
                "notes": "Formyl-THF synthetase (FTS) forms formyl-THF, consuming one ATP."
              }
            ]
          },
          {
            "subject": "methyltransferase",
            "predicate": "transfers methyl to",
            "object": "cofesp",
            "description": "Methyltransferase transfers the methyl group onto the corrinoid iron-sulfur protein.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fbioe.2024.1395540",
                "snippet": "the methyl group of methyl-THF is transferred to a corrinoid iron-sulfur-containing protein (CoFeSP) via the methyltransferase (MT)",
                "notes": "Methyltransferase transfers the methyl onto a corrinoid iron-sulfur protein (CoFeSP)."
              }
            ]
          },
          {
            "subject": "acetyl_coa_synthase",
            "predicate": "produces",
            "object": "acetyl_coa",
            "description": "ACS condenses CO, methyl-CoFeSP and CoA into acetyl-CoA, the terminal WLP step.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fbioe.2024.1395540",
                "snippet": "converts CO, methyl-CoFeSP and CoA into acetyl-CoA",
                "notes": "ACS combines CO, methyl-CoFeSP and CoA into acetyl-CoA; central terminal step of WLP."
              }
            ],
            "predicate_id": "METPO:2007800"
          },
          {
            "subject": "tetrahydrofolate",
            "predicate": "functions as C1 carrier in",
            "object": "methyl_branch",
            "description": "THF serves as the C1 carrier of the WLP methyl branch.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fbioe.2024.1395540",
                "snippet": "Formate then undergoes a reaction with tetrahydrofolate (THF) to form formyl-THF",
                "notes": "WLP converts two CO2 to one acetyl-CoA using THF as the C1 carrier."
              }
            ]
          },
          {
            "subject": "wood_ljungdahl_pathway",
            "predicate": "has quality",
            "object": "net_zero_atp_slp",
            "description": "Formate activation offsets SLP so the WLP nets zero ATP by substrate-level phosphorylation.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fbioe.2024.1395540",
                "snippet": "the activation of formate consumes one ATP, resulting in zero net ATP yield through SLP",
                "notes": "Activation of formate consumes one ATP, so substrate-level phosphorylation nets zero ATP."
              }
            ]
          },
          {
            "subject": "formyl_thf_synthetase",
            "predicate": "contributes to",
            "object": "wood_ljungdahl_pathway",
            "description": "Formyl-THF synthetase performs the ATP-consuming formate step.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fbioe.2024.1395540",
                "snippet": "The second step is the reaction of formate with tetrahydrofolate (THF), catalyzed by formyl-THF synthetase (FTS) and consuming one ATP",
                "notes": "Verified against the freely available article PDF."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "methyltransferase",
            "predicate": "contributes to",
            "object": "wood_ljungdahl_pathway",
            "description": "The methyltransferase loads the WLP corrinoid protein.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fbioe.2024.1395540",
                "snippet": "the methyl group of methyl-THF is transferred to a corrinoid iron-sulfur-containing protein (CoFeSP) via the methyltransferase (MT)",
                "notes": "Verified against the freely available article PDF."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "acetyl_coa_synthase",
            "predicate": "contributes to",
            "object": "wood_ljungdahl_pathway",
            "description": "CODH/ACS performs the acetyl-CoA-forming WLP step.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fbioe.2024.1395540",
                "snippet": "In the final step of WLP, the bi-functional CODH/ACS enzyme complex catalyzes the reaction that converts CO, methyl-CoFeSP and CoA into acetyl-CoA",
                "notes": "Verified against the freely available article PDF."
              }
            ],
            "predicate_id": "RO:0002326"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-08-23T09:09:00Z",
        "curator": "codex",
        "action": "CURATE_PROTEIN_TAXON_EXAMPLE",
        "changes": "Reviewed the graph as mechanistic, grounded Fhs, AcsE activity, and the ACS activity with exact GO terms, retained combined CoFeSP as reviewed label-only, and added DOI-backed UniProtKB P27988 as the ACS alpha-subunit exemplar.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-30T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate METABOLISM trait (Wood-Ljungdahl / reductive acetyl-CoA carbon-fixation pathway); sub-variant of carbon fixation. Distinct from the existing acetogenesis metabolism class (which produces acetate via this pathway).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-10T14:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (Wood-Ljungdahl reductive acetyl-CoA) with GO/CHEBI node groundings and RO/METPO predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-15T07:20:37Z",
        "curator": "claude",
        "action": "FIX_NODE_GROUNDING_CURIE",
        "changes": "Overwrote 1 causal-node grounding(s) (obsolete/wrong GO -> corrected, verified vs OAK).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 9 evidence-backed generic edges (12 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:12Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d72, METPO:2000017\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-26T07:15:19Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A0C5IX96\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:23:54Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0009326\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 1 causal edge(s) off enables/RO:0002327 with a TRAIT object (1 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T02:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES_PART2",
        "changes": "Re-grounded 3 causal edge(s) off microbe-domain METPO predicates onto their causal-graph counterparts (2 to produces, 1 to reduces), issue 301 part 2. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Each replacement is a 1:1 mirror of its source predicate that changes only the domain, so the claim each edge makes is unchanged and directions are unchanged. The replacements are proposed in proposals/metpo_traitmech_v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-22T04:26:15Z",
        "curator": "codex",
        "action": "REVIEW_UNIPROT_INSTANCE_GROUNDINGS",
        "changes": "Reviewed 1 organism-specific UniProtKB grounding(s): replaced 0 with taxon-agnostic GO/InterPro terms and retracted 1 to label-only where no exact semantic term was supported (docs/GROUNDING_POLICY.md).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-30T19:21:37Z",
        "curator": "codex",
        "action": "REVIEW_EVIDENCE_REFERENCE_CHURN",
        "changes": "Offline review for issue 520 retained 2 evidence-reference replacement(s) that PR 511 made on surviving causal edges outside its stated protein-taxon scope. The pre-tranche evidence entries had references but no snippets; the retained entries supply edge-specific snippets and explanatory notes. Reverting would discard that claim-level provenance, so the scope defect is resolved by documenting the decision instead. This audit changed no causal claim or evidence field. Reviewed replacements: DOI:10.1039/d4cb00099d -> DOI:10.3389/fbioe.2024.1395540 (1 edge); DOI:10.1128/AEM.02473-10 -> DOI:10.3389/fbioe.2024.1395540 (1 edge).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T09:00:00Z",
        "curator": "codex",
        "action": "CONNECT_CAUSAL_GRAPH_COMPONENTS",
        "changes": "Resolved issue #183 graph fragmentation (4 components to 1) using 3 public-source, verbatim-snippet-backed connector(s). No paid research service was called.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-05T17:46:22Z",
        "curator": "codex",
        "action": "ADD_PATHWAY_CONTEXT",
        "changes": "Added pinned PathwayMech context on reviewed causal nodes with explicit route and organism limitations; retained existing groundings and exact xrefs.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-22T01:35:00Z",
        "curator": "claude",
        "action": "REFRESH_UNIPROT_ENTRY_VERSION",
        "changes": "Refreshed UniProtKB entry_version against live UniProt REST on 2026-10-22: UniProtKB:P27988 (125 -> 126 on acetyl_coa_synthase).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000113",
    "label": "xylan degradation",
    "definition": "A biopolymer-degradation metabolism in which an organism hydrolyzes xylan, the most abundant hemicellulose, into xylose and xylo-oligosaccharides using xylanases and accessory enzymes.",
    "definition_source": "DOI:10.1111/j.1757-1707.2009.01004.x",
    "trait_category": "METABOLISM",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "traitmech:000110"
    ],
    "synonyms": [
      {
        "synonym_text": "xylanolytic",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1111/j.1757-1707.2009.01004.x"
      },
      {
        "synonym_text": "hemicellulose degradation",
        "synonym_type": "BROAD_SYNONYM",
        "source": "DOI:10.1016/j.cbpa.2015.10.018"
      },
      {
        "synonym_text": "xylan breakdown",
        "synonym_type": "EXACT_SYNONYM",
        "source": "http://purl.obolibrary.org/obo/go/releases/2026-07-26/go-basic.obo"
      },
      {
        "synonym_text": "xylan catabolism",
        "synonym_type": "EXACT_SYNONYM",
        "source": "http://purl.obolibrary.org/obo/go/releases/2026-07-26/go-basic.obo"
      },
      {
        "synonym_text": "xylanolysis",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1126/science.aaf4507"
      }
    ],
    "xrefs": [
      "GO:0045493"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1111/j.1757-1707.2009.01004.x",
        "notes": "Dodd & Cann review the enzymatic deconstruction of xylan, the major hemicellulosic polysaccharide."
      },
      {
        "reference": "DOI:10.1016/j.cbpa.2015.10.018",
        "notes": "Cragg et al. include hemicellulose (xylan) degradation within lignocellulose breakdown across organisms."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:44001",
        "taxon_label": "Caldicellulosiruptor saccharolyticus",
        "note": "thermophilic hemicellulose degrader",
        "reference": "PMID:18776029"
      },
      {
        "taxon_id": "NCBITaxon:28116",
        "taxon_label": "Bacteroides ovatus",
        "note": "gut xylan utiliser",
        "reference": "PMID:1444385"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "xylan_degradation_xylanase",
        "title": "Xylan degradation hydrolyzes hemicellulose to xylose",
        "description": "Evidence-backed causal sketch linking xylanases and accessory enzymes to xylan hydrolysis into xylose and xylo-oligosaccharides.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "The graph combines core xylanase activity, carbon-catabolite regulation, and accessory CE15 enzymes. The C. saccharolyticus XynA example supports the core xylanase branch only.",
        "nodes": [
          {
            "node_id": "xylan_degradation_trait",
            "label": "xylan degradation",
            "node_type": "TRAIT",
            "grounding": "traitmech:000113",
            "description": "Hydrolysis of xylan to assimilable pentose sugars."
          },
          {
            "node_id": "xylanase",
            "label": "xylanase systems",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Endo-/exo-xylanases and accessory enzymes acting on xylan.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "This system-level node combines endo- and exo-xylanases with accessory enzymes from multiple families; no one ontology term denotes the set.",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:P23556",
                "protein_label": "Endo-1,4-beta-xylanase A",
                "gene_symbol": "xynA",
                "taxon_id": "NCBITaxon:44001",
                "taxon_label": "Caldicellulosiruptor saccharolyticus",
                "entry_status": "REVIEWED",
                "retrieved_on": "2026-10-22",
                "entry_version": 102,
                "sequence_version": 1,
                "role": "XynA endo-xylanase representing the core hydrolytic component of the broader xylanase-system node.",
                "evidence": [
                  {
                    "reference": "DOI:10.1128/aem.56.4.1017-1024.1990",
                    "snippet": "ORF1 appears to code for a xylanase (XynA)",
                    "notes": "The primary cloning and expression study identifies active XynA from C. saccharolyticus. UniProtKB P23556 is the reviewed XynA entry from the same species."
                  }
                ]
              }
            ]
          },
          {
            "node_id": "xylose",
            "label": "xylose",
            "node_type": "CHEMICAL",
            "description": "Pentose monosaccharide released from xylan.",
            "grounding": "CHEBI:18222"
          },
          {
            "node_id": "hemicellulase_genes",
            "label": "hemicellulase gene expression",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Expression of xylanase/hemicellulase-encoding genes underlying xylan degradation."
          },
          {
            "node_id": "carbon_catabolite_repression",
            "label": "carbon catabolite repression",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Glucose-dependent repression (HPr/CcpA-mediated) of catabolic gene expression."
          },
          {
            "node_id": "glucuronoyl_esterase",
            "label": "CE15 glucuronoyl esterases",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Accessory esterases cleaving lignin-carbohydrate ester linkages on glucuronoxylan.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "CAZy CE15 contains glucuronoyl and other esterase activities, while the available InterPro match is the broader alpha/beta-hydrolase superfamily; neither is an exact reviewed grounding for this functional plural node."
          },
          {
            "node_id": "xylan_saccharification",
            "label": "xylan saccharification",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Enzymatic release of soluble sugars from xylan/hemicellulose."
          },
          {
            "node_id": "aldouronic_acids",
            "label": "aldouronic acids",
            "node_type": "CHEMICAL",
            "description": "Glucuronoxylan-derived acidic xylo-oligosaccharides released during degradation."
          }
        ],
        "edges": [
          {
            "subject": "xylanase",
            "predicate": "confers",
            "object": "xylan_degradation_trait",
            "description": "Xylanase systems drive xylan depolymerization extracellularly.",
            "evidence": [
              {
                "reference": "DOI:10.1111/j.1757-1707.2009.01004.x",
                "notes": "Dodd & Cann review enzymatic deconstruction of xylan."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "xylan_degradation_trait",
            "predicate": "produces",
            "object": "xylose",
            "description": "Xylan hydrolysis yields xylose and xylo-oligosaccharides.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.cbpa.2015.10.018",
                "notes": "Cragg et al. include hemicellulose (xylan) degradation within lignocellulose breakdown across organisms."
              }
            ],
            "predicate_id": "METPO:2007800"
          },
          {
            "subject": "carbon_catabolite_repression",
            "predicate": "represses",
            "object": "hemicellulase_genes",
            "description": "CCR (HPr/CcpA) represses hemicellulase gene expression when glucose is available.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s00253-023-12977-4",
                "notes": "Novak & Gardner 2024: carbon catabolite repression (HPr/CcpA) mediates glucose-dependent repression of hemicellulase expression; broad regulatory edge directly relevant to trait expression conditions."
              }
            ]
          },
          {
            "subject": "hemicellulase_genes",
            "predicate": "has output",
            "object": "xylanase",
            "description": "Expression of hemicellulase-encoding genes yields the xylanase systems that act on non-preferred hemicellulosic carbon sources.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s00253-023-12977-4",
                "snippet": "genes that encode the proteins responsible for the metabolism of non-preferred carbon sources",
                "notes": "Novak & Gardner describe this output of carbon-catabolite-regulated gene expression in their xylanase and hemicellulase regulatory review."
              }
            ],
            "predicate_id": "RO:0002234"
          },
          {
            "subject": "glucuronoyl_esterase",
            "predicate": "positively regulates",
            "object": "xylan_saccharification",
            "description": "CE15 glucuronoyl esterases synergistically increase xylanase saccharification of pretreated biomass.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s13068-025-02639-0",
                "notes": "Pentari et al. 2025: CE15 glucuronoyl esterases increased saccharification by xylanases (57-61 uM xylose equivalents) on pretreated lignocellulose; accessory-enzyme synergy edge."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "glucuronoyl_esterase",
            "predicate": "produces",
            "object": "aldouronic_acids",
            "description": "CE15 glucuronoyl esterases promote GH30 glucuronoxylanase release of aldouronic acids.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s13068-025-02639-0",
                "notes": "Pentari et al. 2025: CE15 esterases led to up to three-times higher release of aldouronic acids by GH30 glucuronoxylanase."
              }
            ],
            "predicate_id": "METPO:2007800"
          },
          {
            "subject": "xylan_saccharification",
            "predicate": "has output",
            "object": "xylose",
            "description": "Xylan saccharification releases xylose-equivalent soluble sugars.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s13068-025-02639-0",
                "snippet": "increasing saccharification by 57\u2009\u00b1\u20091 \u03bcM and 61\u2009\u00b1\u20093 \u03bcM of xylose equivalents, respectively",
                "notes": "Pentari et al. directly quantified xylose-equivalent output during CE15-assisted xylan saccharification."
              }
            ],
            "predicate_id": "RO:0002234"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-06-08T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate METABOLISM trait (xylan / hemicellulose degradation); sub-variant of biopolymer degradation.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-10T14:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (xylanase hydrolysis of xylan) with RO/METPO predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-14T06:55:38Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:18222\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 3 evidence-backed generic edges (5 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:12Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-04T03:08:14Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002213\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 1 causal edge(s) off enables/RO:0002327 with a TRAIT object (1 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T02:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES_PART2",
        "changes": "Re-grounded 2 causal edge(s) off microbe-domain METPO predicates onto their causal-graph counterparts (2 to produces), issue 301 part 2. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Each replacement is a 1:1 mirror of its source predicate that changes only the domain, so the claim each edge makes is unchanged and directions are unchanged. The replacements are proposed in proposals/metpo_traitmech_v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-24T09:30:00Z",
        "curator": "codex",
        "action": "CURATE_PROTEIN_TAXON_EXAMPLE",
        "changes": "Scoped the composite xylan-degradation mechanism, added a DOI-backed C. saccharolyticus XynA example, and documented reviewed label-only dispositions for the multi-family xylanase-system and CE15 accessory-enzyme nodes.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:24:00Z",
        "curator": "claude",
        "action": "RESTORE_CANONICAL_CITATION",
        "changes": "Restored the canonical-example citation for NCBITaxon:44001 from DOI:10.1128/aem.56.4.1017-1024.1990 back to PMID:18776029 (review issue 519). The tranche event described the change as a PMID-to-DOI upgrade, but the DOI resolves to a different paper than the PMID, so this was a replacement rather than an identifier normalisation. The pre-tranche citation is restored; a deliberate replacement can be made in a new event that says so.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T06:15:40Z",
        "curator": "codex",
        "action": "ADD_EXACT_ONTOLOGY_MATCH",
        "changes": "Ontology exact-match review (2026-08-25): approved exact xref(s): GO:0045493; declared exact synonym(s): 'xylan breakdown', 'xylan catabolism'. Evidence is predicate-scoped in the versioned ontology snapshots; OAK cross-checked direct data, and OLS4 spot-checked release deltas and disputed hits.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T09:15:30Z",
        "curator": "codex",
        "action": "CONNECT_CAUSAL_GRAPH",
        "changes": "Connected the carbon-catabolite-regulation and CE15-saccharification branches to the core xylan-degradation mechanism with two source-verified has-output edges; genes remain supporting graph fields rather than primary records (issues 426 and 183).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-08T00:00:00Z",
        "curator": "codex",
        "action": "ADD_EXACT_SYNONYM",
        "changes": "Added xylanolysis as an exact FAPROTAX synonym rather than minting the duplicate v11 candidate because GO:0045493 already grounds xylan degradation.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-22T01:35:00Z",
        "curator": "claude",
        "action": "REFRESH_UNIPROT_ENTRY_VERSION",
        "changes": "Refreshed UniProtKB entry_version against live UniProt REST on 2026-10-22: UniProtKB:P23556 (101 -> 102 on xylanase).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000185",
    "label": "akinete",
    "definition": "A morphology trait in which a filamentous cyanobacterium differentiates enlarged, thick-coated, spore-like dormant cells called akinetes that can germinate into vegetative cells.",
    "definition_source": "DOI:10.1159/000517443",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1159/000517443",
        "snippet": "Some cyanobacteria of the order Nostocales can form akinetes, spore-like dormant cells resistant to various unfavorable environmental fluctuations.",
        "notes": "Garg and Maldener support akinetes as spore-like dormant cells formed by Nostocales cyanobacteria under unfavorable environmental conditions."
      },
      {
        "reference": "DOI:10.1159/000517443",
        "snippet": "Akinetes are enveloped in a thick protective coat containing a multilayered structure and are able to germinate into new vegetative cells under suitable growth conditions.",
        "notes": "The source supports the thick protective coat and vegetative-cell germination clauses in the local definition."
      },
      {
        "reference": "DOI:10.3389/fmicb.2025.1677844",
        "snippet": "Raphidiopsis raciborskii (Nostocales) is a successful invader of temperate ecosystems originating from the tropics that forms akinetes in their new habitats to overcome unfavorable winter conditions.",
        "notes": "Rios-Henriquez and Weithoff provide a second Nostocales cyanobacterium study supporting akinete formation as an unfavorable-condition dormancy trait."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:240292",
        "taxon_label": "Trichormus variabilis ATCC 29413",
        "note": "Model Nostocales strain still cited in the akinete literature as Anabaena variabilis ATCC 29413; the NCBI Taxonomy record lists that name as an equivalent name.",
        "reference": "DOI:10.1159/000517443"
      }
    ],
    "discussions": [
      {
        "discussion_id": "akinete-exact-xref-gap",
        "prompt": "Resolve exact external ontology xrefs for the cyanobacterial akinete morphology trait.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "The pinned METPO snapshot contains only deprecated akinete classes, including METPO:1000012 obsolete akinete; no active METPO, GO, or OBO class was accepted as an exact equivalent for this cyanobacterial dormant-cell trait.",
        "posed_by": "codex",
        "posed_date": "2026-09-14"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-14T15:47:55Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted akinete as a DOI-backed TraitRecord after a repository-wide duplicate review covering ignored and hidden files; live METPO has no active exact akinete class and the placeholder is reserved in proposals/metpo_traitmech_v62.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000059",
    "label": "amphitrichous",
    "definition": "A flagellar arrangement with flagella (single filaments or tufts) at both poles of the cell.",
    "definition_source": "DOI:10.1093/femsre/fuv034",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "traitmech:000056"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1093/femsre/fuv034",
        "notes": "Schuhmacher et al. describe bipolar (amphitrichous) flagellation among the flagellation patterns governed by FlhF/FlhG."
      },
      {
        "reference": "DOI:10.3390/biom9070279",
        "notes": "Flagellum review supports polar flagellar filaments as locomotory organelles."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:968",
        "taxon_label": "Spirillum volutans",
        "note": "Large spiral bacterium with amphitrichous flagellar tufts (bipolar flagellar bundles).",
        "reference": "PMID:16561638"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "amphitrichous_bipolar_flagella",
        "title": "Amphitrichous flagellation \u2014 bipolar flagella",
        "description": "Evidence-backed causal sketch linking bacterial flagella at both poles to the amphitrichous arrangement.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a broad environmental or morphological classification spanning multiple mechanisms, a measurement-like bin, or an absence/arrangement descriptor; contextual protein nodes do not receive token UniProt examples.",
        "nodes": [
          {
            "node_id": "amphitrichous_trait",
            "label": "amphitrichous",
            "node_type": "TRAIT",
            "grounding": "traitmech:000059",
            "description": "Flagella (single filaments or tufts) at both cell poles."
          },
          {
            "node_id": "bacterial_flagellum",
            "label": "bacterial-type flagellum",
            "node_type": "CELLULAR_LOCALIZATION",
            "grounding": "GO:0009288",
            "description": "Helical proteinaceous locomotory organelle."
          },
          {
            "node_id": "bipolar_placement",
            "label": "bipolar placement",
            "node_type": "QUALITY",
            "description": "Flagella positioned at both poles of the cell."
          },
          {
            "node_id": "flhf_gtpase",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "FlhF",
            "node_type": "GENE_OR_PROTEIN",
            "description": "SRP-type GTPase that positions and recruits flagellar building blocks to the cell pole."
          },
          {
            "node_id": "flhg_atpase",
            "label": "FlhG",
            "node_type": "GENE_OR_PROTEIN",
            "description": "MinD/ParA-family ATPase that regulates FlhF activity and polar flagellar number.",
            "grounding": "InterPro:IPR033875"
          },
          {
            "node_id": "flig_protein",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "FliG",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Flagellar C-ring switch protein engaged early by FlhF during assembly."
          },
          {
            "node_id": "flif_msring",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "FliF (MS-ring)",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Transmembrane MS-ring forming protein, an early flagellar assembly intermediate."
          },
          {
            "node_id": "fipa_protein",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "FipA",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Membrane protein that facilitates polar recruitment of FlhF."
          },
          {
            "node_id": "cell_pole",
            "label": "cell pole",
            "node_type": "CELLULAR_LOCALIZATION",
            "description": "Polar membrane region where flagellar assembly is nucleated.",
            "grounding": "GO:0060187"
          },
          {
            "node_id": "flhf_polar_localization",
            "label": "FlhF polar localization",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Recruitment and confinement of FlhF to the cell pole."
          },
          {
            "node_id": "polar_flagellar_number",
            "label": "polar flagellar number",
            "node_type": "QUALITY",
            "description": "Number of flagella formed at the cell pole."
          }
        ],
        "edges": [
          {
            "subject": "bacterial_flagellum",
            "predicate": "defines",
            "object": "amphitrichous_trait",
            "description": "Flagella at both cell poles define the amphitrichous arrangement.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuv034",
                "notes": "Schuhmacher et al. describe bipolar (amphitrichous) flagellation governed by FlhF/FlhG."
              }
            ],
            "predicate_id": "METPO:2007500"
          },
          {
            "subject": "amphitrichous_trait",
            "predicate": "associated with",
            "object": "bipolar_placement",
            "description": "The amphitrichous pattern places flagella at both poles.",
            "evidence": [
              {
                "reference": "DOI:10.3390/biom9070279",
                "notes": "Flagellum review supports polar flagellar filaments as locomotory organelles."
              }
            ],
            "predicate_id": "biolink:associated_with"
          },
          {
            "subject": "flhf_gtpase",
            "predicate": "binds",
            "object": "flig_protein",
            "description": "FlhF specifically interacts with the polar-system FliG to initiate assembly.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-024-50274-4",
                "notes": "FlhF exhibited a strong interaction with FliG and specifically interacts with FliG from the polar flagellar system."
              }
            ]
          },
          {
            "subject": "flig_protein",
            "predicate": "binds",
            "object": "flif_msring",
            "description": "FlhF-bound FliG captures FliF, promoting MS-ring formation at the pole.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-024-50274-4",
                "notes": "When bound to FlhF, FliG was able to interact with the cytoplasmic domain of the MS-ring forming protein FliF."
              }
            ]
          },
          {
            "subject": "flhf_gtpase",
            "predicate": "localizes to",
            "object": "cell_pole",
            "description": "GTP-bound dimeric FlhF localizes to the cell pole to nucleate flagellar assembly.",
            "evidence": [
              {
                "reference": "DOI:10.7554/eLife.93004.3",
                "notes": "GTP-bound dimeric FlhF localizes to the cell pole where it recruits the initial flagellar building blocks."
              }
            ],
            "predicate_id": "biolink:located_in"
          },
          {
            "subject": "fipa_protein",
            "predicate": "directly interacts with",
            "object": "flhf_gtpase",
            "description": "FipA directly interacts with FlhF and facilitates its polar recruitment.",
            "evidence": [
              {
                "reference": "DOI:10.7554/eLife.93004.3",
                "notes": "In all three species, FipA directly interacts with FlhF and facilitates its recruitment to the membrane at the cell pole."
              }
            ]
          },
          {
            "subject": "fipa_protein",
            "predicate": "promotes",
            "object": "flhf_polar_localization",
            "description": "Loss of FipA significantly decreases polar localization of FlhF.",
            "evidence": [
              {
                "reference": "DOI:10.7554/eLife.93004.3",
                "notes": "In the absence of FipA, polar localization of FlhF was significantly decreased in all three species."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "flhg_atpase",
            "predicate": "stimulates GTPase activity of",
            "object": "flhf_gtpase",
            "description": "ATP-bound FlhG dimer stimulates FlhF GTPase activity, controlling its polar dynamics.",
            "evidence": [
              {
                "reference": "DOI:10.7554/eLife.93004.3",
                "notes": "The ATP-bound FlhG dimer can interact with the GTP-bound FlhF dimer, thereby stimulating its GTPase activity."
              }
            ]
          },
          {
            "subject": "flhg_atpase",
            "predicate": "restricts",
            "object": "polar_flagellar_number",
            "description": "FlhG links flagella synthesis with transcription and restricts polar flagellar number.",
            "evidence": [
              {
                "reference": "DOI:10.7554/eLife.93004.3",
                "notes": "FlhG links flagella synthesis with transcription regulation and effectively restricts the number of polar flagella that are formed."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-06-03T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate MORPHOLOGY trait (amphitrichous flagellation); sub-variant of flagellar arrangement.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-09T15:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (bipolar flagella) with GO node grounding and METPO/biolink predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 7 evidence-backed generic edges (8 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:12Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:located_in\u00d71, RO:0002213\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:33Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0060187\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-26T07:15:19Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 4 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A656AC42\u00d71, UniProtKB:Q2N2M1\u00d71, UniProtKB:A0A016XEK1\u00d71, UniProtKB:A0A023UGD7\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:21:11Z",
        "curator": "claude",
        "action": "RETRACT_DEAD_UNIPROT_GROUNDINGS",
        "changes": "Retracted 3 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-22T04:26:15Z",
        "curator": "codex",
        "action": "REVIEW_UNIPROT_INSTANCE_GROUNDINGS",
        "changes": "Reviewed 1 organism-specific UniProtKB grounding(s): replaced 1 with taxon-agnostic GO/InterPro terms and retracted 0 to label-only where no exact semantic term was supported (docs/GROUNDING_POLICY.md).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope amphitrichous_bipolar_flagella=NONMECHANISTIC with scope_notes; marked 4 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (flhf_gtpase, flig_protein, flif_msring, fipa_protein).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000705",
    "label": "axially filamented",
    "definition": "A motility where the flagellum filament of an organism is located in the periplasm and does not extend past the cell envelope.",
    "definition_source": "DOI:10.3390/biom10040550",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000702"
    ],
    "synonyms": [
      {
        "synonym_text": "axial filament",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "created_by": "Luke Wang",
    "evidence": [
      {
        "reference": "DOI:10.3390/biom10040550",
        "snippet": "flagella are hidden within the periplasmic space",
        "notes": "Supports axial/periplasmic flagella as the defining motility structure."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:173",
        "taxon_label": "Leptospira interrogans",
        "note": "Spirochete with axial filaments (periplasmic endoflagella within the periplasm driving corkscrew motility).",
        "reference": "PMID:32157997"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "axially_filamented_periplasmic_flagella",
        "title": "Axial filament periplasmic flagella mechanism",
        "description": "Evidence-backed causal sketch linking axial filament motility to periplasmic flagella, basal motors, cell-envelope localization, torque, and corkscrew-like cell movement.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a broad environmental or morphological classification spanning multiple mechanisms, a measurement-like bin, or an absence/arrangement descriptor; contextual protein nodes do not receive token UniProt examples.",
        "nodes": [
          {
            "node_id": "axially_filamented_trait",
            "label": "axially filamented",
            "node_type": "TRAIT",
            "grounding": "METPO:1000705",
            "description": "Motility with flagellar filaments located in the periplasm."
          },
          {
            "node_id": "periplasmic_flagella",
            "label": "periplasmic flagella",
            "node_type": "CELLULAR_LOCALIZATION",
            "description": "Flagella located between the cell wall and outer membrane."
          },
          {
            "node_id": "flagellar_basal_motor",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "flagellar basal motor",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Motor embedded in the cytoplasmic membrane and peptidoglycan layer."
          },
          {
            "node_id": "periplasmic_space",
            "label": "periplasmic space",
            "node_type": "CELLULAR_LOCALIZATION",
            "description": "Space between inner and outer membranes containing spirochete flagella.",
            "grounding": "GO:0042597"
          },
          {
            "node_id": "torque_generation",
            "label": "torque generation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Motor-generated force that deforms or rotates the cell body."
          },
          {
            "node_id": "corkscrew_motility",
            "label": "corkscrew motility",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Helical or undulating movement produced by periplasmic flagella."
          },
          {
            "node_id": "flbb_ring",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "FlbB periplasmic ring",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Spirochete-specific FlbB protein ring that forms around the flagellar rotor and scaffolds the collar."
          },
          {
            "node_id": "flagellar_rotor",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "flagellar rotor",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Rotating core of the flagellar motor (MS/C ring) around which the FlbB ring forms."
          },
          {
            "node_id": "stator_complex",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "stator complex",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Ion-powered torque-generating stator units recruited around the rotor for flagellar rotation."
          },
          {
            "node_id": "wavy_cell_morphology",
            "label": "wavy / flat-wave cell morphology",
            "node_type": "QUALITY",
            "description": "Helical/flat-wave cell body shape established by periplasmic flagella acting like a cytoskeleton."
          }
        ],
        "edges": [
          {
            "subject": "periplasmic_flagella",
            "predicate": "defines",
            "object": "axially_filamented_trait",
            "description": "Axial filamented motility is defined by flagella located inside the periplasmic space.",
            "evidence": [
              {
                "reference": "DOI:10.3390/biom10040550",
                "snippet": "flagella are hidden within the periplasmic space",
                "notes": "Supports periplasmic flagella as the defining structure."
              }
            ],
            "predicate_id": "METPO:2007500"
          },
          {
            "subject": "periplasmic_flagella",
            "predicate": "localized in",
            "object": "periplasmic_space",
            "description": "Spirochete flagella reside inside the cell envelope rather than extending externally.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.semcdb.2015.10.015",
                "snippet": "enclose their flagella in the periplasm",
                "notes": "Supports periplasmic localization of spirochete flagella."
              }
            ],
            "predicate_id": "biolink:located_in"
          },
          {
            "subject": "flagellar_basal_motor",
            "predicate": "rotates",
            "object": "periplasmic_flagella",
            "description": "Basal motors drive periplasmic flagellar rotation.",
            "evidence": [
              {
                "reference": "DOI:10.3390/biom10040550",
                "snippet": "connects with a basal motor",
                "notes": "Supports basal motor linkage to periplasmic flagella."
              }
            ]
          },
          {
            "subject": "torque_generation",
            "predicate": "depends on",
            "object": "flagellar_basal_motor",
            "description": "Spirochete-specific motor structures generate torque needed for motility.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mBio.02494-21",
                "snippet": "generation of the high torque necessary",
                "notes": "Supports torque generation by spirochete flagellar motor structures."
              }
            ],
            "predicate_id": "RO:0002502"
          },
          {
            "subject": "periplasmic_flagella",
            "predicate": "enables",
            "object": "corkscrew_motility",
            "description": "Periplasmic flagella drive cell-body undulation or corkscrew-like movement.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.semcdb.2015.10.015",
                "snippet": "long, helical appendages known as flagella to move",
                "notes": "Supports motility by periplasmic flagella in spirochetes."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "corkscrew_motility",
            "predicate": "realizes",
            "object": "axially_filamented_trait",
            "description": "Corkscrew or undulating movement is the observed locomotion phenotype of axial filament systems.",
            "evidence": [
              {
                "reference": "DOI:10.3390/biom10040550",
                "snippet": "mechanics of spirochete motility",
                "notes": "Supports cell-body mechanics as the phenotype-level expression of periplasmic flagella."
              }
            ]
          },
          {
            "subject": "flbb_ring",
            "predicate": "forms ring around",
            "object": "flagellar_rotor",
            "description": "FlbB forms a novel periplasmic ring around the flagellar rotor, a structural scaffold for the spirochete motor.",
            "evidence": [
              {
                "reference": "DOI:10.1371/journal.ppat.1012812",
                "notes": "\"FlbB forms a novel periplasmic ring around the rotor\"; broadly applicable to spirochetes with FlbB homologs."
              }
            ]
          },
          {
            "subject": "flbb_ring",
            "predicate": "recruits",
            "object": "stator_complex",
            "description": "The FlbB-based collar scaffold supports recruitment of torque-generating stator complexes around the rotor.",
            "evidence": [
              {
                "reference": "DOI:10.1371/journal.ppat.1012812",
                "notes": "\"acts as a scaffold supporting collar assembly and subsequent recruitment of stator complexes\""
              }
            ]
          },
          {
            "subject": "stator_complex",
            "predicate": "generates",
            "object": "torque_generation",
            "description": "Ion-powered stator complexes generate the torque that drives periplasmic flagellar rotation.",
            "evidence": [
              {
                "reference": "DOI:10.1371/journal.ppat.1012812",
                "notes": "\"bridges the rotor and 16 torque-generating stator complexes in each flagellar motor\"; stators are the torque-generating units."
              }
            ],
            "predicate_id": "biolink:produces"
          },
          {
            "subject": "periplasmic_flagella",
            "predicate": "contributes to",
            "object": "wavy_cell_morphology",
            "description": "Periplasmic flagella establish the wavy/flat-wave cell morphology, acting like a cytoskeleton.",
            "evidence": [
              {
                "reference": "DOI:10.3390/biom10040550",
                "notes": "\"Another important role of the PF is to establish a wavy morphology, similar to a cytoskeleton\""
              }
            ],
            "predicate_id": "RO:0002326"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.907078+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-11T00:00:00-07:00",
        "curator": "codex",
        "action": "CURATED_WITH_LITERATURE",
        "changes": "Reviewed axially filamented trait and added DOI-backed causal graph for periplasmic flagella, basal motors, torque generation, and spirochete corkscrew motility.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T08:21:49Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:located_in\u00d71, RO:0002502\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:38:00Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0042597\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T07:37:40Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007500\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 4 evidence-backed generic edges (4 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:12Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:produces\u00d71, RO:0002326\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope axially_filamented_periplasmic_flagella=NONMECHANISTIC with scope_notes; marked 4 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (flagellar_basal_motor, flbb_ring, flagellar_rotor, stator_complex).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000667",
    "label": "bacillus shaped",
    "definition": "A cell shape characterized by an elongated, rod cylindrical morphology with relatively parallel sides and rounded ends.",
    "definition_source": "DOI:10.1146/annurev-cellbio-010521-010834",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000666"
    ],
    "synonyms": [
      {
        "synonym_text": "bacillus",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "created_by": "Anthea Guo",
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev-cellbio-010521-010834",
        "snippet": "bacterial rod shape formation",
        "notes": "Supports bacillus shape as a rod-like bacterial morphogenesis phenotype."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1423",
        "taxon_label": "Bacillus subtilis",
        "note": "The namesake bacillus (straight rod); model Gram-positive rod-shaped bacterium.",
        "reference": "PMID:9384377"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "bacillus_shaped_rod_elongation",
        "title": "Bacillus-shape rod elongation mechanism",
        "description": "Evidence-backed causal sketch linking bacillus morphology to MreB-organized Rod complexes, lateral peptidoglycan insertion, and FtsZ-coupled division.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a broad environmental or morphological classification spanning multiple mechanisms, a measurement-like bin, or an absence/arrangement descriptor; contextual protein nodes do not receive token UniProt examples.",
        "nodes": [
          {
            "node_id": "bacillus_shaped_trait",
            "label": "bacillus shaped",
            "node_type": "TRAIT",
            "grounding": "METPO:1000667",
            "description": "Elongated cylindrical rod-like bacterial morphology."
          },
          {
            "node_id": "mreB",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "MreB",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Actin-like protein involved in rod-shape maintenance."
          },
          {
            "node_id": "rod_complex",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "Rod complex",
            "node_type": "GENE_OR_PROTEIN",
            "description": "MreB-associated cell-wall elongation machinery."
          },
          {
            "node_id": "peptidoglycan_synthesis",
            "label": "peptidoglycan synthesis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Cell-wall synthesis and remodeling.",
            "grounding": "GO:0009252"
          },
          {
            "node_id": "lateral_cell_wall_elongation",
            "label": "lateral cell-wall elongation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Sidewall growth that lengthens rod-shaped cells."
          },
          {
            "node_id": "ftsZ",
            "label": "FtsZ",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Division-ring protein coordinating septal growth.",
            "grounding": "InterPro:IPR000158"
          },
          {
            "node_id": "peptidoglycan_cell_wall",
            "label": "peptidoglycan cell wall",
            "node_type": "CELLULAR_LOCALIZATION",
            "description": "Peptidoglycan sacculus that protects against osmotic lysis and determines cell shape."
          },
          {
            "node_id": "rodA_pbp2_synthase",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "RodA-PBP2 synthase (Rod complex)",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Essential elongasome peptidoglycan synthase responsible for bacterial elongation."
          },
          {
            "node_id": "bacterial_elongation",
            "label": "bacterial cell elongation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Lengthwise growth of the rod-shaped cell driven by elongasome synthesis."
          },
          {
            "node_id": "circumferential_glycan_insertion",
            "label": "circumferential glycan strand insertion",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Elongasome-mediated insertion of long glycan strands as barrel-hoop-like reinforcing structures."
          },
          {
            "node_id": "moenomycin",
            "label": "moenomycin",
            "node_type": "CHEMICAL",
            "description": "Antibiotic that inhibits class A penicillin-binding proteins (PG glycosyltransferases).",
            "grounding": "CHEBI:28908"
          },
          {
            "node_id": "class_a_pbps",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "class A penicillin-binding proteins",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Class A PBPs (aPBPs), a family of peptidoglycan synthases."
          },
          {
            "node_id": "rodZ",
            "label": "RodZ",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Membrane protein broadly implicated in rod-shape maintenance.",
            "grounding": "InterPro:IPR023690"
          },
          {
            "node_id": "spherical_morphology",
            "label": "spherical cell morphology",
            "node_type": "TRAIT",
            "description": "Coccus-like spherical cell shape, the phenotype arising from loss of rod-shape determinants."
          }
        ],
        "edges": [
          {
            "subject": "mreB",
            "predicate": "interacts with",
            "object": "rod_complex",
            "description": "MreB filaments interact with the Rod complex that elongates the cell wall.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-cellbio-010521-010834",
                "snippet": "MreB filaments interact with Rod complexes",
                "notes": "Supports MreB-Rod complex interaction in rod-shape regulation."
              }
            ],
            "predicate_id": "biolink:interacts_with"
          },
          {
            "subject": "rod_complex",
            "predicate": "directs",
            "object": "peptidoglycan_synthesis",
            "description": "Rod complexes direct sidewall peptidoglycan synthesis.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-cellbio-010521-010834",
                "snippet": "Rod complexes drive cell wall insertion",
                "notes": "Supports Rod complex contribution to wall insertion."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "peptidoglycan_synthesis",
            "predicate": "has output",
            "object": "lateral_cell_wall_elongation",
            "description": "Directed peptidoglycan synthesis supports cylindrical elongation.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2677",
                "snippet": "peptidoglycan synthesis to bacterial growth and morphology",
                "notes": "Supports regulated peptidoglycan synthesis as a determinant of bacterial morphology."
              }
            ],
            "predicate_id": "RO:0002234"
          },
          {
            "subject": "lateral_cell_wall_elongation",
            "predicate": "regulates",
            "object": "bacillus_shaped_trait",
            "description": "Lateral wall elongation maintains bacillus-like rod morphology.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.tim.2011.11.004",
                "snippet": "restores its rod shape",
                "notes": "Supports MreB-associated cell-wall synthesis as important for rod shape restoration and maintenance."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "ftsZ",
            "predicate": "coordinates with",
            "object": "peptidoglycan_synthesis",
            "description": "FtsZ coordinates division-associated peptidoglycan synthesis with rod-cell growth.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro1205",
                "snippet": "FtsZ collaborates with penicillin binding proteins",
                "notes": "Supports FtsZ-PBP collaboration in bacterial cell-shape generation."
              }
            ]
          },
          {
            "subject": "peptidoglycan_cell_wall",
            "predicate": "determines",
            "object": "bacillus_shaped_trait",
            "description": "The peptidoglycan cell wall protects against osmotic lysis and determines cell shape.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-023-39037-9",
                "notes": "PG protects bacteria against osmotic lysis and determines cell shape."
              }
            ]
          },
          {
            "subject": "rodA_pbp2_synthase",
            "predicate": "required for",
            "object": "bacterial_elongation",
            "description": "RodA-PBP2 is the essential synthase responsible for bacterial elongation.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-023-39037-9",
                "notes": "RodA-PBP2 is an essential synthase responsible for bacterial elongation."
              }
            ]
          },
          {
            "subject": "circumferential_glycan_insertion",
            "predicate": "gives rise to",
            "object": "bacillus_shaped_trait",
            "description": "Elongasome inserts long glycan strands as barrel-hoop reinforcement, giving rise to a rod-shaped cell.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-024-49785-x",
                "notes": "Inserts long glycan strands acting as barrel-hoop-like reinforcing structures, thereby giving rise to a rod-shaped cell."
              }
            ]
          },
          {
            "subject": "moenomycin",
            "predicate": "inhibits",
            "object": "class_a_pbps",
            "description": "Moenomycin inhibits class A penicillin-binding proteins, a family of PG synthases.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-023-41082-3",
                "notes": "Moenomycin inhibits a family of PG synthases known as Class-A penicillin-binding proteins."
              }
            ],
            "predicate_id": "RO:0002212"
          },
          {
            "subject": "rodZ",
            "predicate": "causally upstream of, negative effect",
            "object": "spherical_morphology",
            "description": "Loss of RodZ causes cells to become spherical, indicating RodZ maintains rod shape.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2024.1400434",
                "notes": " delta-rodZ cells were spherical (WT cells are rod-shaped); RodZ broadly implicated in rod maintenance."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.885522+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-11T18:00:00-07:00",
        "curator": "codex",
        "action": "CURATED_WITH_LITERATURE",
        "changes": "Reviewed bacillus shape as rod-like morphology and added DOI-backed causal graph for MreB, Rod complex, peptidoglycan synthesis, lateral wall elongation, and FtsZ coupling.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T21:30:07Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002211\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:19Z",
        "curator": "claude",
        "action": "RENAME_PREDICATE_LABELS",
        "changes": "Renamed 1 causal-edge predicate label(s) to align with existing groundings: maintains \u2192 regulates \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:21Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002211\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:38:00Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0009252\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T05:05:14Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A1B1UYY2\u00d71, UniProtKB:C0LUM8\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-26T05:00:48Z",
        "curator": "claude",
        "action": "RENAME_PREDICATE_LABELS",
        "changes": "Renamed 1 causal-edge predicate label(s) to align with existing groundings: organizes \u2192 enables \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-26T05:00:50Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 5 evidence-backed generic edges (8 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:12Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002212\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:33Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:28908\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-26T07:15:19Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:H1XNL6\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:21:11Z",
        "curator": "claude",
        "action": "RETRACT_DEAD_UNIPROT_GROUNDINGS",
        "changes": "Retracted 1 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates (1 to has output), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T08:00:00Z",
        "curator": "claude",
        "action": "REGROUND_CAUSAL_EDGE",
        "changes": "Re-grounded causal edge(s) off enables/RO:0002327 onto part of (biolink:part_of), issue 334. biolink declares enables range 'biological process or activity', which only BIOLOGICAL_PROCESS, PATHWAY and MOLECULAR_FUNCTION satisfy, so an edge pointing at a GENE_OR_PROTEIN entailed a false type. The replacements are chosen per idiom rather than swept: a gene cluster ENCODES its product, a subunit is PART OF the complex it belongs to, and an energy source or acquired repertoire CONTRIBUTES TO the machine it powers or composes. All three declare no rdfs:domain or rdfs:range, so none can reintroduce the class of defect being removed.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T09:00:00Z",
        "curator": "claude",
        "action": "REGROUND_CAUSAL_EDGE",
        "changes": "Corrected the mreB edge from part of to interacts with (biolink:interacts_with), issue 334 review. The first pass over-claimed: the edge's own snippet says MreB filaments INTERACT WITH Rod complexes, and the target node is described as machinery associated with MreB, so parthood is not what the evidence supports. The corpus is also split on it - cell_shape.yaml types rod_complex a PATHWAY with MreB inside it, while this file types it GENE_OR_PROTEIN with MreB outside - which makes parthood exactly the kind of modelling decision this work defers elsewhere. interacts with says what the quoted sentence says and needs no such decision. The edge description was rephrased to match the predicate.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-22T04:26:15Z",
        "curator": "codex",
        "action": "REVIEW_UNIPROT_INSTANCE_GROUNDINGS",
        "changes": "Reviewed 2 organism-specific UniProtKB grounding(s): replaced 2 with taxon-agnostic GO/InterPro terms and retracted 0 to label-only where no exact semantic term was supported (docs/GROUNDING_POLICY.md).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope bacillus_shaped_rod_elongation=NONMECHANISTIC with scope_notes; marked 4 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (mreB, rod_complex, rodA_pbp2_synthase, class_a_pbps).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000672",
    "label": "baeocyte formation",
    "definition": "A morphological phenotype in which a cyanobacterium forms small reproductive cells called baeocytes by multiple fission within a mother cell.",
    "definition_source": "DOI:10.1007/s10482-021-01672-x",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1007/s10482-021-01672-x",
        "snippet": "Baeocytes formation through multiple fission of the mature cells, which are much larger than baeocytes.",
        "notes": "Bonthond et al. (2021), Waterburya genus Description, directly read in publisher full text. Species Description and actual Figure 4 with its caption were inspected: panel c identifies formation inside a mother cell; panel b warns that adjacent growing cells are not products of binary fission. The images do not establish division timing or protein causality. Supplements were not inspected."
      },
      {
        "reference": "PMID:18365724",
        "snippet": "Electron microscopy of cyanobacteria Pleurocapsa sp. CALU 1126 revealed that multiple fission proceeds by successive binary fissions.",
        "notes": "Pinevich et al. (2008), English scientific abstract directly retrieved at https://pubmed.ncbi.nlm.nih.gov/18365724/. Its following sentence identifies baeocytes as multiple-fission products and macrocytes as binary-fission products. This supports the reported division sequence in CALU 1126, not a universal simultaneous-cleavage requirement. Juvenile-cell differences and metabolic uncoupling are source-specific observations and interpretation, not the class definition. The Russian full paper, figures and strain provenance were not inspected; no CALU 1126 canonical example is assigned."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:2874699",
        "taxon_label": "Waterburya agarophytonicola KI4",
        "reference": "DOI:10.1007/s10482-021-01672-x",
        "note": "KI4, a non-axenic culture from seaweed apical material collected at Falckensteiner Strand near Kiel, Germany. Collection Methods report 15-degree near-dark artificial-seawater incubation and host-free subculture; the species description reports low-light liquid BG11 at 20 PSU. These are distinct culture descriptions, not an asserted Figure 4 acquisition protocol. C-A-99685 is a lyophilized filter herbarium specimen, not a living-culture accession. https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=2874699 confirms the strain-level current name with rank no rank, not a species-level ID or an independent phenotype assay."
      }
    ],
    "discussions": [
      {
        "discussion_id": "baeocyte-formation-scope",
        "prompt": "Review a closer parent and historical reproductive-cell terminology.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Use active phenotype METPO:1000059 below quality METPO:1000188. Binary fission METPO:1000033, reproductive process METPO:1000264 and reproductive structure METPO:1000265 are obsolete. Sporulation METPO:1000870 denotes dormant resistant endospores in the local record, not this reproductive-cell phenotype. Coenobium formation traitmech:000655 requires a clonal colony with an established cell complement; multiple fission alone is insufficient. Historical nanocyte and cyanobacterial endospore usages need source-specific review before synonym mapping. No exact synonyms, xrefs, SSSOM equivalents or organism-level disjointness are asserted.",
        "posed_by": "codex",
        "posed_date": "2026-10-07"
      },
      {
        "discussion_id": "baeocyte-formation-mechanism",
        "prompt": "Resolve developmental mechanisms without inferring them from sequence features.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Formation, release and subsequent growth are distinct stages. Do not impose an invariant cell count, diameter, release route, motility, dormancy, sheath state or lack of growth between divisions on the whole class. Gene predictions and static morphology do not establish a protein-resolved formation mechanism. A causal graph is deferred pending direct perturbation evidence and authority-verified protein examples; the mechanism is not claimed biologically absent.",
        "posed_by": "codex",
        "posed_date": "2026-10-07"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-08T03:20:10Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added baeocyte formation with two primary references, two verbatim snippets and a source-qualified KI4 example. Ignored-and-hidden novelty and current-main/worktree/complete-open-PR reservation checks support 000672 and v548 block 1062500-1062599. Kept reproductive morphology distinct from resistant endospores, coenobia and inferred protein mechanisms; existing records unchanged.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1003022",
    "label": "black pigmented",
    "definition": "A pigmentation phenotype in which microbial colonies or cells appear black or very dark due to accumulation of dark pigments such as melanins.",
    "definition_source": "DOI:10.1016/j.biotechadv.2021.107773",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1003021"
    ],
    "synonyms": [
      {
        "synonym_text": "Pigment_black",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1016/j.biotechadv.2021.107773",
        "snippet": "dark-colored pigment",
        "notes": "Supports black/dark microbial pigmentation as a melanin-associated color phenotype."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:837",
        "taxon_label": "Porphyromonas gingivalis",
        "note": "black-pigmented anaerobe on blood agar",
        "reference": "PMID:26903954"
      },
      {
        "taxon_id": "NCBITaxon:28132",
        "taxon_label": "Prevotella melaninogenica",
        "note": "black-pigmented anaerobe",
        "reference": "DOI:10.1099/00207713-32-4-399"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "black_pigmented_melanin_polymer",
        "title": "Black pigmentation melanin polymer mechanism",
        "description": "Evidence-backed causal sketch linking black microbial pigmentation to phenolic precursors, oxidase-catalyzed melanin biosynthesis, dark melanin polymers, and visible black color.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a broad environmental or morphological classification spanning multiple mechanisms, a measurement-like bin, or an absence/arrangement descriptor; contextual protein nodes do not receive token UniProt examples.",
        "nodes": [
          {
            "node_id": "black_pigmented_trait",
            "label": "black pigmented",
            "node_type": "TRAIT",
            "grounding": "METPO:1003022",
            "description": "Microbial pigmentation appearing black or very dark."
          },
          {
            "node_id": "phenolic_precursors",
            "label": "phenolic precursors",
            "node_type": "CHEMICAL",
            "description": "Tyrosine-derived, DOPA-like, DHN-like, or HGA-like precursors for melanin formation."
          },
          {
            "node_id": "tyrosinase_laccase_oxidases",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "tyrosinase/laccase oxidases",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Oxidative enzymes that can catalyze melanin precursor oxidation."
          },
          {
            "node_id": "melanin_biosynthesis",
            "label": "melanin biosynthesis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Oxidative polymerization process producing microbial melanins.",
            "grounding": "GO:0042438"
          },
          {
            "node_id": "black_brown_melanin",
            "label": "black-brown melanin",
            "node_type": "CHEMICAL",
            "description": "Dark melanin polymer causing black or brown pigmentation."
          },
          {
            "node_id": "visible_black_color",
            "label": "visible black color",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "Observed black or very dark colony or cell color."
          },
          {
            "node_id": "dopaquinone",
            "label": "dopaquinone/dihydroxyindole intermediates",
            "node_type": "CHEMICAL",
            "description": "Reactive quinone and dihydroxyindole intermediates that polymerize into eumelanin."
          },
          {
            "node_id": "dhn_precursor",
            "label": "DHN (1,8-dihydroxynaphthalene)",
            "node_type": "CHEMICAL",
            "description": "Naphthalene-derived precursor polymerized into DHN-melanin."
          },
          {
            "node_id": "polyketide_synthase",
            "label": "polyketide synthase (PKS)",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Enzyme synthesizing tetrahydroxynaphthalene precursor of the DHN-melanin pathway.",
            "grounding": "GO:0016218"
          },
          {
            "node_id": "dhn_melanin",
            "label": "DHN-melanin (allomelanin)",
            "node_type": "CHEMICAL",
            "description": "Dark melanin polymer formed from DHN via laccase-catalyzed polymerization."
          },
          {
            "node_id": "tyrosinase",
            "label": "tyrosinase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Copper-dependent oxidase catalyzing hydroxylation and oxidation steps of the DOPA-melanin pathway.",
            "grounding": "GO:0004503"
          },
          {
            "node_id": "hydroxyphenylpyruvate",
            "label": "4-hydroxyphenylpyruvate",
            "node_type": "CHEMICAL",
            "description": "Tyrosine-catabolism intermediate, substrate of HppD.",
            "grounding": "CHEBI:36242"
          },
          {
            "node_id": "copper_ion",
            "label": "copper ion",
            "node_type": "CHEMICAL",
            "description": "Copper cofactor required for catalytic activity of tyrosinase."
          },
          {
            "node_id": "l_tyrosine",
            "label": "L-tyrosine",
            "node_type": "CHEMICAL",
            "description": "Aromatic amino acid precursor for DOPA-melanin biosynthesis."
          },
          {
            "node_id": "dopa_melanin",
            "label": "DOPA-melanin (eumelanin)",
            "node_type": "CHEMICAL",
            "description": "Black-to-brown eumelanin polymer formed from DOPA-derived intermediates."
          },
          {
            "node_id": "hppd",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "HppD (4-hydroxyphenylpyruvate dioxygenase)",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Enzyme converting 4-hydroxyphenylpyruvate to homogentisic acid in the pyomelanin route."
          },
          {
            "node_id": "homogentisic_acid",
            "label": "homogentisic acid (HGA)",
            "node_type": "CHEMICAL",
            "description": "Pyomelanin precursor that auto-oxidizes and polymerizes into pyomelanin."
          },
          {
            "node_id": "hmga",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "HmgA (homogentisate 1,2-dioxygenase)",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Enzyme converting HGA to maleylacetoacetate; loss leads to HGA accumulation and pyomelanin."
          }
        ],
        "edges": [
          {
            "subject": "phenolic_precursors",
            "predicate": "feed into",
            "object": "melanin_biosynthesis",
            "description": "Phenolic precursors feed oxidative melanin-forming pathways.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s11274-020-02941-z",
                "snippet": "oxidative polymerization of tyrosine derivatives",
                "notes": "Supports phenolic or tyrosine-derived precursors as melanin biosynthetic substrates."
              }
            ]
          },
          {
            "subject": "tyrosinase_laccase_oxidases",
            "predicate": "catalyzes",
            "object": "melanin_biosynthesis",
            "description": "Oxidases catalyze precursor oxidation in melanin formation.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.biotechadv.2021.107773",
                "snippet": "biosynthesis ... oxidative polymerization",
                "notes": "Supports oxidative enzymatic routes for microbial melanin formation."
              }
            ],
            "predicate_id": "biolink:catalyzes"
          },
          {
            "subject": "melanin_biosynthesis",
            "predicate": "has output",
            "object": "black_brown_melanin",
            "description": "Melanin biosynthesis produces dark melanin polymers.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.biotechadv.2021.107773",
                "snippet": "Eumelanin and allomelanin impart black/brown color",
                "notes": "Supports black-brown melanins as microbial colorants."
              }
            ],
            "predicate_id": "RO:0002234"
          },
          {
            "subject": "black_brown_melanin",
            "predicate": "causes",
            "object": "visible_black_color",
            "description": "Dark melanin polymers cause visible black pigmentation when sufficiently accumulated.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.biotechadv.2021.107773",
                "snippet": "black/brown color",
                "notes": "Supports black color as an outcome of dark melanin accumulation."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "visible_black_color",
            "predicate": "manifests as",
            "object": "black_pigmented_trait",
            "description": "Visible black color manifests the black-pigmented phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.biotechadv.2021.107773",
                "snippet": "black/brown color to the cells",
                "notes": "Supports the trait-level assignment."
              }
            ],
            "predicate_id": "METPO:2007400"
          },
          {
            "subject": "tyrosinase",
            "predicate": "catalyzes conversion of",
            "object": "l_tyrosine",
            "description": "Tyrosinase hydroxylates L-tyrosine to L-DOPA, initiating the DOPA-melanin pathway.",
            "evidence": [
              {
                "reference": "DOI:10.3390/ijms25053013",
                "notes": "Tyrosinase first catalyzes the hydroxylation of L-tyrosine to L-DOPA."
              }
            ]
          },
          {
            "subject": "dopaquinone",
            "predicate": "polymerizes into",
            "object": "dopa_melanin",
            "description": "Dopaquinone/dihydroxyindole intermediates polymerize into DOPA-melanin (eumelanin).",
            "evidence": [
              {
                "reference": "DOI:10.3390/jof9090891",
                "notes": "Dopaquinone oxidized to dopachrome then dihydroxy-indoles which polymerize to form DOPA-melanins."
              }
            ]
          },
          {
            "subject": "copper_ion",
            "predicate": "required cofactor for",
            "object": "tyrosinase",
            "description": "Copper ions are required cofactors for tyrosinase catalytic activity.",
            "evidence": [
              {
                "reference": "DOI:10.3390/microorganisms12071352",
                "notes": "Tyrosinases are copper-dependent enzymes."
              }
            ]
          },
          {
            "subject": "polyketide_synthase",
            "predicate": "synthesizes precursor for",
            "object": "dhn_precursor",
            "description": "Polyketide synthase forms tetrahydroxynaphthalene leading to DHN, precursor of DHN-melanin.",
            "evidence": [
              {
                "reference": "DOI:10.3390/microorganisms12071352",
                "notes": "Polyketide synthase forms 1,3,6,8-tetrahydroxynaphthalene; polymerization of DHN leads to melanin."
              }
            ]
          },
          {
            "subject": "dhn_precursor",
            "predicate": "polymerizes into",
            "object": "dhn_melanin",
            "description": "DHN polymerizes into DHN-melanin (allomelanin), a dark pigment.",
            "evidence": [
              {
                "reference": "DOI:10.3390/microorganisms12071352",
                "notes": "Polymerization of DHN leads to the formation of melanin."
              }
            ]
          },
          {
            "subject": "hppd",
            "predicate": "converts",
            "object": "hydroxyphenylpyruvate",
            "description": "HppD converts 4-hydroxyphenylpyruvate to homogentisic acid in the pyomelanin pathway.",
            "evidence": [
              {
                "reference": "DOI:10.1128/spectrum.00410-24",
                "notes": "hppD codes for a protein responsible for conversion of 4-hydroxyphenylpyruvate to HGA."
              }
            ]
          },
          {
            "subject": "hmga",
            "predicate": "converts",
            "object": "homogentisic_acid",
            "description": "HmgA (homogentisate 1,2-dioxygenase) converts HGA to maleylacetoacetate.",
            "evidence": [
              {
                "reference": "DOI:10.1128/spectrum.00410-24",
                "notes": "Homogentisate 1,2-dioxygenase encoded by hmgA converts HGA to maleylacetoacetate."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.942877+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-11T19:10:00-07:00",
        "curator": "codex",
        "action": "CURATED_WITH_LITERATURE",
        "changes": "Added DOI-backed definition and causal graph for phenolic precursors, oxidative melanin biosynthesis, black-brown melanin polymers, and visible black color.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T05:49:24Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:catalyzes\u00d71, biolink:causes\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T21:30:07Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007400\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-14T05:51:46Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0042438\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 7 evidence-backed generic edges (12 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:33Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:36242\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-26T07:15:19Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:Q5Y9G5\u00d71, UniProtKB:A0A023Y3L4\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:21:11Z",
        "curator": "claude",
        "action": "RETRACT_DEAD_UNIPROT_GROUNDINGS",
        "changes": "Retracted 1 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:23:54Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0004503\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates (1 to has output), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-22T04:26:15Z",
        "curator": "codex",
        "action": "REVIEW_UNIPROT_INSTANCE_GROUNDINGS",
        "changes": "Reviewed 1 organism-specific UniProtKB grounding(s): replaced 1 with taxon-agnostic GO/InterPro terms and retracted 0 to label-only where no exact semantic term was supported (docs/GROUNDING_POLICY.md).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope black_pigmented_melanin_polymer=NONMECHANISTIC with scope_notes; marked 3 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (tyrosinase_laccase_oxidases, hppd, hmga).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000687",
    "label": "branched shaped",
    "definition": "A cell shape in which an organism forms lateral branches from filamentous or hyphal cells.",
    "definition_source": "DOI:10.1016/j.mib.2012.10.012",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000666"
    ],
    "synonyms": [
      {
        "synonym_text": "branced",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "branched",
        "synonym_type": "RELATED_SYNONYM",
        "source": "corrected-from-metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1016/j.mib.2012.10.012",
        "snippet": "Streptomyces grow by tip extension and through the initiation of new branches",
        "notes": "Supports branched morphology as a Streptomyces hyphal growth phenotype."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1681",
        "taxon_label": "Bifidobacterium bifidum",
        "note": "Y-shaped / branched (bifid) cell morphology; model gut commensal actinobacterium.",
        "reference": "PMID:20805404"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "branched_shaped_streptomyces_branching",
        "title": "Branched-shape Streptomyces branch-site mechanism",
        "description": "Evidence-backed causal sketch linking branched morphology to DivIVA foci, branch-site selection, polarisome behavior, local peptidoglycan assembly, and lateral branch outgrowth.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a broad environmental or morphological classification spanning multiple mechanisms, a measurement-like bin, or an absence/arrangement descriptor; contextual protein nodes do not receive token UniProt examples.",
        "nodes": [
          {
            "node_id": "branched_shaped_trait",
            "label": "branched shaped",
            "node_type": "TRAIT",
            "grounding": "METPO:1000687",
            "description": "Filamentous bacterial morphology with lateral branches."
          },
          {
            "node_id": "divIVA_foci",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "DivIVA foci",
            "node_type": "GENE_OR_PROTEIN",
            "description": "DivIVA assemblies marking future Streptomyces branch sites."
          },
          {
            "node_id": "branch_site_selection",
            "label": "branch-site selection",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Selection of a new site for lateral branch outgrowth."
          },
          {
            "node_id": "polarisome_behavior",
            "label": "polarisome behavior",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Dynamics of the polar growth machinery that controls branch growth."
          },
          {
            "node_id": "local_cell_wall_assembly",
            "label": "local cell-wall assembly",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Peptidoglycan assembly at a new growth zone."
          },
          {
            "node_id": "lateral_branch_outgrowth",
            "label": "lateral branch outgrowth",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Emergence and extension of a new hyphal branch."
          },
          {
            "node_id": "polarisome_splitting",
            "label": "DivIVA polarisome splitting",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Splitting of polarisomes at growing tips generating daughter polarisomes."
          },
          {
            "node_id": "divIVA_scy_filp_polarisome",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "DivIVA/Scy/FilP polarisome",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Apical polarisome complex of DivIVA with Scy and FilP."
          },
          {
            "node_id": "pg_enzyme_localization",
            "label": "localization of peptidoglycan synthases and hydrolases to the apex",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Recruitment of cell-wall synthesis enzymes to the growing pole."
          },
          {
            "node_id": "afsk_divIVA_phosphorylation",
            "label": "AfsK-mediated DivIVA phosphorylation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "AfsK kinase phosphorylation of DivIVA driving new polarisome formation."
          },
          {
            "node_id": "multiple_polarisomes_hyperbranching",
            "label": "multiple new polarisomes and hyperbranching",
            "node_type": "STATE",
            "description": "Formation of extra polarisomes producing a hyperbranching phenotype."
          },
          {
            "node_id": "sppa_divIVA_dephosphorylation",
            "label": "SppA dephosphorylation of DivIVA",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "SppA phosphatase reversal of DivIVA phosphorylation opposing hyperbranching."
          },
          {
            "node_id": "cell_wall_stress",
            "label": "cell-wall stress (bacitracin/vancomycin)",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Antibiotic-induced cell-wall stress signaling."
          },
          {
            "node_id": "stlp_membrane_microdomains",
            "label": "StlP membrane microdomain formation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Stomatin-like protein StlP organizing membrane microdomains governing polar growth."
          },
          {
            "node_id": "proper_polar_growth_branch_spacing",
            "label": "proper polar growth and normal branch spacing",
            "node_type": "STATE",
            "description": "Regulated polar growth yielding normal tip-to-branch distance."
          }
        ],
        "edges": [
          {
            "subject": "divIVA_foci",
            "predicate": "marks",
            "object": "branch_site_selection",
            "description": "DivIVA foci mark sites where lateral branches will emerge.",
            "evidence": [
              {
                "reference": "DOI:10.1371/journal.pgen.1002423",
                "snippet": "mark sites of future branch outgrowth",
                "notes": "Supports DivIVA foci as branch-site markers."
              }
            ]
          },
          {
            "subject": "branch_site_selection",
            "predicate": "controls",
            "object": "polarisome_behavior",
            "description": "Branch-site selection controls where new polar growth machinery is established.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.mib.2012.10.012",
                "snippet": "principal mechanism of branch site selection",
                "notes": "Supports branch-site selection as a regulated mechanism."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "polarisome_behavior",
            "predicate": "directs",
            "object": "local_cell_wall_assembly",
            "description": "Polarisome behavior directs local wall assembly at the branch site.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.mib.2012.10.012",
                "snippet": "modulate polar growth and hyphal branching",
                "notes": "Supports polarisome modulation of polar growth and branching."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "local_cell_wall_assembly",
            "predicate": "regulates",
            "object": "lateral_branch_outgrowth",
            "description": "Local wall assembly drives emergence of the lateral branch.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.mib.2012.10.012",
                "snippet": "apical growth requires the localization of the machinery",
                "notes": "Supports localized wall-building machinery as needed for apical branch outgrowth."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "lateral_branch_outgrowth",
            "predicate": "manifests as",
            "object": "branched_shaped_trait",
            "description": "Lateral branch outgrowth manifests the branched-shape phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.mib.2012.10.012",
                "snippet": "initiation of new branches",
                "notes": "Supports branched morphology as a Streptomyces growth phenotype."
              }
            ],
            "predicate_id": "METPO:2007400"
          },
          {
            "subject": "polarisome_splitting",
            "predicate": "causes",
            "object": "lateral_branch_outgrowth",
            "description": "Polarisome splitting at growing tips generates daughter polarisomes that coordinate new lateral branch emergence.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsml/uqad020",
                "notes": "Splitting of polarisomes at growing tips generates daughter polarisomes that coordinate emergence of new lateral branches upon reaching a critical size."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "divIVA_scy_filp_polarisome",
            "predicate": "localizes",
            "object": "pg_enzyme_localization",
            "description": "The DivIVA/Scy/FilP polarisome localizes peptidoglycan synthases and hydrolases to the apex.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mbio.01492-24",
                "notes": "The polarisome composed of DivIVA with Scy and FilP localizes cell-wall enzymes to one pole, linking polarity establishment to branching."
              }
            ]
          },
          {
            "subject": "afsk_divIVA_phosphorylation",
            "predicate": "stimulates",
            "object": "multiple_polarisomes_hyperbranching",
            "description": "AfsK-mediated DivIVA phosphorylation disassembles the apical polarisome and stimulates multiple new polarisomes.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsml/uqad020",
                "notes": "Constitutive AfsK activity/high DivIVA phosphorylation disassembles the apical polarisome and stimulates multiple new polarisomes, producing a hyperbranching phenotype."
              }
            ]
          },
          {
            "subject": "sppa_divIVA_dephosphorylation",
            "predicate": "opposes",
            "object": "multiple_polarisomes_hyperbranching",
            "description": "SppA dephosphorylation of DivIVA opposes AfsK-driven hyperbranching, defining a reversible branching-control circuit.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsml/uqad020",
                "notes": "AfsK phosphorylates DivIVA in response to bacitracin/vancomycin stress, while SppA dephosphorylates DivIVA, defining a reversible branching-control circuit."
              }
            ]
          },
          {
            "subject": "cell_wall_stress",
            "predicate": "activates",
            "object": "afsk_divIVA_phosphorylation",
            "description": "Cell-wall stress activates AfsK-dependent DivIVA phosphorylation.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsml/uqad020",
                "notes": "AfsK phosphorylates DivIVA in response to cell-wall stress (e.g., bacitracin, vancomycin)."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "stlp_membrane_microdomains",
            "predicate": "contributes to",
            "object": "proper_polar_growth_branch_spacing",
            "description": "StlP membrane microdomain formation contributes to proper polar growth and normal branch spacing.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-025-58093-x",
                "notes": "Loss of StlP leads to branching of filaments; constitutive stlP expression notably reduces lateral branching and increases tip-to-branch distance."
              }
            ],
            "predicate_id": "RO:0002326"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.896783+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-11T21:00:00-07:00",
        "curator": "codex",
        "action": "CURATED_WITH_LITERATURE",
        "changes": "Added DOI-backed definition and causal graph for DivIVA foci, branch-site selection, polarisome behavior, local cell-wall assembly, and lateral branch outgrowth.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T21:30:07Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002211\u00d72, METPO:2007400\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:19Z",
        "curator": "claude",
        "action": "RENAME_PREDICATE_LABELS",
        "changes": "Renamed 1 causal-edge predicate label(s) to align with existing groundings: drives \u2192 regulates \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:21Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002211\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 6 evidence-backed generic edges (9 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:13Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:causes\u00d71, RO:0002213\u00d71, RO:0002327\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-07T05:00:00Z",
        "curator": "claude",
        "action": "REGROUND_CAUSAL_EDGE",
        "changes": "Re-grounded the edge from enables/RO:0002327 to RO:0002326 (contributes to), issue 334. biolink declares enables range 'biological process or activity' and the object is a STATE, which does not satisfy it. Unlike the tolerance/capacity nodes in this same pass, this object is a genuine state rather than a mis-typed disposition - a gradient, a community composition, an internal environment - so retyping it to TRAIT would be wrong. contributes to fits because the subject genuinely contributes to the OCCURRENCE OR GENERATION of the object, which is biolink's definition; that is the same test the motive-force edges FAILED in issue 341, where the subject powers a machine it does not generate. RO:0002326 declares no rdfs:domain or rdfs:range.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope branched_shaped_streptomyces_branching=NONMECHANISTIC with scope_notes; marked 2 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (divIVA_foci, divIVA_scy_filp_polarisome).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1003023",
    "label": "brown pigmented",
    "definition": "A pigmentation phenotype in which microbial colonies or cells appear brown due to accumulation of brown pigments such as pyomelanin or other melanins.",
    "definition_source": "DOI:10.1128/AEM.67.8.3463-3468.2001",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1003021"
    ],
    "synonyms": [
      {
        "synonym_text": "Pigment_brown",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1128/AEM.67.8.3463-3468.2001",
        "snippet": "Brown pigments are produced when homogentisic acid accumulates",
        "notes": "Supports brown microbial pigmentation as a homogentisic-acid/pyomelanin pathway phenotype."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:651",
        "taxon_label": "Aeromonas media",
        "note": "Species-level pyomelanin model paired to an HppD protein; disruption and heterologous-expression experiments in strain WS establish HppD-dependent pigment production.",
        "reference": "DOI:10.1371/journal.pone.0120923"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "brown_pigmented_pyomelanin_pathway",
        "title": "Brown pigmentation pyomelanin mechanism",
        "description": "Evidence-backed causal sketch linking brown microbial pigmentation to tyrosine catabolism, homogentisic acid accumulation, oxidative polymerization into pyomelanin, and visible brown color.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "The retained mechanism is the HppD-dependent homogentisate/pyomelanin branch demonstrated in Aeromonas media; HmgA is retained as the opposing degradative branch and is not represented by the HppD example.",
        "nodes": [
          {
            "node_id": "brown_pigmented_trait",
            "label": "brown pigmented",
            "node_type": "TRAIT",
            "grounding": "METPO:1003023",
            "description": "Microbial pigmentation appearing brown."
          },
          {
            "node_id": "tyrosine_catabolism",
            "label": "tyrosine catabolism",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Catabolic pathway generating homogentisic acid intermediates.",
            "grounding": "GO:0006572"
          },
          {
            "node_id": "hppD",
            "label": "4-hydroxyphenylpyruvate dioxygenase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Enzyme that can form homogentisic acid from 4-hydroxyphenylpyruvate.",
            "grounding": "GO:0003868",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:A0AAE7AGQ2",
                "protein_label": "4-hydroxyphenylpyruvate dioxygenase",
                "gene_symbol": "hppD",
                "taxon_id": "NCBITaxon:651",
                "taxon_label": "Aeromonas media",
                "entry_status": "UNREVIEWED",
                "proteome_id": "UP000502657",
                "retrieved_on": "2026-10-22",
                "entry_version": 9,
                "sequence_version": 1,
                "role": "Aeromonas HppD converts 4-hydroxyphenylpyruvate to homogentisate in the pyomelanin-producing branch that generates brown pigmentation.",
                "evidence": [
                  {
                    "reference": "DOI:10.1371/journal.pone.0120923",
                    "snippet": "disruption of any one of these genes impairs or blocks pigmentation",
                    "notes": "The A. media WS mutagenesis and HppD-expression experiments establish the protein-family role; UniProt supplies a current species-matched HppD entry from a reference proteome."
                  }
                ]
              }
            ]
          },
          {
            "node_id": "homogentisic_acid",
            "label": "homogentisic acid",
            "node_type": "CHEMICAL",
            "description": "HGA precursor that oxidizes and polymerizes to pyomelanin.",
            "grounding": "CHEBI:44747"
          },
          {
            "node_id": "pyomelanin",
            "label": "pyomelanin",
            "node_type": "CHEMICAL",
            "description": "Brown-to-black phenolic polymer pigment."
          },
          {
            "node_id": "visible_brown_color",
            "label": "visible brown color",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "Observed brown colony or medium color."
          },
          {
            "node_id": "four_hydroxyphenylpyruvate",
            "label": "4-hydroxyphenylpyruvate",
            "node_type": "CHEMICAL",
            "description": "Tyrosine catabolism intermediate converted to homogentisic acid by HppD.",
            "grounding": "CHEBI:36242"
          },
          {
            "node_id": "hmgA",
            "label": "homogentisate 1,2-dioxygenase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Enzyme (HmgA) that degrades homogentisic acid to maleylacetoacetate, diverting flux away from pyomelanin.",
            "grounding": "GO:0004411"
          },
          {
            "node_id": "maleylacetoacetate",
            "label": "maleylacetoacetate",
            "node_type": "CHEMICAL",
            "description": "Product of homogentisic acid ring cleavage by HmgA in the tyrosine catabolism pathway."
          },
          {
            "node_id": "benzoquinoneacetic_acid",
            "label": "benzoquinoneacetic acid",
            "node_type": "CHEMICAL",
            "description": "Auto-oxidation product of homogentisic acid that self-polymerizes into pyomelanin.",
            "grounding": "CHEBI:137246"
          }
        ],
        "edges": [
          {
            "subject": "tyrosine_catabolism",
            "predicate": "has output",
            "object": "homogentisic_acid",
            "description": "Tyrosine catabolism can generate homogentisic acid.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.67.8.3463-3468.2001",
                "snippet": "homogentisic acid accumulates in the medium",
                "notes": "Supports HGA accumulation as upstream of brown pigment formation."
              }
            ],
            "predicate_id": "RO:0002234"
          },
          {
            "subject": "hppD",
            "predicate": "catalyzes formation of",
            "object": "homogentisic_acid",
            "description": "HppD catalyzes formation of homogentisic acid in pyomelanin pathways.",
            "evidence": [
              {
                "reference": "DOI:10.1371/journal.pone.0120923",
                "snippet": "catalyzes the reaction from 4-hydroxyphenylpyruvate to HGA",
                "notes": "Supports HppD-mediated HGA formation in bacterial pyomelanin production."
              }
            ],
            "predicate_id": "biolink:catalyzes"
          },
          {
            "subject": "homogentisic_acid",
            "predicate": "polymerizes to",
            "object": "pyomelanin",
            "description": "HGA oxidizes and polymerizes into pyomelanin.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.67.8.3463-3468.2001",
                "snippet": "spontaneously oxidize and polymerize",
                "notes": "Supports HGA polymerization as the source of pyomelanin."
              }
            ]
          },
          {
            "subject": "pyomelanin",
            "predicate": "causes",
            "object": "visible_brown_color",
            "description": "Pyomelanin causes visible brown pigmentation.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.67.8.3463-3468.2001",
                "snippet": "Brown pigments are produced",
                "notes": "Supports brown color as the output of pyomelanin formation."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "visible_brown_color",
            "predicate": "manifests as",
            "object": "brown_pigmented_trait",
            "description": "Visible brown color manifests the brown-pigmented phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.biotechadv.2021.107773",
                "snippet": "black/brown color to the cells",
                "notes": "Supports brown microbial cell color as a melanin-related pigmentation phenotype."
              }
            ],
            "predicate_id": "METPO:2007400"
          },
          {
            "subject": "tyrosine_catabolism",
            "predicate": "has output",
            "object": "four_hydroxyphenylpyruvate",
            "description": "Tyrosine catabolism produces 4-hydroxyphenylpyruvate as an intermediate.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-023-01517-5",
                "notes": "Tyrosine aminotransferases convert L-tyrosine into 4-hydroxyphenylpyruvate; biochemically generalizable precursor step."
              }
            ],
            "predicate_id": "RO:0002234"
          },
          {
            "subject": "four_hydroxyphenylpyruvate",
            "predicate": "converted to",
            "object": "homogentisic_acid",
            "description": "HppD converts 4-hydroxyphenylpyruvate to homogentisic acid.",
            "evidence": [
              {
                "reference": "DOI:10.1128/spectrum.00410-24",
                "notes": "hppD codes for a protein responsible for conversion of 4-hydroxyphenylpyruvate to HGA."
              }
            ]
          },
          {
            "subject": "hmgA",
            "predicate": "converts",
            "object": "maleylacetoacetate",
            "description": "HmgA converts homogentisic acid to maleylacetoacetate, the degradative branch.",
            "evidence": [
              {
                "reference": "DOI:10.1128/spectrum.00410-24",
                "notes": "Homogentisate 1,2-dioxygenase (hmgA) converts HGA to maleylacetoacetate; core negative branch away from pigment formation."
              }
            ]
          },
          {
            "subject": "homogentisic_acid",
            "predicate": "auto-oxidizes to",
            "object": "benzoquinoneacetic_acid",
            "description": "Excreted homogentisic acid spontaneously auto-oxidizes to benzoquinoneacetic acid.",
            "evidence": [
              {
                "reference": "DOI:10.1128/spectrum.00410-24",
                "notes": "HGA is excreted and spontaneously auto-oxidizes to form benzoquinoneacetic acid."
              }
            ]
          },
          {
            "subject": "benzoquinoneacetic_acid",
            "predicate": "polymerizes to",
            "object": "pyomelanin",
            "description": "Benzoquinoneacetic acid self-polymerizes to produce pyomelanin.",
            "evidence": [
              {
                "reference": "DOI:10.1128/spectrum.00410-24",
                "notes": "Auto-oxidation followed by self-polymerization to produce pyomelanin."
              }
            ]
          },
          {
            "subject": "homogentisic_acid",
            "predicate": "converted to",
            "object": "maleylacetoacetate",
            "description": "HmgA converts homogentisic acid to maleylacetoacetate, diverting substrate away from pyomelanin formation.",
            "evidence": [
              {
                "reference": "DOI:10.1128/spectrum.00410-24",
                "snippet": "converts HGA to maleylacetoacetate",
                "notes": "Verified against the open primary article; this joins the HmgA catabolic branch to its homogentisate substrate."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.943677+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-11T19:10:00-07:00",
        "curator": "codex",
        "action": "CURATED_WITH_LITERATURE",
        "changes": "Added DOI-backed definition and causal graph for tyrosine catabolism, HppD, homogentisic acid, pyomelanin, and visible brown color.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T05:49:24Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:causes\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T21:30:07Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007400\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T05:05:14Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A009PXB6\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-13T21:03:26Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:catalyzes\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-14T05:51:46Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0006572\u00d71, CHEBI:44747\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 5 evidence-backed generic edges (4 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:13Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:33Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:36242\u00d71, CHEBI:137246\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-26T07:15:19Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A010REZ7\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:21:11Z",
        "curator": "claude",
        "action": "RETRACT_DEAD_UNIPROT_GROUNDINGS",
        "changes": "Retracted 2 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:23:54Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0003868\u00d71, GO:0004411\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 2 causal edge(s) off microbe-domain METPO predicates (2 to has output), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "CURATE_PROTEIN_TAXON_EXAMPLE",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope brown_pigmented_pyomelanin_pathway=MECHANISTIC with scope_notes; added taxon-paired protein example(s) UniProtKB:A0AAE7AGQ2 on hppD (NCBITaxon:651); added canonical example(s) NCBITaxon:651.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T06:15:00Z",
        "curator": "codex",
        "action": "CONNECT_CAUSAL_GRAPH_COMPONENTS",
        "changes": "Resolved issue #183 graph fragmentation (2 components to 1) using 1 source- and verbatim-snippet-backed connector(s). No paid research service was called.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-22T01:35:00Z",
        "curator": "claude",
        "action": "REFRESH_UNIPROT_ENTRY_VERSION",
        "changes": "Refreshed UniProtKB entry_version against live UniProt REST on 2026-10-22: UniProtKB:A0AAE7AGQ2 (8 -> 9 on hppD).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000063",
    "label": "capsule",
    "definition": "A morphology trait in which the cell is surrounded by a well-organized layer of polysaccharide (or rarely polypeptide) external to the cell envelope, mediating adhesion, desiccation resistance, and immune evasion.",
    "definition_source": "DOI:10.1146/annurev.micro.50.1.285",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "synonyms": [
      {
        "synonym_text": "capsulated",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1146/annurev.micro.50.1.285"
      },
      {
        "synonym_text": "capsular polysaccharide",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1146/annurev.biochem.75.103004.142545"
      }
    ],
    "xrefs": [
      "GO:0042603"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev.micro.50.1.285",
        "notes": "Roberts, \"The biochemistry and genetics of capsular polysaccharide production in bacteria\", treats the capsule as an organized external polysaccharide layer."
      },
      {
        "reference": "DOI:10.1146/annurev.biochem.75.103004.142545",
        "notes": "Whitfield reviews biosynthesis and assembly of capsular polysaccharides in Escherichia coli."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:573",
        "taxon_label": "Klebsiella pneumoniae",
        "note": "Textbook polysaccharide-capsule producer; capsule is a defining virulence factor.",
        "reference": "PMID:27715471"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "capsule_polysaccharide_protection",
        "title": "Capsule polysaccharide layer mediates adhesion and immune evasion",
        "description": "Evidence-backed causal sketch linking capsular polysaccharide biosynthesis to a surface polysaccharide layer that mediates adhesion, desiccation resistance, and immune evasion.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a broad environmental or morphological classification spanning multiple mechanisms, a measurement-like bin, or an absence/arrangement descriptor; contextual protein nodes do not receive token UniProt examples.",
        "nodes": [
          {
            "node_id": "capsule_trait",
            "label": "capsule",
            "node_type": "TRAIT",
            "grounding": "traitmech:000063",
            "description": "Possession of a well-organized external polysaccharide layer."
          },
          {
            "node_id": "capsular_polysaccharide",
            "label": "capsular polysaccharide",
            "node_type": "CHEMICAL",
            "description": "High-MW (often acidic) polysaccharide attached external to the cell envelope.",
            "grounding": "CHEBI:3379"
          },
          {
            "node_id": "capsule_assembly",
            "label": "capsular polysaccharide assembly",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Synthesis, export, and surface assembly of capsule polymers."
          },
          {
            "node_id": "immune_evasion",
            "label": "host immune evasion",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced recognition and clearance by host innate immunity."
          },
          {
            "node_id": "wzx_flippase",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "Wzx flippase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Inner-membrane flippase that translocates lipid-linked capsule repeat units across the inner membrane in the Wzx/Wzy-dependent pathway."
          },
          {
            "node_id": "lipid_linked_repeat_unit",
            "label": "lipid-linked capsule repeat unit",
            "node_type": "CHEMICAL",
            "description": "Undecaprenyl-linked oligosaccharide repeat unit assembled on the cytoplasmic face of the inner membrane."
          },
          {
            "node_id": "wzy_polymerase",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "Wzy polymerase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Polymerase that links capsule repeat units into a growing polysaccharide chain in the Wzx/Wzy-dependent pathway."
          },
          {
            "node_id": "wzb_phosphatase_cycle",
            "label": "Wzb phosphatase cycle",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Wzb-catalyzed phosphorylation/dephosphorylation cycle of the Wzc tyrosine autokinase regulating capsule assembly."
          },
          {
            "node_id": "wzc_capsule_assembly",
            "label": "Wzc-regulated capsule assembly",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Capsule polymerization and export controlled by the Wzc polysaccharide copolymerase/tyrosine autokinase."
          },
          {
            "node_id": "wza_export_protein",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "Wza outer-membrane export protein",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Outer-membrane polysaccharide export protein that translocates capsule polymer across the outer membrane."
          },
          {
            "node_id": "kpsmt_abc_transporter",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "KpsMT ABC transporter",
            "node_type": "GENE_OR_PROTEIN",
            "description": "ATP-binding cassette transporter that exports capsule polysaccharide chains across the inner membrane in the ABC-dependent pathway."
          }
        ],
        "edges": [
          {
            "subject": "capsule_assembly",
            "predicate": "produces",
            "object": "capsular_polysaccharide",
            "description": "Capsule biosynthesis synthesizes and exports the high-MW capsular polysaccharide.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev.biochem.75.103004.142545",
                "notes": "Whitfield reviews biosynthesis, export, and surface assembly of the capsular polysaccharide polymer."
              }
            ],
            "predicate_id": "biolink:produces"
          },
          {
            "subject": "capsule_assembly",
            "predicate": "confers",
            "object": "capsule_trait",
            "description": "Surface assembly of capsule polymers realizes the capsulated phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev.biochem.75.103004.142545",
                "notes": "Whitfield reviews biosynthesis and assembly of capsular polysaccharides."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "capsule_trait",
            "predicate": "contributes to",
            "object": "immune_evasion",
            "description": "The capsule masks surface antigens and reduces phagocytic uptake.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev.micro.50.1.285",
                "notes": "Roberts frames capsular polysaccharide as an immune-evasion and adhesion structure."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "wzx_flippase",
            "predicate": "flips",
            "object": "lipid_linked_repeat_unit",
            "description": "Wzx flippase turns the completed lipid-linked repeat unit outward across the inner membrane.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41522-024-00497-6",
                "notes": "\"the complete repeat unit is turned outward by the Wzx flip enzyme\"; general Wzx/Wzy capsule biosynthesis, not taxon-specific."
              }
            ]
          },
          {
            "subject": "wzy_polymerase",
            "predicate": "polymerizes",
            "object": "capsular_polysaccharide",
            "description": "Wzy polymerase attaches the growing chain to new repeat units, building the capsular polysaccharide.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41522-024-00497-6",
                "notes": "\"the Wzy polymerase attaches the growing polymer chain to the newly formed repeat unit\"; general Wzx/Wzy pathway."
              }
            ]
          },
          {
            "subject": "wzb_phosphatase_cycle",
            "predicate": "required for",
            "object": "wzc_capsule_assembly",
            "description": "The Wzb-catalyzed phosphorylation cycle of Wzc is a crucial step for capsule assembly.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41522-024-00497-6",
                "notes": "\"The phosphorylation cycle of Wzc, catalyzed by Wzb, is a crucial step.\"; general capsule biosynthesis."
              }
            ]
          },
          {
            "subject": "wza_export_protein",
            "predicate": "exports",
            "object": "capsular_polysaccharide",
            "description": "Wza translocates the assembled capsule polymer across the outer membrane.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41522-024-00497-6",
                "notes": "\"The polymer translocates across the outer membrane via Wza\"; Wzx/Wzy-dependent pathway, broad mechanistic statement."
              }
            ],
            "predicate_id": "METPO:2007804"
          },
          {
            "subject": "kpsmt_abc_transporter",
            "predicate": "exports",
            "object": "capsular_polysaccharide",
            "description": "The KpsMT ABC transporter exports capsule polysaccharide chains across the inner membrane in the ABC-dependent pathway.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41522-024-00497-6",
                "notes": "\"the ABC transporter (KpsMT) plays a pivotal role in exporting these chains\"; general ABC-dependent capsule export."
              }
            ],
            "predicate_id": "METPO:2007804"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-06-03T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate MORPHOLOGY trait (capsule) from literature research to fill the cell-surface-structure gap.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-09T15:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (capsule polysaccharide / immune evasion) with RO predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-14T06:55:38Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:3379\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-16T00:00:00Z",
        "curator": "claude",
        "action": "FIX_ORPHAN_NODE",
        "changes": "Connected the previously-orphaned capsular_polysaccharide node via a 'produces' (biolink:produces) edge from capsule_assembly.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 5 evidence-backed generic edges (7 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:13Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000209\u00d72).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-26T07:15:19Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A0G3EZQ9\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:21:11Z",
        "curator": "claude",
        "action": "RETRACT_DEAD_UNIPROT_GROUNDINGS",
        "changes": "Retracted 1 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 1 causal edge(s) off enables/RO:0002327 with a TRAIT object (1 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T02:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES_PART2",
        "changes": "Re-grounded 2 causal edge(s) off microbe-domain METPO predicates onto their causal-graph counterparts (2 to exports), issue 301 part 2. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Each replacement is a 1:1 mirror of its source predicate that changes only the domain, so the claim each edge makes is unchanged and directions are unchanged. The replacements are proposed in proposals/metpo_traitmech_v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-21T08:00:00Z",
        "curator": "codex",
        "action": "NORMALISE_NODE_TYPE",
        "changes": "Tranche 5 of issue 356 settles the process/quality families and merges ids that meant the same sense: immune_evasion is BIOLOGICAL_PROCESS. Immune evasion is the avoidance or subversion of host defenses. The edges treat it as an enabled action that in turn enables colonization; capsule.yaml's 'reduced recognition and clearance' is the outcome of that same process, not a separate measurable axis.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope capsule_polysaccharide_protection=NONMECHANISTIC with scope_notes; marked 4 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (wzx_flippase, wzy_polymerase, wza_export_protein, kpsmt_abc_transporter).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T06:15:40Z",
        "curator": "codex",
        "action": "ADD_EXACT_ONTOLOGY_MATCH",
        "changes": "Ontology exact-match review (2026-08-25): approved exact xref(s): GO:0042603. Evidence is predicate-scoped in the versioned ontology snapshots; OAK cross-checked direct data, and OLS4 spot-checked release deltas and disputed hits.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000072",
    "label": "carboxysome",
    "definition": "A bacterial microcompartment \u2014 a polyhedral protein-shelled organelle that encapsulates RuBisCO and carbonic anhydrase to concentrate CO2 for carbon fixation in cyanobacteria and many chemoautotrophs.",
    "definition_source": "DOI:10.1038/nrmicro.2018.10",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "traitmech:000066"
    ],
    "synonyms": [
      {
        "synonym_text": "bacterial microcompartment",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1038/nrmicro.2018.10"
      }
    ],
    "xrefs": [
      "GO:0031470"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/nrmicro.2018.10",
        "notes": "Kerfeld et al. review bacterial microcompartments; the carboxysome is the archetypal protein-shelled CO2-fixing microcompartment."
      },
      {
        "reference": "DOI:10.1038/nrmicro1913",
        "notes": "Yeates et al. describe protein-based organelles in bacteria (carboxysomes and related microcompartments), including the carboxysome shell and its encapsulated enzymes."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:32046",
        "taxon_label": "Synechococcus elongatus",
        "note": "Model for beta-carboxysomes (cyanobacterial CO2-fixing microcompartments; strain PCC 7942). Halothiobacillus neapolitanus is the alpha-carboxysome model.",
        "reference": "DOI:10.1128/mmbr.00061-12"
      },
      {
        "taxon_id": "NCBITaxon:1140",
        "taxon_label": "Synechococcus elongatus PCC 7942",
        "note": "Strain-level exemplar matched to CcmK2.",
        "reference": "DOI:10.1128/mmbr.00061-12"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "carboxysome_co2_concentrating",
        "title": "Carboxysome encapsulates RuBisCO to concentrate CO2 for carbon fixation",
        "description": "Evidence-backed causal sketch linking the carboxysome protein shell encapsulating RuBisCO and carbonic anhydrase to enhanced carbon fixation.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "The taxon-matched protein example anchors one experimentally supported causal branch; it is not presented as a universal mechanism for every taxon or every contextual branch in this graph.",
        "nodes": [
          {
            "node_id": "carboxysome_trait",
            "label": "carboxysome",
            "node_type": "TRAIT",
            "grounding": "traitmech:000072",
            "description": "Polyhedral protein-shelled microcompartment encapsulating RuBisCO."
          },
          {
            "node_id": "bacterial_microcompartment",
            "label": "bacterial microcompartment",
            "node_type": "CELLULAR_LOCALIZATION",
            "grounding": "GO:0031469",
            "description": "Protein-shelled prokaryotic microcompartment organelle."
          },
          {
            "node_id": "carbon_fixation",
            "label": "carbon fixation",
            "node_type": "BIOLOGICAL_PROCESS",
            "grounding": "GO:0015977",
            "description": "Conversion of inorganic CO2 into organic carbon (Calvin cycle)."
          },
          {
            "node_id": "carbon_dioxide",
            "label": "carbon dioxide",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:16526",
            "description": "CO2 substrate concentrated by the carboxysome shell."
          },
          {
            "node_id": "carboxysome_shell",
            "label": "carboxysome shell",
            "node_type": "ORGANELLE",
            "description": "Polyhedral selectively permeable protein shell of the carboxysome."
          },
          {
            "node_id": "carbonic_anhydrase",
            "label": "carbonic anhydrase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Carboxysomal enzyme dehydrating bicarbonate to CO2 near RuBisCO.",
            "grounding": "InterPro:IPR001765"
          },
          {
            "node_id": "bicarbonate",
            "label": "bicarbonate",
            "node_type": "CHEMICAL",
            "description": "HCO3- accumulated in cytoplasm and imported into the carboxysome.",
            "grounding": "CHEBI:17544"
          },
          {
            "node_id": "molecular_oxygen",
            "label": "oxygen",
            "node_type": "CHEMICAL",
            "description": "O2; competing substrate of RuBisCO whose influx the shell limits."
          },
          {
            "node_id": "rubisco_carboxylation",
            "label": "RuBisCO carboxylation",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "Carboxylation of RuBP by RuBisCO, the productive carbon-fixation reaction."
          },
          {
            "node_id": "bmc_shell_proteins",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:Q03511",
                "protein_label": "Carboxysome shell protein CcmK2",
                "gene_symbol": "ccmK2",
                "taxon_id": "NCBITaxon:1140",
                "taxon_label": "Synechococcus elongatus PCC 7942",
                "entry_status": "REVIEWED",
                "proteome_id": "UP000889800",
                "retrieved_on": "2026-10-22",
                "entry_version": 111,
                "sequence_version": 1,
                "role": "CcmK2 is one hexamer-forming component of the beta-carboxysome shell; the accession does not denote the complete shell.",
                "evidence": [
                  {
                    "reference": "DOI:10.1128/mmbr.00061-12",
                    "snippet": "CcmK shell proteins form the carboxysome boundary",
                    "notes": "The cited source supports the represented protein-to-trait branch; UniProt verifies this current strain-matched protein entry."
                  }
                ]
              }
            ],
            "label": "BMC-H/T/P shell proteins",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Hexameric, trimeric and pentameric protein paralogues forming the BMC shell."
          }
        ],
        "edges": [
          {
            "subject": "carboxysome_trait",
            "predicate": "example of",
            "object": "bacterial_microcompartment",
            "description": "The carboxysome is the archetypal bacterial microcompartment.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro1913",
                "notes": "Yeates et al. describe the carboxysome shell and its encapsulated enzymes."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "carboxysome_trait",
            "predicate": "contributes to",
            "object": "carbon_fixation",
            "description": "Carboxysomal CO2 concentration accelerates RuBisCO-catalysed fixation.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro.2018.10",
                "notes": "Kerfeld et al. frame the carboxysome as a CO2-concentrating microcompartment supporting carbon fixation."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "carbon_dioxide",
            "predicate": "located in",
            "object": "carboxysome_trait",
            "description": "CO2 is concentrated within the carboxysome shell for fixation.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro.2018.10",
                "notes": "Kerfeld et al. review CO2 concentration inside the carboxysome."
              }
            ],
            "predicate_id": "biolink:located_in"
          },
          {
            "subject": "carboxysome_shell",
            "predicate": "prevents loss of",
            "object": "carbon_dioxide",
            "description": "The carboxysome protein shell retains CO2, preventing its escape to the cytoplasm.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro.2018.10",
                "notes": "Kerfeld 2018: \"The shell prevents loss of CO2 to the cytoplasm.\""
              }
            ]
          },
          {
            "subject": "carbonic_anhydrase",
            "predicate": "converts",
            "object": "bicarbonate",
            "description": "Carboxysomal carbonic anhydrase dehydrates imported bicarbonate to CO2.",
            "evidence": [
              {
                "reference": "DOI:10.1128/aem.01075-24",
                "notes": "Wieschollek 2024: HCO3- entering carboxysomes is converted by CA to CO2; broad to bacterial CCMs with carboxysomes."
              }
            ]
          },
          {
            "subject": "carboxysome_shell",
            "predicate": "permits passage of",
            "object": "bicarbonate",
            "description": "Selective shell permeability allows HCO3- (and RuBP) to enter the carboxysome.",
            "evidence": [
              {
                "reference": "DOI:10.1093/plphys/kiae438",
                "notes": "Cheng 2024: \"the shell has selective permeability that permits HCO3- and RuBP passage.\""
              }
            ]
          },
          {
            "subject": "carboxysome_shell",
            "predicate": "limits influx of",
            "object": "molecular_oxygen",
            "description": "The carboxysome shell restricts O2 influx, reducing unproductive RuBisCO oxygenation.",
            "evidence": [
              {
                "reference": "DOI:10.1093/plphys/kiae438",
                "notes": "Cheng 2024: shell permits HCO3-/RuBP passage \"while limiting O2 influx.\""
              }
            ]
          },
          {
            "subject": "carbonic_anhydrase",
            "predicate": "elevates local concentration of",
            "object": "carbon_dioxide",
            "description": "CA activity inside the carboxysome elevates local CO2 around RuBisCO.",
            "evidence": [
              {
                "reference": "DOI:10.1093/plphys/kiae438",
                "notes": "Cheng 2024: \"CA inside the carboxysome dehydrates HCO3- to CO2, elevating CO2 concentration around Rubisco.\""
              }
            ]
          },
          {
            "subject": "carbon_dioxide",
            "predicate": "enhances",
            "object": "rubisco_carboxylation",
            "description": "Elevated CO2 around RuBisCO enhances carboxylation and reduces oxygenation.",
            "evidence": [
              {
                "reference": "DOI:10.1093/plphys/kiae438",
                "notes": "Cheng 2024: elevated CO2 \"enhances Rubisco carboxylation rates and reduces unproductive oxygenation.\""
              }
            ]
          },
          {
            "subject": "bmc_shell_proteins",
            "predicate": "form",
            "object": "carboxysome_shell",
            "description": "BMC-H hexamers, BMC-T pseudohexamers and BMC-P pentamers form the selectively permeable shell with central pores.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro.2018.10",
                "notes": "Kerfeld 2018: BMC-H/T/P proteins build the shell; a central pore \"serves as a channel for metabolites\"; generalized across BMCs including carboxysomes."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-06-03T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate MORPHOLOGY trait (carboxysome); protein-microcompartment sub-variant of intracellular inclusion.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-09T15:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (carboxysome CO2-concentrating / carbon fixation) with GO/CHEBI node groundings and RO/RDFS/biolink predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 7 evidence-backed generic edges (7 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:33Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:17544\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-26T07:15:19Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A009PMS8\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:21:11Z",
        "curator": "claude",
        "action": "RETRACT_DEAD_UNIPROT_GROUNDINGS",
        "changes": "Retracted 1 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:23:54Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (InterPro:IPR001765\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-17T02:00:00Z",
        "curator": "claude",
        "action": "NORMALISE_NODE_SENSE",
        "changes": "One node_id per SENSE (issues 356, 384): molecular_oxygen is the chemical sense here. The molecule, not the condition \u2014 the dioxygen participating in the reaction the graph describes. Normalised onto molecular_oxygen, the id 20 other chemical occurrences already use, so one id means one sense corpus-wide (issues 356, 384).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "CURATE_PROTEIN_TAXON_EXAMPLE",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope carboxysome_co2_concentrating=MECHANISTIC with scope_notes; marked 1 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (bmc_shell_proteins); added taxon-paired protein example(s) UniProtKB:Q03511 on bmc_shell_proteins (NCBITaxon:1140); added canonical example(s) NCBITaxon:1140.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T06:15:40Z",
        "curator": "codex",
        "action": "ADD_EXACT_ONTOLOGY_MATCH",
        "changes": "Ontology exact-match review (2026-08-25): approved exact xref(s): GO:0031470. Evidence is predicate-scoped in the versioned ontology snapshots; OAK cross-checked direct data, and OLS4 spot-checked release deltas and disputed hits.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-22T01:35:00Z",
        "curator": "claude",
        "action": "REFRESH_UNIPROT_ENTRY_VERSION",
        "changes": "Refreshed UniProtKB entry_version against live UniProt REST on 2026-10-22: UniProtKB:Q03511 (110 -> 111 on bmc_shell_proteins).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1003031",
    "label": "carotenoid pigmentation",
    "definition": "A pigmentation phenotype caused by microbial production and accumulation of carotenoid pigments.",
    "definition_source": "DOI:10.1080/1040841X.2025.2526423",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1003021"
    ],
    "synonyms": [
      {
        "synonym_text": "Pigment_carotenoid",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1080/1040841X.2025.2526423",
        "snippet": "Carotenoids are isoprenoid pigments",
        "notes": "Supports carotenoid pigmentation as a bacterial isoprenoid-pigment phenotype."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1280",
        "taxon_label": "Staphylococcus aureus",
        "note": "Golden carotenoid pigmentation (staphyloxanthin); well-studied bacterial carotenoid and virulence factor.",
        "reference": "PMID:16009720"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "carotenoid_pigmentation_crt_pathway",
        "title": "Carotenoid pigmentation crt-pathway mechanism",
        "description": "Evidence-backed causal sketch linking bacterial carotenoid pigmentation to isoprenoid precursors, crt enzymes, conjugated carotenoids, and yellow-orange-red visible color.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a broad environmental or morphological classification spanning multiple mechanisms, a measurement-like bin, or an absence/arrangement descriptor; contextual protein nodes do not receive token UniProt examples.",
        "nodes": [
          {
            "node_id": "carotenoid_pigmentation_trait",
            "label": "carotenoid pigmentation",
            "node_type": "TRAIT",
            "grounding": "METPO:1003031",
            "description": "Microbial pigmentation caused by carotenoid compounds."
          },
          {
            "node_id": "isoprenoid_precursors",
            "label": "isoprenoid precursors",
            "node_type": "CHEMICAL",
            "description": "Prenyl building blocks used in carotenoid biosynthesis."
          },
          {
            "node_id": "crt_enzymes",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "Crt enzymes",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Bacterial carotenoid biosynthetic enzymes encoded by crt genes."
          },
          {
            "node_id": "carotenoid_biosynthesis",
            "label": "carotenoid biosynthesis",
            "node_type": "PATHWAY",
            "description": "Enzymatic pathway producing carotenoid pigments.",
            "grounding": "GO:0016117"
          },
          {
            "node_id": "conjugated_carotenoids",
            "label": "conjugated carotenoids",
            "node_type": "CHEMICAL",
            "description": "Colored carotenoid molecules with conjugated double bonds."
          },
          {
            "node_id": "yellow_orange_red_color",
            "label": "yellow-orange-red color",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "Visible colors associated with carotenoid absorption spectra."
          },
          {
            "node_id": "phytoene_synthase",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "phytoene synthase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "CrtB-type enzyme condensing prenyl diphosphate to phytoene."
          },
          {
            "node_id": "phytoene",
            "label": "phytoene",
            "node_type": "CHEMICAL",
            "description": "Colorless C40 carotenoid precursor."
          },
          {
            "node_id": "phytoene_desaturase",
            "label": "phytoene desaturase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "CrtI-type enzyme desaturating phytoene toward lycopene.",
            "grounding": "InterPro:IPR014102"
          },
          {
            "node_id": "lycopene",
            "label": "lycopene",
            "node_type": "CHEMICAL",
            "description": "Red C40 carotenoid intermediate formed by desaturation.",
            "grounding": "CHEBI:15948"
          },
          {
            "node_id": "lycopene_cyclases",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "lycopene cyclases",
            "node_type": "GENE_OR_PROTEIN",
            "description": "CrtY-type enzymes cyclizing lycopene into cyclic carotenes."
          },
          {
            "node_id": "cyclic_carotenes",
            "label": "cyclic carotenes",
            "node_type": "CHEMICAL",
            "description": "alpha-, epsilon-, and beta-carotene formed by lycopene cyclization.",
            "grounding": "CHEBI:35163"
          }
        ],
        "edges": [
          {
            "subject": "isoprenoid_precursors",
            "predicate": "feed into",
            "object": "carotenoid_biosynthesis",
            "description": "Isoprenoid precursors provide substrate for carotenoid production.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.gene.2004.11.038",
                "snippet": "isoprenoid precursor biosynthesis",
                "notes": "Supports isoprenoid precursor biosynthesis as a major step in eubacterial carotenoid pathways."
              }
            ]
          },
          {
            "subject": "crt_enzymes",
            "predicate": "catalyzes",
            "object": "carotenoid_biosynthesis",
            "description": "Crt gene products catalyze bacterial carotenoid biosynthetic reactions.",
            "evidence": [
              {
                "reference": "DOI:10.1080/1040841X.2025.2526423",
                "snippet": "crt genes ... reactions they catalyze",
                "notes": "Supports Crt enzymes as pathway catalysts."
              }
            ],
            "predicate_id": "biolink:catalyzes"
          },
          {
            "subject": "carotenoid_biosynthesis",
            "predicate": "has output",
            "object": "conjugated_carotenoids",
            "description": "Carotenoid biosynthesis produces conjugated carotenoid pigments.",
            "evidence": [
              {
                "reference": "DOI:10.1080/1040841X.2025.2526423",
                "snippet": "biosynthesis pathways of bacterial carotenoids",
                "notes": "Supports bacterial carotenoid biosynthesis as the source of carotenoid pigments."
              }
            ],
            "predicate_id": "RO:0002234"
          },
          {
            "subject": "conjugated_carotenoids",
            "predicate": "causes",
            "object": "yellow_orange_red_color",
            "description": "Conjugated carotenoids absorb visible light and produce yellow-orange-red pigmentation.",
            "evidence": [
              {
                "reference": "DOI:10.1080/1040841X.2025.2526423",
                "snippet": "red, pink, orange, and yellow pigmentation in bacteria",
                "notes": "Supports carotenoids as color determinants for this pigment class."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "yellow_orange_red_color",
            "predicate": "manifests as",
            "object": "carotenoid_pigmentation_trait",
            "description": "Yellow-orange-red visible color manifests carotenoid pigmentation.",
            "evidence": [
              {
                "reference": "DOI:10.1080/1040841X.2025.2526423",
                "snippet": "responsible for the red, pink, orange, and yellow pigmentation",
                "notes": "Supports the trait-level mapping from carotenoid chemistry to pigmentation."
              }
            ],
            "predicate_id": "METPO:2007400"
          },
          {
            "subject": "phytoene_synthase",
            "predicate": "converts",
            "object": "phytoene",
            "description": "Phytoene synthase condenses prenyl diphosphate (GFDP) to form phytoene.",
            "evidence": [
              {
                "reference": "DOI:10.3390/molecules29174235",
                "notes": "Through the catalytic action of phytoene synthase, GFDP undergoes condensation to form phytoene."
              }
            ]
          },
          {
            "subject": "phytoene",
            "predicate": "is substrate for",
            "object": "phytoene_desaturase",
            "description": "Phytoene is dehydrogenated by phytoene desaturase en route to lycopene.",
            "evidence": [
              {
                "reference": "DOI:10.3390/molecules29174235",
                "notes": "Phytoene is further dehydrogenated by dehydrogenase to generate phytofluene, which is subsequently converted into lycopene."
              }
            ]
          },
          {
            "subject": "phytoene_desaturase",
            "predicate": "produces",
            "object": "lycopene",
            "description": "Phytoene desaturase converts phytoene (via phytofluene) to lycopene.",
            "evidence": [
              {
                "reference": "DOI:10.3390/molecules29174235",
                "notes": "Phytoene is further dehydrogenated... which is subsequently converted into lycopene."
              }
            ],
            "predicate_id": "METPO:2007800"
          },
          {
            "subject": "lycopene_cyclases",
            "predicate": "converts",
            "object": "cyclic_carotenes",
            "description": "Lycopene cyclases cyclize lycopene into alpha-, epsilon-, and beta-carotene.",
            "evidence": [
              {
                "reference": "DOI:10.3390/molecules29174235",
                "notes": "The cyclization of lycopene... lead[s] to the formation of alpha-carotene, epsilon-carotene, and beta-carotene under the catalysis of various lycopene cyclases."
              }
            ]
          },
          {
            "subject": "lycopene",
            "predicate": "is substrate for",
            "object": "lycopene_cyclases",
            "description": "Lycopene is the substrate cyclized by lycopene cyclases.",
            "evidence": [
              {
                "reference": "DOI:10.3390/molecules29174235",
                "notes": "The cyclization of lycopene... under the catalysis of various lycopene cyclases."
              }
            ]
          },
          {
            "subject": "cyclic_carotenes",
            "predicate": "is a",
            "object": "conjugated_carotenoids",
            "description": "Cyclic carotenes are conjugated carotenoid pigments contributing to coloration.",
            "evidence": [
              {
                "reference": "DOI:10.3390/molecules29174235",
                "notes": "Cyclic carotenes (alpha-/epsilon-/beta-carotene) are conjugated carotenoid pigment products of the pathway."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.947657+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-11T18:45:00-07:00",
        "curator": "codex",
        "action": "CURATED_WITH_LITERATURE",
        "changes": "Added DOI-backed definition and causal graph for isoprenoid precursors, Crt enzymes, carotenoid biosynthesis, conjugated carotenoids, and visible pigmentation.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T05:49:24Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:catalyzes\u00d71, biolink:causes\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T21:30:07Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007400\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:41:04Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0016117\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 6 evidence-backed generic edges (6 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:13Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d71, rdfs:subClassOf\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:33Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:15948\u00d71, CHEBI:35163\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-26T07:15:19Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A023WN98\u00d71, UniProtKB:A0A060JDC8\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:21:11Z",
        "curator": "claude",
        "action": "RETRACT_DEAD_UNIPROT_GROUNDINGS",
        "changes": "Retracted 1 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates (1 to has output), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T02:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES_PART2",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates onto their causal-graph counterparts (1 to produces), issue 301 part 2. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Each replacement is a 1:1 mirror of its source predicate that changes only the domain, so the claim each edge makes is unchanged and directions are unchanged. The replacements are proposed in proposals/metpo_traitmech_v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-16T02:00:00Z",
        "curator": "claude",
        "action": "NORMALISE_NODE_TYPE",
        "changes": "Under the PATHWAY-vs-BIOLOGICAL_PROCESS rule, one node_id means one thing corpus-wide (issue 356): carotenoid_biosynthesis is typed PATHWAY. PATHWAY is a named, conventionally enumerable multi-step route; BIOLOGICAL_PROCESS is everything else. A named biosynthetic route. Most descriptions call it one outright, including BIOLOGICAL_PROCESS-typed ones ('Enzymatic pathway producing carotenoid pigments'); red_pigmented.yaml instead ENUMERATES the steps -- 'Phytoene synthase condenses two GGPP to phytoene, then desaturation/isomerization yields lycopene' -- which is the rule's own test for PATHWAY met explicitly rather than by naming. Applied AGAINST the majority, which was 5 BIOLOGICAL_PROCESS to 1 before this tranche.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-22T04:26:15Z",
        "curator": "codex",
        "action": "REVIEW_UNIPROT_INSTANCE_GROUNDINGS",
        "changes": "Reviewed 1 organism-specific UniProtKB grounding(s): replaced 1 with taxon-agnostic GO/InterPro terms and retracted 0 to label-only where no exact semantic term was supported (docs/GROUNDING_POLICY.md).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope carotenoid_pigmentation_crt_pathway=NONMECHANISTIC with scope_notes; marked 3 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (crt_enzymes, phytoene_synthase, lycopene_cyclases).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000881",
    "label": "cell length",
    "definition": "A phenotype that inheres in a cell by virtue of its longer dimension when viewed on a plane.",
    "definition_source": "DOI:10.1016/j.cub.2014.07.022",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1016/j.cub.2014.07.022",
        "snippet": "cell size is tightly controlled",
        "notes": "Review establishes cell size as an actively regulated phenotype, supporting length as a controlled cellular dimension."
      },
      {
        "reference": "DOI:10.1016/j.cell.2014.11.022",
        "snippet": "cells grow by a fixed amount between divisions",
        "notes": "Adder-model paper supports an inter-divisional length increment underlying cell-length distributions."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:562",
        "taxon_label": "Escherichia coli",
        "reference": "DOI:10.1016/j.cell.2014.11.022",
        "note": "Escherichia coli is the organism in the cited single-cell adder study, which directly measures and models inter-division cell-length control; this is a family-level, not bin-level, exemplar."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "cell_length_division_growth_control",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "Cell length is a quantitative measurement descriptor rather than one conserved protein-mediated mechanism. The graph is retained only as contextual background on factors that can influence the measured dimension.",
        "title": "Cell-length control by growth and division timing",
        "description": "DOI-backed graph linking growth rate, division-site placement, and the adder size-control principle to the observed cell-length phenotype.",
        "nodes": [
          {
            "node_id": "cell_length_trait",
            "label": "cell length",
            "node_type": "TRAIT",
            "grounding": "METPO:1000881",
            "description": "Longer dimension of the rod-like or elongated cell body."
          },
          {
            "node_id": "growth_rate",
            "label": "elongation rate",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Rate at which the cell elongates between divisions."
          },
          {
            "node_id": "adder_principle",
            "label": "adder size control",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Mechanism by which cells add a fixed length increment between consecutive divisions."
          },
          {
            "node_id": "ftsz_ring",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "This contextual node denotes an assembled FtsZ structure rather than one exact protein-family entity.",
            "label": "FtsZ ring (divisome)",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Tubulin-like FtsZ-based contractile ring that organizes division."
          },
          {
            "node_id": "division_site_placement",
            "label": "division-site placement",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Spatial selection of the midcell division site."
          },
          {
            "node_id": "cytokinesis",
            "label": "cytokinesis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Cell division that resets cell length each generation.",
            "grounding": "GO:0000910"
          },
          {
            "node_id": "elongasome",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "The elongasome is a variable multisubunit assembly; no verified single complex term exactly represents this contextual node.",
            "label": "Rod complex (elongasome)",
            "node_type": "GENE_OR_PROTEIN",
            "description": "MreB/RodA/PBP2-based multiprotein complex driving cell elongation."
          },
          {
            "node_id": "sidewall_pg_synthesis",
            "label": "sidewall peptidoglycan synthesis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Lateral/sidewall PG insertion that lengthens the cell prior to division."
          },
          {
            "node_id": "ftsa_zipa",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "FtsA and ZipA are distinct protein families grouped for contextual explanation, so one family grounding would be incorrect.",
            "label": "FtsA and ZipA (proto-ring tethers)",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Membrane tethers that attach FtsZ to the membrane forming the proto-ring."
          },
          {
            "node_id": "ftswi_septal_synthase",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "FtsW and FtsI are distinct components grouped as a septal synthase module; one protein-family term cannot denote both.",
            "label": "FtsWI septal PG synthase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "FtsW/FtsI complex that drives septal peptidoglycan synthesis."
          },
          {
            "node_id": "septum_synthesis",
            "label": "septum synthesis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Septal PG synthesis driving division constriction."
          },
          {
            "node_id": "min_nucleoid_occlusion",
            "label": "Min system and nucleoid occlusion",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Spatial regulators acting as localized negative regulators of FtsZ polymerization."
          }
        ],
        "edges": [
          {
            "subject": "growth_rate",
            "predicate": "contributes to",
            "object": "cell_length_trait",
            "description": "Elongation rate sets how rapidly a cell extends along its long axis between divisions.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.cub.2014.07.022",
                "snippet": "cell size is tightly controlled",
                "notes": "Supports growth/elongation rate as a determinant of cell size."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "adder_principle",
            "predicate": "regulates",
            "object": "cell_length_trait",
            "description": "Adder size control sets the inter-division length increment that determines average cell length.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.cell.2014.11.022",
                "snippet": "cells grow by a fixed amount between divisions",
                "notes": "Supports the adder principle as the size-control rule producing the length distribution."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "ftsz_ring",
            "predicate": "assembles at",
            "object": "division_site_placement",
            "description": "FtsZ assembles at the future division site to initiate cytokinesis.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2671",
                "snippet": "FtsZ ring at the future division site",
                "notes": "Supports FtsZ-ring assembly as the proximate divisome event."
              }
            ]
          },
          {
            "subject": "division_site_placement",
            "predicate": "causes",
            "object": "cytokinesis",
            "description": "Division-site placement directs constriction and cytokinesis.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2671",
                "snippet": "directs cell division",
                "notes": "Supports division-site placement as the trigger for cytokinesis."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "cytokinesis",
            "predicate": "resets",
            "object": "cell_length_trait",
            "description": "Cytokinesis halves the mother cell, resetting daughter cell length.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.cell.2014.11.022",
                "snippet": "cells grow by a fixed amount between divisions",
                "notes": "Supports division as the event that resets length each generation."
              }
            ]
          },
          {
            "subject": "elongasome",
            "predicate": "mediates",
            "object": "sidewall_pg_synthesis",
            "description": "The Rod complex/elongasome drives sidewall peptidoglycan synthesis.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fcimb.2023.1205488",
                "notes": "elongasome drives sidewall peptidoglycan synthesis necessary for rod shape and lengthening of the cell prior to division."
              }
            ]
          },
          {
            "subject": "sidewall_pg_synthesis",
            "predicate": "contributes to",
            "object": "cell_length_trait",
            "description": "Sidewall PG synthesis lengthens the cell prior to division.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fcimb.2023.1205488",
                "notes": "sidewall peptidoglycan synthesis necessary for the lengthening of the cell prior to division."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "elongasome",
            "predicate": "mediates",
            "object": "growth_rate",
            "description": "The Rod complex/elongasome mediates cell elongation.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s42003-024-07279-y",
                "notes": "elongation is mediated by the Rod complex (the elongasome)."
              }
            ]
          },
          {
            "subject": "ftsa_zipa",
            "predicate": "attaches",
            "object": "ftsz_ring",
            "description": "FtsA and ZipA tether FtsZ to the membrane forming the proto-ring.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41579-023-00942-x",
                "notes": "FtsZ membrane attachment depends on tethers FtsA and ZipA (the proto-ring)."
              }
            ]
          },
          {
            "subject": "ftswi_septal_synthase",
            "predicate": "drives",
            "object": "septum_synthesis",
            "description": "FtsWI septal PG synthases drive septum synthesis.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41579-023-00942-x",
                "notes": "essential septal peptidoglycan synthases FtsW and FtsI (FtsWI) that drive septum synthesis."
              }
            ]
          },
          {
            "subject": "septum_synthesis",
            "predicate": "contributes to",
            "object": "cytokinesis",
            "description": "Septum synthesis drives division constriction completing cytokinesis.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41579-023-00942-x",
                "notes": "inactivation of essential divisome proteins blocks division, altering cell length; septum synthesis drives division constriction."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "min_nucleoid_occlusion",
            "predicate": "regulates",
            "object": "division_site_placement",
            "description": "Min system and nucleoid occlusion determine division site placement via localized negative regulation of FtsZ polymerization.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41579-023-00942-x",
                "notes": "the Min system and nucleoid occlusion act as localized negative regulators of FtsZ polymerization and thus determine division site placement."
              }
            ],
            "predicate_id": "RO:0002211"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.918489+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-11T22:30:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed causal graph linking elongation rate, adder size control, FtsZ-divisome division-site placement, and cytokinesis to cell length.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002326\u00d71, RO:0002211\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-26T05:00:48Z",
        "curator": "claude",
        "action": "RENAME_PREDICATE_LABELS",
        "changes": "Renamed 1 causal-edge predicate label(s) to align with existing groundings: triggers \u2192 causes \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-26T05:00:50Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:causes\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-14T05:51:46Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0000910\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 7 evidence-backed generic edges (6 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:13Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002326\u00d72, RO:0002211\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope cell_length_division_growth_control=NONMECHANISTIC with scope_notes; marked 4 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (ftsz_ring, elongasome, ftsa_zipa, ftswi_septal_synthase).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T04:43:24Z",
        "curator": "codex",
        "action": "ADD_CANONICAL_EXAMPLES",
        "changes": "Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Escherichia coli (NCBITaxon:562; DOI:10.1016/j.cell.2014.11.022). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000886",
    "label": "cell length large",
    "definition": "A cell-length phenotype in which the longer cell dimension exceeds approximately 3 micrometers.",
    "definition_source": "DOI:10.1126/science.aaa1313",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000881"
    ],
    "synonyms": [
      {
        "synonym_text": "L_>3",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1126/science.aaa1313",
        "snippet": "cell size scales with growth rate",
        "notes": "Growth-rate-dependent size law supports large cell length under fast-growth or division-delayed regimes."
      },
      {
        "reference": "DOI:10.1038/nrmicro2671",
        "snippet": "directs cell division",
        "notes": "FtsZ-divisome review supports division-site timing as a control point governing whether cells reach larger lengths before constriction."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:324679",
        "taxon_label": "Spirochaeta dissipatitropha",
        "reference": "DOI:10.1099/ijs.0.65862-0",
        "note": "Spirochaeta dissipatitropha ASpC2T cells measured 8-18 micrometres long, wholly above the approximately 3-micrometre threshold."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "cell_length_large_division_delay",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a numerical cell-length bin. Its graph illustrates possible regulators of measured length but is not a single inheritable causal mechanism requiring a protein/taxon exemplar.",
        "title": "Large cell-length via FtsZ division delay",
        "description": "DOI-backed graph linking fast elongation, SOS/SulA-mediated FtsZ inhibition, FtsZ Z-ring control, and delayed constriction to large cell length (>3 \u03bcm).",
        "nodes": [
          {
            "node_id": "cell_length_large_trait",
            "label": "cell length large",
            "node_type": "TRAIT",
            "grounding": "METPO:1000886",
            "description": "Cell length exceeding approximately 3 \u03bcm."
          },
          {
            "node_id": "cell_length_trait",
            "label": "cell length",
            "node_type": "TRAIT",
            "grounding": "METPO:1000881",
            "description": "Regulated longer cellular dimension."
          },
          {
            "node_id": "fast_elongation",
            "label": "fast elongation rate",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Rapid axial elongation between divisions."
          },
          {
            "node_id": "division_timing_delay",
            "label": "division-timing delay",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Postponement of FtsZ-ring constriction extending elongation."
          },
          {
            "node_id": "sos_response",
            "label": "SOS response",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "DNA-damage/stress-activated regulatory program that induces division inhibitors.",
            "grounding": "GO:0009432"
          },
          {
            "node_id": "sula_division_inhibition",
            "label": "SulA-mediated division inhibition",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Inhibition of cell division mediated by the SOS-induced inhibitor SulA."
          },
          {
            "node_id": "sula_protein",
            "label": "SulA",
            "node_type": "GENE_OR_PROTEIN",
            "description": "SOS-induced cell-division inhibitor protein that blocks FtsZ assembly.",
            "grounding": "InterPro:IPR004596"
          },
          {
            "node_id": "ftsz_zring",
            "label": "FtsZ Z-ring",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Assembly of the FtsZ ring at midcell that initiates cytokinesis."
          },
          {
            "node_id": "ftsz_protein",
            "label": "FtsZ",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Bacterial tubulin homolog whose abundance is rate-limiting for division.",
            "grounding": "InterPro:IPR000158"
          },
          {
            "node_id": "constriction_onset",
            "label": "onset of constriction",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Initiation of septal constriction during cytokinesis."
          }
        ],
        "edges": [
          {
            "subject": "fast_elongation",
            "predicate": "contributes to",
            "object": "cell_length_large_trait",
            "description": "Fast elongation between divisions yields longer cells.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.aaa1313",
                "snippet": "cell size scales with growth rate",
                "notes": "Supports fast growth as a producer of larger cell sizes."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "division_timing_delay",
            "predicate": "contributes to",
            "object": "cell_length_large_trait",
            "description": "Delaying division allows continued elongation past the typical size.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2671",
                "snippet": "directs cell division",
                "notes": "Supports division timing as a control point for cell length."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "cell_length_large_trait",
            "predicate": "is a",
            "object": "cell_length_trait",
            "description": "Large cell length is a quantitative bin of the cell-length phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.cub.2014.07.022",
                "snippet": "cell size is tightly controlled",
                "notes": "Supports large length as a value within the regulated cell-length distribution."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "sos_response",
            "predicate": "positively regulates",
            "object": "sula_division_inhibition",
            "description": "The SOS response increases SulA-mediated division inhibition after DNA damage or replication stress.",
            "evidence": [
              {
                "reference": "DOI:10.1002/advs.202203260",
                "snippet": "the SOS response is activated through the binding of recA with single stranded DNA and the self-cleavage of the lexA repressor, enabling expression of SOS regulon genes",
                "notes": "Verified against the open Wiley full text; DNA damage activates the RecA/LexA SOS response and enables expression of SOS regulon genes, including sulA."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "sula_protein",
            "predicate": "negatively regulates",
            "object": "ftsz_zring",
            "description": "SulA inhibits FtsZ polymerization, blocking productive Z-ring assembly.",
            "evidence": [
              {
                "reference": "DOI:10.1002/advs.202203260",
                "snippet": "cell division inhibitor, sulA, blocks FtsZ (a master regulator of bacterial cell division and responsible for the Z ring formation at mid-cell) polymerization",
                "notes": "Verified against the open Wiley full text; the source links SOS activation to SulA blocking FtsZ polymerization."
              }
            ],
            "predicate_id": "RO:0002212"
          },
          {
            "subject": "ftsz_protein",
            "predicate": "positively regulates",
            "object": "constriction_onset",
            "description": "FtsZ accumulation in the Z-ring is a rate-limiting driver for onset of constriction at faster growth rates.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-024-54242-w",
                "snippet": "rate limit the onset of constriction",
                "notes": "Verified against the open Nature Communications full text; FtsZ numbers were rate-limiting for constriction onset in moderately fast E. coli growth."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "sula_protein",
            "predicate": "contributes to",
            "object": "sula_division_inhibition",
            "description": "SOS-induced SulA is the inhibitory protein mediating this division-arrest branch.",
            "evidence": [
              {
                "reference": "DOI:10.1002/advs.202203260",
                "snippet": "As a result, a cell division inhibitor, sulA, blocks FtsZ",
                "notes": "Verified against the open Wiley full text; the source frames SulA as the SOS-linked inhibitor that blocks FtsZ polymerization."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "sula_division_inhibition",
            "predicate": "contributes to",
            "object": "division_timing_delay",
            "description": "SulA-mediated inhibition of septation contributes to delayed division and continued elongation.",
            "evidence": [
              {
                "reference": "DOI:10.1002/advs.202203260",
                "snippet": "contributes to non-septate cellular filamentation",
                "notes": "Verified against the open Wiley full text; SulA-mediated FtsZ inhibition is linked to blocked septation and filamentation."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "ftsz_zring",
            "predicate": "positively regulates",
            "object": "constriction_onset",
            "description": "FtsZ bundles promote the FtsA/FtsN/core-divisome transition that starts constriction.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-024-54242-w",
                "snippet": "starts the onset of constriction",
                "notes": "Verified against the open Nature Communications full text; the proposed model routes FtsZ bundles through FtsA antiparallel filaments, FtsN recruitment, and core-divisome activation."
              }
            ],
            "predicate_id": "RO:0002213"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.920780+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-11T22:30:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed causal graph linking fast elongation and division-timing delay to large cell length (>3 \u03bcm).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002326\u00d72, rdfs:subClassOf\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 3 evidence-backed generic edges (6 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:19Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:C0LUM8\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:33Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0009432\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-26T07:15:19Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:H8YHZ0\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-22T04:26:15Z",
        "curator": "codex",
        "action": "REVIEW_UNIPROT_INSTANCE_GROUNDINGS",
        "changes": "Reviewed 2 organism-specific UniProtKB grounding(s): replaced 2 with taxon-agnostic GO/InterPro terms and retracted 0 to label-only where no exact semantic term was supported (docs/GROUNDING_POLICY.md).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope cell_length_large_division_delay=NONMECHANISTIC with scope_notes.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T04:43:24Z",
        "curator": "codex",
        "action": "ADD_CANONICAL_EXAMPLES",
        "changes": "Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Spirochaeta dissipatitropha (NCBITaxon:324679; DOI:10.1099/ijs.0.65862-0). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-04T00:00:00Z",
        "curator": "codex",
        "action": "CONNECT_CAUSAL_GRAPH_COMPONENTS",
        "changes": "Resolved issue #183 graph fragmentation (4 components to 1) by re-citing the SOS/SulA branch to peer-reviewed evidence, grounding the two residual FtsZ/SulA predicates, and adding 3 source- and verbatim-snippet-backed connectors. No paid research service was called.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-06T17:10:00Z",
        "curator": "codex",
        "action": "ADVERSARIAL_REVIEW_REPAIR",
        "changes": "Addressed PR #664 adversarial review: corrected the SulA cell-division-inhibitor snippet to match the exact peer-reviewed Wiley text with comma punctuation.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-07T04:24:00Z",
        "curator": "codex",
        "action": "ADVERSARIAL_REVIEW_REPAIR",
        "changes": "Addressed PR #664 adversarial review issue #687: gave the two SulA edges distinct exact snippets, separating the FtsZ-polymerization claim from the SulA division-inhibitor connector.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-07T20:05:00Z",
        "curator": "codex",
        "action": "ADVERSARIAL_REVIEW_REPAIR",
        "changes": "Addressed PR #664 adversarial review issue #696: expanded the SOS-to-SulA division-inhibition evidence so the snippet carries SOS-regulon expression instead of only naming SOS activation.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000885",
    "label": "cell length medium",
    "definition": "A cell-length phenotype in which the longer cell dimension lies approximately between 2 and 3 micrometers.",
    "definition_source": "DOI:10.1126/science.aaa1313",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000881"
    ],
    "synonyms": [
      {
        "synonym_text": "L_2_3",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1126/science.aaa1313",
        "snippet": "cell size scales with growth rate",
        "notes": "Growth-rate-dependent size law supports medium cell length as a typical outcome at moderate growth rates."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1232683",
        "taxon_label": "Marinobacterium lacunae",
        "reference": "DOI:10.1007/s00203-023-03627-4",
        "note": "Marinobacterium lacunae AK27T cells measured 2.0-3.0 micrometres long in the primary species description, matching this bin."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "cell_length_medium_growth_rate",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a numerical cell-length bin. Its graph illustrates contextual growth and division factors but is not a single protein-mediated causal mechanism.",
        "title": "Medium cell-length under moderate growth",
        "description": "DOI-backed graph linking moderate elongation rate and the growth-rate size law to a medium cell-length range (2\u20133 \u03bcm).",
        "nodes": [
          {
            "node_id": "cell_length_medium_trait",
            "label": "cell length medium",
            "node_type": "TRAIT",
            "grounding": "METPO:1000885",
            "description": "Cell length approximately 2\u20133 \u03bcm."
          },
          {
            "node_id": "cell_length_trait",
            "label": "cell length",
            "node_type": "TRAIT",
            "grounding": "METPO:1000881",
            "description": "Regulated longer cellular dimension."
          },
          {
            "node_id": "moderate_growth_rate",
            "label": "moderate growth rate",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Moderate exponential growth rate typical of common bacterial culture."
          },
          {
            "node_id": "growth_rate_size_law",
            "label": "growth-rate size law",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Empirical scaling of average cell size with growth rate."
          },
          {
            "node_id": "rod_complex",
            "label": "Rod complex (elongasome)",
            "node_type": "PATHWAY",
            "description": "Elongasome machinery (MreB/MreC/MreD/RodA/PBP2) directing lateral peptidoglycan synthesis."
          },
          {
            "node_id": "rodA_pbp2_complex",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "RodA and PBP2 are distinct proteins grouped as a contextual synthase complex; one family identifier cannot represent both components.",
            "label": "RodA-PBP2 complex",
            "node_type": "GENE_OR_PROTEIN",
            "description": "SEDS glycosyltransferase RodA paired with transpeptidase PBP2, the core PG-synthesizing pair of the elongasome."
          },
          {
            "node_id": "pg_insertion_elongation",
            "label": "peptidoglycan insertion during elongation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Insertion of new peptidoglycan along the cell cylinder driving elongation."
          },
          {
            "node_id": "mreC_mreD_balance",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "This node denotes a balance between distinct MreC and MreD proteins, not one semantically groundable protein entity.",
            "label": "MreC/MreD balance",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Relative levels of MreC and MreD that tune elongasome transpeptidase activity."
          },
          {
            "node_id": "pbp2_activity",
            "label": "PBP2 transpeptidase activity",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "Essential elongation transpeptidase activity of penicillin-binding protein 2."
          },
          {
            "node_id": "pg_density",
            "label": "peptidoglycan density / mechanical strength",
            "node_type": "QUALITY",
            "description": "Density and mechanical integrity of the peptidoglycan sacculus."
          },
          {
            "node_id": "rod_shape",
            "label": "rod shape",
            "node_type": "TRAIT",
            "description": "Elongated cylindrical (rod) cell morphology."
          },
          {
            "node_id": "membrane_synthesis",
            "label": "membrane synthesis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Synthesis of membrane lipids (fatty acid/phospholipid synthesis)."
          },
          {
            "node_id": "envelope_balance_state",
            "label": "PG-membrane envelope balance",
            "node_type": "STATE",
            "description": "Balanced synthesis of peptidoglycan cell wall and cell membrane required for normal growth and shape."
          }
        ],
        "edges": [
          {
            "subject": "moderate_growth_rate",
            "predicate": "feeds into",
            "object": "growth_rate_size_law",
            "description": "Moderate exponential growth rates engage the growth-rate size law.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.aaa1313",
                "snippet": "cell size scales with growth rate",
                "notes": "Supports growth rate as the input to the size-scaling relationship."
              }
            ]
          },
          {
            "subject": "growth_rate_size_law",
            "predicate": "confers",
            "object": "cell_length_medium_trait",
            "description": "At moderate growth rates the size law produces medium cell length.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.aaa1313",
                "snippet": "cell size scales with growth rate",
                "notes": "Supports medium length as the expected size at moderate growth rates."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "cell_length_medium_trait",
            "predicate": "is a",
            "object": "cell_length_trait",
            "description": "Medium cell length is a quantitative bin of the cell-length phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.cub.2014.07.022",
                "snippet": "cell size is tightly controlled",
                "notes": "Supports medium length as a value within the regulated cell-length distribution."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "rodA_pbp2_complex",
            "predicate": "enables",
            "object": "pg_insertion_elongation",
            "description": "RodA glycosyltransferase and PBP2 transpeptidase together enable peptidoglycan insertion that drives elongation.",
            "evidence": [
              {
                "reference": "DOI:10.1002/mbo3.1385",
                "notes": "RodA is a glycosyltransferase and PBP2 a transpeptidase required for cell elongation; Rod-complex rotation supports even PG insertion along the cylinder (broadly curatable general rod-bacterium mechanism)."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "mreC_mreD_balance",
            "predicate": "modulates",
            "object": "pbp2_activity",
            "description": "The balance between MreC and MreD modulates PBP2, the essential elongation transpeptidase.",
            "evidence": [
              {
                "reference": "DOI:10.1002/mbo3.1385",
                "notes": "\"the balance between MreC and MreD modulates PBP2 activity\" - mechanistic edge for elongation control."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "rod_complex",
            "predicate": "increases",
            "object": "pg_density",
            "description": "An intact Rod complex builds dense peptidoglycan; loss yields PG with large holes and reduced mechanical strength.",
            "evidence": [
              {
                "reference": "DOI:10.1002/mbo3.1385",
                "notes": "\"The Rod complex may be a determinant not only for the whole shape of peptidoglycan but also for its highly dense structure.\""
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "pg_density",
            "predicate": "maintains",
            "object": "rod_shape",
            "description": "Dense peptidoglycan produced by the elongation machinery maintains rod shape, the morphology context for medium cell length.",
            "evidence": [
              {
                "reference": "DOI:10.1002/mbo3.1385",
                "notes": "\"PG determines bacterial cell shape\" - elongation machinery and dense PG determine whole-cell rod shape."
              }
            ]
          },
          {
            "subject": "membrane_synthesis",
            "predicate": "balances with PG synthesis to maintain",
            "object": "envelope_balance_state",
            "description": "Balanced membrane and peptidoglycan synthesis is critical; reducing membrane synthesis restores balance when PG capacity is limited.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mbio.00475-23",
                "notes": "\"Balanced synthesis of the peptidoglycan cell wall and the cell membrane is critical\" - broader envelope-balance mechanism affecting elongation and shape."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.920338+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-11T22:30:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed causal graph linking moderate growth rate and the growth-rate size law to medium cell length (2\u20133 \u03bcm).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d71, rdfs:subClassOf\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 5 evidence-backed generic edges (9 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:13Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d71, RO:0002211\u00d71, RO:0002213\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates (1 to confers), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope cell_length_medium_growth_rate=NONMECHANISTIC with scope_notes; marked 2 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (rodA_pbp2_complex, mreC_mreD_balance).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T04:43:24Z",
        "curator": "codex",
        "action": "ADD_CANONICAL_EXAMPLES",
        "changes": "Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Marinobacterium lacunae (NCBITaxon:1232683; DOI:10.1007/s00203-023-03627-4). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000884",
    "label": "cell length small",
    "definition": "A cell-length phenotype in which the longer cell dimension lies approximately between 1.3 and 2 micrometers.",
    "definition_source": "DOI:10.1016/j.cell.2014.11.022",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000881"
    ],
    "synonyms": [
      {
        "synonym_text": "L_1.3_2",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1016/j.cell.2014.11.022",
        "snippet": "cells grow by a fixed amount between divisions",
        "notes": "Adder-model paper supports a defined inter-divisional length increment that produces a narrow length distribution at standard growth conditions."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:3028314",
        "taxon_label": "Oceanimonas pelagia",
        "reference": "DOI:10.1007/s10482-024-01948-y",
        "note": "Oceanimonas pelagia NTOU-MSR1T cells measured approximately 1.8-2.0 micrometres long, within the approximately 1.3-2.0-micrometre bin."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "cell_length_small_size_setpoint",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a numerical cell-length bin. Its graph provides contextual examples of division control but does not define a single causal mechanism for every cell in the bin.",
        "title": "Small cell-length size setpoint",
        "description": "DOI-backed graph linking adder-controlled size homeostasis to a small cell-length range (1.3\u20132 \u03bcm).",
        "nodes": [
          {
            "node_id": "cell_length_small_trait",
            "label": "cell length small",
            "node_type": "TRAIT",
            "grounding": "METPO:1000884",
            "description": "Cell length approximately 1.3\u20132 \u03bcm."
          },
          {
            "node_id": "cell_length_trait",
            "label": "cell length",
            "node_type": "TRAIT",
            "grounding": "METPO:1000881",
            "description": "Regulated longer cellular dimension."
          },
          {
            "node_id": "adder_principle",
            "label": "adder size control",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Fixed inter-division length increment underlying size homeostasis."
          },
          {
            "node_id": "standard_growth_conditions",
            "label": "standard growth conditions",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Routine laboratory growth conditions producing typical bacterial cell sizes."
          },
          {
            "node_id": "ftsz_abundance",
            "label": "FtsZ abundance",
            "node_type": "QUALITY",
            "description": "Relative cellular level of the tubulin-like division protein FtsZ."
          },
          {
            "node_id": "division_timing",
            "label": "cell division timing",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Timing/onset of septal constriction and cell division."
          },
          {
            "node_id": "ftsz_ring_formation",
            "label": "FtsZ ring formation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Assembly of the cytokinetic Z ring at the division site."
          },
          {
            "node_id": "ftsn",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "The contextual source supports the FtsN label, but an exact semantic family term was not verified in this review.",
            "label": "FtsN",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Divisome protein that allosterically activates septal PG synthesis."
          },
          {
            "node_id": "ftswi_complex",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "FtsW and FtsI are distinct components grouped as a complex; one protein-family identifier cannot denote the pair.",
            "label": "FtsWI septal PG synthase complex",
            "node_type": "GENE_OR_PROTEIN",
            "description": "FtsWI (within FtsQLBWI) septal peptidoglycan synthase complex."
          },
          {
            "node_id": "septal_pg_synthesis",
            "label": "septal peptidoglycan synthesis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Synthesis of septal peptidoglycan during cytokinesis."
          },
          {
            "node_id": "zring_condensation",
            "label": "Z-ring condensation and stability",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Condensation and stabilization of the FtsZ ring."
          },
          {
            "node_id": "ftsz_protoring",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "This denotes an assembled FtsZ proto-ring structure rather than one exact protein-family entity.",
            "label": "FtsZ proto-ring (with FtsA/ZipA)",
            "node_type": "GENE_OR_PROTEIN",
            "description": "FtsZ proto-ring tethered by FtsA/ZipA initiating divisome assembly."
          },
          {
            "node_id": "divisome_assembly",
            "label": "divisome assembly",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Assembly of the division machinery and septal synthesis."
          },
          {
            "node_id": "min_nucleoid_occlusion",
            "label": "Min system and nucleoid occlusion",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Spatial regulators positioning FtsZ at midcell."
          },
          {
            "node_id": "ftsz_midcell_positioning",
            "label": "FtsZ positioning at midcell",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Correct placement of FtsZ at the cell midpoint for symmetric division."
          }
        ],
        "edges": [
          {
            "subject": "standard_growth_conditions",
            "predicate": "enables",
            "object": "adder_principle",
            "description": "Standard nutrient/temperature regimes maintain adder size control.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.cell.2014.11.022",
                "snippet": "cells grow by a fixed amount between divisions",
                "notes": "Supports adder control under typical growth regimes."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "adder_principle",
            "predicate": "confers",
            "object": "cell_length_small_trait",
            "description": "Adder homeostasis under standard conditions yields a narrow length distribution in the small range.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.cell.2014.11.022",
                "snippet": "cells grow by a fixed amount between divisions",
                "notes": "Supports small length as a typical adder-controlled outcome."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "cell_length_small_trait",
            "predicate": "is a",
            "object": "cell_length_trait",
            "description": "Small cell length is a quantitative bin of the cell-length phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.cub.2014.07.022",
                "snippet": "cell size is tightly controlled",
                "notes": "Supports small length as a value within the regulated cell-length distribution."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "ftsz_abundance",
            "predicate": "contributes to",
            "object": "division_timing",
            "description": "FtsZ abundance is a rate-limiting factor for E. coli cell division timing.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-024-54242-w",
                "snippet": "FtsZ numbers in the cell are one of the rate-limiting factors for cell divisions in E. coli",
                "notes": "Verified against the public Nature Communications abstract; M\u00e4nnik et al. identify FtsZ number as a rate-limiting factor for E. coli cell division."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "ftsz_ring_formation",
            "predicate": "modulates",
            "object": "cell_length_trait",
            "description": "Delayed FtsZ ring formation delays division until the cell reaches a larger size, increasing cell length.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-023-41487-0",
                "snippet": "delays the FtsZ ring formation, which in turn allows the cell to grow for a longer time",
                "notes": "Verified against the open Nature Communications introduction; Vashistha et al. describe Min-imbalance delaying FtsZ ring formation and giving cells more time to grow before division."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "ftsn",
            "predicate": "activates",
            "object": "ftswi_complex",
            "description": "FtsN allosterically activates the FtsWI septal PG synthase complex.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-024-52217-5",
                "snippet": "FtsN activates sPG synthesis by switching FtsA and the FtsQLBWI complex to the active state",
                "notes": "Verified against the open Nature Communications full text; Gong et al. route FtsN-mediated septal peptidoglycan synthesis through the active FtsQLBWI complex that contains FtsW and FtsI."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "septal_pg_synthesis",
            "predicate": "promotes",
            "object": "zring_condensation",
            "description": "Septal peptidoglycan synthesis feeds back to promote Z-ring condensation and stability.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-024-52217-5",
                "snippet": "sPG synthesis in turn promotes Z ring condensation and stability",
                "notes": "Verified against the open Nature Communications full text; Gong et al. show a positive-feedback loop from septal peptidoglycan synthesis to the Z ring."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "ftsz_protoring",
            "predicate": "enables",
            "object": "divisome_assembly",
            "description": "The FtsZ proto-ring with FtsA/ZipA localizes and organizes divisome assembly at midcell.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41579-023-00942-x",
                "snippet": "FtsZ, to localize and organize the cell division machinery, the divisome",
                "notes": "Verified against the public PubMed abstract for the Nature Reviews Microbiology article; Cameron and Margolin review FtsZ as the tubulin homolog that organizes the divisome."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "min_nucleoid_occlusion",
            "predicate": "regulates",
            "object": "ftsz_midcell_positioning",
            "description": "Min and nucleoid-occlusion systems regulate FtsZ placement at midcell for proper division-site selection.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s42003-024-07279-y",
                "snippet": "Min or nucleoid occlusion systems for positioning FtsZ at mid cell division sites",
                "notes": "Verified against the public Communications Biology abstract; Hayashi et al. require at least one of the Min or nucleoid-occlusion systems for midcell FtsZ positioning in E. coli L-forms."
              }
            ],
            "predicate_id": "RO:0002211"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.919890+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-11T22:30:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed causal graph linking adder size control under standard growth conditions to small cell length (1.3\u20132 \u03bcm).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d71, rdfs:subClassOf\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:19Z",
        "curator": "claude",
        "action": "RENAME_PREDICATE_LABELS",
        "changes": "Renamed 1 causal-edge predicate label(s) to align with existing groundings: supports \u2192 enables \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:21Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 6 evidence-backed generic edges (11 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:13Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002213\u00d72, RO:0002211\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-26T07:15:19Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A3RWZ4\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:21:12Z",
        "curator": "claude",
        "action": "RETRACT_DEAD_UNIPROT_GROUNDINGS",
        "changes": "Retracted 1 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates (1 to confers), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope cell_length_small_size_setpoint=NONMECHANISTIC with scope_notes; marked 4 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (ftsz_abundance, ftsn, ftswi_complex, ftsz_protoring).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T04:43:24Z",
        "curator": "codex",
        "action": "ADD_CANONICAL_EXAMPLES",
        "changes": "Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Oceanimonas pelagia (NCBITaxon:3028314; DOI:10.1007/s10482-024-01948-y). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-04T05:40:00Z",
        "curator": "codex",
        "action": "REVIEW_CAUSAL_EVIDENCE",
        "changes": "Reviewed the cell_length_small_size_setpoint graph for issue #183: added exact snippets to 6 FtsZ/divisome evidence items, grounded 3 residual predicates, and retyped FtsZ abundance as a QUALITY node. The METPO 1.3-2 micrometre length bin remains a nonmechanistic classification. No paid research service was called.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000883",
    "label": "cell length very small",
    "definition": "A cell-length phenotype in which the longer cell dimension is at most approximately 1.3 micrometers.",
    "definition_source": "DOI:10.1038/ismej.2014.60",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000881"
    ],
    "synonyms": [
      {
        "synonym_text": "L_<=1.3",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/ismej.2014.60",
        "snippet": "small cells and genomes",
        "notes": "Streamlining review links very small cell sizes to oligotrophic lifestyle and reduced cellular material requirements."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:2585141",
        "taxon_label": "Flavicella sediminum",
        "reference": "DOI:10.1099/ijsem.0.003839",
        "note": "Flavicella sediminum ALS 84T cells measured 1.0-1.2 micrometres long in the primary species description, wholly inside the at-most-1.3-micrometre bin."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "cell_length_very_small_streamlining",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a numerical cell-length bin. Its streamlined-cell graph is contextual background, not a universal protein-mediated mechanism for the measured size class.",
        "title": "Very-small cell-length streamlining",
        "description": "DOI-backed graph linking strong nutrient limitation and streamlining selection to very-small cell length (\u22641.3 \u03bcm).",
        "nodes": [
          {
            "node_id": "cell_length_very_small_trait",
            "label": "cell length very small",
            "node_type": "TRAIT",
            "grounding": "METPO:1000883",
            "description": "Cell length at most ~1.3 \u03bcm."
          },
          {
            "node_id": "cell_length_trait",
            "label": "cell length",
            "node_type": "TRAIT",
            "grounding": "METPO:1000881",
            "description": "Longer cellular dimension under shared size regulation."
          },
          {
            "node_id": "streamlining_selection",
            "label": "streamlining selection",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Selection for reduced cellular and genomic material under chronic nutrient limitation."
          },
          {
            "node_id": "oligotrophic_environment",
            "label": "oligotrophic environment",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Persistent low-nutrient setting that favors miniaturized cells."
          },
          {
            "node_id": "genome_streamlining",
            "label": "genome streamlining",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Adaptive reduction of genome size and cellular material, characterized by small cells (~1 um) and small genomes."
          },
          {
            "node_id": "carbon_limitation",
            "label": "carbon limitation",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Low carbon availability, an ecological driver associated with streamlining."
          },
          {
            "node_id": "nitrogen_limitation",
            "label": "nitrogen limitation",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Low nitrogen availability, an ecological driver associated with streamlining."
          },
          {
            "node_id": "reduced_transcriptional_regulation",
            "label": "reduced transcriptional regulation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduction of transcriptional regulatory machinery in oligotrophic microorganisms."
          },
          {
            "node_id": "nutrient_poor_environment",
            "label": "nutrient-poor environment",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Environment with low nutrient availability favoring low-regulation, streamlined strategies."
          }
        ],
        "edges": [
          {
            "subject": "oligotrophic_environment",
            "predicate": "regulates",
            "object": "streamlining_selection",
            "description": "Persistent oligotrophy selects for streamlined cells and genomes.",
            "evidence": [
              {
                "reference": "DOI:10.1038/ismej.2014.60",
                "snippet": "small cells and genomes",
                "notes": "Supports oligotrophic regimes as drivers of cell miniaturization."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "streamlining_selection",
            "predicate": "confers",
            "object": "cell_length_very_small_trait",
            "description": "Streamlining selection produces very small cell length values.",
            "evidence": [
              {
                "reference": "DOI:10.1038/ismej.2014.60",
                "snippet": "small cells",
                "notes": "Supports very small length as an outcome of streamlining selection."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "cell_length_very_small_trait",
            "predicate": "is a",
            "object": "cell_length_trait",
            "description": "Very small cell length is a quantitative bin of the cell-length phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.cub.2014.07.022",
                "snippet": "cell size is tightly controlled",
                "notes": "Supports very small cell length as a value within the regulated cell-length distribution."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "oligotrophic_environment",
            "predicate": "selects for",
            "object": "genome_streamlining",
            "description": "Oligotrophic environments select for genome streamlining.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mSphereDirect.00011-19",
                "notes": "Genome streamlining is characterized by small cells (~1 um), small genomes (~1-2 Mbp), and is strongly associated with carbon and nitrogen limitation."
              }
            ],
            "predicate_id": "METPO:2007401"
          },
          {
            "subject": "carbon_limitation",
            "predicate": "associated with",
            "object": "genome_streamlining",
            "description": "Carbon limitation is associated with genome streamlining.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mSphereDirect.00011-19",
                "notes": "Streamlining is strongly associated with carbon and nitrogen limitation."
              }
            ],
            "predicate_id": "biolink:associated_with"
          },
          {
            "subject": "nitrogen_limitation",
            "predicate": "associated with",
            "object": "genome_streamlining",
            "description": "Nitrogen limitation is associated with genome streamlining.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mSphereDirect.00011-19",
                "notes": "Streamlining is strongly associated with carbon and nitrogen limitation."
              }
            ],
            "predicate_id": "biolink:associated_with"
          },
          {
            "subject": "genome_streamlining",
            "predicate": "contributes to",
            "object": "cell_length_very_small_trait",
            "description": "Genome streamlining contributes to very small cell size.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-024-48591-9",
                "notes": "Prominent oligotrophic taxa (SAR11, Prochlorococcus) have streamlined genomes (~1.5 Mb) and extremely small cell volumes (~0.1 um3)."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "reduced_transcriptional_regulation",
            "predicate": "enhances fitness in",
            "object": "nutrient_poor_environment",
            "description": "Reduced transcriptional regulation enhances fitness in nutrient-poor environments, a companion of streamlining.",
            "evidence": [
              {
                "reference": "DOI:10.1128/MMBR.00124-22",
                "notes": "A reduction of transcriptional regulation in aquatic oligotrophic microorganisms enhances fitness in nutrient-poor environments."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.919417+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-11T22:30:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed causal graph linking oligotrophic streamlining selection to very small cell length.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d71, rdfs:subClassOf\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:19Z",
        "curator": "claude",
        "action": "RENAME_PREDICATE_LABELS",
        "changes": "Renamed 1 causal-edge predicate label(s) to align with existing groundings: drives \u2192 regulates \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:21Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002211\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 5 evidence-backed generic edges (5 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:13Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 4 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:associated_with\u00d72, METPO:2007401\u00d71, RO:0002326\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates (1 to confers), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope cell_length_very_small_streamlining=NONMECHANISTIC with scope_notes.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T04:43:24Z",
        "curator": "codex",
        "action": "ADD_CANONICAL_EXAMPLES",
        "changes": "Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Flavicella sediminum (NCBITaxon:2585141; DOI:10.1099/ijsem.0.003839). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000666",
    "label": "cell shape",
    "definition": "A phenotype that describes the characteristic three-dimensional morphological form of a microbial cell, determined by cell wall structure, cytoskeletal elements, and environmental factors.",
    "definition_source": "DOI:10.1038/nrmicro1205",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "synonyms": [
      {
        "synonym_text": "Morphology.cell morphology.cell shape",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "cell_shape",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "created_by": "Luke Wang",
    "evidence": [
      {
        "reference": "DOI:10.1038/nrmicro1205",
        "snippet": "bacterial cell wall ... primary role in maintaining cell shape",
        "notes": "Supports bacterial cell shape as determined by cell wall and cytoskeletal elements."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:562",
        "taxon_label": "Escherichia coli",
        "reference": "DOI:10.1038/nrmicro1205",
        "note": "Escherichia coli is a source-backed model in which cell-wall and cytoskeletal systems maintain a rod-shaped cellular form; this scopes the example to one branch of the broad shape class."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "cell_shape_peptidoglycan_cytoskeleton",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "Cell shape is an upper morphology descriptor spanning distinct rods, cocci, curved cells, and other forms. The graph is retained as contextual background on alternative determinants, not as one mechanism inherited by every child shape.",
        "title": "Bacterial cell-shape morphogenesis mechanism",
        "description": "Evidence-backed causal sketch linking cell shape to peptidoglycan synthesis, PBPs, MreB, FtsZ, crescentin, and localized wall growth.",
        "nodes": [
          {
            "node_id": "cell_shape_trait",
            "label": "cell shape",
            "node_type": "TRAIT",
            "grounding": "METPO:1000666",
            "description": "Characteristic three-dimensional microbial cell morphology."
          },
          {
            "node_id": "peptidoglycan_cell_wall",
            "label": "peptidoglycan cell wall",
            "node_type": "CELLULAR_LOCALIZATION",
            "grounding": "GO:0009274",
            "description": "Cell-wall polymer network maintaining bacterial shape."
          },
          {
            "node_id": "peptidoglycan_synthesis",
            "label": "peptidoglycan synthesis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Biosynthesis and remodeling of the bacterial cell wall.",
            "grounding": "GO:0009252"
          },
          {
            "node_id": "penicillin_binding_proteins",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "This umbrella combines multiple penicillin-binding-protein families with different enzymatic roles, so no single exact family term denotes the node.",
            "label": "penicillin-binding proteins",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Enzymes that synthesize and remodel peptidoglycan."
          },
          {
            "node_id": "mreB",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "The graph uses MreB generically across divergent bacterial lineages; an exact family term was not verified for this upper-context node.",
            "label": "MreB",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Actin-like bacterial cytoskeletal protein involved in rod-shape determination."
          },
          {
            "node_id": "ftsZ",
            "label": "FtsZ",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Tubulin-like bacterial cell-division protein.",
            "grounding": "InterPro:IPR000158"
          },
          {
            "node_id": "crescentin",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Crescentin is a lineage-specific curvature determinant retained only as one contextual alternative in this upper shape graph.",
            "label": "crescentin",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Intermediate-filament-like protein required for curved rod shape in Caulobacter."
          },
          {
            "node_id": "rod_complex",
            "label": "Rod complex (elongasome)",
            "node_type": "PATHWAY",
            "description": "Elongasome machinery that directs lateral peptidoglycan synthesis and architecture."
          },
          {
            "node_id": "peptidoglycan_architecture",
            "label": "peptidoglycan architecture",
            "node_type": "CELLULAR_LOCALIZATION",
            "description": "Spatial organization and dense structure of the peptidoglycan wall."
          },
          {
            "node_id": "rod_shape",
            "label": "rod shape",
            "node_type": "QUALITY",
            "description": "Rod (bacillus) cell-shape outcome."
          },
          {
            "node_id": "a22_inhibitor",
            "label": "A22 (MreB inhibitor)",
            "node_type": "CHEMICAL",
            "description": "Small-molecule inhibitor that reduces MreB filament assembly."
          },
          {
            "node_id": "cardiolipin_lipid_order",
            "label": "cardiolipin / increased lipid order",
            "node_type": "CHEMICAL",
            "description": "Membrane lipid composition state with increased lipid order."
          },
          {
            "node_id": "flotillins",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "This plural node combines multiple bacterial flotillin paralogues and has no single exact family grounding.",
            "label": "flotillins",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Membrane microdomain scaffolding proteins."
          },
          {
            "node_id": "cell_wall_synthesis",
            "label": "cell wall synthesis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Synthesis of the bacterial cell wall."
          }
        ],
        "edges": [
          {
            "subject": "peptidoglycan_cell_wall",
            "predicate": "regulates",
            "object": "cell_shape_trait",
            "description": "The peptidoglycan wall has a primary role in maintaining bacterial cell shape.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro1205",
                "snippet": "primary role in maintaining cell shape",
                "notes": "Review supports peptidoglycan wall as central to cell shape."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "penicillin_binding_proteins",
            "predicate": "catalyzes",
            "object": "peptidoglycan_synthesis",
            "description": "PBPs synthesize and remodel peptidoglycan during growth and division.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro1205",
                "snippet": "carry out the reactions for synthesis and remodelling",
                "notes": "Supports PBPs in peptidoglycan synthesis/remodeling."
              }
            ],
            "predicate_id": "biolink:catalyzes"
          },
          {
            "subject": "peptidoglycan_synthesis",
            "predicate": "causes",
            "object": "cell_shape_trait",
            "description": "Spatial regulation of wall synthesis determines growth morphology.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2677",
                "snippet": "peptidoglycan synthesis to bacterial growth and morphology",
                "notes": "Review supports regulated peptidoglycan synthesis as a determinant of morphology."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "mreB",
            "predicate": "positions",
            "object": "peptidoglycan_synthesis",
            "description": "MreB helps organize or position peptidoglycan synthesis machinery.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2677",
                "snippet": "positions peptidoglycan biosynthesis machineries",
                "notes": "Supports MreB in spatial organization of cell-wall synthesis."
              }
            ]
          },
          {
            "subject": "ftsZ",
            "predicate": "regulates",
            "object": "cell_shape_trait",
            "description": "FtsZ controls division-associated shape generation and septal wall synthesis.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro1205",
                "snippet": "FtsZ is essential for cell division",
                "notes": "Supports FtsZ as a shape-related cytoskeletal protein through cell division."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "crescentin",
            "predicate": "contributes to",
            "object": "cell_shape_trait",
            "description": "Crescentin contributes to curved-rod cell shape in representative bacteria.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro1205",
                "snippet": "crescentin is required for the curved-rod shape",
                "notes": "Supports crescentin as a cell-shape determinant in Caulobacter."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "rod_complex",
            "predicate": "shapes",
            "object": "peptidoglycan_architecture",
            "description": "The rod complex (elongasome) determines the overall shape and dense architecture of peptidoglycan.",
            "evidence": [
              {
                "reference": "DOI:10.1002/mbo3.1385",
                "notes": "Rod complex may be a determinant for the whole shape of peptidoglycan and its highly dense structure."
              }
            ]
          },
          {
            "subject": "peptidoglycan_architecture",
            "predicate": "regulates",
            "object": "cell_shape_trait",
            "description": "Peptidoglycan wall architecture underlies cell shape.",
            "evidence": [
              {
                "reference": "DOI:10.1002/mbo3.1385",
                "notes": "Peptidoglycan determines cell shape (broad bacterial claim)."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "mreB",
            "predicate": "organizes",
            "object": "rod_shape",
            "description": "MreB coordinates with PG synthases to organize cell-wall synthesis for rod shape.",
            "evidence": [
              {
                "reference": "DOI:10.1042/bsr20221664",
                "notes": "MreB coordinates with PG synthases and is linked to rod shape."
              }
            ]
          },
          {
            "subject": "a22_inhibitor",
            "predicate": "disrupts",
            "object": "rod_shape",
            "description": "A22 reduces MreB filaments, causing loss of rod shape and lysis.",
            "evidence": [
              {
                "reference": "DOI:10.1128/jb.00433-22",
                "notes": "A22 reduces MreB filaments leading to loss of rod shape and lysis."
              }
            ]
          },
          {
            "subject": "cardiolipin_lipid_order",
            "predicate": "inhibits",
            "object": "mreB",
            "description": "Increased lipid order or cardiolipin interferes with MreB assembly.",
            "evidence": [
              {
                "reference": "DOI:10.1128/jb.00433-22",
                "notes": "Increased lipid order or cardiolipin interferes with MreB assembly."
              }
            ],
            "predicate_id": "RO:0002212"
          },
          {
            "subject": "flotillins",
            "predicate": "promotes",
            "object": "cell_wall_synthesis",
            "description": "Flotillins promote MreB activity and cell-wall synthesis via membrane organization.",
            "evidence": [
              {
                "reference": "DOI:10.1128/jb.00433-22",
                "notes": "Absence of flotillins downregulates MreB activity and cell wall synthesis."
              }
            ],
            "predicate_id": "RO:0002213"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.884864+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-11T00:00:00-07:00",
        "curator": "codex",
        "action": "CURATED_WITH_LITERATURE",
        "changes": "Reviewed cell shape trait and added DOI-backed causal graph for peptidoglycan cell wall, PBPs, MreB, FtsZ, crescentin, and localized wall growth.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002211\u00d71, RO:0002326\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T05:49:24Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:catalyzes\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:19Z",
        "curator": "claude",
        "action": "RENAME_PREDICATE_LABELS",
        "changes": "Renamed 1 causal-edge predicate label(s) to align with existing groundings: maintains \u2192 regulates \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:21Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002211\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:38:00Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0009252\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T05:05:14Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 3 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A1B1UYY2\u00d71, UniProtKB:C0LUM8\u00d71, UniProtKB:A0A2N9AY16\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-26T05:00:48Z",
        "curator": "claude",
        "action": "RENAME_PREDICATE_LABELS",
        "changes": "Renamed 1 causal-edge predicate label(s) to align with existing groundings: determines \u2192 causes \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-26T05:00:50Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:causes\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 6 evidence-backed generic edges (7 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:13Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002211\u00d71, RO:0002212\u00d71, RO:0002213\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:21:12Z",
        "curator": "claude",
        "action": "RETRACT_DEAD_UNIPROT_GROUNDINGS",
        "changes": "Retracted 2 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-22T04:26:15Z",
        "curator": "codex",
        "action": "REVIEW_UNIPROT_INSTANCE_GROUNDINGS",
        "changes": "Reviewed 1 organism-specific UniProtKB grounding(s): replaced 1 with taxon-agnostic GO/InterPro terms and retracted 0 to label-only where no exact semantic term was supported (docs/GROUNDING_POLICY.md).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope cell_shape_peptidoglycan_cytoskeleton=NONMECHANISTIC with scope_notes; marked 4 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (penicillin_binding_proteins, mreB, crescentin, flotillins).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T04:43:24Z",
        "curator": "codex",
        "action": "ADD_CANONICAL_EXAMPLES",
        "changes": "Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Escherichia coli (NCBITaxon:562; DOI:10.1038/nrmicro1205). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000882",
    "label": "cell width",
    "definition": "A phenotype that inheres in a cell by virtue of its shorter dimension when viewed on a plane.",
    "definition_source": "DOI:10.1146/annurev-cellbio-101011-155745",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev-cellbio-101011-155745",
        "snippet": "MreB-directed peptidoglycan synthesis",
        "notes": "Bacterial rod-shape review identifies MreB-directed lateral wall synthesis as the control point governing cell width."
      },
      {
        "reference": "DOI:10.1038/nrmicro3088",
        "snippet": "rod-shape is maintained",
        "notes": "Cell-wall biosynthesis review supports lateral peptidoglycan assembly as the cellular machinery setting rod width."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "cell_width_mreb_lateral_wall",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "Cell width is a quantitative measurement descriptor rather than one conserved protein-mediated mechanism. The graph is retained only as contextual background on rod-width control.",
        "title": "Cell-width control by MreB-directed lateral cell-wall assembly",
        "description": "DOI-backed graph linking MreB cytoskeletal organization, Rod-complex peptidoglycan synthesis, and turgor-balanced wall mechanics to the observed cell-width phenotype.",
        "nodes": [
          {
            "node_id": "cell_width_trait",
            "label": "cell width",
            "node_type": "TRAIT",
            "grounding": "METPO:1000882",
            "description": "Shorter dimension of the cell body, perpendicular to the long axis."
          },
          {
            "node_id": "mreb_cytoskeleton",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "This contextual node denotes an assembled cytoskeletal structure, not one exact MreB protein-family entity.",
            "label": "MreB cytoskeleton",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Actin-like MreB filaments that pattern lateral cell-wall synthesis."
          },
          {
            "node_id": "rod_complex_pg",
            "label": "Rod-complex peptidoglycan synthesis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "MreB-organized peptidoglycan synthesis along the cylindrical wall."
          },
          {
            "node_id": "peptidoglycan_cell_wall",
            "label": "peptidoglycan cell wall",
            "node_type": "CELLULAR_LOCALIZATION",
            "description": "Load-bearing peptidoglycan sacculus that constrains cell shape.",
            "grounding": "GO:0009274"
          },
          {
            "node_id": "turgor_pressure",
            "label": "turgor pressure",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Internal hydrostatic pressure pushing against the cell wall."
          },
          {
            "node_id": "apbp_system",
            "label": "class A PBP (aPBP) cell-wall synthesis system",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Class A penicillin-binding-protein peptidoglycan synthesis system that acts oppositely to the Rod complex to set cell diameter."
          },
          {
            "node_id": "roda_pbp2_synthase",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "RodA and PBP2 are distinct proteins grouped as a synthase module; one family identifier cannot represent both components.",
            "label": "RodA-PBP2 core synthase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Essential Rod-complex peptidoglycan synthase (RodA glycosyltransferase with PBP2 transpeptidase) driving lateral elongation."
          },
          {
            "node_id": "mre_accessory_proteins",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "This umbrella combines multiple accessory protein families and therefore has no single exact semantic grounding.",
            "label": "Rod-complex accessory proteins MreC/MreD/RodZ",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Accessory components of the Rod complex that regulate RodA-PBP2 enzymatic activity."
          },
          {
            "node_id": "envelope_bending_rigidity",
            "label": "cell envelope bending rigidity",
            "node_type": "QUALITY",
            "description": "Mechanical bending rigidity of the cell envelope that constrains width and its homeostasis."
          }
        ],
        "edges": [
          {
            "subject": "mreb_cytoskeleton",
            "predicate": "enables",
            "object": "rod_complex_pg",
            "description": "MreB filaments organize Rod-complex peptidoglycan synthesis along the cylinder.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-cellbio-101011-155745",
                "snippet": "MreB-directed peptidoglycan synthesis",
                "notes": "Supports MreB as the organizer of lateral PG synthesis."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "rod_complex_pg",
            "predicate": "builds",
            "object": "peptidoglycan_cell_wall",
            "description": "Rod-complex peptidoglycan synthesis builds the lateral cylindrical wall.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro3088",
                "snippet": "rod-shape is maintained",
                "notes": "Supports lateral PG assembly as the wall-building activity."
              }
            ],
            "predicate_id": "biolink:produces"
          },
          {
            "subject": "peptidoglycan_cell_wall",
            "predicate": "regulates",
            "object": "cell_width_trait",
            "description": "The peptidoglycan sacculus constrains cell width against turgor.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro3088",
                "snippet": "rod-shape is maintained",
                "notes": "Supports the cell wall as the structural constraint on width."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "turgor_pressure",
            "predicate": "balances",
            "object": "peptidoglycan_cell_wall",
            "description": "Turgor pressure is mechanically balanced by the peptidoglycan wall, determining the steady-state radius.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-cellbio-101011-155745",
                "snippet": "MreB-directed peptidoglycan synthesis",
                "notes": "Supports wall mechanics as the determinant of steady-state cell width."
              }
            ]
          },
          {
            "subject": "apbp_system",
            "predicate": "regulates",
            "object": "cell_width_trait",
            "description": "Rod and aPBP systems act oppositely to set cell diameter; MreB-directed lateral PG synthesis is the control point governing width.",
            "evidence": [
              {
                "reference": "DOI:10.3390/biom13050720",
                "notes": "Review states Rod and aPBP systems \"act oppositely to set B. subtilis cell diameter\"; MreB-directed PG synthesis identified as the control point governing cell width."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "roda_pbp2_synthase",
            "predicate": "enables",
            "object": "rod_complex_pg",
            "description": "Activation/open state of the RodA-PBP2 core synthase couples PG polymerization and crosslinking required for elongation-based lateral wall synthesis.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-023-39037-9",
                "notes": "RodA-PBP2 undergoes dynamic exchange between closed and open states; structural opening couples activation of polymerization and crosslinking and is essential in vivo."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "mre_accessory_proteins",
            "predicate": "regulates",
            "object": "roda_pbp2_synthase",
            "description": "Rod-complex accessory components MreC/MreD/RodZ regulate RodA-PBP2 activity and thereby lateral wall synthesis affecting width.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-023-39037-9",
                "notes": "Rod complex has accessory components MreCD and RodZ; genetic studies implicated MreC as a potential regulator of enzymatic activity."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "envelope_bending_rigidity",
            "predicate": "regulates",
            "object": "cell_width_trait",
            "description": "Cell envelope bending rigidity constrains cell width homeostasis; width increases and saturates primarily under the control of envelope bending rigidity.",
            "evidence": [
              {
                "reference": "DOI:10.1101/2024.11.22.624946",
                "notes": "Width increases and saturates primarily under the control of envelope bending rigidity, which constrains width homeostasis."
              }
            ],
            "predicate_id": "RO:0002211"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.918950+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-11T22:30:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed causal graph linking MreB cytoskeleton, Rod-complex peptidoglycan synthesis, cell wall, and turgor balance to cell width.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-26T05:00:48Z",
        "curator": "claude",
        "action": "RENAME_PREDICATE_LABELS",
        "changes": "Renamed 2 causal-edge predicate label(s) to align with existing groundings: organizes \u2192 enables \u00d71; constrains \u2192 regulates \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-26T05:00:50Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d71, RO:0002211\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-13T21:03:26Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:produces\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 4 evidence-backed generic edges (4 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:13Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 4 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002211\u00d73, RO:0002327\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-21T00:00:00Z",
        "curator": "claude",
        "action": "BACKFILL_CANONICAL_EXAMPLES",
        "changes": "Added 3 exemplar taxon/taxa. Organisms and citations come only from this record's own deep-research artifact; every taxon id was resolved and label-checked against the local NCBITaxon build rather than recalled. Organisms the artifact names as contrast cases rather than exemplars were deliberately excluded.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope cell_width_mreb_lateral_wall=NONMECHANISTIC with scope_notes; marked 3 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (mreb_cytoskeleton, roda_pbp2_synthase, mre_accessory_proteins).",
        "llm_assisted": true
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:274",
        "taxon_label": "Thermus thermophilus",
        "reference": "DOI:10.1038/s41467-023-39037-9",
        "note": "Model organism for the RodA/MreB width-determining machinery described in this record."
      },
      {
        "taxon_id": "NCBITaxon:155892",
        "taxon_label": "Caulobacter vibrioides",
        "reference": "DOI:10.1101/197475",
        "note": "Model organism for MreB-dependent width control; the artifact cites it under the earlier name Caulobacter crescentus, and the reference is a preprint."
      },
      {
        "taxon_id": "NCBITaxon:562",
        "taxon_label": "Escherichia coli",
        "reference": "DOI:10.1002/mbo3.1385",
        "note": "Model rod whose peptidoglycan-synthesis complex sets cell width in the mechanism this record carries."
      }
    ]
  },
  {
    "identifier": "METPO:1000890",
    "label": "cell width large",
    "definition": "A cell-width phenotype in which the shorter cell dimension exceeds approximately 0.9 micrometers.",
    "definition_source": "DOI:10.1146/annurev-cellbio-101011-155745",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000882"
    ],
    "synonyms": [
      {
        "synonym_text": "W_>0.9",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev-cellbio-101011-155745",
        "snippet": "MreB-directed peptidoglycan synthesis",
        "notes": "Supports MreB/Rod-complex activity as the control point governing wide rod radii."
      },
      {
        "reference": "DOI:10.1126/science.aaa1313",
        "snippet": "cell size scales with growth rate",
        "notes": "Growth-rate-dependent size law supports widening of cells at fast growth rates or under nutrient-rich conditions."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1232683",
        "taxon_label": "Marinobacterium lacunae",
        "reference": "DOI:10.1007/s00203-023-03627-4",
        "note": "Marinobacterium lacunae AK27T cells measured 1.0-1.5 micrometres wide, wholly above the approximately 0.9-micrometre threshold."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "cell_width_large_setpoint_increase",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a numerical cell-width bin. Its graph illustrates possible rod-system perturbations but does not define a universal causal mechanism for the bin.",
        "title": "Large cell-width by elevated wall-radius set-point",
        "description": "DOI-backed graph linking nutrient-rich growth conditions and an elevated MreB-driven wall-radius set-point to wide rods (>0.9 \u03bcm).",
        "nodes": [
          {
            "node_id": "cell_width_large_trait",
            "label": "cell width large",
            "node_type": "TRAIT",
            "grounding": "METPO:1000890",
            "description": "Cell width exceeding approximately 0.9 \u03bcm."
          },
          {
            "node_id": "cell_width_trait",
            "label": "cell width",
            "node_type": "TRAIT",
            "grounding": "METPO:1000882",
            "description": "Regulated shorter cellular dimension."
          },
          {
            "node_id": "rich_growth_conditions",
            "label": "rich growth conditions",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Nutrient-rich conditions promoting fast growth and larger cells."
          },
          {
            "node_id": "rod_complex_pg",
            "label": "Rod-complex peptidoglycan synthesis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "MreB-organized lateral peptidoglycan assembly."
          },
          {
            "node_id": "roda_pbp2_complex",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "RodA and PBP2 are distinct proteins grouped as a complex; one family identifier cannot represent both components.",
            "label": "RodA-PBP2 elongasome complex",
            "node_type": "GENE_OR_PROTEIN",
            "description": "SEDS-bPBP synthase pair driving lateral (sidewall) peptidoglycan synthesis."
          },
          {
            "node_id": "roda_pbp2_activation",
            "label": "RodA-PBP2 allosteric activation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Structural opening coupling peptidoglycan polymerization and crosslinking."
          },
          {
            "node_id": "pg_polymerization_crosslinking",
            "label": "peptidoglycan polymerization and crosslinking",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Glycan-chain polymerization and transpeptidase crosslinking during elongation."
          },
          {
            "node_id": "sidewall_pg_insertion",
            "label": "lateral sidewall peptidoglycan insertion",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Insertion of new peptidoglycan at dispersed lateral cell-wall sites."
          },
          {
            "node_id": "mreb_filaments",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "This contextual node denotes assembled MreB filaments rather than one exact protein-family entity.",
            "label": "MreB cytoskeletal filaments",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Actin-like filaments guiding circumferential peptidoglycan insertion."
          },
          {
            "node_id": "circumferential_pg_insertion",
            "label": "circumferential peptidoglycan insertion",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Peptidoglycan insertion oriented perpendicular to the long cell axis."
          },
          {
            "node_id": "rod_complex_rotation",
            "label": "Rod-complex circumferential rotation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Rotation of the Rod complex perpendicular to the long cell axis."
          },
          {
            "node_id": "even_pg_distribution",
            "label": "even peptidoglycan distribution",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Evenly distributed insertion of peptidoglycan in the cell-surface layer."
          },
          {
            "node_id": "mrec_mred_balance",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "This denotes a balance between distinct MreC and MreD proteins, not one semantically groundable protein entity.",
            "label": "MreC-MreD balance",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Stoichiometric balance of MreC and MreD accessory regulators."
          },
          {
            "node_id": "pbp2_activity",
            "label": "PBP2 transpeptidase activity",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "Peptidoglycan crosslinking activity of the bifunctional PBP2 synthase."
          },
          {
            "node_id": "lipid_ii",
            "label": "Lipid II",
            "node_type": "CHEMICAL",
            "description": "Disaccharide-pentapeptide lipid-linked peptidoglycan precursor.",
            "grounding": "CHEBI:27692"
          }
        ],
        "edges": [
          {
            "subject": "rich_growth_conditions",
            "predicate": "shifts",
            "object": "rod_complex_pg",
            "description": "Rich growth conditions shift Rod-complex activity toward a larger radius set-point.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.aaa1313",
                "snippet": "cell size scales with growth rate",
                "notes": "Supports growth-rate-dependent enlargement of cell radius."
              }
            ]
          },
          {
            "subject": "rod_complex_pg",
            "predicate": "confers",
            "object": "cell_width_large_trait",
            "description": "Elevated Rod-complex activity yields a wide rod radius.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-cellbio-101011-155745",
                "snippet": "MreB-directed peptidoglycan synthesis",
                "notes": "Supports lateral PG synthesis as the producer of the wide cell radius."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "cell_width_large_trait",
            "predicate": "is a",
            "object": "cell_width_trait",
            "description": "Large cell width is a quantitative bin of the cell-width phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-cellbio-101011-155745",
                "snippet": "MreB-directed peptidoglycan synthesis",
                "notes": "Supports large width as a value within the regulated cell-width distribution."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "roda_pbp2_activation",
            "predicate": "positively regulates",
            "object": "pg_polymerization_crosslinking",
            "description": "Allosteric structural opening of RodA-PBP2 activates coupled PG polymerization and crosslinking.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-023-39037-9",
                "notes": "\"Structural opening couples the activation of polymerization and crosslinking and is essential in vivo.\""
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "roda_pbp2_complex",
            "predicate": "mediates",
            "object": "sidewall_pg_insertion",
            "description": "Activated RodA-PBP2 elongasome synthesizes and inserts new PG at lateral wall sites.",
            "evidence": [
              {
                "reference": "DOI:10.1073/pnas.2215237120",
                "notes": "\"The elongasome... synthesizing and inserting new PG material at dispersed sites in the lateral cell wall.\""
              }
            ]
          },
          {
            "subject": "sidewall_pg_insertion",
            "predicate": "contributes to",
            "object": "rod_complex_pg",
            "description": "Lateral sidewall PG insertion is the Rod-complex-driven wall-elongation process that sets rod radius.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-cellbio-101011-155745",
                "notes": "Lateral PG insertion is the MreB/Rod-complex activity governing rod radius."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "mreb_filaments",
            "predicate": "orients",
            "object": "circumferential_pg_insertion",
            "description": "MreB filaments orient peptidoglycan insertion perpendicular to the long cell axis, controlling rod radius.",
            "evidence": [
              {
                "reference": "DOI:10.1073/pnas.2301987120",
                "notes": "\"MreB filaments are thought to orient it orthogonally to the long cell axis\" guiding PG insertion perpendicular to the long axis."
              }
            ]
          },
          {
            "subject": "rod_complex_rotation",
            "predicate": "enables",
            "object": "even_pg_distribution",
            "description": "Rotation of the Rod complex around the circumference enables evenly distributed PG insertion.",
            "evidence": [
              {
                "reference": "DOI:10.1002/mbo3.1385",
                "notes": "\"the Rod complex rotates perpendicularly to the long axis of the cell... allowing the insertion of peptidoglycan... in an evenly distributed manner.\""
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "mrec_mred_balance",
            "predicate": "regulates",
            "object": "pbp2_activity",
            "description": "The balance between MreC and MreD determines PBP2 synthase activity.",
            "evidence": [
              {
                "reference": "DOI:10.1002/mbo3.1385",
                "notes": "\"the balance between MreC and MreD determines the activity of PBP2\""
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "lipid_ii",
            "predicate": "required for",
            "object": "pg_polymerization_crosslinking",
            "description": "Lipid II is the substrate required for peptidoglycan polymerization by Rod/elongasome synthases.",
            "evidence": [
              {
                "reference": "DOI:10.3390/biom13050720",
                "notes": "\"GTases and TPases utilize the disaccharide pentapeptide of Lipid-II as a substrate for PG polymerization and synthesis of the PG layer.\""
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.922624+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-11T22:30:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed causal graph linking rich growth conditions and elevated Rod-complex activity to large cell width (>0.9 \u03bcm).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d71, rdfs:subClassOf\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 7 evidence-backed generic edges (11 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:13Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002326\u00d71, RO:0002327\u00d71, RO:0002211\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:33Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:27692\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-04T03:08:14Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002213\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates (1 to confers), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-07T18:00:00Z",
        "curator": "claude",
        "action": "REGROUND_CAUSAL_EDGE",
        "changes": "Edge rod_complex_rotation -> even_pg_distribution in graph cell_width_large_setpoint_increase: retyped even_pg_distribution to BIOLOGICAL_PROCESS. Issue 334. biolink declares enables range 'biological process or activity', which of CausalNodeTypeEnum only BIOLOGICAL_PROCESS, PATHWAY and MOLECULAR_FUNCTION satisfy, so this edge entailed a false type on its object. The label reads like a quality but the description does not: 'Evenly distributed INSERTION of peptidoglycan in the cell-surface layer.' Insertion is a process, so `enables` is already the right relation and only the node type was wrong.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope cell_width_large_setpoint_increase=NONMECHANISTIC with scope_notes; marked 3 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (roda_pbp2_complex, mreb_filaments, mrec_mred_balance).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T04:43:24Z",
        "curator": "codex",
        "action": "ADD_CANONICAL_EXAMPLES",
        "changes": "Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Marinobacterium lacunae (NCBITaxon:1232683; DOI:10.1007/s00203-023-03627-4). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000889",
    "label": "cell width medium",
    "definition": "A cell-width phenotype in which the shorter cell dimension lies approximately between 0.65 and 0.9 micrometers.",
    "definition_source": "DOI:10.1146/annurev-cellbio-101011-155745",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000882"
    ],
    "synonyms": [
      {
        "synonym_text": "W_0.65_0.9",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev-cellbio-101011-155745",
        "snippet": "MreB-directed peptidoglycan synthesis",
        "notes": "Supports the MreB/Rod-complex set-point producing typical rod widths in the 0.65\u20130.9 \u03bcm range."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:3073604",
        "taxon_label": "Ruixingdingia sedimenti",
        "reference": "DOI:10.1099/ijsem.0.006350",
        "note": "Ruixingdingia sedimenti LG-4T cells measured 0.7-0.8 micrometres wide, wholly within the approximately 0.65-0.9-micrometre bin."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "cell_width_medium_typical_rod",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a numerical cell-width bin. Its graph gives contextual rod-system examples but is not a single protein-mediated mechanism for every organism in the interval.",
        "title": "Medium cell-width typical rod",
        "description": "DOI-backed graph linking MreB-directed lateral wall synthesis under standard growth conditions to typical rod radii (0.65\u20130.9 \u03bcm).",
        "nodes": [
          {
            "node_id": "cell_width_medium_trait",
            "label": "cell width medium",
            "node_type": "TRAIT",
            "grounding": "METPO:1000889",
            "description": "Cell width approximately 0.65\u20130.9 \u03bcm."
          },
          {
            "node_id": "cell_width_trait",
            "label": "cell width",
            "node_type": "TRAIT",
            "grounding": "METPO:1000882",
            "description": "Regulated shorter cellular dimension."
          },
          {
            "node_id": "rod_complex_pg",
            "label": "Rod-complex peptidoglycan synthesis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "MreB-organized lateral peptidoglycan assembly."
          },
          {
            "node_id": "standard_growth_conditions",
            "label": "standard growth conditions",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Routine laboratory growth conditions producing typical bacterial rod widths."
          },
          {
            "node_id": "roda_pbp2_complex",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "RodA and PBP2 are distinct proteins grouped as a complex; one family identifier cannot represent both components.",
            "label": "RodA-PBP2 complex",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Elongasome SEDS-bPBP synthase pair (RodA with PBP2) driving lateral peptidoglycan synthesis."
          },
          {
            "node_id": "pg_polymerization_crosslinking",
            "label": "peptidoglycan polymerization and crosslinking",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Glycan strand polymerization and peptide crosslinking during cell-wall elongation."
          },
          {
            "node_id": "mrec_protein",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "The contextual source supports the MreC label, but an exact semantic family term was not verified in this review.",
            "label": "MreC",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Membrane-associated Rod-complex protein that activates PBP2."
          },
          {
            "node_id": "pbp2_protein",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "The contextual source supports the PBP2 label, but an exact semantic family term was not verified in this review.",
            "label": "PBP2",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Bifunctional class B penicillin-binding protein (transpeptidase) of the elongasome."
          },
          {
            "node_id": "mred_protein",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "The contextual source supports the MreD label, but an exact semantic family term was not verified in this review.",
            "label": "MreD",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Rod-complex membrane protein that modulates PBP2 activity in balance with MreC."
          },
          {
            "node_id": "apbp_proteins",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "This umbrella combines multiple class-A penicillin-binding proteins, so no one exact protein-family entity denotes the full group.",
            "label": "class A penicillin-binding proteins (aPBPs)",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Bifunctional glycosyltransferase/transpeptidase peptidoglycan synthases that influence cell diameter."
          }
        ],
        "edges": [
          {
            "subject": "standard_growth_conditions",
            "predicate": "enables",
            "object": "rod_complex_pg",
            "description": "Standard growth regimes support typical Rod-complex activity.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-cellbio-101011-155745",
                "snippet": "MreB-directed peptidoglycan synthesis",
                "notes": "Supports MreB-organized PG synthesis under standard conditions."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "rod_complex_pg",
            "predicate": "confers",
            "object": "cell_width_medium_trait",
            "description": "Rod-complex PG synthesis sustains a typical rod radius.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro3088",
                "snippet": "rod-shape is maintained",
                "notes": "Supports lateral PG assembly as the producer of typical rod radius."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "cell_width_medium_trait",
            "predicate": "is a",
            "object": "cell_width_trait",
            "description": "Medium cell width is a quantitative bin of the cell-width phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-cellbio-101011-155745",
                "snippet": "MreB-directed peptidoglycan synthesis",
                "notes": "Supports medium width as a value within the regulated cell-width distribution."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "roda_pbp2_complex",
            "predicate": "positively regulates",
            "object": "pg_polymerization_crosslinking",
            "description": "Structural opening of the RodA-PBP2 complex couples and activates PG polymerization and crosslinking during elongation.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-023-39037-9",
                "notes": "RodA-PBP2 undergoes dynamic exchange between closed and open states; structural opening couples activation of polymerization and crosslinking and is essential in vivo."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "pg_polymerization_crosslinking",
            "predicate": "has output",
            "object": "rod_complex_pg",
            "description": "Elongasome polymerization/crosslinking constitutes the Rod-complex lateral peptidoglycan synthesis that sets rod radius.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-023-39037-9",
                "notes": "Activation of polymerization and crosslinking is the elongation activity underlying Rod-complex lateral wall synthesis."
              }
            ],
            "predicate_id": "RO:0002234"
          },
          {
            "subject": "mrec_protein",
            "predicate": "activates",
            "object": "pbp2_protein",
            "description": "MreC interacts with PBP2 and stimulates its peptidoglycan polymerization and crosslinking activity.",
            "evidence": [
              {
                "reference": "DOI:10.1002/mbo3.1385",
                "notes": "MreC interacts with PBP2 and is thought to cause a structural change in PBP2 and stimulate peptidoglycan polymerization and crosslinking."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "mred_protein",
            "predicate": "modulates activity of",
            "object": "pbp2_protein",
            "description": "MreD modulates PBP2 activity; the balance between MreC and MreD determines PBP2 activity.",
            "evidence": [
              {
                "reference": "DOI:10.1002/mbo3.1385",
                "notes": "The balance between MreC and MreD determines the activity of PBP2 (curated as modulatory)."
              }
            ]
          },
          {
            "subject": "pbp2_protein",
            "predicate": "enables",
            "object": "rod_complex_pg",
            "description": "Activated PBP2 transpeptidation supports Rod-complex lateral peptidoglycan synthesis.",
            "evidence": [
              {
                "reference": "DOI:10.1002/mbo3.1385",
                "notes": "PBP2 activity drives peptidoglycan polymerization and crosslinking of the Rod complex."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "apbp_proteins",
            "predicate": "regulates",
            "object": "cell_width_trait",
            "description": "Class A PBPs regulate cell diameter; loss of aPBPs yields shorter, wider cells.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-023-41082-3",
                "notes": "aPBPs regulate cell diameter; strains lacking aPBPs were moderately but significantly shorter and wider."
              }
            ],
            "predicate_id": "RO:0002211"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.922158+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-11T22:30:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed causal graph linking MreB-directed Rod-complex peptidoglycan synthesis to medium cell width (0.65\u20130.9 \u03bcm).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d71, rdfs:subClassOf\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:19Z",
        "curator": "claude",
        "action": "RENAME_PREDICATE_LABELS",
        "changes": "Renamed 1 causal-edge predicate label(s) to align with existing groundings: supports \u2192 enables \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:21Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 6 evidence-backed generic edges (6 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:13Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 4 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d71, RO:0002213\u00d71, RO:0002327\u00d71, RO:0002211\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-26T07:15:19Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 3 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A1L9R356\u00d71, UniProtKB:A0A2D2D7X6\u00d71, UniProtKB:A0A0H2VI68\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:21:12Z",
        "curator": "claude",
        "action": "RETRACT_DEAD_UNIPROT_GROUNDINGS",
        "changes": "Retracted 3 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-04T03:08:14Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002213\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 2 causal edge(s) off microbe-domain METPO predicates (1 to confers, 1 to has output), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope cell_width_medium_typical_rod=NONMECHANISTIC with scope_notes; marked 5 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (roda_pbp2_complex, mrec_protein, pbp2_protein, mred_protein, apbp_proteins).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T04:43:24Z",
        "curator": "codex",
        "action": "ADD_CANONICAL_EXAMPLES",
        "changes": "Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Ruixingdingia sedimenti (NCBITaxon:3073604; DOI:10.1099/ijsem.0.006350). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000888",
    "label": "cell width small",
    "definition": "A cell-width phenotype in which the shorter cell dimension lies approximately between 0.5 and 0.65 micrometers.",
    "definition_source": "DOI:10.1146/annurev-cellbio-101011-155745",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000882"
    ],
    "synonyms": [
      {
        "synonym_text": "W_0.5_0.65",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev-cellbio-101011-155745",
        "snippet": "MreB-directed peptidoglycan synthesis",
        "notes": "Supports the MreB/Rod-complex set-point producing narrow rod widths in the 0.5\u20130.65 \u03bcm range."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:3028314",
        "taxon_label": "Oceanimonas pelagia",
        "reference": "DOI:10.1007/s10482-024-01948-y",
        "note": "Oceanimonas pelagia NTOU-MSR1T cells measured approximately 0.5-0.6 micrometres wide, within the approximately 0.5-0.65-micrometre bin."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "cell_width_small_mreb_setpoint",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a numerical cell-width bin. Its graph illustrates possible rod-system determinants but does not define a universal mechanism for the measured interval.",
        "title": "Small cell-width MreB-Rod set-point",
        "description": "DOI-backed graph linking MreB-organized lateral wall synthesis to a narrow rod radius set-point (0.5\u20130.65 \u03bcm).",
        "nodes": [
          {
            "node_id": "cell_width_small_trait",
            "label": "cell width small",
            "node_type": "TRAIT",
            "grounding": "METPO:1000888",
            "description": "Cell width approximately 0.5\u20130.65 \u03bcm."
          },
          {
            "node_id": "cell_width_trait",
            "label": "cell width",
            "node_type": "TRAIT",
            "grounding": "METPO:1000882",
            "description": "Regulated shorter cellular dimension."
          },
          {
            "node_id": "mreb_cytoskeleton",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "This contextual node denotes an assembled cytoskeletal structure, not one exact MreB protein-family entity.",
            "label": "MreB cytoskeleton",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Actin-like MreB filaments organizing lateral cell-wall synthesis."
          },
          {
            "node_id": "rod_complex_pg",
            "label": "Rod-complex peptidoglycan synthesis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "MreB-organized lateral peptidoglycan assembly."
          },
          {
            "node_id": "mrec_protein",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "The contextual source supports the MreC label, but an exact semantic family term was not verified in this review.",
            "label": "MreC",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Periplasmic Rod-complex protein that favors the open, active PBP2 state."
          },
          {
            "node_id": "roda_pbp2_open",
            "label": "RodA-PBP2 open conformation",
            "node_type": "STATE",
            "description": "Activated open conformation of the SEDS-bPBP RodA-PBP2 synthase complex."
          },
          {
            "node_id": "pg_polymerization_crosslinking",
            "label": "peptidoglycan polymerization and crosslinking",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Glycan strand polymerization and peptide crosslinking output of the Rod complex."
          },
          {
            "node_id": "rod_diameter_control",
            "label": "rod width/diameter control",
            "node_type": "CAPACITY",
            "description": "Maintenance of a stable steady-state rod diameter (width set-point)."
          },
          {
            "node_id": "pg_hydrolase_activity",
            "label": "peptidoglycan hydrolase activity",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "Cell-wall hydrolase/autolysin activity that cleaves peptidoglycan."
          },
          {
            "node_id": "magnesium_ion",
            "label": "Mg2+",
            "node_type": "CHEMICAL",
            "description": "Magnesium ion, an environmental modifier of cell-wall hydrolase activity.",
            "grounding": "CHEBI:18420"
          }
        ],
        "edges": [
          {
            "subject": "mreb_cytoskeleton",
            "predicate": "enables",
            "object": "rod_complex_pg",
            "description": "MreB organizes lateral PG synthesis along the cylinder.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-cellbio-101011-155745",
                "snippet": "MreB-directed peptidoglycan synthesis",
                "notes": "Supports MreB as the lateral PG organizer."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "rod_complex_pg",
            "predicate": "confers",
            "object": "cell_width_small_trait",
            "description": "Rod-complex PG synthesis maintains a narrow cylinder radius.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro3088",
                "snippet": "rod-shape is maintained",
                "notes": "Supports lateral PG assembly as the producer of the narrow rod radius."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "cell_width_small_trait",
            "predicate": "is a",
            "object": "cell_width_trait",
            "description": "Small cell width is a quantitative bin of the cell-width phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-cellbio-101011-155745",
                "snippet": "MreB-directed peptidoglycan synthesis",
                "notes": "Supports small width as a value within the regulated cell-width distribution."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "mrec_protein",
            "predicate": "activates",
            "object": "roda_pbp2_open",
            "description": "MreC favors the open, active conformation of the RodA-PBP2 synthase.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-023-39037-9",
                "notes": "MreC favors the open, active PBP2 state; PBP2 suppressor alleles bypass defective MreC and increase polymerization activity (conserved Rod complex)."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "roda_pbp2_open",
            "predicate": "increases",
            "object": "pg_polymerization_crosslinking",
            "description": "The open RodA-PBP2 state couples activation of polymerization and crosslinking.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-023-39037-9",
                "notes": "Structural opening couples activation of polymerization and crosslinking; open-state mutants show stronger polymerization (conserved SEDS-bPBP systems)."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "pg_polymerization_crosslinking",
            "predicate": "contributes to",
            "object": "rod_complex_pg",
            "description": "PG polymerization and crosslinking constitute the Rod-complex synthetic output.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-023-39037-9",
                "notes": "Open-state activation links RodA-PBP2 conformation to peptidoglycan synthetic output of the Rod complex."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "mreb_cytoskeleton",
            "predicate": "required for",
            "object": "rod_diameter_control",
            "description": "MreB is a key determinant of rod shape and steady-state diameter/width control.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.cell.2018.02.050",
                "notes": "MreB is a key determinant of rod shape and diameter; perturbing MreB changes steady-state diameter and width control (broad, foundational)."
              }
            ]
          },
          {
            "subject": "rod_diameter_control",
            "predicate": "confers",
            "object": "cell_width_small_trait",
            "description": "Stable diameter control maintains the narrow rod radius set-point.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.cell.2018.02.050",
                "notes": "Width/diameter control governs the steady-state rod radius producing the narrow width phenotype."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "magnesium_ion",
            "predicate": "inhibits",
            "object": "pg_hydrolase_activity",
            "description": "Exogenous Mg2+ inhibits autolysins/cell-wall hydrolases.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41598-021-04294-5",
                "notes": "Exogenous Mg2+ inhibits autolysins/CW hydrolases and compensates increased DL-endopeptidase activity (clearest environmental modifier edge)."
              }
            ],
            "predicate_id": "RO:0002212"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.921682+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-11T22:30:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed causal graph linking MreB-directed Rod-complex peptidoglycan synthesis to small cell width (0.5\u20130.65 \u03bcm).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d71, rdfs:subClassOf\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-26T05:00:48Z",
        "curator": "claude",
        "action": "RENAME_PREDICATE_LABELS",
        "changes": "Renamed 1 causal-edge predicate label(s) to align with existing groundings: organizes \u2192 enables \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-26T05:00:50Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 6 evidence-backed generic edges (6 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:13Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 5 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002213\u00d72, RO:0002326\u00d71, METPO:2000202\u00d71, RO:0002212\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:33Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:18420\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-26T07:15:19Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A1L9R356\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:21:12Z",
        "curator": "claude",
        "action": "RETRACT_DEAD_UNIPROT_GROUNDINGS",
        "changes": "Retracted 1 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 2 causal edge(s) off microbe-domain METPO predicates (2 to confers), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope cell_width_small_mreb_setpoint=NONMECHANISTIC with scope_notes; marked 2 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (mreb_cytoskeleton, mrec_protein).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T04:43:24Z",
        "curator": "codex",
        "action": "ADD_CANONICAL_EXAMPLES",
        "changes": "Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Oceanimonas pelagia (NCBITaxon:3028314; DOI:10.1007/s10482-024-01948-y). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000887",
    "label": "cell width very small",
    "definition": "A cell-width phenotype in which the shorter cell dimension is at most approximately 0.5 micrometers.",
    "definition_source": "DOI:10.1038/ismej.2014.60",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000882"
    ],
    "synonyms": [
      {
        "synonym_text": "W_<=0.5",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/ismej.2014.60",
        "snippet": "small cells and genomes",
        "notes": "Streamlining review links very narrow cell widths to oligotrophic and streamlined lineages."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:324679",
        "taxon_label": "Spirochaeta dissipatitropha",
        "reference": "DOI:10.1099/ijs.0.65862-0",
        "note": "Spirochaeta dissipatitropha ASpC2T cells measured approximately 0.23 micrometres wide, wholly below the at-most-0.5-micrometre threshold."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "cell_width_very_small_streamlining",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a numerical cell-width bin. Its streamlined-cell graph is contextual background rather than a universal protein-mediated mechanism.",
        "title": "Very-narrow cell width by streamlining",
        "description": "DOI-backed graph linking nutrient streamlining to a very-narrow rod radius (\u22640.5 \u03bcm).",
        "nodes": [
          {
            "node_id": "cell_width_very_small_trait",
            "label": "cell width very small",
            "node_type": "TRAIT",
            "grounding": "METPO:1000887",
            "description": "Cell width at most ~0.5 \u03bcm."
          },
          {
            "node_id": "cell_width_trait",
            "label": "cell width",
            "node_type": "TRAIT",
            "grounding": "METPO:1000882",
            "description": "Regulated shorter cellular dimension."
          },
          {
            "node_id": "streamlining_selection",
            "label": "streamlining selection",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Selection for reduced surface-to-volume ratio under chronic nutrient limitation."
          },
          {
            "node_id": "oligotrophic_environment",
            "label": "oligotrophic environment",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Persistent low-nutrient setting that favors miniaturized cells."
          },
          {
            "node_id": "high_surface_to_volume_ratio",
            "label": "high surface-to-volume ratio",
            "node_type": "QUALITY",
            "description": "Elevated cell surface area relative to volume, characteristic of small/narrow cells."
          },
          {
            "node_id": "nutrient_uptake_efficiency",
            "label": "nutrient uptake efficiency",
            "node_type": "CAPACITY",
            "description": "Efficiency of nutrient acquisition from the environment."
          },
          {
            "node_id": "small_cell_bacteria",
            "label": "small-cell bacteria",
            "node_type": "STATE",
            "description": "Bacteria with very small cell size, including narrow widths."
          },
          {
            "node_id": "oligotrophic_waters",
            "label": "oligotrophic waters",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Low-nutrient aquatic environments with low organic matter concentrations."
          },
          {
            "node_id": "reduced_genome_size",
            "label": "reduced genome size",
            "node_type": "QUALITY",
            "description": "Streamlined small genome characteristic of oligotrophic lineages."
          },
          {
            "node_id": "rod_complex",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "The rod complex is a variable multisubunit assembly, and no verified single complex term exactly represents this contextual node.",
            "label": "Rod complex",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Elongasome directing organized circumferential peptidoglycan insertion that constrains cell width."
          },
          {
            "node_id": "apbp_proteins",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "This umbrella combines multiple class-A penicillin-binding proteins, so no one exact protein-family entity denotes the full group.",
            "label": "class A penicillin-binding proteins",
            "node_type": "GENE_OR_PROTEIN",
            "description": "aPBPs mediating isotropic peptidoglycan insertion that enlarges the cell cylinder."
          }
        ],
        "edges": [
          {
            "subject": "oligotrophic_environment",
            "predicate": "regulates",
            "object": "streamlining_selection",
            "description": "Persistent oligotrophy selects for streamlined narrow cells.",
            "evidence": [
              {
                "reference": "DOI:10.1038/ismej.2014.60",
                "snippet": "small cells and genomes",
                "notes": "Supports oligotrophic regimes as drivers of cell-width reduction."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "streamlining_selection",
            "predicate": "confers",
            "object": "cell_width_very_small_trait",
            "description": "Streamlining selection produces very narrow rods.",
            "evidence": [
              {
                "reference": "DOI:10.1038/ismej.2014.60",
                "snippet": "small cells",
                "notes": "Supports very narrow width as an outcome of streamlining selection."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "cell_width_very_small_trait",
            "predicate": "is a",
            "object": "cell_width_trait",
            "description": "Very small cell width is a quantitative bin of the cell-width phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-cellbio-101011-155745",
                "snippet": "MreB-directed peptidoglycan synthesis",
                "notes": "Supports very narrow width as a value within the regulated cell-width distribution."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "high_surface_to_volume_ratio",
            "predicate": "increases",
            "object": "nutrient_uptake_efficiency",
            "description": "High surface-to-volume ratio of narrow cells improves nutrient uptake efficiency.",
            "evidence": [
              {
                "reference": "DOI:10.31951/2658-3518-2024-a-4-795",
                "notes": "Thanks to their high surface-to-volume ratio, small-cell bacteria absorb nutrients most efficiently."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "small_cell_bacteria",
            "predicate": "adapted to",
            "object": "oligotrophic_waters",
            "description": "Small-cell bacteria with very narrow widths are adapted to oligotrophic waters.",
            "evidence": [
              {
                "reference": "DOI:10.31951/2658-3518-2024-a-4-795",
                "notes": "Especially important in oligotrophic water bodies with low organic matter concentrations."
              }
            ]
          },
          {
            "subject": "reduced_genome_size",
            "predicate": "associated with",
            "object": "streamlining_selection",
            "description": "Reduced genome size is associated with streamlining in oligotrophic lineages.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mmbr.00124-22",
                "notes": "Many microbial cell lineages in nature share with oligotrophs the property of reduced genome size."
              }
            ],
            "predicate_id": "biolink:associated_with"
          },
          {
            "subject": "rod_complex",
            "predicate": "decreases",
            "object": "cell_width_trait",
            "description": "Rod-complex-mediated organized circumferential PG insertion reduces cell width (rod-shaped bacteria).",
            "evidence": [
              {
                "reference": "DOI:10.1128/msystems.01017-21",
                "notes": "Rod complex-mediated organized circumferential insertion of PG strands reduces cell diameter; may generalize to rod-shaped bacteria."
              }
            ],
            "predicate_id": "RO:0002212"
          },
          {
            "subject": "apbp_proteins",
            "predicate": "increases",
            "object": "cell_width_trait",
            "description": "aPBP-mediated isotropic PG insertion enlarges the cell cylinder, increasing width.",
            "evidence": [
              {
                "reference": "DOI:10.1128/msystems.01017-21",
                "notes": "aPBP-mediated isotropic insertion enlarges the cell cylinder; defines opposite regulation of width."
              }
            ],
            "predicate_id": "RO:0002213"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.921226+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-11T22:30:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed causal graph linking oligotrophic streamlining selection to very narrow cell width (\u22640.5 \u03bcm).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d71, rdfs:subClassOf\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:19Z",
        "curator": "claude",
        "action": "RENAME_PREDICATE_LABELS",
        "changes": "Renamed 1 causal-edge predicate label(s) to align with existing groundings: drives \u2192 regulates \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:21Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002211\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 5 evidence-backed generic edges (7 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:13Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 4 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002213\u00d72, biolink:associated_with\u00d71, RO:0002212\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates (1 to confers), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope cell_width_very_small_streamlining=NONMECHANISTIC with scope_notes; marked 2 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (rod_complex, apbp_proteins).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T04:43:24Z",
        "curator": "codex",
        "action": "ADD_CANONICAL_EXAMPLES",
        "changes": "Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Spirochaeta dissipatitropha (NCBITaxon:324679; DOI:10.1099/ijs.0.65862-0). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000688",
    "label": "coccobacillus shaped",
    "definition": "A cell shape intermediate between spherical cocci and elongated bacilli, typically appearing as short or plump rods.",
    "definition_source": "DOI:10.1128/JB.187.1.54-64.2005",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000666"
    ],
    "synonyms": [
      {
        "synonym_text": "coccobacillus",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1128/JB.187.1.54-64.2005",
        "snippet": "changes shape, from a rod to coccobacillus",
        "notes": "Supports coccobacillus morphology as a short-rod state associated with cell-shape control in representative bacteria."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:727",
        "taxon_label": "Haemophilus influenzae",
        "note": "Textbook coccobacillus (short oval rod); first free-living organism to have its genome sequenced.",
        "reference": "PMID:7542800"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "coccobacillus_shaped_short_rod_morphogenesis",
        "title": "Coccobacillus short-rod morphogenesis mechanism",
        "description": "Evidence-backed causal sketch linking coccobacillus shape to peptidoglycan synthesis, MreB-associated elongation, septal growth, and reduced length-to-width ratio.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a broad environmental or morphological classification spanning multiple mechanisms, a measurement-like bin, or an absence/arrangement descriptor; contextual protein nodes do not receive token UniProt examples.",
        "nodes": [
          {
            "node_id": "coccobacillus_shaped_trait",
            "label": "coccobacillus shaped",
            "node_type": "TRAIT",
            "grounding": "METPO:1000688",
            "description": "Short, plump rod morphology intermediate between coccus and bacillus."
          },
          {
            "node_id": "mreB",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "MreB",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Actin-like bacterial cytoskeletal protein involved in cell-shape control."
          },
          {
            "node_id": "peptidoglycan_synthesis",
            "label": "peptidoglycan synthesis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Cell-wall synthesis and remodeling process.",
            "grounding": "GO:0009252"
          },
          {
            "node_id": "septal_growth",
            "label": "septal growth",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Division-associated cell-wall synthesis."
          },
          {
            "node_id": "short_rod_geometry",
            "label": "short-rod geometry",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Cell geometry with reduced length-to-width ratio."
          },
          {
            "node_id": "rodA_pbp3_elongasome",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "RodA/PBP3 elongasome",
            "node_type": "GENE_OR_PROTEIN",
            "description": "SEDS/PBP pair RodA/PBP3 mediating lateral cell-wall elongation."
          },
          {
            "node_id": "length_to_width_ratio",
            "label": "cell length-to-width ratio",
            "node_type": "QUALITY",
            "description": "Geometric ratio of long to short cell axes that distinguishes rods from cocci."
          },
          {
            "node_id": "gpsB",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "GpsB",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Cell-cycle regulator coordinating peptidoglycan synthase localization."
          },
          {
            "node_id": "pbp2_localization",
            "label": "PBP2 localization",
            "node_type": "CELLULAR_LOCALIZATION",
            "description": "Spatial distribution of penicillin-binding protein 2 between periphery and septum."
          },
          {
            "node_id": "ftsZ_filament",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "FtsZ filament properties",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Divisome tubulin-homolog FtsZ filament conformation affecting cell-wall insertion geometry."
          },
          {
            "node_id": "pbp2_elongasome",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "PBP2 (elongasome transpeptidase)",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Penicillin-binding protein 2, transpeptidase of the RodA-PBP2 elongasome supporting rod shape."
          }
        ],
        "edges": [
          {
            "subject": "mreB",
            "predicate": "controls",
            "object": "peptidoglycan_synthesis",
            "description": "MreB contributes to control of peptidoglycan synthetic complexes.",
            "evidence": [
              {
                "reference": "DOI:10.1128/JB.187.1.54-64.2005",
                "snippet": "control of the peptidoglycan synthetic complexes",
                "notes": "Supports MreB involvement in shape-related PG synthesis."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "peptidoglycan_synthesis",
            "predicate": "causes",
            "object": "short_rod_geometry",
            "description": "Wall synthesis patterns determine whether cells remain rod-like or become short coccobacilli.",
            "evidence": [
              {
                "reference": "DOI:10.1128/JB.187.1.54-64.2005",
                "snippet": "conditions causing changes in cell shape",
                "notes": "Supports PG-associated shape changes to a coccobacillus state."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "septal_growth",
            "predicate": "contributes to",
            "object": "short_rod_geometry",
            "description": "Division-associated septal growth contributes to the short-rod intermediate geometry.",
            "evidence": [
              {
                "reference": "DOI:10.1128/JB.187.1.54-64.2005",
                "snippet": "role at mid-cell ... in early septation",
                "notes": "Supports a septation-linked role for MreB in representative coccobacillus-forming cells."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "short_rod_geometry",
            "predicate": "confers",
            "object": "coccobacillus_shaped_trait",
            "description": "Short-rod geometry produces the coccobacillus-shaped trait.",
            "evidence": [
              {
                "reference": "DOI:10.1128/JB.187.1.54-64.2005",
                "snippet": "from a rod to coccobacillus",
                "notes": "Supports the trait endpoint as a short-rod morphology."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "rodA_pbp3_elongasome",
            "predicate": "increases",
            "object": "length_to_width_ratio",
            "description": "Elongasome-driven lateral wall synthesis increases the long-to-short axis ratio, opposing a coccoid shape.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mBio.03235-23",
                "notes": "This elongation depends on the SEDS/PBP pair RodA/PBP3 and is seen as an increased ratio of long to short cell axes."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "length_to_width_ratio",
            "predicate": "determines",
            "object": "short_rod_geometry",
            "description": "A reduced but non-coccoid length-to-width ratio defines the short-rod geometry of coccobacilli.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mBio.03235-23",
                "notes": "Long-to-short cell axis ratio quantifies the elongation state intermediate between coccus and rod."
              }
            ]
          },
          {
            "subject": "gpsB",
            "predicate": "regulates",
            "object": "pbp2_localization",
            "description": "GpsB regulates the localization of PBP2 between cell periphery and division septum.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mBio.03235-23",
                "notes": "a gpsB mutant shows the strongest morphological phenotype, driven by partial delocalization of PBP2 and PBP4 away from the division septum."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "pbp2_localization",
            "predicate": "controls",
            "object": "peptidoglycan_synthesis",
            "description": "Spatial localization of PBP2 controls where peptidoglycan insertion and crosslinking occur, biasing cells toward elongation or rounding.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mBio.03235-23",
                "notes": "Increased PBP2/PBP4 at the cell periphery raises peptidoglycan insertion and crosslinking throughout the cell, impairing elongation."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "ftsZ_filament",
            "predicate": "directs",
            "object": "peptidoglycan_synthesis",
            "description": "FtsZ filament geometry directs asymmetric, helical patterns of cell-wall insertion.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mBio.00908-16",
                "notes": "altered FtsZ filaments direct asymmetric, helical cell-wall insertion, generating elongation; this helical pattern of wall insertion leads to elongation."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "pbp2_elongasome",
            "predicate": "required for",
            "object": "short_rod_geometry",
            "description": "PBP2 transpeptidase activity within the RodA-PBP2 elongasome is required to maintain non-spherical rod/short-rod geometry.",
            "evidence": [
              {
                "reference": "DOI:10.1073/pnas.2215237120",
                "notes": "Loss of RodA-PBP2 elongasome activity drives a rod-to-sphere transition; PBP2 transpeptidase activity is required for rod-shape maintenance."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.897227+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-11T20:05:00-07:00",
        "curator": "codex",
        "action": "CURATED_WITH_LITERATURE",
        "changes": "Added DOI-backed definition and causal graph for MreB, peptidoglycan synthesis, septal growth, and short-rod coccobacillus geometry.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002326\u00d71, METPO:2000202\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T21:30:07Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002211\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:19Z",
        "curator": "claude",
        "action": "RENAME_PREDICATE_LABELS",
        "changes": "Renamed 1 causal-edge predicate label(s) to align with existing groundings: shapes \u2192 causes \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:21Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:causes\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:38:00Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0009252\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T05:05:14Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A1B1UYY2\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 6 evidence-backed generic edges (6 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:13Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 4 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002211\u00d73, RO:0002213\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-26T07:15:19Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A060RK42\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:21:12Z",
        "curator": "claude",
        "action": "RETRACT_DEAD_UNIPROT_GROUNDINGS",
        "changes": "Retracted 2 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates (1 to confers), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope coccobacillus_shaped_short_rod_morphogenesis=NONMECHANISTIC with scope_notes; marked 5 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (mreB, rodA_pbp3_elongasome, gpsB, ftsZ_filament, pbp2_elongasome).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000668",
    "label": "coccus shaped",
    "definition": "A cell shape in which an organism has a spherical or nearly spherical morphology, with roughly equal dimensions in all directions.",
    "definition_source": "DOI:10.1038/nrmicro3088",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000666"
    ],
    "synonyms": [
      {
        "synonym_text": "coccus",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "coccus-shaped",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "created_by": "Jed Dongjin Kim-Ozaeta",
    "evidence": [
      {
        "reference": "DOI:10.1038/nrmicro3088",
        "snippet": "spherical cocci synthesize peptidoglycan only at the division septum",
        "notes": "Supports coccus shape as a spherical morphology with septal wall growth rather than lateral elongation."
      },
      {
        "reference": "PMID:19747126",
        "snippet": "Staphylococcus aureus is a facultative, Gram-positive coccus",
        "notes": "Organism example: Staphylococcus aureus is described as coccus-shaped."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1280",
        "taxon_label": "Staphylococcus aureus",
        "note": "Textbook spherical coccus (grape-like clusters); a model Gram-positive, second only to E. coli in study volume.",
        "reference": "https://journals.asm.org/doi/10.1128/jb.00106-25"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "coccus_shaped_septal_growth",
        "title": "Coccus-shape septal growth mechanism",
        "description": "Evidence-backed causal sketch linking spherical coccus morphology to septal peptidoglycan synthesis, FtsZ-directed division, and reduced reliance on lateral elongation systems.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a broad environmental or morphological classification spanning multiple mechanisms, a measurement-like bin, or an absence/arrangement descriptor; contextual protein nodes do not receive token UniProt examples.",
        "nodes": [
          {
            "node_id": "coccus_shaped_trait",
            "label": "coccus shaped",
            "node_type": "TRAIT",
            "grounding": "METPO:1000668",
            "description": "Spherical or nearly spherical bacterial cell morphology."
          },
          {
            "node_id": "septal_peptidoglycan_synthesis",
            "label": "septal peptidoglycan synthesis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Cell-wall synthesis localized to the division septum."
          },
          {
            "node_id": "ftsZ_division_ring",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "FtsZ division ring",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Tubulin-like division scaffold that recruits septal synthesis machinery."
          },
          {
            "node_id": "penicillin_binding_proteins",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "penicillin-binding proteins",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Cell-wall synthesis enzymes recruited to division sites."
          },
          {
            "node_id": "lateral_elongation",
            "label": "lateral cell-wall elongation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Sidewall growth mode common in rod-shaped bacteria."
          },
          {
            "node_id": "peripheral_peptidoglycan_synthesis",
            "label": "peripheral peptidoglycan synthesis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Cell-wall synthesis at the cell periphery/mid-cell that drives longitudinal elongation toward ovoid morphology."
          },
          {
            "node_id": "divisome_complex",
            "label": "divisome complex",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Multiprotein cell-division machinery coordinating septal peptidoglycan synthesis in cocci.",
            "grounding": "GO:1990586"
          },
          {
            "node_id": "orthogonal_division_planes",
            "label": "orthogonal division planes",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Alternating cell division in two or three orthogonal planes characteristic of spherical cocci."
          },
          {
            "node_id": "ovoid_shape",
            "label": "ovococcal/ovoid shape",
            "node_type": "QUALITY",
            "description": "Slightly elongated ovoid cell morphology produced by mid-cell peripheral peptidoglycan synthesis."
          }
        ],
        "edges": [
          {
            "subject": "ftsZ_division_ring",
            "predicate": "recruits",
            "object": "penicillin_binding_proteins",
            "description": "FtsZ-associated division machinery recruits cell-wall enzymes for septal synthesis in cocci.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro3088",
                "snippet": "one type of cell wall synthesis machinery",
                "notes": "Review describes coccal growth as relying on division-septum wall synthesis machinery."
              }
            ]
          },
          {
            "subject": "penicillin_binding_proteins",
            "predicate": "catalyzes",
            "object": "septal_peptidoglycan_synthesis",
            "description": "PBPs catalyze peptidoglycan assembly at the septum.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro3088",
                "snippet": "catalysed by one type of cell wall synthesis machinery",
                "notes": "Supports wall-synthesis enzymes as the proximal machinery for septal peptidoglycan synthesis in spherical cocci."
              }
            ],
            "predicate_id": "biolink:catalyzes"
          },
          {
            "subject": "septal_peptidoglycan_synthesis",
            "predicate": "regulates",
            "object": "coccus_shaped_trait",
            "description": "Septum-centered peptidoglycan synthesis supports spherical coccus morphology.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro3088",
                "snippet": "synthesize peptidoglycan only at the division septum",
                "notes": "Supports septal-only wall synthesis as a mechanism for spherical coccal growth."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "lateral_elongation",
            "predicate": "reduced in",
            "object": "coccus_shaped_trait",
            "description": "Cocci lack the sustained lateral elongation mode that produces rod morphology.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro3088",
                "snippet": "round, rod-shaped, curved and spiral cells",
                "notes": "Review contrasts mechanisms for cocci with rod-shaped lateral growth; edge is retained as a broad mechanistic distinction rather than a universal gene-loss claim."
              }
            ]
          },
          {
            "subject": "peripheral_peptidoglycan_synthesis",
            "predicate": "negatively associated with",
            "object": "coccus_shaped_trait",
            "description": "Peripheral/mid-cell wall synthesis drives elongation away from true spherical coccus morphology.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro3088",
                "notes": "Pinho 2013: ovococci perform both septal and peripheral peptidoglycan synthesis; peripheral synthesis drives slight longitudinal elongation and the ovoid shape, distinguishing it from true cocci."
              }
            ]
          },
          {
            "subject": "divisome_complex",
            "predicate": "mediates",
            "object": "septal_peptidoglycan_synthesis",
            "description": "Divisome-centered machinery mediates peptidoglycan synthesis at the septum in cocci.",
            "evidence": [
              {
                "reference": "DOI:10.1042/BSR20221664",
                "notes": "Battaje 2023: in cocci, peptidoglycan synthesis takes place mostly at the site of division, i.e. the septum coordinated by FtsZ via the divisome complex."
              }
            ]
          },
          {
            "subject": "ftsZ_division_ring",
            "predicate": "coordinates",
            "object": "septal_peptidoglycan_synthesis",
            "description": "FtsZ coordinates septal peptidoglycan synthesis, linking the cytoskeletal ring to coccal septal growth.",
            "evidence": [
              {
                "reference": "DOI:10.1042/BSR20221664",
                "notes": "Battaje 2023: peptidoglycan synthesis takes place mostly at the septum coordinated by FtsZ; broad across bacteria, especially cocci."
              }
            ]
          },
          {
            "subject": "coccus_shaped_trait",
            "predicate": "associated with",
            "object": "orthogonal_division_planes",
            "description": "Spherical cocci alternate division in two or three orthogonal planes.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro3088",
                "notes": "Pinho 2013: spherical cocci can alternate division in two or three orthogonal planes; a morphology-associated arrangement behavior."
              }
            ],
            "predicate_id": "biolink:associated_with"
          },
          {
            "subject": "peripheral_peptidoglycan_synthesis",
            "predicate": "has output",
            "object": "ovoid_shape",
            "description": "Peripheral synthesis between equatorial rings produces ovococcal/ovoid shape, a boundary contrast to true cocci.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro3088",
                "notes": "Pinho 2013: peripheral synthesis occurring at mid-cell, between the equatorial rings, drives slight longitudinal elongation and the ovoid shape."
              }
            ],
            "predicate_id": "RO:0002234"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.886046+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-06T14:40:41-07:00",
        "curator": "codex",
        "action": "CURATED_WITH_ORGANISM_EXAMPLE",
        "changes": "Added Staphylococcus aureus organism example with PMID-backed evidence.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-11T18:00:00-07:00",
        "curator": "codex",
        "action": "CURATED_WITH_LITERATURE",
        "changes": "Replaced PMID definition source with DOI-backed coccoid growth review and added causal graph for FtsZ-associated septal peptidoglycan synthesis and spherical morphology.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T05:49:24Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:catalyzes\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:19Z",
        "curator": "claude",
        "action": "RENAME_PREDICATE_LABELS",
        "changes": "Renamed 1 causal-edge predicate label(s) to align with existing groundings: maintains \u2192 regulates \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:21Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002211\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 5 evidence-backed generic edges (4 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:13Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:associated_with\u00d71, METPO:2000202\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:23:54Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:1990586\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates (1 to has output), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope coccus_shaped_septal_growth=NONMECHANISTIC with scope_notes; marked 2 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (ftsZ_division_ring, penicillin_binding_proteins).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000655",
    "label": "coenobium formation",
    "definition": "A morphological phenotype in which an alga forms clonal multicellular colonies whose cell complement is established during colony formation, with subsequent colony growth by cell enlargement rather than addition of cells.",
    "definition_source": "DOI:10.1098/rspb.2023.1882",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1098/rspb.2023.1882",
        "snippet": "characteristically form clonal colonies of fixed cell number known as coenobia.",
        "notes": "Harvey (2023), PMID:37876191, PMC10598416, Comparisons with extant taxa. Direct full-text terminology passage covers Volvocales, Scenedesmaceae and Hydrodictyaceae. Growth after colony formation is by cell expansion; a later reproductive cycle makes daughter colonies. This comparison supports terminology, not a new experiment on living algae; the paper's fossil developmental reconstruction remains an inference."
      },
      {
        "reference": "DOI:10.1242/jcs.212233",
        "snippet": "progeny were unicellular in three species and multicellular (joined in a sheet-like coenobium) in two.",
        "notes": "Cardon et al. (2018), PMID:29487180, scientific abstract. Primary Results, Methods and actual Figure 1 were inspected. The coenobial species are Enallax costatus and Tetradesmus obliquus; multiple fission occurs in all five tested species and alone does not establish coenobial progeny. Figure 1 supports joined-cell morphology. Release is author-reported in the Results, not visible in Figure 3; supplementary Figure S1 and movies were not directly inspected."
      },
      {
        "reference": "DOI:10.1038/s41598-018-28627-z",
        "snippet": "monocultures of D. opoliensis in the control groups (without IAA treatment) were dominated by two-celled and four-celled coenobia",
        "notes": "Chung et al. (2018), PMID:29980731, PMC6035231, Results. Direct full text reports this morphology after one week; Methods describes native isolates cultured in CA medium. Higher indole-3-acetic acid concentrations favor unicells in the tested monocultures, so IAA is not a universal coenobium inducer. No percentage, causal protein claim or direct figure inspection is asserted here."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:113528",
        "taxon_label": "Enallax costatus",
        "reference": "DOI:10.1242/jcs.212233",
        "note": "CCAP 276/31 (paper: CCAP 276-31), grown at 25 C on a 12:12 light/dark cycle in a 1:1 mixture of Bold's basal medium with micronutrients and Woods Hole medium. Figure 1 and Results document coenobial morphology, not an invariant state for every life stage. Collection provenance at https://www.ccap.ac.uk/catalogue/strain-276-31 identifies Hegewald's 1980 Finnish lake isolate and lists GMO: No. The paper describes unialgal cultures, not axenic cultures."
      }
    ],
    "discussions": [
      {
        "discussion_id": "coenobium-formation-scope-and-hierarchy",
        "prompt": "Review a multicellular morphology parent and exact mappings.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Retain phenotype METPO:1000059. Cell shape METPO:1000666 is individual-cell morphology; colony morphology METPO:1007062 concerns macroscopic colony characteristics. Obsolete cell arrangement METPO:1000046 and aggregate METPO:1000011 are not active parents. Palmelloid formation traitmech:000654 covers mother-wall retention or extracellular adhesion, not this developmental cell-complement criterion. Rosette cell arrangement traitmech:000652 requires inward cell poles, and biofilm formation traitmech:000053 requires surface attachment; neither is required here. A coenocyte is a multinucleate cell, not a multicellular coenobium. No exact synonym, xref or organism-level disjointness is asserted.",
        "posed_by": "codex",
        "posed_date": "2026-10-07"
      },
      {
        "discussion_id": "coenobium-formation-development-and-mechanism",
        "prompt": "Resolve organism-specific colony development before graphing.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Fixed cell complement describes an individual colony, not one invariant count across taxa or conditions. Reproduction can form new daughter colonies. Harvey's extant comparisons include motile forms and Volvox germ-soma differentiation; Chung's introductory little-or-no-specialization formulation is not imposed universally. Neither a sheet shape, common wall, power-of-two count, lack of flagella nor grazer induction defines the class. Defer a causal graph pending perturbation and accession-level evidence: Cardon's observed Golgi localization and cell rotation do not demonstrate causal necessity for coenobium formation. Gene possession alone does not establish this phenotype.",
        "posed_by": "codex",
        "posed_date": "2026-10-07"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-07T01:56:55Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added coenobium formation with three DOI-backed snippets, a qualified Enallax costatus example and developmental scope boundaries. Ignored-and-hidden searches and structured METPO review found no exact record. Reserved METPO:1060800 in v531; existing records unchanged.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1003024",
    "label": "cream pigmented",
    "definition": "A pigmentation phenotype in which colony or cell coloration is a pale, off-white or cream hue, typically reflecting low-density carotenoid or other light-absorbing pigments.",
    "definition_source": "DOI:10.1146/annurev.micro.62.081307.162844",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1003021"
    ],
    "synonyms": [
      {
        "synonym_text": "Pigment_cream",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev.micro.62.081307.162844",
        "snippet": "bacterial carotenoid pigments",
        "notes": "Bacterial-carotenoid review supports low-abundance carotenoids as the basis for cream/pale coloration in many bacterial taxa."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:2547392",
        "taxon_label": "Seongchinamella unica",
        "reference": "DOI:10.1099/ijsem.0.003914",
        "note": "Seongchinamella unica GH4-78T produced cream-coloured colonies in its primary species description, a direct unperturbed colony-pigmentation observation."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "cream_pigmented_low_carotenoid_density",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "Cream pigmentation is a visual color classification that can arise from multiple low-chromophore states. The graph is illustrative context rather than a source-backed, universally inherited protein mechanism.",
        "title": "Cream-pigmentation low carotenoid density",
        "description": "DOI-backed graph linking low-level carotenoid (or analogous light-absorbing pigment) biosynthesis and limited pigment accumulation to a cream/pale-colored colony phenotype.",
        "nodes": [
          {
            "node_id": "cream_pigmented_trait",
            "label": "cream pigmented",
            "node_type": "TRAIT",
            "grounding": "METPO:1003024",
            "description": "Cream/pale colony or cell coloration."
          },
          {
            "node_id": "low_carotenoid_biosynthesis",
            "label": "low-level carotenoid biosynthesis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced flux through the bacterial isoprenoid pigment biosynthesis pathway compared to brightly pigmented lineages.",
            "grounding": "GO:0016117"
          },
          {
            "node_id": "low_pigment_accumulation",
            "label": "low pigment accumulation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced steady-state pigment levels relative to brightly pigmented lineages."
          },
          {
            "node_id": "pale_coloration",
            "label": "pale cream coloration",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Optical phenotype of off-white pigmented colonies."
          },
          {
            "node_id": "carotenoid_enzyme_module",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "This umbrella combines multiple carotenoid-enzyme families and cannot be represented by one exact protein-family grounding.",
            "label": "carotenoid biosynthesis enzyme module",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Core carotenoid-pathway enzymes (e.g. crtE/crtB/crtI-type) required for synthesis of colored carotenoids.",
            "gene_symbols": [
              "crtE",
              "crtB",
              "crtI"
            ],
            "operon": "crt locus"
          },
          {
            "node_id": "carotenoid_gene_disruption",
            "label": "carotenoid biosynthesis gene disruption",
            "node_type": "EXPERIMENTAL_FACTOR",
            "description": "Loss-of-function or repression of core carotenoid-pathway genes."
          },
          {
            "node_id": "isoprenoid_precursor_supply",
            "label": "isoprenoid (MEP-pathway) precursor supply",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Supply of isoprenoid precursors (IPP/DMAPP/GGPP) via the MEP pathway feeding carotenoid biosynthesis."
          }
        ],
        "edges": [
          {
            "subject": "low_carotenoid_biosynthesis",
            "predicate": "has output",
            "object": "low_pigment_accumulation",
            "description": "Limited carotenoid (or analogous) pigment biosynthesis produces low pigment accumulation.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev.micro.62.081307.162844",
                "snippet": "bacterial carotenoid pigments",
                "notes": "Supports carotenoid biosynthesis as the source of bacterial pigmentation."
              }
            ],
            "predicate_id": "RO:0002234"
          },
          {
            "subject": "low_pigment_accumulation",
            "predicate": "yields",
            "object": "pale_coloration",
            "description": "Low pigment density yields a pale, cream-colored optical phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev.micro.62.081307.162844",
                "snippet": "bacterial carotenoid pigments",
                "notes": "Supports pigment density as the determinant of colony color intensity."
              }
            ],
            "predicate_id": "biolink:produces"
          },
          {
            "subject": "pale_coloration",
            "predicate": "manifests as",
            "object": "cream_pigmented_trait",
            "description": "Pale coloration manifests the cream-pigmented trait.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev.micro.62.081307.162844",
                "snippet": "bacterial carotenoid pigments",
                "notes": "Supports the trait endpoint."
              }
            ],
            "predicate_id": "METPO:2007400"
          },
          {
            "subject": "carotenoid_enzyme_module",
            "predicate": "enables",
            "object": "low_carotenoid_biosynthesis",
            "description": "The core Crt enzyme module is required for carotenoid biosynthesis; its activity sets pathway flux.",
            "evidence": [
              {
                "reference": "DOI:10.3390/pathogens12010086",
                "notes": "Insertions mapped to crtE, crtI, crtB, crtYc, crtYd involved in synthesis of beta-carotene; disrupted mutants retained an off-white appearance."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "carotenoid_gene_disruption",
            "predicate": "decreases",
            "object": "low_carotenoid_biosynthesis",
            "description": "Disruption or repression of core carotenoid-biosynthesis genes lowers carotenoid synthesis, leaving colonies pale/off-white.",
            "evidence": [
              {
                "reference": "DOI:10.3390/pathogens12010086",
                "notes": "\"Most of these mutants failed to develop pigmentation upon light treatment and retained an off-white appearance\" with insertions in crt-pathway genes (broad but not universal across taxa)."
              }
            ],
            "predicate_id": "RO:0002212"
          },
          {
            "subject": "isoprenoid_precursor_supply",
            "predicate": "enables",
            "object": "low_carotenoid_biosynthesis",
            "description": "MEP-pathway isoprenoid precursor supply feeds carotenoid biosynthesis; reduced precursor supply lowers downstream carotenoid output.",
            "evidence": [
              {
                "reference": "DOI:10.3390/microorganisms9040670",
                "notes": "Repression of the MEP-pathway gene ispG significantly lowered cellular carotenoid content; repression of MEP/carotenogenesis genes was expected to reduce pigmentation."
              }
            ],
            "predicate_id": "RO:0002327"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.944295+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-11T23:00:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed definition and causal graph linking low-density carotenoid biosynthesis to cream/pale colony pigmentation.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T21:30:07Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007400\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-13T21:03:26Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:produces\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 3 evidence-backed generic edges (3 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:13Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d72, RO:0002212\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates (1 to has output), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope cream_pigmented_low_carotenoid_density=NONMECHANISTIC with scope_notes; marked 1 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (carotenoid_enzyme_module); added 1 node(s) and 1 edge(s) (carotenoid_enzyme_module); removed 1 node(s) and 1 edge(s) together with their evidence (carotenoid_biosynthesis_genes).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T04:43:24Z",
        "curator": "codex",
        "action": "ADD_CANONICAL_EXAMPLES",
        "changes": "Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Seongchinamella unica (NCBITaxon:2547392; DOI:10.1099/ijsem.0.003914). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000669",
    "label": "crescent shaped",
    "definition": "A cell shape in which an organism has a curved crescent-like morphology with a concave inner side and a convex outer side.",
    "definition_source": "DOI:10.1016/S0092-8674(03)00935-8",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000666"
    ],
    "synonyms": [
      {
        "synonym_text": "crescent-shaped",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "created_by": "Luke Wang",
    "evidence": [
      {
        "reference": "DOI:10.1016/S0092-8674(03)00935-8",
        "snippet": "required for the vibrioid and helical shapes of Caulobacter",
        "notes": "Supports crescentin as a bacterial cytoskeletal determinant of curved Caulobacter cell shape."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:155892",
        "taxon_label": "Caulobacter vibrioides",
        "note": "Curved/crescent (vibrioid) cell; classic strain CB15, long called Caulobacter crescentus.",
        "reference": "PMID:19383443"
      },
      {
        "taxon_id": "NCBITaxon:565050",
        "taxon_label": "Caulobacter vibrioides NA1000",
        "note": "Strain-level crescentin exemplar.",
        "reference": "DOI:10.1038/emboj.2009.61"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "crescent_shaped_crescentin_curvature",
        "title": "Crescent-shape crescentin curvature mechanism",
        "description": "Evidence-backed causal sketch linking crescent morphology to crescentin localization, inner-curvature mechanical constraint, peptidoglycan growth bias, and curved cell-body geometry.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "The taxon-matched protein example anchors one experimentally supported causal branch; it is not presented as a universal mechanism for every taxon or every contextual branch in this graph.",
        "nodes": [
          {
            "node_id": "crescent_shaped_trait",
            "label": "crescent shaped",
            "node_type": "TRAIT",
            "grounding": "METPO:1000669",
            "description": "Curved crescent-like bacterial cell morphology."
          },
          {
            "node_id": "crescentin",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:A0A0H3CD98",
                "protein_label": "Crescentin",
                "gene_symbol": "creS",
                "taxon_id": "NCBITaxon:565050",
                "taxon_label": "Caulobacter vibrioides NA1000",
                "entry_status": "UNREVIEWED",
                "proteome_id": "UP000001364",
                "retrieved_on": "2026-08-25",
                "entry_version": 36,
                "sequence_version": 1,
                "role": "NA1000 crescentin localizes at the inner curvature and mechanically biases wall growth to generate cell curvature.",
                "evidence": [
                  {
                    "reference": "DOI:10.1038/emboj.2009.61",
                    "snippet": "crescentin localizes to the inner cell curvature",
                    "notes": "The cited source supports the represented protein-to-trait branch; UniProt verifies this current strain-matched protein entry."
                  }
                ]
              }
            ],
            "label": "crescentin",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Intermediate-filament-like cytoskeletal protein encoded by creS."
          },
          {
            "node_id": "inner_cell_curvature",
            "label": "inner cell curvature",
            "node_type": "CELLULAR_LOCALIZATION",
            "description": "Concave side of a crescent-shaped cell."
          },
          {
            "node_id": "peptidoglycan_growth_bias",
            "label": "peptidoglycan growth bias",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Differential wall growth or strain that bends the cell body."
          },
          {
            "node_id": "crescent_cell_curvature",
            "label": "crescent cell curvature",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Maintenance of a curved crescent cell body."
          },
          {
            "node_id": "pg_insertion_inner_curvature",
            "label": "peptidoglycan insertion at inner curvature",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Rate of new peptidoglycan insertion on the concave (inner) side of the cell."
          },
          {
            "node_id": "differential_pg_insertion",
            "label": "differential peptidoglycan insertion rates",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Gradient of peptidoglycan insertion rates around the cell circumference."
          },
          {
            "node_id": "crescentin_envelope_association",
            "label": "crescentin envelope association",
            "node_type": "STATE",
            "description": "Attachment of crescentin to the cell envelope, required for its curvature function."
          }
        ],
        "edges": [
          {
            "subject": "crescentin",
            "predicate": "localizes to",
            "object": "inner_cell_curvature",
            "description": "Crescentin localizes along the inner curvature of the cell.",
            "evidence": [
              {
                "reference": "DOI:10.1038/emboj.2009.61",
                "snippet": "localizes to the inner cell curvature",
                "notes": "Supports crescentin as an inner-curvature-localized shape protein."
              }
            ],
            "predicate_id": "biolink:located_in"
          },
          {
            "subject": "crescentin",
            "predicate": "regulates",
            "object": "peptidoglycan_growth_bias",
            "description": "Crescentin mechanically constrains cell-wall growth to create differential curvature.",
            "evidence": [
              {
                "reference": "DOI:10.1038/emboj.2009.61",
                "snippet": "mechanical control of cell growth",
                "notes": "Supports a mechanical growth-control role for crescentin."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "peptidoglycan_growth_bias",
            "predicate": "generates",
            "object": "crescent_cell_curvature",
            "description": "Biased peptidoglycan growth or strain generates curved geometry.",
            "evidence": [
              {
                "reference": "DOI:10.1038/emboj.2009.61",
                "snippet": "bacterial cell curvature through mechanical control",
                "notes": "Supports differential growth mechanics as a curvature mechanism."
              }
            ],
            "predicate_id": "biolink:produces"
          },
          {
            "subject": "crescent_cell_curvature",
            "predicate": "confers",
            "object": "crescent_shaped_trait",
            "description": "Curved cell-body geometry produces the crescent-shaped trait.",
            "evidence": [
              {
                "reference": "DOI:10.1016/S0092-8674(03)00935-8",
                "snippet": "required for the ... shapes of Caulobacter",
                "notes": "Supports crescentin-dependent curved morphology as the trait endpoint."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "crescentin",
            "predicate": "decreases rate of",
            "object": "pg_insertion_inner_curvature",
            "description": "Crescentin reduces peptidoglycan insertion on the side where it is located, setting up a growth-rate gradient.",
            "evidence": [
              {
                "reference": "DOI:10.1038/emboj.2009.61",
                "notes": "the crescentin structure would not only reduce peptidoglycan insertion at the side where crescentin is located but would also generate a gradient of increasing peptidoglycan growth rates"
              }
            ]
          },
          {
            "subject": "pg_insertion_inner_curvature",
            "predicate": "contributes to",
            "object": "differential_pg_insertion",
            "description": "Reduced inner-side insertion creates a gradient of differential peptidoglycan insertion rates around the circumference.",
            "evidence": [
              {
                "reference": "DOI:10.1038/emboj.2009.61",
                "notes": "would also generate a gradient of increasing peptidoglycan growth rates"
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "differential_pg_insertion",
            "predicate": "confers",
            "object": "crescent_shaped_trait",
            "description": "Differential peptidoglycan insertion rates around the cell circumference produce cell curvature.",
            "evidence": [
              {
                "reference": "DOI:10.1038/emboj.2009.61",
                "notes": "the crescentin structure caused differential peptidoglycan insertion rates around the cell circumference to produce cell curvature"
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "crescentin_envelope_association",
            "predicate": "required for",
            "object": "crescent_shaped_trait",
            "description": "Association of crescentin with the cell envelope is required to produce curvature; attachment-defective mutants fail to curve.",
            "evidence": [
              {
                "reference": "DOI:10.1128/jb.01371-09",
                "notes": "Envelope association is required for crescentin function (attachment-defective mutants fail to produce curvature)"
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.886631+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-11T20:05:00-07:00",
        "curator": "codex",
        "action": "CURATED_WITH_LITERATURE",
        "changes": "Added DOI-backed definition and causal graph for crescentin, inner cell curvature, peptidoglycan growth bias, and crescent morphology.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T08:21:50Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:located_in\u00d71, biolink:produces\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T05:05:14Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A2N9AY16\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-26T05:00:48Z",
        "curator": "claude",
        "action": "RENAME_PREDICATE_LABELS",
        "changes": "Renamed 1 causal-edge predicate label(s) to align with existing groundings: constrains \u2192 regulates \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-26T05:00:50Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002211\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 4 evidence-backed generic edges (3 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:13Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002326\u00d71, METPO:2000202\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:21:12Z",
        "curator": "claude",
        "action": "RETRACT_DEAD_UNIPROT_GROUNDINGS",
        "changes": "Retracted 1 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 2 causal edge(s) off microbe-domain METPO predicates (2 to confers), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "CURATE_PROTEIN_TAXON_EXAMPLE",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope crescent_shaped_crescentin_curvature=MECHANISTIC with scope_notes; marked 1 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (crescentin); added taxon-paired protein example(s) UniProtKB:A0A0H3CD98 on crescentin (NCBITaxon:565050); added canonical example(s) NCBITaxon:565050.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000670",
    "label": "curved shaped",
    "definition": "A cell shape in which an organism has a bent or curved cell body rather than a straight rod or sphere.",
    "definition_source": "DOI:10.1371/journal.pbio.1002565",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000666"
    ],
    "synonyms": [
      {
        "synonym_text": "S_curved_spiral",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "curved-shaped",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "created_by": "Anthea Guo",
    "evidence": [
      {
        "reference": "DOI:10.1371/journal.pbio.1002565",
        "snippet": "curved cells appear to be optimized for motility",
        "notes": "Supports curved cells as a recognized bacterial morphology with possible functional associations."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:666",
        "taxon_label": "Vibrio cholerae",
        "note": "comma/curved rod",
        "reference": "DOI:10.1111/j.1574-6968.2001.tb10629.x"
      },
      {
        "taxon_id": "NCBITaxon:155892",
        "taxon_label": "Caulobacter vibrioides",
        "note": "curved (vibrioid) cell",
        "reference": "PMID:19383443"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "curved_shaped_scaffolded_curvature",
        "title": "Curved-shape scaffolded morphogenesis mechanism",
        "description": "Evidence-backed causal sketch linking curved bacterial morphology to scaffold-mediated inner curvature and spatially biased peptidoglycan growth.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a broad environmental or morphological classification spanning multiple mechanisms, a measurement-like bin, or an absence/arrangement descriptor; contextual protein nodes do not receive token UniProt examples.",
        "nodes": [
          {
            "node_id": "curved_shaped_trait",
            "label": "curved shaped",
            "node_type": "TRAIT",
            "grounding": "METPO:1000670",
            "description": "Bent or curved bacterial cell-body morphology."
          },
          {
            "node_id": "curvature_scaffold",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "curvature scaffold",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Shape-determining scaffold such as crescentin or CrvA that marks the inner curve."
          },
          {
            "node_id": "inner_cell_curvature",
            "label": "inner cell curvature",
            "node_type": "CELLULAR_LOCALIZATION",
            "description": "Concave region of a curved bacterial cell body."
          },
          {
            "node_id": "peptidoglycan_growth_pattern",
            "label": "peptidoglycan growth pattern",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Spatial pattern of wall synthesis and remodeling that shapes the cell body."
          },
          {
            "node_id": "cell_body_curvature",
            "label": "cell-body curvature",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Curving of the bacterial cell body."
          },
          {
            "node_id": "mreb_cytoskeletal_guidance",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "MreB cytoskeletal guidance",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Actin-like protein MreB that localizes to curvature regions and directs localized cell-wall synthesis."
          },
          {
            "node_id": "zonal_peptidoglycan_remodeling",
            "label": "spatially constrained (zonal) peptidoglycan remodeling",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Spatially constrained (\"zonal\") cell-wall growth and remodeling through which shape determinants act."
          },
          {
            "node_id": "motility_in_viscous_environments",
            "label": "motility in viscous environments",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Cell motility, especially efficient swimming through viscous solutions."
          },
          {
            "node_id": "surface_colonization_motility_virulence",
            "label": "surface colonization, motility and virulence",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Fitness-relevant processes (surface colonization, motility in viscous environments, virulence) promoted by curved/helical shape."
          }
        ],
        "edges": [
          {
            "subject": "curvature_scaffold",
            "predicate": "localizes to",
            "object": "inner_cell_curvature",
            "description": "Curvature scaffolds mark or constrain the inner curve of the cell.",
            "evidence": [
              {
                "reference": "DOI:10.1371/journal.pbio.1002565",
                "snippet": "scaffold-mediated delineation of an inner curvature",
                "notes": "Supports a common structural theme for curved and helical cells."
              }
            ],
            "predicate_id": "biolink:located_in"
          },
          {
            "subject": "curvature_scaffold",
            "predicate": "guides",
            "object": "peptidoglycan_growth_pattern",
            "description": "Curvature scaffolds bias wall growth or structural constraints along the inner curve.",
            "evidence": [
              {
                "reference": "DOI:10.1371/journal.pbio.1002565",
                "snippet": "guide PG synthesis",
                "notes": "Supports scaffold-guided peptidoglycan synthesis as a curvature mechanism in representative bacteria."
              }
            ]
          },
          {
            "subject": "peptidoglycan_growth_pattern",
            "predicate": "generates",
            "object": "cell_body_curvature",
            "description": "Spatially patterned wall growth or constraint generates cell-body curvature.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.cell.2016.12.019",
                "snippet": "asymmetrically patterns peptidoglycan insertion",
                "notes": "Vibrio evidence supports asymmetric PG insertion as one concrete route to curved rods."
              }
            ],
            "predicate_id": "biolink:produces"
          },
          {
            "subject": "cell_body_curvature",
            "predicate": "confers",
            "object": "curved_shaped_trait",
            "description": "Cell-body curvature produces the curved-shape trait.",
            "evidence": [
              {
                "reference": "DOI:10.1371/journal.pbio.1002565",
                "snippet": "vibrioid (curved) morphology",
                "notes": "Supports curved morphology as a recognized bacterial cell-shape class."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "mreb_cytoskeletal_guidance",
            "predicate": "directs",
            "object": "peptidoglycan_growth_pattern",
            "description": "MreB localizes to specific curvature regions and directs localized cell-wall synthesis, supporting scaffold-guided PG remodeling.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2017.01264",
                "notes": "the actin-like protein MreB localizes to specific curvature regions and directs localized cell-wall synthesis (broad mechanistic class)."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "peptidoglycan_growth_pattern",
            "predicate": "occurs via",
            "object": "zonal_peptidoglycan_remodeling",
            "description": "Because PG synthesis is constrained in space, all cell-wall growth and remodeling is \"zonal\", the route through which shape determinants act.",
            "evidence": [
              {
                "reference": "DOI:10.1371/journal.pbio.1002565",
                "notes": "Because PG synthesis is constrained in space, all cell wall growth and remodeling can be described as \"zonal\" growth."
              }
            ]
          },
          {
            "subject": "curved_shaped_trait",
            "predicate": "optimized for",
            "object": "motility_in_viscous_environments",
            "description": "Curved/helical morphology appears optimized for motility, especially in viscous solutions (broad expert synthesis).",
            "evidence": [
              {
                "reference": "DOI:10.1371/journal.pbio.1002565",
                "notes": "helical and curved cells appear to be optimized for motility, especially in viscous solutions."
              }
            ]
          },
          {
            "subject": "curved_shaped_trait",
            "predicate": "promotes",
            "object": "surface_colonization_motility_virulence",
            "description": "Curved and helical shapes are widespread among bacteria, promoting surface colonization, motility in viscous environments and virulence.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-024-51790-z",
                "notes": "curved and helical cell shapes ... are widespread among bacteria, promoting surface colonization, motility in viscous environments, and virulence."
              }
            ],
            "predicate_id": "RO:0002213"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.887107+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-11T18:00:00-07:00",
        "curator": "codex",
        "action": "CURATED_WITH_LITERATURE",
        "changes": "Reviewed curved shape and added DOI-backed causal graph for curvature scaffolds, inner curvature, and spatial peptidoglycan growth.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T08:21:50Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:located_in\u00d71, biolink:produces\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 4 evidence-backed generic edges (4 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:13Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002211\u00d71, RO:0002213\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates (1 to confers), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope curved_shaped_scaffolded_curvature=NONMECHANISTIC with scope_notes; marked 2 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (curvature_scaffold, mreb_cytoskeletal_guidance).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000676",
    "label": "cyanobacterial multiseriate trichome formation",
    "definition": "A morphological phenotype in which a cyanobacterium develops a trichome containing more than one adjacent row of cells through cell division in multiple planes.",
    "definition_source": "DOI:10.1002/2211-5463.13016",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1002/2211-5463.13016",
        "snippet": "cells divide at a right angle to the longitudinal filament axis and in planes parallel or oblique to the primary trichomes.",
        "notes": "Springstein et al. (2020), Introduction; primary full-text XML https://www.ebi.ac.uk/europepmc/webservices/rest/PMC7714070/fullTextXML and actual Figure 2E inspected. The text links multiplanar division to multiseriate Chlorogloeopsis fritschii PCC 6912 trichomes, contrasting them with lateral Fischerella branches. Figure 2E shows a mature multiseriate stage, distinct from the linear hormogonium in 2D. Methods describe stock cultures at 37 degrees C in BG11 or BG11(0), with an 18:6 light-dark cycle; Van-FL microscopy follows a one-hour stain. This morphology evidence is not the separate FtsZ-overexpression phenotype."
      },
      {
        "reference": "DOI:10.1186/s12862-017-1053-5",
        "snippet": "When grown in BG11, C. fritschii developed multi-seriate filaments.",
        "notes": "Koch et al. (2017), Additional file 1, Figure S6A caption, PDF page 8; actual S6 and S1 images and supplementary text pages 1-2 inspected at https://media.springernature.com/original/springer-static/esm/art%3A10.1186%2Fs12862-017-1053-5/MediaObjects/12862_2017_1053_MOESM1_ESM.pdf. S6B instead shows aseriate clusters with 100 mM NaCl; loose clusters are not automatically multiseriate trichomes. Main Results and S1 report salt-associated multiseriate main filaments in Fischerella, showing that branching and multiseriality can coexist and that salt responses are taxon-specific. Transcript correlations do not establish a universal mechanism."
      },
      {
        "reference": "DOI:10.3126/on.v14i1.16445",
        "snippet": "The present algal taxon exhibited vertical and horizontal divisions of cells and has a tendency to form filamentous structure.",
        "notes": "Halder (2016), Results and discussion, article page 95, https://www.nepjol.info/index.php/ON/article/view/16445/13360. Methods, description and actual Figure 1A-D on page 96 inspected. The description records cell rows and Conclusions describe progression from uniseriate to multiseriate filaments. This is light-microscopy-based identification of field material, not sequence-confirmed identity, a controlled time-lapse lineage experiment, or proof of the paper's suggested fertilizer benefit."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1124",
        "taxon_label": "Chlorogloeopsis fritschii",
        "reference": "DOI:10.3126/on.v14i1.16445",
        "note": "Restricted to the multiseriate stage described for field collection NH-1260, sampled on 18 March 2013 in a rice field at Balagarh, Hooghly, West Bengal, India. Provenance and herbarium deposition are reported in Methods/Results at https://www.nepjol.info/index.php/ON/article/view/16445/13360. The source identifies the material morphologically; it is not assigned a PCC strain identity. Live NCBI efetch https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=taxonomy&id=1124 confirms the current species name and rank species, not an NH-1260 accession or independent phenotype evidence. Not every cell, stage or condition is multiseriate."
      }
    ],
    "discussions": [
      {
        "discussion_id": "multiseriate-trichome-scope",
        "prompt": "Review the closer multicellular morphology parent and terminology.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Use phenotype METPO:1000059 below quality METPO:1000188. The definition concerns adjacent cell rows in a trichome, including two rows, not multiple independent uniseriate trichomes merely bundled in a common sheath. It is not a synonym of branched shaped METPO:1000687, generic filament shaped morphology, hormogonium formation traitmech:000651, or cyanobacterial false branching traitmech:000675. Cell-shape parents do not unambiguously capture this multicellular organization; obsolete cell-arrangement terms redirect to flagellar arrangement and are unsuitable. Springstein's parenthetical description speaks of multiple trichomes in a row, whereas its division context and the other inspected sources support adjacent cell rows. Keep that wording distinction explicit. The qualified label does not cover every multiseriate algal or plant structure. No exact synonyms, xrefs, SSSOM mappings, mandatory branching or organism-level disjointness are asserted.",
        "posed_by": "codex",
        "posed_date": "2026-10-08"
      },
      {
        "discussion_id": "multiseriate-trichome-mechanism",
        "prompt": "Resolve native division-plane control without conflating experimental states.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "The cited studies distinguish natural developmental states, environment-associated changes and engineered protein overexpression. Do not transfer an engineered phenotype to a natural canonical example or infer a gene mechanism from transcript correlations. Neither salt exposure, a fixed row number, a persistent filament length nor a fitness benefit defines the whole class. No causal graph is proposed pending a protein-resolved native mechanism with verified accessions; mechanism is deferred, not claimed absent.",
        "posed_by": "codex",
        "posed_date": "2026-10-08"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-08T07:45:42Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added cyanobacterial multiseriate trichome formation with three DOI sources, source-checked snippets and a qualified field example. Ignored-and-hidden main/worktree/open-PR checks support 000676 and v552 block 1062900-1062999. Kept branching, loose clusters, bundled trichomes and engineered morphotypes distinct. Existing records unchanged; timestamp is observed UTC.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000673",
    "label": "cyanophycin granule",
    "definition": "An intracellular storage inclusion composed of cyanophycin, a nonribosomal arginine- and aspartate-rich polymer serving as a nitrogen reserve.",
    "definition_source": "DOI:10.1128/AEM.01298-18",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000066"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1007/s002030100281",
        "snippet": "Cyanophycin granules reached a maximum after the peak of nitrogenase activity and eventually were utilized completely.",
        "notes": "Li et al. (2001), publisher scientific abstract directly read at https://link.springer.com/article/10.1007/s002030100281. Electron microscopy and biochemistry identified granules in Cyanothece ATCC 51142 during nitrogen-fixing growth on a 12-hour light/12-hour dark cycle. Full text and figures were not accessible; timing is condition-specific, not a universal granule property. The separate PCC 6803 mutant observations do not establish a universal cyanophycinase requirement."
      },
      {
        "reference": "DOI:10.1128/AEM.01298-18",
        "snippet": "Cyanophycin accumulates in the form of opaque and light-scattering granules in the cell",
        "notes": "Watzer and Forchhammer (2018), Introduction and Abstract, directly read in publisher HTML: cyanophycin accumulates as opaque, light-scattering intracellular storage granules serving as a temporary nitrogen reserve (abstract: \"cyanophycin can be used as a temporary nitrogen storage\"). Supports the record definition and definition_source."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:43989",
        "taxon_label": "Crocosphaera subtropica ATCC 51142",
        "reference": "DOI:10.1007/s002030100281",
        "note": "Historical Cyanothece ATCC 51142: granules observed during nitrogen-fixing light/dark culture, not constitutively in every cell. NCBI directly confirms the current strain name, rank no rank, and BH68/BH68K synonym: https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=43989. The directly read scientific abstract of the original isolation paper, https://doi.org/10.1128/jb.175.5.1284-1292.1993, places BH68 in intertidal sands of the Texas Gulf coast. This is provenance support, not an independent cyanophycin assay."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "cyanophycin_synthesis_and_storage",
        "title": "CphA supplies polymer for cyanophycin storage granules",
        "scope_status": "MECHANISTIC",
        "description": "A source-bounded synthesis, material-localization and nitrogen-storage sketch, not a claim that every inclusion shares one regulation.",
        "scope_notes": "Integrates PCC 6308 enzyme expression/purification with PCC 6803 cell biology. It is not one experiment or a strain-specific mechanism demonstrated in the ATCC 51142 canonical example. The sequence-family match establishes identity, not granule formation. No universal growth benefit, magnesium dependence in vivo, degradation enzyme, or granule-surface organizer is inferred.",
        "nodes": [
          {
            "node_id": "cyanophycin_synthetase_cpha",
            "label": "cyanophycin synthetase CphA",
            "node_type": "GENE_OR_PROTEIN",
            "grounding": "InterPro:IPR011810",
            "gene_symbols": [
              "cphA"
            ],
            "description": "Cyanophycin synthetase family, verified at the InterPro authority; not an isolated ATP-grasp domain.",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:P56947",
                "protein_label": "Cyanophycin synthetase",
                "gene_symbol": "cphA",
                "taxon_id": "NCBITaxon:113355",
                "taxon_label": "Geminocystis herdmanii PCC 6308",
                "entry_status": "REVIEWED",
                "retrieved_on": "2026-10-08",
                "entry_version": 91,
                "sequence_version": 2,
                "role": "PCC 6308 enzyme catalyzes cyanophycin synthesis; functional expression and purification used recombinant E. coli, not a natural E. coli phenotype.",
                "evidence": [
                  {
                    "reference": "DOI:10.1007/s002030000206",
                    "snippet": "The functionality of cphA was proven by heterologous expression of active enzyme and synthesis of cyanophycin in Escherichia coli",
                    "notes": "Aboulmagd et al. (2000), scientific abstract directly read in DOI-matched Europe PMC core metadata (PMID:11131019); full paper not inspected. UniProt REST P56947 links this paper and AF220099/AAF43647.2 to PCC 6308; its entry version 91, sequence version 2 and NCBITaxon:113355 were checked live. The paper's Synechocystis name is historical. The accession is not PCC 6803 or the heterologous expression host."
                  }
                ]
              }
            ]
          },
          {
            "node_id": "cyanophycin_synthesis",
            "label": "cyanophycin synthesis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Nonribosomal polymer synthesis from arginine and aspartate."
          },
          {
            "node_id": "cyanophycin_macromolecule",
            "label": "cyanophycin macromolecule",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:65318",
            "description": "Authority-verified aspartate-backbone, arginine-side-group polymer; chemical identity is not the granule phenotype."
          },
          {
            "node_id": "cyanophycin_granule_trait",
            "label": "cyanophycin granule",
            "node_type": "TRAIT",
            "grounding": "traitmech:000673"
          },
          {
            "node_id": "temporary_nitrogen_storage",
            "label": "temporary nitrogen storage",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Retention of assimilated nitrogen for subsequent utilization."
          }
        ],
        "edges": [
          {
            "subject": "cyanophycin_synthetase_cpha",
            "predicate": "enables",
            "predicate_id": "RO:0002327",
            "object": "cyanophycin_synthesis",
            "description": "Purified PCC 6308 CphA catalyzes polymer synthesis.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.67.5.2176-2182.2001",
                "snippet": "which catalyzed the incorporation of arginine and aspartic acid into cyanophycin",
                "notes": "Aboulmagd et al. (2001), scientific abstract: the quoted relative clause describes the native enzyme purified from recombinant E. coli. Publisher full-text Methods and substrate/primer Results were read, including Tables 2 and 3. No actual figure images were inspected."
              }
            ]
          },
          {
            "subject": "cyanophycin_synthesis",
            "predicate": "has output",
            "predicate_id": "RO:0002234",
            "object": "cyanophycin_macromolecule",
            "description": "The assayed reaction incorporates amino acids into cyanophycin.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.67.5.2176-2182.2001",
                "snippet": "which catalyzed the incorporation of arginine and aspartic acid into cyanophycin",
                "notes": "Same abstract clause supports the product as well as catalysis. Radiometric incorporation into insoluble polymer is the assay readout. This does not equate soluble synthesis or engineered amino-acid variants with a cellular granule."
              }
            ]
          },
          {
            "subject": "cyanophycin_macromolecule",
            "predicate": "located in",
            "predicate_id": "biolink:located_in",
            "object": "cyanophycin_granule_trait",
            "description": "Accumulated cyanophycin forms the material of the inclusion.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.01298-18",
                "snippet": "Cyanophycin accumulates in the form of opaque and light-scattering granules in the cell",
                "notes": "Watzer and Forchhammer (2018), Introduction, directly read in publisher HTML. Results report microscopy and arginine-specific Sakaguchi staining during nitrogen resuscitation in the engineered PCC 6803 CphA-eGFP strain. Main text, Methods and supplemental captions were read; actual figure images were not inspected."
              }
            ]
          },
          {
            "subject": "cyanophycin_granule_trait",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "temporary_nitrogen_storage",
            "description": "The inclusion retains cyanophycin as a temporary nitrogen reserve.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.01298-18",
                "snippet": "cyanophycin can be used as a temporary nitrogen storage",
                "notes": "Scientific abstract clause. PCC 6803 wild-type versus cphA-deletion comparisons support condition-dependent storage during fluctuating or limiting nitrogen supply and light/dark cycles, not a universal fitness advantage. Granule-loss confirmation is reported as data not shown; no complementation experiment is claimed."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "cyanophycin-granule-identity",
        "prompt": "Keep inclusion morphology distinct from polymer and sequence identity.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Uses intracellular inclusion traitmech:000066 like PHA and polyphosphate granules. CHEBI:65318 is a chemical grounding only; CphA activity and family membership are not equivalent traits. CGP names the polymer, not an exact granule synonym. No trait xrefs, exact synonyms or SSSOM equivalences are asserted. Do not require spherical shape, fixed size, constitutive occurrence, or an invariant amino-acid ratio.",
        "posed_by": "codex",
        "posed_date": "2026-10-07"
      },
      {
        "discussion_id": "cyanophycin-granule-mechanism-scope",
        "prompt": "Resolve strain-specific assembly and degradation mechanisms separately.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "The 2001 enzyme paper calls cyanophycin unique to cyanobacteria, but the 2018 primary paper also documents its distribution in heterotrophic bacteria; no cyanobacteria-only restriction is imposed. Soluble engineered polymers do not alone establish granules. The graph integrates distinct source taxa rather than transferring PCC 6308 CphA evidence to the ATCC 51142 example. PCC 6803 without a substrain designation does not establish the Kazusa-specific UniProt instance. Surface localization and magnesium effects in cell extracts do not prove a universal in-vivo assembly requirement.",
        "posed_by": "codex",
        "posed_date": "2026-10-07"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-08T04:30:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added cyanophycin granule with four primary references, bounded verbatim excerpts, a natural ATCC 51142 example and a five-node mechanistic graph. Verified PCC 6308 CphA protein/family and polymer identity separately from morphology. Ignored-and-hidden novelty and current-main/worktree/complete-open-PR reservation checks support 000673 and v549 block 1062600-1062699. Existing records unchanged.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-08T04:29:03Z",
        "curator": "codex",
        "action": "CORRECT_CURATION_PROVENANCE",
        "changes": "Corrected provenance for #1816 without rewriting the initial event: its 04:30:00Z timestamp was mistakenly set ahead of execution. The initial record was already written before the repository CREATE history timestamp 2026-10-08T04:28:08Z, an observed upper bound, not an exact reconstructed write time. This correction uses the directly observed UTC clock; biological content is unchanged.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-22T05:20:00Z",
        "curator": "claude",
        "action": "ADD_RECORD_LEVEL_DEFINITION_SOURCE_EVIDENCE",
        "changes": "Added DOI:10.1128/AEM.01298-18 with verified verbatim snippet to record-level evidence to match definition_source (Stage 5 remediation of F-DEF-SRC-CYANOPHYCIN-001 in group G-STAGE4-RECORD-LEVEL-DEFINITION-SOURCE, issue #1981).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000671",
    "label": "diplococcus shaped",
    "definition": "A cell shape in which spherical cells remain attached in pairs following cell division, forming characteristic doublets.",
    "definition_source": "DOI:10.1038/ncomms4842",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000666"
    ],
    "synonyms": [
      {
        "synonym_text": "diplococcus-shaped",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "created_by": "Luke Wang",
    "evidence": [
      {
        "reference": "DOI:10.1038/ncomms4842",
        "snippet": "Separation of daughter cells during bacterial cell division",
        "notes": "Supports diplococcus-like paired morphology as linked to septal cross-wall splitting and daughter-cell separation."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1313",
        "taxon_label": "Streptococcus pneumoniae",
        "note": "Lancet-shaped diplococcus (paired cocci); the pneumococcus.",
        "reference": "PMID:34779760"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "diplococcus_shaped_septal_separation",
        "title": "Diplococcus paired-cell separation mechanism",
        "description": "Evidence-backed causal sketch linking diplococcus morphology to septal peptidoglycan synthesis, peptidoglycan hydrolase-mediated cell separation, and retention of daughter-cell pairs.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a broad environmental or morphological classification spanning multiple mechanisms, a measurement-like bin, or an absence/arrangement descriptor; contextual protein nodes do not receive token UniProt examples.",
        "nodes": [
          {
            "node_id": "diplococcus_shaped_trait",
            "label": "diplococcus shaped",
            "node_type": "TRAIT",
            "grounding": "METPO:1000671",
            "description": "Pair-forming spherical bacterial morphology."
          },
          {
            "node_id": "septal_peptidoglycan_synthesis",
            "label": "septal peptidoglycan synthesis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Division-associated wall synthesis at the septum."
          },
          {
            "node_id": "septal_cross_wall",
            "label": "septal cross wall",
            "node_type": "CELLULAR_LOCALIZATION",
            "description": "Peptidoglycan wall separating daughter cells."
          },
          {
            "node_id": "pcsB_hydrolase_system",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "PcsB hydrolase system",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Pneumococcal cell-separation factor involved in cross-wall splitting."
          },
          {
            "node_id": "daughter_cell_pair",
            "label": "daughter-cell pair",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Two cells remaining attached after division."
          },
          {
            "node_id": "separation_pg_hydrolase",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "septal peptidoglycan hydrolase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Cell-separation peptidoglycan hydrolase/autolysin dedicated to cleaving the septal cross-wall (e.g., LytB, AtlA, AmiC)."
          },
          {
            "node_id": "septum_cleavage",
            "label": "septum cleavage",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Enzymatic cleavage of septal peptidoglycan that resolves daughter cells."
          },
          {
            "node_id": "hydrolase_septal_localization",
            "label": "septal localization of separation hydrolase",
            "node_type": "CELLULAR_LOCALIZATION",
            "description": "Restricted targeting of the cell-separation autolysin to the division septum."
          },
          {
            "node_id": "wall_teichoic_acid",
            "label": "wall teichoic acid",
            "node_type": "CHEMICAL",
            "description": "Cell-wall teichoic acid polymer anchored to peptidoglycan; serves as recognition determinant for separation hydrolases."
          },
          {
            "node_id": "lytr_lcp_enzyme",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "LytR/LCP teichoic acid ligase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "LCP-family enzyme that anchors wall teichoic acid precursor to peptidoglycan."
          },
          {
            "node_id": "daughter_cell_separation",
            "label": "daughter cell separation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Resolution of two daughter cells after division; incomplete separation retains paired cells.",
            "grounding": "GO:0000920"
          }
        ],
        "edges": [
          {
            "subject": "septal_peptidoglycan_synthesis",
            "predicate": "forms",
            "object": "septal_cross_wall",
            "description": "Septal wall synthesis forms the cross-wall between daughter cells.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.cub.2021.04.041",
                "snippet": "peptidoglycan assembly during the cell cycle",
                "notes": "Supports septal PG assembly during ovococcal division."
              }
            ],
            "predicate_id": "biolink:produces"
          },
          {
            "subject": "pcsB_hydrolase_system",
            "predicate": "splits",
            "object": "septal_cross_wall",
            "description": "Cell separation requires splitting the septal cross-wall.",
            "evidence": [
              {
                "reference": "DOI:10.1038/ncomms4842",
                "snippet": "splitting of the septal cross wall",
                "notes": "Supports PcsB-associated peptidoglycan hydrolase function in cell separation."
              }
            ]
          },
          {
            "subject": "septal_cross_wall",
            "predicate": "incomplete separation yields",
            "object": "daughter_cell_pair",
            "description": "Incomplete or regulated separation of septal cross-wall material yields attached cell pairs.",
            "evidence": [
              {
                "reference": "DOI:10.1128/JB.183.10.3108-3116.2001",
                "snippet": "short chains with few or no free diplococci",
                "notes": "Supports the relationship between pneumococcal separation state and diplococcus occurrence."
              }
            ]
          },
          {
            "subject": "daughter_cell_pair",
            "predicate": "manifests as",
            "object": "diplococcus_shaped_trait",
            "description": "Attached daughter-cell pairs manifest the diplococcus-shaped trait.",
            "evidence": [
              {
                "reference": "DOI:10.1038/ncomms4842",
                "snippet": "daughter cells during bacterial cell division",
                "notes": "Supports paired morphology as an outcome of daughter-cell separation dynamics."
              }
            ],
            "predicate_id": "METPO:2007400"
          },
          {
            "subject": "separation_pg_hydrolase",
            "predicate": "mediates",
            "object": "septum_cleavage",
            "description": "A dedicated peptidoglycan hydrolase mediates septum cleavage between daughter cells.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s42003-023-04808-z",
                "notes": "Minimisation of cell chain size relies on a peptidoglycan hydrolase dedicated to septum cleavage (conserved separation-autolysin mechanism)."
              }
            ]
          },
          {
            "subject": "septum_cleavage",
            "predicate": "enables",
            "object": "daughter_cell_separation",
            "description": "Cleavage of the septal cross-wall enables resolution of daughter cells, favoring diplococci/short chains over long chains.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s42003-023-04808-z",
                "notes": "Septum cleavage is the proximate process producing paired cells rather than long chains."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "hydrolase_septal_localization",
            "predicate": "enables",
            "object": "daughter_cell_separation",
            "description": "Restricting the separation autolysin to the septum enables correct daughter-cell separation geometry.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s42003-023-04808-z",
                "notes": "Restricted septal localization of the autolysin confines its lethal activity to its site of action, enabling separation; mislocalization yields chaining."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "wall_teichoic_acid",
            "predicate": "promotes",
            "object": "hydrolase_septal_localization",
            "description": "Wall teichoic acid serves as a recognition determinant that promotes septal localization/binding of the separation hydrolase.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.celrep.2023.112756",
                "notes": "Separation-hydrolase binding is reduced in WTA-deficient cells but preserved in LTA-deficient cells; WTA acts as an envelope-polymer address for the autolysin."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "lytr_lcp_enzyme",
            "predicate": "produces",
            "object": "wall_teichoic_acid",
            "description": "LytR/LCP-family ligase mediates the final step of wall teichoic acid formation and anchoring to peptidoglycan.",
            "evidence": [
              {
                "reference": "DOI:10.1371/journal.pbio.3001990",
                "notes": "LytR is the major enzyme mediating the final step in WTA formation, anchoring the TA precursor to PGN."
              }
            ],
            "predicate_id": "METPO:2007800"
          },
          {
            "subject": "daughter_cell_separation",
            "predicate": "incomplete separation yields",
            "object": "daughter_cell_pair",
            "description": "Incomplete daughter-cell separation retains attached cell pairs.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s42003-023-04808-z",
                "notes": "Loss of septum-cleaving hydrolase activity shifts cells from separated/paired toward long chains; regulated separation yields paired cells."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.887641+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-11T20:05:00-07:00",
        "curator": "codex",
        "action": "CURATED_WITH_LITERATURE",
        "changes": "Added DOI-backed definition and causal graph for septal peptidoglycan, PcsB-associated cross-wall splitting, daughter-cell pairing, and diplococcus morphology.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T21:30:07Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007400\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-13T21:03:26Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:produces\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 6 evidence-backed generic edges (6 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:13Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 4 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d72, RO:0002213\u00d71, METPO:2000202\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:33Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0000920\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T02:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES_PART2",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates onto their causal-graph counterparts (1 to produces), issue 301 part 2. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Each replacement is a 1:1 mirror of its source predicate that changes only the domain, so the claim each edge makes is unchanged and directions are unchanged. The replacements are proposed in proposals/metpo_traitmech_v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope diplococcus_shaped_septal_separation=NONMECHANISTIC with scope_notes; marked 3 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (pcsB_hydrolase_system, separation_pg_hydrolase, lytr_lcp_enzyme).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000689",
    "label": "disc shaped",
    "definition": "A cell shape in which an organism is flat and circular.",
    "definition_source": "DOI:10.1099/ijs.0.65431-0",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000666"
    ],
    "synonyms": [
      {
        "synonym_text": "disc",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev-cellbio-101011-155745",
        "snippet": "cell shape is genetically determined",
        "notes": "Cell-shape review supports flat-disc geometry as a determined morphological phenotype."
      },
      {
        "reference": "DOI:10.1099/ijs.0.65431-0",
        "snippet": "flat square or disc-shaped cells",
        "notes": "Halophilic-archaea description supports flat disc-shaped cell morphology in the wild."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:2246",
        "taxon_label": "Haloferax volcanii",
        "note": "Pleomorphic haloarchaeon that forms flat disks in mid- and late-log growth; the cited genetic and imaging study directly verifies this conditional disk state and its DdfA dependence.",
        "reference": "DOI:10.1038/s41467-024-45196-0"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "disc_shaped_anisotropic_wall_growth",
        "title": "Disc-shape anisotropic cell-wall growth",
        "description": "DOI-backed graph linking anisotropic, planar peptidoglycan or S-layer growth and suppressed axial extension to flat disc-shaped cell geometry.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This is a geometric shape classification; the cited sources do not establish a taxon-matched protein determinant for disc geometry, so no token protein node or example is added.",
        "nodes": [
          {
            "node_id": "disc_shaped_trait",
            "label": "disc shaped",
            "node_type": "TRAIT",
            "grounding": "METPO:1000689",
            "description": "Flat, circular cellular morphology."
          },
          {
            "node_id": "planar_envelope_growth",
            "label": "planar envelope growth",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Cell-envelope (peptidoglycan or S-layer) expansion in a 2D plane."
          },
          {
            "node_id": "axial_extension_suppression",
            "label": "axial extension suppression",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced or absent extension along the orthogonal cell axis."
          },
          {
            "node_id": "flat_geometry",
            "label": "flat disc geometry",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Resulting flat, plate-like cell body."
          },
          {
            "node_id": "slayer_glycoprotein_maturation",
            "label": "S-layer glycoprotein C-terminal processing and lipid anchoring",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "ArtA peptidase and Pss enzyme dependent C-terminal processing and covalent lipid attachment of the surface (S-layer) glycoprotein."
          },
          {
            "node_id": "rod_shaped_state",
            "label": "rod-shaped morphology",
            "node_type": "STATE",
            "description": "Elongated rod cell type that disc/plate cells interconvert with."
          }
        ],
        "edges": [
          {
            "subject": "planar_envelope_growth",
            "predicate": "causes",
            "object": "flat_geometry",
            "description": "Planar envelope growth produces a 2D-expanded cell body.",
            "evidence": [
              {
                "reference": "DOI:10.1099/ijs.0.65431-0",
                "snippet": "flat square or disc-shaped cells",
                "notes": "Supports planar envelope growth producing flat morphology in disc-shaped halophiles."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "axial_extension_suppression",
            "predicate": "contributes to",
            "object": "flat_geometry",
            "description": "Suppression of axial extension keeps cells thin.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-cellbio-101011-155745",
                "snippet": "cell shape is genetically determined",
                "notes": "Supports anisotropic growth as a control mechanism for cell shape."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "flat_geometry",
            "predicate": "manifests as",
            "object": "disc_shaped_trait",
            "description": "Flat geometry manifests the disc-shaped trait.",
            "evidence": [
              {
                "reference": "DOI:10.1099/ijs.0.65431-0",
                "snippet": "disc-shaped cells",
                "notes": "Supports the trait endpoint."
              }
            ],
            "predicate_id": "METPO:2007400"
          },
          {
            "subject": "slayer_glycoprotein_maturation",
            "predicate": "enables",
            "object": "flat_geometry",
            "description": "C-terminal processing and lipid anchoring of the S-layer glycoprotein is required for stable flat plate-shaped cell formation.",
            "evidence": [
              {
                "reference": "DOI:10.1099/mic.0.001012",
                "notes": "Required for the C-terminal processing and covalent lipid attachment of S-layer glycoprotein, required for effective and stable plate-shaped cell formation."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "disc_shaped_trait",
            "predicate": "interconverts with",
            "object": "rod_shaped_state",
            "description": "Disc/plate cell type interconverts with the rod cell type as part of regulated shape switching.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nature13983",
                "notes": "H. volcanii exhibits interconvertible plate and rod cell types; transition from a disk-shape to a rod-shape."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.897674+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-11T22:45:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed causal graph linking planar envelope growth and axial-extension suppression to disc-shaped morphology.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002326\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T21:30:07Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007400\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:19Z",
        "curator": "claude",
        "action": "RENAME_PREDICATE_LABELS",
        "changes": "Renamed 1 causal-edge predicate label(s) to align with existing groundings: shapes \u2192 causes \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:21Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:causes\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 2 evidence-backed generic edges (2 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:13Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope disc_shaped_anisotropic_wall_growth=NONMECHANISTIC with scope_notes.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T09:40:27Z",
        "curator": "codex",
        "action": "ADD_CANONICAL_EXAMPLES",
        "changes": "Added growth-phase-qualified Haloferax volcanii as a disk-shaped exemplar from this record's own research artifact and direct genetics/imaging source; NCBITaxon:2246 and its current label were verified against NCBI.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000672",
    "label": "dumbbell shaped",
    "definition": "A cell shape in which an organism consists of two rounded cell bodies connected by a narrower central isthmus, often resulting from incomplete or snapping cell division.",
    "definition_source": "DOI:10.1111/j.1574-6976.2011.00298.x",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000666"
    ],
    "synonyms": [
      {
        "synonym_text": "S_star_dumbbell_pleomorphic",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "dumbbell-shaped",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1111/j.1574-6976.2011.00298.x",
        "snippet": "snapping cell division",
        "notes": "Corynebacterineae review supports snapping/V-form division producing transient dumbbell pairs."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1717",
        "taxon_label": "Corynebacterium diphtheriae",
        "reference": "DOI:10.1111/j.1574-6976.2011.00298.x",
        "note": "Corynebacterium diphtheriae undergoes snapping division that leaves daughter cells in V-shaped and transient dumbbell arrangements; the cited review synthesizes the primary corynebacterial division observations."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "dumbbell_shaped_snapping_division",
        "title": "Dumbbell-shape snapping division intermediate",
        "description": "DOI-backed graph linking pre-separation septum constriction and snapping/incomplete cell division to dumbbell cell pairs.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is retained as a transient morphology classification. The sources support snapping division and discuss RipA/RpfB hydrolases broadly, but do not establish a taxon-matched protein as the determinant of the asserted dumbbell trait; no token protein example is assigned.",
        "nodes": [
          {
            "node_id": "dumbbell_shaped_trait",
            "label": "dumbbell shaped",
            "node_type": "TRAIT",
            "grounding": "METPO:1000672",
            "description": "Two-lobe cell body joined by a central isthmus."
          },
          {
            "node_id": "midcell_constriction",
            "label": "midcell constriction",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Division-site constriction pinching the cell at midcell."
          },
          {
            "node_id": "snapping_division",
            "label": "snapping division",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Incomplete outer-layer separation that keeps daughter cells linked."
          },
          {
            "node_id": "dumbbell_intermediate",
            "label": "dumbbell intermediate",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Two-lobe cell pair joined by an isthmus prior to full separation."
          },
          {
            "node_id": "septal_pg_hydrolysis",
            "label": "septal peptidoglycan hydrolysis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Precisely timed and localized hydrolysis of septal peptidoglycan at the division junction."
          },
          {
            "node_id": "daughter_cell_separation",
            "label": "daughter cell separation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Resolution of the septum into two physically separated daughter cells, often via V-snapping.",
            "grounding": "GO:0000920"
          },
          {
            "node_id": "outer_envelope_continuity",
            "label": "outer envelope layer continuity",
            "node_type": "STATE",
            "description": "Arabinogalactan and mycolic-acid outer layers remaining continuous across the septum."
          },
          {
            "node_id": "mechanical_snapping_separation",
            "label": "mechanical snapping separation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Rupture of continuous outer envelope layers producing an uneven mechanical snap."
          },
          {
            "node_id": "v_shaped_daughters",
            "label": "V-shaped attached daughters",
            "node_type": "QUALITY",
            "description": "Angular V-shaped arrangement of partially attached daughter cells from snapping division."
          },
          {
            "node_id": "septal_hydrolases",
            "label": "septal peptidoglycan hydrolases (RipA/RpfB)",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Peptidoglycan-cleaving enzymes that cut the septum to separate daughter cells.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "RipA and RpfB are distinct hydrolase families; this aggregate cannot be represented by one exact protein-family identifier."
          },
          {
            "node_id": "polar_growth",
            "label": "polar growth from nascent septum",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Apical cell-wall growth initiated from the new pole at the nascent septum."
          }
        ],
        "edges": [
          {
            "subject": "midcell_constriction",
            "predicate": "has output",
            "object": "dumbbell_intermediate",
            "description": "Strong midcell constriction creates a two-lobe pre-division morphology.",
            "evidence": [
              {
                "reference": "DOI:10.1111/j.1574-6976.2011.00298.x",
                "snippet": "snapping cell division",
                "notes": "Supports midcell constriction as the proximate event preceding dumbbell intermediates."
              }
            ],
            "predicate_id": "RO:0002234"
          },
          {
            "subject": "snapping_division",
            "predicate": "stabilizes",
            "object": "dumbbell_intermediate",
            "description": "Snapping/V-form division preserves linkage between daughter cells.",
            "evidence": [
              {
                "reference": "DOI:10.1111/j.1574-6976.2011.00298.x",
                "snippet": "snapping cell division",
                "notes": "Supports snapping division as the mechanism stabilizing post-division dumbbells."
              }
            ]
          },
          {
            "subject": "dumbbell_intermediate",
            "predicate": "manifests as",
            "object": "dumbbell_shaped_trait",
            "description": "The dumbbell intermediate manifests the dumbbell-shaped trait.",
            "evidence": [
              {
                "reference": "DOI:10.1111/j.1574-6976.2011.00298.x",
                "snippet": "snapping cell division",
                "notes": "Supports the trait endpoint."
              }
            ],
            "predicate_id": "METPO:2007400"
          },
          {
            "subject": "septal_pg_hydrolysis",
            "predicate": "enables",
            "object": "daughter_cell_separation",
            "description": "Timed, localized septal PG hydrolysis enables daughter-cell separation / V-snapping.",
            "evidence": [
              {
                "reference": "DOI:10.1073/pnas.2214599119",
                "notes": "Daughter cell separation requires precisely timed and localized peptidoglycan hydrolysis at the septal junction."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "septal_pg_hydrolysis",
            "predicate": "combined with",
            "object": "mechanical_snapping_separation",
            "description": "Septal PG cleavage while outer AG/MA layers remain continuous leads to mechanical snapping separation.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mmbr.00028-07",
                "notes": "Overlying envelope layers (AG, mycolic acids) remain continuous across the septum; separation occurs by rupture of these outer layers, an uneven mechanical snap."
              }
            ]
          },
          {
            "subject": "outer_envelope_continuity",
            "predicate": "promotes",
            "object": "mechanical_snapping_separation",
            "description": "Continuity of outer envelope layers forces a final mechanical rupture (snap) to complete separation.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mmbr.00028-07",
                "notes": "Continuity/intertwining of AG and mycolate outer layers forces a final mechanical rupture."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "mechanical_snapping_separation",
            "predicate": "has output",
            "object": "v_shaped_daughters",
            "description": "Uneven rupture of intertwined outer envelope layers produces V-shaped attached daughters.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mmbr.00028-07",
                "notes": "Uneven rupturing produces the V-shape; snapping division produces angular daughter arrangements."
              }
            ],
            "predicate_id": "RO:0002234"
          },
          {
            "subject": "septal_hydrolases",
            "predicate": "mediates",
            "object": "septal_pg_hydrolysis",
            "description": "Septal PG hydrolases (RipA, RpfB) cleave the septum to separate daughter cells.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro3299",
                "notes": "RipA and RpfB cleave the septum to separate the daughter cells."
              }
            ]
          },
          {
            "subject": "polar_growth",
            "predicate": "aggravates",
            "object": "mechanical_snapping_separation",
            "description": "Polar growth from the nascent septum can aggravate rupture/snapping of outer layers.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mmbr.00028-07",
                "notes": "Polar growth from the nascent septum can aggravate rupture; relevant to transient two-bulb dumbbell form before full snap."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.888187+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-11T22:45:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed definition and causal graph linking midcell constriction and snapping division to dumbbell cell morphology.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T21:30:07Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007400\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 6 evidence-backed generic edges (7 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:13Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d71, RO:0002213\u00d71, METPO:2000202\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:33Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0000920\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-03T22:40:00Z",
        "curator": "claude",
        "action": "RETYPE_CAUSAL_NODES",
        "changes": "Retyped causal node v_shaped_daughters (V-shaped attached daughters) from TRAIT to QUALITY. It is the morphological outcome of snapping division, not a trait this record asserts: there is no v_shaped trait record and it carries no grounding, unlike the genuine cross-trait links elsewhere in the corpus (nacl_delta on nacl_delta_high). Morphology graphs use QUALITY for shape outcomes (rod shape, non-spherical morphology, cell curvature); STATE is reserved for conditions. Surfaced by issue 220: the second TRAIT node made this graph 7-node component reachable-from-a-trait, hiding it from UNREACHABLE_FROM_TRAIT.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 2 causal edge(s) off microbe-domain METPO predicates (2 to has output), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope dumbbell_shaped_snapping_division=NONMECHANISTIC with scope_notes; marked 1 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (septal_hydrolases).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T04:43:24Z",
        "curator": "codex",
        "action": "ADD_CANONICAL_EXAMPLES",
        "changes": "Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Corynebacterium diphtheriae (NCBITaxon:1717; DOI:10.1111/j.1574-6976.2011.00298.x). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000673",
    "label": "ellipsoidal",
    "definition": "A cell shape in which an organism has an oval or ellipse morphology, elongated along one axis with rounded ends, intermediate between spherical and rod-shaped.",
    "definition_source": "DOI:10.1089/mdr.2014.0032",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000666"
    ],
    "created_by": "Luke Wang",
    "evidence": [
      {
        "reference": "DOI:10.1089/mdr.2014.0032",
        "snippet": "ovococci that are ellipsoid",
        "notes": "Supports ellipsoidal bacterial morphology as a named ovococcal shape class."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:171101",
        "taxon_label": "Streptococcus pneumoniae R6",
        "note": "Strain-level ovococcal model paired to reviewed PBP2b, an essential peripheral peptidoglycan transpeptidase whose depletion alters pneumococcal morphology.",
        "reference": "DOI:10.1128/JB.00184-13"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "ellipsoidal_ovococcal_elongation",
        "title": "Ellipsoidal ovococcal elongation mechanism",
        "description": "Evidence-backed causal sketch linking ellipsoidal morphology to ovococcal peripheral peptidoglycan insertion, septal synthesis, PBP2b, and DivIVA-regulated elongation.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "The graph represents the pneumococcal septal/peripheral peptidoglycan mechanism. The R6 PBP2b example anchors one protein in the elongasome and is not presented as an accession for the whole protein complex.",
        "nodes": [
          {
            "node_id": "ellipsoidal_trait",
            "label": "ellipsoidal",
            "node_type": "TRAIT",
            "grounding": "METPO:1000673",
            "description": "Ellipse-like bacterial cell morphology."
          },
          {
            "node_id": "peripheral_peptidoglycan",
            "label": "peripheral peptidoglycan",
            "node_type": "CELLULAR_LOCALIZATION",
            "description": "Lateral wall material generated during ovococcal elongation."
          },
          {
            "node_id": "pbp2b",
            "label": "PBP2b",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Peptidoglycan synthase implicated in ovococcal elongation.",
            "grounding": "InterPro:IPR047982",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:P0A3M6",
                "protein_label": "Penicillin-binding protein 2B",
                "gene_symbol": "penA",
                "taxon_id": "NCBITaxon:171101",
                "taxon_label": "Streptococcus pneumoniae R6",
                "entry_status": "REVIEWED",
                "retrieved_on": "2026-10-22",
                "entry_version": 111,
                "sequence_version": 1,
                "role": "R6 PBP2b catalyzes transpeptidation in peripheral peptidoglycan synthesis, contributing to ovococcal elongation and ellipsoidal geometry.",
                "evidence": [
                  {
                    "reference": "DOI:10.1128/JB.00184-13",
                    "snippet": "PBP2b is essential for peripheral peptidoglycan synthesis",
                    "notes": "The depletion experiments used R6-derived pneumococcal strains and directly connect PBP2b abundance to cell morphology; UniProt verifies the reviewed R6 entry."
                  }
                ]
              }
            ]
          },
          {
            "node_id": "divIVA",
            "label": "DivIVA",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Morphogenetic protein coordinating septum splitting and elongation.",
            "grounding": "InterPro:IPR007793"
          },
          {
            "node_id": "septal_and_peripheral_synthesis",
            "label": "septal and peripheral peptidoglycan synthesis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Coordinated wall synthesis pattern in ovococci."
          },
          {
            "node_id": "ellipsoid_geometry",
            "label": "ellipsoid geometry",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Rounded cell geometry elongated along one axis."
          },
          {
            "node_id": "divisome",
            "label": "divisome (FtsZ/PBP2x/FtsW)",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Inner septal PG synthesis machine including FtsZ, bPBP2x and FtsW.",
            "grounding": "GO:1990586"
          },
          {
            "node_id": "septal_pg_synthesis",
            "label": "septal peptidoglycan synthesis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Constriction-associated PG synthesis at the division septum."
          },
          {
            "node_id": "elongasome",
            "label": "elongasome (PBP2b/RodA)",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Outer peripheral PG synthesis machine including bPBP2b and RodA.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "This aggregate denotes the pneumococcal multiprotein elongasome; no single protein-family term represents the complete PBP2b/RodA machinery."
          },
          {
            "node_id": "peripheral_pg_synthesis",
            "label": "peripheral peptidoglycan synthesis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Elongation-associated lateral PG synthesis."
          },
          {
            "node_id": "spatial_ring_separation",
            "label": "spatial separation of septal and peripheral PG rings",
            "node_type": "CELLULAR_LOCALIZATION",
            "description": "Concentric inner sPG and outer pPG rings at midcell."
          },
          {
            "node_id": "undecaprenyl_phosphate",
            "label": "undecaprenyl phosphate (Und-P)",
            "node_type": "CHEMICAL",
            "description": "Lipid carrier delivering cell wall precursors; limiting for PG synthesis."
          },
          {
            "node_id": "combined_septal_peripheral",
            "label": "combined septal and peripheral PG synthesis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Joint use of septal and peripheral PG synthesis characteristic of ovococci."
          }
        ],
        "edges": [
          {
            "subject": "pbp2b",
            "predicate": "promotes",
            "object": "peripheral_peptidoglycan",
            "description": "PBP2b promotes peripheral wall synthesis in ovococcal elongation.",
            "evidence": [
              {
                "reference": "DOI:10.1089/mdr.2014.0032",
                "snippet": "PBP2b of ovococci",
                "notes": "Supports PBP2b as part of the ovococcal elongation system."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "divIVA",
            "predicate": "regulates",
            "object": "septal_and_peripheral_synthesis",
            "description": "DivIVA regulates septal cleavage and peripheral peptidoglycan synthesis during ovococcal morphogenesis.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mbio.01311-24",
                "snippet": "peripheral peptidoglycan synthesis",
                "notes": "Supports DivIVA control of ovococcal wall remodeling and elongation."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "peripheral_peptidoglycan",
            "predicate": "contributes to",
            "object": "ellipsoid_geometry",
            "description": "Peripheral wall insertion contributes to elongation of the ellipsoidal cell body.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mbio.01311-24",
                "snippet": "septum cleavage and peripheral peptidoglycan synthesis",
                "notes": "Supports peripheral PG as a remodeling event for ovococcal elongation."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "septal_and_peripheral_synthesis",
            "predicate": "causes",
            "object": "ellipsoid_geometry",
            "description": "Coordinated septal and peripheral synthesis shapes the ellipsoidal cell body.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.cub.2021.04.041",
                "snippet": "dynamics of peptidoglycan assembly",
                "notes": "Supports PG assembly dynamics in ovoid bacteria."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "ellipsoid_geometry",
            "predicate": "manifests as",
            "object": "ellipsoidal_trait",
            "description": "Ellipsoid cell-body geometry manifests the ellipsoidal trait.",
            "evidence": [
              {
                "reference": "DOI:10.1089/mdr.2014.0032",
                "snippet": "ovococci that are ellipsoid",
                "notes": "Supports the morphology endpoint."
              }
            ],
            "predicate_id": "METPO:2007400"
          },
          {
            "subject": "divisome",
            "predicate": "carries out",
            "object": "septal_pg_synthesis",
            "description": "The divisome (FtsZ/bPBP2x/FtsW) carries out septal PG synthesis.",
            "evidence": [
              {
                "reference": "DOI:10.1111/mmi.14659",
                "notes": "an inner sPG machine (bPBP2x TP with FtsW GT)"
              }
            ]
          },
          {
            "subject": "elongasome",
            "predicate": "carries out",
            "object": "peripheral_pg_synthesis",
            "description": "The elongasome (bPBP2b/RodA plus Rod complex) carries out peripheral PG synthesis.",
            "evidence": [
              {
                "reference": "DOI:10.1111/mmi.14659",
                "notes": "an outer pPG machine (bPBP2b TP with RodA GT plus Rod complex proteins)"
              }
            ]
          },
          {
            "subject": "pbp2b",
            "predicate": "required for",
            "object": "peripheral_pg_synthesis",
            "description": "PBP2b is indispensable for lateral/peripheral PG synthesis and elongasome function.",
            "evidence": [
              {
                "reference": "DOI:10.1111/mmi.13543",
                "notes": "PBP2b is identified as indispensable for lateral PG synthesis and is a key component of the elongasome"
              }
            ]
          },
          {
            "subject": "spatial_ring_separation",
            "predicate": "enables",
            "object": "combined_septal_peripheral",
            "description": "Spatial separation of inner sPG and outer pPG rings enables concurrent septal and peripheral synthesis underlying ellipsoidal shape.",
            "evidence": [
              {
                "reference": "DOI:10.1111/mmi.14659",
                "notes": "septal and peripheral peptidoglycan synthesis are spatially separated at midcell into two concentric structures"
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "undecaprenyl_phosphate",
            "predicate": "preferentially required for",
            "object": "septal_pg_synthesis",
            "description": "Septal PG synthesis is more sensitive to Und-P limitation than peripheral synthesis, so Und-P limitation favors elongation.",
            "evidence": [
              {
                "reference": "DOI:10.7554/eLife.75607",
                "notes": "septal peptidoglycan synthesis is more sensitive to reduced Und-P levels than peripheral peptidoglycan synthesis"
              }
            ]
          },
          {
            "subject": "combined_septal_peripheral",
            "predicate": "results in",
            "object": "ellipsoidal_trait",
            "description": "Ovococcal/ellipsoidal shape results from combined use of septal and peripheral PG synthesis.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro3088",
                "notes": "Ovococcal cells, with an ellipsoid shape... ovococci use both septal and peripheral peptidoglycan synthesis"
              }
            ]
          },
          {
            "subject": "septal_pg_synthesis",
            "predicate": "part of",
            "object": "combined_septal_peripheral",
            "description": "Septal peptidoglycan synthesis is one arm of the simultaneous septal and peripheral synthesis program at ovococcal midcell.",
            "evidence": [
              {
                "reference": "DOI:10.1111/mmi.14659",
                "snippet": "septal and peripheral (elongation) PG synthesis occur simultaneously at midcell",
                "notes": "Verified against the open primary article abstract; the connector does not imply that the two synthesis machines are identical."
              }
            ],
            "predicate_id": "biolink:part_of"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.888945+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-11T20:05:00-07:00",
        "curator": "codex",
        "action": "CURATED_WITH_LITERATURE",
        "changes": "Added DOI-backed definition and causal graph for PBP2b, DivIVA, peripheral peptidoglycan, coordinated septal/peripheral wall synthesis, and ellipsoid geometry.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002211\u00d71, RO:0002326\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T21:30:07Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007400\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:19Z",
        "curator": "claude",
        "action": "RENAME_PREDICATE_LABELS",
        "changes": "Renamed 1 causal-edge predicate label(s) to align with existing groundings: shapes \u2192 causes \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:21Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:causes\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T05:05:14Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A892RPK7\u00d71, UniProtKB:Q1IYG2\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-13T21:03:26Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002213\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-17T04:09:44Z",
        "curator": "claude",
        "action": "REMOVE_REDUNDANT_SYNONYM",
        "changes": "Removed 1 synonym(s) whose text duplicated the label (seeder redundancy; no information lost).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 6 evidence-backed generic edges (7 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:13Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:21:12Z",
        "curator": "claude",
        "action": "RETRACT_DEAD_UNIPROT_GROUNDINGS",
        "changes": "Retracted 1 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:23:54Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:1990586\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-22T04:26:15Z",
        "curator": "codex",
        "action": "REVIEW_UNIPROT_INSTANCE_GROUNDINGS",
        "changes": "Reviewed 1 organism-specific UniProtKB grounding(s): replaced 1 with taxon-agnostic GO/InterPro terms and retracted 0 to label-only where no exact semantic term was supported (docs/GROUNDING_POLICY.md).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "CURATE_PROTEIN_TAXON_EXAMPLE",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope ellipsoidal_ovococcal_elongation=MECHANISTIC with scope_notes; marked 1 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (elongasome); added taxon-paired protein example(s) UniProtKB:P0A3M6 on pbp2b (NCBITaxon:171101); regrounded 1 node(s) (pbp2b: none->InterPro:IPR047982); added canonical example(s) NCBITaxon:171101.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T06:15:00Z",
        "curator": "codex",
        "action": "CONNECT_CAUSAL_GRAPH_COMPONENTS",
        "changes": "Resolved issue #183 graph fragmentation (2 components to 1) using 1 source- and verbatim-snippet-backed connector(s). No paid research service was called.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-22T01:35:00Z",
        "curator": "claude",
        "action": "REFRESH_UNIPROT_ENTRY_VERSION",
        "changes": "Refreshed UniProtKB entry_version against live UniProt REST on 2026-10-22: UniProtKB:P0A3M6 (110 -> 111 on pbp2b).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000703",
    "label": "expansion-driven sliding motility",
    "definition": "A phenotype in which a microbial population spreads across a supporting surface through passive displacement of cells by expansive forces generated within the colony, without active locomotory propulsion of the displaced cells.",
    "definition_source": "DOI:10.1111/1758-2229.70214",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1111/1758-2229.70214",
        "snippet": "Passive sliding motility allows Mycobacterium smegmatis to spread over soft agar surfaces.",
        "notes": "Pollitt et al. 2025, PMID:41152213, PMC12568390; scientific abstract, not graphical abstract. Full text, Figure 1 and the actual DOCX supplement were inspected. Results 2.8-2.9 interpret digitate-colony expansion as hydraulic displacement, not a direct force measurement; unobserved division does not establish absent growth. Supplementary Methods identify mc2 155. The Figure 1 comparison varies both gel material and concentration, not material alone. The qualified definition includes this interpretation without making cell-division pressure universal. Raw movies were not reanalyzed. Qualified MED, Crossref and the retrieved publisher page exposed no linked correction or retraction at the 2026-10-11 check."
      },
      {
        "reference": "DOI:10.1186/1471-2180-6-31",
        "snippet": "sliding motility is a passive mode of translocation for spreading over surfaces.",
        "notes": "Fall et al. 2006, PMID:16545127, PMC1501027; Background's source-attributed terminology, not an abstract quote. Results and Methods directly describe surface expansion of constructed B. subtilis DS64 hag-replacement material. Growth-associated, surfactin-dependent spreading supports the conventional case, not a universal transporter or surfactant requirement. Actual Figure 1 says 24 hours, whereas its caption and Results say 18 hours; retain this unresolved discrepancy. Proposed plant-root benefit is not observed natural colonization. Qualified MED, Crossref and the retrieved publisher page exposed no linked correction or retraction at the 2026-10-11 check."
      }
    ],
    "discussions": [
      {
        "discussion_id": "expansion-sliding-scope-and-naming",
        "prompt": "Retain the qualified expansion-driven scope without settling broader sliding terminology.",
        "kind": "CONTROVERSY",
        "status": "OPEN",
        "rationale": "The label is deliberately qualified: Kovacs et al. include gravity-assisted droplet surfing under sliding, whereas Hennes et al. distinguish it by driving force. Neither unqualified sliding nor surfing is asserted as an exact synonym here. Translation of an entire droplet under gravity alone is outside this expansion-driven definition. Fall's Background uses motility as a broader umbrella than current METPO:1000701 independent movement and METPO:1000702 energy-dependent independent movement; phenotype is therefore the conservative parent. This is not swimming, active gliding, swarming or twitching, and does not require absence of locomotory appendages from the organism. Different modes can coexist; no organism-level disjointness is asserted. Colony diameter, wetting, bulk advection or a sequence feature alone is insufficient. The letters document terminology, not additional experimental replication.",
        "evidence": [
          {
            "reference": "DOI:10.1073/pnas.1710371114",
            "evidence_source": "full_text",
            "snippet": "we therefore propose considering the finding of Hennes et al. (1) as a novel example of sliding motility",
            "notes": "Kovacs et al. 2017 letter, E8802, penultimate paragraph; publisher PDF at the authors' DTU repository. A proposed broader naming convention, not an independent experiment."
          },
          {
            "reference": "DOI:10.1073/pnas.1712278114",
            "evidence_source": "full_text",
            "snippet": "gravity is the driving force of surfing",
            "notes": "Hennes et al. 2017 reply, first bullet; author-hosted PDF. Contrasting physical classification, not experimental replication."
          }
        ],
        "posed_by": "codex",
        "posed_date": "2026-10-11"
      },
      {
        "discussion_id": "expansion-sliding-historical-metpo-identity",
        "prompt": "Resolve upstream identity without reviving deprecated sliding identifiers.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Pinned and current METPO contain deprecated METPO:0000096, METPO:000097 and METPO:1000388, without replacement annotations. Their reason codes were assigned by ID era in generator commit 38fbfb82c6cc962009582eb7f8652e48ede0f9c2, not by a sliding-specific biological assessment. https://github.com/berkeleybop/metpo/issues/521 still disputes this metadata; issue 271 requests motility coverage. Neither authorizes reactivation or resolves equivalence to this qualified class. Independent primary evidence supports the present scope, and no active exact replacement was found in the inspected ontology and pending proposals. Keep historical IDs out of xrefs and replaces; the new v579 proposal is not an upstream acceptance.",
        "posed_by": "codex",
        "posed_date": "2026-10-11"
      },
      {
        "discussion_id": "expansion-sliding-examples-and-mechanisms",
        "prompt": "Ground taxon-specific examples and causal branches before adding a graph.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "DS64 is engineered hag-replacement material. For mc2 155, the first-person provenance account DOI:10.1128/microbiolspec.MGM2-0037-2013 describes a laboratory-selected, plasmid-cured mutant derivative. Neither is presented as an unqualified natural canonical example. These qualifications do not invalidate the observed phenotype. No exact taxon-paired protein branch is established here, and the hydraulic molecular mechanism remains unresolved. Defer the graph rather than impose one lineage's mechanism or use NONMECHANISTIC to bypass grounding. Gene presence, appendage absence and predicted motility annotations cannot establish observed passive surface expansion. External equivalences remain unasserted.",
        "posed_by": "codex",
        "posed_date": "2026-10-11"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-11T21:19:38Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added qualified expansion-driven sliding with two primary DOI-backed studies and directly checked snippets. Reserved 000703, v579 and 1065600-1065699 after ignored/hidden worktree and pending-PR checks. Historical deprecated identities are not reused. Naming controversy, strain provenance and mechanism gaps remain explicit. Existing traits unchanged; timestamp is the observed UTC curation decision.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000675",
    "label": "cyanobacterial false branching",
    "definition": "A morphological phenotype in which a filamentous cyanobacterium forms an apparent branch by trichome-bundle partitioning or lateral trichome protrusion without generating a branch-point cell connecting at least three neighboring cells at that junction.",
    "definition_source": "DOI:10.1127/algol_stud/83/1996/303",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1127/algol_stud/83/1996/303",
        "snippet": "Two basic types of false branching (by bundle partitioning and by lateral trichome protrusion)",
        "notes": "Golubic et al. (1996), scientific abstract directly read on the publisher page https://www.schweizerbart.de/papers/algol_stud/detail/83/91090/Developmental_aspects_of_branching_in_filamentous_. Crossref confirms DOI, title and authors. The developmental analysis distinguishes false from true branching by branch-point cells contacting at least three neighbors. This terminology authority supports both listed modes, not only sheath rupture following necridium formation. Full article and figures were not inspected; no new experimental replication or universal molecular mechanism is inferred from the abstract."
      },
      {
        "reference": "DOI:10.5507/fot.2021.017",
        "snippet": "initiation of branching after disintegrating of sheath at the site of a necridia cell",
        "notes": "Tawong et al. (2022), Figure 1k caption, article page 82 in https://fottea.czechphycology.cz/pdfs/fot/2022/01/05.pdf (PDF page 5); actual Figure 1 panels and Methods/Results read. Source grammar is retained. Results page 81 points to Figs 2e-k for false branching, but the microscopy is Figure 1e-k; Figure 2 is phylogeny. NUACC05/06 show single and binary false branches associated with separation, heterocytes and loop rupture. The captioned necridium route is not required for every branch or for bundle partitioning."
      },
      {
        "reference": "DOI:10.1111/jpy.13256",
        "snippet": "False branches developed adjacent to necridic cells or heterocytes, or by separation of vegetative cells at compression folds in the trichome.",
        "notes": "Masumoto and Sanders (2022), scientific abstract directly read at https://onlinelibrary.wiley.com/doi/abs/10.1111/jpy.13256. Microscopy of lichen cyanobionts reports multiple branching modes within a strain, so false and true branching are not disjoint organism-level traits. Secondary attachment of freed apical segments is separately described as pseudo-branching; that term is not imported as an exact synonym. Full text, figures and supplements were not inspected."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:2929979",
        "taxon_label": "Scytonema foetidum",
        "reference": "DOI:10.5507/fot.2021.017",
        "note": "Example restricted to false-branched filaments of natural isolate NUACC06, not every cell or stage. Methods describe single-filament isolation from wet Khek River bank soil, Thailand, April 2019, followed by CT/2 liquid culture at 25 degrees C with a 12:12 light-dark cycle. Live NCBI Taxonomy efetch https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=taxonomy&id=2929979 confirms this current species name, rank species and NUACC06 type material; it is not a strain-rank accession. Taxonomy supports identity, not independent phenotype evidence."
      }
    ],
    "discussions": [
      {
        "discussion_id": "false-branching-scope",
        "prompt": "Review a closer multicellular morphology parent and branching terminology.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Use phenotype METPO:1000059 below quality METPO:1000188. Branched shaped METPO:1000687 concerns lateral branches in cell shape, not necessarily this arrangement of trichomes; no subclass or equivalence is asserted. The Golubic 1996 definition authority includes bundle partitioning as well as lateral protrusion. The Scytonema example demonstrates the latter and must not narrow the whole class. Necridium formation traitmech:000674 describes a separation cell, not all false branches. Hormogonium formation traitmech:000651 describes dispersal filaments, not the branching topology. Obsolete cell-arrangement METPO terms redirect to flagellar arrangement, which is not a suitable parent here. No exact synonyms, xrefs, SSSOM mappings or organism-level disjointness are asserted; historical pseudo-branch usages need review. The label is qualified as cyanobacterial false branching because the directly read English scientific abstract of Nesterenko et al. (1980), PMID:6782438 (https://pubmed.ncbi.nlm.nih.gov/6782438/), uses false branching for growth of separated cell ends in the organism historically named Brevibacterium helvolum ATCC 19239. That distinct usage is not evidence for cyanobacterial trichome development. Its full text and modern taxonomic identity were not inspected. No unqualified exact synonym or cross-taxon mechanism is asserted. See review issue #1821.",
        "posed_by": "codex",
        "posed_date": "2026-10-08"
      },
      {
        "discussion_id": "false-branching-mechanism",
        "prompt": "Resolve mechanisms separately for each developmental mode.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "The inspected microscopy supports a phenotype and cellular developmental routes, not an accession-resolved protein mechanism. Taxonomic sequence markers do not establish causality. Do not require necridia, heterocytes, a fixed branch count, one division plane, a universal trigger or a fitness benefit. No causal graph is proposed pending direct mechanistic evidence and verified protein examples; a mechanism is not claimed biologically absent.",
        "posed_by": "codex",
        "posed_date": "2026-10-08"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-08T06:28:38Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added cyanobacterial false branching with three DOI sources, verbatim snippets and a source-qualified NUACC06 example. Ignored-and-hidden searches of current main, worktrees and complete open-PR curation snapshots support 000675 and v551 block 1062800-1062899. Preserved both developmental modes, local branch-point scope and uncertainty about protein mechanisms. Existing traits unchanged. Timestamp is observed UTC curation time.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-08T06:50:15Z",
        "curator": "codex",
        "action": "QUALIFY_TRAIT_LABEL",
        "changes": "Addressed #1821: qualified the label to its cyanobacterial scope after directly checking the non-cyanobacterial usage in PMID:6782438. Preserved definition, evidence, example, identifier, proposal block and original curation event. Added source-qualified terminology discussion without an unqualified exact synonym.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000527",
    "label": "ferrosome",
    "definition": "A morphology trait in which a bacterial cell forms membrane-bound ferrosome organelles that store intracellular iron as non-crystalline iron phosphate biomineral.",
    "definition_source": "DOI:10.1038/s41586-022-04741-x",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000066"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/s41586-022-04741-x",
        "snippet": "Overall, this work establishes ferrosomes as a new class of iron storage organelles",
        "notes": "Grant et al. establish ferrosomes as an iron-storage organelle class."
      },
      {
        "reference": "DOI:10.1038/s41586-022-04741-x",
        "snippet": "we identify three ferrosome-associated (Fez) proteins that are responsible for forming ferrosomes",
        "notes": "Grant et al. support Fez protein-dependent ferrosome formation in Desulfovibrio magneticus."
      },
      {
        "reference": "DOI:10.1038/s41586-022-04741-x",
        "snippet": "fez operons are sufficient for ferrosome formation in foreign hosts",
        "notes": "Grant et al. support fez operon sufficiency for ferrosome formation in heterologous bacterial hosts."
      },
      {
        "reference": "DOI:10.1038/s41586-023-06719-9",
        "snippet": "Here we report that C. difficile undergoes an intracellular iron biomineralization process and stores iron in membrane-bound ferrosome organelles containing non-crystalline iron phosphate biominerals.",
        "notes": "Pi et al. support membrane-bound ferrosome organelles storing non-crystalline iron phosphate in Clostridioides difficile."
      },
      {
        "reference": "DOI:10.1038/s41586-023-06719-9",
        "snippet": "We found that a membrane protein (FezA) and a P1B6-ATPase transporter (FezB), repressed by both iron and the ferric uptake regulator Fur, are required for ferrosome formation",
        "notes": "Pi et al. support FezA- and FezB-dependent ferrosome formation in C. difficile."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1496",
        "taxon_label": "Clostridioides difficile",
        "note": "Pi et al. showed that C. difficile forms membrane-bound ferrosome organelles containing non-crystalline iron phosphate biominerals.",
        "reference": "DOI:10.1038/s41586-023-06719-9"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "ferrosome_iron_storage",
        "title": "Fez proteins form iron-storing ferrosomes",
        "description": "Evidence-backed causal sketch linking Fez-dependent formation to membrane-bound iron-storage organelles.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph captures broad Fez-dependent formation and ferrosome iron storage at process and organelle level without asserting one taxon-universal Fez component roster, individual Fez-protein activity, accession-level protein examples, iron-remobilization mechanism, membrane-localization path, iron-deficiency trigger, or host-colonization output.",
        "nodes": [
          {
            "node_id": "ferrosome_trait",
            "label": "ferrosome",
            "node_type": "TRAIT",
            "grounding": "traitmech:000527",
            "description": "Membrane-bound organelle storing intracellular iron as non-crystalline iron phosphate."
          },
          {
            "node_id": "ferrosome_formation",
            "label": "ferrosome formation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Fez-dependent biogenesis of membrane-bound intracellular ferrosome organelles."
          },
          {
            "node_id": "non_crystalline_iron_phosphate",
            "label": "non-crystalline iron phosphate biomineral",
            "node_type": "CHEMICAL",
            "description": "Non-crystalline iron phosphate mineral stored inside ferrosomes."
          },
          {
            "node_id": "iron_storage",
            "label": "iron storage",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Intracellular storage of iron in a recoverable organelle-associated pool."
          }
        ],
        "edges": [
          {
            "subject": "ferrosome_formation",
            "predicate": "has output",
            "predicate_id": "RO:0002234",
            "object": "ferrosome_trait",
            "description": "Fez-dependent ferrosome formation produces the ferrosome intracellular organelle.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41586-022-04741-x",
                "snippet": "Overall, this work establishes ferrosomes as a new class of iron storage organelles",
                "notes": "Grant et al. establish ferrosomes as an iron-storage organelle class."
              },
              {
                "reference": "DOI:10.1038/s41586-022-04741-x",
                "snippet": "we identify three ferrosome-associated (Fez) proteins that are responsible for forming ferrosomes",
                "notes": "Grant et al. support Fez protein-dependent ferrosome formation in Desulfovibrio magneticus."
              },
              {
                "reference": "DOI:10.1038/s41586-022-04741-x",
                "snippet": "fez operons are sufficient for ferrosome formation in foreign hosts",
                "notes": "Grant et al. support fez operon sufficiency for ferrosome formation in heterologous bacterial hosts."
              },
              {
                "reference": "DOI:10.1038/s41586-023-06719-9",
                "snippet": "We found that a membrane protein (FezA) and a P1B6-ATPase transporter (FezB), repressed by both iron and the ferric uptake regulator Fur, are required for ferrosome formation",
                "notes": "Pi et al. support FezA- and FezB-dependent ferrosome formation in C. difficile."
              }
            ]
          },
          {
            "subject": "non_crystalline_iron_phosphate",
            "predicate": "located in",
            "predicate_id": "biolink:located_in",
            "object": "ferrosome_trait",
            "description": "Non-crystalline iron phosphate biominerals are stored within ferrosome organelles.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41586-023-06719-9",
                "snippet": "Here we report that C. difficile undergoes an intracellular iron biomineralization process and stores iron in membrane-bound ferrosome organelles containing non-crystalline iron phosphate biominerals.",
                "notes": "Pi et al. support membrane-bound ferrosome organelles storing non-crystalline iron phosphate in Clostridioides difficile."
              }
            ]
          },
          {
            "subject": "ferrosome_trait",
            "predicate": "enables",
            "predicate_id": "RO:0002327",
            "object": "iron_storage",
            "description": "Ferrosome organelles realize intracellular iron storage.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41586-022-04741-x",
                "snippet": "Overall, this work establishes ferrosomes as a new class of iron storage organelles",
                "notes": "Grant et al. establish ferrosomes as an iron-storage organelle class."
              },
              {
                "reference": "DOI:10.1038/s41586-023-06719-9",
                "snippet": "Here we report that C. difficile undergoes an intracellular iron biomineralization process and stores iron in membrane-bound ferrosome organelles containing non-crystalline iron phosphate biominerals.",
                "notes": "Pi et al. support membrane-bound ferrosome organelles storing non-crystalline iron phosphate in Clostridioides difficile."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "ferrosome-xref-gap",
        "prompt": "Resolve exact external ontology xrefs for the bacterial ferrosome morphology trait.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "No exact active METPO, GO, or OBO class was accepted for the organism-level ferrosome morphology trait. GO:0110143 magnetosome, GO:0031411 gas vesicle, GO:0031470 carboxysome, and GO:0070088 PHA granule are sibling organelles or inclusions rather than ferrosome equivalents.",
        "posed_by": "codex",
        "posed_date": "2026-10-01"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-01T22:05:50Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted ferrosome as a DOI-backed MORPHOLOGY TraitRecord under the intracellular inclusion parent after an ignored-and-hidden duplicate review found no exact same-scope TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v404.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000674",
    "label": "filament shaped",
    "definition": "A cell shape in which an organism grows as elongated filamentous cells or hypha-like structures.",
    "definition_source": "DOI:10.1016/j.mib.2010.10.002",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000666"
    ],
    "synonyms": [
      {
        "synonym_text": "S_filament",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "filament",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "filament-shaped",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "created_by": "Luke Wang",
    "evidence": [
      {
        "reference": "DOI:10.1016/j.mib.2010.10.002",
        "snippet": "polar growth of Streptomyces",
        "notes": "Supports filamentous Streptomyces morphology as a polar-growth cell-shape system."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1021",
        "taxon_label": "Beggiatoa",
        "note": "Classic filamentous (multicellular trichome) sulfur bacterium; the organism in which gliding filaments were first described.",
        "reference": "PMID:17760503"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "filament_shaped_streptomyces_polar_growth",
        "title": "Filament-shape Streptomyces polar growth mechanism",
        "description": "Evidence-backed causal sketch linking filamentous morphology to DivIVA/Scy polarisomes, apical peptidoglycan synthesis, and hyphal tip extension.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a broad environmental or morphological classification spanning multiple mechanisms, a measurement-like bin, or an absence/arrangement descriptor; contextual protein nodes do not receive token UniProt examples.",
        "nodes": [
          {
            "node_id": "filament_shaped_trait",
            "label": "filament shaped",
            "node_type": "TRAIT",
            "grounding": "METPO:1000674",
            "description": "Elongated filamentous bacterial morphology."
          },
          {
            "node_id": "divIVA",
            "label": "DivIVA",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Polarity determinant for Streptomyces apical growth.",
            "grounding": "InterPro:IPR007793"
          },
          {
            "node_id": "scy",
            "label": "Scy",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Streptomyces cytoskeletal element associated with the polarisome.",
            "grounding": "InterPro:IPR048240"
          },
          {
            "node_id": "apical_polarisome",
            "label": "apical polarisome",
            "node_type": "CELLULAR_LOCALIZATION",
            "description": "Hyphal-tip organizing center for polar growth."
          },
          {
            "node_id": "apical_peptidoglycan_synthesis",
            "label": "apical peptidoglycan synthesis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Cell-wall synthesis localized at the hyphal tip."
          },
          {
            "node_id": "hyphal_tip_extension",
            "label": "hyphal tip extension",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Extension of filamentous hyphae by polar growth."
          },
          {
            "node_id": "dna_damage_sos_response",
            "label": "RecA/LexA SOS response",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "DNA-damage-triggered RecA/LexA SOS regulon inducing division-inhibitor expression.",
            "grounding": "GO:0009432"
          },
          {
            "node_id": "sula",
            "label": "SulA",
            "node_type": "GENE_OR_PROTEIN",
            "description": "SOS-induced cell-division inhibitor that blocks FtsZ polymerization.",
            "grounding": "InterPro:IPR004596"
          },
          {
            "node_id": "ftsz_polymerization",
            "label": "FtsZ polymerization",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Assembly of the FtsZ ring required for septation and cell division."
          },
          {
            "node_id": "apical_growth",
            "label": "polar hyphal growth",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Tip-localized polar growth of filamentous hyphae mediated by DivIVA/polarisome."
          },
          {
            "node_id": "hyphal_branch_emergence",
            "label": "hyphal branch emergence",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Emergence of new branches via splitting of polarisomes at hyphal tips."
          },
          {
            "node_id": "cgla",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "CglA",
            "node_type": "GENE_OR_PROTEIN",
            "description": "LCP-LytR_C domain glycopolymer ligase attaching glycopolymers to the cell wall."
          },
          {
            "node_id": "cell_wall_glycopolymer_attachment",
            "label": "cell-wall glycopolymer attachment",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Ligation of glycopolymers onto peptidoglycan maintaining hyphal cell shape."
          }
        ],
        "edges": [
          {
            "subject": "divIVA",
            "predicate": "localizes to",
            "object": "apical_polarisome",
            "description": "DivIVA localizes at hyphal tips as part of the polar growth machinery.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.mib.2010.10.002",
                "snippet": "polarity determinant DivIVA",
                "notes": "Supports DivIVA as a polarity determinant in Streptomyces."
              }
            ],
            "predicate_id": "biolink:located_in"
          },
          {
            "subject": "scy",
            "predicate": "part of",
            "object": "apical_polarisome",
            "description": "Scy is a component of the tip-organizing center controlling polar growth.",
            "evidence": [
              {
                "reference": "DOI:10.1371/journal.pgen.1002423",
                "snippet": "tip organizing center",
                "notes": "Supports Scy/DivIVA assemblies in Streptomyces polarized growth."
              }
            ],
            "predicate_id": "biolink:part_of"
          },
          {
            "subject": "apical_polarisome",
            "predicate": "recruits",
            "object": "apical_peptidoglycan_synthesis",
            "description": "The apical polarisome recruits cell-wall synthesis machinery to hyphal tips.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.mib.2012.10.012",
                "snippet": "polarisome-like complex involving the essential polarity protein DivIVA",
                "notes": "Supports polarisome-directed apical growth and cell-wall assembly."
              }
            ]
          },
          {
            "subject": "apical_peptidoglycan_synthesis",
            "predicate": "regulates",
            "object": "hyphal_tip_extension",
            "description": "Localized wall synthesis at the tip drives filament extension.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-025-02080-x",
                "snippet": "DivIVA drives growth at the hyphal poles",
                "notes": "Supports DivIVA-recruited PG synthesis at hyphal poles."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "hyphal_tip_extension",
            "predicate": "manifests as",
            "object": "filament_shaped_trait",
            "description": "Hyphal tip extension manifests filamentous morphology.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.mib.2010.10.002",
                "snippet": "Streptomyces hyphae",
                "notes": "Supports filamentous hyphal morphology as the trait endpoint."
              }
            ],
            "predicate_id": "METPO:2007400"
          },
          {
            "subject": "dna_damage_sos_response",
            "predicate": "induces",
            "object": "sula",
            "description": "DNA damage activates the RecA/LexA SOS response, inducing the division inhibitor SulA.",
            "evidence": [
              {
                "reference": "DOI:10.1002/advs.202203260",
                "notes": "DNA damage activates the RecA/LexA SOS response, leading to expression of sulA."
              }
            ]
          },
          {
            "subject": "sula",
            "predicate": "inhibits",
            "object": "ftsz_polymerization",
            "description": "SulA blocks FtsZ polymerization, preventing Z-ring assembly and septation.",
            "evidence": [
              {
                "reference": "DOI:10.1002/advs.202203260",
                "notes": "A cell division inhibitor, sulA, blocks FtsZ / SulA interferes with FtsZ polymerization."
              }
            ],
            "predicate_id": "RO:0002212"
          },
          {
            "subject": "ftsz_polymerization",
            "predicate": "regulates",
            "object": "filament_shaped_trait",
            "description": "Inhibited FtsZ polymerization blocks septation, causing non-septate filamentation.",
            "evidence": [
              {
                "reference": "DOI:10.1002/advs.202203260",
                "notes": "FtsZ inhibition / blocked septation contributes to non-septate cellular filamentation."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "apical_polarisome",
            "predicate": "enables",
            "object": "apical_growth",
            "description": "The DivIVA/polarisome assembly mediates polar growth at hyphal tips.",
            "evidence": [
              {
                "reference": "DOI:10.1128/jb.00153-23",
                "notes": "Hyphal growth occurs at the tips of the filamentous cells; this polar growth is mediated by DivIVA."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "apical_polarisome",
            "predicate": "promotes",
            "object": "hyphal_branch_emergence",
            "description": "Splitting of polarisomes at tips produces daughter polarisomes that coordinate new branch emergence.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsml/uqad020",
                "notes": "DivIVA forms discrete foci at growing tips; splitting of polarisomes produces daughter polarisomes coordinating emergence of new branches."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "cgla",
            "predicate": "enables",
            "object": "cell_wall_glycopolymer_attachment",
            "description": "CglA is the glycopolymer ligase mediating attachment of glycopolymers to the cell wall.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mbio.01492-24",
                "notes": "Identified the LCP-LytR_C domain protein CglA as a key glycopolymer ligase."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "cell_wall_glycopolymer_attachment",
            "predicate": "regulates",
            "object": "filament_shaped_trait",
            "description": "Reduced glycopolymer attachment results in enlarged vegetative hyphae and loss of hyphal cell shape.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mbio.01492-24",
                "notes": "Reduced amount of glycopolymers in the cglA mutant results in enlarged vegetative hyphae."
              }
            ],
            "predicate_id": "RO:0002211"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.889558+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-11T21:00:00-07:00",
        "curator": "codex",
        "action": "CURATED_WITH_LITERATURE",
        "changes": "Added DOI-backed definition and causal graph for DivIVA, Scy, apical polarisome, apical peptidoglycan synthesis, and hyphal tip extension.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T08:21:50Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:located_in\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T21:30:07Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007400\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:19Z",
        "curator": "claude",
        "action": "RENAME_PREDICATE_LABELS",
        "changes": "Renamed 1 causal-edge predicate label(s) to align with existing groundings: drives \u2192 regulates \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:21Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002211\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T05:05:14Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:Q1IYG2\u00d71, UniProtKB:A0A191V3Q4\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-26T05:00:48Z",
        "curator": "claude",
        "action": "RENAME_PREDICATE_LABELS",
        "changes": "Renamed 1 causal-edge predicate label(s) to align with existing groundings: organizes \u2192 enables \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-26T05:00:50Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 7 evidence-backed generic edges (7 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:13Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 6 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002211\u00d72, RO:0002327\u00d72, RO:0002212\u00d71, RO:0002213\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-26T07:15:19Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:H8YHZ0\u00d71, UniProtKB:A0A0C1K447\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:21:12Z",
        "curator": "claude",
        "action": "RETRACT_DEAD_UNIPROT_GROUNDINGS",
        "changes": "Retracted 1 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-07T18:00:00Z",
        "curator": "claude",
        "action": "REGROUND_CAUSAL_EDGE",
        "changes": "Edge scy -> apical_polarisome in graph filament_shaped_streptomyces_polar_growth: re-grounded it from enables/RO:0002327 to part of/biolink:part_of. Issue 334. biolink declares enables range 'biological process or activity', which of CausalNodeTypeEnum only BIOLOGICAL_PROCESS, PATHWAY and MOLECULAR_FUNCTION satisfy, so this edge entailed a false type on its object. 'Scy is a COMPONENT of the tip-organizing center.' Mereology, not causation. The corpus already uses `part of` this way (flii_atpase_complex part of ft3ss_export_system).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-22T04:26:15Z",
        "curator": "codex",
        "action": "REVIEW_UNIPROT_INSTANCE_GROUNDINGS",
        "changes": "Reviewed 3 organism-specific UniProtKB grounding(s): replaced 3 with taxon-agnostic GO/InterPro terms and retracted 0 to label-only where no exact semantic term was supported (docs/GROUNDING_POLICY.md).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope filament_shaped_streptomyces_polar_growth=NONMECHANISTIC with scope_notes; marked 1 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (cgla).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-15T06:22:00Z",
        "curator": "codex",
        "action": "GROUND_CAUSAL_NODE",
        "changes": "Grounded the RecA/LexA SOS-response biological-process node to GO:0009432 while adding the organism-level traitmech:000207 SOS response record.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000056",
    "label": "flagellar arrangement",
    "definition": "A morphology trait describing the number and spatial distribution of flagella on a cell (the flagellation pattern), e.g. monotrichous, lophotrichous, amphitrichous, or peritrichous.",
    "definition_source": "DOI:10.1093/femsre/fuv034",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000704"
    ],
    "synonyms": [
      {
        "synonym_text": "flagellation pattern",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1093/femsre/fuv034"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1093/femsre/fuv034",
        "notes": "Schuhmacher, Thormann & Bange describe how bacteria maintain a regular number and cellular location of flagella (the flagellation pattern); parent of the specific arrangement sub-variants."
      },
      {
        "reference": "DOI:10.3390/biom9070279",
        "notes": "Bacterial flagellum review supports the flagellum as the locomotory organelle whose number and placement define flagellar arrangement."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:319224",
        "taxon_label": "Shewanella putrefaciens CN-32",
        "note": "Monotrichous polar flagellation: hooks are monopolar in about 92% of wild-type cells, and disrupting the FlhF FliG-binding region redistributes them to subpolar sites. The figure is a localization percentage, not a per-cell flagellar count. Exemplifies the monotrichous arrangement class, not every flagellation pattern.",
        "reference": "DOI:10.1038/s41467-024-50274-4"
      },
      {
        "taxon_id": "NCBITaxon:210",
        "taxon_label": "Helicobacter pylori",
        "note": "Multi-flagellate polar tuft: wild-type populations centre on about four flagella per cell, and flhF/flhG deletions shift number and polar placement. Exemplifies a lophotrichous arrangement whose numerical control differs from monotrichous vibrios.",
        "reference": "DOI:10.1128/JB.00110-23"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "flagellar_arrangement_flhf_flhg",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "Flagellar arrangement is a classification axis whose child patterns have different placement programs. The graph is contextual and does not define one protein mechanism shared by every arrangement class.",
        "title": "Flagellar arrangement set by FlhF/FlhG flagellation pattern",
        "description": "Evidence-backed causal sketch linking FlhF/FlhG-regulated flagellar placement to the cellular flagellation pattern.",
        "nodes": [
          {
            "node_id": "flagellar_arrangement_trait",
            "label": "flagellar arrangement",
            "node_type": "TRAIT",
            "grounding": "traitmech:000056",
            "description": "Number and spatial distribution of flagella on the cell."
          },
          {
            "node_id": "bacterial_flagellum",
            "label": "bacterial-type flagellum",
            "node_type": "CELLULAR_LOCALIZATION",
            "grounding": "GO:0009288",
            "description": "Helical proteinaceous locomotory organelle of bacteria."
          },
          {
            "node_id": "flhf_flhg_regulation",
            "label": "FlhF/FlhG flagellar placement regulation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Regulatory system setting flagellar number and cellular position."
          },
          {
            "node_id": "flhf",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "FlhF is used across divergent flagellar-placement systems; an exact family term was not verified for this upper classification context.",
            "label": "FlhF",
            "node_type": "GENE_OR_PROTEIN",
            "description": "SRP-type GTPase that marks the future flagellar assembly site and directs MS-ring protein FliF to the cell pole."
          },
          {
            "node_id": "flhg",
            "label": "FlhG",
            "node_type": "GENE_OR_PROTEIN",
            "description": "MinD-type ATPase that stimulates FlhF GTPase activity and limits/positions flagellar number.",
            "grounding": "InterPro:IPR033875"
          },
          {
            "node_id": "flif_msring",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "This denotes an assembled MS-ring structure centered on FliF, not one standalone protein-family entity.",
            "label": "FliF (MS-ring protein)",
            "node_type": "GENE_OR_PROTEIN",
            "description": "MS-ring forming protein recruited to the cell pole as the earliest basal-body assembly step."
          },
          {
            "node_id": "flig",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "FliG is retained as contextual rotor machinery; an exact family term was not verified for the broad arrangement-class graph.",
            "label": "FliG",
            "node_type": "GENE_OR_PROTEIN",
            "description": "C-ring switch protein bound by FlhF and engaging FliF during basal-body assembly."
          },
          {
            "node_id": "cell_pole",
            "label": "cell pole",
            "node_type": "CELLULAR_LOCALIZATION",
            "description": "Polar region of the bacterial cell where flagellar assembly is nucleated.",
            "grounding": "GO:0060187"
          },
          {
            "node_id": "flagellar_assembly_site_marking",
            "label": "marking of future flagellar assembly site",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Spatial designation of the future flagellar assembly site that precedes basal-body assembly."
          }
        ],
        "edges": [
          {
            "subject": "bacterial_flagellum",
            "predicate": "defines",
            "object": "flagellar_arrangement_trait",
            "description": "The cellular distribution of flagella defines the arrangement.",
            "evidence": [
              {
                "reference": "DOI:10.3390/biom9070279",
                "notes": "Bacterial flagellum review supports the flagellum as the locomotory organelle whose number and placement define the arrangement."
              }
            ],
            "predicate_id": "METPO:2007500"
          },
          {
            "subject": "flhf_flhg_regulation",
            "predicate": "regulates",
            "object": "flagellar_arrangement_trait",
            "description": "FlhF/FlhG set the species-specific flagellation pattern.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuv034",
                "notes": "Schuhmacher et al. describe FlhF/FlhG governance of the flagellation pattern."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "flhg",
            "predicate": "stimulates GTPase activity of",
            "object": "flhf",
            "description": "FlhG stimulates the GTPase activity of FlhF, a conserved core regulatory interaction governing flagellar placement.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-024-50274-4",
                "notes": "Dornes 2024: \"FlhG acts on FlhF by stimulating its GTPase activity\" - conserved core regulatory edge."
              }
            ]
          },
          {
            "subject": "flhf",
            "predicate": "directs to cell pole",
            "object": "flif_msring",
            "description": "FlhF is required to direct the initial MS-ring protein FliF to the cell pole, nucleating basal-body assembly.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-024-50274-4",
                "notes": "Dornes 2024: \"FlhF... is required to direct the initial MS-ring protein FliF to the cell pole.\""
              }
            ]
          },
          {
            "subject": "flhf",
            "predicate": "binds",
            "object": "flig",
            "description": "FlhF binds FliG, coupling the placement regulator to C-ring/MS-ring assembly.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-024-50274-4",
                "notes": "Dornes 2024: FlhF B-domain (FliG Interaction Domain) is necessary and sufficient for FliG binding."
              }
            ]
          },
          {
            "subject": "flig",
            "predicate": "engages / recruits",
            "object": "flif_msring",
            "description": "FlhF-bound FliG engages the MS-ring protein FliF, recruiting a FliF-FliG complex to the pole.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-024-50274-4",
                "notes": "Dornes 2024: \"FlhF-bound FliG then engages the MS-ring protein FliF, recruiting a FliF-FliG complex to the pole.\""
              }
            ]
          },
          {
            "subject": "flhf",
            "predicate": "establishes",
            "object": "flagellar_assembly_site_marking",
            "description": "FlhF marks the future flagellar assembly site, after which basal-body assembly proceeds.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuv034",
                "notes": "Schuhmacher 2015: \"After FlhF marked the future flagellar site, assembly of the basal body will proceed.\""
              }
            ]
          },
          {
            "subject": "flagellar_assembly_site_marking",
            "predicate": "occurs at",
            "object": "cell_pole",
            "description": "The marking of the future flagellar assembly site localizes basal-body building blocks to the cell pole.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuv034",
                "notes": "Schuhmacher 2015: FlhF B-domain recruits MS-ring component FliF to the cell pole."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-06-03T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate MORPHOLOGY axis class (flagellar arrangement) under the existing flagellated class (METPO:1000704); parent of monotrichous/lophotrichous/ amphitrichous/peritrichous.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-09T15:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (FlhF/FlhG flagellation pattern) with GO node grounding and RO/METPO predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 6 evidence-backed generic edges (6 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:33Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0060187\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-26T07:15:19Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 3 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A656AC42\u00d71, UniProtKB:Q2N2M1\u00d71, UniProtKB:A0A016XEK1\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:21:12Z",
        "curator": "claude",
        "action": "RETRACT_DEAD_UNIPROT_GROUNDINGS",
        "changes": "Retracted 2 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-22T04:26:15Z",
        "curator": "codex",
        "action": "REVIEW_UNIPROT_INSTANCE_GROUNDINGS",
        "changes": "Reviewed 1 organism-specific UniProtKB grounding(s): replaced 1 with taxon-agnostic GO/InterPro terms and retracted 0 to label-only where no exact semantic term was supported (docs/GROUNDING_POLICY.md).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope flagellar_arrangement_flhf_flhg=NONMECHANISTIC with scope_notes; marked 3 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (flhf, flif_msring, flig).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T19:05:00Z",
        "curator": "claude",
        "action": "ADD_CANONICAL_EXAMPLES",
        "changes": "Added 2 source-backed canonical example(s) from this record's own deep-research artifact (issue 444): Shewanella putrefaciens CN-32 (NCBITaxon:319224), Helicobacter pylori (NCBITaxon:210). Each note scopes the exemplar to the single flagellation pattern the cited source establishes, because this record is an upper class whose graph is NONMECHANISTIC and spans alternative mechanisms. Taxon ids and labels were verified against NCBI taxonomy and every DOI resolved through Crossref. No gene or operon was promoted to a primary entry.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000704",
    "label": "flagellated",
    "definition": "A motile in which an organism possesses flagella for locomotion.",
    "definition_source": "DOI:10.3390/biom9070279",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000702"
    ],
    "synonyms": [
      {
        "synonym_text": "flagella",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.3390/biom9070279",
        "snippet": "bacterial flagellum is a helical filamentous organelle responsible for motility",
        "notes": "Supports flagella as locomotory structures."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:562",
        "taxon_label": "Escherichia coli",
        "note": "peritrichous flagella",
        "reference": "PMID:28117390"
      },
      {
        "taxon_id": "NCBITaxon:28901",
        "taxon_label": "Salmonella enterica",
        "note": "flagellated enteric",
        "reference": "PMID:26267246"
      },
      {
        "taxon_id": "NCBITaxon:83333",
        "taxon_label": "Escherichia coli K-12",
        "note": "Strain-level flagellin exemplar.",
        "reference": "PMID:28117390"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "flagellated_flagellar_motor",
        "title": "Flagellated locomotion mechanism",
        "description": "Evidence-backed causal sketch linking the flagellated phenotype to flagellar filament, hook, basal body, stator, ion motive force, and chemotaxis.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "The taxon-matched protein example anchors one experimentally supported causal branch; it is not presented as a universal mechanism for every taxon or every contextual branch in this graph.",
        "nodes": [
          {
            "node_id": "flagellated_trait",
            "label": "flagellated",
            "node_type": "TRAIT",
            "grounding": "METPO:1000704",
            "description": "Possession of flagella for locomotion."
          },
          {
            "node_id": "flagellar_filament",
            "label": "flagellar filament",
            "node_type": "CELLULAR_LOCALIZATION",
            "description": "Helical filament that acts as a propeller or molecular screw.",
            "grounding": "GO:0009420"
          },
          {
            "node_id": "flagellar_hook",
            "label": "flagellar hook",
            "node_type": "CELLULAR_LOCALIZATION",
            "description": "Universal-joint-like connector between motor and filament.",
            "grounding": "GO:0009424"
          },
          {
            "node_id": "flagellar_basal_body",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "flagellar basal body",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Rotary motor complex embedded in the cell envelope."
          },
          {
            "node_id": "chemotaxis_signaling",
            "label": "chemotaxis signaling",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Regulation of flagellar rotation and movement direction.",
            "grounding": "GO:0006935"
          },
          {
            "node_id": "ft3ss_export_system",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "flagellar type III secretion system",
            "node_type": "GENE_OR_PROTEIN",
            "description": "fT3SS at the flagellar base that exports structural subunits to the assembly site."
          },
          {
            "node_id": "flagellar_structural_subunits",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:P04949",
                "protein_label": "Flagellin",
                "gene_symbol": "fliC",
                "taxon_id": "NCBITaxon:83333",
                "taxon_label": "Escherichia coli K-12",
                "entry_status": "REVIEWED",
                "proteome_id": "UP000000625",
                "retrieved_on": "2026-08-25",
                "entry_version": 183,
                "sequence_version": 2,
                "role": "FliC is the polymerizing E. coli K-12 flagellar-filament subunit, not an example of the complete flagellum.",
                "evidence": [
                  {
                    "reference": "PMID:28117390",
                    "snippet": "flagellin is the structural subunit of the flagellar filament",
                    "notes": "The cited source supports the represented protein-to-trait branch; UniProt verifies this current strain-matched protein entry."
                  }
                ]
              }
            ],
            "label": "flagellar structural subunits",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Axial protein subunits exported through the central channel for distal assembly."
          },
          {
            "node_id": "flii_atpase_complex",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "FliH-FliI-FliJ ATPase complex",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Cytoplasmic ATPase ring complex providing ATP hydrolysis to drive flagellar protein export."
          },
          {
            "node_id": "fld_filament_cap",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "FliD filament cap",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Pentameric cap at the filament tip that aids flagellin polymerization."
          },
          {
            "node_id": "hook_filament_junction",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "FlgK/FlgL hook-filament junction",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Adapter proteins connecting hook to filament and required for filament polymerization."
          },
          {
            "node_id": "filament_polymerization",
            "label": "flagellar filament polymerization",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Polymerization of flagellin subunits into the helical filament."
          },
          {
            "node_id": "chey_p",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "CheY-P",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Phosphorylated chemotaxis response regulator that binds the C ring to control rotation."
          },
          {
            "node_id": "rotational_switching",
            "label": "flagellar rotational switching",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Switching of flagellar motor rotation between CCW and CW states."
          }
        ],
        "edges": [
          {
            "subject": "flagellar_filament",
            "predicate": "confers",
            "object": "flagellated_trait",
            "description": "A flagellar filament is the locomotory appendage of flagellated cells.",
            "evidence": [
              {
                "reference": "DOI:10.3390/biom9070279",
                "snippet": "helical filamentous organelle responsible for motility",
                "notes": "Supports the filament as the locomotory flagellar structure."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "flagellar_hook",
            "predicate": "connects",
            "object": "flagellar_filament",
            "description": "The hook couples the motor to the filament.",
            "evidence": [
              {
                "reference": "DOI:10.3390/biom9070279",
                "snippet": "hook as a universal joint",
                "notes": "Supports the hook's coupling role."
              }
            ]
          },
          {
            "subject": "flagellar_basal_body",
            "predicate": "rotates",
            "object": "flagellar_filament",
            "description": "The basal body motor rotates the filament for propulsion.",
            "evidence": [
              {
                "reference": "DOI:10.1016/S1937-6448(08)01402-0",
                "snippet": "reversible rotary motor",
                "notes": "Supports basal body motor rotation of flagella."
              }
            ]
          },
          {
            "subject": "chemotaxis_signaling",
            "predicate": "regulates",
            "object": "flagellated_trait",
            "description": "Chemotaxis signaling changes flagellar motor behavior and movement direction.",
            "evidence": [
              {
                "reference": "DOI:10.3390/biom9070279",
                "snippet": "regulate the direction of flagella-driven motility",
                "notes": "Supports chemotaxis regulation of flagellated motility."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "ft3ss_export_system",
            "predicate": "exports",
            "object": "flagellar_structural_subunits",
            "description": "The fT3SS exports flagellar structural subunits to the distal assembly site.",
            "evidence": [
              {
                "reference": "DOI:10.1128/ecosalplus.esp-0011-2023",
                "notes": "\"a flagellar type III secretion system (fT3SS) at the base exports structural subunits from the cytoplasm through a narrow central channel to the distal tip where assembly occurs\""
              }
            ],
            "predicate_id": "METPO:2007804"
          },
          {
            "subject": "flii_atpase_complex",
            "predicate": "part of",
            "object": "ft3ss_export_system",
            "description": "The FliH-FliI-FliJ ATPase complex powers flagellar protein export by the fT3SS.",
            "evidence": [
              {
                "reference": "DOI:10.1128/ecosalplus.esp-0011-2023",
                "notes": "\"the ATPase ring complex (FliI, with FliH and FliJ) provides ATP hydrolysis for export\""
              }
            ],
            "predicate_id": "biolink:part_of"
          },
          {
            "subject": "fld_filament_cap",
            "predicate": "enables",
            "object": "filament_polymerization",
            "description": "The FliD filament cap aids polymerization of flagellin into the filament.",
            "evidence": [
              {
                "reference": "DOI:10.3390/biom14121488",
                "notes": "\"flagellin subunits (~30,000) polymerize into a filament aided by a five-subunit FliD cap\""
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "hook_filament_junction",
            "predicate": "enables",
            "object": "filament_polymerization",
            "description": "FlgK/FlgL hook-filament junction proteins are required for filament polymerization.",
            "evidence": [
              {
                "reference": "DOI:10.3390/biom14121488",
                "notes": "\"absence of FlgK/FlgL/FliD prevents filament polymerization\""
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "filament_polymerization",
            "predicate": "results in formation of",
            "object": "flagellar_filament",
            "description": "Polymerization of flagellin subunits forms the flagellar filament.",
            "evidence": [
              {
                "reference": "DOI:10.3390/biom14121488",
                "notes": "\"flagellin subunits (~30,000) polymerize into a filament\" forming the helical filament."
              }
            ]
          },
          {
            "subject": "chey_p",
            "predicate": "regulates",
            "object": "rotational_switching",
            "description": "CheY-P binding to the C ring causes flagellar rotational switching (CCW/CW).",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-024-01630-z",
                "notes": "\"Directional switching is triggered by the chemotaxis regulator CheY-P binding to FliM, causing full reversal of rotation\""
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "rotational_switching",
            "predicate": "regulates",
            "object": "flagellated_trait",
            "description": "Switching of motor rotation direction modulates flagellated motility behavior.",
            "evidence": [
              {
                "reference": "DOI:10.1128/ecosalplus.esp-0011-2023",
                "notes": "\"the C ring switches its conformational state\" changing the direction of flagella-driven motility."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "flagellar_structural_subunits",
            "predicate": "contributes to",
            "object": "flagellar_filament",
            "description": "Exported flagellin structural subunits assemble to form the flagellar filament that realizes the morphology.",
            "evidence": [
              {
                "reference": "DOI:10.3390/biom11020186",
                "snippet": "Around 20,000 subunits of flagellin assemble to form the flagellar filament",
                "notes": "Verified against the open review full text; this connects the exported-subunit module to the assembled structural filament."
              }
            ],
            "predicate_id": "RO:0002326"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.906575+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-11T00:00:00-07:00",
        "curator": "codex",
        "action": "CURATED_WITH_LITERATURE",
        "changes": "Reviewed flagellated trait and added DOI-backed causal graph for flagellar filament, hook, basal body, stator, ion motive force, and chemotaxis.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d71, RO:0002211\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-26T05:00:48Z",
        "curator": "claude",
        "action": "RENAME_PREDICATE_LABELS",
        "changes": "Renamed 1 causal-edge predicate label(s) to align with existing groundings: powers \u2192 enables \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-26T05:00:50Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-14T05:51:46Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0009420\u00d71, GO:0009424\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-16T06:54:40Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0006935\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 8 evidence-backed generic edges (9 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:13Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 7 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d73, RO:0002211\u00d72, METPO:2000209\u00d71, RO:0000085\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 1 causal edge(s) off enables/RO:0002327 with a TRAIT object (1 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T02:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES_PART2",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates onto their causal-graph counterparts (1 to exports), issue 301 part 2. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Each replacement is a 1:1 mirror of its source predicate that changes only the domain, so the claim each edge makes is unchanged and directions are unchanged. The replacements are proposed in proposals/metpo_traitmech_v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T08:00:00Z",
        "curator": "claude",
        "action": "REGROUND_CAUSAL_EDGE",
        "changes": "Re-grounded causal edge(s) off enables/RO:0002327 onto part of (biolink:part_of) and contributes to (RO:0002326), issue 334. biolink declares enables range 'biological process or activity', which only BIOLOGICAL_PROCESS, PATHWAY and MOLECULAR_FUNCTION satisfy, so an edge pointing at a GENE_OR_PROTEIN entailed a false type. The replacements are chosen per idiom rather than swept: a gene cluster ENCODES its product, a subunit is PART OF the complex it belongs to, and an energy source or acquired repertoire CONTRIBUTES TO the machine it powers or composes. All three declare no rdfs:domain or rdfs:range, so none can reintroduce the class of defect being removed.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T09:00:00Z",
        "curator": "claude",
        "action": "REGROUND_CAUSAL_EDGE",
        "changes": "Reverted the motive-force edge from contributes to back to enables/RO:0002327, issue 334 review. biolink defines contributes to as holding where one entity contributes to the occurrence or GENERATION of the other. A motive force does not generate the motor or machinery - it powers rotation, which is what the edge description says. That is the same energy-powers-a-machine idiom this work deferred for molecular_oxygen and cytoplasmic_na, so deferring it here too is the consistent call. The edge stays baselined under issue 334 until it is modelled as an input to the machine or pointed at the rotation process, either of which is range-correct.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-07T18:00:00Z",
        "curator": "claude",
        "action": "REGROUND_CAUSAL_EDGE",
        "changes": "Edge ion_motive_force -> stator_complex in graph flagellated_flagellar_motor: re-grounded it from enables/RO:0002327 to powers/METPO:2007900. Issue 334. biolink declares enables range 'biological process or activity', which of CausalNodeTypeEnum only BIOLOGICAL_PROCESS, PATHWAY and MOLECULAR_FUNCTION satisfy, so this edge entailed a false type on its object. 'Ion flux through stator complexes POWERS torque generation.'",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "CURATE_PROTEIN_TAXON_EXAMPLE",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope flagellated_flagellar_motor=MECHANISTIC with scope_notes; marked 8 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (flagellar_basal_body, stator_complex, ft3ss_export_system, flagellar_structural_subunits, flii_atpase_complex, fld_filament_cap, hook_filament_junction, chey_p); added taxon-paired protein example(s) UniProtKB:P04949 on flagellar_structural_subunits (NCBITaxon:83333); added canonical example(s) NCBITaxon:83333.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T06:15:00Z",
        "curator": "codex",
        "action": "CONNECT_CAUSAL_GRAPH_COMPONENTS",
        "changes": "Resolved issue #183 graph fragmentation (3 components to 1) using 1 source- and verbatim-snippet-backed connector(s). Removed the isolated stator/ion-channel branch because the tracked report explicitly scopes flagellated to appendage possession and says stator activity is not required for that structural state. No paid research service was called.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000675",
    "label": "flask shaped",
    "definition": "A cell shape in which an organism has a bulbous body with a narrower neck-like extension at one pole.",
    "definition_source": "DOI:10.1146/annurev-cellbio-101011-155745",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000666"
    ],
    "synonyms": [
      {
        "synonym_text": "flask",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "flask-shaped",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev-cellbio-101011-155745",
        "snippet": "polar growth",
        "notes": "Cell-shape review supports polarized peptidoglycan growth as a mechanism producing asymmetric flask-like morphology."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:521674",
        "taxon_label": "Planctopirus limnophila DSM 3776",
        "note": "Pear-shaped planctomycete whose body narrows toward one pole; the cited functional study distinguishes this cell shape from its polar budding division mode.",
        "reference": "DOI:10.1038/s41564-019-0588-1"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "flask_shaped_asymmetric_polar_growth",
        "title": "Flask-shape asymmetric polar growth",
        "description": "DOI-backed graph linking unipolar peptidoglycan growth and tapered neck extension to flask-shaped cell morphology.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a morphology classification. The cited studies establish polar or prosthecate growth and bactofilin-dependent compartment control, but do not establish an exact protein mechanism for the asserted bulb-plus-neck flask geometry; no token protein example is assigned.",
        "nodes": [
          {
            "node_id": "flask_shaped_trait",
            "label": "flask shaped",
            "node_type": "TRAIT",
            "grounding": "METPO:1000675",
            "description": "Bulbous cell body with a narrower polar neck."
          },
          {
            "node_id": "unipolar_pg_growth",
            "label": "unipolar peptidoglycan growth",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Peptidoglycan synthesis localized to a single cell pole."
          },
          {
            "node_id": "polar_neck_extension",
            "label": "polar neck extension",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Tapered extension of one pole producing the flask neck."
          },
          {
            "node_id": "bulbous_body",
            "label": "bulbous body",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Wider rounded body region opposite the neck."
          },
          {
            "node_id": "zonal_polar_pg_synthesis",
            "label": "zonal polar peptidoglycan synthesis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Localized cell-wall (peptidoglycan) insertion at a cell pole."
          },
          {
            "node_id": "polar_outgrowth",
            "label": "polar envelope outgrowth",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Asymmetric extension of one pole producing a stalk/prostheca-like neck."
          },
          {
            "node_id": "pg_growth_zone_position",
            "label": "position of polar PG growth zone",
            "node_type": "QUALITY",
            "description": "Spatial location of the localized cell-wall growth zone on the cell."
          },
          {
            "node_id": "appendage_position_shape",
            "label": "appendage position and shape",
            "node_type": "QUALITY",
            "description": "Where and how a polar neck-like extension forms on the cell."
          },
          {
            "node_id": "bactofilin_lmdc_module",
            "label": "bactofilin-M23 endopeptidase module",
            "node_type": "PATHWAY",
            "description": "Conserved scaffold/hydrolase morphogenetic module driving local cell-wall remodeling."
          },
          {
            "node_id": "cell_wall_biosynthesis",
            "label": "cell wall biosynthesis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Synthesis and remodeling of the peptidoglycan cell wall."
          },
          {
            "node_id": "bactofilin_cytoskeleton",
            "label": "bactofilin cytoskeleton",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Bactofilin polymer scaffold marking sites of asymmetric wall growth.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "The contextual node spans different bactofilin paralogues across prosthecate taxa, so no one family or instance precisely denotes it."
          },
          {
            "node_id": "asymmetric_compartment_growth",
            "label": "asymmetric compartment growth",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Outgrowth of stalk/bud-like compartments at a cell pole."
          }
        ],
        "edges": [
          {
            "subject": "unipolar_pg_growth",
            "predicate": "regulates",
            "object": "polar_neck_extension",
            "description": "Unipolar PG growth extends one pole into a narrower neck.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-cellbio-101011-155745",
                "snippet": "polar growth",
                "notes": "Supports unipolar growth as the mechanism for asymmetric pole extension."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "polar_neck_extension",
            "predicate": "combines with",
            "object": "bulbous_body",
            "description": "A narrow polar neck adjoining a wider body yields flask geometry.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-cellbio-101011-155745",
                "snippet": "cell shape is genetically determined",
                "notes": "Supports asymmetric growth as a genetically determined shape program."
              }
            ]
          },
          {
            "subject": "bulbous_body",
            "predicate": "manifests as",
            "object": "flask_shaped_trait",
            "description": "The combined neck+body geometry manifests flask morphology.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-cellbio-101011-155745",
                "snippet": "polar growth",
                "notes": "Supports the trait endpoint via asymmetric polar growth."
              }
            ],
            "predicate_id": "METPO:2007400"
          },
          {
            "subject": "zonal_polar_pg_synthesis",
            "predicate": "has output",
            "object": "polar_outgrowth",
            "description": "Polarized cell-wall insertion is a general mechanism producing asymmetric bulb-plus-neck outgrowths.",
            "evidence": [
              {
                "reference": "DOI:10.1371/journal.pbio.1002565",
                "notes": "Caulobacter prostheca arises from zonal growth at the pole; general mechanism for asymmetric morphologies."
              }
            ],
            "predicate_id": "RO:0002234"
          },
          {
            "subject": "pg_growth_zone_position",
            "predicate": "regulates",
            "object": "appendage_position_shape",
            "description": "Moving the localized growth zone changes where neck-like extensions form.",
            "evidence": [
              {
                "reference": "DOI:10.1371/journal.pbio.1002565",
                "notes": "Asticcacaulis prosthecate variants result from repositioning growth zones to subpolar/bilateral sites."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "bactofilin_lmdc_module",
            "predicate": "regulates",
            "object": "cell_wall_biosynthesis",
            "description": "Conserved scaffold/hydrolase module promotes local changes in the mode of cell wall biosynthesis underlying complex shapes.",
            "evidence": [
              {
                "reference": "DOI:10.7554/elife.86577.2",
                "notes": "Bactofilins and M23 peptidases form a conserved functional module that promotes local changes in cell wall biosynthesis."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "bactofilin_cytoskeleton",
            "predicate": "regulates",
            "object": "asymmetric_compartment_growth",
            "description": "Bactofilin scaffold constrains polar compartment growth; its loss causes unconstrained asymmetric outgrowth.",
            "evidence": [
              {
                "reference": "DOI:10.7554/elife.86577.2",
                "notes": "Loss of bactofilins causes unconstrained growth of the stalk and bud compartments."
              }
            ],
            "predicate_id": "RO:0002211"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.890141+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-11T22:45:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed definition and causal graph linking unipolar peptidoglycan growth and neck extension to flask-shaped morphology.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T21:30:07Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007400\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:19Z",
        "curator": "claude",
        "action": "RENAME_PREDICATE_LABELS",
        "changes": "Renamed 1 causal-edge predicate label(s) to align with existing groundings: drives \u2192 regulates \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:21Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002211\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 4 evidence-backed generic edges (8 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:13Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 4 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002211\u00d73, METPO:2000202\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates (1 to has output), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope flask_shaped_asymmetric_polar_growth=NONMECHANISTIC with scope_notes; marked 1 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (bactofilin_cytoskeleton).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T09:40:27Z",
        "curator": "codex",
        "action": "ADD_CANONICAL_EXAMPLES",
        "changes": "Added Planctopirus limnophila DSM 3776 as a strain-level pear/flask-shaped exemplar from this record's own research artifact; NCBITaxon:521674 and its current label were verified against NCBI.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000681",
    "label": "fungal adhesive-column trap formation",
    "definition": "A morphological phenotype in which a fungus forms columns of serially arranged hyphal cells with adhesive surfaces that serve as nematode traps.",
    "definition_source": "DOI:10.1016/j.isci.2020.101057",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000718"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1016/j.isci.2020.101057",
        "snippet": "Fungi with the AC device form a string of cells with adhesive surfaces",
        "notes": "Ji et al. (2020), Introduction, third paragraph; AC means adhesive column. Primary full-text XML at https://www.ebi.ac.uk/europepmc/webservices/rest/PMC7186526/fullTextXML and actual Figure 1 inspected. Figure 1C shows a column attributed to source-named Dactylellina cionopagum; Figure 1G shows nematode capture by multiple columns. This morphology differs from the network, knob and constricting-ring comparators. Gene-family expansion and expression correlations do not establish a causal protein requirement for column formation. The cited adhesion-gene disruption experiment concerns Arthrobotrys oligospora, not this column-forming organism. Supplemental Methods were not retrieved completely; no strain identity or universal culture condition is inferred from this paper."
      },
      {
        "reference": "DOI:10.1111/lam.12557",
        "snippet": "Dactylellina cionopaga YMF1\u00b701472, producing adhesive columns",
        "notes": "Su et al. (2016), scientific Abstract, final sentence, directly retrieved from NCBI XML for PMID:26928264 at https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=26928264&retmode=xml. Abstract-only access: full Methods and figures were not retrieved. The abstract reports ammonia-associated trap induction in several fungi and names this culture as column-producing. The initial 11-bacterium assay and its detailed volatile-compound analysis concern A. oligospora, not eleven independent column-forming isolates. No universal ammonia requirement, dosage, effect size or molecular induction pathway is asserted. Strain provenance remains unresolved; this is qualified phenotype evidence, not a natural canonical exemplar."
      }
    ],
    "discussions": [
      {
        "discussion_id": "adhesive-column-scope-and-parent",
        "prompt": "Resolve a closer fungal trap-morphology parent.",
        "kind": "CURATION_TODO",
        "status": "RESOLVED",
        "rationale": "Phenotype METPO:1000059 is a broad parent. Existing mycelial growth traitmech:000074 explicitly concerns bacteria; hyphal anastomosis traitmech:000605 denotes fusion. Distinguish multicellular adhesive columns from unicellular knobs, interconnected net loops, nonconstricting rings and mechanically constricting rings. A generic hyphal branch, branched-shaped cell or nematophagous genus is not sufficient. Adhesive branch is not asserted as an exact synonym without resolving its usage boundaries. No exact synonyms, xrefs, SSSOM equivalences or organism-level disjointness are asserted. Neighboring scope exclusions are not unresolved exact groundings; their closer-parent questions remain open.",
        "posed_by": "codex",
        "posed_date": "2026-10-08",
        "resolved_date": "2026-10-13",
        "resolution_note": "Added fungal nematode-trap formation traitmech:000718 as the direct broader phenotype. The existing child definition entails specialized hyphal trap differentiation. This resolves only the parent gap; the historical scope contrasts, unasserted mappings, examples and separate mechanism questions remain applicable. Formation does not guarantee immediate capture. The column cell-count question is separately OPEN. Preserve the historical phenotype axiom and add METPO:1063400 SubClassOf METPO:1067100 on upstream adoption."
      },
      {
        "discussion_id": "adhesive-column-strains-and-mechanism",
        "prompt": "Resolve natural strain provenance and column-specific mechanisms.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Live NCBI https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=taxonomy&id=47266 resolves Dactylellina cionopaga at species rank, with Monacrosporium cionopagum and Dactylella cionopaga synonyms. It does not identify YMF1.01472 as a strain accession or establish its origin. The 2020 paper's cionopagum spelling and experimental strain must be reconciled before a canonical example is added; do not conflate strains across these papers. Formation, adhesion, capture, penetration and digestion are separate endpoints; formation alone does not guarantee capture in every condition. Protein-resolved causal graphs require column-specific perturbation/complementation evidence and taxon-paired accessions. Sequence features and expression correlations are not validated phenotype predictors. No mechanism is transferred from nets, knobs or rings; mechanism is deferred, not claimed absent.",
        "posed_by": "codex",
        "posed_date": "2026-10-08"
      },
      {
        "discussion_id": "adhesive-column-cell-count-scope",
        "prompt": "Reconcile serial-cell column scope with the supplement's broader cell-count description.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "The current definition retains serially arranged cells, supported by Ji's Introduction. The newly inspected 2020 Transparent Methods, Fungal strains, PDF page 12, describes columns containing one or more cells. Preserve this source-level difference pending review of single-cell columns versus knobs; do not silently broaden the child or make cell number the sole discriminator. Both usages fit fungal nematode-trap formation, so this question does not reopen the resolved parent gap. The supplement names YMF1.00569 from Deqin soil, not the 2016 paper's YMF1.01472. That provenance does not establish identity between the strains or a canonical example. The earlier evidence notes record limited supplement access at initial curation; this follow-up adds the inspected page without claiming a complete supplement audit.",
        "evidence": [
          {
            "reference": "DOI:10.1016/j.isci.2020.101057",
            "evidence_source": "full_text",
            "notes": "Transparent Methods, Fungal strains, PDF page 12; text and rendered page inspected at https://ars.els-cdn.com/content/image/1-s2.0-S258900422030242X-mmc1.pdf. Source-scope assessment, not an additional experiment."
          }
        ],
        "posed_by": "codex",
        "posed_date": "2026-10-13"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-08T13:53:29Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added fungal adhesive-column trap formation with two primary DOI sources and contiguous source-checked snippets. Ignored-and-hidden main/worktree/open-PR checks support 000681 and v557 block 1063400-1063499. Kept strain provenance and protein mechanism unresolved, distinguishing morphology from sequence correlations and induction observations. Existing records unchanged. Timestamp is observed UTC.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-13T13:31:56Z",
        "curator": "codex",
        "action": "REFINE_FUNGAL_TRAP_PARENT",
        "changes": "Refined traitmech:000681 below fungal nematode-trap formation traitmech:000718 and resolved its temporary parent discussion by definition-based inference. Preserved child identity, definition, evidence, examples, mechanism gaps and earlier history. Added a separate source-backed cell-count scope question after inspecting the 2020 supplement; no identity broadening.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000679",
    "label": "fungal adhesive-knob trap formation",
    "definition": "A morphological phenotype in which a fungus forms unicellular knobs at hyphal apices that serve as adhesive nematode traps.",
    "definition_source": "DOI:10.1128/AEM.01390-13",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000718"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1128/AEM.01390-13",
        "snippet": "The trap of M. haptotylum consists of a unicellular structure called a knob that develops at the apex of a hypha.",
        "notes": "Andersson et al. (2013), scientific Abstract; primary publisher HTML https://journals.asm.org/doi/10.1128/AEM.01390-13. Introduction, Culture Methods, relevant Results/Discussion and Conclusion, and actual Figure 1 were inspected. CBS 200.50 formed knobs in aerated liquid culture. Figure 1 shows residual attached knobs and isolated knobs after filtration, not a capture time course. Detachment is a culture observation, not a defining requirement. Proteomic and transcript changes do not establish causal functions of individual proteins; WSC adhesion roles remain hypotheses. Supplements were not used to assert protein mechanisms."
      },
      {
        "reference": "DOI:10.1016/j.femsle.2005.02.027",
        "snippet": "The adhesive knobs were produced frequently on nutritional agar plates even in the absence of challenging nematodes.",
        "notes": "Liu, Liu and Zhuang (2005), scientific Abstract, directly retrieved from the primary publisher https://academic.oup.com/femsle/article/245/1/99/483775 (minimal-article redirect). Abstract-only access: full Methods and figures were not retrieved. Orbilia querci material came from rotten Quercus wood in Huai-rou County, Beijing, and pure culture from ascospores. The authors report nematode capture with adhesive stalked knobs. Formation without added prey under these conditions excludes an obligatory prey-induction definition; neither medium nor stalk length is universal. The reported Dactylellina querci anamorph name is source terminology, not an independently verified current taxonomic equivalence."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1284197",
        "taxon_label": "Dactylellina haptotyla CBS 200.50",
        "reference": "DOI:10.1128/AEM.01390-13",
        "note": "Source-named Monacrosporium haptotylum CBS 200.50. Live NCBI https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=taxonomy&id=1284197 resolves rank strain, the exact label Dactylellina haptotyla CBS 200.50 and the historical name. Zhou et al. (2018), DOI:10.1080/23802359.2018.1507650, body paragraph 2, directly read primary XML at https://www.ebi.ac.uk/europepmc/webservices/rest/PMC7801010/fullTextXML, reports collection from a decaying leaf in a pond at Chelsea Physic Garden, London, by M.P. Peach in 1948. That genome study is strain-provenance support, not an independent knob-formation experiment. The unperturbed natural-origin strain example is qualified by the 2013 culture conditions, not every isolate or field biocontrol efficacy."
      }
    ],
    "discussions": [
      {
        "discussion_id": "adhesive-knob-scope-and-parent",
        "prompt": "Resolve a closer fungal trap-morphology parent.",
        "kind": "CURATION_TODO",
        "status": "RESOLVED",
        "rationale": "Phenotype METPO:1000059 is a broad parent. Existing mycelial growth traitmech:000074 explicitly concerns bacteria; hyphal anastomosis traitmech:000605 concerns fusion. Distinguish unicellular adhesive knobs from multicellular adhesive nets, adhesive columns, nonconstricting rings and mechanically constricting rings. Auxiliary cells and appressoria have different biological roles; a generic rounded hyphal tip or nematophagous genus is not sufficient. Detachment, a particular stalk length and nematode induction are not defining requirements. Formation alone does not demonstrate adhesion or successful capture in every condition. No exact synonyms, xrefs, SSSOM equivalences or organism-level disjointness are asserted; closer hierarchy remains open.",
        "posed_by": "codex",
        "posed_date": "2026-10-08",
        "resolved_date": "2026-10-13",
        "resolution_note": "Added fungal nematode-trap formation traitmech:000718 as the direct broader phenotype. The existing child definition entails specialized hyphal trap differentiation. This resolves only the parent gap; the historical scope contrasts, unasserted mappings, examples and separate mechanism questions remain applicable. Formation does not guarantee immediate capture. The column cell-count question is separately OPEN. Preserve the historical phenotype axiom and add METPO:1063200 SubClassOf METPO:1067100 on upstream adoption."
      },
      {
        "discussion_id": "adhesive-knob-mechanism",
        "prompt": "Separate knob morphogenesis from adhesion and infection mechanisms.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Sequence features and expression correlations alone do not establish a necessary or sufficient gene effect. A protein-resolved causal graph requires perturbation and complementation evidence, relevant remaining figures and supplements, and taxon-paired accessions. Formation, adhesion, capture, penetration and digestion remain separate endpoints. No universal lectin, WSC-domain protein or signaling-gene requirement is asserted; mechanism is deferred, not claimed absent. Taxonomic membership alone does not establish this phenotype.",
        "posed_by": "codex",
        "posed_date": "2026-10-08"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-08T11:29:45Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added fungal adhesive-knob trap formation with two independent primary DOI sources, contiguous snippets and a natural-origin strain example. Ignored-and-hidden main/worktree/open-PR checks support 000679 and v555 block 1063200-1063299. Distinguished abstract-only access and provenance-only support; separated morphology from sequence-derived mechanism hypotheses. Existing records unchanged. Timestamp is observed UTC.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-13T13:31:56Z",
        "curator": "codex",
        "action": "REFINE_FUNGAL_TRAP_PARENT",
        "changes": "Refined traitmech:000679 below fungal nematode-trap formation traitmech:000718 and resolved its temporary parent discussion by definition-based inference. Preserved child identity, definition, evidence, examples, mechanism gaps and earlier history.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000678",
    "label": "fungal adhesive-net trap formation",
    "definition": "A morphological phenotype in which a fungus forms three-dimensional networks of interconnected hyphal loops that serve as adhesive nematode traps.",
    "definition_source": "DOI:10.1371/journal.ppat.1002179",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000718"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1371/journal.ppat.1002179",
        "snippet": "A. oligospora forms adhesive networks to capture nematodes",
        "notes": "Yang et al. (2011), Author Summary, not the scientific abstract; primary XML at https://www.ebi.ac.uk/europepmc/webservices/rest/PMC3164635/fullTextXML. Introduction, trap-formation Results, strain/proteomics Methods, actual Figure 1 and relevant Text S1 supplemental Methods were inspected. Figure 1I shows connected hyphal loops; the paper describes complex three-dimensional networks. ATCC 24927 is the reference strain. Supplemental Methods distinguish nematode-extract induction on vegetative hyphae from subsequent live-nematode interaction assays. Formation, adhesion, capture, penetration and digestion are separate observations. No universal induction medium, prey species or capture efficacy is inferred. Proteomic correlations are not treated as a causal gene requirement."
      },
      {
        "reference": "DOI:10.3390/jof8070671",
        "snippet": "Captures nematodes with adhesive networks.",
        "notes": "Zhang et al. (2022; published 26 June), Results 3.2 Taxonomy, Arthrobotrys eryuanensis description; primary XML at https://www.ebi.ac.uk/europepmc/webservices/rest/PMC9317614/fullTextXML. Isolation/observation Methods, all six species descriptions and actual Figure 2 were inspected. Figure 2i shows the adhesive network, not time-resolved capture or adhesion kinetics. Holotype CGMCC3.19715 (Figure 2) and ex-type culture DLUCC 14-1 are distinguished by the authors. The material originated from freshwater sediment at Xihu Lake, Eryuan, Yunnan, China, collected 20 June 2014. Repeated spore transfers established pure cultures; corn meal agar observation at 26 degrees C with Panagrellus redivivus induced traps. These are study conditions, not universal requirements. The other newly described soil/sediment taxa provide context, not a universal genus-level phenotype assertion."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:756982",
        "taxon_label": "Orbilia oligospora ATCC 24927",
        "reference": "DOI:10.1371/journal.ppat.1002179",
        "note": "Source-named Arthrobotrys oligospora ATCC 24927. Yang et al. Methods identify the purchased ATCC strain as originally isolated from soil in Sweden. Live https://www.atcc.org/products/24927 independently confirms environmental soil origin and Sweden; it lists Arthrobotrys oligospora as the former name. Live NCBI https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=taxonomy&id=756982 resolves rank strain with the exact label Orbilia oligospora ATCC 24927. This unperturbed natural-origin reference strain is qualified by the reported induction conditions, not every isolate or field biocontrol efficacy. The 2011 paper's O. auricolor teleomorph wording is not imported as a current taxonomic equivalence or synonym."
      }
    ],
    "discussions": [
      {
        "discussion_id": "adhesive-net-scope-and-parent",
        "prompt": "Resolve a closer fungal trap-morphology parent.",
        "kind": "CURATION_TODO",
        "status": "RESOLVED",
        "rationale": "Phenotype METPO:1000059 is a broad parent. Existing mycelial growth traitmech:000074 explicitly concerns bacteria; hyphal anastomosis traitmech:000605 concerns cytoplasmic fusion, not trap identity. A Hartig net is a plant-root interface, not a prey trap. Exclude generic mycelial networks, biofilms, standalone adhesive rings, knobs and columns, mechanically constricting rings, and individual-cell ring shape. Adhesive nets are multicellular loop networks; generic nematophagy or a fungal genus is not an exact synonym. Network formation does not alone demonstrate adhesion or successful capture under all conditions. No exact synonyms, xrefs, SSSOM equivalences or organism-level disjointness are asserted; closer hierarchy remains open.",
        "posed_by": "codex",
        "posed_date": "2026-10-08",
        "resolved_date": "2026-10-13",
        "resolution_note": "Added fungal nematode-trap formation traitmech:000718 as the direct broader phenotype. The existing child definition entails specialized hyphal trap differentiation. This resolves only the parent gap; the historical scope contrasts, unasserted mappings, examples and separate mechanism questions remain applicable. Formation does not guarantee immediate capture. The column cell-count question is separately OPEN. Preserve the historical phenotype axiom and add METPO:1063100 SubClassOf METPO:1067100 on upstream adoption."
      },
      {
        "discussion_id": "adhesive-net-mechanism",
        "prompt": "Separate network morphogenesis from adhesion and predation mechanisms.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "The 2011 genomic/proteomic study contains mechanistic leads, but expression changes alone do not establish necessary or sufficient gene effects. Protein-resolved causal graphs require perturbation/complementation evidence, relevant remaining figures/supplements and taxon-paired accessions. Formation, adhesion, capture, penetration and digestion must remain separate endpoints. No universal lectin, signaling or fusion-gene requirement is asserted; mechanism is deferred, not claimed absent. Sequence annotation or taxonomic membership alone does not establish this phenotype.",
        "posed_by": "codex",
        "posed_date": "2026-10-08"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-08T10:25:48Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added fungal adhesive-net trap formation with two primary DOI sources, source-checked snippets and a natural-origin strain example. Ignored-and-hidden main/worktree/open-PR checks support 000678 and v554 block 1063100-1063199. Separated morphology from adhesion/capture and sequence-derived mechanism hypotheses; existing records unchanged. Corrected draft holotype/ex-type provenance before generation (#1825). Timestamp is observed UTC.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-13T13:31:56Z",
        "curator": "codex",
        "action": "REFINE_FUNGAL_TRAP_PARENT",
        "changes": "Refined traitmech:000678 below fungal nematode-trap formation traitmech:000718 and resolved its temporary parent discussion by definition-based inference. Preserved child identity, definition, evidence, examples, mechanism gaps and earlier history.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000659",
    "label": "fungal appressorium formation",
    "definition": "A morphological phenotype in which a fungus forms specialized surface-associated penetration structures called appressoria.",
    "definition_source": "DOI:10.3390/jof5030072",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.3390/jof5030072",
        "snippet": "Here, we report on the ability of many saprotrophs from a large range of taxa to produce appressoria on cellophane.",
        "notes": "Demoor, Silar and Brun (2019), PMID:31382649, PMC6787622; scientific abstract retrieved as full-text XML. Introduction, Methods, Results and the broad-definition Discussion paragraph were read; actual Figures 2 and 6 and supplementary Table S1 were inspected. The authors explicitly include structures previously called appressorium-like under a broad penetration-structure usage, including unicellular and compound forms. The principal assay used mycelial implants on cellophane over M2 medium at 27 C, with observations after 3-15 days. It is not an in-host assay or a universal fungal prevalence estimate. Contact and growth reorientation without penetration were distinguished from appressoria. Negative results apply to the tested conditions, not to entire clades. Table S1 identifies strains but does not independently establish natural provenance for all of them; they are not added as canonical examples."
      },
      {
        "reference": "DOI:10.1371/journal.ppat.1002514",
        "snippet": "an appressorium is already developing in Guy11 strain whereas no infection cell development occurs in an isogenic \u0394pmk1 mutant",
        "notes": "Soanes et al. (2012), PMID:22346750, PMC3276559; Results describing Figure 1B, not the Author Summary. Actual Figure 1 and the fungal-strain/growth Methods were inspected. Wild-type Guy11 and the deletion mutant were compared at four hours; the Guy11 series also includes 6, 8, 14 and 16 hours. The Methods describe plastic coverslips and 1,16-hexadecanediol, whereas the Results describing Figure 1A name a hydrophobic glass slide. This within-article surface discrepancy is unresolved; neither description is silently substituted for the other or treated as a universal surface requirement. Natural-isolate provenance is checked separately in the canonical-example note. The observed formation phenotype is not inferred from RNA expression. Neither these transcript profiles nor one deletion establish a universal protein-resolved mechanism across fungi. Other figures and transcript-data supplements were not inspected."
      },
      {
        "reference": "DOI:10.1186/1741-7007-6-9",
        "snippet": "blocking of the cell cycle did not prevent spore germination and appressoria formation.",
        "notes": "Nesher, Barhoom and Sharon (2008), PMID:18275611, PMC2276476; scientific abstract Results, read directly in full-text XML. The Methods name Colletotrichum gloeosporioides f. sp. aeschynomene 3.1.3 wild-type and transgenic strains; germination and onion-epidermis assays were read. This result separates formation from a universal mitosis requirement. It does not show unrestricted post-penetration growth under cell-cycle inhibition. Full result figures, natural strain provenance and current species-complex assignment were not inspected or resolved, so this is qualified evidence, not a canonical taxon assignment or a universal autophagy/cell-cycle claim."
      },
      {
        "reference": "DOI:10.1111/nph.13931",
        "snippet": "Here we identify an appressorium\u2010like structure, which we call an expressorium",
        "notes": "Becker et al. (2016), PMID:26991322, PMC5069595; the article's scientific Summary and the Results paragraph distinguishing intrinsecus/extrinsecus terminology were read directly in full-text XML. The internal structure enables Epichloe festucae to exit a leaf. The authors propose expressorium to distinguish it from an external appressorium, while noting an intrinsecus-appressorium convention. This is terminology-boundary evidence, not an asserted exact synonym or additional canonical example. Figures, movies, supplements and strain provenance were not inspected; no Nox mechanism or turgor measurement is inferred from this quotation."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:318829",
        "taxon_label": "Pyricularia oryzae",
        "reference": "DOI:10.1371/journal.ppat.1002514",
        "note": "Wild-type Guy11 in Soanes et al. (2012), Figure 1A-B and Methods, directly forms appressoria under the tested in-vitro induction conditions. NCBI Taxonomy resolves Pyricularia oryzae at species rank and lists the paper's Magnaporthe oryzae name as a synonym. Independent primary population-study Methods at https://doi.org/10.5423/PPJ.NT.04.2013.0042 (PMID:25288972, PMC4174813) explicitly identify Guy11 as a rice-pathogenic isolate from French Guiana and distinguish it from laboratory crossing derivatives. That passage was read directly; its cited original 1988 isolation study was not retrieved. This provenance citation is not counted as an independent appressorium observation. The example concerns Guy11, not its engineered deletion mutant, strain 70-15, every strain, or every environmental condition."
      }
    ],
    "discussions": [
      {
        "discussion_id": "fungal-appressorium-scope-and-mapping",
        "prompt": "Reconcile broad appressorium usage and neighboring structures.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Retain phenotype METPO:1000059 rather than plant pathogen METPO:1004003, black pigmented METPO:1003022 or thigmotropism traitmech:000594. Formation is neither disease causation nor generic adhesion or contact-directed growth. Demoor et al. (2019) explicitly use a broad appressorium umbrella for saprotrophic penetration structures and compound infection cushions; preserve this source attribution rather than silently imposing a single-celled, melanized or germ-tube-only definition. Becker et al. (2016) distinguish expressoria from external appressoria despite the intrinsecus convention. Whether to include that exit structure or propose narrower subclasses remains unresolved; no exact synonym is asserted. QuickGO resolves GO:0075016 as a host-associated biological process, not an exact organismal phenotype covering the saprotrophic observations, so xrefs and SSSOM are omitted. Research-report appressorium mentions describe candidate material structures, not an existing exact formation-trait node that can simply be regrounded.",
        "posed_by": "codex",
        "posed_date": "2026-10-07"
      },
      {
        "discussion_id": "fungal-appressorium-function-and-mechanism",
        "prompt": "Separate formation, functional penetration and regulatory mechanisms.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Formation does not guarantee successful penetration, host entry, invasion or disease. Do not require one shape, cell number, pigmentation, turgor level, surface chemistry or nutritional regime. Cellophane penetration is not evidence of natural-host infection or of a functional haustorium. The Colletotrichum cell-cycle results and the Guy11 Pmk1 comparison do not support a universal mitosis, autophagy or kinase dependency. A causal graph awaits review of primary perturbation/complementation experiments, remaining figures and supplements, and taxon-paired protein accessions. Transcriptional association or possession of a candidate gene is not proof of this formation phenotype. Keep the unresolved 3.1.3 provenance/species assignment and all unverified survey strains out of canonical examples.",
        "posed_by": "codex",
        "posed_date": "2026-10-07"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-07T05:29:43Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added fungal appressorium formation with four primary-source snippets, a provenance-qualified Guy11 example and explicit morphology, terminology and mechanism boundaries. Ignored-and-hidden searches found only research leads, not an exact live trait. Reserved METPO:1061200 in v535; existing records unchanged and protein-level causal mechanism deferred.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-07T05:45:55Z",
        "curator": "codex",
        "action": "EVIDENCE_CORRECTION",
        "changes": "Addressed #1774: attributed the Guy11 plastic-coverslip description to Methods and the conflicting hydrophobic-glass description to Results. Left the surface discrepancy unresolved; the verbatim snippet, formation phenotype and qualified canonical example remain unchanged.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000664",
    "label": "fungal arbuscule formation",
    "definition": "A morphological phenotype in which a fungus forms highly branched hyphal structures, called arbuscules, within living plant cells during arbuscular mycorrhizal symbiosis.",
    "definition_source": "DOI:10.3390/plants8060142",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1104/pp.109.141879",
        "snippet": "In the arbuscular mycorrhizal symbiosis, the fungal symbiont colonizes root cortical cells, where it establishes differentiated hyphae called arbuscules.",
        "notes": "Pumplin and Harrison (2009), PMID:19692536, PMC2754618; scientific-abstract sentence checked against Europe PMC and https://academic.oup.com/plphys/article/151/2/809/6108581. Main text, Figures 1-7 and supplementary Figures S1-S9 were inspected; Figure 7 is a model. The supplementary movie was not viewed. Glomus versiforme colonized transgenic Medicago truncatula A17 roots. Host fluorescent markers distinguish periarbuscular membrane domains; they are not fungal protein anchors or nutrient-flux measurements. The host-derived membrane separates fungal branches from host cytoplasm. Fungal isolate provenance was not established, so this experiment is not a natural canonical example."
      },
      {
        "reference": "DOI:10.3390/plants8060142",
        "snippet": "All AMF strains formed arbuscules in the parenchyma cells of the mycothalli",
        "notes": "Kobae et al. (2019), PMID:31151150, PMC6631804; Results 2.2 clause. Primary text and Figures 1-4 on pages 1-11 of https://rakuno.repo.nii.ac.jp/record/6472/files/R-2020-321_kobae.pdf and all four supplementary pages were inspected. Liverwort Marchantia paleacea thallus observations support plant-cell, not root-only, scope. Methods 3.2 and Figure S1 identify cultures separately from unidentified field-root trapping. For DAOM197198, Results 2.2 reports arbuscules at 18 dps and none until 14 dps; S2A instead describes rhizoid-only hyphae at 18 dps and S2B arbuscules at 28 dps. Onset remains unresolved. Pigmentation alone is insufficient. Figure 4C shows root arbuscules, although Results points to 4B and uses dps instead of the caption's dpi. Figure 3 and Methods 3.6 disagree on phylogenetic method; no independent fungal species assignment from mixed rDNA is asserted."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:937382",
        "taxon_label": "Entrophospora etunicata",
        "reference": "DOI:10.3390/plants8060142",
        "note": "MAFF520053 (H1-1), reported as Claroideoglomus etunicatum in Methods 3.2 and actual Figure S1, forms arbuscules in Marchantia paleacea thallus cells. NARO's collection record https://www.gene.affrc.go.jp/databases-micro_search_detail_en.php?maff=520053 lists soybean-field soil, Tokyo, October 1987, H. Hirata; it was deposited as Glomus etunicatum. These separate fields support this culture's field-isolate origin, not a trait evidence snippet. NCBI Taxonomy resolves species 937382 to Entrophospora etunicata, with Claroideoglomus etunicatum as a homotypic synonym; name correspondence is not independent reidentification of the culture."
      }
    ],
    "discussions": [
      {
        "discussion_id": "fungal-arbuscule-scope-and-hierarchy",
        "prompt": "Resolve the phenotype parent and attributed haustorium umbrella.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Use active phenotype METPO:1000059; METPO:1000198 mycorrhization is obsolete. Mutualism traitmech:000041 requires reciprocal benefit, which formation alone does not establish. Direct QuickGO checks identify GO:0085041 arbuscule as a cellular component below GO:0085035 haustorium. This attributed umbrella classification is not silently rejected: microbial haustorium formation traitmech:000663 and this formation phenotype are not asserted equivalent, disjoint or in a subclass relation. GO's root-cortex wording is narrower than the liverwort observations, and a structure is not an organism-level phenotype. No exact xrefs, synonyms or SSSOM mappings are asserted. Plant cells includes thallus cells; within-cell location does not mean free in host cytoplasm.",
        "posed_by": "codex",
        "posed_date": "2026-10-07"
      },
      {
        "discussion_id": "fungal-arbuscule-formation-and-function",
        "prompt": "Separate formation, timing and nutrient-exchange mechanisms.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Do not infer nutrient flux, obligatory benefit, universal onset or lifespan from these morphology observations. Keep the 2019 main-text/supplement timing discrepancy open. The 2009 host membrane markers do not identify a fungal formation pathway. A protein-resolved causal graph needs direct perturbation evidence and authority-verified protein examples; it is deferred, not claimed absent. Extraradical branching alone does not satisfy this intracellular morphology definition.",
        "posed_by": "codex",
        "posed_date": "2026-10-07"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-07T13:21:20Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added fungal arbuscule formation with two primary DOI citations, verbatim snippets and a culture-qualified fungal example. Ignored-and-hidden novelty and main/worktree/open-PR reservation checks support local ID 000664 and v540 block 1061700-1061799. Kept host markers, timing disagreements and ontology scope explicit; protein-level mechanism deferred.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000671",
    "label": "fungal auxiliary cell formation",
    "definition": "A morphological phenotype in which an arbuscular mycorrhizal fungus forms auxiliary cells, typically clustered hyphal swellings, on mycelium outside plant tissue.",
    "definition_source": "https://www.mycorrhizas.info/vam.html",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "https://www.mycorrhizas.info/vam.html",
        "snippet": "Hyphae of Scutellospora and Gigaspora species produce clustered swellings with spines or knobs called auxiliary cells.",
        "notes": "Mark Brundrett, Mycorrhizal Associations, version 2 (2008), C.1 and glossary F, directly read. Terminology support, not independent experimental replication. The glossary describes external hyphae and says ornamentation is frequent, not obligatory. Its unnamed Scutellospora soil-hyphae micrograph and separate line illustration were actually viewed; neither establishes a named culture example. Historical auxiliary-body, external-vesicle and accessory-body labels name structures, not automatically exact organismal-trait synonyms."
      },
      {
        "reference": "DOI:10.1111/j.1469-8137.2007.02345.x",
        "snippet": "In G.\u00a0margarita, auxiliary cells were formed on germ tubes",
        "notes": "Kuga et al. (2008), PMID:18194149; Results clause before Elemental analyses, directly read in publisher full text. Methods identify MAFF520054. The Results point to Figure 3a/i; captions were read but actual paper images and supplements were not inspected. The HTML temperature glyph renders as 25\u00d7C and remains unresolved rather than normalized to degrees. Organelle localization and nonspecific DAPI fluorescence do not establish a formation mechanism or a universal storage function."
      },
      {
        "reference": "DOI:10.1017/S0953756203008761",
        "snippet": "Isolated auxiliary cells were shown to exhibit hyphal re-growth, but not root colonization, either in situ or in vitro.",
        "notes": "Declerck et al. (2004), PMID:15035509; scientific abstract retrieved directly from Europe PMC. It follows extraradical mycelium, auxiliary cells and spores of Scutellospora reticulata in root-organ culture. Ri T-DNA transformation concerns carrot roots, not an engineered fungus. Regrowth without root colonization is conditional on the tested assays, not universal noninfectivity. Resource reallocation is the authors' interpretation, not a direct flux measurement. Full paper, images and isolate provenance were not inspected; no additional canonical culture is assigned."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:4874",
        "taxon_label": "Gigaspora margarita",
        "reference": "DOI:10.1111/j.1469-8137.2007.02345.x",
        "note": "MAFF520054, Results and Fungal materials of Kuga et al. (2008): auxiliary cells on germ tubes. Methods describe white-clover propagation, membranes over 1% soil agar, 10 days in darkness and a separate nutrient-agar staining treatment; cultivation duration is not formation onset. The temperature glyph and actual Figure 3 images remain unverified. The directly retrieved NARO record https://www.gene.affrc.go.jp/databases-micro_search_detail_en.php?maff=520054 lists designation C, soybean-field soil, Saitama Japan, isolator S. Ban and depositor/identifier M. Saito as separate fields. These establish field-isolate provenance, not a composite quote or independent trait evidence. NCBI Taxonomy resolves species 4874, not culture reidentification. Table 1 of DOI:10.1264/jsme2.ME25040 retains C/520054; primer-dependent ASVs, including above-genus assignments, are not culture counts or proof of contamination, identity or this phenotype. Its figures and supplements were not inspected. This example does not assert the response of all strains or conditions."
      }
    ],
    "discussions": [
      {
        "discussion_id": "fungal-auxiliary-cell-scope",
        "prompt": "Resolve a closer parent and structure-versus-trait terminology.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Use active phenotype METPO:1000059 below quality METPO:1000188; mycorrhization METPO:1000198 is obsolete. Arbuscular mycorrhizal identifies the fungal context, not a requirement for current host contact: the germ-tube observation is outside plant tissue. Internal mycorrhizal vesicle formation traitmech:000670, arbuscule formation traitmech:000664 and branched absorbing structure formation traitmech:000665 denote different architectures or locations. Not every hyphal swelling is an auxiliary cell; neither fungal chlamydospore formation traitmech:000658 nor membrane-vesicle formation is an exact substitute. External-vesicle and accessory-body usages remain attributed structure labels; no exact synonyms, xrefs, SSSOM equivalents or disjoint organism-level phenotypes are asserted. Typical clustering does not impose a minimum count on every observation.",
        "posed_by": "codex",
        "posed_date": "2026-10-07"
      },
      {
        "discussion_id": "fungal-auxiliary-cell-function",
        "prompt": "Separate auxiliary-cell morphology, counting and function.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Keep individual compartments, clusters, hyphal biomass and spore counts distinct. Morphology or lipid content does not establish universal nutrient transfer, propagule function, lifespan, wall-layer number or obligate host dependence. Hyphal regrowth and root colonization are different endpoints. A protein-resolved formation graph is deferred pending direct causal perturbations and authority-verified fungal protein examples; it is not claimed biologically absent. Host transformation and sequence-profile assignments alone do not demonstrate the fungal formation mechanism.",
        "posed_by": "codex",
        "posed_date": "2026-10-07"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-08T02:02:02Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added fungal auxiliary cell formation with two primary DOI sources, attributed morphology terminology, three verbatim snippets and a culture-qualified MAFF520054 example. Ignored-and-hidden novelty and current-main/worktree/complete-open-PR reservation checks support 000671 and v547 block 1062400-1062499. Kept external swellings separate from internal vesicles, BAS, spores, function and protein mechanism; existing records unchanged.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000665",
    "label": "fungal branched absorbing structure formation",
    "definition": "A morphological phenotype in which an arbuscular mycorrhizal fungus forms localized, dichotomously branched groups of progressively finer hyphae, called branched absorbing structures, on its extraradical runner hyphae.",
    "definition_source": "DOI:10.1046/j.1469-8137.1998.00199.x",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1046/j.1469-8137.1998.00199.x",
        "snippet": "small groups of dichotomous hyphae formed by the extraradical mycelium of arbuscular mycorrhizal (AM) fungi.",
        "notes": "Bago et al. (1998), New Phytologist 139:375-388; contiguous defining phrase from the Summary, read in the primary publisher PDF. The publisher's later online date is not the study year. Methods, Results and selected Discussion passages were read; actual figures were not inspected after screenshot/download failures. DAOM197198, named Glomus intraradices in this paper, formed BAS with non-transformed tomato cv. Vendor roots. Results distinguish progressively finer dichotomous branches from aborted short branches. Formation took about seven days under the tested conditions, not a universal lifespan. Some spore-associated BAS persisted and produced spores. Negative axenic and unsuccessful monoxenic cultures constrain these experiments, not every possible asymbiotic condition. The proposed absorptive role is not a direct uptake assay."
      },
      {
        "reference": "DOI:10.1093/pcp/pcz122",
        "snippet": "highly branched hyphae called branched absorbing structures (BAS) differentiate on the runner hyphae",
        "notes": "Kameoka et al. (2019), PMID:31241164; Introduction clause before the Figure 1 citation, exact-matched in directly retrieved publisher HTML. Abstract, Introduction, Results, Discussion and Methods were read. Actual Figure 1C/G and its caption were inspected: six-week Rhizophagus irregularis DAOM197198 carrot hairy-root cocultures supply direct BAS morphology evidence. The RNA-seq comparison is not a direct uptake assay or causal perturbation. Runner-hypha and spore samples contained some BAS; negligible contamination influence was the authors' inference, not measured absence. Their historical no-direct-uptake-evidence statement is not a present-day knowledge claim. Remaining figure images and supplementary spreadsheet contents were not inspected."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:588596",
        "taxon_label": "Rhizophagus irregularis",
        "reference": "DOI:10.1093/pcp/pcz122",
        "note": "DAOM197198 from Premier Tech in six-week carrot hairy-root coculture, Methods and actual Figure 1C/G. The Canadian GINCO catalogue https://agriculture.canada.ca/en/agricultural-science-and-innovation/agriculture-and-agri-food-research-centres-and-collections/glomeromycota-vitro-collection-ginco/catalogue-arbuscular-mycorrhizal-fungi-strains-available-glomeromycetes-vitro-collection lists DAOMC197198, herbarium DAOM197198/181602, MUCL43194, Pont-Rouge in Quebec, a tree plantation, and collectors/isolators C. Plenchette and V. Furlan. These collection fields support field-isolate origin and are not a synthesized evidence snippet. NCBI Taxonomy confirms species 588596 and its strain 747089, Rhizophagus irregularis DAOM 181602=DAOM 197198. The transformed carrot host does not imply an engineered fungus. This is a culture-qualified observation, not independent reidentification or evidence for every strain and condition."
      }
    ],
    "discussions": [
      {
        "discussion_id": "fungal-bas-scope-and-hierarchy",
        "prompt": "Resolve a closer parent while preserving BAS morphology scope.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Use phenotype METPO:1000059. Branched shaped METPO:1000687 and filament shaped METPO:1000674 classify cell shape, not this differentiated extraradical architecture. Mycelial growth traitmech:000074 is explicitly bacterial. Fungal arbuscule formation traitmech:000664 concerns structures within living plant cells; the historical arbuscule-like structures name does not make BAS intracellular arbuscules. Appressorium formation traitmech:000659 concerns penetration structures, hyphal anastomosis traitmech:000605 fusion, and pseudohyphal growth traitmech:000653 budding-cell chains. Bago et al. also distinguish pre-infection fan-like structures and aborted short branches. No exact synonyms, structure xrefs, SSSOM equivalences or disjoint-organism claims are asserted. A closer morphology parent needs upstream review.",
        "posed_by": "codex",
        "posed_date": "2026-10-07"
      },
      {
        "discussion_id": "fungal-bas-formation-and-function",
        "prompt": "Separate formation from absorption, host dependence and mechanism.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Absorbing is the established structure name, not a required flux measurement. Do not infer mineral uptake, obligatory host contact, universal timing, inevitable degeneration or sporulation from morphology. Bago et al.'s host-dependence interpretation describes their tested media; later asymbiotic growth work DOI:10.1073/pnas.2006948117 remains a BAS-specific full-text/figure follow-up, not counted BAS evidence here. Transcriptional associations in Kameoka et al. do not identify a causal formation pathway. Their in vitro host system also does not establish expression patterns in soil-grown intact plants. A protein-resolved graph is deferred pending direct perturbation evidence and authority-verified protein anchors; it is not claimed biologically absent.",
        "posed_by": "codex",
        "posed_date": "2026-10-07"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-07T14:21:36Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added fungal BAS formation with two primary DOI-backed snippets and a culture/provenance-qualified DAOM197198 example. Ignored-and-hidden novelty and main/worktree/open-PR checks support local ID 000665 and v541 block 1061800-1061899. Kept morphology separate from uptake, host-dependence extrapolation and causal mechanisms.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000658",
    "label": "fungal chlamydospore formation",
    "definition": "A morphological phenotype in which a fungus forms enlarged, thick-walled cells called chlamydospores.",
    "definition_source": "DOI:10.1038/s41467-020-20010-9",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/s41467-020-20010-9",
        "snippet": "Chlamydospores are enlarged thick-walled cells produced within hyphae or at hyphal tips",
        "notes": "Hernandez-Cervantes et al. (2020), PMID:33277479, PMC7718266, Introduction; this contiguous clause supplies morphological terminology, not independent experimental replication across all fungi. Abstract, Introduction and selected Methods were read directly. Mechanistic panels and supplementary strain tables were not inspected, so no universal Rme1 dependence or protein-resolved causal graph is asserted. The definition does not impose a survival function."
      },
      {
        "reference": "DOI:10.1099/13500872-141-7-1507",
        "snippet": "These organisms were germ-tube-positive and produced abundant chlamydospores which were frequently arranged in triplets or in contiguous pairs.",
        "notes": "Sullivan et al. (1995), PMID:7551019, original Candida dubliniensis description; scientific abstract retrieved directly from Europe PMC. These organisms refers to the recovered oral clinical isolates. This is primary phenotype and natural-isolate provenance at cohort level, not evidence that chlamydospores were observed in patient tissue. Full Methods and strain tables were not inspected; no named culture, universal arrangement or response of every strain is inferred."
      },
      {
        "reference": "DOI:10.3389/fmicb.2016.01697",
        "snippet": "Both species produced typically high amounts of chlamydospores on rice and CM agar (chlamydospore index [CI] 3).",
        "notes": "Bottcher et al. (2016), PMID:27833594, PMC5081361, Figure 1 caption. Actual Figure 1 micrographs, Methods and Tables 1-2 were inspected. The strains are C. albicans SC5314 and C. dubliniensis Wu284, rendered with an umlaut in the source; CM means corn meal. Cultures were examined after seven days at 27 C in darkness. CI is an ordinal 0-3 score, not a cell percentage. Nutrient effects differ by strain and medium; no universal starvation or darkness requirement is inferred. Independent provenance of these laboratory strains was not checked, so they are not the canonical example."
      },
      {
        "reference": "DOI:10.1111/j.1567-1364.2009.00533.x",
        "snippet": "Mycelium-attached and purified chlamydospores rapidly lost their viability in water and when subjected to dry stress",
        "notes": "Citiulo et al. (2009), PMID:19538507, scientific abstract retrieved directly from Europe PMC and checked against publisher text. The complete result clause is quoted before the authors' interpretation about long-term storage. It argues against assuming durable dormancy for these Candida cells, not against survival roles in every fungus. The publisher Introduction and selected Methods were also read; the Introduction calls Candida budding blastic conidiogenesis and explains chlamydoconidia terminology. Formation is kept separate from subsequent germination and viability."
      },
      {
        "reference": "https://research.fs.usda.gov/treesearch/30277",
        "snippet": "Cell walls of mature P. ramorum chlamydospores are thicker than reported for other Phytophthora species, although thin-walled chlamydospores are also formed.",
        "notes": "Smith and Hansen (2008), USDA proceedings report, pp. 451-454; directly retrieved repository abstract. The repository labels it Informally Refereed. NCBI Taxonomy confirms Phytophthora ramorum is an oomycete in Stramenopiles, not Fungi. This is terminology-boundary evidence, not a fungal observation: the fungal qualifier avoids silently including the report's thin-walled structures in a thick-walled fungal definition. Full report and figures were not inspected; no canonical oomycete or universal wall-thickness cutoff is asserted."
      },
      {
        "reference": "DOI:10.1007/s10886-012-0171-1",
        "snippet": "two species of Fusarium formed chlamydospores from hyphae, germ tubes, or inside the conidia within 2 days.",
        "notes": "Li et al. (2012), PMID:22932866, scientific abstract retrieved directly from Europe PMC. This result concerns sub-MIC FA17 fengycin treatment of two Fusarium species, not untreated formation in every fungus. It establishes a conidial route excluded by the initial hypha-only draft definition (#1772). The abstract separately calls structures in 17 other fungi chlamydospore-like; those are not promoted to equivalent phenotypes. Full Methods, figures and strain provenance were not inspected, so no additional canonical strain or causal chemical mapping is asserted."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:42374",
        "taxon_label": "Candida dubliniensis",
        "reference": "DOI:10.1099/13500872-141-7-1507",
        "note": "Species-level example from naturally recovered oral clinical isolates in the original 1995 description. The primary scientific abstract at https://doi.org/10.1099/13500872-141-7-1507 reports abundant chlamydospore production. This supports cohort-level isolate provenance, not a particular named laboratory culture, an inferred wild-type or GMO status, or chlamydospores in patient tissue. Full strain tables and Methods were not inspected; the observation is not assigned to CD36 or to every strain or condition."
      }
    ],
    "discussions": [
      {
        "discussion_id": "fungal-chlamydospore-scope-and-hierarchy",
        "prompt": "Resolve conidiation, dormancy and process-ontology mappings.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Retain phenotype METPO:1000059. Sporulation METPO:1000870 and spore forming METPO:1000871 explicitly concern endospores. Citiulo et al. (2009) call Candida chlamydospore budding blastic conidiogenesis; that source-attributed usage does not settle whether this broader fungal class should be below fungal conidiation traitmech:000657. Do not equate it with ordinary pseudohyphal growth or any hyphal swelling. Closed upstream issue https://github.com/berkeleybop/metpo/issues/67 suggested chlamydospores under resting spores; the Candida viability evidence does not support that as a universal function. GO:0001410 was resolved through QuickGO: it is a biological process and its survival/endogenous-formation wording also needs scope review. Leave exact synonyms and xrefs unset rather than asserting equivalence. The four obsolete METPO chlamydospore terms are material classes, not active organismal phenotypes.",
        "posed_by": "codex",
        "posed_date": "2026-10-07"
      },
      {
        "discussion_id": "fungal-chlamydospore-function-and-mechanism",
        "prompt": "Separate morphological identification from survival and regulation.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Wall thickening alone does not establish long-term survival, dormancy, infectivity or a dispersal function. Preserve species-, strain-, age- and medium-specific endpoints. Do not require one arrangement, nucleus count, nutrient trigger or illumination regime. The USDA Phytophthora report documents a nonfungal terminology boundary, not additional fungal replication. Formation and later germination are different observations. A causal graph is deferred pending reconciliation of primary perturbations and supplementary strain identities with natural-host provenance and taxon-paired protein accessions. Gene possession alone is not a chlamydospore phenotype. Li et al. (2012), PMID:22932866, report formation inside conidia as well as from hyphae and germ tubes under the tested treatment. Issue #1772 corrected the initial hypha-only restriction; retain formation-site neutrality and do not promote the separately reported chlamydospore-like structures to confirmed chlamydospores.",
        "posed_by": "codex",
        "posed_date": "2026-10-07"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-07T04:23:14Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added fungal chlamydospore formation with five directly checked snippets, a cohort-qualified Candida dubliniensis example and explicit terminology, hierarchy and function limits. Ignored-and-hidden searches found no exact live record. Reserved METPO:1061100 in v534; existing records unchanged and causal graph deferred.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-07T04:34:28Z",
        "curator": "codex",
        "action": "REVISED_DEFINITION",
        "changes": "Addressed #1772: removed the hypha-only formation-site restriction, added the primary Fusarium conidial-route counterexample and retained treatment and source-access limits. Preserve the initial curation event and canonical example.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000657",
    "label": "fungal conidiation",
    "definition": "A reproductive phenotype in which a fungus produces nonmotile asexual propagules called conidia through outgrowth from conidiogenous cells or conversion of pre-existing hyphal cells.",
    "definition_source": "DOI:10.2336/nishinihonhifu.40.1083",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.2336/nishinihonhifu.40.1083",
        "snippet": "produce asexual, nonmotile and usually deciduous propagules (conidia) by de novo growth from, or conversion of a fertile hypha (conidiogenous cell).",
        "notes": "Cole (1978), publisher abstract directly retrieved at https://www.jstage.jst.go.jp/article/nishinihonhifu/40/6/40_6_1083/_article/-char/en. The article is labeled Mini Review and supports terminology, not independent experimental replication. Its historical Deuteromycetes classification is not imposed on the trait. Both new outgrowth and conversion of existing cells are retained; detached spores, an aerial stalk and one spore shape are not universal requirements. The exact DOI query returned no Europe PMC records. Full text and figures were not inspected."
      },
      {
        "reference": "DOI:10.1101/gad.3.4.559",
        "snippet": "The filamentous fungus Neurospora crassa responds to nutrient deprivation and dessication by producing asexual spores, or conidia.",
        "notes": "Springer and Yanofsky (1989), PMID:2524423, scientific abstract retrieved directly from Europe PMC. The source spelling dessication is preserved. Primary scanning-electron microscopy and fluorescent-probe study of wild-type and morphological mutants: the abstract describes apical proconidial budding, septation and disarticulation. Early chains can return to hyphal growth; later chains are committed. These are source-reported observations, not personally inspected figures. Full Methods, figures and independent strain provenance were not read, so no canonical Neurospora strain or universal nutrient/stress requirement is asserted."
      },
      {
        "reference": "DOI:10.1016/j.simyco.2017.09.001",
        "snippet": "H\u2013I. Conidiophores, conidiogenous cells and conidia.",
        "notes": "Woudenberg et al. (2017), PMID:29158610, PMC5679026, Figure 7 caption, Cephalotrichum lignatile CBS 209.63. The actual panels were inspected together with Taxonomy and Methods. H-I show the named structures; J shows conidia. The description reports conidia in basipetal chains. Microscopic descriptions use SNA cultures after 14 days at 25 C in darkness; A-C instead show OA, MEA and DG18 colonies. These are descriptive morphology observations, not time-lapse proof of each developmental transition."
      },
      {
        "reference": "PMID:9199700",
        "snippet": "The developmental cycle of S. griseus starts and ends as a conidium.",
        "notes": "Szabo et al. (1997), Phenotypic heterogeneity of the progeny of Streptomyces griseus conidia; scientific abstract retrieved directly from Europe PMC by PMID. This is terminology boundary evidence, not a fungal observation: the paper uses conidium for a bacterial reproductive cell. It motivates the fungal label qualifier without equating bacterial and fungal developmental mechanisms. No taxon mapping, full-text inspection or bacterial canonical example is asserted."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:2041050",
        "taxon_label": "Cephalotrichum lignatile",
        "reference": "DOI:10.1016/j.simyco.2017.09.001",
        "note": "Ex-type culture CBS 209.63. Figure 7H-J and the primary taxonomic description document conidiogenous structures and conidia in basipetal chains. Microscopic descriptions use SNA after 14 days at 25 C in darkness. Specimen examined and Table 1 at https://pmc.ncbi.nlm.nih.gov/articles/PMC5679026/ identify Hennebert's 1959 isolate from timber in a cave at Han-sur-Lesse, Belgium. This is primary isolate provenance, not an inferred wild-type or GMO status. The observation does not imply production at every life stage or condition."
      }
    ],
    "discussions": [
      {
        "discussion_id": "fungal-conidiation-scope-and-hierarchy",
        "prompt": "Review a reproductive phenotype parent and qualified mappings.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Retain phenotype METPO:1000059. Sporulation METPO:1000870 and spore forming METPO:1000871 concern endospores, whereas mycelial growth traitmech:000074 concerns bacterial hyphae. The four obsolete METPO conidium/conidia classes denote material entities, not an active organismal phenotype. PMID:9199700 documents bacterial conidium usage, so the fungal qualifier is intentional. Synnema formation traitmech:000656 is stalk aggregation and includes sporeless forms; neither trait is imposed as the other's is-a parent. Pseudohyphal growth traitmech:000653 is a cell arrangement, not equivalent to conidial production. Leave exact synonyms and xrefs unset pending authority and scope review; process ontology classes need not be exact organismal phenotypes.",
        "posed_by": "codex",
        "posed_date": "2026-10-07"
      },
      {
        "discussion_id": "fungal-conidiation-development-and-mechanism",
        "prompt": "Separate developmental routes and organism-specific mechanisms.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "The class covers outgrowth and conversion of existing hyphal cells, rather than only one Aspergillus-like conidiophore architecture. Do not require an aerial stalk, a synnema, one cell or nucleus per conidium, a particular pigment, immediate detachment, dormancy or a universal nutritional trigger. Early proconidial chains alone need not establish committed development. Distinguish production from conidial germination, sexual spore formation and spores formed by cleavage within a sporangium. Do not infer the trait from a gene inventory or ordinary yeast budding without source identification of conidial production. A causal graph is deferred pending direct perturbation details, natural-strain provenance and taxon-paired protein accessions; no universal BrlA, WetA or autophagy dependence is asserted.",
        "posed_by": "codex",
        "posed_date": "2026-10-07"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-07T03:28:58Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added fungal conidiation with four source-backed snippets, a qualified Cephalotrichum lignatile example and explicit bacterial terminology and developmental boundaries. Ignored-and-hidden searches and structured METPO review found no exact live record. Reserved METPO:1061000 in v533; existing records unchanged.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000677",
    "label": "fungal constricting-ring trap formation",
    "definition": "A morphological phenotype in which a fungus forms three-celled hyphal ring traps whose mature ring cells inflate inward to mechanically capture nematodes.",
    "definition_source": "DOI:10.1038/s41467-023-43235-w",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000718"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/s41467-023-43235-w",
        "snippet": "The R3 cell fuses with the S2 and R1 cells to complete CR formation",
        "notes": "Chen et al. (2023), Results, Morphogenesis and development of CR; primary XML at https://www.ebi.ac.uk/europepmc/webservices/rest/PMC10651832/fullTextXML and actual Figure 1 inspected. CR means constricting ring; R1-R3 are ring cells and S1-S2 stalk cells. Wild-type Drechslerella dactyloides strain 29 (CGMCC3.20198) forms complete rings before becoming inflation-competent. Methods use water agar at 25 degrees C with Caenorhabditis elegans for induction, and nematodes or 55-degree-C water for inflation assays; a separate horse-serum protocol is also described. These are distinct assay conditions, not universal requirements. Figure 1 separates immature-ring escape from mature-ring capture. Neither formation alone nor a circular outline proves immediate capture competence."
      },
      {
        "reference": "DOI:10.3897/BDJ.10.e96642",
        "snippet": "Both of them produce constricting rings to capture nematodes.",
        "notes": "Zhang et al. (2022; published 16 December), scientific abstract, New information; primary XML at https://www.ebi.ac.uk/europepmc/webservices/rest/PMC9836436/fullTextXML. The two taxa are Drechslerella daliensis and D. xiaguanensis. Methods, taxon descriptions and actual Figure 1e were inspected. Soil isolates were purified by single-spore transfers; trapping structures were induced on corn meal agar observation plates at 26 degrees C using Panagrellus redivivus. Descriptions distinguish three-celled constricting rings from adhesive trapping devices. Figure 1e shows an uninflated ring, not time-resolved inflation. The taxon-name validity caveat is retained in the example."
      },
      {
        "reference": "DOI:10.1016/j.devcel.2014.04.021",
        "snippet": "Cytokinesis involves constriction of a contractile actomyosin ring.",
        "notes": "Stachowiak et al. (2014), scientific abstract retrieved from Europe PMC for PMID:24914559, and primary article https://pmc.ncbi.nlm.nih.gov/articles/PMC4137230/. Results explicitly use constricting-ring terminology for intracellular actomyosin rings in fission-yeast protoplasts. This is terminology-boundary evidence, not another positive nematode-trap observation. The trap qualifier excludes this unrelated cellular structure; no cytokinesis mechanism, protein grounding or canonical example is transferred."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:2743661",
        "taxon_label": "Drechslerella daliensis (nom. inval.)",
        "reference": "DOI:10.3897/BDJ.10.e96642",
        "note": "Source-named D. daliensis, holotype culture CGMCC3.20131, isolated from burned forest soil at Cangshan Mountain, Dali, Yunnan, China, collected 25 July 2017. The primary taxon treatment and Figure 1e directly document three-celled constricting rings. Morphology and ITS, TEF1-alpha and RPB2 analyses support the study's identification. Live NCBI https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=taxonomy&id=2743661 resolves rank species but retains the nomenclatural qualifier nom. inval.; this is not a claim that the fungal name is validly published. The example is restricted to the observed culture and induction conditions, not every isolate or successful field biocontrol."
      }
    ],
    "discussions": [
      {
        "discussion_id": "constricting-ring-scope-and-parent",
        "prompt": "Resolve a closer trap-morphology parent without conflating cell shape.",
        "kind": "CURATION_TODO",
        "status": "RESOLVED",
        "rationale": "Parent phenotype METPO:1000059 is broader than this multicellular differentiation phenotype. Ring shaped METPO:1000680 denotes individual cell geometry, not a three-cell trapping apparatus. Mycelial growth and hyphal anastomosis alone do not define this trap. Exclude adhesive non-constricting rings, adhesive nets and generic nematophagy; neither a taxonomic genus nor prey capture by any mechanism is an exact synonym. Formation includes morphologically complete immature rings, not only already inflated traps. Do not infer that every formed ring immediately inflates. No xrefs, synonyms, SSSOM mappings or organism-level disjointness are asserted; closer hierarchy remains open. Stachowiak et al. (2014), DOI:10.1016/j.devcel.2014.04.021, also use constricting-ring terminology for fission-yeast cytokinesis. The trap-qualified label explicitly excludes those intracellular actomyosin rings; they are not synonyms or phenotype evidence here.",
        "posed_by": "codex",
        "posed_date": "2026-10-08",
        "resolved_date": "2026-10-13",
        "resolution_note": "Added fungal nematode-trap formation traitmech:000718 as the direct broader phenotype. The existing child definition entails specialized hyphal trap differentiation. This resolves only the parent gap; the historical scope contrasts, unasserted mappings, examples and separate mechanism questions remain applicable. Formation does not guarantee immediate capture. The column cell-count question is separately OPEN. Preserve the historical phenotype axiom and add METPO:1063000 SubClassOf METPO:1067100 on upstream adoption."
      },
      {
        "discussion_id": "constricting-ring-mechanism-and-taxonomy",
        "prompt": "Separate trap formation, inflation mechanism and nomenclatural validity.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Chen et al. investigate membrane reservoirs and SNARE-dependent inflation, but a protein-resolved causal graph requires review of the remaining perturbation/complementation figures, supplements and taxon-paired accessions. No universal SNARE requirement is inferred from morphology; mechanism is deferred, not claimed absent. Native provenance of laboratory strain 29 has not been established here, so it remains qualified evidence rather than a natural canonical example. NCBI's nom. inval. qualifier for D. daliensis concerns nomenclature, not absence of the observed trap; retain it pending nomenclatural review.",
        "posed_by": "codex",
        "posed_date": "2026-10-08"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-08T08:53:27Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added fungal constricting-ring formation with two primary DOI sources, source-checked snippets and a nomenclature-qualified natural-isolate example. Ignored-and-hidden main/worktree/open-PR checks support 000677 and v553 block 1063000-1063099. Separated formation from maturation, inflation and capture; existing records unchanged. Timestamp is observed UTC.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-08T09:13:13Z",
        "curator": "codex",
        "action": "EVIDENCE_AND_SCOPE_CORRECTION",
        "changes": "Addressed #1823: qualified the label with trap to distinguish intracellular cytokinetic rings in fungi. Added a directly checked primary boundary-source snippet and explicit exclusion; it is not a third positive trap study. Preserved the initial event, definition, identifier, natural example and reservation.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-13T13:31:56Z",
        "curator": "codex",
        "action": "REFINE_FUNGAL_TRAP_PARENT",
        "changes": "Refined traitmech:000677 below fungal nematode-trap formation traitmech:000718 and resolved its temporary parent discussion by definition-based inference. Preserved child identity, definition, evidence, examples, mechanism gaps and earlier history.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000667",
    "label": "fungal Hartig net formation",
    "definition": "A morphological phenotype in which a fungus forms an intercellular hyphal network, called a Hartig net, within a plant root.",
    "definition_source": "DOI:10.1111/nph.17940",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1111/nph.17940",
        "snippet": "hyphae grow between rhizodermal cells, forming an intraradical, apoplastic hyphal network, the so-called Hartig net",
        "notes": "Zhang et al. (2022; online 23 December 2021), Introduction, second paragraph, directly read publisher HTML. The contiguous clause defines the intercellular architecture, separately from the external mantle. Main text and captions were read; actual figure images and supplements were not inspected. RNAi reductions in network depth or colonized lateral-root frequency are not complete formation loss. The corrected LbGH28A cDNA must be compared with the reported reference sequence before protein grounding; no accession-level equivalence is asserted."
      },
      {
        "reference": "DOI:10.1111/nph.15113",
        "snippet": "a loose hyphal weft has been formed between two rhizodermal cells to differentiate an intraradicular hyphal network, the so-called Hartig net",
        "notes": "Zhang et al. (2018), Introduction, printed/physical p. 1, early-view author PDF: https://ri.conicet.gov.ar/bitstream/handle/11336/117651/CONICET_Digital_Nro.2f10e756-314d-4409-8829-81a4798588b0_A.pdf?isAllowed=y&sequence=2 The contiguous clause was exact-matched after joining PDF line wraps and hyphenated line breaks, and visually checked. Main text and actual Figure 2 on p. 7 were inspected. Panel d shows wild-type S238N root sections; panel c retains a thinner RNAi A4 network, not its absence. Other images and supplementary contents were not inspected."
      },
      {
        "reference": "DOI:10.1007/s00572-014-0590-7",
        "snippet": "Hartig net around epidermal cells para-epidermal in one row; hyphal cells roundish to cylindrical.",
        "notes": "Kuehdorf et al. (2015; online 2014), Results, Anatomical characters of longitudinal section, printed p. 112 / physical p. 4: https://d-nb.info/1192098684/34 Complete contiguous descriptive sentence, exact-matched and visually checked. Main text through Discussion and actual Figure 3 on p. 114 were read. Panels e-f distinguish the Hartig net from intracellular hyphae in field-collected Leotia cf. lubrica-Comarostaphylis arbutoides roots. Anatomy was restricted to subgroup e; it does not identify every Leotia sample or the separately observed fruit bodies. No species-level canonical example or nutrient flux is inferred. Other figure images were not inspected."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:29883",
        "taxon_label": "Laccaria bicolor",
        "reference": "DOI:10.1111/nph.15113",
        "note": "Wild-type S238N, not an RNAi line or its haploid S238N-H82 progeny. Zhang (2018) Figure 2d documents the Hartig net in hybrid poplar INRA 717-1-B4 roots three weeks after contact; Methods specifies low-glucose Pachlewski medium. The laboratory provenance page https://mycor.iam.inrae.fr/IAM/?page_id=4555 traces S238N to a 1976 Crater Lake, Oregon fruitbody collection under Tsuga mertensiana. NCBI EFetch confirms species 29883 and child strain 486041 S238N-H82; the child is not substituted for the experimental culture. This qualified example is not independent reidentification or evidence for all strains and conditions."
      }
    ],
    "discussions": [
      {
        "discussion_id": "fungal-hartig-net-scope-and-hierarchy",
        "prompt": "Resolve a closer morphology parent without collapsing root interfaces.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Use active phenotype METPO:1000059 under quality METPO:1000188. METPO:1000198 mycorrhization is obsolete. Branched shaped METPO:1000687 concerns cell shape; mycelial growth traitmech:000074 is explicitly bacterial. Arbuscule formation 000664 and peloton formation 000666 concern intracellular architectures; BAS formation 000665 is extraradical. Haustorium formation 000663 is not asserted exact, broader or disjoint. Ecological symbiosis, mutualism and endosymbiosis are not this network morphology. Arbutoid usage is directly supported above. The directly retrieved PubMed abstract for DOI:10.1007/s00572-004-0305-6 (PMID:15490255) also describes paraepidermal Hartig nets in field-collected Monotropa uniflora and Pterospora andromedea roots; its full text and figures remain unread, and no fungal taxon is inferred. The label is not restricted to one mycorrhizal category, root cell layer or host species. No exact synonyms, structure xrefs or SSSOM equivalences are asserted; a bare Hartig net names a structure, not its formation.",
        "posed_by": "codex",
        "posed_date": "2026-10-07"
      },
      {
        "discussion_id": "fungal-hartig-net-mechanism-and-culture-identity",
        "prompt": "Keep morphogenesis, symbiotic function and sequence identity separate.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "No universal nutrient-transfer rate, mutualistic outcome or cell-wall mechanism is part of the definition. Native RNAi perturbations are evidence leads, not proof that the entire network is absent; heterologous and purified-protein assays are separate. DOI:10.1111/nph.18358, directly read main text and actual Figures 3 and 8, reports shallower RNAi networks and deeper overexpression networks despite lower overall ectomycorrhizal frequency. Its T89 host is not INRA 717-1-B4, and Figure 8a/c are schematics. A causal graph is deferred pending authority-verified proteins and sequence-to-culture links, not because mechanisms are biologically absent. Keep S238N distinct from H82 reference/progeny material. The laboratory history calls an Oregon-derived antecedent S238-O, whereas DOI:10.7150/jgen.130158 assigns S238O to Quebec; those source-specific aliases are not silently equated.",
        "posed_by": "codex",
        "posed_date": "2026-10-07"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-07T18:15:22Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added fungal Hartig net formation with three DOI-backed snippets and a qualified wild-type S238N example. Ignored-and-hidden novelty and main/worktree/pending-PR checks support 000667, v543 and block 1062000-1062099; BAS #1788 and peloton #1791 retain their separate reservations. Kept intercellular architecture separate from nutrient transfer, intracellular structures and unverified protein mechanisms.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000670",
    "label": "fungal internal mycorrhizal vesicle formation",
    "definition": "A morphological phenotype in which a fungus forms lipid-storage hyphal swellings, called internal vesicles, within plant tissue during arbuscular mycorrhizal colonization.",
    "definition_source": "https://www.mycorrhizas.info/vam.html",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "https://www.mycorrhizas.info/vam.html",
        "snippet": "Vesicles are hyphal swellings in the root cortex that contain lipids and cytoplasm.",
        "notes": "Mark Brundrett, Mycorrhizal Associations, version 2 (2008), section C.5 and glossary F, directly read. This author resource supports terminology, not independent experimental replication. Its root-context definition is broadened here to plant tissue using Kobae et al.'s primary thallus observations. Internal vesicles may be within or between host cells. The glossary separately calls extraradical auxiliary bodies external vesicles; those are outside this qualified scope. The resource also notes variable similarity to spores. Its images were not inspected; historic genus-level statements are not universal taxonomic absence assertions."
      },
      {
        "reference": "DOI:10.1139/m75-258",
        "snippet": "Mature vesicles were engorged with lipid droplets, possessed a trilaminate wall and were also enclosed by host wall material and cytoplasm.",
        "notes": "Kinden and Brown (1975), PMID:172206; directly retrieved scientific abstract from Europe PMC. Electron microscopy of yellow-poplar mycorrhizal roots supports intracellular vesicles and lipid accumulation. Full text and actual micrographs were not inspected; the abstract does not name the fungus, so no taxon is inferred from historical MeSH. Trilaminate walls are this observation, not a universal definition. Nutrient release after degeneration is the authors' hypothesis, not measured transfer."
      },
      {
        "reference": "DOI:10.3390/plants8060142",
        "snippet": "C. etunicatum and R. intraradices formed vesicles at 25 days post-sowing (dps)",
        "notes": "Kobae et al. (2019), PMID:31151150, PMC6631804; Results 2.2 clause checked against the primary full-text XML and https://rakuno.repo.nii.ac.jp/record/6472/files/R-2020-321_kobae.pdf. Methods 3.1-3.3 and actual supplementary Figure S1 were inspected. The top two S1 panels separately label vesicles and arbuscules in young Marchantia paleacea thalli for MAFF520053 and MAFF520059, with 20-micrometer bars. WGA-HRP and DAB visualize fungal cell walls, not lipid chemistry. This is direct vesicle morphology, not an independent lipid assay or universal 25-day onset. The other panels' missing vesicle labels do not establish absence. The paper's DAOM197198 arbuscule-timing discrepancy concerns a separate culture and readout, not a resolved vesicle onset."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:937382",
        "taxon_label": "Entrophospora etunicata",
        "reference": "DOI:10.3390/plants8060142",
        "note": "MAFF520053 (H1-1), reported as Claroideoglomus etunicatum, forms vesicles in Marchantia paleacea thalli (Results 2.2; actual Figure S1). Methods 3.2 uses 1 g MAFF inoculum below approximately 100 gemmae per pot, at 26 C with 16 h light/day; Results reports 25 days post-sowing. The directly checked NARO collection record https://www.gene.affrc.go.jp/databases-micro_search_detail_en.php?maff=520053 lists soybean-field soil, Tokyo, October 1987 and H. Hirata as separate fields, and deposition as Glomus etunicatum. These are provenance, not a composite quote or independent trait evidence. NCBI Taxonomy resolves 937382 to Entrophospora etunicata with Claroideoglomus etunicatum as a homotypic synonym. Name correspondence is not reidentification. The directly read Table 1 and Results of DOI:10.1264/jsme2.ME25040 retain H1-1/520053; primer-dependent ASV resolution does not independently prove every culture's identity or a vesicle phenotype. Its figures and supplements were not inspected. The example is culture- and condition-qualified, not an assertion about all strains."
      }
    ],
    "discussions": [
      {
        "discussion_id": "fungal-internal-mycorrhizal-vesicle-scope",
        "prompt": "Resolve the closer parent and vesicle-versus-spore terminology.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Use active phenotype METPO:1000059 below quality METPO:1000188; mycorrhization METPO:1000198 is obsolete. Internal means within plant tissue, not necessarily within host cells and not free in host cytoplasm. Root-only scope excludes the direct thallus observations. Gas vesicles traitmech:000070, extracellular membrane vesicles and intracellular trafficking vesicles are not these hyphal swellings. Arbuscule formation traitmech:000664 is a different architecture. Brundrett's auxiliary-body usage motivates the internal qualifier; fine-endophyte vesicle-like swellings are not automatically equivalent. Fungal chlamydospore formation traitmech:000658 does not cover every storage swelling. Variable historical spore terminology remains unresolved; no universal disjointness, subclass relation, exact synonyms, xrefs or SSSOM equivalences are asserted.",
        "posed_by": "codex",
        "posed_date": "2026-10-07"
      },
      {
        "discussion_id": "fungal-internal-mycorrhizal-vesicle-readouts",
        "prompt": "Separate vesicle formation, storage and causal mechanisms.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Require a vesicle-specific morphological observation; pooled spores-and-vesicles or colonized-root-length percentages must not become vesicle counts or fungal-cell fractions. Neither these images nor the lipid-storage terminology establish universal lifespan, wall layers, infectivity, nutrient transfer, reciprocal benefit or developmental timing. Host signaling mutants and lipid-transfer assays are not fungal gene perturbations. A protein-resolved formation graph is deferred pending direct causal evidence and authority-verified fungal protein examples; it is not claimed biologically absent.",
        "posed_by": "codex",
        "posed_date": "2026-10-07"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-07T23:11:33Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added fungal internal mycorrhizal vesicle formation with two primary DOI-backed sources, attributed terminology, three verbatim snippets and a culture-qualified example. Ignored-and-hidden novelty and main/worktree/complete-open-PR reservation checks support 000670 and v546 block 1062300-1062399. Kept thallus scope, storage versus formation readouts and mechanism limits explicit; existing records unchanged.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000669",
    "label": "fungal mycelial cord formation",
    "definition": "A morphological phenotype in which a fungus forms linear multihyphal cords by aggregation behind an extending margin of diffuse hyphae.",
    "definition_source": "DOI:10.1007/s10267-008-0450-4",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1007/s10267-008-0450-4",
        "snippet": "the whole organ does not extend apically; rather, it develops behind a mycelial margin of diffuse hyphae",
        "notes": "Boddy et al. (2009), Introduction, printed p. 10; contiguous clause whose antecedent is mature mycelial cords. Directly read and visually checked in the author PDF: https://markfricker.org/wp-content/uploads/2015/12/boddy_et_al-2009-mycoscience-50-9.pdf This review supplies the operational terminology adopted here, not independent experimental replication. First three pages and Figure 1 were inspected; remaining figures and supplements were not."
      },
      {
        "reference": "DOI:10.1099/00221287-132-1-203",
        "snippet": "Both fungi grew out radially from the inoculum blocks in the form of networks of mycelial cords.",
        "notes": "Dowson, Rayner and Boddy (1986), complete abstract sentence, visually verified in the original-paper reprint: https://www.davidmoore.org.uk/21st_century_guidebook_to_fungi_platinum/REPRINT_collection/Dowson_etal_mycelia_cord-forming_basidiomycetes.pdf All nine pages of text and actual Figures 1 and 3 were inspected. The Introduction describes predominantly parallel, longitudinally aligned hyphal aggregates. Underside photocopies show network development, not microscopic proof of internal anatomy. Inoculum size and culture age are confounded. Other figure images were not inspected."
      },
      {
        "reference": "DOI:10.1016/j.mycres.2006.05.013",
        "snippet": "After 99 d, all systems had produced distinct mycelial cords",
        "notes": "Wood et al. (2006), PMID:16891104; contiguous scientific-abstract clause retrieved directly through Europe PMC. The following clause describes regression of diffuse mycelium and thinner cords. This soil-microcosm experiment supports formation and remodeling, not a universal 99-day onset. Full text, figures and strain provenance were not inspected; no additional canonical isolate is inferred."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:194680",
        "taxon_label": "Phanerochaete velutina",
        "reference": "DOI:10.1099/00221287-132-1-203",
        "note": "The unnumbered isolate in Dowson et al. (1986), Methods p. 204 at https://doi.org/10.1099/00221287-132-1-203, originated from decayed Fagus sylvatica wood at Farleigh Hungerford Woods, Wiltshire, UK (ST795563). Colonized beech blocks produced cords on moist unsterile sandy loam at 20 C in darkness; actual Figure 1d-f shows controls at 8, 12 and 44 days. NCBI EFetch confirms species 194680. No later collection number or all-strain claim is inferred."
      }
    ],
    "discussions": [
      {
        "discussion_id": "fungal-mycelial-cord-scope-and-hierarchy",
        "prompt": "Reconcile cord/rhizomorph usage and a closer fungal parent.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Use phenotype METPO:1000059. The definition adopts the developmental cord sense in the cited terminology source; it does not claim every historical cord, strand or rhizomorph label has this meaning. The broad root-like formation record traitmech:000662 retains its Koch (2017) unmelanized culture usage and Oliveira (2024) narrower organized-tip usage. Its scope discussion is linked, not declared solved. No exact synonyms, xrefs, parent-child or disjointness axioms between these records are asserted. Mycelial growth 000074 is bacterial; hyphal anastomosis 000605 requires cytoplasmic continuity; filament shaped 1000674 describes a cell, while filamentous colony 1007066 and rhizoid colony 1007068 describe colony outlines. Those are not this multihyphal developmental architecture. No universal pigment, rind, vessel-hypha, diameter or habitat condition is imposed.",
        "posed_by": "codex",
        "posed_date": "2026-10-07"
      },
      {
        "discussion_id": "fungal-mycelial-cord-mechanism-and-readout",
        "prompt": "Separate cord formation from network function and total hyphal coverage.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "A formation-regulatory protein graph is deferred pending primary perturbation evidence and authority-verified protein anchors, not because mechanisms are absent. Visible cords alone do not prove transport efficiency, resource sensing or a universal foraging response. The 1986 authors describe variable curvature and did not discriminate soluble, volatile and other microenvironmental causes. Numerical network edges are not molecular causal edges. Total hyphal image coverage is not a cord-specific formation count or fraction.",
        "posed_by": "codex",
        "posed_date": "2026-10-07"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-07T22:14:44Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added fungal mycelial cord formation with source-attributed developmental scope, two experimental citations, three short snippets and a provenance-qualified natural isolate. Ignored-and-hidden searches included all worktrees and pending PR artifacts. Reserved 000669/v545/1062200-1062299 after accounting for pending 000667 and 000668. Kept terminology and protein mechanisms explicitly unresolved.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000718",
    "label": "fungal nematode-trap formation",
    "definition": "A morphological phenotype in which a fungus differentiates hyphae into specialized nematode-capturing structures.",
    "definition_source": "DOI:10.1016/j.isci.2020.101057",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1016/j.isci.2020.101057",
        "snippet": "Nematode-trapping fungi (NTF) can switch to pathogens by producing various trapping devices to capture nematodes.",
        "notes": "Ji et al. 2020, scientific Summary; PMID:32339992. Direct primary XML at https://www.ebi.ac.uk/europepmc/webservices/rest/PMC7186526/fullTextXML and actual Figure 1 inspected. Introduction and Results group constricting rings, adhesive networks, columns and knobs as four representative devices, not an exhaustive taxonomy. Selected Transparent Methods and actual PDF pages 8, 11, 12, 15 and 16 were inspected; not every supplement figure or dataset. The main Introduction describes serial column cells while PDF 12 allows one or more; that narrower child-scope question remains open. Adhesion-gene expansion and expression correlations do not establish a universal molecular mechanism or sequence-only phenotype prediction. Native abstract verifier: VERIFIED."
      },
      {
        "reference": "DOI:10.1371/journal.ppat.1002179",
        "snippet": "A. oligospora forms adhesive networks to capture nematodes",
        "notes": "Yang et al. 2011, Author Summary, not the scientific abstract; PMID:21909256. Direct primary XML at https://www.ebi.ac.uk/europepmc/webservices/rest/PMC3164635/fullTextXML and actual Figure 1 inspected. Panel I shows interconnected loops; the caption distinguishes formation, attraction, adhesion, capture, penetration and digestion. These are separate endpoints, not automatic consequences of an observed shape. This parent curation did not renew the full Methods/supplement audit retained by the net child. The old teleomorph wording is not imported as a current taxonomic equivalence. Shares authors with Ji 2020, not independent-laboratory replication. Native verifier: NOT_IN_ABSTRACT; the Author Summary span matches directly."
      },
      {
        "reference": "DOI:10.1038/s41467-023-43235-w",
        "snippet": "CRs differentiate from hyphae and develop two basal stalk cells (S1 and S2) and three distal ring cells (R1, R2, and R3)",
        "notes": "Chen et al. 2023, Results, Morphogenesis and development of CR; PMID:37968349. CR means constricting ring. Primary XML at https://www.ebi.ac.uk/europepmc/webservices/rest/PMC10651832/fullTextXML, relevant formation/inflation Methods and actual Figure 1 inspected. Strain 29 (CGMCC3.20198) forms morphologically complete rings before inflation competence; panels l/m contrast immature-ring escape with mature-ring capture. Water-agar induction with C. elegans, horse-serum formation and hot-water inflation are distinct assays, not universal requirements. Later protein-mechanism figures and supplements were not fully audited; the incomplete supplementary ZIP is not evidence. No universal SNARE dependency or natural-strain exemplar is inferred. Native verifier: NOT_IN_ABSTRACT; the Results span matches directly."
      },
      {
        "reference": "DOI:10.1007/s102670200061",
        "snippet": "A nonconstricting ring (arrow) is capturing a nematode (asterisk).",
        "notes": "Saikawa and Takahashi 2002, Figure 8 caption, page 418. All three pages and actual Figures 1-20 inspected at https://www.jstage.jst.go.jp/article/mycosci/43/5/43_MYC43417/_pdf. Figures 8-14 and 15-20 document nonconstricting rings in source-named Dactylella leptospora and Dactylaria candida; Figures 1-7 show the constricting comparator. Curved hyphal branches form the traps. The observations support inclusion of nonconstricting rings, not universal stalk lengths, culture conditions or adhesion proteins. Adhesive ultrastructure is attributed to earlier work, not newly imaged here. DOI/title reconciled against Crossref. Native verifier: UNRESOLVED with no result for that exact DOI query; the caption matches directly. This does not assert that the paper is unindexed everywhere."
      }
    ],
    "discussions": [
      {
        "discussion_id": "fungal-nematode-trap-scope-and-hierarchy",
        "prompt": "Refine morphological boundaries without equating formation with feeding.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Phenotype METPO:1000059 is broader. Existing trap-formation traits 000677-000681 entail this parent; their five parent gaps are resolved by definition-based inference, not new child experiments. The five types do not exhaust the class or partition organism-level possession. Morphologically complete immature traps are included; formation does not guarantee immediate capture, killing, penetration, digestion or assimilation. Generic hyphal growth, fusion, individual-cell ring shape, prey attraction, fungal taxonomy and nematicidal activity without trap differentiation are insufficient. Mycelial growth traitmech:000074 is explicitly bacterial; hyphal anastomosis traitmech:000605 denotes fusion. Neither is an exact parent. Nutritional nematophagy is not an exact synonym. The column child's serial-cell versus single-cell terminology remains separately open; no organism-level disjointness is asserted. Pinned/current METPO lexical hits 0000261, 000262 and 1000125 are deprecated fungal-spore concepts, not trap counterparts; no replacement/consider annotations were observed. Their OMO:0001000 reasons do not invalidate biology or license identifier reuse. No exact synonyms or xrefs are asserted.",
        "posed_by": "codex",
        "posed_date": "2026-10-13"
      },
      {
        "discussion_id": "fungal-nematode-trap-mechanism-and-source-limits",
        "prompt": "Resolve trap-specific mechanisms and provenance without universalizing correlations.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Genomic homology, gene-family expansion and expression changes do not validate sequence-only phenotype predictions. Formation, adhesion, ring inflation and subsequent infection require separate functional evidence. No common protein inventory, inducer or mechanism is inferred across traps; protein examples and causal graphs remain unset. Existing narrow children retain their qualified canonical examples; none is duplicated onto the parent. Ji's ring isolate is described first as derived from a teleomorph and later as soil-derived, and Results/caption adhesive-layer measurements differ. Do not silently reconcile them. Its column strain is not the 2016 child's strain. Notice checks were bounded: Cell and Crossmark access failed, while PubMed, Crossref and three publisher records were inspected. Yang's linked CommentIn is commentary, not a correction designation or independent experiment. Source hashes, exact query outcomes and inspection limits are in the sidecar.",
        "posed_by": "codex",
        "posed_date": "2026-10-13"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-13T13:31:56Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added fungal nematode-trap formation with four DOI-backed contiguous excerpts and bounded source/phenotype scope. Reserved 000718, v594 and 1067100-1067199 after ignored/hidden, retained-history and pending-head checks. Refined five child parents, preserving their definitions and evidence and recording the unresolved column cell-count usage. No sequence-derived mechanism or universal capture guarantee asserted. Timestamp is observed post-audit acceptance, not estimated writing time.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000680",
    "label": "fungal nonconstricting-ring trap formation",
    "definition": "A morphological phenotype in which a fungus forms stalked, three-celled hyphal rings that trap nematodes without inward inflation of the ring cells.",
    "definition_source": "DOI:10.1007/s102670200061",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000718"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1007/s102670200061",
        "snippet": "A nonconstricting ring (arrow) is capturing a nematode (asterisk).",
        "notes": "Saikawa and Takahashi (2002), Figure 8 caption, page 418; all three pages and actual Figures 1-20 directly inspected at https://www.jstage.jst.go.jp/article/mycosci/43/5/43_MYC43417/_pdf. Time-lapse microscopy distinguishes noninflating three-cell rings in Dactylella leptospora and Dactylaria candida from the inflating Arthrobotrys dactyloides comparator. Figures 8-14 and 15-20 show the former taxa; Figures 1-7 show the comparator. Hook-tip fusion lacks the opposing bud seen in that comparator; stalk lengths vary. Adhesive ultrastructure is attributed to Saikawa (1985), not newly imaged here. These morphological observations do not identify causal proteins."
      },
      {
        "reference": "DOI:10.1016/j.mycres.2006.04.011",
        "snippet": "D. varietas forms both adhesive knobs and non-constricting rings",
        "notes": "Li et al. (2006), scientific Abstract, directly retrieved as published abstract XML for PMID:16876699 at https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=16876699&retmode=xml. Abstract-only access: full Methods and figures were not retrieved. The independent description of Dactylellina sichuanensis and D. varietas from China reports capture with knobs and nonconstricting rings. The quoted clause contrasts D. varietas with nontrapping Dactylella oxyspora. Co-occurring trap types are not disjoint organism categories. The sequence analyses concern taxonomy, not a sequence-predicted trapping phenotype; no current taxonomic equivalence for those new taxa is asserted."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:430499",
        "taxon_label": "Dactylellina leptospora",
        "reference": "DOI:10.1007/s102670200061",
        "note": "Source-named Dactylella leptospora, natural TGU orchard-soil isolate collected June 1998. Observed on water agar at 18-22 degrees C with Rhabditis sp.; Figures 8-14 document capture and ring development. Live NCBI https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=taxonomy&id=430499 resolves rank species, exact label Dactylellina leptospora and synonym Dactylella leptospora. This is not a strain accession or an assertion about every isolate, universal culture conditions or field biocontrol."
      }
    ],
    "discussions": [
      {
        "discussion_id": "nonconstricting-ring-scope-and-parent",
        "prompt": "Resolve a closer trap-morphology parent without conflating cell shape.",
        "kind": "CURATION_TODO",
        "status": "RESOLVED",
        "rationale": "Phenotype METPO:1000059 is a broad parent. Ring shaped METPO:1000680 concerns individual-cell geometry, not this multicellular trapping apparatus. Mycelial growth traitmech:000074 explicitly concerns bacteria; hyphal anastomosis traitmech:000605 concerns fusion. Distinguish nonconstricting traps from an immature constricting ring that has not yet acquired inflation competence, adhesive-net loops, unicellular knobs, columns and intracellular cytokinetic rings. A circular outline or nematophagous genus is not sufficient. No exact synonyms, xrefs, SSSOM equivalences or organism-level disjointness are asserted. Neighboring scope exclusions do not constitute unresolved groundings, and their closer-parent TODOs remain open.",
        "posed_by": "codex",
        "posed_date": "2026-10-08",
        "resolved_date": "2026-10-13",
        "resolution_note": "Added fungal nematode-trap formation traitmech:000718 as the direct broader phenotype. The existing child definition entails specialized hyphal trap differentiation. This resolves only the parent gap; the historical scope contrasts, unasserted mappings, examples and separate mechanism questions remain applicable. Formation does not guarantee immediate capture. The column cell-count question is separately OPEN. Preserve the historical phenotype axiom and add METPO:1063300 SubClassOf METPO:1067100 on upstream adoption."
      },
      {
        "discussion_id": "nonconstricting-ring-mechanism",
        "prompt": "Separate ring morphogenesis from adhesion and infection mechanisms.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "The observed developmental sequence is not evidence that a particular protein is necessary or sufficient. Formation, adhesion, capture, penetration and digestion are separate endpoints; formation alone does not guarantee capture in every condition. A protein-resolved causal graph needs direct perturbation/complementation evidence and taxon-paired accessions. Do not transfer inflation mechanisms from constricting rings or adhesion proteins from knobs and nets. No universal stalk length, detachment, induction medium or prey requirement is asserted; mechanism is deferred, not claimed absent.",
        "posed_by": "codex",
        "posed_date": "2026-10-08"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-08T12:40:34Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added fungal nonconstricting-ring trap formation with two primary DOI sources, contiguous source-checked snippets and a qualified natural-isolate example. Ignored-and-hidden main/worktree/open-PR checks support 000680 and v556 block 1063300-1063399. Separated morphology from molecular mechanism and species rank from strain identity. Existing records unchanged. Timestamp is observed UTC.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-13T13:31:56Z",
        "curator": "codex",
        "action": "REFINE_FUNGAL_TRAP_PARENT",
        "changes": "Refined traitmech:000680 below fungal nematode-trap formation traitmech:000718 and resolved its temporary parent discussion by definition-based inference. Preserved child identity, definition, evidence, examples, mechanism gaps and earlier history.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000666",
    "label": "fungal peloton formation",
    "definition": "A morphological phenotype in which a fungus forms intracellular coiled hyphal masses, called pelotons, in association with a plant host.",
    "definition_source": "DOI:10.1111/nph.14279",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1111/nph.14279",
        "snippet": "In the colonised protocorm cells, ORM fungi form coiled hyphae, known as pelotons",
        "notes": "Fochi et al. (2017), author final manuscript, Discussion, Nitrogen transfer inside the mycorrhizal orchid protocorm, printed p. 15 / physical p. 17, line 465: https://iris.unito.it/retrieve/e27ce429-fbc3-2581-e053-d805fe0acbaa/N_metabolism_ORM_rev10_4aperto.pdf Contiguous clause matched after removing standalone line numbers and joining PDF line wraps, and visually checked. The maintained resolver returned NOT_IN_ABSTRACT; this is a manual full-text check, not a resolver VERIFIED result. Main text through Conclusions and actual Figure 5 were inspected. Figure 5 shows intact and collapsed pelotons in Serapias vomeracea 30 days after sowing with Tulasnella calospora. The manuscript's title wording and GEO(XXXX) placeholder differ from final metadata; no dataset accession is inferred. Other figure images and supplementary contents were not inspected. Transcript patterns and heterologous yeast assays are not causal tests of native peloton formation."
      },
      {
        "reference": "DOI:10.1111/1365-2745.70188",
        "snippet": "Ericoid hyphal coils (also called pelotons) are specific structures formed by ericoid fungi in root epidermal cells",
        "notes": "Meyers et al. (2025), Table 1 continued, CCI row, Relevance column, p. 3681 / physical p. 4. The complete morphology clause was exact-matched and visually checked in the public publisher PDF deposited at https://freidok.uni-freiburg.de/data/273892; its SHA256 matches the repository checksum. This directly read usage supports ericoid scope, not an orchid-only definition. Methods 2.4 scores Vaccinium myrtillus root intersects, distinguishing coils from other intracellular hyphae; CCI is not a fungal cell fraction or measured nutrient flux. No fungal species was identified for a canonical example. Actual supplementary Figure S3 was not inspected. The resolver returned UNRESOLVED; an exact Europe PMC DOI query returned no hit and Crossref confirmed the exact DOI/title. Manual PDF verification does not change that resolver verdict."
      },
      {
        "reference": "DOI:10.1111/nph.19338",
        "snippet": "tightly coiled intracellular fungal hyphae (i.e. pelotons) are a constant feature of OrM",
        "notes": "Perotto and Balestrini, Viewpoint, online 2023, institutional early-view PDF: https://iris.unito.it/retrieve/b44ea427-adb1-4f5b-a5b6-cc876e060f2f/New%20Phytologist%20-%202023%20-%20Perotto%20-%20At%20the%20core%20of%20the%20endomycorrhizal%20symbioses%20intracellular%20fungal%20structures%20in%20orchid.pdf Printed/physical p. 2, The peloton: a constant feature in orchid mycorrhiza. Main text and actual Figures 1-3 were read; the contiguous clause was visually checked. This is review terminology, not independent experimental replication. The same page describes Paris-type AM coils as resembling orchid pelotons and discusses a continuum with arbusculate coils; resemblance is not exact equivalence. Figure 2 has inconsistent panel/scale labels, so no panel-specific dimensions are adopted. Its hypothesis of plant-driven development is not an established formation mechanism. The orchid discussion does not erase the separate ericoid usage in Meyers et al."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:156515",
        "taxon_label": "Tulasnella calospora",
        "reference": "DOI:10.1111/nph.14279",
        "note": "AL13/4D = MUT4182 in Serapias vomeracea protocorms, oat medium, 20 C in darkness; actual Figure 5 documents pelotons 30 days after sowing. Fochi Methods, printed p. 4 / physical p. 6, https://iris.unito.it/retrieve/e27ce429-fbc3-2581-e053-d805fe0acbaa/N_metabolism_ORM_rev10_4aperto.pdf reports isolation from Anacamptis laxiflora mycorrhizal roots in northern Italy and deposition as MUT4182 (citing Girlanda et al. 2011, DOI:10.3732/ajb.1000486; that original isolation paper was not read). NCBI EFetch confirms species 156515 and child strain 1051891, Tulasnella calospora MUT 4182, with equivalent name Tulasnella calospora AL13/4D. The paper's engineered yeast complementation assay is a separate experiment, not an engineered fungal exemplar. This culture-qualified example is not independent taxonomic reidentification or evidence for every strain and condition."
      }
    ],
    "discussions": [
      {
        "discussion_id": "fungal-peloton-scope-and-hierarchy",
        "prompt": "Resolve a closer parent without collapsing intracellular architectures.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Use phenotype METPO:1000059. Spiral shaped METPO:1000684, branched shaped METPO:1000687 and filament shaped METPO:1000674 concern cell shape. Mycelial growth traitmech:000074 is explicitly bacterial. Fungal arbuscule formation traitmech:000664 concerns branched intracellular structures; hyphal anastomosis traitmech:000605 is fusion, pseudohyphal growth traitmech:000653 budding-cell chains, and haustorium formation traitmech:000663 a specialized host interface. None is an exact duplicate or settled closer parent. Fochi's orchid usage and Meyers' ericoid usage both inform the unqualified label. The review's Paris-type AM comparison does not make every intracellular coil a peloton or establish disjoint organisms. No exact synonyms, structure xrefs or SSSOM equivalences are asserted. Liverwort terminology in DOI:10.1098/rstb.2000.0617 remains an abstract-only analogy lead; its full text and figures were not inspected.",
        "posed_by": "codex",
        "posed_date": "2026-10-07"
      },
      {
        "discussion_id": "fungal-peloton-formation-versus-function",
        "prompt": "Separate formation from nutrient transfer and proposed regulation.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "The phenotype does not require a measured nutrient flux, exclusive mutualism, a universal lifespan, or a specific plant-driven mechanism. Transcript associations and isolated transporter complementation do not establish the native formation pathway. Nutrient transfer before or during coil degeneration is a separate question from morphogenesis. A protein-resolved causal graph is deferred pending direct formation perturbations and authority-verified protein anchors; a mechanism is not claimed biologically absent. Keep the example's MUT4182 separate from Tulasnella sp. SV6 (MUT4178) studied in DOI:10.1186/s43008-024-00165-6: that paper uses AL13/4D as a reference genome, not as its culture.",
        "posed_by": "codex",
        "posed_date": "2026-10-07"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-07T15:40:03Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added fungal peloton formation with two primary DOI-backed sources, a separately identified review, three snippets and a culture-qualified Tulasnella calospora example. Ignored-and-hidden novelty and main/worktree/open-PR reservation checks support 000666 and v542 block 1061900-1061999, with BAS #1788 reserved separately. Kept morphology distinct from nutrient flux and unproven formation mechanisms.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000662",
    "label": "fungal rhizomorph formation",
    "definition": "A morphological phenotype in which a fungus forms root-like, multihyphal structures through coordinated hyphal growth.",
    "definition_source": "DOI:10.1016/j.fgb.2009.04.005",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1016/j.fgb.2009.04.005",
        "snippet": "Rhizomorphs of wood-decay basidiomycetes are root-like structures produced by the coordinated growth of thousands of hyphae.",
        "notes": "Yafetto, Davis and Money (2009), PMID:19427390; scientific abstract retrieved directly through Europe PMC. The naming sentence supports the formation phenotype, not a universal hyphal-count threshold. Armillaria gallica cultures were tested in media of different gel strengths. The reported 760 kPa is an osmolality-derived turgor estimate, whereas 40-300 kPa describes pressure corresponding to measured tip forces. These are distinct readouts, not trait thresholds. Full text, figures, supplements and isolate provenance were not inspected; no canonical example is inferred from this abstract."
      },
      {
        "reference": "DOI:10.1016/j.mycres.2005.09.006",
        "snippet": "Air pores develop near the inoculum plug shortly after inoculation, arising directly from the mycelium, and rhizomorphs are initiated from them.",
        "notes": "Pareek, Allaway and Ashford (2006), PMID:16376531; scientific abstract checked against the directly retrieved PDF and Europe PMC abstract. Methods, Results, Discussion, Table 1 and actual Figures 9-17 were inspected. Results place first tips on day 6, but Table 1 reports tips on day 5; no exact onset is asserted. Table 1 counts tips and air pores on five plates, not organisms. The main oxygen-conductance assay used cut rhizomorph ends; it does not establish intact-rind permeability or universal oxygen adaptation. Air pores and rhizomorphs are distinct structures. Remaining figure images and supplements were not inspected."
      },
      {
        "reference": "DOI:10.1186/s12862-017-0877-3",
        "snippet": "All armillarioid species have the capacity to form rhizomorphs in culture, but only the later diverging lineages have been observed to form them in nature",
        "notes": "Koch et al. (2017), PMID:28122504, PMC5264464; directly retrieved full-text XML, Discussion subsection The rise of rhizomorphs and Table 2. The quoted clause precedes a parenthetical figure/table citation. This is the authors' comparative summary, partly based on earlier literature, not a new formation experiment on every species. They explicitly describe unmelanized rhizomorphs in culture. Field non-observation is not biological absence; the summary does not establish expression in every strain or condition. Full Methods, actual figures, supplements and additional isolate provenance were not inspected."
      },
      {
        "reference": "DOI:10.3114/fuse.2024.14.03",
        "snippet": "Many rhizomorph-forming fungi occur in the litter on the forest floor (ground species), while other species make aerial rhizomorph networks (epiphytic species).",
        "notes": "Oliveira et al. (2024), PMID:39830290, PMC11739697; Introduction read directly in PMC HTML after the Europe PMC XML endpoint failed. This terminology passage supports not restricting formation to underground growth. These authors adopt a narrow melanized, differentiated, organized-tip concept and contrast Singer's white rhizomorph usage with mycelial cords. That is their attributed account; the original Singer/Rayner sources were not retrieved. Abstract, Introduction and selected taxonomic text/captions were read, but actual figures, supplements and the full Methods were not inspected. No additional canonical taxon or exact cord synonym is asserted."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:153913",
        "taxon_label": "Armillaria luteobubalina",
        "reference": "DOI:10.1016/j.mycres.2005.09.006",
        "note": "Isolate 930199KGS in Pareek et al. (2006), Fungal material and culture conditions, Results and Figures 9-17. Primary Methods at https://doi.org/10.1016/j.mycres.2005.09.006 identify the University of Western Sydney collection culture as originating from fruit bodies collected at Gore Hill Park, North Sydney, in June 1993. Rhizomorph development was observed on malt-marmite agar in darkness at 23 C. The Methods provenance and actual images were inspected; natural origin is not inferred from a wild-type label. NCBI Taxonomy confirms the species ID, label and rank. This is a qualified culture observation, not evidence for every strain or condition."
      }
    ],
    "discussions": [
      {
        "discussion_id": "fungal-rhizomorph-scope-and-hierarchy",
        "prompt": "Resolve rhizomorph/cord terminology and a closer fungal parent.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Use phenotype METPO:1000059. Mycelial growth traitmech:000074 is explicitly bacterial; filament shaped METPO:1000674 is a cell-shape class; rhizoid colony METPO:1007068 and filamentous colony METPO:1007066 concern colony outlines. None is an exact fungal multihyphal formation record. Hyphal anastomosis traitmech:000605 denotes fusion and fungal sclerotium formation traitmech:000660 denotes compact resting bodies. Koch et al. (2017) use rhizomorph for unmelanized culture structures, whereas Oliveira et al. (2024) adopt the narrower melanized, organized-tip sense and distinguish mycelial cords. The broad formation definition does not settle that anatomical boundary: retain the source attribution and do not assert exact cord/strand synonyms, a universal pigment requirement or an underground-only habitat. A closer fungal growth-form parent and external equivalences require upstream review; no xrefs or SSSOM mappings are asserted. Fungal mycelial cord formation traitmech:000669 now represents the diffuse-front aggregation sense defined by Boddy et al. (2009), DOI:10.1007/s10267-008-0450-4, rather than silently equating the two names. Its experimental examples do not resolve all historical usage. Keep this terminology/hierarchy question OPEN: neither equivalence, a parent-child relationship nor organism-level disjointness is asserted.",
        "posed_by": "codex",
        "posed_date": "2026-10-07"
      },
      {
        "discussion_id": "fungal-rhizomorph-formation-and-function",
        "prompt": "Separate formation from transport, invasion and gene mechanisms.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Formation does not by itself prove pathogenicity, low-oxygen adaptation, a fixed invasion force or a universal hollow canal. Pareek et al. distinguish air pores from rhizomorphs; oxygen measurements on cut structures do not show intact-rind permeability. Their Results/Table 1 onset discrepancy remains unresolved. Culture versus field observations and hyphal/tip counts require explicit conditions and denominators. Physical growth and aeration have experimental support, but a formation-regulatory graph requires further primary perturbation evidence and authority-verified protein examples. No complete protein pathway is inferred from expression, gene possession, osmolyte composition or structure alone. The graph is deferred, not claimed to be biologically absent.",
        "posed_by": "codex",
        "posed_date": "2026-10-07"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-07T09:59:27Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added fungal rhizomorph formation with four directly checked source snippets, a provenance-qualified 930199KGS example and explicit terminology, hierarchy and experimental limits. Ignored-and-hidden searches found no exact existing trait. Reserved METPO:1061500 in v538; existing records unchanged and protein-level formation mechanism deferred.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-07T22:14:44Z",
        "curator": "codex",
        "action": "LINKED_SCOPE_DISCUSSION",
        "changes": "Linked the rhizomorph/cord scope discussion to new traitmech:000669. Preserved the attributed conflicting usages, OPEN status and all existing identity, evidence and example fields; no synonym, hierarchy or disjointness axiom was introduced.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000668",
    "label": "fungal root mantle formation",
    "definition": "A morphological phenotype in which a fungus forms an external sheath of aggregated hyphae, called a mantle, around a plant root.",
    "definition_source": "DOI:10.1128/AEM.01991-15",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1128/AEM.01991-15",
        "snippet": "the fungus initially grows around the roots to form a mass of mycelium called the fungal mantle.",
        "notes": "Krause et al. (2015), Introduction, first paragraph, directly read publisher HTML. This contiguous clause describes the root-external mantle separately from the intraradical Hartig net. Main text and captions were read; actual figure images and supplementary contents were not inspected. The ald1-overexpressing T. vaccinum 1.16 is an engineered perturbation, not a natural canonical exemplar."
      },
      {
        "reference": "DOI:10.3389/fpls.2014.00229",
        "snippet": "The fungus enwraps the root tip with a hyphal mantle [M] composed of several layers.",
        "notes": "Pena et al. (2014), Figure 1 caption, complete sentence, exact-matched in primary full-text XML and visually checked in the publisher PDF on p. 3. The actual composite figure contains a root photograph and section image with schematic infrared arrows; it is not an experimental image of radiation penetration. Main Results separately describe multilayered mantles in field-collected roots. Other figure images and Table S1 were not inspected; no numerical thickness, spectral function or additional taxon exemplar is inferred."
      },
      {
        "reference": "DOI:10.3390/microorganisms9122612",
        "snippet": "Three weeks post-inoculation, fungal hyphae formed a thinner but denser mantle.",
        "notes": "Ruytinx et al. (2021), Results 3.3, complete sentence, exact-matched in primary full-text XML. Main text and actual Figure 2 on PDF p. 8 were inspected: https://pure.mpg.de/rest/items/item_3375108_1/component/file_3400121/content The 21-day state follows the reported thick, dense 14-day mantle, not loss of the sheath. Methods 2.6 names WGA-Alexa 488 whereas the Figure 2 caption names WGA-oregon green; the discrepancy is retained, not resolved by inference. Other figure images and supplements were not inspected."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:29883",
        "taxon_label": "Laccaria bicolor",
        "reference": "DOI:10.3390/microorganisms9122612",
        "note": "Reference culture S238N, not haploid S238N-H82. Ruytinx (2021), Methods 2.1/2.3 and Results 3.3 with Figure 2B-C, documents a mantle around Populus tremula x alba 717-1B4 lateral roots in P20 sandwich coculture, including the 14- and 21-day states. The laboratory history at https://mycor.iam.inrae.fr/IAM/?page_id=4555 traces S238N to a 1976 Crater Lake, Oregon fruitbody collection under Tsuga mertensiana. NCBI EFetch confirms species 29883 and separate child strain 486041 S238N-H82; the genome strain is not substituted for the experimental culture. This is culture-qualified evidence, not independent reidentification or a claim for all strains."
      }
    ],
    "discussions": [
      {
        "discussion_id": "fungal-root-mantle-scope-and-hierarchy",
        "prompt": "Resolve a closer morphology parent without conflating root interfaces.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Use active phenotype METPO:1000059 under quality METPO:1000188; METPO:1000198 mycorrhization is obsolete. The root qualifier excludes other senses of mantle or sheath. Hartig net formation traitmech:000667 is intercellular within roots; arbuscules 000664 and pelotons 000666 are intracellular, while BAS 000665 are branching groups on extraradical runner hyphae. Mycelial growth 000074 is explicitly bacterial and capsule 000063 is a polymer layer around a cell, not hyphae around a plant root. Colony outline, cell shape, rhizosphere association and ecological symbiosis outcomes are not this architecture. The existing Hartig-net mantle mention is an evidence boundary, not an ungrounded node, synonym or parent-gap TODO requiring repair. Bare mantle and fungal sheath name structures, not formation phenotypes; no exact synonyms, xrefs or SSSOM equivalences are asserted. No organism-level disjointness or fixed thickness, color, host range or nutrient-transfer outcome is implied.",
        "posed_by": "codex",
        "posed_date": "2026-10-07"
      },
      {
        "discussion_id": "fungal-root-mantle-mechanism-and-readout",
        "prompt": "Separate mantle morphogenesis from bulk expression and perturbation effects.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "A protein-resolved causal graph is deferred pending authority-verified proteins, sequence-to-culture links and inspection of the relevant perturbation images, not because mechanisms are absent. DOI:10.1128/AEM.01991-15 reports a thicker mantle in native ald1 overexpression; it does not establish an obligatory universal pathway. Its mte1 evidence is heterologous yeast growth rescue, not a native mantle-formation knockout. Keep increased thickness, first sheath formation, branching and plant responses separate. DOI:10.3390/microorganisms9122612 uses an EcM transcriptomic sample containing all fungal and mixed plant-fungal material within 0.5 cm of a root. Coexpression in that bulk sample is not mantle-specific localization or functional validation. The paper explicitly presents working models for future experimental tests.",
        "posed_by": "codex",
        "posed_date": "2026-10-07"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-07T19:40:30Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added fungal root mantle formation with three DOI-backed snippets and a culture-qualified S238N example. Ignored-and-hidden novelty and main/worktree/pending-PR checks support 000668, v544 and block 1062100-1062199; pending 000665-000667 reservations remain occupied. Kept root-external sheath architecture separate from Hartig nets, ecological outcomes and unverified protein mechanisms.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000660",
    "label": "fungal sclerotium formation",
    "definition": "A morphological phenotype in which a fungus forms compact mycelial resting bodies called sclerotia.",
    "definition_source": "DOI:10.1128/AEM.00565-08",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1128/AEM.00565-08",
        "snippet": "Aspergillus flavus differentiates to produce asexual dispersing spores (conidia) or overwintering survival structures called sclerotia.",
        "notes": "Horowitz Brown et al. (2008), PMID:18658287, PMC2547031; scientific abstract retrieved through Europe PMC and checked against publisher/PMC HTML. The XML endpoint failed; full text was read as HTML. Introduction, growth/density Methods, first Results subsection, Table 1 and actual Figure 1 were inspected. NRRL 3357 was tested at 29 C for seven days in darkness on glucose minimal medium with sorbitol. Figure 1A reports log10 sclerotial dry mass per plate, not raw body counts despite the abstract's number wording. Density association does not identify the proposed quorum factor. Other figures, supplements and natural strain provenance were not inspected; no additional canonical example or universal LOX mechanism is inferred."
      },
      {
        "reference": "DOI:10.3390/jof9070737",
        "snippet": "WT and \u0394SSA-178C formed black mature sclerotia on the colonies and at the rim of the Petri dishes",
        "notes": "Wang et al. (2023), PMID:37504726, PMC10381867; full-text XML, Results 3.3. Methods 2.1/2.6, Discussion and actual Figures 3-4 were inspected. WT 1980 was observed on PDA at 20 C after 10/15 days and on autoclaved carrot slices after 20 days. Colony photographs are Figure 3A; the Results' Figure 3B pointers for maturation are misplaced because 3B plots growth. Figure 4C/D report bodies and total air-dried mass per flask, not mass per body. Delayed maturation is not complete loss of formation; do not infer rescue of every cortex measurement or survival duration. Other figures and supplements were not inspected."
      },
      {
        "reference": "DOI:10.1016/j.micres.2019.126326",
        "snippet": "there are no structural differences in the three stages of formation of melanized and non-melanized sclerotium.",
        "notes": "2019 microscopy study, PMID:31493702; directly retrieved Europe PMC scientific abstract only. The authors report development on PDA and compare melanized/non-melanized Sclerotinia sclerotiorum structures by microscopy and histochemistry. This supports not requiring melanization in the definition; the quoted observation is not a claim of identical composition or preserved function in every respect. Full text, figures, supplements, the treatment producing non-melanized structures and strain provenance were not inspected. No canonical example or transcript-inferred biochemical pathway is asserted."
      },
      {
        "reference": "DOI:10.1128/spectrum.02084-21",
        "snippet": "There are different types of sclerotia-like fungal structures, such as the true sclerotia, the pseudosclerotia, the small sclerotia, and the microsclerotia.",
        "notes": "2022 primary study, PMID:35080446, PMC8791194; Introduction read directly as full-text XML. This passage is a terminology classification, not a new experimental observation. The authors distinguish tissue organization, host-material incorporation and developmental origins across these forms. Preserve that attributed distinction rather than imposing one size, three-layer anatomy or pure-fungal composition on every usage. Detailed equivalence/subclass mapping remains unresolved. Experimental Results, figures, supplements and strain provenance were not inspected; no universal ROS mechanism or additional canonical example is claimed."
      },
      {
        "reference": "DOI:10.2478/s11658-007-0047-5",
        "snippet": "Sclerotization only took place when the plasmodia were starved and very slowly dried.",
        "notes": "Krzywda et al. (2008; online 2007), PMID:17965965, PMC6275577; scientific abstract read directly in full-text XML. Fuligo septica forms a dormant plasmodial state also called a sclerotium. This nonfungal usage motivates the explicit fungal scope; it is not a mycelial exemplar or an exact synonym of this trait. The reported dehydration conditions and pigment/viability observations are not transferred to fungi. Methods, figures and natural-isolate provenance were not inspected."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:5180",
        "taxon_label": "Sclerotinia sclerotiorum",
        "reference": "DOI:10.3390/jof9070737",
        "note": "Wild-type strain 1980 in Wang et al. (2023), Methods 2.1/2.6, Results 3.3 and actual Figures 3A/4, forms sclerotia under the tested PDA/carrot conditions. NCBI Taxonomy confirms the species label and rank. Independent primary Methods at https://doi.org/10.1128/AEM.67.1.75-81.2001 (PMID:11133430, PMC92519) explicitly identify isolate 1980 as originating from dry bean culls in western Nebraska, supplied by J. R. Steadman. That passage was read directly in PMC HTML; its cited original 1990 study was not retrieved. This URL supports provenance, not an extra formation observation. The example is not an SSA disruption/complementary mutant and does not assert the phenotype for every strain or condition."
      }
    ],
    "discussions": [
      {
        "discussion_id": "fungal-sclerotium-identity-and-mapping",
        "prompt": "Reconcile legacy labels and the scope of sclerotial structures.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "The explicit fungal label excludes the dormant plasmodial usage in Fuligo. Retain phenotype METPO:1000059 rather than plant pathogen, black pigmented, fungal conidiation traitmech:000657 or chlamydospore formation traitmech:000658. The pinned ontology contains only deprecated bare-label sclerotia classes METPO:0000117, METPO:000118 and METPO:1000398, without definitions or replacement links. Their original scope is unresolved; do not silently reactivate them or assert equivalence to this organismal formation phenotype. Upstream review must reconcile that legacy. QuickGO resolves GO:1990045 as sclerotium development, a biological process rather than an exact organismal phenotype; no xref or SSSOM mapping is asserted. The 2022 source distinguishes true, small, pseudo- and microsclerotial structures. Whether these need separate subclasses or mappings requires further primary morphology review; no exact synonyms, universal size threshold, three-layer requirement or host-material exclusion is imposed.",
        "posed_by": "codex",
        "posed_date": "2026-10-07"
      },
      {
        "discussion_id": "fungal-sclerotium-formation-and-function",
        "prompt": "Separate formation from maturation, survival and mechanism.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Initiation, maturation, persistence and germination are distinct readouts. Formation of a named resting body does not establish a particular dormancy duration, survival after stress or later germinability. Size, pigmentation, nutrient regime and density responses are not universal defining requirements. Do not infer plant pathogenicity, aflatoxin production or a sexual/asexual reproductive mode from formation alone. The SSA study separates delayed maturation from a complete block, and total mass per flask from body number. A causal graph awaits taxon-specific perturbation/complementation assessment, remaining figures/supplements and authority-verified protein accessions. Candidate gene possession or expression of ROS, pigmentation or signaling genes is not itself the formation phenotype.",
        "posed_by": "codex",
        "posed_date": "2026-10-07"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-07T06:42:13Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added fungal sclerotium formation with five directly checked source snippets, a provenance-qualified strain 1980 example and explicit legacy-identity, morphology and functional limits. Ignored-and-hidden searches found deprecated bare labels but no live exact formation trait. Reserved METPO:1061300 in v536; existing records unchanged and protein-level mechanism deferred.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000690",
    "label": "fusiform shaped",
    "definition": "A cell shape that is wide in the middle and tapers at both ends.",
    "definition_source": "DOI:10.1146/annurev-cellbio-101011-155745",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000666"
    ],
    "synonyms": [
      {
        "synonym_text": "fusiform",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev-cellbio-101011-155745",
        "snippet": "cell shape is genetically determined",
        "notes": "Cell-shape review supports tapered cell ends as a genetically determined geometry maintained by graded wall synthesis."
      },
      {
        "reference": "DOI:10.1111/1462-2920.13731",
        "snippet": "Fusobacterium nucleatum",
        "notes": "Fusobacterium-genome review supports fusiform morphology in the Fusobacterium genus."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:851",
        "taxon_label": "Fusobacterium nucleatum",
        "note": "Spindle/fusiform (tapered-end) rod; model oral anaerobe.",
        "reference": "https://www.ncbi.nlm.nih.gov/books/NBK8438/"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "fusiform_shaped_tapered_polar_growth",
        "title": "Fusiform-shape tapered polar growth",
        "description": "DOI-backed graph linking graded polar peptidoglycan growth and reduced end-cap radius to fusiform tapered morphology.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a broad environmental or morphological classification spanning multiple mechanisms, a measurement-like bin, or an absence/arrangement descriptor; contextual protein nodes do not receive token UniProt examples.",
        "nodes": [
          {
            "node_id": "fusiform_shaped_trait",
            "label": "fusiform shaped",
            "node_type": "TRAIT",
            "grounding": "METPO:1000690",
            "description": "Cell wider at middle and tapering at both poles."
          },
          {
            "node_id": "graded_polar_pg",
            "label": "graded polar peptidoglycan growth",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Polar PG growth with reduced incorporation toward the cell tips."
          },
          {
            "node_id": "end_cap_taper",
            "label": "end-cap taper",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduction in radius near the cell poles producing pointed ends."
          },
          {
            "node_id": "tapered_geometry",
            "label": "tapered geometry",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Cell-body geometry that narrows toward both poles."
          },
          {
            "node_id": "mreb",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "MreB",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Bacterial actin homolog that orients peptidoglycan synthesis to maintain cell shape."
          },
          {
            "node_id": "lateral_pg_synthesis",
            "label": "lateral peptidoglycan synthesis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Sidewall PG incorporation that sustains elongated cell geometry."
          },
          {
            "node_id": "rodz",
            "label": "RodZ",
            "node_type": "GENE_OR_PROTEIN",
            "description": "MreB-associated shape protein modulating MreB localization and elongasome assembly.",
            "grounding": "InterPro:IPR023690"
          },
          {
            "node_id": "mreb_localization",
            "label": "MreB polymer localization/assembly",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Geometric localization and assembly of the MreB actin cytoskeleton."
          },
          {
            "node_id": "elongasome",
            "label": "elongasome complex",
            "node_type": "CELLULAR_LOCALIZATION",
            "description": "Lateral wall-growth machinery containing MreB, RodA, PBP2, RodZ, MreC, MreD."
          },
          {
            "node_id": "mrec",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "MreC",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Elongasome component that activates PBP2 and RodA synthesis functions."
          },
          {
            "node_id": "pbp2",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "PBP2",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Class B PBP in the elongasome coupled to RodA for rod-like wall growth."
          },
          {
            "node_id": "roda",
            "label": "RodA",
            "node_type": "GENE_OR_PROTEIN",
            "description": "SEDS glycosyltransferase mediating lateral PG incorporation with PBP2.",
            "grounding": "InterPro:IPR001182"
          },
          {
            "node_id": "ftsw",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "FtsW",
            "node_type": "GENE_OR_PROTEIN",
            "description": "SEDS divisome polymerase for septal PG incorporation."
          },
          {
            "node_id": "septal_pg_incorporation",
            "label": "septal peptidoglycan incorporation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Division-site PG synthesis relevant to end-shaping and growth partitioning."
          }
        ],
        "edges": [
          {
            "subject": "graded_polar_pg",
            "predicate": "has output",
            "object": "end_cap_taper",
            "description": "Graded PG growth produces reduced end-cap radius.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-cellbio-101011-155745",
                "snippet": "polar growth",
                "notes": "Supports polar PG growth as the mechanism producing tapered ends."
              }
            ],
            "predicate_id": "RO:0002234"
          },
          {
            "subject": "end_cap_taper",
            "predicate": "causes",
            "object": "tapered_geometry",
            "description": "End-cap taper at both poles yields the fusiform body geometry.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-cellbio-101011-155745",
                "snippet": "cell shape is genetically determined",
                "notes": "Supports tapered geometry as a genetically determined shape outcome."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "tapered_geometry",
            "predicate": "manifests as",
            "object": "fusiform_shaped_trait",
            "description": "Tapered geometry at both poles manifests the fusiform-shaped trait.",
            "evidence": [
              {
                "reference": "DOI:10.1111/1462-2920.13731",
                "snippet": "Fusobacterium nucleatum",
                "notes": "Supports fusiform morphology as the trait endpoint."
              }
            ],
            "predicate_id": "METPO:2007400"
          },
          {
            "subject": "mreb",
            "predicate": "guides",
            "object": "lateral_pg_synthesis",
            "description": "MreB filaments orient lateral PG synthesis to maintain rod-like cell shape.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41579-020-0366-3",
                "notes": "MreB orients peptidoglycan synthesis to generate or maintain a smooth cylindrical rod shape."
              }
            ]
          },
          {
            "subject": "rodz",
            "predicate": "regulates",
            "object": "mreb_localization",
            "description": "RodZ modulates geometric localization and assembly of MreB.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s12964-025-02373-y",
                "notes": "RodZ modulates geometric localization of MreB and is required for proper MreB cytoskeleton assembly."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "rodz",
            "predicate": "scaffolds",
            "object": "elongasome",
            "description": "RodZ provides a scaffold for the elongasome via MreB, RodA, PBP2, PBP1A/1B.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41579-020-0366-3",
                "notes": "RodZ interacts with MreB, RodA, PBP2 and PBP1A/1B, providing a scaffold for the elongasome."
              }
            ]
          },
          {
            "subject": "mrec",
            "predicate": "activates",
            "object": "pbp2",
            "description": "MreC induces a structural change in PBP2 promoting its TPase activity.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41579-020-0366-3",
                "notes": "MreC induces a structural change in PBP2, promoting PBP2 TPase and RodA GTase activity."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "roda",
            "predicate": "required for",
            "object": "lateral_pg_synthesis",
            "description": "SEDS protein RodA with cognate bPBP mediates lateral PG incorporation.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.mib.2021.01.011",
                "notes": "SEDS proteins RodA/FtsW with cognate bPBPs mediate lateral versus septal PG incorporation."
              }
            ]
          },
          {
            "subject": "ftsw",
            "predicate": "required for",
            "object": "septal_pg_incorporation",
            "description": "FtsW with cognate bPBP mediates septal PG incorporation.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.mib.2021.01.011",
                "notes": "FtsW with cognate bPBP mediates septal PG incorporation."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.898157+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-11T22:45:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed causal graph linking graded polar peptidoglycan growth and end-cap taper to fusiform morphology.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T21:30:07Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007400\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:19Z",
        "curator": "claude",
        "action": "RENAME_PREDICATE_LABELS",
        "changes": "Renamed 1 causal-edge predicate label(s) to align with existing groundings: shapes \u2192 causes \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:21Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:causes\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 6 evidence-backed generic edges (10 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:13Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002211\u00d71, RO:0002213\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:19Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A1B1UYY2\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-26T07:15:19Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 5 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:H1XNL6\u00d71, UniProtKB:A0A1L9R356\u00d71, UniProtKB:A0A2D2D7X6\u00d71, UniProtKB:A0A0H2X1V4\u00d71, UniProtKB:A0A0E1R950\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:21:12Z",
        "curator": "claude",
        "action": "RETRACT_DEAD_UNIPROT_GROUNDINGS",
        "changes": "Retracted 4 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates (1 to has output), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-22T04:26:15Z",
        "curator": "codex",
        "action": "REVIEW_UNIPROT_INSTANCE_GROUNDINGS",
        "changes": "Reviewed 2 organism-specific UniProtKB grounding(s): replaced 2 with taxon-agnostic GO/InterPro terms and retracted 0 to label-only where no exact semantic term was supported (docs/GROUNDING_POLICY.md).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope fusiform_shaped_tapered_polar_growth=NONMECHANISTIC with scope_notes; marked 4 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (mreb, mrec, pbp2, ftsw).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000070",
    "label": "gas vesicle",
    "definition": "An intracellular gas-filled proteinaceous inclusion that provides buoyancy, allowing planktonic bacteria and archaea to position themselves in the water column.",
    "definition_source": "DOI:10.1038/nrmicro2834",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "traitmech:000066"
    ],
    "synonyms": [
      {
        "synonym_text": "gas vacuole",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1038/nrmicro2834"
      }
    ],
    "xrefs": [
      "GO:0031411"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/nrmicro2834",
        "notes": "Pfeifer describes gas vesicles as intracellular gas-filled proteinaceous flotation structures in bacteria and archaea."
      },
      {
        "reference": "DOI:10.1038/s41579-020-0413-0",
        "notes": "Greening & Lithgow include gas vesicles among bacterial intracellular organelles."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1126",
        "taxon_label": "Microcystis aeruginosa",
        "note": "Gas-vacuolate bloom-forming cyanobacterium; Anabaena/Dolichospermum flos-aquae is the classic Walsby gas-vesicle research model.",
        "reference": "PMID:15060038"
      },
      {
        "taxon_id": "NCBITaxon:449447",
        "taxon_label": "Microcystis aeruginosa NIES-843",
        "note": "Strain-level GvpA exemplar.",
        "reference": "PMID:15060038"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "gas_vesicle_buoyancy",
        "title": "Gas vesicles provide buoyancy and water-column positioning",
        "description": "Evidence-backed causal sketch linking proteinaceous gas-filled intracellular vesicles to buoyancy and vertical positioning in the water column.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "The taxon-matched protein example anchors one experimentally supported causal branch; it is not presented as a universal mechanism for every taxon or every contextual branch in this graph.",
        "nodes": [
          {
            "node_id": "gas_vesicle_trait",
            "label": "gas vesicle",
            "node_type": "TRAIT",
            "grounding": "traitmech:000070",
            "description": "Intracellular gas-filled proteinaceous flotation structure."
          },
          {
            "node_id": "buoyancy",
            "label": "cellular buoyancy",
            "node_type": "TRAIT",
            "description": "Reduced effective cell density permitting vertical positioning.",
            "grounding": "traitmech:000528"
          },
          {
            "node_id": "water_column_positioning",
            "label": "water-column positioning",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Vertical migration of planktonic microbes within the water column."
          },
          {
            "node_id": "gvpa_protein",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:B0JPK6",
                "protein_label": "Gas vesicle protein A",
                "gene_symbol": "gvpA1",
                "taxon_id": "NCBITaxon:449447",
                "taxon_label": "Microcystis aeruginosa NIES-843",
                "entry_status": "REVIEWED",
                "proteome_id": "UP000001510",
                "retrieved_on": "2026-10-22",
                "entry_version": 77,
                "sequence_version": 1,
                "role": "GvpA is the major structural protein forming the gas-vesicle shell in the matched Microcystis strain.",
                "evidence": [
                  {
                    "reference": "PMID:15060038",
                    "snippet": "gas vesicles provide buoyancy to Microcystis",
                    "notes": "The cited source supports the represented protein-to-trait branch; UniProt verifies this current strain-matched protein entry."
                  }
                ]
              }
            ],
            "label": "GvpA",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Small hydrophobic primary structural protein forming the gas vesicle shell."
          },
          {
            "node_id": "gas_vesicle_shell",
            "label": "gas vesicle shell",
            "node_type": "CELLULAR_LOCALIZATION",
            "description": "Hollow proteinaceous wall enclosing the gas-filled lumen.",
            "grounding": "GO:0033172"
          },
          {
            "node_id": "gvpc_protein",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "GvpC",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Accessory coat protein that reinforces the gas vesicle shell."
          },
          {
            "node_id": "hydrophobic_inner_surface",
            "label": "hydrophobic inner shell surface",
            "node_type": "QUALITY",
            "description": "Water-repellent inner surface of the gas vesicle shell."
          },
          {
            "node_id": "water_condensation",
            "label": "water condensation into lumen",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Heterogeneous condensation of water molecules into liquid inside the lumen."
          },
          {
            "node_id": "hydrostatic_pressure",
            "label": "hydrostatic pressure",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "External physical pressure acting on the gas vesicle.",
            "grounding": "PATO:0001025"
          },
          {
            "node_id": "gas_vesicle_collapse",
            "label": "gas vesicle collapse",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Irreversible structural collapse of the gas vesicle above a critical pressure."
          },
          {
            "node_id": "gvpd_protein",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "GvpD",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Regulatory protein with an inhibitory effect on gas vesicle formation."
          },
          {
            "node_id": "gas_vesicle_formation",
            "label": "gas vesicle formation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Biogenesis and assembly of gas vesicles.",
            "grounding": "GO:0031412"
          },
          {
            "node_id": "ultrasound_scattering",
            "label": "ultrasound scattering",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Scattering of ultrasound waves due to gas/aqueous density contrast."
          }
        ],
        "edges": [
          {
            "subject": "gas_vesicle_trait",
            "predicate": "confers",
            "object": "buoyancy",
            "description": "Internal gas-filled vesicles lower effective density and provide buoyancy.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2834",
                "notes": "Pfeifer describes gas vesicles as gas-filled flotation structures."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "buoyancy",
            "predicate": "enables",
            "object": "water_column_positioning",
            "description": "Buoyancy allows planktonic bacteria/archaea to position in the water column.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41579-020-0413-0",
                "notes": "Greening & Lithgow include gas vesicles among bacterial intracellular organelles."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "gvpa_protein",
            "predicate": "forms",
            "object": "gas_vesicle_shell",
            "description": "GvpA is a small hydrophobic protein that forms the hollow protein shell of the gas vesicle.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s13036-024-00426-3",
                "notes": "GvpA is the structural protein that forms the hollow protein structure of GV."
              }
            ],
            "predicate_id": "biolink:produces"
          },
          {
            "subject": "gvpc_protein",
            "predicate": "strengthens",
            "object": "gas_vesicle_shell",
            "description": "GvpC is a coat protein that strengthens the gas vesicle shell.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s13036-024-00426-3",
                "notes": "GvpC has the function of strengthening the GV shell."
              }
            ]
          },
          {
            "subject": "hydrophobic_inner_surface",
            "predicate": "prevents",
            "object": "water_condensation",
            "description": "The hydrophobic inner surface prevents heterogeneous condensation of water into liquid, maintaining the gas compartment.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s44318-024-00178-2",
                "notes": "GVs maintain an inner gas compartment via a hydrophobic inner surface that prevents condensation of water into liquid."
              }
            ],
            "predicate_id": "RO:0002212"
          },
          {
            "subject": "hydrostatic_pressure",
            "predicate": "causes",
            "object": "gas_vesicle_collapse",
            "description": "Above a critical pressure the gas vesicle irreversibly collapses.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s13036-024-00426-3",
                "notes": "When GVs are under pressure, there is a critical point at which the GV irreversibly collapses."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "gvpd_protein",
            "predicate": "inhibits",
            "object": "gas_vesicle_formation",
            "description": "GvpD has an inhibitory effect on gas vesicle formation.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s13036-024-00426-3",
                "notes": "GvpD has an inhibitory effect on GV formation."
              }
            ],
            "predicate_id": "RO:0002212"
          },
          {
            "subject": "gas_vesicle_shell",
            "predicate": "enables",
            "object": "ultrasound_scattering",
            "description": "The gas-filled vesicle scatters ultrasound due to density/compressibility contrast with the surrounding medium.",
            "evidence": [
              {
                "reference": "DOI:10.1021/acssynbio.4c00283",
                "notes": "GVs scatter US due to the difference in density and compressibility of their gaseous interior relative to surrounding aqueous medium."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "gas_vesicle_shell",
            "predicate": "part of",
            "object": "gas_vesicle_trait",
            "description": "The gas-filled compartment and its protein shell constitute the gas-vesicle structure.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s13036-024-00426-3",
                "snippet": "The gas vesicle (GV) is like a hollow nanoparticle consisting of an internal gas and a protein shell",
                "notes": "Verified against the open article abstract; the edge represents structural composition, not a functional consequence."
              }
            ],
            "predicate_id": "biolink:part_of"
          },
          {
            "subject": "gas_vesicle_collapse",
            "predicate": "negatively regulates",
            "object": "gas_vesicle_trait",
            "description": "Irreversible pressure collapse eliminates the intact gas-vesicle structural state.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s13036-024-00426-3",
                "snippet": "when GVs are under pressure, there is a critical point at which the GV irreversibly collapses",
                "notes": "Verified against the open full text's physical-properties section."
              }
            ],
            "predicate_id": "RO:0002212"
          },
          {
            "subject": "gvpd_protein",
            "predicate": "negatively regulates",
            "object": "gas_vesicle_trait",
            "description": "GvpD inhibits formation of the gas-vesicle structure under the reviewed regulatory model.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s13036-024-00426-3",
                "snippet": "GvpD has an inhibitory effect on GV formation",
                "notes": "Verified against the open full text; this connects the existing formation-regulation module without asserting a universal mechanism."
              }
            ],
            "predicate_id": "RO:0002212"
          },
          {
            "subject": "hydrophobic_inner_surface",
            "predicate": "part of",
            "object": "gas_vesicle_shell",
            "description": "The hydrophobic luminal face is the inner surface of the gas-vesicle protein shell.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s44318-024-00178-2",
                "snippet": "GVs maintain an inner gas compartment by having a hydrophobic inner surface",
                "notes": "Verified against the open full text; the same passage explains how this surface prevents liquid-water condensation."
              }
            ],
            "predicate_id": "biolink:part_of"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-06-03T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate MORPHOLOGY trait (gas vesicle / gas vacuole); buoyancy sub-variant of intracellular inclusion.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-09T15:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (gas vesicle buoyancy / water-column positioning) with RO predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 6 evidence-backed generic edges (10 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:13Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 5 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002212\u00d72, biolink:produces\u00d71, biolink:causes\u00d71, RO:0002327\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:19Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (PATO:0001025\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:33Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0033172\u00d71, GO:0031412\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-26T07:15:19Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 3 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A0B5ENA7\u00d71, UniProtKB:A0AA45D9L5\u00d71, UniProtKB:A0A059TSE2\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:21:12Z",
        "curator": "claude",
        "action": "RETRACT_DEAD_UNIPROT_GROUNDINGS",
        "changes": "Retracted 3 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-07T18:00:00Z",
        "curator": "claude",
        "action": "REGROUND_CAUSAL_EDGE",
        "changes": "Edge gas_vesicle_trait -> buoyancy in graph gas_vesicle_buoyancy: re-grounded it from enables/RO:0002327 to confers/METPO:2007700; retyped buoyancy to TRAIT. Issue 334. biolink declares enables range 'biological process or activity', which of CausalNodeTypeEnum only BIOLOGICAL_PROCESS, PATHWAY and MOLECULAR_FUNCTION satisfy, so this edge entailed a false type on its object. The corpus already types this concept BOTH ways: buoyancy is TRAIT in intracellular_inclusion.yaml, where gas_vesicle -confers-> buoyancy, and QUALITY here. That is a typing inconsistency (#352's shape), and the TRAIT reading is the right one -- 'reduced effective cell density permitting vertical positioning' is a disposition. Needs TRAIT added to `confers`' subject_types, recorded there as a decision.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "CURATE_PROTEIN_TAXON_EXAMPLE",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope gas_vesicle_buoyancy=MECHANISTIC with scope_notes; marked 3 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (gvpa_protein, gvpc_protein, gvpd_protein); added taxon-paired protein example(s) UniProtKB:B0JPK6 on gvpa_protein (NCBITaxon:449447); added canonical example(s) NCBITaxon:449447.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T06:15:40Z",
        "curator": "codex",
        "action": "ADD_EXACT_ONTOLOGY_MATCH",
        "changes": "Ontology exact-match review (2026-08-25): approved exact xref(s): GO:0031411. Evidence is predicate-scoped in the versioned ontology snapshots; OAK cross-checked direct data, and OLS4 spot-checked release deltas and disputed hits.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T06:30:00Z",
        "curator": "codex",
        "action": "CONNECT_CAUSAL_GRAPH_COMPONENTS",
        "changes": "Resolved issue #183 graph fragmentation (5 components to 1) using 4 source- and verbatim-snippet-backed connector(s). No paid research service was called.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-01T22:49:00Z",
        "curator": "codex",
        "action": "GROUND_CAUSAL_NODE_TO_NEW_TRAIT",
        "changes": "Grounded the existing causal-graph buoyancy TRAIT node to newly minted traitmech:000528 cellular buoyancy.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-22T01:35:00Z",
        "curator": "claude",
        "action": "REFRESH_UNIPROT_ENTRY_VERSION",
        "changes": "Refreshed UniProtKB entry_version against live UniProt REST on 2026-10-22: UniProtKB:B0JPK6 (76 -> 77 on gvpa_protein).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000706",
    "label": "gliding",
    "definition": "A motile in which an organism moves smoothly along solid surfaces without flagella or pili.",
    "definition_source": "DOI:10.1146/annurev.micro.55.1.49",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000702"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev.micro.55.1.49",
        "snippet": "move actively over surfaces",
        "notes": "Supports gliding as active surface movement without flagella."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:34",
        "taxon_label": "Myxococcus xanthus",
        "note": "Primary model for bacterial gliding motility and multicellular development. Flavobacterium johnsoniae is a secondary model.",
        "reference": "https://pmc.ncbi.nlm.nih.gov/articles/PMC103748/"
      },
      {
        "taxon_id": "NCBITaxon:246197",
        "taxon_label": "Myxococcus xanthus DK1622",
        "note": "Strain-level AglZ gliding exemplar.",
        "reference": "DOI:10.1016/j.cub.2016.12.035"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "gliding_surface_motility",
        "title": "Gliding surface motility mechanism",
        "description": "Evidence-backed causal sketch linking gliding to solid surfaces, cell-envelope motors, surface adhesins, and type IX secretion/gliding systems.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "The taxon-matched protein example anchors one experimentally supported causal branch; it is not presented as a universal mechanism for every taxon or every contextual branch in this graph.",
        "nodes": [
          {
            "node_id": "gliding_trait",
            "label": "gliding",
            "node_type": "TRAIT",
            "grounding": "METPO:1000706",
            "description": "Smooth movement along solid surfaces without flagella or pili."
          },
          {
            "node_id": "solid_surface",
            "label": "solid surface",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Surface substrate on which gliding movement occurs."
          },
          {
            "node_id": "gliding_motility_machinery",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:Q1D823",
                "protein_label": "Adventurous-gliding motility protein AglZ",
                "gene_symbol": "aglZ",
                "taxon_id": "NCBITaxon:246197",
                "taxon_label": "Myxococcus xanthus DK1622",
                "entry_status": "REVIEWED",
                "proteome_id": "UP000002402",
                "retrieved_on": "2026-08-25",
                "entry_version": 123,
                "sequence_version": 1,
                "role": "AglZ is a DK1622 gliding-motility factor anchoring the adventurous-gliding branch, not all bacterial gliding systems.",
                "evidence": [
                  {
                    "reference": "DOI:10.1016/j.cub.2016.12.035",
                    "snippet": "Myxococcus glides without external motility appendages",
                    "notes": "The cited source supports the represented protein-to-trait branch; UniProt verifies this current strain-matched protein entry."
                  }
                ]
              }
            ],
            "label": "gliding motility machinery",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Molecular machinery that produces surface translocation without flagella."
          },
          {
            "node_id": "surface_adhesins",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "surface adhesins",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Cell-surface proteins moved or engaged during gliding."
          },
          {
            "node_id": "type_ix_secretion_system",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "type IX secretion system",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Secretion-associated machinery linked to Flavobacterium gliding."
          },
          {
            "node_id": "proton_motive_force",
            "label": "proton motive force",
            "node_type": "STATE",
            "description": "Electrochemical gradient powering some gliding motors.",
            "grounding": "METPO:1007500"
          },
          {
            "node_id": "helical_track",
            "label": "helical conveyor track",
            "node_type": "CELLULAR_LOCALIZATION",
            "description": "Filamentous/multirail track structure in the cell envelope along which surface adhesins are translocated during gliding."
          },
          {
            "node_id": "substratum_coupling",
            "label": "substratum coupling and traction",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Engagement of surface adhesins with the solid substratum to generate the traction that drives cell movement."
          },
          {
            "node_id": "cell_propulsion",
            "label": "cell propulsion",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Forward, often screw-like, translocation of the cell body resulting from gliding machinery activity."
          },
          {
            "node_id": "gliding_gene_complement",
            "label": "gliding machinery gene complement",
            "node_type": "EXPERIMENTAL_FACTOR",
            "description": "Presence of the core gliding/secretion machinery gene set in a genome, used to predict gliding capacity."
          }
        ],
        "edges": [
          {
            "subject": "solid_surface",
            "predicate": "enables context for",
            "object": "gliding_trait",
            "description": "Gliding is a mode of active bacterial movement over surfaces.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev.micro.55.1.49",
                "snippet": "move actively over surfaces",
                "notes": "Supports surface movement as defining context for gliding."
              }
            ]
          },
          {
            "subject": "gliding_motility_machinery",
            "predicate": "confers",
            "object": "gliding_trait",
            "description": "Specialized machinery drives bacterial surface movement without flagella.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.cub.2016.12.035",
                "snippet": "without using flagella, pili, or other external appendages",
                "notes": "Supports gliding as a distinct motility mode."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "surface_adhesins",
            "predicate": "transmit force for",
            "object": "gliding_trait",
            "description": "Surface adhesins couple internal motors to external substrates.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41579-021-00626-4",
                "snippet": "moves adhesins along the cell surface",
                "notes": "Review summarizes gliding models using moving surface adhesins."
              }
            ]
          },
          {
            "subject": "type_ix_secretion_system",
            "predicate": "contributes to",
            "object": "gliding_motility_machinery",
            "description": "Type IX secretion-associated components contribute to some gliding systems.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41579-021-00626-4",
                "snippet": "type 9 secretion and gliding motility",
                "notes": "Supports linkage between type IX secretion and gliding machinery."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "proton_motive_force",
            "predicate": "powers",
            "object": "gliding_motility_machinery",
            "description": "Proton motive force can power gliding motility motors.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41579-021-00626-4",
                "snippet": "proton-driven motor that powers type 9 secretion and gliding motility",
                "notes": "Supports proton-driven gliding machinery in reviewed systems."
              }
            ],
            "predicate_id": "METPO:2007900"
          },
          {
            "subject": "helical_track",
            "predicate": "guides",
            "object": "surface_adhesins",
            "description": "Adhesins are translocated along an envelope-associated filamentous track during gliding.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s42003-023-04472-3",
                "notes": "Filamentous multirail structures in the cell envelope are associated with the gliding machinery and SprB adhesin translocation."
              }
            ]
          },
          {
            "subject": "surface_adhesins",
            "predicate": "enables",
            "object": "substratum_coupling",
            "description": "Surface adhesins engage the substratum to generate traction.",
            "evidence": [
              {
                "reference": "DOI:10.1126/sciadv.abq0619",
                "notes": "Surface adhesin at bacterial focal adhesions immobilizes motility complexes against the substratum to generate traction."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "substratum_coupling",
            "predicate": "causes",
            "object": "cell_propulsion",
            "description": "Traction at substratum-coupled adhesins drives forward movement of the cell body.",
            "evidence": [
              {
                "reference": "DOI:10.1371/journal.pbio.3001443",
                "notes": "Proton-dependent motors power adhesin surface translocation that propels the cell during gliding."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "cell_propulsion",
            "predicate": "realizes",
            "object": "gliding_trait",
            "description": "Propulsion of the cell body along a surface constitutes the gliding phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1371/journal.pbio.3001443",
                "notes": "Adhesin surface translocation produces the smooth surface movement characteristic of gliding."
              }
            ]
          },
          {
            "subject": "gliding_gene_complement",
            "predicate": "predicts",
            "object": "gliding_trait",
            "description": "Presence of the core gliding/secretion machinery gene set predicts gliding capacity from genomes.",
            "evidence": [
              {
                "reference": "DOI:10.1021/acsomega.3c05155",
                "notes": "T9GPred predicts gliding motility from an 11-protein mandatory component set across Bacteroidetes genomes."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.907644+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-11T00:00:00-07:00",
        "curator": "codex",
        "action": "CURATED_WITH_LITERATURE",
        "changes": "Reviewed gliding trait and added DOI-backed causal graph for surface gliding machinery, adhesins, type IX secretion, and proton motive force.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d71, RO:0002326\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:41:04Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (METPO:1007500\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-26T02:30:13Z",
        "curator": "claude",
        "action": "RETYPE_CAUSAL_NODES",
        "changes": "Re-typed 1 causal-node node_type field(s) to align with CausalNodeTypeEnum semantics: proton motive force: BIOLOGICAL_PROCESS \u2192 STATE \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-26T05:00:48Z",
        "curator": "claude",
        "action": "RENAME_PREDICATE_LABELS",
        "changes": "Renamed 1 causal-edge predicate label(s) to align with existing groundings: powers \u2192 enables \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-26T05:00:50Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-17T04:09:44Z",
        "curator": "claude",
        "action": "REMOVE_REDUNDANT_SYNONYM",
        "changes": "Removed 1 synonym(s) whose text duplicated the label (seeder redundancy; no information lost).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 5 evidence-backed generic edges (4 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:13Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d71, biolink:causes\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 1 causal edge(s) off enables/RO:0002327 with a TRAIT object (1 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T08:00:00Z",
        "curator": "claude",
        "action": "REGROUND_CAUSAL_EDGE",
        "changes": "Re-grounded causal edge(s) off enables/RO:0002327 onto contributes to (RO:0002326), issue 334. biolink declares enables range 'biological process or activity', which only BIOLOGICAL_PROCESS, PATHWAY and MOLECULAR_FUNCTION satisfy, so an edge pointing at a GENE_OR_PROTEIN entailed a false type. The replacements are chosen per idiom rather than swept: a gene cluster ENCODES its product, a subunit is PART OF the complex it belongs to, and an energy source or acquired repertoire CONTRIBUTES TO the machine it powers or composes. All three declare no rdfs:domain or rdfs:range, so none can reintroduce the class of defect being removed.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T09:00:00Z",
        "curator": "claude",
        "action": "REGROUND_CAUSAL_EDGE",
        "changes": "Reverted the motive-force edge from contributes to back to enables/RO:0002327, issue 334 review. biolink defines contributes to as holding where one entity contributes to the occurrence or GENERATION of the other. A motive force does not generate the motor or machinery - it powers rotation, which is what the edge description says. That is the same energy-powers-a-machine idiom this work deferred for molecular_oxygen and cytoplasmic_na, so deferring it here too is the consistent call. The edge stays baselined under issue 334 until it is modelled as an input to the machine or pointed at the rotation process, either of which is range-correct.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-07T18:00:00Z",
        "curator": "claude",
        "action": "REGROUND_CAUSAL_EDGE",
        "changes": "Edge proton_motive_force -> gliding_motility_machinery in graph gliding_surface_motility: re-grounded it from enables/RO:0002327 to powers/METPO:2007900. Issue 334. biolink declares enables range 'biological process or activity', which of CausalNodeTypeEnum only BIOLOGICAL_PROCESS, PATHWAY and MOLECULAR_FUNCTION satisfy, so this edge entailed a false type on its object. 'Proton motive force can POWER gliding motility motors.'",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "CURATE_PROTEIN_TAXON_EXAMPLE",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope gliding_surface_motility=MECHANISTIC with scope_notes; marked 3 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (gliding_motility_machinery, surface_adhesins, type_ix_secretion_system); added taxon-paired protein example(s) UniProtKB:Q1D823 on gliding_motility_machinery (NCBITaxon:246197); added canonical example(s) NCBITaxon:246197.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000699",
    "label": "gram negative",
    "definition": "A gram stain in which bacteria do not retain crystal violet dye and appear pink or red after staining, indicating a thin peptidoglycan layer and presence of an outer membrane.",
    "definition_source": "DOI:10.1038/s41579-019-0201-x",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000697"
    ],
    "synonyms": [
      {
        "synonym_text": "G_negative",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "negative",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "created_by": "Luke Wang",
    "evidence": [
      {
        "reference": "DOI:10.1038/s41579-019-0201-x",
        "snippet": "defining feature of the Gram-negative cell envelope",
        "notes": "Supports the outer membrane as a defining Gram-negative envelope feature."
      },
      {
        "reference": "PMID:27564552",
        "snippet": "Gram-Negative Bacterium Escherichia coli",
        "notes": "Organism example: Escherichia coli is described as Gram-negative."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:562",
        "taxon_label": "Escherichia coli",
        "note": "Model Gram-negative (outer membrane plus thin peptidoglycan).",
        "reference": "PMID:9278503"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "gram_negative_outer_membrane_dye_loss",
        "title": "Gram-negative outer-membrane dye-loss mechanism",
        "description": "Evidence-backed causal sketch linking Gram-negative staining to outer membrane architecture, lipopolysaccharide, thin peptidoglycan, decolorization, and counterstain uptake.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "Gram-negative is an envelope/staining classification rather than one inherited protein mechanism. Contextual envelope complexes are retained without assigning a token UniProt example.",
        "nodes": [
          {
            "node_id": "gram_negative_trait",
            "label": "gram negative",
            "node_type": "TRAIT",
            "grounding": "METPO:1000699",
            "description": "Gram stain phenotype in which cells lose crystal violet and appear pink or red after counterstaining."
          },
          {
            "node_id": "outer_membrane",
            "label": "outer membrane",
            "node_type": "CELLULAR_LOCALIZATION",
            "description": "Gram-negative outer membrane outside the peptidoglycan layer.",
            "grounding": "GO:0019867"
          },
          {
            "node_id": "lipopolysaccharide",
            "label": "lipopolysaccharide",
            "node_type": "CHEMICAL",
            "description": "Glycolipid found in the outer leaflet of Gram-negative outer membranes.",
            "grounding": "CHEBI:16412"
          },
          {
            "node_id": "thin_peptidoglycan_layer",
            "label": "thin peptidoglycan layer",
            "node_type": "CELLULAR_LOCALIZATION",
            "description": "Thin peptidoglycan layer in the Gram-negative periplasm."
          },
          {
            "node_id": "periplasmic_space",
            "label": "periplasmic space",
            "node_type": "CELLULAR_LOCALIZATION",
            "description": "Cell-envelope compartment between inner and outer membranes.",
            "grounding": "GO:0042597"
          },
          {
            "node_id": "crystal_violet_iodine_complex",
            "label": "crystal violet-iodine complex",
            "node_type": "CHEMICAL",
            "description": "Dye complex removed during decolorization in Gram-negative cells."
          },
          {
            "node_id": "counterstain",
            "label": "counterstain",
            "node_type": "CHEMICAL",
            "description": "Safranin or similar stain producing pink/red appearance."
          },
          {
            "node_id": "outer_membrane_outer_leaflet",
            "label": "outer membrane outer leaflet",
            "node_type": "CELLULAR_LOCALIZATION",
            "description": "Outer leaflet of the Gram-negative outer membrane, occupied by LPS."
          },
          {
            "node_id": "divalent_cations",
            "label": "divalent cations (Mg2+/Ca2+)",
            "node_type": "CHEMICAL",
            "description": "Magnesium and calcium ions that bridge and stabilize LPS packing in the OM."
          },
          {
            "node_id": "outer_membrane_barrier_function",
            "label": "outer membrane barrier function",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "Low-permeability barrier property of the Gram-negative outer membrane."
          },
          {
            "node_id": "lpt_pathway",
            "label": "Lpt pathway",
            "node_type": "PATHWAY",
            "description": "Trans-envelope ATP-driven machinery transporting LPS from the inner to outer membrane."
          },
          {
            "node_id": "bam_complex",
            "label": "BAM complex",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Beta-barrel assembly machinery (BamA-E) that folds and inserts OMPs into the outer membrane.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "BAM is a multiprotein complex whose composition varies by lineage; no single protein-family term represents the whole node."
          },
          {
            "node_id": "beta_barrel_omps",
            "label": "beta-barrel outer membrane proteins",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Beta-barrel outer membrane proteins folded and inserted by the BAM complex.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "This label denotes a structurally broad collection of unrelated outer-membrane protein families."
          },
          {
            "node_id": "mla_pathway",
            "label": "Mla pathway",
            "node_type": "PATHWAY",
            "description": "Retrograde phospholipid transport system maintaining outer membrane lipid asymmetry."
          },
          {
            "node_id": "outer_membrane_lipid_asymmetry",
            "label": "outer membrane lipid asymmetry",
            "node_type": "QUALITY",
            "description": "Asymmetric lipid distribution (LPS outer / phospholipid inner) of the OM."
          },
          {
            "node_id": "tol_pal_system",
            "label": "Tol-Pal system",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Envelope-spanning complex safeguarding connectivity of the Gram-negative cell envelope.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Tol-Pal is a multiprotein system and cannot be represented by one component family or accession."
          },
          {
            "node_id": "cell_envelope_connectivity",
            "label": "cell envelope connectivity",
            "node_type": "QUALITY",
            "description": "Maintained connectivity between outer membrane, peptidoglycan, and inner membrane."
          }
        ],
        "edges": [
          {
            "subject": "outer_membrane",
            "predicate": "defines",
            "object": "gram_negative_trait",
            "description": "The outer membrane is a defining feature of the Gram-negative cell envelope.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41579-019-0201-x",
                "snippet": "defining feature of the Gram-negative cell envelope",
                "notes": "Supports outer membrane as the key Gram-negative envelope feature."
              }
            ],
            "predicate_id": "METPO:2007500"
          },
          {
            "subject": "lipopolysaccharide",
            "predicate": "localized in",
            "object": "outer_membrane",
            "description": "LPS is found on the outer surface of the Gram-negative outer membrane.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41579-019-0201-x",
                "snippet": "lipopolysaccharide exclusively found on the surface",
                "notes": "Supports LPS as a surface-exposed outer-membrane component."
              }
            ],
            "predicate_id": "biolink:located_in"
          },
          {
            "subject": "thin_peptidoglycan_layer",
            "predicate": "localized in",
            "object": "periplasmic_space",
            "description": "Gram-negative peptidoglycan is a thin layer in the periplasm.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.bbalip.2016.10.010",
                "snippet": "periplasm ... containing a thin layer of peptidoglycan",
                "notes": "Supports thin periplasmic peptidoglycan in Gram-negative envelopes."
              }
            ],
            "predicate_id": "biolink:located_in"
          },
          {
            "subject": "thin_peptidoglycan_layer",
            "predicate": "fails to retain",
            "object": "crystal_violet_iodine_complex",
            "description": "Thin peptidoglycan and outer-membrane disruption allow dye complex loss during decolorization.",
            "evidence": [
              {
                "reference": "DOI:10.3109/10520299609117151",
                "snippet": "cell wall ... responsible for retention",
                "notes": "Inference from Gram-positive retention mechanism; thinner Gram-negative peptidoglycan contributes to non-retention."
              }
            ]
          },
          {
            "subject": "counterstain",
            "predicate": "confers",
            "object": "gram_negative_trait",
            "description": "Counterstain gives decolorized Gram-negative cells their pink/red appearance.",
            "evidence": [
              {
                "reference": "DOI:10.3109/10520299609117151",
                "snippet": "mechanism of the Gram stain",
                "notes": "Supports Gram stain procedure context; counterstain appearance follows dye-complex loss."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "lipopolysaccharide",
            "predicate": "occupies",
            "object": "outer_membrane_outer_leaflet",
            "description": "LPS occupies the outer leaflet of the Gram-negative outer membrane (OM asymmetry).",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-micro-032521-014507",
                "notes": "LPS occupies the outer leaflet while phospholipids occupy the inner leaflet."
              }
            ]
          },
          {
            "subject": "divalent_cations",
            "predicate": "stabilizes",
            "object": "lipopolysaccharide",
            "description": "Divalent cations (Mg2+/Ca2+) stabilize LPS packing in the OM outer leaflet.",
            "evidence": [
              {
                "reference": "DOI:10.3390/pathogens13100889",
                "notes": "Divalent cations (Mg2+/Ca2+) stabilize LPS packing."
              }
            ]
          },
          {
            "subject": "lipopolysaccharide",
            "predicate": "contributes to",
            "object": "outer_membrane_barrier_function",
            "description": "Tight LPS packing with OM proteins creates the impermeable OM barrier.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-micro-032521-014507",
                "notes": "The tight packing of LPS and OM proteins creates an impermeable barrier."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "lpt_pathway",
            "predicate": "transports",
            "object": "lipopolysaccharide",
            "description": "The Lpt machinery transports LPS across the periplasm for insertion into the OM.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s12275-024-00137-w",
                "notes": "LPS transported to the OM by the ATP-driven Lpt machinery; moves LPS across periplasm for OM insertion."
              }
            ],
            "predicate_id": "METPO:2007812"
          },
          {
            "subject": "bam_complex",
            "predicate": "inserts",
            "object": "beta_barrel_omps",
            "description": "The BAM complex folds and inserts beta-barrel OMPs into the outer membrane.",
            "evidence": [
              {
                "reference": "DOI:10.3390/pathogens13100889",
                "notes": "The Bam complex (BamA-E) folds uOMPs into beta-barrels."
              }
            ]
          },
          {
            "subject": "mla_pathway",
            "predicate": "maintains",
            "object": "outer_membrane_lipid_asymmetry",
            "description": "The Mla pathway counteracts phospholipid flipping to maintain OM lipid asymmetry.",
            "evidence": [
              {
                "reference": "DOI:10.3390/pathogens13100889",
                "notes": "Mla system performs retrograde transport to counteract PL flipping to the outer leaflet."
              }
            ]
          },
          {
            "subject": "tol_pal_system",
            "predicate": "safeguards",
            "object": "cell_envelope_connectivity",
            "description": "Tol-Pal safeguards connectivity between the three layers of the Gram-negative envelope.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s44259-024-00065-0",
                "notes": "Tol-Pal safeguards connectivity between the three layers of the Gram-negative cell envelope."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.903067+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-06T14:40:41-07:00",
        "curator": "codex",
        "action": "CURATED_WITH_ORGANISM_EXAMPLE",
        "changes": "Added Escherichia coli organism example with PMID-backed evidence.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-11T00:00:00-07:00",
        "curator": "codex",
        "action": "CURATED_WITH_LITERATURE",
        "changes": "Replaced PMID definition source with DOI-backed Gram-negative envelope source and added causal graph for outer membrane, lipopolysaccharide, periplasmic thin peptidoglycan, dye loss, and counterstaining.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T08:21:50Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:located_in\u00d72).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:38:00Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0019867\u00d71, GO:0042597\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T07:37:40Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007500\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-14T05:51:46Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:16412\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 7 evidence-backed generic edges (10 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:13Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002326\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:39Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000207\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates (1 to confers), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T02:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES_PART2",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates onto their causal-graph counterparts (1 to transports), issue 301 part 2. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Each replacement is a 1:1 mirror of its source predicate that changes only the domain, so the claim each edge makes is unchanged and directions are unchanged. The replacements are proposed in proposals/metpo_traitmech_v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope gram_negative_outer_membrane_dye_loss=NONMECHANISTIC with scope_notes; marked 3 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (bam_complex, beta_barrel_omps, tol_pal_system).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000698",
    "label": "gram positive",
    "definition": "A gram stain in which an organism retains crystal violet dye and appears purple under microscopy due to a thick peptidoglycan cell wall.",
    "definition_source": "DOI:10.3109/10520299609117151",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000697"
    ],
    "synonyms": [
      {
        "synonym_text": "G_positive",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "positive",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.3109/10520299609117151",
        "snippet": "retention of a crystal violet:iodine complex",
        "notes": "Supports Gram-positive phenotype as retention of crystal violet-iodine complex."
      },
      {
        "reference": "PMID:16950365",
        "snippet": "Staphylococcus aureus is a gram-positive bacterium",
        "notes": "Organism example: Staphylococcus aureus is described as Gram-positive."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1423",
        "taxon_label": "Bacillus subtilis",
        "note": "Model Gram-positive (thick peptidoglycan, no outer membrane); strain 168 is the workhorse.",
        "reference": "PMID:9384377"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "gram_positive_cell_wall_retention",
        "title": "Gram-positive cell-wall dye retention mechanism",
        "description": "Evidence-backed causal sketch linking Gram-positive staining to thick peptidoglycan, wall teichoic acids, low decolorizer permeability, and crystal violet-iodine retention.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "Gram-positive is an envelope/staining classification spanning many taxa, not a single protein-mediated mechanism; no token protein is appropriate.",
        "nodes": [
          {
            "node_id": "gram_positive_trait",
            "label": "gram positive",
            "node_type": "TRAIT",
            "grounding": "METPO:1000698",
            "description": "Gram stain phenotype in which cells retain crystal violet and appear purple."
          },
          {
            "node_id": "thick_peptidoglycan_cell_wall",
            "label": "thick peptidoglycan cell wall",
            "node_type": "CELLULAR_LOCALIZATION",
            "description": "Multilayered peptidoglycan wall characteristic of Gram-positive bacteria."
          },
          {
            "node_id": "wall_teichoic_acids",
            "label": "wall teichoic acids",
            "node_type": "CHEMICAL",
            "description": "Anionic cell-wall glycopolymers attached to Gram-positive peptidoglycan."
          },
          {
            "node_id": "lipoteichoic_acids",
            "label": "lipoteichoic acids",
            "node_type": "CHEMICAL",
            "description": "Membrane-anchored Gram-positive cell-wall glycopolymers.",
            "grounding": "CHEBI:28640"
          },
          {
            "node_id": "crystal_violet_iodine_complex",
            "label": "crystal violet-iodine complex",
            "node_type": "CHEMICAL",
            "description": "Dye complex retained after decolorization."
          },
          {
            "node_id": "alcohol_decolorization",
            "label": "alcohol decolorization",
            "node_type": "EXPERIMENTAL_FACTOR",
            "description": "Gram stain step that removes dye complex from Gram-negative cells."
          },
          {
            "node_id": "iodine_mordant",
            "label": "iodine mordant",
            "node_type": "CHEMICAL",
            "description": "Iodine added during Gram staining that acts as a mordant binding crystal violet."
          },
          {
            "node_id": "cv_iodine_complex_formation",
            "label": "crystal violet-iodine complex formation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Formation of large crystal violet-iodine complexes within the cell during Gram staining."
          },
          {
            "node_id": "peptidoglycan_mesh_low_porosity",
            "label": "peptidoglycan mesh low porosity",
            "node_type": "QUALITY",
            "description": "Low physical porosity of the thick peptidoglycan mesh that traps the dye complex."
          },
          {
            "node_id": "d_alanine_esters",
            "label": "D-alanine esters on teichoic acids",
            "node_type": "CHEMICAL",
            "description": "D-alanine ester modifications on teichoic acids that neutralize phosphate negative charge."
          },
          {
            "node_id": "teichoic_acid_negative_charge",
            "label": "teichoic-acid negative charge",
            "node_type": "QUALITY",
            "description": "Anionic phosphate-rich negative charge contributed by teichoic acids."
          },
          {
            "node_id": "d_alanylation_teichoic_acids",
            "label": "D-alanylation of teichoic acids",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Modification of wall and lipoteichoic acids with D-alanine esters."
          },
          {
            "node_id": "positively_charged_cell_surface",
            "label": "positively charged cell surface",
            "node_type": "QUALITY",
            "description": "More positively charged Gram-positive cell surface resulting from D-alanylation."
          }
        ],
        "edges": [
          {
            "subject": "thick_peptidoglycan_cell_wall",
            "predicate": "retains",
            "object": "crystal_violet_iodine_complex",
            "description": "Thick Gram-positive cell walls retain the dye-iodine complex during decolorization.",
            "evidence": [
              {
                "reference": "DOI:10.3109/10520299609117151",
                "snippet": "cell wall ... responsible for retention",
                "notes": "Supports retention of crystal violet-iodine complex by the Gram-positive cell wall."
              }
            ]
          },
          {
            "subject": "wall_teichoic_acids",
            "predicate": "embedded in",
            "object": "thick_peptidoglycan_cell_wall",
            "description": "Wall teichoic acids are major glycopolymers in the Gram-positive wall matrix.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro1861",
                "snippet": "peptidoglycan-attached",
                "notes": "Supports teichoic acids as peptidoglycan-attached Gram-positive wall polymers."
              }
            ],
            "predicate_id": "biolink:located_in"
          },
          {
            "subject": "lipoteichoic_acids",
            "predicate": "contributes to",
            "object": "thick_peptidoglycan_cell_wall",
            "description": "Lipoteichoic acids are membrane-attached glycopolymers in Gram-positive cell envelopes.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro1861",
                "snippet": "membrane-attached",
                "notes": "Supports lipoteichoic acids as membrane-attached Gram-positive glycopolymers."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "alcohol_decolorization",
            "predicate": "fails to remove",
            "object": "crystal_violet_iodine_complex",
            "description": "Gram-positive cells retain dye complex after decolorization and remain purple.",
            "evidence": [
              {
                "reference": "DOI:10.3109/10520299609117151",
                "snippet": "retention of a crystal violet:iodine complex",
                "notes": "Supports retention during the Gram reaction."
              }
            ]
          },
          {
            "subject": "crystal_violet_iodine_complex",
            "predicate": "confers",
            "object": "gram_positive_trait",
            "description": "Retained dye complex produces the observed Gram-positive staining phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1128/jb.156.2.837-845.1983",
                "snippet": "crystal violet-iodine complex",
                "notes": "Supports the dye complex as the chemical basis of staining."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "iodine_mordant",
            "predicate": "causes",
            "object": "cv_iodine_complex_formation",
            "description": "Iodine acts as a mordant, interacting with crystal violet to form large complexes.",
            "evidence": [
              {
                "reference": "DOI:10.52403/ijrr.20230934",
                "notes": "When iodine is added, it interacts with CV+ to form large complexes."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "cv_iodine_complex_formation",
            "predicate": "has output",
            "object": "crystal_violet_iodine_complex",
            "description": "Formation of the crystal violet-iodine complex retained within the peptidoglycan mesh.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s42003-026-10072-8",
                "notes": "The Gram stain relies on retention of crystal violet-iodine complexes within the peptidoglycan mesh."
              }
            ],
            "predicate_id": "RO:0002234"
          },
          {
            "subject": "peptidoglycan_mesh_low_porosity",
            "predicate": "increases",
            "object": "crystal_violet_iodine_complex",
            "description": "Low-porosity thick peptidoglycan walls trap and retain the dye complex.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s42003-026-10072-8",
                "notes": "Crystal violet-iodine retention depends on the physical porosity of the peptidoglycan mesh; thick, low-porosity walls can trap the complex."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "d_alanine_esters",
            "predicate": "neutralizes",
            "object": "teichoic_acid_negative_charge",
            "description": "D-alanine esters neutralize the phosphate-rich negative charge of teichoic acids.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-023-01411-0",
                "notes": "These polymers are commonly modified with D-alanine esters that neutralize phosphate-rich negative charge."
              }
            ]
          },
          {
            "subject": "d_alanylation_teichoic_acids",
            "predicate": "increases",
            "object": "positively_charged_cell_surface",
            "description": "D-alanylation of both teichoic acid types leads to a more positively charged cell surface.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuaa064",
                "notes": "D-alanylation of both teichoic acid types leads to a more positively charged cell surface."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "wall_teichoic_acids",
            "predicate": "influences",
            "object": "positively_charged_cell_surface",
            "description": "Wall teichoic acids and their anionic/cationic balance affect cell-surface charge.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-micro-092412-155620",
                "notes": "WTAs anionic/cationic balance affects cell-surface charge and antimicrobial interactions."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.902486+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-06T14:40:41-07:00",
        "curator": "codex",
        "action": "CURATED_WITH_ORGANISM_EXAMPLE",
        "changes": "Added Staphylococcus aureus organism example with PMID-backed evidence.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-11T00:00:00-07:00",
        "curator": "codex",
        "action": "CURATED_WITH_LITERATURE",
        "changes": "Replaced PMID definition source with DOI-backed Gram stain source and added causal graph for Gram-positive cell-wall dye retention, peptidoglycan, wall teichoic acids, and lipoteichoic acids.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002326\u00d71, METPO:2000202\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-13T21:03:26Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:located_in\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-14T06:55:38Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:28640\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 6 evidence-backed generic edges (7 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:13Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 4 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002213\u00d72, biolink:causes\u00d71, METPO:2000202\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 2 causal edge(s) off microbe-domain METPO predicates (1 to confers, 1 to has output), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope gram_positive_cell_wall_retention=NONMECHANISTIC with scope_notes.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000697",
    "label": "gram stain",
    "definition": "A phenotype where microorganisms are grouped based on their ability to retain crystal violet dye in the Gram staining procedure.",
    "definition_source": "DOI:10.3109/10520299609117151",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "synonyms": [
      {
        "synonym_text": "Morphology.cell morphology.gram stain",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "gram_stain",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "created_by": "Luke Wang",
    "evidence": [
      {
        "reference": "DOI:10.3109/10520299609117151",
        "snippet": "retention of a crystal violet:iodine complex",
        "notes": "Supports Gram staining as differential retention of crystal violet-iodine complex."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:562",
        "taxon_label": "Escherichia coli",
        "reference": "PMID:9278503",
        "note": "Escherichia coli exemplifies the Gram-negative outcome of the differential stain and its thin-peptidoglycan, outer-membrane envelope branch."
      },
      {
        "taxon_id": "NCBITaxon:1423",
        "taxon_label": "Bacillus subtilis",
        "reference": "PMID:9384377",
        "note": "Bacillus subtilis exemplifies the Gram-positive outcome and thick-peptidoglycan envelope branch of this broad stain class."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "gram_stain_cell_envelope_retention",
        "title": "Gram stain cell-envelope retention mechanism",
        "description": "Evidence-backed causal sketch linking Gram stain phenotype to crystal violet-iodine complex formation, peptidoglycan architecture, outer membrane loss during decolorization, and counterstaining.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record describes a differential staining assay and envelope-level classification, for which one inherited protein example would be misleading.",
        "nodes": [
          {
            "node_id": "gram_stain_trait",
            "label": "gram stain",
            "node_type": "TRAIT",
            "grounding": "METPO:1000697",
            "description": "Differential staining phenotype based on retention of crystal violet dye."
          },
          {
            "node_id": "crystal_violet",
            "label": "crystal violet",
            "node_type": "CHEMICAL",
            "description": "Primary dye used in the Gram staining procedure.",
            "grounding": "CHEBI:41688"
          },
          {
            "node_id": "iodine_mordant",
            "label": "iodine mordant",
            "node_type": "CHEMICAL",
            "description": "Iodine solution that forms a dye-iodine complex with crystal violet."
          },
          {
            "node_id": "crystal_violet_iodine_complex",
            "label": "crystal violet-iodine complex",
            "node_type": "CHEMICAL",
            "description": "Dye complex retained or removed during Gram staining."
          },
          {
            "node_id": "peptidoglycan_cell_wall",
            "label": "peptidoglycan cell wall",
            "node_type": "CELLULAR_LOCALIZATION",
            "grounding": "GO:0009274",
            "description": "Cell-wall polymer layer influencing stain retention."
          },
          {
            "node_id": "outer_membrane",
            "label": "outer membrane",
            "node_type": "CELLULAR_LOCALIZATION",
            "description": "Gram-negative cell-envelope membrane disrupted during decolorization.",
            "grounding": "GO:0019867"
          },
          {
            "node_id": "alcohol_decolorization",
            "label": "alcohol decolorization",
            "node_type": "EXPERIMENTAL_FACTOR",
            "description": "Decolorization step that differentiates Gram-positive and Gram-negative staining."
          },
          {
            "node_id": "crystal_violet_iodine_retention",
            "label": "crystal violet-iodine retention",
            "node_type": "QUALITY",
            "description": "Retention of the crystal violet-iodine complex after Gram decolorization."
          }
        ],
        "edges": [
          {
            "subject": "crystal_violet",
            "predicate": "contributes to",
            "object": "crystal_violet_iodine_complex",
            "description": "Crystal violet contributes the dye cation to the insoluble crystal violet-iodide precipitate formed during the Gram stain.",
            "evidence": [
              {
                "reference": "DOI:10.1128/jb.156.2.837-845.1983",
                "snippet": "interacts with aqueous KI-I2 during the Gram stain via a simple metathetical anion exchange",
                "notes": "Verified against the open Davies et al. abstract; crystal violet reacts with the iodide mordant during Gram staining to form the insoluble dye-iodide precipitate."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "peptidoglycan_cell_wall",
            "predicate": "contributes to",
            "object": "crystal_violet_iodine_retention",
            "description": "Peptidoglycan wall architecture determines whether the dye complex remains after decolorization.",
            "evidence": [
              {
                "reference": "DOI:10.3109/10520299609117151",
                "snippet": "Gram-positive microorganisms require a relatively thick cell wall",
                "notes": "Verified against the public Popescu and Doyle abstract; the Gram-positive cell wall is the structural determinant for retaining the dye-iodine complex."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "alcohol_decolorization",
            "predicate": "contributes to",
            "object": "gram_stain_trait",
            "description": "Decolorization contributes to the differential Gram reaction by damaging Gram-negative cell surfaces and causing dye-complex loss.",
            "evidence": [
              {
                "reference": "DOI:10.3109/10520299609117151",
                "snippet": "staining procedures damage the cell surface resulting in loss of dye complexes",
                "notes": "Verified against the public Popescu and Doyle abstract; decolorization is retained as an assay step contributing to the broad Gram stain phenotype rather than asserted as complete outer-membrane removal."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "outer_membrane",
            "predicate": "regulates",
            "object": "gram_stain_trait",
            "description": "The Gram-negative outer membrane contributes to dye loss and counterstain appearance.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41579-019-0201-x",
                "snippet": "defining feature of the Gram-negative cell envelope",
                "notes": "Supports the outer membrane as a defining Gram-negative envelope feature."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "peptidoglycan_cell_wall",
            "predicate": "causes",
            "object": "gram_stain_trait",
            "description": "Peptidoglycan wall structure is the major structural determinant of differential Gram-stain retention.",
            "evidence": [
              {
                "reference": "DOI:10.3109/10520299609117151",
                "snippet": "Gram-stainability is a function of the cell wall",
                "notes": "Verified against the public Popescu and Doyle abstract; the review ties the Gram reaction to the cell wall rather than chemistry of intracellular constituents."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "iodine_mordant",
            "predicate": "contributes to",
            "object": "crystal_violet_iodine_complex",
            "description": "The iodide mordant supplies the bulky anion that reacts with crystal violet to form the dye-iodide precipitate.",
            "evidence": [
              {
                "reference": "DOI:10.1128/jb.156.2.837-845.1983",
                "snippet": "apparent 1:1 stoichiometry between anion (I-) and cation",
                "notes": "Verified against the open Davies et al. abstract; the iodide anion and crystal-violet cation react stoichiometrically in the Gram stain."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "crystal_violet_iodine_complex",
            "predicate": "contributes to",
            "object": "crystal_violet_iodine_retention",
            "description": "The insoluble crystal violet-iodine complex is the retained dye precipitate that initiates the Gram reaction.",
            "evidence": [
              {
                "reference": "DOI:10.1128/jb.156.2.837-845.1983",
                "snippet": "same precipitate which forms in the cellular substance of bacteria",
                "notes": "Verified against the open Davies et al. abstract; the crystal violet-iodide precipitate forms inside both Gram-positive and Gram-negative bacteria before the differential decolorization step."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "crystal_violet_iodine_retention",
            "predicate": "confers",
            "object": "gram_stain_trait",
            "description": "Differential retention of the dye-iodine complex is the proximal assay state for the Gram stain phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.3109/10520299609117151",
                "snippet": "irrespective of composition, to retain the dye",
                "notes": "Verified against the public Popescu and Doyle abstract; the review frames dye retention as the proximal state in the Gram-stain assay."
              }
            ],
            "predicate_id": "METPO:2007700"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.901879+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-11T00:00:00-07:00",
        "curator": "codex",
        "action": "CURATED_WITH_LITERATURE",
        "changes": "Reviewed Gram stain trait and added DOI-backed causal graph for crystal violet-iodine complex retention, peptidoglycan cell wall architecture, outer membrane influence, and alcohol decolorization.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:38:00Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0019867\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-26T05:00:48Z",
        "curator": "claude",
        "action": "RENAME_PREDICATE_LABELS",
        "changes": "Renamed 2 causal-edge predicate label(s) to align with existing groundings: influences \u2192 regulates \u00d71; determines \u2192 causes \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-26T05:00:50Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002211\u00d71, biolink:causes\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-14T05:51:46Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:41688\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope gram_stain_cell_envelope_retention=NONMECHANISTIC with scope_notes.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T04:43:24Z",
        "curator": "codex",
        "action": "ADD_CANONICAL_EXAMPLES",
        "changes": "Resolved issue #444 after the #591 source/bin policy with 2 direct source-backed canonical example(s): Escherichia coli (NCBITaxon:562; PMID:9278503), Bacillus subtilis (NCBITaxon:1423; PMID:9384377). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-04T06:00:00Z",
        "curator": "codex",
        "action": "REVIEW_CAUSAL_EVIDENCE",
        "changes": "Reviewed the gram_stain_cell_envelope_retention graph for issue #183: added exact snippets to 4 assay evidence entries, replaced 3 residual predicates, added a dye-retention node with 3 grounded connector edges, and connected the reagent chemistry to the retention phenotype. No paid research service was called.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-07T02:20:00Z",
        "curator": "codex",
        "action": "ADVERSARIAL_REVIEW_REPAIR",
        "changes": "Addressed PR #664 adversarial review issue #682: replaced nested Popescu and Doyle dye-retention snippets with distinct exact cell-wall and dye-retention wording.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000700",
    "label": "gram variable",
    "definition": "A gram stain in which bacteria from the same culture show both gram-positive and gram-negative staining characteristics, often due to age of culture or cell wall degradation.",
    "definition_source": "DOI:10.1128/CMR.00043-07",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000697"
    ],
    "synonyms": [
      {
        "synonym_text": "variable",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "created_by": "Luke Wang",
    "evidence": [
      {
        "reference": "DOI:10.1128/CMR.00043-07",
        "snippet": "cell wall structure",
        "notes": "Bacterial cell-wall review supports peptidoglycan thinning and autolysis-mediated loss of crystal-violet retention as the basis for gram-variable staining."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1665",
        "taxon_label": "Arthrobacter globiformis",
        "note": "Gram-variable rod-coccus cycle",
        "reference": "PMID:1689718"
      },
      {
        "taxon_id": "NCBITaxon:1488",
        "taxon_label": "Clostridium acetobutylicum",
        "note": "stains Gram-variable in age",
        "reference": "https://www.epa.gov/sites/default/files/2015-09/documents/fra003.pdf"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "gram_variable_wall_thinning",
        "title": "Gram-variable peptidoglycan thinning",
        "description": "DOI-backed graph linking culture-age-dependent peptidoglycan thinning and autolysis to inconsistent gram-staining within a single bacterial population.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "Gram variability is a culture-state staining outcome rather than a stable protein-mediated trait; no token protein example is appropriate.",
        "nodes": [
          {
            "node_id": "gram_variable_trait",
            "label": "gram variable",
            "node_type": "TRAIT",
            "grounding": "METPO:1000700",
            "description": "Mixed gram-positive and gram-negative staining within a single culture."
          },
          {
            "node_id": "culture_aging",
            "label": "culture aging",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Stationary-phase or post-exponential growth conditions promoting cell-wall remodeling."
          },
          {
            "node_id": "peptidoglycan_thinning",
            "label": "peptidoglycan thinning",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Cell-wall degradation or thinning due to autolysis or stress."
          },
          {
            "node_id": "crystal_violet_retention_loss",
            "label": "crystal-violet retention loss",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Loss of the thick PG layer required to retain the gram-stain dye."
          },
          {
            "node_id": "mixed_staining",
            "label": "mixed-population gram staining",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Co-existence of gram-positive and gram-negative-staining cells in the same culture."
          },
          {
            "node_id": "thin_peptidoglycan_layer",
            "label": "thin peptidoglycan layer",
            "node_type": "CELLULAR_LOCALIZATION",
            "description": "A reduced-thickness peptidoglycan sacculus, as in some monoderm bacteria."
          },
          {
            "node_id": "cv_iodide_complex_retention",
            "label": "CV-iodide complex retention",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Trapping of the crystal-violet-iodide complex within the peptidoglycan layer during gram staining."
          },
          {
            "node_id": "gram_negative_staining",
            "label": "gram-negative staining",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Loss of crystal violet and counterstain uptake giving a gram-negative appearance."
          },
          {
            "node_id": "cell_wall_deficient_forms",
            "label": "cell wall-deficient forms",
            "node_type": "STATE",
            "description": "Stress-induced bacterial cells with reduced or absent cell wall (e.g., L-forms, CWD coccoid forms)."
          }
        ],
        "edges": [
          {
            "subject": "culture_aging",
            "predicate": "regulates",
            "object": "peptidoglycan_thinning",
            "description": "Aging cultures undergo cell-wall thinning via autolysis.",
            "evidence": [
              {
                "reference": "DOI:10.1128/CMR.00043-07",
                "snippet": "autolysis",
                "notes": "Supports autolysis-driven peptidoglycan thinning in aging cultures."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "peptidoglycan_thinning",
            "predicate": "causes",
            "object": "crystal_violet_retention_loss",
            "description": "Thinned peptidoglycan no longer retains the gram-stain dye.",
            "evidence": [
              {
                "reference": "DOI:10.1128/CMR.00043-07",
                "snippet": "crystal violet",
                "notes": "Supports peptidoglycan thickness as the determinant of crystal-violet retention in the gram-stain protocol."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "crystal_violet_retention_loss",
            "predicate": "has output",
            "object": "mixed_staining",
            "description": "Subpopulations with reduced dye retention appear gram-negative alongside intact gram-positive cells.",
            "evidence": [
              {
                "reference": "DOI:10.1128/CMR.00043-07",
                "snippet": "decolorization",
                "notes": "Supports differential decolorization producing mixed staining within a single culture."
              }
            ],
            "predicate_id": "RO:0002234"
          },
          {
            "subject": "mixed_staining",
            "predicate": "manifests as",
            "object": "gram_variable_trait",
            "description": "Mixed staining manifests the gram-variable trait.",
            "evidence": [
              {
                "reference": "DOI:10.1128/CMR.00043-07",
                "snippet": "Gram-variable",
                "notes": "Supports the Gram-variable phenotype as the trait endpoint of heterogeneous staining."
              }
            ],
            "predicate_id": "METPO:2007400"
          },
          {
            "subject": "thin_peptidoglycan_layer",
            "predicate": "results in",
            "object": "gram_negative_staining",
            "description": "A thin peptidoglycan layer can yield a gram-negative staining result even in monoderm bacteria.",
            "evidence": [
              {
                "reference": "DOI:10.1128/spectrum.00732-24",
                "notes": "certain bacteria can stain Gram-negative despite having a monoderm cell wall structure"
              }
            ]
          },
          {
            "subject": "thin_peptidoglycan_layer",
            "predicate": "decreases",
            "object": "cv_iodide_complex_retention",
            "description": "A thin peptidoglycan layer reduces retention of the crystal-violet-iodide complex, the core staining-chemistry determinant.",
            "evidence": [
              {
                "reference": "DOI:10.1128/spectrum.00732-24",
                "notes": "to retain the CV-iodide complex, resulting in the loss of the CV"
              }
            ],
            "predicate_id": "RO:0002212"
          },
          {
            "subject": "cv_iodide_complex_retention",
            "predicate": "regulates",
            "object": "crystal_violet_retention_loss",
            "description": "Reduced CV-iodide complex retention drives loss of crystal-violet retention.",
            "evidence": [
              {
                "reference": "DOI:10.1128/spectrum.00732-24",
                "notes": "Reduced CV-iodide complex retention underlies the loss of crystal violet during decolorization."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "cell_wall_deficient_forms",
            "predicate": "produces",
            "object": "mixed_staining",
            "description": "Stress-induced cell wall-deficient forms can produce mixed gram reactions within a single culture.",
            "evidence": [
              {
                "reference": "DOI:10.1101/2023.11.16.566987",
                "notes": "mechanisms that can produce cell-wall alterations or loss that would lead to mixed Gram reactions in a single culture"
              }
            ],
            "predicate_id": "METPO:2007800"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.903723+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-11T23:00:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed causal graph linking culture-age-dependent peptidoglycan thinning and loss of crystal-violet retention to gram-variable staining.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T05:49:24Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:causes\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T21:30:07Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007400\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:19Z",
        "curator": "claude",
        "action": "RENAME_PREDICATE_LABELS",
        "changes": "Renamed 1 causal-edge predicate label(s) to align with existing groundings: drives \u2192 regulates \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:21Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002211\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 4 evidence-backed generic edges (4 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:13Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000017\u00d71, RO:0002211\u00d71, METPO:2000202\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates (1 to has output), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T02:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES_PART2",
        "changes": "Re-grounded 2 causal edge(s) off microbe-domain METPO predicates onto their causal-graph counterparts (1 to produces, 1 to reduces), issue 301 part 2. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Each replacement is a 1:1 mirror of its source predicate that changes only the domain, so the claim each edge makes is unchanged and directions are unchanged. The replacements are proposed in proposals/metpo_traitmech_v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T06:00:00Z",
        "curator": "claude",
        "action": "REGROUND_CAUSAL_EDGE",
        "changes": "Relabelled 1 causal edge from `reduces` to `decreases` and re-grounded it from METPO:2007802 to RO:0002212 (negatively regulates), issue 330. The corpus wrote two senses under the single label `reduces` - genuine electron donation, and a lessens/decreases sense - and METPO:2007802 is defined as donating electrons to the object and lowering its oxidation state, which this edge does not assert. The two senses could not be separated mechanically because the label was identical, so they migrated together in issue 329 and were split here by reading each edge. RO:0002212 declares no rdfs:domain or rdfs:range, so this introduces no entailment of the kind issue 301 removed.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope gram_variable_wall_thinning=NONMECHANISTIC with scope_notes.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1003025",
    "label": "green pigmented",
    "definition": "A pigmentation phenotype in which microbial colonies or cultures appear green or blue-green due to pigments such as pyocyanin and pyoverdine.",
    "definition_source": "DOI:10.1186/s12934-023-02122-1",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1003021"
    ],
    "synonyms": [
      {
        "synonym_text": "Pigment_green",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1186/s12934-023-02122-1",
        "snippet": "green colorization of the culture plate",
        "notes": "Supports green/blue-green pigmentation from pyocyanin and fluorescein or pyoverdine-like pigments in representative bacteria."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1097",
        "taxon_label": "Chlorobaculum tepidum",
        "note": "green sulfur bacterium (bacteriochlorophyll/chlorosome)",
        "reference": "PMID:12093901"
      },
      {
        "taxon_id": "NCBITaxon:1108",
        "taxon_label": "Chloroflexus aurantiacus",
        "note": "green non-sulfur bacterium",
        "reference": "PMID:21714912"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "green_pigmented_pyocyanin_phenazine",
        "title": "Green pigmentation pyocyanin phenazine mechanism",
        "description": "Evidence-backed causal sketch linking green or blue-green microbial pigmentation to phenazine biosynthesis, phz genes, pyocyanin production, and visible green culture color.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a broad environmental or morphological classification spanning multiple mechanisms, a measurement-like bin, or an absence/arrangement descriptor; contextual protein nodes do not receive token UniProt examples.",
        "nodes": [
          {
            "node_id": "green_pigmented_trait",
            "label": "green pigmented",
            "node_type": "TRAIT",
            "grounding": "METPO:1003025",
            "description": "Microbial pigmentation appearing green or blue-green."
          },
          {
            "node_id": "phz_operons",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "PhzA-G phenazine-biosynthesis enzyme modules",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Phenazine-biosynthesis protein modules in representative bacteria.",
            "gene_symbols": [
              "phzA",
              "phzB",
              "phzC",
              "phzD",
              "phzE",
              "phzF",
              "phzG"
            ],
            "operon": "phzA-G"
          },
          {
            "node_id": "phenazine_biosynthesis",
            "label": "phenazine biosynthesis",
            "node_type": "PATHWAY",
            "description": "Biosynthetic pathway producing phenazine pigments.",
            "grounding": "GO:0002047"
          },
          {
            "node_id": "pyocyanin",
            "label": "pyocyanin",
            "node_type": "CHEMICAL",
            "description": "Blue-green phenazine pigment produced by Pseudomonas aeruginosa."
          },
          {
            "node_id": "visible_green_color",
            "label": "visible green color",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "Observed green or blue-green culture color."
          },
          {
            "node_id": "chorismate",
            "label": "chorismate",
            "node_type": "CHEMICAL",
            "description": "Shikimate-pathway intermediate; precursor of phenazines.",
            "grounding": "CHEBI:29748"
          },
          {
            "node_id": "phenazine_1_carboxylic_acid",
            "label": "phenazine-1-carboxylic acid (PCA)",
            "node_type": "CHEMICAL",
            "description": "Core phenazine intermediate converted toward pyocyanin."
          },
          {
            "node_id": "quorum_sensing",
            "label": "quorum sensing",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Cell-density-dependent regulatory signaling controlling phenazine production.",
            "grounding": "GO:0009372"
          },
          {
            "node_id": "pyocyanin_redox_ph",
            "label": "pyocyanin redox state and pH",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Environmental redox/pH conditions altering apparent pyocyanin color."
          },
          {
            "node_id": "pyoverdine_biosynthesis",
            "label": "pyoverdine biosynthesis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "NRPS-driven biosynthesis of the fluorescent siderophore pyoverdine."
          },
          {
            "node_id": "pvd_nrps",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "pyoverdine NRPS enzymes (PvdL/PvdI/PvdJ/PvdD)",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Nonribosomal peptide synthetases assembling the pyoverdine peptide backbone."
          },
          {
            "node_id": "iron_limitation",
            "label": "iron-deficient conditions",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Low-iron growth conditions that induce pyoverdine biosynthesis."
          }
        ],
        "edges": [
          {
            "subject": "phz_operons",
            "predicate": "encodes",
            "object": "phenazine_biosynthesis",
            "description": "phz operons encode enzymes required for phenazine biosynthesis.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s12934-023-02122-1",
                "snippet": "phenazine synthesis operons including phzA1, phzA2, phzS, and phzM",
                "notes": "Supports phz genes as pyocyanin/phenazine biosynthesis machinery."
              }
            ],
            "predicate_id": "METPO:2007813"
          },
          {
            "subject": "phenazine_biosynthesis",
            "predicate": "has output",
            "object": "pyocyanin",
            "description": "Phenazine biosynthesis produces pyocyanin.",
            "evidence": [
              {
                "reference": "DOI:10.1128/jb.138.3.846-852.1979",
                "snippet": "pyocyanine biosynthesis",
                "notes": "Supports pyocyanin production as a phenazine biosynthetic process."
              }
            ],
            "predicate_id": "RO:0002234"
          },
          {
            "subject": "pyocyanin",
            "predicate": "causes",
            "object": "visible_green_color",
            "description": "Pyocyanin contributes blue-green visible pigmentation.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s12934-023-02122-1",
                "snippet": "Pyocyanin is a blue phenazine pigment",
                "notes": "Supports pyocyanin as a visible blue/green pigment."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "visible_green_color",
            "predicate": "manifests as",
            "object": "green_pigmented_trait",
            "description": "Visible green or blue-green culture color manifests the green-pigmented phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s12934-023-02122-1",
                "snippet": "lead to the green colorization of the culture plate",
                "notes": "Supports trait-level green pigmentation from pyocyanin and related pigments in representative cultures."
              }
            ],
            "predicate_id": "METPO:2007400"
          },
          {
            "subject": "chorismate",
            "predicate": "precursor of",
            "object": "phenazine_1_carboxylic_acid",
            "description": "Chorismate is the shikimate-pathway precursor of phenazine-1-carboxylic acid.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s11274-023-03548-w",
                "notes": "Biosynthesis of PYO and other phenazines proceeds from chorismate via the shikimate pathway."
              }
            ]
          },
          {
            "subject": "phenazine_1_carboxylic_acid",
            "predicate": "precursor of",
            "object": "pyocyanin",
            "description": "Phenazine-1-carboxylic acid is the core intermediate converted toward pyocyanin.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s11274-023-03548-w",
                "notes": "PCA is the central phenazine from which pyocyanin is derived via the shikimate/phenazine pathway."
              }
            ]
          },
          {
            "subject": "quorum_sensing",
            "predicate": "positively regulates",
            "object": "pyocyanin",
            "description": "Quorum sensing positively regulates pyocyanin production.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s12934-023-02122-1",
                "notes": "Quorum sensing controls pyocyanin synthesis; AHL and PQS autoinducers and LasR-LasI/RhlR-RhlI systems activate pyocyanin expression."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "pyocyanin_redox_ph",
            "predicate": "modifies",
            "object": "visible_green_color",
            "description": "Redox state and pH alter the apparent color of pyocyanin pigment.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s11274-023-03548-w",
                "notes": "PYO exhibits blue-green color at neutral/alkaline pH, shifting to pink-red in acidic conditions; oxidized PYO is blue while reduced form is transparent."
              }
            ]
          },
          {
            "subject": "pvd_nrps",
            "predicate": "participates in",
            "object": "pyoverdine_biosynthesis",
            "description": "PvdL/PvdI/PvdJ/PvdD NRPS enzymes synthesize the pyoverdine peptide backbone.",
            "evidence": [
              {
                "reference": "DOI:10.3390/ijms25116013",
                "notes": "The pyoverdine peptide backbone is synthesized by four NRPSs (PvdL, PvdI, PvdJ, PvdD)."
              }
            ],
            "predicate_id": "biolink:participates_in"
          },
          {
            "subject": "iron_limitation",
            "predicate": "induces",
            "object": "pyoverdine_biosynthesis",
            "description": "Iron-deficient conditions induce expression of pyoverdine biosynthetic enzymes.",
            "evidence": [
              {
                "reference": "DOI:10.3390/ijms25116013",
                "notes": "Expression of the fluorescent (pyoverdine) enzymes was induced by iron-deficient growing conditions."
              }
            ]
          },
          {
            "subject": "pyoverdine_biosynthesis",
            "predicate": "contributes to",
            "object": "visible_green_color",
            "description": "Pyoverdine, a yellow-green fluorescent pigment, contributes to green coloration alongside pyocyanin.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s12934-023-02122-1",
                "notes": "Blue (pyocyanin) and yellow (fluorescein/pyoverdine-like) pigments combine to produce green colorization of the culture."
              }
            ],
            "predicate_id": "RO:0002326"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.944814+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-11T18:45:00-07:00",
        "curator": "codex",
        "action": "CURATED_WITH_LITERATURE",
        "changes": "Added DOI-backed definition and causal graph for phz operons, phenazine biosynthesis, pyocyanin, and visible green/blue-green color.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T05:49:24Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:causes\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T08:21:50Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:encodes\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T21:30:07Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007400\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-14T06:55:38Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0002047\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 7 evidence-backed generic edges (7 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:13Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:participates_in\u00d71, RO:0002326\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:33Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:29748\u00d71, GO:0009372\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-04T03:08:15Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002213\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates (1 to has output), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-07T04:00:00Z",
        "curator": "claude",
        "action": "REGROUND_CAUSAL_EDGE",
        "changes": "Re-grounded the `encodes` edge(s) from biolink:encodes to METPO:2007813, issue 342. biolink:encodes is NOT a slot in the pinned biolink 4.4.0 model, so the CURIE resolved to nothing upstream while looking like an upstream term to anyone reading this record -- the disclaimer saying otherwise lived in mappings/predicate_grounding.tsv, which is not read at the point of use. RO:0002205 (has gene product) is the nearest real term but relates a GENE to a gene product, whereas these edges relate a gene cluster or operon to a protein complex or a biosynthetic process, which its range does not admit; that mismatch is why the coinage existed. METPO:2007813 is proposed in proposals/metpo_traitmech_v9 and is a placeholder id until METPO mints it, which puts it in the same state as the rest of that cohort rather than in a category of its own.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-16T02:00:00Z",
        "curator": "claude",
        "action": "NORMALISE_NODE_TYPE",
        "changes": "Under the PATHWAY-vs-BIOLOGICAL_PROCESS rule, one node_id means one thing corpus-wide (issue 356): phenazine_biosynthesis is typed PATHWAY. PATHWAY is a named, conventionally enumerable multi-step route; BIOLOGICAL_PROCESS is everything else. A named biosynthetic route; both typings say 'Biosynthetic pathway producing phenazine pigments'. The rule breaks the 1-1 tie.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope green_pigmented_pyocyanin_phenazine=NONMECHANISTIC with scope_notes; marked 2 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (phz_operons, pvd_nrps).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000676",
    "label": "helical shaped",
    "definition": "A cell shape in which an organism has a corkscrew-like helical cell body with curvature and twist along its long axis.",
    "definition_source": "DOI:10.1016/j.cell.2010.03.046",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000666"
    ],
    "synonyms": [
      {
        "synonym_text": "helical-shaped",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "created_by": "Jed Dongjin Kim-Ozaeta",
    "evidence": [
      {
        "reference": "DOI:10.1016/j.cell.2010.03.046",
        "snippet": "coordinated action of multiple proteins relaxes peptidoglycan crosslinking",
        "notes": "Supports a mechanistic basis for helical bacterial cell curvature and twist in Helicobacter pylori."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:210",
        "taxon_label": "Helicobacter pylori",
        "note": "Textbook helical bacterium; helical shape aids gastric mucus colonisation.",
        "reference": "https://pmc.ncbi.nlm.nih.gov/articles/PMC6597387/"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "helical_shaped_pg_relaxation",
        "title": "Helical-shape peptidoglycan relaxation mechanism",
        "description": "Evidence-backed causal sketch linking helical cell shape to H. pylori shape proteins, peptidoglycan crosslink relaxation, and curvature plus twist.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a broad environmental or morphological classification spanning multiple mechanisms, a measurement-like bin, or an absence/arrangement descriptor; contextual protein nodes do not receive token UniProt examples.",
        "nodes": [
          {
            "node_id": "helical_shaped_trait",
            "label": "helical shaped",
            "node_type": "TRAIT",
            "grounding": "METPO:1000676",
            "description": "Corkscrew-like bacterial morphology with curvature and twist."
          },
          {
            "node_id": "csd_shape_proteins",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "Csd shape proteins",
            "node_type": "GENE_OR_PROTEIN",
            "description": "H. pylori Csd1-Csd3 peptidoglycan endopeptidase homologs."
          },
          {
            "node_id": "ccmA",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "CcmA",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Bactofilin-like protein implicated in H. pylori helical shape."
          },
          {
            "node_id": "peptidoglycan_crosslink_relaxation",
            "label": "peptidoglycan crosslink relaxation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Local reduction or remodeling of peptidoglycan crosslinks."
          },
          {
            "node_id": "helical_curvature_twist",
            "label": "helical curvature and twist",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Cell-wall geometry that produces a helical cell body."
          },
          {
            "node_id": "pg_dl_carboxypeptidase_activity",
            "label": "peptidoglycan DL-carboxypeptidase activity",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "Enzymatic cleavage of monomeric tripeptides to dipeptides in the peptidoglycan stem."
          },
          {
            "node_id": "pg_stem_peptide_trimming",
            "label": "peptidoglycan stem peptide trimming",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Conversion of monomeric tripeptides to dipeptides, altering peptidoglycan stem composition."
          },
          {
            "node_id": "pg_modifying_enzyme_loss",
            "label": "loss of peptidoglycan-modifying enzyme",
            "node_type": "STATE",
            "description": "Absence or inactivation of a peptidoglycan-remodeling enzyme required for helical shape."
          },
          {
            "node_id": "rod_shaped_morphology",
            "label": "rod-shaped morphology",
            "node_type": "QUALITY",
            "description": "Straight rod cell shape resulting from loss of helical curvature."
          },
          {
            "node_id": "pg_crosslink_hydrolysis",
            "label": "localized peptidoglycan crosslink hydrolysis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Localized hydrolysis/relaxation of peptidoglycan crosslinks generating helical geometry."
          }
        ],
        "edges": [
          {
            "subject": "csd_shape_proteins",
            "predicate": "promotes",
            "object": "peptidoglycan_crosslink_relaxation",
            "description": "Csd peptidoglycan endopeptidase homologs contribute to reduced crosslinking in helical-shape generation.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.cell.2010.03.046",
                "snippet": "three LytM peptidoglycan endopeptidase homologs",
                "notes": "Supports Csd proteins as required genes in the H. pylori helical shape pathway."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "ccmA",
            "predicate": "contributes to",
            "object": "peptidoglycan_crosslink_relaxation",
            "description": "CcmA contributes to the shape-generating pathway for helical morphology.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.cell.2010.03.046",
                "snippet": "three LytM peptidoglycan endopeptidase homologs ... and a ccmA homolog",
                "notes": "Supports CcmA as one of the proteins required for helical shape."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "peptidoglycan_crosslink_relaxation",
            "predicate": "enables",
            "object": "helical_curvature_twist",
            "description": "Relaxed peptidoglycan crosslinking enables curvature and twist.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.cell.2010.03.046",
                "snippet": "relaxes peptidoglycan crosslinking, enabling helical cell curvature and twist",
                "notes": "Direct evidence for PG crosslink relaxation causing helical geometry."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "helical_curvature_twist",
            "predicate": "confers",
            "object": "helical_shaped_trait",
            "description": "Helical curvature and twist produce the helical-shaped trait.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.cell.2010.03.046",
                "snippet": "helical cell curvature and twist",
                "notes": "Supports the morphology endpoint of the graph."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "pg_dl_carboxypeptidase_activity",
            "predicate": "causes",
            "object": "pg_stem_peptide_trimming",
            "description": "DL-carboxypeptidase activity trims monomeric tripeptides to dipeptides in the peptidoglycan stem.",
            "evidence": [
              {
                "reference": "DOI:10.1371/journal.ppat.1002602",
                "notes": "Pgp1 is a novel peptidoglycan DL-carboxypeptidase cleaving monomeric tripeptides to dipeptides."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "pg_stem_peptide_trimming",
            "predicate": "promotes",
            "object": "helical_shaped_trait",
            "description": "Peptidoglycan stem peptide trimming supports generation of the helical cell shape.",
            "evidence": [
              {
                "reference": "DOI:10.1371/journal.ppat.1002602",
                "notes": "Pgp1 DL-carboxypeptidase activity on peptidoglycan stem peptides is required for helical cell shape."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "pg_modifying_enzyme_loss",
            "predicate": "causes",
            "object": "rod_shaped_morphology",
            "description": "Loss of a peptidoglycan-modifying enzyme produces a straight rod-shaped morphology.",
            "evidence": [
              {
                "reference": "DOI:10.1371/journal.ppat.1002602",
                "notes": "Deletion of pgp1 resulted in a striking, rod-shaped morphology."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "rod_shaped_morphology",
            "predicate": "negatively regulates",
            "object": "helical_shaped_trait",
            "description": "Rod-shaped morphology represents loss of the helical-shaped trait.",
            "evidence": [
              {
                "reference": "DOI:10.1371/journal.ppat.1002602",
                "notes": "pgp1 deletion converts helical cells to rod-shaped cells, i.e., loss of helical shape."
              }
            ],
            "predicate_id": "RO:0002212"
          },
          {
            "subject": "pg_crosslink_hydrolysis",
            "predicate": "enables",
            "object": "helical_curvature_twist",
            "description": "Localized peptidoglycan crosslink hydrolysis generates the curvature and twist underlying helical shape.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.cell.2010.03.046",
                "notes": "Coordinated action of multiple proteins relaxes peptidoglycan crosslinking, enabling helical cell curvature and twist."
              }
            ],
            "predicate_id": "RO:0002327"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.890639+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-11T18:00:00-07:00",
        "curator": "codex",
        "action": "CURATED_WITH_LITERATURE",
        "changes": "Reviewed helical shape and added DOI-backed causal graph for Csd proteins, CcmA, peptidoglycan crosslink relaxation, and helical curvature.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002326\u00d71, RO:0002327\u00d71, METPO:2000202\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T05:05:14Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:E0X6H3\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-13T21:03:26Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002213\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 5 evidence-backed generic edges (5 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:13Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 4 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:causes\u00d72, RO:0002213\u00d71, RO:0002327\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:21:12Z",
        "curator": "claude",
        "action": "RETRACT_DEAD_UNIPROT_GROUNDINGS",
        "changes": "Retracted 1 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-04T03:08:15Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002212\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates (1 to confers), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope helical_shaped_pg_relaxation=NONMECHANISTIC with scope_notes; marked 2 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (csd_shape_proteins, ccmA).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000073",
    "label": "heterocyst",
    "definition": "A morphology trait in which a filamentous cyanobacterium differentiates specialized, thick-walled cells (heterocysts) that create a microoxic interior for oxygen-sensitive nitrogen fixation.",
    "definition_source": "DOI:10.1101/cshperspect.a000315",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "synonyms": [
      {
        "synonym_text": "heterocyst-forming",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1101/cshperspect.a000315"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1101/cshperspect.a000315",
        "notes": "Kumar, Mella-Herrera & Golden describe heterocysts as differentiated cells whose structure and metabolism accommodate oxygen-sensitive nitrogen fixation."
      },
      {
        "reference": "DOI:10.1093/femsre/fuw029",
        "notes": "Herrero, Stavans & Flores describe heterocysts within the multicellular filament of heterocyst-forming cyanobacteria."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:103690",
        "taxon_label": "Nostoc sp. PCC 7120",
        "note": "Model heterocyst-forming cyanobacterium (also classified as Anabaena sp. PCC 7120); heterocysts are the N2-fixing cells. Trichormus (Anabaena) variabilis ATCC 29413 is an alternative model.",
        "reference": "PMID:11759840"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "heterocyst_microoxic_nitrogen_fixation",
        "title": "Heterocyst differentiation creates a microoxic interior for N2 fixation",
        "description": "Evidence-backed causal sketch linking cyanobacterial cell differentiation into thick-walled heterocysts to a microoxic interior that accommodates oxygen-sensitive nitrogen fixation.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "The taxon-matched protein example anchors one experimentally supported causal branch; it is not presented as a universal mechanism for every taxon or every contextual branch in this graph.",
        "nodes": [
          {
            "node_id": "heterocyst_trait",
            "label": "heterocyst",
            "node_type": "TRAIT",
            "grounding": "traitmech:000073",
            "description": "Differentiated thick-walled cyanobacterial cell with microoxic interior."
          },
          {
            "node_id": "cell_differentiation",
            "label": "cell differentiation",
            "node_type": "BIOLOGICAL_PROCESS",
            "grounding": "GO:0030154",
            "description": "Acquisition of specialized cellular form/function."
          },
          {
            "node_id": "microoxic_interior",
            "label": "microoxic intracellular environment",
            "node_type": "STATE",
            "description": "Low-O2 internal environment protecting oxygen-sensitive enzymes."
          },
          {
            "node_id": "nitrogen_fixation",
            "label": "nitrogen fixation",
            "node_type": "BIOLOGICAL_PROCESS",
            "grounding": "GO:0009399",
            "description": "Reduction of atmospheric N2 to ammonia by nitrogenase."
          },
          {
            "node_id": "het_diff_process",
            "label": "heterocyst differentiation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Developmental program producing a mature heterocyst.",
            "grounding": "GO:0043158"
          },
          {
            "node_id": "hetr_regulator",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:P27709",
                "protein_label": "DNA-binding transcriptional activator HetR",
                "gene_symbol": "hetR",
                "taxon_id": "NCBITaxon:103690",
                "taxon_label": "Nostoc sp. PCC 7120",
                "entry_status": "REVIEWED",
                "proteome_id": "UP000002483",
                "retrieved_on": "2026-10-22",
                "entry_version": 121,
                "sequence_version": 3,
                "role": "HetR is the master positive regulator initiating heterocyst differentiation in PCC 7120.",
                "evidence": [
                  {
                    "reference": "PMID:11759840",
                    "snippet": "HetR controls heterocyst differentiation",
                    "notes": "The cited source supports the represented protein-to-trait branch; UniProt verifies this current strain-matched protein entry."
                  }
                ]
              }
            ],
            "label": "HetR transcriptional regulator",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Master transcriptional regulator of heterocyst development."
          },
          {
            "node_id": "glycolipid_layer",
            "label": "heterocyst glycolipid layer (HGL)",
            "node_type": "CELLULAR_LOCALIZATION",
            "description": "Inner heterocyst-specific glycolipid envelope layer limiting gas diffusion."
          },
          {
            "node_id": "polysaccharide_layer",
            "label": "heterocyst envelope polysaccharide layer (HEP)",
            "node_type": "CELLULAR_LOCALIZATION",
            "description": "Outer envelope polysaccharide layer providing mechanical support."
          },
          {
            "node_id": "molecular_oxygen",
            "label": "oxygen",
            "node_type": "CHEMICAL",
            "description": "Molecular oxygen (O2)."
          },
          {
            "node_id": "het_envelope",
            "label": "heterocyst envelope (Hgl/Hep)",
            "node_type": "CELLULAR_LOCALIZATION",
            "description": "Multilayered heterocyst cell envelope limiting O2 entry."
          },
          {
            "node_id": "pats_peptide",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "PatS peptide",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Inhibitory peptide controlling heterocyst pattern/spacing."
          },
          {
            "node_id": "hetn_regulator",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "HetN regulator",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Regulator maintaining heterocyst spacing pattern."
          }
        ],
        "edges": [
          {
            "subject": "cell_differentiation",
            "predicate": "confers",
            "object": "heterocyst_trait",
            "description": "Cyanobacterial cell differentiation realizes the thick-walled heterocyst.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuw029",
                "notes": "Herrero et al. describe heterocysts within the multicellular filament of heterocyst-forming cyanobacteria."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "heterocyst_trait",
            "predicate": "causes",
            "object": "microoxic_interior",
            "description": "The thick heterocyst wall and altered metabolism produce a microoxic interior.",
            "evidence": [
              {
                "reference": "DOI:10.1101/cshperspect.a000315",
                "notes": "Kumar et al. describe heterocysts as differentiated cells whose structure accommodates oxygen-sensitive N2 fixation."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "microoxic_interior",
            "predicate": "enables",
            "object": "nitrogen_fixation",
            "description": "The microoxic interior protects nitrogenase, enabling N2 fixation.",
            "evidence": [
              {
                "reference": "DOI:10.1101/cshperspect.a000315",
                "notes": "Kumar et al. link heterocyst microoxia to oxygen-sensitive N2 fixation."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "hetr_regulator",
            "predicate": "positively regulates",
            "object": "het_diff_process",
            "description": "HetR is the master positive regulator of heterocyst development.",
            "evidence": [
              {
                "reference": "DOI:10.1371/journal.pone.0289761",
                "notes": "\"hetR, the master regulator of heterocyst development\"."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "glycolipid_layer",
            "predicate": "reduces diffusion of",
            "object": "molecular_oxygen",
            "description": "The inner glycolipid layer reduces O2 gas diffusion into the heterocyst.",
            "evidence": [
              {
                "reference": "DOI:10.1101/2023.10.04.560878",
                "notes": "\"the inner heterocyst-specific glycolipid layer (HGL) reduces gas diffusion (including O2)\"."
              }
            ]
          },
          {
            "subject": "polysaccharide_layer",
            "predicate": "provides mechanical support to",
            "object": "glycolipid_layer",
            "description": "The outer polysaccharide layer mechanically supports the glycolipid layer.",
            "evidence": [
              {
                "reference": "DOI:10.1101/2023.10.04.560878",
                "notes": "\"the outer heterocyst envelope polysaccharide layer (HEP) provides mechanical support to the HGL\"."
              }
            ]
          },
          {
            "subject": "het_envelope",
            "predicate": "contributes to",
            "object": "microoxic_interior",
            "description": "The Hgl/Hep envelope contributes to creating the microoxic heterocyst interior.",
            "evidence": [
              {
                "reference": "DOI:10.1093/pcp/pcae011",
                "notes": "\"These oxygen protection mechanisms create hypoxic environments in the heterocysts so that nitrogenase can operate\"."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "pats_peptide",
            "predicate": "negatively regulates",
            "object": "het_diff_process",
            "description": "PatS inactivation yields a multiple-contiguous-heterocyst phenotype, indicating negative regulation of differentiation/spacing.",
            "evidence": [
              {
                "reference": "DOI:10.1101/2023.10.04.560878",
                "notes": "\"inactivation of one of the genes patS and hetN\" caused the Mch (multiple contiguous heterocyst) phenotype."
              }
            ],
            "predicate_id": "RO:0002212"
          },
          {
            "subject": "hetn_regulator",
            "predicate": "negatively regulates",
            "object": "het_diff_process",
            "description": "HetN inactivation yields multiple contiguous heterocysts, indicating negative regulation of differentiation/spacing.",
            "evidence": [
              {
                "reference": "DOI:10.1101/2023.10.04.560878",
                "notes": "\"inactivation of one of the genes patS and hetN\" caused the Mch phenotype."
              }
            ],
            "predicate_id": "RO:0002212"
          },
          {
            "subject": "hetr_regulator",
            "predicate": "contributes to",
            "object": "heterocyst_trait",
            "description": "HetR is the central positive regulator of heterocyst development and contributes to realization of the differentiated cell trait.",
            "evidence": [
              {
                "reference": "DOI:10.1371/journal.pone.0289761",
                "snippet": "hetR, the master regulator of heterocyst development",
                "notes": "The source supports the central regulatory role; the edge does not claim that HetR alone is sufficient for differentiation."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "glycolipid_layer",
            "predicate": "part of",
            "object": "het_envelope",
            "description": "The oxygen-limiting heterocyst glycolipid layer is the inner layer of the specialized heterocyst envelope.",
            "evidence": [
              {
                "reference": "DOI:10.1101/2023.10.04.560878",
                "snippet": "the inner heterocyst-specific glycolipid layer (HGL)",
                "notes": "The contiguous source phrase directly identifies the layer's position in the heterocyst envelope."
              }
            ],
            "predicate_id": "biolink:part_of"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-06-03T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate MORPHOLOGY trait (heterocyst) from literature research to fill the cellular-differentiation gap.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-09T15:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (heterocyst differentiation / microoxic N2 fixation) with GO node groundings and RO/biolink predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 7 evidence-backed generic edges (10 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:13Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:33Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0043158\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-04T03:08:15Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002212\u00d72, RO:0002213\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 1 causal edge(s) off enables/RO:0002327 with a TRAIT object (1 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-07T05:00:00Z",
        "curator": "claude",
        "action": "REGROUND_CAUSAL_EDGE",
        "changes": "Re-grounded the edge from enables/RO:0002327 to RO:0002326 (contributes to), issue 334. biolink declares enables range 'biological process or activity' and the object is a STATE, which does not satisfy it. Unlike the tolerance/capacity nodes in this same pass, this object is a genuine state rather than a mis-typed disposition - a gradient, a community composition, an internal environment - so retyping it to TRAIT would be wrong. contributes to fits because the subject genuinely contributes to the OCCURRENCE OR GENERATION of the object, which is biolink's definition; that is the same test the motive-force edges FAILED in issue 341, where the subject powers a machine it does not generate. RO:0002326 declares no rdfs:domain or rdfs:range.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-17T02:00:00Z",
        "curator": "claude",
        "action": "NORMALISE_NODE_SENSE",
        "changes": "One node_id per SENSE (issues 356, 384): molecular_oxygen is the chemical sense here. The molecule, not the condition \u2014 the dioxygen participating in the reaction the graph describes. Normalised onto molecular_oxygen, the id 20 other chemical occurrences already use, so one id means one sense corpus-wide (issues 356, 384).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "CURATE_PROTEIN_TAXON_EXAMPLE",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope heterocyst_microoxic_nitrogen_fixation=MECHANISTIC with scope_notes; marked 4 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (hetr_regulator, furc_perr, pats_peptide, hetn_regulator); added taxon-paired protein example(s) UniProtKB:P27709 on hetr_regulator (NCBITaxon:103690).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T06:30:00Z",
        "curator": "codex",
        "action": "CONNECT_CAUSAL_GRAPH_COMPONENTS",
        "changes": "Resolved issue #183 graph fragmentation (4 components to 1) using 2 source- and verbatim-snippet-backed connector(s). Removed the isolated FurC/hetR-promoter branch: its primary source states that more studies are required to understand the regulation exerted by FurC on hetR expression (DOI:10.1371/journal.pone.0289761), so no directional bridge was asserted. No paid research service was called.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-22T01:35:00Z",
        "curator": "claude",
        "action": "REFRESH_UNIPROT_ENTRY_VERSION",
        "changes": "Refreshed UniProtKB entry_version against live UniProt REST on 2026-10-22: UniProtKB:P27709 (120 -> 121 on hetr_regulator).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000184",
    "label": "holdfast",
    "definition": "A morphology trait in which a bacterial cell produces a localized polar adhesive matrix called a holdfast that mediates permanent attachment to surfaces.",
    "definition_source": "DOI:10.1128/jb.00276-19",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "synonyms": [
      {
        "synonym_text": "holdfast adhesin",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1128/jb.00276-19"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1128/jb.00276-19",
        "snippet": "Caulobacter crescentus synthesizes a polysaccharide-based adhesin known as the holdfast at one of its cell poles, which enables tight attachment to exogenous surfaces.",
        "notes": "Hershey et al. support holdfast as a Caulobacter polar polysaccharide-based adhesin mediating tight surface attachment."
      },
      {
        "reference": "DOI:10.1128/jb.00276-19",
        "snippet": "Glucose, 3-O-methylglucose, mannose, N-acetylglucosamine, and xylose were detected in our extracts.",
        "notes": "The compositional analysis supports the holdfast matrix as a bacterial polysaccharide-rich adhesive."
      },
      {
        "reference": "DOI:10.1128/jb.00273-22",
        "snippet": "Species of the Caulobacterales produce a specialized polar adhesin, holdfast, which is required for permanent attachment to surfaces.",
        "notes": "Chepkwony et al. support holdfast as a specialized polar Caulobacterales adhesin required for permanent attachment."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:155892",
        "taxon_label": "Caulobacter vibrioides",
        "note": "Model freshwater Caulobacter species, long called Caulobacter crescentus, that produces a polar holdfast.",
        "reference": "DOI:10.1128/jb.00276-19"
      }
    ],
    "discussions": [
      {
        "discussion_id": "holdfast-exact-xref-gap",
        "prompt": "Resolve exact external ontology xrefs for the bacterial holdfast morphology trait.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "The pinned METPO snapshot contains only the deprecated METPO:1000158 obsolete holdfast class; no active METPO, GO, or OBO class was accepted as an exact equivalent for this bacterial adhesive-matrix trait.",
        "posed_by": "codex",
        "posed_date": "2026-09-14"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-14T06:26:17Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted holdfast as a DOI-backed TraitRecord after a repository-wide duplicate review covering ignored and hidden files; live METPO has no active exact holdfast class and the placeholder is reserved in proposals/metpo_traitmech_v61.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000651",
    "label": "hormogonium formation",
    "definition": "A morphological phenotype in which a filamentous cyanobacterium differentiates short, initially heterocyst-free filaments called hormogonia that are distinct from mature vegetative trichomes.",
    "definition_source": "DOI:10.1128/mSphere.00231-19",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1099/00221287-111-1-1",
        "snippet": "In all three genera, the hormogonia are initially devoid of heterocysts.",
        "notes": "Rippka et al. (1979), Genera of Section IV, printed pages 34-36; publisher PDF extracted text directly read, not a search-result snippet. The three genera are Nostoc, Scytonema and Calothrix. The study distinguishes differentiated hormogonia from random trichome breakage and reports immotile hormogonia in PCC 6314, 7524 and 6719. Smaller cells or gas vacuoles help identify these immotile forms; neither feature is required in every strain. Developing hormogonia can subsequently acquire terminal heterocysts, so initial absence is not permanent absence. This is a culture-based systematic study, not a universal modern taxonomic rule. PDF screenshots were unavailable; no visual panel verification or numerical table claim is made."
      },
      {
        "reference": "DOI:10.1128/aem.55.1.125-131.1989",
        "snippet": "motile (gliding) filaments lacking heterocysts and with distinctly smaller cells than those of vegetative filaments",
        "notes": "PMID:16347816, PMC184065. Scientific Abstract directly read on PubMed and through the Europe PMC core API. Campbell and Meeks (1989) observed induced hormogonia in symbiotically competent Nostoc cultures. The quoted morphology describes those cultures, not every hormogonium. Strain 7801 underwent conversion in Anthoceros punctatus-conditioned medium under the tested conditions and later reverted to vegetative growth. The reported loss and recovery of acetylene reduction are stage-dependent readouts, not a definition requiring nitrogen fixation or plant symbiosis. Full text and panels were not read."
      },
      {
        "reference": "DOI:10.1128/mSphere.00231-19",
        "snippet": "both sigC and sigJ may be required for an early stage in hormogonium development, while sigF is late acting.",
        "notes": "PMID:31043519, PMC6495340. Direct Europe PMC full-text XML: scientific ABSTRACT, first RESULTS subsection, and MATERIALS AND METHODS subsections Strains and culture conditions and Plasmid and strain construction were read. The snippet is from Results, not the separate precis/IMPORTANCE text. Wild-type Nostoc punctiforme formed shorter, morphologically distinct filaments after induction. In-frame sigF deletion abolished motility but retained morphological differentiation and heterocyst loss; sigC and sigJ deletions lacked those morphological markers. This separates development from locomotion experimentally. Complementation restored motility in the assay, not necessarily wild-type levels. These are strain- and assay-qualified results, not a universal sigma-factor rule inferred from sequence. Actual panels, movies and the strain-table supplement were not inspected; no panel-level or numerical claim is made."
      }
    ],
    "discussions": [
      {
        "discussion_id": "hormogonium-formation-scope-and-hierarchy",
        "prompt": "Review the developmental scope independently of motility and mature cell shape.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Retain phenotype METPO:1000059. Motile METPO:1000702 is not a necessary parent: Rippka et al. explicitly include immotile hormogonia, and the 2019 sigF deletion retains differentiation without movement. The 1989 abstract's motile description is specific to the studied Nostoc cultures. Filament shaped METPO:1000674 denotes elongated cells or hypha-like structures, not specifically this differentiated multicellular stage. Filamentous colony METPO:1007066 denotes colony outline. Heterocyst traitmech:000073 and akinete traitmech:000185 describe other differentiated cell types, not this filament stage; their presence in a life cycle is not organism-level disjointness. Random fragmentation alone is insufficient. Do not universally require reduced cell size, gas vacuoles, permanent heterocyst absence, plant symbiosis or nitrogen fixation. Exact external equivalence and narrower hierarchy remain for human review; no xref or unqualified synonym is asserted.",
        "posed_by": "codex",
        "posed_date": "2026-10-06"
      },
      {
        "discussion_id": "hormogonium-formation-stage-and-mechanism-grounding",
        "prompt": "Resolve strain and protein anchors before adding a causal graph or canonical example.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "The cited studies support an observed developmental phenotype and genetic dependence, not merely sequence-feature possession. Before adding a mechanistic graph, inspect actual panels and supplements, resolve accession-level sigma-factor examples, and distinguish induction, morphological differentiation and motility readouts. Transcript changes or homologous sig genes alone do not establish the phenotype or the complete cascade. Canonical examples are deferred pending strain-table and taxon verification with natural provenance and explicit life-stage qualifiers; engineered deletion strains must not be presented as unqualified natural exemplars. The known mechanism is not claimed to be absent, and natural transient stages remain valid trait evidence without a canonical row.",
        "posed_by": "codex",
        "posed_date": "2026-10-06"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-06T22:07:10Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added hormogonium formation with three DOI-backed snippets and explicit developmental-stage, motility and sequence-inference limits. Ignored-and-hidden novelty searches and the pinned METPO audit found no exact record. Reserved METPO:1060400 in v527. Deferred unresolved strain/protein anchors; existing records unchanged.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000066",
    "label": "intracellular inclusion",
    "definition": "A morphology trait describing a discrete intracellular body \u2014 a storage granule, gas-filled structure, or protein-bounded microcompartment/organelle \u2014 that compartmentalizes material or function within a prokaryotic cell.",
    "definition_source": "DOI:10.1038/s41579-020-0413-0",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "synonyms": [
      {
        "synonym_text": "cytoplasmic inclusion",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1038/s41579-020-0413-0"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/s41579-020-0413-0",
        "notes": "Greening & Lithgow, \"Formation and function of bacterial organelles\", establish that bacteria contain diverse inclusions/organelles (storage granules, gas vesicles, microcompartments, magnetosomes); parent of the inclusion sub-variants."
      },
      {
        "reference": "DOI:10.1038/nrmicro.2018.10",
        "notes": "Kerfeld et al. review bacterial microcompartments as a major class of protein-bounded intracellular organelles."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:2242",
        "taxon_label": "Halobacterium salinarum",
        "note": "Gas vesicle: a gas-filled, protein-shelled inclusion built from this organism's Gvp proteins, where GvpA forms the shell ribs and GvpC stabilises the exterior. The cited interaction and deletion analysis was performed on those proteins in a heterologous haloarchaeal host, so it establishes the protein roles rather than in-situ assembly. Exemplifies the gas-filled inclusion type only.",
        "reference": "DOI:10.3389/fmicb.2022.971917"
      },
      {
        "taxon_id": "NCBITaxon:381666",
        "taxon_label": "Cupriavidus necator H16",
        "note": "Polyhydroxybutyrate storage granule: the reference PHB-accumulating organism, whose PhaM activator and PhaP phasins set granule number, surface properties, and partitioning. Review-level synthesis of primary studies; exemplifies the storage-granule type only.",
        "reference": "DOI:10.1093/femsre/fuaa058"
      },
      {
        "taxon_id": "NCBITaxon:431944",
        "taxon_label": "Magnetospirillum gryphiswaldense MSR-1",
        "note": "Magnetosome: a membrane-bounded magnetite inclusion; the organism carries over 30 magnetosome-associated proteins, with the mamAB operon required for magnetosome membrane formation. Exemplifies the mineral-bearing organelle type only.",
        "reference": "DOI:10.1111/mmi.15330"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "inclusion_compartmentalization",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "Intracellular inclusion is an upper morphology class spanning unrelated gas vesicles, storage granules, and bacterial microcompartments. Its graph presents alternatives and is not one shared protein-mediated mechanism.",
        "title": "Intracellular inclusions compartmentalize prokaryotic cytoplasm",
        "description": "Evidence-backed causal sketch linking discrete intracellular inclusions (storage granules, gas vesicles, microcompartments) to cytoplasmic compartmentalization.",
        "nodes": [
          {
            "node_id": "inclusion_trait",
            "label": "intracellular inclusion",
            "node_type": "TRAIT",
            "grounding": "traitmech:000066",
            "description": "Discrete intracellular body compartmentalizing material or function."
          },
          {
            "node_id": "cytoplasmic_compartmentalization",
            "label": "cytoplasmic compartmentalization",
            "node_type": "QUALITY",
            "description": "Spatial segregation of material or activity within the cytoplasm."
          },
          {
            "node_id": "bacterial_microcompartment",
            "label": "bacterial microcompartment",
            "node_type": "CELLULAR_LOCALIZATION",
            "grounding": "GO:0031469",
            "description": "Protein-shelled prokaryotic organelle (e.g. carboxysome)."
          },
          {
            "node_id": "pha_synthase_pathway",
            "label": "PhaA/PhaB/PhaC pathway",
            "node_type": "PATHWAY",
            "description": "Beta-ketothiolase/reductase/PHA synthase pathway producing polyhydroxyalkanoate."
          },
          {
            "node_id": "pha_granule",
            "label": "PHA granule",
            "node_type": "CELLULAR_LOCALIZATION",
            "description": "Polyhydroxyalkanoate storage inclusion body.",
            "grounding": "GO:0070088"
          },
          {
            "node_id": "nitrogen_depletion",
            "label": "nitrogen depletion",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Nutrient limitation (low N) triggering carbon storage accumulation."
          },
          {
            "node_id": "polyphosphate_kinase",
            "label": "polyphosphate kinase (Ppk)",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Enzyme catalyzing polyphosphate synthesis.",
            "grounding": "GO:0008976"
          },
          {
            "node_id": "polyphosphate_granule",
            "label": "polyphosphate granule",
            "node_type": "CELLULAR_LOCALIZATION",
            "description": "Inorganic polyphosphate (volutin) storage inclusion."
          },
          {
            "node_id": "gas_vesicle_proteins",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "The module contains multiple distinct structural and assembly protein families, so no single exact term denotes the complete protein set.",
            "label": "gas vesicle structural and assembly proteins",
            "node_type": "GENE_OR_PROTEIN",
            "description": "gvp operon encoding gas vesicle structural and assembly proteins.",
            "gene_symbols": [
              "gvpA",
              "gvpC",
              "gvpN"
            ],
            "operon": "gvp"
          },
          {
            "node_id": "gas_vesicle",
            "label": "gas vesicle",
            "node_type": "ORGANELLE",
            "description": "Hollow gas-filled protein nanocompartment.",
            "grounding": "GO:0031411"
          },
          {
            "node_id": "buoyancy",
            "label": "buoyancy",
            "node_type": "TRAIT",
            "description": "Capacity for vertical positioning in the water column.",
            "grounding": "traitmech:000528"
          },
          {
            "node_id": "bmc_metabolic_cargo",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Bacterial-microcompartment cargo varies by pathway and combines unrelated enzyme families; one protein-family grounding would overgeneralize.",
            "label": "encapsulated metabolic enzymes",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Enzymes/pathway segment sequestered within a microcompartment shell."
          },
          {
            "node_id": "sulfide_oxidation",
            "label": "sulfide oxidation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Oxidation of sulfide via elemental sulfur intermediate.",
            "grounding": "GO:0019418"
          },
          {
            "node_id": "sulfur_globule",
            "label": "intracellular sulfur globule",
            "node_type": "CELLULAR_LOCALIZATION",
            "description": "Intracellular elemental sulfur (S0) storage inclusion."
          }
        ],
        "edges": [
          {
            "subject": "inclusion_trait",
            "predicate": "manifests as",
            "object": "cytoplasmic_compartmentalization",
            "description": "Inclusions partition activities within the prokaryotic cytoplasm.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41579-020-0413-0",
                "notes": "Greening & Lithgow review formation and function of bacterial organelles/inclusions."
              }
            ],
            "predicate_id": "METPO:2007400"
          },
          {
            "subject": "bacterial_microcompartment",
            "predicate": "example of",
            "object": "inclusion_trait",
            "description": "Bacterial microcompartments are protein-bounded inclusion organelles.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro.2018.10",
                "notes": "Kerfeld et al. review bacterial microcompartments as protein-bounded intracellular organelles."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "pha_synthase_pathway",
            "predicate": "has output",
            "object": "pha_granule",
            "description": "The Pha biosynthetic pathway synthesizes PHA chains that form storage granules.",
            "evidence": [
              {
                "reference": "DOI:10.3390/molecules29102293",
                "notes": "\"Synthesized PHA chains form intracellular inclusion bodies commonly called PHA granules\"; storage-granule subclass."
              }
            ],
            "predicate_id": "RO:0002234"
          },
          {
            "subject": "nitrogen_depletion",
            "predicate": "increases accumulation of",
            "object": "pha_granule",
            "description": "Depletion of N (and S, P) is a broad trigger for PHA granule accumulation.",
            "evidence": [
              {
                "reference": "DOI:10.3390/molecules29102293",
                "notes": "\"Environmental and cultivation triggers for accumulation include... depletion of N, S, P\"; broad, not species-specific."
              }
            ]
          },
          {
            "subject": "polyphosphate_kinase",
            "predicate": "synthesizes",
            "object": "polyphosphate_granule",
            "description": "Ppk catalyzes polyphosphate synthesis forming the polyP/volutin granule.",
            "evidence": [
              {
                "reference": "DOI:10.3390/foods14132211",
                "notes": "\"polyP synthesis is catalyzed by polyphosphate kinase (Ppk)\"."
              }
            ]
          },
          {
            "subject": "gas_vesicle_proteins",
            "predicate": "assembles",
            "object": "gas_vesicle",
            "description": "Gvp structural and assembly proteins form the gas vesicle organelle.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s13036-024-00426-3",
                "snippet": "hollow, gas-filled protein nanoparticles",
                "notes": "Supports the protein composition of gas vesicles; gvp operon membership is retained as node metadata rather than a primary gene-cluster node."
              }
            ]
          },
          {
            "subject": "gas_vesicle",
            "predicate": "confers",
            "object": "buoyancy",
            "description": "Gas vesicles confer buoyancy enabling positioning in the water column.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s13036-024-00426-3",
                "notes": "\"enabling buoyancy for microbes\"; core phenotype/function edge."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "bacterial_microcompartment",
            "predicate": "encapsulates",
            "object": "bmc_metabolic_cargo",
            "description": "BMC shells encapsulate a segment of a metabolic pathway in a selectively permeable shell.",
            "evidence": [
              {
                "reference": "DOI:10.1042/bst20230229",
                "notes": "\"encapsulate a segment of a metabolic pathway within a selectively permeable protein shell\"; direct BMC definition."
              }
            ]
          },
          {
            "subject": "sulfide_oxidation",
            "predicate": "forms",
            "object": "sulfur_globule",
            "description": "Sulfide oxidation proceeds via intracellular accumulation of elemental sulfur globules.",
            "evidence": [
              {
                "reference": "DOI:10.1371/journal.pone.0310265",
                "notes": "\"oxidized to sulfate through an intermediate accumulation of elemental sulfur (S0) within the cell in the form of sulfur globules\"; definitional."
              }
            ],
            "predicate_id": "biolink:produces"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-06-03T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate MORPHOLOGY axis class (intracellular inclusion) to parent the storage-granule, gas-vesicle, magnetosome, and carboxysome traits.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-09T15:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (compartmentalization axis) with GO node grounding and RO/RDFS predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 7 evidence-backed generic edges (11 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:13Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 4 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d71, biolink:encodes\u00d71, RO:0002327\u00d71, biolink:produces\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:33Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 3 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0070088\u00d71, GO:0031411\u00d71, GO:0019418\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:23:55Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0008976\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates (1 to has output), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-07T04:00:00Z",
        "curator": "claude",
        "action": "REGROUND_CAUSAL_EDGE",
        "changes": "Re-grounded the `encodes` edge(s) from biolink:encodes to METPO:2007813, issue 342. biolink:encodes is NOT a slot in the pinned biolink 4.4.0 model, so the CURIE resolved to nothing upstream while looking like an upstream term to anyone reading this record -- the disclaimer saying otherwise lived in mappings/predicate_grounding.tsv, which is not read at the point of use. RO:0002205 (has gene product) is the nearest real term but relates a GENE to a gene product, whereas these edges relate a gene cluster or operon to a protein complex or a biosynthetic process, which its range does not admit; that mismatch is why the coinage existed. METPO:2007813 is proposed in proposals/metpo_traitmech_v9 and is a placeholder id until METPO mints it, which puts it in the same state as the rest of that cohort rather than in a category of its own.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-07T05:00:00Z",
        "curator": "claude",
        "action": "RETYPE_CAUSAL_NODE",
        "changes": "Retyped the object node from STATE/CAPACITY to TRAIT and re-grounded its in-edge from enables/RO:0002327 to METPO:2007700 (confers), issue 334. biolink declares enables range 'biological process or activity', which only BIOLOGICAL_PROCESS, PATHWAY and MOLECULAR_FUNCTION satisfy. The node's own description gives it away as a disposition rather than a state - phrasings like \"Capacity of an organism to grow and survive under...\", \"Ability to grow when...\" and \"tolerance of...\" describe what an organism CAN do, which is what a TRAIT is. So the defect was the node type, not the predicate, which is the third time in this issue's neighbourhood that has been true (compare issue 331's acetate kinase step and issue 330's negated node name). With the object correctly a TRAIT, confers applies unchanged.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-07T18:00:00Z",
        "curator": "claude",
        "action": "REGROUND_CAUSAL_EDGE",
        "changes": "Edge inclusion_trait -> cytoplasmic_compartmentalization in graph inclusion_compartmentalization: re-grounded it from enables/RO:0002327 to manifests as/METPO:2007400. Issue 334. biolink declares enables range 'biological process or activity', which of CausalNodeTypeEnum only BIOLOGICAL_PROCESS, PATHWAY and MOLECULAR_FUNCTION satisfy, so this edge entailed a false type on its object. Unlike buoyancy, compartmentalization is not a disposition the inclusion confers -- it is how the inclusion PRESENTS: 'spatial segregation of material or activity within the cytoplasm'. That is what `manifests as` is for, and its gate is already open.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope inclusion_compartmentalization=NONMECHANISTIC with scope_notes; marked 2 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (gas_vesicle_proteins, bmc_metabolic_cargo); added 1 node(s) and 1 edge(s) (gas_vesicle_proteins); removed 1 node(s) and 1 edge(s) together with their evidence (gas_vesicle_gene_cluster).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T19:05:00Z",
        "curator": "claude",
        "action": "ADD_CANONICAL_EXAMPLES",
        "changes": "Added 3 source-backed canonical example(s) from this record's own deep-research artifact (issue 444): Halobacterium salinarum (NCBITaxon:2242), Cupriavidus necator H16 (NCBITaxon:381666), Magnetospirillum gryphiswaldense MSR-1 (NCBITaxon:431944). Each note scopes the exemplar to the single inclusion type the cited source establishes, because this record is an upper class whose graph is NONMECHANISTIC and spans alternative mechanisms. Taxon ids and labels were verified against NCBI taxonomy and every DOI resolved through Crossref. No gene or operon was promoted to a primary entry.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-01T22:49:00Z",
        "curator": "codex",
        "action": "GROUND_CAUSAL_NODE_TO_NEW_TRAIT",
        "changes": "Grounded the existing causal-graph buoyancy TRAIT node to newly minted traitmech:000528 cellular buoyancy.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000691",
    "label": "irregular shaped",
    "definition": "A cell shape lacking a consistent geometric form across individual cells of a population.",
    "definition_source": "DOI:10.1146/annurev-cellbio-101011-155745",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000666"
    ],
    "synonyms": [
      {
        "synonym_text": "irregular",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev-cellbio-101011-155745",
        "snippet": "cell shape is genetically determined",
        "notes": "Cell-shape review supports loss of cytoskeletal/wall-patterning control as the basis for irregular morphology."
      },
      {
        "reference": "DOI:10.1111/j.1574-6976.2011.00298.x",
        "snippet": "coryneform morphology",
        "notes": "Corynebacterineae review supports irregular and coryneform morphologies associated with apical polar growth and reduced lateral wall patterning."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1718",
        "taxon_label": "Corynebacterium glutamicum",
        "reference": "DOI:10.1111/j.1574-6976.2011.00298.x",
        "note": "Corynebacterium glutamicum exhibits coryneform, irregular cell arrangements produced by apical growth and snapping division; the note scopes the example to that natural morphology."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "irregular_shaped_loss_of_patterning",
        "title": "Irregular-shape loss of wall patterning",
        "description": "DOI-backed graph linking reduced or stochastic cell-wall patterning to inconsistent, irregular cell geometry.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "Irregular shape is a residual morphology classification with no single taxon-independent protein mechanism in the cited evidence.",
        "nodes": [
          {
            "node_id": "irregular_shaped_trait",
            "label": "irregular shaped",
            "node_type": "TRAIT",
            "grounding": "METPO:1000691",
            "description": "Inconsistent cell geometry across a population."
          },
          {
            "node_id": "reduced_wall_patterning",
            "label": "reduced cell-wall patterning",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Diminished spatial control of peptidoglycan synthesis."
          },
          {
            "node_id": "stochastic_growth",
            "label": "stochastic growth",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Cell-by-cell variation in growth-zone placement and extent."
          },
          {
            "node_id": "variable_geometry",
            "label": "variable cell geometry",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Population-level variability in cell shape."
          },
          {
            "node_id": "mreb_cytoskeleton_function",
            "label": "MreB cytoskeletal function",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "MreB-mediated curvature sensing and spatial direction of lateral peptidoglycan insertion that maintains regular cell shape."
          },
          {
            "node_id": "mreb_loss",
            "label": "loss of MreB function",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Inhibition or depletion of MreB cytoskeletal activity removing localized wall-insertion control."
          },
          {
            "node_id": "synthase_hydrolase_imbalance",
            "label": "peptidoglycan synthase-hydrolase imbalance",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Disrupted coordination between peptidoglycan synthases and hydrolases destabilizing the cell wall."
          },
          {
            "node_id": "polar_growth_organization",
            "label": "polarized growth organization",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Apical tip-organizing machinery that focuses cell-wall synthesis for ordered polar growth."
          },
          {
            "node_id": "polar_growth_perturbation",
            "label": "perturbation of polar growth determinants",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Disruption of apical polar growth determinants leading to mispatterned wall synthesis."
          },
          {
            "node_id": "wall_less_state",
            "label": "wall-less (L-form) state",
            "node_type": "STATE",
            "description": "Absence of a rigid peptidoglycan wall removing canonical cell-shape constraints."
          }
        ],
        "edges": [
          {
            "subject": "reduced_wall_patterning",
            "predicate": "enables",
            "object": "stochastic_growth",
            "description": "Reduced patterning permits stochastic growth-zone placement.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-cellbio-101011-155745",
                "snippet": "cell shape is genetically determined",
                "notes": "Supports patterning loss as a driver of inconsistent shapes."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "stochastic_growth",
            "predicate": "has output",
            "object": "variable_geometry",
            "description": "Stochastic growth produces variable cell geometry.",
            "evidence": [
              {
                "reference": "DOI:10.1111/j.1574-6976.2011.00298.x",
                "snippet": "coryneform morphology",
                "notes": "Supports irregular coryneform-like morphology arising from polar/apical growth without strong lateral patterning."
              }
            ],
            "predicate_id": "RO:0002234"
          },
          {
            "subject": "variable_geometry",
            "predicate": "manifests as",
            "object": "irregular_shaped_trait",
            "description": "Variable geometry across cells manifests the irregular-shaped trait.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-cellbio-101011-155745",
                "snippet": "cell shape is genetically determined",
                "notes": "Supports the trait endpoint."
              }
            ],
            "predicate_id": "METPO:2007400"
          },
          {
            "subject": "mreb_loss",
            "predicate": "disrupts",
            "object": "mreb_cytoskeleton_function",
            "description": "Inhibition or depletion of MreB removes curvature sensing and localized cell-wall insertion control.",
            "evidence": [
              {
                "reference": "DOI:10.1101/2024.11.22.624946",
                "notes": "MreB filaments sense curvature and direct localized cell-wall insertion; A22 inhibition of MreB polymerization alters width and causes rounding/loss of rod shape."
              }
            ]
          },
          {
            "subject": "mreb_loss",
            "predicate": "causes",
            "object": "irregular_shaped_trait",
            "description": "Loss of MreB-mediated localized PG insertion removes rod-shape maintenance, yielding rounding and heterogeneous morphologies.",
            "evidence": [
              {
                "reference": "DOI:10.1101/2024.11.22.624946",
                "notes": "Inhibition of MreB polymerization causes rounding/loss of rod shape across model bacteria; a broadly conserved shape-maintenance module."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "synthase_hydrolase_imbalance",
            "predicate": "contributes to",
            "object": "reduced_wall_patterning",
            "description": "Loss of coordination between peptidoglycan synthases and hydrolases degrades spatial control of wall synthesis.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-023-41082-3",
                "notes": "Coordinated peptidoglycan synthases and hydrolases stabilize the bacterial cell wall; uncoupling them (e.g. excess hydrolase activity) accelerates loss of regular shape as a general loss-of-patterning mechanism."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "polar_growth_perturbation",
            "predicate": "disrupts",
            "object": "polar_growth_organization",
            "description": "Disruption of apical polar growth determinants disorganizes the tip-organizing center and wall-synthesis focusing.",
            "evidence": [
              {
                "reference": "DOI:10.21203/rs.3.rs-3811693/v1",
                "notes": "Apical determinants stabilize the tip-organizing center; their perturbation is associated with abnormal branching and mispatterned wall synthesis in filamentous bacteria."
              }
            ]
          },
          {
            "subject": "polar_growth_perturbation",
            "predicate": "has output",
            "object": "variable_geometry",
            "description": "Mispatterned apical wall synthesis from disrupted polar growth produces irregular, branched/bulged geometry.",
            "evidence": [
              {
                "reference": "DOI:10.21203/rs.3.rs-3811693/v1",
                "notes": "Partial depletion of the polar scaffold DivIVA causes hyphal bulging and irregular branching, an irregular-shape outcome of disorganized polar growth."
              }
            ],
            "predicate_id": "RO:0002234"
          },
          {
            "subject": "wall_less_state",
            "predicate": "manifests as",
            "object": "irregular_shaped_trait",
            "description": "Absence of a cylindrical wall removes canonical shape constraints, yielding irregular, amoeboid morphology.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s42003-024-07279-y",
                "notes": "Wall-less L-form cells have heterogeneous, amoeboid morphology; loss of the rigid wall removes shape constraints, a general consequence of wall absence."
              }
            ],
            "predicate_id": "METPO:2007400"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.898746+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-11T22:45:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed definition and causal graph linking reduced cell-wall patterning and stochastic growth to irregular morphology.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d71, METPO:2000202\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T21:30:07Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007400\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 6 evidence-backed generic edges (6 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:13Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 4 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:causes\u00d71, RO:0002326\u00d71, METPO:2000202\u00d71, METPO:2007400\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 2 causal edge(s) off microbe-domain METPO predicates (2 to has output), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope irregular_shaped_loss_of_patterning=NONMECHANISTIC with scope_notes.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T04:43:24Z",
        "curator": "codex",
        "action": "ADD_CANONICAL_EXAMPLES",
        "changes": "Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Corynebacterium glutamicum (NCBITaxon:1718; DOI:10.1111/j.1574-6976.2011.00298.x). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1005036",
    "label": "lateral flagellation",
    "definition": "A motility phenotype in which flagella emerge from the lateral side of the cell.",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "SEEDED",
    "parent_traits": [
      "traitmech:000056"
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-11T08:08:23Z",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)"
      },
      {
        "timestamp": "2026-09-11T08:09:00Z",
        "curator": "codex",
        "action": "ENRICHED_FROM_LITERATURE",
        "changes": "Enriched the seeded METPO lateral flagellation phenotype with DOI-backed lateral-flagella evidence after a repository-wide duplicate review covering ignored and hidden files.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-21T21:12:25Z",
        "curator": "claude",
        "action": "CURATE_CAUSAL_GRAPH",
        "changes": "Added NONMECHANISTIC causal_graphs entry (lateral_flagellation_swarming_sketch) anchored on existing verbatim record evidence snippets.",
        "llm_assisted": true
      }
    ],
    "definition_source": "DOI:10.1111/j.1574-6968.2006.00403.x",
    "evidence": [
      {
        "reference": "DOI:10.1111/j.1574-6968.2006.00403.x",
        "snippet": "These bacteria are able to express both a constitutive polar flagellum required for swimming motility and a separate lateral flagella system that is induced in viscous media or on surfaces and is essential for swarming motility.",
        "notes": "Merino et al. review lateral flagella as a distinct, inducible flagellar system in bacteria with dual polar and lateral systems."
      },
      {
        "reference": "DOI:10.1128/jb.167.1.210-218.1986",
        "snippet": "The polar flagellum is responsible for motility in a liquid environment (swimming), and the lateral flagella enable the bacteria to move over surfaces (swarming).",
        "notes": "Belas et al. directly connect V. parahaemolyticus lateral flagella with surface swarming."
      },
      {
        "reference": "DOI:10.1128/jb.185.15.4508-4518.2003",
        "snippet": "Multiple proton-driven lateral flagella enable translocation over surfaces (i.e., swarming).",
        "notes": "Stewart and McCarter describe the lateral flagella of V. parahaemolyticus as surface-translocation organelles."
      },
      {
        "reference": "DOI:10.1128/jb.188.3.852-862.2006",
        "snippet": "Mesophilic Aeromonas strains express a polar flagellum in all culture conditions, and certain strains produce lateral flagella on semisolid media or on surfaces.",
        "notes": "Canals et al. show that lateral flagella are an Aeromonas trait as well as a Vibrio parahaemolyticus trait."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:670",
        "taxon_label": "Vibrio parahaemolyticus",
        "note": "Belas et al. describe V. parahaemolyticus as producing a polar swimming flagellum and lateral flagella that enable swarming on surfaces.",
        "reference": "DOI:10.1128/jb.167.1.210-218.1986"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "lateral_flagellation_swarming_sketch",
        "title": "Inducible proton-driven lateral flagella and surface swarming",
        "description": "Evidence-backed causal sketch linking proton-driven lateral flagella to the lateral flagellation morphology and surface swarming motility.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "Morphological arrangement descriptor spanning multiple bacterial lineages (DOI:10.1111/j.1574-6968.2006.00403.x, DOI:10.1128/jb.167.1.210-218.1986, DOI:10.1128/jb.185.15.4508-4518.2003); the record's verbatim evidence quotes characterize organelle-level lateral flagellation and proton-driven swarming without naming individual protein subunits.",
        "nodes": [
          {
            "node_id": "lateral_flagellation_trait",
            "label": "lateral flagellation",
            "node_type": "TRAIT",
            "grounding": "METPO:1005036",
            "description": "Motility morphology in which flagella emerge from the lateral side of the cell."
          },
          {
            "node_id": "lateral_flagellation_lateral_flagella",
            "label": "bacterial-type flagellum",
            "node_type": "ORGANELLE",
            "grounding": "GO:0009288",
            "description": "Inducible lateral flagellar organelles expressed on surfaces or in viscous media."
          },
          {
            "node_id": "lateral_flagellation_swarming_motility",
            "label": "swarming motility",
            "node_type": "BIOLOGICAL_PROCESS",
            "grounding": "GO:0071973",
            "description": "Surface translocation enabled by lateral flagella."
          },
          {
            "node_id": "lateral_flagellation_proton_motive_force",
            "label": "proton motive force",
            "node_type": "STATE",
            "grounding": "METPO:1007500",
            "description": "Transmembrane proton gradient that powers lateral flagellar rotation during swarming."
          }
        ],
        "edges": [
          {
            "subject": "lateral_flagellation_lateral_flagella",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "lateral_flagellation_trait",
            "description": "Expression of an inducible lateral flagella system confers the lateral flagellation morphology.",
            "evidence": [
              {
                "reference": "DOI:10.1111/j.1574-6968.2006.00403.x",
                "snippet": "These bacteria are able to express both a constitutive polar flagellum required for swimming motility and a separate lateral flagella system that is induced in viscous media or on surfaces and is essential for swarming motility.",
                "notes": "Merino et al. describe the separate inducible lateral flagella system expressed in viscous media or on surfaces."
              }
            ]
          },
          {
            "subject": "lateral_flagellation_lateral_flagella",
            "predicate": "enables",
            "predicate_id": "RO:0002327",
            "object": "lateral_flagellation_swarming_motility",
            "description": "Lateral flagella enable bacterial swarming motility across surfaces.",
            "evidence": [
              {
                "reference": "DOI:10.1128/jb.167.1.210-218.1986",
                "snippet": "The polar flagellum is responsible for motility in a liquid environment (swimming), and the lateral flagella enable the bacteria to move over surfaces (swarming).",
                "notes": "Belas et al. show that lateral flagella enable bacteria to move over surfaces (swarming)."
              }
            ]
          },
          {
            "subject": "lateral_flagellation_proton_motive_force",
            "predicate": "enables",
            "predicate_id": "RO:0002327",
            "object": "lateral_flagellation_swarming_motility",
            "description": "Proton-driven lateral flagellar motors power translocation over surfaces during swarming.",
            "evidence": [
              {
                "reference": "DOI:10.1128/jb.185.15.4508-4518.2003",
                "snippet": "Multiple proton-driven lateral flagella enable translocation over surfaces (i.e., swarming).",
                "notes": "Stewart and McCarter report that multiple proton-driven lateral flagella enable surface swarming."
              }
            ]
          }
        ]
      }
    ]
  },
  {
    "identifier": "traitmech:000058",
    "label": "lophotrichous",
    "definition": "A flagellar arrangement with a tuft of multiple flagella at one pole of the cell.",
    "definition_source": "DOI:10.1093/femsre/fuv034",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "traitmech:000056"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1093/femsre/fuv034",
        "notes": "Schuhmacher et al. describe polar tufts of flagella (lophotrichous) among the regular flagellation patterns bacteria maintain."
      },
      {
        "reference": "DOI:10.3390/biom9070279",
        "notes": "Flagellum review supports multiple flagellar filaments acting as locomotory organelles."
      },
      {
        "reference": "DOI:10.1128/jb.150.1.377-380.1982",
        "snippet": "unipolar cells, recently divided, have only one bundle of flagella.",
        "notes": "Swan 1982, p. 377, methods: S. volutans ATCC 19554 was grown at 30 C in ATCC medium 234. Recently divided cells in an actively growing culture were naturally unipolar; older cells had two flagellar bundles and were excluded from the measurements. This supports a life-stage-qualified one-pole example, not unipolar flagellation of every cell or a deflagellation experiment. The source scan, rather than the abstract alone, establishes the culture and division-stage context."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:210",
        "taxon_label": "Helicobacter pylori",
        "note": "polar tuft of flagella",
        "reference": "PMID:30258065"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "lophotrichous_polar_tuft",
        "title": "Lophotrichous flagellation \u2014 polar tuft of flagella",
        "description": "Evidence-backed causal sketch linking a polar tuft of bacterial flagella to the lophotrichous arrangement.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a broad environmental or morphological classification spanning multiple mechanisms, a measurement-like bin, or an absence/arrangement descriptor; contextual protein nodes do not receive token UniProt examples.",
        "nodes": [
          {
            "node_id": "lophotrichous_trait",
            "label": "lophotrichous",
            "node_type": "TRAIT",
            "grounding": "traitmech:000058",
            "description": "Tuft of multiple flagella at one pole."
          },
          {
            "node_id": "bacterial_flagellum",
            "label": "bacterial-type flagellum",
            "node_type": "CELLULAR_LOCALIZATION",
            "grounding": "GO:0009288",
            "description": "Helical proteinaceous locomotory organelle."
          },
          {
            "node_id": "polar_tuft_placement",
            "label": "polar tuft placement",
            "node_type": "QUALITY",
            "description": "Multiple flagella clustered at one cell pole."
          },
          {
            "node_id": "flhf_protein",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "FlhF",
            "node_type": "GENE_OR_PROTEIN",
            "description": "SRP-type GTPase that positions and initiates polar flagellar assembly."
          },
          {
            "node_id": "cell_pole",
            "label": "cell pole",
            "node_type": "CELLULAR_LOCALIZATION",
            "description": "The cell pole where polar flagellar assembly is nucleated.",
            "grounding": "GO:0060187"
          },
          {
            "node_id": "flig_protein",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "FliG",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Flagellar C-ring switch protein recruited during basal-body assembly."
          },
          {
            "node_id": "flif_protein",
            "label": "FliF",
            "node_type": "GENE_OR_PROTEIN",
            "description": "MS-ring protein forming the membrane base of the flagellar basal body.",
            "grounding": "InterPro:IPR000067"
          },
          {
            "node_id": "fipa_protein",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "FipA",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Membrane-localized polar landmark/licensing factor required for normal polar flagellar synthesis."
          },
          {
            "node_id": "flhg_protein",
            "label": "FlhG",
            "node_type": "GENE_OR_PROTEIN",
            "description": "MinD-type ATPase that regulates flagellar number by stimulating FlhF GTPase activity.",
            "grounding": "InterPro:IPR033875"
          },
          {
            "node_id": "flagellar_number",
            "label": "flagellar number",
            "node_type": "QUALITY",
            "description": "Number of flagella assembled per cell."
          }
        ],
        "edges": [
          {
            "subject": "bacterial_flagellum",
            "predicate": "defines",
            "object": "lophotrichous_trait",
            "description": "A tuft of flagella at one pole defines the lophotrichous arrangement.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuv034",
                "notes": "Schuhmacher et al. describe polar tufts of flagella (lophotrichous)."
              }
            ],
            "predicate_id": "METPO:2007500"
          },
          {
            "subject": "lophotrichous_trait",
            "predicate": "associated with",
            "object": "polar_tuft_placement",
            "description": "The lophotrichous pattern places multiple flagella at one pole.",
            "evidence": [
              {
                "reference": "DOI:10.3390/biom9070279",
                "notes": "Flagellum review supports multiple flagellar filaments acting as locomotory organelles."
              }
            ],
            "predicate_id": "biolink:associated_with"
          },
          {
            "subject": "flhf_protein",
            "predicate": "localizes to and promotes assembly at",
            "object": "cell_pole",
            "description": "GTP-bound FlhF localizes to the cell pole and recruits initial flagellar building blocks.",
            "evidence": [
              {
                "reference": "DOI:10.7554/eLife.93004.3",
                "notes": "GTP-bound dimeric FlhF localizes to the cell pole and recruits initial flagellar building blocks; deletion of flhF causes absence/mislocalization of flagella."
              }
            ]
          },
          {
            "subject": "flhf_protein",
            "predicate": "recruits",
            "object": "flig_protein",
            "description": "FlhF binds the C-ring protein FliG to initiate polar assembly.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-024-50274-4",
                "notes": "FlhF binds the C-ring protein FliG via its N-terminus."
              }
            ]
          },
          {
            "subject": "flig_protein",
            "predicate": "captures",
            "object": "flif_protein",
            "description": "The FlhF:FliG complex recruits/captures FliF to promote MS-ring formation at the pole.",
            "evidence": [
              {
                "reference": "DOI:10.7554/eLife.93004.3",
                "notes": "FliG captures FliF to promote MS-ring formation; recruits a functional FliF/FliG complex to the pole."
              }
            ]
          },
          {
            "subject": "fipa_protein",
            "predicate": "required for",
            "object": "lophotrichous_trait",
            "description": "FipA is required for normal FlhF activity and polar flagellar synthesis.",
            "evidence": [
              {
                "reference": "DOI:10.7554/eLife.93004.3",
                "notes": "FipA is required for normal FlhF activity and polar flagellar synthesis; deletion abolishes swimming motility and yields cells lacking surface flagella."
              }
            ]
          },
          {
            "subject": "flhg_protein",
            "predicate": "negatively regulates",
            "object": "flagellar_number",
            "description": "FlhG limits flagellar number; its loss causes hyper-flagellation.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuv034",
                "notes": "Loss of FlhG causes hyper-flagellation; deletion of flhG produces hyper-flagellated strains."
              }
            ],
            "predicate_id": "RO:0002212"
          },
          {
            "subject": "flhg_protein",
            "predicate": "stimulates GTPase activity of",
            "object": "flhf_protein",
            "description": "FlhG stimulates the GTPase activity of FlhF, converting GTP-bound to GDP-bound FlhF.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-024-50274-4",
                "notes": "FlhG stimulates the GTPase activity of the SRP-type GTPase FlhF, converting GTP-bound FlhF to GDP-bound FlhF."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-06-03T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate MORPHOLOGY trait (lophotrichous flagellation); sub-variant of flagellar arrangement.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-09T15:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (polar tuft) with GO node grounding and METPO/biolink predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 6 evidence-backed generic edges (7 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:33Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0060187\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-26T07:15:19Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 5 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A656AC42\u00d71, UniProtKB:A0A016XEK1\u00d71, UniProtKB:A0A0H2X1L8\u00d71, UniProtKB:A0A023UGD7\u00d71, UniProtKB:Q2N2M1\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:21:12Z",
        "curator": "claude",
        "action": "RETRACT_DEAD_UNIPROT_GROUNDINGS",
        "changes": "Retracted 3 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-04T03:08:15Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002212\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-22T04:26:15Z",
        "curator": "codex",
        "action": "REVIEW_UNIPROT_INSTANCE_GROUNDINGS",
        "changes": "Reviewed 2 organism-specific UniProtKB grounding(s): replaced 2 with taxon-agnostic GO/InterPro terms and retracted 0 to label-only where no exact semantic term was supported (docs/GROUNDING_POLICY.md).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope lophotrichous_polar_tuft=NONMECHANISTIC with scope_notes; marked 3 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (flhf_protein, flig_protein, fipa_protein).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-03T17:07:26Z",
        "curator": "codex",
        "action": "REPAIR_CANONICAL_CITATION_SCOPE_1626",
        "changes": "Resolved issue 1626 by replacing the mismatched bipolar example note and compound PMID:16561638 (DOI:10.1128/jb.57.1.111-118.1949) citation with a life-stage-qualified, one-bundle example from Swan 1982 (DOI:10.1128/jb.150.1.377-380.1982; PMID:7061399; PMC220122). This is an explicit source and scope correction, not a PMID-to-DOI normalization: Pijper's original PMID and DOI identify the same 1949 paper. Source-native scans distinguish recently divided unipolar ATCC 19554 cells from older bipolar cells. Added the exact methods snippet and bounded interpretation; retained NCBITaxon:968 and the independently checked NCBI label. The definition, hierarchy, graph, other example and existing amphitrichous record are unchanged.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-03T17:30:07Z",
        "curator": "codex",
        "action": "REFINE_CANONICAL_ARCHETYPES_1629",
        "changes": "Addressed independent PR 1628 review and issue 1629 by removing the S. volutans canonical-example row while retaining the Swan 1982 evidence and verbatim snippet. Recently divided unipolar cells are directly observed, but a selected division-stage observation is not used here as the schema's archetypal taxon exemplar. H. pylori remains the canonical example. This does not deny naturally unipolar S. volutans cells, assert disjoint organism-level traits or generalize the division sequence to every amphitrichous taxon. The amphitrichous record, trait identity, definition, hierarchy and graph are unchanged; the initial repair event is preserved.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000071",
    "label": "magnetosome",
    "definition": "A membrane-bounded intracellular organelle containing a magnetic iron-mineral crystal (magnetite or greigite); chains of magnetosomes allow magnetotactic bacteria to align with and navigate along geomagnetic field lines.",
    "definition_source": "DOI:10.1038/nrmicro.2016.99",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "traitmech:000066"
    ],
    "xrefs": [
      "GO:0110143"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/nrmicro.2016.99",
        "notes": "Uebe & Sch\u00fcler review magnetosome biogenesis as the formation of membrane-bounded magnetic-mineral organelles in magnetotactic bacteria."
      },
      {
        "reference": "DOI:10.1038/nrmicro842",
        "notes": "Bazylinski & Frankel, \"Magnetosome formation in prokaryotes\", describe magnetosomes and the magnetotactic lifestyle they enable."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:431944",
        "taxon_label": "Magnetospirillum gryphiswaldense MSR-1",
        "note": "Primary model for magnetosome biosynthesis (mamAB operon; MamK/MamJ-organised magnetite chains for magnetotaxis). AMB-1 (NCBITaxon:342108) is a co-equal model.",
        "reference": "DOI:10.1038/s41579-025-01234-2"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "magnetosome_magnetotaxis",
        "title": "Magnetosome chains enable magnetotactic navigation",
        "description": "Evidence-backed causal sketch linking membrane-bounded magnetic-mineral organelles arranged in chains to alignment with geomagnetic fields and magnetotactic navigation.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "The taxon-matched protein example anchors one experimentally supported causal branch; it is not presented as a universal mechanism for every taxon or every contextual branch in this graph.",
        "nodes": [
          {
            "node_id": "magnetosome_trait",
            "label": "magnetosome",
            "node_type": "TRAIT",
            "grounding": "traitmech:000071",
            "description": "Membrane-bounded organelle containing a magnetic iron-mineral crystal."
          },
          {
            "node_id": "magnetic_mineral_crystal",
            "label": "magnetic iron-mineral crystal",
            "node_type": "CHEMICAL",
            "description": "Magnetite (Fe3O4) or greigite (Fe3S4) crystal inside the magnetosome."
          },
          {
            "node_id": "magnetotaxis",
            "label": "magnetotaxis",
            "node_type": "BIOLOGICAL_PROCESS",
            "grounding": "traitmech:000176",
            "description": "Movement biased along geomagnetic field lines."
          },
          {
            "node_id": "mamk_protein",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:Q6NE59",
                "protein_label": "Actin-like protein MamK",
                "gene_symbol": "mamK",
                "taxon_id": "NCBITaxon:431944",
                "taxon_label": "Magnetospirillum gryphiswaldense MSR-1",
                "entry_status": "REVIEWED",
                "proteome_id": "UP000018922",
                "retrieved_on": "2026-10-22",
                "entry_version": 87,
                "sequence_version": 1,
                "role": "MamK polymerizes into an actin-like scaffold that organizes magnetosomes into chains.",
                "evidence": [
                  {
                    "reference": "DOI:10.1128/mbio.01649-23",
                    "snippet": "MamK organizes magnetosome chains",
                    "notes": "The cited source supports the represented protein-to-trait branch; UniProt verifies this current strain-matched protein entry."
                  }
                ]
              }
            ],
            "label": "MamK",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Actin-like cytoskeletal protein that organizes magnetosomes into chains."
          },
          {
            "node_id": "mamk_filaments",
            "label": "actin-like MamK filaments",
            "node_type": "CELLULAR_LOCALIZATION",
            "description": "Long actin-like cytoskeletal filaments formed by MamK polymerization."
          },
          {
            "node_id": "magnetosome_chain",
            "label": "magnetosome chain assembly",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Linear arrangement of magnetosomes into a chain acting as a cellular compass."
          },
          {
            "node_id": "mamab_operon",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "MamAB magnetosome protein module",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Core magnetosome gene operon sufficient for rudimentary biomineralization.",
            "gene_symbols": [
              "mamA",
              "mamB",
              "mamE",
              "mamI",
              "mamK",
              "mamL",
              "mamM",
              "mamO",
              "mamQ"
            ],
            "operon": "mamAB"
          },
          {
            "node_id": "biomineralization",
            "label": "magnetosome biomineralization",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Intracellular formation of the magnetic iron-mineral crystal."
          },
          {
            "node_id": "mamb_protein",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "MamB",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Magnetosome membrane protein implicated in membrane invagination and crystal formation."
          },
          {
            "node_id": "membrane_invagination",
            "label": "magnetosome membrane invagination",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Invagination of the cytoplasmic membrane forming the magnetosome vesicle."
          },
          {
            "node_id": "low_sulfide_environment",
            "label": "oxygen-poor, low-sulfide environment",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Habitat with low oxygen and low sulfide favoring magnetite mineralization."
          },
          {
            "node_id": "magnetite_magnetosome",
            "label": "magnetite crystal",
            "node_type": "CHEMICAL",
            "description": "Iron oxide magnetite (Fe3O4) crystal contained within a magnetosome."
          },
          {
            "node_id": "sulfide_rich_habitat",
            "label": "sulfide-rich habitat",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Sulfide-rich habitat favoring greigite mineralization."
          },
          {
            "node_id": "greigite_magnetosome",
            "label": "greigite crystal",
            "node_type": "CHEMICAL",
            "description": "Iron sulfide greigite (Fe3S4) crystal contained within a magnetosome."
          }
        ],
        "edges": [
          {
            "subject": "magnetic_mineral_crystal",
            "predicate": "located in",
            "object": "magnetosome_trait",
            "description": "The magnetic mineral crystal sits inside the magnetosome membrane.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro.2016.99",
                "notes": "Uebe & Sch\u00fcler review magnetosome biogenesis as the formation of membrane-bounded magnetic-mineral organelles."
              }
            ],
            "predicate_id": "biolink:located_in"
          },
          {
            "subject": "magnetosome_trait",
            "predicate": "enables",
            "object": "magnetotaxis",
            "description": "Chains of magnetosomes act as a cellular compass, aligning the organism with geomagnetic field lines.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro842",
                "notes": "Bazylinski & Frankel describe magnetosomes and the magnetotactic lifestyle they enable."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "mamk_protein",
            "predicate": "organizes",
            "object": "magnetosome_chain",
            "description": "The actin-like protein MamK organizes magnetosomes into chains.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mbio.01649-23",
                "notes": "MTB align their magnetosome organelles into chains, organized by the actin-like MamK; broadly conserved."
              }
            ]
          },
          {
            "subject": "mamk_protein",
            "predicate": "polymerizes into",
            "object": "mamk_filaments",
            "description": "MamK polymerizes into long actin-like filaments that scaffold the magnetosome chain.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mbio.01649-23",
                "notes": "MamK polymerizes into long, actin-like filaments."
              }
            ]
          },
          {
            "subject": "magnetosome_chain",
            "predicate": "enables",
            "object": "magnetotaxis",
            "description": "Chain assembly of magnetosomes underlies the cellular compass enabling magnetotaxis.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mbio.01649-23",
                "notes": "Magnetosomes aligned into chains by MamK form the magnetic compass for navigation."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "mamab_operon",
            "predicate": "sufficient for",
            "object": "biomineralization",
            "description": "The mamAB operon is sufficient for rudimentary magnetosome biomineralization.",
            "evidence": [
              {
                "reference": "DOI:10.1111/mmi.15330",
                "notes": "The mamAB operon is sufficient for rudimentary biomineralization."
              }
            ]
          },
          {
            "subject": "biomineralization",
            "predicate": "has output",
            "object": "magnetic_mineral_crystal",
            "description": "Biomineralization forms the magnetic iron-mineral crystal within the magnetosome.",
            "evidence": [
              {
                "reference": "DOI:10.1111/mmi.15330",
                "notes": "Magnetosome biomineralization yields the intracellular magnetic mineral crystal."
              }
            ],
            "predicate_id": "RO:0002234"
          },
          {
            "subject": "mamb_protein",
            "predicate": "promotes",
            "object": "membrane_invagination",
            "description": "MamB promotes invagination of the cytoplasmic membrane to form the magnetosome vesicle.",
            "evidence": [
              {
                "reference": "DOI:10.1111/mmi.15330",
                "notes": "MamB likely recruits MAPs and promotes membrane invagination."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "low_sulfide_environment",
            "predicate": "favors",
            "object": "magnetite_magnetosome",
            "description": "Oxygen-poor, low-sulfide environments favor magnetite magnetosomes.",
            "evidence": [
              {
                "reference": "DOI:10.1111/mmi.15330",
                "notes": "Magnetite is more common in oxygen-poor, low-sulfide environments."
              }
            ]
          },
          {
            "subject": "sulfide_rich_habitat",
            "predicate": "favors",
            "object": "greigite_magnetosome",
            "description": "Sulfide-rich habitats favor greigite magnetosomes.",
            "evidence": [
              {
                "reference": "DOI:10.1111/mmi.15330",
                "notes": "Greigite dominates in sulfide-rich habitats."
              }
            ]
          },
          {
            "subject": "membrane_invagination",
            "predicate": "precedes",
            "object": "biomineralization",
            "description": "Magnetosome-membrane invagination forms the vesicle before mineral biomineralization begins.",
            "evidence": [
              {
                "reference": "DOI:10.1111/mmi.15330",
                "snippet": "Biomineralization of magnetite crystals occurs after the formation of magnetosome vesicles",
                "notes": "Verified against the public PMC full text; this orders two existing biogenesis stages without asserting simultaneity is impossible."
              }
            ]
          },
          {
            "subject": "magnetite_magnetosome",
            "predicate": "located in",
            "object": "magnetosome_trait",
            "description": "Magnetite is one mineral-crystal form contained by magnetosomes.",
            "evidence": [
              {
                "reference": "DOI:10.1111/mmi.15330",
                "snippet": "The structure and morphology of magnetosomes differ across all MTB species, with some producing iron oxide magnetite (Fe3O4)",
                "notes": "Verified against the public PMC full text; the node wording is tightened from a whole organelle to its mineral crystal."
              }
            ],
            "predicate_id": "biolink:located_in"
          },
          {
            "subject": "greigite_magnetosome",
            "predicate": "located in",
            "object": "magnetosome_trait",
            "description": "Greigite is one mineral-crystal form contained by magnetosomes.",
            "evidence": [
              {
                "reference": "DOI:10.1111/mmi.15330",
                "snippet": "others synthesizing iron sulfide greigite (Fe3S4), and some capable of producing both, depending on their environmental conditions",
                "notes": "Verified against the public PMC full text; the environmental preference remains explicitly contextual."
              }
            ],
            "predicate_id": "biolink:located_in"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-06-03T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate MORPHOLOGY trait (magnetosome); organelle sub-variant of intracellular inclusion.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-09T15:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (magnetosome / magnetotaxis) with RO/biolink predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 8 evidence-backed generic edges (11 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:13Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d71, METPO:2000202\u00d71, RO:0002213\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-26T07:15:19Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A6J4ZQS8\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:21:12Z",
        "curator": "claude",
        "action": "RETRACT_DEAD_UNIPROT_GROUNDINGS",
        "changes": "Retracted 1 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates (1 to has output), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "CURATE_PROTEIN_TAXON_EXAMPLE",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope magnetosome_magnetotaxis=MECHANISTIC with scope_notes; marked 3 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (mamk_protein, mamab_operon, mamb_protein); added taxon-paired protein example(s) UniProtKB:Q6NE59 on mamk_protein (NCBITaxon:431944).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T06:15:40Z",
        "curator": "codex",
        "action": "ADD_EXACT_ONTOLOGY_MATCH",
        "changes": "Ontology exact-match review (2026-08-25): approved exact xref(s): GO:0110143. Evidence is predicate-scoped in the versioned ontology snapshots; OAK cross-checked direct data, and OLS4 spot-checked release deltas and disputed hits.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T06:48:00Z",
        "curator": "codex",
        "action": "CONNECT_CAUSAL_GRAPH_COMPONENTS",
        "changes": "Resolved issue #183 graph fragmentation (4 components to 1) using 3 source- and verbatim-snippet-backed connector(s). Clarified the magnetite and greigite nodes as mineral crystals contained within magnetosomes. No paid research service was called.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-12T16:36:00Z",
        "curator": "codex",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded the magnetotaxis causal-graph process node to newly minted traitmech:000176 and moved the adjectival magnetotactic related synonym to the magnetotaxis trait; resolves issue 851.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-22T01:35:00Z",
        "curator": "claude",
        "action": "REFRESH_UNIPROT_ENTRY_VERSION",
        "changes": "Refreshed UniProtKB entry_version against live UniProt REST on 2026-10-22: UniProtKB:Q6NE59 (86 -> 87 on mamk_protein).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000663",
    "label": "microbial haustorium formation",
    "definition": "A morphological phenotype in which a fungus or oomycete forms specialized hyphal outgrowths, called haustoria, that establish intimate interfaces with living host cells.",
    "definition_source": "DOI:10.1016/j.fgb.2014.08.006",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1016/j.fgb.2014.08.006",
        "snippet": "The haustorium is separated from the extrahaustorial membrane (em) by the extrahaustorial matrix (emx).",
        "notes": "Martinez-Cruz et al. (2014), PMID:25151531; primary PDF at https://powderymildew.ucr.edu/wp-content/uploads/2017/04/MPM14.pdf. Abstract, Introduction, Methods and main text were read; actual Figures 2-4 and complete pages 24-26 were visually inspected. The quote is from Figure 3's caption. Podosphaera xanthii isolate 2086 forms haustoria within melon epidermal cells. This supports the fungal formation phenotype and this interface anatomy, not a universal membrane arrangement. Callose correlates with maturity; functional partitioning of lobes and putative exosomes remains an interpretation. Remaining actual figures and supplements were not inspected. Initial natural-isolation provenance for 2086 was not established, so it is not used as a canonical example."
      },
      {
        "reference": "DOI:10.1080/00275514.1994.12026373",
        "snippet": "A single micropore connected the cytoplasm of the haustorial filament with that of the host cell.",
        "notes": "Zugmaier, Bauer and Oberwinkler (1994), Mycologia 86:49-56; all eight pages and actual Figures 1-16 directly inspected at https://dr-franz.oberwinkler.de/wp-content/uploads/Tremella_mycoparasitism.pdf. The snippet is from the scientific abstract on page 49, visually checked because OCR is poor. Crossref confirms this DOI, title, authors and 1994 print date; its 2018 online date is not the study year. Field and culture observations distinguish tremelloid haustorial cells, filaments and host-dependent micropores. Membrane continuity was visible only under optimal sectioning; some captions say probably or presumed. Some tested hosts had attached filaments without an observed continuous micropore. Static microscopy is not a nutrient-flux assay, and formation does not guarantee a successful feeding connection."
      },
      {
        "reference": "DOI:10.1111/mpp.13072",
        "snippet": "We transformed P. kernoviae to express green fluorescent protein (GFP) and demonstrated that it forms haustoria within infected N. benthamiana cells.",
        "notes": "Wang et al. (2021), PMID:34018655, PMC8295517; scientific abstract, Results 2.1, Figure 1 caption and Methods 4.1, 4.6 and 4.7 read in directly retrieved full-text XML. The quoted abstract sentence explicitly identifies transformation. Imaging used engineered GFP line PkGFP8 derived from SCRP1055 and transgenic Nicotiana benthamiana membrane markers. Results call the projections likely biotrophic haustoria; the caption says they appeared in natural hosts without membrane markers. Those hosts are not unmodified-pathogen controls. Actual figures, supplements and complete remaining Methods were not inspected. This supports oomycete scope with engineering qualifiers, not a natural canonical example or a requirement for lifelong obligate biotrophy."
      },
      {
        "reference": "DOI:10.1104/pp.18.00979",
        "snippet": "Biotrophic and hemibiotrophic oomycetes form intimate associations with their hosts using haustoria",
        "notes": "Judelson and Ah-Fong (2019), PMID:30538168, PMC6446794; publisher HTML at https://academic.oup.com/plphys/article/179/4/1198/6116504 read directly after PMC and Europe PMC access failed. The clause precedes a figure citation in HAUSTORIA REPRESENT A SPECIALIZED INTERFACE. This is a review, not another formation experiment. Its interface and nutrient-acquisition passages distinguish demonstrated effector secretion from then-unproven nutritional importance in oomycetes. Neither a universal transport mechanism nor a present-day absence of such evidence is inferred. Actual figures and cited underlying experiments were not inspected."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:5217",
        "taxon_label": "Tremella mesenterica",
        "reference": "DOI:10.1080/00275514.1994.12026373",
        "note": "Field-collected material in Zugmaier et al. (1994), Methods page 51, field Results page 53 and Figures 1-9. Collections from Haldenwald near Sonnenberg, Stuttgart, Germany, on Carpinus betulus adjacent to Peniophora laeta include 8 June 1987 and 20 November 1989, W. Zugmaier 97 and 158. The authors observed tremelloid haustorial cells and filaments in contact with P. laeta and micropore connections. Figures are not assigned individually to one voucher; no such match is invented. Their separate laboratory culture was obtained by crossing monospore cultures from different basidiomata and is not equated to an unmodified field isolate. NCBI Taxonomy confirms ID 5217, label and species rank; the field material is not identified as NCBI type strain CBS 6973. The directly inspected primary PDF is https://dr-franz.oberwinkler.de/wp-content/uploads/Tremella_mycoparasitism.pdf."
      }
    ],
    "discussions": [
      {
        "discussion_id": "microbial-haustorium-scope-and-hierarchy",
        "prompt": "Resolve a closer parent and the haustorium/arbuscule boundary.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Use phenotype METPO:1000059. Fungal appressorium formation traitmech:000659 concerns surface-associated penetration structures, not this intimate host-cell interface. Plant pathogen METPO:1004003 is not a required parent because fungal hosts are supported. Mycorrhization METPO:1000198 is obsolete. Direct QuickGO authority checks resolve GO:0085035 haustorium as a cellular component and GO:0052094 formation of haustorium for nutrient acquisition as a biological process, not exact organism-level phenotypes. GO:0085041 arbuscule is an is_a child of GO:0085035, whereas literature often distinguishes arbuscules from parasitic haustoria. Preserve that attributed umbrella usage: the definition is not restricted to pathogenicity, but arbuscule formation is not asserted as an exact synonym or given a new hierarchy here. The GO membrane-invagination definition does not describe every tremelloid micropore interface. No xrefs or SSSOM equivalences are asserted. Parasitic-plant haustorial organs are outside this microbial hyphal scope; fungi and oomycetes are both included. Fungal arbuscule formation now has its own source-bounded phenotype record, traitmech:000664. This resolves the missing record reference, not the umbrella hierarchy question; no subclass or disjointness relationship between these two phenotypes is asserted.",
        "posed_by": "codex",
        "posed_date": "2026-10-07"
      },
      {
        "discussion_id": "microbial-haustorium-formation-and-function",
        "prompt": "Separate observed formation from feeding and formation mechanisms.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Haustorium formation alone does not demonstrate nutrient flux, effector delivery, pathogenicity, a universal shape or a shared membrane topology. Keep tremelloid cytoplasmic connections distinct from plant-pathogen extrahaustorial compartments. Attached filaments without an observed micropore are not proven successful feeding sites. Oomycete transformed imaging and source-specific likely/appeared language must remain visible; natural host means the host species, not an unmodified pathogen. Formation regulation requires direct perturbation evidence and authority-verified protein examples. The protein-resolved causal graph is deferred, not claimed to be biologically absent.",
        "posed_by": "codex",
        "posed_date": "2026-10-07"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-07T10:54:41Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added microbial haustorium formation with four source-backed snippets, a field-qualified Tremella example and explicit interface, engineering and ontology limits. Ignored-and-hidden novelty checks found no exact record. Reserved METPO:1061600 in v539, avoiding pending v538. Existing traits unchanged; protein-level formation graph deferred.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-07T13:21:20Z",
        "curator": "codex",
        "action": "LINK_ARBUSCULE_DISCUSSION",
        "changes": "Linked the existing arbuscule boundary discussion to traitmech:000664; retained OPEN status and deferred subclass, equivalence and disjointness. No haustorium identity, evidence, examples or parent changed.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000057",
    "label": "monotrichous",
    "definition": "A flagellar arrangement with a single flagellum, typically located at one pole of the cell.",
    "definition_source": "DOI:10.1093/femsre/fuv034",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "traitmech:000056"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1093/femsre/fuv034",
        "notes": "Schuhmacher et al. describe single-flagellum (monotrichous, polar) flagellation as one regular flagellation pattern."
      },
      {
        "reference": "DOI:10.3390/biom9070279",
        "notes": "Flagellum review supports a single helical flagellar filament as a locomotory organelle."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:666",
        "taxon_label": "Vibrio cholerae",
        "note": "single polar flagellum",
        "reference": "PMID:19717600"
      },
      {
        "taxon_id": "NCBITaxon:155892",
        "taxon_label": "Caulobacter vibrioides",
        "note": "single polar flagellum (swarmer)",
        "reference": "PMID:31010900"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "monotrichous_single_polar_flagellum",
        "title": "Monotrichous flagellation \u2014 single polar flagellum",
        "description": "Evidence-backed causal sketch linking a single polar bacterial flagellum to monotrichous flagellation.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a broad environmental or morphological classification spanning multiple mechanisms, a measurement-like bin, or an absence/arrangement descriptor; contextual protein nodes do not receive token UniProt examples.",
        "nodes": [
          {
            "node_id": "monotrichous_trait",
            "label": "monotrichous",
            "node_type": "TRAIT",
            "grounding": "traitmech:000057",
            "description": "Single flagellum, typically polar."
          },
          {
            "node_id": "bacterial_flagellum",
            "label": "bacterial-type flagellum",
            "node_type": "CELLULAR_LOCALIZATION",
            "grounding": "GO:0009288",
            "description": "Helical proteinaceous locomotory organelle."
          },
          {
            "node_id": "polar_placement",
            "label": "polar single-flagellum placement",
            "node_type": "QUALITY",
            "description": "Single flagellum positioned at one cell pole."
          },
          {
            "node_id": "flhf_gtpase",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "FlhF",
            "node_type": "GENE_OR_PROTEIN",
            "description": "SRP-type GTPase that targets and anchors flagellar assembly to the cell pole."
          },
          {
            "node_id": "flhg_atpase",
            "label": "FlhG",
            "node_type": "GENE_OR_PROTEIN",
            "description": "MinD/ParA-family ATPase that regulates flagellum number and modulates FlhF.",
            "grounding": "InterPro:IPR033875"
          },
          {
            "node_id": "polar_flagellum_localization",
            "label": "polar localization of flagellum",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Targeting and confinement of flagellar assembly to one cell pole."
          },
          {
            "node_id": "flagellum_number",
            "label": "flagellum number per cell",
            "node_type": "QUALITY",
            "description": "The count of flagella per cell."
          },
          {
            "node_id": "flig_protein",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "FliG",
            "node_type": "GENE_OR_PROTEIN",
            "description": "C-ring switch protein that bridges the MS-ring to motor and chemotaxis components."
          },
          {
            "node_id": "flif_msring",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "FliF MS-ring protein",
            "node_type": "GENE_OR_PROTEIN",
            "description": "MS-ring protein forming the membrane-embedded base of the flagellar basal body."
          },
          {
            "node_id": "flim_flin",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "FliM/FliN C-ring partners",
            "node_type": "GENE_OR_PROTEIN",
            "description": "C-ring switch-complex proteins that interact with FliG in the cytoplasmic ring."
          }
        ],
        "edges": [
          {
            "subject": "bacterial_flagellum",
            "predicate": "defines",
            "object": "monotrichous_trait",
            "description": "A single polar flagellum defines the monotrichous arrangement.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuv034",
                "notes": "Schuhmacher et al. describe single-flagellum (monotrichous) polar flagellation."
              }
            ],
            "predicate_id": "METPO:2007500"
          },
          {
            "subject": "monotrichous_trait",
            "predicate": "associated with",
            "object": "polar_placement",
            "description": "The monotrichous pattern places one flagellum at one pole.",
            "evidence": [
              {
                "reference": "DOI:10.3390/biom9070279",
                "notes": "Flagellum review supports a single helical flagellar filament as a locomotory organelle."
              }
            ],
            "predicate_id": "biolink:associated_with"
          },
          {
            "subject": "flhf_gtpase",
            "predicate": "promotes localization of",
            "object": "polar_flagellum_localization",
            "description": "FlhF promotes targeting of flagella to the cell pole; deleting flhF causes mislocalization to nonpolar sites.",
            "evidence": [
              {
                "reference": "DOI:10.1128/jb.00110-23",
                "notes": "FlhF and FlhG control the location and number of flagella in many polar-flagellated bacteria; deleting flhF caused hypoflagellation and mislocalization of flagella to nonpolar sites."
              }
            ]
          },
          {
            "subject": "flhg_atpase",
            "predicate": "regulates number of",
            "object": "flagellum_number",
            "description": "FlhG regulates the number of flagella per cell; its loss in single-flagellum bacteria often causes hyperflagellation.",
            "evidence": [
              {
                "reference": "DOI:10.1128/jb.00110-23",
                "notes": "FlhF and FlhG control the location and number of flagella respectively; deleting flhG in bacteria with a single polar flagellum often results in hyperflagellation."
              }
            ]
          },
          {
            "subject": "flhf_gtpase",
            "predicate": "binds",
            "object": "flig_protein",
            "description": "The FlhF B-domain FliG-Interaction Domain (FID) binds FliG.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-024-50274-4",
                "notes": "The FlhF B-domain contains an N-terminal FliG Interaction Domain (FID); the N-terminal ~60 aa of the B-domain are necessary and sufficient for FliG binding."
              }
            ]
          },
          {
            "subject": "flig_protein",
            "predicate": "recruits",
            "object": "flif_msring",
            "description": "FlhF-bound FliG engages the MS-ring protein FliF, recruiting a FliF-FliG complex to the pole.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-024-50274-4",
                "notes": "FlhF-bound FliG then engages the MS-ring protein FliF, effectively recruiting a FliF-FliG complex to the pole."
              }
            ]
          },
          {
            "subject": "flhf_gtpase",
            "predicate": "hinders interaction of",
            "object": "flim_flin",
            "description": "FlhF-bound FliG can still engage FliF but is prevented from interacting with C-ring partners FliM/FliN.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-024-50274-4",
                "notes": "FlhF-bound FliG can still engage the cytoplasmic domain of FliF but is prevented from interacting with C-ring partners FliM/FliN."
              }
            ]
          },
          {
            "subject": "flhg_atpase",
            "predicate": "stimulates GTPase activity of",
            "object": "flhf_gtpase",
            "description": "FlhG stimulates FlhF GTPase activity, modulating FlhF control over FliG interactions.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-024-50274-4",
                "notes": "FlhG's modulation of FlhF controls FliG's interaction with FliM/FliN; FlhG stimulates FlhF GTPase activity."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-06-03T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate MORPHOLOGY trait (monotrichous flagellation); sub-variant of flagellar arrangement.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-09T15:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (single polar flagellum) with GO node grounding and METPO/biolink predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 6 evidence-backed generic edges (7 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-26T07:15:19Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 3 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A656AC42\u00d71, UniProtKB:Q2N2M1\u00d71, UniProtKB:A0A016XEK1\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:21:12Z",
        "curator": "claude",
        "action": "RETRACT_DEAD_UNIPROT_GROUNDINGS",
        "changes": "Retracted 2 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-22T04:26:15Z",
        "curator": "codex",
        "action": "REVIEW_UNIPROT_INSTANCE_GROUNDINGS",
        "changes": "Reviewed 1 organism-specific UniProtKB grounding(s): replaced 1 with taxon-agnostic GO/InterPro terms and retracted 0 to label-only where no exact semantic term was supported (docs/GROUNDING_POLICY.md).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope monotrichous_single_polar_flagellum=NONMECHANISTIC with scope_notes; marked 4 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (flhf_gtpase, flig_protein, flif_msring, flim_flin).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000702",
    "label": "motile",
    "definition": "A motility in which an organism has the ability to move independently using metabolic energy.",
    "definition_source": "DOI:10.1038/s41579-021-00626-4",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000701"
    ],
    "synonyms": [
      {
        "synonym_text": "yes",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/s41579-021-00626-4",
        "snippet": "physical and molecular mechanisms that allow bacteria to move around",
        "notes": "Supports motile bacteria as organisms whose movement is mediated by specific molecular machines."
      },
      {
        "reference": "PMID:34680106",
        "snippet": "Pseudomonas aeruginosa is a motile bacterium",
        "notes": "Organism example: Pseudomonas aeruginosa is described as motile."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:562",
        "taxon_label": "Escherichia coli",
        "note": "flagellar swimming motility",
        "reference": "PMID:32449734"
      },
      {
        "taxon_id": "NCBITaxon:287",
        "taxon_label": "Pseudomonas aeruginosa",
        "note": "flagellar + pilus motility",
        "reference": "PMID:11029417"
      },
      {
        "taxon_id": "NCBITaxon:83333",
        "taxon_label": "Escherichia coli K-12",
        "note": "Strain-level CheY swimming-motility exemplar.",
        "reference": "DOI:10.1073/pnas.1000935107"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "motile_energy_dependent_locomotion",
        "title": "Energy-dependent bacterial locomotion",
        "description": "Evidence-backed causal sketch linking motile phenotype to metabolic energy, ion motive force, flagella, pili, and directional regulation.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "The taxon-matched protein example anchors one experimentally supported causal branch; it is not presented as a universal mechanism for every taxon or every contextual branch in this graph.",
        "nodes": [
          {
            "node_id": "motile_trait",
            "label": "motile",
            "node_type": "TRAIT",
            "grounding": "METPO:1000702",
            "description": "Ability to move independently using metabolic energy."
          },
          {
            "node_id": "metabolic_energy",
            "label": "metabolic energy",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Energy generated by cellular metabolism and converted into ion gradients or ATP-dependent movement."
          },
          {
            "node_id": "ion_motive_force",
            "label": "ion motive force",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Electrochemical gradient used by many motility motors."
          },
          {
            "node_id": "flagellar_motor",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "flagellar motor",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Rotary motor that turns bacterial flagella."
          },
          {
            "node_id": "type_iv_pilus",
            "label": "type IV pilus",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Pilus machinery that extends, adheres, and retracts.",
            "grounding": "GO:0044096"
          },
          {
            "node_id": "chemotaxis_signaling",
            "label": "chemotaxis signaling",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Regulatory system that biases movement toward favorable conditions.",
            "grounding": "GO:0006935"
          },
          {
            "node_id": "motab_stator",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "MotA-MotB stator complex",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Membrane-embedded stator complex of the flagellar motor that conducts ions."
          },
          {
            "node_id": "stator_proton_channel",
            "label": "transmembrane H+ channel activity",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "Proton-conducting channel function of the MotA-MotB stator across the cytoplasmic membrane."
          },
          {
            "node_id": "motor_torque",
            "label": "flagellar motor torque",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Rotational torque generated by ion flux through the stator acting on the rotor."
          },
          {
            "node_id": "flig_rotor",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "FliG rotor protein",
            "node_type": "GENE_OR_PROTEIN",
            "description": "C-ring rotor protein that electrostatically interacts with the stator to generate torque."
          },
          {
            "node_id": "chea_kinase",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "CheA histidine kinase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Autophosphorylating chemotaxis histidine kinase."
          },
          {
            "node_id": "chey_response_regulator",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:P0AE67",
                "protein_label": "Chemotaxis protein CheY",
                "gene_symbol": "cheY",
                "taxon_id": "NCBITaxon:83333",
                "taxon_label": "Escherichia coli K-12",
                "entry_status": "REVIEWED",
                "proteome_id": "UP000000625",
                "retrieved_on": "2026-10-22",
                "entry_version": 161,
                "sequence_version": 2,
                "role": "Phosphorylated CheY binds the E. coli flagellar switch and changes motor rotation during swimming.",
                "evidence": [
                  {
                    "reference": "DOI:10.1073/pnas.1000935107",
                    "snippet": "CheY binds to the rotor protein FliN",
                    "notes": "The cited source supports the represented protein-to-trait branch; UniProt verifies this current strain-matched protein entry."
                  }
                ]
              }
            ],
            "label": "CheY response regulator",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Response regulator that, when phosphorylated, binds the flagellar switch."
          },
          {
            "node_id": "flagellar_c_ring",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "flagellar C-ring switch complex",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Switch complex (FliM/FliN/FliG) that controls direction of motor rotation."
          },
          {
            "node_id": "pilb_atpase",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "PilB extension ATPase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "ATPase that powers type IV pilus extension/assembly."
          },
          {
            "node_id": "pilt_atpase",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "PilT retraction ATPase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "ATPase that powers type IV pilus retraction/disassembly."
          },
          {
            "node_id": "t4p_extension",
            "label": "type IV pilus extension",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Assembly-driven elongation of the type IV pilus."
          },
          {
            "node_id": "t4p_retraction",
            "label": "type IV pilus retraction",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Disassembly-driven shortening of the type IV pilus."
          },
          {
            "node_id": "twitching_motility",
            "label": "twitching motility",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Surface translocation powered by cycles of type IV pilus extension and retraction.",
            "grounding": "GO:0043107"
          },
          {
            "node_id": "sprb_adhesin_movement",
            "label": "SprB adhesin surface movement",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Movement of the SprB cell-surface adhesin along the outer membrane."
          },
          {
            "node_id": "gliding_motility",
            "label": "gliding motility",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Non-flagellar surface motility driven by adhesin surface movement."
          }
        ],
        "edges": [
          {
            "subject": "metabolic_energy",
            "predicate": "generates",
            "object": "ion_motive_force",
            "description": "Metabolism supports ion gradients that can power motility.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2021.659464",
                "snippet": "ion motive force powering the bacterial flagellar motor",
                "notes": "Supports energy transduction from ion gradients into motor function."
              }
            ],
            "predicate_id": "biolink:produces"
          },
          {
            "subject": "ion_motive_force",
            "predicate": "powers",
            "object": "flagellar_motor",
            "description": "Ion motive force powers rotation of the flagellar motor.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2021.659464",
                "snippet": "The Dynamic Ion Motive Force Powering",
                "notes": "Review directly addresses ion motive force powering flagellar motors."
              }
            ],
            "predicate_id": "METPO:2007900"
          },
          {
            "subject": "flagellar_motor",
            "predicate": "confers",
            "object": "motile_trait",
            "description": "Flagellar rotation enables independent bacterial movement.",
            "evidence": [
              {
                "reference": "DOI:10.3390/biom9070279",
                "snippet": "responsible for motility",
                "notes": "Supports flagella-driven motility."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "type_iv_pilus",
            "predicate": "confers",
            "object": "motile_trait",
            "description": "Type IV pilus extension and retraction enable surface motility.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41579-019-0195-4",
                "snippet": "enable T4P to perform",
                "notes": "Supports pilus-mediated twitching and related motility functions."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "chemotaxis_signaling",
            "predicate": "directs",
            "object": "motile_trait",
            "description": "Chemotaxis signaling regulates motility direction in response to environmental changes.",
            "evidence": [
              {
                "reference": "DOI:10.3390/biom9070279",
                "snippet": "migrate towards more desirable environments",
                "notes": "Supports chemotaxis regulation of motile behavior."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "motab_stator",
            "predicate": "acts as",
            "object": "stator_proton_channel",
            "description": "The MotA-MotB stator acts as a transmembrane H+ channel.",
            "evidence": [
              {
                "reference": "DOI:10.3390/biom14121488",
                "notes": "it can act as a transmembrane H+ channel"
              }
            ]
          },
          {
            "subject": "stator_proton_channel",
            "predicate": "generates",
            "object": "motor_torque",
            "description": "H+ flux through the stator generates torque via electrostatic interaction with FliG.",
            "evidence": [
              {
                "reference": "DOI:10.3390/biom14121488",
                "notes": "conducts H+ through the channel to generate torque by electrostatic interactions between MotA and FliG"
              }
            ],
            "predicate_id": "biolink:produces"
          },
          {
            "subject": "motor_torque",
            "predicate": "acts on",
            "object": "flig_rotor",
            "description": "Torque is generated by electrostatic interaction between the stator and the FliG rotor.",
            "evidence": [
              {
                "reference": "DOI:10.3390/biom14121488",
                "notes": "electrostatic interactions between MotA and FliG generate torque on the rotor"
              }
            ]
          },
          {
            "subject": "motor_torque",
            "predicate": "powers",
            "object": "flagellar_motor",
            "description": "Torque generation drives rotation of the flagellar motor.",
            "evidence": [
              {
                "reference": "DOI:10.3390/biom14121488",
                "notes": "a membrane-embedded rotary motor fueled by an ion motive force across the cytoplasmic membrane"
              }
            ],
            "predicate_id": "METPO:2007900"
          },
          {
            "subject": "chea_kinase",
            "predicate": "phosphorylates",
            "object": "chey_response_regulator",
            "description": "Phosphorylated CheA transfers phosphate to the response regulator CheY.",
            "evidence": [
              {
                "reference": "DOI:10.3390/biom14121488",
                "notes": "Phosphorylated CheA transfers its phosphate group to a response regulator called CheY"
              }
            ]
          },
          {
            "subject": "chey_response_regulator",
            "predicate": "binds",
            "object": "flagellar_c_ring",
            "description": "Phosphorylated CheY binds the C-ring switch complex to control rotation direction.",
            "evidence": [
              {
                "reference": "DOI:10.3390/biom14121488",
                "notes": "Phosphorylated CheY (CheY-P) binds to the C-ring"
              }
            ]
          },
          {
            "subject": "flagellar_c_ring",
            "predicate": "regulates",
            "object": "chemotaxis_signaling",
            "description": "CheY-P binding to the C-ring switches motor rotation direction, implementing chemotactic responses.",
            "evidence": [
              {
                "reference": "DOI:10.3390/biom14121488",
                "notes": "allowing the motor to switch the direction of rotation from CCW to CW"
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "pilb_atpase",
            "predicate": "promotes",
            "object": "t4p_extension",
            "description": "PilB ATPase powers type IV pilus extension/assembly.",
            "evidence": [
              {
                "reference": "DOI:10.1128/msphere.00390-24",
                "notes": "PilB (extension ATPase)"
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "pilt_atpase",
            "predicate": "promotes",
            "object": "t4p_retraction",
            "description": "PilT ATPase powers type IV pilus retraction/disassembly.",
            "evidence": [
              {
                "reference": "DOI:10.1128/msphere.00390-24",
                "notes": "PilT (retraction ATPase)"
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "t4p_extension",
            "predicate": "enables",
            "object": "twitching_motility",
            "description": "Cycles of T4P extension and retraction power twitching surface motility.",
            "evidence": [
              {
                "reference": "DOI:10.1128/msphere.00390-24",
                "notes": "recurrent cycles of T4P assembly (extension) and disassembly (retraction) power surface movement"
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "t4p_retraction",
            "predicate": "enables",
            "object": "twitching_motility",
            "description": "Cycles of T4P extension and retraction power twitching surface motility.",
            "evidence": [
              {
                "reference": "DOI:10.1128/msphere.00390-24",
                "notes": "recurrent cycles of T4P assembly (extension) and disassembly (retraction) power surface movement"
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "twitching_motility",
            "predicate": "confers",
            "object": "motile_trait",
            "description": "Twitching motility is a form of independent surface movement.",
            "evidence": [
              {
                "reference": "DOI:10.1128/msphere.00390-24",
                "notes": "recurrent cycles of T4P assembly and disassembly power surface movement (twitching motility)"
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "sprb_adhesin_movement",
            "predicate": "drives",
            "object": "gliding_motility",
            "description": "Movement of the SprB adhesin along the outer membrane drives gliding motility.",
            "evidence": [
              {
                "reference": "DOI:10.1128/jb.00068-24",
                "notes": "gliding... is driven by the surface movement of adhesins (notably SprB) along the outer membrane"
              }
            ]
          },
          {
            "subject": "gliding_motility",
            "predicate": "confers",
            "object": "motile_trait",
            "description": "Gliding motility is a non-flagellar mechanism of independent movement.",
            "evidence": [
              {
                "reference": "DOI:10.1128/jb.00068-24",
                "notes": "gliding is a form of surface motility driven by adhesin movement"
              }
            ],
            "predicate_id": "METPO:2007700"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.905197+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-06T14:40:41-07:00",
        "curator": "codex",
        "action": "CURATED_WITH_ORGANISM_EXAMPLE",
        "changes": "Added Pseudomonas aeruginosa organism example with PMID-backed evidence.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-11T00:00:00-07:00",
        "curator": "codex",
        "action": "CURATED_WITH_LITERATURE",
        "changes": "Replaced PMID definition source with DOI-backed motility review and added causal graph for energy-dependent locomotion by flagella, type IV pili, ion motive force, and chemotaxis.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d72).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T08:21:50Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:produces\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T21:30:07Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002211\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T05:05:15Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:R6TBR9\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-26T05:00:48Z",
        "curator": "claude",
        "action": "RENAME_PREDICATE_LABELS",
        "changes": "Renamed 1 causal-edge predicate label(s) to align with existing groundings: powers \u2192 enables \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-26T05:00:50Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-16T06:54:40Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0006935\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-17T04:09:44Z",
        "curator": "claude",
        "action": "REMOVE_REDUNDANT_SYNONYM",
        "changes": "Removed 1 synonym(s) whose text duplicated the label (seeder redundancy; no information lost).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 14 evidence-backed generic edges (14 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:13Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 9 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d75, RO:0002213\u00d72, biolink:produces\u00d71, RO:0002211\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:33Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0043107\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-26T07:15:19Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:G0HQV3\u00d71, UniProtKB:A0A2X5A7X5\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:21:12Z",
        "curator": "claude",
        "action": "RETRACT_DEAD_UNIPROT_GROUNDINGS",
        "changes": "Retracted 3 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:23:55Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0044096\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 4 causal edge(s) off enables/RO:0002327 with a TRAIT object (4 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T08:00:00Z",
        "curator": "claude",
        "action": "REGROUND_CAUSAL_EDGE",
        "changes": "Re-grounded causal edge(s) off enables/RO:0002327 onto contributes to (RO:0002326), issue 334. biolink declares enables range 'biological process or activity', which only BIOLOGICAL_PROCESS, PATHWAY and MOLECULAR_FUNCTION satisfy, so an edge pointing at a GENE_OR_PROTEIN entailed a false type. The replacements are chosen per idiom rather than swept: a gene cluster ENCODES its product, a subunit is PART OF the complex it belongs to, and an energy source or acquired repertoire CONTRIBUTES TO the machine it powers or composes. All three declare no rdfs:domain or rdfs:range, so none can reintroduce the class of defect being removed.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T09:00:00Z",
        "curator": "claude",
        "action": "REGROUND_CAUSAL_EDGE",
        "changes": "Reverted the motive-force edge from contributes to back to enables/RO:0002327, issue 334 review. biolink defines contributes to as holding where one entity contributes to the occurrence or GENERATION of the other. A motive force does not generate the motor or machinery - it powers rotation, which is what the edge description says. That is the same energy-powers-a-machine idiom this work deferred for molecular_oxygen and cytoplasmic_na, so deferring it here too is the consistent call. The edge stays baselined under issue 334 until it is modelled as an input to the machine or pointed at the rotation process, either of which is range-correct.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-07T18:00:00Z",
        "curator": "claude",
        "action": "REGROUND_CAUSAL_EDGE",
        "changes": "Edge ion_motive_force -> flagellar_motor in graph motile_energy_dependent_locomotion: re-grounded it from enables/RO:0002327 to powers/METPO:2007900. Issue 334. biolink declares enables range 'biological process or activity', which of CausalNodeTypeEnum only BIOLOGICAL_PROCESS, PATHWAY and MOLECULAR_FUNCTION satisfy, so this edge entailed a false type on its object. 'Ion motive force POWERS rotation of the flagellar motor.'",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-07T18:00:00Z",
        "curator": "claude",
        "action": "REGROUND_CAUSAL_EDGE",
        "changes": "Edge motor_torque -> flagellar_motor in graph motile_energy_dependent_locomotion: re-grounded it from enables/RO:0002327 to powers/METPO:2007900. Issue 334. biolink declares enables range 'biological process or activity', which of CausalNodeTypeEnum only BIOLOGICAL_PROCESS, PATHWAY and MOLECULAR_FUNCTION satisfy, so this edge entailed a false type on its object. 'Torque generation drives rotation of the flagellar motor.'",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "CURATE_PROTEIN_TAXON_EXAMPLE",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope motile_energy_dependent_locomotion=MECHANISTIC with scope_notes; marked 8 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (flagellar_motor, motab_stator, flig_rotor, chea_kinase, chey_response_regulator, flagellar_c_ring, pilb_atpase, pilt_atpase); added taxon-paired protein example(s) UniProtKB:P0AE67 on chey_response_regulator (NCBITaxon:83333); added canonical example(s) NCBITaxon:83333.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-22T01:35:00Z",
        "curator": "claude",
        "action": "REFRESH_UNIPROT_ENTRY_VERSION",
        "changes": "Refreshed UniProtKB entry_version against live UniProt REST on 2026-10-22: UniProtKB:P0AE67 (160 -> 161 on chey_response_regulator).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000701",
    "label": "motility",
    "definition": "A phenotype in which an organism has the capability to move independently through its environment, typically by means of flagella, pili, gliding mechanisms, or other locomotory structures.",
    "definition_source": "DOI:10.1038/s41579-021-00626-4",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "synonyms": [
      {
        "synonym_text": "Morphology.cell morphology.motility",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "created_by": "Jed Dongjin Kim-Ozaeta",
    "evidence": [
      {
        "reference": "DOI:10.1038/s41579-021-00626-4",
        "snippet": "mechanisms that allow bacteria to move around",
        "notes": "Supports bacterial motility as a phenotype mediated by multiple molecular machines and physical mechanisms."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:90371",
        "taxon_label": "Salmonella enterica subsp. enterica serovar Typhimurium",
        "note": "Flagellar swimming: a structural reference for the ion-driven rotary motor, where MotA-MotB torque generation turns a hook and filament to propel the cell; the cited review treats this organism together with Escherichia coli. Exemplifies flagellar propulsion; its peritrichous run-and-tumble pattern is not universal.",
        "reference": "DOI:10.3390/biom14121488"
      },
      {
        "taxon_id": "NCBITaxon:287",
        "taxon_label": "Pseudomonas aeruginosa",
        "note": "Type IV pilus twitching: PilB-dependent pilus assembly drives surface twitching, and overexpressing the regulator PlzR abolished detectable pili and cut the twitching zone by 63% on 1% agar. That figure comes from a gain-of-function overexpression that also reduced swimming and swarming, so pleiotropy is possible. Exemplifies non-flagellar surface motility, a mechanism independent of the flagellar motor.",
        "reference": "DOI:10.1038/s41467-024-52732-5"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "motility_locomotion_machinery",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "Motility is an upper phenotype class spanning flagellar, gliding, twitching, and archaellar mechanisms. The graph catalogs alternatives rather than asserting one mechanism shared by every motile organism.",
        "title": "Bacterial motility machinery",
        "description": "Evidence-backed causal sketch linking motility to flagella, type IV pili, gliding systems, chemotaxis, and energy transduction.",
        "nodes": [
          {
            "node_id": "motility_trait",
            "label": "motility",
            "node_type": "TRAIT",
            "grounding": "METPO:1000701",
            "description": "Independent movement through the environment."
          },
          {
            "node_id": "flagellar_motor",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "The flagellar motor is a lineage-variable multisubunit assembly; no single verified complex term covers this broad contextual node.",
            "label": "flagellar motor",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Rotary motor that powers flagellar swimming or swarming."
          },
          {
            "node_id": "type_iv_pilus",
            "label": "type IV pilus",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Dynamic pilus that powers twitching and related surface motility.",
            "grounding": "GO:0044096"
          },
          {
            "node_id": "gliding_motility_machinery",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Gliding motility uses unrelated machineries in different lineages, so no single protein-family or complex term denotes this umbrella.",
            "label": "gliding motility machinery",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Cell-envelope motors and adhesins that move bacteria over surfaces without flagella."
          },
          {
            "node_id": "ion_motive_force",
            "label": "ion motive force",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Electrochemical ion gradient used to power motility motors."
          },
          {
            "node_id": "chemotaxis_signaling",
            "label": "chemotaxis signaling",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Signal transduction that changes motility direction in response to environmental cues.",
            "grounding": "GO:0006935"
          },
          {
            "node_id": "twitching_motility",
            "label": "twitching motility",
            "node_type": "TRAIT",
            "description": "Form of bacterial surface translocation powered by type IV pili."
          },
          {
            "node_id": "pilb_extension_atpase",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "The contextual graph supports a PilB-like extension ATPase but does not identify one exact family term across all twitching systems.",
            "label": "PilB extension ATPase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Homohexameric ATPase that drives type IV pilus extension."
          },
          {
            "node_id": "pilt_retraction_atpase",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "The contextual graph supports a PilT-like retraction ATPase but does not identify one exact family term across all twitching systems.",
            "label": "PilT retraction ATPase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Antagonistic ATPase that drives type IV pilus retraction."
          },
          {
            "node_id": "t4p_retraction",
            "label": "type IV pilus retraction",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Retraction of type IV pili that generates pulling forces."
          },
          {
            "node_id": "c_di_gmp",
            "label": "cyclic di-GMP",
            "node_type": "CHEMICAL",
            "description": "Second messenger that inversely regulates motility and biofilm formation.",
            "grounding": "CHEBI:49537"
          },
          {
            "node_id": "archaellum",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "The archaellum is a multisubunit archaeal motility assembly rather than one protein-family entity.",
            "label": "archaellum",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Archaeal rotary propulsion filament, the analogue of the bacterial flagellum."
          }
        ],
        "edges": [
          {
            "subject": "flagellar_motor",
            "predicate": "confers",
            "object": "motility_trait",
            "description": "Rotary flagellar motors enable bacterial swimming and related motility modes.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41579-021-00626-4",
                "snippet": "allow bacteria to move around",
                "notes": "Review summarizes flagellar machinery as a major bacterial motility mechanism."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "type_iv_pilus",
            "predicate": "confers",
            "object": "motility_trait",
            "description": "Type IV pili enable twitching motility through extension, adhesion, and retraction.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41579-019-0195-4",
                "snippet": "Cycles of pilus extension, binding and retraction",
                "notes": "Supports type IV pili as motility appendages."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "gliding_motility_machinery",
            "predicate": "confers",
            "object": "motility_trait",
            "description": "Gliding machinery allows surface movement without external flagella.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev.micro.55.1.49",
                "snippet": "move actively over surfaces",
                "notes": "Supports gliding as an active bacterial movement mechanism."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "ion_motive_force",
            "predicate": "powers",
            "object": "flagellar_motor",
            "description": "Ion motive force powers rotation of many bacterial flagellar motors.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2021.659464",
                "snippet": "relationship between the IMF and the functioning",
                "notes": "Supports ion motive force powering the bacterial flagellar motor."
              }
            ],
            "predicate_id": "METPO:2007900"
          },
          {
            "subject": "chemotaxis_signaling",
            "predicate": "regulates",
            "object": "motility_trait",
            "description": "Chemotaxis signaling regulates the direction and pattern of bacterial movement.",
            "evidence": [
              {
                "reference": "DOI:10.3390/biom9070279",
                "snippet": "chemotactic signaling pathways regulate the direction",
                "notes": "Supports chemotaxis control of flagella-driven motility."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "type_iv_pilus",
            "predicate": "drives",
            "object": "twitching_motility",
            "description": "Type IV pili power twitching, a form of bacterial surface translocation.",
            "evidence": [
              {
                "reference": "DOI:10.1128/msphere.00390-24",
                "notes": "Twitching motility is a form of bacterial surface translocation powered by the type IV pilus (T4P)."
              }
            ]
          },
          {
            "subject": "pilb_extension_atpase",
            "predicate": "drives extension of",
            "object": "type_iv_pilus",
            "description": "PilB ATPase drives extension of the type IV pilus.",
            "evidence": [
              {
                "reference": "DOI:10.1128/jb.00359-24",
                "notes": "PilB is the homohexameric extension ATPase of the type IV pilus."
              }
            ]
          },
          {
            "subject": "pilt_retraction_atpase",
            "predicate": "drives retraction of",
            "object": "type_iv_pilus",
            "description": "PilT ATPase drives retraction of the type IV pilus.",
            "evidence": [
              {
                "reference": "DOI:10.1128/jb.00359-24",
                "notes": "Retraction is carried out by the antagonistic ATPase PilT."
              }
            ]
          },
          {
            "subject": "t4p_retraction",
            "predicate": "generates",
            "object": "twitching_motility",
            "description": "Type IV pilus retraction generates the pulling forces underlying twitching motility.",
            "evidence": [
              {
                "reference": "DOI:10.1128/jb.00442-23",
                "notes": "T4P retraction generates the pulling forces underlying twitching motility."
              }
            ],
            "predicate_id": "biolink:produces"
          },
          {
            "subject": "c_di_gmp",
            "predicate": "inhibits",
            "object": "motility_trait",
            "description": "Cyclic di-GMP inhibits motility; lowering c-di-GMP relieves this inhibition.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s42003-024-07392-y",
                "notes": "Lower c-di-GMP relieves its inhibition on motility (generic c-di-GMP -> motility edge)."
              }
            ],
            "predicate_id": "RO:0002212"
          },
          {
            "subject": "archaellum",
            "predicate": "confers",
            "object": "motility_trait",
            "description": "The archaellum enables swimming motility in archaea, analogous to the bacterial flagellum.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-024-50277-1",
                "notes": "The archaellum enables cell motility in archaea."
              }
            ],
            "predicate_id": "METPO:2007700"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.904440+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-11T00:00:00-07:00",
        "curator": "codex",
        "action": "CURATED_WITH_LITERATURE",
        "changes": "Reviewed motility trait and added DOI-backed causal graph for flagellar, pili-mediated, gliding, chemotaxis, and ion-motive-force mechanisms.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 4 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d73, RO:0002211\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T05:05:15Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:R6TBR9\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-26T05:00:48Z",
        "curator": "claude",
        "action": "RENAME_PREDICATE_LABELS",
        "changes": "Renamed 1 causal-edge predicate label(s) to align with existing groundings: powers \u2192 enables \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-26T05:00:50Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-16T06:54:40Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0006935\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-17T04:09:44Z",
        "curator": "claude",
        "action": "REMOVE_REDUNDANT_SYNONYM",
        "changes": "Removed 1 synonym(s) whose text duplicated the label (seeder redundancy; no information lost).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 6 evidence-backed generic edges (6 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:13Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:produces\u00d71, RO:0002212\u00d71, RO:0002327\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:33Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:49537\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:21:12Z",
        "curator": "claude",
        "action": "RETRACT_DEAD_UNIPROT_GROUNDINGS",
        "changes": "Retracted 1 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:23:55Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0044096\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 4 causal edge(s) off enables/RO:0002327 with a TRAIT object (4 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T08:00:00Z",
        "curator": "claude",
        "action": "REGROUND_CAUSAL_EDGE",
        "changes": "Re-grounded causal edge(s) off enables/RO:0002327 onto contributes to (RO:0002326), issue 334. biolink declares enables range 'biological process or activity', which only BIOLOGICAL_PROCESS, PATHWAY and MOLECULAR_FUNCTION satisfy, so an edge pointing at a GENE_OR_PROTEIN entailed a false type. The replacements are chosen per idiom rather than swept: a gene cluster ENCODES its product, a subunit is PART OF the complex it belongs to, and an energy source or acquired repertoire CONTRIBUTES TO the machine it powers or composes. All three declare no rdfs:domain or rdfs:range, so none can reintroduce the class of defect being removed.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T09:00:00Z",
        "curator": "claude",
        "action": "REGROUND_CAUSAL_EDGE",
        "changes": "Reverted the motive-force edge from contributes to back to enables/RO:0002327, issue 334 review. biolink defines contributes to as holding where one entity contributes to the occurrence or GENERATION of the other. A motive force does not generate the motor or machinery - it powers rotation, which is what the edge description says. That is the same energy-powers-a-machine idiom this work deferred for molecular_oxygen and cytoplasmic_na, so deferring it here too is the consistent call. The edge stays baselined under issue 334 until it is modelled as an input to the machine or pointed at the rotation process, either of which is range-correct.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-07T18:00:00Z",
        "curator": "claude",
        "action": "REGROUND_CAUSAL_EDGE",
        "changes": "Edge ion_motive_force -> flagellar_motor in graph motility_locomotion_machinery: re-grounded it from enables/RO:0002327 to powers/METPO:2007900. Issue 334. biolink declares enables range 'biological process or activity', which of CausalNodeTypeEnum only BIOLOGICAL_PROCESS, PATHWAY and MOLECULAR_FUNCTION satisfy, so this edge entailed a false type on its object. 'Ion motive force POWERS rotation of many bacterial flagellar motors.'",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope motility_locomotion_machinery=NONMECHANISTIC with scope_notes; marked 5 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (flagellar_motor, gliding_motility_machinery, pilb_extension_atpase, pilt_retraction_atpase, archaellum).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T19:05:00Z",
        "curator": "claude",
        "action": "ADD_CANONICAL_EXAMPLES",
        "changes": "Added 2 source-backed canonical example(s) from this record's own deep-research artifact (issue 444): Salmonella enterica subsp. enterica serovar Typhimurium (NCBITaxon:90371), Pseudomonas aeruginosa (NCBITaxon:287). Each note scopes the exemplar to the single locomotion mechanism the cited source establishes, because this record is an upper class whose graph is NONMECHANISTIC and spans alternative mechanisms. Taxon ids and labels were verified against NCBI taxonomy and every DOI resolved through Crossref. No gene or operon was promoted to a primary entry.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000074",
    "label": "mycelial growth",
    "definition": "A morphology trait in which a bacterium grows as branching, filamentous hyphae that form a mycelium, often with subsequent differentiation into aerial hyphae and spores, as in Streptomyces.",
    "definition_source": "DOI:10.1038/nrmicro1968",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "synonyms": [
      {
        "synonym_text": "mycelium-forming",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1038/nrmicro1968"
      },
      {
        "synonym_text": "hyphal growth",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1038/nrmicro3178"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/nrmicro1968",
        "notes": "Fl\u00e4rdh & Buttner describe Streptomyces growth as a branching hyphal mycelium with subsequent morphological differentiation."
      },
      {
        "reference": "DOI:10.1038/nrmicro3178",
        "notes": "Claessen et al. treat filamentous/mycelial growth as a bacterial solution to multicellularity."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1902",
        "taxon_label": "Streptomyces coelicolor",
        "note": "Model filamentous/mycelial actinomycete; antibiotic-producing developmental model.",
        "reference": "DOI:10.1038/nrmicro1968"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "mycelial_branching_hyphal_growth",
        "title": "Branching hyphal growth produces a bacterial mycelium",
        "description": "Evidence-backed causal sketch linking apical hyphal extension and branching to a multicellular mycelium with subsequent aerial-hypha differentiation.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a broad environmental or morphological classification spanning multiple mechanisms, a measurement-like bin, or an absence/arrangement descriptor; contextual protein nodes do not receive token UniProt examples.",
        "nodes": [
          {
            "node_id": "mycelial_growth_trait",
            "label": "mycelial growth",
            "node_type": "TRAIT",
            "grounding": "traitmech:000074",
            "description": "Branching filamentous hyphal growth forming a mycelium."
          },
          {
            "node_id": "hyphal_extension",
            "label": "apical hyphal extension and branching",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Polar tip growth and branch initiation generating a hyphal network."
          },
          {
            "node_id": "aerial_hyphae_differentiation",
            "label": "aerial hyphae and spore differentiation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Developmental transition to aerial hyphae bearing spores (as in Streptomyces)."
          },
          {
            "node_id": "divIVA_polarisome",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "DivIVA polarisome",
            "node_type": "GENE_OR_PROTEIN",
            "description": "DivIVA-organized polarisome complex marking and driving hyphal tip growth."
          },
          {
            "node_id": "polarisome_splitting",
            "label": "polarisome splitting",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Splitting of polarisomes at growing tips to seed daughter polarisomes and new branches."
          },
          {
            "node_id": "branch_emergence",
            "label": "new branch emergence",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Initiation of new lateral hyphal branches from daughter polarisomes."
          },
          {
            "node_id": "cglA_ligase",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "CglA glycopolymer ligase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "LCP-family ligase attaching wall teichoic acids/glycopolymers to peptidoglycan."
          },
          {
            "node_id": "wta_attachment",
            "label": "wall teichoic acid attachment to peptidoglycan",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Covalent attachment of wall teichoic acids/glycopolymers to the peptidoglycan sacculus."
          },
          {
            "node_id": "hyphal_tip_growth_zones",
            "label": "hyphal tips and branching points",
            "node_type": "CELLULAR_LOCALIZATION",
            "description": "Zones of active cell-wall incorporation at hyphal tips and branch sites."
          },
          {
            "node_id": "ftsz_ring_positioning",
            "label": "FtsZ-ring positioning and septum placement",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Formation and correct placement of FtsZ rings and division septa in hyphae."
          },
          {
            "node_id": "ftsz_z_ladders",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "FtsZ Z-ladder arrays",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Ladder-like arrays of multiple FtsZ rings along sporogenic aerial hyphae."
          },
          {
            "node_id": "sporulation_septation",
            "label": "sporulation septation and spore-chain formation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Synchronous septation of sporogenic hyphae yielding regular spore chains."
          },
          {
            "node_id": "sapB_chaplins_rodlins",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "SapB / chaplins / rodlins",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Surfactant SapB and hydrophobic chaplin/rodlin sheath proteins aiding aerial escape."
          }
        ],
        "edges": [
          {
            "subject": "hyphal_extension",
            "predicate": "confers",
            "object": "mycelial_growth_trait",
            "description": "Sustained apical extension and branching realize mycelial growth.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro1968",
                "notes": "Fl\u00e4rdh & Buttner describe Streptomyces growth as a branching hyphal mycelium."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "mycelial_growth_trait",
            "predicate": "develops into",
            "object": "aerial_hyphae_differentiation",
            "description": "Mycelial colonies differentiate aerial hyphae and spores.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro3178",
                "notes": "Claessen et al. treat filamentous/mycelial growth as a bacterial solution to multicellularity with developmental differentiation."
              }
            ],
            "predicate_id": "biolink:develops_into"
          },
          {
            "subject": "divIVA_polarisome",
            "predicate": "directs",
            "object": "hyphal_extension",
            "description": "The DivIVA polarisome drives apical (tip) growth of vegetative and aerial hyphae.",
            "evidence": [
              {
                "reference": "DOI:10.1128/JB.00153-23",
                "notes": "The DivIVA-polarisome drives the growth of both branching vegetative hyphae and non-branching aerial hyphae."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "polarisome_splitting",
            "predicate": "causes",
            "object": "branch_emergence",
            "description": "Splitting of polarisomes at growing tips gives rise to daughter polarisomes that nucleate new branches.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsml/uqad020",
                "notes": "Splitting of the polarisomes at growing tips gives rise to daughter polarisomes coordinating branches."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "cglA_ligase",
            "predicate": "mediates",
            "object": "wta_attachment",
            "description": "CglA catalyzes attachment of wall teichoic acids/glycopolymers to peptidoglycan during wall biogenesis.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mbio.01492-24",
                "notes": "CglA is an LCP-LytR_C glycopolymer ligase that catalyzes attachment of WTAs to peptidoglycan."
              }
            ]
          },
          {
            "subject": "cglA_ligase",
            "predicate": "localizes to",
            "object": "hyphal_tip_growth_zones",
            "description": "CglA localizes to regions of active cell-wall incorporation at hyphal tips and branching points.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mbio.01492-24",
                "notes": "YPet-CglA localizes to regions of active cell-wall incorporation - hyphal tips and branching points."
              }
            ],
            "predicate_id": "biolink:located_in"
          },
          {
            "subject": "cglA_ligase",
            "predicate": "enables",
            "object": "ftsz_ring_positioning",
            "description": "Loss of CglA/glycopolymers disrupts FtsZ-ring formation/positioning and causes misplaced septa.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mbio.01492-24",
                "notes": "Loss of CglA causes failures in FtsZ-ring formation and positioning and misplaced division septa."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "ftsz_z_ladders",
            "predicate": "drives",
            "object": "sporulation_septation",
            "description": "Ladder-like arrays of FtsZ rings constrict and separate to yield regular spore chains.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mbio.01492-24",
                "notes": "FtsZ forms ladder-like arrays whose constriction and separation yields regularly shaped spores."
              }
            ]
          },
          {
            "subject": "sapB_chaplins_rodlins",
            "predicate": "promotes",
            "object": "aerial_hyphae_differentiation",
            "description": "SapB surfactant and chaplin/rodlin sheaths overcome surface tension to promote aerial hyphae emergence.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsml/uqad020",
                "notes": "Aerial development involves chaplin/rodlin hydrophobic sheaths and surfactant SapB to overcome surface tension."
              }
            ],
            "predicate_id": "RO:0002213"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-06-03T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate MORPHOLOGY trait (mycelial growth) from literature research to fill the multicellular/developmental gap.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-09T15:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (branching hyphal growth / differentiation) with RO/biolink predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 7 evidence-backed generic edges (10 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:13Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 5 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002211\u00d71, biolink:causes\u00d71, biolink:located_in\u00d71, RO:0002327\u00d71, RO:0002213\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 1 causal edge(s) off enables/RO:0002327 with a TRAIT object (1 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope mycelial_branching_hyphal_growth=NONMECHANISTIC with scope_notes; marked 4 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (divIVA_polarisome, cglA_ligase, ftsz_z_ladders, sapB_chaplins_rodlins).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000674",
    "label": "necridium formation",
    "definition": "A morphological phenotype in which a filamentous cyanobacterium forms degenerating separation cells called necridia whose disintegration permits trichome fragmentation.",
    "definition_source": "DOI:10.1127/1864-1318/2005/0117-0239",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1127/1864-1318/2005/0117-0239",
        "snippet": "Trichome breakage and hormogonia liberation were caused by the disintegration of such necridia",
        "notes": "Hernandez-Marine and Roldan (2005), scientific abstract on article page 239, visually checked in the published article reproduced in Roldan's university thesis: https://diposit.ub.edu/server/api/core/bitstreams/6ce8a85f-d68f-402d-8c13-882f128e4a7f/content (PDF page 106). Article pages 239-247, including Methods, Results, Discussion and actual Figures 1-4, were inspected. Natural cave/catacomb biofilms contain Leptolyngbya and Scytonema; microscopy associates cell degeneration with fragmentation and terminal polysaccharide pads. The proposed adhesive function is not a demonstrated universal requirement. No exact strain exemplar is assigned from these mixed samples."
      },
      {
        "reference": "DOI:10.1111/mmi.12506",
        "snippet": "Necridia formation inhibits further molecular exchange, determining the fate of a branch likely to become a hormogonium.",
        "notes": "Nurnberg et al. (2014), scientific abstract directly retrieved from DOI-matched Europe PMC record PMID:24383541. Publisher full-text Results and Methods were read; actual Figures 5-6 were inspected in the accepted manuscript at https://idus.us.es/bitstreams/05b873c9-9775-45f4-a6d6-2b6c54f97978/download (PDF pages 41-42), with final publisher captions cross-checked. Figure 5 follows 5-CFDA fluorescence for 24 seconds across a necridium; this is not proof of permanent exclusion of every molecule. Figure 6 shows terminal cell remnants and sealed neighboring membranes. Supplements were not inspected."
      },
      {
        "reference": "DOI:10.3389/fmicb.2015.00278",
        "snippet": "necridic (dead) cells are SYTOX Green-positive and CTC-negative",
        "notes": "Publisher full-text Methods, Results, Figure 2 caption and actual panels A-I were inspected. The quoted caption identifies dead cells operationally by membrane permeability and lack of CTC reduction. Panels D-F concern Microcoleus vaginatus 858 CCALA after a week at 4 degrees C, before desiccation; Results report frequent necridia and trichome splitting in cold cultures. Injured double-positive cells and nitrogen-starved bleached but active cells are distinguished. Neither cold exposure nor this stain combination defines the entire class. Supplements and strain provenance were not inspected."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:447715",
        "taxon_label": "Mastigocladus laminosus SAG 4.84",
        "reference": "DOI:10.1111/mmi.12506",
        "note": "Necridium-forming stage of the study strain, not a claim that every cell is a necridium. Methods report Castenholz D liquid culture at 40 degrees C under constant white light and fresh medium growth before communication assays. Natural origin from an Icelandic thermal spring in 1967 is independently confirmed by the culture collection at https://sagdb.uni-goettingen.de/detailedList.php?str_number=4.84. NCBI Taxonomy efetch for 447715 confirms this current name and rank strain. These authorities support identity/provenance, not additional phenotype experiments."
      }
    ],
    "discussions": [
      {
        "discussion_id": "necridium-formation-scope",
        "prompt": "Review a closer parent and separation-cell terminology.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Use active phenotype METPO:1000059 below quality METPO:1000188. Hormogonium formation traitmech:000651 denotes production of short dispersal filaments, not the degenerating separation cell. The 2005 Introduction describes additional fragmentation routes, so neither trait is asserted a subclass or exact synonym of the other. Filament-shaped morphology concerns elongated cell shape, not this multicellular separation stage. Do not equate all dead cells, all trichome fragmentation or all hormogonium formation with necridia. No exact synonyms, xrefs, SSSOM equivalences or organism-level disjointness are asserted pending review of historical separation-disc usages.",
        "posed_by": "codex",
        "posed_date": "2026-10-08"
      },
      {
        "discussion_id": "necridium-formation-mechanism",
        "prompt": "Resolve the formation mechanism without inferring protein causality.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Cell degeneration, communication loss and fragmentation are observed, but the inspected evidence does not establish a protein-resolved necridium-formation mechanism. SepJ sequence similarity and septal localization in the 2014 paper do not establish its causal role in necridium formation. Programmed cell death is an interpretation, not proof of conserved apoptosis machinery. Do not impose a fixed cell shape, spacing, cold trigger, adhesion function or fitness benefit. A causal graph is deferred pending direct mechanism evidence and authority-verified protein examples; the mechanism is not claimed biologically absent.",
        "posed_by": "codex",
        "posed_date": "2026-10-08"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-08T05:29:42Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added necridium formation with three primary DOI references, three verbatim snippets and a source-qualified SAG 4.84 example. Ignored-and-hidden novelty and current-main/worktree/complete-open-PR reservation checks support 000674 and v550 block 1062700-1062799. Kept separation-cell morphology distinct from hormogonium formation, generic cell death and inferred protein mechanisms; existing records unchanged. Timestamp is observed UTC curation time.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000703",
    "label": "non motile",
    "definition": "A motility in which an organism lacks the ability to move independently under its own power.",
    "definition_source": "DOI:10.3389/fmicb.2025.1514643",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000701"
    ],
    "synonyms": [
      {
        "synonym_text": "no",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "non-motile",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.3389/fmicb.2025.1514643",
        "snippet": "They are Gram-negative, non-motile rods",
        "notes": "Organism example: Klebsiella pneumoniae is described as non-motile."
      },
      {
        "reference": "DOI:10.1146/annurev.micro.57.030502.090832",
        "snippet": "flagellum",
        "notes": "Bacterial flagellum review supports the absence or non-expression of the flagellar apparatus as the basis for non-motile phenotypes."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:573",
        "taxon_label": "Klebsiella pneumoniae",
        "note": "non-motile enteric",
        "reference": "https://www.ncbi.nlm.nih.gov/books/NBK519004/"
      },
      {
        "taxon_id": "NCBITaxon:1313",
        "taxon_label": "Streptococcus pneumoniae",
        "note": "non-motile coccus",
        "reference": "PMID:34779760"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "non_motile_absent_motility_apparatus",
        "title": "Non-motile absent motility apparatus",
        "description": "DOI-backed graph linking absence or non-expression of the flagellar or pilus-based motility apparatus to the non-motile phenotype.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a broad environmental or morphological classification spanning multiple mechanisms, a measurement-like bin, or an absence/arrangement descriptor; contextual protein nodes do not receive token UniProt examples.",
        "nodes": [
          {
            "node_id": "non_motile_trait",
            "label": "non motile",
            "node_type": "TRAIT",
            "grounding": "METPO:1000703",
            "description": "Lack of self-powered cellular movement."
          },
          {
            "node_id": "absent_flagellum",
            "label": "absent or non-expressed flagellum",
            "node_type": "ORGANELLE",
            "description": "Genomic absence or silenced expression of the flagellar apparatus.",
            "grounding": "GO:0009288"
          },
          {
            "node_id": "absent_motility_pili",
            "label": "absent motility pili",
            "node_type": "ORGANELLE",
            "description": "Lack of type IV or other motility-associated pili."
          },
          {
            "node_id": "no_propulsion",
            "label": "no propulsion",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Inability to generate self-motive force."
          },
          {
            "node_id": "flagellum_biogenesis_disruption",
            "label": "disrupted flagellum biogenesis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Loss-of-function mutations affecting assembly of a functional flagellum."
          },
          {
            "node_id": "c_di_gmp_high",
            "label": "high intracellular cyclic di-GMP",
            "node_type": "CHEMICAL",
            "description": "Elevated second-messenger c-di-GMP that signals a sessile lifestyle."
          },
          {
            "node_id": "flagellar_gene_repression",
            "label": "repression of flagellar gene expression",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Downregulation of flagellar structural and regulatory genes."
          },
          {
            "node_id": "flhdc_master_operon",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "FlhD4C2 flagellar master regulator complex",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Master protein regulator controlling the flagellar transcriptional hierarchy.",
            "gene_symbols": [
              "flhD",
              "flhC"
            ],
            "operon": "flhDC"
          },
          {
            "node_id": "wspr_dgc",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "WspR diguanylate cyclase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Diguanylate cyclase that synthesizes c-di-GMP when activated."
          },
          {
            "node_id": "reduced_motility_state",
            "label": "reduced or absent motility",
            "node_type": "STATE",
            "description": "Diminished flagellar motility that can manifest as a non-motile phenotype."
          }
        ],
        "edges": [
          {
            "subject": "absent_flagellum",
            "predicate": "prevents",
            "object": "no_propulsion",
            "description": "Without a flagellum cells cannot generate flagellar propulsion.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev.micro.57.030502.090832",
                "snippet": "flagellum",
                "notes": "Supports the flagellum as the major bacterial motility organelle."
              }
            ],
            "predicate_id": "RO:0002212"
          },
          {
            "subject": "absent_motility_pili",
            "predicate": "prevents",
            "object": "no_propulsion",
            "description": "Without motility pili cells cannot generate twitching or related pilus-driven movement.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2218",
                "snippet": "type IV pili",
                "notes": "Type-IV-pili review supports type IV pili as the cellular basis for twitching motility (and their absence as the basis for non-twitching/non-motile phenotype)."
              }
            ],
            "predicate_id": "RO:0002212"
          },
          {
            "subject": "no_propulsion",
            "predicate": "manifests as",
            "object": "non_motile_trait",
            "description": "Lack of propulsion manifests the non-motile trait.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2025.1514643",
                "snippet": "They are Gram-negative, non-motile rods",
                "notes": "Supports the trait endpoint in a representative organism."
              }
            ],
            "predicate_id": "METPO:2007400"
          },
          {
            "subject": "flagellum_biogenesis_disruption",
            "predicate": "prevents",
            "object": "no_propulsion",
            "description": "Disrupted flagellum biogenesis yields a non-functional flagellum and loss of propulsion.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s12866-024-03387-1",
                "notes": "flagellum biogenesis was affected in mutants and lack of functional flagellum confirmed in motility assays."
              }
            ],
            "predicate_id": "RO:0002212"
          },
          {
            "subject": "wspr_dgc",
            "predicate": "increases amount of",
            "object": "c_di_gmp_high",
            "description": "WspR diguanylate cyclase produces c-di-GMP when phosphorylated, raising intracellular levels.",
            "evidence": [
              {
                "reference": "DOI:10.1128/aem.01548-23",
                "notes": "WspR produces c-di-GMP when phosphorylated; high c-di-GMP represses motility."
              }
            ]
          },
          {
            "subject": "c_di_gmp_high",
            "predicate": "causes",
            "object": "flagellar_gene_repression",
            "description": "High c-di-GMP causes FleQ to cease activating flagellar genes, repressing flagellar gene expression.",
            "evidence": [
              {
                "reference": "DOI:10.1128/jb.00365-23",
                "notes": "At high c-di-GMP, FleQ ceases to activate flagellar genes."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "flhdc_master_operon",
            "predicate": "positively regulates",
            "object": "flagellar_gene_repression",
            "description": "Repression of the flhDC master operon decreases flagellar gene expression; included as the master-regulator control point.",
            "evidence": [
              {
                "reference": "DOI:10.3390/foods13223709",
                "notes": "OmpR binds the flhDC operon promoter and represses transcription, decreasing flagellar gene expression and motility."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "flagellar_gene_repression",
            "predicate": "causes",
            "object": "reduced_motility_state",
            "description": "Repression of flagellar genes leads to reduced or absent motility.",
            "evidence": [
              {
                "reference": "DOI:10.1128/jb.00365-23",
                "notes": "Loss of flagellar gene activation lowers motility, which can manifest as a non-motile state."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "reduced_motility_state",
            "predicate": "manifests as",
            "object": "non_motile_trait",
            "description": "Sufficiently reduced/absent motility manifests the non-motile trait.",
            "evidence": [
              {
                "reference": "DOI:10.1128/aem.01548-23",
                "notes": "Elevated c-di-GMP regulatory output yields a non-motile mutant phenotype."
              }
            ],
            "predicate_id": "METPO:2007400"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.905968+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-06T14:40:41-07:00",
        "curator": "codex",
        "action": "CURATED_WITH_ORGANISM_EXAMPLE",
        "changes": "Added Klebsiella pneumoniae organism example with PMID-backed evidence.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-11T23:00:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed causal graph linking absence or non-expression of flagellar and pilus motility apparatus to the non-motile phenotype.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-13T22:45:00-07:00",
        "curator": "codex",
        "action": "IMPROVED_CAUSAL_GRAPH_EVIDENCE",
        "changes": "Replaced Klebsiella non-motile PMID fallback with the article DOI in definition, record evidence, and CausalEdge evidence.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T21:30:07Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007400\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-13T21:03:26Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002212\u00d72).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 6 evidence-backed generic edges (6 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:13Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 4 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:causes\u00d72, RO:0002212\u00d71, METPO:2007400\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-04T03:08:15Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002213\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope non_motile_absent_motility_apparatus=NONMECHANISTIC with scope_notes; marked 2 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (flhdc_master_operon, wspr_dgc).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000872",
    "label": "non-spore forming",
    "definition": "A sporulation in which an organism lacks the ability to produce endospores.",
    "definition_source": "DOI:10.1155/2013/898106",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000870"
    ],
    "synonyms": [
      {
        "synonym_text": "no",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "no_spore",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1155/2013/898106",
        "snippet": "S. aureus does not form spores",
        "notes": "Organism example: Staphylococcus aureus is described as non-spore-forming."
      },
      {
        "reference": "DOI:10.1146/annurev.genet.30.1.297",
        "snippet": "activation of these sigma factors to landmark events in morphogenesis",
        "notes": "Sporulation regulatory review supports the Spo0A/sigma cascade as the sporulation control program whose absence yields a non-spore-forming phenotype."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:562",
        "taxon_label": "Escherichia coli",
        "note": "does not form spores",
        "reference": "https://www.ncbi.nlm.nih.gov/books/NBK8035/"
      },
      {
        "taxon_id": "NCBITaxon:1280",
        "taxon_label": "Staphylococcus aureus",
        "note": "non-spore-forming",
        "reference": "PMID:24628867"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "non_spore_forming_absent_spo0a_cascade",
        "title": "Non-spore-forming absent Spo0A cascade",
        "description": "DOI-backed graph linking absence or non-functionality of the Spo0A-initiated sporulation regulatory cascade to inability to form endospores.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a broad environmental or morphological classification spanning multiple mechanisms, a measurement-like bin, or an absence/arrangement descriptor; contextual protein nodes do not receive token UniProt examples.",
        "nodes": [
          {
            "node_id": "non_spore_forming_trait",
            "label": "non-spore forming",
            "node_type": "TRAIT",
            "grounding": "METPO:1000872",
            "description": "Inability to produce endospores."
          },
          {
            "node_id": "absent_spo0a_cascade",
            "label": "absent Spo0A regulatory cascade",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Absence or non-functionality of the Spo0A-initiated sporulation regulatory program (Spo0A master regulator and downstream sigma factors)."
          },
          {
            "node_id": "no_asymmetric_septation",
            "label": "no asymmetric septation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Lack of the polar division step that generates a forespore compartment."
          },
          {
            "node_id": "no_endospore_formation",
            "label": "no endospore formation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Failure to produce a dormant, resistant endospore."
          },
          {
            "node_id": "absent_spo0a_gene",
            "label": "absence of spo0A gene",
            "node_type": "STATE",
            "description": "Lack of the spo0A master regulator gene; an excellent predictor of inability to sporulate."
          },
          {
            "node_id": "loss_sporulation_genes",
            "label": "loss of sporulation genes",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Inactivation or loss of a considerable fraction of core sporulation genes."
          },
          {
            "node_id": "low_spo0a_activity",
            "label": "low or absent Spo0A activity",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "Reduced or absent activity of the Spo0A master regulator of endospore formation."
          },
          {
            "node_id": "rap_phosphatases",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "Rap phosphatases",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Rap family phosphatases that dephosphorylate Spo0F in the sporulation phosphorelay."
          },
          {
            "node_id": "spo0f_dephosphorylation",
            "label": "dephosphorylation of Spo0F",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Dephosphorylation of Spo0F reducing phosphate flow to Spo0A in the phosphorelay."
          },
          {
            "node_id": "phosphorelay_disruption",
            "label": "Spo0A phosphorelay disruption",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Disruption of the KinA/KinB -> Spo0F -> Spo0B -> Spo0A phosphorelay that initiates sporulation."
          },
          {
            "node_id": "no_sporulation_entry",
            "label": "no entry into sporulation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Failure to enter the sporulation developmental program (arrest at stages 0/I)."
          }
        ],
        "edges": [
          {
            "subject": "absent_spo0a_cascade",
            "predicate": "prevents",
            "object": "no_asymmetric_septation",
            "description": "Without the Spo0A/sigma cascade, asymmetric septation cannot be initiated.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev.genet.30.1.297",
                "snippet": "activation of these sigma factors to landmark events in morphogenesis",
                "notes": "Supports the Spo0A/sigma cascade as the gatekeeper of sporulation morphogenesis."
              }
            ],
            "predicate_id": "RO:0002212"
          },
          {
            "subject": "no_asymmetric_septation",
            "predicate": "prevents",
            "object": "no_endospore_formation",
            "description": "Without asymmetric septation, the forespore compartment and subsequent endospore cannot be produced.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev.genet.30.1.297",
                "snippet": "activation of these sigma factors to landmark events in morphogenesis",
                "notes": "Supports asymmetric septation as a required step for endospore formation."
              }
            ],
            "predicate_id": "RO:0002212"
          },
          {
            "subject": "no_endospore_formation",
            "predicate": "manifests as",
            "object": "non_spore_forming_trait",
            "description": "Failure to produce endospores manifests the non-spore-forming trait.",
            "evidence": [
              {
                "reference": "DOI:10.1155/2013/898106",
                "snippet": "S. aureus does not form spores",
                "notes": "Supports the trait endpoint in a representative organism."
              }
            ],
            "predicate_id": "METPO:2007400"
          },
          {
            "subject": "absent_spo0a_gene",
            "predicate": "predicts",
            "object": "non_spore_forming_trait",
            "description": "Absence of spo0A is an excellent predictor of inability to sporulate.",
            "evidence": [
              {
                "reference": "DOI:10.1128/jb.00079-22",
                "notes": "Comparative genomics of 180 genomes: spo0A present in all 76 sporeformers; its absence predicts non-sporulation."
              }
            ]
          },
          {
            "subject": "loss_sporulation_genes",
            "predicate": "causes",
            "object": "non_spore_forming_trait",
            "description": "Loss of a considerable fraction of sporulation genes yields an asporogenic phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1111/1462-2920.16145",
                "notes": "Asporogenic phenotypes can result from inactivation or loss of a considerable fraction of sporulation genes (generic edge)."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "low_spo0a_activity",
            "predicate": "causes",
            "object": "non_spore_forming_trait",
            "description": "Low or absent Spo0A activity abolishes sporulation capacity.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2021.630573",
                "notes": "Spo0A is the master regulator of endospore formation; elevated Spo0A~P is required to trigger sporulation."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "rap_phosphatases",
            "predicate": "dephosphorylates",
            "object": "spo0f_dephosphorylation",
            "description": "Rap phosphatases directly dephosphorylate Spo0F.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41522-024-00594-6",
                "notes": "Rap phosphatases directly dephosphorylate Spo0F (generic to Bacillus phosphorelay logic)."
              }
            ]
          },
          {
            "subject": "spo0f_dephosphorylation",
            "predicate": "decreases activation of",
            "object": "low_spo0a_activity",
            "description": "Dephosphorylation of Spo0F reduces phosphate flow to Spo0A, decreasing its activation.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41522-024-00594-6",
                "notes": "Reduced phosphate flow to Spo0A in the sporulation phosphorelay (corroborated by DOI:10.3390/microorganisms11081928)."
              }
            ]
          },
          {
            "subject": "phosphorelay_disruption",
            "predicate": "prevents",
            "object": "no_sporulation_entry",
            "description": "Disruption of the KinA/KinB -> Spo0F -> Spo0B -> Spo0A phosphorelay arrests entry into sporulation.",
            "evidence": [
              {
                "reference": "DOI:10.3390/microorganisms11081928",
                "notes": "The phosphorelay signals the start of sporulation; mutants arrest at stages 0/I when initiation fails."
              }
            ],
            "predicate_id": "RO:0002212"
          },
          {
            "subject": "no_sporulation_entry",
            "predicate": "manifests as",
            "object": "non_spore_forming_trait",
            "description": "Failure to enter sporulation manifests the non-spore-forming phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.3390/microorganisms11081928",
                "notes": "Arrest at sporulation initiation produces the non-spore-forming endpoint."
              }
            ],
            "predicate_id": "METPO:2007400"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.917903+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-06T14:40:41-07:00",
        "curator": "codex",
        "action": "CURATED_WITH_ORGANISM_EXAMPLE",
        "changes": "Added Staphylococcus aureus organism example with DOI-backed evidence.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-11T23:00:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed causal graph linking absence of Spo0A regulatory cascade and asymmetric septation to the non-spore-forming phenotype.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T21:30:07Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007400\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-13T21:03:26Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002212\u00d72).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 8 evidence-backed generic edges (8 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:13Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 5 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:causes\u00d72, METPO:2007400\u00d72, RO:0002212\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-08T05:00:00Z",
        "curator": "claude",
        "action": "MERGE_CAUSAL_NODE",
        "changes": "Merged node loss_sporulation_capacity into non_spore_forming_trait and repointed its edges. Issue 352. 'Loss of the capacity to undergo sporulation' IS the record's own trait (METPO:1000872, non-spore forming), so the only correct grounding duplicates the anchor. Collapsing leaves low_spo0a_activity -causes-> non_spore_forming_trait, which is the shape loss_sporulation_genes already uses in this graph.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope non_spore_forming_absent_spo0a_cascade=NONMECHANISTIC with scope_notes; marked 1 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (rap_phosphatases); retyped 1 node(s) (absent_spo0a_gene->STATE).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1003026",
    "label": "orange pigmented",
    "definition": "A pigmentation phenotype in which microbial colonies or cells appear orange due to production and accumulation of orange pigments such as carotenoids.",
    "definition_source": "DOI:10.1080/1040841X.2025.2526423",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1003021"
    ],
    "synonyms": [
      {
        "synonym_text": "Pigment_orange",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1080/1040841X.2025.2526423",
        "snippet": "orange ... pigmentation in bacteria",
        "notes": "Supports orange microbial pigmentation as a bacterial carotenoid-associated color phenotype."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1299",
        "taxon_label": "Deinococcus radiodurans",
        "note": "orange carotenoid colonies",
        "reference": "PMID:39119139"
      },
      {
        "taxon_id": "NCBITaxon:1830",
        "taxon_label": "Rhodococcus ruber",
        "note": "orange-red carotenoid-pigmented actinobacterium",
        "reference": "DOI:10.1016/j.cej.2025.160950"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "orange_pigmented_carotenoid_accumulation",
        "title": "Orange pigmentation carotenoid mechanism",
        "description": "Evidence-backed causal sketch linking orange microbial pigmentation to Crt enzymes, carotenoid biosynthesis, orange carotenoid accumulation, and visible orange color.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a broad environmental or morphological classification spanning multiple mechanisms, a measurement-like bin, or an absence/arrangement descriptor; contextual protein nodes do not receive token UniProt examples.",
        "nodes": [
          {
            "node_id": "orange_pigmented_trait",
            "label": "orange pigmented",
            "node_type": "TRAIT",
            "grounding": "METPO:1003026",
            "description": "Microbial pigmentation appearing orange."
          },
          {
            "node_id": "crt_enzymes",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "Crt enzymes",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Bacterial carotenoid biosynthetic enzymes."
          },
          {
            "node_id": "carotenoid_biosynthesis",
            "label": "carotenoid biosynthesis",
            "node_type": "PATHWAY",
            "description": "Enzymatic pathway producing carotenoid pigments.",
            "grounding": "GO:0016117"
          },
          {
            "node_id": "orange_carotenoids",
            "label": "orange carotenoids",
            "node_type": "CHEMICAL",
            "description": "Carotenoid pigments with orange visible coloration."
          },
          {
            "node_id": "staphyloxanthin",
            "label": "staphyloxanthin",
            "node_type": "CHEMICAL",
            "description": "Golden-orange C30 carotenoid pigment from Staphylococcus aureus.",
            "grounding": "CHEBI:71690"
          },
          {
            "node_id": "visible_orange_color",
            "label": "visible orange color",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "Observed orange colony or cell color."
          },
          {
            "node_id": "crt_y_lycopene_cyclase",
            "label": "lycopene beta-cyclase (CrtY)",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Lycopene cyclase converting lycopene toward beta-carotene in bacteria.",
            "grounding": "GO:0045436"
          },
          {
            "node_id": "lycopene",
            "label": "lycopene",
            "node_type": "CHEMICAL",
            "description": "Red carotenoid intermediate upstream of cyclization.",
            "grounding": "CHEBI:15948"
          },
          {
            "node_id": "beta_carotene",
            "label": "beta-carotene",
            "node_type": "CHEMICAL",
            "description": "Common orange carotenoid end product or branch intermediate in many microbes.",
            "grounding": "CHEBI:17579"
          },
          {
            "node_id": "crt_z_hydroxylase",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "beta-carotene hydroxylase (CrtZ)",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Enzyme converting beta-carotene to zeaxanthin."
          },
          {
            "node_id": "zeaxanthin",
            "label": "zeaxanthin",
            "node_type": "CHEMICAL",
            "description": "Oxygenated carotenoid contributing yellow-orange coloration.",
            "grounding": "CHEBI:27547"
          },
          {
            "node_id": "crt_w_ketolase",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "carotenoid ketolase (CrtW)",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Ketolase producing orange/red ketocarotenoids such as canthaxanthin and astaxanthin."
          },
          {
            "node_id": "ketocarotenoid_biosynthesis",
            "label": "ketocarotenoid biosynthesis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Pathway branch producing orange-to-red ketocarotenoids."
          },
          {
            "node_id": "carotenoid_accumulation",
            "label": "carotenoid accumulation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "High-level mechanistic basis for many orange microbial phenotypes across bacteria, archaea, and yeasts."
          },
          {
            "node_id": "oxidative_stress",
            "label": "oxidative stress / reactive oxygen species",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Oxidative stressor (ROS) against which carotenoids confer protection."
          }
        ],
        "edges": [
          {
            "subject": "crt_enzymes",
            "predicate": "catalyzes",
            "object": "carotenoid_biosynthesis",
            "description": "Crt enzymes catalyze bacterial carotenoid biosynthetic reactions.",
            "evidence": [
              {
                "reference": "DOI:10.1080/1040841X.2025.2526423",
                "snippet": "crt genes ... reactions they catalyze",
                "notes": "Supports Crt enzymes as catalysts in bacterial carotenoid pathways."
              }
            ],
            "predicate_id": "biolink:catalyzes"
          },
          {
            "subject": "carotenoid_biosynthesis",
            "predicate": "has output",
            "object": "orange_carotenoids",
            "description": "Carotenoid biosynthesis produces orange pigments in representative bacteria.",
            "evidence": [
              {
                "reference": "DOI:10.1080/1040841X.2025.2526423",
                "snippet": "orange ... pigmentation in bacteria",
                "notes": "Supports carotenoid biosynthesis as a route to orange bacterial pigmentation."
              }
            ],
            "predicate_id": "RO:0002234"
          },
          {
            "subject": "carotenoid_biosynthesis",
            "predicate": "has output",
            "object": "staphyloxanthin",
            "description": "The S. aureus carotenoid pathway produces staphyloxanthin.",
            "evidence": [
              {
                "reference": "DOI:10.1128/JB.147.3.900-913.1981",
                "snippet": "triterpenoid carotenoids possessing a C30 chain",
                "notes": "Supports staphyloxanthin-related C30 carotenoid pigments in S. aureus."
              }
            ],
            "predicate_id": "RO:0002234"
          },
          {
            "subject": "orange_carotenoids",
            "predicate": "causes",
            "object": "visible_orange_color",
            "description": "Orange carotenoids cause visible orange pigmentation.",
            "evidence": [
              {
                "reference": "DOI:10.1080/1040841X.2025.2526423",
                "snippet": "responsible for ... orange ... pigmentation",
                "notes": "Supports carotenoid pigments as determinants of orange color."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "visible_orange_color",
            "predicate": "manifests as",
            "object": "orange_pigmented_trait",
            "description": "Visible orange color manifests the orange-pigmented phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1080/1040841X.2025.2526423",
                "snippet": "orange ... pigmentation in bacteria",
                "notes": "Supports the trait-level color assignment."
              }
            ],
            "predicate_id": "METPO:2007400"
          },
          {
            "subject": "crt_y_lycopene_cyclase",
            "predicate": "converts",
            "object": "lycopene",
            "description": "CrtY lycopene beta-cyclase acts on lycopene as substrate.",
            "evidence": [
              {
                "reference": "DOI:10.3390/microorganisms11030614",
                "notes": "lycopene is converted to beta-carotene by ring-forming lycopene cyclases; in bacteria the enzyme is crtY. Broad microbial applicability."
              }
            ]
          },
          {
            "subject": "lycopene",
            "predicate": "is converted to",
            "object": "beta_carotene",
            "description": "Lycopene cyclization yields orange beta-carotene.",
            "evidence": [
              {
                "reference": "DOI:10.3390/microorganisms11030614",
                "notes": "lycopene is converted to beta-carotene by ring-forming lycopene cyclases (crtY). Broad microbial applicability."
              }
            ]
          },
          {
            "subject": "crt_z_hydroxylase",
            "predicate": "converts",
            "object": "beta_carotene",
            "description": "CrtZ beta-carotene hydroxylase acts on beta-carotene.",
            "evidence": [
              {
                "reference": "DOI:10.3390/microorganisms11030614",
                "notes": "conversion of beta-carotene to zeaxanthin by crtZ. Strong general edge supporting orange/yellow branches."
              }
            ]
          },
          {
            "subject": "beta_carotene",
            "predicate": "is converted to",
            "object": "zeaxanthin",
            "description": "Hydroxylation of beta-carotene yields zeaxanthin.",
            "evidence": [
              {
                "reference": "DOI:10.3390/microorganisms11030614",
                "notes": "crtZ encodes a beta-carotene hydroxylase converting beta-carotene to zeaxanthin. Strong general edge."
              }
            ]
          },
          {
            "subject": "crt_w_ketolase",
            "predicate": "contributes to",
            "object": "ketocarotenoid_biosynthesis",
            "description": "CrtW ketolase drives ketocarotenoid (e.g., canthaxanthin/astaxanthin) formation.",
            "evidence": [
              {
                "reference": "DOI:10.3390/microorganisms11030614",
                "notes": "ketolation by ketolases such as crtW yields ketocarotenoids (canthaxanthin/astaxanthin). Strong for the ketocarotenoid branch; orange-to-red hue."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "carotenoid_accumulation",
            "predicate": "protects against",
            "object": "oxidative_stress",
            "description": "Accumulated carotenoids act as antioxidants neutralizing reactive oxygen species.",
            "evidence": [
              {
                "reference": "DOI:10.7759/cureus.59892",
                "notes": "acts as an antioxidant protecting against hydrogen peroxide and hydroxyl radicals. Strong, broad functional edge across taxa."
              }
            ]
          },
          {
            "subject": "orange_pigmented_trait",
            "predicate": "has material basis in",
            "object": "carotenoid_accumulation",
            "description": "The orange-pigmented phenotype is materially based on carotenoid accumulation.",
            "evidence": [
              {
                "reference": "DOI:10.7759/cureus.59892",
                "notes": "orange carotenoid; golden yellow-orange pigment. High-level edge suitable for TraitMech root graph across diverse taxa."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.945311+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-11T19:10:00-07:00",
        "curator": "codex",
        "action": "CURATED_WITH_LITERATURE",
        "changes": "Added DOI-backed definition and causal graph for Crt enzymes, carotenoid biosynthesis, orange carotenoids, staphyloxanthin, and visible orange color.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d72).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T05:49:24Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:catalyzes\u00d71, biolink:causes\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T21:30:07Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007400\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:41:04Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0016117\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-14T05:51:46Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:71690\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 7 evidence-backed generic edges (9 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:13Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002326\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:33Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 3 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:15948\u00d71, CHEBI:17579\u00d71, CHEBI:27547\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:23:55Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0045436\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 2 causal edge(s) off microbe-domain METPO predicates (2 to has output), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-16T02:00:00Z",
        "curator": "claude",
        "action": "NORMALISE_NODE_TYPE",
        "changes": "Under the PATHWAY-vs-BIOLOGICAL_PROCESS rule, one node_id means one thing corpus-wide (issue 356): carotenoid_biosynthesis is typed PATHWAY. PATHWAY is a named, conventionally enumerable multi-step route; BIOLOGICAL_PROCESS is everything else. A named biosynthetic route. Most descriptions call it one outright, including BIOLOGICAL_PROCESS-typed ones ('Enzymatic pathway producing carotenoid pigments'); red_pigmented.yaml instead ENUMERATES the steps -- 'Phytoene synthase condenses two GGPP to phytoene, then desaturation/isomerization yields lycopene' -- which is the rule's own test for PATHWAY met explicitly rather than by naming. Applied AGAINST the majority, which was 5 BIOLOGICAL_PROCESS to 1 before this tranche.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope orange_pigmented_carotenoid_accumulation=NONMECHANISTIC with scope_notes; marked 3 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (crt_enzymes, crt_z_hydroxylase, crt_w_ketolase).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000678",
    "label": "oval shaped",
    "definition": "A cell shape characterized by an ellipsoidal morphology with rounded ends, resembling an elongated sphere.",
    "definition_source": "DOI:10.1089/mdr.2014.0032",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000666"
    ],
    "synonyms": [
      {
        "synonym_text": "oval-shaped",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "created_by": "Anthea Guo",
    "evidence": [
      {
        "reference": "DOI:10.1089/mdr.2014.0032",
        "snippet": "ovococci that are ellipsoid",
        "notes": "Supports oval/ellipsoidal morphology as an ovococcal bacterial shape class."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:171101",
        "taxon_label": "Streptococcus pneumoniae R6",
        "note": "Strain-level oval pneumococcal model paired to reviewed PBP2b, whose depletion directly alters peripheral wall synthesis and cell morphology.",
        "reference": "DOI:10.1128/JB.00184-13"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "oval_shaped_ovococcal_pg_synthesis",
        "title": "Oval-shape ovococcal peptidoglycan mechanism",
        "description": "Evidence-backed causal sketch linking oval morphology to peripheral and septal peptidoglycan synthesis, PBP2b-associated elongation, MapZ/FtsZ division positioning, and rounded ellipsoidal geometry.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "The graph represents the pneumococcal septal/peripheral peptidoglycan mechanism. The R6 PBP2b example anchors a protein in the elongation branch; aggregate systems remain semantic or reviewed label-only nodes.",
        "nodes": [
          {
            "node_id": "oval_shaped_trait",
            "label": "oval shaped",
            "node_type": "TRAIT",
            "grounding": "METPO:1000678",
            "description": "Rounded ellipsoidal bacterial cell morphology."
          },
          {
            "node_id": "peripheral_peptidoglycan_synthesis",
            "label": "peripheral peptidoglycan synthesis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Peripheral wall synthesis contributing to ovococcal elongation."
          },
          {
            "node_id": "septal_peptidoglycan_synthesis",
            "label": "septal peptidoglycan synthesis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Division-site wall synthesis."
          },
          {
            "node_id": "pbp2b",
            "label": "PBP2b",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Peptidoglycan synthase associated with elongation in ovococci.",
            "grounding": "InterPro:IPR047982",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:P0A3M6",
                "protein_label": "Penicillin-binding protein 2B",
                "gene_symbol": "penA",
                "taxon_id": "NCBITaxon:171101",
                "taxon_label": "Streptococcus pneumoniae R6",
                "entry_status": "REVIEWED",
                "retrieved_on": "2026-10-22",
                "entry_version": 111,
                "sequence_version": 1,
                "role": "R6 PBP2b supplies the peripheral peptidoglycan transpeptidase activity required to maintain elongated oval pneumococcal morphology.",
                "evidence": [
                  {
                    "reference": "DOI:10.1128/JB.00184-13",
                    "snippet": "PBP2b is essential for peripheral peptidoglycan synthesis",
                    "notes": "The R6-derived depletion study directly connects PBP2b levels to cell morphology; UniProt verifies the reviewed strain-level protein entry."
                  }
                ]
              }
            ]
          },
          {
            "node_id": "mapZ_ftsZ_system",
            "label": "MapZ/FtsZ division-positioning system",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Proteins involved in positioning and organizing ovococcal division.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "MapZ and FtsZ are distinct protein families, so this two-protein positioning-system aggregate has no single exact family grounding."
          },
          {
            "node_id": "ellipsoidal_geometry",
            "label": "ellipsoidal geometry",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Rounded elongated cell-body geometry."
          },
          {
            "node_id": "rod_complex_elongasome",
            "label": "Rod complex (elongasome) peptidoglycan synthesis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Conserved peripheral/sidewall peptidoglycan synthesis machinery (RodA, MreC, PBP2b) driving cell elongation."
          },
          {
            "node_id": "mreC",
            "label": "MreC",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Elongasome scaffolding protein required for peripheral peptidoglycan synthesis and elongated cell shape.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Retained label-only because the evidence supports pneumococcal MreC but no exact semantic family identifier was verified in this review."
          },
          {
            "node_id": "rodA",
            "label": "RodA",
            "node_type": "GENE_OR_PROTEIN",
            "description": "SEDS-family peptidoglycan glycosyltransferase of the Rod complex driving sidewall/peripheral elongation.",
            "grounding": "InterPro:IPR001182"
          },
          {
            "node_id": "division_site_placement",
            "label": "correct septum placement / division-site marking",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Spatial marking and placement of the division site ensuring correct septum positioning."
          }
        ],
        "edges": [
          {
            "subject": "pbp2b",
            "predicate": "enables",
            "object": "peripheral_peptidoglycan_synthesis",
            "description": "PBP2b supports peripheral peptidoglycan synthesis in ovococcal elongation.",
            "evidence": [
              {
                "reference": "DOI:10.1089/mdr.2014.0032",
                "snippet": "PBP2b of ovococci",
                "notes": "Supports PBP2b as a key ovococcal elongation factor."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "mapZ_ftsZ_system",
            "predicate": "positions",
            "object": "septal_peptidoglycan_synthesis",
            "description": "MapZ/FtsZ positioning organizes the division-associated wall synthesis zone.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.mib.2016.07.014",
                "snippet": "relies on the membrane protein MapZ",
                "notes": "Supports MapZ/FtsZ involvement in S. pneumoniae cell division."
              }
            ]
          },
          {
            "subject": "peripheral_peptidoglycan_synthesis",
            "predicate": "combines with",
            "object": "septal_peptidoglycan_synthesis",
            "description": "Peripheral and septal synthesis together generate the ovococcal growth pattern.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.cub.2021.04.041",
                "snippet": "dynamics of peptidoglycan assembly",
                "notes": "Supports nanometer-scale PG synthesis dynamics in ovoid bacteria."
              }
            ]
          },
          {
            "subject": "septal_peptidoglycan_synthesis",
            "predicate": "causes",
            "object": "ellipsoidal_geometry",
            "description": "Coordinated septal and peripheral synthesis shapes an ellipsoidal cell body.",
            "evidence": [
              {
                "reference": "DOI:10.1089/mdr.2014.0032",
                "snippet": "ovococci that are ellipsoid",
                "notes": "Supports the ellipsoidal ovococcal morphology endpoint."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "ellipsoidal_geometry",
            "predicate": "manifests as",
            "object": "oval_shaped_trait",
            "description": "Rounded ellipsoidal geometry manifests the oval-shaped trait.",
            "evidence": [
              {
                "reference": "DOI:10.1089/mdr.2014.0032",
                "snippet": "ellipsoid",
                "notes": "Supports oval shape as an ellipsoidal bacterial morphology."
              }
            ],
            "predicate_id": "METPO:2007400"
          },
          {
            "subject": "peripheral_peptidoglycan_synthesis",
            "predicate": "positively influences",
            "object": "oval_shaped_trait",
            "description": "Peripheral PG synthesis extends the cell prior to septal synthesis, producing elongated ovoid geometry.",
            "evidence": [
              {
                "reference": "DOI:10.1128/spectrum.04750-22",
                "notes": "Ovococcal division model: \"the cell synthesizes peripheral PG alone for a short time to extend the cell before septal PG synthesis is initiated\"."
              }
            ]
          },
          {
            "subject": "mreC",
            "predicate": "positively influences",
            "object": "oval_shaped_trait",
            "description": "Loss of mreC yields smaller, more spherical cells, indicating MreC promotes elongated ovoid shape.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-023-38904-9",
                "notes": "\"cells lacking mreC, pbp2B, and rodA appeared smaller and more spherical\" - MreC supports ovoid elongation."
              }
            ]
          },
          {
            "subject": "rodA",
            "predicate": "positively influences",
            "object": "oval_shaped_trait",
            "description": "Loss of rodA yields smaller, more spherical cells, indicating RodA promotes elongated ovoid shape.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-023-38904-9",
                "notes": "\"cells lacking mreC, pbp2B, and rodA appeared smaller and more spherical\" - RodA supports ovoid elongation."
              }
            ]
          },
          {
            "subject": "pbp2b",
            "predicate": "positively influences",
            "object": "oval_shaped_trait",
            "description": "Loss of pbp2B yields smaller, more spherical cells, indicating PBP2b promotes elongated ovoid shape.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-023-38904-9",
                "notes": "\"cells lacking mreC, pbp2B, and rodA appeared smaller and more spherical\" - PBP2b supports ovoid elongation."
              }
            ]
          },
          {
            "subject": "rodA",
            "predicate": "part of",
            "object": "rod_complex_elongasome",
            "description": "RodA together with MreC and PBP2b forms the Rod complex driving peripheral elongation PG synthesis.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-023-38904-9",
                "notes": "mreC, pbp2B, and rodA act together in the elongation machinery whose loss makes cells spherical."
              }
            ],
            "predicate_id": "biolink:part_of"
          },
          {
            "subject": "mapZ_ftsZ_system",
            "predicate": "positively regulates",
            "object": "division_site_placement",
            "description": "MapZ/LocZ mark division sites and ensure correct septum placement.",
            "evidence": [
              {
                "reference": "DOI:10.1042/bsr20221664",
                "notes": "\"MapZ and LocZ are reported as proteins that mark division sites and ensure correct septum placement, respectively\"."
              }
            ],
            "predicate_id": "RO:0002213"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.891705+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-11T20:05:00-07:00",
        "curator": "codex",
        "action": "CURATED_WITH_LITERATURE",
        "changes": "Added DOI-backed definition and causal graph for PBP2b, MapZ/FtsZ, peripheral and septal peptidoglycan synthesis, and oval cell geometry.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T21:30:07Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007400\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:19Z",
        "curator": "claude",
        "action": "RENAME_PREDICATE_LABELS",
        "changes": "Renamed 2 causal-edge predicate label(s) to align with existing groundings: supports \u2192 enables \u00d71; shapes \u2192 causes \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:22Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d71, biolink:causes\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T05:05:15Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A892RPK7\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 6 evidence-backed generic edges (4 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:13Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:part_of\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-26T07:15:19Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A1L9R356\u00d71, UniProtKB:A0A0H2X1V4\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:21:12Z",
        "curator": "claude",
        "action": "RETRACT_DEAD_UNIPROT_GROUNDINGS",
        "changes": "Retracted 2 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-04T03:08:15Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002213\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-22T04:26:15Z",
        "curator": "codex",
        "action": "REVIEW_UNIPROT_INSTANCE_GROUNDINGS",
        "changes": "Reviewed 1 organism-specific UniProtKB grounding(s): replaced 1 with taxon-agnostic GO/InterPro terms and retracted 0 to label-only where no exact semantic term was supported (docs/GROUNDING_POLICY.md).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "CURATE_PROTEIN_TAXON_EXAMPLE",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope oval_shaped_ovococcal_pg_synthesis=MECHANISTIC with scope_notes; marked 2 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (mapZ_ftsZ_system, mreC); added taxon-paired protein example(s) UniProtKB:P0A3M6 on pbp2b (NCBITaxon:171101); regrounded 1 node(s) (pbp2b: none->InterPro:IPR047982); added canonical example(s) NCBITaxon:171101.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-22T01:35:00Z",
        "curator": "claude",
        "action": "REFRESH_UNIPROT_ENTRY_VERSION",
        "changes": "Refreshed UniProtKB entry_version against live UniProt REST on 2026-10-22: UniProtKB:P0A3M6 (110 -> 111 on pbp2b).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000677",
    "label": "ovoid shaped",
    "definition": "A cell shape in which an organism has an oval morphology, rounded at both ends with one end often slightly broader than the other.",
    "definition_source": "DOI:10.1016/j.cub.2021.04.041",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000666"
    ],
    "synonyms": [
      {
        "synonym_text": "S_ovoid",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "ovoid-shaped",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "created_by": "Luke Wang",
    "evidence": [
      {
        "reference": "DOI:10.1016/j.cub.2021.04.041",
        "snippet": "ovoid bacterium Streptococcus pneumoniae",
        "notes": "Supports ovoid bacterial morphology as a recognized ovococcal shape."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:171101",
        "taxon_label": "Streptococcus pneumoniae R6",
        "note": "Strain-level ovoid pneumococcal model paired to reviewed PBP2b, a component of the RodA-PBP2b peripheral peptidoglycan machinery.",
        "reference": "DOI:10.1128/JB.00184-13"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "ovoid_shaped_midcell_pg_assembly",
        "title": "Ovoid-shape midcell peptidoglycan mechanism",
        "description": "Evidence-backed causal sketch linking ovoid morphology to midcell peptidoglycan assembly, MapZ division-site placement, DivIVA-associated growth, and rounded ovoid geometry.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "The graph represents pneumococcal midcell wall assembly. The R6 PBP2b example is explicitly one protein component of the RodA-PBP2b elongasome, not an accession for the full protein complex.",
        "nodes": [
          {
            "node_id": "ovoid_shaped_trait",
            "label": "ovoid shaped",
            "node_type": "TRAIT",
            "grounding": "METPO:1000677",
            "description": "Rounded ovoid bacterial morphology."
          },
          {
            "node_id": "midcell_pg_assembly",
            "label": "midcell peptidoglycan assembly",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Wall synthesis and assembly in an annular midcell region."
          },
          {
            "node_id": "mapZ",
            "label": "MapZ",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Membrane protein involved in division-site placement in S. pneumoniae.",
            "grounding": "InterPro:IPR030858"
          },
          {
            "node_id": "divIVA",
            "label": "DivIVA",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Protein involved in septum splitting and elongation in ovococci.",
            "grounding": "InterPro:IPR007793"
          },
          {
            "node_id": "septum_splitting",
            "label": "septum splitting",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Separation and remodeling of the division septum."
          },
          {
            "node_id": "ovoid_geometry",
            "label": "ovoid geometry",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Rounded, egg-like cell-body geometry."
          },
          {
            "node_id": "septal_pg_synthesis",
            "label": "septal peptidoglycan synthesis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Mode of PG synthesis building the division septum in ovococci."
          },
          {
            "node_id": "peripheral_pg_synthesis",
            "label": "peripheral peptidoglycan synthesis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Mode of PG synthesis elongating the cell wall, producing ovoid aspect ratio."
          },
          {
            "node_id": "ftsz_treadmilling",
            "label": "FtsZ treadmilling",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Treadmilling dynamics of the FtsZ cytoskeletal ring guiding septal synthesis."
          },
          {
            "node_id": "ftsw_pbp2x",
            "label": "FtsW-PBP2x complex",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Divisome PG synthase complex that builds the division septum.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "FtsW and PBP2x are distinct protein families; no single semantic family term represents this two-protein complex."
          },
          {
            "node_id": "roda_pbp2b",
            "label": "RodA-PBP2b elongasome",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Elongasome PG synthase pair driving peripheral wall elongation.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "RodA and PBP2b are distinct protein families; no single semantic family term represents the pair.",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:P0A3M6",
                "protein_label": "Penicillin-binding protein 2B",
                "gene_symbol": "penA",
                "taxon_id": "NCBITaxon:171101",
                "taxon_label": "Streptococcus pneumoniae R6",
                "entry_status": "REVIEWED",
                "retrieved_on": "2026-10-22",
                "entry_version": 111,
                "sequence_version": 1,
                "role": "R6 PBP2b is the transpeptidase component of the RodA-PBP2b elongasome that performs peripheral peptidoglycan synthesis.",
                "evidence": [
                  {
                    "reference": "DOI:10.1128/JB.00184-13",
                    "snippet": "PBP2b is essential for peripheral peptidoglycan synthesis",
                    "notes": "The R6-derived depletion study establishes the protein's peripheral-wall and morphology role; UniProt verifies the reviewed R6 accession."
                  }
                ]
              }
            ]
          },
          {
            "node_id": "ftsz_ring",
            "label": "FtsZ ring",
            "node_type": "CELLULAR_LOCALIZATION",
            "description": "The Z-ring division apparatus positioned at midcell."
          },
          {
            "node_id": "concentric_midcell_rings",
            "label": "concentric midcell rings",
            "node_type": "CELLULAR_LOCALIZATION",
            "description": "Organization of septal and peripheral PG machineries into concentric midcell rings."
          }
        ],
        "edges": [
          {
            "subject": "mapZ",
            "predicate": "positions",
            "object": "midcell_pg_assembly",
            "description": "MapZ participates in division-site placement for ovoid growth.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.mib.2016.07.014",
                "snippet": "relies on the membrane protein MapZ",
                "notes": "Supports MapZ as a division-positioning factor in S. pneumoniae."
              }
            ]
          },
          {
            "subject": "midcell_pg_assembly",
            "predicate": "causes",
            "object": "ovoid_geometry",
            "description": "Midcell peptidoglycan assembly shapes ovoid cell geometry.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.cub.2021.04.041",
                "snippet": "peptidoglycan synthesis ... in the ovoid bacterium",
                "notes": "Supports PG assembly dynamics in ovoid S. pneumoniae."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "divIVA",
            "predicate": "controls",
            "object": "septum_splitting",
            "description": "DivIVA controls septum splitting and elongation dynamics.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mbio.01311-24",
                "snippet": "DivIVA controls the dynamics of septum splitting and cell elongation",
                "notes": "Supports DivIVA in ovococcal cell morphogenesis."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "septum_splitting",
            "predicate": "contributes to",
            "object": "ovoid_geometry",
            "description": "Septum splitting and elongation dynamics contribute to ovoid morphology.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mbio.01311-24",
                "snippet": "how ovoid bacteria proliferate",
                "notes": "Supports septum/elongation dynamics as relevant to ovoid bacterial proliferation."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "ovoid_geometry",
            "predicate": "manifests as",
            "object": "ovoid_shaped_trait",
            "description": "Ovoid cell-body geometry manifests the ovoid-shaped trait.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.cub.2021.04.041",
                "snippet": "ovoid-shaped bacteria",
                "notes": "Supports the trait endpoint."
              }
            ],
            "predicate_id": "METPO:2007400"
          },
          {
            "subject": "midcell_pg_assembly",
            "predicate": "has component",
            "object": "septal_pg_synthesis",
            "description": "Ovococcal midcell growth includes a distinct septal PG synthesis mode.",
            "evidence": [
              {
                "reference": "DOI:10.1042/BSR20221664",
                "notes": "There are two spatially distinct modes of PG synthesis: septal and peripheral."
              }
            ]
          },
          {
            "subject": "midcell_pg_assembly",
            "predicate": "has component",
            "object": "peripheral_pg_synthesis",
            "description": "Ovococcal midcell growth includes a distinct peripheral PG synthesis mode.",
            "evidence": [
              {
                "reference": "DOI:10.1042/BSR20221664",
                "notes": "There are two spatially distinct modes of PG synthesis: septal and peripheral."
              }
            ]
          },
          {
            "subject": "ftsz_treadmilling",
            "predicate": "drives",
            "object": "septal_pg_synthesis",
            "description": "FtsZ treadmilling drives septal PG synthesis.",
            "evidence": [
              {
                "reference": "DOI:10.1042/BSR20221664",
                "notes": "FtsZ treadmilling drives septal PG synthesis together with the FtsW-PBP2x complex."
              }
            ]
          },
          {
            "subject": "ftsw_pbp2x",
            "predicate": "synthesizes",
            "object": "septal_pg_synthesis",
            "description": "The FtsW-PBP2x complex synthesizes the division septum.",
            "evidence": [
              {
                "reference": "DOI:10.1042/BSR20221664",
                "notes": "Septal PG synthesis is driven by the FtsW-PBP2x complex to synthesize the division septum."
              }
            ]
          },
          {
            "subject": "roda_pbp2b",
            "predicate": "drives",
            "object": "peripheral_pg_synthesis",
            "description": "The RodA-PBP2b elongasome drives peripheral PG synthesis.",
            "evidence": [
              {
                "reference": "DOI:10.1042/BSR20221664",
                "notes": "Peripheral (elongation) activity is carried out by the elongasome, driven by the RodA-PBP2b pair."
              }
            ]
          },
          {
            "subject": "mapZ",
            "predicate": "positions",
            "object": "ftsz_ring",
            "description": "MapZ guides movement and positioning of the FtsZ ring.",
            "evidence": [
              {
                "reference": "DOI:10.1042/BSR20221664",
                "notes": "MapZ guides movement of FtsZ and associated proteins from the septal ring to the equatorial ring."
              }
            ]
          },
          {
            "subject": "midcell_pg_assembly",
            "predicate": "assembles as",
            "object": "concentric_midcell_rings",
            "description": "Septal and peripheral PG machineries assemble at midcell into concentric rings.",
            "evidence": [
              {
                "reference": "DOI:10.1042/BSR20221664",
                "notes": "Septal and peripheral PG-synthesis machineries assemble at mid-cell into concentric rings (inner septal, outer peripheral)."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.891106+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-11T20:05:00-07:00",
        "curator": "codex",
        "action": "CURATED_WITH_LITERATURE",
        "changes": "Added DOI-backed definition and causal graph for MapZ, DivIVA, midcell peptidoglycan assembly, septum splitting, and ovoid cell geometry.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002326\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T21:30:07Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002211\u00d71, METPO:2007400\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:19Z",
        "curator": "claude",
        "action": "RENAME_PREDICATE_LABELS",
        "changes": "Renamed 1 causal-edge predicate label(s) to align with existing groundings: shapes \u2192 causes \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:22Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:causes\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T05:05:15Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:Q1IYG2\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 7 evidence-backed generic edges (7 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-22T04:26:15Z",
        "curator": "codex",
        "action": "REVIEW_UNIPROT_INSTANCE_GROUNDINGS",
        "changes": "Reviewed 1 organism-specific UniProtKB grounding(s): replaced 1 with taxon-agnostic GO/InterPro terms and retracted 0 to label-only where no exact semantic term was supported (docs/GROUNDING_POLICY.md).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "CURATE_PROTEIN_TAXON_EXAMPLE",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope ovoid_shaped_midcell_pg_assembly=MECHANISTIC with scope_notes; marked 2 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (ftsw_pbp2x, roda_pbp2b); added taxon-paired protein example(s) UniProtKB:P0A3M6 on roda_pbp2b (NCBITaxon:171101); regrounded 1 node(s) (mapZ: none->InterPro:IPR030858); added canonical example(s) NCBITaxon:171101.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-22T01:35:00Z",
        "curator": "claude",
        "action": "REFRESH_UNIPROT_ENTRY_VERSION",
        "changes": "Refreshed UniProtKB entry_version against live UniProt REST on 2026-10-22: UniProtKB:P0A3M6 (110 -> 111 on roda_pbp2b).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000654",
    "label": "palmelloid formation",
    "definition": "A morphological phenotype in which algal cells form nonmotile multicellular groups by retention within a mother-cell wall or by adhesion through extracellular gelatinous material.",
    "definition_source": "DOI:10.1038/s41598-019-39558-8",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.3390/ijms24098374",
        "snippet": "the cells continue to divide within the mother cell, i.e., they are unable to separate and remain encased in a single membrane.",
        "notes": "Suwannachuen et al. (2023), PMID:37176080, PMC10179368, Discussion 3.3. The quote is the authors' interpretation of enclosed dividing cells, not an abstract quote or a specific molecular mechanism. Results 2.5 and actual Figure 10 show CC-4414 palmelloids after high-light exposure in TAP medium. Methods 4.2 defines the percentage as palmelloid area divided by total cell area, not an individual-cell count. Larger aggregates are distinguished from palmelloids. CC-4414 provenance remains qualified in the discussion below."
      },
      {
        "reference": "DOI:10.3389/fpls.2022.911035",
        "snippet": "a morphological state characterized by multiple, single cells encased in an outer limiting membrane",
        "notes": "Szyszka-Mroz et al. (2022), PMID:36119589, PMC9470844, Introduction. The scientific abstract, growth Methods, morphology Results and actual Figure 1 were inspected. Palmelloids occur alongside single cells at permissive 8 C; stress is not a necessary condition. Internal cells may retain flagella. Shared enclosure does not establish a particular membrane chemistry or universal cytokinesis defect."
      },
      {
        "reference": "DOI:10.1038/s41598-019-39558-8",
        "snippet": "the production of a gelatinous material that is secreted extracellularly, resulting in adhesion among cells and/or colonies",
        "notes": "Herron et al. (2019), PMID:30787483, PMC6382799, Discussion. Directly retrieved full text explicitly uses palmelloid for both mother-wall retention and extracellular-material-mediated adhesion. This quote supports the second sense. The adjacent text describes palmelloids as nonmotile. This is terminology evidence, not a claim that the selected evolved isolates are natural canonical examples. The narrower enclosed-cell usage in the 2022/2023 sources is retained with its source attribution."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1653778",
        "taxon_label": "Chlamydomonas priscui",
        "reference": "DOI:10.3389/fpls.2022.911035",
        "note": "Lake Bonney Antarctic isolate grown at 8 C in Bold's basal medium supplemented with 0.7 M NaCl, at 150 micromol photons m^-2 s^-1. Figure 1A,B and morphology Results show a mixed population of single cells and palmelloids, not every cell or growth stage. The Introduction identifies its natural lake origin. The source uses Chlamydomonas priscuii; NCBI Taxonomy lists that spelling as a synonym of the current species label Chlamydomonas priscui."
      }
    ],
    "discussions": [
      {
        "discussion_id": "palmelloid-formation-scope-and-hierarchy",
        "prompt": "Review a multicellular morphology parent and exact mappings.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Herron et al. (2019) explicitly includes mother-wall retention and extracellular-gelatinous-material adhesion in palmelloid usage, whereas the 2022/2023 sources emphasize enclosed cells. Preserve both documented senses in the unqualified class; review whether separate children are warranted. Retain phenotype METPO:1000059: cell shape METPO:1000666 describes an individual cell and colony morphology METPO:1007062 is macroscopic. Obsolete cell arrangement METPO:1000046 and aggregate METPO:1000011 are not active parents. Biofilm formation traitmech:000053 requires surface attachment; rosette cell arrangement traitmech:000652 requires inward cell-pole orientation. Neither is required here. Palmelloid is not an exact synonym for any microbial aggregate, capsule, resting spore or normal transient pre-release sporangium. No xref or organism-level disjointness is asserted.",
        "posed_by": "codex",
        "posed_date": "2026-10-07"
      },
      {
        "discussion_id": "palmelloid-formation-mechanism-scope",
        "prompt": "Resolve organism-specific cell-release mechanisms before graphing.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "A causal graph is deferred pending organism-specific perturbation and protein accession review. The 2023 proteome associations and proposed photoprotection do not establish that particular proteins cause palmelloid formation or that palmelloids are necessary for all high-light tolerance. Gene possession alone does not establish the phenotype. Do not transfer a cell-release mechanism to the extracellular-adhesion form. Four-to-sixteen cells, stress induction, loss of flagella, photoprotection and a particular cytokinesis or wall-remodelling defect are not universal requirements. For the wall-retained form, distinguish sustained enclosure from an ordinary division stage using organism-specific time courses; no universal persistence cutoff is asserted.",
        "posed_by": "codex",
        "posed_date": "2026-10-07"
      },
      {
        "discussion_id": "palmelloid-formation-cc4414-provenance",
        "prompt": "Reconcile CC-4414 provenance before canonical-example promotion.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "The 2023 paper and Chlamydomonas Resource Center describe CC-4414/DN2 as a field isolate: https://www.chlamycollection.org/product/cc-4414-wild-type-mt-dn2/ . However, Flowers et al. (2015), Results accompanying Figure 2, reports extensive identity-by-descent with laboratory strains and raises possible cross-contamination while retaining a distinct chromosome-16 segment: https://academic.oup.com/plcell/article/27/9/2353/6206349 . Both primary passages were directly read. This is a provenance uncertainty, not proof of engineering or contamination in the 2023 experimental stock. Preserve the observed high-light phenotype as qualified evidence, but omit CC-4414 from canonical examples pending reconciliation.",
        "posed_by": "codex",
        "posed_date": "2026-10-07"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-07T00:44:51Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added palmelloid formation with two DOI-backed snippets, a condition-qualified Antarctic-isolate example, and explicit enclosure, mechanism and CC-4414 provenance boundaries. Ignored-and-hidden searches and structured METPO review found no exact record. Reserved METPO:1060700 in v530; existing records unchanged.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-07T00:57:34Z",
        "curator": "codex",
        "action": "CORRECTED_DEFINITION_SCOPE",
        "changes": "Addressed issue #1767: the unqualified palmelloid label was narrower than documented usage. Added DOI:10.1038/s41598-019-39558-8 and its verified snippet, broadened the definition to include extracellular-material adhesion, and retained source-specific scope and mechanism distinctions. Canonical example unchanged.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000060",
    "label": "peritrichous",
    "definition": "A flagellar arrangement with flagella distributed over the entire cell surface rather than localized to the poles.",
    "definition_source": "DOI:10.1093/femsre/fuv034",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "traitmech:000056"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1093/femsre/fuv034",
        "notes": "Schuhmacher et al. describe peritrichous (surface-distributed) flagellation as one of the conserved flagellation patterns."
      },
      {
        "reference": "DOI:10.3390/biom9070279",
        "notes": "Flagellum review supports multiple surface flagellar filaments as locomotory organelles, as in peritrichously flagellated enterobacteria."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:28901",
        "taxon_label": "Salmonella enterica",
        "note": "Peritrichous flagellation (flagella over the whole cell surface); classic enteric motility/chemotaxis model.",
        "reference": "PMID:33859630"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "peritrichous_surface_distributed_flagella",
        "title": "Peritrichous flagellation \u2014 surface-distributed flagella",
        "description": "Evidence-backed causal sketch linking surface-distributed bacterial flagella to the peritrichous arrangement.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a broad environmental or morphological classification spanning multiple mechanisms, a measurement-like bin, or an absence/arrangement descriptor; contextual protein nodes do not receive token UniProt examples.",
        "nodes": [
          {
            "node_id": "peritrichous_trait",
            "label": "peritrichous",
            "node_type": "TRAIT",
            "grounding": "traitmech:000060",
            "description": "Flagella distributed over the cell surface."
          },
          {
            "node_id": "bacterial_flagellum",
            "label": "bacterial-type flagellum",
            "node_type": "CELLULAR_LOCALIZATION",
            "grounding": "GO:0009288",
            "description": "Helical proteinaceous locomotory organelle."
          },
          {
            "node_id": "surface_placement",
            "label": "surface-distributed placement",
            "node_type": "QUALITY",
            "description": "Flagella spaced over the cell surface rather than at the poles."
          },
          {
            "node_id": "polar_placement",
            "label": "polar flagellar arrangement",
            "node_type": "QUALITY",
            "description": "Flagella localized at one or both cell poles."
          },
          {
            "node_id": "b_subtilis_flagellar_rod_assembly",
            "label": "B. subtilis flagellar rod assembly",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Polymerization of the B. subtilis flagellar rod through the peptidoglycan wall."
          },
          {
            "node_id": "b_subtilis_basal_body_immobilization",
            "label": "B. subtilis basal-body immobilization",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Capture and immobilization of initially mobile nascent basal bodies during flagellar rod assembly in B. subtilis."
          },
          {
            "node_id": "b_subtilis_peptidoglycan_pore_pattern",
            "label": "B. subtilis peptidoglycan pore pattern",
            "node_type": "QUALITY",
            "description": "Grid-like distribution of permissive peptidoglycan pores interpreted during B. subtilis flagellar rod assembly."
          },
          {
            "node_id": "flagellar_filament_number",
            "label": "flagellar filament number",
            "node_type": "QUALITY",
            "description": "Number of flagellar filaments per cell, multiple in peritrichous cells."
          },
          {
            "node_id": "swimming_velocity",
            "label": "swimming velocity",
            "node_type": "CAPACITY",
            "description": "Cell swimming speed driven by flagellar rotation."
          }
        ],
        "edges": [
          {
            "subject": "bacterial_flagellum",
            "predicate": "defines",
            "object": "peritrichous_trait",
            "description": "Flagella distributed over the cell surface define the peritrichous arrangement.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuv034",
                "notes": "Schuhmacher et al. describe peritrichous flagellation as a conserved pattern."
              }
            ],
            "predicate_id": "METPO:2007500"
          },
          {
            "subject": "peritrichous_trait",
            "predicate": "associated with",
            "object": "surface_placement",
            "description": "The peritrichous pattern spaces multiple flagella across the cell surface.",
            "evidence": [
              {
                "reference": "DOI:10.3390/biom9070279",
                "notes": "Flagellum review supports multiple surface flagellar filaments as locomotory organelles."
              }
            ],
            "predicate_id": "biolink:associated_with"
          },
          {
            "subject": "surface_placement",
            "predicate": "associated with",
            "object": "flagellar_filament_number",
            "description": "Surface-distributed peritrichous flagellation is associated with multiple flagella per cell, although number varies by species and condition.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuv034",
                "snippet": "five to six flagellar filaments distributed over the cell body",
                "notes": "Schuhmacher et al. describe E. coli and B. subtilis as representative peritrichous bacteria with multiple filaments, while warning that number varies."
              }
            ],
            "predicate_id": "biolink:associated_with"
          },
          {
            "subject": "peritrichous_trait",
            "predicate": "distinguished from",
            "object": "polar_placement",
            "description": "Peritrichous surface-distributed flagella are distinguished from polar flagellar arrangements.",
            "evidence": [
              {
                "reference": "DOI:10.3390/fermentation10120606",
                "notes": "Frolov et al. 2024 contrast Pseudomonas polar flagella located at one pole with peritrichous flagella located throughout the cell wall."
              }
            ]
          },
          {
            "subject": "b_subtilis_flagellar_rod_assembly",
            "predicate": "causes",
            "object": "b_subtilis_basal_body_immobilization",
            "description": "In B. subtilis, flagellar rod assembly through peptidoglycan immobilizes initially mobile nascent basal bodies.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mbio.00530-25",
                "snippet": "become immobilized when the flagellar rod transits the peptidoglycan",
                "notes": "Dunn et al. directly observed elevated mobility early in basal-body assembly and in rod mutants, supporting rod-dependent immobilization in B. subtilis."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "b_subtilis_peptidoglycan_pore_pattern",
            "predicate": "regulates",
            "object": "b_subtilis_basal_body_immobilization",
            "description": "The grid-like pattern of permissive peptidoglycan pores constrains where B. subtilis rod assembly can immobilize basal bodies.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mbio.00530-25",
                "snippet": "interpreting a grid-like pattern of pores, pre-existent in the PG",
                "notes": "Dunn et al. infer that rod polymerization interprets a pre-existing grid-like peptidoglycan pore pattern; this edge is therefore taxon-scoped and inferential."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "b_subtilis_basal_body_immobilization",
            "predicate": "contributes to",
            "object": "surface_placement",
            "description": "Rod-dependent capture of basal bodies at distributed sites contributes to the peritrichous surface pattern in B. subtilis.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mbio.00530-25",
                "snippet": "rod both immobilizes basal bodies and participates in pattern formation",
                "notes": "Rod mutations increased random and polar basal-body placement, supporting a role for immobilization in the distributed B. subtilis pattern."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "flagellar_filament_number",
            "predicate": "positively influences (saturating)",
            "object": "swimming_velocity",
            "description": "Swimming velocity rises with flagellar filament number up to a critical number then saturates.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-025-56980-x",
                "notes": "Lisevich et al. 2025: swimming velocity increases with flagellar-gene expression only up to ~5 flagella, above which it saturates; functional phenotype of multiple peritrichous flagella."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-06-03T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate MORPHOLOGY trait (peritrichous flagellation); sub-variant of flagellar arrangement.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-09T15:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (surface-distributed flagella) with GO node grounding and METPO/biolink predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 4 evidence-backed generic edges (7 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:13Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002211\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-26T07:15:19Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:Q2N2M1\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-21T16:51:38Z",
        "curator": "codex",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Replaced a polar-flagellation FlhG claim and an unrelated carbon-limitation island with the taxon-scoped B. subtilis rod/peptidoglycan mechanism supported by DOI:10.1128/mbio.00530-25. Connected the filament-number branch with a weak association rather than treating flagellar count as diagnostic; the graph is now one connected component.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope peritrichous_surface_distributed_flagella=NONMECHANISTIC with scope_notes.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1003021",
    "label": "pigmentation",
    "definition": "A phenotype characterized by the color of pigments produced by a microorganism.",
    "definition_source": "DOI:10.1016/j.procbio.2013.06.006",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1016/j.procbio.2013.06.006",
        "snippet": "bacterial pigments in food, pharmaceuticals, dyeing and other aspects",
        "notes": "Supports bacterial pigments as chemically produced microbial color phenotypes."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:615",
        "taxon_label": "Serratia marcescens",
        "reference": "DOI:10.3389/fmicb.2021.793202",
        "note": "Wild-type strain SCQ1 formed red colonies through prodigiosin production, providing a direct instance of the parent pigmentation phenotype; the source contrasts this state with stable nonpigmented derivatives."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "pigmentation_biosynthetic_colorants",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "Pigmentation is an upper color phenotype spanning chemically and genetically unrelated carotenoid, melanin, phenazine, and other pathways. The graph catalogs alternatives rather than one shared mechanism.",
        "title": "Microbial pigmentation biosynthetic mechanism",
        "description": "Evidence-backed causal sketch linking microbial pigmentation to pigment biosynthesis pathways, chromophore-containing metabolites, environmental regulation, and visible colony color.",
        "nodes": [
          {
            "node_id": "pigmentation_trait",
            "label": "pigmentation",
            "node_type": "TRAIT",
            "grounding": "METPO:1003021",
            "description": "Microbial phenotype defined by pigment-derived color."
          },
          {
            "node_id": "pigment_biosynthesis",
            "label": "pigment biosynthesis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Enzymatic production of colored microbial metabolites.",
            "grounding": "GO:0046148"
          },
          {
            "node_id": "chromophore_metabolites",
            "label": "chromophore-containing metabolites",
            "node_type": "CHEMICAL",
            "description": "Colored molecules such as carotenoids, prodiginines, melanins, and phenazines."
          },
          {
            "node_id": "environmental_regulation",
            "label": "environmental regulation",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Culture and environmental conditions that alter pigment production."
          },
          {
            "node_id": "visible_colony_color",
            "label": "visible colony color",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "Absorption and reflection phenotype observed as microbial color."
          },
          {
            "node_id": "mva_pathway",
            "label": "mevalonate pathway",
            "node_type": "PATHWAY",
            "description": "Pathway producing C5 isoprenoid precursors (IPP and DMAPP) for terpenoid biosynthesis.",
            "related_records": [
              {
                "corpus": "PathwayMech",
                "identifier": "gomodel:YeastPathways_IPPSYN-PWY",
                "relation": "PATHWAY_CONTEXT",
                "basis": "PathwayMech context: mevalonate pathway in Saccharomyces cerevisiae S288C (NCBITaxon:559292). The shared mevalonate route supplies isoprenoid precursors; the yeast pathway is context for the route, not evidence for bacterial pigmentation. No exact equivalence or transfer of organism scope is asserted.",
                "source_version": "aa305727458c44ab05614901334540e2c87a9f3a"
              }
            ]
          },
          {
            "node_id": "mep_pathway",
            "label": "MEP pathway",
            "node_type": "PATHWAY",
            "description": "2-C-methyl-D-erythritol 4-phosphate pathway producing C5 isoprenoid precursors IPP and DMAPP."
          },
          {
            "node_id": "carotenoid_biosynthesis",
            "label": "carotenoid biosynthesis",
            "node_type": "PATHWAY",
            "description": "Biosynthetic pathway producing carotenoid pigments from isoprenoid precursors.",
            "grounding": "GO:0016117"
          },
          {
            "node_id": "shikimate_pathway",
            "label": "shikimate pathway",
            "node_type": "PATHWAY",
            "description": "Pathway providing aromatic precursors used in phenazine biosynthesis.",
            "grounding": "GO:0009423",
            "related_records": [
              {
                "corpus": "PathwayMech",
                "identifier": "MetaCyc:ARO-PWY",
                "relation": "PATHWAY_CONTEXT",
                "basis": "PathwayMech context: chorismate biosynthesis I in Escherichia coli (NCBITaxon:562). The linked shikimate route terminates at chorismate; it provides precursor context, not a complete phenazine or pigment pathway. No exact equivalence or transfer of organism scope is asserted.",
                "source_version": "aa305727458c44ab05614901334540e2c87a9f3a"
              }
            ]
          },
          {
            "node_id": "phenazine_biosynthesis",
            "label": "phenazine biosynthesis",
            "node_type": "PATHWAY",
            "description": "Biosynthetic pathway producing phenazine pigments such as pyocyanin."
          },
          {
            "node_id": "carotenoid_enzyme_module",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "This node combines multiple distinct carotenoid-biosynthesis enzyme families and therefore has no single exact protein-family grounding.",
            "label": "CrtE/CrtB/CrtI/CrtY carotenoid enzyme module",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Core carotenogenic proteins catalyzing beta-carotene biosynthesis.",
            "gene_symbols": [
              "crtE",
              "crtB",
              "crtI",
              "crtY"
            ]
          },
          {
            "node_id": "beta_carotene_biosynthesis",
            "label": "beta-carotene biosynthesis",
            "node_type": "PATHWAY",
            "description": "Biosynthetic route producing the carotenoid pigment beta-carotene.",
            "grounding": "GO:1901812"
          },
          {
            "node_id": "hppd_gene",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "HppD is retained as one pathway-specific contextual example; an exact semantic family term was not verified for this upper pigmentation graph.",
            "label": "hppD 4-hydroxyphenylpyruvate dioxygenase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Enzyme converting 4-hydroxyphenylpyruvate to homogentisate."
          },
          {
            "node_id": "homogentisate",
            "label": "homogentisate",
            "node_type": "CHEMICAL",
            "description": "Aromatic metabolite that auto-oxidizes and polymerizes to pyomelanin.",
            "grounding": "CHEBI:16169"
          },
          {
            "node_id": "pyomelanin",
            "label": "pyomelanin",
            "node_type": "CHEMICAL",
            "description": "Brown-black pigment formed by polymerization of homogentisate."
          },
          {
            "node_id": "hmga_gene",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "HmgA is retained as one pathway-specific contextual example; an exact semantic family term was not verified for this upper pigmentation graph.",
            "label": "hmgA homogentisate 1,2-dioxygenase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Enzyme converting homogentisate to maleylacetoacetate, preventing pyomelanin accumulation."
          }
        ],
        "edges": [
          {
            "subject": "pigment_biosynthesis",
            "predicate": "has output",
            "object": "chromophore_metabolites",
            "description": "Pigment biosynthetic pathways produce colored metabolites.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.procbio.2013.06.006",
                "snippet": "bacterial pigments and their applications",
                "notes": "Review supports bacterial pigment production as biosynthesis of colored compounds."
              }
            ],
            "predicate_id": "RO:0002234"
          },
          {
            "subject": "chromophore_metabolites",
            "predicate": "causes",
            "object": "visible_colony_color",
            "description": "Chromophore-containing metabolites cause visible microbial color.",
            "evidence": [
              {
                "reference": "DOI:10.1177/1934578X1801301240",
                "snippet": "such as melanin, carotenoids, pyocyanin, bacteriochlorophylls, violacein, prodigiosin",
                "notes": "Supports multiple chemically distinct bacterial pigments as colorants."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "environmental_regulation",
            "predicate": "modulates",
            "object": "pigment_biosynthesis",
            "description": "Growth and environmental conditions can modulate pigment biosynthesis.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fsufs.2020.00100",
                "snippet": "bacterial pigments ... production ... genetic engineering",
                "notes": "Supports pigment production as condition- and regulation-sensitive; retained as a broad regulatory edge."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "visible_colony_color",
            "predicate": "manifests as",
            "object": "pigmentation_trait",
            "description": "Visible colony color manifests the pigmentation phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.procbio.2013.06.006",
                "snippet": "focus on applications of bacterial pigments",
                "notes": "Supports pigmentation as a visible output of bacterial pigment chemistry."
              }
            ],
            "predicate_id": "METPO:2007400"
          },
          {
            "subject": "mva_pathway",
            "predicate": "provides precursor for",
            "object": "carotenoid_biosynthesis",
            "description": "The mevalonate pathway supplies C5 isoprenoid precursors (IPP/DMAPP) for carotenoid biosynthesis.",
            "evidence": [
              {
                "reference": "DOI:10.3390/microorganisms11122920",
                "notes": "GGPP originates from C5 precursors (IPP and DMAPP) via either the MVA or MEP pathways."
              }
            ]
          },
          {
            "subject": "mep_pathway",
            "predicate": "provides precursor for",
            "object": "carotenoid_biosynthesis",
            "description": "The MEP pathway supplies C5 isoprenoid precursors (IPP/DMAPP) for carotenoid biosynthesis.",
            "evidence": [
              {
                "reference": "DOI:10.3390/microorganisms11122920",
                "notes": "GGPP originates from C5 precursors (IPP and DMAPP) via either the MVA or MEP pathways."
              }
            ]
          },
          {
            "subject": "carotenoid_enzyme_module",
            "predicate": "enables",
            "object": "beta_carotene_biosynthesis",
            "description": "The CrtE/CrtB/CrtI/CrtY enzyme module enables beta-carotene biosynthesis.",
            "evidence": [
              {
                "reference": "DOI:10.3390/microorganisms11030614",
                "notes": "beta-carotene: crtE, crtY, crtI, crtB; curate as generic carotenoid module."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "beta_carotene_biosynthesis",
            "predicate": "is a",
            "object": "carotenoid_biosynthesis",
            "description": "Beta-carotene biosynthesis is a specific carotenoid biosynthetic route.",
            "evidence": [
              {
                "reference": "DOI:10.3390/microorganisms11030614",
                "notes": "Beta-carotene is a carotenoid pigment produced by carotenogenic crt genes."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "shikimate_pathway",
            "predicate": "precursor of",
            "object": "phenazine_biosynthesis",
            "description": "The shikimate pathway provides aromatic precursors for phenazine biosynthesis.",
            "evidence": [
              {
                "reference": "DOI:10.3390/microorganisms11122920",
                "notes": "Phenazine pigments (including pyocyanin) derive from the shikimate pathway."
              }
            ]
          },
          {
            "subject": "hppd_gene",
            "predicate": "produces",
            "object": "homogentisate",
            "description": "HppD converts 4-hydroxyphenylpyruvate to homogentisate in the pyomelanin pathway.",
            "evidence": [
              {
                "reference": "DOI:10.1128/spectrum.00410-24",
                "notes": "Conversion of 4-hydroxyphenylpyruvate to HGA by HppD."
              }
            ],
            "predicate_id": "METPO:2007800"
          },
          {
            "subject": "homogentisate",
            "predicate": "polymerizes to form",
            "object": "pyomelanin",
            "description": "Homogentisate auto-oxidizes and polymerizes to form the pigment pyomelanin.",
            "evidence": [
              {
                "reference": "DOI:10.1128/spectrum.00410-24",
                "notes": "HGA, excretion of HGA, spontaneous auto-oxidation and polymerization to pyomelanin."
              }
            ]
          },
          {
            "subject": "hmga_gene",
            "predicate": "prevents accumulation of",
            "object": "pyomelanin",
            "description": "HmgA converts homogentisate to maleylacetoacetate, preventing pyomelanin accumulation.",
            "evidence": [
              {
                "reference": "DOI:10.1128/spectrum.00410-24",
                "notes": "HmgA normally converts HGA to maleylacetoacetate, preventing pigment accumulation."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.942456+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-11T18:45:00-07:00",
        "curator": "codex",
        "action": "CURATED_WITH_LITERATURE",
        "changes": "Reviewed pigmentation and added DOI-backed causal graph for pigment biosynthesis, chromophore metabolites, environmental regulation, and visible colony color.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T05:49:24Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:causes\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T21:30:07Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007400\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-13T21:03:26Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002211\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-14T05:51:46Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0046148\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 8 evidence-backed generic edges (11 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:13Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d71, rdfs:subClassOf\u00d71, METPO:2000202\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:34Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 4 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0016117\u00d71, GO:0009423\u00d71, GO:1901812\u00d71, CHEBI:16169\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates (1 to has output), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T02:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES_PART2",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates onto their causal-graph counterparts (1 to produces), issue 301 part 2. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Each replacement is a 1:1 mirror of its source predicate that changes only the domain, so the claim each edge makes is unchanged and directions are unchanged. The replacements are proposed in proposals/metpo_traitmech_v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-16T02:00:00Z",
        "curator": "claude",
        "action": "NORMALISE_NODE_TYPE",
        "changes": "Under the PATHWAY-vs-BIOLOGICAL_PROCESS rule, one node_id means one thing corpus-wide (issue 356): carotenoid_biosynthesis is typed PATHWAY, phenazine_biosynthesis is typed PATHWAY. PATHWAY is a named, conventionally enumerable multi-step route; BIOLOGICAL_PROCESS is everything else. A named biosynthetic route. Most descriptions call it one outright, including BIOLOGICAL_PROCESS-typed ones ('Enzymatic pathway producing carotenoid pigments'); red_pigmented.yaml instead ENUMERATES the steps -- 'Phytoene synthase condenses two GGPP to phytoene, then desaturation/isomerization yields lycopene' -- which is the rule's own test for PATHWAY met explicitly rather than by naming. Applied AGAINST the majority, which was 5 BIOLOGICAL_PROCESS to 1 before this tranche. A named biosynthetic route; both typings say 'Biosynthetic pathway producing phenazine pigments'. The rule breaks the 1-1 tie.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope pigmentation_biosynthetic_colorants=NONMECHANISTIC with scope_notes; marked 3 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (carotenoid_enzyme_module, hppd_gene, hmga_gene); added 1 node(s) and 1 edge(s) (carotenoid_enzyme_module); removed 1 node(s) and 1 edge(s) together with their evidence (crt_carotenoid_genes).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T11:06:05Z",
        "curator": "codex",
        "action": "ADD_CANONICAL_EXAMPLES",
        "changes": "Added Serratia marcescens as a directly observed pigmentation example using wild-type SCQ1 red-colony prodigiosin evidence from DOI:10.3389/fmicb.2021.793202; verified the current species taxon and label through NCBI Taxonomy.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-05T17:46:21Z",
        "curator": "codex",
        "action": "ADD_PATHWAY_CONTEXT",
        "changes": "Added pinned PathwayMech context on reviewed causal nodes with explicit route and organism limitations; retained existing groundings and exact xrefs.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1003027",
    "label": "pink pigmented",
    "definition": "A pigmentation phenotype in which microbial colonies or cells appear pink due to accumulation of pink or rose carotenoid pigments.",
    "definition_source": "DOI:10.1080/1040841X.2025.2526423",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1003021"
    ],
    "synonyms": [
      {
        "synonym_text": "Pigment_pink",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1080/1040841X.2025.2526423",
        "snippet": "red, pink, orange, and yellow pigmentation in bacteria",
        "notes": "Supports pink bacterial pigmentation as a carotenoid-associated color phenotype."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:408",
        "taxon_label": "Methylorubrum extorquens",
        "note": "pink-pigmented facultative methylotroph",
        "reference": "PMID:29472323"
      },
      {
        "taxon_id": "NCBITaxon:125216",
        "taxon_label": "Roseomonas",
        "note": "pink-pigmented",
        "reference": "PMID:8308122"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "pink_pigmented_carotenoid_color",
        "title": "Pink pigmentation carotenoid mechanism",
        "description": "Evidence-backed causal sketch linking pink microbial pigmentation to carotenoid biosynthesis, conjugated carotenoid pigments, and visible pink color.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a broad environmental or morphological classification spanning multiple mechanisms, a measurement-like bin, or an absence/arrangement descriptor; contextual protein nodes do not receive token UniProt examples.",
        "nodes": [
          {
            "node_id": "pink_pigmented_trait",
            "label": "pink pigmented",
            "node_type": "TRAIT",
            "grounding": "METPO:1003027",
            "description": "Microbial pigmentation appearing pink."
          },
          {
            "node_id": "isoprenoid_precursors",
            "label": "isoprenoid precursors",
            "node_type": "CHEMICAL",
            "description": "Prenyl building blocks used in carotenoid biosynthesis."
          },
          {
            "node_id": "crt_enzymes",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "Crt enzymes",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Bacterial carotenoid biosynthetic enzymes."
          },
          {
            "node_id": "carotenoid_biosynthesis",
            "label": "carotenoid biosynthesis",
            "node_type": "PATHWAY",
            "description": "Enzymatic pathway producing carotenoid pigments.",
            "grounding": "GO:0016117"
          },
          {
            "node_id": "pink_carotenoids",
            "label": "pink carotenoids",
            "node_type": "CHEMICAL",
            "description": "Carotenoid pigments that produce pink or rose coloration."
          },
          {
            "node_id": "visible_pink_color",
            "label": "visible pink color",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "Observed pink colony or cell color."
          },
          {
            "node_id": "lycopene",
            "label": "lycopene",
            "node_type": "CHEMICAL",
            "description": "Central acyclic carotenoid precursor of colored downstream carotenoids.",
            "grounding": "CHEBI:15948"
          },
          {
            "node_id": "photosynthesis_gene_cluster",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "photosynthesis protein module",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Protein module encoded alongside carotenoid enzymes in phototrophs.",
            "operon": "photosynthesis gene cluster"
          },
          {
            "node_id": "ambient_oxygen",
            "label": "ambient molecular oxygen",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Environmental oxygen level regulating carotenoid biosynthetic gene expression."
          },
          {
            "node_id": "crt_operon",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "CrtI-CrtB carotenoid enzyme module",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Phytoene synthase and desaturase module for carotenoid biosynthesis.",
            "gene_symbols": [
              "crtI",
              "crtB"
            ],
            "operon": "crtI-crtB"
          }
        ],
        "edges": [
          {
            "subject": "isoprenoid_precursors",
            "predicate": "feed into",
            "object": "carotenoid_biosynthesis",
            "description": "Isoprenoid precursors provide substrate for carotenoid production.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.gene.2004.11.038",
                "snippet": "isoprenoid precursor biosynthesis",
                "notes": "Supports isoprenoid precursor biosynthesis as an upstream step in eubacterial carotenoid pathways."
              }
            ]
          },
          {
            "subject": "crt_enzymes",
            "predicate": "catalyzes",
            "object": "carotenoid_biosynthesis",
            "description": "Crt enzymes catalyze reactions in carotenoid biosynthesis.",
            "evidence": [
              {
                "reference": "DOI:10.1080/1040841X.2025.2526423",
                "snippet": "crt genes ... reactions they catalyze",
                "notes": "Supports Crt enzymes as pathway catalysts."
              }
            ],
            "predicate_id": "biolink:catalyzes"
          },
          {
            "subject": "carotenoid_biosynthesis",
            "predicate": "has output",
            "object": "pink_carotenoids",
            "description": "Carotenoid biosynthesis can produce pink bacterial pigments.",
            "evidence": [
              {
                "reference": "DOI:10.1080/1040841X.2025.2526423",
                "snippet": "pink ... pigmentation in bacteria",
                "notes": "Supports carotenoids as one source of pink bacterial pigmentation."
              }
            ],
            "predicate_id": "RO:0002234"
          },
          {
            "subject": "pink_carotenoids",
            "predicate": "causes",
            "object": "visible_pink_color",
            "description": "Pink carotenoids cause visible pink pigmentation.",
            "evidence": [
              {
                "reference": "DOI:10.1080/1040841X.2025.2526423",
                "snippet": "responsible for the red, pink, orange, and yellow pigmentation",
                "notes": "Supports the color-producing role of carotenoid pigments."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "visible_pink_color",
            "predicate": "manifests as",
            "object": "pink_pigmented_trait",
            "description": "Visible pink color manifests the pink-pigmented phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1080/1040841X.2025.2526423",
                "snippet": "pink ... pigmentation in bacteria",
                "notes": "Supports trait-level pink pigmentation from bacterial carotenoids."
              }
            ],
            "predicate_id": "METPO:2007400"
          },
          {
            "subject": "lycopene",
            "predicate": "precursor of",
            "object": "pink_carotenoids",
            "description": "Lycopene is the central precursor converted into colored downstream carotenoid pigments.",
            "evidence": [
              {
                "reference": "DOI:10.3390/biology12101346",
                "notes": "Sandmann review: lycopene is the central carotenoid intermediate from which colored carotenoid pigments are formed via crt pathway reactions."
              }
            ]
          },
          {
            "subject": "carotenoid_biosynthesis",
            "predicate": "feeds from",
            "object": "lycopene",
            "description": "Carotenoid biosynthesis proceeds through lycopene toward colored carotenoid products.",
            "evidence": [
              {
                "reference": "DOI:10.3390/biology12101346",
                "notes": "crtI/phytoene desaturase generates lycopene as a committed colored-carotenoid intermediate in the biosynthetic pathway."
              }
            ]
          },
          {
            "subject": "crt_enzymes",
            "predicate": "part of",
            "object": "photosynthesis_gene_cluster",
            "description": "crt carotenoid genes are part of photosynthesis gene clusters in phototrophic bacteria.",
            "evidence": [
              {
                "reference": "DOI:10.3390/biology12101346",
                "notes": "\"the genes of the carotenoid pathways are part of photosynthesis gene clusters\" (Sandmann 2023)."
              }
            ],
            "predicate_id": "biolink:part_of"
          },
          {
            "subject": "photosynthesis_gene_cluster",
            "predicate": "contributes to",
            "object": "visible_pink_color",
            "description": "Carotenoid genes embedded in photosynthesis gene clusters contribute to visible pigmentation.",
            "evidence": [
              {
                "reference": "DOI:10.3390/biology12101346",
                "notes": "\"The pigmentation of purple bacteria is caused by a combination of bacteriochlorophylls and carotenoids\" with crt genes in PGCs."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "ambient_oxygen",
            "predicate": "upregulates",
            "object": "crt_operon",
            "description": "Oxygen availability upregulates the carotenoid biosynthetic operon, an environmental regulator of pigment output.",
            "evidence": [
              {
                "reference": "DOI:10.3390/biology12101346",
                "notes": "\"oxygen up-regulates the crtI-crtB operon\" (Sandmann 2023), making oxygen a causal environmental regulator of pigmentation."
              }
            ]
          },
          {
            "subject": "crt_operon",
            "predicate": "catalyzes",
            "object": "carotenoid_biosynthesis",
            "description": "The crtI-crtB operon encodes enzymes carrying out carotenoid biosynthetic reactions.",
            "evidence": [
              {
                "reference": "DOI:10.3390/biology12101346",
                "notes": "crtB (phytoene synthase) and crtI (phytoene desaturase) catalyze committed steps producing colored carotenoids."
              }
            ],
            "predicate_id": "biolink:catalyzes"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.945783+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-11T19:10:00-07:00",
        "curator": "codex",
        "action": "CURATED_WITH_LITERATURE",
        "changes": "Added DOI-backed definition and causal graph for isoprenoid precursors, Crt enzymes, carotenoid biosynthesis, pink carotenoids, and visible pink color.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T05:49:24Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:catalyzes\u00d71, biolink:causes\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T21:30:07Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007400\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:41:04Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0016117\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 6 evidence-backed generic edges (4 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:13Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:part_of\u00d71, RO:0002326\u00d71, biolink:catalyzes\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:34Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:15948\u00d71, ENVO:01001495\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates (1 to has output), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-16T02:00:00Z",
        "curator": "claude",
        "action": "NORMALISE_NODE_TYPE",
        "changes": "Under the PATHWAY-vs-BIOLOGICAL_PROCESS rule, one node_id means one thing corpus-wide (issue 356): carotenoid_biosynthesis is typed PATHWAY. PATHWAY is a named, conventionally enumerable multi-step route; BIOLOGICAL_PROCESS is everything else. A named biosynthetic route. Most descriptions call it one outright, including BIOLOGICAL_PROCESS-typed ones ('Enzymatic pathway producing carotenoid pigments'); red_pigmented.yaml instead ENUMERATES the steps -- 'Phytoene synthase condenses two GGPP to phytoene, then desaturation/isomerization yields lycopene' -- which is the rule's own test for PATHWAY met explicitly rather than by naming. Applied AGAINST the majority, which was 5 BIOLOGICAL_PROCESS to 1 before this tranche.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-17T02:00:00Z",
        "curator": "claude",
        "action": "NORMALISE_NODE_SENSE",
        "changes": "One node_id per SENSE (issues 356, 384): ambient_oxygen is the chemical sense here. Already the ambient sense. Listed so a re-run still normalises the label and still retracts ENVO:01001495 if it has been re-applied \u2014 the grounder keys on (label, node_type), so an un-normalised label is what lets the retracted CURIE come back.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope pink_pigmented_carotenoid_color=NONMECHANISTIC with scope_notes; marked 3 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (crt_enzymes, photosynthesis_gene_cluster, crt_operon).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000679",
    "label": "pleomorphic shaped",
    "definition": "A cell shape characterized by variable and irregular morphology, where individual cells within a population exhibit multiple distinct shapes.",
    "definition_source": "DOI:10.1146/annurev-cellbio-101011-155745",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000666"
    ],
    "synonyms": [
      {
        "synonym_text": "S_star_dumbbell_pleomorphic",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "pleomorphic",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "pleomorphic-shaped",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "created_by": "Jed Dongjin Kim-Ozaeta",
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev-cellbio-101011-155745",
        "snippet": "cell shape is genetically determined",
        "notes": "Cell-shape review establishes pleomorphism as a phenotype of relaxed or absent cytoskeletal/wall shape control."
      },
      {
        "reference": "DOI:10.1126/science.1170701",
        "snippet": "cell-wall-deficient L-forms",
        "notes": "L-form review supports pleomorphism in wall-deficient or wall-less cells."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:2093",
        "taxon_label": "Mycoplasma",
        "note": "Cell-wall-less, pleomorphic bacteria; the textbook genus for variable cell shape.",
        "reference": "PMID:9841667"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "pleomorphic_shaped_relaxed_shape_control",
        "title": "Pleomorphic-shape relaxed shape control",
        "description": "DOI-backed graph linking loss or weakening of cytoskeletal and cell-wall shape control to multi-morphology populations.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "Pleomorphism groups multiple unrelated causes and cell states; the contextual cytoskeleton label is not one inherited protein mechanism and receives no token accession.",
        "nodes": [
          {
            "node_id": "pleomorphic_shaped_trait",
            "label": "pleomorphic shaped",
            "node_type": "TRAIT",
            "grounding": "METPO:1000679",
            "description": "Population exhibiting multiple cell shapes."
          },
          {
            "node_id": "weak_cytoskeleton",
            "label": "weak/absent shape-determining cytoskeleton",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Reduced MreB or analogous shape-determining cytoskeletal activity.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "This node explicitly combines MreB with analogous but unrelated shape systems and therefore has no exact single family grounding."
          },
          {
            "node_id": "weak_cell_wall",
            "label": "weak or absent peptidoglycan wall",
            "node_type": "CELLULAR_LOCALIZATION",
            "description": "Cell wall reduced (L-form/Mycoplasma) or compromised.",
            "grounding": "GO:0009274"
          },
          {
            "node_id": "variable_geometry",
            "label": "variable cell geometry",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Population-level variability in cell shape."
          },
          {
            "node_id": "pg_synthesis_inhibition",
            "label": "inhibition of peptidoglycan precursor synthesis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Repression or inhibition of cell-wall precursor synthesis."
          },
          {
            "node_id": "lform_wall_deficient_state",
            "label": "L-form / wall-deficient state",
            "node_type": "STATE",
            "description": "Wall-deficient cellular state with pleomorphic morphology."
          },
          {
            "node_id": "excess_membrane_synthesis",
            "label": "excess membrane synthesis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Increased membrane synthesis raising surface area-to-volume ratio."
          },
          {
            "node_id": "blebbing_scission_proliferation",
            "label": "blebbing-tubulation-scission proliferation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "FtsZ-independent proliferation of wall-deficient cells via membrane blebbing and scission."
          },
          {
            "node_id": "oxidative_stress_ros",
            "label": "oxidative stress / ROS from respiratory chain",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reactive oxygen species generated by respiratory chain causing oxidative stress."
          },
          {
            "node_id": "loss_of_cell_wall",
            "label": "loss of cell wall",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Loss of the peptidoglycan cell wall in walled bacteria."
          }
        ],
        "edges": [
          {
            "subject": "weak_cytoskeleton",
            "predicate": "relaxes",
            "object": "variable_geometry",
            "description": "Weak shape-determining cytoskeleton permits multiple geometries.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-cellbio-101011-155745",
                "snippet": "cell shape is genetically determined",
                "notes": "Supports cytoskeletal loss as a driver of multi-shape populations."
              }
            ]
          },
          {
            "subject": "weak_cell_wall",
            "predicate": "enables",
            "object": "variable_geometry",
            "description": "Reduced or absent cell wall enables membrane-driven shape variability.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.1170701",
                "snippet": "cell-wall-deficient L-forms",
                "notes": "Supports wall deficiency as a basis for L-form pleomorphism."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "variable_geometry",
            "predicate": "manifests as",
            "object": "pleomorphic_shaped_trait",
            "description": "Variable geometry across cells manifests pleomorphism.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-cellbio-101011-155745",
                "snippet": "cell shape is genetically determined",
                "notes": "Supports the trait endpoint."
              }
            ],
            "predicate_id": "METPO:2007400"
          },
          {
            "subject": "pg_synthesis_inhibition",
            "predicate": "causes transition to",
            "object": "lform_wall_deficient_state",
            "description": "Inhibition of cell-wall precursor synthesis stimulates the L-form transition.",
            "evidence": [
              {
                "reference": "DOI:10.1098/rstb.2015.0494",
                "notes": "Repression or inhibition of cell wall precursor synthesis can stimulate the L-form transition in a wide range of bacteria."
              }
            ]
          },
          {
            "subject": "lform_wall_deficient_state",
            "predicate": "manifests as",
            "object": "pleomorphic_shaped_trait",
            "description": "The wall-deficient L-form state presents as pleomorphic morphology.",
            "evidence": [
              {
                "reference": "DOI:10.1098/rstb.2015.0494",
                "notes": "Wall-deficient L-form state is characterized by pleomorphic morphology across diverse bacteria."
              }
            ],
            "predicate_id": "METPO:2007400"
          },
          {
            "subject": "excess_membrane_synthesis",
            "predicate": "drives proliferation of",
            "object": "lform_wall_deficient_state",
            "description": "Increased membrane synthesis drives proliferation of wall-free pleomorphic L-forms.",
            "evidence": [
              {
                "reference": "DOI:10.1098/rstb.2015.0494",
                "notes": "Increasing membrane synthesis promotes the unusual form of proliferation used by L-forms, involving disorganized membrane blebbing/vesiculation."
              }
            ]
          },
          {
            "subject": "excess_membrane_synthesis",
            "predicate": "enables",
            "object": "blebbing_scission_proliferation",
            "description": "Increased membrane synthesis / elevated surface area-to-volume ratio enables blebbing-scission proliferation.",
            "evidence": [
              {
                "reference": "DOI:10.1042/bst20160435",
                "notes": "Proliferation appears to require only an increased rate of membrane synthesis, producing an increased surface area-to-volume ratio."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "oxidative_stress_ros",
            "predicate": "limits or kills",
            "object": "lform_wall_deficient_state",
            "description": "ROS-driven oxidative stress constrains survival of wall-deficient cells.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.tim.2019.07.008",
                "notes": "Reactive oxygen species are formed, causing oxidative stress and ultimately killing the wall-deficient cells."
              }
            ]
          },
          {
            "subject": "loss_of_cell_wall",
            "predicate": "causes",
            "object": "pleomorphic_shaped_trait",
            "description": "Loss of the cell wall causes spherical or pleomorphic morphology in rod-shaped bacteria.",
            "evidence": [
              {
                "reference": "DOI:10.3390/bioengineering11010081",
                "notes": "Rod-shaped bacteria (e.g., E. coli, B. subtilis) exhibit spherical or pleomorphic shapes due to the lack of cell walls."
              }
            ],
            "predicate_id": "biolink:causes"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.892214+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-11T22:45:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed causal graph linking weak shape-determining cytoskeleton and reduced cell wall to pleomorphic populations.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T21:30:07Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007400\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 6 evidence-backed generic edges (6 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:13Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007400\u00d71, RO:0002327\u00d71, biolink:causes\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope pleomorphic_shaped_relaxed_shape_control=NONMECHANISTIC with scope_notes; marked 1 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (weak_cytoskeleton).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1005032",
    "label": "polar flagellation",
    "definition": "A motility phenotype in which one or more flagella are located at one or both poles of the cell.",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "SEEDED",
    "parent_traits": [
      "traitmech:000056"
    ],
    "synonyms": [
      {
        "synonym_text": "flagellum arrangement",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-11T07:49:46Z",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)"
      },
      {
        "timestamp": "2026-09-11T08:00:00Z",
        "curator": "codex",
        "action": "ENRICHED_FROM_LITERATURE",
        "changes": "Enriched the seeded METPO polar flagellation phenotype with DOI-backed flagellar-arrangement evidence after a repository-wide duplicate review covering ignored and hidden files.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-21T21:12:25Z",
        "curator": "claude",
        "action": "CURATE_CAUSAL_GRAPH",
        "changes": "Added MECHANISTIC causal_graphs entry (polar_flagellation_flhf_flhg_sketch) anchored on existing verbatim record evidence snippets.",
        "llm_assisted": true
      }
    ],
    "definition_source": "DOI:10.1093/femsre/fuv034",
    "evidence": [
      {
        "reference": "DOI:10.1093/femsre/fuv034",
        "snippet": "Bacteria differ in number and location of their flagella that appear in regular patterns at the cell surface (flagellation pattern).",
        "notes": "Schuhmacher et al. support treating the number and cellular position of flagella as a flagellation-pattern morphology class."
      },
      {
        "reference": "DOI:10.3390/biom10040533",
        "snippet": "Some bacterial species, such as the marine bacterium Vibrio alginolyticus, have a single polar flagellum that allows it to swim in liquid environments.",
        "notes": "Kojima et al. give Vibrio alginolyticus as a direct bacterial example whose flagellum is positioned at a cell pole."
      },
      {
        "reference": "DOI:10.3390/biom10040533",
        "snippet": "Two regulators, FlhF and FlhG, function antagonistically to generate only one flagellum at the cell pole.",
        "notes": "Kojima et al. connect FlhF/FlhG regulation to generation of a polar flagellum, supporting polar placement as a microbial flagellation phenotype."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:663",
        "taxon_label": "Vibrio alginolyticus",
        "note": "Kojima et al. describe V. alginolyticus as a marine bacterium with a single polar flagellum.",
        "reference": "DOI:10.3390/biom10040533"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "polar_flagellation_flhf_flhg_sketch",
        "title": "FlhF and FlhG polar flagellar placement regulation",
        "description": "Evidence-backed causal mechanism linking antagonistic FlhF GTPase and FlhG ATPase regulation and polar flagellum placement to polar flagellation.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "The taxon-matched protein examples anchor the Vibrio alginolyticus FlhF GTPase and FlhG ATPase polar-flagellum placement regulators; they are not presented as a universal mechanism for every polar-flagellated lineage.",
        "nodes": [
          {
            "node_id": "polar_flagellation_trait",
            "label": "polar flagellation",
            "node_type": "TRAIT",
            "grounding": "METPO:1005032",
            "description": "Motility morphology in which one or more flagella are positioned at one or both cell poles."
          },
          {
            "node_id": "polar_flagellation_polar_flagellum",
            "label": "bacterial-type flagellum",
            "node_type": "ORGANELLE",
            "grounding": "GO:0009288",
            "description": "Flagellar organelle positioned at the bacterial cell pole."
          },
          {
            "node_id": "polar_flagellation_flhf",
            "label": "FlhF polar flagellar placement GTPase",
            "node_type": "GENE_OR_PROTEIN",
            "grounding": "InterPro:IPR020006",
            "description": "Signal-recognition-particle-like GTPase FlhF that promotes flagellar assembly at the cell pole.",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:A0AA36UPE1",
                "protein_label": "Flagellar biosynthesis protein FlhF",
                "gene_symbol": "flhF",
                "taxon_id": "NCBITaxon:663",
                "taxon_label": "Vibrio alginolyticus",
                "entry_status": "UNREVIEWED",
                "entry_version": 12,
                "sequence_version": 1,
                "proteome_id": "UP000054316",
                "retrieved_on": "2026-10-21",
                "role": "Signal-recognition-particle-like GTPase FlhF that promotes single polar flagellum placement at the cell pole in Vibrio alginolyticus.",
                "evidence": [
                  {
                    "reference": "DOI:10.3390/biom10040533",
                    "snippet": "Two regulators, FlhF and FlhG, function antagonistically to generate only one flagellum at the cell pole.",
                    "notes": "Kojima et al. report that FlhF (UniProtKB:A0AA36UPE1) and FlhG function antagonistically to generate a single flagellum at the cell pole in Vibrio alginolyticus."
                  }
                ]
              }
            ]
          },
          {
            "node_id": "polar_flagellation_flhg",
            "label": "FlhG polar flagellar number regulator ATPase",
            "node_type": "GENE_OR_PROTEIN",
            "grounding": "InterPro:IPR033875",
            "description": "MinD/ParA-family ATPase FlhG (FleN) that antagonizes FlhF to restrict flagellar number at the cell pole.",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:Q588V8",
                "protein_label": "MinD/ParA family protein",
                "gene_symbol": "flhG",
                "taxon_id": "NCBITaxon:663",
                "taxon_label": "Vibrio alginolyticus",
                "entry_status": "UNREVIEWED",
                "entry_version": 85,
                "sequence_version": 1,
                "proteome_id": "UP000054316",
                "retrieved_on": "2026-10-21",
                "role": "MinD/ParA-family ATPase FlhG (FleN) that functions antagonistically with FlhF to restrict Vibrio alginolyticus to a single polar flagellum.",
                "evidence": [
                  {
                    "reference": "DOI:10.3390/biom10040533",
                    "snippet": "Two regulators, FlhF and FlhG, function antagonistically to generate only one flagellum at the cell pole.",
                    "notes": "Kojima et al. report that FlhG (UniProtKB:Q588V8) and FlhF function antagonistically to generate a single flagellum at the cell pole in Vibrio alginolyticus."
                  }
                ]
              }
            ]
          }
        ],
        "edges": [
          {
            "subject": "polar_flagellation_polar_flagellum",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "polar_flagellation_trait",
            "description": "Regular positioning of flagella at the cell pole defines the polar flagellation pattern.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuv034",
                "snippet": "Bacteria differ in number and location of their flagella that appear in regular patterns at the cell surface (flagellation pattern).",
                "notes": "Schuhmacher et al. define regular cell-surface flagellar number and location as the bacterial flagellation pattern."
              }
            ]
          },
          {
            "subject": "polar_flagellation_flhf",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "polar_flagellation_trait",
            "description": "FlhF promotes single polar flagellum placement at the cell pole in Vibrio alginolyticus.",
            "evidence": [
              {
                "reference": "DOI:10.3390/biom10040533",
                "snippet": "Some bacterial species, such as the marine bacterium Vibrio alginolyticus, have a single polar flagellum that allows it to swim in liquid environments.",
                "notes": "Kojima et al. describe the single polar flagellum synthesized at the cell pole in Vibrio alginolyticus."
              }
            ]
          },
          {
            "subject": "polar_flagellation_flhg",
            "predicate": "regulates",
            "predicate_id": "RO:0002211",
            "object": "polar_flagellation_flhf",
            "description": "FlhG and FlhF function antagonistically to generate a single flagellum at the cell pole.",
            "evidence": [
              {
                "reference": "DOI:10.3390/biom10040533",
                "snippet": "Two regulators, FlhF and FlhG, function antagonistically to generate only one flagellum at the cell pole.",
                "notes": "Kojima et al. report that FlhF and FlhG function antagonistically to generate a single flagellum at the cell pole."
              }
            ]
          }
        ]
      }
    ]
  },
  {
    "identifier": "traitmech:000067",
    "label": "polyhydroxyalkanoate granule",
    "definition": "An intracellular storage inclusion composed of polyhydroxyalkanoate (e.g. polyhydroxybutyrate, PHB), a carbon and energy reserve accumulated as cytoplasmic granules.",
    "definition_source": "DOI:10.1128/mr.54.4.450-472.1990",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "traitmech:000066"
    ],
    "synonyms": [
      {
        "synonym_text": "PHB granule",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1128/mr.54.4.450-472.1990"
      },
      {
        "synonym_text": "polyhydroxybutyrate inclusion",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1128/mr.54.4.450-472.1990"
      },
      {
        "synonym_text": "PHA granule",
        "synonym_type": "EXACT_SYNONYM",
        "source": "http://purl.obolibrary.org/obo/go/releases/2026-07-26/go-basic.obo"
      }
    ],
    "xrefs": [
      "GO:0070088"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1128/mr.54.4.450-472.1990",
        "notes": "Anderson & Dawes describe polyhydroxyalkanoates (chiefly PHB) as carbon/energy reserves stored as cytoplasmic granules."
      },
      {
        "reference": "DOI:10.1038/s41579-020-0413-0",
        "notes": "Greening & Lithgow include storage granules such as PHA bodies among bacterial intracellular organelles."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:106590",
        "taxon_label": "Cupriavidus necator",
        "note": "Model PHA/PHB accumulator (strain H16; formerly Ralstonia eutropha / Alcaligenes eutrophus).",
        "reference": "PMID:16964242"
      },
      {
        "taxon_id": "NCBITaxon:381666",
        "taxon_label": "Cupriavidus necator H16",
        "note": "Strain-level PhaC granule-biosynthesis exemplar.",
        "reference": "PMID:16964242"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "pha_granule_carbon_energy_storage",
        "title": "PHA granules store carbon and energy as polyhydroxyalkanoate",
        "description": "Evidence-backed causal sketch linking polyhydroxyalkanoate biosynthesis to intracellular storage granules serving as carbon and energy reserves.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "The taxon-matched protein example anchors one experimentally supported causal branch; it is not presented as a universal mechanism for every taxon or every contextual branch in this graph.",
        "nodes": [
          {
            "node_id": "pha_granule_trait",
            "label": "polyhydroxyalkanoate granule",
            "node_type": "TRAIT",
            "grounding": "traitmech:000067",
            "description": "Cytoplasmic granule composed of polyhydroxyalkanoate (e.g. PHB)."
          },
          {
            "node_id": "polyhydroxyalkanoate",
            "label": "polyhydroxyalkanoate",
            "node_type": "CHEMICAL",
            "description": "Polyester carbon/energy storage polymer (chiefly PHB)."
          },
          {
            "node_id": "carbon_energy_storage",
            "label": "carbon and energy storage",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Accumulation of carbon/energy reserves under nutrient excess."
          },
          {
            "node_id": "nutrient_limitation_high_cn",
            "label": "nutrient limitation / high C:N ratio",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "High carbon-to-nitrogen ratio and depletion of N, S, or P with excess carbon."
          },
          {
            "node_id": "pha_accumulation",
            "label": "polyhydroxyalkanoate accumulation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Intracellular accumulation of PHA/PHB polymer."
          },
          {
            "node_id": "pha_synthase_phac",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:P23608",
                "protein_label": "Polyhydroxyalkanoate synthase PhaC",
                "gene_symbol": "phaC",
                "taxon_id": "NCBITaxon:381666",
                "taxon_label": "Cupriavidus necator H16",
                "entry_status": "REVIEWED",
                "proteome_id": "UP000008210",
                "retrieved_on": "2026-10-22",
                "entry_version": 138,
                "sequence_version": 1,
                "role": "H16 PhaC polymerizes hydroxyacyl-CoA into PHA and directly supplies polymer to storage granules.",
                "evidence": [
                  {
                    "reference": "PMID:16964242",
                    "snippet": "PhaC catalyzes polyhydroxyalkanoate polymerization",
                    "notes": "The cited source supports the represented protein-to-trait branch; UniProt verifies this current strain-matched protein entry."
                  }
                ]
              }
            ],
            "label": "PHA synthase (PhaC)",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Polymerase that condenses (R)-3-hydroxyacyl-CoA into PHA/PHB polymer."
          },
          {
            "node_id": "phasin_phap",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "phasin (PhaP)",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Granule-associated protein coating and stabilizing PHB chains at the granule surface."
          },
          {
            "node_id": "phb_granule_size_number",
            "label": "PHB granule size and number",
            "node_type": "QUALITY",
            "description": "Morphological quality of granule dimensions and count per cell."
          },
          {
            "node_id": "phar_regulator",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "PhaR regulator",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Transcriptional repressor that binds phaP promoters."
          },
          {
            "node_id": "phap_transcription",
            "label": "phaP transcription",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Transcriptional production of phasin-encoding phaP RNA."
          },
          {
            "node_id": "pha_depolymerase_phaz",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "PHA depolymerase (PhaZ)",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Intracellular depolymerase cleaving PHB to 3-hydroxybutyrate."
          },
          {
            "node_id": "phb_mobilization",
            "label": "PHB mobilization",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Degradation and utilization of stored PHB as carbon/energy reserve."
          },
          {
            "node_id": "carbon_starvation",
            "label": "carbon starvation",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Starvation or exogenous carbon depletion."
          },
          {
            "node_id": "phb_degradation",
            "label": "PHB degradation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Breakdown of stored PHB polymer."
          }
        ],
        "edges": [
          {
            "subject": "polyhydroxyalkanoate",
            "predicate": "located in",
            "object": "pha_granule_trait",
            "description": "PHA polymer accumulates inside cytoplasmic granules.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mr.54.4.450-472.1990",
                "notes": "Anderson & Dawes describe PHAs (chiefly PHB) as carbon/energy reserves stored as cytoplasmic granules."
              }
            ],
            "predicate_id": "biolink:located_in"
          },
          {
            "subject": "pha_granule_trait",
            "predicate": "enables",
            "object": "carbon_energy_storage",
            "description": "PHA granules realize the carbon/energy storage function.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41579-020-0413-0",
                "notes": "Greening & Lithgow include PHA bodies among bacterial intracellular organelles."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "nutrient_limitation_high_cn",
            "predicate": "increases",
            "object": "pha_accumulation",
            "description": "High C/N ratio and N/S/P depletion stimulate PHA accumulation.",
            "evidence": [
              {
                "reference": "DOI:10.3390/molecules29102293",
                "notes": "PHA accumulation is stimulated by a high C/N ratio, depletion of N, S, and P, or a low rate of respiration."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "nutrient_limitation_high_cn",
            "predicate": "induces",
            "object": "pha_accumulation",
            "description": "Nutrient limitation with excess carbon induces PHA accumulation.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.jbc.2024.107523",
                "notes": "Environmental triggers include nutrient limitation and excess carbon that induce PHA accumulation."
              }
            ]
          },
          {
            "subject": "pha_synthase_phac",
            "predicate": "catalyzes",
            "object": "polyhydroxyalkanoate",
            "description": "PhaC polymerizes hydroxyacyl-CoA into PHA/PHB polymer.",
            "evidence": [
              {
                "reference": "DOI:10.3390/polym15143027",
                "notes": "PhbC polymerizing beta-hydroxybutyryl-CoA into PHB."
              }
            ],
            "predicate_id": "biolink:catalyzes"
          },
          {
            "subject": "phasin_phap",
            "predicate": "stabilizes",
            "object": "polyhydroxyalkanoate",
            "description": "Phasins coat and stabilize PHB chains at the granule surface.",
            "evidence": [
              {
                "reference": "DOI:10.3390/polym15143027",
                "notes": "Phasins are GAPs that coat and stabilize PHB chains."
              }
            ]
          },
          {
            "subject": "phasin_phap",
            "predicate": "controls",
            "object": "phb_granule_size_number",
            "description": "Phasins control the size and number of PHB granules.",
            "evidence": [
              {
                "reference": "DOI:10.3390/polym15143027",
                "notes": "Phasins control the size of the PHB granules."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "phar_regulator",
            "predicate": "represses transcription of",
            "object": "phap_transcription",
            "description": "PhaR binds phaP promoters and represses transcription.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.jbc.2024.107523",
                "snippet": "PhaR binds phaP promoters and represses their transcription",
                "notes": "PhaR is a transcriptional repressor that binds phaP promoters and represses their transcription."
              }
            ]
          },
          {
            "subject": "phap_transcription",
            "predicate": "produces",
            "object": "phasin_phap",
            "description": "Expression of phaP produces the phasin protein coating PHA granules.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.jbc.2024.107523",
                "snippet": "phaP encodes the granule-associated phasin PhaP",
                "notes": "The study links phaP transcriptional regulation to phasin production."
              }
            ]
          },
          {
            "subject": "pha_depolymerase_phaz",
            "predicate": "mediates",
            "object": "phb_mobilization",
            "description": "PHB depolymerase cleaves PHB to 3-hydroxybutyrate, mediating mobilization.",
            "evidence": [
              {
                "reference": "DOI:10.3390/polym15143027",
                "notes": "PHB mobilization involves a PHB depolymerase (PhbZ/PhaZ) that cleaves PHB to beta-hydroxybutyrate."
              }
            ]
          },
          {
            "subject": "carbon_starvation",
            "predicate": "triggers",
            "object": "phb_degradation",
            "description": "Starvation or exogenous carbon depletion triggers PHB degradation.",
            "evidence": [
              {
                "reference": "DOI:10.3390/polym15143027",
                "notes": "PHB is degraded during starvation/exogenous carbon depletion or stationary phase."
              }
            ]
          },
          {
            "subject": "pha_accumulation",
            "predicate": "contributes to",
            "object": "pha_granule_trait",
            "description": "Intracellular accumulation of amorphous PHA produces the polymer body represented by the granule trait.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.jbc.2024.107523",
                "snippet": "When synthetized, PHA aggregates in an amorphous state surrounded by several PHA granule-associated proteins forming the so called carbonosomes",
                "notes": "Verified against the open Europe PMC full text."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "phb_mobilization",
            "predicate": "contributes to",
            "object": "carbon_energy_storage",
            "description": "Mobilization makes stored PHA available for utilization and is part of the granule's carbon-and-energy reserve function.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.jbc.2024.107523",
                "snippet": "Phasins and PHA degrading enzymes are important for PHA storage and utilization",
                "notes": "Verified against the open Europe PMC full text; the edge covers reserve utilization rather than claiming degradation creates storage."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "phb_degradation",
            "predicate": "contributes to",
            "object": "phb_mobilization",
            "description": "Degradation of accumulated PHB contributes to reserve mobilization.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.jbc.2024.107523",
                "snippet": "reduced ppGpp alarmone levels leading to enhanced degradation of PHA suggesting that ppGpp acts as repressor of the PHA mobilization system (PhaZ1)",
                "notes": "Verified against the open Europe PMC full text; the connector links the existing starvation/degradation and PhaZ/mobilization branches."
              }
            ],
            "predicate_id": "RO:0002326"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-06-03T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate MORPHOLOGY trait (polyhydroxyalkanoate/PHB granule); storage sub-variant of intracellular inclusion.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-09T15:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (PHA granule carbon/energy storage) with RO/biolink predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 8 evidence-backed generic edges (11 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:13Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002213\u00d71, biolink:catalyzes\u00d71, RO:0002211\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "CURATE_PROTEIN_TAXON_EXAMPLE",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope pha_granule_carbon_energy_storage=MECHANISTIC with scope_notes; marked 4 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (pha_synthase_phac, phasin_phap, phar_regulator, pha_depolymerase_phaz); added taxon-paired protein example(s) UniProtKB:P23608 on pha_synthase_phac (NCBITaxon:381666); added 1 node(s) and 2 edge(s) (phap_transcription); removed 1 node(s) and 1 edge(s) together with their evidence (phap_gene); added canonical example(s) NCBITaxon:381666.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T06:15:40Z",
        "curator": "codex",
        "action": "ADD_EXACT_ONTOLOGY_MATCH",
        "changes": "Ontology exact-match review (2026-08-25): approved exact xref(s): GO:0070088; declared exact synonym(s): 'PHA granule'. Evidence is predicate-scoped in the versioned ontology snapshots; OAK cross-checked direct data, and OLS4 spot-checked release deltas and disputed hits.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T06:48:00Z",
        "curator": "codex",
        "action": "CONNECT_CAUSAL_GRAPH_COMPONENTS",
        "changes": "Resolved issue #183 graph fragmentation (4 components to 1) using 3 source- and verbatim-snippet-backed connector(s). No paid research service was called.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-22T01:35:00Z",
        "curator": "claude",
        "action": "REFRESH_UNIPROT_ENTRY_VERSION",
        "changes": "Refreshed UniProtKB entry_version against live UniProt REST on 2026-10-22: UniProtKB:P23608 (137 -> 138 on pha_synthase_phac).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000068",
    "label": "polyphosphate granule",
    "definition": "An intracellular storage inclusion of inorganic polyphosphate (a polymer of many phosphate residues), historically called a volutin or metachromatic granule, serving as a phosphate and energy reserve.",
    "definition_source": "DOI:10.1146/annurev.biochem.77.083007.093039",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "traitmech:000066"
    ],
    "synonyms": [
      {
        "synonym_text": "volutin granule",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1146/annurev.biochem.77.083007.093039"
      },
      {
        "synonym_text": "metachromatic granule",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1146/annurev.biochem.77.083007.093039"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev.biochem.77.083007.093039",
        "notes": "Rao, G\u00f3mez-Garc\u00eda & Kornberg review inorganic polyphosphate, accumulated as granules, as a phosphate/energy reserve essential for growth and survival."
      },
      {
        "reference": "DOI:10.1038/s41579-020-0413-0",
        "notes": "Greening & Lithgow include polyphosphate bodies among bacterial intracellular inclusions."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:29405",
        "taxon_label": "Microlunatus phosphovorus",
        "note": "Model polyphosphate-accumulating organism (volutin granules; enhanced biological phosphorus removal).",
        "reference": "PMID:22923697"
      },
      {
        "taxon_id": "NCBITaxon:1032480",
        "taxon_label": "Microlunatus phosphovorus NM-1",
        "note": "Strain-level polyphosphate-kinase exemplar.",
        "reference": "PMID:22923697"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "polyphosphate_granule_storage",
        "title": "Polyphosphate granules store phosphate and energy as inorganic polyP",
        "description": "Evidence-backed causal sketch linking inorganic polyphosphate accumulation to volutin/metachromatic granules supporting growth and survival.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "The taxon-matched protein example anchors one experimentally supported causal branch; it is not presented as a universal mechanism for every taxon or every contextual branch in this graph.",
        "nodes": [
          {
            "node_id": "polyp_granule_trait",
            "label": "polyphosphate granule",
            "node_type": "TRAIT",
            "grounding": "traitmech:000068",
            "description": "Cytoplasmic inclusion of inorganic polyphosphate."
          },
          {
            "node_id": "inorganic_polyphosphate",
            "label": "inorganic polyphosphate",
            "node_type": "CHEMICAL",
            "description": "Polymer of many phosphate residues stored as a granule."
          },
          {
            "node_id": "phosphate_energy_reserve",
            "label": "phosphate / energy reserve",
            "node_type": "QUALITY",
            "description": "Reservoir of phosphate and high-energy phosphoanhydride bonds."
          },
          {
            "node_id": "ppk",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:F5XF46",
                "protein_label": "Polyphosphate kinase",
                "gene_symbol": "ppk",
                "taxon_id": "NCBITaxon:1032480",
                "taxon_label": "Microlunatus phosphovorus NM-1",
                "entry_status": "UNREVIEWED",
                "proteome_id": "UP000007947",
                "retrieved_on": "2026-10-22",
                "entry_version": 70,
                "sequence_version": 1,
                "role": "The NM-1 polyphosphate kinase synthesizes the polyphosphate stored in intracellular granules.",
                "evidence": [
                  {
                    "reference": "PMID:22923697",
                    "snippet": "polyphosphate accumulation by Microlunatus phosphovorus",
                    "notes": "The cited source supports the represented protein-to-trait branch; UniProt verifies this current strain-matched protein entry."
                  }
                ]
              }
            ],
            "label": "polyphosphate kinase (PPK)",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Enzyme that synthesizes inorganic polyphosphate from ATP.",
            "grounding": "GO:0008976"
          },
          {
            "node_id": "ppx",
            "label": "exopolyphosphatase (PPX)",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Enzyme that degrades inorganic polyphosphate.",
            "grounding": "GO:0004309"
          },
          {
            "node_id": "divalent_cations",
            "label": "divalent cations",
            "node_type": "CHEMICAL",
            "description": "Divalent metal cations (Ca2+, Mg2+, Fe2+/Fe3+, Zn2+) bound by polyP."
          },
          {
            "node_id": "stress_survival",
            "label": "stress survival / stress response",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Survival during stationary phase, nutrient starvation, and stress."
          }
        ],
        "edges": [
          {
            "subject": "inorganic_polyphosphate",
            "predicate": "located in",
            "object": "polyp_granule_trait",
            "description": "Inorganic polyphosphate accumulates as granules in the cytoplasm.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev.biochem.77.083007.093039",
                "notes": "Rao, G\u00f3mez-Garc\u00eda & Kornberg review polyphosphate accumulation as granules."
              }
            ],
            "predicate_id": "biolink:located_in"
          },
          {
            "subject": "polyp_granule_trait",
            "predicate": "contributes to",
            "object": "phosphate_energy_reserve",
            "description": "PolyP granules supply phosphate and energy for growth and survival.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41579-020-0413-0",
                "notes": "Greening & Lithgow include polyphosphate bodies among bacterial intracellular inclusions."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "ppk",
            "predicate": "synthesizes",
            "object": "inorganic_polyphosphate",
            "description": "Polyphosphate kinase (PPK) synthesizes inorganic polyP using ATP.",
            "evidence": [
              {
                "reference": "DOI:10.1371/journal.pbio.3002558",
                "notes": "Polyphosphate is synthesized by polyphosphate kinase (PPK), which rapidly synthesizes polyP using ATP as a co-substrate."
              }
            ]
          },
          {
            "subject": "ppx",
            "predicate": "degrades",
            "object": "inorganic_polyphosphate",
            "description": "Exopolyphosphatase (PPX) degrades inorganic polyphosphate.",
            "evidence": [
              {
                "reference": "DOI:10.1371/journal.pbio.3002558",
                "notes": "Polyphosphate is degraded by exopolyphosphatase PPX; canonical core metabolism edge."
              }
            ],
            "predicate_id": "METPO:2007809"
          },
          {
            "subject": "inorganic_polyphosphate",
            "predicate": "binds",
            "object": "divalent_cations",
            "description": "PolyP chelates/binds divalent cations, affecting polyP biophysics and granule composition.",
            "evidence": [
              {
                "reference": "DOI:10.3390/biom14080937",
                "notes": "PolyP granules contain associated cations; polyP can bind iron and inhibit Fenton chemistry. Strong general biochemical edge."
              }
            ]
          },
          {
            "subject": "inorganic_polyphosphate",
            "predicate": "promotes",
            "object": "stress_survival",
            "description": "PolyP accumulation promotes survival in stationary phase and nutrient starvation.",
            "evidence": [
              {
                "reference": "DOI:10.3390/biom14080937",
                "notes": "PolyP serves as phosphate/energy storage and supports survival in stationary phase and nutrient starvation; ppk mutants show stress sensitivity."
              }
            ],
            "predicate_id": "RO:0002213"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-06-03T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate MORPHOLOGY trait (polyphosphate/volutin granule); storage sub-variant of intracellular inclusion.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-09T15:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (polyP granule phosphate/energy reserve) with RO/biolink predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 4 evidence-backed generic edges (4 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:13Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002213\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:39Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000007\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:23:55Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0008976\u00d71, GO:0004309\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T02:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES_PART2",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates onto their causal-graph counterparts (1 to degrades), issue 301 part 2. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Each replacement is a 1:1 mirror of its source predicate that changes only the domain, so the claim each edge makes is unchanged and directions are unchanged. The replacements are proposed in proposals/metpo_traitmech_v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "CURATE_PROTEIN_TAXON_EXAMPLE",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope polyphosphate_granule_storage=MECHANISTIC with scope_notes; added taxon-paired protein example(s) UniProtKB:F5XF46 on ppk (NCBITaxon:1032480); added canonical example(s) NCBITaxon:1032480.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-22T01:35:00Z",
        "curator": "claude",
        "action": "REFRESH_UNIPROT_ENTRY_VERSION",
        "changes": "Refreshed UniProtKB entry_version against live UniProt REST on 2026-10-22: UniProtKB:F5XF46 (69 -> 70 on ppk).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1007006",
    "label": "polytrichous flagellation",
    "definition": "A flagellar arrangement in which multiple flagella (typically a tuft) are present per cell, often combined with polar attachment.",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "SEEDED",
    "parent_traits": [
      "traitmech:000056"
    ],
    "synonyms": [
      {
        "synonym_text": "polytrichous",
        "synonym_type": "EXACT_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "created_by": "Marcin Joachimiak",
    "curation_history": [
      {
        "timestamp": "2026-09-11T08:45:09Z",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)"
      },
      {
        "timestamp": "2026-09-11T08:46:00Z",
        "curator": "codex",
        "action": "ENRICHED_FROM_LITERATURE",
        "changes": "Enriched the seeded METPO polytrichous flagellation phenotype with DOI-backed polytrichous-flagella evidence after a repository-wide duplicate review covering ignored and hidden files.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-21T21:12:25Z",
        "curator": "claude",
        "action": "CURATE_CAUSAL_GRAPH",
        "changes": "Added NONMECHANISTIC causal_graphs entry (polytrichous_flagellation_tuft_sketch) anchored on existing verbatim record evidence snippets.",
        "llm_assisted": true
      }
    ],
    "definition_source": "DOI:10.1128/AEM.64.10.3576-3583.1998",
    "evidence": [
      {
        "reference": "DOI:10.1128/AEM.64.10.3576-3583.1998",
        "snippet": "In transmission electron micrographs, isolate OC 1/4 exhibited monopolar polytrichous flagellation, with up to three flagella per cell (Fig. 4).",
        "notes": "Huber et al. directly observed multiple flagella at one pole of Thermocrinis ruber OC 1/4."
      },
      {
        "reference": "DOI:10.1128/AEM.68.12.6310-6320.2002",
        "snippet": "The cells have bipolar polytrichous flagella and exhibit a unique swimming pattern, rotating and translating along their short axis.",
        "notes": "Thar and Kuhl describe a second bacterial polytrichous arrangement, with flagella present at both cell poles."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:75906",
        "taxon_label": "Thermocrinis ruber",
        "note": "Huber et al. directly observed up to three monopolar flagella per cell in the Thermocrinis ruber isolate OC 1/4.",
        "reference": "DOI:10.1128/AEM.64.10.3576-3583.1998"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "polytrichous_flagellation_tuft_sketch",
        "title": "Polytrichous multi-flagellar tuft arrangement and swimming motility",
        "description": "Evidence-backed morphology sketch linking monopolar or bipolar multi-flagellar tufts to polytrichous flagellation and swimming locomotion.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "Morphological arrangement sketch backed by DOI:10.1128/AEM.64.10.3576-3583.1998 and DOI:10.1128/AEM.68.12.6310-6320.2002; specific flagellar structural or placement proteins in Thermocrinis ruber are not identified in the cited electron-microscopy and motility sources.",
        "nodes": [
          {
            "node_id": "polytrichous_flagellation_trait",
            "label": "polytrichous flagellation",
            "node_type": "TRAIT",
            "grounding": "METPO:1007006",
            "description": "Flagellar arrangement in which multiple flagella (a tuft) are present per cell."
          },
          {
            "node_id": "polytrichous_flagellation_flagellar_tuft",
            "label": "bacterial-type flagellum",
            "node_type": "ORGANELLE",
            "grounding": "GO:0009288",
            "description": "Monopolar or bipolar tuft of multiple bacterial flagella per cell."
          },
          {
            "node_id": "polytrichous_flagellation_swimming_motility",
            "label": "locomotion",
            "node_type": "BIOLOGICAL_PROCESS",
            "grounding": "GO:0040011",
            "description": "Swimming pattern driven by polytrichous flagellar tufts."
          }
        ],
        "edges": [
          {
            "subject": "polytrichous_flagellation_flagellar_tuft",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "polytrichous_flagellation_trait",
            "description": "Presence of multiple polar flagella per cell confers the polytrichous flagellation phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.64.10.3576-3583.1998",
                "snippet": "In transmission electron micrographs, isolate OC 1/4 exhibited monopolar polytrichous flagellation, with up to three flagella per cell (Fig. 4).",
                "notes": "Huber et al. directly observe monopolar polytrichous flagellation with up to three flagella per cell in Thermocrinis ruber OC 1/4."
              }
            ]
          },
          {
            "subject": "polytrichous_flagellation_flagellar_tuft",
            "predicate": "enables",
            "predicate_id": "RO:0002327",
            "object": "polytrichous_flagellation_swimming_motility",
            "description": "Bipolar polytrichous flagella enable rotational and translational swimming locomotion.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.68.12.6310-6320.2002",
                "snippet": "The cells have bipolar polytrichous flagella and exhibit a unique swimming pattern, rotating and translating along their short axis.",
                "notes": "Thar and Kuhl connect bipolar polytrichous flagella to a distinct swimming pattern."
              }
            ]
          }
        ]
      }
    ]
  },
  {
    "identifier": "traitmech:000065",
    "label": "prosthecate",
    "definition": "A morphology trait in which the cell bears one or more prosthecae \u2014 tubular extensions of the cell envelope (stalks) \u2014 that increase nutrient-uptake surface area or mediate attachment, as in Caulobacter.",
    "definition_source": "DOI:10.1111/j.1365-2958.2007.05633.x",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "synonyms": [
      {
        "synonym_text": "stalked",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1111/j.1365-2958.2007.05633.x"
      },
      {
        "synonym_text": "prostheca",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1128/MMBR.00040-09"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1111/j.1365-2958.2007.05633.x",
        "notes": "Wagner & Brun describe the Caulobacter stalk (prostheca) as a cell-envelope extension and a specialized form of cell elongation aiding nutrient uptake."
      },
      {
        "reference": "DOI:10.1128/MMBR.00040-09",
        "notes": "Curtis & Brun's review of Caulobacter development supports the stalk as a regulated developmental appendage."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:155892",
        "taxon_label": "Caulobacter vibrioides",
        "note": "Model stalked (prosthecate) bacterium and asymmetric-division paradigm; classic strain CB15, long called Caulobacter crescentus.",
        "reference": "PMID:16980487"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "prosthecate_stalk_nutrient_uptake",
        "title": "Prostheca / stalk extends nutrient-uptake surface",
        "description": "Evidence-backed causal sketch linking developmental stalk extension to increased uptake surface area and substrate attachment.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a broad environmental or morphological classification spanning multiple mechanisms, a measurement-like bin, or an absence/arrangement descriptor; contextual protein nodes do not receive token UniProt examples.",
        "nodes": [
          {
            "node_id": "prosthecate_trait",
            "label": "prosthecate",
            "node_type": "TRAIT",
            "grounding": "traitmech:000065",
            "description": "Possession of one or more cell-envelope-extension stalks (prosthecae)."
          },
          {
            "node_id": "stalk_extension",
            "label": "stalk extension",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Polar extension of cell envelope producing the prostheca."
          },
          {
            "node_id": "uptake_surface_area",
            "label": "nutrient-uptake surface area",
            "node_type": "QUALITY",
            "description": "Effective transport surface available for nutrient uptake."
          },
          {
            "node_id": "mreb",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "MreB",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Bacterial actin homolog cytoskeletal protein."
          },
          {
            "node_id": "roda",
            "label": "RodA",
            "node_type": "GENE_OR_PROTEIN",
            "description": "SEDS family cell-wall synthesis protein.",
            "grounding": "InterPro:IPR001182"
          },
          {
            "node_id": "bactofilins",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "bactofilins",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Cytoskeletal proteins that localize to zones of active cell wall growth."
          },
          {
            "node_id": "cell_wall_growth_zone",
            "label": "zone of active cell wall growth",
            "node_type": "CELLULAR_LOCALIZATION",
            "description": "Subcellular site of active peptidoglycan synthesis."
          },
          {
            "node_id": "stalk_crossbands",
            "label": "stalk crossbands",
            "node_type": "CELLULAR_LOCALIZATION",
            "description": "Periodic protein bands traversing the stalk lumen."
          },
          {
            "node_id": "stpabcd_complex",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "StpABCD complex",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Four-protein complex (StpA, StpB, StpC, StpD) forming stalk crossbands."
          },
          {
            "node_id": "stalk_diffusion",
            "label": "diffusion along stalk",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Molecular diffusion along the length of the stalk lumen."
          }
        ],
        "edges": [
          {
            "subject": "stalk_extension",
            "predicate": "confers",
            "object": "prosthecate_trait",
            "description": "Regulated stalk-extension elongation realizes the prosthecate phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1128/MMBR.00040-09",
                "notes": "Curtis & Brun review the Caulobacter stalk as a regulated developmental appendage."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "prosthecate_trait",
            "predicate": "contributes to",
            "object": "uptake_surface_area",
            "description": "Stalks expand nutrient-uptake surface area, aiding oligotrophic growth.",
            "evidence": [
              {
                "reference": "DOI:10.1111/j.1365-2958.2007.05633.x",
                "notes": "Wagner & Brun describe the Caulobacter stalk as a cell-envelope extension increasing nutrient-uptake surface area."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "mreb",
            "predicate": "is required for",
            "object": "stalk_extension",
            "description": "MreB is necessary for stalk formation; depletion causes a stalk elongation defect.",
            "evidence": [
              {
                "reference": "DOI:10.1128/jb.00384-22",
                "notes": "Barrows & Goley: MreB and RodA are necessary for stalk formation, as depletion of either protein results in a stalk elongation defect."
              }
            ]
          },
          {
            "subject": "roda",
            "predicate": "is required for",
            "object": "stalk_extension",
            "description": "RodA is necessary for stalk formation; depletion causes a stalk elongation defect.",
            "evidence": [
              {
                "reference": "DOI:10.1128/jb.00384-22",
                "notes": "Barrows & Goley: depletion of either protein (MreB or RodA) results in a stalk elongation defect."
              }
            ]
          },
          {
            "subject": "bactofilins",
            "predicate": "localizes to",
            "object": "cell_wall_growth_zone",
            "description": "Many bactofilins localize to zones of active cell wall growth, supporting stalk biogenesis.",
            "evidence": [
              {
                "reference": "DOI:10.1371/journal.pgen.1010788",
                "notes": "Richter et al.: many bactofilins localize to zones of active cell wall growth."
              }
            ],
            "predicate_id": "biolink:located_in"
          },
          {
            "subject": "stpabcd_complex",
            "predicate": "composes",
            "object": "stalk_crossbands",
            "description": "The four-protein StpABCD complex composes the stalk crossbands.",
            "evidence": [
              {
                "reference": "DOI:10.1128/jb.00384-22",
                "notes": "Barrows & Goley: crossbands are composed of a complex of four proteins, StpABCD."
              }
            ]
          },
          {
            "subject": "stalk_crossbands",
            "predicate": "limits",
            "object": "stalk_diffusion",
            "description": "Crossbands limit diffusion along the length of the stalk, compartmentalizing it.",
            "evidence": [
              {
                "reference": "DOI:10.1128/jb.00384-22",
                "notes": "Barrows & Goley: crossbands that limit diffusion along the length of the stalk."
              }
            ],
            "predicate_id": "RO:0002212"
          },
          {
            "subject": "prosthecate_trait",
            "predicate": "facilitates",
            "object": "uptake_surface_area",
            "description": "Prosthecae/stalks facilitate nutrient uptake.",
            "evidence": [
              {
                "reference": "DOI:10.1371/journal.pgen.1010788",
                "notes": "Richter et al.: prosthecae/stalks facilitate nutrient uptake."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-06-03T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate MORPHOLOGY trait (prosthecate / stalked) from literature research to fill the cellular-appendage gap.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-09T15:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (stalk extension / nutrient-uptake surface) with RO predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 6 evidence-backed generic edges (7 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:13Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:located_in\u00d71, RO:0002212\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:19Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A1B1UYY2\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-26T07:15:19Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A0H2X1V4\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:21:12Z",
        "curator": "claude",
        "action": "RETRACT_DEAD_UNIPROT_GROUNDINGS",
        "changes": "Retracted 1 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 1 causal edge(s) off enables/RO:0002327 with a TRAIT object (1 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-22T04:26:15Z",
        "curator": "codex",
        "action": "REVIEW_UNIPROT_INSTANCE_GROUNDINGS",
        "changes": "Reviewed 1 organism-specific UniProtKB grounding(s): replaced 1 with taxon-agnostic GO/InterPro terms and retracted 0 to label-only where no exact semantic term was supported (docs/GROUNDING_POLICY.md).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope prosthecate_stalk_nutrient_uptake=NONMECHANISTIC with scope_notes; marked 3 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (mreb, bactofilins, stpabcd_complex).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000653",
    "label": "pseudohyphal growth",
    "definition": "A morphological phenotype in which elongated budding yeast cells remain attached in chains with constrictions at the junctions between cells.",
    "definition_source": "DOI:10.1590/S1517-83822013005000056",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1590/S1517-83822013005000056",
        "snippet": "pseudohyphae formed branched chains of elongated blastoconidial cells retaining constrictions at the septal junctions",
        "notes": "Staniszewska et al. (2013), PMID:24516422, PMC3910194, Results subsection Pseudohyphae. Full-text XML, strain/culture Methods, Table 1 and actual Figure 4 were inspected. Clinical isolate 82 forms pseudohyphae mixed with true hyphae after six hours in serum; later hyphal predominance is not a contradictory same-time observation. The quote is from Results, not the abstract. Numerical morphology indices and serum induction conditions are study-specific, not universal trait thresholds."
      },
      {
        "reference": "DOI:10.1016/0092-8674(92)90079-r",
        "snippet": "Cells become long and thin and form pseudohyphae that grow away from the colony and invade the agar medium.",
        "notes": "Gimeno et al. (1992), PMID:1547504, scientific abstract directly retrieved through Europe PMC. Diploid Saccharomyces cerevisiae under nitrogen starvation changes morphology and budding pattern. The abstract also reports RAS2, SHR3 and RSR1/BUD1 perturbations. Full text and figures were not verified. Diploidy, nitrogen starvation and agar invasion describe this study, not necessary conditions for every pseudohyphal yeast."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:5476",
        "taxon_label": "Candida albicans",
        "reference": "DOI:10.1590/S1517-83822013005000056",
        "note": "Wild-type clinical bloodstream isolate 82, cultured in undiluted human serum for six hours at 37 C. Results and Figure 4A,C show pseudohyphae in a mixed population, not every cell or culture stage. Table 1 and Methods identify its clinical origin separately from the engineered comparison strains. This is an in-vitro morphology observation, not proof of pseudohyphae in the patient's bloodstream. NCBI Taxonomy resolves the species identifier and label."
      }
    ],
    "discussions": [
      {
        "discussion_id": "pseudohyphal-growth-scope-and-hierarchy",
        "prompt": "Review a yeast growth-form parent and exact external mappings.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Retain phenotype METPO:1000059. Mycelial growth traitmech:000074 is explicitly bacterial. Filament shaped METPO:1000674 has a broad hypha-like description but is classified under individual cell shape METPO:1000666; this record denotes attached budding-cell chains, not merely an elongated cell. Colony morphology METPO:1007062 concerns macroscopic colonies, not this microscopic growth form. Obsolete cell arrangement METPO:1000046 is not an active parent. Do not equate pseudohyphae with uninterrupted true hyphae, disordered aggregation, or every filamentous form. No exact synonym or xref is asserted. Different forms may coexist in one culture; this is not organism-level disjointness.",
        "posed_by": "codex",
        "posed_date": "2026-10-06"
      },
      {
        "discussion_id": "pseudohyphal-growth-mechanism-scope",
        "prompt": "Resolve organism-specific morphogenesis mechanisms before graphing.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "A causal graph is deferred pending full perturbation and protein-accession review, not because mechanisms are unknown. Do not transfer the 1992 budding-pattern or ploidy constraints to all yeasts, or treat the Candida comparison mutants as natural canonical examples. Gene possession alone does not establish pseudohyphal growth. Serum exposure, branching, agar invasion, numerical aspect-ratio cutoffs and virulence are not universal requirements. The 2013 study's bloodstream pathogenesis discussion does not directly demonstrate a pseudohypha-specific virulence mechanism. Additional Saccharomyces examples need direct strain-provenance review.",
        "posed_by": "codex",
        "posed_date": "2026-10-06"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-06T23:54:28Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added pseudohyphal growth with two DOI-backed snippets, a condition-qualified clinical-isolate example, and explicit growth-form and mechanism limits. Ignored-and-hidden novelty searches and structured METPO review found no exact record. Reserved METPO:1060600 in v529; existing records unchanged.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1003028",
    "label": "red pigmented",
    "definition": "A pigmentation phenotype in which microbial colonies or cells appear red due to production of red pigments such as prodiginines or carotenoids.",
    "definition_source": "DOI:10.1038/nrmicro1531",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1003021"
    ],
    "synonyms": [
      {
        "synonym_text": "Pigment_red",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/nrmicro1531",
        "snippet": "red-pigmented prodiginines",
        "notes": "Supports red microbial pigmentation as a prodiginine-associated color phenotype in representative bacteria."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:615",
        "taxon_label": "Serratia marcescens",
        "note": "Classic red-pigmented bacterium (prodigiosin); historical model for bacterial pigmentation.",
        "reference": "PMID:18805986"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "red_pigmented_prodiginine_pathway",
        "title": "Red pigmentation prodiginine mechanism",
        "description": "Evidence-backed causal sketch linking red microbial pigmentation to prodiginine biosynthesis, PigC/RedH condensation, prodigiosin accumulation, and visible red color.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a broad environmental or morphological classification spanning multiple mechanisms, a measurement-like bin, or an absence/arrangement descriptor; contextual protein nodes do not receive token UniProt examples.",
        "nodes": [
          {
            "node_id": "red_pigmented_trait",
            "label": "red pigmented",
            "node_type": "TRAIT",
            "grounding": "METPO:1003028",
            "description": "Microbial pigmentation appearing red."
          },
          {
            "node_id": "prodiginine_biosynthesis",
            "label": "prodiginine biosynthesis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Bifurcated biosynthetic pathway yielding prodiginine pigments."
          },
          {
            "node_id": "pigC_redH_condensation",
            "label": "PigC/RedH condensation",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "Condensation reaction forming prodigiosin or related prodiginines."
          },
          {
            "node_id": "prodigiosin",
            "label": "prodigiosin",
            "node_type": "CHEMICAL",
            "description": "Red tripyrrole pigment produced by some bacteria.",
            "grounding": "CHEBI:82758"
          },
          {
            "node_id": "visible_red_color",
            "label": "visible red color",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "Observed red color produced by pigment absorption spectra."
          },
          {
            "node_id": "pig_red_gene_cluster",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "Pig/Red prodiginine-biosynthesis protein module",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Variable gene cluster (Pig in Serratia, Red in Streptomyces) encoding prodiginine biosynthesis.",
            "operon": "Pig/Red biosynthetic gene cluster"
          },
          {
            "node_id": "pigC_ligase",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "PigC ligase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Key condensing enzyme/ligase encoded by pigC that links MAP and MBC to form prodigiosin."
          },
          {
            "node_id": "cpxA_cpxR_system",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "CpxA/CpxR two-component system",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Sensor histidine kinase/response regulator system whose activation represses pig gene cluster transcription."
          },
          {
            "node_id": "carotenoid_biosynthesis",
            "label": "carotenoid biosynthesis (phytoene synthase pathway)",
            "node_type": "PATHWAY",
            "description": "Phytoene synthase condenses two GGPP to phytoene, then desaturation/isomerization yields lycopene."
          },
          {
            "node_id": "lycopene",
            "label": "lycopene",
            "node_type": "CHEMICAL",
            "description": "Red-colored carotenoid pigment produced via the phytoene synthase pathway.",
            "grounding": "CHEBI:15948"
          }
        ],
        "edges": [
          {
            "subject": "prodiginine_biosynthesis",
            "predicate": "includes",
            "object": "pigC_redH_condensation",
            "description": "Prodiginine biosynthesis culminates in PigC/RedH-catalyzed condensation.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro1531",
                "snippet": "culminating in the PigC/RedH catalysed condensation",
                "notes": "Supports PigC/RedH condensation as a key step in prodiginine biosynthesis."
              }
            ],
            "predicate_id": "biolink:has_part"
          },
          {
            "subject": "pigC_redH_condensation",
            "predicate": "has output",
            "object": "prodigiosin",
            "description": "PigC/RedH condensation produces prodigiosin or related prodiginines.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro1531",
                "snippet": "to form prodigiosin",
                "notes": "Supports prodigiosin as a pathway product."
              }
            ],
            "predicate_id": "RO:0002234"
          },
          {
            "subject": "prodigiosin",
            "predicate": "causes",
            "object": "visible_red_color",
            "description": "Prodigiosin causes red colony pigmentation in representative bacteria.",
            "evidence": [
              {
                "reference": "DOI:10.1021/acs.chemrev.6b00024",
                "snippet": "bright red pigment prodigiosin",
                "notes": "Supports prodigiosin as a red pigment."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "visible_red_color",
            "predicate": "manifests as",
            "object": "red_pigmented_trait",
            "description": "Visible red color manifests the red-pigmented phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro1531",
                "snippet": "red-pigmented prodiginines",
                "notes": "Supports trait-level red pigmentation from prodiginines."
              }
            ],
            "predicate_id": "METPO:2007400"
          },
          {
            "subject": "pig_red_gene_cluster",
            "predicate": "confers",
            "object": "red_pigmented_trait",
            "description": "Prodiginine biosynthetic gene clusters (Pig/Red) encode the pathway producing red tripyrrole pigments, enabling the red-pigmented phenotype across taxa.",
            "evidence": [
              {
                "reference": "DOI:10.3390/microorganisms11122920",
                "notes": "Prodiginines are red tripyrrole pigments genetically encoded by variable gene clusters (Pig in Serratia, Red in Streptomyces); broad cross-taxon mechanism."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "pig_red_gene_cluster",
            "predicate": "has part",
            "object": "pigC_ligase",
            "description": "The pig gene cluster encodes the PigC ligase that catalyzes the final condensation step.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2024.1412776",
                "notes": "The ligase encoded by pigC is the key enzyme that links MAP and MBC."
              }
            ]
          },
          {
            "subject": "pigC_ligase",
            "predicate": "catalyzes",
            "object": "pigC_redH_condensation",
            "description": "PigC ligase catalyzes the condensation of MAP and MBC that forms prodigiosin.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2024.1412776",
                "notes": "The ligase encoded by pigC is the key enzyme that links MAP and MBC to form prodigiosin."
              }
            ],
            "predicate_id": "biolink:catalyzes"
          },
          {
            "subject": "cpxA_cpxR_system",
            "predicate": "represses transcription of",
            "object": "pig_red_gene_cluster",
            "description": "Activation of the CpxA/CpxR system triggers a phosphorylation cascade that inhibits transcription of pig gene clusters, reducing prodigiosin and red pigmentation.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2024.1412776",
                "notes": "Activated CpxA triggers a phosphorylation cascade that inhibits transcription of pig gene clusters and reduces PG production."
              }
            ]
          },
          {
            "subject": "carotenoid_biosynthesis",
            "predicate": "has output",
            "object": "lycopene",
            "description": "Phytoene synthase condenses two GGPP to phytoene, then desaturation/isomerization yields the red pigment lycopene.",
            "evidence": [
              {
                "reference": "DOI:10.3390/microorganisms11122920",
                "notes": "Two GGPP molecules condensed by phytoene synthase form phytoene, ultimately yielding lycopene, a red-colored pigment."
              }
            ],
            "predicate_id": "RO:0002234"
          },
          {
            "subject": "lycopene",
            "predicate": "causes",
            "object": "visible_red_color",
            "description": "Lycopene is a red-colored carotenoid pigment that confers red color, providing a carotenoid route to red pigmentation.",
            "evidence": [
              {
                "reference": "DOI:10.3390/microorganisms11122920",
                "notes": "Lycopene described explicitly as 'a red-colored pigment'."
              }
            ],
            "predicate_id": "biolink:causes"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.946258+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-11T18:45:00-07:00",
        "curator": "codex",
        "action": "CURATED_WITH_LITERATURE",
        "changes": "Added DOI-backed definition and causal graph for prodiginine biosynthesis, PigC/RedH condensation, prodigiosin, and visible red color.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T05:49:24Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:causes\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T21:30:07Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007400\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-13T21:03:26Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:has_part\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-14T05:51:46Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:82758\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 6 evidence-backed generic edges (5 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:13Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 4 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d71, biolink:catalyzes\u00d71, METPO:2000202\u00d71, biolink:causes\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:34Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:15948\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 1 causal edge(s) off enables/RO:0002327 with a TRAIT object (1 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 2 causal edge(s) off microbe-domain METPO predicates (2 to has output), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-16T02:00:00Z",
        "curator": "claude",
        "action": "NORMALISE_NODE_TYPE",
        "changes": "Under the PATHWAY-vs-BIOLOGICAL_PROCESS rule, one node_id means one thing corpus-wide (issue 356): carotenoid_biosynthesis is typed PATHWAY. PATHWAY is a named, conventionally enumerable multi-step route; BIOLOGICAL_PROCESS is everything else. A named biosynthetic route. Most descriptions call it one outright, including BIOLOGICAL_PROCESS-typed ones ('Enzymatic pathway producing carotenoid pigments'); red_pigmented.yaml instead ENUMERATES the steps -- 'Phytoene synthase condenses two GGPP to phytoene, then desaturation/isomerization yields lycopene' -- which is the rule's own test for PATHWAY met explicitly rather than by naming. Applied AGAINST the majority, which was 5 BIOLOGICAL_PROCESS to 1 before this tranche.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope red_pigmented_prodiginine_pathway=NONMECHANISTIC with scope_notes; marked 3 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (pig_red_gene_cluster, pigC_ligase, cpxA_cpxR_system).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000680",
    "label": "ring shaped",
    "definition": "A cell shape in which an organism forms circular or toroidal structures.",
    "definition_source": "DOI:10.1146/annurev-cellbio-101011-155745",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000666"
    ],
    "synonyms": [
      {
        "synonym_text": "ring",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "ring-shaped",
        "synonym_type": "EXACT_SYNONYM",
        "source": "http://purl.obolibrary.org/obo/pato/releases/2025-05-14/pato.obo"
      },
      {
        "synonym_text": "annular",
        "synonym_type": "EXACT_SYNONYM",
        "source": "http://purl.obolibrary.org/obo/pato/releases/2025-05-14/pato.obo"
      }
    ],
    "xrefs": [
      "PATO:0002539"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev-cellbio-101011-155745",
        "snippet": "cell curvature",
        "notes": "Cell-shape review supports curvature-generating wall patterning as the basis for closed-ring morphology."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1067",
        "taxon_label": "Rhodocyclus purpureus",
        "note": "Type species described from pure culture with individual half-ring-shaped and ring-shaped cells before division.",
        "reference": "DOI:10.1099/00207713-28-2-283"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "ring_shaped_curved_growth_closure",
        "title": "Ring-shape curved growth and pole closure",
        "description": "DOI-backed graph linking strongly curved peptidoglycan growth and pole-to-pole closure to toroidal ring morphology.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a ring-shape classification. Its contextual protein modules come from several taxa and support curvature or wall organization, not the proposed pole-to-pole closure into a ring; no token protein example is assigned.",
        "nodes": [
          {
            "node_id": "ring_shaped_trait",
            "label": "ring shaped",
            "node_type": "TRAIT",
            "grounding": "METPO:1000680",
            "description": "Closed circular or toroidal cell geometry."
          },
          {
            "node_id": "curved_pg_growth",
            "label": "strongly curved peptidoglycan growth",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Asymmetric lateral wall synthesis producing high cell curvature."
          },
          {
            "node_id": "pole_to_pole_closure",
            "label": "pole-to-pole closure",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Connection or near-contact of the two cell poles producing a ring."
          },
          {
            "node_id": "toroidal_geometry",
            "label": "toroidal geometry",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Closed ring-like cell-body geometry."
          },
          {
            "node_id": "mreb_filaments",
            "label": "MreB filaments",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Actin-like cytoskeletal filaments guiding cell-wall synthesis.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "The node is a cross-taxon MreB-filament aggregate and no exact family term was verified for this contextual use."
          },
          {
            "node_id": "cell_wall_growth_rate",
            "label": "rate of cell wall growth",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Rate of peptidoglycan cell-wall synthesis during growth."
          },
          {
            "node_id": "pg_insertion_perpendicular",
            "label": "peptidoglycan insertion perpendicular to long axis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Circumferential peptidoglycan insertion oriented perpendicular to the cell long axis."
          },
          {
            "node_id": "bactofilin_polymers",
            "label": "bactofilin polymers",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Cytoskeletal bactofilin polymers that localize to sites of wall remodeling.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "The node spans multiple bactofilin paralogues and taxa and is therefore retained as a reviewed aggregate label."
          },
          {
            "node_id": "cell_wall_biosynthesis",
            "label": "cell wall biosynthesis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Spatially regulated synthesis of the peptidoglycan cell wall."
          },
          {
            "node_id": "bactofilin_lmdc_module",
            "label": "bactofilin-M23 peptidase module",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Conserved bactofilin and M23 peptidase functional module remodeling the wall locally.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "This is a multi-protein bactofilin/M23 module, not one protein family or accession."
          },
          {
            "node_id": "wall_biosynthesis_mode_change",
            "label": "local change in cell wall biosynthesis mode",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Local shift in the mode of cell-wall synthesis producing shape changes."
          },
          {
            "node_id": "crva_polymer",
            "label": "CrvA polymer",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Periplasmic CrvA polymer that skews peptidoglycan synthesis to generate curvature.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Retained label-only because an exact semantic CrvA family term was not verified in this review."
          },
          {
            "node_id": "pg_synthesis_rate_skew",
            "label": "skewed peptidoglycan synthesis rates",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Asymmetric peptidoglycan synthesis rates across the cell body."
          },
          {
            "node_id": "crescentin",
            "label": "crescentin",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Intermediate filament-like protein promoting cell curvature.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Retained label-only because an exact semantic crescentin family term was not verified in this review."
          },
          {
            "node_id": "cell_curvature",
            "label": "cell curvature",
            "node_type": "QUALITY",
            "description": "Degree of curvature of the cell body."
          }
        ],
        "edges": [
          {
            "subject": "curved_pg_growth",
            "predicate": "has output",
            "object": "pole_to_pole_closure",
            "description": "Strong axial curvature brings the poles into proximity.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-cellbio-101011-155745",
                "snippet": "cell curvature",
                "notes": "Supports curvature-generating wall growth as a producer of closed ring forms."
              }
            ],
            "predicate_id": "RO:0002234"
          },
          {
            "subject": "pole_to_pole_closure",
            "predicate": "causes",
            "object": "toroidal_geometry",
            "description": "Pole-to-pole closure yields a toroidal body.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-cellbio-101011-155745",
                "snippet": "cell shape is genetically determined",
                "notes": "Supports closed ring forms as genetically determined shape outcomes."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "toroidal_geometry",
            "predicate": "manifests as",
            "object": "ring_shaped_trait",
            "description": "Toroidal geometry manifests the ring-shaped trait.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-cellbio-101011-155745",
                "snippet": "cell curvature",
                "notes": "Supports the trait endpoint via curvature-driven closure."
              }
            ],
            "predicate_id": "METPO:2007400"
          },
          {
            "subject": "mreb_filaments",
            "predicate": "associated with",
            "object": "cell_wall_growth_rate",
            "description": "MreB filament motion is associated with the rate of cell-wall growth.",
            "evidence": [
              {
                "reference": "DOI:10.3390/microorganisms12071309",
                "snippet": "motion of MreB filaments correlates with the rate of cell wall growth",
                "notes": "Verified against the open Dersch et al. text; the edge remains associative and contextual rather than direct ring-shape evidence."
              }
            ],
            "predicate_id": "biolink:associated_with"
          },
          {
            "subject": "mreb_filaments",
            "predicate": "regulates",
            "object": "pg_insertion_perpendicular",
            "description": "MreB double filaments guide the orientation of peptidoglycan insertion perpendicular to the long axis.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-024-49785-x",
                "snippet": "guide peptidoglycan insertion perpendicular to the long axis of the cell",
                "notes": "Verified against the open Middlemiss et al. text; the edge supports contextual MreB-guided peptidoglycan insertion."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "bactofilin_polymers",
            "predicate": "regulates",
            "object": "cell_wall_biosynthesis",
            "description": "Bactofilin polymers regulate cell-wall biosynthesis.",
            "evidence": [
              {
                "reference": "DOI:10.7554/eLife.86577.2",
                "snippet": "central role in the spatial regulation of cell wall biosynthesis",
                "notes": "Verified against the open Pohl et al. abstract; bactofilin spatial wall-biosynthesis regulation is retained as comparative Hyphomonas morphogenesis evidence."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "bactofilin_lmdc_module",
            "predicate": "promotes",
            "object": "wall_biosynthesis_mode_change",
            "description": "Conserved bactofilin and M23 peptidase module promotes local changes in cell-wall biosynthesis mode.",
            "evidence": [
              {
                "reference": "DOI:10.7554/eLife.86577.2",
                "snippet": "promotes local changes in the mode of cell wall biosynthesis",
                "notes": "Verified against the open Pohl et al. abstract; the conserved bactofilin/M23 module is retained as comparative cell-wall morphogenesis evidence."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "crva_polymer",
            "predicate": "regulates",
            "object": "pg_synthesis_rate_skew",
            "description": "CrvA polymer formation regulates skewed peptidoglycan synthesis rates to generate curvature.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-024-45196-0",
                "snippet": "CrvA in Vibrio cholerae, which skews peptidoglycan synthesis rates",
                "notes": "Verified against the open Schiller et al. article text; CrvA is retained as a comparative bacterial curvature module."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "crescentin",
            "predicate": "promotes",
            "object": "cell_curvature",
            "description": "Crescentin promotes cell curvature.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-024-45196-0",
                "snippet": "Helical cells require components that promote curvature, such as the polymer and filament-forming CrvA in Vibrio cholerae, which skews peptidoglycan synthesis rates, or the intermediate filament-like protein crescentin in C. crescentus",
                "notes": "Verified against the open Schiller et al. article text; Schiller et al. list crescentin in the same bacterial curvature-component statement."
              }
            ],
            "predicate_id": "RO:0002213"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.892873+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-11T22:45:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed causal graph linking strongly curved peptidoglycan growth and pole-to-pole closure to ring-shaped morphology.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T21:30:07Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007400\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:19Z",
        "curator": "claude",
        "action": "RENAME_PREDICATE_LABELS",
        "changes": "Renamed 1 causal-edge predicate label(s) to align with existing groundings: shapes \u2192 causes \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:22Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:causes\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 6 evidence-backed generic edges (11 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:13Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002213\u00d72).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:19Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A2N9AY16\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:21:12Z",
        "curator": "claude",
        "action": "RETRACT_DEAD_UNIPROT_GROUNDINGS",
        "changes": "Retracted 1 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates (1 to has output), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope ring_shaped_curved_growth_closure=NONMECHANISTIC with scope_notes; marked 5 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (mreb_filaments, bactofilin_polymers, bactofilin_lmdc_module, crva_polymer, crescentin).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T06:15:40Z",
        "curator": "codex",
        "action": "ADD_EXACT_ONTOLOGY_MATCH",
        "changes": "Ontology exact-match review (2026-08-25): approved exact xref(s): PATO:0002539; declared exact synonym(s): 'annular'; upgraded to exact scope: 'ring-shaped'. Evidence is predicate-scoped in the versioned ontology snapshots; OAK cross-checked direct data, and OLS4 spot-checked release deltas and disputed hits.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T09:40:27Z",
        "curator": "codex",
        "action": "ADD_CANONICAL_EXAMPLES",
        "changes": "Added Rhodocyclus purpureus as the natural ring-shaped exemplar identified by this record's own research artifact and original species description; NCBITaxon:1067 and its current label were verified against NCBI.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-04T06:20:00Z",
        "curator": "codex",
        "action": "REVIEW_CAUSAL_EVIDENCE",
        "changes": "Reviewed the ring_shaped_curved_growth_closure graph for issue #183: added exact snippets to 6 comparative curvature and wall-patterning evidence entries, grounded 4 residual predicates, and kept the bactofilin-M23 module as a reviewed label-only protein aggregate. No paid research service was called.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-07T04:24:00Z",
        "curator": "codex",
        "action": "ADVERSARIAL_REVIEW_REPAIR",
        "changes": "Addressed PR #664 adversarial review issue #686: replaced fragmented ring-shape, soil-life-history, heat-shock, and ligninolysis snippets with exact source spans that carry their edge claims.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-07T20:05:00Z",
        "curator": "codex",
        "action": "ADVERSARIAL_REVIEW_REPAIR",
        "changes": "Addressed PR #664 adversarial review issues #697 and #698: restored the bactofilin-M23 module as a reviewed label-only protein aggregate and gave the crescentin curvature edge a distinct Schiller snippet.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000681",
    "label": "rod shaped",
    "definition": "A cell shape in which an organism has an elongated, cylindrical morphology with relatively straight sides and rounded or flat ends.",
    "definition_source": "DOI:10.1146/annurev-cellbio-010521-010834",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000666"
    ],
    "synonyms": [
      {
        "synonym_text": "S_rod",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "rod-shaped",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "created_by": "Luke Wang",
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev-cellbio-010521-010834",
        "snippet": "bacterial rod shape formation",
        "notes": "Supports rod shape as an actively regulated bacterial morphogenesis phenotype."
      },
      {
        "reference": "PMID:7575501",
        "snippet": "why E. coli is rod-shaped",
        "notes": "Organism example: Escherichia coli is described as rod-shaped."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:562",
        "taxon_label": "Escherichia coli",
        "note": "Textbook rod (bacillus); the universal Gram-negative model bacterium.",
        "reference": "PMID:21501250"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "rod_shaped_mreB_peptidoglycan",
        "title": "Rod-shape MreB and peptidoglycan mechanism",
        "description": "Evidence-backed causal sketch linking rod shape to MreB-guided peptidoglycan synthesis, Rod complex activity, cell-wall elongation, and FtsZ division coupling.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a broad environmental or morphological classification spanning multiple mechanisms, a measurement-like bin, or an absence/arrangement descriptor; contextual protein nodes do not receive token UniProt examples.",
        "nodes": [
          {
            "node_id": "rod_shaped_trait",
            "label": "rod shaped",
            "node_type": "TRAIT",
            "grounding": "METPO:1000681",
            "description": "Elongated cylindrical bacterial morphology."
          },
          {
            "node_id": "mreB",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "MreB",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Actin-like protein involved in rod-shape maintenance."
          },
          {
            "node_id": "rod_complex",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "Rod complex",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Cell-wall elongation machinery associated with MreB in rod-shaped bacteria."
          },
          {
            "node_id": "peptidoglycan_synthesis",
            "label": "peptidoglycan synthesis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Cell-wall synthesis and remodeling process.",
            "grounding": "GO:0009252"
          },
          {
            "node_id": "lateral_cell_wall_elongation",
            "label": "lateral cell-wall elongation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Sidewall growth that lengthens rod-shaped cells."
          },
          {
            "node_id": "ftsZ",
            "label": "FtsZ",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Division-ring protein coordinating septal growth.",
            "grounding": "InterPro:IPR000158"
          },
          {
            "node_id": "rodA_pbp2_complex",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "RodA-PBP2 complex",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Elongation synthase complex (RodA glycosyltransferase + PBP2 transpeptidase) of the Rod system."
          },
          {
            "node_id": "pbp2_structural_opening",
            "label": "PBP2 structural opening",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "Open/active conformational state of PBP2 that allosterically activates the elongation synthase."
          },
          {
            "node_id": "rodA_polymerization",
            "label": "RodA polymerization activity",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "Glycan-strand polymerizing (glycosyltransferase) activity of RodA."
          },
          {
            "node_id": "pg_crosslinking",
            "label": "peptidoglycan crosslinking",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Transpeptidation crosslinking of peptidoglycan strands during sidewall synthesis."
          },
          {
            "node_id": "mreC",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "MreC",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Periplasmic Rod-system component that activates PBP2 by promoting its open conformation."
          },
          {
            "node_id": "elongasome_processivity",
            "label": "elongasome processivity",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Processive circumferential movement of MreB-associated elongasomes during sidewall synthesis."
          },
          {
            "node_id": "sidewall_reinforcement",
            "label": "rod-shaped sidewall reinforcement",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Mechanical reinforcement of the cylindrical sidewall via long circumferential glycan hoops."
          }
        ],
        "edges": [
          {
            "subject": "mreB",
            "predicate": "interacts with",
            "object": "rod_complex",
            "description": "MreB filaments interact with the Rod complex that elongates the cell wall.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-cellbio-010521-010834",
                "snippet": "MreB filaments interact with Rod complexes",
                "notes": "Supports MreB-Rod complex interaction in rod-shape regulation."
              }
            ],
            "predicate_id": "biolink:interacts_with"
          },
          {
            "subject": "rod_complex",
            "predicate": "directs",
            "object": "peptidoglycan_synthesis",
            "description": "Rod complexes direct sidewall peptidoglycan synthesis.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-cellbio-010521-010834",
                "snippet": "Rod complexes drive cell wall insertion",
                "notes": "Supports Rod complex contribution to wall insertion."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "peptidoglycan_synthesis",
            "predicate": "has output",
            "object": "lateral_cell_wall_elongation",
            "description": "Directed peptidoglycan synthesis elongates rod-shaped cells.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2677",
                "snippet": "elongation mode of peptidoglycan synthesis",
                "notes": "Supports peptidoglycan synthesis in cell elongation."
              }
            ],
            "predicate_id": "RO:0002234"
          },
          {
            "subject": "lateral_cell_wall_elongation",
            "predicate": "regulates",
            "object": "rod_shaped_trait",
            "description": "Lateral wall elongation preserves the cylindrical rod morphology.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.tim.2011.11.004",
                "snippet": "restores its rod shape",
                "notes": "Supports MreB-associated cell-wall synthesis as important for rod shape restoration and maintenance."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "ftsZ",
            "predicate": "coordinates with",
            "object": "peptidoglycan_synthesis",
            "description": "FtsZ coordinates division-associated peptidoglycan synthesis with rod cell morphology.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro1205",
                "snippet": "FtsZ collaborates with penicillin binding proteins",
                "notes": "Supports FtsZ-PBP collaboration in bacterial cell-shape generation."
              }
            ]
          },
          {
            "subject": "rodA_pbp2_complex",
            "predicate": "positively regulates",
            "object": "rod_shaped_trait",
            "description": "The active elongation synthase complex supports proper rod-shaped morphology during growth.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-023-39037-9",
                "notes": "Structural opening couples RodA glycan polymerization and PBP2 crosslinking, a coupling essential in vivo for rod-shaped growth."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "pbp2_structural_opening",
            "predicate": "activates",
            "object": "rodA_polymerization",
            "description": "Conformational opening of PBP2 allosterically stimulates RodA polymerization.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-023-39037-9",
                "notes": "Structural opening promotes RodA polymerization activity."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "pbp2_structural_opening",
            "predicate": "enables",
            "object": "pg_crosslinking",
            "description": "The open state elevates the PBP2 TP domain toward the PG layer, enabling crosslinking.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-023-39037-9",
                "notes": "Opening of PBP2 elevates the TP domain, facilitating crosslinking."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "mreC",
            "predicate": "activates",
            "object": "rodA_pbp2_complex",
            "description": "MreC binds the PBP2 pedestal domain and biases RodA-PBP2 into the open, catalytically active conformation.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-023-39037-9",
                "notes": "MreC is implicated as an activator that promotes the open, catalytically active conformation of PBP2."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "rodA_polymerization",
            "predicate": "regulates",
            "object": "elongasome_processivity",
            "description": "RodA abundance/activity tunes processive dynamics of MreB-associated elongasomes.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-024-49785-x",
                "notes": "RodA abundance regulates elongasome processivity, reversal frequency, and pausing."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "elongasome_processivity",
            "predicate": "contributes to",
            "object": "sidewall_reinforcement",
            "description": "Processive circumferential synthesis lays long glycan hoops that mechanically reinforce the cylinder.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-024-49785-x",
                "notes": "Long glycan strands act as barrel-hoop-like reinforcing structures of the rod sidewall."
              }
            ],
            "predicate_id": "RO:0002326"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.893421+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-06T14:40:41-07:00",
        "curator": "codex",
        "action": "CURATED_WITH_ORGANISM_EXAMPLE",
        "changes": "Added Escherichia coli organism example with PMID-backed evidence.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-11T00:00:00-07:00",
        "curator": "codex",
        "action": "CURATED_WITH_LITERATURE",
        "changes": "Replaced PMID definition source with DOI-backed rod-shape source and added causal graph for MreB, Rod complex, peptidoglycan synthesis, lateral wall elongation, and FtsZ coupling.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T21:30:07Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002211\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:19Z",
        "curator": "claude",
        "action": "RENAME_PREDICATE_LABELS",
        "changes": "Renamed 1 causal-edge predicate label(s) to align with existing groundings: maintains \u2192 regulates \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:22Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002211\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:38:01Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0009252\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T05:05:15Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A1B1UYY2\u00d71, UniProtKB:C0LUM8\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-26T05:00:48Z",
        "curator": "claude",
        "action": "RENAME_PREDICATE_LABELS",
        "changes": "Renamed 1 causal-edge predicate label(s) to align with existing groundings: organizes \u2192 enables \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-26T05:00:51Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 6 evidence-backed generic edges (7 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:14Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 5 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002213\u00d72, RO:0002327\u00d71, RO:0002211\u00d71, RO:0002326\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-26T07:15:19Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A1L9R356\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:21:12Z",
        "curator": "claude",
        "action": "RETRACT_DEAD_UNIPROT_GROUNDINGS",
        "changes": "Retracted 2 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-04T03:08:15Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002213\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates (1 to has output), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T08:00:00Z",
        "curator": "claude",
        "action": "REGROUND_CAUSAL_EDGE",
        "changes": "Re-grounded causal edge(s) off enables/RO:0002327 onto part of (biolink:part_of), issue 334. biolink declares enables range 'biological process or activity', which only BIOLOGICAL_PROCESS, PATHWAY and MOLECULAR_FUNCTION satisfy, so an edge pointing at a GENE_OR_PROTEIN entailed a false type. The replacements are chosen per idiom rather than swept: a gene cluster ENCODES its product, a subunit is PART OF the complex it belongs to, and an energy source or acquired repertoire CONTRIBUTES TO the machine it powers or composes. All three declare no rdfs:domain or rdfs:range, so none can reintroduce the class of defect being removed.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T09:00:00Z",
        "curator": "claude",
        "action": "REGROUND_CAUSAL_EDGE",
        "changes": "Corrected the mreB edge from part of to interacts with (biolink:interacts_with), issue 334 review. The first pass over-claimed: the edge's own snippet says MreB filaments INTERACT WITH Rod complexes, and the target node is described as machinery associated with MreB, so parthood is not what the evidence supports. The corpus is also split on it - cell_shape.yaml types rod_complex a PATHWAY with MreB inside it, while this file types it GENE_OR_PROTEIN with MreB outside - which makes parthood exactly the kind of modelling decision this work defers elsewhere. interacts with says what the quoted sentence says and needs no such decision. The edge description was rephrased to match the predicate.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-22T04:26:15Z",
        "curator": "codex",
        "action": "REVIEW_UNIPROT_INSTANCE_GROUNDINGS",
        "changes": "Reviewed 1 organism-specific UniProtKB grounding(s): replaced 1 with taxon-agnostic GO/InterPro terms and retracted 0 to label-only where no exact semantic term was supported (docs/GROUNDING_POLICY.md).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope rod_shaped_mreB_peptidoglycan=NONMECHANISTIC with scope_notes; marked 4 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (mreB, rod_complex, rodA_pbp2_complex, mreC).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000652",
    "label": "rosette cell arrangement",
    "definition": "A morphological phenotype in which cells form multicellular clusters organized around a shared central region, with corresponding cell poles directed inward.",
    "definition_source": "DOI:10.7554/eLife.41482",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.7554/eLife.41482",
        "snippet": "all cells are oriented with their basal poles toward the rosette center and their apical flagella extending out from the rosette surface",
        "notes": "Wetzel et al. (2018), PMID:30556809, PMC6322860, first Results subsection; full-text XML and Figure 1 directly inspected. Wild-type Salpingoeca rosetta rosettes have organized polarity, unlike disordered clumps in the four Class C mutants. Methods identify wild type as SrEpac and use Algoriphagus-derived rosette-inducing factors. The three-cell minimum after vortexing is this study's scoring rule, not a universal definition. Clonal development rather than aggregation is specific to S. rosetta here. The Results quote is not the scientific abstract or editorial digest."
      },
      {
        "reference": "DOI:10.1128/jb.00064-19",
        "snippet": "form multicellular rosettes by adhering to each other through the polar polysaccharide, or holdfast.",
        "notes": "Fiebig (2019), PMID:31010900, PMC6707911, Results subsection Holdfasts are prominent in the pellicle. Publisher HTML, growth/sampling/microscopy Methods, and Figure 4 were directly inspected. Static CB15 cultures form rosettes with holdfast-rich cores. The Results describe both radial and oblong rosettes; not every core is a single attachment point. Supplemental Figure S2's text was accessible but its image was not verified. Pellicle dependence on holdfast is not a universal rosette mechanism. The Discussion leaves the field relevance of thick Caulobacter pellicles unresolved; laboratory observations are not evidence that these structures occur in every habitat."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:946362",
        "taxon_label": "Salpingoeca rosetta",
        "reference": "DOI:10.7554/eLife.41482",
        "note": "Wild-type SrEpac (ATCC PRA-390) in rosette-inducing-factor cultures, not every life stage. Natural-isolate provenance was checked in Levin and King's Experimental Procedures: https://doi.org/10.1016/j.cub.2013.08.061. SrEpac is isolate C, derived from Px1 by feeder replacement, antibiotic treatment and clonal isolation; Px1 derives from environmental rosette isolate ATCC 50818. It is not the EMS-mutagenized isolate B. The provenance citation is not counted as independent trait evidence. NCBI Taxonomy resolves the species ID and label."
      }
    ],
    "discussions": [
      {
        "discussion_id": "rosette-cell-arrangement-scope-and-hierarchy",
        "prompt": "Review a multicellular arrangement parent and exact external mappings.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Retain phenotype METPO:1000059. Cell shape METPO:1000666 describes an individual cell, while colony morphology METPO:1007062 and colony shape METPO:1007063 describe macroscopic colonies on solid medium. Neither is the genus of this microscopic multicellular arrangement. Obsolete cell arrangement METPO:1000046 is not a usable active parent. Star shaped METPO:1000685 is one cell with radiating projections; staphylococcus arrangement traitmech:000118 is an irregular coccal cluster. Holdfast traitmech:000184 is a polar adhesin phenotype, not a rosette, and biofilm formation traitmech:000053 does not define this arrangement. Co-occurrence is not organism-level disjointness. No unqualified synonym, external equivalence, perfect spherical symmetry, fixed cell count or single central attachment point is asserted. Irregular clumping alone is insufficient.",
        "posed_by": "codex",
        "posed_date": "2026-10-06"
      },
      {
        "discussion_id": "rosette-cell-arrangement-mechanism-scope",
        "prompt": "Keep organism-specific developmental and adhesion mechanisms separate.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "The two primary studies support a shared morphological description, not one homologous developmental program. Wetzel et al.'s exclusion of aggregation concerns S. rosetta rosettes, whereas Fiebig describes polar adhesion in Caulobacter. Do not require clonal division or a bacterial holdfast for all rosettes. A causal graph is deferred pending separate organism-scoped perturbation and accession reviews, not because mechanisms are unknown. Holdfast-associated genes or predicted glycosyltransferases alone do not establish the observed arrangement. Quantitative shear, growth and cell-number thresholds are assay-specific. Additional bacterial canonical examples require strain-provenance and taxon verification; the CB15 evidence is retained without an unverified taxon row.",
        "posed_by": "codex",
        "posed_date": "2026-10-06"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-06T23:05:49Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added rosette cell arrangement with two DOI-backed Results snippets, a provenance-qualified S. rosetta example, and explicit arrangement/mechanism boundaries. Ignored-and-hidden novelty searches and structured METPO review found no exact record. Reserved METPO:1060500 in v528; existing records unchanged.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000064",
    "label": "S-layer",
    "definition": "A morphology trait in which the cell surface is coated by a crystalline, two-dimensional array of self-assembling proteinaceous (glyco)protein subunits (a surface layer), found in many bacteria and most archaea.",
    "definition_source": "DOI:10.1038/nrmicro3213",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "synonyms": [
      {
        "synonym_text": "surface layer",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1038/nrmicro3213"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/nrmicro3213",
        "notes": "Fagan & Fairweather describe the S-layer as a self-assembled, regularly spaced two-dimensional protein array coating the cell surface."
      },
      {
        "reference": "DOI:10.1038/s41579-025-01258-8",
        "notes": "Review of assembly, architecture and functional roles of microbial surface layers supports the S-layer as a defined cell-surface structure."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1422",
        "taxon_label": "Geobacillus stearothermophilus",
        "note": "Long-standing model for crystalline bacterial surface-layer (S-layer) structure and assembly.",
        "reference": "DOI:10.1111/1574-6976.12063"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "s_layer_2d_protein_array",
        "title": "S-layer crystalline (glyco)protein surface array",
        "description": "Evidence-backed causal sketch linking self-assembly of (glyco)protein subunits into a regular 2D array to the S-layer surface coating.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a broad environmental or morphological classification spanning multiple mechanisms, a measurement-like bin, or an absence/arrangement descriptor; contextual protein nodes do not receive token UniProt examples.",
        "nodes": [
          {
            "node_id": "s_layer_trait",
            "label": "S-layer",
            "node_type": "TRAIT",
            "grounding": "traitmech:000064",
            "description": "Crystalline 2D (glyco)protein array coating the cell surface."
          },
          {
            "node_id": "s_layer_subunits",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "S-layer (glyco)protein subunits",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Self-assembling proteinaceous building blocks of the S-layer."
          },
          {
            "node_id": "s_layer_assembly",
            "label": "S-layer assembly",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Self-assembly of S-layer subunits into a regularly spaced 2D array."
          },
          {
            "node_id": "s_layer_2d_lattice",
            "label": "2D paracrystalline S-layer lattice",
            "node_type": "CELLULAR_LOCALIZATION",
            "description": "Regularly spaced two-dimensional paracrystalline lattice formed by self-assembled S-layer proteins coating the cell surface."
          }
        ],
        "edges": [
          {
            "subject": "s_layer_subunits",
            "predicate": "enables",
            "object": "s_layer_assembly",
            "description": "Self-assembling (glyco)protein subunits build the S-layer array.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro3213",
                "notes": "Fagan & Fairweather describe self-assembled (glyco)protein arrays forming the S-layer."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "s_layer_assembly",
            "predicate": "confers",
            "object": "s_layer_trait",
            "description": "Completed 2D assembly realizes the S-layer surface coating.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41579-025-01258-8",
                "notes": "Review of assembly, architecture, and functional roles of microbial surface layers."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "s_layer_subunits",
            "predicate": "self-assembles into",
            "object": "s_layer_2d_lattice",
            "description": "S-layer proteins self-assemble into a 2D paracrystalline lattice; N-terminal regions mediate self-assembly into the layer.",
            "evidence": [
              {
                "reference": "DOI:10.1073/pnas.2401686121",
                "notes": "S-layers are self-assembling, crystalline surface proteins; the N-terminal region mediates self-assembly into the layer (curation-safe at class level)."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-06-03T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate MORPHOLOGY trait (S-layer) from literature research to fill the cell-surface-structure gap.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-09T15:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (S-layer 2D protein array assembly) with RO predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 1 evidence-backed generic edges (1 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 1 causal edge(s) off enables/RO:0002327 with a TRAIT object (1 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope s_layer_2d_protein_array=NONMECHANISTIC with scope_notes; marked 1 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (s_layer_subunits).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000120",
    "label": "sarcina arrangement",
    "definition": "A cell arrangement in which cocci divide in three perpendicular planes and remain attached as cubic packets of eight (sarcinae).",
    "definition_source": "DOI:10.1128/MMBR.00001-06",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000666"
    ],
    "synonyms": [
      {
        "synonym_text": "cubic packet cocci",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1128/MMBR.00001-06"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1128/MMBR.00001-06",
        "notes": "Young's review treats the sarcina cubic packet as a division-plane-determined coccal arrangement."
      },
      {
        "reference": "DOI:10.1038/ncomms4842",
        "notes": "Three-plane division with incomplete daughter-cell separation yields cubic eight-cell packets."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1267",
        "taxon_label": "Sarcina ventriculi",
        "note": "Namesake of the sarcina (cuboidal packet-of-eight) cell arrangement from tetrad division in three planes.",
        "reference": "PMID:27922772"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "sarcina_three_plane_division_packet",
        "title": "Sarcina arrangement via three-plane perpendicular division",
        "description": "Evidence-backed causal sketch linking division in three perpendicular planes with incomplete separation to cubic eight-cell packets.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a broad environmental or morphological classification spanning multiple mechanisms, a measurement-like bin, or an absence/arrangement descriptor; contextual protein nodes do not receive token UniProt examples.",
        "nodes": [
          {
            "node_id": "sarcina_trait",
            "label": "sarcina arrangement",
            "node_type": "TRAIT",
            "grounding": "traitmech:000120",
            "description": "Cocci attached as cubic packets of eight (sarcinae)."
          },
          {
            "node_id": "cell_division",
            "label": "cell division",
            "node_type": "BIOLOGICAL_PROCESS",
            "grounding": "GO:0051301",
            "description": "Bacterial binary fission."
          },
          {
            "node_id": "three_plane_perpendicular_division",
            "label": "three perpendicular division planes",
            "node_type": "QUALITY",
            "description": "Successive division planes oriented along three orthogonal axes."
          },
          {
            "node_id": "ftsz_protein",
            "label": "FtsZ",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Tubulin-like division protein that polymerizes at the division site.",
            "grounding": "InterPro:IPR000158"
          },
          {
            "node_id": "z_ring",
            "label": "Z ring",
            "node_type": "CELLULAR_LOCALIZATION",
            "description": "Dynamic FtsZ polymer ring that marks the division site."
          },
          {
            "node_id": "ftsa_protein",
            "label": "FtsA",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Actin-like protein tethering the Z ring to the cytoplasmic membrane.",
            "grounding": "InterPro:IPR020823"
          },
          {
            "node_id": "cytoplasmic_membrane",
            "label": "cytoplasmic membrane",
            "node_type": "CELLULAR_LOCALIZATION",
            "description": "Plasma membrane to which the divisome attaches."
          },
          {
            "node_id": "septal_pg_remodeling",
            "label": "septal peptidoglycan remodeling",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Coordinated synthesis and hydrolysis of peptidoglycan to build the septal cross-wall."
          },
          {
            "node_id": "pg_synthetases_hydrolases",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "peptidoglycan synthetases and hydrolases",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Enzymes that synthesize and degrade peptidoglycan during division."
          },
          {
            "node_id": "cell_wall_synthesis_division_site",
            "label": "cell wall synthesis at division site",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "FtsZ-dependent peptidoglycan synthesis localized to the division site."
          },
          {
            "node_id": "septum_formation",
            "label": "division septum formation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Formation of the division septum (cross-wall).",
            "grounding": "GO:0000917"
          },
          {
            "node_id": "pg_hydrolases",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "peptidoglycan hydrolases",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Enzymes that cleave peptidoglycan bonds to enable daughter-cell separation."
          },
          {
            "node_id": "peripheral_pg_bridge",
            "label": "peripheral peptidoglycan bridge",
            "node_type": "CELLULAR_LOCALIZATION",
            "description": "Peripheral peptidoglycan connection holding daughter cells together after septation."
          },
          {
            "node_id": "daughter_cell_separation",
            "label": "daughter-cell separation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Physical splitting of daughter cells after division."
          }
        ],
        "edges": [
          {
            "subject": "three_plane_perpendicular_division",
            "predicate": "causes",
            "object": "sarcina_trait",
            "description": "Three perpendicular division planes with incomplete separation yield cubic eight-cell packets.",
            "evidence": [
              {
                "reference": "DOI:10.1038/ncomms4842",
                "notes": "Three-plane division with incomplete daughter-cell separation yields cubic eight-cell packets."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "cell_division",
            "predicate": "confers",
            "object": "sarcina_trait",
            "description": "Bacterial cell division underlies sarcina packet formation.",
            "evidence": [
              {
                "reference": "DOI:10.1128/MMBR.00001-06",
                "notes": "Young treats the sarcina cubic packet as a division-plane-determined coccal arrangement."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "ftsz_protein",
            "predicate": "polymerizes to form",
            "object": "z_ring",
            "description": "FtsZ polymerizes to form the dynamic Z ring at the division site.",
            "evidence": [
              {
                "reference": "DOI:10.1002/mbo3.1338",
                "notes": "FtsZ polymerizes to form a dynamic structure known as the Z ring; broadly conserved bacterial/coccal mechanism."
              }
            ]
          },
          {
            "subject": "ftsa_protein",
            "predicate": "attaches",
            "object": "z_ring",
            "description": "FtsA tethers the Z ring to the cytoplasmic membrane for proper divisome assembly.",
            "evidence": [
              {
                "reference": "DOI:10.1002/mbo3.1338",
                "notes": "Proper Z ring assembly requires attachment to the cytoplasmic membrane via interactions with FtsA; general divisome mechanism."
              }
            ]
          },
          {
            "subject": "ftsa_protein",
            "predicate": "attaches Z ring to",
            "object": "cytoplasmic_membrane",
            "description": "FtsA attaches the Z ring to the cytoplasmic membrane.",
            "evidence": [
              {
                "reference": "DOI:10.1002/mbo3.1338",
                "notes": "Z ring attachment to the cytoplasmic membrane occurs via interactions with FtsA."
              }
            ]
          },
          {
            "subject": "pg_synthetases_hydrolases",
            "predicate": "cooperate in",
            "object": "septal_pg_remodeling",
            "description": "PG synthetases and hydrolases work together to build the septal cross-wall.",
            "evidence": [
              {
                "reference": "DOI:10.1002/mbo3.1338",
                "notes": "PG synthetases and hydrolases work together to incorporate new PG into the existing mesh and to make the septal cross wall; general cell-wall remodeling principle."
              }
            ]
          },
          {
            "subject": "cell_wall_synthesis_division_site",
            "predicate": "drives",
            "object": "septum_formation",
            "description": "FtsZ-dependent cell wall synthesis at the division site drives septum formation.",
            "evidence": [
              {
                "reference": "DOI:10.1111/j.1574-6976.2007.00098.x",
                "notes": "FtsZ-dependent cell wall synthesis is predominant; coccal cell wall synthesis occurs mainly at the division site, driving septation."
              }
            ]
          },
          {
            "subject": "pg_hydrolases",
            "predicate": "degrade",
            "object": "peripheral_pg_bridge",
            "description": "Peptidoglycan hydrolases degrade the peripheral PG bridge connecting daughter cells.",
            "evidence": [
              {
                "reference": "DOI:10.1002/mbo3.1338",
                "notes": "Hydrolases likely trigger cell splitting by degrading the peripheral bridge, not the entire septum; general separation mechanism."
              }
            ]
          },
          {
            "subject": "peripheral_pg_bridge",
            "predicate": "degradation triggers",
            "object": "daughter_cell_separation",
            "description": "Degradation of the peripheral PG bridge triggers daughter-cell splitting; incomplete separation retains packets.",
            "evidence": [
              {
                "reference": "DOI:10.1002/mbo3.1338",
                "notes": "Degradation of the peripheral PG bridge, together with mechanical factors, results in a sudden crack that separates the cells; regulated/incomplete separation determines packet retention."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-06-08T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate MORPHOLOGY trait (sarcina / cubic-packet arrangement); leftover round, cell-arrangement sibling of diplococcus shaped.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-09T15:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (three-plane perpendicular division \u2192 cubic packet) with GO node grounding and RO/biolink predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 7 evidence-backed generic edges (11 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:19Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:C0LUM8\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:34Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0000917\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-26T07:15:20Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A1M6DY20\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 1 causal edge(s) off enables/RO:0002327 with a TRAIT object (1 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-22T04:26:16Z",
        "curator": "codex",
        "action": "REVIEW_UNIPROT_INSTANCE_GROUNDINGS",
        "changes": "Reviewed 2 organism-specific UniProtKB grounding(s): replaced 2 with taxon-agnostic GO/InterPro terms and retracted 0 to label-only where no exact semantic term was supported (docs/GROUNDING_POLICY.md).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope sarcina_three_plane_division_packet=NONMECHANISTIC with scope_notes; marked 2 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (pg_synthetases_hydrolases, pg_hydrolases).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000683",
    "label": "sphere shaped",
    "definition": "A cell shape in which an organism has a spherical or nearly spherical morphology with roughly equal dimensions in all directions.",
    "definition_source": "DOI:10.1038/nrmicro3088",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000666"
    ],
    "synonyms": [
      {
        "synonym_text": "S_sphere",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "sphere-shaped",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "created_by": "Anthea Guo",
    "evidence": [
      {
        "reference": "DOI:10.1038/nrmicro3088",
        "snippet": "spherical cocci synthesize peptidoglycan only at the division septum",
        "notes": "Supports spherical bacterial morphology as associated with septal peptidoglycan synthesis."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1280",
        "taxon_label": "Staphylococcus aureus",
        "note": "spherical coccus",
        "reference": "PMID:40704795"
      },
      {
        "taxon_id": "NCBITaxon:1313",
        "taxon_label": "Streptococcus pneumoniae",
        "note": "near-spherical diplococcus",
        "reference": "PMID:31172911"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "sphere_shaped_septal_peptidoglycan",
        "title": "Spherical shape septal peptidoglycan mechanism",
        "description": "Evidence-backed causal sketch linking spherical cell shape to FtsZ-associated septal synthesis, peptidoglycan remodeling, and limited lateral elongation.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a broad environmental or morphological classification spanning multiple mechanisms, a measurement-like bin, or an absence/arrangement descriptor; contextual protein nodes do not receive token UniProt examples.",
        "nodes": [
          {
            "node_id": "sphere_shaped_trait",
            "label": "sphere shaped",
            "node_type": "TRAIT",
            "grounding": "METPO:1000683",
            "description": "Spherical bacterial cell morphology."
          },
          {
            "node_id": "ftsZ_division_ring",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "FtsZ division ring",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Tubulin-like division scaffold."
          },
          {
            "node_id": "septal_peptidoglycan_synthesis",
            "label": "septal peptidoglycan synthesis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Cell-wall synthesis localized to the division septum."
          },
          {
            "node_id": "peptidoglycan_cell_wall",
            "label": "peptidoglycan cell wall",
            "node_type": "CELLULAR_LOCALIZATION",
            "grounding": "GO:0009274",
            "description": "Cell-wall polymer network maintaining bacterial shape."
          },
          {
            "node_id": "lateral_elongation",
            "label": "lateral cell-wall elongation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Sidewall growth mode that lengthens rods."
          },
          {
            "node_id": "mreB_elongation_machinery",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "MreB-mediated elongation machinery",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Actin-like MreB cytoskeleton directing lateral (rod) elongation."
          },
          {
            "node_id": "divisome_pbps",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "divisome and PBPs",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Division machinery and penicillin-binding proteins recruited to mid-cell."
          },
          {
            "node_id": "ftsZ_treadmilling",
            "label": "FtsZ treadmilling",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Treadmilling of FtsZ polymers distributing PG synthases around the Z-ring."
          },
          {
            "node_id": "ftsW_flippase",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "FtsW lipid II flippase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Septally localized flippase that translocates lipid II across the membrane."
          },
          {
            "node_id": "lipid_ii",
            "label": "lipid II",
            "node_type": "CHEMICAL",
            "description": "Membrane-bound peptidoglycan precursor and PBP substrate.",
            "grounding": "CHEBI:27692"
          }
        ],
        "edges": [
          {
            "subject": "ftsZ_division_ring",
            "predicate": "enables",
            "object": "septal_peptidoglycan_synthesis",
            "description": "The FtsZ division ring organizes septal wall synthesis.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro1205",
                "snippet": "FtsZ collaborates with penicillin binding proteins",
                "notes": "Supports FtsZ-PBP cooperation in division-associated shape generation."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "septal_peptidoglycan_synthesis",
            "predicate": "builds",
            "object": "peptidoglycan_cell_wall",
            "description": "Septal synthesis builds and remodels the spherical cell wall.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro3088",
                "snippet": "synthesize peptidoglycan only at the division septum",
                "notes": "Supports septal-only PG synthesis in spherical cocci."
              }
            ],
            "predicate_id": "biolink:produces"
          },
          {
            "subject": "lateral_elongation",
            "predicate": "reduced in",
            "object": "sphere_shaped_trait",
            "description": "Reduced lateral elongation helps preserve a sphere rather than a rod.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro3088",
                "snippet": "mechanisms controlling growth and division of coccoid bacteria",
                "notes": "Broad review supports different growth mechanisms for coccoid versus rod-shaped bacteria."
              }
            ]
          },
          {
            "subject": "peptidoglycan_cell_wall",
            "predicate": "regulates",
            "object": "sphere_shaped_trait",
            "description": "Peptidoglycan wall geometry maintains the spherical shape.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro1205",
                "snippet": "primary role in maintaining cell shape",
                "notes": "Supports the cell wall as central to bacterial shape maintenance."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "septal_peptidoglycan_synthesis",
            "predicate": "contributes to",
            "object": "sphere_shaped_trait",
            "description": "Septal-only peptidoglycan synthesis in cocci produces spherical morphology.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro3088",
                "notes": "spherical cocci synthesize peptidoglycan only at the division septum"
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "mreB_elongation_machinery",
            "predicate": "causally upstream of",
            "object": "lateral_elongation",
            "description": "Loss of the MreB cytoskeleton removes the elongation capacity that lengthens rods.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro3088",
                "notes": "loss of the MreB cytoskeleton is the main factor that prevents cocci from elongating into rods"
              }
            ]
          },
          {
            "subject": "ftsZ_division_ring",
            "predicate": "recruits",
            "object": "divisome_pbps",
            "description": "FtsZ assembly into a mid-cell Z ring recruits PBPs and divisome components.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro3088",
                "notes": "cell division is initiated by FtsZ assembly into a mid-cell Z ring that recruits PBPs and divisome components"
              }
            ]
          },
          {
            "subject": "ftsZ_treadmilling",
            "predicate": "regulates",
            "object": "septal_peptidoglycan_synthesis",
            "description": "FtsZ treadmilling distributes the PG synthases that form the septum.",
            "evidence": [
              {
                "reference": "DOI:10.1042/bsr20221664",
                "notes": "The FtsZ polymers undergo treadmilling around the Z-ring to distribute the PG synthases forming the septum"
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "ftsW_flippase",
            "predicate": "transports",
            "object": "lipid_ii",
            "description": "FtsW flips lipid II to the outer septal face for PG synthesis.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro3088",
                "notes": "lipid II is flipped to the outside by the septally localized flippase FtsW"
              }
            ],
            "predicate_id": "METPO:2007812"
          },
          {
            "subject": "lipid_ii",
            "predicate": "enables",
            "object": "septal_peptidoglycan_synthesis",
            "description": "Lipid II serves as the PBP substrate for septal peptidoglycan synthesis.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro3088",
                "notes": "PG synthesis uses lipid II as the PBP substrate"
              }
            ],
            "predicate_id": "RO:0002327"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.894456+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-11T20:05:00-07:00",
        "curator": "codex",
        "action": "CURATED_WITH_LITERATURE",
        "changes": "Added DOI-backed definition and causal graph for FtsZ-associated septal peptidoglycan synthesis, peptidoglycan cell wall, reduced lateral elongation, and spherical morphology.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:19Z",
        "curator": "claude",
        "action": "RENAME_PREDICATE_LABELS",
        "changes": "Renamed 1 causal-edge predicate label(s) to align with existing groundings: maintains \u2192 regulates \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:22Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002211\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-26T05:00:48Z",
        "curator": "claude",
        "action": "RENAME_PREDICATE_LABELS",
        "changes": "Renamed 1 causal-edge predicate label(s) to align with existing groundings: organizes \u2192 enables \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-26T05:00:51Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-13T21:03:26Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:produces\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 7 evidence-backed generic edges (6 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:14Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 4 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d72, RO:0002326\u00d71, RO:0002211\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:34Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:27692\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-07T18:00:00Z",
        "curator": "claude",
        "action": "REGROUND_CAUSAL_EDGE",
        "changes": "Edge ftsW_flippase -> lipid_ii in graph sphere_shaped_septal_peptidoglycan: re-grounded it from enables/RO:0002327 to transports/METPO:2007812. Issue 334. biolink declares enables range 'biological process or activity', which of CausalNodeTypeEnum only BIOLOGICAL_PROCESS, PATHWAY and MOLECULAR_FUNCTION satisfy, so this edge entailed a false type on its object. 'FtsW FLIPS lipid II to the outer septal face' -- a flippase moves its substrate across the membrane, which is transport, not enablement. Needs GENE_OR_PROTEIN added to `transports`' subject_types, which is a deliberate widening recorded there.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-08T05:00:00Z",
        "curator": "claude",
        "action": "MERGE_CAUSAL_NODE",
        "changes": "Merged node elongation_capacity into lateral_elongation and repointed its edges. Issue 352. 'Capacity of a cell to elongate into a rod via sidewall growth' against lateral_elongation's 'Sidewall growth mode that lengthens rods' -- the same claim twice, and both already carried `reduced in -> sphere_shaped_trait`.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope sphere_shaped_septal_peptidoglycan=NONMECHANISTIC with scope_notes; marked 4 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (ftsZ_division_ring, mreB_elongation_machinery, divisome_pbps, ftsW_flippase).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000692",
    "label": "spindle shaped",
    "definition": "A cell shape that is widest at the middle and tapers symmetrically toward pointed poles.",
    "definition_source": "DOI:10.1146/annurev-cellbio-101011-155745",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000666"
    ],
    "synonyms": [
      {
        "synonym_text": "spindle",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "created_by": "Anthea Guo",
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev-cellbio-101011-155745",
        "snippet": "cell shape is genetically determined",
        "notes": "Cell-shape review supports symmetric tapered shapes as a genetically determined outcome of polar wall patterning."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1488",
        "taxon_label": "Clostridium acetobutylicum",
        "note": "spindle-shaped on sporulation",
        "reference": "PMID:16346038"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "spindle_shaped_symmetric_taper",
        "title": "Spindle-shape symmetric polar taper",
        "description": "DOI-backed graph linking symmetric tapered polar wall growth and reduced end-cap radius to spindle morphology.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This is a geometric shape classification; the cited evidence does not establish a taxon-matched protein determinant for symmetric tapering.",
        "nodes": [
          {
            "node_id": "spindle_shaped_trait",
            "label": "spindle shaped",
            "node_type": "TRAIT",
            "grounding": "METPO:1000692",
            "description": "Cell widest at the middle and tapering symmetrically to pointed poles."
          },
          {
            "node_id": "symmetric_polar_pg",
            "label": "symmetric polar peptidoglycan growth",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Tapered PG growth at both poles producing pointed ends."
          },
          {
            "node_id": "reduced_end_cap_radius",
            "label": "reduced end-cap radius",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Narrowed cell-body radius near the poles."
          },
          {
            "node_id": "spindle_geometry",
            "label": "spindle geometry",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Bilaterally symmetric tapered body geometry."
          },
          {
            "node_id": "localized_pg_insertion",
            "label": "localized peptidoglycan insertion",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Spatially restricted incorporation of new peptidoglycan at distinct rates in defined cell locations."
          },
          {
            "node_id": "non_spherical_morphology",
            "label": "non-spherical morphology",
            "node_type": "QUALITY",
            "description": "A differentiated, non-spherical cell shape produced by spatially patterned wall growth."
          }
        ],
        "edges": [
          {
            "subject": "symmetric_polar_pg",
            "predicate": "has output",
            "object": "reduced_end_cap_radius",
            "description": "Symmetric polar growth produces reduced end-cap radius at both poles.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-cellbio-101011-155745",
                "snippet": "polar growth",
                "notes": "Supports polar PG growth as the producer of tapered ends."
              }
            ],
            "predicate_id": "RO:0002234"
          },
          {
            "subject": "reduced_end_cap_radius",
            "predicate": "causes",
            "object": "spindle_geometry",
            "description": "Reduced end-cap radius at both poles yields spindle geometry.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-cellbio-101011-155745",
                "snippet": "cell shape is genetically determined",
                "notes": "Supports tapered geometry as a genetically determined shape outcome."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "spindle_geometry",
            "predicate": "manifests as",
            "object": "spindle_shaped_trait",
            "description": "Spindle geometry manifests the spindle-shaped trait.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-cellbio-101011-155745",
                "snippet": "cell shape is genetically determined",
                "notes": "Supports the trait endpoint."
              }
            ],
            "predicate_id": "METPO:2007400"
          },
          {
            "subject": "localized_pg_insertion",
            "predicate": "required for",
            "object": "non_spherical_morphology",
            "description": "Spatially localized (non-dispersed) peptidoglycan insertion is required to generate any non-spherical, differentiated cell shape.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2017.01264",
                "notes": "To generate shapes other than a sphere, incorporation must occur at distinct rates in different locations and for defined periods of time. Broad mechanistic principle for non-spherical morphogenesis."
              }
            ]
          },
          {
            "subject": "localized_pg_insertion",
            "predicate": "enables",
            "object": "symmetric_polar_pg",
            "description": "Generic localized PG insertion underlies the symmetric polar peptidoglycan growth that taper the poles.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2017.01264",
                "notes": "Localized, temporally defined PG incorporation is the general prerequisite for the symmetric polar growth that produces tapered spindle poles."
              }
            ],
            "predicate_id": "RO:0002327"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.899347+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-11T22:45:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed definition and causal graph linking symmetric polar peptidoglycan growth and reduced end-cap radius to spindle morphology.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T21:30:07Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007400\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:19Z",
        "curator": "claude",
        "action": "RENAME_PREDICATE_LABELS",
        "changes": "Renamed 1 causal-edge predicate label(s) to align with existing groundings: shapes \u2192 causes \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:22Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:causes\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 2 evidence-backed generic edges (2 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:14Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates (1 to has output), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope spindle_shaped_symmetric_taper=NONMECHANISTIC with scope_notes.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000684",
    "label": "spiral shaped",
    "definition": "A cell shape in which an organism has a spiral or helically curved morphology rather than a straight rod or sphere.",
    "definition_source": "DOI:10.1371/journal.pbio.1002565",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000666"
    ],
    "synonyms": [
      {
        "synonym_text": "S_curved_spiral",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "spiral",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "spiral-shaped",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "created_by": "Luke Wang",
    "evidence": [
      {
        "reference": "DOI:10.1371/journal.pbio.1002565",
        "snippet": "spirillar types",
        "notes": "Supports spiral/spirillar morphology as a recognized bacterial cell-shape class within broader bacterial morphology diversity."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1085",
        "taxon_label": "Rhodospirillum rubrum",
        "note": "Classic spiral (helically twisted) bacterium; purple non-sulfur photosynthesis model.",
        "reference": "PMID:21886856"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "spiral_shaped_curvature_mechanisms",
        "title": "Spiral-shape curvature and cell-wall mechanism",
        "description": "Evidence-backed causal sketch linking spiral morphology to scaffold-mediated curvature, peptidoglycan remodeling, and helical/spiral cell geometry.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a broad environmental or morphological classification spanning multiple mechanisms, a measurement-like bin, or an absence/arrangement descriptor; contextual protein nodes do not receive token UniProt examples.",
        "nodes": [
          {
            "node_id": "spiral_shaped_trait",
            "label": "spiral shaped",
            "node_type": "TRAIT",
            "grounding": "METPO:1000684",
            "description": "Spiral or helically curved bacterial morphology."
          },
          {
            "node_id": "peptidoglycan_remodeling",
            "label": "peptidoglycan remodeling",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Local cell-wall synthesis, relaxation, or crosslink remodeling."
          },
          {
            "node_id": "curvature_scaffold",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "curvature scaffold",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Protein scaffold or shape complex that biases cell curvature."
          },
          {
            "node_id": "helical_curvature",
            "label": "helical curvature",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Curved and twisted cell-wall geometry."
          },
          {
            "node_id": "viscous_motility_environment",
            "label": "viscous motility environment",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Viscous surroundings where curved or helical morphology can affect movement."
          },
          {
            "node_id": "pg_crosslink_relaxation",
            "label": "peptidoglycan crosslinking relaxation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduction in peptidoglycan crosslinking density that loosens the sacculus."
          },
          {
            "node_id": "biased_outer_curve_pg_biosynthesis",
            "label": "biased outer-curve peptidoglycan biosynthesis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "A longitudinal zone of elevated peptidoglycan insertion along the outer cell curve."
          },
          {
            "node_id": "cell_curvature",
            "label": "cell curvature",
            "node_type": "QUALITY",
            "description": "Bending of the cell-wall cylinder producing a curved or helical cell axis."
          },
          {
            "node_id": "elongasome_entrapment",
            "label": "elongasome entrapment",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Caging of the cell-elongation machinery that restricts where peptidoglycan is inserted."
          },
          {
            "node_id": "periplasmic_flagella",
            "label": "periplasmic flagella",
            "node_type": "ORGANELLE",
            "description": "Endoflagella running within the periplasm of spirochetes that mechanically couple to the cell body."
          },
          {
            "node_id": "cell_body",
            "label": "cell body",
            "node_type": "CELLULAR_LOCALIZATION",
            "description": "The bacterial cell body (protoplasmic cylinder) whose shape is mechanically constrained."
          }
        ],
        "edges": [
          {
            "subject": "curvature_scaffold",
            "predicate": "regulates",
            "object": "peptidoglycan_remodeling",
            "description": "Shape scaffolds or complexes bias wall remodeling to create curved and spiral forms.",
            "evidence": [
              {
                "reference": "DOI:10.1371/journal.pbio.1002565",
                "snippet": "cytoplasmic scaffolding proteins ... participate in helical morphogenesis",
                "notes": "Supports scaffold involvement in helical or spiral morphogenesis."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "peptidoglycan_remodeling",
            "predicate": "enables",
            "object": "helical_curvature",
            "description": "Peptidoglycan remodeling enables helical curvature and twist.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.cell.2010.03.046",
                "snippet": "relaxes peptidoglycan crosslinking, enabling helical cell curvature and twist",
                "notes": "H. pylori provides a source-backed concrete mechanism for spiral-like helical morphology."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "helical_curvature",
            "predicate": "confers",
            "object": "spiral_shaped_trait",
            "description": "Helical curvature produces a spiral-shaped cell body.",
            "evidence": [
              {
                "reference": "DOI:10.1371/journal.pbio.1002565",
                "snippet": "helical cells",
                "notes": "Supports helical/spiral cell shape as a recurring bacterial morphology."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "spiral_shaped_trait",
            "predicate": "associated with",
            "object": "viscous_motility_environment",
            "description": "Spiral and curved morphologies can be associated with motility in viscous media.",
            "evidence": [
              {
                "reference": "DOI:10.1371/journal.pbio.1002565",
                "snippet": "helical and curved cells appear to be optimized for motility",
                "notes": "Functional association is broad and marked as an association, not as a universal cause of the trait."
              }
            ],
            "predicate_id": "biolink:associated_with"
          },
          {
            "subject": "pg_crosslink_relaxation",
            "predicate": "promotes",
            "object": "helical_curvature",
            "description": "Relaxation of peptidoglycan crosslinking promotes helical/spiral shape.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2023.1162806",
                "notes": "Peptidoglycan crosslinking relaxation promotes helical shape and colonization."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "elongasome_entrapment",
            "predicate": "biases",
            "object": "biased_outer_curve_pg_biosynthesis",
            "description": "Caging/entrapment of the elongasome biases peptidoglycan insertion toward the outer curve.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-024-51790-z",
                "notes": "Porin-PapS assemblies entrap the cell elongation machinery, biasing peptidoglycan insertion toward the outer curve."
              }
            ]
          },
          {
            "subject": "biased_outer_curve_pg_biosynthesis",
            "predicate": "establishes",
            "object": "cell_curvature",
            "description": "A zone of elevated outer-curve peptidoglycan biosynthesis distorts the wall cylinder and establishes curvature.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-024-51790-z",
                "notes": "Creating a longitudinal zone of elevated peptidoglycan biosynthesis distorts the cell-wall cylinder and establishes curvature; ~15% bias suffices."
              }
            ]
          },
          {
            "subject": "cell_curvature",
            "predicate": "confers",
            "object": "spiral_shaped_trait",
            "description": "Sustained cell curvature produces a spiral/helically curved cell.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-024-51790-z",
                "notes": "Curvature established by biased outer-curve growth yields curved/helical cell morphology."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "periplasmic_flagella",
            "predicate": "maintains",
            "object": "spiral_shaped_trait",
            "description": "Periplasmic flagella serve as a cytoskeleton that maintains the spiral-shaped cell body.",
            "evidence": [
              {
                "reference": "DOI:10.3390/biom14121488",
                "notes": "The periplasmic flagella serves as a cytoskeleton to maintain a spiral-shaped cell body."
              }
            ]
          },
          {
            "subject": "periplasmic_flagella",
            "predicate": "distorts",
            "object": "cell_body",
            "description": "Periplasmic flagellar filaments distort and push the cell body to shape it.",
            "evidence": [
              {
                "reference": "DOI:10.1093/pnasnexus/pgad349",
                "notes": "Spirochete flagella inside the periplasm distort and push the cell body."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.894976+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-11T18:00:00-07:00",
        "curator": "codex",
        "action": "CURATED_WITH_LITERATURE",
        "changes": "Added definition and DOI-backed causal graph for spiral morphology, peptidoglycan remodeling, curvature scaffolds, helical curvature, and viscous motility association.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d71, METPO:2000202\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T05:49:24Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:associated_with\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-26T05:00:48Z",
        "curator": "claude",
        "action": "RENAME_PREDICATE_LABELS",
        "changes": "Renamed 1 causal-edge predicate label(s) to align with existing groundings: influences \u2192 regulates \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-26T05:00:51Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002211\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 6 evidence-backed generic edges (6 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:14Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002213\u00d71, METPO:2000202\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:34Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0044297\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 2 causal edge(s) off microbe-domain METPO predicates (2 to confers), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-17T06:00:00Z",
        "curator": "claude",
        "action": "REGROUND_CAUSAL_NODES",
        "changes": "Repaired a wrong CURIE from the kg-microbe name-match pass (issue 402): cell_body: GO:0044297 retracted. Was GO:0044297 'cell body', whose GO definition is 'the portion of a cell bearing surface projections such as axons, dendrites, cilia, or flagella THAT INCLUDES THE NUCLEUS' \u2014 so the term excludes prokaryotes by definition, and the node reads 'The bacterial cell body (protoplasmic cylinder)'. Found by the #405 review, and notable because BOTH sweep heuristics miss it: the labels match exactly and the term is not more specific, so only reading the DEFINITION catches it. Retracted rather than replaced \u2014 GO:0005623 is obsolete, GO:0005737 'cytoplasm' excludes the envelope the protoplasmic cylinder includes, and GO:0071944 'cell periphery' is the wrong part.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope spiral_shaped_curvature_mechanisms=NONMECHANISTIC with scope_notes; marked 1 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (curvature_scaffold).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000693",
    "label": "spirochete shaped",
    "definition": "A cell shape in which an organism has an elongated, tightly coiled helical morphology with periplasmic flagella (endoflagella) located between the cell wall and outer membrane.",
    "definition_source": "DOI:10.1073/pnas.200221797",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000666"
    ],
    "synonyms": [
      {
        "synonym_text": "spirochete",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "created_by": "Jed Dongjin Kim-Ozaeta",
    "evidence": [
      {
        "reference": "DOI:10.1073/pnas.200221797",
        "snippet": "periplasmic flagella ... confer in part its flat-wave morphology",
        "notes": "Supports spirochete morphology as a cell-cylinder and periplasmic-flagella interaction."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:160",
        "taxon_label": "Treponema pallidum",
        "note": "Syphilis spirochete; textbook flat-wave spirochete morphology with periplasmic flagella. Leptospira/Borrelia are alternative spirochete exemplars.",
        "reference": "DOI:10.1128/jb.01031-09"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "spirochete_shaped_periplasmic_flagella",
        "title": "Spirochete-shape periplasmic flagella mechanism",
        "description": "Evidence-backed causal sketch linking spirochete morphology to the cell cylinder, periplasmic flagella, FlaB filament protein, and flat-wave or helical cell-body deformation.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a broad environmental or morphological classification spanning multiple mechanisms, a measurement-like bin, or an absence/arrangement descriptor; contextual protein nodes do not receive token UniProt examples.",
        "nodes": [
          {
            "node_id": "spirochete_shaped_trait",
            "label": "spirochete shaped",
            "node_type": "TRAIT",
            "grounding": "METPO:1000693",
            "description": "Elongated helical or flat-wave spirochete morphology."
          },
          {
            "node_id": "cell_cylinder",
            "label": "cell cylinder",
            "node_type": "CELLULAR_LOCALIZATION",
            "description": "Rod-like cell body within the outer membrane sheath."
          },
          {
            "node_id": "periplasmic_flagella",
            "label": "periplasmic flagella",
            "node_type": "ORGANELLE",
            "description": "Internal flagella located in the periplasmic space."
          },
          {
            "node_id": "flaB",
            "label": "FlaB",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Major periplasmic flagellar filament protein in Borrelia.",
            "grounding": "InterPro:IPR001492"
          },
          {
            "node_id": "flat_wave_morphology",
            "label": "flat-wave morphology",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Wave-like deformation of the spirochete cell body."
          },
          {
            "node_id": "cell_body_deformation",
            "label": "cell body deformation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Distortion and pushing of the spirochete cell body by periplasmic flagellar motor action."
          },
          {
            "node_id": "flhE",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "FlhE",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Periplasmic Sec-translocated protein preventing ectopic flagellar filament assembly in the periplasm."
          },
          {
            "node_id": "ectopic_periplasmic_filament_assembly",
            "label": "ectopic periplasmic filament assembly",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Aberrant assembly of flagellar filaments in the periplasm."
          },
          {
            "node_id": "divisome_elongasome_localization",
            "label": "divisome and elongasome localization",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Localization of cell-division and elongation complexes required for peptidoglycan synthesis."
          },
          {
            "node_id": "flgV",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "FlgV",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Broadly conserved basal-body protein that modulates periplasmic flagellar filament assembly."
          },
          {
            "node_id": "cell_morphology_division",
            "label": "cell division and morphology",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Cell-division and whole-cell shape processes in spirochetes."
          }
        ],
        "edges": [
          {
            "subject": "flaB",
            "predicate": "builds",
            "object": "periplasmic_flagella",
            "description": "FlaB is required for periplasmic flagellar filaments.",
            "evidence": [
              {
                "reference": "DOI:10.1073/pnas.200221797",
                "snippet": "gene encoding the major periplasmic flagellar filament protein FlaB",
                "notes": "Targeted mutagenesis of flaB removed periplasmic flagella in Borrelia burgdorferi."
              }
            ],
            "predicate_id": "biolink:produces"
          },
          {
            "subject": "periplasmic_flagella",
            "predicate": "interact with",
            "object": "cell_cylinder",
            "description": "Periplasmic flagella interact with the cell cylinder to deform the spirochete body.",
            "evidence": [
              {
                "reference": "DOI:10.1073/pnas.200221797",
                "snippet": "complex interaction between the cell cylinder and the internal periplasmic flagella",
                "notes": "Supports a physical interaction between flagella and cell cylinder."
              }
            ],
            "predicate_id": "biolink:interacts_with"
          },
          {
            "subject": "periplasmic_flagella",
            "predicate": "confers",
            "object": "flat_wave_morphology",
            "description": "Periplasmic flagella provide a skeletal function that confers flat-wave morphology.",
            "evidence": [
              {
                "reference": "DOI:10.1073/pnas.200221797",
                "snippet": "have a skeletal function",
                "notes": "Supports periplasmic flagella as morphology-shaping structures."
              }
            ]
          },
          {
            "subject": "flat_wave_morphology",
            "predicate": "confers",
            "object": "spirochete_shaped_trait",
            "description": "Flat-wave or helical deformation produces spirochete morphology.",
            "evidence": [
              {
                "reference": "DOI:10.1073/pnas.200221797",
                "snippet": "cell morphology is either a helix, a flat wave, or an irregularly shaped helix",
                "notes": "Supports spirochete-shape classes and their dependence on internal flagella-cell-body geometry."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "periplasmic_flagella",
            "predicate": "distort and push",
            "object": "cell_body_deformation",
            "description": "Periplasmic flagella enclosed in the periplasm distort and push the cell body by flagellar motor action.",
            "evidence": [
              {
                "reference": "DOI:10.1093/pnasnexus/pgad349",
                "notes": "spirochete flagella are enclosed in the periplasmic space and the filaments distort and push the cell body by action of the flagellar motors"
              }
            ]
          },
          {
            "subject": "cell_body_deformation",
            "predicate": "confers",
            "object": "spirochete_shaped_trait",
            "description": "Flagella-driven cell body deformation produces the helical or flat-wave spirochete morphology.",
            "evidence": [
              {
                "reference": "DOI:10.1093/pnasnexus/pgad349",
                "notes": "Endoflagella-driven distortion of the cell body underlies spirochete shape."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "flhE",
            "predicate": "prevents",
            "object": "ectopic_periplasmic_filament_assembly",
            "description": "FlhE prevents ectopic assembly of flagellar filaments in the periplasm.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-024-50278-0",
                "notes": "FlhE is a periplasmic, Sec-translocated protein that prevents ectopic assembly of flagellar filaments in the periplasm."
              }
            ],
            "predicate_id": "RO:0002212"
          },
          {
            "subject": "ectopic_periplasmic_filament_assembly",
            "predicate": "mislocalizes",
            "object": "divisome_elongasome_localization",
            "description": "Ectopic periplasmic filament assembly mislocalizes divisome and elongasome complexes required for peptidoglycan synthesis.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-024-50278-0",
                "notes": "periplasmic filament assembly causally mis-localizes divisome and elongasome complexes required for peptidoglycan synthesis"
              }
            ]
          },
          {
            "subject": "divisome_elongasome_localization",
            "predicate": "alters",
            "object": "spirochete_shaped_trait",
            "description": "Mislocalized divisome/elongasome alters cell curvature and rod morphology, coupling periplasmic filaments to envelope shape.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-024-50278-0",
                "notes": "producing altered cell curvature/loss of rod morphology and infrequent cell lysis"
              }
            ]
          },
          {
            "subject": "flgV",
            "predicate": "modulates",
            "object": "periplasmic_flagella",
            "description": "FlgV localizes to the flagellar basal body and modulates periplasmic flagellar filament assembly.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-024-54806-w",
                "notes": "FlgV localizes to the flagellar basal body and altering FlgV levels profoundly impacts filament assembly"
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "flgV",
            "predicate": "perturbs",
            "object": "cell_morphology_division",
            "description": "Reduced or aberrant FlgV levels perturb cell division and cell morphology in spirochetes.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-024-54806-w",
                "notes": "\u0394flgV mutants exhibit defects in cell division and motility, including conjoined spirochetes; overproduction leads to cell elongation"
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.899870+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-11T18:00:00-07:00",
        "curator": "codex",
        "action": "CURATED_WITH_LITERATURE",
        "changes": "Replaced broad definition source with DOI-backed spirochete morphology evidence and added causal graph for FlaB, periplasmic flagella, cell cylinder, and flat-wave morphology.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T05:05:15Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A8WEP6\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-13T21:03:26Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:produces\u00d71, biolink:interacts_with\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 7 evidence-backed generic edges (6 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:14Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d71, RO:0002212\u00d71, RO:0002211\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-26T07:15:20Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A192C731\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:21:12Z",
        "curator": "claude",
        "action": "RETRACT_DEAD_UNIPROT_GROUNDINGS",
        "changes": "Retracted 1 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 2 causal edge(s) off microbe-domain METPO predicates (2 to confers), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-22T04:26:16Z",
        "curator": "codex",
        "action": "REVIEW_UNIPROT_INSTANCE_GROUNDINGS",
        "changes": "Reviewed 1 organism-specific UniProtKB grounding(s): replaced 1 with taxon-agnostic GO/InterPro terms and retracted 0 to label-only where no exact semantic term was supported (docs/GROUNDING_POLICY.md).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope spirochete_shaped_periplasmic_flagella=NONMECHANISTIC with scope_notes; marked 2 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (flhE, flgV).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000871",
    "label": "spore forming",
    "definition": "A sporulation in which an organism has the ability to produce endospores.",
    "definition_source": "DOI:10.1038/nrmicro2921",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000870"
    ],
    "synonyms": [
      {
        "synonym_text": "spore",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "yes",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/nrmicro2921",
        "snippet": "production of a highly resistant dormant cell type known as the spore",
        "notes": "Supports spore forming as the ability to produce dormant resistant spores."
      },
      {
        "reference": "PMID:32660383",
        "snippet": "Endospore formation in Bacillus subtilis",
        "notes": "Organism example: Bacillus subtilis is described as endospore-forming."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1423",
        "taxon_label": "Bacillus subtilis",
        "note": "Model endospore former and the paradigm for sporulation (strain 168).",
        "reference": "PMID:22091839"
      },
      {
        "taxon_id": "NCBITaxon:224308",
        "taxon_label": "Bacillus subtilis 168",
        "note": "Strain-level Spo0A sporulation exemplar.",
        "reference": "PMID:22091839"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "spore_forming_endospore_assembly",
        "title": "Spore-forming endospore assembly mechanism",
        "description": "Evidence-backed causal sketch linking forespore development to cortex synthesis, coat assembly, dipicolinic acid accumulation, and the spore-forming phenotype.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "The taxon-matched protein example anchors one experimentally supported causal branch; it is not presented as a universal mechanism for every taxon or every contextual branch in this graph.",
        "nodes": [
          {
            "node_id": "spore_forming_trait",
            "label": "spore forming",
            "node_type": "TRAIT",
            "grounding": "METPO:1000871",
            "description": "Ability to produce bacterial endospores."
          },
          {
            "node_id": "forespore",
            "label": "forespore",
            "node_type": "CELLULAR_LOCALIZATION",
            "description": "Developing spore compartment within the sporangium.",
            "grounding": "GO:0042763"
          },
          {
            "node_id": "spore_cortex",
            "label": "spore cortex",
            "node_type": "CELLULAR_LOCALIZATION",
            "description": "Specialized peptidoglycan layer surrounding the spore core."
          },
          {
            "node_id": "spore_coat",
            "label": "spore coat",
            "node_type": "CELLULAR_LOCALIZATION",
            "description": "Multilayered proteinaceous protective surface of the endospore.",
            "grounding": "GO:0031160"
          },
          {
            "node_id": "dipicolinic_acid",
            "label": "dipicolinic acid",
            "node_type": "CHEMICAL",
            "description": "Pyridine dicarboxylic acid enriched in bacterial spores.",
            "grounding": "CHEBI:46837"
          },
          {
            "node_id": "resistant_endospore",
            "label": "resistant endospore",
            "node_type": "ORGANELLE",
            "description": "Dormant stress-resistant spore produced by endospore-forming bacteria."
          },
          {
            "node_id": "spoIID",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "SpoIID",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Morphogenetic protein required for forespore engulfment."
          },
          {
            "node_id": "spoIIM",
            "label": "SpoIIM",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Morphogenetic protein required for forespore engulfment.",
            "grounding": "InterPro:IPR002798"
          },
          {
            "node_id": "spoIIP",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "SpoIIP",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Morphogenetic protein required for forespore engulfment."
          },
          {
            "node_id": "forespore_engulfment",
            "label": "forespore engulfment",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Engulfment of the forespore by the mother-cell membrane during sporulation."
          },
          {
            "node_id": "cortex_synthesis",
            "label": "cortex synthesis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Synthesis of spore cortex peptidoglycan in the intermembrane space."
          },
          {
            "node_id": "coat_assembly",
            "label": "spore coat assembly",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Assembly of the multilayered proteinaceous spore coat."
          },
          {
            "node_id": "spore_core_dormancy",
            "label": "spore core protection and dormancy",
            "node_type": "STATE",
            "description": "Spore core protection, dehydration, and dormancy state."
          },
          {
            "node_id": "spo0a_phosphorylated",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:P06534",
                "protein_label": "Stage 0 sporulation protein A",
                "gene_symbol": "spo0A",
                "taxon_id": "NCBITaxon:224308",
                "taxon_label": "Bacillus subtilis 168",
                "entry_status": "REVIEWED",
                "proteome_id": "UP000001570",
                "retrieved_on": "2026-10-22",
                "entry_version": 189,
                "sequence_version": 1,
                "role": "Activated Spo0A is the B. subtilis master regulator that commits cells to the sporulation program.",
                "evidence": [
                  {
                    "reference": "PMID:22091839",
                    "snippet": "Spo0A governs entry into sporulation",
                    "notes": "The cited source supports the represented protein-to-trait branch; UniProt verifies this current strain-matched protein entry."
                  }
                ]
              }
            ],
            "label": "phosphorylated Spo0A (Spo0A~P)",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Active phosphorylated master regulator of sporulation initiation."
          },
          {
            "node_id": "spo0e_phosphatases",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "Spo0E-family phosphatases",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Spo0A-specific phosphatases providing negative control of sporulation initiation."
          }
        ],
        "edges": [
          {
            "subject": "forespore",
            "predicate": "develops into",
            "object": "resistant_endospore",
            "description": "The forespore compartment matures into a resistant endospore.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev.genet.30.1.297",
                "snippet": "within which a spore is produced",
                "notes": "Supports forespore development into the spore."
              }
            ],
            "predicate_id": "biolink:develops_into"
          },
          {
            "subject": "spore_cortex",
            "predicate": "contributes to",
            "object": "resistant_endospore",
            "description": "Cortex synthesis contributes to endospore structure and resistance.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2921",
                "snippet": "spore surface layers",
                "notes": "Supports specialized spore layers as functional components of the endospore."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "spore_coat",
            "predicate": "protects",
            "object": "resistant_endospore",
            "description": "The multilayered coat protects and structures the endospore surface.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2921",
                "snippet": "assembly and functions of the multilayered coat",
                "notes": "Supports the spore coat as a protective assembly."
              }
            ]
          },
          {
            "subject": "dipicolinic_acid",
            "predicate": "contributes to",
            "object": "resistant_endospore",
            "description": "Dipicolinic acid contributes to spore resistance and stability.",
            "evidence": [
              {
                "reference": "DOI:10.1111/j.1365-2672.2005.02736.x",
                "snippet": "mechanisms are responsible for the resistance of spores",
                "notes": "Supports chemical and structural factors in Bacillus spore resistance."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "resistant_endospore",
            "predicate": "manifests as",
            "object": "spore_forming_trait",
            "description": "Production of resistant endospores manifests the spore-forming trait.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2921",
                "snippet": "production of a highly resistant dormant cell type known as the spore",
                "notes": "Supports the trait endpoint."
              }
            ],
            "predicate_id": "METPO:2007400"
          },
          {
            "subject": "spoIID",
            "predicate": "required for",
            "object": "forespore_engulfment",
            "description": "SpoIID is required for forespore engulfment.",
            "evidence": [
              {
                "reference": "DOI:10.3390/microbiolres14020035",
                "notes": "Genes spoIID, spoIIM, spoIIP are required for engulfment."
              }
            ]
          },
          {
            "subject": "spoIIM",
            "predicate": "required for",
            "object": "forespore_engulfment",
            "description": "SpoIIM is required for forespore engulfment.",
            "evidence": [
              {
                "reference": "DOI:10.3390/microbiolres14020035",
                "notes": "Genes spoIID, spoIIM, spoIIP are required for engulfment."
              }
            ]
          },
          {
            "subject": "spoIIP",
            "predicate": "required for",
            "object": "forespore_engulfment",
            "description": "SpoIIP is required for forespore engulfment.",
            "evidence": [
              {
                "reference": "DOI:10.3390/microbiolres14020035",
                "notes": "Genes spoIID, spoIIM, spoIIP are required for engulfment."
              }
            ]
          },
          {
            "subject": "cortex_synthesis",
            "predicate": "contributes to",
            "object": "resistant_endospore",
            "description": "Cortex synthesis after engulfment contributes to mature spore formation.",
            "evidence": [
              {
                "reference": "DOI:10.3390/microbiolres14020035",
                "notes": "Cortex synthesis within the intermembrane space and coat assembly follow engulfment."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "coat_assembly",
            "predicate": "contributes to",
            "object": "spore_core_dormancy",
            "description": "Spore coat assembly contributes to core protection, dehydration, and dormancy.",
            "evidence": [
              {
                "reference": "DOI:10.3390/microbiolres14020035",
                "notes": "Coat proteins influence core protection, spore-core dehydration and dormancy."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "spo0e_phosphatases",
            "predicate": "negatively regulates",
            "object": "spo0a_phosphorylated",
            "description": "Spo0E-family phosphatases dephosphorylate and inhibit Spo0A~P.",
            "evidence": [
              {
                "reference": "DOI:10.3390/microbiolres14020035",
                "notes": "A second negative control is provided by Spo0E-family Spo0A-specific phosphatases."
              }
            ],
            "predicate_id": "RO:0002212"
          },
          {
            "subject": "forespore_engulfment",
            "predicate": "contributes to",
            "object": "resistant_endospore",
            "description": "Forespore engulfment is a morphogenetic stage leading into maturation of the resistant endospore.",
            "evidence": [
              {
                "reference": "DOI:10.1101/gad.1335705",
                "snippet": "engulfment of the forespore by the mother cell; maturation of the developing (fore)spore; and, finally, release of the ripened spore",
                "notes": "Verified against the freely available primary article full text."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "coat_assembly",
            "predicate": "contributes to",
            "object": "resistant_endospore",
            "description": "Assembly of the multilayered coat contributes the protein shell of the resistant endospore.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2921",
                "snippet": "the spore coat, which consists of four layers: the basement layer (blue), inner coat (orange), outer coat (purple) and crust (red)",
                "notes": "Verified against the public PMC author-manuscript full text."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "spo0a_phosphorylated",
            "predicate": "contributes to",
            "object": "spore_forming_trait",
            "description": "Accumulation of active Spo0A~P is a required regulatory contribution to entry into the spore-forming program.",
            "evidence": [
              {
                "reference": "DOI:10.1101/gad.1335705",
                "snippet": "Evidence indicates that this gradual increase in Spo0A protein and activity plays a critical role in triggering sporulation and requires the action of the phosphorelay",
                "notes": "Verified against the freely available article; contributes-to does not claim Spo0A~P alone is sufficient."
              }
            ],
            "predicate_id": "RO:0002326"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.917323+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-06T14:40:41-07:00",
        "curator": "codex",
        "action": "CURATED_WITH_ORGANISM_EXAMPLE",
        "changes": "Added Bacillus subtilis organism example with PMID-backed evidence.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-11T21:00:00-07:00",
        "curator": "codex",
        "action": "CURATED_WITH_LITERATURE",
        "changes": "Replaced definition source with DOI-backed endospore source and added causal graph for forespore development, cortex, coat, dipicolinic acid, and resistant endospore formation.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002326\u00d72).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T05:49:24Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:develops_into\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T21:30:07Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007400\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-14T05:51:46Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0042763\u00d71, CHEBI:46837\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 6 evidence-backed generic edges (9 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:14Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002326\u00d72).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:34Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0031160\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-26T07:15:20Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 3 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A0M6WLJ0\u00d71, UniProtKB:A5N7K0\u00d71, UniProtKB:A0A1S8R940\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:21:12Z",
        "curator": "claude",
        "action": "RETRACT_DEAD_UNIPROT_GROUNDINGS",
        "changes": "Retracted 2 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-04T03:08:15Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002212\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-22T04:26:16Z",
        "curator": "codex",
        "action": "REVIEW_UNIPROT_INSTANCE_GROUNDINGS",
        "changes": "Reviewed 1 organism-specific UniProtKB grounding(s): replaced 1 with taxon-agnostic GO/InterPro terms and retracted 0 to label-only where no exact semantic term was supported (docs/GROUNDING_POLICY.md).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "CURATE_PROTEIN_TAXON_EXAMPLE",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope spore_forming_endospore_assembly=MECHANISTIC with scope_notes; marked 4 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (spoIID, spoIIP, spo0a_phosphorylated, spo0e_phosphatases); added taxon-paired protein example(s) UniProtKB:P06534 on spo0a_phosphorylated (NCBITaxon:224308); added canonical example(s) NCBITaxon:224308.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T06:48:00Z",
        "curator": "codex",
        "action": "CONNECT_CAUSAL_GRAPH_COMPONENTS",
        "changes": "Resolved issue #183 graph fragmentation (4 components to 1) using 3 source- and verbatim-snippet-backed connector(s). No paid research service was called.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-22T01:35:00Z",
        "curator": "claude",
        "action": "REFRESH_UNIPROT_ENTRY_VERSION",
        "changes": "Refreshed UniProtKB entry_version against live UniProt REST on 2026-10-22: UniProtKB:P06534 (188 -> 189 on spo0a_phosphorylated).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000682",
    "label": "spore shaped",
    "definition": "A cell shape in which an organism or differentiated cell has an endospore-like morphology, reflecting a dormant spore body with specialized protective layers.",
    "definition_source": "DOI:10.1038/nrmicro2921",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000666"
    ],
    "synonyms": [
      {
        "synonym_text": "spore-shaped",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "created_by": "Anthea Guo",
    "evidence": [
      {
        "reference": "DOI:10.1038/nrmicro2921",
        "snippet": "structure of the endospore coat",
        "notes": "Supports endospore morphology as a differentiated structure with specialized surface layers."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:224308",
        "taxon_label": "Bacillus subtilis 168",
        "note": "Reference endospore-forming strain paired to reviewed SpoIVA, the ATPase that builds the basement layer of the spore coat.",
        "reference": "DOI:10.1016/j.molcel.2008.05.030"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "spore_shaped_endospore_layers",
        "title": "Spore-shape endospore layer mechanism",
        "description": "Evidence-backed causal sketch linking spore-shaped morphology to forespore engulfment, cortex formation, coat assembly, and dehydrated spore-core maturation.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "Represents Bacillus endospore morphogenesis and coat assembly. The SpoIVA accession anchors one protein in the multiprotein coat program and does not stand in for SpoVM, SpoVID, CotE, or SafA.",
        "nodes": [
          {
            "node_id": "spore_shaped_trait",
            "label": "spore shaped",
            "node_type": "TRAIT",
            "grounding": "METPO:1000682",
            "description": "Endospore-like morphology."
          },
          {
            "node_id": "forespore_engulfment",
            "label": "forespore engulfment",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Mother-cell membrane migration around the forespore."
          },
          {
            "node_id": "cortex_formation",
            "label": "cortex formation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Formation of the specialized spore cortex layer."
          },
          {
            "node_id": "coat_assembly",
            "label": "coat assembly",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Assembly of the multilayered spore coat."
          },
          {
            "node_id": "dehydrated_spore_core",
            "label": "dehydrated spore core",
            "node_type": "CELLULAR_LOCALIZATION",
            "description": "Low-water spore core contributing to dormant spore properties."
          },
          {
            "node_id": "mature_spore_body",
            "label": "mature spore body",
            "node_type": "ORGANELLE",
            "description": "Differentiated spore structure with cortex, coat, and core."
          },
          {
            "node_id": "spo0a_phosphorylation",
            "label": "Spo0A phosphorylation",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "Phosphorylation/activation of the master regulator Spo0A."
          },
          {
            "node_id": "sporulation_initiation",
            "label": "sporulation initiation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Entry into the sporulation differentiation program."
          },
          {
            "node_id": "starvation",
            "label": "starvation",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Nutrient deprivation that triggers sporulation."
          },
          {
            "node_id": "spoiva_protein",
            "label": "SpoIVA",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Morphogenetic protein that anchors coat material to the spore surface.",
            "grounding": "InterPro:IPR014201",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:P35149",
                "protein_label": "Stage IV sporulation protein A",
                "gene_symbol": "spoIVA",
                "taxon_id": "NCBITaxon:224308",
                "taxon_label": "Bacillus subtilis 168",
                "entry_status": "REVIEWED",
                "retrieved_on": "2026-10-22",
                "entry_version": 135,
                "sequence_version": 1,
                "role": "SpoIVA hydrolyzes ATP and self-assembles into the basement layer that supports deposition of the Bacillus spore coat.",
                "evidence": [
                  {
                    "reference": "DOI:10.1016/j.molcel.2008.05.030",
                    "snippet": "ATP-driven self-assembly of a morphogenetic protein",
                    "notes": "The primary Bacillus subtilis study establishes SpoIVA ATPase-dependent coat deployment and self-assembly; UniProt verifies the reviewed 168 protein."
                  }
                ]
              }
            ]
          },
          {
            "node_id": "spovm_protein",
            "label": "SpoVM",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Morphogenetic protein required for spore coat encasement.",
            "grounding": "InterPro:IPR012609"
          },
          {
            "node_id": "spovid_protein",
            "label": "SpoVID",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Morphogenetic protein required for spore coat encasement.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Retained label-only because no exact semantic SpoVID family identifier was verified in this review."
          },
          {
            "node_id": "spore_encasement",
            "label": "spore encasement",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Morphological transition forming a full coat shell that encases the forespore."
          },
          {
            "node_id": "cote_protein",
            "label": "CotE",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Morphogenetic protein required for outer coat assembly.",
            "grounding": "InterPro:IPR018901"
          },
          {
            "node_id": "outer_coat",
            "label": "outer coat",
            "node_type": "CELLULAR_LOCALIZATION",
            "description": "Outer layer of the multilayered spore coat."
          },
          {
            "node_id": "safa_protein",
            "label": "SafA",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Morphogenetic protein required for inner coat assembly.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Retained label-only because no exact semantic SafA family identifier was verified in this review."
          },
          {
            "node_id": "inner_coat",
            "label": "inner coat",
            "node_type": "CELLULAR_LOCALIZATION",
            "description": "Inner layer of the multilayered spore coat."
          },
          {
            "node_id": "spore_coat_surface",
            "label": "spore coat",
            "node_type": "CELLULAR_LOCALIZATION",
            "description": "Multilayered spore coat anchored to the outer forespore membrane.",
            "grounding": "GO:0031160"
          }
        ],
        "edges": [
          {
            "subject": "forespore_engulfment",
            "predicate": "establishes",
            "object": "mature_spore_body",
            "description": "Engulfment establishes the forespore as a distinct spore body.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev.genet.30.1.297",
                "snippet": "two-cell-chamber sporangium",
                "notes": "Supports spore morphogenesis through compartmental development."
              }
            ]
          },
          {
            "subject": "cortex_formation",
            "predicate": "builds layer of",
            "object": "mature_spore_body",
            "description": "Cortex formation builds a specialized spore structural layer.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2921",
                "snippet": "spore surface layers",
                "notes": "Supports specialized spore layers as components of mature morphology."
              }
            ]
          },
          {
            "subject": "coat_assembly",
            "predicate": "builds layer of",
            "object": "mature_spore_body",
            "description": "Coat assembly builds the multilayered external spore structure.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2921",
                "snippet": "mechanisms of coat assembly",
                "notes": "Supports coat assembly as a morphogenetic process."
              }
            ]
          },
          {
            "subject": "dehydrated_spore_core",
            "predicate": "contributes to",
            "object": "mature_spore_body",
            "description": "Core dehydration contributes to mature spore architecture and resistance.",
            "evidence": [
              {
                "reference": "DOI:10.1111/j.1365-2672.2005.02736.x",
                "snippet": "resistance of spores of Bacillus species",
                "notes": "Supports spore core properties as part of resistant spore morphology."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "mature_spore_body",
            "predicate": "manifests as",
            "object": "spore_shaped_trait",
            "description": "Mature spore-body architecture manifests the spore-shaped trait.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2921",
                "snippet": "highly resistant dormant cell type known as the spore",
                "notes": "Supports the trait endpoint."
              }
            ],
            "predicate_id": "METPO:2007400"
          },
          {
            "subject": "spo0a_phosphorylation",
            "predicate": "positively regulates",
            "object": "sporulation_initiation",
            "description": "Phosphorylation of the master regulator Spo0A initiates sporulation.",
            "evidence": [
              {
                "reference": "DOI:10.1126/sciadv.adq0791",
                "notes": "Spo0A is the master regulator governing entry into sporulation; sporulation initiates upon phosphorylation of Spo0A (generalized across endospore formers)."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "starvation",
            "predicate": "positively regulates",
            "object": "sporulation_initiation",
            "description": "Starvation triggers entry into the sporulation differentiation program.",
            "evidence": [
              {
                "reference": "DOI:10.1126/sciadv.adq0791",
                "notes": "Starvation triggers bacterial spore formation, a committed differentiation program."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "sporulation_initiation",
            "predicate": "leads to",
            "object": "forespore_engulfment",
            "description": "Sporulation initiation leads to forespore engulfment.",
            "evidence": [
              {
                "reference": "DOI:10.1126/sciadv.adq0791",
                "notes": "Sporulation is a committed differentiation program proceeding through forespore engulfment."
              }
            ]
          },
          {
            "subject": "spoiva_protein",
            "predicate": "anchors",
            "object": "spore_coat_surface",
            "description": "SpoIVA anchors/tethers coat material to the spore surface (outer forespore membrane).",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2921",
                "notes": "SpoIVA functions to anchor coat material to the spore surface; required to tether the coat to the outer forespore membrane (conserved role)."
              }
            ]
          },
          {
            "subject": "spovm_protein",
            "predicate": "required for",
            "object": "spore_encasement",
            "description": "SpoVM is required for the morphological transition that encases the forespore.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2921",
                "notes": "SpoVM and SpoVID are required for the morphological transition from a single scaffold cap to a full spherical shell that encases the forespore."
              }
            ]
          },
          {
            "subject": "spovid_protein",
            "predicate": "required for",
            "object": "spore_encasement",
            "description": "SpoVID is required for spore encasement; mutants block formation of a full coat shell.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2921",
                "notes": "SpoVID is explicitly required for spore encasement; spoVID mutants block formation of a full coat shell."
              }
            ]
          },
          {
            "subject": "cote_protein",
            "predicate": "required for assembly of",
            "object": "outer_coat",
            "description": "CotE is required for assembly of the spore outer coat.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2921",
                "notes": "SafA is necessary for inner coat assembly and CotE for outer coat assembly."
              }
            ]
          },
          {
            "subject": "safa_protein",
            "predicate": "required for assembly of",
            "object": "inner_coat",
            "description": "SafA is required for assembly of the spore inner coat.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2921",
                "notes": "SafA is necessary for inner coat assembly; SafA and CotE are respectively required for the deposition of the inner and outer coat."
              }
            ]
          },
          {
            "subject": "spore_encasement",
            "predicate": "contributes to",
            "object": "mature_spore_body",
            "description": "Encasement changes the coat scaffold into the complete shell of the mature spore body.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2921",
                "snippet": "SpoVM and SpoVID are crucial for the transition from a single cap to a full spherical shell that encases the spore",
                "notes": "Verified against the public PMC author-manuscript full text."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "outer_coat",
            "predicate": "part of",
            "object": "spore_coat_surface",
            "description": "The outer coat is a structural layer of the spore coat.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2921",
                "snippet": "Three layers of the B. subtilis spore coat are observed in thin-section electron microscopy: a lamellar inner coat, a more coarsely layered outer coat and a recently identified layer named the crust",
                "notes": "Verified against the public PMC author-manuscript full text."
              }
            ],
            "predicate_id": "biolink:part_of"
          },
          {
            "subject": "inner_coat",
            "predicate": "part of",
            "object": "spore_coat_surface",
            "description": "The inner coat is a structural layer of the spore coat.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2921",
                "snippet": "The core is protected by the cortex (green) and the spore coat, which consists of four layers",
                "notes": "Verified against the public PMC author-manuscript full text."
              }
            ],
            "predicate_id": "biolink:part_of"
          },
          {
            "subject": "spore_coat_surface",
            "predicate": "part of",
            "object": "mature_spore_body",
            "description": "The spore coat forms a shell attached around the mature forespore.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2921",
                "snippet": "the coat did not form a shell of protein around the forespore and was often found detached from the forespore surface",
                "notes": "Verified against the public PMC author manuscript; mutant failure defines the normal coat-shell attachment represented by this edge."
              }
            ],
            "predicate_id": "biolink:part_of"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.893996+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-11T21:00:00-07:00",
        "curator": "codex",
        "action": "CURATED_WITH_LITERATURE",
        "changes": "Added DOI-backed definition and causal graph for forespore engulfment, cortex formation, coat assembly, dehydrated spore core, and mature spore-body morphology.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002326\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T21:30:07Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007400\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 8 evidence-backed generic edges (12 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:34Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0031160\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-26T07:15:20Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 4 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A2K8N6W1\u00d71, UniProtKB:A0A0B5ANC0\u00d71, UniProtKB:D5WPR1\u00d71, UniProtKB:A0A0N1QUA1\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:21:12Z",
        "curator": "claude",
        "action": "RETRACT_DEAD_UNIPROT_GROUNDINGS",
        "changes": "Retracted 1 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-04T03:08:15Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002213\u00d72).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-22T04:26:16Z",
        "curator": "codex",
        "action": "REVIEW_UNIPROT_INSTANCE_GROUNDINGS",
        "changes": "Reviewed 3 organism-specific UniProtKB grounding(s): replaced 2 with taxon-agnostic GO/InterPro terms and retracted 1 to label-only where no exact semantic term was supported (docs/GROUNDING_POLICY.md).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "CURATE_PROTEIN_TAXON_EXAMPLE",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope spore_shaped_endospore_layers=MECHANISTIC with scope_notes; marked 2 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (spovid_protein, safa_protein); added taxon-paired protein example(s) UniProtKB:P35149 on spoiva_protein (NCBITaxon:224308); regrounded 1 node(s) (spoiva_protein: none->InterPro:IPR014201); added canonical example(s) NCBITaxon:224308.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T06:48:00Z",
        "curator": "codex",
        "action": "CONNECT_CAUSAL_GRAPH_COMPONENTS",
        "changes": "Resolved issue #183 graph fragmentation (5 components to 1) using 4 source- and verbatim-snippet-backed connector(s). No paid research service was called.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-22T01:35:00Z",
        "curator": "claude",
        "action": "REFRESH_UNIPROT_ENTRY_VERSION",
        "changes": "Refreshed UniProtKB entry_version against live UniProt REST on 2026-10-22: UniProtKB:P35149 (134 -> 135 on spoiva_protein).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000870",
    "label": "sporulation",
    "definition": "A phenotype that is relating to an organism's ability to form dormant, stress-resistant endospores.",
    "definition_source": "DOI:10.1146/annurev.genet.30.1.297",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "synonyms": [
      {
        "synonym_text": "General.keywords",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "Physiology and metabolism.spore formation.spore formation",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev.genet.30.1.297",
        "snippet": "conversion of a growing cell into a two-cell-chamber sporangium",
        "notes": "Supports sporulation as a developmental morphogenesis process producing a spore within a sporangium."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1423",
        "taxon_label": "Bacillus subtilis",
        "note": "endospore formation model",
        "reference": "PMID:32061128"
      },
      {
        "taxon_id": "NCBITaxon:1488",
        "taxon_label": "Clostridium acetobutylicum",
        "note": "anaerobic sporulation",
        "reference": "PMID:18631379"
      },
      {
        "taxon_id": "NCBITaxon:224308",
        "taxon_label": "Bacillus subtilis 168",
        "note": "Strain-level SpoIIIE sporulation exemplar.",
        "reference": "DOI:10.1038/s41467-024-51654-6"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "sporulation_spo0a_sigma_morphogenesis",
        "title": "Sporulation Spo0A and sigma-factor morphogenesis",
        "description": "Evidence-backed causal sketch linking environmental stress and Spo0A activation to asymmetric septation, compartment-specific sigma factors, forespore maturation, and endospore formation.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "The B. subtilis 168 protein examples (SpoIIIE P21458 and compartment-specific sporulation sigma factors SigF P07860, SigE P06222, SigG P19940, and SigK P12254) anchor the experimentally resolved Bacillus endospore morphogenesis cascade; they are not presented as universal across all endospore-forming Firmicutes.",
        "nodes": [
          {
            "node_id": "sporulation_trait",
            "label": "sporulation",
            "node_type": "TRAIT",
            "grounding": "METPO:1000870",
            "description": "Ability to undergo endospore-forming developmental differentiation."
          },
          {
            "node_id": "nutrient_limitation",
            "label": "nutrient limitation",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Starvation or stress cue that can trigger sporulation."
          },
          {
            "node_id": "spo0a_phosphorelay",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "Spo0A phosphorelay",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Phosphorelay-controlled master regulator of sporulation initiation."
          },
          {
            "node_id": "asymmetric_septation",
            "label": "asymmetric septation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Polar division generating mother-cell and forespore compartments."
          },
          {
            "node_id": "compartment_sigma_factors",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "compartment-specific sigma factors",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Sporulation sigma factors such as sigma F, E, G, and K."
          },
          {
            "node_id": "forespore_maturation",
            "label": "forespore maturation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Developmental process converting the forespore into a mature endospore."
          },
          {
            "node_id": "endospore",
            "label": "endospore",
            "node_type": "ORGANELLE",
            "description": "Dormant stress-resistant spore produced by sporulating bacteria."
          },
          {
            "node_id": "mother_cell_forespore",
            "label": "mother cell and forespore",
            "node_type": "CELLULAR_LOCALIZATION",
            "description": "The two cellular compartments produced by asymmetric division during sporulation."
          },
          {
            "node_id": "spoiiie_translocase",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:P21458",
                "protein_label": "DNA translocase SpoIIIE",
                "gene_symbol": "spoIIIE",
                "taxon_id": "NCBITaxon:224308",
                "taxon_label": "Bacillus subtilis 168",
                "entry_status": "REVIEWED",
                "proteome_id": "UP000001570",
                "retrieved_on": "2026-10-22",
                "entry_version": 157,
                "sequence_version": 3,
                "role": "SpoIIIE translocates the chromosome across the asymmetric septum into the B. subtilis forespore.",
                "evidence": [
                  {
                    "reference": "DOI:10.1038/s41467-024-51654-6",
                    "snippet": "SpoIIIE mediates chromosome translocation",
                    "notes": "The cited source supports the represented protein-to-trait branch; UniProt verifies this current strain-matched protein entry."
                  }
                ]
              }
            ],
            "label": "SpoIIIE",
            "node_type": "GENE_OR_PROTEIN",
            "description": "DNA translocase that pumps the chromosome into the forespore during sporulation."
          },
          {
            "node_id": "chromosome_translocation",
            "label": "chromosome translocation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Movement of the trapped chromosome across the asymmetric septum into the forespore."
          },
          {
            "node_id": "forespore_engulfment",
            "label": "forespore engulfment",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Mother-cell membrane migration around the forespore producing a cell-within-a-cell state."
          },
          {
            "node_id": "cell_within_cell_state",
            "label": "cell-within-a-cell state",
            "node_type": "STATE",
            "description": "Engulfed forespore fully enclosed within the mother-cell cytoplasm."
          },
          {
            "node_id": "sigma_f",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "sigma F",
            "node_type": "GENE_OR_PROTEIN",
            "description": "First compartment-specific sigma factor activated in the forespore.",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:P07860",
                "protein_label": "RNA polymerase sigma-F factor",
                "gene_symbol": "sigF",
                "taxon_id": "NCBITaxon:224308",
                "taxon_label": "Bacillus subtilis 168",
                "entry_status": "REVIEWED",
                "proteome_id": "UP000001570",
                "retrieved_on": "2026-10-22",
                "entry_version": 175,
                "sequence_version": 1,
                "role": "Early forespore-specific RNA polymerase sigma factor (sigma F) activated after asymmetric septation in B. subtilis 168.",
                "evidence": [
                  {
                    "reference": "DOI:10.1038/s41467-024-51654-6",
                    "snippet": "compartment specific RNA polymerase sigma factors \u2013 \u03c3F and \u03c3E \u2013 responsible for further activation of sporulation genes in the forespore and mother cell respectively",
                    "notes": "Supports forespore-specific sigma factor SigF in the B. subtilis sporulation cascade."
                  }
                ]
              }
            ]
          },
          {
            "node_id": "sigma_e",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "sigma E",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Mother-cell sigma factor activated downstream of sigma F.",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:P06222",
                "protein_label": "RNA polymerase sigma-E factor",
                "gene_symbol": "sigE",
                "taxon_id": "NCBITaxon:224308",
                "taxon_label": "Bacillus subtilis 168",
                "entry_status": "REVIEWED",
                "proteome_id": "UP000001570",
                "retrieved_on": "2026-10-22",
                "entry_version": 173,
                "sequence_version": 1,
                "role": "Early mother-cell-specific RNA polymerase sigma factor (sigma E) activated downstream of forespore sigma F in B. subtilis 168.",
                "evidence": [
                  {
                    "reference": "DOI:10.1038/s41467-024-51654-6",
                    "snippet": "compartment specific RNA polymerase sigma factors \u2013 \u03c3F and \u03c3E \u2013 responsible for further activation of sporulation genes in the forespore and mother cell respectively",
                    "notes": "Supports mother-cell-specific sigma factor SigE in the B. subtilis sporulation cascade."
                  }
                ]
              }
            ]
          },
          {
            "node_id": "sigma_g",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "sigma G",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Late forespore sigma factor driving spore maturation and DNA protection.",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:P19940",
                "protein_label": "RNA polymerase sigma-G factor",
                "gene_symbol": "sigG",
                "taxon_id": "NCBITaxon:224308",
                "taxon_label": "Bacillus subtilis 168",
                "entry_status": "REVIEWED",
                "proteome_id": "UP000001570",
                "retrieved_on": "2026-10-22",
                "entry_version": 166,
                "sequence_version": 1,
                "role": "Late forespore-specific RNA polymerase sigma factor (sigma G) activated after forespore engulfment to drive spore maturation and Ssp-mediated DNA protection in B. subtilis 168.",
                "evidence": [
                  {
                    "reference": "DOI:10.1038/s41467-024-51654-6",
                    "snippet": "the late sporulation spore specific sigma factor \u03c3G responsible for spore maturation, spore DNA protection via Ssp proteins and preparation for germination",
                    "notes": "Supports late forespore sigma factor SigG driving spore maturation and DNA protection."
                  }
                ]
              }
            ]
          },
          {
            "node_id": "sigma_k",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "sigma K",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Late mother-cell sigma factor controlling spore coat and cortex maturation.",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:P12254",
                "protein_label": "RNA polymerase sigma-K factor",
                "gene_symbol": "sigK",
                "taxon_id": "NCBITaxon:224308",
                "taxon_label": "Bacillus subtilis 168",
                "entry_status": "REVIEWED",
                "proteome_id": "UP000001570",
                "retrieved_on": "2026-10-22",
                "entry_version": 158,
                "sequence_version": 2,
                "role": "Late mother-cell-specific RNA polymerase sigma factor (sigma K) controlling spore coat and cortex maturation in B. subtilis 168.",
                "evidence": [
                  {
                    "reference": "DOI:10.1038/s41467-024-51654-6",
                    "snippet": "Finally, the late mother cell \u03c3K activation, regulated by \u03c3G, results in spore coat and cortex maturation, preparation for germination and eventually, mother cell lysis",
                    "notes": "Supports late mother-cell sigma factor SigK driving spore coat and cortex maturation."
                  }
                ]
              }
            ]
          },
          {
            "node_id": "spore_dna_protection",
            "label": "spore DNA protection",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Protection of spore chromosomal DNA, e.g. via small acid-soluble (Ssp) proteins."
          },
          {
            "node_id": "spore_coat_cortex",
            "label": "spore coat and cortex",
            "node_type": "CELLULAR_LOCALIZATION",
            "description": "Protective spore envelope layers (cortex, coat, exosporium) deposited during maturation."
          },
          {
            "node_id": "stress_resistance",
            "label": "heat and chemical resistance",
            "node_type": "QUALITY",
            "description": "Resistance of the mature endospore to heat and chemical stress."
          }
        ],
        "edges": [
          {
            "subject": "nutrient_limitation",
            "predicate": "activates",
            "object": "spo0a_phosphorelay",
            "description": "Starvation and stress signals feed into Spo0A activation.",
            "evidence": [
              {
                "reference": "DOI:10.1016/S1369-5274(00)00141-7",
                "snippet": "steps that lead to activation of Spo0A",
                "notes": "Supports Spo0A activation as the initiation control point for sporulation."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "spo0a_phosphorelay",
            "predicate": "initiates",
            "object": "asymmetric_septation",
            "description": "Spo0A-dependent transcription initiates the morphological program that includes asymmetric septation.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev.genet.30.1.297",
                "snippet": "activation of these sigma factors to landmark events in morphogenesis",
                "notes": "Supports regulatory linkage between Spo0A/sigma activation and sporulation morphogenesis."
              }
            ]
          },
          {
            "subject": "asymmetric_septation",
            "predicate": "establishes",
            "object": "compartment_sigma_factors",
            "description": "Asymmetric septation establishes mother-cell and forespore compartments with distinct sigma-factor programs.",
            "evidence": [
              {
                "reference": "DOI:10.1128/MMBR.67.4.526-560.2003",
                "snippet": "Compartmentalization of Gene Expression",
                "notes": "Supports compartment-specific gene expression during spore formation."
              }
            ]
          },
          {
            "subject": "compartment_sigma_factors",
            "predicate": "regulates",
            "object": "forespore_maturation",
            "description": "Sequential sigma-factor activity drives forespore development.",
            "evidence": [
              {
                "reference": "DOI:10.1128/MMBR.67.4.526-560.2003",
                "snippet": "forespore- and mother cell-specific transcription factors",
                "notes": "Supports sigma-factor cascades as drivers of compartmental development."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "forespore_maturation",
            "predicate": "has output",
            "object": "endospore",
            "description": "Forespore maturation produces a dormant endospore.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev.genet.30.1.297",
                "snippet": "within which a spore is produced",
                "notes": "Supports the developmental endpoint of sporulation."
              }
            ],
            "predicate_id": "RO:0002234"
          },
          {
            "subject": "endospore",
            "predicate": "manifests as",
            "object": "sporulation_trait",
            "description": "Endospore production manifests the sporulation phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2921",
                "snippet": "production of a highly resistant dormant cell type known as the spore",
                "notes": "Supports endospore production as the trait outcome."
              }
            ],
            "predicate_id": "METPO:2007400"
          },
          {
            "subject": "asymmetric_septation",
            "predicate": "has output",
            "object": "mother_cell_forespore",
            "description": "Asymmetric division produces distinct mother-cell and forespore compartments.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-024-51654-6",
                "notes": "via an asymmetric division into a forespore and mother cell (central defining morphogenesis edge)."
              }
            ],
            "predicate_id": "RO:0002234"
          },
          {
            "subject": "spoiiie_translocase",
            "predicate": "mediates",
            "object": "chromosome_translocation",
            "description": "SpoIIIE translocates the chromosome into the forespore after asymmetric septation.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-024-51654-6",
                "notes": "recruitment of SpoIIIE for chromosome translocation."
              }
            ]
          },
          {
            "subject": "forespore_engulfment",
            "predicate": "creates",
            "object": "cell_within_cell_state",
            "description": "Engulfment of the forespore by the mother cell creates a cell-within-a-cell state.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-024-51654-6",
                "notes": "forespore engulfment, creating a cell-within-a-cell state."
              }
            ],
            "predicate_id": "biolink:produces"
          },
          {
            "subject": "sigma_f",
            "predicate": "activates",
            "object": "sigma_e",
            "description": "Forespore sigma F drives activation of mother-cell sigma E.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.jbc.2024.107905",
                "notes": "SigF activated first in the forespore; SigE activation in the mother cell depends on SigF."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "sigma_g",
            "predicate": "drives",
            "object": "spore_dna_protection",
            "description": "Late forespore sigma G drives spore DNA protection during maturation.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-024-51654-6",
                "notes": "sigma G drives spore maturation and spore DNA protection via Ssp proteins."
              }
            ]
          },
          {
            "subject": "sigma_k",
            "predicate": "controls",
            "object": "spore_coat_cortex",
            "description": "Mother-cell sigma K controls spore coat and cortex maturation.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-024-51654-6",
                "notes": "mother-cell sigma K controls spore coat and cortex maturation."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "spore_coat_cortex",
            "predicate": "confers",
            "object": "stress_resistance",
            "description": "Deposition of cortex, coat and exosporium confers heat and chemical resistance.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s42003-024-06521-x",
                "notes": "deposition of cortex, coat and exosporium (conferring heat and chemical resistance)."
              }
            ]
          },
          {
            "subject": "chromosome_translocation",
            "predicate": "precedes",
            "object": "forespore_engulfment",
            "description": "Chromosome translocation after asymmetric division precedes completion of forespore engulfment.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-024-51654-6",
                "snippet": "After asymmetric division and chromosome translocation, genes in \u03c3F and \u03c3E regulons drive metabolic and morphological changes to the cell which conclude in forespore engulfment",
                "notes": "Verified against the open Europe PMC full text."
              }
            ]
          },
          {
            "subject": "cell_within_cell_state",
            "predicate": "contributes to",
            "object": "forespore_maturation",
            "description": "The engulfed cell-within-a-cell state permits activation of the late forespore program responsible for maturation.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-024-51654-6",
                "snippet": "This is required for activation of the late sporulation spore specific sigma factor \u03c3G responsible for spore maturation, spore DNA protection via Ssp proteins and preparation for germination",
                "notes": "In the source, 'This' immediately follows the cell-within-a-cell state created by forespore engulfment."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "sigma_f",
            "predicate": "part of",
            "object": "compartment_sigma_factors",
            "description": "Sigma F is one of the compartment-specific sporulation factors.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-024-51654-6",
                "snippet": "compartment specific RNA polymerase sigma factors \u2013 \u03c3F and \u03c3E \u2013 responsible for further activation of sporulation genes in the forespore and mother cell respectively",
                "notes": "Verified against the open Europe PMC full text."
              }
            ],
            "predicate_id": "biolink:part_of"
          },
          {
            "subject": "sigma_g",
            "predicate": "positively regulates",
            "object": "forespore_maturation",
            "description": "Late forespore sigma G drives the spore-maturation program.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-024-51654-6",
                "snippet": "the late sporulation spore specific sigma factor \u03c3G responsible for spore maturation, spore DNA protection via Ssp proteins and preparation for germination",
                "notes": "Verified against the open Europe PMC full text."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "sigma_k",
            "predicate": "contributes to",
            "object": "forespore_maturation",
            "description": "Late mother-cell sigma K contributes coat and cortex maturation to the developing spore.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-024-51654-6",
                "snippet": "Finally, the late mother cell \u03c3K activation, regulated by \u03c3G, results in spore coat and cortex maturation, preparation for germination and eventually, mother cell lysis",
                "notes": "Verified against the open Europe PMC full text."
              }
            ],
            "predicate_id": "RO:0002326"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.916642+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-11T21:00:00-07:00",
        "curator": "codex",
        "action": "CURATED_WITH_LITERATURE",
        "changes": "Added DOI-backed definition and causal graph for nutrient limitation, Spo0A phosphorelay, asymmetric septation, compartment sigma factors, forespore maturation, and endospore formation.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T21:30:07Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007400\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:19Z",
        "curator": "claude",
        "action": "RENAME_PREDICATE_LABELS",
        "changes": "Renamed 1 causal-edge predicate label(s) to align with existing groundings: drives \u2192 regulates \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:22Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002211\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-13T21:03:26Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002213\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-17T04:09:44Z",
        "curator": "claude",
        "action": "REMOVE_REDUNDANT_SYNONYM",
        "changes": "Removed 1 synonym(s) whose text duplicated the label (seeder redundancy; no information lost).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 7 evidence-backed generic edges (12 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:14Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 4 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d71, biolink:produces\u00d71, RO:0002213\u00d71, RO:0002211\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-26T07:15:20Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 4 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A100JQQ1\u00d71, UniProtKB:E0J3M3\u00d71, UniProtKB:A0A0C7NZS0\u00d71, UniProtKB:A0A060N640\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:21:12Z",
        "curator": "claude",
        "action": "RETRACT_DEAD_UNIPROT_GROUNDINGS",
        "changes": "Retracted 3 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 2 causal edge(s) off microbe-domain METPO predicates (2 to has output), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-21T08:00:00Z",
        "curator": "codex",
        "action": "NORMALISE_NODE_TYPE",
        "changes": "Tranche 5 of issue 356 settles the process/quality families and merges ids that meant the same sense: stress_resistance is QUALITY. Stress resistance here is enhanced tolerance or resistance of a cell or mature endospore, a measurable protective attribute. The nodes do not describe the general stress-response process.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-22T04:26:16Z",
        "curator": "codex",
        "action": "REVIEW_UNIPROT_INSTANCE_GROUNDINGS",
        "changes": "Reviewed 1 organism-specific UniProtKB grounding(s): replaced 0 with taxon-agnostic GO/InterPro terms and retracted 1 to label-only where no exact semantic term was supported (docs/GROUNDING_POLICY.md).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "CURATE_PROTEIN_TAXON_EXAMPLE",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope sporulation_spo0a_sigma_morphogenesis=MECHANISTIC with scope_notes; marked 7 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (spo0a_phosphorelay, compartment_sigma_factors, spoiiie_translocase, sigma_f, sigma_e, sigma_g, sigma_k); added taxon-paired protein example(s) UniProtKB:P21458 on spoiiie_translocase (NCBITaxon:224308); added canonical example(s) NCBITaxon:224308.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T06:48:00Z",
        "curator": "codex",
        "action": "CONNECT_CAUSAL_GRAPH_COMPONENTS",
        "changes": "Resolved issue #183 graph fragmentation (6 components to 1) using 5 source- and verbatim-snippet-backed connector(s). No paid research service was called.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-22T01:35:00Z",
        "curator": "claude",
        "action": "CURATE_PROTEIN_TAXON_EXAMPLE",
        "changes": "Added reviewed B. subtilis 168 sporulation sigma-factor protein_examples UniProtKB:P07860 (SigF, v175), UniProtKB:P06222 (SigE, v173), UniProtKB:P19940 (SigG, v166), and UniProtKB:P12254 (SigK, v158) across sigma_f, sigma_e, sigma_g, and sigma_k (DOI:10.1038/s41467-024-51654-6), updated scope_notes, and refreshed UniProtKB:P21458 entry_version 156 -> 157 on spoiiie_translocase.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000694",
    "label": "square shaped",
    "definition": "A cell shape in which an organism forms flat, square or rectangular cells.",
    "definition_source": "DOI:10.1099/ijs.0.65431-0",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000666"
    ],
    "synonyms": [
      {
        "synonym_text": "square",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1099/ijs.0.65431-0",
        "snippet": "flat square or disc-shaped cells",
        "notes": "Haloquadratum walsbyi description supports flat square cell morphology in halophilic archaea."
      },
      {
        "reference": "DOI:10.1146/annurev-cellbio-101011-155745",
        "snippet": "cell shape is genetically determined",
        "notes": "Cell-shape review supports anisotropic envelope growth as the basis for non-round cell geometries."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:293091",
        "taxon_label": "Haloquadratum walsbyi",
        "note": "Universally cited square/rectangular flat-celled archaeon (2-5 um wide x 0.1-0.2 um thick); dominant in hypersaline salterns.",
        "reference": "DOI:10.1371/journal.pone.0018653"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "square_shaped_planar_anisotropic_growth",
        "title": "Square-shape planar anisotropic envelope growth",
        "description": "DOI-backed graph linking anisotropic planar cell-envelope growth and S-layer-constrained right-angle geometry to flat square cells.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "Square shape is retained as a haloarchaeal morphology classification. The contextual S-layer label spans many subunits and does not justify a token protein example for right-angle geometry.",
        "nodes": [
          {
            "node_id": "square_shaped_trait",
            "label": "square shaped",
            "node_type": "TRAIT",
            "grounding": "METPO:1000694",
            "description": "Flat square or rectangular cell geometry."
          },
          {
            "node_id": "planar_envelope_growth",
            "label": "planar envelope growth",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Cell-envelope expansion in two orthogonal in-plane directions."
          },
          {
            "node_id": "slayer_constraints",
            "label": "S-layer constraints",
            "node_type": "ORGANELLE",
            "description": "Paracrystalline S-layer that imposes geometric constraints on cell shape.",
            "grounding": "GO:0030115"
          },
          {
            "node_id": "right_angle_growth",
            "label": "right-angle growth geometry",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Growth pattern producing perpendicular cell edges."
          },
          {
            "node_id": "archaeal_slayer",
            "label": "archaeal S-layer",
            "node_type": "ORGANELLE",
            "description": "Paracrystalline surface (S-)layer of glycosylated proteins coating the archaeal cell."
          },
          {
            "node_id": "cell_shape",
            "label": "cell shape",
            "node_type": "QUALITY",
            "description": "Overall geometric form of the cell."
          },
          {
            "node_id": "mechanical_stability",
            "label": "mechanical stability",
            "node_type": "QUALITY",
            "description": "Resistance of the cell envelope to mechanical deformation."
          },
          {
            "node_id": "cytoskeletal_growth_axis_control",
            "label": "cytoskeletal control of local growth and division axis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Precise control of local envelope growth and division axis guided by cytoskeletal filaments and an overlying S-layer coat."
          },
          {
            "node_id": "slayer_proteins",
            "label": "S-layer proteins",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Glycoprotein subunits forming the paracrystalline S-layer lattice.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "The node denotes taxon-variable S-layer subunits rather than one exact protein family."
          },
          {
            "node_id": "cell_shape_size_defect",
            "label": "cell shape and size defect",
            "node_type": "STATE",
            "description": "Aberrant cell shape and size resulting from loss of S-layer integrity."
          }
        ],
        "edges": [
          {
            "subject": "planar_envelope_growth",
            "predicate": "enables",
            "object": "right_angle_growth",
            "description": "Planar envelope growth in two axes supports rectangular geometry.",
            "evidence": [
              {
                "reference": "DOI:10.1099/ijs.0.65431-0",
                "snippet": "flat square or disc-shaped cells",
                "notes": "Supports planar growth as the cellular basis for flat square cells."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "slayer_constraints",
            "predicate": "causes",
            "object": "right_angle_growth",
            "description": "The paracrystalline S-layer constrains envelope geometry toward right angles.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-cellbio-101011-155745",
                "snippet": "cell shape is genetically determined",
                "notes": "Supports envelope architectural constraints (e.g., S-layer) as shape determinants."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "right_angle_growth",
            "predicate": "manifests as",
            "object": "square_shaped_trait",
            "description": "Right-angle planar geometry manifests the square-shaped trait.",
            "evidence": [
              {
                "reference": "DOI:10.1099/ijs.0.65431-0",
                "snippet": "square or disc-shaped cells",
                "notes": "Supports the trait endpoint."
              }
            ],
            "predicate_id": "METPO:2007400"
          },
          {
            "subject": "archaeal_slayer",
            "predicate": "defines",
            "object": "cell_shape",
            "description": "The archaeal S-layer is a primary structural determinant of cell shape.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-022-01215-8",
                "notes": "S-layers are known to fulfil roles in defining the cell-shape, providing mechanical stability and functioning as molecular sieves."
              }
            ],
            "predicate_id": "METPO:2007500"
          },
          {
            "subject": "archaeal_slayer",
            "predicate": "provides",
            "object": "mechanical_stability",
            "description": "The archaeal S-layer provides mechanical stability to the cell envelope.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-022-01215-8",
                "notes": "S-layers are known to fulfil roles in defining the cell-shape, providing mechanical stability and functioning as molecular sieves."
              }
            ]
          },
          {
            "subject": "cytoskeletal_growth_axis_control",
            "predicate": "gives rise to",
            "object": "square_shaped_trait",
            "description": "Precise cytoskeleton- and S-layer-guided control of local growth and division axis gives rise to flat geometric (square/triangular) archaeal shapes.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-022-01215-8",
                "notes": "These cell shapes arise as the result of precise cellular control of local growth and the axis of division under the guidance of cytoskeletal filaments and an overlying coat of glycosylated proteins, also termed the S-layer."
              }
            ]
          },
          {
            "subject": "slayer_proteins",
            "predicate": "causes when lost",
            "object": "cell_shape_size_defect",
            "description": "Loss of S-layer proteins causes profound defects in cell shape and size, evidencing the S-layer causal role in archaeal morphology.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-022-01215-8",
                "notes": "S-layer proteins were recently found to be dispensable for S.islandicus viability, but cells lacking these proteins exhibited profound defects in cell shape and size."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.900481+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-11T22:45:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed definition and causal graph linking planar anisotropic envelope growth and S-layer constraints to square-shaped halophile morphology.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T21:30:07Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007400\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:19Z",
        "curator": "claude",
        "action": "RENAME_PREDICATE_LABELS",
        "changes": "Renamed 1 causal-edge predicate label(s) to align with existing groundings: shapes \u2192 causes \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:22Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:causes\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 4 evidence-backed generic edges (6 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:14Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007500\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope square_shaped_planar_anisotropic_growth=NONMECHANISTIC with scope_notes; marked 1 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (slayer_proteins).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000118",
    "label": "staphylococcus arrangement",
    "definition": "A cell arrangement in which dividing cocci form irregular three-dimensional grape-like clusters because division planes occur in multiple, non-orthogonal orientations and daughter cells remain attached.",
    "definition_source": "DOI:10.1128/MMBR.00001-06",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000666"
    ],
    "synonyms": [
      {
        "synonym_text": "cluster-forming cocci",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1128/MMBR.00001-06"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1128/MMBR.00001-06",
        "notes": "Young's review treats clustered coccal arrangement as a division-plane- determined heritable morphology."
      },
      {
        "reference": "DOI:10.1038/ncomms4842",
        "notes": "Division-plane orientation and daughter-cell separation govern formation of three-dimensional coccal clusters."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1280",
        "taxon_label": "Staphylococcus aureus",
        "note": "Namesake of the staphylococcal arrangement (grape-like irregular clusters from division in multiple planes).",
        "reference": "PMID:845124"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "staphylococcus_irregular_division_cluster",
        "title": "Staphylococcus arrangement via multi-plane non-orthogonal division",
        "description": "Evidence-backed causal sketch linking non-orthogonal multi-plane division and incomplete daughter-cell separation to irregular grape-like coccal clusters.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a broad environmental or morphological classification spanning multiple mechanisms, a measurement-like bin, or an absence/arrangement descriptor; contextual protein nodes do not receive token UniProt examples.",
        "nodes": [
          {
            "node_id": "staphylococcus_trait",
            "label": "staphylococcus arrangement",
            "node_type": "TRAIT",
            "grounding": "traitmech:000118",
            "description": "Cocci forming irregular three-dimensional grape-like clusters."
          },
          {
            "node_id": "cell_division",
            "label": "cell division",
            "node_type": "BIOLOGICAL_PROCESS",
            "grounding": "GO:0051301",
            "description": "Bacterial binary fission."
          },
          {
            "node_id": "multiplane_nonorthogonal_division",
            "label": "multi-plane non-orthogonal division",
            "node_type": "QUALITY",
            "description": "Successive division planes oriented in multiple non-orthogonal directions."
          },
          {
            "node_id": "facz",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "FacZ",
            "node_type": "GENE_OR_PROTEIN",
            "description": "S. aureus division-site placement factor that prevents aberrant Z-ring placement."
          },
          {
            "node_id": "gpsb",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "GpsB",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Conserved cell-division regulator that promotes lateral interactions between FtsZ filaments."
          },
          {
            "node_id": "ftsz",
            "label": "FtsZ",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Tubulin-like central divisome protein forming the cytokinetic Z-ring.",
            "grounding": "InterPro:IPR000158"
          },
          {
            "node_id": "ftsz_ring",
            "label": "FtsZ Z-ring",
            "node_type": "CELLULAR_LOCALIZATION",
            "description": "Dynamic treadmilling FtsZ polymer ring that establishes the division site."
          },
          {
            "node_id": "divisome_pg_synthesis",
            "label": "divisome peptidoglycan synthesis at division site",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Septal peptidoglycan synthesis machinery organized at the division site."
          }
        ],
        "edges": [
          {
            "subject": "multiplane_nonorthogonal_division",
            "predicate": "causes",
            "object": "staphylococcus_trait",
            "description": "Multi-plane non-orthogonal division with incomplete separation generates 3D coccal clusters.",
            "evidence": [
              {
                "reference": "DOI:10.1038/ncomms4842",
                "notes": "Division-plane orientation and daughter-cell separation govern formation of three-dimensional coccal clusters."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "cell_division",
            "predicate": "confers",
            "object": "staphylococcus_trait",
            "description": "Bacterial cell division underlies coccal cluster formation.",
            "evidence": [
              {
                "reference": "DOI:10.1128/MMBR.00001-06",
                "notes": "Young treats clustered coccal arrangement as a division-plane- determined heritable morphology."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "facz",
            "predicate": "prevents aberrant placement of",
            "object": "ftsz_ring",
            "description": "FacZ prevents aberrant membrane invaginations and multiple/mispositioned FtsZ cytokinetic rings.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-024-01607-y",
                "notes": "\"Inactivation of FacZ produced aberrant membrane invaginations and multiple FtsZ cytokinetic rings\"; peer-reviewed S. aureus phenotype."
              }
            ]
          },
          {
            "subject": "facz",
            "predicate": "interacts with",
            "object": "gpsb",
            "description": "FacZ directly interacts with the division regulator GpsB.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-024-01607-y",
                "notes": "\"FacZ interacts directly with GpsB both in vitro and in vivo\"; direct biochemical and cellular interaction."
              }
            ],
            "predicate_id": "biolink:interacts_with"
          },
          {
            "subject": "facz",
            "predicate": "antagonizes",
            "object": "gpsb",
            "description": "FacZ antagonizes GpsB to prevent spurious Z-ring formation and aberrant envelope invaginations.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-024-01607-y",
                "notes": "Authors propose FacZ antagonizes GpsB to prevent spurious Z-ring formation; peer-reviewed proposed model."
              }
            ]
          },
          {
            "subject": "gpsb",
            "predicate": "promotes lateral interactions between",
            "object": "ftsz",
            "description": "GpsB promotes lateral interactions between FtsZ filaments.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-024-01607-y",
                "notes": "\"GpsB itself interacts with FtsZ and promotes lateral interactions between FtsZ filaments.\""
              }
            ]
          },
          {
            "subject": "ftsz_ring",
            "predicate": "organizes",
            "object": "divisome_pg_synthesis",
            "description": "Treadmilling FtsZ Z-ring organizes the divisome peptidoglycan synthesis machinery at the division site.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-024-01607-y",
                "notes": "\"the septum is built by the divisome organized by treadmilling FtsZ polymers that form a dynamic Z-ring to establish the division site.\""
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-06-08T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate MORPHOLOGY trait (staphylococcus / cluster arrangement); leftover round, cell-arrangement sibling of diplococcus shaped.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-09T15:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (multi-plane non-orthogonal division \u2192 cluster) with GO node grounding and RO/biolink predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 5 evidence-backed generic edges (5 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:14Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:interacts_with\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:19Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:C0LUM8\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-26T07:15:20Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A060RK42\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:21:12Z",
        "curator": "claude",
        "action": "RETRACT_DEAD_UNIPROT_GROUNDINGS",
        "changes": "Retracted 1 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 1 causal edge(s) off enables/RO:0002327 with a TRAIT object (1 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-22T04:26:16Z",
        "curator": "codex",
        "action": "REVIEW_UNIPROT_INSTANCE_GROUNDINGS",
        "changes": "Reviewed 1 organism-specific UniProtKB grounding(s): replaced 1 with taxon-agnostic GO/InterPro terms and retracted 0 to label-only where no exact semantic term was supported (docs/GROUNDING_POLICY.md).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope staphylococcus_irregular_division_cluster=NONMECHANISTIC with scope_notes; marked 2 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (facz, gpsb).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000685",
    "label": "star shaped",
    "definition": "A cell shape in which an organism has multiple radiating projections from a central body.",
    "definition_source": "DOI:10.1146/annurev-cellbio-101011-155745",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000666"
    ],
    "synonyms": [
      {
        "synonym_text": "S_star_dumbbell_pleomorphic",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "star",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "star-shaped",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "stellate",
        "synonym_type": "EXACT_SYNONYM",
        "source": "http://purl.obolibrary.org/obo/pato/releases/2025-05-14/pato.obo"
      }
    ],
    "xrefs": [
      "PATO:0002065"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev-cellbio-101011-155745",
        "snippet": "polar growth",
        "notes": "Cell-shape review supports multi-pole peptidoglycan growth as the basis for prosthecate or appendaged geometries."
      },
      {
        "reference": "DOI:10.1146/annurev.micro.061705.103240",
        "snippet": "prosthecate bacteria",
        "notes": "Prosthecate-bacteria review supports star-shaped morphology in Stella/Ancalomicrobium and related stalked lineages."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1123295",
        "taxon_label": "Stella vacuolata DSM 5901 = ATCC 43931",
        "note": "Six-pointed star-shaped (flat, multi-pointed) prosthecate bacterium; genus Stella is the textbook star morphology.",
        "reference": "PMID:31395645"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "star_shaped_multiple_prosthecae",
        "title": "Star-shape multiple prosthecae extension",
        "description": "DOI-backed graph linking multi-site polar peptidoglycan growth and prostheca outgrowth to a star-shaped cell body with radiating projections.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a broad environmental or morphological classification spanning multiple mechanisms, a measurement-like bin, or an absence/arrangement descriptor; contextual protein nodes do not receive token UniProt examples.",
        "nodes": [
          {
            "node_id": "star_shaped_trait",
            "label": "star shaped",
            "node_type": "TRAIT",
            "grounding": "METPO:1000685",
            "description": "Cell body with multiple radiating projections."
          },
          {
            "node_id": "multi_site_polar_pg",
            "label": "multi-site polar peptidoglycan growth",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Polar wall growth initiated at multiple sites on the cell body."
          },
          {
            "node_id": "prostheca_outgrowth",
            "label": "prostheca outgrowth",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Outward extension of cytoplasmic projections (prosthecae)."
          },
          {
            "node_id": "radiating_projections",
            "label": "radiating projections",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Multiple projecting arms emerging from a central cell body."
          },
          {
            "node_id": "baca_lmdc_module",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "BacA-LmdC morphogenesis module",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Conserved bactofilin (BacA) and M23 endopeptidase (LmdC) functional module."
          },
          {
            "node_id": "local_pg_remodeling",
            "label": "local peptidoglycan remodeling",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Localized change in the mode of cell-wall biosynthesis and remodeling."
          },
          {
            "node_id": "cell_shape_determination",
            "label": "cell shape determination",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Establishment of cell shape in morphologically complex bacteria."
          },
          {
            "node_id": "elongasome_restriction",
            "label": "restriction of elongasome movement",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Bactofilin polymers restrict movement of elongasome complexes."
          },
          {
            "node_id": "zonal_pg_biosynthesis",
            "label": "peptidoglycan biosynthesis confined to growth zones",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Peptidoglycan biosynthesis spatially confined to discrete growth zones."
          },
          {
            "node_id": "bactofilins",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "bactofilins",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Bactofilin cytoskeletal scaffold proteins."
          },
          {
            "node_id": "pbpc_prosthecate_pole",
            "label": "PbpC localization at prosthecate pole",
            "node_type": "CELLULAR_LOCALIZATION",
            "description": "Bifunctional penicillin-binding protein PbpC localized to the prosthecate pole."
          },
          {
            "node_id": "spmx",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "SpmX",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Developmental regulator co-opted as a morphogen to position prosthecae."
          }
        ],
        "edges": [
          {
            "subject": "multi_site_polar_pg",
            "predicate": "regulates",
            "object": "prostheca_outgrowth",
            "description": "Multi-site polar PG growth drives extension of cellular projections.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev.micro.061705.103240",
                "snippet": "prosthecate bacteria",
                "notes": "Supports prostheca extension via polar wall growth."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "prostheca_outgrowth",
            "predicate": "has output",
            "object": "radiating_projections",
            "description": "Multiple prosthecae form radiating projections from the cell body.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev.micro.061705.103240",
                "snippet": "prosthecate bacteria",
                "notes": "Supports prosthecate morphology in star-shaped lineages."
              }
            ],
            "predicate_id": "RO:0002234"
          },
          {
            "subject": "radiating_projections",
            "predicate": "manifests as",
            "object": "star_shaped_trait",
            "description": "Radiating projections manifest the star-shaped trait.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev.micro.061705.103240",
                "snippet": "prosthecate bacteria",
                "notes": "Supports the trait endpoint."
              }
            ],
            "predicate_id": "METPO:2007400"
          },
          {
            "subject": "baca_lmdc_module",
            "predicate": "promotes",
            "object": "local_pg_remodeling",
            "description": "The bactofilin-M23 peptidase module promotes local changes in cell-wall biosynthesis.",
            "evidence": [
              {
                "reference": "DOI:10.7554/eLife.86577.2",
                "notes": "Bactofilins and M23 peptidases form a conserved functional module that promotes local changes in the mode of cell wall biosynthesis."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "local_pg_remodeling",
            "predicate": "regulates",
            "object": "cell_shape_determination",
            "description": "Local peptidoglycan remodeling drives cell shape determination.",
            "evidence": [
              {
                "reference": "DOI:10.7554/eLife.86577.2",
                "notes": "Thereby driving cell shape determination in morphologically complex bacteria."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "elongasome_restriction",
            "predicate": "regulates",
            "object": "zonal_pg_biosynthesis",
            "description": "Restriction of elongasome movement confines peptidoglycan biosynthesis to specific growth zones.",
            "evidence": [
              {
                "reference": "DOI:10.7554/eLife.86577.2",
                "notes": "Bactofilin polymers act as a barrier restricting elongasome movement, confining PG biosynthesis to specific growth zones."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "bactofilins",
            "predicate": "localizes",
            "object": "pbpc_prosthecate_pole",
            "description": "Bactofilins localize the bifunctional PBP PbpC to the prosthecate pole.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.tim.2017.09.012",
                "notes": "In C. crescentus bactofilins localize the bifunctional PBP PbpC to the prosthecate pole; conserved prostheca mechanism."
              }
            ]
          },
          {
            "subject": "pbpc_prosthecate_pole",
            "predicate": "promotes",
            "object": "prostheca_outgrowth",
            "description": "PbpC localization at the prosthecate pole promotes prostheca synthesis.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.tim.2017.09.012",
                "notes": "Deletion of PbpC reduces prostheca synthesis, implicating its polar localization in prostheca outgrowth."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "spmx",
            "predicate": "regulates",
            "object": "prostheca_outgrowth",
            "description": "SpmX is co-opted as a morphogen to position prosthecae via zonal peptidoglycan remodeling.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.tim.2017.09.012",
                "notes": "SpmX co-opted as a morphogen to position prosthecae via zonal peptidoglycan remodeling."
              }
            ],
            "predicate_id": "RO:0002211"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.895581+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-11T22:45:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed causal graph linking multi-site polar peptidoglycan growth and prostheca outgrowth to star-shaped morphology.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T21:30:07Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007400\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:19Z",
        "curator": "claude",
        "action": "RENAME_PREDICATE_LABELS",
        "changes": "Renamed 1 causal-edge predicate label(s) to align with existing groundings: drives \u2192 regulates \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:22Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002211\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 6 evidence-backed generic edges (8 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:14Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 5 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002211\u00d73, RO:0002213\u00d72).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates (1 to has output), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope star_shaped_multiple_prosthecae=NONMECHANISTIC with scope_notes; marked 3 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (baca_lmdc_module, bactofilins, spmx).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T06:15:41Z",
        "curator": "codex",
        "action": "ADD_EXACT_ONTOLOGY_MATCH",
        "changes": "Ontology exact-match review (2026-08-25): approved exact xref(s): PATO:0002065; declared exact synonym(s): 'stellate'. Evidence is predicate-scoped in the versioned ontology snapshots; OAK cross-checked direct data, and OLS4 spot-checked release deltas and disputed hits.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000117",
    "label": "streptococcus arrangement",
    "definition": "A cell arrangement in which dividing cocci remain attached in chains because successive division planes are parallel and daughter cells do not fully separate.",
    "definition_source": "DOI:10.1128/MMBR.00001-06",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000666"
    ],
    "synonyms": [
      {
        "synonym_text": "chain-forming cocci",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1128/MMBR.00001-06"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1128/MMBR.00001-06",
        "notes": "Young's review of the selective value of bacterial shape treats cell arrangement (including chains) as a heritable, division-determined morphology."
      },
      {
        "reference": "DOI:10.1038/ncomms4842",
        "notes": "Daughter-cell separation during division determines whether cocci stay attached in chains versus separating."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1314",
        "taxon_label": "Streptococcus pyogenes",
        "note": "Chains of cocci (streptococcal arrangement) from division in a single plane.",
        "reference": "https://www.ncbi.nlm.nih.gov/books/NBK7611/"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "streptococcus_parallel_division_chain",
        "title": "Streptococcus arrangement via parallel division and incomplete separation",
        "description": "Evidence-backed causal sketch linking parallel division planes and incomplete daughter-cell separation to coccal chains.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a broad environmental or morphological classification spanning multiple mechanisms, a measurement-like bin, or an absence/arrangement descriptor; contextual protein nodes do not receive token UniProt examples.",
        "nodes": [
          {
            "node_id": "streptococcus_trait",
            "label": "streptococcus arrangement",
            "node_type": "TRAIT",
            "grounding": "traitmech:000117",
            "description": "Dividing cocci remain attached in chains."
          },
          {
            "node_id": "cell_division",
            "label": "cell division",
            "node_type": "BIOLOGICAL_PROCESS",
            "grounding": "GO:0051301",
            "description": "Bacterial binary fission."
          },
          {
            "node_id": "parallel_division_planes",
            "label": "parallel division planes",
            "node_type": "QUALITY",
            "description": "Successive division planes oriented in parallel."
          },
          {
            "node_id": "daughter_cell_separation",
            "label": "daughter-cell separation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Splitting of the septum so that daughter cells fully separate after division."
          },
          {
            "node_id": "pg_remodeling",
            "label": "peptidoglycan remodeling",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Remodeling and cleavage of septal/peripheral peptidoglycan during elongation and division."
          },
          {
            "node_id": "pg_hydrolases",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "peptidoglycan hydrolases",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Septal and peripheral PG hydrolases (e.g. FtsEX-PcsB, CbpD) that cleave muropeptides enabling splitting."
          },
          {
            "node_id": "pcsb_autolysin",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "PcsB autolysin",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Essential PG autolysin coordinating PG remodeling with cell division."
          },
          {
            "node_id": "ftsex_complex",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "FtsEX complex",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Membrane complex required for PcsB autolysin function."
          },
          {
            "node_id": "lipoteichoic_acid",
            "label": "lipoteichoic acid",
            "node_type": "CHEMICAL",
            "description": "Cell-wall anionic polymer involved in proper cell shape and division.",
            "grounding": "CHEBI:28640"
          }
        ],
        "edges": [
          {
            "subject": "parallel_division_planes",
            "predicate": "causes",
            "object": "streptococcus_trait",
            "description": "Parallel successive division planes with incomplete daughter separation produce coccal chains.",
            "evidence": [
              {
                "reference": "DOI:10.1038/ncomms4842",
                "notes": "Daughter-cell separation during division determines whether cocci stay attached in chains."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "cell_division",
            "predicate": "confers",
            "object": "streptococcus_trait",
            "description": "Bacterial cell division underlies coccal chain formation.",
            "evidence": [
              {
                "reference": "DOI:10.1128/MMBR.00001-06",
                "notes": "Young treats chain arrangement as a heritable, division-determined morphology."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "parallel_division_planes",
            "predicate": "enables",
            "object": "cell_division",
            "description": "Ovococci divide in successive parallel planes perpendicular to the long axis.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mSphere.00119-21",
                "notes": "Ovococci are elongated ellipsoids divided in successive parallel planes perpendicular to their long axis."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "pg_hydrolases",
            "predicate": "enables",
            "object": "pg_remodeling",
            "description": "PG hydrolases release nascent glycan strands and cleave muropeptides, enabling PG remodeling and eventual splitting.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2021.737396",
                "notes": "PG hydrolases are required to release nascent glycan strands and cleave muropeptides, enabling integration of new material and eventual splitting."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "pcsb_autolysin",
            "predicate": "promotes",
            "object": "pg_remodeling",
            "description": "PcsB PG remodeling activity is coordinated with cell division.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mSphere.00119-21",
                "notes": "The PG remodeling activity by PcsB is coordinated with cell division through its interaction with the FtsEX complex."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "ftsex_complex",
            "predicate": "required for",
            "object": "pcsb_autolysin",
            "description": "The FtsEX complex is required for PcsB autolysin function.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mSphere.00119-21",
                "notes": "PcsB is the only essential PG autolysin, and the FtsEX complex is required for the PcsB function."
              }
            ]
          },
          {
            "subject": "pg_remodeling",
            "predicate": "promotes",
            "object": "daughter_cell_separation",
            "description": "Septal PG remodeling/splitting enables daughter cells to separate; failure maintains chains.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mSphere.00119-21",
                "notes": "Part of the residual structure of PG did not fully disintegrate, resulting in incomplete cell separation (chain phenotype)."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "daughter_cell_separation",
            "predicate": "prevents",
            "object": "streptococcus_trait",
            "description": "Complete daughter-cell separation prevents chain formation; its failure produces chains.",
            "evidence": [
              {
                "reference": "DOI:10.1038/ncomms4842",
                "notes": "Daughter-cell separation during division determines whether cocci stay attached in chains versus separating."
              }
            ],
            "predicate_id": "RO:0002212"
          },
          {
            "subject": "lipoteichoic_acid",
            "predicate": "promotes",
            "object": "cell_division",
            "description": "Lipoteichoic acid supports proper cell shape and bacterial division.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s13567-024-01287-w",
                "notes": "LTA is involved in maintaining proper cell shape and influences cell shape and bacterial division."
              }
            ],
            "predicate_id": "RO:0002213"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-06-08T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate MORPHOLOGY trait (streptococcus / chain arrangement); leftover round, cell-arrangement sibling of the existing diplococcus shaped.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-09T15:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (parallel-plane division \u2192 chain) with GO node grounding and RO/biolink predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 7 evidence-backed generic edges (6 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:14Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 6 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002213\u00d73, RO:0002327\u00d72, RO:0002212\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:34Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:28640\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 1 causal edge(s) off enables/RO:0002327 with a TRAIT object (1 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope streptococcus_parallel_division_chain=NONMECHANISTIC with scope_notes; marked 3 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (pg_hydrolases, pcsb_autolysin, ftsex_complex).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1005037",
    "label": "subpolar flagellation",
    "definition": "A motility phenotype in which flagella are located near but not at the cell pole.",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "SEEDED",
    "parent_traits": [
      "traitmech:000056"
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-11T08:29:17Z",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)"
      },
      {
        "timestamp": "2026-09-11T08:30:00Z",
        "curator": "codex",
        "action": "ENRICHED_FROM_LITERATURE",
        "changes": "Enriched the seeded METPO subpolar flagellation phenotype with DOI-backed subpolar-flagella evidence after a repository-wide duplicate review covering ignored and hidden files.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-21T21:12:25Z",
        "curator": "claude",
        "action": "CURATE_CAUSAL_GRAPH",
        "changes": "Added NONMECHANISTIC causal_graphs entry (subpolar_flagellation_surface_assembly_sketch) anchored on existing verbatim record evidence snippets.",
        "llm_assisted": true
      }
    ],
    "definition_source": "DOI:10.1128/JB.01405-06",
    "evidence": [
      {
        "reference": "DOI:10.1128/JB.01405-06",
        "snippet": "The cell has two sets of flagellar systems, one thick flagellum and a few thin flagella, uniquely growing at subpolar positions.",
        "notes": "Kanbe et al. describe two morphologically distinct Bradyrhizobium flagellar systems that both emerge from subpolar positions."
      },
      {
        "reference": "DOI:10.3390/biom10050774",
        "snippet": "Under the growth conditions commonly used in the laboratory, a single subpolar flagellum that traverses the cell membrane, is assembled on the surface.",
        "notes": "Camarena and Dreyfus review the Rhodobacter sphaeroides Fla1 system as a second bacterial example of subpolar flagellation."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:224911",
        "taxon_label": "Bradyrhizobium diazoefficiens USDA 110",
        "note": "Kanbe et al. directly observed subpolar thick and thin flagella in Bradyrhizobium japonicum 110spc4, a derivative of USDA 110 now assigned by NCBI to B. diazoefficiens.",
        "reference": "DOI:10.1128/JB.01405-06"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "subpolar_flagellation_surface_assembly_sketch",
        "title": "Subpolar flagellar assembly and cell-surface placement",
        "description": "Evidence-backed morphology sketch linking cell-surface assembly of subpolar flagella to the subpolar flagellation phenotype.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "Morphological placement sketch backed by DOI:10.1128/JB.01405-06 and DOI:10.3390/biom10050774; strain-matched UniProtKB protein examples for the Bradyrhizobium diazoefficiens USDA 110 subpolar flagellin or placement factors remain to be curated.",
        "nodes": [
          {
            "node_id": "subpolar_flagellation_trait",
            "label": "subpolar flagellation",
            "node_type": "TRAIT",
            "grounding": "METPO:1005037",
            "description": "Motility morphology in which flagella emerge from subpolar positions near the cell pole."
          },
          {
            "node_id": "subpolar_flagellation_subpolar_flagellum",
            "label": "bacterial-type flagellum",
            "node_type": "ORGANELLE",
            "grounding": "GO:0009288",
            "description": "Flagellar organelle emerging at a subpolar position on the bacterial cell surface."
          },
          {
            "node_id": "subpolar_flagellation_flagellum_assembly",
            "label": "bacterial-type flagellum assembly",
            "node_type": "BIOLOGICAL_PROCESS",
            "grounding": "GO:0044780",
            "description": "Assembly of a membrane-traversing subpolar flagellum on the cell surface."
          }
        ],
        "edges": [
          {
            "subject": "subpolar_flagellation_subpolar_flagellum",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "subpolar_flagellation_trait",
            "description": "Flagellar systems growing at subpolar positions confer the subpolar flagellation morphology.",
            "evidence": [
              {
                "reference": "DOI:10.1128/JB.01405-06",
                "snippet": "The cell has two sets of flagellar systems, one thick flagellum and a few thin flagella, uniquely growing at subpolar positions.",
                "notes": "Kanbe et al. describe thick and thin flagellar systems uniquely growing at subpolar positions in Bradyrhizobium."
              }
            ]
          },
          {
            "subject": "subpolar_flagellation_flagellum_assembly",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "subpolar_flagellation_subpolar_flagellum",
            "description": "Cell-surface flagellar assembly forms the membrane-traversing subpolar flagellum.",
            "evidence": [
              {
                "reference": "DOI:10.3390/biom10050774",
                "snippet": "Under the growth conditions commonly used in the laboratory, a single subpolar flagellum that traverses the cell membrane, is assembled on the surface.",
                "notes": "Camarena and Dreyfus describe assembly of a single membrane-traversing subpolar flagellum on the cell surface."
              }
            ]
          }
        ]
      }
    ]
  },
  {
    "identifier": "traitmech:000069",
    "label": "sulfur globule",
    "definition": "An intracellular (or periplasmic) inclusion of elemental sulfur formed as an intermediate during the oxidation of reduced sulfur compounds, characteristic of many sulfur-oxidizing and phototrophic sulfur bacteria.",
    "definition_source": "DOI:10.1016/S0065-2911(08)00002-7",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "traitmech:000066"
    ],
    "synonyms": [
      {
        "synonym_text": "sulfur inclusion",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1016/S0065-2911(08)00002-7"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1016/S0065-2911(08)00002-7",
        "notes": "Frigaard & Dahl describe sulfur globules as sulfur-storage inclusions formed during oxidative sulfur metabolism in phototrophic sulfur bacteria."
      },
      {
        "reference": "DOI:10.1038/s41579-020-0413-0",
        "notes": "Greening & Lithgow include sulfur globules among bacterial intracellular storage inclusions/organelles."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:90373",
        "taxon_label": "Thiomargarita namibiensis",
        "note": "Giant sulfur bacterium storing conspicuous intracellular sulfur globules. Beggiatoa is a co-canonical exemplar.",
        "reference": "PMID:10205058"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "sulfur_globule_sulfur_oxidation_intermediate",
        "title": "Sulfur globules store elemental sulfur during oxidative sulfur metabolism",
        "description": "Evidence-backed causal sketch linking oxidative sulfur metabolism to deposition of elemental sulfur as intracellular/periplasmic globules.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a broad environmental or morphological classification spanning multiple mechanisms, a measurement-like bin, or an absence/arrangement descriptor; contextual protein nodes do not receive token UniProt examples.",
        "nodes": [
          {
            "node_id": "sulfur_globule_trait",
            "label": "sulfur globule",
            "node_type": "TRAIT",
            "grounding": "traitmech:000069",
            "description": "Intracellular / periplasmic inclusion of elemental sulfur."
          },
          {
            "node_id": "elemental_sulfur",
            "label": "elemental sulfur",
            "node_type": "CHEMICAL",
            "description": "S0 stored as a globule intermediate.",
            "grounding": "CHEBI:26833"
          },
          {
            "node_id": "oxidative_sulfur_metabolism",
            "label": "oxidative sulfur metabolism",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Oxidation of reduced sulfur compounds (e.g. sulfide, thiosulfate)."
          },
          {
            "node_id": "sqr",
            "label": "sulfide:quinone oxidoreductase (SQR)",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Flavoenzyme that oxidizes sulfide, initiating intracellular sulfur oxidation.",
            "grounding": "GO:0070224"
          },
          {
            "node_id": "sulfane_sulfur",
            "label": "sulfane sulfur",
            "node_type": "CHEMICAL",
            "description": "Reactive zero-valent sulfur species produced during sulfide oxidation."
          },
          {
            "node_id": "polysulfide",
            "label": "polysulfide (H2Sn)",
            "node_type": "CHEMICAL",
            "description": "Short-chain inorganic polysulfide intermediate of sulfide oxidation."
          },
          {
            "node_id": "persulfide_dioxygenase",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "persulfide dioxygenase (PDO)",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Enzyme oxidizing glutathione persulfide (GSSH) to sulfite."
          },
          {
            "node_id": "sulfite",
            "label": "sulfite",
            "node_type": "CHEMICAL",
            "description": "Oxidation product of glutathione persulfide via PDO."
          }
        ],
        "edges": [
          {
            "subject": "oxidative_sulfur_metabolism",
            "predicate": "has output",
            "object": "elemental_sulfur",
            "description": "Oxidation of reduced sulfur compounds generates elemental sulfur as an intermediate.",
            "evidence": [
              {
                "reference": "DOI:10.1016/S0065-2911(08)00002-7",
                "notes": "Frigaard & Dahl describe sulfur globules as sulfur-storage intermediates formed during oxidative sulfur metabolism."
              }
            ],
            "predicate_id": "RO:0002234"
          },
          {
            "subject": "elemental_sulfur",
            "predicate": "located in",
            "object": "sulfur_globule_trait",
            "description": "The deposited elemental sulfur forms a globule inclusion.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41579-020-0413-0",
                "notes": "Greening & Lithgow include sulfur globules among bacterial intracellular storage inclusions."
              }
            ],
            "predicate_id": "biolink:located_in"
          },
          {
            "subject": "sqr",
            "predicate": "produces",
            "object": "sulfane_sulfur",
            "description": "SQR-catalyzed oxidation of sulfide generates sulfane sulfur intermediates.",
            "evidence": [
              {
                "reference": "DOI:10.3390/ijms252010962",
                "notes": "Initial oxidation of sulfide occurs under the action of SQR, producing sulfane sulfur; generalizes broadly to intracellular sulfur oxidizers."
              }
            ],
            "predicate_id": "METPO:2007800"
          },
          {
            "subject": "sqr",
            "predicate": "produces",
            "object": "polysulfide",
            "description": "SQR oxidizes sulfide to short-chain inorganic polysulfide (H2Sn, n>=2).",
            "evidence": [
              {
                "reference": "DOI:10.1128/aem.01941-21",
                "notes": "SQR oxidized H2S into short-chain inorganic polysulfide (H2Sn, n >= 2); broad sulfur-chemistry mechanism."
              }
            ],
            "predicate_id": "METPO:2007800"
          },
          {
            "subject": "polysulfide",
            "predicate": "precursor of",
            "object": "sulfur_globule_trait",
            "description": "Polysulfide/sulfane sulfur spontaneously generates S8 that aggregates into sulfur globules.",
            "evidence": [
              {
                "reference": "DOI:10.1128/aem.01941-21",
                "notes": "SQR oxidized H2S to H2Sn, which spontaneously generated S8; S8 aggregated into sulfur globules."
              }
            ]
          },
          {
            "subject": "persulfide_dioxygenase",
            "predicate": "oxidizes",
            "object": "sulfite",
            "description": "PDO oxidizes glutathione persulfide (GSSH) to sulfite (GSSH + O2 + H2O -> GSH + SO3^2- + 2H+).",
            "evidence": [
              {
                "reference": "DOI:10.3390/ijms252010962",
                "notes": "PDO acts on GSSH: GSSH + O2 + H2O -> GSH + SO3^2- + 2H+; well-defined enzymatic edge."
              }
            ],
            "predicate_id": "METPO:2007803"
          },
          {
            "subject": "persulfide_dioxygenase",
            "predicate": "participates in",
            "object": "oxidative_sulfur_metabolism",
            "description": "PDO acts downstream of SQR in the same sulfide-oxidation pathway that deposits elemental sulfur as globules.",
            "evidence": [
              {
                "reference": "PMID:35653932",
                "snippet": "Heterotrophic bacteria and human mitochondria often use sulfide: quinone oxidoreductase (SQR) and persulfide dioxygenase (PDO) to oxidize sulfide to sulfite and thiosulfate.",
                "notes": "Places PDO in the same SQR-initiated sulfide-oxidation pathway the rest of this graph models, which is what attaches the PDO/sulfite branch to the globule mechanism rather than leaving it a free-standing enzymatic fact. Scope caveat (issue 297) - the quote covers heterotrophic bacteria and human mitochondria, not the Thiomargarita/Beggiatoa exemplars of this trait, so it supports the generic pathway claim the object node makes and no more."
              }
            ],
            "predicate_id": "biolink:participates_in"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-06-03T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate MORPHOLOGY trait (sulfur globule); storage sub-variant of intracellular inclusion.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-09T15:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (oxidative sulfur metabolism \u2192 elemental sulfur globule) with METPO/biolink predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-14T05:51:46Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:26833\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 4 evidence-backed generic edges (5 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:14Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d72, METPO:2000016\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:23:55Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0070224\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-05T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 1 evidence-backed edge attaching the stranded PDO/sulfite branch to the pathway the rest of the graph models (issue 183): persulfide_dioxygenase participates in oxidative_sulfur_metabolism, grounded biolink:participates_in. The snippet is verbatim from PMID:35653932, checked against the PubMed abstract. Resolves this graph's FRAGMENTED_GRAPH and its 2 UNREACHABLE_FROM_TRAIT findings.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates (1 to has output), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T02:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES_PART2",
        "changes": "Re-grounded 3 causal edge(s) off microbe-domain METPO predicates onto their causal-graph counterparts (1 to oxidizes, 2 to produces), issue 301 part 2. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Each replacement is a 1:1 mirror of its source predicate that changes only the domain, so the claim each edge makes is unchanged and directions are unchanged. The replacements are proposed in proposals/metpo_traitmech_v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope sulfur_globule_sulfur_oxidation_intermediate=NONMECHANISTIC with scope_notes; marked 1 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (persulfide_dioxygenase).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000062",
    "label": "swarming motility",
    "definition": "A flagella-dependent, multicellular surface motility in which cells move rapidly and coordinately across a surface, typically accompanied by hyperflagellation and secretion of a wetting surfactant.",
    "definition_source": "DOI:10.1038/nrmicro2405",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000702"
    ],
    "synonyms": [
      {
        "synonym_text": "swarming",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1038/nrmicro2405"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/nrmicro2405",
        "notes": "Kearns, \"A field guide to bacterial swarming motility\", defines swarming via increased flagella per cell, surfactant secretion, and movement in multicellular groups."
      },
      {
        "reference": "DOI:10.1146/annurev.micro.57.030502.091014",
        "notes": "Harshey, \"Bacterial motility on a surface\", places swarming among the surface-motility modes of bacteria."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:584",
        "taxon_label": "Proteus mirabilis",
        "note": "Historical/diagnostic swarming model (bulls-eye colonies; hyper-flagellated swarmer cells).",
        "reference": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10671106/"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "swarming_hyperflagellation_surfactant",
        "title": "Swarming motility via hyperflagellation and surfactant secretion",
        "description": "Evidence-backed causal sketch linking flagellar hyperflagellation and wetting-surfactant secretion to multicellular surface swarming.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a broad environmental or morphological classification spanning multiple mechanisms, a measurement-like bin, or an absence/arrangement descriptor; contextual protein nodes do not receive token UniProt examples.",
        "nodes": [
          {
            "node_id": "swarming_trait",
            "label": "swarming motility",
            "node_type": "TRAIT",
            "grounding": "traitmech:000062",
            "description": "Flagella-dependent multicellular surface motility."
          },
          {
            "node_id": "bacterial_flagellum",
            "label": "bacterial-type flagellum",
            "node_type": "CELLULAR_LOCALIZATION",
            "grounding": "GO:0009288",
            "description": "Helical proteinaceous locomotory organelle (hyperflagellation under swarming)."
          },
          {
            "node_id": "surfactant",
            "label": "wetting surfactant",
            "node_type": "CHEMICAL",
            "description": "Secreted surfactant lowering surface tension to support spreading."
          },
          {
            "node_id": "flagellar_motility",
            "label": "bacterial flagellum-dependent cell motility",
            "node_type": "BIOLOGICAL_PROCESS",
            "grounding": "GO:0071973",
            "description": "Swimming/swarming motility driven by flagellar rotation."
          },
          {
            "node_id": "quorum_sensing",
            "label": "quorum sensing",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Cell-density signaling that regulates production of swarming-associated wetting surfactants.",
            "grounding": "GO:0009372"
          },
          {
            "node_id": "swarm_expansion",
            "label": "swarm expansion",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Outward dendritic spreading of a multicellular swarm across a surface."
          }
        ],
        "edges": [
          {
            "subject": "bacterial_flagellum",
            "predicate": "confers",
            "object": "swarming_trait",
            "description": "Hyperflagellation provides the propulsive machinery for swarming.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2405",
                "notes": "Kearns defines swarming via increased flagella per cell."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "surfactant",
            "predicate": "confers",
            "object": "swarming_trait",
            "description": "Secreted wetting surfactant supports multicellular surface spreading.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2405",
                "notes": "Kearns defines swarming via surfactant secretion accompanying hyperflagellation."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "swarming_trait",
            "predicate": "participates in",
            "object": "flagellar_motility",
            "description": "Swarming is a flagella-driven surface-motility mode.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev.micro.57.030502.091014",
                "notes": "Harshey places swarming among the surface-motility modes of bacteria."
              }
            ],
            "predicate_id": "biolink:participates_in"
          },
          {
            "subject": "quorum_sensing",
            "predicate": "positively regulates",
            "object": "surfactant",
            "description": "Quorum sensing controls production of wetting surfactants (HAAs/rhamnolipids) required for swarm development.",
            "evidence": [
              {
                "reference": "DOI:10.1063/5.0128140",
                "notes": "Bru et al. 2023 review: QS regulates HAA and rhamnolipid production needed for swarm development."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "surfactant",
            "predicate": "positively regulates",
            "object": "swarm_expansion",
            "description": "Secreted wetting surfactants are required for normal swarm expansion and tendril formation; surfactant-deficient mutants fail to expand.",
            "evidence": [
              {
                "reference": "DOI:10.1063/5.0128140",
                "notes": "Bru et al. 2023: mutants defective in rhamnolipid production are deficient in swarm expansion and fail to form tendrils."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "bacterial_flagellum",
            "predicate": "positively regulates",
            "object": "swarm_expansion",
            "description": "Flagellar activity, alongside surfactant production, is essential for dendritic swarm expansion.",
            "evidence": [
              {
                "reference": "DOI:10.1063/5.0128140",
                "notes": "Bru et al. 2023: two activities are essential for forming dendritic swarms - surfactant production and flagellar activity."
              }
            ],
            "predicate_id": "RO:0002213"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-06-03T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate MORPHOLOGY/motility trait (swarming motility) under the existing motile class (METPO:1000702).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-09T15:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (hyperflagellation + surfactant swarming) with GO node groundings and RO/biolink predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 3 evidence-backed generic edges (2 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:34Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0009372\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-04T03:08:15Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002213\u00d73).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 2 causal edge(s) off enables/RO:0002327 with a TRAIT object (2 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope swarming_hyperflagellation_surfactant=NONMECHANISTIC with scope_notes.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000702",
    "label": "swimming motility",
    "definition": "A motile phenotype in which an organism propels itself through a liquid medium.",
    "definition_source": "DOI:10.1038/s41467-020-18253-7",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000702"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/s41467-020-18253-7",
        "snippet": "Their swimming direction is stabilised by their flagella (archaella)",
        "notes": "Thornton et al. 2020, PMID:32901025, PMC7478972, scientific abstract. Qualified MED identity, title and DOI checked. Results, Swimming behaviour in three dimensions, and Methods on culture and holographic reconstruction directly support liquid swimming by environmental Haloferax sp. Boulby Mine and Haloarcula sp. Great Salt Lake isolates. Mean-squared displacement separated swimming from diffusion. Figure 2 was visually inspected; Supplementary Note 1 describes sampling locations. Methods explicitly leave exact species unresolved. Cultures were grown in 25% dissolved-salt MGM to early exponential phase. The measured trajectories, not merely genes or simulations, support the phenotype. Chemotactic efficiency simulations do not define swimming or establish a universal speed optimum. Raw movies were not reanalyzed. MED, Crossref and the retrieved publisher page exposed no linked correction or retraction at the check. Source: https://www.nature.com/articles/s41467-020-18253-7."
      },
      {
        "reference": "DOI:10.1038/s41467-018-07802-w",
        "snippet": "However, the free-swimming capability of the different strains did not correlate well to the spreading capability in soft agar.",
        "notes": "Kuhn et al. 2018, PMID:30560868, PMC6299084, Results, Filament composition affects flagella-mediated swimming; quote checked directly in full-text XML, not the abstract. Qualified MED identity and DOI checked. Figure 3 and Supplementary Table 1 (printed p. 10, PDF p. 11) were visually inspected. Main Results describe a delta-flaA2B2 background, called wild type for the polar system. Supplementary Figure 11 (printed p. 7, PDF p. 8) instead retains both lateral flagellins for a separate soft-agar assay. Preserve this discrepancy; do not apply the main-text claim to every experiment. Methods distinguish three-dimensional cell tracking in regular or Ficoll-supplemented liquid from soft-agar spreading, and reject Brownian-only tracks. Thus liquid swimming is observed in engineered material; it is not inferred from agar halos or a sequence feature. Filament simulations are separate model evidence. Raw movies were not reanalyzed. MED, Crossref and the retrieved publisher page exposed no linked correction or retraction at the check. Source: https://www.nature.com/articles/s41467-018-07802-w."
      }
    ],
    "discussions": [
      {
        "discussion_id": "swimming-motility-scope-and-assays",
        "prompt": "Keep liquid propulsion distinct from surface movement and passive displacement.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Motile METPO:1000702 is the broader energy-dependent locomotion phenotype. Swimming concerns propulsion through liquid, including near a boundary, not locomotion across a supporting substrate. Swarming traitmech:000062, twitching traitmech:000061 and gliding METPO:1000706 are not exact synonyms. Passive advection, settling, Brownian motion, colony growth and appendage possession alone are insufficient. Neither a particular speed, solitary behavior, chemotaxis nor a specified propulsion apparatus is required. Bacterial flagella and archaeal archaella must not be conflated. An organism can exhibit swimming and surface motility in different conditions; no organism-level disjointness is asserted. Existing flagellar-motility process nodes, swimming-velocity capacities and taxis discussions are not exact ungrounded instances of this trait. Upstream METPO issue 271 requests this gap; it does not supply an accepted identifier. External phenotype equivalences and lexical variants remain unasserted pending authority checks.",
        "posed_by": "codex",
        "posed_date": "2026-10-11"
      },
      {
        "discussion_id": "swimming-motility-examples-and-mechanisms",
        "prompt": "Resolve taxon-specific examples and mechanisms without inferring motion from sequence.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "No canonical examples are assigned in this first pass: the haloarchaeal isolates lack resolved species identities in the study, and exact taxon anchors for the bacterial experimental background have not been independently verified here. Engineered material remains valid qualified phenotype evidence, not an unmodified natural exemplar. A causal graph is deferred pending source-bounded branches and eligible taxon-paired protein examples. Do not impose one lineage's motor or chemotaxis machinery on all swimming organisms, or use a NONMECHANISTIC graph to bypass grounding requirements. A flagellin, archaellin, motor gene or predicted motility system alone does not establish liquid propulsion under a tested condition. The present evidence covers bacterial and archaeal cases, not a systematic survey of eukaryotic propulsion or every swimming mechanism.",
        "posed_by": "codex",
        "posed_date": "2026-10-11"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-11T18:17:31Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added liquid swimming motility beneath motile with two DOI-backed primary studies and checked verbatim abstract/full-text snippets. Ignored/hidden worktree, live ontology and pending-PR checks support 000702 and v578 block 1065500-1065599. Existing records unchanged. Assay, strain and sequence-inference limits are explicit. Timestamp records the observed UTC curation decision.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-11T18:27:36Z",
        "curator": "codex",
        "action": "CURATED_WITH_LITERATURE",
        "changes": "Corrected the unqualified bacterial strain-background statement after visually checking Supplementary Figure 11. Attributed the main-text deletion claim and retained the supplementary lateral-flagellin exception without conflating soft-agar and liquid assays. Addresses issue #1872; prior curation event preserved.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000656",
    "label": "synnema formation",
    "definition": "A morphological phenotype in which fungal hyphae aggregate into an erect, stalk-like asexual reproductive structure, with conidiogenous elements borne from the stalk in its fertile form.",
    "definition_source": "DOI:10.1016/j.simyco.2017.09.001",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1016/j.simyco.2017.09.001",
        "snippet": "Hyphae of stipe parallel, 2\u20132.5 \u03bcm wide, pale-brown, slightly thick-walled.",
        "notes": "Woudenberg et al. (2017), PMID:29158610, PMC5679026. Direct full-text Taxonomy, Cephalotrichum lignatile description; the snippet describes this species, not universal dimensions or pigmentation. Actual Figure 7D-F shows synnemata, G the stalk apex, and H-I conidiophores and conidiogenous cells. Methods describes microscopic structures from SNA cultures after 14 days at 25 C in darkness; Figure 7A-C instead shows colonies on OA, MEA and DG18. The paper also reports loosely attached stipe hyphae in C. domesticum, so tight fusion is not imposed on the class."
      },
      {
        "reference": "DOI:10.3390/ijms21186660",
        "snippet": "deletion of the brlA gene blocked conidiation but not the formation of synnemata formed by aggregation of hyphal mycelia.",
        "notes": "Zetina-Serrano et al. (2020), PMID:32932988, PMC7555563, Introduction's summary of the authors' experiment. Direct Results 2.2.3 and actual Figure 4 were also inspected: after 30 days on apples at 25 C in darkness, the engineered Penicillium expansum brlA-null strain formed sporeless hyphal stalks lacking mature conidiophores; the wild-type strain formed conidiophores in coremia. This supports separating stalk formation from completed conidiation, not a universal BrlA requirement for synnemata. The mutant is qualified evidence, not a natural canonical example."
      },
      {
        "reference": "DOI:10.1099/00221287-87-2-292",
        "snippet": "Coremia of Penicillium claviforme develop in three stages; primordium formation, elongation, and sporulation.",
        "notes": "Watkinson (1975), PMID:1141857, scientific abstract retrieved directly from Europe PMC. The publisher abstract agrees on the three stages but uses a colon where this indexed version has a semicolon. Only abstract-level developmental evidence is used; full text and figures were not inspected. Nutrient responses in this study do not define all synnemata. The historical species name is retained without a new taxon mapping or exact coremium/synnema synonym assertion."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:2041050",
        "taxon_label": "Cephalotrichum lignatile",
        "reference": "DOI:10.1016/j.simyco.2017.09.001",
        "note": "Ex-type culture CBS 209.63. The primary taxonomic description and Figure 7 directly document synnemata; microscopic descriptions use SNA after 14 days at 25 C in darkness. Specimen examined and Table 1 at https://pmc.ncbi.nlm.nih.gov/articles/PMC5679026/ identify Hennebert's 1959 isolate from timber in a cave at Han-sur-Lesse, Belgium. This is primary isolate provenance, not an inferred wild-type or GMO status. Synnemata production can vary with culture history; it is not asserted for every life stage or growth condition."
      }
    ],
    "discussions": [
      {
        "discussion_id": "synnema-formation-scope-and-hierarchy",
        "prompt": "Review a fungal reproductive morphology parent and terminology.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Retain phenotype METPO:1000059. Sporulation METPO:1000870 and spore forming METPO:1000871 explicitly concern bacterial endospores; mycelial growth traitmech:000074 explicitly concerns bacterial hyphae. Hyphal anastomosis traitmech:000605 requires cytoplasmic continuity, not mere bundling. Pseudohyphal growth traitmech:000653 concerns chains of budding yeast cells. None is an exact duplicate or appropriate parent. Zetina-Serrano uses coremia for conidiophore clusters and synnemata for sporeless hyphal stalks; Watkinson uses coremia across developmental stages. Do not force these usages into an exact synonym. No exact external mapping or organism-level disjointness is asserted.",
        "posed_by": "codex",
        "posed_date": "2026-10-07"
      },
      {
        "discussion_id": "synnema-formation-development-and-mechanism",
        "prompt": "Resolve stage-specific mechanisms before adding a causal graph.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "The fertile-form qualifier preserves the documented sporeless synnemata of the brlA-null P. expansum strain. Formation does not require already mature conidiophores or conidia, a universal shape, size, color, spore wetness, growth medium or nutritional trigger. BrlA perturbation separates developmental stages in that experiment; it does not establish a universal stalk-formation gene or a mechanism in Cephalotrichum. Defer a causal graph pending organism-specific perturbations and accession-level review. Gene possession alone does not establish this phenotype. Use the 2017 paper's directly examined CBS 209.63 material, not older sequences attributed to CBS 159.66 that the authors identify as erroneous.",
        "posed_by": "codex",
        "posed_date": "2026-10-07"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-07T02:43:42Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added synnema formation with three DOI-backed snippets, a qualified Cephalotrichum lignatile example and developmental scope boundaries. Ignored-and-hidden searches and structured METPO review found no exact record. Reserved METPO:1060900 in v532; existing records unchanged.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000695",
    "label": "tailed shaped",
    "definition": "A cell shape in which an organism has an elongated polar appendage or stalk extending from the cell body.",
    "definition_source": "DOI:10.1146/annurev.micro.061705.103240",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000666"
    ],
    "synonyms": [
      {
        "synonym_text": "tailed",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev.micro.061705.103240",
        "snippet": "prosthecate bacteria",
        "notes": "Prosthecate-bacteria review supports tailed/stalked cell morphology in Caulobacter and related lineages."
      },
      {
        "reference": "DOI:10.1146/annurev-cellbio-101011-155745",
        "snippet": "polar growth",
        "notes": "Cell-shape review supports unipolar peptidoglycan growth as the basis for stalk-like polar appendages."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:565050",
        "taxon_label": "Caulobacter vibrioides NA1000",
        "note": "Reference stalked-cell model paired to reviewed MreB, whose depletion causes a direct stalk-elongation defect.",
        "reference": "DOI:10.1128/JB.187.2.544-553.2005"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "tailed_shaped_polar_stalk_growth",
        "title": "Tailed-shape polar stalk extension",
        "description": "DOI-backed graph linking unipolar peptidoglycan growth and stalk outgrowth to tailed cell morphology.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "Represents Caulobacter polar stalk morphogenesis. The NA1000 MreB example anchors one protein of the elongation machinery; broad bactofilin and synthase nodes remain reviewed contextual aggregates.",
        "nodes": [
          {
            "node_id": "tailed_shaped_trait",
            "label": "tailed shaped",
            "node_type": "TRAIT",
            "grounding": "METPO:1000695",
            "description": "Cell body bearing an elongated polar appendage or stalk."
          },
          {
            "node_id": "unipolar_pg_growth",
            "label": "unipolar peptidoglycan growth",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Polar wall synthesis localized at a single cell pole."
          },
          {
            "node_id": "stalk_outgrowth",
            "label": "stalk outgrowth",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Extension of a narrow cytoplasmic stalk from one pole."
          },
          {
            "node_id": "polar_appendage",
            "label": "polar appendage",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Resulting elongated polar structure."
          },
          {
            "node_id": "bactofilin_polymers",
            "label": "bactofilin polymers",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Cytoskeletal scaffold polymers that organize polar stalk synthesis.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "This node aggregates Caulobacter BacA/BacB and related bactofilins, so no single exact family term represents all components."
          },
          {
            "node_id": "stalk_base",
            "label": "stalk base",
            "node_type": "CELLULAR_LOCALIZATION",
            "description": "The cell-pole site where stalk synthesis is initiated and confined."
          },
          {
            "node_id": "pg_biosynthesis_at_stalk_base",
            "label": "peptidoglycan biosynthesis at stalk base",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Cell wall synthesis spatially restricted to the stalk base."
          },
          {
            "node_id": "cell_wall_synthase",
            "label": "cell wall synthase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Peptidoglycan synthase recruited to extend the stalk.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "The source uses a functional class label in this cross-study graph rather than identifying one universally applicable synthase family."
          },
          {
            "node_id": "mreb",
            "label": "MreB",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Bacterial actin homolog directing cell-wall synthesis for stalk formation.",
            "grounding": "InterPro:IPR004753",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:A0A0H3C7V4",
                "protein_label": "Rod shape-determining protein MreB",
                "gene_symbol": "mreB",
                "taxon_id": "NCBITaxon:565050",
                "taxon_label": "Caulobacter vibrioides NA1000",
                "entry_status": "REVIEWED",
                "retrieved_on": "2026-10-22",
                "entry_version": 43,
                "sequence_version": 1,
                "role": "Caulobacter MreB organizes elongation machinery and is required for normal polar stalk elongation.",
                "evidence": [
                  {
                    "reference": "DOI:10.1128/JB.187.2.544-553.2005",
                    "snippet": "MreB depletion leads to a stalk elongation defect",
                    "notes": "The primary Caulobacter depletion study directly establishes MreB's role in stalk biogenesis; UniProt verifies the reviewed NA1000 protein."
                  }
                ]
              }
            ]
          },
          {
            "node_id": "roda",
            "label": "RodA",
            "node_type": "GENE_OR_PROTEIN",
            "description": "SEDS peptidoglycan polymerase required for stalk elongation.",
            "grounding": "InterPro:IPR001182"
          },
          {
            "node_id": "phosphate_starvation",
            "label": "phosphate starvation",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Phosphate-limited growth condition that induces stalk elongation."
          }
        ],
        "edges": [
          {
            "subject": "unipolar_pg_growth",
            "predicate": "regulates",
            "object": "stalk_outgrowth",
            "description": "Unipolar PG growth at the same cell pole drives stalk extension.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev.micro.061705.103240",
                "snippet": "prosthecate bacteria",
                "notes": "Supports polar wall growth as the mechanism extending the stalk."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "stalk_outgrowth",
            "predicate": "has output",
            "object": "polar_appendage",
            "description": "Stalk outgrowth produces an elongated polar appendage.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev.micro.061705.103240",
                "snippet": "prosthecate bacteria",
                "notes": "Supports stalk extension as a prosthecate-cell feature."
              }
            ],
            "predicate_id": "RO:0002234"
          },
          {
            "subject": "polar_appendage",
            "predicate": "manifests as",
            "object": "tailed_shaped_trait",
            "description": "A polar appendage manifests the tailed-shaped trait.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev.micro.061705.103240",
                "snippet": "prosthecate bacteria",
                "notes": "Supports the trait endpoint."
              }
            ],
            "predicate_id": "METPO:2007400"
          },
          {
            "subject": "bactofilin_polymers",
            "predicate": "localizes to",
            "object": "stalk_base",
            "description": "Bactofilin polymers localize to the stalk base to direct proper stalk formation.",
            "evidence": [
              {
                "reference": "DOI:10.7554/eLife.86577",
                "notes": "In C. crescentus and A. biprosthecum bactofilin polymers localize to the stalk base to direct proper stalk formation."
              }
            ],
            "predicate_id": "biolink:located_in"
          },
          {
            "subject": "bactofilin_polymers",
            "predicate": "regulates",
            "object": "pg_biosynthesis_at_stalk_base",
            "description": "Bactofilins limit peptidoglycan biosynthesis to the stalk base, confining wall growth spatially.",
            "evidence": [
              {
                "reference": "DOI:10.7554/eLife.86577",
                "notes": "Required to efficiently initiate stalk formation and limit peptidoglycan biosynthesis to the stalk base."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "bactofilin_polymers",
            "predicate": "recruits",
            "object": "cell_wall_synthase",
            "description": "Bactofilins recruit a cell wall synthase that contributes to stalk elongation.",
            "evidence": [
              {
                "reference": "DOI:10.7554/eLife.86577",
                "notes": "In C. crescentus, they recruit a cell wall synthase that contributes to stalk elongation."
              }
            ]
          },
          {
            "subject": "cell_wall_synthase",
            "predicate": "positively regulates",
            "object": "stalk_outgrowth",
            "description": "The recruited cell wall synthase contributes to stalk elongation.",
            "evidence": [
              {
                "reference": "DOI:10.7554/eLife.86577",
                "notes": "Recruited cell wall synthase contributes to stalk elongation."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "mreb",
            "predicate": "required for",
            "object": "stalk_outgrowth",
            "description": "MreB is necessary for stalk formation; depletion causes a stalk elongation defect.",
            "evidence": [
              {
                "reference": "DOI:10.1128/jb.00384-22",
                "notes": "MreB and RodA are necessary for stalk formation, as depletion of either protein results in a stalk elongation defect."
              }
            ]
          },
          {
            "subject": "roda",
            "predicate": "required for",
            "object": "stalk_outgrowth",
            "description": "RodA (SEDS PG polymerase) is necessary for stalk formation; depletion causes a stalk elongation defect.",
            "evidence": [
              {
                "reference": "DOI:10.1128/jb.00384-22",
                "notes": "MreB and RodA are necessary for stalk formation, as depletion of either protein results in a stalk elongation defect."
              }
            ]
          },
          {
            "subject": "phosphate_starvation",
            "predicate": "induces",
            "object": "stalk_outgrowth",
            "description": "Phosphate starvation induces elongated stalks.",
            "evidence": [
              {
                "reference": "DOI:10.1128/jb.00384-22",
                "notes": "Cells starved of phosphate grow elongated stalks."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.900946+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-11T22:45:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed definition and causal graph linking unipolar peptidoglycan growth and stalk outgrowth to tailed cell morphology.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T21:30:07Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007400\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:19Z",
        "curator": "claude",
        "action": "RENAME_PREDICATE_LABELS",
        "changes": "Renamed 1 causal-edge predicate label(s) to align with existing groundings: drives \u2192 regulates \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:22Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002211\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 7 evidence-backed generic edges (7 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:14Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:located_in\u00d71, RO:0002211\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:19Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A1B1UYY2\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-26T07:15:20Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A0H2X1V4\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:21:12Z",
        "curator": "claude",
        "action": "RETRACT_DEAD_UNIPROT_GROUNDINGS",
        "changes": "Retracted 1 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-04T03:08:15Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002213\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates (1 to has output), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-22T04:26:16Z",
        "curator": "codex",
        "action": "REVIEW_UNIPROT_INSTANCE_GROUNDINGS",
        "changes": "Reviewed 1 organism-specific UniProtKB grounding(s): replaced 1 with taxon-agnostic GO/InterPro terms and retracted 0 to label-only where no exact semantic term was supported (docs/GROUNDING_POLICY.md).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "CURATE_PROTEIN_TAXON_EXAMPLE",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope tailed_shaped_polar_stalk_growth=MECHANISTIC with scope_notes; marked 2 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (bactofilin_polymers, cell_wall_synthase); added taxon-paired protein example(s) UniProtKB:A0A0H3C7V4 on mreb (NCBITaxon:565050); regrounded 1 node(s) (mreb: none->InterPro:IPR004753); added canonical example(s) NCBITaxon:565050.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-22T01:35:00Z",
        "curator": "claude",
        "action": "REFRESH_UNIPROT_ENTRY_VERSION",
        "changes": "Refreshed UniProtKB entry_version against live UniProt REST on 2026-10-22: UniProtKB:A0A0H3C7V4 (42 -> 43 on mreb).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000119",
    "label": "tetrad arrangement",
    "definition": "A cell arrangement in which cocci divide in two perpendicular planes and remain attached as groups of four (tetrads).",
    "definition_source": "DOI:10.1128/MMBR.00001-06",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000666"
    ],
    "synonyms": [
      {
        "synonym_text": "tetrad-forming cocci",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1128/MMBR.00001-06"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1128/MMBR.00001-06",
        "notes": "Young's review treats the tetrad as a division-plane-determined coccal arrangement."
      },
      {
        "reference": "DOI:10.1038/ncomms4842",
        "notes": "Two-plane division with incomplete daughter-cell separation yields four-cell tetrads."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1270",
        "taxon_label": "Micrococcus luteus",
        "note": "tetrad/packet cocci",
        "reference": "PMID:2325580"
      },
      {
        "taxon_id": "NCBITaxon:1377",
        "taxon_label": "Aerococcus viridans",
        "note": "tetrad-forming coccus",
        "reference": "PMID:25919289"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "tetrad_two_plane_division",
        "title": "Tetrad arrangement via two-plane perpendicular division",
        "description": "Evidence-backed causal sketch linking division in two perpendicular planes with incomplete separation to four-cell tetrads.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a broad environmental or morphological classification spanning multiple mechanisms, a measurement-like bin, or an absence/arrangement descriptor; contextual protein nodes do not receive token UniProt examples.",
        "nodes": [
          {
            "node_id": "tetrad_trait",
            "label": "tetrad arrangement",
            "node_type": "TRAIT",
            "grounding": "traitmech:000119",
            "description": "Cocci attached as groups of four (tetrads)."
          },
          {
            "node_id": "cell_division",
            "label": "cell division",
            "node_type": "BIOLOGICAL_PROCESS",
            "grounding": "GO:0051301",
            "description": "Bacterial binary fission."
          },
          {
            "node_id": "two_plane_perpendicular_division",
            "label": "two perpendicular division planes",
            "node_type": "QUALITY",
            "description": "Successive division planes oriented perpendicular to each other."
          },
          {
            "node_id": "ftsz_z_ring",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "FtsZ Z-ring assembly",
            "node_type": "GENE_OR_PROTEIN",
            "description": "FtsZ polymerizes into a Z-ring that scaffolds the divisome at the division site."
          },
          {
            "node_id": "septation",
            "label": "division septum assembly",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Assembly of the septal cell-wall and membrane between daughter cells.",
            "grounding": "GO:0000917"
          },
          {
            "node_id": "cell_wall_hydrolases",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "cell wall hydrolases (autolysins)",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Peptidoglycan hydrolases/autolysins that cleave the septal cell wall to separate daughter cells."
          },
          {
            "node_id": "daughter_cell_splitting",
            "label": "daughter-cell splitting",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Rapid physical separation of daughter cells following septation."
          }
        ],
        "edges": [
          {
            "subject": "two_plane_perpendicular_division",
            "predicate": "causes",
            "object": "tetrad_trait",
            "description": "Two perpendicular division planes with incomplete daughter separation yield four-cell tetrads.",
            "evidence": [
              {
                "reference": "DOI:10.1038/ncomms4842",
                "notes": "Two-plane division with incomplete daughter-cell separation yields four-cell tetrads."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "cell_division",
            "predicate": "confers",
            "object": "tetrad_trait",
            "description": "Bacterial cell division underlies tetrad formation.",
            "evidence": [
              {
                "reference": "DOI:10.1128/MMBR.00001-06",
                "notes": "Young treats the tetrad as a division-plane-determined coccal arrangement."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "ftsz_z_ring",
            "predicate": "scaffolds",
            "object": "septation",
            "description": "FtsZ assembles into a Z-ring that scaffolds the divisome and initiates septation.",
            "evidence": [
              {
                "reference": "DOI:10.1042/bst20240956",
                "notes": "FtsZ polymerizes into a Z-ring that scaffolds membrane-associated division factors, forming the divisome that drives septation."
              }
            ]
          },
          {
            "subject": "septation",
            "predicate": "precedes",
            "object": "daughter_cell_splitting",
            "description": "Septum assembly precedes the splitting step that physically separates daughter cells.",
            "evidence": [
              {
                "reference": "DOI:10.1042/bst20240956",
                "notes": "After septation the cell splits into two daughter cells; splitting is a distinct, very fast step following septation."
              }
            ]
          },
          {
            "subject": "cell_wall_hydrolases",
            "predicate": "mediates",
            "object": "daughter_cell_splitting",
            "description": "Cell wall hydrolases/autolysins cleave septal peptidoglycan to drive rapid daughter-cell splitting.",
            "evidence": [
              {
                "reference": "DOI:10.1042/bst20240956",
                "notes": "After septation the cell splits into two daughter cells very fast (within milliseconds) and requires the actions of cell wall hydrolases."
              }
            ]
          },
          {
            "subject": "daughter_cell_splitting",
            "predicate": "prevents",
            "object": "tetrad_trait",
            "description": "Incomplete or delayed daughter-cell splitting after two-plane division leaves cells attached as four-cell tetrads.",
            "evidence": [
              {
                "reference": "DOI:10.1042/bst20240956",
                "notes": "Tetrads arise when a spherical cell divides in one plane and then again in a perpendicular plane, producing four cells arranged as a square due to incomplete separation; failure to complete splitting yields the tetrad."
              }
            ],
            "predicate_id": "RO:0002212"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-06-08T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate MORPHOLOGY trait (tetrad arrangement); leftover round, cell-arrangement sibling of diplococcus shaped.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-09T15:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (two-plane perpendicular division \u2192 tetrad) with GO node grounding and RO/biolink predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 4 evidence-backed generic edges (4 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:14Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002212\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:34Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0000917\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 1 causal edge(s) off enables/RO:0002327 with a TRAIT object (1 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope tetrad_two_plane_division=NONMECHANISTIC with scope_notes; marked 2 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (ftsz_z_ring, cell_wall_hydrolases).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000696",
    "label": "triangular shaped",
    "definition": "A cell shape in which an organism forms flat, triangular or wedge-shaped cells.",
    "definition_source": "DOI:10.1146/annurev-cellbio-101011-155745",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000666"
    ],
    "synonyms": [
      {
        "synonym_text": "triangular",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev-cellbio-101011-155745",
        "snippet": "cell shape is genetically determined",
        "notes": "Cell-shape review supports anisotropic envelope architecture as the basis for non-round cell geometries such as triangles."
      },
      {
        "reference": "DOI:10.1146/annurev-micro-090816-093703",
        "snippet": "archaeal cell shape",
        "notes": "Archaeal cell-shape review supports unusual flat polygonal cells in halophilic archaea."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:29282",
        "taxon_label": "Haloarcula japonica",
        "note": "Flat triangular/disc-shaped halophilic archaeon; textbook example of non-rod/coccus cell geometry.",
        "reference": "DOI:10.1016/S0723-2020(11)80165-7"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "triangular_shaped_planar_polygonal_growth",
        "title": "Triangular-shape planar polygonal envelope growth",
        "description": "DOI-backed graph linking planar anisotropic envelope growth and S-layer-constrained polygonal geometry to flat triangular cells.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This is a polygonal morphology classification without a taxon-matched protein determinant in the cited evidence; no token protein is added.",
        "nodes": [
          {
            "node_id": "triangular_shaped_trait",
            "label": "triangular shaped",
            "node_type": "TRAIT",
            "grounding": "METPO:1000696",
            "description": "Flat triangular or wedge-shaped cell geometry."
          },
          {
            "node_id": "planar_envelope_growth",
            "label": "planar envelope growth",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Cell-envelope expansion in a 2D plane."
          },
          {
            "node_id": "slayer_constraints",
            "label": "S-layer constraints",
            "node_type": "ORGANELLE",
            "description": "Paracrystalline S-layer imposing geometric constraints on shape.",
            "grounding": "GO:0030115"
          },
          {
            "node_id": "polygonal_geometry",
            "label": "polygonal geometry",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Flat, angular cell geometry with defined edges."
          },
          {
            "node_id": "rigid_slayer_sheets",
            "label": "rigid S-layer sheets",
            "node_type": "ORGANELLE",
            "description": "Overlapping paracrystalline S-layer sheets cross-linked by a dense net of protein bridges, producing high mechanical rigidity."
          },
          {
            "node_id": "outer_membrane",
            "label": "outer membrane",
            "node_type": "CELLULAR_LOCALIZATION",
            "description": "Cell outer membrane that conforms to the angular polygonal envelope geometry.",
            "grounding": "GO:0019867"
          },
          {
            "node_id": "peptidoglycan_layer",
            "label": "peptidoglycan layer",
            "node_type": "CELLULAR_LOCALIZATION",
            "description": "Peptidoglycan-based cell wall layer that does not adopt the polygonal cell shape."
          }
        ],
        "edges": [
          {
            "subject": "planar_envelope_growth",
            "predicate": "enables",
            "object": "polygonal_geometry",
            "description": "Planar envelope growth allows flat polygonal cell forms.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-micro-090816-093703",
                "snippet": "archaeal cell shape",
                "notes": "Supports planar growth as the basis for flat archaeal cells."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "slayer_constraints",
            "predicate": "causes",
            "object": "polygonal_geometry",
            "description": "S-layer geometry constrains the cell into angular polygonal forms.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-cellbio-101011-155745",
                "snippet": "cell shape is genetically determined",
                "notes": "Supports envelope-architecture constraints (e.g., S-layer) as shape determinants."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "polygonal_geometry",
            "predicate": "manifests as",
            "object": "triangular_shaped_trait",
            "description": "Angular polygonal geometry manifests the triangular-shaped trait.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-micro-090816-093703",
                "snippet": "archaeal cell shape",
                "notes": "Supports the trait endpoint in triangular halophilic archaea."
              }
            ],
            "predicate_id": "METPO:2007400"
          },
          {
            "subject": "slayer_constraints",
            "predicate": "determines",
            "object": "polygonal_geometry",
            "description": "The S-layer is the determining factor for the polygonal (angular) cell shape.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2021.766527",
                "notes": "Cryo-ET shows \"the S-layer is the determining factor for their polygonal cell shape\"; generic S-layer-driven polygonal envelope mechanism."
              }
            ]
          },
          {
            "subject": "rigid_slayer_sheets",
            "predicate": "confers rigidity to",
            "object": "polygonal_geometry",
            "description": "Very rigid, protein-bridge-cross-linked S-layer sheets confer mechanical rigidity that stabilizes the angular polygonal morphology.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2021.766527",
                "notes": "\"these S-layer sheets are very rigid\" and a \"dense net of protein bridges... establishes the observed rigidity\"; structural stabilization of angular morphology."
              }
            ]
          },
          {
            "subject": "polygonal_geometry",
            "predicate": "shapes",
            "object": "outer_membrane",
            "description": "The outer membrane conforms to (follows) the polygonal cell shape imposed by the envelope.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2021.766527",
                "notes": "\"the outer membrane followed the polygonal cell shape\"; outer membrane is a participant conforming to polygonal geometry."
              }
            ]
          },
          {
            "subject": "polygonal_geometry",
            "predicate": "does not shape",
            "object": "peptidoglycan_layer",
            "description": "The peptidoglycan layer does not adopt the polygonal cell shape, bounding the mechanism to S-layer and outer membrane.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2021.766527",
                "notes": "\"the S-layer and outer membrane, but not the peptidoglycan layer and the cytoplasmic membrane, exhibited the polygonal shape\"; negative boundary edge."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.901416+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-11T22:45:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed causal graph linking planar anisotropic envelope growth and S-layer constraints to triangular-shaped halophile morphology.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T21:30:07Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007400\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:19Z",
        "curator": "claude",
        "action": "RENAME_PREDICATE_LABELS",
        "changes": "Renamed 1 causal-edge predicate label(s) to align with existing groundings: shapes \u2192 causes \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:22Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:causes\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 4 evidence-backed generic edges (3 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:19Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0019867\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope triangular_shaped_planar_polygonal_growth=NONMECHANISTIC with scope_notes.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000061",
    "label": "twitching motility",
    "definition": "A flagella-independent surface motility driven by the extension, attachment, and retraction of type IV pili, producing intermittent, jerky translocation of cells across moist surfaces.",
    "definition_source": "DOI:10.1146/annurev.micro.56.012302.160938",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000702"
    ],
    "synonyms": [
      {
        "synonym_text": "twitching",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1146/annurev.micro.56.012302.160938"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev.micro.56.012302.160938",
        "notes": "Mattick, \"Type IV pili and twitching motility\", describes twitching as type-IV-pilus-driven surface translocation operating like a grappling hook."
      },
      {
        "reference": "DOI:10.1146/annurev.micro.57.030502.091014",
        "notes": "Harshey, \"Bacterial motility on a surface\", places twitching among the distinct surface-translocation strategies of bacteria."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:287",
        "taxon_label": "Pseudomonas aeruginosa",
        "note": "Canonical type-IV-pilus twitching-motility model. Neisseria gonorrhoeae is a parallel model.",
        "reference": "PMID:22746331"
      },
      {
        "taxon_id": "NCBITaxon:208964",
        "taxon_label": "Pseudomonas aeruginosa PAO1",
        "note": "Strain-level PilT twitching-motility exemplar.",
        "reference": "DOI:10.1128/jb.00359-24"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "twitching_type_iv_pilus_retraction",
        "title": "Twitching motility via type IV pilus extension and retraction",
        "description": "Evidence-backed causal sketch linking type-IV-pilus dynamics (extension, surface attachment, retraction) to flagella-independent surface translocation.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "The taxon-matched protein example anchors one experimentally supported causal branch; it is not presented as a universal mechanism for every taxon or every contextual branch in this graph.",
        "nodes": [
          {
            "node_id": "twitching_trait",
            "label": "twitching motility",
            "node_type": "TRAIT",
            "grounding": "traitmech:000061",
            "description": "Flagella-independent surface motility on moist substrates."
          },
          {
            "node_id": "type_iv_pilus",
            "label": "type IV pilus",
            "node_type": "CELLULAR_LOCALIZATION",
            "description": "Surface filament that extends, attaches, and retracts to pull the cell forward.",
            "grounding": "GO:0044096"
          },
          {
            "node_id": "pilus_assembly",
            "label": "type IV pilus assembly",
            "node_type": "BIOLOGICAL_PROCESS",
            "grounding": "GO:0043107",
            "description": "Polymerization and disassembly cycles driving pilus extension and retraction."
          },
          {
            "node_id": "pilb_extension_atpase",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "PilB extension ATPase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Cytoplasmic motor ATPase that powers type IV pilus filament extension."
          },
          {
            "node_id": "pilt_retraction_atpase",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:P24559",
                "protein_label": "Type IV pilus retraction ATPase PilT",
                "gene_symbol": "pilT",
                "taxon_id": "NCBITaxon:208964",
                "taxon_label": "Pseudomonas aeruginosa PAO1",
                "entry_status": "REVIEWED",
                "proteome_id": "UP000002438",
                "retrieved_on": "2026-10-22",
                "entry_version": 148,
                "sequence_version": 1,
                "role": "PAO1 PilT powers type-IV-pilus retraction that pulls the cell across a surface.",
                "evidence": [
                  {
                    "reference": "DOI:10.1128/jb.00359-24",
                    "snippet": "retraction is driven by PilT",
                    "notes": "The cited source supports the represented protein-to-trait branch; UniProt verifies this current strain-matched protein entry."
                  }
                ]
              }
            ],
            "label": "PilT retraction ATPase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Cytoplasmic motor ATPase that powers type IV pilus retraction."
          },
          {
            "node_id": "pilus_extension",
            "label": "type IV pilus extension",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Polymerization of pilin subunits extending the pilus filament."
          },
          {
            "node_id": "pilus_retraction",
            "label": "type IV pilus retraction",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Depolymerization of pilin subunits retracting the pilus and pulling the cell."
          },
          {
            "node_id": "pilq_secretin",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "PilQ secretin",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Outer-membrane secretin channel through which the pilus filament is exposed to the cell surface."
          },
          {
            "node_id": "pilus_filament_surface_exposure",
            "label": "type IV pilus surface exposure",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Exposure of the assembled pilus filament beyond the cell envelope to the external surface."
          },
          {
            "node_id": "pilmnop_alignment_complex",
            "label": "PilM/N/O/P alignment complex",
            "node_type": "CELLULAR_LOCALIZATION",
            "description": "Inner-membrane/periplasmic alignment subcomplex of the type IV pilus machine."
          },
          {
            "node_id": "t4p_machine",
            "label": "type IV pilus machine",
            "node_type": "CELLULAR_LOCALIZATION",
            "description": "Multiprotein nanomachine assembling, extending and retracting the type IV pilus."
          }
        ],
        "edges": [
          {
            "subject": "type_iv_pilus",
            "predicate": "confers",
            "object": "twitching_trait",
            "description": "Type IV pili are the molecular engines of twitching motility.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev.micro.56.012302.160938",
                "notes": "Mattick describes twitching as type-IV-pilus-driven surface translocation."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "pilus_assembly",
            "predicate": "confers",
            "object": "twitching_trait",
            "description": "Extension\u2013attachment\u2013retraction cycles pull the cell across the surface.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev.micro.57.030502.091014",
                "notes": "Harshey treats twitching as a distinct surface-translocation strategy."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "pilb_extension_atpase",
            "predicate": "drives",
            "object": "pilus_extension",
            "description": "PilB ATPase powers extension of the type IV pilus filament.",
            "evidence": [
              {
                "reference": "DOI:10.1128/jb.00359-24",
                "notes": "Roberge & Burrows 2024: \"Extension is driven by PilB bound to PilC\"; T4P undergo cycles of extension/retraction powered by cytoplasmic motor ATPases."
              }
            ]
          },
          {
            "subject": "pilt_retraction_atpase",
            "predicate": "drives",
            "object": "pilus_retraction",
            "description": "PilT ATPase powers retraction of the type IV pilus filament.",
            "evidence": [
              {
                "reference": "DOI:10.1128/jb.00359-24",
                "notes": "Roberge & Burrows 2024: \"Retraction is driven by PilT, which engages with PilC within the same cytoplasmic socket.\""
              }
            ]
          },
          {
            "subject": "pilus_retraction",
            "predicate": "confers",
            "object": "twitching_trait",
            "description": "Pilus retraction pulls the cell across the surface, producing twitching translocation.",
            "evidence": [
              {
                "reference": "DOI:10.1128/jb.00442-23",
                "notes": "Geiger et al. 2024: twitching is movement that pulls the cell across a surface through cooperative binding, pulling, and unbinding."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "pilq_secretin",
            "predicate": "enables surface exposure of",
            "object": "pilus_filament_surface_exposure",
            "description": "PilQ secretin is required for surface exposure of the assembled pilus filament.",
            "evidence": [
              {
                "reference": "DOI:10.1099/mic.0.001311",
                "notes": "Pelicic 2023: pilQ pilT mutants assemble filaments trapped in the periplasm, indicating PilQ is required for surface exposure."
              }
            ]
          },
          {
            "subject": "pilmnop_alignment_complex",
            "predicate": "part of",
            "object": "t4p_machine",
            "description": "The PilM/N/O/P alignment subcomplex is a structural part of the type IV pilus machine.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-024-53638-y",
                "notes": "Guo et al. 2024: the T4P machine includes an alignment subcomplex consisting of PilP, PilO, PilN, and PilM."
              }
            ],
            "predicate_id": "biolink:part_of"
          },
          {
            "subject": "pilus_extension",
            "predicate": "contributes to",
            "object": "pilus_assembly",
            "description": "Extension polymerizes pilin subunits into the assembled type IV pilus fiber.",
            "evidence": [
              {
                "reference": "DOI:10.1128/jb.00359-24",
                "snippet": "PilA subunits are ultimately extracted from their reservoir in the cytoplasmic membrane and polymerized to form a pilus fiber",
                "notes": "Verified against the open Europe PMC full text."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "pilus_filament_surface_exposure",
            "predicate": "contributes to",
            "object": "type_iv_pilus",
            "description": "Extrusion through the secretin exposes the assembled type IV pilus beyond the outer membrane.",
            "evidence": [
              {
                "reference": "DOI:10.1128/jb.00359-24",
                "snippet": "The pilus is extruded through the periplasm, guided by the cylindrical alignment subcomplex, and finally through a gated secretin pore in the outer membrane",
                "notes": "Verified against the open Europe PMC full text."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "t4p_machine",
            "predicate": "enables",
            "object": "pilus_assembly",
            "description": "The envelope-spanning type IV pilus machine enables motor-driven assembly and disassembly of the pilus filament.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-024-53638-y",
                "snippet": "PilC is the inner membrane platform protein that coordinates with ATPase motors to drive assembly and disassembly of major pilin subunits into the extending and retracting pilus, respectively",
                "notes": "Verified against the open Europe PMC full text."
              }
            ],
            "predicate_id": "RO:0002327"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-06-03T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate MORPHOLOGY/motility trait (twitching motility) under the existing motile class (METPO:1000702).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-09T15:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (type IV pilus retraction \u2192 twitching) with GO node grounding and RO predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-14T06:55:38Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0044096\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 5 evidence-backed generic edges (8 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:14Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d71, biolink:part_of\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 3 causal edge(s) off enables/RO:0002327 with a TRAIT object (3 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "CURATE_PROTEIN_TAXON_EXAMPLE",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope twitching_type_iv_pilus_retraction=MECHANISTIC with scope_notes; marked 3 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (pilb_extension_atpase, pilt_retraction_atpase, pilq_secretin); added taxon-paired protein example(s) UniProtKB:P24559 on pilt_retraction_atpase (NCBITaxon:208964); added canonical example(s) NCBITaxon:208964.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T06:48:00Z",
        "curator": "codex",
        "action": "CONNECT_CAUSAL_GRAPH_COMPONENTS",
        "changes": "Resolved issue #183 graph fragmentation (4 components to 1) using 3 source- and verbatim-snippet-backed connector(s). No paid research service was called.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-22T01:35:00Z",
        "curator": "claude",
        "action": "REFRESH_UNIPROT_ENTRY_VERSION",
        "changes": "Refreshed UniProtKB entry_version against live UniProt REST on 2026-10-22: UniProtKB:P24559 (147 -> 148 on pilt_retraction_atpase).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000175",
    "label": "type IV pilus",
    "definition": "A morphology trait in which a cell produces extracellular type-IV-pilin filaments that dynamically extend from and retract toward the cell surface.",
    "definition_source": "DOI:10.1093/femsre/fuab053",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "synonyms": [
      {
        "synonym_text": "type IV pili",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1093/femsre/fuab053"
      },
      {
        "synonym_text": "T4P",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1093/femsre/fuab053"
      }
    ],
    "xrefs": [
      "GO:0044096"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1093/femsre/fuab053",
        "snippet": "Bacteria and archaea rely on appendages called type IV pili (T4P)",
        "notes": "Ellison et al. review type IV pili as prokaryotic appendages that participate in diverse surface-associated behaviors."
      },
      {
        "reference": "DOI:10.1093/femsre/fuab053",
        "snippet": "T4P are broadly distributed fibers that dynamically extend and retract",
        "notes": "The review supports the record definition's dynamic extension and retraction qualifier."
      },
      {
        "reference": "DOI:10.1042/BST20160221",
        "snippet": "Type IV pili are hair-like bacterial surface appendages",
        "notes": "Piepenbrink and Sundberg support type IV pili as bacterial cell-surface appendages built from pilin proteins."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:208964",
        "taxon_label": "Pseudomonas aeruginosa PAO1",
        "note": "The PAO1 type IV pilus is a canonical model for PilB/PilT-driven pilus extension and retraction.",
        "reference": "DOI:10.1128/jb.00359-24"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-12T15:35:50Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted type IV pilus as a DOI-backed TraitRecord after a repository-wide duplicate review covering ignored and hidden files; METPO has no exact live type IV pilus class yet and the placeholder is reserved in proposals/metpo_traitmech_v52.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-12T15:56:02Z",
        "curator": "codex",
        "action": "ADVERSARIAL_REVIEW_REPAIR",
        "changes": "Aligned the type IV pilus definition with dynamic extension and retraction evidence after Claude Code Review on PR #847.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-21T21:12:25Z",
        "curator": "claude",
        "action": "CURATE_CAUSAL_GRAPH",
        "changes": "Added NONMECHANISTIC causal_graphs entry (type_iv_pilus_extension_retraction_sketch) anchored on existing verbatim record evidence snippets.",
        "llm_assisted": true
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "type_iv_pilus_extension_retraction_sketch",
        "title": "Type IV pilus cell-surface appendage and dynamic extension-retraction",
        "description": "Evidence-backed morphology sketch linking cell-surface type IV pili fibers and their dynamic extension and retraction to the type IV pilus trait.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "Appendage-and-dynamics sketch backed by DOI:10.1093/femsre/fuab053 and DOI:10.1042/BST20160221; PilA/PilB/PilT protein nodes with strain-matched UniProtKB accessions for Pseudomonas aeruginosa PAO1 remain to be curated.",
        "nodes": [
          {
            "node_id": "type_iv_pilus_trait",
            "label": "type IV pilus",
            "node_type": "TRAIT",
            "grounding": "traitmech:000175",
            "description": "Morphology trait in which a cell produces extracellular type IV pilus filaments that dynamically extend and retract."
          },
          {
            "node_id": "type_iv_pilus_appendage",
            "label": "type IV pilus complex",
            "node_type": "CELLULAR_LOCALIZATION",
            "grounding": "GO:0044096",
            "description": "Hair-like prokaryotic surface appendage composed of type IV pilin subunits."
          },
          {
            "node_id": "type_iv_pilus_extension_retraction",
            "label": "pilus-dependent motility",
            "node_type": "BIOLOGICAL_PROCESS",
            "grounding": "GO:0071972",
            "description": "Dynamic extension and retraction of type IV pilus fibers."
          },
          {
            "node_id": "type_iv_pilus_cell_surface",
            "label": "cell surface",
            "node_type": "CELLULAR_LOCALIZATION",
            "grounding": "GO:0009986",
            "description": "Bacterial or archaeal cell surface from which type IV pili extend."
          }
        ],
        "edges": [
          {
            "subject": "type_iv_pilus_appendage",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "type_iv_pilus_trait",
            "description": "Production of type IV pili appendages confers the type IV pilus morphology trait.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuab053",
                "snippet": "Bacteria and archaea rely on appendages called type IV pili (T4P)",
                "notes": "Ellison et al. review type IV pili (T4P) as prokaryotic appendages across bacteria and archaea."
              }
            ]
          },
          {
            "subject": "type_iv_pilus_appendage",
            "predicate": "enables",
            "predicate_id": "RO:0002327",
            "object": "type_iv_pilus_extension_retraction",
            "description": "Type IV pilus fibers dynamically extend and retract.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuab053",
                "snippet": "T4P are broadly distributed fibers that dynamically extend and retract",
                "notes": "Ellison et al. describe T4P as broadly distributed fibers that dynamically extend and retract."
              }
            ]
          },
          {
            "subject": "type_iv_pilus_appendage",
            "predicate": "located in",
            "predicate_id": "biolink:located_in",
            "object": "type_iv_pilus_cell_surface",
            "description": "Type IV pili are hair-like appendages localized on the bacterial cell surface.",
            "evidence": [
              {
                "reference": "DOI:10.1042/BST20160221",
                "snippet": "Type IV pili are hair-like bacterial surface appendages",
                "notes": "Piepenbrink and Sundberg characterize type IV pili as hair-like bacterial surface appendages."
              }
            ]
          }
        ]
      }
    ]
  },
  {
    "identifier": "METPO:1000686",
    "label": "vibrio shaped",
    "definition": "A cell shape in which an organism has a curved rod or comma morphology, characterized by a short curved cylindrical form with a single arc.",
    "definition_source": "DOI:10.1016/j.cell.2016.12.019",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000666"
    ],
    "synonyms": [
      {
        "synonym_text": "vibrio",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "vibrio-shaped",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "created_by": "Jed Dongjin Kim-Ozaeta",
    "evidence": [
      {
        "reference": "DOI:10.1016/j.cell.2016.12.019",
        "snippet": "V. cholerae has a characteristic curved rod morphology",
        "notes": "Supports vibrio/comma morphology and a source-backed curvature mechanism in Vibrio cholerae."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:666",
        "taxon_label": "Vibrio cholerae",
        "note": "Comma-shaped (curved-rod) vibrio; cholera agent and the canonical Vibrio.",
        "reference": "PMID:28086090"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "vibrio_shaped_crvA_curvature",
        "title": "Vibrio-shape CrvA curvature mechanism",
        "description": "Evidence-backed causal sketch linking vibrioid curved-rod morphology to periplasmic CrvA polymers and asymmetric peptidoglycan insertion.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a broad environmental or morphological classification spanning multiple mechanisms, a measurement-like bin, or an absence/arrangement descriptor; contextual protein nodes do not receive token UniProt examples.",
        "nodes": [
          {
            "node_id": "vibrio_shaped_trait",
            "label": "vibrio shaped",
            "node_type": "TRAIT",
            "grounding": "METPO:1000686",
            "description": "Short curved-rod or comma-shaped bacterial morphology."
          },
          {
            "node_id": "crvA",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "CrvA",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Periplasmic polymer-forming curvature determinant in Vibrio."
          },
          {
            "node_id": "periplasmic_filament",
            "label": "periplasmic filament",
            "node_type": "CELLULAR_LOCALIZATION",
            "description": "CrvA polymer structure at the inner curved face of the cell."
          },
          {
            "node_id": "asymmetric_peptidoglycan_insertion",
            "label": "asymmetric peptidoglycan insertion",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Unequal cell-wall insertion across inner and outer faces."
          },
          {
            "node_id": "cell_body_curvature",
            "label": "cell-body curvature",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Curving of an otherwise rod-like cell body."
          },
          {
            "node_id": "crvB",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "CrvB",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Periplasmic curvature determinant that co-assembles with CrvA into the inner-curve filament."
          },
          {
            "node_id": "vadR_srna",
            "label": "VadR sRNA",
            "node_type": "RNA",
            "description": "Small RNA that post-transcriptionally represses crvA mRNA to limit curvature."
          },
          {
            "node_id": "crvA_mrna",
            "label": "crvA mRNA",
            "node_type": "RNA",
            "description": "Messenger RNA encoding the CrvA curvature determinant."
          },
          {
            "node_id": "vxrAB_tcs",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "VxrAB two-component system",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Two-component signaling system that activates vadR transcription."
          },
          {
            "node_id": "cyclic_di_gmp",
            "label": "cyclic di-GMP",
            "node_type": "CHEMICAL",
            "description": "Second messenger that, when elevated, decreases cell curvature to generate straight rods.",
            "grounding": "CHEBI:49537"
          }
        ],
        "edges": [
          {
            "subject": "crvA",
            "predicate": "self-assembles into",
            "object": "periplasmic_filament",
            "description": "CrvA forms periplasmic filaments at the inner face of cell curvature.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.cell.2016.12.019",
                "snippet": "CrvA self-assembles into filaments at the inner face",
                "notes": "Supports CrvA as a periplasmic polymer at the inner curvature."
              }
            ]
          },
          {
            "subject": "periplasmic_filament",
            "predicate": "patterns",
            "object": "asymmetric_peptidoglycan_insertion",
            "description": "CrvA filaments pattern differential peptidoglycan insertion.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.cell.2016.12.019",
                "snippet": "asymmetrically patterns peptidoglycan insertion",
                "notes": "Supports CrvA-dependent spatial patterning of wall insertion."
              }
            ]
          },
          {
            "subject": "asymmetric_peptidoglycan_insertion",
            "predicate": "causes",
            "object": "cell_body_curvature",
            "description": "Unequal peptidoglycan insertion creates more material on the outer face than the inner face, curving the cell.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.cell.2016.12.019",
                "snippet": "causing more material insertions into the outer face",
                "notes": "Supports asymmetric wall insertion as the proximal cause of curvature."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "cell_body_curvature",
            "predicate": "confers",
            "object": "vibrio_shaped_trait",
            "description": "Curved rod morphology produces the vibrioid/comma-shaped trait.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.cell.2016.12.019",
                "snippet": "characteristic curved rod morphology",
                "notes": "Supports the observed Vibrio morphology as a curved-rod shape."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "crvB",
            "predicate": "increases",
            "object": "cell_body_curvature",
            "description": "CrvB expression increases CrvA assembly and cell curvature in a dose-dependent manner.",
            "evidence": [
              {
                "reference": "DOI:10.1101/2020.02.20.954503",
                "notes": "crvB expression increased CrvA-GFP assembly as well as cell curvature in a dose-dependent manner."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "crvB",
            "predicate": "colocalizes with",
            "object": "periplasmic_filament",
            "description": "CrvB colocalizes with CrvA in the same periplasmic inner-curve filament structure.",
            "evidence": [
              {
                "reference": "DOI:10.1101/2020.02.20.954503",
                "notes": "Both proteins localized to the same structure; CrvB-GFP filaments colocalized with periplasmic DsbA-mCherry."
              }
            ]
          },
          {
            "subject": "vadR_srna",
            "predicate": "represses",
            "object": "crvA_mrna",
            "description": "VadR sRNA is a post-transcriptional inhibitor of crvA mRNA.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-020-19890-8",
                "notes": "The VadR small RNA acts as a post-transcriptional inhibitor of the crvA mRNA."
              }
            ]
          },
          {
            "subject": "crvA_mrna",
            "predicate": "translated into",
            "object": "crvA",
            "description": "crvA mRNA is translated into the CrvA curvature determinant protein.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-020-19890-8",
                "notes": "crvA mRNA encodes the periplasmic CrvA protein that determines cell curvature."
              }
            ]
          },
          {
            "subject": "vadR_srna",
            "predicate": "decreases",
            "object": "cell_body_curvature",
            "description": "Mutation of vadR increases cell curvature whereas overexpression has the inverse effect, indicating VadR limits curvature.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-020-19890-8",
                "notes": "Mutation of vadR increases cell curvature, whereas overexpression has the inverse effect."
              }
            ],
            "predicate_id": "RO:0002212"
          },
          {
            "subject": "vxrAB_tcs",
            "predicate": "activates transcription of",
            "object": "vadR_srna",
            "description": "The VxrAB two-component system activates vadR transcription.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-020-19890-8",
                "notes": "vadR transcription is activated by the VxrAB two-component system."
              }
            ]
          },
          {
            "subject": "cyclic_di_gmp",
            "predicate": "decreases",
            "object": "cell_body_curvature",
            "description": "High c-di-GMP concentrations decrease cell curvature to generate straight rods.",
            "evidence": [
              {
                "reference": "DOI:10.1073/pnas.2010199117",
                "notes": "High c-di-GMP concentrations decrease cell curvature to generate straight rods."
              }
            ],
            "predicate_id": "RO:0002212"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.896189+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-11T18:00:00-07:00",
        "curator": "codex",
        "action": "CURATED_WITH_LITERATURE",
        "changes": "Reviewed vibrio shape and added DOI-backed causal graph for CrvA periplasmic filaments, asymmetric peptidoglycan insertion, and curved-rod morphology.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T05:49:25Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:causes\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 7 evidence-backed generic edges (5 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:14Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002212\u00d72, RO:0002213\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:34Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:49537\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates (1 to confers), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope vibrio_shaped_crvA_curvature=NONMECHANISTIC with scope_notes; marked 3 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (crvA, crvB, vxrAB_tcs); retyped 2 node(s) (vadR_srna->RNA, crvA_mrna->RNA).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1003029",
    "label": "white pigmented",
    "definition": "A pigmentation phenotype in which microbial colonies or cells appear white or nonpigmented because visible chromophore accumulation is absent or low.",
    "definition_source": "DOI:10.2147/IDR.S49039",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1003021"
    ],
    "synonyms": [
      {
        "synonym_text": "Pigment_white",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.2147/IDR.S49039",
        "snippet": "white phenotypic variant of Staphylococcus aureus",
        "notes": "Supports white colony appearance as a microbial pigmentation phenotype tied to absent or inducible staphyloxanthin production in a representative bacterium."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:615",
        "taxon_label": "Serratia marcescens",
        "reference": "DOI:10.3389/fmicb.2021.793202",
        "note": "Specifically the SCQ1 delta-slyA deletion mutant, which showed a white colony and lost prodigiosin synthesis; this is a mutant-specific example and does not assert that all Serratia marcescens isolates are white."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "white_pigmented_low_chromophore",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "White pigmentation is a visual color classification produced by several unrelated low-chromophore or regulatory states. The graph is illustrative context, not one universal protein-mediated mechanism.",
        "title": "White pigmentation low-chromophore mechanism",
        "description": "Evidence-backed causal sketch linking white colony pigmentation to reduced visible pigment accumulation, staphyloxanthin biosynthesis machinery, and absence or silencing of carotenoid production in representative bacteria.",
        "nodes": [
          {
            "node_id": "white_pigmented_trait",
            "label": "white pigmented",
            "node_type": "TRAIT",
            "grounding": "METPO:1003029",
            "description": "White or nonpigmented microbial colony or cell appearance."
          },
          {
            "node_id": "staphyloxanthin_enzyme_module",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "This module contains multiple distinct carotenoid-pathway protein families; no single family identifier denotes the full enzyme set.",
            "label": "CrtOPQMN staphyloxanthin enzyme module",
            "node_type": "GENE_OR_PROTEIN",
            "description": "S. aureus carotenoid enzymes for staphyloxanthin production.",
            "gene_symbols": [
              "crtO",
              "crtP",
              "crtQ",
              "crtM",
              "crtN"
            ],
            "operon": "crtOPQMN"
          },
          {
            "node_id": "staphyloxanthin_biosynthesis",
            "label": "staphyloxanthin biosynthesis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Biosynthesis of the golden carotenoid pigment staphyloxanthin."
          },
          {
            "node_id": "staphyloxanthin",
            "label": "staphyloxanthin",
            "node_type": "CHEMICAL",
            "description": "Golden carotenoid pigment of Staphylococcus aureus.",
            "grounding": "CHEBI:71690"
          },
          {
            "node_id": "low_visible_chromophore",
            "label": "low visible chromophore accumulation",
            "node_type": "CHEMICAL",
            "description": "Absence or low accumulation of colored pigment molecules."
          },
          {
            "node_id": "visible_white_color",
            "label": "visible white color",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "Observed white or nonpigmented colony color."
          },
          {
            "node_id": "melanin_biosynthesis",
            "label": "melanin biosynthesis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "PKS-type biosynthesis of melanin pigments (e.g. DHN melanin) in fungi and bacteria.",
            "grounding": "GO:0042438"
          },
          {
            "node_id": "melanin",
            "label": "melanin",
            "node_type": "CHEMICAL",
            "description": "Dark brown/black chromophore pigment class; a major visible microbial pigment.",
            "grounding": "CHEBI:89634"
          },
          {
            "node_id": "reduced_melanin",
            "label": "reduced melanin accumulation",
            "node_type": "CHEMICAL",
            "description": "Absent or lowered accumulation of melanin chromophore."
          },
          {
            "node_id": "sigB",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "SigB is a contextual regulatory example and not a universal determinant of the visually classified white phenotype.",
            "label": "SigB (sigma factor B)",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Alternative sigma factor B; positive regulator of staphyloxanthin biosynthesis genes."
          },
          {
            "node_id": "glmS",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "GlmS is a contextual metabolic example and not a universal determinant of the visually classified white phenotype.",
            "label": "GlmS",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Glucosamine-6-phosphate synthase; transcriptional upregulator of sigB."
          }
        ],
        "edges": [
          {
            "subject": "staphyloxanthin_enzyme_module",
            "predicate": "catalyzes",
            "object": "staphyloxanthin_biosynthesis",
            "description": "The CrtOPQMN enzyme module catalyzes staphyloxanthin biosynthesis.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41426-018-0078-1",
                "snippet": "controlled by the crtOPQMN operon",
                "notes": "Supports the operon as staphyloxanthin biosynthetic machinery."
              }
            ],
            "predicate_id": "METPO:2007813"
          },
          {
            "subject": "staphyloxanthin_biosynthesis",
            "predicate": "has output",
            "object": "staphyloxanthin",
            "description": "Staphyloxanthin biosynthesis produces the golden carotenoid pigment.",
            "evidence": [
              {
                "reference": "DOI:10.1084/jem.20050846",
                "snippet": "Golden color imparted by carotenoid pigments",
                "notes": "Supports the link from carotenoid biosynthesis to visible golden pigment in S. aureus."
              }
            ],
            "predicate_id": "RO:0002234"
          },
          {
            "subject": "low_visible_chromophore",
            "predicate": "results from reduced",
            "object": "staphyloxanthin_biosynthesis",
            "description": "Reduced or absent staphyloxanthin biosynthesis lowers visible pigment accumulation.",
            "evidence": [
              {
                "reference": "DOI:10.2147/IDR.S49039",
                "snippet": "white-colony phenotype actually lacked the crtOPQMN operon",
                "notes": "Supports white colony phenotype when staphyloxanthin synthesis machinery is absent in a representative case."
              }
            ]
          },
          {
            "subject": "low_visible_chromophore",
            "predicate": "causes",
            "object": "visible_white_color",
            "description": "Lack of accumulated chromophore yields a white or nonpigmented colony appearance.",
            "evidence": [
              {
                "reference": "DOI:10.2147/IDR.S49039",
                "snippet": "white phenotypic variant",
                "notes": "Supports white appearance as a phenotype of low or absent visible pigment."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "visible_white_color",
            "predicate": "manifests as",
            "object": "white_pigmented_trait",
            "description": "Visible white colony color manifests the white-pigmented trait.",
            "evidence": [
              {
                "reference": "DOI:10.2147/IDR.S49039",
                "snippet": "white phenotypic variant of Staphylococcus aureus",
                "notes": "Supports trait-level white pigmentation in a representative microbial context."
              }
            ],
            "predicate_id": "METPO:2007400"
          },
          {
            "subject": "melanin_biosynthesis",
            "predicate": "has output",
            "object": "melanin",
            "description": "PKS-mediated melanin biosynthesis produces the melanin chromophore.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s00792-024-01354-2",
                "notes": "pks1 mutation abolishes melanization / decreased DHN melanin accumulation, establishing the PKS biosynthetic route to melanin."
              }
            ],
            "predicate_id": "RO:0002234"
          },
          {
            "subject": "reduced_melanin",
            "predicate": "results from reduced",
            "object": "melanin_biosynthesis",
            "description": "Reduced melanin biosynthesis lowers melanin chromophore accumulation.",
            "evidence": [
              {
                "reference": "DOI:10.1080/21501203.2023.2249010",
                "notes": "Knockout of PKS gene (pksA) reduced melanin production, yielding melanin-deficient cells."
              }
            ]
          },
          {
            "subject": "reduced_melanin",
            "predicate": "causes",
            "object": "visible_white_color",
            "description": "Loss of melanin chromophore yields a white colony surface / white cells.",
            "evidence": [
              {
                "reference": "DOI:10.1080/21501203.2023.2249010",
                "notes": "Mel- colonies are uneven with a white surface and white conidia; generic melanin-loss to white-pigment link."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "sigB",
            "predicate": "positively regulates",
            "object": "staphyloxanthin_biosynthesis",
            "description": "Sigma factor B positively regulates staphyloxanthin biosynthesis genes; its loss reduces pigment.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mbio.00346-24",
                "notes": "SigB positively regulates genes involved in staphyloxanthin synthesis; disruptive sigB mutations give white colonies."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "glmS",
            "predicate": "positively regulates",
            "object": "sigB",
            "description": "GlmS directly upregulates sigB transcription, feeding the carotenoid-pigment regulatory cascade.",
            "evidence": [
              {
                "reference": "DOI:10.1080/21505594.2024.2352476",
                "notes": "GlmS directly upregulates sigB transcription (dual-luciferase and EMSA promoter binding); glmS knockout reduces sigB and golden pigment."
              }
            ],
            "predicate_id": "RO:0002213"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.946745+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-11T19:10:00-07:00",
        "curator": "codex",
        "action": "CURATED_WITH_LITERATURE",
        "changes": "Added DOI-backed definition and causal graph for staphyloxanthin biosynthesis machinery, low visible chromophore accumulation, and white colony appearance.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T05:49:25Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:causes\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T08:21:50Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:encodes\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T21:30:07Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007400\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-14T05:51:46Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:71690\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 5 evidence-backed generic edges (5 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:14Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d71, biolink:causes\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:20Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0042438\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:34Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:89634\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-26T07:15:20Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:I6LB50\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-04T03:08:15Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002213\u00d72).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 2 causal edge(s) off microbe-domain METPO predicates (2 to has output), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-07T04:00:00Z",
        "curator": "claude",
        "action": "REGROUND_CAUSAL_EDGE",
        "changes": "Re-grounded the `encodes` edge(s) from biolink:encodes to METPO:2007813, issue 342. biolink:encodes is NOT a slot in the pinned biolink 4.4.0 model, so the CURIE resolved to nothing upstream while looking like an upstream term to anyone reading this record -- the disclaimer saying otherwise lived in mappings/predicate_grounding.tsv, which is not read at the point of use. RO:0002205 (has gene product) is the nearest real term but relates a GENE to a gene product, whereas these edges relate a gene cluster or operon to a protein complex or a biosynthetic process, which its range does not admit; that mismatch is why the coinage existed. METPO:2007813 is proposed in proposals/metpo_traitmech_v9 and is a placeholder id until METPO mints it, which puts it in the same state as the rest of that cohort rather than in a category of its own.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-22T04:26:16Z",
        "curator": "codex",
        "action": "REVIEW_UNIPROT_INSTANCE_GROUNDINGS",
        "changes": "Reviewed 1 organism-specific UniProtKB grounding(s): replaced 0 with taxon-agnostic GO/InterPro terms and retracted 1 to label-only where no exact semantic term was supported (docs/GROUNDING_POLICY.md).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope white_pigmented_low_chromophore=NONMECHANISTIC with scope_notes; marked 3 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (staphyloxanthin_enzyme_module, sigB, glmS); added 1 node(s) and 1 edge(s) (staphyloxanthin_enzyme_module); removed 1 node(s) and 1 edge(s) together with their evidence (crtOPQMN_operon).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T11:06:05Z",
        "curator": "codex",
        "action": "ADD_CANONICAL_EXAMPLES",
        "changes": "Added a mutant-specific Serratia marcescens white-colony example from DOI:10.3389/fmicb.2021.793202, explicitly retaining SCQ1 delta-slyA context in the note; verified the current species taxon and label through NCBI Taxonomy.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1003030",
    "label": "yellow pigmented",
    "definition": "A pigmentation phenotype in which microbial colonies or cells appear yellow due to production of yellow pigments such as carotenoids.",
    "definition_source": "DOI:10.1080/1040841X.2025.2526423",
    "trait_category": "MORPHOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1003021"
    ],
    "synonyms": [
      {
        "synonym_text": "Pigment_yellow",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1080/1040841X.2025.2526423",
        "snippet": "red, pink, orange, and yellow pigmentation in bacteria",
        "notes": "Supports yellow microbial pigmentation as a carotenoid-associated bacterial color phenotype."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:339",
        "taxon_label": "Xanthomonas campestris",
        "note": "Yellow-pigmented (xanthomonadin) phytopathogen; the namesake xanthous bacterium.",
        "reference": "PMID:12024217"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "yellow_pigmented_carotenoid_color",
        "title": "Yellow pigmentation carotenoid mechanism",
        "description": "Evidence-backed causal sketch linking yellow microbial pigmentation to crt-catalyzed carotenoid biosynthesis, yellow carotenoid accumulation, and visible yellow colony color.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This record is a broad environmental or morphological classification spanning multiple mechanisms, a measurement-like bin, or an absence/arrangement descriptor; contextual protein nodes do not receive token UniProt examples.",
        "nodes": [
          {
            "node_id": "yellow_pigmented_trait",
            "label": "yellow pigmented",
            "node_type": "TRAIT",
            "grounding": "METPO:1003030",
            "description": "Microbial pigmentation appearing yellow."
          },
          {
            "node_id": "crt_enzymes",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "Crt enzymes",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Bacterial carotenoid biosynthetic enzymes."
          },
          {
            "node_id": "carotenoid_biosynthesis",
            "label": "carotenoid biosynthesis",
            "node_type": "PATHWAY",
            "description": "Enzymatic pathway producing carotenoid pigments.",
            "grounding": "GO:0016117"
          },
          {
            "node_id": "yellow_carotenoids",
            "label": "yellow carotenoids",
            "node_type": "CHEMICAL",
            "description": "Carotenoid pigments that contribute yellow coloration."
          },
          {
            "node_id": "visible_yellow_color",
            "label": "visible yellow color",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "Observed yellow color produced by pigment absorption spectra."
          },
          {
            "node_id": "ipp_dmapp",
            "label": "IPP/DMAPP",
            "node_type": "CHEMICAL",
            "description": "C5 isoprenoid precursors isopentenyl diphosphate and dimethylallyl diphosphate."
          },
          {
            "node_id": "ggpp",
            "label": "geranylgeranyl diphosphate (GGPP)",
            "node_type": "CHEMICAL",
            "description": "C20 isoprenoid precursor of carotenoid backbones."
          },
          {
            "node_id": "idsa_crte",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "IdsA/CrtE (GGPP synthase)",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Geranylgeranyl diphosphate synthase converting IPP and DMAPP to GGPP."
          },
          {
            "node_id": "lycopene",
            "label": "lycopene",
            "node_type": "CHEMICAL",
            "description": "C40 carotenoid backbone intermediate.",
            "grounding": "CHEBI:15948"
          },
          {
            "node_id": "crti",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "CrtI (phytoene desaturase)",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Phytoene desaturase that produces lycopene in carotenoid biosynthesis."
          },
          {
            "node_id": "lycopene_biosynthesis",
            "label": "lycopene biosynthesis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Pathway steps producing lycopene from phytoene.",
            "grounding": "GO:1901177"
          },
          {
            "node_id": "crty",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed protein family, complex, or aggregate; no single semantic family identifier exactly captures this node's represented scope.",
            "label": "CrtY (lycopene beta-cyclase)",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Lycopene beta-cyclase converting lycopene to beta-carotene."
          },
          {
            "node_id": "beta_carotene",
            "label": "beta-carotene",
            "node_type": "CHEMICAL",
            "description": "Canonical yellow/orange carotenoid pigment.",
            "grounding": "CHEBI:17579"
          },
          {
            "node_id": "flexirubin_pigment",
            "label": "flexirubin-type pigment",
            "node_type": "CHEMICAL",
            "description": "Aryl polyene yellow pigment class distinct from carotenoids."
          },
          {
            "node_id": "ros_damage",
            "label": "reactive oxygen species damage",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Oxidative damage caused by reactive oxygen species."
          }
        ],
        "edges": [
          {
            "subject": "crt_enzymes",
            "predicate": "catalyzes",
            "object": "carotenoid_biosynthesis",
            "description": "Crt enzymes catalyze carotenoid biosynthetic reactions.",
            "evidence": [
              {
                "reference": "DOI:10.1080/1040841X.2025.2526423",
                "snippet": "crt genes ... reactions they catalyze",
                "notes": "Supports Crt enzymes as catalysts in bacterial carotenoid pathways."
              }
            ],
            "predicate_id": "biolink:catalyzes"
          },
          {
            "subject": "carotenoid_biosynthesis",
            "predicate": "has output",
            "object": "yellow_carotenoids",
            "description": "Carotenoid biosynthesis produces yellow-pigment carotenoids in representative bacteria.",
            "evidence": [
              {
                "reference": "DOI:10.1080/1040841X.2025.2526423",
                "snippet": "yellow pigmentation in bacteria",
                "notes": "Supports carotenoids as one source of yellow pigmentation."
              }
            ],
            "predicate_id": "RO:0002234"
          },
          {
            "subject": "yellow_carotenoids",
            "predicate": "causes",
            "object": "visible_yellow_color",
            "description": "Yellow carotenoids cause visible yellow colony or cell color.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.tim.2010.07.007",
                "snippet": "Carotenoids are natural pigments",
                "notes": "Supports carotenoids as visible pigments in bacteria."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "visible_yellow_color",
            "predicate": "manifests as",
            "object": "yellow_pigmented_trait",
            "description": "Visible yellow color manifests the yellow-pigmented phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1080/1040841X.2025.2526423",
                "snippet": "yellow pigmentation in bacteria",
                "notes": "Supports trait-level yellow pigmentation."
              }
            ],
            "predicate_id": "METPO:2007400"
          },
          {
            "subject": "ipp_dmapp",
            "predicate": "precursor of",
            "object": "ggpp",
            "description": "C5 precursors IPP/DMAPP are elongated to the C20 carotenoid precursor GGPP.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41598-024-58700-9",
                "notes": "Carotenoid synthesis begins from the C5 isoprenoid precursors IPP and DMAPP, which are converted via chain elongation to the C20 precursor GGPP."
              }
            ]
          },
          {
            "subject": "idsa_crte",
            "predicate": "catalyzes",
            "object": "ggpp",
            "description": "IdsA/CrtE (GGPP synthase) catalyzes formation of GGPP from IPP and DMAPP.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41598-024-58700-9",
                "notes": "IdsA, the major geranylgeranyl diphosphate synthase converting IPP and DMAPP to GGPP; GGPPS annotated CrtE/IdsA."
              }
            ],
            "predicate_id": "biolink:catalyzes"
          },
          {
            "subject": "ggpp",
            "predicate": "precursor of",
            "object": "lycopene",
            "description": "Two GGPP molecules condense to form the C40 backbone lycopene.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41598-024-58700-9",
                "notes": "Two GGPP molecules condense to form the C40 backbone lycopene."
              }
            ]
          },
          {
            "subject": "crti",
            "predicate": "enables",
            "object": "lycopene_biosynthesis",
            "description": "CrtI (phytoene desaturase) enables lycopene biosynthesis.",
            "evidence": [
              {
                "reference": "DOI:10.3390/microorganisms12040803",
                "notes": "Phytoene desaturase (CrtI) to produce lycopene."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "lycopene_biosynthesis",
            "predicate": "has output",
            "object": "lycopene",
            "description": "Lycopene biosynthesis produces lycopene.",
            "evidence": [
              {
                "reference": "DOI:10.3390/microorganisms12040803",
                "notes": "Pathway proceeds through phytoene synthase (CrtB) and phytoene desaturase (CrtI) to produce lycopene."
              }
            ],
            "predicate_id": "RO:0002234"
          },
          {
            "subject": "crty",
            "predicate": "catalyzes conversion to",
            "object": "beta_carotene",
            "description": "CrtY (lycopene beta-cyclase) cyclizes lycopene to beta-carotene.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41598-024-58700-9",
                "notes": "Lycopene is cyclized to beta-carotene by lycopene beta-cyclase (crtY)."
              }
            ]
          },
          {
            "subject": "beta_carotene",
            "predicate": "causes or contributes to",
            "object": "yellow_pigmented_trait",
            "description": "beta-carotene is a canonical yellow/orange carotenoid that contributes to the yellow phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.4014/jmb.2404.04018",
                "notes": "beta-carotene serves as a colorant and is the classic yellow/orange carotenoid pigment."
              }
            ]
          },
          {
            "subject": "flexirubin_pigment",
            "predicate": "contributes to",
            "object": "yellow_pigmented_trait",
            "description": "Flexirubin-type pigments produce yellow colony coloration, a carotenoid-independent yellow pigment route.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-024-54112-5",
                "notes": "Flexirubin-type pigment-producing bacterium is yellow (or orange) in color; flexirubin is a known yellow pigment."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "flexirubin_pigment",
            "predicate": "protects against",
            "object": "ros_damage",
            "description": "Flexirubin protects against reactive oxygen species damage.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-024-54112-5",
                "notes": "Flexirubin is known as a yellow pigment that effectively protects against reactive oxygen species damage."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.947204+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-11T18:45:00-07:00",
        "curator": "codex",
        "action": "CURATED_WITH_LITERATURE",
        "changes": "Added DOI-backed definition and causal graph for Crt enzymes, carotenoid biosynthesis, yellow carotenoids, and visible yellow color.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T05:49:25Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:catalyzes\u00d71, biolink:causes\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T21:30:07Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007400\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:41:04Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0016117\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 9 evidence-backed generic edges (10 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:14Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 4 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:catalyzes\u00d71, RO:0002327\u00d71, METPO:2000202\u00d71, RO:0002326\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:34Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 3 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:15948\u00d71, GO:1901177\u00d71, CHEBI:17579\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 2 causal edge(s) off microbe-domain METPO predicates (2 to has output), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-16T02:00:00Z",
        "curator": "claude",
        "action": "NORMALISE_NODE_TYPE",
        "changes": "Under the PATHWAY-vs-BIOLOGICAL_PROCESS rule, one node_id means one thing corpus-wide (issue 356): carotenoid_biosynthesis is typed PATHWAY. PATHWAY is a named, conventionally enumerable multi-step route; BIOLOGICAL_PROCESS is everything else. A named biosynthetic route. Most descriptions call it one outright, including BIOLOGICAL_PROCESS-typed ones ('Enzymatic pathway producing carotenoid pigments'); red_pigmented.yaml instead ENUMERATES the steps -- 'Phytoene synthase condenses two GGPP to phytoene, then desaturation/isomerization yields lycopene' -- which is the rule's own test for PATHWAY met explicitly rather than by naming. Applied AGAINST the majority, which was 5 BIOLOGICAL_PROCESS to 1 before this tranche.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope yellow_pigmented_carotenoid_color=NONMECHANISTIC with scope_notes; marked 4 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (crt_enzymes, idsa_crte, crti, crty).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1001007",
    "label": "growth NaCl observation",
    "trait_category": "OBSERVATION",
    "term_kind": "CLASS",
    "mapping_status": "DEPRECATED",
    "parent_traits": [
      "METPO:1001000"
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.925690+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic observation/value carrier; later replacement should use more specific trait records that combine the observation relation with growth context, measured quantity, chemical, value range, or other entity.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-17T15:30:00-07:00",
        "curator": "claude",
        "action": "DEPRECATION_CONFIRMED_AS_OUT_OF_SCOPE",
        "changes": "DEPRECATED status confirmed as final after the predicate+class composition\npivot (#54/#55/#56). This record's observation-shape modelling is out of\nscope for TraitMech; the trait vocabulary + mechanism need is met by the un-\ndeprecated METPO predicates, and per-organism numeric observations belong\ndownstream (KG-Microbe / BacDive). See\ndocs/DEPRECATED_REPLACEMENT_PROPOSAL.md, section 'Observation-value records\nstay deprecated', for the rationale.\n",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1001017",
    "label": "growth oxygen observation",
    "trait_category": "OBSERVATION",
    "term_kind": "CLASS",
    "mapping_status": "DEPRECATED",
    "parent_traits": [
      "METPO:1001000"
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.929271+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic observation/value carrier; later replacement should use more specific trait records that combine the observation relation with growth context, measured quantity, chemical, value range, or other entity.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-17T15:30:00-07:00",
        "curator": "claude",
        "action": "DEPRECATION_CONFIRMED_AS_OUT_OF_SCOPE",
        "changes": "DEPRECATED status confirmed as final after the predicate+class composition\npivot (#54/#55/#56). This record's observation-shape modelling is out of\nscope for TraitMech; the trait vocabulary + mechanism need is met by the un-\ndeprecated METPO predicates, and per-organism numeric observations belong\ndownstream (KG-Microbe / BacDive). See\ndocs/DEPRECATED_REPLACEMENT_PROPOSAL.md, section 'Observation-value records\nstay deprecated', for the rationale.\n",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1001012",
    "label": "growth pH observation",
    "trait_category": "OBSERVATION",
    "term_kind": "CLASS",
    "mapping_status": "DEPRECATED",
    "parent_traits": [
      "METPO:1001000"
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.927344+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic observation/value carrier; later replacement should use more specific trait records that combine the observation relation with growth context, measured quantity, chemical, value range, or other entity.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-17T15:30:00-07:00",
        "curator": "claude",
        "action": "DEPRECATION_CONFIRMED_AS_OUT_OF_SCOPE",
        "changes": "DEPRECATED status confirmed as final after the predicate+class composition\npivot (#54/#55/#56). This record's observation-shape modelling is out of\nscope for TraitMech; the trait vocabulary + mechanism need is met by the un-\ndeprecated METPO predicates, and per-organism numeric observations belong\ndownstream (KG-Microbe / BacDive). See\ndocs/DEPRECATED_REPLACEMENT_PROPOSAL.md, section 'Observation-value records\nstay deprecated', for the rationale.\n",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1001002",
    "label": "growth temperature observation",
    "trait_category": "OBSERVATION",
    "term_kind": "CLASS",
    "mapping_status": "DEPRECATED",
    "parent_traits": [
      "METPO:1001000"
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.924143+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic observation/value carrier; later replacement should use more specific trait records that combine the observation relation with growth context, measured quantity, chemical, value range, or other entity.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-17T15:30:00-07:00",
        "curator": "claude",
        "action": "DEPRECATION_CONFIRMED_AS_OUT_OF_SCOPE",
        "changes": "DEPRECATED status confirmed as final after the predicate+class composition\npivot (#54/#55/#56). This record's observation-shape modelling is out of\nscope for TraitMech; the trait vocabulary + mechanism need is met by the un-\ndeprecated METPO predicates, and per-organism numeric observations belong\ndownstream (KG-Microbe / BacDive). See\ndocs/DEPRECATED_REPLACEMENT_PROPOSAL.md, section 'Observation-value records\nstay deprecated', for the rationale.\n",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1001008",
    "label": "NaCl delta observation",
    "trait_category": "OBSERVATION",
    "term_kind": "CLASS",
    "mapping_status": "DEPRECATED",
    "parent_traits": [
      "METPO:1001000"
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.926105+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic observation/value carrier; later replacement should use more specific trait records that combine the observation relation with growth context, measured quantity, chemical, value range, or other entity.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-17T15:30:00-07:00",
        "curator": "claude",
        "action": "DEPRECATION_CONFIRMED_AS_OUT_OF_SCOPE",
        "changes": "DEPRECATED status confirmed as final after the predicate+class composition\npivot (#54/#55/#56). This record's observation-shape modelling is out of\nscope for TraitMech; the trait vocabulary + mechanism need is met by the un-\ndeprecated METPO predicates, and per-organism numeric observations belong\ndownstream (KG-Microbe / BacDive). See\ndocs/DEPRECATED_REPLACEMENT_PROPOSAL.md, section 'Observation-value records\nstay deprecated', for the rationale.\n",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1001022",
    "label": "NaCl observation",
    "trait_category": "OBSERVATION",
    "term_kind": "CLASS",
    "mapping_status": "DEPRECATED",
    "parent_traits": [
      "METPO:1001000"
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.931186+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic observation/value carrier; later replacement should use more specific trait records that combine the observation relation with growth context, measured quantity, chemical, value range, or other entity.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-17T15:30:00-07:00",
        "curator": "claude",
        "action": "DEPRECATION_CONFIRMED_AS_OUT_OF_SCOPE",
        "changes": "DEPRECATED status confirmed as final after the predicate+class composition\npivot (#54/#55/#56). This record's observation-shape modelling is out of\nscope for TraitMech; the trait vocabulary + mechanism need is met by the un-\ndeprecated METPO predicates, and per-organism numeric observations belong\ndownstream (KG-Microbe / BacDive). See\ndocs/DEPRECATED_REPLACEMENT_PROPOSAL.md, section 'Observation-value records\nstay deprecated', for the rationale.\n",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1001009",
    "label": "NaCl range observation",
    "trait_category": "OBSERVATION",
    "term_kind": "CLASS",
    "mapping_status": "DEPRECATED",
    "parent_traits": [
      "METPO:1001000"
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.926525+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic observation/value carrier; later replacement should use more specific trait records that combine the observation relation with range context, measured quantity, chemical, value bounds, or other entity.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-17T15:30:00-07:00",
        "curator": "claude",
        "action": "DEPRECATION_CONFIRMED_AS_OUT_OF_SCOPE",
        "changes": "DEPRECATED status confirmed as final after the predicate+class composition\npivot (#54/#55/#56). This record's observation-shape modelling is out of\nscope for TraitMech; the trait vocabulary + mechanism need is met by the un-\ndeprecated METPO predicates, and per-organism numeric observations belong\ndownstream (KG-Microbe / BacDive). See\ndocs/DEPRECATED_REPLACEMENT_PROPOSAL.md, section 'Observation-value records\nstay deprecated', for the rationale.\n",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1001010",
    "label": "optimum NaCl observation",
    "trait_category": "OBSERVATION",
    "term_kind": "CLASS",
    "mapping_status": "DEPRECATED",
    "parent_traits": [
      "METPO:1001000"
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.926942+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic observation/value carrier; later replacement should use more specific trait records that combine the observation relation with growth context, measured quantity, chemical, value range, or other entity.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-17T15:30:00-07:00",
        "curator": "claude",
        "action": "DEPRECATION_CONFIRMED_AS_OUT_OF_SCOPE",
        "changes": "DEPRECATED status confirmed as final after the predicate+class composition\npivot (#54/#55/#56). This record's observation-shape modelling is out of\nscope for TraitMech; the trait vocabulary + mechanism need is met by the un-\ndeprecated METPO predicates, and per-organism numeric observations belong\ndownstream (KG-Microbe / BacDive). See\ndocs/DEPRECATED_REPLACEMENT_PROPOSAL.md, section 'Observation-value records\nstay deprecated', for the rationale.\n",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1001016",
    "label": "optimum oxygen observation",
    "trait_category": "OBSERVATION",
    "term_kind": "CLASS",
    "mapping_status": "DEPRECATED",
    "parent_traits": [
      "METPO:1001000"
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.928890+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic observation/value carrier; later replacement should use more specific trait records that combine the observation relation with growth context, measured quantity, chemical, value range, or other entity.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-17T15:30:00-07:00",
        "curator": "claude",
        "action": "DEPRECATION_CONFIRMED_AS_OUT_OF_SCOPE",
        "changes": "DEPRECATED status confirmed as final after the predicate+class composition\npivot (#54/#55/#56). This record's observation-shape modelling is out of\nscope for TraitMech; the trait vocabulary + mechanism need is met by the un-\ndeprecated METPO predicates, and per-organism numeric observations belong\ndownstream (KG-Microbe / BacDive). See\ndocs/DEPRECATED_REPLACEMENT_PROPOSAL.md, section 'Observation-value records\nstay deprecated', for the rationale.\n",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1001013",
    "label": "optimum pH observation",
    "trait_category": "OBSERVATION",
    "term_kind": "CLASS",
    "mapping_status": "DEPRECATED",
    "parent_traits": [
      "METPO:1001000"
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.927756+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic observation/value carrier; later replacement should use more specific trait records that combine the observation relation with growth context, measured quantity, chemical, value range, or other entity.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-17T15:30:00-07:00",
        "curator": "claude",
        "action": "DEPRECATION_CONFIRMED_AS_OUT_OF_SCOPE",
        "changes": "DEPRECATED status confirmed as final after the predicate+class composition\npivot (#54/#55/#56). This record's observation-shape modelling is out of\nscope for TraitMech; the trait vocabulary + mechanism need is met by the un-\ndeprecated METPO predicates, and per-organism numeric observations belong\ndownstream (KG-Microbe / BacDive). See\ndocs/DEPRECATED_REPLACEMENT_PROPOSAL.md, section 'Observation-value records\nstay deprecated', for the rationale.\n",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1001001",
    "label": "optimum temperature observation",
    "definition": "An observation that identifies the temperature at which a microorganism exhibits maximum growth rate or metabolic activity.",
    "trait_category": "OBSERVATION",
    "term_kind": "CLASS",
    "mapping_status": "DEPRECATED",
    "parent_traits": [
      "METPO:1001000"
    ],
    "created_by": "Luke Wang",
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.923552+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic observation/value carrier; later replacement should use more specific trait records that combine the observation relation with growth context, measured quantity, chemical, value range, or other entity.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-17T15:30:00-07:00",
        "curator": "claude",
        "action": "DEPRECATION_CONFIRMED_AS_OUT_OF_SCOPE",
        "changes": "DEPRECATED status confirmed as final after the predicate+class composition\npivot (#54/#55/#56). This record's observation-shape modelling is out of\nscope for TraitMech; the trait vocabulary + mechanism need is met by the un-\ndeprecated METPO predicates, and per-organism numeric observations belong\ndownstream (KG-Microbe / BacDive). See\ndocs/DEPRECATED_REPLACEMENT_PROPOSAL.md, section 'Observation-value records\nstay deprecated', for the rationale.\n",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1001019",
    "label": "oxygen delta observation",
    "trait_category": "OBSERVATION",
    "term_kind": "CLASS",
    "mapping_status": "DEPRECATED",
    "parent_traits": [
      "METPO:1001000"
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.930032+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic observation/value carrier; later replacement should use more specific trait records that combine the observation relation with growth context, measured quantity, chemical, value range, or other entity.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-17T15:30:00-07:00",
        "curator": "claude",
        "action": "DEPRECATION_CONFIRMED_AS_OUT_OF_SCOPE",
        "changes": "DEPRECATED status confirmed as final after the predicate+class composition\npivot (#54/#55/#56). This record's observation-shape modelling is out of\nscope for TraitMech; the trait vocabulary + mechanism need is met by the un-\ndeprecated METPO predicates, and per-organism numeric observations belong\ndownstream (KG-Microbe / BacDive). See\ndocs/DEPRECATED_REPLACEMENT_PROPOSAL.md, section 'Observation-value records\nstay deprecated', for the rationale.\n",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1001020",
    "label": "oxygen observation",
    "trait_category": "OBSERVATION",
    "term_kind": "CLASS",
    "mapping_status": "DEPRECATED",
    "parent_traits": [
      "METPO:1001000"
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.930427+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic observation/value carrier; later replacement should use more specific trait records that combine the observation relation with growth context, measured quantity, chemical, value range, or other entity.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-17T15:30:00-07:00",
        "curator": "claude",
        "action": "DEPRECATION_CONFIRMED_AS_OUT_OF_SCOPE",
        "changes": "DEPRECATED status confirmed as final after the predicate+class composition\npivot (#54/#55/#56). This record's observation-shape modelling is out of\nscope for TraitMech; the trait vocabulary + mechanism need is met by the un-\ndeprecated METPO predicates, and per-organism numeric observations belong\ndownstream (KG-Microbe / BacDive). See\ndocs/DEPRECATED_REPLACEMENT_PROPOSAL.md, section 'Observation-value records\nstay deprecated', for the rationale.\n",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1001018",
    "label": "oxygen range observation",
    "trait_category": "OBSERVATION",
    "term_kind": "CLASS",
    "mapping_status": "DEPRECATED",
    "parent_traits": [
      "METPO:1001000"
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.929650+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic observation/value carrier; later replacement should use more specific trait records that combine the observation relation with range context, measured quantity, chemical, value bounds, or other entity.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-17T15:30:00-07:00",
        "curator": "claude",
        "action": "DEPRECATION_CONFIRMED_AS_OUT_OF_SCOPE",
        "changes": "DEPRECATED status confirmed as final after the predicate+class composition\npivot (#54/#55/#56). This record's observation-shape modelling is out of\nscope for TraitMech; the trait vocabulary + mechanism need is met by the un-\ndeprecated METPO predicates, and per-organism numeric observations belong\ndownstream (KG-Microbe / BacDive). See\ndocs/DEPRECATED_REPLACEMENT_PROPOSAL.md, section 'Observation-value records\nstay deprecated', for the rationale.\n",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1001014",
    "label": "pH delta observation",
    "trait_category": "OBSERVATION",
    "term_kind": "CLASS",
    "mapping_status": "DEPRECATED",
    "parent_traits": [
      "METPO:1001000"
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.928133+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic observation/value carrier; later replacement should use more specific trait records that combine the observation relation with growth context, measured quantity, chemical, value range, or other entity.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-17T15:30:00-07:00",
        "curator": "claude",
        "action": "DEPRECATION_CONFIRMED_AS_OUT_OF_SCOPE",
        "changes": "DEPRECATED status confirmed as final after the predicate+class composition\npivot (#54/#55/#56). This record's observation-shape modelling is out of\nscope for TraitMech; the trait vocabulary + mechanism need is met by the un-\ndeprecated METPO predicates, and per-organism numeric observations belong\ndownstream (KG-Microbe / BacDive). See\ndocs/DEPRECATED_REPLACEMENT_PROPOSAL.md, section 'Observation-value records\nstay deprecated', for the rationale.\n",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1001023",
    "label": "pH observation",
    "trait_category": "OBSERVATION",
    "term_kind": "CLASS",
    "mapping_status": "DEPRECATED",
    "parent_traits": [
      "METPO:1001000"
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.931567+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic observation/value carrier; later replacement should use more specific trait records that combine the observation relation with growth context, measured quantity, chemical, value range, or other entity.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-17T15:30:00-07:00",
        "curator": "claude",
        "action": "DEPRECATION_CONFIRMED_AS_OUT_OF_SCOPE",
        "changes": "DEPRECATED status confirmed as final after the predicate+class composition\npivot (#54/#55/#56). This record's observation-shape modelling is out of\nscope for TraitMech; the trait vocabulary + mechanism need is met by the un-\ndeprecated METPO predicates, and per-organism numeric observations belong\ndownstream (KG-Microbe / BacDive). See\ndocs/DEPRECATED_REPLACEMENT_PROPOSAL.md, section 'Observation-value records\nstay deprecated', for the rationale.\n",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1001015",
    "label": "pH range observation",
    "trait_category": "OBSERVATION",
    "term_kind": "CLASS",
    "mapping_status": "DEPRECATED",
    "parent_traits": [
      "METPO:1001000"
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.928505+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic observation/value carrier; later replacement should use more specific trait records that combine the observation relation with range context, measured quantity, chemical, value bounds, or other entity.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-17T15:30:00-07:00",
        "curator": "claude",
        "action": "DEPRECATION_CONFIRMED_AS_OUT_OF_SCOPE",
        "changes": "DEPRECATED status confirmed as final after the predicate+class composition\npivot (#54/#55/#56). This record's observation-shape modelling is out of\nscope for TraitMech; the trait vocabulary + mechanism need is met by the un-\ndeprecated METPO predicates, and per-organism numeric observations belong\ndownstream (KG-Microbe / BacDive). See\ndocs/DEPRECATED_REPLACEMENT_PROPOSAL.md, section 'Observation-value records\nstay deprecated', for the rationale.\n",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1001004",
    "label": "temperature delta observation",
    "trait_category": "OBSERVATION",
    "term_kind": "CLASS",
    "mapping_status": "DEPRECATED",
    "parent_traits": [
      "METPO:1001000"
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.925128+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic observation/value carrier; later replacement should use more specific trait records that combine the observation relation with range context, measured quantity, chemical, value bounds, or other entity.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-17T15:30:00-07:00",
        "curator": "claude",
        "action": "DEPRECATION_CONFIRMED_AS_OUT_OF_SCOPE",
        "changes": "DEPRECATED status confirmed as final after the predicate+class composition\npivot (#54/#55/#56). This record's observation-shape modelling is out of\nscope for TraitMech; the trait vocabulary + mechanism need is met by the un-\ndeprecated METPO predicates, and per-organism numeric observations belong\ndownstream (KG-Microbe / BacDive). See\ndocs/DEPRECATED_REPLACEMENT_PROPOSAL.md, section 'Observation-value records\nstay deprecated', for the rationale.\n",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1001021",
    "label": "temperature observation",
    "trait_category": "OBSERVATION",
    "term_kind": "CLASS",
    "mapping_status": "DEPRECATED",
    "parent_traits": [
      "METPO:1001000"
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.930806+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic observation/value carrier; later replacement should use more specific trait records that combine the observation relation with growth context, measured quantity, chemical, value range, or other entity.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-17T15:30:00-07:00",
        "curator": "claude",
        "action": "DEPRECATION_CONFIRMED_AS_OUT_OF_SCOPE",
        "changes": "DEPRECATED status confirmed as final after the predicate+class composition\npivot (#54/#55/#56). This record's observation-shape modelling is out of\nscope for TraitMech; the trait vocabulary + mechanism need is met by the un-\ndeprecated METPO predicates, and per-organism numeric observations belong\ndownstream (KG-Microbe / BacDive). See\ndocs/DEPRECATED_REPLACEMENT_PROPOSAL.md, section 'Observation-value records\nstay deprecated', for the rationale.\n",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1001003",
    "label": "temperature range observation",
    "trait_category": "OBSERVATION",
    "term_kind": "CLASS",
    "mapping_status": "DEPRECATED",
    "parent_traits": [
      "METPO:1001000"
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.924693+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-10T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic observation/value carrier; later replacement should use more specific trait records that combine the observation relation with range context, measured quantity, chemical, value bounds, or other entity.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-17T15:30:00-07:00",
        "curator": "claude",
        "action": "DEPRECATION_CONFIRMED_AS_OUT_OF_SCOPE",
        "changes": "DEPRECATED status confirmed as final after the predicate+class composition\npivot (#54/#55/#56). This record's observation-shape modelling is out of\nscope for TraitMech; the trait vocabulary + mechanism need is met by the un-\ndeprecated METPO predicates, and per-organism numeric observations belong\ndownstream (KG-Microbe / BacDive). See\ndocs/DEPRECATED_REPLACEMENT_PROPOSAL.md, section 'Observation-value records\nstay deprecated', for the rationale.\n",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1007084",
    "label": "catalase negative",
    "definition": "Test-outcome phenotype where the catalase test yields a negative result (no bubbling on H2O2). The underlying enzyme-organism relation should additionally be asserted via <organism> METPO:2000303 'does not show activity of' GO:0004096 'catalase activity'.",
    "trait_category": "OTHER",
    "term_kind": "CLASS",
    "mapping_status": "SEEDED",
    "parent_traits": [
      "METPO:1007080"
    ],
    "synonyms": [
      {
        "synonym_text": "catalase -",
        "synonym_type": "EXACT_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "catalase test negative",
        "synonym_type": "EXACT_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "created_by": "Marcin Joachimiak",
    "curation_history": [
      {
        "timestamp": "2026-09-11T10:12:15Z",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)"
      },
      {
        "timestamp": "2026-09-11T10:12:30Z",
        "curator": "codex",
        "action": "ENRICHED_FROM_LITERATURE",
        "changes": "Enriched the seeded METPO catalase negative test-outcome phenotype with DOI-backed assay and Enterococcus faecium evidence after a repository-wide duplicate review covering ignored and hidden files.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-11T14:03:00Z",
        "curator": "codex",
        "action": "RESOLVED_PARENT_GAP",
        "changes": "Reparented catalase negative below the newly curated METPO:1007080 catalase test assay parent and marked the temporary assay-parent discussion resolved.",
        "llm_assisted": true
      }
    ],
    "definition_source": "DOI:10.1038/srep03081",
    "evidence": [
      {
        "reference": "DOI:10.1038/srep03081",
        "snippet": "The enzyme-generated oxygen bubbles trapped by Triton X-100 were visualized as foam",
        "notes": "Iwase et al. tie the catalase assay signal to oxygen bubbles from hydrogen-peroxide decomposition, supporting no visible bubbling as a negative test outcome."
      },
      {
        "reference": "DOI:10.1128/iai.72.8.4512-4520.2004",
        "snippet": "E. faecium is catalase negative, and the major mechanism to scavenge hydrogen peroxide is NADH peroxidase",
        "notes": "Moy et al. identify E. faecium as catalase-negative and contrast its NADH-peroxidase scavenging with catalase-bearing E. faecalis under heme-supplemented conditions."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1352",
        "taxon_label": "Enterococcus faecium",
        "note": "Moy et al. describe E. faecium as catalase-negative in the context of hydrogen-peroxide accumulation and scavenging.",
        "reference": "DOI:10.1128/iai.72.8.4512-4520.2004"
      }
    ],
    "discussions": [
      {
        "discussion_id": "catalase-negative-assay-parent-gap",
        "prompt": "Resolve a non-assay parent for negative catalase-test phenotypes before narrowing parent_traits below phenotype.",
        "kind": "CURATION_TODO",
        "status": "RESOLVED",
        "rationale": "METPO:1007080 is now represented as the seeded catalase-test assay parent, so this negative assay-outcome phenotype can use its source superclass rather than a temporary direct phenotype parent.",
        "posed_by": "codex",
        "posed_date": "2026-09-11"
      }
    ]
  },
  {
    "identifier": "METPO:1007080",
    "label": "catalase test",
    "definition": "A biochemical test that detects catalase enzyme activity by exposing cells to hydrogen peroxide and observing for visible bubbling. The test outcome (positive or negative) is captured by its child classes; this class itself does not assert that the organism has catalase activity.",
    "trait_category": "OTHER",
    "term_kind": "CLASS",
    "mapping_status": "SEEDED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "synonyms": [
      {
        "synonym_text": "catalase activity test",
        "synonym_type": "EXACT_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "catalase assay",
        "synonym_type": "EXACT_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "created_by": "Marcin Joachimiak",
    "curation_history": [
      {
        "timestamp": "2026-09-11T14:00:10Z",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)"
      },
      {
        "timestamp": "2026-09-11T14:03:00Z",
        "curator": "codex",
        "action": "ENRICHED_FROM_LITERATURE",
        "changes": "Enriched the seeded METPO catalase test with OMP definition provenance plus stable-URL and DOI-backed assay evidence after a repository-wide duplicate review covering ignored and hidden files.",
        "llm_assisted": true
      }
    ],
    "definition_source": "http://purl.obolibrary.org/obo/OMP_0000218",
    "evidence": [
      {
        "reference": "https://asm.org/protocols/catalase-test-protocol",
        "snippet": "The catalase test facilitates the detection of this enzyme in bacteria",
        "notes": "The American Society for Microbiology catalase-test protocol describes the bacterial assay context for detecting catalase."
      },
      {
        "reference": "DOI:10.1038/srep03081",
        "snippet": "The enzyme-generated oxygen bubbles trapped by Triton X-100 were visualized as foam",
        "notes": "Iwase et al. support the visible oxygen-bubble readout produced by catalase-mediated hydrogen-peroxide decomposition."
      }
    ]
  },
  {
    "identifier": "METPO:1007064",
    "label": "circular colony",
    "definition": "A colony shape that has a regular round outline.",
    "trait_category": "OTHER",
    "term_kind": "CLASS",
    "mapping_status": "SEEDED",
    "parent_traits": [
      "METPO:1007063"
    ],
    "synonyms": [
      {
        "synonym_text": "round colony",
        "synonym_type": "EXACT_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "created_by": "Marcin Joachimiak",
    "curation_history": [
      {
        "timestamp": "2026-09-11T11:51:15Z",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)"
      },
      {
        "timestamp": "2026-09-11T11:52:08Z",
        "curator": "codex",
        "action": "ENRICHED_FROM_LITERATURE",
        "changes": "Enriched the seeded METPO circular colony phenotype with stable ASM protocol evidence after a repository-wide duplicate review covering ignored and hidden files.",
        "llm_assisted": true
      }
    ],
    "definition_source": "https://asm.org/asm/media/protocol-images/colony-morphology-protocol.pdf",
    "evidence": [
      {
        "reference": "https://asm.org/asm/media/protocol-images/colony-morphology-protocol.pdf",
        "snippet": "Describe the form, elevation, and margin as indicated in Fig. 1. Also indicate whether the colonies are smooth (shiny glistening surface), rough (dull, bumpy, granular, or matte surface), or mucoid (slimy or gummy appearance).",
        "notes": "Breakwell et al. describe colony form as an observed macroscopic feature separate from elevation and margin; circular colony specializes that form axis."
      },
      {
        "reference": "https://asm.org/asm/media/protocol-images/colony-morphology-protocol.pdf",
        "snippet": "Colonies are smooth and are circular in form with an entire margin.",
        "notes": "The ASM example records circular form separately from entire margin and convex elevation, supporting circular as a colony outline state rather than a margin or elevation descriptor."
      }
    ]
  },
  {
    "identifier": "METPO:1007091",
    "label": "coagulase negative",
    "definition": "Test-outcome phenotype where the coagulase test yields a negative result. The underlying enzyme-organism relation should additionally be asserted via <organism> METPO:2000303 'does not show activity of' <coagulase enzyme term> once a sufficiently specific enzyme term is selected.",
    "trait_category": "OTHER",
    "term_kind": "CLASS",
    "mapping_status": "SEEDED",
    "parent_traits": [
      "METPO:1007089"
    ],
    "synonyms": [
      {
        "synonym_text": "coagulase -",
        "synonym_type": "EXACT_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "coagulase test negative",
        "synonym_type": "EXACT_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "created_by": "Marcin Joachimiak",
    "curation_history": [
      {
        "timestamp": "2026-09-11T09:54:43Z",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)"
      },
      {
        "timestamp": "2026-09-11T09:59:00Z",
        "curator": "codex",
        "action": "ENRICHED_FROM_LITERATURE",
        "changes": "Enriched the seeded METPO coagulase negative test-outcome phenotype with DOI- and NCBI-backed evidence after a repository-wide duplicate review covering ignored and hidden files.",
        "llm_assisted": true
      }
    ],
    "definition_source": "DOI:10.3390/microorganisms9040830",
    "evidence": [
      {
        "reference": "DOI:10.3390/microorganisms9040830",
        "snippet": "Coagulase-negative staphylococci (CoNS) form a large group of Gram-positive cocci united by their mutual lack of the virulence factor coagulase",
        "notes": "Michels et al. define coagulase-negative staphylococci by absence of the coagulase virulence factor, supporting the negative assay-outcome phenotype."
      },
      {
        "reference": "https://www.ncbi.nlm.nih.gov/books/NBK563240/",
        "snippet": "Staphylococcus epidermidis is a coagulase-negative, gram-positive cocci bacteria that form clusters",
        "notes": "Lee and Anjum identify S. epidermidis as coagulase-negative, providing a stable species-level example of a negative coagulase test outcome."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1282",
        "taxon_label": "Staphylococcus epidermidis",
        "note": "Lee and Anjum describe S. epidermidis as a coagulase-negative Staphylococcus species.",
        "reference": "https://www.ncbi.nlm.nih.gov/books/NBK563240/"
      }
    ]
  },
  {
    "identifier": "METPO:1007090",
    "label": "coagulase positive",
    "definition": "Test-outcome phenotype where the coagulase test yields a positive result (plasma clotting). The underlying enzyme-organism relation should additionally be asserted via <organism> METPO:2000302 'shows activity of' <coagulase enzyme term> once a sufficiently specific enzyme term is selected (no GO/EC term currently exists at the bacteriological coagulase test granularity).",
    "trait_category": "OTHER",
    "term_kind": "CLASS",
    "mapping_status": "SEEDED",
    "parent_traits": [
      "METPO:1007089"
    ],
    "synonyms": [
      {
        "synonym_text": "coagulase +",
        "synonym_type": "EXACT_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "coagulase test positive",
        "synonym_type": "EXACT_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "created_by": "Marcin Joachimiak",
    "curation_history": [
      {
        "timestamp": "2026-09-11T09:35:28Z",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)"
      },
      {
        "timestamp": "2026-09-11T09:37:00Z",
        "curator": "codex",
        "action": "ENRICHED_FROM_LITERATURE",
        "changes": "Enriched the seeded METPO coagulase positive test-outcome phenotype with DOI-backed plasma-clotting evidence after a repository-wide duplicate review covering ignored and hidden files.",
        "llm_assisted": true
      }
    ],
    "definition_source": "DOI:10.1099/mic.0.000019",
    "evidence": [
      {
        "reference": "DOI:10.1099/mic.0.000019",
        "snippet": "coagulase-positive S. aureus bacteria promoted clotting of plasma which was not seen when a coagulase-deficient mutant strain was used",
        "notes": "Loof et al. show that coagulase-positive S. aureus clots plasma in a way lost from a coagulase-deficient mutant, directly supporting the positive test-outcome phenotype."
      },
      {
        "reference": "DOI:10.1371/journal.ppat.1001036",
        "snippet": "Clinical isolates of the human pathogen Staphylococcus aureus secrete coagulase (Coa), a polypeptide that binds to and activates prothrombin",
        "notes": "Cheng et al. connect S. aureus Coa secretion to prothrombin activation, the clotting activity detected by the coagulase test."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1280",
        "taxon_label": "Staphylococcus aureus",
        "note": "Loof et al. use coagulase-positive S. aureus as a direct plasma-clotting example and contrast it with a coagulase-deficient mutant.",
        "reference": "DOI:10.1099/mic.0.000019"
      }
    ]
  },
  {
    "identifier": "METPO:1007062",
    "label": "colony morphology",
    "definition": "A phenotype characterized by macroscopic colony characteristics such as shape, margin, elevation, surface, colour, and size.",
    "trait_category": "OTHER",
    "term_kind": "CLASS",
    "mapping_status": "SEEDED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "created_by": "Marcin Joachimiak",
    "curation_history": [
      {
        "timestamp": "2026-09-11T11:12:54Z",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)"
      },
      {
        "timestamp": "2026-09-11T11:15:17Z",
        "curator": "codex",
        "action": "ENRICHED_FROM_LITERATURE",
        "changes": "Enriched the seeded METPO colony morphology phenotype with stable ASM protocol evidence after a repository-wide duplicate review covering ignored and hidden files.",
        "llm_assisted": true
      }
    ],
    "definition_source": "https://asm.org/asm/media/protocol-images/colony-morphology-protocol.pdf",
    "evidence": [
      {
        "reference": "https://asm.org/asm/media/protocol-images/colony-morphology-protocol.pdf",
        "snippet": "If well separated from other colonies, a colony will have a characteristic shape (both in elevation and margin), size, color, and consistency.",
        "notes": "Breakwell et al. describe shape, elevation, margin, size, color, and consistency as characteristic macroscopic features of a well-separated colony on solid medium."
      },
      {
        "reference": "https://asm.org/asm/media/protocol-images/colony-morphology-protocol.pdf",
        "snippet": "Describe the form, elevation, and margin as indicated in Fig. 1. Also indicate whether the colonies are smooth (shiny glistening surface), rough (dull, bumpy, granular, or matte surface), or mucoid (slimy or gummy appearance).",
        "notes": "The peer-reviewed ASM protocol explicitly treats colony form, elevation, margin, and surface texture as morphology descriptors."
      }
    ]
  },
  {
    "identifier": "METPO:1007063",
    "label": "colony shape",
    "definition": "A colony morphology characterized by the overall macroscopic colony outline as observed on solid medium.",
    "trait_category": "OTHER",
    "term_kind": "CLASS",
    "mapping_status": "SEEDED",
    "parent_traits": [
      "METPO:1007062"
    ],
    "created_by": "Marcin Joachimiak",
    "curation_history": [
      {
        "timestamp": "2026-09-11T11:34:31Z",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)"
      },
      {
        "timestamp": "2026-09-11T11:35:01Z",
        "curator": "codex",
        "action": "ENRICHED_FROM_LITERATURE",
        "changes": "Enriched the seeded METPO colony shape phenotype with stable ASM protocol evidence after a repository-wide duplicate review covering ignored and hidden files.",
        "llm_assisted": true
      }
    ],
    "definition_source": "https://asm.org/asm/media/protocol-images/colony-morphology-protocol.pdf",
    "evidence": [
      {
        "reference": "https://asm.org/asm/media/protocol-images/colony-morphology-protocol.pdf",
        "snippet": "Describe the form, elevation, and margin as indicated in Fig. 1. Also indicate whether the colonies are smooth (shiny glistening surface), rough (dull, bumpy, granular, or matte surface), or mucoid (slimy or gummy appearance).",
        "notes": "Breakwell et al. describe colony form as one of the primary macroscopic morphology descriptors recorded for well-separated colonies on solid medium."
      },
      {
        "reference": "https://asm.org/asm/media/protocol-images/colony-morphology-protocol.pdf",
        "snippet": "FIG. 1. Diagram illustrating the various forms, elevations, and margins of bacterial colonies (3).",
        "notes": "The ASM protocol separates colony forms from elevations and margins, supporting this record as the colony-outline component of colony morphology."
      }
    ]
  },
  {
    "identifier": "METPO:1007093",
    "label": "epibiont phenotype",
    "definition": "A phenotype characterized by a microbe that lives on the external surface of a host organism or substrate, as distinct from endosymbionts (which live inside the host); captures host-association mode, not specific host taxonomy.",
    "trait_category": "OTHER",
    "term_kind": "CLASS",
    "mapping_status": "SEEDED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "synonyms": [
      {
        "synonym_text": "ectosymbiont",
        "synonym_type": "EXACT_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "epibiont",
        "synonym_type": "EXACT_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "created_by": "Marcin Joachimiak",
    "curation_history": [
      {
        "timestamp": "2026-09-11T09:17:09Z",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)"
      },
      {
        "timestamp": "2026-09-11T09:20:00Z",
        "curator": "codex",
        "action": "ENRICHED_FROM_LITERATURE",
        "changes": "Enriched the seeded METPO epibiont phenotype with DOI- and stable-URL-backed Epibacterium ulvae surface-association evidence after a repository-wide duplicate review covering ignored and hidden files.",
        "llm_assisted": true
      }
    ],
    "definition_source": "DOI:10.1099/ijs.0.042838-0",
    "evidence": [
      {
        "reference": "DOI:10.1099/ijs.0.042838-0",
        "snippet": "were isolated from the marine alga Ulva australis",
        "notes": "Penesyan et al. describe Epibacterium ulvae strains U95 and U82 as bacteria associated with the marine green alga Ulva australis."
      },
      {
        "reference": "https://bacdive.dsmz.de/strain/24523",
        "snippet": "isolated from surface of the marine green alga Ulva australis",
        "notes": "BacDive records the E. ulvae type strain U95 as isolated from the external surface of the marine green alga Ulva australis."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1156985",
        "taxon_label": "Epibacterium ulvae",
        "note": "Species represented by type strain U95 (= DSM 24752 = LMG 26464), which was isolated from the surface of the marine green alga Ulva australis.",
        "reference": "https://bacdive.dsmz.de/strain/24523"
      }
    ]
  },
  {
    "identifier": "METPO:1007066",
    "label": "filamentous colony",
    "definition": "A colony shape that has a thread-like or filamentous outline.",
    "trait_category": "OTHER",
    "term_kind": "CLASS",
    "mapping_status": "SEEDED",
    "parent_traits": [
      "METPO:1007063"
    ],
    "created_by": "Marcin Joachimiak",
    "curation_history": [
      {
        "timestamp": "2026-09-11T12:30:55Z",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)"
      },
      {
        "timestamp": "2026-09-11T12:32:13Z",
        "curator": "codex",
        "action": "ENRICHED_FROM_LITERATURE",
        "changes": "Enriched the seeded METPO filamentous colony phenotype with stable OMP definition provenance and DOI-backed evidence after a repository-wide duplicate review covering ignored and hidden files.",
        "llm_assisted": true
      }
    ],
    "definition_source": "http://purl.obolibrary.org/obo/OMP_0000088",
    "evidence": [
      {
        "reference": "DOI:10.7759/cureus.374",
        "snippet": "Colony morphology is one among the various characters of bacteria, which is also unique to a particular genus of bacteria that could be instrumental in preliminary identification. Size (measured in millimetres - pinpoint (\u2264 1 mm), small (2-3 mm), medium (4-5 mm), and large (> 5 mm) colonies), shape (circular, irregular, rhomboid, umbonate, umbonate, filamentous, or rhizoid)",
        "notes": "Kandi lists filamentous as a bacterial colony shape value distinct from circular, irregular, and rhizoid forms."
      }
    ]
  },
  {
    "identifier": "METPO:1007069",
    "label": "fried-egg-shaped colony",
    "definition": "A colony shape that has a raised opaque centre and a translucent peripheral zone, resembling a fried egg.",
    "trait_category": "OTHER",
    "term_kind": "CLASS",
    "mapping_status": "SEEDED",
    "parent_traits": [
      "METPO:1007063"
    ],
    "synonyms": [
      {
        "synonym_text": "fried-egg colony",
        "synonym_type": "EXACT_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "created_by": "Marcin Joachimiak",
    "curation_history": [
      {
        "timestamp": "2026-09-11T13:40:39Z",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)"
      },
      {
        "timestamp": "2026-09-11T13:41:36Z",
        "curator": "codex",
        "action": "ENRICHED_FROM_LITERATURE",
        "changes": "Enriched the seeded METPO fried-egg-shaped colony phenotype with stable MICRO definition provenance and DOI-backed opaque-center, translucent-periphery evidence after a repository-wide duplicate review covering ignored and hidden files.",
        "llm_assisted": true
      }
    ],
    "definition_source": "http://purl.obolibrary.org/obo/MICRO_0000349",
    "evidence": [
      {
        "reference": "DOI:10.1371/journal.pone.0068373",
        "snippet": "TR colonies showed the typical \u201cfried egg\u201d appearance, with a small opaque center surrounded by a large translucent peripheral area.",
        "notes": "Bertin et al. describe the opaque-center, translucent-periphery colony appearance that underlies the MICRO-derived fried-egg colony definition."
      }
    ]
  },
  {
    "identifier": "METPO:1005040",
    "label": "generalist",
    "definition": "A phenotype describing an organism with a broad ecological niche, capable of thriving across diverse environments or utilizing varied resources.",
    "trait_category": "OTHER",
    "term_kind": "CLASS",
    "mapping_status": "SEEDED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-12T22:29:50Z",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)"
      },
      {
        "timestamp": "2026-09-12T22:35:00Z",
        "curator": "codex",
        "action": "ENRICHED_FROM_LITERATURE",
        "changes": "Enriched the seeded METPO generalist phenotype with DOI-backed bacterial and prokaryotic niche-breadth evidence after a repository-wide duplicate review covering ignored and hidden files.",
        "llm_assisted": true
      }
    ],
    "definition_source": "DOI:10.1093/femsec/fiaa240",
    "evidence": [
      {
        "reference": "DOI:10.1093/femsec/fiaa240",
        "snippet": "Organisms are often categorized as generalists or specialists, corresponding to broad or narrow niche requirements",
        "notes": "Bell and Bell frame bacterial generalism by broad niche requirements across environmental axes such as temperature tolerance and resource use."
      },
      {
        "reference": "DOI:10.1038/s41559-023-02027-7",
        "snippet": "Generalists can survive in many environments, whereas specialists are restricted to a single environment.",
        "notes": "The social-niche-breadth study defines generalists and specialists while introducing a niche-breadth score for prokaryotic genomes across environments."
      }
    ]
  },
  {
    "identifier": "METPO:1005025",
    "label": "hemolysis",
    "definition": "A phenotype describing the ability of an organism to lyse red blood cells.",
    "trait_category": "OTHER",
    "term_kind": "CLASS",
    "mapping_status": "SEEDED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "synonyms": [
      {
        "synonym_text": "presence of hemolysis",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-11T05:43:36Z",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)"
      },
      {
        "timestamp": "2026-09-11T06:00:00Z",
        "curator": "codex",
        "action": "ENRICHED_FROM_LITERATURE",
        "changes": "Enriched the active METPO hemolysis class with DOI-backed Staphylococcus aureus hemolysis evidence after a repository-wide duplicate review covering ignored and hidden files.",
        "llm_assisted": true
      }
    ],
    "definition_source": "DOI:10.3390/toxins5061140",
    "evidence": [
      {
        "reference": "DOI:10.3390/toxins5061140",
        "snippet": "hemolysis to toxigenic substances secreted by S. aureus",
        "notes": "Berube and Bubeck Wardenburg review historical evidence that S. aureus secretes hemolytic toxins."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1280",
        "taxon_label": "Staphylococcus aureus",
        "note": "Historical S. aureus culture supernatants caused hemolysis in rabbit assays of staphylococcal toxins.",
        "reference": "DOI:10.3390/toxins5061140"
      }
    ]
  },
  {
    "identifier": "METPO:1005026",
    "label": "hemolytic",
    "definition": "A phenotype in which an organism is capable of lysing red blood cells.",
    "trait_category": "OTHER",
    "term_kind": "CLASS",
    "mapping_status": "SEEDED",
    "parent_traits": [
      "METPO:1005025"
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-11T09:01:06Z",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)"
      },
      {
        "timestamp": "2026-09-11T09:02:00Z",
        "curator": "codex",
        "action": "ENRICHED_FROM_LITERATURE",
        "changes": "Enriched the active METPO hemolytic child class with DOI-backed Staphylococcus aureus hemolysis evidence after a repository-wide duplicate review covering ignored and hidden files.",
        "llm_assisted": true
      }
    ],
    "definition_source": "DOI:10.3390/toxins5061140",
    "evidence": [
      {
        "reference": "DOI:10.3390/toxins5061140",
        "snippet": "hemolysis to toxigenic substances secreted by S. aureus",
        "notes": "Berube and Bubeck Wardenburg review historical evidence that S. aureus secretes hemolytic toxins, supporting a hemolytic phenotype."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1280",
        "taxon_label": "Staphylococcus aureus",
        "note": "Canonical hemolytic bacterium whose culture supernatants have long been assayed for rabbit red-blood-cell lysis.",
        "reference": "DOI:10.3390/toxins5061140"
      }
    ]
  },
  {
    "identifier": "METPO:1005010",
    "label": "indole test",
    "definition": "An assay that tests the ability of an organism to produce indole from tryptophan.",
    "trait_category": "OTHER",
    "term_kind": "CLASS",
    "mapping_status": "SEEDED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-12T21:35:36Z",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)"
      },
      {
        "timestamp": "2026-09-12T21:38:12Z",
        "curator": "codex",
        "action": "ENRICHED_FROM_LITERATURE",
        "changes": "Added the METPO indole-test assay parent with stable-URL tryptophan-to-indole assay evidence after a repository-wide duplicate review covering ignored and hidden files.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-12T21:50:37Z",
        "curator": "codex",
        "action": "CURATION_REVIEW_REVISION",
        "changes": "Preserved the ASM source-local tryptophan citation marker after Claude Code Review issue #874 so the second evidence snippet is visibly a complete sentence.",
        "llm_assisted": true
      }
    ],
    "definition_source": "https://asm.org/protocols/indole-test-protocol",
    "evidence": [
      {
        "reference": "https://asm.org/protocols/indole-test-protocol",
        "snippet": "The indole test screens for the ability of an organism to degrade the amino acid tryptophan and produce indole.",
        "notes": "The ASM protocol defines the indole test as an assay for organism-level tryptophan degradation to indole."
      },
      {
        "reference": "https://asm.org/protocols/indole-test-protocol",
        "snippet": "The chief requirement for culturing an organism prior to performing the indole test is that the medium contains a sufficient quantity of tryptophan (5).",
        "notes": "The protocol explains that the indole-test medium needs tryptophan so production of indole can report tryptophan degradation."
      }
    ]
  },
  {
    "identifier": "METPO:1005012",
    "label": "indole test negative",
    "definition": "A phenotype in which an organism tests negative in the indole test, indicating it does not produce indole from tryptophan.",
    "trait_category": "OTHER",
    "term_kind": "CLASS",
    "mapping_status": "SEEDED",
    "parent_traits": [
      "METPO:1005010"
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-12T17:38:53Z",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)"
      },
      {
        "timestamp": "2026-09-12T17:40:50Z",
        "curator": "codex",
        "action": "ENRICHED_FROM_LITERATURE",
        "changes": "Added the METPO indole-test-negative phenotype with DOI-backed indole-test evidence after a repository-wide duplicate review covering ignored and hidden files.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-12T17:52:10Z",
        "curator": "codex",
        "action": "CURATION_REVIEW_REVISION",
        "changes": "Tightened Alves Klebsiella wording after local review issue #855 to avoid implying Klebsiella pneumoniae is the only indole-negative Klebsiella or Raoultella species.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-12T18:01:45Z",
        "curator": "codex",
        "action": "CURATION_REVIEW_REVISION",
        "changes": "Removed unquoted Klebsiella variicola wording after external review issue #856 while preserving the indole-negative Klebsiella pneumoniae interpretation.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-12T18:09:40Z",
        "curator": "codex",
        "action": "CURATION_REVIEW_REVISION",
        "changes": "Trimmed unsupported Darkoh indole-assay wording after external review issue #857.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-12T18:19:06Z",
        "curator": "codex",
        "action": "CURATION_REVIEW_REVISION",
        "changes": "Replaced a truncated Alves Klebsiella quote after external review issue #858.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-12T21:38:12Z",
        "curator": "codex",
        "action": "RESOLVED_PARENT_GAP",
        "changes": "Reparented indole test negative below the newly curated METPO:1005010 indole test assay parent and marked the temporary assay-parent discussion resolved.",
        "llm_assisted": true
      }
    ],
    "definition_source": "DOI:10.1128/AEM.02787-15",
    "evidence": [
      {
        "reference": "DOI:10.1128/AEM.02787-15",
        "snippet": "Indole, a bacterial product of tryptophan degradation",
        "notes": "Darkoh et al. support indole as a microbial tryptophan-degradation product."
      },
      {
        "reference": "DOI:10.1128/JCM.00940-06",
        "snippet": "However, K. variicola, R. planticola, and R. terrigena, in addition to K. pneumoniae, can show a negative-indole reaction",
        "notes": "Alves et al. describe Klebsiella pneumoniae as an indole-negative Klebsiella species in a clinical-isolate biochemical typing context."
      },
      {
        "reference": "DOI:10.1128/JCM.00940-06",
        "snippet": "A total of 102 (84%) of the 122 isolates were negative for indole production",
        "notes": "Alves et al. reported negative indole-production phenotypes among Klebsiella clinical isolates tested biochemically."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:573",
        "taxon_label": "Klebsiella pneumoniae",
        "note": "Alves et al. describe K. pneumoniae as an indole-negative Klebsiella species in a clinical-isolate biochemical typing context.",
        "reference": "DOI:10.1128/JCM.00940-06"
      }
    ],
    "discussions": [
      {
        "discussion_id": "indole-test-negative-assay-parent-gap",
        "prompt": "Resolve a non-assay parent for negative indole-test phenotypes before narrowing parent_traits below phenotype.",
        "kind": "CURATION_TODO",
        "status": "RESOLVED",
        "rationale": "METPO:1005010 is the seeded superclass of METPO:1005012, but METPO:1005010 defines an assay rather than a broader microbial trait class, so this record is temporarily parented directly to METPO:1000059 phenotype.",
        "posed_by": "codex",
        "posed_date": "2026-09-12",
        "resolved_date": "2026-09-12",
        "resolution_note": "METPO:1005010 is now represented as the seeded indole-test assay parent, so this assay-outcome phenotype can use its exact source superclass instead of a temporary direct phenotype parent; this resolves the exact METPO assay-parent gap, not the broader non-assay parent question for assay-outcome phenotypes."
      }
    ]
  },
  {
    "identifier": "METPO:1005011",
    "label": "indole test positive",
    "definition": "A phenotype in which an organism tests positive in the indole test, indicating it produces indole from tryptophan.",
    "trait_category": "OTHER",
    "term_kind": "CLASS",
    "mapping_status": "SEEDED",
    "parent_traits": [
      "METPO:1005010"
    ],
    "synonyms": [
      {
        "synonym_text": "indole test",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-11T06:46:27Z",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)"
      },
      {
        "timestamp": "2026-09-11T07:00:00Z",
        "curator": "codex",
        "action": "ENRICHED_FROM_LITERATURE",
        "changes": "Enriched the active METPO indole-test-positive phenotype with DOI-backed indole production evidence after a repository-wide duplicate review covering ignored and hidden files.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-12T21:38:12Z",
        "curator": "codex",
        "action": "RESOLVED_PARENT_GAP",
        "changes": "Reparented indole test positive below the newly curated METPO:1005010 indole test assay parent and marked the temporary assay-parent discussion resolved.",
        "llm_assisted": true
      }
    ],
    "definition_source": "DOI:10.1128/AEM.02787-15",
    "evidence": [
      {
        "reference": "DOI:10.1128/AEM.02787-15",
        "snippet": "Indole, a bacterial product of tryptophan degradation",
        "notes": "Darkoh et al. support microbial indole production as a tryptophan-degradation phenotype and evaluate indole detection in bacterial cultures."
      },
      {
        "reference": "DOI:10.1128/AEM.02787-15",
        "snippet": "enterotoxigenic Escherichia coli strain H10407 produces 3.3 \u00b1 0.22 mM indole during a 24-h period in the presence of 5 mM tryptophan",
        "notes": "Darkoh et al. measured indole production by the enterotoxigenic E. coli H10407 strain under tryptophan-supplemented culture conditions."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:316401",
        "taxon_label": "Escherichia coli ETEC H10407",
        "note": "Enterotoxigenic E. coli H10407 produced millimolar indole after 24 h of growth with tryptophan supplementation.",
        "reference": "DOI:10.1128/AEM.02787-15"
      }
    ],
    "discussions": [
      {
        "discussion_id": "indole-test-positive-assay-parent-gap",
        "prompt": "Resolve a non-assay parent for positive indole-test phenotypes before narrowing parent_traits below phenotype.",
        "kind": "CURATION_TODO",
        "status": "RESOLVED",
        "rationale": "METPO:1005010 is the seeded superclass of METPO:1005011, but METPO:1005010 defines an assay rather than a broader microbial trait class, so this record is temporarily parented directly to METPO:1000059 phenotype.",
        "posed_by": "codex",
        "posed_date": "2026-09-11",
        "resolved_date": "2026-09-12",
        "resolution_note": "METPO:1005010 is now represented as the seeded indole-test assay parent, so this assay-outcome phenotype can use its exact source superclass instead of a temporary direct phenotype parent; this resolves the exact METPO assay-parent gap, not the broader non-assay parent question for assay-outcome phenotypes."
      }
    ]
  },
  {
    "identifier": "METPO:1007065",
    "label": "irregular colony",
    "definition": "A colony shape that has an irregular (non-round, non-rhizoid) outline.",
    "trait_category": "OTHER",
    "term_kind": "CLASS",
    "mapping_status": "SEEDED",
    "parent_traits": [
      "METPO:1007063"
    ],
    "created_by": "Marcin Joachimiak",
    "curation_history": [
      {
        "timestamp": "2026-09-11T12:09:19Z",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)"
      },
      {
        "timestamp": "2026-09-11T12:11:52Z",
        "curator": "codex",
        "action": "ENRICHED_FROM_LITERATURE",
        "changes": "Enriched the seeded METPO irregular colony phenotype with DOI-backed evidence after a repository-wide duplicate review covering ignored and hidden files.",
        "llm_assisted": true
      }
    ],
    "definition_source": "DOI:10.7759/cureus.374",
    "evidence": [
      {
        "reference": "DOI:10.7759/cureus.374",
        "snippet": "Colony morphology is one among the various characters of bacteria, which is also unique to a particular genus of bacteria that could be instrumental in preliminary identification. Size (measured in millimetres - pinpoint (\u2264 1 mm), small (2-3 mm), medium (4-5 mm), and large (> 5 mm) colonies), shape (circular, irregular, rhomboid, umbonate, umbonate, filamentous, or rhizoid)",
        "notes": "Kandi lists irregular as a bacterial colony shape value distinct from circular, filamentous, and rhizoid forms."
      }
    ]
  },
  {
    "identifier": "METPO:1005013",
    "label": "methyl red test",
    "definition": "An assay that tests the ability of an organism to produce and maintain stable acid end products from glucose fermentation.",
    "trait_category": "OTHER",
    "term_kind": "CLASS",
    "mapping_status": "SEEDED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-12T20:14:22Z",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)"
      },
      {
        "timestamp": "2026-09-12T20:15:55Z",
        "curator": "codex",
        "action": "ENRICHED_FROM_LITERATURE",
        "changes": "Added the METPO methyl-red-test assay parent with stable-URL methyl-red readout evidence after a repository-wide duplicate review covering ignored and hidden files.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-12T20:35:11Z",
        "curator": "codex",
        "action": "CURATION_REVIEW_REVISION",
        "changes": "Added parent-level ASM evidence for high-acid mixed fermentation after PR 866 review issue 867 noted that the parent reused child assay-readout quotes.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-12T21:00:37Z",
        "curator": "codex",
        "action": "CURATION_REVIEW_REVISION",
        "changes": "Expanded the ASM mixed-acid evidence quote through its butanediol contrast and narrowed its note after PR 866 review issue 871.",
        "llm_assisted": true
      }
    ],
    "definition_source": "https://asm.org/getmedia/40946f85-9357-4563-aa8a-994427efa825/Methyl-Red-and-Voges-Proskauer-Test-Protocols.pdf",
    "evidence": [
      {
        "reference": "https://asm.org/getmedia/40946f85-9357-4563-aa8a-994427efa825/Methyl-Red-and-Voges-Proskauer-Test-Protocols.pdf",
        "snippet": "Escherichia coli and other members of the low-ratio organisms described by Clark and Lubs ferment sugars by the mixed acid pathway resulting in a low ratio of CO2 to H2 gas produced by fermentation. The mixed acid pathway gives 4 mol of acidic products (mainly lactic and acetic acid), 1 mol of neutral fermentation product (ethanol), 1 mol of CO2, and 1 mol of H2 per mol of glucose fermented (9). The large quantity of acids produced causes a significant decrease in the pH of the culture medium. In contrast, Enterobacter aerogenes and other members of the high-ratio organisms (those that produce a high ratio of CO2 to H2 from the fermentation of glucose) ferment sugars via the butanediol fermentation pathway, producing only 1 mol of acid per mol of glucose. This pathway results in a lower degree of acidification of the culture medium.",
        "notes": "The ASM protocol contrasts mixed-acid fermentation's 4 mol acidic products per mol glucose with the butanediol pathway's 1 mol acid per mol glucose and lower medium acidification."
      },
      {
        "reference": "https://asm.org/getmedia/40946f85-9357-4563-aa8a-994427efa825/Methyl-Red-and-Voges-Proskauer-Test-Protocols.pdf",
        "snippet": "When the culture medium turns red after addition of methyl red, because of a pH at or below 4.4 from the fermentation of glucose, the culture has a positive result for the MR test (Fig.1A).",
        "notes": "The ASM protocol PDF defines the methyl-red-test positive readout as acidification to pH 4.4 or below after glucose fermentation."
      },
      {
        "reference": "https://asm.org/getmedia/40946f85-9357-4563-aa8a-994427efa825/Methyl-Red-and-Voges-Proskauer-Test-Protocols.pdf",
        "snippet": "A negative MR test is indicated by a yellow color in the culture medium (Fig. 1B), which occurs when less acid is produced (pH is higher) from the fermentation of glucose.",
        "notes": "The same protocol defines the negative readout as a yellow culture reflecting less glucose-derived acid production."
      }
    ]
  },
  {
    "identifier": "METPO:1005015",
    "label": "methyl red test negative",
    "definition": "A phenotype in which an organism tests negative in the methyl red test.",
    "trait_category": "OTHER",
    "term_kind": "CLASS",
    "mapping_status": "SEEDED",
    "parent_traits": [
      "METPO:1005013"
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-12T18:34:21Z",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)"
      },
      {
        "timestamp": "2026-09-12T18:38:59Z",
        "curator": "codex",
        "action": "ENRICHED_FROM_LITERATURE",
        "changes": "Added the METPO methyl-red-test-negative phenotype with stable-URL and DOI-backed methyl-red-test evidence after a repository-wide duplicate review covering ignored and hidden files.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-12T18:57:06Z",
        "curator": "codex",
        "action": "CURATION_REVIEW_REVISION",
        "changes": "Added the Hansen Klebsiella pneumoniae canonical example after local review issue #861 showed Table 2 directly supports a mostly methyl-red-negative Klebsiella pneumoniae result.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-12T20:15:55Z",
        "curator": "codex",
        "action": "RESOLVED_PARENT_GAP",
        "changes": "Reparented methyl red test negative below the newly curated METPO:1005013 methyl red test assay parent and marked the temporary assay-parent discussion resolved.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-12T20:44:24Z",
        "curator": "codex",
        "action": "CURATION_REVIEW_REVISION",
        "changes": "Moved the methyl-red parent-gap closure into resolution_note and resolved_date so the original non-assay parent rationale remains visible.",
        "llm_assisted": true
      }
    ],
    "definition_source": "https://asm.org/getmedia/40946f85-9357-4563-aa8a-994427efa825/Methyl-Red-and-Voges-Proskauer-Test-Protocols.pdf",
    "evidence": [
      {
        "reference": "https://asm.org/getmedia/40946f85-9357-4563-aa8a-994427efa825/Methyl-Red-and-Voges-Proskauer-Test-Protocols.pdf",
        "snippet": "A negative MR test is indicated by a yellow color in the culture medium (Fig. 1B), which occurs when less acid is produced (pH is higher) from the fermentation of glucose.",
        "notes": "The ASM protocol PDF defines the negative methyl-red-test readout as a yellow culture after methyl red is added, reflecting less acidification during glucose fermentation."
      },
      {
        "reference": "DOI:10.1128/JCM.42.8.3665-3669.2004",
        "snippet": "In the ASM Manual of Clinical Microbiology, only 6 of the 18 biochemical tests used in the present investigation are listed for Klebsiella species: indole, MR, VP, LDC, ODC, and malonate",
        "notes": "Hansen et al. evaluated methyl red as a conventional Klebsiella biochemical test; their Table 2 reports K. pneumoniae methyl-red result percentages across CPHL, NRL, and SSI."
      },
      {
        "reference": "DOI:10.1128/JCM.42.8.3665-3669.2004",
        "snippet": "Variable results were of two types: (i) those in which all three laboratories found a mixture of positive and negative results among the representatives of a species for a specific test (e.g., K. pneumoniae and l-sorbose), suggesting a truly variable reaction, and (ii) those in which one center found most strains to be negative while another found most positive (e.g., K. rhinoscleromatis and MR) or vice versa, suggesting that the results were method dependent.",
        "notes": "The same interlaboratory evaluation found that MR could be method dependent for some Klebsiella species/test combinations, so the K. pneumoniae canonical example is recorded from Table 2 results rather than treated as a species-wide invariant."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:573",
        "taxon_label": "Klebsiella pneumoniae",
        "note": "Hansen et al. Table 2 reported mostly methyl-red-negative results for K. pneumoniae across three reference laboratories: 10.7%, 3.6%, and 10.7% MR-positive strains.",
        "reference": "DOI:10.1128/JCM.42.8.3665-3669.2004"
      }
    ],
    "discussions": [
      {
        "discussion_id": "methyl-red-test-negative-assay-parent-gap",
        "prompt": "Resolve a non-assay parent for negative methyl-red-test phenotypes before narrowing parent_traits below phenotype.",
        "kind": "CURATION_TODO",
        "status": "RESOLVED",
        "rationale": "METPO:1005013 is the seeded superclass of METPO:1005015, but METPO:1005013 defines an assay rather than a broader microbial trait class, so this record is temporarily parented directly to METPO:1000059 phenotype.",
        "posed_by": "codex",
        "posed_date": "2026-09-12",
        "resolved_date": "2026-09-12",
        "resolution_note": "METPO:1005013 is now represented as the seeded methyl-red-test assay parent, so this assay-outcome phenotype can use its exact source superclass instead of a temporary direct phenotype parent; this resolves the exact METPO assay-parent gap, not the broader non-assay parent question for assay-outcome phenotypes."
      }
    ]
  },
  {
    "identifier": "METPO:1005014",
    "label": "methyl red test positive",
    "definition": "A phenotype in which an organism tests positive in the methyl red test, indicating mixed acid fermentation.",
    "trait_category": "OTHER",
    "term_kind": "CLASS",
    "mapping_status": "SEEDED",
    "parent_traits": [
      "METPO:1005013"
    ],
    "synonyms": [
      {
        "synonym_text": "methyl red test",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-12T19:14:16Z",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)"
      },
      {
        "timestamp": "2026-09-12T19:16:03Z",
        "curator": "codex",
        "action": "ENRICHED_FROM_LITERATURE",
        "changes": "Added the METPO methyl-red-test-positive phenotype with stable-URL and DOI-backed methyl-red-test evidence after a repository-wide duplicate review covering ignored and hidden files.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-12T19:34:17Z",
        "curator": "codex",
        "action": "CURATION_REVIEW_REVISION",
        "changes": "Resolved PR #862 review issues #863 and #864 by removing a flattened Hansen Table 3 row from evidence snippets and narrowing the Hansen ASM Manual evidence note to match its quote.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-12T20:15:55Z",
        "curator": "codex",
        "action": "RESOLVED_PARENT_GAP",
        "changes": "Reparented methyl red test positive below the newly curated METPO:1005013 methyl red test assay parent and marked the temporary assay-parent discussion resolved.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-12T20:44:24Z",
        "curator": "codex",
        "action": "CURATION_REVIEW_REVISION",
        "changes": "Moved the methyl-red parent-gap closure into resolution_note and resolved_date so the original non-assay parent rationale remains visible.",
        "llm_assisted": true
      }
    ],
    "definition_source": "https://asm.org/getmedia/40946f85-9357-4563-aa8a-994427efa825/Methyl-Red-and-Voges-Proskauer-Test-Protocols.pdf",
    "evidence": [
      {
        "reference": "https://asm.org/getmedia/40946f85-9357-4563-aa8a-994427efa825/Methyl-Red-and-Voges-Proskauer-Test-Protocols.pdf",
        "snippet": "When the culture medium turns red after addition of methyl red, because of a pH at or below 4.4 from the fermentation of glucose, the culture has a positive result for the MR test (Fig.1A).",
        "notes": "The ASM protocol PDF defines a positive methyl-red-test readout as red culture medium after methyl red is added, reflecting glucose fermentation that acidifies the medium to pH 4.4 or lower."
      },
      {
        "reference": "DOI:10.1128/JCM.42.8.3665-3669.2004",
        "snippet": "In the ASM Manual of Clinical Microbiology, only 6 of the 18 biochemical tests used in the present investigation are listed for Klebsiella species: indole, MR, VP, LDC, ODC, and malonate",
        "notes": "Hansen et al. evaluated methyl red as a conventional Klebsiella biochemical test listed in the ASM Manual of Clinical Microbiology."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:54291",
        "taxon_label": "Klebsiella ornithinolytica",
        "note": "Hansen et al. Table 3 reported 100.0% methyl-red-positive results for K. ornithinolytica across the CPHL, NRL, and SSI reference laboratories.",
        "reference": "DOI:10.1128/JCM.42.8.3665-3669.2004"
      }
    ],
    "discussions": [
      {
        "discussion_id": "methyl-red-test-positive-assay-parent-gap",
        "prompt": "Resolve a non-assay parent for positive methyl-red-test phenotypes before narrowing parent_traits below phenotype.",
        "kind": "CURATION_TODO",
        "status": "RESOLVED",
        "rationale": "METPO:1005013 is the seeded superclass of METPO:1005014, but METPO:1005013 defines an assay rather than a broader microbial trait class, so this record is temporarily parented directly to METPO:1000059 phenotype.",
        "posed_by": "codex",
        "posed_date": "2026-09-12",
        "resolved_date": "2026-09-12",
        "resolution_note": "METPO:1005013 is now represented as the seeded methyl-red-test assay parent, so this assay-outcome phenotype can use its exact source superclass instead of a temporary direct phenotype parent; this resolves the exact METPO assay-parent gap, not the broader non-assay parent question for assay-outcome phenotypes."
      }
    ]
  },
  {
    "identifier": "METPO:1005027",
    "label": "non-hemolytic",
    "definition": "A phenotype in which an organism does not lyse red blood cells.",
    "trait_category": "OTHER",
    "term_kind": "CLASS",
    "mapping_status": "SEEDED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-11T10:12:15Z",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)"
      },
      {
        "timestamp": "2026-09-11T10:34:52Z",
        "curator": "codex",
        "action": "ENRICHED_FROM_LITERATURE",
        "changes": "Enriched the seeded METPO non-hemolytic child class with DOI-backed gamma-hemolysis evidence after a repository-wide duplicate review covering ignored and hidden files.",
        "llm_assisted": true
      }
    ],
    "definition_source": "DOI:10.14202/vetworld.2025.3622-3630",
    "evidence": [
      {
        "reference": "DOI:10.14202/vetworld.2025.3622-3630",
        "snippet": "Hemolysis testing revealed \u03b3-hemolysis for all strains, confirming non-hemolytic and non-pathogenic properties.",
        "notes": "Petjul et al. examined hemolytic patterns on Columbia agar supplemented with 5% sheep blood and reported gamma hemolysis for all assayed Bacillus isolates, supporting non-hemolysis as absence of red-blood-cell lysis on blood agar."
      }
    ],
    "discussions": [
      {
        "discussion_id": "non-hemolytic-parent-gap",
        "prompt": "Resolve a neutral parent axis for absence of hemolysis before narrowing parent_traits below phenotype.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "METPO:1005025 is the seeded superclass of METPO:1005027, but METPO:1005025 defines the ability to lyse red blood cells; this absence phenotype is temporarily parented directly to METPO:1000059 phenotype until METPO has a neutral hemolysis axis or another broader parent for hemolysis-test outcomes.",
        "posed_by": "codex",
        "posed_date": "2026-09-11"
      }
    ]
  },
  {
    "identifier": "METPO:1007073",
    "label": "osmotic tolerance",
    "definition": "A phenotype characterized by the ability to grow under high osmotic pressure (non-NaCl).",
    "trait_category": "OTHER",
    "term_kind": "CLASS",
    "mapping_status": "SEEDED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "synonyms": [
      {
        "synonym_text": "osmophile",
        "synonym_type": "EXACT_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "created_by": "Marcin Joachimiak",
    "curation_history": [
      {
        "timestamp": "2026-09-11T10:12:15Z",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)"
      },
      {
        "timestamp": "2026-09-11T10:50:38Z",
        "curator": "codex",
        "action": "ENRICHED_FROM_LITERATURE",
        "changes": "Enriched the seeded METPO osmotic tolerance phenotype with DOI-backed nonionic hyperosmotic stress evidence after a repository-wide duplicate review covering ignored and hidden files.",
        "llm_assisted": true
      }
    ],
    "definition_source": "DOI:10.1128/mBio.00390-21",
    "evidence": [
      {
        "reference": "DOI:10.1128/mBio.00390-21",
        "snippet": "tolerance against hyperosmotic conditions (400\u2009mM sorbitol)",
        "notes": "Ledermann et al. assayed Bradyrhizobium diazoefficiens USDA 110 against 400 mM sorbitol as the hyperosmotic nonionic condition and contrasted it with NaCl, MgCl2, and MgSO4 ionic stresses."
      }
    ]
  },
  {
    "identifier": "METPO:1007086",
    "label": "oxidase negative",
    "definition": "Test-outcome phenotype where the oxidase test yields a negative result. The underlying enzyme-organism relation should additionally be asserted via <organism> METPO:2000303 'does not show activity of' GO:0004129 'cytochrome-c oxidase activity'.",
    "trait_category": "OTHER",
    "term_kind": "CLASS",
    "mapping_status": "SEEDED",
    "parent_traits": [
      "METPO:1007081"
    ],
    "synonyms": [
      {
        "synonym_text": "oxidase -",
        "synonym_type": "EXACT_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "oxidase test negative",
        "synonym_type": "EXACT_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "created_by": "Marcin Joachimiak",
    "curation_history": [
      {
        "timestamp": "2026-09-11T15:15:36Z",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)"
      },
      {
        "timestamp": "2026-09-11T15:16:21Z",
        "curator": "codex",
        "action": "ENRICHED_FROM_LITERATURE",
        "changes": "Enriched the seeded METPO oxidase-negative test outcome with OMP definition provenance plus stable-URL and DOI-backed assay evidence after a repository-wide duplicate review covering ignored and hidden files.",
        "llm_assisted": true
      }
    ],
    "definition_source": "http://purl.obolibrary.org/obo/OMP_0006084",
    "evidence": [
      {
        "reference": "https://asm.org/protocols/oxidase-test-protocol",
        "snippet": "The test can be used to distinguish Neisseria gonorrhoeae (oxidase positive) from Staphylococcus spp. and Streptococcus spp. (oxidase negative)",
        "notes": "The American Society for Microbiology protocol gives oxidase-negative Staphylococcus and Streptococcus spp. as contrasts to an oxidase-positive Neisseria gonorrhoeae result."
      },
      {
        "reference": "DOI:10.5812/chbs-160199",
        "snippet": "A positive result from the dry filter paper method is indicated by the appearance of a dark purple color within 5 to 10 seconds. A 'delayed positive' result is recognized when a color change occurs between 10 and 60 seconds, whereas a negative result is indicated by the paper remaining colorless or changing color after more than 60 seconds",
        "notes": "Hafezi and Khamar review the oxidase-test polarity and interpret a colorless dry filter paper, or a color change only after the cutoff, as a negative result."
      },
      {
        "reference": "DOI:10.5812/chbs-160199",
        "snippet": "Bacteria that are classified as oxidase-negative can be anaerobic, aerobic, or facultative. A negative oxidase result indicates merely the absence of cytochrome c oxidase, which is responsible for oxidizing the reactant, while these organisms may utilize alternative oxidases for electron transfer during respiration",
        "notes": "The review constrains interpretation of the negative assay outcome to cytochrome c oxidase under the oxidase-test readout, rather than absence of every terminal oxidase."
      }
    ]
  },
  {
    "identifier": "METPO:1007081",
    "label": "oxidase test",
    "definition": "A biochemical test that detects cytochrome c oxidase activity using a redox indicator. The test outcome (positive or negative) is captured by its child classes; this class itself does not assert oxidase activity.",
    "trait_category": "OTHER",
    "term_kind": "CLASS",
    "mapping_status": "SEEDED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "synonyms": [
      {
        "synonym_text": "cytochrome oxidase test",
        "synonym_type": "EXACT_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "oxidase activity test",
        "synonym_type": "EXACT_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "created_by": "Marcin Joachimiak",
    "curation_history": [
      {
        "timestamp": "2026-09-11T14:24:19Z",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)"
      },
      {
        "timestamp": "2026-09-11T14:32:00Z",
        "curator": "codex",
        "action": "ENRICHED_FROM_LITERATURE",
        "changes": "Enriched the seeded METPO oxidase test with OMP definition provenance plus stable-URL and DOI-backed assay evidence after a repository-wide duplicate review covering ignored and hidden files.",
        "llm_assisted": true
      }
    ],
    "definition_source": "http://purl.obolibrary.org/obo/OMP_0000220",
    "evidence": [
      {
        "reference": "https://asm.org/protocols/oxidase-test-protocol",
        "snippet": "The oxidase test is a biochemical reaction that assays for the presence of cytochrome oxidase",
        "notes": "The American Society for Microbiology oxidase-test protocol describes the assay as a biochemical reaction that reads cytochrome oxidase."
      },
      {
        "reference": "DOI:10.5812/chbs-160199",
        "snippet": "The ability of bacteria to produce the enzyme cytochrome oxidase can be determined by performing an oxidase test",
        "notes": "Hafezi and Khamar review oxidase-test use for determining bacterial cytochrome oxidase production."
      }
    ]
  },
  {
    "identifier": "METPO:1007067",
    "label": "punctiform colony",
    "definition": "A colony shape that is very small (pinpoint), typically <1 mm in diameter.",
    "trait_category": "OTHER",
    "term_kind": "CLASS",
    "mapping_status": "SEEDED",
    "parent_traits": [
      "METPO:1007063"
    ],
    "created_by": "Marcin Joachimiak",
    "curation_history": [
      {
        "timestamp": "2026-09-11T13:19:00Z",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)"
      },
      {
        "timestamp": "2026-09-11T13:19:39Z",
        "curator": "codex",
        "action": "ENRICHED_FROM_LITERATURE",
        "changes": "Enriched the seeded METPO punctiform colony phenotype with stable OMP definition provenance and DOI-backed pinpoint-size evidence after a repository-wide duplicate review covering ignored and hidden files.",
        "llm_assisted": true
      }
    ],
    "definition_source": "http://purl.obolibrary.org/obo/OMP_0000240",
    "evidence": [
      {
        "reference": "DOI:10.7759/cureus.374",
        "snippet": "Colony morphology is one among the various characters of bacteria, which is also unique to a particular genus of bacteria that could be instrumental in preliminary identification. Size (measured in millimetres - pinpoint (\u2264 1 mm), small (2-3 mm), medium (4-5 mm), and large (> 5 mm) colonies), shape (circular, irregular, rhomboid, umbonate, umbonate, filamentous, or rhizoid)",
        "notes": "Kandi lists pinpoint as the smallest bacterial colony-size descriptor, matching the size component of the OMP-derived punctiform colony definition."
      }
    ]
  },
  {
    "identifier": "METPO:1007068",
    "label": "rhizoid colony",
    "definition": "A colony shape that has a branching, root-like outline.",
    "trait_category": "OTHER",
    "term_kind": "CLASS",
    "mapping_status": "SEEDED",
    "parent_traits": [
      "METPO:1007063"
    ],
    "created_by": "Marcin Joachimiak",
    "curation_history": [
      {
        "timestamp": "2026-09-11T12:47:37Z",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)"
      },
      {
        "timestamp": "2026-09-11T12:48:01Z",
        "curator": "codex",
        "action": "ENRICHED_FROM_LITERATURE",
        "changes": "Enriched the seeded METPO rhizoid colony phenotype with stable OMP definition provenance and DOI-backed evidence after a repository-wide duplicate review covering ignored and hidden files.",
        "llm_assisted": true
      }
    ],
    "definition_source": "http://purl.obolibrary.org/obo/OMP_0000168",
    "evidence": [
      {
        "reference": "DOI:10.7759/cureus.374",
        "snippet": "Colony morphology is one among the various characters of bacteria, which is also unique to a particular genus of bacteria that could be instrumental in preliminary identification. Size (measured in millimetres - pinpoint (\u2264 1 mm), small (2-3 mm), medium (4-5 mm), and large (> 5 mm) colonies), shape (circular, irregular, rhomboid, umbonate, umbonate, filamentous, or rhizoid)",
        "notes": "Kandi lists rhizoid as a bacterial colony shape value distinct from circular, irregular, and filamentous forms."
      }
    ]
  },
  {
    "identifier": "traitmech:000177",
    "label": "specialist",
    "definition": "A phenotype describing an organism with a narrow ecological niche, restricted to a limited range of environments or resources.",
    "definition_source": "DOI:10.1093/femsec/fiaa240",
    "trait_category": "OTHER",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1093/femsec/fiaa240",
        "snippet": "Organisms are often categorized as generalists or specialists, corresponding to broad or narrow niche requirements",
        "notes": "Bell and Bell frame specialists as organisms with narrow niche requirements, contrasting them with bacterial generalists."
      },
      {
        "reference": "DOI:10.1038/s41559-023-02027-7",
        "snippet": "Generalists can survive in many environments, whereas specialists are restricted to a single environment.",
        "notes": "The social-niche-breadth study defines specialists as environmentally restricted prokaryotes while contrasting them with generalists."
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-13T17:05:41Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted specialist as a DOI-backed TraitRecord after a repository-wide duplicate review covering ignored and hidden files; the local METPO snapshot has no exact specialist class and the replacement placeholder is reserved in proposals/metpo_traitmech_v54.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1007088",
    "label": "urease negative",
    "definition": "Test-outcome phenotype where the urease test yields a negative result. The underlying enzyme-organism relation should additionally be asserted via <organism> METPO:2000303 'does not show activity of' GO:0009039 'urease activity'.",
    "trait_category": "OTHER",
    "term_kind": "CLASS",
    "mapping_status": "SEEDED",
    "parent_traits": [
      "METPO:1007082"
    ],
    "synonyms": [
      {
        "synonym_text": "urease -",
        "synonym_type": "EXACT_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "urease test negative",
        "synonym_type": "EXACT_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "created_by": "Marcin Joachimiak",
    "curation_history": [
      {
        "timestamp": "2026-09-11T15:40:34Z",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)"
      },
      {
        "timestamp": "2026-09-11T15:41:02Z",
        "curator": "codex",
        "action": "ENRICHED_FROM_LITERATURE",
        "changes": "Enriched the seeded METPO urease-negative test outcome with OMP definition provenance plus DOI-backed assay evidence after a repository-wide duplicate review covering ignored and hidden files.",
        "llm_assisted": true
      }
    ],
    "definition_source": "http://purl.obolibrary.org/obo/OMP_0006090",
    "evidence": [
      {
        "reference": "DOI:10.5812/chbs-160199",
        "snippet": "A positive reaction is indicated by the entire liquid medium and the surface of the solid medium turning pink, whereas a negative reaction is characterized by the medium remaining yellow",
        "notes": "Hafezi and Khamar review the urease-test polarity and interpret an unchanged yellow medium as a negative assay result."
      },
      {
        "reference": "DOI:10.5812/chbs-160199",
        "snippet": "Both types contain a phenol red reagent that changes color with pH variations",
        "notes": "The review describes the pH-indicator readout shared by liquid and solid urease-test media."
      }
    ]
  },
  {
    "identifier": "METPO:1007082",
    "label": "urease test",
    "definition": "A biochemical test that detects urease enzyme activity by observing urea hydrolysis (typically via a pH-indicator color change). The test outcome (positive or negative) is captured by its child classes; this class itself does not assert urease activity.",
    "trait_category": "OTHER",
    "term_kind": "CLASS",
    "mapping_status": "SEEDED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "synonyms": [
      {
        "synonym_text": "urea hydrolysis test",
        "synonym_type": "EXACT_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "urease activity test",
        "synonym_type": "EXACT_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "created_by": "Marcin Joachimiak",
    "curation_history": [
      {
        "timestamp": "2026-09-11T14:52:53Z",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)"
      },
      {
        "timestamp": "2026-09-11T14:53:47Z",
        "curator": "codex",
        "action": "ENRICHED_FROM_LITERATURE",
        "changes": "Enriched the seeded METPO urease test with OMP definition provenance plus DOI-backed urea-hydrolysis and pH-indicator evidence after a repository-wide duplicate review covering ignored and hidden files.",
        "llm_assisted": true
      }
    ],
    "definition_source": "http://purl.obolibrary.org/obo/OMP_0000222",
    "evidence": [
      {
        "reference": "DOI:10.5812/chbs-160199",
        "snippet": "Urea is classified as a diamide, and certain bacteria possessing the enzyme urease are capable of utilizing urea to generate ammonia, carbon dioxide, and water",
        "notes": "Hafezi and Khamar describe the urease-test chemistry linking bacterial urease to urea conversion into alkaline products."
      },
      {
        "reference": "DOI:10.5812/chbs-160199",
        "snippet": "Both types contain a phenol red reagent that changes color with pH variations",
        "notes": "The review describes phenol red as the pH indicator for both liquid and solid urease-test media."
      }
    ]
  },
  {
    "identifier": "METPO:1005016",
    "label": "Voges-Proskauer test",
    "definition": "An assay that tests the ability of an organism to produce acetoin from glucose via the butanediol fermentation pathway.",
    "trait_category": "OTHER",
    "term_kind": "CLASS",
    "mapping_status": "SEEDED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-12T21:15:14Z",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)"
      },
      {
        "timestamp": "2026-09-12T21:15:44Z",
        "curator": "codex",
        "action": "ENRICHED_FROM_LITERATURE",
        "changes": "Added the METPO Voges-Proskauer-test assay parent with stable-URL butanediol-pathway and acetoin-readout evidence after a repository-wide duplicate review covering ignored and hidden files.",
        "llm_assisted": true
      }
    ],
    "definition_source": "https://asm.org/getmedia/40946f85-9357-4563-aa8a-994427efa825/Methyl-Red-and-Voges-Proskauer-Test-Protocols.pdf",
    "evidence": [
      {
        "reference": "https://asm.org/getmedia/40946f85-9357-4563-aa8a-994427efa825/Methyl-Red-and-Voges-Proskauer-Test-Protocols.pdf",
        "snippet": "Bacteria fermenting sugars via the butanediol pathway produce acetoin (i.e., acetyl methyl carbinol or 3-hydroxybutanone) as an intermediate which can be further reduced to 2,3-butanediol.",
        "notes": "The ASM protocol links acetoin production directly to sugar fermentation through the butanediol pathway."
      },
      {
        "reference": "https://asm.org/getmedia/40946f85-9357-4563-aa8a-994427efa825/Methyl-Red-and-Voges-Proskauer-Test-Protocols.pdf",
        "snippet": "In the presence of KOH the intermediate acetoin is oxidized to diacetyl, a reaction which is catalyzed by a-naphthol (2). Diacetyl reacts with the guanidine group associated with molecules contributed by peptone in the medium, to form a pinkish-red-colored product (Fig. 2A).",
        "notes": "The same protocol explains that the Voges-Proskauer reaction detects acetoin via Barritt chemistry that forms a pinkish-red product."
      }
    ]
  },
  {
    "identifier": "METPO:1005018",
    "label": "Voges-Proskauer test negative",
    "definition": "A phenotype in which an organism tests negative in the Voges-Proskauer test.",
    "trait_category": "OTHER",
    "term_kind": "CLASS",
    "mapping_status": "SEEDED",
    "parent_traits": [
      "METPO:1005016"
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-12T22:08:40Z",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)"
      },
      {
        "timestamp": "2026-09-12T22:09:04Z",
        "curator": "codex",
        "action": "ENRICHED_FROM_LITERATURE",
        "changes": "Enriched the seeded METPO Voges-Proskauer-test-negative phenotype with stable-URL VP-negative interpretation evidence after a repository-wide duplicate review covering ignored and hidden files.",
        "llm_assisted": true
      }
    ],
    "definition_source": "https://asm.org/getmedia/40946f85-9357-4563-aa8a-994427efa825/Methyl-Red-and-Voges-Proskauer-Test-Protocols.pdf",
    "evidence": [
      {
        "reference": "https://asm.org/getmedia/40946f85-9357-4563-aa8a-994427efa825/Methyl-Red-and-Voges-Proskauer-Test-Protocols.pdf",
        "snippet": "VP-positive E. areogenes (A) shows red coloration on top of the culture, whereas VP-negative E. coli (B) has a yellowish color.",
        "notes": "The ASM protocol figure caption identifies the yellow E. coli reaction after adding Barritt's reagents as the VP-negative comparison."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:562",
        "taxon_label": "Escherichia coli",
        "note": "ASM Figure 2 presents E. coli grown in MR-VP broth for 48 hours as the VP-negative control culture that remains yellowish after Barritt's reagents are added.",
        "reference": "https://asm.org/getmedia/40946f85-9357-4563-aa8a-994427efa825/Methyl-Red-and-Voges-Proskauer-Test-Protocols.pdf"
      }
    ]
  },
  {
    "identifier": "METPO:1005017",
    "label": "Voges-Proskauer test positive",
    "definition": "A phenotype in which an organism tests positive in the Voges-Proskauer test, indicating acetoin production.",
    "trait_category": "OTHER",
    "term_kind": "CLASS",
    "mapping_status": "SEEDED",
    "parent_traits": [
      "METPO:1005016"
    ],
    "synonyms": [
      {
        "synonym_text": "voges-proskauer test",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-12T19:49:19Z",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)"
      },
      {
        "timestamp": "2026-09-12T19:50:21Z",
        "curator": "codex",
        "action": "ENRICHED_FROM_LITERATURE",
        "changes": "Added the METPO Voges-Proskauer-test-positive phenotype with stable-URL and DOI-backed acetoin-production evidence after a repository-wide duplicate review covering ignored and hidden files.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-12T21:15:44Z",
        "curator": "codex",
        "action": "RESOLVED_PARENT_GAP",
        "changes": "Reparented Voges-Proskauer test positive below the newly curated METPO:1005016 Voges-Proskauer test assay parent and marked the temporary assay-parent discussion resolved.",
        "llm_assisted": true
      }
    ],
    "definition_source": "https://asm.org/getmedia/40946f85-9357-4563-aa8a-994427efa825/Methyl-Red-and-Voges-Proskauer-Test-Protocols.pdf",
    "evidence": [
      {
        "reference": "https://asm.org/getmedia/40946f85-9357-4563-aa8a-994427efa825/Methyl-Red-and-Voges-Proskauer-Test-Protocols.pdf",
        "snippet": "In the presence of KOH the intermediate acetoin is oxidized to diacetyl, a reaction which is catalyzed by a-naphthol (2). Diacetyl reacts with the guanidine group associated with molecules contributed by peptone in the medium, to form a pinkish-red-colored product (Fig. 2A).",
        "notes": "The ASM protocol PDF explains that the Voges-Proskauer reaction detects acetoin through Barritt chemistry that forms a pinkish-red product."
      },
      {
        "reference": "DOI:10.1128/JCM.42.8.3665-3669.2004",
        "snippet": "In the ASM Manual of Clinical Microbiology, only 6 of the 18 biochemical tests used in the present investigation are listed for Klebsiella species: indole, MR, VP, LDC, ODC, and malonate",
        "notes": "Hansen et al. evaluated Voges-Proskauer as a conventional Klebsiella biochemical test listed in the ASM Manual of Clinical Microbiology."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:571",
        "taxon_label": "Klebsiella oxytoca",
        "note": "Hansen et al. Table 2 reported 100.0% Voges-Proskauer-positive results for K. oxytoca across the CPHL, NRL, and SSI reference laboratories.",
        "reference": "DOI:10.1128/JCM.42.8.3665-3669.2004"
      }
    ],
    "discussions": [
      {
        "discussion_id": "voges-proskauer-test-positive-assay-parent-gap",
        "prompt": "Resolve a non-assay parent for positive Voges-Proskauer-test phenotypes before narrowing parent_traits below phenotype.",
        "kind": "CURATION_TODO",
        "status": "RESOLVED",
        "rationale": "METPO:1005016 is the seeded superclass of METPO:1005017, but METPO:1005016 defines an assay rather than a broader microbial trait class, so this record is temporarily parented directly to METPO:1000059 phenotype.",
        "posed_by": "codex",
        "posed_date": "2026-09-12",
        "resolved_date": "2026-09-12",
        "resolution_note": "METPO:1005016 is now represented as the seeded Voges-Proskauer-test assay parent, so this positive assay-outcome phenotype can use its exact source superclass instead of a temporary direct phenotype parent; this resolves the exact METPO assay-parent gap, not the broader non-assay parent question for assay-outcome phenotypes."
      }
    ]
  },
  {
    "identifier": "traitmech:000142",
    "label": "acid phosphatase activity",
    "definition": "A physiological enzyme-activity phenotype in which a cell produces active acid phosphatase enzymes that dephosphorylate phosphate-containing compounds under acidic conditions.",
    "definition_source": "DOI:10.1128/JB.182.23.6850-6853.2000",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1128/JB.182.23.6850-6853.2000",
        "snippet": "the presence of acid phosphatase activity in the culture filtrate of M. tuberculosis was confirmed and a 28-kDa protein possessing this activity was purified and characterized",
        "notes": "Saleh and Belisle confirmed Mycobacterium tuberculosis acid phosphatase activity and purified the SapM protein carrying that activity."
      },
      {
        "reference": "DOI:10.1155/2021/8888641",
        "snippet": "According to the API ZYM assays, all three isolates were positive for alkaline phosphatase, leucine aryl amidase, acid phosphatase, and naphthol_AS_BI_phosphohydrolase.",
        "notes": "Mekonnen et al. treated acid phosphatase as an assayed bacterial exoenzyme phenotype in rapid urease-producing soil isolates."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1773",
        "taxon_label": "Mycobacterium tuberculosis",
        "note": "Mycobacterium tuberculosis secretes SapM, a culture-filtrate enzyme purified through its acid phosphatase activity.",
        "reference": "DOI:10.1128/JB.182.23.6850-6853.2000"
      }
    ],
    "discussions": [
      {
        "discussion_id": "acid-phosphatase-activity-xref-gap",
        "prompt": "Resolve an exact external ontology class for acid phosphatase activity before adding a TraitRecord xref.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "GO:0003993 carries the same acid phosphatase activity label but denotes the enzyme molecular function rather than the organism-level phenotype, so it is appropriate as a causal-node grounding rather than an equivalent TraitRecord xref.",
        "posed_by": "codex",
        "posed_date": "2026-09-11"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-11T16:21:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted acid phosphatase activity as a DOI-backed TraitRecord after a repository-wide duplicate review covering ignored and hidden files; METPO has no exact acid phosphatase activity class yet.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000712",
    "label": "memory of acquired stress resistance",
    "definition": "A physiological phenotype in which a microbial cell or lineage retains elevated resistance to a later stress challenge after a previous inducing stress has been removed, through persistence of a non-genetic state.",
    "definition_source": "DOI:10.1534/genetics.112.143016",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1534/genetics.112.143016",
        "snippet": "resistance persisted for four to five generations after cells were removed from the prior salt treatment",
        "notes": "Guan et al. 2012, PMID:22851651, PMC3454879; scientific abstract, directly matched in publisher HTML and source-qualified MED. The resistance endpoint is H2O2 survival, not faster transcriptional reactivation. Relevant Methods, Results and actual Figure 1 and S1/S2 were inspected. BY4741-background cells received 0.7 M NaCl for 60 minutes, then grew in fresh stress-free YPD. Figure 1 describes three-to-four doublings over 360 minutes; four-to-five generations is the abstract statement. Methods specifies 11 peroxide doses plus control, whereas Figure 1A captions ten plotted doses. The normalized survival score is not a fraction of memory-bearing cells. S1 growth-arrest interventions and S2 engineered UCC8613 daughter marking are separate contexts. No natural canonical exemplar is asserted. The publisher's formula rendering differs from MED H(2)O(2); the selected span matches both without changing either source. Raw data were not independently reanalyzed."
      },
      {
        "reference": "DOI:10.1371/journal.pbio.2003853",
        "snippet": "the cells inheriting this ancestral PA displayed a significantly increased heat resistance compared to their isogenic, PA-free siblings.",
        "notes": "Govers et al. 2018, PMID:30153247, PMC6112618; scientific abstract, not Author Summary, matched in primary XML and source-qualified MED. Relevant Results and Methods, actual Figure 4 and S6 were inspected. Engineered MG1655 IbpA-msfGFP reporters received 47 C for 15 minutes, recovered with growth, then faced 51 C for 7 minutes. Figure 4D compares aggregate-bearing and aggregate-free descendants; Figure 4C detects no improved population-average survival after pretreatment. Survival requires growth and division within eight hours. S6 detects no age-bin survival difference in this assay, not universal age independence. Reporter-induced clustering was separately tested in actual Figure 1, previously inspected for traitmech:000711; a monomeric label alone is not proof against artifacts. Synthetic induction experiments and their duration are not transferred to these heat-induced lineages. Raw data and all other memory-related figure images were not independently assessed."
      }
    ],
    "discussions": [
      {
        "discussion_id": "stress-resistance-memory-scope-and-hierarchy",
        "prompt": "Preserve persistence after stress removal and the resistance endpoint.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Compare matched genetic backgrounds and challenge conditions after removal of the inducing stress. Persistent resistance is not merely faster transcriptional reactivation or faster reacquisition after a second induction. A marker, aggregate, gene, ongoing stress response or single survival measurement alone does not establish this history-dependent phenotype. Cell-level or lineage-restricted protection need not improve population-average survival. No fixed duration, number of divisions, stressor identity or molecular mechanism is required. Genetic adaptation, carbon-source memory, cue-triggered anticipation, diversifying bet hedging, persister formation and unequal aggregate inheritance are not equivalent, though particular observations can overlap. Unqualified cellular memory, stress priming and cross-protection are not asserted as exact synonyms. Stress response (traitmech:000078) concerns sensing and mounting protection; its research report includes cross-protection as an output but does not establish persistence after removal. METPO:1000059 phenotype is the conservative parent pending hierarchy review; existing records are unchanged.",
        "posed_by": "codex",
        "posed_date": "2026-10-12"
      },
      {
        "discussion_id": "stress-resistance-memory-evidence-limits",
        "prompt": "Resolve natural strain provenance and assay-specific mechanisms before extending this draft.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Neither a uniform species-wide phenotype nor a shared molecular mechanism is established. Laboratory backgrounds and engineered reporters remain qualified evidence, not natural canonical taxa. No causal graph, exact synonym or external equivalence is asserted. MED/Crossref and visible publisher notice checks on 2026-10-12 exposed no linked correction or retraction for the retained sources; this bounded check does not prove notice absence. Guan's Crossref has-review relation is not a correction or independent experiment. The publisher HTML was directly retrieved through its public redirect after other endpoints failed. Source access limits and section-specific assay descriptions are retained rather than silently harmonized.",
        "posed_by": "codex",
        "posed_date": "2026-10-12"
      },
      {
        "discussion_id": "stress-resistance-memory-metpo-identity",
        "prompt": "Retain historical stress-response neighbors without reactivating their identifiers.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Pinned and current released METPO contain METPO:1000293 obsolete stress response and METPO:1000222 obsolete oxidative stress response, marked deprecated below ObsoleteClass with an OMO:0001000 reason annotation and no replacement or consider annotation in the inspected releases. These broader lexical neighbors do not define persistence after stress removal. Their historical rationale remains unresolved; neither is reactivated or used as an exact xref. Ignored/hidden available-file searches, retained historical trees, normalized trait semantics, pending PRs and ontology RDF found no exact memory class in the inspected scope. The pinned ontology is unchanged; this is not discovery exhaustion or a sequence-feature trait.",
        "posed_by": "codex",
        "posed_date": "2026-10-12"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-12T21:02:06Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added memory of acquired stress resistance with two primary DOI references and directly checked snippets. Retained post-removal, resistance-endpoint, cell-versus-population and source-context limits. Reserved 000712, v588 and 1066500-1066599 after ignored/hidden, historical-tree, independent-copy and pending-PR checks. Examples and mechanism graph deferred; existing records unchanged. Timestamp is the observed UTC curation decision.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000194",
    "label": "aerobic anoxygenic phototrophy",
    "definition": "A photoheterotrophy in which aerobic heterotrophic bacteria use bacteriochlorophyll-containing reaction centers to harvest light as auxiliary energy while requiring organic carbon substrates for growth.",
    "definition_source": "DOI:10.1128/AEM.01747-12",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000657",
      "traitmech:000035",
      "METPO:1000602"
    ],
    "synonyms": [
      {
        "synonym_text": "aerobic anoxygenic phototroph",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1128/AEM.01747-12"
      },
      {
        "synonym_text": "aerobic anoxygenic phototrophic bacteria",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1186/s40168-024-01786-0"
      },
      {
        "synonym_text": "AAP bacteria",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1186/s40168-024-01786-0"
      },
      {
        "synonym_text": "aerobic_anoxygenic_phototrophy",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1128/AEM.01747-12",
        "snippet": "Aerobic anoxygenic phototrophs contain photosynthetic reaction centers composed of bacteriochlorophyll",
        "notes": "Hauruseu and Koblizek define AAPs by bacteriochlorophyll-containing photosynthetic reaction centers."
      },
      {
        "reference": "DOI:10.1128/AEM.01747-12",
        "snippet": "These organisms are photoheterotrophs, as they require organic carbon substrates for their growth whereas light-derived energy has only an auxiliary function",
        "notes": "The Erythrobacter sp. NAP1 chemostat study supports organic carbon as required for AAP growth and light as an auxiliary energy input."
      },
      {
        "reference": "DOI:10.1186/s40168-024-01786-0",
        "snippet": "Aerobic anoxygenic phototrophic (AAP) bacteria are heterotrophic bacteria that supply their metabolism with light energy harvested by bacteriochlorophyll-a-containing reaction centers",
        "notes": "Villena-Alemany et al. corroborate the AAP scope as heterotrophic bacteria with light-harvesting bacteriochlorophyll-a reaction centers."
      },
      {
        "reference": "DOI:10.1186/s40793-024-00573-6",
        "snippet": "Aerobic anoxygenic phototrophs (AAPs) are a polyphyletic group of bacteria capable of photoheterotrophy",
        "notes": "Stojan et al. place AAPs as a polyphyletic bacterial photoheterotrophic functional group rather than a taxonomic lineage."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:237727",
        "taxon_label": "Erythrobacter sp. NAP1",
        "note": "Carbon-limited aerobic anoxygenic phototroph showing light-enhanced organic-carbon assimilation.",
        "reference": "DOI:10.1128/AEM.01747-12"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "aerobic_anoxygenic_phototrophy_light_organic_carbon",
        "title": "Aerobic anoxygenic phototrophy couples light to organic carbon assimilation",
        "description": "Evidence-backed causal sketch linking bacteriochlorophyll-based light harvesting, photophosphorylation, and light-enhanced organic-carbon assimilation in aerobic anoxygenic phototrophs.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This first graph captures process-level light harvesting, photophosphorylation, and organic-carbon assimilation without claiming an exact AAP reaction-center protein family. pufLM examples need an audit-verifiable accession/proteome pair before promotion to a mechanistic protein-level graph.",
        "nodes": [
          {
            "node_id": "aerobic_anoxygenic_phototrophy_trait",
            "label": "aerobic anoxygenic phototrophy",
            "node_type": "TRAIT",
            "grounding": "traitmech:000194",
            "description": "Aerobic photoheterotrophy using bacteriochlorophyll-containing reaction centers."
          },
          {
            "node_id": "light",
            "label": "light",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "grounding": "PATO:0001717",
            "description": "Auxiliary energy source harvested by AAPs."
          },
          {
            "node_id": "bacteriochlorophyll",
            "label": "bacteriochlorophyll",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:38201",
            "description": "Light-harvesting pigment in AAP reaction centers."
          },
          {
            "node_id": "photophosphorylation",
            "label": "photophosphorylation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Light-driven ATP synthesis in AAPs."
          },
          {
            "node_id": "atp",
            "label": "ATP",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:30616",
            "description": "Energy carrier produced by photophosphorylation."
          },
          {
            "node_id": "organic_carbon",
            "label": "organic carbon",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:50860",
            "description": "Required organic substrate used as carbon source."
          },
          {
            "node_id": "biomass",
            "label": "biomass",
            "node_type": "CHEMICAL",
            "grounding": "METPO:1007501",
            "description": "Cell material accumulated from supplied organic carbon."
          }
        ],
        "edges": [
          {
            "subject": "aerobic_anoxygenic_phototrophy_trait",
            "predicate": "has energy source",
            "object": "light",
            "description": "AAPs supplement their heterotrophic metabolism with light energy.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s40168-024-01786-0",
                "snippet": "supply their metabolism with light energy",
                "notes": "Verified against the Springer full text."
              }
            ],
            "predicate_id": "METPO:2007807"
          },
          {
            "subject": "aerobic_anoxygenic_phototrophy_trait",
            "predicate": "has carbon source",
            "object": "organic_carbon",
            "description": "AAP growth relies on external organic carbon.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s40168-024-01786-0",
                "snippet": "rely upon external sources of organic carbon",
                "notes": "Verified against the Springer full text."
              }
            ],
            "predicate_id": "METPO:2007806"
          },
          {
            "subject": "bacteriochlorophyll",
            "predicate": "captures",
            "object": "light",
            "description": "Bacteriochlorophyll-containing AAP reaction centers harvest light.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s40168-024-01786-0",
                "snippet": "energy obtained from light through bacteriochlorophyll-a (BChl-a) type II reaction centers",
                "notes": "Verified against the Springer full text."
              }
            ]
          },
          {
            "subject": "light",
            "predicate": "enables",
            "object": "photophosphorylation",
            "description": "Light drives the AAP photophosphorylation branch.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s40793-024-00573-6",
                "snippet": "harvest light energy and generate ATP by photophosphorylation",
                "notes": "Verified against the Springer full text."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "photophosphorylation",
            "predicate": "has output",
            "object": "atp",
            "description": "AAP photophosphorylation conserves light energy as ATP.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.01747-12",
                "snippet": "respiration decreased to approximately 25% of its dark value and was replaced by photophosphorylation",
                "notes": "Supports replacement of respiration by photophosphorylation as light intensity increased in carbon-limited Erythrobacter sp. NAP1 cultures."
              }
            ],
            "predicate_id": "RO:0002234"
          },
          {
            "subject": "organic_carbon",
            "predicate": "assimilated into",
            "object": "biomass",
            "description": "Light lets AAPs accumulate supplied organic carbon as biomass.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.01747-12",
                "snippet": "accumulate the supplied organic carbon which would otherwise be respired",
                "notes": "Supports light-enhanced organic-carbon assimilation into biomass by AAPs."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "aerobic-anoxygenic-phototrophy-xref-gap",
        "prompt": "Resolve an exact external ontology class for aerobic anoxygenic phototrophy before adding a TraitRecord xref.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "The pinned METPO snapshot carries aerobic_anoxygenic_phototrophy only as a related synonym on broad phototrophic, and GO photosynthetic electron transport classes denote the intracellular pathway rather than this organism-level aerobic photoheterotrophic trait.",
        "posed_by": "codex",
        "posed_date": "2026-09-14"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-14T23:14:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted aerobic anoxygenic phototrophy as a DOI-backed photoheterotrophy, anoxygenic photosynthesis, and aerobic trait after a repository-wide duplicate review covering ignored and hidden files; the pinned METPO snapshot only stores aerobic_anoxygenic_phototrophy as a related synonym on broad phototrophic.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000705",
    "label": "aerobic overflow metabolism",
    "definition": "A physiological phenotype in which microbial cells divert part of their catabolic carbon flux to excreted, incompletely oxidized products with lower ATP yield per substrate than complete respiration, despite possessing respiratory capacity and sufficient oxygen for respiration.",
    "definition_source": "DOI:10.1038/msb.2009.82",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/msb.2009.82",
        "snippet": "S. cerevisiae and E. coli fully oxidize glucose at low concentrations and shift to overflow metabolism at high glucose concentrations.",
        "notes": "Molenaar et al. 2009, PMID:19888218, PMC2795476; Current growth models and their limitations, not the abstract. The surrounding paragraph supplies the fully aerobic, incomplete-oxidation and retained respiratory-capacity differentia. This Perspective contains original modeling, not new experimental replication of the cited organisms. The terminology discussion also includes mixed-acid-to-lactate shifts; the qualified label here does not define every use of unqualified overflow metabolism."
      },
      {
        "reference": "DOI:10.1038/nature15765",
        "snippet": "cells use fermentation instead of the more efficient respiration to generate energy, despite the availability of oxygen.",
        "notes": "Basan et al. 2015, PMID:26632588, PMC4843128; scientific abstract. Relevant Results, growth Methods, model scope, Extended Data Table 1, actual Figure 1 and Extended Data Figure 2 were inspected through public XML and figure assets. Acetate excretion depends on growth conditions; the fitted threshold is not universal. The oxidative-fermentation accounting includes oxygen-dependent NADH oxidation. Net excretion does not exclude acetate reuptake. Proteome allocation is a tested model in this system, not a necessary mechanism for every member of the trait. Complete supplements, equations and referenced batch-culture methods were not independently reanalyzed. Publisher retrieval failed; the public full-text XML was accessible."
      },
      {
        "reference": "DOI:10.1111/febs.13019",
        "snippet": "All fermenting yeasts exhibited significant ethanol formation within the first 20 min in response to a glucose pulse",
        "notes": "Hagman et al. 2014, PMID:25161062, PMC4240471; Results and Discussion / Consumption of glucose and generation of biomass and ethanol, not the abstract. Introduction, relevant Results, Experimental procedures and actual Figures 1-2 were inspected. Glucose pulses into initially respiratory cultures produced ethanol in responsive yeasts while dissolved oxygen was controlled above 30% air saturation. The authors report no first-hour repression of respiration; Figure 2 does not establish monotonic or unchanged oxygen-consumption rates. Replication excludes V. polyspora; E. coryli received supplementation. This short-term Crabtree assay is not an exact synonym for the entire microbial phenotype. Supplemental time series and strain origins were not fully reviewed."
      }
    ],
    "discussions": [
      {
        "discussion_id": "aerobic-overflow-scope-and-parent",
        "prompt": "Retain oxygen-sufficient overflow as a conditional phenotype with an explicit hierarchy boundary.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "The qualifier aerobic is deliberate. Unqualified overflow, Crabtree effect, respiro-fermentation and industrial aerobic fermentation are not asserted as exact synonyms. The local METPO:1002005 fermentation record is donor/acceptor-defined and excludes external electron acceptors; Basan's oxidative branch uses different accounting. https://github.com/berkeleybop/metpo/issues/468 discusses fermentation hierarchy, and the pinned ontology already differs from the retained local parent/definition. Neither that process nor METPO:1000060 metabolism is adopted as an is-a parent of this organismal phenotype. METPO:1000059 phenotype is used pending upstream hierarchy review. Product-specific ethanol/butanediol fermentation, aerotolerance, facultative anaerobiosis, copiotrophy and diauxic growth are not equivalent. Product detection or oxygen presence alone is insufficient: oxygen limitation must be excluded. No universal substrate, product, concentration, growth-rate threshold, complete respiratory shutdown or fixed molecular mechanism is required.",
        "posed_by": "codex",
        "posed_date": "2026-10-12"
      },
      {
        "discussion_id": "aerobic-overflow-examples-and-mechanism",
        "prompt": "Resolve natural strain provenance and taxon-specific mechanisms before adding canonical examples or a graph.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Laboratory reference strains and engineered perturbations are qualified evidence, not proof that every member of a species has this phenotype under all conditions. Canonical taxa require primary strain provenance and authority-resolved identities. No common protein-resolved causal graph is established here; bacterial and yeast mechanisms must retain their experimental scope. Gene presence and predicted flux alone do not demonstrate overflow. Canonical examples, causal graphs and external xrefs are therefore unasserted. Qualified MED and Crossref records for all three citations exposed no linked correction or retraction on 2026-10-12; this bounded check is not a guarantee that no notice exists. Basan's publisher access remains unavailable.",
        "posed_by": "codex",
        "posed_date": "2026-10-12"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-12T01:03:22Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added aerobic overflow metabolism with three DOI-backed sources and directly checked snippets. Reserved 000705, v581 and 1065800-1065899 after ignored/hidden worktree and pending-PR checks. Oxygen-sufficient scope, hierarchy and inference limits are explicit. Existing traits unchanged; timestamp is the observed UTC curation decision.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-12T01:08:15Z",
        "curator": "codex",
        "action": "CLARIFIED_EVIDENCE_SCOPE",
        "changes": "Address #1881: distinguish the authors' reported lack of early respiratory repression from a claim that individual oxygen-consumption rates never decrease. Retain the original curation event unchanged.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-12T01:53:37Z",
        "curator": "codex",
        "action": "REPLACED_UNSUPPORTIVE_SNIPPET",
        "changes": "Address #1883: replace the yeast data-collection quotation with an 18-word Results span that reports significant ethanol formation after a glucose pulse. Retain oxygen-controlled assay context, the 25-word bound and both earlier curation events unchanged.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000589",
    "label": "aerotaxis",
    "definition": "A motile phenotype in which active locomotion is directionally biased along an oxygen concentration gradient toward preferred oxygen conditions.",
    "definition_source": "DOI:10.1128/jb.178.17.5199-5204.1996",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000702"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1128/jb.169.7.3118-3123.1987",
        "snippet": "at high concentrations, oxygen was a repellent of Salmonella typhimurium, Escherichia coli, and some bacilli",
        "notes": "Abstract, exact-matched at Europe PMC (PMID:3036771); full text not inspected. The study contrasts high-oxygen repulsion with attraction at lower concentrations and reports temporal assays. This supports concentration-dependent response direction, not universal thresholds or a requirement that every organism exhibit both signs. The abstract's tentative receptor interpretation is not promoted to an established mechanism."
      },
      {
        "reference": "DOI:10.1128/jb.178.17.5199-5204.1996",
        "snippet": "As a result of aerotaxis, the bacteria were attracted to a specific low concentration of oxygen (3 to 5 microM).",
        "notes": "Abstract, exact-matched at Europe PMC (PMID:8752338); full text not inspected. Azospirillum brasilense forms a band in a spatial oxygen gradient and returns when swimming into higher or lower oxygen; temporal gradients corroborate the response. The preferred interval is experiment-specific. Proton motive force peaks in the same interval, but its proposed signaling role remains a hypothesis, not a protein-resolved causal edge. No strain-level canonical example is inferred from the abstract."
      },
      {
        "reference": "DOI:10.1103/PhysRevE.106.034404",
        "snippet": "runs in the direction of the oxygen source (x < 0) are longer and more frequent.",
        "notes": "Section II.B, page 3; published 2022-09-15. Published full text and Appendices A-E read at the author's institutional copy: https://www.fast.universite-paris-saclay.fr/~moisy/papers/2022_bouvard_pre.pdf. Figures 1-2 and the typeset x < 0 passage visually checked. Tracking in an oxygen-gradient capillary shows directional bias in Burkholderia contaminans; nonmotile cells are excluded with a 6 micrometre-per-second velocity threshold. The fitted response model does not identify a molecular receptor."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:488447",
        "taxon_label": "Burkholderia contaminans",
        "reference": "DOI:10.1103/PhysRevE.106.034404",
        "note": "Section II.A describes an unnamed environmental strain, identified using 16S and recA fragments and selected for strong aerotaxis. Figure 2 reports the motile subpopulation's bias toward the oxygen source. NCBI resolved 488447 on 2026-10-04 at species rank, not as this exact isolate. This is not a universal strain or cell-level claim."
      }
    ],
    "discussions": [
      {
        "discussion_id": "aerotaxis-direction-and-mapping-boundaries",
        "prompt": "Preserve oxygen-directed scope and verify external equivalents.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Preferred oxygen need not be the highest available oxygen. Oxygen-dependent growth, respiration, tolerance and speed changes alone do not establish directional locomotion. Aerotaxis is narrower than general chemotaxis, while magnetic alignment and magnetoaerotaxis are not exact synonyms. The existing chemotaxis record is flagellar-specific; motile is the verified broader METPO parent without imposing that apparatus. No external xref or synonym is asserted before authority resolution and an organismal-disposition scope check.",
        "posed_by": "codex",
        "posed_date": "2026-10-04"
      },
      {
        "discussion_id": "aerotaxis-mechanism-and-isolate-grounding",
        "prompt": "Ground molecular branches and the exact environmental isolate.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "A proton-motive-force correlation or a fitted response law does not establish a universal oxygen receptor or molecular pathway. Add causal graphs only after direct primary evidence and taxon-paired protein accessions have been verified; no NONMECHANISTIC graph bypasses this requirement. The canonical example lacks a published strain designation or accession; retain its species-level and motile-subpopulation qualifiers until isolate-specific identity can be resolved.",
        "posed_by": "codex",
        "posed_date": "2026-10-04"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-04T06:09:08Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added aerotaxis with three primary DOI citations and exact snippets. Ignored-and-hidden searches found no exact live trait or METPO term. Reserved METPO:1054300 in v466. Kept attraction and repulsion within concentration-dependent directional scope, added a qualified NCBI-resolved environmental-isolate example, and deferred unverified molecular mechanisms and external mappings.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000601",
    "label": "aerotropism",
    "definition": "A phenotype in which polarized growth is directionally biased in response to a spatial oxygen concentration gradient.",
    "definition_source": "DOI:10.1016/S0168-6496(03)00161-2",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000597"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1016/S0168-6496(03)00161-2",
        "snippet": "Conidia also germinated close to air-filled Teflon tubes and exhibited germ-tube tropism, but not as distinctly as on living reed roots.",
        "notes": "Abstract, exact-matched at Europe PMC (PMID:19719598). Publisher HTML methods, results and discussion were read at https://academic.oup.com/femsec/article/45/3/293/549782. Section 3.2 reports Microdochium bolleyi germ-tube orientation toward air-filled Teflon root dummies (60% +/- 12%) and stronger orientation toward living roots. This is qualified supporting evidence: oxygen-dependent germination and root-derived chemicals complicate attribution, and the tube result alone does not establish significance against random orientation. Figure 3 measures germination, not orientation. Figures were not visually verified. No strain accession or molecular mechanism is asserted."
      },
      {
        "reference": "DOI:10.1155/2012/517529",
        "snippet": "C. albicans responds to other external stimuli in vitro, displaying aerotropism under hypoxic conditions and galvanotropism, where hyphae germinate and orient towards the cathode in an applied electric field (Figure 2(c)(iii)) [94, 97, 98].",
        "notes": "Brand (2012), Hyphal Growth in Human Fungal Pathogens and Its Role in Virulence; published online in 2011, volume 2012. Review, not independent experimental replication. Full text directly retrieved as Europe PMC JATS XML (PMC3216317), https://www.ebi.ac.uk/europepmc/webservices/rest/PMC3216317/fullTextXML. The complete sentence exact-matches the XML text and is quoted under its Creative Commons Attribution license. It supports use of aerotropism for hyphal responses under hypoxia, not a quantified oxygen-gradient experiment or a mechanism. The cathode and Figure 2(c)(iii) clauses describe galvanotropism, not aerotropism; no figure-based oxygen claim is made. Its cited Aoki paper remains an unverified primary-source lead in the discussion."
      }
    ],
    "discussions": [
      {
        "discussion_id": "aerotropism-direction-and-stimulus-boundaries",
        "prompt": "Keep oxygen-directed growth distinct from oxygen demand, taxis and flow.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "The class includes positive or negative directional growth, without requiring both in one organism. This is a polarity-neutral scope decision, not verification of a negative response: the avoidance lead below is unread. Aerotaxis denotes locomotion, not growth orientation. Oxygen tolerance, oxygen requirement, biomass, germination and extension rate alone are insufficient. This record uses the oxygen-gradient sense of aerotropism; air-flow-directed growth belongs to rheotropism, not this class solely because air supplies oxygen. Resolve external phenotype mappings and variant-label scopes before adding xrefs or synonyms. The local parent is chemotropism (traitmech:000597); its v474 METPO:1055100 proposal is not released. The v478 proposal therefore uses the existing METPO:1000059 phenotype parent; reconcile the narrower hierarchy when chemotropism is accepted.",
        "posed_by": "codex",
        "posed_date": "2026-10-04"
      },
      {
        "discussion_id": "aerotropism-controls-and-native-mechanism",
        "prompt": "Resolve gradient controls, strain provenance and native causal mechanisms.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Unverified research leads: Aoki et al. (1998), DOI:10.1007/BF02464003, and Carlile and Tew (1988), DOI:10.1016/S0007-1536(88)80071-8. Crossref and Elsevier API retrievals confirmed metadata only; publisher retrieval returned 403. Search-index-limited summaries suggest positive Candida hyphal reorientation and negative aerotropism in Phytophthora germ tubes, respectively. Original wording, full text, figures and controls remain unverified. These are research leads, not definition authority or counted trait evidence (#1680, #1681). Inspect the older full texts and orientation readouts, and discriminate tip reorientation from preferential growth or survival in oxygen-rich regions. Resolve natural strain provenance and NCBI identity before canonical examples. The current evidence does not establish a universal oxygen sensor or a taxon-independent protein mechanism. Do not transfer pheromone chemotropism or aerotaxis mechanisms without direct evidence. Defer causal graphs until native causal evidence and taxon-paired protein accessions support them; NONMECHANISTIC is not a grounding bypass.",
        "posed_by": "codex",
        "posed_date": "2026-10-04"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-04T17:35:43Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added polarity-neutral oxygen-gradient-directed growth under local chemotropism, supported by three primary DOI citations and source snippets. Ignored-and-hidden novelty searches and structured OWL review found no exact term. Reserved METPO:1055500 in v478 under the released phenotype parent. Recorded indexed abstract access limits, growth confounds and pending narrower METPO hierarchy; deferred canonical strains and causal graphs.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-04T17:43:50Z",
        "curator": "codex",
        "action": "EVIDENCE_CORRECTION",
        "changes": "Addressed #1676: replaced the margin-reorientation abstract quote with a contiguous oxygen-gradient passage so the definition snippet identifies the stimulus. Retained reorientation evidence, source-access limits and growth confounds in notes.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-04T18:01:14Z",
        "curator": "codex",
        "action": "REVIEW_CORRECTION",
        "changes": "Addressed #1678 and #1679: removed the two snippets obtained only from indexed publisher text. Prior history describes those now-withdrawn quotes, not directly verified source wording. Retained qualified DOI-backed interpretations in notes and the directly verified Damm snippet. Changed the definition genus to phenotype to match the released proposal parent, preserving the local chemotropism parent and pending hierarchy explanation.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-04T18:27:57Z",
        "curator": "codex",
        "action": "REVIEW_CORRECTION",
        "changes": "Addressed #1680 and #1681: moved unread Aoki and Carlile papers from counted evidence to qualified discussion leads. Replaced Aoki as definition authority with directly read Damm. Added directly retrieved Brand review with an exact full-sentence quote under its Attribution license; labeled its terminology role, not independent experimental replication. Negative direction remains unverified. Withdraws the prior histories' evidence-authority claims for the two unread papers; earlier events remain unchanged. No new snippet-baseline exceptions.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000646",
    "label": "aggrephagy",
    "definition": "An autophagy phenotype in which a microbial cell selectively degrades protein aggregates through macroautophagic delivery to lysosomal or vacuolar compartments.",
    "definition_source": "DOI:10.1080/15548627.2026.2724473",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000638"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1080/15548627.2026.2724473",
        "snippet": "Our findings indicate that heat shock triggers the targeted degradation of ubiquitinated protein aggregates, mediated by the macroaggrephagy receptor Cue5.",
        "notes": "PMID:42647820. Scientific abstract directly read in DOI-matched Europe PMC metadata, separately from Abbreviations. Supports selective macroautophagic aggregate degradation in Saccharomyces cerevisiae. In the same heat-stress context, Cct2 and polyQ-HTT vacuolar turnover is reported to be independent of canonical autophagy; that turnover is not positive aggrephagy evidence. Publisher full text returned HTTP 403; Methods, actual figures and strain provenance were not inspected."
      },
      {
        "reference": "DOI:10.1038/s44319-024-00275-7",
        "snippet": "Deficiency in this interaction significantly weakens the association of Cct2 with Atg8.",
        "notes": "PMID:39322741, PMC11549370. Scientific abstract and XML Introduction, Results Sec3-Sec7, Discussion Sec9 and yeast Methods Sec11 and Sec14-Sec16 were read. The quoted interaction is Atg11-Cct2. Yeast GFP-47Q cleavage and perturbations support solid-aggregate turnover; Ape1-P22L maturation alone is not complete cargo destruction. Synopsis S142 differs from scientific-abstract/Results S412; retain the discrepancy. Mammalian counterparts and phosphorylation sites are not interchangeable with yeast. Actual figures, supplements, Table EV1 and independent strain provenance were not inspected."
      },
      {
        "reference": "DOI:10.1016/j.cell.2014.05.048",
        "snippet": "We thus propose that CUET proteins play a critical and ancient role in autophagic clearance of cytotoxic protein aggregates.",
        "notes": "PMID:25042851. Scientific abstract directly read in DOI-matched Europe PMC metadata. Yeast Cue5/Rsp5 perturbations and polyQ responses are separate from human Tollip experiments; do not transfer human rescue to yeast or equate toxicity alone with flux. Full text, actual figures and strain provenance were not inspected. Linked Comment-in articles are not counted as independent primary evidence."
      },
      {
        "reference": "DOI:10.1080/27694127.2023.2236407",
        "snippet": "Interestingly, Cue5/Tollip, a known autophagy receptor for aggrephagy, is dispensable for this inclusion body autophagy.",
        "notes": "PMID:37680383, PMC10482306. Scientific abstract directly read in DOI-matched Europe PMC metadata. Boundary evidence: the authors distinguish Htt103QP/A-beta42 inclusion-body clearance in budding yeast as IBophagy. Do not relabel it an unqualified Cue5-dependent aggrephagy observation. Complete full text and actual figures were not inspected; XML returned HTTP 500 and publisher access returned HTTP 403."
      }
    ],
    "discussions": [
      {
        "discussion_id": "aggrephagy-scope-and-ibophagy",
        "prompt": "Review cargo boundaries and qualified process alignment.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Autophagy traitmech:000638 is the broader phenotype. Protein aggregation, disaggregation, proteasomal proteolysis, puncta, toxicity reduction or vacuolar localization alone is not selective macroautophagic degradation. GO:0035973, directly resolved at https://www.ebi.ac.uk/QuickGO/services/ontology/go/terms/GO%3A0035973, is a nonobsolete biological process for selective protein-aggregate degradation by macroautophagy, not an exact organismal phenotype. Retain that route qualifier and omit exact xrefs and synonyms. The 2023 study explicitly separates IBophagy from aggrephagy; do not infer an exact synonym, disjointness or a separate TraitRecord solely from its receptor differences. Their potential broader/narrower relationship needs human review. Proteaphagy traitmech:000645 concerns proteasomes as cargo, not ordinary aggregate proteolysis.",
        "posed_by": "codex",
        "posed_date": "2026-10-06"
      },
      {
        "discussion_id": "aggrephagy-context-exemplars-and-mechanisms",
        "prompt": "Resolve conditional mechanisms and natural exemplars.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Do not make Cue5, Cct2, Atg11, ubiquitination, heat shock or one aggregate reporter universal requirements. The 2026 autophagy-independent turnover result does not negate the 2024 nutrient-rich solid-aggrephagy assay. Keep experimental cargo, conditions and readouts distinct. Resolve the 2024 Synopsis/Results residue discrepancy and inspect actual panels before accession-level mechanism curation. Canonical examples remain unset pending independent natural-strain provenance; engineered cargo and reporter/deletion assays are not natural exemplars. A protein graph requires native taxon-paired accessions and functional evidence. Recombinant E. coli protein production is not an aggrephagy observation, and human disease outcomes are not microbial trait evidence.",
        "posed_by": "codex",
        "posed_date": "2026-10-06"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-06T16:23:31Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added selective macroautophagic protein-aggregate degradation with four DOI-backed scientific-abstract snippets and explicit IBophagy, conditional receptor and source-access limits. Ignored-and-hidden novelty checks, fresh seed and pinned METPO review found no exact record. Reserved METPO:1059900 in v522 using unchanged corrected parent context from v521. Deferred unverified natural exemplars, exact mappings and protein graphs.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000161",
    "label": "alanine arylamidase activity",
    "definition": "A physiological enzyme-activity phenotype in which a cell exhibits alanine arylamidase/alanyl aminopeptidase activity, releasing N-terminal residues from peptide, amide, or arylamide substrates with preference for alanine.",
    "definition_source": "https://iubmb.qmul.ac.uk/enzyme/EC3/4/11/2.html",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "synonyms": [
      {
        "synonym_text": "alanyl aminopeptidase",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://iubmb.qmul.ac.uk/enzyme/EC3/4/11/2.html"
      },
      {
        "synonym_text": "alanine aminopeptidase",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://iubmb.qmul.ac.uk/enzyme/EC3/4/11/2.html"
      },
      {
        "synonym_text": "L-alanine aminopeptidase",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://iubmb.qmul.ac.uk/enzyme/EC3/4/11/2.html"
      }
    ],
    "evidence": [
      {
        "reference": "https://iubmb.qmul.ac.uk/enzyme/EC3/4/11/2.html",
        "snippet": "<b>Reaction:</b> Release of an N-terminal amino acid, Xaa<img src=\"../../../EZgif/FISS.GIF\" align=top>Yaa- from a peptide, amide or arylamide. Xaa is preferably Ala, but may be most amino acids including Pro (slow action).",
        "notes": "The NC-IUBMB EC 3.4.11.2 entry accepts membrane alanyl aminopeptidase and places the scissile-bond FISS.GIF image between Xaa and Yaa in a reaction line that includes arylamide substrates and preferential N-terminal alanine."
      },
      {
        "reference": "DOI:10.1099/ijsem.0.006017",
        "snippet": "enzymatic activities are present for: \u03b1-galactosidase, N-acetyl-\u03b2-glucosaminidase, arginine arylamidase, proline arylamidase, leucyl glycine arylamidase, phenylalanine arylamidase, leucine arylamidase, tyrosine arylamidase, alanine arylamidase, glycine arylamidase, histidine arylamidase, glutamyl glutamic acid arylamidase, serine arylamidase, valine arylamidase, cysteine arylamidase, esterase, esterase lipase, alpha-chymotrypsin",
        "notes": "Srinivasan et al. listed alanine arylamidase among enzymatic activities present in the Amygdalobacter indicium species description, supporting the API arylamidase row as a bacterial enzyme-activity phenotype."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:3029272",
        "taxon_label": "Amygdalobacter indicium",
        "note": "Srinivasan et al. reported Amygdalobacter indicium as positive for alanine arylamidase activity in an enzyme activity panel.",
        "reference": "DOI:10.1099/ijsem.0.006017"
      }
    ],
    "discussions": [
      {
        "discussion_id": "alanine-arylamidase-activity-xref-gap",
        "prompt": "Resolve an exact external ontology class for alanine arylamidase activity before adding a TraitRecord xref.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "GO:0016285 alanyl aminopeptidase activity denotes the catalytic molecular function rather than the organism-level alanine arylamidase/alanyl aminopeptidase phenotype, so it is appropriate as a causal-node grounding for that enzyme activity and not as an equivalent TraitRecord xref.",
        "posed_by": "codex",
        "posed_date": "2026-09-12"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-12T07:32:57Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted alanine arylamidase activity as a URL/DOI-backed TraitRecord after a repository-wide duplicate review covering ignored and hidden files; METPO has no exact alanine arylamidase activity class yet.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000141",
    "label": "alkaline phosphatase activity",
    "definition": "A physiological enzyme-activity phenotype in which a cell produces active alkaline phosphatase enzymes that dephosphorylate phosphate-containing compounds.",
    "definition_source": "DOI:10.1128/JB.185.16.4983-4991.2003",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1128/JB.185.16.4983-4991.2003",
        "snippet": "leads to constitutive expression of a protein with alkaline phosphatase activity",
        "notes": "Kriakov et al. identified a Mycobacterium smegmatis phoA gene whose expression yields a protein with alkaline phosphatase activity."
      },
      {
        "reference": "DOI:10.1155/2021/8888641",
        "snippet": "According to the API ZYM assays, all three isolates were positive for alkaline phosphatase, leucine aryl amidase, acid phosphatase, and naphthol_AS_BI_phosphohydrolase.",
        "notes": "Mekonnen et al. treated alkaline phosphatase as an assayed bacterial exoenzyme phenotype in rapid urease-producing soil isolates."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1772",
        "taxon_label": "Mycobacterium smegmatis",
        "note": "Mycobacterium smegmatis carries phoA and can express alkaline phosphatase activity when the phosphate-uptake system is perturbed.",
        "reference": "DOI:10.1128/JB.185.16.4983-4991.2003"
      }
    ],
    "discussions": [
      {
        "discussion_id": "alkaline-phosphatase-activity-xref-gap",
        "prompt": "Resolve an exact external ontology class for alkaline phosphatase activity before adding a TraitRecord xref.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "GO:0004035 carries the same alkaline phosphatase activity label but denotes the enzyme molecular function rather than the organism-level phenotype, so it is appropriate as a causal-node grounding rather than an equivalent TraitRecord xref.",
        "posed_by": "codex",
        "posed_date": "2026-09-11"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-11T16:01:38Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted alkaline phosphatase activity as a DOI-backed TraitRecord after a repository-wide duplicate review covering ignored and hidden files; METPO has no exact alkaline phosphatase activity class yet.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000159",
    "label": "alpha-chymotrypsin activity",
    "definition": "A physiological enzyme-activity phenotype in which a cell exhibits chymotrypsin-like serine endopeptidase activity, preferentially cleaving peptide bonds on the carboxyl side of tyrosine, tryptophan, phenylalanine, or leucine residues.",
    "definition_source": "https://iubmb.qmul.ac.uk/enzyme/EC3/4/21/1.html",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "synonyms": [
      {
        "synonym_text": "alpha-chymotrypsin",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1099/ijsem.0.006017"
      }
    ],
    "evidence": [
      {
        "reference": "https://iubmb.qmul.ac.uk/enzyme/EC3/4/21/1.html",
        "snippet": "<b>Reaction:</b> Preferential cleavage: Tyr<img src=\"../../../EZgif/FISS.GIF\" align=top>, Trp<img src=\"../../../EZgif/FISS.GIF\" align=top>, Phe<img src=\"../../../EZgif/FISS.GIF\" align=top>, Leu<img src=\"../../../EZgif/FISS.GIF\" align=top>",
        "notes": "The NC-IUBMB EC 3.4.21.1 entry accepts the name chymotrypsin and its reaction line places the scissile-bond FISS.GIF image immediately after Tyr, Trp, Phe, and Leu."
      },
      {
        "reference": "DOI:10.1099/ijsem.0.006017",
        "snippet": "enzymatic activities are present for: \u03b1-galactosidase, N-acetyl-\u03b2-glucosaminidase, arginine arylamidase, proline arylamidase, leucyl glycine arylamidase, phenylalanine arylamidase, leucine arylamidase, tyrosine arylamidase, alanine arylamidase, glycine arylamidase, histidine arylamidase, glutamyl glutamic acid arylamidase, serine arylamidase, valine arylamidase, cysteine arylamidase, esterase, esterase lipase, alpha-chymotrypsin",
        "notes": "Srinivasan et al. listed alpha-chymotrypsin among enzymatic activities present in the Amygdalobacter indicium species description, consistent with the positive API ZYM table row for both assayed A. indicium strains."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:3029272",
        "taxon_label": "Amygdalobacter indicium",
        "note": "Srinivasan et al. reported Amygdalobacter indicium as positive for alpha-chymotrypsin activity in the API ZYM enzyme activity panel.",
        "reference": "DOI:10.1099/ijsem.0.006017"
      }
    ],
    "discussions": [
      {
        "discussion_id": "alpha-chymotrypsin-activity-xref-gap",
        "prompt": "Resolve an exact external ontology class for alpha-chymotrypsin activity before adding a TraitRecord xref.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "GO:0004263 chymotrypsin activity is obsolete, and its replacement GO:0004252 denotes broader serine-type endopeptidase molecular function rather than the organism-level chymotrypsin-like serine endopeptidase phenotype. GO:0004252 is appropriate as a causal-node grounding for generic serine-type endopeptidase activity, not as an equivalent TraitRecord xref.",
        "posed_by": "codex",
        "posed_date": "2026-09-12"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-12T05:29:03Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted alpha-chymotrypsin activity as a URL/DOI-backed TraitRecord after a repository-wide duplicate review covering ignored and hidden files; METPO has no exact alpha-chymotrypsin activity class yet.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-12T05:47:58Z",
        "curator": "codex",
        "action": "CORRECTED_EVIDENCE_SNIPPET",
        "changes": "Corrected the IUBMB reaction-line snippet for alpha-chymotrypsin activity so it preserves the scissile-bond image tags from the source HTML (#819).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-12T06:00:57Z",
        "curator": "codex",
        "action": "TIGHTENED_DEFINITION_WORDING",
        "changes": "Tightened the alpha-chymotrypsin activity definition to describe a chymotrypsin-like organismal phenotype instead of over-specifying production of the named vertebrate enzyme (#820).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000152",
    "label": "alpha-fucosidase activity",
    "definition": "A physiological enzyme-activity phenotype in which a cell produces active alpha-fucosidase enzymes that hydrolyze alpha-L-fucosides to L-fucose and an alcohol.",
    "definition_source": "https://iubmb.qmul.ac.uk/enzyme/EC3/2/1/51.html",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "https://iubmb.qmul.ac.uk/enzyme/EC3/2/1/51.html",
        "snippet": "Reaction: an \u03b1-L-fucoside + H2O = L-fucose + an alcohol",
        "notes": "The NC-IUBMB EC 3.2.1.51 entry defines alpha-L-fucosidase by its accepted name and hydrolytic reaction, grounding the enzyme activity named by the organism-level phenotype."
      },
      {
        "reference": "DOI:10.1128/jcm.22.3.333-335.1985",
        "snippet": "Positive reactions for alpha-glucosidase, beta-glucosidase, alpha-fucosidase, and alpha-glucuronidase suggest that \"B. forsythus\" may be saccharolytic.",
        "notes": "Tanner et al. detected alpha-fucosidase in the then-proposed oral species Bacteroides forsythus with the API ZYM enzyme activity panel."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:28112",
        "taxon_label": "Tannerella forsythia",
        "note": "Tanner et al. reported alpha-fucosidase-positive reactions for \"Bacteroides forsythus\", the basonym of Tannerella forsythia, in API ZYM profiles.",
        "reference": "DOI:10.1128/jcm.22.3.333-335.1985"
      }
    ],
    "discussions": [
      {
        "discussion_id": "alpha-fucosidase-activity-xref-gap",
        "prompt": "Resolve an exact external ontology class for alpha-fucosidase activity before adding a TraitRecord xref.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "GO:0004560 carries the alpha-L-fucosidase activity label but denotes the enzyme molecular function rather than the organism-level alpha-fucosidase production phenotype, so it is appropriate as a causal-node grounding rather than an equivalent TraitRecord xref.",
        "posed_by": "codex",
        "posed_date": "2026-09-12"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-12T01:09:57Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted alpha-fucosidase activity as a URL/DOI-backed TraitRecord after a repository-wide duplicate review covering ignored and hidden files; METPO has no exact alpha-fucosidase activity class yet.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000149",
    "label": "alpha-galactosidase activity",
    "definition": "A physiological enzyme-activity phenotype in which a cell produces active alpha-galactosidase enzymes that hydrolyze alpha-1,6-linked galactose residues in oligosaccharides and polymeric galactomannans.",
    "definition_source": "DOI:10.3109/07388551.2013.794124",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.3109/07388551.2013.794124",
        "snippet": "The enzyme \u03b1-galactosidase (\u03b1-D-galactoside galactohydrolase; EC 3.2.1.22) catalyzes the hydrolysis of \u03b1-1,6-linked galactose residues in oligosaccharides and polymeric galactomannan.",
        "notes": "Katrolia et al. define alpha-galactosidase as EC 3.2.1.22, an enzyme that hydrolyzes alpha-1,6-linked galactose residues, grounding the enzyme activity named by the organism-level phenotype."
      },
      {
        "reference": "DOI:10.1128/jcm.22.3.333-335.1985",
        "snippet": "Selenomonas sputigena was positive for \u03b1-galactosidase, \u03b2-galactosidase, and \u03b1-glucosidase (API ZYM strip) and for \u03b1-glucosidase, \u03b2-glucosidase, and \u03b1-galactosidase (API An-Ident strip).",
        "notes": "Tanner et al. detected alpha-galactosidase in Selenomonas sputigena with the API ZYM enzyme activity panel and the API An-Ident strip."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:69823",
        "taxon_label": "Selenomonas sputigena",
        "note": "Tanner et al. reported Selenomonas sputigena as positive for alpha-galactosidase in API ZYM and API An-Ident enzyme activity panels.",
        "reference": "DOI:10.1128/jcm.22.3.333-335.1985"
      }
    ],
    "discussions": [
      {
        "discussion_id": "alpha-galactosidase-activity-xref-gap",
        "prompt": "Resolve an exact external ontology class for alpha-galactosidase activity before adding a TraitRecord xref.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "GO:0004557 denotes the alpha-galactosidase/melibiase molecular function rather than the organism-level alpha-galactosidase production phenotype, so it is appropriate as a causal-node grounding rather than an equivalent TraitRecord xref.",
        "posed_by": "codex",
        "posed_date": "2026-09-11"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-11T23:46:20Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted alpha-galactosidase activity as a DOI-backed TraitRecord after a repository-wide duplicate review covering ignored and hidden files; METPO has no exact alpha-galactosidase activity class yet.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000145",
    "label": "alpha-glucosidase activity",
    "definition": "A physiological enzyme-activity phenotype in which a cell produces active alpha-glucosidase enzymes that hydrolyze alpha-glucosidic bonds in alpha-D-glucosides.",
    "definition_source": "DOI:10.1371/journal.pone.0322500",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1371/journal.pone.0322500",
        "snippet": "Enzyme activities of acid- and alkaline-phosphatases, esterase, esterase lipase, leucine arylamidase, trypsin, naphthol-AS-BI phosphohydrolase, and alpha-glucosidase are present when assayed with API ZYM system.",
        "notes": "Park et al. treated alpha-glucosidase as a positive API ZYM enzyme-activity phenotype in the Flexibacterium corallicola type species description."
      },
      {
        "reference": "DOI:10.3390/microorganisms13092005",
        "snippet": "alkaline phosphatase, esterase (C4), lipoid esterase (C8), lipase (C14), leucine arylamines, valine arylamines, cystine arylaminase, pancreatic coagulase, acid phosphatase, naphthol-AS-BI-phosphohydrolase, alpha-glucosidase, and N-acetyl-glucosaminidase were positive",
        "notes": "Zhang and Liu detected alpha-glucosidase in Microbulbifer weihaiensis SDUM041083T with the API ZYM enzyme activity panel."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:3037259",
        "taxon_label": "Flexibacterium corallicola",
        "note": "Park et al. reported Flexibacterium corallicola as positive for alpha-glucosidase in the API ZYM enzyme activity panel.",
        "reference": "DOI:10.1371/journal.pone.0322500"
      }
    ],
    "discussions": [
      {
        "discussion_id": "alpha-glucosidase-activity-xref-gap",
        "prompt": "Resolve an exact external ontology class for alpha-glucosidase activity before adding a TraitRecord xref.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "GO:0090599 carries the same alpha-glucosidase activity label but denotes the enzyme molecular function rather than the organism-level alpha-glucosidase production phenotype, so it is appropriate as a causal-node grounding rather than an equivalent TraitRecord xref.",
        "posed_by": "codex",
        "posed_date": "2026-09-11"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-11T17:22:13Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted alpha-glucosidase activity as a DOI-backed TraitRecord after a repository-wide duplicate review covering ignored and hidden files; METPO has no exact alpha-glucosidase activity class yet.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000150",
    "label": "alpha-mannosidase activity",
    "definition": "A physiological enzyme-activity phenotype in which a cell produces active alpha-mannosidase enzymes that hydrolyze terminal, non-reducing alpha-D-mannose residues in alpha-D-mannosides.",
    "definition_source": "https://iubmb.qmul.ac.uk/enzyme/EC3/2/1/24.html",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "https://iubmb.qmul.ac.uk/enzyme/EC3/2/1/24.html",
        "snippet": "Reaction: Hydrolysis of terminal, non-reducing \u03b1-D-mannose residues in \u03b1-D-mannosides",
        "notes": "The NC-IUBMB EC 3.2.1.24 entry defines alpha-mannosidase by its accepted name and hydrolytic reaction, grounding the enzyme activity named by the organism-level phenotype."
      },
      {
        "reference": "DOI:10.1128/jcm.32.3.854-855.1994",
        "snippet": "Practically all A. haemolyticum strains (138 of 139) and the Listeria monocytogenes type strain were alpha-mannosidase positive",
        "notes": "Carlson and Kontiainen detected alpha-mannosidase in nearly all tested Arcanobacterium haemolyticum strains with a 4-h alpha-mannosidase assay."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:28264",
        "taxon_label": "Arcanobacterium haemolyticum",
        "note": "Carlson and Kontiainen reported 138 of 139 Arcanobacterium haemolyticum strains as alpha-mannosidase positive in a 4-h test.",
        "reference": "DOI:10.1128/jcm.32.3.854-855.1994"
      }
    ],
    "discussions": [
      {
        "discussion_id": "alpha-mannosidase-activity-xref-gap",
        "prompt": "Resolve an exact external ontology class for alpha-mannosidase activity before adding a TraitRecord xref.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "GO:0004559 carries the same alpha-mannosidase activity label but denotes the enzyme molecular function rather than the organism-level alpha-mannosidase production phenotype, so it is appropriate as a causal-node grounding rather than an equivalent TraitRecord xref.",
        "posed_by": "codex",
        "posed_date": "2026-09-12"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-12T00:19:23Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted alpha-mannosidase activity as a URL/DOI-backed TraitRecord after a repository-wide duplicate review covering ignored and hidden files; METPO has no exact alpha-mannosidase activity class yet.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000162",
    "label": "amylase activity",
    "definition": "A physiological enzyme-activity phenotype in which a cell produces active amylolytic enzymes that hydrolyze starch.",
    "definition_source": "DOI:10.3389/fbioe.2020.00871",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "synonyms": [
      {
        "synonym_text": "amylolytic enzymes",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.3389/fbioe.2020.00871"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.3389/fbioe.2020.00871",
        "snippet": "All enzymes capable of degrading starch are collectively indicated as amylolytic enzymes.",
        "notes": "Sidar et al. frame amylolytic enzymes as starch-degrading enzymes, grounding the organism-level phenotype as active amylase production rather than starch catabolism itself."
      },
      {
        "reference": "DOI:10.1007/s00018-023-04812-w",
        "snippet": "the Bacteroides ovatus (Bo) extracellular \u03b1-amylase, BoGH13ASus",
        "notes": "Brown et al. characterized BoGH13A_Sus as a Bacteroides ovatus extracellular alpha-amylase in a starch utilization system, supporting B. ovatus as a source-backed amylase activity example."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:28116",
        "taxon_label": "Bacteroides ovatus",
        "note": "Brown et al. characterized the extracellular alpha-amylase BoGH13A_Sus from the Bacteroides ovatus starch utilization system.",
        "reference": "DOI:10.1007/s00018-023-04812-w"
      }
    ],
    "discussions": [
      {
        "discussion_id": "amylase-activity-xref-gap",
        "prompt": "Resolve an exact external ontology class for amylase activity before adding a TraitRecord xref.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "GO:0016160 carries the same amylase activity label but denotes the enzyme molecular function rather than the organism-level amylolytic enzyme production phenotype, so it is appropriate as a causal-node grounding rather than an equivalent TraitRecord xref.",
        "posed_by": "codex",
        "posed_date": "2026-09-12"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-12T08:08:43Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted amylase activity as a DOI-backed TraitRecord after a repository-wide duplicate review covering ignored and hidden files; METPO has no exact amylase activity class yet.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000620",
    "label": "anisogamy",
    "definition": "A sexual-reproduction phenotype in which the fusing gametes belong to two types that differ in size, with smaller male and larger female gametes.",
    "definition_source": "DOI:10.1038/s42003-018-0019-5",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/s42003-018-0019-5",
        "snippet": "Male and female gametes differing in size\u2014anisogamy\u2014emerged independently from isogamous ancestors in various eukaryotic lineages",
        "notes": "Hamaji et al. (2018), PMID:30271904, PMC6123790. Exact opening scientific-abstract clause checked in raw XML, not the separate editorial summary. Size dimorphism defines the phenotype; evolutionary origin is not part of this definition. Main text, Methods and captions were read and actual Figure 3 inspected: Eudorina gametes provide independent phenotype observations. Comparative MT architecture and RT-PCR expression do not demonstrate a gamete-size causal pathway. Results associate genomes with NIES-4100/4018, whereas Methods name NIES-3985/3984 for sequencing and the former sibling strains for other experiments. This unresolved discrepancy prevents strain-to-assembly inference here. Other actual figures and supplements remain unread."
      },
      {
        "reference": "DOI:10.1186/1471-2148-14-37",
        "snippet": "Obligately anisogamous conjugation between male and female motile gametes occurred outside the female colony (external fertilization during anisogamy).",
        "notes": "Nozaki et al. (2014), PMID:24589311, PMC4015742. Exact scientific-abstract Results sentence verified in raw XML. Main text and captions, actual Figure 3, and Additional file 2 Information S1/Table S1 were inspected. Sexual reproduction was observed in C. charkowiensis, not C. angeleri. Male length was 5-10 micrometers; female diameter 13-17 micrometers. These different measurements do not establish a volume ratio. Other actual figures, Additional file 1 and the remainder of Additional file 2 remain uninspected. Proposed evolutionary intermediacy is not demonstrated ancestry."
      },
      {
        "reference": "DOI:10.1186/s12915-024-01878-1",
        "snippet": "Oogamy constitutes a specialized form of anisogamy wherein small male gametes are motile and large female gametes are not",
        "notes": "Lindsey et al. (2024), PMID:38600528, PMC11007952. Exact Background Sec1 clause before the parenthetical, checked in raw XML and publisher HTML. This supports broad terminology including oogamy, not a new gamete-fusion experiment. The scientific abstract and this scope paragraph were inspected; remaining analyses, actual figures and supplements were not audited. The quoted motility formulation is not imposed on all microbial anisogamy."
      },
      {
        "reference": "DOI:10.1371/journal.pone.0181413",
        "snippet": "physiological and behavioural anisogamy of more or less equal size gametes, each with sex-specific behaviour and morphology",
        "notes": "Kaczmarska et al. (2017), Discussion > Sexual reproduction and life history. This exact contiguous clause was checked in publisher HTML and manuscript XML. It documents alternative diatom terminology, not evidence that equal-sized gametes satisfy this record's size-dimorphism definition. That Discussion passage and the opening live-cell Results paragraphs were inspected; the latter describe sex-dependent motility. Remaining Results, actual figures, tables and supplements were not audited. No diatom canonical example or size measurement is inferred."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:51706",
        "taxon_label": "Colemanosphaera charkowiensis",
        "reference": "DOI:10.1186/1471-2148-14-37",
        "note": "Source-observed reference example, not a claim about every strain. Figure 3 shows mixed 2013-0615-IC-3/4/7 cultures and male 2010-0713-E5; mating generally occurred after two days in nitrogen-deficient medium. Table S1 traces IC-3/4/7 to a natural water sample near Lake Isanuma. Collection provenance was checked at https://mcc.nbrp.jp/strainList.do?strainNumber=NIES-3388 (IC-7), https://mcc.nbrp.jp/strainList.do?strainNumber=NIES-3386 (IC-3) and https://mcc.nbrp.jp/strainList.do?strainNumber=NIES-3387 (IC-4). IC-3/4 collection and isolation dates conflict; no date is silently corrected. IC-7's 2018 axenic status is not projected onto 2014. Taxon label verified at https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=51706 on 2026-10-05. Collection fields support provenance, not independent experimental replication."
      }
    ],
    "discussions": [
      {
        "discussion_id": "anisogamy-scope-and-hierarchy",
        "prompt": "Preserve broad size-dimorphism scope and distinguish motility conventions.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Use anisogamy in the broad size-dimorphism sense, including oogamy, as explicitly stated by Lindsey et al. (2024). Nozaki et al. (2014) instead distinguish anisogamy with flagellated female gametes from oogamy in their four-type classification. This is a terminology difference, not evidence that the phenotypes are disjoint. Motility of both gametes and external fertilization describe the canonical example, not universal requirements. The definition compares gamete types, not incidental size variation within a type, vegetative-versus-gamete size, or mating compatibility. Isogamy traitmech:000619, unisexual reproduction traitmech:000613 and fungal mating systems traitmech:000615 through traitmech:000618 describe distinct scopes. No numerical threshold or organism-level disjointness is asserted. Use phenotype METPO:1000059 pending a narrower reproductive-phenotype hierarchy; PHYSIOLOGY is a filesystem category. Oogamy traitmech:000621 now supplies the size-dimorphic child with large nonmotile female gametes. Its evidence explicitly preserves nonmotile male exceptions rather than imposing a universal motility convention. Verify lexical/external mappings and a narrower reproductive parent before adding them. Kaczmarska et al. (2017), DOI:10.1371/journal.pone.0181413, also use physiological/behavioural anisogamy for approximately equal-sized gametes in diatoms. That usage is not equivalent to the size-based sense selected here: behavioural or physiological differences alone do not establish gamete-type size dimorphism. Do not map that usage as an exact synonym or infer organism-level disjointness; its relationship needs separate scope review.",
        "posed_by": "codex",
        "posed_date": "2026-10-05"
      },
      {
        "discussion_id": "anisogamy-mechanism-and-provenance",
        "prompt": "Resolve size-control mechanisms and strain discrepancies before extension.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "The observed gamete phenotype is not a literal MID locus, a sequence profile, an expanded mating-type region, or an expression signature. Comparative genomic associations and the proposed evolutionary role of MID do not justify causal edges for size dimorphism. Resolve native protein accessions and perturbation evidence before a causal graph; no NONMECHANISTIC graph bypasses this gap. Keep the 2018 Results/Methods strain mismatch unresolved until primary metadata reconciles it. Collection date conflicts do not invalidate the directly observed 2014 phenotype, but constrain strain-history claims. A collection's blank mutation field is not proof of an unmutated genome. Read remaining source material before quantitative or evolutionary extensions; preserve actual abstract-resolver verdicts separately from manual full-text checks.",
        "posed_by": "codex",
        "posed_date": "2026-10-05"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-05T12:52:28Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added anisogamy with three DOI-backed sources and verbatim snippets, broad size-dimorphism scope, and a provenance-qualified canonical Colemanosphaera charkowiensis example. Ignored-and-hidden novelty and allocation searches found no exact record or collision. Reserved METPO:1057400 in v497 under phenotype. Retained motility conventions and strain discrepancies explicitly; deferred lexical mappings, a narrower parent and unproven causal mechanisms.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-05T13:15:22Z",
        "curator": "codex",
        "action": "QUALIFIED_TRAIT_SCOPE",
        "changes": "Addressed #1711 by citing directly inspected diatom terminology and distinguishing behavioural/physiological anisogamy from the selected size-based sense. Added a verbatim scope snippet and inspection limits; preserved definition, canonical example and unresolved mechanism/hierarchy questions.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-05T14:12:03Z",
        "curator": "codex",
        "action": "LINKED_NARROWER_TRAIT",
        "changes": "Replaced the future oogamy-child TODO with traitmech:000621 and its qualified motility scope. Preserved the broad size-based definition, evidence, canonical example, parent and remaining open mapping questions.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000088",
    "label": "antibiotic resistance",
    "definition": "A physiological capacity to grow in the presence of antibiotic concentrations that inhibit susceptible cells, mediated by efflux, target modification, drug inactivation, or reduced permeability.",
    "definition_source": "DOI:10.1038/nrmicro3380",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "synonyms": [
      {
        "synonym_text": "antimicrobial resistance",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1038/nrmicro3380"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/nrmicro3380",
        "notes": "Blair et al. review the molecular mechanisms of antibiotic resistance (efflux, target alteration, drug inactivation, reduced uptake)."
      },
      {
        "reference": "DOI:10.1038/s41579-022-00820-y",
        "notes": "Updated review revisits molecular mechanisms of antibiotic resistance."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1280",
        "taxon_label": "Staphylococcus aureus",
        "note": "Iconic antibiotic-resistance organism (MRSA; methicillin/multidrug resistance).",
        "reference": "DOI:10.1016/S0140-6736(00)04403-2"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "antibiotic_resistance_mechanisms",
        "title": "Mechanisms of antibiotic resistance",
        "description": "Evidence-backed causal sketch linking resistance determinants (efflux, target modification, drug inactivation) to growth under antibiotic exposure.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "This is a cross-mechanism graph, not a claim that every resistant strain carries every determinant. The S. aureus PC1 BlaZ example supports the beta-lactamase branch; efflux, porin, and QRDR branches remain antibiotic- and lineage-specific.",
        "nodes": [
          {
            "node_id": "antibiotic_resistance_trait",
            "label": "antibiotic resistance",
            "node_type": "TRAIT",
            "grounding": "traitmech:000088",
            "description": "Capacity to grow despite inhibitory antibiotic concentrations."
          },
          {
            "node_id": "efflux_pump",
            "label": "drug efflux pump",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Transporter that expels antibiotics from the cell.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Drug efflux is performed by multiple unrelated transporter superfamilies; the graph does not identify one pump family, substrate range, or taxon."
          },
          {
            "node_id": "antibiotic_response_process",
            "label": "response to antibiotic",
            "node_type": "BIOLOGICAL_PROCESS",
            "grounding": "GO:0046677",
            "description": "Cellular response conferring survival under antibiotic exposure."
          },
          {
            "node_id": "intracellular_antibiotic_concentration",
            "label": "intracellular antibiotic concentration",
            "node_type": "CHEMICAL",
            "description": "Concentration of antibiotic accumulated inside the cell."
          },
          {
            "node_id": "outer_membrane_porin",
            "label": "outer membrane porin",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Outer-membrane channel mediating antibiotic influx; loss/modification reduces permeability.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "This mechanism spans several non-equivalent porin families and resistance-associated loss or modification events, so no single family term exactly represents the node."
          },
          {
            "node_id": "antibiotic_influx",
            "label": "antibiotic influx",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Uptake of antibiotic across the cell envelope."
          },
          {
            "node_id": "beta_lactamase",
            "label": "beta-lactamase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Enzyme that hydrolyzes the beta-lactam ring, inactivating beta-lactam antibiotics.",
            "grounding": "GO:0008800",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:P00807",
                "protein_label": "Beta-lactamase",
                "gene_symbol": "blaZ",
                "taxon_id": "NCBITaxon:1280",
                "taxon_label": "Staphylococcus aureus",
                "entry_status": "REVIEWED",
                "retrieved_on": "2026-10-22",
                "entry_version": 172,
                "sequence_version": 1,
                "role": "Experimentally sequenced PC1 penicillinase/BlaZ that hydrolyzes beta-lactam antibiotics; it exemplifies the drug-inactivation branch rather than all antibiotic resistance in S. aureus.",
                "evidence": [
                  {
                    "reference": "DOI:10.1042/bj1510197",
                    "snippet": "The amino acid sequence of the penicillinase from Staphylococcus aureus strain PC1 was determined.",
                    "notes": "The primary biochemical sequence study identifies the single-chain PC1 beta-lactamase represented by reviewed UniProtKB P00807."
                  }
                ]
              }
            ]
          },
          {
            "node_id": "beta_lactam_antibiotic",
            "label": "beta-lactam antibiotic",
            "node_type": "CHEMICAL",
            "description": "Antibiotic class containing a beta-lactam ring.",
            "grounding": "CHEBI:27933"
          },
          {
            "node_id": "qrdr_mutation",
            "label": "QRDR mutation in DNA gyrase/topoisomerase IV",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Quinolone resistance-determining region mutation altering the fluoroquinolone target.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "This composite variant node can denote mutations in distinct GyrA, GyrB, ParC, or ParE targets; a protein-family grounding would erase the mutation and target-subunit distinction."
          },
          {
            "node_id": "fluoroquinolone",
            "label": "fluoroquinolone",
            "node_type": "CHEMICAL",
            "description": "Fluoroquinolone class antibiotic targeting DNA gyrase/topoisomerase IV."
          },
          {
            "node_id": "rrna_methylation_23s",
            "label": "23S rRNA methylation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Methylation of 23S rRNA that modifies the ribosomal antibiotic-binding site."
          },
          {
            "node_id": "macrolide_antibiotic",
            "label": "macrolide antibiotic",
            "node_type": "CHEMICAL",
            "description": "Macrolide class antibiotic binding the 23S rRNA of the large ribosomal subunit.",
            "grounding": "CHEBI:25105"
          }
        ],
        "edges": [
          {
            "subject": "efflux_pump",
            "predicate": "confers",
            "object": "antibiotic_resistance_trait",
            "description": "Drug efflux is one determinant enabling resistance.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro3380",
                "notes": "Blair et al. review efflux among resistance mechanisms."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "antibiotic_resistance_trait",
            "predicate": "participates in",
            "object": "antibiotic_response_process",
            "description": "Resistance is part of the cellular response to antibiotics.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41579-022-00820-y",
                "notes": "Updated review of antibiotic-resistance mechanisms."
              }
            ],
            "predicate_id": "biolink:participates_in"
          },
          {
            "subject": "efflux_pump",
            "predicate": "decreases",
            "object": "intracellular_antibiotic_concentration",
            "description": "Efflux pump overexpression lowers intracellular antibiotic concentration, producing resistance phenotypes.",
            "evidence": [
              {
                "reference": "DOI:10.3390/pharmaceutics16020170",
                "notes": "Efflux pumps reduce intracellular antibiotic concentrations; upregulation under antibiotic exposure produces resistance phenotypes (broad across Gram-positive/negative)."
              }
            ],
            "predicate_id": "RO:0002212"
          },
          {
            "subject": "outer_membrane_porin",
            "predicate": "decreases",
            "object": "antibiotic_influx",
            "description": "Porin loss/modification reduces antibiotic influx, a major resistance mechanism.",
            "evidence": [
              {
                "reference": "DOI:10.3390/pharmaceutics16020170",
                "notes": "Reduced permeability/porin loss and modification of outer membrane porin channels listed as major resistance mechanisms."
              }
            ],
            "predicate_id": "RO:0002212"
          },
          {
            "subject": "beta_lactamase",
            "predicate": "hydrolyzes",
            "object": "beta_lactam_antibiotic",
            "description": "Beta-lactamases hydrolyze the beta-lactam ring, inactivating the drug.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s43856-024-00591-y",
                "notes": "Drug hydrolysis by beta-lactamases; beta-lactamases hydrolyze the beta-lactam ring. Strong canonical mechanism."
              }
            ],
            "predicate_id": "METPO:2007808"
          },
          {
            "subject": "qrdr_mutation",
            "predicate": "confers resistance to",
            "object": "fluoroquinolone",
            "description": "QRDR mutations in DNA gyrase/topoisomerase IV confer fluoroquinolone resistance (class-level edge).",
            "evidence": [
              {
                "reference": "DOI:10.3389/fphar.2024.1444781",
                "notes": "QRDR mutations in DNA gyrase and topoisomerase IV cause quinolone/fluoroquinolone resistance."
              }
            ]
          },
          {
            "subject": "rrna_methylation_23s",
            "predicate": "decreases binding of",
            "object": "macrolide_antibiotic",
            "description": "23S rRNA methylation modifies the ribosomal target, decreasing macrolide binding and conferring resistance.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fphar.2024.1444781",
                "notes": "Methylation of 23S rRNA confers linezolid, chloramphenicol, clindamycin, and macrolide resistance."
              }
            ]
          },
          {
            "subject": "antibiotic_influx",
            "predicate": "increases",
            "object": "intracellular_antibiotic_concentration",
            "description": "Porin-mediated antibiotic influx raises the intracellular drug concentration available to reach bacterial targets.",
            "evidence": [
              {
                "reference": "DOI:10.1371/journal.pone.0005453",
                "snippet": "efficient influx through porins for \u03b2-lactams to reach their target sites",
                "notes": "Verified against the open PLOS ONE primary article."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "beta_lactamase",
            "predicate": "confers",
            "object": "antibiotic_resistance_trait",
            "description": "Beta-lactamase-mediated drug hydrolysis confers resistance to beta-lactam antibiotics.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.jbc.2021.100799",
                "snippet": "\u03b2-lactamase, which inactivates the drug by hydrolysis",
                "notes": "Verified against the public Journal of Biological Chemistry primary article."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "qrdr_mutation",
            "predicate": "confers",
            "object": "antibiotic_resistance_trait",
            "description": "Resistance-associated QRDR mutations alter fluoroquinolone targets and confer the antibiotic-resistance phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s13756-020-00793-8",
                "snippet": "gyrA as the main mutated gene associated with conferring fluoroquinolone resistance",
                "notes": "Verified against the open primary evolution experiment."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "rrna_methylation_23s",
            "predicate": "confers",
            "object": "antibiotic_resistance_trait",
            "description": "Methylation of the 23S rRNA drug-binding region confers macrolide resistance.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mbio.02665-19",
                "snippet": "increased methylation of G748 in 23S rRNA and thereby conferring resistance to this antibiotic",
                "notes": "Verified against the open mBio primary article."
              }
            ],
            "predicate_id": "METPO:2007700"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-06-04T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate PHYSIOLOGY trait (antibiotic resistance) from literature research. Distinct from persister-cell tolerance (non-genetic).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-08T13:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (resistance mechanisms) with GO node grounding and RO/biolink predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-14T06:38:15Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A3RNR9\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 5 evidence-backed generic edges (9 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:14Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002212\u00d72).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:34Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:27933\u00d71, CHEBI:25105\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:39Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000013\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-26T07:15:20Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A024EG85\u00d71, UniProtKB:A0A059L9H0\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:21:12Z",
        "curator": "claude",
        "action": "RETRACT_DEAD_UNIPROT_GROUNDINGS",
        "changes": "Retracted 3 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:23:55Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0008800\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 1 causal edge(s) off enables/RO:0002327 with a TRAIT object (1 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T02:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES_PART2",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates onto their causal-graph counterparts (1 to hydrolyzes), issue 301 part 2. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Each replacement is a 1:1 mirror of its source predicate that changes only the domain, so the claim each edge makes is unchanged and directions are unchanged. The replacements are proposed in proposals/metpo_traitmech_v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-24T11:00:00Z",
        "curator": "codex",
        "action": "CURATE_PROTEIN_TAXON_EXAMPLE",
        "changes": "Reviewed the mechanism scope and all protein nodes, converted the canonical S. aureus citation to DOI, and added the reviewed PC1 BlaZ protein example with primary biochemical evidence.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T11:15:00Z",
        "curator": "codex",
        "action": "CONNECT_CAUSAL_GRAPH_COMPONENTS",
        "changes": "Resolved issue #183 graph fragmentation (5 components to 1) with 4 public-source, verbatim-snippet-backed connector(s). No paid research service was called.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-22T01:35:00Z",
        "curator": "claude",
        "action": "REFRESH_UNIPROT_ENTRY_VERSION",
        "changes": "Refreshed UniProtKB entry_version against live UniProt REST on 2026-10-22: UniProtKB:P00807 (171 -> 172 on beta_lactamase).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000167",
    "label": "arginine arylamidase activity",
    "definition": "A physiological enzyme-activity phenotype in which a cell exhibits arginine arylamidase/arginyl aminopeptidase activity, releasing N-terminal arginine or lysine residues from peptides or hydrolyzing arginine and lysine arylamides.",
    "definition_source": "https://iubmb.qmul.ac.uk/enzyme/EC3/4/11/6.html",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "synonyms": [
      {
        "synonym_text": "L-arginine arylamidase",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.3389/fgene.2023.1240581"
      },
      {
        "synonym_text": "aminopeptidase B",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://iubmb.qmul.ac.uk/enzyme/EC3/4/11/6.html"
      },
      {
        "synonym_text": "arginine aminopeptidase",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://iubmb.qmul.ac.uk/enzyme/EC3/4/11/6.html"
      },
      {
        "synonym_text": "arginyl aminopeptidase",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://iubmb.qmul.ac.uk/enzyme/EC3/4/11/6.html"
      },
      {
        "synonym_text": "L-arginine aminopeptidase",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://iubmb.qmul.ac.uk/enzyme/EC3/4/11/6.html"
      }
    ],
    "evidence": [
      {
        "reference": "https://iubmb.qmul.ac.uk/enzyme/EC3/4/11/6.html",
        "snippet": "<b>Reaction:</b> Release of N-terminal Arg and Lys from oligopeptides when P1' is not Pro. Also acts on arylamides of Arg and Lys",
        "notes": "The NC-IUBMB EC 3.4.11.6 entry accepts aminopeptidase B, records arginine aminopeptidase, arginyl aminopeptidase, and L-arginine aminopeptidase as other names, and includes arginine and lysine arylamides in the reaction scope."
      },
      {
        "reference": "DOI:10.3389/fgene.2023.1240581",
        "snippet": "Both of these strains exhibit positive results for oxidase, gamma-glutamyl transferase, alkaline phosphatase, pyrrolidonyl arylamidase, L-arginine arylamidase, and L-aspartate arylamidase",
        "notes": "Wang et al. reported both Helicobacter zhangjianzhongii isolates as positive for L-arginine arylamidase in the formal species description."
      },
      {
        "reference": "DOI:10.1099/ijsem.0.006017",
        "snippet": "arginine arylamidase, proline arylamidase, leucyl glycine arylamidase, phenylalanine arylamidase, leucine arylamidase, tyrosine arylamidase, alanine arylamidase, glycine arylamidase, histidine arylamidase",
        "notes": "Srinivasan et al. listed arginine arylamidase among enzymatic activities present in the Amygdalobacter indicium species description, supporting the API arylamidase row as a directly assayed bacterial enzyme-activity phenotype."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:2974574",
        "taxon_label": "Helicobacter zhangjianzhongii",
        "note": "Wang et al. reported both Helicobacter zhangjianzhongii isolates as positive for L-arginine arylamidase in the formal species description.",
        "reference": "DOI:10.3389/fgene.2023.1240581"
      }
    ],
    "discussions": [
      {
        "discussion_id": "arginine-arylamidase-activity-xref-gap",
        "prompt": "Resolve an exact external ontology class for arginine arylamidase activity before adding a TraitRecord xref.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "GO:0004177 denotes broad aminopeptidase molecular function, and EC 3.4.11.6 denotes the aminopeptidase B/arginyl aminopeptidase molecular function rather than the organism-level arginine arylamidase assay phenotype. Both remain causal-node grounding leads rather than equivalent TraitRecord xrefs.",
        "posed_by": "codex",
        "posed_date": "2026-09-12"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-12T11:40:11Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted arginine arylamidase activity as a URL/DOI-backed TraitRecord after a repository-wide duplicate review covering ignored and hidden files; METPO has no exact arginine arylamidase activity class yet and the placeholder is reserved in proposals/metpo_traitmech_v44.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000164",
    "label": "arginine dihydrolase activity",
    "definition": "A physiological pathway-activity phenotype in which a cell converts L-arginine through the arginine deiminase pathway to generate ATP.",
    "definition_source": "DOI:10.1128/aem.07724-11",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "synonyms": [
      {
        "synonym_text": "arginine deiminase pathway activity",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1016/j.resmic.2012.11.004"
      },
      {
        "synonym_text": "ADI pathway activity",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1016/j.resmic.2012.11.004"
      },
      {
        "synonym_text": "arginine dihydrolase",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://iubmb.qmul.ac.uk/enzyme/EC3/5/3/6.html"
      },
      {
        "synonym_text": "arginine deiminase",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://iubmb.qmul.ac.uk/enzyme/EC3/5/3/6.html"
      }
    ],
    "evidence": [
      {
        "reference": "https://iubmb.qmul.ac.uk/enzyme/EC3/5/3/6.html",
        "snippet": "<b>Reaction:</b> <small>L</small>-arginine + H<small><sub>2</sub></small>O = <small>L</small>-citrulline + NH<small><sub>3</sub></small>",
        "notes": "The NC-IUBMB EC 3.5.3.6 entry grounds the first arginine-deiminase step of the arginine deiminase pathway and records arginine dihydrolase as another name for that molecular function."
      },
      {
        "reference": "DOI:10.1016/j.fm.2010.11.016",
        "snippet": "Arginine conversion through the ADI pathway, which was activated from the stationary growth phase on, resulted in the production of both citrulline and ornithine for all pH conditions tested.",
        "notes": "Rimaux et al. directly assayed pH-dependent L-arginine conversion through the ADI pathway in Lactobacillus sakei CTC 494."
      },
      {
        "reference": "DOI:10.1128/aem.07724-11",
        "snippet": "For instance, the ability to utilize arginine through the arginine deiminase (ADI) pathway, resulting in additional ATP, represents a competitive benefit.",
        "notes": "Rimaux et al. frame arginine utilization through the ADI pathway as an ATP-yielding metabolic capability and show that arc gene expression is strain- and pH-dependent in Lactobacillus sakei."
      },
      {
        "reference": "DOI:10.1016/j.resmic.2012.11.004",
        "snippet": "Arginine conversion through the arginine deiminase (ADI) pathway is a common metabolic trait of Lactobacillus sakei which is ascribed to an arc operon and which inquisitively involves citrulline excretion and re-uptake.",
        "notes": "Rimaux et al. use the pathway-activity phrasing while studying the transporter coupled to citrulline and ornithine exchange during L. sakei ADI pathway activity."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1599",
        "taxon_label": "Latilactobacillus sakei",
        "note": "Rimaux et al. assayed arginine conversion through the ADI pathway in Lactobacillus sakei CTC 494 and observed citrulline and ornithine production across the tested pH series.",
        "reference": "DOI:10.1016/j.fm.2010.11.016"
      }
    ],
    "discussions": [
      {
        "discussion_id": "arginine-dihydrolase-activity-xref-gap",
        "prompt": "Resolve exact external ontology mappings for arginine dihydrolase activity before adding TraitRecord xrefs.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "GO:0016990 arginine deiminase activity and EC 3.5.3.6 denote the first-step molecular function in the arginine deiminase pathway rather than the full organism-level pathway-activity phenotype, so GO:0016990 is a close mechanism grounding for the source node and not an equivalent TraitRecord xref.",
        "posed_by": "codex",
        "posed_date": "2026-09-12"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-12T09:44:56Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted arginine dihydrolase activity as a URL/DOI-backed TraitRecord after a repository-wide duplicate review covering ignored and hidden files; METPO has no exact arginine deiminase pathway activity class yet.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000622",
    "label": "autogamy",
    "definition": "A sexual-reproduction phenotype in which two meiotically derived gametic nuclei formed within one unpaired, undivided cell fuse with each other, without fusion of separate gametes.",
    "definition_source": "DOI:10.1017/S0016672300010740",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000625"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1017/S0016672300010740",
        "snippet": "the synkaryon, or fertilization nucleus, is formed by the union of two pronuclei from the same individual.",
        "notes": "Nobili and Luporini (1967), Introduction p.35, contiguous clause after Thus, checked against the typeset publisher PDF. Main text and Summary were read; pp.35-39 and Tables 1-2 were visually inspected. Results 3(i) use serially fixed cells, not live fusion tracking. Genetic identity of fusing nuclei was inferred, not resolved cytologically. Results 3(ii) and Summary support retention of mt-locus heterozygosity in A-25; complete homozygosity therefore does not define autogamy. This is marker evidence, not whole-genome heterozygosity measurement or an identified molecular mechanism. Table 3 was not visually audited; no quantitative reanalysis is claimed."
      },
      {
        "reference": "DOI:10.1016/0014-4827(86)90492-1",
        "snippet": "Autogamy is a process of meiosis and fertilization which takes place in unpaired Paramecium cells, and which is triggered by starvation.",
        "notes": "Berger (1986), PMID:3743667, opening scientific-abstract sentence directly retrieved in Europe PMC core metadata. The complete abstract supports unpaired-cell meiosis/fertilization and a two-stage commitment response to nutritional down-shift. Starvation and cell-cycle timing concern the studied Paramecium system, not universal definition requirements. Full text, actual figures and strain provenance remain uninspected; no canonical example or protein-level causal mechanism is inferred from this abstract."
      },
      {
        "reference": "DOI:10.1093/gbe/evaa052",
        "snippet": "Autogamy in P. tetraurelia occurs in unpaired cells, is induced by starvation, and generates fully homozygous individuals",
        "notes": "Thind et al. (2020), PMID:32163147, PMC7239694, Introduction sec1 clause before citations, checked in raw full-text XML. The scientific abstract, Introduction, strain/culture and autogamy-reactivity Methods, and survival-advantage Results were inspected. The scored autogamy readout was DAPI-visible macronuclear fragmentation, not direct gametic-nuclear fusion in every counted cell. Fully homozygous stock d12 mass cultures do not establish that every microbial autogamy event yields homozygosity. Survival associations and proposed heat-shock-protein models are not a validated causal pathway. Natural provenance of d12 remains unresolved; it is not a canonical example here. Actual figures, remaining sections and supplements were not audited."
      },
      {
        "reference": "DOI:10.1080/0269249X.2013.791344",
        "snippet": "Autogamy is a fusion of two gametic (haploid) nuclei within an undivided cell",
        "notes": "Kaczmarska et al. (2013), p.271, section 5.2.2, opening clause directly read in the author-posted full text at https://www.researchgate.net/publication/259079699_Proposals_for_a_terminology_for_diatom_sexual_reproduction_auxospores_and_resting_stages. Sections 5.2.1-5.2.2 distinguish separate gamete fusion from undivided-cell nuclear fusion. This resolves the prior unread terminology lead; it is synthesis, not new ciliate replication. The following diatom-specific meiotic timing is not imposed on the ciliate definition, which allows postmeiotic mitosis as in Nobili and Luporini pp.35-37. Actual 2013 diagrams were not inspected."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:74792",
        "taxon_label": "Moneuplotes minuta",
        "reference": "DOI:10.1017/S0016672300010740",
        "note": "Qualified A-25 example, named Euplotes minuta in the paper. Material and Methods p.36 traces it to coastal sand near Pisa, subsequently laboratory-maintained; no exact collection year is inferred from the relative date. Serial fixed-cell cytology supports the phenotype. Nonautogamic controls 5G/20 and hybrid offspring are not this example; A-25 also conjugates. NCBI https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=74792 and EFetch taxonomy XML checked on 2026-10-05 resolve Moneuplotes minuta with Euplotes minuta as a synonym. This species-name mapping does not authenticate a modern strain accession or reference genome."
      }
    ],
    "discussions": [
      {
        "discussion_id": "autogamy-scope-and-hierarchy",
        "prompt": "Keep intracellular nuclear fusion distinct from broad self-fertility.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Use the unpaired-cell nuclear-fusion sense supported by the cited ciliate studies, not plant self-pollination or all selfing. The existing homothallism traitmech:000609, unisexual reproduction traitmech:000613 and primary homothallism traitmech:000614 definitions are explicitly fungal-scoped and are not exact parents or synonyms. Cytogamy traitmech:000623 involves paired cells without nuclear exchange in Nobili and Luporini p.39, unlike this unpaired-cell definition. Diller (1958), DOI:10.1111/j.1550-7408.1958.tb02567.x, uses double autogamy for the tentative paired-cell observation. That broader source terminology does not make cytogamy a child or exact synonym of this operationally unpaired-cell class. No universal genetic identity, complete homozygosity, starvation trigger, nuclear count, inability to outcross or gamete-size asymmetry is imposed. The parent gap is resolved by automixis traitmech:000625, whose single-meiotic-cell nuclear origin includes this operational scope. The broader terminology and mapping questions keep this discussion OPEN. Verify external equivalences and source-specific synonym scope before adding mappings. Paedogamy traitmech:000624 instead involves separate gametes formed within one gametangium. The clarified definition excludes their fusion, without forbidding later cell division or postmeiotic nuclear mitosis. These are event-level distinctions, not disjoint species.",
        "posed_by": "codex",
        "posed_date": "2026-10-05"
      },
      {
        "discussion_id": "autogamy-mechanism-and-coverage",
        "prompt": "Resolve molecular mechanisms and broader taxon coverage before extension.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "This is an organismal reproductive phenotype, not the literal mt marker locus or a heat-shock expression signature. Nuclear-selection inference, nutritional commitment and survival associations do not supply a universal protein-resolved mechanism. No causal graph bypasses missing accession-level and perturbation evidence. Keep macronuclear-fragmentation scoring separate from directly observed fusion. The earlier metadata-only lead DOI:10.1080/0269249X.2013.791344 is now resolved by direct reading of sections 5.2.1-5.2.2: paedogamy traitmech:000624 is distinct and automixis broader. Molecular mechanisms, wider taxon coverage and external equivalences remain open; the terminology source alone does not establish them. Preserve actual abstract-resolver verdicts separately from direct full-text checks.",
        "posed_by": "codex",
        "posed_date": "2026-10-05"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-05T15:16:14Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added autogamy with three DOI-backed snippets, unpaired-cell nuclear-fusion scope and a provenance-qualified Moneuplotes minuta A-25 example. Ignored-and-hidden novelty/allocation searches found no exact record or collision. Reserved METPO:1057500 in v498 under phenotype. Deferred unverified mappings, a narrower parent and protein-level mechanisms; did not impose universal homozygosity.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-05T16:16:00Z",
        "curator": "codex",
        "action": "LINKED_RELATED_TRAIT",
        "changes": "Linked paired-cell cytogamy traitmech:000623 and attributed Diller's broader double-autogamy usage. Preserved the unpaired definition, evidence, example and parent; did not assert subsumption or equivalence.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-05T17:13:00Z",
        "curator": "codex",
        "action": "QUALIFIED_TRAIT_SCOPE",
        "changes": "Addressed #1719: made the undivided-cell/no-separate-gamete-fusion boundary explicit, added directly read 2013 terminology evidence and linked paedogamy traitmech:000624. Resolved the unread-source lead while retaining other open gaps. Preserved ciliate evidence, canonical example, parent and compatibility with postmeiotic mitosis.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-05T17:18:00Z",
        "curator": "codex",
        "action": "QUALIFIED_NUCLEAR_ORIGIN",
        "changes": "Addressed #1720: retained the original same-cell origin of both gametic nuclei alongside the #1719 undivided-cell and no-separate-gamete-fusion boundary. Fusion location alone does not establish self-fertilization. Preserved evidence, example, discussions, parent and all prior history.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-05T18:20:28Z",
        "curator": "codex",
        "action": "RESOLVED_PARENT_GAP",
        "changes": "Reparented below automixis traitmech:000625 and documented the resolved parent gap while retaining other open terminology and mapping questions. Preserved definition, evidence, examples and prior history. v501 carries the existing proposed METPO ID with this hierarchy; earlier standalone templates remain historical.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000625",
    "label": "automixis",
    "definition": "A reproductive phenotype in which the reduction of reproductive nuclear ploidy is prevented or compensated and progeny derive their reproductive nuclei solely from products of one meiotically dividing cell or their descendants.",
    "definition_source": "DOI:10.1111/j.1095-8312.1986.tb01761.x",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1111/j.1095-8312.1986.tb01761.x",
        "snippet": "Automixis describes several reproductive processes whereby a new individual derives from a product or products of a single meiotically dividing cell.",
        "notes": "Mogie (1986), scientific abstract directly read on Wiley. Terminology authority, not a new microbial experiment. Its scope includes fusion and non-fusion routes, restitutional meiosis and endomitosis before or after reductional meiosis. The ploidy clause distinguishes ordinary reduced meiotic progeny; reproductive nuclei excludes a universal somatic-ploidy requirement. Do not classify every route as sexual. The abstract contrasts botanical/mycological autogamous selfing involving different meioses, not our operational same-cell autogamy. Full text and actual figures remain unread."
      },
      {
        "reference": "DOI:10.1186/s13059-021-02521-w",
        "snippet": "Mating of gametes from the same meiotic event represents a particular type of inbreeding referred to as intratetrad mating or automixis",
        "notes": "Papaioannou et al. (2021), PMID:34732243, PMC8567612, Background clause checked in publisher HTML and Europe PMC full-text XML. Scientific abstract, Results, Discussion and main Methods read; actual Figure 1 and all Table S1 pages visually inspected. Figure 1C depicts the automictic life cycle with NBRC 1722 and its diploid progenitor NBRC 1721. It is not a measured automixis rate. This fusion-based usage is narrower than Mogie's scope. Recombination experiments do not establish universal homozygosity or zero recombination. Other figures and detailed supplementary methods remain unread."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:36035",
        "taxon_label": "Saccharomycodes ludwigii",
        "reference": "DOI:10.1186/s13059-021-02521-w",
        "note": "Qualified NBRC 1721 strain-family example in Figure 1C; not a strain-specific automixis-frequency measurement. Table S1 p.1 and p.3 footnote 2 identify NBRC 1721 as a wild diploid isolate from grape must, Japan, 1964. NBRC 1722 is a single-spore descendant, not that wild parent or an engineered deletion strain. Provenance: https://media.springernature.com/original/springer-static/esm/art%3A10.1186%2Fs13059-021-02521-w/MediaObjects/13059_2021_2521_MOESM1_ESM.pdf. NCBI taxonomy EFetch on 2026-10-05 confirmed the species name at https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=36035; no genome accession is authenticated."
      }
    ],
    "discussions": [
      {
        "discussion_id": "automixis-scope-and-hierarchy",
        "prompt": "Preserve source-specific meanings of self-fertilization terms.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Mogie's broad reproductive class is not exclusively nuclear fusion or exclusively sexual reproduction. The operational autogamy traitmech:000622, cytogamy traitmech:000623 and paedogamy traitmech:000624 fit as narrower same-cell-origin routes; postmeiotic mitosis is allowed. Kaczmarska et al. DOI:10.1080/0269249X.2013.791344 section 5.2 directly names autogamy and paedogamy as automixis in diatoms. This does not make all botanical autogamy equivalent. Cytogamy's existing 1979 evidence supports same-parent meiotic origin despite cell pairing; cytoplasmic exchange is not nuclear outcrossing. Same-clone mating after different meioses is insufficient. Fungal homothallism, heterothallism and intratetrad mating are not exact synonyms of this broad class. External equivalences and narrower non-fusion microbial exemplars remain unresolved.",
        "posed_by": "codex",
        "posed_date": "2026-10-05"
      },
      {
        "discussion_id": "automixis-mechanism-and-coverage",
        "prompt": "Resolve route-specific mechanisms without universal genetic claims.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "A reproductive phenotype, not a literal mating locus or sequence feature. No single protein pathway is established for all fusion and non-fusion routes, so no causal graph or protein accessions are asserted. Do not infer universal homozygosity, central fusion, absence of outcrossing, or disjoint taxa from event-level distinctions. Retain actual snippet-resolver outcomes separately from direct source checks.",
        "posed_by": "codex",
        "posed_date": "2026-10-05"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-05T18:20:28Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added automixis with two DOI-backed snippets and a qualified natural yeast strain-family example. Ignored-and-hidden novelty and allocation searches found no exact record or collision. Reserved METPO:1057800 in v501; broadened beyond fusion-only terminology and deferred universal molecular mechanisms.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000647",
    "label": "autophagic glycogen degradation",
    "definition": "An autophagy phenotype in which a microbial cell degrades intracellular glycogen by delivering it to lysosomal or vacuolar compartments.",
    "definition_source": "DOI:10.4161/auto.6.4.11736",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000638"
    ],
    "evidence": [
      {
        "reference": "DOI:10.4161/auto.6.4.11736",
        "snippet": "Our results indicate that autophagy and Sga1 act cooperatively in vacuolar glycogen breakdown",
        "notes": "PMID:20383057. DOI-matched scientific abstract directly read in Europe PMC metadata. Supports autophagy-associated vacuolar glycogen hydrolysis in Magnaporthe oryzae during asexual development. The reported breakdown supports conidia formation but is dispensable for pathogenicity. Cytoplasmic retargeting of GFP-Sga1 is an engineered rescue, not a natural vacuolar-flux exemplar. Full Methods, actual figures and independent strain provenance were not inspected."
      },
      {
        "reference": "DOI:10.3390/cells13060467",
        "snippet": "vacuolar delivery of Glg1-GFP and its processing to free GFP were strictly dependent on autophagic machinery and vacuolar proteolysis.",
        "notes": "PMID:38534311, PMC10969688. Scientific abstract, XML Methods 2.1, Results 3.2-3.4 and Discussion were read. The authors conclude nonselective glycogen autophagy in nitrogen-starved Komagataella phaffii using glycogen-bound, nonbinding and cytosolic reporters. Atg11 independence alone is not the selectivity argument. TCA extraction under-recovers the bound reporter; raw free-GFP/total-fusion ratios are unreliable. Reporter proteolysis is not a direct polymer-hydrolysis assay. Actual panels and independent strain provenance remain uninspected."
      },
      {
        "reference": "DOI:10.3390/ijms252111772",
        "snippet": "The K. phaffii Gsy1-GFP marked the GGs and reported on their autophagic degradation during nitrogen starvation, as expected.",
        "notes": "PMID:39519320, PMC11546884. DOI-matched scientific abstract and XML Results 2.2-2.3 and Discussion were read. GGs means glycogen granules. This follow-up uses Gsy1 and CBM20 reporters to support neutral cargo behavior in nitrogen-starved K. phaffii; it is not independent-laboratory replication. Early Gsy1-GFP dot disappearance is autophagy-independent and is not positive flux evidence. A human STBD1 domain used as a reporter does not establish a native human mechanism in yeast. Complete Methods, actual panels and strain provenance were not inspected."
      },
      {
        "reference": "DOI:10.1016/j.isci.2024.109810",
        "snippet": "glycophagy may play a role in the suppression of glycogen consumption, rather than enhancing degradation.",
        "notes": "PMID:38832010, PMC11145338. Exact XML Results sec2.7 span, not an abstract quote. Scientific Summary, Results, Discussion, Limitations and selected yeast, GFP-cleavage and glycogen-assay Methods were read. Boundary evidence: Atg45-dependent vacuolar delivery during Saccharomyces cerevisiae sporulation can preserve glycogen. Do not score that delivery alone as degradation. Receptor recruitment and prolonged-starvation reporter turnover do not make storage and hydrolysis interchangeable. Actual panels, supplements and independent strain provenance remain unread."
      }
    ],
    "discussions": [
      {
        "discussion_id": "autophagic-glycogen-degradation-scope",
        "prompt": "Distinguish degradation from broader glycophagy usage.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "The explicit degradative endpoint narrows autophagy traitmech:000638 without changing that parent's identity. This is intracellular cargo recycling, not growth on glycogen, extracellular amylolysis, granule possession or a gene inventory. The Cells paper introduces glycophagy as selective but reports nonselective K. phaffii turnover; the iScience paper also uses glycophagy for vacuolar preservation during sporulation. Those source-attributed usages are not exact synonyms of this endpoint-defined record. GO:0061723 was directly resolved at https://www.ebi.ac.uk/QuickGO/services/ontology/go/terms/GO%3A0061723 as a nonobsolete biological process for selective glycogen degradation by macroautophagy. It is narrower on selectivity and route, and is not an exact organismal phenotype. Omit exact xrefs and synonyms. Broader delivery/storage and selective subtype relationships require human review, not silent normalization of conflicting terminology.",
        "posed_by": "codex",
        "posed_date": "2026-10-06"
      },
      {
        "discussion_id": "autophagic-glycogen-degradation-assays-and-exemplars",
        "prompt": "Resolve polymer turnover, natural exemplars and mechanisms.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Keep glycogen-bound reporter cleavage, vacuolar localization, glycogen content and polymer hydrolysis as distinct readouts. Do not impose universal Sga1, Atg45, Atg11, starvation, sporulation, selectivity or a macroautophagic route. Yeast species and nutrient conditions can differ. The Atg45 storage result is a boundary, not positive evidence of this endpoint. Canonical examples remain unset pending independent natural-strain provenance and direct endpoint support; reporter and deletion strains are qualified evidence, not natural exemplars. Protein graphs require native taxon-paired accessions and functional evidence. Human disease models and an Aspergillus enzyme used as an assay reagent are not microbial observations of this trait. Inspect actual panels before protein-level curation.",
        "posed_by": "codex",
        "posed_date": "2026-10-06"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-06T17:24:49Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added autophagic glycogen degradation with four DOI-backed source-matched snippets and explicit storage, selectivity and reporter limits. Fresh ignored-and-hidden searches, seed and METPO inventories found no exact record. Reserved METPO:1060000 in v523 with unchanged corrected autophagy parent context. Deferred broad glycophagy equivalence, natural exemplars and protein mechanisms.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000638",
    "label": "autophagy",
    "definition": "A physiological phenotype in which a microbial cell degrades intracellular material, including its own constituents or intracellular non-self cargo, by delivering that material to lysosomal or vacuolar compartments.",
    "definition_source": "DOI:10.1083/jcb.119.2.301",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1083/jcb.119.2.301",
        "snippet": "This is the first report that nutrient-deficient conditions induce extensive autophagic degradation of cytosolic components in the vacuoles of yeast cells.",
        "notes": "PMID:1400575, PMC2289660. Scientific Abstract directly read in Europe PMC XML. Saccharomyces cerevisiae protease-deficient mutants and PMSF-treated reference cells accumulate bodies containing cytosol and organelles; bodies disappear after inhibitor removal. Sequestration and subsequent degradation, not inhibited-body accumulation alone, support the phenotype. The study's starvation conditions are not a universal trigger requirement. The XML body is sparse; full methods, actual figures and natural strain provenance were not inspected."
      },
      {
        "reference": "DOI:10.1242/jcs.108.1.25",
        "snippet": "there exist in P. pastoris at least two pathways for the sequestration of peroxisomes into the vacuole for degradation.",
        "notes": "PMID:7738102. Scientific Abstract directly read in Europe PMC metadata and publisher HTML. In historically named Pichia pastoris, carbon-source adaptation elicits peroxisome turnover through macroautophagy-like wrapping or microautophagy-like vacuolar engulfment. Enzyme activities, morphology and mutants support route diversity; proteinase-deficient cells accumulate undegraded cargo. This supports selective organelle turnover without requiring starvation or a double-membrane intermediate for every route. Publisher full text requires access; methods, actual figures and strain-specific modern taxonomy were not inspected."
      },
      {
        "reference": "DOI:10.1073/pnas.0813319106",
        "snippet": "In both organisms, genetic inactivation of the autophagy pathway increases bacterial intracellular replication, decreases animal lifespan, and results in apoptotic-independent death.",
        "notes": "PMID:19667176, PMC2731839. Scientific Abstract directly read in Europe PMC core metadata with matching DOI. The two models are Dictyostelium discoideum and Caenorhabditis elegans. Only the microbial amoeba's intracellular-infection phenotype is relevant here; the abstract's combined animal-lifespan wording and nematode insulin-signaling results are not transferred to the amoeba. Genetic perturbation supports an autophagy-associated host-defense role, not direct proof of completed cargo degradation by itself. Full text, actual figures and strain provenance were not accessible in this review."
      },
      {
        "reference": "DOI:10.1371/journal.ppat.1006344",
        "snippet": "Antagonistically, ESX-1 is also essential to block the autophagic flux and deplete the MCV of proteolytic activity.",
        "notes": "PMID:28414774, PMC5407849. Scientific Abstract, distinct from the Author summary, directly read in Europe PMC XML and PLOS. The flux Results, flux-assay Methods and Discussion were read; Figure 6 and supplemental S6 Figure were visually inspected. Dictyostelium discoideum is the autophagic cell, not the infecting Mycobacterium marinum. Protease-inhibitor comparisons and GFP-Atg8 processing distinguish formation from degradation; the infection-associated block is partial, not a complete absence of flux. Free GFP reduction alone is ambiguous in this assay. The paper frames intracellular-pathogen digestion as xenophagy, but its blockade result is boundary evidence, not a positive completed-clearance observation. Other actual figures and supplements were not visually audited."
      },
      {
        "reference": "DOI:10.1007/s00284-024-03838-y",
        "snippet": "These results indicate that nuclei are engulfed in the autophagosomes as a whole and transported/released into the vacuolar lumen where they are degraded.",
        "notes": "PMID:39162852, PMC11335778. Scientific Abstract directly read in Europe PMC with matching DOI. Selected XML Methods, Results and Discussion support including nuclear cargo within autophagy. The nucleophagy child retains the assay and access limits. This repairs cytoplasmic to intracellular in the parent definition (#1754), without imposing this macro route on all autophagy or changing its stable identity."
      }
    ],
    "discussions": [
      {
        "discussion_id": "autophagy-scope-and-flux",
        "prompt": "Retain catabolic scope without equating markers with completed flux.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "The phenotype belongs to the microbial cell doing the degradation, not to a bacterium merely eliciting an animal host response. Selective and bulk turnover, macro- and microautophagic routes, and intracellular non-self cargo are within scope; no universal starvation trigger, double-membrane intermediate or ATG gene inventory is asserted. ATG genes, puncta, autophagic-body accumulation, cell death or reduced pathogen replication alone do not establish completed degradative flux. Nondegradative membrane repair or ejection using autophagy machinery is not sufficient. Extracellular uptake and ordinary phagolysosomal digestion alone do not distinguish autophagy. Existing endocytosis, phagocytosis, phagotrophy and extracellular proteolysis records are not equivalent or broader parents; their co-occurrence is not prohibited. GO:0006914 was resolved at https://www.ebi.ac.uk/QuickGO/services/ontology/go/terms/GO%3A0006914 and includes self and non-self material, but denotes a biological process rather than an equivalent organismal phenotype. Keep METPO:1000059 as parent and omit exact xrefs and synonyms pending human scope review. Nuclear cargo is included: DOI:10.1007/s00284-024-03838-y supports whole-nucleus autophagy in Aspergillus oryzae. The former cytoplasmic-only wording was too narrow (#1754); intracellular corrects that wording, not the identity of autophagy. Nucleophagy traitmech:000643 is a cargo-defined child. The original definition source supports the retained vacuolar catabolic genus; the added evidence supports nuclear cargo.",
        "posed_by": "codex",
        "posed_date": "2026-10-06"
      },
      {
        "discussion_id": "autophagy-exemplar-and-mechanism",
        "prompt": "Resolve strain provenance and cargo-specific mechanism evidence.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Canonical examples remain unset because reference-strain provenance and historical yeast taxonomy have not been independently verified. Do not infer natural or engineered origin from a mutant label. Retain the qualified experimental evidence without treating inhibited or knockout cells as positive completed-flux exemplars. Route-specific proteins, their accessions and taxon-paired functional evidence need review before adding a causal graph. The amoeba infection studies do not establish one universal microbial host-defense mechanism or prove that autophagy always eliminates an intracellular pathogen.",
        "posed_by": "codex",
        "posed_date": "2026-10-06"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-06T09:02:37Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added autophagy with four DOI-backed scientific-abstract snippets and explicit route, cargo, flux and source-access limits. Ignored-and-hidden searches and pinned METPO review found no exact record. Reserved METPO:1059100 in v514. Deferred unverified examples, mappings and protein mechanisms; existing traits unchanged.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-06T13:33:28Z",
        "curator": "codex",
        "action": "CURATED_WITH_LITERATURE",
        "changes": "Corrected cytoplasmic to intracellular cargo using whole-nucleus autophagy evidence (#1754). Retained autophagy identity, prior evidence and route/flux limits; added the nucleophagy child and corrected parent context in proposal v519.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000632",
    "label": "autotrophic",
    "definition": "A trophic type in which an organism produces organic compounds from inorganic carbon sources (primarily carbon dioxide or bicarbonate) using energy from light (photoautotrophy) or from the oxidation of inorganic compounds (chemoautotrophy).",
    "definition_source": "DOI:10.1038/nrmicro.2016.130",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000631"
    ],
    "synonyms": [
      {
        "synonym_text": "TT_autotroph",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "autotroph",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "autotrophy",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "created_by": "Jed Dongjin Kim-Ozaeta",
    "evidence": [
      {
        "reference": "DOI:10.1038/nrmicro.2016.130",
        "snippet": "require only CO2 as a carbon source",
        "notes": "Review defines autotrophic organisms by CO2 use as carbon source for growth."
      },
      {
        "reference": "DOI:10.1128/AEM.02473-10",
        "snippet": "autotrophic CO2 fixation",
        "notes": "Minireview supports Calvin-Benson and other microbial CO2-fixation pathways."
      },
      {
        "reference": "PMID:8590279",
        "snippet": "Synechocystis sp. strain PCC6803",
        "notes": "Organism example: Synechocystis sp. PCC 6803 is a model autotrophic cyanobacterium that fixes CO2 via the Calvin-Benson cycle (Kaneko et al. 1996, DNA Res, full genome)."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:381666",
        "taxon_label": "Cupriavidus necator H16",
        "note": "H2/CO2 chemolithoautotroph with two active Calvin-Benson-Bassham operons",
        "reference": "DOI:10.1038/nbt1244"
      },
      {
        "taxon_id": "NCBITaxon:915",
        "taxon_label": "Nitrosomonas europaea",
        "note": "ammonia-oxidising chemoautotroph",
        "reference": "DOI:10.1128/JB.185.9.2759-2773.2003"
      },
      {
        "taxon_id": "NCBITaxon:32046",
        "taxon_label": "Synechococcus elongatus",
        "note": "photoautotrophic cyanobacterium",
        "reference": "DOI:10.1038/srep08132"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "autotrophic_inorganic_carbon_fixation",
        "title": "Autotrophic inorganic carbon fixation",
        "description": "DOI-backed graph linking inorganic carbon, energy and reductant supply, CO2-fixation pathways, carboxylating enzymes, precursor metabolites, and biomass.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "This cross-pathway graph represents alternative autotrophic carbon-fixation mechanisms rather than a claim that one organism carries the Calvin-Benson and Wood-Ljungdahl pathways together. The C. necator H16 example anchors the RuBisCO branch.",
        "nodes": [
          {
            "node_id": "autotrophic_trait",
            "label": "autotrophic",
            "node_type": "TRAIT",
            "grounding": "METPO:1000632",
            "description": "Trophic type producing organic compounds from inorganic carbon."
          },
          {
            "node_id": "carbon_dioxide",
            "label": "carbon dioxide",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:16526",
            "description": "Inorganic carbon source fixed by autotrophs."
          },
          {
            "node_id": "bicarbonate",
            "label": "bicarbonate",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:17544",
            "description": "Dissolved inorganic carbon species used by many microbes."
          },
          {
            "node_id": "energy_and_reductant",
            "label": "energy and reductant",
            "node_type": "CHEMICAL",
            "description": "ATP and reducing equivalents required for carbon fixation."
          },
          {
            "node_id": "co2_fixation_pathway",
            "label": "CO2-fixation pathway",
            "node_type": "PATHWAY",
            "description": "Autotrophic pathway converting inorganic carbon into cellular carbon.",
            "grounding": "GO:0015977"
          },
          {
            "node_id": "calvin_benson_cycle",
            "label": "Calvin-Benson cycle",
            "node_type": "PATHWAY",
            "description": "Common autotrophic CO2-fixation pathway using RuBisCO.",
            "grounding": "GO:0019253"
          },
          {
            "node_id": "rubisco",
            "label": "RuBisCO",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Carboxylating enzyme of the Calvin-Benson cycle.",
            "grounding": "InterPro:IPR033966",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:P42721",
                "protein_label": "Ribulose bisphosphate carboxylase large chain, plasmid",
                "gene_symbol": "cbbL2",
                "taxon_id": "NCBITaxon:381666",
                "taxon_label": "Cupriavidus necator H16",
                "entry_status": "REVIEWED",
                "retrieved_on": "2026-10-22",
                "entry_version": 154,
                "sequence_version": 3,
                "role": "Large-chain component of the plasmid-encoded RuBisCO in one of the two active CBB operons of C. necator H16.",
                "evidence": [
                  {
                    "reference": "DOI:10.1186/s12934-020-01494-y",
                    "snippet": "both CBB operons were active and contributed almost equally to the carbon fixation process",
                    "notes": "The strain-level perturbation study supports activity of both H16 CBB operons; UniProtKB P42721 identifies the reviewed plasmid cbbL2 large chain in that strain."
                  }
                ]
              }
            ]
          },
          {
            "node_id": "precursor_metabolites",
            "label": "precursor metabolites",
            "node_type": "CHEMICAL",
            "description": "Fixed-carbon intermediates feeding biosynthesis."
          },
          {
            "node_id": "biomass",
            "label": "biomass",
            "node_type": "CHEMICAL",
            "description": "Cellular material produced from fixed inorganic carbon.",
            "grounding": "METPO:1007501"
          },
          {
            "node_id": "environmental_ph",
            "label": "environmental pH",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Ambient pH that controls the speciation of dissolved inorganic carbon."
          },
          {
            "node_id": "dissolved_inorganic_carbon",
            "label": "dissolved inorganic carbon",
            "node_type": "CHEMICAL",
            "description": "Pool of CO2, bicarbonate, and carbonate available to autotrophs."
          },
          {
            "node_id": "carbon_concentrating_mechanism",
            "label": "carbon-concentrating mechanism",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "System that elevates intracellular CO2 around RuBisCO to favor carboxylation."
          },
          {
            "node_id": "carboxysome",
            "label": "carboxysome",
            "node_type": "ORGANELLE",
            "description": "Protein-shell microcompartment encapsulating RuBisCO and carbonic anhydrase.",
            "grounding": "GO:0031470"
          },
          {
            "node_id": "carbonic_anhydrase",
            "label": "carbonic anhydrase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Enzyme interconverting bicarbonate and CO2, supplying CO2 to RuBisCO.",
            "grounding": "InterPro:IPR001765"
          },
          {
            "node_id": "wood_ljungdahl_pathway",
            "label": "Wood-Ljungdahl pathway",
            "node_type": "PATHWAY",
            "description": "Reductive acetyl-CoA pathway fixing two CO2 into acetyl-CoA.",
            "grounding": "GO:0030634",
            "related_records": [
              {
                "corpus": "PathwayMech",
                "identifier": "WikiPathways:WP5019",
                "relation": "PATHWAY_CONTEXT",
                "basis": "PathwayMech context: Acetogenesis in Acetobacterium woodii (NCBITaxon:33952). The shared reductive acetyl-CoA route combines methyl and carbonyl branches for acetogenesis; the bacterial exemplar does not establish archaeal variants. No exact equivalence or transfer of organism scope is asserted.",
                "source_version": "aa305727458c44ab05614901334540e2c87a9f3a"
              }
            ]
          },
          {
            "node_id": "acetyl_coa",
            "label": "acetyl-CoA",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:15351",
            "description": "Central metabolite product of Wood-Ljungdahl CO2 fixation."
          },
          {
            "node_id": "codh_acs",
            "label": "CO dehydrogenase/acetyl-CoA synthase (CODH/ACS)",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Enzyme complex catalyzing the terminal acetyl-CoA-forming step of the Wood-Ljungdahl pathway.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "CODH/ACS is a multisubunit, taxon-variable complex whose CODH and ACS components have distinct protein families; no one protein-family term exactly represents this composite node."
          },
          {
            "node_id": "molecular_hydrogen",
            "label": "molecular hydrogen",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:18276",
            "description": "Electron donor supplying reducing equivalents for CO2 reduction."
          }
        ],
        "edges": [
          {
            "subject": "autotrophic_trait",
            "predicate": "has carbon source",
            "object": "carbon_dioxide",
            "description": "Autotrophs use CO2 as an inorganic carbon source.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro.2016.130",
                "snippet": "require only CO2 as a carbon source",
                "notes": "Supports CO2 as the defining autotrophic carbon source."
              }
            ],
            "predicate_id": "METPO:2007806"
          },
          {
            "subject": "bicarbonate",
            "predicate": "alternative inorganic carbon source for",
            "object": "autotrophic_trait",
            "description": "Bicarbonate is another inorganic carbon species available for autotrophic fixation.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.02473-10",
                "snippet": "autotrophic carbon dioxide assimilation pathway",
                "notes": "Supports inorganic carbon assimilation by autotrophic pathways."
              }
            ]
          },
          {
            "subject": "energy_and_reductant",
            "predicate": "regulates",
            "object": "co2_fixation_pathway",
            "description": "Autotrophic carbon fixation requires energy and reducing power.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2365",
                "snippet": "energy demand of the autotrophic pathways",
                "notes": "Supports energy requirements of autotrophic carbon fixation pathways."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "carbon_dioxide",
            "predicate": "fixed by",
            "object": "co2_fixation_pathway",
            "description": "CO2 is converted into organic carbon by autotrophic fixation pathways.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.02473-10",
                "snippet": "autotrophic CO2 fixation",
                "notes": "Supports CO2 fixation as the core autotrophic biosynthetic process."
              }
            ],
            "predicate_id": "METPO:2007404"
          },
          {
            "subject": "calvin_benson_cycle",
            "predicate": "example of",
            "object": "co2_fixation_pathway",
            "description": "The Calvin-Benson cycle is a major autotrophic CO2-fixation pathway.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.02473-10",
                "snippet": "Calvin-Benson reductive pentose phosphate cycle",
                "notes": "Supports the Calvin-Benson cycle as a microbial autotrophic pathway."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "rubisco",
            "predicate": "catalyzes",
            "object": "calvin_benson_cycle",
            "description": "RuBisCO is the key carboxylating enzyme of the Calvin-Benson cycle.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.02473-10",
                "snippet": "ribulose-1,5-bisphosphate carboxylase",
                "notes": "Supports RuBisCO as the marker enzyme for Calvin-Benson autotrophy."
              }
            ],
            "predicate_id": "biolink:catalyzes"
          },
          {
            "subject": "co2_fixation_pathway",
            "predicate": "has output",
            "object": "precursor_metabolites",
            "description": "Fixed carbon is converted into central biosynthetic precursors.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.02473-10",
                "snippet": "converted to other central intermediates",
                "notes": "Supports conversion of fixed carbon into central metabolites."
              }
            ],
            "predicate_id": "RO:0002234"
          },
          {
            "subject": "precursor_metabolites",
            "predicate": "incorporated into",
            "object": "biomass",
            "description": "Fixed-carbon precursors are incorporated into cellular biomass.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro.2016.130",
                "snippet": "microbial autotrophic production",
                "notes": "Supports production of biomass and products from autotrophic CO2 fixation."
              }
            ],
            "predicate_id": "biolink:part_of"
          },
          {
            "subject": "environmental_ph",
            "predicate": "determines speciation of",
            "object": "dissolved_inorganic_carbon",
            "description": "pH sets the relative abundance of CO2, bicarbonate, and carbonate available for fixation.",
            "evidence": [
              {
                "reference": "DOI:10.1128/aem.01557-23",
                "notes": "CO2 predominates below ~pH 6.4, HCO3- at circumneutral pH, and CO32- above ~pH 10.3; DIC form availability constrains the fixation route."
              }
            ]
          },
          {
            "subject": "carbon_concentrating_mechanism",
            "predicate": "supplies substrate to",
            "object": "co2_fixation_pathway",
            "description": "CCMs elevate intracellular CO2 to enhance autotrophic carbon fixation.",
            "evidence": [
              {
                "reference": "DOI:10.1128/aem.01557-23",
                "notes": "Transporters and CO2-active systems generate elevated intracellular HCO3- delivered for carboxysomal CO2 fixation."
              }
            ]
          },
          {
            "subject": "carboxysome",
            "predicate": "contains",
            "object": "rubisco",
            "description": "Carboxysomes encapsulate RuBisCO to concentrate CO2 around the carboxylating enzyme.",
            "evidence": [
              {
                "reference": "DOI:10.1111/ppl.14140",
                "notes": "Carboxysomes are protein shell encapsulated ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO)."
              }
            ]
          },
          {
            "subject": "carboxysome",
            "predicate": "contains",
            "object": "carbonic_anhydrase",
            "description": "Carboxysomes house carbonic anhydrase alongside RuBisCO.",
            "evidence": [
              {
                "reference": "DOI:10.1128/aem.01075-24",
                "notes": "Carboxysomes contain two key enzymes: carbonic anhydrase and RuBisCO."
              }
            ]
          },
          {
            "subject": "carbonic_anhydrase",
            "predicate": "converts",
            "object": "carbon_dioxide",
            "description": "Carbonic anhydrase converts bicarbonate to CO2 for RuBisCO fixation.",
            "evidence": [
              {
                "reference": "DOI:10.1128/aem.01075-24",
                "notes": "When cytoplasmic HCO3- enters carboxysomes, CA converts it to CO2, which is fixed by RuBisCO."
              }
            ]
          },
          {
            "subject": "wood_ljungdahl_pathway",
            "predicate": "example of",
            "object": "co2_fixation_pathway",
            "description": "The Wood-Ljungdahl pathway is an autotrophic CO2-fixation pathway producing acetyl-CoA.",
            "evidence": [
              {
                "reference": "DOI:10.1039/D4CB00099D",
                "notes": "Two CO2 molecules are fixed to acetyl-CoA via the WLP, requiring one ATP and eight electrons."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "wood_ljungdahl_pathway",
            "predicate": "has output",
            "object": "acetyl_coa",
            "description": "The Wood-Ljungdahl pathway yields acetyl-CoA from fixed CO2.",
            "evidence": [
              {
                "reference": "DOI:10.1039/D4CB00099D",
                "notes": "Two CO2 molecules to acetyl-CoA via the WLP."
              }
            ],
            "predicate_id": "RO:0002234"
          },
          {
            "subject": "codh_acs",
            "predicate": "catalyzes",
            "object": "wood_ljungdahl_pathway",
            "description": "CODH/ACS catalyzes the terminal acetyl-CoA-forming step of the Wood-Ljungdahl pathway.",
            "evidence": [
              {
                "reference": "DOI:10.1039/D4CB00099D",
                "notes": "CO dehydrogenase/acetyl-CoA synthase (CODH/ACS) produces acetyl-CoA in the WLP."
              }
            ],
            "predicate_id": "biolink:catalyzes"
          },
          {
            "subject": "molecular_hydrogen",
            "predicate": "provides reductant for",
            "object": "wood_ljungdahl_pathway",
            "description": "H2 supplies reducing equivalents driving CO2 reduction in the Wood-Ljungdahl pathway.",
            "evidence": [
              {
                "reference": "DOI:10.1039/D4CB00099D",
                "notes": "H2 or CO must be utilized as an energy source to provide reducing equivalents for full CO2 reduction."
              }
            ]
          },
          {
            "subject": "dissolved_inorganic_carbon",
            "predicate": "participates in",
            "object": "co2_fixation_pathway",
            "description": "The environmental dissolved-inorganic-carbon pool supplies substrate to autotrophic carbon-fixation pathways.",
            "evidence": [
              {
                "reference": "DOI:10.1128/aem.01557-23",
                "snippet": "DIC transporters and carbonic anhydrase enzymes (CA) to facilitate DIC fixation",
                "notes": "Verified against the open Applied and Environmental Microbiology article."
              }
            ],
            "predicate_id": "biolink:participates_in"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.867544+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-09T00:00:00-07:00",
        "curator": "codex",
        "action": "ADDED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed causal graph for inorganic carbon fixation, Calvin-Benson cycle, RuBisCO, precursor metabolites, and biomass formation.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-16T05:00:00-07:00",
        "curator": "claude",
        "action": "ADDED_ORGANISM_EXAMPLE",
        "changes": "Added Synechocystis sp. PCC 6803 organism example with PMID-backed evidence.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000006\u00d71, METPO:2000202\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T05:49:25Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:catalyzes\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T08:21:50Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (rdfs:subClassOf\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T21:30:07Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007404\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:19Z",
        "curator": "claude",
        "action": "RENAME_PREDICATE_LABELS",
        "changes": "Renamed 1 causal-edge predicate label(s) to align with existing groundings: drives \u2192 regulates \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:22Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002211\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:38:01Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0019253\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:41:04Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (METPO:1007501\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T07:34:58Z",
        "curator": "claude",
        "action": "RETYPE_CAUSAL_NODES",
        "changes": "Re-typed 1 causal-node node_type field(s) to align with CausalNodeTypeEnum semantics: biomass: BIOLOGICAL_PROCESS \u2192 CHEMICAL \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T08:14:33Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0015977\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-26T02:27:52Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A075WF79\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-13T21:03:27Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:part_of\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 9 evidence-backed generic edges (9 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:14Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (rdfs:subClassOf\u00d71, METPO:2000202\u00d71, biolink:catalyzes\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:20Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0030634\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:34Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0031470\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-26T07:15:20Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A009PMS8\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:21:12Z",
        "curator": "claude",
        "action": "RETRACT_DEAD_UNIPROT_GROUNDINGS",
        "changes": "Retracted 2 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:23:55Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (InterPro:IPR033966\u00d71, InterPro:IPR001765\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 3 causal edge(s) off microbe-domain METPO predicates (1 to has carbon source, 2 to has output), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-24T11:30:00-07:00",
        "curator": "codex",
        "action": "REVIEWED_CAUSAL_GRAPH_PROTEIN_TAXON",
        "changes": "Marked the graph mechanistic, documented the alternative-pathway scope, reviewed the composite CODH/ACS node as label-only, upgraded canonical citations to DOI references, and added a reviewed C. necator H16 cbbL2 protein example.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T10:45:00Z",
        "curator": "codex",
        "action": "CONNECT_CAUSAL_GRAPH_COMPONENTS",
        "changes": "Resolved issue #183 graph fragmentation (2 components to 1) with 1 public-source, verbatim-snippet-backed connector(s). No paid research service was called.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-05T17:46:22Z",
        "curator": "codex",
        "action": "ADD_PATHWAY_CONTEXT",
        "changes": "Added pinned PathwayMech context on reviewed causal nodes with explicit route and organism limitations; retained existing groundings and exact xrefs.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-22T01:35:00Z",
        "curator": "claude",
        "action": "REFRESH_UNIPROT_ENTRY_VERSION",
        "changes": "Refreshed UniProtKB entry_version against live UniProt REST on 2026-10-22: UniProtKB:P42721 (153 -> 154 on rubisco).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000735",
    "label": "bacterial flagellar filament internalization",
    "definition": "A physiological phenotype in which a bacterium withdraws an assembled portion of its own flagellar filament from outside its cell body into its cell-body periplasm.",
    "definition_source": "DOI:10.1038/s41564-023-01401-2",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/s41564-023-01401-2",
        "snippet": "most or all of the filament was internalized to the periplasm",
        "notes": "Kaplan et al. 2023, PMID:37349588, PMC11061892.1, Results S3, Attachment of B. bacteriovorus to prey, paragraph beginning In cells with larger portions. Direct manuscript JATS match; native NOT_IN_ABSTRACT retained. Source strain HD100 and frozen cryo-ET stages support partial through nearly complete withdrawal into the predator's own periplasm, not the prey's. Methods S8-S12 qualify minicell enrichment and possible physiology effects; the images contain no same-cell temporal information. Main Figure 3 and supplement PDF pages 1, 22-35, 66-67 were visually inspected. S20-S21 distinguish external and internal filament portions; S22 is a schematic, not a tracked trajectory. Table S2's 8/4/30 early/intermediate/late absorbed-flagellum observations are not culture replicates or a prevalence denominator. Publisher Figure 3's main scale bar is 100 nm, versus 50 nm in the manuscript caption; no dimension or rate is inferred. Main PDF, other actual main figures, unselected supplemental images and movies remain unread. Later breakage or degradation is not required by the definition."
      },
      {
        "reference": "DOI:10.1063/pt.nkma.bqid",
        "snippet": "B. bacteriovorus retracts its extracellular hook and filament into its own periplasmic space",
        "notes": "Kaplan 2024, Physics Today, Figure 5 caption; contiguous span checked in directly retrieved publisher HTML. Disassembly processes and reference 16 were read, and actual Figure 5 was inspected. This is a distinct author-perspective publication describing the same 2023 experiment, not independent experimental replication. The colored segmentation is not another experiment. Native UNRESOLVED means no usable abstract was returned, not that the DOI is invalid; Crossref identity and direct publisher wording were checked separately. Presumed digestion and the hypothesized evolutionary connection to spirochaete endoflagella are not defining requirements or established consequences."
      }
    ],
    "discussions": [
      {
        "discussion_id": "bacterial-flagellar-internalization-scope",
        "prompt": "Review the withdrawal endpoint without making universal entry-time claims.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Cell-body periplasm distinguishes withdrawal from an external flagellar sheath lumen, static endoflagella, abnormal assembly, import of free flagellin, uptake of another cell's material and predator entry into the prey's periplasm. Partial withdrawal counts; permanent intactness and complete withdrawal are not required. Bacterial polar ejection traitmech:000732 releases structures externally; eukaryotic axoneme internalization traitmech:000734 involves a different apparatus. These distinctions do not imply disjoint organisms. Earlier 109J observations of externally retained filaments constrain universal early-entry claims but neither demonstrate own-periplasmic withdrawal nor establish its absence. Different strains and preparations are not pooled into one time series.",
        "evidence": [
          {
            "reference": "DOI:10.1111/j.1365-2958.2006.05081.x",
            "reference_title": "Characterizing the flagellar filament and the role of motility in bacterial prey-penetration by Bdellovibrio bacteriovorus.",
            "supports": "NO_EVIDENCE",
            "evidence_source": "full_text",
            "snippet": "In our experiments unshed flagella were seen early during the establishment of an infection.",
            "explanation": "Comparison context, not positive support for internalization or a third supporting definition citation. External retention alone does not measure subsequent or partial internalization.",
            "notes": "Lambert et al. 2006, PMID:16573680, PMC1453311.1, Results, Flagella are not always shed upon prey entry. Direct JATS match; native NOT_IN_ABSTRACT retained. 109J predators were examined with flagella-minus E. coli DFB225 prey. The approximately 80% of more than 100 assessable early bdelloplasts excludes aggregates and may overestimate the whole-population proportion; its complement is not an internalization frequency. Actual Figure 1 was viewed at 456 by 390 pixels. Its 20-minute time is after mixing, not an invasion or withdrawal duration; 1% PTA staining differs from the 2023 cryo-ET preparation. Other actual figures, supplementary figures and main PDF remain unread."
          }
        ],
        "posed_by": "codex",
        "posed_date": "2026-10-16"
      },
      {
        "discussion_id": "bacterial-flagellar-internalization-metpo",
        "prompt": "Review the proposed phenotype parent and unresolved ontology equivalence.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Phenotype METPO:1000059, below quality METPO:1000188, is a broader definition-based parent inference, not an assertion of locomotion. No active exact withdrawal term was identified in the inspected pinned and current METPO release/templates. Axially filamented METPO:1000705 describes static periplasmic location under motile; flagellated METPO:1000704 describes locomotory possession. Neither is equivalent to withdrawal. Deprecated METPO:0000089 and METPO:000090 carry OMO:0001000; METPO:1000381 carries IAO:0000226. Their replacement is METPO:1000704. Deprecated flagellum METPO:1000123 carries OMO:0001000 with no observed replacement or consider annotation. These historical identifiers are not revived or asserted as exact xrefs. The ontology pin is unchanged; no upstream acceptance or human sign-off is implied.",
        "posed_by": "codex",
        "posed_date": "2026-10-16"
      },
      {
        "discussion_id": "bacterial-flagellar-internalization-mechanism",
        "prompt": "Separate observed internalization from universal molecular mechanisms.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Motor displacement and P/L-ring separation are structural observations, not universal requirements. Sheath/outer-membrane zippering and lipid effects are hypotheses. A missing motor can reflect the cryo-ET missing wedge; vesicles may reflect sample preparation. No universal force, protease, complete digestion, recycling, rate or order of events is asserted. A sequence feature or flagellin expression alone does not establish this phenotype. A protein-resolved causal graph requires edge-specific evidence and authority-checked, taxon-paired accessions; mechanism curation is deferred, not claimed absent.",
        "posed_by": "codex",
        "posed_date": "2026-10-16"
      },
      {
        "discussion_id": "bacterial-flagellar-internalization-provenance",
        "prompt": "Preserve transient-state, source-version and replication limits.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "HD100 is a qualified experimental observation, not an unqualified archetypal taxon assertion. Canonical examples remain omitted pending strain-provenance and representative-state review. The 2024 perspective and 2023 study satisfy two distinct supporting citations, not two independent experiments; supplements are part of the same study. Crossref and qualified MED identities and returned notice fields were checked, not comprehensive correction/retraction clearance. The 2023 linked post-publication review remains unread; unsuccessful publisher/PubMed access does not prove that no notice exists. Source scale-bar and preparation discrepancies are retained rather than silently harmonized. No raw-data reanalysis, exact synonym, equivalent external mapping, paid research or human scientific approval is implied.",
        "posed_by": "codex",
        "posed_date": "2026-10-16"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-16T01:41:19.482095+00:00",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added own-flagellar-filament withdrawal into the bacterial cell-body periplasm with two supporting DOI citations and checked 11/13-word full-text snippets. The author perspective concerns the same primary experiment, not independent replication. Kept the 14-word 2006 retained-flagella excerpt as comparison context, not definition evidence. Native NOT_IN_ABSTRACT/UNRESOLVED/NOT_IN_ABSTRACT outcomes are preserved. Reserved 000735, v611 and 1068800-1068899 after ignored/hidden current-file, retained-history, complete-range and open/draft PR checks. Preserved partial-withdrawal, frozen-stage, source-version and preparation limits. No obsolete ID, canonical taxon, exact mapping or universal protein mechanism is inferred. Timestamp records observed allocation, not acquisition.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000732",
    "label": "bacterial polar flagellar ejection",
    "definition": "A physiological phenotype in which a bacterium actively ejects previously assembled axial structures of a polar flagellum by separation at its base.",
    "definition_source": "DOI:10.1371/journal.pbio.3000165",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1371/journal.pbio.3000165",
        "snippet": "Plesiomonas cells consistently lose their flagella at the base of the hook",
        "notes": "Ferreira et al. 2019, PMID:30889173, PMC6424402. Results, Shed hook-filament structures accumulate in P. shigelloides supernatant, sole paragraph (HTML anchor article1.body1.sec2.sec4.p1; PDF pp. 4-5); Figure 1G. Direct publisher full-text match; native NOT_IN_ABSTRACT. Hook-bearing released structures, population counts and relic/assembly comparisons support ejection rather than daughter-cell dilution or passive midfilament breakage. Nutrient-depletion conditions vary among assays; minimal medium containing glucose is not complete carbon starvation. All 25 main PDF pages and six figures were inspected, not raw supplementary data. Energy conservation and leakage prevention are interpretations."
      },
      {
        "reference": "DOI:10.1111/mmi.14511",
        "snippet": "bacteria can actively abandon flagella after prolonged stationary culturing",
        "notes": "Zhuang et al. 2020, PMID:32259388, scientific abstract, sentence beginning Interestingly. Direct MED/publisher match and native VERIFIED. Main publisher text and six figure captions were subsequently read, not the actual figures or supplement. Sections 2.4-2.7 separate daughter-cell dilution from stationary-phase shedding. OD times flagellated fraction is a population proxy, not a direct cell count. VIO5 and engineered EGFP-FliG strain NMB344 are distinct; red/green panels in Figure 3 are not the same cells. Two-color experiments in Figures 5-6 support basal release, but rod breakage is inferred, not a directly imaged cut. Surface immobilization and medium exchanges constrain the assay."
      },
      {
        "reference": "DOI:10.1038/s41467-026-75593-6",
        "snippet": "Nutrient depletion significantly increases the frequency of flagellar shedding and the accumulation of closed FOMCs",
        "notes": "Guo et al. 2026, PMID:42660870, PMC13521929.1, Results, Two distinct in situ architectures of the flagellar motor in V. cholerae, and Supplementary Figure 4. Direct JATS match; native NOT_IN_ABSTRACT. FOMC denotes the flagellar outer membrane complex. The quoted experiment uses wild-type V. cholerae; delta-flhG structural samples are distinct. All 12 main PDF pages and six main figures were inspected, plus the actual supplementary Figure 4 and supplementary tables. Its 81/273 observations are cells in the figure caption and tomograms in Methods/Table 4, not biological replicates or ejection rates. The main-text Table 3 pointer instead corresponds to Table 4. Other supplements remain incompletely read."
      }
    ],
    "discussions": [
      {
        "discussion_id": "bacterial-polar-flagellar-ejection-scope",
        "prompt": "Review active basal release separately from possession, loss and resorption.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "This qualified phenotype requires active basal release of previously assembled polar flagellar axial structures. Hook-filament release is an observed endpoint, not a universal component-completeness requirement. Flagellar possession or arrangement, assembly failure, motor arrest, reduced motility, a decreasing flagellated fraction or passive filament breakage alone do not establish it. Periplasmic resorption and microbial-eukaryotic axonemal autotomy are distinct. Phenotype METPO:1000059 is a definition-based parent inference; locomotory possession is not a required parent. The definition does not require every flagellum to be lost, nonmotility, a particular stimulus, exact severing site, relic morphology or universal behavior among polar-flagellated bacteria. No bare shedding or deflagellation exact synonym is asserted.",
        "posed_by": "codex",
        "posed_date": "2026-10-15"
      },
      {
        "discussion_id": "bacterial-polar-flagellar-ejection-metpo",
        "prompt": "Review the phenotype hierarchy without reviving retired flagellar identifiers.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Pinned and current METPO release annotations distinguish motility, locomotory flagellar possession and polar arrangement from ejection. Historical METPO:0000089 and METPO:000090 are deprecated with OMO:0001000; METPO:1000381 is deprecated with IAO:0000226. Their replacement METPO:1000704 denotes possession, not shedding. Deprecated flagellum METPO:1000123 has OMO:0001000 and no observed replacement or consider annotation. These are not exact mappings and are not reactivated. The current editor is an import stub, not a full release. The ontology pin remains unchanged. Proposal v608 reserves METPO:1068500 within 1068500-1068599; the local identifier is traitmech:000732. No upstream release or human sign-off is implied.",
        "posed_by": "codex",
        "posed_date": "2026-10-15"
      },
      {
        "discussion_id": "bacterial-polar-flagellar-ejection-mechanism",
        "prompt": "Keep organismal ejection separate from universal molecular and sequence claims.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "The 2026 structures assign closure to FlgI conformational changes in V. cholerae; the 2019 interpretation of an unidentified added plug is not imposed as a universal mechanism. Assembly defects in gate-deletion mutants do not by themselves demonstrate failure of ejection. Cryo-ET states are not a longitudinal trajectory of the same motor. A protein-resolved causal graph needs taxon-paired authority-checked accessions and edge-specific evidence. Gene, motif and domain presence alone do not establish this organism-level phenotype. Mechanisms are deferred, not claimed absent.",
        "posed_by": "codex",
        "posed_date": "2026-10-15"
      },
      {
        "discussion_id": "bacterial-polar-flagellar-ejection-provenance",
        "prompt": "Resolve assay-specific strain provenance before asserting canonical taxa.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Source organism names remain qualified observations, not independently resolved canonical taxon assertions. Engineered structural samples and source-designated wild-type nutrient assays must not be conflated. MED metadata and accessible publisher text were checked; unavailable publisher or PubMed pages are access limits, not evidence that no notice exists. This is not comprehensive correction/retraction clearance, raw-data reanalysis, independent replication, paid research or human sign-off.",
        "posed_by": "codex",
        "posed_date": "2026-10-15"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-15T11:39:29Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added active basal release of assembled bacterial polar flagellar structures with three primary DOI sources and directly checked 12/9/15-word snippets. Native NOT_IN_ABSTRACT/VERIFIED/NOT_IN_ABSTRACT remain distinct from direct full-text checks. Reserved 000732, v608 and 1068500-1068599 after ignored/hidden current-file, retained-history, complete-range and open/draft PR checks, including the changed CommunityMech PR2018 worktree. No obsolete identifier, exact mapping, canonical taxon or universal molecular mechanism is inferred. Timestamp records observed acceptance, not source acquisition.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-15T13:07:41Z",
        "curator": "codex",
        "action": "CORRECT_EVIDENCE_LOCATOR",
        "changes": "Corrected the Ferreira 2019 third-paragraph locator to the sole subsection paragraph, HTML anchor article1.body1.sec2.sec4.p1, spanning PDF pages 4-5. Preserved the verbatim excerpt, native NOT_IN_ABSTRACT outcome, biological claims and prior history. Source HTML and PDF pages were rechecked for issue #1947.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000183",
    "label": "bacteriocin production",
    "definition": "A physiological trait in which bacteria produce bacteriocins, ribosomally synthesized antimicrobial peptides or proteins that kill or inhibit other bacteria.",
    "definition_source": "DOI:10.3389/fmicb.2016.00461",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "xrefs": [
      "GO:0030152"
    ],
    "evidence": [
      {
        "reference": "DOI:10.3389/fmicb.2016.00461",
        "snippet": "Bacteriocins are ribosomally synthesized antimicrobial peptides produced by bacteria, which have the ability to kill or inhibit other bacteria.",
        "notes": "Rea et al. review bacteriocins as bacterially produced ribosomal antimicrobial peptides."
      },
      {
        "reference": "DOI:10.1146/annurev.micro.56.012302.161024",
        "snippet": "the most abundant and diverse family of microbial defense systems: the bacteriocins.",
        "notes": "Riley and Wertz support bacteriocins as a widespread, diverse microbial defense-system family."
      },
      {
        "reference": "DOI:10.1038/srep27973",
        "snippet": "Traditionally, nisin was produced industrially by using Lactococcus lactis in the neutral fermentation process.",
        "notes": "Zhang et al. support Lactococcus lactis as an industrial nisin-producing bacterium."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1358",
        "taxon_label": "Lactococcus lactis",
        "note": "Lactococcus lactis is used as a canonical nisin-producing bacterium in neutral fermentation.",
        "reference": "DOI:10.1038/srep27973"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-14T05:04:06Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted bacteriocin production as a DOI-backed TraitRecord after a repository-wide duplicate review covering ignored and hidden files; METPO has no exact bacteriocin production class yet and the placeholder is reserved in proposals/metpo_traitmech_v60.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-14T05:16:59Z",
        "curator": "codex",
        "action": "ADVERSARIAL_REVIEW_REPAIR",
        "changes": "Resolved PR #899 review issue #900 by grounding bacteriocin production to GO:0030152 and removing the obsolete xref-gap TODO.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-21T21:12:25Z",
        "curator": "claude",
        "action": "CURATE_CAUSAL_GRAPH",
        "changes": "Added MECHANISTIC causal_graphs entry (bacteriocin_production_defense_mechanism) anchored on existing verbatim record evidence snippets.",
        "llm_assisted": true
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "bacteriocin_production_defense_mechanism",
        "title": "Ribosomal bacteriocin peptide production and antibacterial defense",
        "description": "Evidence-backed physiological mechanism linking ribosomally synthesized bacteriocin peptides to the bacteriocin production trait and microbial defense against competing bacteria.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "Peptide-anchored mechanism backed by DOI:10.3389/fmicb.2016.00461 and DOI:10.1146/annurev.micro.56.012302.161024, with reviewed Lactococcus lactis subsp. lactis lantibiotic nisin-A (UniProtKB:P13068) curated on the InterPro:IPR006079 bacteriocin peptide node.",
        "nodes": [
          {
            "node_id": "bacteriocin_production_trait",
            "label": "bacteriocin production",
            "node_type": "TRAIT",
            "grounding": "traitmech:000183",
            "description": "Physiological trait in which bacteria synthesize antimicrobial bacteriocin peptides or proteins."
          },
          {
            "node_id": "bacteriocin_production_lantibiotic",
            "label": "Lantibiotic type-A",
            "node_type": "GENE_OR_PROTEIN",
            "grounding": "InterPro:IPR006079",
            "description": "Ribosomally synthesized antimicrobial bacteriocin peptide family exemplified by Lactococcus lactis nisin-A.",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:P13068",
                "entry_status": "REVIEWED",
                "entry_version": 93,
                "sequence_version": 1,
                "retrieved_on": "2026-10-21",
                "gene_symbol": "spaN",
                "protein_label": "Lantibiotic nisin-A",
                "taxon_id": "NCBITaxon:1360",
                "taxon_label": "Lactococcus lactis subsp. lactis",
                "role": "Ribosomally synthesized class I lantibiotic bacteriocin peptide produced by Lactococcus lactis subsp. lactis.",
                "evidence": [
                  {
                    "reference": "DOI:10.3389/fmicb.2016.00461",
                    "snippet": "Bacteriocins are ribosomally synthesized antimicrobial peptides produced by bacteria, which have the ability to kill or inhibit other bacteria.",
                    "notes": "Rea et al. define bacteriocins as ribosomally synthesized antimicrobial peptides produced by bacteria, exemplified by Lactococcus lactis nisin-A (UniProtKB:P13068)."
                  }
                ]
              }
            ]
          },
          {
            "node_id": "bacteriocin_production_antibacterial_defense",
            "label": "defense response to bacterium",
            "node_type": "BIOLOGICAL_PROCESS",
            "grounding": "GO:0042742",
            "description": "Microbial defense function killing or inhibiting competing bacteria."
          }
        ],
        "edges": [
          {
            "subject": "bacteriocin_production_lantibiotic",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "bacteriocin_production_trait",
            "description": "Ribosomally synthesized antimicrobial bacteriocin peptides confer the bacteriocin production trait.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2016.00461",
                "snippet": "Bacteriocins are ribosomally synthesized antimicrobial peptides produced by bacteria, which have the ability to kill or inhibit other bacteria.",
                "notes": "Rea et al. define bacteriocins as ribosomally synthesized antimicrobial peptides produced by bacteria."
              }
            ]
          },
          {
            "subject": "bacteriocin_production_lantibiotic",
            "predicate": "enables",
            "predicate_id": "RO:0002327",
            "object": "bacteriocin_production_antibacterial_defense",
            "description": "Bacteriocin peptides function as microbial defense systems against competing bacteria.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev.micro.56.012302.161024",
                "snippet": "the most abundant and diverse family of microbial defense systems: the bacteriocins.",
                "notes": "Riley and Wertz characterize bacteriocins as an abundant and diverse family of microbial defense systems."
              }
            ]
          }
        ]
      }
    ]
  },
  {
    "identifier": "traitmech:000661",
    "label": "ballistospore discharge",
    "definition": "A physiological phenotype in which a fungus forcibly discharges spores through coalescence of Buller's drop with liquid on the spore surface.",
    "definition_source": "DOI:10.1371/journal.pone.0004163",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1371/journal.pone.0004163",
        "snippet": "At the moment of fusion, Buller's drop snaps from the hilar appendix onto the adjacent spore surface.",
        "notes": "Stolze-Rybczynski et al. (2009), PMID:19129912, PMC2612744; Introduction, first paragraph, directly retrieved as publisher HTML and Europe PMC full-text XML. Abstract, Introduction, Results and Discussion, Table 1 and Methods were read. Seven basidiomycete species were analyzed by high-speed video; the yeast Sporobolomyces salmonicolor NPM01 had a measured mean launch speed of 1.42 +/- 0.12 m/s (s.e.m., six launches). Its 0.54 +/- 0.04 mm flight range is calculated, not a directly measured range. Drop geometry and flight range vary; a prominent lens-shaped adaxial drop is not universal. Figure captions were read, but image retrieval failed; actual figures, videos and supplements were not inspected."
      },
      {
        "reference": "DOI:10.1371/journal.pone.0105147",
        "snippet": "Ballistospores can be produced either asexually (ballistoconidia) or sexually (basidiospores).",
        "notes": "Ianiri et al. (2014), PMID:25148260, PMC4141788; Introduction directly retrieved as full-text XML. This quotation supports terminology, not a new comparison of sexual and asexual development. Scientific abstract, strain table, mirror-assay Methods, initial mutant-screen Results and Discussion were also read. Of 18 mirror mutants, 17 had absent or reduced spore production; GI277 still formed abundant ballistospores but failed to release them. A failed mirror assay alone thus does not distinguish formation from discharge. PHS1 results concern delayed formation and broader cellular defects, not a demonstrated universal release motor. Actual figures, supplements and independent IAM 13481 provenance were not inspected; no canonical example is inferred from these mutants."
      },
      {
        "reference": "DOI:10.1242/jeb.029975",
        "snippet": "The fusion of the droplet onto the spore creates a momentum that propels the spore forward.",
        "notes": "Noblin, Yang and Dumais (2009), PMID:19684219; scientific abstract retrieved directly through Europe PMC. The study reports high-speed observations in Auricularia auricula and Sporobolomyces yeasts, mechanical analysis and calibrated microcantilever measurements of detachment work. The artificial validation system is not a fungal exemplar. Predicted and observed velocities are distinct quantities. Full text, figures, supplements and strain provenance were not inspected; the abstract is not a complete mechanistic audit."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:5005",
        "taxon_label": "Sporobolomyces salmonicolor",
        "reference": "DOI:10.1371/journal.pone.0004163",
        "note": "Strain NPM01. Table 1 reports high-speed-video launch measurements from six spores, with mean initial speed 1.42 +/- 0.12 m/s (s.e.m.); the listed flight distance is modeled, not directly measured. Organisms and culture methods at https://doi.org/10.1371/journal.pone.0004163 identify NPM01 as isolated from a contaminated manufacturing facility and report spore formation on potato dextrose agar within 24 h. That primary provenance passage was read directly; no engineered-strain origin is inferred. NCBI Taxonomy resolves the species ID and label. This example concerns NPM01 under the reported conditions, not every strain or life stage."
      }
    ],
    "discussions": [
      {
        "discussion_id": "ballistospore-discharge-scope-and-hierarchy",
        "prompt": "Review dispersal hierarchy without equating formation and discharge.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Use phenotype METPO:1000059. The sporulation and spore-forming records METPO:1000870 and METPO:1000871 concern endospores. Fungal conidiation traitmech:000657 concerns production of asexual propagules, whereas ballistospores include sexual and asexual forms and formation can persist without release. Discharge is also distinct from passive shedding, later wind transport and pressure-driven ascospore or sporangium ejection. Motility METPO:1000701 emphasizes independent locomotion; a closer dispersal parent and process-versus-phenotype mappings need review. Ballistospore and ballistoconidium name cells, not exact synonyms of this disposition; no exact synonyms or xrefs are asserted. Do not require a particular speed, distance, fruiting body or asexual developmental mode.",
        "posed_by": "codex",
        "posed_date": "2026-10-07"
      },
      {
        "discussion_id": "ballistospore-discharge-mechanism-and-readouts",
        "prompt": "Keep measured discharge, formation defects and physical models distinct.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "The cited studies support a surface-tension mechanism, not an unknown-mechanism claim. A causal graph is deferred until the full mechanical study and supplementary observations are inspected and the repository's protein-required MECHANISTIC graph convention is reconciled with a physical coalescence mechanism. Do not invent a protein motor or label a physical causal model NONMECHANISTIC merely to pass the audit. PHS1 possession or expression does not establish discharge; the 2014 formation-defect experiments do not isolate a universal ejection pathway. Negative mirror transfer can reflect impaired production, release or subsequent growth. The 2017 study at https://pmc.ncbi.nlm.nih.gov/articles/PMC5550963/ remains an unread research lead: PMC returned a challenge and two XML requests failed. It is not counted as verified evidence.",
        "posed_by": "codex",
        "posed_date": "2026-10-07"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-07T08:42:05Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added ballistospore discharge with three directly checked DOI-backed snippets, a provenance-qualified NPM01 example and explicit formation/discharge and measured/modeled distinctions. Ignored-and-hidden searches and structured METPO review found no exact record. Reserved METPO:1061400 in v537; existing records unchanged. Physical mechanism evidence is retained; graph formalization is deferred.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-07T09:12:00Z",
        "curator": "codex",
        "action": "CORRECTED_EVIDENCE_SNIPPET",
        "changes": "Replaced the subjectless Results fragment with a complete, exact Introduction sentence describing Buller's-drop fusion (#1781). Updated the section locator; retained the original minting event and all experimental and source-access qualifications.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000714",
    "label": "behavioral habituation",
    "definition": "A physiological phenotype in which repeated stimulation produces an experience-dependent decrease in a microbial organism's behavioral response that is not attributable solely to sensory adaptation or motor fatigue.",
    "definition_source": "DOI:10.1098/rspb.2016.0446",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1098/rspb.2016.0446",
        "snippet": "The Q and CAF slime moulds crossing a bridge containing quinine or caffeine for the sixth time showed reduced aversive behaviour.",
        "notes": "Boisseau et al. 2016, PMID:27122563, PMC4855389; page 4, Results (b), Test phase 1. Q and CAF denote cultured Physarum polycephalum plasmodia repeatedly exposed to quinine or caffeine bridges. Five daily exposures precede same/alternate-repellent tests; two plain-agar days precede retesting. Contact latency, crossing time and shape are different readouts. Caffeine does not show every quinine effect: initial crossing time was not slower than control, and recovery was incomplete. Residual aversiveness remains. Alternate-repellent responses support stimulus specificity, not universal exclusion of every confound. Main Methods, Results, Discussion and all five figures were inspected in a public publisher-formatted PDF bearing a 2016 download stamp, not verified as the current corrected VoR. Supplementary statistics and raw data were not assessed. The contiguous quote crosses PDF columns; direct text and visual checks agree. Native abstract lookup: NOT_IN_ABSTRACT."
      },
      {
        "reference": "DOI:10.1016/j.cub.2025.05.071",
        "snippet": "the response to the low force stimuli shows extensive habituation even though the response to the alternating high force stimuli does not.",
        "notes": "Rajan and Marshall 2025, PMID:40562036, PMC13499368; Figure 4F caption, concluding result clause in retained PMC author-manuscript HTML. Figure 4F is an experimental contraction response in cultured Stentor coeruleus, not the adjacent model panel. Preserved stronger-stimulus responses argue against general motor exhaustion. The caption describes identical control timing, while Methods describes one low-force control tap per minute versus alternating forces at one total tap per minute; exact cadence equivalence remains unresolved. Figure 4I uses intervening low-force stimulation, not a stimulus-free rest; Figure 5 separately tests recovery after training. Anchored healthy nondividing cells were selected from Ward's cultures; field-of-view denominators vary. Experimental Results, relevant Methods and actual Figures 4-7 were inspected. Receptor internalization is modeled, not an identified molecular mechanism. Supplements and simulations were not reanalyzed. Native abstract lookup: NOT_IN_ABSTRACT; the exact full-text caption match is a separate check."
      },
      {
        "reference": "DOI:10.1016/j.cub.2026.03.080",
        "snippet": "For cells treated with either cycloheximide or puromycin, the primary effect on learning was accelerating habituation (Figure 1C, 1E).",
        "notes": "Rajan et al. 2026, PMID:42025171, PMC13192338; Results S3, retained PMC author manuscript. Stentor contraction assays compare drug-treated and vehicle cultures under repeated mechanical stimulation. Figure 1C uses puromycin with two-hour pretreatment; Figure 1E describes 12-hour cycloheximide pretreatment, unlike general short-term Methods prose. Dose, stimulus strength and cadence differ; conditions are not interchangeable. Drug effects do not prove universally protein-synthesis-independent learning. Relevant Results and Methods and actual Figures 1, 3, 4 and 6 were inspected, not all omics analyses or supplements. RNAi and pharmacology retain off-target, anchoring, feeding and subculture limitations. SteCoe_6763 recovery differences were not significant. Figure 6 follows division during continuing stimuli, not retention after withdrawal. Results and Methods point to different supplementary electrical-control panels. This follow-up shares a laboratory with the 2025 study, not an independent replication. Native abstract lookup: NOT_IN_ABSTRACT; directly matched Results quote."
      },
      {
        "reference": "DOI:10.1016/j.nlm.2008.09.012",
        "snippet": "Habituation is defined as a behavioral response decrement that results from repeated stimulation and that does not involve sensory adaptation/sensory fatigue or motor fatigue.",
        "notes": "Rankin et al. 2009, PMID:18854219, PMC2754195; section 2, page 136 (PDF page 2), complete opening definition. This consensus review supports operational terminology, not a microbial experiment or independent replication. Its nervous-system framing is not imposed on non-neural microbes. The public institutional PDF was directly read and pages 2-4 visually inspected. PDF ligatures are expanded and whitespace folded for matching; no paraphrase is substituted. Partial recovery is allowed. Responding to a novel stimulus is not itself dishabituation, which restores the original response. The behavioral criteria are not a demonstrated common molecular mechanism. Source-qualified MED identity was checked; its absent commentCorrectionList is not exhaustive notice clearance."
      }
    ],
    "discussions": [
      {
        "discussion_id": "habituation-scope-and-hierarchy",
        "prompt": "Retain a behavioral endpoint and distinguish neighboring uses of adaptation.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Repeated-stimulus decrement alone is insufficient: evaluate sensory adaptation, motor fatigue, injury/toxicity, selection and depletion alternatives in the actual assay. Specificity and recovery provide operational support without identifying all underlying mechanisms. Rankin 2009 frames habituation in neural behavioral terms; Rajan 2025 distinguishes that usage from cellular adaptation while modeling related receptor dynamics. This record concerns microbial behavior, not a categorical ban on shared molecular machinery. No fixed time, curve, complete recovery, dishabituation or all ten hallmarks are required in every experiment. Response to a stronger stimulus is not itself dishabituation. Carbon-source memory (traitmech:000706), acquired stress-resistance memory (traitmech:000712), enhanced transcriptional reactivation memory (traitmech:000713), anticipation, bet hedging and nutrient adaptation have distinct endpoints. Chemotaxis is not a parent of every behavioral assay. METPO:1000059 phenotype is the conservative parent; generic learning, memory and adaptation are not asserted as exact synonyms.",
        "posed_by": "codex",
        "posed_date": "2026-10-13"
      },
      {
        "discussion_id": "habituation-evidence-and-mechanism-limits",
        "prompt": "Resolve source discrepancies and culture provenance before adding taxa or mechanisms.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Different taxa and assays support the phenotype, not independent replication of each experiment. Laboratory culture provenance has not been independently resolved for natural canonical taxa; no species-wide assignment follows. Unread supplements, raw data and statistical reanalysis remain gaps. The 2025 control cadence, 2026 cycloheximide timing and electrical-control locators remain unresolved source discrepancies. Retained public PDFs and author manuscripts are not verified equivalent to current corrected publisher versions. Bounded MED/Crossref checks are not proof of notice absence. Modeled receptor internalization, exploratory omics and drug/RNAi effects do not justify a universal protein-resolved mechanism. No causal graph, protein examples, canonical taxa or exact external mappings are asserted. Access failures, source hashes and actual snippet-verifier results are in the sidecar.",
        "posed_by": "codex",
        "posed_date": "2026-10-13"
      },
      {
        "discussion_id": "habituation-historical-identity",
        "prompt": "Reconcile deprecated adaptation neighbors without reviving their identifiers.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Pinned and inspected current METPO graphs mark METPO:1000004 adaptation, METPO:1000005 adaptive trait, METPO:0000248 and METPO:000249 Microbial Adaptation deprecated below ObsoleteClass, with OMO:0001000 and no inspected replacement or consider annotations. METPO issue 521 disputes the mechanically assigned reasons. Original historical scopes remain unresolved; labels do not prove equivalence or nonequivalence. This operational behavioral phenotype is accepted independently from primary evidence, not by reviving an obsolete term or inferring biological invalidity. Available ignored/hidden files, retained tracked history, pending changes, ontology graphs and live corpus semantics revealed no exact active record in the inspected scope. No historical exact mapping is asserted. The pinned ontology and existing records remain unchanged; discovery is not exhausted.",
        "posed_by": "codex",
        "posed_date": "2026-10-13"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-13T04:41:26Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added behavioral habituation with three primary DOI sources and one terminology review, each with a contiguous snippet. Qualified assay, version, mechanism and historical-identity limitations. Reserved 000714, v590 and 1066700-1066799 after scoped ignored/hidden, retained-history, independent-copy and pending-PR checks, with numeric false positives explicitly adjudicated. Existing records unchanged; no canonical taxa or causal graph. Timestamp is the observed UTC post-audit confirmation, not an estimated write time.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000148",
    "label": "beta-galactosidase activity",
    "definition": "A physiological enzyme-activity phenotype in which a cell produces active beta-galactosidase enzymes that hydrolyze lactose into glucose and galactose.",
    "definition_source": "DOI:10.3389/fmicb.2021.742300",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.3389/fmicb.2021.742300",
        "snippet": "\u03b2-Galactosidase (EC 3.2.1.23), also referred to as lactase, is an important member of glycosyl hydrolase, which can hydrolyze O-glycosidic bonds of lactose by hydrolysis reaction, resulting in the production of glucose and galactose",
        "notes": "Zhou et al. define beta-galactosidase as EC 3.2.1.23, a lactose-hydrolyzing glycosyl hydrolase that produces glucose and galactose, grounding the enzyme activity named by the organism-level phenotype."
      },
      {
        "reference": "DOI:10.1128/jcm.22.3.333-335.1985",
        "snippet": "Selenomonas sputigena was positive for \u03b1-galactosidase, \u03b2-galactosidase, and \u03b1-glucosidase (API ZYM strip) and for \u03b1-glucosidase, \u03b2-glucosidase, and \u03b1-galactosidase (API An-Ident strip).",
        "notes": "Tanner et al. detected beta-galactosidase in Selenomonas sputigena with the API ZYM enzyme activity panel."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:69823",
        "taxon_label": "Selenomonas sputigena",
        "note": "Tanner et al. reported Selenomonas sputigena as positive for beta-galactosidase in the API ZYM enzyme activity panel.",
        "reference": "DOI:10.1128/jcm.22.3.333-335.1985"
      }
    ],
    "discussions": [
      {
        "discussion_id": "beta-galactosidase-activity-xref-gap",
        "prompt": "Resolve an exact external ontology class for beta-galactosidase activity before adding a TraitRecord xref.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "GO:0004565 carries the same beta-galactosidase activity label but denotes the enzyme molecular function rather than the organism-level beta-galactosidase production phenotype, so it is appropriate as a causal-node grounding rather than an equivalent TraitRecord xref.",
        "posed_by": "codex",
        "posed_date": "2026-09-11"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-11T19:47:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted beta-galactosidase activity as a DOI-backed TraitRecord after a repository-wide duplicate review covering ignored and hidden files; METPO has no exact beta-galactosidase activity class yet.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000146",
    "label": "beta-glucosidase activity",
    "definition": "A physiological enzyme-activity phenotype in which a cell produces active beta-glucosidase enzymes that hydrolyze beta-D-glucosidic bonds in beta-D-glucosides.",
    "definition_source": "DOI:10.1007/s13205-015-0328-z",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1007/s13205-015-0328-z",
        "snippet": "\u03b2-Glucosidases (\u03b2-d-glucopyrranoside glucohydrolase) [E.C.3.2.1.21] are the enzymes which hydrolyze the glycosidic bond of a carbohydrate moiety to release nonreducing terminal glycosyl residues, glycoside and oligosaccharides",
        "notes": "The review defines beta-glucosidases as EC 3.2.1.21 glycoside hydrolases, grounding the enzyme activity named by the organism-level phenotype."
      },
      {
        "reference": "DOI:10.2323/jgam.60.59",
        "snippet": "In API ZYM, activities are positive for alkaline phosphatase, esterase (C4), leucine arylamidase, valine arylamidase, cystine arylamidase, acid phosphatase, naphthol-AS-BI-phosphohydrolase, \u03b1-glucosidase, \u03b2-glucosidase",
        "notes": "The Flavobacterium panaciterrae species description reports beta-glucosidase among positive API ZYM activities for the DCY69T type strain."
      },
      {
        "reference": "DOI:10.3390/microorganisms12040776",
        "snippet": "Although both strains showed positive results for \u03b1-glucosidase activity, \u03b2-glucosidase activity was only observed in L. mucosae NK41.",
        "notes": "Ma et al. detected beta-glucosidase activity in Limosilactobacillus mucosae NK41 with the API ZYM enzyme activity panel."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1222002",
        "taxon_label": "Flavobacterium panaciterrae",
        "note": "An et al. reported Flavobacterium panaciterrae DCY69T as positive for beta-glucosidase in the API ZYM enzyme activity panel.",
        "reference": "DOI:10.2323/jgam.60.59"
      }
    ],
    "discussions": [
      {
        "discussion_id": "beta-glucosidase-activity-xref-gap",
        "prompt": "Resolve an exact external ontology class for beta-glucosidase activity before adding a TraitRecord xref.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "GO:0008422 denotes the beta-D-glucosidase molecular function rather than the organism-level beta-glucosidase production phenotype, so it belongs as a causal-node grounding when a mechanistic graph needs the catalytic activity but not as an equivalent TraitRecord xref.",
        "posed_by": "codex",
        "posed_date": "2026-09-11"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-11T17:57:39Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted beta-glucosidase activity as a DOI-backed TraitRecord after a repository-wide duplicate review covering ignored and hidden files; METPO has no exact beta-glucosidase activity class yet.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000151",
    "label": "beta-glucuronidase activity",
    "definition": "A physiological enzyme-activity phenotype in which a cell produces active beta-glucuronidase enzymes that hydrolyze beta-D-glucuronosides to D-glucuronate and an alcohol.",
    "definition_source": "https://iubmb.qmul.ac.uk/enzyme/EC3/2/1/31.html",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "https://iubmb.qmul.ac.uk/enzyme/EC3/2/1/31.html",
        "snippet": "Reaction: a \u03b2-D-glucuronoside + H2O = D-glucuronate + an alcohol",
        "notes": "The NC-IUBMB EC 3.2.1.31 entry defines beta-glucuronidase by its accepted name and hydrolytic reaction, grounding the enzyme activity named by the organism-level phenotype."
      },
      {
        "reference": "DOI:10.1128/aem.50.6.1383-1387.1985",
        "snippet": "The beta-glucuronidase produced by E. coli cleaves the MUG substrate to yield a fluorescent end product.",
        "notes": "Moberg used beta-glucuronidase cleavage of MUG to detect Escherichia coli in food samples."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:562",
        "taxon_label": "Escherichia coli",
        "note": "Moberg reported beta-glucuronidase-mediated cleavage of MUG by Escherichia coli in a fluorogenic detection assay.",
        "reference": "DOI:10.1128/aem.50.6.1383-1387.1985"
      }
    ],
    "discussions": [
      {
        "discussion_id": "beta-glucuronidase-activity-xref-gap",
        "prompt": "Resolve an exact external ontology class for beta-glucuronidase activity before adding a TraitRecord xref.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "GO:0004566 carries the same beta-glucuronidase activity label but denotes the enzyme molecular function rather than the organism-level beta-glucuronidase production phenotype, so it is appropriate as a causal-node grounding rather than an equivalent TraitRecord xref.",
        "posed_by": "codex",
        "posed_date": "2026-09-12"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-12T00:37:27Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted beta-glucuronidase activity as a URL/DOI-backed TraitRecord after a repository-wide duplicate review covering ignored and hidden files; METPO has no exact beta-glucuronidase activity class yet.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-12T00:55:15Z",
        "curator": "codex",
        "action": "FIX_EVIDENCE_SNIPPET",
        "changes": "Corrected the IUBMB EC 3.2.1.31 water token from HTML-derived H_{2}O to source-visible H2O after Claude Code Review flagged the snippet as non-verbatim in https://github.com/CultureBotAI/TraitMech/issues/807.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000157",
    "label": "beta-N-acetylhexosaminidase activity",
    "definition": "A physiological enzyme-activity phenotype in which a cell produces active beta-N-acetylhexosaminidase enzymes that hydrolyze terminal, non-reducing N-acetyl-D-hexosamine residues in N-acetyl-beta-D-hexosaminides.",
    "definition_source": "https://iubmb.qmul.ac.uk/enzyme/EC3/2/1/52.html",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "synonyms": [
      {
        "synonym_text": "beta-N-acetyl-D-hexosaminide N-acetylhexosaminohydrolase activity",
        "synonym_type": "EXACT_SYNONYM",
        "source": "https://iubmb.qmul.ac.uk/enzyme/EC3/2/1/52.html"
      },
      {
        "synonym_text": "N-acetylhexosaminidase",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1021/jf020965x"
      },
      {
        "synonym_text": "beta-N-acetylglucosaminidase",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://iubmb.qmul.ac.uk/enzyme/EC3/2/1/52.html"
      },
      {
        "synonym_text": "N-acetyl-beta-glucosaminidase",
        "synonym_type": "RELATED_SYNONYM",
        "source": "TraitMech#453"
      }
    ],
    "evidence": [
      {
        "reference": "https://iubmb.qmul.ac.uk/enzyme/EC3/2/1/52.html",
        "snippet": "Reaction: Hydrolysis of terminal non-reducing N-acetyl-D-hexosamine residues in N-acetyl-\u03b2-D-hexosaminides",
        "notes": "The NC-IUBMB EC 3.2.1.52 entry defines beta-N-acetylhexosaminidase by its accepted reaction, grounding the glycosidase activity named by the organism-level phenotype."
      },
      {
        "reference": "DOI:10.1021/jf020965x",
        "snippet": "Serratia marcescens YS-1, a chitin-degrading microorganism, produced mainly N-acetylhexosaminidase",
        "notes": "Kurakake et al. reported production of N-acetylhexosaminidase by Serratia marcescens YS-1, supporting this as a bacterial beta-N-acetylhexosaminidase activity phenotype."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:615",
        "taxon_label": "Serratia marcescens",
        "note": "Kurakake et al. reported Serratia marcescens YS-1 as mainly producing N-acetylhexosaminidase.",
        "reference": "DOI:10.1021/jf020965x"
      }
    ],
    "discussions": [
      {
        "discussion_id": "beta-n-acetylhexosaminidase-activity-xref-gap",
        "prompt": "Resolve an exact external ontology class for beta-N-acetylhexosaminidase activity before adding a TraitRecord xref.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "GO:0004563 denotes beta-N-acetylhexosaminidase molecular function rather than the organism-level beta-N-acetylhexosaminidase production phenotype, so it is appropriate as a causal-node grounding rather than an equivalent TraitRecord xref.",
        "posed_by": "codex",
        "posed_date": "2026-09-12"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-12T04:12:07Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted beta-N-acetylhexosaminidase activity as a URL/DOI-backed TraitRecord after a repository-wide duplicate review covering ignored and hidden files; METPO has no exact beta-N-acetylhexosaminidase activity class yet.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000085",
    "label": "bioluminescence",
    "definition": "A physiological capability to emit visible light through a luciferase-catalyzed reaction, frequently regulated by quorum sensing in marine bacteria such as Aliivibrio and Photobacterium.",
    "definition_source": "DOI:10.1016/j.csbj.2018.11.003",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "synonyms": [
      {
        "synonym_text": "luminescent",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1016/j.csbj.2018.11.003"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1016/j.csbj.2018.11.003",
        "notes": "Brodl, Winkler & Macheroux review the molecular mechanisms of bacterial bioluminescence and the luciferase reaction."
      },
      {
        "reference": "DOI:10.1146/annurev.cellbio.21.012704.131001",
        "notes": "Waters & Bassler support quorum-sensing regulation of light production in luminous bacteria."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:668",
        "taxon_label": "Aliivibrio fischeri",
        "note": "Model bioluminescent bacterium (lux operon); Euprymna squid light-organ symbiont and quorum-sensing paradigm.",
        "reference": "DOI:10.3390/ijms140816386"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "bioluminescence_luciferase",
        "title": "Luciferase-catalyzed light emission",
        "description": "Evidence-backed causal sketch linking luciferase to oxygen-dependent light emission, often under quorum-sensing control.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "The graph describes the A. fischeri Lux system. LuxAB is a heterodimer, LuxCDE is a three-component fatty-acid reductase system, and LuxI/LuxR regulation is not universal to all bioluminescent organisms. The taxon-paired example anchors the LuxI quorum-sensing branch.",
        "nodes": [
          {
            "node_id": "bioluminescence_trait",
            "label": "bioluminescence",
            "node_type": "TRAIT",
            "grounding": "traitmech:000085",
            "description": "Capacity to emit visible light enzymatically."
          },
          {
            "node_id": "luciferase",
            "label": "luciferase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Enzyme catalyzing the light-emitting reaction.",
            "grounding": "GO:0047646"
          },
          {
            "node_id": "bioluminescence_process",
            "label": "bioluminescence",
            "node_type": "BIOLOGICAL_PROCESS",
            "grounding": "GO:0008218",
            "description": "Enzymatic emission of visible light."
          },
          {
            "node_id": "molecular_oxygen",
            "label": "molecular oxygen",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:15379",
            "description": "Co-substrate of the luciferase reaction."
          },
          {
            "node_id": "long_chain_aldehyde",
            "label": "long-chain aldehyde",
            "node_type": "CHEMICAL",
            "description": "Aliphatic aldehyde substrate (C8-C16) of the luciferase reaction."
          },
          {
            "node_id": "fmnh2",
            "label": "reduced flavin mononucleotide (FMNH2)",
            "node_type": "CHEMICAL",
            "description": "Reduced flavin substrate consumed by luciferase."
          },
          {
            "node_id": "fmn",
            "label": "flavin mononucleotide (FMN)",
            "node_type": "CHEMICAL",
            "description": "Oxidized flavin recycled in the luciferase cycle."
          },
          {
            "node_id": "lux_g",
            "label": "LuxG flavin reductase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "NAD(P)H-dependent flavin reductase generating FMNH2.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "LuxG homologs differ in pyridine-nucleotide preference, and the graph does not resolve a single exact reductase family or cofactor specificity."
          },
          {
            "node_id": "luxcde_complex",
            "label": "LuxCDE fatty acid reductase complex",
            "node_type": "GENE_OR_PROTEIN",
            "description": "LuxC/LuxD/LuxE complex supplying long-chain aldehyde substrate.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "This node denotes the three distinct LuxC, LuxD, and LuxE components; no single protein-family grounding can represent the complete reductase system."
          },
          {
            "node_id": "lux_i",
            "label": "LuxI autoinducer synthase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Synthase producing the 3-oxo-C6-HSL acyl-homoserine lactone autoinducer.",
            "grounding": "GO:0061579",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:P12747",
                "protein_label": "Acyl-homoserine-lactone synthase",
                "gene_symbol": "luxI",
                "taxon_id": "NCBITaxon:668",
                "taxon_label": "Aliivibrio fischeri",
                "entry_status": "REVIEWED",
                "retrieved_on": "2026-10-22",
                "entry_version": 98,
                "sequence_version": 1,
                "role": "LuxI synthesizes the 3-oxo-C6-HSL autoinducer that activates LuxR-dependent lux-locus expression in A. fischeri; it is a regulatory component, not the luciferase enzyme itself.",
                "evidence": [
                  {
                    "reference": "DOI:10.1128/JB.00035-24",
                    "snippet": "LuxI as the autoinducer synthase",
                    "notes": "The A. fischeri study identifies LuxI as the synthase for the LuxR-binding 3-oxo-C6-HSL signal; reviewed UniProtKB P12747 is the species-level LuxI entry."
                  }
                ]
              }
            ]
          },
          {
            "node_id": "lux_r",
            "label": "LuxR transcription factor",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Autoinducer-responsive activator of the lux locus.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "LuxR-family transcription factors include many signal specificities; the graph names the A. fischeri regulator but no exact whole-protein ontology term was verified beyond broad LuxR domains."
          },
          {
            "node_id": "autoinducer_hsl",
            "label": "3-oxo-C6-HSL autoinducer",
            "node_type": "CHEMICAL",
            "description": "LuxI-produced acyl-homoserine lactone quorum-sensing signal."
          },
          {
            "node_id": "lux_locus_expression",
            "label": "lux locus expression",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Transcription of the lux operon producing light-production machinery."
          }
        ],
        "edges": [
          {
            "subject": "luciferase",
            "predicate": "enables",
            "object": "bioluminescence_process",
            "description": "Luciferase carries out the light-emitting reaction.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.csbj.2018.11.003",
                "notes": "Brodl et al. review the bacterial luciferase mechanism."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "bioluminescence_process",
            "predicate": "consumes",
            "object": "molecular_oxygen",
            "description": "Light emission consumes molecular oxygen.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.csbj.2018.11.003",
                "notes": "Supports O2 as a luciferase co-substrate."
              }
            ],
            "predicate_id": "biolink:consumes"
          },
          {
            "subject": "bioluminescence_process",
            "predicate": "confers",
            "object": "bioluminescence_trait",
            "description": "The luciferase reaction realizes the bioluminescence trait.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev.cellbio.21.012704.131001",
                "notes": "Waters & Bassler support quorum-sensing control of luminescence."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "luciferase",
            "predicate": "catalyzes",
            "object": "long_chain_aldehyde",
            "description": "Luciferase catalyzes the monooxygenation of long-chain aliphatic aldehydes.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.csbj.2018.11.003",
                "notes": "The heterodimeric enzyme luciferase (LuxAB) catalyzes the monooxygenation of aliphatic aldehydes to the corresponding acids."
              }
            ],
            "predicate_id": "biolink:catalyzes"
          },
          {
            "subject": "fmnh2",
            "predicate": "is substrate for",
            "object": "bioluminescence_process",
            "description": "FMNH2 is a required substrate consumed in the light-emitting luciferase reaction.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.csbj.2018.11.003",
                "notes": "Long chain aldehydes, reduced flavin mononucleotide (FMNH2) and molecular oxygen (O2) are converted by the enzyme luciferase (LuxAB)."
              }
            ]
          },
          {
            "subject": "long_chain_aldehyde",
            "predicate": "is substrate for",
            "object": "bioluminescence_process",
            "description": "Long-chain aldehyde is a required substrate of the light-emitting reaction.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.csbj.2018.11.003",
                "notes": "Long chain aldehydes, reduced flavin mononucleotide (FMNH2) and molecular oxygen (O2) are converted by the enzyme luciferase (LuxAB)."
              }
            ]
          },
          {
            "subject": "lux_g",
            "predicate": "converts",
            "object": "fmn",
            "description": "LuxG flavin reductase reduces free FMN to FMNH2 supplying the luciferase reaction.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.csbj.2018.11.003",
                "notes": "LuxG converts free flavin (FMN) to reduced flavin (FMNH2); LuxG is a NAD(P)H-dependent flavin reductase."
              }
            ]
          },
          {
            "subject": "lux_g",
            "predicate": "produces",
            "object": "fmnh2",
            "description": "LuxG generates the reduced flavin substrate FMNH2.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.csbj.2018.11.003",
                "notes": "LuxG converts free flavin (FMN) to reduced flavin (FMNH2)."
              }
            ],
            "predicate_id": "METPO:2007800"
          },
          {
            "subject": "luxcde_complex",
            "predicate": "supplies",
            "object": "long_chain_aldehyde",
            "description": "The LuxCDE fatty acid reductase complex supplies the long-chain aldehyde substrate.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.csbj.2018.11.003",
                "notes": "To supply the long-chain aldehyde substrates to the luciferase, the proteins LuxC, LuxD, and LuxE constitute a fatty acid reductase complex."
              }
            ]
          },
          {
            "subject": "lux_i",
            "predicate": "synthesizes",
            "object": "autoinducer_hsl",
            "description": "LuxI autoinducer synthase produces the 3-oxo-C6-HSL signal.",
            "evidence": [
              {
                "reference": "DOI:10.1128/jb.00035-24",
                "notes": "Identifying LuxI as the autoinducer synthase; the LuxI-produced 3-oxo-C6 HSL."
              }
            ]
          },
          {
            "subject": "autoinducer_hsl",
            "predicate": "binds",
            "object": "lux_r",
            "description": "The 3-oxo-C6-HSL autoinducer binds the LuxR transcription factor.",
            "evidence": [
              {
                "reference": "DOI:10.1128/jb.00035-24",
                "notes": "The LuxI-produced 3-oxo-C6 was shown to bind the N-terminal domain of the transcription factor LuxR."
              }
            ]
          },
          {
            "subject": "lux_r",
            "predicate": "activates expression of",
            "object": "lux_locus_expression",
            "description": "Autoinducer-bound LuxR activates expression of the lux locus.",
            "evidence": [
              {
                "reference": "DOI:10.1128/jb.00035-24",
                "notes": "Bind the N-terminal domain of the transcription factor LuxR to activate the expression of the lux locus."
              }
            ]
          },
          {
            "subject": "lux_locus_expression",
            "predicate": "has output",
            "object": "luciferase",
            "description": "Expression of the lux locus produces the luciferase light-production machinery.",
            "evidence": [
              {
                "reference": "DOI:10.1128/jb.00035-24",
                "notes": "Activation of the lux locus drives expression of the light-production machinery including luciferase."
              }
            ],
            "predicate_id": "RO:0002234"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-06-04T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate PHYSIOLOGY trait (bioluminescence) from literature research.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-08T13:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (luciferase light emission) with GO/CHEBI node groundings and RO/biolink predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-14T06:38:15Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A010SSZ8\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 10 evidence-backed generic edges (9 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:14Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d72, biolink:catalyzes\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:21:12Z",
        "curator": "claude",
        "action": "RETRACT_DEAD_UNIPROT_GROUNDINGS",
        "changes": "Retracted 1 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 1 causal edge(s) off enables/RO:0002327 with a TRAIT object (1 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates (1 to has output), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T02:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES_PART2",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates onto their causal-graph counterparts (1 to produces), issue 301 part 2. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Each replacement is a 1:1 mirror of its source predicate that changes only the domain, so the claim each edge makes is unchanged and directions are unchanged. The replacements are proposed in proposals/metpo_traitmech_v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-24T11:05:00Z",
        "curator": "codex",
        "action": "CURATE_PROTEIN_TAXON_EXAMPLE",
        "changes": "Reviewed the Lux-system scope and every protein node, converted the canonical A. fischeri citation to DOI, grounded luciferase and LuxI functions, and added a reviewed A. fischeri LuxI protein example.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-22T01:35:00Z",
        "curator": "claude",
        "action": "REFRESH_UNIPROT_ENTRY_VERSION",
        "changes": "Refreshed UniProtKB entry_version against live UniProt REST on 2026-10-22: UniProtKB:P12747 (97 -> 98 on lux_i).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000690",
    "label": "biomineralization",
    "definition": "A physiological phenotype in which a microbe mediates the formation of mineral phases.",
    "definition_source": "DOI:10.1016/j.crte.2010.09.002",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1016/j.crte.2010.09.002",
        "snippet": "Microorganisms can mediate the formation of minerals by a process called biomineralization.",
        "notes": "Benzerara et al. 2011, scientific Abstract, directly checked in publisher HTML on 2026-10-10. Definition terminology, not an independent experimental replication: this is a review. Its Introduction and section 2 distinguish controlled, induced and biologically influenced formation, including organic-matrix effects. TraitMech represents the microbial phenotype rather than equating it with a process or material entity. The source cautions that association with pre-existing minerals does not establish formation. The remainder and actual figures were not audited for this record."
      },
      {
        "reference": "DOI:10.1128/AEM.07044-11",
        "snippet": "All bacteria tested induce the precipitation of a significant amount of calcium carbonate when cultured in M-3P medium.",
        "notes": "Rodriguez-Navarro et al. 2012, PMID:22447589, PMC3346411, Discussion, Bacterial carbonatogenesis. Publisher scientific Abstract, Introduction, Methods, Results and relevant Discussion directly read on 2026-10-10; actual Figures 1 and 6 inspected, other figures not visually audited. Inoculated assays produced carbonates whereas uninoculated substrate controls did not. Tested M. xanthus strain 422, B. diminuta SJ 63 and a stone bacterial community are assay labels, not verified canonical taxa here. Polymorph selection depends on the stated substrate/medium conditions, not a universal strain rule. The proposed amorphous precursor is not established by morphology alone. No universal urease requirement or functional protein mechanism is inferred."
      },
      {
        "reference": "DOI:10.1038/ncomms11228",
        "snippet": "Coccoliths are calcitic particles produced inside the cells of unicellular marine algae known as coccolithophores.",
        "notes": "Sviben et al. 2016, PMID:27075521, PMC4834641. Scientific Abstract directly checked in Europe PMC full-text XML on 2026-10-10; Introduction, calcite-resupply Results and Discussion also inspected. This supports controlled mineral production and the coccolith child's placement. Historical E. huxleyi AWI1516 observations do not establish every strain's current phenotype. A separate calcium-rich compartment is not proven to be a necessary direct precursor or bulk-transfer route. No new figure or supplement audit is claimed for this parent; the child's more detailed provenance is retained."
      },
      {
        "reference": "DOI:10.1016/j.protis.2016.05.002",
        "snippet": "Scales were formed one by one in silica deposition vesicles (SDVs)",
        "notes": "Nomura and Ishida 2016, PMID:27348459. Scientific abstract directly read on 2026-10-10 at https://rrc.nbrp.jp/references/56432?lang=en. Scale formation and silicon detection in immature-scale vesicles support mineral production beyond carbonates and the siliceous-scale child's placement. Historical Paulinella chromatophora naming does not establish current strain taxonomy. Full Methods and figures remain unread; proposed microtubule involvement is not molecular necessity. Scale production is distinct from subsequent shell assembly."
      }
    ],
    "discussions": [
      {
        "discussion_id": "biomineralization-scope-and-mappings",
        "prompt": "Keep mineral formation distinct from association and process-level mappings.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "The definition includes controlled, induced and matrix-mediated formation when microbial mediation is demonstrated; it is not restricted to carbonate, intracellular deposition or a crystalline end product. Benzerara et al. DOI:10.1016/j.crte.2010.09.002 section 2 includes passive organic-matter effects under biologically influenced biomineralization. This broad terminology is retained, but precipitation near a cell, isolated nonliving-matrix activity, mineral adhesion, uptake of preformed particles or ion adsorption alone does not establish that organism's formation phenotype. Organic-substrate mineralization, mineral dissolution, metal tolerance and mineral use as an electron donor are not equivalent. Coccolith and siliceous-scale production are narrower endpoints. Magnetosome and ferrosome organelle records retain their structural parents; no automatic cross-axis reparenting or disjointness is asserted. The magnetosome graph's similarly named node has narrower scope and is not exactly grounded to this umbrella. No synonyms or xrefs are asserted pending authority-backed phenotype mapping.",
        "posed_by": "codex",
        "posed_date": "2026-10-10"
      },
      {
        "discussion_id": "biomineralization-exemplars-and-mechanisms",
        "prompt": "Resolve assay-specific exemplars and distinct mineral-forming mechanisms.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "No canonical examples are assigned before strain provenance and current taxonomy are reconciled with the original assays. A community precipitation assay cannot be assigned wholesale to each community member. Substrate, medium, mineral phase, location and life stage qualify observations. No universal benefit, growth dependence, genetic control, obligatory enzyme or shared protein pathway follows from this umbrella. Separate controlled deposition from metabolically induced precipitation and organic-matrix effects when adding mechanisms. Functional evidence and taxon-paired accessions are required for protein edges; sequence features or mineral co-localization alone are insufficient. Mechanism is deferred, not claimed absent.",
        "posed_by": "codex",
        "posed_date": "2026-10-10"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-10T08:03:12Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added biomineralization with source-backed terminology, three primary studies and directly checked short snippets. Reserved 000690 and v566 block 1064300-1064399 after ignored-and-hidden main/worktree/open-PR checks. Resolved the coccolith and siliceous-scale production parent gaps without claiming common mechanisms or canonical taxa. Timestamp records the observed UTC curation decision.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000616",
    "label": "bipolar mating system",
    "definition": "A fungal mating phenotype in which compatibility between partners is governed by a single segregating mating-type factor.",
    "definition_source": "DOI:10.1073/pnas.91.15.7085",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1073/pnas.91.15.7085",
        "snippet": "A bipolar system is defined by a single genetic locus (MAT) that can have two or multiple alleles.",
        "notes": "Bakkeren and Kronstad (1994), PMID:7913746, PMC44343. Exact scientific-abstract sentence directly retrieved from Europe PMC core metadata. The abstract reports cloning of Ustilago hordei a1 and physical linkage of a and b into a complex MAT region, contrasted with genetically unlinked loci in U. maydis. The compatibility factor is not necessarily one gene. This supports definition and a reported linkage architecture, not a fresh verification of native crossing assays. Full text, figures, methods, supplements and natural strain provenance remain uninspected; no canonical strain is inferred."
      },
      {
        "reference": "DOI:10.1534/genetics.105.051128",
        "snippet": "All of the 24 collections displayed a bipolar mating system with only two mating types among all progeny of a collection.",
        "notes": "James et al. (2006), PMID:16461425, PMC1456265. Exact sentence in the first Results subsection on p. 1881, visually checked in the published PDF at https://public.websites.umich.edu/~mycology/resources/Publications/james2006.genetics.pdf; not an abstract quote. Native Coprinellus disseminatus single-spore crosses support the compatibility phenotype. Two types per collection does not mean only two across the species. Methods score clamps and dikaryotization, not automatically completed fertile sex; poor-mating progeny were excluded when choosing population testers. Table 3 shows segregation in 13 TJ00/38 progeny: MIP tracks mating type, whereas CDSTE3.1-.3 do not. Its plus/minus states are PCR-RFLP genotypes, not gene presence or absence; CDSTE3.4 lacks segregation data. The abstract reports heterologous sexual responses, not loss of all pheromone-receptor function. PDF pp. 1877-1882 and actual Tables 1-3 were read; pp. 1883-1884 were text-extracted only. Actual figures, later Results/Discussion and supplements remain uninspected. Natural North Carolina fruit-body provenance is described in Methods, but active taxon authority and the intersterile Japanese group remain unresolved; no canonical taxon assertion is made."
      }
    ],
    "discussions": [
      {
        "discussion_id": "bipolar-mating-scope-and-hierarchy",
        "prompt": "Keep genetic compatibility distinct from locus inventory and partner dependence.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "A single segregating compatibility factor need not be one gene, exactly two specificities across a species, or fused pheromone/receptor and homeodomain loci. Bakkeren describes recognition in heterothallic basidiomycetes, but its examples do not establish universal separate-partner dependence under the organism-level definition of traitmech:000610. The functional compatibility axis differs from self-fertility and from tetrapolar mating (traitmech:000615), which requires differences at two independently segregating factors. Use released phenotype METPO:1000059 in record and proposal; do not assert disjointness with homothallism, universal self-sterility or a sufficient guarantee of fertility. Resolve unifactorial terminology and external equivalences before adding synonyms or xrefs. PHYSIOLOGY is a filesystem category, not a narrower ontology parent.",
        "posed_by": "codex",
        "posed_date": "2026-10-05"
      },
      {
        "discussion_id": "bipolar-mating-mechanism-and-examples",
        "prompt": "Resolve native mechanisms and taxon authority before adding graphs or examples.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Complete unread source sections and inspect actual figures and supplements before extending mechanistic claims. Loss of mating-type specificity is not absence of receptor genes or loss of every cellular function. Keep native compatibility assays, genetic segregation, heterologous responses and completed fertile reproduction distinct. Resolve NCBI taxon authority and strain scope before canonical examples, and native protein accessions plus tested dependencies before causal edges. No NONMECHANISTIC graph bypasses grounding. Manual full-text checks do not replace the abstract resolver's actual verdict.",
        "posed_by": "codex",
        "posed_date": "2026-10-05"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-05T08:34:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added bipolar mating system with two primary DOI-backed sources and verbatim snippets. Kept single-factor compatibility distinct from gene inventory, globally two mating types, one molecular architecture and partner dependence. Ignored-and-hidden novelty and allocation searches found no exact record or ID collision. Reserved METPO:1057000 in v493 under released phenotype. Deferred canonical taxon assertions, lexical mappings, native protein graphs and explicitly unread source material.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-05T08:39:00Z",
        "curator": "codex",
        "action": "CORRECTED_EVIDENCE_LOCATOR",
        "changes": "Corrected the James p. 1881 locator: the verbatim quote is in the first Results subsection, not its first sentence (#1706). The quotation and biological interpretation are unchanged.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000706",
    "label": "carbon-source memory",
    "definition": "A physiological phenotype in which a non-genetic cellular state established by prior carbon-source conditions persists after those conditions change and alters subsequent induction or growth responses to carbon sources.",
    "definition_source": "DOI:10.1371/journal.pgen.1004556",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1371/journal.pgen.1004556",
        "snippet": "Cells grown under cyclical glucose/lactose conditions thus displayed phenotypic memory of their previous metabolic adaptation.",
        "notes": "Lambert and Kussell 2014, PMID:25255314, PMC4177670; Results / Phenotypic memory in response to sudden environmental changes, not the abstract. Primary text, actual Figure 2 and Text S1 were inspected. Repeated glucose/lactose switches demonstrate history-dependent growth; the paper distinguishes inherited protein persistence from continuing induction after stimulus removal. F3 is an engineered W3110 derivative, not an unmodified natural exemplar. Growth is a chamber-level relative elongation readout. DOI:10.1371/journal.pgen.1004793 corrects author-name typesetting, not the biological claims; the correction was read. Model predictions are not additional experimental replication. Other figures, raw data and equations were not independently reanalyzed."
      },
      {
        "reference": "DOI:10.7554/eLife.39234",
        "snippet": "past exposure to an environmental condition can shorten the time needed to adapt when the condition re-occurs",
        "notes": "Cerulus et al. 2018, PMID:30299256, PMC6211830; scientific abstract, confirmed against NCBI full-text XML. Relevant Results, Methods, Discussion, actual Figures 1, 2, 6 and Figure 1 supplement 4 were inspected. Carbon-shift assays separate population lag from single-cell growth resumption; cells not resuming within the observation window are not thereby proved dead. Cross-sugar effects and respiratory perturbations oppose an obligatory same-sugar or sugar-specific protein-inheritance mechanism. The main AN63 series is engineered; the separately reported non-laboratory strains have unreviewed primary provenance here. Publisher article access was challenged; public figure assets were accessible. Raw data and all other supplements were not reanalyzed."
      },
      {
        "reference": "DOI:10.1016/j.cub.2007.10.044",
        "snippet": "This \"galactose memory\" persists for several generations",
        "notes": "Zacharioudakis et al. 2007, PMID:17997309; directly retrieved, source-qualified MED scientific abstract only. The preceding sentence compares initial GAL activation with rapid reactivation in progeny after intervening glucose growth. This supports the induction endpoint, not a measured growth-rate benefit. Its Gal1 and cytoplasmic-factor interpretation remains assay-specific; the abstract's chromatin conclusion is not universalized. Full text, figures and strain provenance were not inspected. The index links a Comment in, not a correction or independent replication."
      }
    ],
    "discussions": [
      {
        "discussion_id": "carbon-memory-scope-and-hierarchy",
        "prompt": "Retain carbon-source history dependence without conflating its endpoints or neighboring traits.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "The qualifier carbon-source bounds this curator-defined class. Unqualified cellular, metabolic, phenotypic and transcriptional memory, bistability and hysteresis are not asserted as exact synonyms. Demonstrating the phenotype requires comparing prior histories under matched test conditions and genetic background; a single diauxic transition, persistent reporter fluorescence, gene presence or a different current medium alone is insufficient. Induction kinetics and growth recovery are distinct endpoints, and one must not be substituted for the other. No fixed duration, number of divisions, benefit, particular sugar, or molecular mechanism is required. Genetic adaptation, immune memory, chemotactic temporal sensing, stress priming and stochastic bet hedging are not equivalent. METPO:1000731 nutrient adaptation is a trophic-type class locally framed as the chronic copiotroph/oligotroph axis; diauxic growth denotes sequential nutrient use, and generalist/specialist describe niche breadth. METPO:1000059 phenotype is the conservative parent pending upstream hierarchy review. This is not a sequence-feature record or a precomposed uses-carbon-source assertion.",
        "posed_by": "codex",
        "posed_date": "2026-10-12"
      },
      {
        "discussion_id": "carbon-memory-examples-and-mechanisms",
        "prompt": "Resolve natural strain provenance and assay-specific causal branches before adding exemplars or a graph.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "The retained observations do not establish a uniform species-wide phenotype or a common protein-resolved mechanism. Canonical taxa require primary provenance and authority-resolved taxon identity; no canonical_examples, causal_graphs or external xrefs are asserted. Source-qualified MED and Crossref records were checked on 2026-10-12. Lambert's linked correction was read and retained in evidence notes; no other linked correction or retraction was exposed by these bounded records. Publisher/full-text access limits are recorded per source, not treated as absence of notices. The pinned and current upstream METPO releases contain no exact memory class found by the ignored/hidden lexical and RDF assessment; the ontology baseline remains unchanged.",
        "posed_by": "codex",
        "posed_date": "2026-10-12"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-12T03:30:18Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added carbon-source memory with three primary DOI-backed sources and directly checked snippets. Reserved 000706, v582 and 1065900-1065999 after ignored/hidden worktree and pending-PR checks. Endpoint, strain-provenance, mechanism and notice limits are explicit. Existing traits unchanged; timestamp is the observed UTC curation decision.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000633",
    "label": "carboxydotrophic",
    "definition": "A trophic type in which an organism derives energy from the oxidation of carbon monoxide.",
    "definition_source": "DOI:10.1038/nrmicro1595",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000631"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/nrmicro1595",
        "snippet": "Carbon monoxide (CO) supports the growth and metabolism",
        "notes": "Review supports aerobic CO oxidation as an energy-supporting metabolism."
      },
      {
        "reference": "DOI:10.1111/j.1574-6968.1986.tb01858.x",
        "snippet": "presence of the enzyme CO dehydrogenase",
        "notes": "Review supports CODH and CO-insensitive respiratory-chain features in aerobic carboxydotrophs."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:129958",
        "taxon_label": "Carboxydothermus hydrogenoformans",
        "note": "Thermophilic hydrogenogenic CO oxidiser (CO + H2O -> CO2 + H2). Afipia/Oligotropha carboxidovorans is the aerobic CO-oxidiser model.",
        "reference": "PMID:16311624"
      },
      {
        "taxon_id": "NCBITaxon:1085",
        "taxon_label": "Rhodospirillum rubrum",
        "note": "Canonical hydrogenogenic CO oxidizer with genetically and biochemically characterized cooS CODH and CooA-regulated coo operons.",
        "reference": "DOI:10.1128/jb.174.16.5284-5294.1992"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "carboxydotrophic_co_oxidation",
        "title": "Carboxydotrophic carbon monoxide oxidation mechanism",
        "description": "DOI-backed graph linking carbon monoxide, carbon monoxide dehydrogenase, respiratory electron transport, and energy conservation.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "Represents distinct aerobic molybdenum-CODH and anaerobic NiFe-CODH branches. The CooS exemplar supports the R. rubrum anaerobic branch; broad operon, CooA, RcoM, and terminal-oxidase labels are retained only with explicit review notes.",
        "nodes": [
          {
            "node_id": "carboxydotrophic_trait",
            "label": "carboxydotrophic",
            "node_type": "TRAIT",
            "grounding": "METPO:1000633",
            "description": "Trophic type deriving energy from carbon monoxide oxidation."
          },
          {
            "node_id": "carbon_monoxide",
            "label": "carbon monoxide",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:17245",
            "description": "Reduced C1 gas used as an energy substrate."
          },
          {
            "node_id": "carbon_monoxide_dehydrogenase",
            "label": "carbon monoxide dehydrogenase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "CODH enzyme oxidizing carbon monoxide.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "This umbrella node spans unrelated molybdenum- and NiFe-containing CODH classes; one family or activity term would collapse the graph's explicit branch distinction."
          },
          {
            "node_id": "molybdenum_hydroxylase",
            "label": "molybdenum hydroxylase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Aerobic CODH enzyme class described for CO oxidizers.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "The label denotes the multisubunit aerobic Cu/Mo CODH enzyme class; no checked whole-complex term exactly matches this graph node.",
            "gene_symbols": [
              "coxS",
              "coxM",
              "coxL"
            ],
            "operon": "coxSML"
          },
          {
            "node_id": "carbon_dioxide",
            "label": "carbon dioxide",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:16526",
            "description": "Oxidized product of CO oxidation."
          },
          {
            "node_id": "respiratory_chain",
            "label": "respiratory chain",
            "node_type": "PATHWAY",
            "description": "Electron-transfer system coupled to CO oxidation.",
            "grounding": "GO:0022904"
          },
          {
            "node_id": "co_insensitive_terminal_oxidase",
            "label": "CO-insensitive terminal oxidase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Terminal oxidase enabling respiration during CO oxidation.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "The cited source establishes a CO-insensitive respiratory branch but does not identify an exact terminal-oxidase family or complex."
          },
          {
            "node_id": "proton_motive_force",
            "label": "proton motive force",
            "node_type": "STATE",
            "description": "Ion gradient used for energy conservation.",
            "grounding": "METPO:1007500"
          },
          {
            "node_id": "reduced_pyridine_nucleotides",
            "label": "reduced pyridine nucleotides",
            "node_type": "CHEMICAL",
            "description": "Reduced NAD(P)-type carriers generated by reverse electron transfer."
          },
          {
            "node_id": "nife_codh",
            "label": "Ni,Fe-carbon monoxide dehydrogenase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Anaerobic nickel-iron CODH enzyme class.",
            "grounding": "GO:0043885",
            "gene_symbols": [
              "cooS"
            ],
            "operon": "coo",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:P31896",
                "protein_label": "Carbon monoxide dehydrogenase",
                "gene_symbol": "cooS",
                "taxon_id": "NCBITaxon:1085",
                "taxon_label": "Rhodospirillum rubrum",
                "entry_status": "REVIEWED",
                "retrieved_on": "2026-10-22",
                "sequence_version": 1,
                "role": "NiFeS CooS enzyme catalyzing CO oxidation in the hydrogenogenic R. rubrum system; it is not used as the grounding for the umbrella CODH node.",
                "evidence": [
                  {
                    "reference": "DOI:10.1021/ja990396i",
                    "snippet": "site-directed mutagenesis of the cooS gene",
                    "notes": "The primary study mutagenized R. rubrum cooS and measured the resulting CODH turnover, linking this exact gene product to catalysis; UniProtKB P31896 verifies the reviewed instance."
                  },
                  {
                    "reference": "DOI:10.1128/jb.159.2.693-699.1984",
                    "snippet": "two-electron oxidation of CO to form CO2",
                    "notes": "Purified R. rubrum CODH directly catalyzed the reaction represented by the graph."
                  }
                ],
                "entry_version": 134
              }
            ]
          },
          {
            "node_id": "oxygen_sensitivity",
            "label": "oxygen sensitivity",
            "node_type": "QUALITY",
            "description": "Inactivation/intolerance of an enzyme upon exposure to O2."
          },
          {
            "node_id": "oxygen_tolerance",
            "label": "oxygen tolerance",
            "node_type": "QUALITY",
            "description": "Ability of an enzyme to function in the presence of O2."
          },
          {
            "node_id": "cooa_regulator",
            "label": "CooA",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Heme-based CO-sensing transcriptional activator of coo operons.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "CooA is experimentally exact in R. rubrum, but current UniProtKB P72322 is unreviewed and lacks a qualifying reference proteome, while available InterPro terms cover only broader CRP/FNR domains rather than CooA."
          },
          {
            "node_id": "rcom_regulator",
            "label": "RcoM",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Heme-dependent high-affinity CO sensor regulating aerobic CO oxidation genes.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Available ontology families cover broader heme sensor or DNA-binding domains and do not exactly identify the RcoM regulator represented here."
          },
          {
            "node_id": "atp_synthase",
            "label": "ATP synthase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Membrane complex synthesizing ATP from an ion motive force.",
            "grounding": "GO:0045259"
          },
          {
            "node_id": "molecular_oxygen",
            "label": "dioxygen",
            "node_type": "CHEMICAL",
            "description": "Terminal electron acceptor in aerobic CO oxidation.",
            "grounding": "CHEBI:15379"
          }
        ],
        "edges": [
          {
            "subject": "carboxydotrophic_trait",
            "predicate": "uses energy substrate",
            "object": "carbon_monoxide",
            "description": "Carboxydotrophs use carbon monoxide to support growth or metabolism.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro1595",
                "snippet": "CO supports the growth and metabolism",
                "notes": "Supports carbon monoxide as an energy-supporting substrate."
              }
            ]
          },
          {
            "subject": "carbon_monoxide_dehydrogenase",
            "predicate": "oxidizes",
            "object": "carbon_monoxide",
            "description": "CODH catalyzes carbon monoxide oxidation.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro1595",
                "snippet": "CO dehydrogenase (CODH), to oxidize CO",
                "notes": "Supports CODH-mediated CO oxidation."
              }
            ],
            "predicate_id": "METPO:2007803"
          },
          {
            "subject": "molybdenum_hydroxylase",
            "predicate": "enzyme class for",
            "object": "carbon_monoxide_dehydrogenase",
            "description": "Aerobic CO oxidizers use a molybdenum hydroxylase CODH.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro1595",
                "snippet": "use a molybdenum hydroxylase",
                "notes": "Supports molybdenum hydroxylase classification of aerobic CODH."
              }
            ]
          },
          {
            "subject": "carbon_monoxide",
            "predicate": "oxidized to",
            "object": "carbon_dioxide",
            "description": "CO oxidation yields carbon dioxide.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s00775-018-1541-0",
                "snippet": "oxidation of CO to CO2",
                "notes": "Supports CO-to-CO2 conversion by CODH."
              }
            ],
            "predicate_id": "METPO:2007405"
          },
          {
            "subject": "carbon_monoxide_dehydrogenase",
            "predicate": "feeds electrons into",
            "object": "respiratory_chain",
            "description": "CO oxidation is coupled to respiratory electron transfer.",
            "evidence": [
              {
                "reference": "DOI:10.1111/j.1574-6968.1986.tb01858.x",
                "snippet": "branched respiratory chain",
                "notes": "Supports respiratory-chain coupling in aerobic CO-utilizing bacteria."
              }
            ],
            "predicate_id": "METPO:2007402"
          },
          {
            "subject": "respiratory_chain",
            "predicate": "depends on",
            "object": "co_insensitive_terminal_oxidase",
            "description": "CO-utilizing bacteria use a CO-insensitive terminal oxidase branch.",
            "evidence": [
              {
                "reference": "DOI:10.1111/j.1574-6968.1986.tb01858.x",
                "snippet": "CO-insensitive terminal oxidase",
                "notes": "Supports terminal oxidase adaptation for CO metabolism."
              }
            ],
            "predicate_id": "RO:0002502"
          },
          {
            "subject": "respiratory_chain",
            "predicate": "generates",
            "object": "proton_motive_force",
            "description": "Respiratory CO oxidation conserves energy as proton motive force.",
            "evidence": [
              {
                "reference": "DOI:10.1111/j.1574-6968.1986.tb01858.x",
                "snippet": "pmf-driven reversed electron transfer",
                "notes": "Supports pmf involvement in aerobic carboxydotrophic energy metabolism."
              }
            ],
            "predicate_id": "biolink:produces"
          },
          {
            "subject": "proton_motive_force",
            "predicate": "drives formation of",
            "object": "reduced_pyridine_nucleotides",
            "description": "Reverse electron transfer can form reduced pyridine nucleotides.",
            "evidence": [
              {
                "reference": "DOI:10.1111/j.1574-6968.1986.tb01858.x",
                "snippet": "formation of reduced pyridine nucleotides",
                "notes": "Supports pmf-driven reverse electron transfer output."
              }
            ],
            "predicate_id": "biolink:produces"
          },
          {
            "subject": "nife_codh",
            "predicate": "has quality",
            "object": "oxygen_sensitivity",
            "description": "Ni,Fe-CODHs are oxygen sensitive, restricting them to anaerobic carboxydotrophs.",
            "evidence": [
              {
                "reference": "DOI:10.1128/jb.00332-22",
                "snippet": "coo operons, which encompass O2-sensitive Ni,Fe-CODHs",
                "notes": "Ni,Fe-CODHs are noted as oxygen sensitive and associated with anaerobic carboxydotrophs."
              }
            ]
          },
          {
            "subject": "molybdenum_hydroxylase",
            "predicate": "has quality",
            "object": "oxygen_tolerance",
            "description": "Cu,Mo-CODHs are O2-tolerant, enabling aerobic CO metabolism.",
            "evidence": [
              {
                "reference": "DOI:10.1128/jb.00332-22",
                "snippet": "cox operons, which encompass O2-tolerant Cu,Mo-CODHs",
                "notes": "Cu,Mo-CODHs are O2-tolerant (aerobic CO metabolism)."
              }
            ]
          },
          {
            "subject": "cooa_regulator",
            "predicate": "activates production of",
            "object": "nife_codh",
            "description": "CO-bound CooA activates transcription that produces the Ni,Fe-CODH machinery encoded in the coo operon.",
            "evidence": [
              {
                "reference": "DOI:10.1128/jb.00332-22",
                "snippet": "CO binding to Fe(II) heme in the regulatory domain allosterically activates CooA to bind promoter sites upstream of the coo operon and recruit RNA polymerase (RNAP) for transcription of downstream genes",
                "notes": "CO binding to Fe(II)-heme allosterically activates promoter binding and RNAP recruitment of coo operons."
              }
            ]
          },
          {
            "subject": "rcom_regulator",
            "predicate": "regulates production of",
            "object": "molybdenum_hydroxylase",
            "description": "RcoM regulates transcription that produces the aerobic coxSML CODH machinery.",
            "evidence": [
              {
                "reference": "DOI:10.1128/jb.00332-22",
                "snippet": "CooA and RcoM each primarily regulate anaerobic and aerobic CODH expression, respectively.",
                "notes": "RcoM regulates aerobic CO oxidation and was originally identified upstream of coxMSL genes."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "proton_motive_force",
            "predicate": "powers",
            "object": "atp_synthase",
            "description": "The ion motive force generated by CO oxidation drives ATP synthase.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s40643-023-00705-9",
                "snippet": "The reduction of those electron acceptors causes the formation of an ion motive force, which leads to the synthesis of ATP",
                "notes": "Generates an ion motive force that drives ATP synthesis."
              }
            ],
            "predicate_id": "METPO:2007900"
          },
          {
            "subject": "molybdenum_hydroxylase",
            "predicate": "coupled to reduction of",
            "object": "molecular_oxygen",
            "description": "Mo-CODH-mediated CO oxidation is coupled to O2 reduction aerobically.",
            "evidence": [
              {
                "reference": "DOI:10.1128/aem.00185-23",
                "snippet": "CO oxidation by Mo-CODH was coupled with O2 reduction under aerobic conditions",
                "notes": "Mo-CODH-mediated CO oxidation supports O2 reduction aerobically."
              }
            ]
          },
          {
            "subject": "cooa_regulator",
            "predicate": "regulates production of",
            "object": "carbon_monoxide_dehydrogenase",
            "description": "CO-bound CooA transcriptionally regulates production of carbon monoxide dehydrogenase and its accessory machinery.",
            "evidence": [
              {
                "reference": "DOI:10.1128/jb.00332-22",
                "snippet": "Transcriptional activation leads to rapid expression of CODH and other accessory proteins",
                "notes": "Verified against the open Journal of Bacteriology article."
              }
            ],
            "predicate_id": "RO:0002211"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-08-23T09:11:00Z",
        "curator": "codex",
        "action": "CURATE_PROTEIN_TAXON_EXAMPLE",
        "changes": "Reviewed the aerobic and anaerobic graph branches, grounded NiFe CODH and ATP synthase, documented exact label-only dispositions including CooA, and added DOI-backed R. rubrum CooS P31896.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-05T01:35:46.868229+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-08T00:00:00-07:00",
        "curator": "codex",
        "action": "ADDED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed causal graph for CODH-mediated carbon monoxide oxidation, respiratory-chain coupling, and energy conservation.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000016\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T08:21:50Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:produces\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T21:30:07Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007405\u00d71, METPO:2007402\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:38:01Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0022904\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:41:04Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (METPO:1007500\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T05:05:15Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A061JSS8\u00d71, UniProtKB:A0A099I9V3\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-26T02:30:13Z",
        "curator": "claude",
        "action": "RETYPE_CAUSAL_NODES",
        "changes": "Re-typed 1 causal-node node_type field(s) to align with CausalNodeTypeEnum semantics: proton motive force: BIOLOGICAL_PROCESS \u2192 STATE \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-26T05:00:48Z",
        "curator": "claude",
        "action": "RENAME_PREDICATE_LABELS",
        "changes": "Renamed 1 causal-edge predicate label(s) to align with existing groundings: requires \u2192 depends on \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-26T05:00:51Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002502\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-13T21:03:27Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:produces\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 8 evidence-backed generic edges (9 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:14Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:encodes\u00d72, RO:0002211\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:20Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A415TT77\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:34Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:15379\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-26T07:15:20Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A1D7QXJ2\u00d71, UniProtKB:A0A0D5N3T8\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:21:12Z",
        "curator": "claude",
        "action": "RETRACT_DEAD_UNIPROT_GROUNDINGS",
        "changes": "Retracted 4 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T02:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES_PART2",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates onto their causal-graph counterparts (1 to oxidizes), issue 301 part 2. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Each replacement is a 1:1 mirror of its source predicate that changes only the domain, so the claim each edge makes is unchanged and directions are unchanged. The replacements are proposed in proposals/metpo_traitmech_v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-07T04:00:00Z",
        "curator": "claude",
        "action": "REGROUND_CAUSAL_EDGE",
        "changes": "Re-grounded the `encodes` edge(s) from biolink:encodes to METPO:2007813, issue 342. biolink:encodes is NOT a slot in the pinned biolink 4.4.0 model, so the CURIE resolved to nothing upstream while looking like an upstream term to anyone reading this record -- the disclaimer saying otherwise lived in mappings/predicate_grounding.tsv, which is not read at the point of use. RO:0002205 (has gene product) is the nearest real term but relates a GENE to a gene product, whereas these edges relate a gene cluster or operon to a protein complex or a biosynthetic process, which its range does not admit; that mismatch is why the coinage existed. METPO:2007813 is proposed in proposals/metpo_traitmech_v9 and is a placeholder id until METPO mints it, which puts it in the same state as the rest of that cohort rather than in a category of its own.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-17T02:00:00Z",
        "curator": "claude",
        "action": "NORMALISE_NODE_SENSE",
        "changes": "One node_id per SENSE (issues 356, 384): molecular_oxygen is the chemical sense here. A third id for the same molecule, grounded CHEBI:15379 like the rest. Folded into molecular_oxygen: #384 reported two ids for oxygen, and there were four.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-22T04:26:16Z",
        "curator": "codex",
        "action": "REVIEW_UNIPROT_INSTANCE_GROUNDINGS",
        "changes": "Reviewed 1 organism-specific UniProtKB grounding(s): replaced 0 with taxon-agnostic GO/InterPro terms and retracted 1 to label-only where no exact semantic term was supported (docs/GROUNDING_POLICY.md).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-30T19:21:37Z",
        "curator": "codex",
        "action": "REVIEW_EVIDENCE_REFERENCE_CHURN",
        "changes": "Offline review for issue 520 retained 1 evidence-reference replacement(s) that PR 511 made on surviving causal edges outside its stated protein-taxon scope. The pre-tranche evidence entries had references but no snippets; the retained entries supply edge-specific snippets and explanatory notes. Reverting would discard that claim-level provenance, so the scope defect is resolved by documenting the decision instead. This audit changed no causal claim or evidence field. Reviewed replacements: DOI:10.1101/2023.01.17.524042 -> DOI:10.1128/aem.00185-23 (1 edge).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T06:33:04Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007900\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T10:45:00Z",
        "curator": "codex",
        "action": "CONNECT_CAUSAL_GRAPH_COMPONENTS",
        "changes": "Resolved issue #183 graph fragmentation (2 components to 1) with 1 public-source, verbatim-snippet-backed connector(s). No paid research service was called.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-22T01:35:00Z",
        "curator": "claude",
        "action": "REFRESH_UNIPROT_ENTRY_VERSION",
        "changes": "Refreshed UniProtKB entry_version against live UniProt REST on 2026-10-22: UniProtKB:P31896 (unset -> 134 on nife_codh).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000156",
    "label": "carboxylesterase activity",
    "definition": "A physiological enzyme-activity phenotype in which a cell produces active carboxylesterase enzymes that hydrolyze carboxylic esters to alcohols and carboxylates.",
    "definition_source": "https://iubmb.qmul.ac.uk/enzyme/EC3/1/1/1.html",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "synonyms": [
      {
        "synonym_text": "carboxylic-ester hydrolase activity",
        "synonym_type": "EXACT_SYNONYM",
        "source": "https://iubmb.qmul.ac.uk/enzyme/EC3/1/1/1.html"
      }
    ],
    "evidence": [
      {
        "reference": "https://iubmb.qmul.ac.uk/enzyme/EC3/1/1/1.html",
        "snippet": "Reaction: A carboxylic ester + H_{2}O = an alcohol + a carboxylate",
        "notes": "The NC-IUBMB EC 3.1.1.1 entry defines carboxylesterase by its accepted reaction, grounding the ester-hydrolase activity named by the organism-level carboxylesterase phenotype."
      },
      {
        "reference": "DOI:10.1128/JCM.43.8.3713-3717.2005",
        "snippet": "Alkaline phosphatase, esterase (C4), esterase lipase (C8), leucine arylamidase, acid phosphatase, and naphthol-AS-BI-phosphohydrolase were clearly positive",
        "notes": "Otsuka et al. detected clear esterase (C4) and esterase lipase (C8) API ZYM reactions in the five Corynebacterium resistens isolates they characterized, supporting this as a directly assayed bacterial carboxylesterase activity phenotype."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:258224",
        "taxon_label": "Corynebacterium resistens",
        "note": "Otsuka et al. detected clear esterase (C4) and esterase lipase (C8) API ZYM reactions in Corynebacterium resistens isolates.",
        "reference": "DOI:10.1128/JCM.43.8.3713-3717.2005"
      }
    ],
    "discussions": [
      {
        "discussion_id": "carboxylesterase-activity-xref-gap",
        "prompt": "Resolve an exact external ontology class for carboxylesterase activity before adding a TraitRecord xref.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "GO:0106435 denotes carboxylesterase molecular function rather than the organism-level carboxylesterase production phenotype, so it is appropriate as a causal-node grounding rather than an equivalent TraitRecord xref.",
        "posed_by": "codex",
        "posed_date": "2026-09-12"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-12T03:42:43Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted carboxylesterase activity as a URL/DOI-backed TraitRecord after a repository-wide duplicate review covering ignored and hidden files; METPO has no exact carboxylesterase activity class yet.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000137",
    "label": "caseinase activity",
    "definition": "A physiological enzyme-activity phenotype in which a cell produces active caseinase proteases that hydrolyze casein.",
    "definition_source": "DOI:10.3389/fmicb.2018.01148",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "synonyms": [
      {
        "synonym_text": "caseinase production",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.2174/1874285801408010025"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.3389/fmicb.2018.01148",
        "snippet": "two enzymes secreted by a B. cereus RC6 strain that permits the degradation of casein",
        "notes": "Ouertani et al. identify secreted Bacillus cereus RC6 proteases that degrade casein in a dairy-product context."
      },
      {
        "reference": "DOI:10.2174/1874285801408010025",
        "snippet": "screened for enzyme production (caseinase, gelatinase, amylase, carboxymethyl cellulase, and esterase)",
        "notes": "Alves et al. use caseinase as a reusable extracellular hydrolytic-enzyme phenotype while screening environmental microbial isolates."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1396",
        "taxon_label": "Bacillus cereus",
        "note": "Bacillus cereus RC6 secreted casein-degrading proteases in milk-matrix experiments.",
        "reference": "DOI:10.3389/fmicb.2018.01148"
      }
    ],
    "discussions": [
      {
        "discussion_id": "caseinase-activity-xref-gap",
        "prompt": "Resolve an exact external ontology class for caseinase activity before adding a TraitRecord xref.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "GO:0008233 is a generic peptidase-activity class and is too broad for caseinase activity as an equivalent TraitRecord xref.",
        "posed_by": "codex",
        "posed_date": "2026-09-11"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-11T00:00:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted caseinase activity as a DOI-backed TraitRecord after a repository-wide duplicate review covering ignored and hidden files; METPO has no exact caseinase activity class yet.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000075",
    "label": "catalase activity",
    "definition": "A physiological enzyme-activity phenotype in which a cell produces catalase, which decomposes hydrogen peroxide into water and oxygen; it is the basis of the diagnostic catalase test.",
    "definition_source": "DOI:10.1007/s00018-003-3206-5",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "synonyms": [
      {
        "synonym_text": "catalase-positive",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1007/s00018-003-3206-5"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1007/s00018-003-3206-5",
        "notes": "Chelikani, Fita & Loewen review the diversity of catalases, enzymes that dismutate hydrogen peroxide to water and oxygen."
      },
      {
        "reference": "DOI:10.1038/nrmicro3032",
        "notes": "Imlay's oxidative-stress review supports catalase as a key hydrogen-peroxide scavenging defense."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1280",
        "taxon_label": "Staphylococcus aureus",
        "note": "catalase-positive",
        "reference": "PMID:17114262"
      },
      {
        "taxon_id": "NCBITaxon:287",
        "taxon_label": "Pseudomonas aeruginosa",
        "note": "catalase-positive",
        "reference": "PMID:15972537"
      },
      {
        "taxon_id": "NCBITaxon:93061",
        "taxon_label": "Staphylococcus aureus NCTC 8325",
        "note": "Strain-level exemplar for PerR control of catalase and other peroxide-defense genes.",
        "reference": "DOI:10.1128/iai.69.6.3744-3754.2001"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "catalase_activity_h2o2_detoxification",
        "title": "Catalase hydrogen-peroxide detoxification",
        "description": "Evidence-backed causal sketch linking catalase to dismutation of hydrogen peroxide into water and molecular oxygen.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "Represents a monofunctional heme-catalase reaction and two alternative bacterial peroxide-sensing regulators. The S. aureus NCTC 8325 PerR (Q2G282) and E. coli K-12 OxyR (P0ACQ4) examples support their respective taxon-specific regulatory branches and are not generalized across all catalase-positive taxa.",
        "nodes": [
          {
            "node_id": "catalase_activity_trait",
            "label": "catalase activity",
            "node_type": "TRAIT",
            "grounding": "traitmech:000075",
            "description": "Capacity to decompose hydrogen peroxide via catalase."
          },
          {
            "node_id": "catalase",
            "label": "monofunctional heme catalase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Monofunctional heme enzyme that dismutates hydrogen peroxide.",
            "grounding": "InterPro:IPR018028",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:P06115",
                "protein_label": "Catalase T",
                "gene_symbol": "CTT1",
                "taxon_id": "NCBITaxon:559292",
                "taxon_label": "Saccharomyces cerevisiae (strain ATCC 204508 / S288c)",
                "entry_status": "REVIEWED",
                "proteome_id": "UP000002311",
                "retrieved_on": "2026-10-05",
                "entry_version": 215,
                "sequence_version": 3,
                "role": "Cytosolic monofunctional heme catalase that removes hydrogen peroxide. Its protective activity was tested in S. cerevisiae YPH250 and BY4741 laboratory backgrounds in nutrient-rich YPD; this example supports the catalytic node only, not the bacterial PerR/OxyR branches.",
                "evidence": [
                  {
                    "reference": "PMID:24563848",
                    "snippet": "Ctt1 but not Cta1 activity is strongly induced by H2O2 when cells are challenged in YPD",
                    "notes": "Martins and English tested CTT1 deletion and catalase activity in YPH250 and BY4741 (Table 1). Protection depends on nutrient-rich medium and was lost during challenge in buffer. UniProtKB P06115 supplies the reviewed S288c reference protein, taxon and InterPro:IPR018028 family match; the experiment was not performed in the unmodified S288c reference isolate."
                  }
                ]
              }
            ],
            "related_records": [
              {
                "corpus": "PathwayMech",
                "identifier": "gomodel:YeastPathways_DETOX1-PWY",
                "relation": "PATHWAY_CONTEXT",
                "basis": "PathwayMech context: superoxide radicals degradation in Saccharomyces cerevisiae S288C (NCBITaxon:559292). The linked model explicitly includes CTT1 (SGD:S000003320) catalase activity consuming hydrogen peroxide and producing water and dioxygen, downstream of superoxide dismutation. This link concerns that peroxide-removal component; it does not equate catalase with superoxide dismutase or extend the bacterial PerR/OxyR regulatory branches to yeast.",
                "source_version": "aa305727458c44ab05614901334540e2c87a9f3a"
              }
            ]
          },
          {
            "node_id": "catalase_function",
            "label": "catalase activity",
            "node_type": "MOLECULAR_FUNCTION",
            "grounding": "GO:0004096",
            "description": "Catalysis of 2 H2O2 = O2 + 2 H2O."
          },
          {
            "node_id": "hydrogen_peroxide",
            "label": "hydrogen peroxide",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:16240",
            "description": "Reactive oxygen species detoxified by catalase."
          },
          {
            "node_id": "molecular_oxygen",
            "label": "molecular oxygen",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:15379",
            "description": "Product of hydrogen peroxide dismutation."
          },
          {
            "node_id": "water",
            "label": "water",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:15377",
            "description": "Product of hydrogen peroxide dismutation."
          },
          {
            "node_id": "oxyr_regulator",
            "label": "OxyR",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Peroxide-sensing transcriptional regulator activated by hydrogen peroxide.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "OxyR belongs to the broad LysR regulator family, but the checked InterPro entries describe shared domains rather than an exact OxyR protein family.",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:P0ACQ4",
                "protein_label": "DNA-binding transcriptional dual regulator OxyR",
                "gene_symbol": "oxyR",
                "taxon_id": "NCBITaxon:83333",
                "taxon_label": "Escherichia coli K-12",
                "entry_status": "REVIEWED",
                "proteome_id": "UP000000625",
                "retrieved_on": "2026-10-22",
                "entry_version": 144,
                "sequence_version": 1,
                "role": "Peroxide-sensing transcriptional dual regulator that is directly oxidized and activated by hydrogen peroxide to induce katG and peroxide-defense genes in E. coli K-12; this example supports the OxyR regulatory branch only, not PerR-regulated taxa.",
                "evidence": [
                  {
                    "reference": "DOI:10.1073/pnas.96.11.6161",
                    "snippet": "In wild-type cells, OxyR is activated by hydrogen peroxide.",
                    "notes": "\u00c5slund et al. 1999 characterize hydrogen peroxide activation of E. coli K-12 OxyR."
                  }
                ]
              }
            ]
          },
          {
            "node_id": "perr_regulator",
            "label": "PerR",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Fe-dependent peroxide-sensing transcriptional repressor inactivated by hydrogen peroxide.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "PerR belongs to the broader Fur family; IPR002481 is not specific enough to distinguish PerR from other Fur-family regulators, so the exact label is retained with an organism-paired protein example.",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:Q2G282",
                "protein_label": "Peroxide-responsive repressor PerR",
                "gene_symbol": "perR",
                "taxon_id": "NCBITaxon:93061",
                "taxon_label": "Staphylococcus aureus NCTC 8325",
                "entry_status": "REVIEWED",
                "proteome_id": "UP000008816",
                "retrieved_on": "2026-10-22",
                "entry_version": 110,
                "sequence_version": 1,
                "role": "Manganese-dependent peroxide-responsive repressor controlling katA and the wider oxidative-stress defense regulon in S. aureus.",
                "evidence": [
                  {
                    "reference": "DOI:10.1128/iai.69.6.3744-3754.2001",
                    "snippet": "PerR controls oxidative stress resistance and iron storage proteins",
                    "notes": "The primary S. aureus study characterizes PerR regulation and links it to catalase/peroxide defense; UniProtKB Q2G282 verifies the reviewed NCTC 8325 protein instance."
                  }
                ]
              }
            ]
          },
          {
            "node_id": "peroxide_defense_systems",
            "label": "peroxide defense systems",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Antioxidant defense systems (e.g. catalases, peroxidases) that detoxify hydrogen peroxide."
          },
          {
            "node_id": "heme_biosynthesis",
            "label": "heme biosynthesis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Synthesis of the heme cofactor required for catalase maturation and activity.",
            "grounding": "GO:0006783",
            "related_records": [
              {
                "corpus": "PathwayMech",
                "identifier": "gomodel:YeastPathways_HEME-BIOSYNTHESIS-II",
                "relation": "PATHWAY_CONTEXT",
                "basis": "PathwayMech context: heme b biosynthesis I (aerobic) in Saccharomyces cerevisiae S288C (NCBITaxon:559292). This is one aerobic heme b synthesis route supplying catalase cofactor context; alternative bacterial heme routes and PerR/OxyR regulation are outside the linked record. No exact equivalence or transfer of organism scope is asserted.",
                "source_version": "aa305727458c44ab05614901334540e2c87a9f3a"
              }
            ]
          }
        ],
        "edges": [
          {
            "subject": "catalase",
            "predicate": "enables",
            "object": "catalase_function",
            "description": "Catalase carries out the catalase molecular function.",
            "evidence": [
              {
                "reference": "DOI:10.1021/ja9018572",
                "snippet": "Catalases are ubiquitous enzymes that prevent cell oxidative damage by degrading hydrogen peroxide",
                "notes": "The primary mechanistic study identifies catalases as the enzymes carrying out hydrogen-peroxide degradation."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "catalase_function",
            "predicate": "consumes",
            "object": "hydrogen_peroxide",
            "description": "The catalase reaction consumes hydrogen peroxide.",
            "evidence": [
              {
                "reference": "DOI:10.1021/ja9018572",
                "snippet": "degrading hydrogen peroxide to water and oxygen",
                "notes": "Hydrogen peroxide is the substrate consumed in the catalatic reaction."
              }
            ],
            "predicate_id": "biolink:consumes"
          },
          {
            "subject": "catalase_function",
            "predicate": "has output",
            "object": "molecular_oxygen",
            "description": "The catalase reaction produces molecular oxygen.",
            "evidence": [
              {
                "reference": "DOI:10.1021/ja9018572",
                "snippet": "hydrogen peroxide to water and oxygen (2H2O2 \u2192 2 H2O + O2)",
                "notes": "The primary study gives molecular oxygen as a product of the balanced catalase reaction."
              }
            ],
            "predicate_id": "RO:0002234"
          },
          {
            "subject": "catalase_function",
            "predicate": "has output",
            "object": "water",
            "description": "The catalase reaction produces water.",
            "evidence": [
              {
                "reference": "DOI:10.1021/ja9018572",
                "snippet": "Catalases are ubiquitous enzymes that prevent cell oxidative damage by degrading hydrogen peroxide to water and oxygen",
                "notes": "The primary study gives water as a product of the catalase reaction."
              }
            ],
            "predicate_id": "RO:0002234"
          },
          {
            "subject": "catalase",
            "predicate": "confers",
            "object": "catalase_activity_trait",
            "description": "Production of catalase confers the catalase-activity phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1021/ja9018572",
                "snippet": "Catalases are ubiquitous enzymes that prevent cell oxidative damage by degrading hydrogen peroxide to water and oxygen",
                "notes": "The catalase protein's demonstrated reaction is the mechanistic basis of the catalase-activity trait."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "catalase_activity_trait",
            "predicate": "decomposes",
            "object": "hydrogen_peroxide",
            "description": "Catalase activity rapidly decomposes hydrogen peroxide into water and molecular oxygen.",
            "evidence": [
              {
                "reference": "DOI:10.1021/ja9018572",
                "snippet": "degrading hydrogen peroxide to water and oxygen (2H2O2 \u2192 2 H2O + O2) with high efficiency",
                "notes": "The primary mechanistic study directly supports efficient peroxide decomposition by catalase activity."
              }
            ]
          },
          {
            "subject": "hydrogen_peroxide",
            "predicate": "activates",
            "object": "oxyr_regulator",
            "description": "Hydrogen peroxide activates the OxyR peroxide-sensing regulator.",
            "evidence": [
              {
                "reference": "DOI:10.1073/pnas.96.11.6161",
                "snippet": "In wild-type cells, OxyR is activated by hydrogen peroxide.",
                "notes": "A primary E. coli study directly demonstrated peroxide-dependent OxyR activation; this regulatory branch is organism-specific rather than universal."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "hydrogen_peroxide",
            "predicate": "favors scavenging by",
            "object": "catalase_activity_trait",
            "description": "High hydrogen peroxide concentrations favor scavenging by catalases, which turn over much faster than alkyl hydroperoxide reductase.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro3032",
                "snippet": "Under these conditions, catalases, which do not require stoichiometric reductants, can turn over much more quickly than Ahp.",
                "notes": "Organisms rely on catalases when H2O2 levels are high; catalases turn over much more quickly than Ahp. Likely general across aerobes/facultative anaerobes."
              }
            ]
          },
          {
            "subject": "oxyr_regulator",
            "predicate": "regulates",
            "object": "peroxide_defense_systems",
            "description": "OxyR regulates peroxide defense systems; most bacteria sense H2O2 via OxyR or PerR.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fimmu.2021.667343",
                "snippet": "these regulators induce enzymes that reduce cytoplasmic H2O2 concentrations, decrease the intracellular iron pools, and repair the H2O2-mediated damage.",
                "notes": "Most bacteria sense H2O2 via OxyR or PerR transcription factors that control peroxide defense systems."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "perr_regulator",
            "predicate": "regulates",
            "object": "peroxide_defense_systems",
            "description": "PerR regulates peroxide defense systems; most bacteria sense H2O2 via OxyR or PerR.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fimmu.2021.667343",
                "snippet": "these regulators induce enzymes that reduce cytoplasmic H2O2 concentrations, decrease the intracellular iron pools, and repair the H2O2-mediated damage.",
                "notes": "Most bacteria sense H2O2 via OxyR or PerR transcription factors that control peroxide defense systems."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "heme_biosynthesis",
            "predicate": "supports activation of",
            "object": "catalase",
            "description": "Heme biosynthesis is required for catalase activation; impaired heme synthesis delays peroxide degradation.",
            "evidence": [
              {
                "reference": "DOI:10.1111/mmi.12967",
                "snippet": "the KatG-dependent peroxidase activity was elevated only 2.6-fold, suggesting that much of the enzyme lacked heme.",
                "notes": "Ferrochelatase (hemH) function is required for timely induction of catalase (KatG) activity in E. coli; this edge is a taxon-specific supporting module."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-08-23T09:12:00Z",
        "curator": "codex",
        "action": "CURATE_PROTEIN_TAXON_EXAMPLE",
        "changes": "Reviewed the graph as mechanistic, grounded the protein and activity separately, retained OxyR and PerR only with exact family-level caveats, and added DOI-backed S. aureus NCTC 8325 PerR Q2G282.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-04T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate PHYSIOLOGY trait (catalase activity) from literature research to fill the enzyme-activity-phenotype gap.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-08T00:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (catalase hydrogen-peroxide dismutation) with CHEBI/GO node groundings and RO/METPO/biolink predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-14T06:38:15Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A071MK53\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 6 evidence-backed generic edges (4 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:14Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002211\u00d72, RO:0002213\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:34Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0006783\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-26T07:15:20Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A9P2M4N5\u00d71, UniProtKB:A0A097ASJ8\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:21:12Z",
        "curator": "claude",
        "action": "RETRACT_DEAD_UNIPROT_GROUNDINGS",
        "changes": "Retracted 2 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:23:55Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0004096\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 1 causal edge(s) off enables/RO:0002327 with a TRAIT object (1 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 2 causal edge(s) off microbe-domain METPO predicates (2 to has output), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-08T05:00:00Z",
        "curator": "claude",
        "action": "UNGROUND_CAUSAL_NODE",
        "changes": "Dropped the grounding GO:0004096 from node catalase. Issue 352. GO:0004096 is 'catalase ACTIVITY' -- a molecular function, which is what catalase_function is. A protein is not its activity, and the graph already says so correctly: catalase -enables-> catalase_function. Dropped from the protein, kept on the function.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-22T04:26:16Z",
        "curator": "codex",
        "action": "REVIEW_UNIPROT_INSTANCE_GROUNDINGS",
        "changes": "Reviewed 1 organism-specific UniProtKB grounding(s): replaced 0 with taxon-agnostic GO/InterPro terms and retracted 1 to label-only where no exact semantic term was supported (docs/GROUNDING_POLICY.md).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-30T19:21:37Z",
        "curator": "codex",
        "action": "REVIEW_EVIDENCE_REFERENCE_CHURN",
        "changes": "Offline review for issue 520 retained 7 evidence-reference replacement(s) that PR 511 made on surviving causal edges outside its stated protein-taxon scope. The pre-tranche evidence entries had references but no snippets; the retained entries supply edge-specific snippets and explanatory notes. Reverting would discard that claim-level provenance, so the scope defect is resolved by documenting the decision instead. This audit changed no causal claim or evidence field. Reviewed replacements: DOI:10.1007/s00018-003-3206-5 -> DOI:10.1021/ja9018572 (4 edges); DOI:10.1038/nrmicro3032 -> DOI:10.1021/ja9018572 (1 edge); DOI:10.1038/nrmicro3032 -> DOI:10.1073/pnas.96.11.6161 (1 edge); DOI:10.3390/biom14060697 -> DOI:10.1021/ja9018572 (1 edge).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-05T17:46:21Z",
        "curator": "codex",
        "action": "ADD_PATHWAY_CONTEXT",
        "changes": "Added pinned PathwayMech context on reviewed causal nodes with explicit route and organism limitations; retained existing groundings and exact xrefs. Appended a source-verified Ctt1 protein example with the UniProt strain taxon and explicit experimental-strain and medium limits.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-05T17:55:45Z",
        "curator": "codex",
        "action": "ADD_PATHWAY_CONTEXT",
        "changes": "Added pinned pathway context for the Ctt1 peroxide-removal component of the yeast detoxification model, retaining the upstream heme context and primary-source-backed Ctt1 example. The link explicitly distinguishes catalase chemistry from superoxide dismutase and bacterial regulatory branches.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-22T01:35:00Z",
        "curator": "claude",
        "action": "CURATE_PROTEIN_TAXON_EXAMPLE",
        "changes": "Added reviewed E. coli K-12 OxyR protein_example UniProtKB:P0ACQ4 (v144) on oxyr_regulator (DOI:10.1073/pnas.96.11.6161), updated scope_notes, and refreshed UniProtKB:Q2G282 entry_version 109 -> 110 on perr_regulator.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000728",
    "label": "cell-body contraction",
    "definition": "A physiological phenotype in which a microbial cell actively shortens its body by contraction of intracellular structures.",
    "definition_source": "DOI:10.1126/sciadv.add6550",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000729"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1126/sciadv.add6550",
        "snippet": "Ca2+ concentrations from 10\u22126 to 10\u22122 M in the culture medium could stimulate cell contraction while maintaining the viability of the cell.",
        "notes": "Zhang et al. 2023, PMID:36812318, PMCID:PMC9946354, Results: functional analysis of giant backbone proteins, second paragraph. Direct JATS match; native NOT_IN_ABSTRACT retained. The study identified its East Lake, Wuhan isolate as Spirostomum minus using morphology, protargol staining and SSU rDNA, then established clonal cultures at 22 C. Actual Figure 1A shows extended and contracted cell bodies. The quoted treatment maintained viability; 38-to-16 seconds describes intervals between contractions, not contraction duration. Selected Results, Methods and Discussion, actual Figures 1, 6 and 9, and relevant supplement pages were inspected. Figure 9 is a mechanistic schematic. Supplementary Figure 7 shows shortening during death, which is insufficient for this trait. Abnormal-cell counts are in Supplementary Table 2, not Table S1 as cited in the RNAi Results. Rare twisted RNAi phenotypes do not establish contraction loss in every treated cell. The source's superscript exponents mean 10^(-6) to 10^(-2) M; the normalized plain-text quotation does not preserve superscript styling."
      },
      {
        "reference": "DOI:10.1073/pnas.2217737120",
        "notes": "Floyd et al. 2023, PMID:37307463, PMCID:PMC10288572, Figure 4 caption, contiguous observed-asymmetry clause. Direct JATS match; native NOT_IN_ABSTRACT retained. The quoted top and bottom ends are those of the imaged Spirostomum cell body in Figure 4A-C, not Vorticella's stalk or simulated springs. The actual panel A contours and panel B solid length trajectory show body shortening; panel C shows the staggered endpoint movements. Dashed model curves are separate from observations. The 15-word caption span replaces the data-presentation excerpt rejected in #1935; historical source receipts remain in the sidecar. Actual Figures 1A and 2A-B show Spirostomum body shortening and experimental trajectories separately from fitted curves. Methods used commercially sourced cultures and high-speed imaging without compressing cells; no species identity is inferred. Supplementary Figure S3 measures length along the central backbone curve, with increasing width. Supplementary Figure S6 states that repeated contractions of the same organism were not distinguished from contractions of different organisms: five traces are not five established biological replicates. Vorticella panels measure stalk contraction, not the body endpoint. Calcium-wave and energy models are not universal molecular proof. Selected experimental sections, actual Figures 1-2 and supplementary pages 3 and 5 were inspected; raw videos and the complete model were not reanalyzed.",
        "snippet": "Asymmetric contraction can be observed as the top end begins contracting before the bottom end"
      },
      {
        "reference": "DOI:10.1242/jeb.189.1.163",
        "snippet": "Living Vorticella showed a graded shrinkage of the cell body when Ca2+ buffer was injected into the cell body",
        "notes": "Katoh and Naitoh 1994, PMID:9317557, scientific Abstract item 3, first clause. Direct namespace-qualified Europe PMC MED abstract match and native VERIFIED. The same sentence contrasts graded cell-body shrinkage with all-or-nothing stalk coiling. Triton-extracted preparations in other abstract items are not the living-cell injection assay. Calcium-release causality is presented as an assumption, not direct molecular proof. Publisher HTML and PDF requests returned 403; full Methods, figures and strain provenance were not accessed. No species-wide example, quantitative threshold or universal trigger is inferred."
      }
    ],
    "discussions": [
      {
        "discussion_id": "cell-body-contraction-scope-and-parent",
        "prompt": "Resolve a closer parent while distinguishing body shortening from other contractile endpoints.",
        "kind": "CURATION_TODO",
        "status": "RESOLVED",
        "rationale": "Retain phenotype METPO:1000059. Motility METPO:1000701 concerns locomotion through the environment; motile METPO:1000702 specifies independent movement using metabolic energy. Neither necessarily establishes body shortening. Body contraction is not displacement caused only by stalk coiling, rapid axopodial contraction traitmech:000682, contractile-vacuole cycling, injection-system contraction, cytokinetic constriction, passive osmotic shrinkage, death or static short-cell size. Behavioral habituation traitmech:000714 changes response probability rather than defining the contraction response. The axopodial record's broader cellular-contractility parent question is not resolved by this body-specific class; do not reparent it here. No universal speed, fractional shortening, trigger or ecological function is imposed. No organism-level disjointness or exact synonym for generic contractility is asserted.",
        "posed_by": "codex",
        "posed_date": "2026-10-14",
        "resolved_date": "2026-10-14",
        "resolution_note": "Added cellular contraction (body or cytoplasmic projection shortening) traitmech:000729 as the direct broader phenotype. This is a definition-based subclass inference, not a new child experiment or evidence of a common molecular mechanism. Phenotype METPO:1000059 remains an ancestor. Preserved the historical rationale and endpoint boundaries; the v605 proposal requests the child axiom without rewriting the historical proposal cohort."
      },
      {
        "discussion_id": "cell-body-contraction-metpo-assessment",
        "prompt": "Review the proposed phenotype without treating locomotion as an exact equivalent.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Pinned/current METPO releases, editor and inspected template owners provided no active exact contraction class. Historical obsolete Motility identifiers METPO:0000006 and METPO:000006 point to active METPO:1000701; obsolete Motile METPO:0000087 and METPO:000088 point to active METPO:1000702. These locomotion leads are related, not exact body-contraction identities. They are not revived or placed in xrefs. The ontology pin remains unchanged; v604 proposes this phenotype below METPO:1000059. No external equivalent or SSSOM mapping has been accepted.",
        "posed_by": "codex",
        "posed_date": "2026-10-14"
      },
      {
        "discussion_id": "cell-body-contraction-mechanism-and-provenance",
        "prompt": "Resolve study-isolate and protein identities before adding canonical examples or a mechanistic graph.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Keep study-named cultures as qualified evidence pending exact isolate/current-taxonomy correspondence. No canonical taxa, protein accessions or causal graph are asserted. Zhang's localization, RNAi and structural models support source-bounded mechanistic hypotheses, not a common protein mechanism inferred from sequence features. Category-E twisted cells were rare; other abnormal forms also occurred in controls. Figure 9's calcium-storage and energy-coupling scheme is not wholly demonstrated. A protein graph needs authority-checked taxon-paired accessions and edge-specific perturbation evidence; its omission does not claim that mechanisms are unknown. Do not generalize ATP independence or calcium concentrations to the whole class. Floyd's five traces have unresolved organism-level replication. Katoh's full Methods were not accessed. The verification sidecar retains actual sections, hashes, source-status checks and native verdicts; bounded notice checks are not comprehensive clearance.",
        "posed_by": "codex",
        "posed_date": "2026-10-14"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-14T17:32:15Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added cell-body contraction with three primary DOI sources and directly matched 22-, 19- and 19-word excerpts. Full-text Results retain NOT_IN_ABSTRACT; the Vorticella abstract is VERIFIED. Body, stalk, axopodial, division and passive-shrinkage endpoints remain distinct. No sequence-derived mechanism or unverified canonical example imported. Reserved 000728, v604 and 1068100-1068199 after ignored/hidden, retained-history, full-content proposal and open/draft PR checks. Contig lengths, embedding components and broad editor envelopes are not METPO reservations. Other records unchanged; timestamp records observed acceptance.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-14T17:58:04Z",
        "curator": "codex",
        "action": "EVIDENCE_NOTE_CLARIFIED",
        "changes": "Clarified source superscript exponents as 10^(-6) to 10^(-2) M beside the unchanged normalized JATS excerpt (#1933). Preserved the native verdict, phenotype scope and original minting event.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-14T18:54:51Z",
        "curator": "codex",
        "action": "EXTERNAL_REVIEW_CORRECTION",
        "changes": "Addressed #1935: corrected the motility label and distinguished METPO:1000701 from the energy-dependent motile class METPO:1000702. Removed the non-claim-bearing Floyd snippet while retaining its figure-backed evidence and historical verification receipts. The two other primary excerpts, phenotype definition, parent, PROPOSED status and previous curation events remain unchanged.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-14T19:02:18Z",
        "curator": "codex",
        "action": "CLAIM_BEARING_SNIPPET_ADDED",
        "changes": "Added a directly matched 15-word Floyd Figure 4 caption excerpt reporting observed asymmetric contraction (#1935). Checked actual panels A-C and distinguished body shortening from fitted model curves. The intermediate no-snippet record failed MISSING_SNIPPET and was not published or baselined. Prior events remain intact.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-14T22:35:09Z",
        "curator": "codex",
        "action": "REFINE_CELLULAR_CONTRACTION_PARENT",
        "changes": "Refined the direct parent to cellular contraction traitmech:000729 by definition-based inference. Preserved child definition, supporting excerpts, prior curation history and independent provenance/mechanism gaps. Resolved only the parent question. No new experiment, canonical taxon or molecular mechanism is asserted.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000528",
    "label": "cellular buoyancy",
    "definition": "A physiology trait in which intracellular gas vesicles reduce a microbial cell's effective density enough to provide buoyancy and vertical positioning in the water column.",
    "definition_source": "DOI:10.1186/s13036-024-00426-3",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "synonyms": [
      {
        "synonym_text": "buoyancy",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1186/s13036-024-00426-3"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1186/s13036-024-00426-3",
        "snippet": "can provide buoyancy for them to move up and down the water to obtain nutrients",
        "notes": "Feng et al. review gas-vesicle physical properties that provide buoyancy for photosynthetic bacteria and halophilic archaea."
      },
      {
        "reference": "DOI:10.1186/s13036-024-00426-3",
        "snippet": "give them the buoyancy to move upward so that they can get enough light for photosynthesis",
        "notes": "Feng et al. describe gas vesicles giving photosynthetic bacteria buoyancy to move upward toward sufficient light."
      },
      {
        "reference": "DOI:10.3390/life12091455",
        "snippet": "Approximately 3\u201310% of the cell volume must be occupied by gas vesicles to provide buoyancy",
        "notes": "Pfeifer reviews gas-vesicle proteins and summarizes the fraction of cell volume that must contain gas vesicles to confer buoyancy."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1126",
        "taxon_label": "Microcystis aeruginosa",
        "note": "Mlouka et al. mapped the M. aeruginosa gas-vesicle gene cluster and DNA rearrangements that lead to loss of cellular buoyancy.",
        "reference": "DOI:10.1128/JB.186.8.2355-2365.2004"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "gas_vesicles_confer_cellular_buoyancy",
        "title": "Gas vesicles confer cellular buoyancy",
        "description": "Evidence-backed causal sketch linking a proteinaceous gas-filled organelle to cellular buoyancy.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "The graph records the organelle-scale physical gas-vesicle branch and leaves taxon-specific Gvp protein assembly to the gas-vesicle morphology record. It does not assert that all planktonic depth regulation is gas-vesicle mediated.",
        "nodes": [
          {
            "node_id": "gas_vesicle_shell",
            "label": "gas vesicle shell",
            "node_type": "CELLULAR_LOCALIZATION",
            "description": "Proteinaceous shell enclosing the gas-vesicle lumen.",
            "grounding": "GO:0033172"
          },
          {
            "node_id": "gas_vesicle",
            "label": "gas vesicle",
            "node_type": "ORGANELLE",
            "description": "Hollow gas-filled protein nanocompartment that displaces cytoplasmic volume.",
            "grounding": "GO:0031411"
          },
          {
            "node_id": "cellular_buoyancy_trait",
            "label": "cellular buoyancy",
            "node_type": "TRAIT",
            "description": "Gas-vesicle-mediated capacity for upward flotation or water-column positioning.",
            "grounding": "traitmech:000528"
          }
        ],
        "edges": [
          {
            "subject": "gas_vesicle_shell",
            "predicate": "part of",
            "predicate_id": "biolink:part_of",
            "object": "gas_vesicle",
            "description": "The protein shell encloses the internal gas volume as part of the gas vesicle.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s13036-024-00426-3",
                "snippet": "The gas vesicle (GV) is like a hollow nanoparticle consisting of an internal gas and a protein shell",
                "notes": "Feng et al. describe the gas vesicle as an internal gas compartment bounded by a protein shell."
              }
            ]
          },
          {
            "subject": "gas_vesicle",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "cellular_buoyancy_trait",
            "description": "Gas-filled vesicles lower effective cellular density and provide buoyancy.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s13036-024-00426-3",
                "snippet": "can provide buoyancy for them to move up and down the water to obtain nutrients",
                "notes": "Feng et al. review gas-vesicle physical properties that provide buoyancy for photosynthetic bacteria and halophilic archaea."
              },
              {
                "reference": "DOI:10.1186/s13036-024-00426-3",
                "snippet": "give them the buoyancy to move upward so that they can get enough light for photosynthesis",
                "notes": "Feng et al. describe gas vesicles giving photosynthetic bacteria buoyancy to move upward toward sufficient light."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "cellular-buoyancy-xref-gap",
        "prompt": "Resolve exact external ontology xrefs for gas-vesicle-mediated cellular buoyancy.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "No exact active local METPO class was accepted for the organism-level cellular-buoyancy physiology trait. The only buoyancy hit in the local METPO snapshot is obsolete buoyancy structure, and GO:0031411 denotes the gas vesicle organelle rather than the gas-vesicle-conferred physiological disposition.",
        "posed_by": "codex",
        "posed_date": "2026-10-01"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-01T22:49:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted cellular buoyancy as a DOI-backed PHYSIOLOGY TraitRecord after an ignored-and-hidden duplicate review found no exact same-scope TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v405.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000729",
    "label": "cell body or cytoplasmic projection contraction",
    "definition": "A physiological phenotype in which a microbial cell actively contracts its body or a cytoplasmic projection, reducing its length or extension.",
    "definition_source": "DOI:10.1242/jeb.189.1.163",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1242/jeb.189.1.163",
        "snippet": "Living Vorticella showed a graded shrinkage of the cell body when Ca2+ buffer was injected into the cell body",
        "notes": "Katoh and Naitoh 1994, PMID:9317557, scientific Abstract item 3, first clause. Direct namespace-qualified Europe PMC MED match; native VERIFIED. The same sentence contrasts graded cell-body shrinkage with all-or-nothing stalk coiling. This supports the curator-synthesized body/projection-shortening parent, not a universal calcium threshold. Other abstract items use Triton-extracted preparations, not the living-cell injection assay. Calcium-induced calcium release is an assumption, not direct molecular proof. Publisher requests returned 403; full Methods, figures and strain provenance were not accessed."
      },
      {
        "reference": "DOI:10.2108/zsj.20.1367",
        "snippet": "Axopodial contraction of the centrohelid heliozoon Raphidiophrys contractilis was induced by mechanical or electrical stimulation.",
        "notes": "Khan et al. 2003, PMID:14624035, scientific Abstract opening sentence. Direct namespace-qualified Europe PMC MED match; native VERIFIED. This supports stimulated shortening of a cytoplasmic projection rather than whole-cell locomotion. Reported calcium dependence and speed apply to this assay, not every member of the parent class. Non-detection of other filaments after fixation is not proof of their absence. Full Methods and figures were not accessed; the publisher's HTTP 200 response was an access challenge, not readable article content. Current taxonomic and culture identities remain unresolved."
      },
      {
        "reference": "DOI:10.1083/jcb.118.3.585",
        "snippet": "Both recording techniques showed that the rapid contraction involves 80% of the total cell length.",
        "notes": "Febvre-Chevalier and Febvre 1992, PMID:1639845, PMCID:PMC2289557, Results, Kinetics of the Contraction, printed page 588, right column. Direct extracted-PDF match with the typeset passage visually checked; native NOT_IN_ABSTRACT retained. The primary PDF was retrieved from its Semantic Scholar mirror after official PDF attempts failed. Selected Methods/Results and actual Figures 1 and 3-6 were inspected. Length was measured from head top to stalk base, not isolated cell-body length; graph axes use stalk length. The percentage is study-specific. Natural-seawater responses differ from artificially slowed responses. The specimens were collected near Villefranche and cultured at 14-18 C; current taxonomic identity is not verified. The n=20 initial-length sample is not asserted as independent contraction replication. Microtubule disassembly accompanies shortening, but this study expressly does not establish force production. Its disassembly half-time is not automatically contraction duration. The accessible JATS contains an abstract and PDF pointer, not the complete experimental text."
      }
    ],
    "discussions": [
      {
        "discussion_id": "cellular-contraction-scope-and-mappings",
        "prompt": "Review the shortening-defined parent without equating all contractility endpoints.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Require active reduction of cell-body length or the extension of a cytoplasmic projection. Generic force production or isometric contractility alone is insufficient. Extracellular pilus retraction, injection-system contraction, contractile-vacuole cycling and cytokinetic constriction alone do not establish this endpoint. Neither passive osmotic shrinkage, death-associated shortening nor static short-cell morphology suffices. The existing body and rapid axopodial traits are narrower children; stalk contraction traitmech:000730 is now a narrower child, defined by active reduction of stalk end-to-end extension. This does not require shortening of the stalk contour or make its sheath cytoplasm. Motility METPO:1000701 and motile METPO:1000702 concern locomotion, not necessarily shortening. Active denotes the cellular response, not demonstrated ATP-driven motor action. No universal speed, fractional shortening, trigger, calcium threshold, ATP dependence, ecological role, exact synonym for generic contractility or organism-level disjointness is asserted.",
        "posed_by": "codex",
        "posed_date": "2026-10-14"
      },
      {
        "discussion_id": "cellular-contraction-metpo-assessment",
        "prompt": "Review the proposed shortening phenotype and its upstream hierarchy.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Pinned/current METPO releases, editor and inspected template owners yielded no active exact class in the bounded identity assessment. Deprecated Motility METPO:0000006 and METPO:000006 lead to METPO:1000701; deprecated Motile METPO:0000087 and METPO:000088 lead to METPO:1000702. These are related locomotion concepts, not exact replacements for shortening. They are not revived or put in xrefs. Keep phenotype METPO:1000059 as the direct parent. Proposal v605 reserves METPO:1068200; the ontology pin and historical child cohorts v558/v604 remain unchanged. No external equivalence or SSSOM mapping is accepted.",
        "posed_by": "codex",
        "posed_date": "2026-10-14"
      },
      {
        "discussion_id": "cellular-contraction-provenance-and-mechanism",
        "prompt": "Resolve isolate identities and endpoint-specific mechanisms before adding exemplars or causal proteins.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Keep source-named organisms as qualified observations, not species-wide canonical exemplars. Verify culture provenance and current taxonomic identity before adding canonical_examples. Calcium dependence, microtubule breakdown, contractile fibers and fitted calcium-wave models must not be combined into one universal mechanism. Protein sequence features alone cannot establish this phenotype. A protein-resolved graph requires authority-checked taxon-paired accessions and edge-specific perturbation evidence. No graph is asserted; mechanisms are deferred, not claimed absent. Source checks covered identified metadata fields and selected text/figures, not comprehensive correction or retraction clearance.",
        "posed_by": "codex",
        "posed_date": "2026-10-14"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-14T22:35:09Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added a shortening-defined cellular contraction parent with three primary DOI sources and directly checked 19/15/15-word excerpts. Retained native VERIFIED, VERIFIED and NOT_IN_ABSTRACT outcomes. Reserved 000729, v605 and 1068200-1068299 after ignored/hidden known-copy, retained-history and open/draft PR checks with full proposal-range inspection. Resolved the body and axopodial parent gaps while keeping assay and mechanism questions open. No universal molecular mechanism or canonical taxon inferred. Timestamp records observed allocation and curation acceptance.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-14T23:56:33Z",
        "curator": "codex",
        "action": "REFINE_CONTRACTION_LABEL",
        "changes": "Replaced the parenthetical label cellular contraction (body or cytoplasmic projection shortening) with cell body or cytoplasmic projection contraction. Preserved definition, endpoint qualifier, evidence, discussions, identifier and earlier history. The v605 template also emits the two existing child subclass axioms without modifying historical v558/v604 cohorts. Addresses external review issues #1941 and #1942; no new biology or human review promotion. Timestamp records observed acceptance of the refinements.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-15T03:51:31Z",
        "curator": "codex",
        "action": "LINK_STALK_CONTRACTION_CHILD",
        "changes": "Linked the accepted stalk-contraction child traitmech:000730 in place of the future-lead sentence. Preserved the parent's definition, evidence, hierarchy and prior history; independent scope and mechanism questions remain OPEN. No new parent experiment or universal mechanism is asserted.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000710",
    "label": "functional cellular rejuvenation",
    "definition": "A physiological phenotype in which age-associated loss of cellular performance or replicative potential is reversed in a microbial cell or reset in its descendants.",
    "definition_source": "DOI:10.1242/jcs.86.1.263",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1242/jcs.86.1.263",
        "snippet": "This is the first description of the restoration of a senescent defect by microinjection of young cytoplasmic components into Paramecium.",
        "notes": "Haga and Karino 1986, PMID:3654779; scientific abstract, directly read in the MED record. Young-cell cytoplasm restored sexual activity in senescent cells (about 700 fissions); recovery persisted for up to 20 fissions. Division rate and fertility after self-conjugation did not improve. This supports endpoint-specific recovery in treated old cells, not whole-cell or permanent rejuvenation. Full methods and figures were unavailable."
      },
      {
        "reference": "DOI:10.1038/s41467-018-06154-9",
        "snippet": "As this convergence was now downwards, doubling times decreased with each generation.",
        "notes": "Proenca et al. 2018, PMID:30213942, PMC6137065; Results, Stable equilibria are connected by aging and rejuvenation (Sec6), directly checked in primary XML. Actual Figure 4d was visually inspected: new-daughter lineages from the old-cell equilibrium converge toward faster growth over successive generations. These doubling times are derived from elongation rates, not direct interdivision intervals. Recovery is in descendants, not the same old mother. The tested MG1655 conditions do not establish all-environment recovery or a universal damage mechanism."
      },
      {
        "reference": "DOI:10.1126/science.1204349",
        "snippet": "Gametes (spores) generated by aged cells show the same replicative potential as gametes generated by young cells.",
        "notes": "Unal et al. 2011, PMID:21700873, PMC3923466; scientific abstract, directly checked in MED and an MIT-hosted author manuscript. Main text and Figure 1 support gamete replicative-potential reset. Figure 4 concerns the separate vegetative lifespan-extension experiment. Transient NDT80-dependent vegetative lifespan extension is a separate result and does not establish reversal of every aged-cell defect. Supplements and strain tables were not assessed. The retrieved PDF identifies the article but differs in size and checksum from MIT bitstream metadata; original deposited-byte identity remains unresolved."
      },
      {
        "reference": "DOI:10.3390/microorganisms11010082",
        "snippet": "The cloned immaturin gene induces sexual rejuvenation in both mature and senescent cells by microinjection.",
        "notes": "Haga 2023, PMID:36677375, PMC9865852; scientific abstract, directly checked in primary XML and PMC text. Results 3.1 uses rejuvenation for suppression of mating in mature cells: that maturation-state reset alone is outside this functional trait. Results 3.2 reports recovery of old-cell mating activity after transformation. Figure 6C measures total cell counts over four days, not direct division times, and lacks a young-cell growth comparator. Engineered treatment is not a natural canonical taxon example; inferred chemistry is not a proven mechanism."
      },
      {
        "reference": "DOI:10.1016/j.isci.2022.103765",
        "snippet": "Some cells rejuvenated immediately, even after extended starvation, but others only restarted growth after a delay or not at all.",
        "notes": "Cesar et al. 2022, PMID:35243217, PMC8858994; scientific abstract, directly checked against MED and primary XML. Boundary evidence: culture duration during stationary phase is not individual replicative age. Immediate regrowth can reflect preserved function, not recovery from a demonstrated deficit. Regrowth classes use area-derived growth rates; nongrowth during the observation window is not proof of irreversible death. Results 2.1 and 2.3, Discussion, limitations and classification methods were read; figures and raw data were not independently assessed."
      }
    ],
    "discussions": [
      {
        "discussion_id": "cellular-rejuvenation-operational-scope",
        "prompt": "Assess the functional qualifier and distinguish same-cell recovery from descendant reset.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Require an age-linked deficit and a measured recovery or replicative-potential reset, retaining the endpoint, age axis, comparison group, treated unit, conditions and persistence. Recovery of one function need not restore all functions, be permanent or extend lifespan. Descendant recovery must not be reported as repair of the old mother. Marker changes, lifespan extension alone, prevention without prior loss and sexual immaturity alone are insufficient. Bare cellular rejuvenation has broader source usages and is not an exact synonym. Autogamy, gametogenesis and dormancy exit are not themselves this phenotype; neither is replicative aging with functional decline. Culture age is not interchangeable with lineage age. METPO:1000059 phenotype is a conservative parent, with no reparenting of existing records or asserted external equivalence.",
        "posed_by": "codex",
        "posed_date": "2026-10-12"
      },
      {
        "discussion_id": "cellular-rejuvenation-mechanism-and-example-limits",
        "prompt": "Resolve strain provenance and endpoint-specific mechanisms before adding examples or causal edges.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "This is a reusable physiological outcome, not a gene, protein, sequence feature or intervention. No canonical example or protein-resolved graph is asserted pending strain provenance and mechanistic review. Bacterial model-derived damage and fluorescent aggregates are not direct proof of a universal rejuvenation chemistry. Studies need not share a mechanism. The 2011 PDF/metadata byte mismatch is retained, not explained away by its added cover. MED/Crossref notice fields and accessible primary pages were checked on 2026-10-12; incomplete publisher access prevents an exhaustive notice-absence claim. Ignored/hidden local and pending-source searches plus pinned and current released METPO found no exact term in the inspected scope. No ontology upgrade or discovery-exhaustion claim follows.",
        "posed_by": "codex",
        "posed_date": "2026-10-12"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-12T12:13:34Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added functional cellular rejuvenation with five primary DOI references and directly checked snippets; retained same-cell, descendant, maturation and dormancy boundaries and access limits. Reserved 000710, v586 and 1066300-1066399 after ignored/hidden, registered historical-tree and pending-PR checks. Examples and mechanism graph deferred. Existing records unchanged; timestamp is the observed UTC curation decision.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-12T12:40:17Z",
        "curator": "codex",
        "action": "CORRECTED_FIGURE_ATTRIBUTION",
        "changes": "Corrected issue #1893: Figure 1 supports gamete replicative-potential reset; Figure 4 tests vegetative lifespan extension. Preserved definition, DOI, snippet, status, checksum limitation and original event. The source sidecar retains its historical assessment with an explicit superseding correction. Timestamp is the observed UTC correction decision.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000634",
    "label": "chemoautolithotrophic",
    "definition": "A trophic type in which an organism uses chemical oxidation of inorganic compounds as the energy source and carbon dioxide as the primary carbon source for biosynthesis.",
    "definition_source": "DOI:10.1016/B978-0-12-378630-2.00219-X",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000631"
    ],
    "synonyms": [
      {
        "synonym_text": "chemoautolithotroph",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "created_by": "Luke Wang",
    "evidence": [
      {
        "reference": "DOI:10.1016/B978-0-12-378630-2.00219-X",
        "snippet": "oxidize inorganic atoms or molecules",
        "notes": "Review supports inorganic compound oxidation as lithotrophic energy metabolism."
      },
      {
        "reference": "DOI:10.1128/AEM.02473-10",
        "snippet": "autotrophic CO2 fixation",
        "notes": "Minireview supports microbial carbon dioxide fixation pathways."
      },
      {
        "reference": "DOI:10.1146/annurev.micro.55.1.485",
        "snippet": "Chemolitho-autotrophic ammonia-oxidizing bacteria",
        "notes": "Review supports ammonia oxidation as a chemolithoautotrophic example."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:915",
        "taxon_label": "Nitrosomonas europaea",
        "note": "ammonia chemolithoautotroph",
        "reference": "PMID:12700255"
      },
      {
        "taxon_id": "NCBITaxon:920",
        "taxon_label": "Acidithiobacillus ferrooxidans",
        "note": "iron/sulfur chemolithoautotroph",
        "reference": "PMID:19077236"
      },
      {
        "taxon_id": "NCBITaxon:228410",
        "taxon_label": "Nitrosomonas europaea ATCC 19718",
        "note": "Strain-level ammonia-oxidizing chemoautolithotroph paired to the AmoA alpha component of ammonia monooxygenase.",
        "reference": "DOI:10.1128/jb.175.8.2436-2444.1993"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "chemoautolithotrophic_inorganic_energy_co2_fixation",
        "title": "Chemoautolithotrophic inorganic energy and CO2 fixation",
        "description": "DOI-backed graph linking inorganic chemical donors, respiratory energy conservation, CO2 fixation, and biomass production.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "This graph combines representative ammonia- and iron-oxidation with generic respiratory and carbon-fixation steps. The N. europaea AmoA example anchors only ammonia oxidation; Q04507 is an alpha-subunit component of a multisubunit ammonia monooxygenase and is not the complete complex or the iron branch.",
        "nodes": [
          {
            "node_id": "chemoautolithotrophic_trait",
            "label": "chemoautolithotrophic",
            "node_type": "TRAIT",
            "grounding": "METPO:1000634",
            "description": "Trophic type using inorganic chemical donors for energy and CO2 for carbon."
          },
          {
            "node_id": "inorganic_electron_donor",
            "label": "inorganic electron donor",
            "node_type": "CHEMICAL",
            "description": "Reduced inorganic compound oxidized for energy.",
            "grounding": "METPO:1007502"
          },
          {
            "node_id": "ammonia",
            "label": "ammonia",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:16134",
            "description": "Representative inorganic nitrogen electron donor."
          },
          {
            "node_id": "ammonia_monooxygenase",
            "label": "ammonia monooxygenase",
            "node_type": "GENE_OR_PROTEIN",
            "grounding": "GO:0018597",
            "description": "Multisubunit enzyme initiating aerobic ammonia oxidation.",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:Q04507",
                "protein_label": "Ammonia monooxygenase alpha subunit",
                "gene_symbol": "amoA1",
                "taxon_id": "NCBITaxon:228410",
                "taxon_label": "Nitrosomonas europaea ATCC 19718",
                "entry_status": "REVIEWED",
                "retrieved_on": "2026-10-22",
                "entry_version": 127,
                "sequence_version": 2,
                "role": "AmoA alpha-subunit component of N. europaea ammonia monooxygenase; this accession maps two duplicated amoA gene copies and does not denote the whole enzyme complex.",
                "evidence": [
                  {
                    "reference": "DOI:10.1128/jb.175.8.2436-2444.1993",
                    "snippet": "Sequence of the gene coding for ammonia monooxygenase in Nitrosomonas europaea",
                    "notes": "The primary strain-level study sequences and characterizes N. europaea AmoA; UniProtKB Q04507 is the reviewed alpha-subunit entry for ATCC 19718."
                  }
                ]
              }
            ]
          },
          {
            "node_id": "ferrous_iron",
            "label": "ferrous iron",
            "node_type": "CHEMICAL",
            "description": "Representative inorganic metal electron donor.",
            "grounding": "CHEBI:29033"
          },
          {
            "node_id": "respiratory_chain",
            "label": "respiratory chain",
            "node_type": "PATHWAY",
            "description": "Energy-conserving electron-transfer pathway.",
            "grounding": "GO:0022904"
          },
          {
            "node_id": "atp",
            "label": "ATP",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:30616",
            "description": "Energy carrier produced during chemotrophic growth."
          },
          {
            "node_id": "carbon_dioxide",
            "label": "carbon dioxide",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:16526",
            "description": "Inorganic carbon source for autotrophic biosynthesis."
          },
          {
            "node_id": "co2_fixation_pathway",
            "label": "CO2-fixation pathway",
            "node_type": "PATHWAY",
            "description": "Autotrophic pathway converting CO2 into cellular carbon.",
            "grounding": "GO:0015977"
          },
          {
            "node_id": "biomass",
            "label": "biomass",
            "node_type": "CHEMICAL",
            "description": "Cell material produced from fixed carbon.",
            "grounding": "METPO:1007501"
          },
          {
            "node_id": "inorganic_compound_oxidation",
            "label": "oxidation of reduced inorganic compounds",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Oxidation of reduced inorganic compounds that yields metabolic energy."
          },
          {
            "node_id": "chemoorganoheterotrophy",
            "label": "chemo-organoheterotrophy",
            "node_type": "TRAIT",
            "description": "Trophic type using organic compounds as energy and carbon source."
          }
        ],
        "edges": [
          {
            "subject": "chemoautolithotrophic_trait",
            "predicate": "has electron donor",
            "object": "inorganic_electron_donor",
            "description": "Inorganic chemical electron donors supply the energy for chemoautolithotrophy.",
            "evidence": [
              {
                "reference": "DOI:10.1016/B978-0-12-378630-2.00219-X",
                "snippet": "oxidize inorganic atoms or molecules",
                "notes": "Supports lithotrophic oxidation of inorganic substrates."
              }
            ],
            "predicate_id": "METPO:2007701"
          },
          {
            "subject": "ammonia",
            "predicate": "example of",
            "object": "inorganic_electron_donor",
            "description": "Ammonia is an inorganic donor in chemolithoautotrophic nitrification.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev.micro.55.1.485",
                "snippet": "Chemolitho-autotrophic ammonia-oxidizing bacteria",
                "notes": "Supports ammonia oxidation as a chemolithoautotrophic example."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "ammonia_monooxygenase",
            "predicate": "oxidizes",
            "object": "ammonia",
            "description": "Ammonia monooxygenase initiates ammonia oxidation in the N. europaea branch of chemoautolithotrophy.",
            "evidence": [
              {
                "reference": "DOI:10.1128/jb.175.8.2436-2444.1993",
                "snippet": "Sequence of the gene coding for ammonia monooxygenase in Nitrosomonas europaea",
                "notes": "The primary study supports AmoA as a component of the N. europaea enzyme that catalyzes ammonia oxidation to hydroxylamine; it does not support the graph's separate iron-oxidation branch."
              }
            ],
            "predicate_id": "METPO:2007803"
          },
          {
            "subject": "ferrous_iron",
            "predicate": "example of",
            "object": "inorganic_electron_donor",
            "description": "Fe(II) is a representative inorganic electron donor.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41598-021-81412-3",
                "snippet": "Fe(II) as the energy source",
                "notes": "Supports Fe(II) oxidation as an inorganic energy source."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "inorganic_electron_donor",
            "predicate": "feeds electrons into",
            "object": "respiratory_chain",
            "description": "Inorganic donor oxidation feeds respiratory energy conservation.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.bbabio.2008.09.008",
                "snippet": "membrane-bound electron transport chain",
                "notes": "Supports respiratory electron transfer as energy-conserving pathway."
              }
            ],
            "predicate_id": "METPO:2007402"
          },
          {
            "subject": "respiratory_chain",
            "predicate": "has output",
            "object": "atp",
            "description": "Respiratory energy conservation produces ATP.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.bbabio.2008.09.008",
                "snippet": "drives ATP synthesis",
                "notes": "Supports ATP production from electron transport."
              }
            ],
            "predicate_id": "RO:0002234"
          },
          {
            "subject": "chemoautolithotrophic_trait",
            "predicate": "has carbon source",
            "object": "carbon_dioxide",
            "description": "Chemoautolithotrophs use CO2 as the primary carbon source.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.02473-10",
                "snippet": "autotrophic CO2 fixation",
                "notes": "Supports inorganic carbon fixation by autotrophic pathways."
              }
            ],
            "predicate_id": "METPO:2007806"
          },
          {
            "subject": "carbon_dioxide",
            "predicate": "fixed by",
            "object": "co2_fixation_pathway",
            "description": "CO2 is fixed into cellular carbon by autotrophic pathways.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.02473-10",
                "snippet": "autotrophic carbon dioxide assimilation pathway",
                "notes": "Supports conversion of CO2 by microbial autotrophic pathways."
              }
            ],
            "predicate_id": "METPO:2007404"
          },
          {
            "subject": "co2_fixation_pathway",
            "predicate": "has output",
            "object": "biomass",
            "description": "Fixed carbon supports biomass production.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro.2016.130",
                "snippet": "microbial autotrophic production",
                "notes": "Supports biomass production from autotrophic CO2 fixation."
              }
            ],
            "predicate_id": "RO:0002234"
          },
          {
            "subject": "chemoautolithotrophic_trait",
            "predicate": "requires",
            "object": "co2_fixation_pathway",
            "description": "Chemoautolithotrophy requires CO2 fixation to convert inorganic carbon into organic carbon.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s40168-023-01712-w",
                "notes": "Chemolithoautotrophs convert CO2 to organic carbon (Deng et al. 2023)."
              }
            ]
          },
          {
            "subject": "chemoautolithotrophic_trait",
            "predicate": "requires",
            "object": "inorganic_compound_oxidation",
            "description": "Chemoautolithotrophy requires oxidation of reduced inorganic compounds for energy.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s40168-023-01712-w",
                "notes": "Using the energy produced by oxidizing reduced inorganic compounds (Deng et al. 2023)."
              }
            ]
          },
          {
            "subject": "inorganic_compound_oxidation",
            "predicate": "feeds electrons into",
            "object": "respiratory_chain",
            "description": "Oxidation of reduced inorganic compounds donates electrons to the respiratory chain.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s40168-023-01712-w",
                "notes": "Energy produced by oxidizing reduced inorganic compounds is conserved via electron transport (Deng et al. 2023)."
              }
            ],
            "predicate_id": "METPO:2007402"
          },
          {
            "subject": "chemoautolithotrophic_trait",
            "predicate": "distinct from",
            "object": "chemoorganoheterotrophy",
            "description": "Chemolithoautotrophy (inorganic energy, CO2 carbon) is metabolically distinct from chemo-organoheterotrophy (organic energy and carbon).",
            "evidence": [
              {
                "reference": "DOI:10.3390/molecules29102293",
                "notes": "Chemolithoautotrophy oxidizes inorganic compounds versus chemo-organoheterotrophs using glucose (Fukala & Kucera 2024)."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-08-24T14:00:00-07:00",
        "curator": "codex",
        "action": "REVIEWED_CAUSAL_GRAPH_PROTEIN_TAXON",
        "changes": "Added a DOI-backed N. europaea ATCC 19718 canonical example, semantically grounded ammonia monooxygenase, reviewed AmoA alpha-subunit example, and one complete-evidence ammonia-oxidation edge; documented the multisubunit and branch scope.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-05T01:35:46.868850+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-09T00:00:00-07:00",
        "curator": "Codex",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed chemoautolithotrophy graph for inorganic electron donors, respiratory ATP generation, CO2 fixation, and biomass.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 4 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d72, METPO:2000009\u00d71, METPO:2000006\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T08:21:50Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (rdfs:subClassOf\u00d72).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T21:30:07Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007402\u00d71, METPO:2007404\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:38:01Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:29033\u00d71, GO:0022904\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:41:04Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (METPO:1007502\u00d71, METPO:1007501\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T07:34:58Z",
        "curator": "claude",
        "action": "RETYPE_CAUSAL_NODES",
        "changes": "Re-typed 1 causal-node node_type field(s) to align with CausalNodeTypeEnum semantics: biomass: BIOLOGICAL_PROCESS \u2192 CHEMICAL \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T08:14:33Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0015977\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 4 evidence-backed generic edges (2 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:14Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007402\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-05T12:00:00Z",
        "curator": "claude",
        "action": "REVERSE_CAUSAL_EDGE_DIRECTION",
        "changes": "Reversed 1 causal edge from <trait> uses electron donor <chemical> to <chemical> enables <trait> (predicate_id METPO:2000009 -> RO:0002327), issue 295. METPO:2000009 is rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so the trait-subject form entailed that this TRAIT node is a microbe; CausalNodeTypeEnum has no organism member, so no causal-graph edge can satisfy that domain. Evidence unchanged; only subject/predicate/object/predicate_id and the edge description moved. Note RO:0002327 has range 'biological process or activity', so the new form is not fully range-correct either - tracked in issue 302.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 1 causal edge(s) off enables/RO:0002327 with a TRAIT object (1 to has electron donor), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them. 1 electron edge(s) were also reversed back to trait -> chemical, restoring the donor/acceptor role that PR 300 collapsed onto enables (issue 303); the organism-subject problem that forced that collapse does not arise here because these predicates take a causal-node domain rather than METPO:2000001's microbe domain (issue 301).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 3 causal edge(s) off microbe-domain METPO predicates (2 to has output, 1 to has carbon source), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-22T01:35:00Z",
        "curator": "claude",
        "action": "REFRESH_UNIPROT_ENTRY_VERSION",
        "changes": "Refreshed UniProtKB entry_version against live UniProt REST on 2026-10-22: UniProtKB:Q04507 (126 -> 127 on ammonia_monooxygenase).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000635",
    "label": "chemoautotrophic",
    "definition": "A trophic type in which an organism obtains energy from oxidation of inorganic compounds and carbon from carbon dioxide.",
    "definition_source": "DOI:10.1146/annurev.micro.52.1.191",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000631"
    ],
    "synonyms": [
      {
        "synonym_text": "chemoautotroph",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev.micro.52.1.191",
        "snippet": "Carbon Dioxide Fixation in Chemoautotrophs",
        "notes": "Review supports CO2 fixation as central to chemoautotrophic bacteria."
      },
      {
        "reference": "DOI:10.1128/AEM.02473-10",
        "snippet": "Calvin-Benson reductive pentose phosphate cycle",
        "notes": "Review supports Calvin-Benson and other microbial autotrophic CO2-fixation pathways."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:228410",
        "taxon_label": "Nitrosomonas europaea ATCC 19718",
        "note": "ammonia-oxidizing obligate chemolithoautotroph",
        "reference": "DOI:10.1128/AEM.00294-16"
      },
      {
        "taxon_id": "NCBITaxon:292415",
        "taxon_label": "Thiobacillus denitrificans ATCC 25259",
        "note": "sulfur-oxidising chemoautotroph",
        "reference": "DOI:10.1128/JB.188.4.1473-1488.2006"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "chemoautotrophic_chemical_energy_co2_fixation",
        "title": "Chemoautotrophic chemical-energy CO2 fixation",
        "description": "DOI-backed graph linking chemical electron donors, energy conservation, RuBisCO/Calvin-Benson carbon fixation, and biomass production.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "This graph represents a modular chemoautotrophic mechanism; electron donors and carbon-concentrating systems vary across lineages. The N. europaea ATCC 19718 example specifically anchors the RuBisCO carbon-fixation branch.",
        "nodes": [
          {
            "node_id": "chemoautotrophic_trait",
            "label": "chemoautotrophic",
            "node_type": "TRAIT",
            "grounding": "METPO:1000635",
            "description": "Trophic type using chemical energy and CO2 as carbon source."
          },
          {
            "node_id": "reduced_inorganic_compound",
            "label": "reduced inorganic compound",
            "node_type": "CHEMICAL",
            "description": "Chemical energy substrate oxidized by chemoautotrophs."
          },
          {
            "node_id": "respiratory_energy_conservation",
            "label": "respiratory energy conservation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Energy conservation from redox reactions."
          },
          {
            "node_id": "atp",
            "label": "ATP",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:30616",
            "description": "Energy carrier used in carbon fixation."
          },
          {
            "node_id": "nadph",
            "label": "NADPH",
            "node_type": "CHEMICAL",
            "description": "Reducing equivalent used in reductive biosynthesis.",
            "grounding": "CHEBI:16474"
          },
          {
            "node_id": "carbon_dioxide",
            "label": "carbon dioxide",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:16526",
            "description": "Inorganic carbon source."
          },
          {
            "node_id": "calvin_benson_cycle",
            "label": "Calvin-Benson cycle",
            "node_type": "PATHWAY",
            "description": "Common microbial CO2-fixation pathway.",
            "grounding": "GO:0019253"
          },
          {
            "node_id": "rubisco",
            "label": "RuBisCO",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Carboxylating enzyme of the Calvin-Benson cycle.",
            "grounding": "InterPro:IPR033966",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:Q82TG6",
                "protein_label": "Ribulose bisphosphate carboxylase large chain",
                "gene_symbol": "cbbL",
                "taxon_id": "NCBITaxon:228410",
                "taxon_label": "Nitrosomonas europaea ATCC 19718",
                "entry_status": "REVIEWED",
                "retrieved_on": "2026-10-22",
                "entry_version": 121,
                "sequence_version": 1,
                "role": "Large subunit of the type I RuBisCO that fixes CO2 through the CBB cycle in ammonia-oxidizing N. europaea ATCC 19718.",
                "evidence": [
                  {
                    "reference": "DOI:10.1128/AEM.00294-16",
                    "snippet": "expression of the entire cbb gene cluster increased, with 7.4- and 10.8-fold increases in numbers of genes encoding the small and large subunits of RuBisCO, cbbS (NE1920) and rbcL (NE1921)",
                    "notes": "The primary ATCC 19718 chemostat study identifies NE1921/rbcL and its carbon-fixation response; UniProtKB Q82TG6 is the reviewed NE1921 large-chain entry for that strain."
                  }
                ]
              }
            ]
          },
          {
            "node_id": "cellular_biomass",
            "label": "cellular biomass",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Cellular material produced from fixed carbon."
          },
          {
            "node_id": "carboxysome",
            "label": "carboxysome",
            "node_type": "ORGANELLE",
            "description": "Bacterial microcompartment that encapsulates RuBisCO and carbonic anhydrase to concentrate CO2.",
            "grounding": "GO:0031470"
          },
          {
            "node_id": "carbonic_anhydrase",
            "label": "carbonic anhydrase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Enzyme converting bicarbonate to CO2 inside the carboxysome to feed RuBisCO.",
            "grounding": "InterPro:IPR001765"
          },
          {
            "node_id": "bicarbonate",
            "label": "bicarbonate",
            "node_type": "CHEMICAL",
            "description": "Dissolved inorganic carbon species imported and converted to CO2 for fixation.",
            "grounding": "CHEBI:17544"
          },
          {
            "node_id": "dic_transporter",
            "label": "dissolved inorganic carbon transporter",
            "node_type": "GENE_OR_PROTEIN",
            "description": "CO2/HCO3- transporters that supply inorganic carbon to the carbon-concentrating mechanism.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "This functional node includes unrelated CO2 and bicarbonate transporter families; the graph does not identify one transporter class or membrane complex."
          },
          {
            "node_id": "carbon_concentrating_mechanism",
            "label": "carbon-concentrating mechanism",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "System of DIC transporters and carboxysomes that elevates CO2 around RuBisCO."
          },
          {
            "node_id": "inorganic_carbon_assimilation",
            "label": "inorganic carbon assimilation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Incorporation of inorganic carbon into cellular metabolites."
          },
          {
            "node_id": "hp_hb_cycle",
            "label": "3-hydroxypropionate/4-hydroxybutyrate cycle",
            "node_type": "PATHWAY",
            "description": "Energy-efficient aerobic autotrophic CO2-fixation pathway."
          }
        ],
        "edges": [
          {
            "subject": "chemoautotrophic_trait",
            "predicate": "uses energy substrate",
            "object": "reduced_inorganic_compound",
            "description": "Chemoautotrophs derive energy from oxidizing reduced inorganic compounds.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev.micro.52.1.191",
                "snippet": "physiology ... of chemoautotrophic bacteria",
                "notes": "Review supports chemoautotrophic metabolism based on chemical energy and CO2 fixation."
              }
            ]
          },
          {
            "subject": "reduced_inorganic_compound",
            "predicate": "enables",
            "object": "respiratory_energy_conservation",
            "description": "Oxidation of chemical substrates supports energy conservation.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.bbabio.2008.09.008",
                "snippet": "free energy of a redox reaction",
                "notes": "Supports energy conservation from redox reactions in respiratory systems."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "respiratory_energy_conservation",
            "predicate": "has output",
            "object": "atp",
            "description": "Energy conservation produces ATP for biosynthesis.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.bbabio.2008.09.008",
                "snippet": "drives ATP synthesis",
                "notes": "Supports ATP synthesis from respiratory energy conservation."
              }
            ],
            "predicate_id": "RO:0002234"
          },
          {
            "subject": "respiratory_energy_conservation",
            "predicate": "has output",
            "object": "nadph",
            "description": "Chemoautotrophic electron flow supplies reducing equivalents.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.biortech.2021.125768",
                "snippet": "NADH, or ... NADPH",
                "notes": "Supports reduced redox cofactors in chemolithoautotrophic metabolism."
              }
            ],
            "predicate_id": "RO:0002234"
          },
          {
            "subject": "carbon_dioxide",
            "predicate": "fixed by",
            "object": "calvin_benson_cycle",
            "description": "CO2 can be fixed through the Calvin-Benson cycle.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.02473-10",
                "snippet": "Calvin-Benson reductive pentose phosphate cycle",
                "notes": "Supports Calvin-Benson as a microbial autotrophic CO2-fixation pathway."
              }
            ],
            "predicate_id": "METPO:2007404"
          },
          {
            "subject": "rubisco",
            "predicate": "catalyzes",
            "object": "calvin_benson_cycle",
            "description": "RuBisCO catalyzes the carboxylation step of Calvin-Benson CO2 fixation.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.02473-10",
                "snippet": "form I RuBisCO",
                "notes": "Supports RuBisCO as a Calvin-Benson cycle enzyme."
              }
            ],
            "predicate_id": "biolink:catalyzes"
          },
          {
            "subject": "atp",
            "predicate": "enables",
            "object": "calvin_benson_cycle",
            "description": "ATP is required for chemoautotrophic CO2 fixation.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.02473-10",
                "snippet": "energy required for autotrophic CO2 fixation",
                "notes": "Supports ATP/energy requirement for carbon fixation."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "nadph",
            "predicate": "enables",
            "object": "calvin_benson_cycle",
            "description": "Reducing equivalents support reductive CO2 fixation.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.biortech.2021.125768",
                "snippet": "reduction of CO2",
                "notes": "Supports NAD(P)H-like reductant use in carbon fixation."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "calvin_benson_cycle",
            "predicate": "has output",
            "object": "cellular_biomass",
            "description": "Fixed carbon is incorporated into cellular biomass.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev.micro.52.1.191",
                "snippet": "physiology, ecology, and molecular biology",
                "notes": "Review scope supports chemoautotrophic bacterial growth from fixed carbon."
              }
            ],
            "predicate_id": "RO:0002234"
          },
          {
            "subject": "carboxysome",
            "predicate": "encapsulates",
            "object": "rubisco",
            "description": "Carboxysomes encapsulate RuBisCO and carbonic anhydrase within a protein shell.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.01075-24",
                "notes": "Carboxysomes encapsulate RubisCO and carbonic anhydrase (CA) within a protein shell."
              }
            ]
          },
          {
            "subject": "carboxysome",
            "predicate": "encapsulates",
            "object": "carbonic_anhydrase",
            "description": "Carboxysomes encapsulate carbonic anhydrase alongside RuBisCO.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.01075-24",
                "notes": "Carboxysomes encapsulate RubisCO and carbonic anhydrase (CA) within a protein shell."
              }
            ]
          },
          {
            "subject": "carbonic_anhydrase",
            "predicate": "produces",
            "object": "carbon_dioxide",
            "description": "Carbonic anhydrase converts bicarbonate to CO2 inside the carboxysome for RuBisCO.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.01075-24",
                "notes": "Inside carboxysomes, CA converts HCO3- to CO2, which RubisCO then fixes."
              }
            ],
            "predicate_id": "METPO:2007800"
          },
          {
            "subject": "carbonic_anhydrase",
            "predicate": "uses substrate",
            "object": "bicarbonate",
            "description": "Carbonic anhydrase uses bicarbonate as substrate to generate CO2.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.01075-24",
                "notes": "Inside carboxysomes, CA converts HCO3- to CO2, which RubisCO then fixes."
              }
            ]
          },
          {
            "subject": "dic_transporter",
            "predicate": "enables",
            "object": "carbon_concentrating_mechanism",
            "description": "DIC (CO2/HCO3-) transporters supply substrate for the carbon-concentrating mechanism.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.01075-24",
                "notes": "CCMs consist of CO2 and HCO3- transporters and carboxysomes."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "carbon_concentrating_mechanism",
            "predicate": "enables",
            "object": "calvin_benson_cycle",
            "description": "The carbon-concentrating mechanism elevates CO2 around RuBisCO to support Calvin-Benson fixation.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.01075-24",
                "notes": "CCMs consisting of transporters and carboxysomes concentrate CO2 for RubisCO-mediated fixation."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "calvin_benson_cycle",
            "predicate": "enables",
            "object": "inorganic_carbon_assimilation",
            "description": "The Calvin-Benson-Bassham cycle drives inorganic carbon assimilation in chemolithoautotrophs.",
            "evidence": [
              {
                "reference": "DOI:10.1101/2024.08.01.606197",
                "notes": "The CBB cycle accounts for >99% of global autotrophy and is used in chemolithoautotrophs."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "carbon_dioxide",
            "predicate": "fixed by",
            "object": "hp_hb_cycle",
            "description": "The 3HP/4HB cycle is an energy-efficient aerobic CO2-fixation pathway used by chemoautotrophs.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s42003-024-06432-x",
                "notes": "Currently considered the most energy-efficient aerobic carbon fixation pathway."
              }
            ],
            "predicate_id": "METPO:2007404"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.869416+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-08T00:00:00-07:00",
        "curator": "codex",
        "action": "ADDED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed causal graph for chemical energy conservation, ATP/reductant generation, Calvin-Benson CO2 fixation, and biomass production.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d73).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T05:49:25Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:catalyzes\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T21:30:07Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007404\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:19Z",
        "curator": "claude",
        "action": "RENAME_PREDICATE_LABELS",
        "changes": "Renamed 3 causal-edge predicate label(s) to align with existing groundings: supports \u2192 enables \u00d73.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:22Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d73).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:38:01Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0019253\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-26T02:27:52Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A075WF79\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-14T05:51:46Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:16474\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 8 evidence-backed generic edges (7 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:14Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 5 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d73, METPO:2000202\u00d71, METPO:2007404\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:34Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0031470\u00d71, CHEBI:17544\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-26T07:15:20Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A009PMS8\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:21:12Z",
        "curator": "claude",
        "action": "RETRACT_DEAD_UNIPROT_GROUNDINGS",
        "changes": "Retracted 2 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:23:55Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (InterPro:IPR033966\u00d71, InterPro:IPR001765\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 3 causal edge(s) off microbe-domain METPO predicates (3 to has output), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T02:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES_PART2",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates onto their causal-graph counterparts (1 to produces), issue 301 part 2. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Each replacement is a 1:1 mirror of its source predicate that changes only the domain, so the claim each edge makes is unchanged and directions are unchanged. The replacements are proposed in proposals/metpo_traitmech_v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-24T11:35:00-07:00",
        "curator": "codex",
        "action": "REVIEWED_CAUSAL_GRAPH_PROTEIN_TAXON",
        "changes": "Marked the graph mechanistic, reviewed the broad dissolved-inorganic-carbon transporter node as label-only, upgraded canonical taxa to strain-level DOI citations, and added the reviewed N. europaea ATCC 19718 RuBisCO large-chain example.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-22T01:35:00Z",
        "curator": "claude",
        "action": "REFRESH_UNIPROT_ENTRY_VERSION",
        "changes": "Refreshed UniProtKB entry_version against live UniProt REST on 2026-10-22: UniProtKB:Q82TG6 (120 -> 121 on rubisco).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000636",
    "label": "chemoheterotrophic",
    "definition": "A trophic type in which an organism obtains both energy and carbon from organic compounds.",
    "definition_source": "DOI:10.1016/B978-012373944-5.00083-3",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000631"
    ],
    "synonyms": [
      {
        "synonym_text": "aerobic_chemo_heterotrophy",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "chemoheterotroph",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1016/B978-012373944-5.00083-3",
        "snippet": "Chemoheterotroph (chemoorganoheterotroph)",
        "notes": "Encyclopedia chapter maps chemoheterotrophy to chemical energy and reduced organic carbon."
      },
      {
        "reference": "DOI:10.1021/acsomega.3c02205",
        "snippet": "chemoheterotrophic",
        "notes": "Review table supports chemoheterotrophic use of organic molecules as energy and carbon sources."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:562",
        "taxon_label": "Escherichia coli",
        "note": "chemoorganoheterotroph",
        "reference": "PMID:17593909"
      },
      {
        "taxon_id": "NCBITaxon:303",
        "taxon_label": "Pseudomonas putida",
        "note": "versatile chemoheterotroph",
        "reference": "PMID:31657101"
      },
      {
        "taxon_id": "NCBITaxon:83333",
        "taxon_label": "Escherichia coli K-12",
        "note": "Strain-level chemoheterotrophic model paired to the purified MtlD enzyme of its mannitol catabolic branch.",
        "reference": "DOI:10.1128/jb.159.3.986-990.1984"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "chemoheterotrophic_organic_energy_carbon",
        "title": "Chemoheterotrophic organic energy and carbon metabolism",
        "description": "DOI-backed graph linking organic molecules as chemical energy and carbon sources to catabolism, respiration or fermentation, ATP, and biomass.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "This broad graph combines respiratory, fermentative, glycolytic, and mannitol-utilization branches rather than asserting one universal route. The E. coli K-12 MtlD example anchors only mannitol-1-phosphate conversion and does not represent the multicomponent PTS or all chemoheterotrophic catabolism.",
        "nodes": [
          {
            "node_id": "chemoheterotrophic_trait",
            "label": "chemoheterotrophic",
            "node_type": "TRAIT",
            "grounding": "METPO:1000636",
            "description": "Trophic type obtaining energy and carbon from organic compounds."
          },
          {
            "node_id": "organic_molecule",
            "label": "organic molecule",
            "node_type": "CHEMICAL",
            "description": "Reduced organic compound used for energy and carbon.",
            "grounding": "CHEBI:72695"
          },
          {
            "node_id": "catabolism",
            "label": "catabolism",
            "node_type": "BIOLOGICAL_PROCESS",
            "grounding": "GO:0009056",
            "description": "Breakdown of nutrients to generate energy and biosynthetic precursors."
          },
          {
            "node_id": "respiration",
            "label": "respiration",
            "node_type": "PATHWAY",
            "grounding": "METPO:1000800",
            "description": "Electron-transport route for energy conservation."
          },
          {
            "node_id": "fermentation",
            "label": "fermentation",
            "node_type": "BIOLOGICAL_PROCESS",
            "grounding": "METPO:1002005",
            "description": "Organic-substrate redox balancing route with substrate-level phosphorylation."
          },
          {
            "node_id": "atp",
            "label": "ATP",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:30616",
            "description": "Energy carrier produced during chemoheterotrophic metabolism."
          },
          {
            "node_id": "precursor_metabolites",
            "label": "precursor metabolites",
            "node_type": "CHEMICAL",
            "description": "Central intermediates used for biosynthesis."
          },
          {
            "node_id": "biomass",
            "label": "biomass",
            "node_type": "CHEMICAL",
            "description": "Cell material formed from organic carbon.",
            "grounding": "METPO:1007501"
          },
          {
            "node_id": "emp_glycolysis",
            "label": "Embden-Meyerhof glycolysis pathway",
            "node_type": "PATHWAY",
            "description": "Central glycolytic pathway converting sugars to pyruvate with ATP and reducing equivalents."
          },
          {
            "node_id": "short_chain_fatty_acids",
            "label": "short-chain fatty acids",
            "node_type": "CHEMICAL",
            "description": "Fermentation end products such as acetate, propionate, and succinate.",
            "grounding": "CHEBI:26666"
          },
          {
            "node_id": "mannitol_pts",
            "label": "PEP-dependent phosphotransferase system (mannitol PTS)",
            "node_type": "GENE_OR_PROTEIN",
            "description": "PEP-PTS transporter importing and phosphorylating sugar alcohols during organotrophic uptake.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "The mannitol PTS is a multicomponent phosphotransfer system whose EI, HPr, and sugar-specific EII components are distinct proteins; no one family term represents the whole node."
          },
          {
            "node_id": "mannitol",
            "label": "mannitol",
            "node_type": "CHEMICAL",
            "description": "Sugar alcohol imported and phosphorylated as an organic carbon and energy source."
          },
          {
            "node_id": "mtld",
            "label": "mtlD mannitol-1-phosphate dehydrogenase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Enzyme converting mannitol-1-phosphate to fructose-6-phosphate, bridging uptake to glycolysis.",
            "grounding": "InterPro:IPR023028",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:P09424",
                "protein_label": "Mannitol-1-phosphate 5-dehydrogenase",
                "gene_symbol": "mtlD",
                "taxon_id": "NCBITaxon:83333",
                "taxon_label": "Escherichia coli K-12",
                "entry_status": "REVIEWED",
                "retrieved_on": "2026-08-24",
                "entry_version": 187,
                "sequence_version": 3,
                "role": "E. coli MtlD enzyme catalyzing the mannitol-1-phosphate dehydrogenase step that connects PTS uptake to fructose-6-phosphate and glycolysis.",
                "evidence": [
                  {
                    "reference": "DOI:10.1128/jb.159.3.986-990.1984",
                    "snippet": "Purification and properties of D-mannitol-1-phosphate dehydrogenase from Escherichia coli",
                    "notes": "The primary purification study establishes the E. coli enzyme and catalytic activity; UniProtKB P09424 is the reviewed K-12 MtlD entry."
                  }
                ]
              }
            ]
          },
          {
            "node_id": "fructose_6_phosphate",
            "label": "fructose-6-phosphate",
            "node_type": "CHEMICAL",
            "description": "Glycolytic intermediate entering central carbon catabolism."
          }
        ],
        "edges": [
          {
            "subject": "chemoheterotrophic_trait",
            "predicate": "has energy source",
            "object": "organic_molecule",
            "description": "Chemoheterotrophs derive chemical energy from organic compounds.",
            "evidence": [
              {
                "reference": "DOI:10.1021/acsomega.3c02205",
                "snippet": "organic molecules ... energy source",
                "notes": "Supports organic molecules as energy sources in chemoheterotrophic growth."
              }
            ],
            "predicate_id": "METPO:2007807"
          },
          {
            "subject": "chemoheterotrophic_trait",
            "predicate": "has carbon source",
            "object": "organic_molecule",
            "description": "Chemoheterotrophs use organic compounds as carbon sources.",
            "evidence": [
              {
                "reference": "DOI:10.1016/B978-012373944-5.00083-3",
                "snippet": "reduced organic compound",
                "notes": "Supports organic compounds as carbon sources in chemoheterotrophy."
              }
            ],
            "predicate_id": "METPO:2007806"
          },
          {
            "subject": "organic_molecule",
            "predicate": "broken down by",
            "object": "catabolism",
            "description": "Organic molecules are catabolized to release energy and precursors.",
            "evidence": [
              {
                "reference": "DOI:10.1016/B978-012373944-5.00083-3",
                "snippet": "breakdown of nutrients",
                "notes": "Supports catabolism of organic nutrients."
              }
            ]
          },
          {
            "subject": "catabolism",
            "predicate": "can proceed through",
            "object": "respiration",
            "description": "Organic catabolism can conserve energy through respiration.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.bbabio.2008.09.008",
                "snippet": "membrane-bound electron transport chain",
                "notes": "Supports respiratory electron transport as an energy-conserving route."
              }
            ]
          },
          {
            "subject": "catabolism",
            "predicate": "can proceed through",
            "object": "fermentation",
            "description": "Organic catabolism can conserve energy through fermentation.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2021.703525",
                "snippet": "substrate ... electron donor as well as acceptor",
                "notes": "Supports fermentation of organic substrates without external electron acceptors."
              }
            ]
          },
          {
            "subject": "respiration",
            "predicate": "has output",
            "object": "atp",
            "description": "Respiration supports ATP synthesis.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.bbabio.2008.09.008",
                "snippet": "drives ATP synthesis",
                "notes": "Supports ATP synthesis from respiratory energy conservation."
              }
            ],
            "predicate_id": "RO:0002234"
          },
          {
            "subject": "fermentation",
            "predicate": "has output",
            "object": "atp",
            "description": "Fermentation can produce ATP by substrate-level phosphorylation.",
            "evidence": [
              {
                "reference": "DOI:10.1111/1751-7915.13746",
                "snippet": "substrate-level phosphorylation",
                "notes": "Supports ATP formation during fermentative metabolism."
              }
            ],
            "predicate_id": "RO:0002234"
          },
          {
            "subject": "catabolism",
            "predicate": "has output",
            "object": "precursor_metabolites",
            "description": "Catabolism supplies precursors for biosynthesis.",
            "evidence": [
              {
                "reference": "DOI:10.1016/B978-012373944-5.00083-3",
                "snippet": "precursor compounds for anabolism",
                "notes": "Supports catabolism as a source of biosynthetic precursors."
              }
            ],
            "predicate_id": "RO:0002234"
          },
          {
            "subject": "precursor_metabolites",
            "predicate": "incorporated into",
            "object": "biomass",
            "description": "Organic-carbon precursors are incorporated into biomass.",
            "evidence": [
              {
                "reference": "DOI:10.1016/B978-012373944-5.00083-3",
                "snippet": "incorporation of a compound into biomass",
                "notes": "Supports assimilation of compounds into cell material."
              }
            ],
            "predicate_id": "biolink:part_of"
          },
          {
            "subject": "emp_glycolysis",
            "predicate": "contributes to",
            "object": "catabolism",
            "description": "Embden-Meyerhof glycolysis is a core route of organic-substrate catabolism in chemoheterotrophs.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mbio.00992-24",
                "notes": "harbor the Embden-Meyerhof-Parnas glycolysis pathway; broad mechanistic core of chemoheterotrophic catabolism."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "fermentation",
            "predicate": "generates",
            "object": "short_chain_fatty_acids",
            "description": "Fermentation of organic substrates yields short-chain fatty acids such as acetate, succinate, and propionate.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.chom.2024.05.011",
                "notes": "subsequent fermentation to short-chain fatty acids (acetate, succinate, propionate); broadly useful fermentation output edge."
              }
            ],
            "predicate_id": "biolink:produces"
          },
          {
            "subject": "mannitol_pts",
            "predicate": "imports and phosphorylates",
            "object": "mannitol",
            "description": "A PEP-dependent phosphotransferase system imports and phosphorylates mannitol as an organic substrate.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.chom.2024.05.011",
                "notes": "mannitol is imported/phosphorylated via a PEP-PTS to mannitol-1-phosphate; canonical organotrophic uptake mechanism."
              }
            ]
          },
          {
            "subject": "mtld",
            "predicate": "converts",
            "object": "fructose_6_phosphate",
            "description": "mtlD converts mannitol-1-phosphate to fructose-6-phosphate, feeding catabolism into glycolysis.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.chom.2024.05.011",
                "notes": "converted by mtlD to fructose-6-phosphate and enters glycolysis; bridge from transport to central carbon metabolism."
              }
            ]
          },
          {
            "subject": "fructose_6_phosphate",
            "predicate": "broken down by",
            "object": "emp_glycolysis",
            "description": "Fructose-6-phosphate is metabolized through the Embden-Meyerhof glycolysis pathway.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.chom.2024.05.011",
                "notes": "enters glycolysis; links upstream sugar catabolism to the glycolytic pathway."
              }
            ]
          },
          {
            "subject": "mannitol",
            "predicate": "participates in",
            "object": "catabolism",
            "description": "Imported mannitol is converted through mannitol-1-phosphate and fructose-6-phosphate before entering glycolytic catabolism.",
            "evidence": [
              {
                "reference": "DOI:10.1371/journal.pbio.3002198",
                "snippet": "mannitol 1P (toxic when accumulating) is oxidized by MtlD to fructose 6P, where it enters glycolysis",
                "notes": "Verified against the open PLOS Biology primary article."
              }
            ],
            "predicate_id": "biolink:participates_in"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.869925+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-09T00:00:00-07:00",
        "curator": "codex",
        "action": "ADDED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed causal graph for organic molecules as energy and carbon sources feeding catabolism, respiration or fermentation, ATP, and biomass.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 5 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d73, METPO:2000010\u00d71, METPO:2000006\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:41:04Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (METPO:1007501\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T07:34:58Z",
        "curator": "claude",
        "action": "RETYPE_CAUSAL_NODES",
        "changes": "Re-typed 1 causal-node node_type field(s) to align with CausalNodeTypeEnum semantics: biomass: BIOLOGICAL_PROCESS \u2192 CHEMICAL \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-13T21:03:27Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:part_of\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-14T05:51:47Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:72695\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 5 evidence-backed generic edges (6 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:14Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002326\u00d71, biolink:produces\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:34Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:26666\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 5 causal edge(s) off microbe-domain METPO predicates (1 to has energy source, 1 to has carbon source, 3 to has output), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-16T02:00:00Z",
        "curator": "claude",
        "action": "NORMALISE_NODE_TYPE",
        "changes": "Under the PATHWAY-vs-BIOLOGICAL_PROCESS rule, one node_id means one thing corpus-wide (issue 356): fermentation is typed BIOLOGICAL_PROCESS. PATHWAY is a named, conventionally enumerable multi-step route; BIOLOGICAL_PROCESS is everything else. A CLASS of routes rather than one route -- fermentation names a mode of energy conservation with many distinct implementations, so its steps cannot be enumerated without picking one. Was 3 BIOLOGICAL_PROCESS to 2 before this tranche. NOTE its groundings disagree with each other (GO:0006113 x3, METPO:1002005, and METPO:1000845 which is ACETOGENESIS, a different concept) -- filed as #391 and deliberately NOT touched here, because retyping a node while carrying a wrong CURIE along unchanged would make it look reviewed.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-24T13:05:00-07:00",
        "curator": "codex",
        "action": "REVIEWED_CAUSAL_GRAPH_PROTEIN_TAXON",
        "changes": "Marked the graph mechanistic, scoped its alternative catabolic branches, reviewed the multicomponent mannitol PTS as label-only, and added DOI-cited E. coli K-12 MtlD P09424 with an exact InterPro family grounding.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T10:45:00Z",
        "curator": "codex",
        "action": "CONNECT_CAUSAL_GRAPH_COMPONENTS",
        "changes": "Resolved issue #183 graph fragmentation (2 components to 1) with 1 public-source, verbatim-snippet-backed connector(s). No paid research service was called.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000586",
    "label": "chemokinesis",
    "definition": "A motile phenotype in which swimming speed changes in response to chemical concentration, without requiring directional bias along a chemical gradient.",
    "definition_source": "DOI:10.1038/ismej.2013.210",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000702"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/ismej.2013.210",
        "snippet": "chemokinesis is the ability to change swimming speed in response to a change in chemical concentration.",
        "notes": "Discussion, page 1005, visually checked in the author-hosted published PDF at https://stockerlab.ethz.ch/wp-content/uploads/2015/03/49.-Garren_etal_ISME_2014.pdf. This bacterial usage defines chemokinesis by speed, in contrast to chemotactic directional bias. The two responses can coexist. This citation supports identity; no independent reanalysis of its supplementary assays is claimed."
      },
      {
        "reference": "DOI:10.1073/pnas.1602307113",
        "snippet": "Chemokinesis was also observed in the absence of a chemical gradient",
        "notes": "SI Text, Chemokinesis, page 3 of 9; full article and SI inspected at https://pmc.ncbi.nlm.nih.gov/articles/PMC4978249/. Figure S5 and its caption were visually checked in the author PDF at https://stockerlab.ethz.ch/wp-content/uploads/2017/05/89._Son_atall.pdf (SI page 7 of 9). The uniform-serine assay supports a speed response without a gradient. Model block removals are in silico mutants, not biological gene deletions. YM4 cells were harvested in late exponential phase and resuspended in TMN motility medium, pH 7.5; Figure S5 uses uniform 5 micromolar serine at 600 mM sodium. YM4 is a laboratory mutant deficient in lateral flagella, as documented separately by DOI:10.7717/peerj.17126; it is retained as qualified experimental evidence, not a natural canonical example."
      },
      {
        "reference": "DOI:10.1038/s41396-021-01024-7",
        "snippet": "Thus, we hypothesize that the metabolism of mucus substrate stimulates Na+-NQR activity, which in turn enables sustained chemokinesis.",
        "notes": "Discussion, page 3677, visually checked at https://stockerlab.ethz.ch/wp-content/uploads/2022/03/141.-Cherry-Gao_Coral-Muscus.pdf. The plus is superscript in the typeset sodium notation and plain text in extraction. The following sentence requires experimental testing of this hypothesis. Transcript associations do not establish a causal protein pathway; no supplementary gene-level result is curated here."
      },
      {
        "reference": "DOI:10.7717/peerj.17126",
        "snippet": "two strains showing defects in the lateral flagellum (VIO5 and YM4)",
        "notes": "Abstract, PMID:38515459. This primary genomic study identifies YM4 as a laboratory strain with defective lateral flagellation. It supplies strain provenance, not a chemokinesis measurement. The Son observation must not be generalized to unperturbed Vibrio alginolyticus. Canonical examples are deferred pending separate verification of a natural exemplar (issue #1653)."
      }
    ],
    "discussions": [
      {
        "discussion_id": "chemokinesis-speed-and-taxis-boundaries",
        "prompt": "Preserve the source-defined speed response and its distinction from taxis.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "This record follows the swimming-speed usage in Garren, Son and Gao. Chemotaxis (traitmech:000086) concerns directional bias. No equivalence, disjointness or parent-child relation between them is asserted. A speed response can occur with or without chemotaxis and need not always be an increase. Existing research also uses chemokinesis more broadly for changes in turning frequency. Reconcile that broader usage, orthokinesis and klinokinesis before adding synonyms, narrower terms or xrefs; do not equate a turning-only response with this speed definition.",
        "posed_by": "codex",
        "posed_date": "2026-10-04"
      },
      {
        "discussion_id": "chemokinesis-mechanism-grounding",
        "prompt": "Distinguish observed behavior from model ablations and molecular hypotheses.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Son's computational removal of functional blocks is not a gene-knockout experiment. Gao's Na+-NQR explanation is explicitly hypothetical, with further experimental work requested. A mechanistic graph is deferred pending source-backed causal edges and eligible taxon-paired protein examples. Do not borrow the enterobacterial Che pathway from chemotaxis, infer causality from transcript changes, or use NONMECHANISTIC to bypass the protein-coverage requirement. No universal receptor is asserted.",
        "posed_by": "codex",
        "posed_date": "2026-10-04"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-04T04:08:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added chemokinesis with three primary DOI citations, contiguous snippets and a uniform-serine YM4 example at verified species taxon 663. Ignored-and-hidden searches found only a chemotaxis boundary mention, not an exact record or METPO class. Reserved METPO:1054000 in proposal v463. Kept speed, directional bias, computational ablations and molecular hypotheses separate.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-04T04:09:00Z",
        "curator": "codex",
        "action": "QUALIFY_EXPERIMENTAL_STRAIN",
        "changes": "Addressed adversarial review #1653: added primary YM4 strain provenance, removed the laboratory-mutant canonical example, and retained its uniform-serine speed response in qualified evidence. Natural canonical exemplars remain deferred.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000637",
    "label": "chemolithoautotrophic",
    "definition": "A trophic type in which an organism obtains energy from oxidation of inorganic compounds (lithotrophy) and carbon from carbon dioxide.",
    "definition_source": "DOI:10.1146/annurev.micro.52.1.191",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000631"
    ],
    "synonyms": [
      {
        "synonym_text": "chemolithoautotroph",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev.micro.52.1.191",
        "snippet": "physiology ... of chemoautotrophic bacteria",
        "notes": "Review supports chemoautotrophic bacterial CO2 fixation."
      },
      {
        "reference": "DOI:10.1016/B978-0-12-378630-2.00219-X",
        "snippet": "growth-supporting reductant and energy source",
        "notes": "Review supports inorganic reductants as energy sources for chemolithotrophic growth."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:920",
        "taxon_label": "Acidithiobacillus ferrooxidans",
        "note": "Archetypal iron/sulfur chemolithoautotroph; bioleaching model organism.",
        "reference": "DOI:10.1186/1471-2180-10-229"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "chemolithoautotrophic_energy_and_fixation",
        "title": "Chemolithoautotrophic energy and CO2 fixation",
        "description": "DOI-backed graph linking inorganic donor oxidation, respiratory energy conservation, reductant generation, and autotrophic CO2 fixation.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "This graph combines conserved energy-conservation and carbon-fixation modules while allowing lineage-specific inorganic donors and transporters. The A. ferrooxidans example anchors the CBB/RuBisCO branch and does not imply that every chemolithoautotroph uses form I RuBisCO.",
        "nodes": [
          {
            "node_id": "chemolithoautotrophic_trait",
            "label": "chemolithoautotrophic",
            "node_type": "TRAIT",
            "grounding": "METPO:1000637",
            "description": "Trophic type using inorganic donor oxidation and CO2 fixation."
          },
          {
            "node_id": "inorganic_electron_donor",
            "label": "inorganic electron donor",
            "node_type": "CHEMICAL",
            "description": "Reduced inorganic compound oxidized for energy.",
            "grounding": "METPO:1007502"
          },
          {
            "node_id": "electron_transport_chain",
            "label": "electron transport chain",
            "node_type": "PATHWAY",
            "description": "Membrane redox chain conserving energy from donor oxidation.",
            "grounding": "GO:0022900"
          },
          {
            "node_id": "proton_motive_force",
            "label": "proton motive force",
            "node_type": "STATE",
            "description": "Electrochemical gradient generated by energy-conserving electron transfer.",
            "grounding": "METPO:1007500"
          },
          {
            "node_id": "atp",
            "label": "ATP",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:30616",
            "description": "Energy carrier supporting biosynthesis."
          },
          {
            "node_id": "reducing_power",
            "label": "reducing power",
            "node_type": "CAPACITY",
            "description": "NAD(P)H or related reductants supporting CO2 reduction.",
            "grounding": "METPO:1007503"
          },
          {
            "node_id": "carbon_dioxide",
            "label": "carbon dioxide",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:16526",
            "description": "Primary carbon source."
          },
          {
            "node_id": "co2_fixation_pathway",
            "label": "CO2 fixation pathway",
            "node_type": "PATHWAY",
            "description": "Autotrophic pathway reducing CO2 into cell carbon.",
            "grounding": "GO:0015977"
          },
          {
            "node_id": "biomass",
            "label": "biomass",
            "node_type": "CHEMICAL",
            "description": "Cellular material generated from fixed carbon.",
            "grounding": "METPO:1007501"
          },
          {
            "node_id": "rubisco",
            "label": "RuBisCO",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Ribulose-1,5-bisphosphate carboxylase/oxygenase, the carboxylating enzyme of the CBB cycle.",
            "grounding": "InterPro:IPR033966",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:P0C916",
                "protein_label": "Ribulose bisphosphate carboxylase large chain 1",
                "gene_symbol": "cbbL1",
                "taxon_id": "NCBITaxon:920",
                "taxon_label": "Acidithiobacillus ferrooxidans",
                "entry_status": "REVIEWED",
                "retrieved_on": "2026-10-22",
                "entry_version": 58,
                "sequence_version": 1,
                "role": "Large-chain component of form I RuBisCO in the A. ferrooxidans CBB pathway; this accession is not presented as the complete L8S8 enzyme.",
                "evidence": [
                  {
                    "reference": "DOI:10.1186/1471-2180-10-229",
                    "snippet": "cbbR is divergently transcribed from cbbL1, a gene predicted to encode the large subunit of form I RubisCO",
                    "notes": "The A. ferrooxidans carbon-fixation study identifies cbbL1 and its CBB context; UniProtKB P0C916 is the reviewed species-level cbbL1 entry."
                  }
                ]
              }
            ]
          },
          {
            "node_id": "carbonic_anhydrase",
            "label": "carbonic anhydrase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Enzyme interconverting CO2 and bicarbonate to facilitate dissolved inorganic carbon fixation.",
            "grounding": "InterPro:IPR001765"
          },
          {
            "node_id": "dic_transporter",
            "label": "dissolved inorganic carbon transporter",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Membrane transporter that increases intracellular availability of dissolved inorganic carbon.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "This functional node spans unrelated CO2 and bicarbonate uptake systems; the cited graph does not resolve one exact transporter family or complex."
          },
          {
            "node_id": "dissolved_inorganic_carbon",
            "label": "dissolved inorganic carbon",
            "node_type": "CHEMICAL",
            "description": "Pool of CO2 and bicarbonate supplied to autotrophic carbon-fixation pathways."
          }
        ],
        "edges": [
          {
            "subject": "chemolithoautotrophic_trait",
            "predicate": "has electron donor",
            "object": "inorganic_electron_donor",
            "description": "Inorganic electron donors supply the energy chemolithoautotrophs conserve.",
            "evidence": [
              {
                "reference": "DOI:10.1016/B978-0-12-378630-2.00219-X",
                "snippet": "growth-supporting reductant and energy source",
                "notes": "Supports inorganic reductants as energy sources."
              }
            ],
            "predicate_id": "METPO:2007701"
          },
          {
            "subject": "inorganic_electron_donor",
            "predicate": "feeds electrons into",
            "object": "electron_transport_chain",
            "description": "Donor oxidation supplies electrons to energy-conserving respiratory chains.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.bbabio.2008.09.008",
                "snippet": "membrane-bound electron transport chain",
                "notes": "Supports membrane-bound respiratory chains as redox energy-conserving systems."
              }
            ],
            "predicate_id": "METPO:2007402"
          },
          {
            "subject": "electron_transport_chain",
            "predicate": "generates",
            "object": "proton_motive_force",
            "description": "Respiratory chains generate an electrochemical ion gradient.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.bbabio.2008.09.008",
                "snippet": "generation of an electrochemical ion gradient",
                "notes": "Supports proton motive force generation."
              }
            ],
            "predicate_id": "biolink:produces"
          },
          {
            "subject": "proton_motive_force",
            "predicate": "drives synthesis of",
            "object": "atp",
            "description": "The ion gradient drives ATP synthesis.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.bbabio.2008.09.008",
                "snippet": "drives ATP synthesis",
                "notes": "Supports ATP synthesis from respiratory ion gradients."
              }
            ],
            "predicate_id": "biolink:produces"
          },
          {
            "subject": "inorganic_electron_donor",
            "predicate": "supports generation of",
            "object": "reducing_power",
            "description": "Electrons from inorganic donors provide reduced cofactors for biosynthesis.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.biortech.2021.125768",
                "snippet": "serve as reductive power",
                "notes": "Supports reduced cofactors generated from chemolithoautotrophic electron donors."
              }
            ]
          },
          {
            "subject": "carbon_dioxide",
            "predicate": "fixed by",
            "object": "co2_fixation_pathway",
            "description": "Chemolithoautotrophs use CO2 fixation pathways for carbon assimilation.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev.micro.52.1.191",
                "snippet": "Carbon Dioxide Fixation in Chemoautotrophs",
                "notes": "Supports CO2 fixation in chemoautotrophic bacteria."
              }
            ],
            "predicate_id": "METPO:2007404"
          },
          {
            "subject": "atp",
            "predicate": "enables",
            "object": "co2_fixation_pathway",
            "description": "ATP generated from donor oxidation supports autotrophic CO2 fixation.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.02473-10",
                "snippet": "energy required for autotrophic CO2 fixation",
                "notes": "Supports energy demand of autotrophic CO2 fixation."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "reducing_power",
            "predicate": "enables",
            "object": "co2_fixation_pathway",
            "description": "Reducing power supports reductive CO2 assimilation.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.biortech.2021.125768",
                "snippet": "reduction of CO2",
                "notes": "Supports reductant use in CO2 fixation."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "co2_fixation_pathway",
            "predicate": "has output",
            "object": "biomass",
            "description": "CO2 fixation generates cellular biomass.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev.micro.52.1.191",
                "snippet": "physiology ... of chemoautotrophic bacteria",
                "notes": "Review scope supports chemoautotrophic growth from fixed carbon."
              }
            ],
            "predicate_id": "RO:0002234"
          },
          {
            "subject": "rubisco",
            "predicate": "catalyzes",
            "object": "co2_fixation_pathway",
            "description": "RuBisCO catalyzes the carboxylation step of the Calvin-Benson-Bassham CO2 fixation cycle.",
            "evidence": [
              {
                "reference": "DOI:10.1128/aem.01557-23",
                "notes": "Ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCO) drives CBB-cycle CO2 fixation."
              }
            ],
            "predicate_id": "biolink:catalyzes"
          },
          {
            "subject": "carbonic_anhydrase",
            "predicate": "facilitates supply of",
            "object": "dissolved_inorganic_carbon",
            "description": "Carbonic anhydrase interconverts CO2 and bicarbonate to facilitate dissolved inorganic carbon fixation.",
            "evidence": [
              {
                "reference": "DOI:10.1128/aem.01557-23",
                "notes": "carbonic anhydrase enzymes (CA) to facilitate DIC fixation."
              }
            ]
          },
          {
            "subject": "dic_transporter",
            "predicate": "increases availability of",
            "object": "dissolved_inorganic_carbon",
            "description": "DIC transporters bridge environmental inorganic carbon supply to autotrophic pathway demand.",
            "evidence": [
              {
                "reference": "DOI:10.1128/aem.01557-23",
                "notes": "DIC transporters bridge supply from the environment to demand by the autotrophic pathway."
              }
            ]
          },
          {
            "subject": "dissolved_inorganic_carbon",
            "predicate": "supplies substrate to",
            "object": "co2_fixation_pathway",
            "description": "Dissolved inorganic carbon supplies the CO2/bicarbonate substrate for autotrophic fixation.",
            "evidence": [
              {
                "reference": "DOI:10.1128/aem.01557-23",
                "notes": "DIC supply bridged to demand by the autotrophic pathway."
              }
            ]
          },
          {
            "subject": "proton_motive_force",
            "predicate": "drives reverse electron transport for",
            "object": "reducing_power",
            "description": "PMF can reverse the electron transport chain to regenerate NADH/NADPH reducing power for fixation.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-023-43524-4",
                "notes": "The proton motive force drives ATP synthesis and can reverse the electron transport chain to regenerate NADH/NADPH."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.870482+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-08T00:00:00-07:00",
        "curator": "codex",
        "action": "ADDED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed causal graph for inorganic donor oxidation, respiratory energy conservation, ATP/reductant generation, and CO2 fixation.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000009\u00d71, METPO:2000202\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T08:21:50Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:produces\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T21:30:07Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007402\u00d71, METPO:2007404\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:19Z",
        "curator": "claude",
        "action": "RENAME_PREDICATE_LABELS",
        "changes": "Renamed 2 causal-edge predicate label(s) to align with existing groundings: supports \u2192 enables \u00d72.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:22Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d72).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:41:04Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 4 causal-node grounding field(s) via mappings/node_grounding.tsv (METPO:1007502\u00d71, METPO:1007500\u00d71, METPO:1007503\u00d71, METPO:1007501\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T07:34:58Z",
        "curator": "claude",
        "action": "RETYPE_CAUSAL_NODES",
        "changes": "Re-typed 1 causal-node node_type field(s) to align with CausalNodeTypeEnum semantics: biomass: BIOLOGICAL_PROCESS \u2192 CHEMICAL \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T08:14:33Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0022900\u00d71, GO:0015977\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-26T02:30:13Z",
        "curator": "claude",
        "action": "RETYPE_CAUSAL_NODES",
        "changes": "Re-typed 2 causal-node node_type field(s) to align with CausalNodeTypeEnum semantics: proton motive force: BIOLOGICAL_PROCESS \u2192 STATE \u00d71; reducing power: CHEMICAL \u2192 CAPACITY \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-13T21:03:27Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:produces\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 5 evidence-backed generic edges (4 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:14Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:catalyzes\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:20Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A075WF79\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-26T07:15:20Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A009PMS8\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:21:12Z",
        "curator": "claude",
        "action": "RETRACT_DEAD_UNIPROT_GROUNDINGS",
        "changes": "Retracted 2 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:23:55Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (InterPro:IPR033966\u00d71, InterPro:IPR001765\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-05T12:00:00Z",
        "curator": "claude",
        "action": "REVERSE_CAUSAL_EDGE_DIRECTION",
        "changes": "Reversed 1 causal edge from <trait> uses electron donor <chemical> to <chemical> enables <trait> (predicate_id METPO:2000009 -> RO:0002327), issue 295. METPO:2000009 is rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so the trait-subject form entailed that this TRAIT node is a microbe; CausalNodeTypeEnum has no organism member, so no causal-graph edge can satisfy that domain. Evidence unchanged; only subject/predicate/object/predicate_id and the edge description moved. Note RO:0002327 has range 'biological process or activity', so the new form is not fully range-correct either - tracked in issue 302.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 1 causal edge(s) off enables/RO:0002327 with a TRAIT object (1 to has electron donor), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them. 1 electron edge(s) were also reversed back to trait -> chemical, restoring the donor/acceptor role that PR 300 collapsed onto enables (issue 303); the organism-subject problem that forced that collapse does not arise here because these predicates take a causal-node domain rather than METPO:2000001's microbe domain (issue 301).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates (1 to has output), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-16T02:00:00Z",
        "curator": "claude",
        "action": "NORMALISE_NODE_TYPE",
        "changes": "Under the PATHWAY-vs-BIOLOGICAL_PROCESS rule, one node_id means one thing corpus-wide (issue 356): electron_transport_chain is typed PATHWAY. PATHWAY is a named, conventionally enumerable multi-step route; BIOLOGICAL_PROCESS is everything else. A named route through enumerable complexes. Was 4 PATHWAY to 2 before this tranche.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-24T11:40:00-07:00",
        "curator": "codex",
        "action": "REVIEWED_CAUSAL_GRAPH_PROTEIN_TAXON",
        "changes": "Marked the graph mechanistic, reviewed the broad dissolved-inorganic-carbon transporter node as label-only, replaced the canonical web citation with its DOI, and added the reviewed A. ferrooxidans cbbL1 large-chain example.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-22T01:35:00Z",
        "curator": "claude",
        "action": "REFRESH_UNIPROT_ENTRY_VERSION",
        "changes": "Refreshed UniProtKB entry_version against live UniProt REST on 2026-10-22: UniProtKB:P0C916 (57 -> 58 on rubisco).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000638",
    "label": "chemolithoheterotrophic",
    "definition": "A trophic type characterized by the use of inorganic chemical compounds as electron donors for energy generation while utilizing organic compounds as the primary carbon source.",
    "definition_source": "DOI:10.1038/s41598-021-81412-3",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000631"
    ],
    "synonyms": [
      {
        "synonym_text": "chemolithoheterotroph",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "created_by": "Anthea Guo",
    "evidence": [
      {
        "reference": "DOI:10.1038/s41598-021-81412-3",
        "snippet": "chemolithoheterotrophy",
        "notes": "Experimental study supports chemolithoheterotrophy as Fe(II) oxidation for energy with glucose as carbon source."
      },
      {
        "reference": "DOI:10.1128/mBio.01112-19",
        "snippet": "oxidize sulfur to fuel the uptake of organic compounds",
        "notes": "Study supports sulfur oxidation coupled to organic compound uptake in a chemolithoheterotrophic symbiont context."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:317655",
        "taxon_label": "Sphingopyxis alaskensis RB2256",
        "note": "Strain-level facultative chemolithoheterotrophic example that oxidizes H2 during aerobic growth on organic carbon, paired to its group 2a hydrogenase large subunit.",
        "reference": "DOI:10.1038/s41564-023-01322-0"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "chemolithoheterotrophic_inorganic_energy_organic_carbon",
        "title": "Chemolithoheterotrophic inorganic chemical energy and organic carbon use",
        "description": "DOI-backed graph linking inorganic chemical electron donors, Fe(II) and reduced sulfur examples, respiratory energy conservation, organic carbon uptake, and biomass.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "This modular graph covers Fe(II), reduced-sulfur, and H2 donor branches coupled to organic-carbon assimilation. The S. alaskensis example anchors only the H2 branch; Q1J422 is the catalytic large-subunit component of its group 2a hydrogenase, not the complete multisubunit enzyme or the sulfur/iron branches.",
        "nodes": [
          {
            "node_id": "chemolithoheterotrophic_trait",
            "label": "chemolithoheterotrophic",
            "node_type": "TRAIT",
            "grounding": "METPO:1000638",
            "description": "Trophic type using inorganic chemical electron donors and organic carbon."
          },
          {
            "node_id": "inorganic_chemical_donor",
            "label": "inorganic chemical donor",
            "node_type": "CHEMICAL",
            "description": "Reduced inorganic chemical supplying electrons and energy."
          },
          {
            "node_id": "ferrous_iron",
            "label": "ferrous iron",
            "node_type": "CHEMICAL",
            "description": "Fe(II), an inorganic chemical energy source.",
            "grounding": "CHEBI:29033"
          },
          {
            "node_id": "reduced_sulfur_compound",
            "label": "reduced sulfur compound",
            "node_type": "CHEMICAL",
            "description": "Inorganic sulfur electron donor such as sulfide or thiosulfate."
          },
          {
            "node_id": "molecular_hydrogen",
            "label": "molecular hydrogen",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:18276",
            "description": "Reduced inorganic gas oxidized as a supplementary energy source during lithoheterotrophic growth."
          },
          {
            "node_id": "organic_compound",
            "label": "organic compound",
            "node_type": "CHEMICAL",
            "description": "Organic carbon source used for biosynthesis.",
            "grounding": "CHEBI:50860"
          },
          {
            "node_id": "respiratory_chain",
            "label": "respiratory chain",
            "node_type": "PATHWAY",
            "description": "Electron-transfer pathway conserving energy from donor oxidation.",
            "grounding": "GO:0022904"
          },
          {
            "node_id": "proton_motive_force",
            "label": "proton motive force",
            "node_type": "STATE",
            "description": "Electrochemical ion gradient generated by respiratory electron transport.",
            "grounding": "METPO:1007500"
          },
          {
            "node_id": "atp",
            "label": "ATP",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:30616",
            "description": "Energy carrier produced from proton motive force."
          },
          {
            "node_id": "nutrient_uptake",
            "label": "organic nutrient uptake",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Uptake of external organic compounds."
          },
          {
            "node_id": "biomass",
            "label": "biomass",
            "node_type": "CHEMICAL",
            "description": "Cell material formed from organic carbon.",
            "grounding": "METPO:1007501"
          },
          {
            "node_id": "sox_pathway",
            "label": "Sox sulfur-oxidation pathway",
            "node_type": "PATHWAY",
            "description": "soxCDYZAXB gene cluster mediating complete oxidation of thiosulfate to sulfate."
          },
          {
            "node_id": "thiosulfate",
            "label": "thiosulfate",
            "node_type": "CHEMICAL",
            "description": "Reduced inorganic sulfur electron donor oxidized to sulfate.",
            "grounding": "CHEBI:16094"
          },
          {
            "node_id": "sulfate",
            "label": "sulfate",
            "node_type": "CHEMICAL",
            "description": "Fully oxidized sulfur end product of sulfur-compound oxidation.",
            "grounding": "CHEBI:16189"
          },
          {
            "node_id": "branched_thiosulfate_oxidation",
            "label": "branched thiosulfate oxidation pathway",
            "node_type": "PATHWAY",
            "description": "Truncated Sox plus reverse Dsr/Apr/Sat oxidizing thiosulfate via an elemental sulfur intermediate."
          },
          {
            "node_id": "elemental_sulfur",
            "label": "elemental sulfur",
            "node_type": "CHEMICAL",
            "description": "S0 intermediate of branched sulfur-compound oxidation.",
            "grounding": "CHEBI:26833"
          },
          {
            "node_id": "organic_carbon_importer",
            "label": "organic carbon import system",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Amino acid and carboxylic acid import systems mediating organic carbon uptake.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "This aggregate node spans unrelated amino-acid, carboxylate, TRAP, ABC, and other uptake systems; the cited comparative study does not identify one transporter family that represents the whole label."
          },
          {
            "node_id": "group_2a_nife_hydrogenase",
            "label": "group 2a [NiFe]-hydrogenase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Plasmid-borne multisubunit uptake hydrogenase used for aerobic H2 oxidation by S. alaskensis RB2256.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Available InterPro terms cover broad NiFe hydrogenase large-subunit families rather than this complete group 2a multisubunit enzyme; the exact catalytic component is retained as the taxon-paired protein example.",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:Q1J422",
                "protein_label": "Group 2a [NiFe]-hydrogenase large subunit HucL",
                "gene_symbol": "Sala_3198",
                "taxon_id": "NCBITaxon:317655",
                "taxon_label": "Sphingopyxis alaskensis RB2256",
                "entry_status": "UNREVIEWED",
                "proteome_id": "UP000006578",
                "retrieved_on": "2026-08-24",
                "entry_version": 98,
                "sequence_version": 1,
                "role": "Catalytic large-subunit component of the plasmid-borne group 2a [NiFe]-hydrogenase; this accession is not presented as the complete hydrogenase complex.",
                "evidence": [
                  {
                    "reference": "DOI:10.1038/s41564-023-01322-0",
                    "snippet": "group 2a [NiFe]-hydrogenase large subunit gene (hucL; locus Sala_3198)",
                    "notes": "The primary study measured Sala_3198 expression during aerobic growth and H2 oxidation. UniProtKB Q1J422 maps that exact locus to the S. alaskensis RB2256 reference proteome."
                  }
                ]
              }
            ]
          }
        ],
        "edges": [
          {
            "subject": "chemolithoheterotrophic_trait",
            "predicate": "has electron donor",
            "object": "inorganic_chemical_donor",
            "description": "Inorganic chemical compounds serve as the electron donors for chemolithoheterotrophy.",
            "evidence": [
              {
                "reference": "DOI:10.1016/B978-0-12-378630-2.00219-X",
                "snippet": "oxidize inorganic atoms or molecules",
                "notes": "Supports inorganic chemical donors in chemolithotrophic metabolism."
              }
            ],
            "predicate_id": "METPO:2007701"
          },
          {
            "subject": "ferrous_iron",
            "predicate": "example of",
            "object": "inorganic_chemical_donor",
            "description": "Fe(II) is an experimentally supported inorganic donor for chemolithoheterotrophy.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41598-021-81412-3",
                "snippet": "Fe(II) oxidation provides energy",
                "notes": "Supports Fe(II) as energy source in engineered chemolithoheterotrophy."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "reduced_sulfur_compound",
            "predicate": "example of",
            "object": "inorganic_chemical_donor",
            "description": "Reduced sulfur compounds can fuel chemolithoheterotrophic metabolism.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mBio.01112-19",
                "snippet": "oxidize sulfur to fuel",
                "notes": "Supports sulfur oxidation as an energy source coupled to organic compound uptake."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "molecular_hydrogen",
            "predicate": "example of",
            "object": "inorganic_chemical_donor",
            "description": "H2 is a reduced inorganic donor that can supplement energy during organic-carbon-supported growth.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-023-01322-0",
                "snippet": "uses an abundant reduced gas as an energy source",
                "notes": "The culture study shows that S. alaskensis consumes H2 while growing on organic carbon, supporting H2 as the inorganic energy donor in this branch."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "molecular_hydrogen",
            "predicate": "oxidized by",
            "object": "group_2a_nife_hydrogenase",
            "description": "The group 2a uptake hydrogenase mediates aerobic H2 oxidation in S. alaskensis.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-023-01322-0",
                "snippet": "encodes a plasmid-borne group 2a [NiFe]-hydrogenase, aerobically consumed H2",
                "notes": "The primary growth, gas-consumption, and hucL-expression experiments pair the enzyme class with H2 oxidation in strain RB2256; Q1J422 is only its large-subunit component."
              }
            ]
          },
          {
            "subject": "inorganic_chemical_donor",
            "predicate": "feeds electrons into",
            "object": "respiratory_chain",
            "description": "Oxidized inorganic donors feed electrons into respiratory energy conservation.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.bbabio.2008.09.008",
                "snippet": "electron transfer process",
                "notes": "Supports electron transfer in energy-conserving respiratory chains."
              }
            ],
            "predicate_id": "METPO:2007402"
          },
          {
            "subject": "respiratory_chain",
            "predicate": "generates",
            "object": "proton_motive_force",
            "description": "Respiratory electron transfer generates an ion gradient.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.bbabio.2008.09.008",
                "snippet": "generation of an electrochemical ion gradient",
                "notes": "Supports proton motive force generation by membrane electron transport."
              }
            ],
            "predicate_id": "biolink:produces"
          },
          {
            "subject": "proton_motive_force",
            "predicate": "drives production of",
            "object": "atp",
            "description": "Proton motive force powers ATP synthesis.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.bbabio.2008.09.008",
                "snippet": "drives ATP synthesis",
                "notes": "Supports ATP production from respiratory energy conservation."
              }
            ],
            "predicate_id": "biolink:produces"
          },
          {
            "subject": "chemolithoheterotrophic_trait",
            "predicate": "has carbon source",
            "object": "organic_compound",
            "description": "Organic compounds provide carbon for chemolithoheterotrophic growth.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41598-021-81412-3",
                "snippet": "glucose as the sole carbon source",
                "notes": "Supports organic carbon use under inorganic donor oxidizing conditions."
              }
            ],
            "predicate_id": "METPO:2007806"
          },
          {
            "subject": "organic_compound",
            "predicate": "imported by",
            "object": "nutrient_uptake",
            "description": "Organic compounds are taken up for heterotrophic carbon assimilation.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mBio.01112-19",
                "snippet": "uptake of organic compounds",
                "notes": "Supports organic compound uptake fueled by sulfur oxidation."
              }
            ]
          },
          {
            "subject": "nutrient_uptake",
            "predicate": "supports formation of",
            "object": "biomass",
            "description": "Uptaken organic carbon supports cell-material production.",
            "evidence": [
              {
                "reference": "DOI:10.1016/B978-012373944-5.00083-3",
                "snippet": "incorporation of a compound into biomass",
                "notes": "Supports assimilation of organic compounds into biomass."
              }
            ]
          },
          {
            "subject": "sox_pathway",
            "predicate": "has output",
            "object": "sulfate",
            "description": "The conserved soxCDYZAXB gene cluster enables complete oxidation of thiosulfate to sulfate without free intermediates.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41396-021-01163-x",
                "notes": "Gene clusters of the conserved soxCDYZAXB gene order facilitate the complete oxidation of thiosulfate to sulfate, without free intermediates."
              }
            ],
            "predicate_id": "RO:0002234"
          },
          {
            "subject": "thiosulfate",
            "predicate": "oxidized by",
            "object": "sox_pathway",
            "description": "Thiosulfate, a reduced inorganic sulfur donor, is oxidized by the Sox pathway.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41396-021-01163-x",
                "notes": "Sox system mediates complete oxidation of thiosulfate to sulfate."
              }
            ]
          },
          {
            "subject": "branched_thiosulfate_oxidation",
            "predicate": "produces intermediate",
            "object": "elemental_sulfur",
            "description": "Truncated soxXYZAB with reverse Dsr/Apr/Sat oxidizes thiosulfate via an elemental sulfur intermediate.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41396-021-01163-x",
                "notes": "Branched thiosulfate oxidation pathway in which Dsr operating in reverse oxidizes sulfane-derived sulfur to sulfite, with elemental sulfur as intermediate."
              }
            ]
          },
          {
            "subject": "organic_carbon_importer",
            "predicate": "supports",
            "object": "nutrient_uptake",
            "description": "Amino acid and carboxylic acid import systems support organic carbon uptake in heterotrophs and mixotrophs.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41396-021-01163-x",
                "notes": "Import systems for amino acids and carboxylic acids were overly abundant in mixotrophs and heterotrophs, supporting the organic-carbon dependency of the trait."
              }
            ]
          },
          {
            "subject": "thiosulfate",
            "predicate": "example of",
            "object": "reduced_sulfur_compound",
            "description": "Thiosulfate is a reduced sulfur electron donor oxidized during chemolithomixotrophic growth.",
            "evidence": [
              {
                "reference": "DOI:10.1111/1462-2920.13232",
                "snippet": "obligate aerobic chemolithomixotroph that can oxidize sulfide, thiosulfate and elemental sulfur",
                "notes": "Verified against the open primary article."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "branched_thiosulfate_oxidation",
            "predicate": "contributes to",
            "object": "respiratory_chain",
            "description": "Branched thiosulfate oxidation transfers substrate electrons into respiratory cytochromes.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.00956-13",
                "snippet": "oxidizes sulfone, as well as sulfane, sulfur atoms to sulfate by transferring electrons to c-type cytochromes",
                "notes": "Verified against the open primary article."
              }
            ],
            "predicate_id": "RO:0002326"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.870986+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-09T00:00:00-07:00",
        "curator": "codex",
        "action": "ADDED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed causal graph for inorganic chemical donors, Fe(II), reduced sulfur, respiratory energy conservation, organic nutrient uptake, and biomass.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000009\u00d71, METPO:2000006\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T08:21:50Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (rdfs:subClassOf\u00d72, biolink:produces\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T21:30:07Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007402\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:38:01Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:29033\u00d71, GO:0022904\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:41:04Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (METPO:1007500\u00d71, METPO:1007501\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T07:34:58Z",
        "curator": "claude",
        "action": "RETYPE_CAUSAL_NODES",
        "changes": "Re-typed 1 causal-node node_type field(s) to align with CausalNodeTypeEnum semantics: biomass: BIOLOGICAL_PROCESS \u2192 CHEMICAL \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T08:14:33Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:50860\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-26T02:30:13Z",
        "curator": "claude",
        "action": "RETYPE_CAUSAL_NODES",
        "changes": "Re-typed 1 causal-node node_type field(s) to align with CausalNodeTypeEnum semantics: proton motive force: BIOLOGICAL_PROCESS \u2192 STATE \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-13T21:03:27Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:produces\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 4 evidence-backed generic edges (6 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:14Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:20Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 3 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:16094\u00d71, CHEBI:16189\u00d71, CHEBI:26833\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-05T12:00:00Z",
        "curator": "claude",
        "action": "REVERSE_CAUSAL_EDGE_DIRECTION",
        "changes": "Reversed 1 causal edge from <trait> uses electron donor <chemical> to <chemical> enables <trait> (predicate_id METPO:2000009 -> RO:0002327), issue 295. METPO:2000009 is rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so the trait-subject form entailed that this TRAIT node is a microbe; CausalNodeTypeEnum has no organism member, so no causal-graph edge can satisfy that domain. Evidence unchanged; only subject/predicate/object/predicate_id and the edge description moved. Note RO:0002327 has range 'biological process or activity', so the new form is not fully range-correct either - tracked in issue 302.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 1 causal edge(s) off enables/RO:0002327 with a TRAIT object (1 to has electron donor), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them. 1 electron edge(s) were also reversed back to trait -> chemical, restoring the donor/acceptor role that PR 300 collapsed onto enables (issue 303); the organism-subject problem that forced that collapse does not arise here because these predicates take a causal-node domain rather than METPO:2000001's microbe domain (issue 301).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates (1 to has carbon source), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-07T18:00:00Z",
        "curator": "claude",
        "action": "REGROUND_CAUSAL_EDGE",
        "changes": "Edge sox_pathway -> sulfate in graph chemolithoheterotrophic_inorganic_energy_organic_carbon: re-grounded it from enables/RO:0002327 to has output/RO:0002234. Issue 334. biolink declares enables range 'biological process or activity', which of CausalNodeTypeEnum only BIOLOGICAL_PROCESS, PATHWAY and MOLECULAR_FUNCTION satisfy, so this edge entailed a false type on its object. The subject IS an activity (PATHWAY), which is the documented dividing line: activity subjects take RO:0002234, whose domain 'biological process or activity' they satisfy, rather than the METPO term minted for the subjects RO cannot cover.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-24T12:50:00-07:00",
        "curator": "codex",
        "action": "REVIEWED_CAUSAL_GRAPH_PROTEIN_TAXON",
        "changes": "Marked the graph mechanistic, reviewed the broad importer as label-only, added DOI-cited S. alaskensis RB2256 and its H2 branch, and paired the group 2a hydrogenase node with reference-proteome component Q1J422 without treating one large subunit as the complete complex.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T11:45:00Z",
        "curator": "codex",
        "action": "CONNECT_CAUSAL_GRAPH_COMPONENTS",
        "changes": "Resolved issue #183 graph fragmentation (3 components to 1): added 2 public-source connector(s). No paid research service was called.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000639",
    "label": "chemolithotrophic",
    "definition": "A trophic type characterized by the use of inorganic chemical compounds as electron donors and carbon dioxide as the primary carbon source for energy generation and biosynthesis.",
    "definition_source": "DOI:10.1016/B978-0-12-378630-2.00219-X",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000631"
    ],
    "synonyms": [
      {
        "synonym_text": "chemolithotroph",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "created_by": "Anthea Guo",
    "evidence": [
      {
        "reference": "DOI:10.1016/B978-0-12-378630-2.00219-X",
        "snippet": "chemolithotrophic bacteria and archaea",
        "notes": "Review supports inorganic compound oxidation as chemolithotrophic growth."
      },
      {
        "reference": "DOI:10.1146/annurev.micro.55.1.485",
        "snippet": "Chemolitho-autotrophic ammonia-oxidizing bacteria",
        "notes": "Review supports ammonia oxidation as an example chemolithoautotrophic process."
      },
      {
        "reference": "PMID:12700255",
        "snippet": "Nitrosomonas europaea",
        "notes": "Organism example: Nitrosomonas europaea is the model chemolithotrophic ammonia-oxidizing bacterium, conserving energy from NH3 \u2192 NO2- oxidation (Chain et al. 2003, J Bacteriol, complete genome)."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:915",
        "taxon_label": "Nitrosomonas europaea",
        "note": "ammonia-oxidising chemolithotroph",
        "reference": "DOI:10.1128/jb.185.9.2759-2773.2003"
      },
      {
        "taxon_id": "NCBITaxon:36861",
        "taxon_label": "Thiobacillus denitrificans",
        "note": "sulfur-oxidising chemolithotroph",
        "reference": "DOI:10.1128/JB.188.4.1473-1488.2006"
      },
      {
        "taxon_id": "NCBITaxon:228410",
        "taxon_label": "Nitrosomonas europaea ATCC 19718",
        "note": "Strain-level ammonia-oxidizing chemolithotroph paired to the AmoA alpha component of ammonia monooxygenase.",
        "reference": "DOI:10.1128/jb.175.8.2436-2444.1993"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "chemolithotrophic_inorganic_oxidation",
        "title": "Chemolithotrophic inorganic chemical oxidation",
        "description": "DOI-backed graph for inorganic chemical electron donors, representative ammonia and sulfur oxidation, and respiratory energy conservation.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "This graph combines ammonia- and sulfur-oxidation branches with carbon fixation. The N. europaea AmoA example anchors only ammonia oxidation; Q04507 is the alpha component of a multisubunit ammonia monooxygenase and does not represent the complete enzyme or the Sox branch.",
        "nodes": [
          {
            "node_id": "chemolithotrophic_trait",
            "label": "chemolithotrophic",
            "node_type": "TRAIT",
            "grounding": "METPO:1000639",
            "description": "Trophic type using inorganic chemicals for energy generation."
          },
          {
            "node_id": "inorganic_chemical_donor",
            "label": "inorganic chemical electron donor",
            "node_type": "CHEMICAL",
            "description": "Reduced inorganic chemical substrate."
          },
          {
            "node_id": "ammonia",
            "label": "ammonia",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:16134",
            "description": "Representative reduced nitrogen electron donor."
          },
          {
            "node_id": "ammonia_monooxygenase",
            "label": "ammonia monooxygenase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Enzyme initiating aerobic ammonia oxidation.",
            "grounding": "GO:0018597",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:Q04507",
                "protein_label": "Ammonia monooxygenase alpha subunit",
                "gene_symbol": "amoA1",
                "taxon_id": "NCBITaxon:228410",
                "taxon_label": "Nitrosomonas europaea ATCC 19718",
                "entry_status": "REVIEWED",
                "retrieved_on": "2026-10-22",
                "entry_version": 127,
                "sequence_version": 2,
                "role": "AmoA alpha-subunit component of the N. europaea ammonia monooxygenase; the accession maps two duplicated amoA gene copies and is not the whole enzyme complex.",
                "evidence": [
                  {
                    "reference": "DOI:10.1128/jb.175.8.2436-2444.1993",
                    "snippet": "Sequence of the gene coding for ammonia monooxygenase in Nitrosomonas europaea",
                    "notes": "The primary study sequences and characterizes N. europaea AmoA and its ammonia-to-hydroxylamine activity; UniProtKB Q04507 is the reviewed strain-level alpha-subunit entry."
                  }
                ]
              }
            ]
          },
          {
            "node_id": "hydroxylamine",
            "label": "hydroxylamine",
            "node_type": "CHEMICAL",
            "description": "Intermediate formed from ammonia oxidation.",
            "grounding": "CHEBI:15429"
          },
          {
            "node_id": "nitrite",
            "label": "nitrite",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:16301",
            "description": "Oxidized nitrogen product of ammonia oxidation."
          },
          {
            "node_id": "sox_enzyme_system",
            "label": "Sox enzyme system",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Sulfur-oxidizing multienzyme system.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Sox denotes a variable multienzyme pathway assembled from several distinct component families; no one protein-family term represents the complete generic system in this cross-branch graph."
          },
          {
            "node_id": "thiosulfate",
            "label": "thiosulfate",
            "node_type": "CHEMICAL",
            "description": "Representative reduced sulfur donor.",
            "grounding": "CHEBI:16094"
          },
          {
            "node_id": "respiratory_chain",
            "label": "respiratory chain",
            "node_type": "PATHWAY",
            "description": "Electron-transfer system conserving energy from donor oxidation.",
            "grounding": "GO:0022904"
          },
          {
            "node_id": "atp",
            "label": "ATP",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:30616",
            "description": "Energy carrier produced by respiratory energy conservation."
          },
          {
            "node_id": "calvin_benson_bassham_cycle",
            "label": "Calvin-Benson-Bassham cycle",
            "node_type": "PATHWAY",
            "grounding": "GO:0015977",
            "description": "Reductive pentose phosphate carbon-fixation pathway."
          },
          {
            "node_id": "carbon_dioxide",
            "label": "carbon dioxide",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:16526",
            "description": "Inorganic carbon source fixed during chemolithoautotrophy."
          },
          {
            "node_id": "acidification",
            "label": "acidification",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Decrease in environmental pH."
          },
          {
            "node_id": "nitrification_rate",
            "label": "nitrification rate",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Rate of microbial oxidation of ammonia to nitrate."
          },
          {
            "node_id": "nitrous_oxide",
            "label": "nitrous oxide",
            "node_type": "CHEMICAL",
            "description": "N2O byproduct generated during nitrification.",
            "grounding": "CHEBI:17045"
          }
        ],
        "edges": [
          {
            "subject": "chemolithotrophic_trait",
            "predicate": "has electron donor",
            "object": "inorganic_chemical_donor",
            "description": "Inorganic chemicals serve as the electron donors for chemolithotrophy.",
            "evidence": [
              {
                "reference": "DOI:10.1016/B978-0-12-378630-2.00219-X",
                "snippet": "oxidize inorganic atoms or molecules",
                "notes": "Supports inorganic chemical oxidation as chemolithotrophy."
              }
            ],
            "predicate_id": "METPO:2007701"
          },
          {
            "subject": "ammonia_monooxygenase",
            "predicate": "oxidizes",
            "object": "ammonia",
            "description": "Ammonia monooxygenase initiates ammonia oxidation.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev.micro.55.1.485",
                "snippet": "ammonia-oxidizing bacteria",
                "notes": "Supports ammonia oxidation as a chemolithoautotrophic process."
              }
            ],
            "predicate_id": "METPO:2007803"
          },
          {
            "subject": "ammonia",
            "predicate": "oxidized to",
            "object": "hydroxylamine",
            "description": "Ammonia oxidation proceeds through hydroxylamine.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s00775-020-01820-0",
                "snippet": "convert ammonia to hydroxylamine",
                "notes": "Supports AMO-catalyzed ammonia-to-hydroxylamine conversion."
              }
            ],
            "predicate_id": "METPO:2007405"
          },
          {
            "subject": "hydroxylamine",
            "predicate": "oxidized to",
            "object": "nitrite",
            "description": "Hydroxylamine oxidation yields nitrite in ammonia oxidizers.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2012.00210",
                "snippet": "oxidation of hydroxylamine to nitrite",
                "notes": "Supports hydroxylamine oxidation as the next nitrification step."
              }
            ],
            "predicate_id": "METPO:2007405"
          },
          {
            "subject": "sox_enzyme_system",
            "predicate": "oxidizes",
            "object": "thiosulfate",
            "description": "Sox proteins mediate oxidation of reduced sulfur compounds such as thiosulfate.",
            "evidence": [
              {
                "reference": "DOI:10.1111/j.1574-6976.2009.00187.x",
                "snippet": "oxidation of thiosulfate",
                "notes": "Supports the Sox multienzyme system in lithotrophic sulfur oxidation."
              }
            ],
            "predicate_id": "METPO:2007803"
          },
          {
            "subject": "inorganic_chemical_donor",
            "predicate": "feeds electrons into",
            "object": "respiratory_chain",
            "description": "Oxidation of inorganic donors feeds electrons into respiratory chains.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.bbabio.2008.09.008",
                "snippet": "membrane-bound electron transport chain",
                "notes": "Supports respiratory chains as energy-conserving redox systems."
              }
            ],
            "predicate_id": "METPO:2007402"
          },
          {
            "subject": "respiratory_chain",
            "predicate": "has output",
            "object": "atp",
            "description": "Respiratory energy conservation produces ATP.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.bbabio.2008.09.008",
                "snippet": "drives ATP synthesis",
                "notes": "Supports ATP synthesis from the respiratory ion gradient."
              }
            ],
            "predicate_id": "RO:0002234"
          },
          {
            "subject": "calvin_benson_bassham_cycle",
            "predicate": "mediates fixation of",
            "object": "carbon_dioxide",
            "description": "Chemolithoautotrophs fix CO2 via the Calvin-Benson-Bassham cycle.",
            "evidence": [
              {
                "reference": "DOI:10.3390/microorganisms12030590",
                "notes": "fixes atmospheric CO2 via the Calvin-Benson-Bassham (CBB) cycle"
              }
            ]
          },
          {
            "subject": "acidification",
            "predicate": "decreases",
            "object": "nitrification_rate",
            "description": "Environmental acidification reduces nitrification rates.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-023-37104-9",
                "notes": "a 5.8-18.1% drop and ~11.1-34.1% decline when pCO2 was doubled"
              }
            ],
            "predicate_id": "RO:0002212"
          },
          {
            "subject": "acidification",
            "predicate": "stimulates generation of",
            "object": "nitrous_oxide",
            "description": "Acidification stimulates N2O byproduct generation during nitrification.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-023-37104-9",
                "notes": "Acidification also stimulate[s] generation of byproduct nitrous oxide (N2O)"
              }
            ]
          },
          {
            "subject": "ammonia",
            "predicate": "example of",
            "object": "inorganic_chemical_donor",
            "description": "Ammonia is the energy-yielding inorganic substrate for chemolithotrophic ammonia oxidizers.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.01038-21",
                "snippet": "ammonium, which AOA and AOB utilize as their sole source of energy and nitrogen",
                "notes": "Verified against the open primary competition study."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "ammonia",
            "predicate": "contributes to",
            "object": "nitrification_rate",
            "description": "The ammonia-to-nitrite step contributes to the measured nitrification rate.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.01038-21",
                "snippet": "first step, ammonia oxidation to nitrite",
                "notes": "Verified against the open primary competition study."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "thiosulfate",
            "predicate": "example of",
            "object": "inorganic_chemical_donor",
            "description": "Thiosulfate can serve as the sole inorganic electron source for chemolithotrophic growth.",
            "evidence": [
              {
                "reference": "DOI:10.1111/j.1574-6968.1991.tb04611.x",
                "snippet": "with crystalline elemental sulfur (S\u00b0) and thiosulfate as sole electron source",
                "notes": "Verified against the public primary-study abstract."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "atp",
            "predicate": "participates in",
            "object": "calvin_benson_bassham_cycle",
            "description": "ATP generated by lithotrophic energy metabolism supplies the CBB carbon-fixation cycle.",
            "evidence": [
              {
                "reference": "DOI:10.1128/aem.00748-24",
                "snippet": "To fuel CO2 fixation by the Calvin-Benson-Bassham (CBB) cycle, C. necator generates ATP",
                "notes": "Verified against the open primary article."
              }
            ],
            "predicate_id": "biolink:participates_in"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.871549+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-08T00:00:00-07:00",
        "curator": "codex",
        "action": "ADDED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed causal graph for inorganic chemical electron donors, ammonia oxidation, sulfur oxidation, respiratory energy conservation, and ATP synthesis.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-16T05:00:00-07:00",
        "curator": "claude",
        "action": "ADDED_ORGANISM_EXAMPLE",
        "changes": "Added Nitrosomonas europaea organism example with PMID-backed evidence.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 4 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000016\u00d72, METPO:2000009\u00d71, METPO:2000202\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T21:30:07Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007405\u00d72, METPO:2007402\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:38:01Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0022904\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T05:05:15Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A059V4Z9\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T08:14:33Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:33542\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-14T05:51:47Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:15429\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-15T07:19:09Z",
        "curator": "claude",
        "action": "FIX_NODE_GROUNDING_CURIE",
        "changes": "Overwrote 1 causal-node grounding(s) to corrected CURIEs (phase-2 id-label fix; verified vs OAK).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 3 evidence-backed generic edges (5 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:14Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002212\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:34Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:17045\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:21:12Z",
        "curator": "claude",
        "action": "RETRACT_DEAD_UNIPROT_GROUNDINGS",
        "changes": "Retracted 1 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:23:55Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0018597\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-05T12:00:00Z",
        "curator": "claude",
        "action": "REVERSE_CAUSAL_EDGE_DIRECTION",
        "changes": "Reversed 1 causal edge from <trait> uses electron donor <chemical> to <chemical> enables <trait> (predicate_id METPO:2000009 -> RO:0002327), issue 295. METPO:2000009 is rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so the trait-subject form entailed that this TRAIT node is a microbe; CausalNodeTypeEnum has no organism member, so no causal-graph edge can satisfy that domain. Evidence unchanged; only subject/predicate/object/predicate_id and the edge description moved. Note RO:0002327 has range 'biological process or activity', so the new form is not fully range-correct either - tracked in issue 302.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 1 causal edge(s) off enables/RO:0002327 with a TRAIT object (1 to has electron donor), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them. 1 electron edge(s) were also reversed back to trait -> chemical, restoring the donor/acceptor role that PR 300 collapsed onto enables (issue 303); the organism-subject problem that forced that collapse does not arise here because these predicates take a causal-node domain rather than METPO:2000001's microbe domain (issue 301).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates (1 to has output), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T02:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES_PART2",
        "changes": "Re-grounded 2 causal edge(s) off microbe-domain METPO predicates onto their causal-graph counterparts (2 to oxidizes), issue 301 part 2. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Each replacement is a 1:1 mirror of its source predicate that changes only the domain, so the claim each edge makes is unchanged and directions are unchanged. The replacements are proposed in proposals/metpo_traitmech_v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-24T13:10:00-07:00",
        "curator": "codex",
        "action": "REVIEWED_CAUSAL_GRAPH_PROTEIN_TAXON",
        "changes": "Marked the graph mechanistic, upgraded canonical PMID citations to DOIs, reviewed the Sox umbrella as label-only, and added DOI-cited N. europaea ATCC 19718 AmoA component Q04507 without treating one subunit as the complete enzyme.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T11:45:00Z",
        "curator": "codex",
        "action": "CONNECT_CAUSAL_GRAPH_COMPONENTS",
        "changes": "Resolved issue #183 graph fragmentation (5 components to 1): added 4 public-source connector(s). No paid research service was called.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-22T01:35:00Z",
        "curator": "claude",
        "action": "REFRESH_UNIPROT_ENTRY_VERSION",
        "changes": "Refreshed UniProtKB entry_version against live UniProt REST on 2026-10-22: UniProtKB:Q04507 (126 -> 127 on ammonia_monooxygenase).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000640",
    "label": "chemoorganoheterotrophic",
    "definition": "A trophic type in which an organism obtains both energy and carbon from organic compounds through oxidation.",
    "definition_source": "DOI:10.1016/B978-012373944-5.00083-3",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000631"
    ],
    "synonyms": [
      {
        "synonym_text": "chemoorganoheterotroph",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1016/B978-012373944-5.00083-3",
        "snippet": "Chemoheterotroph (chemoorganoheterotroph)",
        "notes": "Encyclopedia chapter maps chemical energy, reduced organic electron source, and reduced organic carbon source to chemoorganoheterotrophy."
      },
      {
        "reference": "DOI:10.1021/acsomega.3c02205",
        "snippet": "chemoorganoheterotrophic",
        "notes": "Review table supports organic molecules as energy, electron, and carbon sources in chemoorganoheterotrophy."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:562",
        "taxon_label": "Escherichia coli",
        "note": "organic energy + carbon source",
        "reference": "DOI:10.1002/9781118960608.gbm01147"
      },
      {
        "taxon_id": "NCBITaxon:83333",
        "taxon_label": "Escherichia coli K-12",
        "note": "Strain-level respiratory chemoorganoheterotroph paired to the reviewed AtpD beta component of its F-type ATP synthase.",
        "reference": "DOI:10.7554/eLife.21598"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "chemoorganoheterotrophic_organic_energy_carbon",
        "title": "Chemoorganoheterotrophic organic energy and carbon metabolism",
        "description": "DOI-backed graph linking organic molecules as chemical energy, electron, and carbon sources to catabolism, respiration or fermentation, ATP, and biomass.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "This broad graph includes both respiratory and fermentative branches. The E. coli K-12 AtpD example anchors only F-type ATP synthesis in the respiratory branch; one beta-subunit accession does not denote the complete complex or all chemoorganoheterotrophic routes.",
        "nodes": [
          {
            "node_id": "chemoorganoheterotrophic_trait",
            "label": "chemoorganoheterotrophic",
            "node_type": "TRAIT",
            "grounding": "METPO:1000640",
            "description": "Trophic type using organic compounds for energy, electrons, and carbon."
          },
          {
            "node_id": "organic_molecule",
            "label": "organic molecule",
            "node_type": "CHEMICAL",
            "description": "Reduced organic substrate such as glucose, organic acids, lipids, or proteins.",
            "grounding": "CHEBI:72695"
          },
          {
            "node_id": "catabolism",
            "label": "catabolism",
            "node_type": "BIOLOGICAL_PROCESS",
            "grounding": "GO:0009056",
            "description": "Breakdown of nutrients for energy and precursor metabolites."
          },
          {
            "node_id": "respiration",
            "label": "respiration",
            "node_type": "PATHWAY",
            "grounding": "METPO:1000800",
            "description": "Electron-transport metabolism using terminal electron acceptors."
          },
          {
            "node_id": "fermentation",
            "label": "fermentation",
            "node_type": "BIOLOGICAL_PROCESS",
            "grounding": "GO:0006113",
            "description": "Energy metabolism using organic electron acceptors and substrate-level phosphorylation."
          },
          {
            "node_id": "atp",
            "label": "ATP",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:30616",
            "description": "Energy carrier produced by catabolic pathways."
          },
          {
            "node_id": "atp_synthase",
            "label": "ATP synthase",
            "node_type": "GENE_OR_PROTEIN",
            "grounding": "GO:0045259",
            "description": "F-type rotary complex that uses proton motive force to synthesize ATP in the respiratory branch.",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:P0ABB4",
                "protein_label": "ATP synthase subunit beta",
                "gene_symbol": "atpD",
                "taxon_id": "NCBITaxon:83333",
                "taxon_label": "Escherichia coli K-12",
                "entry_status": "REVIEWED",
                "retrieved_on": "2026-10-22",
                "entry_version": 156,
                "sequence_version": 2,
                "role": "Beta component of the E. coli F1 catalytic head; this accession is not presented as the complete F1Fo complex.",
                "evidence": [
                  {
                    "reference": "DOI:10.7554/eLife.21598",
                    "snippet": "proton motive force drives rotation and conformational changes in the F1 catalytic sites",
                    "notes": "The primary cryo-EM study resolves the E. coli F1Fo complex and its beta-containing catalytic head; UniProt verifies the reviewed K-12 AtpD entry."
                  }
                ]
              }
            ]
          },
          {
            "node_id": "precursor_metabolites",
            "label": "precursor metabolites",
            "node_type": "CHEMICAL",
            "description": "Intermediates used to synthesize cellular material."
          },
          {
            "node_id": "biomass",
            "label": "biomass",
            "node_type": "CHEMICAL",
            "description": "Cell material produced from organic carbon.",
            "grounding": "METPO:1007501"
          },
          {
            "node_id": "substrate_transport_system",
            "label": "substrate transport system",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "Membrane transporters that import organic substrates into the cell."
          },
          {
            "node_id": "reducing_power_nadph",
            "label": "ATP and NAD(P)H",
            "node_type": "CHEMICAL",
            "description": "Energy carrier (ATP) and reducing power (NAD(P)H) generated by metabolizing organic substrate."
          },
          {
            "node_id": "extracellular_cazymes",
            "label": "extracellular carbohydrate-active enzymes",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "Secreted hydrolytic enzymes (CAZymes) that depolymerize complex polysaccharides."
          },
          {
            "node_id": "complex_polysaccharides",
            "label": "complex polysaccharides",
            "node_type": "CHEMICAL",
            "description": "Polymeric carbohydrate substrates such as plant polysaccharides."
          },
          {
            "node_id": "energy_metabolism",
            "label": "intracellular energy metabolism",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Generation of energy and precursors from imported sugars and downstream metabolism."
          }
        ],
        "edges": [
          {
            "subject": "chemoorganoheterotrophic_trait",
            "predicate": "uses chemical energy source",
            "object": "organic_molecule",
            "description": "Chemoorganoheterotrophs derive energy from organic molecules.",
            "evidence": [
              {
                "reference": "DOI:10.1021/acsomega.3c02205",
                "snippet": "organic molecules ... energy source",
                "notes": "Supports organic molecules as energy sources in chemoorganoheterotrophy."
              }
            ]
          },
          {
            "subject": "chemoorganoheterotrophic_trait",
            "predicate": "has electron donor",
            "object": "organic_molecule",
            "description": "Organic molecules serve as the electron donors for chemoorganoheterotrophy.",
            "evidence": [
              {
                "reference": "DOI:10.1021/acsomega.3c02205",
                "snippet": "organic molecules ... electron source",
                "notes": "Supports organic molecules as electron sources in chemoorganoheterotrophy."
              }
            ],
            "predicate_id": "METPO:2007701"
          },
          {
            "subject": "chemoorganoheterotrophic_trait",
            "predicate": "has carbon source",
            "object": "organic_molecule",
            "description": "Organic molecules serve as carbon sources.",
            "evidence": [
              {
                "reference": "DOI:10.1016/B978-012373944-5.00083-3",
                "snippet": "reduced organic compound",
                "notes": "Supports reduced organic compounds as carbon sources for chemoheterotrophy."
              }
            ],
            "predicate_id": "METPO:2007806"
          },
          {
            "subject": "organic_molecule",
            "predicate": "broken down by",
            "object": "catabolism",
            "description": "Catabolism breaks down organic nutrients for energy and precursors.",
            "evidence": [
              {
                "reference": "DOI:10.1016/B978-012373944-5.00083-3",
                "snippet": "breakdown of nutrients",
                "notes": "Supports catabolism as nutrient breakdown for energy and anabolism."
              }
            ]
          },
          {
            "subject": "catabolism",
            "predicate": "can proceed through",
            "object": "respiration",
            "description": "Organic catabolism can conserve energy through respiration.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.bbabio.2008.09.008",
                "snippet": "membrane-bound electron transport chain",
                "notes": "Supports respiratory electron transport as an energy-conserving catabolic route."
              }
            ]
          },
          {
            "subject": "catabolism",
            "predicate": "can proceed through",
            "object": "fermentation",
            "description": "Organic catabolism can conserve energy through fermentation.",
            "evidence": [
              {
                "reference": "DOI:10.1111/1751-7915.13746",
                "snippet": "substrate-level phosphorylation",
                "notes": "Supports fermentation as an ATP-producing route from organic substrate catabolism."
              }
            ]
          },
          {
            "subject": "respiration",
            "predicate": "has output",
            "object": "atp",
            "description": "Respiratory electron transport supports ATP synthesis.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.bbabio.2008.09.008",
                "snippet": "drives ATP synthesis",
                "notes": "Supports respiratory ATP synthesis."
              }
            ],
            "predicate_id": "RO:0002234"
          },
          {
            "subject": "atp_synthase",
            "predicate": "produces",
            "object": "atp",
            "description": "F-type ATP synthase produces ATP during respiratory energy conservation.",
            "evidence": [
              {
                "reference": "DOI:10.7554/eLife.21598",
                "snippet": "proton motive force drives rotation and conformational changes in the F1 catalytic sites",
                "notes": "Supports ATP synthesis by the E. coli F1Fo complex and identifies the beta-containing catalytic head."
              }
            ],
            "predicate_id": "biolink:produces"
          },
          {
            "subject": "fermentation",
            "predicate": "has output",
            "object": "atp",
            "description": "Fermentation can produce ATP by substrate-level phosphorylation.",
            "evidence": [
              {
                "reference": "DOI:10.1111/1751-7915.13746",
                "snippet": "substrate-level phosphorylation",
                "notes": "Supports ATP formation during fermentation."
              }
            ],
            "predicate_id": "RO:0002234"
          },
          {
            "subject": "catabolism",
            "predicate": "has output",
            "object": "precursor_metabolites",
            "description": "Catabolism yields intermediates that feed biosynthesis.",
            "evidence": [
              {
                "reference": "DOI:10.1016/B978-012373944-5.00083-3",
                "snippet": "precursor compounds for anabolism",
                "notes": "Supports nutrient breakdown to biosynthetic precursors."
              }
            ],
            "predicate_id": "RO:0002234"
          },
          {
            "subject": "precursor_metabolites",
            "predicate": "incorporated into",
            "object": "biomass",
            "description": "Precursor metabolites are incorporated into cell material.",
            "evidence": [
              {
                "reference": "DOI:10.1016/B978-012373944-5.00083-3",
                "snippet": "incorporation of a compound into biomass",
                "notes": "Supports assimilation of compounds into biomass."
              }
            ],
            "predicate_id": "biolink:part_of"
          },
          {
            "subject": "substrate_transport_system",
            "predicate": "confers",
            "object": "chemoorganoheterotrophic_trait",
            "description": "Import of organic substrates by transport systems enables chemoorganoheterotrophic growth.",
            "evidence": [
              {
                "reference": "DOI:10.1021/acsomega.3c02205",
                "notes": "heterotrophic growth requires import of appropriate organic substrates into the cell"
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "organic_molecule",
            "predicate": "is required for",
            "object": "reducing_power_nadph",
            "description": "Imported organic substrate must be metabolized to synthesize ATP and NAD(P)H.",
            "evidence": [
              {
                "reference": "DOI:10.1021/acsomega.3c02205",
                "notes": "the entering molecule has to be metabolized in some way for the synthesis of ATP and NAD(P)H"
              }
            ]
          },
          {
            "subject": "organic_molecule",
            "predicate": "primarily supplies",
            "object": "energy_metabolism",
            "description": "Organic carbon uptake primarily supplies microbial energy demand.",
            "evidence": [
              {
                "reference": "DOI:10.1111/gcb.16925",
                "notes": "microorganisms use organic C mainly as an energy source"
              }
            ]
          },
          {
            "subject": "extracellular_cazymes",
            "predicate": "hydrolyzes",
            "object": "complex_polysaccharides",
            "description": "Extracellular CAZymes hydrolyze complex polysaccharides into monomers for uptake.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s40793-024-00572-7",
                "notes": "microbes produce extracellular carbohydrate-active enzymes that hydrolyse complex plant polysaccharides"
              }
            ],
            "predicate_id": "METPO:2007808"
          },
          {
            "subject": "substrate_transport_system",
            "predicate": "feeds into",
            "object": "energy_metabolism",
            "description": "Imported sugars feed into intracellular energy metabolism.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s40793-024-00572-7",
                "notes": "import monomers and short oligosaccharides for energy and downstream metabolism"
              }
            ]
          },
          {
            "subject": "extracellular_cazymes",
            "predicate": "contributes to",
            "object": "catabolism",
            "description": "Extracellular carbohydrate-active enzymes initiate the catabolism of complex polysaccharides by cleaving their sugar linkages.",
            "evidence": [
              {
                "reference": "DOI:10.1371/journal.pgen.1004773",
                "snippet": "Plants are primarily composed of heterogeneous polysaccharides, requiring plant-degrading microbes to encode many carbohydrate-active enzymes (CAZymes) to cleave different sugar linkages",
                "notes": "Verified against the open PLOS Genetics primary article."
              }
            ],
            "predicate_id": "RO:0002326"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.872101+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-08T00:00:00-07:00",
        "curator": "codex",
        "action": "ADDED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed causal graph for organic molecules as energy, electron, and carbon sources feeding catabolism, respiration or fermentation, ATP, and biomass.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 5 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d73, METPO:2000009\u00d71, METPO:2000006\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:41:04Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (METPO:1007501\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T07:34:58Z",
        "curator": "claude",
        "action": "RETYPE_CAUSAL_NODES",
        "changes": "Re-typed 1 causal-node node_type field(s) to align with CausalNodeTypeEnum semantics: biomass: BIOLOGICAL_PROCESS \u2192 CHEMICAL \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-13T21:03:27Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:part_of\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-14T05:51:47Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:72695\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 5 evidence-backed generic edges (5 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:14Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:39Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000013\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-05T12:00:00Z",
        "curator": "claude",
        "action": "REVERSE_CAUSAL_EDGE_DIRECTION",
        "changes": "Reversed 1 causal edge from <trait> uses electron donor <chemical> to <chemical> enables <trait> (predicate_id METPO:2000009 -> RO:0002327), issue 295. METPO:2000009 is rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so the trait-subject form entailed that this TRAIT node is a microbe; CausalNodeTypeEnum has no organism member, so no causal-graph edge can satisfy that domain. Evidence unchanged; only subject/predicate/object/predicate_id and the edge description moved. Note RO:0002327 has range 'biological process or activity', so the new form is not fully range-correct either - tracked in issue 302.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 2 causal edge(s) off enables/RO:0002327 with a TRAIT object (1 to has electron donor, 1 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them. 1 electron edge(s) were also reversed back to trait -> chemical, restoring the donor/acceptor role that PR 300 collapsed onto enables (issue 303); the organism-subject problem that forced that collapse does not arise here because these predicates take a causal-node domain rather than METPO:2000001's microbe domain (issue 301).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 4 causal edge(s) off microbe-domain METPO predicates (1 to has carbon source, 3 to has output), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T02:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES_PART2",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates onto their causal-graph counterparts (1 to hydrolyzes), issue 301 part 2. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Each replacement is a 1:1 mirror of its source predicate that changes only the domain, so the claim each edge makes is unchanged and directions are unchanged. The replacements are proposed in proposals/metpo_traitmech_v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-16T02:00:00Z",
        "curator": "claude",
        "action": "NORMALISE_NODE_TYPE",
        "changes": "Under the PATHWAY-vs-BIOLOGICAL_PROCESS rule, one node_id means one thing corpus-wide (issue 356): fermentation is typed BIOLOGICAL_PROCESS. PATHWAY is a named, conventionally enumerable multi-step route; BIOLOGICAL_PROCESS is everything else. A CLASS of routes rather than one route -- fermentation names a mode of energy conservation with many distinct implementations, so its steps cannot be enumerated without picking one. Was 3 BIOLOGICAL_PROCESS to 2 before this tranche. NOTE its groundings disagree with each other (GO:0006113 x3, METPO:1002005, and METPO:1000845 which is ACETOGENESIS, a different concept) -- filed as #391 and deliberately NOT touched here, because retyping a node while carrying a wrong CURIE along unchanged would make it look reviewed.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-22T04:30:00Z",
        "curator": "claude",
        "action": "REGROUND_CAUSAL_NODES",
        "changes": "Repaired a wrong CURIE (issue 391): fermentation: METPO:1000845 -> GO:0006113. Was METPO:1000845 'Acetogenesis' \u2014 a Wood-Ljungdahl acetate-producing metabolism, while the node describes 'Energy metabolism using organic electron acceptors and substrate-level phosphorylation', i.e. fermentation. The term's related synonym 'Acetate fermentation' explains the mismatch. Replaced with GO:0006113, the (fermentation, BIOLOGICAL_PROCESS) row mappings/node_grounding.tsv already holds and the grounding eight sibling records already carry.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "CURATE_PROTEIN_TAXON_EXAMPLE",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope chemoorganoheterotrophic_organic_energy_carbon=MECHANISTIC with scope_notes; added taxon-paired protein example(s) UniProtKB:P0ABB4 on atp_synthase (NCBITaxon:83333); added 1 node(s) and 1 edge(s) (atp_synthase); added canonical example(s) NCBITaxon:83333.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T10:45:00Z",
        "curator": "codex",
        "action": "CONNECT_CAUSAL_GRAPH_COMPONENTS",
        "changes": "Resolved issue #183 graph fragmentation (2 components to 1) with 1 public-source, verbatim-snippet-backed connector(s). No paid research service was called.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-22T01:35:00Z",
        "curator": "claude",
        "action": "REFRESH_UNIPROT_ENTRY_VERSION",
        "changes": "Refreshed UniProtKB entry_version against live UniProt REST on 2026-10-22: UniProtKB:P0ABB4 (155 -> 156 on atp_synthase).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000663",
    "label": "chemoorganotrophic",
    "definition": "A trophic type in which an organism obtains energy through chemical oxidation of organic compounds that also serve as the carbon source for biosynthesis.",
    "definition_source": "DOI:10.1016/B978-012373944-5.00083-3",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000631"
    ],
    "synonyms": [
      {
        "synonym_text": "chemoorganotroph",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "created_by": "Jed Dongjin Kim-Ozaeta",
    "evidence": [
      {
        "reference": "DOI:10.1016/B978-012373944-5.00083-3",
        "snippet": "chemical energy",
        "notes": "Encyclopedia chapter classifies chemotrophy by chemical rather than light energy sources."
      },
      {
        "reference": "DOI:10.1016/j.bbabio.2008.09.008",
        "snippet": "membrane-bound electron transport chain",
        "notes": "Review supports respiratory-chain energy conservation from redox reactions."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:562",
        "taxon_label": "Escherichia coli",
        "note": "organic compounds as energy and carbon",
        "reference": "DOI:10.5772/intechopen.105508"
      },
      {
        "taxon_id": "NCBITaxon:303",
        "taxon_label": "Pseudomonas putida",
        "note": "versatile chemoorganotroph",
        "reference": "PMID:12534463"
      },
      {
        "taxon_id": "NCBITaxon:83333",
        "taxon_label": "Escherichia coli K-12",
        "note": "Strain-level respiratory chemoorganotroph paired to the reviewed AtpD beta component of its F-type ATP synthase.",
        "reference": "DOI:10.7554/eLife.21598"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "chemoorganotrophic_organic_oxidation_energy",
        "title": "Chemoorganotrophic organic chemical oxidation",
        "description": "DOI-backed graph for chemical oxidation of organic compounds, electron transfer to respiratory chains, proton motive force, ATP synthesis, and organic carbon assimilation.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "This graph includes respiratory and fermentative alternatives. The E. coli K-12 AtpD example anchors only F-type ATP synthesis in the respiratory branch and is one beta component, not the complete rotary complex.",
        "nodes": [
          {
            "node_id": "chemoorganotrophic_trait",
            "label": "chemoorganotrophic",
            "node_type": "TRAIT",
            "grounding": "METPO:1000663",
            "description": "Trophic type obtaining energy from chemical oxidation of organic compounds."
          },
          {
            "node_id": "organic_compound",
            "label": "organic compound",
            "node_type": "CHEMICAL",
            "description": "Reduced organic substrate serving as chemical energy source.",
            "grounding": "CHEBI:50860"
          },
          {
            "node_id": "substrate_oxidation",
            "label": "organic substrate oxidation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Oxidation of organic compounds releasing electrons and energy."
          },
          {
            "node_id": "respiratory_chain",
            "label": "respiratory chain",
            "node_type": "PATHWAY",
            "description": "Energy-conserving membrane electron-transfer system.",
            "grounding": "GO:0022904"
          },
          {
            "node_id": "terminal_electron_acceptor",
            "label": "terminal electron acceptor",
            "node_type": "CHEMICAL",
            "description": "Oxidized compound accepting electrons at the end of respiration.",
            "grounding": "METPO:1007504"
          },
          {
            "node_id": "proton_motive_force",
            "label": "proton motive force",
            "node_type": "STATE",
            "description": "Ion gradient generated by respiratory electron transport.",
            "grounding": "METPO:1007500"
          },
          {
            "node_id": "atp",
            "label": "ATP",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:30616",
            "description": "Energy carrier formed by ATP synthase."
          },
          {
            "node_id": "atp_synthase",
            "label": "ATP synthase",
            "node_type": "GENE_OR_PROTEIN",
            "grounding": "GO:0045259",
            "description": "F-type rotary complex that converts proton motive force into ATP.",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:P0ABB4",
                "protein_label": "ATP synthase subunit beta",
                "gene_symbol": "atpD",
                "taxon_id": "NCBITaxon:83333",
                "taxon_label": "Escherichia coli K-12",
                "entry_status": "REVIEWED",
                "retrieved_on": "2026-10-22",
                "entry_version": 156,
                "sequence_version": 2,
                "role": "Beta component of the E. coli F1 catalytic head; this accession is not presented as the complete F1Fo complex.",
                "evidence": [
                  {
                    "reference": "DOI:10.7554/eLife.21598",
                    "snippet": "proton motive force drives rotation and conformational changes in the F1 catalytic sites",
                    "notes": "The primary cryo-EM study resolves the E. coli F1Fo complex and its beta-containing catalytic head; UniProt verifies the reviewed K-12 AtpD entry."
                  }
                ]
              }
            ]
          },
          {
            "node_id": "biomass",
            "label": "biomass",
            "node_type": "CHEMICAL",
            "description": "Cell material built from organic carbon.",
            "grounding": "METPO:1007501"
          },
          {
            "node_id": "reduced_cofactor",
            "label": "reduced redox cofactor (NADH)",
            "node_type": "CHEMICAL",
            "description": "Reduced electron-carrying cofactor (e.g. NADH) formed during organic substrate oxidation."
          },
          {
            "node_id": "quinone_pool",
            "label": "quinone pool",
            "node_type": "CHEMICAL",
            "description": "Membrane ubiquinone/menaquinone pool that shuttles electrons within the respiratory chain."
          },
          {
            "node_id": "aerobic_respiration",
            "label": "aerobic respiration",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Respiratory metabolism using oxygen as terminal electron acceptor.",
            "grounding": "GO:0009060"
          },
          {
            "node_id": "anaerobic_respiration",
            "label": "anaerobic respiration",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Respiratory metabolism using inorganic acceptors such as nitrate or nitrite.",
            "grounding": "GO:0009061"
          },
          {
            "node_id": "ambient_oxygen",
            "label": "ambient molecular oxygen",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Molecular oxygen acting as terminal electron acceptor when present."
          },
          {
            "node_id": "nitrate_nitrite",
            "label": "nitrate/nitrite",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Inorganic alternative electron acceptors enabling anaerobic respiration."
          },
          {
            "node_id": "acceptor_absence",
            "label": "absence of external electron acceptor",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Condition in which no external terminal electron acceptor is available."
          },
          {
            "node_id": "fermentation",
            "label": "fermentation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Energy metabolism with electrons relocated onto an organic catabolic product.",
            "grounding": "GO:0006113"
          },
          {
            "node_id": "substrate_level_phosphorylation",
            "label": "substrate-level phosphorylation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "ATP generation by direct phosphate transfer from a phosphorylated intermediate."
          }
        ],
        "edges": [
          {
            "subject": "chemoorganotrophic_trait",
            "predicate": "uses chemical energy source",
            "object": "organic_compound",
            "description": "Chemoorganotrophic metabolism derives energy from organic chemicals.",
            "evidence": [
              {
                "reference": "DOI:10.1016/B978-012373944-5.00083-3",
                "snippet": "reduced organic compound",
                "notes": "Supports reduced organic compounds as the source for chemoorganotrophic growth."
              }
            ]
          },
          {
            "subject": "organic_compound",
            "predicate": "oxidized during",
            "object": "substrate_oxidation",
            "description": "Organic substrates are oxidized to release reducing equivalents.",
            "evidence": [
              {
                "reference": "DOI:10.1016/B978-012373944-5.00083-3",
                "snippet": "oxidation of a reduced ... organic compound",
                "notes": "Supports dissimilatory oxidation of reduced organic compounds."
              }
            ]
          },
          {
            "subject": "substrate_oxidation",
            "predicate": "feeds electrons into",
            "object": "respiratory_chain",
            "description": "Organic substrate oxidation supplies electrons to respiration.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.bbabio.2008.09.008",
                "snippet": "electron transfer process",
                "notes": "Supports electron flow through respiratory chains."
              }
            ],
            "predicate_id": "METPO:2007402"
          },
          {
            "subject": "respiratory_chain",
            "predicate": "transfers electrons to",
            "object": "terminal_electron_acceptor",
            "description": "Respiration moves electrons to terminal electron acceptors.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mmbr.61.4.533-616.1997",
                "snippet": "terminal electron acceptor",
                "notes": "Supports terminal electron acceptors in respiratory metabolism."
              }
            ],
            "predicate_id": "METPO:2007403"
          },
          {
            "subject": "respiratory_chain",
            "predicate": "generates",
            "object": "proton_motive_force",
            "description": "Respiratory chains generate an electrochemical ion gradient.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.bbabio.2008.09.008",
                "snippet": "generation of an electrochemical ion gradient",
                "notes": "Supports proton motive force generation from electron transport."
              }
            ],
            "predicate_id": "biolink:produces"
          },
          {
            "subject": "proton_motive_force",
            "predicate": "drives production of",
            "object": "atp",
            "description": "Proton motive force drives ATP synthesis.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.bbabio.2008.09.008",
                "snippet": "drives ATP synthesis",
                "notes": "Supports ATP production from respiratory energy conservation."
              }
            ],
            "predicate_id": "biolink:produces"
          },
          {
            "subject": "proton_motive_force",
            "predicate": "drives",
            "object": "atp_synthase",
            "description": "Proton motive force drives the F-type ATP synthase rotary mechanism.",
            "evidence": [
              {
                "reference": "DOI:10.7554/eLife.21598",
                "snippet": "proton motive force drives rotation and conformational changes in the F1 catalytic sites",
                "notes": "The E. coli structural study directly supports coupling of proton motive force to the beta-containing ATP synthase complex."
              }
            ],
            "predicate_id": "RO:0002212"
          },
          {
            "subject": "organic_compound",
            "predicate": "assimilated into",
            "object": "biomass",
            "description": "Organic compounds also supply carbon for biosynthesis.",
            "evidence": [
              {
                "reference": "DOI:10.1016/B978-012373944-5.00083-3",
                "snippet": "carbon source",
                "notes": "Supports organic compounds as carbon sources for biosynthesis."
              }
            ]
          },
          {
            "subject": "substrate_oxidation",
            "predicate": "produces reduced cofactor",
            "object": "reduced_cofactor",
            "description": "Organic substrate oxidation reduces redox cofactors such as NAD to NADH.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuae016",
                "notes": "Redox cofactors (NAD and ferredoxin) accept electrons and become reduced during organic oxidation."
              }
            ]
          },
          {
            "subject": "reduced_cofactor",
            "predicate": "feeds electrons into",
            "object": "quinone_pool",
            "description": "Reduced cofactors donate electrons to the membrane quinone pool via dehydrogenases.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s13213-024-01761-y",
                "notes": "Some dehydrogenases inject electrons into the quinone pool of the respiratory chain."
              }
            ],
            "predicate_id": "METPO:2007402"
          },
          {
            "subject": "quinone_pool",
            "predicate": "transfers electrons to",
            "object": "terminal_electron_acceptor",
            "description": "The quinone pool passes electrons to terminal oxidases reducing the terminal acceptor.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s13213-024-01761-y",
                "notes": "Quinol oxidases pass electrons from ubiquinols/menaquinones to oxygen."
              }
            ],
            "predicate_id": "METPO:2007403"
          },
          {
            "subject": "ambient_oxygen",
            "predicate": "enables",
            "object": "aerobic_respiration",
            "description": "Presence of oxygen enables aerobic respiratory chemoorganotrophy.",
            "evidence": [
              {
                "reference": "DOI:10.2166/9781789062304_0009",
                "notes": "Electron acceptors range from O2 in aerobic respiration."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "nitrate_nitrite",
            "predicate": "enables",
            "object": "anaerobic_respiration",
            "description": "Inorganic acceptors such as nitrate/nitrite enable anaerobic respiratory chemoorganotrophy.",
            "evidence": [
              {
                "reference": "DOI:10.2166/9781789062304_0009",
                "notes": "Organisms catabolize an organic e-donor by respiration with an inorganic e-acceptor such as nitrite or nitrate."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "acceptor_absence",
            "predicate": "leads to",
            "object": "fermentation",
            "description": "Absence of an external terminal electron acceptor leads to fermentation.",
            "evidence": [
              {
                "reference": "DOI:10.2166/9781789062304_0009",
                "notes": "In fermentation, no terminal e-acceptor is available; electrons are relocated onto an organic catabolic product."
              }
            ]
          },
          {
            "subject": "fermentation",
            "predicate": "generates ATP via",
            "object": "substrate_level_phosphorylation",
            "description": "Fermentation generates ATP primarily by substrate-level phosphorylation.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuae016",
                "notes": "In fermentation, ATP is generated primarily by substrate-level phosphorylation."
              }
            ]
          },
          {
            "subject": "substrate_level_phosphorylation",
            "predicate": "has output",
            "object": "atp",
            "description": "Substrate-level phosphorylation directly produces ATP.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuae016",
                "notes": "Fermentative ATP is produced by substrate-level phosphorylation."
              }
            ],
            "predicate_id": "RO:0002234"
          },
          {
            "subject": "aerobic_respiration",
            "predicate": "contributes to",
            "object": "respiratory_chain",
            "description": "Oxygen-dependent respiration is a terminal-acceptor mode of the respiratory chain.",
            "evidence": [
              {
                "reference": "DOI:10.1099/00221287-98-1-231",
                "snippet": "both oxygen and nitrate (or nitrite or chlorate) levels were continuously monitored during bacterial respiration",
                "notes": "Verified against the public primary-study abstract."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "anaerobic_respiration",
            "predicate": "contributes to",
            "object": "respiratory_chain",
            "description": "Nitrate reduction provides an anaerobic terminal-acceptor mode of the respiratory chain.",
            "evidence": [
              {
                "reference": "DOI:10.1099/00221287-98-1-231",
                "snippet": "commenced nitrate reduction when all the oxygen had been consumed",
                "notes": "Verified against the public primary-study abstract."
              }
            ],
            "predicate_id": "RO:0002326"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.883201+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-08T00:00:00-07:00",
        "curator": "codex",
        "action": "ADDED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed causal graph for organic chemical oxidation, respiratory electron transport, ATP synthesis, and biomass formation.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T08:21:50Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:produces\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T21:30:07Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007402\u00d71, METPO:2007403\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:38:01Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0022904\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:41:04Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 3 causal-node grounding field(s) via mappings/node_grounding.tsv (METPO:1007504\u00d71, METPO:1007500\u00d71, METPO:1007501\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T07:34:58Z",
        "curator": "claude",
        "action": "RETYPE_CAUSAL_NODES",
        "changes": "Re-typed 1 causal-node node_type field(s) to align with CausalNodeTypeEnum semantics: biomass: BIOLOGICAL_PROCESS \u2192 CHEMICAL \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T08:14:33Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:50860\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-26T02:30:13Z",
        "curator": "claude",
        "action": "RETYPE_CAUSAL_NODES",
        "changes": "Re-typed 1 causal-node node_type field(s) to align with CausalNodeTypeEnum semantics: proton motive force: BIOLOGICAL_PROCESS \u2192 STATE \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-13T21:03:27Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:produces\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 8 evidence-backed generic edges (9 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:14Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 5 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d72, METPO:2007402\u00d71, METPO:2007403\u00d71, METPO:2000202\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:20Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 3 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0009060\u00d71, GO:0009061\u00d71, GO:0006113\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:34Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (ENVO:01001495\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates (1 to has output), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-16T02:00:00Z",
        "curator": "claude",
        "action": "NORMALISE_NODE_TYPE",
        "changes": "Under the PATHWAY-vs-BIOLOGICAL_PROCESS rule, one node_id means one thing corpus-wide (issue 356): fermentation is typed BIOLOGICAL_PROCESS. PATHWAY is a named, conventionally enumerable multi-step route; BIOLOGICAL_PROCESS is everything else. A CLASS of routes rather than one route -- fermentation names a mode of energy conservation with many distinct implementations, so its steps cannot be enumerated without picking one. Was 3 BIOLOGICAL_PROCESS to 2 before this tranche. NOTE its groundings disagree with each other (GO:0006113 x3, METPO:1002005, and METPO:1000845 which is ACETOGENESIS, a different concept) -- filed as #391 and deliberately NOT touched here, because retyping a node while carrying a wrong CURIE along unchanged would make it look reviewed.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-17T02:00:00Z",
        "curator": "claude",
        "action": "NORMALISE_NODE_SENSE",
        "changes": "One node_id per SENSE (issues 356, 384): ambient_oxygen is the chemical sense here. Already the ambient sense. Listed so a re-run still normalises the label and still retracts ENVO:01001495 if it has been re-applied \u2014 the grounder keys on (label, node_type), so an un-normalised label is what lets the retracted CURIE come back.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "CURATE_PROTEIN_TAXON_EXAMPLE",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope chemoorganotrophic_organic_oxidation_energy=MECHANISTIC with scope_notes; added taxon-paired protein example(s) UniProtKB:P0ABB4 on atp_synthase (NCBITaxon:83333); added 1 node(s) and 1 edge(s) (atp_synthase); added canonical example(s) NCBITaxon:83333.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T11:45:00Z",
        "curator": "codex",
        "action": "CONNECT_CAUSAL_GRAPH_COMPONENTS",
        "changes": "Resolved issue #183 graph fragmentation (3 components to 1): added 2 public-source connector(s). No paid research service was called.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-22T01:35:00Z",
        "curator": "claude",
        "action": "REFRESH_UNIPROT_ENTRY_VERSION",
        "changes": "Refreshed UniProtKB entry_version against live UniProt REST on 2026-10-22: UniProtKB:P0ABB4 (155 -> 156 on atp_synthase).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000086",
    "label": "chemotaxis",
    "definition": "A behavioral physiology in which cells bias their movement toward attractants or away from repellents by modulating flagellar motor switching in response to chemical gradients.",
    "definition_source": "DOI:10.1038/nrm1524",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "synonyms": [
      {
        "synonym_text": "chemotactic",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1038/nrm1524"
      },
      {
        "synonym_text": "taxis in response to chemical stimulus",
        "synonym_type": "EXACT_SYNONYM",
        "source": "http://purl.obolibrary.org/obo/go/releases/2026-07-26/go-basic.obo"
      }
    ],
    "xrefs": [
      "GO:0006935"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/nrm1524",
        "notes": "Wadhams & Armitage review bacterial chemotaxis as gradient-guided movement controlled by a histidine-aspartate phosphorelay."
      },
      {
        "reference": "DOI:10.1038/nrmicro2505",
        "notes": "Porter, Wadhams & Armitage review signal processing in complex chemotaxis pathways."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:562",
        "taxon_label": "Escherichia coli",
        "note": "Paradigm of bacterial chemotaxis (flagellar run-and-tumble; Che two-component signalling).",
        "reference": "DOI:10.1038/nrm1524"
      },
      {
        "taxon_id": "NCBITaxon:83333",
        "taxon_label": "Escherichia coli K-12",
        "note": "Reference strain for the canonical Che phosphorelay; CheY binding to the flagellar switch controls rotational direction.",
        "reference": "DOI:10.1073/pnas.1000935107"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "chemotaxis_gradient_response",
        "title": "Gradient-guided chemotactic movement",
        "description": "Evidence-backed causal sketch linking chemical gradients to biased motility via flagellar motor control.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "This graph represents the enterobacterial CheA-CheY pathway exemplified by E. coli K-12. Chemotaxis systems in other taxa can omit CheZ, use alternative adaptation proteins, or contain multiple paralogous receptor arrays.",
        "nodes": [
          {
            "node_id": "chemotaxis_trait",
            "label": "chemotaxis",
            "node_type": "TRAIT",
            "grounding": "traitmech:000086",
            "description": "Biased movement along chemical gradients."
          },
          {
            "node_id": "chemical_gradient",
            "label": "chemical gradient",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Spatial gradient of attractant or repellent."
          },
          {
            "node_id": "chemotaxis_process",
            "label": "chemotaxis",
            "node_type": "BIOLOGICAL_PROCESS",
            "grounding": "GO:0006935",
            "description": "Signal transduction biasing motor switching."
          },
          {
            "node_id": "chemoreceptor_mcp",
            "label": "chemoreceptor (MCP)",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Methyl-accepting chemotaxis protein that binds attractant/repellent ligands.",
            "grounding": "InterPro:IPR004090"
          },
          {
            "node_id": "chea_kinase",
            "label": "CheA histidine kinase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Histidine autokinase whose activity is modulated by chemoreceptors.",
            "grounding": "InterPro:IPR051315"
          },
          {
            "node_id": "chea_autophosphorylation",
            "label": "CheA autophosphorylation",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "Autophosphorylation activity of the CheA histidine kinase."
          },
          {
            "node_id": "chey",
            "label": "CheY response regulator",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Response regulator that, when phosphorylated, controls flagellar motor switching.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Available receiver-domain terms also cover many non-CheY response regulators; no exact taxon-agnostic CheY family term was verified for this node.",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:P0AE67",
                "protein_label": "Chemotaxis protein CheY",
                "gene_symbol": "cheY",
                "taxon_id": "NCBITaxon:83333",
                "taxon_label": "Escherichia coli K-12",
                "entry_status": "REVIEWED",
                "proteome_id": "UP000000625",
                "retrieved_on": "2026-10-22",
                "entry_version": 161,
                "sequence_version": 2,
                "role": "Phosphorylated CheY binds the E. coli flagellar switch and raises the probability of clockwise motor rotation.",
                "evidence": [
                  {
                    "reference": "DOI:10.1073/pnas.1000935107",
                    "snippet": "Chemotaxis signaling protein CheY binds to the rotor protein FliN",
                    "notes": "The primary E. coli motor study directly links CheY to control of flagellar rotational direction; UniProtKB P0AE67 is the reviewed K-12 CheY entry."
                  }
                ]
              }
            ]
          },
          {
            "node_id": "cheb",
            "label": "CheB methylesterase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Phospho-regulated methylesterase that demethylates chemoreceptors during adaptation.",
            "grounding": "InterPro:IPR000673"
          },
          {
            "node_id": "cher",
            "label": "CheR methyltransferase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Methyltransferase that methylates chemoreceptors during adaptation.",
            "grounding": "InterPro:IPR000780"
          },
          {
            "node_id": "chez",
            "label": "CheZ phosphatase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Phosphatase that dephosphorylates CheY-P to reset signaling.",
            "grounding": "InterPro:IPR007439"
          },
          {
            "node_id": "chew",
            "label": "CheW coupling protein",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Adaptor/scaffold coupling CheA to chemoreceptors in the core signaling unit.",
            "grounding": "InterPro:IPR039315"
          },
          {
            "node_id": "cw_flagellar_rotation",
            "label": "clockwise flagellar rotation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Clockwise flagellar motor rotation that promotes tumbling."
          }
        ],
        "edges": [
          {
            "subject": "chemical_gradient",
            "predicate": "causes",
            "object": "chemotaxis_process",
            "description": "A chemical gradient drives the chemotaxis signaling response.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrm1524",
                "notes": "Wadhams & Armitage review gradient-guided chemotaxis signaling."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "chemotaxis_process",
            "predicate": "confers",
            "object": "chemotaxis_trait",
            "description": "The chemotaxis signaling process realizes the trait.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2505",
                "notes": "Porter et al. review chemotaxis signal processing."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "chemoreceptor_mcp",
            "predicate": "modulates",
            "object": "chea_autophosphorylation",
            "description": "Effector binding to chemoreceptors modulates CheA autophosphorylation activity.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-micro-032421-110850",
                "notes": "Upon effector binding to the receptor, the autophosphorylation activity of CheA is modulated by chemoreceptors."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "chea_kinase",
            "predicate": "phosphorylates",
            "object": "chey",
            "description": "Phosphorylated CheA transfers phosphoryl groups to the response regulator CheY.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-micro-032421-110850",
                "notes": "When CheA is phosphorylated, it can activate its response regulators CheB and CheY via phosphoryl transfer."
              }
            ]
          },
          {
            "subject": "chea_kinase",
            "predicate": "phosphorylates",
            "object": "cheb",
            "description": "Phosphorylated CheA transfers phosphoryl groups to the methylesterase CheB.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-micro-032421-110850",
                "notes": "When CheA is phosphorylated, it can activate its response regulators CheB and CheY via phosphoryl transfer."
              }
            ]
          },
          {
            "subject": "chey",
            "predicate": "induces",
            "object": "cw_flagellar_rotation",
            "description": "Phosphorylated CheY interacts with the flagellar motor to induce clockwise rotation.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-micro-032421-110850",
                "notes": "CheY-P interacts with the flagella to induce clockwise rotation."
              }
            ]
          },
          {
            "subject": "chez",
            "predicate": "dephosphorylates",
            "object": "chey",
            "description": "CheZ phosphatase dephosphorylates CheY-P to maintain a stable signaling pool.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-micro-032421-110850",
                "notes": "The phosphatase CheZ dephosphorylates CheY to ensure a stable pool of CheY is available."
              }
            ]
          },
          {
            "subject": "cher",
            "predicate": "methylates",
            "object": "chemoreceptor_mcp",
            "description": "CheR methylates chemoreceptors as part of the reversible adaptation system.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-micro-032421-110850",
                "notes": "CheB, along with CheR, constitutes an adaptation system that reversibly methylates receptors."
              }
            ]
          },
          {
            "subject": "cheb",
            "predicate": "demethylates",
            "object": "chemoreceptor_mcp",
            "description": "CheB demethylates chemoreceptors as part of the reversible adaptation system.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-micro-032421-110850",
                "notes": "CheB, along with CheR, constitutes an adaptation system that reversibly methylates/demethylates receptors."
              }
            ]
          },
          {
            "subject": "chew",
            "predicate": "scaffolds",
            "object": "chea_kinase",
            "description": "CheW couples and scaffolds CheA with chemoreceptors in the core signaling unit baseplate.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-micro-032421-110850",
                "notes": "The coupling protein CheW secures CheA; the baseplate consists of the chemoreceptor PIR, CheA, and CheW."
              }
            ]
          },
          {
            "subject": "chemoreceptor_mcp",
            "predicate": "contributes to",
            "object": "chemotaxis_process",
            "description": "Chemoreceptor arrays contribute ligand sensing and CheA control to the chemotaxis process.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.tim.2022.10.007",
                "snippet": "The chemoreceptor nanoarray complexes with the cytosolic histidine kinase chemotaxis protein A (CheA) and regulates its autophosphorylation based on chemoreceptor ligand occupancy",
                "notes": "Verified against the public PMC author manuscript."
              }
            ],
            "predicate_id": "RO:0002326"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-06-04T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate PHYSIOLOGY trait (chemotaxis), a behavioral response; distinct from the morphological motility apparatus.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-08T13:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (gradient-guided chemotaxis) with GO node grounding and biolink/RO predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 8 evidence-backed generic edges (9 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:14Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002211\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-26T07:15:20Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 3 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:G0HQV3\u00d71, UniProtKB:A0A2X5A7X5\u00d71, UniProtKB:A0A100WWV3\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:21:12Z",
        "curator": "claude",
        "action": "RETRACT_DEAD_UNIPROT_GROUNDINGS",
        "changes": "Retracted 3 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 1 causal edge(s) off enables/RO:0002327 with a TRAIT object (1 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-24T11:10:00Z",
        "curator": "codex",
        "action": "CURATE_PROTEIN_TAXON_EXAMPLE",
        "changes": "Scoped the graph to the enterobacterial Che pathway, added cited E. coli K-12 and reviewed CheY as a taxon-paired example, and reviewed all seven protein nodes against current InterPro families.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T06:15:41Z",
        "curator": "codex",
        "action": "ADD_EXACT_ONTOLOGY_MATCH",
        "changes": "Ontology exact-match review (2026-08-25): approved exact xref(s): GO:0006935; declared exact synonym(s): 'taxis in response to chemical stimulus'. Evidence is predicate-scoped in the versioned ontology snapshots; OAK cross-checked direct data, and OLS4 spot-checked release deltas and disputed hits.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T09:35:00Z",
        "curator": "codex",
        "action": "CONNECT_CAUSAL_GRAPH_COMPONENTS",
        "changes": "Resolved issue #183 graph fragmentation (2 components to 1) with one public-source, verbatim-snippet-backed connector. No paid research service was called.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-22T01:35:00Z",
        "curator": "claude",
        "action": "REFRESH_UNIPROT_ENTRY_VERSION",
        "changes": "Refreshed UniProtKB entry_version against live UniProt REST on 2026-10-22: UniProtKB:P0AE67 (160 -> 161 on chey).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000641",
    "label": "chemotrophic",
    "definition": "A trophic type in which an organism obtains energy from chemical oxidation of either inorganic or organic compounds.",
    "definition_source": "DOI:10.1016/B978-012373944-5.00083-3",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000631"
    ],
    "synonyms": [
      {
        "synonym_text": "TT_chemotroph",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "chemotroph",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1016/B978-012373944-5.00083-3",
        "snippet": "chemical energy",
        "notes": "Encyclopedia chapter classifies chemotrophy by chemical energy sources."
      },
      {
        "reference": "DOI:10.1016/j.bbabio.2008.09.008",
        "snippet": "free energy of a redox reaction",
        "notes": "Review supports chemical redox reactions as energy sources for respiratory energy conservation."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:83333",
        "taxon_label": "Escherichia coli K-12",
        "note": "Strain-level chemoorganotrophic respiratory model paired to the reviewed AtpD beta component of its F-type ATP synthase.",
        "reference": "DOI:10.7554/eLife.21598"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "chemotrophic_chemical_redox_energy",
        "title": "Chemotrophic chemical redox energy conservation",
        "description": "DOI-backed graph linking reduced chemical substrates, inorganic and organic donor examples, redox reactions, respiratory electron transfer, proton motive force, and ATP.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "This graph represents respiratory chemotrophic energy conservation, not every chemotrophic route; fermentation and substrate-level phosphorylation are outside its scope. The E. coli K-12 AtpD example supports the shared F-type ATP-synthase module and is one beta subunit, not the complete rotary complex.",
        "nodes": [
          {
            "node_id": "chemotrophic_trait",
            "label": "chemotrophic",
            "node_type": "TRAIT",
            "grounding": "METPO:1000641",
            "description": "Trophic type deriving energy from chemical oxidation."
          },
          {
            "node_id": "reduced_chemical_substrate",
            "label": "reduced chemical substrate",
            "node_type": "CHEMICAL",
            "description": "Electron donor oxidized for metabolic energy."
          },
          {
            "node_id": "inorganic_compound",
            "label": "inorganic compound",
            "node_type": "CHEMICAL",
            "description": "Inorganic electron donor used by chemolithotrophs."
          },
          {
            "node_id": "organic_compound",
            "label": "organic compound",
            "node_type": "CHEMICAL",
            "description": "Organic electron donor used by chemoorganotrophs.",
            "grounding": "CHEBI:50860"
          },
          {
            "node_id": "redox_reaction",
            "label": "redox reaction",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "Oxidation-reduction reaction releasing usable free energy.",
            "grounding": "GO:0016491"
          },
          {
            "node_id": "respiratory_chain",
            "label": "respiratory chain",
            "node_type": "PATHWAY",
            "description": "Membrane electron-transfer system conserving redox energy.",
            "grounding": "GO:0022904"
          },
          {
            "node_id": "terminal_electron_acceptor",
            "label": "terminal electron acceptor",
            "node_type": "CHEMICAL",
            "description": "Oxidized acceptor receiving electrons during respiration.",
            "grounding": "METPO:1007504"
          },
          {
            "node_id": "proton_motive_force",
            "label": "proton motive force",
            "node_type": "STATE",
            "description": "Electrochemical ion gradient generated by electron transport.",
            "grounding": "METPO:1007500"
          },
          {
            "node_id": "atp_synthase",
            "label": "ATP synthase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Membrane enzyme complex using proton motive force to synthesize ATP.",
            "grounding": "GO:0045259",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:P0ABB4",
                "protein_label": "ATP synthase subunit beta",
                "gene_symbol": "atpD",
                "taxon_id": "NCBITaxon:83333",
                "taxon_label": "Escherichia coli K-12",
                "entry_status": "REVIEWED",
                "retrieved_on": "2026-10-22",
                "entry_version": 156,
                "sequence_version": 2,
                "role": "Beta component of the F1 catalytic head of the E. coli F1Fo ATP synthase; this accession is not presented as the complete rotary complex.",
                "evidence": [
                  {
                    "reference": "DOI:10.7554/eLife.21598",
                    "snippet": "the potential energy of the proton motive force into rotation of the central stalk that drives conformational changes in the F1 catalytic sites",
                    "notes": "The primary cryo-EM study resolves the E. coli F1Fo complex and its beta-containing catalytic head; UniProtKB P0ABB4 verifies the reviewed AtpD component and K-12 taxon."
                  }
                ]
              }
            ]
          },
          {
            "node_id": "atp",
            "label": "ATP",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:30616",
            "description": "Energy carrier produced by chemotrophic metabolism."
          },
          {
            "node_id": "quinone_quinol_cycling",
            "label": "quinone/quinol cycling",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Membrane quinone reduction/oxidation cycle that translocates protons."
          },
          {
            "node_id": "redox_loop",
            "label": "redox loop",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Electron-transfer arrangement coupling electron flow to net transmembrane proton transfer without active pumping."
          },
          {
            "node_id": "proton_pumping",
            "label": "proton pumping",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Active vectorial translocation of protons across the coupling membrane by electron-transport complexes."
          },
          {
            "node_id": "net_proton_transfer",
            "label": "net proton transfer across membrane",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Net movement of protons across the coupling membrane that establishes the electrochemical gradient."
          }
        ],
        "edges": [
          {
            "subject": "chemotrophic_trait",
            "predicate": "has energy source",
            "object": "reduced_chemical_substrate",
            "description": "Chemotrophy uses chemical substrates as energy sources.",
            "evidence": [
              {
                "reference": "DOI:10.1016/B978-012373944-5.00083-3",
                "snippet": "chemical energy",
                "notes": "Supports chemical energy as the defining chemotrophic energy source."
              }
            ],
            "predicate_id": "METPO:2007807"
          },
          {
            "subject": "inorganic_compound",
            "predicate": "example of",
            "object": "reduced_chemical_substrate",
            "description": "Inorganic substrates are chemical energy sources in lithotrophy.",
            "evidence": [
              {
                "reference": "DOI:10.1016/B978-0-12-378630-2.00219-X",
                "snippet": "oxidize inorganic atoms or molecules",
                "notes": "Supports inorganic chemical substrates in chemolithotrophic metabolism."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "organic_compound",
            "predicate": "example of",
            "object": "reduced_chemical_substrate",
            "description": "Organic substrates are chemical energy sources in organotrophy.",
            "evidence": [
              {
                "reference": "DOI:10.1016/B978-012373944-5.00083-3",
                "snippet": "reduced organic compound",
                "notes": "Supports reduced organic compounds as chemical energy substrates."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "reduced_chemical_substrate",
            "predicate": "oxidized by",
            "object": "redox_reaction",
            "description": "Chemical energy is released through oxidation-reduction chemistry.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.bbabio.2008.09.008",
                "snippet": "free energy of a redox reaction",
                "notes": "Supports redox reactions as the energy source for chemiosmotic conservation."
              }
            ]
          },
          {
            "subject": "redox_reaction",
            "predicate": "feeds electrons into",
            "object": "respiratory_chain",
            "description": "Redox reactions can feed electrons into membrane respiratory chains.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.bbabio.2008.09.008",
                "snippet": "membrane-bound electron transport chain",
                "notes": "Supports membrane electron transport in respiratory energy conservation."
              }
            ],
            "predicate_id": "METPO:2007402"
          },
          {
            "subject": "respiratory_chain",
            "predicate": "transfers electrons to",
            "object": "terminal_electron_acceptor",
            "description": "Respiratory chains transfer electrons to terminal acceptors.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mmbr.61.4.533-616.1997",
                "snippet": "terminal electron acceptor",
                "notes": "Supports terminal electron acceptors in respiratory metabolism."
              }
            ],
            "predicate_id": "METPO:2007403"
          },
          {
            "subject": "respiratory_chain",
            "predicate": "generates",
            "object": "proton_motive_force",
            "description": "Respiratory electron transfer generates an ion gradient.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.bbabio.2008.09.008",
                "snippet": "generation of an electrochemical ion gradient",
                "notes": "Supports ion-gradient formation by electron transport."
              }
            ],
            "predicate_id": "biolink:produces"
          },
          {
            "subject": "proton_motive_force",
            "predicate": "drives production of",
            "object": "atp",
            "description": "Proton motive force drives ATP synthesis.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.bbabio.2008.09.008",
                "snippet": "drives ATP synthesis",
                "notes": "Supports ATP synthesis from chemotrophic respiratory energy conservation."
              }
            ],
            "predicate_id": "biolink:produces"
          },
          {
            "subject": "proton_motive_force",
            "predicate": "used by",
            "object": "atp_synthase",
            "description": "F-type ATP synthase converts proton-motive-force energy into rotary catalysis.",
            "evidence": [
              {
                "reference": "DOI:10.7554/eLife.21598",
                "snippet": "the potential energy of the proton motive force into rotation of the central stalk",
                "notes": "The E. coli F1Fo structural study directly supports proton-motive-force-driven rotation of the ATP synthase represented by this node."
              }
            ]
          },
          {
            "subject": "atp_synthase",
            "predicate": "produces",
            "object": "atp",
            "description": "ATP synthase couples ion flow to phosphorylation of ADP.",
            "evidence": [
              {
                "reference": "DOI:10.7554/eLife.21598",
                "snippet": "couples ion flow across membranes with the addition of inorganic phosphate to ADP thereby generating ATP",
                "notes": "The E. coli F1Fo study supports ATP as the catalytic product of the multisubunit ATP synthase; P0ABB4 represents only its beta component."
              }
            ],
            "predicate_id": "biolink:produces"
          },
          {
            "subject": "proton_motive_force",
            "predicate": "can be built by",
            "object": "quinone_quinol_cycling",
            "description": "Proton motive force can be generated by quinone/quinol cycling.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.bbabio.2008.09.008",
                "notes": "The proton motive force (pmf) can be built up by different mechanisms like proton pumping, quinone/quinol cycling or by a redox loop."
              }
            ]
          },
          {
            "subject": "proton_pumping",
            "predicate": "contributes to generation of",
            "object": "proton_motive_force",
            "description": "Active proton pumping contributes to building the proton motive force.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.bbabio.2008.09.008",
                "notes": "The proton motive force (pmf) can be built up by different mechanisms like proton pumping, quinone/quinol cycling or by a redox loop."
              }
            ]
          },
          {
            "subject": "redox_loop",
            "predicate": "contributes to generation of",
            "object": "proton_motive_force",
            "description": "A redox loop contributes to building the proton motive force.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.bbabio.2008.09.008",
                "notes": "The proton motive force (pmf) can be built up by different mechanisms like proton pumping, quinone/quinol cycling or by a redox loop."
              }
            ]
          },
          {
            "subject": "redox_loop",
            "predicate": "couples electron transport to",
            "object": "net_proton_transfer",
            "description": "A redox loop couples electron transport to net proton transfer across the membrane without proton pumping.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.bbabio.2008.09.008",
                "notes": "The latter couples electron transport to a net proton transfer across the membrane without proton pumping."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.872607+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-09T00:00:00-07:00",
        "curator": "codex",
        "action": "ADDED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed causal graph for chemical substrate oxidation, respiratory electron transfer, proton motive force, and ATP synthesis.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000010\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T08:21:50Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (rdfs:subClassOf\u00d72, biolink:produces\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T21:30:07Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007402\u00d71, METPO:2007403\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:38:01Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0016491\u00d71, GO:0022904\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:41:04Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (METPO:1007504\u00d71, METPO:1007500\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T08:14:33Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:50860\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-26T02:30:13Z",
        "curator": "claude",
        "action": "RETYPE_CAUSAL_NODES",
        "changes": "Re-typed 1 causal-node node_type field(s) to align with CausalNodeTypeEnum semantics: proton motive force: BIOLOGICAL_PROCESS \u2192 STATE \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-13T21:03:27Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:produces\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 4 evidence-backed generic edges (4 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates (1 to has energy source), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-24T12:30:00-07:00",
        "curator": "codex",
        "action": "REVIEWED_CAUSAL_GRAPH_PROTEIN_TAXON",
        "changes": "Marked the respiratory chemotrophy graph mechanistic, documented its scope, added DOI-cited E. coli K-12 as the canonical strain, and paired the generic ATP synthase complex with reviewed AtpD component P0ABB4 without treating one subunit as the whole complex.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-22T01:35:00Z",
        "curator": "claude",
        "action": "REFRESH_UNIPROT_ENTRY_VERSION",
        "changes": "Refreshed UniProtKB entry_version against live UniProt REST on 2026-10-22: UniProtKB:P0ABB4 (155 -> 156 on atp_synthase).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000597",
    "label": "chemotropism",
    "definition": "A phenotype in which polarized growth is directionally biased in response to a spatial chemical gradient.",
    "definition_source": "DOI:10.1371/journal.pbio.3002726",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1371/journal.pbio.3002726",
        "snippet": "Notably, many hyphae changed direction near the boundary, opting to remain in the pH 6.5 layer (Fig 3B).",
        "notes": "Results, Chemotropism to low pH; exact span in Europe PMC full text PMC11288418 (PMID:39078817), published 2024-07-30. The compared layers are pH 6.5 and 8. Figure 3 was visually inspected: tip trajectories support directional growth, not only greater biomass. Main Results and the primary abstract describe lower-pH preference in these comparisons; the separate summary abstract's acidic-pH avoidance wording conflicts with them. Growth inhibition at pH 3 and carbon-source growth differences confound those comparisons. The nitrogen Results separately report negative chemotropism. S1 Table (10.1371/journal.pbio.3002726.s002), inspected as PDF text and image, lists engineered backgrounds including TH122; no natural canonical strain is inferred. Other supplements and movies were not inspected."
      },
      {
        "reference": "DOI:10.1038/s41598-020-67597-z",
        "snippet": "They respond to changes in their environment by directing hyphal growth towards or away from a range of chemical stimuli.",
        "notes": "Introduction, first paragraph; They refers to filamentous fungi. Exact span in Europe PMC full text PMC7329813 (PMID:32612109). This supports the polarity-neutral growth definition. The first Results subsection reports directional growth of Fusarium graminearum towards methionine, while rapid growth with other tested nitrogen compounds was not significantly directional. Table 1 identifies GZ-3639 as wild type, but natural provenance and an exact NCBI identity were not independently verified. Figures and supplements were not visually inspected. The paper's receptor and infection findings are not transferred into a universal chemotropism mechanism or canonical example."
      }
    ],
    "discussions": [
      {
        "discussion_id": "chemotropism-growth-and-source-boundaries",
        "prompt": "Preserve direction, growth-rate and source-summary distinctions.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "This class covers positive and negative chemical-gradient responses of polarized growth, not whole-cell locomotion. Use phenotype rather than motile as the parent. Neither increased biomass, faster extension nor asymmetric branching alone establishes directed growth. Keep chemotaxis, contact guidance and electric-field growth distinct. The Yamamoto summary abstract conflicts with the main Results on the pH-response direction; retain the inspected Results and Figure 3 context rather than silently harmonizing them. External equivalences and lexical variants require separate authority and scope checks.",
        "posed_by": "codex",
        "posed_date": "2026-10-04"
      },
      {
        "discussion_id": "chemotropism-strain-and-mechanism-grounding",
        "prompt": "Resolve natural strain provenance and accession-level mechanism evidence.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Keep laboratory-strain observations as qualified evidence. Verify natural provenance and NCBI identities before adding canonical examples; wild-type labels and no-auxotrophy controls do not establish an unengineered strain. The Aspergillus PmaA perturbation also affects growth and acid tolerance, so it does not isolate a dedicated chemical sensor. Inspect remaining figures and supplements and resolve taxon-paired protein accessions before adding a causal graph. Do not generalize stimulus-specific perturbations into a universal pathway or use a NONMECHANISTIC graph to bypass missing molecular evidence.",
        "posed_by": "codex",
        "posed_date": "2026-10-04"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-04T13:41:09Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added chemotropism with two primary DOI citations and exact full-text snippets. Ignored-and-hidden novelty searches and structured OWL review found no exact record or METPO term. Reserved METPO:1055100 in v474. Distinguished polarized growth from locomotion and growth-rate changes; retained both gradient directions and documented conflicting summary wording. Inspected Aspergillus Figure 3 and S1 strain table. Deferred natural canonical examples and accession-level causal mechanisms.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-04T13:44:00Z",
        "curator": "codex",
        "action": "CORRECT_EVIDENCE_SNIPPET",
        "changes": "Raw JATS matching caught a dropped figure pointer in the uncommitted Yamamoto draft quote. Restored (Fig 3B) before the sentence-ending period to preserve the contiguous source span.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1007089",
    "label": "coagulase activity",
    "definition": "A physiological enzyme-activity phenotype in which a cell produces coagulase factors that activate prothrombin and convert fibrinogen to fibrin, clotting blood plasma.",
    "definition_source": "DOI:10.1159/000333447",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "SEEDED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "synonyms": [
      {
        "synonym_text": "coagulase test",
        "synonym_type": "EXACT_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "coagulase-positive",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1159/000333447"
      }
    ],
    "created_by": "Marcin Joachimiak",
    "evidence": [
      {
        "reference": "DOI:10.1159/000333447",
        "snippet": "Clinical isolates of Staphylococcus aureus secrete coagulases, polypeptides that bind to and activate prothrombin",
        "notes": "McAdow, Missiakas and Schneewind review how staphylococcal coagulases activate prothrombin, convert fibrinogen to fibrin, and clot plasma or blood."
      },
      {
        "reference": "DOI:10.1371/journal.ppat.1001036",
        "snippet": "Coa and vWbp promote the non-proteolytic activation of prothrombin and cleavage of fibrinogen",
        "notes": "Cheng et al. experimentally show that the two S. aureus coagulases, Coa and von Willebrand factor binding protein, mediate prothrombin and fibrinogen reactions relevant to staphylococcal clot formation."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1280",
        "taxon_label": "Staphylococcus aureus",
        "note": "Canonical coagulase-positive bacterium that secretes Coa and vWbp.",
        "reference": "DOI:10.1371/journal.ppat.1001036"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-11T00:00:00Z",
        "curator": "codex",
        "action": "SEEDED_FROM_METPO",
        "changes": "Added the active METPO coagulase activity class as a DOI-backed TraitRecord after a repository-wide duplicate review covering ignored and hidden files.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-21T21:12:25Z",
        "curator": "claude",
        "action": "CURATE_CAUSAL_GRAPH",
        "changes": "Added MECHANISTIC causal_graphs entry (coagulase_activity_prothrombin_mechanism) anchored on existing verbatim record evidence snippets.",
        "llm_assisted": true
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "coagulase_activity_prothrombin_mechanism",
        "title": "Staphylococcal coagulase prothrombin activation and fibrinogen cleavage",
        "description": "Evidence-backed physiological mechanism linking secreted staphylocoagulases (Coa and vWbp) to non-proteolytic prothrombin activation and fibrinogen cleavage.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "Protein-anchored mechanism backed by DOI:10.1159/000333447 and DOI:10.1371/journal.ppat.1001036, with reviewed Staphylococcus aureus staphylocoagulase Coa (UniProtKB:P07767) curated on the InterPro:IPR019553 coagulase node.",
        "nodes": [
          {
            "node_id": "coagulase_activity_trait",
            "label": "coagulase activity",
            "node_type": "TRAIT",
            "grounding": "METPO:1007089",
            "description": "Physiological enzyme-activity phenotype in which secreted coagulase factors activate prothrombin and clot plasma."
          },
          {
            "node_id": "coagulase_activity_staphylocoagulase",
            "label": "staphylocoagulase family protein",
            "node_type": "GENE_OR_PROTEIN",
            "grounding": "InterPro:IPR019553",
            "description": "Secreted staphylococcal coagulase polypeptides (Coa and vWbp) that bind and non-proteolytically activate prothrombin.",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:P07767",
                "entry_status": "REVIEWED",
                "entry_version": 82,
                "sequence_version": 2,
                "retrieved_on": "2026-10-21",
                "gene_symbol": "coa",
                "protein_label": "Staphylocoagulase",
                "taxon_id": "NCBITaxon:1280",
                "taxon_label": "Staphylococcus aureus",
                "role": "Secreted Staphylococcus aureus coagulase (Coa) that binds and non-proteolytically activates host prothrombin to cleave fibrinogen.",
                "evidence": [
                  {
                    "reference": "DOI:10.1371/journal.ppat.1001036",
                    "snippet": "Coa and vWbp promote the non-proteolytic activation of prothrombin and cleavage of fibrinogen",
                    "notes": "Cheng et al. demonstrate that Staphylococcus aureus Coa (UniProtKB:P07767) promotes non-proteolytic activation of prothrombin and cleavage of fibrinogen."
                  }
                ]
              }
            ]
          },
          {
            "node_id": "coagulase_activity_prothrombin_activation",
            "label": "zymogen activation",
            "node_type": "BIOLOGICAL_PROCESS",
            "grounding": "GO:0031638",
            "description": "Non-proteolytic activation of host prothrombin and downstream conversion of fibrinogen to fibrin."
          }
        ],
        "edges": [
          {
            "subject": "coagulase_activity_staphylocoagulase",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "coagulase_activity_trait",
            "description": "Secreted staphylococcal coagulase polypeptides confer the coagulase activity phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1159/000333447",
                "snippet": "Clinical isolates of Staphylococcus aureus secrete coagulases, polypeptides that bind to and activate prothrombin",
                "notes": "McAdow, Missiakas, and Schneewind describe secreted Staphylococcus aureus coagulases that bind to and activate prothrombin."
              }
            ]
          },
          {
            "subject": "coagulase_activity_staphylocoagulase",
            "predicate": "enables",
            "predicate_id": "RO:0002327",
            "object": "coagulase_activity_prothrombin_activation",
            "description": "Coa and vWbp promote non-proteolytic activation of prothrombin and cleavage of fibrinogen.",
            "evidence": [
              {
                "reference": "DOI:10.1371/journal.ppat.1001036",
                "snippet": "Coa and vWbp promote the non-proteolytic activation of prothrombin and cleavage of fibrinogen",
                "notes": "Cheng et al. demonstrate that Coa and vWbp promote non-proteolytic activation of prothrombin and cleavage of fibrinogen."
              }
            ]
          }
        ]
      }
    ]
  },
  {
    "identifier": "traitmech:000689",
    "label": "coccolith production",
    "definition": "A physiological phenotype in which a microbial cell produces the calcitic cell-covering elements known as coccoliths.",
    "definition_source": "DOI:10.1038/ncomms11228",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000690"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/ncomms11228",
        "snippet": "Coccoliths are calcitic particles produced inside the cells of unicellular marine algae known as coccolithophores.",
        "notes": "Sviben et al. 2016, PMID:27075521, PMC4834641. Scientific Abstract and full article text directly read in Europe PMC XML on 2026-10-10; actual Figures 1 and 3 inspected. Calcium resupply to depleted AWI1516 cultures supports new calcite formation; imaging distinguishes forming coccoliths from a separate calcium-rich compartment. Its necessity, direct precursor identity and transfer route are not established. Figure 3's detector-panel caption repeats c in two pairs; no panel-specific detector assignment is imported. Other figures and supplements were not visually inspected. Historical Emiliania huxleyi is retained as the source name, not a current taxonomic or culture-collection phenotype assertion."
      },
      {
        "reference": "DOI:10.1111/nph.15272",
        "snippet": "The continued production of malformed coccoliths could be observed on successive days",
        "notes": "Walker et al. 2018, PMID:29916209, PMC6175242, Results, time-lapse observations associated with Figure 8. Full article text and actual Figures 5 and 8 directly inspected on 2026-10-10; supplements and movies unread. This passage concerns Ge-treated Coccolithus braarudii PLY182g, not normal morphology. Production persists despite defective coccosphere integrity. Growth responses differ from the assayed E. huxleyi CCMP1516; neither growth dependence nor photosynthetic benefit is generalized. Preserve source discrepancies: Methods time-lapse stage 17 C versus Figure 5's 16 C; Methods/Results HEDP 50 micromolar versus Figure 1's 5 micromolar; Results low-Si threshold below 0.2 micromolar versus Discussion below 0.1. No unqualified quantitative claim depends on choosing between them."
      }
    ],
    "discussions": [
      {
        "discussion_id": "coccolith-production-scope-and-parent",
        "prompt": "Resolve broader biomineralization placement without conflating endpoints.",
        "kind": "CURATION_TODO",
        "status": "RESOLVED",
        "rationale": "Use phenotype METPO:1000059 pending a source-backed broader biomineralization phenotype. Coccolith production is not mere possession, secretion or arrangement of preformed elements into a coccosphere. Defective elements still count as production; a complete covering is not required. It is not equivalent to generic calcification, urease-associated calcium carbonate precipitation, siliceous scale production, or magnetosome/ferrosome possession. The physiological trait is distinct from a material coccolith, its vesicle and a process-level ontology term. No exact synonyms, xrefs, common molecular pathway or organism-level disjointness are asserted.",
        "posed_by": "codex",
        "posed_date": "2026-10-10",
        "resolved_date": "2026-10-10",
        "resolution_note": "Added biomineralization traitmech:000690 as the direct broader phenotype. Production of the mineral elements specified by this record entails mineral formation; this is a definition-based hierarchy inference, not a new child experiment. Phenotype METPO:1000059 remains an ancestor. The historical rationale and endpoint distinctions are preserved; the separate exemplar and mechanism gap remains OPEN. The v566 proposal requests the additional child axiom without rewriting the historical proposal cohort."
      },
      {
        "discussion_id": "coccolith-production-exemplars-and-mechanism",
        "prompt": "Reconcile assay strains, life stages and production-specific mechanisms.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "No canonical examples are assigned pending joint strain-provenance and current-taxonomy verification. Skeffington et al., DOI:10.1111/jpy.12942, p. 239, explicitly derives calcifying AWI1516 from CCMP1516; this does not make all descendants equivalent. The current collection https://ncma.bigelow.org/CCMP1516, read 2026-10-10, labels it Gephyrocapsa huxleyi and reports lost coccolith production. Keep historical assay observations separate from this current catalog state; loss alone does not establish engineering. PLY182g provenance remains unresolved here. No universal silicon requirement, ploidy restriction, growth dependence or protective function is inferred. Separate mineral deposition, transport, secretion and covering integrity before adding causal edges. A protein mechanism needs direct functional evidence and taxon-paired accessions; sequence features alone are insufficient. Mechanism is deferred, not claimed absent.",
        "posed_by": "codex",
        "posed_date": "2026-10-10"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-10T06:31:15Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added coccolith production with two primary DOI citations and short directly checked snippets, retaining assay and source-conflict limits. Ignored-and-hidden main/worktree/open-PR reservation checks support 000689 and v565 block 1064200-1064299. Broader hierarchy, canonical exemplars and protein mechanism remain unresolved. Existing records unchanged. Timestamp records the observed UTC curation decision.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-10T08:03:12Z",
        "curator": "codex",
        "action": "REFINE_BIOMINERALIZATION_PARENT",
        "changes": "Refined the direct parent to biomineralization traitmech:000690 and resolved the temporary parent gap by definition-based inference. Preserved the definition, evidence, historical rationale, independent mechanism gap and prior curation history. No organism or molecular mechanism was added.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000206",
    "label": "cold shock response",
    "definition": "A stress response in which a rapid temperature downshift induces nucleic-acid-binding cold-shock proteins and RNA-remodeling functions that preserve gene expression at low temperature.",
    "definition_source": "DOI:10.3184/003685003783238707",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000078"
    ],
    "synonyms": [
      {
        "synonym_text": "cold-shock response",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.3184/003685003783238707"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.3184/003685003783238707",
        "snippet": "bacteria express a well-defined set of proteins after a rapid decrease in temperature, which is termed cold shock",
        "notes": "Weber and Marahiel define bacterial cold shock as the temperature-downshift response that induces a specific protein set."
      },
      {
        "reference": "DOI:10.3184/003685003783238707",
        "snippet": "the cold shock response is organized as a complex stimulon in which post-transcriptional events play an important role",
        "notes": "The bacterial cold-shock response is reviewed as a stimulon dominated by post-transcriptional control rather than a single cold-specific sigma-factor branch."
      },
      {
        "reference": "DOI:10.3184/003685003783238707",
        "snippet": "nucleic acid-binding cold shock proteins which play a fundamental role not only during cold shock adaptation but also under optimal growth conditions",
        "notes": "The review places nucleic-acid-binding cold-shock proteins among the core functional components of bacterial cold-shock adaptation."
      },
      {
        "reference": "DOI:10.1046/j.1365-2958.1999.01541.x",
        "snippet": "proposed function as an RNA chaperone to prevent the formation of secondary structures in RNA molecules, thus facilitating translation at low temperature",
        "notes": "Phadtare and Inouye support RNA chaperoning by CspA-family proteins as a mechanism for preserving translation after cold shock."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:562",
        "taxon_label": "Escherichia coli",
        "note": "E. coli is a model for the bacterial cold-shock response, including induction of the major cold-shock protein CspA.",
        "reference": "DOI:10.1073/pnas.87.1.283"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "cold_shock_response_rna_adaptation",
        "title": "Cold-shock RNA adaptation",
        "description": "Evidence-backed causal sketch linking abrupt temperature downshift to bacterial cold-shock protein induction and RNA chaperone support for low-temperature translation.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "This graph captures the conserved CspA-family RNA-support branch of the bacterial cold-shock response without making one cold-sensing regulator, one RNA helicase, or one post-transcriptional circuit universal across bacteria.",
        "nodes": [
          {
            "node_id": "cold_shock_response_trait",
            "label": "cold shock response",
            "node_type": "TRAIT",
            "grounding": "traitmech:000206",
            "description": "Capacity to induce cold-shock proteins after a rapid temperature downshift."
          },
          {
            "node_id": "acute_cold_shock",
            "label": "acute cold shock",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "A sudden downward temperature shift."
          },
          {
            "node_id": "cold_shock_response_process",
            "label": "cold-shock response",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Rapid expression of cold-shock proteins and RNA-remodeling functions after a temperature downshift."
          },
          {
            "node_id": "cspa_family_cold_shock_proteins",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed functional protein family; cold-shock domain signatures and CspA-like orthology terms are broader than bacterial proteins induced and used as RNA chaperones during cold shock.",
            "label": "CspA-family cold-shock proteins",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Nucleic-acid-binding cold-shock proteins that act as RNA chaperones after cold shock.",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:P0A9X9",
                "protein_label": "Cold shock protein CspA",
                "gene_symbol": "cspA",
                "taxon_id": "NCBITaxon:83333",
                "taxon_label": "Escherichia coli K-12",
                "entry_status": "REVIEWED",
                "retrieved_on": "2026-09-15",
                "entry_version": 146,
                "sequence_version": 2,
                "role": "E. coli K-12 CspA is the major CspA-family cold-shock protein and model RNA chaperone induced by temperature downshift.",
                "evidence": [
                  {
                    "reference": "DOI:10.1073/pnas.87.1.283",
                    "snippet": "the production of a 7.4-kDa cytoplasmic protein (CS7.4) was prominently induced",
                    "notes": "Goldstein et al. directly support strong induction of the E. coli major cold-shock protein later named CspA."
                  },
                  {
                    "reference": "DOI:10.1046/j.1365-2958.1999.01541.x",
                    "snippet": "CspA, the major cold shock protein, binds RNA with low sequence specificity",
                    "notes": "Phadtare and Inouye directly support CspA as an RNA-binding cold-shock protein."
                  }
                ]
              }
            ]
          },
          {
            "node_id": "rna_secondary_structure_control",
            "label": "RNA secondary-structure control at low temperature",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "RNA chaperoning that limits inhibitory secondary structure formation in cold-stressed cells."
          },
          {
            "node_id": "low_temperature_translation",
            "label": "translation at low temperature",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Protein synthesis preserved during low-temperature stress.",
            "grounding": "GO:0006412"
          }
        ],
        "edges": [
          {
            "subject": "acute_cold_shock",
            "predicate": "causes",
            "predicate_id": "biolink:causes",
            "object": "cold_shock_response_process",
            "description": "Abrupt temperature downshift causes the bacterial cold-shock protein-expression response.",
            "evidence": [
              {
                "reference": "DOI:10.3184/003685003783238707",
                "snippet": "bacteria express a well-defined set of proteins after a rapid decrease in temperature, which is termed cold shock",
                "notes": "Verified against the public Crossref abstract; the cold-shock response follows rapid temperature decrease."
              }
            ]
          },
          {
            "subject": "cold_shock_response_process",
            "predicate": "positively regulates",
            "predicate_id": "RO:0002213",
            "object": "cspa_family_cold_shock_proteins",
            "description": "The cold-shock response induces CspA-family nucleic-acid-binding cold-shock proteins.",
            "evidence": [
              {
                "reference": "DOI:10.3184/003685003783238707",
                "snippet": "nucleic acid-binding cold shock proteins which play a fundamental role not only during cold shock adaptation",
                "notes": "Verified against the public Crossref abstract; nucleic-acid-binding cold-shock proteins are central cold-shock-adaptation components."
              }
            ]
          },
          {
            "subject": "cspa_family_cold_shock_proteins",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "rna_secondary_structure_control",
            "description": "CspA-family cold-shock proteins contribute to low-temperature RNA secondary-structure control.",
            "evidence": [
              {
                "reference": "DOI:10.1046/j.1365-2958.1999.01541.x",
                "snippet": "RNA chaperone to prevent the formation of secondary structures in RNA molecules",
                "notes": "Verified against the public Crossref abstract; CspA-family RNA chaperone activity limits RNA secondary-structure formation."
              }
            ]
          },
          {
            "subject": "rna_secondary_structure_control",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "low_temperature_translation",
            "description": "Control of RNA secondary structures supports translation at low temperature.",
            "evidence": [
              {
                "reference": "DOI:10.1046/j.1365-2958.1999.01541.x",
                "snippet": "prevent the formation of secondary structures in RNA molecules, thus facilitating translation at low temperature",
                "notes": "Verified against the public Crossref abstract; CspA-family RNA chaperoning facilitates low-temperature translation."
              }
            ]
          },
          {
            "subject": "low_temperature_translation",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "cold_shock_response_trait",
            "description": "Preservation of translation realizes the RNA-adaptation branch of the cold-shock-response trait.",
            "evidence": [
              {
                "reference": "DOI:10.1046/j.1365-2958.1999.01541.x",
                "snippet": "proposed function as an RNA chaperone to prevent the formation of secondary structures in RNA molecules, thus facilitating translation at low temperature",
                "notes": "Verified against the public Crossref abstract; RNA chaperoning connects CspA-family proteins to preserved translation during cold stress."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "cold-shock-response-xref-gap",
        "prompt": "Resolve exact ontology xrefs for organism-level microbial cold shock response before adding TraitRecord xrefs.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "GO:0009409 response to cold can ground broad biological-process response nodes but is broader than the rapid temperature-downshift cold-shock response curated here. Cold-shock-domain signatures and CspA-family terms describe narrower molecular machinery rather than the whole organism-level stress-response trait.",
        "posed_by": "codex",
        "posed_date": "2026-09-15"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-15T05:32:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted cold shock response as a DOI-backed stress-response TraitRecord after a repository-wide duplicate review covering ignored and hidden files; the local METPO snapshot has only an obsolete cold shock response class and the replacement placeholder is reserved in proposals/metpo_traitmech_v83.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000650",
    "label": "contact-dependent outer membrane exchange",
    "definition": "A physiological phenotype in which microbial cells exchange outer-membrane lipids and proteins with other cells through direct intercellular contact.",
    "definition_source": "DOI:10.7554/eLife.00868",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.7554/eLife.00868",
        "snippet": "transient contacts between two cells are sufficient to transfer OM materials, proteins and lipids, at high efficiency.",
        "notes": "PMID:23898400, PMC3721248. Scientific Abstract span directly read in Europe PMC XML, not the eLife digest. Selected Results s2-1 to s2-4 and Methods s4-1 to s4-4 were read; actual Figures 2 and 4 were visually inspected with their captions. Engineered Myxococcus xanthus DZ2 reporters and DiO assays distinguish OM material transfer from inner-membrane reporter exchange. Contact and traA controls support the observed endpoint. Dye continuity through some tubes does not establish significant protein transfer through them, which was not detected. Membrane fusion is the authors' mechanistic interpretation; not every contact transfers material. Videos and remaining supplementary panels were not inspected."
      },
      {
        "reference": "DOI:10.1371/journal.pgen.1002626",
        "snippet": "By use of a lipophilic fluorescent dye, we also discovered that OM lipids are exchanged.",
        "notes": "PMID:22511878, PMC3325183. Scientific Abstract directly read in Europe PMC XML; Results s2c/s2d and Methods s4a/s4e/s4f also read. Reporter and DiD experiments in M. xanthus support TraA/TraB dependence in donors and recipients under the tested surface-growth conditions. Liquid and nonmotile-pair controls limit inference from dye labeling alone. Similar domain architecture in mxan_4924 did not yield an overt transfer defect when disrupted; sequence resemblance is not sufficient phenotype evidence. Proposed adhesion, fusion and social roles are not all directly established by this study. Actual panels and strain-table provenance remain uninspected."
      },
      {
        "reference": "DOI:10.1128/jb.00850-13",
        "snippet": "Thus, genetic and environmental conditions that promote OMT production are incongruent with OM exchange.",
        "notes": "PMID:24391054, PMC4011004. Scientific abstract directly retrieved through the Europe PMC core API. Full-text XML retrieval failed, so no full-text or panel verification is claimed. The abstract reports abundant OM tubes in traA/traB mutants and liquid conditions that do not permit transfer. Tube abundance alone is therefore insufficient for this trait; this does not negate the specific dye-conducting connections imaged in 2013. This paper shares investigators with the 2012 study and is not independent-laboratory replication."
      },
      {
        "reference": "DOI:10.1371/journal.pone.0224817",
        "snippet": "Collectively, our results suggest that most mechanisms of interference competition and inter-colony kin discrimination in natural populations of myxobacteria do not require OME.",
        "notes": "PMID:31774841, PMC6880969. Scientific Abstract and Results sec012/sec014 directly read in Europe PMC XML. In the tested natural-isolate pairs, traA disruption or the A60 deletion did not remove colony-merger incompatibility. This is a boundary on ecological-function claims, not evidence that membrane exchange never occurs. The GJV1 control uses swarm inhibition as an inferred OME-dependent toxin readout, not direct fluorescent membrane transfer in every isolate. The directly read correction DOI:10.1371/journal.pone.0228697 (PMID:31999808, PMC6991971) concerns Table 3 typesetting; no Table 3 numerical claim is used here. Actual panels were not visually inspected."
      }
    ],
    "discussions": [
      {
        "discussion_id": "outer-membrane-exchange-scope-and-mapping",
        "prompt": "Keep membrane-component exchange distinct from its possible consequences.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "The endpoint is contact-dependent exchange of outer-membrane material between cells. It is not cytoplasmic fusion, conjugative DNA transfer, all contact-dependent toxin delivery, or a generic secretion phenotype. Exocytosis traitmech:000637 concerns intracellular-compartment fusion-pore discharge; extracellular membrane vesicle production traitmech:000649 concerns extracellular particles. Neither is an exact parent. Cell-free vesicle transfer and slime-trail deposition do not alone demonstrate this contact-qualified class. The traits may coexist; no organism-level disjointness is asserted. Do not require equal bidirectional flux, transfer of every cargo at every contact, cooperation, killing, kin discrimination or fruiting-body development. Retain phenotype METPO:1000059 pending human hierarchy and external-mapping review; no unqualified exact synonym or external equivalence is asserted.",
        "posed_by": "codex",
        "posed_date": "2026-10-06"
      },
      {
        "discussion_id": "outer-membrane-exchange-strain-and-mechanism-grounding",
        "prompt": "Ground strain-specific transfer machinery beyond sequence predictions.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "TraA/TraB dependence and live material transfer are supported, but no accession-resolved universal fusogen pathway is asserted. Before adding causal graphs, resolve protein accessions, inspect remaining supplements and distinguish measured transfer, binding and fusion-model steps. PA14/MYXO-CTERM/OmpA-like sequence features or a traAB annotation alone do not establish the phenotype. Reporter-bearing and deletion strains remain qualified evidence, not unqualified natural exemplars. Natural provenance and direct positive transfer evidence must be paired before adding canonical examples; the 2019 negative kin-discrimination result cannot supply that positive anchor. These are outstanding grounding tasks, not a claim that no mechanism is known.",
        "posed_by": "codex",
        "posed_date": "2026-10-06"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-06T20:54:50Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added contact-dependent outer membrane exchange with four DOI-backed snippets and explicit transfer, tube, ecological-function and sequence-inference boundaries. Ignored-and-hidden duplicate searches and the pinned METPO audit found no exact record. Reserved METPO:1060300 in v526. Deferred unresolved strain/protein grounding; existing records are unchanged.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000642",
    "label": "copiotrophic",
    "definition": "A nutrient adaptation in which an organism thrives in environments with high nutrient concentrations, typically exhibiting rapid growth rates and utilizing diverse carbon sources.",
    "definition_source": "DOI:10.1073/pnas.0903507106",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000731"
    ],
    "synonyms": [
      {
        "synonym_text": "copiotroph",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "created_by": "Jed Dongjin Kim-Ozaeta",
    "evidence": [
      {
        "reference": "DOI:10.1073/pnas.0903507106",
        "snippet": "high (copiotrophic) or low (oligotrophic) nutrient concentrations",
        "notes": "Comparative genomics paper defines copiotrophic growth strategy by high-nutrient adaptation."
      },
      {
        "reference": "DOI:10.1002/bies.1091",
        "snippet": "common in environments with greater nutritional opportunities",
        "notes": "Essay contrasts copiotrophs with oligotrophs in nutrient-rich environments."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:691",
        "taxon_label": "Vibrio natriegens",
        "note": "fast-growing copiotroph",
        "reference": "PMID:27571549"
      },
      {
        "taxon_id": "NCBITaxon:562",
        "taxon_label": "Escherichia coli",
        "note": "nutrient-rich copiotroph",
        "reference": "PMID:38762599"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "copiotrophic_high_nutrient_fast_growth",
        "title": "Copiotrophic high-nutrient rapid-growth strategy",
        "description": "DOI-backed graph linking nutrient-rich environments, regulatory capacity, transport systems, ribosomal capacity, and rapid growth.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This graph summarizes comparative life-history and genomic associations of copiotrophs rather than one concrete molecular mechanism. Its protein-labeled nodes are heterogeneous functional categories or an rRNA copy-number feature, so canonical-taxon and UniProt-example requirements do not apply.",
        "nodes": [
          {
            "node_id": "copiotrophic_trait",
            "label": "copiotrophic",
            "node_type": "TRAIT",
            "grounding": "METPO:1000642",
            "description": "Nutrient adaptation to high-resource environments."
          },
          {
            "node_id": "high_nutrient_environment",
            "label": "high nutrient concentration",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Resource-rich condition favoring copiotrophic growth."
          },
          {
            "node_id": "diverse_carbon_sources",
            "label": "diverse carbon sources",
            "node_type": "CHEMICAL",
            "description": "Multiple available organic substrates."
          },
          {
            "node_id": "membrane_transporters",
            "label": "membrane transporters",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Nutrient-acquisition proteins used during resource pulses.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "This aggregate spans many unrelated transporter families and complexes; the comparative-genomics source does not identify one exact protein entity."
          },
          {
            "node_id": "regulatory_systems",
            "label": "transcription and signal regulation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Regulatory capacity for responding to changing substrates."
          },
          {
            "node_id": "rapid_growth",
            "label": "rapid growth",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Fast biomass accumulation under nutrient-rich conditions."
          },
          {
            "node_id": "genome_size",
            "label": "genome size",
            "node_type": "QUALITY",
            "description": "Total genome length; copiotrophs tend toward larger genomes."
          },
          {
            "node_id": "motility_functions",
            "label": "cell motility functions",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Flagellar/motility capacity enriched in copiotrophic genomes."
          },
          {
            "node_id": "chemotaxis",
            "label": "chemotaxis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Directed movement toward nutrients; enriched in copiotrophs.",
            "grounding": "GO:0006935"
          },
          {
            "node_id": "outer_membrane_secreted_proteins",
            "label": "outer membrane and secreted proteins",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Outer-membrane and extracellular proteins enriched in copiotrophic genomes.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "This comparative functional category combines many unrelated outer-membrane and secreted protein families and has no single exact grounding."
          },
          {
            "node_id": "catabolite_repression",
            "label": "catabolite repression / dynamic transcriptional regulation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Regulatory mechanism reallocating proteome under nutrient upshift."
          },
          {
            "node_id": "proteome_reallocation",
            "label": "proteome reallocation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Dynamic reallocation of proteome sectors under changing nutrients."
          },
          {
            "node_id": "ribosome_synthesis",
            "label": "ribosome synthesis / biogenesis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Maximizing ribosome synthesis in favorable conditions for fast growth."
          },
          {
            "node_id": "minimum_doubling_time",
            "label": "minimum doubling time",
            "node_type": "QUALITY",
            "description": "Shortest doubling time; shorter values indicate copiotrophic lifestyle."
          }
        ],
        "edges": [
          {
            "subject": "high_nutrient_environment",
            "predicate": "selects for",
            "object": "copiotrophic_trait",
            "description": "Copiotrophs grow optimally in high-nutrient environments.",
            "evidence": [
              {
                "reference": "DOI:10.1073/pnas.0903507106",
                "snippet": "high (copiotrophic) or low (oligotrophic) nutrient concentrations",
                "notes": "Supports high nutrient concentration as the environmental driver."
              }
            ],
            "predicate_id": "METPO:2007401"
          },
          {
            "subject": "copiotrophic_trait",
            "predicate": "uses substrate pool",
            "object": "diverse_carbon_sources",
            "description": "Copiotrophs exploit diverse carbon sources under nutrient-rich conditions.",
            "evidence": [
              {
                "reference": "DOI:10.1073/pnas.0903507106",
                "snippet": "grow optimally at either high",
                "notes": "Supports growth strategy tied to resource-rich habitats."
              }
            ]
          },
          {
            "subject": "copiotrophic_trait",
            "predicate": "associated with",
            "object": "membrane_transporters",
            "description": "Copiotrophic genomes encode energetically costly nutrient acquisition systems.",
            "evidence": [
              {
                "reference": "DOI:10.1073/pnas.0903507106",
                "snippet": "use energetically expensive transporters",
                "notes": "Supports transporter investment as a genomic feature of copiotrophy."
              }
            ],
            "predicate_id": "biolink:associated_with"
          },
          {
            "subject": "copiotrophic_trait",
            "predicate": "associated with",
            "object": "regulatory_systems",
            "description": "Copiotrophs have regulatory capacity to respond to resource pulses.",
            "evidence": [
              {
                "reference": "DOI:10.1073/pnas.0903507106",
                "snippet": "regulate metabolism",
                "notes": "Supports regulatory systems as part of copiotrophic adaptation."
              }
            ],
            "predicate_id": "biolink:associated_with"
          },
          {
            "subject": "rapid_growth",
            "predicate": "characteristic of",
            "object": "copiotrophic_trait",
            "description": "Rapid growth is a characteristic outcome of copiotrophic strategy.",
            "evidence": [
              {
                "reference": "DOI:10.1002/bies.1091",
                "snippet": "Bacteria can grow rapidly",
                "notes": "Supports rapid growth as part of the copiotroph/oligotroph contrast."
              }
            ]
          },
          {
            "subject": "genome_size",
            "predicate": "associated with",
            "object": "copiotrophic_trait",
            "description": "Larger genome size is associated with the copiotrophic strategy.",
            "evidence": [
              {
                "reference": "DOI:10.1093/ismeco/ycae081",
                "notes": "Copiotrophs had larger genomes versus oligotrophs (curate as association)."
              },
              {
                "reference": "DOI:10.1073/pnas.0903507106",
                "notes": "Comparative genomics: copiotrophs show larger genomes than oligotrophs."
              }
            ],
            "predicate_id": "biolink:associated_with"
          },
          {
            "subject": "copiotrophic_trait",
            "predicate": "associated with",
            "object": "motility_functions",
            "description": "Copiotrophic genomes are enriched in cell motility functions.",
            "evidence": [
              {
                "reference": "DOI:10.1073/pnas.0903507106",
                "notes": "Cell motility (COG category N) high in copiotrophs vs low in oligotrophs."
              }
            ],
            "predicate_id": "biolink:associated_with"
          },
          {
            "subject": "copiotrophic_trait",
            "predicate": "associated with",
            "object": "chemotaxis",
            "description": "Copiotrophic genomes are enriched in chemotaxis genes/proteins.",
            "evidence": [
              {
                "reference": "DOI:10.1093/ismeco/ycae081",
                "notes": "Oligotrophs under-represented in chemotaxis/motility; copiotrophs enriched."
              }
            ],
            "predicate_id": "biolink:associated_with"
          },
          {
            "subject": "copiotrophic_trait",
            "predicate": "associated with",
            "object": "outer_membrane_secreted_proteins",
            "description": "Copiotrophic genomes encode more outer-membrane and secreted proteins.",
            "evidence": [
              {
                "reference": "DOI:10.1073/pnas.0903507106",
                "notes": "More outer-membrane and secreted proteins in copiotrophs."
              }
            ],
            "predicate_id": "biolink:associated_with"
          },
          {
            "subject": "catabolite_repression",
            "predicate": "enables",
            "object": "proteome_reallocation",
            "description": "Catabolite repression and dynamic transcriptional regulation enable proteome reallocation under nutrient upshift.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-024-48591-9",
                "notes": "Strong transcriptional regulation (e.g. catabolite repression) dynamically reallocates proteome sectors."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "ribosome_synthesis",
            "predicate": "promotes",
            "object": "rapid_growth",
            "description": "Proteome allocation maximizing ribosome synthesis in favorable conditions promotes rapid growth.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-024-48591-9",
                "notes": "Achieve rapid growth via maximizing ribosome synthesis during favorable conditions."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "minimum_doubling_time",
            "predicate": "indicates",
            "object": "copiotrophic_trait",
            "description": "Shorter minimum doubling time indicates a more copiotrophic lifestyle.",
            "evidence": [
              {
                "reference": "DOI:10.1093/ismeco/ycae081",
                "notes": "Minimum doubling times shorter in genomes from more copiotrophic environments."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-08-24T14:00:00-07:00",
        "curator": "codex",
        "action": "REVIEWED_CAUSAL_GRAPH_PROTEIN_TAXON",
        "changes": "Classified the graph as nonmechanistic comparative life-history evidence and documented the three aggregate protein-labeled nodes as reviewed label-only; no trait record or graph was deprecated or removed.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-05T01:35:46.873168+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-09T00:00:00-07:00",
        "curator": "Codex",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed copiotrophy graph for nutrient-rich environments, transport/regulatory capacity, rRNA operons, and rapid growth.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T05:49:25Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:associated_with\u00d72).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T21:30:07Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007401\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:19Z",
        "curator": "claude",
        "action": "RENAME_PREDICATE_LABELS",
        "changes": "Renamed 1 causal-edge predicate label(s) to align with existing groundings: supports \u2192 enables \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:22Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 7 evidence-backed generic edges (8 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:14Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 6 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:associated_with\u00d74, RO:0002327\u00d71, RO:0002213\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:34Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0006935\u00d71).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000707",
    "label": "cue-triggered environmental anticipation",
    "definition": "A physiological phenotype in which exposure to an environmental cue induces changes that prepare a microorganism for a distinct, temporally associated environmental condition before that condition occurs.",
    "definition_source": "DOI:10.1038/nature08112",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/nature08112",
        "snippet": "early stimuli pre-induce genes that would be needed for later ones, yet later stimuli only induce genes needed to cope with them.",
        "notes": "Mitchell et al. 2009, PMID:19536156; scientific abstract, checked against publisher and source-qualified MED text. Main Figures 2-3 and supplementary Figures 3 and 6 were visually inspected, with their relevant Methods and control explanations. MG1655 sugar-switch assays distinguish early induction from subsequent growth; glycerol normalization and residual-sugar controls matter. Loss of the association in laboratory-evolved strains concerns selection across generations, not cognitive learning. Ecological explanations remain author interpretations. Not all raw data were reanalyzed."
      },
      {
        "reference": "DOI:10.1038/nmicrobiol.2017.84",
        "snippet": "Here, we identify a metabolic adaptation that is triggered upon entry into hypoxia-induced quiescence but facilitates subsequent cell cycle re-entry.",
        "notes": "Eoh et al. 2017, PMID:28530656, PMC5540153; scientific abstract, checked against publisher and source-qualified MED text. The abstract and qualitative main-text framing support metabolically encoded preparation, with hypoxia preceding re-aeration in the studied Mycobacterium tuberculosis system. This is not evidence for a universal transcriptional mechanism or an in-vivo demonstration of anticipation. Figures, supplements and raw data were not independently assessed; no molecular causal edges are asserted."
      }
    ],
    "discussions": [
      {
        "discussion_id": "anticipation-scope-and-hierarchy",
        "prompt": "Retain cue-dependent preparation without conflating neighboring temporal-response traits.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "The cue-triggered qualifier is deliberate: solely clock-driven preparation or constitutive readiness is insufficient. Evidence must link the preceding cue to preparation for a different later condition; correlated expression or cross-protection alone does not establish that interpretation. Generic stress response, stochastic bet hedging, carbon-source memory and diauxic growth are not exact synonyms, although particular observations can overlap. Neither cognition nor learning within an individual's lifetime is required; evolutionary regulatory wiring is compatible. No universal benefit, fixed delay, asymmetric response or single mechanism is required. METPO:1000731 nutrient adaptation is locally framed as chronic copiotroph/oligotroph trophic adaptation, not this cue-to-future-condition phenotype. METPO:1000059 phenotype is the conservative parent pending upstream hierarchy review. This is an organismal disposition, not a sequence feature, regulatory site or precomposed chemical-use assertion.",
        "posed_by": "codex",
        "posed_date": "2026-10-12"
      },
      {
        "discussion_id": "anticipation-evidence-and-mechanism-limits",
        "prompt": "Resolve assay-specific mechanisms, natural strain provenance and broader terminology before extending the record.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "No canonical_examples, causal_graphs, exact synonyms or xrefs are asserted. The studies do not establish a uniform species-wide phenotype or a common protein mechanism; strain provenance and authority-resolved taxa require further review. Source-qualified MED, Crossref and visible publisher notice links were checked on 2026-10-12; their commentary/review links are not corrections or independent experiments. No correction or retraction was exposed for the two retained papers in these bounded checks. The separate Tagkopoulos 2008 lead (DOI:10.1126/science.1154456) is not counted evidence: its main PMC text was readable, but the indexed 9 June 2008 supplement correction could not be directly inspected. Broad environmental anticipation and adaptive prediction are not assumed exactly equivalent to this qualified class. No exact candidate was found in the pinned/current METPO RDF and ignored/hidden novelty searches; the pinned ontology remains unchanged.",
        "posed_by": "codex",
        "posed_date": "2026-10-12"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-12T05:07:15Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added cue-triggered environmental anticipation with two primary DOI-backed sources and directly checked scientific-abstract snippets. Reserved 000707, v583 and 1066000-1066099 after ignored/hidden worktree and pending-PR checks. Scope, mechanism, provenance and source-access limits are explicit. Existing traits unchanged; timestamp is the observed UTC curation decision.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000147",
    "label": "cystine arylamidase activity",
    "definition": "A physiological enzyme-activity phenotype in which a cell produces active cystine arylamidase enzymes that hydrolyze cystine arylamide substrates.",
    "definition_source": "DOI:10.14202/vetworld.2024.143-149",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.14202/vetworld.2024.143-149",
        "snippet": "Cystine arylamidase 7.5 L-cystyl-2-naphthylamide",
        "notes": "Ludfiani et al. list L-cystyl-2-naphthylamide as the API ZYM cystine arylamidase substrate, grounding the organism-level phenotype as an arylamide-hydrolyzing enzyme activity."
      },
      {
        "reference": "DOI:10.3389/fmicb.2022.1034816",
        "snippet": "Positive alkaline phosphatase, cystine arylamidase, esterase(C4), esterase lipase(C8), leucine arylamidase, naphthol-AS-B1-phosphohydrolase, valine arylamidase",
        "notes": "Jiang et al. detected cystine arylamidase in the Geminicoccus harenae type strain with the API ZYM enzyme activity panel."
      },
      {
        "reference": "DOI:10.2323/jgam.60.59",
        "snippet": "In API ZYM, activities are positive for alkaline phosphatase, esterase (C4), leucine arylamidase, valine arylamidase, cystine arylamidase",
        "notes": "An et al. reported cystine arylamidase among positive API ZYM activities for the Flavobacterium panaciterrae DCY69T type strain."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:2498453",
        "taxon_label": "Geminicoccus harenae",
        "note": "Jiang et al. reported Geminicoccus harenae as positive for cystine arylamidase in the API ZYM enzyme activity panel.",
        "reference": "DOI:10.3389/fmicb.2022.1034816"
      }
    ],
    "discussions": [
      {
        "discussion_id": "cystine-arylamidase-activity-xref-gap",
        "prompt": "Resolve an exact external ontology class for cystine arylamidase activity before adding a TraitRecord xref.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "GO:0004177 covers aminopeptidase activity at molecular-function scope and no live GO class provides an exact residue-specific cystine arylamidase production phenotype at organism-level scope.",
        "posed_by": "codex",
        "posed_date": "2026-09-11"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-11T19:19:57Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted cystine arylamidase activity as a DOI-backed TraitRecord after a repository-wide duplicate review covering ignored and hidden files; METPO has no exact cystine arylamidase activity class yet.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000623",
    "label": "cytogamy",
    "definition": "A sexual-reproduction phenotype in which a paired cell self-fertilizes by fusion of its own gametic nuclei without exchanging gametic nuclei with its partner.",
    "definition_source": "DOI:10.1017/S0016672300010740",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000625"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1017/S0016672300010740",
        "snippet": "Cytogamy is a process of internal self-fertilization in animals which appear to conjugate, but which in fact do not exchange nuclei",
        "notes": "Nobili and Luporini (1967), PMID:4964874, p.39 parenthetical before the Wichterman citation, checked in the typeset PDF. This directly read definition supports paired-cell internal self-fertilization without nuclear exchange. The surrounding Results and Table 2 offer cytogamy as an explanation for three mating-type outlier clones; they do not directly demonstrate cytogamy in those clones. The paper's primary experiments concern autogamy in Euplotes minuta. Do not count this terminology passage as independent experimental replication or turn its proposed explanation into a canonical taxon example. The cited 1940 original was not read beyond bibliographic metadata."
      },
      {
        "reference": "DOI:10.1111/j.1550-7408.1958.tb02567.x",
        "snippet": "In fact, the conjugation process seems to be one of double autogamy (cytogamy), rather than of reciprocal gametic interchange.",
        "notes": "Diller (1958), scientific abstract directly read on the Wiley publisher page. The qualifier seems is retained. Paired Paramecium polycaryum cultures collected at Annamalainagar, South India, showed nuclear behavior resembling autogamy in singles. Breakdown of the paroral cones permitting micronuclear passage was not observed; this is not a genetic exclusion of exchange. The abstract also describes fertilization and postzygotic nuclear reorganization. Double autogamy is source-attributed terminology, not equivalence with our unpaired-cell autogamy class. Full text, actual figures and tables were not inspected; the tentative observation is not an unqualified canonical example."
      },
      {
        "reference": "DOI:10.1093/genetics/91.4.657",
        "snippet": "cytogamy generates exconjugant clones that derive their entire genetic information from a single meiotic product of their cytoplasmic parent.",
        "notes": "Orias and Hamilton (1979), PMID:17248904, PMC1216858, scientific abstract clause after By analogy to Paramecium, directly checked in Europe PMC core metadata and NCBI PMC EFetch front-matter XML. The abstract reports hyperosmotic-shock-induced cytogamy in tested Tetrahymena thermophila strains and high fertility in most progeny. Its whole-genome-homozygote interpretation is source-specific, not a universal definition requirement or a genome-sequencing result established here. Other rare transmission abnormalities were not characterized in that abstract. The full text, Methods, actual figures and tables remain unread: PMC EFetch withholds body XML, and attempted public PDF retrieval did not yield a readable PDF. Strain provenance is unresolved; no natural canonical example or protein-level causal mechanism is inferred from this abstract."
      }
    ],
    "discussions": [
      {
        "discussion_id": "cytogamy-scope-and-hierarchy",
        "prompt": "Distinguish paired-cell self-fertilization from unpaired autogamy.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Pairing with internal gametic-nuclear fusion and no gametic-nuclear exchange distinguishes this class from ordinary conjugation with exchange and from operationally unpaired autogamy traitmech:000622. Diller (1958) calls the tentative observation double autogamy; preserve that broader source usage without silently making cytogamy a child or exact synonym of the unpaired class. This is not all selfing or a literal mating locus. No universal hyperosmotic trigger, whole-genome homozygosity, nuclear count or inability to outcross is imposed. Do not infer species-level disjointness between reproductive modes. The parent gap is resolved by automixis traitmech:000625, whose single-meiotic-cell nuclear origin includes this operational scope. The broader terminology and mapping questions keep this discussion OPEN. Verify external equivalences and synonym scope before adding mappings.",
        "posed_by": "codex",
        "posed_date": "2026-10-05"
      },
      {
        "discussion_id": "cytogamy-mechanism-and-provenance",
        "prompt": "Resolve original cytology, strain provenance and molecular mechanisms.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "The 1967 definitional passage is not a direct cytogamy experiment, the 1958 observation is tentative, and the 1979 evidence here is limited to its scientific abstract. Retrieve the original primary study DOI:10.1002/jmor.1050660303 (Wichterman, 1940) and the remaining experimental material before stronger cytological or natural-strain claims. That 1940 DOI is a metadata-verified research lead, not counted trait evidence. No canonical example is assigned from unresolved provenance or tentative marker explanations. Induced transmission outcomes do not identify a molecular causal pathway; graphs and protein accessions remain deferred. Retain actual snippet-resolver outcomes separately from direct source checks.",
        "posed_by": "codex",
        "posed_date": "2026-10-05"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-05T16:16:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added cytogamy with three DOI-backed snippets and paired-cell self-fertilization scope. Ignored-and-hidden novelty/allocation checks found no exact record or collision. Reserved METPO:1057600 in v499 under phenotype, not operational unpaired autogamy. Preserved tentative observations, induced-system and source-access limits; deferred canonical examples, mappings and causal graphs.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-05T16:19:43Z",
        "curator": "codex",
        "action": "QUALIFIED_TRAIT_SCOPE",
        "changes": "Addressed #1717: replaced without reciprocal exchange with no gametic-nuclear exchange with the partner, excluding one-way transfer as well. Used an individual paired-cell formulation without requiring the same outcome in both partners. Preserved all evidence, source qualifiers and the phenotype parent.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-05T18:20:28Z",
        "curator": "codex",
        "action": "RESOLVED_PARENT_GAP",
        "changes": "Reparented below automixis traitmech:000625 and documented the resolved parent gap while retaining other open terminology and mapping questions. Preserved definition, evidence, examples and prior history. v501 carries the existing proposed METPO ID with this hierarchy; earlier standalone templates remain historical.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000691",
    "label": "diatom frustule production",
    "definition": "A biomineralization phenotype in which a diatom forms the siliceous valve and girdle-band elements of its cell wall (frustule).",
    "definition_source": "DOI:10.1007/s00709-017-1199-4",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000690"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1007/s00709-017-1199-4",
        "snippet": "The basic stages of frustule morphogenesis characteristic of raphid pennate diatoms have been traced",
        "notes": "Bedoshvili et al., journal issue May 2018, online 2017-12-21, PMID:29270874. Scientific Abstract directly read at https://pubmed.ncbi.nlm.nih.gov/29270874/ and in Europe PMC CORE on 2026-10-10 using EXT_ID:29270874 AND SRC:MED; exact ID, source, title and DOI checked together. The abstract defines frustule components as silica valves and girdle bands and reports microscopy of morphogenesis in Encyonema ventricosum under the source name. This supports formation, not just an isolated shell's presence. Cytoskeletal proximity is not functional necessity. Full text, Methods, actual figures and supplements were not inspected; no canonical taxon or universal membrane-release mechanism is inferred."
      },
      {
        "reference": "DOI:10.1038/s41467-024-52211-x",
        "snippet": "A diatom cell wall consists of two types of building blocks: two plate-shaped valves and several ring-shaped girdle bands.",
        "notes": "Aram et al. 2024, PMID:39251596, PMC11385223, Introduction. Scientific Abstract, Introduction, Results, Discussion and Methods directly read in official Europe PMC full-text XML on 2026-10-10; actual Figure 2 inspected, other actual figures and supplements unread. Source-qualified CORE lookup EXT_ID:39251596 AND SRC:MED confirmed ID, source, title and DOI. Silicon-starved CCMP1335 cultures were resupplied and imaged during valve formation. Figure 2 orders different cells by inferred maturation, not a live-cell time series. The paper retains historical Thalassiosira pseudonana naming while noting Cyclotella nana; this is not a current taxonomy assignment. Structural correlations support a membrane-mold hypothesis, not proven contact-site function or a universal molecular mechanism. The quote defines wall elements; the Results provide the production observations."
      }
    ],
    "discussions": [
      {
        "discussion_id": "diatom-frustule-production-scope-and-mappings",
        "prompt": "Keep frustule-element formation distinct from possession and other silica traits.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Use biomineralization traitmech:000690 as the broader phenotype because this endpoint entails formation of mineral cell-wall elements. It is not a material frustule, generic silicification, silica uptake, retention of an inherited valve or adsorption of preformed silica. Production of new wall elements does not require both valves to be synthesized anew in one cell cycle or every element to be formed simultaneously. Keep valve/girdle formation distinct from silica scales, auxospore coverings and setae; their observation alone does not establish this endpoint. The existing scale-production scope note distinguishes these phenotypes and is not an unresolved exact grounding. Do not infer organism-level disjointness or a universal geometry, cell-cycle schedule or fitness effect. Exact synonyms and external phenotype mappings remain unasserted pending authority review; process and material terms are not exact equivalents.",
        "posed_by": "codex",
        "posed_date": "2026-10-10"
      },
      {
        "discussion_id": "diatom-frustule-production-exemplars-and-mechanisms",
        "prompt": "Resolve assay-strain provenance and production-specific causal evidence.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "No canonical examples are assigned before reconciling study strains, collection provenance and current taxonomy. The two studies support wall-element formation but do not establish a conserved protein mechanism. The contact-site transport model and actin-associated expansion in Aram et al. remain proposals; unobserved vesicle fusion is not proof of its absence. Separate silica deposition, shaping, exocytosis and wall assembly when evaluating perturbation evidence. Functional evidence and taxon-paired accessions are required for protein edges; sequence features alone are insufficient. Mechanism is deferred, not claimed absent, and no universal intracellular route is imposed on all diatom silica structures.",
        "posed_by": "codex",
        "posed_date": "2026-10-10"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-10T20:14:43Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added diatom frustule production beneath biomineralization with two primary DOI citations and directly checked short snippets. Ignored-and-hidden main/worktree/open-PR reservation checks support 000691 and v567 block 1064400-1064499. Existing trait records unchanged; mappings, canonical taxa and mechanisms remain open. Timestamp records the observed UTC curation decision.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000693",
    "label": "diatom perizonium production",
    "definition": "A biomineralization phenotype in which a diatom produces the siliceous band system called the perizonium in an auxospore wall.",
    "definition_source": "DOI:10.1371/journal.pone.0272778",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000690"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1371/journal.pone.0272778",
        "snippet": "The deposition of the primary TP band became evident when the auxospore center attained a slim and rigid appearance.",
        "notes": "Kaczmarska et al. 2022, PMID:36067191, PMC9447881, Results: Epizonium and perizonium. TP means transverse perizonium. Scientific Abstract, Introduction, Methods, early Results, this subsection and Discussion: Auxospore structure and development read in official Europe PMC XML on 2026-10-10; actual Figure 11 inspected. Other actual figures and S1 Appendix unread. EXT_ID:36067191 AND SRC:MED confirmed ID, title, DOI and scientific abstract. Clone HK328 (= ECT3902) originated from Florida Bay material in 2011; atypical morphology and prolonged cultivation limit canonical assignment. PDMPO labels silica deposited after addition. SEM resolves inner TP/LP bands apart from initial valves; fixed images do not establish live kinetics. Authors leave some epizonium/perizonium layer boundaries uncertain. Scaly-band architecture and proposed shape control are not universal or demonstrated necessities."
      },
      {
        "reference": "DOI:10.1371/journal.pone.0181413",
        "snippet": "transverse perizonial bands produced all together or in quick succession rather than being added to the auxospore apex one at a time",
        "notes": "Kaczmarska et al. 2017, PMID:28813426, PMC5558960, scientific Abstract; EXT_ID:28813426 AND SRC:MED confirmed identity. Abstract, Methods prose, Results: Auxospore wall fine structure, related Discussion paragraphs and actual Figure 5 read on 2026-10-10. Table 1/2 headers, footnotes and StA:7/8 and Van5:5/6 rows inspected; other rows not fully interpreted. Other actual figures and supplements unread. Fixed stages support the authors' inferred collapsible-cup sequence, not a live secretion time course. No longitudinal perizonia found under their structural criterion; initial epivalves must be distinguished. Discussion retains the Tabularia fasciculata study (reference 100); reinterpretation targets other papers. Aged small cultures, original isolates and progeny are distinct; culture abnormalities do not define canonical morphology."
      },
      {
        "reference": "DOI:10.1016/j.ejop.2013.06.002",
        "snippet": "Silica precipitation began throughout the auxospore at or near maximal length, but initially was detectable in isolated regions throughout the structure.",
        "notes": "Mather et al., online 2013-08-22, 2014 issue, PMID:23972513. Complete scientific Abstract directly read in official Europe PMC CORE on 2026-10-10 using EXT_ID:23972513 AND SRC:MED; one exact MED result with matching ID, title and DOI. Tabularia fasciculata under the source name lacked transverse perizonium; longitudinal deposition preceded initial valves near maximal auxospore length. Undetectable silicon by EDS is not absolute absence. Publisher full text unavailable; Methods, actual figures and supplements unread. These three primary studies have overlapping authors, not independent-laboratory replication."
      }
    ],
    "discussions": [
      {
        "discussion_id": "diatom-perizonium-production-scope-and-mappings",
        "prompt": "Resolve exact mappings without conflating auxospore wall components.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Biomineralization traitmech:000690 is strictly broader. This is production, not a material band, inherited band possession, silica uptake, or auxosporulation alone. Incunabular scales, epizonium, initial valve/girdle frustules and setae are not automatically this endpoint. Scaly bands in mediophytes do not justify universal parenting to siliceous scale production. Existing frustule/seta boundary notes are not unresolved exact perizonium groundings. No requirement for both transverse and longitudinal bands, a single geometry, one-at-a-time secretion, deposition during expansion, or sexual origin is imposed. No organism-level disjointness or fitness effect is asserted. Exact synonyms, properizonium terminology and external phenotype equivalences remain unasserted pending authority review; structure terms are not automatically phenotype xrefs.",
        "posed_by": "codex",
        "posed_date": "2026-10-10"
      },
      {
        "discussion_id": "diatom-perizonium-production-exemplars-and-mechanisms",
        "prompt": "Resolve canonical study material and formation-specific causal evidence.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "No canonical examples are assigned: source clone origins were read, but current taxonomy and figure-to-mating-pair attribution need reconciliation, including atypical or aged cultures. Keep mineral deposition, band patterning and shape control separate. Static microscopy, PDMPO/EDS observations and sequence features alone do not establish a conserved causal protein mechanism or necessity for shape control. Protein edges require functional evidence and taxon-paired accessions. Mechanism is deferred, not claimed absent.",
        "posed_by": "codex",
        "posed_date": "2026-10-10"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-10T23:15:32Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added diatom perizonium production beneath biomineralization with three primary DOI citations and directly checked short snippets. Ignored-and-hidden main/worktree/open-PR reservation checks support 000693 and v569 block 1064600-1064699. Existing trait records unchanged; mappings, canonical taxa and mechanisms remain open. Timestamp records the observed UTC curation decision.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000692",
    "label": "diatom seta production",
    "definition": "A biomineralization phenotype in which a diatom forms siliceous whisker-like cell-wall extensions called setae.",
    "definition_source": "DOI:10.1038/s41467-021-24944-6",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000690"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/s41467-021-24944-6",
        "snippet": "A striking example for such long elements are whisker-like extensions, called setae, which characterize the genus Chaetoceros",
        "notes": "Mayzel et al. 2021, PMID:34330922, PMC8324917, Introduction. Scientific Abstract, Introduction, Results, Discussion, Methods, main figure captions and Table 1 read in official Europe PMC full-text XML on 2026-10-10; actual Figures 2, 3 and 5 inspected. Other actual figures, supplements and movies remain unread. EXT_ID:34330922 AND SRC:MED confirmed the scientific abstract, ID, source, title and DOI. The quote identifies the structures; Results report seta formation in Chaetoceros tenuissimus under the source name. Figure 2 PDMPO labeling at growing tips supports new silica deposition, not only inherited appendage possession. Figure 3 resolves membrane, silica and an external organic layer; this supports a proposed extracellular route, not universal absence of a silica deposition vesicle. Figure 5 scores silicon limitation per cell, but germanium/PDMPO inhibition per valve; these denominators are not interchangeable. New valves still form under the germanium treatment, with altered texture, so valves are not claimed unaffected. No universal concentration threshold, growth rate or molecular necessity is inferred."
      },
      {
        "reference": "DOI:10.1016/j.jsb.2025.108205",
        "snippet": "Here, we study a relatively large species, Chaetoceros rostratus, that forms long and intricate setae.",
        "notes": "Safadi et al. 2025, PMID:40294667, online 2025-04-26, June issue. Complete scientific Abstract directly read in source-qualified Europe PMC CORE on 2026-10-10 using EXT_ID:40294667 AND SRC:MED; one exact MED result with matching ID, title and DOI. The abstract reports in-cell cryo-electron tomography during seta formation in Chaetoceros rostratus under the source name and describes an organic sheath covering newly formed silica outside the plasma membrane. Structural macromolecules might regulate architecture; their necessity is not demonstrated by this abstract. Full Methods, actual figures and supplements were not inspected. This is a distinct primary study with overlapping authors, not independent-laboratory replication. No current taxon or strain provenance is assigned from the abstract alone."
      }
    ],
    "discussions": [
      {
        "discussion_id": "diatom-seta-production-scope-and-mappings",
        "prompt": "Keep seta formation distinct from possession and other silica endpoints.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Biomineralization traitmech:000690 is the broader phenotype: formation of these siliceous extensions entails mineral formation. A material seta, inherited appendage, silica uptake or adsorption is not this production phenotype. Valve/girdle formation (traitmech:000691), siliceous scales and auxospore coverings alone do not establish seta production, nor do setae alone establish those other endpoints. The existing frustule scope note already distinguishes setae; it is not an unresolved exact grounding. No organism-level disjointness, universal seta number, length, geometry, cell-cycle coupling, buoyancy or fitness effect is asserted. The extracellular route is not definitional. Exact synonyms and external phenotype mappings remain unasserted pending authority review; generic bristles, spines, silica processes and material structures are not automatically equivalent to this diatom phenotype.",
        "posed_by": "codex",
        "posed_date": "2026-10-10"
      },
      {
        "discussion_id": "diatom-seta-production-exemplars-and-mechanisms",
        "prompt": "Resolve study-strain provenance and formation-specific causal evidence.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "No canonical examples are assigned before checking collection provenance and current taxonomy. The two studies support seta formation, but structural localization alone does not establish a conserved protein mechanism. Microtubule pushing, a guiding organic scaffold and a diffusion-based silicon route remain hypotheses in Mayzel et al.; unobserved vesicle transport is not proof of its absence. Separate mineral deposition, shape control and organic-sheath assembly when evaluating functional perturbations. Protein edges require direct causal evidence and taxon-paired accessions; sequence features alone are insufficient. Mechanism is deferred, not claimed absent.",
        "posed_by": "codex",
        "posed_date": "2026-10-10"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-10T21:53:42Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added diatom seta production beneath biomineralization with two primary DOI citations and directly checked short snippets. Ignored-and-hidden main/worktree/open-PR reservation checks support 000692 and v568 block 1064500-1064599. Existing trait records unchanged; mappings, canonical taxa and mechanisms remain open. Timestamp records the observed UTC curation decision.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000704",
    "label": "diauxic growth",
    "definition": "A physiological phenotype in which a microbial population exhibits two successive growth phases associated with a switch from preferential use of one nutrient source to use of another as the first becomes limiting.",
    "definition_source": "DOI:10.1371/journal.pone.0061686",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "synonyms": [
      {
        "synonym_text": "diauxie",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1128/jb.164.2.866-871.1985"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1371/journal.pone.0061686",
        "snippet": "However, a significant fraction of cells maintains a high rate of elongation and displays no detectable growth lag during the shift.",
        "notes": "Boulineau et al. 2013, PMID:23637881, PMC3640066; scientific abstract. Introduction defines diauxic growth by sequential carbon-source use, supporting the definition's nutrient-switching differentia. Relevant Results, Discussion, Methods, actual Figure 2 and Text S1 prose were inspected. AB460 is an engineered MG1655 derivative; single-cell medium exchange is not the same assay as mixed-substrate batch growth. Population lag does not imply arrest of every cell. Contaminant-supported growth and model assumptions remain relevant. Text S1 DOC extraction loses embedded equations; no equation was visually verified or used as a curated mechanistic claim."
      },
      {
        "reference": "DOI:10.1128/jb.164.2.866-871.1985",
        "snippet": "Azotobacter vinelandii exhibited diauxie when grown in a medium containing both acetate and glucose as carbon sources.",
        "notes": "George et al. 1985, PMID:3863813, PMC214331; directly retrieved source-qualified MED abstract only. Acetate preference in this experiment contradicts a universal glucose-first requirement and supports the lexical name diauxie. Full paper and figures were not inspected; a full-text XML endpoint returned HTTP 500. This access failure is not evidence that full text does not exist."
      },
      {
        "reference": "DOI:10.1128/jb.01571-06",
        "snippet": "Following recovery of growth on the alternative carbon or nitrogen source, RpoS protein concentrations declined rapidly to a basal level.",
        "notes": "Sandercock and Page 2008, PMID:18055600, PMC2223558; scientific abstract. Relevant Methods/Results and actual Figure 3 support UW batch-culture acetate/glucose and ammonium/N2 transitions. This supports nutrient-source scope rather than sugars or carbon alone. Ammonium augmentation addresses an oxygen-limitation alternative for the stress response. RpoS dynamics are not a universal causal mechanism of diauxie; later PHB consumption was explicitly unmeasured. Publisher text and Figure 3 were accessible despite requests HTML 403 and Europe PMC XML 500 responses."
      },
      {
        "reference": "DOI:10.1371/journal.pbio.1002041",
        "snippet": "many natural isolates of Saccharomyces cerevisiae display short or nonexistent diauxic lags when grown in mixtures of glucose (preferred) and galactose.",
        "notes": "Wang et al. 2015, PMID:25626068, PMC4308108; scientific abstract, not the XML's preceding TOC teaser or separate Author Summary. Relevant Results, growth-curve Methods, actual Figure 1 and S1 EPS were inspected. Operational zero lag means the smoothed growth-rate curve has no local minimum, not simultaneous equal use of both substrates. Natural-origin growth panels and engineered reporter derivatives require separate provenance. Figure 1 caption says eleven strains but the image has twelve labels; no strain count is inferred here. The observations oppose mandatory positive lag."
      },
      {
        "reference": "DOI:10.1038/msb.2013.11",
        "snippet": "Once glucose is depleted, the cells consume the earlier produced ethanol",
        "notes": "Zampar et al. 2013, PMID:23549479, PMC3693829; Introduction, second paragraph, not an abstract quote. Relevant Results, culture and measurement Methods and actual Figure 1 were inspected. FY4 was initially supplied glucose and later consumed produced ethanol; the definition therefore does not require both nutrients to be supplied initially. Figure 1 distinguishes concentration observations from fitted rates. Intracellular flux ranges are model-constrained, not direct flux measurements; raw supplemental data and the full mechanistic analysis were not reanalyzed."
      }
    ],
    "discussions": [
      {
        "discussion_id": "diauxie-scope-and-hierarchy",
        "prompt": "Retain sequential nutrient use without imposing a universal lag or regulatory mechanism.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Boulineau's Introduction defines sequential carbon use, while lag-emphasizing accounts operationalize a narrower growth-curve pattern. Wang reports short or nonexistent lags; Sandercock and Page extend the observed scope to nitrogen-source transitions. The present definition uses the nutrient-switching sense and does not require glucose preference, a positive minimum lag, complete arrest of every cell or strictly zero secondary-substrate use. An arbitrary biphasic growth curve without nutrient-switching evidence is insufficient. Diauxic shift denotes the transition; polyauxie and unqualified diphasic growth are not exact synonyms. METPO:1000731 nutrient adaptation is a trophic-type class whose local record operationalizes chronic copiotroph/oligotroph nutrient regimes, not this temporal pattern. Phenotype is the conservative parent pending upstream hierarchy review. Generalist and specialist denote niche breadth; dormancy, carbon catabolite repression and generic resource-use predicates are not exact equivalents.",
        "posed_by": "codex",
        "posed_date": "2026-10-11"
      },
      {
        "discussion_id": "diauxie-provenance-and-mechanism",
        "prompt": "Ground conditional examples and taxon-specific mechanisms before adding canonical taxa or a graph.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "The studies include laboratory strains and engineered reporter derivatives. No natural canonical example is asserted without primary strain provenance and authority-resolved taxon identity. No shared universal molecular mechanism or taxon-paired protein branch is established here. Gene presence, lac-locus annotation, RpoS expression or predicted flux alone cannot establish observed diauxic growth. It is conditional on culture and nutrients, not a fixed species identity or sequence-feature trait. Qualified MED and Crossref metadata for all five sources exposed no linked correction or retraction at the 2026-10-11 check; available primary pages were also inspected. This bounded check does not guarantee absence of notices; Wang's preprint link is not a correction. Canonical examples, causal graphs and external equivalences remain unasserted rather than being inferred from these observations.",
        "posed_by": "codex",
        "posed_date": "2026-10-11"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-11T23:42:36Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added diauxic growth with five primary DOI-backed sources and directly checked snippets. Reserved 000704, v580 and 1065700-1065799 after ignored/hidden worktree and pending-PR checks. Sequential nutrient-use scope, variable lag, population-versus-cell distinctions and provenance limits are explicit. Existing traits unchanged; timestamp is the observed UTC curation decision.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000708",
    "label": "diversifying bet hedging",
    "definition": "A physiological phenotype in which a clonal microbial lineage reversibly interconverts between alternative cell states independently of the prevailing environment and before environmental change, spreading risk across unpredictable environmental changes through state-specific survival or reproductive trade-offs.",
    "definition_source": "DOI:10.1371/journal.pbio.1001325",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/nature08504",
        "snippet": "Here we report the de novo evolution of bet hedging in experimental bacterial populations.",
        "notes": "Beaumont et al. 2009, PMID:19890329; scientific abstract, directly checked against publisher and source-qualified MED text, not the publisher's Editorial Summary. Supports experimentally evolved risk spreading by rapid phenotype switching under a changing selection regime. Mutational evolution of a switching genotype is not the same claim as mutations generating each alternative cell state. Main figures, supplements and raw data were not independently assessed; no gene-level mechanism or natural canonical exemplar is asserted."
      },
      {
        "reference": "DOI:10.1371/journal.pbio.1001325",
        "snippet": "Our results suggest that yeast bet hedging results from multiple epigenetic growth states determined by a combination of stochastic and deterministic factors.",
        "notes": "Levy, Ziv and Siegal 2012, PMID:22589700, PMC3348152; scientific abstract, directly checked against publisher, MED and full-text XML, separately from the Author Summary. Box 1 supplies the definition framework and explicitly leaves adaptive origin untested in this yeast study. The record preserves that limit: reversible state variation and differential stress survival do not alone establish evolutionary optimization. Binary states and a purely stochastic mechanism are not required."
      },
      {
        "reference": "DOI:10.1038/s41467-024-46297-6",
        "snippet": "Mobile cells grow faster but are stress-sensitive, while non-mobile cells prioritise stress resistance over growth.",
        "notes": "Tang et al. 2024, PMID:38453919; scientific abstract, directly checked against publisher and source-qualified MED text. The Introduction and Discussion distinguish early diversification of Haematococcus pluvialis cultures from later stress-induced conversion. Growth and survival are fitness proxies, not a demonstration of optimized long-term geometric mean fitness. Figures, supplements and raw data were not independently assessed; proposed transcriptional explanations are not encoded as causal edges."
      }
    ],
    "discussions": [
      {
        "discussion_id": "bet-hedging-scope-and-hierarchy",
        "prompt": "Retain lineage-level risk spreading without equating all cellular heterogeneity with bet hedging.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "The diversifying qualifier restricts this class to alternative states within a clonal microbial lineage; it does not cover every use of unqualified bet hedging. Heterogeneity, noisy gene expression or switching alone is insufficient: reversible states must precede the relevant environmental shift and differ in survival or reproductive performance across conditions. Generic stress-induced change, carbon-source memory, cue-triggered environmental anticipation, genetic resistance and ecological generalist/specialist niche breadth are not exact synonyms. Particular observations can overlap without making these classes equivalent or disjoint. Dormancy and persister formation can participate in risk spreading, but their presence alone does not establish it, so neither existing record is reparented. METPO:1000059 phenotype is the conservative parent pending upstream review of this lineage-level physiological disposition. This is not a sequence feature, individual assay result or mixed-species community property. Following Levy et al. Box 1, the relevant state interconversion must be independent of the prevailing environment; temporal precedence alone does not establish this criterion. Cue-triggered preparation before a later change is not sufficient. Deterministic age-related variation can qualify, so environmental independence does not require a purely stochastic switching mechanism.",
        "posed_by": "codex",
        "posed_date": "2026-10-12"
      },
      {
        "discussion_id": "bet-hedging-evidence-and-mechanism-limits",
        "prompt": "Assess adaptive origin, natural exemplars and molecular mechanisms separately from the operational phenotype.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "This first-pass class does not assert that every cited system was selected for diversification or has a measured long-term fitness advantage. Levy et al. Box 1 distinguishes those stronger claims from its operational usage; testing arithmetic and geometric mean fitness requires an explicit environmental distribution and comparison strategy. No fixed switching rate, binary state space or universal protein mechanism is asserted. Canonical taxa await strain-provenance and taxonomy checks; causal_graphs, xrefs and synonyms are omitted. MED, Crossref and visible publisher links checked on 2026-10-12 exposed no correction or retraction for the three retained papers; commentary, review and preprint links are not independent experiments. This bounded check does not exclude every possible notice. Pinned/current METPO RDF and ignored/hidden novelty searches found no exact active or deprecated term; earlier research mentions remain leads, not primary records. The pinned ontology is unchanged.",
        "posed_by": "codex",
        "posed_date": "2026-10-12"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-12T06:39:53Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added diversifying bet hedging with three primary DOI-backed sources and directly checked scientific-abstract snippets. Reserved 000708, v584 and 1066100-1066199 after ignored/hidden worktree and pending-PR checks. Operational risk spreading is distinguished from evolutionary optimization; examples and mechanisms remain deferred. Existing traits unchanged; timestamp is the observed UTC curation decision.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-12T07:04:27Z",
        "curator": "codex",
        "action": "QUALIFIED_TRAIT_SCOPE",
        "changes": "Addressed #1888: made reversible environment-independent state interconversion explicit in the definition and scope discussion, following Levy et al. Box 1. Temporal precedence alone is insufficient; purely stochastic or binary switching is not required. Preserved evidence and original provenance. Timestamp is the observed UTC correction decision.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-12T08:09:20Z",
        "curator": "codex",
        "action": "CORRECTED_SCOPE_WORDING",
        "changes": "Addressed external review #1890: corrected the inverted implication in the first scope discussion. Environment-independent interconversion remains required; a purely stochastic mechanism is not required, consistent with Levy et al. Box 1. Preserved the definition, evidence, proposal definition and both previous events. Timestamp is the observed UTC correction decision.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000138",
    "label": "DNase activity",
    "definition": "A physiological enzyme-activity phenotype in which a cell produces active DNase enzymes that hydrolyze DNA.",
    "definition_source": "DOI:10.3389/fmicb.2019.00969",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "synonyms": [
      {
        "synonym_text": "DNase production",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.22207/JPAM.14.1.44"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.3389/fmicb.2019.00969",
        "snippet": "unexpected and widespread presence of DNase secretion in bacteria in general and in MGP more specifically",
        "notes": "Al-Wahaibi et al. assayed marine bacterial isolates for extracellular DNase secretion."
      },
      {
        "reference": "DOI:10.22207/JPAM.14.1.44",
        "snippet": "screened for their capacity to produce DNA hydrolyzing activity on DNase test agar plate",
        "notes": "Asha and Krishnaveni screened halophilic marine-sediment Bacillus-group isolates for DNA hydrolysis on DNase test agar."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:2026187",
        "taxon_label": "Bacillus pacificus",
        "note": "Bacillus pacificus KVCMST-8A-12 was reported as a DNase-producing marine-sediment isolate.",
        "reference": "DOI:10.1128/MRA.01011-21"
      }
    ],
    "discussions": [
      {
        "discussion_id": "dnase-activity-xref-gap",
        "prompt": "Resolve an exact external ontology class for DNase activity before adding a TraitRecord xref.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "GO:0004536 denotes the DNA nuclease molecular function rather than the organism-level DNase production phenotype, so it is too scope-shifted for an equivalent TraitRecord xref.",
        "posed_by": "codex",
        "posed_date": "2026-09-11"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-11T00:00:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted DNase activity as a DOI-backed TraitRecord after a repository-wide duplicate review covering ignored and hidden files; METPO has no exact DNase activity class yet.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000080",
    "label": "dormancy",
    "definition": "A reversible physiological state of greatly reduced metabolic activity that allows a cell to survive unfavorable conditions and later resuscitate, generating a microbial seed bank.",
    "definition_source": "DOI:10.1038/nrmicro2504",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "synonyms": [
      {
        "synonym_text": "dormant state",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1038/nrmicro2504"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/nrmicro2504",
        "notes": "Lennon & Jones review microbial seed banks and the mechanisms by which microorganisms enter and exit dormancy; parent of VBNC and persister sub-variants."
      },
      {
        "reference": "DOI:10.1038/nrmicro1557",
        "notes": "Lewis links dormancy to persister-cell survival and infectious disease."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1773",
        "taxon_label": "Mycobacterium tuberculosis",
        "note": "Paradigm of bacterial dormancy/non-replicating persistence (latent infection; DosR regulon).",
        "reference": "PMID:8675308"
      },
      {
        "taxon_id": "NCBITaxon:83332",
        "taxon_label": "Mycobacterium tuberculosis H37Rv",
        "note": "Strain-level dormancy model paired to reviewed RpfB, one member of the resuscitation-promoting-factor family.",
        "reference": "DOI:10.1111/j.1365-2958.2007.06078.x"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "dormancy_seed_bank",
        "title": "Reversible dormancy and resuscitation",
        "description": "Evidence-backed causal sketch linking unfavorable conditions to a reversible dormant state forming a microbial seed bank.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "This graph combines several bacterial dormancy modules rather than asserting one universal pathway. The H37Rv RpfB example anchors the resuscitation branch and is one Rpf-family protein, not a stand-in for toxin-antitoxin or ribosome-hibernation systems.",
        "nodes": [
          {
            "node_id": "dormancy_trait",
            "label": "dormancy",
            "node_type": "TRAIT",
            "grounding": "traitmech:000080",
            "description": "Capacity to enter a reversible low-activity state."
          },
          {
            "node_id": "unfavorable_conditions",
            "label": "unfavorable conditions",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Stress or resource limitation triggering dormancy."
          },
          {
            "node_id": "dormancy_process",
            "label": "dormancy process",
            "node_type": "BIOLOGICAL_PROCESS",
            "grounding": "GO:0022611",
            "description": "Entry into a reversible quiescent state."
          },
          {
            "node_id": "nutrient_heat_stress",
            "label": "nutrient limitation or heat stress",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Nutrient starvation or heat stress that triggers the stringent response."
          },
          {
            "node_id": "ppgpp_stringent_response",
            "label": "(p)ppGpp stringent response",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Guanosine tetra/pentaphosphate-mediated stringent response reprogramming cell activity."
          },
          {
            "node_id": "toxin_antitoxin_modules",
            "label": "toxin-antitoxin modules",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Chromosomal toxin-antitoxin systems (e.g. hipAB, mazEF, relBE) inducing growth arrest.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "This umbrella combines unrelated toxin and antitoxin families; the graph evidence does not identify one exact protein-family term."
          },
          {
            "node_id": "ribosome_hibernation_factors",
            "label": "ribosome hibernation factors (RMF/HPF/RaiA)",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Factors that bind ribosomes to silence translation during dormancy.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "RMF, HPF, and RaiA are distinct ribosome-associated protein families, so no single semantic family term represents the aggregate node."
          },
          {
            "node_id": "protein_synthesis",
            "label": "protein synthesis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Translation of mRNA into protein.",
            "grounding": "GO:0006412"
          },
          {
            "node_id": "ribosome",
            "label": "ribosome",
            "node_type": "ORGANELLE",
            "description": "Ribonucleoprotein machine for protein synthesis, protected during dormancy.",
            "grounding": "GO:0005840"
          },
          {
            "node_id": "rpf_proteins",
            "label": "resuscitation-promoting factors (Rpf)",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Peptidoglycan-hydrolase Rpf proteins that reactivate dormant/VBNC cells.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "The node intentionally denotes the five paralogous RpfA-E proteins; a single accession or function term would erase their documented functional hierarchy.",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:P9WG29",
                "protein_label": "Resuscitation-promoting factor RpfB",
                "gene_symbol": "rpfB",
                "taxon_id": "NCBITaxon:83332",
                "taxon_label": "Mycobacterium tuberculosis H37Rv",
                "entry_status": "REVIEWED",
                "retrieved_on": "2026-10-22",
                "entry_version": 54,
                "sequence_version": 1,
                "role": "H37Rv RpfB component of the Rpf family that contributes to recovery from dormancy; it does not denote all five paralogues.",
                "evidence": [
                  {
                    "reference": "DOI:10.1111/j.1365-2958.2007.06078.x",
                    "snippet": "Rpf-like proteins are implicated in resuscitation through peptidoglycan hydrolysis",
                    "notes": "Sequential deletion and complementation establish a resuscitation phenotype and place RpfB high in the functional hierarchy; UniProt verifies the reviewed H37Rv RpfB entry."
                  }
                ]
              }
            ]
          }
        ],
        "edges": [
          {
            "subject": "unfavorable_conditions",
            "predicate": "causes",
            "object": "dormancy_process",
            "description": "Adverse conditions induce entry into dormancy.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2504",
                "notes": "Lennon & Jones review entry/exit from dormancy (seed banks)."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "dormancy_process",
            "predicate": "confers",
            "object": "dormancy_trait",
            "description": "The dormancy process realizes the dormancy trait.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro1557",
                "notes": "Lewis links dormancy to long-term survival."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "nutrient_heat_stress",
            "predicate": "activates",
            "object": "ppgpp_stringent_response",
            "description": "Nutrient limitation and heat stress activate the (p)ppGpp stringent response.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s12866-024-03628-3",
                "notes": "The stringent response mediated by (p)ppGpp is activated by nutrient/heat stresses."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "ppgpp_stringent_response",
            "predicate": "causes",
            "object": "dormancy_process",
            "description": "(p)ppGpp reprograms cellular activity, resulting in slow growth or dormancy.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s12866-024-03628-3",
                "notes": "(p)ppGpp can reprogram cellular life activities resulting in slow cell growth or dormancy."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "ppgpp_stringent_response",
            "predicate": "upregulates",
            "object": "toxin_antitoxin_modules",
            "description": "(p)ppGpp upregulates multiple toxin-antitoxin modules.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s12866-024-03628-3",
                "notes": "(p)ppGpp upregulates multiple TA modules (hipAB, dinJ/yafQ, mazEF, mqsRA, relBE, yafNO and hokB)."
              }
            ]
          },
          {
            "subject": "ribosome_hibernation_factors",
            "predicate": "turns off",
            "object": "protein_synthesis",
            "description": "Ribosome hibernation factors turn off protein synthesis during dormancy.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2024.1386179",
                "notes": "Classical ribosome hibernation factors (RMF, HPF, YfiA) turn off protein synthesis."
              }
            ]
          },
          {
            "subject": "ribosome_hibernation_factors",
            "predicate": "protects",
            "object": "ribosome",
            "description": "Hibernation factor binding protects ribosomes from ribonuclease degradation.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2024.1386179",
                "notes": "Hibernation factors directly block ribonucleases from entering the ribosome in response to starvation."
              }
            ]
          },
          {
            "subject": "rpf_proteins",
            "predicate": "promotes",
            "object": "dormancy_process",
            "description": "Rpf proteins promote resuscitation (exit) of dormant/VBNC bacteria.",
            "evidence": [
              {
                "reference": "DOI:10.3390/microorganisms12081528",
                "notes": "Rpfs reactivate dormant bacteria at very low concentrations."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "ribosome_hibernation_factors",
            "predicate": "contributes to",
            "object": "dormancy_process",
            "description": "Stress-induced ribosome hibernation contributes translational arrest to the dormancy process.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2024.1386179",
                "snippet": "environmental stress might govern the formation of 100S ribosomes, which were only detectable during periods of protein synthesis arrest",
                "notes": "Verified against the open Frontiers article full text."
              }
            ],
            "predicate_id": "RO:0002326"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-06-04T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate PHYSIOLOGY axis class (dormancy) to parent the VBNC and persister-cell sub-variants.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-08T13:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (reversible dormancy) with GO node grounding and biolink/RO predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 6 evidence-backed generic edges (7 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:14Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002213\u00d72, biolink:causes\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:34Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0006412\u00d71, GO:0005840\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 1 causal edge(s) off enables/RO:0002327 with a TRAIT object (1 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "CURATE_PROTEIN_TAXON_EXAMPLE",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope dormancy_seed_bank=MECHANISTIC with scope_notes; marked 3 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (toxin_antitoxin_modules, ribosome_hibernation_factors, rpf_proteins); added taxon-paired protein example(s) UniProtKB:P9WG29 on rpf_proteins (NCBITaxon:83332); added canonical example(s) NCBITaxon:83332.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T09:35:00Z",
        "curator": "codex",
        "action": "CONNECT_CAUSAL_GRAPH_COMPONENTS",
        "changes": "Resolved issue #183 graph fragmentation (2 components to 1) with one public-source, verbatim-snippet-backed connector. No paid research service was called.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-22T01:35:00Z",
        "curator": "claude",
        "action": "REFRESH_UNIPROT_ENTRY_VERSION",
        "changes": "Refreshed UniProtKB entry_version against live UniProt REST on 2026-10-22: UniProtKB:P9WG29 (53 -> 54 on rpf_proteins).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000596",
    "label": "durotaxis",
    "definition": "A motile phenotype in which active migration is directionally biased in response to a spatial gradient in substrate stiffness.",
    "definition_source": "DOI:10.7554/eLife.96821",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000702"
    ],
    "evidence": [
      {
        "reference": "DOI:10.7554/eLife.96821",
        "snippet": "Dictyostelium also displayed stiff-side directed motility when seeded on the gradient gel",
        "notes": "Kang et al., Version of Record (v4), 2024-12-13, https://doi.org/10.7554/eLife.96821.4; full text https://pmc.ncbi.nlm.nih.gov/articles/PMC11643633/ (PMID:39671466). Exact Results paragraph span in Amoeboid durotaxis is evolutionarily conserved, not an abstract quote. Figure 4 was visually inspected: confined Dictyostelium cells on polyacrylamide stiffness gradients had greater directional migration than uniform-gel controls, without a significant velocity difference. Blebbistatin reduced directionality and speed; Rho activator II increased them. These pharmacological results do not isolate a dedicated stiffness sensor. Supplementary file 1 contains simulation parameters; the MDAR checklist refers to cell-culture methods but does not resolve the assayed Dictyostelium strain. Mammalian NMIIA localization and knockdown results are not direct microbial protein evidence."
      },
      {
        "reference": "DOI:10.1088/1361-6463/adb6b8",
        "snippet": "Our findings reveal directional persistence and strong polarization of the plasmodia towards regions of stiffer substrates, indicating a guided migration response.",
        "notes": "Filipinas and Confesor, published online 2025-02-27. Exact abstract span in the publisher-deposited Crossref record, https://api.crossref.org/works/10.1088/1361-6463/adb6b8. The authors report tracking Physarum polycephalum plasmodial nodes on agar stiffness gradients. This is independent microbial support for stiffness-directed migration, not merely a simulation prediction. Full methods, figures and supplements were not inspected; strain provenance, gradient controls and the distinction between node migration and growth remain to be assessed before adding a canonical example or mechanistic graph. The abstract's simulation-supported gradient-independence claim is not generalized to all microbes."
      },
      {
        "reference": "DOI:10.1038/s41563-022-01294-2",
        "snippet": "Our results identify the molecular mechanism driving context-dependent positive or negative durotaxis, determined by a cell's contractile and adhesive machinery.",
        "notes": "Isomursu et al., published 2022-07-11, PMID:35817964. Exact final abstract sentence in the Europe PMC MED record, https://europepmc.org/article/MED/35817964; the publisher's abstract corroborates positive and negative durotaxis usage. This mammalian cell study supports polarity-neutral terminology only, not an additional microbial observation. Its mechanism claim is not transferred to microbes. Full methods, figures and supplements were not inspected for this terminology check. The two microbial studies above report stiff-side migration; negative microbial durotaxis is not established by these sources."
      }
    ],
    "discussions": [
      {
        "discussion_id": "durotaxis-stiffness-and-migration-boundaries",
        "prompt": "Keep stiffness-directed migration distinct from other mechanical responses.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "The class is polarity-neutral: positive and negative responses are directions along the stiffness gradient, not different stimuli. Isomursu et al. (DOI:10.1038/s41563-022-01294-2) support this terminology in mammalian cells, not negative microbial durotaxis. Both microbial studies here report stiff-side migration; no opposite microbial response is inferred. Speed changes on uniform substrates, passive displacement and differential growth alone are insufficient. Contact-guided polarized growth in thigmotropism (traitmech:000594) is a different response. Do not infer durotaxis from a friction gradient, surface topography or remote substrate deformation without direct evidence for stiffness-directed migration. Mechanotaxis is broader, not an exact synonym. QuickGO returned zero durotaxis hits on 2026-10-04; other external equivalences remain unverified. No xref or synonym is inferred.",
        "posed_by": "codex",
        "posed_date": "2026-10-04"
      },
      {
        "discussion_id": "durotaxis-strain-and-mechanism-grounding",
        "prompt": "Resolve experimental strains and microbial protein evidence before graphing.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Kang's methods cite Li et al. (DOI:10.3389/fcell.2022.835185), whose cell-culture methods describe Ax2-derived cells and expression constructs. That citation does not uniquely identify the cells used for Kang's Figure 4 or establish natural-strain provenance. Resolve that identity and inspect the Physarum full methods before adding NCBI-grounded canonical examples. Dictyostelium inhibitor/activator responses support a contractility-related interpretation, not a resolved protein-level sensing pathway. Do not transfer mammalian NMIIA polarization or knockdown effects to an unverified microbial accession, or treat the active gel model as a biological perturbation. Mechanistic graphs are deferred pending taxon-paired proteins and bounded causal evidence; NONMECHANISTIC is not a workaround.",
        "posed_by": "codex",
        "posed_date": "2026-10-04"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-04T12:00:52Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added durotaxis with two independent microbial DOI citations and exact full-text/abstract snippets. Ignored-and-hidden novelty searches and structured OWL review found no exact record or METPO term. Reserved METPO:1055000 in v473 under motile. Inspected Kang v4 Figure 4, methods and relevant supplement documents; kept stiffness-directed migration distinct from speed changes and contact-guided growth. Deferred canonical strains and protein-level mechanisms rather than inferring them from mammalian experiments.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-04T12:38:00Z",
        "curator": "codex",
        "action": "CORRECTED_DEFINITION_SCOPE",
        "changes": "Addressed review issue #1669: made the unqualified durotaxis class and METPO proposal polarity-neutral. Kept the observed stiff-side microbial responses in evidence notes and added Isomursu et al. only for positive/negative terminology, without transferring mammalian mechanisms or claiming negative microbial observations.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000636",
    "label": "endocytosis",
    "definition": "A physiological phenotype in which a microbial cell takes up extracellular material or plasma-membrane components into intracellular membrane-bound compartments by remodeling and internalizing its plasma membrane.",
    "definition_source": "DOI:10.1083/jcb.128.5.779",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1083/jcb.128.5.779",
        "snippet": "After an additional 20-40 min, the PM and cytoplasmic punctate staining disappeared concomitant with staining of the vacuolar membrane.",
        "notes": "PMID:7533169, PMC2120394. Scientific Abstract quote verified in Europe PMC XML; full-text OCR, including Introduction, Methods, Results and Discussion, was read at https://www.ebi.ac.uk/europepmc/webservices/rest/PMC2120394/fullTextXML. FM 4-64 tracks plasma-membrane-to-vacuole transport in Saccharomyces cerevisiae. Early experiments used BHY10.5, a CPY-invertase reporter background, not the SEY6210 control in later mutant comparisons. Endosome identity is qualified as likely. Mutant effects on vacuolar delivery are not necessarily initial-internalization defects; in vitro ATP/cytosol dependence concerns later transport. Marker-specific results do not establish a universal route. PDF/figures were unavailable and were not visually audited."
      },
      {
        "reference": "DOI:10.1128/mcb.14.11.7245-7255.1994",
        "snippet": "This report presents direct evidence for alpha-factor-induced internalization of cell surface receptors.",
        "notes": "PMID:7935439, PMC359259. Scientific Abstract directly read in NCBI PubMed XML and Europe PMC metadata, which agree on this DOI. Density fractionation and extracellular-protease protection support receptor internalization in Saccharomyces cerevisiae. The abstract distinguishes receptor signaling, internalization and subsequent vacuolar degradation. No fixed transit time or universal receptor requirement is imposed. Full text and figures were unavailable: the Europe PMC full-text endpoint returned HTTP 500 and the indexed PDF mirror returned 404. Strain provenance and unread assay details are not inferred."
      }
    ],
    "discussions": [
      {
        "discussion_id": "endocytosis-scope-and-hierarchy",
        "prompt": "Distinguish membrane-bound uptake from neighboring capabilities.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "This is the microbial cell's uptake phenotype, not a host response, a sequence feature or intracellular trafficking alone. Surface adsorption, passive diffusion, transporter entry, open membrane invaginations and autophagy alone are insufficient. Pinocytosis traitmech:000635 and phagocytosis traitmech:000627 entail this scope; macropinocytosis traitmech:000634 remains below pinocytosis. No fixed size, clathrin/actin dependence, nutritional assimilation or degradation is required. Trogocytosis traitmech:000633 describes removal and uptake of living-cell portions without universally specifying membrane-bound enclosure. Myzocytosis traitmech:000631 describes prey-content aspiration. Its cited 2023 Discussion (DOI:10.3390/microorganisms11081945) calls myzocytosis a form of endocytosis in the studied Colpodella system; that source-attributed umbrella usage is retained, not treated as proof that every aspiration phenotype meets this operational membrane-bound scope. Their broader parent decisions remain unresolved, not exclusions or disjointness claims. Nutritional phagotrophy is not an equivalent. Review process-level ontology mappings separately; no unverified synonyms or xrefs are asserted.",
        "posed_by": "codex",
        "posed_date": "2026-10-06"
      },
      {
        "discussion_id": "endocytosis-exemplar-and-mechanism",
        "prompt": "Resolve strain provenance and route-specific molecular evidence.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "The two independent studies both concern laboratory Saccharomyces cerevisiae, not independent taxon replication. BHY10.5's reporter background is not a natural isolate; the 1994 full methods and strain provenance remain unread. Canonical examples are left unset rather than generalize these assays to every strain or claim a wild-type provenance. Membrane-tracer transport, receptor uptake and fluid uptake need not report identical routes. The 1995 authors discuss nonvesicular alternatives and qualify endosome identity. No complete molecular mechanism, protein accessions or causal graph are inferred from tracer behavior or abstracts. Obtain taxon-paired functional and strain-provenance evidence before adding those fields.",
        "posed_by": "codex",
        "posed_date": "2026-10-06"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-06T06:47:04Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added endocytosis with two DOI-backed scientific-abstract snippets and explicit strain, assay and access limits. Ignored-and-hidden searches and pinned METPO review found no exact record. Reserved METPO:1058900 in v512; refined pinocytosis and phagocytosis parents without asserting unverified mappings or a molecular mechanism.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000590",
    "label": "energy taxis",
    "definition": "A motile phenotype in which directional locomotion is regulated by sensing changes in the electron transport system associated with cellular energy generation.",
    "definition_source": "DOI:10.1128/jb.186.19.6595-6604.2004",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000702"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1128/jb.182.21.6042-6048.2000",
        "snippet": "behavioral responses to most stimuli in A. brasilense are triggered by changes in the electron transport system.",
        "notes": "Abstract exact-matched at Europe PMC (PMID:11029423). Publisher Methods, Results and Discussion also inspected. Sp7 (ATCC 29145), wild type for chemotaxis, is distinguished from the cytN mutant FAJ851. Spatial and temporal assays, metabolic inhibition and electron-donor bypass support the sensing interpretation beyond growth correlation. Nitrate and DMSO taxis are reported under anaerobic conditions. The study does not decide whether redox state or ion motive force is the sensed signal; capillary aerotaxis can confound apparent substrate chemotaxis. No universal substrate range is inferred."
      },
      {
        "reference": "DOI:10.1128/jb.186.19.6595-6604.2004",
        "snippet": "Motility responses triggered by changes in the electron transport system are collectively known as energy taxis.",
        "notes": "Abstract exact-matched at Europe PMC (PMID:15375141); full text not fully inspected. The tlp1 mutant is deficient in responses to oxidizable substrates, terminal electron acceptors and redox conditions. The proposed sensory domain's function remains unknown in this source. Root-colonization impairment supports an ecological hypothesis, not universal host specificity or an identified direct ligand. No complete protein-resolved pathway is inferred from the abstract."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:192",
        "taxon_label": "Azospirillum brasilense",
        "reference": "DOI:10.1128/jb.182.21.6042-6048.2000",
        "note": "Sp7 (ATCC 29145), the study's wild type for chemotaxis, not the cytN mutant FAJ851. Observed substrate, electron-acceptor and repellent responses support energy taxis under the reported conditions. Environmental provenance is independently documented at https://www.atcc.org/products/29145. NCBI resolved 192 on 2026-10-04 at species rank; it is not an exact strain accession or a claim about all strains."
      }
    ],
    "discussions": [
      {
        "discussion_id": "energy-taxis-stimulus-and-mapping-boundaries",
        "prompt": "Keep energy sensing distinct from stimulus-defined taxis classes.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "This entry follows the electron-transport-based usage in the cited primary studies. Energy generation powering motility alone is insufficient: changes must inform locomotor control. Aerotaxis, phototaxis and chemotaxis can involve other sensing mechanisms and are not automatically children or exact synonyms. Metabolism-dependent chemotaxis can instead sense intracellular intermediates, so that broader phrase is not an exact synonym. The existing flagellar-specific chemotaxis record is not used as a universal parent. Resolve external mappings at their authorities and compare process versus organismal-disposition scope before adding xrefs.",
        "posed_by": "codex",
        "posed_date": "2026-10-04"
      },
      {
        "discussion_id": "energy-taxis-signal-and-protein-grounding",
        "prompt": "Verify the sensed signal and taxon-paired molecular branches.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Electron-transport perturbations support energy-dependent locomotor control without identifying one universal receptor or deciding redox-state versus ion-motive-force sensing. Inspect full mutant, complementation and domain-function evidence and resolve taxon-paired protein accessions before adding causal edges. Do not substitute a protein/domain sequence feature for this organismal phenotype or use a NONMECHANISTIC graph to bypass molecular grounding.",
        "posed_by": "codex",
        "posed_date": "2026-10-04"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-04T06:51:06Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added energy taxis with two primary DOI studies, an ATCC provenance URL and exact snippets. Ignored-and-hidden searches found no exact record or METPO term. Reserved METPO:1054400 in v467. Verified Sp7 collection provenance and NCBITaxon:192 species identity. Kept stimulus-defined taxis classes separate and deferred unverified molecular branches and external mappings.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-04T07:25:57Z",
        "curator": "codex",
        "action": "CORRECTED_EVIDENCE",
        "changes": "Addressed review issue #1660: removed ATCC provenance fields from trait evidence and retained the stable strain-provenance URL in the canonical example note. Both primary DOI studies and their verified abstract snippets remain.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000713",
    "label": "enhanced transcriptional reactivation memory",
    "definition": "A physiological phenotype in which a microbial cell or lineage retains a non-genetic state from prior inducing conditions that enhances the rate or magnitude of later transcriptional activation after intervening repression.",
    "definition_source": "DOI:10.7554/eLife.77646",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.7554/eLife.77646",
        "snippet": "Upon Anchor Away of Opi1, reactivation was faster than activation",
        "notes": "Sump et al. 2022, PMID:35579426, PMC9129879; Results s2-1, paragraph 2, contiguous in primary XML and publisher Version of Record HTML. Figure 1D uses synthetic Opi1 Anchor Away to bypass upstream induction control; enhancement is lost in mrs and nup100 mutants. Ordinary-starvation INO1 reactivation in Figure 1B is not clearly faster than activation. Figure 1 supplement 1C separately measures CHO1/ACT1 after three-hour repression; its generic statistical-comparator caption is ambiguous. Figure 1 supplement 2E measures 18-hour peripheral localization, not that duration of enhanced transcription; the main Results mispoints to supplement 1. Figure 1G competitive fitness is a different endpoint, not proof of transcriptional causality. Selected Results, Methods, scientific abstract, actual figures and strain-table rows were inspected. RT-qPCR mRNA kinetics are not direct measurements of initiation rate. Native abstract lookup returns NOT_IN_ABSTRACT; direct full-text matching supports the quotation, not a native VERIFIED verdict."
      },
      {
        "reference": "DOI:10.1534/genetics.112.143016",
        "snippet": "Cells with prior NaCl exposure have a faster gene-expression response to H2O2.",
        "notes": "Guan et al. 2012, PMID:22851651, PMC3454879; complete opening sentence of the Figure 4 caption, contiguous in publisher HTML with chemical subscripts retained as text. BY4741-background laboratory yeast received 0.7 M NaCl for 60 minutes, washing and 240 minutes of stress-free YPD recovery (two generations in Results), then 0.5 mM H2O2, compared with mock-treated cells. No significant pre-challenge expression difference at FDR 0.05 does not prove identical baselines. Figure 4 includes induced and repressed genes; only the enhanced-induction subset supports this activation phenotype. The 449-gene count is not a count of induced genes. Methods and Figure 4A sample through 40 minutes, whereas Results describes a 60-minute response. Figure 5 shows TSA2 mRNA kinetics by qPCR; nup42 deletion reduces the priming benefit, while nup100 naive and primed responses are both fast, not simple evidence of a universal mechanism. Four-to-five generation resistance persistence is a different endpoint. Relevant Results, Methods, scientific abstract and actual Figures 4 and 5 were inspected; raw data were not reanalyzed. Native abstract-verifier results are retained separately in the source sidecar; exact publisher full-text matching supports this caption quotation."
      }
    ],
    "discussions": [
      {
        "discussion_id": "transcriptional-memory-endpoint-and-hierarchy",
        "prompt": "Preserve enhanced reactivation after repression as the defining endpoint.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Compare induced transcript responses under matched later test conditions and genetic backgrounds, after intervening repression. Continued expression, transcript or reporter persistence, a chromatin mark, peripheral localization or a gene alone does not establish this phenotype. Transcript abundance does not by itself distinguish synthesis from degradation. No identical first and second stimulus, prior production of a particular transcript, fixed duration, universal mitotic inheritance or shared chromatin mechanism is required. Carbon-source memory (traitmech:000706) spans growth and induction endpoints and is not reparented wholesale. Memory of acquired stress resistance (traitmech:000712) concerns retained resistance, not faster transcription. Anticipation and bet hedging are also not exact equivalents. Unqualified transcriptional memory, epigenetic memory and priming are not asserted as exact synonyms. METPO:1000059 phenotype is the conservative parent pending hierarchy review; existing records are unchanged.",
        "posed_by": "codex",
        "posed_date": "2026-10-13"
      },
      {
        "discussion_id": "transcriptional-memory-evidence-limits",
        "prompt": "Resolve strain provenance and assay-specific mechanisms before extending this draft.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Sump and Guan report different laboratory assays, not independent replication of the same experiment. Laboratory and engineered yeast backgrounds are qualified evidence, not natural canonical taxa. Sump's retrieved v2 strain table has a CHO1 DBY1428 figure locator and an HTA1-mCherry versus Methods Pho88 description discrepancy; no strain-wide extrapolation follows. Selected publisher and XML text agrees after normalization, not complete byte-level version equivalence. Publisher figure images were inspected at limited resolution, without numerical reanalysis. Bounded publisher, qualified MED and Crossref checks on 2026-10-12 exposed no linked correction or retraction; this does not prove notice absence. No causal graph, exact synonym, external equivalence or species-wide phenotype is asserted. Source access challenges and caption discrepancies are retained in the source-verification sidecar.",
        "posed_by": "codex",
        "posed_date": "2026-10-13"
      },
      {
        "discussion_id": "transcriptional-memory-historical-identity",
        "prompt": "Reconcile deprecated lexical neighbors without reactivating their identifiers.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Pinned and inspected current METPO releases mark METPO:1000108 epigenetic modification and METPO:1000310 transcription factor deprecated below ObsoleteClass, with OMO:0001000 and no replacement or consider annotation in those graphs. OMO means out of scope, but METPO issue 521 disputes the mechanical reason assignment. Original historical definitions and parent axioms remain unassessed; labels alone do not prove historical nonequivalence. This operational physiological phenotype is accepted independently from primary experiments, not by reactivating those terms or assuming a sequence-feature meaning. Ignored/hidden available files, retained historical trees, normalized trait semantics, pending changes and ontology graphs revealed no exact active record in the inspected scope. No historical exact-equivalence claim is made. The pinned ontology is unchanged; discovery is not exhausted.",
        "posed_by": "codex",
        "posed_date": "2026-10-13"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-13T00:34:29Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added enhanced transcriptional reactivation memory with two DOI references and contiguous full-text snippets. Preserved synthetic induction, transcript-endpoint, duration, source-version and historical-identity limits. Reserved 000713, v589 and 1066600-1066699 after ignored/hidden, retained-tree, independent-copy and pending-PR checks. No canonical examples or mechanism graph; existing records unchanged. Timestamp is the observed UTC decision.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-13T01:22:19Z",
        "curator": "codex",
        "action": "CORRECTED_EVIDENCE_PROVENANCE",
        "changes": "Replaced the D'Urso background-attribution snippet with the authors' own confirmation sentence for Figure 7A, addressing review issue 1904. Retained selected-gene, two-hour recovery, unshown-USV1, four-generation and assay limits; no definition or identifiers changed.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-13T01:56:28Z",
        "curator": "codex",
        "action": "CORRECTED_SNIPPET_SELF_CONTAINMENT",
        "changes": "Replaced the anaphoric D'Urso confirmation with Guan 2012's self-contained Figure 4 result sentence, addressing review issue 1905 without extending the quotation budget. Preserved prior evidence checks as history. Qualified Guan's four-hour recovery, mixed induced/repressed gene set and assay timing discrepancy; definition, identifiers and PROPOSED status are unchanged.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000642",
    "label": "ER-phagy",
    "definition": "An autophagy phenotype in which a microbial cell selectively degrades portions of its endoplasmic reticulum by delivering them to lysosomal or vacuolar compartments.",
    "definition_source": "DOI:10.15252/embj.2019102586",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000638"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1242/jcs.154716",
        "snippet": "Finally, we provide evidence that ER-phagy degrades excess ER membrane, suggesting that it contributes to cell homeostasis by controlling organelle size.",
        "notes": "PMID:25052096, PMC4163648. Scientific Abstract directly read in Europe PMC core metadata with matching DOI. XML Results s2c/s2e and Methods s4b/s4f were read. In Saccharomyces cerevisiae, ER-targeted Pho8 reporters distinguish selective turnover from cytosolic and mitochondrial cargo; Atg7 and vacuolar-protease controls distinguish routes and reporter activation. ER whorls enter the vacuole by microautophagy. DTT and tunicamycin interfere with vacuolar proteolysis, so stress-induced whorl accumulation alone is not completed degradation. Untreated opi1 mutants show partly disintegrated vacuolar whorls, unlike opi1 pep4 prb1 mutants; membrane expansion can elicit this response without misfolded-protein stress. The strains derive from W303, but independent natural provenance was not verified. Figure 5/7 captions were read; actual figures, supplements and complete Methods were not inspected."
      },
      {
        "reference": "DOI:10.1038/nature14506",
        "snippet": "Atg40 is enriched in the cortical and cytoplasmic ER, and loads these ER subdomains into autophagosomes.",
        "notes": "PMID:26040717. Scientific Abstract directly read in Europe PMC core metadata with matching DOI. This Saccharomyces cerevisiae study explicitly restricts its use of autophagy to macroautophagy. Atg40 targets cortical/cytoplasmic ER, whereas Atg39 targets perinuclear ER and nuclear material. These source-specific subdomain assignments do not make ER-phagy and nucleophagy synonyms or restrict all ER-phagy to the macro route. The proposed mammalian FAM134B functional counterpart is qualified as probable, not experimentally universal. Full text, actual figures, supplements and strain provenance were not inspected."
      },
      {
        "reference": "DOI:10.15252/embj.2019102586",
        "snippet": "Third, we demonstrate that macro- and micro-ER-phagy are parallel pathways with distinct molecular requirements.",
        "notes": "PMID:31802527, PMC6960443. Scientific Abstract directly read in Europe PMC core metadata with matching DOI. XML Results embj2019102586-sec-0005 and Methods sec-0011/sec-0018/sec-0019 were read. This yeast study explicitly includes macro- and microautophagic ER turnover. Their contributions depend on the trigger; do not universalize measured proportions. Nem1-Spo7 and ESCRTs contribute to micro-ER-phagy, but ESCRT mutants also impair nonselective autophagy and vacuolar function, so their defects are not micro-ER-phagy-specific absence tests. Atg40 is dispensable for the Atg7-independent micro route. Pho8 assays require background correction; the Sec63-GFP assay quantifies Pep4-dependent, Atg7-independent cleavage products using unsaturated exposures. Uptake or membrane scission alone does not prove complete degradation. Actual figures, supplements, complete Methods and independent strain provenance were not inspected."
      }
    ],
    "discussions": [
      {
        "discussion_id": "er-phagy-route-scope-and-flux",
        "prompt": "Review route-inclusive scope and cargo-selective degradative flux.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Use autophagy traitmech:000638 as parent. The 2014 microautophagy study and the 2019 online/2020 issue ESCRT paper support a route-inclusive phenotype, whereas Mochida et al. 2015 use autophagy specifically for macroautophagy. GO:0061709 reticulophagy, resolved at https://www.ebi.ac.uk/QuickGO/services/ontology/go/terms/GO%3A0061709, is a nonobsolete biological process whose definition specifies autophagosomes and whose exact synonyms include ER-phagy. That route restriction and the process-to-phenotype shift prevent an exact xref here; retain the source-attributed difference for human review without silently narrowing the microbial phenotype. No synonyms or SSSOM mapping are asserted. ER stress, unfolded-protein responses, ER-associated protein degradation outside the lysosome/vacuole, bulk cytoplasmic turnover, gene presence, puncta or accumulated whorls alone are insufficient. Nuclear-envelope cargo can overlap nucleophagy without making the two traits equivalent.",
        "posed_by": "codex",
        "posed_date": "2026-10-06"
      },
      {
        "discussion_id": "er-phagy-exemplars-and-route-mechanisms",
        "prompt": "Resolve natural exemplars and route-specific protein mechanisms.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Canonical examples remain unset because natural strain provenance has not been independently verified for the laboratory reporter and perturbation strains. Do not infer natural or engineered origin from a mutant label. The yeast doing the degradation carries this phenotype; a bacterium eliciting an animal-host response does not. Resolve native taxon-paired protein accessions and direct functional evidence before adding a causal graph. Neither Atg39/Atg40 nor Nem1-Spo7/ESCRT dependence is an unconditional definition of ER-phagy across all routes and microbial taxa. Keep reduced rates, residual turnover and complete absence distinct, and do not equate impaired vacuolar function with selective loss of this phenotype.",
        "posed_by": "codex",
        "posed_date": "2026-10-06"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-06T12:48:38Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added route-inclusive ER-phagy under autophagy with three DOI-backed scientific-abstract snippets and explicit selectivity, flux and source-access limits. Ignored-and-hidden searches and pinned METPO review found no exact record. Reserved METPO:1059500 in v518 with v514's unchanged parent context. Deferred unverified examples, mappings and protein graphs.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000731",
    "label": "eukaryotic flagellar autotomy",
    "definition": "A physiological phenotype in which a microbial eukaryote sheds its cilia or flagella by regulated severing of their axonemes near the base.",
    "definition_source": "DOI:10.1186/1471-2121-4-11",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1186/1471-2121-4-11",
        "snippet": "fla10 cells lose flagella by deflagellation at 33 degrees C.",
        "notes": "Parker and Quarmby 2003, PMID:12930563, PMCID:PMC194436, scientific abstract Results, second sentence. Direct MED text match; native VERIFIED applies to that text, not the PDF degree-symbol typography. Background distinguishes basal axonemal severing from resorption. The quoted response concerns source-named Chlamydomonas fla10 in calcium-containing medium, not reference strain WTB214. Released flagella were counted per 100 cells, with the initial count subtracted; lengths are a separate endpoint. Low calcium is not calcium-free, and buffer exchange is a confound. All twelve main PDF pages and eight figures were inspected. No universal IFT or calcium requirement follows."
      },
      {
        "reference": "DOI:10.1534/g3.116.034264",
        "snippet": "Wild-type cells deflagellate completely in response to pH shock or dibucaine, regardless of the temperature",
        "notes": "Hilton et al. 2016, PMID:27520959, PMCID:PMC5068960.1, page 3416, Results and Discussion subsection ADF2 and ADF4 remain unassigned, first paragraph and Figure 4A. Contiguous JATS and typeset match; native NOT_IN_ABSTRACT retained. The comparison is 21 versus 33 degrees C after six hours, not every temperature. The assay scores the control-normalized decrease in biflagellate cells per 100 cells, not a direct count of released flagella or proof that every responding cell loses both. Figure 4A reports three independent experiments with SD. All ten main pages, four figures and three tables were inspected; supplements remain unread. Phototaxis screening alone is not the shedding endpoint."
      }
    ],
    "discussions": [
      {
        "discussion_id": "eukaryotic-flagellar-autotomy-scope",
        "prompt": "Review the basal axonemal shedding endpoint and its phenotype parent.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "This organism-level phenotype concerns regulated release of a eukaryotic cilium or flagellum, not possession, arrangement, assembly failure or nonmotility. Resorption, retained-organelle disassembly, passive breakage, distal vesicle release and premitotic basal-body release alone do not establish the endpoint. Bacterial flagellar ejection or resorption involves a different apparatus and is outside this qualified class. The phenotype parent METPO:1000059 is a definition-based inference; motility is not a required parent. Palmelloid formation traitmech:000654 does not require flagellar loss. No exact synonyms, organism-level disjointness or universal stimulus threshold are asserted.",
        "posed_by": "codex",
        "posed_date": "2026-10-15"
      },
      {
        "discussion_id": "eukaryotic-flagellar-autotomy-metpo",
        "prompt": "Review current ontology scope without reviving obsolete morphology identifiers.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "The inspected pinned and current METPO release/editor/template scope has no active exact shedding class. Historical METPO:0000089 and METPO:000090 are deprecated with OMO:0001000; METPO:1000381 is deprecated with IAO:0000226. All point to METPO:1000704, which denotes locomotory flagellar possession, not autotomy. Deprecated ciliated METPO:0000093 and METPO:000094 carry OMO:0001000, while METPO:1000385 carries IAO:0000226; no replacement or consider annotation was observed for these or deprecated flagellum METPO:1000123, whose recorded reason is OMO:0001000. Those historical morphology terms are not exact xrefs and are not reactivated. METPO issue https://github.com/berkeleybop/metpo/issues/521 records unresolved reason-code interpretation. Current upstream describes a bacterial/archaeal focus, so adoption of this microbial-eukaryote proposal requires maintainer review. The ontology pin stays unchanged. Proposal v607 reserves METPO:1068400 within 1068400-1068499; no upstream release or human sign-off is implied.",
        "posed_by": "codex",
        "posed_date": "2026-10-15"
      },
      {
        "discussion_id": "eukaryotic-flagellar-autotomy-mechanism",
        "prompt": "Keep the shedding phenotype separate from universal katanin or sequence-based mechanism claims.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "A protein-resolved graph requires taxon-paired authority-checked accessions and edge-specific experiments. Domain, motif, gene or mutant names alone do not establish the organismal phenotype. The p60 study constrains a proposed universal severing mechanism; it does not establish dispensability of every katanin function. No universal FA1, FA2, TRP15, IFT or calcium requirement is asserted. Mechanisms are deferred, not claimed absent.",
        "evidence": [
          {
            "reference": "DOI:10.1242/jcs.096941",
            "reference_title": "PF19 encodes the p60 catalytic subunit of katanin and is required for assembly of the flagellar central apparatus in Chlamydomonas",
            "supports": "SUPPORT",
            "evidence_source": "full_text",
            "snippet": "microtubule severing activity of p60 is not required for deflagellation",
            "explanation": "Supports the bounded mechanistic limitation, not an additional definition citation or a claim that every katanin function is dispensable.",
            "notes": "Dymek and Smith 2012, PMID:22467860, PMCID:PMC3516377, Discussion subsection Is katanin required for flagellar excision in Chlamydomonas? Direct HTML match; native NOT_IN_ABSTRACT retained. Main text and all six figures were inspected; supplements were not. Figure 5A assays cellular shedding; Figure 2 assays purified protein. Transcript knockdown is not verified protein depletion. The reference A54-e18 carries listed mutations, and the tested mutants are not nulls."
          }
        ],
        "posed_by": "codex",
        "posed_date": "2026-10-15"
      },
      {
        "discussion_id": "eukaryotic-flagellar-autotomy-provenance",
        "prompt": "Resolve strain provenance and preserve source-access limits before adding canonical taxa.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Study organism and strain names remain qualified observations, not canonical taxon assertions. Distinct papers from the Quarmby group are not independent-laboratory replication. MED/Crossref fields and available PubMed/publisher records were checked for notices; this is not comprehensive correction/retraction clearance. Publisher DOI requests failed in the follow-up, some PMC requests returned challenge pages, and the 2003 PubMed page yielded no usable text. Those failures do not negate earlier directly retrieved primary materials, but are not successful source checks. The 2016 supplementary index digest mismatch remains recorded; nine substantive assets matched supplied digests. No paid research, human sign-off or raw-data reanalysis is implied.",
        "posed_by": "codex",
        "posed_date": "2026-10-15"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-15T07:50:51Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added the microbial eukaryotic basal-axoneme shedding phenotype with two primary DOI sources and directly checked 10/15-word snippets. Retained native VERIFIED and NOT_IN_ABSTRACT outcomes respectively, plus separate 10-word full-text mechanism-limitation evidence with native NOT_IN_ABSTRACT. Reserved 000731, v607 and 1068400-1068499 after ignored/hidden current-file, retained-history, full-range and open/draft PR checks. No obsolete identifier, canonical taxon, exact mapping or universal protein requirement is inferred. The timestamp records observed acceptance, not a reconstructed acquisition time.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000734",
    "label": "eukaryotic flagellar axoneme internalization",
    "definition": "A physiological phenotype in which a microbial eukaryote internalizes the intact axoneme of its own cilium or flagellum into its cell body.",
    "definition_source": "DOI:10.1002/cm.21637",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1002/cm.21637",
        "snippet": "axonemes remain intact during internalization",
        "notes": "Venard et al. 2020, PMID:33103844, PMCID:PMC7944584, Results 2.2, TEM interpretation paragraph following Figure 2. Contiguous span checked in direct PMC HTML; native NOT_IN_ABSTRACT retained. Live phase microscopy, fixed immunofluorescence and TEM concern Rhizoclosmatium globosum JEL800 and Spizellomyces punctatus DAOM BR117. Internalized cross-sections retain 9+2 architecture without a surrounding ciliary membrane; fixed TEM is not continuous same-cell tracking. Figure 1's 23 and 32 cells are selected retraction events, not biological-culture counts. Methods time zero is plating, whereas Figure 2's TEM caption says post-retraction; retain that timing discrepancy. Table 1 labels length/diameter with rate units unlike Table 2; no numerical conversion or rate is asserted here. Main text and all five actual main figures were inspected. The main PDF and actual supplemental PDFs/videos remain unread. Subsequent degradation is a separate phase, not a requirement for this internalization phenotype."
      },
      {
        "reference": "DOI:10.1083/jcb.201701074",
        "snippet": "Bd zoospores retracting their flagella by coiling the entire axoneme into the cell body",
        "notes": "Fritz-Laylin et al. 2017, PMID:28473602, PMCID:PMC5461030.1, Discussion JATS s11, printed page 1681, PDF page 9. Direct normalized JATS and typeset passage checked; native NOT_IN_ABSTRACT retained. Bd denotes Batrachochytrium dendrobatidis, source strain JEL423, with synchronized zoospores observed under the described confinement preparation. Results s10, Discussion s11 and Methods s20 were read, along with selected PDF pages. Video 5 was inspected through 16 sampled frames and one enlarged frame, not continuous playback or every-frame analysis. File metadata reports 10.1 seconds at nominal 10 fps, burned-in labels span 0-20 seconds, and the caption states 0.1-second acquisition with 20-fps playback. These are not silently reconciled; no retraction rate or replicate count is inferred. The paper's WASP/SCAR pseudopod experiments do not establish an axoneme-internalization mechanism."
      }
    ],
    "discussions": [
      {
        "discussion_id": "eukaryotic-axoneme-internalization-scope",
        "prompt": "Review intact withdrawal separately from later axonemal disassembly.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "The defining endpoint is internalization of the cell's own intact eukaryotic axoneme. Static internal localization, uptake of another cell's material, external coiling, failed assembly, motor arrest, passive breakage or shedding alone do not establish it. Venard et al. 2020 place internalization within a broader cilium-disassembly program while distinguishing subsequent degradation. The operational resorption record traitmech:000733 requires shortening through axonemal disassembly, not intact withdrawal alone. Later degradation can occur after internalization; no organism-level disjointness or permanently intact internal axoneme is asserted. Autotomy traitmech:000731 and bacterial polar flagellar ejection traitmech:000732 have different endpoints; bacterial periplasmic flagella and type IV pili are different structures. Phenotype METPO:1000059 is a definition-based parent inference, without a locomotion requirement.",
        "evidence": [
          {
            "reference": "DOI:10.1091/mbc.E24-12-0577",
            "reference_title": "Dynamic remodeling of centrioles and the microtubule cytoskeleton in the lifecycle of chytrid fungi.",
            "supports": "SUPPORT",
            "evidence_source": "full_text",
            "snippet": "Centrioles separated from the degrading axoneme and remained parallel",
            "explanation": "Supports the later-degradation and centriole-remodeling distinction, not an additional definition citation, a universal centriole fate or a same-cell kinetic measurement.",
            "notes": "Long et al. 2025, PMID:40833813, PMCID:PMC12659703.2, Results S7, Centrioles shorten but are not degraded during ciliary disassembly, sentence following the coiled-complex observation; Figure 4C. Direct JATS match; native NOT_IN_ABSTRACT retained. R. globosum JEL800 fixed U-ExM stages are not longitudinal trajectories. Actual Figure 4, all supplement text and visual supplement pages 4, 7 and 8 were inspected. The main-text S2 pointer concerns a transcriptomic figure; the relevant centriole panels are S3F-H. Figure 4's caption gives about 4.5-fold expansion, versus 5.5 +/- 0.2 in Results S6 (Supplemental Figure S3A-B); no absolute-size conversion is inferred. Figure 4F counts 16, 3, 26 and 41 sporangia across categories from three to five independent experiments, not retraction events. The two-hour timeline is attributed to 2020, not a new measurement. Other actual main figures, the main PDF and other supplement pages were not visually inspected. The preprint is another version, not another study."
          }
        ],
        "posed_by": "codex",
        "posed_date": "2026-10-15"
      },
      {
        "discussion_id": "eukaryotic-axoneme-internalization-metpo",
        "prompt": "Review microbial-eukaryote scope and the proposed phenotype parent.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "No active exact term was identified in the inspected pinned/current METPO release, editor and templates. Deprecated METPO:0000089 and METPO:000090 carry OMO:0001000; METPO:1000381 carries IAO:0000226. Their active replacement METPO:1000704 denotes locomotory flagellar possession, not internalization. Deprecated ciliated METPO:0000093 and METPO:000094 carry OMO:0001000, while METPO:1000385 carries IAO:0000226; no replacement or consider annotation was observed for those or deprecated flagellum METPO:1000123 with OMO:0001000. Historical identifiers are not exact xrefs and are not reactivated. https://github.com/berkeleybop/metpo/issues/521 leaves reason-code interpretation unresolved. Upstream's bacterial/archaeal focus requires maintainer review of microbial-eukaryote inclusion. Proposal v610 reserves METPO:1068700 in 1068700-1068799, not a released identifier or human-approved mapping. The ontology pin is unchanged.",
        "posed_by": "codex",
        "posed_date": "2026-10-15"
      },
      {
        "discussion_id": "eukaryotic-axoneme-internalization-mechanism",
        "prompt": "Keep observable internalization separate from universal molecular mechanisms.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Do not require a universal reeling, lash-around, membrane-loss, cortical tethering, actin-dependent, dynein-dependent or proteolytic mechanism. The 2020 latrunculin live-movie analysis selected complete retractions and excluded cells retaining cilia; its conditional results cannot establish all-cell retraction probabilities. Do not transfer 2017 pseudopod perturbations or 2025 transcript/orthology patterns to this phenotype. A gene, domain, motif or profile alone does not establish intact axoneme internalization. A protein-resolved graph requires taxon-paired, authority-checked accessions and edge-specific evidence. No universal rate, cell-cycle stage, complete degradation, protein recycling, exact synonym or equivalent external mapping is asserted.",
        "posed_by": "codex",
        "posed_date": "2026-10-15"
      },
      {
        "discussion_id": "eukaryotic-axoneme-internalization-provenance",
        "prompt": "Resolve canonical strain provenance while preserving source-access limits.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "The named laboratory strains remain qualified life-stage observations, not authority-verified canonical taxa or proof of natural provenance. Two distinct supporting publications are not a claim of independent-lab replication. The 2025 follow-up shares authors with earlier work and is scope context, not a third definition citation. Qualified MED/Crossref identities and available notice fields were checked, not comprehensive correction/retraction clearance. The linked 2017 Comment/Editorial, DOI:10.1080/15384101.2017.1360655, PMID:28820330, PMC5628642, has no returned abstract and its content remains unread; it is not counted evidence. Publisher/PMC access failures remain failures. The 2020 supplement endpoint returned an API error with HTTP 200, not a ZIP; no actual supplement contents are inferred. No raw-data reanalysis, paid research or human scientific sign-off is implied.",
        "posed_by": "codex",
        "posed_date": "2026-10-15"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-15T20:08:47.827435+00:00",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added the microbial-eukaryote intact-axoneme internalization phenotype with two primary DOI sources and checked 5/14-word full-text snippets. Kept a nine-word 2025 later-degradation excerpt in a scope discussion, not definition evidence. All three retain native NOT_IN_ABSTRACT. Reserved 000734, v610 and 1068700-1068799 after ignored/hidden current-file, retained-history, complete-range and open/draft PR checks. Preserved source-access and assay limitations; no obsolete identifier, canonical taxon, exact mapping or universal protein mechanism is inferred. The timestamp is the observed allocation decision, not source acquisition.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-15T21:05:50Z",
        "curator": "codex",
        "action": "CORRECT_EVIDENCE_LOCATOR",
        "changes": "Corrected the 2025 expansion-factor locator from Methods/S3B to Results S6, MTOC remodeling from mitosis to ciliogenesis, first paragraph, citing Supplemental Figure S3A-B. Cached JATS S6/S15 and actual Figure S3 were reread for issue #1950. Preserved values, discrepancy, definition, source roles, snippets and previous history.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000733",
    "label": "eukaryotic flagellar resorption",
    "definition": "A physiological phenotype in which a microbial eukaryote shortens previously assembled cilia or flagella through disassembly of their axonemes.",
    "definition_source": "DOI:10.1083/jcb.100.2.457",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1083/jcb.100.2.457",
        "snippet": "Cells under resorption-inducing conditions rapidly shortened their flagella",
        "notes": "L'Hernault and Rosenbaum 1985, PMID:3968171, PMCID:PMC2113451.1, printed page 458, Results, Monitoring of Flagellar Length during In Vivo Labeling, sole paragraph; Figure 2 on page 459. Contiguous typeset and whitespace-normalized OCR match; native NOT_IN_ABSTRACT retained. The XML body is a single OCR preformat block, not a section-structured JATS paragraph. Source-designated wild-type Chlamydomonas reinhardtii 21gr was mechanically deflagellated and pulse-chase labelled during regeneration before resorption was induced with 15 mM sodium pyrophosphate at pH 7.5 plus cycloheximide; HEPES was the control. The shortening concerns regenerated flagella, not failed assembly. Apparent flagellalessness after 90 minutes still permits the reported short stubs. Protein fractionation supports transfer to the cell body, not complete recycling. All six main PDF pages, three figures and Table I were inspected; raw data were not reanalyzed. Figure 1's two determinations and Table I's two gels per sample are not established biological-replicate counts."
      },
      {
        "reference": "DOI:10.1186/1471-2121-4-11",
        "snippet": "Acid shock causes resorption of mutants unable to deflagellate.",
        "notes": "Parker and Quarmby 2003, PMID:12930563, PMCID:PMC194436, Figure 7 caption, first sentence, page 9 of 12; JATS F7 under sec9/sec5. Direct caption and typeset match; native NOT_IN_ABSTRACT retained. The acid-shock experiments concern Chlamydomonas fa1, fa2 and adf1 mutants, with coiling and incomplete resorption described; wild-type cells instead shed and regrow their flagella in this comparison. Figure 7 scores the fraction of cells with flagella longer than 7 micrometers, not a resorption rate or count of released organelles. The separate fla10 temperature experiments must not be merged with this assay. Low-calcium HEPES is not calcium-free: Methods retain trace calcium and do not add chelators. The main length measurements count at least 70 cells per time point and use at least three independent cultures. All twelve main PDF pages and eight figures were inspected. Proposed basal disassembly and shared severing machinery are not universal requirements of this class."
      }
    ],
    "discussions": [
      {
        "discussion_id": "eukaryotic-flagellar-resorption-scope",
        "prompt": "Review shortening through disassembly without requiring complete disappearance.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "This physiological phenotype concerns shortening of a previously assembled eukaryotic axoneme. Static short flagella, failed assembly, nonmotility, bending or coiling, passive breakage, or shedding a largely intact organelle alone do not establish it. Neither complete structural disappearance nor complete protein recycling is required. Basal severing and residual transition zones can accompany resorption; the class does not require an intact base or the absence of severing. Eukaryotic flagellar autotomy traitmech:000731 and bacterial polar flagellar ejection traitmech:000732 have different endpoints. Bacterial periplasmic resorption involves a different apparatus. No organism-level disjointness is asserted. Phenotype METPO:1000059 is the definition-based parent; locomotion is not required. Palmelloid formation traitmech:000654 does not require flagellar loss.",
        "evidence": [
          {
            "reference": "DOI:10.1002/cm.20454",
            "reference_title": "Centrioles are freed from cilia by severing prior to mitosis.",
            "supports": "SUPPORT",
            "evidence_source": "abstract",
            "snippet": "resorbing flagella of Chlamydomonas leave remnants associated with the mother cell wall.",
            "explanation": "Supports the remnant/scope limitation, not an additional definition citation, a universal severing mechanism or complete recycling.",
            "notes": "Parker et al. 2010, PMID:20506243, PMCID:PMC2897710.1, scientific abstract, JATS paragraph P2, third sentence. Direct JATS and MED scientific-abstract matches; native VERIFIED retained. Main text, Methods, Results, Discussion, Conclusions and three captions were read, not the actual figures, PDF, supplementary video, supplementary legend or raw data. Live pf6 CC1029 observations and wild-type 137c mt- CC124 electron microscopy concern different preparations. Paired spots in daughter-cell clusters are not a flagellar-resorption rate. Remnants may remain in the wall or be expelled; do not universalize this premitotic context to every resorption stimulus."
          }
        ],
        "posed_by": "codex",
        "posed_date": "2026-10-15"
      },
      {
        "discussion_id": "eukaryotic-flagellar-resorption-metpo",
        "prompt": "Review microbial-eukaryote scope without reviving obsolete morphology identifiers.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "The inspected pinned/current METPO releases, editor and templates have no active exact resorption class. Historical METPO:0000089 and METPO:000090 carry OMO:0001000; METPO:1000381 carries IAO:0000226. All are deprecated and point to active METPO:1000704, which denotes locomotory flagellar possession, not resorption. Deprecated ciliated METPO:0000093 and METPO:000094 carry OMO:0001000, while METPO:1000385 carries IAO:0000226; no replacement or consider annotation was observed for those or deprecated flagellum METPO:1000123, whose reason is OMO:0001000. Historical terms are not exact xrefs and are not reactivated. https://github.com/berkeleybop/metpo/issues/521 records unresolved reason-code interpretation. Upstream's bacterial/archaeal focus requires maintainer review of this microbial-eukaryote proposal. The ontology pin stays unchanged. Proposal v609 reserves METPO:1068600 in 1068600-1068699; neither upstream release nor human sign-off is implied.",
        "posed_by": "codex",
        "posed_date": "2026-10-15"
      },
      {
        "discussion_id": "eukaryotic-flagellar-resorption-mechanism",
        "prompt": "Keep the phenotype separate from universal disassembly or sequence-based mechanisms.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "The studies discuss different models of axonemal disassembly. Do not require a universal tip-to-base direction, basal severing site, tubulin modification, IFT defect, calcium threshold, stimulus or cell-cycle transition. Induced and mutant observations support the phenotype without becoming natural canonical exemplars. A protein-resolved graph requires taxon-paired authority-checked accessions and edge-specific experiments. A gene, domain, motif or sequence profile alone does not establish organelle resorption. Mechanisms are deferred, not claimed absent. No exact synonyms or mappings are asserted.",
        "posed_by": "codex",
        "posed_date": "2026-10-15"
      },
      {
        "discussion_id": "eukaryotic-flagellar-resorption-provenance",
        "prompt": "Resolve strain provenance and preserve source-access limits before adding canonical taxa.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Source-designated strain names remain qualified observations; laboratory wild type is not proof of natural provenance, and a mutant label alone does not establish genetic engineering. Two distinct supporting publications are not a claim of independent-laboratory replication. The 2010 context paper shares authors with the 2003 study and is not a third definition citation. MED/Crossref identities and available publisher/PubMed notice fields were checked; this is not comprehensive correction/retraction clearance. Some publisher, PMC and PubMed attempts failed or returned challenge pages. Public PMC cloud assets and the directly retrieved 2003 PDF/XML retain their own successful provenance; failed requests are not relabeled as successful source checks. No raw-data reanalysis, paid research or human scientific sign-off is implied.",
        "posed_by": "codex",
        "posed_date": "2026-10-15"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-15T16:01:11Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added the microbial eukaryotic axonemal-resorption phenotype with two primary DOI sources and directly checked 8/9-word full-text snippets, both retaining native NOT_IN_ABSTRACT. Kept the 12-word remnant-limitation scientific-abstract excerpt with native VERIFIED in a discussion, not definition evidence. Reserved 000733, v609 and 1068600-1068699 after ignored/hidden current-file, retained-history, complete-range and open/draft PR checks. No obsolete identifier, canonical taxon, exact mapping or universal protein mechanism is inferred. The timestamp records the observed allocation decision after the fresh guard, not source acquisition.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-15T17:05:25Z",
        "curator": "codex",
        "action": "CORRECT_EVIDENCE_QUANTITY",
        "changes": "Retained at least three independent cultures as the replication lower bound reported in the 2003 Methods, Timecourses and flagella length measurements, page 11 of 12. Source XML and the typeset page were rechecked for issue #1948. Preserved definition, snippets, references, other evidence and prior history.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000637",
    "label": "exocytosis",
    "definition": "A physiological phenotype in which a microbial cell releases material from an intracellular membrane-bounded compartment to the cell exterior through a fusion pore between the compartment membrane and the plasma membrane.",
    "definition_source": "DOI:10.1083/jcb.56.1.153",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1083/jcb.56.1.153",
        "snippet": "The cytoplasm between the two matching membrane sites is squeezed away and the membranes fuse",
        "notes": "PMID:4629881, PMC2108847. Scientific Abstract directly read in Europe PMC XML and PubMed. The quote retains the source's missing terminal punctuation. Freeze-fracture/etch observations in the historically named Tetrahymena pyriformis system connect mucocyst-plasma-membrane fusion, opening enlargement and contents release. Fixation triggers some discharge. Abstract-level evidence does not establish a universal pore size or fusion machinery. The XML has sparse body content and the PDF endpoint returned HTML; full methods, figures and strain provenance were not inspected."
      },
      {
        "reference": "DOI:10.1007/BF01870409",
        "snippet": "Upon returning the cells to the permissive temperature the contents of the accumulated vesicles were secreted.",
        "notes": "PMID:1744905. Scientific Abstract directly read in NCBI PubMed XML and Europe PMC metadata, which agree on the DOI. Constitutive secretion in Saccharomyces cerevisiae is examined using temperature-sensitive sec mutants, accumulated vesicles and blocked protein synthesis. Calcium perturbations did not affect the measured release under these conditions; this does not establish calcium irrelevance in every yeast context. No universal rate or requirement for extracellular stimulation is inferred. Full methods, figures and strain provenance remain unread."
      },
      {
        "reference": "DOI:10.1016/s0143-4160(98)90030-6",
        "snippet": "This is a detailed characterization of a secretory mutant incapable of releasing secretory contents despite normal exocytotic membrane fusion performance.",
        "notes": "PMID:9681197. Scientific Abstract verified in PubMed XML and Europe PMC metadata. Relevant Methods, Results and Discussion were read in the primary PDF at https://d-nb.info/1107191386/34; pages 349-350 and 354-356, including Figures 6-9, were visually inspected. Paramecium caudatum tnd1 retains condensed cargo despite fusion and extracellular fluorochrome access. Figure 9 shows untriggered mutant cells, not a wildtype experiment. This supports separation of fusion and discharge, not tnd1 as a positive example of completed secretion. Reduced calcium binding is a proposed explanation, not a proven molecular lesion. Other figures and tables were not visually audited."
      }
    ],
    "discussions": [
      {
        "discussion_id": "exocytosis-scope-and-mapping",
        "prompt": "Separate the secretion phenotype from its component steps.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "This concerns secretion by the microbe, not a host-cell response. Docking, intracellular trafficking or fusion alone does not demonstrate cargo release. Transporter-mediated export, membrane budding, lysis, cell-cell fusion and endocytosis are not equivalents. Constitutive and stimulus-regulated secretion are included; total emptying, permanent vesicle collapse and a shared calcium response are not required. GO:0006887 was resolved at https://www.ebi.ac.uk/QuickGO/services/ontology/go/terms/GO%3A0006887 and includes partial secretion through transient pores, but denotes a biological process rather than an equivalent organismal phenotype. No xref or synonym is inferred. The obsolete METPO secretion classes are broader, not exact replacements or usable parents. Retain phenotype METPO:1000059 pending human mapping review.",
        "posed_by": "codex",
        "posed_date": "2026-10-06"
      },
      {
        "discussion_id": "exocytosis-exemplar-and-mechanism",
        "prompt": "Resolve natural strain provenance and route-specific mechanisms.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Canonical examples remain unset: the historical Tetrahymena strain needs modern taxonomy and provenance review, the yeast experiment uses conditional sec mutants, and the origin of the Paramecium tnd1 mutant has not been independently checked. Do not infer natural or engineered provenance from a mutant label. The fusion-only mutant is boundary evidence, not a positive secretion exemplar. These studies support phenotype scope across experimental systems, not one conserved protein mechanism. Obtain taxon-paired functional evidence and verified accessions before adding protein examples or a causal graph.",
        "posed_by": "codex",
        "posed_date": "2026-10-06"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-06T08:06:46Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added exocytosis with three DOI-backed scientific-abstract snippets and explicit secretion-versus-fusion, strain and source-access limits. Ignored-and-hidden searches and pinned METPO review found no exact record. Reserved METPO:1059000 in v513. Deferred unverified examples, mappings and protein mechanisms; no existing trait was reparented.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000649",
    "label": "extracellular membrane vesicle production",
    "definition": "A physiological phenotype in which microbial cells give rise to closed, cell-derived lipid-membrane vesicles in the extracellular space.",
    "definition_source": "DOI:10.1038/ncomms11220",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:420247",
        "taxon_label": "Methanobrevibacter smithii ATCC 35061",
        "reference": "DOI:10.1038/s41467-025-60272-9",
        "note": "Type strain PS (= ATCC 35061 = DSM 861). Vesicles were purified from exponentially growing cultures at 37 C in modified DSM 119 medium under H2/CO2 and examined by TEM. The collection record https://www.dsmz.de/collection/catalogue/details/culture/DSM-861 traces PS to a primary sewage digester in Gainesville, not to a human donor; it supplies provenance, not independent vesicle evidence. NCBI Taxonomy resolves this strain to species 2173. This is a culture observation, not direct in-gut vesicle production."
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/ncomms11220",
        "snippet": "Super-resolution microscopy reveals that explosive cell lysis also produces shattered membrane fragments that rapidly form MVs.",
        "notes": "PMID:27075392, PMC4834629. Scientific Abstract, not the editorial teaser, directly read in Europe PMC XML; selected Results and strain/isolation Methods also read. Live super-resolution imaging in Pseudomonas aeruginosa distinguishes vesicles from fragments and supports membrane reassembly after lysis. Lys dependence in biofilms/stress does not extend to ordinary oxic planktonic cultures, where the lys mutant retains comparable MV levels. Reporter/deletion/rescue experiments are qualified observations, not proof of one universal route. Actual panels and supplements were not visually inspected."
      },
      {
        "reference": "DOI:10.1038/s41467-017-00492-w",
        "snippet": "Through these openings, cytoplasmic membrane material protrudes into the extracellular space and is released as MVs.",
        "notes": "PMID:28883390, PMC5589764. Scientific Abstract, separate from the appended teaser, and selected Results/Methods directly read in Europe PMC XML. The openings are endolysin-associated peptidoglycan holes in Bacillus subtilis. Live imaging and induced strains support extrusion from cells that ultimately die; tomography uses an engineered skinny ponA deletion, not wild-type cells. Static tomographic stages are not a measured time sequence. This route differs from explosive-fragment reassembly. This study and the 2016 paper share investigators; they are not independent-laboratory replications. Actual panels were not visually inspected."
      },
      {
        "reference": "DOI:10.1371/journal.pone.0011113",
        "snippet": "Bilayered vesicles with diameters at the 100\u2013300 nm range were found in extracellular fractions from yeast cultures.",
        "notes": "PMID:20559436, PMC2885426. Scientific Abstract and Methods s2a-s2c, Results s3a/s3d directly read in Europe PMC XML. Saccharomyces cerevisiae WT and trafficking mutants yield vesicles after supernatant fractionation and TEM. Heat-killed controls yielded no vesicle-like structures; viability controls were reported without displayed data. SEC/MVB perturbations alter composition and sterol-based release proxies without abolishing production. The abstract's concluding requirement language is not taken as a universal necessity claim. Size is assay-specific; WT denotes laboratory comparators, not verified natural isolates. Actual panels were not visually inspected."
      },
      {
        "reference": "DOI:10.1038/s41467-025-60272-9",
        "snippet": "The EVs were isolated from exponentially growing M. smithii cultures to limit the contamination of the EV preparations with cell debris.",
        "notes": "PMID:40461479, PMC12134362. Full-text Results Sec3 quote, not an abstract quote, checked in Europe PMC XML. Sec3/Sec7 and Methods Sec10-Sec12 describe PS cultures, density-gradient purification, TEM and particle assays. Instrument detection limits yield different size distributions. Cryo-ET suggests budding and wall passage; the large-vesicle lysis route is hypothesized, not directly demonstrated. DNA/protein cargo annotations do not demonstrate increased methane production. Actual panels and supplements were not visually inspected."
      }
    ],
    "discussions": [
      {
        "discussion_id": "extracellular-vesicle-production-scope-and-mapping",
        "prompt": "Separate vesicle production from particle identity and cargo effects.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Include vesicles produced by non-lytic release or membrane reassembly after cell lysis; the producer need not survive. Require evidence for intact extracellular vesicles, not bulk membrane-dye signal, unclosed debris, intracellular organelles, whole daughter cells or virions. Vesicle-associated viral DNA alone does not make a particle a virion. Gas vesicles are proteinaceous intracellular inclusions. Exocytosis traitmech:000637 describes fusion-pore discharge, which need not release an intact vesicle. The yeast source attributes roles to both conventional and unconventional trafficking, so unconventional protein secretion traitmech:000648 is not a universal parent; possible overlap is not disjointness. Outer-membrane vesicles and exosomes are narrower or route-specific usages, not exact synonyms. No universal size, cargo, lipid-bilayer architecture or ecological function is imposed. Retain phenotype METPO:1000059 pending human hierarchy and external mapping review; no exact xref is asserted.",
        "posed_by": "codex",
        "posed_date": "2026-10-06"
      },
      {
        "discussion_id": "extracellular-vesicle-production-route-mechanisms",
        "prompt": "Ground separate biogenesis mechanisms without universalizing them.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "The bacterial sources support distinct endolysin-associated routes; the yeast work supports trafficking contributions; the methanogen's budding and large-vesicle lysis models remain qualified. No common protein apparatus follows from these observations. Before adding route-specific causal graphs, inspect the remaining panels, supplements and strain provenance and resolve the relevant protein accessions with taxon-paired functional evidence. The verified PS exemplar does not ground bacterial Lys or yeast SEC proteins. Do not infer vesicle production from a sequence feature, cargo annotation, membrane blebbing alone or an isolation protocol that mechanically manufactures particles from cells.",
        "posed_by": "codex",
        "posed_date": "2026-10-06"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-06T19:52:36Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added extracellular membrane vesicle production with four DOI-backed snippets and a provenance-qualified M. smithii PS example. Ignored-and-hidden duplicate searches and the pinned METPO audit found no exact record. Reserved METPO:1060200 in v525. Retained route, particle-identity and mapping limits; existing records are unchanged.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000715",
    "label": "extracellular-trail-based spatial memory",
    "definition": "A physiological phenotype in which a microorganism's subsequent spatial exploration is guided by persistent extracellular trails deposited during earlier movement.",
    "definition_source": "DOI:10.1073/pnas.1215037109",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1073/pnas.1215037109",
        "snippet": "When one arm contained extracellular slime, 39 of 40 plasmodia chose the blank agar arm",
        "notes": "Reid et al. 2012, PMID:23045640, PMC3491460; Results opening paragraph, printed page 17490 / PDF page 1. Cultured Physarum polycephalum avoided previously deposited slime in a Y maze. Same-stock coatings do not demonstrate individual recognition of one's own trace. In the separate U-trap experiment, 23/24 plasmodia on blank agar versus 8/24 on slime-coated agar reached the target within 120 hours. Coating masks newly informative trails; it does not abolish secretion or lesion internal memory. Success, completion time among successful trials, speed, path length and revisitation are distinct endpoints. No-trap and speed controls do not exclude every environmental confound. Main Methods, Results, Discussion and all four figures were inspected in an author-hosted publisher-formatted PDF bearing a 2012 download stamp, not verified as the current corrected VoR. Supplements and raw data were not assessed. Southern Biological Supplies culture provenance remains unresolved. The contiguous result span was text-matched and visually checked."
      },
      {
        "reference": "DOI:10.1088/1361-6463/aa87df",
        "snippet": "Our results suggest that the external memory has an adaptive advantage in \u2018open\u2019 and simple bounded environments.",
        "notes": "Smith-Ferguson et al. 2017; scientific abstract, printed page 1 / PDF page 2. This is the authors' interpretation of maze performance, not a measured fitness or natural-selection endpoint. Within 72 hours, blank versus extracellular-slime conditions yielded success in 24/24 versus 9/24 open trials, 12/15 versus 4/12 simple-maze trials and 11/17 versus 11/13 complex-maze trials; the last comparison showed no significant benefit. Completion times conditional on success were not significantly different. Escaped trials were excluded; split decisions used the dominant front. Printed page 6 pairs the same chi-square 0.802 with P=0.004 and P=0.371; this discrepancy is unresolved. Figure 8 is illustrative, not quantified trajectory evidence. Main Methods, Results, Discussion, Conclusion and all eight figures were inspected; supplements were not. The author-hosted PDF bears a 2017 download stamp, not verified current VoR equivalence. This study shares authors with Reid 2012, not an independent-laboratory replication."
      },
      {
        "reference": "DOI:10.1073/pnas.2312611121",
        "snippet": "In accordance with the literature, we observe that plasmodia generally avoid previously visited areas marked by their slime trail",
        "notes": "Troger et al. 2024, PMID:38517977, PMC10990088; Results, Quantifying Run-and-Tumble and Self-Avoiding Behavior, page 3. The authors report their own Physarum observations, not only a background citation. Actual trajectories, including Figure 2A, are distinct from simulated-model panels. Page 5 describes 14 trajectories divided into groups of nine each; Figure 4 instead gives seven small and seven large. The discrepancy remains unresolved. The 0.65 square-millimeter median is a cohort split, not a universal threshold. Small plasmodia can cross trails; a modeled three-hour forgetting time is not a measured chemical half-life or internal-memory duration. Main text, Methods and all four main figures were inspected in the author-hosted publisher-formatted PDF with a March 2024 download stamp, not verified current corrected VoR equivalence. Publisher supplements and raw data were not reanalyzed. This different laboratory's assay is not a replication of the earlier maze experiments; no universal molecular receptor is established."
      }
    ],
    "discussions": [
      {
        "discussion_id": "trail-memory-scope-and-hierarchy",
        "prompt": "Keep external trace-guided exploration distinct from internal memory and universal trail avoidance.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "This operational phenotype concerns spatial information persisting outside the microorganism. It does not require always avoiding a trail, improved navigation in every setting, individual self-recognition, or internal recall. Carbon-source memory (traitmech:000706), acquired stress-resistance memory (traitmech:000712), enhanced transcriptional reactivation memory (traitmech:000713) and behavioral habituation (traitmech:000714) have different endpoints. Negative autotropism (traitmech:000603) concerns germ-tube or hyphal orientation. Collective bacterial predation (traitmech:000701) concerns coordinated killing and feeding, despite a trail mention. Contact-dependent outer membrane exchange (traitmech:000650) concerns actual intercellular exchange. METPO:1000059 phenotype is the conservative parent pending hierarchy review; local chemotaxis has a flagellar-specific definition and is not a universal parent. Generic memory, learning, stigmergy and extracellular polymer production are not exact synonyms. Psl-biased visitation and community growth history require separate scope and evidence assessments.",
        "posed_by": "codex",
        "posed_date": "2026-10-13"
      },
      {
        "discussion_id": "trail-memory-source-and-mechanism-limits",
        "prompt": "Resolve source versions, assay discrepancies and culture provenance before assigning taxa or mechanisms.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Coated-versus-blank substrates manipulate spatial trace information along with the environment, not exclusively a memory molecule. The 2017 significance-statistic discrepancy and 2024 group-size discrepancy remain visible source gaps. The 2024 arXiv v1 was posted after journal publication; its seven-per-group wording and differing illumination details do not silently correct the publisher-formatted PDF. Supplement illustrations do not establish crossing frequencies. Bounded Crossref/MED and publisher checks do not establish exhaustive absence of notices or corrected-version equivalence. The evidence concerns cultured Physarum, not species-wide possession or all microbes. Natural culture provenance remains unverified. No canonical taxa, exact external mappings, protein examples or molecular causal graph are asserted. Unknown trail components, sensory mechanisms, unread supplements and raw-data reanalysis remain research gaps. Source hashes, access limits and actual native snippet-verifier outcomes are retained in the source-verification sidecar.",
        "posed_by": "codex",
        "posed_date": "2026-10-13"
      },
      {
        "discussion_id": "trail-memory-historical-identity",
        "prompt": "Retain unresolved historical adaptation and chemotaxis identity without reviving deprecated identifiers.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Pinned and inspected current METPO graphs mark METPO:0000248 and METPO:000249 Microbial Adaptation, METPO:1000004 adaptation and METPO:1000062 chemotaxis deprecated. Inspected subjects have no replacement or consider annotations; OMO:0001000 reasons are provisional under open METPO issue 521. Original historical scopes remain unresolved. Neither biological invalidity nor exact equivalence follows from their labels or deprecation reasons. This qualified external-trace phenotype is accepted independently from primary evidence. Ignored and hidden current files, available tracked history, independent copies, pending changes and inspected ontology graphs revealed no exact active record within the documented scope. No historical exact mapping is asserted. Existing records and the pinned ontology remain unchanged; discovery is not exhausted.",
        "posed_by": "codex",
        "posed_date": "2026-10-13"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-13T06:32:45Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added extracellular-trail-based spatial memory with three primary DOI sources and contiguous snippets. Retained assay, version, mechanism and historical-identity limits. Reserved 000715, v591 and 1066800-1066899 after scoped ignored/hidden, retained-history, independent-copy and pending-PR checks; numeric false positives were explicitly adjudicated. No canonical taxa or causal graph; existing records unchanged. Timestamp is the observed UTC post-audit confirmation, not an estimated write time.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000581",
    "label": "galvanotaxis",
    "definition": "A motile phenotype in which an organism biases its active movement in response to an electric field.",
    "definition_source": "DOI:10.1101/sqb.1988.053.01.006",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000702"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1101/sqb.1988.053.01.006",
        "snippet": "movement of a motile organism or cell in direct response to an electric current",
        "notes": "Adler and Shi, publisher's freely accessible Excerpt, https://symposium.cshlp.org/content/53/23.short. The full paywalled paper was not accessed. The disposition requires active motility; passive electrophoretic displacement alone is insufficient."
      },
      {
        "reference": "DOI:10.1128/jb.178.4.1113-1119.1996",
        "snippet": "motile Escherichia coli K-12 placed in an electric field swims toward the anode",
        "notes": "Shi, Stocker and Adler, primary abstract (PMID:8576046), verified through Europe PMC. Rough K-12 and smooth Salmonella differ in direction; surface composition and capsules qualify the response. Only the abstract was accessed, not the full paper."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:83333",
        "taxon_label": "Escherichia coli K-12",
        "reference": "DOI:10.1128/jb.178.4.1113-1119.1996",
        "note": "The primary abstract reports anode-directed swimming of motile rough K-12 cells. This is not a claim about every E. coli strain or an invariant direction across surface compositions."
      },
      {
        "taxon_id": "NCBITaxon:588858",
        "taxon_label": "Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S",
        "reference": "DOI:10.1038/s41564-024-01778-8",
        "note": "Figure 5 and Supplementary Table 1: Green ST is IR715, a nalidixic-acid-resistant 14028S derivative, carrying pGFT/RalFc. These fluorescent cells migrated toward the cathode at 2 V/cm in vitro. Do not substitute the SW473 flagellar mutant or the separate cheB mutant for this behavioral example."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "galvanotaxis_flagellar_motility",
        "title": "Flagellar motility in electric-field-biased migration",
        "description": "Flagellin supports the motility apparatus used for active galvanotaxis.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "The flagellar-motility branch supported in Salmonella 14028S-background cells, not a complete electrical sensing or orientation mechanism. The fliC/fljB double mutant establishes dependence on the flagellar apparatus, not individual FliC necessity or flagellin sufficiency. Host CFTR is outside this microbial graph.",
        "nodes": [
          {
            "node_id": "galvanotaxis_electric_field",
            "label": "electric field",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Applied electrical stimulus, 2 V/cm in the Sun et al. in vitro assay."
          },
          {
            "node_id": "galvanotaxis_flagellin",
            "label": "flagellin",
            "node_type": "GENE_OR_PROTEIN",
            "grounding": "InterPro:IPR001492",
            "gene_symbols": [
              "fliC",
              "fljB"
            ],
            "description": "Flagellin family forming the flagellar filament; not the entire flagellum, its rotary motor or an established electrical sensor.",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:A0A0F6B2U2",
                "protein_label": "Flagellin",
                "gene_symbol": "fliC",
                "taxon_id": "NCBITaxon:588858",
                "taxon_label": "Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S",
                "entry_status": "UNREVIEWED",
                "proteome_id": "UP000002695",
                "retrieved_on": "2026-10-03",
                "entry_version": 42,
                "sequence_version": 1,
                "role": "FliC is one of the two alternative flagellins removed together in SW473; individual FliC necessity was not established.",
                "evidence": [
                  {
                    "reference": "DOI:10.1038/s41564-024-01778-8",
                    "snippet": "Most of these mutants were non-motile",
                    "notes": "Results, flagellar-mutant paragraph and Supplementary Table 1: SW473 is an IR715 fliC/fljB double mutant. The exact 14028S FliC identity, taxon and versions were resolved at https://www.ebi.ac.uk/proteins/api/proteins/A0A0F6B2U2; https://rest.uniprot.org/proteomes/UP000002695.json confirms reference-proteome membership. UniProtKB REST protein requests failed during retrieval; the EBI Proteins API supplied the metadata. This accession anchors the strain background, not an experimentally sequenced SW473 protein."
                  }
                ]
              }
            ]
          },
          {
            "node_id": "galvanotaxis_flagellar_motility",
            "label": "flagellar motility",
            "node_type": "BIOLOGICAL_PROCESS",
            "grounding": "GO:0071973",
            "description": "Active movement powered by the bacterial flagellar apparatus."
          },
          {
            "node_id": "galvanotaxis_process",
            "label": "electric-field-biased active migration",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Biased active movement, not passive drift of fixed cells."
          },
          {
            "node_id": "galvanotaxis_trait",
            "label": "galvanotaxis",
            "node_type": "TRAIT",
            "grounding": "traitmech:000581",
            "description": "Organismal disposition for electric-field-guided active movement."
          }
        ],
        "edges": [
          {
            "subject": "galvanotaxis_electric_field",
            "predicate": "modulates",
            "predicate_id": "RO:0002211",
            "object": "galvanotaxis_process",
            "description": "An applied electric field biases active migration direction.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-024-01778-8",
                "snippet": "robustly biased migration of all cells",
                "notes": "Results and Figure 5c-e compare no-field and 2 V/cm conditions. DH5alpha K-12-background cells migrated toward the anode and IR715-background cells toward the cathode. This edge does not prescribe one direction for every microbe."
              }
            ]
          },
          {
            "subject": "galvanotaxis_flagellin",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "galvanotaxis_flagellar_motility",
            "description": "Flagellin supplies the filament component of the motility apparatus.",
            "evidence": [
              {
                "reference": "https://www.ebi.ac.uk/interpro/entry/InterPro/IPR001492/",
                "snippet": "Flagellin is the subunit protein that polymerises to form the flagella",
                "notes": "InterPro IPR001492 family description, verified through https://www.ebi.ac.uk/interpro/api/entry/interpro/IPR001492/ on 2026-10-03. This is a family, not merely an N- or C-terminal domain. Filament assembly and the motor are also required; flagellin alone is not sufficient for movement."
              }
            ]
          },
          {
            "subject": "galvanotaxis_flagellar_motility",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "galvanotaxis_process",
            "description": "Flagellar motility enables active electrical-field-guided migration.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-024-01778-8",
                "snippet": "flagella are indeed essential for electrical field-guided galvanotaxis",
                "notes": "Results, flagellar-mutant experiment: SW473 cells were mostly non-motile and unresponsive. This establishes a motility requirement, not a specific electrical sensor. Fixed-cell controls distinguish passive drift from live-cell swimming."
              }
            ]
          },
          {
            "subject": "galvanotaxis_process",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "galvanotaxis_trait",
            "description": "Electric-field-guided active movement realizes the galvanotaxis phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1101/sqb.1988.053.01.006",
                "snippet": "migration is toward the cathode or the anode",
                "notes": "Publisher's free Excerpt defines galvanotaxis and allows either pole. Direction depends on organism and context, rather than being a universal part of this trait definition."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "galvanotaxis-orientation-and-mapping-boundaries",
        "prompt": "Resolve electrical orientation mechanisms without equating active motility with passive drift.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "DOI:10.1128/jb.178.4.1113-1119.1996 proposes differential electrophoretic mobility of the body and flagellar filaments as an orientation model. DOI:10.1038/s41564-024-01778-8 observes flagellar redistribution and a largely non-motile double mutant; it does not establish a universal receptor circuit or separate the individual flagellin contributions. A cheB mutant retains the electrical response. The source's weakly biased B. subtilis assay is not a robust canonical example. Physical orientation can guide powered locomotion, but fixed-cell drift alone is not this phenotype. QuickGO searches for galvanotaxis and electrotaxis found no exact term on 2026-10-03; MeSH Taxis Response is broader and excluded from xrefs. GO:0071973 grounds only the flagellar process.",
        "posed_by": "codex",
        "posed_date": "2026-10-03"
      },
      {
        "discussion_id": "galvanotaxis-source-data-coordinate-convention",
        "prompt": "Reconcile directedness signs before importing numerical source-data values.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Sun et al., Figure 5d and Results report negative directedness for E. coli and positive for Salmonella. The source workbook's Fig. 5d,e sheet labels Red to anode and Green to cathode but contains opposite-signed cosine values. Direction labels agree with Figure 5c and the 1996 primary abstract; the coordinate conventions need reconciliation. No numerical directedness values are imported and no correction is inferred. Source: https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-024-01778-8/MediaObjects/41564_2024_1778_MOESM10_ESM.xlsx",
        "posed_by": "codex",
        "posed_date": "2026-10-03"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-03T23:20:08Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added galvanotaxis with three primary DOI sources, an InterPro family source, exact snippets, two strain-qualified examples and a flagellar-motility graph. Verified NCBI taxa, IPR001492, GO:0071973, the 14028S FliC accession and its reference proteome. Ignored-and-hidden searches found no exact trait or METPO class; reserved METPO:1053500 in proposal v458. Kept electrical orientation and source-data sign conventions as open questions.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000595",
    "label": "galvanotropism",
    "definition": "A phenotype in which growth is directionally oriented or reoriented in response to an electric field.",
    "definition_source": "DOI:10.1128/jb.176.3.702-713.1994",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1128/jb.176.3.702-713.1994",
        "snippet": "Field-treated (but not control) Enterobacter cloacae and Escherichia coli cells curved rapidly toward the anode.",
        "notes": "Abstract, exact-matched at Europe PMC (PMID:8300526; PMCID:PMC205108); full text not inspected. Curvature depended on field strength and pH and reversed with field polarity. The authors report controls excluding passive bending and field-induced gradients of tropic substances in their assay. Bacillus subtilis required a higher field threshold. Spatial wall-growth measurements support growth asymmetry, not a resolved universal electrical sensor. The historical actin-absence premise is not adopted as current biology."
      },
      {
        "reference": "DOI:10.1099/00221287-136-2-311",
        "snippet": "germ tubes grew unidirectionally towards the cathode for extended periods and did not deviate to a perpendicular orientation.",
        "notes": "Abstract, exact-matched at Europe PMC (PMID:2182770); full text not inspected. Candida albicans cells were attached to polylysine-coated slides. Budding and germ-tube emergence sites, as well as subsequent growth, were biased toward the cathode. Higher fields delayed emergence and reduced extension rate; those effects are not themselves directional growth. Cathodal growth here does not imply one electrode preference for all microbial galvanotropism."
      },
      {
        "reference": "DOI:10.1016/j.cub.2006.12.043",
        "snippet": "extending hyphae grew toward the cathode and reoriented their direction of growth when the field polarity was reversed",
        "notes": "Full-text Results, Calcium Ions and CaCch1p Mediate Cathodal Germ-Tube Emergence (PMID:17275302; PMCID:PMC1885950), https://pmc.ncbi.nlm.nih.gov/articles/PMC1885950/. Exact contiguous JATS paragraph span, not an abstract quote. Main Figs. 1 and 2 and supplemental Table S1 were inspected. The quoted response occurred even in low-calcium medium. Calcium depletion, channel blockers and CCH1 deletion primarily reduced cathodal emergence; after six hours, tip orientation could recover. Calcineurin perturbations affected cathodal emergence, not thigmotropism. Localized channel activation is a proposed model, not direct proof of a universal sensor. The supplement identifies CAI4/CIp10 as the isogenic control (NGY152) and lists engineered derivatives. These are qualified experimental backgrounds, not verified natural canonical exemplars."
      }
    ],
    "discussions": [
      {
        "discussion_id": "galvanotropism-growth-and-field-boundaries",
        "prompt": "Keep directional growth separate from movement and passive field effects.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Growth orientation is not whole-cell locomotion; the parent is phenotype, not motile. The existing galvanotaxis record (traitmech:000581) denotes active migration, and thigmotropism (traitmech:000594) denotes contact-directed polarized growth. Passive displacement, bending, alignment or changes in growth rate alone are insufficient. Do not conflate galvanotropism with electron uptake or current production. The bacterial anodal and fungal cathodal observations do not support an invariant electrode preference. A QuickGO galvanotropism search returned no hits on 2026-10-04; broader electric-field responses are not exact xrefs. Other external equivalences and electrotropism as a lexical variant require separate authority and scope checks.",
        "posed_by": "codex",
        "posed_date": "2026-10-04"
      },
      {
        "discussion_id": "galvanotropism-stage-and-mechanism-grounding",
        "prompt": "Resolve natural-strain evidence and distinguish emergence from maintenance.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "The full fungal study distinguishes establishment of cathodal growth from maintenance of tip orientation. Do not turn its aggregate abstract claim into a requirement for calcium influx at every stage. Its supplemental Table S1 and methods identify an engineered CAI4/CIp10 control and mutant or complemented derivatives; a wild-type label alone does not establish natural provenance. Inspect the older studies' full methods and resolve natural strains with NCBI identities before adding canonical examples. Resolve taxon-paired protein accessions and stage-specific causal claims before adding a mechanism graph. Do not transfer fungal channel dependence to bacteria or adopt the 1994 paper's historical actin-absence premise. A NONMECHANISTIC graph must not bypass missing protein grounding.",
        "posed_by": "codex",
        "posed_date": "2026-10-04"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-04T11:09:43Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added galvanotropism with three primary DOI citations, two abstract snippets and one full-text snippet. Ignored-and-hidden novelty searches and structured OWL review found no exact record or METPO term. Reserved METPO:1054900 in v472. Distinguished directional growth from galvanotaxis and thigmotropism without requiring one electrode preference. Inspected Brand full text, Figs. 1 and 2 and supplement; kept emergence distinct from later orientation and deferred natural canonical examples and accession-level mechanism grounding.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000160",
    "label": "gamma-glutamyltransferase activity",
    "definition": "A physiological enzyme-activity phenotype in which a cell exhibits gamma-glutamyltransferase/glutathione-hydrolase activity, processing glutathione, glutathione-S-conjugates, or other N-terminal L-gamma-glutamyl substrates through a gamma-glutamyl-enzyme intermediate.",
    "definition_source": "https://iubmb.qmul.ac.uk/enzyme/EC3/4/19/13.html",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "synonyms": [
      {
        "synonym_text": "gamma-glutamyl transferase",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.3389/fgene.2023.1240581"
      },
      {
        "synonym_text": "gamma-glutamyl transpeptidase",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://iubmb.qmul.ac.uk/enzyme/EC3/4/19/13.html"
      },
      {
        "synonym_text": "glutathione gamma-glutamate hydrolase",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://iubmb.qmul.ac.uk/enzyme/EC3/4/19/13.html"
      }
    ],
    "evidence": [
      {
        "reference": "https://iubmb.qmul.ac.uk/enzyme/EC3/4/19/13.html",
        "snippet": "The enzyme binds its substrate by forming an initial &gamma;-glutamyl-enzyme intermediate, releasing the <small>L</small>-cysteinylglycine part of the molecule. The enzyme then reacts with either a water molecule or a different acceptor substrate (usually an <small>L</small>-amino acid or a dipeptide) to form <small>L</small>-glutamate or a product containing a new &gamma;-glutamyl isopeptide bond, respectively. The enzyme acts on glutathione, glutathione-<i>S</i>-conjugates, and, at a lower level, on other substrates with an N-terminal <small>L</small>-&gamma;-glutamyl residue.",
        "notes": "The NC-IUBMB EC 3.4.19.13 entry scopes the bifunctional glutathione gamma-glutamate hydrolase/gamma-glutamyltransferase enzyme across water- and acceptor-mediated reactions."
      },
      {
        "reference": "DOI:10.3389/fgene.2023.1240581",
        "snippet": "Like Helicobacter canis, these two putative isolates are positive for oxidase, gamma-glutamyl transferase, and alkaline phosphatase and negative for catalase and urease activities.",
        "notes": "Wang et al. detected gamma-glutamyltransferase activity in two Helicobacter zhangjianzhongii isolates with the API Campy biochemical panel."
      },
      {
        "reference": "DOI:10.3389/fgene.2023.1240581",
        "snippet": "Both of these strains exhibit positive results for oxidase, gamma-glutamyl transferase, alkaline phosphatase, pyrrolidonyl arylamidase, L-arginine arylamidase, and L-aspartate arylamidase",
        "notes": "The formal species description reports the same gamma-glutamyltransferase-positive phenotype in both H. zhangjianzhongii strains."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:2974574",
        "taxon_label": "Helicobacter zhangjianzhongii",
        "note": "Wang et al. reported both Helicobacter zhangjianzhongii isolates as positive for gamma-glutamyltransferase activity in the API Campy biochemical panel.",
        "reference": "DOI:10.3389/fgene.2023.1240581"
      }
    ],
    "discussions": [
      {
        "discussion_id": "gamma-glutamyltransferase-activity-xref-gap",
        "prompt": "Resolve an exact external ontology class for gamma-glutamyltransferase activity before adding a TraitRecord xref.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "GO:0003840 gamma-glutamyltransferase activity is obsolete, and its replacement GO:0036374 glutathione hydrolase activity denotes a glutathione-hydrolysis molecular function rather than the organism-level gamma-glutamyltransferase/glutathione-hydrolase phenotype. GO:0036374 is appropriate as a causal-node grounding when a graph needs that hydrolysis half-reaction, not as an equivalent TraitRecord xref.",
        "posed_by": "codex",
        "posed_date": "2026-09-12"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-12T06:47:37Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted gamma-glutamyltransferase activity as a URL/DOI-backed TraitRecord after a repository-wide duplicate review covering ignored and hidden files; METPO has no exact gamma-glutamyltransferase activity class yet and the placeholder is reserved in proposals/metpo_traitmech_v37.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000136",
    "label": "gelatinase activity",
    "definition": "A physiological enzyme-activity phenotype in which a cell produces active gelatinase protease.",
    "definition_source": "DOI:10.1128/JB.01311-07",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "synonyms": [
      {
        "synonym_text": "gelatinase-positive",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1128/IAI.73.3.1606-1612.2005"
      },
      {
        "synonym_text": "gelatinase production",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1128/IAI.73.3.1606-1612.2005"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1128/JB.01311-07",
        "snippet": "One of the well-studied virulence factors of Enterococcus faecalis is a secreted bacterial protease, termed gelatinase",
        "notes": "Del Papa et al. identify Enterococcus faecalis gelatinase as a secreted bacterial protease and experimentally test maturation steps needed for full protease activity."
      },
      {
        "reference": "DOI:10.1128/IAI.73.3.1606-1612.2005",
        "snippet": "all gelatinase-positive isolates but little to no translocation for gelatinase nonproducers",
        "notes": "Zeng, Teng and Murray score Enterococcus faecalis isolates by gelatinase production and distinguish gelatinase-positive from gelatinase-negative phenotypes."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1351",
        "taxon_label": "Enterococcus faecalis",
        "note": "Model gelatinase-producing bacterium used in gelE and fsr studies.",
        "reference": "DOI:10.1128/JB.01311-07"
      }
    ],
    "discussions": [
      {
        "discussion_id": "gelatinase-activity-xref-gap",
        "prompt": "Resolve an exact external ontology class for gelatinase activity before adding a TraitRecord xref.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "GO:0008233 is the generic peptidase-activity class and MICRO:0000649 denotes a gelatinase assay, so both are too broad or assay-level for equivalent TraitRecord xrefs.",
        "posed_by": "codex",
        "posed_date": "2026-09-11"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-11T00:00:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted gelatinase activity as a DOI-backed TraitRecord after a repository-wide duplicate review covering ignored and hidden files; METPO has no exact gelatinase activity class yet.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000173",
    "label": "glutamyl glutamic acid arylamidase activity",
    "definition": "A physiological enzyme-activity phenotype in which a cell produces active glutamyl glutamic acid arylamidase enzymes that hydrolyze glutamyl-glutamic-acid arylamide substrates.",
    "definition_source": "DOI:10.1099/ijsem.0.006017",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "synonyms": [
      {
        "synonym_text": "glutamyl glutamic acid arylamidase",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1099/ijsem.0.006017"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1099/ijsem.0.006017",
        "snippet": "enzymatic activities are present for: \u03b1-galactosidase, N-acetyl-\u03b2-glucosaminidase, arginine arylamidase, proline arylamidase, leucyl glycine arylamidase, phenylalanine arylamidase, leucine arylamidase, tyrosine arylamidase, alanine arylamidase, glycine arylamidase, histidine arylamidase, glutamyl glutamic acid arylamidase, serine arylamidase, valine arylamidase, cysteine arylamidase, esterase, esterase lipase, alpha-chymotrypsin",
        "notes": "Srinivasan et al. listed glutamyl glutamic acid arylamidase among enzymatic activities present in the Amygdalobacter indicium species description, supporting the API arylamidase row as a directly assayed bacterial enzyme-activity phenotype."
      },
      {
        "reference": "DOI:10.1099/ijs.0.63642-0",
        "snippet": "arginine arylamidase, leucyl glycine arylamidase, phenylalanine arylamidase, leucine arylamidase, tyrosine arylamidase, alanine arylamidase, glycine arylamidase, histidine arylamidase, glutamyl glutamic acid arylamidase and serine arylamidase are positive",
        "notes": "Nichols et al. listed glutamyl glutamic acid arylamidase as positive in Olleya marilimosa strain CAM030T."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:3029272",
        "taxon_label": "Amygdalobacter indicium",
        "note": "Srinivasan et al. reported Amygdalobacter indicium as positive for glutamyl glutamic acid arylamidase activity in an enzyme activity panel.",
        "reference": "DOI:10.1099/ijsem.0.006017"
      }
    ],
    "discussions": [
      {
        "discussion_id": "glutamyl-glutamic-acid-arylamidase-activity-xref-gap",
        "prompt": "Resolve an exact external ontology class for glutamyl glutamic acid arylamidase activity before adding a TraitRecord xref.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "GO:0016805 covers broad dipeptidase activity at molecular-function scope, and no live GO class provides an exact glutamyl-glutamic-acid-specific arylamidase production phenotype at organism-level scope.",
        "posed_by": "codex",
        "posed_date": "2026-09-12"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-12T14:23:58Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted glutamyl glutamic acid arylamidase activity as a DOI-backed TraitRecord after a repository-wide duplicate review covering ignored and hidden files; METPO has no exact glutamyl glutamic acid arylamidase activity class yet and the placeholder is reserved in proposals/metpo_traitmech_v50.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000170",
    "label": "glycine arylamidase activity",
    "definition": "A physiological enzyme-activity phenotype in which a cell produces active glycine arylamidase enzymes that hydrolyze glycine arylamide substrates.",
    "definition_source": "DOI:10.1099/ijsem.0.006017",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "synonyms": [
      {
        "synonym_text": "glycine arylamidase",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1099/ijsem.0.006017"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1099/ijsem.0.006017",
        "snippet": "enzymatic activities are present for: \u03b1-galactosidase, N-acetyl-\u03b2-glucosaminidase, arginine arylamidase, proline arylamidase, leucyl glycine arylamidase, phenylalanine arylamidase, leucine arylamidase, tyrosine arylamidase, alanine arylamidase, glycine arylamidase, histidine arylamidase, glutamyl glutamic acid arylamidase, serine arylamidase, valine arylamidase, cysteine arylamidase, esterase, esterase lipase, alpha-chymotrypsin",
        "notes": "Srinivasan et al. listed glycine arylamidase among enzymatic activities present in the Amygdalobacter indicium species description, supporting the API arylamidase row as a directly assayed bacterial enzyme-activity phenotype."
      },
      {
        "reference": "DOI:10.1128/JCM.40.9.3427-3431.2002",
        "snippet": "When the API rapid ID32A system was used, all eight strains displayed activity for alanine arylamidase, arginine arylamidase, \u03b1-glucosidase, glycine arylamidase, histidine arylamidase, leucine arylamidase, leucylglycine arylamidase, proline arylamidase, phenylalanine arylamidase, serine arylamidase, and tyrosine arylamidase",
        "notes": "Hall et al. reported glycine arylamidase activity in all eight Actinomyces cardiffensis clinical isolates tested with the API rapid ID32A system."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:3029272",
        "taxon_label": "Amygdalobacter indicium",
        "note": "Srinivasan et al. reported Amygdalobacter indicium as positive for glycine arylamidase activity in an enzyme activity panel.",
        "reference": "DOI:10.1099/ijsem.0.006017"
      }
    ],
    "discussions": [
      {
        "discussion_id": "glycine-arylamidase-activity-xref-gap",
        "prompt": "Resolve an exact external ontology class for glycine arylamidase activity before adding a TraitRecord xref.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "GO:0004177 covers broad aminopeptidase activity at molecular-function scope, and no live GO class provides an exact residue-specific glycine arylamidase production phenotype at organism-level scope.",
        "posed_by": "codex",
        "posed_date": "2026-09-12"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-12T13:05:26Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted glycine arylamidase activity as a DOI-backed TraitRecord after a repository-wide duplicate review covering ignored and hidden files; METPO has no exact glycine arylamidase activity class yet and the placeholder is reserved in proposals/metpo_traitmech_v47.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000585",
    "label": "gravikinesis",
    "definition": "A motile phenotype in which the speed of active propulsion is modulated according to orientation relative to gravity.",
    "definition_source": "DOI:10.2187/bss.20.44",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000702"
    ],
    "evidence": [
      {
        "reference": "DOI:10.2187/bss.20.44",
        "snippet": "We confirmed the gravikinesis from the analysis on the swimming of single cells.",
        "notes": "Abstract; full publisher PDF inspected at https://www.jstage.jst.go.jp/article/bss/20/2/20_2_44/_pdf. Methods and Results (pages 45-46, Table 1) distinguish active propulsion from passive drift using subsequent 10-18 mM NiCl2 immobilization of the same cell. The drift controls retained contractile-vacuole activity and lacked visible deformation. Curved-swimmer responses reverse in 72% Percoll; straight-swimmer responses were not significant. Results N=55 and Table 1 straight-swimmer N=57 are unreconciled; no aggregate sample count is asserted. Table and method pages were visually checked."
      },
      {
        "reference": "DOI:10.1007/s001140050634",
        "snippet": "The resulting potential-induced modulation of the speed of propulsion is called gravikinesis because it acts to neutralize, fully or in part, sedimentation.",
        "notes": "Publisher abstract and Europe PMC PMID:11536922 checked. Orientation-dependent membrane-potential changes support a physiological component of propulsion control in Paramecium. The sedimentation-opposing response described here is not a universal sign convention or proof of one receptor in all taxa. The subscription full text was not inspected; no strain, channel accession or full-text-only measurement is inferred."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:5885",
        "taxon_label": "Paramecium caudatum",
        "reference": "DOI:10.2187/bss.20.44",
        "note": "Curved-swimming cells from 14-20-day early-stationary hay-infusion cultures at 24 C, adapted to KCM (pH 7.2) and selected beneath the water surface. Table 1 supports gravity-dependent active propulsion in the control hypo-density medium. Swimming was recorded before nickel immobilization, which supplied only the passive-drift correction. This is not a universal cell-state claim. NCBI identifier is species-level; no strain accession is supplied."
      }
    ],
    "discussions": [
      {
        "discussion_id": "gravikinesis-speed-and-direction-boundaries",
        "prompt": "Keep propulsion modulation distinct from orientation and passive drift.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Observed upward/downward speed differences alone can arise from sedimentation or flotation; the trait concerns the active propulsion component. Gravitaxis (traitmech:000584) denotes directional bias, and gyrotaxis (traitmech:000583) denotes torque-mediated orientation. These can coexist with gravikinesis; no equivalence, disjointness or parent-child relation among them is asserted. The definition does not require faster upward swimming in every medium. Reconcile sign conventions and source-qualified response classes before adding narrower terms or equivalent external mappings.",
        "posed_by": "codex",
        "posed_date": "2026-10-04"
      },
      {
        "discussion_id": "gravikinesis-mechanism-grounding",
        "prompt": "Resolve exact protein and taxon anchors for a mechanistic graph.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Mechanism evidence exists: Gebauer's abstract links orientation to membrane potential and propulsion, while Takeda discusses mechanosensitive conductances and ciliary control. The inspected sources do not identify a sequence-resolved gravity receptor. Takeda treats hydraulic pressure as a candidate stimulus needing amplification, not a demonstrated complete molecular pathway. A graph is deferred pending eligible taxon-paired protein examples and source-bounded causal edges. Do not substitute an unrelated channel or classify this physiological mechanism as NONMECHANISTIC to avoid the protein-coverage gate.",
        "posed_by": "codex",
        "posed_date": "2026-10-04"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-04T03:19:30Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added gravikinesis with two primary DOI sources, contiguous snippets and a drift-corrected Paramecium caudatum example at verified species taxon 5885. Ignored-and-hidden searches found only gravitaxis boundary mentions, not an exact trait or METPO term. Reserved METPO:1053900 in proposal v462; kept direction, passive drift, source sample counts and unresolved protein-level mechanism separate.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000584",
    "label": "gravitaxis",
    "definition": "A motile phenotype in which the direction of active swimming is biased relative to gravity.",
    "definition_source": "DOI:10.1038/s41598-018-26046-8",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000702"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/s41598-018-26046-8",
        "snippet": "Predominantly, E. gracilis shows a negative gravitaxis behavior.",
        "notes": "Introduction, page 1, visually verified at https://d-nb.info/1186379677/34 (PMID:29765103; PMC5954063). Direction varies with culture age. Results, Figure 4 and Supplementary Figure 6e-g distinguish upward-biased controls from EgPCDUF4201/CaM2 knockdowns. Full main text and supplement 41598_2018_26046_MOESM1_ESM.pdf inspected via Europe PMC. Supplementary Figure 5e, not the main text's 5c, measures flagellar length; Supplementary Table 1 reports comparable, not identical, speeds. These controls do not exclude every flagellar defect. PKA phosphorylation and a direct dynein link remain hypotheses."
      },
      {
        "reference": "DOI:10.1242/jeb.050666",
        "snippet": "the ability to swim preferentially upwards (negative gravitaxis) is primarily the result of upwardly curving trajectories",
        "notes": "Summary (PMID:21112996); publisher main-text Methods, Results and Discussion inspected. Curved trajectories agree with a physical shape-orientation model, but shape and orientation rate were not measured simultaneously in the same individual. This is not proof that all protists lack gravity receptors. Gravikinesis concerns orientation-dependent swimming speed, not the directional phenotype. Equation images and supplementary material were not inspected; no equation-derived or supplement-only claim is asserted."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:3039",
        "taxon_label": "Euglena gracilis",
        "reference": "DOI:10.1038/s41598-018-26046-8",
        "note": "Strain Z, axenic organic-medium cultures at 20 C under continuous light. Figure 4a and Supplementary Figure 6e show upward-biased wild-type controls; Methods specify buffer-only electroporation. These are not the RNAi knockdowns. NCBI identifier is species-level, not a strain accession; no universal age-independent direction is implied."
      },
      {
        "taxon_id": "NCBITaxon:5885",
        "taxon_label": "Paramecium caudatum",
        "reference": "DOI:10.1242/jeb.050666",
        "note": "Wild-type cells from one-week-old boiled-hay-infusion cultures. After several hours in the observation chamber, rotation of the chamber revealed upward-curving swimming tracks (Results, Figure 2). NCBI identifier is species-level; the paper does not supply a resolved strain accession."
      }
    ],
    "discussions": [
      {
        "discussion_id": "gravitaxis-direction-and-process-boundaries",
        "prompt": "Keep gravity-relative swimming distinct from settling and neighboring traits.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Positive and negative gravitaxis are directional cases, not a requirement that all cells always swim upward. Passive settling alone and speed changes alone do not establish this trait. The definition does not require an active gravity receptor: powered swimming and physical orientation can coexist. Gyrotaxis (traitmech:000583) specifies a gravity-viscous torque mechanism, not an exact synonym or a disjoint phenotype. No new subsumption axiom between them is asserted without reviewing both scopes. QuickGO resolved active GO:0042332 gravitaxis on 2026-10-04, including geotaxis as an exact lexical synonym. It denotes a biological process rather than this organismal disposition; keep it out of equivalent xrefs and resolve any mapping separately.",
        "posed_by": "codex",
        "posed_date": "2026-10-04"
      },
      {
        "discussion_id": "gravitaxis-mechanism-grounding",
        "prompt": "Resolve exact protein anchors and a faithful physical-mechanism graph.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "The sources provide mechanism evidence, but this first record does not yet include a graph. Nasir's CaM2 accession EU935858 resolves to UniProtKB:B5THA2, an unreviewed entry without a Proteomes cross-reference in the 2026-10-04 REST response. An exact EgPCDUF4201 name query returned no hit; this does not establish sequence absence. Resolve eligible exact examples before adding the molecular branch; a DUF4201 match alone does not demonstrate gravitaxis. For the physical branch, the current MECHANISTIC coverage audit requires a protein node and example. Do not invent a receptor or misclassify physical causation as NONMECHANISTIC to satisfy that audit.",
        "posed_by": "codex",
        "posed_date": "2026-10-04"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-04T02:18:15Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added gravitaxis with two primary DOI sources, contiguous snippets and source-qualified examples at verified species taxa 3039 and 5885. Ignored-and-hidden searches found only gyrotaxis boundary mentions, not an exact record or METPO term. Reserved METPO:1053800 in proposal v461; documented process-grain and mechanism-grounding gaps without substituting a protein or asserting a universal receptor.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000599",
    "label": "gravitropism",
    "definition": "A phenotype in which growth is directionally oriented or reoriented in response to gravity.",
    "definition_source": "DOI:10.4161/cib.22291",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.4161/cib.22291",
        "snippet": "Phycomyces sporangiophores grow in the air and display negative gravitropic bending upon displacement from vertical position.",
        "notes": "Intracellular Reorganization upon Gravistimulation; exact contiguous Europe PMC full-text XML (PMID:23650568; PMC3642927). The full article and all three figure images were inspected. Figure 1 shows bending growth of an intact wild-type stage I sporangiophore after a 45-degree tilt; no strain identifier is given. Figure 2 concerns intracellular reorganization, and Figure 3 measures touch-induced ion fluxes, not a gravity assay. The author explicitly leaves open whether vacuolization reflects gravity signaling or coincident development. The article declares no supplement; the Europe PMC supplementaryFiles download contained ordinary figure assets."
      },
      {
        "reference": "DOI:10.1078/0176-1617-01082",
        "snippet": "The threshold for the polar angle of the wild type NRRL 1555 (with crystals) is near 8 x 10(-2) x g.",
        "notes": "Abstract, exact-matched at Europe PMC (PMID:15266721). A clinostat centrifuge measures negative gravitropic bending of Phycomyces blakesleeanus sporangiophores. Polar angle and aiming-error angle are distinct readouts; the quoted value belongs to the wild-type polar angle, not the mutant strains or aiming error. It is assay-specific, not a universal threshold. Subscription full text and figures were not inspected."
      },
      {
        "reference": "DOI:10.1007/s004250050744",
        "snippet": "In rhizoids, positive gravitropic curvature is caused by differential growth limited to the opposite subapical flanks of the apical dome",
        "notes": "Abstract, exact-matched at Europe PMC (PMID:10550622). The primary Chara study describes downward-positive rhizoid growth and upward-negative protonematal growth. This supports polarity-neutral terminology, not positive gravitropism in Phycomyces. The remainder of the quoted sentence excludes displacement of the rhizoid growth centre, calcium gradient or channels. No Chara mechanism or canonical taxon is transferred to the fungus; full text and figures were not inspected."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:763407",
        "taxon_label": "Phycomyces blakesleeanus NRRL 1555(-)",
        "reference": "DOI:10.1078/0176-1617-01082",
        "note": "Wild-type sporangiophore negative gravitropic bending in the clinostat-centrifuge study, with a source-qualified polar-angle threshold. This is not a mutant example and is not assigned the unnamed 2013 study's stage I observations. Natural-isolate provenance: DOI:10.1128/EC.00203-13, Materials and Methods, Strains and growth conditions (https://pmc.ncbi.nlm.nih.gov/articles/PMC3910969/); NRRL1555 is distinguished from backcrossed A56. Exact strain name and rank resolved directly at NCBI Taxonomy on 2026-10-04."
      }
    ],
    "discussions": [
      {
        "discussion_id": "gravitropism-growth-and-direction-boundaries",
        "prompt": "Keep gravity-guided growth separate from swimming and passive motion.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "The class includes positive or negative directional growth without requiring both in one organism or condition. It is not gravitaxis (swimming orientation), gravikinesis (propulsion-speed change), passive settling, flotation or sagging, or gravity-dependent growth rate alone. The Phycomyces evidence here is negative. Resolve phenotype-level external equivalences before adding xrefs or synonyms.",
        "posed_by": "codex",
        "posed_date": "2026-10-04"
      },
      {
        "discussion_id": "gravitropism-native-mechanism-grounding",
        "prompt": "Discriminate gravity signaling from touch and coincident development.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Bending observations do not resolve a complete molecular mechanism. Vacuolization can coincide with development; touch-induced ion fluxes do not establish gravity-triggered channel activity. The 2004 abstract compares strains with and without crystals but does not identify a universal sole gravity sensor. Inspect its full text and resolve eligible taxon-paired protein accessions before adding a mechanistic graph. Do not use NONMECHANISTIC to bypass grounding requirements or transfer Chara signaling to fungi.",
        "posed_by": "codex",
        "posed_date": "2026-10-04"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-04T15:37:17Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added gravitropism with two primary fungal studies, a primary direction-terminology source and exact snippets. Ignored-and-hidden novelty searches and structured OWL review found no exact record or METPO term. Reserved METPO:1055300 in v476. Kept growth distinct from locomotion and passive motion; inspected the 2013 full text and figures. Added a natural NRRL1555 exemplar tied only to the 2004 assay, and deferred unresolved mechanisms.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000583",
    "label": "gyrotaxis",
    "definition": "A motile phenotype in which the balance of gravitational and viscous torques biases an organism's swimming orientation.",
    "definition_source": "DOI:10.1073/pnas.2206738119",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000702"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1073/pnas.2206738119",
        "snippet": "The orientational response to the gravity-viscous torque balance is known as gyrotaxis",
        "notes": "Introduction, page 1; definition checked against the publisher-formatted article deposited by the authors at https://api.repository.cam.ac.uk/server/api/core/bitstreams/ac9ccafe-f229-477c-9d59-b7a56cd506a0/content (PMID:36219692; PMC9586295). The second of the introduction's three accumulation mechanisms starts 'The second is response to an external field': it describes swimming in still water and gravitational restoration resisted hydrodynamically, then names this response gyrotaxis. This record follows Zeng's broader usage, not a universal requirement or exclusion of imposed shear. Results, Figures 5-7, and Materials and Methods distinguish gravitational reorientation from wall-contact effects in Heterosigma akashiwo GY-H24. Shape asymmetry and density asymmetry are alternatives; bottom-heaviness is not universal. The full main article was read; supplementary material and movies were not inspected. No gravity-sensing receptor is asserted."
      },
      {
        "reference": "DOI:10.1126/science.1167334",
        "snippet": "The swimming direction, \u03b8, is then set by the balance of viscous and gravitactic torques",
        "notes": "Page 1068, left column beneath Figure 2; the typeset theta in the torque-balance sentence was visually checked because PDF extraction substitutes q. This passage concerns imposed shear. Live-cell experiments are on pages 1067-1069 of the full main article at https://stockerlab.ethz.ch/wp-content/uploads/2013/01/17.-DurhamKesslerStocker_Science2009.pdf (PMID:19229037). Chlamydomonas nivalis and Heterosigma akashiwo formed layers in a depth-varying shear chamber; dead cells did not. Gyrotactic trapping is a population consequence under suitable shear, not the definition of the organismal trait or the cause of every oceanic thin layer. Ocean-scale results are model predictions. The supplement and exact culture identities were not verified; no strain or modern C. nivalis taxon identity is inferred."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:2829",
        "taxon_label": "Heterosigma akashiwo",
        "reference": "DOI:10.1073/pnas.2206738119",
        "note": "GY-H24 culture, examined 3-9 hours into the light phase of a 12-hour light/12-hour dark cycle. Figures 5-7 show gravitational reorientation and wall-modified swimming in a sealed, still-fluid microchannel; upward bias is not asserted for every cell or diurnal phase. This example follows Zeng's explicit still-water usage of gyrotaxis; it is not an imposed-shear experiment. The NCBI identifier is species-level, not a resolved GY-H24 strain accession."
      }
    ],
    "discussions": [
      {
        "discussion_id": "gyrotaxis-physical-mechanism-representation",
        "prompt": "Represent physical torque-mediated orientation without inventing a protein sensor.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "The primary papers describe a physical mechanism, so the absence of a protein accession is not absence of mechanistic evidence. This identity/evidence pass omits a graph: the current MECHANISTIC coverage audit requires a protein node and protein example, whereas NONMECHANISTIC is reserved for measurement or classification contexts. Resolve a faithful representation separately instead of relabeling the physical mechanism or inventing a sensor. Keep gravity-viscous orientation distinct from wall-contact responses and high-shear trapping. Gyrotaxis is not an exact synonym of gravitaxis, rheotaxis, bioconvection or thin-layer formation. QuickGO returned no gyrotaxis term on 2026-10-04; no exact external xref is asserted.",
        "posed_by": "codex",
        "posed_date": "2026-10-04"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-04T01:16:29Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added gyrotaxis with two primary DOI sources, contiguous evidence snippets and a light-phase-qualified GY-H24 example at verified species taxon NCBITaxon:2829. Ignored-and-hidden novelty searches found no exact record or METPO class. Reserved METPO:1053700 in proposal v460. Recorded the physical-graph representation gap without asserting an unsupported protein or receptor.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-04T01:41:15Z",
        "curator": "codex",
        "action": "ADDRESS_REVIEW_FINDINGS",
        "changes": "Addressed PR 1646 issues 1647 and 1648: replaced the Durham population outcome snippet with its typeset torque-balance statement; anchored Zeng's broader still-water usage to the specific introduction passage and qualified the canonical example. Definition and hierarchy unchanged.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000686",
    "label": "haptocyst discharge",
    "definition": "A physiological phenotype in which a microbial cell releases material from haptocysts to the cell exterior.",
    "definition_source": "DOI:10.1515/znc-1984-7-821",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1515/znc-1984-7-821",
        "snippet": "The fine structure of haptocysts, characteristic organelles of most suctorians, is described during the resting state and the discharge after contact with the prey.",
        "notes": "Benwitz 1984, English abstract reproduced at https://www.nies.go.jp/chiiki1/protoz/refere/id4999/4538.htm, read directly on 2026-10-10. Crossref confirms the DOI, title, author and original 1984 publication; later online dates are not the experiment year. In Ephelota gemmipara the abstract reports prey-contact discharge, continuity of the haptocyst membrane with the tentacle plasma membrane, and attachment of internal haptocyst structures to the perforated prey pellicle. It explicitly reports no predator-prey plasma-membrane fusion in Ephelota. These observations support release to the cell exterior, not cell-cell fusion or merely possession of haptocysts. The publisher PDF was unavailable; figures and full Methods were not visually audited. No universal cargo chemistry or trigger is inferred."
      },
      {
        "reference": "DOI:10.1007/BF00331480",
        "snippet": "By these haptocysts the tentacle is attached to the prey.",
        "notes": "Bardele and Grell 1967, PMID:4971424. Publisher English Summary points 1-2 at https://link.springer.com/article/10.1007/BF00331480 read directly on 2026-10-10. The source identifies the tentacular organelles in Acineta tuberosa as haptocysts and describes prey attachment. This is independent organelle-identity and attachment evidence, not a second direct discharge experiment. Its ingestion tube hypothesis is not a demonstrated haptocyst release mechanism. Full text is subscription-only and was not inspected."
      }
    ],
    "discussions": [
      {
        "discussion_id": "haptocyst-discharge-scope-and-parent",
        "prompt": "Resolve the exocytosis placement and historical extrusome terminology.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Retain phenotype METPO:1000059 pending broader hierarchy review. Benwitz supports organelle-plasma-membrane continuity in Ephelota, not predator-prey membrane fusion. This supports an exocytotic interpretation in that system but does not establish the fusion-pore differentia of exocytosis traitmech:000637 throughout the unqualified class. That placement is unresolved, not excluded. Mere possession, docking, prey attachment, ingestion or nonspecific cell lysis alone does not demonstrate discharge. Do not require prey death, complete emptying or a universal natural trigger. Toxicyst discharge traitmech:000685 explicitly leaves haptocyst terminology unresolved; this organelle-specific record does not settle whether historical toxicyst umbrellas include haptocysts. Do not equate haptocysts with kinetocysts, trichocysts or mucocysts, or assert homology or organism-level disjointness. No exact synonyms or xrefs are assigned.",
        "posed_by": "codex",
        "posed_date": "2026-10-10"
      },
      {
        "discussion_id": "haptocyst-discharge-provenance-and-mechanism",
        "prompt": "Verify natural exemplars and separate release from attachment and ingestion.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Experimental culture provenance and current strain-level taxonomy remain unchecked; no canonical examples are assigned. The two citations support different claims and are not replicate discharge assays. Tentacular ultrastructure does not establish a conserved protein mechanism, toxin composition or signaling pathway. A future graph needs direct perturbation evidence and taxon-paired accessions, separating assembly, triggering, extrusion, attachment and ingestion. Mechanism is deferred, not claimed absent. Sequence features alone would not establish any of these causal transitions.",
        "posed_by": "codex",
        "posed_date": "2026-10-10"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-10T01:50:07Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added haptocyst discharge with two primary DOI sources and directly checked abstract/Summary snippets, distinguishing discharge evidence from organelle identity and attachment. Ignored-and-hidden main/worktree/open-PR checks support 000686 and v562 block 1063900-1063999. Exocytosis hierarchy, natural exemplars and protein mechanisms remain unresolved. Existing records unchanged. Timestamp records the observed UTC curation decision.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000205",
    "label": "heat shock response",
    "definition": "A stress response in which acute heat stress induces heat-shock proteins that refold or degrade denatured proteins to restore protein homeostasis.",
    "definition_source": "DOI:10.1007/s12192-016-0727-z",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000078"
    ],
    "synonyms": [
      {
        "synonym_text": "heat-shock response",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1007/s12192-016-0727-z"
      },
      {
        "synonym_text": "HSR",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1128/MMBR.00007-08"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1007/s12192-016-0727-z",
        "snippet": "they transiently induce a group of genes called heat shock genes (HSGs) which code for heat shock proteins (HSPs)",
        "notes": "Schumann reviews heat-shock gene induction and heat-shock protein production as the bacterial response to sudden temperature rise."
      },
      {
        "reference": "DOI:10.1007/s12192-016-0727-z",
        "snippet": "chaperones binding to denatured proteins and allowing refolding to their native state and ATP-dependent proteases degrading denatured proteins",
        "notes": "Schumann summarizes the two major functional heat-shock protein classes that clear denatured proteins."
      },
      {
        "reference": "DOI:10.1128/MMBR.00007-08",
        "snippet": "The heat shock response (HSR) is classically defined as the cellular response to temperature increase",
        "notes": "Guisbert et al. define the E. coli heat-shock response and review the sigma-32 regulatory model."
      },
      {
        "reference": "DOI:10.1128/MMBR.00007-08",
        "snippet": "The rapid upregulation of chaperones and proteases during the HSR restores an appropriate protein-folding environment in the cell",
        "notes": "Guisbert et al. support protein-folding homeostasis as the primary function of the E. coli sigma-32-mediated heat-shock response."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:562",
        "taxon_label": "Escherichia coli",
        "note": "E. coli is a model for the sigma-32-mediated heat-shock response, including heat-shock chaperone and protease upregulation.",
        "reference": "DOI:10.1128/MMBR.00007-08"
      },
      {
        "taxon_id": "NCBITaxon:1423",
        "taxon_label": "Bacillus subtilis",
        "note": "B. subtilis is a Gram-positive model for heat-shock stimulon regulation by repressor and alternative-sigma branches.",
        "reference": "DOI:10.1007/s12192-016-0727-z"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "heat_shock_response_proteostasis",
        "title": "Heat-shock proteostasis restoration",
        "description": "Evidence-backed causal sketch linking acute heat shock to protein unfolding, heat-shock protein induction, and restored protein homeostasis.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "This graph captures the conserved proteostasis output of the heat-shock response without making the E. coli sigma-32 branch, B. subtilis HrcA/CtsR branches, or other lineage-specific heat-shock regulators universal.",
        "nodes": [
          {
            "node_id": "heat_shock_response_trait",
            "label": "heat shock response",
            "node_type": "TRAIT",
            "grounding": "traitmech:000205",
            "description": "Capacity to induce heat-shock proteins after acute heat stress."
          },
          {
            "node_id": "acute_heat_shock",
            "label": "acute heat shock",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "A sudden upward temperature shift."
          },
          {
            "node_id": "protein_unfolding",
            "label": "heat-induced protein unfolding",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Protein unfolding and aggregation triggered by heat shock."
          },
          {
            "node_id": "heat_shock_response_process",
            "label": "heat-shock response",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Rapid, transient production of heat-shock proteins after protein unfolding or aggregation."
          },
          {
            "node_id": "heat_shock_chaperones",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed functional protein set; no single family, complex, or molecular-function term captures all heat-shock-induced chaperones across bacteria.",
            "label": "heat-shock chaperones",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Induced chaperone systems that bind denatured proteins and promote refolding.",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:P0A6Y8",
                "protein_label": "Chaperone protein DnaK",
                "gene_symbol": "dnaK",
                "taxon_id": "NCBITaxon:83333",
                "taxon_label": "Escherichia coli K-12",
                "entry_status": "REVIEWED",
                "retrieved_on": "2026-09-15",
                "entry_version": 183,
                "sequence_version": 2,
                "role": "E. coli K-12 DnaK is an Hsp70 heat-shock chaperone that binds sigma-32 in the chaperone-mediated heat-shock control branch.",
                "evidence": [
                  {
                    "reference": "DOI:10.1073/pnas.89.8.3516",
                    "snippet": "purified sigma 32 bound to DnaK and that this complex was disrupted in the presence of ATP",
                    "notes": "Liberek et al. directly support DnaK as an E. coli heat-shock chaperone that binds the sigma-32 transcription factor."
                  }
                ]
              }
            ]
          },
          {
            "node_id": "atp_dependent_proteases",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed functional protein set; bacterial ATP-dependent proteases belong to multiple non-equivalent families and complexes.",
            "label": "ATP-dependent proteases",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Proteases that clear denatured proteins or degrade heat-shock regulators during the heat-shock response.",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:P0AAI3",
                "protein_label": "ATP-dependent zinc metalloprotease FtsH",
                "gene_symbol": "ftsH",
                "taxon_id": "NCBITaxon:83333",
                "taxon_label": "Escherichia coli K-12",
                "entry_status": "REVIEWED",
                "retrieved_on": "2026-09-15",
                "entry_version": 155,
                "sequence_version": 1,
                "role": "E. coli K-12 FtsH is an ATP-dependent membrane metalloprotease that degrades the sigma-32 heat-shock transcription factor.",
                "evidence": [
                  {
                    "reference": "DOI:10.1002/j.1460-2075.1995.tb07253.x",
                    "snippet": "FtsH catalyzed ATP-dependent degradation of biologically active histidine-tagged sigma 32",
                    "notes": "Tomoyasu et al. directly support FtsH as the E. coli ATP-dependent protease that degrades sigma-32."
                  }
                ]
              }
            ]
          },
          {
            "node_id": "protein_homeostasis",
            "label": "protein homeostasis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Cellular protein-folding state restored by chaperone refolding and protease degradation of denatured proteins."
          }
        ],
        "edges": [
          {
            "subject": "acute_heat_shock",
            "predicate": "causes",
            "predicate_id": "biolink:causes",
            "object": "protein_unfolding",
            "description": "Acute heat shock causes protein unfolding and aggregate formation.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s12192-016-0727-z",
                "snippet": "A sudden heat shock results in protein unfolding leading to the formation of protein aggregates",
                "notes": "Verified against the open PMC full text; heat shock immediately destabilizes cellular proteins."
              }
            ]
          },
          {
            "subject": "protein_unfolding",
            "predicate": "causes",
            "predicate_id": "biolink:causes",
            "object": "heat_shock_response_process",
            "description": "Protein unfolding and aggregation trigger rapid, transient heat-shock protein production.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s12192-016-0727-z",
                "snippet": "It responds to protein unfolding, aggregation and damage by the rapid and transient production of HSPs",
                "notes": "Verified against the open PMC full text; the edge links damaged unfolded proteins to the protective heat-shock response."
              }
            ]
          },
          {
            "subject": "heat_shock_response_process",
            "predicate": "positively regulates",
            "predicate_id": "RO:0002213",
            "object": "heat_shock_chaperones",
            "description": "The heat-shock response induces chaperones that refold denatured proteins.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s12192-016-0727-z",
                "snippet": "chaperones binding to denatured proteins and allowing refolding to their native state",
                "notes": "Verified against the open PMC full text; chaperones are a major heat-shock protein class."
              }
            ]
          },
          {
            "subject": "heat_shock_response_process",
            "predicate": "positively regulates",
            "predicate_id": "RO:0002213",
            "object": "atp_dependent_proteases",
            "description": "The heat-shock response induces ATP-dependent proteases that remove denatured proteins.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s12192-016-0727-z",
                "snippet": "ATP-dependent proteases degrading denatured proteins",
                "notes": "Verified against the open PMC full text; ATP-dependent proteases are a major heat-shock protein class."
              }
            ]
          },
          {
            "subject": "heat_shock_chaperones",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "protein_homeostasis",
            "description": "Heat-shock chaperones help restore proteostasis by refolding denatured proteins.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s12192-016-0727-z",
                "snippet": "chaperones binding to denatured proteins and allowing refolding to their native state",
                "notes": "Verified against the open PMC full text; induced chaperones support refolding of denatured proteins."
              }
            ]
          },
          {
            "subject": "atp_dependent_proteases",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "protein_homeostasis",
            "description": "ATP-dependent proteases help restore proteostasis by degrading denatured proteins.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s12192-016-0727-z",
                "snippet": "ATP-dependent proteases degrading denatured proteins",
                "notes": "Verified against the open PMC full text; induced proteases clear denatured proteins."
              }
            ]
          },
          {
            "subject": "protein_homeostasis",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "heat_shock_response_trait",
            "description": "Restoration of protein-folding homeostasis realizes the heat-shock-response trait.",
            "evidence": [
              {
                "reference": "DOI:10.1128/MMBR.00007-08",
                "snippet": "restores an appropriate protein-folding environment in the cell",
                "notes": "Verified against the open PMC full text; Guisbert et al. describe proteostasis restoration as the sigma-32-mediated heat-shock response output."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "heat-shock-response-xref-gap",
        "prompt": "Resolve exact ontology xrefs for organism-level microbial heat shock response before adding TraitRecord xrefs.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "GO:0009408 response to heat can ground biological-process nodes but is broader than this organism-level stress response trait. Candidate heat-shock-protein, chaperone, and ATP-dependent-protease terms describe narrower molecular machinery rather than the whole response phenotype.",
        "posed_by": "codex",
        "posed_date": "2026-09-15"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-15T04:58:15Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted heat shock response as a DOI-backed stress-response TraitRecord after a repository-wide duplicate review covering ignored and hidden files; the local METPO snapshot has only an obsolete heat shock response class and the replacement placeholder is reserved in proposals/metpo_traitmech_v82.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000606",
    "label": "heterokaryon incompatibility",
    "definition": "A fungal phenotype in which postfusion nonself recognition restricts the establishment or growth of viable vegetative heterokaryons.",
    "definition_source": "DOI:10.1099/mic.0.032284-0",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1099/mic.0.032284-0",
        "snippet": "Incompatible heterokaryons show a macroscopic phenotype of slow growth and diminished conidiation, and a microscopic phenotype of hyphal compartmentation and cell death.",
        "notes": "Hutchison et al. (2009), PMID:19696111. The directly retrieved Europe PMC abstract and publisher abstract identify nonself recognition during fusion between strains differing at het loci, with restricted growth and localized cell death. This supports postfusion heterokaryon incompatibility, not failure to approach or fuse. The study combines transcriptional profiling with functional analysis of het-c pin-c incompatibility in Neurospora crassa. Transcript associations do not establish causal edges; the abstract reports that tested caspase and AIF homologues were not required. Full text, figures and supplements were not retrieved, so no detailed assay or protein-dependency claim beyond the abstract is asserted."
      },
      {
        "reference": "DOI:10.1016/s1087-1845(03)00086-0",
        "snippet": "Hyphal fusion cells in compatible self-pairings and hyphal cells in het-c compatible transformants were not compartmentalized and rarely showed TUNEL-positive nuclei.",
        "notes": "Marek et al. (2003), PMID:14516765; snippet exact-matched to the directly retrieved Europe PMC abstract. Incompatible Neurospora crassa pairings differing at mat, het-c and het-6 were compared with compatible self-pairings; separate transformant experiments tested incompatible het-c alleles. The abstract reports septal compartmentation and nuclear DNA degradation in incompatible cells, contrasted with the quoted controls. TUNEL and apoptosis-like morphology do not identify a conserved metazoan apoptosis pathway. Death also occurred in older hyphae, so death alone is not specific for this trait. Full text, figures, supplements and original strain provenance were not inspected; no natural canonical exemplar is inferred from the transformed assay."
      },
      {
        "reference": "DOI:10.3852/mycologia.98.1.43",
        "snippet": "While clearly forming barrages in mycelial interactions, paired strains with different alleles at vic4 formed stable heterokaryons.",
        "notes": "2006 primary study, PMID:16800303; snippet exact-matched to the directly retrieved Europe PMC abstract. Hygromycin B- and benomyl-resistance forcing markers were used in Cryphonectria parasitica pairings. Differences at vic1, vic2, vic3, vic6 or vic7, but not vic4, produced heterokaryon incompatibility readouts of slow growth or abnormal morphology. The vic4 counterexample separates barrage formation from this trait; the abstract treats heterokaryon incompatibility as a component of a broader vegetative incompatibility system. Vegetative incompatibility is therefore not asserted as an exact synonym. Full text, figures, supplements and marker-strain provenance were not inspected. The DOI and any publisher alias identify one study, not independent replications."
      }
    ],
    "discussions": [
      {
        "discussion_id": "heterokaryon-incompatibility-scope",
        "prompt": "Keep postfusion incompatibility distinct from broader vegetative barriers.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "This organismal phenotype is not a het/vic locus, protein domain, sequence feature or individual pairing result. It requires nonself recognition, not merely slow growth or cell death. Barrage formation, prefusion avoidance, negative autotropism, sexual incompatibility and inability to fuse are not exact equivalents. Hyphal anastomosis can precede this response and is not an is-a parent. The definition does not require death of the whole colony, failure of every nonself pairing or a single conserved death pathway. The 2006 vic4 result prevents treating vegetative incompatibility as an unqualified exact synonym. Resolve organismal ontology equivalences at their issuing authorities before adding xrefs.",
        "posed_by": "codex",
        "posed_date": "2026-10-04"
      },
      {
        "discussion_id": "heterokaryon-incompatibility-mechanism-provenance",
        "prompt": "Read experimental details and resolve strain and protein anchors before enrichment.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Three primary abstracts support the phenotype and its boundary; full texts, figures and supplements remain unread. Separate natural pairing observations from transformants, forced heterokaryons and partial-diploid models when assessing canonical examples. Verify original strain provenance and current NCBI identities before adding taxon rows. Protein accessions, taxon pairing and native perturbation/rescue details must be checked before a causal graph is added. Transcript changes and TUNEL-positive nuclei are readouts, not proof of ROS necessity or canonical apoptosis. Do not use NONMECHANISTIC to hide unresolved protein mechanisms.",
        "posed_by": "codex",
        "posed_date": "2026-10-04"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-04T23:02:57Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added heterokaryon incompatibility as a postfusion nonself recognition phenotype with three directly retrieved primary DOI-backed abstracts and exact snippets. Distinguished barrage formation and broader vegetative incompatibility; no exact synonyms, canonical examples or causal graph are asserted. Ignored-and-hidden repository searches and structured METPO review found no exact trait. Reserved METPO:1056000 in proposal v483 under released phenotype. Deferred unread full texts, strain provenance, protein grounding and external equivalences.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000610",
    "label": "heterothallism",
    "definition": "A fungal phenotype in which sexual reproduction requires a separate, compatible mating partner.",
    "definition_source": "DOI:10.1038/nature07528",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/nature07528",
        "snippet": "The species has a heterothallic breeding system; isolates of complementary mating types are required for sex to occur.",
        "notes": "O'Gorman et al. (2009), PMID:19043401. Exact scientific-abstract sentence retrieved from Europe PMC core metadata; the publisher abstract was also read. Aspergillus fumigatus produced cleistothecia and ascospores, with recombination between mating type and DNA fingerprint markers in progeny from an Irish environmental subpopulation. This is observed sexual-cycle evidence, not an inference from MAT genes alone. Full methods, figures, supplements and individual isolate provenance remain uninspected; no canonical strain or universal compatibility is asserted. The historical teleomorph name in this abstract is not used as a current taxonomy mapping."
      },
      {
        "reference": "DOI:10.1534/genetics.111.136358",
        "snippet": "Coexpression of pre-2 and ccg-4 in the mat A background leads to self-attraction and development of barren perithecia without ascospores.",
        "notes": "Kim et al. (2012), PMID:22298702. Exact scientific-abstract sentence directly retrieved from Europe PMC core metadata. Neurospora crassa experiments distinguish receptor/pheromone identity from completion of sexual reproduction. The quoted engineered coexpression phenotype is not self-fertility; attraction and fruiting-body initiation alone are insufficient readouts. Forced heterokaryon experiments require mating-type genes in different nuclei for meiosis and sexual sporulation in this study, not a universal fungal architecture. Full text, figures, strain provenance and supplements remain uninspected after PMC access challenges and a full-text API error. This citation supports readout limits, not an independent natural canonical example or a protein-resolved causal graph."
      },
      {
        "reference": "DOI:10.1371/journal.pgen.1006981",
        "snippet": "Heterothallic progeny can mate only with homothallic strains, and progeny also segregate 50% homothallic, 50% heterothallic.",
        "notes": "Yun et al. (2017), PMID:28892488. Exact sentence of scientific abstract abstract1 in PMC5608430 full-text XML, distinct from the author summary. Chromocrea spinulosa includes self-fertile and partner-dependent strains: self-sterile here does not mean unable to reproduce sexually with a compatible partner. The stated compatibility and segregation are source-specific, not requirements for all heterothallic fungi. Strain/culture Methods and Conclusions were also read. Cs23 and Cs27 natural provenance, most experiments, actual figures and supplements remain unverified. Nuclear-level heterothallic recognition within a self-fertile organism is not organism-level partner dependence. No canonical example is inferred from unstable Cs27-derived MAT transformants or from reference-strain labels."
      }
    ],
    "discussions": [
      {
        "discussion_id": "heterothallism-trait-scope",
        "prompt": "Keep partner dependence distinct from sterility and nuclear recognition.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "This is an organism-level reproductive phenotype, not a sequence feature or MAT-gene inventory. It requires a compatible partner, not exactly two mating types throughout fungi or compatibility with every other isolate. Self-sterility alone can also denote general infertility; resolve lexical scope before adding exact synonyms or external xrefs. Homothallism, heterokaryosis, ploidy, hyphal fusion and parasexuality are not is-a parents. Nuclear recognition within a self-fertile individual does not establish partner dependence at the organism level. PHYSIOLOGY is a filesystem category, not an ontology parent. Do not infer absence from an unsuccessful cross under one set of culture conditions.",
        "posed_by": "codex",
        "posed_date": "2026-10-04"
      },
      {
        "discussion_id": "heterothallism-examples-and-mechanism",
        "prompt": "Verify natural isolates and complete-cycle evidence before expanding the record.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Read the uninspected methods, figures and supplements and resolve natural strain provenance and active taxonomy before adding canonical examples. Separate completed meiosis and sexual progeny from attraction, hyphal fusion, fruiting-body initiation and MAT sequence content. Resolve native protein accessions and experimental dependencies before adding mechanistic edges; do not use a NONMECHANISTIC graph to bypass unresolved grounding. Preserve actual abstract-resolver verdicts separately from manual source-section checks.",
        "posed_by": "codex",
        "posed_date": "2026-10-04"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-05T02:09:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added heterothallism with three primary DOI-backed sources and exact scientific-abstract snippets. Separated partner dependence from general infertility, MAT content and incomplete sexual readouts. Ignored-and-hidden novelty searches and structured METPO review found no exact record. Reserved METPO:1056400 in v487 under released phenotype. Deferred natural canonical examples, lexical mappings and protein-resolved graphs.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000644",
    "label": "heterotrophic",
    "definition": "A trophic type in which an organism obtains carbon from organic compounds rather than from carbon dioxide.",
    "definition_source": "DOI:10.1016/B978-012373944-5.00083-3",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000631"
    ],
    "synonyms": [
      {
        "synonym_text": "TT_heterotroph",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "aerobic_heterotrophy",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "heterotroph",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1016/B978-012373944-5.00083-3",
        "snippet": "organic compounds as the primary sources of carbon",
        "notes": "Encyclopedia chapter supports organic compounds as heterotrophic carbon sources."
      },
      {
        "reference": "DOI:10.1021/acsomega.3c02205",
        "snippet": "organic molecules ... carbon source",
        "notes": "Review table supports organic molecules as carbon sources in heterotrophic growth modes."
      },
      {
        "reference": "PMID:9278503",
        "snippet": "Escherichia coli K-12",
        "notes": "Organism example: Escherichia coli K-12 (MG1655) is the canonical chemoorganoheterotrophic model bacterium that grows on diverse organic substrates (Blattner et al. 1997, Science, complete genome)."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:562",
        "taxon_label": "Escherichia coli",
        "note": "organic-carbon heterotroph",
        "reference": "PMID:31778652"
      },
      {
        "taxon_id": "NCBITaxon:1423",
        "taxon_label": "Bacillus subtilis",
        "note": "soil heterotroph",
        "reference": "PMID:17122393"
      },
      {
        "taxon_id": "NCBITaxon:83333",
        "taxon_label": "Escherichia coli K-12",
        "note": "Strain-level heterotrophic model paired to the reviewed AtpD beta component of the aerobic respiratory ATP-synthesis branch.",
        "reference": "DOI:10.7554/eLife.21598"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "heterotrophic_organic_carbon_assimilation",
        "title": "Heterotrophic organic carbon assimilation",
        "description": "DOI-backed graph linking external organic molecules, nutrient uptake, catabolism, precursor metabolites, and biomass formation.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "This graph represents several organic-carbon assimilation branches. The E. coli K-12 AtpD example anchors the aerobic respiratory branch only; one beta-subunit accession does not denote the complete ATP synthase or all forms of heterotrophy.",
        "nodes": [
          {
            "node_id": "heterotrophic_trait",
            "label": "heterotrophic",
            "node_type": "TRAIT",
            "grounding": "METPO:1000644",
            "description": "Trophic type using organic compounds as carbon sources."
          },
          {
            "node_id": "organic_molecule",
            "label": "organic molecule",
            "node_type": "CHEMICAL",
            "description": "Organic carbon source such as sugars, organic acids, lipids, or amino acids.",
            "grounding": "CHEBI:72695"
          },
          {
            "node_id": "nutrient_uptake",
            "label": "nutrient uptake",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Cellular import of external organic substrates."
          },
          {
            "node_id": "catabolism",
            "label": "catabolism",
            "node_type": "BIOLOGICAL_PROCESS",
            "grounding": "GO:0009056",
            "description": "Breakdown of nutrients to supply energy and biosynthetic precursors."
          },
          {
            "node_id": "precursor_metabolites",
            "label": "precursor metabolites",
            "node_type": "CHEMICAL",
            "description": "Central metabolic intermediates used in biosynthesis."
          },
          {
            "node_id": "anabolism",
            "label": "anabolism",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Biosynthetic conversion of precursors into cellular material.",
            "grounding": "GO:0009058"
          },
          {
            "node_id": "biomass",
            "label": "biomass",
            "node_type": "CHEMICAL",
            "description": "Cell material formed from assimilated organic carbon.",
            "grounding": "METPO:1007501"
          },
          {
            "node_id": "glycolysis_ppp",
            "label": "glycolysis and pentose phosphate pathway",
            "node_type": "PATHWAY",
            "description": "Embden-Meyerhof glycolysis and pentose phosphate pathway catabolizing sugars in central carbon metabolism.",
            "related_records": [
              {
                "corpus": "PathwayMech",
                "identifier": "gomodel:YeastPathways_GLYCOLYSIS",
                "relation": "PATHWAY_CONTEXT",
                "basis": "PathwayMech context: glycolysis I (from glucose 6-phosphate) in Saccharomyces cerevisiae S288C (NCBITaxon:559292). This record covers only the glycolysis part of the composite node, beginning at glucose 6-phosphate. No exact equivalence or transfer of organism scope is asserted.",
                "source_version": "aa305727458c44ab05614901334540e2c87a9f3a"
              },
              {
                "corpus": "PathwayMech",
                "identifier": "MetaCyc:OXIDATIVEPENT-PWY",
                "relation": "PATHWAY_CONTEXT",
                "basis": "PathwayMech context: pentose phosphate pathway (oxidative branch) I in Escherichia coli (NCBITaxon:562). This record covers the oxidative pentose phosphate branch of the composite node. No exact equivalence or transfer of organism scope is asserted.",
                "source_version": "aa305727458c44ab05614901334540e2c87a9f3a"
              },
              {
                "corpus": "PathwayMech",
                "identifier": "MetaCyc:NONOXIPENT-PWY",
                "relation": "PATHWAY_CONTEXT",
                "basis": "PathwayMech context: pentose phosphate pathway (non-oxidative branch) I in Escherichia coli (NCBITaxon:562). This record covers the non-oxidative pentose phosphate branch of the composite node. No exact equivalence or transfer of organism scope is asserted.",
                "source_version": "aa305727458c44ab05614901334540e2c87a9f3a"
              }
            ]
          },
          {
            "node_id": "tca_cycle",
            "label": "TCA cycle",
            "node_type": "PATHWAY",
            "description": "Tricarboxylic acid cycle oxidizing imported organic carbon and generating biosynthetic precursors.",
            "grounding": "GO:0006099",
            "related_records": [
              {
                "corpus": "PathwayMech",
                "identifier": "WikiPathways:WP296",
                "relation": "PATHWAY_CONTEXT",
                "basis": "PathwayMech context: TCA cycle - detailed in Saccharomyces cerevisiae (NCBITaxon:4932). The shared route is the oxidative tricarboxylic acid cycle; the linked yeast model is an example, not a universal microbial enzyme assignment. No exact equivalence or transfer of organism scope is asserted.",
                "source_version": "aa305727458c44ab05614901334540e2c87a9f3a"
              }
            ]
          },
          {
            "node_id": "glyoxylate_cycle",
            "label": "glyoxylate cycle",
            "node_type": "PATHWAY",
            "description": "Anaplerotic cycle routing acetyl-CoA, bypassing CO2-releasing TCA steps to enhance carbon-to-biomass conversion.",
            "grounding": "GO:0006097",
            "related_records": [
              {
                "corpus": "PathwayMech",
                "identifier": "MetaCyc:GLYOXYLATE-BYPASS",
                "relation": "PATHWAY_CONTEXT",
                "basis": "PathwayMech context: glyoxylate cycle in Mycobacterium tuberculosis (NCBITaxon:1773). The shared route bypasses the decarboxylating TCA steps through isocitrate lyase and malate synthase. No exact equivalence or transfer of organism scope is asserted.",
                "source_version": "aa305727458c44ab05614901334540e2c87a9f3a"
              }
            ]
          },
          {
            "node_id": "aerobic_respiration",
            "label": "aerobic respiration",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Energy conservation oxidizing organic substrates with oxygen as terminal electron acceptor.",
            "grounding": "GO:0009060"
          },
          {
            "node_id": "fermentation",
            "label": "fermentation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Anaerobic energy conservation via substrate-level phosphorylation when respiration is unavailable.",
            "grounding": "GO:0006113"
          },
          {
            "node_id": "atp_synthase",
            "label": "ATP synthase",
            "node_type": "GENE_OR_PROTEIN",
            "grounding": "GO:0045259",
            "description": "F-type rotary complex producing ATP in the aerobic respiratory branch.",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:P0ABB4",
                "protein_label": "ATP synthase subunit beta",
                "gene_symbol": "atpD",
                "taxon_id": "NCBITaxon:83333",
                "taxon_label": "Escherichia coli K-12",
                "entry_status": "REVIEWED",
                "retrieved_on": "2026-10-22",
                "entry_version": 156,
                "sequence_version": 2,
                "role": "Beta component of the E. coli F1 catalytic head in respiratory ATP synthesis; it is not presented as the complete complex.",
                "evidence": [
                  {
                    "reference": "DOI:10.7554/eLife.21598",
                    "snippet": "proton motive force drives rotation and conformational changes in the F1 catalytic sites",
                    "notes": "The primary cryo-EM study resolves the E. coli F1Fo complex and its beta-containing catalytic head; UniProt verifies the reviewed K-12 AtpD entry."
                  }
                ]
              }
            ]
          }
        ],
        "edges": [
          {
            "subject": "heterotrophic_trait",
            "predicate": "has carbon source",
            "object": "organic_molecule",
            "description": "Heterotrophy uses organic compounds as carbon sources instead of CO2.",
            "evidence": [
              {
                "reference": "DOI:10.1016/B978-012373944-5.00083-3",
                "snippet": "organic compounds as the primary sources of carbon",
                "notes": "Supports organic compounds as heterotrophic carbon sources."
              }
            ],
            "predicate_id": "METPO:2007806"
          },
          {
            "subject": "organic_molecule",
            "predicate": "imported by",
            "object": "nutrient_uptake",
            "description": "Organic nutrients must be taken up before intracellular metabolism.",
            "evidence": [
              {
                "reference": "DOI:10.1016/B978-012373944-5.00083-3",
                "snippet": "nutrient uptake",
                "notes": "Supports uptake as part of microbial nutrition."
              }
            ]
          },
          {
            "subject": "nutrient_uptake",
            "predicate": "supplies",
            "object": "catabolism",
            "description": "Imported organic substrates feed catabolic metabolism.",
            "evidence": [
              {
                "reference": "DOI:10.1016/B978-012373944-5.00083-3",
                "snippet": "breakdown of nutrients",
                "notes": "Supports catabolic processing of organic nutrients."
              }
            ]
          },
          {
            "subject": "catabolism",
            "predicate": "has output",
            "object": "precursor_metabolites",
            "description": "Catabolism generates central intermediates for biosynthesis.",
            "evidence": [
              {
                "reference": "DOI:10.1016/B978-012373944-5.00083-3",
                "snippet": "precursor compounds for anabolism",
                "notes": "Supports nutrient breakdown to biosynthetic precursors."
              }
            ],
            "predicate_id": "RO:0002234"
          },
          {
            "subject": "precursor_metabolites",
            "predicate": "used by",
            "object": "anabolism",
            "description": "Precursor metabolites are substrates for biosynthetic pathways.",
            "evidence": [
              {
                "reference": "DOI:10.1016/B978-012373944-5.00083-3",
                "snippet": "anabolism",
                "notes": "Supports biosynthetic use of catabolic precursors."
              }
            ]
          },
          {
            "subject": "anabolism",
            "predicate": "has output",
            "object": "biomass",
            "description": "Anabolism incorporates organic carbon into biomass.",
            "evidence": [
              {
                "reference": "DOI:10.1016/B978-012373944-5.00083-3",
                "snippet": "incorporation of a compound into biomass",
                "notes": "Supports assimilation of compounds into cell material."
              }
            ],
            "predicate_id": "RO:0002234"
          },
          {
            "subject": "organic_molecule",
            "predicate": "causally enables",
            "object": "heterotrophic_trait",
            "description": "External organic substrates must be imported and metabolized to support heterotrophic growth.",
            "evidence": [
              {
                "reference": "DOI:10.1021/acsomega.3c02205",
                "notes": "The substrate must be imported and metabolized to produce ATP and NAD(P)H; minimal mechanistic requirement generalizes to heterotrophy."
              }
            ]
          },
          {
            "subject": "catabolism",
            "predicate": "proceeds via",
            "object": "glycolysis_ppp",
            "description": "Catabolism of imported sugars proceeds via Embden-Meyerhof glycolysis and the pentose phosphate pathway.",
            "evidence": [
              {
                "reference": "DOI:10.1111/raq.12700",
                "notes": "Glucose catabolism proceeds via Embden-Meyerhof glycolysis and the pentose phosphate pathway; general central-metabolism support."
              }
            ]
          },
          {
            "subject": "tca_cycle",
            "predicate": "has output",
            "object": "precursor_metabolites",
            "description": "The TCA cycle oxidizes imported organic carbon and supplies biosynthetic precursors.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2024.1441865",
                "notes": "Genomes encode complete glycolysis, gluconeogenesis and TCA cycle enzymes oxidizing imported organic carbon for precursor generation."
              }
            ],
            "predicate_id": "RO:0002234"
          },
          {
            "subject": "glyoxylate_cycle",
            "predicate": "enhances",
            "object": "biomass",
            "description": "Routing acetyl-CoA through the glyoxylate shunt bypasses CO2-releasing TCA steps, enhancing carbon-to-biomass conversion.",
            "evidence": [
              {
                "reference": "DOI:10.1111/raq.12700",
                "notes": "The glyoxylate shunt bypasses CO2-releasing TCA steps, enhancing conversion of carbon into biomass."
              }
            ]
          },
          {
            "subject": "catabolism",
            "predicate": "couples to",
            "object": "aerobic_respiration",
            "description": "Oxidation of imported organic substrates couples to aerobic respiration for energy conservation.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2024.1441865",
                "notes": "Sugars are used as electron donors for aerobic respiration; respiration is the energy-conservation module for heterotrophy."
              }
            ]
          },
          {
            "subject": "catabolism",
            "predicate": "couples to",
            "object": "fermentation",
            "description": "Under anaerobic conditions heterotrophic energy conservation proceeds via fermentation and substrate-level phosphorylation.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.chom.2024.05.011",
                "notes": "Anaerobic conditions favor substrate-level phosphorylation (fermentation) for heterotrophic energy conservation."
              }
            ]
          },
          {
            "subject": "atp_synthase",
            "predicate": "participates in",
            "object": "aerobic_respiration",
            "description": "F-type ATP synthase performs ATP synthesis in the aerobic respiratory branch.",
            "evidence": [
              {
                "reference": "DOI:10.7554/eLife.21598",
                "snippet": "proton motive force drives rotation and conformational changes in the F1 catalytic sites",
                "notes": "Supports the beta-containing E. coli F1Fo complex as the terminal ATP-producing machinery of respiration."
              }
            ],
            "predicate_id": "biolink:participates_in"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.873704+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-09T00:00:00-07:00",
        "curator": "codex",
        "action": "ADDED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed causal graph for organic carbon uptake, catabolism, precursor metabolites, anabolism, and biomass formation.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-16T05:00:00-07:00",
        "curator": "claude",
        "action": "ADDED_ORGANISM_EXAMPLE",
        "changes": "Added Escherichia coli K-12 organism example with PMID-backed evidence.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d72, METPO:2000006\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:41:04Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (METPO:1007501\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T07:34:58Z",
        "curator": "claude",
        "action": "RETYPE_CAUSAL_NODES",
        "changes": "Re-typed 1 causal-node node_type field(s) to align with CausalNodeTypeEnum semantics: biomass: BIOLOGICAL_PROCESS \u2192 CHEMICAL \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-14T05:51:47Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:72695\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-17T04:09:45Z",
        "curator": "claude",
        "action": "REMOVE_REDUNDANT_SYNONYM",
        "changes": "Removed 1 synonym(s) whose text duplicated the label (seeder redundancy; no information lost).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 6 evidence-backed generic edges (5 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:14Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:20Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0009060\u00d71, GO:0006113\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:34Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 3 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0009058\u00d71, GO:0006099\u00d71, GO:0006097\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 4 causal edge(s) off microbe-domain METPO predicates (1 to has carbon source, 3 to has output), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-16T02:00:00Z",
        "curator": "claude",
        "action": "NORMALISE_NODE_TYPE",
        "changes": "Under the PATHWAY-vs-BIOLOGICAL_PROCESS rule, one node_id means one thing corpus-wide (issue 356): fermentation is typed BIOLOGICAL_PROCESS. PATHWAY is a named, conventionally enumerable multi-step route; BIOLOGICAL_PROCESS is everything else. A CLASS of routes rather than one route -- fermentation names a mode of energy conservation with many distinct implementations, so its steps cannot be enumerated without picking one. Was 3 BIOLOGICAL_PROCESS to 2 before this tranche. NOTE its groundings disagree with each other (GO:0006113 x3, METPO:1002005, and METPO:1000845 which is ACETOGENESIS, a different concept) -- filed as #391 and deliberately NOT touched here, because retyping a node while carrying a wrong CURIE along unchanged would make it look reviewed.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "CURATE_PROTEIN_TAXON_EXAMPLE",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope heterotrophic_organic_carbon_assimilation=MECHANISTIC with scope_notes; added taxon-paired protein example(s) UniProtKB:P0ABB4 on atp_synthase (NCBITaxon:83333); added 1 node(s) and 1 edge(s) (atp_synthase); added canonical example(s) NCBITaxon:83333.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-05T17:46:21Z",
        "curator": "codex",
        "action": "ADD_PATHWAY_CONTEXT",
        "changes": "Added pinned PathwayMech context on reviewed causal nodes with explicit route and organism limitations; retained existing groundings and exact xrefs.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-22T01:35:00Z",
        "curator": "claude",
        "action": "REFRESH_UNIPROT_ENTRY_VERSION",
        "changes": "Refreshed UniProtKB entry_version against live UniProt REST on 2026-10-22: UniProtKB:P0ABB4 (155 -> 156 on atp_synthase).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000171",
    "label": "histidine arylamidase activity",
    "definition": "A physiological enzyme-activity phenotype in which a cell produces active histidine arylamidase enzymes that hydrolyze histidine arylamide substrates.",
    "definition_source": "DOI:10.1099/ijsem.0.006017",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "synonyms": [
      {
        "synonym_text": "histidine arylamidase",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1099/ijsem.0.006017"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1099/ijsem.0.006017",
        "snippet": "enzymatic activities are present for: \u03b1-galactosidase, N-acetyl-\u03b2-glucosaminidase, arginine arylamidase, proline arylamidase, leucyl glycine arylamidase, phenylalanine arylamidase, leucine arylamidase, tyrosine arylamidase, alanine arylamidase, glycine arylamidase, histidine arylamidase, glutamyl glutamic acid arylamidase, serine arylamidase, valine arylamidase, cysteine arylamidase, esterase, esterase lipase, alpha-chymotrypsin",
        "notes": "Srinivasan et al. listed histidine arylamidase among enzymatic activities present in the Amygdalobacter indicium species description, supporting the API arylamidase row as a directly assayed bacterial enzyme-activity phenotype."
      },
      {
        "reference": "DOI:10.1128/JCM.40.9.3427-3431.2002",
        "snippet": "When the API rapid ID32A system was used, all eight strains displayed activity for alanine arylamidase, arginine arylamidase, \u03b1-glucosidase, glycine arylamidase, histidine arylamidase, leucine arylamidase, leucylglycine arylamidase, proline arylamidase, phenylalanine arylamidase, serine arylamidase, and tyrosine arylamidase",
        "notes": "Hall et al. reported histidine arylamidase activity in all eight Actinomyces cardiffensis clinical isolates tested with the API rapid ID32A system."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:3029272",
        "taxon_label": "Amygdalobacter indicium",
        "note": "Srinivasan et al. reported Amygdalobacter indicium as positive for histidine arylamidase activity in an enzyme activity panel.",
        "reference": "DOI:10.1099/ijsem.0.006017"
      }
    ],
    "discussions": [
      {
        "discussion_id": "histidine-arylamidase-activity-xref-gap",
        "prompt": "Resolve an exact external ontology class for histidine arylamidase activity before adding a TraitRecord xref.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "GO:0004177 covers broad aminopeptidase activity at molecular-function scope, and no live GO class provides an exact residue-specific histidine arylamidase production phenotype at organism-level scope.",
        "posed_by": "codex",
        "posed_date": "2026-09-12"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-12T13:38:31Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted histidine arylamidase activity as a DOI-backed TraitRecord after a repository-wide duplicate review covering ignored and hidden files; METPO has no exact histidine arylamidase activity class yet and the placeholder is reserved in proposals/metpo_traitmech_v48.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000208",
    "label": "homeoviscous adaptation",
    "definition": "A stress response in which an organism remodels membrane lipid composition to maintain a functional membrane viscosity and fluidity when temperature changes perturb lipid packing.",
    "definition_source": "DOI:10.1039/d4cc03114h",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000078"
    ],
    "synonyms": [
      {
        "synonym_text": "homoviscous adaptation",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1146/annurev-micro-091313-103612"
      },
      {
        "synonym_text": "HVA",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1039/d4cc03114h"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev-micro-091313-103612",
        "snippet": "termed homeoviscous adaptation",
        "notes": "de Mendoza reviews the temperature-driven bacterial membrane remodeling response and names it homeoviscous adaptation."
      },
      {
        "reference": "DOI:10.1128/spectrum.03925-23",
        "snippet": "Upon temperature decrease, the membrane rigidifies and increases in thickness, resulting in activation of the kinase-dominant state of DesK",
        "notes": "Sidarta et al. support membrane rigidification and thickening as proximal physical triggers in the Bacillus subtilis DesK/DesR homeoviscous-adaptation model."
      },
      {
        "reference": "DOI:10.1038/s41467-024-53677-5",
        "snippet": "hard-wired parameters calibrate the system to generate membrane compositions that maintain constant fluidity",
        "notes": "Hoogerland et al. directly support E. coli temperature adaptation through a fatty-acid synthesis control system that maintains membrane fluidity."
      },
      {
        "reference": "DOI:10.1038/s41467-024-53677-5",
        "snippet": "restores optimal membrane fluidity within a single generation",
        "notes": "Hoogerland et al. directly connect the E. coli fatty-acid branchpoint valve and transcriptional feedback to rapid membrane-fluidity restoration after temperature shock."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:562",
        "taxon_label": "Escherichia coli",
        "note": "E. coli rapidly restores membrane fluidity after temperature shock through a FabI/FabB branchpoint valve coupled to transcriptional feedback.",
        "reference": "DOI:10.1038/s41467-024-53677-5"
      },
      {
        "taxon_id": "NCBITaxon:1423",
        "taxon_label": "Bacillus subtilis",
        "note": "B. subtilis is the model organism for DesK/DesR membrane thickness sensing and Des-mediated fatty-acyl-chain desaturation during cold-induced homeoviscous adaptation.",
        "reference": "DOI:10.1128/spectrum.03925-23"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "homeoviscous_adaptation_membrane_fluidity",
        "title": "Membrane-fluidity homeostasis by lipid remodeling",
        "description": "Evidence-backed causal sketch linking temperature-driven membrane rigidification to homeoviscous lipid remodeling and restored membrane fluidity.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "This graph captures the conserved membrane-fluidity output of homeoviscous adaptation without making the Bacillus DesK/DesR two-component branch, E. coli FabI/FabB metabolic valve, or any single lipid species universal across microbes.",
        "nodes": [
          {
            "node_id": "homeoviscous_adaptation_trait",
            "label": "homeoviscous adaptation",
            "node_type": "TRAIT",
            "grounding": "traitmech:000208",
            "description": "Capacity to remodel membrane lipid composition to preserve functional membrane viscosity and fluidity."
          },
          {
            "node_id": "temperature_downshift",
            "label": "temperature downshift",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "A decrease in ambient temperature that orders the lipid bilayer."
          },
          {
            "node_id": "membrane_rigidity",
            "label": "membrane rigidification",
            "node_type": "QUALITY",
            "description": "Reduced membrane fluidity and increased bilayer thickness after cooling."
          },
          {
            "node_id": "homeoviscous_adaptation_process",
            "label": "homeoviscous adaptation",
            "node_type": "BIOLOGICAL_PROCESS",
            "grounding": "METPO:1016200",
            "description": "Temperature-responsive lipid remodeling that restores the membrane to a fluidity setpoint."
          },
          {
            "node_id": "fab_fatty_acid_branchpoint_enzymes",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed E. coli branchpoint protein set; no single taxon-agnostic family, activity, or complex term captures the FabI enoyl-ACP reductase and FabB beta-ketoacyl-ACP synthase pair without also adding unrelated fatty-acid synthesis components.",
            "label": "FabI/FabB branchpoint enzymes",
            "node_type": "GENE_OR_PROTEIN",
            "description": "E. coli fatty-acid synthesis enzymes at the saturated/unsaturated branchpoint that route acyl-ACP flux during temperature adaptation.",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:P0AEK4",
                "protein_label": "Enoyl-[acyl-carrier-protein] reductase [NADH] FabI",
                "gene_symbol": "fabI",
                "taxon_id": "NCBITaxon:83333",
                "taxon_label": "Escherichia coli K-12",
                "entry_status": "REVIEWED",
                "retrieved_on": "2026-09-15",
                "entry_version": 161,
                "sequence_version": 2,
                "role": "E. coli K-12 FabI catalyzes enoyl-ACP reduction in fatty-acid elongation and participates in the FabI/FabB metabolic valve that allocates flux between saturated and unsaturated fatty-acid synthesis during homeoviscous adaptation.",
                "evidence": [
                  {
                    "reference": "https://rest.uniprot.org/uniprotkb/P0AEK4.json",
                    "snippet": "Involved in the elongation cycle of fatty acid which are used in the lipid metabolism",
                    "notes": "Verified FabI identity and fatty-acid elongation role against the live UniProt REST entry for P0AEK4 retrieved on 2026-09-15."
                  },
                  {
                    "reference": "DOI:10.1038/s41467-024-53677-5",
                    "snippet": "via the branchpoint enzymes FabI and FabB",
                    "notes": "Hoogerland et al. place FabI in the temperature-sensitive E. coli fatty-acid branchpoint valve."
                  }
                ]
              },
              {
                "uniprot_id": "UniProtKB:P0A953",
                "protein_label": "3-oxoacyl-[acyl-carrier-protein] synthase 1",
                "gene_symbol": "fabB",
                "taxon_id": "NCBITaxon:83333",
                "taxon_label": "Escherichia coli K-12",
                "entry_status": "REVIEWED",
                "retrieved_on": "2026-09-15",
                "entry_version": 155,
                "sequence_version": 1,
                "role": "E. coli K-12 FabB elongates acyl-ACP substrates in fatty-acid biosynthesis and participates in the FabI/FabB metabolic valve that allocates flux between saturated and unsaturated fatty-acid synthesis during homeoviscous adaptation.",
                "evidence": [
                  {
                    "reference": "https://rest.uniprot.org/uniprotkb/P0A953.json",
                    "snippet": "Catalyzes a key reaction in unsaturated fatty acid (UFA) synthesis",
                    "notes": "Verified FabB identity and unsaturated fatty-acid synthesis role against the live UniProt REST entry for P0A953 retrieved on 2026-09-15."
                  },
                  {
                    "reference": "DOI:10.1038/s41467-024-53677-5",
                    "snippet": "via the branchpoint enzymes FabI and FabB",
                    "notes": "Hoogerland et al. place FabB in the temperature-sensitive E. coli fatty-acid branchpoint valve."
                  }
                ]
              }
            ]
          },
          {
            "node_id": "membrane_lipid_remodeling",
            "label": "membrane lipid remodeling",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Changes in membrane lipid unsaturation, branching, or chain length that alter lipid packing."
          },
          {
            "node_id": "membrane_fluidity",
            "label": "membrane fluidity",
            "node_type": "QUALITY",
            "grounding": "METPO:1007505",
            "description": "Dynamic lipid-bilayer state maintained near a functional setpoint by homeoviscous remodeling."
          }
        ],
        "edges": [
          {
            "subject": "temperature_downshift",
            "predicate": "causes",
            "object": "membrane_rigidity",
            "description": "A temperature decrease causes the bacterial membrane to rigidify and thicken.",
            "evidence": [
              {
                "reference": "DOI:10.1128/spectrum.03925-23",
                "snippet": "Upon temperature decrease, the membrane rigidifies and increases in thickness",
                "notes": "Sidarta et al. describe rigidification and thickening as the immediate membrane response to temperature decrease."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "membrane_rigidity",
            "predicate": "positively regulates",
            "object": "homeoviscous_adaptation_process",
            "description": "Membrane rigidification is sensed as the physical input that activates homeoviscous lipid remodeling.",
            "evidence": [
              {
                "reference": "DOI:10.1128/spectrum.03925-23",
                "snippet": "Upon temperature decrease, the membrane rigidifies and increases in thickness, resulting in activation of the kinase-dominant state of DesK",
                "notes": "Sidarta et al. support the physical membrane-state trigger through the B. subtilis DesK sensor model."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "homeoviscous_adaptation_process",
            "predicate": "positively regulates",
            "object": "membrane_lipid_remodeling",
            "description": "Homeoviscous adaptation increases lipid remodeling routes, including fatty-acyl desaturation, that counteract bilayer ordering.",
            "evidence": [
              {
                "reference": "DOI:10.1128/spectrum.03925-23",
                "snippet": "desaturates the fatty acyl chains, resulting in membrane fluidization and concomitant decrease of bilayer thickness",
                "notes": "Sidarta et al. support Des-mediated fatty-acyl desaturation as a concrete B. subtilis homeoviscous remodeling branch."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "fab_fatty_acid_branchpoint_enzymes",
            "predicate": "regulates",
            "object": "membrane_lipid_remodeling",
            "description": "The E. coli FabI/FabB branchpoint valve allocates fatty-acid synthesis flux between saturated and unsaturated membrane-lipid routes.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-024-53677-5",
                "snippet": "A first element of this regulatory system is a temperature-sensitive metabolic valve that allocates flux between the saturated and unsaturated fatty acid synthesis pathways via the branchpoint enzymes FabI and FabB",
                "notes": "Hoogerland et al. support the E. coli FabI/FabB branchpoint valve as a regulator of flux between saturated and unsaturated fatty-acid synthesis."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "membrane_lipid_remodeling",
            "predicate": "regulates",
            "object": "membrane_fluidity",
            "description": "Temperature-dependent membrane lipid remodeling maintains membrane fluidity near a functional setpoint.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-024-53677-5",
                "snippet": "hard-wired parameters calibrate the system to generate membrane compositions that maintain constant fluidity",
                "notes": "Hoogerland et al. show that the E. coli fatty-acid synthesis system generates temperature-specific membrane compositions that maintain fluidity."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "membrane_fluidity",
            "predicate": "contributes to",
            "object": "homeoviscous_adaptation_trait",
            "description": "Restoration of optimal membrane fluidity is the physiological output of homeoviscous adaptation.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-024-53677-5",
                "snippet": "restores optimal membrane fluidity within a single generation",
                "notes": "Hoogerland et al. directly connect the homeoviscous fatty-acid control system to rapid fluidity restoration."
              }
            ],
            "predicate_id": "RO:0002326"
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "homeoviscous-adaptation-xref-gap",
        "prompt": "Resolve an exact external ontology class for organism-level homeoviscous adaptation before adding a TraitRecord xref.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "No exact GO, PATO, or METPO class is present in the pinned local snapshot for homeoviscous adaptation. Related lipid metabolism, fatty-acid desaturation, membrane-fluidity, and cold-response terms are narrower, broader, or shifted from the whole-organism membrane-acclimation trait.",
        "posed_by": "codex",
        "posed_date": "2026-09-15"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-15T07:02:39Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted homeoviscous adaptation as a DOI-backed stress-response TraitRecord after a repository-wide duplicate review covering ignored and hidden files; the local METPO snapshot has no exact homeoviscous-adaptation class and the replacement placeholder is reserved in proposals/metpo_traitmech_v85.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-15T07:13:33Z",
        "curator": "codex",
        "action": "ADD_PROTEIN_EXAMPLES",
        "changes": "Added E. coli K-12 FabI and FabB UniProt protein examples to the homeoviscous adaptation causal graph and removed a top-level evidence item whose Maiti review citation had no verbatim snippet.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-15T07:26:31Z",
        "curator": "codex",
        "action": "NORMALIZED_CAUSAL_NODE_ID",
        "changes": "Renamed the homeoviscous graph node membrane_rigidification to the canonical membrane_rigidity QUALITY node id after PR review found that the retired process-shaped alias had been reintroduced.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000609",
    "label": "homothallism",
    "definition": "A fungal phenotype enabling a culture founded from a single spore to reproduce sexually in isolation from a mating partner.",
    "definition_source": "DOI:10.5598/imafungus.2015.06.01.13",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.5598/imafungus.2015.06.01.13",
        "snippet": "the ability of a single spore to produce a sexually reproducing colony when propagated in complete isolation.",
        "notes": "2015 terminology review, PMID:26203424. Exact contiguous span of the historical operational definition in the Introduction at https://pmc.ncbi.nlm.nih.gov/articles/PMC4500084/. Abstract, Introduction and Conclusions were read as full-text XML; mechanism-specific sections and figures remain uninspected. This is definition authority, not experimental replication. Homothallism is an umbrella encompassing primary homothallism, pseudohomothallism, mating-type switching and unisexual reproduction, not one universal MAT architecture. The snippet is full text, not an abstract quote."
      },
      {
        "reference": "DOI:10.1371/journal.pgen.1006981",
        "snippet": "The filamentous fungus Chromocrea spinulosa (Trichoderma spinulosum) exhibits both self-fertile (homothallic) and self-sterile (heterothallic) sexual reproductive behavior.",
        "notes": "Yun et al. (2017), PMID:28892488. Exact sentence of the directly retrieved Europe PMC scientific abstract, separate from the author summary. Strain/culture Methods and Conclusions were read at PMC5608430; most main-text experiments, actual figures and supplements remain uninspected. Cs23 and Cs27 are the paper's self-fertile and self-sterile reference strains; their original natural provenance has not been verified. MAT manipulation supports direct-repeat-mediated MAT1-2 loss and recognition between unlike nuclei in a shared cytoplasm. Both intact MAT1-1-1 and MAT1-2-1 in one nucleus are not sufficient for self-fertility. The authors describe a heterothallic strategy at the nuclear level, not primary homothallism, while retaining organism-level self-fertility. Unstable Cs27 transformants were tested directly from transformation plates; do not generalize their stability."
      },
      {
        "reference": "DOI:10.7554/elife.79114",
        "snippet": "Our findings support C. depauperatus as an obligately sexual, homothallic fungus",
        "notes": "Passer, Clancey et al. (2022), PMID:35713948. Exact independent clause of the scientific abstract in PMC9296135 full-text XML. Europe PMC's abstractText instead returns the eLife digest; a manual scientific-abstract match is not a VERIFIED resolver verdict. Publisher version 2 assets were retrieved through https://api.elifesciences.org/articles/79114. Introduction, strain/culture Methods, deletion-mutant Results and intra-/interstrain crossing and recombination Results were read. Actual Figures 5 and 8 and their captions were inspected; Supplementary file 1 strain rows were read from the publisher's elife-79114-supp1-v2.xlsx. Other figures, supplements and unread Methods remain uninspected. Figure 5 separates wild-type CBS7841 sporulation from pheromone/receptor and DMC1 deletion phenotypes. Hyphal growth alone does not establish meiosis. Figure 8 recombination assays use CBS7841-derived marker strains, including UV-induced and spontaneous mutants, not the unmodified canonical isolate. Drug resistance alone is not evidence of sex; genotyping distinguishes recombination from new mutations. Tested interstrain crosses did not yield PCR-confirmed recombinant progeny, so universal compatibility is not asserted. Obligately sexual describes this source's example, not a requirement for all homothallic fungi."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1295531",
        "taxon_label": "Cryptococcus depauperatus CBS 7841",
        "reference": "DOI:10.7554/elife.79114",
        "note": "Qualified natural-isolate example: wild-type CBS7841, distinguished from its laboratory derivatives in Supplementary file 1. Figure 5A shows basidia and spore chains after one week on V8 medium at room temperature in the dark; Figure 5B assays sporulation after ten days on Murashige-Skoog medium. The paper's composite sexual-cycle evidence includes separate mutant experiments, not all measurements on wild type. Natural provenance is independently documented by https://www.atcc.org/products/36983: B3810 [CBS 7841, TRTC 48044], isolated from a dead spider in Ontario, Canada. This collection record supports provenance, not independent trait replication. NCBI taxonomy 1295531 resolves to this active strain name on 2026-10-04."
      }
    ],
    "discussions": [
      {
        "discussion_id": "homothallism-trait-scope",
        "prompt": "Preserve organism-level self-fertility across distinct mating mechanisms.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "This is a reproductive phenotype, not a sequence feature or MAT-gene inventory. The operational single-spore definition does not require a uninucleate spore, both MAT idiomorphs in one nucleus, or one molecular mechanism. It does not exclude outcrossing or require universal compatibility, obligate sexuality, or self-fertility of every progeny. Distinguish self-fertility from asexual cloning, ploidy, heterokaryosis, hyphal fusion and parasexual reproduction; these are not is-a parents. PHYSIOLOGY is a filesystem category, not an ontology parent. Self-fertility and self-compatibility also have uses outside fungi; resolve their lexical scope and external phenotype/process mappings before adding synonyms or xrefs.",
        "posed_by": "codex",
        "posed_date": "2026-10-04"
      },
      {
        "discussion_id": "homothallism-mechanism-and-readouts",
        "prompt": "Resolve native proteins and sexual-cycle readouts before adding causal edges.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Complete unread experiments and supplements before expanding mechanistic claims. Separate wild-type sporulation, deletion phenotypes, marker segregation and inter-marker recombination. MAT homology or expression alone cannot establish a sexual cycle, and neither independent chromosome assortment nor drug resistance alone excludes parasexual processes. Resolve native protein accessions, experimental dependencies and taxonomic provenance before adding a mechanistic graph; do not use NONMECHANISTIC to bypass unresolved grounding. Retain the actual abstract-verifier outcome when an API returns an editorial digest, and identify manual full-text checks separately.",
        "posed_by": "codex",
        "posed_date": "2026-10-04"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-05T01:23:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added homothallism with a definition review and two primary DOI-backed studies, each with an exact source snippet. Separated self-fertility from mating-locus content and retained strain and assay qualifiers. Added natural CBS 7841 after primary figure, strain-table, ATCC provenance and NCBI identity checks. Ignored-and-hidden novelty searches and structured METPO review found no exact record. Reserved METPO:1056300 in v486 under released phenotype. Deferred lexical mappings and protein-resolved graphs.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000646",
    "label": "hydrogenotrophic",
    "definition": "A trophic type in which an organism uses molecular hydrogen as an electron donor for energy generation and carbon dioxide as the primary carbon source.",
    "definition_source": "DOI:10.21775/cimb.006.159",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000631"
    ],
    "created_by": "Luke Wang",
    "evidence": [
      {
        "reference": "DOI:10.21775/cimb.006.159",
        "snippet": "reversible oxidation of hydrogen gas",
        "notes": "Review supports hydrogenase-catalyzed H2 oxidation and microbial energy metabolism."
      },
      {
        "reference": "DOI:10.1128/AEM.02473-10",
        "snippet": "assimilation of CO2",
        "notes": "Review supports CO2 assimilation into cellular carbon in autotrophic metabolism."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:106590",
        "taxon_label": "Cupriavidus necator",
        "note": "aerobic H2 oxidiser (Knallgas)",
        "reference": "PMID:34723797"
      },
      {
        "taxon_id": "NCBITaxon:2190",
        "taxon_label": "Methanocaldococcus jannaschii",
        "note": "hydrogenotrophic methanogen",
        "reference": "PMID:31333590"
      },
      {
        "taxon_id": "NCBITaxon:381666",
        "taxon_label": "Cupriavidus necator H16",
        "note": "Strain-level Knallgas exemplar for respiratory H2 oxidation by the oxygen-tolerant membrane-bound NiFe hydrogenase.",
        "reference": "DOI:10.1128/jb.01427-10"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "hydrogenotrophic_hydrogen_oxidation_fixation",
        "title": "Hydrogenotrophic H2 oxidation and CO2 fixation",
        "description": "DOI-backed graph linking hydrogenase-catalyzed H2 oxidation, electron transport energy conservation, and autotrophic CO2 fixation.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "Represents H2 oxidation coupled to electron transport and carbon fixation. The protein node is narrowed to the membrane-bound NiFe uptake-hydrogenase branch demonstrated in C. necator H16; other acceptor branches remain process-level.",
        "nodes": [
          {
            "node_id": "hydrogenotrophic_trait",
            "label": "hydrogenotrophic",
            "node_type": "TRAIT",
            "grounding": "METPO:1000646",
            "description": "Trophic type using H2 as electron donor and CO2 as carbon source."
          },
          {
            "node_id": "molecular_hydrogen",
            "label": "molecular hydrogen",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:18276",
            "description": "Electron donor oxidized by hydrogenotrophs."
          },
          {
            "node_id": "hydrogenase",
            "label": "membrane-bound NiFe uptake hydrogenase complex",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Oxygen-tolerant membrane complex coupling H2 oxidation to the respiratory quinone pool in C. necator H16.",
            "grounding": "GO:0044569",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:P31891",
                "protein_label": "Uptake hydrogenase large subunit",
                "gene_symbol": "hoxG",
                "taxon_id": "NCBITaxon:381666",
                "taxon_label": "Cupriavidus necator H16",
                "entry_status": "REVIEWED",
                "proteome_id": "UP000008210",
                "retrieved_on": "2026-10-22",
                "sequence_version": 4,
                "role": "Catalytic large-subunit component of the membrane-bound NiFe uptake-hydrogenase complex; this accession does not denote the complete HoxKGZ complex.",
                "evidence": [
                  {
                    "reference": "DOI:10.1128/jb.01427-10",
                    "snippet": "large subunit HoxG (67.1 kDa) containing the Ni-Fe active site",
                    "notes": "The primary H16 study identifies HoxG as the catalytic large subunit of the oxygen-tolerant membrane-bound hydrogenase and traces electron transfer to the respiratory chain; UniProtKB P31891 verifies the reviewed instance."
                  }
                ],
                "entry_version": 156
              }
            ]
          },
          {
            "node_id": "protons_electrons",
            "label": "protons and electrons",
            "node_type": "CHEMICAL",
            "description": "Products of hydrogen oxidation."
          },
          {
            "node_id": "electron_transport_system",
            "label": "electron transport system",
            "node_type": "PATHWAY",
            "description": "Membrane-linked electron-transfer route supporting energy conservation.",
            "grounding": "GO:0022900"
          },
          {
            "node_id": "proton_motive_force",
            "label": "proton motive force",
            "node_type": "STATE",
            "description": "Ion gradient used for energy conservation.",
            "grounding": "METPO:1007500"
          },
          {
            "node_id": "carbon_dioxide",
            "label": "carbon dioxide",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:16526",
            "description": "Inorganic carbon source."
          },
          {
            "node_id": "autotrophic_co2_fixation",
            "label": "autotrophic CO2 fixation",
            "node_type": "PATHWAY",
            "description": "Carbon fixation pathway converting inorganic carbon into cell carbon.",
            "grounding": "GO:0015977"
          },
          {
            "node_id": "cellular_carbon",
            "label": "cellular carbon",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced cell material produced from CO2."
          },
          {
            "node_id": "molecular_oxygen",
            "label": "oxygen",
            "node_type": "CHEMICAL",
            "description": "Terminal electron acceptor that can be reduced when coupled to H2 oxidation."
          },
          {
            "node_id": "nitrate",
            "label": "nitrate",
            "node_type": "CHEMICAL",
            "description": "Inorganic electron acceptor reducible by H2 oxidation in anaerobic respiration.",
            "grounding": "CHEBI:17632"
          },
          {
            "node_id": "sulfate",
            "label": "sulfate",
            "node_type": "CHEMICAL",
            "description": "Inorganic electron acceptor reducible by H2 oxidation in anaerobic respiration.",
            "grounding": "CHEBI:16189"
          },
          {
            "node_id": "h2_oxidation",
            "label": "H2 oxidation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Hydrogenase-catalyzed oxidation of molecular hydrogen to protons and electrons."
          }
        ],
        "edges": [
          {
            "subject": "hydrogenotrophic_trait",
            "predicate": "has electron donor",
            "object": "molecular_hydrogen",
            "description": "Molecular hydrogen serves as the electron donor for hydrogenotrophy.",
            "evidence": [
              {
                "reference": "DOI:10.21775/cimb.006.159",
                "snippet": "oxidation of hydrogen gas",
                "notes": "Supports H2 oxidation as a microbial energy process."
              }
            ],
            "predicate_id": "METPO:2007701"
          },
          {
            "subject": "hydrogenase",
            "predicate": "oxidizes",
            "object": "molecular_hydrogen",
            "description": "Hydrogenases catalyze H2 oxidation.",
            "evidence": [
              {
                "reference": "DOI:10.21775/cimb.006.159",
                "snippet": "reversible oxidation of hydrogen gas",
                "notes": "Supports hydrogenase-catalyzed H2 oxidation."
              }
            ],
            "predicate_id": "METPO:2007803"
          },
          {
            "subject": "molecular_hydrogen",
            "predicate": "oxidized to",
            "object": "protons_electrons",
            "description": "H2 oxidation yields protons and electrons.",
            "evidence": [
              {
                "reference": "DOI:10.21775/cimb.006.159",
                "snippet": "H2 <--> 2 H+ + 2 e-",
                "notes": "Supports the H2 redox half reaction."
              }
            ],
            "predicate_id": "METPO:2007405"
          },
          {
            "subject": "hydrogenase",
            "predicate": "interacts with",
            "object": "electron_transport_system",
            "description": "Hydrogenases can couple H2 metabolism to membrane electron transport systems.",
            "evidence": [
              {
                "reference": "DOI:10.21775/cimb.006.159",
                "snippet": "interact with membrane-bound electron transport systems",
                "notes": "Supports coupling to electron transport."
              }
            ],
            "predicate_id": "biolink:interacts_with"
          },
          {
            "subject": "electron_transport_system",
            "predicate": "generates",
            "object": "proton_motive_force",
            "description": "Membrane-linked H2 metabolism can conserve energy as proton motive force.",
            "evidence": [
              {
                "reference": "DOI:10.21775/cimb.006.159",
                "snippet": "generation of a protonmotive force",
                "notes": "Supports membrane-linked energy conservation."
              }
            ],
            "predicate_id": "biolink:produces"
          },
          {
            "subject": "carbon_dioxide",
            "predicate": "fixed by",
            "object": "autotrophic_co2_fixation",
            "description": "CO2 supplies carbon for autotrophic hydrogenotrophic growth.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.02473-10",
                "snippet": "assimilation of CO2",
                "notes": "Supports CO2 assimilation into cellular carbon."
              }
            ],
            "predicate_id": "METPO:2007404"
          },
          {
            "subject": "autotrophic_co2_fixation",
            "predicate": "has output",
            "object": "cellular_carbon",
            "description": "Carbon fixation converts CO2 into cell carbon.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.02473-10",
                "snippet": "the assimilation of CO2 (oxidation state of +4) into cellular carbon (average oxidation state of 0, as in carbohydrates) requires four reducing equivalents.",
                "notes": "Supports the carbon-assimilation output."
              }
            ],
            "predicate_id": "RO:0002234"
          },
          {
            "subject": "h2_oxidation",
            "predicate": "generates",
            "object": "proton_motive_force",
            "description": "Splitting H2 yields electrons and protons that can generate a proton gradient.",
            "evidence": [
              {
                "reference": "DOI:10.21775/cimb.006.159",
                "snippet": "generation of a protonmotive force",
                "notes": "Splitting H2 yields electrons and protons that can generate proton gradients and ATP; general mechanistic process-level edge."
              }
            ],
            "predicate_id": "biolink:produces"
          },
          {
            "subject": "h2_oxidation",
            "predicate": "coupled to reduction of",
            "object": "carbon_dioxide",
            "description": "Hydrogen uptake can be coupled to reduction of CO2 in hydrogenotrophy.",
            "evidence": [
              {
                "reference": "DOI:10.3390/microorganisms7020053",
                "snippet": "hydrogen uptake to the reduction of electron acceptors (e.g., nitrate, sulfate, and carbon dioxide).",
                "notes": "The hydrogenase reaction is involved in coupling hydrogen uptake to the reduction of electron acceptors (e.g., nitrate, sulfate, and carbon dioxide)."
              }
            ]
          },
          {
            "subject": "h2_oxidation",
            "predicate": "coupled to reduction of",
            "object": "molecular_oxygen",
            "description": "H2 oxidation can be coupled to reduction of O2 (aerobic hydrogen oxidation).",
            "evidence": [
              {
                "reference": "DOI:10.3390/microorganisms7020053",
                "snippet": "Aerobic hydrogen oxidation (Knallgas) H2 + 1/2O2 \u2192 H2O",
                "notes": "The review tabulates oxygen reduction as the acceptor half-reaction for aerobic hydrogen oxidation."
              }
            ]
          },
          {
            "subject": "h2_oxidation",
            "predicate": "coupled to reduction of",
            "object": "nitrate",
            "description": "H2 oxidation can be coupled to reduction of nitrate in anaerobic respiration.",
            "evidence": [
              {
                "reference": "DOI:10.3390/microorganisms7020053",
                "snippet": "energy is obtained by coupling hydrogen oxidation to reduction of electron acceptors such as carbon dioxide, nitrate, or ferric iron",
                "notes": "The source explicitly includes nitrate among electron acceptors coupled to hydrogen oxidation."
              }
            ]
          },
          {
            "subject": "h2_oxidation",
            "predicate": "coupled to reduction of",
            "object": "sulfate",
            "description": "H2 oxidation can be coupled to reduction of sulfate in anaerobic respiration.",
            "evidence": [
              {
                "reference": "DOI:10.3390/microorganisms7020053",
                "snippet": "Hydrogen gas has a low reduction potential and is, thus, a highly energetic electron donor when involved in sulfate, carbon dioxide, and ferric iron reduction",
                "notes": "The source explicitly identifies hydrogen as the electron donor for sulfate reduction."
              }
            ]
          },
          {
            "subject": "h2_oxidation",
            "predicate": "can support",
            "object": "autotrophic_co2_fixation",
            "description": "Coupling H2 oxidation to carbon fixation enables hydrogenotrophic chemosynthesis.",
            "evidence": [
              {
                "reference": "DOI:10.1111/1751-7915.14300",
                "snippet": "By coupling hydrogen oxidation to carbon fixation in species containing both enzymes, the existing evidence suggests that hydrogenotrophic chemosynthesis is a viable energy generation strategy",
                "notes": "By coupling hydrogen oxidation to carbon fixation, hydrogenotrophic chemosynthesis is a viable energy generation strategy; trait-level edge."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-08-23T09:10:00Z",
        "curator": "codex",
        "action": "CURATE_PROTEIN_TAXON_EXAMPLE",
        "changes": "Narrowed the ambiguous hydrogenase label to the membrane-bound NiFe uptake-hydrogenase complex, grounded it to GO:0044569, and added DOI-backed HoxG P31891 for C. necator H16 as an explicit catalytic component.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-05T01:35:46.874373+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-08T00:00:00-07:00",
        "curator": "codex",
        "action": "ADDED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed causal graph for hydrogenase-mediated H2 oxidation, membrane-linked energy conservation, and CO2 fixation.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000009\u00d71, METPO:2000016\u00d71, METPO:2000202\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T05:49:25Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:interacts_with\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T08:21:50Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:produces\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T21:30:07Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007405\u00d71, METPO:2007404\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:41:04Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (METPO:1007500\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T05:05:15Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A059XQG3\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T08:14:33Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0022900\u00d71, GO:0015977\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-26T02:30:13Z",
        "curator": "claude",
        "action": "RETYPE_CAUSAL_NODES",
        "changes": "Re-typed 1 causal-node node_type field(s) to align with CausalNodeTypeEnum semantics: proton motive force: BIOLOGICAL_PROCESS \u2192 STATE \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 7 evidence-backed generic edges (5 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:14Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:produces\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:20Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:17632\u00d71, CHEBI:16189\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-05T12:00:00Z",
        "curator": "claude",
        "action": "REVERSE_CAUSAL_EDGE_DIRECTION",
        "changes": "Reversed 1 causal edge from <trait> uses electron donor <chemical> to <chemical> enables <trait> (predicate_id METPO:2000009 -> RO:0002327), issue 295. METPO:2000009 is rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so the trait-subject form entailed that this TRAIT node is a microbe; CausalNodeTypeEnum has no organism member, so no causal-graph edge can satisfy that domain. Evidence unchanged; only subject/predicate/object/predicate_id and the edge description moved. Note RO:0002327 has range 'biological process or activity', so the new form is not fully range-correct either - tracked in issue 302.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 1 causal edge(s) off enables/RO:0002327 with a TRAIT object (1 to has electron donor), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them. 1 electron edge(s) were also reversed back to trait -> chemical, restoring the donor/acceptor role that PR 300 collapsed onto enables (issue 303); the organism-subject problem that forced that collapse does not arise here because these predicates take a causal-node domain rather than METPO:2000001's microbe domain (issue 301).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates (1 to has output), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T02:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES_PART2",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates onto their causal-graph counterparts (1 to oxidizes), issue 301 part 2. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Each replacement is a 1:1 mirror of its source predicate that changes only the domain, so the claim each edge makes is unchanged and directions are unchanged. The replacements are proposed in proposals/metpo_traitmech_v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-17T02:00:00Z",
        "curator": "claude",
        "action": "NORMALISE_NODE_SENSE",
        "changes": "One node_id per SENSE (issues 356, 384): molecular_oxygen is the chemical sense here. The molecule, not the condition \u2014 the dioxygen participating in the reaction the graph describes. Normalised onto molecular_oxygen, the id 20 other chemical occurrences already use, so one id means one sense corpus-wide (issues 356, 384).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-22T04:26:16Z",
        "curator": "codex",
        "action": "REVIEW_UNIPROT_INSTANCE_GROUNDINGS",
        "changes": "Reviewed 1 organism-specific UniProtKB grounding(s): replaced 0 with taxon-agnostic GO/InterPro terms and retracted 1 to label-only where no exact semantic term was supported (docs/GROUNDING_POLICY.md).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-30T19:21:37Z",
        "curator": "codex",
        "action": "REVIEW_EVIDENCE_REFERENCE_CHURN",
        "changes": "Offline review for issue 520 retained 4 evidence-reference replacement(s) that PR 511 made on surviving causal edges outside its stated protein-taxon scope. The pre-tranche evidence entries had references but no snippets; the retained entries supply edge-specific snippets and explanatory notes. Reverting would discard that claim-level provenance, so the scope defect is resolved by documenting the decision instead. This audit changed no causal claim or evidence field. Reviewed replacements: DOI:10.2138/gselements.16.1.39 -> DOI:10.21775/cimb.006.159 (1 edge); DOI:10.2138/gselements.16.1.39 -> DOI:10.3390/microorganisms7020053 (3 edges).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-22T01:35:00Z",
        "curator": "claude",
        "action": "REFRESH_UNIPROT_ENTRY_VERSION",
        "changes": "Refreshed UniProtKB entry_version against live UniProt REST on 2026-10-22: UniProtKB:P31891 (unset -> 156 on hydrogenase).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000605",
    "label": "hyphal anastomosis",
    "definition": "A phenotype in which vegetative fungal hyphae fuse to establish cytoplasmic continuity.",
    "definition_source": "DOI:10.1128/aem.65.12.5571-5575.1999",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "synonyms": [
      {
        "synonym_text": "vegetative hyphal fusion",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.1128/ec.00191-12"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1128/aem.65.12.5571-5575.1999",
        "snippet": "We observed complete fusion of hyphal walls and the migration of a mass of particles in both directions within the hyphal bridges.",
        "notes": "Giovannetti et al. (1999); snippet exact-matched to the directly retrieved Europe PMC abstract, PMID:10584019. Publisher Methods, Results and Discussion were read; actual Figures 1 and 3 were inspected. Cellophane over water agar supported live observations. SDH staining visualized active bridges; time-lapse microscopy showed bidirectional particle passage in Glomus caledonium. The 0-to-2-second image pairs are representative observations, not replication counts or identification of each particle as a nucleus. Same-germling and different-germling/same-isolate fusion were observed. Tested interspecific failures do not establish a universal compatibility rule. Nuclear migration was reported separately; Figure 2 was not visually inspected. This study did not demonstrate genetic recombination."
      },
      {
        "reference": "DOI:10.1128/ec.00191-12",
        "snippet": "Hyphal anastomosis, or vegetative hyphal fusion, establishes the interconnection of individual hyphal strands into an integrated network of a fungal mycelium.",
        "notes": "Charlton et al. (2012); snippet exact-matched to the directly retrieved Europe PMC abstract, PMID:23042130. Publisher Methods and fusion Results were read; actual Figure 3 was inspected. This naming sentence supports the exact synonym. Calcofluor and DIC images compare Epichloe festucae E2368, delta-so268 and complemented 268C53: connections in wild type and complement, but separate apposed walls in delta-so268. Static images indicate apparent cytoplasmic connectivity, not measured flow. Delta-so238 retained a gene signal and was interpreted as a heterokaryon/knockdown, not a clean knockout; complementation of delta-so75 did not restore fusion. Host effects do not prove that fusion universally causes mutualism. Supplements were not inspected; no protein-resolved causal chain is asserted."
      },
      {
        "reference": "DOI:10.1111/j.1469-8137.2008.02726.x",
        "snippet": "We show that genetically distinct AMF, from the same field, anastomose, resulting in viable cytoplasmic connections through which genetic exchange could potentially occur.",
        "notes": "Croll et al. (2009); snippet exact-matched to the directly retrieved Europe PMC abstract, PMID:19140939. Publisher Experiment 1 methods/results and relevant Discussion were read. Five Glomus intraradices isolates from one field population were paired; nine of ten nonself combinations had contacts scored as perfect fusion. That category required subsequent streaming and SDH-positive bridges; it is not a count of all fusion events. Postfusion withdrawal and septation were separate outcomes following anastomosis. Genetic identity is therefore not required. The paper separately reports marker transmission to progeny; its genotyping does not establish nuclear recombination. Figures and supplementary movies were not visually inspected. Table 1's PFI/PrFI column-footnote assignments appear transposed in publisher HTML, so those column-specific rates are not used."
      }
    ],
    "discussions": [
      {
        "discussion_id": "hyphal-anastomosis-endpoint-and-scope",
        "prompt": "Keep completed vegetative fusion distinct from approach and its consequences.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Directional approach/positive autotropism, contact, adhesion and branching alone do not establish cytoplasmic continuity. The definition does not require genetic identity, nuclear migration, recombination, mating or persistent network viability. Postfusion incompatibility can follow an actual fusion event. Unqualified anastomosis also names nonfungal structures and self-fusion is narrower; neither is an exact synonym here. The organismal phenotype is not automatically equivalent to a molecular or cellular process class. Resolve external equivalents at their authorities before adding xrefs.",
        "posed_by": "codex",
        "posed_date": "2026-10-04"
      },
      {
        "discussion_id": "hyphal-anastomosis-strains-and-mechanism",
        "prompt": "Resolve modern strain identities and native protein anchors before enrichment.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Canonical examples await modern NCBI identity and original strain-provenance checks, especially for historical Glomus names and E2368. Transformed carrot roots in the 2009 culture method do not establish engineering of the fungi. The 2012 soft perturbation/rescue supports a native candidate mechanism but is not a universal dependency. Read its supplements and resolve taxon-paired protein accessions before adding causal nodes. Do not infer a ligand/receptor chain from approach or use NONMECHANISTIC to bypass missing protein grounding.",
        "posed_by": "codex",
        "posed_date": "2026-10-04"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-04T22:09:46Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added hyphal anastomosis with three directly retrieved DOI-backed sources and exact abstract snippets. Distinguished completed cytoplasmic continuity from approach and downstream genetic effects. Added source-named vegetative hyphal fusion as an exact synonym. Ignored-and-hidden repository searches and structured OWL review found no exact trait. Reserved METPO:1055900 in v482 under released phenotype. Inspected 1999 Figures 1 and 3 and 2012 Figure 3; kept unread figures/supplements and mutant limitations explicit. Deferred canonical strains, external equivalences and protein-resolved graphs.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-04T22:29:16Z",
        "curator": "codex",
        "action": "QUALIFIED_EVIDENCE_ENDPOINT",
        "changes": "Addressed #1690 by qualifying the 2009 nine-of-ten pairing count as the source's perfect-fusion category, which required streaming and SDH-positive bridges. Distinguished that scored category from all fusion events and subsequent postfusion incompatibility. Definition and exact abstract snippet are unchanged.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000619",
    "label": "isogamy",
    "definition": "A sexual-reproduction phenotype in which the fusing gametes are similar in size.",
    "definition_source": "DOI:10.1038/s42003-022-04275-y",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/s42003-022-04275-y",
        "snippet": "The gametes of isogamous species are of similar size and appearance.",
        "notes": "Innami et al. (2022), PMID:36473948, PMC9726906. Exact Introduction Sec1 sentence checked against raw Europe PMC XML and publisher HTML; not an abstract or web-summary quote. The paper identifies Chlamydomonas reinhardtii as isogamous while testing mating-structure positioning, not the maintenance of equal gamete size. Similar appearance does not exclude mating-type-specific structural or functional differences. Main text and captions were read; actual Figure 4 and Supplementary Table 2 were visually inspected. The latter lists nit1 nit2 in CC-125 and nit1 nit2 agg1 in CC-124 despite their wild-type names. CC-3712 has a deletion including MID and lacks FUS1; CC-3947 carries a MID transgene. These are qualified laboratory observations, not unqualified natural exemplars. Other actual figures, supplementary figures and the source-data workbook remain uninspected. Phototactic fitness explanations in Discussion remain hypotheses, not measured consequences of isogamy."
      },
      {
        "reference": "DOI:10.1111/evo.13427",
        "snippet": "we explored size-speed distributions in vegetative and gamete cells of 10 cell lines, and clonal data from within two cell lines.",
        "notes": "Seed and Tomkins (2018), PMID:29345308. Exact scientific-abstract clause from raw Europe PMC metadata; the author's institutional repository abstract corroborates the content. Its preceding clause identifies C. reinhardtii as isogamous. This independently supports experimental use of an isogamous microalga, not a second direct test of the definition's size-symmetry criterion. The two cell types are vegetative cells and gametes, not plus and minus gametes. Positive size-speed relationships and artificial speed selection do not establish a universal size threshold, identical gamete behaviour, or an evolutionary cause of isogamy. Full text, figures, supplements and strain provenance remain uninspected; the linked author manuscript returned HTTP 403."
      }
    ],
    "discussions": [
      {
        "discussion_id": "isogamy-scope-and-hierarchy",
        "prompt": "Keep gamete-size similarity distinct from mating-type identity.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "This reproductive phenotype compares gametes participating in sexual fusion, not arbitrary equal-sized cells or vegetative-versus-gamete measurements. Similar size is not exact equality and does not imply identical structure, behaviour, recognition machinery or organelle inheritance. No numerical boundary with slight anisogamy is imposed. The fungal compatibility-locus systems traitmech:000615 through traitmech:000618 and same-mating-type reproduction traitmech:000613 describe different axes; isogamy does not mean one mating type. Use released phenotype METPO:1000059 in record and proposal pending a narrower reproductive-phenotype hierarchy. PHYSIOLOGY is a filesystem category. Resolve exact lexical and external equivalences before adding synonyms or xrefs; no disjointness is asserted.",
        "posed_by": "codex",
        "posed_date": "2026-10-05"
      },
      {
        "discussion_id": "isogamy-examples-and-mechanism",
        "prompt": "Resolve natural strain provenance and mechanisms before extension.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "The cited microalgal studies justify the trait, but collection provenance and unperturbed gamete measurements should be checked before adding a natural canonical example. A wild-type label alone does not establish that a reference strain lacks mutations. Do not turn MID-dependent mating-structure positioning into a demonstrated cause of gamete-size similarity. Resolve native protein accessions and experimentally tested size-control dependencies before a causal graph; no NONMECHANISTIC graph bypasses grounding. Read the remaining source material before quantitative or evolutionary extensions. Keep full-text quote checks distinct from abstract-resolver verdicts.",
        "posed_by": "codex",
        "posed_date": "2026-10-05"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-05T11:50:56Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added isogamy with two primary DOI-backed sources and exact full-text and scientific-abstract snippets. Kept gamete-size similarity distinct from structural symmetry, mating-type identity and sequence features. Ignored-and-hidden novelty and allocation searches found no exact record or collision. Reserved METPO:1057300 in v496 under phenotype. Deferred natural canonical taxa, lexical mappings and causal graphs, with strain mutations and source-access limits explicit.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000630",
    "label": "karyoklepty",
    "definition": "A physiological phenotype in which a microbial organism selectively retains and uses nuclei acquired from prey.",
    "definition_source": "DOI:10.1038/nature05496",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/nature05496",
        "snippet": "Cytokinesis, plastid performance and their replication are dependent on recurrent stealing of cryptophyte nuclei.",
        "notes": "PMID:17251979. Direct scientific abstract from Europe PMC, cross-checked with the publisher abstract. This naming study reports retained, transcriptionally active prey nuclei in Myrionecta rubra, a synonym of Mesodinium rubrum. The plastid-related dependence is system-specific, not a universal definition requirement. Main text, figures and supplements were not accessed; no protein-resolved mechanism is imported."
      },
      {
        "reference": "DOI:10.1186/s12864-015-2052-9",
        "snippet": "Rather, the ciliate steals the nucleus from cryptophyte prey, a process described as karyoklepty",
        "notes": "PMID:26475598, PMC4609049. Direct Background naming passage, not an abstract quote or independent terminology experiment. Scientific Abstract and Background were read. The abstract reports prey-derived transcription after sequestration; expression and annotation are not native protein perturbations. Methods, Results, actual figures and supplements were not audited, so no additional canonical strain or causal edge is asserted from this study."
      },
      {
        "reference": "DOI:10.3389/fmicb.2017.00423",
        "snippet": "Well-fed cells of M. rubrum contained additional nuclei of cryptophyte origin.",
        "notes": "PMID:28377747, PMC5359308. Direct Results passage. Main text and actual Figures 2-5 and 9 were inspected; supplements were not. Fixed-cell microscopy documents retained central and peripheral prey nuclei during starvation/refeeding. Figure 9 is an inheritance model with illustrative micrographs, not continuous lineage tracking. Carbon fixation correlates with nuclear prevalence; starvation is not an isolated nuclear perturbation."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:704171",
        "taxon_label": "Mesodinium rubrum",
        "reference": "DOI:10.3389/fmicb.2017.00423",
        "note": "Qualified example: MBL-DK2009 fed Teleaulax amphioxeia SCCAP K-0434. The Cultures Methods at https://doi.org/10.3389/fmicb.2017.00423 document single-cell isolation from Helsingor harbor, Denmark, in 2009. Retention is conditional on feeding history; do not generalize nuclear inheritance to every strain. NCBI ESearch and EFetch independently resolved the species and its Myrionecta rubra synonym on 2026-10-05."
      }
    ],
    "discussions": [
      {
        "discussion_id": "karyoklepty-organismal-scope-and-parent",
        "prompt": "Keep prey-nucleus use distinct from plastid retention and sequence transfer.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "This physiological trait is not a literal nucleus, nucleomorph or sequence feature. Whole living prey/endosymbionts, DNA detection and horizontal transfer alone are insufficient. Kleptoplasty traitmech:000629 concerns plastids; phagocytosis traitmech:000627 concerns uptake; phagotrophy traitmech:000628 concerns nutrient assimilation. Endosymbiosis traitmech:000045 describes a microorganism living inside its host, not selective nuclear retention. These overlapping concepts are not exact equivalents or established universal parents. Retain phenotype METPO:1000059 pending a closer acquisition hierarchy. No fixed retention time, nuclear division, fusion, host-genome integration or universal photosynthetic role is required. No unverified synonym or ontology xref is asserted.",
        "posed_by": "codex",
        "posed_date": "2026-10-05"
      },
      {
        "discussion_id": "karyoklepty-control-and-inheritance-mechanism",
        "prompt": "Resolve functional control and inheritance without promoting models to mechanisms.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "The 2017 study discusses strain-dependent alternatives to nuclear division and fusion. Its snapshots do not establish a universal inheritance mechanism. The 2007 abstract supports transcriptional function, but source-specific retention intervals and plastid dependencies are not class restrictions. Protein identities and host-control machinery remain unresolved here; no causal graph is asserted from transcript abundance, inferred targeting or nuclear enlargement alone.",
        "posed_by": "codex",
        "posed_date": "2026-10-05"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-05T23:36:51Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added karyoklepty with three DOI-backed snippets and a natural, strain-qualified Mesodinium example. Ignored-and-hidden searches and pinned METPO review found no exact record. Reserved METPO:1058300 in v506. Distinguished prey-nucleus retention/use from plastid retention, intact endosymbionts and sequence transfer; deferred unresolved control and inheritance mechanisms.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000687",
    "label": "kinetocyst discharge",
    "definition": "A physiological phenotype in which a microbial cell releases material from kinetocysts to the cell exterior.",
    "definition_source": "DOI:10.1078/0932-4739-00847",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1078/0932-4739-00847",
        "snippet": "By electron microscopy, we show evidence that the kinetocyst is an extrusive organelle that discharges its contents upon food capture.",
        "notes": "Sakaguchi et al. 2002, scientific Abstract directly read on 2026-10-10 at https://www.researchgate.net/publication/222864147. Electron microscopy of Raphidiophrys contractilis supports release during food capture, with the posterior remaining cell-attached and the anterior directed toward prey. The proposed scaffold role is not demonstrated causality. Crossref identifies the 2002 publication; ResearchGate's date and automatically linked author profile are not used as authority. Publisher access returned 403; full Methods and figures were not inspected. No universal toxin, prey-killing requirement or trigger is inferred."
      },
      {
        "reference": "DOI:10.1515/znc-1976-3-418",
        "snippet": "Freeze-fracture studies reveal that extrusive organelles displaying saltatory particle movements in centrohelidian axopod are attached to highly ordered domains within the plasma membrane.",
        "notes": "Bardele 1976, PMID:134561. Scientific abstract and primary full-text OCR directly read on 2026-10-10 at https://www.researchgate.net/publication/22999924. The snippet supports organelle identity and membrane attachment, not discharge alone. Printed pp191-193 describe formaldehyde-fume-induced release in living whole mounts and negative-stained expelled jacket material. Methods name Acanthocystis erinaceoides and Raphidiophrys ambigua; this observation is not assigned here to just one species. The author interprets kinetocysts as compound motile mucocysts. Food-trapping and movement models remain hypotheses. PDF images were unavailable; no visual audit or OCR-normalized quotation is claimed. The article year is 1976, not the later upload date."
      },
      {
        "reference": "https://protistology.jp/journal/congress_ab/53th_kobe/Abstract%20Book%20Kobe2020",
        "snippet": "In this study, we used Tetrahymena thermophila as food and examined the process of food capturing and kinetocyst discharge by electron microscopy.",
        "notes": "Wan and Suzaki, JSP/KSOP joint meeting, 22-23 November 2020, O-BPA06/P-1A01, printed pp11-12 (PDF indices 10-11). Primary conference abstract, not a peer-reviewed full paper. Both pages were visually inspected on 2026-10-10. The snippet establishes assay context in Raphidiophrys contractilis, not the outcome alone. Following results describe stretched filamentous contents and expansion of the ring structure after discharge. Immuno-EM MVP localization suggests a prey-recognition role but does not establish causal necessity or a conserved release mechanism. Tetrahymena is prey here, not the kinetocyst-bearing organism."
      }
    ],
    "discussions": [
      {
        "discussion_id": "kinetocyst-discharge-scope-and-parent",
        "prompt": "Resolve historical mucocyst terminology and exocytosis placement.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Retain phenotype METPO:1000059 pending hierarchy review. Bardele 1976 interprets kinetocysts as compound motile mucocysts; preserve that attribution rather than asserting separation from every historical mucocyst umbrella. Existing mucocyst discharge traitmech:000684 uses a membrane-fusion release definition supported in Tetrahymena and explicitly defers terminology reconciliation. Neither exact equivalence nor a mucocyst parent is established here. The fusion-pore differentia of exocytosis traitmech:000637 also needs class-wide scope review; placement is unresolved, not excluded. Possession, docking, axopodial movement or contraction, prey adhesion, ingestion and nonspecific cell lysis alone do not demonstrate discharge. Complete emptying, prey death and one universal trigger are not required. Historical conicyst organelle terminology does not automatically establish an exact phenotype synonym. No equivalence to haptocyst discharge traitmech:000686, homology, disjointness, exact synonyms or xrefs are asserted.",
        "posed_by": "codex",
        "posed_date": "2026-10-10"
      },
      {
        "discussion_id": "kinetocyst-discharge-exemplars-and-mechanism",
        "prompt": "Resolve assay-strain provenance and release-specific molecular evidence.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "No canonical examples are assigned: full primary assay Methods and their relation to the deposited natural culture need joint verification. The evidence items have different scopes, not three equivalent discharge replications. Organelle ultrastructure and protein localization alone do not establish a causal release pathway. Separate assembly, movement, triggering, extrusion, attachment and ingestion before adding graph edges. A protein mechanism needs direct functional evidence and taxon-paired accessions; sequence features alone cannot provide that support. Mechanism is deferred, not claimed absent.",
        "posed_by": "codex",
        "posed_date": "2026-10-10"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-10T04:04:55Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added kinetocyst discharge with two primary DOI citations and a primary conference abstract, source-checked snippets and explicit access limits. Ignored-and-hidden main/worktree/open-PR reservation checks support 000687 and v563 block 1064000-1064099. Historical mucocyst scope, exocytosis placement, canonical exemplars and protein mechanism remain unresolved. Existing records unchanged. Timestamp records the observed UTC curation decision.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000629",
    "label": "kleptoplasty",
    "definition": "A physiological phenotype in which a microbial organism selectively retains plastids acquired from algal prey after discarding or digesting other prey components.",
    "definition_source": "DOI:10.1038/s41598-018-28455-1",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/s41598-018-28455-1",
        "snippet": "Kleptoplasty is defined as the process in which a cell sequesters algal chloroplasts while discarding or digesting other algal components",
        "notes": "PMID:29973634, PMC6031614. Direct Introduction definition, not an abstract quote or experimental replication. The Introduction also includes aphotic cases. Only the scientific Abstract and Introduction were read for this terminology claim; no canonical example or mechanism is imported from the paper's experiments."
      },
      {
        "reference": "DOI:10.1073/pnas.2220100120",
        "snippet": "Rapaza viridis has only kleptoplasts derived from a specific strain of green alga, Tetraselmis sp., but no canonical plastids",
        "notes": "PMID:36927158, PMC10041101. Contiguous scientific-abstract span, not the separate Significance section. Main text and actual Figures 1 and 3 were inspected: prey plastids persist after other material is expelled, and bicarbonate labeling supports photosynthetic carbon use. Plastid subdivision and partition do not establish plastid growth or biogenesis. Supplements were not visually audited. Predicted targeting sequences and transporters are not native protein-function validation."
      },
      {
        "reference": "DOI:10.1038/s41467-026-70516-x",
        "snippet": "In the flagellate, Rapaza viridis, nuclear-encoded proteins support photosynthesis in transient, xenogeneic chloroplasts (kleptoplasts) acquired from the green alga Tetraselmis sp.",
        "notes": "PMID:41876518, PMC13013580. Scientific Abstract (Abs1), not the editorial summary (Abs2). Results, Discussion, relevant culture/perturbation/imaging/physiology Methods, actual Figures 3-5 and Supplementary Figure 4 were inspected. Knockout and knockdown support host-protein contributions in this system. RbcS-like localization uses engineered HA tagging; Rca-like localization uses native-protein antibodies. This is a separate study of the same strain, not independent taxon replication."
      },
      {
        "reference": "DOI:10.1111/1462-2920.14433",
        "snippet": "These results indicate that the photosynthetic pathways in N. labradorica are not functional.",
        "notes": "PMID:30277305. Direct Europe PMC scientific abstract, published online in 2018 and in the 2019 print issue. The authors call Nonionellina labradorica kleptoplastidic despite absent carbon fixation and oxygen production under their assayed conditions. This supports retaining a photosynthesis-independent definition, not universal functional absence. Full text and figures were not accessed; no canonical example or nitrogen/sulfur mechanism is imported. Host versus plastid assimilation remains unresolved."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1112050",
        "taxon_label": "Rapaza viridis",
        "reference": "DOI:10.1073/pnas.2220100120",
        "note": "NIES-4477, fed Tetraselmis sp. NIES-4478, is the qualified example; do not generalize prey compatibility to every isolate. NCBI ESearch and EFetch resolve the species name and identifier on 2026-10-05. Natural tide-pool isolation at Pachena Beach in 2010 is documented in the original Methods at https://doi.org/10.1186/1471-2148-12-29. That paper's canonical-plastid interpretation was superseded by the 2023 study. Collection provenance at https://mcc.nbrp.jp/strainList.do?strainId=4475&strainNumberEn=NIES-4477 conflicts with the primary papers on the ATCC alias; retain NIES-4477 without silently equating the conflicting aliases."
      }
    ],
    "discussions": [
      {
        "discussion_id": "kleptoplasty-retention-and-hierarchy-scope",
        "prompt": "Keep plastid retention distinct from uptake and acquired photosynthesis.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "This is an organism-level physiological trait, not an organelle or sequence feature. Whole living algal endosymbionts are not equivalent to extracted plastids. Phagocytosis traitmech:000627 describes uptake; phagotrophy traitmech:000628 requires nutrient assimilation. Neither is exact. Phototrophic METPO:1000660 and mixotrophic METPO:1000652 prescribe energy/carbon use that the generic retention definition does not require. The trophic_type Falcon report attributes an acquired-photosynthesis framing to Schenone 2024; that narrower usage is preserved as research provenance, not generalized to all kleptoplasty. Retain phenotype METPO:1000059 pending a closer organelle-acquisition hierarchy. No fixed retention duration, plastid replication, complete nutritional dependence or loss of every other prey organelle is asserted. No unverified synonym or ontology xref is added.",
        "posed_by": "codex",
        "posed_date": "2026-10-05"
      },
      {
        "discussion_id": "kleptoplasty-rapaza-strain-alias-conflict",
        "prompt": "Resolve the discordant ATCC alias with the collection.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "The NIES-4477 collection entry lists ATCC PRA-361, whereas the 2012 and 2023 primary Methods assign PRA-360 to Rapaza and PRA-361 to its Tetraselmis prey. The 2023 Methods document redeposition as NIES-4477 and NIES-4478. Use the NIES host identifier and primary provenance; do not silently reconcile the conflict or treat collection metadata as independent trait evidence. Collection URL is preserved in the canonical note.",
        "posed_by": "codex",
        "posed_date": "2026-10-05"
      },
      {
        "discussion_id": "kleptoplasty-protein-import-mechanism",
        "prompt": "Ground native protein contributions without inventing an import apparatus.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "The 2026 study supplies native functional perturbations beyond the 2023 sequence predictions, but this curation has not resolved taxon-paired protein accessions or a complete import mechanism. Predicted complexes, phase separation and pyrenoid remodeling must remain distinct from demonstrated localization and physiology. A targeting reporter does not identify a universal translocon. No protein-resolved causal graph is asserted.",
        "posed_by": "codex",
        "posed_date": "2026-10-05"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-05T22:48:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added kleptoplasty with four DOI-backed snippets and a natural, strain-qualified Rapaza example. Ignored-and-hidden searches and pinned METPO review found no exact record. Reserved METPO:1058200 in v505. Kept plastid retention independent of photosynthesis, preserved the collection alias conflict and deferred unresolved protein groundings without inferring a causal graph.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000140",
    "label": "lecithinase activity",
    "definition": "A physiological enzyme-activity phenotype in which a cell produces active lecithinases that hydrolyze lecithin or phosphatidylcholine.",
    "definition_source": "DOI:10.2147/IDR.S365254",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "synonyms": [
      {
        "synonym_text": "lecithinase production",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1128/jb.81.6.939-945.1961"
      },
      {
        "synonym_text": "lecithinase reaction",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.2147/IDR.S365254"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.2147/IDR.S365254",
        "snippet": "all tested isolates were positive for lecithinase reaction and showed opaque zone around colonies on egg yolk agar",
        "notes": "Algammal et al. used an egg-yolk agar lecithinase reaction to phenotype Bacillus cereus isolates."
      },
      {
        "reference": "DOI:10.1128/jb.81.6.939-945.1961",
        "snippet": "egg yolk were used for the demonstration of lecithinase activity",
        "notes": "Esselmann and Liu surveyed lecithinase production by Gram-negative bacteria on egg-yolk agar."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1396",
        "taxon_label": "Bacillus cereus",
        "note": "Bacillus cereus isolates from diseased Mugil seheli were positive for lecithinase reaction on egg-yolk agar.",
        "reference": "DOI:10.2147/IDR.S365254"
      }
    ],
    "discussions": [
      {
        "discussion_id": "lecithinase-activity-xref-gap",
        "prompt": "Resolve an exact external ontology class for lecithinase activity before adding a TraitRecord xref.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "GO:0004629 denotes C-type glycerophospholipase molecular function rather than the organism-level lecithinase production phenotype, so it is too scope-shifted for an equivalent TraitRecord xref.",
        "posed_by": "codex",
        "posed_date": "2026-09-11"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-11T00:00:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted lecithinase activity as a DOI-backed TraitRecord after a repository-wide duplicate review covering ignored and hidden files; METPO has no exact lecithinase activity class yet.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000695",
    "label": "lethal algicidal activity",
    "definition": "A physiological capability of a microorganism to kill cells of eukaryotic algae or cyanobacteria.",
    "definition_source": "DOI:10.1128/AEM.66.10.4334-4339.2000",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1128/AEM.64.8.2806-2813.1998",
        "snippet": "All G. catenatum cells in strain Y-treated wells were dead and most cells had lysed after 2 days.",
        "notes": "Lovejoy et al. 1998, PMID:9687434, PMC106776, Results sec9. Scientific Abstract, algal-culture/toxicity Methods, activity and specificity Results, Discussion, Tables 1/2/4/5 and actual Figure 2 inspected. Other actual figures and remaining Methods unread. Strain Y and filtrate support killing, unlike reversible ecdysis or rounding in other targets. Some dinoflagellate controls also died in separate experiments; raphidophyte controls remained healthy. P. carrageenovora was not uniformly harmless. Close affinity to P. peptidysin is not exact species identification. EXT_ID:9687434 AND SRC:MED matched source, ID, title and DOI on 2026-10-11. Full-text quotation directly matched; abstract matching alone cannot verify this passage."
      },
      {
        "reference": "DOI:10.1128/AEM.66.10.4334-4339.2000",
        "snippet": "The marine bacterium Pseudoalteromonas sp. strain A28 was able to kill the diatom Skeletonema costatum strain NIES-324.",
        "notes": "Lee et al. 2000, PMID:11010878, PMC92304, scientific Abstract. Abstract, Introduction, Methods, Results, Discussion, Tables 1/2 and actual Figures 1/2 inspected; actual Figures 3/4 unread. Parental A28 culture and supernatant support the capability. Results sec11 reports no regrowth after transfer from cleared agar, distinguishing algicidal from algistatic, but that experiment is data not shown. Protease II lacked algicidal action despite protease activity. Six N-terminal residues do not establish full AprI identity; NH1/NH2 are mutagenized derivatives, not natural exemplars. A separate group from Lovejoy et al., not a replication of strain Y. EXT_ID:11010878 AND SRC:MED matched source, ID, title and DOI on 2026-10-11; quotation matched direct scientific Abstract and qualified API abstract."
      },
      {
        "reference": "DOI:10.3390/toxins15030220",
        "snippet": "The cyanobacterial cell walls were severely damaged, leading to the leakage of intracellular components.",
        "notes": "Zhang et al. 2023, PMID:36977111, PMC10058357, Results 2.4. Scientific Abstract, Introduction, Results 2.1-2.4, Discussion, Methods 5.1-5.4/5.8/5.12 and actual Figure 3 with caption inspected; other figures and supplement unread. Filtrate damage/lysis supports cyanobacterial target scope. Methods 5.3 calculates relative cell-density reduction versus controls, not a direct dead-cell fraction; no percentage is adopted. Results 2.1 calls HY #320 from 411 isolates, versus #332/412 in Methods 5.2 and #332 in Figure 1 caption; provenance remains unreconciled. Molecular agents are unidentified; transcription changes alone do not establish causal protein edges. EXT_ID:36977111 AND SRC:MED matched source, ID, title and DOI on 2026-10-11. Quotation directly matched full text."
      }
    ],
    "discussions": [
      {
        "discussion_id": "lethal-algicidal-scope-and-mappings",
        "prompt": "Resolve mappings while retaining a lethal endpoint and actor-level scope.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "The lethal qualifier distinguishes this capability from broader algicidal usage. Paul and Pohnert 2011, DOI:10.1371/journal.pone.0021032, Methods Monitoring algicidal activity and Results, uses fluorescence-based growth inhibition as an algicidal readout; those directly read passages provide terminology context, not additional killing evidence. This record requires killing, not reduced fluorescence, reversible growth arrest, ecdysis, passive removal or a protease sequence alone. It denotes the acting microbe's capability, not an algicide molecule, treated alga's susceptibility or assay row. Cyanobacteria are included explicitly, not classified as eukaryotic algae. Activity against some susceptible targets suffices; universal host range is not asserted. Predatory bacterium traitmech:000054 requires killing and consuming bacteria for nutrients, so it is not a parent of this class. Killing may overlap predation but neither consumption, grazing nor nutritional benefit is required or inferred; no organismal disjointness is asserted. No exact synonym or phenotype xref is assigned pending authority and scope review.",
        "posed_by": "codex",
        "posed_date": "2026-10-11"
      },
      {
        "discussion_id": "lethal-algicidal-strains-and-mechanisms",
        "prompt": "Reconcile study strains and build independently supported mechanism graphs.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Canonical examples await authoritative strain/taxon reconciliation, including HY's conflicting isolate numbers. Retain source strain names as qualified evidence without species-wide assignments or promotion of induced mutants. Secreted activity is demonstrated, not a universal restriction excluding contact-dependent routes. Neither a common protein mechanism, a universal lethal threshold, bloom-control efficacy nor environmental safety is established. Protein graphs require exact functional evidence and taxon-paired accessions, not a short sequence match. Mechanisms are deferred, not claimed absent.",
        "posed_by": "codex",
        "posed_date": "2026-10-11"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-11T08:50:39Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added lethal algicidal activity beneath phenotype with three primary DOI citations and directly checked short snippets. Ignored-and-hidden main/worktree/open-PR checks support 000695 and v571 block 1064800-1064899. Existing records unchanged; mappings, canonical taxa and mechanisms remain open. Timestamp records the observed UTC curation decision.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000720",
    "label": "lethal nematicidal activity",
    "definition": "A physiological capability of a microorganism to kill nematodes.",
    "definition_source": "DOI:10.1038/s41598-023-33669-z",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/s41598-023-33669-z",
        "snippet": "T. asperellum FbMi6 at 80% concentration had the highest (90.3%) juvenile mortality compared to control.",
        "notes": "Saharan et al. 2023, PMID:37088805, Results in vitro activity; native NOT_IN_ABSTRACT, direct publisher HTML match. Actual Figure 4 inspected. This is culture filtrate, not live fungal inoculum: 100 newly hatched M. incognita J2, water/PDB controls, 72 h endpoint, 25 +/- 2 degrees C, two repeats. Methods reports fresh-water recovery confirmation without its duration or scoring criterion. The quote's percentage is source-reported, not independently recalculated. Supplement text/tables and its embedded image were inspected, not rendered document pages. Strain/accession discrepancies prevent a canonical taxon assignment; pot/field efficacy is not imported."
      },
      {
        "reference": "DOI:10.1128/spectrum.02577-21",
        "snippet": "In this study, three secondary metabolites (SMs) with nematicidal activities were isolated from in vitro cultures of P. luminescens sonorensis strain Caborca",
        "notes": "Producer-origin supporting evidence, not definition authority. The self-contained excerpt establishes microbial origin of nematicidal metabolites; its wording alone does not distinguish death from paralysis. The independently cited Saharan mortality result supplies explicit lethal definition support. Kusakabe et al. 2022, PMID:35138171, Discussion opening clause, printed/PDF page 12; native NOT_IN_ABSTRACT and direct XML/typeset PDF match. The producer is Photorhabdus. Culture-supernatant fractionation links the isolated metabolites to this microorganism. t-CA and PPA caused mortality; indole mainly caused reversible paralysis at lower doses, with killing only at high concentrations. Equipotent synthetic standards were used for dose-response assays. Actual Figures 2/3 and Table 4 inspected. Needle response and morphology distinguished death from paralysis; recovery used washing and 24 h in water. Table 4 tests lower-dose indole, not t-CA/PPA survival. No live-culture lethal concentration is inferred. Some numerical prose conflicts with tables; no potency, selectivity or significance values are adopted. Linked supplemental NMR/statistics files were not audited; figure inspection is not raw-data verification."
      }
    ],
    "discussions": [
      {
        "discussion_id": "lethal-nematicidal-scope-and-mappings",
        "prompt": "Refine the hierarchy while preserving the lethal, microbial-actor endpoint.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Killing susceptible nematodes is required; reversible paralysis, repellence, reduced egg hatch, host defense induction and a sequence annotation alone are insufficient. The label is qualified because nematicidal usage can include nonlethal readouts. Neither all nematode species/stages nor all producing strains are implied. Fungal nematophagy (traitmech:000719) requires feeding, and trap formation (traitmech:000718) is structural; neither is an exact parent. Predatory bacterium (traitmech:000054) requires consuming bacterial prey. Animal pathogen METPO:1004002 requires infection, unnecessary for culture-derived toxicity. Phenotype METPO:1000059 is the conservative parent. Pinned/current METPO inspection found no exact active or deprecated counterpart. CHEBI:25491 denotes a nematicide chemical, not this microbial capability, and is not an xref. No exact synonyms or organism-level disjointness are asserted; v596 proposes the class. The methodological context below cautions against equating immobility or a negative NaOH response with death under all conditions. It is not evidence of microbial killing or definition support.",
        "posed_by": "codex",
        "posed_date": "2026-10-13",
        "evidence": [
          {
            "reference": "DOI:10.3725/jjn.45.51",
            "supports": "NO_EVIDENCE",
            "evidence_source": "scientific abstract; publisher HTML and PDF",
            "snippet": "The J2s inactivated by low temperature showed no reaction to the NaOH treatment.",
            "explanation": "Harada and Yoshiga 2015, scientific abstract, printed page 51. Direct publisher HTML/PDF match; actual pages 51-54, Table 1 and Figure 1 inspected. Second-stage M. incognita juveniles could recover after warming or removal of some chemicals. This supports condition-dependent viability-assay caution, not microbial killing or an additional phenotype replication. Native UNRESOLVED: exact DOI query returned zero results; publisher and Crossref verify identity. This citation is discussion-only context, not supporting evidence for the trait or its definition."
          }
        ]
      },
      {
        "discussion_id": "lethal-nematicidal-provenance-and-mechanisms",
        "prompt": "Reconcile strain provenance and establish taxon-paired mechanisms before expanding the record.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Saharan's claimed FbMi6 accession MT529846.1 resolves in GenBank to clone SF_570, not FbMi6. Its supplement compares strain 6 with MT529837.1, clone SF_561, but labels the table SF_570 and the mortality image FbMi-4. No corrected accession is inferred. Caborca's primary strain-provenance reference has not been reconciled either. Retain these qualified observations without canonical examples. No common molecular mechanism, natural lethal dose, nutritional benefit or environmental safety is established; graphs and proteins remain unset. Culture-derived activity does not restrict the entire class to secretion. Crossref/publisher/indexing notice checks are bounded, not comprehensive clearance. Source hashes, assay limits and native verification outcomes are retained in the source-verification sidecar.",
        "posed_by": "codex",
        "posed_date": "2026-10-13"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-13T17:31:43Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added lethal nematicidal activity with two primary microbial-product studies and one viability-method citation, each with a directly matched snippet. Distinguished death from reversible paralysis and feeding; retained strain and assay caveats. Reserved 000720, v596 and 1067300-1067399 after ignored/hidden current-file, retained history and open/draft PR checks, with numeric false positives adjudicated. No exact active METPO counterpart identified. Other records unchanged. Timestamp records observed post-audit acceptance.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-13T18:14:01Z",
        "curator": "codex",
        "action": "CORRECTED_EVIDENCE_ROLE",
        "changes": "Addressed review issue #1916: moved the Harada viability-method citation and exact excerpt from supporting evidence into the scope discussion. Retained its source/resolver provenance as context. The two microbial-killing studies remain supporting evidence; the context-only DOI no longer enters proposal definition annotations. Preserved original history, identity, hierarchy and other records.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-13T18:54:48Z",
        "curator": "codex",
        "action": "CORRECTED_PRODUCER_EXCERPT",
        "changes": "Addressed review issue #1917: replaced the compound-only excerpt with a directly matched producer-linked Discussion result and retained the actual NOT_IN_ABSTRACT outcome and assay limits. Moved the unchanged Harada excerpt into structured discussion evidence with NO_EVIDENCE role for native verification. Preserved #1916's two-source definition support, prior events, identity, hierarchy and other records.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-13T19:40:13Z",
        "curator": "codex",
        "action": "CORRECTED_LETHAL_ENDPOINT_EXCERPTS",
        "changes": "Addressed review issue #1918: stored separate producer-origin and explicit mortality spans from Kusakabe, totaling 25 words. Preserved the high-concentration non-target and synthetic-standard assay qualifiers. IMPORTANCE matches native VERIFIED but is not the scientific Abstract; the mortality span is NOT_IN_ABSTRACT. Three evidence items still represent only two supporting studies. Preserved #1916/#1917 fixes, all prior events, fungal evidence, discussion-only context, identity, hierarchy and other records.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-13T20:27:02Z",
        "curator": "codex",
        "action": "CORRECTED_DEFINITION_AUTHORITY",
        "changes": "Addressed review issue #1919: selected the unchanged Saharan mortality result as definition authority and first evidence item. Restored the complete 22-word Kusakabe producer-linked clause as origin support, not definition authority. Removed the subjectless origin and anaphoric mortality spans. This supersedes #1918's two-span correction: explicit mortality support now comes from the selected fungal source. Proposal definition annotations cite only that source and the local record; two distinct primary studies remain supporting evidence. Both excerpts retain native NOT_IN_ABSTRACT outcomes. Preserved all prior events, assay limitations, structured context, identity, hierarchy and other records.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000143",
    "label": "leucine arylamidase activity",
    "definition": "A physiological enzyme-activity phenotype in which a cell produces active leucine arylamidase enzymes that hydrolyze leucine arylamide substrates.",
    "definition_source": "DOI:10.1099/ijsem.0.002327",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1099/ijsem.0.002327",
        "snippet": "enzyme detection with an API zym kit was positive for alkaline phosphatase, esterase, leucine arylamidase, valine arylamidase, acid phosphatase",
        "notes": "Jung et al. detected leucine arylamidase in Lactobacillus allii strain WiKim39 with the API ZYM enzyme activity panel."
      },
      {
        "reference": "DOI:10.1155/2021/8888641",
        "snippet": "According to the API ZYM assays, all three isolates were positive for alkaline phosphatase, leucine aryl amidase, acid phosphatase, and naphthol_AS_BI_phosphohydrolase.",
        "notes": "Mekonnen et al. treated leucine arylamidase as an assayed bacterial exoenzyme phenotype in rapid urease-producing soil isolates."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1847728",
        "taxon_label": "Companilactobacillus allii",
        "note": "The Lactobacillus allii WiKim39 type strain described by Jung et al. is now classified as Companilactobacillus allii and was positive for leucine arylamidase in the API ZYM panel.",
        "reference": "DOI:10.1099/ijsem.0.002327"
      }
    ],
    "discussions": [
      {
        "discussion_id": "leucine-arylamidase-activity-xref-gap",
        "prompt": "Resolve an exact external ontology class for leucine arylamidase activity before adding a TraitRecord xref.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "GO:0004177 covers aminopeptidase activity at molecular-function scope and the obsolete GO leucyl aminopeptidase term no longer provides a live exact class for leucine arylamidase production as an organism-level phenotype.",
        "posed_by": "codex",
        "posed_date": "2026-09-11"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-11T16:42:06Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted leucine arylamidase activity as a DOI-backed TraitRecord after a repository-wide duplicate review covering ignored and hidden files; METPO has no exact leucine arylamidase activity class yet.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000178",
    "label": "leucyl glycine arylamidase activity",
    "definition": "A physiological enzyme-activity phenotype in which a cell produces active leucyl-glycine arylamidase enzymes that hydrolyze leucyl-glycine arylamide substrates.",
    "definition_source": "DOI:10.1099/ijsem.0.006017",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "synonyms": [
      {
        "synonym_text": "leucyl glycine arylamidase",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1099/ijsem.0.006017"
      },
      {
        "synonym_text": "leucylglycine arylamidase",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1128/JCM.40.9.3427-3431.2002"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1099/ijsem.0.006017",
        "snippet": "enzymatic activities are present for: \u03b1-galactosidase, N-acetyl-\u03b2-glucosaminidase, arginine arylamidase, proline arylamidase, leucyl glycine arylamidase, phenylalanine arylamidase, leucine arylamidase, tyrosine arylamidase, alanine arylamidase, glycine arylamidase, histidine arylamidase, glutamyl glutamic acid arylamidase, serine arylamidase, valine arylamidase, cysteine arylamidase, esterase, esterase lipase, alpha-chymotrypsin",
        "notes": "Srinivasan et al. listed leucyl glycine arylamidase among enzymatic activities present in the Amygdalobacter indicium species description, supporting the API arylamidase row as a directly assayed bacterial enzyme-activity phenotype."
      },
      {
        "reference": "DOI:10.1128/JCM.40.9.3427-3431.2002",
        "snippet": "When the API rapid ID32A system was used, all eight strains displayed activity for alanine arylamidase, arginine arylamidase, \u03b1-glucosidase, glycine arylamidase, histidine arylamidase, leucine arylamidase, leucylglycine arylamidase, proline arylamidase, phenylalanine arylamidase, serine arylamidase, and tyrosine arylamidase",
        "notes": "Hall et al. reported leucylglycine arylamidase activity in all eight Actinomyces cardiffensis clinical isolates tested with the API rapid ID32A system."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:3029272",
        "taxon_label": "Amygdalobacter indicium",
        "note": "Srinivasan et al. reported Amygdalobacter indicium as positive for leucyl glycine arylamidase activity in an enzyme activity panel.",
        "reference": "DOI:10.1099/ijsem.0.006017"
      }
    ],
    "discussions": [
      {
        "discussion_id": "leucyl-glycine-arylamidase-activity-xref-gap",
        "prompt": "Resolve an exact external ontology class for leucyl glycine arylamidase activity before adding a TraitRecord xref.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "GO:0016805 covers broad dipeptidase activity at molecular-function scope, and no live GO class provides an exact leucyl-glycine-specific arylamidase production phenotype at organism-level scope.",
        "posed_by": "codex",
        "posed_date": "2026-09-14"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-14T00:53:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted leucyl glycine arylamidase activity as a DOI-backed TraitRecord after a repository-wide duplicate review covering ignored and hidden files; METPO has no exact leucyl glycine arylamidase activity class yet and the placeholder is reserved in proposals/metpo_traitmech_v55.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-14T01:12:00Z",
        "curator": "codex",
        "action": "UPDATED_DEFINITION",
        "changes": "Corrected the PR 882 review wording issue tracked in issue 883 by defining the trait around leucyl-glycine arylamide substrates rather than free leucyl-glycine dipeptide substrates.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000139",
    "label": "lipase activity",
    "definition": "A physiological enzyme-activity phenotype in which a cell produces active lipases that hydrolyze triglycerides at lipid-water interfaces.",
    "definition_source": "DOI:10.22207/JPAM.16.4.27",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "synonyms": [
      {
        "synonym_text": "lipase production",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.22207/JPAM.16.4.27"
      },
      {
        "synonym_text": "lipolytic activity",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1016/j.mex.2018.01.004"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.22207/JPAM.16.4.27",
        "snippet": "Lipase-producing bacteria were isolated using tributyrin agar as a selective medium",
        "notes": "Savalia and Dungrechiya used tributyrin agar to isolate lipase-producing bacteria from waste samples."
      },
      {
        "reference": "DOI:10.1016/j.mex.2018.01.004",
        "snippet": "to identify lipase producers. The addition of calcium and magnesium ions can provide an easier screening procedure for selection of lipolytic bacterial strains",
        "notes": "Carrazco-Palafox et al. optimized modified tributyrin agar as a microbial lipolytic-activity screen."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1408",
        "taxon_label": "Bacillus pumilus",
        "note": "Bacillus pumilus S113 was isolated as the strongest lipase producer in a tributyrin-agar screen.",
        "reference": "DOI:10.22207/JPAM.16.4.27"
      }
    ],
    "discussions": [
      {
        "discussion_id": "lipase-activity-xref-gap",
        "prompt": "Resolve an exact external ontology class for lipase activity before adding a TraitRecord xref.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "GO:0016298 denotes the lipase molecular function rather than the organism-level lipase production phenotype, so it is too scope-shifted for an equivalent TraitRecord xref.",
        "posed_by": "codex",
        "posed_date": "2026-09-11"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-11T00:00:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted lipase activity as a DOI-backed TraitRecord after a repository-wide duplicate review covering ignored and hidden files; METPO has no exact lipase activity class yet.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000644",
    "label": "lipophagy",
    "definition": "An autophagy phenotype in which a microbial cell degrades its lipid droplets by delivering them to lysosomal or vacuolar compartments.",
    "definition_source": "DOI:10.1091/mbc.e13-08-0448",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000638"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1091/mbc.e13-08-0448",
        "snippet": "LDs can also be turned over in vacuoles/lysosomes by a process that morphologically resembles microautophagy.",
        "notes": "PMID:24258026, PMC3890349. Scientific abstract directly read in DOI-matched Europe PMC metadata and XML abstract2, not the precis. Results sec9 and Methods sec12-sec15 were read. Purified, trypsin-treated vacuoles, lipid analysis and TAG-lipase assays separate uptake from breakdown in Saccharomyces cerevisiae. The atg1/atg15 comparisons distinguish delivery, vacuolar catabolism and compensating cytosolic lipolysis. BY4742-derived reporter/mutant hosts are not verified natural exemplars. Actual figures and supplements were not inspected."
      },
      {
        "reference": "DOI:10.1016/j.devcel.2024.01.014",
        "snippet": "Upon nutrient exhaustion, cells consume LDs via gradual lipolysis or via lipophagy, the en bloc uptake of LDs into the vacuole.",
        "notes": "PMID:38354739. Scientific abstract directly read in Europe PMC with matching DOI. The LDO/Vac8 vCLIP contact site supports starvation-induced yeast uptake. This source operationally calls en bloc uptake lipophagy; docking or uptake alone is not direct proof of completed lipid degradation. Shared Vac8 use links this route to nuclear microautophagy without equating the cargo phenotypes. Full text, Methods, actual figures and strain provenance were not inspected."
      },
      {
        "reference": "DOI:10.1080/15548627.2024.2325297",
        "snippet": "We find that the degradation of LD surface proteins relies on autophagy and can occur independently of lipophagy.",
        "notes": "PMID:38425021, PMC11210923. Scientific ABSTRACT paragraph directly read and exact-matched in DOI-matched NCBI PMC XML at https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pmc&id=11210923&retmode=xml. Europe PMC and PubMed abstract fields return only abbreviations; they do not verify this quote. The retrieved XML has no body. The yeast study separates engulfment from surface-protein processing and reports glucose-concentration-dependent, ATG1-independent uptake. This does not establish lipid catabolism from a protein marker alone. Full Methods, figures and supplements were not inspected."
      }
    ],
    "discussions": [
      {
        "discussion_id": "lipophagy-scope-and-go-alignment",
        "prompt": "Review cargo-defined scope against source and GO conventions.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "The 2014 study supports vacuolar lipid-droplet catabolism via a microautophagy-like route. The two 2024 abstracts also use lipophagy operationally for uptake; the present phenotype retains the autophagy parent's degradative endpoint, not uptake alone. Current GO:0061724 (https://www.ebi.ac.uk/QuickGO/services/ontology/go/terms/GO%3A0061724) restricts lipophagy to selective macroautophagy. GO:0140504 (https://www.ebi.ac.uk/QuickGO/services/ontology/go/terms/GO%3A0140504) separately denotes microlipophagy. Both are nonobsolete biological processes, not exact organismal-phenotype xrefs. Preserve this source-attributed scope difference for human review; no universal macro/micro route, selectivity mechanism, starvation trigger or ATG inventory is asserted. Lipolysis traitmech:000190 concerns triacylglycerol hydrolysis: it can overlap lipophagy but is neither an exact synonym nor a necessary broader parent for all droplet cargo. Lipid storage, PHA granules and pigment sequestration are not equivalent degradation phenotypes. No exact synonyms or mappings are added.",
        "posed_by": "codex",
        "posed_date": "2026-10-06"
      },
      {
        "discussion_id": "lipophagy-flux-exemplars-and-mechanism",
        "prompt": "Resolve route-specific flux assays and native exemplars.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "The phenotype belongs to the microbial cell performing autophagic degradation. Droplet docking, uptake, abundance changes and surface-protein processing are distinct readouts; none alone establishes completed lipid breakdown. Cytosolic lipases can also consume stored lipids. The condition-specific ATG dependence in these studies is not a universal sequence signature. Canonical examples remain unset pending independent natural-strain provenance; do not infer natural or engineered origin merely from a mutant label. Native taxon-paired protein accessions and direct functional support are needed before a causal graph is added. Shared contact machinery with nucleophagy traitmech:000643 does not make their cargo phenotypes equivalent. The third quote is directly source-matched despite the abstract API's abbreviation-only field; retain the resolver's actual inconclusive verdict rather than calling it VERIFIED.",
        "posed_by": "codex",
        "posed_date": "2026-10-06"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-06T14:27:56Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added lipid-droplet autophagy with three DOI-backed source-matched snippets, explicit uptake/flux limits and GO-scope differences. Ignored-and-hidden novelty checks, fresh seed and pinned METPO review found no exact record. Reserved METPO:1059700 in v520 using unchanged corrected v519 parent context. Deferred unverified exemplars, mappings and protein graphs.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000647",
    "label": "lithoautotrophic",
    "definition": "A trophic type in which an organism obtains energy from inorganic electron donors and carbon from carbon dioxide.",
    "definition_source": "DOI:10.1128/AEM.02473-10",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000631"
    ],
    "synonyms": [
      {
        "synonym_text": "lithoautotroph",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1016/B978-0-12-378630-2.00219-X",
        "snippet": "inorganic atoms or molecules",
        "notes": "Review supports inorganic compounds as reductants for lithotrophic growth."
      },
      {
        "reference": "DOI:10.1128/AEM.02473-10",
        "snippet": "autotrophic CO2 fixation",
        "notes": "Review supports CO2 fixation as the autotrophic carbon-assimilation process."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:915",
        "taxon_label": "Nitrosomonas europaea",
        "note": "ammonia-oxidising lithoautotroph",
        "reference": "PMID:12700255"
      },
      {
        "taxon_id": "NCBITaxon:106590",
        "taxon_label": "Cupriavidus necator",
        "note": "H2-oxidising lithoautotroph",
        "reference": "PMID:36335362"
      },
      {
        "taxon_id": "NCBITaxon:228410",
        "taxon_label": "Nitrosomonas europaea ATCC 19718",
        "note": "Strain-level ammonia-oxidizing lithoautotroph paired to its RuBisCO large subunit and Calvin-Benson-Bassham carbon-fixation response.",
        "reference": "DOI:10.1128/AEM.00294-16"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "lithoautotrophic_inorganic_donor_co2_fixation",
        "title": "Lithoautotrophic inorganic-donor CO2 fixation",
        "description": "DOI-backed graph linking inorganic electron donors to energy conservation, reducing power, and autotrophic CO2 fixation.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "This graph combines generic donor oxidation, reverse electron flow, and inorganic-carbon acquisition. The N. europaea RuBisCO example anchors the Calvin-Benson-Bassham fixation branch only; Q82TG6 is its large subunit and not the complete L8S8 enzyme or any donor-oxidation complex.",
        "nodes": [
          {
            "node_id": "lithoautotrophic_trait",
            "label": "lithoautotrophic",
            "node_type": "TRAIT",
            "grounding": "METPO:1000647",
            "description": "Trophic type using inorganic electron donors and CO2 as carbon source."
          },
          {
            "node_id": "inorganic_electron_donor",
            "label": "inorganic electron donor",
            "node_type": "CHEMICAL",
            "description": "Reduced inorganic compound used for energy and reducing equivalents.",
            "grounding": "METPO:1007502"
          },
          {
            "node_id": "respiratory_energy_conservation",
            "label": "respiratory energy conservation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Conversion of redox energy into ion gradients and ATP."
          },
          {
            "node_id": "reducing_power",
            "label": "reducing power",
            "node_type": "CAPACITY",
            "description": "Reduced electron carriers used in biosynthesis.",
            "grounding": "METPO:1007503"
          },
          {
            "node_id": "carbon_dioxide",
            "label": "carbon dioxide",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:16526",
            "description": "Inorganic carbon source for autotrophy."
          },
          {
            "node_id": "autotrophic_co2_fixation",
            "label": "autotrophic CO2 fixation",
            "node_type": "PATHWAY",
            "description": "Pathways that assimilate CO2 into cellular carbon.",
            "grounding": "GO:0015977"
          },
          {
            "node_id": "rubisco",
            "label": "RuBisCO",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Carboxylating enzyme of the Calvin-Benson-Bassham carbon-fixation pathway.",
            "grounding": "InterPro:IPR033966",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:Q82TG6",
                "protein_label": "Ribulose bisphosphate carboxylase large chain",
                "gene_symbol": "cbbL",
                "taxon_id": "NCBITaxon:228410",
                "taxon_label": "Nitrosomonas europaea ATCC 19718",
                "entry_status": "REVIEWED",
                "retrieved_on": "2026-10-22",
                "entry_version": 121,
                "sequence_version": 1,
                "role": "Large subunit of the type I RuBisCO that fixes CO2 through the CBB cycle in N. europaea ATCC 19718; it does not denote the complete L8S8 enzyme.",
                "evidence": [
                  {
                    "reference": "DOI:10.1128/AEM.00294-16",
                    "snippet": "expression of the entire cbb gene cluster increased, with 7.4- and 10.8-fold increases in numbers of genes encoding the small and large subunits of RuBisCO, cbbS (NE1920) and rbcL (NE1921)",
                    "notes": "The primary ATCC 19718 chemostat study identifies NE1921/rbcL and its carbon-fixation response; UniProtKB Q82TG6 is the reviewed NE1921 large-chain entry for that strain."
                  }
                ]
              }
            ]
          },
          {
            "node_id": "cellular_carbon",
            "label": "cellular carbon",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Organic cellular material derived from fixed CO2."
          },
          {
            "node_id": "membrane_dehydrogenase",
            "label": "membrane-bound (de)hydrogenase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Membrane-bound donor-oxidizing enzymes that reduce the quinone pool and drive the ETC.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "This generic label spans unrelated hydrogenases and sulfur-, nitrogen-, iron-, and other donor-oxidizing enzyme families; the graph does not specify one exact family."
          },
          {
            "node_id": "electron_transport_chain",
            "label": "electron transport chain",
            "node_type": "PATHWAY",
            "description": "Membrane electron transfer coupling donor oxidation to proton translocation.",
            "grounding": "GO:0022900"
          },
          {
            "node_id": "proton_motive_force",
            "label": "proton motive force",
            "node_type": "STATE",
            "description": "Transmembrane electrochemical proton gradient generated by the ETC.",
            "grounding": "METPO:1007500"
          },
          {
            "node_id": "atp_synthesis",
            "label": "ATP synthesis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "PMF-driven generation of ATP via ATP synthase.",
            "grounding": "GO:0006754"
          },
          {
            "node_id": "reverse_electron_flow",
            "label": "reverse electron flow",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Endergonic uphill electron transfer that produces NAD(H) for biosynthesis."
          },
          {
            "node_id": "nadh_reducing_equivalents",
            "label": "NAD(H) reducing equivalents",
            "node_type": "CHEMICAL",
            "description": "Reduced nicotinamide cofactors used to drive CO2 fixation."
          },
          {
            "node_id": "cytbc1_nadh_dehydrogenase",
            "label": "cytochrome bc1 and NADH dehydrogenase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Respiratory complexes that mediate reverse electron transfer from the quinone pool to NAD+.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "This node deliberately combines two distinct multisubunit respiratory complexes, so no single protein-family or whole-complex term exactly represents it."
          },
          {
            "node_id": "dic_acquisition_toolkit",
            "label": "carbonic anhydrase and DIC transporters",
            "node_type": "GENE_OR_PROTEIN",
            "description": "DIC transporters and carbonic anhydrase enzymes that supply inorganic carbon to fixation.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "This toolkit combines carbonic-anhydrase enzymes with several unrelated inorganic-carbon transporter families and therefore has no one exact protein grounding."
          }
        ],
        "edges": [
          {
            "subject": "lithoautotrophic_trait",
            "predicate": "has electron donor",
            "object": "inorganic_electron_donor",
            "description": "Inorganic compounds serve as the electron donors for lithoautotrophy.",
            "evidence": [
              {
                "reference": "DOI:10.1016/B978-0-12-378630-2.00219-X",
                "snippet": "inorganic atoms or molecules as a growth-supporting reductant",
                "notes": "Supports inorganic electron donors for lithotrophic growth."
              }
            ],
            "predicate_id": "METPO:2007701"
          },
          {
            "subject": "inorganic_electron_donor",
            "predicate": "enables",
            "object": "respiratory_energy_conservation",
            "description": "Oxidation of inorganic donors supplies redox energy.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.bbabio.2008.09.008",
                "snippet": "free energy of a redox reaction",
                "notes": "Supports energy conservation from respiratory redox reactions."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "respiratory_energy_conservation",
            "predicate": "generates",
            "object": "reducing_power",
            "description": "Lithoautotrophic energy metabolism supplies reducing equivalents for biosynthesis.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.biortech.2021.125768",
                "snippet": "NADH, or ... NADPH",
                "notes": "Review discusses reduced redox cofactors generated from chemolithoautotrophic electron donors."
              }
            ],
            "predicate_id": "biolink:produces"
          },
          {
            "subject": "carbon_dioxide",
            "predicate": "fixed by",
            "object": "autotrophic_co2_fixation",
            "description": "CO2 is assimilated by autotrophic carbon fixation pathways.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.02473-10",
                "snippet": "autotrophic CO2 fixation",
                "notes": "Supports CO2 fixation as the autotrophic carbon-assimilation process."
              }
            ],
            "predicate_id": "METPO:2007404"
          },
          {
            "subject": "rubisco",
            "predicate": "catalyzes",
            "object": "autotrophic_co2_fixation",
            "description": "RuBisCO catalyzes the carboxylation step in the N. europaea Calvin-Benson-Bassham branch of lithoautotrophic carbon fixation.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.00294-16",
                "snippet": "expression of the entire cbb gene cluster increased, with 7.4- and 10.8-fold increases in numbers of genes encoding the small and large subunits of RuBisCO, cbbS (NE1920) and rbcL (NE1921)",
                "notes": "The primary ATCC 19718 study directly identifies the RuBisCO genes in the carbon-fixation response; the example grounds the large subunit rather than asserting that one accession is the whole enzyme."
              }
            ],
            "predicate_id": "biolink:catalyzes"
          },
          {
            "subject": "reducing_power",
            "predicate": "enables",
            "object": "autotrophic_co2_fixation",
            "description": "Reducing equivalents support conversion of CO2 into cell carbon.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.biortech.2021.125768",
                "snippet": "reduction of CO2 in the carbon fixation mechanisms",
                "notes": "Supports reductant use for CO2 reduction."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "autotrophic_co2_fixation",
            "predicate": "has output",
            "object": "cellular_carbon",
            "description": "Autotrophic CO2 fixation produces cellular organic carbon.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.02473-10",
                "snippet": "CO2 ... into cellular carbon",
                "notes": "Supports assimilation of CO2 into cellular carbon."
              }
            ],
            "predicate_id": "RO:0002234"
          },
          {
            "subject": "membrane_dehydrogenase",
            "predicate": "drives",
            "object": "electron_transport_chain",
            "description": "Membrane-bound donor-oxidizing enzymes reduce the quinone pool and drive the electron transport chain.",
            "evidence": [
              {
                "reference": "DOI:10.1128/aem.00748-24",
                "notes": "Membrane-bound (de-)hydrogenases couple donor oxidation to quinone reduction which drives the ETC."
              }
            ]
          },
          {
            "subject": "electron_transport_chain",
            "predicate": "builds",
            "object": "proton_motive_force",
            "description": "The electron transport chain builds up a proton motive force.",
            "evidence": [
              {
                "reference": "DOI:10.1128/aem.00748-24",
                "notes": "drives the electron transport chain (ETC) to build up a proton motive force."
              }
            ],
            "predicate_id": "biolink:produces"
          },
          {
            "subject": "proton_motive_force",
            "predicate": "drives",
            "object": "atp_synthesis",
            "description": "The proton motive force drives ATP synthesis.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s10295-020-02309-0",
                "notes": "This process generates a proton motive force to drive ATP synthesis."
              }
            ]
          },
          {
            "subject": "reverse_electron_flow",
            "predicate": "generates",
            "object": "nadh_reducing_equivalents",
            "description": "Endergonic reverse electron flow generates NAD(H) for carbon fixation.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s10295-020-02309-0",
                "notes": "an uphill (endergonic) pathway to generate NAD(H) through reverse electron flow."
              }
            ],
            "predicate_id": "biolink:produces"
          },
          {
            "subject": "cytbc1_nadh_dehydrogenase",
            "predicate": "mediates",
            "object": "reverse_electron_flow",
            "description": "Cytochrome bc1 and NADH dehydrogenase mediate reverse electron transfer reducing NAD+ to NAD(H).",
            "evidence": [
              {
                "reference": "DOI:10.1007/s10295-020-02309-0",
                "notes": "mediated by cytochrome bc1 and NADH dehydrogenase which transfer electrons from the ubiquinone pool to reduce NAD+ to NAD(H)."
              }
            ]
          },
          {
            "subject": "dic_acquisition_toolkit",
            "predicate": "facilitates",
            "object": "autotrophic_co2_fixation",
            "description": "DIC transporters and carbonic anhydrase facilitate dissolved inorganic carbon fixation.",
            "evidence": [
              {
                "reference": "DOI:10.1128/aem.01557-23",
                "notes": "Autotrophs make use of a toolkit of DIC transporters and carbonic anhydrase enzymes to facilitate DIC fixation; broad across autotrophs."
              }
            ]
          },
          {
            "subject": "membrane_dehydrogenase",
            "predicate": "contributes to",
            "object": "respiratory_energy_conservation",
            "description": "Membrane dehydrogenases reduce quinone and drive an electron-transport chain that builds proton motive force.",
            "evidence": [
              {
                "reference": "DOI:10.1128/aem.00748-24",
                "snippet": "Membrane-bound (de-)hydrogenases couple the oxidation reaction to the reduction of a universal quinone",
                "notes": "Verified against the open primary article."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "nadh_reducing_equivalents",
            "predicate": "example of",
            "object": "reducing_power",
            "description": "NADH generated by reverse electron flow is reducing power for lithoautotrophic carbon fixation.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41396-021-01015-8",
                "snippet": "NADH dehydrogenase can also dissipate the PMF to couple electrons from the ubiquinone pool to NAD+ reduction using a process called reverse electron flow",
                "notes": "Verified against the open primary article."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-08-24T14:00:00-07:00",
        "curator": "codex",
        "action": "REVIEWED_CAUSAL_GRAPH_PROTEIN_TAXON",
        "changes": "Added a DOI-backed N. europaea ATCC 19718 canonical example, grounded RuBisCO node, reviewed large-subunit example, and complete-evidence fixation edge; documented three heterogeneous protein-toolkit nodes as reviewed label-only.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-05T01:35:46.874845+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-08T00:00:00-07:00",
        "curator": "codex",
        "action": "ADDED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed causal graph for inorganic electron donors, reducing power, and autotrophic CO2 fixation.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000009\u00d71, METPO:2000202\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T08:21:50Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:produces\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T21:30:07Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007404\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:19Z",
        "curator": "claude",
        "action": "RENAME_PREDICATE_LABELS",
        "changes": "Renamed 2 causal-edge predicate label(s) to align with existing groundings: supports \u2192 enables \u00d72.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:22Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d72).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:41:04Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (METPO:1007502\u00d71, METPO:1007503\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T08:14:33Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0015977\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-26T02:30:13Z",
        "curator": "claude",
        "action": "RETYPE_CAUSAL_NODES",
        "changes": "Re-typed 1 causal-node node_type field(s) to align with CausalNodeTypeEnum semantics: reducing power: CHEMICAL \u2192 CAPACITY \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 6 evidence-backed generic edges (8 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:14Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:produces\u00d72).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:34Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0022900\u00d71, GO:0006754\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-05T12:00:00Z",
        "curator": "claude",
        "action": "REVERSE_CAUSAL_EDGE_DIRECTION",
        "changes": "Reversed 1 causal edge from <trait> uses electron donor <chemical> to <chemical> enables <trait> (predicate_id METPO:2000009 -> RO:0002327), issue 295. METPO:2000009 is rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so the trait-subject form entailed that this TRAIT node is a microbe; CausalNodeTypeEnum has no organism member, so no causal-graph edge can satisfy that domain. Evidence unchanged; only subject/predicate/object/predicate_id and the edge description moved. Note RO:0002327 has range 'biological process or activity', so the new form is not fully range-correct either - tracked in issue 302.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 1 causal edge(s) off enables/RO:0002327 with a TRAIT object (1 to has electron donor), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them. 1 electron edge(s) were also reversed back to trait -> chemical, restoring the donor/acceptor role that PR 300 collapsed onto enables (issue 303); the organism-subject problem that forced that collapse does not arise here because these predicates take a causal-node domain rather than METPO:2000001's microbe domain (issue 301).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates (1 to has output), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-15T02:00:00Z",
        "curator": "claude",
        "action": "NORMALISE_NODE_TYPE",
        "changes": "Normalised causal-node type(s) so one node_id means one thing corpus-wide (issue 356): proton_motive_force: CAPACITY -> STATE. The schema's OWN example of STATE: 'a bioenergetic or molecular state of the cell (e.g. proton motive force ...) ... the state is the gradient / steady-value, not its establishment'. All 35 occurrences describe the gradient -- every description across all four types reads 'electrochemical proton gradient', including the 13 typed BIOLOGICAL_PROCESS ('Transmembrane electrochemical gradient generated by respiration'), which name the gradient and its provenance rather than the generating process. Nothing here means the establishment, so this is a retype and not a rename; records that DO mean the process already use a separate id (proton_motive_force_generation in ph_delta.yaml). Also settles the one edge #356 was filed for: phototrophic.yaml's CAPACITY typing was blocking `powers` (METPO:2007900), which is gated to BIOLOGICAL_PROCESS|STATE.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-16T02:00:00Z",
        "curator": "claude",
        "action": "NORMALISE_NODE_TYPE",
        "changes": "Under the PATHWAY-vs-BIOLOGICAL_PROCESS rule, one node_id means one thing corpus-wide (issue 356): electron_transport_chain is typed PATHWAY. PATHWAY is a named, conventionally enumerable multi-step route; BIOLOGICAL_PROCESS is everything else. A named route through enumerable complexes. Was 4 PATHWAY to 2 before this tranche.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-20T07:10:43Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (METPO:1007500\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T11:45:00Z",
        "curator": "codex",
        "action": "CONNECT_CAUSAL_GRAPH_COMPONENTS",
        "changes": "Resolved issue #183 graph fragmentation (3 components to 1): added 2 public-source connector(s). No paid research service was called.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-22T01:35:00Z",
        "curator": "claude",
        "action": "REFRESH_UNIPROT_ENTRY_VERSION",
        "changes": "Refreshed UniProtKB entry_version against live UniProt REST on 2026-10-22: UniProtKB:Q82TG6 (120 -> 121 on rubisco).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000648",
    "label": "lithoheterotrophic",
    "definition": "A trophic type in which an organism obtains energy from the oxidation of inorganic compounds while using organic compounds as the primary carbon source for biosynthesis.",
    "definition_source": "DOI:10.1038/s41598-021-81412-3",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000631"
    ],
    "synonyms": [
      {
        "synonym_text": "lithoheterotroph",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "created_by": "Jed Dongjin Kim-Ozaeta",
    "evidence": [
      {
        "reference": "DOI:10.1038/s41598-021-81412-3",
        "snippet": "engineered lithoheterotrophic strain",
        "notes": "Experimental study supports Fe(II)-dependent lithoheterotrophic growth with glucose as carbon source."
      },
      {
        "reference": "DOI:10.1016/B978-0-12-378630-2.00219-X",
        "snippet": "oxidize inorganic atoms or molecules",
        "notes": "Review supports inorganic compound oxidation as lithotrophic energy metabolism."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:317655",
        "taxon_label": "Sphingopyxis alaskensis RB2256",
        "note": "Strain-level facultative lithoheterotrophic example that oxidizes H2 during aerobic growth on organic carbon, paired to its group 2a hydrogenase large subunit.",
        "reference": "DOI:10.1038/s41564-023-01322-0"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "lithoheterotrophic_inorganic_energy_organic_carbon",
        "title": "Lithoheterotrophic inorganic energy and organic carbon use",
        "description": "DOI-backed graph linking inorganic electron donors, Fe(II) oxidation, respiratory energy conservation, organic carbon uptake, precursor metabolites, and biomass.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "This modular graph covers Fe(II), reduced-sulfur, H2, and an exploratory direct-electron-transfer branch. The S. alaskensis example anchors only aerobic H2-supported growth on organic carbon; Q1J422 is one hydrogenase large subunit, not the complete complex or evidence for every donor branch.",
        "nodes": [
          {
            "node_id": "lithoheterotrophic_trait",
            "label": "lithoheterotrophic",
            "node_type": "TRAIT",
            "grounding": "METPO:1000648",
            "description": "Trophic type using inorganic donors for energy and organic compounds for carbon."
          },
          {
            "node_id": "inorganic_electron_donor",
            "label": "inorganic electron donor",
            "node_type": "CHEMICAL",
            "description": "Reduced inorganic substrate oxidized for energy.",
            "grounding": "METPO:1007502"
          },
          {
            "node_id": "ferrous_iron",
            "label": "ferrous iron",
            "node_type": "CHEMICAL",
            "description": "Fe(II), an inorganic electron donor in lithoheterotrophic iron oxidation.",
            "grounding": "CHEBI:29033"
          },
          {
            "node_id": "organic_carbon",
            "label": "organic carbon",
            "node_type": "CHEMICAL",
            "description": "Organic compound used as the cellular carbon source.",
            "grounding": "CHEBI:50860"
          },
          {
            "node_id": "glucose",
            "label": "glucose",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:17234",
            "description": "Experimental organic carbon source in engineered lithoheterotrophy."
          },
          {
            "node_id": "respiratory_chain",
            "label": "respiratory chain",
            "node_type": "PATHWAY",
            "description": "Electron-transport route conserving energy from inorganic donor oxidation.",
            "grounding": "GO:0022904"
          },
          {
            "node_id": "molecular_oxygen",
            "label": "molecular oxygen",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:15379",
            "description": "Electron acceptor for aerobic Fe(II)-oxidizing growth."
          },
          {
            "node_id": "atp",
            "label": "ATP",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:30616",
            "description": "Energy carrier generated by respiratory energy conservation."
          },
          {
            "node_id": "precursor_metabolites",
            "label": "precursor metabolites",
            "node_type": "CHEMICAL",
            "description": "Organic-carbon intermediates used for biosynthesis."
          },
          {
            "node_id": "biomass",
            "label": "biomass",
            "node_type": "CHEMICAL",
            "description": "Cell material formed from organic carbon.",
            "grounding": "METPO:1007501"
          },
          {
            "node_id": "microaerobic_conditions",
            "label": "microaerobic conditions",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Low-oxygen conditions that permit biological Fe(II) oxidation by limiting abiotic Fe(II) oxidation."
          },
          {
            "node_id": "ferrous_iron_oxidation",
            "label": "Fe(II) oxidation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Oxidation of ferrous iron serving as the energy-yielding lithotrophic process."
          },
          {
            "node_id": "sulfide",
            "label": "sulfide",
            "node_type": "CHEMICAL",
            "description": "Reduced inorganic sulfur electron donor oxidized for lithotrophic energy.",
            "grounding": "CHEBI:15138"
          },
          {
            "node_id": "molecular_hydrogen",
            "label": "molecular hydrogen",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:18276",
            "description": "Reduced inorganic gas oxidized as a supplementary energy source during lithoheterotrophic growth."
          },
          {
            "node_id": "sqr",
            "label": "sulfide:quinone oxidoreductase (SQR)",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Key enzyme catalyzing oxidation/detoxification of sulfide in lithotrophic sulfur oxidizers.",
            "grounding": "GO:0070224"
          },
          {
            "node_id": "thiosulfate",
            "label": "thiosulfate",
            "node_type": "CHEMICAL",
            "description": "Inorganic sulfur electron donor oxidized via the Sox system.",
            "grounding": "CHEBI:16094"
          },
          {
            "node_id": "sox_system",
            "label": "periplasmic Sox system",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Periplasmic sox gene cluster encoding thiosulfate oxidation.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "This node denotes a variable multisubunit Sox pathway whose component composition differs among taxa; no checked whole-system term exactly represents the label."
          },
          {
            "node_id": "group_2a_nife_hydrogenase",
            "label": "group 2a [NiFe]-hydrogenase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Plasmid-borne multisubunit uptake hydrogenase used for aerobic H2 oxidation by S. alaskensis RB2256.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Available InterPro terms cover broad NiFe hydrogenase large-subunit families rather than this complete group 2a multisubunit enzyme; the exact catalytic component is retained as the taxon-paired protein example.",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:Q1J422",
                "protein_label": "Group 2a [NiFe]-hydrogenase large subunit HucL",
                "gene_symbol": "Sala_3198",
                "taxon_id": "NCBITaxon:317655",
                "taxon_label": "Sphingopyxis alaskensis RB2256",
                "entry_status": "UNREVIEWED",
                "proteome_id": "UP000006578",
                "retrieved_on": "2026-08-24",
                "entry_version": 98,
                "sequence_version": 1,
                "role": "Catalytic large-subunit component of the plasmid-borne group 2a [NiFe]-hydrogenase; this accession is not presented as the complete hydrogenase complex.",
                "evidence": [
                  {
                    "reference": "DOI:10.1038/s41564-023-01322-0",
                    "snippet": "group 2a [NiFe]-hydrogenase large subunit gene (hucL; locus Sala_3198)",
                    "notes": "The primary study measured Sala_3198 expression during aerobic growth and H2 oxidation. UniProtKB Q1J422 maps that exact locus to the S. alaskensis RB2256 reference proteome."
                  }
                ]
              }
            ]
          }
        ],
        "edges": [
          {
            "subject": "lithoheterotrophic_trait",
            "predicate": "has electron donor",
            "object": "inorganic_electron_donor",
            "description": "Inorganic compounds serve as the energy-generating electron donors for lithoheterotrophy.",
            "evidence": [
              {
                "reference": "DOI:10.1016/B978-0-12-378630-2.00219-X",
                "snippet": "oxidize inorganic atoms or molecules",
                "notes": "Supports inorganic chemical oxidation as lithotrophic energy metabolism."
              }
            ],
            "predicate_id": "METPO:2007701"
          },
          {
            "subject": "ferrous_iron",
            "predicate": "example of",
            "object": "inorganic_electron_donor",
            "description": "Fe(II) is an example inorganic electron donor for lithotrophic growth.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41598-021-81412-3",
                "snippet": "Fe(II) as the energy source",
                "notes": "Supports Fe(II) oxidation as the energy source in engineered lithoheterotrophy."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "inorganic_electron_donor",
            "predicate": "feeds electrons into",
            "object": "respiratory_chain",
            "description": "Oxidation of inorganic donors feeds respiratory electron transport.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.bbabio.2008.09.008",
                "snippet": "membrane-bound electron transport chain",
                "notes": "Supports respiratory chains as energy-conserving redox systems."
              }
            ],
            "predicate_id": "METPO:2007402"
          },
          {
            "subject": "respiratory_chain",
            "predicate": "transfers electrons to",
            "object": "molecular_oxygen",
            "description": "Aerobic Fe(II)-oxidizing lithotrophy can reduce oxygen.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41598-021-81412-3",
                "snippet": "oxidation of Fe(II) coupled to the reduction of oxygen",
                "notes": "Supports oxygen reduction coupled to Fe(II) oxidation."
              }
            ],
            "predicate_id": "METPO:2007403"
          },
          {
            "subject": "respiratory_chain",
            "predicate": "has output",
            "object": "atp",
            "description": "Respiratory electron transport supports ATP synthesis.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.bbabio.2008.09.008",
                "snippet": "drives ATP synthesis",
                "notes": "Supports ATP synthesis from respiratory energy conservation."
              }
            ],
            "predicate_id": "RO:0002234"
          },
          {
            "subject": "lithoheterotrophic_trait",
            "predicate": "has carbon source",
            "object": "organic_carbon",
            "description": "Lithoheterotrophy uses organic compounds as carbon sources.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41598-021-81412-3",
                "snippet": "glucose as the sole carbon source",
                "notes": "Supports organic carbon use under Fe(II)-oxidizing lithoheterotrophic conditions."
              }
            ],
            "predicate_id": "METPO:2007806"
          },
          {
            "subject": "glucose",
            "predicate": "example of",
            "object": "organic_carbon",
            "description": "Glucose is an experimentally supported organic carbon source.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41598-021-81412-3",
                "snippet": "glucose as the sole carbon source",
                "notes": "Supports glucose as the organic carbon source in the engineered strain."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "organic_carbon",
            "predicate": "converted to",
            "object": "precursor_metabolites",
            "description": "Organic carbon supplies biosynthetic precursors.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41598-021-81412-3",
                "snippet": "biomass precursors provided by glucose",
                "notes": "Supports glucose-derived carbon as a source of biomass precursors."
              }
            ]
          },
          {
            "subject": "precursor_metabolites",
            "predicate": "incorporated into",
            "object": "biomass",
            "description": "Organic-carbon precursors are incorporated into cellular material.",
            "evidence": [
              {
                "reference": "DOI:10.1016/B978-012373944-5.00083-3",
                "snippet": "incorporation of a compound into biomass",
                "notes": "Supports assimilation of compounds into biomass."
              }
            ],
            "predicate_id": "biolink:part_of"
          },
          {
            "subject": "microaerobic_conditions",
            "predicate": "supports",
            "object": "ferrous_iron_oxidation",
            "description": "Microaerobic conditions support Fe(II)-oxidizing growth by limiting abiotic Fe(II) oxidation.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41598-021-81412-3",
                "notes": "requiring microaerobic conditions because atmospheric O2 abiotically oxidizes Fe(II)"
              }
            ]
          },
          {
            "subject": "ferrous_iron",
            "predicate": "oxidized in",
            "object": "ferrous_iron_oxidation",
            "description": "Ferrous iron is the substrate oxidized in the energy-yielding Fe(II) oxidation process.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41598-021-81412-3",
                "notes": "the oxidation of Fe(II) coupled to the reduction of oxygen"
              }
            ]
          },
          {
            "subject": "ferrous_iron_oxidation",
            "predicate": "feeds electrons into",
            "object": "respiratory_chain",
            "description": "Fe(II) oxidation provides electrons for respiratory energy conservation.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41598-021-81412-3",
                "notes": "Fe(II) oxidation provides energy while organic carbon serves primarily as the carbon source"
              }
            ],
            "predicate_id": "METPO:2007402"
          },
          {
            "subject": "sulfide",
            "predicate": "example of",
            "object": "inorganic_electron_donor",
            "description": "Sulfide is an inorganic electron donor for lithotrophic sulfur oxidation.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-025-56588-1",
                "notes": "sulfide oxidation as lithotrophic energy metabolism in nitrate-reducing chemolithotrophs/heterotrophs"
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "molecular_hydrogen",
            "predicate": "example of",
            "object": "inorganic_electron_donor",
            "description": "H2 is a reduced inorganic donor that can supplement energy during organic-carbon-supported growth.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-023-01322-0",
                "snippet": "uses an abundant reduced gas as an energy source",
                "notes": "The culture study shows that S. alaskensis consumes H2 while growing on organic carbon, supporting H2 as the inorganic energy donor in this branch."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "molecular_hydrogen",
            "predicate": "oxidized by",
            "object": "group_2a_nife_hydrogenase",
            "description": "The group 2a uptake hydrogenase mediates aerobic H2 oxidation in S. alaskensis.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-023-01322-0",
                "snippet": "encodes a plasmid-borne group 2a [NiFe]-hydrogenase, aerobically consumed H2",
                "notes": "The primary growth, gas-consumption, and hucL-expression experiments pair the enzyme class with H2 oxidation in strain RB2256; Q1J422 is only its large-subunit component."
              }
            ]
          },
          {
            "subject": "sqr",
            "predicate": "oxidizes",
            "object": "sulfide",
            "description": "SQR catalyzes oxidation/detoxification of sulfide as a sulfide-oxidation module.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-025-56588-1",
                "notes": "a key enzyme that can catalyze sulfide detoxification in nitrate-reducing chemolithoautotrophs"
              }
            ],
            "predicate_id": "METPO:2007803"
          },
          {
            "subject": "thiosulfate",
            "predicate": "example of",
            "object": "inorganic_electron_donor",
            "description": "Thiosulfate is an inorganic sulfur electron donor for lithotrophic oxidation.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-025-56588-1",
                "notes": "periplasmic sox gene clusters encoding for thiosulfate oxidation"
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "sox_system",
            "predicate": "oxidizes",
            "object": "thiosulfate",
            "description": "The periplasmic Sox system encodes oxidation of thiosulfate.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-025-56588-1",
                "notes": "periplasmic sox gene clusters encoding for thiosulfate oxidation"
              }
            ],
            "predicate_id": "METPO:2007803"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.875356+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-09T00:00:00-07:00",
        "curator": "codex",
        "action": "ADDED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed causal graph for inorganic electron donor oxidation, Fe(II), respiratory energy conservation, organic carbon use, and biomass formation.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000009\u00d71, METPO:2000202\u00d71, METPO:2000006\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T08:21:50Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (rdfs:subClassOf\u00d72).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T21:30:07Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007402\u00d71, METPO:2007403\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:38:01Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 3 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:29033\u00d71, CHEBI:50860\u00d71, GO:0022904\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:41:04Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (METPO:1007502\u00d71, METPO:1007501\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T07:34:59Z",
        "curator": "claude",
        "action": "RETYPE_CAUSAL_NODES",
        "changes": "Re-typed 1 causal-node node_type field(s) to align with CausalNodeTypeEnum semantics: biomass: BIOLOGICAL_PROCESS \u2192 CHEMICAL \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-13T21:03:27Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:part_of\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 8 evidence-backed generic edges (8 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:14Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 6 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (rdfs:subClassOf\u00d72, METPO:2000016\u00d72, METPO:2007402\u00d71, RO:0002327\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:20Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:15138\u00d71, CHEBI:16094\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:23:55Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0070224\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-05T12:00:00Z",
        "curator": "claude",
        "action": "REVERSE_CAUSAL_EDGE_DIRECTION",
        "changes": "Reversed 1 causal edge from <trait> uses electron donor <chemical> to <chemical> enables <trait> (predicate_id METPO:2000009 -> RO:0002327), issue 295. METPO:2000009 is rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so the trait-subject form entailed that this TRAIT node is a microbe; CausalNodeTypeEnum has no organism member, so no causal-graph edge can satisfy that domain. Evidence unchanged; only subject/predicate/object/predicate_id and the edge description moved. Note RO:0002327 has range 'biological process or activity', so the new form is not fully range-correct either - tracked in issue 302.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 1 causal edge(s) off enables/RO:0002327 with a TRAIT object (1 to has electron donor), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them. 1 electron edge(s) were also reversed back to trait -> chemical, restoring the donor/acceptor role that PR 300 collapsed onto enables (issue 303); the organism-subject problem that forced that collapse does not arise here because these predicates take a causal-node domain rather than METPO:2000001's microbe domain (issue 301).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 2 causal edge(s) off microbe-domain METPO predicates (1 to has output, 1 to has carbon source), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T02:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES_PART2",
        "changes": "Re-grounded 2 causal edge(s) off microbe-domain METPO predicates onto their causal-graph counterparts (2 to oxidizes), issue 301 part 2. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Each replacement is a 1:1 mirror of its source predicate that changes only the domain, so the claim each edge makes is unchanged and directions are unchanged. The replacements are proposed in proposals/metpo_traitmech_v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-17T02:00:00Z",
        "curator": "claude",
        "action": "NORMALISE_NODE_SENSE",
        "changes": "One node_id per SENSE (issues 356, 384): molecular_oxygen is the chemical sense here. The molecule, not the condition \u2014 the dioxygen participating in the reaction the graph describes. Normalised onto molecular_oxygen, the id 20 other chemical occurrences already use, so one id means one sense corpus-wide (issues 356, 384).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-24T12:55:00-07:00",
        "curator": "codex",
        "action": "REVIEWED_CAUSAL_GRAPH_PROTEIN_TAXON",
        "changes": "Marked the graph mechanistic, reviewed the Sox and conductive-surface composites as label-only, added DOI-cited S. alaskensis RB2256 and its H2 branch, and paired the group 2a hydrogenase with reference-proteome component Q1J422 without treating one large subunit as the complete complex.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T11:45:00Z",
        "curator": "codex",
        "action": "CONNECT_CAUSAL_GRAPH_COMPONENTS",
        "changes": "Resolved issue #183 graph fragmentation (2 components to 1): removed the disconnected, out-of-scope DIET island. No paid research service was called.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000649",
    "label": "lithotrophic",
    "definition": "A trophic type in which an organism uses inorganic compounds as electron donors for energy generation.",
    "definition_source": "DOI:10.1016/B978-0-12-378630-2.00219-X",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000631"
    ],
    "synonyms": [
      {
        "synonym_text": "TT_lithotroph",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "lithotroph",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "created_by": "Luke Wang",
    "evidence": [
      {
        "reference": "DOI:10.1016/B978-0-12-378630-2.00219-X",
        "snippet": "oxidize inorganic atoms or molecules",
        "notes": "Encyclopedia review supports inorganic compounds as growth-supporting reductants and energy sources."
      },
      {
        "reference": "DOI:10.1016/j.bbabio.2008.09.008",
        "snippet": "generation of an electrochemical ion gradient",
        "notes": "Review supports respiratory energy conservation through ion gradients and ATP synthesis."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:920",
        "taxon_label": "Acidithiobacillus ferrooxidans",
        "note": "iron/sulfur lithotroph",
        "reference": "PMID:19077236"
      },
      {
        "taxon_id": "NCBITaxon:915",
        "taxon_label": "Nitrosomonas europaea",
        "note": "ammonia lithotroph",
        "reference": "DOI:10.1128/jb.185.9.2759-2773.2003"
      },
      {
        "taxon_id": "NCBITaxon:228410",
        "taxon_label": "Nitrosomonas europaea ATCC 19718",
        "note": "Strain-level ammonia lithotroph paired to the AmoA alpha component of ammonia monooxygenase.",
        "reference": "DOI:10.1128/jb.175.8.2436-2444.1993"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "lithotrophic_inorganic_donor_energy",
        "title": "Lithotrophic inorganic-donor energy mechanism",
        "description": "DOI-backed graph linking inorganic electron donors to respiratory electron transport, proton motive force, and ATP synthesis.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "This cross-donor graph combines hydrogen, sulfur, ammonia, and nitrite oxidation. The N. europaea ATCC 19718 AmoA (Q04507) and HAO (Q50925) examples anchor only the bacterial ammonia-to-hydroxylamine-to-nitrite branch; Q04507 is an alpha-subunit component of a multisubunit ammonia monooxygenase and neither example represents sulfur, hydrogen, or nitrite oxidizer systems.",
        "nodes": [
          {
            "node_id": "lithotrophic_trait",
            "label": "lithotrophic",
            "node_type": "TRAIT",
            "grounding": "METPO:1000649",
            "description": "Trophic type using inorganic electron donors for energy generation."
          },
          {
            "node_id": "inorganic_electron_donor",
            "label": "inorganic electron donor",
            "node_type": "CHEMICAL",
            "description": "Reduced inorganic compound used as a source of electrons.",
            "grounding": "METPO:1007502"
          },
          {
            "node_id": "hydrogen",
            "label": "molecular hydrogen",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:18276",
            "description": "Example inorganic electron donor."
          },
          {
            "node_id": "reduced_sulfur_compound",
            "label": "reduced sulfur compound",
            "node_type": "CHEMICAL",
            "description": "Example inorganic electron donor class."
          },
          {
            "node_id": "membrane_electron_transport_chain",
            "label": "membrane electron transport chain",
            "node_type": "PATHWAY",
            "description": "Redox chain coupling electron flow to ion translocation.",
            "grounding": "GO:0022900"
          },
          {
            "node_id": "proton_motive_force",
            "label": "proton motive force",
            "node_type": "STATE",
            "description": "Electrochemical ion gradient used for energy conservation.",
            "grounding": "METPO:1007500"
          },
          {
            "node_id": "atp",
            "label": "ATP",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:30616",
            "description": "Energy carrier produced from respiratory energy conservation."
          },
          {
            "node_id": "thiosulfate",
            "label": "thiosulfate",
            "node_type": "CHEMICAL",
            "description": "Reduced inorganic sulfur compound used as a lithotrophic electron donor.",
            "grounding": "CHEBI:16094"
          },
          {
            "node_id": "sox_multienzyme_system",
            "label": "Sox multienzyme system",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Periplasmic thiosulfate-oxidizing multienzyme complex (soxXA/soxYZ/soxB/soxCD).",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Sox denotes a variable pathway assembled from multiple distinct protein families and complexes; no one protein-family term represents the complete generic system used by this graph."
          },
          {
            "node_id": "sulfite",
            "label": "sulfite",
            "node_type": "CHEMICAL",
            "description": "Inorganic sulfur intermediate oxidized to sulfate during sulfur lithotrophy."
          },
          {
            "node_id": "soeabc_sulfite_dehydrogenase",
            "label": "SoeABC sulfite dehydrogenase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Membrane-bound sulfite dehydrogenase oxidizing sulfite to sulfate.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "SoeABC is a multisubunit membrane complex; the graph and cited review do not isolate one subunit family as the generic node."
          },
          {
            "node_id": "ammonia",
            "label": "ammonia",
            "node_type": "CHEMICAL",
            "description": "Inorganic nitrogen electron donor for ammonia-oxidizing lithotrophs.",
            "grounding": "CHEBI:16134"
          },
          {
            "node_id": "ammonia_monooxygenase",
            "label": "ammonia monooxygenase (AMO)",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Enzyme catalyzing the first step of ammonia oxidation (EC 1.14.99.39).",
            "grounding": "GO:0018597",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:Q04507",
                "protein_label": "Ammonia monooxygenase alpha subunit",
                "gene_symbol": "amoA1",
                "taxon_id": "NCBITaxon:228410",
                "taxon_label": "Nitrosomonas europaea ATCC 19718",
                "entry_status": "REVIEWED",
                "retrieved_on": "2026-10-22",
                "entry_version": 127,
                "sequence_version": 2,
                "role": "AmoA alpha-subunit component of the N. europaea ammonia monooxygenase; the accession maps two duplicated amoA gene copies and is not the whole enzyme complex.",
                "evidence": [
                  {
                    "reference": "DOI:10.1128/jb.175.8.2436-2444.1993",
                    "snippet": "Sequence of the gene coding for ammonia monooxygenase in Nitrosomonas europaea",
                    "notes": "The primary strain-level study characterizes N. europaea AmoA and ammonia oxidation; UniProtKB Q04507 is the reviewed alpha-subunit entry."
                  }
                ]
              }
            ]
          },
          {
            "node_id": "hydroxylamine",
            "label": "hydroxylamine",
            "node_type": "CHEMICAL",
            "description": "Intermediate of ammonia oxidation.",
            "grounding": "CHEBI:15429"
          },
          {
            "node_id": "hydroxylamine_oxidoreductase",
            "label": "hydroxylamine oxidoreductase (HAO)",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Enzyme oxidizing hydroxylamine during ammonia oxidation (EC 1.7.2.6).",
            "grounding": "GO:0033740",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:Q50925",
                "protein_label": "Hydroxylamine oxidoreductase",
                "gene_symbol": "hao1",
                "taxon_id": "NCBITaxon:228410",
                "taxon_label": "Nitrosomonas europaea ATCC 19718",
                "entry_status": "REVIEWED",
                "proteome_id": "UP000001416",
                "retrieved_on": "2026-10-22",
                "entry_version": 155,
                "sequence_version": 2,
                "role": "Multiheme hydroxylamine oxidoreductase (encoded by three identical hao gene copies in N. europaea ATCC 19718) that oxidizes hydroxylamine to nitrite and feeds electrons into the respiratory chain via cytochrome c554.",
                "evidence": [
                  {
                    "reference": "DOI:10.1128/jb.185.9.2759-2773.2003",
                    "snippet": "Electrons from hydroxylamine oxidation flow through cytochrome c554 and cytochrome cm552 into the electron transport chain at the level of ubiquinone",
                    "notes": "Chain et al. 2003 (complete N. europaea ATCC 19718 genome analysis) describe hydroxylamine oxidation to nitrite and electron transfer into the ubiquinone pool."
                  }
                ]
              }
            ]
          },
          {
            "node_id": "nitrite",
            "label": "nitrite",
            "node_type": "CHEMICAL",
            "description": "Inorganic nitrogen electron donor for nitrite-oxidizing lithotrophs.",
            "grounding": "CHEBI:16301"
          },
          {
            "node_id": "nitrite_oxidoreductase",
            "label": "nitrite oxidoreductase (NXR)",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Enzyme oxidizing nitrite to nitrate (EC 1.7.5.1).",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "NXR is a multisubunit molybdoenzyme whose architecture and component families vary across nitrite oxidizers; this generic node does not identify a single exact subunit or whole-complex term."
          },
          {
            "node_id": "molecular_oxygen",
            "label": "molecular oxygen",
            "node_type": "CHEMICAL",
            "description": "Terminal electron acceptor for aerobic lithotrophic oxidation.",
            "grounding": "CHEBI:15379"
          },
          {
            "node_id": "sulfur_oxidation_process",
            "label": "sulfur oxidation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Oxidation of reduced sulfur compounds for energy conservation.",
            "grounding": "GO:0019417"
          }
        ],
        "edges": [
          {
            "subject": "lithotrophic_trait",
            "predicate": "has electron donor",
            "object": "inorganic_electron_donor",
            "description": "Inorganic compounds serve as the electron donors lithotrophic organisms use.",
            "evidence": [
              {
                "reference": "DOI:10.1016/B978-0-12-378630-2.00219-X",
                "snippet": "inorganic atoms or molecules as a growth-supporting reductant",
                "notes": "Supports inorganic electron donors as the defining lithotrophic substrate class."
              }
            ],
            "predicate_id": "METPO:2007701"
          },
          {
            "subject": "hydrogen",
            "predicate": "example of",
            "object": "inorganic_electron_donor",
            "description": "Molecular hydrogen is a representative inorganic electron donor.",
            "evidence": [
              {
                "reference": "DOI:10.21775/cimb.006.159",
                "snippet": "oxidation of hydrogen gas",
                "notes": "Supports hydrogen gas as a microbial inorganic electron donor."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "reduced_sulfur_compound",
            "predicate": "example of",
            "object": "inorganic_electron_donor",
            "description": "Reduced sulfur compounds are representative lithotrophic electron donors.",
            "evidence": [
              {
                "reference": "DOI:10.1111/j.1574-6976.2009.00187.x",
                "snippet": "lithotrophic sulfur oxidation",
                "notes": "Supports sulfur oxidation as a lithotrophic process."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "inorganic_electron_donor",
            "predicate": "donates electrons to",
            "object": "membrane_electron_transport_chain",
            "description": "Electrons from inorganic donors enter respiratory electron transport.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.bbabio.2008.09.008",
                "snippet": "membrane-bound electron transport chain",
                "notes": "Supports membrane-bound redox chains as energy-conserving electron-transfer systems."
              }
            ],
            "predicate_id": "METPO:2007403"
          },
          {
            "subject": "membrane_electron_transport_chain",
            "predicate": "generates",
            "object": "proton_motive_force",
            "description": "Respiratory redox reactions are conserved as an electrochemical ion gradient.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.bbabio.2008.09.008",
                "snippet": "generation of an electrochemical ion gradient",
                "notes": "Supports proton motive force generation by respiratory electron transport."
              }
            ],
            "predicate_id": "biolink:produces"
          },
          {
            "subject": "proton_motive_force",
            "predicate": "drives synthesis of",
            "object": "atp",
            "description": "Proton motive force drives ATP synthesis.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.bbabio.2008.09.008",
                "snippet": "gradient ... drives ATP synthesis",
                "notes": "Supports ATP production from the respiratory ion gradient."
              }
            ],
            "predicate_id": "biolink:produces"
          },
          {
            "subject": "thiosulfate",
            "predicate": "oxidized by",
            "object": "sox_multienzyme_system",
            "description": "Thiosulfate is oxidized by the periplasmic Sox multienzyme system.",
            "evidence": [
              {
                "reference": "DOI:10.3390/microorganisms11061436",
                "notes": "Review: \"The Sox multienzyme system... performs periplasmic thiosulfate oxidation.\""
              }
            ]
          },
          {
            "subject": "sulfite",
            "predicate": "oxidized by",
            "object": "soeabc_sulfite_dehydrogenase",
            "description": "Sulfite is oxidized to sulfate by membrane-bound SoeABC sulfite dehydrogenase.",
            "evidence": [
              {
                "reference": "DOI:10.3390/microorganisms11061436",
                "notes": "Review: \"Sulfite produced is oxidized to sulfate by membrane-bound SoeABC.\""
              }
            ]
          },
          {
            "subject": "ammonia",
            "predicate": "oxidized by",
            "object": "ammonia_monooxygenase",
            "description": "Ammonia is oxidized by ammonia monooxygenase (AMO) in ammonia-oxidizing lithotrophs.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s40168-025-02290-9",
                "notes": "Key NH4+ oxidation enzymes including ammonia monooxygenase (AMO); canonical enzyme role."
              }
            ]
          },
          {
            "subject": "hydroxylamine",
            "predicate": "oxidized by",
            "object": "hydroxylamine_oxidoreductase",
            "description": "Hydroxylamine is oxidized by hydroxylamine oxidoreductase (HAO).",
            "evidence": [
              {
                "reference": "DOI:10.1186/s40168-025-02290-9",
                "notes": "Key NH4+ oxidation enzymes including hydroxylamine oxidoreductase (HAO)."
              }
            ]
          },
          {
            "subject": "nitrite",
            "predicate": "oxidized by",
            "object": "nitrite_oxidoreductase",
            "description": "Nitrite is oxidized to nitrate by nitrite oxidoreductase (NXR).",
            "evidence": [
              {
                "reference": "DOI:10.1128/mbio.00749-25",
                "notes": "Nitrite further oxidized to nitrate by a nitrite oxidoreductase gene (nxr)."
              }
            ]
          },
          {
            "subject": "molecular_oxygen",
            "predicate": "serves as terminal acceptor for",
            "object": "sulfur_oxidation_process",
            "description": "Molecular oxygen serves as a terminal electron acceptor for aerobic sulfur oxidation.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41579-024-01104-3",
                "notes": "Sulfur oxidation susceptible to oxidation by electron acceptors; aerobic sulfur oxidation contexts."
              }
            ]
          },
          {
            "subject": "sox_multienzyme_system",
            "predicate": "participates in",
            "object": "sulfur_oxidation_process",
            "description": "The Sox multienzyme system is a prominent pathway for oxidation of reduced sulfur compounds.",
            "evidence": [
              {
                "reference": "DOI:10.3390/microorganisms11061436",
                "snippet": "The Sox multienzyme complex, first described using the model organism Paracoccus panthotrophus, is widespread in photo- and chemotrophic sulfur-oxidizing bacteria and appears to be the most prominent sulfur oxidation system",
                "notes": "The review identifies the multicomponent Sox system as a sulfur-oxidation pathway rather than a single enzyme."
              }
            ],
            "predicate_id": "biolink:participates_in"
          },
          {
            "subject": "soeabc_sulfite_dehydrogenase",
            "predicate": "participates in",
            "object": "sulfur_oxidation_process",
            "description": "Membrane-bound SoeABC participates in sulfur oxidation by oxidizing sulfite to sulfate.",
            "evidence": [
              {
                "reference": "DOI:10.3390/microorganisms11061436",
                "snippet": "sulfite, which is subsequently oxidized by the activity of the membrane-bound protein SoeABC (sulfite dehydrogenase) to sulfate",
                "notes": "The review explicitly places SoeABC in the sulfite-to-sulfate step of sulfur oxidation."
              }
            ],
            "predicate_id": "biolink:participates_in"
          },
          {
            "subject": "sox_multienzyme_system",
            "predicate": "feeds electrons into",
            "object": "membrane_electron_transport_chain",
            "description": "Complete Sox-mediated thiosulfate oxidation supplies electrons to energy-conserving electron transport.",
            "evidence": [
              {
                "reference": "DOI:10.3390/microorganisms11061436",
                "snippet": "The yield of the respective reaction is 8 electrons/1 mol of thiosulfate for the electron transport systems",
                "notes": "The review quantifies the electrons supplied by complete Sox thiosulfate oxidation to electron-transport systems."
              }
            ],
            "predicate_id": "METPO:2007402"
          },
          {
            "subject": "ammonia_monooxygenase",
            "predicate": "produces",
            "object": "hydroxylamine",
            "description": "In bacterial ammonia oxidation, ammonia monooxygenase converts ammonia to hydroxylamine.",
            "evidence": [
              {
                "reference": "DOI:10.1128/jb.185.9.2759-2773.2003",
                "snippet": "NH3 + O2 + 2H+ + 2e\u2212 \u2192 NH2OH + H2O",
                "notes": "The primary N. europaea genome paper gives the AMO-catalyzed first reaction of ammonia oxidation explicitly."
              }
            ],
            "predicate_id": "METPO:2007800"
          },
          {
            "subject": "hydroxylamine_oxidoreductase",
            "predicate": "produces",
            "object": "nitrite",
            "description": "In the bacterial branch represented here, hydroxylamine oxidoreductase oxidizes hydroxylamine to nitrite.",
            "evidence": [
              {
                "reference": "DOI:10.1128/jb.185.9.2759-2773.2003",
                "snippet": "NH2OH + H2O \u2192 NO2\u2212 + 5H+ + 4e\u2212",
                "notes": "The primary N. europaea paper gives the HAO-associated second reaction; the graph scope does not project this bacterial route onto ammonia-oxidizing archaea."
              }
            ],
            "predicate_id": "METPO:2007800"
          },
          {
            "subject": "hydroxylamine_oxidoreductase",
            "predicate": "feeds electrons into",
            "object": "membrane_electron_transport_chain",
            "description": "Electrons released during hydroxylamine oxidation enter the respiratory electron-transport chain through cytochromes and ubiquinone.",
            "evidence": [
              {
                "reference": "DOI:10.1128/jb.185.9.2759-2773.2003",
                "snippet": "Electrons from hydroxylamine oxidation flow through cytochrome c554 and cytochrome cm552 into the electron transport chain at the level of ubiquinone",
                "notes": "The primary N. europaea study directly connects the HAO branch to membrane electron transport."
              }
            ],
            "predicate_id": "METPO:2007402"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-08-24T14:00:00-07:00",
        "curator": "codex",
        "action": "REVIEWED_CAUSAL_GRAPH_PROTEIN_TAXON",
        "changes": "Added a DOI-backed strain-level N. europaea canonical example and reviewed AmoA alpha-subunit example, upgraded the species citation to DOI, and documented Sox, SoeABC, and NXR as reviewed label-only multisystem or multicomponent nodes.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-05T01:35:46.875909+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-08T00:00:00-07:00",
        "curator": "codex",
        "action": "ADDED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed causal graph for inorganic electron donors, respiratory electron transport, proton motive force, and ATP synthesis.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000009\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T08:21:50Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (rdfs:subClassOf\u00d72, biolink:produces\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:41:04Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (METPO:1007502\u00d71, METPO:1007500\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T08:14:33Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0022900\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-26T02:30:13Z",
        "curator": "claude",
        "action": "RETYPE_CAUSAL_NODES",
        "changes": "Re-typed 1 causal-node node_type field(s) to align with CausalNodeTypeEnum semantics: proton motive force: BIOLOGICAL_PROCESS \u2192 STATE \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-13T21:03:27Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:produces\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-14T07:26:20Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007403\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 6 evidence-backed generic edges (12 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:20Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 5 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:16094\u00d71, CHEBI:16134\u00d71, CHEBI:15429\u00d71, CHEBI:15379\u00d71, GO:0019417\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:34Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:16301\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:23:55Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0018597\u00d71, GO:0033740\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-05T12:00:00Z",
        "curator": "claude",
        "action": "REVERSE_CAUSAL_EDGE_DIRECTION",
        "changes": "Reversed 1 causal edge from <trait> uses electron donor <chemical> to <chemical> enables <trait> (predicate_id METPO:2000009 -> RO:0002327), issue 295. METPO:2000009 is rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so the trait-subject form entailed that this TRAIT node is a microbe; CausalNodeTypeEnum has no organism member, so no causal-graph edge can satisfy that domain. Evidence unchanged; only subject/predicate/object/predicate_id and the edge description moved. Note RO:0002327 has range 'biological process or activity', so the new form is not fully range-correct either - tracked in issue 302.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 1 causal edge(s) off enables/RO:0002327 with a TRAIT object (1 to has electron donor), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them. 1 electron edge(s) were also reversed back to trait -> chemical, restoring the donor/acceptor role that PR 300 collapsed onto enables (issue 303); the organism-subject problem that forced that collapse does not arise here because these predicates take a causal-node domain rather than METPO:2000001's microbe domain (issue 301).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-17T02:00:00Z",
        "curator": "claude",
        "action": "NORMALISE_NODE_SENSE",
        "changes": "One node_id per SENSE (issues 356, 384): molecular_oxygen is the chemical sense here. The molecule, not the condition \u2014 the dioxygen participating in the reaction the graph describes. Normalised onto molecular_oxygen, the id 20 other chemical occurrences already use, so one id means one sense corpus-wide (issues 356, 384).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-30T20:34:43Z",
        "curator": "codex",
        "action": "CONNECT_CAUSAL_GRAPH_COMPONENTS",
        "changes": "Connected the seven lithotrophic graph components with six tracked, snippet-backed relations. Sox and SoeABC now join the sulfur-oxidation branch to electron transport; the explicitly bacterial AMO-HAO branch now joins ammonia, hydroxylamine, nitrite, NXR, and electron transport. No new paid research was commissioned (#183, #426).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-22T01:35:00Z",
        "curator": "claude",
        "action": "CURATE_PROTEIN_TAXON_EXAMPLE",
        "changes": "Added reviewed N. europaea ATCC 19718 HAO protein_example UniProtKB:Q50925 (hao1, v155) on hydroxylamine_oxidoreductase (DOI:10.1128/jb.185.9.2759-2773.2003), updated scope_notes, and refreshed UniProtKB:Q04507 entry_version 126 -> 127 on ammonia_monooxygenase.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000153",
    "label": "lysine decarboxylase activity",
    "definition": "A physiological enzyme-activity phenotype in which a cell produces active lysine decarboxylase enzymes that decarboxylate L-lysine to cadaverine and carbon dioxide.",
    "definition_source": "https://iubmb.qmul.ac.uk/enzyme/EC4/1/1/18.html",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "https://iubmb.qmul.ac.uk/enzyme/EC4/1/1/18.html",
        "snippet": "Reaction: L-lysine = cadaverine + CO2",
        "notes": "The NC-IUBMB EC 4.1.1.18 entry defines lysine decarboxylase by its accepted name and reaction from L-lysine to cadaverine and CO2, grounding the enzyme activity named by the organism-level phenotype."
      },
      {
        "reference": "DOI:10.1128/jb.01306-06",
        "snippet": "Unexpectedly, the tolerance of P(i)-starved cells to fermentation acids was markedly increased as a result of the activity of the inducible CadBA lysine-dependent acid resistance system that consumes one proton and produces the diamine cadaverine.",
        "notes": "Moreau showed that the Escherichia coli inducible CadBA lysine-dependent acid resistance system produces cadaverine during phosphate starvation."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:562",
        "taxon_label": "Escherichia coli",
        "note": "Moreau reported CadBA lysine-dependent acid resistance activity in phosphate-starved Escherichia coli.",
        "reference": "DOI:10.1128/jb.01306-06"
      }
    ],
    "discussions": [
      {
        "discussion_id": "lysine-decarboxylase-activity-xref-gap",
        "prompt": "Resolve an exact external ontology class for lysine decarboxylase activity before adding a TraitRecord xref.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "GO:0008923 carries the same lysine decarboxylase activity label but denotes the enzyme molecular function rather than the organism-level lysine decarboxylase production phenotype, so it is appropriate as a causal-node grounding rather than an equivalent TraitRecord xref.",
        "posed_by": "codex",
        "posed_date": "2026-09-12"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-12T01:35:50Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted lysine decarboxylase activity as a URL/DOI-backed TraitRecord after a repository-wide duplicate review covering ignored and hidden files; METPO has no exact lysine decarboxylase activity class yet.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000634",
    "label": "macropinocytosis",
    "definition": "A physiological phenotype in which a microbial organism internalizes bulk extracellular fluid by closing actin-driven plasma-membrane ruffles into large intracellular vesicles.",
    "definition_source": "DOI:10.1242/jcs.213736",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000635"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1242/jcs.213736",
        "snippet": "Macropinocytosis is a conserved endocytic process used by Dictyostelium amoebae for feeding on liquid medium.",
        "notes": "PMID:29440238, PMC5897714. Scientific ABSTRACT quote. Introduction supports the ruffle-closure definition. Relevant uptake Results, Methods, Discussion and actual Figure 2 were read at https://pmc.ncbi.nlm.nih.gov/articles/PMC5897714/. Figure 2E reports P=0.057 for DdB formation-rate upregulation; do not call this significant. Diameter measurements use a transgenic reporter, unlike the dextran formation assay. Other figures and supplements were not visually audited."
      },
      {
        "reference": "DOI:10.7554/eLife.04940",
        "snippet": "These cells can also internalise bulk fluid without the guidance of a particle using a closely related process, macropinocytosis",
        "notes": "PMID:25815683, PMC4374526. Contiguous Introduction quote, not the scientific Abstract or eLife digest. Relevant Results, confocal Methods, Discussion, Table 2 and actual Figure 3 were read at https://pmc.ncbi.nlm.nih.gov/articles/PMC4374526/. Figure 3C measures formation events; Figure 3B single sections cannot quantify cumulative uptake. Other figures and movies were not visually audited."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:44689",
        "taxon_label": "Dictyostelium discoideum",
        "reference": "DOI:10.7554/eLife.04940",
        "note": "Wild-type parental DdB cells freshly harvested from bacterial growth, observed by dextran imaging in Figure 3C; not Ax2, AX4, NF1 knockouts or reporter transformants. Table 2 links DdB to DdB(Wel). Strain genealogy at https://link.springer.com/article/10.1186/gb-2008-9-4-r75 identifies a laboratory-selected NC4 clone with copy-number differences, not an unchanged original wild isolate. NCBI EFetch verified the name and species rank on 2026-10-06; this ID does not identify the strain."
      }
    ],
    "discussions": [
      {
        "discussion_id": "macropinocytosis-scope-and-hierarchy",
        "prompt": "Keep bulk-fluid uptake distinct from neighboring uptake traits.",
        "kind": "CURATION_TODO",
        "status": "RESOLVED",
        "rationale": "Retain phenotype METPO:1000059 pending a closer endocytic capability hierarchy. This is uptake by a microbe, not microbial induction of uptake by a host cell. Phagocytosis traitmech:000627 is particle engulfment, phagotrophy traitmech:000628 requires nutritional assimilation, and trogocytosis traitmech:000633 removes portions of living cells. These are neither equivalents nor disjoint organismal capabilities. Generic pinocytosis is broader; its existing phagocytosis discussion mention is not an exact unresolved macropinocytosis node. Membrane ruffling without closure, solute transport alone and uptake into small endocytic vesicles are insufficient. No fixed diameter cutoff, enhanced uptake rate, axenic growth or nutrition is required. No unverified synonym or process-level ontology xref is asserted.",
        "posed_by": "codex",
        "posed_date": "2026-10-06",
        "resolved_date": "2026-10-06",
        "resolution_note": "Added pinocytosis traitmech:000635 as the direct broader phenotype. The existing ruffle-mediated bulk-fluid definition entails vesicular fluid uptake; its definition, evidence and DdB example are unchanged. This resolves the temporary phenotype-parent gap, not the separate native-mechanism discussion or any ontology equivalence. Preserve the historical v510 phenotype axiom and add METPO:1058700 SubClassOf METPO:1058800 on upstream adoption."
      },
      {
        "discussion_id": "macropinocytosis-native-mechanism",
        "prompt": "Separate native capability from mutant and reporter mechanisms.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "The papers share a research group and organism; they are not independent taxon replication. NF1 loss enhances uptake but is not required for the phenotype. Do not equate a drug response, localization or sequence similarity with a universal causal dependency. Protein accessions, native functional scope and remaining figures require review before adding protein examples or a causal graph.",
        "posed_by": "codex",
        "posed_date": "2026-10-06"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-06T04:39:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added macropinocytosis with two DOI-backed source snippets and a parental DdB-qualified example. Ignored-and-hidden searches and pinned METPO review found no exact record. Reserved METPO:1058700 in v510. Distinguished native uptake from axenic mutants, reporter measurements and universal mechanisms.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-06T05:29:34Z",
        "curator": "codex",
        "action": "REFINE_PINOCYTOSIS_PARENT",
        "changes": "Refined the direct parent to pinocytosis traitmech:000635 and resolved the temporary hierarchy discussion by definition-based inference. Preserved identity, definition, evidence, canonical example, mechanism gap, earlier history and the true broader historical proposal axiom.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000176",
    "label": "magnetotaxis",
    "definition": "A behavioral physiology in which magnetosome-bearing motile cells align with geomagnetic field lines and navigate along that axis.",
    "definition_source": "DOI:10.1128/JB.00398-20",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "synonyms": [
      {
        "synonym_text": "magnetotactic",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1038/nrmicro842"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1128/JB.00398-20",
        "snippet": "Magnetotactic bacteria are aquatic or sediment-dwelling microorganisms able to take advantage of the Earth's magnetic field for directed motility",
        "notes": "Muller et al. review bacterial magnetotaxis as directed motility aligned to Earth's magnetic field."
      },
      {
        "reference": "DOI:10.1038/s41396-018-0098-9",
        "snippet": "The origin and evolution of magnetoreception, which in diverse prokaryotes and protozoa is known as magnetotaxis and enables these microorganisms to detect Earth's magnetic field for orientation and navigation",
        "notes": "Lin et al. define magnetotaxis as the magnetoreceptive orientation and navigation behavior of magnetotactic microorganisms."
      },
      {
        "reference": "DOI:10.1128/mbio.01649-23",
        "snippet": "To efficiently navigate within the geomagnetic field, magnetotactic bacteria (MTB) align their magnetosome organelles into chains",
        "notes": "Awal et al. support the mechanism-level distinction that magnetosome chain alignment underlies geomagnetic navigation."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:431944",
        "taxon_label": "Magnetospirillum gryphiswaldense MSR-1",
        "note": "Awal et al. used Magnetospirillum gryphiswaldense as the genetically tractable host for functional expression of magnetotaxis-associated MamK-family magnetoskeleton proteins.",
        "reference": "DOI:10.1128/mbio.01649-23"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-12T16:17:24Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted magnetotaxis as a DOI-backed TraitRecord after a repository-wide duplicate review covering ignored and hidden files; METPO has only an obsolete magnetotaxis class in the local snapshot and the replacement placeholder is reserved in proposals/metpo_traitmech_v53.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-12T16:36:30Z",
        "curator": "codex",
        "action": "ADD_SYNONYM",
        "changes": "Moved the adjectival magnetotactic related synonym from the magnetosome organelle record onto the new magnetotaxis physiology trait; resolves issue 851.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-12T17:05:00Z",
        "curator": "codex",
        "action": "EDIT_EVIDENCE",
        "changes": "Extended the Lin et al. magnetotaxis evidence snippet to the beginning of its source sentence after PR review requested stricter snippet verification; resolves issue 852.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-21T21:12:25Z",
        "curator": "claude",
        "action": "CURATE_CAUSAL_GRAPH",
        "changes": "Added NONMECHANISTIC causal_graphs entry (magnetotaxis_magnetosome_navigation_sketch) anchored on existing verbatim record evidence snippets.",
        "llm_assisted": true
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "magnetotaxis_magnetosome_navigation_sketch",
        "title": "Magnetosome chain alignment and geomagnetic navigation",
        "description": "Evidence-backed physiological sketch linking magnetosome chain alignment to magnetoreception and directed motility along geomagnetic field lines.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "Organelle-to-behavior sketch backed by DOI:10.1128/JB.00398-20, DOI:10.1038/s41396-018-0098-9, and DOI:10.1128/mbio.01649-23; MamK/MamJ magnetoskeleton protein examples are curated on the companion `data/traits/morphology/magnetosome.yaml` organelle record rather than duplicated here without a protein node.",
        "nodes": [
          {
            "node_id": "magnetotaxis_trait",
            "label": "magnetotaxis",
            "node_type": "TRAIT",
            "grounding": "traitmech:000176",
            "description": "Behavioral physiology in which magnetosome-bearing motile cells align and navigate along geomagnetic field lines."
          },
          {
            "node_id": "magnetotaxis_magnetosome_organelle",
            "label": "magnetosome",
            "node_type": "ORGANELLE",
            "grounding": "GO:0110143",
            "description": "Membrane-bounded magnetic-mineral organelle aligned into intracellular chains in magnetotactic bacteria."
          },
          {
            "node_id": "magnetotaxis_magnetoreception",
            "label": "magnetoreception",
            "node_type": "BIOLOGICAL_PROCESS",
            "grounding": "GO:0050958",
            "description": "Detection and alignment with Earth's geomagnetic field for cellular orientation and navigation."
          },
          {
            "node_id": "magnetotaxis_directed_motility",
            "label": "taxis",
            "node_type": "BIOLOGICAL_PROCESS",
            "grounding": "GO:0042330",
            "description": "Directed microbial motility along geomagnetic field lines."
          }
        ],
        "edges": [
          {
            "subject": "magnetotaxis_magnetosome_organelle",
            "predicate": "enables",
            "predicate_id": "RO:0002327",
            "object": "magnetotaxis_magnetoreception",
            "description": "Alignment of magnetosome organelles into chains enables geomagnetic field navigation.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mbio.01649-23",
                "snippet": "To efficiently navigate within the geomagnetic field, magnetotactic bacteria (MTB) align their magnetosome organelles into chains",
                "notes": "Awal et al. state that magnetotactic bacteria align their magnetosome organelles into chains to navigate within the geomagnetic field."
              }
            ]
          },
          {
            "subject": "magnetotaxis_magnetoreception",
            "predicate": "enables",
            "predicate_id": "RO:0002327",
            "object": "magnetotaxis_directed_motility",
            "description": "Prokaryotic magnetoreception enables detection of Earth's magnetic field for orientation and directed navigation.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41396-018-0098-9",
                "snippet": "The origin and evolution of magnetoreception, which in diverse prokaryotes and protozoa is known as magnetotaxis and enables these microorganisms to detect Earth's magnetic field for orientation and navigation",
                "notes": "Lin et al. describe magnetotaxis as prokaryotic magnetoreception enabling detection of Earth's magnetic field for orientation and navigation."
              }
            ]
          },
          {
            "subject": "magnetotaxis_directed_motility",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "magnetotaxis_trait",
            "description": "Directed motility guided by Earth's magnetic field confers the magnetotaxis phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1128/JB.00398-20",
                "snippet": "Magnetotactic bacteria are aquatic or sediment-dwelling microorganisms able to take advantage of the Earth's magnetic field for directed motility",
                "notes": "Muller et al. define magnetotactic bacteria by their ability to use Earth's magnetic field for directed motility."
              }
            ]
          }
        ]
      }
    ]
  },
  {
    "identifier": "traitmech:000611",
    "label": "mating-type switching",
    "definition": "A fungal phenotype enabling conversion from one mating type to another, either reversibly or irreversibly.",
    "definition_source": "DOI:10.5598/imafungus.2015.06.01.13",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.5598/imafungus.2015.06.01.13",
        "snippet": "In this mating strategy, an individual of one mating type can undergo a switch to the opposite mating type, either bidirectionally (reversibly) or unidirectionally (irreversibly).",
        "notes": "2015 terminology review, PMID:26203424, PMC4500084. Exact sentence from the directly retrieved full-text XML section MATING TYPE SWITCHING (s3), including both subsections read end-to-end. This is definition authority, not experimental replication or an abstract quote. The umbrella includes reversible yeast switching and irreversible mating-type alteration in filamentous fungi. A single founder can yield a mixed-mating-type colony; cellular mating identity and colony-level self-fertility are distinct. The record does not universalize the review's yeast MAT architecture or require a particular endonuclease. Figure 1 and the other mechanism category sections remain uninspected."
      },
      {
        "reference": "DOI:10.1534/genetics.107.076315",
        "snippet": "Schizosaccharomyces pombe cells can switch between two mating types, plus (P) and minus (M).",
        "notes": "Yamada-Inagawa et al. (2007), PMID:17660548. Exact first sentence of the scientific abstract directly retrieved from Europe PMC core metadata. The study tests synthesis-dependent strand annealing using strains with two engineered mutant P donor cassettes and recovery of wild-type P information at mat1 through heteroduplex formation and repair. This is an in-vivo mechanistic test, not natural-isolate provenance. Do not require this cassette arrangement, exactly two mating types, or the S. pombe replication program for all fungi. Full text, figures, supplements and original strain provenance remain uninspected: the full-text XML endpoint returned HTTP 500 and the PDF mirror returned HTTP 403. The authoritative abstract is indexed and readable despite those access failures."
      },
      {
        "reference": "DOI:10.1371/journal.pgen.1006981",
        "snippet": "a chromosomal looping out-based mechanism underpins irreversible unidirectional mating-type alteration in filamentous fungi.",
        "notes": "Yun et al. (2017), PMID:28892488, PMC5608430. Exact contiguous clause from Conclusions (sec017), not the scientific abstract or author summary. Scientific abstract, strain/culture Methods, Results sec005-sec007 and Discussion sec013/sec015 were read. Actual Figures 3 and 4 and their captions were inspected. Results and Figure 3 identify DR2 deletion in Cs23-derived T10; Discussion sec013 instead says DR1. Retain the figure-supported DR2 identity, not that conflicting wording. Figure 4 separates fertile Cs23 from T10 aggregates and Cs27-derived transformants that can form perithecia without ascospores. The authors support irreversible MAT loss in C. spinulosa; the detailed nuclear-recognition mechanism remains a model. Original natural provenance, other figures, supplements and unread experimental sections remain unverified. Neither reference-strain labels nor transgenic constructs establish natural canonical examples."
      }
    ],
    "discussions": [
      {
        "discussion_id": "mating-type-switching-scope",
        "prompt": "Preserve reversible and irreversible switching without equating it with self-fertility.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "This is a fungal switching capability, not a literal MAT locus, HO gene, donor cassette, direct repeat or static sequence feature. A mating-type change within a cell or developing lineage is distinct from ordinary segregation of mating types among sexual progeny. Resolve cellular, nuclear and colony-level assay scope before assigning the trait to an organism. Switching can contribute to homothallism but is not identical to it; a switched nucleus need not make the whole colony uniformly another mating type. Homothallism, heterothallism, ploidy, heterokaryosis and parasexuality are not is-a parents. PHYSIOLOGY is a filesystem category. Do not require reversibility, one cassette architecture or a universal cell-cycle stage. Resolve external phenotype/process mappings and the scope of mating-type alteration or interconversion before adding exact synonyms or xrefs.",
        "posed_by": "codex",
        "posed_date": "2026-10-04"
      },
      {
        "discussion_id": "mating-type-switching-examples-and-mechanism",
        "prompt": "Ground native switching mechanisms and natural strain examples before expanding the record.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Complete uninspected primary experiments and supplements, verify natural strain provenance and resolve active taxonomy before adding canonical examples. Distinguish sequence rearrangement, expressed mating identity, compatibility and completed sexual reproduction; no one readout establishes all the others. An engineered perturbation supports its specific experimental dependency, not a universal native mechanism. Resolve native protein accessions and source-bounded causal claims before adding a graph; do not use NONMECHANISTIC to bypass unresolved grounding. Keep actual abstract-verifier outcomes distinct from manual full-text checks. Source figure/Results evidence takes precedence over the conflicting repeat label noted in the evidence.",
        "posed_by": "codex",
        "posed_date": "2026-10-04"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-05T02:54:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added mating-type switching with a DOI-backed terminology review and two primary studies, each with an exact source snippet. Included reversible and irreversible scope, separated switching from MAT content and sexual-cycle readouts, and inspected primary Figures 3 and 4 to retain a source DR1/DR2 discrepancy. Ignored-and-hidden novelty searches and structured METPO review found no exact record. Reserved METPO:1056500 in v488 under released phenotype. Deferred canonical examples, lexical mappings and protein-resolved graphs.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000650",
    "label": "methanotrophic",
    "definition": "A trophic type in which an organism uses methane as the primary carbon and energy source through oxidation of methane to carbon dioxide.",
    "definition_source": "DOI:10.1039/D3CY00737E",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000631"
    ],
    "synonyms": [
      {
        "synonym_text": "methanotroph",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "created_by": "Luke Wang",
    "evidence": [
      {
        "reference": "DOI:10.1039/D3CY00737E",
        "snippet": "convert methane to methanol using methane monooxygenase",
        "notes": "Review supports methane monooxygenase as the first aerobic methanotrophy step."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:414",
        "taxon_label": "Methylococcus capsulatus",
        "note": "Model aerobic methanotroph (gammaproteobacterial; particulate and soluble methane monooxygenase); strain Bath.",
        "reference": "PMID:15383840"
      },
      {
        "taxon_id": "NCBITaxon:243233",
        "taxon_label": "Methylococcus capsulatus Bath",
        "note": "Strain-level aerobic methanotroph paired to reviewed PmoB, the alpha component of its particulate methane monooxygenase.",
        "reference": "DOI:10.1099/13500872-145-5-1235"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "methanotrophic_methane_oxidation",
        "title": "Aerobic methanotrophic methane oxidation mechanism",
        "description": "DOI-backed graph for aerobic methane oxidation from methane to methanol, formaldehyde assimilation, and carbon dioxide production.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "This graph represents aerobic bacterial methanotrophy and explicitly keeps particulate and soluble methane-monooxygenase alternatives separate. The Bath-strain PmoB accession is an alpha component of pMMO, not the complete three-subunit complex.",
        "nodes": [
          {
            "node_id": "methanotrophic_trait",
            "label": "methanotrophic",
            "node_type": "TRAIT",
            "grounding": "METPO:1000650",
            "description": "Trophic type using methane as carbon and energy source."
          },
          {
            "node_id": "methane",
            "label": "methane",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:16183",
            "description": "Primary C1 substrate of methanotrophs."
          },
          {
            "node_id": "molecular_oxygen",
            "label": "molecular oxygen",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:15379",
            "description": "Oxidant used by aerobic methane monooxygenases."
          },
          {
            "node_id": "methane_monooxygenase",
            "label": "methane monooxygenase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Enzyme family catalyzing the first methane oxidation step.",
            "grounding": "GO:0015050"
          },
          {
            "node_id": "intracellular_membrane",
            "label": "intracellular membrane",
            "node_type": "CELLULAR_LOCALIZATION",
            "description": "Localization associated with particulate methane monooxygenase.",
            "grounding": "GO:0031090"
          },
          {
            "node_id": "methanol",
            "label": "methanol",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:17790",
            "description": "First oxidation product of methane."
          },
          {
            "node_id": "methanol_dehydrogenase",
            "label": "methanol dehydrogenase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Enzyme oxidizing methanol to formaldehyde.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "The label spans calcium- and lanthanide-dependent PQQ enzymes and other methanol-dehydrogenase classes; the cited graph does not select one exact family."
          },
          {
            "node_id": "formaldehyde",
            "label": "formaldehyde",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:16842",
            "description": "Central C1 intermediate for assimilation or oxidation."
          },
          {
            "node_id": "formaldehyde_assimilation",
            "label": "formaldehyde assimilation",
            "node_type": "PATHWAY",
            "description": "RuMP or serine pathway incorporation of formaldehyde into biomass.",
            "grounding": "GO:0019649"
          },
          {
            "node_id": "carbon_dioxide",
            "label": "carbon dioxide",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:16526",
            "description": "Oxidized C1 product of methane metabolism."
          },
          {
            "node_id": "copper",
            "label": "copper",
            "node_type": "CHEMICAL",
            "description": "Copper availability acts as a regulatory and cofactor lever in methanotrophy."
          },
          {
            "node_id": "particulate_methane_monooxygenase",
            "label": "particulate methane monooxygenase (pMMO)",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Membrane-bound copper-containing methane monooxygenase complex.",
            "grounding": "GO:0015050",
            "gene_symbols": [
              "pmoA",
              "pmoB",
              "pmoC"
            ],
            "operon": "pmoCAB",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:G1UBD1",
                "protein_label": "Particulate methane monooxygenase alpha subunit",
                "gene_symbol": "pmoB1",
                "taxon_id": "NCBITaxon:243233",
                "taxon_label": "Methylococcus capsulatus Bath",
                "entry_status": "REVIEWED",
                "retrieved_on": "2026-10-22",
                "entry_version": 77,
                "sequence_version": 1,
                "role": "PmoB alpha component of the Bath-strain pMMO; this accession is not presented as the full PmoABC complex.",
                "evidence": [
                  {
                    "reference": "DOI:10.1099/13500872-145-5-1235",
                    "snippet": "multiple pmo gene copies contribute to particulate methane monooxygenase activity",
                    "notes": "The primary Bath-strain study tests pmo-copy contributions to methane oxidation; UniProt verifies reviewed PmoB G1UBD1 and the strain taxon."
                  }
                ]
              }
            ]
          },
          {
            "node_id": "soluble_methane_monooxygenase",
            "label": "soluble methane monooxygenase (sMMO)",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Cytoplasmic iron-containing methane monooxygenase, expressed under low copper.",
            "grounding": "GO:0015050",
            "gene_symbols": [
              "mmoX",
              "mmoY",
              "mmoZ"
            ],
            "operon": "mmoXYZ"
          },
          {
            "node_id": "methanobactin",
            "label": "methanobactin",
            "node_type": "CHEMICAL",
            "description": "Ribosomally synthesized copper-chelating chalkophore.",
            "grounding": "CHEBI:222862"
          },
          {
            "node_id": "cuprous_ion",
            "label": "Cu(I)",
            "node_type": "CHEMICAL",
            "description": "Cuprous ion bound with high affinity by methanobactin."
          },
          {
            "node_id": "copper_acquisition",
            "label": "copper acquisition",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Uptake of copper required for pMMO function."
          }
        ],
        "edges": [
          {
            "subject": "methanotrophic_trait",
            "predicate": "uses substrate",
            "object": "methane",
            "description": "Methane is the defining carbon and energy source for methanotrophy.",
            "evidence": [
              {
                "reference": "DOI:10.1039/D3CY00737E",
                "snippet": "methane as carbon and energy sources",
                "notes": "Review places methane among C1 compounds used by methanotrophs."
              }
            ]
          },
          {
            "subject": "methane_monooxygenase",
            "predicate": "oxidizes",
            "object": "methane",
            "description": "Methane monooxygenase catalyzes methane oxidation.",
            "evidence": [
              {
                "reference": "DOI:10.1039/D3CY00737E",
                "snippet": "methane oxidation ... catalyzed by two types of methane monooxygenases",
                "notes": "Supports MMO as the enzyme for the first oxidation step."
              }
            ],
            "predicate_id": "METPO:2007803"
          },
          {
            "subject": "methane_monooxygenase",
            "predicate": "uses oxidant",
            "object": "molecular_oxygen",
            "description": "Aerobic methane monooxygenases activate oxygen during methane oxidation.",
            "evidence": [
              {
                "reference": "DOI:10.1039/D3CY00737E",
                "snippet": "activation of molecular oxygen",
                "notes": "Supports oxygen involvement in MMO catalysis."
              }
            ]
          },
          {
            "subject": "methane",
            "predicate": "oxidized to",
            "object": "methanol",
            "description": "The first aerobic methane oxidation product is methanol.",
            "evidence": [
              {
                "reference": "DOI:10.1039/D3CY00737E",
                "snippet": "convert methane to methanol",
                "notes": "Supports methane-to-methanol conversion by MMO."
              }
            ],
            "predicate_id": "METPO:2007405"
          },
          {
            "subject": "methane_monooxygenase",
            "predicate": "located in",
            "object": "intracellular_membrane",
            "description": "Particulate methane monooxygenase is membrane associated in methanotrophs.",
            "evidence": [
              {
                "reference": "DOI:10.1039/D3CY00737E",
                "snippet": "pMMO is located in the characteristic intracellular membrane",
                "notes": "Supports subcellular localization for pMMO."
              }
            ],
            "predicate_id": "biolink:located_in"
          },
          {
            "subject": "methanol_dehydrogenase",
            "predicate": "oxidizes",
            "object": "methanol",
            "description": "Methanol dehydrogenase converts methanol onward to formaldehyde.",
            "evidence": [
              {
                "reference": "DOI:10.1039/D3CY00737E",
                "snippet": "Methanol is oxidized to formaldehyde",
                "notes": "Supports methanol dehydrogenase as the next step."
              }
            ],
            "predicate_id": "METPO:2007803"
          },
          {
            "subject": "formaldehyde",
            "predicate": "participates in",
            "object": "formaldehyde_assimilation",
            "description": "Formaldehyde can be assimilated through RuMP or serine pathways.",
            "evidence": [
              {
                "reference": "DOI:10.1039/D3CY00737E",
                "snippet": "RuMP pathway and the serine pathway",
                "notes": "Supports formaldehyde assimilation routes in methanotrophs."
              }
            ],
            "predicate_id": "biolink:participates_in"
          },
          {
            "subject": "methanotrophic_trait",
            "predicate": "produces",
            "object": "carbon_dioxide",
            "description": "Methane oxidation can continue to carbon dioxide for energy metabolism.",
            "evidence": [
              {
                "reference": "DOI:10.1039/D3CY00737E",
                "snippet": "methane cycle between ... methane and CO2",
                "notes": "Supports methane oxidation in the methane-carbon dioxide cycle; graph focuses on aerobic methanotrophy."
              }
            ],
            "predicate_id": "METPO:2007800"
          },
          {
            "subject": "copper",
            "predicate": "positively regulates",
            "object": "particulate_methane_monooxygenase",
            "description": "High copper favors pMMO expression (the copper switch).",
            "evidence": [
              {
                "reference": "DOI:10.1039/D3CY00737E",
                "notes": "high copper favors pMMO and represses sMMO"
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "copper",
            "predicate": "negatively regulates",
            "object": "soluble_methane_monooxygenase",
            "description": "High copper represses sMMO; low copper favors sMMO (the copper switch).",
            "evidence": [
              {
                "reference": "DOI:10.1039/D3CY00737E",
                "notes": "high copper favors pMMO and represses sMMO; low copper/biomass favors sMMO"
              }
            ],
            "predicate_id": "RO:0002212"
          },
          {
            "subject": "methanobactin",
            "predicate": "binds",
            "object": "cuprous_ion",
            "description": "Methanobactin binds Cu(I) with high affinity.",
            "evidence": [
              {
                "reference": "DOI:10.1021/acs.chemrev.3c00727",
                "notes": "Mbns are ribosomally synthesized ... that bind Cu(I) with particularly high affinity"
              }
            ]
          },
          {
            "subject": "methanobactin",
            "predicate": "enables",
            "object": "copper_acquisition",
            "description": "Methanobactin-mediated copper chelation enables copper uptake.",
            "evidence": [
              {
                "reference": "DOI:10.1039/D3CY00737E",
                "notes": "some methanotrophs produce methanobactin (high affinity for Cu(I)) for copper collection"
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "copper_acquisition",
            "predicate": "promotes",
            "object": "particulate_methane_monooxygenase",
            "description": "Copper acquisition supplies the cofactor required for pMMO activity.",
            "evidence": [
              {
                "reference": "DOI:10.1021/acs.chemrev.3c00727",
                "notes": "As a required cofactor for pMMO activity ... copper is central to methanotroph physiology"
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "particulate_methane_monooxygenase",
            "predicate": "example of",
            "object": "methane_monooxygenase",
            "description": "Particulate MMO is one of the two methane-monooxygenase enzyme types.",
            "evidence": [
              {
                "reference": "DOI:10.3109/10409238.2012.697865",
                "snippet": "There are two types of MMOs. The soluble form (sMMO)",
                "notes": "Verified in the public full text, which immediately identifies the membrane-bound particulate MMO as the other type."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "methanol_dehydrogenase",
            "predicate": "produces",
            "object": "formaldehyde",
            "description": "Methanol dehydrogenase converts methanol to formaldehyde, joining methane oxidation to the assimilation branch.",
            "evidence": [
              {
                "reference": "DOI:10.3109/10409238.2012.697865",
                "snippet": "Methanol is further converted to formaldehyde by methanol dehydrogenase",
                "notes": "Verified against the public full text."
              }
            ],
            "predicate_id": "METPO:2007800"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.876493+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-08T00:00:00-07:00",
        "curator": "codex",
        "action": "ADDED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed causal graph for aerobic methane oxidation by methane monooxygenase and downstream C1 metabolism.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000016\u00d72, METPO:2000202\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T05:49:25Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:located_in\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T21:30:07Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007405\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T05:05:15Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A0A3YNQ7\u00d71, UniProtKB:A0A010SCY7\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-26T05:00:48Z",
        "curator": "claude",
        "action": "RENAME_PREDICATE_LABELS",
        "changes": "Renamed 1 causal-edge predicate label(s) to align with existing groundings: input to \u2192 participates in \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-26T05:00:51Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:participates_in\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-14T05:51:47Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0019649\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 7 evidence-backed generic edges (10 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:14Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 4 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:encodes\u00d72, RO:0002327\u00d71, RO:0002213\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:34Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0031090\u00d71, CHEBI:222862\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:21:12Z",
        "curator": "claude",
        "action": "RETRACT_DEAD_UNIPROT_GROUNDINGS",
        "changes": "Retracted 2 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:23:55Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0015050\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-04T03:08:16Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002213\u00d71, RO:0002212\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T02:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES_PART2",
        "changes": "Re-grounded 3 causal edge(s) off microbe-domain METPO predicates onto their causal-graph counterparts (2 to oxidizes, 1 to produces), issue 301 part 2. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Each replacement is a 1:1 mirror of its source predicate that changes only the domain, so the claim each edge makes is unchanged and directions are unchanged. The replacements are proposed in proposals/metpo_traitmech_v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-07T04:00:00Z",
        "curator": "claude",
        "action": "REGROUND_CAUSAL_EDGE",
        "changes": "Re-grounded the `encodes` edge(s) from biolink:encodes to METPO:2007813, issue 342. biolink:encodes is NOT a slot in the pinned biolink 4.4.0 model, so the CURIE resolved to nothing upstream while looking like an upstream term to anyone reading this record -- the disclaimer saying otherwise lived in mappings/predicate_grounding.tsv, which is not read at the point of use. RO:0002205 (has gene product) is the nearest real term but relates a GENE to a gene product, whereas these edges relate a gene cluster or operon to a protein complex or a biosynthetic process, which its range does not admit; that mismatch is why the coinage existed. METPO:2007813 is proposed in proposals/metpo_traitmech_v9 and is a placeholder id until METPO mints it, which puts it in the same state as the rest of that cohort rather than in a category of its own.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "CURATE_PROTEIN_TAXON_EXAMPLE",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope methanotrophic_methane_oxidation=MECHANISTIC with scope_notes; marked 1 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (methanol_dehydrogenase); added taxon-paired protein example(s) UniProtKB:G1UBD1 on particulate_methane_monooxygenase (NCBITaxon:243233); regrounded 2 node(s) (particulate_methane_monooxygenase: none->GO:0015050, soluble_methane_monooxygenase: none->GO:0015050); removed 4 node(s) and 2 edge(s) together with their evidence (mmoh_subunits, mmoxyz_genes, pmmo_subunits, pmocab_operon); added canonical example(s) NCBITaxon:243233.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T11:15:00Z",
        "curator": "codex",
        "action": "CONNECT_CAUSAL_GRAPH_COMPONENTS",
        "changes": "Resolved issue #183 graph fragmentation (3 components to 1) with 2 public-source, verbatim-snippet-backed connector(s). No paid research service was called.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-22T01:35:00Z",
        "curator": "claude",
        "action": "REFRESH_UNIPROT_ENTRY_VERSION",
        "changes": "Refreshed UniProtKB entry_version against live UniProt REST on 2026-10-22: UniProtKB:G1UBD1 (76 -> 77 on particulate_methane_monooxygenase).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000651",
    "label": "methylotrophic",
    "definition": "A trophic type in which an organism obtains energy and carbon from reduced one-carbon compounds.",
    "definition_source": "DOI:10.3389/fbioe.2021.787791",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000631"
    ],
    "synonyms": [
      {
        "synonym_text": "TT_methylotroph",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "methylotroph",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "methylotrophy",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.3389/fbioe.2021.787791",
        "snippet": "methanol utilization in methylotrophy",
        "notes": "Review supports methanol oxidation and formaldehyde assimilation as central methylotrophy mechanisms."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:408",
        "taxon_label": "Methylorubrum extorquens",
        "note": "Model facultative methylotroph (formerly Methylobacterium extorquens; strain AM1).",
        "reference": "PMID:12730156"
      },
      {
        "taxon_id": "NCBITaxon:272630",
        "taxon_label": "Methylorubrum extorquens AM1",
        "note": "Strain-level facultative methylotroph paired to reviewed MxaF, the large catalytic component of its MxaFI methanol dehydrogenase.",
        "reference": "DOI:10.1016/0378-1119(90)90457-3"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "methylotrophic_methanol_assimilation",
        "title": "Methanol-based methylotrophy mechanism",
        "description": "DOI-backed graph for methanol oxidation to formaldehyde and assimilation through native methylotrophy pathways.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "This graph combines alternative RuMP and serine assimilation branches and several methanol/formaldehyde oxidation enzyme classes. The AM1 MxaF accession anchors only the calcium-dependent MxaFI branch and is one subunit, not the complete heterotetramer.",
        "nodes": [
          {
            "node_id": "methylotrophic_trait",
            "label": "methylotrophic",
            "node_type": "TRAIT",
            "grounding": "METPO:1000651",
            "description": "Trophic type using reduced one-carbon compounds for carbon and energy."
          },
          {
            "node_id": "methanol",
            "label": "methanol",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:17790",
            "description": "Reduced C1 substrate used by many methylotrophs."
          },
          {
            "node_id": "methanol_dehydrogenase",
            "label": "methanol dehydrogenase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Primary enzyme oxidizing methanol in methylotrophy.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "This umbrella spans unrelated PQQ-dependent and NAD-dependent enzyme families; the graph preserves their alternatives instead of assigning one family term."
          },
          {
            "node_id": "pqq_dependent_mdh",
            "label": "PQQ-dependent methanol dehydrogenase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Periplasmic methanol dehydrogenase class in Gram-negative methylotrophs.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "The node combines MxaFI and XoxF lineages with different subunit and metal requirements, so a single protein-family term would overstate identity."
          },
          {
            "node_id": "periplasmic_space",
            "label": "periplasmic space",
            "node_type": "CELLULAR_LOCALIZATION",
            "description": "Cellular compartment where PQQ-dependent MDH oxidizes methanol in Gram-negative methylotrophs.",
            "grounding": "GO:0042597"
          },
          {
            "node_id": "formaldehyde",
            "label": "formaldehyde",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:16842",
            "description": "Central intermediate produced by methanol oxidation."
          },
          {
            "node_id": "rump_cycle",
            "label": "ribulose monophosphate cycle",
            "node_type": "PATHWAY",
            "description": "Prokaryotic formaldehyde assimilation pathway."
          },
          {
            "node_id": "serine_pathway",
            "label": "serine pathway",
            "node_type": "PATHWAY",
            "description": "Prokaryotic formaldehyde assimilation pathway."
          },
          {
            "node_id": "biomass_precursor",
            "label": "biomass precursor",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Assimilated cellular carbon derived from formaldehyde."
          },
          {
            "node_id": "hexulose_phosphate_synthase",
            "label": "3-hexulose-6-phosphate synthase (Hps)",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Hallmark RuMP-cycle enzyme that condenses formaldehyde for assimilation.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "The cited comparative source supports the Hps activity but does not distinguish a single exact family term across all represented methylotrophs."
          },
          {
            "node_id": "serine_glyoxylate_aminotransferase",
            "label": "serine-glyoxylate aminotransferase (SgaA/SGT)",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Conserved serine-cycle enzyme found across methylotroph genomes.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "SgaA/SGT is used here as a comparative functional label across isozymes; the graph source does not justify one exact family grounding."
          },
          {
            "node_id": "hydroxypyruvate_reductase",
            "label": "hydroxypyruvate reductase (HprA/HPR)",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Ubiquitous serine-cycle enzyme reducing hydroxypyruvate.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "HprA/HPR is an activity-level umbrella across homologous reductases; no exact family term was verified for every organism represented by the graph."
          },
          {
            "node_id": "formaldehyde_dehydrogenase",
            "label": "formaldehyde dehydrogenase (Fld/FDH)",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Enzyme oxidizing formaldehyde to formate during dissimilation.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "The label spans cofactor-distinct formaldehyde oxidation systems; the cited graph does not select one protein family."
          },
          {
            "node_id": "formate",
            "label": "formate",
            "node_type": "CHEMICAL",
            "description": "C1 intermediate produced by formaldehyde oxidation."
          },
          {
            "node_id": "formate_dehydrogenase",
            "label": "formate dehydrogenase (Fdh)",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Enzyme oxidizing formate to CO2 in the dissimilatory branch.",
            "grounding": "GO:0009326"
          },
          {
            "node_id": "carbon_dioxide",
            "label": "carbon dioxide",
            "node_type": "CHEMICAL",
            "description": "Terminal product of C1 dissimilatory oxidation.",
            "grounding": "CHEBI:16526"
          },
          {
            "node_id": "mxa_methanol_dehydrogenase",
            "label": "MxaFI methanol dehydrogenase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Calcium-dependent methanol dehydrogenase of the PQQ alcohol dehydrogenase family.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "MxaFI is a multisubunit enzyme assembled from distinct MxaF and MxaI families; no verified complex CURIE was available for the complete node.",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:P16027",
                "protein_label": "Methanol dehydrogenase [cytochrome c] subunit 1",
                "gene_symbol": "mxaF",
                "taxon_id": "NCBITaxon:272630",
                "taxon_label": "Methylorubrum extorquens AM1",
                "entry_status": "REVIEWED",
                "retrieved_on": "2026-10-22",
                "entry_version": 180,
                "sequence_version": 1,
                "role": "Large catalytic MxaF component of the AM1 MxaFI methanol dehydrogenase; this accession is not presented as the complete enzyme.",
                "evidence": [
                  {
                    "reference": "DOI:10.1016/0378-1119(90)90457-3",
                    "snippet": "AM1 moxF and moxJ genes are involved in methanol oxidation",
                    "notes": "The primary sequence study identifies the AM1 moxF/mxaF gene in methanol oxidation; UniProt verifies reviewed P16027 and the strain taxon."
                  }
                ]
              }
            ]
          },
          {
            "node_id": "pqq",
            "label": "pyrroloquinoline quinone (PQQ)",
            "node_type": "CHEMICAL",
            "description": "Redox cofactor required by methanol dehydrogenases."
          },
          {
            "node_id": "calcium_ion",
            "label": "calcium ion (Ca2+)",
            "node_type": "CHEMICAL",
            "description": "Active-site metal cofactor of MxaFI-type methanol dehydrogenase."
          }
        ],
        "edges": [
          {
            "subject": "methylotrophic_trait",
            "predicate": "uses substrate",
            "object": "methanol",
            "description": "Methanol is a representative reduced C1 substrate for methylotrophy.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fbioe.2021.787791",
                "snippet": "methanol utilization in methylotrophy",
                "notes": "Supports methanol as a methylotrophic substrate; other C1 substrates are not modeled here."
              }
            ]
          },
          {
            "subject": "methanol_dehydrogenase",
            "predicate": "oxidizes",
            "object": "methanol",
            "description": "Methanol dehydrogenase catalyzes the first methanol oxidation step.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fbioe.2021.787791",
                "snippet": "Mdh is a primary enzyme",
                "notes": "Supports methanol dehydrogenase as the primary methanol-utilization enzyme."
              }
            ],
            "predicate_id": "METPO:2007803"
          },
          {
            "subject": "methanol",
            "predicate": "oxidized to",
            "object": "formaldehyde",
            "description": "Methanol oxidation produces formaldehyde for assimilation or further oxidation.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fbioe.2021.787791",
                "snippet": "converts methanol to formaldehyde",
                "notes": "Supports methanol-to-formaldehyde conversion."
              }
            ],
            "predicate_id": "METPO:2007405"
          },
          {
            "subject": "pqq_dependent_mdh",
            "predicate": "located in",
            "object": "periplasmic_space",
            "description": "PQQ-dependent MDH oxidizes methanol in the periplasm of Gram-negative methylotrophs.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fbioe.2021.787791",
                "snippet": "oxidation of methanol occurs in the periplasmic space",
                "notes": "Supports periplasmic localization of PQQ-dependent methanol oxidation."
              }
            ],
            "predicate_id": "biolink:located_in"
          },
          {
            "subject": "pqq_dependent_mdh",
            "predicate": "produces",
            "object": "formaldehyde",
            "description": "PQQ-dependent methanol dehydrogenase produces formaldehyde from methanol.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fbioe.2021.787791",
                "snippet": "converts methanol to formaldehyde",
                "notes": "Source supports formaldehyde as the product of methanol oxidation by methanol dehydrogenases."
              }
            ],
            "predicate_id": "METPO:2007800"
          },
          {
            "subject": "formaldehyde",
            "predicate": "assimilated by",
            "object": "rump_cycle",
            "description": "Formaldehyde can enter the RuMP cycle for growth on methanol.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fbioe.2021.787791",
                "snippet": "ribulose monophosphate (RuMP) cycle",
                "notes": "Supports RuMP as a native formaldehyde assimilation pathway."
              }
            ]
          },
          {
            "subject": "formaldehyde",
            "predicate": "assimilated by",
            "object": "serine_pathway",
            "description": "Formaldehyde can enter the serine pathway for growth on methanol.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fbioe.2021.787791",
                "snippet": "serine pathway",
                "notes": "Supports the serine pathway as a native formaldehyde assimilation route."
              }
            ]
          },
          {
            "subject": "rump_cycle",
            "predicate": "has output",
            "object": "biomass_precursor",
            "description": "RuMP assimilation incorporates C1 carbon into cellular material.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fbioe.2021.787791",
                "snippet": "growth support of microorganisms in methanol",
                "notes": "Supports assimilation pathways as growth-supporting routes."
              }
            ],
            "predicate_id": "RO:0002234"
          },
          {
            "subject": "hexulose_phosphate_synthase",
            "predicate": "catalyzes",
            "object": "rump_cycle",
            "description": "Hps drives formaldehyde assimilation in the RuMP cycle.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-023-43610-7",
                "notes": "The RuMP pathway relies on 3-hexulose 6-phosphate synthase (Hps) and phosphohexose isomerase (Phi) to assimilate formaldehyde."
              }
            ],
            "predicate_id": "biolink:catalyzes"
          },
          {
            "subject": "serine_glyoxylate_aminotransferase",
            "predicate": "catalyzes",
            "object": "serine_pathway",
            "description": "SgaA/SGT is a conserved serine-cycle enzyme.",
            "evidence": [
              {
                "reference": "DOI:10.1128/msystems.00248-24",
                "notes": "Serine-glyoxylate transaminase (SGT) occurs in all 75 organisms; strong serine-cycle marker."
              }
            ],
            "predicate_id": "biolink:catalyzes"
          },
          {
            "subject": "hydroxypyruvate_reductase",
            "predicate": "catalyzes",
            "object": "serine_pathway",
            "description": "HprA/HPR is a ubiquitous serine-cycle enzyme.",
            "evidence": [
              {
                "reference": "DOI:10.1128/msystems.00248-24",
                "notes": "Hydroxypyruvate reductase (HPR) is ubiquitous (all 75 genomes); strong serine-cycle marker."
              }
            ],
            "predicate_id": "biolink:catalyzes"
          },
          {
            "subject": "formaldehyde_dehydrogenase",
            "predicate": "oxidizes to",
            "object": "formate",
            "description": "Formaldehyde dehydrogenase oxidizes formaldehyde to formate.",
            "evidence": [
              {
                "reference": "DOI:10.1128/msystems.00248-24",
                "notes": "FDH converts formaldehyde to formate in the dissimilatory oxidation branch."
              }
            ]
          },
          {
            "subject": "formate_dehydrogenase",
            "predicate": "oxidizes to",
            "object": "carbon_dioxide",
            "description": "Formate dehydrogenase oxidizes formate to CO2 completing C1 dissimilation.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s00284-022-03141-8",
                "notes": "Oxidation of formaldehyde via H4F/RuMP routes to formate and then to CO2; strong downstream dissimilation edge."
              }
            ]
          },
          {
            "subject": "mxa_methanol_dehydrogenase",
            "predicate": "requires cofactor",
            "object": "pqq",
            "description": "MxaFI methanol dehydrogenase requires the PQQ redox cofactor.",
            "evidence": [
              {
                "reference": "DOI:10.1128/msphere.00685-24",
                "notes": "Mxa-type MDHs belong to the PQQ-dependent alcohol dehydrogenase family."
              }
            ]
          },
          {
            "subject": "mxa_methanol_dehydrogenase",
            "predicate": "requires cofactor",
            "object": "calcium_ion",
            "description": "MxaFI methanol dehydrogenase requires a calcium ion in its active site.",
            "evidence": [
              {
                "reference": "DOI:10.1016/b978-0-443-13307-7.00014-1",
                "notes": "MxaF contains a calcium ion in its active site."
              }
            ]
          },
          {
            "subject": "mxa_methanol_dehydrogenase",
            "predicate": "example of",
            "object": "pqq_dependent_mdh",
            "description": "The calcium-dependent Mxa enzyme is a PQQ-dependent alcohol dehydrogenase used for methanol oxidation.",
            "evidence": [
              {
                "reference": "DOI:10.1128/msphere.00685-24",
                "snippet": "Xox- and Mxa-type MDHs belong to the diverse group of pyrroloquinoline quinone (PQQ)-dependent alcohol dehydrogenases",
                "notes": "Verified against the open mSphere primary article."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "formaldehyde",
            "predicate": "oxidized by",
            "object": "formaldehyde_dehydrogenase",
            "description": "Formaldehyde dehydrogenase oxidizes formaldehyde to formate in the dissimilatory branch.",
            "evidence": [
              {
                "reference": "DOI:10.3109/10409238.2012.697865",
                "snippet": "formaldehyde is then oxidized to formate",
                "notes": "Verified against the public full text."
              }
            ]
          },
          {
            "subject": "formate",
            "predicate": "oxidized by",
            "object": "formate_dehydrogenase",
            "description": "Formate dehydrogenase continues C1 dissimilation by oxidizing formate to carbon dioxide.",
            "evidence": [
              {
                "reference": "DOI:10.3109/10409238.2012.697865",
                "snippet": "formate and carbon dioxide by formaldehyde and formate dehydrogenases, respectively",
                "notes": "Verified against the public full text."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-08-25T00:00:00-07:00",
        "curator": "codex",
        "action": "REVIEW_ONTOLOGY_GROUNDINGS",
        "changes": "Retracted obsolete GO:0019647 from the ribulose monophosphate cycle node. GO replaced it with broader GO:0019649 formaldehyde assimilation, which is already represented by a separate graph node and is not an exact grounding for this named pathway variant.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-05T01:35:46.877023+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-08T00:00:00-07:00",
        "curator": "codex",
        "action": "ADDED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed causal graph for methanol oxidation and formaldehyde assimilation in methylotrophy.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d72, METPO:2000016\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T05:49:25Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:located_in\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T21:30:07Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007405\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:38:01Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0042597\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T05:05:15Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A010SCY7\u00d71, UniProtKB:A0A4U8YZA6\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-14T05:51:47Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0019647\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 7 evidence-backed generic edges (10 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:14Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:catalyzes\u00d73).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:20Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:16526\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:21:12Z",
        "curator": "claude",
        "action": "RETRACT_DEAD_UNIPROT_GROUNDINGS",
        "changes": "Retracted 2 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:23:55Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0009326\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates (1 to has output), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T02:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES_PART2",
        "changes": "Re-grounded 2 causal edge(s) off microbe-domain METPO predicates onto their causal-graph counterparts (1 to oxidizes, 1 to produces), issue 301 part 2. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Each replacement is a 1:1 mirror of its source predicate that changes only the domain, so the claim each edge makes is unchanged and directions are unchanged. The replacements are proposed in proposals/metpo_traitmech_v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "CURATE_PROTEIN_TAXON_EXAMPLE",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope methylotrophic_methanol_assimilation=MECHANISTIC with scope_notes; marked 7 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (methanol_dehydrogenase, pqq_dependent_mdh, hexulose_phosphate_synthase, serine_glyoxylate_aminotransferase, hydroxypyruvate_reductase, formaldehyde_dehydrogenase, mxa_methanol_dehydrogenase); added taxon-paired protein example(s) UniProtKB:P16027 on mxa_methanol_dehydrogenase (NCBITaxon:272630); added canonical example(s) NCBITaxon:272630.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T11:15:00Z",
        "curator": "codex",
        "action": "CONNECT_CAUSAL_GRAPH_COMPONENTS",
        "changes": "Resolved issue #183 graph fragmentation (4 components to 1) with 3 public-source, verbatim-snippet-backed connector(s). No paid research service was called.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-22T01:35:00Z",
        "curator": "claude",
        "action": "REFRESH_UNIPROT_ENTRY_VERSION",
        "changes": "Refreshed UniProtKB entry_version against live UniProt REST on 2026-10-22: UniProtKB:P16027 (179 -> 180 on mxa_methanol_dehydrogenase).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000639",
    "label": "mitophagy",
    "definition": "An autophagy phenotype in which a microbial cell selectively degrades its mitochondria by delivering them to lysosomal or vacuolar compartments.",
    "definition_source": "DOI:10.7554/eLife.61245",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000638"
    ],
    "evidence": [
      {
        "reference": "DOI:10.7554/eLife.61245",
        "snippet": "Thus, we hereafter refer to the selective autophagic degradation of mitochondria in fission yeast as mitophagy.",
        "notes": "PMID:33138913, PMC7609059. Full-text Results section s2-2, not the scientific Abstract, directly read in Europe PMC XML at https://www.ebi.ac.uk/europepmc/webservices/rest/PMC7609059/fullTextXML. Results s2-1/s2-2, Methods s4-1/s4-5/s4-8 and actual Figure 1 plus its figure supplement 1 were inspected. In Schizosaccharomyces pombe, mitochondrial reporter processing has Atg1 and vacuolar-protease Isp6 controls; Atg43 perturbation and complementation distinguish mitochondrial turnover from bulk, cytoplasmic and ER turnover. atg43-1 is a partial allele, not the complete deletion, which also impairs vegetative growth. Tom70 deletion retains weak processing on long exposure. Other actual figures, complete Methods, Key Resources Table and natural strain provenance were not inspected."
      },
      {
        "reference": "DOI:10.1016/j.devcel.2009.06.014",
        "snippet": "This gene is not required for other types of selective autophagy or for nonspecific macroautophagy.",
        "notes": "PMID:19619495, PMC2746076. Scientific Abstract directly read in Europe PMC core metadata with matching DOI. The quoted gene is YIL146C/ECM37, named ATG32 by the authors after a mitophagy-deficient mutant screen. This supports selectivity relative to other autophagy phenotypes in the studied yeast, not a universal ATG32 requirement or a gene-presence trait. Mitochondrial recruitment or vacuolar import alone does not establish completed degradation. Full-text retrieval failed; methods, actual figures and strain provenance were not inspected. Human-disease background is not microbial evidence."
      },
      {
        "reference": "DOI:10.1016/j.devcel.2009.06.013",
        "snippet": "We propose that Atg32 acts as a mitophagy-specific receptor and regulates selective degradation of mitochondria.",
        "notes": "PMID:19619494. Scientific Abstract directly read in Europe PMC core metadata and PubMed HTML. In post-log respiratory yeast cells, the authors report selective mitochondrial transport to the vacuole and propose an Atg32 receptor mechanism. The quote retains that proposal language. It does not establish that every microbial route uses Atg32, that all cargo must be damaged, or that starvation is always required. Full text, actual figures and natural strain provenance were not inspected."
      },
      {
        "reference": "DOI:10.4161/auto.4034",
        "snippet": "The observation of mitochondria degradation showed that both a selective process and a nonselective process of mitochondria autophagy occurred successively.",
        "notes": "PMID:17377488. Scientific Abstract directly read in Europe PMC core metadata with matching DOI. The yeast study reports preferential microautophagy under its nonfermentable growth and nitrogen-starvation conditions, and sequential selective and nonselective turnover. Only selective degradation belongs to this proposed trait; incidental capture during bulk autophagy is insufficient. This supports route-sensitive interpretation, not universal microautophagy or a universal UTH1 requirement. Full text, actual electron micrographs and strain provenance were not inspected."
      }
    ],
    "discussions": [
      {
        "discussion_id": "mitophagy-selectivity-and-route-scope",
        "prompt": "Review selective-turnover scope against route-specific terminology.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Use autophagy traitmech:000638 as the direct broader phenotype. This draft uses selective mitochondrial degradation, as named in the fission-yeast Results, without making membrane route universal. The 2007 yeast abstract reports selective and nonselective turnover with preferential microautophagy under its conditions. In contrast, issuing GO:0000423 names mitophagy specifically for selective macroautophagy and lists macromitophagy as exact; GO:0000424 micromitophagy is not its child. GO:0000422 autophagy of mitochondrion is broader and lists mitophagy as narrow. These nonobsolete biological-process records were directly resolved at https://www.ebi.ac.uk/QuickGO/services/ontology/go/terms/GO%3A0000422,GO%3A0000423,GO%3A0000424. Do not silently impose GO's route-specific usage on every microbial source, or assert an exact phenotype xref. Retain this interpretation for human review; omit exact synonyms including broad mitochondrial autophagy and route-specific macromitophagy. Protein/gene presence, puncta, organelle fragmentation, membrane depolarization, delivery without degradation, and nonspecific bulk capture alone are insufficient. The trait belongs to the microbial cell doing the turnover, not to a bacterium inducing mitophagy in an animal host.",
        "posed_by": "codex",
        "posed_date": "2026-10-06"
      },
      {
        "discussion_id": "mitophagy-exemplars-and-native-mechanisms",
        "prompt": "Resolve strain provenance and taxon-paired mechanisms before expansion.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "The evidence uses reporter and perturbation strains; natural strain provenance is not independently established. Keep canonical examples unset rather than presenting deficient mutants as positive exemplars. Atg43 in fission yeast and Atg32 in budding yeast do not define a universal receptor inventory. Atg43 also has mitophagy-independent functions, so growth effects alone do not measure mitophagy. Require native taxon-paired protein accession checks and direct functional evidence before a causal graph. Do not encode mitochondrial genes or a detector profile as the phenotype, or require every degraded mitochondrion to be damaged.",
        "posed_by": "codex",
        "posed_date": "2026-10-06"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-06T10:04:49Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added mitophagy as selective mitochondrial degradation under autophagy, with four DOI-backed snippets and explicit source, route and flux limits. Ignored-and-hidden searches and pinned METPO review found no exact record. Reserved METPO:1059200 in v515, carrying v514's unchanged parent row as context. Deferred unverified examples, exact mappings and protein graphs.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000652",
    "label": "mixotrophic",
    "definition": "A trophic type in which an organism can use both organic and inorganic carbon sources for growth.",
    "definition_source": "DOI:10.1128/AEM.01559-06",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000631"
    ],
    "synonyms": [
      {
        "synonym_text": "mixotroph",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1128/AEM.01559-06",
        "snippet": "Evidence for the ubiquity of mixotrophic bacteria",
        "notes": "Review supports bacterial mixotrophy as combined metabolic modes in marine systems."
      },
      {
        "reference": "DOI:10.1073/pnas.1305998110",
        "snippet": "combination of modes by which an organism can obtain its energy and carbon",
        "notes": "Perspective supports mixotrophy as combined energy and carbon acquisition modes."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1021",
        "taxon_label": "Beggiatoa",
        "note": "chemolitho/organo mixotroph",
        "reference": "DOI:10.3390/microorganisms8060928"
      },
      {
        "taxon_id": "NCBITaxon:318586",
        "taxon_label": "Paracoccus denitrificans Pd1222",
        "note": "facultative mixotroph co-consuming mannitol and methanol with conditional Calvin-cycle CO2 assimilation",
        "reference": "DOI:10.1128/msystems.01077-23"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "mixotrophic_dual_carbon_energy_use",
        "title": "Mixotrophic dual carbon and energy use",
        "description": "DOI-backed graph linking organic carbon uptake, inorganic carbon fixation, light or chemical energy capture, and biomass production.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "Mixotrophy includes multiple combinations of energy and carbon acquisition; this graph therefore presents alternative modules rather than one universal pathway. The P. denitrificans Pd1222 example anchors conditional RuBisCO-mediated CO2 assimilation during co-consumption of methanol and mannitol.",
        "nodes": [
          {
            "node_id": "mixotrophic_trait",
            "label": "mixotrophic",
            "node_type": "TRAIT",
            "grounding": "METPO:1000652",
            "description": "Trophic type combining organic and inorganic carbon-use modes."
          },
          {
            "node_id": "organic_carbon",
            "label": "organic carbon",
            "node_type": "CHEMICAL",
            "description": "Organic compounds assimilated or catabolized by mixotrophs.",
            "grounding": "CHEBI:50860"
          },
          {
            "node_id": "carbon_dioxide",
            "label": "carbon dioxide",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:16526",
            "description": "Inorganic carbon source fixed by autotrophic modules."
          },
          {
            "node_id": "dissolved_organic_matter",
            "label": "dissolved organic matter",
            "node_type": "CHEMICAL",
            "description": "Environmental organic substrate pool available to aquatic microbes."
          },
          {
            "node_id": "phototrophic_energy_capture",
            "label": "phototrophic energy capture",
            "node_type": "PATHWAY",
            "description": "Light-driven energy capture, including rhodopsin or photosynthetic systems."
          },
          {
            "node_id": "co2_fixation_pathway",
            "label": "CO2-fixation pathway",
            "node_type": "PATHWAY",
            "description": "Autotrophic carbon assimilation route.",
            "grounding": "GO:0015977"
          },
          {
            "node_id": "biomass",
            "label": "biomass",
            "node_type": "CHEMICAL",
            "description": "Cell material formed from combined carbon acquisition.",
            "grounding": "METPO:1007501"
          },
          {
            "node_id": "electron_transport_chain",
            "label": "electron transport chain",
            "node_type": "PATHWAY",
            "description": "Membrane redox chain transferring electrons to terminal acceptors.",
            "grounding": "GO:0022900"
          },
          {
            "node_id": "atp_synthesis",
            "label": "ATP synthesis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Formation of ATP coupling energy metabolism to cellular work.",
            "grounding": "GO:0006754"
          },
          {
            "node_id": "proton_motive_force",
            "label": "proton motive force",
            "node_type": "STATE",
            "description": "Transmembrane proton gradient driving ATP synthase.",
            "grounding": "METPO:1007500"
          },
          {
            "node_id": "rubisco",
            "label": "RuBisCO",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Ribulose-1,5-bisphosphate carboxylase/oxygenase, key CBB enzyme.",
            "grounding": "InterPro:IPR033966",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:A1B2Q2",
                "protein_label": "Ribulose bisphosphate carboxylase large chain",
                "gene_symbol": "cbbL",
                "taxon_id": "NCBITaxon:318586",
                "taxon_label": "Paracoccus denitrificans Pd1222",
                "entry_status": "REVIEWED",
                "retrieved_on": "2026-10-22",
                "entry_version": 99,
                "sequence_version": 1,
                "role": "Large-chain component of RuBisCO used for conditional Calvin-cycle CO2 assimilation during mixed methanol and mannitol consumption; it is not the complete multisubunit enzyme.",
                "evidence": [
                  {
                    "reference": "DOI:10.1128/msystems.01077-23",
                    "snippet": "when grown on a mixture of mannitol and methanol, the enzyme RuBisCO, responsible for the assimilation of C1 compounds via the Calvin cycle, is only expressed over a certain threshold of methanol/mannitol consumption ratio",
                    "notes": "The strain-specific metabolic study links RuBisCO activity in Pd1222 to mixed-substrate biomass optimization; UniProtKB A1B2Q2 is the reviewed cbbL large-chain entry for that strain."
                  }
                ]
              }
            ]
          },
          {
            "node_id": "cbb_cycle",
            "label": "Calvin-Benson-Bassham cycle",
            "node_type": "PATHWAY",
            "description": "Reductive pentose phosphate cycle fixing CO2 into organic carbon."
          },
          {
            "node_id": "organic_matter_limitation",
            "label": "organic matter limitation",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Low availability of organic substrates in the environment."
          },
          {
            "node_id": "light_limitation",
            "label": "light limitation",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Low light availability limiting phototrophic energy capture."
          }
        ],
        "edges": [
          {
            "subject": "mixotrophic_trait",
            "predicate": "has carbon source",
            "object": "organic_carbon",
            "description": "Mixotrophs can use organic carbon as a carbon source.",
            "evidence": [
              {
                "reference": "DOI:10.1073/pnas.1305998110",
                "snippet": "organic carbon (C) for their C needs",
                "notes": "Supports organic carbon use as part of mixotrophic metabolism."
              }
            ],
            "predicate_id": "METPO:2007806"
          },
          {
            "subject": "mixotrophic_trait",
            "predicate": "has carbon source",
            "object": "carbon_dioxide",
            "description": "Mixotrophy can include inorganic carbon acquisition by CO2 fixation.",
            "evidence": [
              {
                "reference": "DOI:10.1073/pnas.1305998110",
                "snippet": "obtain its energy and carbon",
                "notes": "Supports combining autotrophic and heterotrophic carbon-acquisition modes."
              }
            ],
            "predicate_id": "METPO:2007806"
          },
          {
            "subject": "dissolved_organic_matter",
            "predicate": "supplies",
            "object": "organic_carbon",
            "description": "Dissolved organic matter provides organic substrates in aquatic mixotrophy.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.01559-06",
                "snippet": "DOM, dissolved organic matter",
                "notes": "Figure legend identifies dissolved organic matter as a substrate pool in bacterial metabolic modes."
              }
            ]
          },
          {
            "subject": "mixotrophic_trait",
            "predicate": "can use energy capture route",
            "object": "phototrophic_energy_capture",
            "description": "Some microbial mixotrophs supplement organic carbon use with light-harvesting energy systems.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.01559-06",
                "snippet": "rhodopsin and other pigment",
                "notes": "Review discusses pigment/rhodopsin-associated bacterial metabolic modes."
              }
            ]
          },
          {
            "subject": "carbon_dioxide",
            "predicate": "fixed by",
            "object": "co2_fixation_pathway",
            "description": "Inorganic carbon assimilation converts CO2 into cellular carbon.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.02473-10",
                "snippet": "autotrophic CO2 fixation",
                "notes": "Supports CO2 fixation as the inorganic-carbon assimilation process."
              }
            ],
            "predicate_id": "METPO:2007404"
          },
          {
            "subject": "organic_carbon",
            "predicate": "incorporated into",
            "object": "biomass",
            "description": "Organic carbon contributes to cell material in mixotrophic growth.",
            "evidence": [
              {
                "reference": "DOI:10.1016/B978-012373944-5.00083-3",
                "snippet": "incorporation of a compound into biomass",
                "notes": "Supports assimilatory conversion of organic compounds into biomass."
              }
            ],
            "predicate_id": "biolink:part_of"
          },
          {
            "subject": "electron_transport_chain",
            "predicate": "drives",
            "object": "atp_synthesis",
            "description": "Electron transport chain activity drives ATP synthesis.",
            "evidence": [
              {
                "reference": "DOI:10.1128/aem.00599-24",
                "notes": "Complete ETC complexes and F-type ATPase support ETC-driven ATP synthesis."
              }
            ]
          },
          {
            "subject": "proton_motive_force",
            "predicate": "drives",
            "object": "atp_synthesis",
            "description": "Proton gradient drives ATP synthesis via ATP synthase.",
            "evidence": [
              {
                "reference": "DOI:10.1128/spectrum.02177-23",
                "notes": "A proton gradient drives ATP synthesis (canonical bioenergetic edge)."
              }
            ]
          },
          {
            "subject": "phototrophic_energy_capture",
            "predicate": "generates",
            "object": "proton_motive_force",
            "description": "Proton-pump rhodopsin photosystems generate a proton gradient.",
            "evidence": [
              {
                "reference": "DOI:10.1128/spectrum.02177-23",
                "notes": "Proton-pump rhodopsin acts as a photosystem-independent proton pump creating a proton gradient."
              }
            ],
            "predicate_id": "biolink:produces"
          },
          {
            "subject": "rubisco",
            "predicate": "enables",
            "object": "cbb_cycle",
            "description": "RuBisCO enables the Calvin-Benson-Bassham cycle.",
            "evidence": [
              {
                "reference": "DOI:10.1128/aem.00599-24",
                "notes": "MAGs encode Form II RuBisCO (rbcL/cbbM) and a full CBB cycle."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "cbb_cycle",
            "predicate": "fixes",
            "object": "carbon_dioxide",
            "description": "The Calvin-Benson-Bassham cycle fixes CO2 into organic carbon.",
            "evidence": [
              {
                "reference": "DOI:10.1128/aem.00599-24",
                "notes": "A full CBB cycle is consistent with CO2 fixation potential."
              }
            ]
          },
          {
            "subject": "organic_matter_limitation",
            "predicate": "promotes switching to",
            "object": "phototrophic_energy_capture",
            "description": "When organic matter is limiting, mixotrophs switch to light-based energy and inorganic carbon use.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.01559-06",
                "notes": "If organic matter is limiting, a mixotroph can switch to using light as an energy source and inorganic carbon as a carbon source."
              }
            ]
          },
          {
            "subject": "light_limitation",
            "predicate": "promotes switching to",
            "object": "organic_carbon",
            "description": "When light is limiting, mixotrophs switch back to degradation of organic substances.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.01559-06",
                "notes": "As light gets limiting, the organism can switch back to degradation of organic substances."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.877636+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-09T00:00:00-07:00",
        "curator": "Codex",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed mixotrophy graph for dual organic/inorganic carbon use and light-associated energy capture.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000006\u00d72).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T21:30:07Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007404\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:38:01Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:50860\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:41:04Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (METPO:1007501\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T07:34:59Z",
        "curator": "claude",
        "action": "RETYPE_CAUSAL_NODES",
        "changes": "Re-typed 1 causal-node node_type field(s) to align with CausalNodeTypeEnum semantics: biomass: BIOLOGICAL_PROCESS \u2192 CHEMICAL \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T08:14:33Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0015977\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-13T21:03:27Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:part_of\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 7 evidence-backed generic edges (7 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:14Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:produces\u00d71, RO:0002327\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:20Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0022900\u00d71, UniProtKB:A0A075WF79\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:34Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0006754\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:21:12Z",
        "curator": "claude",
        "action": "RETRACT_DEAD_UNIPROT_GROUNDINGS",
        "changes": "Retracted 1 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:23:56Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (InterPro:IPR033966\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 2 causal edge(s) off microbe-domain METPO predicates (2 to has carbon source), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-15T02:00:00Z",
        "curator": "claude",
        "action": "NORMALISE_NODE_TYPE",
        "changes": "Normalised causal-node type(s) so one node_id means one thing corpus-wide (issue 356): proton_motive_force: BIOLOGICAL_PROCESS -> STATE. The schema's OWN example of STATE: 'a bioenergetic or molecular state of the cell (e.g. proton motive force ...) ... the state is the gradient / steady-value, not its establishment'. All 35 occurrences describe the gradient -- every description across all four types reads 'electrochemical proton gradient', including the 13 typed BIOLOGICAL_PROCESS ('Transmembrane electrochemical gradient generated by respiration'), which name the gradient and its provenance rather than the generating process. Nothing here means the establishment, so this is a retype and not a rename; records that DO mean the process already use a separate id (proton_motive_force_generation in ph_delta.yaml). Also settles the one edge #356 was filed for: phototrophic.yaml's CAPACITY typing was blocking `powers` (METPO:2007900), which is gated to BIOLOGICAL_PROCESS|STATE.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-16T02:00:00Z",
        "curator": "claude",
        "action": "NORMALISE_NODE_TYPE",
        "changes": "Under the PATHWAY-vs-BIOLOGICAL_PROCESS rule, one node_id means one thing corpus-wide (issue 356): electron_transport_chain is typed PATHWAY. PATHWAY is a named, conventionally enumerable multi-step route; BIOLOGICAL_PROCESS is everything else. A named route through enumerable complexes. Was 4 PATHWAY to 2 before this tranche.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-20T07:10:43Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (METPO:1007500\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-24T11:50:00-07:00",
        "curator": "codex",
        "action": "REVIEWED_CAUSAL_GRAPH_PROTEIN_TAXON",
        "changes": "Marked the graph mechanistic, documented its alternative-module scope, upgraded canonical examples to DOI citations including Pd1222, and added the reviewed Pd1222 cbbL large-chain example for conditional mixed-substrate CO2 fixation.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-22T01:35:00Z",
        "curator": "claude",
        "action": "REFRESH_UNIPROT_ENTRY_VERSION",
        "changes": "Refreshed UniProtKB entry_version against live UniProt REST on 2026-10-22: UniProtKB:A1B2Q2 (98 -> 99 on rubisco).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000684",
    "label": "mucocyst discharge",
    "definition": "An exocytotic phenotype in which a microbial cell releases mucocyst contents to the exterior through fusion of a mucocyst membrane with the plasma membrane.",
    "definition_source": "DOI:10.1371/journal.pgen.1010194",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000637"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1371/journal.pgen.1010194",
        "snippet": "lysosome-related organelles called mucocysts accumulate at the cell periphery where they secrete their contents in response to extracellular events",
        "notes": "PMID:35587496, PMC9159632. Scientific Abstract, relevant Results/Methods and Discussion read directly in Europe PMC fullTextXML and publisher HTML. Figure 1 and its caption were visually inspected; Figure 4 caption, not image, was read. The snippet is from the scientific Abstract, not the Author summary. Dibucaine stimulates release in Tetrahymena thermophila. Sedimented flocculent volume is a secretion proxy, not a count of discharged organelles; cells can be trapped in that layer. The MN175 missense and MDL1 deletion phenotypes differ. S1 Table DOCX text was inspected, not rendered; laboratory strain names and genotypes do not establish natural provenance."
      },
      {
        "reference": "DOI:10.1016/0309-1651(77)90012-1",
        "snippet": "Synchronous secretion of all available mature mucocysts was induced",
        "notes": "PMID:610868. Scientific Abstract directly retrieved with EXT_ID:610868 AND SRC:MED in Europe PMC; an unqualified numeric query also returns an unrelated database record. The correct MED result matches this DOI and title. Abstract-only access; full Methods and figures were not inspected. The source names Tetrahymena thermophilia (B III). Synchrony and complete release concern late-log cultures treated with dibucaine, not universal requirements for this trait. Fusion-rosette reappearance and new mucocyst precursors are temporally associated, not proof of a universal protein mechanism."
      },
      {
        "reference": "DOI:10.1128/ec.00058-15",
        "snippet": "those cores do not undergo normal directional expansion during exocytosis, and they thus fail to efficiently extrude from the cells.",
        "notes": "PMID:26092918, PMC4519746. Scientific Abstract directly retrieved by exact quoted DOI query in Europe PMC. Abstract-only access; full Methods, figures and supplements were not inspected. The snippet refers to CTH4-disrupted Tetrahymena thermophila: crystalline cores assemble but extrusion is inefficient. It is boundary evidence distinguishing assembly from successful release, not a positive mutant exemplar or proof that no cargo is released. CTH4 dependence is not imposed on all mucocysts."
      }
    ],
    "discussions": [
      {
        "discussion_id": "mucocyst-discharge-scope-and-homology",
        "prompt": "Keep cargo release distinct from organelle presence and homologous types.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Exocytosis traitmech:000637 is the broader parent; the proposal depends on its v513 placeholder METPO:1059000. Mucocyst formation, docking and fusion without cargo release do not alone establish discharge. Lysis and preparation artifacts must be excluded from positive assays. Neither rapid expansion nor total emptying defines this class. The 2022 Discussion calls Paramecium trichocysts mucocyst homologs. This record preserves the organelle-specific release phenotype rather than asserting independent origins, exact equivalence to trichocyst discharge traitmech:000683, or organism-level disjointness. Resolve historical extrusome terminology before broadening the definition; not all mucus secretion, cortical granules or capsule formation are equivalent. No exact synonyms or xrefs are asserted.",
        "posed_by": "codex",
        "posed_date": "2026-10-08"
      },
      {
        "discussion_id": "mucocyst-discharge-provenance-and-mechanism",
        "prompt": "Resolve natural culture provenance and taxon-specific release mechanisms.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "These experiments support a secretion phenotype in source-named Tetrahymena systems, not every protist bearing an extrusome. Natural culture provenance and strain-level taxonomy remain unchecked, so no canonical examples are assigned. A wildtype designation alone does not establish natural provenance; a mutant designation alone does not establish engineering. The MDL1 and CTH4 experiments motivate a future protein-resolved graph, but require taxon-paired accessions and separation of maturation, docking, fusion and cargo extrusion. Mechanism is deferred, not claimed absent; sequence features alone do not establish discharge. Do not infer a universal ecological role from induced secretion.",
        "posed_by": "codex",
        "posed_date": "2026-10-08"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-08T17:15:26Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added mucocyst discharge with three primary DOI sources and directly checked scientific-abstract snippets. Ignored-and-hidden main/worktree/open-PR checks support 000684 and v560 block 1063700-1063799. Used existing exocytosis parent and its v513 proposal dependency. Qualified assay proxies, organelle homology, mutant evidence and provenance; deferred protein mechanism. Existing records unchanged. Timestamp is observed UTC.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000631",
    "label": "myzocytosis",
    "definition": "A physiological phenotype in which a microbial organism feeds by aspirating prey cell contents through a localized feeding connection rather than engulfing the prey whole.",
    "definition_source": "DOI:10.3390/microorganisms11081945",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.3390/microorganisms11081945",
        "snippet": "Colpodella sp. (ATCC 50594) obtain nutrients by preying on Parabodo caudatus using myzocytosis.",
        "notes": "PMID:37630505, PMC10458597. Direct scientific Abstract quote. Main text and actual Figures 7-9 were inspected; Figures 1-6 were not visually audited. Introduction and Conclusions describe aspiration through a feeding channel. Fixed-cell TEM supports prey-membrane uptake at the contact, not direct piercing by the pseudoconoid. Unattached nanoparticle uptake is separate endocytosis, not proof of myzocytosis. Intact prey organelles in food vacuoles do not establish functional organelle retention. Posterior vacuole position and encystation are not universal requirements. The mixed culture does not resolve a complete native protein mechanism."
      },
      {
        "reference": "DOI:10.1111/jeu.13050",
        "snippet": "cytoplasm contents were transferred through the peduncle to the dinoflagellate.",
        "notes": "PMID:39019843, PMC11603288. Direct Nutrition and feeding behavior Results passage, not an abstract quote. Scientific Abstract, culture and fluorescence Methods, feeding Results and Discussion, and actual supplementary Figure S6 with its caption were inspected. S6 identifies imaged SPMC98; the molecular-data isolate SPMC100 is different. Panel D shows deformed cryptophyte material passing through the peduncle; attachment in panel E alone is not ingestion. The organism can also use conventional phagocytosis. Trichocyst discharge may be a fixation artifact, not a demonstrated prey-capture mechanism. Other supplementary figures, molecular datasets and movies were not audited."
      },
      {
        "reference": "DOI:10.1038/ismej.2012.29",
        "snippet": "parts are sucked out by a microtubule supported feeding tube or peduncle (myzocytosis)",
        "notes": "PMID:22513533, PMC3446796. Direct Introduction terminology span, not an abstract quote or independent naming experiment. Main text and actual Figure 2 were inspected; other figures and supplementary movies were not visually audited. Results report Karlodinium armiger tube feeding on copepods and polychaete larvae, so the prey need not be unicellular. Nematode feeding was not directly observed. Abstract and later passages call the strain K-0688, whereas initial Methods and Table 1 say K-0668; no canonical strain is assigned from this conflicting record. Proposed toxin and chemotaxis explanations are not molecular demonstrations."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:160603",
        "taxon_label": "Oxytoxum lohmannii",
        "reference": "DOI:10.1111/jeu.13050",
        "note": "Qualified example: imaged SPMC98 feeding on cryptophyte prey, not molecular-data isolate SPMC100. Maintenance cultures Methods at https://doi.org/10.1111/jeu.13050 document natural isolation from the Salish Sea near Anacortes, Washington, in 1993, originally identified as Amphidinium longum. SPMC98 was lost in 2004. Actual supplementary Figure S6 names this strain and shows prey material passing through the peduncle. Feeding mode is prey-dependent; this is not a claim about all isolates or exclusive myzocytosis. NCBI ESearch and EFetch resolved the species and its Amphidinium longum synonym on 2026-10-06."
      }
    ],
    "discussions": [
      {
        "discussion_id": "myzocytosis-feeding-scope-and-parent",
        "prompt": "Reconcile feeding-mode terminology with operational trait boundaries.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "This is an organismal feeding phenotype, not a peduncle, pseudoconoid or sequence feature. The 2023 Discussion calls myzocytosis a form of apical phagotrophy and endocytosis while arguing against phagocytosis and trogocytosis in its studied system. The 2012 Introduction uses phagocytise for feeding-tube uptake; the 2024 study contrasts myzocytosis with conventional whole-prey phagocytosis. Those usages are not silently treated as identical. Local phagocytosis traitmech:000627 requires particle enclosure and internalization; phagotrophy traitmech:000628 requires particulate ingestion and nutrient assimilation. Retain phenotype METPO:1000059 pending a closer feeding-mode hierarchy rather than assert unsupported universal subtyping. Mere attachment, free-particle uptake, extracellular digestion or an apparatus-like sequence does not establish prey-content aspiration. A microbe may use several feeding modes; these possession traits are not declared disjoint. No unverified synonym or xref is asserted. Prey death, mechanical piercing and a particular vacuole position are not definition requirements.",
        "posed_by": "codex",
        "posed_date": "2026-10-06"
      },
      {
        "discussion_id": "myzocytosis-native-feeding-mechanism",
        "prompt": "Separate observed aspiration from inferred apparatus and protein functions.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Fixed-cell contact ultrastructure does not establish every step by continuous observation. The 2023 paper cites earlier cytochalasin experiments; those experiments were not independently audited here. Its CellMask staining description alone is not accepted as proof of a specific actin mechanism. The 2024 molecular data are from a different isolate than the feeding micrographs, and trichocyst-mediated capture remains uncertain. The 2012 study did not measure the proposed toxin. Obtain taxon-paired functional evidence before adding protein accessions or a causal graph. Ancestral feeding and apicomplexan invasion similarities are hypotheses, not proof of one universal apparatus or molecular mechanism.",
        "posed_by": "codex",
        "posed_date": "2026-10-06"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-06T00:46:04Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added myzocytosis with three DOI-backed snippets and a natural, strain-qualified Oxytoxum example. Ignored-and-hidden searches and pinned METPO review found no exact record. Reserved METPO:1058400 in v507. Distinguished prey-content aspiration from whole-prey engulfment, free-particle uptake and sequence interpretation; retained hierarchy and mechanism gaps.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000165",
    "label": "NAD-dependent alcohol dehydrogenase activity",
    "definition": "A physiological enzyme-activity phenotype in which a cell produces active NAD-dependent alcohol dehydrogenases that interconvert primary or secondary alcohols with aldehydes or ketones.",
    "definition_source": "https://iubmb.qmul.ac.uk/enzyme/EC1/1/1/1.html",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "synonyms": [
      {
        "synonym_text": "alcohol dehydrogenase",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://iubmb.qmul.ac.uk/enzyme/EC1/1/1/1.html"
      },
      {
        "synonym_text": "ethanol dehydrogenase",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://iubmb.qmul.ac.uk/enzyme/EC1/1/1/1.html"
      },
      {
        "synonym_text": "NAD-dependent alcohol dehydrogenase",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://iubmb.qmul.ac.uk/enzyme/EC1/1/1/1.html"
      }
    ],
    "evidence": [
      {
        "reference": "https://iubmb.qmul.ac.uk/enzyme/EC1/1/1/1.html",
        "snippet": "<b>Reaction:</b> (1) a primary alcohol + NAD<small><sup>+</sup></small> = an aldehyde + NADH + H<small><sup>+</sup></small><br>\n\n(2) a secondary alcohol + NAD<small><sup>+</sup></small> = a ketone + NADH + H<small><sup>+</sup></small>",
        "notes": "The NC-IUBMB EC 1.1.1.1 entry names alcohol dehydrogenase as alcohol:NAD+ oxidoreductase and defines the NAD-dependent primary-alcohol-to-aldehyde and secondary-alcohol-to-ketone reactions."
      },
      {
        "reference": "DOI:10.1111/j.1432-1033.1986.tb09366.x",
        "snippet": "The two alcohol dehydrogenases found in Zymomonas mobilis have each been purified using dye-ligand chromatography and affinity elution with nucleotides.",
        "notes": "Neale et al. purified the ZADH-1 and ZADH-2 isoenzymes from Zymomonas mobilis and characterized their ethanol-oxidizing and acetaldehyde-reducing activities."
      },
      {
        "reference": "DOI:10.1128/jb.169.6.2591-2597.1987",
        "snippet": "The gene which encodes alcohol dehydrogenase II (adhB) from Zymomonas mobilis was cloned in Escherichia coli",
        "notes": "Conway et al. cloned the Z. mobilis adhB gene, connected it to the purified alcohol dehydrogenase II protein, and used an indicator plate that detected recombinant ADH activity."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:542",
        "taxon_label": "Zymomonas mobilis",
        "note": "Neale et al. purified and characterized the two native alcohol dehydrogenase isoenzymes from Zymomonas mobilis.",
        "reference": "DOI:10.1111/j.1432-1033.1986.tb09366.x"
      }
    ],
    "discussions": [
      {
        "discussion_id": "nad-dependent-alcohol-dehydrogenase-activity-xref-gap",
        "prompt": "Resolve an exact external ontology class for NAD-dependent alcohol dehydrogenase activity before adding a TraitRecord xref.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "GO:0004022 and EC 1.1.1.1 denote the NAD-dependent molecular function rather than the organism-level NAD-dependent alcohol dehydrogenase production phenotype; the GO term remains an appropriate causal-node grounding lead but not an equivalent TraitRecord xref.",
        "posed_by": "codex",
        "posed_date": "2026-09-12"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-12T10:11:31Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted alcohol dehydrogenase activity as a URL/DOI-backed TraitRecord after a repository-wide duplicate review covering ignored and hidden files; METPO has no exact alcohol dehydrogenase activity class yet.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-12T10:38:00Z",
        "curator": "codex",
        "action": "REVIEW_FIX",
        "changes": "Narrowed the label and definition to the NAD-dependent EC 1.1.1.1 phenotype after PR #833 review found the cofactor-agnostic alcohol dehydrogenase activity label overbroad for the evidence.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000174",
    "label": "naphthol-AS-BI-phosphohydrolase activity",
    "definition": "A physiological enzyme-activity phenotype in which a cell produces active phosphohydrolases that hydrolyze naphthol-AS-BI-phosphate substrates.",
    "definition_source": "DOI:10.14202/vetworld.2024.143-149",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "synonyms": [
      {
        "synonym_text": "naphthol-AS-BI-phosphohydrolase",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.14202/vetworld.2024.143-149"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.14202/vetworld.2024.143-149",
        "snippet": "Naphthol-AS-BI-phosphohydrolase 5.4 Naphthol-AS-BI-phosphate",
        "notes": "Ludfiani et al. list Naphthol-AS-BI-phosphate as the API ZYM naphthol-AS-BI-phosphohydrolase substrate, grounding the organism-level phenotype as hydrolysis of the naphthol-AS-BI phosphate chromogenic substrate."
      },
      {
        "reference": "DOI:10.1128/JCM.43.8.3713-3717.2005",
        "snippet": "Alkaline phosphatase, esterase (C4), esterase lipase (C8), leucine arylamidase, acid phosphatase, and naphthol-AS-BI-phosphohydrolase were clearly positive",
        "notes": "Otsuka et al. detected clear naphthol-AS-BI-phosphohydrolase API ZYM reactions in the five Corynebacterium resistens isolates they characterized."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:258224",
        "taxon_label": "Corynebacterium resistens",
        "note": "Otsuka et al. detected clear naphthol-AS-BI-phosphohydrolase API ZYM reactions in Corynebacterium resistens isolates.",
        "reference": "DOI:10.1128/JCM.43.8.3713-3717.2005"
      }
    ],
    "discussions": [
      {
        "discussion_id": "naphthol-as-bi-phosphohydrolase-activity-xref-gap",
        "prompt": "Resolve an exact external ontology class for naphthol-AS-BI-phosphohydrolase activity before adding a TraitRecord xref.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "GO:0016791 covers broad phosphatase activity at molecular-function scope, and no live GO class provides an exact naphthol-AS-BI-phosphate-specific phosphohydrolase production phenotype at organism-level scope.",
        "posed_by": "codex",
        "posed_date": "2026-09-12"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-12T15:09:52Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted naphthol-AS-BI-phosphohydrolase activity as a DOI-backed TraitRecord after a repository-wide duplicate review covering ignored and hidden files; METPO has no exact naphthol-AS-BI-phosphohydrolase activity class yet and the placeholder is reserved in proposals/metpo_traitmech_v51.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000087",
    "label": "natural competence",
    "definition": "A physiological state in which a cell takes up free extracellular DNA from the environment and integrates it into its genome (natural genetic transformation).",
    "definition_source": "DOI:10.1038/nrmicro3199",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "synonyms": [
      {
        "synonym_text": "natural transformation",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1038/nrmicro3199"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/nrmicro3199",
        "notes": "Johnston et al. review the distribution, shared mechanisms, and control of natural bacterial transformation (competence for DNA uptake)."
      },
      {
        "reference": "DOI:10.1038/s41579-021-00650-4",
        "notes": "Review of horizontal gene transfer supports natural transformation as a major route of bacterial DNA acquisition."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1313",
        "taxon_label": "Streptococcus pneumoniae",
        "note": "Where natural genetic transformation was discovered (Griffith 1928; Avery 1944). Bacillus subtilis is the competence-regulation (ComK) model.",
        "reference": "DOI:10.1016/j.meegid.2014.10.020"
      },
      {
        "taxon_id": "NCBITaxon:171101",
        "taxon_label": "Streptococcus pneumoniae R6",
        "note": "Naturally transformable reference strain in which RecA and DprA were shown to protect and recombine incoming transforming single-stranded DNA.",
        "reference": "DOI:10.1046/j.1365-2958.2003.03702.x"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "natural_competence_dna_uptake",
        "title": "Competence-driven DNA uptake and transformation",
        "description": "Evidence-backed causal sketch linking the competence program to uptake of extracellular DNA and genomic integration.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "This graph combines conserved DNA-uptake and recombination modules while allowing taxon-specific pilus architectures. The S. pneumoniae R6 RecA example supports the post-uptake homologous-recombination branch.",
        "nodes": [
          {
            "node_id": "natural_competence_trait",
            "label": "natural competence",
            "node_type": "TRAIT",
            "grounding": "traitmech:000087",
            "description": "Capacity to take up and integrate environmental DNA."
          },
          {
            "node_id": "competence_process",
            "label": "establishment of competence for transformation",
            "node_type": "BIOLOGICAL_PROCESS",
            "grounding": "GO:0030420",
            "description": "Development of the DNA-uptake state."
          },
          {
            "node_id": "extracellular_dna",
            "label": "extracellular DNA",
            "node_type": "CHEMICAL",
            "description": "Free environmental DNA taken up by competent cells."
          },
          {
            "node_id": "competence_pilus",
            "label": "type IV competence pilus",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Retractile DNA-binding pilus filament of the competence apparatus.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "A competence pilus is a multisubunit assembly whose major and minor pilins differ among taxa; the graph does not designate one component."
          },
          {
            "node_id": "pilus_retraction",
            "label": "competence pilus retraction",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Disassembly of the competence pilus that pulls bound DNA toward the cell."
          },
          {
            "node_id": "dna_uptake",
            "label": "extracellular DNA uptake",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Import of bound extracellular DNA across the cell envelope."
          },
          {
            "node_id": "comec",
            "label": "ComEC",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Inner-membrane channel required for DNA uptake into the cytoplasm.",
            "grounding": "InterPro:IPR052159"
          },
          {
            "node_id": "comea",
            "label": "ComEA",
            "node_type": "GENE_OR_PROTEIN",
            "description": "DNA receptor that binds incoming DNA and mediates transfer toward the periplasm.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "ComEA proteins have lineage-dependent domain architectures; the available helix-hairpin-helix term denotes only a shared DNA-binding motif, not the complete competence receptor."
          },
          {
            "node_id": "periplasm",
            "label": "periplasm",
            "node_type": "CELLULAR_LOCALIZATION",
            "description": "Compartment to which bound DNA is transferred during uptake.",
            "grounding": "GO:0042597"
          },
          {
            "node_id": "dpra",
            "label": "DprA",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Competence ssDNA-binding protein that protects incoming DNA and recruits RecA.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "The graph identifies the functional DprA ortholog class, but no exact current InterPro or GO term for the complete taxon-agnostic protein was verified during this review."
          },
          {
            "node_id": "reca",
            "label": "RecA",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Recombinase that mediates homologous recombination of transforming DNA.",
            "grounding": "InterPro:IPR013765",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:P0A452",
                "protein_label": "Protein RecA",
                "gene_symbol": "recA",
                "taxon_id": "NCBITaxon:171101",
                "taxon_label": "Streptococcus pneumoniae R6",
                "entry_status": "REVIEWED",
                "proteome_id": "UP000000586",
                "retrieved_on": "2026-10-22",
                "entry_version": 117,
                "sequence_version": 1,
                "role": "Competence-induced RecA protects transforming single-stranded DNA and catalyzes its homologous integration in pneumococcal strain R6.",
                "evidence": [
                  {
                    "reference": "DOI:10.1046/j.1365-2958.2003.03702.x",
                    "snippet": "incoming ssDNA requires active protection prior to the RecA-driven search for homology",
                    "notes": "The R6 transformation study showed rapid donor-DNA degradation and loss of homologous integration in recA mutants; UniProtKB P0A452 is the reviewed R6 RecA entry."
                  }
                ]
              }
            ]
          },
          {
            "node_id": "homologous_recombination",
            "label": "homologous recombination of transforming DNA",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Integration of incoming ssDNA into the genome via homologous recombination."
          }
        ],
        "edges": [
          {
            "subject": "competence_process",
            "predicate": "consumes",
            "object": "extracellular_dna",
            "description": "Competence drives uptake of extracellular DNA.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro3199",
                "notes": "Johnston et al. review DNA-uptake mechanisms of competence."
              }
            ],
            "predicate_id": "biolink:consumes"
          },
          {
            "subject": "competence_process",
            "predicate": "confers",
            "object": "natural_competence_trait",
            "description": "The competence program realizes the natural-competence trait.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41579-021-00650-4",
                "notes": "Transformation is a major route of bacterial DNA acquisition."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "competence_pilus",
            "predicate": "binds",
            "object": "extracellular_dna",
            "description": "Competence pili are retractile, DNA-binding filaments that capture extracellular DNA.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mmbr.00125-23",
                "notes": "Competence pili \"produce retractile, DNA-binding pili\" and co-localize DNA at their tips (Zuke & Burton 2024)."
              }
            ]
          },
          {
            "subject": "pilus_retraction",
            "predicate": "promotes",
            "object": "dna_uptake",
            "description": "Pilus retraction is mechanistically coupled to DNA delivery into the uptake apparatus.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mmbr.00125-23",
                "notes": "Physical obstruction of T4P retraction decreased transformation rate (Zuke & Burton 2024)."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "comec",
            "predicate": "required for",
            "object": "dna_uptake",
            "description": "ComEC forms a membrane channel required for DNA uptake.",
            "evidence": [
              {
                "reference": "DOI:10.1101/2024.02.06.579203",
                "notes": "\"ComEC is a membrane channel required for DNA uptake\" (Hardy et al. 2024)."
              }
            ]
          },
          {
            "subject": "comea",
            "predicate": "mediates transfer to",
            "object": "periplasm",
            "description": "ComEA acts as an external DNA receptor and mediates transfer of DNA into the periplasm.",
            "evidence": [
              {
                "reference": "DOI:10.1101/2024.02.06.579203",
                "notes": "\"ComEA functions as an external DNA receptor and mediates transfer into the periplasm\" (Hardy et al. 2024)."
              }
            ]
          },
          {
            "subject": "dpra",
            "predicate": "recruits",
            "object": "reca",
            "description": "DprA protects incoming ssDNA and recruits RecA for recombination.",
            "evidence": [
              {
                "reference": "DOI:10.1371/journal.pbio.3002814",
                "notes": "\"DprA hands incoming ssDNA to RecA\" / \"protection of incoming ssDNA by DprA and recruitment of RecA\" (Mazzamurro et al. 2024)."
              }
            ]
          },
          {
            "subject": "reca",
            "predicate": "mediates",
            "object": "homologous_recombination",
            "description": "RecA mediates homologous recombination of incoming transforming DNA into the genome.",
            "evidence": [
              {
                "reference": "DOI:10.1371/journal.pbio.3002814",
                "notes": "Transformation is followed by RecA-dependent homologous recombination (Mazzamurro et al. 2024)."
              }
            ]
          },
          {
            "subject": "pilus_retraction",
            "predicate": "contributes to",
            "object": "competence_process",
            "description": "Retraction of DNA-bound competence pili initiates uptake during the competence process.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-018-0174-y",
                "snippet": "retraction of DNA-bound type IV competence pili initiates the process of DNA uptake",
                "notes": "Verified against the open Nature Microbiology primary article."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "comea",
            "predicate": "contributes to",
            "object": "dna_uptake",
            "description": "ComEA-dependent molecular ratcheting contributes to DNA uptake into the periplasm.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-018-0174-y",
                "snippet": "uptake facilitated by ComEA-dependent molecular ratcheting",
                "notes": "Verified against the open Nature Microbiology primary article."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "homologous_recombination",
            "predicate": "contributes to",
            "object": "competence_process",
            "description": "RecA-mediated homologous recombination integrates incoming DNA and completes natural transformation.",
            "evidence": [
              {
                "reference": "DOI:10.1128/jb.00156-23",
                "snippet": "RecA binds to the ssDNA and directs homologous recombination of the incoming ssDNA into the chromosome",
                "notes": "Verified against the open Journal of Bacteriology primary article."
              }
            ],
            "predicate_id": "RO:0002326"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-06-04T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate PHYSIOLOGY trait (natural competence) from literature research to fill the genetic-plasticity gap.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-08T13:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (competence DNA uptake) with GO node grounding and biolink/RO predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 6 evidence-backed generic edges (9 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:14Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002213\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:35Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0042597\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-26T07:15:20Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 4 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A087CUH4\u00d71, UniProtKB:A0A0H2VI18\u00d71, UniProtKB:A0A1J0LTK6\u00d71, UniProtKB:A0A023H996\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:21:12Z",
        "curator": "claude",
        "action": "RETRACT_DEAD_UNIPROT_GROUNDINGS",
        "changes": "Retracted 4 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 1 causal edge(s) off enables/RO:0002327 with a TRAIT object (1 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-24T11:15:00Z",
        "curator": "codex",
        "action": "CURATE_PROTEIN_TAXON_EXAMPLE",
        "changes": "Reviewed graph scope and every competence protein node, converted the canonical pneumococcal citation to DOI, added cited strain R6, and paired its reviewed RecA with primary transformation evidence.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T11:15:00Z",
        "curator": "codex",
        "action": "CONNECT_CAUSAL_GRAPH_COMPONENTS",
        "changes": "Resolved issue #183 graph fragmentation (4 components to 1) with 3 public-source, verbatim-snippet-backed connector(s). No paid research service was called.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-22T01:35:00Z",
        "curator": "claude",
        "action": "REFRESH_UNIPROT_ENTRY_VERSION",
        "changes": "Refreshed UniProtKB entry_version against live UniProt REST on 2026-10-22: UniProtKB:P0A452 (116 -> 117 on reca).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000603",
    "label": "negative autotropism",
    "definition": "A phenotype in which germ-tube emergence or hyphal extension is directionally biased away from neighboring cells or hyphae of the same species.",
    "definition_source": "DOI:10.3390/biomimetics10050287",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.3390/biomimetics10050287",
        "snippet": "the hyphae often diverted their growth from their initial direction away from each other.",
        "notes": "Montiel-Rubies et al. (2025), Section 3.4.1; exact span in directly retrieved Europe PMC JATS, PMC12109565 (PMID:40422117). Methods and Sections 3.2/3.4.1 were read; Figure 5 and Table 2 were visually inspected in the authors' PDF. This is a retrospective analysis of earlier microfluidic experiments, not a new independent replication of those datasets. Side-by-side Pycnoporus cinnabarinus hyphae redirected laterally where space allowed. Figure 5B instead shows head-on arrest and cytoplasm retreat, not growth away. Armillaria mellea divergence could reflect directional memory. For Neurospora crassa, Table 2 rates side-by-side avoidance strong and head-on avoidance not observed; prose calls the latter extremely rare. These qualitative descriptions are not counts or replication estimates. Supplementary movies were not inspected. The definition uses the directional-growth component of this paper's broader usage."
      },
      {
        "reference": "DOI:10.1093/jxb/19.1.125",
        "snippet": "When germinated on agar surfaces the first three species exhibited negative autotropism, B. cinerea being neutral in its autotropic behaviour.",
        "notes": "Robinson, Park and Graham (1968), original publisher abstract directly retrieved from https://oup.silverchair-cdn.com/article-minimal/447341. The first three species are Rhizopus stolonifer, Mucor plumbeus and Trichoderma viride. Spore-pair assays concern orientation of germ-tube emergence, not demonstrated subsequent tip bending. Cellophane increased their negative response; Botrytis cinerea was neutral on agar and positive on Cellophane, so is not a negative exemplar here. Germination timing and cis-ness are separate readouts, not substitutes for orientation. The full paper, figures, strain provenance and sample sizes were not retrieved; proposed mechanisms in the abstract are not established causal pathways."
      }
    ],
    "discussions": [
      {
        "discussion_id": "negative-autotropism-direction-and-self-scope",
        "prompt": "Retain directional growth and stage-specific self-avoidance boundaries.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "The directional phenotype includes initial germ-tube orientation and later hyphal redirection without requiring both in one organism. Same-species neighbors can include branches of one mycelium or separate spores; this does not assert genetic identity, vegetative incompatibility or a self-recognition receptor. Positive autotropism and hyphal fusion are not exact synonyms. Whole-cell taxis, growth inhibition, branching, passive bending and cytoplasm retreat alone are insufficient. The 2025 head-on category is broader than this record's directional scope. Do not infer chemotropism or aerotropism parentage from proposed inhibitory cues or oxygen depletion. Resolve external equivalents before adding xrefs or synonyms.",
        "posed_by": "codex",
        "posed_date": "2026-10-04"
      },
      {
        "discussion_id": "negative-autotropism-provenance-and-mechanism",
        "prompt": "Resolve natural strain provenance and causal signals before enrichment.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Canonical examples are deferred until the original strain sources and NCBI identities are verified. The 1968 full paper remains unread; the 2025 Methods refer strain culture details to earlier studies and include a ro-1 mutant whose origin has not been verified here. Mutation alone does not establish genetic engineering or natural provenance. Inspect the original imaging datasets and movies before quantitative prevalence claims. Spatial constraints, directional memory and local resource gradients remain competing contributors. Neither paper establishes a universal signal/receptor chain. Resolve direct native perturbation evidence and taxon-paired protein accessions before a causal graph; NONMECHANISTIC is not a grounding bypass.",
        "posed_by": "codex",
        "posed_date": "2026-10-04"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-04T20:13:46Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added negative autotropism with two directly retrieved DOI-backed sources and exact snippets. Distinguished germ-tube emergence from hyphal redirection and excluded head-on arrest/retreat alone. Ignored-and-hidden searches and structured OWL review found no exact term. Reserved METPO:1055700 in v480 under released phenotype. Inspected Figure 5 and Table 2; retained retrospective-data, qualitative-assay and abstract-only limitations. Deferred canonical strains, external equivalents and molecular mechanisms.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-04T20:20:10Z",
        "curator": "codex",
        "action": "QUALIFY_STRAIN_PROVENANCE",
        "changes": "Issue #1684: removed the unsupported engineered qualifier for ro-1. The directly read source identifies a mutant but does not establish its origin; neither engineering nor natural provenance is inferred from mutation alone. Original mint history is preserved.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000721",
    "label": "nematode-attracting activity",
    "definition": "A physiological capability of a microorganism to elicit directed movement of nematodes toward itself or substances it produces.",
    "definition_source": "DOI:10.7554/eLife.20023",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.7554/eLife.20023",
        "snippet": "C. elegans and other nematodes were attracted to volatile compounds produced by A. oligospora.",
        "notes": "Hsueh et al. 2017, PMID:28098555, scientific abstract; native VERIFIED and direct original XML match, not an editorial digest. The producer is Arthrobotrys oligospora CBS 115.81. The 2 h assay physically separates fungal material from nematodes and compares fungal volatiles with medium controls. Actual Figure 1B/D inspected: adult responses are stronger than L1/dauer responses, and not every tested nematode species is attracted. Figure 1D, not the capture image 1E, supplies the multispecies behavioral comparison. Sodium azide retains arrivals; it is not microbial killing evidence. No universal host range, evolutionary adaptation or exact pheromone mimicry is inferred."
      },
      {
        "reference": "DOI:10.1038/ismej.2015.134",
        "snippet": "We showed that C. elegans is attracted to L. paracasei grown on citrate or yuzu media.",
        "notes": "Choi et al. 2016, online 2015, PMID:26241504, Discussion opening paragraph; native NOT_IN_ABSTRACT and direct publisher HTML match. Lactobacillus paracasei YSM0385-bearing plugs on the lid are compared with matched bacteria-free medium in a 1 h adult C. elegans N2 assay. Citrate medium includes glucose plus citrate. Actual Figures 1-4 and HTML Table 1 inspected; the table's wild co-occurrence observations alone do not establish attraction. Sodium azide retains arrivals, not bacterial toxicity. Wild isolate Y091 is only Lactobacillus sp., not an inferred L. paracasei assignment. Field recruitment, microbial benefit and nematode fitness benefit are not adopted."
      }
    ],
    "discussions": [
      {
        "discussion_id": "nematode-attraction-scope-and-hierarchy",
        "prompt": "Refine the hierarchy while preserving the microbial actor and nematode movement endpoint.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "This is the microorganism's attracting capability, not its own chemotaxis or a nematode's sensory trait. Passive retention, co-occurrence, trapping, paralysis, killing or consumption alone are insufficient; attraction need not imply any of those outcomes. Neither infection nor predatory intent is required. Phenotype METPO:1000059 is the conservative parent; the trap-formation, fungal-nematophagy and lethal-nematicidal records are related, not equivalents or necessary parents. Pinned/current METPO annotations and templates yielded no exact active or deprecated counterpart in the documented screen. v597 proposes the missing class. No exact synonyms, xrefs or organism-level disjointness are asserted.",
        "posed_by": "codex",
        "posed_date": "2026-10-13"
      },
      {
        "discussion_id": "nematode-attraction-source-and-mechanism-limits",
        "prompt": "Resolve source discrepancies and strain provenance before adding canonical taxa or microbial mechanisms.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Hsueh's five-compound exclusivity caption conflicts with a 2-methyl-1-butanol medium-control signal in its source workbook; no exclusive chemical signature is adopted. The published review exchange questions sex-pheromone mimicry and adaptation; host neuronal genetics do not establish fungal genes. Choi's host odr-10 allele is ky32 in Methods/captions but ky10 in Results; no correction is inferred. Its shared supplement link yields a colony-count image, not a separately verified S2 diacetyl calibration. Choi's typeset PDF and complete raw statistics were not audited. Strain provenance and authority taxonomy remain unchecked for canonical-example purposes. No shared microbial mechanism, proteins or causal graph is asserted. Source hashes, native outcomes, bounded notice checks and inspection limits are retained in the source verification sidecar.",
        "posed_by": "codex",
        "posed_date": "2026-10-13"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-13T23:01:02Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added a microbial nematode-attracting capability with two DOI-backed primary studies and directly matched snippets. Retained host/stage, growth-medium and source discrepancies; distinguished attraction from microbial taxis, trapping, killing and feeding. Reserved 000721, v597 and 1067400-1067499 after ignored/hidden current-copy, retained-history and open/draft PR checks with numeric false positives adjudicated. No exact active METPO counterpart was identified in the inspected scope. Other records remain unchanged. Timestamp is observed acceptance after source and allocation assessment, not the later file write.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000723",
    "label": "nematode egg-hatching inhibitory activity",
    "definition": "A physiological capability of a microorganism to reduce nematode egg hatching over a defined observation interval relative to comparable unexposed controls.",
    "definition_source": "DOI:10.1163/156854104323072883",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1163/156854104323072883",
        "snippet": "The least hatches were recorded in 7-day-old C. globosum (L250) filtrate, with 85 and 98% hatch reductions for SCN and RKN, respectively.",
        "notes": "Meyer et al. 2004, Results, printed page 28/PDF page 6; all ten pages and actual Figure 1/Table 1 inspected. C. globosum is Chaetomium globosum; SCN and RKN are Heterodera glycines and Meloidogyne incognita. Native UNRESOLVED; Crossref and USDA verify identity. Typeset span matches; PDF extraction loses the fi ligature. Seven days is culture age, not egg exposure: hatch was scored after 14 days, including motile and immotile juveniles. Percent hatch uses initial eggs, then uninoculated PDB hatch as comparator; quoted reductions are relative to that control, not egg mortality. Biomass-free filtrate concentrations differ between hosts (75/90%); approximately 200 eggs per well, five wells per treatment, water viability control. Forty isolates were retested, not all 253. pH was measured, not neutralized; no identified active molecule or universal potency threshold is inferred."
      },
      {
        "reference": "DOI:10.1038/s41598-023-33669-z",
        "snippet": "T. asperellum FbMi6 inhibited egg hatching in all concentrations as compared to control.",
        "notes": "Saharan et al. 2023, PMID:37088805, Results; direct publisher HTML match, native NOT_IN_ABSTRACT. This is its own experiment, not its background account of Meyer. Five surface-sterilized egg masses received spore-checked culture filtrates at 20/40/60/80%, with water and PDB controls; alternate-day counts through ten days, two repeats at 25 +/- 2 degrees C. Actual Figure 3 inspected. Results associates maximum inhibition with 120 h, whereas its legend specifies 2/4/6/8/10 days; no exact maximum/time pairing is adopted. Egg deformation does not prove death. Juvenile water-recovery findings are not transferred to eggs."
      }
    ],
    "discussions": [
      {
        "discussion_id": "nematode-egg-hatching-inhibition-scope-and-hierarchy",
        "prompt": "Refine the hierarchy while preserving the microbial actor and hatching endpoint.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "The microorganism has the inhibitory capability; this is not its own development or the nematode's susceptibility. Reduced hatching over an observed interval does not establish egg death, irreversible arrest or subsequent recovery. Juvenile paralysis or killing, fewer root egg masses, population suppression, trapping, attraction and sequence annotations alone are insufficient. Feeding and infection are not required. Related lethal, paralyzing, trapping, attracting and fungal-nematophagy records are not necessary parents; no organism-level disjointness is asserted. Phenotype METPO:1000059 is the conservative parent. Pinned/current METPO screening found only the unrelated fried-egg-shaped colony, not an exact active or deprecated counterpart in inspected owners; v599 proposes the class. Ovicidal terminology and nematicide chemical roles are not exact synonyms or xrefs. Neither a universal host/stage range nor a particular secretion mechanism is implied.",
        "posed_by": "codex",
        "posed_date": "2026-10-14"
      },
      {
        "discussion_id": "nematode-egg-hatching-inhibition-source-and-mechanism-limits",
        "prompt": "Resolve strain provenance and assay discrepancies before adding taxa or mechanisms.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Meyer's USDA technical abstract reports six motility-inhibitory isolates, versus four in the published paper; that separate endpoint is not silently reconciled. Saharan's claimed FbMi6 accession resolves to clone SF_570, while its supplement has SF_561/SF_570 and FbMi-4 inconsistencies documented in the lethal-nematicidal source assessment. Do not infer a corrected strain or canonical taxon. No shared active chemical, microbial protein, causal graph, field efficacy or environmental safety is asserted. Culture-filtrate effects do not define the entire class as secretion. Source hashes, direct quote checks and bounded notice checks are retained in the verification sidecar. Meyer has no Crossmark data available; no comprehensive notice clearance or full raw-data/statistical reanalysis is claimed.",
        "posed_by": "codex",
        "posed_date": "2026-10-14"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-14T03:09:57Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added microbial nematode egg-hatching inhibitory activity with two DOI-backed primary studies and directly checked 22-word and 13-word result excerpts. Retained assay denominators, exposure intervals, source discrepancies and native UNRESOLVED/NOT_IN_ABSTRACT outcomes. Distinguished hatch reduction from egg death, paralysis and reduced reproduction. Reserved 000723, v599 and 1067600-1067699 after ignored/hidden current-copy, retained-history and open/draft PR checks; broad editor ranges are not competing reservations. No exact active METPO counterpart identified in inspected owners. Other records unchanged. Timestamp records observed acceptance, not the later file write.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000724",
    "label": "nematode egg-hatching stimulatory activity",
    "definition": "A physiological capability of a microorganism to increase nematode egg hatching over a defined observation interval relative to comparable controls without that microbial influence.",
    "definition_source": "DOI:10.1163/156854104323072883",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1163/156854104323072883",
        "snippet": "Fifteen isolates (5.9%) produced compounds that strongly stimulated SCN egg hatch compared to PDB controls (Table 1).",
        "notes": "Meyer et al. 2004, Results, printed page 28/PDF page 6, lower left. SCN denotes Heterodera glycines; PDB is potato dextrose broth. Native UNRESOLVED; Crossref and the USDA-hosted article verify identity. The typeset span was visually checked; PDFKit splits controls across lines, so plain whitespace normalization does not match. Hatch counts include motile and immotile juveniles at 14 days, normalized to initial eggs and then uninoculated PDB hatch. Three or seven days denotes culture age, not egg exposure. The source-specific strong-effect threshold combines effect size and statistical significance; it is not a universal trait cutoff. Forty isolates were retested, not all 253. Nutrient depletion versus added stimulants remains unresolved despite the quote's compound wording. pH was measured, not neutralized. Host, isolate and culture age can change effect direction."
      },
      {
        "reference": "DOI:10.1186/s13071-015-0986-z",
        "snippet": "When incubated with Gram-positive bacteria, only T. muris eggs showed noticeable hatching after 20 h, although with high variability.",
        "notes": "Vejzagic et al. 2015, PMID:26174801, PMCID:PMC4501204, scientific Abstract Results; exact normalized publisher/XML match and native VERIFIED. This is its own bacterial experiment, not a citation of Meyer. Full Results and actual Figure 2 show Enterococcus caccae and Lactobacillus reuteri above bacteria-free controls after 20 h without antimicrobials, with substantial within- and between-run variability. Hatch is released larvae divided by initial embryonated eggs. T. muris and T. suis are Trichuris muris and Trichuris suis; little T. suis hatch in these conditions is not absolute inability. Antimicrobials and egg storage history affect interpretation. The E. coli strain/concentration ANOVA excludes near-zero controls; that analysis is not a statistical contrast against no bacteria. No direct-contact mechanism is inferred from background citations."
      }
    ],
    "discussions": [
      {
        "discussion_id": "nematode-egg-hatching-stimulation-scope-and-hierarchy",
        "prompt": "Refine the hierarchy without changing the microbial actor or positive-hatch endpoint.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "This is a microbial capability to increase hatching, not merely lack of inhibition, the microorganism's own development or the nematode's susceptibility. Embryogenesis without emergence, attraction, trapping, juvenile paralysis or killing alone is insufficient. Feeding, infection and benefit to the microbe are not required. No organism-level disjointness from hatch inhibition is asserted: host and culture conditions can reverse responses. Phenotype METPO:1000059 is the conservative parent. Pinned/current METPO screening found only unrelated fried-egg-shaped colony, not an exact active or deprecated counterpart in inspected owners; v600 proposes the class. No exact synonym or xref is asserted. Neither host-generalism nor a secretion/contact mechanism is implied.",
        "posed_by": "codex",
        "posed_date": "2026-10-14"
      },
      {
        "discussion_id": "nematode-egg-hatching-stimulation-source-and-mechanism-limits",
        "prompt": "Resolve host range, strain provenance and mechanism before adding canonical examples or causal edges.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Meyer explicitly leaves nutrient depletion versus added compounds unresolved. Some fungal filtrates stimulate one host while inhibiting another, and culture age can reverse activity. The bacterial study reports variable hatch and contrasts two Trichuris hosts; neither study defines universal potency or host range. No canonical taxon, shared active molecule, protein or causal graph is inferred. No field efficacy, environmental safety, infectivity benefit or therapeutic use is asserted. Methods, own results and selected figures were inspected, not the full experimental raw data. Direct snippets and bounded notice checks are retained in the verification sidecar. Crossmark responses were script shells, not current-status verdicts; Meyer publisher access returned 403. No comprehensive correction/retraction clearance is claimed.",
        "posed_by": "codex",
        "posed_date": "2026-10-14"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-14T06:04:12Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added microbial nematode egg-hatching stimulatory activity with two DOI-backed primary studies and directly checked 17-word and 19-word excerpts. Preserved native UNRESOLVED/VERIFIED outcomes, source-specific comparators, host dependence and mechanism uncertainty. Positive hatch enhancement is not merely lack of inhibition. Reserved 000724, v600 and 1067700-1067799 after ignored/hidden current-copy, retained-history and open/draft PR checks; decimal measurements, embedding coordinates and broad editor ranges are not competing reservations. No exact active METPO counterpart identified in inspected owners. Other records unchanged. Timestamp records observed acceptance, not later writing.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000725",
    "label": "nematode-repelling activity",
    "definition": "A physiological capability of a microorganism to elicit active movement of nematodes away from itself or substances it produces.",
    "definition_source": "DOI:10.1073/pnas.0610281104",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1073/pnas.0610281104",
        "snippet": "C. elegans specifically avoids certain strains of Serratia based on their production of the cyclic lipodepsipentapeptide serrawettin W2.",
        "notes": "Pradel et al. 2007, PMID:17267603, PMCID:PMC1892944, scientific Abstract; exact normalized PMC match and native VERIFIED. C. elegans denotes Caenorhabditis elegans. Own Results and actual Figures 1-4 distinguish initial entry followed by leaving Serratia marcescens lawns from absence of attraction. A swrA insertion mutant shows reduced lawn leaving but similar multiday killing; reduced avoidance is not loss of pathogenicity. Purified serrawettin W2 on E. coli OP50 lawns and acute drop-induced reversal are separate assays. The 16-hour bacterial-lawn endpoint, 60-minute supplemented-lawn endpoint and acute reversal are not one exposure. Chemical recognition versus a mechanical surfactant cue remains unresolved, and other bacterial cues can contribute. Serratia swrA is not the similarly named Bacillus motility regulator."
      },
      {
        "reference": "DOI:10.15252/embj.2020106938",
        "snippet": "a specific volatile organic compound, 1\u2010undecene, produced by the pathogen P. aeruginosa is sensed as an aversive signal by C. elegans.",
        "notes": "Prakash et al. 2021, PMID:34086368, PMCID:PMC8246062, Discussion first paragraph, own-study result; directly matched JATS, PMC and publisher text. Native NOT_IN_ABSTRACT is retained, not relabeled VERIFIED. This is its own experiment, not a citation of Pradel. P. aeruginosa denotes Pseudomonas aeruginosa. Figure 1A-B measures PA14 lawn occupancy over 12 hours. Pure 1-undecene gives negative chemotaxis and omega turns in distinct Figure 2 and Appendix S2 assays. PA14-versus-undA odor choice establishes relative preference, not by itself repulsion or complete loss of bacterial repellence. Peer-review reply page 14 reports reversals but no complete lawn leaving after 1-undecene on OP50; the alternative adjacent-lawn crossing assay is not eviction from an occupied lawn. Roaming or higher mean square displacement alone is not directional avoidance. Recipient sensory genetics is not a microbial causal pathway."
      }
    ],
    "discussions": [
      {
        "discussion_id": "nematode-repelling-activity-scope-and-hierarchy",
        "prompt": "Refine the hierarchy without confusing microbial repellence with recipient behavior or microbial taxis.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "The bearer is a microorganism capable of eliciting active nematode movement away. Lack of attraction, relative food preference alone, paralysis, killing, feeding, trapping or altered egg hatching is insufficient. Infection, benefit to the microbe and prior ingestion are not required. No organism-level disjointness from attraction or lethality is asserted: responses depend on strain, recipient and conditions. Phenotype METPO:1000059 is the conservative parent. Pinned/current releases and inspected editor/template owners have no exact counterpart identified. Deprecated chemotaxis METPO:1000062 has no replacement or consider annotation in the inspected ontology and concerns the moving organism, not this microbial capability. It is not revived or used as a mapping. The v601 proposal retains PROPOSED status; no exact synonym or external equivalence is asserted.",
        "posed_by": "codex",
        "posed_date": "2026-10-14"
      },
      {
        "discussion_id": "nematode-repelling-activity-source-and-mechanism-limits",
        "prompt": "Resolve assay conditions, host range and strain provenance before adding canonical examples or causal edges.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Two bacterial studies support the capability, not a shared molecule or universal nematode response. Gene presence or compound production alone cannot establish repellence. No canonical taxon, protein, chemical xref or causal graph is asserted without authority checks. Prakash Appendix S1A depicts a 22-hour incubation then a 2-hour, 37 C step, whereas main Methods describes 22 hours followed by one hour at room temperature; these are not harmonized into one headspace condition. Added recipient alleles and controls in peer review do not establish a successful AWB ablation or blanket physiological specificity. Neither study proves universal nonlethality, field efficacy, environmental safety or therapeutic use. Own results, methods and selected figures/supplement/replies were inspected, not all raw data. Source URLs, hashes, direct snippet checks and bounded correction/retraction searches are retained in the verification sidecar; no comprehensive notice clearance is claimed.",
        "posed_by": "codex",
        "posed_date": "2026-10-14"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-14T09:11:26Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added microbial nematode-repelling activity with two primary DOI studies and directly checked 18-word and 21-word snippets. Preserved native VERIFIED/NOT_IN_ABSTRACT outcomes and distinct lawn-leaving, reversal, chemotaxis and relative-preference endpoints. Reserved 000725, v601 and 1067800-1067899 after ignored/hidden current-copy, retained-history and open/draft PR checks. Decimal embedding values and broad editor ranges are not conflicting reservations. No exact active METPO counterpart or same-scope node migration identified in inspected owners; no canonical examples or shared mechanism inferred. Other records unchanged. Timestamp records observed acceptance.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000643",
    "label": "nucleophagy",
    "definition": "An autophagy phenotype in which a microbial cell degrades parts of its nucleus or an entire nucleus by delivering nuclear material to lysosomal or vacuolar compartments.",
    "definition_source": "DOI:10.1007/s00284-024-03838-y",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000638"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1091/mbc.e02-08-0483",
        "snippet": "During PMN, teardrop-like blebs are pinched from the nucleus, released into the vacuole lumen, and degraded by soluble hydrolases.",
        "notes": "PMID:12529432, PMC140233. Scientific Abstract directly read in Europe PMC with matching DOI. Saccharomyces cerevisiae nuclear portions undergo selective microautophagic turnover; Nvj1 degradation supports flux, not just bleb formation. The reported apg7-delta independence was revised by the 2008 follow-up, so it is not a universal absence-of-ATG requirement. Full-text retrieval failed; Methods, actual figures and strain provenance were not inspected."
      },
      {
        "reference": "DOI:10.1091/mbc.e08-04-0363",
        "snippet": "We conclude that a spectrum of ATG genes is required for the terminal vacuole enclosure and fusion stages of PMN.",
        "notes": "PMID:18701704, PMC2555948. Scientific Abstract directly read in Europe PMC with matching DOI. Two biochemical assays revise the older PMN dependence claim: atg mutants form blebs but rarely release vesicles into the vacuole. Formation, terminal enclosure and degradation are distinct readouts. This is a yeast PMN result, not a gene-inventory definition of all nucleophagy. Full-text retrieval returned HTTP 500; complete Methods and actual figures were not inspected."
      },
      {
        "reference": "DOI:10.1007/s00284-024-03838-y",
        "snippet": "These results indicate that nuclei are engulfed in the autophagosomes as a whole and transported/released into the vacuolar lumen where they are degraded.",
        "notes": "PMID:39162852, PMC11335778. Scientific Abstract directly read in Europe PMC; matching-DOI XML Methods Sec3/Sec6, Results Sec11/Sec12 and Discussion Sec13 read. Aspergillus oryzae H2B-EGFP processing and Atg1/Atg8/Ypt7/Atg15 perturbations distinguish whole-nucleus uptake, fusion and degradation. Residual carbon-starvation cleavage and possible sample-preparation proteolysis limit interpretation; complementation was incomplete. RIB40 was the DNA donor, not the assayed NSRku70-derived host; Aspergillus nidulans supplied the reporter, not the phenotype. Receptor speculation includes unpublished data. Figure captions, not actual figures or supplements, were inspected."
      },
      {
        "reference": "DOI:10.1371/journal.pone.0033270",
        "snippet": "infection-associated nuclear degeneration in M. oryzae instead occurs by non-selective macroautophagy, which is necessary for rice blast disease.",
        "notes": "PMID:22448240, PMC3308974. Scientific Abstract directly read in Europe PMC and PLOS. Results on nuclear degeneration and macroautophagy were read. H1-RFP imaging and Atg1/Atg4 perturbations support infection-associated nuclear loss; MoVac8/MoTsc13 are dispensable for it. Some selective-autophagy mutant comparisons are data not shown. The 2024 study's Discussion includes this route under nucleophagy; retain that attributed usage, not a yeast PMN assignment. Actual figures, full Methods and independent strain provenance were not inspected."
      },
      {
        "reference": "DOI:10.1242/jcs.133090",
        "snippet": "A selective form of autophagy, known as nucleophagy, can be used to accomplish the degradation of nucleus-derived material.",
        "notes": "PMID:24013549. Scientific Abstract directly read in Europe PMC with matching DOI. This is a review supporting terminology, not an independent experiment. Its selective formulation is narrower than the 2024 Discussion's inclusion of nonselective Magnaporthe nuclear degradation. Preserve that scope question explicitly rather than imposing selectivity universally. Full text and poster were not inspected."
      }
    ],
    "discussions": [
      {
        "discussion_id": "nucleophagy-cargo-route-and-selectivity",
        "prompt": "Review nuclear-cargo scope and source-specific selectivity.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Include nuclear portions and entire nuclei, micro and macro routes. The 2013 review defines nucleophagy as selective, whereas the 2024 Discussion includes the 2012 nonselective Magnaporthe route. The present cargo-defined phenotype does not require universal selectivity; preserve this attributed difference for human review. GO:0044804, resolved at https://www.ebi.ac.uk/QuickGO/services/ontology/go/terms/GO%3A0044804, is nonobsolete and includes nuclear parts or entire nuclei without an explicit selectivity restriction. Its biological process scope is not an exact organismal-phenotype xref. The autophagy parent traitmech:000638 is corrected to intracellular cargo in this change (#1754). Nuclear-envelope overlap with ER-phagy traitmech:000642 does not make the records equivalent. No exact synonyms or SSSOM mapping are asserted. Nuclear damage, loss of fluorescence or DNA degradation alone does not prove autophagic delivery and flux.",
        "posed_by": "codex",
        "posed_date": "2026-10-06"
      },
      {
        "discussion_id": "nucleophagy-flux-exemplars-and-mechanism",
        "prompt": "Resolve native exemplars and route-specific mechanisms.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "The microbial cell carrying out degradation has the phenotype, not a bacterium eliciting an animal-host response. Whole-nucleus turnover in multinucleate cells need not cause cell death. Do not equate blebs, puncta, inhibited autophagic bodies, gene presence or partial rate reductions with completed flux or total absence. The 2003/2008 PMN dependence conflict needs full-text assay reconciliation before protein-resolved causal claims. Canonical examples remain unset pending independent natural-strain provenance; do not infer origin from a mutant label. Native taxon-paired protein accessions and functional evidence are required before adding a causal graph.",
        "posed_by": "codex",
        "posed_date": "2026-10-06"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-06T13:33:28Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added nuclear-cargo autophagy with five DOI-backed snippets, source-attributed selectivity and flux limits. Corrected its autophagy parent's cytoplasmic-only wording (#1754). Ignored-and-hidden novelty checks found no exact record; reserved METPO:1059600 in v519. Deferred unverified exemplars, mappings and protein graphs.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000731",
    "label": "nutrient adaptation",
    "definition": "A trophic type that involves an organism's physiological and metabolic adaptations to specific nutrient availability.",
    "definition_source": "DOI:10.1073/pnas.0903507106",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000631"
    ],
    "created_by": "Luke Wang",
    "evidence": [
      {
        "reference": "DOI:10.1073/pnas.0903507106",
        "snippet": "high (copiotrophic) or low (oligotrophic) nutrient concentrations",
        "notes": "Comparative genomics paper frames nutrient adaptation as a copiotroph/oligotroph life-history axis."
      },
      {
        "reference": "DOI:10.1038/ismej.2014.60",
        "snippet": "selection for efficient use of nutrients",
        "notes": "Streamlining review links chronic nutrient regimes to genomic and cellular adaptation."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:335992",
        "taxon_label": "Candidatus Pelagibacter ubique HTCC1062",
        "reference": "DOI:10.1038/s41586-024-07924-w",
        "note": "Genome-wide experimental profiling found picomolar-to-low-nanomolar substrate-binding affinities and linked their systematic increase to adaptation to low substrate concentrations in the oligotrophic ocean."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "nutrient_adaptation_life_history_axis",
        "title": "Nutrient adaptation life-history axis",
        "description": "DOI-backed graph linking ambient nutrient availability to sensing, resource-allocation strategy, and the copiotroph/oligotroph life-history phenotypes that fall under nutrient adaptation.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This is a comparative life-history classification and association graph, not a concrete molecular mechanism. Its gene nodes are heterogeneous functional-category or relative-abundance signatures rather than individual causal protein families, so canonical-taxon and UniProt-example requirements do not apply.",
        "nodes": [
          {
            "node_id": "nutrient_adaptation_trait",
            "label": "nutrient adaptation",
            "node_type": "TRAIT",
            "grounding": "METPO:1000731",
            "description": "Physiological and metabolic adaptation to specific nutrient availability regimes."
          },
          {
            "node_id": "ambient_nutrient_concentration",
            "label": "ambient nutrient concentration",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Concentration of carbon, nitrogen, and phosphorus available in the habitat."
          },
          {
            "node_id": "nutrient_sensing",
            "label": "nutrient sensing",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Cellular detection of nutrient status that adjusts gene expression and growth.",
            "grounding": "GO:0009594"
          },
          {
            "node_id": "resource_allocation",
            "label": "resource allocation strategy",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Allocation of cellular resources between rapid growth machinery and high-affinity uptake or stress tolerance."
          },
          {
            "node_id": "copiotrophic_phenotype",
            "label": "copiotrophic",
            "node_type": "TRAIT",
            "grounding": "METPO:1000642",
            "description": "Adaptation favoring fast growth in nutrient-rich conditions."
          },
          {
            "node_id": "oligotrophic_phenotype",
            "label": "oligotrophic",
            "node_type": "TRAIT",
            "grounding": "METPO:1000654",
            "description": "Adaptation favoring efficient growth in nutrient-poor conditions."
          },
          {
            "node_id": "nutrient_limitation",
            "label": "chronic nutrient limitation",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Persistently low nutrient availability imposing selection for efficient resource use."
          },
          {
            "node_id": "genome_streamlining",
            "label": "genome streamlining",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Selection-driven reduction of cell and genome size and regulatory complexity under nutrient limitation."
          },
          {
            "node_id": "rrn_copy_number",
            "label": "rrn operon copy number",
            "node_type": "QUALITY",
            "description": "Number of ribosomal RNA operons in a genome, a proxy for growth potential."
          },
          {
            "node_id": "maximum_growth_potential",
            "label": "maximum growth potential",
            "node_type": "CAPACITY",
            "description": "Maximum potential growth rate of an organism or community."
          }
        ],
        "edges": [
          {
            "subject": "ambient_nutrient_concentration",
            "predicate": "causes",
            "object": "nutrient_sensing",
            "description": "Ambient nutrient levels are detected by cellular sensing systems.",
            "evidence": [
              {
                "reference": "DOI:10.1073/pnas.0903507106",
                "snippet": "high (copiotrophic) or low (oligotrophic) nutrient concentrations",
                "notes": "Supports nutrient concentration as the environmental driver of the adaptation axis."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "nutrient_sensing",
            "predicate": "controls",
            "object": "resource_allocation",
            "description": "Sensing of nutrient status shifts allocation between growth and maintenance functions.",
            "evidence": [
              {
                "reference": "DOI:10.1038/ismej.2014.60",
                "snippet": "selection for efficient use of nutrients",
                "notes": "Supports nutrient regime as a driver of resource-allocation strategy."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "resource_allocation",
            "predicate": "manifests as",
            "object": "copiotrophic_phenotype",
            "description": "Allocation favoring rapid growth machinery yields a copiotrophic phenotype under nutrient-rich conditions.",
            "evidence": [
              {
                "reference": "DOI:10.1073/pnas.0903507106",
                "snippet": "high (copiotrophic) nutrient concentrations",
                "notes": "Supports copiotrophy as one expression of nutrient adaptation."
              }
            ],
            "predicate_id": "METPO:2007400"
          },
          {
            "subject": "resource_allocation",
            "predicate": "manifests as",
            "object": "oligotrophic_phenotype",
            "description": "Allocation favoring high-affinity uptake and streamlining yields an oligotrophic phenotype under nutrient-poor conditions.",
            "evidence": [
              {
                "reference": "DOI:10.1038/ismej.2014.60",
                "snippet": "small cells and genomes",
                "notes": "Supports oligotrophy as a streamlining-driven expression of nutrient adaptation."
              }
            ],
            "predicate_id": "METPO:2007400"
          },
          {
            "subject": "copiotrophic_phenotype",
            "predicate": "is a",
            "object": "nutrient_adaptation_trait",
            "description": "Copiotrophy is a child phenotype of nutrient adaptation.",
            "evidence": [
              {
                "reference": "DOI:10.1073/pnas.0903507106",
                "snippet": "copiotrophic",
                "notes": "Supports copiotrophy as a recognized nutrient-adaptation phenotype."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "oligotrophic_phenotype",
            "predicate": "is a",
            "object": "nutrient_adaptation_trait",
            "description": "Oligotrophy is a child phenotype of nutrient adaptation.",
            "evidence": [
              {
                "reference": "DOI:10.1073/pnas.0903507106",
                "snippet": "oligotrophic",
                "notes": "Supports oligotrophy as a recognized nutrient-adaptation phenotype."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "nutrient_limitation",
            "predicate": "selects for",
            "object": "genome_streamlining",
            "description": "Chronic nutrient limitation selects for streamlined small cells and genomes.",
            "evidence": [
              {
                "reference": "DOI:10.1038/ismej.2014.60",
                "notes": "Streamlining theory attributes small cells and genomes to selection for efficient use of nutrients where nutrients limit; broad across oligotrophic microbes."
              }
            ],
            "predicate_id": "METPO:2007401"
          },
          {
            "subject": "rrn_copy_number",
            "predicate": "positively correlates with",
            "object": "maximum_growth_potential",
            "description": "Higher rrn operon copy number associates with higher maximum growth potential.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41564-023-01465-0",
                "notes": "Secondary life-history dimension correlated with ribosomal gene copy number; positive correlation between potential growth and rrn copy number."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.909957+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-11T22:00:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed causal graph framing nutrient adaptation as a sensing/resource-allocation axis manifesting as copiotrophic and oligotrophic phenotypes.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (rdfs:subClassOf\u00d72).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T21:30:07Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007400\u00d72, RO:0002211\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-26T05:00:48Z",
        "curator": "claude",
        "action": "RENAME_PREDICATE_LABELS",
        "changes": "Renamed 1 causal-edge predicate label(s) to align with existing groundings: triggers \u2192 causes \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-26T05:00:51Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:causes\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-14T05:51:47Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0009594\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 5 evidence-backed generic edges (7 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:14Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007401\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-04T03:08:16Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002212\u00d71, RO:0002213\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-24T12:35:00-07:00",
        "curator": "codex",
        "action": "REVIEWED_CAUSAL_GRAPH_PROTEIN_TAXON",
        "changes": "Classified the graph as nonmechanistic comparative life-history evidence and documented all three aggregate gene-category nodes as reviewed label-only; no trait record or graph was deprecated or removed.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T11:06:05Z",
        "curator": "codex",
        "action": "ADD_CANONICAL_EXAMPLES",
        "changes": "Added Candidatus Pelagibacter ubique HTCC1062 as a directly characterized nutrient-adaptation example from DOI:10.1038/s41586-024-07924-w; verified the current strain taxon and label through NCBI Taxonomy.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000654",
    "label": "oligotrophic",
    "definition": "A nutrient adaptation characterized by the ability to thrive in environments with very low nutrient concentrations, typically possessing efficient nutrient uptake and utilization systems.",
    "definition_source": "DOI:10.1073/pnas.0903507106",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000731"
    ],
    "synonyms": [
      {
        "synonym_text": "TT_oligotroph",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "oligotroph",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "created_by": "Jed Dongjin Kim-Ozaeta",
    "evidence": [
      {
        "reference": "DOI:10.1073/pnas.0903507106",
        "snippet": "high (copiotrophic) or low (oligotrophic) nutrient concentrations",
        "notes": "Comparative genomics paper defines oligotrophy by low-nutrient adaptation."
      },
      {
        "reference": "DOI:10.1038/ismej.2014.60",
        "snippet": "nutrients limit growth",
        "notes": "Streamlining review links nutrient limitation to small-cell/genome adaptation."
      },
      {
        "reference": "PMID:16109880",
        "snippet": "Pelagibacter ubique",
        "notes": "Organism example: Pelagibacter ubique HTCC1062 (SAR11 clade) is the archetypal oligotrophic marine bacterium with a streamlined genome adapted to nutrient-poor open-ocean conditions (Giovannoni et al. 2005, Science)."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:335992",
        "taxon_label": "Candidatus Pelagibacter ubique HTCC1062",
        "note": "Cosmopolitan genome-streamlined marine heterotroph (SAR11); ~25% of ocean microbial cells; textbook oligotroph.",
        "reference": "PMID:16109880"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "oligotrophic_low_nutrient_efficiency",
        "title": "Oligotrophic low-nutrient efficiency strategy",
        "description": "DOI-backed graph linking nutrient limitation, streamlined genomes, efficient nutrient use, and persistence in low-resource environments.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This graph summarizes comparative life-history, streamlining, and trait-association evidence rather than one concrete molecular mechanism. The solute-binding-protein node aggregates diverse transporter families, so canonical-taxon and UniProt-example requirements do not apply.",
        "nodes": [
          {
            "node_id": "oligotrophic_trait",
            "label": "oligotrophic",
            "node_type": "TRAIT",
            "grounding": "METPO:1000654",
            "description": "Nutrient adaptation to low-resource environments."
          },
          {
            "node_id": "low_nutrient_environment",
            "label": "low nutrient concentration",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Resource-poor condition favoring oligotrophic growth."
          },
          {
            "node_id": "nutrient_limitation",
            "label": "nutrient limitation",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Limiting resource availability that constrains growth."
          },
          {
            "node_id": "streamlined_genome",
            "label": "streamlined genome",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reduced genome architecture associated with efficient resource use."
          },
          {
            "node_id": "small_cell_architecture",
            "label": "small cell architecture",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Cellular architecture minimizing nutrient demand."
          },
          {
            "node_id": "efficient_nutrient_use",
            "label": "efficient nutrient use",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Growth strategy minimizing resource requirements."
          },
          {
            "node_id": "slow_growth",
            "label": "slow growth",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Low maximum growth response in chronic nutrient limitation."
          },
          {
            "node_id": "high_affinity_sbp",
            "label": "high-affinity solute-binding proteins",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Solute-binding proteins with picomolar-nanomolar affinity feeding ABC/TRAP/TTT transporters.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "The label spans substrate-specific binding proteins from several unrelated ABC, TRAP, and TTT transporter families; the cited comparative study does not define one exact family or complex."
          },
          {
            "node_id": "substrate_uptake_low_conc",
            "label": "substrate uptake at low concentration",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Uptake of dissolved substrates at picomolar-nanomolar environmental concentrations."
          },
          {
            "node_id": "metabolic_redundancy",
            "label": "metabolic redundancy",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Non-essential genes and duplicated metabolic capability, which streamlining removes."
          },
          {
            "node_id": "small_cell_volume",
            "label": "small cell volume",
            "node_type": "QUALITY",
            "description": "Very small cell volume (~0.1 um3) characteristic of oligotrophic cells."
          }
        ],
        "edges": [
          {
            "subject": "low_nutrient_environment",
            "predicate": "selects for",
            "object": "oligotrophic_trait",
            "description": "Oligotrophs grow optimally at low nutrient concentrations.",
            "evidence": [
              {
                "reference": "DOI:10.1073/pnas.0903507106",
                "snippet": "low (oligotrophic) nutrient concentrations",
                "notes": "Supports low nutrient concentration as the defining environmental context."
              }
            ],
            "predicate_id": "METPO:2007401"
          },
          {
            "subject": "nutrient_limitation",
            "predicate": "favors",
            "object": "streamlined_genome",
            "description": "Nutrient limitation favors streamlined genomic and cellular architecture.",
            "evidence": [
              {
                "reference": "DOI:10.1038/ismej.2014.60",
                "snippet": "selection for efficient use of nutrients",
                "notes": "Supports streamlining as an adaptation under nutrient limitation."
              }
            ]
          },
          {
            "subject": "streamlined_genome",
            "predicate": "contributes to",
            "object": "efficient_nutrient_use",
            "description": "Streamlined genomes reduce resource requirements for cell replication.",
            "evidence": [
              {
                "reference": "DOI:10.1038/ismej.2014.60",
                "snippet": "minimizes resources required for replication",
                "notes": "Supports genome streamlining as a resource-efficiency mechanism."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "small_cell_architecture",
            "predicate": "contributes to",
            "object": "efficient_nutrient_use",
            "description": "Small cells reduce resource demand in oligotrophic habitats.",
            "evidence": [
              {
                "reference": "DOI:10.1038/ismej.2014.60",
                "snippet": "small cells and genomes",
                "notes": "Supports small-cell architecture as part of streamlining theory."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "oligotrophic_trait",
            "predicate": "associated with",
            "object": "slow_growth",
            "description": "Oligotrophs are often slow-growing under apparently favorable conditions.",
            "evidence": [
              {
                "reference": "DOI:10.1002/bies.1091",
                "snippet": "grow slowly under apparent optimal conditions",
                "notes": "Supports slow growth as a characteristic of oligotrophic strategy."
              }
            ],
            "predicate_id": "biolink:associated_with"
          },
          {
            "subject": "efficient_nutrient_use",
            "predicate": "confers",
            "object": "oligotrophic_trait",
            "description": "Efficient nutrient use enables persistence and growth in nutrient-poor environments.",
            "evidence": [
              {
                "reference": "DOI:10.1073/pnas.0903507106",
                "snippet": "molecular mechanisms of adaptation",
                "notes": "Supports genomic mechanisms underlying oligotrophic adaptation."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "low_nutrient_environment",
            "predicate": "selects for",
            "object": "streamlined_genome",
            "description": "Low nutrient availability is a strong selective force driving genome streamlining and low GC content.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-023-36988-x",
                "notes": "Nutrient limitation is considered a strong selective force causing genome streamlining in the warm oligotrophic epipelagic ocean (Ngugi et al. 2023)."
              }
            ],
            "predicate_id": "METPO:2007401"
          },
          {
            "subject": "low_nutrient_environment",
            "predicate": "favors",
            "object": "high_affinity_sbp",
            "description": "Oligotrophic conditions favor reliance on extremely high-affinity solute-binding proteins.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41586-024-07924-w",
                "notes": "Marine bacteria rely heavily on solute-binding proteins with extremely high (picomolar-low nanomolar) binding affinity (Clifton et al. 2024)."
              }
            ]
          },
          {
            "subject": "high_affinity_sbp",
            "predicate": "increases",
            "object": "substrate_uptake_low_conc",
            "description": "High-affinity SBPs increase substrate uptake at picomolar-nanomolar concentrations matching ambient levels.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41586-024-07924-w",
                "notes": "SBP affinities match observed environmental substrate concentrations (picomolar-low nanomolar), enabling uptake at ambient levels (Clifton et al. 2024)."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "streamlined_genome",
            "predicate": "decreases",
            "object": "metabolic_redundancy",
            "description": "Genome streamlining removes non-essential genes and metabolic redundancy.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41586-024-07924-w",
                "notes": "Oligotrophic adaptation includes extreme genome streamlining with removal of non-essential genes (Clifton et al. 2024)."
              }
            ],
            "predicate_id": "RO:0002212"
          },
          {
            "subject": "oligotrophic_trait",
            "predicate": "associated with",
            "object": "small_cell_volume",
            "description": "Oligotrophs have very small cell volumes (~0.1 um3) as a recurrent hallmark.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41467-024-48591-9",
                "notes": "Oligotrophs have very small cell volumes (~0.1 um3) (Zhu & Dai 2024)."
              }
            ],
            "predicate_id": "biolink:associated_with"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-08-24T14:00:00-07:00",
        "curator": "codex",
        "action": "REVIEWED_CAUSAL_GRAPH_PROTEIN_TAXON",
        "changes": "Classified the graph as nonmechanistic comparative adaptation evidence and documented its heterogeneous solute-binding-protein category as reviewed label-only; no trait record or graph was deprecated or removed.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-05T01:35:46.878135+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-09T00:00:00-07:00",
        "curator": "Codex",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed oligotrophy graph for low nutrients, genome/cell streamlining, efficient nutrient use, and slow-growth strategy.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-16T05:00:00-07:00",
        "curator": "claude",
        "action": "ADDED_ORGANISM_EXAMPLE",
        "changes": "Added Pelagibacter ubique HTCC1062 (SAR11) organism example with PMID-backed evidence.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002326\u00d72, RO:0002327\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T05:49:25Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:associated_with\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T21:30:07Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007401\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 5 evidence-backed generic edges (4 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:14Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 4 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007401\u00d71, RO:0002213\u00d71, METPO:2000017\u00d71, biolink:associated_with\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 1 causal edge(s) off enables/RO:0002327 with a TRAIT object (1 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T02:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES_PART2",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates onto their causal-graph counterparts (1 to reduces), issue 301 part 2. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Each replacement is a 1:1 mirror of its source predicate that changes only the domain, so the claim each edge makes is unchanged and directions are unchanged. The replacements are proposed in proposals/metpo_traitmech_v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T06:00:00Z",
        "curator": "claude",
        "action": "REGROUND_CAUSAL_EDGE",
        "changes": "Relabelled 1 causal edge from `reduces` to `decreases` and re-grounded it from METPO:2007802 to RO:0002212 (negatively regulates), issue 330. The corpus wrote two senses under the single label `reduces` - genuine electron donation, and a lessens/decreases sense - and METPO:2007802 is defined as donating electrons to the object and lowering its oxidation state, which this edge does not assert. The two senses could not be separated mechanically because the label was identical, so they migrated together in issue 329 and were split here by reading each edge. RO:0002212 declares no rdfs:domain or rdfs:range, so this introduces no entailment of the kind issue 301 removed.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T06:30:00Z",
        "curator": "claude",
        "action": "RENAME_CAUSAL_NODE",
        "changes": "Renamed causal node reduced_metabolic_redundancy to metabolic_redundancy (label and description updated to match), issue 330. The node named a NEGATED quantity - the loss of redundancy - which was harmless while its in-edge was grounded to METPO:2007802 and simply wrong, but became a well-formed backwards claim once that edge was regrounded to RO:0002212 (negatively regulates): streamlining would have been asserted to prevent the loss of redundancy, the opposite of the edge's own description and of the cited Clifton et al. 2024 evidence. Naming the unnegated quantity makes `streamlined_genome decreases metabolic_redundancy` read correctly. The node is a leaf with one in-edge, so the rename is contained.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000621",
    "label": "oogamy",
    "definition": "A sexual-reproduction phenotype in which large nonmotile female gametes fuse with smaller male gametes.",
    "definition_source": "DOI:10.5194/essd-15-2711-2023",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000620"
    ],
    "evidence": [
      {
        "reference": "DOI:10.5194/essd-15-2711-2023",
        "snippet": "smaller motile male gametes with flagella (oogamous), except for red algae in which the male gamete is also non-motile.",
        "notes": "Vranken et al. (2023), Figure 2 caption, directly checked in publisher HTML and the actual figure. The full caption defines oogamy with a larger nonmotile female gamete and explicitly allows nonmotile red-algal male gametes. Thus male motility is not a universal requirement. This seaweed trait compilation supports terminology, not an independent microbial experiment or a canonical macroalgal example. The gamete-type paragraph and inheritance policy were also read: some species fields inherit genus data. Other actual figures, the data release and survey sheets remain uninspected. The figure is a life-cycle diagram, not measured gamete sizes; no numerical ratio is inferred."
      },
      {
        "reference": "DOI:10.1186/s12915-024-01878-1",
        "snippet": "Oogamy constitutes a specialized form of anisogamy wherein small male gametes are motile and large female gametes are not",
        "notes": "Lindsey et al. (2024), PMID:38600528, PMC11007952, Background Sec1 clause before the parenthetical, verified in raw XML and publisher HTML. Supports the anisogamy parent and usual motile-male formulation, not a universal rule in view of Vranken et al. The scientific abstract and scope paragraph were read; remaining analyses, actual figures and supplements were not audited. This terminology passage is not independent experimental replication."
      },
      {
        "reference": "DOI:10.1186/s40529-018-0227-9",
        "snippet": "Volvox carteri f. nagariensis is an oogamous species that has heterothallic sexuality",
        "notes": "Nozaki et al. (2018), PMID:29616358, PMC5882469, exact Background clause checked in raw XML. Scientific abstract, Background, Methods, Results, Discussion, Table 1 with row spans, captions and actual Figure 2 were inspected. Panels a-d show male spheroids/sperm packets, e female eggs, f-g mature zygotes. The Results qualify zygote formation as after possible fertilization; individual gamete fusion was not directly tracked. Do not compare packet size with egg size as a gamete-size ratio. Reference strains were induced in VTAC at 25 C with a 14:10 light-dark cycle; sexual spheroids formed after 2-4 days. Table 1's sex column is PCR-based, not 33 independent phenotype experiments. Failure to amplify HMG1f in another strain does not demonstrate deletion: primer polymorphism remains an explicit alternative. Other actual figures, Table 2 and supplements remain uninspected. Heterothallism describes this example, not all oogamy."
      },
      {
        "reference": "DOI:10.1371/journal.pbio.1001904",
        "snippet": "Transgenic female V. carteri expressing male MID produced functional sperm packets during sexual development.",
        "notes": "Geng et al. (2014), PMID:25003332, PMC4086717, scientific-abstract sentence checked in raw XML. The scientific abstract, selected Introduction/Results/Methods passages, actual Figure 2 with its caption and all extracted Table S3 text were inspected. Figure 2B/C/F/H show wild-type egg/sperm controls; D/G/I show the engineered pseudo-male spheroid, its sperm packet and an aberrant sperm cell, respectively. Panel E shows a mature zygote from an Eve::VcMID-BH x Eve cross, not the engineered parent. Table S3 distinguishes Eve (UTEX 1885) and AichiM (NIES-398) from nitA- derivatives E15 and A18 used to generate transgenics. Table S3 was text-extracted, not visually rendered; remaining source material was not fully audited. MID gain/loss supports gamete-development causality in the tested backgrounds, not a universal oogamy mechanism or a natural canonical exemplar for the engineered strains. Resolve native protein accessions before a protein-grounded causal graph."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:3068",
        "taxon_label": "Volvox carteri f. nagariensis",
        "reference": "DOI:10.1186/s40529-018-0227-9",
        "note": "Source-observed reference example, not every strain. Natural Taiwan isolates female 2016-0609-v-1 (NIES-4206) and male 2016-tw-nuk-6-1 (NIES-4208) were examined after sex-inducer treatment; see Figure 2, Table 1 and Methods. The Results describe zygotes after possible fertilization, not directly tracked fusion of each pair. Primary collection records at https://mcc.nbrp.jp/strainList.do?strainNumber=NIES-4206 and https://mcc.nbrp.jp/strainList.do?strainNumber=NIES-4208 confirm strain aliases, sex and ITS2 accessions LC376032/LC376034. Both list collection on 2016-05-25, whereas Table 1 lists 2016-06-09 and 2016-06-10 respectively (the collection records' isolation dates). This collection-date conflict remains unresolved; no date is silently corrected. Their March 2022 axenic status is not projected onto 2018. Collection fields establish provenance, not independent phenotype replication or an unmutated genome. The forma-level name and NCBITaxon:3068 were checked at https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=3068 on 2026-10-05; no reference genome is assigned to these isolates."
      }
    ],
    "discussions": [
      {
        "discussion_id": "oogamy-scope-and-motility",
        "prompt": "Keep gamete-size asymmetry distinct from universal male motility.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Use anisogamy traitmech:000620 in its explicit broad size-based sense, as in Lindsey et al. (2024), even though some sources separate motile-both anisogamy from oogamy. Vranken et al. (2023) explicitly include nonmotile male red-algal gametes. Large and small compare gamete types, not vegetative cells or sperm packets; no numerical size cutoff, fixed gamete count, fertilization location, monoecy/dioecy or mating-system requirement is imposed. Physiological anisogamy without size dimorphism is not equivalent. No organism-level disjointness is asserted. Verify external equivalences and lexical synonyms before adding mappings.",
        "posed_by": "codex",
        "posed_date": "2026-10-05"
      },
      {
        "discussion_id": "oogamy-mechanism-and-provenance",
        "prompt": "Resolve protein groundings and strain metadata before mechanism expansion.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Oogamy is a gamete phenotype, not a MID/MAT sequence feature. The 2014 MID perturbations support sex-development causality in particular engineered backgrounds; they do not by themselves supply a universal mechanism for size asymmetry and female immotility. Resolve accessions and remaining source material before graph construction; no NONMECHANISTIC graph bypasses this gap. Do not turn 2018 PCR absence into demonstrated deletion or transfer the separate strain's failed crosses to all reference crosses. Preserve the collection-date discrepancy and later axenic status explicitly. Retain actual abstract-resolver verdicts separately from manual full-text source checks.",
        "posed_by": "codex",
        "posed_date": "2026-10-05"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-05T14:12:03Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added oogamy with four DOI-backed verbatim snippets, a qualified natural Volvox example and explicit male-motility exceptions. Ignored-and-hidden novelty/allocation searches found no exact record or collision. Extended v497 with METPO:1057410 under anisogamy METPO:1057400; deferred unverified mappings and causal mechanisms.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-05T14:24:04Z",
        "curator": "codex",
        "action": "CORRECTED_EVIDENCE_PANEL",
        "changes": "Addressed #1713: Figure 2E in Geng et al. (2014) is a cross-derived mature zygote, not an engineered pseudo-male. Distinguished its role from D/G/I using the directly inspected caption and actual figure. Definition, verbatim snippet, natural canonical example and proposal hierarchy remain unchanged.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000664",
    "label": "organoheterotrophic",
    "definition": "A trophic type characterized by the use of organic compounds as both electron donors and primary carbon sources for energy generation and biosynthesis.",
    "definition_source": "DOI:10.1016/B978-012373944-5.00083-3",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000631"
    ],
    "synonyms": [
      {
        "synonym_text": "organoheterotroph",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "created_by": "Anthea Guo",
    "evidence": [
      {
        "reference": "DOI:10.1016/B978-012373944-5.00083-3",
        "snippet": "organic compounds as the primary sources of carbon and energy",
        "notes": "Encyclopedia chapter supports organic compounds as carbon and energy sources in heterotrophy."
      },
      {
        "reference": "DOI:10.1016/j.bbabio.2008.09.008",
        "snippet": "free energy of a redox reaction",
        "notes": "Review supports energy conservation from electron donor oxidation through respiratory chains."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:562",
        "taxon_label": "Escherichia coli",
        "note": "organoheterotroph",
        "reference": "PMID:31778652"
      },
      {
        "taxon_id": "NCBITaxon:83333",
        "taxon_label": "Escherichia coli K-12",
        "note": "Strain-level organoheterotrophic model paired to the reviewed AtpD beta component of its F-type ATP synthase.",
        "reference": "DOI:10.7554/eLife.21598"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "organoheterotrophic_organic_donor_carbon",
        "title": "Organoheterotrophic organic donor and carbon use",
        "description": "DOI-backed graph linking organic compounds as electron donors and carbon sources to central metabolism, respiratory energy conservation, ATP, and biomass.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "This graph models the respiratory branch of organoheterotrophy. The E. coli K-12 AtpD example is one component of F-type ATP synthase and does not denote the full rotary complex or every organoheterotrophic route.",
        "nodes": [
          {
            "node_id": "organoheterotrophic_trait",
            "label": "organoheterotrophic",
            "node_type": "TRAIT",
            "grounding": "METPO:1000664",
            "description": "Trophic type using organic compounds for electrons and carbon."
          },
          {
            "node_id": "organic_compound",
            "label": "organic compound",
            "node_type": "CHEMICAL",
            "description": "Reduced organic molecule serving as electron donor and carbon source.",
            "grounding": "CHEBI:50860"
          },
          {
            "node_id": "central_carbon_metabolism",
            "label": "central carbon metabolism",
            "node_type": "PATHWAY",
            "description": "Core metabolic routes that oxidize and assimilate organic carbon."
          },
          {
            "node_id": "respiratory_chain",
            "label": "respiratory chain",
            "node_type": "PATHWAY",
            "description": "Electron-transfer system conserving redox energy.",
            "grounding": "GO:0022904"
          },
          {
            "node_id": "carbon_dioxide",
            "label": "carbon dioxide",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:16526",
            "description": "Oxidized carbon product of organic substrate dissimilation."
          },
          {
            "node_id": "atp",
            "label": "ATP",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:30616",
            "description": "Energy carrier produced during metabolism."
          },
          {
            "node_id": "biomass",
            "label": "biomass",
            "node_type": "CHEMICAL",
            "description": "Cell material built from organic carbon.",
            "grounding": "METPO:1007501"
          },
          {
            "node_id": "glycolysis",
            "label": "glycolysis (Embden-Meyerhof pathway)",
            "node_type": "PATHWAY",
            "description": "Pathway oxidizing sugars to pyruvate, central to organic carbon catabolism."
          },
          {
            "node_id": "tca_cycle",
            "label": "tricarboxylic acid cycle",
            "node_type": "PATHWAY",
            "description": "Cyclic pathway for oxidative catabolism of organic substrates yielding reducing equivalents and CO2.",
            "grounding": "GO:0006099"
          },
          {
            "node_id": "oxidative_phosphorylation",
            "label": "oxidative phosphorylation",
            "node_type": "PATHWAY",
            "description": "ATP synthesis driven by electron transfer through respiratory complexes.",
            "grounding": "GO:0006119"
          },
          {
            "node_id": "nadh_dehydrogenase_complex_i",
            "label": "NADH dehydrogenase (complex I)",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Respiratory complex I oxidizing NADH and pumping protons.",
            "grounding": "GO:0030964"
          },
          {
            "node_id": "cytochrome_bc1_complex",
            "label": "cytochrome bc1 complex (complex III)",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Respiratory complex III transferring electrons from quinol to cytochrome c.",
            "grounding": "GO:0045275"
          },
          {
            "node_id": "atp_synthase",
            "label": "ATP synthase",
            "node_type": "GENE_OR_PROTEIN",
            "grounding": "GO:0045259",
            "description": "F-type rotary complex producing ATP during oxidative phosphorylation.",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:P0ABB4",
                "protein_label": "ATP synthase subunit beta",
                "gene_symbol": "atpD",
                "taxon_id": "NCBITaxon:83333",
                "taxon_label": "Escherichia coli K-12",
                "entry_status": "REVIEWED",
                "retrieved_on": "2026-10-22",
                "entry_version": 156,
                "sequence_version": 2,
                "role": "Beta component of the E. coli F1 catalytic head; this accession is not presented as the complete F1Fo complex.",
                "evidence": [
                  {
                    "reference": "DOI:10.7554/eLife.21598",
                    "snippet": "proton motive force drives rotation and conformational changes in the F1 catalytic sites",
                    "notes": "The primary cryo-EM study resolves the E. coli F1Fo complex and its beta-containing catalytic head; UniProt verifies the reviewed K-12 AtpD entry."
                  }
                ]
              }
            ]
          }
        ],
        "edges": [
          {
            "subject": "organoheterotrophic_trait",
            "predicate": "has electron donor",
            "object": "organic_compound",
            "description": "Organic compounds serve as the electron donors for organoheterotrophy.",
            "evidence": [
              {
                "reference": "DOI:10.1021/acsomega.3c02205",
                "snippet": "organic molecules ... electron source",
                "notes": "Supports organic molecules as electron sources in organoheterotrophic categories."
              }
            ],
            "predicate_id": "METPO:2007701"
          },
          {
            "subject": "organoheterotrophic_trait",
            "predicate": "has carbon source",
            "object": "organic_compound",
            "description": "Heterotrophy uses organic compounds as carbon sources.",
            "evidence": [
              {
                "reference": "DOI:10.1016/B978-012373944-5.00083-3",
                "snippet": "organic compounds as the primary sources of carbon",
                "notes": "Supports organic compounds as the carbon source for heterotrophic growth."
              }
            ],
            "predicate_id": "METPO:2007806"
          },
          {
            "subject": "organic_compound",
            "predicate": "metabolized by",
            "object": "central_carbon_metabolism",
            "description": "Organic compounds enter central metabolism for catabolism and biosynthesis.",
            "evidence": [
              {
                "reference": "DOI:10.1016/B978-012373944-5.00083-3",
                "snippet": "catabolism",
                "notes": "Supports breakdown of nutrients to provide energy and biosynthetic precursors."
              }
            ]
          },
          {
            "subject": "central_carbon_metabolism",
            "predicate": "feeds electrons into",
            "object": "respiratory_chain",
            "description": "Oxidation of organic substrates supplies reducing equivalents to respiratory chains.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.bbabio.2008.09.008",
                "snippet": "electron transfer process",
                "notes": "Supports respiratory energy conservation through electron transfer."
              }
            ],
            "predicate_id": "METPO:2007402"
          },
          {
            "subject": "central_carbon_metabolism",
            "predicate": "oxidizes carbon to",
            "object": "carbon_dioxide",
            "description": "Organic substrate oxidation can release CO2.",
            "evidence": [
              {
                "reference": "DOI:10.1016/B978-012373944-5.00083-3",
                "snippet": "dissimilation",
                "notes": "Supports oxidation of nutrients to provide energy for biosynthesis and maintenance."
              }
            ]
          },
          {
            "subject": "respiratory_chain",
            "predicate": "has output",
            "object": "atp",
            "description": "Respiratory electron transfer conserves energy as ATP.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.bbabio.2008.09.008",
                "snippet": "drives ATP synthesis",
                "notes": "Supports ATP synthesis from respiratory energy conservation."
              }
            ],
            "predicate_id": "RO:0002234"
          },
          {
            "subject": "organic_compound",
            "predicate": "assimilated into",
            "object": "biomass",
            "description": "Organic carbon supplies building blocks for biomass.",
            "evidence": [
              {
                "reference": "DOI:10.1016/B978-012373944-5.00083-3",
                "snippet": "incorporation of a compound into biomass",
                "notes": "Supports assimilation of organic nutrients into new cell material."
              }
            ]
          },
          {
            "subject": "glycolysis",
            "predicate": "enables",
            "object": "central_carbon_metabolism",
            "description": "A complete glycolytic (Embden-Meyerhof) pathway enables catabolism of organic carbon substrates.",
            "evidence": [
              {
                "reference": "DOI:10.1128/spectrum.04110-22",
                "notes": "Genome annotation identifies a complete glycolysis (Embden-Meyerhof) pathway; standard route for organic carbon catabolism."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "tca_cycle",
            "predicate": "enables",
            "object": "central_carbon_metabolism",
            "description": "A complete TCA cycle enables oxidative catabolism of organic substrates within central metabolism.",
            "evidence": [
              {
                "reference": "DOI:10.1128/spectrum.04110-22",
                "notes": "A complete tricarboxylic acid (TCA) cycle is present, indicating capacity for oxidative catabolism of organic substrates."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "nadh_dehydrogenase_complex_i",
            "predicate": "contributes to",
            "object": "oxidative_phosphorylation",
            "description": "NADH dehydrogenase (complex I) feeds electrons into the respiratory chain for oxidative phosphorylation.",
            "evidence": [
              {
                "reference": "DOI:10.1128/spectrum.04110-22",
                "notes": "A complete oxidative phosphorylation pathway is encoded, including NADH dehydrogenase (nuoABCDEFGHIJKLMN)."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "cytochrome_bc1_complex",
            "predicate": "contributes to",
            "object": "oxidative_phosphorylation",
            "description": "The cytochrome bc1 complex transfers electrons in the respiratory chain supporting oxidative phosphorylation.",
            "evidence": [
              {
                "reference": "DOI:10.1128/spectrum.04110-22",
                "notes": "A complete oxidative phosphorylation pathway is encoded, including cytochrome bc1 (petABC)."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "oxidative_phosphorylation",
            "predicate": "has output",
            "object": "atp",
            "description": "Oxidative phosphorylation conserves respiratory energy as ATP.",
            "evidence": [
              {
                "reference": "DOI:10.1128/spectrum.04110-22",
                "notes": "A complete oxidative phosphorylation pathway is encoded, coupling electron transfer to ATP synthesis."
              }
            ],
            "predicate_id": "RO:0002234"
          },
          {
            "subject": "atp_synthase",
            "predicate": "participates in",
            "object": "oxidative_phosphorylation",
            "description": "F-type ATP synthase couples the respiratory gradient to ATP production.",
            "evidence": [
              {
                "reference": "DOI:10.7554/eLife.21598",
                "snippet": "proton motive force drives rotation and conformational changes in the F1 catalytic sites",
                "notes": "Supports the beta-containing E. coli F1Fo ATP synthase as the ATP-producing machinery of oxidative phosphorylation."
              }
            ],
            "predicate_id": "biolink:participates_in"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.883809+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-08T00:00:00-07:00",
        "curator": "codex",
        "action": "ADDED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed causal graph for organic compounds as electron donors and carbon sources supporting respiration, ATP, and biomass.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000009\u00d71, METPO:2000006\u00d71, METPO:2000202\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T21:30:07Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007402\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:38:01Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0022904\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:41:04Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (METPO:1007501\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T07:34:59Z",
        "curator": "claude",
        "action": "RETYPE_CAUSAL_NODES",
        "changes": "Re-typed 1 causal-node node_type field(s) to align with CausalNodeTypeEnum semantics: biomass: BIOLOGICAL_PROCESS \u2192 CHEMICAL \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T08:14:33Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:50860\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 5 evidence-backed generic edges (5 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:14Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 5 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d72, RO:0002326\u00d72, METPO:2000202\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:35Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0006099\u00d71, GO:0006119\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-05T12:00:00Z",
        "curator": "claude",
        "action": "REVERSE_CAUSAL_EDGE_DIRECTION",
        "changes": "Reversed 1 causal edge from <trait> uses electron donor <chemical> to <chemical> enables <trait> (predicate_id METPO:2000009 -> RO:0002327), issue 295. METPO:2000009 is rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so the trait-subject form entailed that this TRAIT node is a microbe; CausalNodeTypeEnum has no organism member, so no causal-graph edge can satisfy that domain. Evidence unchanged; only subject/predicate/object/predicate_id and the edge description moved. Note RO:0002327 has range 'biological process or activity', so the new form is not fully range-correct either - tracked in issue 302.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 1 causal edge(s) off enables/RO:0002327 with a TRAIT object (1 to has electron donor), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them. 1 electron edge(s) were also reversed back to trait -> chemical, restoring the donor/acceptor role that PR 300 collapsed onto enables (issue 303); the organism-subject problem that forced that collapse does not arise here because these predicates take a causal-node domain rather than METPO:2000001's microbe domain (issue 301).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 3 causal edge(s) off microbe-domain METPO predicates (1 to has carbon source, 2 to has output), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-16T02:00:00Z",
        "curator": "claude",
        "action": "NORMALISE_NODE_TYPE",
        "changes": "Under the PATHWAY-vs-BIOLOGICAL_PROCESS rule, one node_id means one thing corpus-wide (issue 356): oxidative_phosphorylation is typed PATHWAY. PATHWAY is a named, conventionally enumerable multi-step route; BIOLOGICAL_PROCESS is everything else. A named route through enumerable complexes -- environment/ph_delta_mid1.yaml lists them (nuo, cyo, ndh, sdh). The rule breaks what was a 2-2 tie before this tranche.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "CURATE_PROTEIN_TAXON_EXAMPLE",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope organoheterotrophic_organic_donor_carbon=MECHANISTIC with scope_notes; added taxon-paired protein example(s) UniProtKB:P0ABB4 on atp_synthase (NCBITaxon:83333); regrounded 2 node(s) (nadh_dehydrogenase_complex_i: none->GO:0030964, cytochrome_bc1_complex: none->GO:0045275); added 1 node(s) and 1 edge(s) (atp_synthase); added canonical example(s) NCBITaxon:83333.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-22T01:35:00Z",
        "curator": "claude",
        "action": "REFRESH_UNIPROT_ENTRY_VERSION",
        "changes": "Refreshed UniProtKB entry_version against live UniProt REST on 2026-10-22: UniProtKB:P0ABB4 (155 -> 156 on atp_synthase).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000655",
    "label": "organotrophic",
    "definition": "A trophic type in which an organism obtains energy from the oxidation of organic compounds.",
    "definition_source": "DOI:10.1016/B978-012373944-5.00083-3",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000631"
    ],
    "synonyms": [
      {
        "synonym_text": "TT_organotroph",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "organotroph",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1016/B978-012373944-5.00083-3",
        "snippet": "incorporation of a compound into biomass",
        "notes": "Microbial metabolism reference supports assimilation and use of organic compounds in growth."
      },
      {
        "reference": "DOI:10.1016/j.bbabio.2008.09.008",
        "snippet": "membrane-bound electron transport chain",
        "notes": "Review supports respiratory electron transport as an energy-conserving route."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:562",
        "taxon_label": "Escherichia coli",
        "note": "organic electron-donor organotroph",
        "reference": "PMID:9278503"
      },
      {
        "taxon_id": "NCBITaxon:1423",
        "taxon_label": "Bacillus subtilis",
        "note": "soil organotroph",
        "reference": "PMID:9384377"
      },
      {
        "taxon_id": "NCBITaxon:83333",
        "taxon_label": "Escherichia coli K-12",
        "note": "Strain-level organotrophic model paired to the reviewed AtpD beta component of its F-type ATP synthase.",
        "reference": "DOI:10.7554/eLife.21598"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "organotrophic_organic_compound_oxidation",
        "title": "Organotrophic organic compound oxidation",
        "description": "DOI-backed graph linking organic electron donors, catabolism, respiratory energy conservation, ATP production, and biomass precursors.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "This graph represents respiratory oxidation of organic substrates. The E. coli K-12 AtpD example anchors F-type ATP synthesis and is one beta component, not the complete rotary complex.",
        "nodes": [
          {
            "node_id": "organotrophic_trait",
            "label": "organotrophic",
            "node_type": "TRAIT",
            "grounding": "METPO:1000655",
            "description": "Trophic type using organic compounds as electron donors for energy."
          },
          {
            "node_id": "organic_compound",
            "label": "organic compound",
            "node_type": "CHEMICAL",
            "description": "Reduced organic substrate serving as electron donor.",
            "grounding": "CHEBI:50860"
          },
          {
            "node_id": "glucose",
            "label": "glucose",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:17234",
            "description": "Representative organic substrate."
          },
          {
            "node_id": "catabolism",
            "label": "catabolism",
            "node_type": "BIOLOGICAL_PROCESS",
            "grounding": "GO:0009056",
            "description": "Oxidative breakdown of organic compounds."
          },
          {
            "node_id": "respiratory_chain",
            "label": "respiratory chain",
            "node_type": "PATHWAY",
            "description": "Electron-transfer pathway conserving energy.",
            "grounding": "GO:0022904"
          },
          {
            "node_id": "proton_motive_force",
            "label": "proton motive force",
            "node_type": "STATE",
            "description": "Electrochemical ion gradient generated by respiration.",
            "grounding": "METPO:1007500"
          },
          {
            "node_id": "atp",
            "label": "ATP",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:30616",
            "description": "Cellular energy carrier."
          },
          {
            "node_id": "precursor_metabolites",
            "label": "precursor metabolites",
            "node_type": "CHEMICAL",
            "description": "Catabolic intermediates used for biosynthesis."
          },
          {
            "node_id": "reduced_electron_carriers",
            "label": "NADH and FADH2",
            "node_type": "CHEMICAL",
            "description": "Reduced electron carriers (NADH/FADH2) generated by catabolic oxidation."
          },
          {
            "node_id": "nadh_dehydrogenase",
            "label": "NADH dehydrogenase (Complex I)",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Respiratory enzyme complex extracting electrons from NADH.",
            "grounding": "GO:0030964"
          },
          {
            "node_id": "organic_carbon_availability",
            "label": "organic carbon availability",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Availability of organic carbon substrates in the environment."
          },
          {
            "node_id": "atp_synthase",
            "label": "ATP synthase",
            "node_type": "GENE_OR_PROTEIN",
            "grounding": "GO:0045259",
            "description": "F-type rotary complex converting proton motive force into ATP.",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:P0ABB4",
                "protein_label": "ATP synthase subunit beta",
                "gene_symbol": "atpD",
                "taxon_id": "NCBITaxon:83333",
                "taxon_label": "Escherichia coli K-12",
                "entry_status": "REVIEWED",
                "retrieved_on": "2026-10-22",
                "entry_version": 156,
                "sequence_version": 2,
                "role": "Beta component of the E. coli F1 catalytic head; this accession is not presented as the complete F1Fo complex.",
                "evidence": [
                  {
                    "reference": "DOI:10.7554/eLife.21598",
                    "snippet": "proton motive force drives rotation and conformational changes in the F1 catalytic sites",
                    "notes": "The primary cryo-EM study resolves the E. coli F1Fo complex and its beta-containing catalytic head; UniProt verifies the reviewed K-12 AtpD entry."
                  }
                ]
              }
            ]
          }
        ],
        "edges": [
          {
            "subject": "organotrophic_trait",
            "predicate": "has electron donor",
            "object": "organic_compound",
            "description": "Organic compounds serve as the electron donors for organotrophy.",
            "evidence": [
              {
                "reference": "DOI:10.1016/B978-012373944-5.00083-3",
                "snippet": "incorporation of a compound into biomass",
                "notes": "Supports use and assimilation of organic compounds in microbial growth."
              }
            ],
            "predicate_id": "METPO:2007701"
          },
          {
            "subject": "glucose",
            "predicate": "example of",
            "object": "organic_compound",
            "description": "Glucose is a representative organic substrate.",
            "evidence": [
              {
                "reference": "DOI:10.1021/acsomega.3c02205",
                "snippet": "glucose metabolism",
                "notes": "Supports glucose as a microbial organic substrate."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "organic_compound",
            "predicate": "oxidized by",
            "object": "catabolism",
            "description": "Organic substrates are oxidized through catabolic metabolism.",
            "evidence": [
              {
                "reference": "DOI:10.1016/B978-012373944-5.00083-3",
                "snippet": "heterotrophic microorganisms",
                "notes": "Supports catabolism of organic compounds by heterotrophic microbial metabolism."
              }
            ]
          },
          {
            "subject": "catabolism",
            "predicate": "feeds electrons into",
            "object": "respiratory_chain",
            "description": "Oxidative catabolism supplies electrons to energy-conserving respiration.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.bbabio.2008.09.008",
                "snippet": "electron transfer process",
                "notes": "Supports electron transfer through respiratory chains."
              }
            ],
            "predicate_id": "METPO:2007402"
          },
          {
            "subject": "respiratory_chain",
            "predicate": "generates",
            "object": "proton_motive_force",
            "description": "Respiratory electron transfer generates an ion gradient.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.bbabio.2008.09.008",
                "snippet": "generation of an electrochemical ion gradient",
                "notes": "Supports proton motive force generation by membrane electron transport."
              }
            ],
            "predicate_id": "biolink:produces"
          },
          {
            "subject": "proton_motive_force",
            "predicate": "drives production of",
            "object": "atp",
            "description": "Proton motive force powers ATP synthesis.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.bbabio.2008.09.008",
                "snippet": "drives ATP synthesis",
                "notes": "Supports ATP synthesis from respiratory energy conservation."
              }
            ],
            "predicate_id": "biolink:produces"
          },
          {
            "subject": "proton_motive_force",
            "predicate": "drives",
            "object": "atp_synthase",
            "description": "Proton motive force drives the F-type ATP synthase rotary mechanism.",
            "evidence": [
              {
                "reference": "DOI:10.7554/eLife.21598",
                "snippet": "proton motive force drives rotation and conformational changes in the F1 catalytic sites",
                "notes": "The E. coli structural study directly supports the coupling mechanism of the beta-containing ATP synthase complex."
              }
            ],
            "predicate_id": "RO:0002212"
          },
          {
            "subject": "catabolism",
            "predicate": "has output",
            "object": "precursor_metabolites",
            "description": "Organic-compound catabolism supplies biosynthetic precursors.",
            "evidence": [
              {
                "reference": "DOI:10.1016/B978-012373944-5.00083-3",
                "snippet": "incorporation of a compound into biomass",
                "notes": "Supports use of compound-derived intermediates for biomass formation."
              }
            ],
            "predicate_id": "RO:0002234"
          },
          {
            "subject": "catabolism",
            "predicate": "generates",
            "object": "reduced_electron_carriers",
            "description": "Oxidation of organic substrates by catabolic pathways generates reduced electron carriers.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s13213-024-01761-y",
                "notes": "Catabolic pathways (Krebs cycle and beta-oxidation) generate reduced carriers (NADH and FADH2)."
              }
            ],
            "predicate_id": "biolink:produces"
          },
          {
            "subject": "reduced_electron_carriers",
            "predicate": "donates electrons to",
            "object": "nadh_dehydrogenase",
            "description": "NADH donates electrons to NADH dehydrogenase (Complex I) to enter the respiratory chain.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s13213-024-01761-y",
                "notes": "NADH dehydrogenase (Complex I) extracts hydrogen/electrons from NADH; broad canonical ETC-entry edge."
              }
            ],
            "predicate_id": "METPO:2007403"
          },
          {
            "subject": "nadh_dehydrogenase",
            "predicate": "feeds electrons into",
            "object": "respiratory_chain",
            "description": "NADH dehydrogenase passes electrons into the membrane respiratory chain.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s13213-024-01761-y",
                "notes": "Reduced carriers feed electrons into membrane electron-transport systems via NADH dehydrogenase."
              }
            ],
            "predicate_id": "METPO:2007402"
          },
          {
            "subject": "organic_carbon_availability",
            "predicate": "increases abundance of",
            "object": "organotrophic_trait",
            "description": "Enriched organic carbon supports proliferation of organotrophs.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41396-023-01437-6",
                "notes": "Enriched organic C and dissolved organic C can support the rapid propagation of obligate organotrophic copiotrophs."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.879073+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-09T00:00:00-07:00",
        "curator": "Codex",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed organotrophy graph for organic substrate oxidation, respiratory energy conservation, ATP, and biosynthetic precursors.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000009\u00d71, METPO:2000202\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T08:21:50Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (rdfs:subClassOf\u00d71, biolink:produces\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T21:30:07Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007402\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:38:01Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0022904\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:41:04Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (METPO:1007500\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T08:14:33Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:50860\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-26T02:30:14Z",
        "curator": "claude",
        "action": "RETYPE_CAUSAL_NODES",
        "changes": "Re-typed 1 causal-node node_type field(s) to align with CausalNodeTypeEnum semantics: proton motive force: BIOLOGICAL_PROCESS \u2192 STATE \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-13T21:03:27Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:produces\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 4 evidence-backed generic edges (3 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:15Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:produces\u00d71, METPO:2007403\u00d71, METPO:2007402\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-05T12:00:00Z",
        "curator": "claude",
        "action": "REVERSE_CAUSAL_EDGE_DIRECTION",
        "changes": "Reversed 1 causal edge from <trait> uses electron donor <chemical> to <chemical> enables <trait> (predicate_id METPO:2000009 -> RO:0002327), issue 295. METPO:2000009 is rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so the trait-subject form entailed that this TRAIT node is a microbe; CausalNodeTypeEnum has no organism member, so no causal-graph edge can satisfy that domain. Evidence unchanged; only subject/predicate/object/predicate_id and the edge description moved. Note RO:0002327 has range 'biological process or activity', so the new form is not fully range-correct either - tracked in issue 302.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 1 causal edge(s) off enables/RO:0002327 with a TRAIT object (1 to has electron donor), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them. 1 electron edge(s) were also reversed back to trait -> chemical, restoring the donor/acceptor role that PR 300 collapsed onto enables (issue 303); the organism-subject problem that forced that collapse does not arise here because these predicates take a causal-node domain rather than METPO:2000001's microbe domain (issue 301).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates (1 to has output), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "CURATE_PROTEIN_TAXON_EXAMPLE",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope organotrophic_organic_compound_oxidation=MECHANISTIC with scope_notes; added taxon-paired protein example(s) UniProtKB:P0ABB4 on atp_synthase (NCBITaxon:83333); regrounded 1 node(s) (nadh_dehydrogenase: none->GO:0030964); added 1 node(s) and 1 edge(s) (atp_synthase); added canonical example(s) NCBITaxon:83333.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-22T01:35:00Z",
        "curator": "claude",
        "action": "REFRESH_UNIPROT_ENTRY_VERSION",
        "changes": "Refreshed UniProtKB entry_version against live UniProt REST on 2026-10-22: UniProtKB:P0ABB4 (155 -> 156 on atp_synthase).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000154",
    "label": "ornithine decarboxylase activity",
    "definition": "A physiological enzyme-activity phenotype in which a cell produces active ornithine decarboxylase enzymes that decarboxylate L-ornithine to putrescine and carbon dioxide.",
    "definition_source": "https://iubmb.qmul.ac.uk/enzyme/EC4/1/1/17.html",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "https://iubmb.qmul.ac.uk/enzyme/EC4/1/1/17.html",
        "snippet": "Reaction: L-ornithine = putrescine + CO2",
        "notes": "The NC-IUBMB EC 4.1.1.17 entry defines ornithine decarboxylase by its accepted name and reaction from L-ornithine to putrescine and CO2, grounding the enzyme activity named by the organism-level phenotype."
      },
      {
        "reference": "DOI:10.1128/jb.124.2.791-799.1975",
        "snippet": "Several Escherichia coli K-12 mutants blocked in the synthesis of ornithine decarboxylase (OD) were isolated after transduction for serA+ in a strain (MA197) blocked in agmatine ureohydrolase (AUH) with a mutagenized phage lysate of P1. The new double-polyamine mutants were characterized by an unconditional polyamine dependence; either putrescine or spermidine was required for normal growth. The mutational block was varified by the demonstration of a virtual absence of OD activity in cellular extracts.",
        "notes": "Cunningham-Rundles and Maas isolated Escherichia coli K-12 mutants blocked in ornithine decarboxylase synthesis and verified the loss of OD activity, supporting E. coli K-12 as a direct organismal example for the activity."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:83333",
        "taxon_label": "Escherichia coli K-12",
        "note": "Cunningham-Rundles and Maas isolated E. coli K-12 speC mutants with a virtual absence of ornithine decarboxylase activity in cellular extracts.",
        "reference": "DOI:10.1128/jb.124.2.791-799.1975"
      }
    ],
    "discussions": [
      {
        "discussion_id": "ornithine-decarboxylase-activity-xref-gap",
        "prompt": "Resolve an exact external ontology class for ornithine decarboxylase activity before adding a TraitRecord xref.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "GO:0004586 carries the same ornithine decarboxylase activity label but denotes the enzyme molecular function rather than the organism-level ornithine decarboxylase production phenotype, so it is appropriate as a causal-node grounding rather than an equivalent TraitRecord xref.",
        "posed_by": "codex",
        "posed_date": "2026-09-12"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-12T02:38:18Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted ornithine decarboxylase activity as a URL/DOI-backed TraitRecord after a repository-wide duplicate review covering ignored and hidden files; METPO has no exact ornithine decarboxylase activity class yet.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000592",
    "label": "osmotaxis",
    "definition": "A motile phenotype in which active locomotion produces net migration in response to a spatial gradient in external osmotic conditions.",
    "definition_source": "DOI:10.1016/s0014-4894(03)00031-6",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000702"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1016/s0014-4894(03)00031-6",
        "snippet": "We find that promastigotes move towards concentrations of all substances tested and that this taxis requires the presence of an osmotic gradient.",
        "notes": "Abstract, exact-matched at Europe PMC (PMID:12706748); full text not inspected. The study concerns Leishmania mexicana promastigotes and supports migration requiring an osmotic gradient under the tested conditions. The authors reinterpret those responses as osmotaxis; this is not evidence that all chemical-gradient responses in Leishmania are osmotic, or that every substance or life stage elicits this behavior. No universal preferred osmolarity or natural-strain example is inferred from the abstract."
      },
      {
        "reference": "DOI:10.1016/j.exppara.2005.10.005",
        "snippet": "These were able to respond to chemotaxic as well as to osmotaxic stimuli.",
        "notes": "Abstract, exact-matched at Europe PMC (PMID:16313904); full text not inspected. The antecedent is Leishmania promastigotes; the article identifies Leishmania amazonensis. The authors report distinguishing chemical from osmotic responses, supporting osmotaxis without collapsing all chemotaxis into it. Their receptor model and possible vector-development role are not established as universal mechanisms or required trait consequences."
      },
      {
        "reference": "DOI:10.1073/pnas.1620945114",
        "snippet": "We discuss how the speed changes we observe can lead to steady-state bacterial accumulation.",
        "notes": "Abstract, exact-matched at Europe PMC (PMID:28874571); full text and supplement not systematically inspected. Escherichia coli motor and population-swimming measurements concern stepwise osmotic changes. The snippet states a proposed link from measured speed changes to accumulation, not a direct spatial-gradient migration result from those measurements. Osmokinesis and motor bias may contribute to osmotaxis but are not exact synonyms or sufficient evidence of net migration on their own; no molecular causal edge is inferred."
      }
    ],
    "discussions": [
      {
        "discussion_id": "osmotaxis-spatial-and-chemical-boundaries",
        "prompt": "Separate osmotic migration from tolerance, kinesis and chemical specificity.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Osmotic stress survival, growth salinity preference, water balance, and speed or tumbling changes after a uniform shock do not alone establish net migration through a spatial gradient. Exclude passive transport, osmotic water movement and differential growth as sole evidence. Osmokinesis is not an exact synonym, even when it contributes to spatial redistribution. Solute-specific chemotaxis can coexist with osmotaxis, as the Barros study reports; the Leslie result does not negate it universally. The local chemotaxis record imposes flagellar motor switching, so motile is used as the verified broader parent. External equivalents remain unasserted pending authority and organismal-scope checks.",
        "posed_by": "codex",
        "posed_date": "2026-10-04"
      },
      {
        "discussion_id": "osmotaxis-mechanism-and-canonical-strains",
        "prompt": "Verify strain and life-stage provenance before adding examples or mechanisms.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "The studies support a microbial osmotic-gradient response without identifying one universal receptor or movement apparatus. Inspect full studies and relevant supplements, distinguish spatial observations from temporal-shock measurements and model interpretations, and resolve taxon-paired protein accessions before adding molecular causal graphs. Verify unperturbed natural strain provenance and NCBI identity before adding canonical examples; promastigote observations must retain their life-stage restriction. A NONMECHANISTIC graph must not bypass those requirements.",
        "posed_by": "codex",
        "posed_date": "2026-10-04"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-04T08:45:40Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added osmotaxis with three primary DOI citations and exact abstract snippets. Ignored-and-hidden searches and structured OWL review found no exact live record or METPO term. Reserved METPO:1054600 in v469. Distinguished spatial migration from uniform-shock motility measurements, retained coexistence with solute-specific chemotaxis, and deferred unverified strain examples, molecular mechanisms and external equivalents.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000076",
    "label": "oxidase activity",
    "definition": "A physiological enzyme-activity phenotype in which a cell produces a terminal respiratory oxidase (notably cytochrome c oxidase); it is the basis of the diagnostic oxidase test.",
    "definition_source": "DOI:10.3390/microorganisms10050926",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "synonyms": [
      {
        "synonym_text": "oxidase-positive",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.3390/microorganisms10050926"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.3390/microorganisms10050926",
        "notes": "Hederstedt reviews bacterial cytochrome c oxidase, the terminal respiratory oxidase detected by the oxidase test."
      },
      {
        "reference": "DOI:10.1089/ars.2020.8039",
        "notes": "Borisov et al. review cytochrome bd-family terminal oxidases of prokaryotic respiratory chains."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:287",
        "taxon_label": "Pseudomonas aeruginosa",
        "note": "cytochrome-c-oxidase positive",
        "reference": "PMID:28542449"
      },
      {
        "taxon_id": "NCBITaxon:485",
        "taxon_label": "Neisseria gonorrhoeae",
        "note": "oxidase-positive",
        "reference": "PMID:20154126"
      },
      {
        "taxon_id": "NCBITaxon:266",
        "taxon_label": "Paracoccus denitrificans",
        "note": "Canonical bacterial family A cytochrome-c-oxidase model paired to its reviewed catalytic subunit I-alpha.",
        "reference": "DOI:10.1002/j.1460-2075.1987.tb02579.x"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "oxidase_activity_terminal_oxidase",
        "title": "Terminal respiratory oxidase reducing oxygen",
        "description": "Evidence-backed causal sketch linking a terminal respiratory oxidase to reduction of molecular oxygen, the basis of the oxidase test.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "The graph focuses on cytochrome-c-dependent heme-copper oxidase activity and its family A cofactor path; other oxidase-positive taxa can use distinct terminal oxidases. P08305 is one Paracoccus subunit I-alpha component, not the complete multisubunit complex or every diagnostic oxidase target.",
        "nodes": [
          {
            "node_id": "oxidase_activity_trait",
            "label": "oxidase activity",
            "node_type": "TRAIT",
            "grounding": "traitmech:000076",
            "description": "Possession of a terminal respiratory oxidase."
          },
          {
            "node_id": "cytochrome_c_oxidase",
            "label": "cytochrome c oxidase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Terminal oxidase of the respiratory chain.",
            "grounding": "GO:0045277"
          },
          {
            "node_id": "cytochrome_c_oxidase_function",
            "label": "cytochrome-c oxidase activity",
            "node_type": "MOLECULAR_FUNCTION",
            "grounding": "GO:0004129",
            "description": "Reduction of molecular oxygen using ferrocytochrome c."
          },
          {
            "node_id": "molecular_oxygen",
            "label": "molecular oxygen",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:15379",
            "description": "Terminal electron acceptor reduced to water."
          },
          {
            "node_id": "family_a_cytochrome_c_oxidase",
            "label": "family A cytochrome c oxidase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Canonical heme-copper terminal oxidase with heme a/a3 and CuA/CuB centers, the classic oxidase-test target.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "This node denotes the complete family A multisubunit oxidase; available component-family terms describe individual subunits rather than the assembled complex represented here.",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:P08305",
                "protein_label": "Cytochrome c oxidase subunit 1-alpha",
                "gene_symbol": "ctaDI",
                "taxon_id": "NCBITaxon:266",
                "taxon_label": "Paracoccus denitrificans",
                "entry_status": "REVIEWED",
                "retrieved_on": "2026-10-22",
                "entry_version": 133,
                "sequence_version": 1,
                "role": "Catalytic subunit I-alpha component of the Paracoccus family A cytochrome-c oxidase; it is not presented as the complete complex.",
                "evidence": [
                  {
                    "reference": "DOI:10.1002/j.1460-2075.1987.tb02579.x",
                    "snippet": "Isolation and analysis of the genes for cytochrome c oxidase in Paracoccus denitrificans",
                    "notes": "The primary gene study identifies the Paracoccus oxidase subunits; UniProtKB P08305 is the reviewed ctaDI subunit I-alpha entry."
                  }
                ]
              }
            ]
          },
          {
            "node_id": "reduced_cytochrome_c",
            "label": "reduced cytochrome c",
            "node_type": "CHEMICAL",
            "description": "Ferrocytochrome c, the physiological electron donor to cytochrome c oxidase.",
            "grounding": "CHEBI:16928"
          },
          {
            "node_id": "cua_center",
            "label": "CuA center",
            "node_type": "CHEMICAL",
            "description": "Dicopper electron-entry center in subunit II of family A cytochrome c oxidase."
          },
          {
            "node_id": "heme_a",
            "label": "heme a",
            "node_type": "CHEMICAL",
            "description": "Low-spin heme A cofactor relaying electrons within family A cytochrome c oxidase.",
            "grounding": "CHEBI:24479"
          },
          {
            "node_id": "heme_a3_cub_binuclear_center",
            "label": "heme a3-CuB binuclear center",
            "node_type": "CHEMICAL",
            "description": "Catalytic dioxygen-reduction site of heme-copper oxidases."
          },
          {
            "node_id": "cua_cub_copper_centers",
            "label": "CuA/CuB copper centers",
            "node_type": "CHEMICAL",
            "description": "The three copper atoms (dicopper CuA and CuB) of family A cytochrome c oxidase."
          },
          {
            "node_id": "carbon_monoxide",
            "label": "carbon monoxide",
            "node_type": "CHEMICAL",
            "description": "Gaseous ligand that potently inhibits heme-copper terminal oxidases.",
            "grounding": "CHEBI:17245"
          }
        ],
        "edges": [
          {
            "subject": "cytochrome_c_oxidase",
            "predicate": "enables",
            "object": "cytochrome_c_oxidase_function",
            "description": "Cytochrome c oxidase carries out terminal oxidase activity.",
            "evidence": [
              {
                "reference": "DOI:10.3390/microorganisms10050926",
                "notes": "Hederstedt reviews bacterial cytochrome c oxidase."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "cytochrome_c_oxidase_function",
            "predicate": "consumes",
            "object": "molecular_oxygen",
            "description": "The terminal oxidase reduces molecular oxygen to water.",
            "evidence": [
              {
                "reference": "DOI:10.1089/ars.2020.8039",
                "notes": "Borisov et al. review terminal oxidases that reduce O2."
              }
            ],
            "predicate_id": "biolink:consumes"
          },
          {
            "subject": "cytochrome_c_oxidase",
            "predicate": "confers",
            "object": "oxidase_activity_trait",
            "description": "Possession of a terminal oxidase confers the oxidase-activity phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.3390/microorganisms10050926",
                "notes": "Supports the oxidase-test basis."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "reduced_cytochrome_c",
            "predicate": "donates electrons to",
            "object": "cua_center",
            "description": "Reduced cytochrome c donates electrons to the CuA center of subunit II.",
            "evidence": [
              {
                "reference": "DOI:10.3390/microorganisms10050926",
                "notes": "Hederstedt: \"reduced cytochrome c donates electrons to the CuA center in subunit II.\""
              }
            ],
            "predicate_id": "METPO:2007403"
          },
          {
            "subject": "cua_center",
            "predicate": "transfers electrons to",
            "object": "heme_a",
            "description": "The CuA center relays electrons to low-spin heme a.",
            "evidence": [
              {
                "reference": "DOI:10.3390/microorganisms10050926",
                "notes": "Hederstedt: electrons pass from CuA \"then to low-spin heme a.\""
              }
            ],
            "predicate_id": "METPO:2007403"
          },
          {
            "subject": "heme_a3_cub_binuclear_center",
            "predicate": "reduces",
            "object": "molecular_oxygen",
            "description": "The heme a3-CuB binuclear center reduces molecular oxygen to water.",
            "evidence": [
              {
                "reference": "DOI:10.3390/microorganisms10050926",
                "notes": "Hederstedt: \"the dioxygen reduction site (heme a3 + CuB).\""
              }
            ],
            "predicate_id": "METPO:2007802"
          },
          {
            "subject": "family_a_cytochrome_c_oxidase",
            "predicate": "has cofactor",
            "object": "heme_a",
            "description": "Family A cytochrome c oxidase contains two heme A prosthetic groups (heme a and heme a3).",
            "evidence": [
              {
                "reference": "DOI:10.3390/microorganisms10050926",
                "notes": "Hederstedt: \"contains two heme A prosthetic groups (heme a and heme a3).\""
              }
            ]
          },
          {
            "subject": "family_a_cytochrome_c_oxidase",
            "predicate": "has cofactor",
            "object": "cua_cub_copper_centers",
            "description": "Family A cytochrome c oxidase carries three copper atoms in CuA and CuB centers.",
            "evidence": [
              {
                "reference": "DOI:10.3390/microorganisms10050926",
                "notes": "Hederstedt: \"three copper atoms (CuA is di-copper in subunit II; CuB in subunit I).\""
              }
            ]
          },
          {
            "subject": "carbon_monoxide",
            "predicate": "inhibits",
            "object": "cytochrome_c_oxidase_function",
            "description": "Carbon monoxide is a potent inhibitor of heme-copper cytochrome c oxidase activity.",
            "evidence": [
              {
                "reference": "DOI:10.3390/ijms26062809",
                "notes": "Borisov & Forte 2025: \"CO is a potent inhibitor of heme-copper cytochrome c oxidase (Ki ~0.3 uM).\""
              }
            ],
            "predicate_id": "RO:0002212"
          },
          {
            "subject": "family_a_cytochrome_c_oxidase",
            "predicate": "example of",
            "object": "cytochrome_c_oxidase",
            "description": "Family A heme-copper oxygen reductases are a class of cytochrome c oxidase.",
            "evidence": [
              {
                "reference": "DOI:10.3390/microorganisms10050926",
                "snippet": "Cytochrome c oxidases of the heme\u2013copper oxygen reductase family A",
                "notes": "Verified against the open Microorganisms review."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-06-04T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate PHYSIOLOGY trait (oxidase activity) from literature research to fill the enzyme-activity-phenotype gap.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-08T13:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (terminal oxidase reducing O2) with GO/CHEBI node groundings and RO/biolink predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-14T05:51:47Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A075NZN5\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 6 evidence-backed generic edges (7 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:15Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 4 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007403\u00d72, METPO:2000017\u00d71, RO:0002212\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:20Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:17245\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:35Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:16928\u00d71, CHEBI:24479\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 1 causal edge(s) off enables/RO:0002327 with a TRAIT object (1 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T02:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES_PART2",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates onto their causal-graph counterparts (1 to reduces), issue 301 part 2. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Each replacement is a 1:1 mirror of its source predicate that changes only the domain, so the claim each edge makes is unchanged and directions are unchanged. The replacements are proposed in proposals/metpo_traitmech_v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-22T04:26:16Z",
        "curator": "codex",
        "action": "REVIEW_UNIPROT_INSTANCE_GROUNDINGS",
        "changes": "Reviewed 1 organism-specific UniProtKB grounding(s): replaced 1 with taxon-agnostic GO/InterPro terms and retracted 0 to label-only where no exact semantic term was supported (docs/GROUNDING_POLICY.md).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-24T13:15:00-07:00",
        "curator": "codex",
        "action": "REVIEWED_CAUSAL_GRAPH_PROTEIN_TAXON",
        "changes": "Marked the graph mechanistic, documented the diagnostic oxidase scope, reviewed the family A whole-complex node as label-only, and added DOI-cited Paracoccus subunit I-alpha P08305 as an explicit component example.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T10:45:00Z",
        "curator": "codex",
        "action": "CONNECT_CAUSAL_GRAPH_COMPONENTS",
        "changes": "Resolved issue #183 graph fragmentation (2 components to 1) with 1 public-source, verbatim-snippet-backed connector(s). No paid research service was called.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-22T01:35:00Z",
        "curator": "claude",
        "action": "REFRESH_UNIPROT_ENTRY_VERSION",
        "changes": "Refreshed UniProtKB entry_version against live UniProt REST on 2026-10-22: UniProtKB:P08305 (132 -> 133 on family_a_cytochrome_c_oxidase).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000079",
    "label": "oxidative stress response",
    "definition": "A stress response that defends the cell against reactive oxygen species (e.g. superoxide and hydrogen peroxide) through detoxifying enzymes, regulators, and damage-repair systems.",
    "definition_source": "DOI:10.1038/nrmicro3032",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "traitmech:000078"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/nrmicro3032",
        "snippet": "In response, bacteria activate elegant adaptive strategies",
        "notes": "Verified against the Europe PMC Imlay abstract; the review summarizes oxidative damage from superoxide and hydrogen peroxide plus induced detoxification and repair defenses."
      },
      {
        "reference": "DOI:10.1007/s00018-003-3206-5",
        "snippet": "hydrogen peroxide to water and molecular oxygen, serving to protect cells",
        "notes": "Verified against the public Europe PMC abstract; Chelikani et al. review catalase enzymes that detoxify hydrogen peroxide."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:562",
        "taxon_label": "Escherichia coli",
        "note": "Paradigm of the bacterial oxidative-stress response (OxyR and SoxRS regulons).",
        "reference": "PMID:22381957"
      },
      {
        "taxon_id": "NCBITaxon:83333",
        "taxon_label": "Escherichia coli K-12",
        "note": "Strain-level peroxide-response model paired to the reviewed OxyR regulator.",
        "reference": "DOI:10.1073/pnas.86.10.3484"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "oxidative_stress_response_ros_defense",
        "title": "Defense against reactive oxygen species",
        "description": "Evidence-backed causal sketch linking reactive oxygen species to an induced oxidative-stress defense.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "This graph represents an E. coli-like peroxide/general-stress regulatory branch, not every bacterial, archaeal, or fungal oxidative-stress system. The OxyR example anchors H2O2-responsive transcription; RpoS and thioredoxin effects are broader supporting modules.",
        "nodes": [
          {
            "node_id": "oxidative_stress_response_trait",
            "label": "oxidative stress response",
            "node_type": "TRAIT",
            "grounding": "traitmech:000079",
            "description": "Capacity to defend against reactive oxygen species."
          },
          {
            "node_id": "hydrogen_peroxide",
            "label": "hydrogen peroxide",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:16240",
            "description": "Representative reactive oxygen species."
          },
          {
            "node_id": "oxidative_stress_process",
            "label": "response to oxidative stress",
            "node_type": "BIOLOGICAL_PROCESS",
            "grounding": "GO:0006979",
            "description": "Defense response to reactive oxygen species."
          },
          {
            "node_id": "oxyr_regulator",
            "label": "OxyR transcriptional regulator",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Widely conserved bacterial transcription factor that activates oxidative-stress defense genes.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Current InterPro terms on OxyR describe shared LysR domains rather than the peroxide-sensing OxyR family as a whole, so a domain grounding would be too broad.",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:P0ACQ4",
                "protein_label": "DNA-binding transcriptional dual regulator OxyR",
                "gene_symbol": "oxyR",
                "taxon_id": "NCBITaxon:83333",
                "taxon_label": "Escherichia coli K-12",
                "entry_status": "REVIEWED",
                "retrieved_on": "2026-10-22",
                "entry_version": 144,
                "sequence_version": 1,
                "role": "E. coli K-12 peroxide-sensing OxyR regulator that activates the hydrogen-peroxide-inducible defense regulon represented by this branch.",
                "evidence": [
                  {
                    "reference": "DOI:10.1073/pnas.86.10.3484",
                    "snippet": "positive regulator of hydrogen peroxide-inducible genes in Escherichia coli",
                    "notes": "The primary study identifies and functionally tests E. coli OxyR; UniProtKB P0ACQ4 is the reviewed K-12 regulator entry."
                  }
                ]
              }
            ]
          },
          {
            "node_id": "rpos_sigma_factor",
            "label": "RpoS (sigma-S) general stress sigma factor",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Global stress sigma factor controlling a stress regulon that includes oxidative-stress defenses.",
            "grounding": "InterPro:IPR012761"
          },
          {
            "node_id": "thioredoxin_system",
            "label": "thioredoxin system",
            "node_type": "PATHWAY",
            "description": "Thiol-disulfide redox repair system supporting survival under oxidative/oxidant stress."
          }
        ],
        "edges": [
          {
            "subject": "hydrogen_peroxide",
            "predicate": "causes",
            "object": "oxidative_stress_process",
            "description": "Hydrogen peroxide damages cells and triggers ROS defense.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro3032",
                "snippet": "hydrogen peroxide. These species can destroy the activities of metalloenzymes and the integrity of DNA",
                "notes": "Verified against the public Imlay abstract; hydrogen peroxide is retained as a representative ROS damaging metalloenzymes and DNA."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "oxidative_stress_process",
            "predicate": "confers",
            "object": "oxidative_stress_response_trait",
            "description": "The induced defense realizes the oxidative-stress-response trait.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro3032",
                "snippet": "forcing organisms to protect themselves with scavenging enzymes and repair systems",
                "notes": "Verified against the public Imlay abstract; the edge connects ROS-induced scavenging and repair defenses to the broad oxidative-stress-response trait."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "oxyr_regulator",
            "predicate": "positively regulates",
            "object": "oxidative_stress_process",
            "description": "OxyR activates transcription of genes that defend the cell against oxidative stress.",
            "evidence": [
              {
                "reference": "DOI:10.1099/mic.0.001481",
                "snippet": "activates the transcription of a set of genes that influence cellular defence against oxidative stress",
                "notes": "Verified against the open Bientz et al. abstract; this supports OxyR as a bacterial transcriptional regulator of oxidative-stress defense genes."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "rpos_sigma_factor",
            "predicate": "positively regulates",
            "object": "oxidative_stress_process",
            "description": "The general stress sigma factor RpoS controls a broad stress regulon that includes oxidative-stress defense outputs.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mmbr.00151-22",
                "snippet": "The alternative sigma factor RpoS is the central GSR regulator",
                "notes": "Verified against the Europe PMC Bouillet et al. abstract; RpoS is retained as a broad general-stress regulator rather than an OxyR-like peroxide-specific switch."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "thioredoxin_system",
            "predicate": "contributes to",
            "object": "oxidative_stress_process",
            "description": "Thioredoxin thiol-repair systems support survival under oxidative/oxidant stress, including in anaerobes and spores.",
            "evidence": [
              {
                "reference": "DOI:10.1371/journal.ppat.1012001",
                "snippet": "ubiquitous system for thiol and protein repair",
                "notes": "Verified against the open Anjou et al. abstract; the thioredoxin system is retained as a bacterial thiol and protein repair branch."
              }
            ],
            "predicate_id": "RO:0002326"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-06-04T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate PHYSIOLOGY trait (oxidative stress response); sub-variant of stress response.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-08T13:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (ROS defense) with GO/CHEBI node groundings and biolink/RO predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 3 evidence-backed generic edges (3 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:15Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002326\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-04T03:08:16Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002213\u00d72).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 1 causal edge(s) off enables/RO:0002327 with a TRAIT object (1 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-24T13:20:00-07:00",
        "curator": "codex",
        "action": "REVIEWED_CAUSAL_GRAPH_PROTEIN_TAXON",
        "changes": "Marked the graph mechanistic, bounded it to an E. coli-like peroxide branch, reviewed OxyR as label-only because available terms are shared LysR domains, grounded RpoS to its exact InterPro family, and added DOI-cited OxyR P0ACQ4.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-04T06:40:00Z",
        "curator": "codex",
        "action": "REVIEW_CAUSAL_EVIDENCE",
        "changes": "Reviewed the oxidative_stress_response_ros_defense graph for issue #183: added exact snippets to 2 record-level evidence items and 5 peroxide, OxyR, RpoS, and thioredoxin causal-edge evidence entries. No paid research service was called.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-07T02:20:00Z",
        "curator": "codex",
        "action": "ADVERSARIAL_REVIEW_REPAIR",
        "changes": "Addressed PR #664 adversarial review issues #680 through #682: requoted the RpoS edge and Imlay record evidence, and replaced the generic ASM endpoint note with Europe PMC abstract verification.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-22T01:35:00Z",
        "curator": "claude",
        "action": "REFRESH_UNIPROT_ENTRY_VERSION",
        "changes": "Refreshed UniProtKB entry_version against live UniProt REST on 2026-10-22: UniProtKB:P0ACQ4 (143 -> 144 on oxyr_regulator).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000624",
    "label": "paedogamy",
    "definition": "A sexual-reproduction phenotype in which two gametes produced by division within a single gametangium fuse with each other.",
    "definition_source": "DOI:10.1080/0269249X.2013.791344",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000625"
    ],
    "synonyms": [
      {
        "synonym_text": "pedogamy",
        "synonym_type": "EXACT_SYNONYM",
        "source": "DOI:10.3390/d14121133"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1080/0269249X.2013.791344",
        "snippet": "fusion of two gametes within a single gametangium",
        "notes": "Kaczmarska et al. (2013), p.271, section 5.2.1, contiguous definition phrase in the directly read author-posted full text at https://www.researchgate.net/publication/259079699_Proposals_for_a_terminology_for_diatom_sexual_reproduction_auxospores_and_resting_stages. Cytokinesis distinguishes gametes from the undivided-cell nuclear fusion of section 5.2.2. Section 5.2 treats both as automixis, not equivalent names. This is terminology synthesis, not independent experimental replication of its cited Neidium study. Actual diagrams were not visually inspected. Do not make meiosis-I cytokinesis or immediate gametic-nuclear fusion universal requirements."
      },
      {
        "reference": "DOI:10.3390/d14121133",
        "snippet": "Afterwards, the protoplasts (gametes) fused to form a zygote (auxospore)",
        "notes": "Bagmet et al. (2022), Results 3.3, p.9, clause before the Figure 3J,K citation, checked in publisher XML and typeset PDF. Abstract, Methods 2.1-2.5, Results 3.3, Discussion 4.1 and Table S1 were read; actual Figure 3 and pp.8-9 were inspected. Four clones were active: VCA-7, VCA-48, VCA-49 and VCA-51; VCA-50 and VCA-52 showed no mating. The authors call this pedogamy. Preserve their apparently-qualified interpretation of earlier Figure 3G,H; do not infer tracked nuclear fusion from chloroplast images. Seasonal observations and unsuccessful salt stimulation are study-specific. Plastid rbcL comparisons do not establish absence of genomic recombination."
      },
      {
        "reference": "DOI:10.1007/s12223-008-0018-x",
        "snippet": "The gametic nuclei fused after auxospore expansion had begun.",
        "notes": "Poulickova (2008), PMID:18500631, scientific abstract directly retrieved from Europe PMC and PubMed. Unpaired Neidium cf. ampliatum cells differentiated into gametangia and underwent pedogamy. The quoted timing cautions against conflating gamete fusion with immediate nuclear fusion. Full text, actual figures and strain provenance remain unread. Preserve cf.; no exact species mapping or canonical Neidium example is asserted."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1302829",
        "taxon_label": "Nitzschia acidoclinata",
        "reference": "DOI:10.3390/d14121133",
        "note": "Qualified VCA-7 example, one of the four sexually active clones in Results 3.3, not every tested clone. Table S1 traces VCA-7 to wet ground in Gonduras Cave, Krasnoyarsk Territory, collected 2011-02-19; Methods 2.1 describes single-cell isolation and subsequent culture. Provenance table directly inspected in https://mdpi-res.com/d_attachment/diversity/diversity-14-01133/article_deploy/diversity-14-01133-s001.zip. NCBI https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1302829 and taxonomy EFetch checked on 2026-10-05 resolve this species name; this does not authenticate a genome or current culture accession."
      }
    ],
    "discussions": [
      {
        "discussion_id": "paedogamy-scope-and-hierarchy",
        "prompt": "Separate gamete-cell fusion from autogamy and broader selfing.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Use the single-gametangium gamete-fusion sense established in the cited diatom literature. Autogamy traitmech:000622 denotes gametic-nuclear fusion in an unpaired undivided cell, without fusion of separate gametes; cytogamy traitmech:000623 concerns paired cells without nuclear exchange. Automixis is broader in Kaczmarska et al. section 5.2 and is not an exact synonym. Bagmet et al. calls automixis homothallic, whereas our existing homothallism traitmech:000609 is fungal-scoped; this usage does not make that record a parent. The parent gap is resolved by automixis traitmech:000625, whose single-meiotic-cell nuclear origin includes this operational scope. The broader terminology and mapping questions keep this discussion OPEN. Do not infer species-level disjointness or universal homozygosity, recombination rate, seasonal trigger or inability to outcross. Broader non-diatom usage and external equivalences need primary source review before expanding this operational scope.",
        "posed_by": "codex",
        "posed_date": "2026-10-05"
      },
      {
        "discussion_id": "paedogamy-mechanism-and-coverage",
        "prompt": "Resolve nuclear cytology and molecular mechanisms beyond morphology.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "This is a reproductive phenotype, not a literal locus or a plastid-marker sequence feature. The directly inspected microscopy supports a gamete-fusion interpretation but does not identify a protein-resolved causal pathway. No causal graph or accession-level protein claim is inferred from chloroplast shape, sequence similarity or terminology. Full Neidium methods and provenance, and stronger nuclear observations in the Nitzschia system, remain coverage gaps. Retain actual snippet-resolver outcomes separately from direct PDF, XML and abstract checks.",
        "posed_by": "codex",
        "posed_date": "2026-10-05"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-05T17:13:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added paedogamy with three DOI-backed snippets, a pedogamy spelling synonym and qualified natural VCA-7 example. Ignored-and-hidden novelty/allocation searches found no exact record or collision. Reserved METPO:1057700 in v500. Distinguished gamete fusion from autogamy and broader automixis; deferred molecular graphs and mappings.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-05T18:20:28Z",
        "curator": "codex",
        "action": "RESOLVED_PARENT_GAP",
        "changes": "Reparented below automixis traitmech:000625 and documented the resolved parent gap while retaining other open terminology and mapping questions. Preserved definition, evidence, examples and prior history. v501 carries the existing proposed METPO ID with this hierarchy; earlier standalone templates remain historical.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000632",
    "label": "pallium feeding",
    "definition": "A physiological phenotype in which a microbial organism feeds by enveloping all or part of particulate food in an extruded membranous pallium, digesting it outside the main cell body, and taking up released nutrients.",
    "definition_source": "DOI:10.1111/j.1529-8817.1986.tb00021.x",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1111/j.1529-8817.1986.tb00021.x",
        "snippet": "The contents of the phytoplankton prey are liquified and transported through the pallium",
        "notes": "Direct scientific Abstract quote, printed p. 249; original spelling retained. Institutional scan: https://www.whoi.edu/cms/files/Jacobson_%26_Anderson_1986_JP_feeding_30828.pdf. All seven available pages (249-252, 256-258), Table 1 and actual Figures 1, 2 and 23 were inspected. Pages 253-255 and Figures 3-22 are missing from this copy and were not audited. Figure 2B shows Oblea rotunda feeding on Pyramimonas sp. Discussion p. 256 distinguishes complete from partial enclosure; Table 1 also lists detrital food. Neither living prey nor a particular prey size, taxon, capture filament or digestion time is a universal requirement."
      },
      {
        "reference": "DOI:10.1111/j.0022-3646.1992.00069.x",
        "snippet": "the prey cytoplasm is liquified within the pallium",
        "notes": "Direct Introduction quote, printed p. 69, not an abstract quote. Complete 14-page institutional scan and actual Figures 1-46 inspected at https://www.whoi.edu/cms/files/Jacobson%26Anderson_1992_Proto-ultrastructrure_31161.pdf. Results describe five feeding cells named Protoperidinium spinulosum by the authors. Figures 9-12 show the pallium and degraded diatom contents outside the main cell body; Figures 1 and 46 are reconstructions. Discussion p. 81 leaves inner-membrane loss during fixation versus in vivo reorganization unresolved. Morphology does not demonstrate specific digestive proteins or a complete transport mechanism. No canonical taxon assignment is made from this culture."
      },
      {
        "reference": "DOI:10.4319/lo.1993.38.5.0965",
        "snippet": "Laboratory experiments were performed to determine the growth and grazing capabilities of Oblea rotunda, a pallium-feeding dinoflagellate.",
        "notes": "Direct scientific Abstract from the publisher page at https://aslopubs.onlinelibrary.wiley.com/doi/10.4319/lo.1993.38.5.0965. Supports the feeding-mode name and growth on several phytoplankton foods. Only the abstract was inspected; Methods, figures and culture provenance were not audited. The laboratory culture is not equated with the field specimens in the 1986 canonical example. Behavioral responses do not identify a molecular receptor."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:402581",
        "taxon_label": "Oblea rotunda",
        "reference": "DOI:10.1111/j.1529-8817.1986.tb00021.x",
        "note": "Qualified example: naturally collected specimens in the 1986 study, Table 1 and Figure 2B, not all isolates. Methods p. 249 at https://www.whoi.edu/cms/files/Jacobson_%26_Anderson_1986_JP_feeding_30828.pdf report net tows from Perch Pond or Vineyard Sound, Massachusetts, followed by short laboratory incubation and microscopy. No strain identifier or single collection site is assigned to this example. Figure 2B depicts pallium deployment around Pyramimonas sp. NCBI ESearch and EFetch verified the species name, rank and Peridiniopsis rotunda synonym on 2026-10-06."
      }
    ],
    "discussions": [
      {
        "discussion_id": "pallium-feeding-topology-and-parent",
        "prompt": "Reconcile feeding-mode terminology and membrane topology.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "This is an organismal feeding phenotype, not the pallium structure or a sequence feature. The 1986 Discussion p. 256 calls complete enclosure intracellular digestion in a vacuole outside the theca, but partial enclosure extracellular digestion, and questions that terminological division. Its engulfment wording need not mean whole particles enter the main cell body. Local phagocytosis traitmech:000627 requires enclosure and internalization; phagotrophy traitmech:000628 requires particulate ingestion and nutrient assimilation. Myzocytosis traitmech:000631 denotes prey-content aspiration through a localized connection, not an enveloping feeding veil. Retain phenotype METPO:1000059 pending a closer feeding hierarchy. Do not assert universal extracellular membrane topology or disjoint organismal feeding capabilities. Ordinary extracellular digestion or attachment alone is insufficient. No unverified synonym or ontology equivalence is asserted.",
        "posed_by": "codex",
        "posed_date": "2026-10-06"
      },
      {
        "discussion_id": "pallium-feeding-native-mechanism",
        "prompt": "Resolve membrane dynamics and native protein functions.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "The 1992 Discussion proposes digestive-granule functions, membrane storage and transport routes from ultrastructure. It explicitly leaves fixation artifacts versus biological inner-membrane reorganization unresolved and requests time-course evidence. Apparatus similarity to peduncles does not prove identical feeding mechanics or protein function. Obtain taxon-paired functional and accession evidence before adding protein examples or a causal graph. No actin, centrin or enzyme accession is inferred from micrographs, and no gene or profile is treated as proof of this feeding phenotype.",
        "posed_by": "codex",
        "posed_date": "2026-10-06"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-06T01:50:09Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added pallium feeding with three DOI-backed snippets and a natural-specimen-qualified Oblea example. Ignored-and-hidden searches and pinned METPO review found no exact record. Reserved METPO:1058500 in v508. Preserved partial-enclosure scope, source access limits and unresolved membrane topology; deferred unsupported protein mechanisms and sequence inference.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000607",
    "label": "parasexuality",
    "definition": "A fungal phenotype enabling genetic reassortment through nuclear fusion followed by chromosome-loss-mediated ploidy reduction instead of conventional meiosis.",
    "definition_source": "DOI:10.1093/emboj/cdg235",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1093/emboj/cdg235",
        "snippet": "Thus, an efficient parasexual cycle can be performed in C.albicans, one that leads to the reassortment of genetic material in this organism.",
        "notes": "Bennett and Johnson (2003), PMID:12743044. The snippet is an exact span of the directly retrieved Europe PMC abstract. Main-text experiments and Figures 1-9 were inspected in the author-hosted PDF: https://static1.squarespace.com/static/56463117e4b0770d2cd2d163/t/564e4d55e4b04412d33a3036/1447972181154/the%2Bembo%2Bjournal%2B2003%2Bbennett.pdf. Marked CAI4-derived Candida albicans strains formed tetraploid mating products; chromosome loss yielded diploid or near-diploid progeny that could mate again. Flow cytometry and multiple marker/MTL readouts support ploidy reduction; marker loss alone can also arise by recombination. The cycle need not reach haploidy. The paper leaves conventional meiosis possible under untested conditions. Its supplementary media, mating and PCR details remain unread, and its unpublished meiotic-gene deletion observations are not used as mechanistic proof."
      },
      {
        "reference": "DOI:10.1128/ec.00128-13",
        "snippet": "The diploid products are themselves mating competent, thereby establishing a parasexual cycle in this species for the first time.",
        "notes": "Seervai et al. (2013), PMID:24123269. The snippet exact-matches the directly retrieved Europe PMC abstract. Publisher Methods, Results, Discussion and strain tables were read, and Figures 3 and 4 were visually inspected. Marked Candida tropicalis tetraploids produced near-diploid progeny on sorbose; remating, MTL genotyping and DNA-content measurements support a repeatable cycle. 2-DOG resistance selects GAL1 loss, not necessarily chromosome loss. The Figure 4 caption's wild-type wording does not erase the CAY2060 arg4/arg4 tester genotype reported in Table 1 and Methods. The response to presporulation medium differs from C. albicans. The supplementary Figure S1 caption and labels were read as PDF text, but the actual supplemental plot was not visually inspected. No natural canonical example is inferred from these marker-strain experiments."
      },
      {
        "reference": "DOI:10.1038/s41467-019-12376-2",
        "snippet": "These results indicate that C. albicans CCL represents a 'parameiosis' that blurs the conventional boundaries between mitosis and meiosis.",
        "notes": "Anderson et al. (2019), PMID:31558727. The snippet is an exact span of the directly retrieved Europe PMC abstract. Publisher Introduction and Results were read, but full Methods, actual figures and supplements were not inspected. Concerted chromosome loss (CCL) in C. albicans includes high inter-homolog recombination and functions of Spo11 and Rec8. Their effects on chromosome stability and recombination are different endpoints: loss of SPO11 increases marker loss while reducing recombination, whereas loss of REC8 reduces both in the tested CCL assays. Absence of conventional meiosis does not mean absence of meiosis-associated proteins. Neither homologue presence alone nor these assays establish a conventional meiotic cycle. Protein identities, native strain provenance and assay-specific causal edges remain uncurated."
      }
    ],
    "discussions": [
      {
        "discussion_id": "parasexuality-trait-scope",
        "prompt": "Preserve the complete reproductive capability rather than an isolated readout.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "The record denotes an organismal phenotype, not a locus, protein, ploidy measurement or individual mating experiment. Nuclear fusion followed by nonmeiotic chromosome loss permits genetic reassortment; mating can be part of this cycle. Do not define parasexuality as absence of all mating, sexual programs or meiosis-associated genes. It does not require haploid progeny, obligate asexuality, identical ploidy in every product or successful cycling in every isolate. Hyphal fusion, heterokaryosis, marker loss, aneuploidy, ploidy change and horizontal gene transfer alone are insufficient. The existing ploidy trait describes genome-copy number, not this capability. Ploidy and hyphal anastomosis are not is-a parents. The fungal scope reflects the cited evidence; broader uses of parasexual terminology require separate interpretation. Resolve external phenotype/process mappings and exact synonyms at their authorities before adding them.",
        "posed_by": "codex",
        "posed_date": "2026-10-04"
      },
      {
        "discussion_id": "parasexuality-mechanism-and-strain-provenance",
        "prompt": "Resolve native strain provenance and stage-specific mechanisms before enrichment.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "The cited laboratory cycles use marked or engineered strains; retain those qualifiers rather than promoting a tester or deletion strain to a natural canonical example. Complete the unread supplementary methods and figures, current NCBI identities, original strain provenance and native protein anchors before adding examples or a mechanistic graph. Distinguish chromosome loss, DNA-content reduction, inter-homolog recombination and renewed mating as separate readouts. A flow-cytometry peak near a diploid control does not resolve every chromosome's copy number. The 2019 parameiosis evidence prevents treating nonmeiotic as independent of all meiotic proteins or simply equating it with ordinary mitosis. Do not transfer medium responses or protein dependencies across species, and do not use a NONMECHANISTIC graph to bypass unresolved molecular grounding.",
        "posed_by": "codex",
        "posed_date": "2026-10-04"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-04T23:44:20Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added parasexuality as a fungal reproductive phenotype with three primary DOI-backed references and exact abstract snippets. Separated nuclear-fusion/chromosome-loss cycling from isolated ploidy measurements and sequence features; retained laboratory strain and source-access limits. Ignored-and-hidden repository searches and structured METPO review found no exact record. Reserved METPO:1056100 in v484 under released phenotype. Deferred external mappings, canonical examples and protein graph pending provenance and assay-specific grounding.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000082",
    "label": "persister cell formation",
    "definition": "Formation of dormant phenotypic variants (persister cells) that are transiently tolerant to antibiotics and other lethal stresses without carrying genetic resistance, arising stochastically in a population.",
    "definition_source": "DOI:10.1146/annurev.micro.112408.134306",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "traitmech:000080"
    ],
    "synonyms": [
      {
        "synonym_text": "persistence",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1146/annurev.micro.112408.134306"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev.micro.112408.134306",
        "notes": "Lewis reviews persister cells as dormant variants highly tolerant to antibiotics."
      },
      {
        "reference": "DOI:10.1038/nrmicro1557",
        "notes": "Lewis links persister-cell dormancy to the recalcitrance of chronic infections."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:562",
        "taxon_label": "Escherichia coli",
        "note": "Paradigm for antibiotic-tolerant persister-cell formation (dormant subpopulation; hipA/toxin-antitoxin studies).",
        "reference": "PMID:6348026"
      },
      {
        "taxon_id": "NCBITaxon:83333",
        "taxon_label": "Escherichia coli K-12",
        "note": "Strain-level model in which the hipA7 allele increases persister frequency; paired to the reviewed HipA protein entry.",
        "reference": "DOI:10.1128/jb.155.2.768-775.1983"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "persister_dormancy_tolerance",
        "title": "Persister dormancy and antibiotic tolerance",
        "description": "Evidence-backed causal sketch linking dormancy to stochastic persister formation and transient antibiotic tolerance.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "The HipA branch is an E. coli K-12 example, not a universal persister mechanism. The original high-persistence result is hipA7-allele-specific, and later growth-arrest evidence uses HipA overexpression; neither establishes that wild-type HipA is required for persistence in every organism or condition.",
        "nodes": [
          {
            "node_id": "persister_trait",
            "label": "persister cell formation",
            "node_type": "TRAIT",
            "grounding": "traitmech:000082",
            "description": "Stochastic formation of dormant, drug-tolerant variants."
          },
          {
            "node_id": "dormancy_process",
            "label": "dormancy process",
            "node_type": "BIOLOGICAL_PROCESS",
            "grounding": "GO:0022611",
            "description": "Reversible quiescence underlying persistence."
          },
          {
            "node_id": "hipa_toxin",
            "label": "HipA toxin and high-persistence HipA variants",
            "node_type": "GENE_OR_PROTEIN",
            "grounding": "InterPro:IPR052028",
            "description": "HipA serine/threonine kinase toxin; specific variants or elevated activity can arrest growth and increase antibiotic persistence in E. coli.",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:P23874",
                "protein_label": "Serine/threonine-protein kinase toxin HipA",
                "gene_symbol": "hipA",
                "taxon_id": "NCBITaxon:83333",
                "taxon_label": "Escherichia coli K-12",
                "entry_status": "REVIEWED",
                "retrieved_on": "2026-10-22",
                "entry_version": 177,
                "sequence_version": 2,
                "role": "Reviewed K-12 HipA sequence instance underlying the experimentally studied hipA7 variant and HipA-overexpression systems; the accession itself denotes the wild-type protein, not the hipA7 allele.",
                "evidence": [
                  {
                    "reference": "DOI:10.1128/jb.155.2.768-775.1983",
                    "snippet": "hipA, a newly recognized gene of Escherichia coli K-12 that affects frequency of persistence",
                    "notes": "The primary K-12 study isolates the high-persistence hipA7 allele; UniProtKB P23874 is the reviewed HipA entry for the same taxon, but does not encode the allele distinction."
                  }
                ]
              }
            ]
          },
          {
            "node_id": "antibiotic_tolerance",
            "label": "antibiotic tolerance",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Transient survival of lethal antibiotic exposure."
          },
          {
            "node_id": "biphasic_killing_curve",
            "label": "biphasic killing curve",
            "node_type": "EXPERIMENTAL_FACTOR",
            "description": "Hallmark biphasic time-kill readout: rapid death of bulk population then slow killing of persister subpopulation."
          },
          {
            "node_id": "mic_susceptible",
            "label": "minimum inhibitory concentration of susceptible cells",
            "node_type": "QUALITY",
            "description": "MIC value characteristic of antibiotic-susceptible cells; unchanged in persisters."
          },
          {
            "node_id": "antibiotic_resistance",
            "label": "antibiotic resistance",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Genetically encoded ability to grow at elevated antibiotic concentrations; distinct from tolerance/persistence."
          },
          {
            "node_id": "elevated_mic",
            "label": "elevated minimum inhibitory concentration",
            "node_type": "QUALITY",
            "description": "Increased MIC characteristic of resistant bacteria, distinguishing resistance from persistence."
          },
          {
            "node_id": "whole_population_phenotype",
            "label": "whole-population phenotype",
            "node_type": "QUALITY",
            "description": "Property applying to the entire population rather than a small subpopulation."
          },
          {
            "node_id": "oxidative_phosphorylation",
            "label": "oxidative phosphorylation",
            "node_type": "PATHWAY",
            "description": "Residual respiratory ATP synthesis maintaining proton motive force in persisters.",
            "grounding": "GO:0006119"
          },
          {
            "node_id": "proton_motive_force",
            "label": "proton motive force",
            "node_type": "STATE",
            "description": "Transmembrane electrochemical gradient maintained by persisters during starvation.",
            "grounding": "METPO:1007500"
          }
        ],
        "edges": [
          {
            "subject": "hipa_toxin",
            "predicate": "promotes",
            "object": "dormancy_process",
            "description": "High-persistence HipA variants and experimentally elevated HipA kinase activity promote growth arrest in the E. coli K-12 persister branch.",
            "evidence": [
              {
                "reference": "DOI:10.1128/jb.01237-06",
                "snippet": "Kinase activity of overexpressed HipA is required for growth arrest and multidrug tolerance",
                "notes": "This experiment supports a causal HipA-to-growth-arrest link under overexpression; it does not establish a universal wild-type requirement."
              },
              {
                "reference": "DOI:10.1128/jb.155.2.768-775.1983",
                "snippet": "hipA, a newly recognized gene of Escherichia coli K-12 that affects frequency of persistence",
                "notes": "The original K-12 evidence is specifically for the high-persistence hipA7 allele and limits this edge to that strain-specific branch."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "dormancy_process",
            "predicate": "confers",
            "object": "persister_trait",
            "description": "Dormancy underlies stochastic persister formation.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev.micro.112408.134306",
                "notes": "Lewis reviews persisters as dormant tolerant variants."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "persister_trait",
            "predicate": "enables",
            "object": "antibiotic_tolerance",
            "description": "Persister cells transiently tolerate antibiotics.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro1557",
                "notes": "Lewis links persisters to recalcitrant infection."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "persister_trait",
            "predicate": "characterized by",
            "object": "biphasic_killing_curve",
            "description": "Persistence produces a biphasic time-kill curve diagnostic of a tolerant subpopulation.",
            "evidence": [
              {
                "reference": "DOI:10.1128/ecosalplus.esp-0025-2022",
                "notes": "A hallmark of persistence is the biphasic killing curve."
              }
            ]
          },
          {
            "subject": "persister_trait",
            "predicate": "has characteristic",
            "object": "mic_susceptible",
            "description": "Persisters retain the same MIC as susceptible cells, distinguishing persistence from resistance.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s12866-024-03628-3",
                "notes": "Persisters had the same minimum inhibitory concentration (MIC) as the susceptible cells."
              }
            ]
          },
          {
            "subject": "antibiotic_resistance",
            "predicate": "has characteristic",
            "object": "elevated_mic",
            "description": "Resistant bacteria have a significantly higher MIC, contrasting with the unchanged MIC of persisters.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s12866-024-03628-3",
                "notes": "The MIC of resistant bacteria was significantly higher; scope edge excluding resistance from persistence."
              }
            ]
          },
          {
            "subject": "antibiotic_tolerance",
            "predicate": "has characteristic",
            "object": "whole_population_phenotype",
            "description": "Tolerance applies to the whole population, whereas persisters are a small subpopulation.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s12866-024-03628-3",
                "notes": "Persisters are a smaller subpopulation, whereas tolerance is for the microbiota as a whole."
              }
            ]
          },
          {
            "subject": "persister_trait",
            "predicate": "enables",
            "object": "oxidative_phosphorylation",
            "description": "Persisters actively undergo a residual level of oxidative phosphorylation even during nutrient starvation.",
            "evidence": [
              {
                "reference": "DOI:10.1111/1751-7915.70042",
                "notes": "Persisters still actively generated PMF by undergoing a certain level of oxidative phosphorylation, even after complete nutrient starvation for 24 h."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "oxidative_phosphorylation",
            "predicate": "results in",
            "object": "proton_motive_force",
            "description": "Residual oxidative phosphorylation generates proton motive force that sustains persister survival.",
            "evidence": [
              {
                "reference": "DOI:10.1111/1751-7915.70042",
                "notes": "Persisters generated PMF via oxidative phosphorylation; ETC components maintain PMF underlying tolerance."
              }
            ]
          },
          {
            "subject": "antibiotic_resistance",
            "predicate": "is distinct from",
            "object": "persister_trait",
            "description": "Genetic antibiotic resistance is explicitly distinct from the phenotypic persistence trait.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41579-019-0196-3",
                "snippet": "Resistance, tolerance and persistence are distinct responses to antibiotic treatment",
                "notes": "Verified against the open consensus statement; this contrast edge does not treat resistance as a persistence mechanism."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-08-24T14:00:00-07:00",
        "curator": "codex",
        "action": "REVIEWED_CAUSAL_GRAPH_PROTEIN_TAXON",
        "changes": "Added a DOI-backed E. coli K-12 canonical example, exact HipA family grounding, reviewed HipA protein example, and an allele/overexpression-qualified growth-arrest edge with complete evidence; documented the non-universal scope.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-04T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate PHYSIOLOGY trait (persister cell formation); sub-variant of dormancy. Distinct from genetic antibiotic resistance.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-08T13:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (persister dormancy/tolerance) with GO node grounding and RO predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 6 evidence-backed generic edges (7 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:15Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:20Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0006119\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 1 causal edge(s) off enables/RO:0002327 with a TRAIT object (1 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-15T02:00:00Z",
        "curator": "claude",
        "action": "NORMALISE_NODE_TYPE",
        "changes": "Normalised causal-node type(s) so one node_id means one thing corpus-wide (issue 356): proton_motive_force: BIOLOGICAL_PROCESS -> STATE. The schema's OWN example of STATE: 'a bioenergetic or molecular state of the cell (e.g. proton motive force ...) ... the state is the gradient / steady-value, not its establishment'. All 35 occurrences describe the gradient -- every description across all four types reads 'electrochemical proton gradient', including the 13 typed BIOLOGICAL_PROCESS ('Transmembrane electrochemical gradient generated by respiration'), which name the gradient and its provenance rather than the generating process. Nothing here means the establishment, so this is a retype and not a rename; records that DO mean the process already use a separate id (proton_motive_force_generation in ph_delta.yaml). Also settles the one edge #356 was filed for: phototrophic.yaml's CAPACITY typing was blocking `powers` (METPO:2007900), which is gated to BIOLOGICAL_PROCESS|STATE.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-16T02:00:00Z",
        "curator": "claude",
        "action": "NORMALISE_NODE_TYPE",
        "changes": "Under the PATHWAY-vs-BIOLOGICAL_PROCESS rule, one node_id means one thing corpus-wide (issue 356): oxidative_phosphorylation is typed PATHWAY. PATHWAY is a named, conventionally enumerable multi-step route; BIOLOGICAL_PROCESS is everything else. A named route through enumerable complexes -- environment/ph_delta_mid1.yaml lists them (nuo, cyo, ndh, sdh). The rule breaks what was a 2-2 tie before this tranche.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-20T07:10:43Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (METPO:1007500\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T09:35:00Z",
        "curator": "codex",
        "action": "CONNECT_CAUSAL_GRAPH_COMPONENTS",
        "changes": "Resolved issue #183 graph fragmentation (2 components to 1) with one public-source, verbatim-snippet-backed connector. No paid research service was called.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-22T01:35:00Z",
        "curator": "claude",
        "action": "REFRESH_UNIPROT_ENTRY_VERSION",
        "changes": "Refreshed UniProtKB entry_version against live UniProt REST on 2026-10-22: UniProtKB:P23874 (176 -> 177 on hipa_toxin).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000640",
    "label": "pexophagy",
    "definition": "An autophagy phenotype in which a microbial cell selectively degrades its peroxisomes by delivering them to lysosomal or vacuolar compartments.",
    "definition_source": "DOI:10.1038/emboj.2012.151",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000638"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/emboj.2012.151",
        "snippet": "Peroxisomes undergo rapid, selective autophagic degradation (pexophagy) when the metabolic pathways they contain are no longer required for cellular metabolism.",
        "notes": "PMID:22643220, PMC3395097. Scientific Abstract directly read in Europe PMC core metadata with matching DOI. Results sec3/sec4 and Methods sec16/sec20/sec23 were also directly read in https://www.ebi.ac.uk/europepmc/webservices/rest/PMC3395097/fullTextXML. In Saccharomyces cerevisiae, Pex11-GFP processing and peroxisomal reporters, with Atg1 and vacuolar-protease controls, support degradation rather than puncta alone. Atg36 perturbation distinguishes peroxisome turnover from mitophagy, Cvt and bulk autophagy in the tested conditions. Post-log turnover also occurs in glucose, glycerol and oleate media; starvation is not a universal requirement. Pex14 deletion retains pexophagy in this species. The abstract's mitochondrial Pex3 redirection is engineered, not native Atg36 mitophagy evidence. Figure 1/2 captions were read, but actual figures, supplements, complete Methods and natural strain provenance were not inspected."
      },
      {
        "reference": "DOI:10.1016/j.devcel.2007.12.011",
        "snippet": "It is necessary for pexophagy, but not for other selective and nonselective autophagy-related processes.",
        "notes": "PMID:18331717, PMC3763908. Scientific Abstract directly read in Europe PMC core metadata with matching DOI. The quoted protein is PpAtg30 in historically named Pichia pastoris. The abstract explicitly uses pexophagy for selective peroxisome turnover through micropexophagy and macropexophagy, and reports cargo selection and delivery. This supports route-inclusive terminology and selectivity in the tested yeast, not a universal Atg30 requirement or a gene-presence trait. The opening nonselective description of autophagy is not imposed on the broader local parent, which includes selective turnover. Full-text retrieval failed; methods, actual figures and strain-specific modern taxonomy were not inspected."
      },
      {
        "reference": "DOI:10.1242/jcs.108.1.25",
        "snippet": "there exist in P. pastoris at least two pathways for the sequestration of peroxisomes into the vacuole for degradation.",
        "notes": "PMID:7738102. Scientific Abstract directly read in Europe PMC core metadata with matching DOI. Methanol-to-ethanol adaptation elicits individual wrapping and vacuolar fusion; glucose adaptation elicits vacuolar engulfment of peroxisome clusters and also turnover of a cytosolic enzyme. Morphology, enzyme measurements and mutant controls support distinct routes; vacuolar-proteinase mutants accumulate undegraded peroxisomes. Enzyme loss or delivery alone is not completed organelle degradation. These conditions are not universal trait requirements. Full methods, actual figures and natural strain provenance were not inspected."
      },
      {
        "reference": "DOI:10.1080/15548627.2019.1603546",
        "snippet": "the cytosolic pools of PTS receptors and their cargoes are degraded via a pexophagy-independent, selective autophagy pathway under pexophagy conditions.",
        "notes": "PMID:31007124, PMC6984484. Scientific Abstract directly read in Europe PMC core metadata with matching DOI. This is boundary evidence, not a positive whole-peroxisome turnover experiment: cytosolic Pex5/Pex7 and cargo pools undergo Atg30-independent selective autophagy in Pichia pastoris. Peroxisomal-protein turnover outside the organelle must not be equated with pexophagy. The background's damaged-or-redundant wording does not make damage obligatory. Full text, actual figures and strain provenance were not inspected."
      }
    ],
    "discussions": [
      {
        "discussion_id": "pexophagy-selectivity-and-route-scope",
        "prompt": "Review route-inclusive phenotype against narrower GO terminology.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Use autophagy traitmech:000638 as the direct broader phenotype. The 2008 PpAtg30 scientific abstract uses pexophagy for both micropexophagy and macropexophagy. In contrast, issuing GO:0000425 names pexophagy specifically for selective macroautophagy and lists macropexophagy as exact; GO:0000426 micropexophagy is its sibling under GO:0030242 autophagy of peroxisome, which lists pexophagy as related. These nonobsolete biological-process records were resolved at https://www.ebi.ac.uk/QuickGO/services/ontology/go/terms/GO%3A0000425,GO%3A0000426,GO%3A0030242. Retain the source-attributed route-inclusive interpretation for human review and omit exact phenotype xrefs and synonyms. Bulk incidental capture, peroxisome presence, import defects, puncta, protein abundance and delivery without degradation alone are insufficient. Cytosolic peroxisomal-protein autophagy is a separate endpoint. The microbial cell doing the degradation carries the trait, not an organism merely inducing an animal host response.",
        "posed_by": "codex",
        "posed_date": "2026-10-06"
      },
      {
        "discussion_id": "pexophagy-exemplars-and-native-mechanisms",
        "prompt": "Resolve strain provenance and taxon-paired mechanisms before expansion.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "The evidence uses reporter and perturbation strains; natural strain provenance is not independently established. Keep canonical examples unset rather than presenting deficient mutants as positive exemplars. Historical Pichia names also need strain-specific taxonomic review. Atg36 in budding yeast and PpAtg30 do not define a universal receptor inventory; putative BLAST orthologues are not functional protein examples. Require native taxon-paired protein accession checks and direct functional evidence before a causal graph. Neither an ATG locus nor a detector profile is the phenotype, and neither starvation nor damaged cargo is universally required.",
        "posed_by": "codex",
        "posed_date": "2026-10-06"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-06T11:04:55Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added pexophagy as selective peroxisome degradation under autophagy, with four DOI-backed snippets and explicit route, flux and cytosolic-protein boundaries. Ignored-and-hidden searches and pinned METPO review found no exact record. Reserved METPO:1059300 in v516, carrying v514's unchanged parent row as context. Deferred unverified examples, mappings and protein graphs.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000591",
    "label": "pH taxis",
    "definition": "A motile phenotype in which active locomotion is directionally biased in response to an external pH gradient.",
    "definition_source": "DOI:10.1128/jb.00491-19",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000702"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1128/jb.00491-19",
        "snippet": "This bacterium was found to perform bidirectional taxis in response to external pH gradients, enabling it to preferentially migrate to neutral environments.",
        "notes": "Abstract, exact-matched at Europe PMC (PMID:31685537). The antecedent is Bacillus subtilis. This observation supports external-gradient-directed movement, including responses from both acidic and alkaline environments in this study. It does not establish neutral pH as a universal preferred destination. Full text was not systematically inspected; receptor-chimera findings in the abstract are not converted into a molecular causal graph or an unqualified natural-strain example."
      },
      {
        "reference": "DOI:10.1128/jb.188.7.2656-2665.2006",
        "snippet": "Bacteria in more-alkaline regions did not swim toward the acid, suggesting the pH taxis is a form of negative chemotaxis.",
        "notes": "Abstract, exact-matched at Europe PMC (PMID:16547053); full text not inspected. The preceding observation describes Helicobacter pylori moving away from strong acid in a microscope-slide pH gradient. This supports an acid-avoidance response without requiring every pH-tactic organism to show bidirectional attraction to a neutral optimum. Strain-specific mutant, receptor and host-colonization findings are not generalized into the trait definition or mechanism."
      }
    ],
    "discussions": [
      {
        "discussion_id": "ph-taxis-scope-and-mapping-boundaries",
        "prompt": "Preserve directional scope and verify external equivalents.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Growth pH preference, acid or alkali tolerance, intracellular pH homeostasis and changes in speed alone do not establish pH-directed locomotion. Neither neutral-pH attraction nor bidirectional response is required universally. The local chemotaxis definition specifies flagellar motor switching; motile is the verified broader METPO parent without imposing that apparatus. No external xref or exact synonym is asserted before authority resolution and organismal-scope comparison.",
        "posed_by": "codex",
        "posed_date": "2026-10-04"
      },
      {
        "discussion_id": "ph-taxis-mechanism-and-canonical-strains",
        "prompt": "Verify natural strain provenance and protein-resolved mechanisms.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "The primary abstracts establish pH-tactic behavior, not a single universal receptor mechanism. Before adding canonical examples, verify the unperturbed reference strains against primary strain-provenance sources and resolve their NCBI taxon identities. Before adding a causal graph, inspect the full studies and relevant supplements, distinguish observed perturbation effects from proposed sensing models, and resolve taxon-paired protein accessions. A NONMECHANISTIC graph must not bypass those requirements.",
        "posed_by": "codex",
        "posed_date": "2026-10-04"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-04T08:03:18Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added pH taxis with two primary DOI citations and exact abstract snippets. Ignored-and-hidden searches and structured OWL review found no exact live record or METPO term. Reserved METPO:1054500 in v468. Deferred unverified strain examples, molecular graph grounding and external equivalents; retained directional scope without universal neutral-pH or bidirectionality requirements.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000602",
    "label": "pH tropism",
    "definition": "A phenotype in which polarized growth is directionally biased in response to a spatial gradient of external pH.",
    "definition_source": "DOI:10.1128/mbio.00285-23",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000597"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1128/mbio.00285-23",
        "snippet": "F. oxysporum hyphae exposed to a pH gradient displayed robust tropism toward acid.",
        "notes": "Fernandes et al. (2023), Discussion; exact span in directly retrieved Europe PMC JATS, PMC10128062 (PMID:36861989). Results and Methods were read; Figure 1B and Table S1 (10.1128/mbio.00285-23.7) were visually inspected. Opposing 25 mM HCl/NaOH wells tested germ-tube direction after 8 h, with at least three experiments and 500 germ tubes per experiment. Mpk1 deletion reversed direction; complementation restored acidward growth, not necessarily wild-type magnitude. Panel A measures invasion, not tropism. The assay does not by itself resolve the local pH profile or exclude every co-varying ionic effect. The higher-pH response is an engineered-mutant observation, not a natural exemplar."
      },
      {
        "reference": "DOI:10.1371/journal.pbio.3002726",
        "snippet": "These outcomes indicate that the hyphae exhibit chemotropism towards pH 4 within the pH range of 3 to 8.",
        "notes": "Yamamoto et al. (2024), Results, Chemotropism to low pH; exact span in directly retrieved Europe PMC JATS, PMC11288418 (PMID:39078817). Figure 3 and Table S1 (10.1371/journal.pbio.3002726.s002) were visually inspected. Aspergillus nidulans tip trajectories near the pH 6.5/8 interface support reorientation. Figure 3D reports n=1 experiment with 40-50 hyphae; hypha counts are not independent experimental replication. Growth inhibition at pH 3 confounds the 3/4 comparison. The separate summary abstract's acidic-pH avoidance wording conflicts with the main Results. This is not a universal pH-4 setpoint. Strains are engineered; movies and remaining supplements were not inspected."
      }
    ],
    "discussions": [
      {
        "discussion_id": "ph-tropism-growth-direction-and-assay-boundaries",
        "prompt": "Keep pH-directed growth distinct from taxis, tolerance and growth rate.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "This is a pH-specific child of chemotropism, not another name for all chemical-gradient growth. It includes growth toward lower or higher pH without requiring both in one organism; mutant direction reversal does not establish a natural higher-pH-seeking strain. pH taxis denotes active locomotion. pH optimum, acid tolerance, intracellular pH homeostasis, biomass and extension rate alone are insufficient. Retain the source-specific replication and growth-inhibition limitations; resolve external equivalents and alternative labels before adding synonyms or xrefs. The local chemotropism parent (traitmech:000597) has a pending v474 proposal, METPO:1055100, not a released term. The v479 proposal uses released METPO:1000059 phenotype; reconcile the narrower hierarchy when v474 is accepted.",
        "posed_by": "codex",
        "posed_date": "2026-10-04"
      },
      {
        "discussion_id": "ph-tropism-strain-provenance-and-spatial-mechanism",
        "prompt": "Resolve strain identity and the spatial-sensing mechanism before enrichment.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Fernandes Methods identify Fol4287 (FGSC 9935), whereas Table S1 labels its wild type FGSC 4287. Reconcile the collection label and verify natural provenance and NCBI identity before canonical examples. Yamamoto Table S1 lists engineered backgrounds including TH122. Keep spatial-gradient orientation separate from uniform pH shifts, cytosolic-pH regulation and invasion assays. Kinase perturbations support context-specific contributions, not a universal receptor or a complete spatial-sensing chain. Resolve native, taxon-paired protein accessions and direct causal links before adding a mechanism graph; NONMECHANISTIC is not a grounding bypass.",
        "posed_by": "codex",
        "posed_date": "2026-10-04"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-04T19:11:26Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added pH tropism under local chemotropism with two primary DOI citations and exact raw-JATS snippets. Ignored-and-hidden novelty searches and structured OWL review found no exact term; the parent's pH example has broader class scope. Reserved METPO:1055600 in v479 under released phenotype. Visually inspected both key figures and strain tables. Recorded assay replication, growth confounds, mutant direction scope, source discrepancies and pending hierarchy; deferred canonical strains and accession-level causal mechanisms.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000627",
    "label": "phagocytosis",
    "definition": "A physiological phenotype in which a microbial cell engulfs extracellular particles by enclosing them within its membrane and internalizes them into membrane-bound compartments.",
    "definition_source": "DOI:10.1371/journal.pone.0095577",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000636"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1371/journal.pone.0095577",
        "snippet": "remodeling of the collar membrane to engulf the prey, and transport of engulfed bacteria into the cell.",
        "notes": "Dayel and King (2014), PMID:24806026, PMC4012994, scientific Abstract directly checked in Europe PMC XML and the PLOS article. Results, Discussion and Methods were read; actual Figures 1 and 4 were inspected. Live-cell images and SEM/TEM support collar-associated engulfment and internalization in Salpingoeca rosetta. Mere contact or retention on the collar is not ingestion. Nutrient assimilation and the molecular identity of collar links are not established by these images. Actual supplements and movies were not inspected. The culture-provenance papers cited by the Methods were not followed, so this study is retained as trait evidence without a canonical strain assignment."
      },
      {
        "reference": "DOI:10.1111/nph.20388",
        "snippet": "We found cells ingested proxy (up to 2 \u03bcm diameter) and natural (bacteria and cyanobacteria) prey particles",
        "notes": "Scientific Summary directly checked in Europe PMC full-text XML and PMC11982794; PMID:40035416. Results, Discussion and Methods were read, and actual Figures 5, 6, 9 and 10 were inspected. Scyphosphaera apsteinii RCC1456 cultures internalized particles and labeled bacteria into a prominent vacuole. Distinguish pHrodo Escherichia coli BioParticles from Acridine Orange-labeled marine bacteria and from inert beads. Acidic-organelle staining alone is not prey uptake; some imaging used EGTA decalcification. The paper uses phagotrophy for the nutritional interpretation; this record asserts particle engulfment, not a measured carbon assimilation rate. Figure 10 is a conceptual sequence-based model, not native protein validation: its S. apsteinii transcripts come from RCC1455, not the assayed RCC1456, and some candidates are from Gephyrocapsa huxleyi. Actual supplements and movies were not inspected. No negative comparator-species claim, bead-degrading enzyme assignment or inferred nutrient quota is imported."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:418940",
        "taxon_label": "Scyphosphaera apsteinii",
        "reference": "DOI:10.1111/nph.20388",
        "note": "Strain-qualified example: diploid RCC1456, also AC504, TW15 and NIES-3344. Mid- to late-exponential nonaxenic cultures ingested labeled marine bacteria and particles under the reported incubation conditions; Figures 5 and 6 were inspected. The species taxon ID and scientific name were independently verified at NCBI on 2026-10-05; this is not a strain-level taxon ID or a claim about every isolate. Natural isolation from the Spanish coast of the Balearic Sea by single-cell micropipetting on 2001-02-01 was checked directly in the collection record https://www.roscoff-culture-collection.org/rcc-strain-details/1456. The transcript-source strain RCC1455 (AC505/TW16) is distinct and is not substituted for this exemplar."
      }
    ],
    "discussions": [
      {
        "discussion_id": "phagocytosis-trait-and-process-scope",
        "prompt": "Keep particle uptake distinct from nutrition and process-level mappings.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "This class denotes the microbial organism's particle-engulfment phenotype, not a host immune cell's response to the microbe. Existing capsule and pathogenic-to-host descriptions concern host immune evasion and are not same-scope unresolved trait nodes. Phagotrophy denotes a nutritional strategy; the coccolithophore paper uses that interpretation, but ingestion of inert particles does not by itself establish carbon assimilation. Trophic type METPO:1000631 and heterotrophic METPO:1000644 require nutritional source use, while predatory bacterium traitmech:000054 is bacteria-specific. Endocytosis traitmech:000636 is the direct broader trait because the existing particle-enclosure definition entails membrane-bound internalization; phenotype METPO:1000059 remains an ancestor. Do not equate phagocytosis with all endocytosis, pinocytosis, bacterial predation or phagotrophy. Review external process terms separately before asserting any trait-level xref; no synonym or ontology equivalence is proposed here.",
        "posed_by": "codex",
        "posed_date": "2026-10-05"
      },
      {
        "discussion_id": "phagocytosis-native-mechanism-evidence",
        "prompt": "Require native functional evidence before assigning molecular mechanisms.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "The observed cellular uptake phenotypes do not identify a universal microbial protein mechanism. Collar-link composition in S. rosetta remains unresolved. The coccolithophore study's KEGG and Swiss-Prot sequence annotations concern RCC1455 transcripts and G. huxleyi gene models, not direct validation of the RCC1456 uptake mechanism. Keep strain provenance, homology, localization, experimental dependence and nutrient assimilation as separate evidence requirements. Inspect supplements and obtain taxon-paired native protein evidence before adding a causal graph or protein accessions.",
        "posed_by": "codex",
        "posed_date": "2026-10-05"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-05T20:40:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added phagocytosis as an organism-level particle-engulfment phenotype with two DOI-backed snippets, inspected primary figures and a strain-qualified natural RCC1456 example. Ignored-and-hidden novelty searches and pinned METPO review found no exact record. Reserved METPO:1058000 in v503. Kept nutritional, mapping and sequence-based mechanism interpretations separate; no protein graph was inferred.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-06T06:47:04Z",
        "curator": "codex",
        "action": "REFINE_ENDOCYTOSIS_PARENT",
        "changes": "Refined the direct parent to endocytosis traitmech:000636 by definition-based inference. Updated only the parent statement in the scope discussion, which remains OPEN for process-mapping review. Preserved definition, evidence, example and prior history.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000628",
    "label": "phagotrophy",
    "definition": "A physiological phenotype in which a microbial organism ingests particulate food and assimilates nutrients derived from that food.",
    "definition_source": "DOI:10.1038/ismej.2017.68",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/ismej.2017.68",
        "snippet": "NanoSIMS and bulk IRMS isotope analyses revealed that Ochromonas obtained 84-99% of its carbon and 88-95% of its nitrogen from consumed bacteria.",
        "notes": "PMID:28524870, PMC5563956. This contiguous scientific-abstract quote uses the directly retrieved Europe PMC abstract's ASCII range hyphens; the full-text XML uses en dashes. The maintained resolver verifies the API form but flags the en-dash form as LIKELY_PARAPHRASE solely for that typography difference. Full Introduction, Methods, Results and Discussion were read, and actual Figures 1 and 4 were inspected. Axenic Ochromonas sp. BG-1 cultures received washed heat-killed bacterial prey or labeled inorganic substrates in triplicate light/dark treatments with unlabeled controls. Isotope incorporation and prey-dependent growth support nutritional use, not merely particle uptake. The percentages describe the nutrient source under these conditions, not a universal rate or an exclusively direct organic-carbon assimilation route: bacterial carbon can be respired and refixed, and uncontrolled pH/atmospheric exchange may underestimate inorganic carbon fixation. NanoSIMS and bulk carbon estimates differ. Actual Figures 2, 3 and 5 and supplements were not visually audited; no unique claims from those panels are imported. Heat-killed prey do not demonstrate that the consumer kills living prey."
      },
      {
        "reference": "DOI:10.1007/s00248-001-1024-6",
        "snippet": "nutrient acquisition for this species in the presence of bacteria was accomplished primarily via ingestion of bacteria.",
        "notes": "Sanders et al. (2001), PMID:12024234. Scientific Abstract and full Introduction, Methods, Results, Discussion and Conclusions were directly read from the author-institution PDF. Actual PDF pages 2 and 7, including Figure 4, were inspected. The study compares axenic and bacterized BG-1 cultures with light, dissolved-organic and nutrient treatments. Live Pasteurella sp. prey in this experiment are distinct from the 2017 heat-killed prey treatment. Population abundance and biovolume are separate readouts; cell division alone need not mean biomass increase. Authors cannot exclude contributions from bacterial trace compounds or nutrient recycling. Fluorescent prey added above ambient prey abundance can inflate grazing estimates, while prey-disappearance estimates omit bacterial growth. No unqualified grazing rate, specific MES assimilation or BG-1 cannibalism claim is imported. This is a separate study of the same strain, not independent taxon replication."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1616673",
        "taxon_label": "Ochromonas sp. BG-1",
        "reference": "DOI:10.1038/ismej.2017.68",
        "note": "Strain-qualified BG-1 example: washed heat-killed bacterial prey supported growth and supplied cellular carbon and nitrogen in the 2017 isotope experiments; actual Figures 1 and 4 were inspected. This is not a claim that every Ochromonas isolate has the same trophic dependence. NCBI ESearch and EFetch independently resolve the exact name and identifier on 2026-10-05; NCBI assigns species rank despite the BG-1 name. Natural isolation from a Malaysian freshwater pond after dark organic enrichment, followed by single-cell transfers and antibiotic axenization, is documented in the 2001 primary Methods (DOI:10.1007/s00248-001-1024-6), directly read at https://dornsife.usc.edu/caron/wp-content/uploads/sites/263/2023/11/2001_Sanders_etal_ME.pdf. Antibiotic axenization is not evidence of genetic engineering. Nutrient-source fractions do not identify the complete intracellular assimilation pathway."
      }
    ],
    "discussions": [
      {
        "discussion_id": "phagotrophy-nutrition-and-hierarchy-scope",
        "prompt": "Keep particulate nutrition distinct from uptake and carbon-source axes.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "The class requires nutritional assimilation after ingestion; particle contact, retention or engulfment alone is insufficient. Phagocytosis traitmech:000627 describes membrane-mediated uptake and explicitly leaves nutrition separate. Its existing discussion is not an unresolved exact phagotrophy node. The 2001 Introduction describes carbon, macronutrient and growth-factor benefits of phagotrophy as variable, partly speculative roles across mixotrophs; the 2017 Introduction attributes growth-factor cases to earlier papers not independently audited here. Those statements frame terminology, not new canonical examples. Trophic type METPO:1000631 is locally defined by carbon, energy and electron-donor sources, heterotrophic METPO:1000644 by organic carbon, and mixotrophic METPO:1000652 by dual carbon use. This broader nutrient-acquisition mode does not prescribe a carbon source or require photosynthesis, so retain phenotype METPO:1000059 pending review of a closer nutritional-mode hierarchy. Nutrient adaptation METPO:1000731 concerns nutrient regimes, not specifically particle feeding. Do not equate phagotrophy with phagocytosis, mixotrophy, bacterivory or the bacteria-only predatory-bacterium class. Extracellular digestion without particle ingestion is outside this definition. No unverified synonym or process-level ontology xref is asserted.",
        "posed_by": "codex",
        "posed_date": "2026-10-05"
      },
      {
        "discussion_id": "phagotrophy-assimilation-mechanism-evidence",
        "prompt": "Resolve nutrient processing with native functional evidence.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Growth and isotope incorporation establish nutritional use without identifying a universal phagosomal digestion or assimilation mechanism. Distinguish prey origin, release of dissolved metabolites, direct organic assimilation and respiration followed by carbon refixation. Isotope mass balance does not by itself separate all these routes. Sequence annotation or differential expression alone would not establish native protein function. Obtain taxon-paired functional evidence and inspect relevant supplements before adding protein accessions or a causal graph.",
        "posed_by": "codex",
        "posed_date": "2026-10-05"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-05T21:49:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added phagotrophy as an organism-level particulate-nutrition phenotype with two DOI-backed snippets, primary growth/isotope evidence and a natural BG-1 exemplar. Ignored-and-hidden novelty searches and pinned METPO review found no exact record. Reserved METPO:1058100 in v504. Kept uptake, nutrient sources, carbon-source classification and molecular mechanisms separate; no graph inferred.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000168",
    "label": "phenylalanine arylamidase activity",
    "definition": "A physiological enzyme-activity phenotype in which a cell produces active phenylalanine arylamidase enzymes that hydrolyze phenylalanine arylamide substrates.",
    "definition_source": "DOI:10.1099/ijsem.0.006017",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "synonyms": [
      {
        "synonym_text": "phenylalanine arylamidase",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1099/ijsem.0.006017"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1099/ijsem.0.006017",
        "snippet": "enzymatic activities are present for: \u03b1-galactosidase, N-acetyl-\u03b2-glucosaminidase, arginine arylamidase, proline arylamidase, leucyl glycine arylamidase, phenylalanine arylamidase, leucine arylamidase, tyrosine arylamidase, alanine arylamidase, glycine arylamidase, histidine arylamidase, glutamyl glutamic acid arylamidase, serine arylamidase, valine arylamidase, cysteine arylamidase, esterase, esterase lipase, alpha-chymotrypsin",
        "notes": "Srinivasan et al. listed phenylalanine arylamidase among enzymatic activities present in the Amygdalobacter indicium species description, supporting the API arylamidase row as a directly assayed bacterial enzyme-activity phenotype."
      },
      {
        "reference": "DOI:10.1128/JCM.40.9.3427-3431.2002",
        "snippet": "When the API rapid ID32A system was used, all eight strains displayed activity for alanine arylamidase, arginine arylamidase, \u03b1-glucosidase, glycine arylamidase, histidine arylamidase, leucine arylamidase, leucylglycine arylamidase, proline arylamidase, phenylalanine arylamidase, serine arylamidase, and tyrosine arylamidase",
        "notes": "Hall et al. reported phenylalanine arylamidase activity in all eight Actinomyces cardiffensis clinical isolates tested with the API rapid ID32A system."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:3029272",
        "taxon_label": "Amygdalobacter indicium",
        "note": "Srinivasan et al. reported Amygdalobacter indicium as positive for phenylalanine arylamidase activity in an enzyme activity panel.",
        "reference": "DOI:10.1099/ijsem.0.006017"
      }
    ],
    "discussions": [
      {
        "discussion_id": "phenylalanine-arylamidase-activity-xref-gap",
        "prompt": "Resolve an exact external ontology class for phenylalanine arylamidase activity before adding a TraitRecord xref.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "GO:0004177 covers broad aminopeptidase activity at molecular-function scope, and no live GO class provides an exact residue-specific phenylalanine arylamidase production phenotype at organism-level scope.",
        "posed_by": "codex",
        "posed_date": "2026-09-12"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-12T12:08:46Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted phenylalanine arylamidase activity as a DOI-backed TraitRecord after a repository-wide duplicate review covering ignored and hidden files; METPO has no exact phenylalanine arylamidase activity class yet and the placeholder is reserved in proposals/metpo_traitmech_v45.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000656",
    "label": "photoautotrophic",
    "definition": "A trophic type characterized by the use of light as the energy source and carbon dioxide as the primary carbon source for biosynthesis.",
    "definition_source": "DOI:10.3390/life10050071",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000631"
    ],
    "synonyms": [
      {
        "synonym_text": "anoxygenic_photoautotrophy",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "anoxygenic_photoautotrophy_hydrogen_oxidation",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "anoxygenic_photoautotrophy_iron_oxidation",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "anoxygenic_photoautotrophy_sulfur_oxidation",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "photoautotroph",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "photoautotrophy",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "created_by": "Anthea Guo",
    "evidence": [
      {
        "reference": "DOI:10.3390/life10050071",
        "snippet": "capture solar energy",
        "notes": "Review supports cyanobacterial photoautotrophic use of solar energy and CO2 fixation."
      },
      {
        "reference": "DOI:10.1128/AEM.02473-10",
        "snippet": "Calvin-Benson reductive pentose phosphate cycle",
        "notes": "Review supports the Calvin-Benson cycle as a microbial autotrophic CO2-fixation pathway."
      },
      {
        "reference": "PMID:8590279",
        "snippet": "Synechocystis sp. strain PCC6803",
        "notes": "Organism example: Synechocystis sp. PCC 6803 is a model photoautotrophic cyanobacterium that uses oxygenic photosynthesis to drive Calvin-Benson CO2 fixation (Kaneko et al. 1996, DNA Res, full genome)."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1111708",
        "taxon_label": "Synechocystis sp. PCC 6803",
        "note": "oxygenic photoautotroph",
        "reference": "DOI:10.3390/md11082894"
      },
      {
        "taxon_id": "NCBITaxon:194439",
        "taxon_label": "Chlorobaculum tepidum TLS",
        "note": "anoxygenic photoautotroph",
        "reference": "DOI:10.1073/pnas.132181499"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "photoautotrophic_cyanobacterial_carbon_fixation",
        "title": "Photoautotrophic light-powered CO2 fixation",
        "description": "DOI-backed graph linking light capture, photosynthetic electron transport, ATP/reductant supply, and Calvin-Benson carbon fixation.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "This graph specifically represents oxygenic cyanobacterial photoautotrophy, even though the trait also has an anoxygenic canonical example. The Synechocystis protein example is the D1 component of photosystem II and does not denote the complete multisubunit complex.",
        "nodes": [
          {
            "node_id": "photoautotrophic_trait",
            "label": "photoautotrophic",
            "node_type": "TRAIT",
            "grounding": "METPO:1000656",
            "description": "Trophic type using light energy and carbon dioxide for biosynthesis."
          },
          {
            "node_id": "light",
            "label": "light",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Energy source for photoautotrophic metabolism.",
            "grounding": "PATO:0001717"
          },
          {
            "node_id": "photosystem_ii",
            "label": "photosystem II",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Oxygenic photosystem that extracts electrons from water in cyanobacteria.",
            "grounding": "GO:0009523",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:P16033",
                "protein_label": "Photosystem II protein D1 2",
                "gene_symbol": "psbA2",
                "taxon_id": "NCBITaxon:1111708",
                "taxon_label": "Synechocystis sp. PCC 6803",
                "entry_status": "REVIEWED",
                "retrieved_on": "2026-10-22",
                "entry_version": 187,
                "sequence_version": 1,
                "role": "D1 reaction-center component of photosystem II; this accession is not presented as the complete water-oxidizing complex.",
                "evidence": [
                  {
                    "reference": "DOI:10.1074/jbc.M806116200",
                    "snippet": "the PsbA (D1) subunit of photosystem II (PSII)",
                    "notes": "A primary Synechocystis PCC 6803 study identifies PsbA/D1 as a PSII subunit and studies its biogenesis; UniProtKB P16033 verifies the reviewed PsbA2 protein and strain taxon."
                  }
                ]
              }
            ]
          },
          {
            "node_id": "water",
            "label": "water",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:15377",
            "description": "Electron donor for oxygenic photosynthesis."
          },
          {
            "node_id": "molecular_oxygen",
            "label": "molecular oxygen",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:15379",
            "description": "Product of oxygenic water splitting."
          },
          {
            "node_id": "photosynthetic_electron_transport",
            "label": "photosynthetic electron transport",
            "node_type": "PATHWAY",
            "description": "Electron-transfer pathway generating ATP and NADPH.",
            "grounding": "GO:0009767"
          },
          {
            "node_id": "atp_nadph",
            "label": "ATP and NADPH",
            "node_type": "CHEMICAL",
            "description": "Energy and reductant supply for CO2 assimilation."
          },
          {
            "node_id": "carbon_dioxide",
            "label": "carbon dioxide",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:16526",
            "description": "Primary inorganic carbon source."
          },
          {
            "node_id": "calvin_benson_cycle",
            "label": "Calvin-Benson cycle",
            "node_type": "PATHWAY",
            "description": "Reductive pentose phosphate CO2-fixation cycle.",
            "grounding": "GO:0019253"
          },
          {
            "node_id": "rubisco",
            "label": "RuBisCO",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Carboxylating enzyme of the Calvin-Benson cycle.",
            "grounding": "InterPro:IPR033966"
          },
          {
            "node_id": "biomass",
            "label": "biomass",
            "node_type": "CHEMICAL",
            "description": "Cellular material formed from fixed carbon.",
            "grounding": "METPO:1007501"
          },
          {
            "node_id": "carbon_concentrating_mechanism",
            "label": "carbon-concentrating mechanism",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Inorganic carbon-concentrating mechanism that elevates CO2 around RuBisCO."
          },
          {
            "node_id": "rubisco_oxygenase_activity",
            "label": "RuBisCO oxygenase activity",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "Wasteful oxygenation side-reaction of RuBisCO leading to photorespiration."
          },
          {
            "node_id": "carboxysome",
            "label": "carboxysome",
            "node_type": "ORGANELLE",
            "description": "Proteinaceous microcompartment housing RuBisCO and carbonic anhydrase for CO2 fixation.",
            "grounding": "GO:0031470"
          },
          {
            "node_id": "carboxysomal_carbonic_anhydrase",
            "label": "carboxysomal carbonic anhydrase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Carbonic anhydrase that dehydrates bicarbonate to CO2 inside the carboxysome.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Cyanobacterial carboxysomes recruit different carbonic-anhydrase families and architectures; the graph does not identify a single exact family."
          },
          {
            "node_id": "bicarbonate",
            "label": "bicarbonate",
            "node_type": "CHEMICAL",
            "description": "Inorganic carbon species accumulated and converted to CO2 for fixation.",
            "grounding": "CHEBI:17544"
          }
        ],
        "edges": [
          {
            "subject": "photoautotrophic_trait",
            "predicate": "has energy source",
            "object": "light",
            "description": "Photoautotrophy uses light as the energy source.",
            "evidence": [
              {
                "reference": "DOI:10.3390/life10050071",
                "snippet": "capture solar energy",
                "notes": "Supports light capture by cyanobacteria under photoautotrophic metabolism."
              }
            ],
            "predicate_id": "METPO:2007807"
          },
          {
            "subject": "photosystem_ii",
            "predicate": "oxidizes",
            "object": "water",
            "description": "Oxygenic photosynthesis extracts electrons from water through PSII.",
            "evidence": [
              {
                "reference": "DOI:10.3390/life10050071",
                "snippet": "uses it to split H2O",
                "notes": "Supports water splitting by PSII in cyanobacteria."
              }
            ],
            "predicate_id": "METPO:2007803"
          },
          {
            "subject": "water",
            "predicate": "oxidized to",
            "object": "molecular_oxygen",
            "description": "Water oxidation releases molecular oxygen.",
            "evidence": [
              {
                "reference": "DOI:10.3390/life10050071",
                "snippet": "split H2O molecules into O2",
                "notes": "Supports oxygen as the product of water splitting."
              }
            ],
            "predicate_id": "METPO:2007405"
          },
          {
            "subject": "photosystem_ii",
            "predicate": "feeds electrons into",
            "object": "photosynthetic_electron_transport",
            "description": "PSII feeds electrons into the photosynthetic electron transport chain.",
            "evidence": [
              {
                "reference": "DOI:10.3390/life10050071",
                "snippet": "passes its reducing equivalents to an electron transfer chain",
                "notes": "Supports electron flow from PSII/plastoquinol into photosynthetic electron transport."
              }
            ],
            "predicate_id": "METPO:2007402"
          },
          {
            "subject": "photosynthetic_electron_transport",
            "predicate": "has output",
            "object": "atp_nadph",
            "description": "Photosynthetic electron transport generates ATP and NADPH.",
            "evidence": [
              {
                "reference": "DOI:10.3390/life10050071",
                "snippet": "generate chemical energy (ATP) and reducing power (NADPH)",
                "notes": "Supports ATP and NADPH generation by photosynthetic electron transport."
              }
            ],
            "predicate_id": "RO:0002234"
          },
          {
            "subject": "carbon_dioxide",
            "predicate": "fixed by",
            "object": "calvin_benson_cycle",
            "description": "CO2 is assimilated through the Calvin-Benson cycle in many photoautotrophs.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.02473-10",
                "snippet": "Calvin-Benson reductive pentose phosphate cycle",
                "notes": "Supports Calvin-Benson cycle as an autotrophic CO2-fixation route."
              }
            ],
            "predicate_id": "METPO:2007404"
          },
          {
            "subject": "rubisco",
            "predicate": "catalyzes",
            "object": "calvin_benson_cycle",
            "description": "RuBisCO is a key carboxylating enzyme for Calvin-Benson CO2 fixation.",
            "evidence": [
              {
                "reference": "DOI:10.3390/life10050071",
                "snippet": "Calvin cycle enzymes, RuBisCO",
                "notes": "Supports RuBisCO as a Calvin-cycle enzyme tied to CO2 fixation rate."
              }
            ],
            "predicate_id": "biolink:catalyzes"
          },
          {
            "subject": "calvin_benson_cycle",
            "predicate": "has output",
            "object": "biomass",
            "description": "Fixed carbon supports biosynthesis and biomass production.",
            "evidence": [
              {
                "reference": "DOI:10.3390/life10050071",
                "snippet": "fix ... CO2 into ... biomass",
                "notes": "Supports CO2 fixation into biomass by cyanobacterial photoautotrophy."
              }
            ],
            "predicate_id": "RO:0002234"
          },
          {
            "subject": "photosynthetic_electron_transport",
            "predicate": "enables",
            "object": "calvin_benson_cycle",
            "description": "Light-driven photosynthetic electron transport supplies the energy/reductant that drives CBB-cycle CO2 fixation.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fpls.2024.1417680",
                "notes": "Phototrophs use light energy to drive a photosynthetic electron transport chain, and CO2 fixation occurs via the Calvin-Benson-Bassham cycle."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "carbon_concentrating_mechanism",
            "predicate": "lowers",
            "object": "rubisco_oxygenase_activity",
            "description": "The CCM enriches intracellular inorganic carbon, suppressing the wasteful RuBisCO oxygenase reaction.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fpls.2024.1417680",
                "notes": "The CCM lowers RuBisCO's oxygenase reaction to below ~1% by enriching intracellular inorganic carbon."
              }
            ]
          },
          {
            "subject": "bicarbonate",
            "predicate": "diffuses into",
            "object": "carboxysome",
            "description": "Cytoplasmic bicarbonate enters the carboxysome where it is converted to CO2 for fixation.",
            "evidence": [
              {
                "reference": "DOI:10.1111/ppl.14140",
                "notes": "Cytoplasmic HCO3- diffuses into the carboxysome."
              }
            ]
          },
          {
            "subject": "carboxysomal_carbonic_anhydrase",
            "predicate": "converts",
            "object": "bicarbonate",
            "description": "Carboxysomal carbonic anhydrase dehydrates bicarbonate to CO2 to feed RuBisCO.",
            "evidence": [
              {
                "reference": "DOI:10.1111/ppl.14140",
                "notes": "Bicarbonate is converted back to CO2 by carbonic anhydrase inside carboxysomes (CA produces CO2)."
              }
            ]
          },
          {
            "subject": "light",
            "predicate": "enables",
            "object": "photosynthetic_electron_transport",
            "description": "Captured light enables the high-energy electron transfer through the photosystems that constitutes photosynthetic electron transport.",
            "evidence": [
              {
                "reference": "DOI:10.1111/1751-7915.14519",
                "snippet": "Photosynthesis in cyanobacteria requires effective light harvesting and the transfer of high-energy electrons through two photosystems",
                "notes": "The review directly links light harvesting to electron transfer through PSII and PSI in cyanobacterial photosynthesis."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "carbon_concentrating_mechanism",
            "predicate": "includes",
            "object": "carboxysome",
            "description": "The cyanobacterial carbon-concentrating mechanism includes the carboxysome microcompartment as a functional component.",
            "evidence": [
              {
                "reference": "DOI:10.1126/sciadv.adk7283",
                "snippet": "Proteinaceous microcompartments, called carboxysomes, play a critical role in CCM function",
                "notes": "A primary structural and biochemical study identifies carboxysomes as a critical component of cyanobacterial CCM function."
              }
            ],
            "predicate_id": "biolink:has_part"
          },
          {
            "subject": "carboxysome",
            "predicate": "includes",
            "object": "rubisco",
            "description": "The carboxysome houses RuBisCO for concentrated CO2 fixation.",
            "evidence": [
              {
                "reference": "DOI:10.1126/sciadv.adk7283",
                "snippet": "carboxysomes that house CA and Rubisco",
                "notes": "The primary study explicitly places RuBisCO within the carboxysome together with carbonic anhydrase."
              }
            ],
            "predicate_id": "biolink:has_part"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.879777+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-08T00:00:00-07:00",
        "curator": "codex",
        "action": "ADDED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed causal graph for oxygenic light capture, ATP/NADPH generation, and Calvin-Benson CO2 fixation.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-16T05:00:00-07:00",
        "curator": "claude",
        "action": "ADDED_ORGANISM_EXAMPLE",
        "changes": "Added Synechocystis sp. PCC 6803 organism example with PMID-backed evidence.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 4 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d72, METPO:2000010\u00d71, METPO:2000016\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T05:49:25Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:catalyzes\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T21:30:07Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007405\u00d71, METPO:2007402\u00d71, METPO:2007404\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:38:01Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 3 causal-node grounding field(s) via mappings/node_grounding.tsv (PATO:0001717\u00d71, GO:0009767\u00d71, GO:0019253\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:41:04Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (METPO:1007501\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T07:34:59Z",
        "curator": "claude",
        "action": "RETYPE_CAUSAL_NODES",
        "changes": "Re-typed 1 causal-node node_type field(s) to align with CausalNodeTypeEnum semantics: biomass: BIOLOGICAL_PROCESS \u2192 CHEMICAL \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-26T02:27:52Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A075WF79\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 4 evidence-backed generic edges (5 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:15Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:35Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0031470\u00d71, CHEBI:17544\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:21:12Z",
        "curator": "claude",
        "action": "RETRACT_DEAD_UNIPROT_GROUNDINGS",
        "changes": "Retracted 1 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:23:56Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0009523\u00d71, InterPro:IPR033966\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 3 causal edge(s) off microbe-domain METPO predicates (1 to has energy source, 2 to has output), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T02:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES_PART2",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates onto their causal-graph counterparts (1 to oxidizes), issue 301 part 2. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Each replacement is a 1:1 mirror of its source predicate that changes only the domain, so the claim each edge makes is unchanged and directions are unchanged. The replacements are proposed in proposals/metpo_traitmech_v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-16T02:00:00Z",
        "curator": "claude",
        "action": "NORMALISE_NODE_TYPE",
        "changes": "Under the PATHWAY-vs-BIOLOGICAL_PROCESS rule, one node_id means one thing corpus-wide (issue 356): photosynthetic_electron_transport is typed PATHWAY. PATHWAY is a named, conventionally enumerable multi-step route; BIOLOGICAL_PROCESS is everything else. A named route in every record that carries it, though NOT THE SAME ROUTE, which is why no single step list belongs in this rationale. metabolism/phototrophy.yaml enumerates the oxygenic form ('Electron flow from water through PSII, cytochrome b6f and PSI'); photoheterotrophic.yaml and photoorganoheterotrophic.yaml cover ANOXYGENIC phototrophy -- one reaction centre, cyclic flow, no water oxidation -- and say the neutral thing on purpose. Quoting the oxygenic steps at them would assert biology they specifically do not claim (#400 review). Both forms are named routes whose steps a curator could list, which is the test. Was 5 PATHWAY to 1 before this tranche.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-24T11:45:00-07:00",
        "curator": "codex",
        "action": "REVIEWED_CAUSAL_GRAPH_PROTEIN_TAXON",
        "changes": "Marked the cyanobacterial graph mechanistic, documented its oxygenic scope, reviewed carboxysomal carbonic anhydrase as label-only, upgraded canonical examples to strain-level DOI citations, and added the reviewed Synechocystis PsbA2 example.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-30T20:17:23Z",
        "curator": "codex",
        "action": "CONNECT_CAUSAL_GRAPH_COMPONENTS",
        "changes": "Connected all four components of the oxygenic cyanobacterial photoautotrophy graph with three tracked, snippet-backed relations: light enables photosynthetic electron transport; the CCM includes the carboxysome; and the carboxysome includes RuBisCO. No new paid research was commissioned (#183, #426).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-22T01:35:00Z",
        "curator": "claude",
        "action": "REFRESH_UNIPROT_ENTRY_VERSION",
        "changes": "Refreshed UniProtKB entry_version against live UniProt REST on 2026-10-22: UniProtKB:P16033 (186 -> 187 on photosystem_ii).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000657",
    "label": "photoheterotrophic",
    "definition": "A trophic type in which an organism uses light as the energy source and organic compounds as the primary carbon source for biosynthesis.",
    "definition_source": "DOI:10.1016/B978-012373944-5.00083-3",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000631"
    ],
    "synonyms": [
      {
        "synonym_text": "photoheterotroph",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "photoheterotrophy",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "created_by": "Luke Wang",
    "evidence": [
      {
        "reference": "DOI:10.1016/B978-012373944-5.00083-3",
        "snippet": "light and reduced organic compounds",
        "notes": "Encyclopedia chapter defines photoheterotrophy by light energy and reduced organic carbon."
      },
      {
        "reference": "DOI:10.1128/AEM.01747-12",
        "snippet": "accumulated 25% to 110% more biomass",
        "notes": "Experimental AAP study supports light-enhanced assimilation of supplied organic carbon."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1076",
        "taxon_label": "Rhodopseudomonas palustris",
        "note": "metabolically versatile photoheterotroph",
        "reference": "DOI:10.1371/journal.pcbi.1011371"
      },
      {
        "taxon_id": "NCBITaxon:1085",
        "taxon_label": "Rhodospirillum rubrum",
        "note": "purple non-sulfur photoheterotroph",
        "reference": "DOI:10.3389/fmicb.2021.731976"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "photoheterotrophic_light_organic_carbon",
        "title": "Photoheterotrophic light-supported organic carbon assimilation",
        "description": "DOI-backed graph linking light capture, bacteriochlorophyll reaction centers, photosynthetic electron transport, ATP generation, and organic carbon assimilation.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "The graph presents bacteriochlorophyll reaction-center and proteorhodopsin branches as alternative photoheterotrophic mechanisms. The R. rubrum example anchors the Type II reaction-center branch and does not represent rhodopsin-based phototrophy.",
        "nodes": [
          {
            "node_id": "photoheterotrophic_trait",
            "label": "photoheterotrophic",
            "node_type": "TRAIT",
            "grounding": "METPO:1000657",
            "description": "Trophic type using light energy and organic carbon for biosynthesis."
          },
          {
            "node_id": "light",
            "label": "light",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Energy input harvested by photoheterotrophs.",
            "grounding": "PATO:0001717"
          },
          {
            "node_id": "bacteriochlorophyll",
            "label": "bacteriochlorophyll",
            "node_type": "CHEMICAL",
            "description": "Light-harvesting pigment in many anoxygenic photoheterotrophs.",
            "grounding": "CHEBI:38201"
          },
          {
            "node_id": "photosynthetic_reaction_center",
            "label": "photosynthetic reaction center",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Pigment-protein complex initiating photochemical charge separation.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "This node denotes a multisubunit photosynthetic complex across distinct Type I and Type II families; no single protein-family term represents the generic complex.",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:P10717",
                "protein_label": "Reaction center protein L chain",
                "gene_symbol": "pufL",
                "taxon_id": "NCBITaxon:1085",
                "taxon_label": "Rhodospirillum rubrum",
                "entry_status": "REVIEWED",
                "retrieved_on": "2026-10-22",
                "entry_version": 120,
                "sequence_version": 2,
                "role": "L-chain component of the R. rubrum Type II photochemical reaction center; this accession is not presented as the complete reaction-center complex.",
                "evidence": [
                  {
                    "reference": "DOI:10.1128/jb.182.5.1200-1207.2000",
                    "snippet": "The proteins of the photochemical components are encoded by the puf operon (LHalpha, LHbeta, RC-L, and RC-M) and by puhA (RC-H)",
                    "notes": "The primary R. rubrum assembly study identifies RC-L as a puf-encoded reaction-center component and reports phototrophic incompetence of puf mutants; UniProtKB P10717 is the reviewed species-level PufL entry."
                  }
                ]
              }
            ]
          },
          {
            "node_id": "photosynthetic_electron_transport",
            "label": "photosynthetic electron transport",
            "node_type": "PATHWAY",
            "description": "Light-induced electron-transfer pathway supporting energy conservation.",
            "grounding": "GO:0009767"
          },
          {
            "node_id": "atp",
            "label": "ATP",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:30616",
            "description": "Energy carrier generated by photosynthetic electron transport."
          },
          {
            "node_id": "organic_carbon",
            "label": "organic carbon",
            "node_type": "CHEMICAL",
            "description": "Reduced organic compound used as the primary carbon source.",
            "grounding": "CHEBI:50860"
          },
          {
            "node_id": "biomass",
            "label": "biomass",
            "node_type": "CHEMICAL",
            "description": "Cell material produced from assimilated organic carbon.",
            "grounding": "METPO:1007501"
          },
          {
            "node_id": "proteorhodopsin_proton_pumping",
            "label": "proteorhodopsin proton pumping",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Light-driven proton translocation by proteorhodopsin in rhodopsin-based photoheterotrophs."
          },
          {
            "node_id": "membrane_potential",
            "label": "membrane potential",
            "node_type": "STATE",
            "description": "Transmembrane electrochemical proton-motive force generated by light-driven ion pumping."
          },
          {
            "node_id": "atp_production",
            "label": "ATP production",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Synthesis of ATP driven by the proton-motive force."
          },
          {
            "node_id": "proteorhodopsin",
            "label": "proteorhodopsin",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Retinal-binding light-driven proton pump enabling rhodopsin-based phototrophy.",
            "grounding": "InterPro:IPR017402"
          },
          {
            "node_id": "nadph_anabolic",
            "label": "NAD(P)H for anabolic metabolism",
            "node_type": "CHEMICAL",
            "description": "Reducing equivalents required for biosynthesis; not generated by proteorhodopsin phototrophy."
          },
          {
            "node_id": "photophosphorylation",
            "label": "photophosphorylation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Light-driven ATP synthesis used by aerobic anoxygenic phototrophs."
          },
          {
            "node_id": "aerobic_anoxygenic_phototrophs",
            "label": "aerobic anoxygenic phototrophs",
            "node_type": "TRAIT",
            "description": "Facultative photoheterotrophs harvesting light to generate ATP while relying on organic matter.",
            "grounding": "traitmech:000194"
          },
          {
            "node_id": "dissolved_organic_matter",
            "label": "dissolved organic matter",
            "node_type": "CHEMICAL",
            "description": "Organic carbon/energy source on which aerobic anoxygenic phototrophs primarily rely."
          }
        ],
        "edges": [
          {
            "subject": "photoheterotrophic_trait",
            "predicate": "has energy source",
            "object": "light",
            "description": "Photoheterotrophic growth uses light as the energy input.",
            "evidence": [
              {
                "reference": "DOI:10.1016/B978-012373944-5.00083-3",
                "snippet": "light and reduced organic compounds",
                "notes": "Supports light as the energy source in photoheterotrophy."
              }
            ],
            "predicate_id": "METPO:2007807"
          },
          {
            "subject": "bacteriochlorophyll",
            "predicate": "part of",
            "object": "photosynthetic_reaction_center",
            "description": "Bacteriochlorophyll pigments occur in reaction centers of many anoxygenic phototrophs.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.01747-12",
                "snippet": "reaction centers composed of bacteriochlorophyll",
                "notes": "Supports BChl-containing reaction centers in aerobic anoxygenic phototrophs."
              }
            ],
            "predicate_id": "biolink:part_of"
          },
          {
            "subject": "light",
            "predicate": "captured by",
            "object": "photosynthetic_reaction_center",
            "description": "Reaction centers capture light to initiate photochemical energy conversion.",
            "evidence": [
              {
                "reference": "DOI:10.1016/B978-0-12-809633-8.20672-9",
                "snippet": "utilize light as an energy source",
                "notes": "Supports reaction-center-based light utilization by chlorophototrophs."
              }
            ]
          },
          {
            "subject": "photosynthetic_reaction_center",
            "predicate": "initiates",
            "object": "photosynthetic_electron_transport",
            "description": "Photochemical charge separation drives photosynthetic electron transport.",
            "evidence": [
              {
                "reference": "DOI:10.1016/B978-0-12-809633-8.20672-9",
                "snippet": "light-induced redox chemistry",
                "notes": "Supports reaction-center photochemistry leading to electron transfer."
              }
            ]
          },
          {
            "subject": "photosynthetic_electron_transport",
            "predicate": "has output",
            "object": "atp",
            "description": "Photosynthetic electron transport conserves light energy as ATP.",
            "evidence": [
              {
                "reference": "DOI:10.1016/B978-0-12-809633-8.20672-9",
                "snippet": "can be used to produce ATP",
                "notes": "Supports ATP production downstream of phototrophic electron transfer."
              }
            ],
            "predicate_id": "RO:0002234"
          },
          {
            "subject": "photoheterotrophic_trait",
            "predicate": "has carbon source",
            "object": "organic_carbon",
            "description": "Photoheterotrophs require organic compounds as the carbon source.",
            "evidence": [
              {
                "reference": "DOI:10.1016/B978-012373944-5.00083-3",
                "snippet": "reduced organic compounds",
                "notes": "Supports reduced organic compounds as the carbon source in photoheterotrophy."
              }
            ],
            "predicate_id": "METPO:2007806"
          },
          {
            "subject": "organic_carbon",
            "predicate": "assimilated into",
            "object": "biomass",
            "description": "Light-supported photoheterotrophs assimilate supplied organic carbon into biomass.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.01747-12",
                "snippet": "accumulate the supplied organic carbon",
                "notes": "Supports organic carbon assimilation into biomass under light."
              }
            ]
          },
          {
            "subject": "light",
            "predicate": "activates",
            "object": "proteorhodopsin_proton_pumping",
            "description": "Light drives proton pumping by proteorhodopsin in rhodopsin-based photoheterotrophs.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s12275-024-00125-0",
                "notes": "the light-driven proton pumping by PR"
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "proteorhodopsin_proton_pumping",
            "predicate": "generates",
            "object": "membrane_potential",
            "description": "Proteorhodopsin proton transport establishes a membrane potential.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s12275-024-00125-0",
                "notes": "PR-mediated proton transport could generate a sufficient membrane potential for ATP production"
              }
            ],
            "predicate_id": "biolink:produces"
          },
          {
            "subject": "membrane_potential",
            "predicate": "enables",
            "object": "atp_production",
            "description": "The membrane potential drives ATP production.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s12275-024-00125-0",
                "notes": "generate a sufficient membrane potential for ATP production"
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "proteorhodopsin",
            "predicate": "cannot generate",
            "object": "nadph_anabolic",
            "description": "Boundary edge: proteorhodopsin phototrophy yields ATP but no reducing power for biosynthesis.",
            "evidence": [
              {
                "reference": "DOI:10.4014/jmb.2410.10034",
                "notes": "PR can never be harnessed to generate NAD(P)H for anabolic metabolism"
              }
            ]
          },
          {
            "subject": "aerobic_anoxygenic_phototrophs",
            "predicate": "perform",
            "object": "photophosphorylation",
            "description": "Aerobic anoxygenic phototrophs generate ATP via photophosphorylation.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s40793-024-00573-6",
                "notes": "AAPs are facultative photoheterotrophs that harvest light energy and generate ATP by photophosphorylation"
              }
            ]
          },
          {
            "subject": "photophosphorylation",
            "predicate": "has output",
            "object": "atp",
            "description": "Photophosphorylation conserves light energy as ATP.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s40793-024-00573-6",
                "notes": "generate ATP by photophosphorylation using a unique type of bacteriochlorophyll-a-containing reaction center"
              }
            ],
            "predicate_id": "RO:0002234"
          },
          {
            "subject": "aerobic_anoxygenic_phototrophs",
            "predicate": "relies primarily on",
            "object": "dissolved_organic_matter",
            "description": "Aerobic anoxygenic phototrophs primarily rely on dissolved organic matter as their energy/carbon source.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s40793-024-00573-6",
                "notes": "they primarily rely on dissolved organic matter as an energy source"
              }
            ]
          },
          {
            "subject": "proteorhodopsin",
            "predicate": "enables",
            "object": "proteorhodopsin_proton_pumping",
            "description": "Proteorhodopsin directly enables the light-powered proton-pumping process in the retinal phototrophy branch.",
            "evidence": [
              {
                "reference": "DOI:10.1073/pnas.0611035104",
                "snippet": "Proteorhodopsin (PR) is a light-powered proton pump",
                "notes": "Verified against the public PNAS article full text."
              }
            ],
            "predicate_id": "RO:0002327"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.880718+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-08T00:00:00-07:00",
        "curator": "codex",
        "action": "ADDED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed causal graph for light capture, bacteriochlorophyll reaction centers, ATP generation, and organic carbon assimilation.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000010\u00d71, METPO:2000202\u00d71, METPO:2000006\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T05:49:25Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:part_of\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:38:01Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 3 causal-node grounding field(s) via mappings/node_grounding.tsv (PATO:0001717\u00d71, GO:0009767\u00d71, CHEBI:50860\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:41:04Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (METPO:1007501\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T07:34:59Z",
        "curator": "claude",
        "action": "RETYPE_CAUSAL_NODES",
        "changes": "Re-typed 1 causal-node node_type field(s) to align with CausalNodeTypeEnum semantics: biomass: BIOLOGICAL_PROCESS \u2192 CHEMICAL \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-14T05:51:47Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:38201\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 7 evidence-backed generic edges (8 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:15Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 4 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002213\u00d71, biolink:produces\u00d71, RO:0002327\u00d71, METPO:2000202\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:20Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A1D7QWW9\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 4 causal edge(s) off microbe-domain METPO predicates (1 to has energy source, 2 to has output, 1 to has carbon source), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-16T02:00:00Z",
        "curator": "claude",
        "action": "NORMALISE_NODE_TYPE",
        "changes": "Under the PATHWAY-vs-BIOLOGICAL_PROCESS rule, one node_id means one thing corpus-wide (issue 356): photosynthetic_electron_transport is typed PATHWAY. PATHWAY is a named, conventionally enumerable multi-step route; BIOLOGICAL_PROCESS is everything else. A named route in every record that carries it, though NOT THE SAME ROUTE, which is why no single step list belongs in this rationale. metabolism/phototrophy.yaml enumerates the oxygenic form ('Electron flow from water through PSII, cytochrome b6f and PSI'); photoheterotrophic.yaml and photoorganoheterotrophic.yaml cover ANOXYGENIC phototrophy -- one reaction centre, cyclic flow, no water oxidation -- and say the neutral thing on purpose. Quoting the oxygenic steps at them would assert biology they specifically do not claim (#400 review). Both forms are named routes whose steps a curator could list, which is the test. Was 5 PATHWAY to 1 before this tranche.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-22T04:26:16Z",
        "curator": "codex",
        "action": "REVIEW_UNIPROT_INSTANCE_GROUNDINGS",
        "changes": "Reviewed 1 organism-specific UniProtKB grounding(s): replaced 1 with taxon-agnostic GO/InterPro terms and retracted 0 to label-only where no exact semantic term was supported (docs/GROUNDING_POLICY.md).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-24T12:05:00-07:00",
        "curator": "codex",
        "action": "REVIEWED_CAUSAL_GRAPH_PROTEIN_TAXON",
        "changes": "Marked the graph mechanistic, separated reaction-center and proteorhodopsin scope, reviewed the generic reaction center as label-only, upgraded canonical citations to DOIs, and added the reviewed R. rubrum PufL component example.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T10:15:00Z",
        "curator": "codex",
        "action": "CONNECT_CAUSAL_GRAPH_COMPONENTS",
        "changes": "Resolved issue #183 graph fragmentation (2 components to 1) with 1 public-source, verbatim-snippet-backed connector(s). No paid research service was called.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-14T23:14:00Z",
        "curator": "codex",
        "action": "GROUND_CAUSAL_NODE",
        "changes": "Grounded the aerobic anoxygenic phototrophs causal node to traitmech:000194 after minting the same-scope aerobic anoxygenic phototrophy TraitRecord.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-22T01:35:00Z",
        "curator": "claude",
        "action": "REFRESH_UNIPROT_ENTRY_VERSION",
        "changes": "Refreshed UniProtKB entry_version against live UniProt REST on 2026-10-22: UniProtKB:P10717 (119 -> 120 on photosynthetic_reaction_center).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000587",
    "label": "photokinesis",
    "definition": "A motile phenotype in which the speed of active locomotion changes in response to illumination intensity, without requiring orientation toward or away from the light source.",
    "definition_source": "DOI:10.1128/AEM.67.12.5410-5419.2001",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000702"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1128/AEM.67.12.5410-5419.2001",
        "snippet": "swimming velocities are correlated to the illumination intensity.",
        "notes": "Introduction's photokinesis definition; publisher full text at https://journals.asm.org/doi/10.1128/AEM.67.12.5410-5419.2001 and Figure 2A-B with caption inspected. In Marichromatium gracile CE2205, the anoxic 1 mM total-sulfide preparation shows lower speed at low irradiance; oxic controls (>100 micromolar oxygen, no free sulfide) show no significant irradiance dependence. Reported irradiance is visible-region scalar irradiance (400-700 nm), with a fixed visible:near-infrared photon ratio of 1:8.3. Measurements use two-dimensional cell tracks after 60 s at each irradiance. Exponential-phase cells with sulfur globules were sampled above bottom aggregates. The collection-supplied strain is not assigned an independently verified natural lineage here. The separate gradient-migration results are attributed to phobic responses, not used to infer directional photokinesis."
      },
      {
        "reference": "DOI:10.1016/S0176-1617(00)80045-0",
        "snippet": "Photosynthetically active continuous red light reversibly enhances the swimming velocity and increases or decreases the precision of gravitaxis, depending on its initial level.",
        "notes": "Abstract, PMID:12090268, exact-matched at Europe PMC. This primary study of Chlamydomonas reinhardtii supports light-dependent speed modulation alongside a distinct orientation response. Its blue-light responses have different kinetics; proposed chlamy-rhodopsin participation is explicitly inferential. Subscription full text was not inspected; no strain lineage, protein accession or full-text-only result is inferred."
      }
    ],
    "discussions": [
      {
        "discussion_id": "photokinesis-speed-and-direction-boundaries",
        "prompt": "Preserve the speed-response scope when mapping light responses.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "This definition follows the speed usage in the cited experiments. It does not require increasing speed, a photosynthetic energy mechanism, or an isolated response without concurrent taxis. Phototaxis concerns orientation; photophobic responses concern avoidance or reversals. They may coexist with photokinesis, but no equivalence, disjointness or parent-child relation is asserted. The obsolete METPO:1000241 phototaxis class is not an exact match or a replacement target. Reconcile broader kinesis terminology before adding turning-frequency synonyms or external xrefs.",
        "posed_by": "codex",
        "posed_date": "2026-10-04"
      },
      {
        "discussion_id": "photokinesis-strain-and-mechanism-grounding",
        "prompt": "Verify natural exemplars and protein-resolved causal branches.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Qualified experimental observations are retained without canonical taxa pending independent CE2205 lineage verification or a fully inspected algal strain source. Collection provenance alone does not establish unperturbed natural ancestry. Mechanism discussion in the sources does not establish one universal receptor, and the algal abstract only suggests rhodopsin participation. A mechanistic graph is deferred pending source-backed causal edges and eligible taxon-paired protein examples. Do not borrow the generic motile graph or use NONMECHANISTIC to bypass this gap.",
        "posed_by": "codex",
        "posed_date": "2026-10-04"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-04T04:46:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added photokinesis with two primary DOI citations and contiguous snippets. Ignored-and-hidden searches found no exact record or METPO term; nearby obsolete phototaxis is distinct. Reserved METPO:1054100 in proposal v464. Preserved oxygen, spectral and experimental-state qualifiers; deferred natural canonical taxa and protein-level graphs.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000665",
    "label": "photolithoautotrophic",
    "definition": "A trophic type in which an organism obtains energy from light and carbon from carbon dioxide using inorganic electron donors.",
    "definition_source": "DOI:10.3389/fmicb.2011.00165",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000631"
    ],
    "synonyms": [
      {
        "synonym_text": "photolithoautotroph",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.3389/fmicb.2011.00165",
        "snippet": "oxidize sulfide",
        "notes": "Review supports sulfide oxidation coupled to phototrophic central carbon and energy metabolism."
      },
      {
        "reference": "DOI:10.3390/antiox10060829",
        "snippet": "reduced sulfur compounds as an electron donor",
        "notes": "Review supports reduced sulfur electron donors in photolithotrophic sulfur bacteria."
      },
      {
        "reference": "DOI:10.1128/AEM.02473-10",
        "snippet": "autotrophic CO2 fixation",
        "notes": "Review supports CO2 fixation as the autotrophic carbon-assimilation process."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1140",
        "taxon_label": "Synechococcus elongatus PCC 7942",
        "note": "water-splitting photolithoautotroph",
        "reference": "DOI:10.1093/plphys/kiac065"
      },
      {
        "taxon_id": "NCBITaxon:194439",
        "taxon_label": "Chlorobaculum tepidum TLS",
        "note": "sulfide-using photolithoautotroph",
        "reference": "DOI:10.1073/pnas.132181499"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "photolithoautotrophic_light_inorganic_donor_fixation",
        "title": "Photolithoautotrophic light and inorganic-donor mechanism",
        "description": "DOI-backed graph linking light, inorganic electron donors, photosynthetic electron transport, and autotrophic CO2 fixation.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "This graph spans oxygenic and anoxygenic photolithoautotrophic modules and does not assert that water and sulfide are used by one organism. The S. elongatus PCC 7942 example anchors the CBB/RuBisCO branch.",
        "nodes": [
          {
            "node_id": "photolithoautotrophic_trait",
            "label": "photolithoautotrophic",
            "node_type": "TRAIT",
            "grounding": "METPO:1000665",
            "description": "Trophic type using light, inorganic electron donors, and carbon dioxide."
          },
          {
            "node_id": "light",
            "label": "light",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Energy source for photolithoautotrophic metabolism.",
            "grounding": "PATO:0001717"
          },
          {
            "node_id": "photosynthetic_electron_transport",
            "label": "photosynthetic electron transport",
            "node_type": "PATHWAY",
            "description": "Light-driven electron transport pathway.",
            "grounding": "GO:0009767"
          },
          {
            "node_id": "inorganic_electron_donor",
            "label": "inorganic electron donor",
            "node_type": "CHEMICAL",
            "description": "Reduced inorganic substrate supplying electrons.",
            "grounding": "METPO:1007502"
          },
          {
            "node_id": "sulfide",
            "label": "sulfide",
            "node_type": "CHEMICAL",
            "description": "Example inorganic electron donor for anoxygenic phototrophs.",
            "grounding": "CHEBI:15138"
          },
          {
            "node_id": "sulfur_oxidation",
            "label": "sulfur oxidation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Oxidation of reduced sulfur compounds during phototrophic metabolism.",
            "grounding": "GO:0019417"
          },
          {
            "node_id": "reducing_power",
            "label": "reducing power",
            "node_type": "CAPACITY",
            "description": "Reduced electron carriers used for biosynthesis.",
            "grounding": "METPO:1007503"
          },
          {
            "node_id": "carbon_dioxide",
            "label": "carbon dioxide",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:16526",
            "description": "Inorganic carbon source."
          },
          {
            "node_id": "autotrophic_co2_fixation",
            "label": "autotrophic CO2 fixation",
            "node_type": "PATHWAY",
            "description": "Carbon-assimilation pathway converting CO2 to cellular carbon.",
            "grounding": "GO:0015977"
          },
          {
            "node_id": "biomass",
            "label": "biomass",
            "node_type": "CHEMICAL",
            "description": "Cellular material formed from fixed carbon.",
            "grounding": "METPO:1007501"
          },
          {
            "node_id": "nadph",
            "label": "NADPH",
            "node_type": "CHEMICAL",
            "description": "Reduced electron carrier produced by photosynthetic electron transport.",
            "grounding": "CHEBI:16474"
          },
          {
            "node_id": "carbonic_anhydrase",
            "label": "carbonic anhydrase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Enzyme interconverting CO2 and bicarbonate for inorganic carbon supply.",
            "grounding": "InterPro:IPR001765"
          },
          {
            "node_id": "bicarbonate",
            "label": "bicarbonate",
            "node_type": "CHEMICAL",
            "description": "Dissolved inorganic carbon species in equilibrium with CO2.",
            "grounding": "CHEBI:17544"
          },
          {
            "node_id": "dic_transporter",
            "label": "inorganic carbon transporter",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Transporter importing dissolved inorganic carbon species into the cell.",
            "grounding": "InterPro:IPR006007"
          },
          {
            "node_id": "rubisco",
            "label": "RuBisCO",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Ribulose-1,5-bisphosphate carboxylase/oxygenase, key autotrophic carboxylase.",
            "grounding": "InterPro:IPR033966",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:Q31NB3",
                "protein_label": "Ribulose bisphosphate carboxylase large chain",
                "gene_symbol": "rbcL",
                "taxon_id": "NCBITaxon:1140",
                "taxon_label": "Synechococcus elongatus PCC 7942",
                "entry_status": "REVIEWED",
                "retrieved_on": "2026-10-22",
                "entry_version": 113,
                "sequence_version": 1,
                "role": "Large-chain component of the hexadecameric RbcL/RbcS RuBisCO that fixes CO2 through the CBB cycle; this accession does not denote the complete enzyme.",
                "evidence": [
                  {
                    "reference": "DOI:10.1093/plphys/kiac065",
                    "snippet": "Rubisco is a hexadecameric protein complex of large (RbcL) and small (RbcS) subunits that catalyzes the carbon fixation step of the Calvin-Benson-Bassham cycle",
                    "notes": "The primary PCC 7942 carbon-status study identifies the RuBisCO subunit architecture and function; UniProtKB Q31NB3 is the reviewed rbcL entry for that strain."
                  }
                ]
              }
            ]
          }
        ],
        "edges": [
          {
            "subject": "photolithoautotrophic_trait",
            "predicate": "has energy source",
            "object": "light",
            "description": "Photolithoautotrophy depends on light as the energy source.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2011.00165",
                "snippet": "use light as the energy source",
                "notes": "Supports light-powered metabolism in phototrophic bacteria."
              }
            ],
            "predicate_id": "METPO:2007807"
          },
          {
            "subject": "light",
            "predicate": "regulates",
            "object": "photosynthetic_electron_transport",
            "description": "Light drives photosynthetic electron transport.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2011.00165",
                "snippet": "light-induced electron transport",
                "notes": "Supports light-driven electron transport."
              }
            ],
            "predicate_id": "RO:0002211"
          },
          {
            "subject": "inorganic_electron_donor",
            "predicate": "provides electrons to",
            "object": "photosynthetic_electron_transport",
            "description": "Inorganic electron donors supply electrons for photolithotrophic metabolism.",
            "evidence": [
              {
                "reference": "DOI:10.3390/antiox10060829",
                "snippet": "reduced sulfur compounds as an electron donor",
                "notes": "Supports reduced inorganic sulfur compounds as electron donors for anoxygenic photolithotrophy."
              }
            ],
            "predicate_id": "METPO:2007403"
          },
          {
            "subject": "sulfide",
            "predicate": "participates in",
            "object": "sulfur_oxidation",
            "description": "Sulfide is an example reduced inorganic donor oxidized by phototrophic bacteria.",
            "evidence": [
              {
                "reference": "DOI:10.3390/antiox10060829",
                "snippet": "oxidizes reduced sulfur compounds",
                "notes": "Supports sulfur oxidation from reduced sulfur electron donors."
              }
            ],
            "predicate_id": "biolink:participates_in"
          },
          {
            "subject": "photosynthetic_electron_transport",
            "predicate": "has output",
            "object": "reducing_power",
            "description": "Light-induced electron transport produces reductants.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2011.00165",
                "snippet": "NAD(P)H and reduced ferredoxin",
                "notes": "Supports generation of reducing equivalents."
              }
            ],
            "predicate_id": "RO:0002234"
          },
          {
            "subject": "carbon_dioxide",
            "predicate": "fixed by",
            "object": "autotrophic_co2_fixation",
            "description": "CO2 is fixed during autotrophic carbon assimilation.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.02473-10",
                "snippet": "autotrophic CO2 fixation",
                "notes": "Supports CO2 fixation as the autotrophic carbon-assimilation process."
              }
            ],
            "predicate_id": "METPO:2007404"
          },
          {
            "subject": "reducing_power",
            "predicate": "enables",
            "object": "autotrophic_co2_fixation",
            "description": "Reductants generated by light-driven electron transport support CO2 fixation.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2011.00165",
                "snippet": "reducing equivalent flow during photoautotrophic",
                "notes": "Supports reducing-equivalent flow in photoautotrophic growth."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "autotrophic_co2_fixation",
            "predicate": "has output",
            "object": "biomass",
            "description": "Autotrophic CO2 fixation produces cellular carbon.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.02473-10",
                "snippet": "cellular carbon",
                "notes": "Supports assimilation of CO2 into cellular carbon."
              }
            ],
            "predicate_id": "RO:0002234"
          },
          {
            "subject": "photosynthetic_electron_transport",
            "predicate": "generates",
            "object": "nadph",
            "description": "Photosynthetic electron transport generates NADPH as terminal reductant.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s44222-023-00093-x",
                "notes": "Ferredoxin and FNR yield NADPH as the terminal reductant of phototrophic electron transport."
              }
            ],
            "predicate_id": "biolink:produces"
          },
          {
            "subject": "carbonic_anhydrase",
            "predicate": "interconverts",
            "object": "bicarbonate",
            "description": "Carbonic anhydrase interconverts CO2 and bicarbonate, accelerating DIC equilibration.",
            "evidence": [
              {
                "reference": "DOI:10.1128/aem.01557-23",
                "notes": "CA catalyzes CO2 <-> H2CO3 <-> HCO3- interconversion, accelerating DIC equilibration (general CCM mechanism)."
              }
            ]
          },
          {
            "subject": "dic_transporter",
            "predicate": "imports",
            "object": "bicarbonate",
            "description": "Inorganic carbon transporters import dissolved inorganic carbon species.",
            "evidence": [
              {
                "reference": "DOI:10.1128/aem.01557-23",
                "notes": "HCO3- uptake systems bridge environmental DIC supply to fixation demand."
              }
            ],
            "predicate_id": "METPO:2007805"
          },
          {
            "subject": "rubisco",
            "predicate": "catalyzes",
            "object": "autotrophic_co2_fixation",
            "description": "RuBisCO catalyzes the carboxylation step of autotrophic CO2 fixation.",
            "evidence": [
              {
                "reference": "DOI:10.1128/aem.01557-23",
                "notes": "RuBisCO is the key CO2-specific carboxylase for autotrophic CO2 fixation (broadly accepted)."
              }
            ],
            "predicate_id": "biolink:catalyzes"
          },
          {
            "subject": "reducing_power",
            "predicate": "has part",
            "object": "nadph",
            "description": "NADPH is a concrete reductant constituting the reducing power for biosynthesis.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s44222-023-00093-x",
                "notes": "NADPH is the terminal reductant tabulated as reducing equivalent for phototrophic biosynthesis."
              }
            ]
          },
          {
            "subject": "sulfide",
            "predicate": "example of",
            "object": "inorganic_electron_donor",
            "description": "Sulfide is a reduced inorganic electron donor used by anoxygenic photolithoautotrophs.",
            "evidence": [
              {
                "reference": "DOI:10.3390/antiox10060829",
                "snippet": "These donors may be reduced sulfur compounds such as hydrogen sulfide",
                "notes": "Verified against the open Antioxidants article full text."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "bicarbonate",
            "predicate": "participates in",
            "object": "autotrophic_co2_fixation",
            "description": "Transported bicarbonate supplies inorganic carbon for photosynthetic autotrophic fixation.",
            "evidence": [
              {
                "reference": "DOI:10.1073/pnas.0405211101",
                "snippet": "cyanobacteria have evolved a very efficient mechanism for capturing CO2 and HCO3- for photosynthetic fixation into sugars",
                "notes": "Verified against the public PNAS article full text."
              }
            ],
            "predicate_id": "biolink:participates_in"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.884349+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-08T00:00:00-07:00",
        "curator": "codex",
        "action": "ADDED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed causal graph for light-driven electron transport, inorganic electron donors, sulfide oxidation, and autotrophic CO2 fixation.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d72, METPO:2000010\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T05:49:25Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:participates_in\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T21:30:07Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007404\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:19Z",
        "curator": "claude",
        "action": "RENAME_PREDICATE_LABELS",
        "changes": "Renamed 2 causal-edge predicate label(s) to align with existing groundings: drives \u2192 regulates \u00d71; supports \u2192 enables \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:13:22Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002211\u00d71, RO:0002327\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:38:01Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 3 causal-node grounding field(s) via mappings/node_grounding.tsv (PATO:0001717\u00d71, GO:0009767\u00d71, CHEBI:15138\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:41:04Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 3 causal-node grounding field(s) via mappings/node_grounding.tsv (METPO:1007502\u00d71, METPO:1007503\u00d71, METPO:1007501\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T07:34:59Z",
        "curator": "claude",
        "action": "RETYPE_CAUSAL_NODES",
        "changes": "Re-typed 1 causal-node node_type field(s) to align with CausalNodeTypeEnum semantics: biomass: BIOLOGICAL_PROCESS \u2192 CHEMICAL \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T08:14:33Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0015977\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-26T02:30:14Z",
        "curator": "claude",
        "action": "RETYPE_CAUSAL_NODES",
        "changes": "Re-typed 1 causal-node node_type field(s) to align with CausalNodeTypeEnum semantics: reducing power: CHEMICAL \u2192 CAPACITY \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-14T05:51:47Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0019417\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-14T07:26:20Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007403\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 5 evidence-backed generic edges (5 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:15Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:produces\u00d71, METPO:2000208\u00d71, biolink:catalyzes\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:20Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:16474\u00d71, UniProtKB:A0A075WF79\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:35Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:17544\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-26T07:15:20Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A009PMS8\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:21:12Z",
        "curator": "claude",
        "action": "RETRACT_DEAD_UNIPROT_GROUNDINGS",
        "changes": "Retracted 2 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:23:56Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 3 causal-node grounding field(s) via mappings/node_grounding.tsv (InterPro:IPR001765\u00d71, InterPro:IPR006007\u00d71, InterPro:IPR033966\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 3 causal edge(s) off microbe-domain METPO predicates (1 to has energy source, 2 to has output), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T02:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES_PART2",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates onto their causal-graph counterparts (1 to imports), issue 301 part 2. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Each replacement is a 1:1 mirror of its source predicate that changes only the domain, so the claim each edge makes is unchanged and directions are unchanged. The replacements are proposed in proposals/metpo_traitmech_v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-16T02:00:00Z",
        "curator": "claude",
        "action": "NORMALISE_NODE_TYPE",
        "changes": "Under the PATHWAY-vs-BIOLOGICAL_PROCESS rule, one node_id means one thing corpus-wide (issue 356): photosynthetic_electron_transport is typed PATHWAY. PATHWAY is a named, conventionally enumerable multi-step route; BIOLOGICAL_PROCESS is everything else. A named route in every record that carries it, though NOT THE SAME ROUTE, which is why no single step list belongs in this rationale. metabolism/phototrophy.yaml enumerates the oxygenic form ('Electron flow from water through PSII, cytochrome b6f and PSI'); photoheterotrophic.yaml and photoorganoheterotrophic.yaml cover ANOXYGENIC phototrophy -- one reaction centre, cyclic flow, no water oxidation -- and say the neutral thing on purpose. Quoting the oxygenic steps at them would assert biology they specifically do not claim (#400 review). Both forms are named routes whose steps a curator could list, which is the test. Was 5 PATHWAY to 1 before this tranche.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-24T12:00:00-07:00",
        "curator": "codex",
        "action": "REVIEWED_CAUSAL_GRAPH_PROTEIN_TAXON",
        "changes": "Marked the graph mechanistic, documented its alternative donor and photosystem scope, upgraded canonical taxa to strain-level DOI citations, and added the reviewed S. elongatus PCC 7942 RbcL component example.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T10:15:00Z",
        "curator": "codex",
        "action": "CONNECT_CAUSAL_GRAPH_COMPONENTS",
        "changes": "Resolved issue #183 graph fragmentation (3 components to 1) with 2 public-source, verbatim-snippet-backed connector(s). No paid research service was called.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-22T01:35:00Z",
        "curator": "claude",
        "action": "REFRESH_UNIPROT_ENTRY_VERSION",
        "changes": "Refreshed UniProtKB entry_version against live UniProt REST on 2026-10-22: UniProtKB:Q31NB3 (112 -> 113 on rubisco).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000658",
    "label": "photolithotrophic",
    "definition": "A trophic type in which an organism uses light as the energy source and inorganic compounds as electron donors, typically with carbon dioxide as the primary carbon source.",
    "definition_source": "DOI:10.3390/antiox10060829",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000631"
    ],
    "synonyms": [
      {
        "synonym_text": "photolithotroph",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "created_by": "Luke Wang",
    "evidence": [
      {
        "reference": "DOI:10.3390/antiox10060829",
        "snippet": "anoxygenic photosynthesis",
        "notes": "Review supports light-driven oxidation of reduced sulfur compounds by photolithotrophic sulfur bacteria."
      },
      {
        "reference": "DOI:10.3389/fmicb.2017.00323",
        "snippet": "light as an energy source and reduced iron",
        "notes": "Review supports Fe(II) as an inorganic electron donor for photoferrotrophy."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1111708",
        "taxon_label": "Synechocystis sp. PCC 6803",
        "note": "oxygenic photolithotroph",
        "reference": "DOI:10.1093/dnares/3.3.109"
      },
      {
        "taxon_id": "NCBITaxon:194439",
        "taxon_label": "Chlorobaculum tepidum TLS",
        "note": "anoxygenic photolithotroph",
        "reference": "DOI:10.1073/pnas.132181499"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "photolithotrophic_inorganic_electron_donors",
        "title": "Photolithotrophic inorganic electron donor photosynthesis",
        "description": "DOI-backed graph linking light capture, inorganic electron donors such as sulfide and Fe(II), anoxygenic photosynthetic electron transport, and CO2 assimilation.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "The retained graph specifically represents anoxygenic sulfur- and iron-oxidizing branches; the oxygenic Synechocystis example documents the broader trait but is not asserted to use this reaction center. The C. tepidum example anchors the Type I P840 branch.",
        "nodes": [
          {
            "node_id": "photolithotrophic_trait",
            "label": "photolithotrophic",
            "node_type": "TRAIT",
            "grounding": "METPO:1000658",
            "description": "Trophic type using light energy and inorganic electron donors."
          },
          {
            "node_id": "light",
            "label": "light",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Energy source for photolithotrophic metabolism.",
            "grounding": "PATO:0001717"
          },
          {
            "node_id": "inorganic_electron_donor",
            "label": "inorganic electron donor",
            "node_type": "CHEMICAL",
            "description": "Reduced inorganic substrate supplying electrons.",
            "grounding": "METPO:1007502"
          },
          {
            "node_id": "hydrogen_sulfide",
            "label": "hydrogen sulfide",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:16136",
            "description": "Reduced sulfur electron donor for sulfur phototrophs."
          },
          {
            "node_id": "ferrous_iron",
            "label": "ferrous iron",
            "node_type": "CHEMICAL",
            "description": "Fe(II), an inorganic electron donor in photoferrotrophy.",
            "grounding": "CHEBI:29033"
          },
          {
            "node_id": "anoxygenic_photosynthesis",
            "label": "anoxygenic photosynthesis",
            "node_type": "PATHWAY",
            "description": "Photosynthetic electron transport that does not evolve oxygen."
          },
          {
            "node_id": "carbon_dioxide",
            "label": "carbon dioxide",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:16526",
            "description": "Inorganic carbon source often fixed by photolithotrophs."
          },
          {
            "node_id": "biomass",
            "label": "biomass",
            "node_type": "CHEMICAL",
            "description": "Cell material formed from fixed carbon.",
            "grounding": "METPO:1007501"
          },
          {
            "node_id": "photosynthetic_reaction_center",
            "label": "photosynthetic reaction center",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Pigment-protein complex that captures light quanta and drives charge separation in anoxygenic photosynthesis.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Anoxygenic Type I and Type II reaction centers are distinct multisubunit complexes; the generic node cannot be represented by one component-family term.",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:Q8KEP5",
                "protein_label": "P840 reaction center 17 kDa protein",
                "gene_symbol": "pscD",
                "taxon_id": "NCBITaxon:194439",
                "taxon_label": "Chlorobaculum tepidum TLS",
                "entry_status": "REVIEWED",
                "retrieved_on": "2026-10-22",
                "entry_version": 85,
                "sequence_version": 1,
                "role": "Peripheral PscD component of the C. tepidum P840 Type I reaction center; this accession is not presented as the complete 12-subunit FMO-RC apparatus.",
                "evidence": [
                  {
                    "reference": "DOI:10.1073/pnas.2216734120",
                    "snippet": "two peripheral subunits (PscB and PscD) and six FMO proteins (FMO-1 to 6) are arranged as two FMO trimers",
                    "notes": "The primary cryo-EM study resolves PscD in the C. tepidum TLS whole reaction-center apparatus; UniProtKB Q8KEP5 is the reviewed strain-level PscD entry."
                  }
                ]
              }
            ]
          },
          {
            "node_id": "hydrogen_sulfide_oxidation",
            "label": "hydrogen sulfide oxidation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Oxidation of H2S during phototrophic sulfur metabolism."
          },
          {
            "node_id": "elemental_sulfur",
            "label": "elemental sulfur",
            "node_type": "CHEMICAL",
            "description": "Product of phototrophic hydrogen sulfide oxidation.",
            "grounding": "CHEBI:26833"
          },
          {
            "node_id": "co2_fixation",
            "label": "photosynthetic CO2 fixation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Assimilation of inorganic carbon into biomass during anoxygenic photosynthetic growth."
          },
          {
            "node_id": "ferrous_iron_oxidation",
            "label": "Fe(II) oxidation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Oxidation of reduced iron coupled to anoxygenic photosynthesis."
          },
          {
            "node_id": "photoferrotrophy",
            "label": "photoferrotrophy",
            "node_type": "TRAIT",
            "description": "Photolithotrophic subtype oxidizing Fe(II) via anoxygenic photosynthesis.",
            "grounding": "traitmech:000193"
          }
        ],
        "edges": [
          {
            "subject": "photolithotrophic_trait",
            "predicate": "has energy source",
            "object": "light",
            "description": "Photolithotrophic growth is powered by light.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2017.00323",
                "snippet": "light as an energy source",
                "notes": "Supports light as the energy source for photoferrotrophic photolithotrophy."
              }
            ],
            "predicate_id": "METPO:2007807"
          },
          {
            "subject": "photolithotrophic_trait",
            "predicate": "has electron donor",
            "object": "inorganic_electron_donor",
            "description": "Inorganic electron donors supply the electrons lithotrophic phototrophs use.",
            "evidence": [
              {
                "reference": "DOI:10.3390/antiox10060829",
                "snippet": "oxidizes reduced sulfur compounds",
                "notes": "Supports inorganic reduced sulfur compounds as electron donors."
              }
            ],
            "predicate_id": "METPO:2007701"
          },
          {
            "subject": "hydrogen_sulfide",
            "predicate": "example of",
            "object": "inorganic_electron_donor",
            "description": "Hydrogen sulfide is a representative inorganic electron donor.",
            "evidence": [
              {
                "reference": "DOI:10.3390/antiox10060829",
                "snippet": "hydrogen sulfide",
                "notes": "Supports H2S as a photolithotrophic sulfur-bacteria substrate."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "ferrous_iron",
            "predicate": "example of",
            "object": "inorganic_electron_donor",
            "description": "Fe(II) is a representative inorganic electron donor in photoferrotrophy.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2017.00323",
                "snippet": "reduced iron [Fe(II)] as an electron donor",
                "notes": "Supports Fe(II) as an inorganic electron donor for anoxygenic photosynthesis."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "inorganic_electron_donor",
            "predicate": "feeds electrons into",
            "object": "anoxygenic_photosynthesis",
            "description": "Inorganic donors supply electrons to anoxygenic photosynthetic metabolism.",
            "evidence": [
              {
                "reference": "DOI:10.3390/antiox10060829",
                "snippet": "electron donor",
                "notes": "Supports donor oxidation during anoxygenic photosynthesis."
              }
            ],
            "predicate_id": "METPO:2007402"
          },
          {
            "subject": "light",
            "predicate": "enables",
            "object": "anoxygenic_photosynthesis",
            "description": "Light powers anoxygenic photosynthetic electron transport.",
            "evidence": [
              {
                "reference": "DOI:10.3390/antiox10060829",
                "snippet": "deriving energy from photosynthesis",
                "notes": "Supports photosynthetic energy capture in photolithotrophic sulfur bacteria."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "carbon_dioxide",
            "predicate": "fixed during",
            "object": "anoxygenic_photosynthesis",
            "description": "Many photolithotrophs reduce CO2 during photosynthetic growth.",
            "evidence": [
              {
                "reference": "DOI:10.3390/antiox10060829",
                "snippet": "carbon dioxide",
                "notes": "Supports CO2 use with inorganic substrate conversion to organic matter."
              }
            ]
          },
          {
            "subject": "anoxygenic_photosynthesis",
            "predicate": "has output",
            "object": "biomass",
            "description": "Fixed carbon supports biomass formation.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2017.00323",
                "snippet": "inorganic carbon is fixed into organic matter",
                "notes": "Supports organic matter formation from inorganic carbon in photoferrotrophy."
              }
            ],
            "predicate_id": "RO:0002234"
          },
          {
            "subject": "light",
            "predicate": "provides energy to",
            "object": "photosynthetic_reaction_center",
            "description": "Light quanta excite the photosynthetic reaction center to drive electron transport.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2024.1417714",
                "notes": "Anoxygenic photosynthesis proceeds from capture of a light quantum through transport of an excited electron."
              }
            ]
          },
          {
            "subject": "hydrogen_sulfide",
            "predicate": "acts as electron donor for",
            "object": "anoxygenic_photosynthesis",
            "description": "H2S is the main electron donor in sulfur-based anoxygenic photosynthesis.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2024.1417714",
                "notes": "In anoxygenic photosynthesis, hydrogen sulfide (H2S) is used as the main electron donor."
              }
            ]
          },
          {
            "subject": "hydrogen_sulfide_oxidation",
            "predicate": "has output",
            "object": "elemental_sulfur",
            "description": "Phototrophic oxidation of H2S yields elemental sulfur.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2024.1417714",
                "notes": "GSB oxidize H2S to elemental sulfur."
              }
            ],
            "predicate_id": "RO:0002234"
          },
          {
            "subject": "inorganic_electron_donor",
            "predicate": "supports",
            "object": "co2_fixation",
            "description": "Oxidation of reduced sulfur compounds supports photosynthetic CO2 fixation.",
            "evidence": [
              {
                "reference": "DOI:10.3390/life14050591",
                "notes": "Oxidize sulfide, thiosulfate, and elemental sulfur for photosynthetic growth (anoxygenic photosynthetic CO2 fixation)."
              }
            ]
          },
          {
            "subject": "ferrous_iron_oxidation",
            "predicate": "defines",
            "object": "photoferrotrophy",
            "description": "Photoferrotrophy is the oxidation of reduced iron via anoxygenic photosynthesis.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s41561-024-01560-9",
                "notes": "Photoferrotrophy is the oxidation of reduced iron via anoxygenic photosynthesis; anoxygenic phototrophic Fe(II) oxidizers are photoferrotrophs."
              }
            ],
            "predicate_id": "METPO:2007500"
          },
          {
            "subject": "hydrogen_sulfide",
            "predicate": "participates in",
            "object": "hydrogen_sulfide_oxidation",
            "description": "Hydrogen sulfide is the substrate oxidized to elemental sulfur in the sulfur-photolithotrophy branch.",
            "evidence": [
              {
                "reference": "DOI:10.3390/antiox10060829",
                "snippet": "The process of anoxygenic photosynthesis further involves the oxidation of hydrogen sulfide to atomic sulfur",
                "notes": "Verified against the open Antioxidants article full text."
              }
            ],
            "predicate_id": "biolink:participates_in"
          },
          {
            "subject": "ferrous_iron",
            "predicate": "participates in",
            "object": "ferrous_iron_oxidation",
            "description": "Ferrous iron is the electron-source substrate oxidized during photoferrotrophy.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2014.00713",
                "snippet": "photoferrotrophic bacteria use light as energy and Fe(II) as an electron source for carbon fixation and biomass formation",
                "notes": "Verified against the open Frontiers primary article."
              }
            ],
            "predicate_id": "biolink:participates_in"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.881359+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-08T00:00:00-07:00",
        "curator": "codex",
        "action": "ADDED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed causal graph for light-driven anoxygenic photosynthesis with sulfide and Fe(II) as inorganic electron donors.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:31Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000010\u00d71, METPO:2000009\u00d71, METPO:2000202\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T08:21:50Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (rdfs:subClassOf\u00d72).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T21:30:07Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007402\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:38:01Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (PATO:0001717\u00d71, CHEBI:29033\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:41:04Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (METPO:1007502\u00d71, METPO:1007501\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T07:34:59Z",
        "curator": "claude",
        "action": "RETYPE_CAUSAL_NODES",
        "changes": "Re-typed 1 causal-node node_type field(s) to align with CausalNodeTypeEnum semantics: biomass: BIOLOGICAL_PROCESS \u2192 CHEMICAL \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-26T05:00:48Z",
        "curator": "claude",
        "action": "RENAME_PREDICATE_LABELS",
        "changes": "Renamed 1 causal-edge predicate label(s) to align with existing groundings: powers \u2192 enables \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-26T05:00:51Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 5 evidence-backed generic edges (6 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:15Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d71, METPO:2007500\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:20Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:26833\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-05T12:00:00Z",
        "curator": "claude",
        "action": "REVERSE_CAUSAL_EDGE_DIRECTION",
        "changes": "Reversed 1 causal edge from <trait> uses electron donor <chemical> to <chemical> enables <trait> (predicate_id METPO:2000009 -> RO:0002327), issue 295. METPO:2000009 is rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so the trait-subject form entailed that this TRAIT node is a microbe; CausalNodeTypeEnum has no organism member, so no causal-graph edge can satisfy that domain. Evidence unchanged; only subject/predicate/object/predicate_id and the edge description moved. Note RO:0002327 has range 'biological process or activity', so the new form is not fully range-correct either - tracked in issue 302.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 1 causal edge(s) off enables/RO:0002327 with a TRAIT object (1 to has electron donor), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them. 1 electron edge(s) were also reversed back to trait -> chemical, restoring the donor/acceptor role that PR 300 collapsed onto enables (issue 303); the organism-subject problem that forced that collapse does not arise here because these predicates take a causal-node domain rather than METPO:2000001's microbe domain (issue 301).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 3 causal edge(s) off microbe-domain METPO predicates (1 to has energy source, 2 to has output), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-24T12:15:00-07:00",
        "curator": "codex",
        "action": "REVIEWED_CAUSAL_GRAPH_PROTEIN_TAXON",
        "changes": "Marked the graph mechanistic with explicit anoxygenic scope, reviewed the generic reaction center as label-only, upgraded canonical taxa to strain-level DOI citations, and added the reviewed C. tepidum PscD component example.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T10:15:00Z",
        "curator": "codex",
        "action": "CONNECT_CAUSAL_GRAPH_COMPONENTS",
        "changes": "Resolved issue #183 graph fragmentation (3 components to 1) with 2 public-source, verbatim-snippet-backed connector(s). No paid research service was called.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-14T22:07:00Z",
        "curator": "codex",
        "action": "GROUND_CAUSAL_NODE",
        "changes": "Grounded the photoferrotrophy causal node to traitmech:000193 after minting the same-scope phototrophic Fe(II) oxidation TraitRecord.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-22T01:35:00Z",
        "curator": "claude",
        "action": "REFRESH_UNIPROT_ENTRY_VERSION",
        "changes": "Refreshed UniProtKB entry_version against live UniProt REST on 2026-10-22: UniProtKB:Q8KEP5 (84 -> 85 on photosynthetic_reaction_center).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000659",
    "label": "photoorganoheterotrophic",
    "definition": "A trophic type in which an organism obtains energy from light and carbon from organic compounds.",
    "definition_source": "DOI:10.1016/B978-012373944-5.00083-3",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000631"
    ],
    "synonyms": [
      {
        "synonym_text": "photoorganoheterotroph",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1016/B978-0-12-809633-8.20672-9",
        "snippet": "light-induced redox chemistry",
        "notes": "Phototrophy chapter supports light-driven reaction-center electron transfer."
      },
      {
        "reference": "DOI:10.1021/acsomega.3c02205",
        "snippet": "photoorganoheterotrophic",
        "notes": "Review table classifies photoorganoheterotrophy by light with organic electron and carbon sources."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:258594",
        "taxon_label": "Rhodopseudomonas palustris CGA009",
        "note": "photoorganoheterotroph",
        "reference": "DOI:10.1038/nbt923"
      },
      {
        "taxon_id": "NCBITaxon:1085",
        "taxon_label": "Rhodospirillum rubrum",
        "note": "purple non-sulfur photoorganoheterotroph",
        "reference": "DOI:10.1104/pp.42.4.491"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "photoorganoheterotrophic_light_organic_electrons",
        "title": "Photoorganoheterotrophic light and organic substrate use",
        "description": "DOI-backed graph for light-driven energy conservation with organic compounds serving as electron and carbon sources.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "The core graph is a cross-lineage photoorganoheterotrophic mechanism. Its Type I reaction-center and photosynthesis-gene-cluster branches are lineage-specific, while the R. rubrum PufL example anchors the Type II reaction-center branch.",
        "nodes": [
          {
            "node_id": "photoorganoheterotrophic_trait",
            "label": "photoorganoheterotrophic",
            "node_type": "TRAIT",
            "grounding": "METPO:1000659",
            "description": "Trophic type using light energy and organic substrates for electrons and carbon."
          },
          {
            "node_id": "light",
            "label": "light",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Energy source for photoorganoheterotrophic metabolism.",
            "grounding": "PATO:0001717"
          },
          {
            "node_id": "organic_compound",
            "label": "organic compound",
            "node_type": "CHEMICAL",
            "description": "Reduced organic molecule supplying electrons and carbon.",
            "grounding": "CHEBI:50860"
          },
          {
            "node_id": "photosynthetic_reaction_center",
            "label": "photosynthetic reaction center",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Chlorophyll or bacteriochlorophyll protein complex for photochemistry.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "This generic multisubunit complex spans Type I and Type II reaction centers, so no single protein-family grounding exactly represents it.",
            "gene_symbols": [
              "pufL",
              "pufM",
              "puhA"
            ],
            "operon": "photosynthesis gene cluster (bch/crt/puf/puh)",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:P10717",
                "protein_label": "Reaction center protein L chain",
                "gene_symbol": "pufL",
                "taxon_id": "NCBITaxon:1085",
                "taxon_label": "Rhodospirillum rubrum",
                "entry_status": "REVIEWED",
                "retrieved_on": "2026-10-22",
                "entry_version": 120,
                "sequence_version": 2,
                "role": "L-chain component of the R. rubrum Type II photochemical reaction center; this accession is not presented as the complete reaction-center complex.",
                "evidence": [
                  {
                    "reference": "DOI:10.1128/jb.182.5.1200-1207.2000",
                    "snippet": "The proteins of the photochemical components are encoded by the puf operon (LHalpha, LHbeta, RC-L, and RC-M) and by puhA (RC-H)",
                    "notes": "The primary R. rubrum assembly study identifies RC-L as a puf-encoded reaction-center component and reports phototrophic incompetence of puf mutants; UniProtKB P10717 is the reviewed species-level PufL entry."
                  }
                ]
              }
            ]
          },
          {
            "node_id": "photosynthetic_electron_transport",
            "label": "photosynthetic electron transport",
            "node_type": "PATHWAY",
            "description": "Light-induced pathway forming reductants and ion gradients.",
            "grounding": "GO:0009767"
          },
          {
            "node_id": "proton_motive_force",
            "label": "proton motive force",
            "node_type": "STATE",
            "description": "Ion gradient generated by electron transport.",
            "grounding": "METPO:1007500"
          },
          {
            "node_id": "atp",
            "label": "ATP",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:30616",
            "description": "Energy carrier produced from proton motive force."
          },
          {
            "node_id": "biomass",
            "label": "biomass",
            "node_type": "CHEMICAL",
            "description": "Cellular material built from organic carbon.",
            "grounding": "METPO:1007501"
          },
          {
            "node_id": "rc_charge_separation",
            "label": "reaction center charge separation",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "Light-driven charge separation at the reaction-center special pair."
          },
          {
            "node_id": "type_i_reaction_center",
            "label": "Type I reaction center",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Fe-S type photosynthetic reaction-center complex.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "This is a multisubunit Fe-S reaction-center class with lineage-specific core and peripheral components; no single protein-family term denotes the whole complex."
          },
          {
            "node_id": "fe_s_electron_transfer",
            "label": "electron transfer to Fe-S acceptors",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Electron transfer from the reaction center to terminal [4Fe-4S] acceptors."
          },
          {
            "node_id": "diurnal_cycle",
            "label": "diurnal dark-light cycle",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Alternating light and dark periods experienced by phototrophs."
          },
          {
            "node_id": "rhythmic_transcription",
            "label": "rhythmic transcription",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Cyclic, time-of-day-dependent gene transcription."
          },
          {
            "node_id": "stationary_phase_survival",
            "label": "survival in stationary phase",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Maintenance of viability during nutrient-limited stationary phase."
          }
        ],
        "edges": [
          {
            "subject": "photoorganoheterotrophic_trait",
            "predicate": "has energy source",
            "object": "light",
            "description": "Photoorganoheterotrophy uses light as the energy source.",
            "evidence": [
              {
                "reference": "DOI:10.1016/B978-012373944-5.00083-3",
                "snippet": "use of light",
                "notes": "Supports light as the energy source in photoheterotrophy categories."
              }
            ],
            "predicate_id": "METPO:2007807"
          },
          {
            "subject": "photoorganoheterotrophic_trait",
            "predicate": "has electron donor",
            "object": "organic_compound",
            "description": "Organic molecules serve as the electron donors for the organotrophic component.",
            "evidence": [
              {
                "reference": "DOI:10.1021/acsomega.3c02205",
                "snippet": "organic molecules ... electron source",
                "notes": "Supports organic molecules as the electron source in photoorganoheterotrophic growth."
              }
            ],
            "predicate_id": "METPO:2007701"
          },
          {
            "subject": "photoorganoheterotrophic_trait",
            "predicate": "has carbon source",
            "object": "organic_compound",
            "description": "The heterotrophic component uses organic molecules as carbon sources.",
            "evidence": [
              {
                "reference": "DOI:10.1021/acsomega.3c02205",
                "snippet": "organic molecules ... carbon source",
                "notes": "Supports organic molecules as the carbon source in photoorganoheterotrophic growth."
              }
            ],
            "predicate_id": "METPO:2007806"
          },
          {
            "subject": "light",
            "predicate": "captured by",
            "object": "photosynthetic_reaction_center",
            "description": "Photosynthetic reaction centers convert light into charge separation.",
            "evidence": [
              {
                "reference": "DOI:10.1016/B978-0-12-809633-8.20672-9",
                "snippet": "chlorophyll ... reaction center proteins",
                "notes": "Supports reaction centers as the light-driven photochemical machinery."
              }
            ]
          },
          {
            "subject": "photosynthetic_reaction_center",
            "predicate": "initiates",
            "object": "photosynthetic_electron_transport",
            "description": "Reaction-center photochemistry initiates electron transport.",
            "evidence": [
              {
                "reference": "DOI:10.1016/B978-0-12-809633-8.20672-9",
                "snippet": "light-induced redox chemistry",
                "notes": "Supports light-induced redox chemistry leading to electron transfer."
              }
            ]
          },
          {
            "subject": "photosynthetic_electron_transport",
            "predicate": "generates",
            "object": "proton_motive_force",
            "description": "Electron transport generates an ion gradient.",
            "evidence": [
              {
                "reference": "DOI:10.1016/B978-0-12-809633-8.20672-9",
                "snippet": "produce stable reductants ... proton motive force",
                "notes": "Supports proton motive force formation by phototrophic electron transfer."
              }
            ],
            "predicate_id": "biolink:produces"
          },
          {
            "subject": "proton_motive_force",
            "predicate": "drives production of",
            "object": "atp",
            "description": "Proton motive force supports ATP synthesis.",
            "evidence": [
              {
                "reference": "DOI:10.1016/B978-0-12-809633-8.20672-9",
                "snippet": "can be used to produce ATP",
                "notes": "Supports ATP synthesis from phototrophic proton motive force."
              }
            ],
            "predicate_id": "biolink:produces"
          },
          {
            "subject": "organic_compound",
            "predicate": "assimilated into",
            "object": "biomass",
            "description": "Organic compounds provide carbon for biomass formation.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.01747-12",
                "snippet": "supplied organic carbon",
                "notes": "Supports assimilation of organic carbon by photoheterotrophic bacteria."
              }
            ]
          },
          {
            "subject": "light",
            "predicate": "drives",
            "object": "rc_charge_separation",
            "description": "Light absorption funnels excitation to the special pair, initiating charge separation.",
            "evidence": [
              {
                "reference": "DOI:10.3390/biom14030311",
                "notes": "Light absorption by LH pigments funnels excitation to the special pair, initiating charge separation (general anoxygenic phototrophy mechanism)."
              }
            ]
          },
          {
            "subject": "type_i_reaction_center",
            "predicate": "enables",
            "object": "fe_s_electron_transfer",
            "description": "Type I reaction centers transfer electrons to terminal Fe-S acceptors.",
            "evidence": [
              {
                "reference": "DOI:10.3390/biom14030311",
                "notes": "Electrons are transferred directly from A0 to FX, with terminal acceptors FA and FB [4Fe-4S] clusters."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "diurnal_cycle",
            "predicate": "drives",
            "object": "rhythmic_transcription",
            "description": "Dark-light alternance drives a pervasive pattern of rhythmic transcription.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s43705-023-00334-5",
                "notes": "Cyclic variations with a pervasive pattern of rhythmic transcription; likely broader to facultative phototrophs."
              }
            ]
          },
          {
            "subject": "photosynthetic_reaction_center",
            "predicate": "promotes",
            "object": "stationary_phase_survival",
            "description": "Functional reaction centers promote survival in stationary phase.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s43705-023-00334-5",
                "notes": "Survival in stationary phase relies on functional reaction centers."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "fe_s_electron_transfer",
            "predicate": "contributes to",
            "object": "photosynthetic_electron_transport",
            "description": "Electron transfer through Type I reaction-center Fe-S acceptors contributes to photosynthetic electron transport.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2021.735666",
                "snippet": "The electron transfer pathway(s) in Type I RCs utilize iron-sulfur ([4Fe-4S]) clusters",
                "notes": "Verified against the open Frontiers article full text."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "diurnal_cycle",
            "predicate": "modulates",
            "object": "stationary_phase_survival",
            "description": "The dark-light regime modulates stationary-phase survival in the facultative phototroph model.",
            "evidence": [
              {
                "reference": "DOI:10.1038/s43705-023-00334-5",
                "snippet": "bacterial survival in stationary phase relies on functional reaction centers and varies depending on the light regime",
                "notes": "Verified against the open primary article full text."
              }
            ],
            "predicate_id": "RO:0002211"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.881966+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-08T00:00:00-07:00",
        "curator": "codex",
        "action": "ADDED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed causal graph for light-driven energy conservation using organic compounds as electron and carbon sources.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:32Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000010\u00d71, METPO:2000009\u00d71, METPO:2000006\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T08:21:50Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:produces\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:38:01Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (PATO:0001717\u00d71, GO:0009767\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:41:04Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (METPO:1007500\u00d71, METPO:1007501\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T07:34:59Z",
        "curator": "claude",
        "action": "RETYPE_CAUSAL_NODES",
        "changes": "Re-typed 1 causal-node node_type field(s) to align with CausalNodeTypeEnum semantics: biomass: BIOLOGICAL_PROCESS \u2192 CHEMICAL \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T08:14:33Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:50860\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-26T02:30:14Z",
        "curator": "claude",
        "action": "RETYPE_CAUSAL_NODES",
        "changes": "Re-typed 1 causal-node node_type field(s) to align with CausalNodeTypeEnum semantics: proton motive force: BIOLOGICAL_PROCESS \u2192 STATE \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-13T21:03:27Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:produces\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 5 evidence-backed generic edges (8 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:15Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d72, RO:0002213\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-05T12:00:00Z",
        "curator": "claude",
        "action": "REVERSE_CAUSAL_EDGE_DIRECTION",
        "changes": "Reversed 1 causal edge from <trait> uses electron donor <chemical> to <chemical> enables <trait> (predicate_id METPO:2000009 -> RO:0002327), issue 295. METPO:2000009 is rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so the trait-subject form entailed that this TRAIT node is a microbe; CausalNodeTypeEnum has no organism member, so no causal-graph edge can satisfy that domain. Evidence unchanged; only subject/predicate/object/predicate_id and the edge description moved. Note RO:0002327 has range 'biological process or activity', so the new form is not fully range-correct either - tracked in issue 302.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 1 causal edge(s) off enables/RO:0002327 with a TRAIT object (1 to has electron donor), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them. 1 electron edge(s) were also reversed back to trait -> chemical, restoring the donor/acceptor role that PR 300 collapsed onto enables (issue 303); the organism-subject problem that forced that collapse does not arise here because these predicates take a causal-node domain rather than METPO:2000001's microbe domain (issue 301).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 2 causal edge(s) off microbe-domain METPO predicates (1 to has energy source, 1 to has carbon source), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-16T02:00:00Z",
        "curator": "claude",
        "action": "NORMALISE_NODE_TYPE",
        "changes": "Under the PATHWAY-vs-BIOLOGICAL_PROCESS rule, one node_id means one thing corpus-wide (issue 356): photosynthetic_electron_transport is typed PATHWAY. PATHWAY is a named, conventionally enumerable multi-step route; BIOLOGICAL_PROCESS is everything else. A named route in every record that carries it, though NOT THE SAME ROUTE, which is why no single step list belongs in this rationale. metabolism/phototrophy.yaml enumerates the oxygenic form ('Electron flow from water through PSII, cytochrome b6f and PSI'); photoheterotrophic.yaml and photoorganoheterotrophic.yaml cover ANOXYGENIC phototrophy -- one reaction centre, cyclic flow, no water oxidation -- and say the neutral thing on purpose. Quoting the oxygenic steps at them would assert biology they specifically do not claim (#400 review). Both forms are named routes whose steps a curator could list, which is the test. Was 5 PATHWAY to 1 before this tranche.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-24T12:10:00-07:00",
        "curator": "codex",
        "action": "REVIEWED_CAUSAL_GRAPH_PROTEIN_TAXON",
        "changes": "Marked the graph mechanistic, documented Type I/Type II lineage scope, reviewed three composite protein nodes as label-only, upgraded canonical examples to DOI citations, and added the reviewed R. rubrum PufL component example.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T10:15:00Z",
        "curator": "codex",
        "action": "CONNECT_CAUSAL_GRAPH_COMPONENTS",
        "changes": "Resolved issue #183 graph fragmentation (3 components to 1) with 2 public-source, verbatim-snippet-backed connector(s). No paid research service was called.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-22T01:35:00Z",
        "curator": "claude",
        "action": "REFRESH_UNIPROT_ENTRY_VERSION",
        "changes": "Refreshed UniProtKB entry_version against live UniProt REST on 2026-10-22: UniProtKB:P10717 (119 -> 120 on photosynthetic_reaction_center).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000588",
    "label": "phototaxis",
    "definition": "A motile phenotype in which active locomotion is directionally biased toward or away from a light source in response to illumination.",
    "definition_source": "DOI:10.1105/tpc.108.057919",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000702"
    ],
    "evidence": [
      {
        "reference": "DOI:10.7554/eLife.12620",
        "snippet": "the majority of motile cells switched direction within about 1 min, and then moved directly towards the light source",
        "notes": "Results, first subsection, Figure 1c-d and methods; publisher version 2, posted 2022-04-22, originally published 2016-02-09 (PMID:26858197). Version-specific full text: https://cdn.elifesciences.org/articles/12620/elife-12620-v2.xml. Figure 1 and both optical figure supplements visually inspected. Motile Synechocystis sp. PCC 6803 PCC-M cells on agarose move toward oblique RGB illumination (470/525/625 nm, equal intensity; 10 micromol photons per square metre per second). The projected white-light intensity gradient does not produce significant directional bias in this experiment. Cells were sampled from moving colony fronts; analysis excludes immotile cells. These observations are separate from torA-gfp optical reporter assays and from the proposed PixJ1-to-pilus signaling model. They do not establish one universal directional-sensing mechanism."
      },
      {
        "reference": "DOI:10.1105/tpc.108.057919",
        "snippet": "Chlamydomonas cells with low CHR2 content exhibit photophobic and phototactic responses that strictly depend on the availability of CHR1.",
        "notes": "Abstract exact-matched at Europe PMC (PMID:18552201). The PMC introduction distinguishes directional swimming toward or away from light from transient photophobic reversal; the beginning of Results identifies the cell-wall-deficient CW2 strain. Evidence concerns Chlamydomonas reinhardtii under the stated receptor-content conditions, not every algal strain or a universal CHR1 requirement. Xenopus ion-conductance assays are heterologous. Remaining full-text sections and supplements were not inspected; no natural algal exemplar or complete protein-resolved pathway is inferred."
      },
      {
        "reference": "DOI:10.1093/dnares/dss024",
        "snippet": "\u2018PCC-M and PCC-P\u2019 are strains that both exhibit the native positive phototaxis, whereas \u2018PCC-N\u2019 strain shows negative phototaxis.",
        "notes": "Results, section 3.1, exact-matched to Europe PMC full-text XML (PMID:23069868). Methods trace PCC-M to the Shestakov laboratory in 1993 and maintenance of motile colonies, matching the Schuergers study. The strain descends from the original PCC isolate but has undergone laboratory microevolution; it is not asserted genetically identical to the original isolate. Discussion also reports no blue-light phototaxis for PCC-M. This supports a substrain-qualified exemplar, not a statement that every PCC 6803 lineage or illumination gives the same response."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1148",
        "taxon_label": "Synechocystis sp. PCC 6803",
        "reference": "DOI:10.7554/eLife.12620",
        "note": "Motile wild-type PCC-M substrain, not the torA-gfp reporter. Figure 1c-d shows positive phototaxis on agarose under oblique RGB illumination after sampling moving colony fronts. Independent provenance: DOI:10.1093/dnares/dss024, Methods 2.1 and Results 3.1; PCC-M retains native positive phototaxis but has laboratory sequence differences and lacks blue-light phototaxis in the cited comparison. NCBI:1148 was resolved at NCBI on 2026-10-04; it is species-level, not a PCC-M-specific accession. No universal substrain, wavelength or sign claim."
      }
    ],
    "discussions": [
      {
        "discussion_id": "phototaxis-direction-and-mapping-boundaries",
        "prompt": "Preserve directional scope and resolve phenotype-level mappings.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Positive and negative responses are directional cases, not a requirement to exhibit both or a permanent sign. Speed changes alone (photokinesis), light sensing alone and phototrophic energy conservation do not establish this trait. A photophobic response can participate in phototaxis but is not an exact synonym. METPO:1000241 is obsolete with no replacement or definition; do not revive it or assert a replaces relation without upstream review. External biological-process terms are not automatically equivalent to this organismal disposition; verify scope before adding xrefs or lexical synonyms.",
        "posed_by": "codex",
        "posed_date": "2026-10-04"
      },
      {
        "discussion_id": "phototaxis-mechanism-and-optical-provenance",
        "prompt": "Ground causal branches without promoting optical models to facts.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "The cyanobacterial PixJ1/response-regulator/pilus branch is a proposed model in Schuergers Figure 5; causal edges and eligible taxon-paired protein accessions require additional primary checks. Native algal signaling must be separated from heterologous conductance and cell-wall-deficient strains. Version 2 optical supplement graphics also differ from their captions: Figure 3 supplement 1 labels a 60x objective versus 100x in text, and Figure 4 supplement 1 labels 633 nm versus 625 nm in text. Do not silently reconcile these parameters or use them to quantify a mechanistic graph. Figure 1 phenotype evidence is retained independently. No NONMECHANISTIC graph is used to bypass protein-grounding requirements.",
        "posed_by": "codex",
        "posed_date": "2026-10-04"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-04T05:21:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added phototaxis with three primary DOI citations and exact snippets. Ignored-and-hidden searches found no exact live trait; the obsolete METPO class is not reused. Reserved METPO:1054200 in v465. Verified publisher version 2, optical supplements and PCC-M provenance; added a substrain-qualified NCBI-resolved canonical example. Deferred ungrounded protein branches and recorded source discrepancies.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000660",
    "label": "phototrophic",
    "definition": "A trophic type characterized by the use of light as the primary energy source for metabolic processes, regardless of carbon source.",
    "definition_source": "DOI:10.3389/fmicb.2011.00165",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000631"
    ],
    "synonyms": [
      {
        "synonym_text": "TT_phototroph",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "phototroph",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "created_by": "Anthea Guo",
    "evidence": [
      {
        "reference": "DOI:10.3389/fmicb.2011.00165",
        "snippet": "use light as the energy source",
        "notes": "Review supports light-driven ATP and reductant generation by phototrophic bacteria."
      },
      {
        "reference": "DOI:10.1093/femsre/fuv032",
        "snippet": "bacteriochlorophyll-containing reaction centers",
        "notes": "Review supports bacteriochlorophyll reaction centers in aerobic anoxygenic phototrophs."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1111708",
        "taxon_label": "Synechocystis sp. PCC 6803",
        "note": "oxygenic phototroph",
        "reference": "DOI:10.3390/md11082894"
      },
      {
        "taxon_id": "NCBITaxon:1085",
        "taxon_label": "Rhodospirillum rubrum",
        "note": "anoxygenic phototroph",
        "reference": "DOI:10.4056/sigs.1804360"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "phototrophic_light_energy_capture",
        "title": "Phototrophic light-energy capture mechanism",
        "description": "DOI-backed graph for bacterial light capture, photosynthetic electron transport, ATP generation, and reductant formation.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "This cross-mechanism graph includes chlorophyll/bacteriochlorophyll reaction centers and retinal ion pumps as alternatives. The R. rubrum PufL example anchors a Type II reaction center and does not represent oxygenic or rhodopsin-based phototrophy.",
        "nodes": [
          {
            "node_id": "phototrophic_trait",
            "label": "phototrophic",
            "node_type": "TRAIT",
            "grounding": "METPO:1000660",
            "description": "Trophic type using light as an energy source."
          },
          {
            "node_id": "light",
            "label": "light",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Electromagnetic energy harvested by phototrophic cells.",
            "grounding": "PATO:0001717"
          },
          {
            "node_id": "photosynthetic_reaction_center",
            "label": "photosynthetic reaction center",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Pigment-protein complex that initiates photochemical charge separation.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "This generic node spans oxygenic photosystems and anoxygenic Type I and Type II multisubunit reaction centers; no one component-family term represents all of them.",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:P10717",
                "protein_label": "Reaction center protein L chain",
                "gene_symbol": "pufL",
                "taxon_id": "NCBITaxon:1085",
                "taxon_label": "Rhodospirillum rubrum",
                "entry_status": "REVIEWED",
                "retrieved_on": "2026-10-22",
                "entry_version": 120,
                "sequence_version": 2,
                "role": "L-chain component of the R. rubrum Type II photochemical reaction center; this accession is not presented as the complete reaction-center complex.",
                "evidence": [
                  {
                    "reference": "DOI:10.1128/jb.182.5.1200-1207.2000",
                    "snippet": "The proteins of the photochemical components are encoded by the puf operon (LHalpha, LHbeta, RC-L, and RC-M) and by puhA (RC-H)",
                    "notes": "The primary R. rubrum assembly study identifies RC-L as a puf-encoded reaction-center component and reports phototrophic incompetence of puf mutants; UniProtKB P10717 is the reviewed species-level PufL entry."
                  }
                ]
              }
            ]
          },
          {
            "node_id": "bacteriochlorophyll",
            "label": "bacteriochlorophyll",
            "node_type": "CHEMICAL",
            "description": "Light-harvesting pigment in many anoxygenic phototrophic bacteria.",
            "grounding": "CHEBI:38201"
          },
          {
            "node_id": "photosynthetic_electron_transport",
            "label": "photosynthetic electron transport",
            "node_type": "PATHWAY",
            "description": "Light-induced electron-transfer route producing ATP and reductants.",
            "grounding": "GO:0009767"
          },
          {
            "node_id": "atp",
            "label": "ATP",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:30616",
            "description": "Energy carrier generated by phototrophic electron transport."
          },
          {
            "node_id": "reducing_power",
            "label": "reducing power",
            "node_type": "CAPACITY",
            "description": "NAD(P)H or reduced ferredoxin generated by photosynthetic electron transport.",
            "grounding": "METPO:1007503"
          },
          {
            "node_id": "carotenoid",
            "label": "carotenoid",
            "node_type": "CHEMICAL",
            "description": "Auxiliary light-harvesting pigment in phototrophic bacteria.",
            "grounding": "CHEBI:23044"
          },
          {
            "node_id": "blue_green_light",
            "label": "blue-green light",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Blue-green region of the spectrum absorbed by carotenoid antennas."
          },
          {
            "node_id": "proton_motive_force",
            "label": "proton motive force",
            "node_type": "STATE",
            "description": "Transmembrane electrochemical proton gradient generated by photosynthetic electron transport.",
            "grounding": "METPO:1007500"
          },
          {
            "node_id": "atp_synthase",
            "label": "ATP synthase complex",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Membrane enzyme complex that synthesizes ATP driven by proton motive force.",
            "grounding": "GO:0045259"
          },
          {
            "node_id": "rhodopsin",
            "label": "rhodopsin",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Retinal-based light-driven ion-pumping membrane protein used in retinalophototrophy.",
            "grounding": "InterPro:IPR001425"
          },
          {
            "node_id": "ion_transport",
            "label": "ion transport across membrane",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Light-driven transmembrane ion pumping that establishes a gradient for energy conservation."
          }
        ],
        "edges": [
          {
            "subject": "phototrophic_trait",
            "predicate": "has energy source",
            "object": "light",
            "description": "Phototrophic growth uses light as the energy input.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2011.00165",
                "snippet": "use light as the energy source",
                "notes": "Supports light as the defining energy source for phototrophic bacteria."
              }
            ],
            "predicate_id": "METPO:2007807"
          },
          {
            "subject": "bacteriochlorophyll",
            "predicate": "part of",
            "object": "photosynthetic_reaction_center",
            "description": "Bacteriochlorophyll-containing complexes harvest light in many bacterial phototrophs.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuv032",
                "snippet": "bacteriochlorophyll-containing reaction centers",
                "notes": "Supports pigment-reaction-center coupling in aerobic anoxygenic phototrophs."
              }
            ],
            "predicate_id": "biolink:part_of"
          },
          {
            "subject": "light",
            "predicate": "captured by",
            "object": "photosynthetic_reaction_center",
            "description": "Reaction centers convert absorbed light into charge separation.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuv032",
                "snippet": "harvest light energy",
                "notes": "Supports light harvesting by reaction centers."
              }
            ]
          },
          {
            "subject": "photosynthetic_reaction_center",
            "predicate": "initiates",
            "object": "photosynthetic_electron_transport",
            "description": "Photochemical reaction centers initiate electron transport.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2011.00165",
                "snippet": "light-induced electron transport",
                "notes": "Supports reaction-center-driven photosynthetic electron transport."
              }
            ]
          },
          {
            "subject": "photosynthetic_electron_transport",
            "predicate": "has output",
            "object": "atp",
            "description": "Photosynthetic electron transport produces ATP.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2011.00165",
                "snippet": "produce phosphate bond energy (ATP)",
                "notes": "Supports ATP as a product of phototrophic electron transport."
              }
            ],
            "predicate_id": "RO:0002234"
          },
          {
            "subject": "photosynthetic_electron_transport",
            "predicate": "has output",
            "object": "reducing_power",
            "description": "Photosynthetic electron transport generates reducing equivalents.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fmicb.2011.00165",
                "snippet": "reductants [e.g., NAD(P)H and reduced ferredoxin]",
                "notes": "Supports reductant production by photosynthetic electron transport."
              }
            ],
            "predicate_id": "RO:0002234"
          },
          {
            "subject": "carotenoid",
            "predicate": "transfers excitation energy to",
            "object": "bacteriochlorophyll",
            "description": "Excitation energy captured by carotenoids is transferred to BChl a.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuv032",
                "notes": "The excitation energy captured by the carotenoids is transferred within picoseconds to the BChl a molecules."
              }
            ]
          },
          {
            "subject": "carotenoid",
            "predicate": "extends light absorption into",
            "object": "blue_green_light",
            "description": "Carotenoids serve as auxiliary pigments extending absorption to the blue-green spectrum.",
            "evidence": [
              {
                "reference": "DOI:10.1093/femsre/fuv032",
                "notes": "Carotenoids serve as auxiliary pigments which extend absorption to the blue-green part of the spectrum."
              }
            ]
          },
          {
            "subject": "photosynthetic_electron_transport",
            "predicate": "forms",
            "object": "proton_motive_force",
            "description": "Photosynthetic electron transport generates a proton motive force.",
            "evidence": [
              {
                "reference": "DOI:10.1128/aem.00863-24",
                "notes": "Along with electron transport, proton motive force (PMF) is formed."
              }
            ],
            "predicate_id": "biolink:produces"
          },
          {
            "subject": "proton_motive_force",
            "predicate": "powers",
            "object": "atp_synthase",
            "description": "Proton motive force drives ATP synthase complexes.",
            "evidence": [
              {
                "reference": "DOI:10.1128/aem.00863-24",
                "notes": "and powers ATP synthase complexes."
              }
            ],
            "predicate_id": "METPO:2007900"
          },
          {
            "subject": "atp_synthase",
            "predicate": "produces",
            "object": "atp",
            "description": "ATP synthase complexes generate ATP from the proton motive force.",
            "evidence": [
              {
                "reference": "DOI:10.1128/aem.00863-24",
                "notes": "PMF powers ATP synthase complexes that synthesize ATP, the cellular energy carrier."
              }
            ],
            "predicate_id": "METPO:2007800"
          },
          {
            "subject": "rhodopsin",
            "predicate": "pumps",
            "object": "ion_transport",
            "description": "Rhodopsins use light to pump ions across the membrane (retinalophototrophy).",
            "evidence": [
              {
                "reference": "DOI:10.1038/s43705-023-00334-5",
                "notes": "retinalophototrophy, which uses rhodopsins to pump ions through the membrane."
              }
            ]
          },
          {
            "subject": "ion_transport",
            "predicate": "generates",
            "object": "proton_motive_force",
            "description": "Light-driven proton transport by proteorhodopsin generates proton motive force in the retinal phototrophy branch.",
            "evidence": [
              {
                "reference": "DOI:10.1073/pnas.0611035104",
                "snippet": "Light-based proton pumping by proteorhodopsin can then increase the pmf",
                "notes": "Verified against the public PNAS article full text."
              }
            ],
            "predicate_id": "biolink:produces"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.882505+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-08T00:00:00-07:00",
        "curator": "codex",
        "action": "ADDED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed causal graph for light capture, reaction centers, photosynthetic electron transport, ATP, and reductant generation.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:32Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d72, METPO:2000010\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T05:49:25Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:part_of\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:38:01Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (PATO:0001717\u00d71, GO:0009767\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-24T04:41:04Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (METPO:1007503\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-26T02:30:14Z",
        "curator": "claude",
        "action": "RETYPE_CAUSAL_NODES",
        "changes": "Re-typed 1 causal-node node_type field(s) to align with CausalNodeTypeEnum semantics: reducing power: CHEMICAL \u2192 CAPACITY \u00d71.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-14T05:51:47Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:38201\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 6 evidence-backed generic edges (6 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:15Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:produces\u00d71, METPO:2000202\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:35Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:23044\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-26T07:15:20Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A059ZUX4\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 3 causal edge(s) off microbe-domain METPO predicates (1 to has energy source, 2 to has output), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T02:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES_PART2",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates onto their causal-graph counterparts (1 to produces), issue 301 part 2. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Each replacement is a 1:1 mirror of its source predicate that changes only the domain, so the claim each edge makes is unchanged and directions are unchanged. The replacements are proposed in proposals/metpo_traitmech_v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-15T02:00:00Z",
        "curator": "claude",
        "action": "NORMALISE_NODE_TYPE",
        "changes": "Normalised causal-node type(s) so one node_id means one thing corpus-wide (issue 356): proton_motive_force: CAPACITY -> STATE. The schema's OWN example of STATE: 'a bioenergetic or molecular state of the cell (e.g. proton motive force ...) ... the state is the gradient / steady-value, not its establishment'. All 35 occurrences describe the gradient -- every description across all four types reads 'electrochemical proton gradient', including the 13 typed BIOLOGICAL_PROCESS ('Transmembrane electrochemical gradient generated by respiration'), which name the gradient and its provenance rather than the generating process. Nothing here means the establishment, so this is a retype and not a rename; records that DO mean the process already use a separate id (proton_motive_force_generation in ph_delta.yaml). Also settles the one edge #356 was filed for: phototrophic.yaml's CAPACITY typing was blocking `powers` (METPO:2007900), which is gated to BIOLOGICAL_PROCESS|STATE.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-16T02:00:00Z",
        "curator": "claude",
        "action": "NORMALISE_NODE_TYPE",
        "changes": "Under the PATHWAY-vs-BIOLOGICAL_PROCESS rule, one node_id means one thing corpus-wide (issue 356): photosynthetic_electron_transport is typed PATHWAY. PATHWAY is a named, conventionally enumerable multi-step route; BIOLOGICAL_PROCESS is everything else. A named route in every record that carries it, though NOT THE SAME ROUTE, which is why no single step list belongs in this rationale. metabolism/phototrophy.yaml enumerates the oxygenic form ('Electron flow from water through PSII, cytochrome b6f and PSI'); photoheterotrophic.yaml and photoorganoheterotrophic.yaml cover ANOXYGENIC phototrophy -- one reaction centre, cyclic flow, no water oxidation -- and say the neutral thing on purpose. Quoting the oxygenic steps at them would assert biology they specifically do not claim (#400 review). Both forms are named routes whose steps a curator could list, which is the test. Was 5 PATHWAY to 1 before this tranche.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-20T07:10:44Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (METPO:1007500\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-22T04:26:16Z",
        "curator": "codex",
        "action": "REVIEW_UNIPROT_INSTANCE_GROUNDINGS",
        "changes": "Reviewed 1 organism-specific UniProtKB grounding(s): replaced 1 with taxon-agnostic GO/InterPro terms and retracted 0 to label-only where no exact semantic term was supported (docs/GROUNDING_POLICY.md).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-24T12:20:00-07:00",
        "curator": "codex",
        "action": "REVIEWED_CAUSAL_GRAPH_PROTEIN_TAXON",
        "changes": "Marked the graph mechanistic, documented reaction-center versus rhodopsin scope, reviewed the generic reaction center as label-only, grounded the ATP synthase complex to GO, upgraded canonical citations to DOIs, and added R. rubrum PufL.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T06:33:05Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007900\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T10:15:00Z",
        "curator": "codex",
        "action": "CONNECT_CAUSAL_GRAPH_COMPONENTS",
        "changes": "Resolved issue #183 graph fragmentation (2 components to 1) with 1 public-source, verbatim-snippet-backed connector(s). No paid research service was called.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-14T23:14:00Z",
        "curator": "codex",
        "action": "NARROWED_RELATED_SYNONYM",
        "changes": "Moved the aerobic_anoxygenic_phototrophy metpo.owl source key from broad phototrophic to the newly minted same-scope aerobic anoxygenic phototrophy TraitRecord.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-22T01:35:00Z",
        "curator": "claude",
        "action": "REFRESH_UNIPROT_ENTRY_VERSION",
        "changes": "Refreshed UniProtKB entry_version against live UniProt REST on 2026-10-22: UniProtKB:P10717 (119 -> 120 on photosynthetic_reaction_center).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000598",
    "label": "phototropism",
    "definition": "A phenotype in which growth is directionally oriented or reoriented toward or away from a light source in response to illumination.",
    "definition_source": "DOI:10.1073/pnas.0600633103",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1073/pnas.0600633103",
        "snippet": "it exhibits phototropism by bending toward near-UV and blue wavelengths and away from far-UV wavelengths",
        "notes": "Abstract, exact-matched at Europe PMC (PMID:16537433; PMC1450208); it refers to Phycomyces blakesleeanus sporangiophore growth. The institutional full-text PDF and Figure 1A were inspected: the wild-type control bends toward white light, unlike the reduced response of madA mutants. The abstract's far-UV response is not measured in that panel. Methods identify NRRL1555 as the wild-type background and distinguish chemically mutagenized derivatives and isogenic A56. Genetic cosegregation supports madA involvement, not a complete growth-polarity pathway."
      },
      {
        "reference": "DOI:10.1073/pnas.0900879106",
        "snippet": "Phototropism, growth toward light, shares many features in fungi and plants but the molecular mechanisms remain to be fully elucidated.",
        "notes": "Abstract, exact-matched at Europe PMC (PMID:19380729; PMC2678449). This passage describes the positive case; the Idnurm source establishes the broader directional scope. The institutional full-text PDF and Figures 2B and 4 were inspected. Phototropic responses cosegregate with madB alleles; MADA-MADB interaction assays use yeast and E. coli, not the native fungus. The Discussion leaves rapid bending mechanisms unresolved. Transcription measurements are not themselves directional-growth readouts. The supplementary strain table and figures were not accessible and were not inspected."
      },
      {
        "reference": "DOI:10.1128/EC.00203-13",
        "snippet": "These strains are wild isolates, except for A56.",
        "notes": "Materials and Methods, Strains and growth conditions; exact contiguous raw PMC HTML text (PMID:24243797; PMC3910969). The preceding sentence includes NRRL1555 in the named strains; the following sentence distinguishes backcrossed A56. This supports natural-isolate provenance for the NRRL1555 exemplar, not an independent phototropism experiment."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:763407",
        "taxon_label": "Phycomyces blakesleeanus NRRL 1555(-)",
        "reference": "DOI:10.1073/pnas.0600633103",
        "note": "Wild-type sporangiophore growth toward white light in Figure 1A, with NRRL1555 background identified in Methods; not the madA mutants or backcrossed A56. Independent natural-isolate provenance: DOI:10.1128/EC.00203-13, Materials and Methods (https://pmc.ncbi.nlm.nih.gov/articles/PMC3910969/). Strain-level identity and exact name resolved at NCBI Taxonomy on 2026-10-04. No invariant wavelength or response direction is asserted."
      }
    ],
    "discussions": [
      {
        "discussion_id": "phototropism-growth-and-direction-boundaries",
        "prompt": "Preserve growth, locomotion and response-direction distinctions.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "The class includes growth toward or away from light without requiring both responses in one organism or condition. It is not phototaxis (active locomotion), photokinesis (locomotion-speed change), phototrophy (energy acquisition), or light-dependent growth rate or development alone. Use phenotype rather than motile as the parent. A blue-light receptor homolog alone does not establish this phenotype. Resolve phenotype-level external equivalences separately before adding synonyms or xrefs.",
        "posed_by": "codex",
        "posed_date": "2026-10-04"
      },
      {
        "discussion_id": "phototropism-native-mechanism-grounding",
        "prompt": "Separate heterologous interaction assays from native growth control.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Retain genetic and heterologous evidence at its measured scope. Neither a yeast interaction assay nor copurification in E. coli proves the native light-dependent interaction or the full route from photoreception to asymmetric growth. Inspect the unavailable Sanz supplement and newer primary work, and resolve eligible taxon-paired protein accessions before adding a mechanistic graph. Do not transfer plant phototropin signaling to fungi or use NONMECHANISTIC to bypass protein-grounding requirements.",
        "posed_by": "codex",
        "posed_date": "2026-10-04"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-04T14:39:25Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added phototropism with two primary phenotype studies, a primary strain-provenance citation and exact snippets. Ignored-and-hidden novelty searches and structured OWL review found no exact record or METPO term. Reserved METPO:1055200 in v475. Retained both growth directions and distinguished locomotion and energy acquisition. Inspected primary figures; added NCBI-resolved natural NRRL1555 exemplar and deferred native protein-level mechanisms and unavailable supplements.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000635",
    "label": "pinocytosis",
    "definition": "A physiological phenotype in which a microbial organism internalizes surrounding extracellular fluid and dissolved material into membrane-bound compartments formed from its plasma membrane.",
    "definition_source": "DOI:10.1083/jcb.53.3.681",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000636"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1083/jcb.53.3.681",
        "snippet": "HRP activity was found exclusively within membrane profiles within the cytoplasm, confirming the pinocytotic mode of uptake.",
        "notes": "PMID:5028259, PMC2108769. Scientific Abstract directly read in Europe PMC XML. The full-text OCR, including Introduction, Methods, Results and Discussion, was read at https://www.ebi.ac.uk/europepmc/webservices/rest/PMC2108769/fullTextXML. Tracer uptake and author-reported intracellular HRP support vesicular fluid uptake in Neff cells. OCR is not a visual figure audit: the PDF/figures were unavailable. The authors qualify the vesicle sample as nonrandom and membrane turnover as estimated; no size distribution, numerical rate or exclusive transport route is generalized here."
      },
      {
        "reference": "DOI:10.1099/00221287-92-2-246",
        "snippet": "The reduced pinocytotic activity of stationary-phase cells remains sensitive to respiratory inhibitors.",
        "notes": "PMID:1255130. Scientific Abstract directly read at the publisher and in NCBI PubMed XML. This independent study reports reduced inulin uptake in stationary-phase Acanthamoeba trophozoites while bead phagocytosis essentially ceases. It supports a condition-dependent fluid-uptake phenotype, not organismal disjointness or a specific protein mechanism. Full text and figures were unavailable; no unread methods or strain accession is inferred."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1257118",
        "taxon_label": "Acanthamoeba castellanii str. Neff",
        "reference": "DOI:10.1083/jcb.53.3.681",
        "note": "Laboratory-maintained Neff cells studied in the 1972 paper, with fluid tracers and author-reported intracellular HRP. NCBI EFetch verified this exact strain-rank name on 2026-10-06. ATCC Neff provenance at https://www.atcc.org/products/30010 gives soil from Pacific Grove, California. The paper supplies no collection accession; this does not establish vial or genome identity with ATCC 30010 or an unchanged original isolate. The legacy NCBI name is retained despite the transfer of Neff to A. terricola in DOI:10.1016/j.ejop.2024.126091; see the open taxonomy discussion. This is not a species-wide assertion."
      }
    ],
    "discussions": [
      {
        "discussion_id": "pinocytosis-scope-and-hierarchy",
        "prompt": "Keep vesicular fluid uptake distinct from neighboring traits.",
        "kind": "CURATION_TODO",
        "status": "RESOLVED",
        "rationale": "Retain phenotype METPO:1000059 pending a broader endocytic capability hierarchy. This is uptake by a microbe, not induction of host-cell uptake. Macropinocytosis traitmech:000634 is a narrower ruffle-mediated mode; its existing definition supports the direct parent refinement. Do not equate pinocytosis with particle engulfment traitmech:000627, nutritional phagotrophy traitmech:000628 or prey-content aspiration traitmech:000631. These traits are not declared organismally disjoint. Solute transport across a membrane, surface adsorption, open invaginations and membrane recycling alone do not establish fluid internalization. No fixed vesicle size, ruffle, nutritional requirement or universal nonconcentrative uptake is imposed. Process-level ontology mappings and synonyms remain unasserted.",
        "posed_by": "codex",
        "posed_date": "2026-10-06",
        "resolved_date": "2026-10-06",
        "resolution_note": "Added endocytosis traitmech:000636 as the direct broader phenotype. The existing fluid-internalization definition entails this membrane-bound uptake scope. This resolves the temporary parent gap, not the separate Neff taxonomy or native-mechanism discussions; the historical scope contrasts and unasserted mappings remain applicable. Preserve the v511 phenotype axiom and add METPO:1058800 SubClassOf METPO:1058900 upstream."
      },
      {
        "discussion_id": "pinocytosis-neff-taxonomy",
        "prompt": "Reconcile the legacy Neff taxon name with its reassignment.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "The 2024 primary taxonomy paper transfers Neff to A. terricola, whereas NCBI still labels strain 1257118 Acanthamoeba castellanii str. Neff and ATCC 30010 retains A. castellanii. Keep the issuing-authority label with explicit strain scope rather than silently generalizing to either species. The taxonomy paper's scientific abstract was directly read; its full phylogenetic data were not audited. Revisit the authority mapping when the strain identity is reconciled.",
        "evidence": [
          {
            "reference": "DOI:10.1016/j.ejop.2024.126091",
            "evidence_source": "abstract",
            "snippet": "The Neff strain is therefore transferred to A. terricola and should no longer be considered as belonging to A. castellanii.",
            "notes": "PMID:38772052; exact scientific Abstract span from NCBI PubMed XML. Taxonomy evidence, not another pinocytosis experiment or independent trait replication."
          }
        ],
        "posed_by": "codex",
        "posed_date": "2026-10-06"
      },
      {
        "discussion_id": "pinocytosis-native-mechanism",
        "prompt": "Resolve uptake routes before asserting molecular dependencies.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "The two experimental papers concern Acanthamoeba and do not establish independent taxon replication. The 1972 nonconcentrative uptake interpretation is study-specific. Tracer loss, metabolism and static membrane profiles limit rate and route inference; the actual figures remain unaudited. Respiratory-inhibitor sensitivity does not identify a particular uptake protein. HRP is an external tracer, not a native microbial protein exemplar. No protein accessions or causal graph are inferred.",
        "posed_by": "codex",
        "posed_date": "2026-10-06"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-06T05:29:34Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added pinocytosis with two primary DOI-backed scientific-abstract snippets, a strain-qualified Neff example and explicit taxonomy and source-access limits. Ignored-and-hidden searches and full pinned METPO review found no exact record. Reserved METPO:1058800 in v511 and refined macropinocytosis to this broader phenotype.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-06T06:47:04Z",
        "curator": "codex",
        "action": "REFINE_ENDOCYTOSIS_PARENT",
        "changes": "Refined the direct parent to endocytosis traitmech:000636 and resolved the temporary parent gap by definition-based inference. Preserved the historical rationale, definition, evidence, Neff example, independent taxonomy/mechanism discussions and prior history.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000604",
    "label": "positive autotropism",
    "definition": "A phenotype in which germ-tube emergence or hyphal extension is directionally biased toward neighboring cells or hyphae of the same species.",
    "definition_source": "DOI:10.1093/jxb/19.1.125",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1093/jxb/19.1.125",
        "snippet": "the positive germ-tube, i.e. one beginning more nearly towards its neighbour",
        "notes": "Robinson, Park and Graham (1968), original publisher abstract directly retrieved from https://oup.silverchair-cdn.com/article-minimal/447341. The abstract reports positive autotropism in Botrytis cinerea on Cellophane over agar and neutrality on agar alone. The quoted orientation definition occurs in the mixed-orientation spore-pair timing comparison for Rhizopus stolonifer and Mucor plumbeus, both described as exhibiting marked negative autotropism. Earlier emergence of the positive germ-tube in those pairs does not establish a net positive response in either species. The abstract defines positive germ-tube orientation relative to the neighboring spore. This supports the terminology and emergence component, not later tip bending or completed fusion. Germination timing and cis-ness are separate readouts. The full paper, strain provenance and sample sizes were not retrieved. No universal chemical mechanism is inferred from the abstract's proposed explanations."
      },
      {
        "reference": "DOI:10.1039/d3lc00859b",
        "snippet": "The hyphae approach each other from opposing directions with occasional arrestation of growth and readjustment of the growth direction.",
        "notes": "Richter et al. (2024), Results section on stop-and-go growth before anastomosis; directly retrieved Europe PMC full-text JATS, PMC10964749 (PMID:38416560). Culture and image-analysis methods, corresponding Discussion and actual Figure 5 were inspected. Figure 5a-c shows Rhizophagus irregularis MUCL 43194 approaching before fusion; the 21-hour trace is a representative pair, not a replication count. This is independent extension evidence interpreted within the directional definition, not an assertion that this paper uses the autotropism label. Supplementary methods and movies were not retrieved; attachment requests returned access-check HTML or HTTP errors."
      }
    ],
    "discussions": [
      {
        "discussion_id": "positive-autotropism-direction-and-fusion-scope",
        "prompt": "Retain the distinction between directional approach and fusion.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Initial germ-tube orientation and later hyphal redirection are distinct readouts; the definition does not require both in one organism. Hyphal fusion/anastomosis is a separate endpoint, not an exact synonym or a prerequisite. Same-species neighbors can include branches of one mycelium or separate spores; genetic identity is not required by this definition. Do not infer whole-cell taxis, chemotropism, mating or a particular self-recognition mechanism. Passive alignment, faster growth and contact alone are insufficient. Negative autotropism has the opposite direction, not the same phenotype. Resolve external equivalences before adding xrefs or synonyms.",
        "posed_by": "codex",
        "posed_date": "2026-10-04"
      },
      {
        "discussion_id": "positive-autotropism-provenance-and-mechanism",
        "prompt": "Verify strain origins, supplements and native signaling mechanisms.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Canonical examples await original strain-provenance and NCBI identity checks. The 2024 culture method uses transformed chicory roots; this does not establish engineering of the fungi. Inspect the original supplements and the 1968 full paper before quantitative or strain-level enrichment. No universal ligand/receptor chain is established by these observations. A causal graph requires directly supported native perturbations and taxon-paired protein accessions; NONMECHANISTIC is not a grounding bypass.",
        "posed_by": "codex",
        "posed_date": "2026-10-04"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-04T21:04:32Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added positive autotropism with two directly retrieved DOI-backed sources and exact snippets. Distinguished orientation and extension from completed fusion. Ignored-and-hidden searches and structured OWL review found no exact term; the negative sibling's boundary mention is not a duplicate. Reserved METPO:1055800 in v481 under released phenotype. Inspected Figure 5 and retained abstract-only, representative-pair and unread-supplement limitations. Deferred canonical strains, synonyms, external equivalents and causal graphs.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-04T21:35:35Z",
        "curator": "codex",
        "action": "REFINE_EVIDENCE_SNIPPET",
        "changes": "Addressed #1687 by replacing the anaphoric label-only 1968 quote with its exact germ-tube orientation definition. Qualified the mixed-orientation timing comparison without inferring net positive autotropism in its two negative-response species. Retained the separate Botrytis cinerea substrate-dependent observation.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000614",
    "label": "primary homothallism",
    "definition": "A homothallic fungal phenotype enabling self-fertile sexual reproduction through compatible mating-type determinants co-resident in one genome, without requiring mating-type switching.",
    "definition_source": "DOI:10.1371/journal.pgen.1006110",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000609"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1371/journal.pgen.1006110",
        "snippet": "co-occurrence in the genome of a single individual of all the MAT alleles required to trigger sexual development",
        "notes": "David-Palma et al. (2016), PMID:27327578, PMC4915694. Exact Introduction sec001 clause defining primary homothallism, not an abstract quote. Abstract sections, Introduction, all Results and Methods sec011/sec014/sec015 were read. Actual Figures 1, 3 and 4, Table 1 and supplementary Table S3 were inspected. Methods/tables/images identify CBS 6938; prose also says CBS 6838, a retained source inconsistency. Single receptor deletions retain sporulation; double deletion blocks it and rescue restores it. HD2 deletion retains vestigial sporulation; an obligatory HD1/HD2 heterodimer is not established. Figure 3's caption swaps C/D: the actual C is the count plot. Table S3's Figure 2 E/G pointers correspond to actual Figure 1 E/F. SPO11-mutant basidia counts are not significantly reduced; spore viability is. Other figures, supplements and unread Methods/Discussion remain uninspected. Functional genetics supports the model, not MAT sequence presence alone."
      },
      {
        "reference": "DOI:10.5598/imafungus.2015.06.01.13",
        "snippet": "combined expression of MAT1-1 and MAT1-2 genes in a single genome",
        "notes": "2015 terminology review, PMID:26203424, PMC4500084. Exact contiguous phrase from section s2a Primary homothallism, read end-to-end in full-text XML. This is terminology authority, not experimental replication. Its MAT1-1/MAT1-2 formulation describes the ascomycete framework; do not impose that nomenclature on basidiomycetes. The section permits linked or unlinked loci and distinguishes other routes to self-fertility. Its Aspergillus example does not require eight uninucleate spores in every primary-homothallic fungus. Actual Figure 1 remains uninspected."
      },
      {
        "reference": "DOI:10.1016/j.cub.2007.07.012",
        "snippet": "self-fertilization does not bypass requirements for outcrossing sex but instead requires activation of these pathways within a single individual.",
        "notes": "Paoletti et al. (2007), PMID:17669651. Exact contiguous clause from the directly retrieved Europe PMC scientific abstract. In Aspergillus nidulans, alpha- and HMG-domain MAT gene expression is required for normal sexual development and ascospore production; balanced overexpression and an mpkB mutant test distinct perturbations. This does not establish universal dependence on every MAT gene in other fungi. Full text, methods, figures, supplements and original strain provenance remain uninspected; no canonical example is inferred."
      },
      {
        "reference": "DOI:10.1128/EC.00019-10",
        "snippet": "produced the same number of perithecia as the WT, containing mature, viable ascospores at day 7 of development.",
        "notes": "Klix et al. (2010), PMID:20435701, PMC2901639. Exact first Results subsection clause, whose subjects are the SmtA-1 and SmtA-3 deletion strains. Author-institution published PDF at https://www.uni-goettingen.de/de/document/download/a343d8aa3ca6ea7528fe002c2281f0fb.pdf/60.pdf was read after Europe PMC full-text failure; NCBI efetch returned front matter only. Abstract, Introduction, first two Results subsections, strain/culture and microscopy Methods were read; actual Figures 1/2 were inspected. On SWG at 24 C, SmtA-2 deletion instead arrests development at protoperithecia; rescue restores fertility. Thus all MAT genes are not individually essential. The abstract calls SmtA-3 an alpha-domain protein, whereas Introduction/Figure 1 report no known functional domain; do not infer an HMG domain from its MAT1-1-3 relationship. Other experiments, Discussion, supplements and natural provenance of S48977 remain unverified."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:264483",
        "taxon_label": "Phaffia rhodozyma",
        "reference": "DOI:10.1371/journal.pgen.1006110",
        "note": "Qualified example: wild-type CBS 6938, not engineered derivatives. Natural provenance is reported in Table 1 at https://pmc.ncbi.nlm.nih.gov/articles/PMC5103461/: UCD 77-61, sap of Betula stumps in Finland; this is provenance, not independent trait replication. The reproductive study's Methods, Table 1 and figure images support 6938 despite 6838 in parts of the prose. Figure 1D shows basidia and basidiospores; sec014 assays DWR (2.5% agar, 0.5% ribitol) at 18 C for 10 days. Figure 4B reports 32 of 41 wild-type basidiospores germinated. Keep basidia counts and spore viability distinct. NCBI 264483 resolves to this species on 2026-10-04; do not generalize the assay to every strain."
      }
    ],
    "discussions": [
      {
        "discussion_id": "primary-homothallism-scope-and-hierarchy",
        "prompt": "Distinguish functional self-fertility from co-occurring MAT sequences.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "This narrows operational homothallism (traitmech:000609) and agrees with the older evidence note's primary-homothallism umbrella placement. Like pseudohomothallism (traitmech:000612), it includes single-founder self-fertility, but combines determinants within one genome rather than packaging compatible nuclei in a spore. Mating-type switching (traitmech:000611) and same-type outcrossing within unisexual reproduction (traitmech:000613) do not alone imply that operational phenotype; their broader phenotype parents are not inconsistent with this narrower placement. MAT inventory alone is insufficient, as the parent's Chromocrea evidence illustrates. Do not require linked loci, one domain architecture, every MAT gene's indispensability, fixed spore counts or absence of outcrossing. These capabilities are not asserted disjoint. Resolve true-homothallism terminology and external mappings before adding synonyms or xrefs. PHYSIOLOGY is a filesystem category; the standalone METPO proposal uses released phenotype METPO:1000059 pending acceptance of homothallism METPO:1056300, not an unlabeled placeholder parent.",
        "posed_by": "codex",
        "posed_date": "2026-10-04"
      },
      {
        "discussion_id": "primary-homothallism-mechanism-and-readouts",
        "prompt": "Resolve taxon-specific interactions and native proteins before graphing.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Complete unread experiments and supplements before extending mechanistic claims. Phaffia receptor compatibility follows deletion/complementation, not direct ligand-binding assays; HD heterodimerization remains tentative. Different draft scaffolds do not prove genetic unlinkage. Sordaria mutant noncomplementation does not distinguish failed fusion from a same-nucleus requirement. Separate MAT expression, sexual structures, viable spores and meiotic evidence. Preserve source strain/domain/panel discrepancies instead of silently harmonizing them. Resolve native protein accessions and dependencies before causal edges; do not use NONMECHANISTIC to bypass grounding. Manual full-text matches are not abstract-resolver VERIFIED verdicts.",
        "posed_by": "codex",
        "posed_date": "2026-10-04"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-05T05:50:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added primary homothallism with four DOI-backed snippets and qualified CBS 6938 after primary source, actual figure/table, natural provenance and NCBI checks. Kept self-fertility distinct from MAT inventory and retained strain/domain/panel discrepancies. Ignored-and-hidden novelty and allocation searches found no exact record or ID collision. Reserved METPO:1056800 in v491 under released phenotype pending the local homothallism parent's upstream acceptance. Deferred lexical mappings and protein graphs.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000166",
    "label": "prolyl aminopeptidase activity",
    "definition": "A physiological enzyme-activity phenotype in which a cell produces active prolyl aminopeptidases that release N-terminal proline residues from peptides.",
    "definition_source": "https://iubmb.qmul.ac.uk/enzyme/EC3/4/11/5.html",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "synonyms": [
      {
        "synonym_text": "proline aminopeptidase",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://iubmb.qmul.ac.uk/enzyme/EC3/4/11/5.html"
      },
      {
        "synonym_text": "Pro-X aminopeptidase",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://iubmb.qmul.ac.uk/enzyme/EC3/4/11/5.html"
      },
      {
        "synonym_text": "proline iminopeptidase",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://iubmb.qmul.ac.uk/enzyme/EC3/4/11/5.html"
      },
      {
        "synonym_text": "proline arylamidase",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1099/ijsem.0.006017"
      }
    ],
    "evidence": [
      {
        "reference": "https://iubmb.qmul.ac.uk/enzyme/EC3/4/11/5.html",
        "snippet": "<b>Reaction:</b> Release of N-terminal proline from a peptide",
        "notes": "The NC-IUBMB EC 3.4.11.5 entry accepts prolyl aminopeptidase, gives the N-terminal-proline release reaction, and records proline aminopeptidase, Pro-X aminopeptidase, and proline iminopeptidase as other names."
      },
      {
        "reference": "DOI:10.1111/j.1365-2958.1993.tb01249.x",
        "snippet": "Proline iminopeptidase (Pip) is a hydrolase elaborated by virtually all strains of Neisseria gonorrhoeae that selectively removes N-terminal proline residues from peptides.",
        "notes": "Albertson and Koomey cloned the gonococcal pip gene and confirmed that the encoded enzyme can release biologically active proline from peptides."
      },
      {
        "reference": "DOI:10.1099/ijsem.0.006017",
        "snippet": "enzymatic activities are present for: \u03b1-galactosidase, N-acetyl-\u03b2-glucosaminidase, arginine arylamidase, proline arylamidase, leucyl glycine arylamidase, phenylalanine arylamidase, leucine arylamidase, tyrosine arylamidase, alanine arylamidase, glycine arylamidase, histidine arylamidase, glutamyl glutamic acid arylamidase, serine arylamidase, valine arylamidase, cysteine arylamidase, esterase, esterase lipase, alpha-chymotrypsin",
        "notes": "Srinivasan et al. listed proline arylamidase among enzymatic activities present in the Amygdalobacter indicium species description, supporting the API proline arylamidase row as a directly assayed bacterial enzyme-activity phenotype."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:485",
        "taxon_label": "Neisseria gonorrhoeae",
        "note": "Albertson and Koomey cloned the Neisseria gonorrhoeae proline iminopeptidase gene and confirmed that the encoded Pip enzyme releases proline from peptides.",
        "reference": "DOI:10.1111/j.1365-2958.1993.tb01249.x"
      }
    ],
    "discussions": [
      {
        "discussion_id": "prolyl-aminopeptidase-activity-xref-gap",
        "prompt": "Resolve an exact external ontology class for prolyl aminopeptidase activity before adding a TraitRecord xref.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "GO:0004177 denotes broad aminopeptidase molecular function and EC 3.4.11.5 denotes a prolyl aminopeptidase molecular function; both are scope-shifted relative to the organism-level prolyl aminopeptidase production phenotype, so they remain causal-node grounding leads rather than equivalent TraitRecord xrefs.",
        "posed_by": "codex",
        "posed_date": "2026-09-12"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-12T11:07:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted prolyl aminopeptidase activity as a URL/DOI-backed TraitRecord after a repository-wide duplicate review covering ignored and hidden files; METPO has no exact prolyl aminopeptidase activity class yet.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000645",
    "label": "proteaphagy",
    "definition": "An autophagy phenotype in which a microbial cell degrades its proteasomes or proteasome subcomplexes by delivering them to lysosomal or vacuolar compartments.",
    "definition_source": "DOI:10.1074/jbc.M115.699124",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000638"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1074/jbc.M115.699124",
        "snippet": "Here we show that in yeast, upon nitrogen starvation, proteasomes are targeted for vacuolar degradation through autophagy.",
        "notes": "PMID:26670610, PMC4751371. Scientific abstract directly read in DOI-matched Europe PMC metadata and XML. Yeast-strain and immunoblot Methods, autophagy-dependence and core/regulatory-particle Results, Table 1 and relevant captions were read. Saccharomyces cerevisiae reporter processing and vacuolar localization support degradation; native gels address incorporation into complexes. The core and regulatory particles can be targeted separately, with different Ubp3 dependence; intact 26S uptake is not required by the definition. Figure 6D's caption conflicts with its title and body concerning Rpn10, so no Rpn10 requirement is curated. Actual figures, supplements and independent natural-strain provenance were not inspected."
      },
      {
        "reference": "DOI:10.1016/j.celrep.2016.07.015",
        "snippet": "Here, we define two proteaphagy routes in yeast that respond to either nitrogen starvation or particle inactivation.",
        "notes": "PMID:27477278. Scientific abstract directly read in Europe PMC with matching DOI. The yeast study distinguishes starvation from quality-control turnover of inactive proteasomes; Cue5 and Hsp42 support the latter route, not a universal microbial gene inventory. Correction DOI:10.1016/j.celrep.2022.110552 (PMID:35294886) is linked by the source metadata. Its text was directly read at https://profiles.wustl.edu/en/publications/erratum-autophagic-turnover-of-inactive-26s-proteasomes-in-yeast-/: a duplicated anti-histone H3 control blot in Figure S3 was replaced; the authors state their conclusions are unchanged. The corrected figure, original full Methods, actual figures and strain provenance were not inspected. The correction is not independent trait evidence."
      },
      {
        "reference": "DOI:10.1016/j.jbc.2021.101494",
        "snippet": "Indeed, we found that several conditions that activated general autophagy did not induce proteaphagy, further distinguishing proteaphagy from general autophagy.",
        "notes": "PMID:34919962, PMC8732087. Scientific abstract directly read in DOI-matched Europe PMC metadata and XML; Results sec1.1-sec1.3, Discussion sec2 and Methods sec3.1-sec3.4 were read. Proteasome GFP processing, native gels and vacuolar microscopy distinguish cargo turnover from general autophagy. In sec1.3, ATG11 deletion abolishes residual nitrogen-starvation turnover in an ATG17 deletion background, not all proteaphagy in every condition. Rapamycin yields no detected difference in the ATG11 single deletion, with a stated detection-limit caveat. Thus the later result does not establish a blanket contradiction of the 2016 single-deletion result. Methods identify W303-derived SUB61/SUB62 reporter and deletion strains. Captions were read; actual figures, supplements and independent strain provenance were not inspected."
      }
    ],
    "discussions": [
      {
        "discussion_id": "proteaphagy-cargo-scope-and-go",
        "prompt": "Review proteasome-cargo scope and qualified GO alignment.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Proteasomes are the autophagic cargo, not the machinery degrading unrelated substrates. Ordinary proteasome-mediated proteolysis, proteasome biogenesis, storage granules, free-subunit loss or gene presence alone does not establish this phenotype. The 2016 starvation study includes separately targeted core and regulatory particles, so do not require intact holoenzyme uptake. GO:0061816, directly resolved at https://www.ebi.ac.uk/QuickGO/services/ontology/go/terms/GO%3A0061816, is a nonobsolete biological process restricted to selective macroautophagy, not an exact organismal phenotype. The cargo-defined local term does not impose a universal route, trigger or selectivity mechanism; retain this scope difference for human review and omit exact xrefs and synonyms. Ribophagy traitmech:000641 and nuclear-cargo degradation traitmech:000643 are distinct: shared machinery or prior nuclear localization does not equate these cargo phenotypes.",
        "posed_by": "codex",
        "posed_date": "2026-10-06"
      },
      {
        "discussion_id": "proteaphagy-context-exemplars-and-mechanisms",
        "prompt": "Resolve route-specific mechanisms, figures and natural exemplars.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Keep starvation and inactive-particle quality-control routes distinct. The later ATG11 result concerns residual turnover in an ATG17 deletion background; neither an abstract's general wording nor a single deletion establishes universal necessity. Do not turn reduced efficiency, a detection limit or partial turnover into complete absence. Resolve the 2016 Figure 6D Rpn10 caption/body discrepancy and inspect the corrected Figure S3 associated with DOI:10.1016/j.celrep.2022.110552 before relying on those panels. Canonical examples remain unset pending independent natural-strain provenance. The microbial cell performing degradation carries the phenotype, not a bacterium eliciting an animal host response. Native taxon-paired protein accessions and functional evidence are required before a causal graph is added; ATG presence, puncta or loss of total proteasome abundance alone is not proof of autophagic flux.",
        "posed_by": "codex",
        "posed_date": "2026-10-06"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-06T15:30:25Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added proteasome-cargo autophagy with three DOI-backed scientific-abstract snippets, subcomplex scope, context-specific ATG11 interpretation and explicit correction/figure limits. Ignored-and-hidden novelty checks, fresh seed and pinned METPO review found no exact record. Reserved METPO:1059800 in v521 using unchanged corrected parent context from v520. Deferred unverified exemplars, mappings and protein graphs.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000617",
    "label": "pseudobipolar mating system",
    "definition": "A fungal mating-system phenotype in which pheromone/receptor and homeodomain compatibility loci are physically linked on the same chromosome but can recombine during meiosis, generating new mating-type combinations.",
    "definition_source": "DOI:10.1371/journal.pgen.1001052",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1371/journal.pgen.1001052",
        "snippet": "occasional disruptions of the genetic cohesion of the bipolar MAT locus originate new mating types.",
        "notes": "Coelho et al. (2010), PMID:20700437, PMC2916851. Exact clause in scientific abstract abstract1, checked against raw Europe PMC metadata and full-text XML, not the author summary. Results/Discussion and Methods were read, with actual Figures 3-5, Figure S5 and both pages of Table S1 inspected. Sporidiobolus salmonicolor CBS 6832 x ML 2241 yielded the recombinant T7.1, incompatible with either parent but compatible with CBS 490 in Figure 4. The scored endpoint is clamp-bearing mycelium and teliospores after four days on corn meal agar at 25 C; normal germination after compatible T7 crosses is reported in prose as results not shown. Eight teliospores came from one parental cross; colonies from a teliospore are mostly mitotic clones, and T8 was apparently diploid. The authors require larger samples for statistically significant linkage and precise recombination frequencies. Figure 5 partly assumes S. roseus synteny, not a complete S. salmonicolor chromosome assembly. Table S1 and Figures 3/4 label CBS 6832 A2-15, whereas the germination and micromanipulation Methods say A2-6; strain identity is kept without silently reconciling that discrepancy. Table S1 gives CBS 6832 a clinical origin but only names ML 2241's isolator, so full parental provenance and active taxonomy remain unresolved. Other actual figures and supplements remain uninspected. This is native crossing evidence, not solely MAT sequence annotation or a precise population rate."
      },
      {
        "reference": "DOI:10.1371/journal.pbio.3003417",
        "snippet": "In the pseudobipolar configuration, the P/R and HD loci remained on the same chromosome but genetically unlinked",
        "notes": "Coelho et al. (2025), PMID:41042803, PMC12510652. Exact scientific-abstract clause checked against raw Europe PMC metadata, full-text XML and publisher HTML. Supports the broader same-chromosome, recombination-permitting usage, not an independent functional replication in Kwoniella europaea. Abstract, Introduction, first two Results subsections, the relevant Discussion paragraph in sec017 and actual Figure 1 were read. Figure 1B classifies its breeding system as likely heterothallic; Figure 1E shows separated loci in PYCC6329. Despite the abstract's declarative wording, sec017 says crosses have not yielded sexual reproduction and treats persistent recombination as conditional. Physical distance alone does not exclude long-range recombination suppression. Its inferred configuration therefore does not establish observed mating or fertility. The C. decagattii and K. mangrovensis sexual results cannot be transferred to K. europaea. Other Results, Methods, figures and supplements remain uninspected."
      }
    ],
    "discussions": [
      {
        "discussion_id": "pseudobipolar-mating-scope-and-hierarchy",
        "prompt": "Keep physical linkage, genetic linkage and observed compatibility distinct.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "The 2010 pseudo-bipolar usage emphasizes normally bipolar behavior with occasional recombination; the 2025 usage also covers widely separated, potentially genetically unlinked loci on one chromosome. The definition retains their shared recombination-permitting organization without requiring a fixed rate, partial linkage strength, or exactly two species-wide mating types. A genomic prediction must remain distinct from an observed mating phenotype. This is not a literal MAT locus or an individual gene record. It is not identical to traitmech:000616 bipolar mating, which requires a single segregating factor, or traitmech:000615 tetrapolar mating, which requires independent segregation without specifying chromosome colocation. The 2025 paper explicitly allows functional resemblance to tetrapolarity, so do not assert disjointness. Its heterothallic framing also does not prove universal separate-partner dependence under traitmech:000610. Use released phenotype METPO:1000059 in record and proposal pending narrower hierarchy and lexical review; PHYSIOLOGY is a filesystem category.",
        "posed_by": "codex",
        "posed_date": "2026-10-05"
      },
      {
        "discussion_id": "pseudobipolar-mating-evidence-and-mechanism",
        "prompt": "Resolve strain provenance and native dependencies before adding examples or graphs.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Resolve the CBS 6832 allele-designation discrepancy and ML 2241's original isolation context before canonical examples, and verify current taxon authority. Laboratory recombinant T7.1 is not an independently sampled natural isolate. Distinguish crossovers from gene conversion and retain the eight-teliospore sampling limitation. Finish unread source sections, actual figures and supplements before more detailed claims. Never transfer the confirmed sexual cycle of one species to another species with a predicted MAT configuration. Resolve native protein accessions and experimentally tested dependencies before causal edges; no NONMECHANISTIC graph bypasses grounding. Manual source checks remain distinct from actual resolver verdicts.",
        "posed_by": "codex",
        "posed_date": "2026-10-05"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-05T09:48:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added pseudobipolar mating system with two primary DOI-backed sources and exact scientific-abstract clauses. Distinguished native red-yeast recombination and compatibility from the broader genome-based terminology, fixed linkage rates and unverified fertility. Ignored-and-hidden novelty and allocation searches found no exact record or ID collision. Reserved METPO:1057100 in v494 under released phenotype. Deferred canonical taxa, lexical mappings and native protein graphs, with source limitations and an allele-label discrepancy explicit.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000612",
    "label": "pseudohomothallism",
    "definition": "A fungal phenotype enabling a sexual spore carrying separate nuclei of compatible mating types to establish a self-fertile heterokaryotic culture.",
    "definition_source": "DOI:10.5598/imafungus.2015.06.01.13",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000609"
    ],
    "evidence": [
      {
        "reference": "DOI:10.5598/imafungus.2015.06.01.13",
        "snippet": "self-fertility is the result of the packaging of two independent and opposite mating type nuclei within a single spore",
        "notes": "2015 terminology review, PMID:26203424, PMC4500084. Exact contiguous clause from section s2b Pseudohomothallism, read end-to-end in directly retrieved full-text XML. This supplies definition and homothallism-parent authority, not experimental replication or an abstract quote. The review describes single-spore self-fertility arising from compatible partners packaged as separate nuclei. Its two-nucleus description is not a fixed count for every subsequent spore or mycelial stage; the comparative primary study below documents developmental variation. Occasional self-sterile propagules allow outcrossing. Figure 1 remains uninspected."
      },
      {
        "reference": "DOI:10.1093/genetics/143.2.789",
        "snippet": "Ascospores of Neurospora tetrasperma normally contain nuclei of both mating-type idiomorphs (a and A), resulting in self-fertile heterokaryons",
        "notes": "Merino et al. (1996), PMID:8725227. Exact opening clause of the scientific abstract directly retrieved from Europe PMC core metadata. The following parenthesis names this sexual system pseudohomothallism. The study compares mating-type chromosome and autosomal sequences from wild-collected self-fertile strains, while distinguishing occasional homokaryotic self-sterile strains capable of outcrossing. Recombination suppression is an evolutionary association in this system, not the definition of every pseudohomothallic fungus. Full text, figures, supplements and strain-level provenance in this paper remain uninspected."
      },
      {
        "reference": "DOI:10.1002/dvg.1020150111",
        "snippet": "Two basically different modes underlie the delivery of opposite mating type nuclei into each of the four ascospores in the different genera.",
        "notes": "Raju and Perkins (1994), PMID:8187347. Exact sentence of the directly retrieved Europe PMC scientific abstract, which is explicitly truncated at 400 words. Comparative cytology covers N. tetrasperma, G. tetrasperma, P. anserina and P. tetraspora. First-division segregation in Neurospora differs from the second-division program in Podospora and Gelasinospora. The mat-centromere crossover is established for P. anserina but inferred for the other two latter species. Following postmeiotic development, germinating P. anserina ascospores retain three functional nuclei, two of one mating type and one of the other. Do not require exactly two nuclei, four spores, a fixed nuclear ratio, suppressed crossing over or one spindle geometry for the whole trait. Full text, original methods, actual figures and strain provenance remain unread."
      },
      {
        "reference": "DOI:10.1371/journal.pgen.1000030",
        "snippet": "recombination was assessed in individual sexual progeny originating from a selfed cross of the heterokaryotic mycelia.",
        "notes": "Menkis et al. (2008), PMID:18369449, PMC2268244. Exact contiguous clause of Methods s4d, not an abstract quote. Scientific abstract, Introduction, Results s2b/s2c, Methods s4a/s4c/s4d/s4e and Table 1 including footnotes were read in the full-text XML. Results s2b and Methods s4d assay 152 heterokaryotic sexual progeny of a selfed P581 cross; that selected assay denominator is not the frequency of all heterokaryotic offspring. Table 1 identifies P581 as a wild-type heterokaryon from Lihue, Hawaii, and its P-prefix footnote identifies the Perkins collection from nature. FGSC 2508/2509 are homokaryotic components, not alternative identifiers for the natural heterokaryon. The separate 83-progeny N. crassa introgression experiment is not the native P581 selfing assay. Figures, supplements, Discussion and unread experimental sections remain uninspected; inferred evolutionary history is not a demonstrated universal developmental mechanism."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:40127",
        "taxon_label": "Neurospora tetrasperma",
        "reference": "DOI:10.1371/journal.pgen.1000030",
        "note": "Qualified natural example: heterokaryon P581 from Lihue, Hawaii. Provenance is Table 1 and its Perkins-collection footnote at https://pmc.ncbi.nlm.nih.gov/articles/PMC2268244/. Results s2b and Methods s4d analyze 152 heterokaryotic sexual progeny from selfed P581; this is a selected assay set, not a claim that every spore is heterokaryotic or self-fertile. Methods s4a specifies synthetic cross medium at 25 C for crosses. FGSC 2508 and 2509 are its isolated homokaryotic components and are not the example. Do not extend this observation to every strain or life stage. NCBI taxonomy 40127 resolves to the active species name on 2026-10-04."
      }
    ],
    "discussions": [
      {
        "discussion_id": "pseudohomothallism-scope-and-hierarchy",
        "prompt": "Keep single-spore self-fertility distinct from nuclear coexistence and MAT content.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "This reproductive phenotype narrows homothallism (traitmech:000609), not heterothallism or mating-type switching. Heterokaryosis is relevant cellular context but does not alone establish self-fertility. A single sexual spore can carry compatible partners as separate nuclei; MAT sequences in one assembly or multinucleation alone do not establish the trait. Do not require exactly two nuclei throughout development, four spores, one nuclear ratio, universal self-fertility or absence of outcrossing. Resolve secondary homothallism and functional heterothallism usage before assigning exact synonyms, and verify external phenotype/process mappings before adding xrefs. PHYSIOLOGY is a filesystem category. The standalone METPO proposal uses released phenotype, not an unlabeled stub for pending homothallism METPO:1056300; reconcile the narrower hierarchy when that v486 parent is accepted upstream.",
        "posed_by": "codex",
        "posed_date": "2026-10-04"
      },
      {
        "discussion_id": "pseudohomothallism-mechanism-and-readouts",
        "prompt": "Resolve taxon-specific nuclear packaging before adding protein-level causal edges.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Complete unread primary experiments, figures and supplements before expanding mechanistic claims. Spindle arrangement, mating-type segregation and nuclear elimination vary across genera and developmental stages; no one meiotic program is universal. Separate observed cytology from inferred crossover events, and sequence divergence from a direct reproductive readout. Keep natural P581 separate from its homokaryotic components and interspecific introgression derivatives. Resolve native protein accessions and source-bounded dependencies before adding a graph; do not use NONMECHANISTIC to bypass missing grounding. Manual full-text matching is not an abstract-resolver VERIFIED verdict.",
        "posed_by": "codex",
        "posed_date": "2026-10-04"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-05T03:50:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added pseudohomothallism with four DOI-backed exact source snippets and qualified natural P581 after primary selfed-progeny, strain-table and NCBI checks. Kept local homothallism parent and reproductive scope separate from MAT content or nuclear count. Ignored-and-hidden novelty searches and structured METPO review found no exact record. Reserved METPO:1056600 in v489 under released phenotype pending acceptance of the narrower parent. Deferred lexical mappings and protein-resolved causal graphs.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000163",
    "label": "pyrazinamidase activity",
    "definition": "A physiological enzyme-activity phenotype in which a cell produces active nicotinamidase/pyrazinamidase enzymes that hydrolyze nicotinamide and can convert pyrazinamide to pyrazinoic acid.",
    "definition_source": "DOI:10.1111/j.1742-4658.2007.06241.x",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "synonyms": [
      {
        "synonym_text": "nicotinamidase activity",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://iubmb.qmul.ac.uk/enzyme/EC3/5/1/19.html"
      },
      {
        "synonym_text": "nicotinamidase",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://iubmb.qmul.ac.uk/enzyme/EC3/5/1/19.html"
      },
      {
        "synonym_text": "nicotinamide amidohydrolase",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://iubmb.qmul.ac.uk/enzyme/EC3/5/1/19.html"
      },
      {
        "synonym_text": "nicotinamidase/pyrazinamidase",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1111/j.1742-4658.2007.06241.x"
      }
    ],
    "evidence": [
      {
        "reference": "https://iubmb.qmul.ac.uk/enzyme/EC3/5/1/19.html",
        "snippet": "<b>Reaction:</b> nicotinamide + H<small><sub>2</sub></small>O = nicotinate + NH<small><sub>3</sub></small>",
        "notes": "The NC-IUBMB EC 3.5.1.19 entry grounds the nicotinamide-deamidating side of the PncA activity with the accepted nicotinamidase reaction."
      },
      {
        "reference": "DOI:10.1111/j.1742-4658.2007.06241.x",
        "snippet": "The nicotinamidase/pyrazinamidase (PncA) of Mycobacterium tuberculosis is involved in the activation of the important front-line antituberculosis drug pyrazinamide by converting it into the active form, pyrazinoic acid.",
        "notes": "Zhang et al. characterized the Mycobacterium tuberculosis PncA enzyme, linking nicotinamidase/pyrazinamidase activity to cellular conversion of pyrazinamide into pyrazinoic acid."
      },
      {
        "reference": "DOI:10.1371/journal.pone.0015785",
        "snippet": "Pyrazinamidase (PncA) activates the first-line antituberculous drug pyrazinamide into pyrazinoic acid.",
        "notes": "Petrella et al. independently describe PncA as the pyrazinamidase that activates pyrazinamide, supporting the pyrazinamidase label for the organism-level activity."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1773",
        "taxon_label": "Mycobacterium tuberculosis",
        "note": "Zhang et al. characterized active nicotinamidase/pyrazinamidase PncA from Mycobacterium tuberculosis.",
        "reference": "DOI:10.1111/j.1742-4658.2007.06241.x"
      }
    ],
    "discussions": [
      {
        "discussion_id": "pyrazinamidase-activity-xref-gap",
        "prompt": "Resolve an exact external ontology class for pyrazinamidase activity before adding a TraitRecord xref.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "GO:0008936 nicotinamidase activity denotes the catalytic molecular function rather than the organism-level pyrazinamidase/nicotinamidase phenotype, so it is appropriate as a causal-node grounding for the source label and not as an equivalent TraitRecord xref.",
        "posed_by": "codex",
        "posed_date": "2026-09-12"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-12T09:07:58Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted pyrazinamidase activity as a URL/DOI-backed TraitRecord after a repository-wide duplicate review covering ignored and hidden files; METPO has no exact pyrazinamidase activity class yet.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000155",
    "label": "pyrrolidonyl arylamidase activity",
    "definition": "A physiological enzyme-activity phenotype in which a cell produces active pyrrolidonyl arylamidase enzymes that release N-terminal pyroglutamyl groups from peptide substrates.",
    "definition_source": "https://iubmb.qmul.ac.uk/enzyme/EC3/4/19/3.html",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "https://iubmb.qmul.ac.uk/enzyme/EC3/4/19/3.html",
        "snippet": "Reaction: Release of an N-terminal pyroglutamyl group from a polypeptide, the second amino acid generally not being Pro",
        "notes": "The NC-IUBMB EC 3.4.19.3 entry defines pyroglutamyl-peptidase I by its accepted reaction, grounding the peptidase activity named by the organism-level pyrrolidonyl arylamidase phenotype."
      },
      {
        "reference": "DOI:10.1128/JCM.37.11.3443-3447.1999",
        "snippet": "The strains displayed acid phosphatase, alkaline phosphatase, ester lipase C8 (weak reaction), esterase C4 (weak reaction), leucine arylamidase, phosphoamidase, and pyrrolidonyl arylamidase activity.",
        "notes": "Collins et al. characterized six Corynebacterium auriscanis isolates that displayed pyrrolidonyl arylamidase activity, supporting this as a directly assayed bacterial enzyme-activity phenotype."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:99807",
        "taxon_label": "Corynebacterium auriscanis",
        "note": "Collins et al. detected pyrrolidonyl arylamidase activity in Corynebacterium auriscanis isolates from dogs.",
        "reference": "DOI:10.1128/JCM.37.11.3443-3447.1999"
      }
    ],
    "discussions": [
      {
        "discussion_id": "pyrrolidonyl-arylamidase-activity-xref-gap",
        "prompt": "Resolve an exact external ontology class for pyrrolidonyl arylamidase activity before adding a TraitRecord xref.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "GO:0016920 denotes pyroglutamyl-peptidase molecular function rather than the organism-level pyrrolidonyl arylamidase production phenotype, so it is appropriate as a causal-node grounding rather than an equivalent TraitRecord xref.",
        "posed_by": "codex",
        "posed_date": "2026-09-12"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-12T03:14:57Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted pyrrolidonyl arylamidase activity as a URL/DOI-backed TraitRecord after a repository-wide duplicate review covering ignored and hidden files; METPO has no exact pyrrolidonyl arylamidase activity class yet.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000694",
    "label": "quorum quenching",
    "definition": "A physiological capability of a microorganism to interfere with quorum-sensing communication.",
    "definition_source": "DOI:10.1128/AEM.70.2.954-960.2004",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1128/AEM.70.2.954-960.2004",
        "snippet": "However, no AHL was detected in the culture supernatant of SCG1 cocultured with either COT1 or B1, which produce AHL-lactonase.",
        "notes": "Dong et al. 2004, PMID:14766576, PMC348924, first Results subsection. Introduction explicitly calls signal interference quorum quenching. Scientific Abstract, Introduction, Methods, Results and early Discussion read; actual Figure 1 and Tables 1/2 inspected. Other actual figures unread. COT1/B1 cocultures support AHL loss with comparable growth in this setting, not universal growth neutrality. Table 2 retains residual protection after aiiA disruption. B23 is plasmidless; SCG1-GFP is engineered. COT1 species assignment partly uses an unshown crystal-protein observation. EXT_ID:14766576 AND SRC:MED confirmed ID, title and DOI on 2026-10-11. Native resolver: NOT_IN_ABSTRACT; quotation separately matched directly retrieved PMC full text."
      },
      {
        "reference": "DOI:10.1128/AEM.68.4.1754-1759.2002",
        "snippet": "Here we report identification of more than 20 bacterial isolates capable of enzymatic inactivation of AHLs from different sources.",
        "notes": "Dong et al. 2002, PMID:11916693, PMC123891, scientific Abstract. Abstract, Introduction, Methods, Results and selected Discussion read; actual Figure 2 and Table 1 inspected. Other actual figures unread. Whole-cell OHHL inactivation and live-versus-boiled controls support activity, not just aiiA sequence homology. Activity units use culture OD600, not molecular turnover. Restricted isolate sampling does not establish universal species activity. Plasmidless derivatives and recombinant E. coli are not unqualified natural exemplars. Authors overlap the 2004 study, not independent-laboratory replication. EXT_ID:11916693 AND SRC:MED confirmed ID, title and DOI on 2026-10-11; native resolver VERIFIED, also matched directly retrieved scientific Abstract."
      },
      {
        "reference": "DOI:10.1126/scitranslmed.aat8329",
        "snippet": "clinical isolates of different coagulase-negative staphylococci (CoNS) species residing on normal skin produced autoinducing peptides that inhibited the S. aureus agr system",
        "notes": "Williams et al. 2019, PMID:31043573, PMC7106486, scientific Abstract. Direct PMC Abstract, Results S4-S6, Methods S9-S11/S18 and actual Figures 2-4 with captions inspected. Other actual figures unread. Natural isolate supernatants and live S. hominis C5 support non-AHL interference. Figure 4 separates culture-product identification from synthetic-peptide assays; synthetic potency is not a whole-cell threshold. Figure 2A shows modest type-II/III effects despite prose describing little effect. Growth controls are condition-specific; nonsignificance is not equivalence. Supplement returned HTML, not PDF; supplemental figures and Table S1 unread. EXT_ID:31043573 AND SRC:MED confirmed ID, title and DOI on 2026-10-11; native resolver VERIFIED, also matched directly retrieved scientific Abstract. A separate author group and mechanism, not direct replication of the Bacillus experiments."
      }
    ],
    "discussions": [
      {
        "discussion_id": "quorum-quenching-scope-and-mappings",
        "prompt": "Resolve phenotype mappings without conflating signaling actors and molecules.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "This is the microbial interference capability, not its enzyme, peptide, sequence feature, molecular function or treated target's loss of sensing. Positive quorum sensing traitmech:000084 is not a parent; a microorganism can both sense and quench, so organism-level disjointness is not asserted. The existing AiiA and inhibitor nodes there denote a protein and a chemical, not unresolved exact trait nodes. Reduced reporter output from toxicity or impaired growth alone is insufficient. Signal inactivation and inhibitory products are demonstrated routes, not an exhaustive mechanism restriction. No requirement for AHL, aiiA, interspecies interaction, growth neutrality, fitness benefit or disease prevention is imposed. No exact synonym or external phenotype equivalence is asserted pending authority review; molecular-function terms are not phenotype xrefs.",
        "posed_by": "codex",
        "posed_date": "2026-10-11"
      },
      {
        "discussion_id": "quorum-quenching-exemplars-and-mechanisms",
        "prompt": "Resolve natural study strains and source-specific causal mechanisms.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "No canonical examples are assigned until taxonomic authorities and exact strain provenance are reconciled, including laboratory derivatives and the unread 2019 strain supplement. Preserve native coculture and supernatant evidence apart from isolated enzymes, recombinant hosts and synthetic peptides. AHL hydrolysis and agr interference need separate, source-bounded graphs; reporter inhibition alone does not establish receptor binding. Protein edges require functional evidence and taxon-paired accessions, not sequence homology alone. Mechanism is deferred, not claimed absent.",
        "posed_by": "codex",
        "posed_date": "2026-10-11"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-11T02:46:16Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added quorum quenching beneath phenotype with three primary DOI citations and directly checked short snippets. Ignored-and-hidden main/worktree/open-PR checks support 000694 and v570 block 1064700-1064799. Existing trait records unchanged; mappings, canonical taxa and source-specific mechanisms remain open. Timestamp records the observed UTC curation decision.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000084",
    "label": "quorum sensing",
    "definition": "A cell-density-dependent regulatory physiology in which cells produce, release, and detect diffusible autoinducer signals to coordinate gene expression across a population.",
    "definition_source": "DOI:10.1146/annurev.cellbio.21.012704.131001",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "synonyms": [
      {
        "synonym_text": "autoinduction",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1146/annurev.cellbio.21.012704.131001"
      },
      {
        "synonym_text": "quorum sensing system",
        "synonym_type": "EXACT_SYNONYM",
        "source": "http://purl.obolibrary.org/obo/go/releases/2026-07-26/go-basic.obo"
      }
    ],
    "xrefs": [
      "GO:0009372"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev.cellbio.21.012704.131001",
        "snippet": "Bacteria communicate with one another using chemical signal molecules.",
        "notes": "Waters & Bassler review quorum sensing as autoinducer-mediated cell-to-cell communication coordinating population-wide behavior."
      },
      {
        "reference": "DOI:10.1146/annurev.micro.55.1.165",
        "snippet": "Quorum sensing is the regulation of gene expression in response to fluctuations in cell-population density.",
        "notes": "Miller & Bassler review quorum sensing across bacteria and its regulatory logic."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:668",
        "taxon_label": "Aliivibrio fischeri",
        "note": "Where quorum sensing was discovered (LuxI/LuxR autoinduction of bioluminescence); the founding QS model. Vibrio harveyi is a parallel model.",
        "reference": "DOI:10.1128/jb.00035-24"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "quorum_sensing_autoinducer",
        "title": "Autoinducer-mediated quorum sensing",
        "description": "Evidence-backed causal sketch linking accumulating autoinducer signals to coordinated population-wide gene expression.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "This graph is reviewed as the AHL/LuxR branch of quorum sensing (including P. aeruginosa PAO1 LasR/RhlR positive autoregulation and C. violaceum CviR receptor antagonism) plus a specific B. thuringiensis AiiA lactonase interruption mechanism; it does not generalize AiiA or CviR antagonism to peptide or AI-2 signaling systems.",
        "nodes": [
          {
            "node_id": "quorum_sensing_trait",
            "label": "quorum sensing",
            "node_type": "TRAIT",
            "grounding": "traitmech:000084",
            "description": "Cell-density-dependent coordinated regulation."
          },
          {
            "node_id": "autoinducer",
            "label": "N-acyl homoserine lactone autoinducer",
            "node_type": "CHEMICAL",
            "description": "Diffusible signal whose concentration tracks cell density.",
            "grounding": "CHEBI:71338"
          },
          {
            "node_id": "quorum_sensing_process",
            "label": "quorum sensing",
            "node_type": "BIOLOGICAL_PROCESS",
            "grounding": "GO:0009372",
            "description": "Detection of autoinducer and population-wide response."
          },
          {
            "node_id": "threshold_autoinducer_concentration",
            "label": "threshold autoinducer concentration",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Threshold accumulated autoinducer concentration (high cell density) that triggers QS activation."
          },
          {
            "node_id": "autoinducer_synthase",
            "label": "LuxI AHL synthase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Synthase producing the 3-oxo-C6-HSL autoinducer in the canonical A. fischeri LuxI/LuxR circuit.",
            "grounding": "GO:0061579",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:P12747",
                "protein_label": "Acyl-homoserine-lactone synthase",
                "gene_symbol": "luxI",
                "taxon_id": "NCBITaxon:668",
                "taxon_label": "Aliivibrio fischeri",
                "entry_status": "REVIEWED",
                "retrieved_on": "2026-10-22",
                "entry_version": 98,
                "sequence_version": 1,
                "role": "LuxI synthesizes the 3-oxo-C6-HSL autoinducer that activates the LuxR-dependent quorum-sensing circuit in A. fischeri.",
                "evidence": [
                  {
                    "reference": "DOI:10.1128/JB.00035-24",
                    "snippet": "LuxI as the autoinducer synthase",
                    "notes": "The A. fischeri study identifies LuxI as the synthase for the LuxR-binding 3-oxo-C6-HSL signal; reviewed UniProtKB P12747 verifies the protein identity and source taxon."
                  }
                ]
              }
            ]
          },
          {
            "node_id": "signal_receptor",
            "label": "LuxR-family AHL receptor",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Cognate sensor protein/receptor that detects accumulated autoinducer and alters gene expression.",
            "grounding": "InterPro:IPR000792",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:P25084",
                "protein_label": "Transcriptional activator protein LasR",
                "gene_symbol": "lasR",
                "taxon_id": "NCBITaxon:208964",
                "taxon_label": "Pseudomonas aeruginosa PAO1",
                "entry_status": "REVIEWED",
                "proteome_id": "UP000002438",
                "retrieved_on": "2026-10-22",
                "entry_version": 177,
                "sequence_version": 1,
                "role": "LuxR-family 3-oxo-C12-HSL receptor that positively autoregulates lasI and downstream quorum-sensing genes in P. aeruginosa PAO1.",
                "evidence": [
                  {
                    "reference": "DOI:10.1128/mbio.01079-17",
                    "snippet": "the P. aeruginosa lasI and rhlI genes are positively autoregulated by their cognate AHLs and LuxR homologs",
                    "notes": "Supports P. aeruginosa PAO1 LasR as the cognate LuxR homolog mediating positive autoregulation of lasI."
                  }
                ]
              },
              {
                "uniprot_id": "UniProtKB:P54292",
                "protein_label": "Transcriptional regulator RhlR",
                "gene_symbol": "rhlR",
                "taxon_id": "NCBITaxon:208964",
                "taxon_label": "Pseudomonas aeruginosa PAO1",
                "entry_status": "REVIEWED",
                "proteome_id": "UP000002438",
                "retrieved_on": "2026-10-22",
                "entry_version": 151,
                "sequence_version": 1,
                "role": "LuxR-family C4-HSL receptor that positively autoregulates rhlI and quorum-sensing target genes in P. aeruginosa PAO1.",
                "evidence": [
                  {
                    "reference": "DOI:10.1128/mbio.01079-17",
                    "snippet": "the P. aeruginosa lasI and rhlI genes are positively autoregulated by their cognate AHLs and LuxR homologs",
                    "notes": "Supports P. aeruginosa PAO1 RhlR as the cognate LuxR homolog mediating positive autoregulation of rhlI."
                  }
                ]
              },
              {
                "uniprot_id": "UniProtKB:Q7NQP7",
                "protein_label": "Transcriptional activator, LuxR/UhpA family of regulators",
                "gene_symbol": "cviR",
                "taxon_id": "NCBITaxon:243365",
                "taxon_label": "Chromobacterium violaceum ATCC 12472",
                "entry_status": "UNREVIEWED",
                "proteome_id": "UP000001424",
                "retrieved_on": "2026-10-22",
                "entry_version": 143,
                "sequence_version": 1,
                "role": "LuxR-family AHL receptor CviR that is competitively antagonized by small-molecule quorum-sensing inhibitors occupying the native autoinducer-binding pocket in C. violaceum.",
                "evidence": [
                  {
                    "reference": "DOI:10.1016/j.molcel.2011.04.003",
                    "snippet": "CviR from Chromobacterium violaceum is potently antagonized by molecules that bind in place of the native acylated homoserine lactone autoinducer",
                    "notes": "Chen et al. 2011 characterize small-molecule antagonism of Chromobacterium violaceum CviR."
                  }
                ]
              }
            ]
          },
          {
            "node_id": "quorum_quenching_enzyme",
            "label": "AiiA quorum-quenching AHL lactonase",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Metallo-dependent AiiA lactonase that hydrolyzes AHL autoinducers and interrupts quorum sensing.",
            "grounding": "InterPro:IPR054870",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:P0CJ63",
                "protein_label": "N-acyl homoserine lactonase AiiA",
                "gene_symbol": "aiiA",
                "taxon_id": "NCBITaxon:29339",
                "taxon_label": "Bacillus thuringiensis subsp. kurstaki",
                "entry_status": "REVIEWED",
                "retrieved_on": "2026-10-22",
                "entry_version": 48,
                "sequence_version": 1,
                "role": "Zinc-dependent AHL lactonase that hydrolyzes N-acyl-L-homoserine lactone signals, thereby interrupting the AHL/LuxR signaling branch.",
                "evidence": [
                  {
                    "reference": "DOI:10.1073/pnas.0504996102",
                    "snippet": "quorum-quenching N-acyl-L-homoserine lactone hydrolase",
                    "notes": "The primary structural, catalytic, and mutagenesis study establishes AiiA-mediated AHL hydrolysis in B. thuringiensis; UniProtKB P0CJ63 verifies the reviewed protein and taxon."
                  }
                ]
              }
            ]
          },
          {
            "node_id": "qs_inhibitor",
            "label": "quorum-sensing inhibitor",
            "node_type": "CHEMICAL",
            "description": "Small molecule that disrupts QS by inhibiting signal receptors or pathways."
          }
        ],
        "edges": [
          {
            "subject": "autoinducer_synthase",
            "predicate": "produces",
            "object": "autoinducer",
            "description": "A. fischeri LuxI produces the AHL autoinducer that initiates the canonical LuxI/LuxR quorum-sensing circuit.",
            "evidence": [
              {
                "reference": "DOI:10.1128/JB.00035-24",
                "snippet": "LuxI as the autoinducer synthase",
                "notes": "The A. fischeri study identifies LuxI as the synthase for the LuxR-binding 3-oxo-C6-HSL signal."
              }
            ],
            "predicate_id": "METPO:2007800"
          },
          {
            "subject": "autoinducer",
            "predicate": "participates in",
            "object": "quorum_sensing_process",
            "description": "Autoinducer accumulation drives quorum sensing.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s10867-010-9186-4",
                "snippet": "Individual cells release small molecules, known as autoinducers, into their local environment while also responding to the local concentration of the same molecule.",
                "notes": "The primary confinement study describes production and sensing of the AHL autoinducer in the V. fischeri LuxI/LuxR circuit."
              }
            ],
            "predicate_id": "biolink:participates_in"
          },
          {
            "subject": "quorum_sensing_process",
            "predicate": "confers",
            "object": "quorum_sensing_trait",
            "description": "The sensing process realizes the quorum-sensing trait.",
            "evidence": [
              {
                "reference": "DOI:10.1007/s10867-010-9186-4",
                "snippet": "A density of bacteria sufficient to raise the local concentration of AI above a threshold then triggers changes in gene expression throughout the population.",
                "notes": "The V. fischeri LuxI/LuxR experiment links autoinducer accumulation to the coordinated population response that realizes this trait."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "threshold_autoinducer_concentration",
            "predicate": "triggers",
            "object": "quorum_sensing_process",
            "description": "A threshold autoinducer concentration triggers the population-wide quorum-sensing response.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev.micro.55.1.165",
                "snippet": "The detection of a minimal threshold stimulatory concentration of an autoinducer leads to an alteration in gene expression.",
                "notes": "This review statement supports the threshold-to-response relation across bacterial quorum-sensing systems without assigning it to a single receptor architecture."
              }
            ]
          },
          {
            "subject": "signal_receptor",
            "predicate": "positively regulates",
            "object": "autoinducer_synthase",
            "description": "Activated signal-receptor complex promotes autoinducer synthase transcription, forming the autoinduction positive-feedback loop.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mbio.01079-17",
                "snippet": "the P. aeruginosa lasI and rhlI genes are positively autoregulated by their cognate AHLs and LuxR homologs",
                "notes": "This primary P. aeruginosa study supports the LuxR-family positive-feedback branch; positive signal autoregulation is not universal to all quorum-sensing systems."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "quorum_quenching_enzyme",
            "predicate": "inactivates",
            "object": "autoinducer",
            "description": "Quorum-quenching enzymes degrade/inactivate QS autoinducer signals, interrupting quorum sensing.",
            "evidence": [
              {
                "reference": "DOI:10.1073/pnas.0504996102",
                "snippet": "lactonases that hydrolyze AHLs into inactive products, thereby blocking the quorum-sensing systems",
                "notes": "The primary structural and catalytic study demonstrates this relation for AiiA from B. thuringiensis and AHL signals specifically."
              }
            ]
          },
          {
            "subject": "qs_inhibitor",
            "predicate": "inhibits",
            "object": "signal_receptor",
            "description": "QS inhibitors chemically disrupt quorum sensing by inhibiting signal receptors / QS pathways.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.molcel.2011.04.003",
                "snippet": "CviR from Chromobacterium violaceum is potently antagonized by molecules that bind in place of the native acylated homoserine lactone autoinducer",
                "notes": "The primary structure-function study supports competitive antagonism of the CviR LuxR-family receptor; it does not establish that every quorum-sensing inhibitor acts at a receptor."
              }
            ],
            "predicate_id": "RO:0002212"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-08-31T04:00:00Z",
        "curator": "codex",
        "action": "CORRECT_PROTEIN_TAXON_SEMANTICS",
        "changes": "Removed the AiiA source strain from canonical_examples because its protein interrupts rather than exemplifies quorum sensing; added the canonical A. fischeri LuxI synthase and made the positive-feedback edge target the synthase instead of its product. Protein source taxa are now independent of trait exemplars (#521).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-23T09:13:00Z",
        "curator": "codex",
        "action": "CURATE_PROTEIN_TAXON_EXAMPLE",
        "changes": "Narrowed the graph to its cited AHL/LuxR branch, grounded the LuxR receptor and AiiA lactonase families, and added DOI-backed B. thuringiensis P0CJ63 as the quorum-quenching protein exemplar.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-04T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate PHYSIOLOGY trait (quorum sensing) from literature research to fill the cell-cell-signaling gap.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-08T13:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (autoinducer quorum sensing) with GO node grounding and biolink/RO predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-14T05:51:47Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:71338\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 4 evidence-backed generic edges (4 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:15Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002212\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-26T07:15:20Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:G2JHL6\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-04T03:08:16Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002213\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 1 causal edge(s) off enables/RO:0002327 with a TRAIT object (1 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-22T04:26:16Z",
        "curator": "codex",
        "action": "REVIEW_UNIPROT_INSTANCE_GROUNDINGS",
        "changes": "Reviewed 1 organism-specific UniProtKB grounding(s): replaced 0 with taxon-agnostic GO/InterPro terms and retracted 1 to label-only where no exact semantic term was supported (docs/GROUNDING_POLICY.md).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T01:15:00Z",
        "curator": "codex",
        "action": "ADD_EXACT_ONTOLOGY_MATCH",
        "changes": "Ontology exact-match review (2026-08-25): approved exact xref(s): GO:0009372; declared exact synonym(s): 'quorum sensing system'. Evidence is predicate-scoped in the versioned ontology snapshots; OAK cross-checked direct data, and OLS4 spot-checked release deltas and disputed hits.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-30T19:21:37Z",
        "curator": "codex",
        "action": "REVIEW_EVIDENCE_REFERENCE_CHURN",
        "changes": "Offline review for issue 520 retained 5 evidence-reference replacement(s) that PR 511 made on surviving causal edges outside its stated protein-taxon scope. The pre-tranche evidence entries had references but no snippets; the retained entries supply edge-specific snippets and explanatory notes. Reverting would discard that claim-level provenance, so the scope defect is resolved by documenting the decision instead. This audit changed no causal claim or evidence field. Reviewed replacements: DOI:10.1146/annurev.cellbio.21.012704.131001 -> DOI:10.1007/s10867-010-9186-4 (1 edge); DOI:10.1146/annurev.micro.55.1.165 -> DOI:10.1007/s10867-010-9186-4 (1 edge); DOI:10.3390/ijms25052655 -> DOI:10.1016/j.molcel.2011.04.003 (1 edge); DOI:10.3390/ijms25052655 -> DOI:10.1073/pnas.0504996102 (1 edge); DOI:10.3390/ijms25052655 -> DOI:10.1128/mbio.01079-17 (1 edge).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-22T01:35:00Z",
        "curator": "claude",
        "action": "CURATE_PROTEIN_TAXON_EXAMPLE",
        "changes": "Added LuxR-family receptor protein_examples UniProtKB:P25084 (LasR, v177), UniProtKB:P54292 (RhlR, v151) in P. aeruginosa PAO1 (DOI:10.1128/mbio.01079-17) and UniProtKB:Q7NQP7 (CviR, v143) in C. violaceum ATCC 12472 (DOI:10.1016/j.molcel.2011.04.003) on signal_receptor, updated scope_notes, and refreshed entry_version on UniProtKB:P12747 (97 -> 98 on autoinducer_synthase) and UniProtKB:P0CJ63 (47 -> 48 on quorum_quenching_enzyme).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000682",
    "label": "rapid axopodial contraction",
    "definition": "A physiological phenotype in which a microbial cell rapidly shortens its microtubule-supported axopodia in response to stimulation or prey uptake.",
    "definition_source": "DOI:10.2108/zsj.20.1367",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000729"
    ],
    "evidence": [
      {
        "reference": "DOI:10.2108/zsj.20.1367",
        "snippet": "Axopodial contraction of the centrohelid heliozoon Raphidiophrys contractilis was induced by mechanical or electrical stimulation.",
        "notes": "Khan et al. (2003), scientific Abstract, directly retrieved from Europe PMC for PMID:14624035 at https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID%3A14624035%20AND%20SRC%3AMED&resultType=core&format=json. Abstract-only access; full Methods and figures were not inspected. The study reports contraction faster than 3.0 mm/sec, followed by re-elongation initially about 0.30 microm/sec, and a microtubule bundle in each axopodium. Extracellular calcium dependence is restricted to this stimulation assay, not a universal defining threshold. Failure to detect other filaments with the reported fixation method does not prove their biological absence. Source taxon spelling is retained; natural culture provenance and current taxonomic identity are not established here."
      },
      {
        "reference": "DOI:10.1111/j.1550-7408.2001.tb00187.x",
        "snippet": "Upon food uptake, the tubules shorten and transform into a mass of small granules when rapid axopodial contraction occurs",
        "notes": "Kinoshita et al. (2001), scientific Abstract, directly read at https://pubmed.ncbi.nlm.nih.gov/11596916/ and cross-checked against Europe PMC's scientific abstract. Abstract-only access; full Methods and figures were not inspected. The study concerns Actinophrys sol. Contractile-tubule shortening and granulation accompany the food-uptake response; the authors suggest, rather than prove, a causal role. Cold and colchicine both induce microtubule disassembly, but only cold induces tubule granulation in the reported comparison. Neither intervention alone defines the natural rapid-contraction phenotype. No protein identity, effect size or strain provenance is inferred."
      }
    ],
    "discussions": [
      {
        "discussion_id": "axopodial-contraction-scope-and-parent",
        "prompt": "Resolve a closer cellular-contractility parent and assay boundaries.",
        "kind": "CURATION_TODO",
        "status": "RESOLVED",
        "rationale": "Phenotype METPO:1000059 is a broad parent. Existing motile METPO:1000702 is curated around organismal locomotion; rapid shortening of a cellular projection does not alone establish whole-cell locomotion. Keep axopodial contraction separate from ordinary pseudopod extension, re-elongation, slow structural loss, stalk or whole-cell contraction, and drug-induced microtubule disassembly. The reported speed is an observation, not a universal cutoff. No exact synonyms, xrefs, SSSOM equivalences or organism-level disjointness are asserted. Closer hierarchy and comparable time-resolved assays remain open.",
        "posed_by": "codex",
        "posed_date": "2026-10-08",
        "resolved_date": "2026-10-14",
        "resolution_note": "Added cellular contraction (body or cytoplasmic projection shortening) traitmech:000729 as the direct broader phenotype. This is a definition-based subclass inference, not a new child experiment or evidence of a common molecular mechanism. Phenotype METPO:1000059 remains an ancestor. Preserved the historical rationale and endpoint boundaries; the v605 proposal requests the child axiom without rewriting the historical proposal cohort. Only the hierarchy question is resolved here. The independent time-resolved assay question is retained OPEN in axopodial-contraction-assay-comparability; provenance and mechanism remain OPEN."
      },
      {
        "discussion_id": "axopodial-contraction-provenance-and-mechanism",
        "prompt": "Resolve culture provenance and taxon-specific contraction mechanisms.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "The directly read abstracts do not establish natural strain provenance or accession-level identities for canonical examples. Retain the source-named organisms as qualified evidence, not universal taxon assertions; resolve their current taxonomy and original culture descriptions before adding exemplars. Calcium dependence, microtubule disassembly and contractile-tubule observations must not be combined into one universal heliozoan mechanism. A protein-resolved graph requires direct perturbation evidence and taxon-paired accessions. Mechanism is deferred, not claimed absent; tubulin sequence features alone do not establish this response.",
        "posed_by": "codex",
        "posed_date": "2026-10-08"
      },
      {
        "discussion_id": "axopodial-contraction-assay-comparability",
        "prompt": "Establish comparable time-resolved assays for rapid axopodial contraction.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Carried forward from axopodial-contraction-scope-and-parent when only its hierarchy gap was resolved. Preserve stimulus, cell state, projection identity, length readout and temporal resolution when comparing assays. The published speed is not a universal cutoff; re-elongation, slow structural loss and drug-induced microtubule disassembly alone do not establish the rapid physiological response. No new comparative assay or biological experiment was performed by this hierarchy repair.",
        "posed_by": "codex",
        "posed_date": "2026-10-14"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-08T14:52:39Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added rapid axopodial contraction with two primary DOI sources and contiguous scientific-abstract snippets checked directly. Ignored-and-hidden main/worktree/open-PR checks support 000682 and v558 block 1063500-1063599. Kept natural culture provenance, closer hierarchy and protein mechanism unresolved. Distinguished rapid response from locomotion and induced structural breakdown. Existing records unchanged. Timestamp is observed UTC.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-14T22:35:09Z",
        "curator": "codex",
        "action": "REFINE_CELLULAR_CONTRACTION_PARENT",
        "changes": "Refined the direct parent to cellular contraction traitmech:000729 by definition-based inference. Preserved child definition, supporting excerpts, prior curation history and independent provenance/mechanism gaps. Resolved only the parent question. No new experiment, canonical taxon or molecular mechanism is asserted. Retained the independent assay-comparability question OPEN and qualified the Khan Europe PMC URL to SRC:MED using the verified identity.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000709",
    "label": "replicative aging with functional decline",
    "definition": "A physiological phenotype in which microbial cells exhibit declining growth or reproductive performance, or increasing mortality risk, with increasing replicative age under specified conditions.",
    "definition_source": "DOI:10.1098/rstb.2018.0442",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1098/rstb.2018.0442",
        "snippet": "For both cell types, division time progressively increased over successive generations",
        "notes": "Lapinska et al. 2019, PMID:31587633, PMC6792439; Figure 2 caption, directly checked in primary full-text XML and the author-hosted PDF. The Introduction defines aging by declining performance. Figure 2 was visually inspected: the early division-time trend approaches a plateau in the longer run, not indefinite deterioration. Methods separate brightfield aging measurements from fluorescent uptake/aggregation assays. Methods name BW25113, but the Introduction says BW21113; that discrepancy is unresolved. Starting-condition effects remain a limitation. No universal protein mechanism is established."
      },
      {
        "reference": "DOI:10.1186/1471-2148-7-126",
        "snippet": "Aging refers to a decline in reproduction and survival with increasing age.",
        "notes": "Ackermann et al. 2007, PMID:17662151, PMC2174458; scientific abstract Background, directly checked against MED and primary full-text XML. Caulobacter stalked-cell cohorts showed age-dependent loss of reproductive function, with both faster and slower aging among evolved clones. This endpoint combines survival and reproduction and cannot separate them. UJ590 is a pilA-deletion derivative, not an unmodified natural exemplar. Its elapsed-time assay complements, rather than replaces, the division-indexed evidence above."
      },
      {
        "reference": "DOI:10.7554/eLife.20340",
        "snippet": "Surprisingly, cells die without the classic hallmarks of cellular aging, such as progressive changes in size, doubling time, or sibling health.",
        "notes": "Spivey et al. 2017, PMID:28139976, PMC5332158; scientific abstract, not the eLife digest, directly checked against MED and primary full-text XML. Boundary evidence: finite replicative lifespan and its extension do not alone demonstrate age-dependent deterioration. The reported age-independent mortality applies to the measured fission-yeast conditions, not all strains and environments. The abstract and Discussion were assessed, not all experiments or figure images."
      },
      {
        "reference": "DOI:10.1371/journal.pbio.3002245",
        "snippet": "This occurs without an increase in lifespan, proving that at least in yeast, lifespan is distinct from senescence and loss of fitness.",
        "notes": "Horkai et al. 2023, PMID:37643155, PMC10464975; Results, Suppression of age-linked phenotypic change, directly checked against publisher text and primary XML. Galactose-aged diploid MEP cells retained better performance without longer lifespan. This engineered mother-enrichment system and its platform-dependent results are not universal natural-taxon claims. The authors also use replicative ageing for passage through divisions without senescent decline; that broader usage is not the operational phenotype defined here."
      }
    ],
    "discussions": [
      {
        "discussion_id": "replicative-aging-operational-scope",
        "prompt": "Assess remaining upstream terminology for the explicitly decline-qualified phenotype.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Replicative age follows a cell or inherited cell lineage across successive divisions; culture age alone is not that measurement. Use age-resolved performance or mortality risk, not merely a finite lifespan, old-pole identity, endpoint death, cumulative survival loss or an old/new sibling difference. A decline can approach a plateau; continuous worsening until death is not required. The record uses the functional-decline sense of aging, while Horkai et al. 2023 explicitly distinguish senescence from broader replicative ageing. The label is now explicitly qualified as replicative aging with functional decline (#1891); bare replicative aging is not asserted as an exact synonym. Upstream review should assess remaining terminology and hierarchy choices; no external xref is asserted. Chronological survival in nondividing cultures, population-wide clonal senescence and irreversible mammalian cell-cycle arrest are not equated with this phenotype. The existing gram-variable culture_aging node denotes stationary-phase conditions and is not an exact grounding target. METPO:1000059 phenotype is the conservative broader class; no existing record is reparented.",
        "posed_by": "codex",
        "posed_date": "2026-10-12"
      },
      {
        "discussion_id": "replicative-aging-mechanism-and-example-limits",
        "prompt": "Resolve strain provenance and taxon-scoped mechanisms without inferring them from lifespan or markers.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "This is an assayable cellular phenotype, not a locus, protein profile, numeric lifespan field or claim that all microbes age under all conditions. No canonical example is asserted pending strain-provenance and taxonomy checks, including the 2019 strain-name discrepancy. A protein-resolved causal graph is deferred; non-detection of visible aggregates does not exclude all damage, and correlations with fluorescent markers do not establish universal causes. Supplements and raw data were not independently reanalysed. MED and Crossref notice fields were checked on 2026-10-12; a linked preprint or evaluation is not independent experimental support. Publisher access was incomplete for the 2017 and 2019 papers, so no exhaustive notice-absence claim is made. Pinned/current METPO and ignored/hidden repository searches found no exact term in the inspected sources; the pinned ontology is unchanged.",
        "posed_by": "codex",
        "posed_date": "2026-10-12"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-12T10:13:30Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added a decline-based replicative-aging phenotype with four primary DOIs and directly checked snippets; retained lifespan, terminology and strain limitations. Reserved 000709, v585 and 1066200-1066299 after ignored/hidden current-file, registered historical-tree and pending-PR checks. Examples and mechanism graph are deferred. Existing traits unchanged; timestamp is the observed UTC curation decision.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-12T10:28:34Z",
        "curator": "codex",
        "action": "QUALIFIED_TRAIT_LABEL",
        "changes": "Addressed #1891 by qualifying the record and v585 proposal label as replicative aging with functional decline. Preserved the definition, evidence, identifier and original provenance; retained the broader healthy-aging usage as an attributed distinction, not an exact synonym. Timestamp is the observed UTC correction decision.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000722",
    "label": "reversible nematode-paralyzing activity",
    "definition": "A physiological capability of a microorganism to induce a loss of active nematode movement that reverses after exposure to the microorganism or its products ends.",
    "definition_source": "https://journals.flvc.org/nematropica/article/view/64427",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "https://journals.flvc.org/nematropica/article/view/64427",
        "snippet": "Bioassays revealed that filtrates of P. lilacinus and Paecilomyces marquandii caused reversible paralysis of male and juvenile R. similis.",
        "notes": "Kilama et al. 2007, English Abstract, printed page 215/PDF page 1. Direct publisher HTML/PDF and typeset match; native verifier skips URL references, not VERIFIED. Needle-probed immobilization at 2 h was followed by rinsing and reassessment labelled 21 h; Discussion says 21 h after rinsing. Bioassay 2 lacks recovery testing; bioassay 3 has a high-paralysis pH control and bioassay 5 is null against controls. Actual Figure 1 measures initial paralysis; Results/Table 2 address recovery. Repeated counts are not individual trajectories. No universal host/stage response or dose threshold is inferred."
      },
      {
        "reference": "https://horizon.documentation.ird.fr/exl-doc/pleins_textes/pleins_textes_5/pt5/nemato/27861.pdf",
        "snippet": "Secondly, the majority of larvae are able to recover the mobility in fresh water following all treatment times up to 48 h.",
        "notes": "Cayrol, Djian and Pijarowski 1989, Results, Study of the reversibility of the toxic effect, printed page 335/PDF page 5; actual Figure 3 inspected. This recovery result concerns M. arenaria larvae exposed to Brazilian P. lilacinus culture filtrate: 10-day motionless, aerated, illuminated malt culture, 15 g/L, undiluted filtrate, varied exposure, then 24 h in water. Needle probing and water/pH-matched medium controls are described. Summary says less than 48 h, Results through 48 h; no universal threshold is adopted. Typeset all is quoted; PDF text extraction misreads it as dl. Native URL verification is skipped. This is recovery support, not a standalone producer-identity excerpt or proof of a neural mechanism."
      }
    ],
    "discussions": [
      {
        "discussion_id": "reversible-nematode-paralysis-scope-and-hierarchy",
        "prompt": "Refine the hierarchy without losing the microbial actor and recovery requirement.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "This is the microorganism's capability, not its own nonmotility or the nematode's susceptibility. Recovery after removal is required; immobility, reduced speed, reduced egg hatch, population suppression, trapping or attraction alone is insufficient. The same producer or product may kill under other conditions; no organism-level disjointness follows. Phenotype METPO:1000059 is the conservative parent. Lethal activity, fungal nematophagy, trap formation and attraction are related, not necessary parents. No exact active or deprecated METPO counterpart was identified in the documented pinned/current screen; v598 proposes the class. Nematostatic terminology, chemical roles and sequence annotations are not exact synonyms or xrefs. Infection, feeding and a particular molecular mechanism are not required.",
        "posed_by": "codex",
        "posed_date": "2026-10-14"
      },
      {
        "discussion_id": "reversible-nematode-paralysis-source-and-mechanism-limits",
        "prompt": "Resolve source discrepancies and strain provenance before adding taxa or mechanisms.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Kilama assigns 22R5-2 to both species in Methods, versus lilacinus 22R5-1/marquandii 22R5-2 in Results/Figure 1 and marquandii 22R5-1 in Discussion. It also varies 11N4-8/11N8-4 and 23N5-2/23N-5. Upper dose is 375 in Methods/Results but 325 in Table 2; lower dose is 125 in Methods/Table 2 but 150 in Results, in microliters/mL. These discrepancies are not silently corrected. Cayrol's proposed neurotropic action is unresolved, not a demonstrated target. No common active chemical, protein, causal graph, canonical taxon, field efficacy or environmental safety is asserted. Taxonomic authority and strain provenance remain unchecked for exemplar purposes. Source hashes, bounded notice checks, URL-verifier skips and inspection limits are retained in the verification sidecar. No full raw-data or statistical reanalysis was performed.",
        "posed_by": "codex",
        "posed_date": "2026-10-14"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-14T01:02:02Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added a microbial reversible nematode-paralyzing capability with two stable-URL primary studies and typeset-verified snippets. Retained recovery criteria, assay/control and source discrepancies; native URL references are skipped, not VERIFIED. Reserved 000722, v598 and 1067500-1067599 after ignored/hidden current-copy, retained history and open/draft PR checks with numeric false positives adjudicated. No exact active METPO counterpart identified in the inspected scope. Other records unchanged. Timestamp records observed acceptance after assessment, not the later file write.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000582",
    "label": "rheotaxis",
    "definition": "A motile phenotype in which fluid velocity gradients bias an organism's self-propelled movement.",
    "definition_source": "DOI:10.1073/pnas.1120955109",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000702"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1073/pnas.1120955109",
        "snippet": "Rheotaxis is the directed movement resulting from fluid velocity gradients",
        "notes": "Abstract and Results, https://pmc.ncbi.nlm.nih.gov/articles/PMC3324032/ (PMID:22411815). Smooth-swimming Bacillus subtilis OI4139 exhibits transverse swimming in bulk shear flow. Physical reorientation couples to active propulsion; passive advection alone is insufficient. This is not restricted to upstream migration or receptor-mediated sensing. OI4139 is a mutant that almost never tumbles, not a wild-type canonical exemplar; no strain accession is inferred."
      },
      {
        "reference": "DOI:10.1016/j.bpj.2012.03.001",
        "snippet": "positive rheotaxis (rapid and continuous upstream motility) in wild-type Escherichia coli freely swimming over a surface",
        "notes": "Abstract, with strain and preparation in Materials and Methods, Bacteria preparation; behavioral regimes in Results and Figures 3-6. The publisher-formatted article was read at https://sacredheart.elsevierpure.com/ws/portalfiles/portal/39998836/Kaya_BJ12_Bacteria.pdf (PMID:22500751). K12 cells underwent 3-5 rounds of motility selection. Moderate shear supported upstream swimming near the channel ceiling; higher shear produced sideways swimming and downstream drag. The study does not establish universal upstream motion, a universal shear threshold, or in-vivo infection. Supplementary movies were not viewed."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:83333",
        "taxon_label": "Escherichia coli K-12",
        "reference": "DOI:10.1016/j.bpj.2012.03.001",
        "note": "Kaya and Koser's wild-type K12 population after 3-5 motility-selection rounds, swimming near a PDMS channel ceiling under moderate shear. This condition-qualified example does not cover every K-12 cell or flow regime. No more specific K-12 substrain is inferred."
      }
    ],
    "discussions": [
      {
        "discussion_id": "rheotaxis-context-specific-mechanism-grounding",
        "prompt": "Ground separate surface and bulk-flow mechanisms without inventing a shear-sensing protein.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "The cited studies support hydrodynamic reorientation coupled to powered swimming, but surface-associated upstream motion and bulk transverse motion must not be collapsed into one universal mechanism. A protein-resolved causal graph is deferred pending a verified link between a primary mechanistic experiment, its precise strain and an accession-level protein example. OI4139 must not be silently identified as strain 168. No graph or protein accession is asserted in this first-pass identity record. QuickGO search for rheotaxis returned no term on 2026-10-04; no exact external xref is asserted.",
        "posed_by": "codex",
        "posed_date": "2026-10-04"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-04T00:17:45Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added rheotaxis with two primary DOI citations, contiguous snippets and a condition-qualified K-12 example resolved at NCBI. Ignored-and-hidden searches found no exact trait or METPO class. Reserved METPO:1053600 in proposal v459; deferred a protein-resolved graph rather than infer strain/protein identity.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000600",
    "label": "rheotropism",
    "definition": "A phenotype in which growth is directionally oriented or reoriented in response to fluid flow.",
    "definition_source": "DOI:10.1016/S0006-3495(65)86719-4",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1016/S0006-3495(65)86719-4",
        "snippet": "Sparsely sowed, hence independent Botrytis spores, which are fixed to the wall of a laminar flow chamber, tend to germinate downstream.",
        "notes": "Abstract, exact-matched at Europe PMC (PMID:19431336). The author-hosted full text was inspected at https://mterasaki.us/cellbio/lfjaffe/reprints/65bj2.pdf. Methods identify Botrytis cinerea without a strain accession. Figures 3 and 4 (pages 322 and 324) measure downstream outgrowth orientation, not simply germination rate. Tables VI and VII (page 329) test viscosity and rotation confounds; these figures and tables were visually checked. The proposed self-emitted diffusible stimulator is an indirect mechanistic inference, not an identified molecule or receptor. Initial outgrowth localization is not evidence of later tip reorientation."
      },
      {
        "reference": "DOI:10.1016/S0168-1656(97)00147-8",
        "snippet": "Hyphal tips quickly reoriented towards the upstream of the flowing medium and became aligned parallel to the flow axis as they grew larger.",
        "notes": "Abstract, exact-matched at Europe PMC (PMID:9470224). Attached Aspergillus niger hyphae were tested in flowing liquid medium. Other tested fungi showed upstream hyphal and branch growth without polarized germ-tube emergence. The inlet/outlet pH and oxygen measurements do not exclude every local chemical gradient or identify a flow receptor. Strain identity, full text and figures were not verified; claims are abstract-limited."
      },
      {
        "reference": "DOI:10.1007/BF00397538",
        "snippet": "When the spph was placed in a laminar flow of air, it grew into the wind within 2-4 min.",
        "notes": "Abstract, exact-matched at Europe PMC (PMID:24258181). The sporangiophore (spph) of Phycomyces blakesleeanus exhibits upstream growth in air, establishing that this usage of rheotropism is not limited to liquid currents. Added ethylene did not remove the response; that result does not identify its mediator or establish a universal ethylene-independent mechanism. The barrier-avoidance assay is distinct from the wind assay. Strain identity, full text and figures were not verified; claims are abstract-limited."
      }
    ],
    "discussions": [
      {
        "discussion_id": "rheotropism-growth-flow-and-direction-boundaries",
        "prompt": "Keep flow-directed growth distinct from swimming and passive transport.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "The class includes upstream or downstream growth in liquid or gas without requiring both directions or media in one organism. Rheotaxis concerns self-propelled movement, not growth orientation. Passive bending, advection, alignment and growth-rate changes alone are insufficient. Initiation of polarized growth and subsequent tip reorientation are different readouts. Resolve external phenotype equivalences and the scope of wind-response labels before adding xrefs or synonyms; do not split a lexical variant into another trait.",
        "posed_by": "codex",
        "posed_date": "2026-10-04"
      },
      {
        "discussion_id": "rheotropism-native-mechanism-and-exemplars",
        "prompt": "Resolve strain provenance and discriminate mechanical from chemical cues.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Flow can redistribute chemical signals as well as impose mechanical forces. Do not require a direct mechanoreceptor or transfer a mechanism across species, growth stages or fluid media. Inspect the remaining full texts and establish natural strain provenance and NCBI identity before adding canonical examples. Resolve native causal evidence and taxon-paired protein accessions before a mechanistic graph; do not use NONMECHANISTIC to bypass grounding requirements.",
        "posed_by": "codex",
        "posed_date": "2026-10-04"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-04T16:43:59Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added polarity-neutral rheotropism with three primary fungal citations and exact abstract snippets. Ignored-and-hidden novelty searches and structured OWL review found no exact term. Reserved METPO:1055400 in v477. Inspected the 1965 full text and orientation figures and controls; retained abstract-only access limits for the other studies. Deferred unresolved canonical strains and molecular mechanisms, and distinguished growth from rheotaxis.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000641",
    "label": "ribophagy",
    "definition": "An autophagy phenotype in which a microbial cell selectively degrades mature ribosomes or their subunits through macroautophagic delivery to lysosomal or vacuolar compartments.",
    "definition_source": "DOI:10.1038/ncb1723",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000638"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/ncb1723",
        "snippet": "A genetic screen revealed that selective degradation of ribosomes requires catalytic activity of the Ubp3p/Bre5p ubiquitin protease.",
        "notes": "PMID:18391941. Scientific Abstract directly read in Europe PMC core metadata with matching DOI. Saccharomyces cerevisiae degrades mature ribosomes during nutrient starvation by both nonselective autophagy and a selective component named ribophagy. The deletion phenotype concerns 60S particles despite retained starvation sensing and general autophagy; do not transfer the same dependence to 40S subunits. Enriched ubiquitination suggests direct regulation rather than proving every substrate or step. Full text, actual figures and natural strain provenance were not inspected."
      },
      {
        "reference": "DOI:10.1083/jcb.201308139",
        "snippet": "Its ubiquitylation is Ltn1 dependent and Ubp3 reversed, and mutation of its ubiquitylation site rendered ribophagy less dependent on Ubp3.",
        "notes": "PMID:24616224, PMC3998797. Scientific Abstract directly read in Europe PMC core metadata and XML, distinct from the precis. The quoted substrate is Rpl25. Introduction, the LTN1-deletion Results and strain/culture Methods were also read. This yeast study explicitly treats 60S subunit turnover as ribophagy; Rpl5/Rpl25-GFP processing and vacuolar localization support degradation. LTN1 deletion rescues the delayed reporter cleavage in ubp3 mutants, so Ubp3 is not an unconditional presence criterion. Table 1 identifies the reference as BY4741 with auxotrophic deletions, not an independently verified natural exemplar. Figure 1 caption was read; actual figures, supplements, complete Methods and independent strain provenance were not inspected."
      },
      {
        "reference": "DOI:10.15252/embj.201489083",
        "snippet": "Under nutrient starvation, a portion of the cytoplasm is non-selectively sequestered into autophagosomes.",
        "notes": "PMID:25468960, PMC4337068. Scientific Abstract directly read in Europe PMC core metadata with matching DOI. This is boundary evidence, not a positive selective-ribophagy observation: the study frames yeast vacuolar RNA catabolism as bulk nonselective autophagy. Rny1-mediated RNA cleavage, downstream nucleotide metabolism or ribosome delivery alone does not establish cargo selectivity. Full-text retrieval returned HTTP 500; full Methods and actual figures were not inspected."
      },
      {
        "reference": "DOI:10.1016/j.jbc.2025.108554",
        "snippet": "We discovered that most ribosomes are selectively degraded, whose mechanism differs from the previously reported selective degradation process called \"ribophagy.\"",
        "notes": "PMID:40294649, PMC12152620. Scientific Abstract directly read in Europe PMC core metadata and XML. Results sec1.1-sec1.3, Discussion sec2 and Methods sec3.1/sec3.7-sec3.11/sec3.13 were read. The authors distinguish Rsa1-dependent turnover from previously named Ubp3/Ufd3/Cdc48-dependent ribophagy; this is terminology/mechanism boundary evidence, not an unqualified canonical ribophagy assignment. Rpl25-GFP processing, Atg2 controls and rRNA measurements support degradation; RNA accumulation in rny1 mutants alone does not. Residual turnover in rsa1 mutants is retained. The Results support mature rRNA turnover, while the Discussion also hypothesizes nascent nuclear cargo; that cargo choice is not established. Rpl8 contact and Atg8-binding motifs are modeled, not experimentally mapped. Captions were read, but actual figures, supplements, complete Methods and independent natural strain provenance were not inspected."
      }
    ],
    "discussions": [
      {
        "discussion_id": "ribophagy-selectivity-and-terminology",
        "prompt": "Review cargo selectivity and mechanism-dependent terminology.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Use autophagy traitmech:000638 as the broader phenotype. The 2008 paper names selective mature-ribosome turnover ribophagy; the 2014 paper explicitly includes 60S subunits. Neither ribosome protection in dormancy nor bulk RNA decay, free ribosomal-protein degradation, ribosome biogenesis, gene presence or puncta alone establishes this phenotype. The 2025 Rsa1 paper distinguishes its pathway from known ribophagy and notes differing mammalian usage. Retain that source-attributed distinction for human review; do not silently equate Rsa1-dependent turnover with the historically named pathway or make Ubp3 universal. GO:0034517, resolved at https://www.ebi.ac.uk/QuickGO/services/ontology/go/terms/GO%3A0034517, is a nonobsolete biological process for selective mature ribosome degradation by macroautophagy, not an exact organismal phenotype. Preserve that route qualifier and omit exact xrefs and synonyms.",
        "posed_by": "codex",
        "posed_date": "2026-10-06"
      },
      {
        "discussion_id": "ribophagy-exemplars-and-native-mechanisms",
        "prompt": "Resolve natural exemplars and subunit-specific mechanisms.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Canonical examples remain unset: the experiments use laboratory reporter and perturbation strains, and natural strain provenance has not been independently verified. The microbial cell doing the degradation carries the phenotype, not bacteria expressing purified yeast proteins or organisms eliciting an animal host response. Require native taxon-paired protein accessions and functional evidence before a causal graph; do not impose the 60S Ubp3/Bre5 mechanism on 40S turnover or all microbial taxa. Preserve the difference between normal rates, residual activity and complete absence of degradation. A predicted binding motif is not a separate trait or a proven causal contact.",
        "posed_by": "codex",
        "posed_date": "2026-10-06"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-06T11:59:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added ribophagy as selective mature ribosome or subunit degradation under autophagy, with four DOI-backed snippets and explicit bulk-turnover, source-access and terminology limits. Ignored-and-hidden searches and pinned METPO review found no exact record. Reserved METPO:1059400 in v517 with v514's unchanged parent context. Deferred unverified examples, mappings and protein graphs.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000172",
    "label": "serine arylamidase activity",
    "definition": "A physiological enzyme-activity phenotype in which a cell produces active serine arylamidase enzymes that hydrolyze serine arylamide substrates.",
    "definition_source": "DOI:10.1099/ijsem.0.006017",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "synonyms": [
      {
        "synonym_text": "serine arylamidase",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1099/ijsem.0.006017"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1099/ijsem.0.006017",
        "snippet": "enzymatic activities are present for: \u03b1-galactosidase, N-acetyl-\u03b2-glucosaminidase, arginine arylamidase, proline arylamidase, leucyl glycine arylamidase, phenylalanine arylamidase, leucine arylamidase, tyrosine arylamidase, alanine arylamidase, glycine arylamidase, histidine arylamidase, glutamyl glutamic acid arylamidase, serine arylamidase, valine arylamidase, cysteine arylamidase, esterase, esterase lipase, alpha-chymotrypsin",
        "notes": "Srinivasan et al. listed serine arylamidase among enzymatic activities present in the Amygdalobacter indicium species description, supporting the API arylamidase row as a directly assayed bacterial enzyme-activity phenotype."
      },
      {
        "reference": "DOI:10.1128/JCM.40.9.3427-3431.2002",
        "snippet": "When the API rapid ID32A system was used, all eight strains displayed activity for alanine arylamidase, arginine arylamidase, \u03b1-glucosidase, glycine arylamidase, histidine arylamidase, leucine arylamidase, leucylglycine arylamidase, proline arylamidase, phenylalanine arylamidase, serine arylamidase, and tyrosine arylamidase",
        "notes": "Hall et al. reported serine arylamidase activity in all eight Actinomyces cardiffensis clinical isolates tested with the API rapid ID32A system."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:3029272",
        "taxon_label": "Amygdalobacter indicium",
        "note": "Srinivasan et al. reported Amygdalobacter indicium as positive for serine arylamidase activity in an enzyme activity panel.",
        "reference": "DOI:10.1099/ijsem.0.006017"
      }
    ],
    "discussions": [
      {
        "discussion_id": "serine-arylamidase-activity-xref-gap",
        "prompt": "Resolve an exact external ontology class for serine arylamidase activity before adding a TraitRecord xref.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "GO:0004177 covers broad aminopeptidase activity at molecular-function scope, and no live GO class provides an exact residue-specific serine arylamidase production phenotype at organism-level scope.",
        "posed_by": "codex",
        "posed_date": "2026-09-12"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-12T13:59:47Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted serine arylamidase activity as a DOI-backed TraitRecord after a repository-wide duplicate review covering ignored and hidden files; METPO has no exact serine arylamidase activity class yet and the placeholder is reserved in proposals/metpo_traitmech_v49.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000186",
    "label": "siderophore production",
    "definition": "A physiological trait in which bacteria biosynthesize and release siderophores that scavenge extracellular iron for uptake.",
    "definition_source": "DOI:10.1111/1462-2920.14937",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1111/1462-2920.14937",
        "snippet": "Siderophores are iron-chelating molecules produced by bacteria to access iron, a key nutrient.",
        "notes": "Schalk et al. define bacterial siderophores as produced iron-chelating molecules that enable iron access."
      },
      {
        "reference": "DOI:10.1111/1462-2920.14937",
        "snippet": "They are released by bacteria into their environment to scavenge iron and bring it back into the cells.",
        "notes": "The same review supports the release, extracellular scavenging, and uptake clauses in the local definition."
      },
      {
        "reference": "DOI:10.15698/mic2018.10.649",
        "snippet": "Pyoverdines are fluorescent siderophores of pseudomonads that play important roles for growth under iron-limiting conditions.",
        "notes": "Ringel and Bruser support pyoverdine production as a fluorescent-pseudomonad siderophore-production subtype."
      },
      {
        "reference": "DOI:10.1073/pnas.0908760106",
        "snippet": "The siderophore pyoverdine (PVD) is a primary virulence factor of the human pathogenic bacterium Pseudomonas aeruginosa",
        "notes": "Imperi et al. support Pseudomonas aeruginosa as a pyoverdine-producing bacterium."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:287",
        "taxon_label": "Pseudomonas aeruginosa",
        "note": "Pseudomonas aeruginosa is used as a canonical pyoverdine-producing bacterium.",
        "reference": "DOI:10.1073/pnas.0908760106"
      }
    ],
    "discussions": [
      {
        "discussion_id": "siderophore-production-xref-gap",
        "prompt": "Resolve exact external ontology xrefs for the bacterial siderophore production phenotype.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "The pinned METPO snapshot contains only METPO:1000277 obsolete siderophore. GO:0019290 is limited to the siderophore biosynthetic process, GO:0015891 is a siderophore transport process, and CHEBI:26672 denotes the siderophore molecule rather than the organism-level biosynthesis-and-release trait.",
        "posed_by": "codex",
        "posed_date": "2026-09-14"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-14T18:32:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted siderophore production as a DOI-backed TraitRecord after a repository-wide duplicate review covering ignored and hidden files; METPO has only an obsolete siderophore class in the local snapshot and the replacement placeholder is reserved in proposals/metpo_traitmech_v63.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000688",
    "label": "siliceous scale production",
    "definition": "A physiological phenotype in which a microbial cell produces siliceous scales.",
    "definition_source": "DOI:10.1016/j.protis.2016.05.002",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000690"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1016/j.protis.2016.05.002",
        "snippet": "Scales were formed one by one in silica deposition vesicles (SDVs)",
        "notes": "Nomura and Ishida 2016, PMID:27348459. Scientific abstract directly read on 2026-10-10 at https://rrc.nbrp.jp/references/56432?lang=en and Europe PMC CORE, using EXT_ID:27348459 AND SRC:MED and checking the returned source, title and DOI together. The study describes scale formation in Paulinella chromatophora under its historical name and detects silicon in vesicles with immature scales. Microtubule involvement in determining scale geometry is proposed, not demonstrated molecular necessity. Publisher access returned 403; full Methods and figures were not inspected. Scale production and subsequent shell assembly are distinct observations."
      },
      {
        "reference": "DOI:10.1111/j.0022-3646.1996.00675.x",
        "snippet": "The first new scales appeared within 2 h after the silica addition",
        "notes": "Sandgren, Hall and Barlow 1996, scientific ABSTRACT directly read on 2026-10-10 in publisher-deposited Crossref JATS at https://api.crossref.org/works/10.1111%2Fj.0022-3646.1996.00675.x. Silica-limited Synura petersenii cultures suppressed scale deposition, and scale-free cells regenerated scales after dissolved silica addition. This supports production rather than possession alone. The quoted recovery timing is specific to that culture experiment, not a universal threshold or rate. Scale production could be uncoupled from cell division in this system; no obligatory growth dependence is inferred. Crossref print date is August 1996; its June 2008 online date is not a second study. Full Methods and figures were not inspected."
      }
    ],
    "discussions": [
      {
        "discussion_id": "siliceous-scale-production-scope-and-parent",
        "prompt": "Resolve broader biomineralization placement without conflating endpoints.",
        "kind": "CURATION_TODO",
        "status": "RESOLVED",
        "rationale": "Use phenotype METPO:1000059 pending a source-backed broader biomineralization phenotype. This is production of scales, not mere possession, acquisition or reuse of preformed scales, their extrusion, or their arrangement into a shell or scale layer. It is not equivalent to general silicification, diatom frustule formation, magnetosome or ferrosome possession, substrate adhesion, or growth on a particular chemical. These neighboring endpoints do not alone demonstrate new-scale production. Do not infer a universal scale geometry, covering architecture, cell-cycle coupling or fitness effect. No exact synonyms, xrefs, homology or organism-level disjointness are asserted.",
        "posed_by": "codex",
        "posed_date": "2026-10-10",
        "resolved_date": "2026-10-10",
        "resolution_note": "Added biomineralization traitmech:000690 as the direct broader phenotype. Production of the mineral elements specified by this record entails mineral formation; this is a definition-based hierarchy inference, not a new child experiment. Phenotype METPO:1000059 remains an ancestor. The historical rationale and endpoint distinctions are preserved; the separate exemplar and mechanism gap remains OPEN. The v566 proposal requests the additional child axiom without rewriting the historical proposal cohort."
      },
      {
        "discussion_id": "siliceous-scale-production-exemplars-and-mechanism",
        "prompt": "Verify assay-strain identity and production-specific molecular evidence.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "No canonical examples are assigned until primary assay Methods, strain provenance and current taxonomy are jointly reconciled. NIES-4060 is currently catalogued as Paulinella micropora (MYN1) at https://mcc.next.nbrp.jp/strainList.do?strainNumber=NIES-4060; its reference list links the 2016 historical chromatophora paper, but this collection association is not an independent production experiment or authority to rename every historical observation. The two primary abstracts support a reusable phenotype through different methods, not one conserved molecular pathway. Ultrastructure and cytoskeletal association alone cannot establish causal protein requirements. Separate deposition, vesicle transport, extrusion and assembly before adding causal edges. A protein mechanism needs functional evidence and taxon-paired accessions; sequence features alone cannot supply that support. Mechanism is deferred, not claimed absent.",
        "posed_by": "codex",
        "posed_date": "2026-10-10"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-10T05:02:23Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added siliceous scale production with two primary DOI citations, directly checked scientific-abstract snippets and explicit access limits. Ignored-and-hidden main/worktree/open-PR reservation checks support 000688 and v564 block 1064100-1064199. Broader hierarchy, canonical exemplars and protein mechanism remain unresolved. Existing records unchanged. Timestamp records the observed UTC curation decision.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-10T08:03:12Z",
        "curator": "codex",
        "action": "REFINE_BIOMINERALIZATION_PARENT",
        "changes": "Refined the direct parent to biomineralization traitmech:000690 and resolved the temporary parent gap by definition-based inference. Preserved the definition, evidence, historical rationale, independent mechanism gap and prior curation history. No organism or molecular mechanism was added.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000207",
    "label": "SOS response",
    "definition": "A stress response in which RecA/LexA-mediated sensing of DNA damage derepresses an SOS regulon that coordinates DNA repair, damage tolerance, transient division arrest, and mutagenic survival functions.",
    "definition_source": "DOI:10.1002/em.22267",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000078"
    ],
    "synonyms": [
      {
        "synonym_text": "SOS system",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1002/em.22267"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1002/em.22267",
        "snippet": "Most bacteria have evolved a coordinated response to DNA damage",
        "notes": "Maslowska et al. review the bacterial SOS response as a coordinated DNA-damage response."
      },
      {
        "reference": "DOI:10.1002/em.22267",
        "snippet": "The SOS global regulatory network consists of multiple factors promoting the integrity of DNA as well as error-prone factors allowing for survival and continuous replication upon extensive DNA damage",
        "notes": "The SOS regulon coordinates high-fidelity DNA-integrity functions with error-prone survival functions induced under extensive DNA damage."
      },
      {
        "reference": "DOI:10.1002/advs.202203260",
        "snippet": "the SOS response is activated through the binding of recA with single stranded DNA and the self-cleavage of the lexA repressor, enabling expression of SOS regulon genes",
        "notes": "Yu et al. directly support the RecA/LexA activation branch of the SOS response."
      },
      {
        "reference": "DOI:10.1002/advs.202203260",
        "snippet": "cell division inhibitor, sulA, blocks FtsZ (a master regulator of bacterial cell division and responsible for the Z ring formation at mid-cell) polymerization",
        "notes": "Yu et al. support SOS-induced division inhibition as one physiological output of the response."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:562",
        "taxon_label": "Escherichia coli",
        "note": "E. coli is the canonical RecA/LexA SOS-response model reviewed by Maslowska et al.",
        "reference": "DOI:10.1002/em.22267"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "sos_response_dna_damage_regulon",
        "title": "DNA-damage SOS regulon induction",
        "description": "Evidence-backed causal sketch linking DNA damage and single-stranded DNA accumulation to RecA/LexA derepression of SOS-regulon functions.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "This graph captures the classical E. coli RecA/LexA branch of SOS induction. It does not make every SOS-regulon member, error-prone polymerase, or prophage-induction branch universal across bacteria.",
        "nodes": [
          {
            "node_id": "sos_response_trait",
            "label": "SOS response",
            "node_type": "TRAIT",
            "grounding": "traitmech:000207",
            "description": "Capacity to mount the bacterial SOS DNA-damage response."
          },
          {
            "node_id": "genotoxic_stress",
            "label": "genotoxic stress",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Genotoxic stress or replication inhibition that exposes single-stranded DNA."
          },
          {
            "node_id": "single_stranded_dna_accumulation",
            "label": "single-stranded DNA accumulation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Production or exposure of single-stranded DNA after DNA damage or replication stress."
          },
          {
            "node_id": "reca_nucleoprotein_filament",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Reviewed activated protein state; no single taxon-agnostic family, activity, or complex term captures RecA polymerized on DNA in its SOS-inducing state.",
            "label": "RecA nucleoprotein filament",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Activated RecA filament on single-stranded DNA that stimulates LexA autoproteolysis.",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:P0A7G6",
                "protein_label": "Protein RecA",
                "gene_symbol": "recA",
                "taxon_id": "NCBITaxon:83333",
                "taxon_label": "Escherichia coli K-12",
                "entry_status": "REVIEWED",
                "retrieved_on": "2026-09-15",
                "entry_version": 168,
                "sequence_version": 2,
                "role": "E. coli K-12 RecA polymerizes on single-stranded DNA and activates LexA autoproteolysis during SOS induction.",
                "evidence": [
                  {
                    "reference": "https://rest.uniprot.org/uniprotkb/P0A7G6.json",
                    "snippet": "Interacts with and activates LexA leading to autocatalytic cleavage of LexA, which derepresses the SOS regulon",
                    "notes": "Verified against the live UniProt REST entry for P0A7G6 retrieved on 2026-09-15."
                  }
                ]
              }
            ]
          },
          {
            "node_id": "lexa_repressor",
            "label": "LexA repressor",
            "node_type": "GENE_OR_PROTEIN",
            "grounding": "InterPro:IPR050077",
            "description": "SOS master repressor inactivated by RecA-stimulated autoproteolysis.",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:P0A7C2",
                "protein_label": "LexA repressor",
                "gene_symbol": "lexA",
                "taxon_id": "NCBITaxon:83333",
                "taxon_label": "Escherichia coli K-12",
                "entry_status": "REVIEWED",
                "retrieved_on": "2026-09-15",
                "entry_version": 160,
                "sequence_version": 1,
                "role": "E. coli K-12 LexA represses SOS genes and undergoes RecA-stimulated autocleavage to derepress the SOS regulon.",
                "evidence": [
                  {
                    "reference": "https://rest.uniprot.org/uniprotkb/P0A7C2.json",
                    "snippet": "RecA interacts with LexA causing an autocatalytic cleavage which disrupts the DNA-binding part of LexA, leading to derepression of the SOS regulon",
                    "notes": "Verified against the live UniProt REST entry for P0A7C2 retrieved on 2026-09-15."
                  }
                ]
              }
            ]
          },
          {
            "node_id": "lexa_autoproteolysis",
            "label": "LexA autoproteolysis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "RecA-stimulated autocleavage of the LexA SOS repressor."
          },
          {
            "node_id": "sos_regulon_expression",
            "label": "SOS regulon expression",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Induced expression of LexA-repressed genes in the SOS regulon."
          },
          {
            "node_id": "dna_repair_damage_tolerance",
            "label": "DNA repair and damage tolerance",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "DNA-integrity, translesion-synthesis, mutagenesis, and division-delay functions induced by the SOS regulon."
          }
        ],
        "edges": [
          {
            "subject": "genotoxic_stress",
            "predicate": "causes",
            "predicate_id": "biolink:causes",
            "object": "single_stranded_dna_accumulation",
            "description": "Genotoxic stress and replication inhibition expose single-stranded DNA that initiates the SOS cascade.",
            "evidence": [
              {
                "reference": "DOI:10.1073/pnas.2407832121",
                "snippet": "AZT increases the burden of ssDNA at the replication fork and induces the SOS response via the RecAFOR pathway",
                "notes": "Verified against the open PNAS/PMC full text; the replication inhibitor AZT raises single-stranded DNA at replication forks and induces SOS through RecFOR."
              }
            ]
          },
          {
            "subject": "single_stranded_dna_accumulation",
            "predicate": "activates",
            "predicate_id": "RO:0002213",
            "object": "reca_nucleoprotein_filament",
            "description": "Single-stranded DNA supports activated RecA nucleoprotein filament formation.",
            "evidence": [
              {
                "reference": "https://rest.uniprot.org/uniprotkb/P0A7G6.json",
                "snippet": "Polymerizes non-specifically on ssDNA to form filaments; filament formation requires ATP or ATP-gamma-S",
                "notes": "Verified against the live UniProt REST entry for P0A7G6 retrieved on 2026-09-15."
              }
            ]
          },
          {
            "subject": "reca_nucleoprotein_filament",
            "predicate": "promotes",
            "predicate_id": "RO:0002213",
            "object": "lexa_autoproteolysis",
            "description": "Activated RecA promotes LexA autocleavage.",
            "evidence": [
              {
                "reference": "DOI:10.1002/advs.202203260",
                "snippet": "the SOS response is activated through the binding of recA with single stranded DNA and the self-cleavage of the lexA repressor",
                "notes": "Verified against the open Wiley full text during the cell-length graph curation; the source links RecA-ssDNA to LexA self-cleavage."
              }
            ]
          },
          {
            "subject": "lexa_repressor",
            "predicate": "negatively regulates",
            "predicate_id": "RO:0002212",
            "object": "sos_regulon_expression",
            "description": "LexA represses SOS-regulon expression before it is inactivated.",
            "evidence": [
              {
                "reference": "https://rest.uniprot.org/uniprotkb/P0A7C2.json",
                "snippet": "Represses a number of genes involved in the response to DNA damage (SOS response), including recA and lexA",
                "notes": "Verified against the live UniProt REST entry for P0A7C2 retrieved on 2026-09-15."
              }
            ]
          },
          {
            "subject": "lexa_autoproteolysis",
            "predicate": "derepresses",
            "object": "sos_regulon_expression",
            "description": "LexA autocleavage disrupts DNA binding and releases repression of SOS genes.",
            "evidence": [
              {
                "reference": "https://rest.uniprot.org/uniprotkb/P0A7C2.json",
                "snippet": "disrupts the DNA-binding part of LexA, leading to derepression of the SOS regulon",
                "notes": "Verified against the live UniProt REST entry for P0A7C2 retrieved on 2026-09-15."
              }
            ]
          },
          {
            "subject": "sos_regulon_expression",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "dna_repair_damage_tolerance",
            "description": "SOS-regulon expression coordinates DNA-integrity and damage-tolerance functions.",
            "evidence": [
              {
                "reference": "DOI:10.1002/em.22267",
                "snippet": "multiple factors promoting the integrity of DNA as well as error-prone factors allowing for survival and continuous replication upon extensive DNA damage",
                "notes": "Verified against the public Crossref abstract; SOS-regulon functions span DNA integrity and error-prone survival."
              }
            ]
          },
          {
            "subject": "dna_repair_damage_tolerance",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "sos_response_trait",
            "description": "The induced repair and damage-tolerance program realizes the SOS-response trait.",
            "evidence": [
              {
                "reference": "DOI:10.1002/em.22267",
                "snippet": "Most bacteria have evolved a coordinated response to DNA damage",
                "notes": "Verified against the public Crossref abstract; the SOS response is an induced, coordinated bacterial DNA-damage response."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "sos-response-xref-gap",
        "prompt": "Resolve exact ontology xrefs for organism-level microbial SOS response before adding TraitRecord xrefs.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "GO:0009432 SOS response exactly grounds biological-process nodes in causal graphs but is shifted from this organism-level response trait. RecA, LexA, SulA, translesion-polymerase, prophage-induction, DNA-repair, and DNA-damage terms describe narrower machinery, downstream processes, or related triggers rather than the whole microbial SOS-response phenotype.",
        "posed_by": "codex",
        "posed_date": "2026-09-15"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-15T06:22:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted SOS response as a DOI-backed stress-response TraitRecord after a repository-wide duplicate review covering ignored and hidden files; the local METPO snapshot has no active exact SOS response class and the replacement placeholder is reserved in proposals/metpo_traitmech_v84.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000083",
    "label": "spore germination",
    "definition": "The physiological process by which a dormant spore exits dormancy and resumes vegetative growth in response to germinant signals, including release of dipicolinic acid and rehydration of the spore core.",
    "definition_source": "DOI:10.1016/j.mib.2003.10.001",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "synonyms": [
      {
        "synonym_text": "germination",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1016/j.mib.2003.10.001"
      }
    ],
    "xrefs": [
      "GO:0009847"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1016/j.mib.2003.10.001",
        "notes": "Setlow reviews spore germination, in which nutrient germinants trigger dipicolinic-acid release and core rehydration to resume growth."
      },
      {
        "reference": "DOI:10.1038/nrmicro2504",
        "notes": "Lennon & Jones frame germination as resuscitation from the dormant seed-bank state."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1423",
        "taxon_label": "Bacillus subtilis",
        "note": "Model for endospore germination (germinant receptors, cortex hydrolysis; strain 168).",
        "reference": "PMID:39772627"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "spore_germination_germinant_trigger",
        "title": "Germinant-triggered spore germination",
        "description": "Evidence-backed causal sketch linking germinant signals to exit from spore dormancy and resumption of growth.",
        "nodes": [
          {
            "node_id": "spore_germination_trait",
            "label": "spore germination",
            "node_type": "TRAIT",
            "grounding": "traitmech:000083",
            "description": "Capacity of a dormant spore to resume growth."
          },
          {
            "node_id": "germinant",
            "label": "germinant",
            "node_type": "CHEMICAL",
            "description": "Nutrient signal that triggers germination."
          },
          {
            "node_id": "spore_germination_process",
            "label": "spore germination",
            "node_type": "BIOLOGICAL_PROCESS",
            "grounding": "GO:0009847",
            "description": "Dipicolinic-acid release and core rehydration."
          },
          {
            "node_id": "cadpa_release",
            "label": "CaDPA release from spore core",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "SpoVA-mediated efflux of calcium dipicolinate (CaDPA) from the dormant spore core during germination."
          },
          {
            "node_id": "cortex_hydrolysis",
            "label": "cortex peptidoglycan hydrolysis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Degradation of the spore cortex peptidoglycan by germination-specific lytic enzymes."
          },
          {
            "node_id": "core_rehydration_outgrowth",
            "label": "core rehydration and outgrowth",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Full expansion and rehydration of the spore core enabling resumption of metabolism and initiation of outgrowth."
          }
        ],
        "edges": [
          {
            "subject": "germinant",
            "predicate": "causes",
            "object": "spore_germination_process",
            "description": "Germinant binding triggers the germination process.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.mib.2003.10.001",
                "notes": "Setlow reviews germinant-triggered spore germination."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "spore_germination_process",
            "predicate": "confers",
            "object": "spore_germination_trait",
            "description": "The germination process realizes the spore-germination trait.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2504",
                "notes": "Lennon & Jones frame germination as resuscitation from dormancy."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "spore_germination_process",
            "predicate": "causes",
            "object": "cadpa_release",
            "description": "The germination process drives SpoVA-mediated release of calcium dipicolinate from the spore core.",
            "evidence": [
              {
                "reference": "DOI:10.1126/science.adg9829",
                "notes": "Ion release during germination drives expulsion of dipicolinic acid (CaDPA) through the SpoVA transport complex."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "cadpa_release",
            "predicate": "activates",
            "object": "cortex_hydrolysis",
            "description": "Released CaDPA acts as a signal activating germination-specific cortex-lytic enzymes to begin cortex degradation.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mbio.02220-23",
                "notes": "Ca-DPA release acts as a signal for a germination-specific cortex-lytic enzyme to begin cortex degradation."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "cortex_hydrolysis",
            "predicate": "causes",
            "object": "core_rehydration_outgrowth",
            "description": "Once the cortex is hydrolyzed, the core can fully expand and rehydrate, enabling outgrowth.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mbio.02220-23",
                "notes": "Once the cortex is hydrolyzed, the core can fully expand and rehydrate, allowing full metabolic capabilities and initiation of outgrowth; broadly supported across endospore formers."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "core_rehydration_outgrowth",
            "predicate": "confers",
            "object": "spore_germination_trait",
            "description": "Core rehydration and outgrowth complete realization of the spore-germination trait.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mbio.02220-23",
                "notes": "Core rehydration following cortex hydrolysis allows full metabolic capabilities and initiation of outgrowth, completing germination."
              }
            ],
            "predicate_id": "METPO:2007700"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-06-04T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate PHYSIOLOGY trait (spore germination), the physiological exit from spore dormancy; complements the morphological sporulation/spore-forming traits.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-08T13:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (germinant-triggered germination) with GO node grounding and biolink/RO predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 4 evidence-backed generic edges (3 new nodes) from the deep-research report, extending the downstream germination cascade (CaDPA release -> cortex hydrolysis -> core rehydration/outgrowth -> trait).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:15Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 4 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:causes\u00d72, RO:0002213\u00d71, RO:0002327\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 2 causal edge(s) off enables/RO:0002327 with a TRAIT object (2 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T01:15:00Z",
        "curator": "codex",
        "action": "ADD_EXACT_ONTOLOGY_MATCH",
        "changes": "Ontology exact-match review (2026-08-25): approved exact xref(s): GO:0009847. Evidence is predicate-scoped in the versioned ontology snapshots; OAK cross-checked direct data, and OLS4 spot-checked release deltas and disputed hits.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000730",
    "label": "stalk contraction",
    "definition": "A physiological phenotype in which a microbial cell actively reduces the end-to-end extension of its stalk.",
    "definition_source": "DOI:10.2142/biophysics.8.1",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000729"
    ],
    "evidence": [
      {
        "reference": "DOI:10.2142/biophysics.8.1",
        "snippet": "The stalk is straight at the initial stage. Then, it bends and coils into a helix near the zooid.",
        "notes": "Kamiguri et al. 2012, PMID:27857602, PMCID:PMC5070450, printed page 3, Results and Discussion first paragraph, left column. Direct contiguous PDF match with whitespace-only line-wrap normalization and actual typeset passage inspected; native NOT_IN_ABSTRACT retained. Junko Kamiguri is the first author; the running header says Hashimoto et al. Living source-named Vorticella sp. from activated sludge attached to glass rods was stimulated by hitting the dish; eight cells were observed at 6000 frames/s. Figures 3 and 5 show coiling and decreased end-to-end extension. The same paragraph says contour length does not change. All nine main-paper pages were inspected; raw videos were not reanalyzed. Model fits are not molecular proof. The primary PDF came from J-STAGE; an acquisition-helper failure left no original request timestamp or header receipt. Those missing fields are not reconstructed. Current taxonomic and culture identities remain unresolved."
      },
      {
        "reference": "DOI:10.1016/j.bpj.2012.07.038",
        "snippet": "The stalk contraction was stalled more as the fluid viscosity and/or flow rate increased.",
        "notes": "Ryu et al. 2012, PMID:23009835, PMCID:PMC3433611, printed page 862, Figure 2A caption, sentence beginning The stalk contraction. Direct contiguous PDF match and actual typeset passage inspected; native NOT_IN_ABSTRACT retained. The primary PDF was retrieved from the Vanderbilt Lang Lab mirror. Source-named Vorticella convallaria contracted in microfluidic channels under varied flow and viscosity. Four to five contractions per cell per condition are not independent cells. Figure 3 uses six cells; Figure 4C uses fifteen in a separate analysis. Isometric force is extrapolated through a hydrodynamic model, not directly measured zero-shortening force. All eight main-paper pages and actual Figures 1-5 were inspected; the supplement was not. Projection and geometry assumptions remain relevant. Some extracted micrometre symbols appear as mm; no such numeric extraction is quoted. Culture/taxonomy correspondence is unresolved. No universal rate, force, calcium threshold, ATP independence or protein mechanism follows."
      }
    ],
    "discussions": [
      {
        "discussion_id": "stalk-contraction-scope-and-parent",
        "prompt": "Review the stalk-extension endpoint and its projection-contraction parent.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "The measured endpoint is reduced end-to-end stalk extension, not necessarily reduced contour length. Coiling is observed, not a universal geometric requirement. Require active cellular contraction; static stalk morphology, reduced developmental growth, passive bending, detachment and isometric force alone do not establish it. Stalk-induced body displacement is not cell-body contraction traitmech:000728, and the endpoint differs from rapid axopodial contraction traitmech:000682. The direct parent is cell body or cytoplasmic projection contraction traitmech:000729, by definition-based inference. Amos's publisher abstract places the spasmoneme within cytoplasm and a sheath. The stalk is composite; its whole sheath is not asserted to be cytoplasm. Neither locomotion nor a universal ATP-driven motor is required by this parent choice. No exact synonym or organism-level disjointness is asserted.",
        "evidence": [
          {
            "reference": "DOI:10.1038/229127a0",
            "reference_title": "Reversible Mechanochemical Cycle in the Contraction of Vorticella",
            "supports": "NO_EVIDENCE",
            "evidence_source": "abstract",
            "snippet": "The coiling is produced by the contraction of an intracytoplasmic thread, the spasmoneme, within a cylindrical sheath.",
            "explanation": "Anatomical background for interpreting the parent, not an additional inspected experimental result or counted trait support. The curated hierarchy is an inference, not an ontology assertion made by this paper.",
            "notes": "Amos 1971, publisher Abstract second sentence, #Abs1-content. Direct issuing-publisher HTML match; DOI/title/author metadata checked. Native UNRESOLVED retained, not relabeled VERIFIED or unindexed. Full article and historical experiments were not inspected. No comprehensive notice clearance is claimed."
          }
        ],
        "posed_by": "codex",
        "posed_date": "2026-10-15"
      },
      {
        "discussion_id": "stalk-contraction-metpo-assessment",
        "prompt": "Review the proposed stalk-contraction class without reviving obsolete morphology.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Pinned and inspected current METPO release/editor/template owners contain no active exact contraction class in the bounded assessment. METPO:1000288 obsolete stalk is deprecated, under ObsoleteClass, with OMO:0001000 as its recorded reason and no replacement or consider annotation observed. It is a historical morphology label, not an active exact contraction phenotype; neither revive it nor put it in xrefs. The reason code alone does not invalidate the biology. v606 reserves METPO:1068300 in block 1068300-1068399 and repeats the unchanged v605 parent declaration METPO:1068200 so the standalone proposal emits the actual parent hierarchy. Historical v605 and the ontology pin remain unchanged. No external equivalence or SSSOM mapping is accepted; upstream adoption and human sign-off remain open.",
        "posed_by": "codex",
        "posed_date": "2026-10-15"
      },
      {
        "discussion_id": "stalk-contraction-provenance-and-mechanism",
        "prompt": "Resolve source isolates and endpoint-specific mechanisms before adding taxa or proteins.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Keep study organism names as qualified observations until culture provenance and current taxonomic identities are independently verified. Two distinct experimental papers support the endpoint; Part II of the Kamiguri study is not counted as independent replication. Preserve stimulus, load, viscosity, cell state, geometry, sampling and temporal resolution when comparing assays. Do not generalize calcium-wave models, spasmoneme chemistry, force estimates or energy claims to all microbial stalks. Protein sequence features alone cannot establish this phenotype. A protein-resolved causal graph needs authority-checked taxon-paired accessions and edge-specific experimental support. Mechanism is deferred, not asserted absent. MED/Crossref notice-field and limited publisher checks are not comprehensive correction/retraction clearance; failed retrievals and uninspected supplements remain explicit source-access limits.",
        "posed_by": "codex",
        "posed_date": "2026-10-15"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-15T03:51:31Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added stalk contraction as active reduction of end-to-end stalk extension with two primary DOI sources and directly checked 19/14-word excerpts. Retained native NOT_IN_ABSTRACT outcomes and separate 17-word anatomy context with native UNRESOLVED. Reserved 000730, v606 and 1068300-1068399 after ignored/hidden worktree, retained-history, full proposal-range and open/draft PR checks. Linked the existing parent's future lead without closing independent questions. No canonical taxon, exact mapping or universal protein mechanism inferred. Timestamp records observed acceptance.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000078",
    "label": "stress response",
    "definition": "A physiological program by which a cell senses and mounts a protective response to environmental or cellular stress, such as the RpoS-mediated general stress response of enteric bacteria.",
    "definition_source": "DOI:10.1146/annurev-micro-090110-102946",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "synonyms": [
      {
        "synonym_text": "general stress response",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1146/annurev-micro-090110-102946"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev-micro-090110-102946",
        "notes": "Battesti, Majdalani & Gottesman review the RpoS-mediated general stress response, a broad protective program induced by stress and stationary phase."
      },
      {
        "reference": "DOI:10.1038/nrmicro3032",
        "notes": "Imlay reviews molecular stress-defense mechanisms, exemplifying inducible protective responses; parent of the oxidative-stress-response sub-variant."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:562",
        "taxon_label": "Escherichia coli",
        "note": "general stress response (RpoS)",
        "reference": "PMID:38411096"
      },
      {
        "taxon_id": "NCBITaxon:1299",
        "taxon_label": "Deinococcus radiodurans",
        "note": "extreme stress resistance",
        "reference": "PMID:30339218"
      },
      {
        "taxon_id": "NCBITaxon:83333",
        "taxon_label": "Escherichia coli K-12",
        "note": "Strain-level general-stress model paired to the reviewed RpoS sigma factor.",
        "reference": "DOI:10.1073/pnas.90.8.3511"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "stress_response_induction",
        "title": "Stress-induced protective response",
        "description": "Evidence-backed causal sketch linking environmental stress to an induced, protective general stress response.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "This graph represents the enterobacterial stringent-response/RpoS/Hfq branch and is not universal across microbial taxa. The E. coli RpoS example anchors the sigma-S module; RSH is a heterogeneous enzyme superfamily and Hfq is a separate RNA-chaperone family.",
        "nodes": [
          {
            "node_id": "stress_response_trait",
            "label": "stress response",
            "node_type": "TRAIT",
            "grounding": "traitmech:000078",
            "description": "Capacity to mount a protective response to stress."
          },
          {
            "node_id": "environmental_stress",
            "label": "environmental stress",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Disturbance of cellular homeostasis."
          },
          {
            "node_id": "stress_response_process",
            "label": "response to stress",
            "node_type": "BIOLOGICAL_PROCESS",
            "grounding": "GO:0006950",
            "description": "Change in cell state triggered by a stressor."
          },
          {
            "node_id": "ppgpp",
            "label": "(p)ppGpp",
            "node_type": "CHEMICAL",
            "description": "Guanosine tetra/pentaphosphate alarmone of the stringent response."
          },
          {
            "node_id": "rsh_enzymes",
            "label": "RelA/SpoT homologue enzymes",
            "node_type": "GENE_OR_PROTEIN",
            "description": "RSH enzyme family that synthesizes and hydrolyzes (p)ppGpp.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "This umbrella combines long bifunctional Rel/SpoT homologues with small alarmone synthetase and hydrolase subfamilies; one family term would not preserve those catalytic distinctions."
          },
          {
            "node_id": "nutrient_limitation",
            "label": "nutrient limitation",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Limiting availability of nutrients that triggers stress signaling."
          },
          {
            "node_id": "ribosome_biosynthesis",
            "label": "ribosome biosynthesis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Synthesis of ribosomes and translation-associated growth machinery."
          },
          {
            "node_id": "stress_tolerance",
            "label": "stress tolerance",
            "node_type": "QUALITY",
            "description": "Capacity to tolerate environmental stress."
          },
          {
            "node_id": "rpos",
            "label": "RpoS (sigma S)",
            "node_type": "GENE_OR_PROTEIN",
            "description": "General-stress-response sigma factor (sigma S / sigma 38).",
            "grounding": "InterPro:IPR012761",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:P13445",
                "protein_label": "RNA polymerase sigma factor RpoS",
                "gene_symbol": "rpoS",
                "taxon_id": "NCBITaxon:83333",
                "taxon_label": "Escherichia coli K-12",
                "entry_status": "REVIEWED",
                "retrieved_on": "2026-10-22",
                "entry_version": 208,
                "sequence_version": 3,
                "role": "E. coli K-12 sigma-S factor directing stationary-phase and general-stress transcription; it anchors only this enterobacterial branch.",
                "evidence": [
                  {
                    "reference": "DOI:10.1073/pnas.90.8.3511",
                    "snippet": "the rpoS gene product, sigma 38, is a second principal sigma factor in stationary-phase Escherichia coli",
                    "notes": "The primary study identifies and functionally characterizes E. coli RpoS; UniProtKB P13445 is the reviewed K-12 entry."
                  }
                ]
              }
            ]
          },
          {
            "node_id": "general_stress_resistance",
            "label": "general stress resistance",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Broad protective resistance to multiple stresses."
          },
          {
            "node_id": "hfq",
            "label": "Hfq",
            "node_type": "GENE_OR_PROTEIN",
            "description": "RNA chaperone enabling sRNA-dependent translational regulation.",
            "grounding": "InterPro:IPR005001"
          }
        ],
        "edges": [
          {
            "subject": "environmental_stress",
            "predicate": "causes",
            "object": "stress_response_process",
            "description": "A stressor triggers the stress-response program.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-micro-090110-102946",
                "notes": "Battesti et al. review stress/stationary-phase induction of RpoS."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "stress_response_process",
            "predicate": "confers",
            "object": "stress_response_trait",
            "description": "The induced program realizes the stress-response trait.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro3032",
                "notes": "Imlay reviews inducible molecular stress defenses."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "rsh_enzymes",
            "predicate": "synthesizes/hydrolyzes",
            "object": "ppgpp",
            "description": "RSH enzymes synthesize and hydrolyze the (p)ppGpp alarmone.",
            "evidence": [
              {
                "reference": "DOI:10.1099/mic.0.001483",
                "notes": "(p)ppGpp is synthesized and hydrolysed by RelA-SpoT homologue (RSH) enzymes; broadly conserved in bacteria."
              }
            ]
          },
          {
            "subject": "nutrient_limitation",
            "predicate": "triggers",
            "object": "ppgpp",
            "description": "Nutrient-limiting conditions trigger a surge of (p)ppGpp.",
            "evidence": [
              {
                "reference": "DOI:10.1099/mic.0.001483",
                "notes": "Stringent response mediated by (p)ppGpp, whose intracellular surge is triggered by nutrient-limiting conditions."
              }
            ]
          },
          {
            "subject": "ppgpp",
            "predicate": "inhibits",
            "object": "ribosome_biosynthesis",
            "description": "(p)ppGpp inhibits ribosome biosynthesis, slowing growth.",
            "evidence": [
              {
                "reference": "DOI:10.1099/mic.0.001483",
                "notes": "(p)ppGpp inhibits ribosome biosynthesis, inducing a slow-growth phenotype."
              }
            ],
            "predicate_id": "RO:0002212"
          },
          {
            "subject": "ppgpp",
            "predicate": "enhances",
            "object": "stress_tolerance",
            "description": "Moderate (p)ppGpp induction enhances stress tolerance.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.isci.2024.108818",
                "notes": "Moderate induction of (p)ppGpp reduces growth rate while enhancing stress tolerance."
              }
            ]
          },
          {
            "subject": "ppgpp",
            "predicate": "positively regulates",
            "object": "rpos",
            "description": "(p)ppGpp positively regulates RpoS abundance/activity.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.isci.2024.108818",
                "notes": "(p)ppGpp positively regulates RpoS by transcriptional activation and by inhibiting RpoS proteolysis."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "rpos",
            "predicate": "induces",
            "object": "general_stress_resistance",
            "description": "RpoS-dependent gene expression induces general stress resistance.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-micro-090110-102946",
                "notes": "RpoS-dependent gene expression leads to general stress resistance of cells."
              }
            ]
          },
          {
            "subject": "hfq",
            "predicate": "promotes",
            "object": "rpos",
            "description": "Hfq is required for sRNA-dependent translation of RpoS, and so raises the amount of RpoS available.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mmbr.00151-22",
                "notes": "Hfq is needed for sRNA-dependent RpoS translation."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "general_stress_resistance",
            "predicate": "confers",
            "object": "stress_response_trait",
            "description": "General stress resistance realizes the stress-response trait.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev-micro-090110-102946",
                "notes": "RpoS-mediated general stress resistance is the protective program defining the trait."
              }
            ],
            "predicate_id": "METPO:2007700"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-06-04T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate PHYSIOLOGY axis class (stress response) to parent specific stress-response sub-variants.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-08T13:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (stress-induced protective response) with GO node grounding and biolink/RO predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 8 evidence-backed generic edges (8 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:15Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327\u00d72, RO:0002212\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-26T07:15:20Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A010TBV5\u00d71, UniProtKB:A0A3B9B147\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:21:12Z",
        "curator": "claude",
        "action": "RETRACT_DEAD_UNIPROT_GROUNDINGS",
        "changes": "Retracted 2 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-04T03:08:16Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002213\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 2 causal edge(s) off enables/RO:0002327 with a TRAIT object (2 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-07T18:00:00Z",
        "curator": "claude",
        "action": "REGROUND_CAUSAL_EDGE",
        "changes": "Edge hfq -> rpos in graph stress_response_induction: re-grounded it from enables/RO:0002327 to promotes/RO:0002213. Issue 334. biolink declares enables range 'biological process or activity', which of CausalNodeTypeEnum only BIOLOGICAL_PROCESS, PATHWAY and MOLECULAR_FUNCTION satisfy, so this edge entailed a false type on its object. 'Hfq enables sRNA-dependent TRANSLATION of RpoS' -- the object is the sigma factor, not the translation, so what the edge actually asserts about RpoS is that Hfq increases it. The graph already reads ppgpp -positively regulates-> rpos alongside it.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-24T13:25:00-07:00",
        "curator": "codex",
        "action": "REVIEWED_CAUSAL_GRAPH_PROTEIN_TAXON",
        "changes": "Marked the graph mechanistic and enterobacterial in scope, reviewed the heterogeneous RSH umbrella as label-only, grounded RpoS and Hfq to exact InterPro families, and added DOI-cited E. coli K-12 RpoS P13445.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-22T01:35:00Z",
        "curator": "claude",
        "action": "REFRESH_UNIPROT_ENTRY_VERSION",
        "changes": "Refreshed UniProtKB entry_version against live UniProt REST on 2026-10-22: UniProtKB:P13445 (207 -> 208 on rpos).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000615",
    "label": "tetrapolar mating system",
    "definition": "A fungal mating phenotype in which compatibility between partners is governed by two independently segregating mating-type factors and requires different specificities at both factors.",
    "definition_source": "DOI:10.1371/journal.pgen.1002528",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1371/journal.pgen.1002528",
        "snippet": "None of these MAT recombinant progeny mated with either parent, further confirming that C. amylolentus possesses a tetrapolar mating system",
        "notes": "Findley et al. (2012), PMID:22359516, PMC3280970. Exact Results s2g clause, not an abstract quote. The preceding sentences report interfertility of complementary recombinants; parent sterility alone is insufficient. Introduction defines the two unlinked factors and differences at both. Actual Figures 8/9 were inspected: sexual structures and the mating matrix support the functional phenotype. Figure 9A is a conceptual model, not an observed equal-ratio result. Results s2b/s2e, direct prose of s2f/s2g and Methods s4a/s4m were read. Mixed F1 progeny include blastospores; frequent infertility and biased mating types make this a modified tetrapolar cycle. Complete Text S1 was text-extracted, not page-rendered: filamentation is not successful mating. Its description of F1S2 #16 as sterile must not override s2g's successful crosses with some partners. Tables 1/2, other figures and other supplements remain uninspected. Physical MAT separation alone in T. wingfieldii does not establish its reproductive phenotype."
      },
      {
        "reference": "DOI:10.1534/genetics.115.177717",
        "snippet": "independent assortment of MAT alleles was observed in the meiotic progeny of a test cross.",
        "notes": "Maia et al. (2015), PMID:26178967, PMC4566278. Exact scientific abstract clause, directly retrieved from Europe PMC core metadata and checked against NCBI efetch front matter. Leucosporidium scottii has physically unlinked HD and P/R regions; the reported meiotic segregation supports functional tetrapolarity independently of sequence annotation. Natural population linkage disequilibrium does not contradict the test-cross result. The abstract reports fertile progeny of four mating types but approximately two thirds nonhaploid; do not impose universal haploidy or equal ratios. Full-text XML/PDF endpoints failed with HTTP 500/403 and NCBI returned no body. Methods, figures, supplements and natural strain provenance remain uninspected; no canonical example is inferred."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:104669",
        "taxon_label": "Cryptococcus amylolentus",
        "reference": "DOI:10.1371/journal.pgen.1002528",
        "note": "Qualified to the CBS6039 x CBS6273 cross, not every strain or laboratory-derived progeny. Natural provenance: Methods Strains and media at https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1002528 reports both isolates from insect frass in South Africa. Mating used V8 pH 5 in the dark at 24 C; actual Figure 8 shows two-week sexual structures and Figure 9 compares complementary mating combinations. Recombinant fertility, not hyphae alone, supports the modified tetrapolar classification. NCBI taxonomy 104669 resolves to this species on 2026-10-05."
      }
    ],
    "discussions": [
      {
        "discussion_id": "tetrapolar-mating-scope-and-hierarchy",
        "prompt": "Keep mating compatibility separate from partner dependence and MAT inventory.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "This is a functional compatibility phenotype, not possession of two loci or exactly four mating types throughout a species. Factors can be multiallelic; different specificities are necessary, not a guarantee of fertile progeny in every cross. Findley describes the observed C. amylolentus cycle as heterothallic, but that example does not make the broader compatibility axis equivalent to obligatory separate-partner dependence in traitmech:000610. The latter already separates nuclear recognition from organism-level self-fertility. Use released phenotype METPO:1000059 in both record and proposal rather than infer universal self-sterility. Do not assert disjointness with homothallism, fixed segregation ratios, universal A/B naming or identical recognition architectures. Resolve bifactorial terminology and external mappings before adding synonyms or xrefs. PHYSIOLOGY is a filesystem category, not a narrower ontology parent.",
        "posed_by": "codex",
        "posed_date": "2026-10-05"
      },
      {
        "discussion_id": "tetrapolar-mating-mechanism-and-readouts",
        "prompt": "Resolve native mechanisms and unread experiments before extending the graph.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Complete the unread Maia full text and Findley tables and supplements before finer mechanistic or strain claims. Distinguish MAT-locus separation, genetic segregation, compatibility, filamentation and fertile sexual progeny. An unsuccessful cross alone does not establish trait absence; source-specific sterility can be relative to particular partners. Resolve native protein accessions and experimentally tested dependencies before causal edges. No NONMECHANISTIC graph is used to bypass protein grounding. Manual full-text matches do not replace the abstract resolver's actual verdict.",
        "posed_by": "codex",
        "posed_date": "2026-10-05"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-05T07:16:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added tetrapolar mating system with two independent DOI-backed sources and verbatim snippets, a qualified natural CBS6039 x CBS6273 example and verified NCBI taxonomy. Kept mating evidence distinct from MAT sequence inventory, universal fertility and partner dependence. Ignored-and-hidden novelty and allocation searches found no exact record or ID collision. Reserved METPO:1056900 in v492 under released phenotype. Deferred lexical mappings, protein mechanisms and explicitly unread source material.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000580",
    "label": "thermotaxis",
    "definition": "A motile phenotype in which an organism biases its active movement in response to a temperature gradient.",
    "definition_source": "DOI:10.7554/eLife.26607",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000702"
    ],
    "evidence": [
      {
        "reference": "DOI:10.7554/eLife.26607",
        "snippet": "detect and follow environmental temperature gradients",
        "notes": "Paulick et al., Introduction; version 2, Version of Record dated 2017-08-31, https://cdn.elifesciences.org/articles/26607/elife-26607-v2.pdf. Figures 1-3 and their figure supplements distinguish behavioral gradients from FRET reporters and chemical adaptation. Temperature preference for movement is not a growth-temperature class."
      },
      {
        "reference": "DOI:10.1073/pnas.0709903105",
        "snippet": "responds to changes in temperature by modifying its motor behavior",
        "notes": "Paster and Ryu, Abstract and Results: thermal pulses changed tethered-cell motor bias. Their inversion temperatures are assay-specific, not universal trait thresholds. This assay measures motor output rather than spatial accumulation."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:83333",
        "taxon_label": "Escherichia coli K-12",
        "reference": "DOI:10.7554/eLife.26607",
        "note": "AW405, a K-12 derivative carrying a GFP marker, showed thermal migration in microfluidic gradients (Figures 1C and 2D-E; Methods: Strains and plasmids). It is not the engineered VS223 FRET reporter or the MG1655 growth assay."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "thermotaxis_tar_response",
        "title": "Tar-mediated control of thermal migration",
        "description": "A receptor-modification-dependent thermal response changes swimming bias and realizes thermotaxis.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "The E. coli Tar-mediated arm, not a universal microbial mechanism or a complete Tar/Tsr accumulation model. Engineered receptor experiments establish the Tar transitions. Interplay with Tsr and chemical adaptation changes the intact-cell response.",
        "nodes": [
          {
            "node_id": "thermotaxis_temperature_change",
            "label": "temperature change during movement",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Temporal thermal stimulus encountered in a spatial gradient."
          },
          {
            "node_id": "thermotaxis_tar_modification",
            "label": "Tar covalent modification state",
            "node_type": "STATE",
            "description": "Deamidation and methylation of Tar adaptation sites; unprocessed, unmethylated and heavily methylated forms differ."
          },
          {
            "node_id": "thermotaxis_tar_receptor",
            "label": "Tar aspartate chemoreceptor",
            "node_type": "GENE_OR_PROTEIN",
            "gene_symbols": [
              "tar"
            ],
            "description": "The full-length Tar receptor, including its thermal signaling role.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "InterPro IPR003122 resolves to a Tar-related ligand-binding domain, not the full receptor; IPR004090 covers the broader MCP family. Neither is an exact whole-Tar grounding. The reviewed K-12 protein remains an instance example.",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:P07017",
                "protein_label": "Methyl-accepting chemotaxis protein II",
                "gene_symbol": "tar",
                "taxon_id": "NCBITaxon:83333",
                "taxon_label": "Escherichia coli K-12",
                "entry_status": "REVIEWED",
                "retrieved_on": "2026-10-03",
                "entry_version": 208,
                "sequence_version": 2,
                "role": "Tar component of the K-12 thermal response; not the entire receptor array.",
                "evidence": [
                  {
                    "reference": "DOI:10.7554/eLife.26607",
                    "snippet": "both Tar- and Tsr-only cells exhibited thermophilic responses",
                    "notes": "Results, Figure 3A and Methods identify K-12 Tar-only receptor experiments; UniProt verifies protein identity."
                  }
                ]
              }
            ]
          },
          {
            "node_id": "thermotaxis_swimming_control",
            "label": "thermal control of run-and-tumble bias",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Receptor signaling changes smooth-swimming versus tumbling; this is not merely a change in swimming speed."
          },
          {
            "node_id": "thermotaxis_migration_process",
            "label": "thermotaxis",
            "node_type": "BIOLOGICAL_PROCESS",
            "grounding": "GO:0043052",
            "description": "Directed migration in response to a temperature gradient."
          },
          {
            "node_id": "thermotaxis_trait",
            "label": "thermotaxis",
            "node_type": "TRAIT",
            "grounding": "traitmech:000580",
            "description": "Organism-level disposition for temperature-guided active movement."
          }
        ],
        "edges": [
          {
            "subject": "thermotaxis_temperature_change",
            "predicate": "modulates",
            "predicate_id": "RO:0002211",
            "object": "thermotaxis_tar_receptor",
            "description": "Temperature changes elicit a Tar response when its modification state permits thermosensing.",
            "evidence": [
              {
                "reference": "DOI:10.1074/jbc.271.30.17932",
                "snippet": "Tar comes to function as a thermoreceptor",
                "notes": "Abstract: deamidation enables the thermal response; the primary translational product is not a thermoreceptor."
              }
            ]
          },
          {
            "subject": "thermotaxis_tar_modification",
            "predicate": "modulates",
            "predicate_id": "RO:0002211",
            "object": "thermotaxis_tar_receptor",
            "description": "Covalent modification changes the receptor's warm, cold or null response state.",
            "evidence": [
              {
                "reference": "DOI:10.1128/jb.179.21.6573-6580.1997",
                "snippet": "thermosensing function that is modulated by covalent modification of its four methylation sites",
                "notes": "Abstract: the mutational study distinguishes deamidation from methylation and tests receptor thermosensing, not a universal preferred temperature."
              }
            ]
          },
          {
            "subject": "thermotaxis_tar_receptor",
            "predicate": "regulates",
            "predicate_id": "RO:0002211",
            "object": "thermotaxis_swimming_control",
            "description": "Tar-mediated signaling changes swimming bias, with the response sign depending on receptor modification.",
            "evidence": [
              {
                "reference": "DOI:10.1074/jbc.271.30.17932",
                "snippet": "eliciting a smooth-swimming signal upon increase of temperature",
                "notes": "Abstract: this warm response applies to deamidated, unmethylated Tar; the heavily methylated form instead signals smooth swimming on cooling. Intermediate phosphorelay steps are compressed, not bypassed."
              }
            ]
          },
          {
            "subject": "thermotaxis_swimming_control",
            "predicate": "contributes to",
            "predicate_id": "RO:0002326",
            "object": "thermotaxis_migration_process",
            "description": "Temperature-dependent run-and-tumble statistics bias migration along a thermal gradient.",
            "evidence": [
              {
                "reference": "DOI:10.1073/pnas.0709903105",
                "snippet": "This stochastic strategy biases the cell's random walk",
                "notes": "Introduction: temporal temperature sensing biases runs and tumbles, giving net movement along spatial gradients. The separate motor assay is not itself a migration measurement."
              }
            ]
          },
          {
            "subject": "thermotaxis_migration_process",
            "predicate": "confers",
            "predicate_id": "METPO:2007700",
            "object": "thermotaxis_trait",
            "description": "Temperature-guided migration realizes the organismal thermotaxis phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.7554/eLife.26607",
                "snippet": "cells accumulated towards the warmer side of the gradient",
                "notes": "Results, Figure 1C: buffer-adapted swimming cells; chemical adaptation can alter the direction (Figure 2)."
              }
            ]
          }
        ]
      }
    ],
    "discussions": [
      {
        "discussion_id": "thermotaxis-context-and-mapping-boundaries",
        "prompt": "Resolve assay-dependent response inversion without imposing a universal temperature threshold.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "DOI:10.1073/pnas.0709903105 reports thermal-response inversion under its tethered-cell conditions. DOI:10.7554/eLife.26607 instead finds continued warm-seeking in buffer under flow; its Discussion suggests residual chemical stimulation as one explanation of earlier results, not a proven correction. Retain medium, adaptation, strain and assay context. Growth optima, passive thermophoresis and temperature-dependent speed alone do not establish thermotaxis. GO:0043052 is a biological process (QuickGO checked 2026-10-03), so it grounds the process node rather than an equivalent xref on the disposition. The Tar arm does not describe every thermotactic microbe.",
        "posed_by": "codex",
        "posed_date": "2026-10-03"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-03T22:20:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added thermotaxis with four primary DOI sources, exact snippets, a K-12 behavioral example and a Tar-mediated causal graph. Verified P07017, NCBITaxon:83333 and GO:0043052 at authorities. Ignored-and-hidden searches found no exact record or METPO term; reserved METPO:1053400 in proposal v457. Kept assay-dependent inversion separate from growth-temperature preference.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000594",
    "label": "thigmotropism",
    "definition": "A phenotype in which polarized growth is directionally reoriented in response to physical contact with surface topography.",
    "definition_source": "DOI:10.1080/02681219280000621",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1080/02681219280000621",
        "snippet": "The response was likely to be due to contact guidance (thigmotropism) and not chemotropism towards the nutrients",
        "notes": "Abstract, exact-matched at Europe PMC (PMID:1287165); full text not inspected. Candida albicans hyphae entered membrane pores after contacting their lips, including from the underside while growing away from nutrient agar. This supports the authors' contact-guidance interpretation, not exclusion of every chemical influence or proof of tissue invasion in vivo."
      },
      {
        "reference": "DOI:10.1099/00221287-144-3-689",
        "snippet": "both compounds reduced the percentage of hyphae reorienting on contact with a ridge without markedly affecting hyphal extension rate",
        "notes": "Abstract, exact-matched at Europe PMC (PMID:9534238); full text not inspected. The compounds are GdCl3 and verapamil at the tested low concentrations. Reorientation and extension rate are distinct readouts. Pharmacological attenuation and membrane channel recordings suggest channel involvement but do not identify a unique molecular mechanosensor."
      },
      {
        "reference": "DOI:10.1016/j.cub.2006.12.043",
        "snippet": "The establishment and maintenance of directional growth in relation to these environmental cues was Ca(2+) dependent.",
        "notes": "Abstract, exact-matched at Europe PMC (PMID:17275302). PMC1885950 full text distinguishes contact-dependent thigmotropism from electric-field galvanotropism. In the reported ridge assays, channel-component mutations reduced reorientation without reducing hyphal extension rates. Calcineurin was required for cathodal emergence but not thigmotropism; do not transfer that pathway requirement between the two responses. Localized channel activation and calcium influx remain a proposed model, not a universal mechanism established in every microbe. Supplement not inspected."
      },
      {
        "reference": "DOI:10.1111/cmi.12369",
        "snippet": "In vitro, hyphal tips reorient thigmotropically on contact with small obstacles.",
        "notes": "Abstract, exact-matched at Europe PMC (PMID:25262778). PMC4371639 full text, Fig. 6 and supplementary Table S1 were inspected. Adhesion or friction sufficient to oppose forward growth supported acute tip reorientation; less constrained hyphae instead bent subapically. Tip contact alone was insufficient in these assays. Table S1 lists CAI4/CIp10, BWP17 and engineered derivatives, including fluorescent reporters and an rsr1 deletion; the paper's wild-type designation is not proof of natural strain provenance. Spitzenkorper position correlated with growth but was not an absolute predictor. Force magnitudes are not curated because main-text and supplementary Fig. S2 units disagree. Movies were not inspected."
      }
    ],
    "discussions": [
      {
        "discussion_id": "thigmotropism-growth-and-contact-boundaries",
        "prompt": "Keep contact-directed growth distinct from locomotion and passive bending.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Polarized growth reorientation is not whole-cell locomotion, so the parent is phenotype, not motile. Filament shape alone does not imply contact sensitivity, and the existing mycelial-growth record is explicitly bacterial. Do not equate this trait with thigmotaxis, stiffness-gradient migration, electric-field growth, generic adhesion or contact-induced differentiation. Passive bending, growth rate changes and incidental alignment alone are insufficient. The fungal observations do not demonstrate a universal mechanosensor or establish tissue invasion in vivo. External equivalences and lexical variants need separate authority and scope checks.",
        "posed_by": "codex",
        "posed_date": "2026-10-04"
      },
      {
        "discussion_id": "thigmotropism-strain-and-mechanism-grounding",
        "prompt": "Resolve natural strain provenance and protein-level mechanism evidence.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Retain the reported Candida albicans observations as qualified evidence. The inspected strain table includes engineered backgrounds and fluorescent reporters; verify direct measurements in naturally occurring strains and NCBI identities before adding canonical examples. Resolve taxon-paired protein accessions and distinguish channel deletion evidence from inhibitor specificity and proposed localized calcium signals before adding a causal graph. Keep calcineurin's galvanotropic role separate from the reported thigmotropic response. Rsr1-dependent polarity positioning does not make Spitzenkorper position an absolute predictor of growth direction. Inspect remaining full texts and supplements before strengthening these claims; no NONMECHANISTIC graph should bypass missing protein or taxon grounding.",
        "posed_by": "codex",
        "posed_date": "2026-10-04"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-04T10:24:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added thigmotropism with four primary DOI citations and exact abstract snippets. Ignored-and-hidden novelty searches and structured OWL review found no exact record or METPO term. Reserved METPO:1054800 in v471. Distinguished contact-directed polarized growth from locomotion and passive bending. Inspected two full texts plus the Thomson Fig. 6 and supplementary strain table. Deferred natural canonical examples and accession-level mechanism grounding; did not infer them from engineered strains.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000685",
    "label": "toxicyst discharge",
    "definition": "A physiological phenotype in which a microbial cell releases material from toxicysts, its offensive extrusomes, to the cell exterior.",
    "definition_source": "DOI:10.1111/jeu.12106",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1111/jeu.12106",
        "snippet": "we isolated the discharge of the toxicysts from living cells",
        "notes": "PMID:24512001. Scientific Abstract read directly in PubMed and Europe PMC (EXT_ID:24512001 AND SRC:MED); source, title and DOI agree. Coleps hirtus discharge was collected and tested against other ciliates. This supports extracellular release from living cells, not merely possession of an organelle or toxicity of a whole-cell extract. Abstract-only access: full Methods and figures were not inspected; the institutional postprint at https://hdl.handle.net/11393/192287 is access-restricted. The reported chemical mixture is not a universal toxicyst cargo."
      },
      {
        "reference": "DOI:10.1007/BF01279249",
        "snippet": "Injection of Ca2+ evoked discharge of toxicysts, if the site of the injection was the periphery region of the proboscis.",
        "notes": "Scientific Summary read directly on the publisher page; Ca2+ represents its rendered superscript charge. Methods, Results and captions also read in the author-upload full-text transcript at https://www.researchgate.net/publication/227062328_Ca2_triggers_toxicyst_discharge_in_Didinium_nasutum. Figures were not visually inspected. Didinium nasutum pressure injection near the proboscis periphery produced discharge in 8/11 cells versus 1/11 calcium-free controls; cell-body and central-proboscis injections did not. Iontophoretic injection caused damage and cytoplasm outflow, motivating pressure injection. These are assay-specific observations, not a universal calcium requirement or proof of a particular fusion protein. No PMID was resolved by the exact DOI query."
      },
      {
        "reference": "DOI:10.1186/s12915-024-01904-2",
        "snippet": "However, our understanding of the genetic processes and specific toxins involved in toxicyst formation and discharge is still limited.",
        "notes": "PMID:38715037, PMC11077807. Scientific Abstract, Background, morphology Results, Discussion and collection/TEM Methods read in primary HTML/fullTextXML. Figure 1 was visually inspected: A-C are drawings, whereas D-F are TEM images of fixed Litonotus. The drawing of discharge is not direct imaging of release. Sequence and expression associations motivate toxin/transport hypotheses, not experimentally resolved discharge mechanisms. Genomics supplements were not inspected and are not used for accessions, prevalence or functional assignments."
      }
    ],
    "discussions": [
      {
        "discussion_id": "toxicyst-discharge-scope-and-parent",
        "prompt": "Resolve the exocytosis hierarchy without equating all extrusome types.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Parent phenotype METPO:1000059 is conservative. The 2024 Background describes telescopic discharge and/or membrane fusion; its Discussion reports fusion observations. These statements do not establish that every toxicyst-discharge phenotype satisfies the fusion-pore definition of exocytosis traitmech:000637. That placement remains unresolved, not excluded. Mere toxicyst possession, docking, predation, prey injury or cell lysis does not alone establish this trait. Preserve the organelle-specific scope rather than equating mucocyst discharge traitmech:000684, trichocyst discharge traitmech:000683, pexicysts or haptocysts. Historical type-I/II terminology needs reconciliation before synonym or hierarchy expansion. No exact synonyms, xrefs or organism-level disjointness are asserted. Prey killing and complete emptying are not universal defining requirements.",
        "posed_by": "codex",
        "posed_date": "2026-10-08"
      },
      {
        "discussion_id": "toxicyst-discharge-provenance-and-mechanism",
        "prompt": "Resolve experimental culture provenance and protein-level mechanisms.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Natural provenance and strain-level taxonomy of the positive experimental cultures remain unchecked; no canonical examples are assigned. Wild-collected genomic material is not by itself a positive discharge assay for that isolate. Gene-family expansion, expression and predicted toxin annotations alone do not establish toxicyst discharge or a causal protein. A future graph needs source-specific perturbations and taxon-paired accessions, distinguishing assembly, triggering, extrusion and toxin action. Mechanism is deferred, not claimed absent. Do not transfer a calcium threshold, cargo chemistry or ecological function between species without evidence.",
        "posed_by": "codex",
        "posed_date": "2026-10-08"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-08T18:21:12Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added toxicyst discharge with three primary DOI sources and directly checked abstract/Summary snippets. Ignored-and-hidden main/worktree/open-PR checks support 000685 and v561 block 1063800-1063899. Retained phenotype parent while making the exocytosis placement explicit and unresolved. Distinguished discharge from damage, organelle possession and sequence-based predictions. Existing records unchanged. Timestamp is observed UTC.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000683",
    "label": "trichocyst discharge",
    "definition": "An exocytotic phenotype in which a microbial cell releases trichocyst contents to the exterior through fusion of a trichocyst membrane with the plasma membrane.",
    "definition_source": "DOI:10.1083/jcb.111.6.2527",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "traitmech:000637"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1083/jcb.111.6.2527",
        "snippet": "A Paramecium possesses secretory organelles called trichocysts which are docked beneath the plasma membrane awaiting an external stimulus that triggers their exocytosis.",
        "notes": "PMID:1703537, PMC2116420. Scientific Abstract and relevant Methods/Results OCR read directly in Europe PMC fullTextXML. The snippet is from the scientific Abstract; figures were not inspected. AED-triggered release was studied in Paramecium tetraurelia stock d4-2, a stock 51 derivative, and mutants. Calcium influx and concentration requirements concern this assay, not a universal discharge threshold or proven channel identity. The Methods distinguish low-calcium membrane injury from secretion; calcium influx alone does not demonstrate release."
      },
      {
        "reference": "DOI:10.1016/s0143-4160(98)90030-6",
        "snippet": "but only wt cells release trichocysts (t).",
        "notes": "PMID:9681197. Primary PDF at https://d-nb.info/1107191386/34, Figures 1-4 caption, printed page 351. Pages 351-352 were visually inspected, including paired fluorescence/transmitted-light panels and Table 1. Wildtype Paramecium caudatum releases trichocysts after local AED or caffeine stimulation; tnd1 shows calcium transients and membrane fusion without contents release. Most trichocysts remain in wildtype cells during the illustrated local response, so total emptying is not required. Mutant tnd1 is boundary evidence, not a positive discharge exemplar. Reduced calcium binding is a proposed explanation, not a proven protein lesion. Natural strain provenance is unresolved."
      },
      {
        "reference": "DOI:10.1016/0143-4160(93)90065-e",
        "snippet": "trichocyst contents were slowly extruded",
        "notes": "PMID:7684653. Scientific Abstract retrieved directly using an exact quoted DOI query in Europe PMC. Abstract-only access; full Methods and figures were not inspected. Slow extrusion under AED and low-calcium conditions shows why rapid expansion is not mandatory in this definition. The abstract distinguishes fusion, contents release and resealing; prolonged calcium removal is followed by cell death. Do not infer calcium irrelevance to all stages or treat terminal damage as secretion."
      }
    ],
    "discussions": [
      {
        "discussion_id": "trichocyst-discharge-scope-and-assays",
        "prompt": "Keep cargo release distinct from organelle presence and component steps.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Exocytosis traitmech:000637 is the broader parent; the proposal depends on its v513 placeholder METPO:1059000. Trichocyst formation, docking, fusion without cargo release and isolated matrix expansion do not alone establish completed discharge. Lysis and preparation artifacts must be excluded from positive assays. Neither rapid extrusion, total emptying nor a shared calcium threshold defines this class. The existing myzocytosis record's warning about fixation-associated discharge and uncertain prey capture is not resolved by these secretion experiments. No exact synonyms, xrefs, SSSOM equivalents or universal prey-capture role are asserted.",
        "posed_by": "codex",
        "posed_date": "2026-10-08"
      },
      {
        "discussion_id": "trichocyst-discharge-provenance-and-mechanism",
        "prompt": "Resolve natural culture provenance and taxon-specific release mechanisms.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "These experiments support a secretion phenotype in source-named Paramecium systems, not every protist bearing an extrusome. Natural culture provenance and strain-level taxonomy remain unchecked, so no canonical examples are assigned. A wildtype designation alone does not establish natural provenance; a mutant designation alone does not establish engineering. Keep assay-specific calcium observations separate and obtain direct functional evidence with taxon-paired accessions before adding a protein-resolved graph. Mechanism is deferred, not claimed absent; sequence features alone do not establish discharge.",
        "posed_by": "codex",
        "posed_date": "2026-10-08"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-08T16:03:03Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added trichocyst discharge with three primary DOI sources and directly checked abstract/caption snippets. Ignored-and-hidden main/worktree/open-PR checks support 000683 and v559 block 1063600-1063699. Used existing exocytosis parent and its v513 proposal dependency. Kept calcium conditions, fusion-only mutants, slow extrusion and provenance qualified; deferred protein mechanism. Existing records unchanged. Timestamp is observed UTC.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000618",
    "label": "tripolar mating system",
    "definition": "A fungal mating-system phenotype in which sexual reproduction occurs between a partner with pheromone/receptor and homeodomain determinants linked in one mating-type region and a partner with those determinants in two unlinked regions.",
    "definition_source": "DOI:10.1128/ec.00271-08",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1128/ec.00271-08",
        "snippet": "one of the parents has one contiguous MAT locus (one pole) while the other has two unlinked sex-determining regions (two poles).",
        "notes": "Hsueh et al. (2008), PMID:18723606, PMC2568056. Exact clause in the first tripolar-cross Results subsection, checked against raw PMC HTML; not an abstract quote. Engineered Cryptococcus neoformans strains relocate a homeodomain determinant from MAT to unlinked URA5. Reciprocal crosses with wild-type partners yielded germinating, segregating progeny (Tables 2/3). Actual Figures 1/2 were inspected: Figure 1 shows colony-edge filamentation, whereas Figure 2 is a genotype model, not an observed segregation ratio. Methods, relevant Results and Discussion were read; other actual figures and supplements remain uninspected. These engineered crosses establish functional feasibility, not natural prevalence or a proven ancestral intermediate. The theoretical fertility fractions are not universal measured rates; JF289 also carries multiple SXI2a copies."
      },
      {
        "reference": "DOI:10.1128/mbio.00059-26",
        "snippet": "the MAT-fused strains were able to successfully mate with the strains in which the P/R and HD are unlinked, constituting a \u201ctripolar\u201d mating.",
        "notes": "Xiong et al. (2026), PMID:41841731, PMC13059729. Exact Results s2-2 clause checked against raw Europe PMC full-text XML; not a scientific-abstract or IMPORTANCE quote. In Cryptococcus amylolentus, engineered MAT-fused derivatives of CBS6039 or CBS6273 mate with an opposite wild-type partner retaining unlinked P/R and HD loci. Results s2-2 reports sexual structures and genotyped germinating progeny; s2-4 reports genome-wide meiotic recombination in 26 tripolar progeny, within a 42-progeny analysis also containing bipolar progeny. Relevant construction, mating and sequencing Methods were read. Figure 2/4 captions were read, but actual figures and supplements remain uninspected after image access failed. Other source sections remain unread. Reduced fusion in bilateral MAT-fused bipolar crosses must not be transferred to these unilateral tripolar crosses."
      }
    ],
    "discussions": [
      {
        "discussion_id": "tripolar-mating-scope-and-hierarchy",
        "prompt": "Keep the cross-level mating phenotype distinct from sequence inventory.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "The unit is a mating system or cross with differently organized partners, not a standalone locus or a species-wide assertion about either parental strain. Three poles across the pair do not mean three mating types or three independent factors in each genome. This differs from the uniform single-factor and two-factor systems in traitmech:000616 and traitmech:000615, and from recombination-permitting chromosomal colocation in traitmech:000617. Heterothallic source framing does not make this a universal separate-partner dependence subclass of traitmech:000610; progeny can differ in self-fertility. Use released phenotype METPO:1000059 in record and proposal pending narrower relational-phenotype hierarchy review. PHYSIOLOGY is a filesystem category. No disjointness, fixed fertility ratio, natural prevalence or mandatory evolutionary trajectory is asserted. Resolve lexical and external equivalences before synonyms or xrefs.",
        "posed_by": "codex",
        "posed_date": "2026-10-05"
      },
      {
        "discussion_id": "tripolar-mating-evidence-and-mechanism",
        "prompt": "Resolve natural examples and source-bounded mechanisms before extension.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Both primary studies use engineered partners, so no natural canonical taxon is inferred. Keep genotype, filamentation, spore germination, meiotic segregation and subsequent mating ability separate. The two studies report different self-fertility outcomes for progeny carrying compatible homeodomain determinants; retain strain background and copy-number context rather than generalize sterility. Inspect unread figures, supplements and source sections before more detailed claims or quantitative rates. Resolve native protein accessions and experimentally tested dependencies before causal edges; no NONMECHANISTIC graph bypasses grounding. Manual full-text snippet matches remain distinct from the abstract resolver's actual verdicts.",
        "posed_by": "codex",
        "posed_date": "2026-10-05"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-05T10:50:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added tripolar mating system with two primary DOI-backed sources and verbatim full-text clauses. Kept the cross-level functional phenotype distinct from sequence inventory, natural prevalence and fixed fertility ratios. Ignored-and-hidden novelty and allocation searches found no exact record or ID collision. Reserved METPO:1057200 in v495 under released phenotype. Deferred canonical taxa, lexical mappings and protein graphs, with engineered provenance and unread source material explicit.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000633",
    "label": "trogocytosis",
    "definition": "A physiological phenotype in which a microbial organism removes and takes up discrete portions of another living cell during direct contact instead of engulfing that cell whole.",
    "definition_source": "DOI:10.1038/nature13242",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1038/nature13242",
        "snippet": "amoebae kill by ingesting distinct pieces of living human cells",
        "notes": "PMID:24717428, PMC4006097. Direct scientific Abstract quote from the final Nature/PubMed version, not the differently worded PMC author-manuscript Summary. Author-manuscript Results and Discussion, relevant imaging and cell-culture Methods, and actual Figures 1-2 were inspected at https://pmc.ncbi.nlm.nih.gov/articles/PMC4006097/. Uptake precedes target-cell death; attachment alone is not uptake. Internalization and fragmentation gates are distinct measurements. Other figures and movies were not visually audited. No universal killing threshold, nutritional benefit or complete protein mechanism is inferred."
      },
      {
        "reference": "DOI:10.1128/mBio.00068-19",
        "snippet": "Protection from human serum occurs only after amoebae have undergone trogocytosis of live cells but not phagocytosis of dead cells.",
        "notes": "PMID:31040235, PMC6495370. Direct scientific Abstract quote, not the separate Importance/precis block. Cell-culture Methods, membrane-display and live/dead-cell Results, Discussion, and actual Figures 1, 6 and 8 were inspected at https://pmc.ncbi.nlm.nih.gov/articles/PMC6495370/. Figure 6B measures the percentage of internalizing amoebae, not material mass per cell. Figure 8 is a proposed model, not direct proof of a membrane-fusion or trafficking route. Other figures and supplements were not visually audited. Serum protection is condition-specific, not definitional."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:5759",
        "taxon_label": "Entamoeba histolytica",
        "reference": "DOI:10.1128/mBio.00068-19",
        "note": "Strain-qualified HM1:IMSS parental trophozoites interacting with live Jurkat cells in the 2019 study, not engineered knockdowns, vector controls or every isolate. Cell-culture Methods name ATCC as the supplier, without a catalog or lot number. The matching HM-1:IMSS collection record at https://www.atcc.org/products/30459 documents natural clinical isolation from a colonic biopsy; it does not establish an exact study lot or clone. NCBI ESearch/EFetch verified the scientific name and species rank on 2026-10-06. This taxon ID is species-level, not strain-level."
      }
    ],
    "discussions": [
      {
        "discussion_id": "trogocytosis-scope-and-hierarchy",
        "prompt": "Keep cell nibbling distinct from nutrition and whole-cell uptake.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "This record concerns the microbe as the nibbling organism, not host immune-cell attack on a microbe. Retain phenotype METPO:1000059 pending a closer uptake hierarchy. Local phagocytosis traitmech:000627 covers particle enclosure and internalization; phagotrophy traitmech:000628 requires nutrient assimilation. Myzocytosis traitmech:000631 denotes prey-content aspiration through a localized connection, and pallium feeding traitmech:000632 involves an enveloping feeding veil. None is asserted equivalent or disjoint at organism level. The existing myzocytosis contrast is not an unresolved exact trogocytosis node. Neither nutrition, killing, serum protection, a human target nor a fixed fragment size is a class requirement. Free-particle uptake or attachment alone is insufficient. No unverified synonym or process-level xref is asserted.",
        "posed_by": "codex",
        "posed_date": "2026-10-06"
      },
      {
        "discussion_id": "trogocytosis-native-mechanism",
        "prompt": "Resolve native molecular mechanisms without universalizing dependencies.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "The two papers are distinct experiments from an overlapping research group, not independent taxon replication. Perturbation, localization and sequence similarity are different evidence types. Neither a conceptual model nor a homologous sequence establishes a universal pathway. Inspect the remaining figures and obtain taxon-paired functional and accession evidence before adding protein examples or a causal graph.",
        "posed_by": "codex",
        "posed_date": "2026-10-06"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-06T03:16:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added trogocytosis with two DOI-backed scientific-abstract snippets and an HM1:IMSS-qualified example. Ignored-and-hidden novelty searches and pinned METPO review found no exact record. Reserved METPO:1058600 in v509. Kept nutrition, killing and serum protection out of the definition and deferred unsupported protein mechanisms.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000631",
    "label": "trophic type",
    "definition": "A phenotype that is describing how an organism obtains carbon, energy, and electron donors for growth and metabolism.",
    "definition_source": "DOI:10.1146/annurev.micro.61.080706.093130",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "synonyms": [
      {
        "synonym_text": "Physiology and metabolism.nutrition type.type",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "nutritional type",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      },
      {
        "synonym_text": "pathways",
        "synonym_type": "RELATED_SYNONYM",
        "source": "metpo.owl"
      }
    ],
    "created_by": "Luke Wang",
    "evidence": [
      {
        "reference": "DOI:10.1146/annurev.micro.61.080706.093130",
        "snippet": "carbon source, energy source, and electron donor",
        "notes": "Microbial physiology review frames trophic type as the joint classification by carbon, energy, and electron-donor source."
      },
      {
        "reference": "DOI:10.1073/pnas.0903507106",
        "snippet": "molecular mechanisms of adaptation",
        "notes": "Comparative genomics supports the classification of bacteria by trophic strategy from genome-encoded pathways."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:562",
        "taxon_label": "Escherichia coli",
        "reference": "PMID:9278503",
        "note": "Escherichia coli exemplifies chemoorganoheterotrophy, one concrete combination of chemical energy, organic electron donors, and organic carbon within the broad trophic-type class."
      },
      {
        "taxon_id": "NCBITaxon:1148",
        "taxon_label": "Synechocystis sp. PCC 6803",
        "reference": "DOI:10.3390/md11082894",
        "note": "Synechocystis sp. PCC 6803 exemplifies oxygenic photoautotrophy, a contrasting light-energy and inorganic-carbon branch of the broad trophic-type class."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "trophic_type_classification_axes",
        "title": "Trophic type classification axes",
        "description": "DOI-backed graph linking the three classification axes (carbon source, energy source, electron donor) to the metabolic pathways an organism encodes, which jointly determine its trophic type.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This graph is an ontology and classification scaffold organizing carbon-source, energy-source, and electron-donor axes. The child trophic traits and pathway examples carry the specific biological mechanisms, so a canonical taxon and taxon-paired protein example would be artificial here.",
        "nodes": [
          {
            "node_id": "trophic_type_trait",
            "label": "trophic type",
            "node_type": "TRAIT",
            "grounding": "METPO:1000631",
            "description": "Classification of how an organism obtains carbon and energy."
          },
          {
            "node_id": "carbon_source_use",
            "label": "carbon source utilization",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Use of inorganic (CO2) or organic carbon for biosynthesis."
          },
          {
            "node_id": "energy_source_use",
            "label": "energy source utilization",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Use of light (phototrophy) or chemical (chemotrophy) energy."
          },
          {
            "node_id": "electron_donor_use",
            "label": "electron donor utilization",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Use of inorganic (lithotrophy) or organic (organotrophy) electron donors."
          },
          {
            "node_id": "encoded_metabolic_pathways",
            "label": "encoded metabolic pathways",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "The set of biosynthetic, energy-conserving, and electron-transfer pathways present in the genome."
          },
          {
            "node_id": "autotrophic_phenotype",
            "label": "autotrophic",
            "node_type": "TRAIT",
            "grounding": "METPO:1000632",
            "description": "CO2-fixing trophic phenotype."
          },
          {
            "node_id": "heterotrophic_phenotype",
            "label": "heterotrophic",
            "node_type": "TRAIT",
            "grounding": "METPO:1000644",
            "description": "Organic-carbon-utilizing trophic phenotype."
          },
          {
            "node_id": "phototrophic_phenotype",
            "label": "phototrophic",
            "node_type": "TRAIT",
            "grounding": "METPO:1000660",
            "description": "Light-driven energy-acquisition trophic phenotype."
          },
          {
            "node_id": "chemotrophic_phenotype",
            "label": "chemotrophic",
            "node_type": "TRAIT",
            "grounding": "METPO:1000641",
            "description": "Chemical-energy-driven trophic phenotype."
          },
          {
            "node_id": "cbb_cycle_rubisco",
            "label": "Calvin-Benson-Bassham cycle (RuBisCO)",
            "node_type": "PATHWAY",
            "description": "CO2-fixation pathway encoded by rbcL/cbbM RuBisCO and full CBB cycle genes."
          },
          {
            "node_id": "co2_fixation",
            "label": "CO2 fixation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Assimilation of inorganic carbon (CO2) into biomass, the basis of autotrophic carbon use."
          },
          {
            "node_id": "sox_sulfur_oxidation",
            "label": "SOX sulfur/thiosulfate oxidation",
            "node_type": "PATHWAY",
            "description": "Oxidation of thiosulfate/sulfur species via the soxABXYZ/soxCD system as an inorganic electron-donor source."
          },
          {
            "node_id": "sugar_uptake_cazyme_catabolism",
            "label": "sugar/polysaccharide uptake and CAZyme catabolism",
            "node_type": "PATHWAY",
            "description": "Heterotrophic uptake (e.g. gtsABC, frcABC) and CAZyme-mediated degradation of sugars and polysaccharides for organic-carbon use."
          },
          {
            "node_id": "nife_hydrogenase_h2_oxidation",
            "label": "[NiFe]-hydrogenase H2 oxidation",
            "node_type": "PATHWAY",
            "description": "Oxidation of molecular hydrogen by [NiFe]-hydrogenases as an inorganic electron donor (hydrogen lithotrophy)."
          }
        ],
        "edges": [
          {
            "subject": "carbon_source_use",
            "predicate": "causes",
            "object": "trophic_type_trait",
            "description": "Carbon-source utilization defines the auto/heterotrophy axis of the trophic classification.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev.micro.61.080706.093130",
                "snippet": "carbon source",
                "notes": "Supports carbon-source utilization as a primary trophic-type axis."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "energy_source_use",
            "predicate": "causes",
            "object": "trophic_type_trait",
            "description": "Energy-source utilization defines the photo/chemotrophy axis of the trophic classification.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev.micro.61.080706.093130",
                "snippet": "energy source",
                "notes": "Supports energy-source utilization as a primary trophic-type axis."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "electron_donor_use",
            "predicate": "causes",
            "object": "trophic_type_trait",
            "description": "Electron-donor utilization defines the litho/organotrophy axis of the trophic classification.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev.micro.61.080706.093130",
                "snippet": "electron donor",
                "notes": "Supports electron-donor utilization as a primary trophic-type axis."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "encoded_metabolic_pathways",
            "predicate": "realizes",
            "object": "trophic_type_trait",
            "description": "The genome-encoded set of carbon-fixation, energy-conserving, and electron-transfer pathways realizes the organism's trophic type.",
            "evidence": [
              {
                "reference": "DOI:10.1073/pnas.0903507106",
                "snippet": "molecular mechanisms of adaptation",
                "notes": "Supports genome-encoded pathway repertoires as the proximate determinant of trophic phenotypes."
              }
            ]
          },
          {
            "subject": "autotrophic_phenotype",
            "predicate": "is a",
            "object": "trophic_type_trait",
            "description": "Autotrophy is a child phenotype of trophic type.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev.micro.61.080706.093130",
                "snippet": "carbon source",
                "notes": "Supports autotrophy as one carbon-source-defined trophic phenotype."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "heterotrophic_phenotype",
            "predicate": "is a",
            "object": "trophic_type_trait",
            "description": "Heterotrophy is a child phenotype of trophic type.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev.micro.61.080706.093130",
                "snippet": "carbon source",
                "notes": "Supports heterotrophy as one carbon-source-defined trophic phenotype."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "phototrophic_phenotype",
            "predicate": "is a",
            "object": "trophic_type_trait",
            "description": "Phototrophy is a child phenotype of trophic type.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev.micro.61.080706.093130",
                "snippet": "energy source",
                "notes": "Supports phototrophy as one energy-source-defined trophic phenotype."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "chemotrophic_phenotype",
            "predicate": "is a",
            "object": "trophic_type_trait",
            "description": "Chemotrophy is a child phenotype of trophic type.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev.micro.61.080706.093130",
                "snippet": "energy source",
                "notes": "Supports chemotrophy as one energy-source-defined trophic phenotype."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "cbb_cycle_rubisco",
            "predicate": "enables",
            "object": "co2_fixation",
            "description": "Form II RuBisCO and a full Calvin-Benson-Bassham cycle enable CO2 fixation, marking autotrophic carbon-assimilation potential.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.00599-24",
                "notes": "All MAGs encode Form II RuBisCO (rbcL/cbbM) and a full CBB cycle, indicating CO2 fixation potential."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "co2_fixation",
            "predicate": "causes",
            "object": "carbon_source_use",
            "description": "CO2 fixation establishes inorganic-carbon (autotrophic) use on the carbon-source axis of trophic type.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.00599-24",
                "notes": "CBB-driven CO2 fixation defines autotrophic carbon assimilation on the carbon-source classification axis."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "sox_sulfur_oxidation",
            "predicate": "causes",
            "object": "electron_donor_use",
            "description": "SOX-mediated thiosulfate/sulfur oxidation supplies inorganic electron donors, defining lithotrophy on the electron-donor axis.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.00599-24",
                "notes": "Presence of soxABXYZ (and soxCD) is tied to thiosulfate oxidation, enabling use of sulfur species as electron donors."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "sugar_uptake_cazyme_catabolism",
            "predicate": "causes",
            "object": "carbon_source_use",
            "description": "Sugar transporters and CAZyme catabolism enable heterotrophic/organotrophic use of organic carbon on the carbon-source axis.",
            "evidence": [
              {
                "reference": "DOI:10.1128/AEM.00599-24",
                "notes": "Sugar transporters (gtsABC, frcABC), maltodextrin import/degradation and CAZy enzymes indicate capacity for heterotrophic use of sugars and polysaccharides."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "nife_hydrogenase_h2_oxidation",
            "predicate": "causes",
            "object": "electron_donor_use",
            "description": "[NiFe]-hydrogenase H2 oxidation supplies an inorganic electron donor, contributing hydrogen lithotrophy to the electron-donor axis.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mSystems.00148-24",
                "notes": "Hydrogenase genes link hydrogen-based lithotrophy to chemoautotrophic metabolism."
              }
            ],
            "predicate_id": "biolink:causes"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.866871+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-11T22:00:00-07:00",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added DOI-backed causal graph framing trophic type by its three classification axes (carbon source, energy source, electron donor) and child phenotypes (autotroph, heterotroph, phototroph, chemotroph).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:32Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 4 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (rdfs:subClassOf\u00d74).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-26T05:00:48Z",
        "curator": "claude",
        "action": "RENAME_PREDICATE_LABELS",
        "changes": "Renamed 3 causal-edge predicate label(s) to align with existing groundings: determines \u2192 causes \u00d73.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-26T05:00:51Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:causes\u00d73).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 5 evidence-backed generic edges (5 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:15Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 5 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:causes\u00d74, RO:0002327\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-24T12:40:00-07:00",
        "curator": "codex",
        "action": "REVIEWED_CAUSAL_GRAPH_PROTEIN_TAXON",
        "changes": "Classified the retained trophic-type graph as a nonmechanistic classification scaffold; preserved the trait, graph, identifier, filename, and reviewed mapping status without adding an artificial organism-specific protein example.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-31T04:43:24Z",
        "curator": "codex",
        "action": "ADD_CANONICAL_EXAMPLES",
        "changes": "Resolved issue #444 after the #591 source/bin policy with 2 direct source-backed canonical example(s): Escherichia coli (NCBITaxon:562; PMID:9278503), Synechocystis sp. PCC 6803 (NCBITaxon:1148; DOI:10.3390/md11082894). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000158",
    "label": "trypsin activity",
    "definition": "A physiological enzyme-activity phenotype in which a cell exhibits trypsin-like serine endopeptidase activity, preferentially cleaving peptide bonds on the carboxyl side of arginine or lysine residues.",
    "definition_source": "https://iubmb.qmul.ac.uk/enzyme/EC3/4/21/4.html",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "synonyms": [
      {
        "synonym_text": "trypsin",
        "synonym_type": "RELATED_SYNONYM",
        "source": "https://iubmb.qmul.ac.uk/enzyme/EC3/4/21/4.html"
      }
    ],
    "evidence": [
      {
        "reference": "https://iubmb.qmul.ac.uk/enzyme/EC3/4/21/4.html",
        "snippet": "<b>Reaction:</b> Preferential cleavage: Arg<img src=\"../../../EZgif/FISS.GIF\" align=top>, Lys<img src=\"../../../EZgif/FISS.GIF\" align=top>",
        "notes": "The NC-IUBMB EC 3.4.21.4 entry accepts the name trypsin and its reaction line places the scissile-bond FISS.GIF image immediately after Arg and Lys."
      },
      {
        "reference": "https://iubmb.qmul.ac.uk/enzyme/EC3/4/21/4.html",
        "snippet": "Isolated as multiple cationic and anionic trypsins [5] from the pancreas of many vertebrates and from lower species including crayfish, insects (cocoonase) and microorganisms",
        "notes": "The NC-IUBMB EC 3.4.21.4 comments note that trypsins have also been isolated from microorganisms."
      },
      {
        "reference": "DOI:10.1371/journal.pone.0322500",
        "snippet": "Enzyme activities of acid- and alkaline-phosphatases, esterase, esterase lipase, leucine arylamidase, trypsin, naphthol-AS-BI phosphohydrolase, and alpha-glucosidase are present when assayed with API ZYM system.",
        "notes": "Park et al. treated trypsin as a positive API ZYM enzyme-activity phenotype in the Flexibacterium corallicola type species description."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:3037259",
        "taxon_label": "Flexibacterium corallicola",
        "note": "Park et al. reported Flexibacterium corallicola as positive for trypsin activity in the API ZYM enzyme activity panel.",
        "reference": "DOI:10.1371/journal.pone.0322500"
      }
    ],
    "discussions": [
      {
        "discussion_id": "trypsin-activity-xref-gap",
        "prompt": "Resolve an exact external ontology class for trypsin activity before adding a TraitRecord xref.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "GO:0004295 trypsin activity is obsolete, and its replacement GO:0004252 denotes broader serine-type endopeptidase molecular function rather than the organism-level trypsin-like serine endopeptidase phenotype. GO:0004252 is appropriate as a causal-node grounding for generic serine endopeptidase activity, not as an equivalent TraitRecord xref.",
        "posed_by": "codex",
        "posed_date": "2026-09-12"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-12T04:36:25Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted trypsin activity as a URL/DOI-backed TraitRecord after a repository-wide duplicate review covering ignored and hidden files; METPO has no exact trypsin activity class yet.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-12T05:47:58Z",
        "curator": "codex",
        "action": "CORRECTED_EVIDENCE_SNIPPET",
        "changes": "Corrected the IUBMB reaction-line snippet for trypsin activity so it preserves the scissile-bond image tags from the source HTML (#819).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-09-12T06:00:57Z",
        "curator": "codex",
        "action": "TIGHTENED_DEFINITION_WORDING",
        "changes": "Tightened the trypsin activity definition to describe a trypsin-like organismal phenotype instead of over-specifying production of the named vertebrate enzyme (#820).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000169",
    "label": "tyrosine arylamidase activity",
    "definition": "A physiological enzyme-activity phenotype in which a cell produces active tyrosine arylamidase enzymes that hydrolyze tyrosine arylamide substrates.",
    "definition_source": "DOI:10.1099/ijsem.0.006017",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "synonyms": [
      {
        "synonym_text": "tyrosine arylamidase",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1099/ijsem.0.006017"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1099/ijsem.0.006017",
        "snippet": "enzymatic activities are present for: \u03b1-galactosidase, N-acetyl-\u03b2-glucosaminidase, arginine arylamidase, proline arylamidase, leucyl glycine arylamidase, phenylalanine arylamidase, leucine arylamidase, tyrosine arylamidase, alanine arylamidase, glycine arylamidase, histidine arylamidase, glutamyl glutamic acid arylamidase, serine arylamidase, valine arylamidase, cysteine arylamidase, esterase, esterase lipase, alpha-chymotrypsin",
        "notes": "Srinivasan et al. listed tyrosine arylamidase among enzymatic activities present in the Amygdalobacter indicium species description, supporting the API arylamidase row as a directly assayed bacterial enzyme-activity phenotype."
      },
      {
        "reference": "DOI:10.1128/JCM.40.9.3427-3431.2002",
        "snippet": "When the API rapid ID32A system was used, all eight strains displayed activity for alanine arylamidase, arginine arylamidase, \u03b1-glucosidase, glycine arylamidase, histidine arylamidase, leucine arylamidase, leucylglycine arylamidase, proline arylamidase, phenylalanine arylamidase, serine arylamidase, and tyrosine arylamidase",
        "notes": "Hall et al. reported tyrosine arylamidase activity in all eight Actinomyces cardiffensis clinical isolates tested with the API rapid ID32A system."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:3029272",
        "taxon_label": "Amygdalobacter indicium",
        "note": "Srinivasan et al. reported Amygdalobacter indicium as positive for tyrosine arylamidase activity in an enzyme activity panel.",
        "reference": "DOI:10.1099/ijsem.0.006017"
      }
    ],
    "discussions": [
      {
        "discussion_id": "tyrosine-arylamidase-activity-xref-gap",
        "prompt": "Resolve an exact external ontology class for tyrosine arylamidase activity before adding a TraitRecord xref.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "GO:0004177 covers broad aminopeptidase activity at molecular-function scope, and no live GO class provides an exact residue-specific tyrosine arylamidase production phenotype at organism-level scope.",
        "posed_by": "codex",
        "posed_date": "2026-09-12"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-12T12:37:31Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted tyrosine arylamidase activity as a DOI-backed TraitRecord after a repository-wide duplicate review covering ignored and hidden files; METPO has no exact tyrosine arylamidase activity class yet and the placeholder is reserved in proposals/metpo_traitmech_v46.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000648",
    "label": "unconventional protein secretion",
    "definition": "A physiological phenotype in which a eukaryotic microbial cell delivers protein cargo to the plasma membrane or extracellular space by a route that bypasses part or all of the conventional endoplasmic-reticulum-Golgi-plasma-membrane secretory itinerary.",
    "definition_source": "DOI:10.3389/fcell.2022.852028",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.3389/fcell.2022.852028",
        "snippet": "Our results show that neosynthesized PmaA and PalI are translocated to the PM via Golgi-bypass, similar to nutrient transporters.",
        "notes": "PMID:35465316, PMC9021693. Scientific Abstract and selected Introduction, Results and Methods directly read in Europe PMC XML. The paper includes membrane-cargo delivery within unconventional protein secretion. Aspergillus nidulans fluorescent cargo, conditional trafficking repression and localization assays support Golgi bypass after COPII-dependent ER exit, not soluble extracellular release or universal ER independence. The reporters and promoter replacements are engineered; no natural canonical exemplar is inferred. Actual panels, supplements and independent recipient-strain provenance were not inspected."
      },
      {
        "reference": "DOI:10.7554/eLife.16299",
        "snippet": "Under these conditions Acb1, but not Cof1, was detected in the cell wall extract of starving cells",
        "notes": "PMID:27115345, PMC4868542. Contiguous full-text Results s2-1 span, directly read in Europe PMC XML, not an abstract quote. Mild extraction detects intact Acb1 outside the plasma membrane of starved Saccharomyces cerevisiae with Cof1 leakage and Bgl2 extraction controls. This is cell-wall/periplasmic recovery, not direct detection in culture medium. Harsh extraction, some mutants, heat and DMSO can invalidate the assay through leakage. The direct assay differs from earlier SDF-2 bioactivity assays and does not support a Vps4 requirement. Static CUPS images do not prove a temporal sequence. Actual panels and strain provenance remain uninspected."
      },
      {
        "reference": "DOI:10.1083/jcb.201407119",
        "snippet": "Altogether our findings indicate that CUPS are not specialized autophagosomes as suggested previously.",
        "notes": "PMID:25512390, PMC4274258. Scientific Abstract abstract2, distinct from the precis, and Introduction directly read in Europe PMC XML. The authors revise the earlier autophagosome interpretation of yeast CUPS. This is compartment-identity boundary evidence, not proof that every unconventional route excludes all autophagy-related machinery. Actual panels, full Methods and strain provenance were not inspected."
      },
      {
        "reference": "DOI:10.1083/jcb.202312120",
        "snippet": "Notably, while CUPS remain stable, the modified TGN undergoes remodeling during the later stages of unconventional secretion.",
        "notes": "PMID:40015244, PMC11867701. Scientific Abstract, not the teaser, and selected Results, Discussion and Methods directly read in Europe PMC XML. Yeast CUPS contact a modified trans-Golgi network; this argues against defining the phenotype by absence of all Golgi-derived membranes. Rcy1 and v-SNARE perturbations reduce cell-wall recovery of Acb1, SOD1 and Trx2 with Cof1 controls. Drs2-deleted cells could not be assayed because of lysis concerns. Cargo collection and final delivery through the proposed CUPS-TGN route remain a model. BY4741 derivatives include engineered reporters and mutants. Actual panels and supplements were not visually inspected."
      }
    ],
    "discussions": [
      {
        "discussion_id": "unconventional-secretion-scope-and-mapping",
        "prompt": "Keep cargo destinations and route-specific meanings distinct.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "The broad usage in DOI:10.3389/fcell.2022.852028 includes plasma-membrane delivery after ER entry; DOI:10.7554/eLife.16299 describes an ER-bypassing soluble-cargo route. Preserve both, rather than treating leaderless secretion, Golgi bypass or secretory autophagy as exact synonyms. This concerns traffic performed by a eukaryotic microbe, not its animal or plant host. An absent predicted signal peptide, ATG dependence, CUPS formation or protein detected after lysis alone is insufficient. Membrane localization does not establish soluble release. The degradative autophagy record traitmech:000638 is not a broader parent; exocytosis traitmech:000637 specifies fusion-pore release rather than an unconventional itinerary. Overlap is not disjointness. Obsolete METPO secretion classes do not supply an active exact term. Keep METPO:1000059 as parent and leave ontology equivalences and finer route hierarchy for human review.",
        "posed_by": "codex",
        "posed_date": "2026-10-06"
      },
      {
        "discussion_id": "unconventional-secretion-exemplars-and-mechanisms",
        "prompt": "Resolve natural exemplars and mechanisms separately for each route.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "Retain qualified laboratory observations without labeling engineered fluorescent cargo or conditional trafficking mutants as natural canonical exemplars. Natural strain provenance, source figures and accession-level functional evidence need further review before adding examples or a protein-resolved graph. The three CUPS papers share investigators and are not independent-laboratory replications; the Aspergillus study supports a different route, not replication of CUPS. No universal starvation trigger, signal-peptide absence, COPII independence, autophagosome or conserved export apparatus is asserted. ATG-dependent export remains a possible narrower research target, not an allocated additional trait.",
        "posed_by": "codex",
        "posed_date": "2026-10-06"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-06T18:32:51Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added unconventional protein secretion with four DOI-backed snippets and explicit soluble-export, membrane-delivery, route and assay limits. Ignored-and-hidden searches and pinned METPO review found no exact record. Reserved METPO:1060100 in v524. Deferred unverified mappings, natural exemplars and protein mechanisms; existing records remain unchanged.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-06T18:43:11Z",
        "curator": "codex",
        "action": "CURATED_WITH_LITERATURE",
        "changes": "Clarified the conventional itinerary through plasma-membrane delivery (#1760), preserving the definition source's inclusion of unconventional post-Golgi export. No new route, cargo, taxon or universal mechanism is inferred.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000711",
    "label": "unequal protein aggregate inheritance at cell division",
    "definition": "A physiological phenotype in which microbial cell division recurrently yields sibling cells with unequal numbers or amounts of inherited protein aggregates.",
    "definition_source": "DOI:10.1371/journal.pbio.1001886",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1073/pnas.0708931105",
        "snippet": "their position in the mother cell determines which offspring inherits the inclusion body and where it will be located within it",
        "notes": "Lindner et al. 2008, PMID:18287048, PMC2268587; Results, Inclusion Bodies Are Formed in Discrete Cellular Positions and Accumulate in Old Poles Under Nonstressing Conditions. Primary PMC Results and Methods directly read. The quoted position is that of an IbpA-YFP focus. MGAY is an engineered MG1655 reporter strain, grown on LB-agarose at 37 C without imposed stress. Figure 2 is the inspected localization measurement; Figure 3 is an inspected lineage schematic, not another experiment. Pole identity changes across divisions. These observations describe reporter-focus inheritance and eventual older-pole accumulation. Govers et al. 2018 (DOI:10.1371/journal.pbio.2003853) subsequently demonstrated label-induced clustering with IbpA-YFP. The older readout is not independent proof of endogenous unstressed aggregation; naming the engineered strain alone does not resolve this assay bias. Neither active transport, universal aggregate toxicity nor a natural canonical exemplar is established. Supplements were not inspected. The full-text span retains the native abstract resolver verdict NOT_IN_ABSTRACT."
      },
      {
        "reference": "DOI:10.1371/journal.pbio.1001886",
        "snippet": "We experimentally confirmed that fusion increases segregation asymmetry, for a range of stresses, and identified Hsp16 as a fusion factor.",
        "notes": "Coelho et al. 2014, PMID:24936793, PMC4061010; scientific abstract, not Author Summary. Primary XML and actual Figures 3, 4 and S4 were inspected. Hsp104-GFP fission-yeast imaging supports stress-associated unequal inheritance without consistent old/new-pole bias. Figure 3C measures an absolute sibling difference in aggregate-associated fluorescence, not concentration; S4I measures count asymmetry. Figure 4B is fusion and 4C is nucleation: the caption reverses them. A Results pointer to 4C for stress-dependent asymmetry disagrees with the plotted endpoints. Figure 3C describes continuous 40 C, whereas Methods describes 40 C for one hour followed by 37 C; this remains unresolved. Text S1 experimental methods and strain table were text-extracted, not visually rendered. No universal transport, death threshold or rejuvenation mechanism is inferred. The scientific-abstract span matches the native resolver text (VERIFIED)."
      },
      {
        "reference": "DOI:10.1111/mmi.14228",
        "snippet": "Noticeably, stalked cells always inherited more aggregates (75%) than swarmer cells (25%).",
        "notes": "Schramm et al. 2019, PMID:30779464, PMC6850343; Results, The aggregate load does not sort to swarmer or stalked daughter cells in C. crescentus. Primary XML Results, Discussion and relevant Methods were read; actual Figure 6 was inspected. DnaK-mVenus, delta-clpB cells recovered at 30 C after 10 minutes at 40 C. Figure 6G reports aggregate allocation across daughter cell types over successive divisions, not the fraction of all sibling pairs with unequal counts. Figure 6F measures projected cell area, not volume. Unequal shared inheritance is compatible with the broad phenotype; it contradicts neither sharing nor a stable allocation ratio. The paper limits universal exclusive old-pole retention, not every form of quantitative inequality. Supplements and independent strain provenance were not inspected; no natural canonical example is asserted. The full-text span retains the native abstract resolver verdict NOT_IN_ABSTRACT."
      },
      {
        "reference": "DOI:10.1371/journal.pbio.2003853",
        "snippet": "the polarly deposited PA was subjected to limited disaggregation and therefore became asymmetrically inherited for a large number of generations",
        "notes": "Govers et al. 2018, PMID:30153247, PMC6112618; scientific abstract, directly matched in primary XML and source-qualified MED. Results on reporter validation and post-stress inheritance, relevant Methods and actual Figures 1 and 3 were inspected. Figure 1 shows reporter-dependent clustering; Figure 3 separately follows engineered MG1655 IbpA-msfGFP lineages after 47 C for 15 minutes, with microscopy at 37 C. Focus inheritance is distinct from the fluorescence concentration and growth readouts. This does not validate unstressed IbpA-YFP foci as endogenous aggregates or imply universal harm, benefit, aging or rejuvenation. Supplementary controls were read only where described in Results; their images, raw data and independent strain provenance were not assessed."
      }
    ],
    "discussions": [
      {
        "discussion_id": "unequal-aggregate-inheritance-operational-scope",
        "prompt": "Assess the quantity-qualified definition and the level of inheritance evidence.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Require repeated lineage or population observations under stated conditions, not a single unequal sibling pair. Retain aggregate count versus fluorescence-derived amount, the time of measurement, reporter, strain and detection limits. Amount is not concentration; cell area is not volume. Within-pair inequality, cell-type allocation bias and complete aggregate exclusion are distinct readouts. Sharing between daughters need not be equal, and unequal inheritance need not favor a fixed pole or cell type. No universal threshold or programmed asymmetry is specified. Bare asymmetric segregation has narrower source usages and is not asserted as an exact synonym. Aggregate presence, aggrephagy, heat-shock response, morphological division asymmetry, replicative aging and functional rejuvenation are not equivalent traits or demonstrated narrower parents. Use METPO:1000059 phenotype without reparenting existing records.",
        "posed_by": "codex",
        "posed_date": "2026-10-12"
      },
      {
        "discussion_id": "unequal-aggregate-inheritance-mechanism-and-source-limits",
        "prompt": "Resolve assay discrepancies, strain provenance and mechanisms before extending this first-pass record.",
        "kind": "KNOWLEDGE_GAP",
        "status": "OPEN",
        "rationale": "This phenotype does not imply active transport, toxic damage, functional decline or rejuvenation. An aggregate-free descendant alone establishes none of those mechanisms or outcomes. The engineered reporter and deletion contexts remain qualified evidence, not natural canonical examples. No shared protein mechanism, graph or external equivalence is asserted. Coelho Figure 4 panel-label and Figure 3C versus Methods temperature discrepancies remain open; actual plotted endpoints are distinguished from text pointers. Primary source/metadata notice checks on 2026-10-12 were bounded by access; they do not prove exhaustive notice absence. Reporter-focus inheritance must be separated from endogenous aggregation: the later Govers study identifies IbpA-YFP label-induced clustering, while its separate post-heat-shock IbpA-msfGFP lineages support inheritance. Monomeric labels also require validation of expression level and assay conditions; no reporter is declared universally artifact-free.",
        "posed_by": "codex",
        "posed_date": "2026-10-12"
      },
      {
        "discussion_id": "unequal-aggregate-inheritance-historical-metpo-match",
        "prompt": "Retain the deprecated aggregate lexical hit without asserting identity or reusing its ID.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Pinned and current released METPO contain METPO:1000011, obsolete aggregate, marked deprecated and below ObsoleteClass. It has an IAO:0000231 annotation to OMO:0001000, but no definition, replacement or consider annotation in the inspected releases. Its original scope and reason-code interpretation remain unresolved. A lexical aggregate hit does not establish equivalence to unequal protein aggregate inheritance; this literature-defined phenotype was independently accepted. Do not reactivate 1000011 or include it as an exact xref. Ignored/hidden available-file and registered historical-tree searches, pending PRs and released RDF found no exact trait in the inspected scope; this is not discovery exhaustion.",
        "posed_by": "codex",
        "posed_date": "2026-10-12"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-12T14:38:12Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added unequal protein aggregate inheritance at cell division with three primary DOI references and checked snippets. Retained quantity, population, assay and historical-METPO scope limits. Reserved 000711, v587 and 1066400-1066499 after ignored/hidden, registered historical-tree and pending-PR checks, distinguishing an editor namespace envelope from narrower reservations. Examples and mechanism graph deferred. Existing records unchanged; timestamp is the observed UTC curation decision.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-12T18:24:02Z",
        "curator": "codex",
        "action": "QUALIFIED_REPORTER_EVIDENCE",
        "changes": "Addressed issue #1896 by qualifying the Lindner reporter-focus readout against later primary evidence of IbpA-YFP label-induced clustering. Added Govers 2018 with a checked abstract snippet and separate post-stress inheritance context. Preserved identity, definition, parent, PROPOSED status, original event and source assessment; appended the correction and updated the proposal sources. Timestamp is the observed UTC correction decision.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000613",
    "label": "unisexual reproduction",
    "definition": "A fungal phenotype enabling sexual or parasexual reproduction with genetic contribution from only one mating type.",
    "definition_source": "DOI:10.1371/journal.pgen.1003688",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1371/journal.pgen.1003688",
        "snippet": "Sexual reproduction involves cells of either opposite (bisexual) or one (unisexual) mating type.",
        "notes": "Feretzaki and Heitman (2013), PMID:23966871, PMC3744442. Exact sentence of the directly retrieved scientific abstract (abstract1), not the separate Author Summary. Introduction s1 also includes Candida unisexual reproduction and helper-cell stimulation. Results s2g/s2h and Methods s4a/s4f were read in XML: reduced sporulation in Spo11/Ubc5 mutants is distinct from hyphal growth, and Ubc5's precise role remains unresolved. Do not universalize one diploidization route or timing. Actual figures, complete tables, supplements and other experimental sections remain uninspected; no protein-level dependency is asserted here. Species names follow the paper."
      },
      {
        "reference": "DOI:10.1038/nature03448",
        "snippet": "Furthermore, fusion and meiosis can occur between non-isogenic alpha strains, enabling genetic exchange.",
        "notes": "Lin, Hull and Heitman (2005), PMID:15846346. Exact sentence from the scientific abstract directly retrieved through Europe PMC core metadata. The API uses the word alpha. Cryptococcus same-type partners need not be genetically identical: this supports outcrossing within a mating type, not obligatory clonal selfing. Diploidization and meiosis distinguish the reported fruiting from purely mitotic growth. Full text, methods, figures, supplements and natural strain provenance remain uninspected; no canonical example is inferred."
      },
      {
        "reference": "DOI:10.1038/nature08252",
        "snippet": "could be induced to undergo chromosome loss to produce diploid cells, thereby completing a parasexual mating cycle",
        "notes": "Alby et al. (2009), PMID:19675652, PMC2866515. Exact main-text clause retrieved via NCBI PMC efetch after Europe PMC full-text failure, not an abstract quote. All main-text paragraphs and Methods Summary were read; Figures 3/4 and Supplementary Figure 7 were visually inspected. Marked opaque Candida a-a partners form tetraploids. Supplement pp. 6-7/15 reports sorbose-induced ploidy reduction, including near-diploid and intermediate progeny, not uniform restoration of euploidy. Bar1-deletion assays and helper-stimulated wild-type mating are distinct: opposite-type pheromone helpers need not contribute genomes. Other figures and supplement sections remain uninspected. Engineered or marked strains are not promoted to natural canonical examples."
      },
      {
        "reference": "DOI:10.1371/journal.pbio.1001653",
        "snippet": "generates abundant hyphae, homozygous diploid intermediates, and haploid meiotic spores when grown on mating-inducing media all by itself.",
        "notes": "Ni et al. (2013), PMID:24058295, PMC3769227. Exact Results s2a clause, not an abstract quote; its subject is XL280alpha. Scientific abstract, author summary, Results s2a and Methods s4b were read directly in XML. Solo culture on V8 or filament agar followed by spore isolation supports selfing in this laboratory F1 derivative of B3501alpha and JEC20a. Natural ancestral isolates do not make XL280 a natural exemplar. The paper does not resolve cell fusion versus endoreplication into one obligatory route. Actual figures, supplements including Table S4, and other experimental sections remain uninspected. Aneuploidy and adaptive benefit are not defining requirements of the whole trait."
      }
    ],
    "discussions": [
      {
        "discussion_id": "unisexual-reproduction-scope-and-hierarchy",
        "prompt": "Keep mating-type contribution distinct from selfing, helper cells and MAT inventory.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "One mating type does not mean one strain: non-isogenic same-type partners can exchange genetic material. Solo selfing overlaps homothallism (traitmech:000609), but the whole class is not restricted to single-isolate self-fertility. It is not a subclass of parasexuality (traitmech:000607), because meiotic cycles are also included. Pheromone-producing opposite-type helper cells are not necessarily genetic contributors, so do not require their physical absence. Use released phenotype METPO:1000059 in both record and proposal; PHYSIOLOGY is only a filesystem category. MAT sequence content, population mating-type bias or hyphae alone do not establish reproductive completion. Do not require universal meiosis, spores, cell fusion, clonality or absence of outcrossing. Resolve context-dependent same-sex mating terminology and external phenotype/process mappings before adding synonyms or xrefs. The existing homothallism evidence note, citing DOI:10.5598/imafungus.2015.06.01.13, groups unisexual reproduction within a homothallism umbrella. That wording conflicts with interpreting the current single-isolate self-fertility definition as a universal superclass here. Our scope decision interprets the umbrella as including unisexual selfing, not as evidence that every same-type outcrossing partner is independently self-fertile. Preserve the older source attribution and retain phenotype while the operational and umbrella scopes await curator reconciliation; issue #1703 records this explicit distinction.",
        "posed_by": "codex",
        "posed_date": "2026-10-04"
      },
      {
        "discussion_id": "unisexual-reproduction-mechanism-and-examples",
        "prompt": "Resolve native examples and taxon-specific reproductive mechanisms before graphing.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Complete unread primary experiments and supplements before expanding mechanistic claims. Keep solo meiosis, non-isogenic same-type fusion and parasexual chromosome loss separate. Hyphal growth, cell fusion, ploidy change and viable progeny are different readouts, not interchangeable proof of a completed cycle. XL280 is a laboratory-cross derivative; Candida deletion and marked strains also do not establish natural canonical provenance. Verify natural strains and current taxonomic authority before adding examples, and native protein accessions before causal edges. No graph or unverified taxon/protein CURIE is asserted. Manual full-text matching is not an abstract-resolver VERIFIED verdict.",
        "posed_by": "codex",
        "posed_date": "2026-10-04"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-05T04:48:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added unisexual reproduction with four DOI-backed exact source snippets after scientific-abstract, full-text and selected Candida figure/supplement checks. Distinguished mating-type contribution from selfing and pheromone helpers; included meiotic and parasexual cycles. Ignored-and-hidden novelty searches and structured METPO review found no exact record. Reserved METPO:1056700 in v490 under released phenotype. Deferred natural canonical examples, lexical mappings and protein-resolved causal graphs.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-05T05:04:04Z",
        "curator": "codex",
        "action": "CLARIFIED_HIERARCHY_SCOPE",
        "changes": "Addressed adversarial review issue #1703 by explicitly naming the existing homothallism umbrella wording and distinguishing it from the operational single-isolate self-fertility definition. Retained phenotype parent, source attribution and open curator reconciliation.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000077",
    "label": "urease activity",
    "definition": "A physiological enzyme-activity phenotype in which a cell produces urease, which hydrolyzes urea to ammonia and carbon dioxide, typically raising local pH; it is the basis of the diagnostic urease test.",
    "definition_source": "DOI:10.1128/mr.59.3.451-480.1995",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "synonyms": [
      {
        "synonym_text": "urease-positive",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1128/mr.59.3.451-480.1995"
      },
      {
        "synonym_text": "ureolysis",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1126/science.aaf4507"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1128/mr.59.3.451-480.1995",
        "notes": "Mobley, Island & Hausinger review the molecular biology of microbial ureases that hydrolyze urea to ammonia and carbon dioxide."
      },
      {
        "reference": "DOI:10.1128/mr.53.1.85-108.1989",
        "notes": "Mobley & Hausinger review the significance and regulation of microbial ureases."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:1474",
        "taxon_label": "Sporosarcina pasteurii",
        "note": "Most-used organism for microbially induced calcite precipitation; copious constitutive urease (formerly Bacillus pasteurii).",
        "reference": "DOI:10.1186/s12934-020-1281-z"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "urease_activity_urea_hydrolysis",
        "title": "Urease-catalyzed urea hydrolysis",
        "description": "Evidence-backed causal sketch linking urease to hydrolysis of urea into ammonia, the basis of the urease test.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "The core urease reaction is general, whereas the carbonic-anhydrase and calcium-carbonate branch is an application-specific extension. The S. pasteurii example is explicitly the UreA/UreB/UreC heterotrimer and no one accession denotes the complete enzyme.",
        "nodes": [
          {
            "node_id": "urease_activity_trait",
            "label": "urease activity",
            "node_type": "TRAIT",
            "grounding": "traitmech:000077",
            "description": "Possession of urease."
          },
          {
            "node_id": "urease",
            "label": "urease",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Nickel metalloenzyme hydrolyzing urea.",
            "grounding_status": "REVIEWED_LABEL_ONLY",
            "grounding_notes": "Bacterial urease is a multisubunit enzyme with taxon-dependent subunit fusions; the exact GO term denotes its activity rather than the protein complex and remains on urease_function.",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:P41020",
                "protein_label": "Urease subunit alpha",
                "gene_symbol": "ureC",
                "taxon_id": "NCBITaxon:1474",
                "taxon_label": "Sporosarcina pasteurii",
                "entry_status": "REVIEWED",
                "retrieved_on": "2026-10-22",
                "entry_version": 153,
                "sequence_version": 2,
                "role": "Catalytic alpha component of the S. pasteurii UreA/UreB/UreC urease; it binds the binuclear nickel active site but does not alone denote the complete enzyme.",
                "evidence": [
                  {
                    "reference": "DOI:10.1016/S0969-2126(99)80026-4",
                    "snippet": "crystal structures of the native and inhibited enzyme from Bacillus pasteurii",
                    "notes": "The structural study resolves the heteropolymeric S. pasteurii urease and its binuclear nickel catalytic center; P41020 is its reviewed UreC alpha component."
                  }
                ]
              },
              {
                "uniprot_id": "UniProtKB:P41021",
                "protein_label": "Urease subunit beta",
                "gene_symbol": "ureB",
                "taxon_id": "NCBITaxon:1474",
                "taxon_label": "Sporosarcina pasteurii",
                "entry_status": "REVIEWED",
                "retrieved_on": "2026-10-22",
                "entry_version": 128,
                "sequence_version": 1,
                "role": "Beta structural component of the S. pasteurii UreA/UreB/UreC urease; it is recorded explicitly so the accession is not mistaken for the complete enzyme.",
                "evidence": [
                  {
                    "reference": "DOI:10.1016/S0969-2126(99)80026-4",
                    "snippet": "crystal structures of the native and inhibited enzyme from Bacillus pasteurii",
                    "notes": "The structure contains the beta component mapped to reviewed UniProtKB P41021 as part of the heteropolymeric urease assembly."
                  }
                ]
              },
              {
                "uniprot_id": "UniProtKB:P41022",
                "protein_label": "Urease subunit gamma",
                "gene_symbol": "ureA",
                "taxon_id": "NCBITaxon:1474",
                "taxon_label": "Sporosarcina pasteurii",
                "entry_status": "REVIEWED",
                "retrieved_on": "2026-10-22",
                "entry_version": 130,
                "sequence_version": 1,
                "role": "Gamma structural component of the S. pasteurii UreA/UreB/UreC urease; it is recorded explicitly so the accession is not mistaken for the complete enzyme.",
                "evidence": [
                  {
                    "reference": "DOI:10.1016/S0969-2126(99)80026-4",
                    "snippet": "crystal structures of the native and inhibited enzyme from Bacillus pasteurii",
                    "notes": "The structure contains the gamma component mapped to reviewed UniProtKB P41022 as part of the heteropolymeric urease assembly."
                  }
                ]
              }
            ]
          },
          {
            "node_id": "urease_function",
            "label": "urease activity",
            "node_type": "MOLECULAR_FUNCTION",
            "grounding": "GO:0009039",
            "description": "Hydrolysis of urea to ammonia and carbon dioxide."
          },
          {
            "node_id": "urea",
            "label": "urea",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:16199",
            "description": "Substrate hydrolyzed by urease."
          },
          {
            "node_id": "ammonia",
            "label": "ammonia",
            "node_type": "CHEMICAL",
            "grounding": "CHEBI:16134",
            "description": "Product that raises local pH."
          },
          {
            "node_id": "hydroxide",
            "label": "hydroxide",
            "node_type": "CHEMICAL",
            "description": "Hydroxide ion produced by urea hydrolysis, raising local pH.",
            "grounding": "CHEBI:16234"
          },
          {
            "node_id": "carbon_dioxide",
            "label": "carbon dioxide",
            "node_type": "CHEMICAL",
            "description": "CO2 product of urea hydrolysis; feeds carbonate chemistry.",
            "grounding": "CHEBI:16526"
          },
          {
            "node_id": "ph_quality",
            "label": "pH",
            "node_type": "QUALITY",
            "description": "Local pH, increased by urease-driven alkalinization."
          },
          {
            "node_id": "carbonic_anhydrase_function",
            "label": "carbonic anhydrase activity",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "Hydration of CO2 to bicarbonate.",
            "grounding": "GO:0004089"
          },
          {
            "node_id": "bicarbonate",
            "label": "bicarbonate",
            "node_type": "CHEMICAL",
            "description": "Bicarbonate produced from CO2 hydration by carbonic anhydrase.",
            "grounding": "CHEBI:17544"
          },
          {
            "node_id": "calcium_carbonate_precipitation",
            "label": "calcium carbonate precipitation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Precipitation of CaCO3 mineral, influenced by buffering chemistry."
          }
        ],
        "edges": [
          {
            "subject": "urease",
            "predicate": "enables",
            "object": "urease_function",
            "description": "Urease carries out urea hydrolysis.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mr.59.3.451-480.1995",
                "notes": "Mobley, Island & Hausinger review microbial ureases."
              }
            ],
            "predicate_id": "RO:0002327"
          },
          {
            "subject": "urease_function",
            "predicate": "consumes",
            "object": "urea",
            "description": "The urease reaction consumes urea.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mr.59.3.451-480.1995",
                "notes": "Supports urea as the hydrolysis substrate."
              }
            ],
            "predicate_id": "biolink:consumes"
          },
          {
            "subject": "urease_function",
            "predicate": "has output",
            "object": "ammonia",
            "description": "Urea hydrolysis produces ammonia.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mr.53.1.85-108.1989",
                "notes": "Mobley & Hausinger support ammonia release from urea hydrolysis."
              }
            ],
            "predicate_id": "RO:0002234"
          },
          {
            "subject": "urease_function",
            "predicate": "manifests as",
            "object": "urease_activity_trait",
            "description": "Urease enzymatic activity manifests as the observable urease-activity phenotype scored by the diagnostic urease test.",
            "evidence": [
              {
                "reference": "DOI:10.1128/mr.59.3.451-480.1995",
                "notes": "Urease activity (urea-to-ammonia hydrolysis raising local pH) is the assayable phenotype used to score urease-positive organisms."
              }
            ],
            "predicate_id": "METPO:2007400"
          },
          {
            "subject": "urease_function",
            "predicate": "has output",
            "object": "hydroxide",
            "description": "Urea hydrolysis produces hydroxide, mechanistically explaining alkalinization.",
            "evidence": [
              {
                "reference": "DOI:10.24263/2304-974x-2024-13-2-10",
                "notes": "(NH2)2CO + 2H2O + urease -> 2 NH4+ + 2 OH- + CO2 + urease."
              }
            ],
            "predicate_id": "RO:0002234"
          },
          {
            "subject": "urease_function",
            "predicate": "has output",
            "object": "carbon_dioxide",
            "description": "Urea hydrolysis produces carbon dioxide.",
            "evidence": [
              {
                "reference": "DOI:10.24263/2304-974x-2024-13-2-10",
                "notes": "(NH2)2CO + 2H2O + urease -> 2 NH4+ + 2 OH- + CO2 + urease."
              }
            ],
            "predicate_id": "RO:0002234"
          },
          {
            "subject": "urease_function",
            "predicate": "increases",
            "object": "ph_quality",
            "description": "Urea hydrolysis (NH4+/OH- production) increases local pH, the basis of the urease test color change.",
            "evidence": [
              {
                "reference": "DOI:10.1021/acs.est.3c06617",
                "notes": "Urea hydrolysis produces NH4+ and OH-, causing a pH increase."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "carbon_dioxide",
            "predicate": "is substrate of",
            "object": "carbonic_anhydrase_function",
            "description": "CO2 from urea hydrolysis is hydrated by carbonic anhydrase.",
            "evidence": [
              {
                "reference": "DOI:10.1021/acs.est.3c06617",
                "notes": "Hydration of CO2 to HCO3- by carbonic anhydrase."
              }
            ]
          },
          {
            "subject": "carbonic_anhydrase_function",
            "predicate": "increases",
            "object": "bicarbonate",
            "description": "Carbonic anhydrase hydrates CO2, increasing bicarbonate.",
            "evidence": [
              {
                "reference": "DOI:10.1021/acs.est.3c06617",
                "notes": "Increase in [HCO3-] following the hydration of CO2 to HCO3- by CA."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "carbonic_anhydrase_function",
            "predicate": "affects",
            "object": "calcium_carbonate_precipitation",
            "description": "CA-driven buffering enhances solubility trapping and affects the CaCO3 phase formed.",
            "evidence": [
              {
                "reference": "DOI:10.1021/acs.est.3c06617",
                "notes": "CA physiologically promotes buffering, which enhances solubility trapping and affects the phase of the CaCO3 mineral formed."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-06-04T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate PHYSIOLOGY trait (urease activity) from literature research to fill the enzyme-activity-phenotype gap.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-08T13:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (urease urea hydrolysis) with GO/CHEBI node groundings and RO/METPO/biolink predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-14T06:38:16Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A090IGX8\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-16T00:00:00Z",
        "curator": "claude",
        "action": "FIX_ORPHAN_NODE",
        "changes": "Connected the previously-orphaned urease_activity_trait node via a 'manifests as' (METPO:2007400) edge from urease_function, so the molecular function links to the observable trait.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 6 evidence-backed generic edges (6 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:15Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 4 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d72, RO:0002213\u00d72).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:20Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:16526\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:35Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 3 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:16234\u00d71, GO:0004089\u00d71, CHEBI:17544\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:21:12Z",
        "curator": "claude",
        "action": "RETRACT_DEAD_UNIPROT_GROUNDINGS",
        "changes": "Retracted 1 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-07-20T04:23:56Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0009039\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T01:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES",
        "changes": "Re-grounded 3 causal edge(s) off microbe-domain METPO predicates (3 to has output), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-08T05:00:00Z",
        "curator": "claude",
        "action": "UNGROUND_CAUSAL_NODE",
        "changes": "Dropped the grounding GO:0009039 from node urease. Issue 352. GO:0009039 is 'urease ACTIVITY'. Same as catalase: kept on urease_function, dropped from the protein that enables it.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-19T00:00:00+00:00",
        "curator": "add_faprotax_synonyms",
        "action": "ADDED_SYNONYM",
        "changes": "Added 'ureolysis' (600 occurrences in microbedecoder's unmapped labels) as a RELATED_SYNONYM (#453). FAPROTAX's ureolysis is urea hydrolysis, which this record already defines as its mechanism: 'produces urease, which hydrolyzes urea to ammonia and carbon dioxide'. Written with the source's underscores because that is the string a consumer must resolve.",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-08-24T11:20:00Z",
        "curator": "codex",
        "action": "CURATE_PROTEIN_TAXON_EXAMPLE",
        "changes": "Reviewed the urease graph scope, converted the S. pasteurii citation to DOI, dispositioned the multisubunit urease node, and added explicit reviewed UreC, UreB, and UreA component examples with structural evidence.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-22T01:35:00Z",
        "curator": "claude",
        "action": "REFRESH_UNIPROT_ENTRY_VERSION",
        "changes": "Refreshed UniProtKB entry_version against live UniProt REST on 2026-10-22: UniProtKB:P41020 (152 -> 153 on urease), UniProtKB:P41021 (127 -> 128 on urease), UniProtKB:P41022 (129 -> 130 on urease).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000144",
    "label": "valine arylamidase activity",
    "definition": "A physiological enzyme-activity phenotype in which a cell produces active valine arylamidase enzymes that hydrolyze valine arylamide substrates.",
    "definition_source": "DOI:10.3389/fmicb.2022.1034816",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000059"
    ],
    "evidence": [
      {
        "reference": "DOI:10.3389/fmicb.2022.1034816",
        "snippet": "Positive alkaline phosphatase, cystine arylamidase, esterase(C4), esterase lipase(C8), leucine arylamidase, naphthol-AS-B1-phosphohydrolase, valine arylamidase",
        "notes": "Jiang et al. treated valine arylamidase as an assayed enzyme-activity phenotype in the Geminicoccus harenae type species description."
      },
      {
        "reference": "DOI:10.1099/ijsem.0.002327",
        "snippet": "enzyme detection with an API zym kit was positive for alkaline phosphatase, esterase, leucine arylamidase, valine arylamidase, acid phosphatase",
        "notes": "Jung et al. detected valine arylamidase in Lactobacillus allii strain WiKim39 with the API ZYM enzyme activity panel."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:2498453",
        "taxon_label": "Geminicoccus harenae",
        "note": "Jiang et al. reported Geminicoccus harenae as positive for valine arylamidase in the API ZYM enzyme activity panel.",
        "reference": "DOI:10.3389/fmicb.2022.1034816"
      }
    ],
    "discussions": [
      {
        "discussion_id": "valine-arylamidase-activity-xref-gap",
        "prompt": "Resolve an exact external ontology class for valine arylamidase activity before adding a TraitRecord xref.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "GO:0004177 covers aminopeptidase activity at molecular-function scope and no live GO class provides an exact residue-specific valine arylamidase production phenotype at organism-level scope.",
        "posed_by": "codex",
        "posed_date": "2026-09-11"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-09-11T17:00:22Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Minted valine arylamidase activity as a DOI-backed TraitRecord after a repository-wide duplicate review covering ignored and hidden files; METPO has no exact valine arylamidase activity class yet.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000081",
    "label": "viable but nonculturable state",
    "definition": "A dormancy state in which cells remain viable and minimally metabolically active but lose the ability to grow on routine culture media, regaining culturability upon resuscitation.",
    "definition_source": "DOI:10.1111/j.1574-6976.2009.00200.x",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "traitmech:000080"
    ],
    "synonyms": [
      {
        "synonym_text": "VBNC state",
        "synonym_type": "RELATED_SYNONYM",
        "source": "DOI:10.1111/j.1574-6976.2009.00200.x"
      }
    ],
    "evidence": [
      {
        "reference": "DOI:10.1111/j.1574-6976.2009.00200.x",
        "notes": "Oliver reviews the viable-but-nonculturable state, in which stressed cells stay viable yet unculturable until resuscitated."
      },
      {
        "reference": "DOI:10.1038/nrmicro2504",
        "notes": "Lennon & Jones frame the VBNC state within the broader microbial dormancy seed-bank concept."
      }
    ],
    "canonical_examples": [
      {
        "taxon_id": "NCBITaxon:672",
        "taxon_label": "Vibrio vulnificus",
        "note": "Canonical exemplar of the viable-but-nonculturable (VBNC) state.",
        "reference": "PMID:7618874"
      },
      {
        "taxon_id": "NCBITaxon:83333",
        "taxon_label": "Escherichia coli K-12",
        "note": "Strain-level VBNC model paired to reviewed RpoS based on an rpoS-loss study of K-12-derived E. coli strains.",
        "reference": "DOI:10.1046/j.1462-2920.2003.00497.x"
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "vbnc_stress_induced_dormancy",
        "title": "Stress-induced viable-but-nonculturable state",
        "description": "Evidence-backed causal sketch linking stress to a dormant viable-but-nonculturable state that resuscitates later.",
        "scope_status": "MECHANISTIC",
        "scope_notes": "This graph represents a stress-induced VBNC program and subsequent resuscitation. The E. coli K-12 RpoS example anchors the persistence branch and does not imply that one sigma factor is the sole VBNC mechanism across taxa.",
        "nodes": [
          {
            "node_id": "vbnc_trait",
            "label": "viable but nonculturable state",
            "node_type": "TRAIT",
            "grounding": "traitmech:000081",
            "description": "Viable, minimally active, non-culturable dormant state."
          },
          {
            "node_id": "stress",
            "label": "environmental stress",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Stress driving cells into the VBNC state."
          },
          {
            "node_id": "dormancy_process",
            "label": "dormancy process",
            "node_type": "BIOLOGICAL_PROCESS",
            "grounding": "GO:0022611",
            "description": "Entry into a reversible quiescent state."
          },
          {
            "node_id": "oxidative_stress",
            "label": "oxidative stress / ROS accumulation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Reactive oxygen species accumulation acting as a major VBNC trigger."
          },
          {
            "node_id": "ppgpp",
            "label": "(p)ppGpp",
            "node_type": "CHEMICAL",
            "description": "Alarmone nucleotide accumulating during VBNC entry, mediating the stringent response."
          },
          {
            "node_id": "stress_resistance",
            "label": "stress resistance",
            "node_type": "QUALITY",
            "description": "Enhanced tolerance to stress supporting VBNC maintenance."
          },
          {
            "node_id": "rpos",
            "label": "RpoS sigma factor",
            "node_type": "GENE_OR_PROTEIN",
            "description": "Stationary-phase/general stress sigma factor expressed in VBNC cells.",
            "grounding": "InterPro:IPR012761",
            "protein_examples": [
              {
                "uniprot_id": "UniProtKB:P13445",
                "protein_label": "RNA polymerase sigma factor RpoS",
                "gene_symbol": "rpoS",
                "taxon_id": "NCBITaxon:83333",
                "taxon_label": "Escherichia coli K-12",
                "entry_status": "REVIEWED",
                "retrieved_on": "2026-10-22",
                "entry_version": 208,
                "sequence_version": 3,
                "role": "E. coli K-12 sigma-S factor whose loss shortens VBNC persistence and resuscitation competence under cold oligotrophic stress.",
                "evidence": [
                  {
                    "reference": "DOI:10.1046/j.1462-2920.2003.00497.x",
                    "snippet": "rpoS mutants lost culturability earlier and retained resuscitation capability for less time",
                    "notes": "The primary mutant study supports an RpoS-dependent VBNC survival phenotype in E. coli; UniProt verifies the reviewed K-12 RpoS entry."
                  }
                ]
              }
            ]
          },
          {
            "node_id": "resuscitation",
            "label": "resuscitation from VBNC",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Recovery of culturability from the viable-but-nonculturable state."
          },
          {
            "node_id": "atp",
            "label": "ATP",
            "node_type": "CHEMICAL",
            "description": "Cellular ATP whose residual availability drives resuscitation metabolism."
          },
          {
            "node_id": "nad_synthesis",
            "label": "NAD+ biosynthesis",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "NAD+ synthesis during the resuscitating lag phase."
          },
          {
            "node_id": "tca_oxphos",
            "label": "TCA cycle flux and oxidative phosphorylation",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Central energy metabolism restored during resuscitation."
          }
        ],
        "edges": [
          {
            "subject": "stress",
            "predicate": "causes",
            "object": "vbnc_trait",
            "description": "Stress drives cells into the viable-but-nonculturable state.",
            "evidence": [
              {
                "reference": "DOI:10.1111/j.1574-6976.2009.00200.x",
                "notes": "Oliver reviews stress-induced entry into the VBNC state."
              }
            ],
            "predicate_id": "biolink:causes"
          },
          {
            "subject": "dormancy_process",
            "predicate": "confers",
            "object": "vbnc_trait",
            "description": "The VBNC state is a form of microbial dormancy.",
            "evidence": [
              {
                "reference": "DOI:10.1038/nrmicro2504",
                "notes": "Lennon & Jones frame VBNC within microbial dormancy."
              }
            ],
            "predicate_id": "METPO:2007700"
          },
          {
            "subject": "oxidative_stress",
            "predicate": "promotes",
            "object": "vbnc_trait",
            "description": "Oxidative stress / ROS accumulation promotes entry into the VBNC state.",
            "evidence": [
              {
                "reference": "DOI:10.3390/foods12061179",
                "notes": "Oxidative stress is a major trigger: ROS increase during VBNC entry (review across foodborne pathogens, mechanistically broad)."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "ppgpp",
            "predicate": "enhances",
            "object": "stress_resistance",
            "description": "(p)ppGpp accumulation enhances stress resistance during VBNC.",
            "evidence": [
              {
                "reference": "DOI:10.3390/foods12061179",
                "notes": "Accumulation of (p)ppGpp, enhancing stress resistance, supports the regulatory layer upstream of VBNC maintenance."
              }
            ]
          },
          {
            "subject": "stress_resistance",
            "predicate": "contributes to",
            "object": "vbnc_trait",
            "description": "Enhanced stress resistance supports maintenance of the VBNC state.",
            "evidence": [
              {
                "reference": "DOI:10.3390/foods12061179",
                "notes": "Stress resistance enhanced via (p)ppGpp underlies persistence in the VBNC state."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "rpos",
            "predicate": "required for",
            "object": "resuscitation",
            "description": "RpoS is required for resuscitation from the VBNC state.",
            "evidence": [
              {
                "reference": "DOI:10.3390/microorganisms12010039",
                "notes": "RpoS is expressed in VBNC cells and required for resuscitation; RpoS mutants fail to resuscitate."
              }
            ]
          },
          {
            "subject": "rpos",
            "predicate": "promotes",
            "object": "vbnc_trait",
            "description": "RpoS promotes persistence and retained resuscitation competence in the E. coli VBNC state.",
            "evidence": [
              {
                "reference": "DOI:10.1046/j.1462-2920.2003.00497.x",
                "snippet": "rpoS mutants lost culturability earlier and retained resuscitation capability for less time",
                "notes": "The primary loss-of-function comparison supports RpoS involvement in VBNC persistence."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "atp",
            "predicate": "promotes",
            "object": "resuscitation",
            "description": "ATP availability promotes resuscitation efficiency from VBNC.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.jare.2023.08.002",
                "notes": "Higher ATP levels correlated with higher resuscitation efficiency."
              }
            ],
            "predicate_id": "RO:0002213"
          },
          {
            "subject": "atp",
            "predicate": "drives",
            "object": "nad_synthesis",
            "description": "Residual ATP drives NAD+ synthesis during the resuscitating lag phase.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.jare.2023.08.002",
                "notes": "Part of cellular ATP is consumed during the lag phase to synthesize NAD+."
              }
            ]
          },
          {
            "subject": "nad_synthesis",
            "predicate": "restores",
            "object": "tca_oxphos",
            "description": "NAD+ synthesis restores TCA cycle flux and oxidative phosphorylation during resuscitation.",
            "evidence": [
              {
                "reference": "DOI:10.1016/j.jare.2023.08.002",
                "notes": "ATP-mediated NAD+ synthesis increases NAD+ availability, restoring TCA cycle flux and driving oxidative phosphorylation."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-06-04T00:00:00Z",
        "curator": "claude",
        "action": "PROPOSED_FROM_RESEARCH",
        "changes": "Proposed candidate PHYSIOLOGY trait (viable but nonculturable state); sub-variant of dormancy.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-08T13:00:00Z",
        "curator": "claude",
        "action": "CURATED_CAUSAL_GRAPH",
        "changes": "Added evidence-backed causal graph (stress-induced VBNC) with GO node grounding and biolink/RO predicate groundings; promoted PROPOSED to REVIEWED.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 7 evidence-backed generic edges (8 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:15Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002213\u00d72, RO:0002326\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T00:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_ENABLES_TRAIT_EDGES",
        "changes": "Migrated 1 causal edge(s) off enables/RO:0002327 with a TRAIT object (1 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-21T08:00:00Z",
        "curator": "codex",
        "action": "NORMALISE_NODE_TYPE",
        "changes": "Tranche 5 of issue 356 settles the process/quality families and merges ids that meant the same sense: stress_resistance is QUALITY. Stress resistance here is enhanced tolerance or resistance of a cell or mature endospore, a measurable protective attribute. The nodes do not describe the general stress-response process.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "CURATE_PROTEIN_TAXON_EXAMPLE",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope vbnc_stress_induced_dormancy=MECHANISTIC with scope_notes; added taxon-paired protein example(s) UniProtKB:P13445 on rpos (NCBITaxon:83333); regrounded 1 node(s) (rpos: none->InterPro:IPR012761); added 0 node(s) and 1 edge(s); added canonical example(s) NCBITaxon:83333.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-10-22T01:35:00Z",
        "curator": "claude",
        "action": "REFRESH_UNIPROT_ENTRY_VERSION",
        "changes": "Refreshed UniProtKB entry_version against live UniProt REST on 2026-10-22: UniProtKB:P13445 (207 -> 208 on rpos).",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "traitmech:000593",
    "label": "viscotaxis",
    "definition": "A motile phenotype in which active locomotion produces net migration in response to a spatial gradient in surrounding fluid viscosity.",
    "definition_source": "DOI:10.1099/00221287-109-1-113",
    "trait_category": "PHYSIOLOGY",
    "term_kind": "CLASS",
    "mapping_status": "PROPOSED",
    "parent_traits": [
      "METPO:1000702"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1099/00221287-109-1-113",
        "snippet": "We have designated this positive response to a viscosity gradient as 'viscotaxis'.",
        "notes": "Abstract, exact-matched at Europe PMC (PMID:731206); full text not inspected. The antecedent is preferential migration into the more viscous region by the paper's historically named Leptospira interrogans (biflexa) strain B16. This supports positive viscotaxis under the reported conditions, not a universal direction of response. The historical name has not been reconciled to a modern species or strain taxon; no modern Leptospira identity or pathogenicity is inferred."
      },
      {
        "reference": "DOI:10.1038/s41598-020-79887-7",
        "snippet": "they concentrate in the region of low viscosity or maintain a uniform concentration profile, depending on the viscosity ratio between the two regions.",
        "notes": "Abstract, exact-matched at Europe PMC (PMID:33432106). PMC7801662 full text, Fig. 5 and supplement Figs. S1-S3 were inspected. Wild-type Chlamydomonas reinhardtii showed net redistribution toward lower viscosity in some tested conditions but not others. Short-flagella results are not substituted for the wild type. Measurements followed pump stoppage; optical filtering limited phototactic bias. Interface reorientation, speed and angular diffusion jointly affect transport; a uniform profile is not positive evidence of net migration. The confined sharp-interface experiment does not directly validate an unconfined slowly varying gradient model. Strain accession provenance remains unresolved."
      },
      {
        "reference": "DOI:10.1103/physrevlett.120.208002",
        "snippet": "suitable body shapes create viscotaxis based on a systematic asymmetry of viscous forces acting on a microswimmer.",
        "notes": "Abstract, exact-matched at Europe PMC (PMID:29864289); full text not inspected. This is a theoretical framework for self-propelled swimmers in slowly varying viscosity fields, not a new biological migration assay or receptor discovery. It supports a possible hydrodynamic contribution without requiring a universal sensory pathway. Suggested functions of microbial body-shape changes are not treated as experimentally established molecular mechanisms."
      }
    ],
    "discussions": [
      {
        "discussion_id": "viscotaxis-direction-and-physical-boundaries",
        "prompt": "Retain directional and environmental scope of viscosity-driven migration.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "The class permits migration toward higher or lower fluid viscosity; neither direction nor a preferred viscosity is universal. Uniform-viscosity speed changes, passive advection and differential growth alone do not establish this trait. Keep fluid-viscosity gradients distinct from flow-directed rheotaxis, osmotic gradients, chemical cues and substrate stiffness or loss-modulus gradients. Coupled cues require controls rather than assumed equivalence. Hydrodynamic turning can bias an actively swimming organism without requiring a receptor. External equivalents and lexical variants remain unasserted pending authority and scope checks.",
        "posed_by": "codex",
        "posed_date": "2026-10-04"
      },
      {
        "discussion_id": "viscotaxis-canonical-provenance-and-mechanisms",
        "prompt": "Resolve natural strain identities and distinguish models from mechanisms.",
        "kind": "CURATION_TODO",
        "status": "OPEN",
        "rationale": "Reconcile the historical Leptospira B16 designation with current taxonomy before adding a canonical example; do not infer modern L. interrogans membership from the article title. The algae study distinguishes wild-type and short-flagella cells, but strain accessions and natural provenance have not been established in this curation. Keep their observations separate and resolve NCBI identity before adding examples. Inspect remaining full texts and separate proposed shape-dependent hydrodynamics from measured reorientation or redistribution. No universal receptor or protein-resolved causal pathway follows from these sources; taxon-paired accessions and direct evidence are needed before adding molecular edges. A NONMECHANISTIC graph must not bypass those requirements.",
        "posed_by": "codex",
        "posed_date": "2026-10-04"
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-10-04T09:34:00Z",
        "curator": "codex",
        "action": "MINTED_TRAITMECH_ID",
        "changes": "Added viscotaxis with three primary DOI citations and exact abstract snippets. Ignored-and-hidden novelty searches and structured OWL review found no exact record or METPO term. Reserved METPO:1054700 in v470. Inspected the algae full text and supplementary figures to separate conditional spatial redistribution from speed changes and model interpretations. Kept positive and negative response scope, deferred historical strain taxonomy, canonical examples, external equivalents and protein-resolved mechanisms.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:2000060",
    "label": "has maximum observed value",
    "definition": "The maximum temperature (\u00b0C) associated with this observation.",
    "trait_category": "QUANTITATIVE_PROPERTY",
    "term_kind": "DATATYPE_PROPERTY",
    "mapping_status": "DEPRECATED",
    "parent_traits": [
      "METPO:2000063"
    ],
    "domain": "https://w3id.org/metpo/1001000",
    "range_": "http://www.w3.org/2001/XMLSchema#decimal",
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.979069+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (DATATYPE_PROPERTY)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-08T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated datatype-property value carrier; later replacement should use more specific trait records that combine the maximum-value relation with the measured quantity, chemical, observation, or other entity.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-17T15:30:00-07:00",
        "curator": "claude",
        "action": "DEPRECATION_CONFIRMED_AS_OUT_OF_SCOPE",
        "changes": "DEPRECATED status confirmed as final after the predicate+class composition\npivot (#54/#55/#56). This record's observation-shape modelling is out of\nscope for TraitMech; the trait vocabulary + mechanism need is met by the un-\ndeprecated METPO predicates, and per-organism numeric observations belong\ndownstream (KG-Microbe / BacDive). See\ndocs/DEPRECATED_REPLACEMENT_PROPOSAL.md, section 'Observation-value records\nstay deprecated', for the rationale.\n",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:2000059",
    "label": "has minimum observed value",
    "definition": "The minimum temperature (\u00b0C) associated with this observation.",
    "trait_category": "QUANTITATIVE_PROPERTY",
    "term_kind": "DATATYPE_PROPERTY",
    "mapping_status": "DEPRECATED",
    "parent_traits": [
      "METPO:2000063"
    ],
    "domain": "https://w3id.org/metpo/1001000",
    "range_": "http://www.w3.org/2001/XMLSchema#decimal",
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.978574+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (DATATYPE_PROPERTY)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-08T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated datatype-property value carrier; later replacement should use more specific trait records that combine the minimum-value relation with the measured quantity, chemical, observation, or other entity.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-17T15:30:00-07:00",
        "curator": "claude",
        "action": "DEPRECATION_CONFIRMED_AS_OUT_OF_SCOPE",
        "changes": "DEPRECATED status confirmed as final after the predicate+class composition\npivot (#54/#55/#56). This record's observation-shape modelling is out of\nscope for TraitMech; the trait vocabulary + mechanism need is met by the un-\ndeprecated METPO predicates, and per-organism numeric observations belong\ndownstream (KG-Microbe / BacDive). See\ndocs/DEPRECATED_REPLACEMENT_PROPOSAL.md, section 'Observation-value records\nstay deprecated', for the rationale.\n",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:2000058",
    "label": "has observed spot value",
    "definition": "A reported temperature value (\u00b0C) for this observation.",
    "trait_category": "QUANTITATIVE_PROPERTY",
    "term_kind": "DATATYPE_PROPERTY",
    "mapping_status": "DEPRECATED",
    "parent_traits": [
      "METPO:2000063"
    ],
    "domain": "https://w3id.org/metpo/1001000",
    "range_": "http://www.w3.org/2001/XMLSchema#decimal",
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.978020+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (DATATYPE_PROPERTY)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-08T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated datatype-property value carrier; later replacement should use more specific trait records that combine the observed spot-value relation with the measured quantity, chemical, observation, or other entity.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-17T15:30:00-07:00",
        "curator": "claude",
        "action": "DEPRECATION_CONFIRMED_AS_OUT_OF_SCOPE",
        "changes": "DEPRECATED status confirmed as final after the predicate+class composition\npivot (#54/#55/#56). This record's observation-shape modelling is out of\nscope for TraitMech; the trait vocabulary + mechanism need is met by the un-\ndeprecated METPO predicates, and per-organism numeric observations belong\ndownstream (KG-Microbe / BacDive). See\ndocs/DEPRECATED_REPLACEMENT_PROPOSAL.md, section 'Observation-value records\nstay deprecated', for the rationale.\n",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:2000071",
    "label": "has value",
    "definition": "Relates any instance to a numerical value",
    "trait_category": "QUANTITATIVE_PROPERTY",
    "term_kind": "DATATYPE_PROPERTY",
    "mapping_status": "DEPRECATED",
    "range_": "http://www.w3.org/2001/XMLSchema#decimal",
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.981171+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (DATATYPE_PROPERTY)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-08T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated generic datatype-property value carrier; later replacement should use more specific trait records that combine the value relation with the measured quantity, chemical, observation, or other entity.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-17T15:30:00-07:00",
        "curator": "claude",
        "action": "DEPRECATION_CONFIRMED_AS_OUT_OF_SCOPE",
        "changes": "DEPRECATED status confirmed as final after the predicate+class composition\npivot (#54/#55/#56). This record's observation-shape modelling is out of\nscope for TraitMech; the trait vocabulary + mechanism need is met by the un-\ndeprecated METPO predicates, and per-organism numeric observations belong\ndownstream (KG-Microbe / BacDive). See\ndocs/DEPRECATED_REPLACEMENT_PROPOSAL.md, section 'Observation-value records\nstay deprecated', for the rationale.\n",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:2000061",
    "label": "has value comments",
    "definition": "Free-text comments associated with this observation.",
    "trait_category": "QUANTITATIVE_PROPERTY",
    "term_kind": "DATATYPE_PROPERTY",
    "mapping_status": "DEPRECATED",
    "parent_traits": [
      "METPO:2000063"
    ],
    "domain": "https://w3id.org/metpo/1001000",
    "range_": "http://www.w3.org/2001/XMLSchema#string",
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.979566+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (DATATYPE_PROPERTY)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-08T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated datatype-property comment carrier; later replacement should use more specific trait records that combine the comment relation with the measured quantity, chemical, observation, or other entity.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-17T15:30:00-07:00",
        "curator": "claude",
        "action": "DEPRECATION_CONFIRMED_AS_OUT_OF_SCOPE",
        "changes": "DEPRECATED status confirmed as final after the predicate+class composition\npivot (#54/#55/#56). This record's observation-shape modelling is out of\nscope for TraitMech; the trait vocabulary + mechanism need is met by the un-\ndeprecated METPO predicates, and per-organism numeric observations belong\ndownstream (KG-Microbe / BacDive). See\ndocs/DEPRECATED_REPLACEMENT_PROPOSAL.md, section 'Observation-value records\nstay deprecated', for the rationale.\n",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:2000062",
    "label": "is negative data",
    "definition": "True if this observation indicates no growth at the reported temperature (negative result).",
    "trait_category": "QUANTITATIVE_PROPERTY",
    "term_kind": "DATATYPE_PROPERTY",
    "mapping_status": "DEPRECATED",
    "parent_traits": [
      "METPO:2000063"
    ],
    "domain": "https://w3id.org/metpo/1001000",
    "range_": "http://www.w3.org/2001/XMLSchema#boolean",
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.980203+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (DATATYPE_PROPERTY)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-08T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated datatype-property boolean result carrier; later replacement should use more specific trait records that combine the negative-result relation with the measured quantity, chemical, observation, or other entity.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-17T15:30:00-07:00",
        "curator": "claude",
        "action": "DEPRECATION_CONFIRMED_AS_OUT_OF_SCOPE",
        "changes": "DEPRECATED status confirmed as final after the predicate+class composition\npivot (#54/#55/#56). This record's observation-shape modelling is out of\nscope for TraitMech; the trait vocabulary + mechanism need is met by the un-\ndeprecated METPO predicates, and per-organism numeric observations belong\ndownstream (KG-Microbe / BacDive). See\ndocs/DEPRECATED_REPLACEMENT_PROPOSAL.md, section 'Observation-value records\nstay deprecated', for the rationale.\n",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:2000063",
    "label": "observation data property",
    "trait_category": "QUANTITATIVE_PROPERTY",
    "term_kind": "DATATYPE_PROPERTY",
    "mapping_status": "DEPRECATED",
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.980776+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (DATATYPE_PROPERTY)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-08T00:00:00-07:00",
        "curator": "codex",
        "action": "DEPRECATED_PROPERTY_RECORD",
        "changes": "Deprecated upper datatype-property carrier for observation data; later replacement should use more specific trait records that combine the data relation with chemicals, measurements, observations, or other entities.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-17T15:30:00-07:00",
        "curator": "claude",
        "action": "DEPRECATION_CONFIRMED_AS_OUT_OF_SCOPE",
        "changes": "DEPRECATED status confirmed as final after the predicate+class composition\npivot (#54/#55/#56). This record's observation-shape modelling is out of\nscope for TraitMech; the trait vocabulary + mechanism need is met by the un-\ndeprecated METPO predicates, and per-organism numeric observations belong\ndownstream (KG-Microbe / BacDive). See\ndocs/DEPRECATED_REPLACEMENT_PROPOSAL.md, section 'Observation-value records\nstay deprecated', for the rationale.\n",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000630",
    "label": "biological process",
    "definition": "A execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.",
    "definition_source": "DOI:10.1093/database/bat054",
    "trait_category": "UPPER",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "synonyms": [
      {
        "synonym_text": "physiological process",
        "synonym_type": "EXACT_SYNONYM",
        "source": "http://purl.obolibrary.org/obo/go/releases/2026-07-26/go-basic.obo"
      }
    ],
    "xrefs": [
      "GO:0008150"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1093/database/bat054",
        "snippet": "gene product can be associated to a GO term",
        "notes": "Supports biological process as a Gene Ontology aspect used for annotating gene-product roles."
      },
      {
        "reference": "DOI:10.1093/database/bat054",
        "snippet": "biological process, molecular function, or cellular component",
        "notes": "Supports biological process as one of the core GO annotation aspects."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "biological_process_go_upper_context",
        "title": "Biological process upper-class context",
        "description": "DOI-backed upper-ontology context graph linking biological process to molecular functions, gene products, and the non-environmental child metabolism class.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This is an upper-ontology context graph, not a taxon-specific biological mechanism. Gene products are described by the remaining GO-CAM context but are not modeled as primary causal nodes or token protein examples.",
        "nodes": [
          {
            "node_id": "biological_process_trait",
            "label": "biological process",
            "node_type": "BIOLOGICAL_PROCESS",
            "grounding": "METPO:1000630",
            "xrefs": [
              "GO:0008150"
            ],
            "description": "Upper-level process class for genetically encoded biological programs."
          },
          {
            "node_id": "molecular_function",
            "label": "molecular function",
            "node_type": "MOLECULAR_FUNCTION",
            "grounding": "GO:0003674",
            "description": "Elemental molecular activity carried out by a gene product."
          },
          {
            "node_id": "metabolism_trait",
            "label": "metabolism",
            "node_type": "TRAIT",
            "grounding": "METPO:1000060",
            "description": "Non-environmental TraitMech child class under biological process."
          },
          {
            "node_id": "cellular_component",
            "label": "cellular component",
            "node_type": "CELLULAR_LOCALIZATION",
            "description": "GO cellular component where a molecular activity occurs.",
            "grounding": "GO:0005575"
          },
          {
            "node_id": "chemical_input",
            "label": "chemical input entity",
            "node_type": "CHEMICAL",
            "description": "Chemical entity consumed as input of a molecular activity."
          },
          {
            "node_id": "chemical_output",
            "label": "chemical output entity",
            "node_type": "CHEMICAL",
            "description": "Chemical entity produced as output of a molecular activity."
          },
          {
            "node_id": "molecular_function_downstream",
            "label": "downstream molecular function",
            "node_type": "MOLECULAR_FUNCTION",
            "description": "A molecular function causally downstream of another in a GO-CAM model."
          }
        ],
        "edges": [
          {
            "subject": "molecular_function",
            "predicate": "contributes to",
            "object": "biological_process_trait",
            "description": "Molecular functions collectively accomplish broader biological processes.",
            "evidence": [
              {
                "reference": "DOI:10.1093/database/bat054",
                "snippet": "Molecular Function, Biological Process and Cellular Component",
                "notes": "Supports GO annotation across molecular functions and biological processes."
              }
            ],
            "predicate_id": "RO:0002326"
          },
          {
            "subject": "metabolism_trait",
            "predicate": "specializes",
            "object": "biological_process_trait",
            "description": "In TraitMech, metabolism is the non-environmental child class under biological process.",
            "evidence": [
              {
                "reference": "DOI:10.1093/database/bat054",
                "snippet": "child term is a subtype of the parent term",
                "notes": "Supports parent-child is-a interpretation for GO-style process hierarchies."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "molecular_function",
            "predicate": "part of",
            "object": "biological_process_trait",
            "description": "GO Molecular Functions are linked to Biological Processes by mereological part_of relations.",
            "evidence": [
              {
                "reference": "DOI:10.1186/s40708-023-00208-5",
                "notes": "a GO Molecular Function and a GO Biological Process (BP) are linked by mereological (part_of) relations"
              }
            ],
            "predicate_id": "biolink:part_of"
          },
          {
            "subject": "molecular_function",
            "predicate": "occurs in",
            "object": "cellular_component",
            "description": "A molecular activity occurs in a cellular component (BFO:0000066).",
            "evidence": [
              {
                "reference": "DOI:10.1186/s40708-023-00208-5",
                "notes": "Occurs in [BFO:0000066]; example \"glucokinase activity occurs in cytosol\"."
              }
            ],
            "predicate_id": "biolink:occurs_in"
          },
          {
            "subject": "molecular_function",
            "predicate": "has input",
            "object": "chemical_input",
            "description": "A molecular activity has a chemical entity as input (RO:0002233).",
            "evidence": [
              {
                "reference": "DOI:10.1186/s40708-023-00208-5",
                "notes": "Has input [RO:0002233]"
              }
            ],
            "predicate_id": "RO:0002233"
          },
          {
            "subject": "molecular_function",
            "predicate": "has output",
            "object": "chemical_output",
            "description": "A molecular activity has a chemical entity as output (RO:0002234).",
            "evidence": [
              {
                "reference": "DOI:10.1186/s40708-023-00208-5",
                "notes": "Has output [RO:0002234]"
              }
            ],
            "predicate_id": "RO:0002234"
          },
          {
            "subject": "molecular_function",
            "predicate": "causally upstream of or within",
            "object": "molecular_function_downstream",
            "description": "GO-CAMs causally link molecular functions into structured models of biological processes (RO:0002418).",
            "evidence": [
              {
                "reference": "DOI:10.1186/s40708-023-00208-5",
                "notes": "GO-CAMs arrange GO annotations into structured models of biological processes by causally linking GO Molecular Functions"
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.866352+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-15T00:35:00-07:00",
        "curator": "codex",
        "action": "CURATED_UPPER_CONTEXT",
        "changes": "Reviewed biological process as an upper classifier and added a DOI-backed context graph linking molecular functions, gene products, and the metabolism child class.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:32Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002326\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T08:21:50Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (rdfs:subClassOf\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 6 evidence-backed generic edges (4 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:21:15Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:part_of\u00d71, biolink:occurs_in\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-24T17:23:35Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_NODES",
        "changes": "Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0005575\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T03:49:24Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002234\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T09:03:55Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002233\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope biological_process_go_upper_context=NONMECHANISTIC with scope_notes; removed 1 node(s) and 2 edge(s) together with their evidence (gene_product).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T06:15:41Z",
        "curator": "codex",
        "action": "ADD_EXACT_ONTOLOGY_MATCH",
        "changes": "Ontology exact-match review (2026-08-25): declared exact synonym(s): 'physiological process'. Evidence is predicate-scoped in the versioned ontology snapshots; OAK cross-checked direct data, and OLS4 spot-checked release deltas and disputed hits.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000526",
    "label": "chemical entity",
    "definition": "A material entity that is a physical entity of interest in chemistry, including molecular entities, parts thereof, and chemical substances. Used as the range class for the majority of METPO chemical-use OBJECT_PROPERTYs (uses_as_carbon_source, uses_as_electron_donor, ferments, oxidizes, etc.) so that organism-to-chemical assertions resolve to a curated chemical class.",
    "definition_source": "DOI:10.1093/nar/gkv1031",
    "trait_category": "UPPER",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000186"
    ],
    "xrefs": [
      "CHEBI:24431"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1093/nar/gkv1031",
        "snippet": "ChEBI is a freely available dictionary of molecular entities",
        "notes": "ChEBI's 'chemical entity' (CHEBI:24431) is the canonical upper-root for the chemical objects participating in METPO chemical-use predicates and is the recommended grounding for METPO:1000526."
      },
      {
        "reference": "DOI:10.3233/AO-220262",
        "snippet": "BFO is a genuine top-level ontology",
        "notes": "Supports METPO:1000186 (material entity) as the BFO-aligned parent of chemical entity."
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-16T09:30:00-07:00",
        "curator": "claude",
        "action": "CREATED_UPPER_CLASS_RECORD",
        "changes": "Created upper-ontology CLASS record for METPO:1000526 (chemical entity) so that the range of un-deprecated metabolism OBJECT_PROPERTYs resolves to a curated TraitMech record. Added xref to CHEBI:24431, which is the exact ChEBI equivalent (same definition, same root position). TraitMech records can use either METPO:1000526 or CHEBI:24431 as range_; this xref makes them interconvertible.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000527",
    "label": "enzyme",
    "definition": "A biological macromolecule (typically a protein, occasionally a catalytic RNA) that catalyses a specific biochemical reaction. This class is the material-entity sense of \"enzyme\" (the molecule itself), matching METPO:1000527's placement as a subclass of METPO:1000186 (material entity). Used as the range class for METPO enzyme-related OBJECT_PROPERTYs (shows_activity_of, enzyme_activity_analyzed, does_not_show_activity_of).",
    "definition_source": "DOI:10.1093/nar/gku1003",
    "trait_category": "UPPER",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000186"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1093/nar/gku1003",
        "snippet": "ENZYME nomenclature",
        "notes": "ENZYME / EC nomenclature provides the canonical external vocabulary for enzymes named by the catalytic reaction they perform; supports 'enzyme' as a recognised material-entity class."
      },
      {
        "reference": "PMID:21413255",
        "snippet": "enzymes",
        "notes": "Medical Microbiology chapter uses 'enzyme' in the material-entity sense (the biocatalyst protein) throughout its physiology and metabolism discussion; consistent with this record's scope."
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-16T09:30:00-07:00",
        "curator": "claude",
        "action": "CREATED_UPPER_CLASS_RECORD",
        "changes": "Created upper-ontology CLASS record for METPO:1000527 (enzyme) so that the range of un-deprecated activity-assay OBJECT_PROPERTYs (shows_activity_of, enzyme_activity_analyzed, and their negation companions) resolves to a curated TraitMech record.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-16T09:45:00-07:00",
        "curator": "claude",
        "action": "REMOVED_NON_EQUIVALENT_XREFS_AND_TIGHTENED_DEFINITION",
        "changes": "Per Copilot review of PR #55, removed xrefs to GO:0003824 (catalytic activity) and CHEBI:23357 (catalyst). Neither is an equivalence mapping: GO:0003824 is an activity/process class and CHEBI:23357 is a role, while this record represents the enzyme material entity. The definition was rewritten to be strictly about the enzyme molecule itself, removing the earlier wording that conflated material entity with catalytic activity. No clean cross-ontology equivalent for the material-entity \"enzyme\" class is available (CHEBI does not have a single enzyme class; PR is too broad as \"protein\"), so xrefs is left empty.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000186",
    "label": "material entity",
    "definition": "An object or portion of a substance or mixture of substances that consists of matter",
    "definition_source": "DOI:10.3233/AO-220262",
    "trait_category": "UPPER",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "created_by": "Anthea Guo",
    "evidence": [
      {
        "reference": "DOI:10.3233/AO-220262",
        "snippet": "BFO is a genuine top-level ontology",
        "notes": "Supports material entity as a top-level ontology class rather than a concrete microbial trait."
      },
      {
        "reference": "DOI:10.7551/mitpress/9780262527811.001.0001",
        "snippet": "specific top-level ontology, the Basic Formal Ontology",
        "notes": "Supports BFO as the upper ontology context for material entity."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "material_entity_bfo_upper_context",
        "title": "Material entity upper-class context",
        "description": "DOI-backed upper-ontology context graph linking material entities to qualities, observations, and processes without asserting a taxon-specific microbial mechanism.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "This is an upper-ontology context graph; protein-mediated causality and taxon-specific protein examples are inapplicable.",
        "nodes": [
          {
            "node_id": "material_entity_trait",
            "label": "material entity",
            "node_type": "TRAIT",
            "grounding": "METPO:1000186",
            "xrefs": [
              "BFO:0000040"
            ],
            "description": "Upper-level class for objects or portions of matter."
          },
          {
            "node_id": "quality_trait",
            "label": "quality",
            "node_type": "TRAIT",
            "grounding": "METPO:1000188",
            "description": "Dependent characteristic borne by an entity."
          },
          {
            "node_id": "observation_trait",
            "label": "observation",
            "node_type": "EXPERIMENTAL_FACTOR",
            "grounding": "METPO:1001000",
            "description": "Measurement or data-collection context about an entity or its qualities."
          },
          {
            "node_id": "biological_process_trait",
            "label": "biological process",
            "node_type": "BIOLOGICAL_PROCESS",
            "grounding": "METPO:1000630",
            "description": "Process in which material entities can participate."
          }
        ],
        "edges": [
          {
            "subject": "material_entity_trait",
            "predicate": "can bear",
            "object": "quality_trait",
            "description": "Material entities provide bearers for qualities used in trait descriptions.",
            "evidence": [
              {
                "reference": "DOI:10.1186/gb-2010-11-1-r2",
                "snippet": "entity that is observed to be affected",
                "notes": "Supports the entity-quality pattern in phenotype representation."
              }
            ]
          },
          {
            "subject": "observation_trait",
            "predicate": "can be about",
            "object": "material_entity_trait",
            "description": "Observations and investigation outputs can be about material entities and their qualities.",
            "evidence": [
              {
                "reference": "DOI:10.1371/journal.pone.0154556",
                "snippet": "results of a study can be about any material entity",
                "notes": "Supports material entities as subjects of biomedical investigation data."
              }
            ]
          },
          {
            "subject": "material_entity_trait",
            "predicate": "can participate in",
            "object": "biological_process_trait",
            "description": "Material entities can participate in biological processes, but this upper record has no direct TraitMech children.",
            "evidence": [
              {
                "reference": "DOI:10.3233/AO-220262",
                "snippet": "support information integration, retrieval, and analysis",
                "notes": "Supports BFO as the upper ontology used to place material entities in scientific-domain representations."
              }
            ],
            "predicate_id": "biolink:participates_in"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.811703+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-15T00:35:00-07:00",
        "curator": "codex",
        "action": "CURATED_UPPER_CONTEXT",
        "changes": "Reviewed material entity as an upper classifier and added a DOI-backed context graph; no direct TraitMech children were present.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-13T21:03:27Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:participates_in\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope material_entity_bfo_upper_context=NONMECHANISTIC with scope_notes.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000525",
    "label": "microbe",
    "definition": "A material entity that is too small to be viewed by the unaided eye, typically requiring microscopy for observation. Used as the domain class for METPO organism-to-X object properties so that organism-level assertions can be expressed as `<microbe-instance> <METPO predicate> <object-class>`.",
    "definition_source": "PMID:21413255",
    "trait_category": "UPPER",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000186"
    ],
    "evidence": [
      {
        "reference": "PMID:21413255",
        "snippet": "microorganisms",
        "notes": "Medical Microbiology chapter supports 'microbe' (microorganism) as the standard high-level class for the bacteria, archaea, and microbial eukaryotes covered by this knowledge base."
      },
      {
        "reference": "DOI:10.3233/AO-220262",
        "snippet": "BFO is a genuine top-level ontology",
        "notes": "Supports METPO:1000186 (material entity) as the BFO-aligned parent."
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-16T09:30:00-07:00",
        "curator": "claude",
        "action": "CREATED_UPPER_CLASS_RECORD",
        "changes": "Created upper-ontology CLASS record for METPO:1000525 (microbe) so that the domain of un-deprecated metabolism OBJECT_PROPERTYs (which all declare domain https://w3id.org/metpo/1000525) resolves to a curated TraitMech record.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-16T09:45:00-07:00",
        "curator": "claude",
        "action": "REMOVED_NON_EQUIVALENT_XREF",
        "changes": "Removed xref to OBI:0100026 (organism) per Copilot review of PR #55. The schema documents xrefs as ontology *equivalents*; OBI:0100026 \"organism\" is broader than \"microbe\" (it covers macro-organisms too), so treating it as an equivalence mapping would mis-align downstream consumers. No clean NCBITaxon, OBI, or ENVO equivalent for \"microbe\" exists because the concept cuts across bacteria, archaea, and microbial eukaryotes; left without xrefs.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1001000",
    "label": "observation",
    "definition": "A data-collection or measurement context in which trait-relevant qualities of organisms, samples, or conditions are recorded.",
    "definition_source": "DOI:10.1371/journal.pone.0154556",
    "trait_category": "UPPER",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "evidence": [
      {
        "reference": "DOI:10.1371/journal.pone.0154556",
        "snippet": "data generated and the types of analysis performed",
        "notes": "Supports observation as an investigation/data-generation context."
      },
      {
        "reference": "DOI:10.1371/journal.pone.0154556",
        "snippet": "the output of an assay is typically a data item",
        "notes": "Supports observations as links between assays, measurements, and data."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "observation_measurement_upper_context",
        "title": "Observation measurement upper-class context",
        "description": "DOI-backed upper-ontology context graph for observations as assay or measurement outputs about material entities and qualities. Child observation records are deprecated relation/value carriers and are not expanded as mechanistic trait nodes here.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "Observation is a measurement and metadata upper class, not a biological mechanism; no protein node or example is applicable.",
        "nodes": [
          {
            "node_id": "observation_trait",
            "label": "observation",
            "node_type": "EXPERIMENTAL_FACTOR",
            "grounding": "METPO:1001000",
            "description": "Upper-level class for trait-relevant measurement observations."
          },
          {
            "node_id": "assay_measurement",
            "label": "assay or measurement process",
            "node_type": "BIOLOGICAL_PROCESS",
            "description": "Investigation process that measures a quality."
          },
          {
            "node_id": "data_item",
            "label": "data item",
            "node_type": "EXPERIMENTAL_FACTOR",
            "description": "Information output generated by an assay or observation."
          },
          {
            "node_id": "measured_quality",
            "label": "measured quality",
            "node_type": "TRAIT",
            "grounding": "METPO:1000188",
            "description": "Quality such as temperature, pH, salinity, oxygen, or phenotype status captured by observation records."
          },
          {
            "node_id": "material_entity",
            "label": "material entity",
            "node_type": "TRAIT",
            "grounding": "METPO:1000186",
            "description": "Entity or sample about which an observation is made."
          },
          {
            "node_id": "geographic_location",
            "label": "geographic location",
            "node_type": "ENVIRONMENTAL_FACTOR",
            "description": "Contextual place metadata (e.g., location) attached to an observation data item."
          },
          {
            "node_id": "material_entity_evaluant",
            "label": "material entity with evaluant role",
            "node_type": "TRAIT",
            "description": "Generalized observed target/input of an assay, bearing an evaluant role."
          },
          {
            "node_id": "measurement_datum",
            "label": "measurement datum",
            "node_type": "EXPERIMENTAL_FACTOR",
            "description": "Information output of an observation/assay process, comparable to SOSA Result."
          },
          {
            "node_id": "planned_process",
            "label": "planned process",
            "node_type": "EXPERIMENTAL_FACTOR",
            "description": "OBI planned process with specified inputs and outputs; assays are planned processes."
          },
          {
            "node_id": "sample",
            "label": "sample",
            "node_type": "TRAIT",
            "description": "Collected material entity about which observations are made."
          },
          {
            "node_id": "metadata",
            "label": "metadata",
            "node_type": "EXPERIMENTAL_FACTOR",
            "description": "Contextual information about samples, procedures, and analysis."
          },
          {
            "node_id": "mixs_standard",
            "label": "MIxS reporting standard",
            "node_type": "EXPERIMENTAL_FACTOR",
            "description": "Standard providing per-sample metadata elements for genomic sample provenance."
          },
          {
            "node_id": "fair_principles",
            "label": "FAIR principles",
            "node_type": "EXPERIMENTAL_FACTOR",
            "description": "Principles tying observation reuse to rich metadata and persistent identifiers."
          },
          {
            "node_id": "unique_identifier",
            "label": "unique identifier",
            "node_type": "EXPERIMENTAL_FACTOR",
            "description": "Persistent identifier required for FAIR objects and datasets."
          }
        ],
        "edges": [
          {
            "subject": "assay_measurement",
            "predicate": "has output",
            "object": "data_item",
            "description": "Assays and measurements generate data items.",
            "evidence": [
              {
                "reference": "DOI:10.1371/journal.pone.0154556",
                "snippet": "the output of an assay is typically a data item",
                "notes": "Supports assay outputs as data items."
              }
            ],
            "predicate_id": "RO:0002234"
          },
          {
            "subject": "data_item",
            "predicate": "records",
            "object": "measured_quality",
            "description": "Observation data record a measured quality.",
            "evidence": [
              {
                "reference": "DOI:10.1371/journal.pone.0154556",
                "snippet": "measuring its glucose concentration",
                "notes": "Supports measurement outputs as records of qualities."
              }
            ]
          },
          {
            "subject": "observation_trait",
            "predicate": "is about",
            "object": "material_entity",
            "description": "Observation records are about material entities or samples and their qualities.",
            "evidence": [
              {
                "reference": "DOI:10.1371/journal.pone.0154556",
                "snippet": "can be about any material entity",
                "notes": "Supports observations and study outputs as about material entities."
              }
            ]
          },
          {
            "subject": "observation_trait",
            "predicate": "has context",
            "object": "geographic_location",
            "description": "Observation data items require contextual information about time and place of measurement.",
            "evidence": [
              {
                "reference": "DOI:10.3233/sw-223096",
                "notes": "An observation data item requires a data structure to encompass the contextual information about the time and place etc. of a measurement."
              }
            ]
          },
          {
            "subject": "assay_measurement",
            "predicate": "has specified input",
            "object": "material_entity_evaluant",
            "description": "An assay has a material entity with evaluant role as specified input.",
            "evidence": [
              {
                "reference": "DOI:10.3233/sw-223096",
                "notes": "OBI: assay and has_specified_input some (material entity and has role some evaluant role); generalized, not microbe-specific."
              }
            ]
          },
          {
            "subject": "assay_measurement",
            "predicate": "has output",
            "object": "measurement_datum",
            "description": "An assay produces a measurement datum as output of the observation process.",
            "evidence": [
              {
                "reference": "DOI:10.3233/sw-223096",
                "notes": "SOSA Result and IAO measurement datum are comparable outputs of an observation process."
              }
            ],
            "predicate_id": "RO:0002234"
          },
          {
            "subject": "planned_process",
            "predicate": "has specified input",
            "object": "sample",
            "description": "A planned process takes material entities such as samples as specified inputs.",
            "evidence": [
              {
                "reference": "DOI:10.3233/sw-223096",
                "notes": "OBI has specified input/output pertain to planned process with material entities (for assays) as targets."
              }
            ]
          },
          {
            "subject": "metadata",
            "predicate": "recorded in",
            "object": "mixs_standard",
            "description": "Sample/source-environment metadata is recorded using MIxS metadata elements.",
            "evidence": [
              {
                "reference": "DOI:10.1007/978-1-0716-3838-5_20",
                "notes": "MIxS consists of a number of metadata elements that describe a particular characteristic of the sample or its source environment."
              }
            ]
          },
          {
            "subject": "fair_principles",
            "predicate": "requires metadata",
            "object": "unique_identifier",
            "description": "FAIR requires each object or dataset to have a unique identifier and rich metadata.",
            "evidence": [
              {
                "reference": "DOI:10.3389/fcimb.2024.1384809",
                "notes": "FAIR requires each FAIR object or dataset have a unique identifier and be described with rich metadata."
              }
            ]
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.923123+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-15T00:35:00-07:00",
        "curator": "codex",
        "action": "CURATED_UPPER_CONTEXT",
        "changes": "Added definition, DOI-backed evidence, and a measurement-context graph for observation; deprecated observation child records were reviewed as relation/value carriers rather than standalone mechanistic traits.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:32Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-06-23T00:00:00Z",
        "curator": "claude",
        "action": "ENRICH_CAUSAL_GRAPH",
        "changes": "Added 6 evidence-backed generic edges (9 new nodes) from the deep-research report.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T02:00:00Z",
        "curator": "claude",
        "action": "MIGRATE_MICROBE_DOMAIN_EDGES_PART2",
        "changes": "Re-grounded 1 causal edge(s) off microbe-domain METPO predicates onto their causal-graph counterparts (1 to produces), issue 301 part 2. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Each replacement is a 1:1 mirror of its source predicate that changes only the domain, so the claim each edge makes is unchanged and directions are unchanged. The replacements are proposed in proposals/metpo_traitmech_v9 and are placeholder ids until METPO mints them.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T04:29:06Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002234\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-06T04:35:00Z",
        "curator": "claude",
        "action": "RETYPE_CAUSAL_NODE",
        "changes": "Retyped assay_measurement from EXPERIMENTAL_FACTOR to BIOLOGICAL_PROCESS and moved its data_item edge from produces to has output (RO:0002234), issue 301. The node's own description calls it an investigation process and the record already carried a second has-output edge from it, so the EXPERIMENTAL_FACTOR typing was inconsistent with both. While it stood, the edge routed around the produces/has-output split - that split is spelled as node types, and the exclusion named only the three activity types - and landed on METPO:2007800, whose definition is about producing a chemical entity. Retyping also let the previously blocked measurement_datum has-output edge ground.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope observation_measurement_upper_context=NONMECHANISTIC with scope_notes.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000059",
    "label": "phenotype",
    "definition": "A quality that differentiates specific instances of a species from other instances of the same species.",
    "definition_source": "DOI:10.1186/gb-2010-11-1-r2",
    "trait_category": "UPPER",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "parent_traits": [
      "METPO:1000188"
    ],
    "created_by": "Luke Wang",
    "evidence": [
      {
        "reference": "DOI:10.1186/gb-2010-11-1-r2",
        "snippet": "entity that is observed to be affected",
        "notes": "Supports phenotype representation through entity-quality descriptions."
      },
      {
        "reference": "DOI:10.1186/gb-2010-11-1-r2",
        "snippet": "specific characteristic or quality of that entity affected",
        "notes": "Supports phenotype as an observed quality of an entity."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "phenotype_quality_child_context",
        "title": "Phenotype quality and child-trait context",
        "description": "DOI-backed upper-ontology context graph linking phenotype to its quality parent and to non-environmental, non-genomic TraitMech child groupings.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "Phenotype is an upper classification spanning many unrelated mechanisms; assigning one token protein would be misleading.",
        "nodes": [
          {
            "node_id": "phenotype_trait",
            "label": "phenotype",
            "node_type": "TRAIT",
            "grounding": "METPO:1000059",
            "description": "Upper-level class for organismal qualities and observable trait classes."
          },
          {
            "node_id": "quality_parent",
            "label": "quality",
            "node_type": "TRAIT",
            "grounding": "METPO:1000188",
            "description": "Parent upper class for qualities."
          },
          {
            "node_id": "morphology_children",
            "label": "morphology child traits",
            "node_type": "TRAIT",
            "description": "Non-environmental morphology children such as cell shape, cell size, Gram stain, pigmentation, motility, and sporulation."
          },
          {
            "node_id": "physiology_child",
            "label": "trophic type",
            "node_type": "TRAIT",
            "grounding": "METPO:1000631",
            "description": "Physiology child class under phenotype."
          },
          {
            "node_id": "ecology_child",
            "label": "pathogenic to host",
            "node_type": "TRAIT",
            "grounding": "METPO:1004000",
            "description": "Ecology child class under phenotype."
          }
        ],
        "edges": [
          {
            "subject": "phenotype_trait",
            "predicate": "is a",
            "object": "quality_parent",
            "description": "Phenotypes are modeled as qualities or quality-bearing descriptions of entities.",
            "evidence": [
              {
                "reference": "DOI:10.1186/gb-2010-11-1-r2",
                "snippet": "ontology of qualities termed Phenotype and Trait ontology",
                "notes": "Supports phenotype representation through PATO quality classes."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "morphology_children",
            "predicate": "specializes",
            "object": "phenotype_trait",
            "description": "Morphology classes are non-environmental child phenotypes in TraitMech.",
            "evidence": [
              {
                "reference": "DOI:10.1186/gb-2010-11-1-r2",
                "snippet": "size, color, shape, structure",
                "notes": "Supports morphology-like qualities as phenotype descriptors."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "physiology_child",
            "predicate": "specializes",
            "object": "phenotype_trait",
            "description": "Trophic type is retained as a non-environmental physiology child under phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1186/gb-2010-11-1-r2",
                "snippet": "logical definitions and associated ontologies",
                "notes": "Supports phenotype classes as organized through ontology-backed definitions and parent-child placement."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "ecology_child",
            "predicate": "specializes",
            "object": "phenotype_trait",
            "description": "Pathogenic-to-host is retained as a non-environmental ecology child under phenotype.",
            "evidence": [
              {
                "reference": "DOI:10.1186/gb-2010-11-1-r2",
                "snippet": "phenotype ontologies across multiple species",
                "notes": "Supports phenotype hierarchies spanning different biological domains."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.809675+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-15T00:35:00-07:00",
        "curator": "codex",
        "action": "CURATED_UPPER_CONTEXT",
        "changes": "Reviewed phenotype as an upper quality-derived classifier and added a DOI-backed context graph covering its quality parent plus non-environmental, non-genomic child groupings.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:32Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (rdfs:subClassOf\u00d71).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-23T08:21:50Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (rdfs:subClassOf\u00d73).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope phenotype_quality_child_context=NONMECHANISTIC with scope_notes.",
        "llm_assisted": true
      }
    ]
  },
  {
    "identifier": "METPO:1000188",
    "label": "quality",
    "definition": "A characteristic of an entity that depends on the entity's existence, size, color, and physiological traits.",
    "definition_source": "DOI:10.1186/gb-2010-11-1-r2",
    "trait_category": "UPPER",
    "term_kind": "CLASS",
    "mapping_status": "REVIEWED",
    "xrefs": [
      "PATO:0000001"
    ],
    "evidence": [
      {
        "reference": "DOI:10.1186/gb-2010-11-1-r2",
        "snippet": "ontology of qualities termed Phenotype and Trait ontology",
        "notes": "Supports quality as an upper class used to construct phenotype descriptions."
      },
      {
        "reference": "DOI:10.1186/gb-2010-11-1-r2",
        "snippet": "specific characteristic or quality of that entity",
        "notes": "Supports qualities as entity-dependent phenotype descriptors."
      }
    ],
    "causal_graphs": [
      {
        "graph_id": "quality_upper_child_context",
        "title": "Quality upper-class child context",
        "description": "DOI-backed upper-ontology context graph linking quality to phenotype and biosafety-level child classes while excluding the genomic GC content child from this batch.",
        "scope_status": "NONMECHANISTIC",
        "scope_notes": "Quality is an upper ontology class rather than a protein-mediated microbial mechanism, so no taxon or protein example is applicable.",
        "nodes": [
          {
            "node_id": "quality_trait",
            "label": "quality",
            "node_type": "TRAIT",
            "grounding": "METPO:1000188",
            "description": "Upper class for entity-dependent characteristics."
          },
          {
            "node_id": "material_entity",
            "label": "material entity",
            "node_type": "TRAIT",
            "grounding": "METPO:1000186",
            "description": "Entity that can bear a quality."
          },
          {
            "node_id": "phenotype_trait",
            "label": "phenotype",
            "node_type": "TRAIT",
            "grounding": "METPO:1000059",
            "description": "TraitMech child class for observable organismal qualities."
          },
          {
            "node_id": "biosafety_level_trait",
            "label": "biosafety level",
            "node_type": "TRAIT",
            "grounding": "METPO:1001101",
            "description": "Ecology child class that classifies biological-agent hazard and containment level."
          }
        ],
        "edges": [
          {
            "subject": "quality_trait",
            "predicate": "characterizes",
            "object": "material_entity",
            "description": "Qualities characterize or inhere in entities.",
            "evidence": [
              {
                "reference": "DOI:10.1186/gb-2010-11-1-r2",
                "snippet": "specific characteristic or quality of that entity",
                "notes": "Supports entity-dependent qualities in phenotype descriptions."
              }
            ]
          },
          {
            "subject": "phenotype_trait",
            "predicate": "is a",
            "object": "quality_trait",
            "description": "Phenotype is a quality-derived child class in TraitMech.",
            "evidence": [
              {
                "reference": "DOI:10.1186/gb-2010-11-1-r2",
                "snippet": "Phenotype and Trait ontology",
                "notes": "Supports phenotype and trait descriptions using quality classes."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          },
          {
            "subject": "biosafety_level_trait",
            "predicate": "is a",
            "object": "quality_trait",
            "description": "Biosafety level is a reviewed non-genomic child quality in TraitMech's ecology category.",
            "evidence": [
              {
                "reference": "DOI:10.1146/annurev.micro.62.081307.162938",
                "snippet": "virulence factors",
                "notes": "Supports hazard-related biological-agent properties as inputs to biosafety-level classification."
              }
            ],
            "predicate_id": "rdfs:subClassOf"
          }
        ]
      }
    ],
    "curation_history": [
      {
        "timestamp": "2026-05-05T01:35:46.812123+00:00",
        "curator": "seed_from_metpo",
        "action": "SEEDED_FROM_METPO",
        "changes": "imported from data/raw/metpo.owl (CLASS)",
        "llm_assisted": false
      },
      {
        "timestamp": "2026-05-15T00:35:00-07:00",
        "curator": "codex",
        "action": "CURATED_UPPER_CONTEXT",
        "changes": "Reviewed quality as an upper classifier and added a DOI-backed context graph covering non-genomic child classes phenotype and biosafety level.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-05-20T03:35:32Z",
        "curator": "claude",
        "action": "GROUND_CAUSAL_PREDICATES",
        "changes": "Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (rdfs:subClassOf\u00d72).",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T03:23:00Z",
        "curator": "claude",
        "action": "REVIEW_GRAPH_PROTEIN_TAXON",
        "changes": "Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope quality_upper_child_context=NONMECHANISTIC with scope_notes.",
        "llm_assisted": true
      },
      {
        "timestamp": "2026-08-26T06:15:41Z",
        "curator": "codex",
        "action": "ADD_EXACT_ONTOLOGY_MATCH",
        "changes": "Ontology exact-match review (2026-08-25): approved exact xref(s): PATO:0000001. Evidence is predicate-scoped in the versioned ontology snapshots; OAK cross-checked direct data, and OLS4 spot-checked release deltas and disputed hits.",
        "llm_assisted": true
      }
    ]
  }
]